0
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1 Release 0.6.2 (19 June, 2012)
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2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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3
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4 This is largely a bug-fix release. Notable changes in BWA-short and BWA-SW:
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5
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6 * Bugfix: BWA-SW may give bad alignments due to incorrect band width.
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7
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8 * Bugfix: A segmentation fault due to an out-of-boundary error. The fix is a
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9 temporary solution. The real cause has not been identified.
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10
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11 * Attempt to read index from prefix.64.bwt, such that the 32-bit and 64-bit
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12 index can coexist.
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13
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14 * Added options '-I' and '-S' to control BWA-SW pairing.
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15
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16 (0.6.2: 19 June 2012, r126)
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17
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18
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19
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20 Release 0.6.1 (28 November, 2011)
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21 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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22
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23 Notable changes to BWA-short:
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24
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25 * Bugfix: duplicated alternative hits in the XA tag.
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26
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27 * Bugfix: when trimming enabled, bwa-aln trims 1bp less.
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28
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29 * Disabled the color-space alignment. 0.6.x is not working with SOLiD reads at
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30 present.
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31
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32 Notable changes to BWA-SW:
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33
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34 * Bugfix: segfault due to excessive ambiguous bases.
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35
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36 * Bugfix: incorrect mate position in the SE mode.
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37
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38 * Bugfix: rare segfault in the PE mode
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39
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40 * When macro _NO_SSE2 is in use, fall back to the standard Smith-Waterman
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41 instead of SSE2-SW.
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42
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43 * Optionally mark split hits with lower alignment scores as secondary.
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44
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45 Changes to fastmap:
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46
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47 * Bugfix: infinite loop caused by ambiguous bases.
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48
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49 * Optionally output the query sequence.
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50
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51 (0.6.1: 28 November 2011, r104)
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52
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53
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54
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55 Release 0.5.10 and 0.6.0 (12 November, 2011)
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56 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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57
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58 The 0.6.0 release comes with two major changes. Firstly, the index data
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59 structure has been changed to support genomes longer than 4GB. The forward and
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60 reverse backward genome is now integrated in one index. This change speeds up
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61 BWA-short by about 20% and BWA-SW by 90% with the mapping acccuracy largely
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62 unchanged. A tradeoff is BWA requires more memory, but this is the price almost
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63 all mappers that index the genome have to pay.
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64
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65 Secondly, BWA-SW in 0.6.0 now works with paired-end data. It is more accurate
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66 for highly unique reads and more robust to long indels and structural
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67 variations. However, BWA-short still has edges for reads with many suboptimal
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68 hits. It is yet to know which algorithm is the best for variant calling.
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69
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70 0.5.10 is a bugfix release only and is likely to be the last release in the 0.5
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71 branch unless I find critical bugs in future.
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72
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73 Other notable changes:
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74
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75 * Added the `fastmap' command that finds super-maximal exact matches. It does
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76 not give the final alignment, but runs much faster. It can be a building
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77 block for other alignment algorithms. [0.6.0 only]
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78
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79 * Output the timing information before BWA exits. This also tells users that
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80 the task has been finished instead of being killed or aborted. [0.6.0 only]
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81
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82 * Sped up multi-threading when using many (>20) CPU cores.
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83
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84 * Check I/O error.
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85
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86 * Increased the maximum barcode length to 63bp.
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87
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88 * Automatically choose the indexing algorithm.
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89
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90 * Bugfix: very rare segfault due to an uninitialized variable. The bug also
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91 affects the placement of suboptimal alignments. The effect is very minor.
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92
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93 This release involves quite a lot of tricky changes. Although it has been
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94 tested on a few data sets, subtle bugs may be still hidden. It is *NOT*
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95 recommended to use this release in a production pipeline. In future, however,
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96 BWA-SW may be better when reads continue to go longer. I would encourage users
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97 to try the 0.6 release. I would also like to hear the users' experience. Thank
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98 you.
