annotate bwa-0.6.2/ChangeLog @ 0:dd1186b11b3b draft

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author ashvark
date Fri, 18 Jul 2014 07:55:14 -0400
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1 ------------------------------------------------------------------------
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2 r1605 | lh3 | 2010-12-29 20:20:20 -0500 (Wed, 29 Dec 2010) | 3 lines
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3 Changed paths:
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4 M /branches/prog/bwa/bwtsw2_aux.c
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5 M /branches/prog/bwa/main.c
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6
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7 * bwa-0.5.9rc1-2 (r1605)
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8 * fixed a typo/bug in bwasw
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11 r1587 | lh3 | 2010-12-21 18:48:30 -0500 (Tue, 21 Dec 2010) | 2 lines
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12 Changed paths:
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13 M /branches/prog/bwa/bwa.1
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14
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15 a typo in the manual
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17 ------------------------------------------------------------------------
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18 r1586 | lh3 | 2010-12-21 18:47:48 -0500 (Tue, 21 Dec 2010) | 3 lines
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19 Changed paths:
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20 M /branches/prog/bwa/bwape.c
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21 M /branches/prog/bwa/bwase.c
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22 M /branches/prog/bwa/bwtaln.c
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23 M /branches/prog/bwa/bwtsw2_main.c
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24 M /branches/prog/bwa/main.c
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25 M /branches/prog/bwa/utils.c
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26 M /branches/prog/bwa/utils.h
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27
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28 * bwa-0.5.9rc1-1 (r1586)
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29 * a few patches by John
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30
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31 ------------------------------------------------------------------------
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32 r1562 | lh3 | 2010-12-10 01:02:06 -0500 (Fri, 10 Dec 2010) | 2 lines
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33 Changed paths:
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34 M /branches/prog/bwa/bwa.1
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35 M /branches/prog/bwa/bwape.c
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36 M /branches/prog/bwa/bwase.c
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37
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38 documentation on specifying @RG
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41 r1561 | lh3 | 2010-12-10 00:45:40 -0500 (Fri, 10 Dec 2010) | 2 lines
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42 Changed paths:
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43 M /branches/prog/bwa/ChangeLog
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44 M /branches/prog/bwa/NEWS
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45 M /branches/prog/bwa/bwa.1
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46 M /branches/prog/bwa/main.c
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47
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48 Release bwa-0.5.9rc1 (r1561)
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49
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51 r1560 | lh3 | 2010-12-10 00:29:08 -0500 (Fri, 10 Dec 2010) | 3 lines
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52 Changed paths:
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53 M /branches/prog/bwa/bwaseqio.c
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54 M /branches/prog/bwa/main.c
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55
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56 * fixed a small memory leak caused by the BAM reader
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57 * fixed a memory violation, also in the BAM reader
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61 Changed paths:
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62 M /branches/prog/bwa/ChangeLog
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63 M /branches/prog/bwa/Makefile
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64
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65 change Makefile gcc options
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69 Changed paths:
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70 M /branches/prog/bwa/bwtsw2_aux.c
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71 M /branches/prog/bwa/bwtsw2_core.c
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72 M /branches/prog/bwa/main.c
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73
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74 * bwa-0.5.8-6 (r1557)
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75 * added a little more comments to BWA-SW
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76 * randomly choosing a mapping if there are more than one
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79 r1557 | lh3 | 2010-12-09 21:58:00 -0500 (Thu, 09 Dec 2010) | 2 lines
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80 Changed paths:
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81 M /branches/prog/bwa/Makefile
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82 M /branches/prog/bwa/bwtsw2_aux.c
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83
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84 sometimes unmapped reads may not be printed...
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85
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87 r1556 | lh3 | 2010-12-09 21:50:26 -0500 (Thu, 09 Dec 2010) | 2 lines
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88 Changed paths:
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89 M /branches/prog/bwa/Makefile
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90 M /branches/prog/bwa/bwtsw2_aux.c
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91
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92 print unmapped reads
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95 r1555 | lh3 | 2010-12-09 21:17:20 -0500 (Thu, 09 Dec 2010) | 3 lines
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96 Changed paths:
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97 M /branches/prog/bwa/ChangeLog
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98 M /branches/prog/bwa/bwa.1
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99 M /branches/prog/bwa/bwtaln.c
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100 M /branches/prog/bwa/main.c
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101
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102 * bwa-0.5.8-5 (r1555)
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103 * BAM input documentation
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104
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105 ------------------------------------------------------------------------
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106 r1544 | lh3 | 2010-11-23 11:01:41 -0500 (Tue, 23 Nov 2010) | 3 lines
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107 Changed paths:
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108 M /branches/prog/bwa/bwape.c
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109 M /branches/prog/bwa/bwase.c
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110 M /branches/prog/bwa/main.c
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111
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112 * bwa-0.5.8-4 (r1544)
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113 * supporting adding RG tags and RG lines
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114
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116 r1543 | lh3 | 2010-11-23 00:16:40 -0500 (Tue, 23 Nov 2010) | 3 lines
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117 Changed paths:
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118 M /branches/prog/bwa/bwtaln.c
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119 M /branches/prog/bwa/main.c
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120
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121 * bwa-0.5.8-3 (r1543)
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122 * fixed a memory leak
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123
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125 r1542 | lh3 | 2010-11-22 23:50:56 -0500 (Mon, 22 Nov 2010) | 3 lines
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127 M /branches/prog/bwa/bwase.c
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128 M /branches/prog/bwa/main.c
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129
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130 * bwa-0.5.8-2 (r1542)
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131 * fixed a long existing bug in random placement of reads
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132
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134 r1541 | lh3 | 2010-11-22 23:27:29 -0500 (Mon, 22 Nov 2010) | 2 lines
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135 Changed paths:
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136 M /branches/prog/bwa/Makefile
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137 A /branches/prog/bwa/bamlite.c
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138 A /branches/prog/bwa/bamlite.h
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139 M /branches/prog/bwa/bwape.c
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140 M /branches/prog/bwa/bwase.c
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141 M /branches/prog/bwa/bwaseqio.c
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142 M /branches/prog/bwa/bwtaln.c
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143 M /branches/prog/bwa/bwtaln.h
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144 M /branches/prog/bwa/main.c
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145
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146 preliminary BAM input support
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147
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149 r1537 | lh3 | 2010-10-16 23:46:20 -0400 (Sat, 16 Oct 2010) | 2 lines
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150 Changed paths:
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151 M /branches/prog/bwa/ChangeLog
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152 M /branches/prog/bwa/bwa.1
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153
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154 change version number and ChangeLog
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156 ------------------------------------------------------------------------
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157 r1536 | lh3 | 2010-10-16 23:35:10 -0400 (Sat, 16 Oct 2010) | 3 lines
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159 M /branches/prog/bwa/bwape.c
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160 M /branches/prog/bwa/main.c
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161 M /branches/prog/bwa/stdaln.c
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162
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163 * fixed a bug in the scoring matrix
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164 * release bwa-0.5.8c (r1536)
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165
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167 r1451 | lh3 | 2010-06-15 09:43:52 -0400 (Tue, 15 Jun 2010) | 2 lines
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168 Changed paths:
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169 M /branches/prog/bwa/bwa.1
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170
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171 version change
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174 r1450 | lh3 | 2010-06-15 09:42:21 -0400 (Tue, 15 Jun 2010) | 3 lines
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176 M /branches/prog/bwa/main.c
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177 M /branches/prog/bwa/stdaln.c
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178
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179 * bwa-0.5.8b (r1450)
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180 * fixed a bug in scoring matrix
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181
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183 r1445 | lh3 | 2010-06-11 08:58:33 -0400 (Fri, 11 Jun 2010) | 2 lines
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185 M /branches/prog/bwa/bwa.1
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186 M /branches/prog/bwa/bwape.c
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187
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188 fixed a serious bug
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189
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191 r1442 | lh3 | 2010-06-08 10:22:14 -0400 (Tue, 08 Jun 2010) | 2 lines
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193 M /branches/prog/bwa/ChangeLog
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194 M /branches/prog/bwa/NEWS
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195 M /branches/prog/bwa/main.c
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196
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197 Release bwa-0.5.8 (r1442)
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198
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199 ------------------------------------------------------------------------
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200 r1440 | lh3 | 2010-05-19 13:43:50 -0400 (Wed, 19 May 2010) | 3 lines
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201 Changed paths:
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202 M /branches/prog/bwa/bwtsw2_core.c
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203 M /branches/prog/bwa/main.c
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204
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205 * bwa-r1440
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206 * sorry, forget to remove a debugging line
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207
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208 ------------------------------------------------------------------------
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209 r1439 | lh3 | 2010-05-19 13:43:08 -0400 (Wed, 19 May 2010) | 4 lines
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210 Changed paths:
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211 M /branches/prog/bwa/bwape.c
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212 M /branches/prog/bwa/bwtsw2_core.c
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213 M /branches/prog/bwa/main.c
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214
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215 * bwa-r1439
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216 * fixed a bug in bwasw caused by a recent modification
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217 * throwing insane insert size when estimating isize
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218
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219 ------------------------------------------------------------------------
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220 r1425 | lh3 | 2010-04-29 15:15:23 -0400 (Thu, 29 Apr 2010) | 10 lines
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221 Changed paths:
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222 M /branches/prog/bwa/bwtsw2_core.c
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223 M /branches/prog/bwa/bwtsw2_main.c
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224 M /branches/prog/bwa/main.c
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225
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226 * bwa-0.5.7-7 (r1425)
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227 * fixed a minor bug in bwasw command-line parsing
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228 * When band-width is not large enough, bwasw may find two highly
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229 overlapping but not completely overlapping alignments. The old
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230 version will filter out one of them, which leads to false
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231 negatives. The current outputs both. This solution is obviously not
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232 ideal. The ideal one would be to increase the band-width and redo the
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233 alignment.
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234
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235
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236 ------------------------------------------------------------------------
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237 r1399 | lh3 | 2010-04-16 09:20:49 -0400 (Fri, 16 Apr 2010) | 3 lines
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238 Changed paths:
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239 M /branches/prog/bwa/ChangeLog
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240 M /branches/prog/bwa/bwase.c
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241 M /branches/prog/bwa/main.c
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242
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243 * bwa-0.5.7-6 (r1399)
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244 * fixed a typo/bug (by Vaughn Iverson)
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245
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246 ------------------------------------------------------------------------
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247 r1329 | lh3 | 2010-03-19 23:32:46 -0400 (Fri, 19 Mar 2010) | 2 lines
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248 Changed paths:
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249 M /branches/prog/bwa/bwape.c
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250 M /branches/prog/bwa/main.c
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251
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252 small correction
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253
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254 ------------------------------------------------------------------------
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255 r1328 | lh3 | 2010-03-19 23:28:44 -0400 (Fri, 19 Mar 2010) | 3 lines
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256 Changed paths:
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257 M /branches/prog/bwa/bwape.c
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258 M /branches/prog/bwa/main.c
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259
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260 * bwa-0.5.7-4 (r1328)
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261 * automatically adjust ap_prior based on alignment
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262
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263 ------------------------------------------------------------------------
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264 r1327 | lh3 | 2010-03-19 23:02:40 -0400 (Fri, 19 Mar 2010) | 3 lines
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265 Changed paths:
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266 M /branches/prog/bwa/bwape.c
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267 M /branches/prog/bwa/main.c
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268 M /branches/prog/bwa/stdaln.c
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269 M /branches/prog/bwa/stdaln.h
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270
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271 * bwa-0.5.7-3 (r1327)
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272 * evaluate hits obtained from SW alignment in a more proper way.
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273
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274 ------------------------------------------------------------------------
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275 r1320 | lh3 | 2010-03-17 15:13:22 -0400 (Wed, 17 Mar 2010) | 2 lines
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276 Changed paths:
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277 M /branches/prog/bwa/bwape.c
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278
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279 fixed a potential out-of-boundary error. Need more testing.
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280
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281 ------------------------------------------------------------------------
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282 r1319 | lh3 | 2010-03-14 22:44:46 -0400 (Sun, 14 Mar 2010) | 2 lines
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283 Changed paths:
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284 M /branches/prog/bwa/bwape.c
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285
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286 insert size is `weird' if the 3rd quatile larger than 100,000bp
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287
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288 ------------------------------------------------------------------------
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289 r1318 | lh3 | 2010-03-14 22:37:35 -0400 (Sun, 14 Mar 2010) | 3 lines
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290 Changed paths:
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291 M /branches/prog/bwa/bwape.c
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292 M /branches/prog/bwa/bwtaln.h
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293 M /branches/prog/bwa/main.c
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294
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295 * bwa-0.5.7-2 (r1318)
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296 * in sampe, allow to disable insert size estimate
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297
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298 ------------------------------------------------------------------------
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299 r1317 | lh3 | 2010-03-14 22:14:14 -0400 (Sun, 14 Mar 2010) | 5 lines
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300 Changed paths:
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301 M /branches/prog/bwa/bwape.c
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302 M /branches/prog/bwa/bwase.c
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303 M /branches/prog/bwa/main.c
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304 M /branches/prog/bwa/solid2fastq.pl
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305
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306 * bwa-0.5.7-1 (r1317)
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307 * fixed a potential bug in solid2fastq.pl
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308 * fixed a bug in calculating mapping quality (by Rodrigo Goya)
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309 * fixed a very rare bug (if ever occur) about pairing
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310
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311 ------------------------------------------------------------------------
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312 r1310 | lh3 | 2010-03-01 10:35:45 -0500 (Mon, 01 Mar 2010) | 2 lines
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313 Changed paths:
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314 M /branches/prog/bwa/ChangeLog
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315 M /branches/prog/bwa/NEWS
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316 M /branches/prog/bwa/main.c
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317
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318 Release bwa-0.5.7
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319
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320 ------------------------------------------------------------------------
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321 r1309 | lh3 | 2010-02-26 21:42:22 -0500 (Fri, 26 Feb 2010) | 4 lines
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322 Changed paths:
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323 M /branches/prog/bwa/bwape.c
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324 M /branches/prog/bwa/bwtaln.c
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325 M /branches/prog/bwa/main.c
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326
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327 * bwa-0.5.6-2 (r1309)
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328 * fixed an unfixed bug (by Carol Scott)
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329 * fixed some tiny formatting
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330
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331 ------------------------------------------------------------------------
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332 r1305 | lh3 | 2010-02-25 13:47:58 -0500 (Thu, 25 Feb 2010) | 3 lines
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333 Changed paths:
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334 M /branches/prog/bwa/bwape.c
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335 M /branches/prog/bwa/bwase.c
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336 M /branches/prog/bwa/bwtaln.c
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337 M /branches/prog/bwa/bwtsw2_main.c
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338 M /branches/prog/bwa/main.c
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339
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340 * bwa-0.5.6-1 (r1304)
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341 * optionally write output to a file (by Tim Fennel)
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342
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343 ------------------------------------------------------------------------
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344 r1303 | lh3 | 2010-02-10 23:43:48 -0500 (Wed, 10 Feb 2010) | 2 lines
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345 Changed paths:
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346 M /branches/prog/bwa/ChangeLog
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347 M /branches/prog/bwa/NEWS
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348 M /branches/prog/bwa/bwa.1
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349 M /branches/prog/bwa/bwtsw2_main.c
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350 M /branches/prog/bwa/main.c
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351
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352 Release bwa-0.5.6
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353
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354 ------------------------------------------------------------------------
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355 r1302 | lh3 | 2010-02-10 11:11:49 -0500 (Wed, 10 Feb 2010) | 3 lines
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356 Changed paths:
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357 M /branches/prog/bwa/ChangeLog
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358 M /branches/prog/bwa/NEWS
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359 M /branches/prog/bwa/bwape.c
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362
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363 * bwa-0.5.5-10 (r1302)
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364 * improve max insert size estimate (method suggested by Gerton Lunter)
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365
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366 ------------------------------------------------------------------------
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367 r1301 | lh3 | 2010-02-09 16:15:28 -0500 (Tue, 09 Feb 2010) | 5 lines
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368 Changed paths:
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369 M /branches/prog/bwa/bwape.c
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370 M /branches/prog/bwa/bwase.c
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372
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373 * bwa-0.5.5-9 (r1301)
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374 * improve mapping quality calculation for abnomalous pairs
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375 * fixed a bug in multiple hits
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376 * SOLiD multiple hits should work now
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377
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378 ------------------------------------------------------------------------
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379 r1300 | lh3 | 2010-02-09 12:50:02 -0500 (Tue, 09 Feb 2010) | 3 lines
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380 Changed paths:
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381 M /branches/prog/bwa/bwape.c
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382 M /branches/prog/bwa/main.c
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383
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384 * bwa-0.5.5-8 (r1300)
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385 * output kurtosis
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386
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388 r1299 | lh3 | 2010-02-09 12:33:34 -0500 (Tue, 09 Feb 2010) | 5 lines
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389 Changed paths:
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390 M /branches/prog/bwa/bwape.c
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391 M /branches/prog/bwa/main.c
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392
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393 * bwa-0.5.5-7 (r1299)
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394 * calculate skewness in sampe
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395 * increase min_len in SW to 20
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396 * perform more SW to fix discordant pairs
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397
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398 ------------------------------------------------------------------------
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399 r1298 | lh3 | 2010-02-08 12:40:31 -0500 (Mon, 08 Feb 2010) | 3 lines
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400 Changed paths:
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408
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409 * bwa-0.5.5-6 (r1297)
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410 * prepare to replace all 16-bit CIGAR (patches by Rodrigo Goya)
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411
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412 ------------------------------------------------------------------------
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413 r1297 | lh3 | 2010-02-05 22:26:11 -0500 (Fri, 05 Feb 2010) | 2 lines
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414 Changed paths:
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415 M /branches/prog/bwa/solid2fastq.pl
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416
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417 the old fix seems not working!
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418
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419 ------------------------------------------------------------------------
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420 r1296 | lh3 | 2010-02-05 21:51:03 -0500 (Fri, 05 Feb 2010) | 3 lines
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421 Changed paths:
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422 M /branches/prog/bwa/bwa.1
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423 M /branches/prog/bwa/bwape.c
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425
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426 * bwa-0.5.5-5 (r1296)
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427 * fixed a minor issue that the lower bound of insert size is not correctly set.
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428
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429 ------------------------------------------------------------------------
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430 r1295 | lh3 | 2010-02-05 21:01:10 -0500 (Fri, 05 Feb 2010) | 5 lines
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431 Changed paths:
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432 M /branches/prog/bwa/bwape.c
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434 M /branches/prog/bwa/bwaseqio.c
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435 M /branches/prog/bwa/main.c
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436
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437 * bwa-0.5.5-4 (r1295)
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438 * fixed a memory leak
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439 * change the behaviour of -n (samse and sampe)
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440 * change the default of -n
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441
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442 ------------------------------------------------------------------------
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443 r1294 | lh3 | 2010-02-05 17:24:06 -0500 (Fri, 05 Feb 2010) | 3 lines
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444 Changed paths:
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445 M /branches/prog/bwa/bwape.c
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450
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451 * bwa-0.5.5-3 (r1294)
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452 * improved multi-hit report
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453
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454 ------------------------------------------------------------------------
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455 r1293 | lh3 | 2010-02-05 12:57:38 -0500 (Fri, 05 Feb 2010) | 5 lines
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456 Changed paths:
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457 M /branches/prog/bwa/bwape.c
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458 M /branches/prog/bwa/bwase.c
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459 M /branches/prog/bwa/cs2nt.c
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460 M /branches/prog/bwa/main.c
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461 M /branches/prog/bwa/solid2fastq.pl
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462
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463 * bwa-0.5.5-2 (r1293)
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464 * bugfix: truncated quality string
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465 * bugfix: quality -1 in solid->fastq conversion
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466 * bugfix: color reads on the reverse strand is not complemented
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467
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468 ------------------------------------------------------------------------
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469 r1279 | lh3 | 2009-11-23 22:42:34 -0500 (Mon, 23 Nov 2009) | 3 lines
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470 Changed paths:
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471 M /branches/prog/bwa/bntseq.c
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472 M /branches/prog/bwa/bntseq.h
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473 M /branches/prog/bwa/bwase.c
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474 A /branches/prog/bwa/bwase.h
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475 M /branches/prog/bwa/bwtaln.c
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476 M /branches/prog/bwa/bwtaln.h
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477 M /branches/prog/bwa/bwtsw2_aux.c
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479
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480 * bwa-0.5.5-1 (r1279)
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481 * incorporate changes from Matt Hanna for Java bindings.
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482
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483 ------------------------------------------------------------------------
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484 r1275 | lh3 | 2009-11-10 22:13:10 -0500 (Tue, 10 Nov 2009) | 2 lines
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485 Changed paths:
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486 M /branches/prog/bwa/ChangeLog
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487
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488 update ChangeLog
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489
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490 ------------------------------------------------------------------------
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491 r1273 | lh3 | 2009-11-10 22:08:16 -0500 (Tue, 10 Nov 2009) | 2 lines
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492 Changed paths:
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493 M /branches/prog/bwa/NEWS
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494 M /branches/prog/bwa/bwa.1
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495 M /branches/prog/bwa/main.c
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496 A /branches/prog/bwa/qualfa2fq.pl
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497
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498 Release bwa-0.5.5 (r1273)
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499
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500 ------------------------------------------------------------------------
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501 r1272 | lh3 | 2009-11-10 22:02:50 -0500 (Tue, 10 Nov 2009) | 3 lines
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502 Changed paths:
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503 M /branches/prog/bwa/bwape.c
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504 M /branches/prog/bwa/main.c
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505
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506 * bwa-0.5.4-3 (r1272)
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507 * fixed another typo which may lead to incorrect single-end mapping quality
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508
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509 ------------------------------------------------------------------------
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510 r1271 | lh3 | 2009-11-10 21:59:47 -0500 (Tue, 10 Nov 2009) | 4 lines
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511 Changed paths:
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512 M /branches/prog/bwa/bwtaln.c
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513 M /branches/prog/bwa/main.c
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514
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515 * bwa-0.5.4-2 (r1271)
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516 * fixed a serious typo/bug which does not hurt if we allow one gap open
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517 and work with <200bp reads, but causes segfault for long reads.
