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1 ------------------------------------------------------------------------
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2 r925 | lh3lh3 | 2011-02-28 15:45:17 -0500 (Mon, 28 Feb 2011) | 2 lines
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3 Changed paths:
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4 M /trunk/samtools/phase.c
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5
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6 minor changes to a heuristic rule
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7
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8 ------------------------------------------------------------------------
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9 r924 | lh3lh3 | 2011-02-28 15:24:04 -0500 (Mon, 28 Feb 2011) | 4 lines
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10 Changed paths:
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11 M /trunk/samtools/bam.h
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12 M /trunk/samtools/bcftools/vcfutils.pl
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13 M /trunk/samtools/phase.c
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14
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15 * 0.1.12-r924:126
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16 * fixed a bug in phase (due to recent changes)
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17 * fixed a bug in vcf2fq
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18
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19 ------------------------------------------------------------------------
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20 r923 | lh3lh3 | 2011-02-28 12:57:39 -0500 (Mon, 28 Feb 2011) | 5 lines
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21 Changed paths:
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22 M /trunk/samtools/Makefile
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23 M /trunk/samtools/bam.h
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24 M /trunk/samtools/bam_plcmd.c
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25 M /trunk/samtools/bamtk.c
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26 M /trunk/samtools/phase.c
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27
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28 * put version number in bam.h
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29 * write version to BCF
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30 * in phase, change the default -q to 37
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31 * output a little more information during phasing
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32
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33 ------------------------------------------------------------------------
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34 r922 | lh3lh3 | 2011-02-25 16:40:09 -0500 (Fri, 25 Feb 2011) | 3 lines
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35 Changed paths:
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36 M /trunk/samtools/bam2bcf.c
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37 M /trunk/samtools/bamtk.c
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38 M /trunk/samtools/bcftools/bcf.c
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39 M /trunk/samtools/bcftools/bcf.tex
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40 M /trunk/samtools/bcftools/bcf2qcall.c
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41 M /trunk/samtools/bcftools/bcfutils.c
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42 M /trunk/samtools/bcftools/ld.c
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43 M /trunk/samtools/bcftools/prob1.c
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44 M /trunk/samtools/bcftools/vcf.c
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45 M /trunk/samtools/cut_target.c
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46
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47 * change the order of PL/GL according to the latest VCF spec
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48 * change the type of SP to int32_t
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49
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50 ------------------------------------------------------------------------
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51 r921 | lh3lh3 | 2011-02-25 14:40:56 -0500 (Fri, 25 Feb 2011) | 2 lines
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52 Changed paths:
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53 M /trunk/samtools/bcftools/bcf.tex
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54
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55 update the BCF spec
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56
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57 ------------------------------------------------------------------------
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58 r920 | lh3lh3 | 2011-02-25 00:59:27 -0500 (Fri, 25 Feb 2011) | 2 lines
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59 Changed paths:
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60 M /trunk/samtools/Makefile
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61 M /trunk/samtools/bam_md.c
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62 M /trunk/samtools/bam_plcmd.c
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63 M /trunk/samtools/bam_sort.c
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64 M /trunk/samtools/bamtk.c
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65 A /trunk/samtools/cut_target.c
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66 M /trunk/samtools/errmod.h
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67 M /trunk/samtools/faidx.c
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68 M /trunk/samtools/khash.h
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69 M /trunk/samtools/kstring.c
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70 M /trunk/samtools/kstring.h
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71 A /trunk/samtools/phase.c
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72 M /trunk/samtools/samtools.1
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73
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74 added the phase command
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75
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76 ------------------------------------------------------------------------
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77 r918 | lh3lh3 | 2011-02-24 10:05:54 -0500 (Thu, 24 Feb 2011) | 2 lines
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78 Changed paths:
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79 M /trunk/samtools/bcftools/prob1.c
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80 M /trunk/samtools/bcftools/prob1.h
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81
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82 added "const" to bcf_p1_cal()
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83
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84 ------------------------------------------------------------------------
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85 r917 | lh3lh3 | 2011-02-24 09:36:30 -0500 (Thu, 24 Feb 2011) | 2 lines
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86 Changed paths:
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87 M /trunk/samtools/bam.c
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88
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89 more meaningful BAM truncation message
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90
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91 ------------------------------------------------------------------------
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92 r916 | lh3lh3 | 2011-02-24 09:35:06 -0500 (Thu, 24 Feb 2011) | 3 lines
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93 Changed paths:
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94 M /trunk/samtools/bcftools/bcf.c
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95 M /trunk/samtools/bcftools/vcf.c
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96
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97 * automatically fix errors in GL
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98 * output unrecognized FORMAT as "."
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99
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100 ------------------------------------------------------------------------
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101 r913 | lh3lh3 | 2011-02-10 22:59:47 -0500 (Thu, 10 Feb 2011) | 2 lines
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102 Changed paths:
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103 M /trunk/samtools/bcftools/bcf.h
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104 M /trunk/samtools/bcftools/call1.c
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105 M /trunk/samtools/bcftools/vcf.c
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106
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107 finished VCF->BCF conversion
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108
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109 ------------------------------------------------------------------------
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110 r910 | petulda | 2011-02-03 03:13:48 -0500 (Thu, 03 Feb 2011) | 1 line
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111 Changed paths:
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112 M /trunk/samtools/bcftools/vcfutils.pl
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113
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114 Prevent division by zero
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115 ------------------------------------------------------------------------
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116 r909 | lh3lh3 | 2011-02-02 11:29:20 -0500 (Wed, 02 Feb 2011) | 2 lines
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117 Changed paths:
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118 M /trunk/samtools/bcftools/call1.c
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119
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120 fixed a typo in the VCF header
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121
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122 ------------------------------------------------------------------------
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123 r908 | lh3lh3 | 2011-02-02 11:28:24 -0500 (Wed, 02 Feb 2011) | 3 lines
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124 Changed paths:
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125 M /trunk/samtools/bam2bcf.c
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126 M /trunk/samtools/bam_index.c
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127
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128 * fixed an out-of-boundary bug
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129 * improved sorting order checking in index
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130
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131 ------------------------------------------------------------------------
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132 r907 | lh3lh3 | 2011-01-29 22:59:20 -0500 (Sat, 29 Jan 2011) | 4 lines
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133 Changed paths:
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134 M /trunk/samtools/INSTALL
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135 M /trunk/samtools/bam_tview.c
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136 M /trunk/samtools/knetfile.c
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137
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138 * avoid a segfault when network connect fails
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139 * update INSTALL
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140 * fixed a bug in tview on big-endian by Nathan Weeks
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141
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142 ------------------------------------------------------------------------
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143 r903 | lh3lh3 | 2011-01-27 14:50:02 -0500 (Thu, 27 Jan 2011) | 3 lines
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144 Changed paths:
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145 M /trunk/samtools/bam2bcf_indel.c
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146 M /trunk/samtools/bam_md.c
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147
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148 * fixed a rare memory issue in bam_md.c
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149 * fixed a bug in indel calling related to unmapped and refskip reads
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150
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151 ------------------------------------------------------------------------
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152 r902 | lh3lh3 | 2011-01-23 21:46:18 -0500 (Sun, 23 Jan 2011) | 2 lines
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153 Changed paths:
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154 M /trunk/samtools/bcftools/fet.c
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155
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156 fixed two minor bugs in Fisher's exact test
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157
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158 ------------------------------------------------------------------------
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159 r899 | petulda | 2011-01-19 09:28:02 -0500 (Wed, 19 Jan 2011) | 1 line
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160 Changed paths:
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161 M /trunk/samtools/bcftools/vcfutils.pl
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162
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163 Skip sites with unknown ref
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164 ------------------------------------------------------------------------
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165 r898 | lh3lh3 | 2011-01-15 12:56:05 -0500 (Sat, 15 Jan 2011) | 2 lines
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166 Changed paths:
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167 M /trunk/samtools/ChangeLog
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168 M /trunk/samtools/bam_maqcns.c
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169 M /trunk/samtools/bam_md.c
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170
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171 move bam_nt16_nt4_table[] from bam_maqcns.c to bam_md.c
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172
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173 ------------------------------------------------------------------------
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174 r896 | lh3lh3 | 2011-01-06 10:52:15 -0500 (Thu, 06 Jan 2011) | 3 lines
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175 Changed paths:
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176 M /trunk/samtools/bam_plcmd.c
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177 M /trunk/samtools/bamtk.c
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178 M /trunk/samtools/bcftools/bcf.h
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179 M /trunk/samtools/bcftools/bcfutils.c
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180 M /trunk/samtools/bcftools/call1.c
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181
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182 * samtools-0.1.12-10 (r896)
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183 * allow to exclude read groups in mpileup
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184
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185 ------------------------------------------------------------------------
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186 r895 | lh3lh3 | 2011-01-04 11:31:29 -0500 (Tue, 04 Jan 2011) | 2 lines
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187 Changed paths:
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188 M /trunk/samtools/bcftools/bcf.tex
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189
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190 sorry. It is SP not ST
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191
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192 ------------------------------------------------------------------------
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193 r894 | lh3lh3 | 2011-01-04 11:29:06 -0500 (Tue, 04 Jan 2011) | 2 lines
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194 Changed paths:
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195 M /trunk/samtools/bcftools/bcf.tex
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196
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197 added ST
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198
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199 ------------------------------------------------------------------------
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200 r893 | petulda | 2011-01-04 06:55:56 -0500 (Tue, 04 Jan 2011) | 1 line
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201 Changed paths:
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202 M /trunk/samtools/bcftools/call1.c
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203
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204 Fixed a typo in read_samples
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205 ------------------------------------------------------------------------
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206 r892 | jmarshall | 2010-12-28 08:06:49 -0500 (Tue, 28 Dec 2010) | 9 lines
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207 Changed paths:
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208 M /trunk/samtools/Makefile
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209 M /trunk/samtools/bcftools/Makefile
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210 M /trunk/samtools/examples/Makefile
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211
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212 System libraries go *after* user libraries in link commands, because
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213 the user libraries may themselves have dependencies that are satisfied
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214 by the system libraries. It's not rocket science!
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215
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216 This makes a difference with some linkers; or with -static or --as-needed.
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217
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218 The examples/Makefile fix is from Charles Plessy.
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219 See also http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=606004
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220
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221 ------------------------------------------------------------------------
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222 r891 | lh3lh3 | 2010-12-21 12:16:33 -0500 (Tue, 21 Dec 2010) | 3 lines
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223 Changed paths:
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224 M /trunk/samtools/bamtk.c
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225 M /trunk/samtools/bcftools/bcf.h
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226 M /trunk/samtools/bcftools/bcfutils.c
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227 M /trunk/samtools/bcftools/call1.c
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228
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229 * samtools-0.1.12-9 (r891)
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230 * allow to call SNPs from a subset of samples
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231
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232 ------------------------------------------------------------------------
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233 r889 | lh3lh3 | 2010-12-15 11:28:16 -0500 (Wed, 15 Dec 2010) | 3 lines
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234 Changed paths:
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235 M /trunk/samtools/bam2bcf.c
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236 M /trunk/samtools/bamtk.c
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237
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238 * samtools-0.1.12-12 (r889)
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239 * set mapQ as 20 if it equals 255
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240
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241 ------------------------------------------------------------------------
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242 r888 | lh3lh3 | 2010-12-14 22:41:09 -0500 (Tue, 14 Dec 2010) | 2 lines
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243 Changed paths:
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244 M /trunk/samtools/bam_plcmd.c
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245 M /trunk/samtools/bamtk.c
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246
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247 When -B is applied to mpileup, still use paired reads only unless -A is flagged.
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248
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249 ------------------------------------------------------------------------
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250 r887 | lh3lh3 | 2010-12-14 22:37:05 -0500 (Tue, 14 Dec 2010) | 3 lines
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251 Changed paths:
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252 M /trunk/samtools/bam_md.c
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253 M /trunk/samtools/bam_plcmd.c
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254 M /trunk/samtools/bamtk.c
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255
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256 * samtools-0.1.12-6 (r887)
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257 * added a hidden option -E to mpileup/calmd. -E triggers an alternative way to apply BAQ.
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258
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259 ------------------------------------------------------------------------
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260 r886 | lh3lh3 | 2010-12-14 12:51:03 -0500 (Tue, 14 Dec 2010) | 2 lines
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261 Changed paths:
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262 M /trunk/samtools/bam2bcf_indel.c
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263 M /trunk/samtools/bamtk.c
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264
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265 (Arguably) improved the indel caller a tiny bit for lowCov data.
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266
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267 ------------------------------------------------------------------------
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268 r885 | petulda | 2010-12-14 04:55:46 -0500 (Tue, 14 Dec 2010) | 1 line
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269 Changed paths:
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270 M /trunk/samtools/bcftools/call1.c
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271
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272 Fixed the VCF header to pass validation
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273 ------------------------------------------------------------------------
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274 r884 | lh3lh3 | 2010-12-12 23:02:19 -0500 (Sun, 12 Dec 2010) | 3 lines
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275 Changed paths:
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276 M /trunk/samtools/bam2bcf_indel.c
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277 M /trunk/samtools/bamtk.c
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278 M /trunk/samtools/bcftools/vcfutils.pl
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279
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280 * samtools-0.1.12-4 (r884)
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281 * fixed a long-existing flaw in the INDEL calling model
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282
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283 ------------------------------------------------------------------------
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284 r883 | lh3lh3 | 2010-12-11 20:05:42 -0500 (Sat, 11 Dec 2010) | 2 lines
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285 Changed paths:
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286 M /trunk/samtools/bcftools/bcfutils.c
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287 M /trunk/samtools/bcftools/call1.c
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288 M /trunk/samtools/bcftools/vcfutils.pl
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289
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290 compute max SP and max GQ from sample genotypes
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291
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292 ------------------------------------------------------------------------
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293 r880 | lh3lh3 | 2010-12-10 10:50:54 -0500 (Fri, 10 Dec 2010) | 2 lines
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294 Changed paths:
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295 D /trunk/samtools/bcftools/bcf-fix.pl
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296
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297 drop bcf-fix.pl as it is redundant by the latest changes
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298
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299 ------------------------------------------------------------------------
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300 r879 | lh3lh3 | 2010-12-10 10:50:29 -0500 (Fri, 10 Dec 2010) | 3 lines
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301 Changed paths:
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302 M /trunk/samtools/bcftools/call1.c
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303 M /trunk/samtools/bcftools/vcf.c
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304
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305 * fixed a minor issue in printing VCFs
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306 * write bcftools specific INFO and FORMAT in the header
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307
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308 ------------------------------------------------------------------------
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309 r878 | lh3lh3 | 2010-12-10 10:09:14 -0500 (Fri, 10 Dec 2010) | 2 lines
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310 Changed paths:
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311 M /trunk/samtools/bamtk.c
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312 M /trunk/samtools/bcftools/bcfutils.c
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313 M /trunk/samtools/bcftools/call1.c
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314
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315 Make sure that the GT genotype field is the first
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316
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317 ------------------------------------------------------------------------
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318 r877 | lh3lh3 | 2010-12-08 17:27:05 -0500 (Wed, 08 Dec 2010) | 7 lines
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319 Changed paths:
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320 M /trunk/samtools/bam2bcf.c
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321 M /trunk/samtools/bam2bcf.h
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322 M /trunk/samtools/bam2bcf_indel.c
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323 M /trunk/samtools/bam_plcmd.c
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324 M /trunk/samtools/bamtk.c
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325
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326 * samtools-0.1.12-2 (r877)
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327
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328 * allow to fine control the selection of indel candidates. The current
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329 setting is okay for lowCov and highCov with ~100 samples, but it
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330 skips too many indels for highCov with >250 samples.
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331
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332
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333 ------------------------------------------------------------------------
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334 r874 | lh3lh3 | 2010-12-07 22:40:35 -0500 (Tue, 07 Dec 2010) | 2 lines
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335 Changed paths:
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336 M /trunk/samtools/bam_plcmd.c
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337
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338 a spelling error..
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339
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340 ------------------------------------------------------------------------
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341 r873 | lh3lh3 | 2010-12-07 22:39:57 -0500 (Tue, 07 Dec 2010) | 3 lines
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342 Changed paths:
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343 M /trunk/samtools/bam_plcmd.c
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344 M /trunk/samtools/bamtk.c
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345
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346 * samtools-0.1.12-1 (r873)
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347 * added a switch to allow anomalous read pairs in calling
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348
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349 ------------------------------------------------------------------------
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350 r872 | lh3lh3 | 2010-12-07 14:43:54 -0500 (Tue, 07 Dec 2010) | 2 lines
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351 Changed paths:
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352 M /trunk/samtools/bcftools/vcfutils.pl
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353
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354 fixed a bug in vcf2fq
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355
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356 ------------------------------------------------------------------------
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357 r869 | lh3lh3 | 2010-12-05 01:18:06 -0500 (Sun, 05 Dec 2010) | 2 lines
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358 Changed paths:
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359 M /trunk/samtools/bamtk.c
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360
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361 added a warning for the Windows version
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362
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363 ------------------------------------------------------------------------
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364 r868 | lh3lh3 | 2010-12-05 01:05:51 -0500 (Sun, 05 Dec 2010) | 4 lines
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365 Changed paths:
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366 M /trunk/samtools/bcftools/call1.c
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367
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368 In ksprintf(), change "%lf" and "%lg" to "%f" and "%g", respectively.
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369 According to the manual page, this change is valid. However, MinGW seems
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370 to interpret "%lf" as "%Lf".
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371
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372 ------------------------------------------------------------------------
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373 r867 | lh3lh3 | 2010-12-05 00:35:43 -0500 (Sun, 05 Dec 2010) | 2 lines
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374 Changed paths:
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375 M /trunk/samtools/Makefile.mingw
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376 M /trunk/samtools/bam_aux.c
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377
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378 bring back the windows support
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379
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380 ------------------------------------------------------------------------
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381 r866 | lh3lh3 | 2010-12-04 23:33:51 -0500 (Sat, 04 Dec 2010) | 2 lines
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382 Changed paths:
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383 M /trunk/samtools/bam_reheader.c
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384 M /trunk/samtools/bcftools/vcfutils.pl
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385
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386 Fixed a compiling error when knetfile is not used.
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387
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388 ------------------------------------------------------------------------
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389 r865 | lh3lh3 | 2010-12-04 00:13:22 -0500 (Sat, 04 Dec 2010) | 2 lines
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390 Changed paths:
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391 M /trunk/samtools/bcftools/vcfutils.pl
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392
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393 vcf->fastq
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394
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395 ------------------------------------------------------------------------
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396 r864 | lh3lh3 | 2010-12-03 17:12:30 -0500 (Fri, 03 Dec 2010) | 3 lines
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397 Changed paths:
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398 M /trunk/samtools/bcftools/call1.c
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399 M /trunk/samtools/bcftools/prob1.c
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400 M /trunk/samtools/bcftools/prob1.h
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401
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402 * remove "-f". Instead always compute consensus quality
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403 * increase the upper limit of quality
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404
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405 ------------------------------------------------------------------------
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406 r863 | lh3lh3 | 2010-12-03 15:28:15 -0500 (Fri, 03 Dec 2010) | 2 lines
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407 Changed paths:
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408 M /trunk/samtools/bcftools/bcf.c
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409
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410 more informative error message
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411
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412 ------------------------------------------------------------------------
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413 r862 | lh3lh3 | 2010-12-02 16:16:08 -0500 (Thu, 02 Dec 2010) | 2 lines
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414 Changed paths:
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415 M /trunk/samtools/NEWS
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416 M /trunk/samtools/bamtk.c
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417
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418 Release samtools-0.1.12a
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419
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420 ------------------------------------------------------------------------
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421 r861 | lh3lh3 | 2010-12-02 15:55:06 -0500 (Thu, 02 Dec 2010) | 2 lines
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422 Changed paths:
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423 M /trunk/samtools/bcftools/call1.c
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424
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425 a possible fix to DP4=0,0,0,0; have not tested, but should have no side-effect
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426
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427 ------------------------------------------------------------------------
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428 r859 | lh3lh3 | 2010-12-02 11:39:57 -0500 (Thu, 02 Dec 2010) | 2 lines
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429 Changed paths:
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430 M /trunk/samtools/NEWS
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431 M /trunk/samtools/bam_index.c
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432 M /trunk/samtools/bamtk.c
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433 M /trunk/samtools/samtools.1
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434
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435 Release samtools-0.1.12
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436
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437 ------------------------------------------------------------------------
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438 r858 | lh3lh3 | 2010-12-02 11:24:41 -0500 (Thu, 02 Dec 2010) | 4 lines
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439 Changed paths:
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440 M /trunk/samtools/bam_plcmd.c
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441 M /trunk/samtools/bamtk.c
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442 M /trunk/samtools/bcftools/bcf.c
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443
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444 * samtools-0.1.11-1 (r858)
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445 * fixed a bug in mpileup which causes segfaults
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446 * bcftools: do not segfault when BCF contains errors
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447
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448 ------------------------------------------------------------------------
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449 r857 | lh3lh3 | 2010-11-30 23:52:50 -0500 (Tue, 30 Nov 2010) | 2 lines
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450 Changed paths:
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451 M /trunk/samtools/bam_index.c
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452
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453 fixed a memory leak in bam_fetch()
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454
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455 ------------------------------------------------------------------------
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456 r856 | lh3lh3 | 2010-11-26 00:07:31 -0500 (Fri, 26 Nov 2010) | 3 lines
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457 Changed paths:
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458 M /trunk/samtools/bam2bcf_indel.c
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459 M /trunk/samtools/bcftools/vcfutils.pl
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460
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461 * fixed a memory violation
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462 * added splitchr to vcfutils.pl
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463
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464 ------------------------------------------------------------------------
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465 r854 | lh3lh3 | 2010-11-23 09:05:08 -0500 (Tue, 23 Nov 2010) | 2 lines
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466 Changed paths:
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467 M /trunk/samtools/bcftools/ld.c
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468
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469 fixed a typo/bug in r^2 computation
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470
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471 ------------------------------------------------------------------------
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472 r852 | lh3lh3 | 2010-11-21 22:20:20 -0500 (Sun, 21 Nov 2010) | 2 lines
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473 Changed paths:
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474 M /trunk/samtools/bamtk.c
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475
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476 forget to change the version information
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477
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478 ------------------------------------------------------------------------
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479 r851 | lh3lh3 | 2010-11-21 22:16:52 -0500 (Sun, 21 Nov 2010) | 2 lines
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480 Changed paths:
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481 M /trunk/samtools/ChangeLog
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482 M /trunk/samtools/NEWS
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483 M /trunk/samtools/bcftools/bcftools.1
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484 M /trunk/samtools/samtools.1
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485
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486 Release samtools-0.1.11
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487
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488 ------------------------------------------------------------------------
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489 r844 | lh3lh3 | 2010-11-19 23:16:08 -0500 (Fri, 19 Nov 2010) | 3 lines
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490 Changed paths:
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491 M /trunk/samtools/bamtk.c
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492 M /trunk/samtools/bcftools/call1.c
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493 M /trunk/samtools/bcftools/prob1.c
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494 M /trunk/samtools/bcftools/prob1.h
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495
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496 * samtools-0.1.10-9 (r844)
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497 * added the "folded" or reference-free mode for variant calling
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498
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499 ------------------------------------------------------------------------
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500 r843 | lh3lh3 | 2010-11-19 22:26:36 -0500 (Fri, 19 Nov 2010) | 2 lines
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501 Changed paths:
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502 M /trunk/samtools/NEWS
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503 M /trunk/samtools/bam_sort.c
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504
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505 In merging, if -R is specified, do not abort if the sequence dictionary is different.
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506
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507 ------------------------------------------------------------------------
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508 r842 | jmarshall | 2010-11-19 21:24:28 -0500 (Fri, 19 Nov 2010) | 5 lines
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509 Changed paths:
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510 M /trunk/samtools/bam_sort.c
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511
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512 When merging BAM headers, compare the list of target reference sequences
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513 strictly (and fail/abort if there is a mismatch), but allow one list to be a
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514 prefix of the other. (i.e., check that the lists are identical up until the
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515 shorter runs out, and add the excess targets from the longer to the output.)
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516
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517 ------------------------------------------------------------------------
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518 r841 | lh3lh3 | 2010-11-19 14:49:27 -0500 (Fri, 19 Nov 2010) | 4 lines
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519 Changed paths:
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520 M /trunk/samtools/bam_index.c
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521 M /trunk/samtools/bam_pileup.c
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522 M /trunk/samtools/bamtk.c
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523
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524 * samtools-0.1.10 (r841)
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525 * fixed a bug in pileup when the first CIGAR operation is D
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526 * fixed a bug in view with range query
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527
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528 ------------------------------------------------------------------------
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529 r840 | lh3lh3 | 2010-11-19 13:45:51 -0500 (Fri, 19 Nov 2010) | 10 lines
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530 Changed paths:
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531 M /trunk/samtools/ChangeLog
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532 M /trunk/samtools/bam2bcf.c
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533 M /trunk/samtools/bam2bcf.h
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534 M /trunk/samtools/bam2bcf_indel.c
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535 M /trunk/samtools/bam_plcmd.c
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536 M /trunk/samtools/bamtk.c
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537
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538 * samtools-0.1.10-4 (r840)
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539
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540 * drop the MNP caller. It is slow while does not diliver too much
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541 benefit. Possibly I will work on it in future given more time.
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542
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543 * there is a segfault in pileup
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544
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545 * someone has reported segfault from view/index/sort
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546
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547
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548 ------------------------------------------------------------------------
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549 r839 | lh3lh3 | 2010-11-18 17:30:11 -0500 (Thu, 18 Nov 2010) | 9 lines
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550 Changed paths:
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551 M /trunk/samtools/bam2bcf.h
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552 M /trunk/samtools/bam2bcf_indel.c
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553 M /trunk/samtools/bamtk.c
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554
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555 * samtools-0.1.10-6 (r839)
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556
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557 * call MNPs without realignment because it seems to me that it is not
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558 worthwhile to significantly slow down SNP calling.
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559
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560 * the result looks quite different from the previous version. I have
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561 work to do...
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562
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563
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564 ------------------------------------------------------------------------
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565 r838 | lh3lh3 | 2010-11-18 11:26:09 -0500 (Thu, 18 Nov 2010) | 2 lines
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566 Changed paths:
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567 M /trunk/samtools/knetfile.c
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568
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569 Apply a patch by Rob Davis, which improves fault detection.
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570
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571 ------------------------------------------------------------------------
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572 r836 | lh3lh3 | 2010-11-18 11:09:23 -0500 (Thu, 18 Nov 2010) | 3 lines
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573 Changed paths:
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574 M /trunk/samtools/bam2bcf_indel.c
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575 M /trunk/samtools/bamtk.c
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576
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577 * samtools-r836
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578 * initiate MNP realignment when the MNP has at least 0.2% frequency (otherwise too slow)
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579
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580 ------------------------------------------------------------------------
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581 r835 | lh3lh3 | 2010-11-18 00:25:13 -0500 (Thu, 18 Nov 2010) | 3 lines
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582 Changed paths:
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583 M /trunk/samtools/bcftools/vcfutils.pl
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584
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585 * modify the filtering rule: also filter SNPs around filtered indels
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586 * added MNP filter
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587
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588 ------------------------------------------------------------------------
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589 r834 | lh3lh3 | 2010-11-17 23:13:52 -0500 (Wed, 17 Nov 2010) | 4 lines
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590 Changed paths:
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591 M /trunk/samtools/bam2bcf.c
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592 M /trunk/samtools/bam2bcf_indel.c
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593 M /trunk/samtools/bamtk.c
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594
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595 * samtools-0.1.10-4 (r834)
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596 * fixed a silly bug in printing MNP
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597 * restrict to at most 1 alternative allele
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598
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599 ------------------------------------------------------------------------
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600 r833 | lh3lh3 | 2010-11-17 21:58:58 -0500 (Wed, 17 Nov 2010) | 2 lines
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601 Changed paths:
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602 M /trunk/samtools/bam2bcf.c
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603 M /trunk/samtools/bamtk.c
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604
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605 fixed a bug in printing MNPs
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606
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607 ------------------------------------------------------------------------
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608 r832 | lh3lh3 | 2010-11-17 21:47:20 -0500 (Wed, 17 Nov 2010) | 2 lines
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609 Changed paths:
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610 M /trunk/samtools/bam2bcf_indel.c
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611 M /trunk/samtools/bamtk.c
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612
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613 minor change to how seqQ is applied
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614
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615 ------------------------------------------------------------------------
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616 r831 | lh3lh3 | 2010-11-17 21:41:12 -0500 (Wed, 17 Nov 2010) | 3 lines
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617 Changed paths:
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618 M /trunk/samtools/bam2bcf.c
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619 M /trunk/samtools/bam2bcf.h
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620 M /trunk/samtools/bam2bcf_indel.c
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621 M /trunk/samtools/bam_plcmd.c
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622 M /trunk/samtools/bamtk.c
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623
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624 * samtools-0.1.10 (r831)
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625 * initial MNP caller
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626
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627 ------------------------------------------------------------------------
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628 r829 | lh3lh3 | 2010-11-16 23:14:15 -0500 (Tue, 16 Nov 2010) | 2 lines
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629 Changed paths:
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630 M /trunk/samtools/ChangeLog
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631 M /trunk/samtools/NEWS
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632 M /trunk/samtools/bamtk.c
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633
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634 Release samtools-0.1.10 (r829)
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635
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636 ------------------------------------------------------------------------
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637 r828 | lh3lh3 | 2010-11-16 20:48:49 -0500 (Tue, 16 Nov 2010) | 2 lines
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638 Changed paths:
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639 M /trunk/samtools/bamtk.c
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640
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641 update version information: samtools-0.1.9-20 (r828)
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642
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643 ------------------------------------------------------------------------
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644 r827 | lh3lh3 | 2010-11-16 15:32:50 -0500 (Tue, 16 Nov 2010) | 2 lines
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645 Changed paths:
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646 M /trunk/samtools/bcftools/call1.c
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647
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648 bcftools: allow to skip indels
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649
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650 ------------------------------------------------------------------------
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651 r826 | lh3lh3 | 2010-11-16 14:11:58 -0500 (Tue, 16 Nov 2010) | 2 lines
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652 Changed paths:
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653 M /trunk/samtools/bam_md.c
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654
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655 remove ZQ if both BQ and ZQ are present
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656
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657 ------------------------------------------------------------------------
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658 r825 | lh3lh3 | 2010-11-16 13:51:33 -0500 (Tue, 16 Nov 2010) | 3 lines
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659 Changed paths:
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660 M /trunk/samtools/bam2bcf_indel.c
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661 M /trunk/samtools/bam_md.c
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662 M /trunk/samtools/bamtk.c
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663 M /trunk/samtools/samtools.1
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664
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665 * samtools-0.1.9-18 (r825)
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666 * change the behaviour of calmd such that by default it does not change the base quality
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667
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668 ------------------------------------------------------------------------
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669 r824 | lh3lh3 | 2010-11-15 23:31:53 -0500 (Mon, 15 Nov 2010) | 4 lines
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670 Changed paths:
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671 M /trunk/samtools/bam_plcmd.c
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672 M /trunk/samtools/bamtk.c
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673 M /trunk/samtools/bcftools/call1.c
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674 M /trunk/samtools/samtools.1
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675
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676 * samtools-0.1.9-17 (r824)
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677 * added command line options to change the default parameters in indel calling
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678 * update the manual
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679
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680 ------------------------------------------------------------------------
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681 r823 | lh3lh3 | 2010-11-15 12:20:13 -0500 (Mon, 15 Nov 2010) | 3 lines
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682 Changed paths:
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683 M /trunk/samtools/bam2bcf_indel.c
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684 M /trunk/samtools/bam_md.c
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685 M /trunk/samtools/bamtk.c
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686
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687 * samtools-0.1.9-r823
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688 * the BQ tag is now 64 shifted, not 33 shifted
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689
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690 ------------------------------------------------------------------------
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691 r822 | lh3lh3 | 2010-11-15 00:30:18 -0500 (Mon, 15 Nov 2010) | 3 lines
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692 Changed paths:
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693 M /trunk/samtools/bam2bcf.c
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694 M /trunk/samtools/bam2bcf.h
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695 M /trunk/samtools/bamtk.c
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696 M /trunk/samtools/bcftools/vcfutils.pl
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697 M /trunk/samtools/misc/samtools.pl
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698
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699 * samtools-0.1.9-16 (r822)
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700 * keep the raw depth because in indel calling, DP4 may be way off the true depth
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701
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702 ------------------------------------------------------------------------
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703 r821 | lh3lh3 | 2010-11-13 01:18:31 -0500 (Sat, 13 Nov 2010) | 4 lines
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704 Changed paths:
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705 M /trunk/samtools/bam_md.c
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706 M /trunk/samtools/bamtk.c
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707
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708 * samtools-0.1.9-15 (r821)
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709 * calmd: write BQ
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710 * skip realignment if BQ is present
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711
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712 ------------------------------------------------------------------------
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713 r820 | lh3lh3 | 2010-11-13 01:08:26 -0500 (Sat, 13 Nov 2010) | 3 lines
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714 Changed paths:
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715 M /trunk/samtools/bam2bcf_indel.c
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716 M /trunk/samtools/bamtk.c
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717
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718 * samtools-0.1.9-14 (r820)
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719 * penalize reads with excessive differences in indel calling
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720
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721 ------------------------------------------------------------------------
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722 r819 | lh3lh3 | 2010-11-12 21:36:27 -0500 (Fri, 12 Nov 2010) | 3 lines
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723 Changed paths:
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724 M /trunk/samtools/bam_maqcns.c
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725 M /trunk/samtools/bamtk.c
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726
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727 * samtools-0.1.9-13 (r819)
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728 * fixed a bug in pileup given refskip
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729
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730 ------------------------------------------------------------------------
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731 r818 | lh3lh3 | 2010-11-12 13:04:53 -0500 (Fri, 12 Nov 2010) | 3 lines
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732 Changed paths:
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733 M /trunk/samtools/bam2bcf_indel.c
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734 M /trunk/samtools/bamtk.c
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735
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736 * samtools-r818
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737 * for indel calling, do two rounds of probabilistic realignments
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738
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739 ------------------------------------------------------------------------
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740 r817 | lh3lh3 | 2010-11-11 20:04:07 -0500 (Thu, 11 Nov 2010) | 3 lines
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741 Changed paths:
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742 M /trunk/samtools/bam2bcf_indel.c
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743 M /trunk/samtools/bamtk.c
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744 M /trunk/samtools/bcftools/vcfutils.pl
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745
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746 * samtools-0.1.19-11 (r817)
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747 * only initiate indel calling when 0.2% of reads contain a gap
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748
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749 ------------------------------------------------------------------------
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750 r816 | lh3lh3 | 2010-11-11 01:22:59 -0500 (Thu, 11 Nov 2010) | 7 lines
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751 Changed paths:
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752 M /trunk/samtools/bam2bcf_indel.c
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753 M /trunk/samtools/bamtk.c
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754
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755 * samtools-0.1.9-10 (r816)
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756
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757 * I know why the forward method fails. it is because of zero base
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758 qualities. when that is fixed, the forward method seems to give
|
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759 better results than Viterbi, as it should be. I am tired...
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760
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761
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762 ------------------------------------------------------------------------
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763 r815 | lh3lh3 | 2010-11-11 00:57:15 -0500 (Thu, 11 Nov 2010) | 2 lines
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764 Changed paths:
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765 M /trunk/samtools/ChangeLog
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766 M /trunk/samtools/bam2bcf_indel.c
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767
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768 effectively revert to the viterbi version. The forward realignment gives too many false positives.
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769
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770 ------------------------------------------------------------------------
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771 r814 | lh3lh3 | 2010-11-11 00:18:02 -0500 (Thu, 11 Nov 2010) | 4 lines
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772 Changed paths:
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773 M /trunk/samtools/bam2bcf_indel.c
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774 M /trunk/samtools/bam_md.c
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775 M /trunk/samtools/bam_plcmd.c
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776 M /trunk/samtools/bamtk.c
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777
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778 * samtools-0.1.9-9 (r810)
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779 * use forward, instead of viterbi, for realignment
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780 * realignment is now quality aware
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781
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782 ------------------------------------------------------------------------
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783 r813 | lh3lh3 | 2010-11-10 22:45:24 -0500 (Wed, 10 Nov 2010) | 2 lines
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784 Changed paths:
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785 M /trunk/samtools/bam2bcf_indel.c
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786 M /trunk/samtools/kprobaln.c
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787 M /trunk/samtools/kprobaln.h
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788
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789 * prepare to replace kaln with kprobaln in realignment
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790
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791 ------------------------------------------------------------------------
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792 r812 | lh3lh3 | 2010-11-10 17:28:50 -0500 (Wed, 10 Nov 2010) | 2 lines
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793 Changed paths:
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794 M /trunk/samtools/bcftools/bcf.c
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795
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796 fixed a typo
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797
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798 ------------------------------------------------------------------------
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799 r811 | lh3lh3 | 2010-11-10 16:54:46 -0500 (Wed, 10 Nov 2010) | 2 lines
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800 Changed paths:
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801 M /trunk/samtools/bcftools/bcf.c
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802 M /trunk/samtools/bcftools/bcf.h
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803
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804 use zlib for direct reading when BCF_LITE is in use
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805
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806 ------------------------------------------------------------------------
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807 r810 | lh3lh3 | 2010-11-10 16:32:13 -0500 (Wed, 10 Nov 2010) | 3 lines
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808 Changed paths:
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809 M /trunk/samtools/bam2bcf_indel.c
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810
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811 * do not use reads containing too many mismatches for indel calling
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812 * fixed a trivial bug in case of multi-allelic indels
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813
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814 ------------------------------------------------------------------------
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815 r809 | lh3lh3 | 2010-11-10 13:23:02 -0500 (Wed, 10 Nov 2010) | 3 lines
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816 Changed paths:
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817 M /trunk/samtools/bam2bcf.c
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818 M /trunk/samtools/bam2bcf_indel.c
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819 M /trunk/samtools/bam_plcmd.c
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820 M /trunk/samtools/bamtk.c
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821
|
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822 * samtools-0.1.9-8 (r809)
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823 * fixed a bug in the indel caller
|
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824
|
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825 ------------------------------------------------------------------------
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826 r808 | lh3lh3 | 2010-11-10 12:24:10 -0500 (Wed, 10 Nov 2010) | 2 lines
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827 Changed paths:
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828 M /trunk/samtools/Makefile
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829
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830 minor change to makefile
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831
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832 ------------------------------------------------------------------------
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833 r807 | lh3lh3 | 2010-11-10 12:10:21 -0500 (Wed, 10 Nov 2010) | 4 lines
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834 Changed paths:
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835 M /trunk/samtools/Makefile
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836 M /trunk/samtools/bam2bcf.h
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837 M /trunk/samtools/bam2bcf_indel.c
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838 M /trunk/samtools/bam_plcmd.c
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839 M /trunk/samtools/bamtk.c
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840 M /trunk/samtools/bcftools/vcfutils.pl
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841
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842 * samtools-0.1.9-8 (r807)
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843 * collect indel candidates only from specified platforms (@RG-PL)
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844 * merge varFilter and filter4vcf in vcfutils.pl
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845
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846 ------------------------------------------------------------------------
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847 r806 | lh3lh3 | 2010-11-09 22:05:46 -0500 (Tue, 09 Nov 2010) | 2 lines
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848 Changed paths:
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849 M /trunk/samtools/bcftools/call1.c
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850 M /trunk/samtools/bcftools/prob1.c
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851 M /trunk/samtools/bcftools/prob1.h
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852
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853 bcftools: compute equal-tail (Bayesian) credible interval
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854
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855 ------------------------------------------------------------------------
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856 r805 | lh3lh3 | 2010-11-09 16:28:39 -0500 (Tue, 09 Nov 2010) | 2 lines
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857 Changed paths:
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858 M /trunk/samtools/bcftools/vcfutils.pl
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859
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860 added a double-hit filter to avoid overestimated indel likelihood
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861
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862 ------------------------------------------------------------------------
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863 r804 | lh3lh3 | 2010-11-09 14:12:06 -0500 (Tue, 09 Nov 2010) | 3 lines
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864 Changed paths:
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865 M /trunk/samtools/bam2bcf_indel.c
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866 M /trunk/samtools/bamtk.c
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867
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868 * samtools-0.1.9-7 (r804)
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869 * fixed a bug in the gap caller
|
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870
|
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871 ------------------------------------------------------------------------
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872 r803 | lh3lh3 | 2010-11-09 10:45:33 -0500 (Tue, 09 Nov 2010) | 4 lines
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873 Changed paths:
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874 M /trunk/samtools/bam2bcf.c
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875 M /trunk/samtools/bam2bcf_indel.c
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876 M /trunk/samtools/bamtk.c
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877 M /trunk/samtools/bcftools/bcf.c
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878 M /trunk/samtools/bcftools/bcf.h
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879 M /trunk/samtools/bcftools/prob1.c
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880
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881 * samtools-0.1.9-6 (r803)
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882 * mpileup: apply homopolymer correction when calculating GL, instead of before
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883 * bcftools: apply a different prior to indels
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884
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885 ------------------------------------------------------------------------
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886 r802 | lh3lh3 | 2010-11-08 23:53:15 -0500 (Mon, 08 Nov 2010) | 3 lines
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887 Changed paths:
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888 M /trunk/samtools/bam2bcf.c
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889 M /trunk/samtools/bamtk.c
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890
|
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891 * samtools-0.1.9-5 (r802)
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892 * relax tandem penalty. this will be made a command-line option in future.