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99
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100 (0.6.0: 12 November 2011, r85)
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101
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102
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103
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104 Beta Release 0.5.9 (24 January, 2011)
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105 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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106
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107 Notable changes:
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108
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109 * Feature: barcode support via the `-B' option.
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110
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111 * Feature: Illumina 1.3+ read format support via the `-I' option.
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112
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113 * Bugfix: RG tags are not attached to unmapped reads.
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114
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115 * Bugfix: very rare bwasw mismappings
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116
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117 * Recommend options for PacBio reads in bwasw help message.
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118
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119
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120 Also, since January 13, the BWA master repository has been moved to github:
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121
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122 https://github.com/lh3/bwa
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123
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124 The revision number has been reset. All recent changes will be first
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125 committed to this repository.
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126
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127 (0.5.9: 24 January 2011, r16)
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128
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129
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130
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131 Beta Release Candidate 0.5.9rc1 (10 December, 2010)
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132 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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133
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134 Notable changes in bwasw:
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135
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136 * Output unmapped reads.
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137
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138 * For a repetitive read, choose a random hit instead of a fixed
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139 one. This is not well tested.
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140
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141 Notable changes in bwa-short:
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142
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143 * Fixed a bug in the SW scoring system, which may lead to unexpected
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144 gaps towards the end of a read.
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145
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146 * Fixed a bug which invalidates the randomness of repetitive reads.
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147
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148 * Fixed a rare memory leak.
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149
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150 * Allowed to specify the read group at the command line.
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151
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152 * Take name-grouped BAM files as input.
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153
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154 Changes to this release are usually safe in that they do not interfere
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155 with the key functionality. However, the release has only been tested on
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156 small samples instead of on large-scale real data. If anything weird
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157 happens, please report the bugs to the bio-bwa-help mailing list.
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158
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159 (0.5.9rc1: 10 December 2010, r1561)
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160
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161
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162
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163 Beta Release 0.5.8 (8 June, 2010)
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164 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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165
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166 Notable changes in bwasw:
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167
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168 * Fixed an issue of missing alignments. This should happen rarely and
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169 only when the contig/read alignment is multi-part. Very rarely, bwasw
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170 may still miss a segment in a multi-part alignment. This is difficult
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171 to fix, although possible.
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172
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173 Notable changes in bwa-short:
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174
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175 * Discard the SW alignment when the best single-end alignment is much
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176 better. Such a SW alignment may caused by structural variations and
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177 forcing it to be aligned leads to false alignment. This fix has not
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178 been tested thoroughly. It would be great to receive more users
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179 feedbacks on this issue.
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180
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181 * Fixed a typo/bug in sampe which leads to unnecessarily large memory
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182 usage in some cases.
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183
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184 * Further reduced the chance of reporting `weird pairing'.
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185
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186 (0.5.8: 8 June 2010, r1442)
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187
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188
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189
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190 Beta Release 0.5.7 (1 March, 2010)
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191 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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192
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193 This release only has an effect on paired-end data with fat insert-size
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194 distribution. Users are still recommended to update as the new release
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195 improves the robustness to poor data.
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196
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197 * The fix for `weird pairing' was not working in version 0.5.6, pointed
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198 out by Carol Scott. It should work now.
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199
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200 * Optionally output to a normal file rather than to stdout (by Tim
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201 Fennel).
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202
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203 (0.5.7: 1 March 2010, r1310)
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204
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205
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206
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207 Beta Release 0.5.6 (10 Feburary, 2010)
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208 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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209
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210 Notable changes in bwa-short:
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211
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212 * Report multiple hits in the SAM format at a new tag XA encoded as:
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213 (chr,pos,CIGAR,NM;)*. By default, if a paired or single-end read has
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214 4 or fewer hits, they will all be reported; if a read in a anomalous
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215 pair has 11 or fewer hits, all of them will be reported.
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216
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217 * Perform Smith-Waterman alignment also for anomalous read pairs when
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218 both ends have quality higher than 17. This reduces false positives
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219 for some SV discovery algorithms.
