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2 r1309 | lh3 | 2010-02-26 21:42:22 -0500 (Fri, 26 Feb 2010) | 4 lines
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3 Changed paths:
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6 M /branches/prog/bwa/main.c
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7
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8 * bwa-0.5.6-2 (r1309)
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9 * fixed an unfixed bug (by Carol Scott)
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10 * fixed some tiny formatting
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11
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12 ------------------------------------------------------------------------
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13 r1305 | lh3 | 2010-02-25 13:47:58 -0500 (Thu, 25 Feb 2010) | 3 lines
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14 Changed paths:
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15 M /branches/prog/bwa/bwape.c
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16 M /branches/prog/bwa/bwase.c
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17 M /branches/prog/bwa/bwtaln.c
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18 M /branches/prog/bwa/bwtsw2_main.c
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19 M /branches/prog/bwa/main.c
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20
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21 * bwa-0.5.6-1 (r1304)
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22 * optionally write output to a file (by Tim Fennel)
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23
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24 ------------------------------------------------------------------------
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25 r1303 | lh3 | 2010-02-10 23:43:48 -0500 (Wed, 10 Feb 2010) | 2 lines
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26 Changed paths:
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27 M /branches/prog/bwa/ChangeLog
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28 M /branches/prog/bwa/NEWS
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29 M /branches/prog/bwa/bwa.1
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30 M /branches/prog/bwa/bwtsw2_main.c
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31 M /branches/prog/bwa/main.c
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32
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33 Release bwa-0.5.6
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34
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35 ------------------------------------------------------------------------
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36 r1302 | lh3 | 2010-02-10 11:11:49 -0500 (Wed, 10 Feb 2010) | 3 lines
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37 Changed paths:
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38 M /branches/prog/bwa/ChangeLog
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39 M /branches/prog/bwa/NEWS
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40 M /branches/prog/bwa/bwape.c
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41 M /branches/prog/bwa/bwtaln.h
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42 M /branches/prog/bwa/main.c
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43
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44 * bwa-0.5.5-10 (r1302)
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45 * improve max insert size estimate (method suggested by Gerton Lunter)
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46
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47 ------------------------------------------------------------------------
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48 r1301 | lh3 | 2010-02-09 16:15:28 -0500 (Tue, 09 Feb 2010) | 5 lines
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49 Changed paths:
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50 M /branches/prog/bwa/bwape.c
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51 M /branches/prog/bwa/bwase.c
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52 M /branches/prog/bwa/main.c
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53
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54 * bwa-0.5.5-9 (r1301)
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55 * improve mapping quality calculation for abnomalous pairs
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56 * fixed a bug in multiple hits
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57 * SOLiD multiple hits should work now
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58
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59 ------------------------------------------------------------------------
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60 r1300 | lh3 | 2010-02-09 12:50:02 -0500 (Tue, 09 Feb 2010) | 3 lines
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61 Changed paths:
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62 M /branches/prog/bwa/bwape.c
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63 M /branches/prog/bwa/main.c
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64
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65 * bwa-0.5.5-8 (r1300)
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66 * output kurtosis
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67
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68 ------------------------------------------------------------------------
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69 r1299 | lh3 | 2010-02-09 12:33:34 -0500 (Tue, 09 Feb 2010) | 5 lines
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70 Changed paths:
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71 M /branches/prog/bwa/bwape.c
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72 M /branches/prog/bwa/main.c
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73
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74 * bwa-0.5.5-7 (r1299)
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75 * calculate skewness in sampe
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76 * increase min_len in SW to 20
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77 * perform more SW to fix discordant pairs
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78
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79 ------------------------------------------------------------------------
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80 r1298 | lh3 | 2010-02-08 12:40:31 -0500 (Mon, 08 Feb 2010) | 3 lines
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81 Changed paths:
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82 M /branches/prog/bwa/bwape.c
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83 M /branches/prog/bwa/bwase.c
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84 M /branches/prog/bwa/bwtaln.c
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85 M /branches/prog/bwa/bwtaln.h
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86 M /branches/prog/bwa/cs2nt.c
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87 M /branches/prog/bwa/main.c
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88 M /branches/prog/bwa/stdaln.h
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89
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90 * bwa-0.5.5-6 (r1297)
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91 * prepare to replace all 16-bit CIGAR (patches by Rodrigo Goya)
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92
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93 ------------------------------------------------------------------------
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94 r1297 | lh3 | 2010-02-05 22:26:11 -0500 (Fri, 05 Feb 2010) | 2 lines
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95 Changed paths:
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96 M /branches/prog/bwa/solid2fastq.pl
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97
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98 the old fix seems not working!
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99
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100 ------------------------------------------------------------------------
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101 r1296 | lh3 | 2010-02-05 21:51:03 -0500 (Fri, 05 Feb 2010) | 3 lines
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102 Changed paths:
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103 M /branches/prog/bwa/bwa.1
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104 M /branches/prog/bwa/bwape.c
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105 M /branches/prog/bwa/main.c
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106
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107 * bwa-0.5.5-5 (r1296)
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108 * fixed a minor issue that the lower bound of insert size is not correctly set.
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109
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110 ------------------------------------------------------------------------
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111 r1295 | lh3 | 2010-02-05 21:01:10 -0500 (Fri, 05 Feb 2010) | 5 lines
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112 Changed paths:
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113 M /branches/prog/bwa/bwape.c
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114 M /branches/prog/bwa/bwase.c
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115 M /branches/prog/bwa/bwaseqio.c
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116 M /branches/prog/bwa/main.c
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117
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118 * bwa-0.5.5-4 (r1295)
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119 * fixed a memory leak
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120 * change the behaviour of -n (samse and sampe)
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121 * change the default of -n
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122
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123 ------------------------------------------------------------------------
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124 r1294 | lh3 | 2010-02-05 17:24:06 -0500 (Fri, 05 Feb 2010) | 3 lines
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125 Changed paths:
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126 M /branches/prog/bwa/bwape.c
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127 M /branches/prog/bwa/bwase.c
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128 M /branches/prog/bwa/bwaseqio.c
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129 M /branches/prog/bwa/bwtaln.h
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130 M /branches/prog/bwa/main.c
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131
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132 * bwa-0.5.5-3 (r1294)
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133 * improved multi-hit report
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134
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135 ------------------------------------------------------------------------
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136 r1293 | lh3 | 2010-02-05 12:57:38 -0500 (Fri, 05 Feb 2010) | 5 lines
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137 Changed paths:
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138 M /branches/prog/bwa/bwape.c
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139 M /branches/prog/bwa/bwase.c
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140 M /branches/prog/bwa/cs2nt.c
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141 M /branches/prog/bwa/main.c
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142 M /branches/prog/bwa/solid2fastq.pl
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143
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144 * bwa-0.5.5-2 (r1293)
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145 * bugfix: truncated quality string
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146 * bugfix: quality -1 in solid->fastq conversion
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147 * bugfix: color reads on the reverse strand is not complemented
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148
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149 ------------------------------------------------------------------------
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150 r1279 | lh3 | 2009-11-23 22:42:34 -0500 (Mon, 23 Nov 2009) | 3 lines
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151 Changed paths:
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152 M /branches/prog/bwa/bntseq.c
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153 M /branches/prog/bwa/bntseq.h
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154 M /branches/prog/bwa/bwase.c
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155 A /branches/prog/bwa/bwase.h
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156 M /branches/prog/bwa/bwtaln.c
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157 M /branches/prog/bwa/bwtaln.h
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158 M /branches/prog/bwa/bwtsw2_aux.c
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159 M /branches/prog/bwa/main.c
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160
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161 * bwa-0.5.5-1 (r1279)
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162 * incorporate changes from Matt Hanna for Java bindings.
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163
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164 ------------------------------------------------------------------------
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165 r1275 | lh3 | 2009-11-10 22:13:10 -0500 (Tue, 10 Nov 2009) | 2 lines
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166 Changed paths:
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167 M /branches/prog/bwa/ChangeLog
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168
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169 update ChangeLog
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170
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171 ------------------------------------------------------------------------
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172 r1273 | lh3 | 2009-11-10 22:08:16 -0500 (Tue, 10 Nov 2009) | 2 lines
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173 Changed paths:
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174 M /branches/prog/bwa/NEWS
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175 M /branches/prog/bwa/bwa.1
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176 M /branches/prog/bwa/main.c
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177 A /branches/prog/bwa/qualfa2fq.pl
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178
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179 Release bwa-0.5.5 (r1273)
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180
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181 ------------------------------------------------------------------------
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182 r1272 | lh3 | 2009-11-10 22:02:50 -0500 (Tue, 10 Nov 2009) | 3 lines
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183 Changed paths:
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184 M /branches/prog/bwa/bwape.c
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185 M /branches/prog/bwa/main.c
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186
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187 * bwa-0.5.4-3 (r1272)
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188 * fixed another typo which may lead to incorrect single-end mapping quality
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189
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190 ------------------------------------------------------------------------
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191 r1271 | lh3 | 2009-11-10 21:59:47 -0500 (Tue, 10 Nov 2009) | 4 lines
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192 Changed paths:
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193 M /branches/prog/bwa/bwtaln.c
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194 M /branches/prog/bwa/main.c
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195
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196 * bwa-0.5.4-2 (r1271)
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197 * fixed a serious typo/bug which does not hurt if we allow one gap open
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198 and work with <200bp reads, but causes segfault for long reads.
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199
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200 ------------------------------------------------------------------------
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201 r1270 | lh3 | 2009-11-09 23:12:42 -0500 (Mon, 09 Nov 2009) | 3 lines
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202 Changed paths:
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203 M /branches/prog/bwa/cs2nt.c
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204 M /branches/prog/bwa/main.c
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205
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206 * bwa-0.5.4-1 (r1270)
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207 * fixed a bug in color alignment
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208
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209 ------------------------------------------------------------------------
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210 r1245 | lh3 | 2009-10-09 07:42:52 -0400 (Fri, 09 Oct 2009) | 2 lines
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211 Changed paths:
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212 M /branches/prog/bwa/ChangeLog
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213 M /branches/prog/bwa/NEWS
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214 M /branches/prog/bwa/bwa.1
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215 M /branches/prog/bwa/bwape.c
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216 M /branches/prog/bwa/bwase.c
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217 M /branches/prog/bwa/bwaseqio.c
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218 M /branches/prog/bwa/main.c
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219
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220 Release bwa-0.5.4
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221
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222 ------------------------------------------------------------------------
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223 r1244 | lh3 | 2009-10-09 05:53:52 -0400 (Fri, 09 Oct 2009) | 5 lines
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224 Changed paths:
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225 M /branches/prog/bwa/ChangeLog
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226 M /branches/prog/bwa/bwape.c
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227 M /branches/prog/bwa/bwase.c
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228 M /branches/prog/bwa/bwaseqio.c
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229 M /branches/prog/bwa/bwtaln.h
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230 M /branches/prog/bwa/main.c
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231 M /branches/prog/bwa/stdaln.c
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232
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233 * bwa-0.5.3-4 (r1244)
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234 * output the clipped length in XC:i: tag
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235 * skip mate alignment when stdaln is buggy
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236 * fixed a bug in NM:i: tag
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237
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238 ------------------------------------------------------------------------
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239 r1243 | lh3 | 2009-10-07 08:15:04 -0400 (Wed, 07 Oct 2009) | 3 lines
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240 Changed paths:
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241 M /branches/prog/bwa/bwape.c
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242 M /branches/prog/bwa/main.c
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243
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244 * bwa-0.5.3-3 (r1243)
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245 * sampe: fixed a bug when a read sequence is identical its reverse complement.
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246
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247 ------------------------------------------------------------------------
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248 r1242 | lh3 | 2009-10-07 07:49:13 -0400 (Wed, 07 Oct 2009) | 4 lines
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249 Changed paths:
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250 M /branches/prog/bwa/bntseq.c
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251 M /branches/prog/bwa/bwape.c
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252 M /branches/prog/bwa/bwtaln.c
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253 M /branches/prog/bwa/bwtaln.h
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254 M /branches/prog/bwa/main.c
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255
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256 * bwa-0.5.3-2 (r1242)
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257 * sampe: optionall preload the full index into memory
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258 * aln: change the default seed length to 32bp
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259
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260 ------------------------------------------------------------------------
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261 r1238 | lh3 | 2009-09-26 18:38:15 -0400 (Sat, 26 Sep 2009) | 2 lines
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262 Changed paths:
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263 M /branches/prog/bwa/khash.h
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264
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265 Improve portability of khash.h
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266
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267 ------------------------------------------------------------------------
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268 r1228 | lh3 | 2009-09-15 09:20:22 -0400 (Tue, 15 Sep 2009) | 2 lines
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269 Changed paths:
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270 M /branches/prog/bwa/main.c
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271
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272 fixed a typo
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273
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274 ------------------------------------------------------------------------
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275 r1227 | lh3 | 2009-09-15 09:19:35 -0400 (Tue, 15 Sep 2009) | 3 lines
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276 Changed paths:
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278 M /branches/prog/bwa/bwtsw2_aux.c
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279 M /branches/prog/bwa/bwtsw2_main.c
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280 M /branches/prog/bwa/main.c
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281
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282 * bwa-0.5.3-1 (r1226)
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283 * in dBWT-SW, optionall use hard clipping instead of soft clipping
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284
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285 ------------------------------------------------------------------------
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286 r1225 | lh3 | 2009-09-15 08:32:30 -0400 (Tue, 15 Sep 2009) | 2 lines
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287 Changed paths:
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288 M /branches/prog/bwa/NEWS
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289 M /branches/prog/bwa/bwase.c
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290 M /branches/prog/bwa/main.c
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291
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292 Release bwa-0.5.3 (r1225)
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293
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294 ------------------------------------------------------------------------
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295 r1223 | lh3 | 2009-09-13 07:30:41 -0400 (Sun, 13 Sep 2009) | 2 lines
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296 Changed paths:
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297 M /branches/prog/bwa/ChangeLog
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298 M /branches/prog/bwa/NEWS
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299 M /branches/prog/bwa/bwa.1
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300 M /branches/prog/bwa/main.c
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301
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302 Release bwa-0.5.2
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303
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304 ------------------------------------------------------------------------
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305 r1222 | lh3 | 2009-09-11 09:11:39 -0400 (Fri, 11 Sep 2009) | 3 lines
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306 Changed paths:
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307 M /branches/prog/bwa/bwtaln.c
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308 M /branches/prog/bwa/main.c
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309
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310 * bwa-0.5.1-5 (r1222)
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311 * fixed a typo. No real change
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312
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313 ------------------------------------------------------------------------
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314 r1221 | lh3 | 2009-09-11 09:09:44 -0400 (Fri, 11 Sep 2009) | 3 lines
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315 Changed paths:
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318 M /branches/prog/bwa/bwase.c
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319 M /branches/prog/bwa/bwaseqio.c
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320 M /branches/prog/bwa/bwtaln.c
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321 M /branches/prog/bwa/bwtaln.h
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322 M /branches/prog/bwa/main.c
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323
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324 * bwa-0.5.1-4 (r1221)
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325 * trim reads before alignment
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326
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327 ------------------------------------------------------------------------
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328 r1216 | lh3 | 2009-09-08 17:50:15 -0400 (Tue, 08 Sep 2009) | 4 lines
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329 Changed paths:
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330 M /branches/prog/bwa/bwape.c
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331 M /branches/prog/bwa/bwase.c
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332 M /branches/prog/bwa/bwtaln.h
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333 M /branches/prog/bwa/main.c
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334
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335 * bwa-0.5.1-3 (r1216)
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336 * fixed a bug about NM tags for gapped alignment
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337 * print SAM header
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338
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339 ------------------------------------------------------------------------
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340 r1215 | lh3 | 2009-09-08 17:14:42 -0400 (Tue, 08 Sep 2009) | 3 lines
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341 Changed paths:
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342 M /branches/prog/bwa/bwtaln.c
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343 M /branches/prog/bwa/main.c
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344
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345 * bwa-0.5.1-2 (r1215)
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346 * fixed a bug when read lengths vary (by John Marshall)
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347
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348 ------------------------------------------------------------------------
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349 r1213 | lh3 | 2009-09-06 18:58:15 -0400 (Sun, 06 Sep 2009) | 3 lines
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350 Changed paths:
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351 M /branches/prog/bwa/bwtsw2_aux.c
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352 M /branches/prog/bwa/main.c
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353
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354 * bwa-0.5.1-1 (r1213)
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355 * change default -T to 30
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356
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357 ------------------------------------------------------------------------
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358 r1209 | lh3 | 2009-09-02 06:06:02 -0400 (Wed, 02 Sep 2009) | 2 lines
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359 Changed paths:
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360 M /branches/prog/bwa/NEWS
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361 M /branches/prog/bwa/bwa.1
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362 M /branches/prog/bwa/main.c
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363
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364 Release bwa-0.5.1
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365
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366 ------------------------------------------------------------------------
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367 r1208 | lh3 | 2009-09-02 05:56:33 -0400 (Wed, 02 Sep 2009) | 2 lines
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368 Changed paths:
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369 M /branches/prog/bwa/ChangeLog
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370
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371 * ChangeLog
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372
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373 ------------------------------------------------------------------------
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374 r1206 | lh3 | 2009-08-30 18:27:30 -0400 (Sun, 30 Aug 2009) | 3 lines
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375 Changed paths:
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377 M /branches/prog/bwa/main.c
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378
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379 * bwa-0.5.0-6 (r1206)
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380 * fixed two bugs caused by previous modification
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381
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382 ------------------------------------------------------------------------
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383 r1205 | lh3 | 2009-08-30 17:28:36 -0400 (Sun, 30 Aug 2009) | 4 lines
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384 Changed paths:
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385 M /branches/prog/bwa/ChangeLog
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386 M /branches/prog/bwa/bwtsw2_aux.c
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387 M /branches/prog/bwa/main.c
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388
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389 * bwa-0.5.0-4 (r1205)
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390 * reduce false coordinates and CIGAR when a query bridges two reference
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391 sequences, although some very rare cases may fail bwa.
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392
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393 ------------------------------------------------------------------------
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394 r1204 | lh3 | 2009-08-30 06:06:16 -0400 (Sun, 30 Aug 2009) | 3 lines
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395 Changed paths:
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397 M /branches/prog/bwa/bwtsw2_core.c
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398 M /branches/prog/bwa/main.c
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399
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400 * bwa-0.5.0-3 (r1204)
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401 * choose one repetitive hit to extend
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402
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403 ------------------------------------------------------------------------
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404 r1203 | lh3 | 2009-08-29 18:11:51 -0400 (Sat, 29 Aug 2009) | 4 lines
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405 Changed paths:
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406 M /branches/prog/bwa/bwase.c
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407 M /branches/prog/bwa/bwtsw2_aux.c
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408 M /branches/prog/bwa/main.c
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409
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410 * bwa-0.5.0-2 (r1203)
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411 * dBWT-SW: change a parameter in calculating mapping quality
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412 * fixed a bug in samse
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413
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414 ------------------------------------------------------------------------
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415 r1202 | lh3 | 2009-08-28 19:48:41 -0400 (Fri, 28 Aug 2009) | 4 lines
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416 Changed paths:
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417 M /branches/prog/bwa/bwtsw2_aux.c
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418 M /branches/prog/bwa/main.c
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419
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420 * bwa-0.5.0-1 (r1202)
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421 * change default band width to 50
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422 * improve mapping quality a bit
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423
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424 ------------------------------------------------------------------------
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425 r1200 | lh3 | 2009-08-20 06:21:24 -0400 (Thu, 20 Aug 2009) | 2 lines
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426 Changed paths:
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427 M /branches/prog/bwa/NEWS
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428 M /branches/prog/bwa/main.c
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429
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430 Release bwa-0.5.0 (r1200)
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431
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432 ------------------------------------------------------------------------
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433 r1199 | lh3 | 2009-08-20 04:49:15 -0400 (Thu, 20 Aug 2009) | 2 lines
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434 Changed paths:
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435 M /branches/prog/bwa/ChangeLog
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436 M /branches/prog/bwa/bwa.1
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437
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438 Updated ChangeLog and the manual
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439
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440 ------------------------------------------------------------------------
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441 r1198 | lh3 | 2009-08-19 11:09:15 -0400 (Wed, 19 Aug 2009) | 3 lines
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442 Changed paths:
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443 M /branches/prog/bwa/bwtsw2_aux.c
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444 M /branches/prog/bwa/bwtsw2_core.c
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445 M /branches/prog/bwa/main.c
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446
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447 * bwa-0.4.9-36 (r1198)
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448 * simplify duphits removal. The accuracy is changed a tiny bit, sometimes better, sometimes worse.
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449
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450 ------------------------------------------------------------------------
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451 r1197 | lh3 | 2009-08-19 08:15:05 -0400 (Wed, 19 Aug 2009) | 3 lines
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452 Changed paths:
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453 M /branches/prog/bwa/Makefile
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454 M /branches/prog/bwa/bwtsw2_aux.c
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455 A /branches/prog/bwa/bwtsw2_chain.c
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456 M /branches/prog/bwa/main.c
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457
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458 * bwa-0.4.9-35 (r1197)
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459 * further heuristic acceleration for long queries
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460
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461 ------------------------------------------------------------------------
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462 r1196 | lh3 | 2009-08-18 06:54:03 -0400 (Tue, 18 Aug 2009) | 4 lines
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463 Changed paths:
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464 M /branches/prog/bwa/bwa.1
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465 M /branches/prog/bwa/bwtsw2_aux.c
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466 M /branches/prog/bwa/main.c
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467
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468 * bwa-0.4.9-34 (r1196)
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469 * updated the manual page
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470 * output base quality if the input is fastq
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471
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472 ------------------------------------------------------------------------
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473 r1195 | lh3 | 2009-08-18 06:23:00 -0400 (Tue, 18 Aug 2009) | 4 lines
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474 Changed paths:
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475 M /branches/prog/bwa/bwase.c
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476 M /branches/prog/bwa/bwtsw2_main.c
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477 M /branches/prog/bwa/main.c
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478 M /branches/prog/bwa/simple_dp.c
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479
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480 * bwa-0.4.9-33 (r1191)
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481 * fixed a bug in sampe/samse when gaps occur to the 5'-end in SW alignment
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482 * in dbwtsw adjust -T and -c according to -a
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483
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484 ------------------------------------------------------------------------
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485 r1192 | lh3 | 2009-08-13 05:37:28 -0400 (Thu, 13 Aug 2009) | 2 lines
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486 Changed paths:
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487 M /branches/prog/bwa/bwa.1
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488
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489 update manual
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490
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491 ------------------------------------------------------------------------
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492 r1191 | lh3 | 2009-08-12 19:40:51 -0400 (Wed, 12 Aug 2009) | 2 lines
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493 Changed paths:
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494 M /branches/prog/bwa/bwa.1
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495 M /branches/prog/bwa/bwtsw2_main.c
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496
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497 update documentation
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498
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499 ------------------------------------------------------------------------
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500 r1190 | lh3 | 2009-08-12 08:56:10 -0400 (Wed, 12 Aug 2009) | 3 lines
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501 Changed paths:
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502 M /branches/prog/bwa/bwtsw2_main.c
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503 M /branches/prog/bwa/main.c
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504
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505 * bwa-0.4.9-32 (r1190)
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506 * only help messages are changed
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507
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508 ------------------------------------------------------------------------
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509 r1189 | lh3 | 2009-08-11 09:28:55 -0400 (Tue, 11 Aug 2009) | 4 lines
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510 Changed paths:
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511 M /branches/prog/bwa/bwase.c
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512 M /branches/prog/bwa/bwtsw2.h
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513 M /branches/prog/bwa/bwtsw2_aux.c
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514 M /branches/prog/bwa/bwtsw2_core.c
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515 M /branches/prog/bwa/main.c
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516
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517 * bwa-0.4.9-31 (r1189)
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518 * in bwape/bwase, print CIGAR "*" if the read is unmapped
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519 * improved the calculation of mapping quality
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520
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521 ------------------------------------------------------------------------
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522 r1181 | lh3 | 2009-08-03 12:09:41 -0400 (Mon, 03 Aug 2009) | 2 lines
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523 Changed paths:
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524 M /branches/prog/bwa/bwtsw2_aux.c
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525
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526 fflush()
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527
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528 ------------------------------------------------------------------------
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529 r1180 | lh3 | 2009-08-03 12:08:46 -0400 (Mon, 03 Aug 2009) | 4 lines
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530 Changed paths:
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531 M /branches/prog/bwa/bwtsw2_aux.c
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532 M /branches/prog/bwa/main.c
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533
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534 * bwa-0.4.9-30 (r1180)
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535 * fixed a memory problem
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536 * multi-threading sometimes does not work...