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893
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894 ------------------------------------------------------------------------
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895 r801 | lh3lh3 | 2010-11-08 23:35:52 -0500 (Mon, 08 Nov 2010) | 3 lines
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896 Changed paths:
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897 M /trunk/samtools/bam2bcf.c
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898 M /trunk/samtools/bamtk.c
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899
|
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900 * samtools-0.1.9-4 (r801)
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901 * fixed a minor issue in printing indel VCF
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902
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903 ------------------------------------------------------------------------
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904 r800 | lh3lh3 | 2010-11-08 15:28:14 -0500 (Mon, 08 Nov 2010) | 2 lines
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905 Changed paths:
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906 M /trunk/samtools/bam2bcf_indel.c
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907 M /trunk/samtools/bcftools/vcfutils.pl
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908
|
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909 fixed another silly bug in mpileup's indel caller
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910
|
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911 ------------------------------------------------------------------------
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912 r799 | lh3lh3 | 2010-11-08 14:28:27 -0500 (Mon, 08 Nov 2010) | 2 lines
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913 Changed paths:
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914 M /trunk/samtools/bam2bcf.c
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915
|
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916 fixed a silly bug in the indel caller
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917
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918 ------------------------------------------------------------------------
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|
919 r798 | lh3lh3 | 2010-11-08 14:07:33 -0500 (Mon, 08 Nov 2010) | 2 lines
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920 Changed paths:
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921 M /trunk/samtools/ChangeLog
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922 M /trunk/samtools/sam_view.c
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923 M /trunk/samtools/samtools.1
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924
|
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925 Incorporate patches by Marcel Martin for read counting.
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926
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927 ------------------------------------------------------------------------
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928 r797 | lh3lh3 | 2010-11-08 13:39:52 -0500 (Mon, 08 Nov 2010) | 3 lines
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929 Changed paths:
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930 M /trunk/samtools/bam2bcf.c
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931 M /trunk/samtools/bam2bcf.h
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932 M /trunk/samtools/bam2bcf_indel.c
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933 M /trunk/samtools/bam_plcmd.c
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934 M /trunk/samtools/bamtk.c
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935
|
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|
936 * samtools-0.1.9-2 (r797)
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937 * mpileup: indel calling seems to be working
|
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938
|
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|
939 ------------------------------------------------------------------------
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940 r796 | lh3lh3 | 2010-11-08 10:54:46 -0500 (Mon, 08 Nov 2010) | 2 lines
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941 Changed paths:
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|
942 M /trunk/samtools/bam2bcf.c
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943 M /trunk/samtools/bam2bcf.h
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944 M /trunk/samtools/bam2bcf_indel.c
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945 M /trunk/samtools/bam_plcmd.c
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946 M /trunk/samtools/kaln.c
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947
|
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948 indel calling is apparently working, but more information needs to be collected
|
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949
|
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950 ------------------------------------------------------------------------
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951 r795 | lh3lh3 | 2010-11-08 00:39:18 -0500 (Mon, 08 Nov 2010) | 2 lines
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952 Changed paths:
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953 M /trunk/samtools/bam2bcf.c
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954 M /trunk/samtools/bam2bcf_indel.c
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955
|
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|
956 fixed a few bugs in the indel caller. Probably there are more.
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957
|
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958 ------------------------------------------------------------------------
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|
959 r794 | lh3lh3 | 2010-11-07 22:23:16 -0500 (Sun, 07 Nov 2010) | 2 lines
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960 Changed paths:
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961 M /trunk/samtools/Makefile
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962 M /trunk/samtools/bam.h
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963 M /trunk/samtools/bam2bcf.c
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964 M /trunk/samtools/bam2bcf.h
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965 A /trunk/samtools/bam2bcf_indel.c
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966 M /trunk/samtools/bam_plcmd.c
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967 M /trunk/samtools/kaln.c
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968 M /trunk/samtools/kaln.h
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969
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970 prepare for the indel caller. It is not ready yet.
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971
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|
972 ------------------------------------------------------------------------
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|
973 r793 | lh3lh3 | 2010-11-05 11:28:23 -0400 (Fri, 05 Nov 2010) | 2 lines
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974 Changed paths:
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975 M /trunk/samtools/bam2bcf.c
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976 M /trunk/samtools/bam2bcf.h
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977 M /trunk/samtools/bam_plcmd.c
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978
|
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|
979 Revert to r790. The recent changes are not good...
|
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980
|
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|
981 ------------------------------------------------------------------------
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|
982 r792 | lh3lh3 | 2010-11-05 00:19:14 -0400 (Fri, 05 Nov 2010) | 6 lines
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983 Changed paths:
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984 M /trunk/samtools/bam2bcf.c
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985 M /trunk/samtools/bam2bcf.h
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986 M /trunk/samtools/bam_plcmd.c
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987
|
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|
988 * this revision is UNSTABLE
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|
989
|
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|
990 * indel caller seems working, but it is very insensitive and has
|
|
|
991 several things I do not quite understand.
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992
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993
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994 ------------------------------------------------------------------------
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995 r791 | lh3lh3 | 2010-11-04 22:58:43 -0400 (Thu, 04 Nov 2010) | 2 lines
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996 Changed paths:
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997 M /trunk/samtools/bam2bcf.c
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998 M /trunk/samtools/bam2bcf.h
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999 M /trunk/samtools/bam_plcmd.c
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1000
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1001 for backup. no effective changes
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1002
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1003 ------------------------------------------------------------------------
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1004 r790 | lh3lh3 | 2010-11-03 15:51:24 -0400 (Wed, 03 Nov 2010) | 2 lines
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1005 Changed paths:
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1006 M /trunk/samtools/bcftools/vcfutils.pl
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1007 M /trunk/samtools/kprobaln.c
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1008
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1009 fixed a minor problem in the example coming with kprobaln.c
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1010
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1011 ------------------------------------------------------------------------
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1012 r789 | lh3lh3 | 2010-11-02 15:41:27 -0400 (Tue, 02 Nov 2010) | 4 lines
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1013 Changed paths:
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1014 M /trunk/samtools/Makefile
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1015 M /trunk/samtools/bam_md.c
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1016 M /trunk/samtools/kaln.c
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1017 M /trunk/samtools/kaln.h
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1018 A /trunk/samtools/kprobaln.c
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1019 A /trunk/samtools/kprobaln.h
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1020
|
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1021 Separate kaln and kprobaln as I am preparing further changes. At
|
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1022 present, the results should be identical to the previous.
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1023
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1024
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1025 ------------------------------------------------------------------------
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1026 r788 | petulda | 2010-11-02 12:19:04 -0400 (Tue, 02 Nov 2010) | 1 line
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1027 Changed paths:
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1028 M /trunk/samtools/bam_plcmd.c
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1029
|
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1030 Added -b option: read file names from a file
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|
|
1031 ------------------------------------------------------------------------
|
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|
1032 r787 | lh3lh3 | 2010-10-29 23:17:22 -0400 (Fri, 29 Oct 2010) | 7 lines
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1033 Changed paths:
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1034 M /trunk/samtools/bam.h
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1035 M /trunk/samtools/bam_pileup.c
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1036 M /trunk/samtools/bam_plcmd.c
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1037 M /trunk/samtools/bamtk.c
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1038
|
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|
1039 * samtools-0.1.9-2 (r787)
|
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1040
|
|
|
1041 * Allow to set a maximum per-sample depth to reduce memory. However,
|
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1042 BAQ computation is still applied to every read. The speed is not
|
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1043 improved.
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1044
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1045
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1046 ------------------------------------------------------------------------
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1047 r786 | lh3lh3 | 2010-10-29 12:10:40 -0400 (Fri, 29 Oct 2010) | 3 lines
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1048 Changed paths:
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1049 M /trunk/samtools/bam2bcf.c
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1050 M /trunk/samtools/bam2bcf.h
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1051 M /trunk/samtools/bam_plcmd.c
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1052 M /trunk/samtools/bamtk.c
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1053 M /trunk/samtools/bcftools/bcf.c
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1054 M /trunk/samtools/bcftools/vcf.c
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1055
|
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|
1056 * samtools-0.1.9-1 (r786)
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1057 * samtools: optionally perform exact test for each sample
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1058
|
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|
1059 ------------------------------------------------------------------------
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1060 r785 | lh3lh3 | 2010-10-29 09:42:25 -0400 (Fri, 29 Oct 2010) | 2 lines
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1061 Changed paths:
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1062 M /trunk/samtools/bam2bcf.c
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1063 M /trunk/samtools/bam2bcf.h
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1064 M /trunk/samtools/bam_plcmd.c
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1065 M /trunk/samtools/bcftools/bcf.c
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1066
|
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1067 Optionally output "DP", the individual read depth
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1068
|
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|
1069 ------------------------------------------------------------------------
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1070 r784 | lh3lh3 | 2010-10-27 23:10:27 -0400 (Wed, 27 Oct 2010) | 2 lines
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1071 Changed paths:
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1072 M /trunk/samtools/samtools.1
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1073
|
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|
1074 acknowledge Petr and John who have greatly contributed to the project.
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1075
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1076 ------------------------------------------------------------------------
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1077 r783 | lh3lh3 | 2010-10-27 22:47:47 -0400 (Wed, 27 Oct 2010) | 2 lines
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1078 Changed paths:
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1079 M /trunk/samtools/ChangeLog
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1080 M /trunk/samtools/NEWS
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1081 M /trunk/samtools/bamtk.c
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1082 M /trunk/samtools/samtools.1
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1083
|
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1084 Release samtools-0.1.9 (r783)
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1085
|
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|
1086 ------------------------------------------------------------------------
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1087 r782 | lh3lh3 | 2010-10-27 19:58:54 -0400 (Wed, 27 Oct 2010) | 2 lines
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1088 Changed paths:
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1089 M /trunk/samtools/bam_plcmd.c
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1090
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1091 fixed a silly bug in pileup
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1092
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1093 ------------------------------------------------------------------------
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1094 r781 | lh3lh3 | 2010-10-27 14:39:48 -0400 (Wed, 27 Oct 2010) | 5 lines
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1095 Changed paths:
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1096 M /trunk/samtools/ChangeLog
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1097 M /trunk/samtools/bam_plcmd.c
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1098 M /trunk/samtools/bam_sort.c
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1099 M /trunk/samtools/bamtk.c
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1100 M /trunk/samtools/samtools.1
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1101
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1102 * samtools-0.1.8-22 (r781)
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1103 * made BAQ the default behavior of mpileup
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1104 * updated manual
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1105 * in merge, force to exit given inconsistent header when "-R" is not in use.
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1106
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1107 ------------------------------------------------------------------------
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1108 r780 | lh3lh3 | 2010-10-27 11:01:11 -0400 (Wed, 27 Oct 2010) | 3 lines
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1109 Changed paths:
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1110 M /trunk/samtools/bam.h
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1111 M /trunk/samtools/bam_plcmd.c
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1112 M /trunk/samtools/bamtk.c
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1113
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1114 * samtools-0.1.8-21 (r780)
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1115 * minor speedup to pileup
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1116
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1117 ------------------------------------------------------------------------
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1118 r779 | lh3lh3 | 2010-10-27 09:58:56 -0400 (Wed, 27 Oct 2010) | 2 lines
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1119 Changed paths:
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1120 M /trunk/samtools/bam_pileup.c
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1121 M /trunk/samtools/bam_plcmd.c
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1122 M /trunk/samtools/examples/toy.sam
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1123
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1124 improve pileup a little bit
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1125
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1126 ------------------------------------------------------------------------
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1127 r778 | lh3lh3 | 2010-10-27 00:14:43 -0400 (Wed, 27 Oct 2010) | 3 lines
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1128 Changed paths:
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1129 M /trunk/samtools/bam.h
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1130 M /trunk/samtools/bam_pileup.c
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1131 M /trunk/samtools/bam_plcmd.c
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1132 M /trunk/samtools/bam_tview.c
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1133 M /trunk/samtools/bamtk.c
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1134
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1135 * samtools-0.1.8-20 (r778)
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1136 * speed up pileup, although I do not know how much is the improvement
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1137
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1138 ------------------------------------------------------------------------
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1139 r777 | lh3lh3 | 2010-10-26 17:26:04 -0400 (Tue, 26 Oct 2010) | 3 lines
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1140 Changed paths:
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1141 M /trunk/samtools/bam_maqcns.c
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1142 M /trunk/samtools/bam_maqcns.h
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1143 M /trunk/samtools/bam_plcmd.c
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1144 M /trunk/samtools/bamtk.c
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1145 M /trunk/samtools/examples/Makefile
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1146
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1147 * samtools-0.1.8-19 (r777)
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1148 * integrate mpileup features to pileup: min_baseQ, capQ, prob_realn, paired-only and biased prior
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1149
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1150 ------------------------------------------------------------------------
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1151 r776 | lh3lh3 | 2010-10-26 15:27:46 -0400 (Tue, 26 Oct 2010) | 2 lines
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1152 Changed paths:
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1153 M /trunk/samtools/bam_md.c
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1154
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1155 remove local realignment (probabilistic realignment is still there)
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1156
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1157 ------------------------------------------------------------------------
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1158 r774 | jmarshall | 2010-10-21 06:52:38 -0400 (Thu, 21 Oct 2010) | 3 lines
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1159 Changed paths:
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1160 M /trunk/samtools/sam_view.c
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1161
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1162 Add the relevant filename or region to error messages, and cause a failure
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1163 exit status where appropriate. Based on a patch provided by Marcel Martin.
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1164
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1165 ------------------------------------------------------------------------
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1166 r773 | lh3lh3 | 2010-10-19 19:44:31 -0400 (Tue, 19 Oct 2010) | 3 lines
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1167 Changed paths:
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1168 M /trunk/samtools/examples/toy.sam
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1169 M /trunk/samtools/kaln.c
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1170
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1171 * Minor code changes. No real effect.
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1172 * change quality to 30 in toy.sam
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1173
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1174 ------------------------------------------------------------------------
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1175 r772 | lh3lh3 | 2010-10-18 23:40:13 -0400 (Mon, 18 Oct 2010) | 2 lines
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1176 Changed paths:
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1177 M /trunk/samtools/examples/toy.fa
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1178 M /trunk/samtools/examples/toy.sam
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1179
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1180 added another toy example
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1181
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1182 ------------------------------------------------------------------------
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1183 r771 | lh3lh3 | 2010-10-13 23:32:12 -0400 (Wed, 13 Oct 2010) | 2 lines
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1184 Changed paths:
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1185 M /trunk/samtools/bcftools/call1.c
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1186 M /trunk/samtools/bcftools/ld.c
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1187 M /trunk/samtools/bcftools/vcfutils.pl
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1188
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1189 improve the LD statistics
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1190
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1191 ------------------------------------------------------------------------
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1192 r770 | lh3lh3 | 2010-10-12 23:49:26 -0400 (Tue, 12 Oct 2010) | 3 lines
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1193 Changed paths:
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1194 M /trunk/samtools/bcftools/call1.c
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1195 M /trunk/samtools/bcftools/vcfutils.pl
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1196
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1197 * a minor fix to the -L option
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1198 * add ldstats to vcfutils.pl
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1199
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1200 ------------------------------------------------------------------------
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1201 r769 | lh3lh3 | 2010-10-12 15:51:57 -0400 (Tue, 12 Oct 2010) | 2 lines
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1202 Changed paths:
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1203 M /trunk/samtools/bcftools/bcf.c
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1204
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1205 a minor change
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1206
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1207 ------------------------------------------------------------------------
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1208 r768 | lh3lh3 | 2010-10-12 15:49:06 -0400 (Tue, 12 Oct 2010) | 2 lines
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1209 Changed paths:
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1210 M /trunk/samtools/bcftools/Makefile
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1211 A /trunk/samtools/bcftools/ld.c
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1212
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1213 forget to add the key file
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1214
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1215 ------------------------------------------------------------------------
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1216 r767 | lh3lh3 | 2010-10-12 15:48:46 -0400 (Tue, 12 Oct 2010) | 4 lines
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1217 Changed paths:
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1218 M /trunk/samtools/bcftools/Makefile
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1219 M /trunk/samtools/bcftools/bcf.c
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1220 M /trunk/samtools/bcftools/bcf.h
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1221 M /trunk/samtools/bcftools/call1.c
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1222 M /trunk/samtools/bcftools/prob1.c
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1223 M /trunk/samtools/bcftools/vcfutils.pl
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1224
|
|
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1225 * vcfutils.pl: fixed a typo in help message
|
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|
1226 * added APIs: bcf_append_info() and bcf_cpy()
|
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1227 * calculate adjacent LD
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1228
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1229 ------------------------------------------------------------------------
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1230 r766 | lh3lh3 | 2010-10-11 11:06:40 -0400 (Mon, 11 Oct 2010) | 2 lines
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1231 Changed paths:
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1232 M /trunk/samtools/bcftools/vcfutils.pl
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1233
|
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1234 added filter for samtools/bcftools genetated VCFs
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1235
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1236 ------------------------------------------------------------------------
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1237 r765 | lh3lh3 | 2010-10-05 14:05:18 -0400 (Tue, 05 Oct 2010) | 3 lines
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1238 Changed paths:
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1239 M /trunk/samtools/bcftools/vcfutils.pl
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1240 M /trunk/samtools/kaln.c
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1241
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1242 * removed a comment line in kaln.c
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1243 * vcfutils.pl fillac works when GT is not the first field
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1244
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1245 ------------------------------------------------------------------------
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1246 r764 | petulda | 2010-10-05 08:59:36 -0400 (Tue, 05 Oct 2010) | 1 line
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1247 Changed paths:
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1248 A /trunk/samtools/bcftools/bcf-fix.pl
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1249
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1250 Convert VCF output of "bcftools view -bgcv" to a valid VCF file
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1251 ------------------------------------------------------------------------
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1252 r763 | lh3lh3 | 2010-10-02 22:51:03 -0400 (Sat, 02 Oct 2010) | 4 lines
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1253 Changed paths:
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1254 M /trunk/samtools/bam_plcmd.c
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1255 M /trunk/samtools/bamtk.c
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1256 A /trunk/samtools/bcftools/bcftools.1
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1257 M /trunk/samtools/bcftools/call1.c
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1258 M /trunk/samtools/samtools.1
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1259
|
|
|
1260 * samtools-0.1.8-18 (r763)
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|
|
1261 * added bcftools manual page
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1262 * minor fix to mpileup and view command lines
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1263
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1264 ------------------------------------------------------------------------
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1265 r762 | lh3lh3 | 2010-10-02 21:46:25 -0400 (Sat, 02 Oct 2010) | 3 lines
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1266 Changed paths:
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1267 M /trunk/samtools/bcftools/bcf.c
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1268 M /trunk/samtools/bcftools/call1.c
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1269 M /trunk/samtools/bcftools/vcfutils.pl
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1270
|
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1271 * vcfutils.pl qstats: calculate marginal ts/tv
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1272 * allow to call genotypes at variant sites
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1273
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1274 ------------------------------------------------------------------------
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1275 r761 | lh3lh3 | 2010-10-01 00:29:55 -0400 (Fri, 01 Oct 2010) | 3 lines
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1276 Changed paths:
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1277 M /trunk/samtools/kaln.c
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1278 M /trunk/samtools/misc/HmmGlocal.java
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1279
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|
1280 I am changing the gap open probability back to 0.001. It seems that
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|
1281 being conservative here is a good thing...
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1282
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1283 ------------------------------------------------------------------------
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1284 r760 | lh3lh3 | 2010-10-01 00:11:27 -0400 (Fri, 01 Oct 2010) | 5 lines
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1285 Changed paths:
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1286 M /trunk/samtools/bamtk.c
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1287 M /trunk/samtools/kaln.c
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1288 A /trunk/samtools/misc/HmmGlocal.java
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1289
|
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|
1290 * samtools-0.1.8-17 (r760)
|
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|
1291 * the default gap open penalty is too small (a typo)
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|
1292 * added comments on hmm_realn
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1293 * Java implementation
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1294
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1295 ------------------------------------------------------------------------
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1296 r759 | lh3lh3 | 2010-09-30 10:12:54 -0400 (Thu, 30 Sep 2010) | 2 lines
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1297 Changed paths:
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1298 M /trunk/samtools/bamtk.c
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1299
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|
1300 mark samtools-0.1.8-16 (r759)
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1301
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1302 ------------------------------------------------------------------------
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1303 r758 | lh3lh3 | 2010-09-30 10:12:02 -0400 (Thu, 30 Sep 2010) | 2 lines
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1304 Changed paths:
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1305 M /trunk/samtools/kaln.c
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1306
|
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|
1307 round to the nearest integer
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1308
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1309 ------------------------------------------------------------------------
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1310 r757 | lh3lh3 | 2010-09-28 17:16:43 -0400 (Tue, 28 Sep 2010) | 4 lines
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1311 Changed paths:
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1312 M /trunk/samtools/kaln.c
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1313
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|
1314 I was trying to accelerate ka_prob_glocal() as this will be the
|
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|
1315 bottleneck. After an hour, the only gain is to change division to
|
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|
1316 multiplication. OK. I will stop.
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1317
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1318 ------------------------------------------------------------------------
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1319 r756 | lh3lh3 | 2010-09-28 16:57:49 -0400 (Tue, 28 Sep 2010) | 2 lines
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1320 Changed paths:
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1321 M /trunk/samtools/kaln.c
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1322
|
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|
1323 this is interesting. multiplication is much faster than division, at least on my Mac
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1324
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1325 ------------------------------------------------------------------------
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1326 r755 | lh3lh3 | 2010-09-28 16:19:13 -0400 (Tue, 28 Sep 2010) | 2 lines
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1327 Changed paths:
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1328 M /trunk/samtools/kaln.c
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1329
|
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|
1330 minor changes
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1331
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1332 ------------------------------------------------------------------------
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1333 r754 | lh3lh3 | 2010-09-28 15:44:16 -0400 (Tue, 28 Sep 2010) | 2 lines
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1334 Changed paths:
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1335 M /trunk/samtools/bam_md.c
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1336 M /trunk/samtools/bam_plcmd.c
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1337 M /trunk/samtools/kaln.c
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1338
|
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|
1339 prob_realn() seems working!
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1340
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|
1341 ------------------------------------------------------------------------
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1342 r753 | lh3lh3 | 2010-09-28 12:48:23 -0400 (Tue, 28 Sep 2010) | 2 lines
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1343 Changed paths:
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1344 M /trunk/samtools/kaln.c
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1345
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1346 minor
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1347
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1348 ------------------------------------------------------------------------
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1349 r752 | lh3lh3 | 2010-09-28 12:47:41 -0400 (Tue, 28 Sep 2010) | 2 lines
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1350 Changed paths:
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1351 M /trunk/samtools/kaln.c
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1352 M /trunk/samtools/kaln.h
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1353
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1354 Convert phredQ to probabilities
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1355
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1356 ------------------------------------------------------------------------
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1357 r751 | lh3lh3 | 2010-09-28 12:32:08 -0400 (Tue, 28 Sep 2010) | 2 lines
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1358 Changed paths:
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1359 M /trunk/samtools/kaln.c
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1360 M /trunk/samtools/kaln.h
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1361
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1362 Implement the glocal HMM; discard the extention HMM
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1363
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1364 ------------------------------------------------------------------------
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1365 r750 | lh3lh3 | 2010-09-28 00:06:11 -0400 (Tue, 28 Sep 2010) | 2 lines
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1366 Changed paths:
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1367 M /trunk/samtools/kaln.c
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1368
|
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1369 improve numerical stability
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1370
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1371 ------------------------------------------------------------------------
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1372 r749 | lh3lh3 | 2010-09-27 23:27:54 -0400 (Mon, 27 Sep 2010) | 2 lines
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1373 Changed paths:
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1374 M /trunk/samtools/kaln.c
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1375
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1376 more comments
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1377
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1378 ------------------------------------------------------------------------
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1379 r748 | lh3lh3 | 2010-09-27 23:17:16 -0400 (Mon, 27 Sep 2010) | 2 lines
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1380 Changed paths:
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1381 M /trunk/samtools/kaln.c
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1382
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|
1383 fixed a bug in banded DP
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1384
|
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|
1385 ------------------------------------------------------------------------
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1386 r747 | lh3lh3 | 2010-09-27 23:05:12 -0400 (Mon, 27 Sep 2010) | 3 lines
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1387 Changed paths:
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1388 M /trunk/samtools/kaln.c
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1389
|
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|
1390 * fixed that weird issue.
|
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|
1391 * the banded version is NOT working
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1392
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|
1393 ------------------------------------------------------------------------
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1394 r746 | lh3lh3 | 2010-09-27 22:57:05 -0400 (Mon, 27 Sep 2010) | 2 lines
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1395 Changed paths:
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1396 M /trunk/samtools/kaln.c
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1397
|
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|
1398 More comments. This version seems working, but something is a little weird...
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1399
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1400 ------------------------------------------------------------------------
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1401 r745 | lh3lh3 | 2010-09-27 17:21:40 -0400 (Mon, 27 Sep 2010) | 6 lines
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1402 Changed paths:
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1403 M /trunk/samtools/kaln.c
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1404
|
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|
1405 A little code cleanup. Now the forward and backback algorithms give
|
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|
1406 nearly identical P(x), which means both are close to the correct
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|
1407 forms. However, I have only tested on toy examples. Minor errors in
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1408 the implementation may not be obvious.
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1409
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1410
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1411 ------------------------------------------------------------------------
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1412 r744 | lh3lh3 | 2010-09-27 16:55:15 -0400 (Mon, 27 Sep 2010) | 2 lines
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1413 Changed paths:
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1414 M /trunk/samtools/bam_plcmd.c
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|
1415 M /trunk/samtools/bam_sort.c
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|
1416 M /trunk/samtools/kaln.c
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|
1417 M /trunk/samtools/kaln.h
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1418
|
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|
1419 ...
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1420
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1421 ------------------------------------------------------------------------
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1422 r743 | jmarshall | 2010-09-27 08:19:06 -0400 (Mon, 27 Sep 2010) | 6 lines
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1423 Changed paths:
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1424 M /trunk/samtools/bam_sort.c
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1425
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|
1426 Abort if merge -h's INH.SAM cannot be opened, just as we abort
|
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|
1427 if any of the IN#.BAM input files cannot be opened.
|
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|
1428
|
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1429 Also propagate any error indication returned by bam_merge_core()
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1430 to samtools merge's exit status.
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1431
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|
1432 ------------------------------------------------------------------------
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|
1433 r741 | jmarshall | 2010-09-24 11:08:24 -0400 (Fri, 24 Sep 2010) | 5 lines
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1434 Changed paths:
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|
1435 M /trunk/samtools/bam_index.c
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|
1436
|
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|
1437 Use bam_validate1() to detect garbage records in the event of a corrupt
|
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|
1438 BAI index file that causes a bam_seek() to an invalid position. At most
|
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1439 one record (namely, the bam_iter_read terminator) is tested per bam_fetch()
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1440 call, so the cost is insignificant in the normal case.
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1441
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1442 ------------------------------------------------------------------------
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1443 r740 | jmarshall | 2010-09-24 11:00:19 -0400 (Fri, 24 Sep 2010) | 2 lines
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1444 Changed paths:
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1445 M /trunk/samtools/bam.c
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1446 M /trunk/samtools/bam.h
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1447
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1448 Add bam_validate1().
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1449
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1450 ------------------------------------------------------------------------
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1451 r739 | lh3lh3 | 2010-09-22 12:07:50 -0400 (Wed, 22 Sep 2010) | 3 lines
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1452 Changed paths:
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1453 M /trunk/samtools/bam_md.c
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1454 M /trunk/samtools/bamtk.c
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1455
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1456 * samtools-0.1.8-15 (r379)
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1457 * allow to change capQ parameter in calmd
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1458
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1459 ------------------------------------------------------------------------
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1460 r738 | jmarshall | 2010-09-22 11:15:33 -0400 (Wed, 22 Sep 2010) | 13 lines
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1461 Changed paths:
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1462 M /trunk/samtools/bam_index.c
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1463 M /trunk/samtools/sam_view.c
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1464
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1465 When bam_read1() returns an error (return value <= -2), propagate that error
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1466 to bam_iter_read()'s own return value. Similarly, also propagate it up to
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1467 bam_fetch()'s return value. Previously bam_fetch() always returned 0, and
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1468 callers ignored its return value anyway. With this change, 0 continues to
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1469 indicate success, while <= -2 (which can be written as < 0, as -1 is never
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1470 returned) indicates corrupted input.
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1471
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1472 bam_iter_read() ought also to propagate errors returned by bam_seek().
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1473
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1474 main_samview() can now print an error message and fail when bam_fetch()
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1475 detects that a .bai index file is corrupted or otherwise does not correspond
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1476 to the .bam file it is being used with.
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1477
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1478 ------------------------------------------------------------------------
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1479 r737 | jmarshall | 2010-09-22 10:47:42 -0400 (Wed, 22 Sep 2010) | 3 lines
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1480 Changed paths:
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1481 M /trunk/samtools/bam_index.c
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1482
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1483 0 is a successful return value from bam_read1(). (In practice, it never
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1484 returns 0 anyway; but all the other callers treat 0 as successful.)
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1485
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1486 ------------------------------------------------------------------------
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1487 r736 | lh3lh3 | 2010-09-20 17:43:08 -0400 (Mon, 20 Sep 2010) | 2 lines
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1488 Changed paths:
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1489 M /trunk/samtools/bam.h
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1490 M /trunk/samtools/bam_index.c
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1491 M /trunk/samtools/bam_sort.c
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1492
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1493 * merge files region-by-region. work on small examples but more tests are needed.
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1494
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1495 ------------------------------------------------------------------------
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1496 r735 | lh3lh3 | 2010-09-20 16:56:24 -0400 (Mon, 20 Sep 2010) | 2 lines
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1497 Changed paths:
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1498 M /trunk/samtools/bcftools/vcfutils.pl
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1499
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1500 improve qstats by checking the alleles as well
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1501
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1502 ------------------------------------------------------------------------
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1503 r734 | lh3lh3 | 2010-09-17 18:12:13 -0400 (Fri, 17 Sep 2010) | 2 lines
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1504 Changed paths:
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1505 M /trunk/samtools/bcftools/vcfutils.pl
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1506
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1507 convert UCSC SNP SQL dump to VCF
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1508
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1509 ------------------------------------------------------------------------
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1510 r733 | lh3lh3 | 2010-09-17 13:02:11 -0400 (Fri, 17 Sep 2010) | 2 lines
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1511 Changed paths:
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1512 M /trunk/samtools/bcftools/vcfutils.pl
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1513
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1514 hapmap2vcf convertor
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1515
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1516 ------------------------------------------------------------------------
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1517 r732 | lh3lh3 | 2010-09-17 10:11:37 -0400 (Fri, 17 Sep 2010) | 3 lines
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1518 Changed paths:
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1519 M /trunk/samtools/bcftools/Makefile
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1520 M /trunk/samtools/bcftools/bcf.c
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1521 M /trunk/samtools/bcftools/bcf.h
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1522 M /trunk/samtools/bcftools/vcf.c
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1523
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1524 * added comments
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1525 * VCF->BCF is not possible without knowing the sequence dictionary before hand...
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1526
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1527 ------------------------------------------------------------------------
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1528 r731 | lh3lh3 | 2010-09-17 09:15:53 -0400 (Fri, 17 Sep 2010) | 2 lines
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1529 Changed paths:
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1530 M /trunk/samtools/bam2bcf.c
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1531 M /trunk/samtools/bcftools/bcf.c
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1532 M /trunk/samtools/bcftools/bcf.h
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1533 M /trunk/samtools/bcftools/bcfutils.c
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1534 M /trunk/samtools/bcftools/call1.c
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1535 M /trunk/samtools/bcftools/vcf.c
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1536
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1537 * put n_smpl to "bcf1_t" to simplify API a little
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1538
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1539 ------------------------------------------------------------------------
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1540 r730 | lh3lh3 | 2010-09-16 21:36:01 -0400 (Thu, 16 Sep 2010) | 2 lines
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1541 Changed paths:
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1542 M /trunk/samtools/bcftools/bcf.h
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1543 M /trunk/samtools/bcftools/call1.c
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1544 M /trunk/samtools/bcftools/index.c
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1545
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1546 fixed a bug in indexing
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1547
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1548 ------------------------------------------------------------------------
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1549 r729 | lh3lh3 | 2010-09-16 16:54:48 -0400 (Thu, 16 Sep 2010) | 3 lines
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1550 Changed paths:
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1551 M /trunk/samtools/bam.c
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1552 M /trunk/samtools/bam_md.c
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1553 M /trunk/samtools/bam_pileup.c
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1554
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1555 * fixed a bug in capQ
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1556 * valgrind identifies a use of uninitialised value, but I have not fixed it.
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1557
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1558 ------------------------------------------------------------------------
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1559 r728 | lh3lh3 | 2010-09-16 15:03:59 -0400 (Thu, 16 Sep 2010) | 3 lines
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1560 Changed paths:
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1561 M /trunk/samtools/bgzip.c
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1562 M /trunk/samtools/razip.c
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1563
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1564 * fixed a bug in razip: -c will delete the input file
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1565 * copy tabix/bgzip to here
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1566
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1567 ------------------------------------------------------------------------
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1568 r727 | lh3lh3 | 2010-09-16 13:45:49 -0400 (Thu, 16 Sep 2010) | 3 lines
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1569 Changed paths:
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1570 M /trunk/samtools/bam_md.c
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1571 M /trunk/samtools/bam_plcmd.c
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1572 M /trunk/samtools/bamtk.c
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1573
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1574 * samtools-0.1.8-14 (r727)
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1575 * allow to change the capQ parameter at the command line
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1576
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1577 ------------------------------------------------------------------------
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1578 r726 | lh3lh3 | 2010-09-16 13:38:43 -0400 (Thu, 16 Sep 2010) | 4 lines
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1579 Changed paths:
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1580 M /trunk/samtools/bam_md.c
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1581 M /trunk/samtools/bam_plcmd.c
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1582 M /trunk/samtools/bcftools/vcfutils.pl
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1583 M /trunk/samtools/misc/samtools.pl
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1584
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1585 * added varFilter to vcfutils.pl
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|
1586 * reimplement realn(). now it performs a local alignment
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1587 * added cap_mapQ() to cap mapping quality when there are many substitutions
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1588
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1589 ------------------------------------------------------------------------
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1590 r724 | lh3lh3 | 2010-09-15 00:18:31 -0400 (Wed, 15 Sep 2010) | 2 lines
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1591 Changed paths:
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1592 M /trunk/samtools/bcftools/Makefile
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1593 A /trunk/samtools/bcftools/bcf2qcall.c
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1594 M /trunk/samtools/bcftools/call1.c
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1595
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1596 * convert BCF to QCALL input
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1597
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1598 ------------------------------------------------------------------------
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1599 r723 | lh3lh3 | 2010-09-14 22:41:50 -0400 (Tue, 14 Sep 2010) | 2 lines
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1600 Changed paths:
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1601 M /trunk/samtools/bam_md.c
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1602
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1603 dynamic band width in realignment
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1604
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1605 ------------------------------------------------------------------------
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1606 r722 | lh3lh3 | 2010-09-14 22:05:32 -0400 (Tue, 14 Sep 2010) | 2 lines
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1607 Changed paths:
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1608 M /trunk/samtools/bam_md.c
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1609 M /trunk/samtools/bam_plcmd.c
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1610
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1611 fixed a bug in realignment
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1612
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1613 ------------------------------------------------------------------------
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1614 r721 | lh3lh3 | 2010-09-14 20:54:09 -0400 (Tue, 14 Sep 2010) | 2 lines
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1615 Changed paths:
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1616 M /trunk/samtools/bcftools/prob1.c
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1617
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1618 fixed a minor issue
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1619
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1620 ------------------------------------------------------------------------
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1621 r720 | lh3lh3 | 2010-09-14 19:25:10 -0400 (Tue, 14 Sep 2010) | 2 lines
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1622 Changed paths:
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1623 M /trunk/samtools/Makefile
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1624 M /trunk/samtools/bam_maqcns.c
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1625 M /trunk/samtools/bam_md.c
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1626
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1627 fixed a bug in realignment
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1628
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1629 ------------------------------------------------------------------------
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1630 r719 | lh3lh3 | 2010-09-14 19:18:24 -0400 (Tue, 14 Sep 2010) | 2 lines
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1631 Changed paths:
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1632 M /trunk/samtools/bam_plcmd.c
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1633
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1634 minor changes. It is BUGGY now!
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1635
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1636 ------------------------------------------------------------------------
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1637 r718 | lh3lh3 | 2010-09-14 16:32:33 -0400 (Tue, 14 Sep 2010) | 4 lines
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1638 Changed paths:
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1639 M /trunk/samtools/bam_md.c
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1640 M /trunk/samtools/bam_pileup.c
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1641 M /trunk/samtools/kaln.c
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1642 M /trunk/samtools/kaln.h
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1643
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1644 * aggressive gapped aligner is implemented in calmd.
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1645 * distinguish gap_open and gap_end_open in banded alignment
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1646 * make tview accepts alignment with heading and tailing D
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1647
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1648 ------------------------------------------------------------------------
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1649 r717 | jmarshall | 2010-09-14 09:04:28 -0400 (Tue, 14 Sep 2010) | 2 lines
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1650 Changed paths:
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1651 M /trunk/samtools
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1652
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1653 Add svn:ignore properties for generated files that don't appear in "make all".
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1654
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1655 ------------------------------------------------------------------------
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1656 r716 | jmarshall | 2010-09-13 08:37:53 -0400 (Mon, 13 Sep 2010) | 3 lines
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1657 Changed paths:
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1658 M /trunk/samtools
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1659 M /trunk/samtools/bcftools
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|
1660 M /trunk/samtools/misc
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1661
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|
1662 Add svn:ignore properties listing the generated files.
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1663 (Except for *.o, which we'll assume is in global-ignores.)
