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1 ------------------------------------------------------------------------
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2 r451 | lh3lh3 | 2009-09-02 10:44:48 +0100 (Wed, 02 Sep 2009) | 4 lines
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3 Changed paths:
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4 M /trunk/samtools/bam_md.c
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5 M /trunk/samtools/bam_rmdup.c
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6 M /trunk/samtools/bam_rmdupse.c
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7 M /trunk/samtools/bam_sort.c
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8 M /trunk/samtools/bamtk.c
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9 M /trunk/samtools/samtools.1
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10
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11 * samtools-0.1.5-34 (r451)
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12 * applied the patch by John
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13 * improved the help message a little bit
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14
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15 ------------------------------------------------------------------------
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16 r450 | lh3lh3 | 2009-09-02 09:55:55 +0100 (Wed, 02 Sep 2009) | 3 lines
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17 Changed paths:
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18 M /trunk/samtools/bam_color.c
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19 M /trunk/samtools/bamtk.c
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20
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21 * samtools-0.1.5-33 (r450)
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22 * fixed a bug in bam_color.c (on behalf of Nils Homer)
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23
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24 ------------------------------------------------------------------------
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25 r449 | lh3lh3 | 2009-08-29 20:36:41 +0100 (Sat, 29 Aug 2009) | 4 lines
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26 Changed paths:
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27 M /trunk/samtools/bam_import.c
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28 M /trunk/samtools/bam_md.c
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29 M /trunk/samtools/bamtk.c
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30 M /trunk/samtools/misc/samtools.pl
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31
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32 * samtools-0.1.5-32 (r449)
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33 * fillmd: fixed a bug in modifying MD/NM tags
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34 * in import, give a warning if the read is aligned but there is no CIGAR.
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35
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36 ------------------------------------------------------------------------
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37 r448 | lh3lh3 | 2009-08-19 09:44:28 +0100 (Wed, 19 Aug 2009) | 3 lines
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38 Changed paths:
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39 M /trunk/samtools/ChangeLog
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40 M /trunk/samtools/bam_pileup.c
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41 M /trunk/samtools/bamtk.c
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42 M /trunk/samtools/misc/wgsim_eval.pl
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43
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44 * samtools-0.1.5-31 (r448)
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45 * fixed an issue when the last CIGAR is I or D
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46
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47 ------------------------------------------------------------------------
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48 r447 | lh3lh3 | 2009-08-17 09:34:57 +0100 (Mon, 17 Aug 2009) | 3 lines
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49 Changed paths:
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50 M /trunk/samtools/bam_aux.c
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51 M /trunk/samtools/bamtk.c
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52
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53 * samtools-0.1.5-30 (r447)
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54 * fixed a bug in bam_aux_get(): 'A' is not checked
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55
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56 ------------------------------------------------------------------------
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57 r446 | lh3lh3 | 2009-08-17 09:33:17 +0100 (Mon, 17 Aug 2009) | 2 lines
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58 Changed paths:
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59 M /trunk/samtools/bam_aux.c
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60 M /trunk/samtools/bamtk.c
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61
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62 *
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63
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64 ------------------------------------------------------------------------
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65 r444 | lh3lh3 | 2009-08-11 10:02:36 +0100 (Tue, 11 Aug 2009) | 3 lines
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66 Changed paths:
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67 M /trunk/samtools/bam_sort.c
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68 M /trunk/samtools/bamtk.c
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69
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70 * samtools-0.1.5-28 (r444)
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71 * bug in "merge -n"
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72
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73 ------------------------------------------------------------------------
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74 r443 | lh3lh3 | 2009-08-11 09:29:11 +0100 (Tue, 11 Aug 2009) | 4 lines
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75 Changed paths:
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76 M /trunk/samtools/bam.c
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77 M /trunk/samtools/bam_import.c
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78 M /trunk/samtools/bamtk.c
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79
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80 * samtools-0.1.5-27 (r443)
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81 * SEQ and QUAL can be "*"
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82 * parse CIGAR "=" and "X" as "M"
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83
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84 ------------------------------------------------------------------------
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85 r442 | lh3lh3 | 2009-08-07 21:56:38 +0100 (Fri, 07 Aug 2009) | 4 lines
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86 Changed paths:
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87 M /trunk/samtools/bam_pileup.c
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88 M /trunk/samtools/bamtk.c
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89 M /trunk/samtools/misc/md5.c
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90 M /trunk/samtools/misc/md5.h
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91 M /trunk/samtools/misc/md5fa.c
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92
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93 * samtools-0.1.5-26 (r442)
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94 * replace RSA Inc md5.* with ones under permissive lincense
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95 * fixed a bug in detecting unsorted bam in pileup
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96
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97 ------------------------------------------------------------------------
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98 r441 | bhandsaker | 2009-08-05 14:41:28 +0100 (Wed, 05 Aug 2009) | 2 lines
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99 Changed paths:
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100 M /trunk/samtools/bgzf.c
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101 M /trunk/samtools/bgzf.h
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102 M /trunk/samtools/bgzip.c
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103
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104 Change copyright notices now that MIT has approved open source distribution.
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105
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106 ------------------------------------------------------------------------
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107 r440 | lh3lh3 | 2009-08-05 10:44:24 +0100 (Wed, 05 Aug 2009) | 3 lines
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108 Changed paths:
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109 M /trunk/samtools/bam_stat.c
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110 M /trunk/samtools/bamtk.c
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111
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112 * samtools-0.1.5-25 (r436)
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113 * in flagstats, do not report singletons if both ends are unmapped
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114
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115 ------------------------------------------------------------------------
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116 r439 | lh3lh3 | 2009-08-04 22:16:51 +0100 (Tue, 04 Aug 2009) | 2 lines
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117 Changed paths:
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118 M /trunk/samtools/misc/maq2sam.c
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119
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120 fixed a SERIOUS bug in setting 0x20 flag
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121
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122 ------------------------------------------------------------------------
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123 r438 | lh3lh3 | 2009-08-04 21:50:43 +0100 (Tue, 04 Aug 2009) | 2 lines
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124 Changed paths:
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125 M /trunk/samtools/misc/samtools.pl
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126
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127 fixed two minor bugs (suggested by Tim M Storm)
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128
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129 ------------------------------------------------------------------------
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130 r437 | lh3lh3 | 2009-08-04 09:13:24 +0100 (Tue, 04 Aug 2009) | 3 lines
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131 Changed paths:
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132 M /trunk/samtools/bamtk.c
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133 M /trunk/samtools/misc/samtools.pl
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134 M /trunk/samtools/sam_view.c
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135
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136 * samtools-0.1.5-24 (r435)
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137 * fixed a typo
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138
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139 ------------------------------------------------------------------------
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140 r434 | lh3lh3 | 2009-08-03 10:40:42 +0100 (Mon, 03 Aug 2009) | 3 lines
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141 Changed paths:
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142 M /trunk/samtools/bam_tview.c
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143 M /trunk/samtools/bamtk.c
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144
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145 * samtools-0.1.5-23 (r434)
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146 * in tview, press 'r' to show read names rather than sequences
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147
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148 ------------------------------------------------------------------------
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149 r433 | lh3lh3 | 2009-08-02 19:13:35 +0100 (Sun, 02 Aug 2009) | 3 lines
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150 Changed paths:
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151 M /trunk/samtools/knetfile.c
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152
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153 * tried to fixed the buggy FTP random access in Windows. FAILED.
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154 * anyway, MinGW seems to have problem with "%lld".
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155
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156 ------------------------------------------------------------------------
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157 r432 | lh3lh3 | 2009-08-02 00:32:07 +0100 (Sun, 02 Aug 2009) | 5 lines
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158 Changed paths:
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159 M /trunk/samtools/Makefile.mingw
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160 M /trunk/samtools/bamtk.c
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161 M /trunk/samtools/faidx.c
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162 M /trunk/samtools/razf.c
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163 A /trunk/samtools/win32/libcurses.a
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164 A /trunk/samtools/win32/xcurses.h
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165
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166 * samtools-0.1.5-22 (r432)
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167 * faidx: fixed compitability issue with _WIN32
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168 * razf: fixed potential compitability issue with _WIN32
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169 * PDCurses support in Windows
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170
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171 ------------------------------------------------------------------------
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172 r431 | lh3lh3 | 2009-08-01 23:34:54 +0100 (Sat, 01 Aug 2009) | 2 lines
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173 Changed paths:
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174 M /trunk/samtools/win32/libz.a
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175
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176 replace the GnuWin32 version of libz.a with my own build with MinGW.
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177
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178 ------------------------------------------------------------------------
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179 r430 | lh3lh3 | 2009-08-01 23:21:07 +0100 (Sat, 01 Aug 2009) | 2 lines
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180 Changed paths:
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181 M /trunk/samtools/knetfile.c
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182
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183 add comments
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184
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185 ------------------------------------------------------------------------
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186 r429 | lh3lh3 | 2009-08-01 22:41:19 +0100 (Sat, 01 Aug 2009) | 3 lines
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187 Changed paths:
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188 M /trunk/samtools/Makefile.mingw
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189 M /trunk/samtools/bamtk.c
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190 M /trunk/samtools/knetfile.c
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191 M /trunk/samtools/knetfile.h
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192
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193 * samtools-0.1.5-21 (r428)
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194 * knetfile.c is now compatible with mingw-winsock
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195
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196 ------------------------------------------------------------------------
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197 r428 | lh3lh3 | 2009-08-01 00:39:07 +0100 (Sat, 01 Aug 2009) | 2 lines
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198 Changed paths:
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199 M /trunk/samtools/Makefile.mingw
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200
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201 simplify MinGW Makefile
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202
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203 ------------------------------------------------------------------------
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204 r427 | lh3lh3 | 2009-08-01 00:30:54 +0100 (Sat, 01 Aug 2009) | 5 lines
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205 Changed paths:
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206 A /trunk/samtools/Makefile.mingw
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207 M /trunk/samtools/bam_import.c
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208 M /trunk/samtools/bamtk.c
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209 A /trunk/samtools/win32
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210 A /trunk/samtools/win32/libz.a
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211 A /trunk/samtools/win32/zconf.h
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212 A /trunk/samtools/win32/zlib.h
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213
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214 * samtools-0.1.5-20 (r427)
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215 * MinGW support. At least SAM<->BAM conversion is working. Other
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216 functionality are not tested at the moment.
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217 * zlib headers and Windows version of libz.a are included in win32/
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218
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219 ------------------------------------------------------------------------
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220 r426 | lh3lh3 | 2009-07-31 23:32:09 +0100 (Fri, 31 Jul 2009) | 3 lines
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221 Changed paths:
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222 M /trunk/samtools/bamtk.c
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223 M /trunk/samtools/sam_view.c
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224
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225 * samtools-0.1.5-19 (r426)
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226 * fixed a bug caused by recent modifications. Sorry.
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227
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228 ------------------------------------------------------------------------
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229 r425 | lh3lh3 | 2009-07-31 23:23:51 +0100 (Fri, 31 Jul 2009) | 2 lines
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230 Changed paths:
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231 M /trunk/samtools/bgzf.c
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232
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233 compatible with Windows binary files
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234
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235 ------------------------------------------------------------------------
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236 r424 | lh3lh3 | 2009-07-31 10:19:59 +0100 (Fri, 31 Jul 2009) | 5 lines
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237 Changed paths:
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238 M /trunk/samtools/bam_maqcns.c
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239 M /trunk/samtools/bam_maqcns.h
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240 M /trunk/samtools/bam_plcmd.c
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241 M /trunk/samtools/bam_tview.c
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242 M /trunk/samtools/bamtk.c
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243 M /trunk/samtools/misc/samtools.pl
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244
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245 * samtools-0.1.5-18 (r423)
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246 * output additional information in pileup indel lines, for the purepose
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247 of debugging at the moment
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248 * in tview, optionally allow to treat reference skip as deletion
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249
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250 ------------------------------------------------------------------------
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251 r423 | lh3lh3 | 2009-07-30 22:00:36 +0100 (Thu, 30 Jul 2009) | 2 lines
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252 Changed paths:
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253 A /trunk/samtools/misc/psl2sam.pl
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254
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255 convert BLAT psl to SAM.
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256
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257 ------------------------------------------------------------------------
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258 r422 | lh3lh3 | 2009-07-30 11:24:39 +0100 (Thu, 30 Jul 2009) | 6 lines
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259 Changed paths:
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260 M /trunk/samtools/ChangeLog
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261 M /trunk/samtools/bam.c
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262 M /trunk/samtools/bamtk.c
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263 M /trunk/samtools/bgzf.c
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264 M /trunk/samtools/bgzf.h
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265 M /trunk/samtools/knetfile.c
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266 M /trunk/samtools/sam.c
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267 M /trunk/samtools/sam_view.c
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268
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269 * samtools-0.1.5-17 (r422)
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270 * fixed a but in knetfile.c when seek type is not SEEK_SET
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271 * write an empty BGZF block to every BGZF file
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272 * check BGZF EOF marker in bam_header_read()
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273 * update ChangeLog
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274
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275 ------------------------------------------------------------------------
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276 r421 | lh3lh3 | 2009-07-30 10:03:39 +0100 (Thu, 30 Jul 2009) | 3 lines
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277 Changed paths:
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278 M /trunk/samtools/bam_import.c
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279 M /trunk/samtools/bam_plcmd.c
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280 M /trunk/samtools/bamtk.c
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281 M /trunk/samtools/misc/samtools.pl
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282 M /trunk/samtools/sam.c
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283 M /trunk/samtools/sam.h
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284 M /trunk/samtools/sam_view.c
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285
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286 * samtools-0.1.5-16 (r421)
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287 * in view and pileup, load header from FASTA index if the input is SAM.
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288
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289 ------------------------------------------------------------------------
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290 r420 | lh3lh3 | 2009-07-29 09:18:55 +0100 (Wed, 29 Jul 2009) | 2 lines
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291 Changed paths:
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292 M /trunk/samtools/misc/maq2sam.c
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293
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294 do not set "read 1" if reads are not mapped in the PE mode of maq
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295
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296 ------------------------------------------------------------------------
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297 r419 | lh3lh3 | 2009-07-28 09:52:33 +0100 (Tue, 28 Jul 2009) | 5 lines
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298 Changed paths:
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299 M /trunk/samtools/bam_import.c
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300 M /trunk/samtools/bamtk.c
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301 M /trunk/samtools/misc/samtools.pl
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302 M /trunk/samtools/misc/wgsim_eval.pl
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303
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304 * samtools-0.1.5-15 (r419)
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305 * in sam_open(), return NULL when the file cannot be opened.
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306 * make wgsim_eval.pl more robust to imperfect SAM
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307 * add "unique" command to samtools.pl
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308
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309 ------------------------------------------------------------------------
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310 r418 | lh3lh3 | 2009-07-24 14:04:19 +0100 (Fri, 24 Jul 2009) | 2 lines
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311 Changed paths:
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312 M /trunk/samtools/misc/wgsim_eval.pl
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313
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314 skip @header lines in SAM
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315
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316 ------------------------------------------------------------------------
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317 r417 | lh3lh3 | 2009-07-24 12:42:38 +0100 (Fri, 24 Jul 2009) | 3 lines
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318 Changed paths:
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319 M /trunk/samtools/bamtk.c
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320 M /trunk/samtools/sam_view.c
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321
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322 * samtools-0.1.5-14 (r417)
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323 * more help in "samtools view" due to the recent changes.
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324
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325 ------------------------------------------------------------------------
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326 r416 | lh3lh3 | 2009-07-24 12:34:30 +0100 (Fri, 24 Jul 2009) | 3 lines
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327 Changed paths:
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328 M /trunk/samtools/bam.c
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329 M /trunk/samtools/bam.h
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330 M /trunk/samtools/bam_import.c
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331 M /trunk/samtools/bamtk.c
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332 M /trunk/samtools/sam.c
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333 M /trunk/samtools/sam.h
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334 M /trunk/samtools/sam_view.c
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335
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336 * samtools-0.1.5-17 (r416)
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337 * support import/export SAM with string tags
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338
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339 ------------------------------------------------------------------------
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340 r415 | lh3lh3 | 2009-07-24 11:39:26 +0100 (Fri, 24 Jul 2009) | 3 lines
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341 Changed paths:
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342 M /trunk/samtools/bam.c
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343 M /trunk/samtools/bam.h
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344 M /trunk/samtools/bam_import.c
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345 M /trunk/samtools/bamtk.c
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346 M /trunk/samtools/sam.c
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347 M /trunk/samtools/sam.h
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348 M /trunk/samtools/sam_view.c
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349
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350 * samtools-0.1.5-12 (r415)
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351 * FLAG now can be in HEX
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352
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353 ------------------------------------------------------------------------
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354 r414 | lh3lh3 | 2009-07-22 22:03:49 +0100 (Wed, 22 Jul 2009) | 2 lines
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355 Changed paths:
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356 M /trunk/samtools/kstring.h
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357
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358 fixed a compiling error (thank Ken for fixing it)
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359
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360 ------------------------------------------------------------------------
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361 r412 | lh3lh3 | 2009-07-21 22:19:40 +0100 (Tue, 21 Jul 2009) | 2 lines
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362 Changed paths:
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363 M /trunk/samtools/kstring.c
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364 M /trunk/samtools/kstring.h
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365
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366 Implemented Boyer-Moore search in the kstring library.