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537
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538 ------------------------------------------------------------------------
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539 r1179 | lh3 | 2009-08-03 11:04:39 -0400 (Mon, 03 Aug 2009) | 3 lines
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540 Changed paths:
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541 M /branches/prog/bwa/Makefile
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542 M /branches/prog/bwa/bwtsw2.h
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543 M /branches/prog/bwa/bwtsw2_aux.c
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544 M /branches/prog/bwa/bwtsw2_main.c
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545 M /branches/prog/bwa/main.c
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546
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547 * bwa-0.4.9-29 (r1179)
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548 * preliminary mutli-threading support in dbwtsw
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549
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550 ------------------------------------------------------------------------
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551 r1178 | lh3 | 2009-08-03 09:14:54 -0400 (Mon, 03 Aug 2009) | 3 lines
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552 Changed paths:
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554 M /branches/prog/bwa/bwtsw2_main.c
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555 M /branches/prog/bwa/main.c
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556
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557 * bwa-0.4.9-28 (r1178)
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558 * fixed a bug in printing repetitive hits
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559
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560 ------------------------------------------------------------------------
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561 r1177 | lh3 | 2009-08-03 05:03:42 -0400 (Mon, 03 Aug 2009) | 3 lines
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562 Changed paths:
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563 M /branches/prog/bwa/bwtsw2_core.c
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564 M /branches/prog/bwa/main.c
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565
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566 * bwa-0.4.9-27 (r1177)
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567 * bwtsw2: fixed a hidden memory leak
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568
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569 ------------------------------------------------------------------------
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570 r1176 | lh3 | 2009-07-31 10:58:24 -0400 (Fri, 31 Jul 2009) | 3 lines
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571 Changed paths:
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573 M /branches/prog/bwa/bwtsw2_main.c
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574 M /branches/prog/bwa/main.c
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575
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576 * bwa-0.4.9-26
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577 * change the way mapping quality is calculated
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578
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579 ------------------------------------------------------------------------
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580 r1175 | lh3 | 2009-07-31 09:15:54 -0400 (Fri, 31 Jul 2009) | 4 lines
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581 Changed paths:
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584 M /branches/prog/bwa/bwtsw2_core.c
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585 M /branches/prog/bwa/bwtsw2_main.c
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586 M /branches/prog/bwa/main.c
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587
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588 * bwa-0.4.9-25
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589 * code clean up
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590 * automatically adjust ->t and ->is_rev based on input
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591
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592 ------------------------------------------------------------------------
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593 r1174 | lh3 | 2009-07-30 08:50:25 -0400 (Thu, 30 Jul 2009) | 3 lines
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594 Changed paths:
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596 M /branches/prog/bwa/main.c
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597
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598 * bwa-0.4.9-24
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599 * fixed a bug in printing the hits
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600
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601 ------------------------------------------------------------------------
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602 r1173 | lh3 | 2009-07-29 18:32:43 -0400 (Wed, 29 Jul 2009) | 4 lines
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603 Changed paths:
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606 M /branches/prog/bwa/bwtsw2_main.c
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607 M /branches/prog/bwa/main.c
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608
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609 * bwa-0.4.9-23
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610 * allow to skip reverse alignment
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611 * increase opt->t to 37
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612
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613 ------------------------------------------------------------------------
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614 r1172 | lh3 | 2009-07-29 17:22:39 -0400 (Wed, 29 Jul 2009) | 3 lines
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615 Changed paths:
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617 M /branches/prog/bwa/bwtsw2_main.c
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618 M /branches/prog/bwa/main.c
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619
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620 * bwa-0.4.9-22
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621 * report if the hit is found in both directions
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622
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623 ------------------------------------------------------------------------
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624 r1171 | lh3 | 2009-07-29 17:12:02 -0400 (Wed, 29 Jul 2009) | 3 lines
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625 Changed paths:
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627 M /branches/prog/bwa/bwtsw2_aux.c
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628 M /branches/prog/bwa/bwtsw2_main.c
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629 M /branches/prog/bwa/main.c
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630
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631 * bwa-0.4.9-21
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632 * dbwtsw: map to both forward and reverse BWT to reduce false alignment
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633
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634 ------------------------------------------------------------------------
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635 r1170 | lh3 | 2009-07-29 15:25:14 -0400 (Wed, 29 Jul 2009) | 2 lines
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636 Changed paths:
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637 M /branches/prog/bwa/bwtsw2_core.c
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638 M /branches/prog/bwa/main.c
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639
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640 save hits before cut_tail()
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641
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642 ------------------------------------------------------------------------
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643 r1169 | lh3 | 2009-07-29 08:06:01 -0400 (Wed, 29 Jul 2009) | 3 lines
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644 Changed paths:
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647 M /branches/prog/bwa/bwtsw2_core.c
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648 M /branches/prog/bwa/main.c
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649 M /branches/prog/bwa/stdaln.c
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650 M /branches/prog/bwa/stdaln.h
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651
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652 * bwa-0.4.9-19
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653 * use a global memory pool to reduce the CPU time spent on malloc/free().
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654
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655 ------------------------------------------------------------------------
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656 r1168 | lh3 | 2009-07-29 06:13:29 -0400 (Wed, 29 Jul 2009) | 5 lines
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657 Changed paths:
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660 M /branches/prog/bwa/bwtsw2_core.c
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661 M /branches/prog/bwa/bwtsw2_main.c
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662 M /branches/prog/bwa/main.c
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663
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664 * bwa-0.4.9-18
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665 * reduce unnecessary extension to the 5'-end
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666 * allow to use different interval size for the 2 rounds
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667 * change default parameters
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668
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669 ------------------------------------------------------------------------
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670 r1167 | lh3 | 2009-07-28 19:06:17 -0400 (Tue, 28 Jul 2009) | 3 lines
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671 Changed paths:
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672 M /branches/prog/bwa/bwtsw2_core.c
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673 M /branches/prog/bwa/main.c
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674
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675 * bwa-0.4.9-17
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676 * dbwtsw: fixed THE memory leak.
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677
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678 ------------------------------------------------------------------------
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679 r1166 | lh3 | 2009-07-28 16:31:41 -0400 (Tue, 28 Jul 2009) | 5 lines
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680 Changed paths:
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681 M /branches/prog/bwa/bwtsw2_aux.c
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682 M /branches/prog/bwa/bwtsw2_core.c
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683 M /branches/prog/bwa/bwtsw2_main.c
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684 M /branches/prog/bwa/main.c
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685 M /branches/prog/bwa/stdaln.c
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686
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687 * bwa-0.4.9-16
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688 * fixed a memory leak
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689 * a small memory leak still occurs to bwtsw2_core(). I will work on that later.
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690 * changed the default parameters
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691
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692 ------------------------------------------------------------------------
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693 r1165 | lh3 | 2009-07-28 10:15:40 -0400 (Tue, 28 Jul 2009) | 4 lines
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694 Changed paths:
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695 M /branches/prog/bwa/bwtsw2_aux.c
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696 M /branches/prog/bwa/bwtsw2_core.c
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697 M /branches/prog/bwa/main.c
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698 M /branches/prog/bwa/stdaln.c
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699
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700 * bwa-0.4.9-15
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701 * generate CIGAR right before output. This saves unnecessary computation.
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702 * this version may be buggy as I have not tested it.
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703
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704 ------------------------------------------------------------------------
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705 r1164 | lh3 | 2009-07-28 09:04:14 -0400 (Tue, 28 Jul 2009) | 11 lines
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706 Changed paths:
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707 M /branches/prog/bwa/bwtsw2.h
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708 M /branches/prog/bwa/bwtsw2_aux.c
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709 M /branches/prog/bwa/bwtsw2_core.c
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710 M /branches/prog/bwa/main.c
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711 M /branches/prog/bwa/stdaln.c
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712 M /branches/prog/bwa/stdaln.h
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713
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714 * bwa-0.4.9-14
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715
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716 * deplete unique hits in dbwtsw and postprocess them with standard sw
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717
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718 * in principle, this stratgy should be faster and more accurate, but I
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719 have not tested this point. I may switch back to the old method if
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720 this does not work.
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721
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722 * the code looks quite nasty now. it needs clean up...
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723
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724
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725 ------------------------------------------------------------------------
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726 r1163 | lh3 | 2009-07-27 17:41:10 -0400 (Mon, 27 Jul 2009) | 2 lines
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727 Changed paths:
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728 M /branches/prog/bwa/bwtsw2_aux.c
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729
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730 change a default parameter
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731
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732 ------------------------------------------------------------------------
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733 r1162 | lh3 | 2009-07-27 17:04:35 -0400 (Mon, 27 Jul 2009) | 3 lines
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734 Changed paths:
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735 M /branches/prog/bwa/bwtsw2.h
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736 M /branches/prog/bwa/bwtsw2_aux.c
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737 M /branches/prog/bwa/bwtsw2_core.c
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738 M /branches/prog/bwa/bwtsw2_main.c
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739 M /branches/prog/bwa/main.c
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740
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741 * bwa-0.4.9-13
|
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742 * dbwtsw: switch between small and large Z-best
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743
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744 ------------------------------------------------------------------------
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745 r1161 | lh3 | 2009-07-27 12:17:41 -0400 (Mon, 27 Jul 2009) | 4 lines
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746 Changed paths:
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747 M /branches/prog/bwa/bwtsw2_aux.c
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748 M /branches/prog/bwa/bwtsw2_core.c
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749 M /branches/prog/bwa/main.c
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750
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751 * bwa-0.4.9-12
|
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752 * changed the default -z to 100
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753 * heuristically speed up alignments for polyA reads
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754
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755 ------------------------------------------------------------------------
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756 r1160 | lh3 | 2009-07-27 07:50:57 -0400 (Mon, 27 Jul 2009) | 6 lines
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757 Changed paths:
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758 M /branches/prog/bwa/bwtsw2.h
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759 M /branches/prog/bwa/bwtsw2_aux.c
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760 M /branches/prog/bwa/bwtsw2_core.c
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761 M /branches/prog/bwa/main.c
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762
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763 * bwa-0.4.9-11
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764
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765 * dbwtsw potentially generates less false alignments, although in
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766 practice, the modification brings no improvement.
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767
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768
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769 ------------------------------------------------------------------------
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770 r1159 | lh3 | 2009-07-27 04:37:02 -0400 (Mon, 27 Jul 2009) | 4 lines
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771 Changed paths:
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772 M /branches/prog/bwa/bwase.c
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773 M /branches/prog/bwa/bwtsw2_aux.c
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774 M /branches/prog/bwa/bwtsw2_core.c
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775 M /branches/prog/bwa/main.c
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776
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777 * bwa-0.4.9-10
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778 * disabled debugging code
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779 * add "BAM_FMU" if both ends are unmapped
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780
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781 ------------------------------------------------------------------------
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782 r1158 | lh3 | 2009-07-24 09:36:52 -0400 (Fri, 24 Jul 2009) | 2 lines
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783 Changed paths:
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784 M /branches/prog/bwa/main.c
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785
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786 nothing, really
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787
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788 ------------------------------------------------------------------------
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789 r1157 | lh3 | 2009-07-24 09:05:44 -0400 (Fri, 24 Jul 2009) | 3 lines
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790 Changed paths:
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791 M /branches/prog/bwa/bwtsw2_aux.c
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792 M /branches/prog/bwa/bwtsw2_core.c
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793 M /branches/prog/bwa/main.c
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794
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795 * bwa-0.4.9-9
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796 * bwtsw2: generate SAM output
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797
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798 ------------------------------------------------------------------------
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799 r1156 | lh3 | 2009-07-24 05:42:47 -0400 (Fri, 24 Jul 2009) | 6 lines
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800 Changed paths:
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801 M /branches/prog/bwa/bwape.c
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802 M /branches/prog/bwa/main.c
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803
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804 * bwa-0.4.9-8
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805
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806 * fixed a weird deadloop which only happens to icc -O3. Thanks John
|
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807 Marshall for the fix.
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808
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809
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810 ------------------------------------------------------------------------
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811 r1155 | lh3 | 2009-07-24 05:28:40 -0400 (Fri, 24 Jul 2009) | 8 lines
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812 Changed paths:
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813 M /branches/prog/bwa/bwtsw2_aux.c
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814 M /branches/prog/bwa/bwtsw2_core.c
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815 M /branches/prog/bwa/main.c
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816
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|
817 * bwa-0.4.9-7
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818
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819 * fixed a typo in bwtsw2 alignment. Now score from the standard SW
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820 seems to agree with score from bwtsw2, except that in reporting
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821 alignments, bwtsw2 may report non-optimal segments. This is expected,
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822 though. I will improve in future.
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823
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824
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825 ------------------------------------------------------------------------
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826 r1154 | lh3 | 2009-07-23 17:40:20 -0400 (Thu, 23 Jul 2009) | 3 lines
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827 Changed paths:
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828 M /branches/prog/bwa/stdaln.c
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829 M /branches/prog/bwa/stdaln.h
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830
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831 * aln_left_core() seems to work properly
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832 * aln_local_core() has a bug... AN EVER EXISTING BUG!!!!!!!!!!!
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833
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834 ------------------------------------------------------------------------
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835 r1153 | lh3 | 2009-07-23 17:06:09 -0400 (Thu, 23 Jul 2009) | 2 lines
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836 Changed paths:
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837 M /branches/prog/bwa/stdaln.c
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838
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839 removed debugging code...
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840
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841 ------------------------------------------------------------------------
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842 r1152 | lh3 | 2009-07-23 17:01:00 -0400 (Thu, 23 Jul 2009) | 3 lines
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843 Changed paths:
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844 M /branches/prog/bwa/stdaln.c
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845
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846 * radical changes failed...
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|
847 * fixed a bug
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848
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849 ------------------------------------------------------------------------
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850 r1151 | lh3 | 2009-07-23 14:46:35 -0400 (Thu, 23 Jul 2009) | 2 lines
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851 Changed paths:
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852 M /branches/prog/bwa/stdaln.c
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853
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854 temporary changes. Will apply some radical changes to this file...
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855
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856 ------------------------------------------------------------------------
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857 r1150 | lh3 | 2009-07-23 10:09:56 -0400 (Thu, 23 Jul 2009) | 2 lines
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858 Changed paths:
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859 M /branches/prog/bwa/bwtsw2_aux.c
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860 M /branches/prog/bwa/bwtsw2_main.c
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861 M /branches/prog/bwa/stdaln.c
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862
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863 fixed a long-existing bug in Smith-Waterman alignment
|
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864
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865 ------------------------------------------------------------------------
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866 r1149 | lh3 | 2009-07-23 08:50:52 -0400 (Thu, 23 Jul 2009) | 3 lines
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867 Changed paths:
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868 M /branches/prog/bwa/bwtsw2.h
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869 M /branches/prog/bwa/bwtsw2_aux.c
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870 M /branches/prog/bwa/bwtsw2_main.c
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871 M /branches/prog/bwa/main.c
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872 M /branches/prog/bwa/simple_dp.c
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873 M /branches/prog/bwa/stdaln.c
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874 M /branches/prog/bwa/stdaln.h
|
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|
875
|
|
|
876 * bwa-0.4.9-6
|
|
|
877 * unexplained inconsistency still occurs, but the results largely look reasonable.
|
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878
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879 ------------------------------------------------------------------------
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880 r1148 | lh3 | 2009-07-23 08:07:29 -0400 (Thu, 23 Jul 2009) | 2 lines
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881 Changed paths:
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882 M /branches/prog/bwa/stdaln.c
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883
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884 half DP
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885
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886 ------------------------------------------------------------------------
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887 r1147 | lh3 | 2009-07-22 08:03:06 -0400 (Wed, 22 Jul 2009) | 2 lines
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888 Changed paths:
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|
889 M /branches/prog/bwa/bwtsw2.h
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890 M /branches/prog/bwa/bwtsw2_aux.c
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891 M /branches/prog/bwa/bwtsw2_core.c
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892 M /branches/prog/bwa/bwtsw2_main.c
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893
|
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|
894 a bit code clean up
|
|
|
895
|
|
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896 ------------------------------------------------------------------------
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897 r1145 | lh3 | 2009-07-21 15:52:05 -0400 (Tue, 21 Jul 2009) | 4 lines
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898 Changed paths:
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|
899 M /branches/prog/bwa/bwtsw2_aux.c
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900 M /branches/prog/bwa/bwtsw2_core.c
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901 M /branches/prog/bwa/main.c
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902
|
|
|
903 * bwa-0.4.9-5
|
|
|
904 * fixed a bug in determining sub-optimal hits
|
|
|
905 * removed some debugging codes
|
|
|
906
|
|
|
907 ------------------------------------------------------------------------
|
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|
908 r1144 | lh3 | 2009-07-21 10:17:29 -0400 (Tue, 21 Jul 2009) | 4 lines
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909 Changed paths:
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910 M /branches/prog/bwa/bwtsw2.h
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911 M /branches/prog/bwa/bwtsw2_aux.c
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912 M /branches/prog/bwa/bwtsw2_core.c
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913 M /branches/prog/bwa/bwtsw2_main.c
|
|
|
914 M /branches/prog/bwa/main.c
|
|
|
915
|
|
|
916 * bwa-0.4.9-4
|
|
|
917 * better cmd interface
|
|
|
918 * faster speed
|
|
|
919
|
|
|
920 ------------------------------------------------------------------------
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|
921 r1143 | lh3 | 2009-07-20 16:38:18 -0400 (Mon, 20 Jul 2009) | 3 lines
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922 Changed paths:
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923 M /branches/prog/bwa/bwtsw2.h
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924 M /branches/prog/bwa/bwtsw2_aux.c
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|
925 M /branches/prog/bwa/bwtsw2_core.c
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926 M /branches/prog/bwa/bwtsw2_main.c
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|
|
927 M /branches/prog/bwa/main.c
|
|
|
928
|
|
|
929 bwtsw2 (dBWT-SW) is working apparently...
|
|
|
930
|
|
|
931
|
|
|
932 ------------------------------------------------------------------------
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933 r1139 | lh3 | 2009-07-15 05:52:18 -0400 (Wed, 15 Jul 2009) | 4 lines
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934 Changed paths:
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935 M /branches/prog/bwa/bwtsw2_core.c
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|
936 M /branches/prog/bwa/main.c
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|
937
|
|
|
938 * bwa-0.4.9-2
|
|
|
939 * bwtsw2: change cut_tail() such that it is faster but more likely to
|
|
|
940 miss true hits
|
|
|
941
|
|
|
942 ------------------------------------------------------------------------
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|
943 r1138 | lh3 | 2009-07-15 05:18:42 -0400 (Wed, 15 Jul 2009) | 3 lines
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944 Changed paths:
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945 M /branches/prog/bwa/Makefile
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946 A /branches/prog/bwa/bwt_lite.c
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947 A /branches/prog/bwa/bwt_lite.h
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|
948 A /branches/prog/bwa/bwtsw2.h
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949 A /branches/prog/bwa/bwtsw2_aux.c
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|
950 A /branches/prog/bwa/bwtsw2_core.c
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951 A /branches/prog/bwa/bwtsw2_main.c
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|
952 M /branches/prog/bwa/main.c
|
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|
953 M /branches/prog/bwa/main.h
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|
954
|
|
|
955 * bwa-0.4.9-1
|
|
|
956 * added back bwtsw2
|
|
|
957
|
|
|
958 ------------------------------------------------------------------------
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|
959 r1075 | lh3 | 2009-05-19 05:14:50 -0400 (Tue, 19 May 2009) | 2 lines
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960 Changed paths:
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961 M /branches/prog/bwa/NEWS
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962 M /branches/prog/bwa/bwase.c
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963 M /branches/prog/bwa/main.c
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964
|
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|
965 Release bwa-0.4.9
|
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|
966
|
|
|
967 ------------------------------------------------------------------------
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968 r1073 | lh3 | 2009-05-18 17:13:19 -0400 (Mon, 18 May 2009) | 2 lines
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969 Changed paths:
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970 M /branches/prog/bwa/NEWS
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971 M /branches/prog/bwa/bwa.1
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972 M /branches/prog/bwa/main.c
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973
|
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|
974 Release bwa-0.4.8
|
|
|
975
|
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|
976 ------------------------------------------------------------------------
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|
977 r1069 | lh3 | 2009-05-14 09:54:54 -0400 (Thu, 14 May 2009) | 3 lines
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978 Changed paths:
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|
979 M /branches/prog/bwa/bwtaln.c
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|
980 M /branches/prog/bwa/main.c
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981
|
|
|
982 * bwa-0.4.7-2
|
|
|
983 * change the default of "aln -R" to 30
|
|
|
984
|
|
|
985 ------------------------------------------------------------------------
|
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|
986 r1068 | lh3 | 2009-05-14 09:27:55 -0400 (Thu, 14 May 2009) | 3 lines
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987 Changed paths:
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|
988 M /branches/prog/bwa/bwape.c
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989 M /branches/prog/bwa/bwase.c
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990 M /branches/prog/bwa/bwtaln.c
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991 M /branches/prog/bwa/bwtaln.h
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992 M /branches/prog/bwa/bwtgap.c
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993 M /branches/prog/bwa/main.c
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|
994
|
|
|
995 * bwa-0.4.7-1
|
|
|
996 * search for suboptimal hits if the top hit is not so repetitive
|
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|
997
|
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|
998 ------------------------------------------------------------------------
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999 r1066 | lh3 | 2009-05-12 15:31:31 -0400 (Tue, 12 May 2009) | 2 lines
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1000 Changed paths:
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|
1001 M /branches/prog/bwa/ChangeLog
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1002 M /branches/prog/bwa/NEWS
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1003 M /branches/prog/bwa/bwase.c
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1004 M /branches/prog/bwa/main.c
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1005
|
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|
1006 Release bwa-0.4.7
|
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1007
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1008 ------------------------------------------------------------------------
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1009 r1065 | lh3 | 2009-05-12 15:20:40 -0400 (Tue, 12 May 2009) | 3 lines
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1010 Changed paths:
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|
1011 M /branches/prog/bwa/bwape.c
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1012 M /branches/prog/bwa/bwase.c
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1013 M /branches/prog/bwa/main.c
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|
1014
|
|
|
1015 * bwa-0.4.6-9
|
|
|
1016 * fixed compiling errors on some Linux machines
|
|
|
1017
|
|
|
1018 ------------------------------------------------------------------------
|
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|
1019 r1064 | lh3 | 2009-05-12 07:30:46 -0400 (Tue, 12 May 2009) | 3 lines
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|
1020 Changed paths:
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|
1021 M /branches/prog/bwa/bwtaln.c
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|
1022 M /branches/prog/bwa/main.c
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1023
|
|
|
1024 * bwa-0.4.6-8
|
|
|
1025 * avoid compilation error on some systems.
