Mercurial > repos > ashvark > qiime_1_8_0
comparison bwa-0.6.2/NEWS @ 2:a294fbfcb1db draft default tip
Uploaded BWA
author | ashvark |
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date | Fri, 18 Jul 2014 07:55:59 -0400 |
parents | dd1186b11b3b |
children |
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1:a9636dc1e99a | 2:a294fbfcb1db |
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1 Release 0.6.2 (19 June, 2012) | |
2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
3 | |
4 This is largely a bug-fix release. Notable changes in BWA-short and BWA-SW: | |
5 | |
6 * Bugfix: BWA-SW may give bad alignments due to incorrect band width. | |
7 | |
8 * Bugfix: A segmentation fault due to an out-of-boundary error. The fix is a | |
9 temporary solution. The real cause has not been identified. | |
10 | |
11 * Attempt to read index from prefix.64.bwt, such that the 32-bit and 64-bit | |
12 index can coexist. | |
13 | |
14 * Added options '-I' and '-S' to control BWA-SW pairing. | |
15 | |
16 (0.6.2: 19 June 2012, r126) | |
17 | |
18 | |
19 | |
20 Release 0.6.1 (28 November, 2011) | |
21 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
22 | |
23 Notable changes to BWA-short: | |
24 | |
25 * Bugfix: duplicated alternative hits in the XA tag. | |
26 | |
27 * Bugfix: when trimming enabled, bwa-aln trims 1bp less. | |
28 | |
29 * Disabled the color-space alignment. 0.6.x is not working with SOLiD reads at | |
30 present. | |
31 | |
32 Notable changes to BWA-SW: | |
33 | |
34 * Bugfix: segfault due to excessive ambiguous bases. | |
35 | |
36 * Bugfix: incorrect mate position in the SE mode. | |
37 | |
38 * Bugfix: rare segfault in the PE mode | |
39 | |
40 * When macro _NO_SSE2 is in use, fall back to the standard Smith-Waterman | |
41 instead of SSE2-SW. | |
42 | |
43 * Optionally mark split hits with lower alignment scores as secondary. | |
44 | |
45 Changes to fastmap: | |
46 | |
47 * Bugfix: infinite loop caused by ambiguous bases. | |
48 | |
49 * Optionally output the query sequence. | |
50 | |
51 (0.6.1: 28 November 2011, r104) | |
52 | |
53 | |
54 | |
55 Release 0.5.10 and 0.6.0 (12 November, 2011) | |
56 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
57 | |
58 The 0.6.0 release comes with two major changes. Firstly, the index data | |
59 structure has been changed to support genomes longer than 4GB. The forward and | |
60 reverse backward genome is now integrated in one index. This change speeds up | |
61 BWA-short by about 20% and BWA-SW by 90% with the mapping acccuracy largely | |
62 unchanged. A tradeoff is BWA requires more memory, but this is the price almost | |
63 all mappers that index the genome have to pay. | |
64 | |
65 Secondly, BWA-SW in 0.6.0 now works with paired-end data. It is more accurate | |
66 for highly unique reads and more robust to long indels and structural | |
67 variations. However, BWA-short still has edges for reads with many suboptimal | |
68 hits. It is yet to know which algorithm is the best for variant calling. | |
69 | |
70 0.5.10 is a bugfix release only and is likely to be the last release in the 0.5 | |
71 branch unless I find critical bugs in future. | |
72 | |
73 Other notable changes: | |
74 | |
75 * Added the `fastmap' command that finds super-maximal exact matches. It does | |
76 not give the final alignment, but runs much faster. It can be a building | |
77 block for other alignment algorithms. [0.6.0 only] | |
78 | |
79 * Output the timing information before BWA exits. This also tells users that | |
80 the task has been finished instead of being killed or aborted. [0.6.0 only] | |
81 | |
82 * Sped up multi-threading when using many (>20) CPU cores. | |
83 | |
84 * Check I/O error. | |
85 | |
86 * Increased the maximum barcode length to 63bp. | |
87 | |
88 * Automatically choose the indexing algorithm. | |
89 | |
90 * Bugfix: very rare segfault due to an uninitialized variable. The bug also | |
91 affects the placement of suboptimal alignments. The effect is very minor. | |