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220
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221 * Do not report "weird pairing" when the insert size distribution is
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222 too fat or has a mean close to zero.
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223
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224 * If a read is bridging two adjacent chromsomes, flag it as unmapped.
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225
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226 * Fixed a small but long existing memory leak in paired-end mapping.
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227
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228 * Multiple bug fixes in SOLiD mapping: a) quality "-1" can be correctly
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229 parsed by solid2fastq.pl; b) truncated quality string is resolved; c)
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230 SOLiD read mapped to the reverse strand is complemented.
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231
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232 * Bwa now calculates skewness and kurtosis of the insert size
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233 distribution.
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234
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235 * Deploy a Bayesian method to estimate the maximum distance for a read
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236 pair considered to be paired properly. The method is proposed by
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237 Gerton Lunter, but bwa only implements a simplified version.
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238
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239 * Export more functions for Java bindings, by Matt Hanna (See:
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240 http://www.broadinstitute.org/gsa/wiki/index.php/Sting_BWA/C_bindings)
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241
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242 * Abstract bwa CIGAR for further extension, by Rodrigo Goya.
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243
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244 (0.5.6: 10 Feburary 2010, r1303)
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245
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246
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247
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248 Beta Release 0.5.5 (10 November, 2009)
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249 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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250
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251 This is a bug fix release:
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252
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253 * Fixed a serious bug/typo in aln which does not occur given short
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254 reads, but will lead to segfault for >500bp reads. Of course, the aln
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255 command is not recommended for reads longer than 200bp, but this is a
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256 bug anyway.
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257
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258 * Fixed a minor bug/typo which leads to incorrect single-end mapping
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259 quality when one end is moved to meet the mate-pair requirement.
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260
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261 * Fixed a bug in samse for mapping in the color space. This bug is
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262 caused by quality filtration added since 0.5.1.
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263
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264 (0.5.5: 10 November 2009, r1273)
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265
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266
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267
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268 Beta Release 0.5.4 (9 October, 2009)
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269 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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270
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271 Since this version, the default seed length used in the "aln" command is
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272 changed to 32.
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273
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274 Notable changes in bwa-short:
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275
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276 * Added a new tag "XC:i" which gives the length of clipped reads.
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277
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278 * In sampe, skip alignments in case of a bug in the Smith-Waterman
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279 alignment module.
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280
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281 * In sampe, fixed a bug in pairing when the read sequence is identical
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282 to its reverse complement.
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283
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284 * In sampe, optionally preload the entire FM-index into memory to
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285 reduce disk operations.
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286
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287 Notable changes in dBWT-SW/BWA-SW:
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288
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289 * Changed name dBWT-SW to BWA-SW.
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290
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291 * Optionally use "hard clipping" in the SAM output.
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292
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293 (0.5.4: 9 October 2009, r1245)
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294
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295
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296
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297 Beta Release 0.5.3 (15 September, 2009)
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298 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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299
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300 Fixed a critical bug in bwa-short: reads mapped to the reverse strand
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301 are not complemented.
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302
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303 (0.5.3: 15 September 2009, r1225)
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304
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305
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306
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307 Beta Release 0.5.2 (13 September, 2009)
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308 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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309
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310 Notable changes in bwa-short:
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311
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312 * Optionally trim reads before alignment. See the manual page on `aln
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313 -q' for detailed description.
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314
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315 * Fixed a bug in calculating the NM tag for a gapped alignment.
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316
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317 * Fixed a bug given a mixture of reads with some longer than the seed
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318 length and some shorter.
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319
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320 * Print SAM header.
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321
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322 Notable changes in dBWT-SW:
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323
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324 * Changed the default value of -T to 30. As a result, the accuracy is a
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325 little higher for short reads at the cost of speed.