|
|
|
1026
|
|
|
1027 ------------------------------------------------------------------------
|
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|
1028 r1035 | lh3 | 2009-05-09 05:41:33 -0400 (Sat, 09 May 2009) | 4 lines
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1029 Changed paths:
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|
1030 M /branches/prog/bwa/bwape.c
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1031 M /branches/prog/bwa/bwase.c
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|
1032 M /branches/prog/bwa/main.c
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|
1033
|
|
|
1034 * bwa-0.4.6-7
|
|
|
1035 * fixed an integer overflow caused by previous modifications
|
|
|
1036 * made insert size estimation more robust
|
|
|
1037
|
|
|
1038 ------------------------------------------------------------------------
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|
1039 r1008 | lh3 | 2009-04-29 05:41:58 -0400 (Wed, 29 Apr 2009) | 4 lines
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1040 Changed paths:
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|
1041 M /branches/prog/bwa/bwase.c
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1042 M /branches/prog/bwa/main.c
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1043
|
|
|
1044 * bwa-0.4.6-5
|
|
|
1045 * fixed a integer overflow problem which may cause seg fault in very rare cases
|
|
|
1046 * made XN tags more accurate
|
|
|
1047
|
|
|
1048 ------------------------------------------------------------------------
|
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|
1049 r1005 | lh3 | 2009-04-27 07:37:23 -0400 (Mon, 27 Apr 2009) | 4 lines
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1050 Changed paths:
|
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|
1051 M /branches/prog/bwa/bwape.c
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1052 M /branches/prog/bwa/main.c
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1053 M /branches/prog/bwa/simple_dp.c
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|
1054 M /branches/prog/bwa/stdaln.c
|
|
|
1055 M /branches/prog/bwa/stdaln.h
|
|
|
1056
|
|
|
1057 * bwa-0.4.6-4
|
|
|
1058 * heuristic rules to detect suboptimal alignment
|
|
|
1059 * stdsw: support double-strand and protein alignment
|
|
|
1060
|
|
|
1061 ------------------------------------------------------------------------
|
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|
1062 r1003 | lh3 | 2009-04-26 12:48:19 -0400 (Sun, 26 Apr 2009) | 4 lines
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|
1063 Changed paths:
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|
1064 M /branches/prog/bwa/main.c
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1065 M /branches/prog/bwa/simple_dp.c
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|
1066 M /branches/prog/bwa/stdaln.c
|
|
|
1067 M /branches/prog/bwa/stdaln.h
|
|
|
1068
|
|
|
1069 * bwa-0.4.6-2
|
|
|
1070 * improve the functionality of stdsw
|
|
|
1071 * allow to add a threshold on SW alignment. Hope this does not incur new bugs...
|
|
|
1072
|
|
|
1073 ------------------------------------------------------------------------
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1074 r1002 | lh3 | 2009-04-22 03:56:15 -0400 (Wed, 22 Apr 2009) | 3 lines
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1075 Changed paths:
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1076 M /branches/prog/bwa/bwa.1
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1077 M /branches/prog/bwa/bwape.c
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1078 M /branches/prog/bwa/bwase.c
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|
1079 M /branches/prog/bwa/bwtaln.h
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|
1080 M /branches/prog/bwa/main.c
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1081
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1082 * bwa-0.4.6-1
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1083 * output SM and AM tag
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1084
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1085 ------------------------------------------------------------------------
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1086 r914 | lh3 | 2009-03-09 17:53:50 -0400 (Mon, 09 Mar 2009) | 2 lines
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1087 Changed paths:
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1088 M /branches/prog/bwa/ChangeLog
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1089 M /branches/prog/bwa/NEWS
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1090 M /branches/prog/bwa/main.c
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1091
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1092 Release bwa-0.4.6
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1093
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1094 ------------------------------------------------------------------------
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1095 r913 | lh3 | 2009-03-09 17:23:24 -0400 (Mon, 09 Mar 2009) | 4 lines
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1096 Changed paths:
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1097 M /branches/prog/bwa/bwa.1
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1098 M /branches/prog/bwa/bwape.c
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1099 A /branches/prog/bwa/solid2fastq.pl
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1100
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1101 * added notes to bwa
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1102 * added a script to convert SOLiD reads
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1103 * updated documentations
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1104
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1105 ------------------------------------------------------------------------
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1106 r912 | lh3 | 2009-03-09 16:57:05 -0400 (Mon, 09 Mar 2009) | 2 lines
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1107 Changed paths:
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1108 M /branches/prog/bwa/ChangeLog
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1109 M /branches/prog/bwa/kstring.c
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1110 M /branches/prog/bwa/main.c
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1111
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1112 fixed a bug in kstring
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1113
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1114 ------------------------------------------------------------------------
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1115 r881 | lh3 | 2009-03-02 15:36:06 -0500 (Mon, 02 Mar 2009) | 3 lines
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1116 Changed paths:
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1117 M /branches/prog/bwa/bwtmisc.c
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1118 M /branches/prog/bwa/main.c
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1119
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1120 * bwa-0.4.5-7
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1121 * fixed a bug in pac2cspac
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1122
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1123 ------------------------------------------------------------------------
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1124 r880 | lh3 | 2009-03-01 16:34:08 -0500 (Sun, 01 Mar 2009) | 2 lines
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1125 Changed paths:
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1126 M /branches/prog/bwa/Makefile
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1127
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1128 disable debugging
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1129
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1130 ------------------------------------------------------------------------
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1131 r879 | lh3 | 2009-03-01 16:28:04 -0500 (Sun, 01 Mar 2009) | 3 lines
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1132 Changed paths:
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1133 M /branches/prog/bwa/bwase.c
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1134 M /branches/prog/bwa/cs2nt.c
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1135 M /branches/prog/bwa/main.c
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1136
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1137 * bwa-0.4.5-6
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1138 * fixed problems with coordinates for color gapped alignment
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1139
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1140 ------------------------------------------------------------------------
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1141 r878 | lh3 | 2009-03-01 13:43:09 -0500 (Sun, 01 Mar 2009) | 3 lines
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1142 Changed paths:
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1143 M /branches/prog/bwa/bwase.c
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1144 M /branches/prog/bwa/cs2nt.c
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1145 M /branches/prog/bwa/main.c
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1146
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1147 * bwa-0.4.5-5
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1148 * added support for gapped color alignment
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1149
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1150 ------------------------------------------------------------------------
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1151 r877 | lh3 | 2009-03-01 10:27:52 -0500 (Sun, 01 Mar 2009) | 2 lines
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1152 Changed paths:
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1153 M /branches/prog/bwa/Makefile
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1154 M /branches/prog/bwa/bwape.c
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1155 M /branches/prog/bwa/bwase.c
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1156 M /branches/prog/bwa/bwtaln.h
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1157 M /branches/prog/bwa/cs2nt.c
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1158 M /branches/prog/bwa/main.c
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1159
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1160 * convert cs read to nt read (for ungapped alignment only)
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1161
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1162 ------------------------------------------------------------------------
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1163 r860 | lh3 | 2009-02-27 08:58:39 -0500 (Fri, 27 Feb 2009) | 2 lines
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1164 Changed paths:
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1165 M /branches/prog/bwa/Makefile
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1166 M /branches/prog/bwa/bwase.c
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1167 A /branches/prog/bwa/cs2nt.c
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1168
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1169 prepare to implement cs->nt conversion (have not yet...)
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1170
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1171 ------------------------------------------------------------------------
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1172 r859 | lh3 | 2009-02-27 07:00:03 -0500 (Fri, 27 Feb 2009) | 3 lines
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1173 Changed paths:
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1174 M /branches/prog/bwa/bntseq.c
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1175 M /branches/prog/bwa/bntseq.h
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1176 M /branches/prog/bwa/bwtindex.c
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1177 M /branches/prog/bwa/bwtmisc.c
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1178 M /branches/prog/bwa/main.c
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1179 M /branches/prog/bwa/main.h
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1180
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1181 * bwa-0.4.5-3
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1182 * generate color index from nucleotide fasta reference
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1183
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1184 ------------------------------------------------------------------------
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1185 r857 | lh3 | 2009-02-26 10:22:58 -0500 (Thu, 26 Feb 2009) | 4 lines
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1186 Changed paths:
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1187 M /branches/prog/bwa/bwape.c
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1188 M /branches/prog/bwa/main.c
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1189
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1190 * bwa-0.4.5-2
|
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1191 * improved mapping quality a bit if one end falls in a tandem repeat
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1192 but the mate is unique.
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1193
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1194 ------------------------------------------------------------------------
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1195 r856 | lh3 | 2009-02-26 10:02:29 -0500 (Thu, 26 Feb 2009) | 3 lines
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1196 Changed paths:
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1197 M /branches/prog/bwa/bwape.c
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1198 M /branches/prog/bwa/bwtaln.h
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1199 M /branches/prog/bwa/main.c
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1200
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1201 * bwa-0.4.5-1
|
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1202 * make bwa work for SOLiD reads
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1203
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1204 ------------------------------------------------------------------------
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1205 r828 | lh3 | 2009-02-18 17:36:41 -0500 (Wed, 18 Feb 2009) | 2 lines
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1206 Changed paths:
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1207 M /branches/prog/bwa/ChangeLog
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1208 M /branches/prog/bwa/NEWS
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1209 M /branches/prog/bwa/bwa.1
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1210 M /branches/prog/bwa/main.c
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1211
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1212 Release bwa-0.4.5
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1213
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1214 ------------------------------------------------------------------------
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1215 r827 | lh3 | 2009-02-18 16:48:48 -0500 (Wed, 18 Feb 2009) | 3 lines
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1216 Changed paths:
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1217 M /branches/prog/bwa/main.c
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1218 M /branches/prog/bwa/stdaln.c
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1219 M /branches/prog/bwa/stdaln.h
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1220
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1221 * bwa-0.4.4-6
|
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1222 * fixed a bug in SW alignment when no residue matches
|
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1223
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1224 ------------------------------------------------------------------------
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1225 r824 | lh3 | 2009-02-17 05:33:07 -0500 (Tue, 17 Feb 2009) | 3 lines
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1226 Changed paths:
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1227 M /branches/prog/bwa/bwape.c
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1228 M /branches/prog/bwa/main.c
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1229
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1230 * bwa-0.4.4-5
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1231 * fixed that bounary bug
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1232
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1233 ------------------------------------------------------------------------
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1234 r823 | lh3 | 2009-02-17 04:54:18 -0500 (Tue, 17 Feb 2009) | 2 lines
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1235 Changed paths:
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1236 M /branches/prog/bwa/ChangeLog
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1237 M /branches/prog/bwa/bwape.c
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1238
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1239 just change some logging information
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1240
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1241 ------------------------------------------------------------------------
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1242 r822 | lh3 | 2009-02-17 04:20:39 -0500 (Tue, 17 Feb 2009) | 2 lines
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1243 Changed paths:
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1244 M /branches/prog/bwa/bwa.1
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1245
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1246 update manual
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1247
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1248 ------------------------------------------------------------------------
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1249 r821 | lh3 | 2009-02-17 04:11:14 -0500 (Tue, 17 Feb 2009) | 3 lines
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1250 Changed paths:
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1251 M /branches/prog/bwa/bwape.c
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1252 M /branches/prog/bwa/bwase.c
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1253 M /branches/prog/bwa/main.c
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1254
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1255 * bwa-0.4.4-4
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1256 * fixed a bug on boundary check in pair_sw
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1257
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1258 ------------------------------------------------------------------------
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1259 r820 | lh3 | 2009-02-16 17:43:37 -0500 (Mon, 16 Feb 2009) | 3 lines
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1260 Changed paths:
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1261 M /branches/prog/bwa/bwtaln.c
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1262 M /branches/prog/bwa/main.c
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1263
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1264 * bwa-0.4.4-3
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1265 * allow to change mismatch penalty
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1266
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1267 ------------------------------------------------------------------------
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1268 r819 | lh3 | 2009-02-16 17:40:28 -0500 (Mon, 16 Feb 2009) | 4 lines
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1269 Changed paths:
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1270 M /branches/prog/bwa/bwtaln.c
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1271 M /branches/prog/bwa/main.c
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1272
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1273 * bwa-0.4.4-2
|
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1274 * remove timer
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1275 * allow to change default gapo and gape penalty at the command line
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1276
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1277 ------------------------------------------------------------------------
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1278 r818 | lh3 | 2009-02-16 09:30:51 -0500 (Mon, 16 Feb 2009) | 2 lines
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1279 Changed paths:
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1280 M /branches/prog/bwa/bwa.1
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1281
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1282 update benchmark
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1283
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1284 ------------------------------------------------------------------------
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1285 r817 | lh3 | 2009-02-16 08:44:40 -0500 (Mon, 16 Feb 2009) | 4 lines
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1286 Changed paths:
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1287 M /branches/prog/bwa/bwape.c
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1288 M /branches/prog/bwa/bwtaln.c
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1289 M /branches/prog/bwa/kvec.h
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1290 M /branches/prog/bwa/main.c
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1291
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1292 * bwa-0.4.4-1
|
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1293 * automatically detect insert size
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1294 * use insert size in pairing. This may potentially improve accuracy (untested!)
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1295
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1296 ------------------------------------------------------------------------
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1297 r814 | lh3 | 2009-02-15 11:10:23 -0500 (Sun, 15 Feb 2009) | 2 lines
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1298 Changed paths:
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1299 M /branches/prog/bwa/ChangeLog
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1300 M /branches/prog/bwa/NEWS
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1301 M /branches/prog/bwa/main.c
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1302
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1303 Release bwa-0.4.4
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1304
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1305 ------------------------------------------------------------------------
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1306 r813 | lh3 | 2009-02-15 10:22:50 -0500 (Sun, 15 Feb 2009) | 3 lines
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1307 Changed paths:
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1309 M /branches/prog/bwa/bwase.c
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1310 M /branches/prog/bwa/main.c
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1311
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1312 * bwa-0.4.3-5
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1313 * impose boundary check in refine_gapped
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1314
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1315 ------------------------------------------------------------------------
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1316 r811 | lh3 | 2009-02-14 09:46:13 -0500 (Sat, 14 Feb 2009) | 3 lines
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1317 Changed paths:
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1318 M /branches/prog/bwa/bwase.c
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1319 M /branches/prog/bwa/main.c
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1320
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1321 * bwa-0.4.3-4
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1322 * change MD tag to match the latest SAM specification
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1323
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1324 ------------------------------------------------------------------------
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1325 r810 | lh3 | 2009-02-13 04:46:04 -0500 (Fri, 13 Feb 2009) | 2 lines
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1326 Changed paths:
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1327 M /branches/prog/bwa/ChangeLog
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1328
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1329 update ChangeLog
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1330
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1331 ------------------------------------------------------------------------
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1332 r799 | lh3 | 2009-02-05 12:01:17 -0500 (Thu, 05 Feb 2009) | 2 lines
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1333 Changed paths:
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1334 M /branches/prog/bwa/bwase.c
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1335 M /branches/prog/bwa/main.c
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1336
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1337 change MD tag to meet the latest SAM specification
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1338
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1339 ------------------------------------------------------------------------
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1340 r796 | lh3 | 2009-02-05 08:35:13 -0500 (Thu, 05 Feb 2009) | 3 lines
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1341 Changed paths:
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1342 M /branches/prog/bwa/bntseq.c
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1343 M /branches/prog/bwa/bwase.c
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1344 M /branches/prog/bwa/main.c
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1345
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1346 * bwa-0.4.3-2
|
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|
1347 * fixed a bug on counting 'N'
|
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1348
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1349 ------------------------------------------------------------------------
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1350 r795 | lh3 | 2009-02-05 07:41:27 -0500 (Thu, 05 Feb 2009) | 4 lines
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1351 Changed paths:
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1354 M /branches/prog/bwa/main.c
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1355
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1356 * bwa-0.4.3-1
|
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|
1357 * fixed potential boundary problems
|
|
|
1358 * update benchmark result
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1359
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1360 ------------------------------------------------------------------------
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1361 r791 | lh3 | 2009-01-25 05:20:47 -0500 (Sun, 25 Jan 2009) | 2 lines
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1362 Changed paths:
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1363 M /branches/prog/bwa/bwa.1
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1364
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1365 update some numbers
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1366
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1367 ------------------------------------------------------------------------
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1368 r790 | lh3 | 2009-01-24 15:13:03 -0500 (Sat, 24 Jan 2009) | 2 lines
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1369 Changed paths:
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1370 M /branches/prog/bwa/bwa.1
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1371
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1372 update benchmark
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1373
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1374 ------------------------------------------------------------------------
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1375 r789 | lh3 | 2009-01-22 10:18:44 -0500 (Thu, 22 Jan 2009) | 2 lines
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1376 Changed paths:
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1377 M /branches/prog/bwa/bwtindex.c
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1378
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1379 a warning message for index
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1380
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1381 ------------------------------------------------------------------------
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1382 r788 | lh3 | 2009-01-22 09:54:06 -0500 (Thu, 22 Jan 2009) | 2 lines
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1383 Changed paths:
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1384 M /branches/prog/bwa/main.c
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1385
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1386 forget to change release number
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1387
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1388 ------------------------------------------------------------------------
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1389 r786 | lh3 | 2009-01-22 06:27:39 -0500 (Thu, 22 Jan 2009) | 2 lines
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1390 Changed paths:
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1391 M /branches/prog/bwa/NEWS
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1392
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1393 Release bwa-0.4.3
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1394
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1395 ------------------------------------------------------------------------
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1396 r785 | lh3 | 2009-01-22 06:27:16 -0500 (Thu, 22 Jan 2009) | 2 lines
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1397 Changed paths:
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1398 M /branches/prog/bwa/ChangeLog
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1399 M /branches/prog/bwa/NEWS
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1400
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1401 Release bwa-0.4.3
|
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1402
|
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|
1403 ------------------------------------------------------------------------
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1404 r784 | lh3 | 2009-01-22 06:19:59 -0500 (Thu, 22 Jan 2009) | 4 lines
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1405 Changed paths:
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1407 M /branches/prog/bwa/bwase.c
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1408 M /branches/prog/bwa/main.c
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1409
|
|
|
1410 * bwa-0.4.2-10
|
|
|
1411 * update documentation
|
|
|
1412 * fixed a bug on generating MD tags for SW alignment
|
|
|
1413
|
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|
1414 ------------------------------------------------------------------------
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1415 r782 | lh3 | 2009-01-19 12:08:38 -0500 (Mon, 19 Jan 2009) | 3 lines
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1416 Changed paths:
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1417 M /branches/prog/bwa/bwase.c
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1418 M /branches/prog/bwa/main.c
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1419
|
|
|
1420 * bwa-0.4.2-9
|
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|
1421 * fixed a bug in samse -n...
|
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|
1422
|
|
|
1423 ------------------------------------------------------------------------
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1424 r781 | lh3 | 2009-01-19 11:26:37 -0500 (Mon, 19 Jan 2009) | 3 lines
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1425 Changed paths:
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1427 M /branches/prog/bwa/main.c
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1428
|
|
|
1429 * bwa-0.4.2-8
|
|
|
1430 * given -N, the previous version would stop if the top hit is a repeat. Now changed.
