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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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9
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10 ------------------------------------------------------------------------
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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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16
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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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39
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40 ------------------------------------------------------------------------
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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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50 ------------------------------------------------------------------------
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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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58
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59 ------------------------------------------------------------------------
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60 r1559 | lh3 | 2010-12-10 00:10:48 -0500 (Fri, 10 Dec 2010) | 2 lines
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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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66
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67 ------------------------------------------------------------------------
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68 r1558 | lh3 | 2010-12-10 00:09:22 -0500 (Fri, 10 Dec 2010) | 4 lines
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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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77
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78 ------------------------------------------------------------------------
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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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86 ------------------------------------------------------------------------
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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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93
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94 ------------------------------------------------------------------------
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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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115 ------------------------------------------------------------------------
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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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124 ------------------------------------------------------------------------
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125 r1542 | lh3 | 2010-11-22 23:50:56 -0500 (Mon, 22 Nov 2010) | 3 lines
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126 Changed paths:
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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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133 ------------------------------------------------------------------------
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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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148 ------------------------------------------------------------------------
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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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155
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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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158 Changed paths:
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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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166 ------------------------------------------------------------------------
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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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172
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173 ------------------------------------------------------------------------
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174 r1450 | lh3 | 2010-06-15 09:42:21 -0400 (Tue, 15 Jun 2010) | 3 lines
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175 Changed paths:
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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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182 ------------------------------------------------------------------------
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183 r1445 | lh3 | 2010-06-11 08:58:33 -0400 (Fri, 11 Jun 2010) | 2 lines
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184 Changed paths:
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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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190 ------------------------------------------------------------------------
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191 r1442 | lh3 | 2010-06-08 10:22:14 -0400 (Tue, 08 Jun 2010) | 2 lines
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192 Changed paths:
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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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360 M /branches/prog/bwa/bwtaln.h
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361 M /branches/prog/bwa/main.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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371 M /branches/prog/bwa/main.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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387 ------------------------------------------------------------------------
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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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401 M /branches/prog/bwa/bwape.c
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402 M /branches/prog/bwa/bwase.c
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403 M /branches/prog/bwa/bwtaln.c
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404 M /branches/prog/bwa/bwtaln.h
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405 M /branches/prog/bwa/cs2nt.c
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406 M /branches/prog/bwa/main.c
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407 M /branches/prog/bwa/stdaln.h
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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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424 M /branches/prog/bwa/main.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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433 M /branches/prog/bwa/bwase.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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446 M /branches/prog/bwa/bwase.c
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447 M /branches/prog/bwa/bwaseqio.c
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448 M /branches/prog/bwa/bwtaln.h
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449 M /branches/prog/bwa/main.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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478 M /branches/prog/bwa/main.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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537 M /branches/prog/bwa/main.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)
|
|
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
|
|
708 * bwa-0.5.0-4 (r1205)
|
|
709 * reduce false coordinates and CIGAR when a query bridges two reference
|
|
710 sequences, although some very rare cases may fail bwa.
|
|
711
|
|
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
|
|
729 * bwa-0.5.0-2 (r1203)
|
|
730 * dBWT-SW: change a parameter in calculating mapping quality
|
|
731 * fixed a bug in samse
|
|
732
|
|
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
|
|
739 * bwa-0.5.0-1 (r1202)
|
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740 * change default band width to 50
|
|
741 * improve mapping quality a bit
|
|
742
|
|
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)
|
|
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
|
|
766 * bwa-0.4.9-36 (r1198)
|
|
767 * simplify duphits removal. The accuracy is changed a tiny bit, sometimes better, sometimes worse.
|
|
768
|
|
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
|
|
777 * bwa-0.4.9-35 (r1197)
|
|
778 * further heuristic acceleration for long queries
|
|
779
|
|
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
|
|
787 * bwa-0.4.9-34 (r1196)
|
|
788 * updated the manual page
|
|
789 * output base quality if the input is fastq
|
|
790
|
|
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
|
|
799 * bwa-0.4.9-33 (r1191)
|
|
800 * fixed a bug in sampe/samse when gaps occur to the 5'-end in SW alignment
|
|
801 * in dbwtsw adjust -T and -c according to -a
|
|
802
|
|
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
|
|
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)
|
|
825 * only help messages are changed
|
|
826
|
|
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)
|
|
837 * in bwape/bwase, print CIGAR "*" if the read is unmapped
|
|
838 * improved the calculation of mapping quality
|
|
839
|
|
840 ------------------------------------------------------------------------
|
|
841 r1181 | lh3 | 2009-08-03 12:09:41 -0400 (Mon, 03 Aug 2009) | 2 lines
|
|
842 Changed paths:
|
|
843 M /branches/prog/bwa/bwtsw2_aux.c
|
|
844
|
|
845 fflush()
|
|
846
|
|
847 ------------------------------------------------------------------------
|
|
848 r1180 | lh3 | 2009-08-03 12:08:46 -0400 (Mon, 03 Aug 2009) | 4 lines
|
|
849 Changed paths:
|
|
850 M /branches/prog/bwa/bwtsw2_aux.c
|
|
851 M /branches/prog/bwa/main.c
|
|
852
|
|
853 * bwa-0.4.9-30 (r1180)
|
|
854 * fixed a memory problem
|
|
855 * multi-threading sometimes does not work...
|
|
856
|
|
857 ------------------------------------------------------------------------
|
|
858 r1179 | lh3 | 2009-08-03 11:04:39 -0400 (Mon, 03 Aug 2009) | 3 lines
|
|
859 Changed paths:
|
|
860 M /branches/prog/bwa/Makefile
|
|
861 M /branches/prog/bwa/bwtsw2.h
|
|
862 M /branches/prog/bwa/bwtsw2_aux.c
|
|
863 M /branches/prog/bwa/bwtsw2_main.c
|
|
864 M /branches/prog/bwa/main.c
|
|
865
|
|
866 * bwa-0.4.9-29 (r1179)
|
|
867 * preliminary mutli-threading support in dbwtsw
|
|
868
|
|
869 ------------------------------------------------------------------------
|
|
870 r1178 | lh3 | 2009-08-03 09:14:54 -0400 (Mon, 03 Aug 2009) | 3 lines
|
|
871 Changed paths:
|
|
872 M /branches/prog/bwa/bwtsw2_aux.c
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|
873 M /branches/prog/bwa/bwtsw2_main.c
|
|
874 M /branches/prog/bwa/main.c
|
|
875
|
|
876 * bwa-0.4.9-28 (r1178)
|
|
877 * fixed a bug in printing repetitive hits
|
|
878
|
|
879 ------------------------------------------------------------------------
|
|
880 r1177 | lh3 | 2009-08-03 05:03:42 -0400 (Mon, 03 Aug 2009) | 3 lines
|
|
881 Changed paths:
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|
882 M /branches/prog/bwa/bwtsw2_core.c
|
|
883 M /branches/prog/bwa/main.c
|
|
884
|
|
885 * bwa-0.4.9-27 (r1177)
|
|
886 * bwtsw2: fixed a hidden memory leak
|
|
887
|
|
888 ------------------------------------------------------------------------
|
|
889 r1176 | lh3 | 2009-07-31 10:58:24 -0400 (Fri, 31 Jul 2009) | 3 lines
|
|
890 Changed paths:
|
|
891 M /branches/prog/bwa/bwtsw2_aux.c
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|
892 M /branches/prog/bwa/bwtsw2_main.c
|
|
893 M /branches/prog/bwa/main.c
|
|
894
|
|
895 * bwa-0.4.9-26
|
|
896 * change the way mapping quality is calculated
|
|
897
|
|
898 ------------------------------------------------------------------------
|
|
899 r1175 | lh3 | 2009-07-31 09:15:54 -0400 (Fri, 31 Jul 2009) | 4 lines
|
|
900 Changed paths:
|
|
901 M /branches/prog/bwa/bwtsw2.h
|
|
902 M /branches/prog/bwa/bwtsw2_aux.c
|
|
903 M /branches/prog/bwa/bwtsw2_core.c
|
|
904 M /branches/prog/bwa/bwtsw2_main.c
|
|
905 M /branches/prog/bwa/main.c
|
|
906
|
|
907 * bwa-0.4.9-25
|
|
908 * code clean up
|
|
909 * automatically adjust ->t and ->is_rev based on input
|
|
910
|
|
911 ------------------------------------------------------------------------
|
|
912 r1174 | lh3 | 2009-07-30 08:50:25 -0400 (Thu, 30 Jul 2009) | 3 lines
|
|
913 Changed paths:
|
|
914 M /branches/prog/bwa/bwtsw2_aux.c
|
|
915 M /branches/prog/bwa/main.c
|
|
916
|
|
917 * bwa-0.4.9-24
|
|
918 * fixed a bug in printing the hits
|
|
919
|
|
920 ------------------------------------------------------------------------
|
|
921 r1173 | lh3 | 2009-07-29 18:32:43 -0400 (Wed, 29 Jul 2009) | 4 lines
|
|
922 Changed paths:
|
|
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
|
|
926 M /branches/prog/bwa/main.c
|
|
927
|
|
928 * bwa-0.4.9-23
|
|
929 * allow to skip reverse alignment
|
|
930 * increase opt->t to 37
|
|
931
|
|
932 ------------------------------------------------------------------------
|
|
933 r1172 | lh3 | 2009-07-29 17:22:39 -0400 (Wed, 29 Jul 2009) | 3 lines
|
|
934 Changed paths:
|
|
935 M /branches/prog/bwa/bwtsw2_aux.c
|
|
936 M /branches/prog/bwa/bwtsw2_main.c
|
|
937 M /branches/prog/bwa/main.c
|
|
938
|
|
939 * bwa-0.4.9-22
|
|
940 * report if the hit is found in both directions
|
|
941
|
|
942 ------------------------------------------------------------------------
|
|
943 r1171 | lh3 | 2009-07-29 17:12:02 -0400 (Wed, 29 Jul 2009) | 3 lines
|
|
944 Changed paths:
|
|
945 M /branches/prog/bwa/bwtsw2.h
|
|
946 M /branches/prog/bwa/bwtsw2_aux.c
|
|
947 M /branches/prog/bwa/bwtsw2_main.c
|
|
948 M /branches/prog/bwa/main.c
|
|
949
|
|
950 * bwa-0.4.9-21
|
|
951 * dbwtsw: map to both forward and reverse BWT to reduce false alignment
|
|
952
|
|
953 ------------------------------------------------------------------------
|
|
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
|
|
957 M /branches/prog/bwa/main.c
|
|
958
|
|
959 save hits before cut_tail()
|
|
960
|
|
961 ------------------------------------------------------------------------
|
|
962 r1169 | lh3 | 2009-07-29 08:06:01 -0400 (Wed, 29 Jul 2009) | 3 lines
|
|
963 Changed paths:
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|
964 M /branches/prog/bwa/bwtsw2.h
|
|
965 M /branches/prog/bwa/bwtsw2_aux.c
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|
966 M /branches/prog/bwa/bwtsw2_core.c
|
|
967 M /branches/prog/bwa/main.c
|
|
968 M /branches/prog/bwa/stdaln.c
|
|
969 M /branches/prog/bwa/stdaln.h
|
|
970
|
|
971 * bwa-0.4.9-19
|
|
972 * use a global memory pool to reduce the CPU time spent on malloc/free().
|
|
973
|
|
974 ------------------------------------------------------------------------
|
|
975 r1168 | lh3 | 2009-07-29 06:13:29 -0400 (Wed, 29 Jul 2009) | 5 lines
|
|
976 Changed paths:
|
|
977 M /branches/prog/bwa/bwtsw2.h
|
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978 M /branches/prog/bwa/bwtsw2_aux.c
|
|
979 M /branches/prog/bwa/bwtsw2_core.c
|
|
980 M /branches/prog/bwa/bwtsw2_main.c
|
|
981 M /branches/prog/bwa/main.c
|
|
982
|
|
983 * bwa-0.4.9-18
|
|
984 * reduce unnecessary extension to the 5'-end
|
|
985 * allow to use different interval size for the 2 rounds
|
|
986 * change default parameters
|
|
987
|
|
988 ------------------------------------------------------------------------
|
|
989 r1167 | lh3 | 2009-07-28 19:06:17 -0400 (Tue, 28 Jul 2009) | 3 lines
|
|
990 Changed paths:
|
|
991 M /branches/prog/bwa/bwtsw2_core.c
|
|
992 M /branches/prog/bwa/main.c
|
|
993
|
|
994 * bwa-0.4.9-17
|
|
995 * dbwtsw: fixed THE memory leak.
|
|
996
|
|
997 ------------------------------------------------------------------------
|
|
998 r1166 | lh3 | 2009-07-28 16:31:41 -0400 (Tue, 28 Jul 2009) | 5 lines
|
|
999 Changed paths:
|
|
1000 M /branches/prog/bwa/bwtsw2_aux.c
|
|
1001 M /branches/prog/bwa/bwtsw2_core.c
|
|
1002 M /branches/prog/bwa/bwtsw2_main.c
|
|
1003 M /branches/prog/bwa/main.c
|
|
1004 M /branches/prog/bwa/stdaln.c
|
|
1005
|
|
1006 * bwa-0.4.9-16
|
|
1007 * fixed a memory leak
|
|
1008 * a small memory leak still occurs to bwtsw2_core(). I will work on that later.
|
|
1009 * changed the default parameters
|
|
1010
|
|
1011 ------------------------------------------------------------------------
|
|
1012 r1165 | lh3 | 2009-07-28 10:15:40 -0400 (Tue, 28 Jul 2009) | 4 lines
|
|
1013 Changed paths:
|
|
1014 M /branches/prog/bwa/bwtsw2_aux.c
|
|
1015 M /branches/prog/bwa/bwtsw2_core.c
|
|
1016 M /branches/prog/bwa/main.c
|
|
1017 M /branches/prog/bwa/stdaln.c
|
|
1018
|
|
1019 * bwa-0.4.9-15
|
|
1020 * generate CIGAR right before output. This saves unnecessary computation.
|
|
1021 * this version may be buggy as I have not tested it.
|
|
1022
|
|
1023 ------------------------------------------------------------------------
|
|
1024 r1164 | lh3 | 2009-07-28 09:04:14 -0400 (Tue, 28 Jul 2009) | 11 lines
|
|
1025 Changed paths:
|
|
1026 M /branches/prog/bwa/bwtsw2.h
|
|
1027 M /branches/prog/bwa/bwtsw2_aux.c
|
|
1028 M /branches/prog/bwa/bwtsw2_core.c
|
|
1029 M /branches/prog/bwa/main.c
|
|
1030 M /branches/prog/bwa/stdaln.c
|
|
1031 M /branches/prog/bwa/stdaln.h
|
|
1032
|
|
1033 * bwa-0.4.9-14
|
|
1034
|
|
1035 * deplete unique hits in dbwtsw and postprocess them with standard sw
|
|
1036
|
|
1037 * in principle, this stratgy should be faster and more accurate, but I
|
|
1038 have not tested this point. I may switch back to the old method if
|
|
1039 this does not work.
|
|
1040
|
|
1041 * the code looks quite nasty now. it needs clean up...
|
|
1042
|
|
1043
|
|
1044 ------------------------------------------------------------------------
|
|
1045 r1163 | lh3 | 2009-07-27 17:41:10 -0400 (Mon, 27 Jul 2009) | 2 lines
|
|
1046 Changed paths:
|
|
1047 M /branches/prog/bwa/bwtsw2_aux.c
|
|
1048
|
|
1049 change a default parameter
|
|
1050
|
|
1051 ------------------------------------------------------------------------
|
|
1052 r1162 | lh3 | 2009-07-27 17:04:35 -0400 (Mon, 27 Jul 2009) | 3 lines
|
|
1053 Changed paths:
|
|
1054 M /branches/prog/bwa/bwtsw2.h
|
|
1055 M /branches/prog/bwa/bwtsw2_aux.c
|
|
1056 M /branches/prog/bwa/bwtsw2_core.c
|
|
1057 M /branches/prog/bwa/bwtsw2_main.c
|
|
1058 M /branches/prog/bwa/main.c
|
|
1059
|
|
1060 * bwa-0.4.9-13
|
|
1061 * dbwtsw: switch between small and large Z-best
|
|
1062
|
|
1063 ------------------------------------------------------------------------
|
|
1064 r1161 | lh3 | 2009-07-27 12:17:41 -0400 (Mon, 27 Jul 2009) | 4 lines
|
|
1065 Changed paths:
|
|
1066 M /branches/prog/bwa/bwtsw2_aux.c
|
|
1067 M /branches/prog/bwa/bwtsw2_core.c
|
|
1068 M /branches/prog/bwa/main.c
|
|
1069
|
|
1070 * bwa-0.4.9-12
|
|
1071 * changed the default -z to 100
|
|
1072 * heuristically speed up alignments for polyA reads
|
|
1073
|
|
1074 ------------------------------------------------------------------------
|
|
1075 r1160 | lh3 | 2009-07-27 07:50:57 -0400 (Mon, 27 Jul 2009) | 6 lines
|
|
1076 Changed paths:
|
|
1077 M /branches/prog/bwa/bwtsw2.h
|
|
1078 M /branches/prog/bwa/bwtsw2_aux.c
|
|
1079 M /branches/prog/bwa/bwtsw2_core.c
|
|
1080 M /branches/prog/bwa/main.c
|
|
1081
|
|
1082 * bwa-0.4.9-11
|
|
1083
|
|
1084 * dbwtsw potentially generates less false alignments, although in
|
|
1085 practice, the modification brings no improvement.