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326
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327 (0.5.2: 13 September 2009, r1223)
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328
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329
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330
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331 Beta Release 0.5.1 (2 September, 2009)
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332 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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333
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334 Notable changes in the short read alignment component:
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335
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336 * Fixed a bug in samse: do not write mate coordinates.
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337
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338 Notable changes in dBWT-SW:
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339
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340 * Randomly choose one alignment if the read is a repetitive.
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341
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342 * Fixed a flaw when a read is mapped across two adjacent reference
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343 sequences. However, wrong alignment reports may still occur rarely in
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344 this case.
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345
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346 * Changed the default band width to 50. The speed is slower due to this
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347 change.
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348
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349 * Improved the mapping quality a little given long query sequences.
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350
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351 (0.5.1: 2 September 2009, r1209)
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352
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353
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354
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355 Beta Release 0.5.0 (20 August, 2009)
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356 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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357
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358 This release implements a novel algorithm, dBWT-SW, specifically
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359 designed for long reads. It is 10-50 times faster than SSAHA2, depending
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360 on the characteristics of the input data, and achieves comparable
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361 alignment accuracy while allowing chimera detection. In comparison to
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362 BLAT, dBWT-SW is several times faster and much more accurate especially
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363 when the error rate is high. Please read the manual page for more
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364 information.
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365
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366 The dBWT-SW algorithm is kind of developed for future sequencing
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367 technologies which produce much longer reads with a little higher error
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368 rate. It is still at its early development stage. Some features are
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369 missing and it may be buggy although I have evaluated on several
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370 simulated and real data sets. But following the "release early"
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371 paradigm, I would like the users to try it first.
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372
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373 Other notable changes in BWA are:
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374
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375 * Fixed a rare bug in the Smith-Waterman alignment module.
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376
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377 * Fixed a rare bug about the wrong alignment coordinate when a read is
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378 poorly aligned.
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379
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380 * Fixed a bug in generating the "mate-unmap" SAM tag when both ends in
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381 a pair are unmapped.
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382
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383 (0.5.0: 20 August 2009, r1200)
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384
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385
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386
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387 Beta Release 0.4.9 (19 May, 2009)
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388 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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389
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390 Interestingly, the integer overflow bug claimed to be fixed in 0.4.7 has
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391 not in fact. Now I have fixed the bug. Sorry for this and thank Quan
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392 Long for pointing out the bug (again).
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393
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394 (0.4.9: 19 May 2009, r1075)
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395
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396
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397
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398 Beta Release 0.4.8 (18 May, 2009)
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399 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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400
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401 One change to "aln -R". Now by default, if there are no more than `-R'
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402 equally best hits, bwa will search for suboptimal hits. This change
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403 affects the ability in finding SNPs in segmental duplications.
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404
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405 I have not tested this option thoroughly, but this simple change is less
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406 likely to cause new bugs. Hope I am right.
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407
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408 (0.4.8: 18 May 2009, r1073)
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409
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410
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411
|
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412 Beta Release 0.4.7 (12 May, 2009)
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413 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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414
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415 Notable changes:
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416
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417 * Output SM (single-end mapping quality) and AM (smaller mapping
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418 quality among the two ends) tag from sam output.
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419
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420 * Improved the functionality of stdsw.
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421
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422 * Made the XN tag more accurate.
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423
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424 * Fixed a very rare segfault caused by integer overflow.
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425
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426 * Improve the insert size estimation.
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427
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428 * Fixed compiling errors for some Linux systems.
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429
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430 (0.4.7: 12 May 2009, r1066)
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431
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432
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433
|
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434 Beta Release 0.4.6 (9 March, 2009)
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435 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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436
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437 This release improves the SOLiD support. First, a script for converting
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438 SOLiD raw data is provided. This script is adapted from solid2fastq.pl
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439 in the MAQ package. Second, a nucleotide reference file can be directly
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440 used with `bwa index'. Third, SOLiD paired-end support is
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441 completed. Fourth, color-space reads will be converted to nucleotides
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442 when SAM output is generated. Color errors are corrected in this
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443 process. Please note that like MAQ, BWA cannot make use of the primer
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444 base and the first color.