92 | |
93 This release involves quite a lot of tricky changes. Although it has been | |
94 tested on a few data sets, subtle bugs may be still hidden. It is *NOT* | |
95 recommended to use this release in a production pipeline. In future, however, | |
96 BWA-SW may be better when reads continue to go longer. I would encourage users | |
97 to try the 0.6 release. I would also like to hear the users' experience. Thank | |
98 you. | |
99 | |
100 (0.6.0: 12 November 2011, r85) | |
101 | |
102 | |
103 | |
104 Beta Release 0.5.9 (24 January, 2011) | |
105 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
106 | |
107 Notable changes: | |
108 | |
109 * Feature: barcode support via the `-B' option. | |
110 | |
111 * Feature: Illumina 1.3+ read format support via the `-I' option. | |
112 | |
113 * Bugfix: RG tags are not attached to unmapped reads. | |
114 | |
115 * Bugfix: very rare bwasw mismappings | |
116 | |
117 * Recommend options for PacBio reads in bwasw help message. | |
118 | |
119 | |
120 Also, since January 13, the BWA master repository has been moved to github: | |
121 | |
122 https://github.com/lh3/bwa | |
123 | |
124 The revision number has been reset. All recent changes will be first | |
125 committed to this repository. | |
126 | |
127 (0.5.9: 24 January 2011, r16) | |
128 | |
129 | |
130 | |
131 Beta Release Candidate 0.5.9rc1 (10 December, 2010) | |
132 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
133 | |
134 Notable changes in bwasw: | |
135 | |
136 * Output unmapped reads. | |
137 | |
138 * For a repetitive read, choose a random hit instead of a fixed | |
139 one. This is not well tested. | |
140 | |
141 Notable changes in bwa-short: | |
142 | |
143 * Fixed a bug in the SW scoring system, which may lead to unexpected | |
144 gaps towards the end of a read. | |
145 | |
146 * Fixed a bug which invalidates the randomness of repetitive reads. | |
147 | |
148 * Fixed a rare memory leak. | |
149 | |
150 * Allowed to specify the read group at the command line. | |
151 | |
152 * Take name-grouped BAM files as input. | |
153 | |
154 Changes to this release are usually safe in that they do not interfere | |
155 with the key functionality. However, the release has only been tested on | |
156 small samples instead of on large-scale real data. If anything weird | |
157 happens, please report the bugs to the bio-bwa-help mailing list. | |
158 | |
159 (0.5.9rc1: 10 December 2010, r1561) | |
160 | |
161 | |
162 | |
163 Beta Release 0.5.8 (8 June, 2010) | |
164 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
165 | |
166 Notable changes in bwasw: | |
167 | |
168 * Fixed an issue of missing alignments. This should happen rarely and | |
169 only when the contig/read alignment is multi-part. Very rarely, bwasw | |
170 may still miss a segment in a multi-part alignment. This is difficult | |
171 to fix, although possible. | |
172 | |
173 Notable changes in bwa-short: | |
174 | |
175 * Discard the SW alignment when the best single-end alignment is much | |
176 better. Such a SW alignment may caused by structural variations and | |
177 forcing it to be aligned leads to false alignment. This fix has not | |
178 been tested thoroughly. It would be great to receive more users | |
179 feedbacks on this issue. | |
180 | |
181 * Fixed a typo/bug in sampe which leads to unnecessarily large memory | |
182 usage in some cases. | |
183 | |
184 * Further reduced the chance of reporting `weird pairing'. | |
185 | |
186 (0.5.8: 8 June 2010, r1442) | |
187 | |
188 | |
189 | |
190 Beta Release 0.5.7 (1 March, 2010) | |
191 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
192 | |
193 This release only has an effect on paired-end data with fat insert-size | |
194 distribution. Users are still recommended to update as the new release | |
195 improves the robustness to poor data. | |
196 | |
197 * The fix for `weird pairing' was not working in version 0.5.6, pointed | |