|
|
1086
|
|
1087
|
|
1088 ------------------------------------------------------------------------
|
|
1089 r1159 | lh3 | 2009-07-27 04:37:02 -0400 (Mon, 27 Jul 2009) | 4 lines
|
|
1090 Changed paths:
|
|
1091 M /branches/prog/bwa/bwase.c
|
|
1092 M /branches/prog/bwa/bwtsw2_aux.c
|
|
1093 M /branches/prog/bwa/bwtsw2_core.c
|
|
1094 M /branches/prog/bwa/main.c
|
|
1095
|
|
1096 * bwa-0.4.9-10
|
|
1097 * disabled debugging code
|
|
1098 * add "BAM_FMU" if both ends are unmapped
|
|
1099
|
|
1100 ------------------------------------------------------------------------
|
|
1101 r1158 | lh3 | 2009-07-24 09:36:52 -0400 (Fri, 24 Jul 2009) | 2 lines
|
|
1102 Changed paths:
|
|
1103 M /branches/prog/bwa/main.c
|
|
1104
|
|
1105 nothing, really
|
|
1106
|
|
1107 ------------------------------------------------------------------------
|
|
1108 r1157 | lh3 | 2009-07-24 09:05:44 -0400 (Fri, 24 Jul 2009) | 3 lines
|
|
1109 Changed paths:
|
|
1110 M /branches/prog/bwa/bwtsw2_aux.c
|
|
1111 M /branches/prog/bwa/bwtsw2_core.c
|
|
1112 M /branches/prog/bwa/main.c
|
|
1113
|
|
1114 * bwa-0.4.9-9
|
|
1115 * bwtsw2: generate SAM output
|
|
1116
|
|
1117 ------------------------------------------------------------------------
|
|
1118 r1156 | lh3 | 2009-07-24 05:42:47 -0400 (Fri, 24 Jul 2009) | 6 lines
|
|
1119 Changed paths:
|
|
1120 M /branches/prog/bwa/bwape.c
|
|
1121 M /branches/prog/bwa/main.c
|
|
1122
|
|
1123 * bwa-0.4.9-8
|
|
1124
|
|
1125 * fixed a weird deadloop which only happens to icc -O3. Thanks John
|
|
1126 Marshall for the fix.
|
|
1127
|
|
1128
|
|
1129 ------------------------------------------------------------------------
|
|
1130 r1155 | lh3 | 2009-07-24 05:28:40 -0400 (Fri, 24 Jul 2009) | 8 lines
|
|
1131 Changed paths:
|
|
1132 M /branches/prog/bwa/bwtsw2_aux.c
|
|
1133 M /branches/prog/bwa/bwtsw2_core.c
|
|
1134 M /branches/prog/bwa/main.c
|
|
1135
|
|
1136 * bwa-0.4.9-7
|
|
1137
|
|
1138 * fixed a typo in bwtsw2 alignment. Now score from the standard SW
|
|
1139 seems to agree with score from bwtsw2, except that in reporting
|
|
1140 alignments, bwtsw2 may report non-optimal segments. This is expected,
|
|
1141 though. I will improve in future.
|
|
1142
|
|
1143
|
|
1144 ------------------------------------------------------------------------
|
|
1145 r1154 | lh3 | 2009-07-23 17:40:20 -0400 (Thu, 23 Jul 2009) | 3 lines
|
|
1146 Changed paths:
|
|
1147 M /branches/prog/bwa/stdaln.c
|
|
1148 M /branches/prog/bwa/stdaln.h
|
|
1149
|
|
1150 * aln_left_core() seems to work properly
|
|
1151 * aln_local_core() has a bug... AN EVER EXISTING BUG!!!!!!!!!!!
|
|
1152
|
|
1153 ------------------------------------------------------------------------
|
|
1154 r1153 | lh3 | 2009-07-23 17:06:09 -0400 (Thu, 23 Jul 2009) | 2 lines
|
|
1155 Changed paths:
|
|
1156 M /branches/prog/bwa/stdaln.c
|
|
1157
|
|
1158 removed debugging code...
|
|
1159
|
|
1160 ------------------------------------------------------------------------
|
|
1161 r1152 | lh3 | 2009-07-23 17:01:00 -0400 (Thu, 23 Jul 2009) | 3 lines
|
|
1162 Changed paths:
|
|
1163 M /branches/prog/bwa/stdaln.c
|
|
1164
|
|
1165 * radical changes failed...
|
|
1166 * fixed a bug
|
|
1167
|
|
1168 ------------------------------------------------------------------------
|
|
1169 r1151 | lh3 | 2009-07-23 14:46:35 -0400 (Thu, 23 Jul 2009) | 2 lines
|
|
1170 Changed paths:
|
|
1171 M /branches/prog/bwa/stdaln.c
|
|
1172
|
|
1173 temporary changes. Will apply some radical changes to this file...
|
|
1174
|
|
1175 ------------------------------------------------------------------------
|
|
1176 r1150 | lh3 | 2009-07-23 10:09:56 -0400 (Thu, 23 Jul 2009) | 2 lines
|
|
1177 Changed paths:
|
|
1178 M /branches/prog/bwa/bwtsw2_aux.c
|
|
1179 M /branches/prog/bwa/bwtsw2_main.c
|
|
1180 M /branches/prog/bwa/stdaln.c
|
|
1181
|
|
1182 fixed a long-existing bug in Smith-Waterman alignment
|
|
1183
|
|
1184 ------------------------------------------------------------------------
|
|
1185 r1149 | lh3 | 2009-07-23 08:50:52 -0400 (Thu, 23 Jul 2009) | 3 lines
|
|
1186 Changed paths:
|
|
1187 M /branches/prog/bwa/bwtsw2.h
|
|
1188 M /branches/prog/bwa/bwtsw2_aux.c
|
|
1189 M /branches/prog/bwa/bwtsw2_main.c
|
|
1190 M /branches/prog/bwa/main.c
|
|
1191 M /branches/prog/bwa/simple_dp.c
|
|
1192 M /branches/prog/bwa/stdaln.c
|
|
1193 M /branches/prog/bwa/stdaln.h
|
|
1194
|
|
1195 * bwa-0.4.9-6
|
|
1196 * unexplained inconsistency still occurs, but the results largely look reasonable.
|
|
1197
|
|
1198 ------------------------------------------------------------------------
|
|
1199 r1148 | lh3 | 2009-07-23 08:07:29 -0400 (Thu, 23 Jul 2009) | 2 lines
|
|
1200 Changed paths:
|
|
1201 M /branches/prog/bwa/stdaln.c
|
|
1202
|
|
1203 half DP
|
|
1204
|
|
1205 ------------------------------------------------------------------------
|
|
1206 r1147 | lh3 | 2009-07-22 08:03:06 -0400 (Wed, 22 Jul 2009) | 2 lines
|
|
1207 Changed paths:
|
|
1208 M /branches/prog/bwa/bwtsw2.h
|
|
1209 M /branches/prog/bwa/bwtsw2_aux.c
|
|
1210 M /branches/prog/bwa/bwtsw2_core.c
|
|
1211 M /branches/prog/bwa/bwtsw2_main.c
|
|
1212
|
|
1213 a bit code clean up
|
|
1214
|
|
1215 ------------------------------------------------------------------------
|
|
1216 r1145 | lh3 | 2009-07-21 15:52:05 -0400 (Tue, 21 Jul 2009) | 4 lines
|
|
1217 Changed paths:
|
|
1218 M /branches/prog/bwa/bwtsw2_aux.c
|
|
1219 M /branches/prog/bwa/bwtsw2_core.c
|
|
1220 M /branches/prog/bwa/main.c
|
|
1221
|
|
1222 * bwa-0.4.9-5
|
|
1223 * fixed a bug in determining sub-optimal hits
|
|
1224 * removed some debugging codes
|
|
1225
|
|
1226 ------------------------------------------------------------------------
|
|
1227 r1144 | lh3 | 2009-07-21 10:17:29 -0400 (Tue, 21 Jul 2009) | 4 lines
|
|
1228 Changed paths:
|
|
1229 M /branches/prog/bwa/bwtsw2.h
|
|
1230 M /branches/prog/bwa/bwtsw2_aux.c
|
|
1231 M /branches/prog/bwa/bwtsw2_core.c
|
|
1232 M /branches/prog/bwa/bwtsw2_main.c
|
|
1233 M /branches/prog/bwa/main.c
|
|
1234
|
|
1235 * bwa-0.4.9-4
|
|
1236 * better cmd interface
|
|
1237 * faster speed
|
|
1238
|
|
1239 ------------------------------------------------------------------------
|
|
1240 r1143 | lh3 | 2009-07-20 16:38:18 -0400 (Mon, 20 Jul 2009) | 3 lines
|
|
1241 Changed paths:
|
|
1242 M /branches/prog/bwa/bwtsw2.h
|
|
1243 M /branches/prog/bwa/bwtsw2_aux.c
|
|
1244 M /branches/prog/bwa/bwtsw2_core.c
|
|
1245 M /branches/prog/bwa/bwtsw2_main.c
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1246 M /branches/prog/bwa/main.c
|
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1247
|
|
1248 bwtsw2 (dBWT-SW) is working apparently...
|
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1249
|
|
1250
|
|
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
|
|
1255 M /branches/prog/bwa/main.c
|
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1256
|
|
1257 * bwa-0.4.9-2
|
|
1258 * bwtsw2: change cut_tail() such that it is faster but more likely to
|
|
1259 miss true hits
|
|
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
|
|
1272 M /branches/prog/bwa/main.h
|
|
1273
|
|
1274 * bwa-0.4.9-1
|
|
1275 * added back bwtsw2
|
|
1276
|
|
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
|
|
1281 M /branches/prog/bwa/bwase.c
|
|
1282 M /branches/prog/bwa/main.c
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1283
|
|
1284 Release bwa-0.4.9
|
|
1285
|
|
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
|
|
1293 Release bwa-0.4.8
|
|
1294
|
|
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
|
|
1301 * bwa-0.4.7-2
|
|
1302 * change the default of "aln -R" to 30
|
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1303
|
|
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
|
|
1312 M /branches/prog/bwa/main.c
|
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1313
|
|
1314 * bwa-0.4.7-1
|
|
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
|
|
1325 Release bwa-0.4.7
|
|
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
|
|
1334 * bwa-0.4.6-9
|
|
1335 * fixed compiling errors on some Linux machines
|
|
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
|
|
1343 * bwa-0.4.6-8
|
|
1344 * avoid compilation error on some systems.
|
|
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
|
|
1353 * bwa-0.4.6-7
|
|
1354 * fixed an integer overflow caused by previous modifications
|
|
1355 * made insert size estimation more robust
|
|
1356
|
|
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
|
|
1361 M /branches/prog/bwa/main.c
|
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1362
|
|
1363 * bwa-0.4.6-5
|
|
1364 * fixed a integer overflow problem which may cause seg fault in very rare cases
|
|
1365 * made XN tags more accurate
|
|
1366
|
|
1367 ------------------------------------------------------------------------
|
|
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
|
|
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
|
|
1374 M /branches/prog/bwa/stdaln.h
|
|
1375
|
|
1376 * bwa-0.4.6-4
|
|
1377 * heuristic rules to detect suboptimal alignment
|
|
1378 * stdsw: support double-strand and protein alignment
|
|
1379
|
|
1380 ------------------------------------------------------------------------
|
|
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
|
|
1386 M /branches/prog/bwa/stdaln.h
|
|
1387
|
|
1388 * bwa-0.4.6-2
|
|
1389 * improve the functionality of stdsw
|
|
1390 * allow to add a threshold on SW alignment. Hope this does not incur new bugs...
|
|
1391
|
|
1392 ------------------------------------------------------------------------
|
|
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
|
|
1398 M /branches/prog/bwa/bwtaln.h
|
|
1399 M /branches/prog/bwa/main.c
|
|
1400
|
|
1401 * bwa-0.4.6-1
|
|
1402 * output SM and AM tag
|
|
1403
|
|
1404 ------------------------------------------------------------------------
|
|
1405 r914 | lh3 | 2009-03-09 17:53:50 -0400 (Mon, 09 Mar 2009) | 2 lines
|
|
1406 Changed paths:
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1407 M /branches/prog/bwa/ChangeLog
|
|
1408 M /branches/prog/bwa/NEWS
|
|
1409 M /branches/prog/bwa/main.c
|
|
1410
|
|
1411 Release bwa-0.4.6
|
|
1412
|
|
1413 ------------------------------------------------------------------------
|
|
1414 r913 | lh3 | 2009-03-09 17:23:24 -0400 (Mon, 09 Mar 2009) | 4 lines
|
|
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
|
|
1418 A /branches/prog/bwa/solid2fastq.pl
|
|
1419
|
|
1420 * added notes to bwa
|
|
1421 * added a script to convert SOLiD reads
|
|
1422 * updated documentations
|
|
1423
|
|
1424 ------------------------------------------------------------------------
|
|
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
|
|
1430
|
|
1431 fixed a bug in kstring
|
|
1432
|
|
1433 ------------------------------------------------------------------------
|
|
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
|
|
1437 M /branches/prog/bwa/main.c
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1438
|
|
1439 * bwa-0.4.5-7
|
|
1440 * fixed a bug in pac2cspac
|
|
1441
|
|
1442 ------------------------------------------------------------------------
|
|
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
|
|
1447 disable debugging
|
|
1448
|
|
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
|
|
1454 M /branches/prog/bwa/main.c
|
|
1455
|
|
1456 * bwa-0.4.5-6
|
|
1457 * fixed problems with coordinates for color gapped alignment
|
|
1458
|
|
1459 ------------------------------------------------------------------------
|
|
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
|
|
1464 M /branches/prog/bwa/main.c
|
|
1465
|
|
1466 * bwa-0.4.5-5
|
|
1467 * added support for gapped color alignment
|
|
1468
|
|
1469 ------------------------------------------------------------------------
|
|
1470 r877 | lh3 | 2009-03-01 10:27:52 -0500 (Sun, 01 Mar 2009) | 2 lines
|
|
1471 Changed paths:
|
|
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
|
|
1477 M /branches/prog/bwa/main.c
|
|
1478
|
|
1479 * convert cs read to nt read (for ungapped alignment only)
|
|
1480
|
|
1481 ------------------------------------------------------------------------
|
|
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
|
|
1485 M /branches/prog/bwa/bwase.c
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|
1486 A /branches/prog/bwa/cs2nt.c
|
|
1487
|
|
1488 prepare to implement cs->nt conversion (have not yet...)
|
|
1489
|
|
1490 ------------------------------------------------------------------------
|
|
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
|
|
1494 M /branches/prog/bwa/bntseq.h
|
|
1495 M /branches/prog/bwa/bwtindex.c
|
|
1496 M /branches/prog/bwa/bwtmisc.c
|
|
1497 M /branches/prog/bwa/main.c
|
|
1498 M /branches/prog/bwa/main.h
|
|
1499
|
|
1500 * bwa-0.4.5-3
|
|
1501 * generate color index from nucleotide fasta reference
|
|
1502
|
|
1503 ------------------------------------------------------------------------
|
|
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
|
|
1507 M /branches/prog/bwa/main.c
|
|
1508
|
|
1509 * bwa-0.4.5-2
|
|
1510 * improved mapping quality a bit if one end falls in a tandem repeat
|
|
1511 but the mate is unique.