|
|
|
1431
|
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|
1432 ------------------------------------------------------------------------
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1433 r780 | lh3 | 2009-01-19 11:20:18 -0500 (Mon, 19 Jan 2009) | 4 lines
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1434 Changed paths:
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1435 M /branches/prog/bwa/bwape.c
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1436 M /branches/prog/bwa/bwase.c
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1437 M /branches/prog/bwa/bwtaln.c
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1438 M /branches/prog/bwa/bwtaln.h
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1439 M /branches/prog/bwa/bwtgap.c
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1440 M /branches/prog/bwa/main.c
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1441
|
|
|
1442 * bwa-0.4.2-7
|
|
|
1443 * use a bit-wise flag to replace some member variables in the option struct
|
|
|
1444 * allow to switch off the iterative strategy
|
|
|
1445
|
|
|
1446 ------------------------------------------------------------------------
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|
1447 r779 | lh3 | 2009-01-19 10:45:57 -0500 (Mon, 19 Jan 2009) | 3 lines
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1448 Changed paths:
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1449 M /branches/prog/bwa/bwa.1
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1450 M /branches/prog/bwa/bwase.c
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1451 M /branches/prog/bwa/main.c
|
|
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1452
|
|
|
1453 * bwa-0.4.2-6
|
|
|
1454 * allow to dump multiple hits from samse, in another format, though
|
|
|
1455
|
|
|
1456 ------------------------------------------------------------------------
|
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|
1457 r778 | lh3 | 2009-01-19 06:24:29 -0500 (Mon, 19 Jan 2009) | 5 lines
|
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1458 Changed paths:
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1459 M /branches/prog/bwa/Makefile
|
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1460 M /branches/prog/bwa/bwape.c
|
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1461 M /branches/prog/bwa/bwase.c
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1462 M /branches/prog/bwa/bwaseqio.c
|
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1463 M /branches/prog/bwa/bwtaln.h
|
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1464 M /branches/prog/bwa/kseq.h
|
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1465 A /branches/prog/bwa/kstring.c
|
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1466 A /branches/prog/bwa/kstring.h
|
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1467 M /branches/prog/bwa/main.c
|
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1468 M /branches/prog/bwa/simple_dp.c
|
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|
1469
|
|
|
1470 * bwa-0.4.2-5
|
|
|
1471 * update kseq.h to the latest version
|
|
|
1472 * generate MD tag
|
|
|
1473 * print mate coordinate if only one end is unmapped
|
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1474
|
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1475 ------------------------------------------------------------------------
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|
1476 r775 | lh3 | 2009-01-18 05:40:35 -0500 (Sun, 18 Jan 2009) | 3 lines
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1477 Changed paths:
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1478 M /branches/prog/bwa/bwase.c
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1479 M /branches/prog/bwa/main.c
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1480
|
|
|
1481 * bwa-0.4.2-4
|
|
|
1482 * fixed a bug for SAM format
|
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1483
|
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1484 ------------------------------------------------------------------------
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1485 r774 | lh3 | 2009-01-17 13:48:52 -0500 (Sat, 17 Jan 2009) | 4 lines
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1486 Changed paths:
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1487 M /branches/prog/bwa/bwtaln.c
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1488 M /branches/prog/bwa/main.c
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1489
|
|
|
1490 * bwa-0.4.2-3
|
|
|
1491 * change default fnr to 0.04
|
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1492 * print max_diff for valid fnr
|
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1493
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1494 ------------------------------------------------------------------------
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1495 r773 | lh3 | 2009-01-17 05:54:37 -0500 (Sat, 17 Jan 2009) | 3 lines
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1496 Changed paths:
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1497 M /branches/prog/bwa/bwape.c
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1498 M /branches/prog/bwa/bwase.c
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1499 M /branches/prog/bwa/bwtaln.c
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1500 M /branches/prog/bwa/bwtaln.h
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1501 M /branches/prog/bwa/main.c
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1502
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|
1503 * bwa-0.4.2-2
|
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1504 * automatically choose max_diff
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1505
|
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1506 ------------------------------------------------------------------------
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1507 r772 | lh3 | 2009-01-16 18:16:14 -0500 (Fri, 16 Jan 2009) | 3 lines
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1508 Changed paths:
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1509 M /branches/prog/bwa/bwaseqio.c
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1510 M /branches/prog/bwa/bwt.c
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1511 M /branches/prog/bwa/bwtaln.c
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1512 M /branches/prog/bwa/bwtaln.h
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1513 M /branches/prog/bwa/bwtgap.c
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1514 M /branches/prog/bwa/main.c
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1515
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|
1516 * bwa-0.4.2-1
|
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1517 * take N as a mismatch
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1518
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1519 ------------------------------------------------------------------------
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1520 r768 | lh3 | 2009-01-09 11:57:23 -0500 (Fri, 09 Jan 2009) | 2 lines
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1521 Changed paths:
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1522 M /branches/prog/bwa/ChangeLog
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1523 M /branches/prog/bwa/NEWS
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1524 M /branches/prog/bwa/bntseq.c
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1525 M /branches/prog/bwa/main.c
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1526
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1527 Release bwa-0.4.2
|
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1528
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1529 ------------------------------------------------------------------------
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1530 r759 | lh3 | 2009-01-07 09:55:43 -0500 (Wed, 07 Jan 2009) | 2 lines
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1531 Changed paths:
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1532 M /branches/prog/bwa/ChangeLog
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1533 M /branches/prog/bwa/NEWS
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1534 M /branches/prog/bwa/bwa.1
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1535 M /branches/prog/bwa/bwape.c
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1536 M /branches/prog/bwa/bwtaln.h
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1537 M /branches/prog/bwa/main.c
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1538
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1539 Release bwa-0.4.1
|
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1540
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|
1541 ------------------------------------------------------------------------
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1542 r758 | lh3 | 2009-01-07 05:36:06 -0500 (Wed, 07 Jan 2009) | 3 lines
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1543 Changed paths:
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1544 M /branches/prog/bwa/bwape.c
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1545 M /branches/prog/bwa/bwase.c
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1546 M /branches/prog/bwa/bwtaln.h
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1547 M /branches/prog/bwa/main.c
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1548
|
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|
1549 * bwa-0.4.0-2
|
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|
1550 * make mate_sw fully working
|
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1551
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1552 ------------------------------------------------------------------------
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1553 r757 | lh3 | 2009-01-06 18:04:29 -0500 (Tue, 06 Jan 2009) | 5 lines
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1554 Changed paths:
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1555 M /branches/prog/bwa/bwape.c
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1556 M /branches/prog/bwa/bwase.c
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1557 M /branches/prog/bwa/bwaseqio.c
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1558 M /branches/prog/bwa/bwtaln.h
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1559 M /branches/prog/bwa/main.c
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1560
|
|
|
1561 * bwa-0.4.0-1
|
|
|
1562 * do SW alignment for unmapped mate. It is working.
|
|
|
1563 * I still need to do some extra work for SW alignment, but it is too late
|
|
|
1564 and I am getting tired... I will do tomorrow.
|
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1565
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1566 ------------------------------------------------------------------------
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1567 r755 | lh3 | 2009-01-06 10:23:29 -0500 (Tue, 06 Jan 2009) | 2 lines
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1568 Changed paths:
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1569 M /branches/prog/bwa/ChangeLog
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1570 M /branches/prog/bwa/NEWS
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1571 M /branches/prog/bwa/bwa.1
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1572 M /branches/prog/bwa/main.c
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1573
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|
1574 Release bwa-0.4.0
|
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1575
|
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|
1576 ------------------------------------------------------------------------
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1577 r754 | lh3 | 2009-01-06 07:45:02 -0500 (Tue, 06 Jan 2009) | 3 lines
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1578 Changed paths:
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1579 M /branches/prog/bwa/bwtaln.c
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1580 M /branches/prog/bwa/bwtgap.c
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1581 M /branches/prog/bwa/bwtgap.h
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1582 M /branches/prog/bwa/main.c
|
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1583
|
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|
1584 * bwa-0.3.0-12
|
|
|
1585 * better lock
|
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1586
|
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|
1587 ------------------------------------------------------------------------
|
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|
1588 r753 | lh3 | 2009-01-06 06:17:21 -0500 (Tue, 06 Jan 2009) | 5 lines
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1589 Changed paths:
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1590 M /branches/prog/bwa/Makefile
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1591 M /branches/prog/bwa/bwaseqio.c
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1592 M /branches/prog/bwa/bwtaln.c
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1593 M /branches/prog/bwa/bwtaln.h
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1594 M /branches/prog/bwa/bwtgap.c
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1595 M /branches/prog/bwa/main.c
|
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|
1596
|
|
|
1597 * bwa-0.3.0-11
|
|
|
1598 * fixed a small memory leak in bwa_seq_close()
|
|
|
1599 * fixed "uninitialized memory" from bwt_aln1_t
|
|
|
1600 * multithreading for "aln" command
|
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|
1601
|
|
|
1602 ------------------------------------------------------------------------
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|
1603 r752 | lh3 | 2009-01-05 17:34:13 -0500 (Mon, 05 Jan 2009) | 3 lines
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1604 Changed paths:
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1605 M /branches/prog/bwa/Makefile
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1606 D /branches/prog/bwa/bwt2fmv.c
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1607 M /branches/prog/bwa/bwt_gen/bwt_gen.c
|
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|
1608 A /branches/prog/bwa/bwtmisc.c (from /branches/prog/bwa/pac2bwt.c:748)
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1609 M /branches/prog/bwa/main.c
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1610 M /branches/prog/bwa/main.h
|
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|
1611 D /branches/prog/bwa/pac2bwt.c
|
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|
1612
|
|
|
1613 * bwa-0.3.0-10
|
|
|
1614 * a little bit code clean up
|
|
|
1615
|
|
|
1616 ------------------------------------------------------------------------
|
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|
1617 r751 | lh3 | 2009-01-05 17:19:04 -0500 (Mon, 05 Jan 2009) | 3 lines
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1618 Changed paths:
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1619 M /branches/prog/bwa/bwt.c
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1620 M /branches/prog/bwa/main.c
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1621
|
|
|
1622 * bwa-0.3.0-9
|
|
|
1623 * use 64-bit integer to speed up Occ calculate, although just a little bit
|
|
|
1624
|
|
|
1625 ------------------------------------------------------------------------
|
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|
1626 r750 | lh3 | 2009-01-05 16:44:26 -0500 (Mon, 05 Jan 2009) | 3 lines
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1627 Changed paths:
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1628 M /branches/prog/bwa/bwt.c
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1629 M /branches/prog/bwa/main.c
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1630
|
|
|
1631 * bwa-0.3.0-8
|
|
|
1632 * a little bit code cleanup
|
|
|
1633
|
|
|
1634 ------------------------------------------------------------------------
|
|
|
1635 r749 | lh3 | 2009-01-05 16:37:28 -0500 (Mon, 05 Jan 2009) | 3 lines
|
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1636 Changed paths:
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|
1637 M /branches/prog/bwa/bwt.c
|
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1638 M /branches/prog/bwa/main.c
|
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1639
|
|
|
1640 * bwa-0.1.0-7
|
|
|
1641 * accelerate Occ calculation
|
|
|
1642
|
|
|
1643 ------------------------------------------------------------------------
|
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|
1644 r748 | lh3 | 2009-01-05 16:12:28 -0500 (Mon, 05 Jan 2009) | 4 lines
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1645 Changed paths:
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1646 M /branches/prog/bwa/bwape.c
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1647 M /branches/prog/bwa/bwase.c
|
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1648 M /branches/prog/bwa/bwt.c
|
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|
1649 M /branches/prog/bwa/bwt.h
|
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|
1650 M /branches/prog/bwa/bwt2fmv.c
|
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|
1651 M /branches/prog/bwa/bwtaln.c
|
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|
1652 M /branches/prog/bwa/bwtindex.c
|
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|
1653 M /branches/prog/bwa/bwtio.c
|
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|
1654 M /branches/prog/bwa/main.c
|
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|
1655 M /branches/prog/bwa/main.h
|
|
|
1656 M /branches/prog/bwa/pac2bwt.c
|
|
|
1657
|
|
|
1658 * bwa-0.3.0-6
|
|
|
1659 * put occ table along with bwt to save another cache miss
|
|
|
1660 * this version is already faster than the previous and I can still improve it...
|
|
|
1661
|
|
|
1662 ------------------------------------------------------------------------
|
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|
1663 r747 | lh3 | 2009-01-05 10:16:18 -0500 (Mon, 05 Jan 2009) | 5 lines
|
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1664 Changed paths:
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1665 M /branches/prog/bwa/bwt.c
|
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1666 M /branches/prog/bwa/bwt.h
|
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|
1667 M /branches/prog/bwa/bwtio.c
|
|
|
1668 M /branches/prog/bwa/main.c
|
|
|
1669
|
|
|
1670 * bwa-0.3.0-5
|
|
|
1671 * remove occ_major to save a cache miss; however, OCC_INTERVAL has to be
|
|
|
1672 increased to keep the same memory. As a result, the speed is a little
|
|
|
1673 slower in fact.
|
|
|
1674
|
|
|
1675 ------------------------------------------------------------------------
|
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|
1676 r746 | lh3 | 2009-01-05 09:50:53 -0500 (Mon, 05 Jan 2009) | 3 lines
|
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1677 Changed paths:
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|
1678 M /branches/prog/bwa/bwt.c
|
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|
1679 M /branches/prog/bwa/main.c
|
|
|
1680
|
|
|
1681 * bwa-0.3.0-4
|
|
|
1682 * added back optimization codes (it is a pain...)
|
|
|
1683
|
|
|
1684 ------------------------------------------------------------------------
|
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|
1685 r745 | lh3 | 2009-01-05 08:23:00 -0500 (Mon, 05 Jan 2009) | 3 lines
|
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1686 Changed paths:
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|
1687 M /branches/prog/bwa/bwt.c
|
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|
1688 M /branches/prog/bwa/bwtaln.c
|
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|
1689 M /branches/prog/bwa/main.c
|
|
|
1690
|
|
|
1691 * bwa-0.3.0-3
|
|
|
1692 * faster bit operations
|
|
|
1693
|
|
|
1694 ------------------------------------------------------------------------
|
|
|
1695 r744 | lh3 | 2009-01-05 05:58:46 -0500 (Mon, 05 Jan 2009) | 4 lines
|
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|
1696 Changed paths:
|
|
|
1697 M /branches/prog/bwa/bwt.c
|
|
|
1698 M /branches/prog/bwa/main.c
|
|
|
1699
|
|
|
1700 * bwa-0.3.0-2
|
|
|
1701 * removed optimization codes again...
|
|
|
1702 * use a new method to count the bits
|
|
|
1703
|
|
|
1704 ------------------------------------------------------------------------
|
|
|
1705 r743 | lh3 | 2009-01-04 17:18:38 -0500 (Sun, 04 Jan 2009) | 5 lines
|
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|
1706 Changed paths:
|
|
|
1707 M /branches/prog/bwa/bwa.1
|
|
|
1708 M /branches/prog/bwa/bwt.c
|
|
|
1709 M /branches/prog/bwa/bwtaln.c
|
|
|
1710 M /branches/prog/bwa/bwtaln.h
|
|
|
1711 M /branches/prog/bwa/bwtgap.c
|
|
|
1712 M /branches/prog/bwa/main.c
|
|
|
1713
|
|
|
1714 * bwa-0.3.0-1
|
|
|
1715 * added back the optimization codes
|
|
|
1716 * added a new option to aln: max_entries, although this is disabled by default
|
|
|
1717 * updated benchmark
|
|
|
1718
|
|
|
1719 ------------------------------------------------------------------------
|
|
|
1720 r742 | lh3 | 2009-01-04 07:56:12 -0500 (Sun, 04 Jan 2009) | 2 lines
|
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|
1721 Changed paths:
|
|
|
1722 M /branches/prog/bwa/bwa.1
|
|
|
1723
|
|
|
1724 add URL
|
|
|
1725
|
|
|
1726 ------------------------------------------------------------------------
|
|
|
1727 r740 | lh3 | 2009-01-04 07:39:43 -0500 (Sun, 04 Jan 2009) | 2 lines
|
|
|
1728 Changed paths:
|
|
|
1729 M /branches/prog/bwa/ChangeLog
|
|
|
1730 M /branches/prog/bwa/NEWS
|
|
|
1731 M /branches/prog/bwa/bwa.1
|
|
|
1732 M /branches/prog/bwa/main.c
|
|
|
1733
|
|
|
1734 Release bwa-0.3.0
|
|
|
1735
|
|
|
1736 ------------------------------------------------------------------------
|
|
|
1737 r739 | lh3 | 2009-01-04 06:55:06 -0500 (Sun, 04 Jan 2009) | 2 lines
|
|
|
1738 Changed paths:
|
|
|
1739 A /branches/prog/bwa/COPYING
|
|
|
1740 M /branches/prog/bwa/ChangeLog
|
|
|
1741 M /branches/prog/bwa/bntseq.c
|
|
|
1742 M /branches/prog/bwa/bntseq.h
|
|
|
1743 M /branches/prog/bwa/bwa.1
|
|
|
1744 M /branches/prog/bwa/bwt.c
|
|
|
1745 M /branches/prog/bwa/bwt.h
|
|
|
1746 M /branches/prog/bwa/bwtindex.c
|
|
|
1747 M /branches/prog/bwa/utils.c
|
|
|
1748 M /branches/prog/bwa/utils.h
|
|
|
1749
|
|
|
1750 added licensing information
|
|
|
1751
|
|
|
1752 ------------------------------------------------------------------------
|
|
|
1753 r738 | lh3 | 2009-01-04 06:18:25 -0500 (Sun, 04 Jan 2009) | 4 lines
|
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|
1754 Changed paths:
|
|
|
1755 M /branches/prog/bwa/bwa.1
|
|
|
1756 M /branches/prog/bwa/bwape.c
|
|
|
1757 M /branches/prog/bwa/main.c
|
|
|
1758
|
|
|
1759 * bwa-0.2.0-31
|
|
|
1760 * better mapping quality
|
|
|
1761 * update benchmark
|
|
|
1762
|
|
|
1763 ------------------------------------------------------------------------
|
|
|
1764 r737 | lh3 | 2009-01-03 16:00:58 -0500 (Sat, 03 Jan 2009) | 2 lines
|
|
|
1765 Changed paths:
|
|
|
1766 M /branches/prog/bwa/ChangeLog
|
|
|
1767 M /branches/prog/bwa/bwa.1
|
|
|
1768
|
|
|
1769 update documentation
|
|
|
1770
|
|
|
1771 ------------------------------------------------------------------------
|
|
|
1772 r736 | lh3 | 2009-01-02 10:26:38 -0500 (Fri, 02 Jan 2009) | 2 lines
|
|
|
1773 Changed paths:
|
|
|
1774 M /branches/prog/bwa/bwa.1
|
|
|
1775
|
|
|
1776 update documentation
|
|
|
1777
|
|
|
1778 ------------------------------------------------------------------------
|
|
|
1779 r735 | lh3 | 2009-01-02 07:10:20 -0500 (Fri, 02 Jan 2009) | 4 lines
|
|
|
1780 Changed paths:
|
|
|
1781 M /branches/prog/bwa/bwa.1
|
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|
1782 M /branches/prog/bwa/bwape.c
|
|
|
1783 M /branches/prog/bwa/bwtaln.c
|
|
|
1784 M /branches/prog/bwa/main.c
|
|
|
1785
|
|
|
1786 * bwa-0.2.0-30
|
|
|
1787 * reduce memory a little bit
|
|
|
1788 * update documentation
|
|
|
1789
|
|
|
1790 ------------------------------------------------------------------------
|
|
|
1791 r734 | lh3 | 2009-01-01 13:45:45 -0500 (Thu, 01 Jan 2009) | 8 lines
|
|
|
1792 Changed paths:
|
|
|
1793 M /branches/prog/bwa/bwa.1
|
|
|
1794 M /branches/prog/bwa/bwape.c
|
|
|
1795 M /branches/prog/bwa/bwase.c
|
|
|
1796 M /branches/prog/bwa/bwtaln.c
|
|
|
1797 M /branches/prog/bwa/bwtaln.h
|
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1798 M /branches/prog/bwa/bwtgap.c
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1799 M /branches/prog/bwa/main.c
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1800
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1801 * bwa-0.2.0-29
|
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1802 * sampe: removed -O option; changed default -o to 100000
|
|
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1803 * sampe: fixed a bug in calculating paired mapping quality
|
|
|
1804 * aln: added an option to search for suboptimal hits even if the best is a repeat.
|
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1805 This option will make sampe MUCH SLOWER.
|
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|
1806 * sampe: set isize as zero if mapped to two different chr
|
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1807 * update manual (unfinished)
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1808
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1809 ------------------------------------------------------------------------
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1810 r733 | lh3 | 2009-01-01 11:01:20 -0500 (Thu, 01 Jan 2009) | 3 lines
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1811 Changed paths:
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1812 M /branches/prog/bwa/bwape.c
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1813 M /branches/prog/bwa/main.c
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1814
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1815 * bwa-0.2.0-28
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1816 * fixed a bug in calculating paired mapping quality
|
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1817
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1818 ------------------------------------------------------------------------
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1819 r732 | lh3 | 2009-01-01 09:27:46 -0500 (Thu, 01 Jan 2009) | 3 lines
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1820 Changed paths:
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1821 M /branches/prog/bwa/bwape.c
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1822 A /branches/prog/bwa/khash.h (from /branches/prog/sclib/khash/khash.h:675)
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1823 M /branches/prog/bwa/main.c
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1824
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1825 * bwa-0.2.0-27
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1826 * accelerate sampe by storing visited large intervals
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1827
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1828 ------------------------------------------------------------------------
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1829 r731 | lh3 | 2009-01-01 06:51:21 -0500 (Thu, 01 Jan 2009) | 3 lines
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1830 Changed paths:
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1831 M /branches/prog/bwa/bwt.c
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1832 M /branches/prog/bwa/main.c
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1833
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1834 * bwa-0.2.0-26
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1835 * remove the optimation codes
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1836
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1837 ------------------------------------------------------------------------
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1838 r730 | lh3 | 2009-01-01 06:48:59 -0500 (Thu, 01 Jan 2009) | 4 lines
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1839 Changed paths:
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1840 M /branches/prog/bwa/bwt.c
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1841 M /branches/prog/bwa/main.c
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1842
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1843 * bwa-0.2.0-25
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1844 * accelerate OCC calculation by ~7%. However, it seems not worth doing
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1845 this by complicate the codes. I will change back later.
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1846
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1847 ------------------------------------------------------------------------
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1848 r729 | lh3 | 2008-12-31 16:43:56 -0500 (Wed, 31 Dec 2008) | 6 lines
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1849 Changed paths:
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1850 M /branches/prog/bwa/bntseq.c
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1851 M /branches/prog/bwa/bwape.c
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1852 M /branches/prog/bwa/bwase.c
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1853 M /branches/prog/bwa/main.c
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1854
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1855 * bwa-0.2.0-24
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1856 * change command "sai2sam_pe" to "sampe"
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1857 * print usage for sampe command
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1858 * in sampe: change default max_occ to 1000
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1859 * fixed a few compiling warnings in bntseq.c
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1860
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1861 ------------------------------------------------------------------------
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1862 r728 | lh3 | 2008-12-27 07:14:59 -0500 (Sat, 27 Dec 2008) | 3 lines
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1863 Changed paths:
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1864 M /branches/prog/bwa/bwape.c
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1865 M /branches/prog/bwa/bwase.c
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1866 M /branches/prog/bwa/main.c
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1867
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1868 * bwa-0.2.0-22
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1869 * mating information can be printed to SAM
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1870
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1871 ------------------------------------------------------------------------
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1872 r727 | lh3 | 2008-12-26 18:10:59 -0500 (Fri, 26 Dec 2008) | 4 lines
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1873 Changed paths:
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1874 M /branches/prog/bwa/bwape.c
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1875 M /branches/prog/bwa/bwase.c
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1876 M /branches/prog/bwa/bwaseqio.c
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1877 M /branches/prog/bwa/bwtaln.c
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1878 M /branches/prog/bwa/bwtaln.h
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1879 M /branches/prog/bwa/main.c
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1880
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1881 * bwa-0.2.0-21
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1882 * implement pairing (still UNFINISHED)
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1883 * output all reads even if full of N
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1884
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1885 ------------------------------------------------------------------------
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1886 r726 | lh3 | 2008-12-26 13:31:27 -0500 (Fri, 26 Dec 2008) | 5 lines
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1887 Changed paths:
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1888 M /branches/prog/bwa/Makefile
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1889 A /branches/prog/bwa/bwape.c
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1890 M /branches/prog/bwa/bwase.c
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1891 M /branches/prog/bwa/bwt2fmv.c
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1892 M /branches/prog/bwa/bwtaln.c
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1893 M /branches/prog/bwa/bwtaln.h
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1894 M /branches/prog/bwa/bwtgap.c
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1895 M /branches/prog/bwa/main.c
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1896 M /branches/prog/bwa/main.h
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1897
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1898 * bwa-0.2.0-20
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1899 * remove "-t" from aln cmd
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|
1900 * code clean up: move some functions in bwt2fmv.c to other source files
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1901 * added sai2sam_pe cmd: *UNFINISHED*
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1902
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1903 ------------------------------------------------------------------------
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1904 r725 | lh3 | 2008-12-26 07:04:11 -0500 (Fri, 26 Dec 2008) | 3 lines
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1905 Changed paths:
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1906 M /branches/prog/bwa/Makefile
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1907 A /branches/prog/bwa/bwase.c
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1908 A /branches/prog/bwa/bwaseqio.c
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1909 M /branches/prog/bwa/bwt2fmv.c
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1910 M /branches/prog/bwa/bwtaln.c
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1911 M /branches/prog/bwa/bwtaln.h
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1912 M /branches/prog/bwa/bwtgap.c
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1913 M /branches/prog/bwa/kseq.h
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1914 A /branches/prog/bwa/ksort.h (from /branches/prog/sclib/ksort/ksort.h:712)
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1915 A /branches/prog/bwa/kvec.h (from /branches/prog/sclib/kvec/kvec.h:537)
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1916 M /branches/prog/bwa/main.c
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1917
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1918 * bwa-0.2.0-19
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1919 * considerable code cleanup; no actual changes
|
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1920
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1921 ------------------------------------------------------------------------
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1922 r724 | lh3 | 2008-12-25 11:32:11 -0500 (Thu, 25 Dec 2008) | 3 lines
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1923 Changed paths:
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1924 M /branches/prog/bwa/bwtaln.c
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1925 M /branches/prog/bwa/bwtaln.h
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1926 M /branches/prog/bwa/main.c
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1927
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|
1928 * bwa-0.2.0-18
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1929 * generate SAM output
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1930
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1931 ------------------------------------------------------------------------
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1932 r723 | lh3 | 2008-12-25 10:48:31 -0500 (Thu, 25 Dec 2008) | 4 lines
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1933 Changed paths:
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1934 M /branches/prog/bwa/bwt2fmv.c
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1935 M /branches/prog/bwa/bwtaln.c
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1936 M /branches/prog/bwa/main.c
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1937 M /branches/prog/bwa/main.h
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1938
|
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|
1939 * bwa-0.2.0-17
|
|
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1940 * remove bwtsw2 related codes
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|
|
1941 * separate searching for SA interval from generating alignments
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1942
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1943 ------------------------------------------------------------------------
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1944 r722 | lh3 | 2008-12-25 08:57:13 -0500 (Thu, 25 Dec 2008) | 3 lines
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1945 Changed paths:
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1946 M /branches/prog/bwa/Makefile
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1947 M /branches/prog/bwa/bwt2fmv.c
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1948 D /branches/prog/bwa/bwt_lite.c
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1949 D /branches/prog/bwa/bwt_lite.h
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1950 M /branches/prog/bwa/bwtgap.c
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1951 D /branches/prog/bwa/bwtsw2.h
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1952 D /branches/prog/bwa/bwtsw2_aux.c
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1953 D /branches/prog/bwa/bwtsw2_core.c
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1954 D /branches/prog/bwa/bwtsw2_main.c
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1955 D /branches/prog/bwa/khash.h
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1956 D /branches/prog/bwa/ksort.h
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1957 D /branches/prog/bwa/kvec.h
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1958 M /branches/prog/bwa/main.c
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1959
|
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|
1960 * added interface to "aln -t"
|
|
|
1961 * remove bwtsw2 related codes
|
|
|
1962
|
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|
1963 ------------------------------------------------------------------------
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|
1964 r666 | lh3 | 2008-11-18 18:34:29 -0500 (Tue, 18 Nov 2008) | 4 lines
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1965 Changed paths:
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1966 M /branches/prog/bwa/bwt2fmv.c
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1967 M /branches/prog/bwa/bwtaln.c
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|
1968 M /branches/prog/bwa/bwtaln.h
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|
1969 M /branches/prog/bwa/main.c
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|
1970
|
|
|
1971 * bwa-0.2.0-16
|
|
|
1972 * allow to set max mismatches based on read length, but I do not know
|
|
|
1973 whether this really works
|
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|
1974
|
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|
1975 ------------------------------------------------------------------------
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|
1976 r665 | lh3 | 2008-11-18 08:34:03 -0500 (Tue, 18 Nov 2008) | 3 lines
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1977 Changed paths:
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1978 M /branches/prog/bwa/bwtaln.c
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|
1979 M /branches/prog/bwa/main.c
|
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|
1980
|
|
|
1981 * bwa-0.2.0-15
|
|
|
1982 * fixed a bug in sequence parser.