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1664
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|
1665 ------------------------------------------------------------------------
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1666 r715 | lh3lh3 | 2010-09-08 12:53:55 -0400 (Wed, 08 Sep 2010) | 5 lines
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1667 Changed paths:
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1668 M /trunk/samtools/bamtk.c
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1669 M /trunk/samtools/bcftools/call1.c
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1670 M /trunk/samtools/bcftools/prob1.c
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1671 M /trunk/samtools/sample.c
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|
1672 M /trunk/samtools/sample.h
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1673
|
|
|
1674 * samtools-0.1.8-13 (r715)
|
|
|
1675 * fixed a bug in identifying SM across files
|
|
|
1676 * bcftools: estimate heterozygosity
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1677 * bcftools: allow to skip sites without reference bases
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1678
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1679 ------------------------------------------------------------------------
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1680 r713 | lh3lh3 | 2010-09-03 17:19:12 -0400 (Fri, 03 Sep 2010) | 2 lines
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1681 Changed paths:
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1682 M /trunk/samtools/bcftools/Makefile
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1683 M /trunk/samtools/bcftools/call1.c
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1684 M /trunk/samtools/bcftools/prob1.c
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1685 M /trunk/samtools/bcftools/prob1.h
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1686
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|
1687 quite a lot changes to the contrast caller, but I still feel something is missing...
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1688
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1689 ------------------------------------------------------------------------
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1690 r711 | lh3lh3 | 2010-09-03 00:30:48 -0400 (Fri, 03 Sep 2010) | 4 lines
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1691 Changed paths:
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1692 M /trunk/samtools/bcftools/Makefile
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1693 M /trunk/samtools/bcftools/call1.c
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1694 M /trunk/samtools/bcftools/prob1.c
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1695 M /trunk/samtools/bcftools/vcfutils.pl
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|
|
1696
|
|
|
1697 * changed 3.434 to 4.343 (typo!)
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|
1698 * fixed a bug in the contrast caller
|
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|
1699 * calculate heterozygosity
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1700
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1701 ------------------------------------------------------------------------
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1702 r710 | lh3lh3 | 2010-09-01 23:24:47 -0400 (Wed, 01 Sep 2010) | 2 lines
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1703 Changed paths:
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1704 M /trunk/samtools/bcftools/bcf.h
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1705 M /trunk/samtools/bcftools/bcfutils.c
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1706 M /trunk/samtools/bcftools/call1.c
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1707
|
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1708 SNP calling from the GL field
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1709
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1710 ------------------------------------------------------------------------
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1711 r709 | lh3lh3 | 2010-09-01 18:52:30 -0400 (Wed, 01 Sep 2010) | 2 lines
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1712 Changed paths:
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1713 M /trunk/samtools/bcftools/vcf.c
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1714
|
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|
1715 fixed another problem
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1716
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1717 ------------------------------------------------------------------------
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1718 r708 | lh3lh3 | 2010-09-01 18:31:17 -0400 (Wed, 01 Sep 2010) | 3 lines
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1719 Changed paths:
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1720 M /trunk/samtools/bcftools/bcf.c
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|
1721 M /trunk/samtools/bcftools/vcf.c
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1722
|
|
|
1723 * fixed bugs in parsing VCF
|
|
|
1724 * parser now works with GT/GQ/DP/PL/GL
|
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1725
|
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|
1726 ------------------------------------------------------------------------
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|
1727 r707 | lh3lh3 | 2010-09-01 15:28:29 -0400 (Wed, 01 Sep 2010) | 2 lines
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1728 Changed paths:
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|
1729 M /trunk/samtools/bcftools/Makefile
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|
1730 M /trunk/samtools/bcftools/prob1.c
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1731
|
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1732 Do not compile _BCF_QUAD by default
|
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1733
|
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|
1734 ------------------------------------------------------------------------
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|
1735 r706 | lh3lh3 | 2010-09-01 15:21:41 -0400 (Wed, 01 Sep 2010) | 2 lines
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1736 Changed paths:
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1737 M /trunk/samtools/bcftools/bcf.c
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1738 M /trunk/samtools/bcftools/bcf.h
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1739 M /trunk/samtools/bcftools/bcfutils.c
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|
1740 M /trunk/samtools/bcftools/call1.c
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1741
|
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1742 Write the correct ALT and PL in the SNP calling mode.
|
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1743
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|
1744 ------------------------------------------------------------------------
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|
1745 r705 | lh3lh3 | 2010-09-01 12:50:33 -0400 (Wed, 01 Sep 2010) | 2 lines
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1746 Changed paths:
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1747 M /trunk/samtools/bcftools/vcfutils.pl
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1748
|
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|
1749 more commands for my own uses
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1750
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1751 ------------------------------------------------------------------------
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1752 r704 | lh3lh3 | 2010-09-01 09:26:10 -0400 (Wed, 01 Sep 2010) | 2 lines
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1753 Changed paths:
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1754 A /trunk/samtools/bcftools/vcfutils.pl
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1755
|
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1756 Utilities for processing VCF
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1757
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1758 ------------------------------------------------------------------------
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1759 r703 | lh3lh3 | 2010-08-31 16:44:57 -0400 (Tue, 31 Aug 2010) | 2 lines
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1760 Changed paths:
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1761 M /trunk/samtools/bcftools/Makefile
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|
1762 M /trunk/samtools/bcftools/call1.c
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1763 M /trunk/samtools/bcftools/prob1.c
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1764 M /trunk/samtools/bcftools/prob1.h
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1765
|
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|
1766 preliminary contrast variant caller
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1767
|
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1768 ------------------------------------------------------------------------
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1769 r702 | lh3lh3 | 2010-08-31 12:28:39 -0400 (Tue, 31 Aug 2010) | 2 lines
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1770 Changed paths:
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1771 M /trunk/samtools/bcftools/call1.c
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1772 M /trunk/samtools/bcftools/prob1.c
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|
1773 M /trunk/samtools/bcftools/prob1.h
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1774
|
|
|
1775 z' and z'' can be calculated
|
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1776
|
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|
1777 ------------------------------------------------------------------------
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1778 r701 | lh3lh3 | 2010-08-31 10:20:57 -0400 (Tue, 31 Aug 2010) | 3 lines
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1779 Changed paths:
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|
1780 M /trunk/samtools/bcftools/Makefile
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1781 A /trunk/samtools/bcftools/call1.c (from /trunk/samtools/bcftools/vcfout.c:699)
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1782 M /trunk/samtools/bcftools/prob1.c
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1783 D /trunk/samtools/bcftools/vcfout.c
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1784
|
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|
1785 * rename vcfout.c as call1.c
|
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|
1786 * prepare to add two-sample comparison
|
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1787
|
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|
1788 ------------------------------------------------------------------------
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1789 r699 | lh3lh3 | 2010-08-24 15:28:16 -0400 (Tue, 24 Aug 2010) | 2 lines
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1790 Changed paths:
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|
1791 M /trunk/samtools/bcftools/vcfout.c
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1792
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1793 fixed a bug in calculating the t statistics
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1794
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1795 ------------------------------------------------------------------------
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1796 r698 | lh3lh3 | 2010-08-24 14:05:50 -0400 (Tue, 24 Aug 2010) | 3 lines
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1797 Changed paths:
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1798 M /trunk/samtools/bam2bcf.c
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1799 M /trunk/samtools/bam2bcf.h
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1800 M /trunk/samtools/bamtk.c
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1801 M /trunk/samtools/bcftools/kfunc.c
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1802 M /trunk/samtools/bcftools/vcfout.c
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1803
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1804 * samtools-0.1.8-13 (r698)
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1805 * perform one-tailed t-test for baseQ, mapQ and endDist
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1806
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1807 ------------------------------------------------------------------------
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1808 r697 | lh3lh3 | 2010-08-24 12:30:13 -0400 (Tue, 24 Aug 2010) | 2 lines
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1809 Changed paths:
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1810 M /trunk/samtools/bcftools/kfunc.c
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1811
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1812 added regularized incomplete beta function
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1813
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1814 ------------------------------------------------------------------------
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1815 r695 | lh3lh3 | 2010-08-23 17:36:17 -0400 (Mon, 23 Aug 2010) | 2 lines
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1816 Changed paths:
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1817 M /trunk/samtools/bam_maqcns.c
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1818 M /trunk/samtools/bam_plcmd.c
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1819
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1820 change the default correlation coefficient
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1821
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1822 ------------------------------------------------------------------------
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1823 r694 | lh3lh3 | 2010-08-23 14:46:52 -0400 (Mon, 23 Aug 2010) | 2 lines
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1824 Changed paths:
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1825 M /trunk/samtools/bcftools/bcf.c
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1826 M /trunk/samtools/bcftools/vcfout.c
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1827
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1828 print QUAL as floating numbers
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1829
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1830 ------------------------------------------------------------------------
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1831 r693 | lh3lh3 | 2010-08-23 14:06:07 -0400 (Mon, 23 Aug 2010) | 3 lines
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1832 Changed paths:
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1833 M /trunk/samtools/Makefile
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1834 M /trunk/samtools/bam_plcmd.c
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1835 M /trunk/samtools/bamtk.c
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1836 M /trunk/samtools/examples/Makefile
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1837 A /trunk/samtools/sample.c
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1838 A /trunk/samtools/sample.h
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1839
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1840 * samtools-0.1.8-12 (r692)
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1841 * group data by samples in "mpileup -g"
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1842
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1843 ------------------------------------------------------------------------
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1844 r692 | lh3lh3 | 2010-08-23 10:58:53 -0400 (Mon, 23 Aug 2010) | 2 lines
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1845 Changed paths:
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1846 M /trunk/samtools/Makefile
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1847 D /trunk/samtools/bam_mcns.c
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1848 D /trunk/samtools/bam_mcns.h
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1849 M /trunk/samtools/bam_plcmd.c
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1850
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1851 remove VCF output in mpileup
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1852
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1853 ------------------------------------------------------------------------
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1854 r691 | lh3lh3 | 2010-08-23 10:48:20 -0400 (Mon, 23 Aug 2010) | 3 lines
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1855 Changed paths:
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1856 M /trunk/samtools/bam2bcf.c
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1857 M /trunk/samtools/bam2bcf.h
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1858
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1859 * use the revised MAQ error model for mpileup
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1860 * prepare to remove the independent model from mpileup
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1861
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1862 ------------------------------------------------------------------------
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1863 r690 | lh3lh3 | 2010-08-20 15:46:40 -0400 (Fri, 20 Aug 2010) | 2 lines
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1864 Changed paths:
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1865 M /trunk/samtools/Makefile
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1866 M /trunk/samtools/bam_maqcns.c
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1867 M /trunk/samtools/bam_maqcns.h
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1868 M /trunk/samtools/bam_plcmd.c
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1869 A /trunk/samtools/errmod.c
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1870 A /trunk/samtools/errmod.h
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1871 M /trunk/samtools/ksort.h
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1872
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1873 added revised MAQ error model
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1874
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1875 ------------------------------------------------------------------------
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1876 r689 | lh3lh3 | 2010-08-18 09:55:20 -0400 (Wed, 18 Aug 2010) | 2 lines
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1877 Changed paths:
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1878 M /trunk/samtools/bcftools/prob1.c
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1879 M /trunk/samtools/bcftools/prob1.h
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1880 M /trunk/samtools/bcftools/vcfout.c
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1881
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1882 allow to read the prior from the error output. EM iteration is working.
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1883
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1884 ------------------------------------------------------------------------
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1885 r688 | lh3lh3 | 2010-08-17 12:12:20 -0400 (Tue, 17 Aug 2010) | 3 lines
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1886 Changed paths:
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1887 M /trunk/samtools/bcftools/main.c
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1888 M /trunk/samtools/bcftools/vcf.c
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1889
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1890 * write a little more VCF header
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1891 * concatenate BCFs
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1892
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1893 ------------------------------------------------------------------------
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1894 r687 | lh3lh3 | 2010-08-16 20:53:16 -0400 (Mon, 16 Aug 2010) | 2 lines
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1895 Changed paths:
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1896 M /trunk/samtools/bcftools/bcf.c
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1897 M /trunk/samtools/bcftools/bcf.h
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1898 M /trunk/samtools/bcftools/bcf.tex
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1899
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1900 use float for QUAL
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1901
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1902 ------------------------------------------------------------------------
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1903 r686 | lh3lh3 | 2010-08-14 00:11:13 -0400 (Sat, 14 Aug 2010) | 2 lines
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1904 Changed paths:
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1905 M /trunk/samtools/bcftools/bcf.c
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1906 M /trunk/samtools/bcftools/prob1.c
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1907
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1908 faster for large sample size (in principle)
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1909
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1910 ------------------------------------------------------------------------
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1911 r685 | lh3lh3 | 2010-08-13 23:28:31 -0400 (Fri, 13 Aug 2010) | 4 lines
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1912 Changed paths:
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1913 M /trunk/samtools/bcftools/prob1.c
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1914
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1915 * a numerically stable method to calculate z_{jk}
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1916 * currently slower than the old method but will be important for large sample size
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1917 * in principle, we can speed up for large n, but have not tried
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1918
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1919 ------------------------------------------------------------------------
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1920 r684 | lh3lh3 | 2010-08-11 21:58:31 -0400 (Wed, 11 Aug 2010) | 2 lines
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1921 Changed paths:
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1922 M /trunk/samtools/bcftools/vcfout.c
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1923
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1924 fixed an issue in parsing integer
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1925
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1926 ------------------------------------------------------------------------
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1927 r683 | lh3lh3 | 2010-08-09 13:05:07 -0400 (Mon, 09 Aug 2010) | 2 lines
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1928 Changed paths:
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1929 M /trunk/samtools/bcftools/bcf.c
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1930
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1931 do not print refname if file is converted from VCF
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1932
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1933 ------------------------------------------------------------------------
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1934 r682 | lh3lh3 | 2010-08-09 12:59:47 -0400 (Mon, 09 Aug 2010) | 3 lines
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1935 Changed paths:
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1936 M /trunk/samtools/bcftools/vcf.c
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1937
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1938 * parse PL
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1939 * fixed a bug in parsing VCF
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1940
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1941 ------------------------------------------------------------------------
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1942 r681 | lh3lh3 | 2010-08-09 12:49:23 -0400 (Mon, 09 Aug 2010) | 4 lines
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1943 Changed paths:
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1944 M /trunk/samtools/bcftools/bcf.c
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1945 M /trunk/samtools/bcftools/bcf.h
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1946 M /trunk/samtools/bcftools/bcfutils.c
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1947 M /trunk/samtools/bcftools/main.c
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1948 M /trunk/samtools/bcftools/vcf.c
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1949 M /trunk/samtools/bcftools/vcfout.c
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1950 M /trunk/samtools/bgzf.c
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1951 M /trunk/samtools/kstring.c
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1952
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1953 * fixed a bug in kstrtok@kstring.c
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1954 * preliminary VCF parser (not parse everything for now)
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1955 * improved view interface
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1956
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1957 ------------------------------------------------------------------------
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1958 r680 | lh3lh3 | 2010-08-09 10:43:13 -0400 (Mon, 09 Aug 2010) | 4 lines
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1959 Changed paths:
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1960 M /trunk/samtools/bcftools/bcf.c
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1961 M /trunk/samtools/bcftools/bcf.h
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1962 M /trunk/samtools/bcftools/vcfout.c
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1963 M /trunk/samtools/kstring.c
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1964 M /trunk/samtools/kstring.h
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1965
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1966 * improved kstring (added kstrtok)
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1967 * removed the limit on the format string length in bcftools
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1968 * use kstrtok to parse format which fixed a bug in the old code
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1969
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1970 ------------------------------------------------------------------------
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1971 r679 | lh3lh3 | 2010-08-09 01:12:05 -0400 (Mon, 09 Aug 2010) | 2 lines
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1972 Changed paths:
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1973 A /trunk/samtools/bcftools/README
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1974 M /trunk/samtools/bcftools/vcfout.c
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1975
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1976 help messages
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1977
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1978 ------------------------------------------------------------------------
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1979 r678 | lh3lh3 | 2010-08-09 00:01:52 -0400 (Mon, 09 Aug 2010) | 2 lines
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1980 Changed paths:
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1981 M /trunk/samtools/bcftools/vcfout.c
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1982
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1983 perform single-tail test for ED4
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1984
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1985 ------------------------------------------------------------------------
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1986 r677 | lh3lh3 | 2010-08-08 23:48:35 -0400 (Sun, 08 Aug 2010) | 2 lines
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1987 Changed paths:
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1988 M /trunk/samtools/bcftools/Makefile
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1989 M /trunk/samtools/bcftools/kfunc.c
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1990 M /trunk/samtools/bcftools/vcfout.c
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1991
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1992 * test depth, end distance and HWE
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1993
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1994 ------------------------------------------------------------------------
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1995 r676 | lh3lh3 | 2010-08-08 02:04:15 -0400 (Sun, 08 Aug 2010) | 2 lines
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1996 Changed paths:
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1997 M /trunk/samtools/bcftools/kfunc.c
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1998
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1999 reimplement incomplete gamma functions. no copy-paste
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2000
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2001 ------------------------------------------------------------------------
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2002 r675 | lh3lh3 | 2010-08-06 22:42:54 -0400 (Fri, 06 Aug 2010) | 3 lines
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2003 Changed paths:
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2004 M /trunk/samtools/bam2bcf.c
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2005 M /trunk/samtools/bam2bcf.h
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2006 M /trunk/samtools/bcftools/fet.c
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2007 M /trunk/samtools/bcftools/prob1.c
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2008 M /trunk/samtools/bcftools/prob1.h
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2009 M /trunk/samtools/bcftools/vcfout.c
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2010
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2011 * bcftools: add HWE (no testing for now)
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2012 * record end dist in a 2x2 table, not avg, std any more
|
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2013
|
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|
2014 ------------------------------------------------------------------------
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2015 r674 | lh3lh3 | 2010-08-06 17:30:16 -0400 (Fri, 06 Aug 2010) | 3 lines
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2016 Changed paths:
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2017 A /trunk/samtools/bcftools/kfunc.c
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2018
|
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|
2019 * Special functions: log(gamma()), erfc(), P(a,x) (incomplete gamma)
|
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2020 * Not using Numerical Recipe due to licensing issues
|
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2021
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2022 ------------------------------------------------------------------------
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2023 r673 | lh3lh3 | 2010-08-05 23:46:53 -0400 (Thu, 05 Aug 2010) | 2 lines
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2024 Changed paths:
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2025 A /trunk/samtools/bcftools/fet.c
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2026
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2027 Fisher's exact test
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2028
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2029 ------------------------------------------------------------------------
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2030 r672 | lh3lh3 | 2010-08-05 21:48:33 -0400 (Thu, 05 Aug 2010) | 3 lines
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2031 Changed paths:
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2032 M /trunk/samtools/bam2bcf.c
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2033 M /trunk/samtools/bam2bcf.h
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2034 M /trunk/samtools/bamtk.c
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2035 M /trunk/samtools/examples/Makefile
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2036
|
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|
2037 * samtools-0.1.8-11 (r672)
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2038 * collect more stats for allele balance test in bcftools (not yet)
|
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2039
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2040 ------------------------------------------------------------------------
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2041 r671 | lh3lh3 | 2010-08-05 16:17:58 -0400 (Thu, 05 Aug 2010) | 3 lines
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2042 Changed paths:
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2043 M /trunk/samtools/bam_plcmd.c
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2044 M /trunk/samtools/bcftools/bcf.c
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2045 M /trunk/samtools/bcftools/main.c
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2046
|
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|
2047 * the code base is stablized again.
|
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2048 * I will delay the vcf parser, which is quite complicated but with little value for now
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2049
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2050 ------------------------------------------------------------------------
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2051 r670 | lh3lh3 | 2010-08-05 16:03:23 -0400 (Thu, 05 Aug 2010) | 2 lines
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2052 Changed paths:
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2053 M /trunk/samtools/examples/Makefile
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2054
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2055 minor
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2056
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2057 ------------------------------------------------------------------------
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2058 r669 | lh3lh3 | 2010-08-05 16:03:08 -0400 (Thu, 05 Aug 2010) | 2 lines
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2059 Changed paths:
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2060 M /trunk/samtools/bcftools/vcf.c
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2061
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2062 unfinished vcf parser
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2063
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2064 ------------------------------------------------------------------------
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2065 r668 | lh3lh3 | 2010-08-05 15:46:40 -0400 (Thu, 05 Aug 2010) | 3 lines
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2066 Changed paths:
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2067 M /trunk/samtools/bcftools/Makefile
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2068 M /trunk/samtools/bcftools/bcf.c
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2069 M /trunk/samtools/bcftools/bcf.h
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2070 M /trunk/samtools/bcftools/bcfutils.c
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2071 M /trunk/samtools/bcftools/index.c
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2072 M /trunk/samtools/bcftools/main.c
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2073 A /trunk/samtools/bcftools/vcf.c
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2074 M /trunk/samtools/bcftools/vcfout.c
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2075
|
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2076 * added prelimiary VCF parser (not finished)
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2077 * change struct a bit
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2078
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2079 ------------------------------------------------------------------------
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2080 r667 | lh3lh3 | 2010-08-03 22:35:27 -0400 (Tue, 03 Aug 2010) | 3 lines
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2081 Changed paths:
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2082 M /trunk/samtools/bam2bcf.c
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2083 M /trunk/samtools/bam2bcf.h
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2084 M /trunk/samtools/bam_plcmd.c
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|
2085 M /trunk/samtools/bcftools/bcf.c
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|
2086
|
|
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2087 * allow to set min base q
|
|
|
2088 * fixed a bug in mpileup -u
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2089
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2090 ------------------------------------------------------------------------
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2091 r666 | lh3lh3 | 2010-08-03 22:08:44 -0400 (Tue, 03 Aug 2010) | 2 lines
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2092 Changed paths:
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2093 A /trunk/samtools/bcftools/bcf.tex
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2094
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2095 spec
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2096
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2097 ------------------------------------------------------------------------
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2098 r665 | lh3lh3 | 2010-08-03 21:18:57 -0400 (Tue, 03 Aug 2010) | 2 lines
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2099 Changed paths:
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2100 M /trunk/samtools/examples/Makefile
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2101
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2102 added more examples
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2103
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2104 ------------------------------------------------------------------------
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2105 r664 | lh3lh3 | 2010-08-03 21:13:00 -0400 (Tue, 03 Aug 2010) | 2 lines
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2106 Changed paths:
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2107 M /trunk/samtools/Makefile
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2108 M /trunk/samtools/bam2bcf.c
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2109 M /trunk/samtools/bam2bcf.h
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|
2110 M /trunk/samtools/bcftools/Makefile
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2111
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2112 fixed compilation error
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2113
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2114 ------------------------------------------------------------------------
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2115 r662 | lh3lh3 | 2010-08-03 21:04:00 -0400 (Tue, 03 Aug 2010) | 2 lines
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2116 Changed paths:
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2117 M /trunk/samtools/Makefile
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2118 D /trunk/samtools/bcf.c
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2119 D /trunk/samtools/bcf.h
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2120 A /trunk/samtools/bcftools
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2121 A /trunk/samtools/bcftools/Makefile
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2122 A /trunk/samtools/bcftools/bcf.c
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2123 A /trunk/samtools/bcftools/bcf.h
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2124 A /trunk/samtools/bcftools/bcfutils.c
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2125 A /trunk/samtools/bcftools/index.c
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|
2126 A /trunk/samtools/bcftools/main.c
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2127 A /trunk/samtools/bcftools/prob1.c
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|
2128 A /trunk/samtools/bcftools/prob1.h
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|
2129 A /trunk/samtools/bcftools/vcfout.c
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2130
|
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|
2131 move bcftools to samtools
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2132
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|
2133 ------------------------------------------------------------------------
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2134 r660 | lh3lh3 | 2010-08-03 15:58:32 -0400 (Tue, 03 Aug 2010) | 2 lines
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2135 Changed paths:
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2136 M /trunk/samtools/bam2bcf.c
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2137
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|
2138 fixed another minor bug
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2139
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2140 ------------------------------------------------------------------------
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2141 r658 | lh3lh3 | 2010-08-03 15:06:45 -0400 (Tue, 03 Aug 2010) | 3 lines
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2142 Changed paths:
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2143 M /trunk/samtools/bamtk.c
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2144 M /trunk/samtools/bcf.c
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2145
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2146 * samtools-0.1.8-10 (r658)
|
|
|
2147 * fixed a bug in bam2bcf when the reference is N
|
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2148
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2149 ------------------------------------------------------------------------
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2150 r657 | lh3lh3 | 2010-08-03 14:50:23 -0400 (Tue, 03 Aug 2010) | 3 lines
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2151 Changed paths:
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2152 M /trunk/samtools/bam2bcf.c
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2153 M /trunk/samtools/bam2bcf.h
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2154
|
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2155 * fixed a bug
|
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2156 * treat ambiguous ref base as the fifth base
|
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2157
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2158 ------------------------------------------------------------------------
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2159 r654 | lh3lh3 | 2010-08-02 17:38:27 -0400 (Mon, 02 Aug 2010) | 2 lines
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2160 Changed paths:
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2161 M /trunk/bcftools/bcf.c
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2162 M /trunk/samtools/bcf.c
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2163
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2164 missing a column in VCF output...
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2165
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2166 ------------------------------------------------------------------------
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2167 r653 | lh3lh3 | 2010-08-02 17:31:33 -0400 (Mon, 02 Aug 2010) | 2 lines
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2168 Changed paths:
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2169 M /trunk/samtools/bcf.c
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2170
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2171 fixed a memory leak
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2172
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2173 ------------------------------------------------------------------------
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2174 r651 | lh3lh3 | 2010-08-02 17:27:31 -0400 (Mon, 02 Aug 2010) | 2 lines
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2175 Changed paths:
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2176 M /trunk/samtools/bcf.c
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2177
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2178 fixed a bug in bcf reader
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2179
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2180 ------------------------------------------------------------------------
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2181 r650 | lh3lh3 | 2010-08-02 17:00:41 -0400 (Mon, 02 Aug 2010) | 2 lines
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2182 Changed paths:
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2183 M /trunk/samtools/bam2bcf.c
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2184
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2185 fixed a bug
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2186
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2187 ------------------------------------------------------------------------
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2188 r649 | lh3lh3 | 2010-08-02 16:49:35 -0400 (Mon, 02 Aug 2010) | 3 lines
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2189 Changed paths:
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2190 M /trunk/samtools/Makefile
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2191 M /trunk/samtools/bam2bcf.c
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2192 M /trunk/samtools/bam2bcf.h
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2193 M /trunk/samtools/bamtk.c
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2194
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2195 * samtools-0.1.8-9 (r649)
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2196 * lossless representation of PL in BCF output
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2197
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2198 ------------------------------------------------------------------------
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2199 r648 | lh3lh3 | 2010-08-02 16:07:25 -0400 (Mon, 02 Aug 2010) | 2 lines
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2200 Changed paths:
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2201 M /trunk/samtools/Makefile
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2202 A /trunk/samtools/bam2bcf.c
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2203 A /trunk/samtools/bam2bcf.h
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2204 M /trunk/samtools/bam_plcmd.c
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2205 A /trunk/samtools/bcf.c
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2206 A /trunk/samtools/bcf.h
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2207
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2208 Generate binary VCF
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2209
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2210 ------------------------------------------------------------------------
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2211 r644 | lh3lh3 | 2010-07-28 11:59:19 -0400 (Wed, 28 Jul 2010) | 5 lines
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2212 Changed paths:
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2213 M /trunk/samtools/bam_mcns.c
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2214 M /trunk/samtools/bamtk.c
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2215
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2216 * samtools-0.1.8-8 (r644)
|
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2217 * mpileup becomes a little stable again
|
|
|
2218 * the method is slightly different, but is more theoretically correct
|
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2219 * snp calling is O(n^2) instead of O(n^3)
|
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2220
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2221 ------------------------------------------------------------------------
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2222 r643 | lh3lh3 | 2010-07-28 11:54:15 -0400 (Wed, 28 Jul 2010) | 3 lines
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2223 Changed paths:
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2224 M /trunk/samtools/bam_mcns.c
|
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2225
|
|
|
2226 * fixed a STUPID bug, which cost me a lot of time.
|
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2227 * I am going to clean up mcns a little bit
|
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2228
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2229 ------------------------------------------------------------------------
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2230 r642 | lh3lh3 | 2010-07-27 23:23:07 -0400 (Tue, 27 Jul 2010) | 2 lines
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2231 Changed paths:
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2232 M /trunk/samtools/bam_mcns.c
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2233 M /trunk/samtools/bam_mcns.h
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2234 M /trunk/samtools/bam_plcmd.c
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2235
|
|
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2236 supposedly this is THE correct implementation, but more testing is needed
|
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2237
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2238 ------------------------------------------------------------------------
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2239 r641 | lh3lh3 | 2010-07-27 22:43:39 -0400 (Tue, 27 Jul 2010) | 2 lines
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2240 Changed paths:
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2241 M /trunk/samtools/bam_mcns.c
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2242
|
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|
2243 NOT ready yet. Going to make further changes...
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2244
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2245 ------------------------------------------------------------------------
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2246 r639 | lh3lh3 | 2010-07-25 22:18:38 -0400 (Sun, 25 Jul 2010) | 3 lines
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2247 Changed paths:
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2248 M /trunk/samtools/bam_mcns.c
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2249 M /trunk/samtools/bam_plcmd.c
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2250 M /trunk/samtools/bamtk.c
|
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2251
|
|
|
2252 * samtools-0.1.8-7 (r639)
|
|
|
2253 * fixed the reference allele assignment
|
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2254
|
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|
2255 ------------------------------------------------------------------------
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2256 r638 | lh3lh3 | 2010-07-25 12:01:26 -0400 (Sun, 25 Jul 2010) | 5 lines
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2257 Changed paths:
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2258 M /trunk/samtools/bam_mcns.c
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2259 M /trunk/samtools/bam_mcns.h
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2260 M /trunk/samtools/bam_plcmd.c
|
|
|
2261 M /trunk/samtools/bamtk.c
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2262
|
|
|
2263 * samtools-0.1.8-6 (r638)
|
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|
2264 * skip isnan/isinf in case of float underflow
|
|
|
2265 * added the flat prior
|
|
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2266 * fixed an issue where there are no reads supporting the reference
|
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2267
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2268 ------------------------------------------------------------------------
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2269 r637 | lh3lh3 | 2010-07-24 14:16:27 -0400 (Sat, 24 Jul 2010) | 2 lines
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2270 Changed paths:
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2271 M /trunk/samtools/bam_plcmd.c
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2272
|
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|
2273 minor changes
|
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2274
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2275 ------------------------------------------------------------------------
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2276 r636 | lh3lh3 | 2010-07-24 14:07:27 -0400 (Sat, 24 Jul 2010) | 2 lines
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2277 Changed paths:
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2278 M /trunk/samtools/bam_mcns.c
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2279 M /trunk/samtools/bam_mcns.h
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2280 M /trunk/samtools/bam_plcmd.c
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2281 M /trunk/samtools/bamtk.c
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2282
|
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2283 minor tweaks
|
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2284
|
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2285 ------------------------------------------------------------------------
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2286 r635 | lh3lh3 | 2010-07-24 01:49:49 -0400 (Sat, 24 Jul 2010) | 2 lines
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2287 Changed paths:
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2288 M /trunk/samtools/bam_mcns.c
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2289 M /trunk/samtools/bam_mcns.h
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2290 M /trunk/samtools/bam_plcmd.c
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2291
|
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|
2292 posterior expectation FINALLY working. I am so tired...
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2293
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2294 ------------------------------------------------------------------------
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2295 r633 | lh3lh3 | 2010-07-23 13:50:48 -0400 (Fri, 23 Jul 2010) | 2 lines
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2296 Changed paths:
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2297 M /trunk/samtools/bam_plcmd.c
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2298
|
|
|
2299 another minor fix to mpileup
|
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2300
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2301 ------------------------------------------------------------------------
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2302 r632 | lh3lh3 | 2010-07-23 13:43:31 -0400 (Fri, 23 Jul 2010) | 2 lines
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2303 Changed paths:
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2304 M /trunk/samtools/bam_plcmd.c
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2305
|
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|
2306 added the format column
|
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2307
|
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2308 ------------------------------------------------------------------------
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2309 r631 | lh3lh3 | 2010-07-23 13:25:44 -0400 (Fri, 23 Jul 2010) | 2 lines
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2310 Changed paths:
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|
|
2311 M /trunk/samtools/bam_mcns.c
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2312 M /trunk/samtools/bam_mcns.h
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2313 M /trunk/samtools/bam_plcmd.c
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|
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2314 M /trunk/samtools/bamtk.c
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2315
|
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|
2316 added an alternative prior
|
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2317
|
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|
2318 ------------------------------------------------------------------------
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2319 r628 | lh3lh3 | 2010-07-23 11:48:51 -0400 (Fri, 23 Jul 2010) | 2 lines
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2320 Changed paths:
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|
2321 M /trunk/samtools/bam_mcns.c
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2322 M /trunk/samtools/bam_mcns.h
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2323 M /trunk/samtools/bam_plcmd.c
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2324
|
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2325 calculate posterior allele frequency
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2326
|
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|
2327 ------------------------------------------------------------------------
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2328 r627 | lh3lh3 | 2010-07-22 21:39:13 -0400 (Thu, 22 Jul 2010) | 3 lines
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2329 Changed paths:
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|
|
2330 M /trunk/samtools/bam_mcns.c
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2331 M /trunk/samtools/bam_plcmd.c
|
|
|
2332 M /trunk/samtools/bamtk.c
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|
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2333
|
|
|
2334 * samtools-0.1.8-3 (r627)
|
|
|
2335 * multi-sample snp calling appears to work. More tests needed.
|
|
|
2336
|
|
|
2337 ------------------------------------------------------------------------
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|
2338 r626 | lh3lh3 | 2010-07-22 16:37:56 -0400 (Thu, 22 Jul 2010) | 3 lines
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2339 Changed paths:
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|
|
2340 M /trunk/samtools/bam_mcns.c
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|
2341 M /trunk/samtools/bam_mcns.h
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|
2342 M /trunk/samtools/bam_plcmd.c
|
|
|
2343 M /trunk/samtools/bam_tview.c
|
|
|
2344
|
|
|
2345 * preliminary multisample SNP caller.
|
|
|
2346 * something looks not so right, but it largely works
|
|
|
2347
|
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|
2348 ------------------------------------------------------------------------
|
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|
2349 r617 | lh3lh3 | 2010-07-14 16:26:27 -0400 (Wed, 14 Jul 2010) | 3 lines
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|
2350 Changed paths:
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|
|
2351 M /trunk/samtools/bam_mcns.c
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|
2352 M /trunk/samtools/bam_plcmd.c
|
|
|
2353 M /trunk/samtools/bamtk.c
|
|
|
2354
|
|
|
2355 * samtools-0.1.8-2 (r617)
|
|
|
2356 * allele frequency calculation apparently works...
|
|
|
2357
|
|
|
2358 ------------------------------------------------------------------------
|
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|
2359 r616 | lh3lh3 | 2010-07-14 13:33:51 -0400 (Wed, 14 Jul 2010) | 3 lines
|
|
|
2360 Changed paths:
|
|
|
2361 M /trunk/samtools/Makefile
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|
|
2362 A /trunk/samtools/bam_mcns.c
|
|
|
2363 A /trunk/samtools/bam_mcns.h
|
|
|
2364 M /trunk/samtools/bam_plcmd.c
|
|
|
2365
|
|
|
2366 * added mutli-sample framework. It is not working, yet.
|
|
|
2367 * improved the mpileup interface
|
|
|
2368
|
|
|
2369 ------------------------------------------------------------------------
|
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|
2370 r615 | lh3lh3 | 2010-07-13 14:50:12 -0400 (Tue, 13 Jul 2010) | 3 lines
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|
2371 Changed paths:
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|
|
2372 M /trunk/samtools/bam_plcmd.c
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2373 M /trunk/samtools/bamtk.c
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|
|
2374 M /trunk/samtools/misc/Makefile
|
|
|
2375
|
|
|
2376 * samtools-0.1.8-1 (r615)
|
|
|
2377 * allow to get mpileup at required sites
|
|
|
2378
|
|
|
2379 ------------------------------------------------------------------------
|
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|
2380 r613 | lh3lh3 | 2010-07-11 22:40:56 -0400 (Sun, 11 Jul 2010) | 2 lines
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|
2381 Changed paths:
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|
|
2382 M /trunk/samtools/ChangeLog
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2383 M /trunk/samtools/NEWS
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|
2384 M /trunk/samtools/bam_plcmd.c
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|
|
2385 M /trunk/samtools/bamtk.c
|
|
|
2386 M /trunk/samtools/samtools.1
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2387
|
|
|
2388 Release samtools-0.1.8
|
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2389
|
|
|
2390 ------------------------------------------------------------------------
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|
2391 r612 | lh3lh3 | 2010-07-11 21:08:56 -0400 (Sun, 11 Jul 2010) | 2 lines
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|
2392 Changed paths:
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|
2393 M /trunk/samtools/knetfile.c
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2394
|
|
|
2395 fixed a compiling issue for Windows
|
|
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2396
|
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|
2397 ------------------------------------------------------------------------
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|
2398 r611 | lh3lh3 | 2010-07-11 20:59:15 -0400 (Sun, 11 Jul 2010) | 2 lines
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|
2399 Changed paths:
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|
2400 M /trunk/samtools/bam_sort.c
|
|
|
2401
|
|
|
2402 fixed a bug in sorting when output to stdout (by Peter Chines)
|
|
|
2403
|
|
|
2404 ------------------------------------------------------------------------
|
|
|
2405 r610 | lh3lh3 | 2010-07-09 17:05:10 -0400 (Fri, 09 Jul 2010) | 2 lines
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|
2406 Changed paths:
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2407 M /trunk/samtools/NEWS
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2408 M /trunk/samtools/bam_plcmd.c
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2409
|
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|
2410 change the command line option of pileup
|
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2411
|
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|
2412 ------------------------------------------------------------------------
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2413 r609 | lh3lh3 | 2010-07-09 00:39:34 -0400 (Fri, 09 Jul 2010) | 2 lines
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2414 Changed paths:
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|
|
2415 M /trunk/samtools/bam_pileup.c
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2416 A /trunk/samtools/examples/toy.fa
|
|
|
2417 A /trunk/samtools/examples/toy.sam
|
|
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2418
|
|
|
2419 make pileup work with CIGAR with I/D at the beginning or in the end
|
|
|
2420
|
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|
2421 ------------------------------------------------------------------------
|
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|
2422 r608 | lh3lh3 | 2010-07-08 22:36:12 -0400 (Thu, 08 Jul 2010) | 3 lines
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2423 Changed paths:
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|
|
2424 M /trunk/samtools/bam_maqcns.c
|
|
|
2425 M /trunk/samtools/bam_maqcns.h
|
|
|
2426 M /trunk/samtools/bam_plcmd.c
|
|
|
2427 M /trunk/samtools/bam_tview.c
|
|
|
2428
|
|
|
2429 * make tview more friendly
|
|
|
2430 * a temporary remedy for an issue in indel calling
|
|
|
2431
|
|
|
2432 ------------------------------------------------------------------------
|
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|
2433 r607 | lh3lh3 | 2010-07-08 14:43:52 -0400 (Thu, 08 Jul 2010) | 4 lines
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2434 Changed paths:
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|
2435 M /trunk/samtools/bam_maqcns.c
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2436 M /trunk/samtools/bam_plcmd.c
|
|
|
2437 M /trunk/samtools/bamtk.c
|
|
|
2438
|
|
|
2439 * samtools-0.1.7-r607
|
|
|
2440 * improved the genotype accuracy for indels
|
|
|
2441 * use the SOAPsnp model for SNP calling by default.
|
|
|
2442
|
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|
2443 ------------------------------------------------------------------------
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|
2444 r606 | lh3lh3 | 2010-07-08 01:05:19 -0400 (Thu, 08 Jul 2010) | 2 lines
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2445 Changed paths:
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|
2446 M /trunk/samtools/misc/Makefile
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|
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2447
|
|
|
2448 removed a debugging example
|
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|
2449
|
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|
2450 ------------------------------------------------------------------------
|
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|
2451 r605 | lh3lh3 | 2010-07-08 01:04:09 -0400 (Thu, 08 Jul 2010) | 4 lines
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2452 Changed paths:
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|
|
2453 M /trunk/samtools/bam_maqcns.c
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|
2454 M /trunk/samtools/bamtk.c
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2455
|
|
|
2456 * samtools-.1.7-18 (r605)
|
|
|
2457 * fixed an issue when a deletion and mismatch occur at the same time
|
|
|
2458 and the base quality is higher than 40 (if -I40).
|
|
|
2459
|
|
|
2460 ------------------------------------------------------------------------
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|
2461 r604 | lh3lh3 | 2010-07-02 19:32:24 -0400 (Fri, 02 Jul 2010) | 2 lines
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2462 Changed paths:
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|
2463 M /trunk/samtools/bam.h
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|
|
2464 M /trunk/samtools/bam_index.c
|
|
|
2465 M /trunk/samtools/misc/Makefile
|
|
|
2466
|
|
|
2467 fixed a minor bug in idxstats
|
|
|
2468
|
|
|
2469 ------------------------------------------------------------------------
|
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|
2470 r601 | lh3lh3 | 2010-06-16 09:03:59 -0400 (Wed, 16 Jun 2010) | 2 lines
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|
2471 Changed paths:
|
|
|
2472 M /trunk/samtools/bam_index.c
|
|
|
2473
|
|
|
2474 fixed a minor bug in indexing
|
|
|
2475
|
|
|
2476 ------------------------------------------------------------------------
|
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|
2477 r600 | lh3lh3 | 2010-06-15 10:17:53 -0400 (Tue, 15 Jun 2010) | 2 lines
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2478 Changed paths:
|
|
|
2479 M /trunk/samtools/ChangeLog
|
|
|
2480 M /trunk/samtools/bam.c
|
|
|
2481
|
|
|
2482 change printf() to puts in exporting
|
|
|
2483
|
|
|
2484 ------------------------------------------------------------------------
|
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|
2485 r599 | lh3lh3 | 2010-06-13 21:41:11 -0400 (Sun, 13 Jun 2010) | 2 lines
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2486 Changed paths:
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|
2487 M /trunk/samtools/bamtk.c
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|
2488
|
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|
2489 minor fix. No actual effect.
|
|
|
2490
|
|
|
2491 ------------------------------------------------------------------------
|
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|
2492 r598 | lh3lh3 | 2010-06-13 21:32:45 -0400 (Sun, 13 Jun 2010) | 2 lines
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2493 Changed paths:
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|
2494 M /trunk/samtools/Makefile
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|
|
2495
|
|
|
2496 added Makefile targets to compile shared/dynamic library
|
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|
2497
|
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|
2498 ------------------------------------------------------------------------
|
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|
2499 r596 | lh3lh3 | 2010-06-13 19:48:07 -0400 (Sun, 13 Jun 2010) | 3 lines
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2500 Changed paths:
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|
2501 M /trunk/samtools/ChangeLog
|
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|
2502 M /trunk/samtools/bam_index.c
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|
2503 M /trunk/samtools/bamtk.c
|
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2504
|
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2505 * samtools-0.1.7-17 (r596)
|
|
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2506 * also keep the number of coor-less reads in the index file
|
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2507
|
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2508 ------------------------------------------------------------------------
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2509 r595 | lh3lh3 | 2010-06-13 18:54:26 -0400 (Sun, 13 Jun 2010) | 3 lines
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2510 Changed paths:
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2511 M /trunk/samtools/bam_index.c
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2512 M /trunk/samtools/bamtk.c
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2513
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2514 * samtools-0.1.7-16 (r595)
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2515 * write additional information to bam index
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2516
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2517 ------------------------------------------------------------------------
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2518 r594 | lh3lh3 | 2010-06-13 17:29:52 -0400 (Sun, 13 Jun 2010) | 2 lines
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2519 Changed paths:
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2520 M /trunk/samtools/bam_index.c
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2521
|
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2522 fixed a bug for unmapped sequences in indexing
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2523
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2524 ------------------------------------------------------------------------
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2525 r593 | lh3lh3 | 2010-06-12 18:11:32 -0400 (Sat, 12 Jun 2010) | 2 lines
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2526 Changed paths:
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2527 M /trunk/samtools/bam.h
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2528 M /trunk/samtools/bam_index.c
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2529 M /trunk/samtools/bam_plcmd.c
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2530 M /trunk/samtools/samtools.1
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2531
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2532 rename iterf as iter
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2533
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2534 ------------------------------------------------------------------------
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2535 r592 | lh3lh3 | 2010-06-12 18:02:38 -0400 (Sat, 12 Jun 2010) | 4 lines
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2536 Changed paths:
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2537 M /trunk/samtools/ChangeLog
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2538 M /trunk/samtools/bam_aux.c
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2539 M /trunk/samtools/bam_index.c
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2540 M /trunk/samtools/bam_pileup.c
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2541 M /trunk/samtools/bam_plcmd.c
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2542 M /trunk/samtools/bamtk.c
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2543
|
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|
2544 * samtools-0.1.7-15 (r592)
|
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|
2545 * fixed a few minor memory leaks in the new pileup code
|
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|
2546 * improved the functionality of mpileup
|
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2547
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2548 ------------------------------------------------------------------------
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2549 r591 | lh3lh3 | 2010-06-12 14:09:22 -0400 (Sat, 12 Jun 2010) | 3 lines
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2550 Changed paths:
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2551 M /trunk/samtools/bam.h
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2552 M /trunk/samtools/bam_pileup.c
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2553 M /trunk/samtools/bam_plcmd.c
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2554 M /trunk/samtools/bamtk.c
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2555
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2556 * samtools-0.1.7-14 (r591)
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2557 * elementary multi-way pileup. More testing and more functionality to be done.