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518
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519 ------------------------------------------------------------------------
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520 r1270 | lh3 | 2009-11-09 23:12:42 -0500 (Mon, 09 Nov 2009) | 3 lines
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521 Changed paths:
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522 M /branches/prog/bwa/cs2nt.c
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523 M /branches/prog/bwa/main.c
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524
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525 * bwa-0.5.4-1 (r1270)
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526 * fixed a bug in color alignment
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527
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528 ------------------------------------------------------------------------
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529 r1245 | lh3 | 2009-10-09 07:42:52 -0400 (Fri, 09 Oct 2009) | 2 lines
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530 Changed paths:
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531 M /branches/prog/bwa/ChangeLog
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532 M /branches/prog/bwa/NEWS
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533 M /branches/prog/bwa/bwa.1
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534 M /branches/prog/bwa/bwape.c
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535 M /branches/prog/bwa/bwase.c
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536 M /branches/prog/bwa/bwaseqio.c
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538
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539 Release bwa-0.5.4
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540
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541 ------------------------------------------------------------------------
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542 r1244 | lh3 | 2009-10-09 05:53:52 -0400 (Fri, 09 Oct 2009) | 5 lines
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543 Changed paths:
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544 M /branches/prog/bwa/ChangeLog
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545 M /branches/prog/bwa/bwape.c
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546 M /branches/prog/bwa/bwase.c
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547 M /branches/prog/bwa/bwaseqio.c
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548 M /branches/prog/bwa/bwtaln.h
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549 M /branches/prog/bwa/main.c
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550 M /branches/prog/bwa/stdaln.c
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551
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552 * bwa-0.5.3-4 (r1244)
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553 * output the clipped length in XC:i: tag
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554 * skip mate alignment when stdaln is buggy
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555 * fixed a bug in NM:i: tag
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556
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557 ------------------------------------------------------------------------
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558 r1243 | lh3 | 2009-10-07 08:15:04 -0400 (Wed, 07 Oct 2009) | 3 lines
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559 Changed paths:
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560 M /branches/prog/bwa/bwape.c
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561 M /branches/prog/bwa/main.c
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562
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563 * bwa-0.5.3-3 (r1243)
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564 * sampe: fixed a bug when a read sequence is identical its reverse complement.
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565
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566 ------------------------------------------------------------------------
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567 r1242 | lh3 | 2009-10-07 07:49:13 -0400 (Wed, 07 Oct 2009) | 4 lines
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568 Changed paths:
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569 M /branches/prog/bwa/bntseq.c
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570 M /branches/prog/bwa/bwape.c
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571 M /branches/prog/bwa/bwtaln.c
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572 M /branches/prog/bwa/bwtaln.h
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573 M /branches/prog/bwa/main.c
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574
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575 * bwa-0.5.3-2 (r1242)
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576 * sampe: optionall preload the full index into memory
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577 * aln: change the default seed length to 32bp
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578
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579 ------------------------------------------------------------------------
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580 r1238 | lh3 | 2009-09-26 18:38:15 -0400 (Sat, 26 Sep 2009) | 2 lines
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581 Changed paths:
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582 M /branches/prog/bwa/khash.h
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583
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584 Improve portability of khash.h
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585
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586 ------------------------------------------------------------------------
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587 r1228 | lh3 | 2009-09-15 09:20:22 -0400 (Tue, 15 Sep 2009) | 2 lines
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588 Changed paths:
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589 M /branches/prog/bwa/main.c
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590
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591 fixed a typo
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592
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593 ------------------------------------------------------------------------
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594 r1227 | lh3 | 2009-09-15 09:19:35 -0400 (Tue, 15 Sep 2009) | 3 lines
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595 Changed paths:
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596 M /branches/prog/bwa/bwtsw2.h
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597 M /branches/prog/bwa/bwtsw2_aux.c
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598 M /branches/prog/bwa/bwtsw2_main.c
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599 M /branches/prog/bwa/main.c
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600
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601 * bwa-0.5.3-1 (r1226)
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602 * in dBWT-SW, optionall use hard clipping instead of soft clipping
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603
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604 ------------------------------------------------------------------------
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605 r1225 | lh3 | 2009-09-15 08:32:30 -0400 (Tue, 15 Sep 2009) | 2 lines
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606 Changed paths:
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607 M /branches/prog/bwa/NEWS
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608 M /branches/prog/bwa/bwase.c
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609 M /branches/prog/bwa/main.c
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610
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611 Release bwa-0.5.3 (r1225)
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612
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613 ------------------------------------------------------------------------
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614 r1223 | lh3 | 2009-09-13 07:30:41 -0400 (Sun, 13 Sep 2009) | 2 lines
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615 Changed paths:
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616 M /branches/prog/bwa/ChangeLog
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617 M /branches/prog/bwa/NEWS
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618 M /branches/prog/bwa/bwa.1
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619 M /branches/prog/bwa/main.c
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620
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621 Release bwa-0.5.2
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622
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623 ------------------------------------------------------------------------
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624 r1222 | lh3 | 2009-09-11 09:11:39 -0400 (Fri, 11 Sep 2009) | 3 lines
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625 Changed paths:
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626 M /branches/prog/bwa/bwtaln.c
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627 M /branches/prog/bwa/main.c
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628
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629 * bwa-0.5.1-5 (r1222)
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630 * fixed a typo. No real change
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631
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632 ------------------------------------------------------------------------
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633 r1221 | lh3 | 2009-09-11 09:09:44 -0400 (Fri, 11 Sep 2009) | 3 lines
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634 Changed paths:
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635 M /branches/prog/bwa/bwa.1
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636 M /branches/prog/bwa/bwape.c
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637 M /branches/prog/bwa/bwase.c
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638 M /branches/prog/bwa/bwaseqio.c
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639 M /branches/prog/bwa/bwtaln.c
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640 M /branches/prog/bwa/bwtaln.h
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641 M /branches/prog/bwa/main.c
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642
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643 * bwa-0.5.1-4 (r1221)
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644 * trim reads before alignment
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645
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646 ------------------------------------------------------------------------
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647 r1216 | lh3 | 2009-09-08 17:50:15 -0400 (Tue, 08 Sep 2009) | 4 lines
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648 Changed paths:
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649 M /branches/prog/bwa/bwape.c
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650 M /branches/prog/bwa/bwase.c
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651 M /branches/prog/bwa/bwtaln.h
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652 M /branches/prog/bwa/main.c
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653
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654 * bwa-0.5.1-3 (r1216)
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655 * fixed a bug about NM tags for gapped alignment
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656 * print SAM header
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657
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658 ------------------------------------------------------------------------
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659 r1215 | lh3 | 2009-09-08 17:14:42 -0400 (Tue, 08 Sep 2009) | 3 lines
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660 Changed paths:
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661 M /branches/prog/bwa/bwtaln.c
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662 M /branches/prog/bwa/main.c
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663
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664 * bwa-0.5.1-2 (r1215)
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665 * fixed a bug when read lengths vary (by John Marshall)
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666
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667 ------------------------------------------------------------------------
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668 r1213 | lh3 | 2009-09-06 18:58:15 -0400 (Sun, 06 Sep 2009) | 3 lines
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669 Changed paths:
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670 M /branches/prog/bwa/bwtsw2_aux.c
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671 M /branches/prog/bwa/main.c
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672
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673 * bwa-0.5.1-1 (r1213)
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674 * change default -T to 30
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675
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676 ------------------------------------------------------------------------
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677 r1209 | lh3 | 2009-09-02 06:06:02 -0400 (Wed, 02 Sep 2009) | 2 lines
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678 Changed paths:
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679 M /branches/prog/bwa/NEWS
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680 M /branches/prog/bwa/bwa.1
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681 M /branches/prog/bwa/main.c
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682
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683 Release bwa-0.5.1
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684
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685 ------------------------------------------------------------------------
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686 r1208 | lh3 | 2009-09-02 05:56:33 -0400 (Wed, 02 Sep 2009) | 2 lines
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687 Changed paths:
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688 M /branches/prog/bwa/ChangeLog
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689
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690 * ChangeLog
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691
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692 ------------------------------------------------------------------------
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693 r1206 | lh3 | 2009-08-30 18:27:30 -0400 (Sun, 30 Aug 2009) | 3 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/main.c
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697
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698 * bwa-0.5.0-6 (r1206)
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699 * fixed two bugs caused by previous modification
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700
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701 ------------------------------------------------------------------------
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702 r1205 | lh3 | 2009-08-30 17:28:36 -0400 (Sun, 30 Aug 2009) | 4 lines
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703 Changed paths:
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704 M /branches/prog/bwa/ChangeLog
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705 M /branches/prog/bwa/bwtsw2_aux.c
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706 M /branches/prog/bwa/main.c
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707
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708 * bwa-0.5.0-4 (r1205)
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709 * reduce false coordinates and CIGAR when a query bridges two reference
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710 sequences, although some very rare cases may fail bwa.
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711
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712 ------------------------------------------------------------------------
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713 r1204 | lh3 | 2009-08-30 06:06:16 -0400 (Sun, 30 Aug 2009) | 3 lines
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714 Changed paths:
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715 M /branches/prog/bwa/bwtsw2_aux.c
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716 M /branches/prog/bwa/bwtsw2_core.c
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717 M /branches/prog/bwa/main.c
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718
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719 * bwa-0.5.0-3 (r1204)
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720 * choose one repetitive hit to extend
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721
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722 ------------------------------------------------------------------------
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723 r1203 | lh3 | 2009-08-29 18:11:51 -0400 (Sat, 29 Aug 2009) | 4 lines
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724 Changed paths:
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725 M /branches/prog/bwa/bwase.c
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726 M /branches/prog/bwa/bwtsw2_aux.c
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727 M /branches/prog/bwa/main.c
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728
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729 * bwa-0.5.0-2 (r1203)
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730 * dBWT-SW: change a parameter in calculating mapping quality
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731 * fixed a bug in samse
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732
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733 ------------------------------------------------------------------------
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734 r1202 | lh3 | 2009-08-28 19:48:41 -0400 (Fri, 28 Aug 2009) | 4 lines
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735 Changed paths:
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736 M /branches/prog/bwa/bwtsw2_aux.c
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737 M /branches/prog/bwa/main.c
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738
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739 * bwa-0.5.0-1 (r1202)
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740 * change default band width to 50
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741 * improve mapping quality a bit
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742
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743 ------------------------------------------------------------------------
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744 r1200 | lh3 | 2009-08-20 06:21:24 -0400 (Thu, 20 Aug 2009) | 2 lines
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745 Changed paths:
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746 M /branches/prog/bwa/NEWS
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747 M /branches/prog/bwa/main.c
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748
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749 Release bwa-0.5.0 (r1200)
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750
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751 ------------------------------------------------------------------------
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752 r1199 | lh3 | 2009-08-20 04:49:15 -0400 (Thu, 20 Aug 2009) | 2 lines
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753 Changed paths:
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754 M /branches/prog/bwa/ChangeLog
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755 M /branches/prog/bwa/bwa.1
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756
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757 Updated ChangeLog and the manual
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758
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759 ------------------------------------------------------------------------
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760 r1198 | lh3 | 2009-08-19 11:09:15 -0400 (Wed, 19 Aug 2009) | 3 lines
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761 Changed paths:
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762 M /branches/prog/bwa/bwtsw2_aux.c
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763 M /branches/prog/bwa/bwtsw2_core.c
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764 M /branches/prog/bwa/main.c
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765
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766 * bwa-0.4.9-36 (r1198)
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767 * simplify duphits removal. The accuracy is changed a tiny bit, sometimes better, sometimes worse.
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768
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769 ------------------------------------------------------------------------
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770 r1197 | lh3 | 2009-08-19 08:15:05 -0400 (Wed, 19 Aug 2009) | 3 lines
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771 Changed paths:
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772 M /branches/prog/bwa/Makefile
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773 M /branches/prog/bwa/bwtsw2_aux.c
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774 A /branches/prog/bwa/bwtsw2_chain.c
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775 M /branches/prog/bwa/main.c
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776
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777 * bwa-0.4.9-35 (r1197)
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778 * further heuristic acceleration for long queries
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779
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780 ------------------------------------------------------------------------
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781 r1196 | lh3 | 2009-08-18 06:54:03 -0400 (Tue, 18 Aug 2009) | 4 lines
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782 Changed paths:
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783 M /branches/prog/bwa/bwa.1
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784 M /branches/prog/bwa/bwtsw2_aux.c
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785 M /branches/prog/bwa/main.c
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786
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787 * bwa-0.4.9-34 (r1196)
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788 * updated the manual page
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789 * output base quality if the input is fastq
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790
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791 ------------------------------------------------------------------------
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792 r1195 | lh3 | 2009-08-18 06:23:00 -0400 (Tue, 18 Aug 2009) | 4 lines
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793 Changed paths:
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794 M /branches/prog/bwa/bwase.c
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795 M /branches/prog/bwa/bwtsw2_main.c
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796 M /branches/prog/bwa/main.c
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797 M /branches/prog/bwa/simple_dp.c
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798
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799 * bwa-0.4.9-33 (r1191)
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800 * fixed a bug in sampe/samse when gaps occur to the 5'-end in SW alignment
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801 * in dbwtsw adjust -T and -c according to -a
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802
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803 ------------------------------------------------------------------------
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804 r1192 | lh3 | 2009-08-13 05:37:28 -0400 (Thu, 13 Aug 2009) | 2 lines
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805 Changed paths:
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806 M /branches/prog/bwa/bwa.1
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807
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808 update manual
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809
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810 ------------------------------------------------------------------------
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811 r1191 | lh3 | 2009-08-12 19:40:51 -0400 (Wed, 12 Aug 2009) | 2 lines
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812 Changed paths:
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813 M /branches/prog/bwa/bwa.1
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814 M /branches/prog/bwa/bwtsw2_main.c
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815
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816 update documentation
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817
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818 ------------------------------------------------------------------------
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819 r1190 | lh3 | 2009-08-12 08:56:10 -0400 (Wed, 12 Aug 2009) | 3 lines
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820 Changed paths:
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821 M /branches/prog/bwa/bwtsw2_main.c
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822 M /branches/prog/bwa/main.c
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823
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824 * bwa-0.4.9-32 (r1190)
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825 * only help messages are changed
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826
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827 ------------------------------------------------------------------------
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828 r1189 | lh3 | 2009-08-11 09:28:55 -0400 (Tue, 11 Aug 2009) | 4 lines
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829 Changed paths:
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830 M /branches/prog/bwa/bwase.c
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831 M /branches/prog/bwa/bwtsw2.h
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832 M /branches/prog/bwa/bwtsw2_aux.c
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833 M /branches/prog/bwa/bwtsw2_core.c
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834 M /branches/prog/bwa/main.c
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835
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836 * bwa-0.4.9-31 (r1189)
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837 * in bwape/bwase, print CIGAR "*" if the read is unmapped
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838 * improved the calculation of mapping quality
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839
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840 ------------------------------------------------------------------------
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841 r1181 | lh3 | 2009-08-03 12:09:41 -0400 (Mon, 03 Aug 2009) | 2 lines
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842 Changed paths:
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843 M /branches/prog/bwa/bwtsw2_aux.c
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844
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845 fflush()
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846
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847 ------------------------------------------------------------------------
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848 r1180 | lh3 | 2009-08-03 12:08:46 -0400 (Mon, 03 Aug 2009) | 4 lines
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849 Changed paths:
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850 M /branches/prog/bwa/bwtsw2_aux.c
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851 M /branches/prog/bwa/main.c
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852
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853 * bwa-0.4.9-30 (r1180)
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854 * fixed a memory problem
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855 * multi-threading sometimes does not work...
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856
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857 ------------------------------------------------------------------------
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858 r1179 | lh3 | 2009-08-03 11:04:39 -0400 (Mon, 03 Aug 2009) | 3 lines
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859 Changed paths:
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860 M /branches/prog/bwa/Makefile
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861 M /branches/prog/bwa/bwtsw2.h
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862 M /branches/prog/bwa/bwtsw2_aux.c
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863 M /branches/prog/bwa/bwtsw2_main.c
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864 M /branches/prog/bwa/main.c
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865
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866 * bwa-0.4.9-29 (r1179)
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867 * preliminary mutli-threading support in dbwtsw
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868
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869 ------------------------------------------------------------------------
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870 r1178 | lh3 | 2009-08-03 09:14:54 -0400 (Mon, 03 Aug 2009) | 3 lines
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871 Changed paths:
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872 M /branches/prog/bwa/bwtsw2_aux.c
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873 M /branches/prog/bwa/bwtsw2_main.c
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874 M /branches/prog/bwa/main.c
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875
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876 * bwa-0.4.9-28 (r1178)
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877 * fixed a bug in printing repetitive hits
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878
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879 ------------------------------------------------------------------------
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880 r1177 | lh3 | 2009-08-03 05:03:42 -0400 (Mon, 03 Aug 2009) | 3 lines
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881 Changed paths:
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882 M /branches/prog/bwa/bwtsw2_core.c
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883 M /branches/prog/bwa/main.c
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884
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885 * bwa-0.4.9-27 (r1177)
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886 * bwtsw2: fixed a hidden memory leak
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887
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888 ------------------------------------------------------------------------
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889 r1176 | lh3 | 2009-07-31 10:58:24 -0400 (Fri, 31 Jul 2009) | 3 lines
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890 Changed paths:
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891 M /branches/prog/bwa/bwtsw2_aux.c
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892 M /branches/prog/bwa/bwtsw2_main.c
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893 M /branches/prog/bwa/main.c
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894
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895 * bwa-0.4.9-26
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896 * change the way mapping quality is calculated
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897
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898 ------------------------------------------------------------------------
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899 r1175 | lh3 | 2009-07-31 09:15:54 -0400 (Fri, 31 Jul 2009) | 4 lines
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900 Changed paths:
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901 M /branches/prog/bwa/bwtsw2.h
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902 M /branches/prog/bwa/bwtsw2_aux.c
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903 M /branches/prog/bwa/bwtsw2_core.c
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904 M /branches/prog/bwa/bwtsw2_main.c
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905 M /branches/prog/bwa/main.c
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906
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907 * bwa-0.4.9-25
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908 * code clean up
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909 * automatically adjust ->t and ->is_rev based on input
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910
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911 ------------------------------------------------------------------------
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912 r1174 | lh3 | 2009-07-30 08:50:25 -0400 (Thu, 30 Jul 2009) | 3 lines
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913 Changed paths:
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914 M /branches/prog/bwa/bwtsw2_aux.c
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915 M /branches/prog/bwa/main.c
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916
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917 * bwa-0.4.9-24
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918 * fixed a bug in printing the hits
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919
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920 ------------------------------------------------------------------------
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921 r1173 | lh3 | 2009-07-29 18:32:43 -0400 (Wed, 29 Jul 2009) | 4 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_main.c
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926 M /branches/prog/bwa/main.c
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927
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928 * bwa-0.4.9-23
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929 * allow to skip reverse alignment
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930 * increase opt->t to 37
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931
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932 ------------------------------------------------------------------------
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933 r1172 | lh3 | 2009-07-29 17:22:39 -0400 (Wed, 29 Jul 2009) | 3 lines
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934 Changed paths:
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935 M /branches/prog/bwa/bwtsw2_aux.c
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936 M /branches/prog/bwa/bwtsw2_main.c
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937 M /branches/prog/bwa/main.c
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938
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939 * bwa-0.4.9-22
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940 * report if the hit is found in both directions
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941
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942 ------------------------------------------------------------------------
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943 r1171 | lh3 | 2009-07-29 17:12:02 -0400 (Wed, 29 Jul 2009) | 3 lines
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944 Changed paths:
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945 M /branches/prog/bwa/bwtsw2.h
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946 M /branches/prog/bwa/bwtsw2_aux.c
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947 M /branches/prog/bwa/bwtsw2_main.c
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948 M /branches/prog/bwa/main.c
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949
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950 * bwa-0.4.9-21
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951 * dbwtsw: map to both forward and reverse BWT to reduce false alignment
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952
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953 ------------------------------------------------------------------------
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954 r1170 | lh3 | 2009-07-29 15:25:14 -0400 (Wed, 29 Jul 2009) | 2 lines
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955 Changed paths:
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956 M /branches/prog/bwa/bwtsw2_core.c
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957 M /branches/prog/bwa/main.c
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958
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959 save hits before cut_tail()
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960
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961 ------------------------------------------------------------------------
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962 r1169 | lh3 | 2009-07-29 08:06:01 -0400 (Wed, 29 Jul 2009) | 3 lines
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963 Changed paths:
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964 M /branches/prog/bwa/bwtsw2.h
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965 M /branches/prog/bwa/bwtsw2_aux.c
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966 M /branches/prog/bwa/bwtsw2_core.c
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967 M /branches/prog/bwa/main.c
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968 M /branches/prog/bwa/stdaln.c
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969 M /branches/prog/bwa/stdaln.h
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970
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971 * bwa-0.4.9-19
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972 * use a global memory pool to reduce the CPU time spent on malloc/free().
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973
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974 ------------------------------------------------------------------------
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975 r1168 | lh3 | 2009-07-29 06:13:29 -0400 (Wed, 29 Jul 2009) | 5 lines
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976 Changed paths:
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977 M /branches/prog/bwa/bwtsw2.h
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978 M /branches/prog/bwa/bwtsw2_aux.c
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979 M /branches/prog/bwa/bwtsw2_core.c
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980 M /branches/prog/bwa/bwtsw2_main.c
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981 M /branches/prog/bwa/main.c
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982
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983 * bwa-0.4.9-18
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984 * reduce unnecessary extension to the 5'-end
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985 * allow to use different interval size for the 2 rounds
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986 * change default parameters
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987
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988 ------------------------------------------------------------------------
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989 r1167 | lh3 | 2009-07-28 19:06:17 -0400 (Tue, 28 Jul 2009) | 3 lines
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990 Changed paths:
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991 M /branches/prog/bwa/bwtsw2_core.c
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992 M /branches/prog/bwa/main.c
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993
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994 * bwa-0.4.9-17
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995 * dbwtsw: fixed THE memory leak.
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996
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997 ------------------------------------------------------------------------
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998 r1166 | lh3 | 2009-07-28 16:31:41 -0400 (Tue, 28 Jul 2009) | 5 lines
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999 Changed paths:
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1000 M /branches/prog/bwa/bwtsw2_aux.c
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1001 M /branches/prog/bwa/bwtsw2_core.c
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1002 M /branches/prog/bwa/bwtsw2_main.c
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1003 M /branches/prog/bwa/main.c
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1004 M /branches/prog/bwa/stdaln.c
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1005
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1006 * bwa-0.4.9-16
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1007 * fixed a memory leak
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1008 * a small memory leak still occurs to bwtsw2_core(). I will work on that later.
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1009 * changed the default parameters
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1010
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1011 ------------------------------------------------------------------------
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1012 r1165 | lh3 | 2009-07-28 10:15:40 -0400 (Tue, 28 Jul 2009) | 4 lines
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1013 Changed paths:
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1014 M /branches/prog/bwa/bwtsw2_aux.c
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1015 M /branches/prog/bwa/bwtsw2_core.c
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1016 M /branches/prog/bwa/main.c
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1017 M /branches/prog/bwa/stdaln.c
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1018
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1019 * bwa-0.4.9-15
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1020 * generate CIGAR right before output. This saves unnecessary computation.