|
|
1512
|
|
1513 ------------------------------------------------------------------------
|
|
1514 r856 | lh3 | 2009-02-26 10:02:29 -0500 (Thu, 26 Feb 2009) | 3 lines
|
|
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
|
|
1518 M /branches/prog/bwa/main.c
|
|
1519
|
|
1520 * bwa-0.4.5-1
|
|
1521 * make bwa work for SOLiD reads
|
|
1522
|
|
1523 ------------------------------------------------------------------------
|
|
1524 r828 | lh3 | 2009-02-18 17:36:41 -0500 (Wed, 18 Feb 2009) | 2 lines
|
|
1525 Changed paths:
|
|
1526 M /branches/prog/bwa/ChangeLog
|
|
1527 M /branches/prog/bwa/NEWS
|
|
1528 M /branches/prog/bwa/bwa.1
|
|
1529 M /branches/prog/bwa/main.c
|
|
1530
|
|
1531 Release bwa-0.4.5
|
|
1532
|
|
1533 ------------------------------------------------------------------------
|
|
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
|
|
1538 M /branches/prog/bwa/stdaln.h
|
|
1539
|
|
1540 * bwa-0.4.4-6
|
|
1541 * fixed a bug in SW alignment when no residue matches
|
|
1542
|
|
1543 ------------------------------------------------------------------------
|
|
1544 r824 | lh3 | 2009-02-17 05:33:07 -0500 (Tue, 17 Feb 2009) | 3 lines
|
|
1545 Changed paths:
|
|
1546 M /branches/prog/bwa/bwape.c
|
|
1547 M /branches/prog/bwa/main.c
|
|
1548
|
|
1549 * bwa-0.4.4-5
|
|
1550 * fixed that bounary bug
|
|
1551
|
|
1552 ------------------------------------------------------------------------
|
|
1553 r823 | lh3 | 2009-02-17 04:54:18 -0500 (Tue, 17 Feb 2009) | 2 lines
|
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1554 Changed paths:
|
|
1555 M /branches/prog/bwa/ChangeLog
|
|
1556 M /branches/prog/bwa/bwape.c
|
|
1557
|
|
1558 just change some logging information
|
|
1559
|
|
1560 ------------------------------------------------------------------------
|
|
1561 r822 | lh3 | 2009-02-17 04:20:39 -0500 (Tue, 17 Feb 2009) | 2 lines
|
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1562 Changed paths:
|
|
1563 M /branches/prog/bwa/bwa.1
|
|
1564
|
|
1565 update manual
|
|
1566
|
|
1567 ------------------------------------------------------------------------
|
|
1568 r821 | lh3 | 2009-02-17 04:11:14 -0500 (Tue, 17 Feb 2009) | 3 lines
|
|
1569 Changed paths:
|
|
1570 M /branches/prog/bwa/bwape.c
|
|
1571 M /branches/prog/bwa/bwase.c
|
|
1572 M /branches/prog/bwa/main.c
|
|
1573
|
|
1574 * bwa-0.4.4-4
|
|
1575 * fixed a bug on boundary check in pair_sw
|
|
1576
|
|
1577 ------------------------------------------------------------------------
|
|
1578 r820 | lh3 | 2009-02-16 17:43:37 -0500 (Mon, 16 Feb 2009) | 3 lines
|
|
1579 Changed paths:
|
|
1580 M /branches/prog/bwa/bwtaln.c
|
|
1581 M /branches/prog/bwa/main.c
|
|
1582
|
|
1583 * bwa-0.4.4-3
|
|
1584 * allow to change mismatch penalty
|
|
1585
|
|
1586 ------------------------------------------------------------------------
|
|
1587 r819 | lh3 | 2009-02-16 17:40:28 -0500 (Mon, 16 Feb 2009) | 4 lines
|
|
1588 Changed paths:
|
|
1589 M /branches/prog/bwa/bwtaln.c
|
|
1590 M /branches/prog/bwa/main.c
|
|
1591
|
|
1592 * bwa-0.4.4-2
|
|
1593 * remove timer
|
|
1594 * allow to change default gapo and gape penalty at the command line
|
|
1595
|
|
1596 ------------------------------------------------------------------------
|
|
1597 r818 | lh3 | 2009-02-16 09:30:51 -0500 (Mon, 16 Feb 2009) | 2 lines
|
|
1598 Changed paths:
|
|
1599 M /branches/prog/bwa/bwa.1
|
|
1600
|
|
1601 update benchmark
|
|
1602
|
|
1603 ------------------------------------------------------------------------
|
|
1604 r817 | lh3 | 2009-02-16 08:44:40 -0500 (Mon, 16 Feb 2009) | 4 lines
|
|
1605 Changed paths:
|
|
1606 M /branches/prog/bwa/bwape.c
|
|
1607 M /branches/prog/bwa/bwtaln.c
|
|
1608 M /branches/prog/bwa/kvec.h
|
|
1609 M /branches/prog/bwa/main.c
|
|
1610
|
|
1611 * bwa-0.4.4-1
|
|
1612 * automatically detect insert size
|
|
1613 * use insert size in pairing. This may potentially improve accuracy (untested!)
|
|
1614
|
|
1615 ------------------------------------------------------------------------
|
|
1616 r814 | lh3 | 2009-02-15 11:10:23 -0500 (Sun, 15 Feb 2009) | 2 lines
|
|
1617 Changed paths:
|
|
1618 M /branches/prog/bwa/ChangeLog
|
|
1619 M /branches/prog/bwa/NEWS
|
|
1620 M /branches/prog/bwa/main.c
|
|
1621
|
|
1622 Release bwa-0.4.4
|
|
1623
|
|
1624 ------------------------------------------------------------------------
|
|
1625 r813 | lh3 | 2009-02-15 10:22:50 -0500 (Sun, 15 Feb 2009) | 3 lines
|
|
1626 Changed paths:
|
|
1627 M /branches/prog/bwa/bwa.1
|
|
1628 M /branches/prog/bwa/bwase.c
|
|
1629 M /branches/prog/bwa/main.c
|
|
1630
|
|
1631 * bwa-0.4.3-5
|
|
1632 * impose boundary check in refine_gapped
|
|
1633
|
|
1634 ------------------------------------------------------------------------
|
|
1635 r811 | lh3 | 2009-02-14 09:46:13 -0500 (Sat, 14 Feb 2009) | 3 lines
|
|
1636 Changed paths:
|
|
1637 M /branches/prog/bwa/bwase.c
|
|
1638 M /branches/prog/bwa/main.c
|
|
1639
|
|
1640 * bwa-0.4.3-4
|
|
1641 * change MD tag to match the latest SAM specification
|
|
1642
|
|
1643 ------------------------------------------------------------------------
|
|
1644 r810 | lh3 | 2009-02-13 04:46:04 -0500 (Fri, 13 Feb 2009) | 2 lines
|
|
1645 Changed paths:
|
|
1646 M /branches/prog/bwa/ChangeLog
|
|
1647
|
|
1648 update ChangeLog
|
|
1649
|
|
1650 ------------------------------------------------------------------------
|
|
1651 r799 | lh3 | 2009-02-05 12:01:17 -0500 (Thu, 05 Feb 2009) | 2 lines
|
|
1652 Changed paths:
|
|
1653 M /branches/prog/bwa/bwase.c
|
|
1654 M /branches/prog/bwa/main.c
|
|
1655
|
|
1656 change MD tag to meet the latest SAM specification
|
|
1657
|
|
1658 ------------------------------------------------------------------------
|
|
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
|
|
1665 * bwa-0.4.3-2
|
|
1666 * fixed a bug on counting 'N'
|
|
1667
|
|
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
|
|
1675 * bwa-0.4.3-1
|
|
1676 * fixed potential boundary problems
|
|
1677 * update benchmark result
|
|
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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1702 Changed paths:
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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
|
|
1729 * bwa-0.4.2-10
|
|
1730 * update documentation
|
|
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
|
|
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
|
|
1748 * bwa-0.4.2-8
|
|
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
|
|
1762 * use a bit-wise flag to replace some member variables in the option struct
|
|
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
|
|
1773 * allow to dump multiple hits from samse, in another format, though
|
|
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
|
|
1787 M /branches/prog/bwa/simple_dp.c
|
|
1788
|
|
1789 * bwa-0.4.2-5
|
|
1790 * update kseq.h to the latest version
|
|
1791 * generate MD tag
|
|
1792 * print mate coordinate if only one end is unmapped
|
|
1793
|
|
1794 ------------------------------------------------------------------------
|
|
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
|
|
1801 * fixed a bug for SAM format
|
|
1802
|
|
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
|
|
1810 * change default fnr to 0.04
|
|
1811 * print max_diff for valid fnr
|
|
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
|
|
1822 * bwa-0.4.2-2
|
|
1823 * automatically choose max_diff
|
|
1824
|
|
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
|
|
1834
|
|
1835 * bwa-0.4.2-1
|
|
1836 * take N as a mismatch
|
|
1837
|
|
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
|
|
1858 Release bwa-0.4.1
|
|
1859
|
|
1860 ------------------------------------------------------------------------
|
|
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
|
|
1868 * bwa-0.4.0-2
|
|
1869 * make mate_sw fully working
|
|
1870
|
|
1871 ------------------------------------------------------------------------
|
|
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
|
|
1880 * bwa-0.4.0-1
|
|
1881 * do SW alignment for unmapped mate. It is working.
|
|
1882 * I still need to do some extra work for SW alignment, but it is too late
|
|
1883 and I am getting tired... I will do tomorrow.
|
|
1884
|
|
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
|
|
1893 Release bwa-0.4.0
|
|
1894
|
|
1895 ------------------------------------------------------------------------
|
|
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
|
|
1901 M /branches/prog/bwa/main.c
|
|
1902
|
|
1903 * bwa-0.3.0-12
|
|
1904 * better lock
|
|
1905
|
|
1906 ------------------------------------------------------------------------
|
|
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
|
|
1916 * bwa-0.3.0-11
|
|
1917 * fixed a small memory leak in bwa_seq_close()
|
|
1918 * fixed "uninitialized memory" from bwt_aln1_t
|
|
1919 * multithreading for "aln" command
|
|
1920
|
|
1921 ------------------------------------------------------------------------
|
|
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
|
|
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
|
|
1929 M /branches/prog/bwa/main.h
|
|
1930 D /branches/prog/bwa/pac2bwt.c
|
|
1931
|
|
1932 * bwa-0.3.0-10
|
|
1933 * a little bit code clean up
|
|
1934
|
|
1935 ------------------------------------------------------------------------
|
|
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
|
|
1940
|
|
1941 * bwa-0.3.0-9
|
|
1942 * use 64-bit integer to speed up Occ calculate, although just a little bit
|
|
1943
|
|
1944 ------------------------------------------------------------------------
|
|
1945 r750 | lh3 | 2009-01-05 16:44:26 -0500 (Mon, 05 Jan 2009) | 3 lines
|
|
1946 Changed paths:
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1947 M /branches/prog/bwa/bwt.c
|
|
1948 M /branches/prog/bwa/main.c
|
|
1949
|
|
1950 * bwa-0.3.0-8
|
|
1951 * a little bit code cleanup
|
|
1952
|
|
1953 ------------------------------------------------------------------------
|
|
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
|
|
1957 M /branches/prog/bwa/main.c
|
|
1958
|
|
1959 * bwa-0.1.0-7
|
|
1960 * accelerate Occ calculation
|
|
1961
|
|
1962 ------------------------------------------------------------------------
|
|
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
|
|
1967 M /branches/prog/bwa/bwt.c
|
|
1968 M /branches/prog/bwa/bwt.h
|
|
1969 M /branches/prog/bwa/bwt2fmv.c
|
|
1970 M /branches/prog/bwa/bwtaln.c
|
|
1971 M /branches/prog/bwa/bwtindex.c
|
|
1972 M /branches/prog/bwa/bwtio.c
|
|
1973 M /branches/prog/bwa/main.c
|
|
1974 M /branches/prog/bwa/main.h
|
|
1975 M /branches/prog/bwa/pac2bwt.c
|
|
1976
|
|
1977 * bwa-0.3.0-6
|
|
1978 * put occ table along with bwt to save another cache miss
|
|
1979 * this version is already faster than the previous and I can still improve it...
|
|
1980
|
|
1981 ------------------------------------------------------------------------
|
|
1982 r747 | lh3 | 2009-01-05 10:16:18 -0500 (Mon, 05 Jan 2009) | 5 lines
|
|
1983 Changed paths:
|
|
1984 M /branches/prog/bwa/bwt.c
|
|
1985 M /branches/prog/bwa/bwt.h
|
|
1986 M /branches/prog/bwa/bwtio.c
|
|
1987 M /branches/prog/bwa/main.c
|
|
1988
|
|
1989 * bwa-0.3.0-5
|
|
1990 * remove occ_major to save a cache miss; however, OCC_INTERVAL has to be
|
|
1991 increased to keep the same memory. As a result, the speed is a little
|
|
1992 slower in fact.
|
|
1993
|
|
1994 ------------------------------------------------------------------------
|
|
1995 r746 | lh3 | 2009-01-05 09:50:53 -0500 (Mon, 05 Jan 2009) | 3 lines
|
|
1996 Changed paths:
|
|
1997 M /branches/prog/bwa/bwt.c
|
|
1998 M /branches/prog/bwa/main.c
|
|
1999
|
|
2000 * bwa-0.3.0-4
|
|
2001 * added back optimization codes (it is a pain...)
|
|
2002
|
|
2003 ------------------------------------------------------------------------
|
|
2004 r745 | lh3 | 2009-01-05 08:23:00 -0500 (Mon, 05 Jan 2009) | 3 lines
|
|
2005 Changed paths:
|
|
2006 M /branches/prog/bwa/bwt.c
|
|
2007 M /branches/prog/bwa/bwtaln.c
|
|
2008 M /branches/prog/bwa/main.c
|
|
2009
|
|
2010 * bwa-0.3.0-3
|
|
2011 * faster bit operations
|
|
2012
|
|
2013 ------------------------------------------------------------------------
|
|
2014 r744 | lh3 | 2009-01-05 05:58:46 -0500 (Mon, 05 Jan 2009) | 4 lines
|
|
2015 Changed paths:
|
|
2016 M /branches/prog/bwa/bwt.c
|
|
2017 M /branches/prog/bwa/main.c
|
|
2018
|
|
2019 * bwa-0.3.0-2
|
|
2020 * removed optimization codes again...
|
|
2021 * use a new method to count the bits
|
|
2022
|
|
2023 ------------------------------------------------------------------------
|
|
2024 r743 | lh3 | 2009-01-04 17:18:38 -0500 (Sun, 04 Jan 2009) | 5 lines
|
|
2025 Changed paths:
|
|
2026 M /branches/prog/bwa/bwa.1
|
|
2027 M /branches/prog/bwa/bwt.c
|
|
2028 M /branches/prog/bwa/bwtaln.c
|
|
2029 M /branches/prog/bwa/bwtaln.h
|
|
2030 M /branches/prog/bwa/bwtgap.c
|
|
2031 M /branches/prog/bwa/main.c
|
|
2032
|
|
2033 * bwa-0.3.0-1
|
|
2034 * added back the optimization codes
|
|
2035 * added a new option to aln: max_entries, although this is disabled by default
|
|
2036 * updated benchmark
|
|
2037
|
|
2038 ------------------------------------------------------------------------
|
|
2039 r742 | lh3 | 2009-01-04 07:56:12 -0500 (Sun, 04 Jan 2009) | 2 lines
|
|
2040 Changed paths:
|
|
2041 M /branches/prog/bwa/bwa.1
|
|
2042
|
|
2043 add URL
|
|
2044
|
|
2045 ------------------------------------------------------------------------
|
|
2046 r740 | lh3 | 2009-01-04 07:39:43 -0500 (Sun, 04 Jan 2009) | 2 lines
|
|
2047 Changed paths:
|
|
2048 M /branches/prog/bwa/ChangeLog
|
|
2049 M /branches/prog/bwa/NEWS
|
|
2050 M /branches/prog/bwa/bwa.1
|
|
2051 M /branches/prog/bwa/main.c
|
|
2052
|
|
2053 Release bwa-0.3.0
|
|
2054
|
|
2055 ------------------------------------------------------------------------
|
|
2056 r739 | lh3 | 2009-01-04 06:55:06 -0500 (Sun, 04 Jan 2009) | 2 lines
|
|
2057 Changed paths:
|
|
2058 A /branches/prog/bwa/COPYING
|
|
2059 M /branches/prog/bwa/ChangeLog
|
|
2060 M /branches/prog/bwa/bntseq.c
|
|
2061 M /branches/prog/bwa/bntseq.h
|
|
2062 M /branches/prog/bwa/bwa.1
|
|
2063 M /branches/prog/bwa/bwt.c
|
|
2064 M /branches/prog/bwa/bwt.h
|
|
2065 M /branches/prog/bwa/bwtindex.c
|
|
2066 M /branches/prog/bwa/utils.c
|
|
2067 M /branches/prog/bwa/utils.h
|
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2068
|
|
2069 added licensing information
|
|
2070
|
|
2071 ------------------------------------------------------------------------
|
|
2072 r738 | lh3 | 2009-01-04 06:18:25 -0500 (Sun, 04 Jan 2009) | 4 lines
|
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2073 Changed paths:
|
|
2074 M /branches/prog/bwa/bwa.1
|
|
2075 M /branches/prog/bwa/bwape.c
|
|
2076 M /branches/prog/bwa/main.c
|
|
2077
|
|
2078 * bwa-0.2.0-31
|
|
2079 * better mapping quality
|
|
2080 * update benchmark
|
|
2081
|
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2082 ------------------------------------------------------------------------
|
|
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
|
|
2088 update documentation
|
|
2089
|
|
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
|
|
2095 update documentation
|
|
2096
|
|
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
|
|
2103 M /branches/prog/bwa/main.c
|
|
2104
|
|
2105 * bwa-0.2.0-30
|
|
2106 * reduce memory a little bit
|
|
2107 * update documentation
|
|
2108
|
|
2109 ------------------------------------------------------------------------
|
|
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
|
|
2114 M /branches/prog/bwa/bwase.c
|
|
2115 M /branches/prog/bwa/bwtaln.c
|
|
2116 M /branches/prog/bwa/bwtaln.h
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|
2117 M /branches/prog/bwa/bwtgap.c
|
|
2118 M /branches/prog/bwa/main.c
|
|
2119
|
|
2120 * bwa-0.2.0-29
|
|
2121 * sampe: removed -O option; changed default -o to 100000
|
|
2122 * sampe: fixed a bug in calculating paired mapping quality
|
|
2123 * aln: added an option to search for suboptimal hits even if the best is a repeat.