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367
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368 ------------------------------------------------------------------------
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369 r409 | lh3lh3 | 2009-07-17 17:10:20 +0100 (Fri, 17 Jul 2009) | 2 lines
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370 Changed paths:
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371 M /trunk/samtools/bam_index.c
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372
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373 do not include knetfile.h when _USE_KNETFILE is not defined
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374
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375 ------------------------------------------------------------------------
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376 r408 | lh3lh3 | 2009-07-17 15:29:21 +0100 (Fri, 17 Jul 2009) | 5 lines
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377 Changed paths:
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378 M /trunk/samtools/bam_md.c
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379 M /trunk/samtools/bam_tview.c
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380 M /trunk/samtools/bamtk.c
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381 M /trunk/samtools/bgzf.c
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382
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383 * samtools-0.1.5-11 (r408)
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384 * force to overwirte existing MD if it is different from the one calculated
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385 from fillmd.
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386 * bgzf.c: improved the compatibility with Windows headers
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387
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388 ------------------------------------------------------------------------
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389 r407 | lh3lh3 | 2009-07-17 14:46:56 +0100 (Fri, 17 Jul 2009) | 5 lines
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390 Changed paths:
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391 M /trunk/samtools/bam.h
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392 M /trunk/samtools/bam_aux.c
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393 M /trunk/samtools/bam_md.c
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394 M /trunk/samtools/bamtk.c
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395 M /trunk/samtools/sam.h
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396
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397 * samtools-0.1.5-10 (r407)
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398 * implemented bam_aux_del() to remove a tag
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399 * fillmd: generate the NM tag
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400 * fillmd: cmd interface improvement
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401
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402 ------------------------------------------------------------------------
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403 r406 | lh3lh3 | 2009-07-16 23:30:40 +0100 (Thu, 16 Jul 2009) | 2 lines
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404 Changed paths:
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405 M /trunk/samtools/Makefile
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406
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407 Sorry. The old Makefile is for PDCurses...
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408
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409 ------------------------------------------------------------------------
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410 r405 | lh3lh3 | 2009-07-16 23:30:11 +0100 (Thu, 16 Jul 2009) | 3 lines
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411 Changed paths:
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412 M /trunk/samtools/Makefile
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413 M /trunk/samtools/bam_tview.c
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414 M /trunk/samtools/bamtk.c
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415
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416 * samtools-0.1.5-9 (r405)
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417 * improved the compatibility with PDCurses a little bit
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418
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419 ------------------------------------------------------------------------
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420 r404 | lh3lh3 | 2009-07-16 23:23:52 +0100 (Thu, 16 Jul 2009) | 3 lines
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421 Changed paths:
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422 M /trunk/samtools/Makefile
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423 M /trunk/samtools/bam_tview.c
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424 M /trunk/samtools/bamtk.c
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425
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426 * samtools-0.1.5-8 (r404)
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427 * compatible with PDCurses
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428
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429 ------------------------------------------------------------------------
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430 r403 | lh3lh3 | 2009-07-16 22:39:39 +0100 (Thu, 16 Jul 2009) | 3 lines
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431 Changed paths:
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432 M /trunk/samtools/bamtk.c
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433 M /trunk/samtools/kseq.h
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434
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435 * samtools-0.1.5-7 (r403)
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436 * fixed a bug in kseq.h for binary files (text files are fine)
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437
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438 ------------------------------------------------------------------------
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439 r402 | lh3lh3 | 2009-07-16 11:49:53 +0100 (Thu, 16 Jul 2009) | 4 lines
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440 Changed paths:
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441 M /trunk/samtools/bam_import.c
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442 M /trunk/samtools/bam_index.c
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443 M /trunk/samtools/bamtk.c
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444 M /trunk/samtools/bgzf.c
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445
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446 * samtools-0.1.5-6 (r402)
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447 * fixed compiling error when "-D_USE_NETFILE" is not applied
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448 * improve portability to MinGW
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449
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450 ------------------------------------------------------------------------
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451 r398 | lh3lh3 | 2009-07-13 10:21:36 +0100 (Mon, 13 Jul 2009) | 3 lines
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452 Changed paths:
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453 A /trunk/bam-lite/bam.h (from /trunk/samtools/bam.h:395)
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454 A /trunk/bam-lite/bam_lite.c (from /trunk/samtools/bam_lite.c:395)
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455 D /trunk/samtools/bam_lite.c
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456
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457 * move bam_lite.c to bam-lite
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458 * copy bam.h to bam-lite
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459
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460 ------------------------------------------------------------------------
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461 r395 | lh3lh3 | 2009-07-13 10:12:57 +0100 (Mon, 13 Jul 2009) | 3 lines
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462 Changed paths:
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463 M /trunk/samtools/bam.h
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464 M /trunk/samtools/bam_lite.c
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465 M /trunk/samtools/bam_lpileup.c
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466 M /trunk/samtools/bam_pileup.c
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467 M /trunk/samtools/bamtk.c
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468
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469 * samtools-0.1.5-5 (r395)
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470 * added bam_pileup_file() and removed bam_lpileup_file()
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471
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472 ------------------------------------------------------------------------
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473 r394 | lh3lh3 | 2009-07-13 00:35:10 +0100 (Mon, 13 Jul 2009) | 3 lines
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474 Changed paths:
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475 M /trunk/samtools/bamtk.c
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476 M /trunk/samtools/knetfile.c
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477 M /trunk/samtools/knetfile.h
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478
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479 * samtools-0.1.5-4 (r394)
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480 * http_proxy support in knetfile library (check http_proxy ENV)
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481
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482 ------------------------------------------------------------------------
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483 r393 | lh3lh3 | 2009-07-12 23:57:07 +0100 (Sun, 12 Jul 2009) | 5 lines
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484 Changed paths:
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485 M /trunk/samtools/bam_index.c
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486 M /trunk/samtools/bam_tview.c
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487 M /trunk/samtools/bamtk.c
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488 M /trunk/samtools/knetfile.c
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489 M /trunk/samtools/knetfile.h
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490
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491 * samtools-0.1.5-3 (r393)
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492 * knetfile now supports HTTP (no proxy at the moment)
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493 * fixed a potential issue in knetfile on opening ordinary file, although I have
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494 not seen the sideeffect so far.
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495
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496 ------------------------------------------------------------------------
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497 r392 | lh3lh3 | 2009-07-12 18:50:55 +0100 (Sun, 12 Jul 2009) | 2 lines
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498 Changed paths:
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499 M /trunk/samtools/samtools.1
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500
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501 Remove the warning in tview
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502
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503 ------------------------------------------------------------------------
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504 r391 | lh3lh3 | 2009-07-12 18:42:43 +0100 (Sun, 12 Jul 2009) | 3 lines
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505 Changed paths:
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506 M /trunk/samtools/bam_tview.c
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507 M /trunk/samtools/bamtk.c
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508
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509 * samtools-0.1.5-2 (r391)
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510 * do not show a blank screen when no reads mapped
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511
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512 ------------------------------------------------------------------------
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513 r390 | lh3lh3 | 2009-07-09 14:01:42 +0100 (Thu, 09 Jul 2009) | 4 lines
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514 Changed paths:
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515 M /trunk/samtools/bam.h
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516 A /trunk/samtools/bam_lite.c
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517 M /trunk/samtools/bamtk.c
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518
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519 * samtools-0.1.5-1 (r390)
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520 * removed useless _IOLIB in bam.h. This should cause no change at all.
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521 * added bam_lite.c for light-weight BAM reading
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522
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523 ------------------------------------------------------------------------
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524 r385 | lh3lh3 | 2009-07-07 16:53:29 +0100 (Tue, 07 Jul 2009) | 2 lines
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525 Changed paths:
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526 M /trunk/samtools/bamtk.c
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527 M /trunk/samtools/knetfile.c
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528
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529 Release samtools-0.1.5c (fixed a bug in piping)
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530
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531 ------------------------------------------------------------------------
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532 r383 | lh3lh3 | 2009-07-07 11:39:55 +0100 (Tue, 07 Jul 2009) | 2 lines
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533 Changed paths:
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534 M /trunk/samtools/bamtk.c
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535 M /trunk/samtools/sam.c
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536
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537 Release samtools-0.1.5b (BUG! so embarrassing!)
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538
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539 ------------------------------------------------------------------------
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540 r381 | lh3lh3 | 2009-07-07 11:20:06 +0100 (Tue, 07 Jul 2009) | 2 lines
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541 Changed paths:
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542 M /trunk/samtools/Makefile
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543 M /trunk/samtools/bam.h
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544 M /trunk/samtools/bam_aux.c
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545 M /trunk/samtools/bamtk.c
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546
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547 Release samtools-0.1.5a (for compatibility with Bio::DB::Sam)
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548
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549 ------------------------------------------------------------------------
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550 r373 | lh3lh3 | 2009-07-07 10:26:57 +0100 (Tue, 07 Jul 2009) | 2 lines
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551 Changed paths:
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552 M /trunk/samtools/ChangeLog
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553 M /trunk/samtools/NEWS
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554 M /trunk/samtools/bamtk.c
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555 M /trunk/samtools/samtools.1
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556
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557 Release samtools-0.1.5
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558
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559 ------------------------------------------------------------------------
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560 r372 | lh3lh3 | 2009-07-07 09:49:27 +0100 (Tue, 07 Jul 2009) | 3 lines
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561 Changed paths:
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562 M /trunk/samtools/bamtk.c
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563 M /trunk/samtools/sam.c
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564
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565 * samtools-0.1.4-23 (r372)
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566 * keep header text if "view -t" is used (by Gerton)
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567
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568 ------------------------------------------------------------------------
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569 r371 | lh3lh3 | 2009-07-07 01:13:32 +0100 (Tue, 07 Jul 2009) | 2 lines
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570 Changed paths:
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571 M /trunk/samtools/samtools.1
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572
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573 update documentation
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574
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575 ------------------------------------------------------------------------
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576 r370 | bhandsaker | 2009-07-02 22:24:34 +0100 (Thu, 02 Jul 2009) | 2 lines
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577 Changed paths:
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578 M /trunk/samtools/Makefile
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579
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580 Introduced LIBPATH variable so this could be overridden to allow samtools to build correct at the Broad.
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581
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582 ------------------------------------------------------------------------
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583 r369 | lh3lh3 | 2009-07-02 13:36:53 +0100 (Thu, 02 Jul 2009) | 4 lines
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584 Changed paths:
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585 M /trunk/samtools/ChangeLog
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586 M /trunk/samtools/bam_aux.c
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587 M /trunk/samtools/bam_plcmd.c
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588 M /trunk/samtools/bamtk.c
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589
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590 * samtools-0.1.4-22 (r369)
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591 * in pileup, optionally print E2 and U2
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592 * remove the debugging code in bam_aux_get() (Drat!)
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593
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594 ------------------------------------------------------------------------
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595 r368 | lh3lh3 | 2009-07-02 11:32:26 +0100 (Thu, 02 Jul 2009) | 6 lines
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596 Changed paths:
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597 M /trunk/samtools/bam.c
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598 M /trunk/samtools/bam.h
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599 M /trunk/samtools/bam_aux.c
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600 M /trunk/samtools/bam_index.c
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601 M /trunk/samtools/bam_lpileup.c
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602 M /trunk/samtools/bam_md.c
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603 M /trunk/samtools/bam_pileup.c
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604 M /trunk/samtools/bam_rmdup.c
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605 M /trunk/samtools/bam_stat.c
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606 M /trunk/samtools/bam_tview.c
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607 M /trunk/samtools/bamtk.c
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608 M /trunk/samtools/faidx.c
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609 M /trunk/samtools/faidx.h
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610 M /trunk/samtools/glf.c
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611
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612 * samtools-0.1.4-21 (r368)
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613 * propagate errors rather than exit or complain assertion failure. Assertion
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614 should be only used for checking internal bugs, but not for external input
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615 inconsistency. I was just a bit lazy.
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616 * small memory leak may be present on failure, though
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617
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618 ------------------------------------------------------------------------
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619 r367 | lh3lh3 | 2009-06-30 16:18:42 +0100 (Tue, 30 Jun 2009) | 2 lines
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620 Changed paths:
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621 M /trunk/samtools/knetfile.c
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622
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623 reduce the chance of blocking in FTP connection
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624
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625 ------------------------------------------------------------------------
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626 r366 | lh3lh3 | 2009-06-30 15:35:21 +0100 (Tue, 30 Jun 2009) | 2 lines
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627 Changed paths:
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628 M /trunk/samtools/knetfile.c
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629
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630 minor changes to knetfile: invalid fd equals -1 rather than 0
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631
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632 ------------------------------------------------------------------------
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633 r365 | lh3lh3 | 2009-06-30 14:04:30 +0100 (Tue, 30 Jun 2009) | 3 lines
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634 Changed paths:
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635 M /trunk/samtools/bam_index.c
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636 M /trunk/samtools/bamtk.c
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637 M /trunk/samtools/knetfile.c
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638 M /trunk/samtools/knetfile.h
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639
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640 * samtools-0.1.4-20 (r365)
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641 * download the BAM index file if it is not found in the current working directory.
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642
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643 ------------------------------------------------------------------------
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644 r364 | lh3lh3 | 2009-06-30 12:39:07 +0100 (Tue, 30 Jun 2009) | 3 lines
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645 Changed paths:
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646 M /trunk/samtools/bamtk.c
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647 M /trunk/samtools/knetfile.c
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648
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649 * samtools-0.1.4-19 (r364)
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650 * knetfile: report error when the file is not present on FTP
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651
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652 ------------------------------------------------------------------------
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653 r363 | lh3lh3 | 2009-06-29 23:23:32 +0100 (Mon, 29 Jun 2009) | 4 lines
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654 Changed paths:
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655 M /trunk/samtools/bam_tview.c
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656 M /trunk/samtools/bamtk.c
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657 M /trunk/samtools/bgzf.c
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658 M /trunk/samtools/bgzf.h
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659 M /trunk/samtools/knetfile.c
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660 M /trunk/samtools/knetfile.h
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661
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662 * samtools-0.1.4-18 (r363)
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663 * knetfile: do not trigger network communication in FTP seek (lazy seek)
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664 * bgzf: cache recent blocks (disabled by default)
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665
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666 ------------------------------------------------------------------------
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667 r362 | lh3lh3 | 2009-06-25 21:04:34 +0100 (Thu, 25 Jun 2009) | 2 lines
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668 Changed paths:
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669 M /trunk/samtools/bgzf.c
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670
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671 write changelog
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672
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673 ------------------------------------------------------------------------
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674 r361 | lh3lh3 | 2009-06-25 21:03:10 +0100 (Thu, 25 Jun 2009) | 3 lines
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675 Changed paths:
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676 M /trunk/samtools/bam_index.c
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677 M /trunk/samtools/bamtk.c
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678
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679 * samtools-0.1.4-17 (r361)
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680 * if a file is given on FTP, search locally for the BAM index
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681
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682 ------------------------------------------------------------------------
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683 r360 | lh3lh3 | 2009-06-25 20:44:52 +0100 (Thu, 25 Jun 2009) | 5 lines
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684 Changed paths:
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685 M /trunk/samtools/Makefile
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686 M /trunk/samtools/bam_import.c
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687 M /trunk/samtools/bam_index.c
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688 M /trunk/samtools/bamtk.c
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689 M /trunk/samtools/bgzf.c
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690 M /trunk/samtools/bgzf.h
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691 M /trunk/samtools/knetfile.c
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692 M /trunk/samtools/knetfile.h
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693
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694 * samtools-0.1.4-16 (r360)
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695 * report more information in index when the input is not sorted
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696 * change the behaviour of knet_seek() such that it returns 0 on success
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697 * support knetfile library in BGZF
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698
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699 ------------------------------------------------------------------------
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700 r359 | lh3lh3 | 2009-06-25 17:10:55 +0100 (Thu, 25 Jun 2009) | 2 lines
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701 Changed paths:
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702 M /trunk/samtools/knetfile.c
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703 M /trunk/samtools/knetfile.h
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704
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705 fixed bugs in knetfile.*
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706
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707 ------------------------------------------------------------------------
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708 r358 | lh3lh3 | 2009-06-25 13:53:19 +0100 (Thu, 25 Jun 2009) | 2 lines
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709 Changed paths:
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710 A /trunk/samtools/knetfile.h
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711
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712 this is the header file
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713
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714 ------------------------------------------------------------------------
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715 r357 | lh3lh3 | 2009-06-25 13:52:03 +0100 (Thu, 25 Jun 2009) | 3 lines
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716 Changed paths:
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717 A /trunk/samtools/knetfile.c
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718
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719 * open a file at FTP
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720 * preliminary version
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721
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722 ------------------------------------------------------------------------
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723 r354 | lh3lh3 | 2009-06-24 14:02:25 +0100 (Wed, 24 Jun 2009) | 3 lines
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724 Changed paths:
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725 M /trunk/samtools/bam.c
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726 M /trunk/samtools/bamtk.c
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727
|
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728 * samtools-0.1.4-15 (r354)
|
|
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729 * fixed a memory leak in bam_view1(), although samtools is not using this routine.