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1021 * this version may be buggy as I have not tested it.
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1022
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1023 ------------------------------------------------------------------------
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1024 r1164 | lh3 | 2009-07-28 09:04:14 -0400 (Tue, 28 Jul 2009) | 11 lines
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1025 Changed paths:
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1026 M /branches/prog/bwa/bwtsw2.h
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1027 M /branches/prog/bwa/bwtsw2_aux.c
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1028 M /branches/prog/bwa/bwtsw2_core.c
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1029 M /branches/prog/bwa/main.c
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1030 M /branches/prog/bwa/stdaln.c
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1031 M /branches/prog/bwa/stdaln.h
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1032
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1033 * bwa-0.4.9-14
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1034
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1035 * deplete unique hits in dbwtsw and postprocess them with standard sw
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1036
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1037 * in principle, this stratgy should be faster and more accurate, but I
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1038 have not tested this point. I may switch back to the old method if
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1039 this does not work.
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1040
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1041 * the code looks quite nasty now. it needs clean up...
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1042
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1043
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1044 ------------------------------------------------------------------------
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1045 r1163 | lh3 | 2009-07-27 17:41:10 -0400 (Mon, 27 Jul 2009) | 2 lines
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1046 Changed paths:
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1047 M /branches/prog/bwa/bwtsw2_aux.c
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1048
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1049 change a default parameter
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1050
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1051 ------------------------------------------------------------------------
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1052 r1162 | lh3 | 2009-07-27 17:04:35 -0400 (Mon, 27 Jul 2009) | 3 lines
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1053 Changed paths:
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1054 M /branches/prog/bwa/bwtsw2.h
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1055 M /branches/prog/bwa/bwtsw2_aux.c
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1056 M /branches/prog/bwa/bwtsw2_core.c
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1057 M /branches/prog/bwa/bwtsw2_main.c
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1058 M /branches/prog/bwa/main.c
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1059
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1060 * bwa-0.4.9-13
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1061 * dbwtsw: switch between small and large Z-best
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1062
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1063 ------------------------------------------------------------------------
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1064 r1161 | lh3 | 2009-07-27 12:17:41 -0400 (Mon, 27 Jul 2009) | 4 lines
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1065 Changed paths:
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1066 M /branches/prog/bwa/bwtsw2_aux.c
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1067 M /branches/prog/bwa/bwtsw2_core.c
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1068 M /branches/prog/bwa/main.c
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1069
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1070 * bwa-0.4.9-12
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1071 * changed the default -z to 100
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1072 * heuristically speed up alignments for polyA reads
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1073
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1074 ------------------------------------------------------------------------
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1075 r1160 | lh3 | 2009-07-27 07:50:57 -0400 (Mon, 27 Jul 2009) | 6 lines
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1076 Changed paths:
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1077 M /branches/prog/bwa/bwtsw2.h
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1078 M /branches/prog/bwa/bwtsw2_aux.c
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1079 M /branches/prog/bwa/bwtsw2_core.c
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1080 M /branches/prog/bwa/main.c
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1081
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1082 * bwa-0.4.9-11
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1083
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1084 * dbwtsw potentially generates less false alignments, although in
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1085 practice, the modification brings no improvement.
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1086
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1087
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1088 ------------------------------------------------------------------------
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1089 r1159 | lh3 | 2009-07-27 04:37:02 -0400 (Mon, 27 Jul 2009) | 4 lines
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1090 Changed paths:
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1091 M /branches/prog/bwa/bwase.c
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1092 M /branches/prog/bwa/bwtsw2_aux.c
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1093 M /branches/prog/bwa/bwtsw2_core.c
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1094 M /branches/prog/bwa/main.c
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1095
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1096 * bwa-0.4.9-10
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1097 * disabled debugging code
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1098 * add "BAM_FMU" if both ends are unmapped
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1099
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1100 ------------------------------------------------------------------------
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1101 r1158 | lh3 | 2009-07-24 09:36:52 -0400 (Fri, 24 Jul 2009) | 2 lines
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1102 Changed paths:
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1103 M /branches/prog/bwa/main.c
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1104
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1105 nothing, really
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1106
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1107 ------------------------------------------------------------------------
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1108 r1157 | lh3 | 2009-07-24 09:05:44 -0400 (Fri, 24 Jul 2009) | 3 lines
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1109 Changed paths:
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1110 M /branches/prog/bwa/bwtsw2_aux.c
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1111 M /branches/prog/bwa/bwtsw2_core.c
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1112 M /branches/prog/bwa/main.c
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1113
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1114 * bwa-0.4.9-9
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1115 * bwtsw2: generate SAM output
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1116
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1117 ------------------------------------------------------------------------
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1118 r1156 | lh3 | 2009-07-24 05:42:47 -0400 (Fri, 24 Jul 2009) | 6 lines
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1119 Changed paths:
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1120 M /branches/prog/bwa/bwape.c
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1121 M /branches/prog/bwa/main.c
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1122
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1123 * bwa-0.4.9-8
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1124
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1125 * fixed a weird deadloop which only happens to icc -O3. Thanks John
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1126 Marshall for the fix.
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1127
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1128
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1129 ------------------------------------------------------------------------
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1130 r1155 | lh3 | 2009-07-24 05:28:40 -0400 (Fri, 24 Jul 2009) | 8 lines
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1131 Changed paths:
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1132 M /branches/prog/bwa/bwtsw2_aux.c
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1133 M /branches/prog/bwa/bwtsw2_core.c
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1134 M /branches/prog/bwa/main.c
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1135
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1136 * bwa-0.4.9-7
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1137
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1138 * fixed a typo in bwtsw2 alignment. Now score from the standard SW
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1139 seems to agree with score from bwtsw2, except that in reporting
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1140 alignments, bwtsw2 may report non-optimal segments. This is expected,
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1141 though. I will improve in future.
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1142
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1143
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1144 ------------------------------------------------------------------------
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1145 r1154 | lh3 | 2009-07-23 17:40:20 -0400 (Thu, 23 Jul 2009) | 3 lines
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1146 Changed paths:
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1147 M /branches/prog/bwa/stdaln.c
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1148 M /branches/prog/bwa/stdaln.h
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1149
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1150 * aln_left_core() seems to work properly
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1151 * aln_local_core() has a bug... AN EVER EXISTING BUG!!!!!!!!!!!
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1152
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1153 ------------------------------------------------------------------------
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1154 r1153 | lh3 | 2009-07-23 17:06:09 -0400 (Thu, 23 Jul 2009) | 2 lines
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1155 Changed paths:
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1156 M /branches/prog/bwa/stdaln.c
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1157
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1158 removed debugging code...
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1159
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1160 ------------------------------------------------------------------------
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1161 r1152 | lh3 | 2009-07-23 17:01:00 -0400 (Thu, 23 Jul 2009) | 3 lines
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1162 Changed paths:
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1163 M /branches/prog/bwa/stdaln.c
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1164
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1165 * radical changes failed...
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1166 * fixed a bug
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1167
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1168 ------------------------------------------------------------------------
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1169 r1151 | lh3 | 2009-07-23 14:46:35 -0400 (Thu, 23 Jul 2009) | 2 lines
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1170 Changed paths:
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1171 M /branches/prog/bwa/stdaln.c
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1172
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1173 temporary changes. Will apply some radical changes to this file...
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1174
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1175 ------------------------------------------------------------------------
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1176 r1150 | lh3 | 2009-07-23 10:09:56 -0400 (Thu, 23 Jul 2009) | 2 lines
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1177 Changed paths:
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1178 M /branches/prog/bwa/bwtsw2_aux.c
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1179 M /branches/prog/bwa/bwtsw2_main.c
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1180 M /branches/prog/bwa/stdaln.c
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1181
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1182 fixed a long-existing bug in Smith-Waterman alignment
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1183
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1184 ------------------------------------------------------------------------
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1185 r1149 | lh3 | 2009-07-23 08:50:52 -0400 (Thu, 23 Jul 2009) | 3 lines
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1186 Changed paths:
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1187 M /branches/prog/bwa/bwtsw2.h
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1188 M /branches/prog/bwa/bwtsw2_aux.c
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1189 M /branches/prog/bwa/bwtsw2_main.c
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1190 M /branches/prog/bwa/main.c
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1191 M /branches/prog/bwa/simple_dp.c
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1192 M /branches/prog/bwa/stdaln.c
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1193 M /branches/prog/bwa/stdaln.h
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1194
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1195 * bwa-0.4.9-6
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1196 * unexplained inconsistency still occurs, but the results largely look reasonable.
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1197
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1198 ------------------------------------------------------------------------
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1199 r1148 | lh3 | 2009-07-23 08:07:29 -0400 (Thu, 23 Jul 2009) | 2 lines
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1200 Changed paths:
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1201 M /branches/prog/bwa/stdaln.c
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1202
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1203 half DP
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1204
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1205 ------------------------------------------------------------------------
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1206 r1147 | lh3 | 2009-07-22 08:03:06 -0400 (Wed, 22 Jul 2009) | 2 lines
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1207 Changed paths:
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1208 M /branches/prog/bwa/bwtsw2.h
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1209 M /branches/prog/bwa/bwtsw2_aux.c
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1210 M /branches/prog/bwa/bwtsw2_core.c
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1211 M /branches/prog/bwa/bwtsw2_main.c
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1212
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1213 a bit code clean up
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1214
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1215 ------------------------------------------------------------------------
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1216 r1145 | lh3 | 2009-07-21 15:52:05 -0400 (Tue, 21 Jul 2009) | 4 lines
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1217 Changed paths:
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1218 M /branches/prog/bwa/bwtsw2_aux.c
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1219 M /branches/prog/bwa/bwtsw2_core.c
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1220 M /branches/prog/bwa/main.c
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1221
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1222 * bwa-0.4.9-5
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1223 * fixed a bug in determining sub-optimal hits
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1224 * removed some debugging codes
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1225
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1226 ------------------------------------------------------------------------
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1227 r1144 | lh3 | 2009-07-21 10:17:29 -0400 (Tue, 21 Jul 2009) | 4 lines
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1228 Changed paths:
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1229 M /branches/prog/bwa/bwtsw2.h
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1230 M /branches/prog/bwa/bwtsw2_aux.c
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1231 M /branches/prog/bwa/bwtsw2_core.c
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1232 M /branches/prog/bwa/bwtsw2_main.c
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1233 M /branches/prog/bwa/main.c
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1234
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1235 * bwa-0.4.9-4
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1236 * better cmd interface
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1237 * faster speed
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1238
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1239 ------------------------------------------------------------------------
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1240 r1143 | lh3 | 2009-07-20 16:38:18 -0400 (Mon, 20 Jul 2009) | 3 lines
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1241 Changed paths:
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1242 M /branches/prog/bwa/bwtsw2.h
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1243 M /branches/prog/bwa/bwtsw2_aux.c
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1244 M /branches/prog/bwa/bwtsw2_core.c
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1245 M /branches/prog/bwa/bwtsw2_main.c
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1246 M /branches/prog/bwa/main.c
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1247
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1248 bwtsw2 (dBWT-SW) is working apparently...
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1249
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1250
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1251 ------------------------------------------------------------------------
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1252 r1139 | lh3 | 2009-07-15 05:52:18 -0400 (Wed, 15 Jul 2009) | 4 lines
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1253 Changed paths:
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1254 M /branches/prog/bwa/bwtsw2_core.c
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1255 M /branches/prog/bwa/main.c
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1256
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1257 * bwa-0.4.9-2
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1258 * bwtsw2: change cut_tail() such that it is faster but more likely to
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1259 miss true hits
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1260
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1261 ------------------------------------------------------------------------
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1262 r1138 | lh3 | 2009-07-15 05:18:42 -0400 (Wed, 15 Jul 2009) | 3 lines
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1263 Changed paths:
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1264 M /branches/prog/bwa/Makefile
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1265 A /branches/prog/bwa/bwt_lite.c
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1266 A /branches/prog/bwa/bwt_lite.h
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1267 A /branches/prog/bwa/bwtsw2.h
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1268 A /branches/prog/bwa/bwtsw2_aux.c
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1269 A /branches/prog/bwa/bwtsw2_core.c
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1270 A /branches/prog/bwa/bwtsw2_main.c
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1271 M /branches/prog/bwa/main.c
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1272 M /branches/prog/bwa/main.h
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1273
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1274 * bwa-0.4.9-1
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1275 * added back bwtsw2
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1276
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1277 ------------------------------------------------------------------------
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1278 r1075 | lh3 | 2009-05-19 05:14:50 -0400 (Tue, 19 May 2009) | 2 lines
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1279 Changed paths:
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1280 M /branches/prog/bwa/NEWS
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1281 M /branches/prog/bwa/bwase.c
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1282 M /branches/prog/bwa/main.c
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1283
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1284 Release bwa-0.4.9
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1285
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1286 ------------------------------------------------------------------------
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1287 r1073 | lh3 | 2009-05-18 17:13:19 -0400 (Mon, 18 May 2009) | 2 lines
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1288 Changed paths:
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1289 M /branches/prog/bwa/NEWS
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1290 M /branches/prog/bwa/bwa.1
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1291 M /branches/prog/bwa/main.c
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1292
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1293 Release bwa-0.4.8
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1294
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1295 ------------------------------------------------------------------------
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1296 r1069 | lh3 | 2009-05-14 09:54:54 -0400 (Thu, 14 May 2009) | 3 lines
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1297 Changed paths:
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1298 M /branches/prog/bwa/bwtaln.c
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1299 M /branches/prog/bwa/main.c
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1300
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1301 * bwa-0.4.7-2
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1302 * change the default of "aln -R" to 30
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1303
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1304 ------------------------------------------------------------------------
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1305 r1068 | lh3 | 2009-05-14 09:27:55 -0400 (Thu, 14 May 2009) | 3 lines
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1306 Changed paths:
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1307 M /branches/prog/bwa/bwape.c
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1308 M /branches/prog/bwa/bwase.c
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1309 M /branches/prog/bwa/bwtaln.c
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1310 M /branches/prog/bwa/bwtaln.h
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1311 M /branches/prog/bwa/bwtgap.c
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1312 M /branches/prog/bwa/main.c
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1313
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1314 * bwa-0.4.7-1
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1315 * search for suboptimal hits if the top hit is not so repetitive
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1316
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1317 ------------------------------------------------------------------------
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1318 r1066 | lh3 | 2009-05-12 15:31:31 -0400 (Tue, 12 May 2009) | 2 lines
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1319 Changed paths:
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1320 M /branches/prog/bwa/ChangeLog
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1321 M /branches/prog/bwa/NEWS
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1322 M /branches/prog/bwa/bwase.c
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1323 M /branches/prog/bwa/main.c
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1324
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1325 Release bwa-0.4.7
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1326
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1327 ------------------------------------------------------------------------
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1328 r1065 | lh3 | 2009-05-12 15:20:40 -0400 (Tue, 12 May 2009) | 3 lines
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1329 Changed paths:
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1330 M /branches/prog/bwa/bwape.c
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1331 M /branches/prog/bwa/bwase.c
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1332 M /branches/prog/bwa/main.c
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1333
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1334 * bwa-0.4.6-9
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1335 * fixed compiling errors on some Linux machines
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1336
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1337 ------------------------------------------------------------------------
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1338 r1064 | lh3 | 2009-05-12 07:30:46 -0400 (Tue, 12 May 2009) | 3 lines
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1339 Changed paths:
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1340 M /branches/prog/bwa/bwtaln.c
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1341 M /branches/prog/bwa/main.c
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1342
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1343 * bwa-0.4.6-8
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1344 * avoid compilation error on some systems.
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1345
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1346 ------------------------------------------------------------------------
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1347 r1035 | lh3 | 2009-05-09 05:41:33 -0400 (Sat, 09 May 2009) | 4 lines
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1348 Changed paths:
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1349 M /branches/prog/bwa/bwape.c
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1350 M /branches/prog/bwa/bwase.c
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1351 M /branches/prog/bwa/main.c
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1352
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1353 * bwa-0.4.6-7
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1354 * fixed an integer overflow caused by previous modifications
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1355 * made insert size estimation more robust
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1356
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1357 ------------------------------------------------------------------------
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1358 r1008 | lh3 | 2009-04-29 05:41:58 -0400 (Wed, 29 Apr 2009) | 4 lines
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1359 Changed paths:
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1360 M /branches/prog/bwa/bwase.c
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1361 M /branches/prog/bwa/main.c
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1362
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1363 * bwa-0.4.6-5
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1364 * fixed a integer overflow problem which may cause seg fault in very rare cases
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1365 * made XN tags more accurate
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1366
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1367 ------------------------------------------------------------------------
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1368 r1005 | lh3 | 2009-04-27 07:37:23 -0400 (Mon, 27 Apr 2009) | 4 lines
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1369 Changed paths:
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1370 M /branches/prog/bwa/bwape.c
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1371 M /branches/prog/bwa/main.c
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1372 M /branches/prog/bwa/simple_dp.c
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1373 M /branches/prog/bwa/stdaln.c
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1374 M /branches/prog/bwa/stdaln.h
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1375
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1376 * bwa-0.4.6-4
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1377 * heuristic rules to detect suboptimal alignment
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1378 * stdsw: support double-strand and protein alignment
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1379
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1380 ------------------------------------------------------------------------
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1381 r1003 | lh3 | 2009-04-26 12:48:19 -0400 (Sun, 26 Apr 2009) | 4 lines
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1382 Changed paths:
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1383 M /branches/prog/bwa/main.c
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1384 M /branches/prog/bwa/simple_dp.c
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1385 M /branches/prog/bwa/stdaln.c
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1386 M /branches/prog/bwa/stdaln.h
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1387
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1388 * bwa-0.4.6-2
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1389 * improve the functionality of stdsw
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1390 * allow to add a threshold on SW alignment. Hope this does not incur new bugs...
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1391
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1392 ------------------------------------------------------------------------
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1393 r1002 | lh3 | 2009-04-22 03:56:15 -0400 (Wed, 22 Apr 2009) | 3 lines
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1394 Changed paths:
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1395 M /branches/prog/bwa/bwa.1
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1396 M /branches/prog/bwa/bwape.c
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1397 M /branches/prog/bwa/bwase.c
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1398 M /branches/prog/bwa/bwtaln.h
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1399 M /branches/prog/bwa/main.c
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1400
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1401 * bwa-0.4.6-1
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1402 * output SM and AM tag
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1403
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1404 ------------------------------------------------------------------------
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1405 r914 | lh3 | 2009-03-09 17:53:50 -0400 (Mon, 09 Mar 2009) | 2 lines
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1406 Changed paths:
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1407 M /branches/prog/bwa/ChangeLog
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1408 M /branches/prog/bwa/NEWS
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1409 M /branches/prog/bwa/main.c
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1410
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1411 Release bwa-0.4.6
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1412
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1413 ------------------------------------------------------------------------
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1414 r913 | lh3 | 2009-03-09 17:23:24 -0400 (Mon, 09 Mar 2009) | 4 lines
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1415 Changed paths:
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1416 M /branches/prog/bwa/bwa.1
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1417 M /branches/prog/bwa/bwape.c
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1418 A /branches/prog/bwa/solid2fastq.pl
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1419
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1420 * added notes to bwa
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1421 * added a script to convert SOLiD reads
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1422 * updated documentations
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1423
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1424 ------------------------------------------------------------------------
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1425 r912 | lh3 | 2009-03-09 16:57:05 -0400 (Mon, 09 Mar 2009) | 2 lines
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1426 Changed paths:
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1427 M /branches/prog/bwa/ChangeLog
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1428 M /branches/prog/bwa/kstring.c
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1429 M /branches/prog/bwa/main.c
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1430
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1431 fixed a bug in kstring
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1432
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1433 ------------------------------------------------------------------------
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1434 r881 | lh3 | 2009-03-02 15:36:06 -0500 (Mon, 02 Mar 2009) | 3 lines
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1435 Changed paths:
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1436 M /branches/prog/bwa/bwtmisc.c
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1437 M /branches/prog/bwa/main.c
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1438
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1439 * bwa-0.4.5-7
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1440 * fixed a bug in pac2cspac
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1441
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1442 ------------------------------------------------------------------------
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1443 r880 | lh3 | 2009-03-01 16:34:08 -0500 (Sun, 01 Mar 2009) | 2 lines
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1444 Changed paths:
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1445 M /branches/prog/bwa/Makefile
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1446
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1447 disable debugging
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1448
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1449 ------------------------------------------------------------------------
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1450 r879 | lh3 | 2009-03-01 16:28:04 -0500 (Sun, 01 Mar 2009) | 3 lines
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1451 Changed paths:
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1452 M /branches/prog/bwa/bwase.c
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1453 M /branches/prog/bwa/cs2nt.c
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1454 M /branches/prog/bwa/main.c
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1455
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1456 * bwa-0.4.5-6
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1457 * fixed problems with coordinates for color gapped alignment
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1458
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1459 ------------------------------------------------------------------------
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1460 r878 | lh3 | 2009-03-01 13:43:09 -0500 (Sun, 01 Mar 2009) | 3 lines
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1461 Changed paths:
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1462 M /branches/prog/bwa/bwase.c
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1463 M /branches/prog/bwa/cs2nt.c
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1464 M /branches/prog/bwa/main.c
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1465
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1466 * bwa-0.4.5-5
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1467 * added support for gapped color alignment
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1468
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1469 ------------------------------------------------------------------------
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1470 r877 | lh3 | 2009-03-01 10:27:52 -0500 (Sun, 01 Mar 2009) | 2 lines
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1471 Changed paths:
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1472 M /branches/prog/bwa/Makefile
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1473 M /branches/prog/bwa/bwape.c
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1474 M /branches/prog/bwa/bwase.c
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1475 M /branches/prog/bwa/bwtaln.h
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1476 M /branches/prog/bwa/cs2nt.c
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1477 M /branches/prog/bwa/main.c
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1478
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1479 * convert cs read to nt read (for ungapped alignment only)
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1480
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1481 ------------------------------------------------------------------------
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1482 r860 | lh3 | 2009-02-27 08:58:39 -0500 (Fri, 27 Feb 2009) | 2 lines
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1483 Changed paths:
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1484 M /branches/prog/bwa/Makefile
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1485 M /branches/prog/bwa/bwase.c
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1486 A /branches/prog/bwa/cs2nt.c
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1487
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1488 prepare to implement cs->nt conversion (have not yet...)