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445
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446 In addition, the calculation of mapping quality is also improved a
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447 little bit, although end-users may barely observe the difference.
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448
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449 (0.4.6: 9 March 2009, r915)
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450
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451
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452
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453 Beta Release 0.4.5 (18 Feburary, 2009)
|
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454 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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455
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456 Not much happened, but I think it would be good to let the users use the
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457 latest version.
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458
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459 Notable changes (Thank Bob Handsaker for catching the two bugs):
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460
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461 * Improved bounary check. Previous version may still give incorrect
|
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462 alignment coordinates in rare cases.
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463
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464 * Fixed a bug in SW alignment when no residue matches. This only
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465 affects the `sampe' command.
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466
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467 * Robustly estimate insert size without setting the maximum on the
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468 command line. Since this release `sampe -a' only has an effect if
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469 there are not enough good pairs to infer the insert size
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470 distribution.
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471
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472 * Reduced false PE alignments a little bit by using the inferred insert
|
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473 size distribution. This fix may be more important for long insert
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474 size libraries.
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475
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476 (0.4.5: 18 Feburary 2009, r829)
|
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477
|
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478
|
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479
|
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480 Beta Release 0.4.4 (15 Feburary, 2009)
|
|
481 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
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482
|
|
483 This is mainly a bug fix release. Notable changes are:
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484
|
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485 * Imposed boundary check for extracting subsequence from the
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486 genome. Previously this causes memory problem in rare cases.
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487
|
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488 * Fixed a bug in failing to find whether an alignment overlapping with
|
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489 N on the genome.
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490
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491 * Changed MD tag to meet the latest SAM specification.
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492
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493 (0.4.4: 15 Feburary 2009, r815)
|
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494
|
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495
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496
|
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497 Beta Release 0.4.3 (22 January, 2009)
|
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498 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
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499
|
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500 Notable changes:
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501
|
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502 * Treat an ambiguous base N as a mismatch. Previous versions will not
|
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503 map reads containing any N.
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504
|
|
505 * Automatically choose the maximum allowed number of differences. This
|
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506 is important when reads of different lengths are mixed together.
|
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507
|
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508 * Print mate coordinate if only one end is unmapped.
|
|
509
|
|
510 * Generate MD tag. This tag encodes the mismatching positions and the
|
|
511 reference bases at these positions. Deletions from the reference will
|
|
512 also be printed.
|
|
513
|
|
514 * Optionally dump multiple hits from samse, in another concise format
|
|
515 rather than SAM.
|
|
516
|
|
517 * Optionally disable iterative search. This is VERY SLOOOOW, though.
|
|
518
|
|
519 * Fixed a bug in generate SAM.
|
|
520
|
|
521 (0.4.3: 22 January 2009, r787)
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|
522
|
|
523
|
|
524
|
|
525 Beta Release 0.4.2 (9 January, 2009)
|
|
526 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
527
|
|
528 Aaron Quinlan found a bug in the indexer: the bwa indexer segfaults if
|
|
529 there are no comment texts in the FASTA header. This is a critical
|
|
530 bug. Nothing else was changed.
|
|
531
|
|
532 (0.4.2: 9 January 2009, r769)
|
|
533
|
|
534
|
|
535
|
|
536 Beta Release 0.4.1 (7 January, 2009)
|
|
537 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
538
|
|
539 I am sorry for the quick updates these days. I like to set a milestone
|
|
540 for BWA and this release seems to be. For paired end reads, BWA also
|
|
541 does Smith-Waterman alignment for an unmapped read whose mate can be
|
|
542 mapped confidently. With this strategy BWA achieves similar accuracy to
|
|
543 maq. Benchmark is also updated accordingly.