|
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730
|
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731 ------------------------------------------------------------------------
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732 r351 | lh3lh3 | 2009-06-18 00:16:26 +0100 (Thu, 18 Jun 2009) | 4 lines
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733 Changed paths:
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734 M /trunk/samtools/bamtk.c
|
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735 M /trunk/samtools/faidx.c
|
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|
736
|
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737 * samtools-0.1.4-13 (r351)
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|
|
738 * make faidx more tolerant to empty lines right before or after > lines
|
|
|
739 * hope this does not introduce new bugs...
|
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740
|
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741 ------------------------------------------------------------------------
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742 r350 | lh3lh3 | 2009-06-16 14:37:01 +0100 (Tue, 16 Jun 2009) | 3 lines
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743 Changed paths:
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744 M /trunk/samtools/bam_plcmd.c
|
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745 M /trunk/samtools/bamtk.c
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746
|
|
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747 * samtools-0.1.4-13 (r350)
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748 * fixed a small memory leak in pileup, caused by recent modifications
|
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749
|
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750 ------------------------------------------------------------------------
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751 r347 | lh3lh3 | 2009-06-13 21:20:49 +0100 (Sat, 13 Jun 2009) | 3 lines
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752 Changed paths:
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753 M /trunk/samtools/bam_plcmd.c
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754 M /trunk/samtools/bamtk.c
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755 M /trunk/samtools/sam_view.c
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756
|
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757 * samtools-0.1.4-12 (r347)
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758 * added `-S' to pileup, similar to `view -S'
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759
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760 ------------------------------------------------------------------------
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761 r346 | lh3lh3 | 2009-06-13 17:52:31 +0100 (Sat, 13 Jun 2009) | 3 lines
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762 Changed paths:
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763 M /trunk/samtools/Makefile
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764 M /trunk/samtools/bamtk.c
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765 M /trunk/samtools/sam_view.c
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766 M /trunk/samtools/samtools.1
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767
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768 * samtools-0.1.4-11 (r346)
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769 * allow to select a read group at view command-line
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770
|
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771 ------------------------------------------------------------------------
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772 r344 | lh3lh3 | 2009-06-13 14:06:24 +0100 (Sat, 13 Jun 2009) | 2 lines
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773 Changed paths:
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774 M /trunk/samtools/examples/calDepth.c
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775
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776 added more comments
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777
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778 ------------------------------------------------------------------------
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779 r343 | lh3lh3 | 2009-06-13 14:01:22 +0100 (Sat, 13 Jun 2009) | 2 lines
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780 Changed paths:
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781 M /trunk/samtools/examples/calDepth.c
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782
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783 nothing really
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784
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785 ------------------------------------------------------------------------
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786 r342 | lh3lh3 | 2009-06-13 13:58:48 +0100 (Sat, 13 Jun 2009) | 2 lines
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787 Changed paths:
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788 M /trunk/samtools/examples/Makefile
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789 A /trunk/samtools/examples/calDepth.c
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790
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791 added an example of calculating read depth
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792
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793 ------------------------------------------------------------------------
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794 r341 | lh3lh3 | 2009-06-13 13:00:08 +0100 (Sat, 13 Jun 2009) | 6 lines
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795 Changed paths:
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796 M /trunk/samtools/Makefile
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797 M /trunk/samtools/bam.h
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798 M /trunk/samtools/bam_aux.c
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799 A /trunk/samtools/bam_color.c
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800 M /trunk/samtools/bam_plcmd.c
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801 M /trunk/samtools/bam_sort.c
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802 M /trunk/samtools/bam_tview.c
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803 M /trunk/samtools/bamtk.c
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804 M /trunk/samtools/sam.c
|
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805 M /trunk/samtools/sam.h
|
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806
|
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807 * samtools-0.1.4-10 (r341)
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808 * only include key APIs in libbam.a
|
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|
809 * move color-specific routines to bam_color.c
|
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810 * update documentations
|
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|
811 * remove the support of -q in pileup
|
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812
|
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813 ------------------------------------------------------------------------
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814 r340 | lh3lh3 | 2009-06-13 11:17:14 +0100 (Sat, 13 Jun 2009) | 6 lines
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815 Changed paths:
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816 M /trunk/samtools/INSTALL
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817 M /trunk/samtools/Makefile
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818 M /trunk/samtools/bam_aux.c
|
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819 M /trunk/samtools/bam_import.c
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820 M /trunk/samtools/bam_tview.c
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821 M /trunk/samtools/bamtk.c
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822 M /trunk/samtools/razf.c
|
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|
823 M /trunk/samtools/sam_view.c
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824
|
|
|
825 * samtools-0.1.4-9 (r340)
|
|
|
826 * added a warning to razf.c if zlib<1.2.2.1
|
|
|
827 * fixed a compilation warning
|
|
|
828 * fixed a segfault caused by @RG parsing
|
|
|
829 * detect NCURSES in bam_tview.c
|
|
|
830
|
|
|
831 ------------------------------------------------------------------------
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832 r339 | lh3lh3 | 2009-06-13 10:35:19 +0100 (Sat, 13 Jun 2009) | 2 lines
|
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833 Changed paths:
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834 M /trunk/samtools/INSTALL
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835
|
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|
836 update INSTALL
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837
|
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838 ------------------------------------------------------------------------
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839 r338 | lh3lh3 | 2009-06-13 00:15:24 +0100 (Sat, 13 Jun 2009) | 4 lines
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840 Changed paths:
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|
841 M /trunk/samtools/bam.c
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842 M /trunk/samtools/bam.h
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843 M /trunk/samtools/bam_aux.c
|
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844 M /trunk/samtools/bam_import.c
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845 M /trunk/samtools/bamtk.c
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846 M /trunk/samtools/kstring.h
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847 M /trunk/samtools/sam.c
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848 M /trunk/samtools/sam_view.c
|
|
|
849
|
|
|
850 * samtools-0.1.4-8 (r338)
|
|
|
851 * parse the @RG header lines and allow to choose library at the "samtools view"
|
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|
852 command line
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853
|
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854 ------------------------------------------------------------------------
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855 r337 | lh3lh3 | 2009-06-12 21:25:50 +0100 (Fri, 12 Jun 2009) | 4 lines
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856 Changed paths:
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857 M /trunk/samtools/bamtk.c
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858 M /trunk/samtools/bgzf.c
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859 M /trunk/samtools/bgzf.h
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860 M /trunk/samtools/sam.c
|
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861 M /trunk/samtools/sam_view.c
|
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862
|
|
|
863 * samtools-0.1.4-7 (r337)
|
|
|
864 * bgzf.c: support mode string "wu": uncompressed output
|
|
|
865 * "samtools view" support "-u" command-line option
|
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|
866
|
|
|
867 ------------------------------------------------------------------------
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868 r336 | lh3lh3 | 2009-06-12 17:20:12 +0100 (Fri, 12 Jun 2009) | 5 lines
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869 Changed paths:
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|
870 M /trunk/samtools/Makefile
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871 M /trunk/samtools/misc/Makefile
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|
872 M /trunk/samtools/razf.c
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873 M /trunk/samtools/razf.h
|
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874 M /trunk/samtools/razip.c
|
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|
875
|
|
|
876 * no changes to samtools itself
|
|
|
877 * remove zlib source codes
|
|
|
878 * make RAZF reading compatible with old version of zlib
|
|
|
879 * on old version of zlib, writing is not available
|
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880
|
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881 ------------------------------------------------------------------------
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882 r335 | lh3lh3 | 2009-06-12 16:47:33 +0100 (Fri, 12 Jun 2009) | 2 lines
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883 Changed paths:
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884 D /trunk/samtools/zlib
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885
|
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|
886 remove zlib for simplification...
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887
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888 ------------------------------------------------------------------------
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889 r334 | lh3lh3 | 2009-06-12 15:43:36 +0100 (Fri, 12 Jun 2009) | 5 lines
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890 Changed paths:
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891 M /trunk/samtools/bam.h
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892 M /trunk/samtools/bam_aux.c
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893 M /trunk/samtools/bamtk.c
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|
894
|
|
|
895 * samtools-0.1.4-6 (r334)
|
|
|
896 * do not export bam_aux_get_core() for Bio::DB::Sam because it has already
|
|
|
897 been implemented in that.
|
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|
898 * this version works with the latest Bio::DB::Sam (20090612)
|
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899
|
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|
900 ------------------------------------------------------------------------
|
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|
901 r333 | lh3lh3 | 2009-06-12 15:33:42 +0100 (Fri, 12 Jun 2009) | 2 lines
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902 Changed paths:
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903 M /trunk/samtools/ChangeLog
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|
904
|
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|
905 update ChangeLog
|
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|
906
|
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907 ------------------------------------------------------------------------
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908 r332 | lh3lh3 | 2009-06-12 15:21:21 +0100 (Fri, 12 Jun 2009) | 2 lines
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909 Changed paths:
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910 M /trunk/samtools/AUTHORS
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911 M /trunk/samtools/Makefile
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912 M /trunk/samtools/misc/Makefile
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913
|
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|
914 fixed minor things in Makefile
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915
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916 ------------------------------------------------------------------------
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|
917 r331 | lh3lh3 | 2009-06-12 15:07:05 +0100 (Fri, 12 Jun 2009) | 4 lines
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|
918 Changed paths:
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|
919 M /trunk/samtools/bamtk.c
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920
|
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|
921 * samtools-0.1.4-5 (r3310
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|
|
922 * no change to samtools itself. Version number is increased to reflect the
|
|
|
923 changes in the Makefile building system.
|
|
|
924
|
|
|
925 ------------------------------------------------------------------------
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|
926 r330 | lh3lh3 | 2009-06-12 15:03:38 +0100 (Fri, 12 Jun 2009) | 2 lines
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927 Changed paths:
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928 M /trunk/samtools/AUTHORS
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929 D /trunk/samtools/README
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930
|
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|
931 update information...
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932
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933 ------------------------------------------------------------------------
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934 r329 | lh3lh3 | 2009-06-12 14:52:21 +0100 (Fri, 12 Jun 2009) | 3 lines
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935 Changed paths:
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936 M /trunk/samtools/misc/novo2sam.pl
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937
|
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|
938 * updated novoalign converter by Colin Hercus et al.
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939 * this version works with indels
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940
|
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|
941 ------------------------------------------------------------------------
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942 r328 | lh3lh3 | 2009-06-12 14:50:53 +0100 (Fri, 12 Jun 2009) | 3 lines
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943 Changed paths:
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944 M /trunk/samtools/INSTALL
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945 M /trunk/samtools/Makefile
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946 M /trunk/samtools/misc/Makefile
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947 M /trunk/samtools/zlib/Makefile
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948
|
|
|
949 * update Makefile
|
|
|
950 * update INSTALL instruction
|
|
|
951
|
|
|
952 ------------------------------------------------------------------------
|
|
|
953 r327 | lh3lh3 | 2009-06-12 14:18:29 +0100 (Fri, 12 Jun 2009) | 4 lines
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|
954 Changed paths:
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|
955 A /trunk/samtools/Makefile (from /trunk/samtools/Makefile.generic:325)
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956 D /trunk/samtools/Makefile.am
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957 D /trunk/samtools/Makefile.generic
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958 D /trunk/samtools/Makefile.lite
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959 D /trunk/samtools/autogen.sh
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960 D /trunk/samtools/cleanup.sh
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961 D /trunk/samtools/configure.ac
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962 A /trunk/samtools/misc/Makefile (from /trunk/samtools/misc/Makefile.generic:305)
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963 D /trunk/samtools/misc/Makefile.am
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964 D /trunk/samtools/misc/Makefile.generic
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965 M /trunk/samtools/razf.c
|
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966 A /trunk/samtools/zlib
|
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967 A /trunk/samtools/zlib/Makefile
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968 A /trunk/samtools/zlib/adler32.c
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969 A /trunk/samtools/zlib/compress.c
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970 A /trunk/samtools/zlib/crc32.c
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971 A /trunk/samtools/zlib/crc32.h
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972 A /trunk/samtools/zlib/deflate.c
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973 A /trunk/samtools/zlib/deflate.h
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974 A /trunk/samtools/zlib/gzio.c
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975 A /trunk/samtools/zlib/infback.c
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976 A /trunk/samtools/zlib/inffast.c
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977 A /trunk/samtools/zlib/inffast.h
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978 A /trunk/samtools/zlib/inffixed.h
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979 A /trunk/samtools/zlib/inflate.c
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980 A /trunk/samtools/zlib/inflate.h
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|
981 A /trunk/samtools/zlib/inftrees.c
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982 A /trunk/samtools/zlib/inftrees.h
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983 A /trunk/samtools/zlib/trees.c
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984 A /trunk/samtools/zlib/trees.h
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|
985 A /trunk/samtools/zlib/uncompr.c
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986 A /trunk/samtools/zlib/zconf.h
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987 A /trunk/samtools/zlib/zlib.h
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988 A /trunk/samtools/zlib/zutil.c
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989 A /trunk/samtools/zlib/zutil.h
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990 D /trunk/samtools/zutil.h
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991
|
|
|
992 * added zlib-1.2.3 as razip requires that
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|
|
993 * prepare to changed back to the Makefile building system
|
|
|
994 * unfinished! (will be soon)
|
|
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995
|
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996 ------------------------------------------------------------------------
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997 r326 | lh3lh3 | 2009-06-12 14:12:03 +0100 (Fri, 12 Jun 2009) | 2 lines
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998 Changed paths:
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999 M /trunk/samtools/misc/samtools.pl
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1000
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1001 Unfinished
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1002
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1003 ------------------------------------------------------------------------
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1004 r325 | lh3lh3 | 2009-06-10 16:27:59 +0100 (Wed, 10 Jun 2009) | 3 lines
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1005 Changed paths:
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1006 M /trunk/samtools/bam_maqcns.c
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1007 M /trunk/samtools/bamtk.c
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1008
|
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1009 * samtools-0.1.4-4 (r325)
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1010 * further avoid wrong consensus calls in repetitive regions.
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1011
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1012 ------------------------------------------------------------------------
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1013 r324 | lh3lh3 | 2009-06-10 15:56:17 +0100 (Wed, 10 Jun 2009) | 4 lines
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1014 Changed paths:
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1015 M /trunk/samtools/bam_maqcns.c
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1016 M /trunk/samtools/bam_plcmd.c
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1017 M /trunk/samtools/bamtk.c
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1018 M /trunk/samtools/sam.c
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1019 M /trunk/samtools/sam.h
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1020
|
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|
1021 * samtools-0.1.4-3 (r324)
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|
1022 * make maqcns generate the correct call in repetitive regions.