|
|
2124 This option will make sampe MUCH SLOWER.
|
|
2125 * sampe: set isize as zero if mapped to two different chr
|
|
2126 * update manual (unfinished)
|
|
2127
|
|
2128 ------------------------------------------------------------------------
|
|
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
|
|
2132 M /branches/prog/bwa/main.c
|
|
2133
|
|
2134 * bwa-0.2.0-28
|
|
2135 * fixed a bug in calculating paired mapping quality
|
|
2136
|
|
2137 ------------------------------------------------------------------------
|
|
2138 r732 | lh3 | 2009-01-01 09:27:46 -0500 (Thu, 01 Jan 2009) | 3 lines
|
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2139 Changed paths:
|
|
2140 M /branches/prog/bwa/bwape.c
|
|
2141 A /branches/prog/bwa/khash.h (from /branches/prog/sclib/khash/khash.h:675)
|
|
2142 M /branches/prog/bwa/main.c
|
|
2143
|
|
2144 * bwa-0.2.0-27
|
|
2145 * accelerate sampe by storing visited large intervals
|
|
2146
|
|
2147 ------------------------------------------------------------------------
|
|
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
|
|
2151 M /branches/prog/bwa/main.c
|
|
2152
|
|
2153 * bwa-0.2.0-26
|
|
2154 * remove the optimation codes
|
|
2155
|
|
2156 ------------------------------------------------------------------------
|
|
2157 r730 | lh3 | 2009-01-01 06:48:59 -0500 (Thu, 01 Jan 2009) | 4 lines
|
|
2158 Changed paths:
|
|
2159 M /branches/prog/bwa/bwt.c
|
|
2160 M /branches/prog/bwa/main.c
|
|
2161
|
|
2162 * bwa-0.2.0-25
|
|
2163 * accelerate OCC calculation by ~7%. However, it seems not worth doing
|
|
2164 this by complicate the codes. I will change back later.
|
|
2165
|
|
2166 ------------------------------------------------------------------------
|
|
2167 r729 | lh3 | 2008-12-31 16:43:56 -0500 (Wed, 31 Dec 2008) | 6 lines
|
|
2168 Changed paths:
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|
2169 M /branches/prog/bwa/bntseq.c
|
|
2170 M /branches/prog/bwa/bwape.c
|
|
2171 M /branches/prog/bwa/bwase.c
|
|
2172 M /branches/prog/bwa/main.c
|
|
2173
|
|
2174 * bwa-0.2.0-24
|
|
2175 * change command "sai2sam_pe" to "sampe"
|
|
2176 * print usage for sampe command
|
|
2177 * in sampe: change default max_occ to 1000
|
|
2178 * fixed a few compiling warnings in bntseq.c
|
|
2179
|
|
2180 ------------------------------------------------------------------------
|
|
2181 r728 | lh3 | 2008-12-27 07:14:59 -0500 (Sat, 27 Dec 2008) | 3 lines
|
|
2182 Changed paths:
|
|
2183 M /branches/prog/bwa/bwape.c
|
|
2184 M /branches/prog/bwa/bwase.c
|
|
2185 M /branches/prog/bwa/main.c
|
|
2186
|
|
2187 * bwa-0.2.0-22
|
|
2188 * mating information can be printed to SAM
|
|
2189
|
|
2190 ------------------------------------------------------------------------
|
|
2191 r727 | lh3 | 2008-12-26 18:10:59 -0500 (Fri, 26 Dec 2008) | 4 lines
|
|
2192 Changed paths:
|
|
2193 M /branches/prog/bwa/bwape.c
|
|
2194 M /branches/prog/bwa/bwase.c
|
|
2195 M /branches/prog/bwa/bwaseqio.c
|
|
2196 M /branches/prog/bwa/bwtaln.c
|
|
2197 M /branches/prog/bwa/bwtaln.h
|
|
2198 M /branches/prog/bwa/main.c
|
|
2199
|
|
2200 * bwa-0.2.0-21
|
|
2201 * implement pairing (still UNFINISHED)
|
|
2202 * output all reads even if full of N
|
|
2203
|
|
2204 ------------------------------------------------------------------------
|
|
2205 r726 | lh3 | 2008-12-26 13:31:27 -0500 (Fri, 26 Dec 2008) | 5 lines
|
|
2206 Changed paths:
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|
2207 M /branches/prog/bwa/Makefile
|
|
2208 A /branches/prog/bwa/bwape.c
|
|
2209 M /branches/prog/bwa/bwase.c
|
|
2210 M /branches/prog/bwa/bwt2fmv.c
|
|
2211 M /branches/prog/bwa/bwtaln.c
|
|
2212 M /branches/prog/bwa/bwtaln.h
|
|
2213 M /branches/prog/bwa/bwtgap.c
|
|
2214 M /branches/prog/bwa/main.c
|
|
2215 M /branches/prog/bwa/main.h
|
|
2216
|
|
2217 * bwa-0.2.0-20
|
|
2218 * remove "-t" from aln cmd
|
|
2219 * code clean up: move some functions in bwt2fmv.c to other source files
|
|
2220 * added sai2sam_pe cmd: *UNFINISHED*
|
|
2221
|
|
2222 ------------------------------------------------------------------------
|
|
2223 r725 | lh3 | 2008-12-26 07:04:11 -0500 (Fri, 26 Dec 2008) | 3 lines
|
|
2224 Changed paths:
|
|
2225 M /branches/prog/bwa/Makefile
|
|
2226 A /branches/prog/bwa/bwase.c
|
|
2227 A /branches/prog/bwa/bwaseqio.c
|
|
2228 M /branches/prog/bwa/bwt2fmv.c
|
|
2229 M /branches/prog/bwa/bwtaln.c
|
|
2230 M /branches/prog/bwa/bwtaln.h
|
|
2231 M /branches/prog/bwa/bwtgap.c
|
|
2232 M /branches/prog/bwa/kseq.h
|
|
2233 A /branches/prog/bwa/ksort.h (from /branches/prog/sclib/ksort/ksort.h:712)
|
|
2234 A /branches/prog/bwa/kvec.h (from /branches/prog/sclib/kvec/kvec.h:537)
|
|
2235 M /branches/prog/bwa/main.c
|
|
2236
|
|
2237 * bwa-0.2.0-19
|
|
2238 * considerable code cleanup; no actual changes
|
|
2239
|
|
2240 ------------------------------------------------------------------------
|
|
2241 r724 | lh3 | 2008-12-25 11:32:11 -0500 (Thu, 25 Dec 2008) | 3 lines
|
|
2242 Changed paths:
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|
2243 M /branches/prog/bwa/bwtaln.c
|
|
2244 M /branches/prog/bwa/bwtaln.h
|
|
2245 M /branches/prog/bwa/main.c
|
|
2246
|
|
2247 * bwa-0.2.0-18
|
|
2248 * generate SAM output
|
|
2249
|
|
2250 ------------------------------------------------------------------------
|
|
2251 r723 | lh3 | 2008-12-25 10:48:31 -0500 (Thu, 25 Dec 2008) | 4 lines
|
|
2252 Changed paths:
|
|
2253 M /branches/prog/bwa/bwt2fmv.c
|
|
2254 M /branches/prog/bwa/bwtaln.c
|
|
2255 M /branches/prog/bwa/main.c
|
|
2256 M /branches/prog/bwa/main.h
|
|
2257
|
|
2258 * bwa-0.2.0-17
|
|
2259 * remove bwtsw2 related codes
|
|
2260 * separate searching for SA interval from generating alignments
|
|
2261
|
|
2262 ------------------------------------------------------------------------
|
|
2263 r722 | lh3 | 2008-12-25 08:57:13 -0500 (Thu, 25 Dec 2008) | 3 lines
|
|
2264 Changed paths:
|
|
2265 M /branches/prog/bwa/Makefile
|
|
2266 M /branches/prog/bwa/bwt2fmv.c
|
|
2267 D /branches/prog/bwa/bwt_lite.c
|
|
2268 D /branches/prog/bwa/bwt_lite.h
|
|
2269 M /branches/prog/bwa/bwtgap.c
|
|
2270 D /branches/prog/bwa/bwtsw2.h
|
|
2271 D /branches/prog/bwa/bwtsw2_aux.c
|
|
2272 D /branches/prog/bwa/bwtsw2_core.c
|
|
2273 D /branches/prog/bwa/bwtsw2_main.c
|
|
2274 D /branches/prog/bwa/khash.h
|
|
2275 D /branches/prog/bwa/ksort.h
|
|
2276 D /branches/prog/bwa/kvec.h
|
|
2277 M /branches/prog/bwa/main.c
|
|
2278
|
|
2279 * added interface to "aln -t"
|
|
2280 * remove bwtsw2 related codes
|
|
2281
|
|
2282 ------------------------------------------------------------------------
|
|
2283 r666 | lh3 | 2008-11-18 18:34:29 -0500 (Tue, 18 Nov 2008) | 4 lines
|
|
2284 Changed paths:
|
|
2285 M /branches/prog/bwa/bwt2fmv.c
|
|
2286 M /branches/prog/bwa/bwtaln.c
|
|
2287 M /branches/prog/bwa/bwtaln.h
|
|
2288 M /branches/prog/bwa/main.c
|
|
2289
|
|
2290 * bwa-0.2.0-16
|
|
2291 * allow to set max mismatches based on read length, but I do not know
|
|
2292 whether this really works
|
|
2293
|
|
2294 ------------------------------------------------------------------------
|
|
2295 r665 | lh3 | 2008-11-18 08:34:03 -0500 (Tue, 18 Nov 2008) | 3 lines
|
|
2296 Changed paths:
|
|
2297 M /branches/prog/bwa/bwtaln.c
|
|
2298 M /branches/prog/bwa/main.c
|
|
2299
|
|
2300 * bwa-0.2.0-15
|
|
2301 * fixed a bug in sequence parser.
|
|
2302
|
|
2303 ------------------------------------------------------------------------
|
|
2304 r612 | lh3 | 2008-10-28 06:50:53 -0400 (Tue, 28 Oct 2008) | 3 lines
|
|
2305 Changed paths:
|
|
2306 M /branches/prog/bwa/bntseq.c
|
|
2307 M /branches/prog/bwa/bwtindex.c
|
|
2308 M /branches/prog/bwa/main.c
|
|
2309 M /branches/prog/bwa/utils.c
|
|
2310
|
|
2311 * bwa-0.2.0-14
|
|
2312 * fixed a bug caused by the change of the FASTA/Q parser
|
|
2313
|
|
2314 ------------------------------------------------------------------------
|
|
2315 r611 | lh3 | 2008-10-28 06:24:56 -0400 (Tue, 28 Oct 2008) | 2 lines
|
|
2316 Changed paths:
|
|
2317 M /branches/prog/bwa/Makefile
|
|
2318 M /branches/prog/bwa/bntseq.c
|
|
2319 M /branches/prog/bwa/bntseq.h
|
|
2320 M /branches/prog/bwa/bwtaln.c
|
|
2321 M /branches/prog/bwa/bwtsw2_core.c
|
|
2322 A /branches/prog/bwa/kseq.h
|
|
2323 D /branches/prog/bwa/seq.c
|
|
2324 D /branches/prog/bwa/seq.h
|
|
2325 M /branches/prog/bwa/simple_dp.c
|
|
2326 M /branches/prog/bwa/utils.c
|
|
2327 M /branches/prog/bwa/utils.h
|
|
2328
|
|
2329 replace seq.* with kseq.h
|
|
2330
|
|
2331 ------------------------------------------------------------------------
|
|
2332 r610 | lh3 | 2008-10-27 13:00:04 -0400 (Mon, 27 Oct 2008) | 3 lines
|
|
2333 Changed paths:
|
|
2334 M /branches/prog/bwa/bwtsw2.h
|
|
2335 M /branches/prog/bwa/bwtsw2_aux.c
|
|
2336 M /branches/prog/bwa/bwtsw2_core.c
|
|
2337 M /branches/prog/bwa/main.c
|
|
2338
|
|
2339 * bwa-0.2.0-13
|
|
2340 * make bwtsw2 output sub-optimal hits. not completed
|
|
2341
|
|
2342 ------------------------------------------------------------------------
|
|
2343 r609 | lh3 | 2008-10-24 16:52:00 -0400 (Fri, 24 Oct 2008) | 2 lines
|
|
2344 Changed paths:
|
|
2345 M /branches/prog/bwa/kvec.h
|
|
2346
|
|
2347 little...
|
|
2348
|
|
2349 ------------------------------------------------------------------------
|
|
2350 r532 | lh3 | 2008-09-19 05:28:45 -0400 (Fri, 19 Sep 2008) | 2 lines
|
|
2351 Changed paths:
|
|
2352 M /branches/prog/bwa/bwtsw2_core.c
|
|
2353 M /branches/prog/bwa/khash.h
|
|
2354
|
|
2355 improve interface of khash
|
|
2356
|
|
2357 ------------------------------------------------------------------------
|
|
2358 r531 | lh3 | 2008-09-18 06:52:59 -0400 (Thu, 18 Sep 2008) | 2 lines
|
|
2359 Changed paths:
|
|
2360 M /branches/prog/bwa/bwtsw2_core.c
|
|
2361
|
|
2362 improve minor things, which make bwtsw2 slower, but should miss less true hits
|
|
2363
|
|
2364 ------------------------------------------------------------------------
|
|
2365 r530 | lh3 | 2008-09-17 18:19:26 -0400 (Wed, 17 Sep 2008) | 3 lines
|
|
2366 Changed paths:
|
|
2367 M /branches/prog/bwa/bwtsw2_core.c
|
|
2368
|
|
2369 * fixed a bug in calculating ->D
|
|
2370 * enforce band-width checking
|
|
2371
|
|
2372 ------------------------------------------------------------------------
|
|
2373 r529 | lh3 | 2008-09-17 18:06:49 -0400 (Wed, 17 Sep 2008) | 2 lines
|
|
2374 Changed paths:
|
|
2375 M /branches/prog/bwa/bwtsw2_core.c
|
|
2376
|
|
2377 delete a line of code that is never visited
|
|
2378
|
|
2379 ------------------------------------------------------------------------
|
|
2380 r528 | lh3 | 2008-09-17 17:58:51 -0400 (Wed, 17 Sep 2008) | 2 lines
|
|
2381 Changed paths:
|
|
2382 M /branches/prog/bwa/bwtsw2_core.c
|
|
2383
|
|
2384 a bit code clean up
|
|
2385
|
|
2386 ------------------------------------------------------------------------
|
|
2387 r527 | lh3 | 2008-09-17 10:55:45 -0400 (Wed, 17 Sep 2008) | 3 lines
|
|
2388 Changed paths:
|
|
2389 M /branches/prog/bwa/bwtsw2_core.c
|
|
2390 M /branches/prog/bwa/bwtsw2_main.c
|
|
2391 M /branches/prog/bwa/main.c
|
|
2392
|
|
2393 * bwa-0.2.0-12
|
|
2394 * max-depth can be set, although it does not help the speed at all
|
|
2395
|
|
2396 ------------------------------------------------------------------------
|
|
2397 r526 | lh3 | 2008-09-16 17:59:36 -0400 (Tue, 16 Sep 2008) | 2 lines
|
|
2398 Changed paths:
|
|
2399 M /branches/prog/bwa/bwtsw2_core.c
|
|
2400
|
|
2401 cut_tail after remove duplicate
|
|
2402
|
|
2403 ------------------------------------------------------------------------
|
|
2404 r525 | lh3 | 2008-09-16 17:56:11 -0400 (Tue, 16 Sep 2008) | 3 lines
|
|
2405 Changed paths:
|
|
2406 M /branches/prog/bwa/bwtsw2.h
|
|
2407 M /branches/prog/bwa/bwtsw2_aux.c
|
|
2408 M /branches/prog/bwa/bwtsw2_core.c
|
|
2409 M /branches/prog/bwa/bwtsw2_main.c
|
|
2410 M /branches/prog/bwa/khash.h
|
|
2411 M /branches/prog/bwa/main.c
|
|
2412
|
|
2413 * bwa-0.2.0-11
|
|
2414 * improved cut_tail()
|
|
2415
|
|
2416 ------------------------------------------------------------------------
|
|
2417 r524 | lh3 | 2008-09-15 16:53:22 -0400 (Mon, 15 Sep 2008) | 3 lines
|
|
2418 Changed paths:
|
|
2419 M /branches/prog/bwa/bwtsw2_aux.c
|
|
2420 M /branches/prog/bwa/bwtsw2_core.c
|
|
2421 M /branches/prog/bwa/bwtsw2_main.c
|
|
2422 M /branches/prog/bwa/main.c
|
|
2423
|
|
2424 * bwa-0.2.0-10
|
|
2425 * fixed a bug in cut_tail()
|
|
2426
|
|
2427 ------------------------------------------------------------------------
|
|
2428 r518 | lh3 | 2008-09-15 04:35:59 -0400 (Mon, 15 Sep 2008) | 2 lines
|
|
2429 Changed paths:
|
|
2430 M /branches/prog/bwa/bwtsw2_core.c
|
|
2431
|
|
2432 a bit code clean up
|
|
2433
|
|
2434 ------------------------------------------------------------------------
|
|
2435 r517 | lh3 | 2008-09-14 18:18:11 -0400 (Sun, 14 Sep 2008) | 2 lines
|
|
2436 Changed paths:
|
|
2437 M /branches/prog/bwa/bwtsw2_core.c
|
|
2438
|
|
2439 improve speed (<1%)
|
|
2440
|
|
2441 ------------------------------------------------------------------------
|
|
2442 r516 | lh3 | 2008-09-14 18:08:55 -0400 (Sun, 14 Sep 2008) | 3 lines
|
|
2443 Changed paths:
|
|
2444 M /branches/prog/bwa/bwtsw2_core.c
|
|
2445
|
|
2446 * fixed two potential bugs, although I have not seen their effects
|
|
2447 * improve speed a bit (<2%)
|
|
2448
|
|
2449 ------------------------------------------------------------------------
|
|
2450 r515 | lh3 | 2008-09-14 17:26:49 -0400 (Sun, 14 Sep 2008) | 2 lines
|
|
2451 Changed paths:
|
|
2452 M /branches/prog/bwa/bwtsw2_core.c
|
|
2453 M /branches/prog/bwa/bwtsw2_main.c
|
|
2454
|
|
2455 nothing, really
|
|
2456
|
|
2457 ------------------------------------------------------------------------
|
|
2458 r514 | lh3 | 2008-09-14 17:10:13 -0400 (Sun, 14 Sep 2008) | 2 lines
|
|
2459 Changed paths:
|
|
2460 M /branches/prog/bwa/bwtsw2_core.c
|
|
2461
|
|
2462 disable X-drop, which has to be reimplemented in the current algorithm
|
|
2463
|
|
2464 ------------------------------------------------------------------------
|
|
2465 r513 | lh3 | 2008-09-14 16:49:42 -0400 (Sun, 14 Sep 2008) | 4 lines
|
|
2466 Changed paths:
|
|
2467 M /branches/prog/bwa/bwt_lite.c
|
|
2468 M /branches/prog/bwa/bwt_lite.h
|
|
2469 M /branches/prog/bwa/bwtsw2_core.c
|
|
2470 M /branches/prog/bwa/bwtsw2_main.c
|
|
2471
|
|
2472 * temporarily disable cut_tail()