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2558
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2559 ------------------------------------------------------------------------
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2560 r590 | lh3lh3 | 2010-06-12 01:00:24 -0400 (Sat, 12 Jun 2010) | 3 lines
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2561 Changed paths:
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2562 M /trunk/samtools/bam.h
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2563 M /trunk/samtools/bam_pileup.c
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2564 M /trunk/samtools/bamtk.c
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2565
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2566 * samtools-0.1.7-13 (r590)
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2567 * added mpileup APIs. No compiling errors, but not tested at all. It is late.
|
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2568
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2569 ------------------------------------------------------------------------
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2570 r589 | lh3lh3 | 2010-06-11 22:37:09 -0400 (Fri, 11 Jun 2010) | 3 lines
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2571 Changed paths:
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2572 M /trunk/samtools/bam.h
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2573 M /trunk/samtools/bam_pileup.c
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2574 M /trunk/samtools/bamtk.c
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2575
|
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2576 * samtools-0.1.7-12 (r589)
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2577 * added iterator-like APIs for pileup
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2578
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2579 ------------------------------------------------------------------------
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2580 r588 | lh3lh3 | 2010-06-11 17:41:13 -0400 (Fri, 11 Jun 2010) | 3 lines
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2581 Changed paths:
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2582 M /trunk/samtools/bam_index.c
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2583 M /trunk/samtools/bamtk.c
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2584
|
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2585 * samtools-0.1.7-11 (r588)
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2586 * ported a few improvements from tabix back to samtools
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2587
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2588 ------------------------------------------------------------------------
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2589 r587 | lh3lh3 | 2010-06-11 17:33:16 -0400 (Fri, 11 Jun 2010) | 3 lines
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2590 Changed paths:
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2591 M /trunk/samtools/bam.h
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2592 M /trunk/samtools/bam_index.c
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2593 M /trunk/samtools/bamtk.c
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2594
|
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2595 * samtools-0.1.7-10 (r587)
|
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2596 * added iterator interface for bam_fetch (ported back from tabix)
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2597
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2598 ------------------------------------------------------------------------
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2599 r586 | lh3lh3 | 2010-06-11 13:23:53 -0400 (Fri, 11 Jun 2010) | 3 lines
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2600 Changed paths:
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2601 M /trunk/samtools/Makefile
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2602 A /trunk/samtools/bam_reheader.c
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2603 M /trunk/samtools/bamtk.c
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2604 M /trunk/samtools/bgzf.c
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2605
|
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2606 * samtools-0.1.7-9 (r586)
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2607 * added "reheader" to replace the BAM header
|
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2608
|
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2609 ------------------------------------------------------------------------
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2610 r585 | lh3lh3 | 2010-06-11 12:22:06 -0400 (Fri, 11 Jun 2010) | 3 lines
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2611 Changed paths:
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2612 M /trunk/samtools/bam.c
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2613 M /trunk/samtools/bamtk.c
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2614 M /trunk/samtools/kstring.h
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2615
|
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2616 * samtools-0.1.7-8 (r585)
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2617 * speed up "view"
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2618
|
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2619 ------------------------------------------------------------------------
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2620 r584 | lh3lh3 | 2010-06-11 12:00:41 -0400 (Fri, 11 Jun 2010) | 4 lines
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2621 Changed paths:
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2622 M /trunk/samtools/bam.c
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2623 M /trunk/samtools/bamtk.c
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2624 M /trunk/samtools/bgzf.c
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2625 M /trunk/samtools/bgzf.h
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2626 M /trunk/samtools/kstring.h
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2627 M /trunk/samtools/misc/wgsim_eval.pl
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2628
|
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2629 * samtools-0.1.7-7 (r584)
|
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2630 * ported tabix BGZF to samtools
|
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|
2631 * flush BGZF after writing the BAM header and between alignment boundaries
|
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2632
|
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2633 ------------------------------------------------------------------------
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2634 r583 | petulda | 2010-06-11 11:58:20 -0400 (Fri, 11 Jun 2010) | 1 line
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2635 Changed paths:
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2636 A /trunk/samtools/misc/varfilter.py
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2637
|
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2638 Initial release on behalf of Aylwyn Scally
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2639 ------------------------------------------------------------------------
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2640 r561 | petulda | 2010-05-07 08:41:56 -0400 (Fri, 07 May 2010) | 1 line
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2641 Changed paths:
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2642 M /trunk/samtools/samtools.1
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2643
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2644 Added a note about the indels coordinates
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2645 ------------------------------------------------------------------------
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2646 r551 | petulda | 2010-04-23 09:42:13 -0400 (Fri, 23 Apr 2010) | 1 line
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2647 Changed paths:
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2648 M /trunk/samtools/misc/sam2vcf.pl
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2649
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2650 Added the possibility to print or not to print the reference allele
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2651 ------------------------------------------------------------------------
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2652 r546 | petulda | 2010-04-15 04:33:55 -0400 (Thu, 15 Apr 2010) | 1 line
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2653 Changed paths:
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2654 M /trunk/samtools/sam_header.c
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2655
|
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2656 More descriptive message for space separated tags
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2657 ------------------------------------------------------------------------
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2658 r545 | petulda | 2010-04-14 11:44:50 -0400 (Wed, 14 Apr 2010) | 1 line
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2659 Changed paths:
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2660 M /trunk/samtools/misc/sam2vcf.pl
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2661
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2662 Speedup with -i, no need to query the reference all the time
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2663 ------------------------------------------------------------------------
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2664 r541 | petulda | 2010-03-15 10:03:51 -0400 (Mon, 15 Mar 2010) | 1 line
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2665 Changed paths:
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2666 M /trunk/samtools/sam_header.c
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2667
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2668 Fixed the order of sequences in the header
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2669 ------------------------------------------------------------------------
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2670 r540 | petulda | 2010-03-04 06:28:35 -0500 (Thu, 04 Mar 2010) | 1 line
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2671 Changed paths:
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2672 M /trunk/samtools/misc/sam2vcf.pl
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2673
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2674 Added possibility to select indels only and fixed a bug in reporting homozygous indels.
|
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2675 ------------------------------------------------------------------------
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2676 r539 | jmarshall | 2010-02-27 06:48:17 -0500 (Sat, 27 Feb 2010) | 4 lines
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2677 Changed paths:
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2678 M /trunk/samtools/bam.c
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2679
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2680 Improve the invalid 'BAM\1' magic number error message, and also print it
|
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2681 when no bytes can be read from the alleged BAM file, e.g., in the common
|
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2682 user error case when a SAM file has accidentally been supplied.
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2683
|
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2684 ------------------------------------------------------------------------
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2685 r538 | petulda | 2010-02-26 10:51:40 -0500 (Fri, 26 Feb 2010) | 1 line
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2686 Changed paths:
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2687 M /trunk/samtools/AUTHORS
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2688 M /trunk/samtools/bam.h
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2689 M /trunk/samtools/bam_import.c
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2690 M /trunk/samtools/sam_header.c
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2691
|
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2692 Improved efficiency of header parsing
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2693 ------------------------------------------------------------------------
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2694 r537 | lh3lh3 | 2010-02-23 21:08:48 -0500 (Tue, 23 Feb 2010) | 3 lines
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2695 Changed paths:
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2696 M /trunk/samtools/misc/export2sam.pl
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2697
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2698 Updated export2sam.pl by Chris Saunders from Illumina.
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2699
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2700
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2701 ------------------------------------------------------------------------
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2702 r536 | petulda | 2010-02-17 08:32:53 -0500 (Wed, 17 Feb 2010) | 1 line
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2703 Changed paths:
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2704 M /trunk/samtools/misc/samtools.pl
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2705
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2706 Fixed filtering of SNPs near indels. Added min indel and SNP quality filter.
|
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2707 ------------------------------------------------------------------------
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2708 r535 | petulda | 2010-02-12 04:52:37 -0500 (Fri, 12 Feb 2010) | 1 line
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2709 Changed paths:
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2710 M /trunk/samtools/misc/sam2vcf.pl
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2711
|
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2712 Print an error for pileups in simple format
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2713 ------------------------------------------------------------------------
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2714 r534 | lh3lh3 | 2010-02-11 14:01:41 -0500 (Thu, 11 Feb 2010) | 2 lines
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2715 Changed paths:
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2716 M /trunk/samtools/bam_plcmd.c
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2717
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2718 added a hidden option in pileup to output the base position (for Erin)
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2719
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2720 ------------------------------------------------------------------------
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2721 r533 | petulda | 2010-02-09 10:12:14 -0500 (Tue, 09 Feb 2010) | 1 line
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2722 Changed paths:
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2723 M /trunk/samtools/misc/sam2vcf.pl
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2724
|
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|
2725 Added possibility to specify a custom column title for the data column
|
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2726 ------------------------------------------------------------------------
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2727 r532 | petulda | 2010-02-09 09:46:09 -0500 (Tue, 09 Feb 2010) | 1 line
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2728 Changed paths:
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2729 M /trunk/samtools/bam_plcmd.c
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2730
|
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2731 Added the -d option to limit maximum depth for indels.
|
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2732 ------------------------------------------------------------------------
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2733 r531 | petulda | 2010-02-03 07:57:27 -0500 (Wed, 03 Feb 2010) | 1 line
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2734 Changed paths:
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2735 M /trunk/samtools/misc/sam2vcf.pl
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2736
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2737 Added VCF header
|
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2738 ------------------------------------------------------------------------
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2739 r530 | lh3lh3 | 2010-02-01 09:13:19 -0500 (Mon, 01 Feb 2010) | 3 lines
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2740 Changed paths:
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2741 M /trunk/samtools/ChangeLog
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2742 M /trunk/samtools/bam_plcmd.c
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2743 M /trunk/samtools/bamtk.c
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2744 M /trunk/samtools/misc/samtools.pl
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2745 M /trunk/samtools/misc/wgsim.c
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2746
|
|
|
2747 * samtools-0.1.7-6
|
|
|
2748 * fixed a bug in faidx
|
|
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2749
|
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2750 ------------------------------------------------------------------------
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2751 r529 | jmarshall | 2010-01-11 18:51:49 -0500 (Mon, 11 Jan 2010) | 2 lines
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2752 Changed paths:
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2753 M /trunk/samtools/faidx.c
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2754
|
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|
2755 Put the right filename in the error message.
|
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2756
|
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2757 ------------------------------------------------------------------------
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2758 r528 | lh3lh3 | 2009-12-14 11:26:47 -0500 (Mon, 14 Dec 2009) | 3 lines
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2759 Changed paths:
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2760 M /trunk/samtools/bam_plcmd.c
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2761 M /trunk/samtools/bamtk.c
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2762
|
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|
2763 * samtools-0.1.7-5 (r528)
|
|
|
2764 * further add new consensus generation strategy
|
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2765
|
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2766 ------------------------------------------------------------------------
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2767 r527 | petulda | 2009-12-11 12:31:05 -0500 (Fri, 11 Dec 2009) | 1 line
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2768 Changed paths:
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2769 M /trunk/samtools/knetfile.c
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2770
|
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2771 Fixed a bug in knet_seek
|
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2772 ------------------------------------------------------------------------
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|
2773 r526 | petulda | 2009-12-11 07:51:18 -0500 (Fri, 11 Dec 2009) | 1 line
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2774 Changed paths:
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2775 M /trunk/samtools/misc/sam2vcf.pl
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2776
|
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|
2777 Small fix in VCF format: dot for the empty INFO field
|
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|
2778 ------------------------------------------------------------------------
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2779 r525 | petulda | 2009-12-11 04:36:18 -0500 (Fri, 11 Dec 2009) | 1 line
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2780 Changed paths:
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2781 M /trunk/samtools/sam_header.c
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2782
|
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2783 Allow tabs in the CO header field
|
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2784 ------------------------------------------------------------------------
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2785 r524 | jmarshall | 2009-12-10 10:03:58 -0500 (Thu, 10 Dec 2009) | 3 lines
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2786 Changed paths:
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2787 M /trunk/samtools/Makefile
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2788 M /trunk/samtools/Makefile.mingw
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|
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2789
|
|
|
2790 Depend on libbam.a rather than the phony target, so that samtools is not
|
|
|
2791 unnecessarily rebuilt every time. Also clean bgzip.
|
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2792
|
|
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2793 ------------------------------------------------------------------------
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2794 r523 | jmarshall | 2009-12-10 09:45:32 -0500 (Thu, 10 Dec 2009) | 4 lines
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2795 Changed paths:
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2796 M /trunk/samtools/Makefile
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2797 M /trunk/samtools/Makefile.mingw
|
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2798
|
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|
2799 Fix a bug in compiling bgzip: this also needs knetfile.o when _USE_KNETFILE
|
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|
2800 is defined. Also introduce $(KNETFILE_O) which can be set to empty to
|
|
|
2801 facilitate non-knet builds.
|
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2802
|
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2803 ------------------------------------------------------------------------
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2804 r522 | lh3lh3 | 2009-12-01 13:02:36 -0500 (Tue, 01 Dec 2009) | 4 lines
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2805 Changed paths:
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2806 M /trunk/samtools/bamtk.c
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2807 M /trunk/samtools/sam_view.c
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2808
|
|
|
2809 * samtools-0.1.7-4 (r522)
|
|
|
2810 * fixed a bug in "view -r"
|
|
|
2811 * added a new option "view -R" to read required read groups from a file
|
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2812
|
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|
2813 ------------------------------------------------------------------------
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2814 r521 | lh3lh3 | 2009-12-01 10:00:12 -0500 (Tue, 01 Dec 2009) | 3 lines
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2815 Changed paths:
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2816 M /trunk/samtools/bam_md.c
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|
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2817 M /trunk/samtools/bamtk.c
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|
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2818
|
|
|
2819 * samtools-0.1.7-3 (r521)
|
|
|
2820 * calmd: optionally mask matching bases as N
|
|
|
2821
|
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|
2822 ------------------------------------------------------------------------
|
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|
2823 r520 | lh3lh3 | 2009-12-01 09:37:17 -0500 (Tue, 01 Dec 2009) | 4 lines
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2824 Changed paths:
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2825 M /trunk/samtools/bam_plcmd.c
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2826 M /trunk/samtools/bamtk.c
|
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|
2827 M /trunk/samtools/misc/samtools.pl
|
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2828
|
|
|
2829 * samtools-0.1.7-2 (r520)
|
|
|
2830 * fixed a few issues with compilation in Windows (on behalf of John)
|
|
|
2831 * choose a random base as the consensus (for population genetics studies)
|
|
|
2832
|
|
|
2833 ------------------------------------------------------------------------
|
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|
2834 r519 | jmarshall | 2009-11-30 10:53:02 -0500 (Mon, 30 Nov 2009) | 6 lines
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2835 Changed paths:
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2836 M /trunk/samtools/Makefile
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2837
|
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|
2838 Put libraries at the end, so they can resolve references from libbam.a
|
|
|
2839 as well, even with old-fashioned linkers.
|
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|
2840
|
|
|
2841 Also use libbam.a explicitly rather than "-L. -lbam" to ensure that we get
|
|
|
2842 the freshly built library, not some other libbam.a lying around the system.
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2843
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2844 ------------------------------------------------------------------------
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2845 r518 | jmarshall | 2009-11-30 08:44:56 -0500 (Mon, 30 Nov 2009) | 2 lines
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2846 Changed paths:
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2847 M /trunk/samtools/Makefile
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2848 M /trunk/samtools/misc/Makefile
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2849
|
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|
2850 Also clean *.exe (for Cygwin users using this makefile).
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2851
|
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2852 ------------------------------------------------------------------------
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|
2853 r517 | jmarshall | 2009-11-30 07:09:04 -0500 (Mon, 30 Nov 2009) | 2 lines
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2854 Changed paths:
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|
2855 M /trunk/samtools/bam_index.c
|
|
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2856
|
|
|
2857 Index files should be opened in binary mode, not text mode.
|
|
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2858
|
|
|
2859 ------------------------------------------------------------------------
|
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|
2860 r516 | lh3lh3 | 2009-11-27 15:18:59 -0500 (Fri, 27 Nov 2009) | 2 lines
|
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2861 Changed paths:
|
|
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2862 A /trunk/samtools/examples/bam2bed.c
|
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2863
|
|
|
2864 another example program
|
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2865
|
|
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2866 ------------------------------------------------------------------------
|
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2867 r515 | lh3lh3 | 2009-11-27 10:44:56 -0500 (Fri, 27 Nov 2009) | 3 lines
|
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2868 Changed paths:
|
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2869 M /trunk/samtools/bam_import.c
|
|
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2870 M /trunk/samtools/bamtk.c
|
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2871 M /trunk/samtools/misc/wgsim_eval.pl
|
|
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2872 M /trunk/samtools/sam.c
|
|
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2873
|
|
|
2874 * samtools-0.1.7-1 (r515)
|
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2875 * report an error when .fai contains duplicated names, instead of segfault
|
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2876
|
|
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2877 ------------------------------------------------------------------------
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2878 r514 | jmarshall | 2009-11-24 09:45:35 -0500 (Tue, 24 Nov 2009) | 2 lines
|
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2879 Changed paths:
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2880 M /trunk/samtools/bam.c
|
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2881
|
|
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2882 Format 'c'-encoded auxiliary fields correctly, as *signed* integers.
|
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2883
|
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2884 ------------------------------------------------------------------------
|
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2885 r513 | lh3lh3 | 2009-11-16 10:13:07 -0500 (Mon, 16 Nov 2009) | 2 lines
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2886 Changed paths:
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2887 M /trunk/samtools/Makefile.mingw
|
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2888
|
|
|
2889 Update Makefile.mingw for the same reason
|
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2890
|
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2891 ------------------------------------------------------------------------
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2892 r512 | lh3lh3 | 2009-11-16 10:00:08 -0500 (Mon, 16 Nov 2009) | 2 lines
|
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2893 Changed paths:
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2894 M /trunk/samtools/Makefile
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2895
|
|
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2896 Fixed a bug in compiling razip
|
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2897
|
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2898 ------------------------------------------------------------------------
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2899 r510 | lh3lh3 | 2009-11-10 10:55:41 -0500 (Tue, 10 Nov 2009) | 2 lines
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2900 Changed paths:
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2901 M /trunk/samtools/ChangeLog
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2902 M /trunk/samtools/NEWS
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2903 M /trunk/samtools/bamtk.c
|
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2904 M /trunk/samtools/samtools.1
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2905
|
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2906 Release samtools-0.1.7 (r510)
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2907
|
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2908 ------------------------------------------------------------------------
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2909 r509 | lh3lh3 | 2009-11-06 09:17:09 -0500 (Fri, 06 Nov 2009) | 3 lines
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2910 Changed paths:
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2911 M /trunk/samtools/bam_plcmd.c
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2912 M /trunk/samtools/bamtk.c
|
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2913
|
|
|
2914 * samtools-0.1.6-22 (r509)
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2915 * forget to fix a similar problem in glfgen
|
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2916
|
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2917 ------------------------------------------------------------------------
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2918 r508 | lh3lh3 | 2009-11-06 09:06:40 -0500 (Fri, 06 Nov 2009) | 3 lines
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2919 Changed paths:
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2920 M /trunk/samtools/bam_maqcns.c
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2921 M /trunk/samtools/bam_plcmd.c
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2922 M /trunk/samtools/bamtk.c
|
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2923 M /trunk/samtools/sam_view.c
|
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2924
|
|
|
2925 * samtools-0.1.6-21 (r508)
|
|
|
2926 * fixed a potential bug in the indel caller towards the end of a chromosome
|
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|
2927
|
|
|
2928 ------------------------------------------------------------------------
|
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|
2929 r494 | lh3lh3 | 2009-10-26 11:38:00 -0400 (Mon, 26 Oct 2009) | 3 lines
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2930 Changed paths:
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2931 M /trunk/samtools/bamtk.c
|
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2932 M /trunk/samtools/sam_view.c
|
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2933
|
|
|
2934 * samtools-0.1.6-19 (r494)
|
|
|
2935 * allow to convert Illumina quality (64 based) to the BAM quality
|
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2936
|
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|
2937 ------------------------------------------------------------------------
|
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2938 r493 | lh3lh3 | 2009-10-26 10:24:39 -0400 (Mon, 26 Oct 2009) | 4 lines
|
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2939 Changed paths:
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2940 M /trunk/samtools/Makefile
|
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|
2941 M /trunk/samtools/bam.c
|
|
|
2942 M /trunk/samtools/bam_import.c
|
|
|
2943 M /trunk/samtools/bamtk.c
|
|
|
2944 M /trunk/samtools/sam.c
|
|
|
2945 M /trunk/samtools/sam_header.c
|
|
|
2946
|
|
|
2947 * samtools-0.1.6-18 (r493)
|
|
|
2948 * fixed the bugs due to improperly incorporating Petr's header parser
|
|
|
2949 * a little code clean up in sam_header.c
|
|
|
2950
|
|
|
2951 ------------------------------------------------------------------------
|
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2952 r492 | petulda | 2009-10-24 09:43:25 -0400 (Sat, 24 Oct 2009) | 1 line
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2953 Changed paths:
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2954 M /trunk/samtools/sam_header.c
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2955
|
|
|
2956 Added sam_header_line_free call for sam_header_parse2
|
|
|
2957 ------------------------------------------------------------------------
|
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|
2958 r491 | lh3lh3 | 2009-10-24 00:50:16 -0400 (Sat, 24 Oct 2009) | 3 lines
|
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2959 Changed paths:
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2960 M /trunk/samtools/sam_view.c
|
|
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2961
|
|
|
2962 * BUGGY VERSION
|
|
|
2963 * fixed a minor bug
|
|
|
2964
|
|
|
2965 ------------------------------------------------------------------------
|
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|
2966 r490 | lh3lh3 | 2009-10-24 00:45:12 -0400 (Sat, 24 Oct 2009) | 4 lines
|
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2967 Changed paths:
|
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|
2968 M /trunk/samtools/bam.c
|
|
|
2969 M /trunk/samtools/bam.h
|
|
|
2970 M /trunk/samtools/bam_import.c
|
|
|
2971 M /trunk/samtools/sam.c
|
|
|
2972
|
|
|
2973 * BUGGY VERSION
|
|
|
2974 * improved the interface a bit
|
|
|
2975 * bug unfixed
|
|
|
2976
|
|
|
2977 ------------------------------------------------------------------------
|
|
|
2978 r489 | lh3lh3 | 2009-10-24 00:41:50 -0400 (Sat, 24 Oct 2009) | 3 lines
|
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|
2979 Changed paths:
|
|
|
2980 M /trunk/samtools/bam_import.c
|
|
|
2981 M /trunk/samtools/sam_header.c
|
|
|
2982 M /trunk/samtools/sam_header.h
|
|
|
2983
|
|
|
2984 * BUGGY VERSION. Please NOT use it.
|
|
|
2985 * Fixed a minor bug, but the major bug is still there.
|
|
|
2986
|
|
|
2987 ------------------------------------------------------------------------
|
|
|
2988 r488 | lh3lh3 | 2009-10-24 00:17:10 -0400 (Sat, 24 Oct 2009) | 3 lines
|
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2989 Changed paths:
|
|
|
2990 M /trunk/samtools/Makefile
|
|
|
2991 M /trunk/samtools/bam.c
|
|
|
2992 M /trunk/samtools/bam.h
|
|
|
2993 M /trunk/samtools/bam_aux.c
|
|
|
2994 M /trunk/samtools/bam_import.c
|
|
|
2995 M /trunk/samtools/bam_rmdup.c
|
|
|
2996 M /trunk/samtools/bam_rmdupse.c
|
|
|
2997 M /trunk/samtools/kaln.c
|
|
|
2998 M /trunk/samtools/sam.c
|
|
|
2999 M /trunk/samtools/sam_header.c
|
|
|
3000 M /trunk/samtools/sam_header.h
|
|
|
3001 M /trunk/samtools/sam_view.c
|
|
|
3002
|
|
|
3003 * This revision is SERIOUSLY BUGGY. Please NOT use it.
|
|
|
3004 * Start to incorporate header parsing from Petr Danecek
|
|
|
3005
|
|
|
3006 ------------------------------------------------------------------------
|
|
|
3007 r487 | petulda | 2009-10-23 11:44:32 -0400 (Fri, 23 Oct 2009) | 1 line
|
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3008 Changed paths:
|
|
|
3009 M /trunk/samtools/sam_header.c
|
|
|
3010 M /trunk/samtools/sam_header.h
|
|
|
3011
|
|
|
3012 Now possible to merge multiple HeaderDict dictionaries
|
|
|
3013 ------------------------------------------------------------------------
|
|
|
3014 r486 | petulda | 2009-10-22 11:46:58 -0400 (Thu, 22 Oct 2009) | 1 line
|
|
|
3015 Changed paths:
|
|
|
3016 M /trunk/samtools/sam_header.c
|
|
|
3017
|
|
|
3018
|
|
|
3019 ------------------------------------------------------------------------
|
|
|
3020 r485 | petulda | 2009-10-22 11:41:56 -0400 (Thu, 22 Oct 2009) | 1 line
|
|
|
3021 Changed paths:
|
|
|
3022 A /trunk/samtools/sam_header.c
|
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3023 A /trunk/samtools/sam_header.h
|
|
|
3024
|
|
|
3025
|
|
|
3026 ------------------------------------------------------------------------
|
|
|
3027 r484 | lh3lh3 | 2009-10-19 14:31:32 -0400 (Mon, 19 Oct 2009) | 5 lines
|
|
|
3028 Changed paths:
|
|
|
3029 M /trunk/samtools/bam_import.c
|
|
|
3030 M /trunk/samtools/bam_rmdupse.c
|
|
|
3031 M /trunk/samtools/bamtk.c
|
|
|
3032 M /trunk/samtools/examples/Makefile
|
|
|
3033
|
|
|
3034 * samtools-0.1.6-17 (r484)
|
|
|
3035 * fixed a memory leak in rmdupse
|
|
|
3036 * fixed a bug in parsing @RG header lines
|
|
|
3037 * test rmdup in examples/
|
|
|
3038
|
|
|
3039 ------------------------------------------------------------------------
|
|
|
3040 r483 | lh3lh3 | 2009-10-19 13:22:48 -0400 (Mon, 19 Oct 2009) | 4 lines
|
|
|
3041 Changed paths:
|
|
|
3042 M /trunk/samtools/bam_rmdup.c
|
|
|
3043 M /trunk/samtools/bam_rmdupse.c
|
|
|
3044 M /trunk/samtools/bamtk.c
|
|
|
3045
|
|
|
3046 * samtools-0.1.6-16 (r483)
|
|
|
3047 * unify the interface of rmdup and rmdupse
|
|
|
3048 * a new bug found in rg2lib(). Have not been fixed yet.
|
|
|
3049
|
|
|
3050 ------------------------------------------------------------------------
|
|
|
3051 r482 | lh3lh3 | 2009-10-19 13:03:34 -0400 (Mon, 19 Oct 2009) | 4 lines
|
|
|
3052 Changed paths:
|
|
|
3053 M /trunk/samtools/bam.h
|
|
|
3054 M /trunk/samtools/bam_rmdup.c
|
|
|
3055 M /trunk/samtools/bam_rmdupse.c
|
|
|
3056 M /trunk/samtools/bamtk.c
|
|
|
3057 A /trunk/samtools/klist.h
|
|
|
3058
|
|
|
3059 * samtools-0.1.6-15 (r482)
|
|
|
3060 * rewrite rmdupse
|
|
|
3061 * rmdupse is now library aware
|
|
|
3062
|
|
|
3063 ------------------------------------------------------------------------
|
|
|
3064 r481 | lh3lh3 | 2009-10-18 00:07:21 -0400 (Sun, 18 Oct 2009) | 3 lines
|
|
|
3065 Changed paths:
|
|
|
3066 M /trunk/samtools/bam_rmdup.c
|
|
|
3067 M /trunk/samtools/bamtk.c
|
|
|
3068
|
|
|
3069 * samtools-0.1.6-14 (r480)
|
|
|
3070 * rmdup is now RG aware
|
|
|
3071
|
|
|
3072 ------------------------------------------------------------------------
|
|
|
3073 r480 | lh3lh3 | 2009-10-17 22:05:20 -0400 (Sat, 17 Oct 2009) | 2 lines
|
|
|
3074 Changed paths:
|
|
|
3075 M /trunk/samtools/misc/samtools.pl
|
|
|
3076
|
|
|
3077 added a small unitity to parse SRA XML files
|
|
|
3078
|
|
|
3079 ------------------------------------------------------------------------
|
|
|
3080 r479 | lh3lh3 | 2009-10-17 20:57:26 -0400 (Sat, 17 Oct 2009) | 3 lines
|
|
|
3081 Changed paths:
|
|
|
3082 M /trunk/samtools/bam_maqcns.c
|
|
|
3083 M /trunk/samtools/bam_maqcns.h
|
|
|
3084 M /trunk/samtools/bam_plcmd.c
|
|
|
3085 M /trunk/samtools/bam_sort.c
|
|
|
3086 M /trunk/samtools/bamtk.c
|
|
|
3087
|
|
|
3088 * samtools-0.1.6-13 (r479)
|
|
|
3089 * merge: optionally use file names as RG tags
|
|
|
3090
|
|
|
3091 ------------------------------------------------------------------------
|
|
|
3092 r478 | lh3lh3 | 2009-10-14 14:18:12 -0400 (Wed, 14 Oct 2009) | 3 lines
|
|
|
3093 Changed paths:
|
|
|
3094 M /trunk/samtools/bam.c
|
|
|
3095 M /trunk/samtools/bam.h
|
|
|
3096 M /trunk/samtools/bam_maqcns.c
|
|
|
3097 M /trunk/samtools/bamtk.c
|
|
|
3098 M /trunk/samtools/kaln.c
|
|
|
3099
|
|
|
3100 * samtools-0.1.6-12 (r478)
|
|
|
3101 * fixed a bug in the indel caller
|
|
|
3102
|
|
|
3103 ------------------------------------------------------------------------
|
|
|
3104 r477 | lh3lh3 | 2009-10-10 06:12:26 -0400 (Sat, 10 Oct 2009) | 3 lines
|
|
|
3105 Changed paths:
|
|
|
3106 M /trunk/samtools/bam_index.c
|
|
|
3107 M /trunk/samtools/bamtk.c
|
|
|
3108
|
|
|
3109 * samtools-0.1.6-11 (r477)
|
|
|
3110 * fixed a bug due to recent change in bam_index.c (thank Nicole Washington for the patch)
|
|
|
3111
|
|
|
3112 ------------------------------------------------------------------------
|
|
|
3113 r476 | petulda | 2009-10-09 11:45:36 -0400 (Fri, 09 Oct 2009) | 1 line
|
|
|
3114 Changed paths:
|
|
|
3115 A /trunk/samtools/misc/sam2vcf.pl
|
|
|
3116
|
|
|
3117 Added the sam2vcf.pl script.
|
|
|
3118 ------------------------------------------------------------------------
|
|
|
3119 r475 | lh3lh3 | 2009-10-08 10:19:16 -0400 (Thu, 08 Oct 2009) | 2 lines
|
|
|
3120 Changed paths:
|
|
|
3121 M /trunk/samtools/Makefile
|
|
|
3122 M /trunk/samtools/bam.c
|
|
|
3123 M /trunk/samtools/bam.h
|
|
|
3124 M /trunk/samtools/bam_maqcns.c
|
|
|
3125 M /trunk/samtools/bamtk.c
|
|
|
3126 A /trunk/samtools/kaln.c
|
|
|
3127 A /trunk/samtools/kaln.h
|
|
|
3128
|
|
|
3129 Unfinished modification. Please do not use this revision...
|
|
|
3130
|
|
|
3131 ------------------------------------------------------------------------
|
|
|
3132 r474 | petulda | 2009-10-08 06:39:54 -0400 (Thu, 08 Oct 2009) | 1 line
|
|
|
3133 Changed paths:
|
|
|
3134 M /trunk/samtools/knetfile.c
|
|
|
3135
|
|
|
3136 Removed the offending knet_seek message.
|
|
|
3137 ------------------------------------------------------------------------
|
|
|
3138 r473 | petulda | 2009-10-06 09:26:35 -0400 (Tue, 06 Oct 2009) | 1 line
|
|
|
3139 Changed paths:
|
|
|
3140 M /trunk/samtools/knetfile.c
|
|
|
3141 M /trunk/samtools/razf.c
|
|
|
3142
|
|
|
3143 Bug fix - faidx on RAZF compressed files now working.
|
|
|
3144 ------------------------------------------------------------------------
|
|
|
3145 r472 | lh3lh3 | 2009-10-02 08:42:57 -0400 (Fri, 02 Oct 2009) | 2 lines
|
|
|
3146 Changed paths:
|
|
|
3147 M /trunk/samtools/samtools.1
|
|
|
3148
|
|
|
3149 Clarify the meaning of a region like "chr2:1,000,000".
|
|
|
3150
|
|
|
3151 ------------------------------------------------------------------------
|
|
|
3152 r471 | lh3lh3 | 2009-10-02 05:42:19 -0400 (Fri, 02 Oct 2009) | 2 lines
|
|
|
3153 Changed paths:
|
|
|
3154 M /trunk/samtools/misc/novo2sam.pl
|
|
|
3155
|
|
|
3156 Fixed minor bugs in novo2sam.pl (on behalf of Ken Chen and Colin Hercus)
|
|
|
3157
|
|
|
3158 ------------------------------------------------------------------------
|
|
|
3159 r470 | lh3lh3 | 2009-09-29 15:01:27 -0400 (Tue, 29 Sep 2009) | 3 lines
|
|
|
3160 Changed paths:
|
|
|
3161 M /trunk/samtools/Makefile.mingw
|
|
|
3162 M /trunk/samtools/bamtk.c
|
|
|
3163 M /trunk/samtools/knetfile.c
|
|
|
3164 M /trunk/samtools/knetfile.h
|
|
|
3165
|
|
|
3166 * samtools-0.1.6-9 (r470)
|
|
|
3167 * make knetfile.c compatible with MinGW (thank Martin Morgan for the patch)
|
|
|
3168
|
|
|
3169 ------------------------------------------------------------------------
|
|
|
3170 r469 | lh3lh3 | 2009-09-29 08:07:44 -0400 (Tue, 29 Sep 2009) | 3 lines
|
|
|
3171 Changed paths:
|
|
|
3172 M /trunk/samtools/bam_index.c
|
|
|
3173 M /trunk/samtools/bamtk.c
|
|
|
3174
|
|
|
3175 * samtools-0.1.6-9 (r469)
|
|
|
3176 * refactor bam_fetch() for Python binding. On behalf of Leo Goodstadt.