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1023 * allow filtering on mapQ at the pileup command line
|
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1024
|
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|
1025 ------------------------------------------------------------------------
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|
1026 r323 | lh3lh3 | 2009-06-10 10:04:21 +0100 (Wed, 10 Jun 2009) | 3 lines
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1027 Changed paths:
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1028 M /trunk/samtools/misc/samtools.pl
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1029
|
|
|
1030 * samtools.pl-0.3.2 (r322)
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1031 * indels and SNPs use different mapping quality threshold
|
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1032
|
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|
1033 ------------------------------------------------------------------------
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1034 r322 | lh3lh3 | 2009-06-10 10:03:22 +0100 (Wed, 10 Jun 2009) | 2 lines
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1035 Changed paths:
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1036 M /trunk/samtools/misc/export2sam.pl
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1037
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1038 fixed a typo
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1039
|
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1040 ------------------------------------------------------------------------
|
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|
1041 r321 | lh3lh3 | 2009-06-09 09:21:48 +0100 (Tue, 09 Jun 2009) | 2 lines
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1042 Changed paths:
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1043 M /trunk/samtools/misc/samtools.pl
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1044
|
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|
1045 just typo. no real change
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1046
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1047 ------------------------------------------------------------------------
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1048 r320 | lh3lh3 | 2009-06-08 14:32:51 +0100 (Mon, 08 Jun 2009) | 2 lines
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1049 Changed paths:
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1050 M /trunk/samtools/misc/samtools.pl
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1051
|
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1052 a little bit code cleanup
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1053
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1054 ------------------------------------------------------------------------
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1055 r319 | lh3lh3 | 2009-06-08 14:22:33 +0100 (Mon, 08 Jun 2009) | 4 lines
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1056 Changed paths:
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1057 M /trunk/samtools/misc/samtools.pl
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1058
|
|
|
1059 * samtools.pl-0.3.1
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1060 * change default parameters
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|
|
1061 * optionally print filtered variants
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1062
|
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|
1063 ------------------------------------------------------------------------
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1064 r318 | lh3lh3 | 2009-06-08 14:14:26 +0100 (Mon, 08 Jun 2009) | 3 lines
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1065 Changed paths:
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1066 M /trunk/samtools/misc/samtools.pl
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1067
|
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|
1068 * samtools.pl-0.3.0
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1069 * combine snpFilter and indelFilter
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1070
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1071 ------------------------------------------------------------------------
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1072 r317 | lh3lh3 | 2009-06-08 11:31:42 +0100 (Mon, 08 Jun 2009) | 3 lines
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1073 Changed paths:
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1074 M /trunk/samtools/misc/samtools.pl
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1075
|
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1076 * samtools.pl-0.2.3
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1077 * change a default parameter
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1078
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1079 ------------------------------------------------------------------------
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1080 r316 | lh3lh3 | 2009-06-08 11:11:06 +0100 (Mon, 08 Jun 2009) | 5 lines
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1081 Changed paths:
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|
1082 M /trunk/samtools/bam_maqcns.c
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1083 M /trunk/samtools/bam_maqcns.h
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1084 M /trunk/samtools/bam_plcmd.c
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1085 M /trunk/samtools/bamtk.c
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1086 M /trunk/samtools/sam.c
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1087
|
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1088 * samtools-0.1.4-2 (r316)
|
|
|
1089 * pileup: cap mapping quality at 60 (by default)
|
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|
1090 * pileup: always calculate RMS mapq
|
|
|
1091 * pileup: allow to output variant sites only
|
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1092
|
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1093 ------------------------------------------------------------------------
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1094 r312 | lh3lh3 | 2009-06-04 13:01:10 +0100 (Thu, 04 Jun 2009) | 3 lines
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1095 Changed paths:
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1096 M /trunk/samtools/misc/samtools.pl
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1097
|
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1098 * samtools.pl-0.2.2
|
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1099 * added pileup2fq
|
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1100
|
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1101 ------------------------------------------------------------------------
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1102 r311 | lh3lh3 | 2009-06-03 09:40:40 +0100 (Wed, 03 Jun 2009) | 2 lines
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1103 Changed paths:
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1104 M /trunk/samtools/misc/samtools.pl
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1105
|
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1106 * in snpFilter, suppress non-SNP sites
|
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1107
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1108 ------------------------------------------------------------------------
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1109 r310 | lh3lh3 | 2009-06-01 14:35:13 +0100 (Mon, 01 Jun 2009) | 3 lines
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1110 Changed paths:
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1111 M /trunk/samtools/misc/samtools.pl
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1112
|
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1113 * samtools.pl-0.2.1
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1114 * fixed a typo
|
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1115
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1116 ------------------------------------------------------------------------
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1117 r309 | lh3lh3 | 2009-06-01 14:04:39 +0100 (Mon, 01 Jun 2009) | 3 lines
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1118 Changed paths:
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1119 M /trunk/samtools/misc/samtools.pl
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1120
|
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1121 * samtools.pl-0.2.0
|
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1122 * snpFilter
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1123
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1124 ------------------------------------------------------------------------
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1125 r306 | lh3lh3 | 2009-05-28 11:49:35 +0100 (Thu, 28 May 2009) | 3 lines
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1126 Changed paths:
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1127 M /trunk/samtools/bgzf.c
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1128
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1129 * minor changes to bgzf: return NULL if fd == -1
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1130 * suggested by {kdj,jm18}@sanger.ac.uk
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1131
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1132 ------------------------------------------------------------------------
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1133 r305 | lh3lh3 | 2009-05-28 11:16:08 +0100 (Thu, 28 May 2009) | 2 lines
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1134 Changed paths:
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1135 A /trunk/samtools/misc/interpolate_sam.pl
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1136
|
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1137 Script for paired-end pileup, contributed by Stephen Montgomery.
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1138
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1139 ------------------------------------------------------------------------
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1140 r304 | lh3lh3 | 2009-05-28 11:08:49 +0100 (Thu, 28 May 2009) | 3 lines
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1141 Changed paths:
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1142 M /trunk/samtools/bamtk.c
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1143 M /trunk/samtools/sam.c
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1144
|
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1145 * samtools-0.1.4-1 (r304)
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1146 * fixed a minor bug in printing headers
|
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1147
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1148 ------------------------------------------------------------------------
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1149 r297 | lh3lh3 | 2009-05-21 16:06:16 +0100 (Thu, 21 May 2009) | 2 lines
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1150 Changed paths:
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1151 M /trunk/samtools/ChangeLog
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1152 M /trunk/samtools/NEWS
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1153 M /trunk/samtools/bam_plcmd.c
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1154 M /trunk/samtools/bamtk.c
|
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1155 M /trunk/samtools/misc/maq2sam.c
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1156 M /trunk/samtools/samtools.1
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1157
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1158 Release samtools-0.1.4
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1159
|
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1160 ------------------------------------------------------------------------
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1161 r296 | lh3lh3 | 2009-05-21 12:53:14 +0100 (Thu, 21 May 2009) | 3 lines
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1162 Changed paths:
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1163 M /trunk/samtools/bam_maqcns.c
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1164 M /trunk/samtools/bamtk.c
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1165
|
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|
1166 * samtools-0.1.3-24 (r296)
|
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1167 * another similar bug in the indel caller
|
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1168
|
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1169 ------------------------------------------------------------------------
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1170 r295 | lh3lh3 | 2009-05-21 12:50:28 +0100 (Thu, 21 May 2009) | 3 lines
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1171 Changed paths:
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1172 M /trunk/samtools/bam_maqcns.c
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1173 M /trunk/samtools/bamtk.c
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1174
|
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|
1175 * samtools-0.1.3-23 (r295)
|
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1176 * fixed a critical bug in the indel caller
|
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1177
|
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1178 ------------------------------------------------------------------------
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1179 r294 | lh3lh3 | 2009-05-20 13:00:20 +0100 (Wed, 20 May 2009) | 2 lines
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1180 Changed paths:
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1181 M /trunk/samtools/bam_stat.c
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1182
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1183 added a missing header file
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1184
|
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1185 ------------------------------------------------------------------------
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1186 r293 | lh3lh3 | 2009-05-19 23:44:25 +0100 (Tue, 19 May 2009) | 3 lines
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1187 Changed paths:
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1188 M /trunk/samtools/bam_tview.c
|
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1189 M /trunk/samtools/bamtk.c
|
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1190
|
|
|
1191 * samtools-0.1.3-22 (r293)
|
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1192 * open tview in the dot-view mode by default
|
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1193
|
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1194 ------------------------------------------------------------------------
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1195 r292 | lh3lh3 | 2009-05-18 21:01:23 +0100 (Mon, 18 May 2009) | 6 lines
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1196 Changed paths:
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1197 M /trunk/samtools/samtools.1
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1198
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|
1199 Added a note to the manual. Currently SAMtools used unaligned words in
|
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|
1200 several places. Although this does not cause bus errors to me, it may
|
|
|
1201 affect portability. Please see the "Bus error" wiki page for more
|
|
|
1202 information. Also thank James Bonfields for pointing this out.
|
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1203
|
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1204
|
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|
1205 ------------------------------------------------------------------------
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|
1206 r286 | lh3lh3 | 2009-05-14 15:23:13 +0100 (Thu, 14 May 2009) | 3 lines
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1207 Changed paths:
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|
1208 M /trunk/samtools/bam.h
|
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1209 M /trunk/samtools/bam_aux.c
|
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1210 M /trunk/samtools/bamtk.c
|
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1211
|
|
|
1212 * samtools-0.1.3-21 (286)
|
|
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1213 * declare bam_aux_get_core() in bam.h
|
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1214
|
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|
1215 ------------------------------------------------------------------------
|
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|
1216 r276 | lh3lh3 | 2009-05-13 10:07:55 +0100 (Wed, 13 May 2009) | 5 lines
|
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1217 Changed paths:
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|
1218 M /trunk/samtools/bam.h
|
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1219 M /trunk/samtools/bam_index.c
|
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1220 M /trunk/samtools/bamtk.c
|
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1221
|
|
|
1222 * samtools-0.1.3-20 (r276)
|
|
|
1223 * remove bam1_t::hash again. We need to modify the Perl API anyway to
|
|
|
1224 make it work with the latest SVN.
|
|
|
1225 * As is suggested by Tim, scan "{base}.bai" and "{base}.bam.bai" for index
|
|
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1226
|
|
|
1227 ------------------------------------------------------------------------
|
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|
1228 r275 | lh3lh3 | 2009-05-12 21:14:10 +0100 (Tue, 12 May 2009) | 4 lines
|
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1229 Changed paths:
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1230 M /trunk/samtools/ChangeLog
|
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1231 M /trunk/samtools/bam.h
|
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1232 M /trunk/samtools/bamtk.c
|
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1233
|
|
|
1234 * samtools-0.1.3-19 (r275)
|
|
|
1235 * a minor change to the bam1_t struct: added back "void *hash" for the
|
|
|
1236 backward compatibility with Bio::DB::Sam
|
|
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1237
|
|
|
1238 ------------------------------------------------------------------------
|
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|
1239 r273 | lh3lh3 | 2009-05-12 14:28:39 +0100 (Tue, 12 May 2009) | 3 lines
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1240 Changed paths:
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1241 M /trunk/samtools/bam_rmdupse.c
|
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1242 M /trunk/samtools/bamtk.c
|
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1243
|
|
|
1244 * samtools-0.1.3-18 (r273)
|
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1245 * rmdupse: do not remove unmapped reads
|
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1246
|
|
|
1247 ------------------------------------------------------------------------
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1248 r272 | lh3lh3 | 2009-05-12 14:20:00 +0100 (Tue, 12 May 2009) | 2 lines
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1249 Changed paths:
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1250 M /trunk/samtools/bam_rmdupse.c
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1251
|
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1252 change a parameter. It does nothing
|
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1253
|
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1254 ------------------------------------------------------------------------
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1255 r271 | lh3lh3 | 2009-05-12 14:17:58 +0100 (Tue, 12 May 2009) | 3 lines
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1256 Changed paths:
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1257 M /trunk/samtools/Makefile.am
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1258 M /trunk/samtools/Makefile.generic
|
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1259 M /trunk/samtools/Makefile.lite
|
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1260 A /trunk/samtools/bam_rmdupse.c
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1261 M /trunk/samtools/bamtk.c
|
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1262 M /trunk/samtools/configure.ac
|
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1263
|
|
|
1264 * samtools-0.1.3-17 (r271)
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1265 * added 'rmdupse' command
|
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1266
|
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|
1267 ------------------------------------------------------------------------
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1268 r267 | lh3lh3 | 2009-05-05 22:31:41 +0100 (Tue, 05 May 2009) | 3 lines
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1269 Changed paths:
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1270 M /trunk/samtools/bamtk.c
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1271 M /trunk/samtools/sam_view.c
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1272
|
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1273 * samtools-0.1.3-16 (r267)
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1274 * in sam_view.c, changed g_flag_on based on the suggestion by Angie Hinrichs
|
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1275
|
|
|
1276 ------------------------------------------------------------------------
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1277 r266 | lh3lh3 | 2009-05-05 22:23:27 +0100 (Tue, 05 May 2009) | 3 lines
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1278 Changed paths:
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1279 M /trunk/samtools/bam_import.c
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1280 M /trunk/samtools/bamtk.c
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1281
|
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1282 * samtools-0.1.3-15 (r266)
|
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1283 * report an error if a non-* reference is present while @SQ is absent
|
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1284
|
|
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1285 ------------------------------------------------------------------------
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1286 r265 | lh3lh3 | 2009-05-05 22:09:00 +0100 (Tue, 05 May 2009) | 3 lines
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1287 Changed paths:
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1288 M /trunk/samtools/bam.h
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1289 M /trunk/samtools/bam_import.c
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1290 M /trunk/samtools/bamtk.c
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1291 M /trunk/samtools/sam.c
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1292 M /trunk/samtools/sam_view.c
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1293
|
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|
1294 * samtools-0.1.3-14 (r262)
|
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1295 * make samopen() recognize @SQ header lines
|
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1296
|
|
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1297 ------------------------------------------------------------------------
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1298 r261 | lh3lh3 | 2009-05-05 15:10:30 +0100 (Tue, 05 May 2009) | 3 lines
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1299 Changed paths:
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1300 M /trunk/samtools/bam_plcmd.c
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1301 M /trunk/samtools/bamtk.c
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1302 M /trunk/samtools/bgzf.c
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1303 M /trunk/samtools/sam.c
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1304 M /trunk/samtools/sam_view.c
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1305
|
|
|
1306 * samtools-0.1.3-13 (r260)
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1307 * report error for file I/O error
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1308
|
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1309 ------------------------------------------------------------------------
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1310 r260 | lh3lh3 | 2009-05-05 15:01:16 +0100 (Tue, 05 May 2009) | 2 lines
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1311 Changed paths:
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1312 M /trunk/samtools/Makefile.am
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1313
|
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1314 update Makefile.am
|
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1315
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1316 ------------------------------------------------------------------------
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1317 r259 | lh3lh3 | 2009-05-05 14:52:25 +0100 (Tue, 05 May 2009) | 3 lines
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1318 Changed paths:
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1319 M /trunk/samtools/bam.h
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1320 M /trunk/samtools/bam_pileup.c
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1321 M /trunk/samtools/bam_plcmd.c
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1322 M /trunk/samtools/bamtk.c
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1323 M /trunk/samtools/sam.c
|
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|
1324 M /trunk/samtools/sam.h
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1325
|
|
|
1326 * samtools-0.1.3-12 (r259)
|
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1327 * use the new I/O interface in pileup
|
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1328
|
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|
1329 ------------------------------------------------------------------------
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1330 r258 | lh3lh3 | 2009-05-05 14:33:22 +0100 (Tue, 05 May 2009) | 3 lines
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1331 Changed paths:
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1332 M /trunk/samtools/Makefile.generic
|
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1333 M /trunk/samtools/Makefile.lite
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1334 M /trunk/samtools/bam.c
|
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1335 M /trunk/samtools/bam.h
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1336 M /trunk/samtools/bam_import.c
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1337 M /trunk/samtools/bamtk.c
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1338 A /trunk/samtools/sam.c
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1339 A /trunk/samtools/sam.h
|
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1340 A /trunk/samtools/sam_view.c
|
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1341
|
|
|
1342 * samtools-0.1.3-11 (r258)
|
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1343 * unify the interface to BAM and SAM I/O
|
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1344
|
|
|
1345 ------------------------------------------------------------------------
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1346 r257 | lh3lh3 | 2009-05-05 09:53:35 +0100 (Tue, 05 May 2009) | 3 lines
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1347 Changed paths:
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1348 M /trunk/samtools/Makefile.lite
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1349 M /trunk/samtools/bam_plcmd.c
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1350 M /trunk/samtools/bamtk.c
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1351
|
|
|
1352 * samtools-0.1.3-10 (r257)
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1353 * allow hex with "pileup -m"
|
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1354
|
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1355 ------------------------------------------------------------------------
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1356 r256 | lh3lh3 | 2009-05-04 19:16:50 +0100 (Mon, 04 May 2009) | 4 lines