|
|
2473 * calculate SA in bwt_lite.c
|
|
2474 * fixed a bug in reversing the sequence
|
|
2475
|
|
2476 ------------------------------------------------------------------------
|
|
2477 r512 | lh3 | 2008-09-13 17:35:40 -0400 (Sat, 13 Sep 2008) | 2 lines
|
|
2478 Changed paths:
|
|
2479 M /branches/prog/bwa/bwtsw2.h
|
|
2480 M /branches/prog/bwa/bwtsw2_aux.c
|
|
2481 M /branches/prog/bwa/bwtsw2_core.c
|
|
2482 M /branches/prog/bwa/bwtsw2_main.c
|
|
2483 A /branches/prog/bwa/ksort.h
|
|
2484
|
|
2485 n-best method
|
|
2486
|
|
2487 ------------------------------------------------------------------------
|
|
2488 r507 | lh3 | 2008-09-13 09:06:54 -0400 (Sat, 13 Sep 2008) | 2 lines
|
|
2489 Changed paths:
|
|
2490 M /branches/prog/bwa/Makefile
|
|
2491 M /branches/prog/bwa/bwtsw2_core.c
|
|
2492
|
|
2493 give correct result again
|
|
2494
|
|
2495 ------------------------------------------------------------------------
|
|
2496 r506 | lh3 | 2008-09-13 08:12:07 -0400 (Sat, 13 Sep 2008) | 2 lines
|
|
2497 Changed paths:
|
|
2498 M /branches/prog/bwa/bwtsw2_core.c
|
|
2499
|
|
2500 I think I know the reason. It needs more work...
|
|
2501
|
|
2502 ------------------------------------------------------------------------
|
|
2503 r505 | lh3 | 2008-09-13 06:20:43 -0400 (Sat, 13 Sep 2008) | 2 lines
|
|
2504 Changed paths:
|
|
2505 M /branches/prog/bwa/Makefile
|
|
2506 M /branches/prog/bwa/bwtsw2_core.c
|
|
2507
|
|
2508 fixed another bug, but still have
|
|
2509
|
|
2510 ------------------------------------------------------------------------
|
|
2511 r504 | lh3 | 2008-09-12 18:13:37 -0400 (Fri, 12 Sep 2008) | 2 lines
|
|
2512 Changed paths:
|
|
2513 M /branches/prog/bwa/bwtsw2_core.c
|
|
2514
|
|
2515 fixed another bug
|
|
2516
|
|
2517 ------------------------------------------------------------------------
|
|
2518 r503 | lh3 | 2008-09-12 17:15:56 -0400 (Fri, 12 Sep 2008) | 3 lines
|
|
2519 Changed paths:
|
|
2520 M /branches/prog/bwa/bwtsw2_core.c
|
|
2521 M /branches/prog/bwa/khash.h
|
|
2522
|
|
2523 * do not segfault, but the result is WRONG!
|
|
2524 * prepare to remove bsw2_connectivity_check()
|
|
2525
|
|
2526 ------------------------------------------------------------------------
|
|
2527 r502 | lh3 | 2008-09-12 15:52:41 -0400 (Fri, 12 Sep 2008) | 2 lines
|
|
2528 Changed paths:
|
|
2529 M /branches/prog/bwa/bwtsw2_core.c
|
|
2530 M /branches/prog/bwa/kvec.h
|
|
2531
|
|
2532 more revisions
|
|
2533
|
|
2534 ------------------------------------------------------------------------
|
|
2535 r501 | lh3 | 2008-09-11 18:06:15 -0400 (Thu, 11 Sep 2008) | 2 lines
|
|
2536 Changed paths:
|
|
2537 M /branches/prog/bwa/bwtsw2_core.c
|
|
2538
|
|
2539 further simply codes with kvec.h
|
|
2540
|
|
2541 ------------------------------------------------------------------------
|
|
2542 r500 | lh3 | 2008-09-11 17:42:15 -0400 (Thu, 11 Sep 2008) | 2 lines
|
|
2543 Changed paths:
|
|
2544 M /branches/prog/bwa/bwtsw2_core.c
|
|
2545
|
|
2546 part of revisions... have not finished
|
|
2547
|
|
2548 ------------------------------------------------------------------------
|
|
2549 r499 | lh3 | 2008-09-11 17:24:15 -0400 (Thu, 11 Sep 2008) | 2 lines
|
|
2550 Changed paths:
|
|
2551 M /branches/prog/bwa/bwtsw2.h
|
|
2552 M /branches/prog/bwa/bwtsw2_core.c
|
|
2553 M /branches/prog/bwa/bwtsw2_main.c
|
|
2554 M /branches/prog/bwa/khash.h
|
|
2555 A /branches/prog/bwa/kvec.h
|
|
2556
|
|
2557 prepare for abrupt change
|
|
2558
|
|
2559 ------------------------------------------------------------------------
|
|
2560 r496 | lh3 | 2008-09-11 10:34:38 -0400 (Thu, 11 Sep 2008) | 2 lines
|
|
2561 Changed paths:
|
|
2562 M /branches/prog/bwa/bwtsw2_core.c
|
|
2563
|
|
2564 fixed a bug; now "bwtsw2 -d" is useless
|
|
2565
|
|
2566 ------------------------------------------------------------------------
|
|
2567 r495 | lh3 | 2008-09-11 09:22:03 -0400 (Thu, 11 Sep 2008) | 2 lines
|
|
2568 Changed paths:
|
|
2569 M /branches/prog/bwa/bwtsw2_core.c
|
|
2570 M /branches/prog/bwa/simple_dp.c
|
|
2571 M /branches/prog/bwa/stdaln.c
|
|
2572 M /branches/prog/bwa/stdaln.h
|
|
2573
|
|
2574 improve speed a little bit
|
|
2575
|
|
2576 ------------------------------------------------------------------------
|
|
2577 r494 | lh3 | 2008-09-11 08:28:08 -0400 (Thu, 11 Sep 2008) | 2 lines
|
|
2578 Changed paths:
|
|
2579 M /branches/prog/bwa/bwtsw2_core.c
|
|
2580
|
|
2581 remove debug codes
|
|
2582
|
|
2583 ------------------------------------------------------------------------
|
|
2584 r493 | lh3 | 2008-09-11 07:49:53 -0400 (Thu, 11 Sep 2008) | 3 lines
|
|
2585 Changed paths:
|
|
2586 M /branches/prog/bwa/bwtsw2_core.c
|
|
2587
|
|
2588 * improve the speed a little bit (<5%)
|
|
2589 * prepare to remove BSW_DEBUG
|
|
2590
|
|
2591 ------------------------------------------------------------------------
|
|
2592 r492 | lh3 | 2008-09-11 06:15:56 -0400 (Thu, 11 Sep 2008) | 4 lines
|
|
2593 Changed paths:
|
|
2594 M /branches/prog/bwa/bwtsw2.h
|
|
2595 M /branches/prog/bwa/bwtsw2_aux.c
|
|
2596 M /branches/prog/bwa/bwtsw2_core.c
|
|
2597 M /branches/prog/bwa/bwtsw2_main.c
|
|
2598 M /branches/prog/bwa/main.c
|
|
2599
|
|
2600 * bwa-0.2.0-9
|
|
2601 * support reverse strand
|
|
2602 * fixed a bug that causes missing hits
|
|
2603
|
|
2604 ------------------------------------------------------------------------
|
|
2605 r491 | lh3 | 2008-09-11 05:46:16 -0400 (Thu, 11 Sep 2008) | 3 lines
|
|
2606 Changed paths:
|
|
2607 M /branches/prog/bwa/bwtsw2_core.c
|
|
2608 M /branches/prog/bwa/main.c
|
|
2609
|
|
2610 * bwa-0.2.0-8
|
|
2611 * better progress report
|
|
2612
|
|
2613 ------------------------------------------------------------------------
|
|
2614 r490 | lh3 | 2008-09-10 17:04:49 -0400 (Wed, 10 Sep 2008) | 4 lines
|
|
2615 Changed paths:
|
|
2616 M /branches/prog/bwa/bwtsw2.h
|
|
2617 M /branches/prog/bwa/bwtsw2_aux.c
|
|
2618 M /branches/prog/bwa/bwtsw2_core.c
|
|
2619 M /branches/prog/bwa/bwtsw2_main.c
|
|
2620 M /branches/prog/bwa/main.c
|
|
2621
|
|
2622 * bwa-0.2.0-7
|
|
2623 * avoid some missing hits
|
|
2624 * add maximum depth
|
|
2625
|
|
2626 ------------------------------------------------------------------------
|
|
2627 r489 | lh3 | 2008-09-10 11:51:13 -0400 (Wed, 10 Sep 2008) | 4 lines
|
|
2628 Changed paths:
|
|
2629 M /branches/prog/bwa/bwtsw2_core.c
|
|
2630 M /branches/prog/bwa/main.c
|
|
2631
|
|
2632 * bwa-0.2.0-6
|
|
2633 * bwtsw2 works although on the forward strand only for now
|
|
2634 * better progress information
|
|
2635
|
|
2636 ------------------------------------------------------------------------
|
|
2637 r488 | lh3 | 2008-09-10 10:21:53 -0400 (Wed, 10 Sep 2008) | 3 lines
|
|
2638 Changed paths:
|
|
2639 M /branches/prog/bwa/bwtsw2_core.c
|
|
2640
|
|
2641 * implement memory pool
|
|
2642 * avoid some rehashing
|
|
2643
|
|
2644 ------------------------------------------------------------------------
|
|
2645 r487 | lh3 | 2008-09-10 09:23:38 -0400 (Wed, 10 Sep 2008) | 3 lines
|
|
2646 Changed paths:
|
|
2647 M /branches/prog/bwa/bwtsw2.h
|
|
2648 M /branches/prog/bwa/bwtsw2_aux.c
|
|
2649 M /branches/prog/bwa/bwtsw2_main.c
|
|
2650
|
|
2651 * fixed a memory leak
|
|
2652 * prepare to implement mempool
|
|
2653
|
|
2654 ------------------------------------------------------------------------
|
|
2655 r486 | lh3 | 2008-09-10 09:10:09 -0400 (Wed, 10 Sep 2008) | 4 lines
|
|
2656 Changed paths:
|
|
2657 M /branches/prog/bwa/bwtsw2.h
|
|
2658 M /branches/prog/bwa/bwtsw2_aux.c
|
|
2659 M /branches/prog/bwa/bwtsw2_core.c
|
|
2660 M /branches/prog/bwa/bwtsw2_main.c
|
|
2661 M /branches/prog/bwa/khash.h
|
|
2662
|
|
2663 * add X-dropoff
|
|
2664 * remove duplicated results
|
|
2665 * switch to simple stack
|
|
2666
|
|
2667 ------------------------------------------------------------------------
|
|
2668 r485 | lh3 | 2008-09-10 06:31:20 -0400 (Wed, 10 Sep 2008) | 3 lines
|
|
2669 Changed paths:
|
|
2670 M /branches/prog/bwa/bwtsw2.h
|
|
2671 M /branches/prog/bwa/bwtsw2_aux.c
|
|
2672 M /branches/prog/bwa/bwtsw2_core.c
|
|
2673 M /branches/prog/bwa/bwtsw2_main.c
|
|
2674
|
|
2675 * check whether t-node has been visited
|
|
2676 * prepare to remove two-level stack
|
|
2677
|
|
2678 ------------------------------------------------------------------------
|
|
2679 r484 | lh3 | 2008-09-10 05:00:57 -0400 (Wed, 10 Sep 2008) | 2 lines
|
|
2680 Changed paths:
|
|
2681 A /branches/prog/bwa/khash.h
|
|
2682
|
|
2683 khash library
|
|
2684
|
|
2685 ------------------------------------------------------------------------
|
|
2686 r483 | lh3 | 2008-09-10 04:22:53 -0400 (Wed, 10 Sep 2008) | 2 lines
|
|
2687 Changed paths:
|
|
2688 M /branches/prog/bwa/bwtsw2_core.c
|
|
2689
|
|
2690 add inline
|
|
2691
|
|
2692 ------------------------------------------------------------------------
|
|
2693 r482 | lh3 | 2008-09-09 16:34:57 -0400 (Tue, 09 Sep 2008) | 2 lines
|
|
2694 Changed paths:
|
|
2695 M /branches/prog/bwa/Makefile
|
|
2696 M /branches/prog/bwa/bwtsw2_aux.c
|
|
2697 M /branches/prog/bwa/bwtsw2_core.c
|
|
2698
|
|
2699 improve speed
|
|
2700
|
|
2701 ------------------------------------------------------------------------
|
|
2702 r481 | lh3 | 2008-09-09 13:13:00 -0400 (Tue, 09 Sep 2008) | 4 lines
|
|
2703 Changed paths:
|
|
2704 M /branches/prog/bwa/bwtsw2_core.c
|
|
2705
|
|
2706 Use a 128bit hash table to keep all (tk,tl,qk,ql). This is slow. Just
|
|
2707 keep a copy in case I may need this in future.
|
|
2708
|
|
2709
|
|
2710 ------------------------------------------------------------------------
|
|
2711 r480 | lh3 | 2008-09-09 12:53:32 -0400 (Tue, 09 Sep 2008) | 2 lines
|
|
2712 Changed paths:
|
|
2713 M /branches/prog/bwa/bwtsw2.h
|
|
2714 M /branches/prog/bwa/bwtsw2_core.c
|
|
2715
|
|
2716 * no principal modification
|
|
2717
|
|
2718 ------------------------------------------------------------------------
|
|
2719 r479 | lh3 | 2008-09-09 11:01:45 -0400 (Tue, 09 Sep 2008) | 4 lines
|
|
2720 Changed paths:
|
|
2721 M /branches/prog/bwa/Makefile
|
|
2722 M /branches/prog/bwa/bwtsw2_core.c
|
|
2723
|
|
2724 * fixed a bug which may cause duplicated matching
|
|
2725 * accelerate the speed a bit, although using hash in avoiding duplications
|
|
2726 slows the speed down in the end
|
|
2727
|
|
2728 ------------------------------------------------------------------------
|
|
2729 r474 | lh3 | 2008-09-03 17:22:57 -0400 (Wed, 03 Sep 2008) | 4 lines
|
|
2730 Changed paths:
|
|
2731 M /branches/prog/bwa/Makefile
|
|
2732 M /branches/prog/bwa/bwtsw2.h
|
|
2733 M /branches/prog/bwa/bwtsw2_aux.c
|
|
2734 M /branches/prog/bwa/bwtsw2_core.c
|
|
2735 M /branches/prog/bwa/bwtsw2_main.c
|
|
2736 M /branches/prog/bwa/main.c
|
|
2737
|
|
2738 * bwa-0.2.0-5
|
|
2739 * indel seems to work on toy example
|
|
2740 * add band
|
|
2741
|
|
2742 ------------------------------------------------------------------------
|
|
2743 r469 | lh3 | 2008-09-01 09:18:45 -0400 (Mon, 01 Sep 2008) | 3 lines
|
|
2744 Changed paths:
|
|
2745 M /branches/prog/bwa/ChangeLog
|
|
2746 M /branches/prog/bwa/Makefile
|
|
2747 M /branches/prog/bwa/bwt_lite.c
|
|
2748 M /branches/prog/bwa/bwt_lite.h
|
|
2749 M /branches/prog/bwa/bwtgap.c
|
|
2750 M /branches/prog/bwa/bwtsw2.h
|
|
2751 A /branches/prog/bwa/bwtsw2_aux.c
|
|
2752 M /branches/prog/bwa/bwtsw2_core.c
|
|
2753 M /branches/prog/bwa/bwtsw2_main.c
|
|
2754 M /branches/prog/bwa/is.c
|
|
2755 M /branches/prog/bwa/main.c
|
|
2756 M /branches/prog/bwa/main.h
|
|
2757 M /branches/prog/bwa/simple_dp.c
|
|
2758
|
|
2759 * bwa-0.2.0-4
|
|
2760 * updated bwtsw2, which seems to work properly on toy examples
|
|
2761
|
|
2762 ------------------------------------------------------------------------
|
|
2763 r447 | lh3 | 2008-08-27 10:05:09 -0400 (Wed, 27 Aug 2008) | 3 lines
|
|
2764 Changed paths:
|
|
2765 M /branches/prog/bwa/bwt2fmv.c
|
|
2766 M /branches/prog/bwa/bwtaln.c
|
|
2767 M /branches/prog/bwa/bwtaln.h
|
|
2768 M /branches/prog/bwa/bwtgap.c
|
|
2769 M /branches/prog/bwa/main.c
|
|
2770
|
|
2771 * bwa-0.2.0-3
|
|
2772 * tune for longer gaps, but it does not really work with kilo-bp gaps...