|
|
544
|
|
545 (0.4.1: 7 January 2009, r760)
|
|
546
|
|
547
|
|
548
|
|
549 Beta Release 0.4.0 (6 January, 2009)
|
|
550 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
551
|
|
552 In comparison to the release two days ago, this release is mainly tuned
|
|
553 for performance with some tricks I learnt from Bowtie. However, as the
|
|
554 indexing format has also been changed, I have to increase the version
|
|
555 number to 0.4.0 to emphasize that *DATABASE MUST BE RE-INDEXED* with
|
|
556 `bwa index'.
|
|
557
|
|
558 * Improved the speed by about 20%.
|
|
559
|
|
560 * Added multi-threading to `bwa aln'.
|
|
561
|
|
562 (0.4.0: 6 January 2009, r756)
|
|
563
|
|
564
|
|
565
|
|
566 Beta Release 0.3.0 (4 January, 2009)
|
|
567 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
568
|
|
569 * Added paired-end support by separating SA calculation and alignment
|
|
570 output.
|
|
571
|
|
572 * Added SAM output.
|
|
573
|
|
574 * Added evaluation to the documentation.
|
|
575
|
|
576 (0.3.0: 4 January 2009, r741)
|
|
577
|
|
578
|
|
579
|
|
580 Beta Release 0.2.0 (15 Augusst, 2008)
|
|
581 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
582
|
|
583 * Take the subsequence at the 5'-end as seed. Seeding strategy greatly
|
|
584 improves the speed for long reads, at the cost of missing a few true
|
|
585 hits that contain many differences in the seed. Seeding also increase
|
|
586 the memory by 800MB.
|
|
587
|
|
588 * Fixed a bug which may miss some gapped alignments. Fixing the bug
|
|
589 also slows the speed a little.
|
|
590
|
|
591 (0.2.0: 15 August 2008, r428)
|
|
592
|
|
593
|
|
594
|
|
595 Beta Release 0.1.6 (08 Augusst, 2008)
|
|
596 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
597
|
|
598 * Give accurate CIGAR string.
|
|
599
|
|
600 * Add a simple interface to SW/NW alignment
|
|
601
|
|
602 (0.1.6: 08 August 2008, r414)
|
|
603
|
|
604
|
|
605
|
|
606 Beta Release 0.1.5 (27 July, 2008)
|
|
607 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
608
|
|
609 * Improve the speed. This version is expected to give the same results.
|
|
610
|
|
611 (0.1.5: 27 July 2008, r400)
|
|
612
|
|
613
|
|
614
|
|
615 Beta Release 0.1.4 (22 July, 2008)
|
|
616 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
617
|
|
618 * Fixed a bug which may cause missing gapped alignments.
|
|
619
|
|
620 * More clearly define what alignments can be found by BWA (See
|
|
621 manual). Now BWA runs a little slower because it will visit more
|
|
622 potential gapped alignments.
|
|
623
|
|
624 * A bit code clean up.
|
|
625
|
|
626 (0.1.4: 22 July 2008, r387)
|
|
627
|
|
628
|
|
629
|
|
630 Beta Release 0.1.3 (21 July, 2008)
|
|
631 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
632
|
|
633 Improve the speed with some tricks on retrieving occurences. The results
|
|
634 should be exactly the same as that of 0.1.2.
|
|
635
|
|
636 (0.1.3: 21 July 2008, r382)
|
|
637
|
|
638
|
|
639
|
|
640 Beta Release 0.1.2 (17 July, 2008)
|
|
641 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
642
|
|
643 Support gapped alignment. Codes for ungapped alignment has been removed.
|
|
644
|
|
645 (0.1.2: 17 July 2008, r371)
|
|
646
|
|
647
|
|
648
|
|
649 Beta Release 0.1.1 (03 June, 2008)
|
|
650 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
651
|
|
652 This is the first release of BWA, Burrows-Wheeler Alignment tool. Please
|
|
653 read man page for more information about this software.
|
|
654
|
|
655 (0.1.1: 03 June 2008, r349)
|
|
656
|
|
657
|
|
658
|