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1357 Changed paths:
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1358 M /trunk/samtools/bam_lpileup.c
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1359 M /trunk/samtools/bamtk.c
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1360
|
|
|
1361 * samtools-0.1.3-9 (r256)
|
|
|
1362 * fixed a bug in bam_lpileup.c
|
|
|
1363 * I do not know if this also fixes the bug causing assertion failure in the tview
|
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1364
|
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|
1365 ------------------------------------------------------------------------
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1366 r251 | lh3lh3 | 2009-04-28 13:53:23 +0100 (Tue, 28 Apr 2009) | 3 lines
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1367 Changed paths:
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1368 M /trunk/samtools/bam_pileup.c
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1369 M /trunk/samtools/bamtk.c
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1370
|
|
|
1371 * samtools-0.1.3-8 (r251)
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1372 * fixed a bug when there are reads without coordinates
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1373
|
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|
1374 ------------------------------------------------------------------------
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1375 r250 | lh3lh3 | 2009-04-28 13:43:33 +0100 (Tue, 28 Apr 2009) | 2 lines
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1376 Changed paths:
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1377 A /trunk/samtools/AUTHORS
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1378 A /trunk/samtools/README
|
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1379 M /trunk/samtools/cleanup.sh
|
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1380
|
|
|
1381 added missing files
|
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|
1382
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|
1383 ------------------------------------------------------------------------
|
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|
1384 r249 | lh3lh3 | 2009-04-28 13:37:16 +0100 (Tue, 28 Apr 2009) | 2 lines
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1385 Changed paths:
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|
1386 M /trunk/samtools/Makefile.generic
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|
1387 M /trunk/samtools/Makefile.lite
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1388 M /trunk/samtools/configure.ac
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1389 M /trunk/samtools/misc/Makefile.generic
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1390
|
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1391 improve large file support in compilation
|
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1392
|
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|
1393 ------------------------------------------------------------------------
|
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|
1394 r248 | lh3lh3 | 2009-04-28 13:33:24 +0100 (Tue, 28 Apr 2009) | 2 lines
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1395 Changed paths:
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|
1396 M /trunk/samtools/INSTALL
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1397
|
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1398 update INSTALL
|
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1399
|
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|
1400 ------------------------------------------------------------------------
|
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|
1401 r247 | lh3lh3 | 2009-04-28 13:28:50 +0100 (Tue, 28 Apr 2009) | 2 lines
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1402 Changed paths:
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1403 M /trunk/samtools/Makefile.am
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1404 M /trunk/samtools/autogen.sh
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1405 M /trunk/samtools/cleanup.sh
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1406 M /trunk/samtools/configure.ac
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1407 A /trunk/samtools/misc/Makefile.am
|
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1408
|
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|
1409 fixed various issues about the GNU building scripts
|
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1410
|
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1411 ------------------------------------------------------------------------
|
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|
1412 r246 | lh3lh3 | 2009-04-28 13:10:23 +0100 (Tue, 28 Apr 2009) | 4 lines
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1413 Changed paths:
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|
1414 M /trunk/samtools/ChangeLog
|
|
|
1415 D /trunk/samtools/Makefile
|
|
|
1416 A /trunk/samtools/Makefile.am
|
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|
1417 A /trunk/samtools/Makefile.generic
|
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|
1418 A /trunk/samtools/autogen.sh
|
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|
1419 M /trunk/samtools/bam.h
|
|
|
1420 M /trunk/samtools/bam_aux.c
|
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|
1421 M /trunk/samtools/bam_tview.c
|
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|
1422 M /trunk/samtools/bamtk.c
|
|
|
1423 A /trunk/samtools/cleanup.sh
|
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1424 A /trunk/samtools/configure.ac
|
|
|
1425 D /trunk/samtools/misc/Makefile
|
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|
1426 A /trunk/samtools/misc/Makefile.generic (from /trunk/samtools/misc/Makefile:245)
|
|
|
1427
|
|
|
1428 * samtools-0.1.3-7 (r246)
|
|
|
1429 * incorporated revisions from Nils Homer
|
|
|
1430 * enhanced support of displaying color-space reads
|
|
|
1431
|
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|
1432 ------------------------------------------------------------------------
|
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|
1433 r244 | lh3lh3 | 2009-04-25 11:49:40 +0100 (Sat, 25 Apr 2009) | 3 lines
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1434 Changed paths:
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1435 M /trunk/samtools/bam_md.c
|
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|
1436 M /trunk/samtools/bamtk.c
|
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1437
|
|
|
1438 * samtools-0.1.3-6 (r244)
|
|
|
1439 * fixed segfault for unmapped reads
|
|
|
1440
|
|
|
1441 ------------------------------------------------------------------------
|
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1442 r243 | lh3lh3 | 2009-04-24 21:27:26 +0100 (Fri, 24 Apr 2009) | 5 lines
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1443 Changed paths:
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1444 M /trunk/samtools/bam.h
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1445 M /trunk/samtools/bam_maqcns.c
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1446 M /trunk/samtools/bam_md.c
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1447 M /trunk/samtools/bamtk.c
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1448
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1449 * samtools-0.1.3-5 (r243)
|
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1450 * fixed a long existing bug which may cause memory leak
|
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1451 * check MD
|
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1452 * consensus calling now works with "=", but indel calling not
|
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1453
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1454 ------------------------------------------------------------------------
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1455 r242 | lh3lh3 | 2009-04-24 20:44:46 +0100 (Fri, 24 Apr 2009) | 3 lines
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1456 Changed paths:
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1457 M /trunk/samtools/bam_md.c
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1458 M /trunk/samtools/bamtk.c
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1459
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1460 * samtools-0.1.3-4 (r242)
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1461 * fixed a memory leak
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1462
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1463 ------------------------------------------------------------------------
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1464 r240 | lh3lh3 | 2009-04-24 16:40:18 +0100 (Fri, 24 Apr 2009) | 5 lines
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1465 Changed paths:
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1466 M /trunk/samtools/Makefile
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1467 M /trunk/samtools/Makefile.lite
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1468 M /trunk/samtools/bam.h
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1469 M /trunk/samtools/bam_aux.c
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1470 A /trunk/samtools/bam_md.c
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1471 M /trunk/samtools/bam_plcmd.c
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1472 M /trunk/samtools/bamtk.c
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1473
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1474 * samtools-0.1.3-3 (r240)
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1475 * generate MD tag
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1476 * generate "=" bases
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1477 * the plain pileup now support "=" bases, but consensus calling and glfgen may fail
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1478
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1479 ------------------------------------------------------------------------
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1480 r239 | lh3lh3 | 2009-04-24 12:08:20 +0100 (Fri, 24 Apr 2009) | 5 lines
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1481 Changed paths:
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1482 M /trunk/samtools/bam.h
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1483 M /trunk/samtools/bam_aux.c
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1484 M /trunk/samtools/bamtk.c
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1485
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1486 * samtools-0.1.3-2 (r239)
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1487 * fixed bugs in bam_aux.c (these functions nevered used by samtools)
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1488 * removed bam_aux_init()/bam_aux_destroy()
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1489 * added tagview for testing bam_aux
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1490
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1491 ------------------------------------------------------------------------
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1492 r235 | lh3lh3 | 2009-04-21 23:17:39 +0100 (Tue, 21 Apr 2009) | 3 lines
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1493 Changed paths:
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1494 M /trunk/samtools/bam_pileup.c
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1495 M /trunk/samtools/bamtk.c
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1496
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1497 * samtools-0.1.3-1
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1498 * fixed a bug in pileup: the first read in a chromosome may not be printed
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1499
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1500 ------------------------------------------------------------------------
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1501 r232 | lh3lh3 | 2009-04-16 15:25:43 +0100 (Thu, 16 Apr 2009) | 2 lines
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1502 Changed paths:
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1503 M /trunk/samtools/Makefile.lite
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1504
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1505 a missing file in Makefile.lite
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1506
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1507 ------------------------------------------------------------------------
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1508 r227 | lh3lh3 | 2009-04-15 22:02:53 +0100 (Wed, 15 Apr 2009) | 2 lines
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1509 Changed paths:
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1510 M /trunk/samtools/NEWS
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1511 M /trunk/samtools/bamtk.c
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1512
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1513 Release samtools-0.1.3
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1514
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1515 ------------------------------------------------------------------------
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1516 r223 | lh3lh3 | 2009-04-15 14:31:32 +0100 (Wed, 15 Apr 2009) | 3 lines
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1517 Changed paths:
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1518 M /trunk/samtools/bam_plcmd.c
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1519 M /trunk/samtools/bamtk.c
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1520
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1521 * samtools-0.1.2-28
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1522 * make samtools more robust to weird input such as empty file
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1523
|
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1524 ------------------------------------------------------------------------
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1525 r222 | lh3lh3 | 2009-04-15 14:05:33 +0100 (Wed, 15 Apr 2009) | 2 lines
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1526 Changed paths:
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1527 M /trunk/samtools/ChangeLog
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1528 M /trunk/samtools/NEWS
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1529 M /trunk/samtools/samtools.1
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1530
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1531 prepare for release 0.1.3
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1532
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1533 ------------------------------------------------------------------------
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1534 r221 | lh3lh3 | 2009-04-15 13:32:14 +0100 (Wed, 15 Apr 2009) | 2 lines
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1535 Changed paths:
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1536 A /trunk/samtools/misc/blast2sam.pl
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1537
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1538 convert NCBI-BLASTN to SAM
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1539
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1540 ------------------------------------------------------------------------
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1541 r220 | lh3lh3 | 2009-04-15 13:18:19 +0100 (Wed, 15 Apr 2009) | 3 lines
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1542 Changed paths:
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1543 M /trunk/samtools/bam_lpileup.c
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1544 M /trunk/samtools/bamtk.c
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1545
|
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1546 * samtools-0.1.2-27
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1547 * fixed a small memory leak in tview
|
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1548
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1549 ------------------------------------------------------------------------
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1550 r219 | lh3lh3 | 2009-04-15 13:00:08 +0100 (Wed, 15 Apr 2009) | 3 lines
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1551 Changed paths:
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1552 M /trunk/samtools/bam_rmdup.c
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1553 M /trunk/samtools/bamtk.c
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1554
|
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1555 * samtools-0.1.2-26
|
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1556 * fixed a bug in rmdup when there are unmapped reads
|
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1557
|
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1558 ------------------------------------------------------------------------
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1559 r218 | lh3lh3 | 2009-04-14 22:28:58 +0100 (Tue, 14 Apr 2009) | 2 lines
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1560 Changed paths:
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1561 M /trunk/samtools/ChangeLog
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1562 M /trunk/samtools/NEWS
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1563
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1564 proposed NEWS for the new release (have not yet)
|
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1565
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1566 ------------------------------------------------------------------------
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1567 r216 | lh3lh3 | 2009-04-14 22:10:46 +0100 (Tue, 14 Apr 2009) | 4 lines
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1568 Changed paths:
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1569 M /trunk/samtools/misc/samtools.pl
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1570
|
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1571 * samtools.pl-0.1.1
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1572 * improve indelFilter to avoid filtering true indels. The new filter relies
|
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1573 on the new pileup indel line implemented in samtools-0.1.2-25
|
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1574
|
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1575 ------------------------------------------------------------------------
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1576 r215 | lh3lh3 | 2009-04-14 22:04:19 +0100 (Tue, 14 Apr 2009) | 4 lines
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1577 Changed paths:
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1578 M /trunk/samtools/bam_maqcns.c
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1579 M /trunk/samtools/bam_plcmd.c
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1580 M /trunk/samtools/bamtk.c
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1581 M /trunk/samtools/samtools.1
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1582
|
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1583 * samtools-0.1.2-25
|
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1584 * change the pileup indel line to shows the number of alignments actually
|
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|
1585 containing indels
|
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1586
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1587 ------------------------------------------------------------------------
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1588 r211 | lh3lh3 | 2009-04-13 12:07:13 +0100 (Mon, 13 Apr 2009) | 2 lines
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1589 Changed paths:
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1590 M /trunk/samtools/ChangeLog
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1591
|
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1592 update ChangeLog from "svn log"
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1593
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1594 ------------------------------------------------------------------------
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1595 r210 | lh3lh3 | 2009-04-12 20:57:05 +0100 (Sun, 12 Apr 2009) | 4 lines
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1596 Changed paths:
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1597 M /trunk/samtools/bam.c
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1598 M /trunk/samtools/bam_import.c
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1599 M /trunk/samtools/bam_sort.c
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1600 M /trunk/samtools/bamtk.c
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1601 M /trunk/samtools/kseq.h
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1602
|
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1603 * samtools-0.1.2-24
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1604 * in merge, gives a warning rather than error if the target sequence length is different
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1605 * allow empty header
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1606
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1607 ------------------------------------------------------------------------
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1608 r209 | lh3lh3 | 2009-04-12 20:32:44 +0100 (Sun, 12 Apr 2009) | 3 lines
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1609 Changed paths:
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1610 M /trunk/samtools/bam.c
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1611 M /trunk/samtools/bam_import.c
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1612 M /trunk/samtools/bamtk.c
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1613
|
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1614 * samtools-0.1.2-23
|
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1615 * recognize '*' at the QUAL field
|
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1616
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1617 ------------------------------------------------------------------------
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1618 r208 | lh3lh3 | 2009-04-12 20:08:02 +0100 (Sun, 12 Apr 2009) | 3 lines
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1619 Changed paths:
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1620 M /trunk/samtools/bam_import.c
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1621 M /trunk/samtools/bamtk.c
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1622 M /trunk/samtools/kseq.h
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1623
|
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1624 * samtools-0.1.2-22
|
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1625 * the field separater is TAB only, now
|
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1626
|
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1627 ------------------------------------------------------------------------
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1628 r207 | lh3lh3 | 2009-04-08 15:18:03 +0100 (Wed, 08 Apr 2009) | 2 lines
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1629 Changed paths:
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1630 M /trunk/samtools/examples/ex1.sam.gz
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1631
|
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1632 * fixed the problem in the example alignment due to the bug in fixmate
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1633
|
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1634 ------------------------------------------------------------------------
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1635 r206 | lh3lh3 | 2009-04-08 15:15:05 +0100 (Wed, 08 Apr 2009) | 3 lines
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1636 Changed paths:
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1637 M /trunk/samtools/bam_mate.c
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1638 M /trunk/samtools/bamtk.c
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1639 M /trunk/samtools/misc/soap2sam.pl
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1640
|
|
|
1641 * samtools-0.1.2-21
|
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1642 * fixed a nasty bug in `fixmate'
|
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1643
|
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1644 ------------------------------------------------------------------------
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1645 r205 | lh3lh3 | 2009-04-08 10:57:08 +0100 (Wed, 08 Apr 2009) | 2 lines
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1646 Changed paths:
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1647 M /trunk/samtools/misc/bowtie2sam.pl
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1648 M /trunk/samtools/misc/soap2sam.pl
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1649 M /trunk/samtools/misc/wgsim_eval.pl
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1650
|
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|
1651 make the script robust to the bugs in SOAP-2.1.7
|
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1652
|
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1653 ------------------------------------------------------------------------
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1654 r200 | lh3lh3 | 2009-04-02 15:14:56 +0100 (Thu, 02 Apr 2009) | 3 lines
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1655 Changed paths:
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1656 M /trunk/samtools/bam_stat.c
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1657 M /trunk/samtools/bamtk.c
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1658
|
|
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1659 * samtools-0.1.2-20
|
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1660 * check if file is truncated in flagstat
|
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1661
|
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|
1662 ------------------------------------------------------------------------
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1663 r199 | lh3lh3 | 2009-04-02 15:09:10 +0100 (Thu, 02 Apr 2009) | 3 lines
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1664 Changed paths:
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1665 M /trunk/samtools/bamtk.c
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1666
|
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|
1667 * samtools-0.1.2-19
|
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1668 * print the header if requested
|
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1669
|
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1670 ------------------------------------------------------------------------
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1671 r193 | lh3lh3 | 2009-03-27 15:09:50 +0000 (Fri, 27 Mar 2009) | 3 lines
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1672 Changed paths:
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1673 M /trunk/samtools/bam_plcmd.c
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1674 M /trunk/samtools/bamtk.c
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1675
|
|
|
1676 * samtools-0.1.2-18
|
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1677 * fixed a minor bug reported by Nils Homer
|
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1678
|
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|
1679 ------------------------------------------------------------------------
|
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1680 r185 | lh3lh3 | 2009-03-24 11:50:32 +0000 (Tue, 24 Mar 2009) | 2 lines
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1681 Changed paths:
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1682 A /trunk/samtools/Makefile (from /trunk/samtools/Makefile.std:184)
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1683 D /trunk/samtools/Makefile.std
|
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1684 A /trunk/samtools/misc/Makefile (from /trunk/samtools/misc/Makefile.std:184)
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1685 D /trunk/samtools/misc/Makefile.std
|
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1686
|
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|
1687 rename Makefile.std as Makefile. GNU building systerm is not ready and may take some time...