|
|
|
3177
|
|
|
3178 ------------------------------------------------------------------------
|
|
|
3179 r468 | lh3lh3 | 2009-09-28 05:18:29 -0400 (Mon, 28 Sep 2009) | 3 lines
|
|
|
3180 Changed paths:
|
|
|
3181 M /trunk/samtools/bam_sort.c
|
|
|
3182 M /trunk/samtools/bamtk.c
|
|
|
3183 M /trunk/samtools/misc/samtools.pl
|
|
|
3184
|
|
|
3185 * samtools-0.1.6-7 (r468)
|
|
|
3186 * make merge stable
|
|
|
3187
|
|
|
3188 ------------------------------------------------------------------------
|
|
|
3189 r467 | petulda | 2009-09-28 04:51:29 -0400 (Mon, 28 Sep 2009) | 1 line
|
|
|
3190 Changed paths:
|
|
|
3191 M /trunk/samtools/bgzf.c
|
|
|
3192 M /trunk/samtools/bgzip.c
|
|
|
3193 M /trunk/samtools/razf.c
|
|
|
3194 M /trunk/samtools/razip.c
|
|
|
3195
|
|
|
3196 Changed the mode for newly created files to 0666. This allows less strict permissions with umask properly set (e.g. 0002 vs. 0022).
|
|
|
3197 ------------------------------------------------------------------------
|
|
|
3198 r466 | lh3lh3 | 2009-09-24 06:29:19 -0400 (Thu, 24 Sep 2009) | 3 lines
|
|
|
3199 Changed paths:
|
|
|
3200 M /trunk/samtools/ChangeLog
|
|
|
3201 M /trunk/samtools/bam_md.c
|
|
|
3202 M /trunk/samtools/bamtk.c
|
|
|
3203
|
|
|
3204 * samtools-0.1.6-6 (r466)
|
|
|
3205 * do not crash calmd when some sequences are absent from the reference.
|
|
|
3206
|
|
|
3207 ------------------------------------------------------------------------
|
|
|
3208 r464 | jmarshall | 2009-09-23 06:14:32 -0400 (Wed, 23 Sep 2009) | 3 lines
|
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3209 Changed paths:
|
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|
3210 M /trunk/samtools/bam.c
|
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|
3211 M /trunk/samtools/knetfile.c
|
|
|
3212
|
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|
3213 Suppress bgzf_check_EOF() messages when reading from a pipe, as there is
|
|
|
3214 no way to seek on a pipe and the messages always appear.
|
|
|
3215
|
|
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3216 ------------------------------------------------------------------------
|
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3217 r463 | petulda | 2009-09-16 07:05:41 -0400 (Wed, 16 Sep 2009) | 1 line
|
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3218 Changed paths:
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3219 M /trunk/samtools/knetfile.c
|
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3220 M /trunk/samtools/razf.c
|
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3221
|
|
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3222 A bug fix, "samtools view" is now working again.
|
|
|
3223 ------------------------------------------------------------------------
|
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3224 r462 | lh3lh3 | 2009-09-16 04:51:07 -0400 (Wed, 16 Sep 2009) | 3 lines
|
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3225 Changed paths:
|
|
|
3226 M /trunk/samtools/bamtk.c
|
|
|
3227 M /trunk/samtools/faidx.c
|
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3228 M /trunk/samtools/knetfile.c
|
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3229 M /trunk/samtools/knetfile.h
|
|
|
3230 M /trunk/samtools/razf.c
|
|
|
3231 M /trunk/samtools/razf.h
|
|
|
3232
|
|
|
3233 * samtools-0.1.6-5 (r462)
|
|
|
3234 * Added knetfile support in razf and faidx (on behalf of Petr Danecek)
|
|
|
3235
|
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|
3236 ------------------------------------------------------------------------
|
|
|
3237 r460 | lh3lh3 | 2009-09-09 07:06:22 -0400 (Wed, 09 Sep 2009) | 2 lines
|
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3238 Changed paths:
|
|
|
3239 M /trunk/samtools/samtools.1
|
|
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3240
|
|
|
3241 fixed a formatting issue
|
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3242
|
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|
3243 ------------------------------------------------------------------------
|
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3244 r459 | lh3lh3 | 2009-09-08 18:14:08 -0400 (Tue, 08 Sep 2009) | 3 lines
|
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3245 Changed paths:
|
|
|
3246 M /trunk/samtools/bam_sort.c
|
|
|
3247 M /trunk/samtools/bamtk.c
|
|
|
3248
|
|
|
3249 * samtools-0.1.6-4 (r459)
|
|
|
3250 * make sort output the result to stdout when -o is in use
|
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|
3251
|
|
|
3252 ------------------------------------------------------------------------
|
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|
3253 r458 | lh3lh3 | 2009-09-07 05:10:28 -0400 (Mon, 07 Sep 2009) | 4 lines
|
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3254 Changed paths:
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|
3255 M /trunk/samtools/bamtk.c
|
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|
3256 M /trunk/samtools/faidx.c
|
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|
3257 M /trunk/samtools/faidx.h
|
|
|
3258 M /trunk/samtools/samtools.1
|
|
|
3259
|
|
|
3260 * samtools-0.1.6-2 (r458)
|
|
|
3261 * added more interface to faidx (by Nils)
|
|
|
3262 * updated documentation
|
|
|
3263
|
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|
3264 ------------------------------------------------------------------------
|
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3265 r457 | lh3lh3 | 2009-09-05 16:12:04 -0400 (Sat, 05 Sep 2009) | 3 lines
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3266 Changed paths:
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|
3267 M /trunk/samtools/bam_sort.c
|
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3268 M /trunk/samtools/bamtk.c
|
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3269
|
|
|
3270 * samtools-0.1.6-2 (r457)
|
|
|
3271 * get rid of three assert() in bam_sort.c
|
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3272
|
|
|
3273 ------------------------------------------------------------------------
|
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3274 r456 | jmarshall | 2009-09-04 12:46:25 -0400 (Fri, 04 Sep 2009) | 3 lines
|
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3275 Changed paths:
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|
3276 M /trunk/samtools/razf.c
|
|
|
3277
|
|
|
3278 Return NULL from _razf_open() (and hence razf_open()/razf_open2())
|
|
|
3279 when opening the file fails.
|
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|
3280
|
|
|
3281 ------------------------------------------------------------------------
|
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3282 r453 | lh3lh3 | 2009-09-02 08:56:33 -0400 (Wed, 02 Sep 2009) | 2 lines
|
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3283 Changed paths:
|
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3284 M /trunk/samtools/ChangeLog
|
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|
3285 M /trunk/samtools/NEWS
|
|
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3286 M /trunk/samtools/bamtk.c
|
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3287 M /trunk/samtools/samtools.1
|
|
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3288 D /trunk/samtools/source.dot
|
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3289
|
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|
3290 Release samtools-0.1.6
|
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3291
|
|
|
3292 ------------------------------------------------------------------------
|
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|
3293 r451 | lh3lh3 | 2009-09-02 05:44:48 -0400 (Wed, 02 Sep 2009) | 4 lines
|
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3294 Changed paths:
|
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|
3295 M /trunk/samtools/bam_md.c
|
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3296 M /trunk/samtools/bam_rmdup.c
|
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3297 M /trunk/samtools/bam_rmdupse.c
|
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3298 M /trunk/samtools/bam_sort.c
|
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3299 M /trunk/samtools/bamtk.c
|
|
|
3300 M /trunk/samtools/samtools.1
|
|
|
3301
|
|
|
3302 * samtools-0.1.5-34 (r451)
|
|
|
3303 * applied the patch by John
|
|
|
3304 * improved the help message a little bit
|
|
|
3305
|
|
|
3306 ------------------------------------------------------------------------
|
|
|
3307 r450 | lh3lh3 | 2009-09-02 04:55:55 -0400 (Wed, 02 Sep 2009) | 3 lines
|
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|
3308 Changed paths:
|
|
|
3309 M /trunk/samtools/bam_color.c
|
|
|
3310 M /trunk/samtools/bamtk.c
|
|
|
3311
|
|
|
3312 * samtools-0.1.5-33 (r450)
|
|
|
3313 * fixed a bug in bam_color.c (on behalf of Nils Homer)
|
|
|
3314
|
|
|
3315 ------------------------------------------------------------------------
|
|
|
3316 r449 | lh3lh3 | 2009-08-29 15:36:41 -0400 (Sat, 29 Aug 2009) | 4 lines
|
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3317 Changed paths:
|
|
|
3318 M /trunk/samtools/bam_import.c
|
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|
3319 M /trunk/samtools/bam_md.c
|
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3320 M /trunk/samtools/bamtk.c
|
|
|
3321 M /trunk/samtools/misc/samtools.pl
|
|
|
3322
|
|
|
3323 * samtools-0.1.5-32 (r449)
|
|
|
3324 * fillmd: fixed a bug in modifying MD/NM tags
|
|
|
3325 * in import, give a warning if the read is aligned but there is no CIGAR.
|
|
|
3326
|
|
|
3327 ------------------------------------------------------------------------
|
|
|
3328 r448 | lh3lh3 | 2009-08-19 04:44:28 -0400 (Wed, 19 Aug 2009) | 3 lines
|
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|
3329 Changed paths:
|
|
|
3330 M /trunk/samtools/ChangeLog
|
|
|
3331 M /trunk/samtools/bam_pileup.c
|
|
|
3332 M /trunk/samtools/bamtk.c
|
|
|
3333 M /trunk/samtools/misc/wgsim_eval.pl
|
|
|
3334
|
|
|
3335 * samtools-0.1.5-31 (r448)
|
|
|
3336 * fixed an issue when the last CIGAR is I or D
|
|
|
3337
|
|
|
3338 ------------------------------------------------------------------------
|
|
|
3339 r447 | lh3lh3 | 2009-08-17 04:34:57 -0400 (Mon, 17 Aug 2009) | 3 lines
|
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3340 Changed paths:
|
|
|
3341 M /trunk/samtools/bam_aux.c
|
|
|
3342 M /trunk/samtools/bamtk.c
|
|
|
3343
|
|
|
3344 * samtools-0.1.5-30 (r447)
|
|
|
3345 * fixed a bug in bam_aux_get(): 'A' is not checked
|
|
|
3346
|
|
|
3347 ------------------------------------------------------------------------
|
|
|
3348 r446 | lh3lh3 | 2009-08-17 04:33:17 -0400 (Mon, 17 Aug 2009) | 2 lines
|
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|
3349 Changed paths:
|
|
|
3350 M /trunk/samtools/bam_aux.c
|
|
|
3351 M /trunk/samtools/bamtk.c
|
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3352
|
|
|
3353 *
|
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|
3354
|
|
|
3355 ------------------------------------------------------------------------
|
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|
3356 r444 | lh3lh3 | 2009-08-11 05:02:36 -0400 (Tue, 11 Aug 2009) | 3 lines
|
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3357 Changed paths:
|
|
|
3358 M /trunk/samtools/bam_sort.c
|
|
|
3359 M /trunk/samtools/bamtk.c
|
|
|
3360
|
|
|
3361 * samtools-0.1.5-28 (r444)
|
|
|
3362 * bug in "merge -n"
|
|
|
3363
|
|
|
3364 ------------------------------------------------------------------------
|
|
|
3365 r443 | lh3lh3 | 2009-08-11 04:29:11 -0400 (Tue, 11 Aug 2009) | 4 lines
|
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3366 Changed paths:
|
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|
3367 M /trunk/samtools/bam.c
|
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3368 M /trunk/samtools/bam_import.c
|
|
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3369 M /trunk/samtools/bamtk.c
|
|
|
3370
|
|
|
3371 * samtools-0.1.5-27 (r443)
|
|
|
3372 * SEQ and QUAL can be "*"
|
|
|
3373 * parse CIGAR "=" and "X" as "M"
|
|
|
3374
|
|
|
3375 ------------------------------------------------------------------------
|
|
|
3376 r442 | lh3lh3 | 2009-08-07 16:56:38 -0400 (Fri, 07 Aug 2009) | 4 lines
|
|
|
3377 Changed paths:
|
|
|
3378 M /trunk/samtools/bam_pileup.c
|
|
|
3379 M /trunk/samtools/bamtk.c
|
|
|
3380 M /trunk/samtools/misc/md5.c
|
|
|
3381 M /trunk/samtools/misc/md5.h
|
|
|
3382 M /trunk/samtools/misc/md5fa.c
|
|
|
3383
|
|
|
3384 * samtools-0.1.5-26 (r442)
|
|
|
3385 * replace RSA Inc md5.* with ones under permissive lincense
|
|
|
3386 * fixed a bug in detecting unsorted bam in pileup
|
|
|
3387
|
|
|
3388 ------------------------------------------------------------------------
|
|
|
3389 r441 | bhandsaker | 2009-08-05 09:41:28 -0400 (Wed, 05 Aug 2009) | 2 lines
|
|
|
3390 Changed paths:
|
|
|
3391 M /trunk/samtools/bgzf.c
|
|
|
3392 M /trunk/samtools/bgzf.h
|
|
|
3393 M /trunk/samtools/bgzip.c
|
|
|
3394
|
|
|
3395 Change copyright notices now that MIT has approved open source distribution.
|
|
|
3396
|
|
|
3397 ------------------------------------------------------------------------
|
|
|
3398 r440 | lh3lh3 | 2009-08-05 05:44:24 -0400 (Wed, 05 Aug 2009) | 3 lines
|
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|
3399 Changed paths:
|
|
|
3400 M /trunk/samtools/bam_stat.c
|
|
|
3401 M /trunk/samtools/bamtk.c
|
|
|
3402
|
|
|
3403 * samtools-0.1.5-25 (r436)
|
|
|
3404 * in flagstats, do not report singletons if both ends are unmapped
|
|
|
3405
|
|
|
3406 ------------------------------------------------------------------------
|
|
|
3407 r439 | lh3lh3 | 2009-08-04 17:16:51 -0400 (Tue, 04 Aug 2009) | 2 lines
|
|
|
3408 Changed paths:
|
|
|
3409 M /trunk/samtools/misc/maq2sam.c
|
|
|
3410
|
|
|
3411 fixed a SERIOUS bug in setting 0x20 flag
|
|
|
3412
|
|
|
3413 ------------------------------------------------------------------------
|
|
|
3414 r438 | lh3lh3 | 2009-08-04 16:50:43 -0400 (Tue, 04 Aug 2009) | 2 lines
|
|
|
3415 Changed paths:
|
|
|
3416 M /trunk/samtools/misc/samtools.pl
|
|
|
3417
|
|
|
3418 fixed two minor bugs (suggested by Tim M Storm)
|
|
|
3419
|
|
|
3420 ------------------------------------------------------------------------
|
|
|
3421 r437 | lh3lh3 | 2009-08-04 04:13:24 -0400 (Tue, 04 Aug 2009) | 3 lines
|
|
|
3422 Changed paths:
|
|
|
3423 M /trunk/samtools/bamtk.c
|
|
|
3424 M /trunk/samtools/misc/samtools.pl
|
|
|
3425 M /trunk/samtools/sam_view.c
|
|
|
3426
|
|
|
3427 * samtools-0.1.5-24 (r435)
|
|
|
3428 * fixed a typo
|
|
|
3429
|
|
|
3430 ------------------------------------------------------------------------
|
|
|
3431 r434 | lh3lh3 | 2009-08-03 05:40:42 -0400 (Mon, 03 Aug 2009) | 3 lines
|
|
|
3432 Changed paths:
|
|
|
3433 M /trunk/samtools/bam_tview.c
|
|
|
3434 M /trunk/samtools/bamtk.c
|
|
|
3435
|
|
|
3436 * samtools-0.1.5-23 (r434)
|
|
|
3437 * in tview, press 'r' to show read names rather than sequences
|
|
|
3438
|
|
|
3439 ------------------------------------------------------------------------
|
|
|
3440 r433 | lh3lh3 | 2009-08-02 14:13:35 -0400 (Sun, 02 Aug 2009) | 3 lines
|
|
|
3441 Changed paths:
|
|
|
3442 M /trunk/samtools/knetfile.c
|
|
|
3443
|
|
|
3444 * tried to fixed the buggy FTP random access in Windows. FAILED.
|
|
|
3445 * anyway, MinGW seems to have problem with "%lld".
|
|
|
3446
|
|
|
3447 ------------------------------------------------------------------------
|
|
|
3448 r432 | lh3lh3 | 2009-08-01 19:32:07 -0400 (Sat, 01 Aug 2009) | 5 lines
|
|
|
3449 Changed paths:
|
|
|
3450 M /trunk/samtools/Makefile.mingw
|
|
|
3451 M /trunk/samtools/bamtk.c
|
|
|
3452 M /trunk/samtools/faidx.c
|
|
|
3453 M /trunk/samtools/razf.c
|
|
|
3454 A /trunk/samtools/win32/libcurses.a
|
|
|
3455 A /trunk/samtools/win32/xcurses.h
|
|
|
3456
|
|
|
3457 * samtools-0.1.5-22 (r432)
|
|
|
3458 * faidx: fixed compitability issue with _WIN32
|
|
|
3459 * razf: fixed potential compitability issue with _WIN32
|
|
|
3460 * PDCurses support in Windows
|
|
|
3461
|
|
|
3462 ------------------------------------------------------------------------
|
|
|
3463 r431 | lh3lh3 | 2009-08-01 18:34:54 -0400 (Sat, 01 Aug 2009) | 2 lines
|
|
|
3464 Changed paths:
|
|
|
3465 M /trunk/samtools/win32/libz.a
|
|
|
3466
|
|
|
3467 replace the GnuWin32 version of libz.a with my own build with MinGW.
|
|
|
3468
|
|
|
3469 ------------------------------------------------------------------------
|
|
|
3470 r430 | lh3lh3 | 2009-08-01 18:21:07 -0400 (Sat, 01 Aug 2009) | 2 lines
|
|
|
3471 Changed paths:
|
|
|
3472 M /trunk/samtools/knetfile.c
|
|
|
3473
|
|
|
3474 add comments
|
|
|
3475
|
|
|
3476 ------------------------------------------------------------------------
|
|
|
3477 r429 | lh3lh3 | 2009-08-01 17:41:19 -0400 (Sat, 01 Aug 2009) | 3 lines
|
|
|
3478 Changed paths:
|
|
|
3479 M /trunk/samtools/Makefile.mingw
|
|
|
3480 M /trunk/samtools/bamtk.c
|
|
|
3481 M /trunk/samtools/knetfile.c
|
|
|
3482 M /trunk/samtools/knetfile.h
|
|
|
3483
|
|
|
3484 * samtools-0.1.5-21 (r428)
|
|
|
3485 * knetfile.c is now compatible with mingw-winsock
|
|
|
3486
|
|
|
3487 ------------------------------------------------------------------------
|
|
|
3488 r428 | lh3lh3 | 2009-07-31 19:39:07 -0400 (Fri, 31 Jul 2009) | 2 lines
|
|
|
3489 Changed paths:
|
|
|
3490 M /trunk/samtools/Makefile.mingw
|
|
|
3491
|
|
|
3492 simplify MinGW Makefile
|
|
|
3493
|
|
|
3494 ------------------------------------------------------------------------
|
|
|
3495 r427 | lh3lh3 | 2009-07-31 19:30:54 -0400 (Fri, 31 Jul 2009) | 5 lines
|
|
|
3496 Changed paths:
|
|
|
3497 A /trunk/samtools/Makefile.mingw
|
|
|
3498 M /trunk/samtools/bam_import.c
|
|
|
3499 M /trunk/samtools/bamtk.c
|
|
|
3500 A /trunk/samtools/win32
|
|
|
3501 A /trunk/samtools/win32/libz.a
|
|
|
3502 A /trunk/samtools/win32/zconf.h
|
|
|
3503 A /trunk/samtools/win32/zlib.h
|
|
|
3504
|
|
|
3505 * samtools-0.1.5-20 (r427)
|
|
|
3506 * MinGW support. At least SAM<->BAM conversion is working. Other
|
|
|
3507 functionality are not tested at the moment.
|
|
|
3508 * zlib headers and Windows version of libz.a are included in win32/
|
|
|
3509
|
|
|
3510 ------------------------------------------------------------------------
|
|
|
3511 r426 | lh3lh3 | 2009-07-31 18:32:09 -0400 (Fri, 31 Jul 2009) | 3 lines
|
|
|
3512 Changed paths:
|
|
|
3513 M /trunk/samtools/bamtk.c
|
|
|
3514 M /trunk/samtools/sam_view.c
|
|
|
3515
|
|
|
3516 * samtools-0.1.5-19 (r426)
|
|
|
3517 * fixed a bug caused by recent modifications. Sorry.
|
|
|
3518
|
|
|
3519 ------------------------------------------------------------------------
|
|
|
3520 r425 | lh3lh3 | 2009-07-31 18:23:51 -0400 (Fri, 31 Jul 2009) | 2 lines
|
|
|
3521 Changed paths:
|
|
|
3522 M /trunk/samtools/bgzf.c
|
|
|
3523
|
|
|
3524 compatible with Windows binary files
|
|
|
3525
|
|
|
3526 ------------------------------------------------------------------------
|
|
|
3527 r424 | lh3lh3 | 2009-07-31 05:19:59 -0400 (Fri, 31 Jul 2009) | 5 lines
|
|
|
3528 Changed paths:
|
|
|
3529 M /trunk/samtools/bam_maqcns.c
|
|
|
3530 M /trunk/samtools/bam_maqcns.h
|
|
|
3531 M /trunk/samtools/bam_plcmd.c
|
|
|
3532 M /trunk/samtools/bam_tview.c
|
|
|
3533 M /trunk/samtools/bamtk.c
|
|
|
3534 M /trunk/samtools/misc/samtools.pl
|
|
|
3535
|
|
|
3536 * samtools-0.1.5-18 (r423)
|
|
|
3537 * output additional information in pileup indel lines, for the purepose
|
|
|
3538 of debugging at the moment
|
|
|
3539 * in tview, optionally allow to treat reference skip as deletion
|
|
|
3540
|
|
|
3541 ------------------------------------------------------------------------
|
|
|
3542 r423 | lh3lh3 | 2009-07-30 17:00:36 -0400 (Thu, 30 Jul 2009) | 2 lines
|
|
|
3543 Changed paths:
|
|
|
3544 A /trunk/samtools/misc/psl2sam.pl
|
|
|
3545
|
|
|
3546 convert BLAT psl to SAM.
|
|
|
3547
|
|
|
3548 ------------------------------------------------------------------------
|
|
|
3549 r422 | lh3lh3 | 2009-07-30 06:24:39 -0400 (Thu, 30 Jul 2009) | 6 lines
|
|
|
3550 Changed paths:
|
|
|
3551 M /trunk/samtools/ChangeLog
|
|
|
3552 M /trunk/samtools/bam.c
|
|
|
3553 M /trunk/samtools/bamtk.c
|
|
|
3554 M /trunk/samtools/bgzf.c
|
|
|
3555 M /trunk/samtools/bgzf.h
|
|
|
3556 M /trunk/samtools/knetfile.c
|
|
|
3557 M /trunk/samtools/sam.c
|
|
|
3558 M /trunk/samtools/sam_view.c
|
|
|
3559
|
|
|
3560 * samtools-0.1.5-17 (r422)
|
|
|
3561 * fixed a but in knetfile.c when seek type is not SEEK_SET
|
|
|
3562 * write an empty BGZF block to every BGZF file
|
|
|
3563 * check BGZF EOF marker in bam_header_read()
|
|
|
3564 * update ChangeLog
|
|
|
3565
|
|
|
3566 ------------------------------------------------------------------------
|
|
|
3567 r421 | lh3lh3 | 2009-07-30 05:03:39 -0400 (Thu, 30 Jul 2009) | 3 lines
|
|
|
3568 Changed paths:
|
|
|
3569 M /trunk/samtools/bam_import.c
|
|
|
3570 M /trunk/samtools/bam_plcmd.c
|
|
|
3571 M /trunk/samtools/bamtk.c
|
|
|
3572 M /trunk/samtools/misc/samtools.pl
|
|
|
3573 M /trunk/samtools/sam.c
|
|
|
3574 M /trunk/samtools/sam.h
|
|
|
3575 M /trunk/samtools/sam_view.c
|
|
|
3576
|
|
|
3577 * samtools-0.1.5-16 (r421)
|
|
|
3578 * in view and pileup, load header from FASTA index if the input is SAM.
|
|
|
3579
|
|
|
3580 ------------------------------------------------------------------------
|
|
|
3581 r420 | lh3lh3 | 2009-07-29 04:18:55 -0400 (Wed, 29 Jul 2009) | 2 lines
|
|
|
3582 Changed paths:
|
|
|
3583 M /trunk/samtools/misc/maq2sam.c
|
|
|
3584
|
|
|
3585 do not set "read 1" if reads are not mapped in the PE mode of maq
|
|
|
3586
|
|
|
3587 ------------------------------------------------------------------------
|
|
|
3588 r419 | lh3lh3 | 2009-07-28 04:52:33 -0400 (Tue, 28 Jul 2009) | 5 lines
|
|
|
3589 Changed paths:
|
|
|
3590 M /trunk/samtools/bam_import.c
|
|
|
3591 M /trunk/samtools/bamtk.c
|
|
|
3592 M /trunk/samtools/misc/samtools.pl
|
|
|
3593 M /trunk/samtools/misc/wgsim_eval.pl
|
|
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3594
|
|
|
3595 * samtools-0.1.5-15 (r419)
|
|
|
3596 * in sam_open(), return NULL when the file cannot be opened.
|
|
|
3597 * make wgsim_eval.pl more robust to imperfect SAM
|
|
|
3598 * add "unique" command to samtools.pl
|
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3599
|
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|
3600 ------------------------------------------------------------------------
|
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|
3601 r418 | lh3lh3 | 2009-07-24 09:04:19 -0400 (Fri, 24 Jul 2009) | 2 lines
|
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3602 Changed paths:
|
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3603 M /trunk/samtools/misc/wgsim_eval.pl
|
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3604
|
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|
3605 skip @header lines in SAM
|
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3606
|
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|
3607 ------------------------------------------------------------------------
|
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3608 r417 | lh3lh3 | 2009-07-24 07:42:38 -0400 (Fri, 24 Jul 2009) | 3 lines
|
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3609 Changed paths:
|
|
|
3610 M /trunk/samtools/bamtk.c
|
|
|
3611 M /trunk/samtools/sam_view.c
|
|
|
3612
|
|
|
3613 * samtools-0.1.5-14 (r417)
|
|
|
3614 * more help in "samtools view" due to the recent changes.
|
|
|
3615
|
|
|
3616 ------------------------------------------------------------------------
|
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|
3617 r416 | lh3lh3 | 2009-07-24 07:34:30 -0400 (Fri, 24 Jul 2009) | 3 lines
|
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|
3618 Changed paths:
|
|
|
3619 M /trunk/samtools/bam.c
|
|
|
3620 M /trunk/samtools/bam.h
|
|
|
3621 M /trunk/samtools/bam_import.c
|
|
|
3622 M /trunk/samtools/bamtk.c
|
|
|
3623 M /trunk/samtools/sam.c
|
|
|
3624 M /trunk/samtools/sam.h
|
|
|
3625 M /trunk/samtools/sam_view.c
|
|
|
3626
|
|
|
3627 * samtools-0.1.5-17 (r416)
|
|
|
3628 * support import/export SAM with string tags
|
|
|
3629
|
|
|
3630 ------------------------------------------------------------------------
|
|
|
3631 r415 | lh3lh3 | 2009-07-24 06:39:26 -0400 (Fri, 24 Jul 2009) | 3 lines
|
|
|
3632 Changed paths:
|
|
|
3633 M /trunk/samtools/bam.c
|
|
|
3634 M /trunk/samtools/bam.h
|
|
|
3635 M /trunk/samtools/bam_import.c
|
|
|
3636 M /trunk/samtools/bamtk.c
|
|
|
3637 M /trunk/samtools/sam.c
|
|
|
3638 M /trunk/samtools/sam.h
|
|
|
3639 M /trunk/samtools/sam_view.c
|
|
|
3640
|
|
|
3641 * samtools-0.1.5-12 (r415)
|
|
|
3642 * FLAG now can be in HEX
|
|
|
3643
|
|
|
3644 ------------------------------------------------------------------------
|
|
|
3645 r414 | lh3lh3 | 2009-07-22 17:03:49 -0400 (Wed, 22 Jul 2009) | 2 lines
|
|
|
3646 Changed paths:
|
|
|
3647 M /trunk/samtools/kstring.h
|
|
|
3648
|
|
|
3649 fixed a compiling error (thank Ken for fixing it)
|
|
|
3650
|
|
|
3651 ------------------------------------------------------------------------
|
|
|
3652 r412 | lh3lh3 | 2009-07-21 17:19:40 -0400 (Tue, 21 Jul 2009) | 2 lines
|
|
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3653 Changed paths:
|
|
|
3654 M /trunk/samtools/kstring.c
|
|
|
3655 M /trunk/samtools/kstring.h
|
|
|
3656
|
|
|
3657 Implemented Boyer-Moore search in the kstring library.
|
|
|
3658
|
|
|
3659 ------------------------------------------------------------------------
|
|
|
3660 r409 | lh3lh3 | 2009-07-17 12:10:20 -0400 (Fri, 17 Jul 2009) | 2 lines
|
|
|
3661 Changed paths:
|
|
|
3662 M /trunk/samtools/bam_index.c
|
|
|
3663
|
|
|
3664 do not include knetfile.h when _USE_KNETFILE is not defined
|
|
|
3665
|
|
|
3666 ------------------------------------------------------------------------
|
|
|
3667 r408 | lh3lh3 | 2009-07-17 10:29:21 -0400 (Fri, 17 Jul 2009) | 5 lines
|
|
|
3668 Changed paths:
|
|
|
3669 M /trunk/samtools/bam_md.c
|
|
|
3670 M /trunk/samtools/bam_tview.c
|
|
|
3671 M /trunk/samtools/bamtk.c
|
|
|
3672 M /trunk/samtools/bgzf.c
|
|
|
3673
|
|
|
3674 * samtools-0.1.5-11 (r408)
|
|
|
3675 * force to overwirte existing MD if it is different from the one calculated
|
|
|
3676 from fillmd.
|
|
|
3677 * bgzf.c: improved the compatibility with Windows headers
|
|
|
3678
|
|
|
3679 ------------------------------------------------------------------------
|
|
|
3680 r407 | lh3lh3 | 2009-07-17 09:46:56 -0400 (Fri, 17 Jul 2009) | 5 lines
|
|
|
3681 Changed paths:
|
|
|
3682 M /trunk/samtools/bam.h
|
|
|
3683 M /trunk/samtools/bam_aux.c
|
|
|
3684 M /trunk/samtools/bam_md.c
|
|
|
3685 M /trunk/samtools/bamtk.c
|
|
|
3686 M /trunk/samtools/sam.h
|
|
|
3687
|
|
|
3688 * samtools-0.1.5-10 (r407)
|
|
|
3689 * implemented bam_aux_del() to remove a tag
|
|
|
3690 * fillmd: generate the NM tag
|
|
|
3691 * fillmd: cmd interface improvement
|
|
|
3692
|
|
|
3693 ------------------------------------------------------------------------
|
|
|
3694 r406 | lh3lh3 | 2009-07-16 18:30:40 -0400 (Thu, 16 Jul 2009) | 2 lines
|
|
|
3695 Changed paths:
|
|
|
3696 M /trunk/samtools/Makefile
|
|
|
3697
|
|
|
3698 Sorry. The old Makefile is for PDCurses...
|
|
|
3699
|
|
|
3700 ------------------------------------------------------------------------
|
|
|
3701 r405 | lh3lh3 | 2009-07-16 18:30:11 -0400 (Thu, 16 Jul 2009) | 3 lines
|
|
|
3702 Changed paths:
|
|
|
3703 M /trunk/samtools/Makefile
|
|
|
3704 M /trunk/samtools/bam_tview.c
|
|
|
3705 M /trunk/samtools/bamtk.c
|
|
|
3706
|
|
|
3707 * samtools-0.1.5-9 (r405)
|
|
|
3708 * improved the compatibility with PDCurses a little bit
|
|
|
3709
|
|
|
3710 ------------------------------------------------------------------------
|
|
|
3711 r404 | lh3lh3 | 2009-07-16 18:23:52 -0400 (Thu, 16 Jul 2009) | 3 lines
|
|
|
3712 Changed paths:
|
|
|
3713 M /trunk/samtools/Makefile
|
|
|
3714 M /trunk/samtools/bam_tview.c
|
|
|
3715 M /trunk/samtools/bamtk.c
|
|
|
3716
|
|
|
3717 * samtools-0.1.5-8 (r404)
|
|
|
3718 * compatible with PDCurses
|
|
|
3719
|
|
|
3720 ------------------------------------------------------------------------
|
|
|
3721 r403 | lh3lh3 | 2009-07-16 17:39:39 -0400 (Thu, 16 Jul 2009) | 3 lines
|
|
|
3722 Changed paths:
|
|
|
3723 M /trunk/samtools/bamtk.c
|
|
|
3724 M /trunk/samtools/kseq.h
|
|
|
3725
|
|
|
3726 * samtools-0.1.5-7 (r403)
|
|
|
3727 * fixed a bug in kseq.h for binary files (text files are fine)
|
|
|
3728
|
|
|
3729 ------------------------------------------------------------------------
|
|
|
3730 r402 | lh3lh3 | 2009-07-16 06:49:53 -0400 (Thu, 16 Jul 2009) | 4 lines
|
|
|
3731 Changed paths:
|
|
|
3732 M /trunk/samtools/bam_import.c
|
|
|
3733 M /trunk/samtools/bam_index.c
|
|
|
3734 M /trunk/samtools/bamtk.c
|
|
|
3735 M /trunk/samtools/bgzf.c
|
|
|
3736
|
|
|
3737 * samtools-0.1.5-6 (r402)
|
|
|
3738 * fixed compiling error when "-D_USE_NETFILE" is not applied
|
|
|
3739 * improve portability to MinGW
|
|
|
3740
|
|
|
3741 ------------------------------------------------------------------------
|
|
|
3742 r398 | lh3lh3 | 2009-07-13 05:21:36 -0400 (Mon, 13 Jul 2009) | 3 lines
|
|
|
3743 Changed paths:
|
|
|
3744 A /trunk/bam-lite/bam.h (from /trunk/samtools/bam.h:395)
|
|
|
3745 A /trunk/bam-lite/bam_lite.c (from /trunk/samtools/bam_lite.c:395)
|
|
|
3746 D /trunk/samtools/bam_lite.c
|
|
|
3747
|
|
|
3748 * move bam_lite.c to bam-lite
|
|
|
3749 * copy bam.h to bam-lite
|
|
|
3750
|
|
|
3751 ------------------------------------------------------------------------
|
|
|
3752 r395 | lh3lh3 | 2009-07-13 05:12:57 -0400 (Mon, 13 Jul 2009) | 3 lines
|
|
|
3753 Changed paths:
|
|
|
3754 M /trunk/samtools/bam.h
|
|
|
3755 M /trunk/samtools/bam_lite.c
|
|
|
3756 M /trunk/samtools/bam_lpileup.c
|
|
|
3757 M /trunk/samtools/bam_pileup.c
|
|
|
3758 M /trunk/samtools/bamtk.c
|
|
|
3759
|
|
|
3760 * samtools-0.1.5-5 (r395)
|
|
|
3761 * added bam_pileup_file() and removed bam_lpileup_file()
|
|
|
3762
|
|
|
3763 ------------------------------------------------------------------------
|
|
|
3764 r394 | lh3lh3 | 2009-07-12 19:35:10 -0400 (Sun, 12 Jul 2009) | 3 lines
|
|
|
3765 Changed paths:
|
|
|
3766 M /trunk/samtools/bamtk.c
|
|
|
3767 M /trunk/samtools/knetfile.c
|
|
|
3768 M /trunk/samtools/knetfile.h
|
|
|
3769
|
|
|
3770 * samtools-0.1.5-4 (r394)
|
|
|
3771 * http_proxy support in knetfile library (check http_proxy ENV)
|
|
|
3772
|
|
|
3773 ------------------------------------------------------------------------
|
|
|
3774 r393 | lh3lh3 | 2009-07-12 18:57:07 -0400 (Sun, 12 Jul 2009) | 5 lines
|
|
|
3775 Changed paths:
|
|
|
3776 M /trunk/samtools/bam_index.c
|
|
|
3777 M /trunk/samtools/bam_tview.c
|
|
|
3778 M /trunk/samtools/bamtk.c
|
|
|
3779 M /trunk/samtools/knetfile.c
|
|
|
3780 M /trunk/samtools/knetfile.h
|
|
|
3781
|
|
|
3782 * samtools-0.1.5-3 (r393)
|
|
|
3783 * knetfile now supports HTTP (no proxy at the moment)
|
|
|
3784 * fixed a potential issue in knetfile on opening ordinary file, although I have
|
|
|
3785 not seen the sideeffect so far.
|
|
|
3786
|
|
|
3787 ------------------------------------------------------------------------
|
|
|
3788 r392 | lh3lh3 | 2009-07-12 13:50:55 -0400 (Sun, 12 Jul 2009) | 2 lines
|
|
|
3789 Changed paths:
|
|
|
3790 M /trunk/samtools/samtools.1
|
|
|
3791
|
|
|
3792 Remove the warning in tview
|
|
|
3793
|
|
|
3794 ------------------------------------------------------------------------
|
|
|
3795 r391 | lh3lh3 | 2009-07-12 13:42:43 -0400 (Sun, 12 Jul 2009) | 3 lines
|
|
|
3796 Changed paths:
|
|
|
3797 M /trunk/samtools/bam_tview.c
|
|
|
3798 M /trunk/samtools/bamtk.c
|
|
|
3799
|
|
|
3800 * samtools-0.1.5-2 (r391)
|
|
|
3801 * do not show a blank screen when no reads mapped
|
|
|
3802
|
|
|
3803 ------------------------------------------------------------------------
|
|
|
3804 r390 | lh3lh3 | 2009-07-09 09:01:42 -0400 (Thu, 09 Jul 2009) | 4 lines
|
|
|
3805 Changed paths:
|
|
|
3806 M /trunk/samtools/bam.h
|
|
|
3807 A /trunk/samtools/bam_lite.c
|
|
|
3808 M /trunk/samtools/bamtk.c
|
|
|
3809
|
|
|
3810 * samtools-0.1.5-1 (r390)
|
|
|
3811 * removed useless _IOLIB in bam.h. This should cause no change at all.