|
|
2773
|
|
2774 ------------------------------------------------------------------------
|
|
2775 r446 | lh3 | 2008-08-26 13:30:41 -0400 (Tue, 26 Aug 2008) | 3 lines
|
|
2776 Changed paths:
|
|
2777 M /branches/prog/bwa/bwt2fmv.c
|
|
2778 M /branches/prog/bwa/bwtaln.c
|
|
2779 M /branches/prog/bwa/bwtaln.h
|
|
2780 M /branches/prog/bwa/bwtgap.c
|
|
2781 M /branches/prog/bwa/main.c
|
|
2782
|
|
2783 * bwa-0.2.0-2
|
|
2784 * changed the way to extend long deletions. Now use max_del_occ.
|
|
2785
|
|
2786 ------------------------------------------------------------------------
|
|
2787 r445 | lh3 | 2008-08-26 13:05:58 -0400 (Tue, 26 Aug 2008) | 2 lines
|
|
2788 Changed paths:
|
|
2789 M /branches/prog/bwa/bwt_lite.c
|
|
2790 M /branches/prog/bwa/bwt_lite.h
|
|
2791
|
|
2792 updated from bwtsw2_lite
|
|
2793
|
|
2794 ------------------------------------------------------------------------
|
|
2795 r436 | lh3 | 2008-08-23 12:28:44 -0400 (Sat, 23 Aug 2008) | 4 lines
|
|
2796 Changed paths:
|
|
2797 M /branches/prog/bwa/Makefile
|
|
2798 M /branches/prog/bwa/bwt.h
|
|
2799 A /branches/prog/bwa/bwt_lite.c
|
|
2800 A /branches/prog/bwa/bwt_lite.h
|
|
2801 A /branches/prog/bwa/bwtsw2.h
|
|
2802 A /branches/prog/bwa/bwtsw2_core.c
|
|
2803 A /branches/prog/bwa/bwtsw2_main.c
|
|
2804 M /branches/prog/bwa/main.c
|
|
2805
|
|
2806 * bwa-0.2.0-1
|
|
2807 * add bwt_lite: a light-weighted version of bwt (NOT TESTED!)
|
|
2808 * add core codes for bwtsw2: NOT TESTED!!!
|
|
2809
|
|
2810 ------------------------------------------------------------------------
|
|
2811 r427 | lh3 | 2008-08-15 05:38:12 -0400 (Fri, 15 Aug 2008) | 2 lines
|
|
2812 Changed paths:
|
|
2813 M /branches/prog/bwa/ChangeLog
|
|
2814 M /branches/prog/bwa/NEWS
|
|
2815 M /branches/prog/bwa/bwa.1
|
|
2816 M /branches/prog/bwa/bwtaln.c
|
|
2817 M /branches/prog/bwa/main.c
|
|
2818
|
|
2819 Release bwa-0.2.0
|
|
2820
|
|
2821 ------------------------------------------------------------------------
|
|
2822 r426 | lh3 | 2008-08-14 11:26:19 -0400 (Thu, 14 Aug 2008) | 4 lines
|
|
2823 Changed paths:
|
|
2824 M /branches/prog/bwa/bwt2fmv.c
|
|
2825 M /branches/prog/bwa/bwtaln.c
|
|
2826 M /branches/prog/bwa/bwtaln.h
|
|
2827 M /branches/prog/bwa/main.c
|
|
2828
|
|
2829 * bwa-0.1.6-7
|
|
2830 * change default seed length to 31
|
|
2831 * add incomplete support to color sequences (not tested yet!)
|
|
2832
|
|
2833 ------------------------------------------------------------------------
|
|
2834 r425 | lh3 | 2008-08-14 06:23:11 -0400 (Thu, 14 Aug 2008) | 3 lines
|
|
2835 Changed paths:
|
|
2836 M /branches/prog/bwa/bwtaln.c
|
|
2837 M /branches/prog/bwa/main.c
|
|
2838
|
|
2839 * bwa-0.1.6-6
|
|
2840 * change default seed length to 33bp
|
|
2841
|
|
2842 ------------------------------------------------------------------------
|
|
2843 r424 | lh3 | 2008-08-14 05:55:33 -0400 (Thu, 14 Aug 2008) | 6 lines
|
|
2844 Changed paths:
|
|
2845 M /branches/prog/bwa/bwtaln.c
|
|
2846 M /branches/prog/bwa/bwtgap.c
|
|
2847 M /branches/prog/bwa/main.c
|
|
2848
|
|
2849 * bwa-0.1.6-5
|
|
2850 * fixed a bug that may miss true alignments. this bugs exists in most
|
|
2851 early versions.
|
|
2852 * fixed a bug that yields wrong coordinates for reads mapped on the forward
|
|
2853 strands with gaps.
|
|
2854
|
|
2855 ------------------------------------------------------------------------
|
|
2856 r423 | lh3 | 2008-08-14 04:07:28 -0400 (Thu, 14 Aug 2008) | 2 lines
|
|
2857 Changed paths:
|
|
2858 D /branches/prog/bwa/Makefile.div
|
|
2859
|
|
2860 useless
|
|
2861
|
|
2862 ------------------------------------------------------------------------
|
|
2863 r422 | lh3 | 2008-08-13 19:21:14 -0400 (Wed, 13 Aug 2008) | 4 lines
|
|
2864 Changed paths:
|
|
2865 M /branches/prog/bwa/bwtaln.c
|
|
2866 M /branches/prog/bwa/main.c
|
|
2867
|
|
2868 * bwa-0.1.6-4
|
|
2869 * fixed one bug
|
|
2870 * there is another one...
|
|
2871
|
|
2872 ------------------------------------------------------------------------
|
|
2873 r421 | lh3 | 2008-08-13 18:23:33 -0400 (Wed, 13 Aug 2008) | 3 lines
|
|
2874 Changed paths:
|
|
2875 M /branches/prog/bwa/bwtaln.c
|
|
2876 M /branches/prog/bwa/bwtaln.h
|
|
2877 M /branches/prog/bwa/bwtgap.c
|
|
2878 M /branches/prog/bwa/bwtgap.h
|
|
2879 M /branches/prog/bwa/bwtindex.c
|
|
2880 M /branches/prog/bwa/main.c
|
|
2881
|
|
2882 * bwa-0.1.6-3
|
|
2883 * almost there, but not quite right
|
|
2884
|
|
2885 ------------------------------------------------------------------------
|
|
2886 r419 | lh3 | 2008-08-13 17:27:02 -0400 (Wed, 13 Aug 2008) | 3 lines
|
|
2887 Changed paths:
|
|
2888 M /branches/prog/bwa/bwtaln.c
|
|
2889 M /branches/prog/bwa/bwtaln.h
|
|
2890 M /branches/prog/bwa/bwtgap.c
|
|
2891 M /branches/prog/bwa/bwtgap.h
|
|
2892 M /branches/prog/bwa/main.c
|
|
2893
|
|
2894 * improve the seeding method
|
|
2895 * prepare to load two BWTs into memory. A BIG change!
|
|
2896
|
|
2897 ------------------------------------------------------------------------
|
|
2898 r418 | lh3 | 2008-08-13 10:56:54 -0400 (Wed, 13 Aug 2008) | 3 lines
|
|
2899 Changed paths:
|
|
2900 M /branches/prog/bwa/bwt2fmv.c
|
|
2901 M /branches/prog/bwa/bwtaln.c
|
|
2902 M /branches/prog/bwa/bwtaln.h
|
|
2903 M /branches/prog/bwa/bwtgap.c
|
|
2904 M /branches/prog/bwa/bwtgap.h
|
|
2905 M /branches/prog/bwa/main.c
|
|
2906
|
|
2907 * added seeding
|
|
2908 * unfinished yet
|
|
2909
|
|
2910 ------------------------------------------------------------------------
|
|
2911 r413 | lh3 | 2008-08-08 11:48:35 -0400 (Fri, 08 Aug 2008) | 2 lines
|
|
2912 Changed paths:
|
|
2913 M /branches/prog/bwa/ChangeLog
|
|
2914 M /branches/prog/bwa/NEWS
|
|
2915 M /branches/prog/bwa/main.c
|
|
2916
|
|
2917 Release bwa-0.1.6
|
|
2918
|
|
2919 ------------------------------------------------------------------------
|
|
2920 r410 | lh3 | 2008-08-06 15:48:22 -0400 (Wed, 06 Aug 2008) | 2 lines
|
|
2921 Changed paths:
|
|
2922 M /branches/prog/bwa/simple_dp.c
|
|
2923
|
|
2924 sw: output alignment score
|
|
2925
|
|
2926 ------------------------------------------------------------------------
|
|
2927 r407 | lh3 | 2008-08-04 10:01:20 -0400 (Mon, 04 Aug 2008) | 4 lines
|
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2928 Changed paths:
|
|
2929 M /branches/prog/bwa/Makefile
|
|
2930 M /branches/prog/bwa/main.c
|
|
2931 M /branches/prog/bwa/main.h
|
|
2932 A /branches/prog/bwa/simple_dp.c
|
|
2933 M /branches/prog/bwa/stdaln.c
|
|
2934 M /branches/prog/bwa/stdaln.h
|
|
2935
|
|
2936 * bwa-0.1.5-3
|
|
2937 * added a simple interface to SW/NW alignment
|
|
2938 * stdaln-0.9.8 (see header for more details)
|
|
2939
|
|
2940 ------------------------------------------------------------------------
|
|
2941 r406 | lh3 | 2008-08-01 19:21:59 -0400 (Fri, 01 Aug 2008) | 3 lines
|
|
2942 Changed paths:
|
|
2943 M /branches/prog/bwa/Makefile
|
|
2944 M /branches/prog/bwa/bwtaln.c
|
|
2945 M /branches/prog/bwa/bwtaln.h
|
|
2946 M /branches/prog/bwa/main.c
|
|
2947 A /branches/prog/bwa/stdaln.c
|
|
2948 A /branches/prog/bwa/stdaln.h
|
|
2949
|
|
2950 * bwa-0.1.5-2
|
|
2951 * give accurate gap positions
|
|
2952
|
|
2953 ------------------------------------------------------------------------
|
|
2954 r405 | lh3 | 2008-08-01 19:06:19 -0400 (Fri, 01 Aug 2008) | 2 lines
|
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2955 Changed paths:
|
|
2956 M /branches/prog/bwa/Makefile
|
|
2957 M /branches/prog/bwa/bwtaln.c
|
|
2958 M /branches/prog/bwa/bwtaln.h
|
|
2959
|
|
2960 unfinished, but I am tired...
|
|
2961
|
|
2962 ------------------------------------------------------------------------
|
|
2963 r401 | lh3 | 2008-07-30 05:59:24 -0400 (Wed, 30 Jul 2008) | 4 lines
|
|
2964 Changed paths:
|
|
2965 M /branches/prog/bwa/bntseq.c
|
|
2966 M /branches/prog/bwa/main.c
|
|
2967
|
|
2968 * bwa-0.1.5-1
|
|
2969 * fixed a potential bug which may produce an alignment in N regions,
|
|
2970 although extremely rare.
|
|
2971
|
|
2972 ------------------------------------------------------------------------
|
|
2973 r399 | lh3 | 2008-07-27 11:41:52 -0400 (Sun, 27 Jul 2008) | 2 lines
|
|
2974 Changed paths:
|
|
2975 M /branches/prog/bwa/ChangeLog
|
|
2976 M /branches/prog/bwa/NEWS
|
|
2977 M /branches/prog/bwa/main.c
|
|
2978
|
|
2979 Release bwa-0.1.5
|
|
2980
|
|
2981 ------------------------------------------------------------------------
|
|
2982 r398 | lh3 | 2008-07-25 12:14:47 -0400 (Fri, 25 Jul 2008) | 2 lines
|
|
2983 Changed paths:
|
|
2984 M /branches/prog/bwa/bwa.1
|
|
2985
|
|
2986 update documentation
|
|
2987
|
|
2988 ------------------------------------------------------------------------
|
|
2989 r397 | lh3 | 2008-07-25 09:58:56 -0400 (Fri, 25 Jul 2008) | 2 lines
|
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2990 Changed paths:
|
|
2991 M /branches/prog/bwa/bwt2fmv.c
|
|
2992 M /branches/prog/bwa/bwtaln.c
|
|
2993 M /branches/prog/bwa/main.c
|
|
2994
|
|
2995 *
|
|
2996
|
|
2997 ------------------------------------------------------------------------
|
|
2998 r396 | lh3 | 2008-07-25 06:42:01 -0400 (Fri, 25 Jul 2008) | 3 lines
|
|
2999 Changed paths:
|
|
3000 M /branches/prog/bwa/bwtaln.c
|
|
3001 M /branches/prog/bwa/main.c
|
|
3002
|
|
3003 * bwa-0.1.4-4
|
|
3004 * add timer for debugging
|
|
3005
|
|
3006 ------------------------------------------------------------------------
|
|
3007 r395 | lh3 | 2008-07-24 05:46:21 -0400 (Thu, 24 Jul 2008) | 4 lines
|
|
3008 Changed paths:
|
|
3009 M /branches/prog/bwa/bwtgap.c
|
|
3010 M /branches/prog/bwa/main.c
|
|
3011
|
|
3012 * bwa-0.1.4-3
|
|
3013 * fixed a bug in the previous code
|
|
3014 * this version gives identical result to bwa-0.1.4, just 10% faster
|
|
3015
|
|
3016 ------------------------------------------------------------------------
|
|
3017 r394 | lh3 | 2008-07-24 05:18:53 -0400 (Thu, 24 Jul 2008) | 4 lines
|
|
3018 Changed paths:
|
|
3019 M /branches/prog/bwa/bwtaln.c
|
|
3020 M /branches/prog/bwa/bwtgap.c
|
|
3021 M /branches/prog/bwa/bwtgap.h
|
|
3022 M /branches/prog/bwa/main.c
|
|
3023
|
|
3024 * bwa-0.1.4-2
|
|
3025 * further improve the speed
|
|
3026 * The result is slightly different from bwa-0.1.4 now. I need to check...
|
|
3027
|
|
3028 ------------------------------------------------------------------------
|
|
3029 r393 | lh3 | 2008-07-23 12:04:16 -0400 (Wed, 23 Jul 2008) | 2 lines
|
|
3030 Changed paths:
|
|
3031 M /branches/prog/bwa/bwt.c
|
|
3032
|
|
3033 comments only
|
|
3034
|
|
3035 ------------------------------------------------------------------------
|
|
3036 r392 | lh3 | 2008-07-23 10:34:03 -0400 (Wed, 23 Jul 2008) | 2 lines
|
|
3037 Changed paths:
|
|
3038 M /branches/prog/bwa/bwt.c
|
|
3039 M /branches/prog/bwa/main.c
|
|
3040
|
|
3041 further improve the speed in Occ functions
|
|
3042
|
|
3043 ------------------------------------------------------------------------
|
|
3044 r386 | lh3 | 2008-07-22 10:03:54 -0400 (Tue, 22 Jul 2008) | 2 lines
|
|
3045 Changed paths:
|
|
3046 M /branches/prog/bwa/NEWS
|
|
3047 M /branches/prog/bwa/main.c
|
|
3048
|
|
3049 Release bwa-0.1.4
|
|
3050
|
|
3051 ------------------------------------------------------------------------
|
|
3052 r385 | lh3 | 2008-07-22 09:44:50 -0400 (Tue, 22 Jul 2008) | 2 lines
|
|
3053 Changed paths:
|
|
3054 M /branches/prog/bwa/ChangeLog
|
|
3055 M /branches/prog/bwa/bwa.1
|
|
3056
|
|
3057 update documentation and ChangeLog
|
|
3058
|
|
3059 ------------------------------------------------------------------------
|
|
3060 r384 | lh3 | 2008-07-22 08:50:03 -0400 (Tue, 22 Jul 2008) | 4 lines
|
|
3061 Changed paths:
|
|
3062 M /branches/prog/bwa/Makefile
|
|
3063 M /branches/prog/bwa/bwt2fmv.c
|
|
3064 M /branches/prog/bwa/bwtaln.c
|
|
3065 M /branches/prog/bwa/bwtaln.h
|
|
3066 M /branches/prog/bwa/bwtgap.c
|
|
3067 M /branches/prog/bwa/main.c
|
|
3068
|
|
3069 * bwa-0.1.3-2
|
|
3070 * fixed the bug in the last modification
|
|
3071 * now the alignment should be more clearly defined
|
|
3072
|
|
3073 ------------------------------------------------------------------------
|
|
3074 r383 | lh3 | 2008-07-21 18:32:21 -0400 (Mon, 21 Jul 2008) | 4 lines
|
|
3075 Changed paths:
|
|
3076 M /branches/prog/bwa/bwt2fmv.c
|
|
3077 M /branches/prog/bwa/bwtaln.c
|
|
3078 M /branches/prog/bwa/bwtgap.c
|
|
3079 M /branches/prog/bwa/main.c
|
|
3080
|
|
3081 * bwa-0.1.3-1
|
|
3082 * this is a buggy verion!