|
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1688
|
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1689 ------------------------------------------------------------------------
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1690 r184 | lh3lh3 | 2009-03-24 10:36:38 +0000 (Tue, 24 Mar 2009) | 4 lines
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1691 Changed paths:
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1692 D /trunk/samtools/Makefile
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1693 A /trunk/samtools/Makefile.std (from /trunk/samtools/Makefile:183)
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1694 M /trunk/samtools/bam_sort.c
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1695 M /trunk/samtools/bam_tview.c
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1696 M /trunk/samtools/bamtk.c
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1697 D /trunk/samtools/misc/Makefile
|
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1698 A /trunk/samtools/misc/Makefile.std (from /trunk/samtools/misc/Makefile:182)
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1699 M /trunk/samtools/samtools.1
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1700
|
|
|
1701 * samtools-0.1.2-17
|
|
|
1702 * incorporating Nils' changes
|
|
|
1703 * rename Makefile to Makefile.std and prepare to add the GNU building systerms (also by Nils)
|
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1704
|
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|
1705 ------------------------------------------------------------------------
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1706 r183 | lh3lh3 | 2009-03-24 10:30:23 +0000 (Tue, 24 Mar 2009) | 4 lines
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1707 Changed paths:
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1708 M /trunk/samtools/Makefile
|
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1709 M /trunk/samtools/bam_import.c
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1710 M /trunk/samtools/bam_maqcns.c
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1711 M /trunk/samtools/bam_maqcns.h
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1712 M /trunk/samtools/bam_plcmd.c
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1713 M /trunk/samtools/bamtk.c
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1714 M /trunk/samtools/kseq.h
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1715 A /trunk/samtools/kstring.c
|
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1716 A /trunk/samtools/kstring.h
|
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1717
|
|
|
1718 * samtools-0.1.2-16
|
|
|
1719 * made pileup take a list of proposed indels. An insertion is N at the moment.
|
|
|
1720 * added my kstring library for a bit complex parsing of the position list.
|
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1721
|
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|
1722 ------------------------------------------------------------------------
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|
1723 r169 | lh3lh3 | 2009-03-12 13:40:14 +0000 (Thu, 12 Mar 2009) | 3 lines
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1724 Changed paths:
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1725 M /trunk/samtools/misc/soap2sam.pl
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1726
|
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1727 * soap2sam.pl-0.1.2
|
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1728 * more robust to truncated soap output
|
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1729
|
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|
1730 ------------------------------------------------------------------------
|
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|
1731 r168 | lh3lh3 | 2009-03-11 10:49:00 +0000 (Wed, 11 Mar 2009) | 2 lines
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1732 Changed paths:
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1733 M /trunk/samtools/Makefile.lite
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1734
|
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|
1735 added bam_stat.o to Makefile.lite
|
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1736
|
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|
1737 ------------------------------------------------------------------------
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1738 r167 | lh3lh3 | 2009-03-10 22:11:31 +0000 (Tue, 10 Mar 2009) | 3 lines
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1739 Changed paths:
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1740 M /trunk/samtools/bam_maqcns.c
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1741 M /trunk/samtools/bamtk.c
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1742
|
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1743 * samtools-0.1.2-15
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1744 * generate RMS of mapQ instead of max mapQ
|
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1745
|
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|
1746 ------------------------------------------------------------------------
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1747 r166 | lh3lh3 | 2009-03-10 22:06:45 +0000 (Tue, 10 Mar 2009) | 3 lines
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1748 Changed paths:
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1749 M /trunk/samtools/bam_plcmd.c
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1750 M /trunk/samtools/bamtk.c
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|
1751 M /trunk/samtools/glf.c
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1752 M /trunk/samtools/glf.h
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1753 M /trunk/samtools/misc/Makefile
|
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1754
|
|
|
1755 * samtools-0.1.2-14
|
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|
1756 * implemented GLFv3
|
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1757
|
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|
1758 ------------------------------------------------------------------------
|
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1759 r159 | lh3lh3 | 2009-03-03 11:26:08 +0000 (Tue, 03 Mar 2009) | 3 lines
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1760 Changed paths:
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1761 M /trunk/samtools/bam_plcmd.c
|
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1762 M /trunk/samtools/bamtk.c
|
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1763
|
|
|
1764 * samtools-0.1.2-13
|
|
|
1765 * fixed a minor bug in displaying pileup
|
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1766
|
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|
1767 ------------------------------------------------------------------------
|
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1768 r158 | lh3lh3 | 2009-03-03 11:24:16 +0000 (Tue, 03 Mar 2009) | 3 lines
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1769 Changed paths:
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1770 M /trunk/samtools/ChangeLog
|
|
|
1771 M /trunk/samtools/bamtk.c
|
|
|
1772
|
|
|
1773 * samtools-0.1.2-12
|
|
|
1774 * optionally print SAM header
|
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|
1775
|
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|
1776 ------------------------------------------------------------------------
|
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|
1777 r153 | lh3lh3 | 2009-03-02 10:45:28 +0000 (Mon, 02 Mar 2009) | 3 lines
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1778 Changed paths:
|
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|
1779 M /trunk/samtools/bamtk.c
|
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|
1780 M /trunk/samtools/glf.c
|
|
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1781
|
|
|
1782 * samtools-0.1.2-11
|
|
|
1783 * use "GLF\3" as the magic for GLFv3 files
|
|
|
1784
|
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|
1785 ------------------------------------------------------------------------
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1786 r152 | lh3lh3 | 2009-03-02 10:39:09 +0000 (Mon, 02 Mar 2009) | 5 lines
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1787 Changed paths:
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|
1788 M /trunk/samtools/Makefile
|
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|
1789 M /trunk/samtools/bam_import.c
|
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1790 M /trunk/samtools/bam_index.c
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|
1791 M /trunk/samtools/bam_plcmd.c
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1792 M /trunk/samtools/bamtk.c
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1793 M /trunk/samtools/glf.c
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1794 M /trunk/samtools/glf.h
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1795
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1796 * samtools-0.1.2-10
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1797 * fixed a bug in import: core.bin is undefined for unmapped reads
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1798 * this bug can be alleviated (not completely solved) in bam_index.c
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1799 * update to GLFv3: pos is changed to offset for better compression
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1800
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1801 ------------------------------------------------------------------------
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1802 r151 | lh3lh3 | 2009-03-01 15:18:43 +0000 (Sun, 01 Mar 2009) | 3 lines
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1803 Changed paths:
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1804 M /trunk/samtools/misc/wgsim.c
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1805
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1806 * wgsim-0.2.3
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1807 * fixed a bug in simulating indels
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1808
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1809 ------------------------------------------------------------------------
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1810 r145 | lh3lh3 | 2009-02-26 19:43:57 +0000 (Thu, 26 Feb 2009) | 4 lines
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1811 Changed paths:
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1812 M /trunk/samtools/misc/wgsim.c
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1813
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1814 * wgsim-0.2.2
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1815 * allow to print mismatch information as fastq comment. MAQ does
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1816 not like long read names.
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1817
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1818 ------------------------------------------------------------------------
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1819 r141 | lh3lh3 | 2009-02-26 14:53:03 +0000 (Thu, 26 Feb 2009) | 6 lines
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1820 Changed paths:
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1821 M /trunk/samtools/ChangeLog
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1822 M /trunk/samtools/misc/wgsim.c
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1823 M /trunk/samtools/misc/wgsim_eval.pl
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1824
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1825 * wgsim-0.2.1
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1826 * fixed a bug about color read coordinates
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1827 * fixed a bug in read names
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1828 * wgsim_eval.pl-0.1.3
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1829 * make the script work with color reads
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1830
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1831 ------------------------------------------------------------------------
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1832 r140 | lh3lh3 | 2009-02-26 14:02:57 +0000 (Thu, 26 Feb 2009) | 2 lines
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1833 Changed paths:
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1834 M /trunk/samtools/misc/Makefile
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1835 M /trunk/samtools/misc/wgsim.c
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1836
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1837 * wgsim: added a note
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1838
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1839 ------------------------------------------------------------------------
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1840 r139 | lh3lh3 | 2009-02-26 11:39:08 +0000 (Thu, 26 Feb 2009) | 7 lines
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1841 Changed paths:
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1842 M /trunk/samtools/misc/wgsim.c
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1843 M /trunk/samtools/misc/wgsim_eval.pl
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1844
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1845 * wgsim-0.2.0
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1846 * considerable code clean up
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1847 * print number of substitutions/indels/errors on each read
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1848 * potentially support SOLiD simulation, though not tested at the moment
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1849 * wgsim_eval.pl-0.1.2
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1850 * change in accordant with wgsim
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1851
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1852 ------------------------------------------------------------------------
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1853 r129 | lh3lh3 | 2009-02-18 22:23:27 +0000 (Wed, 18 Feb 2009) | 3 lines
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1854 Changed paths:
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1855 M /trunk/samtools/bam_index.c
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1856 M /trunk/samtools/bamtk.c
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1857
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1858 * samtools-0.1.2-9
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1859 * fixed a bug in bam_fetch, caused by completely contained adjacent chunks
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1860
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1861 ------------------------------------------------------------------------
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1862 r128 | bhandsaker | 2009-02-18 19:06:57 +0000 (Wed, 18 Feb 2009) | 2 lines
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1863 Changed paths:
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1864 M /trunk/samtools/bamtk.c
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1865
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1866 Fix annoying segv when invalid region specified.
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1867
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1868 ------------------------------------------------------------------------
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1869 r127 | lh3lh3 | 2009-02-17 10:49:55 +0000 (Tue, 17 Feb 2009) | 2 lines
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1870 Changed paths:
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1871 D /trunk/samtools/misc/indel_filter.pl
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1872 A /trunk/samtools/misc/samtools.pl
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1873
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1874 * move indel_filter.pl to samtools.pl
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1875
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1876 ------------------------------------------------------------------------
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1877 r126 | lh3lh3 | 2009-02-14 21:22:30 +0000 (Sat, 14 Feb 2009) | 3 lines
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1878 Changed paths:
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1879 M /trunk/samtools/bam_mate.c
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1880 M /trunk/samtools/bamtk.c
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1881
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1882 * samtools-0.1.2-7
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1883 * fixed a bug in fixmate: SE reads are flagged as BAM_FMUNMAP
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1884
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1885 ------------------------------------------------------------------------
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1886 r125 | lh3lh3 | 2009-02-13 09:54:45 +0000 (Fri, 13 Feb 2009) | 3 lines
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1887 Changed paths:
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1888 M /trunk/samtools/bam_stat.c
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1889 M /trunk/samtools/bamtk.c
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1890
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1891 * samtools-0.1.2-7
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1892 * fixed a minor bug in flagstat
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1893
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1894 ------------------------------------------------------------------------
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1895 r124 | lh3lh3 | 2009-02-12 11:15:32 +0000 (Thu, 12 Feb 2009) | 3 lines
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1896 Changed paths:
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1897 M /trunk/samtools/bam_maqcns.c
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1898 M /trunk/samtools/bamtk.c
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1899 M /trunk/samtools/misc/indel_filter.pl
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1900
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1901 * samtools-0.1.2-6
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1902 * improve indel caller by setting maximum window size
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1903
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1904 ------------------------------------------------------------------------
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1905 r123 | lh3lh3 | 2009-02-12 10:30:29 +0000 (Thu, 12 Feb 2009) | 2 lines
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1906 Changed paths:
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1907 M /trunk/samtools/bam_plcmd.c
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1908 M /trunk/samtools/bamtk.c
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1909
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1910 * output max mapping quality in indel line
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1911
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1912 ------------------------------------------------------------------------
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1913 r122 | lh3lh3 | 2009-02-11 10:59:10 +0000 (Wed, 11 Feb 2009) | 2 lines
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1914 Changed paths:
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1915 M /trunk/samtools/misc/maq2sam.c
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1916
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1917 fixed a bug in generating tag AM
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1918
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1919 ------------------------------------------------------------------------
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1920 r121 | lh3lh3 | 2009-02-03 10:43:11 +0000 (Tue, 03 Feb 2009) | 2 lines
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1921 Changed paths:
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1922 M /trunk/samtools/bam_index.c
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1923 M /trunk/samtools/bamtk.c
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1924
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1925 fixed a potential memory problem in indexing
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1926
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1927 ------------------------------------------------------------------------
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1928 r120 | bhandsaker | 2009-02-02 15:52:52 +0000 (Mon, 02 Feb 2009) | 2 lines
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1929 Changed paths:
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1930 M /trunk/samtools/Makefile
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1931
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1932 Pass LIBS to recursive targets to facilitate building at Broad.
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1933
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1934 ------------------------------------------------------------------------
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1935 r119 | lh3lh3 | 2009-02-02 10:12:15 +0000 (Mon, 02 Feb 2009) | 4 lines
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1936 Changed paths:
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1937 M /trunk/samtools/ChangeLog
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1938 M /trunk/samtools/bam_plcmd.c
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1939 M /trunk/samtools/bam_stat.c
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1940 M /trunk/samtools/bamtk.c
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1941
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1942 * samtools-0.1.2-3
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1943 * fixed a bug in generating GLFv2 for indels
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1944 * improve flagstat report a little bit
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1945
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1946 ------------------------------------------------------------------------
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1947 r118 | lh3lh3 | 2009-01-29 12:33:23 +0000 (Thu, 29 Jan 2009) | 3 lines
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1948 Changed paths:
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1949 M /trunk/samtools/Makefile
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1950 A /trunk/samtools/bam_stat.c
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1951 M /trunk/samtools/bamtk.c
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1952
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1953 * samtools-0.1.2-1
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1954 * added flagstat command
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1955
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1956 ------------------------------------------------------------------------
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1957 r116 | lh3lh3 | 2009-01-28 13:31:12 +0000 (Wed, 28 Jan 2009) | 2 lines
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1958 Changed paths:
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1959 M /trunk/samtools/ChangeLog
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1960 M /trunk/samtools/NEWS
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1961 M /trunk/samtools/bamtk.c
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1962 M /trunk/samtools/samtools.1
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1963
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1964 Release SAMtools-0.1.2
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1965
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1966 ------------------------------------------------------------------------
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1967 r115 | lh3lh3 | 2009-01-28 12:54:08 +0000 (Wed, 28 Jan 2009) | 2 lines
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1968 Changed paths:
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1969 A /trunk/samtools/misc/indel_filter.pl
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1970
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1971 Script for filtering indel results
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1972
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1973 ------------------------------------------------------------------------
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1974 r114 | lh3lh3 | 2009-01-25 11:45:37 +0000 (Sun, 25 Jan 2009) | 2 lines
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1975 Changed paths:
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1976 A /trunk/samtools/misc/zoom2sam.pl
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1977
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1978 convert ZOOM to SAM
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1979
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1980 ------------------------------------------------------------------------
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1981 r113 | lh3lh3 | 2009-01-24 14:25:07 +0000 (Sat, 24 Jan 2009) | 2 lines
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1982 Changed paths:
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1983 A /trunk/samtools/misc/novo2sam.pl
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1984
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1985 add a script to convert novo alignment to SAM
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1986
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1987 ------------------------------------------------------------------------
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1988 r112 | lh3lh3 | 2009-01-23 20:57:39 +0000 (Fri, 23 Jan 2009) | 2 lines
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1989 Changed paths:
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1990 M /trunk/samtools/ChangeLog
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1991 M /trunk/samtools/ChangeLog.old
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1992 M /trunk/samtools/samtools.1
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1993
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1994 update documentation and ChangeLog
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1995
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1996 ------------------------------------------------------------------------
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1997 r111 | lh3lh3 | 2009-01-23 19:22:59 +0000 (Fri, 23 Jan 2009) | 3 lines
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1998 Changed paths:
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1999 M /trunk/samtools/bam_sort.c
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2000 M /trunk/samtools/bamtk.c
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2001
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2002 * samtools-0.1.1-19
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2003 * fixed a bug in "merge" command line
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2004
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2005 ------------------------------------------------------------------------
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2006 r110 | lh3lh3 | 2009-01-22 15:36:48 +0000 (Thu, 22 Jan 2009) | 3 lines
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2007 Changed paths:
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2008 M /trunk/samtools/misc/Makefile
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2009 A /trunk/samtools/misc/bowtie2sam.pl (from /branches/dev/samtools/misc/bowtie2sam.pl:108)
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2010 M /trunk/samtools/misc/export2sam.pl
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2011 A /trunk/samtools/misc/soap2sam.pl (from /branches/dev/samtools/misc/soap2sam.pl:108)
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2012 A /trunk/samtools/misc/wgsim.c (from /branches/dev/samtools/misc/wgsim.c:108)
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2013 A /trunk/samtools/misc/wgsim_eval.pl (from /branches/dev/samtools/misc/wgsim_eval.pl:108)
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2014
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2015 * merge from branches/dev/
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2016 * all future development will happen here
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2017
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2018 ------------------------------------------------------------------------
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2019 r109 | lh3lh3 | 2009-01-22 15:14:27 +0000 (Thu, 22 Jan 2009) | 3 lines
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2020 Changed paths:
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2021 M /trunk/samtools/COPYING
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2022 M /trunk/samtools/ChangeLog
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2023 A /trunk/samtools/INSTALL (from /branches/dev/samtools/INSTALL:108)
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2024 M /trunk/samtools/Makefile
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2025 A /trunk/samtools/Makefile.lite (from /branches/dev/samtools/Makefile.lite:108)
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2026 M /trunk/samtools/bam.c
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2027 M /trunk/samtools/bam.h
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2028 M /trunk/samtools/bam_import.c
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2029 M /trunk/samtools/bam_index.c
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2030 M /trunk/samtools/bam_lpileup.c
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2031 M /trunk/samtools/bam_maqcns.c
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2032 M /trunk/samtools/bam_maqcns.h
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2033 A /trunk/samtools/bam_mate.c (from /branches/dev/samtools/bam_mate.c:108)
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2034 M /trunk/samtools/bam_pileup.c
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2035 M /trunk/samtools/bam_plcmd.c
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2036 A /trunk/samtools/bam_rmdup.c (from /branches/dev/samtools/bam_rmdup.c:108)
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2037 M /trunk/samtools/bam_sort.c
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2038 M /trunk/samtools/bamtk.c
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2039 M /trunk/samtools/bgzf.h
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2040 M /trunk/samtools/examples/00README.txt
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2041 A /trunk/samtools/examples/Makefile (from /branches/dev/samtools/examples/Makefile:108)
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2042 D /trunk/samtools/examples/ex1.fa.fai
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2043 M /trunk/samtools/examples/ex1.sam.gz
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2044 M /trunk/samtools/faidx.c
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2045 A /trunk/samtools/glf.c (from /branches/dev/samtools/glf.c:108)
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2046 M /trunk/samtools/glf.h
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2047 M /trunk/samtools/misc/Makefile
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2048 M /trunk/samtools/misc/maq2sam.c
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2049 M /trunk/samtools/razf.c
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2050 M /trunk/samtools/source.dot
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2051
|
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2052 * Merge from branches/dev/
|
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2053 * all future development will happen here at trunk/
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2054
|
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2055 ------------------------------------------------------------------------
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2056 r79 | bhandsaker | 2009-01-07 21:42:15 +0000 (Wed, 07 Jan 2009) | 2 lines
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2057 Changed paths:
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2058 M /trunk/samtools/bam_maqcns.c
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2059 M /trunk/samtools/bam_tview.c
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2060
|
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2061 Fix problem with compiling without curses.