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1489
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1490 ------------------------------------------------------------------------
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1491 r859 | lh3 | 2009-02-27 07:00:03 -0500 (Fri, 27 Feb 2009) | 3 lines
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1492 Changed paths:
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1493 M /branches/prog/bwa/bntseq.c
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1494 M /branches/prog/bwa/bntseq.h
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1495 M /branches/prog/bwa/bwtindex.c
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1496 M /branches/prog/bwa/bwtmisc.c
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1497 M /branches/prog/bwa/main.c
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1498 M /branches/prog/bwa/main.h
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1499
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1500 * bwa-0.4.5-3
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1501 * generate color index from nucleotide fasta reference
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1502
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1503 ------------------------------------------------------------------------
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1504 r857 | lh3 | 2009-02-26 10:22:58 -0500 (Thu, 26 Feb 2009) | 4 lines
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1505 Changed paths:
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1506 M /branches/prog/bwa/bwape.c
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1507 M /branches/prog/bwa/main.c
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1508
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1509 * bwa-0.4.5-2
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1510 * improved mapping quality a bit if one end falls in a tandem repeat
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1511 but the mate is unique.
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1512
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1513 ------------------------------------------------------------------------
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1514 r856 | lh3 | 2009-02-26 10:02:29 -0500 (Thu, 26 Feb 2009) | 3 lines
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1515 Changed paths:
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1516 M /branches/prog/bwa/bwape.c
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1517 M /branches/prog/bwa/bwtaln.h
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1518 M /branches/prog/bwa/main.c
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1519
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1520 * bwa-0.4.5-1
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1521 * make bwa work for SOLiD reads
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1522
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1523 ------------------------------------------------------------------------
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1524 r828 | lh3 | 2009-02-18 17:36:41 -0500 (Wed, 18 Feb 2009) | 2 lines
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1525 Changed paths:
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1526 M /branches/prog/bwa/ChangeLog
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1527 M /branches/prog/bwa/NEWS
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1528 M /branches/prog/bwa/bwa.1
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1529 M /branches/prog/bwa/main.c
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1530
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1531 Release bwa-0.4.5
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1532
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1533 ------------------------------------------------------------------------
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1534 r827 | lh3 | 2009-02-18 16:48:48 -0500 (Wed, 18 Feb 2009) | 3 lines
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1535 Changed paths:
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1536 M /branches/prog/bwa/main.c
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1537 M /branches/prog/bwa/stdaln.c
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1538 M /branches/prog/bwa/stdaln.h
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1539
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1540 * bwa-0.4.4-6
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1541 * fixed a bug in SW alignment when no residue matches
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1542
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1543 ------------------------------------------------------------------------
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1544 r824 | lh3 | 2009-02-17 05:33:07 -0500 (Tue, 17 Feb 2009) | 3 lines
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1545 Changed paths:
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1546 M /branches/prog/bwa/bwape.c
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1547 M /branches/prog/bwa/main.c
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1548
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1549 * bwa-0.4.4-5
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1550 * fixed that bounary bug
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1551
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1552 ------------------------------------------------------------------------
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1553 r823 | lh3 | 2009-02-17 04:54:18 -0500 (Tue, 17 Feb 2009) | 2 lines
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1554 Changed paths:
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1555 M /branches/prog/bwa/ChangeLog
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1556 M /branches/prog/bwa/bwape.c
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1557
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1558 just change some logging information
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1559
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1560 ------------------------------------------------------------------------
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1561 r822 | lh3 | 2009-02-17 04:20:39 -0500 (Tue, 17 Feb 2009) | 2 lines
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1562 Changed paths:
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1563 M /branches/prog/bwa/bwa.1
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1564
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1565 update manual
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1566
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1567 ------------------------------------------------------------------------
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1568 r821 | lh3 | 2009-02-17 04:11:14 -0500 (Tue, 17 Feb 2009) | 3 lines
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1569 Changed paths:
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1570 M /branches/prog/bwa/bwape.c
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1571 M /branches/prog/bwa/bwase.c
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1572 M /branches/prog/bwa/main.c
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1573
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1574 * bwa-0.4.4-4
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1575 * fixed a bug on boundary check in pair_sw
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1576
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1577 ------------------------------------------------------------------------
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1578 r820 | lh3 | 2009-02-16 17:43:37 -0500 (Mon, 16 Feb 2009) | 3 lines
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1579 Changed paths:
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1580 M /branches/prog/bwa/bwtaln.c
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1581 M /branches/prog/bwa/main.c
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1582
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1583 * bwa-0.4.4-3
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1584 * allow to change mismatch penalty
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1585
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1586 ------------------------------------------------------------------------
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1587 r819 | lh3 | 2009-02-16 17:40:28 -0500 (Mon, 16 Feb 2009) | 4 lines
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1588 Changed paths:
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1589 M /branches/prog/bwa/bwtaln.c
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1590 M /branches/prog/bwa/main.c
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1591
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1592 * bwa-0.4.4-2
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1593 * remove timer
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1594 * allow to change default gapo and gape penalty at the command line
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1595
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1596 ------------------------------------------------------------------------
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1597 r818 | lh3 | 2009-02-16 09:30:51 -0500 (Mon, 16 Feb 2009) | 2 lines
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1598 Changed paths:
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1599 M /branches/prog/bwa/bwa.1
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1600
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1601 update benchmark
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1602
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1603 ------------------------------------------------------------------------
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1604 r817 | lh3 | 2009-02-16 08:44:40 -0500 (Mon, 16 Feb 2009) | 4 lines
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1605 Changed paths:
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1606 M /branches/prog/bwa/bwape.c
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1607 M /branches/prog/bwa/bwtaln.c
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1608 M /branches/prog/bwa/kvec.h
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1610
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1611 * bwa-0.4.4-1
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1612 * automatically detect insert size
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1613 * use insert size in pairing. This may potentially improve accuracy (untested!)
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1614
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1615 ------------------------------------------------------------------------
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1616 r814 | lh3 | 2009-02-15 11:10:23 -0500 (Sun, 15 Feb 2009) | 2 lines
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1617 Changed paths:
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1618 M /branches/prog/bwa/ChangeLog
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1619 M /branches/prog/bwa/NEWS
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1620 M /branches/prog/bwa/main.c
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1621
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1622 Release bwa-0.4.4
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1623
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1624 ------------------------------------------------------------------------
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1625 r813 | lh3 | 2009-02-15 10:22:50 -0500 (Sun, 15 Feb 2009) | 3 lines
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1626 Changed paths:
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1627 M /branches/prog/bwa/bwa.1
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1628 M /branches/prog/bwa/bwase.c
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1629 M /branches/prog/bwa/main.c
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1630
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1631 * bwa-0.4.3-5
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1632 * impose boundary check in refine_gapped
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1633
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1634 ------------------------------------------------------------------------
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1635 r811 | lh3 | 2009-02-14 09:46:13 -0500 (Sat, 14 Feb 2009) | 3 lines
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1636 Changed paths:
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1637 M /branches/prog/bwa/bwase.c
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1638 M /branches/prog/bwa/main.c
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1639
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1640 * bwa-0.4.3-4
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1641 * change MD tag to match the latest SAM specification
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1642
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1643 ------------------------------------------------------------------------
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1644 r810 | lh3 | 2009-02-13 04:46:04 -0500 (Fri, 13 Feb 2009) | 2 lines
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1645 Changed paths:
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1646 M /branches/prog/bwa/ChangeLog
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1647
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1648 update ChangeLog
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1649
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1650 ------------------------------------------------------------------------
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1651 r799 | lh3 | 2009-02-05 12:01:17 -0500 (Thu, 05 Feb 2009) | 2 lines
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1652 Changed paths:
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1653 M /branches/prog/bwa/bwase.c
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1654 M /branches/prog/bwa/main.c
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1655
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1656 change MD tag to meet the latest SAM specification
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1657
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1658 ------------------------------------------------------------------------
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1659 r796 | lh3 | 2009-02-05 08:35:13 -0500 (Thu, 05 Feb 2009) | 3 lines
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1660 Changed paths:
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1661 M /branches/prog/bwa/bntseq.c
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1662 M /branches/prog/bwa/bwase.c
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1663 M /branches/prog/bwa/main.c
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1664
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1665 * bwa-0.4.3-2
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1666 * fixed a bug on counting 'N'
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1667
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1668 ------------------------------------------------------------------------
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1669 r795 | lh3 | 2009-02-05 07:41:27 -0500 (Thu, 05 Feb 2009) | 4 lines
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1670 Changed paths:
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1671 M /branches/prog/bwa/bwa.1
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1672 M /branches/prog/bwa/bwape.c
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1673 M /branches/prog/bwa/main.c
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1674
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1675 * bwa-0.4.3-1
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1676 * fixed potential boundary problems
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1677 * update benchmark result
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1678
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1679 ------------------------------------------------------------------------
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1680 r791 | lh3 | 2009-01-25 05:20:47 -0500 (Sun, 25 Jan 2009) | 2 lines
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1681 Changed paths:
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1682 M /branches/prog/bwa/bwa.1
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1683
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1684 update some numbers
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1685
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1686 ------------------------------------------------------------------------
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1687 r790 | lh3 | 2009-01-24 15:13:03 -0500 (Sat, 24 Jan 2009) | 2 lines
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1688 Changed paths:
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1689 M /branches/prog/bwa/bwa.1
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1690
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1691 update benchmark
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1692
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1693 ------------------------------------------------------------------------
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1694 r789 | lh3 | 2009-01-22 10:18:44 -0500 (Thu, 22 Jan 2009) | 2 lines
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1695 Changed paths:
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1696 M /branches/prog/bwa/bwtindex.c
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1697
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1698 a warning message for index
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1699
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1700 ------------------------------------------------------------------------
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1701 r788 | lh3 | 2009-01-22 09:54:06 -0500 (Thu, 22 Jan 2009) | 2 lines
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1703 M /branches/prog/bwa/main.c
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1704
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1705 forget to change release number
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1706
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1707 ------------------------------------------------------------------------
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1708 r786 | lh3 | 2009-01-22 06:27:39 -0500 (Thu, 22 Jan 2009) | 2 lines
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1709 Changed paths:
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1710 M /branches/prog/bwa/NEWS
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1711
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1712 Release bwa-0.4.3
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1713
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1714 ------------------------------------------------------------------------
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1715 r785 | lh3 | 2009-01-22 06:27:16 -0500 (Thu, 22 Jan 2009) | 2 lines
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1716 Changed paths:
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1717 M /branches/prog/bwa/ChangeLog
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1718 M /branches/prog/bwa/NEWS
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1719
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1720 Release bwa-0.4.3
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1721
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1722 ------------------------------------------------------------------------
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1723 r784 | lh3 | 2009-01-22 06:19:59 -0500 (Thu, 22 Jan 2009) | 4 lines
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1724 Changed paths:
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1725 M /branches/prog/bwa/bwa.1
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1726 M /branches/prog/bwa/bwase.c
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1727 M /branches/prog/bwa/main.c
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1728
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1729 * bwa-0.4.2-10
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1730 * update documentation
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1731 * fixed a bug on generating MD tags for SW alignment
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1732
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1733 ------------------------------------------------------------------------
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1734 r782 | lh3 | 2009-01-19 12:08:38 -0500 (Mon, 19 Jan 2009) | 3 lines
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1735 Changed paths:
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1736 M /branches/prog/bwa/bwase.c
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1737 M /branches/prog/bwa/main.c
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1738
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1739 * bwa-0.4.2-9
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1740 * fixed a bug in samse -n...
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1741
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1742 ------------------------------------------------------------------------
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1743 r781 | lh3 | 2009-01-19 11:26:37 -0500 (Mon, 19 Jan 2009) | 3 lines
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1744 Changed paths:
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1745 M /branches/prog/bwa/bwtaln.c
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1746 M /branches/prog/bwa/main.c
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1747
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1748 * bwa-0.4.2-8
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1749 * given -N, the previous version would stop if the top hit is a repeat. Now changed.
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1750
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1751 ------------------------------------------------------------------------
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1752 r780 | lh3 | 2009-01-19 11:20:18 -0500 (Mon, 19 Jan 2009) | 4 lines
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1753 Changed paths:
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1754 M /branches/prog/bwa/bwape.c
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1755 M /branches/prog/bwa/bwase.c
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1756 M /branches/prog/bwa/bwtaln.c
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1757 M /branches/prog/bwa/bwtaln.h
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1758 M /branches/prog/bwa/bwtgap.c
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1759 M /branches/prog/bwa/main.c
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1760
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1761 * bwa-0.4.2-7
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1762 * use a bit-wise flag to replace some member variables in the option struct
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1763 * allow to switch off the iterative strategy
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1764
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1765 ------------------------------------------------------------------------
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1766 r779 | lh3 | 2009-01-19 10:45:57 -0500 (Mon, 19 Jan 2009) | 3 lines
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1767 Changed paths:
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1768 M /branches/prog/bwa/bwa.1
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1769 M /branches/prog/bwa/bwase.c
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1770 M /branches/prog/bwa/main.c
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1771
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1772 * bwa-0.4.2-6
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1773 * allow to dump multiple hits from samse, in another format, though
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1774
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1775 ------------------------------------------------------------------------
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1776 r778 | lh3 | 2009-01-19 06:24:29 -0500 (Mon, 19 Jan 2009) | 5 lines
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1777 Changed paths:
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1778 M /branches/prog/bwa/Makefile
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1779 M /branches/prog/bwa/bwape.c
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1780 M /branches/prog/bwa/bwase.c
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1781 M /branches/prog/bwa/bwaseqio.c
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1782 M /branches/prog/bwa/bwtaln.h
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1783 M /branches/prog/bwa/kseq.h
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1784 A /branches/prog/bwa/kstring.c
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1785 A /branches/prog/bwa/kstring.h
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1786 M /branches/prog/bwa/main.c
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1787 M /branches/prog/bwa/simple_dp.c
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1788
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1789 * bwa-0.4.2-5
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1790 * update kseq.h to the latest version
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1791 * generate MD tag
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1792 * print mate coordinate if only one end is unmapped
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1793
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1794 ------------------------------------------------------------------------
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1795 r775 | lh3 | 2009-01-18 05:40:35 -0500 (Sun, 18 Jan 2009) | 3 lines
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1796 Changed paths:
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1797 M /branches/prog/bwa/bwase.c
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1798 M /branches/prog/bwa/main.c
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1799
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1800 * bwa-0.4.2-4
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1801 * fixed a bug for SAM format
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1802
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1803 ------------------------------------------------------------------------
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1804 r774 | lh3 | 2009-01-17 13:48:52 -0500 (Sat, 17 Jan 2009) | 4 lines
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1805 Changed paths:
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1806 M /branches/prog/bwa/bwtaln.c
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1807 M /branches/prog/bwa/main.c
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1808
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1809 * bwa-0.4.2-3
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1810 * change default fnr to 0.04
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1811 * print max_diff for valid fnr
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1812
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1813 ------------------------------------------------------------------------
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1814 r773 | lh3 | 2009-01-17 05:54:37 -0500 (Sat, 17 Jan 2009) | 3 lines
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1815 Changed paths:
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1816 M /branches/prog/bwa/bwape.c
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1817 M /branches/prog/bwa/bwase.c
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1818 M /branches/prog/bwa/bwtaln.c
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1819 M /branches/prog/bwa/bwtaln.h
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1820 M /branches/prog/bwa/main.c
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1821
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1822 * bwa-0.4.2-2
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1823 * automatically choose max_diff
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1824
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1825 ------------------------------------------------------------------------
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1826 r772 | lh3 | 2009-01-16 18:16:14 -0500 (Fri, 16 Jan 2009) | 3 lines
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1827 Changed paths:
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1828 M /branches/prog/bwa/bwaseqio.c
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1829 M /branches/prog/bwa/bwt.c
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1830 M /branches/prog/bwa/bwtaln.c
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1831 M /branches/prog/bwa/bwtaln.h
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1832 M /branches/prog/bwa/bwtgap.c
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1833 M /branches/prog/bwa/main.c
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1834
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1835 * bwa-0.4.2-1
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1836 * take N as a mismatch
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1837
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1838 ------------------------------------------------------------------------
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1839 r768 | lh3 | 2009-01-09 11:57:23 -0500 (Fri, 09 Jan 2009) | 2 lines
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1840 Changed paths:
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1841 M /branches/prog/bwa/ChangeLog
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1842 M /branches/prog/bwa/NEWS
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1843 M /branches/prog/bwa/bntseq.c
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1844 M /branches/prog/bwa/main.c
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1845
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1846 Release bwa-0.4.2
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1847
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1848 ------------------------------------------------------------------------
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1849 r759 | lh3 | 2009-01-07 09:55:43 -0500 (Wed, 07 Jan 2009) | 2 lines
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1850 Changed paths:
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1851 M /branches/prog/bwa/ChangeLog
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1852 M /branches/prog/bwa/NEWS
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1853 M /branches/prog/bwa/bwa.1
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1854 M /branches/prog/bwa/bwape.c
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1855 M /branches/prog/bwa/bwtaln.h
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1856 M /branches/prog/bwa/main.c
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1857
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1858 Release bwa-0.4.1
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1859
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1860 ------------------------------------------------------------------------
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1861 r758 | lh3 | 2009-01-07 05:36:06 -0500 (Wed, 07 Jan 2009) | 3 lines
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1862 Changed paths:
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1863 M /branches/prog/bwa/bwape.c
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1864 M /branches/prog/bwa/bwase.c
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1865 M /branches/prog/bwa/bwtaln.h
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1866 M /branches/prog/bwa/main.c
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1867
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1868 * bwa-0.4.0-2
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1869 * make mate_sw fully working
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1870
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1871 ------------------------------------------------------------------------
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1872 r757 | lh3 | 2009-01-06 18:04:29 -0500 (Tue, 06 Jan 2009) | 5 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.h
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1878 M /branches/prog/bwa/main.c
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1879
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1880 * bwa-0.4.0-1
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1881 * do SW alignment for unmapped mate. It is working.
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1882 * I still need to do some extra work for SW alignment, but it is too late
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1883 and I am getting tired... I will do tomorrow.
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1884
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1885 ------------------------------------------------------------------------
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1886 r755 | lh3 | 2009-01-06 10:23:29 -0500 (Tue, 06 Jan 2009) | 2 lines
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1887 Changed paths:
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1888 M /branches/prog/bwa/ChangeLog
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1889 M /branches/prog/bwa/NEWS
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1890 M /branches/prog/bwa/bwa.1
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1891 M /branches/prog/bwa/main.c
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1892
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1893 Release bwa-0.4.0
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1894
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1895 ------------------------------------------------------------------------
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1896 r754 | lh3 | 2009-01-06 07:45:02 -0500 (Tue, 06 Jan 2009) | 3 lines
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1897 Changed paths:
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1898 M /branches/prog/bwa/bwtaln.c
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1899 M /branches/prog/bwa/bwtgap.c
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1900 M /branches/prog/bwa/bwtgap.h
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1901 M /branches/prog/bwa/main.c
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1902
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1903 * bwa-0.3.0-12
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1904 * better lock
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1905
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1906 ------------------------------------------------------------------------
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1907 r753 | lh3 | 2009-01-06 06:17:21 -0500 (Tue, 06 Jan 2009) | 5 lines
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1908 Changed paths:
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1909 M /branches/prog/bwa/Makefile
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1910 M /branches/prog/bwa/bwaseqio.c
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1911 M /branches/prog/bwa/bwtaln.c
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1912 M /branches/prog/bwa/bwtaln.h
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1913 M /branches/prog/bwa/bwtgap.c
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1914 M /branches/prog/bwa/main.c
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1915
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1916 * bwa-0.3.0-11
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1917 * fixed a small memory leak in bwa_seq_close()
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1918 * fixed "uninitialized memory" from bwt_aln1_t
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1919 * multithreading for "aln" command
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1920
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1921 ------------------------------------------------------------------------
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1922 r752 | lh3 | 2009-01-05 17:34:13 -0500 (Mon, 05 Jan 2009) | 3 lines
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1923 Changed paths:
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1924 M /branches/prog/bwa/Makefile
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1925 D /branches/prog/bwa/bwt2fmv.c
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1926 M /branches/prog/bwa/bwt_gen/bwt_gen.c
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1927 A /branches/prog/bwa/bwtmisc.c (from /branches/prog/bwa/pac2bwt.c:748)
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1928 M /branches/prog/bwa/main.c
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1929 M /branches/prog/bwa/main.h
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1930 D /branches/prog/bwa/pac2bwt.c
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1931
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1932 * bwa-0.3.0-10
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1933 * a little bit code clean up
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1934
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1935 ------------------------------------------------------------------------
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1936 r751 | lh3 | 2009-01-05 17:19:04 -0500 (Mon, 05 Jan 2009) | 3 lines
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1937 Changed paths:
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1938 M /branches/prog/bwa/bwt.c
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1939 M /branches/prog/bwa/main.c
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1940
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1941 * bwa-0.3.0-9
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1942 * use 64-bit integer to speed up Occ calculate, although just a little bit
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1943
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1944 ------------------------------------------------------------------------
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1945 r750 | lh3 | 2009-01-05 16:44:26 -0500 (Mon, 05 Jan 2009) | 3 lines
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1946 Changed paths:
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1947 M /branches/prog/bwa/bwt.c
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1948 M /branches/prog/bwa/main.c
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1949
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1950 * bwa-0.3.0-8
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1951 * a little bit code cleanup
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1952
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1953 ------------------------------------------------------------------------
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1954 r749 | lh3 | 2009-01-05 16:37:28 -0500 (Mon, 05 Jan 2009) | 3 lines
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1955 Changed paths:
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1956 M /branches/prog/bwa/bwt.c
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1957 M /branches/prog/bwa/main.c
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1958
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1959 * bwa-0.1.0-7
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1960 * accelerate Occ calculation
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1961
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1962 ------------------------------------------------------------------------
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1963 r748 | lh3 | 2009-01-05 16:12:28 -0500 (Mon, 05 Jan 2009) | 4 lines
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1964 Changed paths:
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1965 M /branches/prog/bwa/bwape.c
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1966 M /branches/prog/bwa/bwase.c
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1967 M /branches/prog/bwa/bwt.c
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1968 M /branches/prog/bwa/bwt.h
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1969 M /branches/prog/bwa/bwt2fmv.c
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1970 M /branches/prog/bwa/bwtaln.c
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1971 M /branches/prog/bwa/bwtindex.c
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1972 M /branches/prog/bwa/bwtio.c
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1973 M /branches/prog/bwa/main.c
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1974 M /branches/prog/bwa/main.h
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1975 M /branches/prog/bwa/pac2bwt.c
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1976
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1977 * bwa-0.3.0-6
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1978 * put occ table along with bwt to save another cache miss
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1979 * this version is already faster than the previous and I can still improve it...