|
|
|
3812 * added bam_lite.c for light-weight BAM reading
|
|
|
3813
|
|
|
3814 ------------------------------------------------------------------------
|
|
|
3815 r385 | lh3lh3 | 2009-07-07 11:53:29 -0400 (Tue, 07 Jul 2009) | 2 lines
|
|
|
3816 Changed paths:
|
|
|
3817 M /trunk/samtools/bamtk.c
|
|
|
3818 M /trunk/samtools/knetfile.c
|
|
|
3819
|
|
|
3820 Release samtools-0.1.5c (fixed a bug in piping)
|
|
|
3821
|
|
|
3822 ------------------------------------------------------------------------
|
|
|
3823 r383 | lh3lh3 | 2009-07-07 06:39:55 -0400 (Tue, 07 Jul 2009) | 2 lines
|
|
|
3824 Changed paths:
|
|
|
3825 M /trunk/samtools/bamtk.c
|
|
|
3826 M /trunk/samtools/sam.c
|
|
|
3827
|
|
|
3828 Release samtools-0.1.5b (BUG! so embarrassing!)
|
|
|
3829
|
|
|
3830 ------------------------------------------------------------------------
|
|
|
3831 r381 | lh3lh3 | 2009-07-07 06:20:06 -0400 (Tue, 07 Jul 2009) | 2 lines
|
|
|
3832 Changed paths:
|
|
|
3833 M /trunk/samtools/Makefile
|
|
|
3834 M /trunk/samtools/bam.h
|
|
|
3835 M /trunk/samtools/bam_aux.c
|
|
|
3836 M /trunk/samtools/bamtk.c
|
|
|
3837
|
|
|
3838 Release samtools-0.1.5a (for compatibility with Bio::DB::Sam)
|
|
|
3839
|
|
|
3840 ------------------------------------------------------------------------
|
|
|
3841 r373 | lh3lh3 | 2009-07-07 05:26:57 -0400 (Tue, 07 Jul 2009) | 2 lines
|
|
|
3842 Changed paths:
|
|
|
3843 M /trunk/samtools/ChangeLog
|
|
|
3844 M /trunk/samtools/NEWS
|
|
|
3845 M /trunk/samtools/bamtk.c
|
|
|
3846 M /trunk/samtools/samtools.1
|
|
|
3847
|
|
|
3848 Release samtools-0.1.5
|
|
|
3849
|
|
|
3850 ------------------------------------------------------------------------
|
|
|
3851 r372 | lh3lh3 | 2009-07-07 04:49:27 -0400 (Tue, 07 Jul 2009) | 3 lines
|
|
|
3852 Changed paths:
|
|
|
3853 M /trunk/samtools/bamtk.c
|
|
|
3854 M /trunk/samtools/sam.c
|
|
|
3855
|
|
|
3856 * samtools-0.1.4-23 (r372)
|
|
|
3857 * keep header text if "view -t" is used (by Gerton)
|
|
|
3858
|
|
|
3859 ------------------------------------------------------------------------
|
|
|
3860 r371 | lh3lh3 | 2009-07-06 20:13:32 -0400 (Mon, 06 Jul 2009) | 2 lines
|
|
|
3861 Changed paths:
|
|
|
3862 M /trunk/samtools/samtools.1
|
|
|
3863
|
|
|
3864 update documentation
|
|
|
3865
|
|
|
3866 ------------------------------------------------------------------------
|
|
|
3867 r370 | bhandsaker | 2009-07-02 17:24:34 -0400 (Thu, 02 Jul 2009) | 2 lines
|
|
|
3868 Changed paths:
|
|
|
3869 M /trunk/samtools/Makefile
|
|
|
3870
|
|
|
3871 Introduced LIBPATH variable so this could be overridden to allow samtools to build correct at the Broad.
|
|
|
3872
|
|
|
3873 ------------------------------------------------------------------------
|
|
|
3874 r369 | lh3lh3 | 2009-07-02 08:36:53 -0400 (Thu, 02 Jul 2009) | 4 lines
|
|
|
3875 Changed paths:
|
|
|
3876 M /trunk/samtools/ChangeLog
|
|
|
3877 M /trunk/samtools/bam_aux.c
|
|
|
3878 M /trunk/samtools/bam_plcmd.c
|
|
|
3879 M /trunk/samtools/bamtk.c
|
|
|
3880
|
|
|
3881 * samtools-0.1.4-22 (r369)
|
|
|
3882 * in pileup, optionally print E2 and U2
|
|
|
3883 * remove the debugging code in bam_aux_get() (Drat!)
|
|
|
3884
|
|
|
3885 ------------------------------------------------------------------------
|
|
|
3886 r368 | lh3lh3 | 2009-07-02 06:32:26 -0400 (Thu, 02 Jul 2009) | 6 lines
|
|
|
3887 Changed paths:
|
|
|
3888 M /trunk/samtools/bam.c
|
|
|
3889 M /trunk/samtools/bam.h
|
|
|
3890 M /trunk/samtools/bam_aux.c
|
|
|
3891 M /trunk/samtools/bam_index.c
|
|
|
3892 M /trunk/samtools/bam_lpileup.c
|
|
|
3893 M /trunk/samtools/bam_md.c
|
|
|
3894 M /trunk/samtools/bam_pileup.c
|
|
|
3895 M /trunk/samtools/bam_rmdup.c
|
|
|
3896 M /trunk/samtools/bam_stat.c
|
|
|
3897 M /trunk/samtools/bam_tview.c
|
|
|
3898 M /trunk/samtools/bamtk.c
|
|
|
3899 M /trunk/samtools/faidx.c
|
|
|
3900 M /trunk/samtools/faidx.h
|
|
|
3901 M /trunk/samtools/glf.c
|
|
|
3902
|
|
|
3903 * samtools-0.1.4-21 (r368)
|
|
|
3904 * propagate errors rather than exit or complain assertion failure. Assertion
|
|
|
3905 should be only used for checking internal bugs, but not for external input
|
|
|
3906 inconsistency. I was just a bit lazy.
|
|
|
3907 * small memory leak may be present on failure, though
|
|
|
3908
|
|
|
3909 ------------------------------------------------------------------------
|
|
|
3910 r367 | lh3lh3 | 2009-06-30 11:18:42 -0400 (Tue, 30 Jun 2009) | 2 lines
|
|
|
3911 Changed paths:
|
|
|
3912 M /trunk/samtools/knetfile.c
|
|
|
3913
|
|
|
3914 reduce the chance of blocking in FTP connection
|
|
|
3915
|
|
|
3916 ------------------------------------------------------------------------
|
|
|
3917 r366 | lh3lh3 | 2009-06-30 10:35:21 -0400 (Tue, 30 Jun 2009) | 2 lines
|
|
|
3918 Changed paths:
|
|
|
3919 M /trunk/samtools/knetfile.c
|
|
|
3920
|
|
|
3921 minor changes to knetfile: invalid fd equals -1 rather than 0
|
|
|
3922
|
|
|
3923 ------------------------------------------------------------------------
|
|
|
3924 r365 | lh3lh3 | 2009-06-30 09:04:30 -0400 (Tue, 30 Jun 2009) | 3 lines
|
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|
3925 Changed paths:
|
|
|
3926 M /trunk/samtools/bam_index.c
|
|
|
3927 M /trunk/samtools/bamtk.c
|
|
|
3928 M /trunk/samtools/knetfile.c
|
|
|
3929 M /trunk/samtools/knetfile.h
|
|
|
3930
|
|
|
3931 * samtools-0.1.4-20 (r365)
|
|
|
3932 * download the BAM index file if it is not found in the current working directory.
|
|
|
3933
|
|
|
3934 ------------------------------------------------------------------------
|
|
|
3935 r364 | lh3lh3 | 2009-06-30 07:39:07 -0400 (Tue, 30 Jun 2009) | 3 lines
|
|
|
3936 Changed paths:
|
|
|
3937 M /trunk/samtools/bamtk.c
|
|
|
3938 M /trunk/samtools/knetfile.c
|
|
|
3939
|
|
|
3940 * samtools-0.1.4-19 (r364)
|
|
|
3941 * knetfile: report error when the file is not present on FTP
|
|
|
3942
|
|
|
3943 ------------------------------------------------------------------------
|
|
|
3944 r363 | lh3lh3 | 2009-06-29 18:23:32 -0400 (Mon, 29 Jun 2009) | 4 lines
|
|
|
3945 Changed paths:
|
|
|
3946 M /trunk/samtools/bam_tview.c
|
|
|
3947 M /trunk/samtools/bamtk.c
|
|
|
3948 M /trunk/samtools/bgzf.c
|
|
|
3949 M /trunk/samtools/bgzf.h
|
|
|
3950 M /trunk/samtools/knetfile.c
|
|
|
3951 M /trunk/samtools/knetfile.h
|
|
|
3952
|
|
|
3953 * samtools-0.1.4-18 (r363)
|
|
|
3954 * knetfile: do not trigger network communication in FTP seek (lazy seek)
|
|
|
3955 * bgzf: cache recent blocks (disabled by default)
|
|
|
3956
|
|
|
3957 ------------------------------------------------------------------------
|
|
|
3958 r362 | lh3lh3 | 2009-06-25 16:04:34 -0400 (Thu, 25 Jun 2009) | 2 lines
|
|
|
3959 Changed paths:
|
|
|
3960 M /trunk/samtools/bgzf.c
|
|
|
3961
|
|
|
3962 write changelog
|
|
|
3963
|
|
|
3964 ------------------------------------------------------------------------
|
|
|
3965 r361 | lh3lh3 | 2009-06-25 16:03:10 -0400 (Thu, 25 Jun 2009) | 3 lines
|
|
|
3966 Changed paths:
|
|
|
3967 M /trunk/samtools/bam_index.c
|
|
|
3968 M /trunk/samtools/bamtk.c
|
|
|
3969
|
|
|
3970 * samtools-0.1.4-17 (r361)
|
|
|
3971 * if a file is given on FTP, search locally for the BAM index
|
|
|
3972
|
|
|
3973 ------------------------------------------------------------------------
|
|
|
3974 r360 | lh3lh3 | 2009-06-25 15:44:52 -0400 (Thu, 25 Jun 2009) | 5 lines
|
|
|
3975 Changed paths:
|
|
|
3976 M /trunk/samtools/Makefile
|
|
|
3977 M /trunk/samtools/bam_import.c
|
|
|
3978 M /trunk/samtools/bam_index.c
|
|
|
3979 M /trunk/samtools/bamtk.c
|
|
|
3980 M /trunk/samtools/bgzf.c
|
|
|
3981 M /trunk/samtools/bgzf.h
|
|
|
3982 M /trunk/samtools/knetfile.c
|
|
|
3983 M /trunk/samtools/knetfile.h
|
|
|
3984
|
|
|
3985 * samtools-0.1.4-16 (r360)
|
|
|
3986 * report more information in index when the input is not sorted
|
|
|
3987 * change the behaviour of knet_seek() such that it returns 0 on success
|
|
|
3988 * support knetfile library in BGZF
|
|
|
3989
|
|
|
3990 ------------------------------------------------------------------------
|
|
|
3991 r359 | lh3lh3 | 2009-06-25 12:10:55 -0400 (Thu, 25 Jun 2009) | 2 lines
|
|
|
3992 Changed paths:
|
|
|
3993 M /trunk/samtools/knetfile.c
|
|
|
3994 M /trunk/samtools/knetfile.h
|
|
|
3995
|
|
|
3996 fixed bugs in knetfile.*
|
|
|
3997
|
|
|
3998 ------------------------------------------------------------------------
|
|
|
3999 r358 | lh3lh3 | 2009-06-25 08:53:19 -0400 (Thu, 25 Jun 2009) | 2 lines
|
|
|
4000 Changed paths:
|
|
|
4001 A /trunk/samtools/knetfile.h
|
|
|
4002
|
|
|
4003 this is the header file
|
|
|
4004
|
|
|
4005 ------------------------------------------------------------------------
|
|
|
4006 r357 | lh3lh3 | 2009-06-25 08:52:03 -0400 (Thu, 25 Jun 2009) | 3 lines
|
|
|
4007 Changed paths:
|
|
|
4008 A /trunk/samtools/knetfile.c
|
|
|
4009
|
|
|
4010 * open a file at FTP
|
|
|
4011 * preliminary version
|
|
|
4012
|
|
|
4013 ------------------------------------------------------------------------
|
|
|
4014 r354 | lh3lh3 | 2009-06-24 09:02:25 -0400 (Wed, 24 Jun 2009) | 3 lines
|
|
|
4015 Changed paths:
|
|
|
4016 M /trunk/samtools/bam.c
|
|
|
4017 M /trunk/samtools/bamtk.c
|
|
|
4018
|
|
|
4019 * samtools-0.1.4-15 (r354)
|
|
|
4020 * fixed a memory leak in bam_view1(), although samtools is not using this routine.
|
|
|
4021
|
|
|
4022 ------------------------------------------------------------------------
|
|
|
4023 r351 | lh3lh3 | 2009-06-17 19:16:26 -0400 (Wed, 17 Jun 2009) | 4 lines
|
|
|
4024 Changed paths:
|
|
|
4025 M /trunk/samtools/bamtk.c
|
|
|
4026 M /trunk/samtools/faidx.c
|
|
|
4027
|
|
|
4028 * samtools-0.1.4-13 (r351)
|
|
|
4029 * make faidx more tolerant to empty lines right before or after > lines
|
|
|
4030 * hope this does not introduce new bugs...
|
|
|
4031
|
|
|
4032 ------------------------------------------------------------------------
|
|
|
4033 r350 | lh3lh3 | 2009-06-16 09:37:01 -0400 (Tue, 16 Jun 2009) | 3 lines
|
|
|
4034 Changed paths:
|
|
|
4035 M /trunk/samtools/bam_plcmd.c
|
|
|
4036 M /trunk/samtools/bamtk.c
|
|
|
4037
|
|
|
4038 * samtools-0.1.4-13 (r350)
|
|
|
4039 * fixed a small memory leak in pileup, caused by recent modifications
|
|
|
4040
|
|
|
4041 ------------------------------------------------------------------------
|
|
|
4042 r347 | lh3lh3 | 2009-06-13 16:20:49 -0400 (Sat, 13 Jun 2009) | 3 lines
|
|
|
4043 Changed paths:
|
|
|
4044 M /trunk/samtools/bam_plcmd.c
|
|
|
4045 M /trunk/samtools/bamtk.c
|
|
|
4046 M /trunk/samtools/sam_view.c
|
|
|
4047
|
|
|
4048 * samtools-0.1.4-12 (r347)
|
|
|
4049 * added `-S' to pileup, similar to `view -S'
|
|
|
4050
|
|
|
4051 ------------------------------------------------------------------------
|
|
|
4052 r346 | lh3lh3 | 2009-06-13 12:52:31 -0400 (Sat, 13 Jun 2009) | 3 lines
|
|
|
4053 Changed paths:
|
|
|
4054 M /trunk/samtools/Makefile
|
|
|
4055 M /trunk/samtools/bamtk.c
|
|
|
4056 M /trunk/samtools/sam_view.c
|
|
|
4057 M /trunk/samtools/samtools.1
|
|
|
4058
|
|
|
4059 * samtools-0.1.4-11 (r346)
|
|
|
4060 * allow to select a read group at view command-line
|
|
|
4061
|
|
|
4062 ------------------------------------------------------------------------
|
|
|
4063 r344 | lh3lh3 | 2009-06-13 09:06:24 -0400 (Sat, 13 Jun 2009) | 2 lines
|
|
|
4064 Changed paths:
|
|
|
4065 M /trunk/samtools/examples/calDepth.c
|
|
|
4066
|
|
|
4067 added more comments
|
|
|
4068
|
|
|
4069 ------------------------------------------------------------------------
|
|
|
4070 r343 | lh3lh3 | 2009-06-13 09:01:22 -0400 (Sat, 13 Jun 2009) | 2 lines
|
|
|
4071 Changed paths:
|
|
|
4072 M /trunk/samtools/examples/calDepth.c
|
|
|
4073
|
|
|
4074 nothing really
|
|
|
4075
|
|
|
4076 ------------------------------------------------------------------------
|
|
|
4077 r342 | lh3lh3 | 2009-06-13 08:58:48 -0400 (Sat, 13 Jun 2009) | 2 lines
|
|
|
4078 Changed paths:
|
|
|
4079 M /trunk/samtools/examples/Makefile
|
|
|
4080 A /trunk/samtools/examples/calDepth.c
|
|
|
4081
|
|
|
4082 added an example of calculating read depth
|
|
|
4083
|
|
|
4084 ------------------------------------------------------------------------
|
|
|
4085 r341 | lh3lh3 | 2009-06-13 08:00:08 -0400 (Sat, 13 Jun 2009) | 6 lines
|
|
|
4086 Changed paths:
|
|
|
4087 M /trunk/samtools/Makefile
|
|
|
4088 M /trunk/samtools/bam.h
|
|
|
4089 M /trunk/samtools/bam_aux.c
|
|
|
4090 A /trunk/samtools/bam_color.c
|
|
|
4091 M /trunk/samtools/bam_plcmd.c
|
|
|
4092 M /trunk/samtools/bam_sort.c
|
|
|
4093 M /trunk/samtools/bam_tview.c
|
|
|
4094 M /trunk/samtools/bamtk.c
|
|
|
4095 M /trunk/samtools/sam.c
|
|
|
4096 M /trunk/samtools/sam.h
|
|
|
4097
|
|
|
4098 * samtools-0.1.4-10 (r341)
|
|
|
4099 * only include key APIs in libbam.a
|
|
|
4100 * move color-specific routines to bam_color.c
|
|
|
4101 * update documentations
|
|
|
4102 * remove the support of -q in pileup
|
|
|
4103
|
|
|
4104 ------------------------------------------------------------------------
|
|
|
4105 r340 | lh3lh3 | 2009-06-13 06:17:14 -0400 (Sat, 13 Jun 2009) | 6 lines
|
|
|
4106 Changed paths:
|
|
|
4107 M /trunk/samtools/INSTALL
|
|
|
4108 M /trunk/samtools/Makefile
|
|
|
4109 M /trunk/samtools/bam_aux.c
|
|
|
4110 M /trunk/samtools/bam_import.c
|
|
|
4111 M /trunk/samtools/bam_tview.c
|
|
|
4112 M /trunk/samtools/bamtk.c
|
|
|
4113 M /trunk/samtools/razf.c
|
|
|
4114 M /trunk/samtools/sam_view.c
|
|
|
4115
|
|
|
4116 * samtools-0.1.4-9 (r340)
|
|
|
4117 * added a warning to razf.c if zlib<1.2.2.1
|
|
|
4118 * fixed a compilation warning
|
|
|
4119 * fixed a segfault caused by @RG parsing
|
|
|
4120 * detect NCURSES in bam_tview.c
|
|
|
4121
|
|
|
4122 ------------------------------------------------------------------------
|
|
|
4123 r339 | lh3lh3 | 2009-06-13 05:35:19 -0400 (Sat, 13 Jun 2009) | 2 lines
|
|
|
4124 Changed paths:
|
|
|
4125 M /trunk/samtools/INSTALL
|
|
|
4126
|
|
|
4127 update INSTALL
|
|
|
4128
|
|
|
4129 ------------------------------------------------------------------------
|
|
|
4130 r338 | lh3lh3 | 2009-06-12 19:15:24 -0400 (Fri, 12 Jun 2009) | 4 lines
|
|
|
4131 Changed paths:
|
|
|
4132 M /trunk/samtools/bam.c
|
|
|
4133 M /trunk/samtools/bam.h
|
|
|
4134 M /trunk/samtools/bam_aux.c
|
|
|
4135 M /trunk/samtools/bam_import.c
|
|
|
4136 M /trunk/samtools/bamtk.c
|
|
|
4137 M /trunk/samtools/kstring.h
|
|
|
4138 M /trunk/samtools/sam.c
|
|
|
4139 M /trunk/samtools/sam_view.c
|
|
|
4140
|
|
|
4141 * samtools-0.1.4-8 (r338)
|
|
|
4142 * parse the @RG header lines and allow to choose library at the "samtools view"
|
|
|
4143 command line
|
|
|
4144
|
|
|
4145 ------------------------------------------------------------------------
|
|
|
4146 r337 | lh3lh3 | 2009-06-12 16:25:50 -0400 (Fri, 12 Jun 2009) | 4 lines
|
|
|
4147 Changed paths:
|
|
|
4148 M /trunk/samtools/bamtk.c
|
|
|
4149 M /trunk/samtools/bgzf.c
|
|
|
4150 M /trunk/samtools/bgzf.h
|
|
|
4151 M /trunk/samtools/sam.c
|
|
|
4152 M /trunk/samtools/sam_view.c
|
|
|
4153
|
|
|
4154 * samtools-0.1.4-7 (r337)
|
|
|
4155 * bgzf.c: support mode string "wu": uncompressed output
|
|
|
4156 * "samtools view" support "-u" command-line option
|
|
|
4157
|
|
|
4158 ------------------------------------------------------------------------
|
|
|
4159 r336 | lh3lh3 | 2009-06-12 12:20:12 -0400 (Fri, 12 Jun 2009) | 5 lines
|
|
|
4160 Changed paths:
|
|
|
4161 M /trunk/samtools/Makefile
|
|
|
4162 M /trunk/samtools/misc/Makefile
|
|
|
4163 M /trunk/samtools/razf.c
|
|
|
4164 M /trunk/samtools/razf.h
|
|
|
4165 M /trunk/samtools/razip.c
|
|
|
4166
|
|
|
4167 * no changes to samtools itself
|
|
|
4168 * remove zlib source codes
|
|
|
4169 * make RAZF reading compatible with old version of zlib
|
|
|
4170 * on old version of zlib, writing is not available
|
|
|
4171
|
|
|
4172 ------------------------------------------------------------------------
|
|
|
4173 r335 | lh3lh3 | 2009-06-12 11:47:33 -0400 (Fri, 12 Jun 2009) | 2 lines
|
|
|
4174 Changed paths:
|
|
|
4175 D /trunk/samtools/zlib
|
|
|
4176
|
|
|
4177 remove zlib for simplification...
|
|
|
4178
|
|
|
4179 ------------------------------------------------------------------------
|
|
|
4180 r334 | lh3lh3 | 2009-06-12 10:43:36 -0400 (Fri, 12 Jun 2009) | 5 lines
|
|
|
4181 Changed paths:
|
|
|
4182 M /trunk/samtools/bam.h
|
|
|
4183 M /trunk/samtools/bam_aux.c
|
|
|
4184 M /trunk/samtools/bamtk.c
|
|
|
4185
|
|
|
4186 * samtools-0.1.4-6 (r334)
|
|
|
4187 * do not export bam_aux_get_core() for Bio::DB::Sam because it has already
|
|
|
4188 been implemented in that.
|
|
|
4189 * this version works with the latest Bio::DB::Sam (20090612)
|
|
|
4190
|
|
|
4191 ------------------------------------------------------------------------
|
|
|
4192 r333 | lh3lh3 | 2009-06-12 10:33:42 -0400 (Fri, 12 Jun 2009) | 2 lines
|
|
|
4193 Changed paths:
|
|
|
4194 M /trunk/samtools/ChangeLog
|
|
|
4195
|
|
|
4196 update ChangeLog
|
|
|
4197
|
|
|
4198 ------------------------------------------------------------------------
|
|
|
4199 r332 | lh3lh3 | 2009-06-12 10:21:21 -0400 (Fri, 12 Jun 2009) | 2 lines
|
|
|
4200 Changed paths:
|
|
|
4201 M /trunk/samtools/AUTHORS
|
|
|
4202 M /trunk/samtools/Makefile
|
|
|
4203 M /trunk/samtools/misc/Makefile
|
|
|
4204
|
|
|
4205 fixed minor things in Makefile
|
|
|
4206
|
|
|
4207 ------------------------------------------------------------------------
|
|
|
4208 r331 | lh3lh3 | 2009-06-12 10:07:05 -0400 (Fri, 12 Jun 2009) | 4 lines
|
|
|
4209 Changed paths:
|
|
|
4210 M /trunk/samtools/bamtk.c
|
|
|
4211
|
|
|
4212 * samtools-0.1.4-5 (r3310
|
|
|
4213 * no change to samtools itself. Version number is increased to reflect the
|
|
|
4214 changes in the Makefile building system.
|
|
|
4215
|
|
|
4216 ------------------------------------------------------------------------
|
|
|
4217 r330 | lh3lh3 | 2009-06-12 10:03:38 -0400 (Fri, 12 Jun 2009) | 2 lines
|
|
|
4218 Changed paths:
|
|
|
4219 M /trunk/samtools/AUTHORS
|
|
|
4220 D /trunk/samtools/README
|
|
|
4221
|
|
|
4222 update information...
|
|
|
4223
|
|
|
4224 ------------------------------------------------------------------------
|
|
|
4225 r329 | lh3lh3 | 2009-06-12 09:52:21 -0400 (Fri, 12 Jun 2009) | 3 lines
|
|
|
4226 Changed paths:
|
|
|
4227 M /trunk/samtools/misc/novo2sam.pl
|
|
|
4228
|
|
|
4229 * updated novoalign converter by Colin Hercus et al.
|
|
|
4230 * this version works with indels
|
|
|
4231
|
|
|
4232 ------------------------------------------------------------------------
|
|
|
4233 r328 | lh3lh3 | 2009-06-12 09:50:53 -0400 (Fri, 12 Jun 2009) | 3 lines
|
|
|
4234 Changed paths:
|
|
|
4235 M /trunk/samtools/INSTALL
|
|
|
4236 M /trunk/samtools/Makefile
|
|
|
4237 M /trunk/samtools/misc/Makefile
|
|
|
4238 M /trunk/samtools/zlib/Makefile
|
|
|
4239
|
|
|
4240 * update Makefile
|
|
|
4241 * update INSTALL instruction
|
|
|
4242
|
|
|
4243 ------------------------------------------------------------------------
|
|
|
4244 r327 | lh3lh3 | 2009-06-12 09:18:29 -0400 (Fri, 12 Jun 2009) | 4 lines
|
|
|
4245 Changed paths:
|
|
|
4246 A /trunk/samtools/Makefile (from /trunk/samtools/Makefile.generic:325)
|
|
|
4247 D /trunk/samtools/Makefile.am
|
|
|
4248 D /trunk/samtools/Makefile.generic
|
|
|
4249 D /trunk/samtools/Makefile.lite
|
|
|
4250 D /trunk/samtools/autogen.sh
|
|
|
4251 D /trunk/samtools/cleanup.sh
|
|
|
4252 D /trunk/samtools/configure.ac
|
|
|
4253 A /trunk/samtools/misc/Makefile (from /trunk/samtools/misc/Makefile.generic:305)
|
|
|
4254 D /trunk/samtools/misc/Makefile.am
|
|
|
4255 D /trunk/samtools/misc/Makefile.generic
|
|
|
4256 M /trunk/samtools/razf.c
|
|
|
4257 A /trunk/samtools/zlib
|
|
|
4258 A /trunk/samtools/zlib/Makefile
|
|
|
4259 A /trunk/samtools/zlib/adler32.c
|
|
|
4260 A /trunk/samtools/zlib/compress.c
|
|
|
4261 A /trunk/samtools/zlib/crc32.c
|
|
|
4262 A /trunk/samtools/zlib/crc32.h
|
|
|
4263 A /trunk/samtools/zlib/deflate.c
|
|
|
4264 A /trunk/samtools/zlib/deflate.h
|
|
|
4265 A /trunk/samtools/zlib/gzio.c
|
|
|
4266 A /trunk/samtools/zlib/infback.c
|
|
|
4267 A /trunk/samtools/zlib/inffast.c
|
|
|
4268 A /trunk/samtools/zlib/inffast.h
|
|
|
4269 A /trunk/samtools/zlib/inffixed.h
|
|
|
4270 A /trunk/samtools/zlib/inflate.c
|
|
|
4271 A /trunk/samtools/zlib/inflate.h
|
|
|
4272 A /trunk/samtools/zlib/inftrees.c
|
|
|
4273 A /trunk/samtools/zlib/inftrees.h
|
|
|
4274 A /trunk/samtools/zlib/trees.c
|
|
|
4275 A /trunk/samtools/zlib/trees.h
|
|
|
4276 A /trunk/samtools/zlib/uncompr.c
|
|
|
4277 A /trunk/samtools/zlib/zconf.h
|
|
|
4278 A /trunk/samtools/zlib/zlib.h
|
|
|
4279 A /trunk/samtools/zlib/zutil.c
|
|
|
4280 A /trunk/samtools/zlib/zutil.h
|
|
|
4281 D /trunk/samtools/zutil.h
|
|
|
4282
|
|
|
4283 * added zlib-1.2.3 as razip requires that
|
|
|
4284 * prepare to changed back to the Makefile building system
|
|
|
4285 * unfinished! (will be soon)
|
|
|
4286
|
|
|
4287 ------------------------------------------------------------------------
|
|
|
4288 r326 | lh3lh3 | 2009-06-12 09:12:03 -0400 (Fri, 12 Jun 2009) | 2 lines
|
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4289 Changed paths:
|
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|
4290 M /trunk/samtools/misc/samtools.pl
|
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4291
|
|
|
4292 Unfinished
|
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4293
|
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|
4294 ------------------------------------------------------------------------
|
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4295 r325 | lh3lh3 | 2009-06-10 11:27:59 -0400 (Wed, 10 Jun 2009) | 3 lines
|
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4296 Changed paths:
|
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4297 M /trunk/samtools/bam_maqcns.c
|
|
|
4298 M /trunk/samtools/bamtk.c
|
|
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4299
|
|
|
4300 * samtools-0.1.4-4 (r325)
|
|
|
4301 * further avoid wrong consensus calls in repetitive regions.
|
|
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4302
|
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|
4303 ------------------------------------------------------------------------
|
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|
4304 r324 | lh3lh3 | 2009-06-10 10:56:17 -0400 (Wed, 10 Jun 2009) | 4 lines
|
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4305 Changed paths:
|
|
|
4306 M /trunk/samtools/bam_maqcns.c
|
|
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4307 M /trunk/samtools/bam_plcmd.c
|
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|
4308 M /trunk/samtools/bamtk.c
|
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|
4309 M /trunk/samtools/sam.c
|
|
|
4310 M /trunk/samtools/sam.h
|
|
|
4311
|
|
|
4312 * samtools-0.1.4-3 (r324)
|
|
|
4313 * make maqcns generate the correct call in repetitive regions.
|
|
|
4314 * allow filtering on mapQ at the pileup command line
|
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|
4315
|
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|
4316 ------------------------------------------------------------------------
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|
4317 r323 | lh3lh3 | 2009-06-10 05:04:21 -0400 (Wed, 10 Jun 2009) | 3 lines
|
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4318 Changed paths:
|
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|
4319 M /trunk/samtools/misc/samtools.pl
|
|
|
4320
|
|
|
4321 * samtools.pl-0.3.2 (r322)
|
|
|
4322 * indels and SNPs use different mapping quality threshold
|
|
|
4323
|
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|
4324 ------------------------------------------------------------------------
|
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|
4325 r322 | lh3lh3 | 2009-06-10 05:03:22 -0400 (Wed, 10 Jun 2009) | 2 lines
|
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4326 Changed paths:
|
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|
4327 M /trunk/samtools/misc/export2sam.pl
|
|
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4328
|
|
|
4329 fixed a typo
|
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4330
|
|
|
4331 ------------------------------------------------------------------------
|
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|
4332 r321 | lh3lh3 | 2009-06-09 04:21:48 -0400 (Tue, 09 Jun 2009) | 2 lines
|
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4333 Changed paths:
|
|
|
4334 M /trunk/samtools/misc/samtools.pl
|
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4335
|
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|
4336 just typo. no real change
|
|
|
4337
|
|
|
4338 ------------------------------------------------------------------------
|
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|
4339 r320 | lh3lh3 | 2009-06-08 09:32:51 -0400 (Mon, 08 Jun 2009) | 2 lines
|
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|
4340 Changed paths:
|
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|
4341 M /trunk/samtools/misc/samtools.pl
|
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|
4342
|
|
|
4343 a little bit code cleanup
|
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|
4344
|
|
|
4345 ------------------------------------------------------------------------
|
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|
4346 r319 | lh3lh3 | 2009-06-08 09:22:33 -0400 (Mon, 08 Jun 2009) | 4 lines
|
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|
4347 Changed paths:
|
|
|
4348 M /trunk/samtools/misc/samtools.pl
|
|
|
4349
|
|
|
4350 * samtools.pl-0.3.1
|
|
|
4351 * change default parameters
|
|
|
4352 * optionally print filtered variants
|
|
|
4353
|
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|
4354 ------------------------------------------------------------------------
|
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|
4355 r318 | lh3lh3 | 2009-06-08 09:14:26 -0400 (Mon, 08 Jun 2009) | 3 lines
|
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|
4356 Changed paths:
|
|
|
4357 M /trunk/samtools/misc/samtools.pl
|
|
|
4358
|
|
|
4359 * samtools.pl-0.3.0
|
|
|
4360 * combine snpFilter and indelFilter
|
|
|
4361
|
|
|
4362 ------------------------------------------------------------------------
|
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|
4363 r317 | lh3lh3 | 2009-06-08 06:31:42 -0400 (Mon, 08 Jun 2009) | 3 lines
|
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|
4364 Changed paths:
|
|
|
4365 M /trunk/samtools/misc/samtools.pl
|
|
|
4366
|
|
|
4367 * samtools.pl-0.2.3
|
|
|
4368 * change a default parameter
|
|
|
4369
|
|
|
4370 ------------------------------------------------------------------------
|
|
|
4371 r316 | lh3lh3 | 2009-06-08 06:11:06 -0400 (Mon, 08 Jun 2009) | 5 lines
|
|
|
4372 Changed paths:
|
|
|
4373 M /trunk/samtools/bam_maqcns.c
|
|
|
4374 M /trunk/samtools/bam_maqcns.h
|
|
|
4375 M /trunk/samtools/bam_plcmd.c
|
|
|
4376 M /trunk/samtools/bamtk.c
|
|
|
4377 M /trunk/samtools/sam.c
|
|
|
4378
|
|
|
4379 * samtools-0.1.4-2 (r316)
|
|
|
4380 * pileup: cap mapping quality at 60 (by default)
|
|
|
4381 * pileup: always calculate RMS mapq
|
|
|
4382 * pileup: allow to output variant sites only
|
|
|
4383
|
|
|
4384 ------------------------------------------------------------------------
|
|
|
4385 r312 | lh3lh3 | 2009-06-04 08:01:10 -0400 (Thu, 04 Jun 2009) | 3 lines
|
|
|
4386 Changed paths:
|
|
|
4387 M /trunk/samtools/misc/samtools.pl
|
|
|
4388
|
|
|
4389 * samtools.pl-0.2.2
|
|
|
4390 * added pileup2fq
|
|
|
4391
|
|
|
4392 ------------------------------------------------------------------------
|
|
|
4393 r311 | lh3lh3 | 2009-06-03 04:40:40 -0400 (Wed, 03 Jun 2009) | 2 lines
|
|
|
4394 Changed paths:
|
|
|
4395 M /trunk/samtools/misc/samtools.pl
|
|
|
4396
|
|
|
4397 * in snpFilter, suppress non-SNP sites
|
|
|
4398
|
|
|
4399 ------------------------------------------------------------------------
|
|
|
4400 r310 | lh3lh3 | 2009-06-01 09:35:13 -0400 (Mon, 01 Jun 2009) | 3 lines
|
|
|
4401 Changed paths:
|
|
|
4402 M /trunk/samtools/misc/samtools.pl
|
|
|
4403
|
|
|
4404 * samtools.pl-0.2.1
|
|
|
4405 * fixed a typo
|
|
|
4406
|
|
|
4407 ------------------------------------------------------------------------
|
|
|
4408 r309 | lh3lh3 | 2009-06-01 09:04:39 -0400 (Mon, 01 Jun 2009) | 3 lines
|
|
|
4409 Changed paths:
|
|
|
4410 M /trunk/samtools/misc/samtools.pl
|
|
|
4411
|
|
|
4412 * samtools.pl-0.2.0
|
|
|
4413 * snpFilter
|
|
|
4414
|
|
|
4415 ------------------------------------------------------------------------
|
|
|
4416 r306 | lh3lh3 | 2009-05-28 06:49:35 -0400 (Thu, 28 May 2009) | 3 lines
|
|
|
4417 Changed paths:
|
|
|
4418 M /trunk/samtools/bgzf.c
|
|
|
4419
|
|
|
4420 * minor changes to bgzf: return NULL if fd == -1
|
|
|
4421 * suggested by {kdj,jm18}@sanger.ac.uk
|
|
|
4422
|
|
|
4423 ------------------------------------------------------------------------
|
|
|
4424 r305 | lh3lh3 | 2009-05-28 06:16:08 -0400 (Thu, 28 May 2009) | 2 lines
|
|
|
4425 Changed paths:
|
|
|
4426 A /trunk/samtools/misc/interpolate_sam.pl
|
|
|
4427
|
|
|
4428 Script for paired-end pileup, contributed by Stephen Montgomery.
|
|
|
4429
|
|
|
4430 ------------------------------------------------------------------------
|
|
|
4431 r304 | lh3lh3 | 2009-05-28 06:08:49 -0400 (Thu, 28 May 2009) | 3 lines
|
|
|
4432 Changed paths:
|
|
|
4433 M /trunk/samtools/bamtk.c
|
|
|
4434 M /trunk/samtools/sam.c
|
|
|
4435
|
|
|
4436 * samtools-0.1.4-1 (r304)
|
|
|
4437 * fixed a minor bug in printing headers
|
|
|
4438
|
|
|
4439 ------------------------------------------------------------------------
|
|
|
4440 r297 | lh3lh3 | 2009-05-21 11:06:16 -0400 (Thu, 21 May 2009) | 2 lines
|
|
|
4441 Changed paths:
|
|
|
4442 M /trunk/samtools/ChangeLog
|
|
|
4443 M /trunk/samtools/NEWS
|
|
|
4444 M /trunk/samtools/bam_plcmd.c
|
|
|
4445 M /trunk/samtools/bamtk.c
|
|
|
4446 M /trunk/samtools/misc/maq2sam.c
|
|
|
4447 M /trunk/samtools/samtools.1
|
|
|
4448
|
|
|
4449 Release samtools-0.1.4
|
|
|
4450
|
|
|
4451 ------------------------------------------------------------------------
|
|
|
4452 r296 | lh3lh3 | 2009-05-21 07:53:14 -0400 (Thu, 21 May 2009) | 3 lines
|
|
|
4453 Changed paths:
|
|
|
4454 M /trunk/samtools/bam_maqcns.c
|
|
|
4455 M /trunk/samtools/bamtk.c
|
|
|
4456
|
|
|
4457 * samtools-0.1.3-24 (r296)
|
|
|
4458 * another similar bug in the indel caller
|
|
|
4459
|
|
|
4460 ------------------------------------------------------------------------
|
|
|
4461 r295 | lh3lh3 | 2009-05-21 07:50:28 -0400 (Thu, 21 May 2009) | 3 lines
|
|
|
4462 Changed paths:
|
|
|
4463 M /trunk/samtools/bam_maqcns.c
|
|
|
4464 M /trunk/samtools/bamtk.c
|
|
|
4465
|
|
|
4466 * samtools-0.1.3-23 (r295)
|
|
|
4467 * fixed a critical bug in the indel caller
|
|
|
4468
|
|
|
4469 ------------------------------------------------------------------------
|
|
|
4470 r294 | lh3lh3 | 2009-05-20 08:00:20 -0400 (Wed, 20 May 2009) | 2 lines
|
|
|
4471 Changed paths:
|
|
|
4472 M /trunk/samtools/bam_stat.c
|
|
|
4473
|
|
|
4474 added a missing header file
|
|
|
4475
|
|
|
4476 ------------------------------------------------------------------------
|
|
|
4477 r293 | lh3lh3 | 2009-05-19 18:44:25 -0400 (Tue, 19 May 2009) | 3 lines
|
|
|
4478 Changed paths:
|
|
|
4479 M /trunk/samtools/bam_tview.c
|
|
|
4480 M /trunk/samtools/bamtk.c
|
|
|
4481
|
|
|
4482 * samtools-0.1.3-22 (r293)
|
|
|
4483 * open tview in the dot-view mode by default
|
|
|
4484
|
|
|
4485 ------------------------------------------------------------------------
|
|
|
4486 r292 | lh3lh3 | 2009-05-18 16:01:23 -0400 (Mon, 18 May 2009) | 6 lines
|
|
|
4487 Changed paths:
|
|
|
4488 M /trunk/samtools/samtools.1
|
|
|
4489
|
|
|
4490 Added a note to the manual. Currently SAMtools used unaligned words in
|
|
|
4491 several places. Although this does not cause bus errors to me, it may
|
|
|
4492 affect portability. Please see the "Bus error" wiki page for more
|
|
|
4493 information. Also thank James Bonfields for pointing this out.