|
|
|
1983
|
|
|
1984 ------------------------------------------------------------------------
|
|
|
1985 r612 | lh3 | 2008-10-28 06:50:53 -0400 (Tue, 28 Oct 2008) | 3 lines
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|
1986 Changed paths:
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|
1987 M /branches/prog/bwa/bntseq.c
|
|
|
1988 M /branches/prog/bwa/bwtindex.c
|
|
|
1989 M /branches/prog/bwa/main.c
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|
|
1990 M /branches/prog/bwa/utils.c
|
|
|
1991
|
|
|
1992 * bwa-0.2.0-14
|
|
|
1993 * fixed a bug caused by the change of the FASTA/Q parser
|
|
|
1994
|
|
|
1995 ------------------------------------------------------------------------
|
|
|
1996 r611 | lh3 | 2008-10-28 06:24:56 -0400 (Tue, 28 Oct 2008) | 2 lines
|
|
|
1997 Changed paths:
|
|
|
1998 M /branches/prog/bwa/Makefile
|
|
|
1999 M /branches/prog/bwa/bntseq.c
|
|
|
2000 M /branches/prog/bwa/bntseq.h
|
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|
2001 M /branches/prog/bwa/bwtaln.c
|
|
|
2002 M /branches/prog/bwa/bwtsw2_core.c
|
|
|
2003 A /branches/prog/bwa/kseq.h
|
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|
2004 D /branches/prog/bwa/seq.c
|
|
|
2005 D /branches/prog/bwa/seq.h
|
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|
2006 M /branches/prog/bwa/simple_dp.c
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|
|
2007 M /branches/prog/bwa/utils.c
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|
|
2008 M /branches/prog/bwa/utils.h
|
|
|
2009
|
|
|
2010 replace seq.* with kseq.h
|
|
|
2011
|
|
|
2012 ------------------------------------------------------------------------
|
|
|
2013 r610 | lh3 | 2008-10-27 13:00:04 -0400 (Mon, 27 Oct 2008) | 3 lines
|
|
|
2014 Changed paths:
|
|
|
2015 M /branches/prog/bwa/bwtsw2.h
|
|
|
2016 M /branches/prog/bwa/bwtsw2_aux.c
|
|
|
2017 M /branches/prog/bwa/bwtsw2_core.c
|
|
|
2018 M /branches/prog/bwa/main.c
|
|
|
2019
|
|
|
2020 * bwa-0.2.0-13
|
|
|
2021 * make bwtsw2 output sub-optimal hits. not completed
|
|
|
2022
|
|
|
2023 ------------------------------------------------------------------------
|
|
|
2024 r609 | lh3 | 2008-10-24 16:52:00 -0400 (Fri, 24 Oct 2008) | 2 lines
|
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|
2025 Changed paths:
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|
2026 M /branches/prog/bwa/kvec.h
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|
2027
|
|
|
2028 little...
|
|
|
2029
|
|
|
2030 ------------------------------------------------------------------------
|
|
|
2031 r532 | lh3 | 2008-09-19 05:28:45 -0400 (Fri, 19 Sep 2008) | 2 lines
|
|
|
2032 Changed paths:
|
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|
2033 M /branches/prog/bwa/bwtsw2_core.c
|
|
|
2034 M /branches/prog/bwa/khash.h
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|
|
2035
|
|
|
2036 improve interface of khash
|
|
|
2037
|
|
|
2038 ------------------------------------------------------------------------
|
|
|
2039 r531 | lh3 | 2008-09-18 06:52:59 -0400 (Thu, 18 Sep 2008) | 2 lines
|
|
|
2040 Changed paths:
|
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|
2041 M /branches/prog/bwa/bwtsw2_core.c
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|
|
2042
|
|
|
2043 improve minor things, which make bwtsw2 slower, but should miss less true hits
|
|
|
2044
|
|
|
2045 ------------------------------------------------------------------------
|
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|
2046 r530 | lh3 | 2008-09-17 18:19:26 -0400 (Wed, 17 Sep 2008) | 3 lines
|
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2047 Changed paths:
|
|
|
2048 M /branches/prog/bwa/bwtsw2_core.c
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|
|
2049
|
|
|
2050 * fixed a bug in calculating ->D
|
|
|
2051 * enforce band-width checking
|
|
|
2052
|
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|
2053 ------------------------------------------------------------------------
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|
2054 r529 | lh3 | 2008-09-17 18:06:49 -0400 (Wed, 17 Sep 2008) | 2 lines
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2055 Changed paths:
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|
2056 M /branches/prog/bwa/bwtsw2_core.c
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|
|
2057
|
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|
2058 delete a line of code that is never visited
|
|
|
2059
|
|
|
2060 ------------------------------------------------------------------------
|
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|
2061 r528 | lh3 | 2008-09-17 17:58:51 -0400 (Wed, 17 Sep 2008) | 2 lines
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2062 Changed paths:
|
|
|
2063 M /branches/prog/bwa/bwtsw2_core.c
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|
2064
|
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|
2065 a bit code clean up
|
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|
2066
|
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|
2067 ------------------------------------------------------------------------
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|
2068 r527 | lh3 | 2008-09-17 10:55:45 -0400 (Wed, 17 Sep 2008) | 3 lines
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2069 Changed paths:
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|
2070 M /branches/prog/bwa/bwtsw2_core.c
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|
2071 M /branches/prog/bwa/bwtsw2_main.c
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|
2072 M /branches/prog/bwa/main.c
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|
2073
|
|
|
2074 * bwa-0.2.0-12
|
|
|
2075 * max-depth can be set, although it does not help the speed at all
|
|
|
2076
|
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|
2077 ------------------------------------------------------------------------
|
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|
2078 r526 | lh3 | 2008-09-16 17:59:36 -0400 (Tue, 16 Sep 2008) | 2 lines
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2079 Changed paths:
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|
2080 M /branches/prog/bwa/bwtsw2_core.c
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|
2081
|
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|
2082 cut_tail after remove duplicate
|
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2083
|
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|
2084 ------------------------------------------------------------------------
|
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|
2085 r525 | lh3 | 2008-09-16 17:56:11 -0400 (Tue, 16 Sep 2008) | 3 lines
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2086 Changed paths:
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|
2087 M /branches/prog/bwa/bwtsw2.h
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|
2088 M /branches/prog/bwa/bwtsw2_aux.c
|
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|
2089 M /branches/prog/bwa/bwtsw2_core.c
|
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|
2090 M /branches/prog/bwa/bwtsw2_main.c
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|
2091 M /branches/prog/bwa/khash.h
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|
|
2092 M /branches/prog/bwa/main.c
|
|
|
2093
|
|
|
2094 * bwa-0.2.0-11
|
|
|
2095 * improved cut_tail()
|
|
|
2096
|
|
|
2097 ------------------------------------------------------------------------
|
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|
2098 r524 | lh3 | 2008-09-15 16:53:22 -0400 (Mon, 15 Sep 2008) | 3 lines
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2099 Changed paths:
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|
2100 M /branches/prog/bwa/bwtsw2_aux.c
|
|
|
2101 M /branches/prog/bwa/bwtsw2_core.c
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|
2102 M /branches/prog/bwa/bwtsw2_main.c
|
|
|
2103 M /branches/prog/bwa/main.c
|
|
|
2104
|
|
|
2105 * bwa-0.2.0-10
|
|
|
2106 * fixed a bug in cut_tail()
|
|
|
2107
|
|
|
2108 ------------------------------------------------------------------------
|
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|
2109 r518 | lh3 | 2008-09-15 04:35:59 -0400 (Mon, 15 Sep 2008) | 2 lines
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|
2110 Changed paths:
|
|
|
2111 M /branches/prog/bwa/bwtsw2_core.c
|
|
|
2112
|
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|
2113 a bit code clean up
|
|
|
2114
|
|
|
2115 ------------------------------------------------------------------------
|
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|
2116 r517 | lh3 | 2008-09-14 18:18:11 -0400 (Sun, 14 Sep 2008) | 2 lines
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2117 Changed paths:
|
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|
2118 M /branches/prog/bwa/bwtsw2_core.c
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|
2119
|
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|
2120 improve speed (<1%)
|
|
|
2121
|
|
|
2122 ------------------------------------------------------------------------
|
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|
2123 r516 | lh3 | 2008-09-14 18:08:55 -0400 (Sun, 14 Sep 2008) | 3 lines
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2124 Changed paths:
|
|
|
2125 M /branches/prog/bwa/bwtsw2_core.c
|
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|
2126
|
|
|
2127 * fixed two potential bugs, although I have not seen their effects
|
|
|
2128 * improve speed a bit (<2%)
|
|
|
2129
|
|
|
2130 ------------------------------------------------------------------------
|
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|
2131 r515 | lh3 | 2008-09-14 17:26:49 -0400 (Sun, 14 Sep 2008) | 2 lines
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2132 Changed paths:
|
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|
2133 M /branches/prog/bwa/bwtsw2_core.c
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|
|
2134 M /branches/prog/bwa/bwtsw2_main.c
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|
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2135
|
|
|
2136 nothing, really
|
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2137
|
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|
2138 ------------------------------------------------------------------------
|
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2139 r514 | lh3 | 2008-09-14 17:10:13 -0400 (Sun, 14 Sep 2008) | 2 lines
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2140 Changed paths:
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|
2141 M /branches/prog/bwa/bwtsw2_core.c
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2142
|
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|
2143 disable X-drop, which has to be reimplemented in the current algorithm
|
|
|
2144
|
|
|
2145 ------------------------------------------------------------------------
|
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|
2146 r513 | lh3 | 2008-09-14 16:49:42 -0400 (Sun, 14 Sep 2008) | 4 lines
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2147 Changed paths:
|
|
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2148 M /branches/prog/bwa/bwt_lite.c
|
|
|
2149 M /branches/prog/bwa/bwt_lite.h
|
|
|
2150 M /branches/prog/bwa/bwtsw2_core.c
|
|
|
2151 M /branches/prog/bwa/bwtsw2_main.c
|
|
|
2152
|
|
|
2153 * temporarily disable cut_tail()
|
|
|
2154 * calculate SA in bwt_lite.c
|
|
|
2155 * fixed a bug in reversing the sequence
|
|
|
2156
|
|
|
2157 ------------------------------------------------------------------------
|
|
|
2158 r512 | lh3 | 2008-09-13 17:35:40 -0400 (Sat, 13 Sep 2008) | 2 lines
|
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2159 Changed paths:
|
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|
2160 M /branches/prog/bwa/bwtsw2.h
|
|
|
2161 M /branches/prog/bwa/bwtsw2_aux.c
|
|
|
2162 M /branches/prog/bwa/bwtsw2_core.c
|
|
|
2163 M /branches/prog/bwa/bwtsw2_main.c
|
|
|
2164 A /branches/prog/bwa/ksort.h
|
|
|
2165
|
|
|
2166 n-best method
|
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|
2167
|
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|
2168 ------------------------------------------------------------------------
|
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|
2169 r507 | lh3 | 2008-09-13 09:06:54 -0400 (Sat, 13 Sep 2008) | 2 lines
|
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2170 Changed paths:
|
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2171 M /branches/prog/bwa/Makefile
|
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2172 M /branches/prog/bwa/bwtsw2_core.c
|
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|
2173
|
|
|
2174 give correct result again
|
|
|
2175
|
|
|
2176 ------------------------------------------------------------------------
|
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|
2177 r506 | lh3 | 2008-09-13 08:12:07 -0400 (Sat, 13 Sep 2008) | 2 lines
|
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2178 Changed paths:
|
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2179 M /branches/prog/bwa/bwtsw2_core.c
|
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|
2180
|
|
|
2181 I think I know the reason. It needs more work...
|
|
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2182
|
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2183 ------------------------------------------------------------------------
|
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2184 r505 | lh3 | 2008-09-13 06:20:43 -0400 (Sat, 13 Sep 2008) | 2 lines
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2185 Changed paths:
|
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2186 M /branches/prog/bwa/Makefile
|
|
|
2187 M /branches/prog/bwa/bwtsw2_core.c
|
|
|
2188
|
|
|
2189 fixed another bug, but still have
|
|
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2190
|
|
|
2191 ------------------------------------------------------------------------
|
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|
2192 r504 | lh3 | 2008-09-12 18:13:37 -0400 (Fri, 12 Sep 2008) | 2 lines
|
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|
2193 Changed paths:
|
|
|
2194 M /branches/prog/bwa/bwtsw2_core.c
|
|
|
2195
|
|
|
2196 fixed another bug
|
|
|
2197
|
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|
2198 ------------------------------------------------------------------------
|
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2199 r503 | lh3 | 2008-09-12 17:15:56 -0400 (Fri, 12 Sep 2008) | 3 lines
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2200 Changed paths:
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2201 M /branches/prog/bwa/bwtsw2_core.c
|
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|
2202 M /branches/prog/bwa/khash.h
|
|
|
2203
|
|
|
2204 * do not segfault, but the result is WRONG!
|
|
|
2205 * prepare to remove bsw2_connectivity_check()
|
|
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2206
|
|
|
2207 ------------------------------------------------------------------------
|
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|
2208 r502 | lh3 | 2008-09-12 15:52:41 -0400 (Fri, 12 Sep 2008) | 2 lines
|
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2209 Changed paths:
|
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|
2210 M /branches/prog/bwa/bwtsw2_core.c
|
|
|
2211 M /branches/prog/bwa/kvec.h
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2212
|
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|
2213 more revisions
|
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2214
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|
2215 ------------------------------------------------------------------------
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|
2216 r501 | lh3 | 2008-09-11 18:06:15 -0400 (Thu, 11 Sep 2008) | 2 lines
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2217 Changed paths:
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2218 M /branches/prog/bwa/bwtsw2_core.c
|
|
|
2219
|
|
|
2220 further simply codes with kvec.h
|
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2221
|
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|
2222 ------------------------------------------------------------------------
|
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|
2223 r500 | lh3 | 2008-09-11 17:42:15 -0400 (Thu, 11 Sep 2008) | 2 lines
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2224 Changed paths:
|
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|
2225 M /branches/prog/bwa/bwtsw2_core.c
|
|
|
2226
|
|
|
2227 part of revisions... have not finished
|
|
|
2228
|
|
|
2229 ------------------------------------------------------------------------
|
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|
2230 r499 | lh3 | 2008-09-11 17:24:15 -0400 (Thu, 11 Sep 2008) | 2 lines
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2231 Changed paths:
|
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2232 M /branches/prog/bwa/bwtsw2.h
|
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|
2233 M /branches/prog/bwa/bwtsw2_core.c
|
|
|
2234 M /branches/prog/bwa/bwtsw2_main.c
|
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|
2235 M /branches/prog/bwa/khash.h
|
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|
2236 A /branches/prog/bwa/kvec.h
|
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|
2237
|
|
|
2238 prepare for abrupt change
|
|
|
2239
|
|
|
2240 ------------------------------------------------------------------------
|
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|
2241 r496 | lh3 | 2008-09-11 10:34:38 -0400 (Thu, 11 Sep 2008) | 2 lines
|
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2242 Changed paths:
|
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|
2243 M /branches/prog/bwa/bwtsw2_core.c
|
|
|
2244
|
|
|
2245 fixed a bug; now "bwtsw2 -d" is useless
|
|
|
2246
|
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|
2247 ------------------------------------------------------------------------
|
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|
2248 r495 | lh3 | 2008-09-11 09:22:03 -0400 (Thu, 11 Sep 2008) | 2 lines
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2249 Changed paths:
|
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|
2250 M /branches/prog/bwa/bwtsw2_core.c
|
|
|
2251 M /branches/prog/bwa/simple_dp.c
|
|
|
2252 M /branches/prog/bwa/stdaln.c
|
|
|
2253 M /branches/prog/bwa/stdaln.h
|
|
|
2254
|
|
|
2255 improve speed a little bit
|
|
|
2256
|
|
|
2257 ------------------------------------------------------------------------
|
|
|
2258 r494 | lh3 | 2008-09-11 08:28:08 -0400 (Thu, 11 Sep 2008) | 2 lines
|
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|
2259 Changed paths:
|
|
|
2260 M /branches/prog/bwa/bwtsw2_core.c
|
|
|
2261
|
|
|
2262 remove debug codes
|
|
|
2263
|
|
|
2264 ------------------------------------------------------------------------
|
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|
2265 r493 | lh3 | 2008-09-11 07:49:53 -0400 (Thu, 11 Sep 2008) | 3 lines
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2266 Changed paths:
|
|
|
2267 M /branches/prog/bwa/bwtsw2_core.c
|
|
|
2268
|
|
|
2269 * improve the speed a little bit (<5%)
|
|
|
2270 * prepare to remove BSW_DEBUG
|
|
|
2271
|
|
|
2272 ------------------------------------------------------------------------
|
|
|
2273 r492 | lh3 | 2008-09-11 06:15:56 -0400 (Thu, 11 Sep 2008) | 4 lines
|
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|
2274 Changed paths:
|
|
|
2275 M /branches/prog/bwa/bwtsw2.h
|
|
|
2276 M /branches/prog/bwa/bwtsw2_aux.c
|
|
|
2277 M /branches/prog/bwa/bwtsw2_core.c
|
|
|
2278 M /branches/prog/bwa/bwtsw2_main.c
|
|
|
2279 M /branches/prog/bwa/main.c
|
|
|
2280
|
|
|
2281 * bwa-0.2.0-9
|
|
|
2282 * support reverse strand
|
|
|
2283 * fixed a bug that causes missing hits
|
|
|
2284
|
|
|
2285 ------------------------------------------------------------------------
|
|
|
2286 r491 | lh3 | 2008-09-11 05:46:16 -0400 (Thu, 11 Sep 2008) | 3 lines
|
|
|
2287 Changed paths:
|
|
|
2288 M /branches/prog/bwa/bwtsw2_core.c
|
|
|
2289 M /branches/prog/bwa/main.c
|
|
|
2290
|
|
|
2291 * bwa-0.2.0-8
|
|
|
2292 * better progress report
|
|
|
2293
|
|
|
2294 ------------------------------------------------------------------------
|
|
|
2295 r490 | lh3 | 2008-09-10 17:04:49 -0400 (Wed, 10 Sep 2008) | 4 lines
|
|
|
2296 Changed paths:
|
|
|
2297 M /branches/prog/bwa/bwtsw2.h
|
|
|
2298 M /branches/prog/bwa/bwtsw2_aux.c
|
|
|
2299 M /branches/prog/bwa/bwtsw2_core.c
|
|
|
2300 M /branches/prog/bwa/bwtsw2_main.c
|
|
|
2301 M /branches/prog/bwa/main.c
|
|
|
2302
|
|
|
2303 * bwa-0.2.0-7
|
|
|
2304 * avoid some missing hits
|
|
|
2305 * add maximum depth
|
|
|
2306
|
|
|
2307 ------------------------------------------------------------------------
|
|
|
2308 r489 | lh3 | 2008-09-10 11:51:13 -0400 (Wed, 10 Sep 2008) | 4 lines
|
|
|
2309 Changed paths:
|
|
|
2310 M /branches/prog/bwa/bwtsw2_core.c
|
|
|
2311 M /branches/prog/bwa/main.c
|
|
|
2312
|
|
|
2313 * bwa-0.2.0-6
|
|
|
2314 * bwtsw2 works although on the forward strand only for now
|
|
|
2315 * better progress information
|
|
|
2316
|
|
|
2317 ------------------------------------------------------------------------
|
|
|
2318 r488 | lh3 | 2008-09-10 10:21:53 -0400 (Wed, 10 Sep 2008) | 3 lines
|
|
|
2319 Changed paths:
|
|
|
2320 M /branches/prog/bwa/bwtsw2_core.c
|
|
|
2321
|
|
|
2322 * implement memory pool
|
|
|
2323 * avoid some rehashing
|
|
|
2324
|
|
|
2325 ------------------------------------------------------------------------
|
|
|
2326 r487 | lh3 | 2008-09-10 09:23:38 -0400 (Wed, 10 Sep 2008) | 3 lines
|
|
|
2327 Changed paths:
|
|
|
2328 M /branches/prog/bwa/bwtsw2.h
|
|
|
2329 M /branches/prog/bwa/bwtsw2_aux.c
|
|
|
2330 M /branches/prog/bwa/bwtsw2_main.c
|
|
|
2331
|
|
|
2332 * fixed a memory leak
|
|
|
2333 * prepare to implement mempool
|
|
|
2334
|
|
|
2335 ------------------------------------------------------------------------
|
|
|
2336 r486 | lh3 | 2008-09-10 09:10:09 -0400 (Wed, 10 Sep 2008) | 4 lines
|
|
|
2337 Changed paths:
|
|
|
2338 M /branches/prog/bwa/bwtsw2.h
|
|
|
2339 M /branches/prog/bwa/bwtsw2_aux.c
|
|
|
2340 M /branches/prog/bwa/bwtsw2_core.c
|
|
|
2341 M /branches/prog/bwa/bwtsw2_main.c
|
|
|
2342 M /branches/prog/bwa/khash.h
|
|
|
2343
|
|
|
2344 * add X-dropoff
|
|
|
2345 * remove duplicated results
|
|
|
2346 * switch to simple stack
|
|
|
2347
|
|
|
2348 ------------------------------------------------------------------------
|
|
|
2349 r485 | lh3 | 2008-09-10 06:31:20 -0400 (Wed, 10 Sep 2008) | 3 lines
|
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|
2350 Changed paths:
|
|
|
2351 M /branches/prog/bwa/bwtsw2.h
|
|
|
2352 M /branches/prog/bwa/bwtsw2_aux.c
|
|
|
2353 M /branches/prog/bwa/bwtsw2_core.c
|
|
|
2354 M /branches/prog/bwa/bwtsw2_main.c
|
|
|
2355
|
|
|
2356 * check whether t-node has been visited
|
|
|
2357 * prepare to remove two-level stack
|
|
|
2358
|
|
|
2359 ------------------------------------------------------------------------
|
|
|
2360 r484 | lh3 | 2008-09-10 05:00:57 -0400 (Wed, 10 Sep 2008) | 2 lines
|
|
|
2361 Changed paths:
|
|
|
2362 A /branches/prog/bwa/khash.h
|
|
|
2363
|
|
|
2364 khash library
|
|
|
2365
|
|
|
2366 ------------------------------------------------------------------------
|
|
|
2367 r483 | lh3 | 2008-09-10 04:22:53 -0400 (Wed, 10 Sep 2008) | 2 lines
|
|
|
2368 Changed paths:
|
|
|
2369 M /branches/prog/bwa/bwtsw2_core.c
|
|
|
2370
|
|
|
2371 add inline
|
|
|
2372
|
|
|
2373 ------------------------------------------------------------------------
|
|
|
2374 r482 | lh3 | 2008-09-09 16:34:57 -0400 (Tue, 09 Sep 2008) | 2 lines
|
|
|
2375 Changed paths:
|
|
|
2376 M /branches/prog/bwa/Makefile
|
|
|
2377 M /branches/prog/bwa/bwtsw2_aux.c
|
|
|
2378 M /branches/prog/bwa/bwtsw2_core.c
|
|
|
2379
|
|
|
2380 improve speed
|
|
|
2381
|
|
|
2382 ------------------------------------------------------------------------
|
|
|
2383 r481 | lh3 | 2008-09-09 13:13:00 -0400 (Tue, 09 Sep 2008) | 4 lines
|
|
|
2384 Changed paths:
|
|
|
2385 M /branches/prog/bwa/bwtsw2_core.c
|
|
|
2386
|
|
|
2387 Use a 128bit hash table to keep all (tk,tl,qk,ql). This is slow. Just
|
|
|
2388 keep a copy in case I may need this in future.