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1980
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1981 ------------------------------------------------------------------------
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1982 r747 | lh3 | 2009-01-05 10:16:18 -0500 (Mon, 05 Jan 2009) | 5 lines
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1983 Changed paths:
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1984 M /branches/prog/bwa/bwt.c
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1985 M /branches/prog/bwa/bwt.h
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1986 M /branches/prog/bwa/bwtio.c
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1987 M /branches/prog/bwa/main.c
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1988
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1989 * bwa-0.3.0-5
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1990 * remove occ_major to save a cache miss; however, OCC_INTERVAL has to be
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1991 increased to keep the same memory. As a result, the speed is a little
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1992 slower in fact.
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1993
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1994 ------------------------------------------------------------------------
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1995 r746 | lh3 | 2009-01-05 09:50:53 -0500 (Mon, 05 Jan 2009) | 3 lines
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1996 Changed paths:
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1997 M /branches/prog/bwa/bwt.c
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1998 M /branches/prog/bwa/main.c
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1999
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2000 * bwa-0.3.0-4
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2001 * added back optimization codes (it is a pain...)
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2002
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2003 ------------------------------------------------------------------------
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2004 r745 | lh3 | 2009-01-05 08:23:00 -0500 (Mon, 05 Jan 2009) | 3 lines
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2005 Changed paths:
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2006 M /branches/prog/bwa/bwt.c
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2007 M /branches/prog/bwa/bwtaln.c
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2008 M /branches/prog/bwa/main.c
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2009
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2010 * bwa-0.3.0-3
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2011 * faster bit operations
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2012
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2013 ------------------------------------------------------------------------
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2014 r744 | lh3 | 2009-01-05 05:58:46 -0500 (Mon, 05 Jan 2009) | 4 lines
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2015 Changed paths:
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2016 M /branches/prog/bwa/bwt.c
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2017 M /branches/prog/bwa/main.c
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2018
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2019 * bwa-0.3.0-2
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2020 * removed optimization codes again...
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2021 * use a new method to count the bits
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2022
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2023 ------------------------------------------------------------------------
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2024 r743 | lh3 | 2009-01-04 17:18:38 -0500 (Sun, 04 Jan 2009) | 5 lines
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2025 Changed paths:
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2026 M /branches/prog/bwa/bwa.1
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2027 M /branches/prog/bwa/bwt.c
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2028 M /branches/prog/bwa/bwtaln.c
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2029 M /branches/prog/bwa/bwtaln.h
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2030 M /branches/prog/bwa/bwtgap.c
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2031 M /branches/prog/bwa/main.c
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2032
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2033 * bwa-0.3.0-1
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2034 * added back the optimization codes
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2035 * added a new option to aln: max_entries, although this is disabled by default
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2036 * updated benchmark
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2037
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2038 ------------------------------------------------------------------------
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2039 r742 | lh3 | 2009-01-04 07:56:12 -0500 (Sun, 04 Jan 2009) | 2 lines
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2040 Changed paths:
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2041 M /branches/prog/bwa/bwa.1
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2042
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2043 add URL
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2044
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2045 ------------------------------------------------------------------------
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2046 r740 | lh3 | 2009-01-04 07:39:43 -0500 (Sun, 04 Jan 2009) | 2 lines
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2047 Changed paths:
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2048 M /branches/prog/bwa/ChangeLog
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2049 M /branches/prog/bwa/NEWS
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2050 M /branches/prog/bwa/bwa.1
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2051 M /branches/prog/bwa/main.c
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2052
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2053 Release bwa-0.3.0
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2054
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2055 ------------------------------------------------------------------------
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2056 r739 | lh3 | 2009-01-04 06:55:06 -0500 (Sun, 04 Jan 2009) | 2 lines
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2057 Changed paths:
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2058 A /branches/prog/bwa/COPYING
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2059 M /branches/prog/bwa/ChangeLog
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2060 M /branches/prog/bwa/bntseq.c
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2061 M /branches/prog/bwa/bntseq.h
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2062 M /branches/prog/bwa/bwa.1
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2063 M /branches/prog/bwa/bwt.c
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2064 M /branches/prog/bwa/bwt.h
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2065 M /branches/prog/bwa/bwtindex.c
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2066 M /branches/prog/bwa/utils.c
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2067 M /branches/prog/bwa/utils.h
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2068
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2069 added licensing information
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2070
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2071 ------------------------------------------------------------------------
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2072 r738 | lh3 | 2009-01-04 06:18:25 -0500 (Sun, 04 Jan 2009) | 4 lines
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2073 Changed paths:
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2074 M /branches/prog/bwa/bwa.1
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2075 M /branches/prog/bwa/bwape.c
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2076 M /branches/prog/bwa/main.c
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2077
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2078 * bwa-0.2.0-31
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2079 * better mapping quality
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2080 * update benchmark
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2081
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2082 ------------------------------------------------------------------------
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2083 r737 | lh3 | 2009-01-03 16:00:58 -0500 (Sat, 03 Jan 2009) | 2 lines
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2084 Changed paths:
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2085 M /branches/prog/bwa/ChangeLog
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2086 M /branches/prog/bwa/bwa.1
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2087
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2088 update documentation
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2089
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2090 ------------------------------------------------------------------------
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2091 r736 | lh3 | 2009-01-02 10:26:38 -0500 (Fri, 02 Jan 2009) | 2 lines
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2092 Changed paths:
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2093 M /branches/prog/bwa/bwa.1
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2094
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2095 update documentation
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2096
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2097 ------------------------------------------------------------------------
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2098 r735 | lh3 | 2009-01-02 07:10:20 -0500 (Fri, 02 Jan 2009) | 4 lines
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2099 Changed paths:
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2100 M /branches/prog/bwa/bwa.1
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2101 M /branches/prog/bwa/bwape.c
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2102 M /branches/prog/bwa/bwtaln.c
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2103 M /branches/prog/bwa/main.c
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2104
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2105 * bwa-0.2.0-30
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2106 * reduce memory a little bit
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2107 * update documentation
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2108
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2109 ------------------------------------------------------------------------
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2110 r734 | lh3 | 2009-01-01 13:45:45 -0500 (Thu, 01 Jan 2009) | 8 lines
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2111 Changed paths:
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2112 M /branches/prog/bwa/bwa.1
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2113 M /branches/prog/bwa/bwape.c
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2114 M /branches/prog/bwa/bwase.c
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2115 M /branches/prog/bwa/bwtaln.c
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2116 M /branches/prog/bwa/bwtaln.h
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2117 M /branches/prog/bwa/bwtgap.c
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2118 M /branches/prog/bwa/main.c
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2119
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2120 * bwa-0.2.0-29
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2121 * sampe: removed -O option; changed default -o to 100000
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2122 * sampe: fixed a bug in calculating paired mapping quality
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2123 * aln: added an option to search for suboptimal hits even if the best is a repeat.
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2124 This option will make sampe MUCH SLOWER.
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2125 * sampe: set isize as zero if mapped to two different chr
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2126 * update manual (unfinished)
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2127
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2128 ------------------------------------------------------------------------
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2129 r733 | lh3 | 2009-01-01 11:01:20 -0500 (Thu, 01 Jan 2009) | 3 lines
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2130 Changed paths:
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2131 M /branches/prog/bwa/bwape.c
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2132 M /branches/prog/bwa/main.c
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2133
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2134 * bwa-0.2.0-28
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2135 * fixed a bug in calculating paired mapping quality
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2136
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2137 ------------------------------------------------------------------------
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2138 r732 | lh3 | 2009-01-01 09:27:46 -0500 (Thu, 01 Jan 2009) | 3 lines
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2139 Changed paths:
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2140 M /branches/prog/bwa/bwape.c
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2141 A /branches/prog/bwa/khash.h (from /branches/prog/sclib/khash/khash.h:675)
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2142 M /branches/prog/bwa/main.c
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2143
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2144 * bwa-0.2.0-27
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2145 * accelerate sampe by storing visited large intervals
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2146
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2147 ------------------------------------------------------------------------
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2148 r731 | lh3 | 2009-01-01 06:51:21 -0500 (Thu, 01 Jan 2009) | 3 lines
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2149 Changed paths:
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2150 M /branches/prog/bwa/bwt.c
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2151 M /branches/prog/bwa/main.c
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2152
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2153 * bwa-0.2.0-26
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2154 * remove the optimation codes
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2155
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2156 ------------------------------------------------------------------------
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2157 r730 | lh3 | 2009-01-01 06:48:59 -0500 (Thu, 01 Jan 2009) | 4 lines
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2158 Changed paths:
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2159 M /branches/prog/bwa/bwt.c
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2160 M /branches/prog/bwa/main.c
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2161
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2162 * bwa-0.2.0-25
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2163 * accelerate OCC calculation by ~7%. However, it seems not worth doing
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2164 this by complicate the codes. I will change back later.
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2165
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2166 ------------------------------------------------------------------------
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2167 r729 | lh3 | 2008-12-31 16:43:56 -0500 (Wed, 31 Dec 2008) | 6 lines
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2168 Changed paths:
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2169 M /branches/prog/bwa/bntseq.c
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2170 M /branches/prog/bwa/bwape.c
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2171 M /branches/prog/bwa/bwase.c
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2172 M /branches/prog/bwa/main.c
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2173
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2174 * bwa-0.2.0-24
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2175 * change command "sai2sam_pe" to "sampe"
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2176 * print usage for sampe command
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2177 * in sampe: change default max_occ to 1000
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2178 * fixed a few compiling warnings in bntseq.c
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2179
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2180 ------------------------------------------------------------------------
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2181 r728 | lh3 | 2008-12-27 07:14:59 -0500 (Sat, 27 Dec 2008) | 3 lines
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2182 Changed paths:
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2183 M /branches/prog/bwa/bwape.c
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2184 M /branches/prog/bwa/bwase.c
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2185 M /branches/prog/bwa/main.c
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2186
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2187 * bwa-0.2.0-22
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2188 * mating information can be printed to SAM
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2189
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2190 ------------------------------------------------------------------------
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2191 r727 | lh3 | 2008-12-26 18:10:59 -0500 (Fri, 26 Dec 2008) | 4 lines
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2192 Changed paths:
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2193 M /branches/prog/bwa/bwape.c
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2194 M /branches/prog/bwa/bwase.c
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2195 M /branches/prog/bwa/bwaseqio.c
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2196 M /branches/prog/bwa/bwtaln.c
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2197 M /branches/prog/bwa/bwtaln.h
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2198 M /branches/prog/bwa/main.c
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2199
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2200 * bwa-0.2.0-21
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2201 * implement pairing (still UNFINISHED)
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2202 * output all reads even if full of N
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2203
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2204 ------------------------------------------------------------------------
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2205 r726 | lh3 | 2008-12-26 13:31:27 -0500 (Fri, 26 Dec 2008) | 5 lines
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2206 Changed paths:
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2207 M /branches/prog/bwa/Makefile
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2208 A /branches/prog/bwa/bwape.c
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2209 M /branches/prog/bwa/bwase.c
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2210 M /branches/prog/bwa/bwt2fmv.c
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2211 M /branches/prog/bwa/bwtaln.c
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2212 M /branches/prog/bwa/bwtaln.h
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2213 M /branches/prog/bwa/bwtgap.c
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2214 M /branches/prog/bwa/main.c
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2215 M /branches/prog/bwa/main.h
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2216
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2217 * bwa-0.2.0-20
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2218 * remove "-t" from aln cmd
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2219 * code clean up: move some functions in bwt2fmv.c to other source files
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2220 * added sai2sam_pe cmd: *UNFINISHED*
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2221
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2222 ------------------------------------------------------------------------
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2223 r725 | lh3 | 2008-12-26 07:04:11 -0500 (Fri, 26 Dec 2008) | 3 lines
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2224 Changed paths:
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2225 M /branches/prog/bwa/Makefile
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2226 A /branches/prog/bwa/bwase.c
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2227 A /branches/prog/bwa/bwaseqio.c
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2228 M /branches/prog/bwa/bwt2fmv.c
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2229 M /branches/prog/bwa/bwtaln.c
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2230 M /branches/prog/bwa/bwtaln.h
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2231 M /branches/prog/bwa/bwtgap.c
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2232 M /branches/prog/bwa/kseq.h
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2233 A /branches/prog/bwa/ksort.h (from /branches/prog/sclib/ksort/ksort.h:712)
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2234 A /branches/prog/bwa/kvec.h (from /branches/prog/sclib/kvec/kvec.h:537)
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2235 M /branches/prog/bwa/main.c
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2236
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2237 * bwa-0.2.0-19
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2238 * considerable code cleanup; no actual changes
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2239
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2240 ------------------------------------------------------------------------
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2241 r724 | lh3 | 2008-12-25 11:32:11 -0500 (Thu, 25 Dec 2008) | 3 lines
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2242 Changed paths:
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2243 M /branches/prog/bwa/bwtaln.c
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2244 M /branches/prog/bwa/bwtaln.h
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2245 M /branches/prog/bwa/main.c
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2246
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2247 * bwa-0.2.0-18
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2248 * generate SAM output
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2249
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2250 ------------------------------------------------------------------------
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2251 r723 | lh3 | 2008-12-25 10:48:31 -0500 (Thu, 25 Dec 2008) | 4 lines
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2252 Changed paths:
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2253 M /branches/prog/bwa/bwt2fmv.c
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2254 M /branches/prog/bwa/bwtaln.c
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2255 M /branches/prog/bwa/main.c
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2256 M /branches/prog/bwa/main.h
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2257
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2258 * bwa-0.2.0-17
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2259 * remove bwtsw2 related codes
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2260 * separate searching for SA interval from generating alignments
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2261
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2262 ------------------------------------------------------------------------
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2263 r722 | lh3 | 2008-12-25 08:57:13 -0500 (Thu, 25 Dec 2008) | 3 lines
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2264 Changed paths:
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2265 M /branches/prog/bwa/Makefile
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2266 M /branches/prog/bwa/bwt2fmv.c
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2267 D /branches/prog/bwa/bwt_lite.c
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2268 D /branches/prog/bwa/bwt_lite.h
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2269 M /branches/prog/bwa/bwtgap.c
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2270 D /branches/prog/bwa/bwtsw2.h
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2271 D /branches/prog/bwa/bwtsw2_aux.c
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2272 D /branches/prog/bwa/bwtsw2_core.c
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2273 D /branches/prog/bwa/bwtsw2_main.c
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2274 D /branches/prog/bwa/khash.h
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2275 D /branches/prog/bwa/ksort.h
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2276 D /branches/prog/bwa/kvec.h
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2277 M /branches/prog/bwa/main.c
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2278
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2279 * added interface to "aln -t"
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2280 * remove bwtsw2 related codes
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2281
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2282 ------------------------------------------------------------------------
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2283 r666 | lh3 | 2008-11-18 18:34:29 -0500 (Tue, 18 Nov 2008) | 4 lines
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2284 Changed paths:
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2285 M /branches/prog/bwa/bwt2fmv.c
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2286 M /branches/prog/bwa/bwtaln.c
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2287 M /branches/prog/bwa/bwtaln.h
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2288 M /branches/prog/bwa/main.c
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2289
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2290 * bwa-0.2.0-16
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2291 * allow to set max mismatches based on read length, but I do not know
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2292 whether this really works
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2293
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2294 ------------------------------------------------------------------------
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2295 r665 | lh3 | 2008-11-18 08:34:03 -0500 (Tue, 18 Nov 2008) | 3 lines
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2296 Changed paths:
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2297 M /branches/prog/bwa/bwtaln.c
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2298 M /branches/prog/bwa/main.c
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2299
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2300 * bwa-0.2.0-15
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2301 * fixed a bug in sequence parser.
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2302
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2303 ------------------------------------------------------------------------
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2304 r612 | lh3 | 2008-10-28 06:50:53 -0400 (Tue, 28 Oct 2008) | 3 lines
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2305 Changed paths:
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2306 M /branches/prog/bwa/bntseq.c
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2307 M /branches/prog/bwa/bwtindex.c
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2308 M /branches/prog/bwa/main.c
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2309 M /branches/prog/bwa/utils.c
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2310
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2311 * bwa-0.2.0-14
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2312 * fixed a bug caused by the change of the FASTA/Q parser
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2313
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2314 ------------------------------------------------------------------------
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2315 r611 | lh3 | 2008-10-28 06:24:56 -0400 (Tue, 28 Oct 2008) | 2 lines
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2316 Changed paths:
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2317 M /branches/prog/bwa/Makefile
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2318 M /branches/prog/bwa/bntseq.c
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2319 M /branches/prog/bwa/bntseq.h
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2320 M /branches/prog/bwa/bwtaln.c
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2321 M /branches/prog/bwa/bwtsw2_core.c
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2322 A /branches/prog/bwa/kseq.h
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2323 D /branches/prog/bwa/seq.c
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2324 D /branches/prog/bwa/seq.h
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2325 M /branches/prog/bwa/simple_dp.c
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2326 M /branches/prog/bwa/utils.c
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2327 M /branches/prog/bwa/utils.h
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2328
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2329 replace seq.* with kseq.h
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2330
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2331 ------------------------------------------------------------------------
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2332 r610 | lh3 | 2008-10-27 13:00:04 -0400 (Mon, 27 Oct 2008) | 3 lines
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2333 Changed paths:
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2334 M /branches/prog/bwa/bwtsw2.h
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2335 M /branches/prog/bwa/bwtsw2_aux.c
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2336 M /branches/prog/bwa/bwtsw2_core.c
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2337 M /branches/prog/bwa/main.c
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2338
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2339 * bwa-0.2.0-13
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2340 * make bwtsw2 output sub-optimal hits. not completed
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2341
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2342 ------------------------------------------------------------------------
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2343 r609 | lh3 | 2008-10-24 16:52:00 -0400 (Fri, 24 Oct 2008) | 2 lines
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2344 Changed paths:
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2345 M /branches/prog/bwa/kvec.h
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2346
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2347 little...
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2348
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2349 ------------------------------------------------------------------------
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2350 r532 | lh3 | 2008-09-19 05:28:45 -0400 (Fri, 19 Sep 2008) | 2 lines
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2351 Changed paths:
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2352 M /branches/prog/bwa/bwtsw2_core.c
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2353 M /branches/prog/bwa/khash.h
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2354
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2355 improve interface of khash
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2356
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2357 ------------------------------------------------------------------------
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2358 r531 | lh3 | 2008-09-18 06:52:59 -0400 (Thu, 18 Sep 2008) | 2 lines
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2359 Changed paths:
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2360 M /branches/prog/bwa/bwtsw2_core.c
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2361
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2362 improve minor things, which make bwtsw2 slower, but should miss less true hits
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2363
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2364 ------------------------------------------------------------------------
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2365 r530 | lh3 | 2008-09-17 18:19:26 -0400 (Wed, 17 Sep 2008) | 3 lines
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2366 Changed paths:
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2367 M /branches/prog/bwa/bwtsw2_core.c
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2368
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2369 * fixed a bug in calculating ->D
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2370 * enforce band-width checking
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2371
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2372 ------------------------------------------------------------------------
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2373 r529 | lh3 | 2008-09-17 18:06:49 -0400 (Wed, 17 Sep 2008) | 2 lines
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2374 Changed paths:
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2375 M /branches/prog/bwa/bwtsw2_core.c
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2376
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2377 delete a line of code that is never visited
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2378
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2379 ------------------------------------------------------------------------
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2380 r528 | lh3 | 2008-09-17 17:58:51 -0400 (Wed, 17 Sep 2008) | 2 lines
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2381 Changed paths:
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2382 M /branches/prog/bwa/bwtsw2_core.c
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2383
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2384 a bit code clean up
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2385
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2386 ------------------------------------------------------------------------
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2387 r527 | lh3 | 2008-09-17 10:55:45 -0400 (Wed, 17 Sep 2008) | 3 lines
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2388 Changed paths:
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2389 M /branches/prog/bwa/bwtsw2_core.c
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2390 M /branches/prog/bwa/bwtsw2_main.c
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2391 M /branches/prog/bwa/main.c
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2392
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2393 * bwa-0.2.0-12
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2394 * max-depth can be set, although it does not help the speed at all
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2395
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2396 ------------------------------------------------------------------------
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2397 r526 | lh3 | 2008-09-16 17:59:36 -0400 (Tue, 16 Sep 2008) | 2 lines
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2398 Changed paths:
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2399 M /branches/prog/bwa/bwtsw2_core.c
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2400
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2401 cut_tail after remove duplicate
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2402
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2403 ------------------------------------------------------------------------
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2404 r525 | lh3 | 2008-09-16 17:56:11 -0400 (Tue, 16 Sep 2008) | 3 lines
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2405 Changed paths:
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2406 M /branches/prog/bwa/bwtsw2.h
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2407 M /branches/prog/bwa/bwtsw2_aux.c
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2408 M /branches/prog/bwa/bwtsw2_core.c
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2409 M /branches/prog/bwa/bwtsw2_main.c
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2410 M /branches/prog/bwa/khash.h
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2411 M /branches/prog/bwa/main.c
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2412
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2413 * bwa-0.2.0-11
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2414 * improved cut_tail()
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2415
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2416 ------------------------------------------------------------------------
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2417 r524 | lh3 | 2008-09-15 16:53:22 -0400 (Mon, 15 Sep 2008) | 3 lines
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2418 Changed paths:
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2419 M /branches/prog/bwa/bwtsw2_aux.c
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2420 M /branches/prog/bwa/bwtsw2_core.c
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2421 M /branches/prog/bwa/bwtsw2_main.c
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2422 M /branches/prog/bwa/main.c
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2423
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2424 * bwa-0.2.0-10
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2425 * fixed a bug in cut_tail()
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2426
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2427 ------------------------------------------------------------------------
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2428 r518 | lh3 | 2008-09-15 04:35:59 -0400 (Mon, 15 Sep 2008) | 2 lines
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2429 Changed paths:
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2430 M /branches/prog/bwa/bwtsw2_core.c
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2431
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2432 a bit code clean up
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2433
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2434 ------------------------------------------------------------------------
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2435 r517 | lh3 | 2008-09-14 18:18:11 -0400 (Sun, 14 Sep 2008) | 2 lines
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2436 Changed paths:
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2437 M /branches/prog/bwa/bwtsw2_core.c
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2438
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2439 improve speed (<1%)
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2440
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2441 ------------------------------------------------------------------------
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2442 r516 | lh3 | 2008-09-14 18:08:55 -0400 (Sun, 14 Sep 2008) | 3 lines
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2443 Changed paths:
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2444 M /branches/prog/bwa/bwtsw2_core.c
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2445
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2446 * fixed two potential bugs, although I have not seen their effects
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2447 * improve speed a bit (<2%)
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2448
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2449 ------------------------------------------------------------------------
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2450 r515 | lh3 | 2008-09-14 17:26:49 -0400 (Sun, 14 Sep 2008) | 2 lines
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2451 Changed paths:
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2452 M /branches/prog/bwa/bwtsw2_core.c
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2453 M /branches/prog/bwa/bwtsw2_main.c
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2454
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2455 nothing, really
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2456
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2457 ------------------------------------------------------------------------
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2458 r514 | lh3 | 2008-09-14 17:10:13 -0400 (Sun, 14 Sep 2008) | 2 lines
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2459 Changed paths:
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2460 M /branches/prog/bwa/bwtsw2_core.c
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2461
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2462 disable X-drop, which has to be reimplemented in the current algorithm
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2463
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2464 ------------------------------------------------------------------------
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2465 r513 | lh3 | 2008-09-14 16:49:42 -0400 (Sun, 14 Sep 2008) | 4 lines
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2466 Changed paths:
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2467 M /branches/prog/bwa/bwt_lite.c
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2468 M /branches/prog/bwa/bwt_lite.h
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2469 M /branches/prog/bwa/bwtsw2_core.c
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2470 M /branches/prog/bwa/bwtsw2_main.c
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2471
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2472 * temporarily disable cut_tail()
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2473 * calculate SA in bwt_lite.c
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2474 * fixed a bug in reversing the sequence
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2475
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2476 ------------------------------------------------------------------------
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2477 r512 | lh3 | 2008-09-13 17:35:40 -0400 (Sat, 13 Sep 2008) | 2 lines
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2478 Changed paths:
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2479 M /branches/prog/bwa/bwtsw2.h
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2480 M /branches/prog/bwa/bwtsw2_aux.c
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2481 M /branches/prog/bwa/bwtsw2_core.c
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2482 M /branches/prog/bwa/bwtsw2_main.c
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2483 A /branches/prog/bwa/ksort.h
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2484
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2485 n-best method
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2486
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2487 ------------------------------------------------------------------------
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2488 r507 | lh3 | 2008-09-13 09:06:54 -0400 (Sat, 13 Sep 2008) | 2 lines
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2489 Changed paths:
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2490 M /branches/prog/bwa/Makefile
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2491 M /branches/prog/bwa/bwtsw2_core.c
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2492
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2493 give correct result again
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2494
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2495 ------------------------------------------------------------------------
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2496 r506 | lh3 | 2008-09-13 08:12:07 -0400 (Sat, 13 Sep 2008) | 2 lines
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2497 Changed paths:
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2498 M /branches/prog/bwa/bwtsw2_core.c
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2499
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2500 I think I know the reason. It needs more work...