|
|
|
4494
|
|
|
4495
|
|
|
4496 ------------------------------------------------------------------------
|
|
|
4497 r286 | lh3lh3 | 2009-05-14 10:23:13 -0400 (Thu, 14 May 2009) | 3 lines
|
|
|
4498 Changed paths:
|
|
|
4499 M /trunk/samtools/bam.h
|
|
|
4500 M /trunk/samtools/bam_aux.c
|
|
|
4501 M /trunk/samtools/bamtk.c
|
|
|
4502
|
|
|
4503 * samtools-0.1.3-21 (286)
|
|
|
4504 * declare bam_aux_get_core() in bam.h
|
|
|
4505
|
|
|
4506 ------------------------------------------------------------------------
|
|
|
4507 r276 | lh3lh3 | 2009-05-13 05:07:55 -0400 (Wed, 13 May 2009) | 5 lines
|
|
|
4508 Changed paths:
|
|
|
4509 M /trunk/samtools/bam.h
|
|
|
4510 M /trunk/samtools/bam_index.c
|
|
|
4511 M /trunk/samtools/bamtk.c
|
|
|
4512
|
|
|
4513 * samtools-0.1.3-20 (r276)
|
|
|
4514 * remove bam1_t::hash again. We need to modify the Perl API anyway to
|
|
|
4515 make it work with the latest SVN.
|
|
|
4516 * As is suggested by Tim, scan "{base}.bai" and "{base}.bam.bai" for index
|
|
|
4517
|
|
|
4518 ------------------------------------------------------------------------
|
|
|
4519 r275 | lh3lh3 | 2009-05-12 16:14:10 -0400 (Tue, 12 May 2009) | 4 lines
|
|
|
4520 Changed paths:
|
|
|
4521 M /trunk/samtools/ChangeLog
|
|
|
4522 M /trunk/samtools/bam.h
|
|
|
4523 M /trunk/samtools/bamtk.c
|
|
|
4524
|
|
|
4525 * samtools-0.1.3-19 (r275)
|
|
|
4526 * a minor change to the bam1_t struct: added back "void *hash" for the
|
|
|
4527 backward compatibility with Bio::DB::Sam
|
|
|
4528
|
|
|
4529 ------------------------------------------------------------------------
|
|
|
4530 r273 | lh3lh3 | 2009-05-12 09:28:39 -0400 (Tue, 12 May 2009) | 3 lines
|
|
|
4531 Changed paths:
|
|
|
4532 M /trunk/samtools/bam_rmdupse.c
|
|
|
4533 M /trunk/samtools/bamtk.c
|
|
|
4534
|
|
|
4535 * samtools-0.1.3-18 (r273)
|
|
|
4536 * rmdupse: do not remove unmapped reads
|
|
|
4537
|
|
|
4538 ------------------------------------------------------------------------
|
|
|
4539 r272 | lh3lh3 | 2009-05-12 09:20:00 -0400 (Tue, 12 May 2009) | 2 lines
|
|
|
4540 Changed paths:
|
|
|
4541 M /trunk/samtools/bam_rmdupse.c
|
|
|
4542
|
|
|
4543 change a parameter. It does nothing
|
|
|
4544
|
|
|
4545 ------------------------------------------------------------------------
|
|
|
4546 r271 | lh3lh3 | 2009-05-12 09:17:58 -0400 (Tue, 12 May 2009) | 3 lines
|
|
|
4547 Changed paths:
|
|
|
4548 M /trunk/samtools/Makefile.am
|
|
|
4549 M /trunk/samtools/Makefile.generic
|
|
|
4550 M /trunk/samtools/Makefile.lite
|
|
|
4551 A /trunk/samtools/bam_rmdupse.c
|
|
|
4552 M /trunk/samtools/bamtk.c
|
|
|
4553 M /trunk/samtools/configure.ac
|
|
|
4554
|
|
|
4555 * samtools-0.1.3-17 (r271)
|
|
|
4556 * added 'rmdupse' command
|
|
|
4557
|
|
|
4558 ------------------------------------------------------------------------
|
|
|
4559 r267 | lh3lh3 | 2009-05-05 17:31:41 -0400 (Tue, 05 May 2009) | 3 lines
|
|
|
4560 Changed paths:
|
|
|
4561 M /trunk/samtools/bamtk.c
|
|
|
4562 M /trunk/samtools/sam_view.c
|
|
|
4563
|
|
|
4564 * samtools-0.1.3-16 (r267)
|
|
|
4565 * in sam_view.c, changed g_flag_on based on the suggestion by Angie Hinrichs
|
|
|
4566
|
|
|
4567 ------------------------------------------------------------------------
|
|
|
4568 r266 | lh3lh3 | 2009-05-05 17:23:27 -0400 (Tue, 05 May 2009) | 3 lines
|
|
|
4569 Changed paths:
|
|
|
4570 M /trunk/samtools/bam_import.c
|
|
|
4571 M /trunk/samtools/bamtk.c
|
|
|
4572
|
|
|
4573 * samtools-0.1.3-15 (r266)
|
|
|
4574 * report an error if a non-* reference is present while @SQ is absent
|
|
|
4575
|
|
|
4576 ------------------------------------------------------------------------
|
|
|
4577 r265 | lh3lh3 | 2009-05-05 17:09:00 -0400 (Tue, 05 May 2009) | 3 lines
|
|
|
4578 Changed paths:
|
|
|
4579 M /trunk/samtools/bam.h
|
|
|
4580 M /trunk/samtools/bam_import.c
|
|
|
4581 M /trunk/samtools/bamtk.c
|
|
|
4582 M /trunk/samtools/sam.c
|
|
|
4583 M /trunk/samtools/sam_view.c
|
|
|
4584
|
|
|
4585 * samtools-0.1.3-14 (r262)
|
|
|
4586 * make samopen() recognize @SQ header lines
|
|
|
4587
|
|
|
4588 ------------------------------------------------------------------------
|
|
|
4589 r261 | lh3lh3 | 2009-05-05 10:10:30 -0400 (Tue, 05 May 2009) | 3 lines
|
|
|
4590 Changed paths:
|
|
|
4591 M /trunk/samtools/bam_plcmd.c
|
|
|
4592 M /trunk/samtools/bamtk.c
|
|
|
4593 M /trunk/samtools/bgzf.c
|
|
|
4594 M /trunk/samtools/sam.c
|
|
|
4595 M /trunk/samtools/sam_view.c
|
|
|
4596
|
|
|
4597 * samtools-0.1.3-13 (r260)
|
|
|
4598 * report error for file I/O error
|
|
|
4599
|
|
|
4600 ------------------------------------------------------------------------
|
|
|
4601 r260 | lh3lh3 | 2009-05-05 10:01:16 -0400 (Tue, 05 May 2009) | 2 lines
|
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4602 Changed paths:
|
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|
4603 M /trunk/samtools/Makefile.am
|
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4604
|
|
|
4605 update Makefile.am
|
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|
4606
|
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|
4607 ------------------------------------------------------------------------
|
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4608 r259 | lh3lh3 | 2009-05-05 09:52:25 -0400 (Tue, 05 May 2009) | 3 lines
|
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4609 Changed paths:
|
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4610 M /trunk/samtools/bam.h
|
|
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4611 M /trunk/samtools/bam_pileup.c
|
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4612 M /trunk/samtools/bam_plcmd.c
|
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4613 M /trunk/samtools/bamtk.c
|
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4614 M /trunk/samtools/sam.c
|
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4615 M /trunk/samtools/sam.h
|
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4616
|
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|
4617 * samtools-0.1.3-12 (r259)
|
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|
4618 * use the new I/O interface in pileup
|
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4619
|
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4620 ------------------------------------------------------------------------
|
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4621 r258 | lh3lh3 | 2009-05-05 09:33:22 -0400 (Tue, 05 May 2009) | 3 lines
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4622 Changed paths:
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4623 M /trunk/samtools/Makefile.generic
|
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4624 M /trunk/samtools/Makefile.lite
|
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4625 M /trunk/samtools/bam.c
|
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|
4626 M /trunk/samtools/bam.h
|
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4627 M /trunk/samtools/bam_import.c
|
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4628 M /trunk/samtools/bamtk.c
|
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4629 A /trunk/samtools/sam.c
|
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4630 A /trunk/samtools/sam.h
|
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4631 A /trunk/samtools/sam_view.c
|
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4632
|
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|
4633 * samtools-0.1.3-11 (r258)
|
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|
4634 * unify the interface to BAM and SAM I/O
|
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4635
|
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4636 ------------------------------------------------------------------------
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4637 r257 | lh3lh3 | 2009-05-05 04:53:35 -0400 (Tue, 05 May 2009) | 3 lines
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4638 Changed paths:
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4639 M /trunk/samtools/Makefile.lite
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4640 M /trunk/samtools/bam_plcmd.c
|
|
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4641 M /trunk/samtools/bamtk.c
|
|
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4642
|
|
|
4643 * samtools-0.1.3-10 (r257)
|
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|
4644 * allow hex with "pileup -m"
|
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4645
|
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4646 ------------------------------------------------------------------------
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4647 r256 | lh3lh3 | 2009-05-04 14:16:50 -0400 (Mon, 04 May 2009) | 4 lines
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4648 Changed paths:
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4649 M /trunk/samtools/bam_lpileup.c
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4650 M /trunk/samtools/bamtk.c
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4651
|
|
|
4652 * samtools-0.1.3-9 (r256)
|
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|
4653 * fixed a bug in bam_lpileup.c
|
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|
4654 * I do not know if this also fixes the bug causing assertion failure in the tview
|
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4655
|
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|
4656 ------------------------------------------------------------------------
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4657 r251 | lh3lh3 | 2009-04-28 08:53:23 -0400 (Tue, 28 Apr 2009) | 3 lines
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4658 Changed paths:
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4659 M /trunk/samtools/bam_pileup.c
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4660 M /trunk/samtools/bamtk.c
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4661
|
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|
4662 * samtools-0.1.3-8 (r251)
|
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4663 * fixed a bug when there are reads without coordinates
|
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4664
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4665 ------------------------------------------------------------------------
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4666 r250 | lh3lh3 | 2009-04-28 08:43:33 -0400 (Tue, 28 Apr 2009) | 2 lines
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4667 Changed paths:
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4668 A /trunk/samtools/AUTHORS
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4669 A /trunk/samtools/README
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4670 M /trunk/samtools/cleanup.sh
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4671
|
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4672 added missing files
|
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4673
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4674 ------------------------------------------------------------------------
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4675 r249 | lh3lh3 | 2009-04-28 08:37:16 -0400 (Tue, 28 Apr 2009) | 2 lines
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4676 Changed paths:
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4677 M /trunk/samtools/Makefile.generic
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4678 M /trunk/samtools/Makefile.lite
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4679 M /trunk/samtools/configure.ac
|
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4680 M /trunk/samtools/misc/Makefile.generic
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4681
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4682 improve large file support in compilation
|
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4683
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4684 ------------------------------------------------------------------------
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4685 r248 | lh3lh3 | 2009-04-28 08:33:24 -0400 (Tue, 28 Apr 2009) | 2 lines
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4686 Changed paths:
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4687 M /trunk/samtools/INSTALL
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4688
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4689 update INSTALL
|
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4690
|
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|
4691 ------------------------------------------------------------------------
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4692 r247 | lh3lh3 | 2009-04-28 08:28:50 -0400 (Tue, 28 Apr 2009) | 2 lines
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4693 Changed paths:
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4694 M /trunk/samtools/Makefile.am
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4695 M /trunk/samtools/autogen.sh
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4696 M /trunk/samtools/cleanup.sh
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4697 M /trunk/samtools/configure.ac
|
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4698 A /trunk/samtools/misc/Makefile.am
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4699
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4700 fixed various issues about the GNU building scripts
|
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4701
|
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4702 ------------------------------------------------------------------------
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4703 r246 | lh3lh3 | 2009-04-28 08:10:23 -0400 (Tue, 28 Apr 2009) | 4 lines
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4704 Changed paths:
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4705 M /trunk/samtools/ChangeLog
|
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4706 D /trunk/samtools/Makefile
|
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4707 A /trunk/samtools/Makefile.am
|
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4708 A /trunk/samtools/Makefile.generic
|
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4709 A /trunk/samtools/autogen.sh
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4710 M /trunk/samtools/bam.h
|
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4711 M /trunk/samtools/bam_aux.c
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4712 M /trunk/samtools/bam_tview.c
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4713 M /trunk/samtools/bamtk.c
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4714 A /trunk/samtools/cleanup.sh
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4715 A /trunk/samtools/configure.ac
|
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4716 D /trunk/samtools/misc/Makefile
|
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4717 A /trunk/samtools/misc/Makefile.generic (from /trunk/samtools/misc/Makefile:245)
|
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4718
|
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|
4719 * samtools-0.1.3-7 (r246)
|
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|
4720 * incorporated revisions from Nils Homer
|
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|
4721 * enhanced support of displaying color-space reads
|
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4722
|
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|
4723 ------------------------------------------------------------------------
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4724 r244 | lh3lh3 | 2009-04-25 06:49:40 -0400 (Sat, 25 Apr 2009) | 3 lines
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4725 Changed paths:
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4726 M /trunk/samtools/bam_md.c
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4727 M /trunk/samtools/bamtk.c
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4728
|
|
|
4729 * samtools-0.1.3-6 (r244)
|
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|
4730 * fixed segfault for unmapped reads
|
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4731
|
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4732 ------------------------------------------------------------------------
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4733 r243 | lh3lh3 | 2009-04-24 16:27:26 -0400 (Fri, 24 Apr 2009) | 5 lines
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4734 Changed paths:
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4735 M /trunk/samtools/bam.h
|
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4736 M /trunk/samtools/bam_maqcns.c
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4737 M /trunk/samtools/bam_md.c
|
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4738 M /trunk/samtools/bamtk.c
|
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4739
|
|
|
4740 * samtools-0.1.3-5 (r243)
|
|
|
4741 * fixed a long existing bug which may cause memory leak
|
|
|
4742 * check MD
|
|
|
4743 * consensus calling now works with "=", but indel calling not
|
|
|
4744
|
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|
4745 ------------------------------------------------------------------------
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4746 r242 | lh3lh3 | 2009-04-24 15:44:46 -0400 (Fri, 24 Apr 2009) | 3 lines
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4747 Changed paths:
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4748 M /trunk/samtools/bam_md.c
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4749 M /trunk/samtools/bamtk.c
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4750
|
|
|
4751 * samtools-0.1.3-4 (r242)
|
|
|
4752 * fixed a memory leak
|
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|
4753
|
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|
4754 ------------------------------------------------------------------------
|
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4755 r240 | lh3lh3 | 2009-04-24 11:40:18 -0400 (Fri, 24 Apr 2009) | 5 lines
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4756 Changed paths:
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4757 M /trunk/samtools/Makefile
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4758 M /trunk/samtools/Makefile.lite
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4759 M /trunk/samtools/bam.h
|
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4760 M /trunk/samtools/bam_aux.c
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4761 A /trunk/samtools/bam_md.c
|
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4762 M /trunk/samtools/bam_plcmd.c
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4763 M /trunk/samtools/bamtk.c
|
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4764
|
|
|
4765 * samtools-0.1.3-3 (r240)
|
|
|
4766 * generate MD tag
|
|
|
4767 * generate "=" bases
|
|
|
4768 * the plain pileup now support "=" bases, but consensus calling and glfgen may fail
|
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4769
|
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|
4770 ------------------------------------------------------------------------
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4771 r239 | lh3lh3 | 2009-04-24 07:08:20 -0400 (Fri, 24 Apr 2009) | 5 lines
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4772 Changed paths:
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4773 M /trunk/samtools/bam.h
|
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4774 M /trunk/samtools/bam_aux.c
|
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4775 M /trunk/samtools/bamtk.c
|
|
|
4776
|
|
|
4777 * samtools-0.1.3-2 (r239)
|
|
|
4778 * fixed bugs in bam_aux.c (these functions nevered used by samtools)
|
|
|
4779 * removed bam_aux_init()/bam_aux_destroy()
|
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|
4780 * added tagview for testing bam_aux
|
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4781
|
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|
4782 ------------------------------------------------------------------------
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4783 r235 | lh3lh3 | 2009-04-21 18:17:39 -0400 (Tue, 21 Apr 2009) | 3 lines
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4784 Changed paths:
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4785 M /trunk/samtools/bam_pileup.c
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4786 M /trunk/samtools/bamtk.c
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4787
|
|
|
4788 * samtools-0.1.3-1
|
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|
4789 * fixed a bug in pileup: the first read in a chromosome may not be printed
|
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4790
|
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|
4791 ------------------------------------------------------------------------
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4792 r232 | lh3lh3 | 2009-04-16 10:25:43 -0400 (Thu, 16 Apr 2009) | 2 lines
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4793 Changed paths:
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4794 M /trunk/samtools/Makefile.lite
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4795
|
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|
4796 a missing file in Makefile.lite
|
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4797
|
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|
4798 ------------------------------------------------------------------------
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4799 r227 | lh3lh3 | 2009-04-15 17:02:53 -0400 (Wed, 15 Apr 2009) | 2 lines
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4800 Changed paths:
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4801 M /trunk/samtools/NEWS
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4802 M /trunk/samtools/bamtk.c
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4803
|
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|
4804 Release samtools-0.1.3
|
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4805
|
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|
4806 ------------------------------------------------------------------------
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4807 r223 | lh3lh3 | 2009-04-15 09:31:32 -0400 (Wed, 15 Apr 2009) | 3 lines
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4808 Changed paths:
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4809 M /trunk/samtools/bam_plcmd.c
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4810 M /trunk/samtools/bamtk.c
|
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4811
|
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|
4812 * samtools-0.1.2-28
|
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|
4813 * make samtools more robust to weird input such as empty file
|
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|
4814
|
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|
4815 ------------------------------------------------------------------------
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4816 r222 | lh3lh3 | 2009-04-15 09:05:33 -0400 (Wed, 15 Apr 2009) | 2 lines
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4817 Changed paths:
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4818 M /trunk/samtools/ChangeLog
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4819 M /trunk/samtools/NEWS
|
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4820 M /trunk/samtools/samtools.1
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4821
|
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|
4822 prepare for release 0.1.3
|
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4823
|
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|
4824 ------------------------------------------------------------------------
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4825 r221 | lh3lh3 | 2009-04-15 08:32:14 -0400 (Wed, 15 Apr 2009) | 2 lines
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4826 Changed paths:
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4827 A /trunk/samtools/misc/blast2sam.pl
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4828
|
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|
4829 convert NCBI-BLASTN to SAM
|
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4830
|
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|
4831 ------------------------------------------------------------------------
|
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4832 r220 | lh3lh3 | 2009-04-15 08:18:19 -0400 (Wed, 15 Apr 2009) | 3 lines
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4833 Changed paths:
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4834 M /trunk/samtools/bam_lpileup.c
|
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4835 M /trunk/samtools/bamtk.c
|
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4836
|
|
|
4837 * samtools-0.1.2-27
|
|
|
4838 * fixed a small memory leak in tview
|
|
|
4839
|
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|
4840 ------------------------------------------------------------------------
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4841 r219 | lh3lh3 | 2009-04-15 08:00:08 -0400 (Wed, 15 Apr 2009) | 3 lines
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4842 Changed paths:
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4843 M /trunk/samtools/bam_rmdup.c
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4844 M /trunk/samtools/bamtk.c
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4845
|
|
|
4846 * samtools-0.1.2-26
|
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|
4847 * fixed a bug in rmdup when there are unmapped reads
|
|
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4848
|
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|
4849 ------------------------------------------------------------------------
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4850 r218 | lh3lh3 | 2009-04-14 17:28:58 -0400 (Tue, 14 Apr 2009) | 2 lines
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4851 Changed paths:
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4852 M /trunk/samtools/ChangeLog
|
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4853 M /trunk/samtools/NEWS
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4854
|
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|
4855 proposed NEWS for the new release (have not yet)
|
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4856
|
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|
4857 ------------------------------------------------------------------------
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4858 r216 | lh3lh3 | 2009-04-14 17:10:46 -0400 (Tue, 14 Apr 2009) | 4 lines
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4859 Changed paths:
|
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|
4860 M /trunk/samtools/misc/samtools.pl
|
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|
4861
|
|
|
4862 * samtools.pl-0.1.1
|
|
|
4863 * improve indelFilter to avoid filtering true indels. The new filter relies
|
|
|
4864 on the new pileup indel line implemented in samtools-0.1.2-25
|
|
|
4865
|
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|
4866 ------------------------------------------------------------------------
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4867 r215 | lh3lh3 | 2009-04-14 17:04:19 -0400 (Tue, 14 Apr 2009) | 4 lines
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4868 Changed paths:
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4869 M /trunk/samtools/bam_maqcns.c
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|
4870 M /trunk/samtools/bam_plcmd.c
|
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4871 M /trunk/samtools/bamtk.c
|
|
|
4872 M /trunk/samtools/samtools.1
|
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4873
|
|
|
4874 * samtools-0.1.2-25
|
|
|
4875 * change the pileup indel line to shows the number of alignments actually
|
|
|
4876 containing indels
|
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|
4877
|
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|
4878 ------------------------------------------------------------------------
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4879 r211 | lh3lh3 | 2009-04-13 07:07:13 -0400 (Mon, 13 Apr 2009) | 2 lines
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4880 Changed paths:
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|
4881 M /trunk/samtools/ChangeLog
|
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4882
|
|
|
4883 update ChangeLog from "svn log"
|
|
|
4884
|
|
|
4885 ------------------------------------------------------------------------
|
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|
4886 r210 | lh3lh3 | 2009-04-12 15:57:05 -0400 (Sun, 12 Apr 2009) | 4 lines
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4887 Changed paths:
|
|
|
4888 M /trunk/samtools/bam.c
|
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4889 M /trunk/samtools/bam_import.c
|
|
|
4890 M /trunk/samtools/bam_sort.c
|
|
|
4891 M /trunk/samtools/bamtk.c
|
|
|
4892 M /trunk/samtools/kseq.h
|
|
|
4893
|
|
|
4894 * samtools-0.1.2-24
|
|
|
4895 * in merge, gives a warning rather than error if the target sequence length is different
|
|
|
4896 * allow empty header
|
|
|
4897
|
|
|
4898 ------------------------------------------------------------------------
|
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|
4899 r209 | lh3lh3 | 2009-04-12 15:32:44 -0400 (Sun, 12 Apr 2009) | 3 lines
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4900 Changed paths:
|
|
|
4901 M /trunk/samtools/bam.c
|
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|
4902 M /trunk/samtools/bam_import.c
|
|
|
4903 M /trunk/samtools/bamtk.c
|
|
|
4904
|
|
|
4905 * samtools-0.1.2-23
|
|
|
4906 * recognize '*' at the QUAL field
|
|
|
4907
|
|
|
4908 ------------------------------------------------------------------------
|
|
|
4909 r208 | lh3lh3 | 2009-04-12 15:08:02 -0400 (Sun, 12 Apr 2009) | 3 lines
|
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4910 Changed paths:
|
|
|
4911 M /trunk/samtools/bam_import.c
|
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|
4912 M /trunk/samtools/bamtk.c
|
|
|
4913 M /trunk/samtools/kseq.h
|
|
|
4914
|
|
|
4915 * samtools-0.1.2-22
|
|
|
4916 * the field separater is TAB only, now
|
|
|
4917
|
|
|
4918 ------------------------------------------------------------------------
|
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|
4919 r207 | lh3lh3 | 2009-04-08 10:18:03 -0400 (Wed, 08 Apr 2009) | 2 lines
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4920 Changed paths:
|
|
|
4921 M /trunk/samtools/examples/ex1.sam.gz
|
|
|
4922
|
|
|
4923 * fixed the problem in the example alignment due to the bug in fixmate
|
|
|
4924
|
|
|
4925 ------------------------------------------------------------------------
|
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|
4926 r206 | lh3lh3 | 2009-04-08 10:15:05 -0400 (Wed, 08 Apr 2009) | 3 lines
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4927 Changed paths:
|
|
|
4928 M /trunk/samtools/bam_mate.c
|
|
|
4929 M /trunk/samtools/bamtk.c
|
|
|
4930 M /trunk/samtools/misc/soap2sam.pl
|
|
|
4931
|
|
|
4932 * samtools-0.1.2-21
|
|
|
4933 * fixed a nasty bug in `fixmate'
|
|
|
4934
|
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|
4935 ------------------------------------------------------------------------
|
|
|
4936 r205 | lh3lh3 | 2009-04-08 05:57:08 -0400 (Wed, 08 Apr 2009) | 2 lines
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4937 Changed paths:
|
|
|
4938 M /trunk/samtools/misc/bowtie2sam.pl
|
|
|
4939 M /trunk/samtools/misc/soap2sam.pl
|
|
|
4940 M /trunk/samtools/misc/wgsim_eval.pl
|
|
|
4941
|
|
|
4942 make the script robust to the bugs in SOAP-2.1.7
|
|
|
4943
|
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|
4944 ------------------------------------------------------------------------
|
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|
4945 r200 | lh3lh3 | 2009-04-02 10:14:56 -0400 (Thu, 02 Apr 2009) | 3 lines
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4946 Changed paths:
|
|
|
4947 M /trunk/samtools/bam_stat.c
|
|
|
4948 M /trunk/samtools/bamtk.c
|
|
|
4949
|
|
|
4950 * samtools-0.1.2-20
|
|
|
4951 * check if file is truncated in flagstat
|
|
|
4952
|
|
|
4953 ------------------------------------------------------------------------
|
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4954 r199 | lh3lh3 | 2009-04-02 10:09:10 -0400 (Thu, 02 Apr 2009) | 3 lines
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4955 Changed paths:
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4956 M /trunk/samtools/bamtk.c
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4957
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4958 * samtools-0.1.2-19
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4959 * print the header if requested
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4960
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4961 ------------------------------------------------------------------------
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4962 r193 | lh3lh3 | 2009-03-27 11:09:50 -0400 (Fri, 27 Mar 2009) | 3 lines
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4963 Changed paths:
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4964 M /trunk/samtools/bam_plcmd.c
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4965 M /trunk/samtools/bamtk.c
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4966
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4967 * samtools-0.1.2-18
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4968 * fixed a minor bug reported by Nils Homer
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4969
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4970 ------------------------------------------------------------------------
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4971 r185 | lh3lh3 | 2009-03-24 07:50:32 -0400 (Tue, 24 Mar 2009) | 2 lines
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4972 Changed paths:
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4973 A /trunk/samtools/Makefile (from /trunk/samtools/Makefile.std:184)
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4974 D /trunk/samtools/Makefile.std
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4975 A /trunk/samtools/misc/Makefile (from /trunk/samtools/misc/Makefile.std:184)
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4976 D /trunk/samtools/misc/Makefile.std
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4977
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4978 rename Makefile.std as Makefile. GNU building systerm is not ready and may take some time...
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4979
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4980 ------------------------------------------------------------------------
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4981 r184 | lh3lh3 | 2009-03-24 06:36:38 -0400 (Tue, 24 Mar 2009) | 4 lines
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4982 Changed paths:
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4983 D /trunk/samtools/Makefile
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4984 A /trunk/samtools/Makefile.std (from /trunk/samtools/Makefile:183)
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4985 M /trunk/samtools/bam_sort.c
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4986 M /trunk/samtools/bam_tview.c
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4987 M /trunk/samtools/bamtk.c
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4988 D /trunk/samtools/misc/Makefile
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4989 A /trunk/samtools/misc/Makefile.std (from /trunk/samtools/misc/Makefile:182)
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4990 M /trunk/samtools/samtools.1
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4991
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4992 * samtools-0.1.2-17
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4993 * incorporating Nils' changes
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4994 * rename Makefile to Makefile.std and prepare to add the GNU building systerms (also by Nils)
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4995
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4996 ------------------------------------------------------------------------
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4997 r183 | lh3lh3 | 2009-03-24 06:30:23 -0400 (Tue, 24 Mar 2009) | 4 lines
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4998 Changed paths:
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4999 M /trunk/samtools/Makefile
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5000 M /trunk/samtools/bam_import.c
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5001 M /trunk/samtools/bam_maqcns.c
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5002 M /trunk/samtools/bam_maqcns.h
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5003 M /trunk/samtools/bam_plcmd.c
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5004 M /trunk/samtools/bamtk.c
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5005 M /trunk/samtools/kseq.h
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5006 A /trunk/samtools/kstring.c
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5007 A /trunk/samtools/kstring.h
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5008
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5009 * samtools-0.1.2-16
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5010 * made pileup take a list of proposed indels. An insertion is N at the moment.
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5011 * added my kstring library for a bit complex parsing of the position list.
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5012
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5013 ------------------------------------------------------------------------
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5014 r169 | lh3lh3 | 2009-03-12 09:40:14 -0400 (Thu, 12 Mar 2009) | 3 lines
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5015 Changed paths:
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5016 M /trunk/samtools/misc/soap2sam.pl
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5017
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5018 * soap2sam.pl-0.1.2
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5019 * more robust to truncated soap output
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5020
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5021 ------------------------------------------------------------------------
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5022 r168 | lh3lh3 | 2009-03-11 06:49:00 -0400 (Wed, 11 Mar 2009) | 2 lines
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5023 Changed paths:
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5024 M /trunk/samtools/Makefile.lite
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5025
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5026 added bam_stat.o to Makefile.lite
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5027
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5028 ------------------------------------------------------------------------
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5029 r167 | lh3lh3 | 2009-03-10 18:11:31 -0400 (Tue, 10 Mar 2009) | 3 lines
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5030 Changed paths:
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5031 M /trunk/samtools/bam_maqcns.c
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5032 M /trunk/samtools/bamtk.c
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5033
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5034 * samtools-0.1.2-15
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5035 * generate RMS of mapQ instead of max mapQ
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5036
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5037 ------------------------------------------------------------------------
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5038 r166 | lh3lh3 | 2009-03-10 18:06:45 -0400 (Tue, 10 Mar 2009) | 3 lines
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5039 Changed paths:
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5040 M /trunk/samtools/bam_plcmd.c
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5041 M /trunk/samtools/bamtk.c
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5042 M /trunk/samtools/glf.c
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5043 M /trunk/samtools/glf.h
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5044 M /trunk/samtools/misc/Makefile
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5045
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5046 * samtools-0.1.2-14
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5047 * implemented GLFv3
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5048
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5049 ------------------------------------------------------------------------
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5050 r159 | lh3lh3 | 2009-03-03 06:26:08 -0500 (Tue, 03 Mar 2009) | 3 lines
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5051 Changed paths:
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5052 M /trunk/samtools/bam_plcmd.c
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5053 M /trunk/samtools/bamtk.c
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5054
|
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5055 * samtools-0.1.2-13
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5056 * fixed a minor bug in displaying pileup
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5057
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5058 ------------------------------------------------------------------------
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5059 r158 | lh3lh3 | 2009-03-03 06:24:16 -0500 (Tue, 03 Mar 2009) | 3 lines
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5060 Changed paths:
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5061 M /trunk/samtools/ChangeLog
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5062 M /trunk/samtools/bamtk.c
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5063
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5064 * samtools-0.1.2-12
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5065 * optionally print SAM header
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5066
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5067 ------------------------------------------------------------------------
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5068 r153 | lh3lh3 | 2009-03-02 05:45:28 -0500 (Mon, 02 Mar 2009) | 3 lines
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5069 Changed paths:
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5070 M /trunk/samtools/bamtk.c
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5071 M /trunk/samtools/glf.c
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5072
|
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5073 * samtools-0.1.2-11
|
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5074 * use "GLF\3" as the magic for GLFv3 files
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5075
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5076 ------------------------------------------------------------------------
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5077 r152 | lh3lh3 | 2009-03-02 05:39:09 -0500 (Mon, 02 Mar 2009) | 5 lines
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5078 Changed paths:
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5079 M /trunk/samtools/Makefile
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5080 M /trunk/samtools/bam_import.c
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5081 M /trunk/samtools/bam_index.c
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5082 M /trunk/samtools/bam_plcmd.c
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5083 M /trunk/samtools/bamtk.c
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5084 M /trunk/samtools/glf.c
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5085 M /trunk/samtools/glf.h
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5086
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5087 * samtools-0.1.2-10
|
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5088 * fixed a bug in import: core.bin is undefined for unmapped reads
|
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|
5089 * this bug can be alleviated (not completely solved) in bam_index.c
|
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5090 * update to GLFv3: pos is changed to offset for better compression
|
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5091
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5092 ------------------------------------------------------------------------
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5093 r151 | lh3lh3 | 2009-03-01 10:18:43 -0500 (Sun, 01 Mar 2009) | 3 lines
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5094 Changed paths:
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5095 M /trunk/samtools/misc/wgsim.c
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5096
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5097 * wgsim-0.2.3
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5098 * fixed a bug in simulating indels
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5099
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5100 ------------------------------------------------------------------------
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5101 r145 | lh3lh3 | 2009-02-26 14:43:57 -0500 (Thu, 26 Feb 2009) | 4 lines
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5102 Changed paths:
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5103 M /trunk/samtools/misc/wgsim.c
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5104
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5105 * wgsim-0.2.2
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5106 * allow to print mismatch information as fastq comment. MAQ does
|
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5107 not like long read names.
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5108
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5109 ------------------------------------------------------------------------
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5110 r141 | lh3lh3 | 2009-02-26 09:53:03 -0500 (Thu, 26 Feb 2009) | 6 lines
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5111 Changed paths:
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5112 M /trunk/samtools/ChangeLog
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5113 M /trunk/samtools/misc/wgsim.c
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5114 M /trunk/samtools/misc/wgsim_eval.pl
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5115
|
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5116 * wgsim-0.2.1
|
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5117 * fixed a bug about color read coordinates
|
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|
5118 * fixed a bug in read names
|
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5119 * wgsim_eval.pl-0.1.3
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5120 * make the script work with color reads
|
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5121
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5122 ------------------------------------------------------------------------
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5123 r140 | lh3lh3 | 2009-02-26 09:02:57 -0500 (Thu, 26 Feb 2009) | 2 lines
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5124 Changed paths:
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5125 M /trunk/samtools/misc/Makefile
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5126 M /trunk/samtools/misc/wgsim.c
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5127
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5128 * wgsim: added a note
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5129
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5130 ------------------------------------------------------------------------
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5131 r139 | lh3lh3 | 2009-02-26 06:39:08 -0500 (Thu, 26 Feb 2009) | 7 lines
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5132 Changed paths:
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5133 M /trunk/samtools/misc/wgsim.c
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5134 M /trunk/samtools/misc/wgsim_eval.pl
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5135
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5136 * wgsim-0.2.0
|
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5137 * considerable code clean up
|
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|
5138 * print number of substitutions/indels/errors on each read
|
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|
5139 * potentially support SOLiD simulation, though not tested at the moment
|
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|
5140 * wgsim_eval.pl-0.1.2
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5141 * change in accordant with wgsim
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5142
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5143 ------------------------------------------------------------------------
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5144 r129 | lh3lh3 | 2009-02-18 17:23:27 -0500 (Wed, 18 Feb 2009) | 3 lines
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5145 Changed paths:
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5146 M /trunk/samtools/bam_index.c
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5147 M /trunk/samtools/bamtk.c
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5148
|
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|
5149 * samtools-0.1.2-9
|
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5150 * fixed a bug in bam_fetch, caused by completely contained adjacent chunks
|
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5151
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5152 ------------------------------------------------------------------------
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5153 r128 | bhandsaker | 2009-02-18 14:06:57 -0500 (Wed, 18 Feb 2009) | 2 lines
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5154 Changed paths:
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5155 M /trunk/samtools/bamtk.c
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5156
|
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5157 Fix annoying segv when invalid region specified.