|
|
|
2389
|
|
|
2390
|
|
|
2391 ------------------------------------------------------------------------
|
|
|
2392 r480 | lh3 | 2008-09-09 12:53:32 -0400 (Tue, 09 Sep 2008) | 2 lines
|
|
|
2393 Changed paths:
|
|
|
2394 M /branches/prog/bwa/bwtsw2.h
|
|
|
2395 M /branches/prog/bwa/bwtsw2_core.c
|
|
|
2396
|
|
|
2397 * no principal modification
|
|
|
2398
|
|
|
2399 ------------------------------------------------------------------------
|
|
|
2400 r479 | lh3 | 2008-09-09 11:01:45 -0400 (Tue, 09 Sep 2008) | 4 lines
|
|
|
2401 Changed paths:
|
|
|
2402 M /branches/prog/bwa/Makefile
|
|
|
2403 M /branches/prog/bwa/bwtsw2_core.c
|
|
|
2404
|
|
|
2405 * fixed a bug which may cause duplicated matching
|
|
|
2406 * accelerate the speed a bit, although using hash in avoiding duplications
|
|
|
2407 slows the speed down in the end
|
|
|
2408
|
|
|
2409 ------------------------------------------------------------------------
|
|
|
2410 r474 | lh3 | 2008-09-03 17:22:57 -0400 (Wed, 03 Sep 2008) | 4 lines
|
|
|
2411 Changed paths:
|
|
|
2412 M /branches/prog/bwa/Makefile
|
|
|
2413 M /branches/prog/bwa/bwtsw2.h
|
|
|
2414 M /branches/prog/bwa/bwtsw2_aux.c
|
|
|
2415 M /branches/prog/bwa/bwtsw2_core.c
|
|
|
2416 M /branches/prog/bwa/bwtsw2_main.c
|
|
|
2417 M /branches/prog/bwa/main.c
|
|
|
2418
|
|
|
2419 * bwa-0.2.0-5
|
|
|
2420 * indel seems to work on toy example
|
|
|
2421 * add band
|
|
|
2422
|
|
|
2423 ------------------------------------------------------------------------
|
|
|
2424 r469 | lh3 | 2008-09-01 09:18:45 -0400 (Mon, 01 Sep 2008) | 3 lines
|
|
|
2425 Changed paths:
|
|
|
2426 M /branches/prog/bwa/ChangeLog
|
|
|
2427 M /branches/prog/bwa/Makefile
|
|
|
2428 M /branches/prog/bwa/bwt_lite.c
|
|
|
2429 M /branches/prog/bwa/bwt_lite.h
|
|
|
2430 M /branches/prog/bwa/bwtgap.c
|
|
|
2431 M /branches/prog/bwa/bwtsw2.h
|
|
|
2432 A /branches/prog/bwa/bwtsw2_aux.c
|
|
|
2433 M /branches/prog/bwa/bwtsw2_core.c
|
|
|
2434 M /branches/prog/bwa/bwtsw2_main.c
|
|
|
2435 M /branches/prog/bwa/is.c
|
|
|
2436 M /branches/prog/bwa/main.c
|
|
|
2437 M /branches/prog/bwa/main.h
|
|
|
2438 M /branches/prog/bwa/simple_dp.c
|
|
|
2439
|
|
|
2440 * bwa-0.2.0-4
|
|
|
2441 * updated bwtsw2, which seems to work properly on toy examples
|
|
|
2442
|
|
|
2443 ------------------------------------------------------------------------
|
|
|
2444 r447 | lh3 | 2008-08-27 10:05:09 -0400 (Wed, 27 Aug 2008) | 3 lines
|
|
|
2445 Changed paths:
|
|
|
2446 M /branches/prog/bwa/bwt2fmv.c
|
|
|
2447 M /branches/prog/bwa/bwtaln.c
|
|
|
2448 M /branches/prog/bwa/bwtaln.h
|
|
|
2449 M /branches/prog/bwa/bwtgap.c
|
|
|
2450 M /branches/prog/bwa/main.c
|
|
|
2451
|
|
|
2452 * bwa-0.2.0-3
|
|
|
2453 * tune for longer gaps, but it does not really work with kilo-bp gaps...
|
|
|
2454
|
|
|
2455 ------------------------------------------------------------------------
|
|
|
2456 r446 | lh3 | 2008-08-26 13:30:41 -0400 (Tue, 26 Aug 2008) | 3 lines
|
|
|
2457 Changed paths:
|
|
|
2458 M /branches/prog/bwa/bwt2fmv.c
|
|
|
2459 M /branches/prog/bwa/bwtaln.c
|
|
|
2460 M /branches/prog/bwa/bwtaln.h
|
|
|
2461 M /branches/prog/bwa/bwtgap.c
|
|
|
2462 M /branches/prog/bwa/main.c
|
|
|
2463
|
|
|
2464 * bwa-0.2.0-2
|
|
|
2465 * changed the way to extend long deletions. Now use max_del_occ.
|
|
|
2466
|
|
|
2467 ------------------------------------------------------------------------
|
|
|
2468 r445 | lh3 | 2008-08-26 13:05:58 -0400 (Tue, 26 Aug 2008) | 2 lines
|
|
|
2469 Changed paths:
|
|
|
2470 M /branches/prog/bwa/bwt_lite.c
|
|
|
2471 M /branches/prog/bwa/bwt_lite.h
|
|
|
2472
|
|
|
2473 updated from bwtsw2_lite
|
|
|
2474
|
|
|
2475 ------------------------------------------------------------------------
|
|
|
2476 r436 | lh3 | 2008-08-23 12:28:44 -0400 (Sat, 23 Aug 2008) | 4 lines
|
|
|
2477 Changed paths:
|
|
|
2478 M /branches/prog/bwa/Makefile
|
|
|
2479 M /branches/prog/bwa/bwt.h
|
|
|
2480 A /branches/prog/bwa/bwt_lite.c
|
|
|
2481 A /branches/prog/bwa/bwt_lite.h
|
|
|
2482 A /branches/prog/bwa/bwtsw2.h
|
|
|
2483 A /branches/prog/bwa/bwtsw2_core.c
|
|
|
2484 A /branches/prog/bwa/bwtsw2_main.c
|
|
|
2485 M /branches/prog/bwa/main.c
|
|
|
2486
|
|
|
2487 * bwa-0.2.0-1
|
|
|
2488 * add bwt_lite: a light-weighted version of bwt (NOT TESTED!)
|
|
|
2489 * add core codes for bwtsw2: NOT TESTED!!!
|
|
|
2490
|
|
|
2491 ------------------------------------------------------------------------
|
|
|
2492 r427 | lh3 | 2008-08-15 05:38:12 -0400 (Fri, 15 Aug 2008) | 2 lines
|
|
|
2493 Changed paths:
|
|
|
2494 M /branches/prog/bwa/ChangeLog
|
|
|
2495 M /branches/prog/bwa/NEWS
|
|
|
2496 M /branches/prog/bwa/bwa.1
|
|
|
2497 M /branches/prog/bwa/bwtaln.c
|
|
|
2498 M /branches/prog/bwa/main.c
|
|
|
2499
|
|
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2500 Release bwa-0.2.0
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2501
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2502 ------------------------------------------------------------------------
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2503 r426 | lh3 | 2008-08-14 11:26:19 -0400 (Thu, 14 Aug 2008) | 4 lines
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2504 Changed paths:
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2505 M /branches/prog/bwa/bwt2fmv.c
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2506 M /branches/prog/bwa/bwtaln.c
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2507 M /branches/prog/bwa/bwtaln.h
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2508 M /branches/prog/bwa/main.c
|
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2509
|
|
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2510 * bwa-0.1.6-7
|
|
|
2511 * change default seed length to 31
|
|
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2512 * add incomplete support to color sequences (not tested yet!)
|
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2513
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2514 ------------------------------------------------------------------------
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2515 r425 | lh3 | 2008-08-14 06:23:11 -0400 (Thu, 14 Aug 2008) | 3 lines
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2516 Changed paths:
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2517 M /branches/prog/bwa/bwtaln.c
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2518 M /branches/prog/bwa/main.c
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2519
|
|
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2520 * bwa-0.1.6-6
|
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|
2521 * change default seed length to 33bp
|
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2522
|
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2523 ------------------------------------------------------------------------
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2524 r424 | lh3 | 2008-08-14 05:55:33 -0400 (Thu, 14 Aug 2008) | 6 lines
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2525 Changed paths:
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2526 M /branches/prog/bwa/bwtaln.c
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2527 M /branches/prog/bwa/bwtgap.c
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2528 M /branches/prog/bwa/main.c
|
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2529
|
|
|
2530 * bwa-0.1.6-5
|
|
|
2531 * fixed a bug that may miss true alignments. this bugs exists in most
|
|
|
2532 early versions.
|
|
|
2533 * fixed a bug that yields wrong coordinates for reads mapped on the forward
|
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2534 strands with gaps.
|
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2535
|
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2536 ------------------------------------------------------------------------
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2537 r423 | lh3 | 2008-08-14 04:07:28 -0400 (Thu, 14 Aug 2008) | 2 lines
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2538 Changed paths:
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2539 D /branches/prog/bwa/Makefile.div
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2540
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2541 useless
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2542
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2543 ------------------------------------------------------------------------
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2544 r422 | lh3 | 2008-08-13 19:21:14 -0400 (Wed, 13 Aug 2008) | 4 lines
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2545 Changed paths:
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2546 M /branches/prog/bwa/bwtaln.c
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2547 M /branches/prog/bwa/main.c
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2548
|
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2549 * bwa-0.1.6-4
|
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|
2550 * fixed one bug
|
|
|
2551 * there is another one...
|
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2552
|
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2553 ------------------------------------------------------------------------
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2554 r421 | lh3 | 2008-08-13 18:23:33 -0400 (Wed, 13 Aug 2008) | 3 lines
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2555 Changed paths:
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2556 M /branches/prog/bwa/bwtaln.c
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2557 M /branches/prog/bwa/bwtaln.h
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2558 M /branches/prog/bwa/bwtgap.c
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2559 M /branches/prog/bwa/bwtgap.h
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2560 M /branches/prog/bwa/bwtindex.c
|
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2561 M /branches/prog/bwa/main.c
|
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2562
|
|
|
2563 * bwa-0.1.6-3
|
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|
2564 * almost there, but not quite right
|
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2565
|
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2566 ------------------------------------------------------------------------
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2567 r419 | lh3 | 2008-08-13 17:27:02 -0400 (Wed, 13 Aug 2008) | 3 lines
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2568 Changed paths:
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2569 M /branches/prog/bwa/bwtaln.c
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2570 M /branches/prog/bwa/bwtaln.h
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2571 M /branches/prog/bwa/bwtgap.c
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2572 M /branches/prog/bwa/bwtgap.h
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2573 M /branches/prog/bwa/main.c
|
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2574
|
|
|
2575 * improve the seeding method
|
|
|
2576 * prepare to load two BWTs into memory. A BIG change!
|
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2577
|
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2578 ------------------------------------------------------------------------
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2579 r418 | lh3 | 2008-08-13 10:56:54 -0400 (Wed, 13 Aug 2008) | 3 lines
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2580 Changed paths:
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2581 M /branches/prog/bwa/bwt2fmv.c
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2582 M /branches/prog/bwa/bwtaln.c
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2583 M /branches/prog/bwa/bwtaln.h
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2584 M /branches/prog/bwa/bwtgap.c
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2585 M /branches/prog/bwa/bwtgap.h
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2586 M /branches/prog/bwa/main.c
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2587
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|
2588 * added seeding
|
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|
2589 * unfinished yet
|
|
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2590
|
|
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2591 ------------------------------------------------------------------------
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2592 r413 | lh3 | 2008-08-08 11:48:35 -0400 (Fri, 08 Aug 2008) | 2 lines
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2593 Changed paths:
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2594 M /branches/prog/bwa/ChangeLog
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2595 M /branches/prog/bwa/NEWS
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2596 M /branches/prog/bwa/main.c
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2597
|
|
|
2598 Release bwa-0.1.6
|
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2599
|
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2600 ------------------------------------------------------------------------
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2601 r410 | lh3 | 2008-08-06 15:48:22 -0400 (Wed, 06 Aug 2008) | 2 lines
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2602 Changed paths:
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2603 M /branches/prog/bwa/simple_dp.c
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2604
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2605 sw: output alignment score
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2606
|
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2607 ------------------------------------------------------------------------
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2608 r407 | lh3 | 2008-08-04 10:01:20 -0400 (Mon, 04 Aug 2008) | 4 lines
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2609 Changed paths:
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2610 M /branches/prog/bwa/Makefile
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2611 M /branches/prog/bwa/main.c
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2612 M /branches/prog/bwa/main.h
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2613 A /branches/prog/bwa/simple_dp.c
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2614 M /branches/prog/bwa/stdaln.c
|
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2615 M /branches/prog/bwa/stdaln.h
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|
2616
|
|
|
2617 * bwa-0.1.5-3
|
|
|
2618 * added a simple interface to SW/NW alignment
|
|
|
2619 * stdaln-0.9.8 (see header for more details)
|
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2620
|
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|
2621 ------------------------------------------------------------------------
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2622 r406 | lh3 | 2008-08-01 19:21:59 -0400 (Fri, 01 Aug 2008) | 3 lines
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2623 Changed paths:
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2624 M /branches/prog/bwa/Makefile
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2625 M /branches/prog/bwa/bwtaln.c
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2626 M /branches/prog/bwa/bwtaln.h
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2627 M /branches/prog/bwa/main.c
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2628 A /branches/prog/bwa/stdaln.c
|
|
|
2629 A /branches/prog/bwa/stdaln.h
|
|
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2630
|
|
|
2631 * bwa-0.1.5-2
|
|
|
2632 * give accurate gap positions
|
|
|
2633
|
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|
2634 ------------------------------------------------------------------------
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2635 r405 | lh3 | 2008-08-01 19:06:19 -0400 (Fri, 01 Aug 2008) | 2 lines
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2636 Changed paths:
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2637 M /branches/prog/bwa/Makefile
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2638 M /branches/prog/bwa/bwtaln.c
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2639 M /branches/prog/bwa/bwtaln.h
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2640
|
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|
2641 unfinished, but I am tired...
|
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2642
|
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2643 ------------------------------------------------------------------------
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2644 r401 | lh3 | 2008-07-30 05:59:24 -0400 (Wed, 30 Jul 2008) | 4 lines
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2645 Changed paths:
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2646 M /branches/prog/bwa/bntseq.c
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2647 M /branches/prog/bwa/main.c
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2648
|
|
|
2649 * bwa-0.1.5-1
|
|
|
2650 * fixed a potential bug which may produce an alignment in N regions,
|
|
|
2651 although extremely rare.
|
|
|
2652
|
|
|
2653 ------------------------------------------------------------------------
|
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2654 r399 | lh3 | 2008-07-27 11:41:52 -0400 (Sun, 27 Jul 2008) | 2 lines
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2655 Changed paths:
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2656 M /branches/prog/bwa/ChangeLog
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2657 M /branches/prog/bwa/NEWS
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2658 M /branches/prog/bwa/main.c
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2659
|
|
|
2660 Release bwa-0.1.5
|
|
|
2661
|
|
|
2662 ------------------------------------------------------------------------
|
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|
2663 r398 | lh3 | 2008-07-25 12:14:47 -0400 (Fri, 25 Jul 2008) | 2 lines
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2664 Changed paths:
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2665 M /branches/prog/bwa/bwa.1
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2666
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|
2667 update documentation
|
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|
2668
|
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|
2669 ------------------------------------------------------------------------
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2670 r397 | lh3 | 2008-07-25 09:58:56 -0400 (Fri, 25 Jul 2008) | 2 lines
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2671 Changed paths:
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2672 M /branches/prog/bwa/bwt2fmv.c
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2673 M /branches/prog/bwa/bwtaln.c
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2674 M /branches/prog/bwa/main.c
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2675
|
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|
2676 *
|
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|
2677
|
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|
2678 ------------------------------------------------------------------------
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2679 r396 | lh3 | 2008-07-25 06:42:01 -0400 (Fri, 25 Jul 2008) | 3 lines
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2680 Changed paths:
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2681 M /branches/prog/bwa/bwtaln.c
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2682 M /branches/prog/bwa/main.c
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2683
|
|
|
2684 * bwa-0.1.4-4
|
|
|
2685 * add timer for debugging
|
|
|
2686
|
|
|
2687 ------------------------------------------------------------------------
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|
2688 r395 | lh3 | 2008-07-24 05:46:21 -0400 (Thu, 24 Jul 2008) | 4 lines
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2689 Changed paths:
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2690 M /branches/prog/bwa/bwtgap.c
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2691 M /branches/prog/bwa/main.c
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2692
|
|
|
2693 * bwa-0.1.4-3
|
|
|
2694 * fixed a bug in the previous code
|
|
|
2695 * this version gives identical result to bwa-0.1.4, just 10% faster
|
|
|
2696
|
|
|
2697 ------------------------------------------------------------------------
|
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|
2698 r394 | lh3 | 2008-07-24 05:18:53 -0400 (Thu, 24 Jul 2008) | 4 lines
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2699 Changed paths:
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2700 M /branches/prog/bwa/bwtaln.c
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2701 M /branches/prog/bwa/bwtgap.c
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2702 M /branches/prog/bwa/bwtgap.h
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|
2703 M /branches/prog/bwa/main.c
|
|
|
2704
|
|
|
2705 * bwa-0.1.4-2
|
|
|
2706 * further improve the speed
|
|
|
2707 * The result is slightly different from bwa-0.1.4 now. I need to check...
|
|
|
2708
|
|
|
2709 ------------------------------------------------------------------------
|
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|
2710 r393 | lh3 | 2008-07-23 12:04:16 -0400 (Wed, 23 Jul 2008) | 2 lines
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2711 Changed paths:
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|
2712 M /branches/prog/bwa/bwt.c
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2713
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|
2714 comments only
|
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2715
|
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|
2716 ------------------------------------------------------------------------
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2717 r392 | lh3 | 2008-07-23 10:34:03 -0400 (Wed, 23 Jul 2008) | 2 lines
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2718 Changed paths:
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2719 M /branches/prog/bwa/bwt.c
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2720 M /branches/prog/bwa/main.c
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2721
|
|
|
2722 further improve the speed in Occ functions
|
|
|
2723
|
|
|
2724 ------------------------------------------------------------------------
|
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|
2725 r386 | lh3 | 2008-07-22 10:03:54 -0400 (Tue, 22 Jul 2008) | 2 lines
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2726 Changed paths:
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2727 M /branches/prog/bwa/NEWS
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2728 M /branches/prog/bwa/main.c
|
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2729
|
|
|
2730 Release bwa-0.1.4
|
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2731
|
|
|
2732 ------------------------------------------------------------------------
|
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|
2733 r385 | lh3 | 2008-07-22 09:44:50 -0400 (Tue, 22 Jul 2008) | 2 lines
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2734 Changed paths:
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|
2735 M /branches/prog/bwa/ChangeLog
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|
2736 M /branches/prog/bwa/bwa.1
|
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2737
|
|
|
2738 update documentation and ChangeLog
|
|
|
2739
|
|
|
2740 ------------------------------------------------------------------------
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|
2741 r384 | lh3 | 2008-07-22 08:50:03 -0400 (Tue, 22 Jul 2008) | 4 lines
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2742 Changed paths:
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|
2743 M /branches/prog/bwa/Makefile
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2744 M /branches/prog/bwa/bwt2fmv.c
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|
2745 M /branches/prog/bwa/bwtaln.c
|
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|
2746 M /branches/prog/bwa/bwtaln.h
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|
2747 M /branches/prog/bwa/bwtgap.c
|
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|
2748 M /branches/prog/bwa/main.c
|
|
|
2749
|
|
|
2750 * bwa-0.1.3-2
|
|
|
2751 * fixed the bug in the last modification
|
|
|
2752 * now the alignment should be more clearly defined
|
|
|
2753
|
|
|
2754 ------------------------------------------------------------------------
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|
2755 r383 | lh3 | 2008-07-21 18:32:21 -0400 (Mon, 21 Jul 2008) | 4 lines
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2756 Changed paths:
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|
2757 M /branches/prog/bwa/bwt2fmv.c
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|
|
2758 M /branches/prog/bwa/bwtaln.c
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|
|
2759 M /branches/prog/bwa/bwtgap.c
|
|
|
2760 M /branches/prog/bwa/main.c
|
|
|
2761
|
|
|
2762 * bwa-0.1.3-1
|
|
|
2763 * this is a buggy verion!