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2501
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2502 ------------------------------------------------------------------------
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2503 r505 | lh3 | 2008-09-13 06:20:43 -0400 (Sat, 13 Sep 2008) | 2 lines
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2504 Changed paths:
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2505 M /branches/prog/bwa/Makefile
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2506 M /branches/prog/bwa/bwtsw2_core.c
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2507
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2508 fixed another bug, but still have
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2509
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2510 ------------------------------------------------------------------------
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2511 r504 | lh3 | 2008-09-12 18:13:37 -0400 (Fri, 12 Sep 2008) | 2 lines
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2512 Changed paths:
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2513 M /branches/prog/bwa/bwtsw2_core.c
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2514
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2515 fixed another bug
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2516
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2517 ------------------------------------------------------------------------
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2518 r503 | lh3 | 2008-09-12 17:15:56 -0400 (Fri, 12 Sep 2008) | 3 lines
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2519 Changed paths:
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2520 M /branches/prog/bwa/bwtsw2_core.c
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2521 M /branches/prog/bwa/khash.h
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2522
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2523 * do not segfault, but the result is WRONG!
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2524 * prepare to remove bsw2_connectivity_check()
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2525
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2526 ------------------------------------------------------------------------
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2527 r502 | lh3 | 2008-09-12 15:52:41 -0400 (Fri, 12 Sep 2008) | 2 lines
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2528 Changed paths:
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2529 M /branches/prog/bwa/bwtsw2_core.c
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2530 M /branches/prog/bwa/kvec.h
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2531
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2532 more revisions
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2533
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2534 ------------------------------------------------------------------------
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2535 r501 | lh3 | 2008-09-11 18:06:15 -0400 (Thu, 11 Sep 2008) | 2 lines
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2536 Changed paths:
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2537 M /branches/prog/bwa/bwtsw2_core.c
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2538
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2539 further simply codes with kvec.h
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2540
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2541 ------------------------------------------------------------------------
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2542 r500 | lh3 | 2008-09-11 17:42:15 -0400 (Thu, 11 Sep 2008) | 2 lines
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2543 Changed paths:
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2544 M /branches/prog/bwa/bwtsw2_core.c
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2545
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2546 part of revisions... have not finished
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2547
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2548 ------------------------------------------------------------------------
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2549 r499 | lh3 | 2008-09-11 17:24:15 -0400 (Thu, 11 Sep 2008) | 2 lines
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2550 Changed paths:
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2551 M /branches/prog/bwa/bwtsw2.h
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2552 M /branches/prog/bwa/bwtsw2_core.c
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2553 M /branches/prog/bwa/bwtsw2_main.c
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2554 M /branches/prog/bwa/khash.h
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2555 A /branches/prog/bwa/kvec.h
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2556
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2557 prepare for abrupt change
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2558
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2559 ------------------------------------------------------------------------
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2560 r496 | lh3 | 2008-09-11 10:34:38 -0400 (Thu, 11 Sep 2008) | 2 lines
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2561 Changed paths:
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2562 M /branches/prog/bwa/bwtsw2_core.c
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2563
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2564 fixed a bug; now "bwtsw2 -d" is useless
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2565
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2566 ------------------------------------------------------------------------
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2567 r495 | lh3 | 2008-09-11 09:22:03 -0400 (Thu, 11 Sep 2008) | 2 lines
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2568 Changed paths:
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2569 M /branches/prog/bwa/bwtsw2_core.c
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2570 M /branches/prog/bwa/simple_dp.c
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2571 M /branches/prog/bwa/stdaln.c
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2572 M /branches/prog/bwa/stdaln.h
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2573
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2574 improve speed a little bit
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2575
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2576 ------------------------------------------------------------------------
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2577 r494 | lh3 | 2008-09-11 08:28:08 -0400 (Thu, 11 Sep 2008) | 2 lines
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2578 Changed paths:
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2579 M /branches/prog/bwa/bwtsw2_core.c
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2580
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2581 remove debug codes
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2582
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2583 ------------------------------------------------------------------------
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2584 r493 | lh3 | 2008-09-11 07:49:53 -0400 (Thu, 11 Sep 2008) | 3 lines
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2585 Changed paths:
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2586 M /branches/prog/bwa/bwtsw2_core.c
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2587
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2588 * improve the speed a little bit (<5%)
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2589 * prepare to remove BSW_DEBUG
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2590
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2591 ------------------------------------------------------------------------
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2592 r492 | lh3 | 2008-09-11 06:15:56 -0400 (Thu, 11 Sep 2008) | 4 lines
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2593 Changed paths:
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2594 M /branches/prog/bwa/bwtsw2.h
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2595 M /branches/prog/bwa/bwtsw2_aux.c
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2596 M /branches/prog/bwa/bwtsw2_core.c
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2597 M /branches/prog/bwa/bwtsw2_main.c
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2598 M /branches/prog/bwa/main.c
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2599
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2600 * bwa-0.2.0-9
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2601 * support reverse strand
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2602 * fixed a bug that causes missing hits
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2603
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2604 ------------------------------------------------------------------------
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2605 r491 | lh3 | 2008-09-11 05:46:16 -0400 (Thu, 11 Sep 2008) | 3 lines
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2606 Changed paths:
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2607 M /branches/prog/bwa/bwtsw2_core.c
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2608 M /branches/prog/bwa/main.c
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2609
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2610 * bwa-0.2.0-8
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2611 * better progress report
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2612
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2613 ------------------------------------------------------------------------
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2614 r490 | lh3 | 2008-09-10 17:04:49 -0400 (Wed, 10 Sep 2008) | 4 lines
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2615 Changed paths:
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2616 M /branches/prog/bwa/bwtsw2.h
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2617 M /branches/prog/bwa/bwtsw2_aux.c
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2618 M /branches/prog/bwa/bwtsw2_core.c
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2619 M /branches/prog/bwa/bwtsw2_main.c
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2620 M /branches/prog/bwa/main.c
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2621
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2622 * bwa-0.2.0-7
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2623 * avoid some missing hits
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2624 * add maximum depth
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2625
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2626 ------------------------------------------------------------------------
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2627 r489 | lh3 | 2008-09-10 11:51:13 -0400 (Wed, 10 Sep 2008) | 4 lines
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2628 Changed paths:
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2629 M /branches/prog/bwa/bwtsw2_core.c
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2630 M /branches/prog/bwa/main.c
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2631
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2632 * bwa-0.2.0-6
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2633 * bwtsw2 works although on the forward strand only for now
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2634 * better progress information
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2635
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2636 ------------------------------------------------------------------------
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2637 r488 | lh3 | 2008-09-10 10:21:53 -0400 (Wed, 10 Sep 2008) | 3 lines
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2638 Changed paths:
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2639 M /branches/prog/bwa/bwtsw2_core.c
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2640
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2641 * implement memory pool
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2642 * avoid some rehashing
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2643
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2644 ------------------------------------------------------------------------
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2645 r487 | lh3 | 2008-09-10 09:23:38 -0400 (Wed, 10 Sep 2008) | 3 lines
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2646 Changed paths:
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2647 M /branches/prog/bwa/bwtsw2.h
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2648 M /branches/prog/bwa/bwtsw2_aux.c
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2649 M /branches/prog/bwa/bwtsw2_main.c
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2650
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2651 * fixed a memory leak
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2652 * prepare to implement mempool
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2653
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2654 ------------------------------------------------------------------------
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2655 r486 | lh3 | 2008-09-10 09:10:09 -0400 (Wed, 10 Sep 2008) | 4 lines
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2656 Changed paths:
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2657 M /branches/prog/bwa/bwtsw2.h
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2658 M /branches/prog/bwa/bwtsw2_aux.c
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2659 M /branches/prog/bwa/bwtsw2_core.c
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2660 M /branches/prog/bwa/bwtsw2_main.c
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2661 M /branches/prog/bwa/khash.h
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2662
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2663 * add X-dropoff
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2664 * remove duplicated results
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2665 * switch to simple stack
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2666
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2667 ------------------------------------------------------------------------
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2668 r485 | lh3 | 2008-09-10 06:31:20 -0400 (Wed, 10 Sep 2008) | 3 lines
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2669 Changed paths:
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2670 M /branches/prog/bwa/bwtsw2.h
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2671 M /branches/prog/bwa/bwtsw2_aux.c
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2672 M /branches/prog/bwa/bwtsw2_core.c
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2673 M /branches/prog/bwa/bwtsw2_main.c
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2674
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2675 * check whether t-node has been visited
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2676 * prepare to remove two-level stack
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2677
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2678 ------------------------------------------------------------------------
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2679 r484 | lh3 | 2008-09-10 05:00:57 -0400 (Wed, 10 Sep 2008) | 2 lines
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2680 Changed paths:
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2681 A /branches/prog/bwa/khash.h
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2682
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2683 khash library
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2684
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2685 ------------------------------------------------------------------------
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2686 r483 | lh3 | 2008-09-10 04:22:53 -0400 (Wed, 10 Sep 2008) | 2 lines
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2687 Changed paths:
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2688 M /branches/prog/bwa/bwtsw2_core.c
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2689
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2690 add inline
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2691
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2692 ------------------------------------------------------------------------
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2693 r482 | lh3 | 2008-09-09 16:34:57 -0400 (Tue, 09 Sep 2008) | 2 lines
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2694 Changed paths:
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2695 M /branches/prog/bwa/Makefile
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2696 M /branches/prog/bwa/bwtsw2_aux.c
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2697 M /branches/prog/bwa/bwtsw2_core.c
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2698
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2699 improve speed
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2700
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2701 ------------------------------------------------------------------------
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2702 r481 | lh3 | 2008-09-09 13:13:00 -0400 (Tue, 09 Sep 2008) | 4 lines
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2703 Changed paths:
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2704 M /branches/prog/bwa/bwtsw2_core.c
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2705
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2706 Use a 128bit hash table to keep all (tk,tl,qk,ql). This is slow. Just
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2707 keep a copy in case I may need this in future.
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2708
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2709
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2710 ------------------------------------------------------------------------
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2711 r480 | lh3 | 2008-09-09 12:53:32 -0400 (Tue, 09 Sep 2008) | 2 lines
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2712 Changed paths:
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2713 M /branches/prog/bwa/bwtsw2.h
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2714 M /branches/prog/bwa/bwtsw2_core.c
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2715
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2716 * no principal modification
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2717
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2718 ------------------------------------------------------------------------
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2719 r479 | lh3 | 2008-09-09 11:01:45 -0400 (Tue, 09 Sep 2008) | 4 lines
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2720 Changed paths:
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2721 M /branches/prog/bwa/Makefile
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2722 M /branches/prog/bwa/bwtsw2_core.c
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2723
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2724 * fixed a bug which may cause duplicated matching
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2725 * accelerate the speed a bit, although using hash in avoiding duplications
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2726 slows the speed down in the end
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2727
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2728 ------------------------------------------------------------------------
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2729 r474 | lh3 | 2008-09-03 17:22:57 -0400 (Wed, 03 Sep 2008) | 4 lines
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2730 Changed paths:
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2731 M /branches/prog/bwa/Makefile
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2732 M /branches/prog/bwa/bwtsw2.h
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2733 M /branches/prog/bwa/bwtsw2_aux.c
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2734 M /branches/prog/bwa/bwtsw2_core.c
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2735 M /branches/prog/bwa/bwtsw2_main.c
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2736 M /branches/prog/bwa/main.c
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2737
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2738 * bwa-0.2.0-5
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2739 * indel seems to work on toy example
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2740 * add band
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2741
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2742 ------------------------------------------------------------------------
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2743 r469 | lh3 | 2008-09-01 09:18:45 -0400 (Mon, 01 Sep 2008) | 3 lines
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2744 Changed paths:
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2745 M /branches/prog/bwa/ChangeLog
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2746 M /branches/prog/bwa/Makefile
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2747 M /branches/prog/bwa/bwt_lite.c
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2748 M /branches/prog/bwa/bwt_lite.h
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2749 M /branches/prog/bwa/bwtgap.c
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2750 M /branches/prog/bwa/bwtsw2.h
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2751 A /branches/prog/bwa/bwtsw2_aux.c
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2752 M /branches/prog/bwa/bwtsw2_core.c
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2753 M /branches/prog/bwa/bwtsw2_main.c
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2754 M /branches/prog/bwa/is.c
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2755 M /branches/prog/bwa/main.c
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2756 M /branches/prog/bwa/main.h
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2757 M /branches/prog/bwa/simple_dp.c
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2758
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2759 * bwa-0.2.0-4
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2760 * updated bwtsw2, which seems to work properly on toy examples
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2761
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2762 ------------------------------------------------------------------------
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2763 r447 | lh3 | 2008-08-27 10:05:09 -0400 (Wed, 27 Aug 2008) | 3 lines
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2764 Changed paths:
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2765 M /branches/prog/bwa/bwt2fmv.c
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2766 M /branches/prog/bwa/bwtaln.c
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2767 M /branches/prog/bwa/bwtaln.h
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2768 M /branches/prog/bwa/bwtgap.c
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2769 M /branches/prog/bwa/main.c
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2770
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2771 * bwa-0.2.0-3
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2772 * tune for longer gaps, but it does not really work with kilo-bp gaps...
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2773
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2774 ------------------------------------------------------------------------
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2775 r446 | lh3 | 2008-08-26 13:30:41 -0400 (Tue, 26 Aug 2008) | 3 lines
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2776 Changed paths:
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2777 M /branches/prog/bwa/bwt2fmv.c
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2778 M /branches/prog/bwa/bwtaln.c
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2779 M /branches/prog/bwa/bwtaln.h
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2780 M /branches/prog/bwa/bwtgap.c
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2781 M /branches/prog/bwa/main.c
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2782
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2783 * bwa-0.2.0-2
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2784 * changed the way to extend long deletions. Now use max_del_occ.
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2785
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2786 ------------------------------------------------------------------------
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2787 r445 | lh3 | 2008-08-26 13:05:58 -0400 (Tue, 26 Aug 2008) | 2 lines
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2788 Changed paths:
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2789 M /branches/prog/bwa/bwt_lite.c
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2790 M /branches/prog/bwa/bwt_lite.h
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2791
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2792 updated from bwtsw2_lite
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2793
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2794 ------------------------------------------------------------------------
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2795 r436 | lh3 | 2008-08-23 12:28:44 -0400 (Sat, 23 Aug 2008) | 4 lines
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2796 Changed paths:
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2797 M /branches/prog/bwa/Makefile
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2798 M /branches/prog/bwa/bwt.h
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2799 A /branches/prog/bwa/bwt_lite.c
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2800 A /branches/prog/bwa/bwt_lite.h
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2801 A /branches/prog/bwa/bwtsw2.h
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2802 A /branches/prog/bwa/bwtsw2_core.c
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2803 A /branches/prog/bwa/bwtsw2_main.c
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2804 M /branches/prog/bwa/main.c
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2805
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2806 * bwa-0.2.0-1
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2807 * add bwt_lite: a light-weighted version of bwt (NOT TESTED!)
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2808 * add core codes for bwtsw2: NOT TESTED!!!
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2809
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2810 ------------------------------------------------------------------------
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2811 r427 | lh3 | 2008-08-15 05:38:12 -0400 (Fri, 15 Aug 2008) | 2 lines
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2812 Changed paths:
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2813 M /branches/prog/bwa/ChangeLog
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2814 M /branches/prog/bwa/NEWS
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2815 M /branches/prog/bwa/bwa.1
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2816 M /branches/prog/bwa/bwtaln.c
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2817 M /branches/prog/bwa/main.c
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2818
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2819 Release bwa-0.2.0
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2820
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2821 ------------------------------------------------------------------------
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2822 r426 | lh3 | 2008-08-14 11:26:19 -0400 (Thu, 14 Aug 2008) | 4 lines
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2823 Changed paths:
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2824 M /branches/prog/bwa/bwt2fmv.c
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2825 M /branches/prog/bwa/bwtaln.c
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2826 M /branches/prog/bwa/bwtaln.h
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2827 M /branches/prog/bwa/main.c
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2828
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2829 * bwa-0.1.6-7
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2830 * change default seed length to 31
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2831 * add incomplete support to color sequences (not tested yet!)
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2832
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2833 ------------------------------------------------------------------------
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2834 r425 | lh3 | 2008-08-14 06:23:11 -0400 (Thu, 14 Aug 2008) | 3 lines
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2835 Changed paths:
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2836 M /branches/prog/bwa/bwtaln.c
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2837 M /branches/prog/bwa/main.c
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2838
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2839 * bwa-0.1.6-6
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2840 * change default seed length to 33bp
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2841
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2842 ------------------------------------------------------------------------
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2843 r424 | lh3 | 2008-08-14 05:55:33 -0400 (Thu, 14 Aug 2008) | 6 lines
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2844 Changed paths:
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2845 M /branches/prog/bwa/bwtaln.c
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2846 M /branches/prog/bwa/bwtgap.c
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2847 M /branches/prog/bwa/main.c
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2848
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2849 * bwa-0.1.6-5
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2850 * fixed a bug that may miss true alignments. this bugs exists in most
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2851 early versions.
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2852 * fixed a bug that yields wrong coordinates for reads mapped on the forward
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2853 strands with gaps.
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2854
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2855 ------------------------------------------------------------------------
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2856 r423 | lh3 | 2008-08-14 04:07:28 -0400 (Thu, 14 Aug 2008) | 2 lines
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2857 Changed paths:
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2858 D /branches/prog/bwa/Makefile.div
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2859
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2860 useless
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2861
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2862 ------------------------------------------------------------------------
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2863 r422 | lh3 | 2008-08-13 19:21:14 -0400 (Wed, 13 Aug 2008) | 4 lines
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2864 Changed paths:
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2865 M /branches/prog/bwa/bwtaln.c
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2866 M /branches/prog/bwa/main.c
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2867
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2868 * bwa-0.1.6-4
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2869 * fixed one bug
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2870 * there is another one...
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2871
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2872 ------------------------------------------------------------------------
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2873 r421 | lh3 | 2008-08-13 18:23:33 -0400 (Wed, 13 Aug 2008) | 3 lines
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2874 Changed paths:
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2875 M /branches/prog/bwa/bwtaln.c
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2876 M /branches/prog/bwa/bwtaln.h
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2877 M /branches/prog/bwa/bwtgap.c
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2878 M /branches/prog/bwa/bwtgap.h
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2879 M /branches/prog/bwa/bwtindex.c
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2880 M /branches/prog/bwa/main.c
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2881
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2882 * bwa-0.1.6-3
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2883 * almost there, but not quite right
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2884
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2885 ------------------------------------------------------------------------
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2886 r419 | lh3 | 2008-08-13 17:27:02 -0400 (Wed, 13 Aug 2008) | 3 lines
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2887 Changed paths:
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2888 M /branches/prog/bwa/bwtaln.c
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2889 M /branches/prog/bwa/bwtaln.h
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2890 M /branches/prog/bwa/bwtgap.c
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2891 M /branches/prog/bwa/bwtgap.h
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2892 M /branches/prog/bwa/main.c
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2893
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2894 * improve the seeding method
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2895 * prepare to load two BWTs into memory. A BIG change!