|
|
3083 * i will fix the bug tomorrow. It is late...
|
|
3084
|
|
3085 ------------------------------------------------------------------------
|
|
3086 r381 | lh3 | 2008-07-21 06:45:32 -0400 (Mon, 21 Jul 2008) | 2 lines
|
|
3087 Changed paths:
|
|
3088 M /branches/prog/bwa/ChangeLog
|
|
3089 M /branches/prog/bwa/NEWS
|
|
3090 M /branches/prog/bwa/bwa.1
|
|
3091 M /branches/prog/bwa/main.c
|
|
3092
|
|
3093 Release bwa-0.1.3
|
|
3094
|
|
3095 ------------------------------------------------------------------------
|
|
3096 r380 | lh3 | 2008-07-21 06:07:43 -0400 (Mon, 21 Jul 2008) | 4 lines
|
|
3097 Changed paths:
|
|
3098 M /branches/prog/bwa/ChangeLog
|
|
3099 M /branches/prog/bwa/bwa.1
|
|
3100 M /branches/prog/bwa/bwt.c
|
|
3101 M /branches/prog/bwa/bwt2fmv.c
|
|
3102 M /branches/prog/bwa/main.c
|
|
3103
|
|
3104 * bwa-0.1.2-3
|
|
3105 * improve the speed for gcc on Intel Mac OS X, but not really on icc on Linux
|
|
3106 * aln: more command-line options
|
|
3107
|
|
3108 ------------------------------------------------------------------------
|
|
3109 r373 | lh3 | 2008-07-17 09:09:46 -0400 (Thu, 17 Jul 2008) | 4 lines
|
|
3110 Changed paths:
|
|
3111 M /branches/prog/bwa/bwt.c
|
|
3112 M /branches/prog/bwa/bwt.h
|
|
3113 M /branches/prog/bwa/bwtio.c
|
|
3114 M /branches/prog/bwa/main.c
|
|
3115
|
|
3116 * bwa-0.1.2-2
|
|
3117 * further improve the speed
|
|
3118 * this version gives exactly the same result as bwa-0.1.2
|
|
3119
|
|
3120 ------------------------------------------------------------------------
|
|
3121 r372 | lh3 | 2008-07-17 07:51:08 -0400 (Thu, 17 Jul 2008) | 3 lines
|
|
3122 Changed paths:
|
|
3123 M /branches/prog/bwa/bwt.c
|
|
3124 M /branches/prog/bwa/main.c
|
|
3125
|
|
3126 * bwa-0.1.2-1
|
|
3127 * speed up by about 5%
|
|
3128
|
|
3129 ------------------------------------------------------------------------
|
|
3130 r370 | lh3 | 2008-07-17 05:12:00 -0400 (Thu, 17 Jul 2008) | 2 lines
|
|
3131 Changed paths:
|
|
3132 M /branches/prog/bwa/NEWS
|
|
3133 M /branches/prog/bwa/bwa.1
|
|
3134 M /branches/prog/bwa/main.c
|
|
3135
|
|
3136 Release bwa-0.1.2
|
|
3137
|
|
3138 ------------------------------------------------------------------------
|
|
3139 r368 | lh3 | 2008-07-16 08:51:25 -0400 (Wed, 16 Jul 2008) | 4 lines
|
|
3140 Changed paths:
|
|
3141 M /branches/prog/bwa/Makefile
|
|
3142 D /branches/prog/bwa/bwt1away.c
|
|
3143 M /branches/prog/bwa/bwt2fmv.c
|
|
3144 M /branches/prog/bwa/bwtaln.c
|
|
3145 M /branches/prog/bwa/bwtaln.h
|
|
3146 M /branches/prog/bwa/bwtgap.c
|
|
3147 M /branches/prog/bwa/bwtgap.h
|
|
3148 D /branches/prog/bwa/bwttop2.c
|
|
3149 M /branches/prog/bwa/main.c
|
|
3150
|
|
3151 * bwa-0.1.1-9
|
|
3152 * some code cleanup
|
|
3153 * remove 1away and top2
|
|
3154
|
|
3155 ------------------------------------------------------------------------
|
|
3156 r367 | lh3 | 2008-07-16 08:24:34 -0400 (Wed, 16 Jul 2008) | 2 lines
|
|
3157 Changed paths:
|
|
3158 M /branches/prog/bwa/is.c
|
|
3159
|
|
3160 Yuta Mori's implementation of IS algorithm.
|
|
3161
|
|
3162 ------------------------------------------------------------------------
|
|
3163 r365 | lh3 | 2008-07-16 06:58:04 -0400 (Wed, 16 Jul 2008) | 6 lines
|
|
3164 Changed paths:
|
|
3165 M /branches/prog/bwa/bwtaln.c
|
|
3166 M /branches/prog/bwa/bwtgap.c
|
|
3167 M /branches/prog/bwa/bwtgap.h
|
|
3168 M /branches/prog/bwa/main.c
|
|
3169
|
|
3170 * bwa-0.1.1-8
|
|
3171 * improve gapped alignment
|
|
3172 * this version will miss more gapped alignments, but the speed is much faster
|
|
3173 * prepare to remove top2 and 1away algorithms
|
|
3174 * prepare to add SAIS algorithm for bwt construction
|
|
3175
|
|
3176 ------------------------------------------------------------------------
|
|
3177 r358 | lh3 | 2008-06-09 06:03:04 -0400 (Mon, 09 Jun 2008) | 4 lines
|
|
3178 Changed paths:
|
|
3179 M /branches/prog/bwa/bwt2fmv.c
|
|
3180 M /branches/prog/bwa/bwtgap.c
|
|
3181 M /branches/prog/bwa/main.c
|
|
3182
|
|
3183 * bwa-0.1.1-7
|
|
3184 * change END_SKIP from 3 to 5, but still gaps may be wrongly added
|
|
3185 * change default '-g' from 5 to 3
|
|
3186
|
|
3187 ------------------------------------------------------------------------
|
|
3188 r357 | lh3 | 2008-06-09 05:18:36 -0400 (Mon, 09 Jun 2008) | 3 lines
|
|
3189 Changed paths:
|
|
3190 M /branches/prog/bwa/bntseq.c
|
|
3191 M /branches/prog/bwa/bwt2fmv.c
|
|
3192 M /branches/prog/bwa/bwtgap.c
|
|
3193 M /branches/prog/bwa/main.c
|
|
3194
|
|
3195 * bwa-0.1.1-6
|
|
3196 * fix a bug in nested stack
|
|
3197
|
|
3198 ------------------------------------------------------------------------
|
|
3199 r356 | lh3 | 2008-06-08 18:43:13 -0400 (Sun, 08 Jun 2008) | 4 lines
|
|
3200 Changed paths:
|
|
3201 M /branches/prog/bwa/Makefile
|
|
3202 M /branches/prog/bwa/bwtaln.c
|
|
3203 M /branches/prog/bwa/bwtaln.h
|
|
3204 M /branches/prog/bwa/bwtgap.c
|
|
3205 A /branches/prog/bwa/bwtgap.h
|
|
3206 M /branches/prog/bwa/main.c
|
|
3207
|
|
3208 * bwa-0.1.1-5
|
|
3209 * replace heap with nested stacks
|
|
3210 * there are still obvious bugs...
|
|
3211
|
|
3212 ------------------------------------------------------------------------
|
|
3213 r355 | lh3 | 2008-06-08 17:13:44 -0400 (Sun, 08 Jun 2008) | 4 lines
|
|
3214 Changed paths:
|
|
3215 M /branches/prog/bwa/bwt2fmv.c
|
|
3216 M /branches/prog/bwa/bwtaln.c
|
|
3217 M /branches/prog/bwa/bwtaln.h
|
|
3218 M /branches/prog/bwa/bwtgap.c
|
|
3219 M /branches/prog/bwa/main.c
|
|
3220 M /branches/prog/bwa/main.h
|
|
3221
|
|
3222 * bwa-0.1.1-4
|
|
3223 * add interface to affine gap alignment
|
|
3224 * there are obvious bugs and I will fix them later
|
|
3225
|
|
3226 ------------------------------------------------------------------------
|
|
3227 r354 | lh3 | 2008-06-08 15:39:05 -0400 (Sun, 08 Jun 2008) | 3 lines
|
|
3228 Changed paths:
|
|
3229 M /branches/prog/bwa/bwtaln.c
|
|
3230 M /branches/prog/bwa/bwtaln.h
|
|
3231 M /branches/prog/bwa/bwtgap.c
|
|
3232 M /branches/prog/bwa/main.c
|
|
3233
|
|
3234 * bwa-0.1.1-3
|
|
3235 * affine gap seems to work, at least partially
|
|
3236
|
|
3237 ------------------------------------------------------------------------
|
|
3238 r353 | lh3 | 2008-06-08 09:27:18 -0400 (Sun, 08 Jun 2008) | 3 lines
|
|
3239 Changed paths:
|
|
3240 M /branches/prog/bwa/Makefile
|
|
3241 M /branches/prog/bwa/bwt2fmv.c
|
|
3242 M /branches/prog/bwa/bwtaln.c
|
|
3243 M /branches/prog/bwa/bwtaln.h
|
|
3244 A /branches/prog/bwa/bwtgap.c
|
|
3245 M /branches/prog/bwa/bwttop2.c
|
|
3246 M /branches/prog/bwa/main.c
|
|
3247
|
|
3248 * bwa-0.1.1-2
|
|
3249 * initial gapped alignment. not work at the moment
|
|
3250
|
|
3251 ------------------------------------------------------------------------
|
|
3252 r352 | lh3 | 2008-06-06 04:37:34 -0400 (Fri, 06 Jun 2008) | 3 lines
|
|
3253 Changed paths:
|
|
3254 M /branches/prog/bwa/bwttop2.c
|
|
3255 M /branches/prog/bwa/main.c
|
|
3256
|
|
3257 * bwa-0.1.1-1
|
|
3258 * ungap: remove a useless varible in top2_entry_t
|
|
3259
|
|
3260 ------------------------------------------------------------------------
|
|
3261 r348 | lh3 | 2008-06-03 09:04:12 -0400 (Tue, 03 Jun 2008) | 2 lines
|
|
3262 Changed paths:
|
|
3263 M /branches/prog/bwa/ChangeLog
|
|
3264 A /branches/prog/bwa/NEWS
|
|
3265 M /branches/prog/bwa/bwa.1
|
|
3266 M /branches/prog/bwa/main.c
|
|
3267
|
|
3268 Release bwa-0.1.1
|
|
3269
|
|
3270 ------------------------------------------------------------------------
|
|
3271 r347 | lh3 | 2008-06-03 05:45:08 -0400 (Tue, 03 Jun 2008) | 2 lines
|
|
3272 Changed paths:
|
|
3273 M /branches/prog/bwa/bwa.1
|
|
3274
|
|
3275 update documentation
|
|
3276
|
|
3277 ------------------------------------------------------------------------
|
|
3278 r346 | lh3 | 2008-06-02 18:59:50 -0400 (Mon, 02 Jun 2008) | 5 lines
|
|
3279 Changed paths:
|
|
3280 A /branches/prog/bwa/ChangeLog
|
|
3281 A /branches/prog/bwa/bwa.1
|
|
3282 M /branches/prog/bwa/bwtaln.c
|
|
3283 M /branches/prog/bwa/main.c
|
|
3284
|
|
3285 * bwa-0.1.0-11
|
|
3286 * improve approximating mapping qualities
|
|
3287 * add documentation
|
|
3288 * add ChangeLog
|
|
3289
|
|
3290 ------------------------------------------------------------------------
|
|
3291 r345 | lh3 | 2008-06-02 16:04:39 -0400 (Mon, 02 Jun 2008) | 3 lines
|
|
3292 Changed paths:
|
|
3293 M /branches/prog/bwa/bwtaln.c
|
|
3294 M /branches/prog/bwa/bwttop2.c
|
|
3295 M /branches/prog/bwa/main.c
|
|
3296
|
|
3297 * bwa-0.1.0-10
|
|
3298 * output a random position for repetitive reads
|
|
3299
|
|
3300 ------------------------------------------------------------------------
|
|
3301 r344 | lh3 | 2008-06-02 15:03:54 -0400 (Mon, 02 Jun 2008) | 4 lines
|
|
3302 Changed paths:
|
|
3303 M /branches/prog/bwa/bntseq.c
|
|
3304 M /branches/prog/bwa/bwtaln.c
|
|
3305 M /branches/prog/bwa/main.c
|
|
3306 M /branches/prog/bwa/pac2bwt.c
|
|
3307
|
|
3308 * bwa-0.1.0-9
|
|
3309 * fix memory leaks
|
|
3310 * fix a potential bug in coverting to the real coordinate
|
|
3311
|
|
3312 ------------------------------------------------------------------------
|
|
3313 r343 | lh3 | 2008-06-02 13:44:51 -0400 (Mon, 02 Jun 2008) | 5 lines
|
|
3314 Changed paths:
|
|
3315 M /branches/prog/bwa/Makefile.div
|
|
3316 M /branches/prog/bwa/bwt.c
|
|
3317 M /branches/prog/bwa/bwt.h
|
|
3318 M /branches/prog/bwa/bwt2fmv.c
|
|
3319 M /branches/prog/bwa/bwtaln.c
|
|
3320 M /branches/prog/bwa/bwttop2.c
|
|
3321 M /branches/prog/bwa/main.c
|
|
3322
|
|
3323 * bwa-0.1.0-8
|
|
3324 * fix a bug about strand
|
|
3325 * update Makefile.div
|
|
3326 * change top2b as the default method
|
|
3327
|
|
3328 ------------------------------------------------------------------------
|
|
3329 r342 | lh3 | 2008-06-02 11:23:26 -0400 (Mon, 02 Jun 2008) | 3 lines
|
|
3330 Changed paths:
|
|
3331 M /branches/prog/bwa/bwt.c
|
|
3332 M /branches/prog/bwa/bwt1away.c
|
|
3333 M /branches/prog/bwa/bwtaln.c
|
|
3334 M /branches/prog/bwa/main.c
|
|
3335
|
|
3336 * bwa-0.1.0-7
|
|
3337 * use bwt_2occ() and bwt_2occ4() in other functions
|
|
3338
|
|
3339 ------------------------------------------------------------------------
|
|
3340 r341 | lh3 | 2008-06-02 09:31:39 -0400 (Mon, 02 Jun 2008) | 3 lines
|
|
3341 Changed paths:
|
|
3342 M /branches/prog/bwa/bwttop2.c
|
|
3343 M /branches/prog/bwa/main.c
|
|
3344
|
|
3345 * bwa-0.1.0-6
|
|
3346 * fix a bug for missing hits
|
|
3347
|
|
3348 ------------------------------------------------------------------------
|
|
3349 r340 | lh3 | 2008-06-02 09:10:18 -0400 (Mon, 02 Jun 2008) | 3 lines
|
|
3350 Changed paths:
|
|
3351 M /branches/prog/bwa/bwttop2.c
|
|
3352 M /branches/prog/bwa/main.c
|
|
3353
|
|
3354 * bwa-0.1.0-5
|
|
3355 * accelerate comparisons in heap, a bit
|
|
3356
|
|
3357 ------------------------------------------------------------------------
|
|
3358 r339 | lh3 | 2008-06-02 08:41:31 -0400 (Mon, 02 Jun 2008) | 3 lines
|
|
3359 Changed paths:
|
|
3360 M /branches/prog/bwa/bwt.c
|
|
3361 M /branches/prog/bwa/bwt.h
|
|
3362 M /branches/prog/bwa/bwttop2.c
|
|
3363 M /branches/prog/bwa/main.c
|
|
3364
|
|
3365 * bwa-0.1.0-4
|
|
3366 * avoid marginal repeated calculation in occ
|
|
3367
|
|
3368 ------------------------------------------------------------------------
|
|
3369 r338 | lh3 | 2008-06-02 06:46:51 -0400 (Mon, 02 Jun 2008) | 5 lines
|
|
3370 Changed paths:
|
|
3371 M /branches/prog/bwa/Makefile
|
|
3372 M /branches/prog/bwa/bwt.c
|
|
3373 M /branches/prog/bwa/bwttop2.c
|
|
3374 M /branches/prog/bwa/main.c
|
|
3375
|
|
3376 * bwa-0.1.0-3
|
|
3377 * fix a bug caused by previours change
|
|
3378 * fix a bug in heap
|
|
3379 * order the heap by more criteria
|
|
3380
|
|
3381 ------------------------------------------------------------------------
|
|
3382 r337 | lh3 | 2008-06-01 19:11:15 -0400 (Sun, 01 Jun 2008) | 4 lines
|
|
3383 Changed paths:
|
|
3384 M /branches/prog/bwa/bwttop2.c
|
|
3385 M /branches/prog/bwa/main.c
|
|
3386
|
|
3387 * bwa-0.1.0-2
|
|
3388 * also sort sa range in heapsort, in attempt to improve cache performance.