|
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5158
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5159 ------------------------------------------------------------------------
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5160 r127 | lh3lh3 | 2009-02-17 05:49:55 -0500 (Tue, 17 Feb 2009) | 2 lines
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5161 Changed paths:
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5162 D /trunk/samtools/misc/indel_filter.pl
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5163 A /trunk/samtools/misc/samtools.pl
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5164
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5165 * move indel_filter.pl to samtools.pl
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5166
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5167 ------------------------------------------------------------------------
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5168 r126 | lh3lh3 | 2009-02-14 16:22:30 -0500 (Sat, 14 Feb 2009) | 3 lines
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5169 Changed paths:
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5170 M /trunk/samtools/bam_mate.c
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5171 M /trunk/samtools/bamtk.c
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5172
|
|
|
5173 * samtools-0.1.2-7
|
|
|
5174 * fixed a bug in fixmate: SE reads are flagged as BAM_FMUNMAP
|
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5175
|
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|
5176 ------------------------------------------------------------------------
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5177 r125 | lh3lh3 | 2009-02-13 04:54:45 -0500 (Fri, 13 Feb 2009) | 3 lines
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5178 Changed paths:
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5179 M /trunk/samtools/bam_stat.c
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5180 M /trunk/samtools/bamtk.c
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5181
|
|
|
5182 * samtools-0.1.2-7
|
|
|
5183 * fixed a minor bug in flagstat
|
|
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5184
|
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|
5185 ------------------------------------------------------------------------
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5186 r124 | lh3lh3 | 2009-02-12 06:15:32 -0500 (Thu, 12 Feb 2009) | 3 lines
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5187 Changed paths:
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5188 M /trunk/samtools/bam_maqcns.c
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5189 M /trunk/samtools/bamtk.c
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5190 M /trunk/samtools/misc/indel_filter.pl
|
|
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5191
|
|
|
5192 * samtools-0.1.2-6
|
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|
5193 * improve indel caller by setting maximum window size
|
|
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5194
|
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|
5195 ------------------------------------------------------------------------
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5196 r123 | lh3lh3 | 2009-02-12 05:30:29 -0500 (Thu, 12 Feb 2009) | 2 lines
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5197 Changed paths:
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5198 M /trunk/samtools/bam_plcmd.c
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5199 M /trunk/samtools/bamtk.c
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5200
|
|
|
5201 * output max mapping quality in indel line
|
|
|
5202
|
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|
5203 ------------------------------------------------------------------------
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5204 r122 | lh3lh3 | 2009-02-11 05:59:10 -0500 (Wed, 11 Feb 2009) | 2 lines
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5205 Changed paths:
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5206 M /trunk/samtools/misc/maq2sam.c
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|
|
5207
|
|
|
5208 fixed a bug in generating tag AM
|
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|
5209
|
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5210 ------------------------------------------------------------------------
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5211 r121 | lh3lh3 | 2009-02-03 05:43:11 -0500 (Tue, 03 Feb 2009) | 2 lines
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5212 Changed paths:
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5213 M /trunk/samtools/bam_index.c
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5214 M /trunk/samtools/bamtk.c
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5215
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5216 fixed a potential memory problem in indexing
|
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5217
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5218 ------------------------------------------------------------------------
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5219 r120 | bhandsaker | 2009-02-02 10:52:52 -0500 (Mon, 02 Feb 2009) | 2 lines
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5220 Changed paths:
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5221 M /trunk/samtools/Makefile
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5222
|
|
|
5223 Pass LIBS to recursive targets to facilitate building at Broad.
|
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5224
|
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5225 ------------------------------------------------------------------------
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5226 r119 | lh3lh3 | 2009-02-02 05:12:15 -0500 (Mon, 02 Feb 2009) | 4 lines
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5227 Changed paths:
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5228 M /trunk/samtools/ChangeLog
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5229 M /trunk/samtools/bam_plcmd.c
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5230 M /trunk/samtools/bam_stat.c
|
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5231 M /trunk/samtools/bamtk.c
|
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5232
|
|
|
5233 * samtools-0.1.2-3
|
|
|
5234 * fixed a bug in generating GLFv2 for indels
|
|
|
5235 * improve flagstat report a little bit
|
|
|
5236
|
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|
5237 ------------------------------------------------------------------------
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5238 r118 | lh3lh3 | 2009-01-29 07:33:23 -0500 (Thu, 29 Jan 2009) | 3 lines
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5239 Changed paths:
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5240 M /trunk/samtools/Makefile
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5241 A /trunk/samtools/bam_stat.c
|
|
|
5242 M /trunk/samtools/bamtk.c
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|
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5243
|
|
|
5244 * samtools-0.1.2-1
|
|
|
5245 * added flagstat command
|
|
|
5246
|
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|
5247 ------------------------------------------------------------------------
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5248 r116 | lh3lh3 | 2009-01-28 08:31:12 -0500 (Wed, 28 Jan 2009) | 2 lines
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5249 Changed paths:
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5250 M /trunk/samtools/ChangeLog
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5251 M /trunk/samtools/NEWS
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5252 M /trunk/samtools/bamtk.c
|
|
|
5253 M /trunk/samtools/samtools.1
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5254
|
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|
5255 Release SAMtools-0.1.2
|
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5256
|
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|
5257 ------------------------------------------------------------------------
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5258 r115 | lh3lh3 | 2009-01-28 07:54:08 -0500 (Wed, 28 Jan 2009) | 2 lines
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5259 Changed paths:
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5260 A /trunk/samtools/misc/indel_filter.pl
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5261
|
|
|
5262 Script for filtering indel results
|
|
|
5263
|
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|
5264 ------------------------------------------------------------------------
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5265 r114 | lh3lh3 | 2009-01-25 06:45:37 -0500 (Sun, 25 Jan 2009) | 2 lines
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5266 Changed paths:
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5267 A /trunk/samtools/misc/zoom2sam.pl
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5268
|
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5269 convert ZOOM to SAM
|
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5270
|
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5271 ------------------------------------------------------------------------
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5272 r113 | lh3lh3 | 2009-01-24 09:25:07 -0500 (Sat, 24 Jan 2009) | 2 lines
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5273 Changed paths:
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5274 A /trunk/samtools/misc/novo2sam.pl
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5275
|
|
|
5276 add a script to convert novo alignment to SAM
|
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5277
|
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5278 ------------------------------------------------------------------------
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|
5279 r112 | lh3lh3 | 2009-01-23 15:57:39 -0500 (Fri, 23 Jan 2009) | 2 lines
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5280 Changed paths:
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5281 M /trunk/samtools/ChangeLog
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5282 M /trunk/samtools/ChangeLog.old
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5283 M /trunk/samtools/samtools.1
|
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5284
|
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|
5285 update documentation and ChangeLog
|
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|
5286
|
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|
5287 ------------------------------------------------------------------------
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|
5288 r111 | lh3lh3 | 2009-01-23 14:22:59 -0500 (Fri, 23 Jan 2009) | 3 lines
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5289 Changed paths:
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5290 M /trunk/samtools/bam_sort.c
|
|
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5291 M /trunk/samtools/bamtk.c
|
|
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5292
|
|
|
5293 * samtools-0.1.1-19
|
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|
5294 * fixed a bug in "merge" command line
|
|
|
5295
|
|
|
5296 ------------------------------------------------------------------------
|
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5297 r110 | lh3lh3 | 2009-01-22 10:36:48 -0500 (Thu, 22 Jan 2009) | 3 lines
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5298 Changed paths:
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5299 M /trunk/samtools/misc/Makefile
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5300 A /trunk/samtools/misc/bowtie2sam.pl (from /branches/dev/samtools/misc/bowtie2sam.pl:108)
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|
5301 M /trunk/samtools/misc/export2sam.pl
|
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5302 A /trunk/samtools/misc/soap2sam.pl (from /branches/dev/samtools/misc/soap2sam.pl:108)
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5303 A /trunk/samtools/misc/wgsim.c (from /branches/dev/samtools/misc/wgsim.c:108)
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5304 A /trunk/samtools/misc/wgsim_eval.pl (from /branches/dev/samtools/misc/wgsim_eval.pl:108)
|
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5305
|
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5306 * merge from branches/dev/
|
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|
5307 * all future development will happen here
|
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5308
|
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|
5309 ------------------------------------------------------------------------
|
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5310 r109 | lh3lh3 | 2009-01-22 10:14:27 -0500 (Thu, 22 Jan 2009) | 3 lines
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5311 Changed paths:
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5312 M /trunk/samtools/COPYING
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5313 M /trunk/samtools/ChangeLog
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5314 A /trunk/samtools/INSTALL (from /branches/dev/samtools/INSTALL:108)
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5315 M /trunk/samtools/Makefile
|
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5316 A /trunk/samtools/Makefile.lite (from /branches/dev/samtools/Makefile.lite:108)
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5317 M /trunk/samtools/bam.c
|
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5318 M /trunk/samtools/bam.h
|
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5319 M /trunk/samtools/bam_import.c
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5320 M /trunk/samtools/bam_index.c
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5321 M /trunk/samtools/bam_lpileup.c
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5322 M /trunk/samtools/bam_maqcns.c
|
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5323 M /trunk/samtools/bam_maqcns.h
|
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5324 A /trunk/samtools/bam_mate.c (from /branches/dev/samtools/bam_mate.c:108)
|
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5325 M /trunk/samtools/bam_pileup.c
|
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5326 M /trunk/samtools/bam_plcmd.c
|
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5327 A /trunk/samtools/bam_rmdup.c (from /branches/dev/samtools/bam_rmdup.c:108)
|
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5328 M /trunk/samtools/bam_sort.c
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5329 M /trunk/samtools/bamtk.c
|
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5330 M /trunk/samtools/bgzf.h
|
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5331 M /trunk/samtools/examples/00README.txt
|
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5332 A /trunk/samtools/examples/Makefile (from /branches/dev/samtools/examples/Makefile:108)
|
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5333 D /trunk/samtools/examples/ex1.fa.fai
|
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|
5334 M /trunk/samtools/examples/ex1.sam.gz
|
|
|
5335 M /trunk/samtools/faidx.c
|
|
|
5336 A /trunk/samtools/glf.c (from /branches/dev/samtools/glf.c:108)
|
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|
5337 M /trunk/samtools/glf.h
|
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|
5338 M /trunk/samtools/misc/Makefile
|
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5339 M /trunk/samtools/misc/maq2sam.c
|
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5340 M /trunk/samtools/razf.c
|
|
|
5341 M /trunk/samtools/source.dot
|
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|
5342
|
|
|
5343 * Merge from branches/dev/
|
|
|
5344 * all future development will happen here at trunk/
|
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5345
|
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|
5346 ------------------------------------------------------------------------
|
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|
5347 r79 | bhandsaker | 2009-01-07 16:42:15 -0500 (Wed, 07 Jan 2009) | 2 lines
|
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5348 Changed paths:
|
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|
5349 M /trunk/samtools/bam_maqcns.c
|
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|
5350 M /trunk/samtools/bam_tview.c
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5351
|
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|
5352 Fix problem with compiling without curses.
|
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5353
|
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|
5354 ------------------------------------------------------------------------
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5355 r63 | lh3lh3 | 2008-12-22 10:58:02 -0500 (Mon, 22 Dec 2008) | 2 lines
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5356 Changed paths:
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|
5357 A /trunk/samtools (from /branches/dev/samtools:62)
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5358
|
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|
5359 Create trunk copy
|
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5360
|
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|
5361 ------------------------------------------------------------------------
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5362 r62 | lh3lh3 | 2008-12-22 10:55:13 -0500 (Mon, 22 Dec 2008) | 2 lines
|
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5363 Changed paths:
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|
5364 A /branches/dev/samtools/NEWS
|
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5365 M /branches/dev/samtools/bamtk.c
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5366 M /branches/dev/samtools/samtools.1
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5367
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|
5368 Release samtools-0.1.1
|
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5369
|
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|
5370 ------------------------------------------------------------------------
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5371 r61 | lh3lh3 | 2008-12-22 10:46:08 -0500 (Mon, 22 Dec 2008) | 10 lines
|
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5372 Changed paths:
|
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|
5373 M /branches/dev/samtools/bam_aux.c
|
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5374 M /branches/dev/samtools/bam_index.c
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5375 M /branches/dev/samtools/bam_plcmd.c
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5376 M /branches/dev/samtools/bam_tview.c
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5377 M /branches/dev/samtools/bamtk.c
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5378 M /branches/dev/samtools/razf.c
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5379 M /branches/dev/samtools/samtools.1
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5380
|
|
|
5381 * samtools-0.1.0-66
|
|
|
5382 * fixed a bug in razf.c: reset z_eof when razf_seek() is called
|
|
|
5383 * fixed a memory leak in parsing a region
|
|
|
5384 * changed pileup a little bit when -s is in use: output ^ and $
|
|
|
5385 * when a bam is not indexed, output more meaningful error message
|
|
|
5386 * fixed a bug in indexing for small alignment
|
|
|
5387 * fixed a bug in the viewer when we come to the end of a reference file
|
|
|
5388 * updated documentation
|
|
|
5389 * prepare to release 0.1.1
|
|
|
5390
|
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|
5391 ------------------------------------------------------------------------
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|
5392 r60 | lh3lh3 | 2008-12-22 10:10:16 -0500 (Mon, 22 Dec 2008) | 2 lines
|
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5393 Changed paths:
|
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|
5394 A /branches/dev/samtools/examples
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5395 A /branches/dev/samtools/examples/00README.txt
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5396 A /branches/dev/samtools/examples/ex1.fa
|
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|
5397 A /branches/dev/samtools/examples/ex1.fa.fai
|
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5398 A /branches/dev/samtools/examples/ex1.sam.gz
|
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5399
|
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|
5400 example
|
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|
5401
|
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|
5402 ------------------------------------------------------------------------
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5403 r59 | lh3lh3 | 2008-12-22 04:38:15 -0500 (Mon, 22 Dec 2008) | 2 lines
|
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5404 Changed paths:
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|
5405 M /branches/dev/samtools/ChangeLog
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5406
|
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|
5407 update ChangeLog
|
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|
5408
|
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|
5409 ------------------------------------------------------------------------
|
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5410 r58 | lh3lh3 | 2008-12-20 18:06:00 -0500 (Sat, 20 Dec 2008) | 3 lines
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5411 Changed paths:
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5412 M /branches/dev/samtools/misc/export2sam.pl
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5413
|
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|
5414 * added comments
|
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|
5415 * fixed several bugs
|
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5416
|
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5417 ------------------------------------------------------------------------
|
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|
5418 r57 | lh3lh3 | 2008-12-20 10:44:20 -0500 (Sat, 20 Dec 2008) | 2 lines
|
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5419 Changed paths:
|
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5420 A /branches/dev/samtools/misc/export2sam.pl
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5421
|
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|
5422 convert Export format to SAM; not thoroughly tested
|
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5423
|
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|
5424 ------------------------------------------------------------------------
|
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|
5425 r56 | lh3lh3 | 2008-12-19 17:13:28 -0500 (Fri, 19 Dec 2008) | 6 lines
|
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5426 Changed paths:
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|
5427 M /branches/dev/samtools/bam_import.c
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5428 M /branches/dev/samtools/bam_plcmd.c
|
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5429 M /branches/dev/samtools/bam_tview.c
|
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5430 M /branches/dev/samtools/bamtk.c
|
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5431 A /branches/dev/samtools/source.dot
|
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|
5432
|
|
|
5433 * samtools-0.1.0-65
|
|
|
5434 * pileup: generate maq-like simple output
|
|
|
5435 * pileup: allow to output pileup at required sites
|
|
|
5436 * source.dot: source file relationship graph
|
|
|
5437 * tview: fixed a minor bug
|
|
|
5438
|
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|
5439 ------------------------------------------------------------------------
|
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|
5440 r55 | lh3lh3 | 2008-12-19 15:10:26 -0500 (Fri, 19 Dec 2008) | 2 lines
|
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5441 Changed paths:
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|
5442 D /branches/dev/samtools/misc/all2sam.pl
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5443
|
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|
5444 remove all2sam.pl
|
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5445
|
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|
5446 ------------------------------------------------------------------------
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|
5447 r54 | lh3lh3 | 2008-12-16 17:34:25 -0500 (Tue, 16 Dec 2008) | 2 lines
|
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5448 Changed paths:
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|
5449 A /branches/dev/samtools/COPYING
|
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5450 M /branches/dev/samtools/bam.h
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5451 M /branches/dev/samtools/faidx.h
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5452 M /branches/dev/samtools/khash.h
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5453 M /branches/dev/samtools/kseq.h
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5454 M /branches/dev/samtools/ksort.h
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5455 M /branches/dev/samtools/samtools.1
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5456
|
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|
5457 Added copyright information and a bit more documentation. No code change.
|
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5458
|
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|
5459 ------------------------------------------------------------------------
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|
5460 r53 | lh3lh3 | 2008-12-16 08:40:18 -0500 (Tue, 16 Dec 2008) | 3 lines
|
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5461 Changed paths:
|
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|
5462 M /branches/dev/samtools/bam.c
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5463 M /branches/dev/samtools/bam.h
|
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|
5464 M /branches/dev/samtools/bam_index.c
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5465 M /branches/dev/samtools/bam_maqcns.c
|
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5466 M /branches/dev/samtools/bamtk.c
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5467
|
|
|
5468 * samtools-0.1.0-64
|
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|
5469 * improved efficiency of the indel caller for spliced alignments
|
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|
5470
|
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|
5471 ------------------------------------------------------------------------
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|
5472 r52 | lh3lh3 | 2008-12-16 05:28:20 -0500 (Tue, 16 Dec 2008) | 3 lines
|
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5473 Changed paths:
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|
5474 M /branches/dev/samtools/bam.c
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5475 M /branches/dev/samtools/bam.h
|
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|
5476 M /branches/dev/samtools/bam_aux.c
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5477 M /branches/dev/samtools/bam_index.c
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|
5478 M /branches/dev/samtools/bamtk.c
|
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|
5479
|
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|
5480 * samtools-0.1.0-63
|
|
|
5481 * a bit code cleanup: reduce the dependency between source files
|
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5482
|
|
|
5483 ------------------------------------------------------------------------
|
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|
5484 r51 | lh3lh3 | 2008-12-15 09:29:32 -0500 (Mon, 15 Dec 2008) | 3 lines
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5485 Changed paths:
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|
5486 M /branches/dev/samtools/bam_maqcns.c
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5487 M /branches/dev/samtools/bam_plcmd.c
|
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5488 M /branches/dev/samtools/bamtk.c
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5489
|
|
|
5490 * samtools-0.1.0-62
|
|
|
5491 * fixed a memory leak
|
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|
5492
|
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|
5493 ------------------------------------------------------------------------
|
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5494 r50 | lh3lh3 | 2008-12-15 09:00:13 -0500 (Mon, 15 Dec 2008) | 2 lines
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5495 Changed paths:
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|
5496 M /branches/dev/samtools/ChangeLog
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5497 M /branches/dev/samtools/bam.h
|
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5498 M /branches/dev/samtools/samtools.1
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5499
|
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|
5500 update documentation, ChangeLog and a comment
|
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5501
|
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|
5502 ------------------------------------------------------------------------
|
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|
5503 r49 | lh3lh3 | 2008-12-15 08:36:43 -0500 (Mon, 15 Dec 2008) | 6 lines
|
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5504 Changed paths:
|
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|
5505 M /branches/dev/samtools/Makefile
|
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|
5506 M /branches/dev/samtools/bam.h
|
|
|
5507 M /branches/dev/samtools/bam_maqcns.c
|
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|
5508 M /branches/dev/samtools/bam_maqcns.h
|
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|
5509 M /branches/dev/samtools/bam_pileup.c
|
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5510 A /branches/dev/samtools/bam_plcmd.c
|
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5511 M /branches/dev/samtools/bamtk.c
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5512 M /branches/dev/samtools/samtools.1
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5513
|
|
|
5514 * samtools-0.1.0-61
|
|
|
5515 * moved pileup command to a separate source file
|
|
|
5516 * added indel caller
|
|
|
5517 * added bam_cal_segend(). (NOT WORKING for spliced alignment!!!)
|
|
|
5518 * updated documentation
|
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|
5519
|
|
|
5520 ------------------------------------------------------------------------
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|
5521 r48 | lh3lh3 | 2008-12-12 08:55:36 -0500 (Fri, 12 Dec 2008) | 3 lines
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5522 Changed paths:
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5523 M /branches/dev/samtools/bam_maqcns.c
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|
5524 M /branches/dev/samtools/bamtk.c
|
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5525
|
|
|
5526 * samtools-0.1.0-60
|
|
|
5527 * fixed another bug in maqcns when there is a nearby deletion
|
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|
5528
|
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|
5529 ------------------------------------------------------------------------
|
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|
5530 r47 | lh3lh3 | 2008-12-12 08:42:16 -0500 (Fri, 12 Dec 2008) | 5 lines
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5531 Changed paths:
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|
5532 M /branches/dev/samtools/bam_maqcns.c
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5533 M /branches/dev/samtools/bam_pileup.c
|
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|
5534 M /branches/dev/samtools/bamtk.c
|
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5535
|
|
|
5536 * samtools-0.1.0-59
|
|
|
5537 * pileup: outputing consensus is now optional
|
|
|
5538 * fixed a bug in glfgen. This bug also exists in maq's glfgen. However,
|
|
|
5539 I am not quite sure why the previous version may have problem.
|
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|
5540
|
|
|
5541 ------------------------------------------------------------------------
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5542 r46 | lh3lh3 | 2008-12-12 06:44:56 -0500 (Fri, 12 Dec 2008) | 6 lines
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5543 Changed paths:
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|
5544 M /branches/dev/samtools/bam_pileup.c
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5545 M /branches/dev/samtools/bamtk.c
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5546
|
|
|
5547 * samtools-0.1.0-58
|
|
|
5548 * add maq consensus to pileup. However, I will move this part to a new
|
|
|
5549 command as strictly speaking, consensus callin is not part of pileup,
|
|
|
5550 and imposing it would make it harder to generate for other language
|
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|
5551 bindings.
|
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|
5552
|
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|
5553 ------------------------------------------------------------------------
|
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|
5554 r45 | bhandsaker | 2008-12-11 15:43:56 -0500 (Thu, 11 Dec 2008) | 2 lines
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5555 Changed paths:
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|
5556 M /branches/dev/samtools/bgzf.c
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5557
|
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|
5558 Fix bug in tell() after reads that consume to the exact end of a block.
|
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|
5559
|
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|
5560 ------------------------------------------------------------------------
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5561 r44 | lh3lh3 | 2008-12-11 04:36:53 -0500 (Thu, 11 Dec 2008) | 2 lines
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5562 Changed paths:
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5563 M /branches/dev/samtools/samtools.1
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5564
|
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|
5565 update manual
|
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|
5566
|
|
|
5567 ------------------------------------------------------------------------
|
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|
5568 r43 | lh3lh3 | 2008-12-11 04:25:36 -0500 (Thu, 11 Dec 2008) | 4 lines
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|
5569 Changed paths:
|
|
|
5570 M /branches/dev/samtools/bam_import.c
|
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|
5571 M /branches/dev/samtools/bamtk.c
|
|
|
5572
|
|
|
5573 * samtools-0.1.0-57
|
|
|
5574 * fixed a bug in parser when there is auxiliary fields
|
|
|
5575 * made the parser a bit more robust
|
|
|
5576
|
|
|
5577 ------------------------------------------------------------------------
|
|
|
5578 r42 | lh3lh3 | 2008-12-10 09:57:29 -0500 (Wed, 10 Dec 2008) | 5 lines
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5579 Changed paths:
|
|
|
5580 M /branches/dev/samtools/bam_index.c
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|
5581 M /branches/dev/samtools/bamtk.c
|
|
|
5582 M /branches/dev/samtools/bgzf.c
|
|
|
5583
|
|
|
5584 * samtools-0.1.0-56
|
|
|
5585 * fixed a bug in bgzf (only reading is affected)
|
|
|
5586 * fixed a typo in bam_index.c
|
|
|
5587 * in bam_index.c, check potential bugs in the underlying I/O library
|
|
|
5588
|
|
|
5589 ------------------------------------------------------------------------
|
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5590 r41 | lh3lh3 | 2008-12-10 07:53:08 -0500 (Wed, 10 Dec 2008) | 2 lines
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5591 Changed paths:
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|
5592 M /branches/dev/samtools/samtools.1
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5593
|
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|
5594 update manual
|
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|
5595
|
|
|
5596 ------------------------------------------------------------------------
|
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5597 r40 | lh3lh3 | 2008-12-10 06:52:10 -0500 (Wed, 10 Dec 2008) | 5 lines
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5598 Changed paths:
|
|
|
5599 M /branches/dev/samtools/bam.h
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5600 M /branches/dev/samtools/bam_pileup.c
|
|
|
5601 M /branches/dev/samtools/bamtk.c
|
|
|
5602
|
|
|
5603 * samtools-0.1.0-55
|
|
|
5604 * tried to make pileup work with clipping (previously not), though NOT tested
|
|
|
5605 * removed -v from pileup
|
|
|
5606 * made pileup take the reference sequence
|
|
|
5607
|
|
|
5608 ------------------------------------------------------------------------
|
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|
5609 r39 | lh3lh3 | 2008-12-09 06:59:28 -0500 (Tue, 09 Dec 2008) | 4 lines
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5610 Changed paths:
|
|
|
5611 M /branches/dev/samtools/bam_import.c
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5612 M /branches/dev/samtools/bamtk.c
|
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|
5613 M /branches/dev/samtools/samtools.1
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|
5614
|
|
|
5615 * samtools-0.1.0-54
|
|
|
5616 * in parser, recognize "=", rather than ",", as a match
|
|
|
5617 * in parser, correctl parse "=" at the MRNM field.
|
|
|
5618
|
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|
5619 ------------------------------------------------------------------------
|
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|
5620 r38 | lh3lh3 | 2008-12-09 06:39:07 -0500 (Tue, 09 Dec 2008) | 2 lines
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5621 Changed paths:
|
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|
5622 M /branches/dev/samtools/misc/maq2sam.c
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|
5623
|
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|
5624 fixed a bug in handling maq flag 64 and 192
|
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|
5625
|
|
|
5626 ------------------------------------------------------------------------
|
|
|
5627 r37 | lh3lh3 | 2008-12-09 04:53:46 -0500 (Tue, 09 Dec 2008) | 2 lines
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5628 Changed paths:
|
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|
5629 M /branches/dev/samtools/misc/md5fa.c
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5630
|
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|
5631 also calculate unordered md5sum check
|
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5632
|
|
|
5633 ------------------------------------------------------------------------
|
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|
5634 r36 | lh3lh3 | 2008-12-09 04:46:21 -0500 (Tue, 09 Dec 2008) | 2 lines
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5635 Changed paths:
|
|
|
5636 M /branches/dev/samtools/misc/md5fa.c
|
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|
5637
|
|
|
5638 fixed a minor bug when there are space in the sequence
|
|
|
5639
|
|
|
5640 ------------------------------------------------------------------------
|
|
|
5641 r35 | lh3lh3 | 2008-12-09 04:40:45 -0500 (Tue, 09 Dec 2008) | 2 lines
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5642 Changed paths:
|
|
|
5643 M /branches/dev/samtools/misc/md5fa.c
|
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5644
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|
5645 fixed a potential memory leak
|
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5646
|
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|
5647 ------------------------------------------------------------------------
|
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5648 r34 | lh3lh3 | 2008-12-08 09:52:17 -0500 (Mon, 08 Dec 2008) | 2 lines
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5649 Changed paths:
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5650 M /branches/dev/samtools/bam_import.c
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5651 M /branches/dev/samtools/bam_index.c
|
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|
5652 M /branches/dev/samtools/bamtk.c
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5653
|
|
|
5654 * fixed a bug in import: bin is wrongly calculated
|
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5655
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5656 ------------------------------------------------------------------------
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5657 r33 | lh3lh3 | 2008-12-08 09:08:01 -0500 (Mon, 08 Dec 2008) | 2 lines
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5658 Changed paths:
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5659 M /branches/dev/samtools/misc/all2sam.pl
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5660
|
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5661 nothing, really
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5662
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5663 ------------------------------------------------------------------------
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5664 r32 | lh3lh3 | 2008-12-08 07:56:02 -0500 (Mon, 08 Dec 2008) | 3 lines
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5665 Changed paths:
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5666 M /branches/dev/samtools/Makefile
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5667 M /branches/dev/samtools/kseq.h
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5668 M /branches/dev/samtools/misc/Makefile
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5669 A /branches/dev/samtools/misc/md5.c
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5670 A /branches/dev/samtools/misc/md5.h
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5671 A /branches/dev/samtools/misc/md5fa.c
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5672
|
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|
5673 * fixed two warnings in kseq.h
|
|
|
5674 * added md5sum utilities
|
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5675
|
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5676 ------------------------------------------------------------------------
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5677 r31 | lh3lh3 | 2008-12-08 06:35:29 -0500 (Mon, 08 Dec 2008) | 5 lines
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5678 Changed paths:
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5679 M /branches/dev/samtools/Makefile
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5680 M /branches/dev/samtools/bam_import.c
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5681 M /branches/dev/samtools/bamtk.c
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5682 A /branches/dev/samtools/kseq.h
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5683 D /branches/dev/samtools/kstream.h
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5684
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5685 * samtools-0.1.0-52
|
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|
5686 * replace kstream with kseq. kseq is a superset of kstream. I need the
|
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5687 extra functions in kseq.h.
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5688 * also compile stand-alone faidx
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5689
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5690 ------------------------------------------------------------------------
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5691 r30 | lh3lh3 | 2008-12-08 06:17:04 -0500 (Mon, 08 Dec 2008) | 3 lines
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5692 Changed paths:
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5693 M /branches/dev/samtools/bam.h
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5694 M /branches/dev/samtools/bam_sort.c
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5695 M /branches/dev/samtools/bamtk.c
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5696
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5697 * samtools-0.1.0-51
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5698 * sorting by read names is available
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5699
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5700 ------------------------------------------------------------------------
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5701 r29 | lh3lh3 | 2008-12-08 05:29:02 -0500 (Mon, 08 Dec 2008) | 3 lines
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5702 Changed paths:
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5703 M /branches/dev/samtools/bam.c
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5704 M /branches/dev/samtools/bam.h
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5705 M /branches/dev/samtools/bam_import.c
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5706 M /branches/dev/samtools/bam_maqcns.c
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5707 M /branches/dev/samtools/bam_pileup.c
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5708 M /branches/dev/samtools/bam_sort.c
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5709 M /branches/dev/samtools/bam_tview.c
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5710 M /branches/dev/samtools/bamtk.c
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5711 M /branches/dev/samtools/misc/maq2sam.c
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5712
|
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|
5713 * samtools-0.1.0-50
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5714 * format change to meet the latest specification
|
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5715
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|
5716 ------------------------------------------------------------------------
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5717 r28 | lh3lh3 | 2008-12-04 11:09:21 -0500 (Thu, 04 Dec 2008) | 3 lines
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5718 Changed paths:
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|
5719 M /branches/dev/samtools/bam_maqcns.c
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5720 M /branches/dev/samtools/misc/maq2sam.c
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5721
|
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|
5722 * minor change in maqcns: special care when n==0
|
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|
5723 * change maq2sam to meet the latest specification
|
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5724
|
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|
5725 ------------------------------------------------------------------------
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|
5726 r27 | lh3lh3 | 2008-12-04 10:55:44 -0500 (Thu, 04 Dec 2008) | 2 lines
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5727 Changed paths:
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5728 M /branches/dev/samtools/razf.c
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5729 M /branches/dev/samtools/razf.h
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5730
|
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|
5731 considerable code clean up in razf
|
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5732
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|
5733 ------------------------------------------------------------------------
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|
5734 r26 | lh3lh3 | 2008-12-04 10:08:18 -0500 (Thu, 04 Dec 2008) | 2 lines
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5735 Changed paths:
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|
5736 M /branches/dev/samtools/ChangeLog
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|
5737 M /branches/dev/samtools/Makefile
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|
5738 M /branches/dev/samtools/faidx.c
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5739
|
|
|
5740 make RAZF optional in faidx.c
|
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5741
|
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|
5742 ------------------------------------------------------------------------
|
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|
5743 r25 | lh3lh3 | 2008-12-01 10:27:22 -0500 (Mon, 01 Dec 2008) | 3 lines
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|
5744 Changed paths:
|
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|
5745 M /branches/dev/samtools/Makefile
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|
5746 M /branches/dev/samtools/bam.h
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|
5747 M /branches/dev/samtools/bam_aux.c
|
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|
5748 M /branches/dev/samtools/bamtk.c
|
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|
5749 M /branches/dev/samtools/samtools.1
|
|
|
5750
|
|
|
5751 * samtools-0.1.0-49
|
|
|
5752 * added routines for retrieving aux data, NOT TESTED YET!
|
|
|
5753
|
|
|
5754 ------------------------------------------------------------------------
|
|
|
5755 r24 | lh3lh3 | 2008-12-01 09:29:43 -0500 (Mon, 01 Dec 2008) | 5 lines
|
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|
5756 Changed paths:
|
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|
5757 M /branches/dev/samtools/bam.c
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|
5758 M /branches/dev/samtools/bam_import.c
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|
5759 M /branches/dev/samtools/bam_maqcns.c
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|
5760 M /branches/dev/samtools/bamtk.c
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5761 M /branches/dev/samtools/bgzf.c
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|
5762 M /branches/dev/samtools/samtools.1
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|
5763
|
|
|
5764 * samtools-0.1.0-48
|
|
|
5765 * bgzf: fixed a potential integer overflow on 32-it machines
|
|
|
5766 * maqcns: set the minimum combined quality as 0
|
|
|
5767 * supporting hex strings
|
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|
5768
|
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|
5769 ------------------------------------------------------------------------
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|
5770 r23 | lh3lh3 | 2008-11-27 12:14:37 -0500 (Thu, 27 Nov 2008) | 3 lines
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5771 Changed paths:
|
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|
5772 M /branches/dev/samtools/bam_maqcns.c
|
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|
5773 M /branches/dev/samtools/bamtk.c
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|
5774
|
|
|
5775 * samtools-0.1.0-47
|
|
|
5776 * fixed the bug in maqcns
|
|
|
5777
|
|
|
5778 ------------------------------------------------------------------------
|
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|
5779 r22 | lh3lh3 | 2008-11-27 12:08:11 -0500 (Thu, 27 Nov 2008) | 3 lines
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5780 Changed paths:
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|
5781 M /branches/dev/samtools/Makefile
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5782 M /branches/dev/samtools/bam.h
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5783 A /branches/dev/samtools/bam_maqcns.c
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5784 A /branches/dev/samtools/bam_maqcns.h
|
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|
5785 M /branches/dev/samtools/bam_tview.c
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5786 M /branches/dev/samtools/bamtk.c
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|
5787 A /branches/dev/samtools/glf.h
|
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5788
|
|
|
5789 * samtools-0.1.0-46
|
|
|
5790 * add MAQ consensus caller, currently BUGGY!
|
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|
5791
|
|
|
5792 ------------------------------------------------------------------------
|
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|
5793 r21 | lh3lh3 | 2008-11-27 08:51:28 -0500 (Thu, 27 Nov 2008) | 4 lines
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5794 Changed paths:
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|
5795 M /branches/dev/samtools/bam_pileup.c
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5796 M /branches/dev/samtools/bam_tview.c
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|
5797 M /branches/dev/samtools/bamtk.c
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|
5798
|
|
|
5799 * samtools-0.1.0-45
|
|
|
5800 * tview: display padded alignment (but not P operation)
|
|
|
5801 * better coordinates and reference sequence
|
|
|
5802
|
|
|
5803 ------------------------------------------------------------------------
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|
5804 r19 | lh3lh3 | 2008-11-27 04:26:05 -0500 (Thu, 27 Nov 2008) | 2 lines
|
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|
5805 Changed paths:
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|
5806 A /branches/dev/samtools/ChangeLog
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5807
|
|
|
5808 new ChangeLog
|
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|
5809
|
|
|
5810 ------------------------------------------------------------------------
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5811 r18 | lh3lh3 | 2008-11-27 04:24:45 -0500 (Thu, 27 Nov 2008) | 3 lines
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|
5812 Changed paths:
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|
5813 D /branches/dev/samtools/ChangeLog
|
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|
5814 A /branches/dev/samtools/ChangeLog.old (from /branches/dev/samtools/ChangeLog:6)
|
|
|
5815
|
|
|
5816 Rename ChangeLog to ChangeLog.old. This old ChangeLog is generated from
|
|
|
5817 the log of my personal SVN repository.
|
|
|
5818
|
|
|
5819 ------------------------------------------------------------------------
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|
5820 r17 | lh3lh3 | 2008-11-27 04:22:55 -0500 (Thu, 27 Nov 2008) | 6 lines
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|
5821 Changed paths:
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|
5822 M /branches/dev/samtools/Makefile
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5823 M /branches/dev/samtools/bamtk.c
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|
5824 M /branches/dev/samtools/bgzf.c
|
|
|
5825
|
|
|
5826 * samtools-0.1.0-44
|
|
|
5827 * declare fseeko and ftello as some Linux may not do this by default and
|
|
|
5828 missing these declarations will make bgzf buggy
|
|
|
5829 * get rid of some harmless warings
|
|
|
5830 * use BGZF by default, now
|
|
|
5831
|
|
|
5832 ------------------------------------------------------------------------
|
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|
5833 r16 | lh3lh3 | 2008-11-26 16:19:11 -0500 (Wed, 26 Nov 2008) | 4 lines
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5834 Changed paths:
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|
5835 M /branches/dev/samtools/bam_index.c
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5836 M /branches/dev/samtools/bamtk.c
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|
5837 M /branches/dev/samtools/razf.c
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|
|
5838
|
|
|
5839 * samtools-0.1.0-43
|
|
|
5840 * fixed a bug in razf_read()
|
|
|
5841 * give more warnings when the file is truncated (or due to bugs in I/O library)
|
|
|
5842
|
|
|
5843 ------------------------------------------------------------------------
|
|
|
5844 r15 | lh3lh3 | 2008-11-26 15:41:39 -0500 (Wed, 26 Nov 2008) | 2 lines
|
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|
5845 Changed paths:
|
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|
5846 M /branches/dev/samtools/bgzf.c
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|
|
5847
|
|
|
5848 fixed a bug in bgzf.c at the end of the file
|
|
|
5849
|
|
|
5850 ------------------------------------------------------------------------
|
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|
5851 r14 | lh3lh3 | 2008-11-26 12:05:18 -0500 (Wed, 26 Nov 2008) | 4 lines
|
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|
5852 Changed paths:
|
|
|
5853 M /branches/dev/samtools/bamtk.c
|
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|
5854
|
|
|
5855 * samtools-0.1.0-42
|
|
|
5856 * a lot happened to RAZF, although samtools itself is untouched. Better
|
|
|
5857 also update the version number anyway to avoid confusion
|
|
|
5858
|
|
|
5859 ------------------------------------------------------------------------
|
|
|
5860 r13 | lh3lh3 | 2008-11-26 12:03:48 -0500 (Wed, 26 Nov 2008) | 2 lines
|
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|
5861 Changed paths:
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|
5862 M /branches/dev/samtools/razf.c
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|
5863
|
|
|
5864 a change from Jue, but I think it should not matter
|
|
|
5865
|
|
|
5866 ------------------------------------------------------------------------
|
|
|
5867 r12 | lh3lh3 | 2008-11-26 11:48:14 -0500 (Wed, 26 Nov 2008) | 3 lines
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|
5868 Changed paths:
|
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|
5869 M /branches/dev/samtools/razf.c
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|
5870
|
|
|
5871 fixed a potential bug in razf. However, it seems still buggy, just
|
|
|
5872 rarely happens, very rarely.
|
|
|
5873
|
|
|
5874 ------------------------------------------------------------------------
|
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|
5875 r11 | lh3lh3 | 2008-11-26 09:02:56 -0500 (Wed, 26 Nov 2008) | 2 lines
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|
5876 Changed paths:
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|
5877 M /branches/dev/samtools/razf.c
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|
5878
|
|
|
5879 fixed a bug in razf, with the help of Jue
|
|
|
5880
|
|
|
5881 ------------------------------------------------------------------------
|
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|
5882 r10 | lh3lh3 | 2008-11-26 06:55:32 -0500 (Wed, 26 Nov 2008) | 2 lines
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|
5883 Changed paths:
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|
5884 M /branches/dev/samtools/bam_index.c
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|
5885
|
|
|
5886 remove a comment
|
|
|
5887
|
|
|
5888 ------------------------------------------------------------------------
|
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|
5889 r9 | lh3lh3 | 2008-11-26 06:37:05 -0500 (Wed, 26 Nov 2008) | 2 lines
|
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|
5890 Changed paths:
|
|
|
5891 M /branches/dev/samtools/Makefile
|
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|
5892 M /branches/dev/samtools/bam.h
|
|
|
5893 M /branches/dev/samtools/razf.c
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|
|
5894 M /branches/dev/samtools/razf.h
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|
5895
|
|
|
5896 * Jue has updated razf to realize Bob's scheme
|
|
|
5897
|
|
|
5898 ------------------------------------------------------------------------
|
|
|
5899 r7 | lh3lh3 | 2008-11-25 15:37:37 -0500 (Tue, 25 Nov 2008) | 2 lines
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5900 Changed paths:
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|
5901 A /branches/dev/samtools/samtools.1
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5902
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|
5903 the manual page
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|
5904
|
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|
5905 ------------------------------------------------------------------------
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5906 r6 | lh3lh3 | 2008-11-25 15:37:16 -0500 (Tue, 25 Nov 2008) | 3 lines
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5907 Changed paths:
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|
5908 A /branches/dev/samtools/ChangeLog
|
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|
5909 A /branches/dev/samtools/Makefile
|
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|
5910 A /branches/dev/samtools/bam.c
|
|
|
5911 A /branches/dev/samtools/bam.h
|
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|
5912 A /branches/dev/samtools/bam_aux.c
|
|
|
5913 A /branches/dev/samtools/bam_endian.h
|
|
|
5914 A /branches/dev/samtools/bam_import.c
|
|
|
5915 A /branches/dev/samtools/bam_index.c
|
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|
5916 A /branches/dev/samtools/bam_lpileup.c
|
|
|
5917 A /branches/dev/samtools/bam_pileup.c
|
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|
5918 A /branches/dev/samtools/bam_sort.c
|
|
|
5919 A /branches/dev/samtools/bam_tview.c
|
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|
5920 A /branches/dev/samtools/bamtk.c
|
|
|
5921 A /branches/dev/samtools/bgzf.c
|
|
|
5922 A /branches/dev/samtools/bgzf.h
|
|
|
5923 A /branches/dev/samtools/bgzip.c
|
|
|
5924 A /branches/dev/samtools/faidx.c
|
|
|
5925 A /branches/dev/samtools/faidx.h
|
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|
5926 A /branches/dev/samtools/khash.h
|
|
|
5927 A /branches/dev/samtools/ksort.h
|
|
|
5928 A /branches/dev/samtools/kstream.h
|
|
|
5929 A /branches/dev/samtools/misc
|
|
|
5930 A /branches/dev/samtools/misc/Makefile
|
|
|
5931 A /branches/dev/samtools/misc/all2sam.pl
|
|
|
5932 A /branches/dev/samtools/misc/maq2sam.c
|
|
|
5933 A /branches/dev/samtools/razf.c
|
|
|
5934 A /branches/dev/samtools/razf.h
|
|
|
5935 A /branches/dev/samtools/razip.c
|
|
|
5936 A /branches/dev/samtools/zutil.h
|
|
|
5937
|
|
|
5938 The initial version of samtools, replicated from my local SVN repository.
|
|
|
5939 The current version is: 0.1.0-42. All future development will happen here.
|
|
|
5940
|
|
|
5941 ------------------------------------------------------------------------
|
|
|
5942 r5 | lh3lh3 | 2008-11-25 15:30:49 -0500 (Tue, 25 Nov 2008) | 2 lines
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5943 Changed paths:
|
|
|
5944 A /branches/dev/samtools
|
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5945
|
|
|
5946 samtools (C version)
|
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|
5947
|
|
|
5948 ------------------------------------------------------------------------
|