|
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2062
|
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2063 ------------------------------------------------------------------------
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2064 r63 | lh3lh3 | 2008-12-22 15:58:02 +0000 (Mon, 22 Dec 2008) | 2 lines
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2065 Changed paths:
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2066 A /trunk/samtools (from /branches/dev/samtools:62)
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2067
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2068 Create trunk copy
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2069
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2070 ------------------------------------------------------------------------
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2071 r62 | lh3lh3 | 2008-12-22 15:55:13 +0000 (Mon, 22 Dec 2008) | 2 lines
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2072 Changed paths:
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2073 A /branches/dev/samtools/NEWS
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2074 M /branches/dev/samtools/bamtk.c
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2075 M /branches/dev/samtools/samtools.1
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2076
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2077 Release samtools-0.1.1
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2078
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2079 ------------------------------------------------------------------------
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2080 r61 | lh3lh3 | 2008-12-22 15:46:08 +0000 (Mon, 22 Dec 2008) | 10 lines
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2081 Changed paths:
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2082 M /branches/dev/samtools/bam_aux.c
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2083 M /branches/dev/samtools/bam_index.c
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2084 M /branches/dev/samtools/bam_plcmd.c
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2085 M /branches/dev/samtools/bam_tview.c
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2086 M /branches/dev/samtools/bamtk.c
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2087 M /branches/dev/samtools/razf.c
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2088 M /branches/dev/samtools/samtools.1
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2089
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2090 * samtools-0.1.0-66
|
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|
2091 * fixed a bug in razf.c: reset z_eof when razf_seek() is called
|
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|
2092 * fixed a memory leak in parsing a region
|
|
|
2093 * changed pileup a little bit when -s is in use: output ^ and $
|
|
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2094 * when a bam is not indexed, output more meaningful error message
|
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|
2095 * fixed a bug in indexing for small alignment
|
|
|
2096 * fixed a bug in the viewer when we come to the end of a reference file
|
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|
2097 * updated documentation
|
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|
2098 * prepare to release 0.1.1
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2099
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2100 ------------------------------------------------------------------------
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2101 r60 | lh3lh3 | 2008-12-22 15:10:16 +0000 (Mon, 22 Dec 2008) | 2 lines
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2102 Changed paths:
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2103 A /branches/dev/samtools/examples
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2104 A /branches/dev/samtools/examples/00README.txt
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2105 A /branches/dev/samtools/examples/ex1.fa
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2106 A /branches/dev/samtools/examples/ex1.fa.fai
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2107 A /branches/dev/samtools/examples/ex1.sam.gz
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2108
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2109 example
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2110
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2111 ------------------------------------------------------------------------
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2112 r59 | lh3lh3 | 2008-12-22 09:38:15 +0000 (Mon, 22 Dec 2008) | 2 lines
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2113 Changed paths:
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2114 M /branches/dev/samtools/ChangeLog
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2115
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2116 update ChangeLog
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2117
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2118 ------------------------------------------------------------------------
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2119 r58 | lh3lh3 | 2008-12-20 23:06:00 +0000 (Sat, 20 Dec 2008) | 3 lines
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2120 Changed paths:
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2121 M /branches/dev/samtools/misc/export2sam.pl
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2122
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2123 * added comments
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2124 * fixed several bugs
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2125
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2126 ------------------------------------------------------------------------
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2127 r57 | lh3lh3 | 2008-12-20 15:44:20 +0000 (Sat, 20 Dec 2008) | 2 lines
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2128 Changed paths:
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2129 A /branches/dev/samtools/misc/export2sam.pl
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2130
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2131 convert Export format to SAM; not thoroughly tested
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2132
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2133 ------------------------------------------------------------------------
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2134 r56 | lh3lh3 | 2008-12-19 22:13:28 +0000 (Fri, 19 Dec 2008) | 6 lines
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2135 Changed paths:
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2136 M /branches/dev/samtools/bam_import.c
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2137 M /branches/dev/samtools/bam_plcmd.c
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2138 M /branches/dev/samtools/bam_tview.c
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2139 M /branches/dev/samtools/bamtk.c
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2140 A /branches/dev/samtools/source.dot
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2141
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2142 * samtools-0.1.0-65
|
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2143 * pileup: generate maq-like simple output
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2144 * pileup: allow to output pileup at required sites
|
|
|
2145 * source.dot: source file relationship graph
|
|
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2146 * tview: fixed a minor bug
|
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2147
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2148 ------------------------------------------------------------------------
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2149 r55 | lh3lh3 | 2008-12-19 20:10:26 +0000 (Fri, 19 Dec 2008) | 2 lines
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2150 Changed paths:
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2151 D /branches/dev/samtools/misc/all2sam.pl
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2152
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2153 remove all2sam.pl
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2154
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2155 ------------------------------------------------------------------------
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2156 r54 | lh3lh3 | 2008-12-16 22:34:25 +0000 (Tue, 16 Dec 2008) | 2 lines
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2157 Changed paths:
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2158 A /branches/dev/samtools/COPYING
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2159 M /branches/dev/samtools/bam.h
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2160 M /branches/dev/samtools/faidx.h
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2161 M /branches/dev/samtools/khash.h
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2162 M /branches/dev/samtools/kseq.h
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2163 M /branches/dev/samtools/ksort.h
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2164 M /branches/dev/samtools/samtools.1
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2165
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2166 Added copyright information and a bit more documentation. No code change.
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2167
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2168 ------------------------------------------------------------------------
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2169 r53 | lh3lh3 | 2008-12-16 13:40:18 +0000 (Tue, 16 Dec 2008) | 3 lines
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2170 Changed paths:
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2171 M /branches/dev/samtools/bam.c
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2172 M /branches/dev/samtools/bam.h
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2173 M /branches/dev/samtools/bam_index.c
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2174 M /branches/dev/samtools/bam_maqcns.c
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2175 M /branches/dev/samtools/bamtk.c
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2176
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2177 * samtools-0.1.0-64
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2178 * improved efficiency of the indel caller for spliced alignments
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2179
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2180 ------------------------------------------------------------------------
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2181 r52 | lh3lh3 | 2008-12-16 10:28:20 +0000 (Tue, 16 Dec 2008) | 3 lines
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2182 Changed paths:
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2183 M /branches/dev/samtools/bam.c
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2184 M /branches/dev/samtools/bam.h
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2185 M /branches/dev/samtools/bam_aux.c
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2186 M /branches/dev/samtools/bam_index.c
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2187 M /branches/dev/samtools/bamtk.c
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2188
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2189 * samtools-0.1.0-63
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2190 * a bit code cleanup: reduce the dependency between source files
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2191
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2192 ------------------------------------------------------------------------
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2193 r51 | lh3lh3 | 2008-12-15 14:29:32 +0000 (Mon, 15 Dec 2008) | 3 lines
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2194 Changed paths:
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2195 M /branches/dev/samtools/bam_maqcns.c
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2196 M /branches/dev/samtools/bam_plcmd.c
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2197 M /branches/dev/samtools/bamtk.c
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2198
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2199 * samtools-0.1.0-62
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2200 * fixed a memory leak
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2201
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2202 ------------------------------------------------------------------------
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2203 r50 | lh3lh3 | 2008-12-15 14:00:13 +0000 (Mon, 15 Dec 2008) | 2 lines
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2204 Changed paths:
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2205 M /branches/dev/samtools/ChangeLog
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2206 M /branches/dev/samtools/bam.h
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2207 M /branches/dev/samtools/samtools.1
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2208
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2209 update documentation, ChangeLog and a comment
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2210
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2211 ------------------------------------------------------------------------
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2212 r49 | lh3lh3 | 2008-12-15 13:36:43 +0000 (Mon, 15 Dec 2008) | 6 lines
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2213 Changed paths:
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2214 M /branches/dev/samtools/Makefile
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2215 M /branches/dev/samtools/bam.h
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2216 M /branches/dev/samtools/bam_maqcns.c
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2217 M /branches/dev/samtools/bam_maqcns.h
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2218 M /branches/dev/samtools/bam_pileup.c
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2219 A /branches/dev/samtools/bam_plcmd.c
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2220 M /branches/dev/samtools/bamtk.c
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2221 M /branches/dev/samtools/samtools.1
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2222
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2223 * samtools-0.1.0-61
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2224 * moved pileup command to a separate source file
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2225 * added indel caller
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2226 * added bam_cal_segend(). (NOT WORKING for spliced alignment!!!)
|
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2227 * updated documentation
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2228
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2229 ------------------------------------------------------------------------
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2230 r48 | lh3lh3 | 2008-12-12 13:55:36 +0000 (Fri, 12 Dec 2008) | 3 lines
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2231 Changed paths:
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2232 M /branches/dev/samtools/bam_maqcns.c
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2233 M /branches/dev/samtools/bamtk.c
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2234
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2235 * samtools-0.1.0-60
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2236 * fixed another bug in maqcns when there is a nearby deletion
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2237
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2238 ------------------------------------------------------------------------
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2239 r47 | lh3lh3 | 2008-12-12 13:42:16 +0000 (Fri, 12 Dec 2008) | 5 lines
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2240 Changed paths:
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2241 M /branches/dev/samtools/bam_maqcns.c
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2242 M /branches/dev/samtools/bam_pileup.c
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2243 M /branches/dev/samtools/bamtk.c
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2244
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2245 * samtools-0.1.0-59
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2246 * pileup: outputing consensus is now optional
|
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2247 * fixed a bug in glfgen. This bug also exists in maq's glfgen. However,
|
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2248 I am not quite sure why the previous version may have problem.
|
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2249
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2250 ------------------------------------------------------------------------
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2251 r46 | lh3lh3 | 2008-12-12 11:44:56 +0000 (Fri, 12 Dec 2008) | 6 lines
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2252 Changed paths:
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2253 M /branches/dev/samtools/bam_pileup.c
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2254 M /branches/dev/samtools/bamtk.c
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2255
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2256 * samtools-0.1.0-58
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2257 * add maq consensus to pileup. However, I will move this part to a new
|
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2258 command as strictly speaking, consensus callin is not part of pileup,
|
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2259 and imposing it would make it harder to generate for other language
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2260 bindings.
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2261
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2262 ------------------------------------------------------------------------
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2263 r45 | bhandsaker | 2008-12-11 20:43:56 +0000 (Thu, 11 Dec 2008) | 2 lines
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2264 Changed paths:
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2265 M /branches/dev/samtools/bgzf.c
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2266
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2267 Fix bug in tell() after reads that consume to the exact end of a block.
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2268
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2269 ------------------------------------------------------------------------
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2270 r44 | lh3lh3 | 2008-12-11 09:36:53 +0000 (Thu, 11 Dec 2008) | 2 lines
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2271 Changed paths:
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2272 M /branches/dev/samtools/samtools.1
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2273
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2274 update manual
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2275
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2276 ------------------------------------------------------------------------
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2277 r43 | lh3lh3 | 2008-12-11 09:25:36 +0000 (Thu, 11 Dec 2008) | 4 lines
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2278 Changed paths:
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2279 M /branches/dev/samtools/bam_import.c
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2280 M /branches/dev/samtools/bamtk.c
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2281
|
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2282 * samtools-0.1.0-57
|
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2283 * fixed a bug in parser when there is auxiliary fields
|
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2284 * made the parser a bit more robust
|
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2285
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2286 ------------------------------------------------------------------------
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2287 r42 | lh3lh3 | 2008-12-10 14:57:29 +0000 (Wed, 10 Dec 2008) | 5 lines
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2288 Changed paths:
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2289 M /branches/dev/samtools/bam_index.c
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2290 M /branches/dev/samtools/bamtk.c
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2291 M /branches/dev/samtools/bgzf.c
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2292
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2293 * samtools-0.1.0-56
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2294 * fixed a bug in bgzf (only reading is affected)
|
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2295 * fixed a typo in bam_index.c
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2296 * in bam_index.c, check potential bugs in the underlying I/O library
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2297
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2298 ------------------------------------------------------------------------
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2299 r41 | lh3lh3 | 2008-12-10 12:53:08 +0000 (Wed, 10 Dec 2008) | 2 lines
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2300 Changed paths:
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2301 M /branches/dev/samtools/samtools.1
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2302
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2303 update manual
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2304
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2305 ------------------------------------------------------------------------
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2306 r40 | lh3lh3 | 2008-12-10 11:52:10 +0000 (Wed, 10 Dec 2008) | 5 lines
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2307 Changed paths:
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2308 M /branches/dev/samtools/bam.h
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2309 M /branches/dev/samtools/bam_pileup.c
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2310 M /branches/dev/samtools/bamtk.c
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2311
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2312 * samtools-0.1.0-55
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2313 * tried to make pileup work with clipping (previously not), though NOT tested
|
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2314 * removed -v from pileup
|
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2315 * made pileup take the reference sequence
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2316
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2317 ------------------------------------------------------------------------
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2318 r39 | lh3lh3 | 2008-12-09 11:59:28 +0000 (Tue, 09 Dec 2008) | 4 lines
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2319 Changed paths:
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2320 M /branches/dev/samtools/bam_import.c
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2321 M /branches/dev/samtools/bamtk.c
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2322 M /branches/dev/samtools/samtools.1
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2323
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2324 * samtools-0.1.0-54
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2325 * in parser, recognize "=", rather than ",", as a match
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2326 * in parser, correctl parse "=" at the MRNM field.