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2896
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2897 ------------------------------------------------------------------------
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2898 r418 | lh3 | 2008-08-13 10:56:54 -0400 (Wed, 13 Aug 2008) | 3 lines
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2899 Changed paths:
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2900 M /branches/prog/bwa/bwt2fmv.c
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2901 M /branches/prog/bwa/bwtaln.c
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2902 M /branches/prog/bwa/bwtaln.h
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2903 M /branches/prog/bwa/bwtgap.c
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2904 M /branches/prog/bwa/bwtgap.h
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2905 M /branches/prog/bwa/main.c
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2906
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2907 * added seeding
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2908 * unfinished yet
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2909
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2910 ------------------------------------------------------------------------
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2911 r413 | lh3 | 2008-08-08 11:48:35 -0400 (Fri, 08 Aug 2008) | 2 lines
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2912 Changed paths:
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2913 M /branches/prog/bwa/ChangeLog
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2914 M /branches/prog/bwa/NEWS
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2915 M /branches/prog/bwa/main.c
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2916
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2917 Release bwa-0.1.6
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2918
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2919 ------------------------------------------------------------------------
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2920 r410 | lh3 | 2008-08-06 15:48:22 -0400 (Wed, 06 Aug 2008) | 2 lines
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2921 Changed paths:
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2922 M /branches/prog/bwa/simple_dp.c
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2923
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2924 sw: output alignment score
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2925
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2926 ------------------------------------------------------------------------
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2927 r407 | lh3 | 2008-08-04 10:01:20 -0400 (Mon, 04 Aug 2008) | 4 lines
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2928 Changed paths:
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2929 M /branches/prog/bwa/Makefile
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2930 M /branches/prog/bwa/main.c
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2931 M /branches/prog/bwa/main.h
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2932 A /branches/prog/bwa/simple_dp.c
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2933 M /branches/prog/bwa/stdaln.c
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2934 M /branches/prog/bwa/stdaln.h
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2935
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2936 * bwa-0.1.5-3
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2937 * added a simple interface to SW/NW alignment
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2938 * stdaln-0.9.8 (see header for more details)
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2939
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2940 ------------------------------------------------------------------------
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2941 r406 | lh3 | 2008-08-01 19:21:59 -0400 (Fri, 01 Aug 2008) | 3 lines
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2942 Changed paths:
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2943 M /branches/prog/bwa/Makefile
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2944 M /branches/prog/bwa/bwtaln.c
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2945 M /branches/prog/bwa/bwtaln.h
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2946 M /branches/prog/bwa/main.c
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2947 A /branches/prog/bwa/stdaln.c
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2948 A /branches/prog/bwa/stdaln.h
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2949
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2950 * bwa-0.1.5-2
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2951 * give accurate gap positions
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2952
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2953 ------------------------------------------------------------------------
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2954 r405 | lh3 | 2008-08-01 19:06:19 -0400 (Fri, 01 Aug 2008) | 2 lines
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2955 Changed paths:
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2956 M /branches/prog/bwa/Makefile
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2957 M /branches/prog/bwa/bwtaln.c
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2958 M /branches/prog/bwa/bwtaln.h
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2959
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2960 unfinished, but I am tired...
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2961
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2962 ------------------------------------------------------------------------
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2963 r401 | lh3 | 2008-07-30 05:59:24 -0400 (Wed, 30 Jul 2008) | 4 lines
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2964 Changed paths:
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2965 M /branches/prog/bwa/bntseq.c
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2966 M /branches/prog/bwa/main.c
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2967
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2968 * bwa-0.1.5-1
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2969 * fixed a potential bug which may produce an alignment in N regions,
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2970 although extremely rare.
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2971
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2972 ------------------------------------------------------------------------
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2973 r399 | lh3 | 2008-07-27 11:41:52 -0400 (Sun, 27 Jul 2008) | 2 lines
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2974 Changed paths:
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2975 M /branches/prog/bwa/ChangeLog
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2976 M /branches/prog/bwa/NEWS
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2977 M /branches/prog/bwa/main.c
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2978
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2979 Release bwa-0.1.5
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2980
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2981 ------------------------------------------------------------------------
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2982 r398 | lh3 | 2008-07-25 12:14:47 -0400 (Fri, 25 Jul 2008) | 2 lines
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2983 Changed paths:
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2984 M /branches/prog/bwa/bwa.1
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2985
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2986 update documentation
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2987
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2988 ------------------------------------------------------------------------
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2989 r397 | lh3 | 2008-07-25 09:58:56 -0400 (Fri, 25 Jul 2008) | 2 lines
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2990 Changed paths:
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2991 M /branches/prog/bwa/bwt2fmv.c
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2992 M /branches/prog/bwa/bwtaln.c
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2993 M /branches/prog/bwa/main.c
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2994
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2995 *
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2996
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2997 ------------------------------------------------------------------------
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2998 r396 | lh3 | 2008-07-25 06:42:01 -0400 (Fri, 25 Jul 2008) | 3 lines
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2999 Changed paths:
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3000 M /branches/prog/bwa/bwtaln.c
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3001 M /branches/prog/bwa/main.c
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3002
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3003 * bwa-0.1.4-4
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3004 * add timer for debugging
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3005
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3006 ------------------------------------------------------------------------
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3007 r395 | lh3 | 2008-07-24 05:46:21 -0400 (Thu, 24 Jul 2008) | 4 lines
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3008 Changed paths:
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3009 M /branches/prog/bwa/bwtgap.c
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3010 M /branches/prog/bwa/main.c
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3011
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3012 * bwa-0.1.4-3
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3013 * fixed a bug in the previous code
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3014 * this version gives identical result to bwa-0.1.4, just 10% faster
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3015
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3016 ------------------------------------------------------------------------
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3017 r394 | lh3 | 2008-07-24 05:18:53 -0400 (Thu, 24 Jul 2008) | 4 lines
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3018 Changed paths:
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3019 M /branches/prog/bwa/bwtaln.c
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3020 M /branches/prog/bwa/bwtgap.c
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3021 M /branches/prog/bwa/bwtgap.h
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3022 M /branches/prog/bwa/main.c
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3023
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3024 * bwa-0.1.4-2
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3025 * further improve the speed
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3026 * The result is slightly different from bwa-0.1.4 now. I need to check...
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3027
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3028 ------------------------------------------------------------------------
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3029 r393 | lh3 | 2008-07-23 12:04:16 -0400 (Wed, 23 Jul 2008) | 2 lines
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3030 Changed paths:
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3031 M /branches/prog/bwa/bwt.c
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3032
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3033 comments only
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3034
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3035 ------------------------------------------------------------------------
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3036 r392 | lh3 | 2008-07-23 10:34:03 -0400 (Wed, 23 Jul 2008) | 2 lines
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3037 Changed paths:
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3038 M /branches/prog/bwa/bwt.c
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3039 M /branches/prog/bwa/main.c
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3040
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3041 further improve the speed in Occ functions
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3042
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3043 ------------------------------------------------------------------------
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3044 r386 | lh3 | 2008-07-22 10:03:54 -0400 (Tue, 22 Jul 2008) | 2 lines
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3045 Changed paths:
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3046 M /branches/prog/bwa/NEWS
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3047 M /branches/prog/bwa/main.c
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3048
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3049 Release bwa-0.1.4
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3050
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3051 ------------------------------------------------------------------------
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3052 r385 | lh3 | 2008-07-22 09:44:50 -0400 (Tue, 22 Jul 2008) | 2 lines
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3053 Changed paths:
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3054 M /branches/prog/bwa/ChangeLog
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3055 M /branches/prog/bwa/bwa.1
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3056
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3057 update documentation and ChangeLog
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3058
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3059 ------------------------------------------------------------------------
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3060 r384 | lh3 | 2008-07-22 08:50:03 -0400 (Tue, 22 Jul 2008) | 4 lines
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3061 Changed paths:
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3062 M /branches/prog/bwa/Makefile
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3063 M /branches/prog/bwa/bwt2fmv.c
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3064 M /branches/prog/bwa/bwtaln.c
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3065 M /branches/prog/bwa/bwtaln.h
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3066 M /branches/prog/bwa/bwtgap.c
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3067 M /branches/prog/bwa/main.c
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3068
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3069 * bwa-0.1.3-2
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3070 * fixed the bug in the last modification
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3071 * now the alignment should be more clearly defined
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3072
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3073 ------------------------------------------------------------------------
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3074 r383 | lh3 | 2008-07-21 18:32:21 -0400 (Mon, 21 Jul 2008) | 4 lines
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3075 Changed paths:
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3076 M /branches/prog/bwa/bwt2fmv.c
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3077 M /branches/prog/bwa/bwtaln.c
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3078 M /branches/prog/bwa/bwtgap.c
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3079 M /branches/prog/bwa/main.c
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3080
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3081 * bwa-0.1.3-1
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3082 * this is a buggy verion!
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3083 * i will fix the bug tomorrow. It is late...
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3084
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3085 ------------------------------------------------------------------------
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3086 r381 | lh3 | 2008-07-21 06:45:32 -0400 (Mon, 21 Jul 2008) | 2 lines
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3087 Changed paths:
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3088 M /branches/prog/bwa/ChangeLog
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3089 M /branches/prog/bwa/NEWS
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3090 M /branches/prog/bwa/bwa.1
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3091 M /branches/prog/bwa/main.c
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3092
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3093 Release bwa-0.1.3
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3094
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3095 ------------------------------------------------------------------------
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3096 r380 | lh3 | 2008-07-21 06:07:43 -0400 (Mon, 21 Jul 2008) | 4 lines
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3097 Changed paths:
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3098 M /branches/prog/bwa/ChangeLog
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3099 M /branches/prog/bwa/bwa.1
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3100 M /branches/prog/bwa/bwt.c
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3101 M /branches/prog/bwa/bwt2fmv.c
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3102 M /branches/prog/bwa/main.c
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3103
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3104 * bwa-0.1.2-3
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3105 * improve the speed for gcc on Intel Mac OS X, but not really on icc on Linux
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3106 * aln: more command-line options
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3107
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3108 ------------------------------------------------------------------------
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3109 r373 | lh3 | 2008-07-17 09:09:46 -0400 (Thu, 17 Jul 2008) | 4 lines
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3110 Changed paths:
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3111 M /branches/prog/bwa/bwt.c
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3112 M /branches/prog/bwa/bwt.h
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3113 M /branches/prog/bwa/bwtio.c
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3114 M /branches/prog/bwa/main.c
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3115
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3116 * bwa-0.1.2-2
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3117 * further improve the speed
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3118 * this version gives exactly the same result as bwa-0.1.2
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3119
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3120 ------------------------------------------------------------------------
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3121 r372 | lh3 | 2008-07-17 07:51:08 -0400 (Thu, 17 Jul 2008) | 3 lines
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3122 Changed paths:
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3123 M /branches/prog/bwa/bwt.c
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3124 M /branches/prog/bwa/main.c
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3125
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3126 * bwa-0.1.2-1
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3127 * speed up by about 5%
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3128
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3129 ------------------------------------------------------------------------
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3130 r370 | lh3 | 2008-07-17 05:12:00 -0400 (Thu, 17 Jul 2008) | 2 lines
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3131 Changed paths:
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3132 M /branches/prog/bwa/NEWS
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3133 M /branches/prog/bwa/bwa.1
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3134 M /branches/prog/bwa/main.c
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3135
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3136 Release bwa-0.1.2
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3137
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3138 ------------------------------------------------------------------------
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3139 r368 | lh3 | 2008-07-16 08:51:25 -0400 (Wed, 16 Jul 2008) | 4 lines
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3140 Changed paths:
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3141 M /branches/prog/bwa/Makefile
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3142 D /branches/prog/bwa/bwt1away.c
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3143 M /branches/prog/bwa/bwt2fmv.c
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3144 M /branches/prog/bwa/bwtaln.c
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3145 M /branches/prog/bwa/bwtaln.h
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3146 M /branches/prog/bwa/bwtgap.c
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3147 M /branches/prog/bwa/bwtgap.h
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3148 D /branches/prog/bwa/bwttop2.c
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3149 M /branches/prog/bwa/main.c
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3150
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3151 * bwa-0.1.1-9
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3152 * some code cleanup
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3153 * remove 1away and top2
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3154
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3155 ------------------------------------------------------------------------
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3156 r367 | lh3 | 2008-07-16 08:24:34 -0400 (Wed, 16 Jul 2008) | 2 lines
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3157 Changed paths:
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3158 M /branches/prog/bwa/is.c
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3159
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3160 Yuta Mori's implementation of IS algorithm.
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3161
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3162 ------------------------------------------------------------------------
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3163 r365 | lh3 | 2008-07-16 06:58:04 -0400 (Wed, 16 Jul 2008) | 6 lines
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3164 Changed paths:
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3165 M /branches/prog/bwa/bwtaln.c
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3166 M /branches/prog/bwa/bwtgap.c
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3167 M /branches/prog/bwa/bwtgap.h
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3168 M /branches/prog/bwa/main.c
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3169
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3170 * bwa-0.1.1-8
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3171 * improve gapped alignment
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3172 * this version will miss more gapped alignments, but the speed is much faster
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3173 * prepare to remove top2 and 1away algorithms
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3174 * prepare to add SAIS algorithm for bwt construction
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3175
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3176 ------------------------------------------------------------------------
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3177 r358 | lh3 | 2008-06-09 06:03:04 -0400 (Mon, 09 Jun 2008) | 4 lines
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3178 Changed paths:
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3179 M /branches/prog/bwa/bwt2fmv.c
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3180 M /branches/prog/bwa/bwtgap.c
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3181 M /branches/prog/bwa/main.c
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3182
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3183 * bwa-0.1.1-7
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3184 * change END_SKIP from 3 to 5, but still gaps may be wrongly added
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3185 * change default '-g' from 5 to 3
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3186
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3187 ------------------------------------------------------------------------
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3188 r357 | lh3 | 2008-06-09 05:18:36 -0400 (Mon, 09 Jun 2008) | 3 lines
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3189 Changed paths:
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3190 M /branches/prog/bwa/bntseq.c
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3191 M /branches/prog/bwa/bwt2fmv.c
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3192 M /branches/prog/bwa/bwtgap.c
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3193 M /branches/prog/bwa/main.c
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3194
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3195 * bwa-0.1.1-6
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3196 * fix a bug in nested stack
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3197
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3198 ------------------------------------------------------------------------
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3199 r356 | lh3 | 2008-06-08 18:43:13 -0400 (Sun, 08 Jun 2008) | 4 lines
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3200 Changed paths:
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3201 M /branches/prog/bwa/Makefile
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3202 M /branches/prog/bwa/bwtaln.c
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3203 M /branches/prog/bwa/bwtaln.h
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3204 M /branches/prog/bwa/bwtgap.c
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3205 A /branches/prog/bwa/bwtgap.h
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3206 M /branches/prog/bwa/main.c
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3207
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3208 * bwa-0.1.1-5
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3209 * replace heap with nested stacks
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3210 * there are still obvious bugs...
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3211
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3212 ------------------------------------------------------------------------
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3213 r355 | lh3 | 2008-06-08 17:13:44 -0400 (Sun, 08 Jun 2008) | 4 lines
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3214 Changed paths:
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3215 M /branches/prog/bwa/bwt2fmv.c
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3216 M /branches/prog/bwa/bwtaln.c
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3217 M /branches/prog/bwa/bwtaln.h
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3218 M /branches/prog/bwa/bwtgap.c
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3219 M /branches/prog/bwa/main.c
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3220 M /branches/prog/bwa/main.h
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3221
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3222 * bwa-0.1.1-4
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3223 * add interface to affine gap alignment
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3224 * there are obvious bugs and I will fix them later
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3225
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3226 ------------------------------------------------------------------------
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3227 r354 | lh3 | 2008-06-08 15:39:05 -0400 (Sun, 08 Jun 2008) | 3 lines
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3228 Changed paths:
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3229 M /branches/prog/bwa/bwtaln.c
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3230 M /branches/prog/bwa/bwtaln.h
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3231 M /branches/prog/bwa/bwtgap.c
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3232 M /branches/prog/bwa/main.c
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3233
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3234 * bwa-0.1.1-3
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3235 * affine gap seems to work, at least partially
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3236
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3237 ------------------------------------------------------------------------
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3238 r353 | lh3 | 2008-06-08 09:27:18 -0400 (Sun, 08 Jun 2008) | 3 lines
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3239 Changed paths:
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3240 M /branches/prog/bwa/Makefile
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3241 M /branches/prog/bwa/bwt2fmv.c
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3242 M /branches/prog/bwa/bwtaln.c
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3243 M /branches/prog/bwa/bwtaln.h
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3244 A /branches/prog/bwa/bwtgap.c
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3245 M /branches/prog/bwa/bwttop2.c
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3246 M /branches/prog/bwa/main.c
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3247
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3248 * bwa-0.1.1-2
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3249 * initial gapped alignment. not work at the moment
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3250
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3251 ------------------------------------------------------------------------
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3252 r352 | lh3 | 2008-06-06 04:37:34 -0400 (Fri, 06 Jun 2008) | 3 lines
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3253 Changed paths:
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3254 M /branches/prog/bwa/bwttop2.c
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3255 M /branches/prog/bwa/main.c
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3256
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3257 * bwa-0.1.1-1
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3258 * ungap: remove a useless varible in top2_entry_t
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3259
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3260 ------------------------------------------------------------------------
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3261 r348 | lh3 | 2008-06-03 09:04:12 -0400 (Tue, 03 Jun 2008) | 2 lines
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3262 Changed paths:
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3263 M /branches/prog/bwa/ChangeLog
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3264 A /branches/prog/bwa/NEWS
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3265 M /branches/prog/bwa/bwa.1
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3266 M /branches/prog/bwa/main.c
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3267
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3268 Release bwa-0.1.1
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3269
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3270 ------------------------------------------------------------------------
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3271 r347 | lh3 | 2008-06-03 05:45:08 -0400 (Tue, 03 Jun 2008) | 2 lines
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3272 Changed paths:
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3273 M /branches/prog/bwa/bwa.1
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3274
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3275 update documentation
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3276
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3277 ------------------------------------------------------------------------
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3278 r346 | lh3 | 2008-06-02 18:59:50 -0400 (Mon, 02 Jun 2008) | 5 lines
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3279 Changed paths:
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3280 A /branches/prog/bwa/ChangeLog
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3281 A /branches/prog/bwa/bwa.1
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3282 M /branches/prog/bwa/bwtaln.c
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3283 M /branches/prog/bwa/main.c
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3284
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3285 * bwa-0.1.0-11
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3286 * improve approximating mapping qualities
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3287 * add documentation
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3288 * add ChangeLog
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3289
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3290 ------------------------------------------------------------------------
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3291 r345 | lh3 | 2008-06-02 16:04:39 -0400 (Mon, 02 Jun 2008) | 3 lines
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3292 Changed paths:
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3293 M /branches/prog/bwa/bwtaln.c
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3294 M /branches/prog/bwa/bwttop2.c
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3295 M /branches/prog/bwa/main.c
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3296
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3297 * bwa-0.1.0-10
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3298 * output a random position for repetitive reads
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3299
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3300 ------------------------------------------------------------------------
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3301 r344 | lh3 | 2008-06-02 15:03:54 -0400 (Mon, 02 Jun 2008) | 4 lines
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3302 Changed paths:
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3303 M /branches/prog/bwa/bntseq.c
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3304 M /branches/prog/bwa/bwtaln.c
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3305 M /branches/prog/bwa/main.c
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3306 M /branches/prog/bwa/pac2bwt.c
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3307
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3308 * bwa-0.1.0-9
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3309 * fix memory leaks
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3310 * fix a potential bug in coverting to the real coordinate
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3311
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3312 ------------------------------------------------------------------------
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3313 r343 | lh3 | 2008-06-02 13:44:51 -0400 (Mon, 02 Jun 2008) | 5 lines
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3314 Changed paths:
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3315 M /branches/prog/bwa/Makefile.div
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3316 M /branches/prog/bwa/bwt.c
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3317 M /branches/prog/bwa/bwt.h
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3318 M /branches/prog/bwa/bwt2fmv.c
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3319 M /branches/prog/bwa/bwtaln.c
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3320 M /branches/prog/bwa/bwttop2.c
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3321 M /branches/prog/bwa/main.c
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3322
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3323 * bwa-0.1.0-8
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3324 * fix a bug about strand
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3325 * update Makefile.div
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3326 * change top2b as the default method
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3327
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3328 ------------------------------------------------------------------------
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3329 r342 | lh3 | 2008-06-02 11:23:26 -0400 (Mon, 02 Jun 2008) | 3 lines
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3330 Changed paths:
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3331 M /branches/prog/bwa/bwt.c
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3332 M /branches/prog/bwa/bwt1away.c
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3333 M /branches/prog/bwa/bwtaln.c
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3334 M /branches/prog/bwa/main.c
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3335
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3336 * bwa-0.1.0-7
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3337 * use bwt_2occ() and bwt_2occ4() in other functions
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3338
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3339 ------------------------------------------------------------------------
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3340 r341 | lh3 | 2008-06-02 09:31:39 -0400 (Mon, 02 Jun 2008) | 3 lines
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3341 Changed paths:
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3342 M /branches/prog/bwa/bwttop2.c
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3343 M /branches/prog/bwa/main.c
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3344
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3345 * bwa-0.1.0-6
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3346 * fix a bug for missing hits
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3347
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3348 ------------------------------------------------------------------------
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3349 r340 | lh3 | 2008-06-02 09:10:18 -0400 (Mon, 02 Jun 2008) | 3 lines
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3350 Changed paths:
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3351 M /branches/prog/bwa/bwttop2.c
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3352 M /branches/prog/bwa/main.c
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3353
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3354 * bwa-0.1.0-5
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3355 * accelerate comparisons in heap, a bit
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3356
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3357 ------------------------------------------------------------------------
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3358 r339 | lh3 | 2008-06-02 08:41:31 -0400 (Mon, 02 Jun 2008) | 3 lines
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3359 Changed paths:
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3360 M /branches/prog/bwa/bwt.c
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3361 M /branches/prog/bwa/bwt.h
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3362 M /branches/prog/bwa/bwttop2.c
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3363 M /branches/prog/bwa/main.c
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3364
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3365 * bwa-0.1.0-4
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3366 * avoid marginal repeated calculation in occ
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3367
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3368 ------------------------------------------------------------------------
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3369 r338 | lh3 | 2008-06-02 06:46:51 -0400 (Mon, 02 Jun 2008) | 5 lines
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3370 Changed paths:
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3371 M /branches/prog/bwa/Makefile
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3372 M /branches/prog/bwa/bwt.c
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3373 M /branches/prog/bwa/bwttop2.c
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3374 M /branches/prog/bwa/main.c
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3375
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3376 * bwa-0.1.0-3
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3377 * fix a bug caused by previours change
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3378 * fix a bug in heap
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3379 * order the heap by more criteria
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3380
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3381 ------------------------------------------------------------------------
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3382 r337 | lh3 | 2008-06-01 19:11:15 -0400 (Sun, 01 Jun 2008) | 4 lines
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3383 Changed paths:
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3384 M /branches/prog/bwa/bwttop2.c
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3385 M /branches/prog/bwa/main.c
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3386
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3387 * bwa-0.1.0-2
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3388 * also sort sa range in heapsort, in attempt to improve cache performance.
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3389 Unfortunately, it does not work well at all.