|
|
|
2764 * i will fix the bug tomorrow. It is late...
|
|
|
2765
|
|
|
2766 ------------------------------------------------------------------------
|
|
|
2767 r381 | lh3 | 2008-07-21 06:45:32 -0400 (Mon, 21 Jul 2008) | 2 lines
|
|
|
2768 Changed paths:
|
|
|
2769 M /branches/prog/bwa/ChangeLog
|
|
|
2770 M /branches/prog/bwa/NEWS
|
|
|
2771 M /branches/prog/bwa/bwa.1
|
|
|
2772 M /branches/prog/bwa/main.c
|
|
|
2773
|
|
|
2774 Release bwa-0.1.3
|
|
|
2775
|
|
|
2776 ------------------------------------------------------------------------
|
|
|
2777 r380 | lh3 | 2008-07-21 06:07:43 -0400 (Mon, 21 Jul 2008) | 4 lines
|
|
|
2778 Changed paths:
|
|
|
2779 M /branches/prog/bwa/ChangeLog
|
|
|
2780 M /branches/prog/bwa/bwa.1
|
|
|
2781 M /branches/prog/bwa/bwt.c
|
|
|
2782 M /branches/prog/bwa/bwt2fmv.c
|
|
|
2783 M /branches/prog/bwa/main.c
|
|
|
2784
|
|
|
2785 * bwa-0.1.2-3
|
|
|
2786 * improve the speed for gcc on Intel Mac OS X, but not really on icc on Linux
|
|
|
2787 * aln: more command-line options
|
|
|
2788
|
|
|
2789 ------------------------------------------------------------------------
|
|
|
2790 r373 | lh3 | 2008-07-17 09:09:46 -0400 (Thu, 17 Jul 2008) | 4 lines
|
|
|
2791 Changed paths:
|
|
|
2792 M /branches/prog/bwa/bwt.c
|
|
|
2793 M /branches/prog/bwa/bwt.h
|
|
|
2794 M /branches/prog/bwa/bwtio.c
|
|
|
2795 M /branches/prog/bwa/main.c
|
|
|
2796
|
|
|
2797 * bwa-0.1.2-2
|
|
|
2798 * further improve the speed
|
|
|
2799 * this version gives exactly the same result as bwa-0.1.2
|
|
|
2800
|
|
|
2801 ------------------------------------------------------------------------
|
|
|
2802 r372 | lh3 | 2008-07-17 07:51:08 -0400 (Thu, 17 Jul 2008) | 3 lines
|
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|
2803 Changed paths:
|
|
|
2804 M /branches/prog/bwa/bwt.c
|
|
|
2805 M /branches/prog/bwa/main.c
|
|
|
2806
|
|
|
2807 * bwa-0.1.2-1
|
|
|
2808 * speed up by about 5%
|
|
|
2809
|
|
|
2810 ------------------------------------------------------------------------
|
|
|
2811 r370 | lh3 | 2008-07-17 05:12:00 -0400 (Thu, 17 Jul 2008) | 2 lines
|
|
|
2812 Changed paths:
|
|
|
2813 M /branches/prog/bwa/NEWS
|
|
|
2814 M /branches/prog/bwa/bwa.1
|
|
|
2815 M /branches/prog/bwa/main.c
|
|
|
2816
|
|
|
2817 Release bwa-0.1.2
|
|
|
2818
|
|
|
2819 ------------------------------------------------------------------------
|
|
|
2820 r368 | lh3 | 2008-07-16 08:51:25 -0400 (Wed, 16 Jul 2008) | 4 lines
|
|
|
2821 Changed paths:
|
|
|
2822 M /branches/prog/bwa/Makefile
|
|
|
2823 D /branches/prog/bwa/bwt1away.c
|
|
|
2824 M /branches/prog/bwa/bwt2fmv.c
|
|
|
2825 M /branches/prog/bwa/bwtaln.c
|
|
|
2826 M /branches/prog/bwa/bwtaln.h
|
|
|
2827 M /branches/prog/bwa/bwtgap.c
|
|
|
2828 M /branches/prog/bwa/bwtgap.h
|
|
|
2829 D /branches/prog/bwa/bwttop2.c
|
|
|
2830 M /branches/prog/bwa/main.c
|
|
|
2831
|
|
|
2832 * bwa-0.1.1-9
|
|
|
2833 * some code cleanup
|
|
|
2834 * remove 1away and top2
|
|
|
2835
|
|
|
2836 ------------------------------------------------------------------------
|
|
|
2837 r367 | lh3 | 2008-07-16 08:24:34 -0400 (Wed, 16 Jul 2008) | 2 lines
|
|
|
2838 Changed paths:
|
|
|
2839 M /branches/prog/bwa/is.c
|
|
|
2840
|
|
|
2841 Yuta Mori's implementation of IS algorithm.
|
|
|
2842
|
|
|
2843 ------------------------------------------------------------------------
|
|
|
2844 r365 | lh3 | 2008-07-16 06:58:04 -0400 (Wed, 16 Jul 2008) | 6 lines
|
|
|
2845 Changed paths:
|
|
|
2846 M /branches/prog/bwa/bwtaln.c
|
|
|
2847 M /branches/prog/bwa/bwtgap.c
|
|
|
2848 M /branches/prog/bwa/bwtgap.h
|
|
|
2849 M /branches/prog/bwa/main.c
|
|
|
2850
|
|
|
2851 * bwa-0.1.1-8
|
|
|
2852 * improve gapped alignment
|
|
|
2853 * this version will miss more gapped alignments, but the speed is much faster
|
|
|
2854 * prepare to remove top2 and 1away algorithms
|
|
|
2855 * prepare to add SAIS algorithm for bwt construction
|
|
|
2856
|
|
|
2857 ------------------------------------------------------------------------
|
|
|
2858 r358 | lh3 | 2008-06-09 06:03:04 -0400 (Mon, 09 Jun 2008) | 4 lines
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2859 Changed paths:
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2860 M /branches/prog/bwa/bwt2fmv.c
|
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2861 M /branches/prog/bwa/bwtgap.c
|
|
|
2862 M /branches/prog/bwa/main.c
|
|
|
2863
|
|
|
2864 * bwa-0.1.1-7
|
|
|
2865 * change END_SKIP from 3 to 5, but still gaps may be wrongly added
|
|
|
2866 * change default '-g' from 5 to 3
|
|
|
2867
|
|
|
2868 ------------------------------------------------------------------------
|
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|
2869 r357 | lh3 | 2008-06-09 05:18:36 -0400 (Mon, 09 Jun 2008) | 3 lines
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2870 Changed paths:
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2871 M /branches/prog/bwa/bntseq.c
|
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2872 M /branches/prog/bwa/bwt2fmv.c
|
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2873 M /branches/prog/bwa/bwtgap.c
|
|
|
2874 M /branches/prog/bwa/main.c
|
|
|
2875
|
|
|
2876 * bwa-0.1.1-6
|
|
|
2877 * fix a bug in nested stack
|
|
|
2878
|
|
|
2879 ------------------------------------------------------------------------
|
|
|
2880 r356 | lh3 | 2008-06-08 18:43:13 -0400 (Sun, 08 Jun 2008) | 4 lines
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2881 Changed paths:
|
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2882 M /branches/prog/bwa/Makefile
|
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2883 M /branches/prog/bwa/bwtaln.c
|
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|
2884 M /branches/prog/bwa/bwtaln.h
|
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2885 M /branches/prog/bwa/bwtgap.c
|
|
|
2886 A /branches/prog/bwa/bwtgap.h
|
|
|
2887 M /branches/prog/bwa/main.c
|
|
|
2888
|
|
|
2889 * bwa-0.1.1-5
|
|
|
2890 * replace heap with nested stacks
|
|
|
2891 * there are still obvious bugs...
|
|
|
2892
|
|
|
2893 ------------------------------------------------------------------------
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|
2894 r355 | lh3 | 2008-06-08 17:13:44 -0400 (Sun, 08 Jun 2008) | 4 lines
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2895 Changed paths:
|
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2896 M /branches/prog/bwa/bwt2fmv.c
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2897 M /branches/prog/bwa/bwtaln.c
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2898 M /branches/prog/bwa/bwtaln.h
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2899 M /branches/prog/bwa/bwtgap.c
|
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2900 M /branches/prog/bwa/main.c
|
|
|
2901 M /branches/prog/bwa/main.h
|
|
|
2902
|
|
|
2903 * bwa-0.1.1-4
|
|
|
2904 * add interface to affine gap alignment
|
|
|
2905 * there are obvious bugs and I will fix them later
|
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|
2906
|
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2907 ------------------------------------------------------------------------
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2908 r354 | lh3 | 2008-06-08 15:39:05 -0400 (Sun, 08 Jun 2008) | 3 lines
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2909 Changed paths:
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2910 M /branches/prog/bwa/bwtaln.c
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2911 M /branches/prog/bwa/bwtaln.h
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2912 M /branches/prog/bwa/bwtgap.c
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2913 M /branches/prog/bwa/main.c
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2914
|
|
|
2915 * bwa-0.1.1-3
|
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|
2916 * affine gap seems to work, at least partially
|
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2917
|
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2918 ------------------------------------------------------------------------
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2919 r353 | lh3 | 2008-06-08 09:27:18 -0400 (Sun, 08 Jun 2008) | 3 lines
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2920 Changed paths:
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2921 M /branches/prog/bwa/Makefile
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2922 M /branches/prog/bwa/bwt2fmv.c
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2923 M /branches/prog/bwa/bwtaln.c
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2924 M /branches/prog/bwa/bwtaln.h
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2925 A /branches/prog/bwa/bwtgap.c
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2926 M /branches/prog/bwa/bwttop2.c
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2927 M /branches/prog/bwa/main.c
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|
2928
|
|
|
2929 * bwa-0.1.1-2
|
|
|
2930 * initial gapped alignment. not work at the moment
|
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2931
|
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2932 ------------------------------------------------------------------------
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2933 r352 | lh3 | 2008-06-06 04:37:34 -0400 (Fri, 06 Jun 2008) | 3 lines
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2934 Changed paths:
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2935 M /branches/prog/bwa/bwttop2.c
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2936 M /branches/prog/bwa/main.c
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2937
|
|
|
2938 * bwa-0.1.1-1
|
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|
2939 * ungap: remove a useless varible in top2_entry_t
|
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2940
|
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2941 ------------------------------------------------------------------------
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2942 r348 | lh3 | 2008-06-03 09:04:12 -0400 (Tue, 03 Jun 2008) | 2 lines
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2943 Changed paths:
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2944 M /branches/prog/bwa/ChangeLog
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2945 A /branches/prog/bwa/NEWS
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2946 M /branches/prog/bwa/bwa.1
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2947 M /branches/prog/bwa/main.c
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2948
|
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2949 Release bwa-0.1.1
|
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2950
|
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2951 ------------------------------------------------------------------------
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2952 r347 | lh3 | 2008-06-03 05:45:08 -0400 (Tue, 03 Jun 2008) | 2 lines
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2953 Changed paths:
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2954 M /branches/prog/bwa/bwa.1
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2955
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2956 update documentation
|
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2957
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2958 ------------------------------------------------------------------------
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2959 r346 | lh3 | 2008-06-02 18:59:50 -0400 (Mon, 02 Jun 2008) | 5 lines
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2960 Changed paths:
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2961 A /branches/prog/bwa/ChangeLog
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2962 A /branches/prog/bwa/bwa.1
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2963 M /branches/prog/bwa/bwtaln.c
|
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|
2964 M /branches/prog/bwa/main.c
|
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2965
|
|
|
2966 * bwa-0.1.0-11
|
|
|
2967 * improve approximating mapping qualities
|
|
|
2968 * add documentation
|
|
|
2969 * add ChangeLog
|
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2970
|
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2971 ------------------------------------------------------------------------
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2972 r345 | lh3 | 2008-06-02 16:04:39 -0400 (Mon, 02 Jun 2008) | 3 lines
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2973 Changed paths:
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2974 M /branches/prog/bwa/bwtaln.c
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2975 M /branches/prog/bwa/bwttop2.c
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2976 M /branches/prog/bwa/main.c
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2977
|
|
|
2978 * bwa-0.1.0-10
|
|
|
2979 * output a random position for repetitive reads
|
|
|
2980
|
|
|
2981 ------------------------------------------------------------------------
|
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2982 r344 | lh3 | 2008-06-02 15:03:54 -0400 (Mon, 02 Jun 2008) | 4 lines
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2983 Changed paths:
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2984 M /branches/prog/bwa/bntseq.c
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2985 M /branches/prog/bwa/bwtaln.c
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2986 M /branches/prog/bwa/main.c
|
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2987 M /branches/prog/bwa/pac2bwt.c
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2988
|
|
|
2989 * bwa-0.1.0-9
|
|
|
2990 * fix memory leaks
|
|
|
2991 * fix a potential bug in coverting to the real coordinate
|
|
|
2992
|
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2993 ------------------------------------------------------------------------
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2994 r343 | lh3 | 2008-06-02 13:44:51 -0400 (Mon, 02 Jun 2008) | 5 lines
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2995 Changed paths:
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2996 M /branches/prog/bwa/Makefile.div
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2997 M /branches/prog/bwa/bwt.c
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2998 M /branches/prog/bwa/bwt.h
|
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2999 M /branches/prog/bwa/bwt2fmv.c
|
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|
3000 M /branches/prog/bwa/bwtaln.c
|
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3001 M /branches/prog/bwa/bwttop2.c
|
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|
3002 M /branches/prog/bwa/main.c
|
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|
3003
|
|
|
3004 * bwa-0.1.0-8
|
|
|
3005 * fix a bug about strand
|
|
|
3006 * update Makefile.div
|
|
|
3007 * change top2b as the default method
|
|
|
3008
|
|
|
3009 ------------------------------------------------------------------------
|
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|
3010 r342 | lh3 | 2008-06-02 11:23:26 -0400 (Mon, 02 Jun 2008) | 3 lines
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3011 Changed paths:
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3012 M /branches/prog/bwa/bwt.c
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3013 M /branches/prog/bwa/bwt1away.c
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3014 M /branches/prog/bwa/bwtaln.c
|
|
|
3015 M /branches/prog/bwa/main.c
|
|
|
3016
|
|
|
3017 * bwa-0.1.0-7
|
|
|
3018 * use bwt_2occ() and bwt_2occ4() in other functions
|
|
|
3019
|
|
|
3020 ------------------------------------------------------------------------
|
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|
3021 r341 | lh3 | 2008-06-02 09:31:39 -0400 (Mon, 02 Jun 2008) | 3 lines
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3022 Changed paths:
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3023 M /branches/prog/bwa/bwttop2.c
|
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|
3024 M /branches/prog/bwa/main.c
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3025
|
|
|
3026 * bwa-0.1.0-6
|
|
|
3027 * fix a bug for missing hits
|
|
|
3028
|
|
|
3029 ------------------------------------------------------------------------
|
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|
3030 r340 | lh3 | 2008-06-02 09:10:18 -0400 (Mon, 02 Jun 2008) | 3 lines
|
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|
3031 Changed paths:
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|
3032 M /branches/prog/bwa/bwttop2.c
|
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3033 M /branches/prog/bwa/main.c
|
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|
3034
|
|
|
3035 * bwa-0.1.0-5
|
|
|
3036 * accelerate comparisons in heap, a bit
|
|
|
3037
|
|
|
3038 ------------------------------------------------------------------------
|
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|
3039 r339 | lh3 | 2008-06-02 08:41:31 -0400 (Mon, 02 Jun 2008) | 3 lines
|
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|
3040 Changed paths:
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|
3041 M /branches/prog/bwa/bwt.c
|
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|
3042 M /branches/prog/bwa/bwt.h
|
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|
3043 M /branches/prog/bwa/bwttop2.c
|
|
|
3044 M /branches/prog/bwa/main.c
|
|
|
3045
|
|
|
3046 * bwa-0.1.0-4
|
|
|
3047 * avoid marginal repeated calculation in occ
|
|
|
3048
|
|
|
3049 ------------------------------------------------------------------------
|
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|
3050 r338 | lh3 | 2008-06-02 06:46:51 -0400 (Mon, 02 Jun 2008) | 5 lines
|
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|
3051 Changed paths:
|
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|
3052 M /branches/prog/bwa/Makefile
|
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|
3053 M /branches/prog/bwa/bwt.c
|
|
|
3054 M /branches/prog/bwa/bwttop2.c
|
|
|
3055 M /branches/prog/bwa/main.c
|
|
|
3056
|
|
|
3057 * bwa-0.1.0-3
|
|
|
3058 * fix a bug caused by previours change
|
|
|
3059 * fix a bug in heap
|
|
|
3060 * order the heap by more criteria
|
|
|
3061
|
|
|
3062 ------------------------------------------------------------------------
|
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|
3063 r337 | lh3 | 2008-06-01 19:11:15 -0400 (Sun, 01 Jun 2008) | 4 lines
|
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|
3064 Changed paths:
|
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|
3065 M /branches/prog/bwa/bwttop2.c
|
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|
3066 M /branches/prog/bwa/main.c
|
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|
3067
|
|
|
3068 * bwa-0.1.0-2
|
|
|
3069 * also sort sa range in heapsort, in attempt to improve cache performance.
|
|
|
3070 Unfortunately, it does not work well at all.
|
|
|
3071
|
|
|
3072 ------------------------------------------------------------------------
|
|
|
3073 r336 | lh3 | 2008-06-01 17:45:23 -0400 (Sun, 01 Jun 2008) | 3 lines
|
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|
3074 Changed paths:
|
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|
3075 M /branches/prog/bwa/Makefile
|
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|
3076 M /branches/prog/bwa/Makefile.div
|
|
|
3077 M /branches/prog/bwa/bntseq.c
|
|
|
3078 M /branches/prog/bwa/main.c
|
|
|
3079
|
|
|
3080 * 0.1.0-1
|
|
|
3081 * fix a bug in calculating the real coordinate
|
|
|
3082
|
|
|
3083 ------------------------------------------------------------------------
|
|
|
3084 r335 | lh3 | 2008-06-01 16:03:09 -0400 (Sun, 01 Jun 2008) | 2 lines
|
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|
3085 Changed paths:
|
|
|
3086 M /branches/prog/bwa/Makefile
|
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|
3087
|
|
|
3088 nothing, really
|
|
|
3089
|
|
|
3090 ------------------------------------------------------------------------
|
|
|
3091 r334 | lh3 | 2008-06-01 15:59:13 -0400 (Sun, 01 Jun 2008) | 2 lines
|
|
|
3092 Changed paths:
|
|
|
3093 M /branches/prog/bwa/Makefile
|
|
|
3094 A /branches/prog/bwa/Makefile.div
|
|
|
3095 M /branches/prog/bwa/bwtindex.c
|
|
|
3096 M /branches/prog/bwa/pac2bwt.c
|
|
|
3097
|
|
|
3098 use IS algorithm by default
|
|
|
3099
|
|
|
3100 ------------------------------------------------------------------------
|
|
|
3101 r333 | lh3 | 2008-06-01 15:05:15 -0400 (Sun, 01 Jun 2008) | 3 lines
|
|
|
3102 Changed paths:
|
|
|
3103 M /branches/prog/bwa/Makefile
|
|
|
3104 M /branches/prog/bwa/bwtindex.c
|
|
|
3105 M /branches/prog/bwa/is.c
|
|
|
3106 M /branches/prog/bwa/pac2bwt.c
|
|
|
3107
|
|
|
3108 * a bit code clean up in is.c
|
|
|
3109 * add IS algorithm for constructing BWT, albeit slower
|
|
|
3110
|
|
|
3111 ------------------------------------------------------------------------
|
|
|
3112 r332 | lh3 | 2008-06-01 13:23:08 -0400 (Sun, 01 Jun 2008) | 2 lines
|
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|
3113 Changed paths:
|
|
|
3114 A /branches/prog/bwa/is.c
|
|
|
3115
|
|
|
3116 IS linear-time algorithm for constructing SA/BWT
|
|
|
3117
|
|
|
3118 ------------------------------------------------------------------------
|
|
|
3119 r331 | lh3 | 2008-06-01 10:35:26 -0400 (Sun, 01 Jun 2008) | 3 lines
|
|
|
3120 Changed paths:
|
|
|
3121 M /branches/prog/bwa/Makefile
|
|
|
3122 M /branches/prog/bwa/bntseq.c
|
|
|
3123 A /branches/prog/bwa/bwtindex.c
|
|
|
3124 M /branches/prog/bwa/main.c
|
|
|
3125 M /branches/prog/bwa/main.h
|
|
|
3126
|
|
|
3127 * fix a bug in generating .pac
|
|
|
3128 * index in one go
|
|
|
3129
|
|
|
3130 ------------------------------------------------------------------------
|
|
|
3131 r330 | lh3 | 2008-06-01 09:17:05 -0400 (Sun, 01 Jun 2008) | 2 lines
|
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|
3132 Changed paths:
|
|
|
3133 M /branches/prog/bwa/bntseq.c
|
|
|
3134 M /branches/prog/bwa/bntseq.h
|
|
|
3135 M /branches/prog/bwa/bwtaln.c
|
|
|
3136 M /branches/prog/bwa/bwttop2.c
|
|
|
3137
|
|
|
3138 real coordinates can be ouput
|
|
|
3139
|
|
|
3140 ------------------------------------------------------------------------
|
|
|
3141 r329 | lh3 | 2008-05-31 19:21:02 -0400 (Sat, 31 May 2008) | 2 lines
|
|
|
3142 Changed paths:
|
|
|
3143 M /branches/prog/bwa/bwt2fmv.c
|
|
|
3144 M /branches/prog/bwa/bwtaln.h
|
|
|
3145 M /branches/prog/bwa/bwttop2.c
|
|
|
3146
|
|
|
3147 add top2e which is similar to 1away
|
|
|
3148
|
|
|
3149 ------------------------------------------------------------------------
|
|
|
3150 r328 | lh3 | 2008-05-31 18:46:12 -0400 (Sat, 31 May 2008) | 3 lines
|
|
|
3151 Changed paths:
|
|
|
3152 M /branches/prog/bwa/bwt2fmv.c
|
|
|
3153 M /branches/prog/bwa/bwtaln.c
|
|
|
3154 M /branches/prog/bwa/bwtaln.h
|
|
|
3155 M /branches/prog/bwa/bwttop2.c
|
|
|
3156 M /branches/prog/bwa/main.c
|
|
|
3157 M /branches/prog/bwa/main.h
|
|
|
3158
|
|
|
3159 * unified cmd-line interface for ungapped alignment
|
|
|
3160 * add two alternatives to top2 algorithm
|
|
|
3161
|
|
|
3162 ------------------------------------------------------------------------
|
|
|
3163 r327 | lh3 | 2008-05-31 18:14:46 -0400 (Sat, 31 May 2008) | 2 lines
|
|
|
3164 Changed paths:
|
|
|
3165 M /branches/prog/bwa/bwt2fmv.c
|
|
|
3166 M /branches/prog/bwa/bwtaln.c
|
|
|
3167 M /branches/prog/bwa/bwtaln.h
|
|
|
3168 M /branches/prog/bwa/main.c
|
|
|
3169 M /branches/prog/bwa/main.h
|
|
|
3170
|
|
|
3171 add cmd-line interface to alntop2
|
|
|
3172
|
|
|
3173 ------------------------------------------------------------------------
|
|
|
3174 r326 | lh3 | 2008-05-31 17:59:31 -0400 (Sat, 31 May 2008) | 2 lines
|
|
|
3175 Changed paths:
|
|
|
3176 M /branches/prog/bwa/Makefile
|
|
|
3177 M /branches/prog/bwa/bwt1away.c
|
|
|
3178 M /branches/prog/bwa/bwtaln.c
|
|
|
3179 M /branches/prog/bwa/bwtaln.h
|
|
|
3180 A /branches/prog/bwa/bwttop2.c
|
|
|
3181
|
|
|
3182 top2 algorithm seems to work. I need to change interface, though
|
|
|
3183
|
|
|
3184 ------------------------------------------------------------------------
|
|
|
3185 r325 | lh3 | 2008-05-31 15:11:49 -0400 (Sat, 31 May 2008) | 2 lines
|
|
|
3186 Changed paths:
|
|
|
3187 M /branches/prog/bwa/bwt1away.c
|
|
|
3188
|
|
|
3189 change the variable in the structure
|
|
|
3190
|
|
|
3191 ------------------------------------------------------------------------
|
|
|
3192 r324 | lh3 | 2008-05-31 14:52:13 -0400 (Sat, 31 May 2008) | 2 lines
|
|
|
3193 Changed paths:
|
|
|
3194 M /branches/prog/bwa/bwt1away.c
|
|
|
3195
|
|
|
3196 set a slightly better bound on the maximum allowed mismatches
|
|
|
3197
|
|
|
3198 ------------------------------------------------------------------------
|
|
|
3199 r323 | lh3 | 2008-05-30 18:40:21 -0400 (Fri, 30 May 2008) | 2 lines
|
|
|
3200 Changed paths:
|
|
|
3201 M /branches/prog/bwa/bwtaln.c
|
|
|
3202
|
|
|
3203 * output time statistics
|
|
|
3204
|
|
|
3205 ------------------------------------------------------------------------
|
|
|
3206 r322 | lh3 | 2008-05-30 17:58:25 -0400 (Fri, 30 May 2008) | 4 lines
|
|
|
3207 Changed paths:
|
|
|
3208 M /branches/prog/bwa/Makefile
|
|
|
3209 M /branches/prog/bwa/bwt.c
|
|
|
3210 M /branches/prog/bwa/bwt.h
|
|
|
3211 A /branches/prog/bwa/bwt1away.c
|
|
|
3212 M /branches/prog/bwa/bwtaln.c
|
|
|
3213 M /branches/prog/bwa/bwtaln.h
|
|
|
3214
|
|
|
3215 * presumably better way to make use of prefix. But for the moment I do
|
|
|
3216 not know whether it is correct or not.