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2327
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2328 ------------------------------------------------------------------------
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2329 r38 | lh3lh3 | 2008-12-09 11:39:07 +0000 (Tue, 09 Dec 2008) | 2 lines
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2330 Changed paths:
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2331 M /branches/dev/samtools/misc/maq2sam.c
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2332
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2333 fixed a bug in handling maq flag 64 and 192
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2334
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2335 ------------------------------------------------------------------------
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2336 r37 | lh3lh3 | 2008-12-09 09:53:46 +0000 (Tue, 09 Dec 2008) | 2 lines
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2337 Changed paths:
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2338 M /branches/dev/samtools/misc/md5fa.c
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2339
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2340 also calculate unordered md5sum check
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2341
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2342 ------------------------------------------------------------------------
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2343 r36 | lh3lh3 | 2008-12-09 09:46:21 +0000 (Tue, 09 Dec 2008) | 2 lines
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2344 Changed paths:
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2345 M /branches/dev/samtools/misc/md5fa.c
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2346
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2347 fixed a minor bug when there are space in the sequence
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2348
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2349 ------------------------------------------------------------------------
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2350 r35 | lh3lh3 | 2008-12-09 09:40:45 +0000 (Tue, 09 Dec 2008) | 2 lines
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2351 Changed paths:
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2352 M /branches/dev/samtools/misc/md5fa.c
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2353
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2354 fixed a potential memory leak
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2355
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2356 ------------------------------------------------------------------------
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2357 r34 | lh3lh3 | 2008-12-08 14:52:17 +0000 (Mon, 08 Dec 2008) | 2 lines
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2358 Changed paths:
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2359 M /branches/dev/samtools/bam_import.c
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2360 M /branches/dev/samtools/bam_index.c
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2361 M /branches/dev/samtools/bamtk.c
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2362
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2363 * fixed a bug in import: bin is wrongly calculated
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2364
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2365 ------------------------------------------------------------------------
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2366 r33 | lh3lh3 | 2008-12-08 14:08:01 +0000 (Mon, 08 Dec 2008) | 2 lines
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2367 Changed paths:
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2368 M /branches/dev/samtools/misc/all2sam.pl
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2369
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2370 nothing, really
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2371
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2372 ------------------------------------------------------------------------
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2373 r32 | lh3lh3 | 2008-12-08 12:56:02 +0000 (Mon, 08 Dec 2008) | 3 lines
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2374 Changed paths:
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2375 M /branches/dev/samtools/Makefile
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2376 M /branches/dev/samtools/kseq.h
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2377 M /branches/dev/samtools/misc/Makefile
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2378 A /branches/dev/samtools/misc/md5.c
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2379 A /branches/dev/samtools/misc/md5.h
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2380 A /branches/dev/samtools/misc/md5fa.c
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2381
|
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2382 * fixed two warnings in kseq.h
|
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2383 * added md5sum utilities
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2384
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2385 ------------------------------------------------------------------------
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2386 r31 | lh3lh3 | 2008-12-08 11:35:29 +0000 (Mon, 08 Dec 2008) | 5 lines
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2387 Changed paths:
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2388 M /branches/dev/samtools/Makefile
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2389 M /branches/dev/samtools/bam_import.c
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2390 M /branches/dev/samtools/bamtk.c
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2391 A /branches/dev/samtools/kseq.h
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2392 D /branches/dev/samtools/kstream.h
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2393
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2394 * samtools-0.1.0-52
|
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|
2395 * replace kstream with kseq. kseq is a superset of kstream. I need the
|
|
|
2396 extra functions in kseq.h.
|
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|
2397 * also compile stand-alone faidx
|
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2398
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2399 ------------------------------------------------------------------------
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2400 r30 | lh3lh3 | 2008-12-08 11:17:04 +0000 (Mon, 08 Dec 2008) | 3 lines
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2401 Changed paths:
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2402 M /branches/dev/samtools/bam.h
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2403 M /branches/dev/samtools/bam_sort.c
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2404 M /branches/dev/samtools/bamtk.c
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2405
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2406 * samtools-0.1.0-51
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2407 * sorting by read names is available
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2408
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2409 ------------------------------------------------------------------------
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2410 r29 | lh3lh3 | 2008-12-08 10:29:02 +0000 (Mon, 08 Dec 2008) | 3 lines
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2411 Changed paths:
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2412 M /branches/dev/samtools/bam.c
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2413 M /branches/dev/samtools/bam.h
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2414 M /branches/dev/samtools/bam_import.c
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2415 M /branches/dev/samtools/bam_maqcns.c
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2416 M /branches/dev/samtools/bam_pileup.c
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2417 M /branches/dev/samtools/bam_sort.c
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2418 M /branches/dev/samtools/bam_tview.c
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2419 M /branches/dev/samtools/bamtk.c
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2420 M /branches/dev/samtools/misc/maq2sam.c
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2421
|
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2422 * samtools-0.1.0-50
|
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|
2423 * format change to meet the latest specification
|
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2424
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2425 ------------------------------------------------------------------------
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2426 r28 | lh3lh3 | 2008-12-04 16:09:21 +0000 (Thu, 04 Dec 2008) | 3 lines
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2427 Changed paths:
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2428 M /branches/dev/samtools/bam_maqcns.c
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2429 M /branches/dev/samtools/misc/maq2sam.c
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2430
|
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|
2431 * minor change in maqcns: special care when n==0
|
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|
2432 * change maq2sam to meet the latest specification
|
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2433
|
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2434 ------------------------------------------------------------------------
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2435 r27 | lh3lh3 | 2008-12-04 15:55:44 +0000 (Thu, 04 Dec 2008) | 2 lines
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2436 Changed paths:
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2437 M /branches/dev/samtools/razf.c
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2438 M /branches/dev/samtools/razf.h
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2439
|
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|
2440 considerable code clean up in razf
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2441
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2442 ------------------------------------------------------------------------
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2443 r26 | lh3lh3 | 2008-12-04 15:08:18 +0000 (Thu, 04 Dec 2008) | 2 lines
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2444 Changed paths:
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2445 M /branches/dev/samtools/ChangeLog
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2446 M /branches/dev/samtools/Makefile
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2447 M /branches/dev/samtools/faidx.c
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2448
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2449 make RAZF optional in faidx.c
|
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2450
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2451 ------------------------------------------------------------------------
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2452 r25 | lh3lh3 | 2008-12-01 15:27:22 +0000 (Mon, 01 Dec 2008) | 3 lines
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2453 Changed paths:
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2454 M /branches/dev/samtools/Makefile
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2455 M /branches/dev/samtools/bam.h
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2456 M /branches/dev/samtools/bam_aux.c
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2457 M /branches/dev/samtools/bamtk.c
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2458 M /branches/dev/samtools/samtools.1
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2459
|
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2460 * samtools-0.1.0-49
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2461 * added routines for retrieving aux data, NOT TESTED YET!
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2462
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2463 ------------------------------------------------------------------------
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2464 r24 | lh3lh3 | 2008-12-01 14:29:43 +0000 (Mon, 01 Dec 2008) | 5 lines
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2465 Changed paths:
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2466 M /branches/dev/samtools/bam.c
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2467 M /branches/dev/samtools/bam_import.c
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2468 M /branches/dev/samtools/bam_maqcns.c
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2469 M /branches/dev/samtools/bamtk.c
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2470 M /branches/dev/samtools/bgzf.c
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2471 M /branches/dev/samtools/samtools.1
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2472
|
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|
2473 * samtools-0.1.0-48
|
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|
2474 * bgzf: fixed a potential integer overflow on 32-it machines
|
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|
2475 * maqcns: set the minimum combined quality as 0
|
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|
2476 * supporting hex strings
|
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2477
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2478 ------------------------------------------------------------------------
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2479 r23 | lh3lh3 | 2008-11-27 17:14:37 +0000 (Thu, 27 Nov 2008) | 3 lines
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2480 Changed paths:
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2481 M /branches/dev/samtools/bam_maqcns.c
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2482 M /branches/dev/samtools/bamtk.c
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2483
|
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2484 * samtools-0.1.0-47
|
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2485 * fixed the bug in maqcns
|
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2486
|
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2487 ------------------------------------------------------------------------
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2488 r22 | lh3lh3 | 2008-11-27 17:08:11 +0000 (Thu, 27 Nov 2008) | 3 lines
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2489 Changed paths:
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2490 M /branches/dev/samtools/Makefile
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2491 M /branches/dev/samtools/bam.h
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2492 A /branches/dev/samtools/bam_maqcns.c
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2493 A /branches/dev/samtools/bam_maqcns.h
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2494 M /branches/dev/samtools/bam_tview.c
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2495 M /branches/dev/samtools/bamtk.c
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2496 A /branches/dev/samtools/glf.h
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2497
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2498 * samtools-0.1.0-46
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2499 * add MAQ consensus caller, currently BUGGY!
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2500
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2501 ------------------------------------------------------------------------
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2502 r21 | lh3lh3 | 2008-11-27 13:51:28 +0000 (Thu, 27 Nov 2008) | 4 lines
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2503 Changed paths:
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2504 M /branches/dev/samtools/bam_pileup.c
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2505 M /branches/dev/samtools/bam_tview.c
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2506 M /branches/dev/samtools/bamtk.c
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2507
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2508 * samtools-0.1.0-45
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2509 * tview: display padded alignment (but not P operation)
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2510 * better coordinates and reference sequence
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2511
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2512 ------------------------------------------------------------------------
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2513 r19 | lh3lh3 | 2008-11-27 09:26:05 +0000 (Thu, 27 Nov 2008) | 2 lines
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2514 Changed paths:
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2515 A /branches/dev/samtools/ChangeLog
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2516
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2517 new ChangeLog
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2518
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2519 ------------------------------------------------------------------------
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2520 r18 | lh3lh3 | 2008-11-27 09:24:45 +0000 (Thu, 27 Nov 2008) | 3 lines
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2521 Changed paths:
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2522 D /branches/dev/samtools/ChangeLog
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2523 A /branches/dev/samtools/ChangeLog.old (from /branches/dev/samtools/ChangeLog:6)
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2524
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2525 Rename ChangeLog to ChangeLog.old. This old ChangeLog is generated from
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2526 the log of my personal SVN repository.
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2527
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2528 ------------------------------------------------------------------------
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2529 r17 | lh3lh3 | 2008-11-27 09:22:55 +0000 (Thu, 27 Nov 2008) | 6 lines
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2530 Changed paths:
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2531 M /branches/dev/samtools/Makefile
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2532 M /branches/dev/samtools/bamtk.c
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2533 M /branches/dev/samtools/bgzf.c
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2534
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2535 * samtools-0.1.0-44
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2536 * declare fseeko and ftello as some Linux may not do this by default and
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2537 missing these declarations will make bgzf buggy
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2538 * get rid of some harmless warings
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2539 * use BGZF by default, now
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2540
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2541 ------------------------------------------------------------------------
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2542 r16 | lh3lh3 | 2008-11-26 21:19:11 +0000 (Wed, 26 Nov 2008) | 4 lines
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2543 Changed paths:
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2544 M /branches/dev/samtools/bam_index.c
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2545 M /branches/dev/samtools/bamtk.c
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2546 M /branches/dev/samtools/razf.c
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2547
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2548 * samtools-0.1.0-43
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2549 * fixed a bug in razf_read()
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2550 * give more warnings when the file is truncated (or due to bugs in I/O library)
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2551
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2552 ------------------------------------------------------------------------
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2553 r15 | lh3lh3 | 2008-11-26 20:41:39 +0000 (Wed, 26 Nov 2008) | 2 lines
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2554 Changed paths:
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2555 M /branches/dev/samtools/bgzf.c
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2556
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2557 fixed a bug in bgzf.c at the end of the file
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2558
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2559 ------------------------------------------------------------------------
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2560 r14 | lh3lh3 | 2008-11-26 17:05:18 +0000 (Wed, 26 Nov 2008) | 4 lines
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2561 Changed paths:
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2562 M /branches/dev/samtools/bamtk.c
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2563
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2564 * samtools-0.1.0-42
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2565 * a lot happened to RAZF, although samtools itself is untouched. Better
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2566 also update the version number anyway to avoid confusion
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2567
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2568 ------------------------------------------------------------------------
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2569 r13 | lh3lh3 | 2008-11-26 17:03:48 +0000 (Wed, 26 Nov 2008) | 2 lines
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2570 Changed paths:
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2571 M /branches/dev/samtools/razf.c
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2572
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2573 a change from Jue, but I think it should not matter
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2574
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2575 ------------------------------------------------------------------------
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2576 r12 | lh3lh3 | 2008-11-26 16:48:14 +0000 (Wed, 26 Nov 2008) | 3 lines
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2577 Changed paths:
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2578 M /branches/dev/samtools/razf.c
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2579
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2580 fixed a potential bug in razf. However, it seems still buggy, just
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2581 rarely happens, very rarely.
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2582
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2583 ------------------------------------------------------------------------
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2584 r11 | lh3lh3 | 2008-11-26 14:02:56 +0000 (Wed, 26 Nov 2008) | 2 lines
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2585 Changed paths:
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2586 M /branches/dev/samtools/razf.c
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2587
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2588 fixed a bug in razf, with the help of Jue
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2589
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2590 ------------------------------------------------------------------------
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2591 r10 | lh3lh3 | 2008-11-26 11:55:32 +0000 (Wed, 26 Nov 2008) | 2 lines
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2592 Changed paths:
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2593 M /branches/dev/samtools/bam_index.c
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2594
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2595 remove a comment
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2596
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2597 ------------------------------------------------------------------------
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2598 r9 | lh3lh3 | 2008-11-26 11:37:05 +0000 (Wed, 26 Nov 2008) | 2 lines
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2599 Changed paths:
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2600 M /branches/dev/samtools/Makefile
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2601 M /branches/dev/samtools/bam.h
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2602 M /branches/dev/samtools/razf.c
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2603 M /branches/dev/samtools/razf.h
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2604
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2605 * Jue has updated razf to realize Bob's scheme
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2606
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2607 ------------------------------------------------------------------------
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2608 r7 | lh3lh3 | 2008-11-25 20:37:37 +0000 (Tue, 25 Nov 2008) | 2 lines
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2609 Changed paths:
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2610 A /branches/dev/samtools/samtools.1
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2611
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2612 the manual page
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2613
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2614 ------------------------------------------------------------------------
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2615 r6 | lh3lh3 | 2008-11-25 20:37:16 +0000 (Tue, 25 Nov 2008) | 3 lines
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2616 Changed paths:
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2617 A /branches/dev/samtools/ChangeLog
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2618 A /branches/dev/samtools/Makefile
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2619 A /branches/dev/samtools/bam.c
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2620 A /branches/dev/samtools/bam.h
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2621 A /branches/dev/samtools/bam_aux.c
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2622 A /branches/dev/samtools/bam_endian.h
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2623 A /branches/dev/samtools/bam_import.c
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2624 A /branches/dev/samtools/bam_index.c
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2625 A /branches/dev/samtools/bam_lpileup.c
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2626 A /branches/dev/samtools/bam_pileup.c
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2627 A /branches/dev/samtools/bam_sort.c
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2628 A /branches/dev/samtools/bam_tview.c
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2629 A /branches/dev/samtools/bamtk.c
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2630 A /branches/dev/samtools/bgzf.c
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2631 A /branches/dev/samtools/bgzf.h
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2632 A /branches/dev/samtools/bgzip.c
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2633 A /branches/dev/samtools/faidx.c
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2634 A /branches/dev/samtools/faidx.h
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2635 A /branches/dev/samtools/khash.h
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2636 A /branches/dev/samtools/ksort.h
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2637 A /branches/dev/samtools/kstream.h
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2638 A /branches/dev/samtools/misc
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2639 A /branches/dev/samtools/misc/Makefile
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2640 A /branches/dev/samtools/misc/all2sam.pl
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2641 A /branches/dev/samtools/misc/maq2sam.c
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2642 A /branches/dev/samtools/razf.c
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2643 A /branches/dev/samtools/razf.h
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2644 A /branches/dev/samtools/razip.c
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2645 A /branches/dev/samtools/zutil.h
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2646
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2647 The initial version of samtools, replicated from my local SVN repository.
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2648 The current version is: 0.1.0-42. All future development will happen here.
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2649
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2650 ------------------------------------------------------------------------
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2651 r5 | lh3lh3 | 2008-11-25 20:30:49 +0000 (Tue, 25 Nov 2008) | 2 lines
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2652 Changed paths:
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2653 A /branches/dev/samtools
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2654
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2655 samtools (C version)
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2656
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2657 ------------------------------------------------------------------------
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