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3390
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3391 ------------------------------------------------------------------------
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3392 r336 | lh3 | 2008-06-01 17:45:23 -0400 (Sun, 01 Jun 2008) | 3 lines
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3393 Changed paths:
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3394 M /branches/prog/bwa/Makefile
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3395 M /branches/prog/bwa/Makefile.div
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3396 M /branches/prog/bwa/bntseq.c
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3397 M /branches/prog/bwa/main.c
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3398
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3399 * 0.1.0-1
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3400 * fix a bug in calculating the real coordinate
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3401
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3402 ------------------------------------------------------------------------
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3403 r335 | lh3 | 2008-06-01 16:03:09 -0400 (Sun, 01 Jun 2008) | 2 lines
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3404 Changed paths:
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3405 M /branches/prog/bwa/Makefile
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3406
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3407 nothing, really
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3408
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3409 ------------------------------------------------------------------------
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3410 r334 | lh3 | 2008-06-01 15:59:13 -0400 (Sun, 01 Jun 2008) | 2 lines
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3411 Changed paths:
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3412 M /branches/prog/bwa/Makefile
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3413 A /branches/prog/bwa/Makefile.div
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3414 M /branches/prog/bwa/bwtindex.c
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3415 M /branches/prog/bwa/pac2bwt.c
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3416
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3417 use IS algorithm by default
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3418
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3419 ------------------------------------------------------------------------
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3420 r333 | lh3 | 2008-06-01 15:05:15 -0400 (Sun, 01 Jun 2008) | 3 lines
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3421 Changed paths:
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3422 M /branches/prog/bwa/Makefile
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3423 M /branches/prog/bwa/bwtindex.c
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3424 M /branches/prog/bwa/is.c
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3425 M /branches/prog/bwa/pac2bwt.c
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3426
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3427 * a bit code clean up in is.c
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3428 * add IS algorithm for constructing BWT, albeit slower
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3429
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3430 ------------------------------------------------------------------------
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3431 r332 | lh3 | 2008-06-01 13:23:08 -0400 (Sun, 01 Jun 2008) | 2 lines
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3432 Changed paths:
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3433 A /branches/prog/bwa/is.c
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3434
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3435 IS linear-time algorithm for constructing SA/BWT
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3436
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3437 ------------------------------------------------------------------------
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3438 r331 | lh3 | 2008-06-01 10:35:26 -0400 (Sun, 01 Jun 2008) | 3 lines
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3439 Changed paths:
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3440 M /branches/prog/bwa/Makefile
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3441 M /branches/prog/bwa/bntseq.c
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3442 A /branches/prog/bwa/bwtindex.c
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3443 M /branches/prog/bwa/main.c
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3444 M /branches/prog/bwa/main.h
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3445
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3446 * fix a bug in generating .pac
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3447 * index in one go
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3448
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3449 ------------------------------------------------------------------------
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3450 r330 | lh3 | 2008-06-01 09:17:05 -0400 (Sun, 01 Jun 2008) | 2 lines
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3451 Changed paths:
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3452 M /branches/prog/bwa/bntseq.c
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3453 M /branches/prog/bwa/bntseq.h
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3454 M /branches/prog/bwa/bwtaln.c
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3455 M /branches/prog/bwa/bwttop2.c
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3456
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3457 real coordinates can be ouput
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3458
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3459 ------------------------------------------------------------------------
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3460 r329 | lh3 | 2008-05-31 19:21:02 -0400 (Sat, 31 May 2008) | 2 lines
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3461 Changed paths:
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3462 M /branches/prog/bwa/bwt2fmv.c
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3463 M /branches/prog/bwa/bwtaln.h
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3464 M /branches/prog/bwa/bwttop2.c
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3465
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3466 add top2e which is similar to 1away
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3467
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3468 ------------------------------------------------------------------------
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3469 r328 | lh3 | 2008-05-31 18:46:12 -0400 (Sat, 31 May 2008) | 3 lines
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3470 Changed paths:
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3471 M /branches/prog/bwa/bwt2fmv.c
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3472 M /branches/prog/bwa/bwtaln.c
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3473 M /branches/prog/bwa/bwtaln.h
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3474 M /branches/prog/bwa/bwttop2.c
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3475 M /branches/prog/bwa/main.c
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3476 M /branches/prog/bwa/main.h
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3477
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3478 * unified cmd-line interface for ungapped alignment
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3479 * add two alternatives to top2 algorithm
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3480
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3481 ------------------------------------------------------------------------
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3482 r327 | lh3 | 2008-05-31 18:14:46 -0400 (Sat, 31 May 2008) | 2 lines
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3483 Changed paths:
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3484 M /branches/prog/bwa/bwt2fmv.c
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3485 M /branches/prog/bwa/bwtaln.c
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3486 M /branches/prog/bwa/bwtaln.h
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3487 M /branches/prog/bwa/main.c
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3488 M /branches/prog/bwa/main.h
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3489
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3490 add cmd-line interface to alntop2
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3491
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3492 ------------------------------------------------------------------------
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3493 r326 | lh3 | 2008-05-31 17:59:31 -0400 (Sat, 31 May 2008) | 2 lines
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3494 Changed paths:
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3495 M /branches/prog/bwa/Makefile
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3496 M /branches/prog/bwa/bwt1away.c
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3497 M /branches/prog/bwa/bwtaln.c
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3498 M /branches/prog/bwa/bwtaln.h
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3499 A /branches/prog/bwa/bwttop2.c
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3500
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3501 top2 algorithm seems to work. I need to change interface, though
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3502
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3503 ------------------------------------------------------------------------
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3504 r325 | lh3 | 2008-05-31 15:11:49 -0400 (Sat, 31 May 2008) | 2 lines
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3505 Changed paths:
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3506 M /branches/prog/bwa/bwt1away.c
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3507
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3508 change the variable in the structure
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3509
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3510 ------------------------------------------------------------------------
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3511 r324 | lh3 | 2008-05-31 14:52:13 -0400 (Sat, 31 May 2008) | 2 lines
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3512 Changed paths:
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3513 M /branches/prog/bwa/bwt1away.c
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3514
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3515 set a slightly better bound on the maximum allowed mismatches
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3516
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3517 ------------------------------------------------------------------------
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3518 r323 | lh3 | 2008-05-30 18:40:21 -0400 (Fri, 30 May 2008) | 2 lines
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3519 Changed paths:
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3520 M /branches/prog/bwa/bwtaln.c
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3521
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3522 * output time statistics
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3523
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3524 ------------------------------------------------------------------------
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3525 r322 | lh3 | 2008-05-30 17:58:25 -0400 (Fri, 30 May 2008) | 4 lines
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3526 Changed paths:
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3527 M /branches/prog/bwa/Makefile
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3528 M /branches/prog/bwa/bwt.c
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3529 M /branches/prog/bwa/bwt.h
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3530 A /branches/prog/bwa/bwt1away.c
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3531 M /branches/prog/bwa/bwtaln.c
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3532 M /branches/prog/bwa/bwtaln.h
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3533
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3534 * presumably better way to make use of prefix. But for the moment I do
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3535 not know whether it is correct or not.
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3536 * a bit code clean up: separate alignment part
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3537
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3538 ------------------------------------------------------------------------
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3539 r321 | lh3 | 2008-05-30 13:57:43 -0400 (Fri, 30 May 2008) | 3 lines
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3540 Changed paths:
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3541 M /branches/prog/bwa/Makefile
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3542 M /branches/prog/bwa/bwt.c
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3543 M /branches/prog/bwa/bwt.h
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3544 M /branches/prog/bwa/bwt_gen/Makefile
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3545 M /branches/prog/bwa/bwt_gen/bwt_gen.c
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3546 M /branches/prog/bwa/bwtaln.c
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3547 M /branches/prog/bwa/main.c
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3548 M /branches/prog/bwa/main.h
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3549 M /branches/prog/bwa/pac2bwt.c
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3550
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diff changeset
3551 * a bit code clean up
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diff changeset
3552 * put bwt_gen in bwa
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3553
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3554 ------------------------------------------------------------------------
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3555 r320 | lh3 | 2008-05-30 11:40:11 -0400 (Fri, 30 May 2008) | 4 lines
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3556 Changed paths:
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3557 M /branches/prog/bwa/bwt.c
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3558 M /branches/prog/bwa/bwt2fmv.c
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3559 M /branches/prog/bwa/bwtaln.c
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3560 M /branches/prog/bwa/bwtaln.h
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3561 M /branches/prog/bwa/bwtio.c
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3562
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diff changeset
3563 * improve cmd-line interface
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diff changeset
3564 * fix a bug in loading .sa
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3565 * change default sa interval to 32
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3566
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3567 ------------------------------------------------------------------------
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3568 r319 | lh3 | 2008-05-30 10:31:37 -0400 (Fri, 30 May 2008) | 3 lines
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3569 Changed paths:
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3570 M /branches/prog/bwa/bwtaln.c
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3571
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3572 * fix memory leak (I know that. Just a bit lazy)
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3573 * change to another method to do 1-away alignment
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3574
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3575 ------------------------------------------------------------------------
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3576 r318 | lh3 | 2008-05-30 09:21:49 -0400 (Fri, 30 May 2008) | 2 lines
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3577 Changed paths:
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3578 M /branches/prog/bwa/bwt.c
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3579 M /branches/prog/bwa/bwt.h
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3580 M /branches/prog/bwa/bwt2fmv.c
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3581 M /branches/prog/bwa/bwtaln.c
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3582 M /branches/prog/bwa/bwtaln.h
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3583 M /branches/prog/bwa/main.c
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3584 M /branches/prog/bwa/main.h
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3585
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3586 best unique match is partially finished
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3587
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3588 ------------------------------------------------------------------------
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3589 r317 | lh3 | 2008-05-30 06:33:28 -0400 (Fri, 30 May 2008) | 2 lines
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3590 Changed paths:
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3591 M /branches/prog/bwa/bwt.c
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3592 M /branches/prog/bwa/bwt2fmv.c
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3593 M /branches/prog/bwa/bwtaln.c
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3594 M /branches/prog/bwa/bwtaln.h
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3595 M /branches/prog/bwa/main.c
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3596 M /branches/prog/bwa/main.h
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3597
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3598 remove "ungapped" command and related codes
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3599
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3600 ------------------------------------------------------------------------
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3601 r316 | lh3 | 2008-05-30 06:05:20 -0400 (Fri, 30 May 2008) | 2 lines
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3602 Changed paths:
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3603 M /branches/prog/bwa/Makefile
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3604 M /branches/prog/bwa/bwt.c
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3605 M /branches/prog/bwa/bwtaln.c
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3606 M /branches/prog/bwa/bwtaln.h
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3607
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3608 change variable name thick to width
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3609
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3610 ------------------------------------------------------------------------
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3611 r315 | lh3 | 2008-05-29 19:06:13 -0400 (Thu, 29 May 2008) | 2 lines
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3612 Changed paths:
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3613 M /branches/prog/bwa/bntseq.c
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3614 M /branches/prog/bwa/bwt.c
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3615 M /branches/prog/bwa/bwt.h
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3616 M /branches/prog/bwa/bwt2fmv.c
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3617 M /branches/prog/bwa/bwtaln.c
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3618 M /branches/prog/bwa/bwtaln.h
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3619 M /branches/prog/bwa/bwtio.c
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3620 M /branches/prog/bwa/main.c
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3621 M /branches/prog/bwa/main.h
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3622 M /branches/prog/bwa/pac2bwt.c
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3623
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3624 revised algorithm for ungapped alignment. the old one can still be used.
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3625
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3626 ------------------------------------------------------------------------
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3627 r314 | lh3 | 2008-05-29 16:36:11 -0400 (Thu, 29 May 2008) | 2 lines
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3628 Changed paths:
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3629 M /branches/prog/bwa/bwt2fmv.c
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3630 M /branches/prog/bwa/bwt_gen/bwt_gen.c
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3631 M /branches/prog/bwa/bwtio.c
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3632 M /branches/prog/bwa/pac2bwt.c
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3633
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3634 * make commands more independent, but ungapped does not work at the moment
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3635
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3636 ------------------------------------------------------------------------
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3637 r313 | lh3 | 2008-05-29 15:56:14 -0400 (Thu, 29 May 2008) | 2 lines
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3638 Changed paths:
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3639 M /branches/prog/bwa/bwt_gen/bwt_gen.c
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3640
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3641 little...
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3642
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3643 ------------------------------------------------------------------------
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3644 r312 | lh3 | 2008-05-29 15:54:01 -0400 (Thu, 29 May 2008) | 3 lines
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3645 Changed paths:
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3646 M /branches/prog/bwa/bwt_gen/bwt_gen.c
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3647 M /branches/prog/bwa/bwt_gen/bwt_gen.h
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3648
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3649 * add CopyRight information from the original codes
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3650 * do not dump .fmv files
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3651
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3652 ------------------------------------------------------------------------
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3653 r311 | lh3 | 2008-05-29 15:44:36 -0400 (Thu, 29 May 2008) | 2 lines
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3654 Changed paths:
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3655 A /branches/prog/bwa/bwt_gen
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3656 A /branches/prog/bwa/bwt_gen/Makefile
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3657 A /branches/prog/bwa/bwt_gen/QSufSort.c
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3658 A /branches/prog/bwa/bwt_gen/QSufSort.h
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3659 A /branches/prog/bwa/bwt_gen/bwt_gen.c
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3660 A /branches/prog/bwa/bwt_gen/bwt_gen.h
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3661
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3662 codes from BWT-SW, for building BWT from packed file
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3663
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3664 ------------------------------------------------------------------------
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3665 r310 | lh3 | 2008-05-28 17:03:35 -0400 (Wed, 28 May 2008) | 4 lines
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3666 Changed paths:
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3667 M /branches/prog/bwa/bwt.c
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3668 M /branches/prog/bwa/bwt.h
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3669 M /branches/prog/bwa/bwt2fmv.c
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3670 M /branches/prog/bwa/bwtio.c
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3671 M /branches/prog/bwa/main.c
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3672 M /branches/prog/bwa/main.h
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3673
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3674 * change OCC_INTERVAL to 0x40, which makes bwa twice as fast.
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3675 * write Occ file as ".occ" as it is using a different interval from
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3676 .fmv, the BWT-SW correspondance of .occ
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3677
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3678 ------------------------------------------------------------------------
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3679 r309 | lh3 | 2008-05-28 11:39:37 -0400 (Wed, 28 May 2008) | 2 lines
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3680 Changed paths:
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3681 M /branches/prog/bwa/bwt.c
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3682 M /branches/prog/bwa/bwt2fmv.c
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3683
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diff changeset
3684 fix a bug
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3685
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3686 ------------------------------------------------------------------------
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3687 r308 | lh3 | 2008-05-28 09:56:16 -0400 (Wed, 28 May 2008) | 4 lines
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3688 Changed paths:
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3689 M /branches/prog/bwa/bwt.c
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3690 M /branches/prog/bwa/bwt2fmv.c
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3691
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3692 add heuristics to improve the speed, but I have not tested whether the
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3693 results are correct or not.
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3694
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3695
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3696 ------------------------------------------------------------------------
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3697 r307 | lh3 | 2008-05-28 06:31:34 -0400 (Wed, 28 May 2008) | 5 lines
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3698 Changed paths:
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3699 M /branches/prog/bwa/bwt.c
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3700 M /branches/prog/bwa/bwt2fmv.c
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3701 M /branches/prog/bwa/bwtaln.c
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3702 M /branches/prog/bwa/bwtaln.h
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3703 M /branches/prog/bwa/main.c
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3704 M /branches/prog/bwa/main.h
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3705
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3706 * make ungapped alignment basically works...
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3707 * but it is very slow in comparison to others...
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3708 * also I need to improve the interface...
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3709 * a lot of things to keep me busy today...
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3710
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3711 ------------------------------------------------------------------------
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3712 r306 | lh3 | 2008-05-27 18:41:27 -0400 (Tue, 27 May 2008) | 3 lines
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3713 Changed paths:
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3714 M /branches/prog/bwa/bwt.c
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3715 M /branches/prog/bwa/bwt.h
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3716 M /branches/prog/bwa/bwtaln.c
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3717
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3718 * remove recursion
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3719 * fixed a bug in bwt_occ()
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3720
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3721 ------------------------------------------------------------------------
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3722 r305 | lh3 | 2008-05-27 16:59:44 -0400 (Tue, 27 May 2008) | 5 lines
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3723 Changed paths:
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3724 M /branches/prog/bwa/bwt.c
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3725 M /branches/prog/bwa/bwt.h
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3726 M /branches/prog/bwa/bwtaln.c
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3727
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3728 * bwa now tells whether a sequenced can be mapped with maximum allowed
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3729 mismatches. ONLY ungapped.
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3730 * this is a recursive version. I will remove recursion later.
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3731
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3732
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3733 ------------------------------------------------------------------------
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3734 r304 | lh3 | 2008-05-27 09:12:17 -0400 (Tue, 27 May 2008) | 3 lines
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3735 Changed paths:
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3736 M /branches/prog/bwa/Makefile
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3737 M /branches/prog/bwa/bwt.c
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3738 M /branches/prog/bwa/bwt.h
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3739 M /branches/prog/bwa/bwt2fmv.c
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3740 A /branches/prog/bwa/bwtaln.c
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3741 A /branches/prog/bwa/bwtaln.h
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3742 M /branches/prog/bwa/bwtio.c
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3743 M /branches/prog/bwa/main.c
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3744 M /branches/prog/bwa/main.h
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3745 M /branches/prog/bwa/utils.c
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3746
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3747 * load .sa and .fmv files
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3748 * exact alignment now works
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3749
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3750 ------------------------------------------------------------------------
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3751 r303 | lh3 | 2008-05-27 06:33:38 -0400 (Tue, 27 May 2008) | 2 lines
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3752 Changed paths:
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3753 M /branches/prog/bwa/bntseq.c
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3754 M /branches/prog/bwa/bwt.c
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3755 M /branches/prog/bwa/bwtio.c
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3756 M /branches/prog/bwa/utils.c
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3757 M /branches/prog/bwa/utils.h
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3758
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diff changeset
3759 add xassert and fix a bug
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3760
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3761 ------------------------------------------------------------------------
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3762 r302 | lh3 | 2008-05-27 06:23:20 -0400 (Tue, 27 May 2008) | 2 lines
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3763 Changed paths:
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3764 M /branches/prog/bwa/Makefile
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3765 M /branches/prog/bwa/bntseq.c
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3766 M /branches/prog/bwa/bwt.c
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3767 M /branches/prog/bwa/bwtio.c
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3768 A /branches/prog/bwa/utils.c
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3769 A /branches/prog/bwa/utils.h
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3770
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diff changeset
3771 improve error message and error handling
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3772
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3773 ------------------------------------------------------------------------
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3774 r301 | lh3 | 2008-05-27 05:37:51 -0400 (Tue, 27 May 2008) | 4 lines
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3775 Changed paths:
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3776 M /branches/prog/bwa/Makefile
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3777 M /branches/prog/bwa/bwt.c
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3778 M /branches/prog/bwa/bwt.h
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3779 M /branches/prog/bwa/bwt2fmv.c
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3780 A /branches/prog/bwa/bwtio.c
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3781 M /branches/prog/bwa/main.c
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3782 M /branches/prog/bwa/main.h
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3783
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3784 * move I/O codes to bwtio.c
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3785 * SA can be dumped and interestingly, it is identical to BWTSW
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3786 * now, .fmv is still different from BWTSW
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3787
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3788 ------------------------------------------------------------------------
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3789 r299 | lh3 | 2008-05-26 18:07:44 -0400 (Mon, 26 May 2008) | 2 lines
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3790 Changed paths:
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3791 M /branches/prog/bwa/Makefile
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3792 M /branches/prog/bwa/bwt.c
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3793 M /branches/prog/bwa/bwt.h
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3794 M /branches/prog/bwa/bwt2fmv.c
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3795
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3796 generate/retrieve SA and Occ
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3797
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3798 ------------------------------------------------------------------------
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3799 r298 | lh3 | 2008-05-26 13:16:49 -0400 (Mon, 26 May 2008) | 3 lines
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3800 Changed paths:
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3801 M /branches/prog/bwa/bntseq.h
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3802 M /branches/prog/bwa/bwt.c
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3803 M /branches/prog/bwa/bwt.h
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3804 M /branches/prog/bwa/bwt2fmv.c
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3805
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3806 * retrieve occ value at any position
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3807 * move bwt_cal_occ() to bwt.c
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3808
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3809 ------------------------------------------------------------------------
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3810 r297 | lh3 | 2008-05-25 17:43:58 -0400 (Sun, 25 May 2008) | 6 lines
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3811 Changed paths:
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3812 M /branches/prog/bwa/Makefile
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3813 A /branches/prog/bwa/bwt.c
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3814 A /branches/prog/bwa/bwt.h
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3815 A /branches/prog/bwa/bwt2fmv.c
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3816 M /branches/prog/bwa/main.c
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3817 M /branches/prog/bwa/main.h
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3818 M /branches/prog/bwa/pac2bwt.c
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3819
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3820 * add bwt2fmv. It works to some extend. However, I do not understand
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3821 the purpose of some weird codes in BWT-SW. As a consequence, bwt2fmv
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3822 could generate a file almost identical, but not exactly identical, to
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3823 the .fmv file from BWT-SW.
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3824
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3825
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3826 ------------------------------------------------------------------------
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3827 r296 | lh3 | 2008-05-24 18:35:02 -0400 (Sat, 24 May 2008) | 5 lines
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3828 Changed paths:
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3829 M /branches/prog/bwa/Makefile
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3830 M /branches/prog/bwa/bntseq.c
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3831 M /branches/prog/bwa/bntseq.h
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3832 M /branches/prog/bwa/main.c
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3833 M /branches/prog/bwa/main.h
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3834 A /branches/prog/bwa/pac2bwt.c
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3835
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3836 Burrows-Wheeler Transform now works. At least on one example, the
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3837 current code generates the same BWT as BWT-SW. Kind of magical, I would
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3838 say. :)
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3839
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3840
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3841 ------------------------------------------------------------------------
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3842 r295 | lh3 | 2008-05-24 11:25:31 -0400 (Sat, 24 May 2008) | 3 lines
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3843 Changed paths:
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3844 A /branches/prog/bwa/Makefile
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3845 M /branches/prog/bwa/bntseq.c
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3846 A /branches/prog/bwa/main.c
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3847 A /branches/prog/bwa/main.h
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3848
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3849 * add Makefile and main.*
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3850 * improve interface to fa2bns, a bit
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3851
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3852 ------------------------------------------------------------------------
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3853 r293 | lh3 | 2008-05-24 10:57:03 -0400 (Sat, 24 May 2008) | 3 lines
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3854 Changed paths:
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3855 A /branches/prog/bwa
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3856 A /branches/prog/bwa/bntseq.c
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3857 A /branches/prog/bwa/bntseq.h
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3858 A /branches/prog/bwa/seq.c
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3859 A /branches/prog/bwa/seq.h
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3860
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3861 * Burrow-Wheeler Alignment
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3862 * initial codes
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3863
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3864 ------------------------------------------------------------------------