|
|
|
3217 * a bit code clean up: separate alignment part
|
|
|
3218
|
|
|
3219 ------------------------------------------------------------------------
|
|
|
3220 r321 | lh3 | 2008-05-30 13:57:43 -0400 (Fri, 30 May 2008) | 3 lines
|
|
|
3221 Changed paths:
|
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|
3222 M /branches/prog/bwa/Makefile
|
|
|
3223 M /branches/prog/bwa/bwt.c
|
|
|
3224 M /branches/prog/bwa/bwt.h
|
|
|
3225 M /branches/prog/bwa/bwt_gen/Makefile
|
|
|
3226 M /branches/prog/bwa/bwt_gen/bwt_gen.c
|
|
|
3227 M /branches/prog/bwa/bwtaln.c
|
|
|
3228 M /branches/prog/bwa/main.c
|
|
|
3229 M /branches/prog/bwa/main.h
|
|
|
3230 M /branches/prog/bwa/pac2bwt.c
|
|
|
3231
|
|
|
3232 * a bit code clean up
|
|
|
3233 * put bwt_gen in bwa
|
|
|
3234
|
|
|
3235 ------------------------------------------------------------------------
|
|
|
3236 r320 | lh3 | 2008-05-30 11:40:11 -0400 (Fri, 30 May 2008) | 4 lines
|
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|
3237 Changed paths:
|
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|
3238 M /branches/prog/bwa/bwt.c
|
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3239 M /branches/prog/bwa/bwt2fmv.c
|
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|
3240 M /branches/prog/bwa/bwtaln.c
|
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|
3241 M /branches/prog/bwa/bwtaln.h
|
|
|
3242 M /branches/prog/bwa/bwtio.c
|
|
|
3243
|
|
|
3244 * improve cmd-line interface
|
|
|
3245 * fix a bug in loading .sa
|
|
|
3246 * change default sa interval to 32
|
|
|
3247
|
|
|
3248 ------------------------------------------------------------------------
|
|
|
3249 r319 | lh3 | 2008-05-30 10:31:37 -0400 (Fri, 30 May 2008) | 3 lines
|
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|
3250 Changed paths:
|
|
|
3251 M /branches/prog/bwa/bwtaln.c
|
|
|
3252
|
|
|
3253 * fix memory leak (I know that. Just a bit lazy)
|
|
|
3254 * change to another method to do 1-away alignment
|
|
|
3255
|
|
|
3256 ------------------------------------------------------------------------
|
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|
3257 r318 | lh3 | 2008-05-30 09:21:49 -0400 (Fri, 30 May 2008) | 2 lines
|
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|
3258 Changed paths:
|
|
|
3259 M /branches/prog/bwa/bwt.c
|
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3260 M /branches/prog/bwa/bwt.h
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3261 M /branches/prog/bwa/bwt2fmv.c
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3262 M /branches/prog/bwa/bwtaln.c
|
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3263 M /branches/prog/bwa/bwtaln.h
|
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3264 M /branches/prog/bwa/main.c
|
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|
3265 M /branches/prog/bwa/main.h
|
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3266
|
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|
3267 best unique match is partially finished
|
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3268
|
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|
3269 ------------------------------------------------------------------------
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|
3270 r317 | lh3 | 2008-05-30 06:33:28 -0400 (Fri, 30 May 2008) | 2 lines
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3271 Changed paths:
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3272 M /branches/prog/bwa/bwt.c
|
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3273 M /branches/prog/bwa/bwt2fmv.c
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3274 M /branches/prog/bwa/bwtaln.c
|
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3275 M /branches/prog/bwa/bwtaln.h
|
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3276 M /branches/prog/bwa/main.c
|
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|
3277 M /branches/prog/bwa/main.h
|
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3278
|
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|
3279 remove "ungapped" command and related codes
|
|
|
3280
|
|
|
3281 ------------------------------------------------------------------------
|
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|
3282 r316 | lh3 | 2008-05-30 06:05:20 -0400 (Fri, 30 May 2008) | 2 lines
|
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|
3283 Changed paths:
|
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|
3284 M /branches/prog/bwa/Makefile
|
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3285 M /branches/prog/bwa/bwt.c
|
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3286 M /branches/prog/bwa/bwtaln.c
|
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|
3287 M /branches/prog/bwa/bwtaln.h
|
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|
3288
|
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|
3289 change variable name thick to width
|
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3290
|
|
|
3291 ------------------------------------------------------------------------
|
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|
3292 r315 | lh3 | 2008-05-29 19:06:13 -0400 (Thu, 29 May 2008) | 2 lines
|
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3293 Changed paths:
|
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|
3294 M /branches/prog/bwa/bntseq.c
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3295 M /branches/prog/bwa/bwt.c
|
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|
3296 M /branches/prog/bwa/bwt.h
|
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|
3297 M /branches/prog/bwa/bwt2fmv.c
|
|
|
3298 M /branches/prog/bwa/bwtaln.c
|
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|
3299 M /branches/prog/bwa/bwtaln.h
|
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|
3300 M /branches/prog/bwa/bwtio.c
|
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|
3301 M /branches/prog/bwa/main.c
|
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|
3302 M /branches/prog/bwa/main.h
|
|
|
3303 M /branches/prog/bwa/pac2bwt.c
|
|
|
3304
|
|
|
3305 revised algorithm for ungapped alignment. the old one can still be used.
|
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|
3306
|
|
|
3307 ------------------------------------------------------------------------
|
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|
3308 r314 | lh3 | 2008-05-29 16:36:11 -0400 (Thu, 29 May 2008) | 2 lines
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|
3309 Changed paths:
|
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|
3310 M /branches/prog/bwa/bwt2fmv.c
|
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|
3311 M /branches/prog/bwa/bwt_gen/bwt_gen.c
|
|
|
3312 M /branches/prog/bwa/bwtio.c
|
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|
3313 M /branches/prog/bwa/pac2bwt.c
|
|
|
3314
|
|
|
3315 * make commands more independent, but ungapped does not work at the moment
|
|
|
3316
|
|
|
3317 ------------------------------------------------------------------------
|
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|
3318 r313 | lh3 | 2008-05-29 15:56:14 -0400 (Thu, 29 May 2008) | 2 lines
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3319 Changed paths:
|
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|
3320 M /branches/prog/bwa/bwt_gen/bwt_gen.c
|
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|
3321
|
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|
3322 little...
|
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|
3323
|
|
|
3324 ------------------------------------------------------------------------
|
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|
3325 r312 | lh3 | 2008-05-29 15:54:01 -0400 (Thu, 29 May 2008) | 3 lines
|
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|
3326 Changed paths:
|
|
|
3327 M /branches/prog/bwa/bwt_gen/bwt_gen.c
|
|
|
3328 M /branches/prog/bwa/bwt_gen/bwt_gen.h
|
|
|
3329
|
|
|
3330 * add CopyRight information from the original codes
|
|
|
3331 * do not dump .fmv files
|
|
|
3332
|
|
|
3333 ------------------------------------------------------------------------
|
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|
3334 r311 | lh3 | 2008-05-29 15:44:36 -0400 (Thu, 29 May 2008) | 2 lines
|
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|
3335 Changed paths:
|
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|
3336 A /branches/prog/bwa/bwt_gen
|
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3337 A /branches/prog/bwa/bwt_gen/Makefile
|
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|
3338 A /branches/prog/bwa/bwt_gen/QSufSort.c
|
|
|
3339 A /branches/prog/bwa/bwt_gen/QSufSort.h
|
|
|
3340 A /branches/prog/bwa/bwt_gen/bwt_gen.c
|
|
|
3341 A /branches/prog/bwa/bwt_gen/bwt_gen.h
|
|
|
3342
|
|
|
3343 codes from BWT-SW, for building BWT from packed file
|
|
|
3344
|
|
|
3345 ------------------------------------------------------------------------
|
|
|
3346 r310 | lh3 | 2008-05-28 17:03:35 -0400 (Wed, 28 May 2008) | 4 lines
|
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|
3347 Changed paths:
|
|
|
3348 M /branches/prog/bwa/bwt.c
|
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|
3349 M /branches/prog/bwa/bwt.h
|
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|
3350 M /branches/prog/bwa/bwt2fmv.c
|
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|
3351 M /branches/prog/bwa/bwtio.c
|
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|
3352 M /branches/prog/bwa/main.c
|
|
|
3353 M /branches/prog/bwa/main.h
|
|
|
3354
|
|
|
3355 * change OCC_INTERVAL to 0x40, which makes bwa twice as fast.
|
|
|
3356 * write Occ file as ".occ" as it is using a different interval from
|
|
|
3357 .fmv, the BWT-SW correspondance of .occ
|
|
|
3358
|
|
|
3359 ------------------------------------------------------------------------
|
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|
3360 r309 | lh3 | 2008-05-28 11:39:37 -0400 (Wed, 28 May 2008) | 2 lines
|
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3361 Changed paths:
|
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|
3362 M /branches/prog/bwa/bwt.c
|
|
|
3363 M /branches/prog/bwa/bwt2fmv.c
|
|
|
3364
|
|
|
3365 fix a bug
|
|
|
3366
|
|
|
3367 ------------------------------------------------------------------------
|
|
|
3368 r308 | lh3 | 2008-05-28 09:56:16 -0400 (Wed, 28 May 2008) | 4 lines
|
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|
3369 Changed paths:
|
|
|
3370 M /branches/prog/bwa/bwt.c
|
|
|
3371 M /branches/prog/bwa/bwt2fmv.c
|
|
|
3372
|
|
|
3373 add heuristics to improve the speed, but I have not tested whether the
|
|
|
3374 results are correct or not.
|
|
|
3375
|
|
|
3376
|
|
|
3377 ------------------------------------------------------------------------
|
|
|
3378 r307 | lh3 | 2008-05-28 06:31:34 -0400 (Wed, 28 May 2008) | 5 lines
|
|
|
3379 Changed paths:
|
|
|
3380 M /branches/prog/bwa/bwt.c
|
|
|
3381 M /branches/prog/bwa/bwt2fmv.c
|
|
|
3382 M /branches/prog/bwa/bwtaln.c
|
|
|
3383 M /branches/prog/bwa/bwtaln.h
|
|
|
3384 M /branches/prog/bwa/main.c
|
|
|
3385 M /branches/prog/bwa/main.h
|
|
|
3386
|
|
|
3387 * make ungapped alignment basically works...
|
|
|
3388 * but it is very slow in comparison to others...
|
|
|
3389 * also I need to improve the interface...
|
|
|
3390 * a lot of things to keep me busy today...
|
|
|
3391
|
|
|
3392 ------------------------------------------------------------------------
|
|
|
3393 r306 | lh3 | 2008-05-27 18:41:27 -0400 (Tue, 27 May 2008) | 3 lines
|
|
|
3394 Changed paths:
|
|
|
3395 M /branches/prog/bwa/bwt.c
|
|
|
3396 M /branches/prog/bwa/bwt.h
|
|
|
3397 M /branches/prog/bwa/bwtaln.c
|
|
|
3398
|
|
|
3399 * remove recursion
|
|
|
3400 * fixed a bug in bwt_occ()
|
|
|
3401
|
|
|
3402 ------------------------------------------------------------------------
|
|
|
3403 r305 | lh3 | 2008-05-27 16:59:44 -0400 (Tue, 27 May 2008) | 5 lines
|
|
|
3404 Changed paths:
|
|
|
3405 M /branches/prog/bwa/bwt.c
|
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|
3406 M /branches/prog/bwa/bwt.h
|
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|
3407 M /branches/prog/bwa/bwtaln.c
|
|
|
3408
|
|
|
3409 * bwa now tells whether a sequenced can be mapped with maximum allowed
|
|
|
3410 mismatches. ONLY ungapped.
|
|
|
3411 * this is a recursive version. I will remove recursion later.
|
|
|
3412
|
|
|
3413
|
|
|
3414 ------------------------------------------------------------------------
|
|
|
3415 r304 | lh3 | 2008-05-27 09:12:17 -0400 (Tue, 27 May 2008) | 3 lines
|
|
|
3416 Changed paths:
|
|
|
3417 M /branches/prog/bwa/Makefile
|
|
|
3418 M /branches/prog/bwa/bwt.c
|
|
|
3419 M /branches/prog/bwa/bwt.h
|
|
|
3420 M /branches/prog/bwa/bwt2fmv.c
|
|
|
3421 A /branches/prog/bwa/bwtaln.c
|
|
|
3422 A /branches/prog/bwa/bwtaln.h
|
|
|
3423 M /branches/prog/bwa/bwtio.c
|
|
|
3424 M /branches/prog/bwa/main.c
|
|
|
3425 M /branches/prog/bwa/main.h
|
|
|
3426 M /branches/prog/bwa/utils.c
|
|
|
3427
|
|
|
3428 * load .sa and .fmv files
|
|
|
3429 * exact alignment now works
|
|
|
3430
|
|
|
3431 ------------------------------------------------------------------------
|
|
|
3432 r303 | lh3 | 2008-05-27 06:33:38 -0400 (Tue, 27 May 2008) | 2 lines
|
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|
3433 Changed paths:
|
|
|
3434 M /branches/prog/bwa/bntseq.c
|
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|
3435 M /branches/prog/bwa/bwt.c
|
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|
3436 M /branches/prog/bwa/bwtio.c
|
|
|
3437 M /branches/prog/bwa/utils.c
|
|
|
3438 M /branches/prog/bwa/utils.h
|
|
|
3439
|
|
|
3440 add xassert and fix a bug
|
|
|
3441
|
|
|
3442 ------------------------------------------------------------------------
|
|
|
3443 r302 | lh3 | 2008-05-27 06:23:20 -0400 (Tue, 27 May 2008) | 2 lines
|
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|
3444 Changed paths:
|
|
|
3445 M /branches/prog/bwa/Makefile
|
|
|
3446 M /branches/prog/bwa/bntseq.c
|
|
|
3447 M /branches/prog/bwa/bwt.c
|
|
|
3448 M /branches/prog/bwa/bwtio.c
|
|
|
3449 A /branches/prog/bwa/utils.c
|
|
|
3450 A /branches/prog/bwa/utils.h
|
|
|
3451
|
|
|
3452 improve error message and error handling
|
|
|
3453
|
|
|
3454 ------------------------------------------------------------------------
|
|
|
3455 r301 | lh3 | 2008-05-27 05:37:51 -0400 (Tue, 27 May 2008) | 4 lines
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|
3456 Changed paths:
|
|
|
3457 M /branches/prog/bwa/Makefile
|
|
|
3458 M /branches/prog/bwa/bwt.c
|
|
|
3459 M /branches/prog/bwa/bwt.h
|
|
|
3460 M /branches/prog/bwa/bwt2fmv.c
|
|
|
3461 A /branches/prog/bwa/bwtio.c
|
|
|
3462 M /branches/prog/bwa/main.c
|
|
|
3463 M /branches/prog/bwa/main.h
|
|
|
3464
|
|
|
3465 * move I/O codes to bwtio.c
|
|
|
3466 * SA can be dumped and interestingly, it is identical to BWTSW
|
|
|
3467 * now, .fmv is still different from BWTSW
|
|
|
3468
|
|
|
3469 ------------------------------------------------------------------------
|
|
|
3470 r299 | lh3 | 2008-05-26 18:07:44 -0400 (Mon, 26 May 2008) | 2 lines
|
|
|
3471 Changed paths:
|
|
|
3472 M /branches/prog/bwa/Makefile
|
|
|
3473 M /branches/prog/bwa/bwt.c
|
|
|
3474 M /branches/prog/bwa/bwt.h
|
|
|
3475 M /branches/prog/bwa/bwt2fmv.c
|
|
|
3476
|
|
|
3477 generate/retrieve SA and Occ
|
|
|
3478
|
|
|
3479 ------------------------------------------------------------------------
|
|
|
3480 r298 | lh3 | 2008-05-26 13:16:49 -0400 (Mon, 26 May 2008) | 3 lines
|
|
|
3481 Changed paths:
|
|
|
3482 M /branches/prog/bwa/bntseq.h
|
|
|
3483 M /branches/prog/bwa/bwt.c
|
|
|
3484 M /branches/prog/bwa/bwt.h
|
|
|
3485 M /branches/prog/bwa/bwt2fmv.c
|
|
|
3486
|
|
|
3487 * retrieve occ value at any position
|
|
|
3488 * move bwt_cal_occ() to bwt.c
|
|
|
3489
|
|
|
3490 ------------------------------------------------------------------------
|
|
|
3491 r297 | lh3 | 2008-05-25 17:43:58 -0400 (Sun, 25 May 2008) | 6 lines
|
|
|
3492 Changed paths:
|
|
|
3493 M /branches/prog/bwa/Makefile
|
|
|
3494 A /branches/prog/bwa/bwt.c
|
|
|
3495 A /branches/prog/bwa/bwt.h
|
|
|
3496 A /branches/prog/bwa/bwt2fmv.c
|
|
|
3497 M /branches/prog/bwa/main.c
|
|
|
3498 M /branches/prog/bwa/main.h
|
|
|
3499 M /branches/prog/bwa/pac2bwt.c
|
|
|
3500
|
|
|
3501 * add bwt2fmv. It works to some extend. However, I do not understand
|
|
|
3502 the purpose of some weird codes in BWT-SW. As a consequence, bwt2fmv
|
|
|
3503 could generate a file almost identical, but not exactly identical, to
|
|
|
3504 the .fmv file from BWT-SW.
|
|
|
3505
|
|
|
3506
|
|
|
3507 ------------------------------------------------------------------------
|
|
|
3508 r296 | lh3 | 2008-05-24 18:35:02 -0400 (Sat, 24 May 2008) | 5 lines
|
|
|
3509 Changed paths:
|
|
|
3510 M /branches/prog/bwa/Makefile
|
|
|
3511 M /branches/prog/bwa/bntseq.c
|
|
|
3512 M /branches/prog/bwa/bntseq.h
|
|
|
3513 M /branches/prog/bwa/main.c
|
|
|
3514 M /branches/prog/bwa/main.h
|
|
|
3515 A /branches/prog/bwa/pac2bwt.c
|
|
|
3516
|
|
|
3517 Burrows-Wheeler Transform now works. At least on one example, the
|
|
|
3518 current code generates the same BWT as BWT-SW. Kind of magical, I would
|
|
|
3519 say. :)
|
|
|
3520
|
|
|
3521
|
|
|
3522 ------------------------------------------------------------------------
|
|
|
3523 r295 | lh3 | 2008-05-24 11:25:31 -0400 (Sat, 24 May 2008) | 3 lines
|
|
|
3524 Changed paths:
|
|
|
3525 A /branches/prog/bwa/Makefile
|
|
|
3526 M /branches/prog/bwa/bntseq.c
|
|
|
3527 A /branches/prog/bwa/main.c
|
|
|
3528 A /branches/prog/bwa/main.h
|
|
|
3529
|
|
|
3530 * add Makefile and main.*
|
|
|
3531 * improve interface to fa2bns, a bit
|
|
|
3532
|
|
|
3533 ------------------------------------------------------------------------
|
|
|
3534 r293 | lh3 | 2008-05-24 10:57:03 -0400 (Sat, 24 May 2008) | 3 lines
|
|
|
3535 Changed paths:
|
|
|
3536 A /branches/prog/bwa
|
|
|
3537 A /branches/prog/bwa/bntseq.c
|
|
|
3538 A /branches/prog/bwa/bntseq.h
|
|
|
3539 A /branches/prog/bwa/seq.c
|
|
|
3540 A /branches/prog/bwa/seq.h
|
|
|
3541
|
|
|
3542 * Burrow-Wheeler Alignment
|
|
|
3543 * initial codes
|
|
|
3544
|
|
|
3545 ------------------------------------------------------------------------
|