|
|
3389 Unfortunately, it does not work well at all.
|
|
3390
|
|
3391 ------------------------------------------------------------------------
|
|
3392 r336 | lh3 | 2008-06-01 17:45:23 -0400 (Sun, 01 Jun 2008) | 3 lines
|
|
3393 Changed paths:
|
|
3394 M /branches/prog/bwa/Makefile
|
|
3395 M /branches/prog/bwa/Makefile.div
|
|
3396 M /branches/prog/bwa/bntseq.c
|
|
3397 M /branches/prog/bwa/main.c
|
|
3398
|
|
3399 * 0.1.0-1
|
|
3400 * fix a bug in calculating the real coordinate
|
|
3401
|
|
3402 ------------------------------------------------------------------------
|
|
3403 r335 | lh3 | 2008-06-01 16:03:09 -0400 (Sun, 01 Jun 2008) | 2 lines
|
|
3404 Changed paths:
|
|
3405 M /branches/prog/bwa/Makefile
|
|
3406
|
|
3407 nothing, really
|
|
3408
|
|
3409 ------------------------------------------------------------------------
|
|
3410 r334 | lh3 | 2008-06-01 15:59:13 -0400 (Sun, 01 Jun 2008) | 2 lines
|
|
3411 Changed paths:
|
|
3412 M /branches/prog/bwa/Makefile
|
|
3413 A /branches/prog/bwa/Makefile.div
|
|
3414 M /branches/prog/bwa/bwtindex.c
|
|
3415 M /branches/prog/bwa/pac2bwt.c
|
|
3416
|
|
3417 use IS algorithm by default
|
|
3418
|
|
3419 ------------------------------------------------------------------------
|
|
3420 r333 | lh3 | 2008-06-01 15:05:15 -0400 (Sun, 01 Jun 2008) | 3 lines
|
|
3421 Changed paths:
|
|
3422 M /branches/prog/bwa/Makefile
|
|
3423 M /branches/prog/bwa/bwtindex.c
|
|
3424 M /branches/prog/bwa/is.c
|
|
3425 M /branches/prog/bwa/pac2bwt.c
|
|
3426
|
|
3427 * a bit code clean up in is.c
|
|
3428 * add IS algorithm for constructing BWT, albeit slower
|
|
3429
|
|
3430 ------------------------------------------------------------------------
|
|
3431 r332 | lh3 | 2008-06-01 13:23:08 -0400 (Sun, 01 Jun 2008) | 2 lines
|
|
3432 Changed paths:
|
|
3433 A /branches/prog/bwa/is.c
|
|
3434
|
|
3435 IS linear-time algorithm for constructing SA/BWT
|
|
3436
|
|
3437 ------------------------------------------------------------------------
|
|
3438 r331 | lh3 | 2008-06-01 10:35:26 -0400 (Sun, 01 Jun 2008) | 3 lines
|
|
3439 Changed paths:
|
|
3440 M /branches/prog/bwa/Makefile
|
|
3441 M /branches/prog/bwa/bntseq.c
|
|
3442 A /branches/prog/bwa/bwtindex.c
|
|
3443 M /branches/prog/bwa/main.c
|
|
3444 M /branches/prog/bwa/main.h
|
|
3445
|
|
3446 * fix a bug in generating .pac
|
|
3447 * index in one go
|
|
3448
|
|
3449 ------------------------------------------------------------------------
|
|
3450 r330 | lh3 | 2008-06-01 09:17:05 -0400 (Sun, 01 Jun 2008) | 2 lines
|
|
3451 Changed paths:
|
|
3452 M /branches/prog/bwa/bntseq.c
|
|
3453 M /branches/prog/bwa/bntseq.h
|
|
3454 M /branches/prog/bwa/bwtaln.c
|
|
3455 M /branches/prog/bwa/bwttop2.c
|
|
3456
|
|
3457 real coordinates can be ouput
|
|
3458
|
|
3459 ------------------------------------------------------------------------
|
|
3460 r329 | lh3 | 2008-05-31 19:21:02 -0400 (Sat, 31 May 2008) | 2 lines
|
|
3461 Changed paths:
|
|
3462 M /branches/prog/bwa/bwt2fmv.c
|
|
3463 M /branches/prog/bwa/bwtaln.h
|
|
3464 M /branches/prog/bwa/bwttop2.c
|
|
3465
|
|
3466 add top2e which is similar to 1away
|
|
3467
|
|
3468 ------------------------------------------------------------------------
|
|
3469 r328 | lh3 | 2008-05-31 18:46:12 -0400 (Sat, 31 May 2008) | 3 lines
|
|
3470 Changed paths:
|
|
3471 M /branches/prog/bwa/bwt2fmv.c
|
|
3472 M /branches/prog/bwa/bwtaln.c
|
|
3473 M /branches/prog/bwa/bwtaln.h
|
|
3474 M /branches/prog/bwa/bwttop2.c
|
|
3475 M /branches/prog/bwa/main.c
|
|
3476 M /branches/prog/bwa/main.h
|
|
3477
|
|
3478 * unified cmd-line interface for ungapped alignment
|
|
3479 * add two alternatives to top2 algorithm
|
|
3480
|
|
3481 ------------------------------------------------------------------------
|
|
3482 r327 | lh3 | 2008-05-31 18:14:46 -0400 (Sat, 31 May 2008) | 2 lines
|
|
3483 Changed paths:
|
|
3484 M /branches/prog/bwa/bwt2fmv.c
|
|
3485 M /branches/prog/bwa/bwtaln.c
|
|
3486 M /branches/prog/bwa/bwtaln.h
|
|
3487 M /branches/prog/bwa/main.c
|
|
3488 M /branches/prog/bwa/main.h
|
|
3489
|
|
3490 add cmd-line interface to alntop2
|
|
3491
|
|
3492 ------------------------------------------------------------------------
|
|
3493 r326 | lh3 | 2008-05-31 17:59:31 -0400 (Sat, 31 May 2008) | 2 lines
|
|
3494 Changed paths:
|
|
3495 M /branches/prog/bwa/Makefile
|
|
3496 M /branches/prog/bwa/bwt1away.c
|
|
3497 M /branches/prog/bwa/bwtaln.c
|
|
3498 M /branches/prog/bwa/bwtaln.h
|
|
3499 A /branches/prog/bwa/bwttop2.c
|
|
3500
|
|
3501 top2 algorithm seems to work. I need to change interface, though
|
|
3502
|
|
3503 ------------------------------------------------------------------------
|
|
3504 r325 | lh3 | 2008-05-31 15:11:49 -0400 (Sat, 31 May 2008) | 2 lines
|
|
3505 Changed paths:
|
|
3506 M /branches/prog/bwa/bwt1away.c
|
|
3507
|
|
3508 change the variable in the structure
|
|
3509
|
|
3510 ------------------------------------------------------------------------
|
|
3511 r324 | lh3 | 2008-05-31 14:52:13 -0400 (Sat, 31 May 2008) | 2 lines
|
|
3512 Changed paths:
|
|
3513 M /branches/prog/bwa/bwt1away.c
|
|
3514
|
|
3515 set a slightly better bound on the maximum allowed mismatches
|
|
3516
|
|
3517 ------------------------------------------------------------------------
|
|
3518 r323 | lh3 | 2008-05-30 18:40:21 -0400 (Fri, 30 May 2008) | 2 lines
|
|
3519 Changed paths:
|
|
3520 M /branches/prog/bwa/bwtaln.c
|
|
3521
|
|
3522 * output time statistics
|
|
3523
|
|
3524 ------------------------------------------------------------------------
|
|
3525 r322 | lh3 | 2008-05-30 17:58:25 -0400 (Fri, 30 May 2008) | 4 lines
|
|
3526 Changed paths:
|
|
3527 M /branches/prog/bwa/Makefile
|
|
3528 M /branches/prog/bwa/bwt.c
|
|
3529 M /branches/prog/bwa/bwt.h
|
|
3530 A /branches/prog/bwa/bwt1away.c
|
|
3531 M /branches/prog/bwa/bwtaln.c
|
|
3532 M /branches/prog/bwa/bwtaln.h
|
|
3533
|
|
3534 * presumably better way to make use of prefix. But for the moment I do
|
|
3535 not know whether it is correct or not.
|
|
3536 * a bit code clean up: separate alignment part
|
|
3537
|
|
3538 ------------------------------------------------------------------------
|
|
3539 r321 | lh3 | 2008-05-30 13:57:43 -0400 (Fri, 30 May 2008) | 3 lines
|
|
3540 Changed paths:
|
|
3541 M /branches/prog/bwa/Makefile
|
|
3542 M /branches/prog/bwa/bwt.c
|
|
3543 M /branches/prog/bwa/bwt.h
|
|
3544 M /branches/prog/bwa/bwt_gen/Makefile
|
|
3545 M /branches/prog/bwa/bwt_gen/bwt_gen.c
|
|
3546 M /branches/prog/bwa/bwtaln.c
|
|
3547 M /branches/prog/bwa/main.c
|
|
3548 M /branches/prog/bwa/main.h
|
|
3549 M /branches/prog/bwa/pac2bwt.c
|
|
3550
|
|
3551 * a bit code clean up
|
|
3552 * put bwt_gen in bwa
|
|
3553
|
|
3554 ------------------------------------------------------------------------
|
|
3555 r320 | lh3 | 2008-05-30 11:40:11 -0400 (Fri, 30 May 2008) | 4 lines
|
|
3556 Changed paths:
|
|
3557 M /branches/prog/bwa/bwt.c
|
|
3558 M /branches/prog/bwa/bwt2fmv.c
|
|
3559 M /branches/prog/bwa/bwtaln.c
|
|
3560 M /branches/prog/bwa/bwtaln.h
|
|
3561 M /branches/prog/bwa/bwtio.c
|
|
3562
|
|
3563 * improve cmd-line interface
|
|
3564 * fix a bug in loading .sa
|
|
3565 * change default sa interval to 32
|
|
3566
|
|
3567 ------------------------------------------------------------------------
|
|
3568 r319 | lh3 | 2008-05-30 10:31:37 -0400 (Fri, 30 May 2008) | 3 lines
|
|
3569 Changed paths:
|
|
3570 M /branches/prog/bwa/bwtaln.c
|
|
3571
|
|
3572 * fix memory leak (I know that. Just a bit lazy)
|
|
3573 * change to another method to do 1-away alignment
|
|
3574
|
|
3575 ------------------------------------------------------------------------
|
|
3576 r318 | lh3 | 2008-05-30 09:21:49 -0400 (Fri, 30 May 2008) | 2 lines
|
|
3577 Changed paths:
|
|
3578 M /branches/prog/bwa/bwt.c
|
|
3579 M /branches/prog/bwa/bwt.h
|
|
3580 M /branches/prog/bwa/bwt2fmv.c
|
|
3581 M /branches/prog/bwa/bwtaln.c
|
|
3582 M /branches/prog/bwa/bwtaln.h
|
|
3583 M /branches/prog/bwa/main.c
|
|
3584 M /branches/prog/bwa/main.h
|
|
3585
|
|
3586 best unique match is partially finished
|
|
3587
|
|
3588 ------------------------------------------------------------------------
|
|
3589 r317 | lh3 | 2008-05-30 06:33:28 -0400 (Fri, 30 May 2008) | 2 lines
|
|
3590 Changed paths:
|
|
3591 M /branches/prog/bwa/bwt.c
|
|
3592 M /branches/prog/bwa/bwt2fmv.c
|
|
3593 M /branches/prog/bwa/bwtaln.c
|
|
3594 M /branches/prog/bwa/bwtaln.h
|
|
3595 M /branches/prog/bwa/main.c
|
|
3596 M /branches/prog/bwa/main.h
|
|
3597
|
|
3598 remove "ungapped" command and related codes
|
|
3599
|
|
3600 ------------------------------------------------------------------------
|
|
3601 r316 | lh3 | 2008-05-30 06:05:20 -0400 (Fri, 30 May 2008) | 2 lines
|
|
3602 Changed paths:
|
|
3603 M /branches/prog/bwa/Makefile
|
|
3604 M /branches/prog/bwa/bwt.c
|
|
3605 M /branches/prog/bwa/bwtaln.c
|
|
3606 M /branches/prog/bwa/bwtaln.h
|
|
3607
|
|
3608 change variable name thick to width
|
|
3609
|
|
3610 ------------------------------------------------------------------------
|
|
3611 r315 | lh3 | 2008-05-29 19:06:13 -0400 (Thu, 29 May 2008) | 2 lines
|
|
3612 Changed paths:
|
|
3613 M /branches/prog/bwa/bntseq.c
|
|
3614 M /branches/prog/bwa/bwt.c
|
|
3615 M /branches/prog/bwa/bwt.h
|
|
3616 M /branches/prog/bwa/bwt2fmv.c
|
|
3617 M /branches/prog/bwa/bwtaln.c
|
|
3618 M /branches/prog/bwa/bwtaln.h
|
|
3619 M /branches/prog/bwa/bwtio.c
|
|
3620 M /branches/prog/bwa/main.c
|
|
3621 M /branches/prog/bwa/main.h
|
|
3622 M /branches/prog/bwa/pac2bwt.c
|
|
3623
|
|
3624 revised algorithm for ungapped alignment. the old one can still be used.
|
|
3625
|
|
3626 ------------------------------------------------------------------------
|
|
3627 r314 | lh3 | 2008-05-29 16:36:11 -0400 (Thu, 29 May 2008) | 2 lines
|
|
3628 Changed paths:
|
|
3629 M /branches/prog/bwa/bwt2fmv.c
|
|
3630 M /branches/prog/bwa/bwt_gen/bwt_gen.c
|
|
3631 M /branches/prog/bwa/bwtio.c
|
|
3632 M /branches/prog/bwa/pac2bwt.c
|
|
3633
|
|
3634 * make commands more independent, but ungapped does not work at the moment
|
|
3635
|
|
3636 ------------------------------------------------------------------------
|
|
3637 r313 | lh3 | 2008-05-29 15:56:14 -0400 (Thu, 29 May 2008) | 2 lines
|
|
3638 Changed paths:
|
|
3639 M /branches/prog/bwa/bwt_gen/bwt_gen.c
|
|
3640
|
|
3641 little...
|
|
3642
|
|
3643 ------------------------------------------------------------------------
|
|
3644 r312 | lh3 | 2008-05-29 15:54:01 -0400 (Thu, 29 May 2008) | 3 lines
|
|
3645 Changed paths:
|
|
3646 M /branches/prog/bwa/bwt_gen/bwt_gen.c
|
|
3647 M /branches/prog/bwa/bwt_gen/bwt_gen.h
|
|
3648
|
|
3649 * add CopyRight information from the original codes
|
|
3650 * do not dump .fmv files
|
|
3651
|
|
3652 ------------------------------------------------------------------------
|
|
3653 r311 | lh3 | 2008-05-29 15:44:36 -0400 (Thu, 29 May 2008) | 2 lines
|
|
3654 Changed paths:
|
|
3655 A /branches/prog/bwa/bwt_gen
|
|
3656 A /branches/prog/bwa/bwt_gen/Makefile
|
|
3657 A /branches/prog/bwa/bwt_gen/QSufSort.c
|
|
3658 A /branches/prog/bwa/bwt_gen/QSufSort.h
|
|
3659 A /branches/prog/bwa/bwt_gen/bwt_gen.c
|
|
3660 A /branches/prog/bwa/bwt_gen/bwt_gen.h
|
|
3661
|
|
3662 codes from BWT-SW, for building BWT from packed file
|
|
3663
|
|
3664 ------------------------------------------------------------------------
|
|
3665 r310 | lh3 | 2008-05-28 17:03:35 -0400 (Wed, 28 May 2008) | 4 lines
|
|
3666 Changed paths:
|
|
3667 M /branches/prog/bwa/bwt.c
|
|
3668 M /branches/prog/bwa/bwt.h
|
|
3669 M /branches/prog/bwa/bwt2fmv.c
|
|
3670 M /branches/prog/bwa/bwtio.c
|
|
3671 M /branches/prog/bwa/main.c
|
|
3672 M /branches/prog/bwa/main.h
|
|
3673
|
|
3674 * change OCC_INTERVAL to 0x40, which makes bwa twice as fast.
|
|
3675 * write Occ file as ".occ" as it is using a different interval from
|
|
3676 .fmv, the BWT-SW correspondance of .occ
|
|
3677
|
|
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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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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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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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 ------------------------------------------------------------------------
|