198 out by Carol Scott. It should work now. | |
199 | |
200 * Optionally output to a normal file rather than to stdout (by Tim | |
201 Fennel). | |
202 | |
203 (0.5.7: 1 March 2010, r1310) | |
204 | |
205 | |
206 | |
207 Beta Release 0.5.6 (10 Feburary, 2010) | |
208 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
209 | |
210 Notable changes in bwa-short: | |
211 | |
212 * Report multiple hits in the SAM format at a new tag XA encoded as: | |
213 (chr,pos,CIGAR,NM;)*. By default, if a paired or single-end read has | |
214 4 or fewer hits, they will all be reported; if a read in a anomalous | |
215 pair has 11 or fewer hits, all of them will be reported. | |
216 | |
217 * Perform Smith-Waterman alignment also for anomalous read pairs when | |
218 both ends have quality higher than 17. This reduces false positives | |
219 for some SV discovery algorithms. | |
220 | |
221 * Do not report "weird pairing" when the insert size distribution is | |
222 too fat or has a mean close to zero. | |
223 | |
224 * If a read is bridging two adjacent chromsomes, flag it as unmapped. | |
225 | |
226 * Fixed a small but long existing memory leak in paired-end mapping. | |
227 | |
228 * Multiple bug fixes in SOLiD mapping: a) quality "-1" can be correctly | |
229 parsed by solid2fastq.pl; b) truncated quality string is resolved; c) | |
230 SOLiD read mapped to the reverse strand is complemented. | |
231 | |
232 * Bwa now calculates skewness and kurtosis of the insert size | |
233 distribution. | |
234 | |
235 * Deploy a Bayesian method to estimate the maximum distance for a read | |
236 pair considered to be paired properly. The method is proposed by | |
237 Gerton Lunter, but bwa only implements a simplified version. | |
238 | |
239 * Export more functions for Java bindings, by Matt Hanna (See: | |
240 http://www.broadinstitute.org/gsa/wiki/index.php/Sting_BWA/C_bindings) | |
241 | |
242 * Abstract bwa CIGAR for further extension, by Rodrigo Goya. | |
243 | |
244 (0.5.6: 10 Feburary 2010, r1303) | |
245 | |
246 | |
247 | |
248 Beta Release 0.5.5 (10 November, 2009) | |
249 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
250 | |
251 This is a bug fix release: | |
252 | |
253 * Fixed a serious bug/typo in aln which does not occur given short | |
254 reads, but will lead to segfault for >500bp reads. Of course, the aln | |
255 command is not recommended for reads longer than 200bp, but this is a | |
256 bug anyway. | |
257 | |
258 * Fixed a minor bug/typo which leads to incorrect single-end mapping | |
259 quality when one end is moved to meet the mate-pair requirement. | |
260 | |
261 * Fixed a bug in samse for mapping in the color space. This bug is | |
262 caused by quality filtration added since 0.5.1. | |
263 | |
264 (0.5.5: 10 November 2009, r1273) | |
265 | |
266 | |
267 | |
268 Beta Release 0.5.4 (9 October, 2009) | |
269 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
270 | |
271 Since this version, the default seed length used in the "aln" command is | |
272 changed to 32. | |
273 | |
274 Notable changes in bwa-short: | |
275 | |
276 * Added a new tag "XC:i" which gives the length of clipped reads. | |
277 | |
278 * In sampe, skip alignments in case of a bug in the Smith-Waterman | |
279 alignment module. | |
280 | |
281 * In sampe, fixed a bug in pairing when the read sequence is identical | |
282 to its reverse complement. | |
283 | |
284 * In sampe, optionally preload the entire FM-index into memory to | |
285 reduce disk operations. | |
286 | |
287 Notable changes in dBWT-SW/BWA-SW: | |
288 | |
289 * Changed name dBWT-SW to BWA-SW. | |
290 | |
291 * Optionally use "hard clipping" in the SAM output. | |
292 | |
293 (0.5.4: 9 October 2009, r1245) | |
294 | |
295 | |
296 | |
297 Beta Release 0.5.3 (15 September, 2009) | |
298 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
299 | |
300 Fixed a critical bug in bwa-short: reads mapped to the reverse strand | |
301 are not complemented. | |
302 | |
303 (0.5.3: 15 September 2009, r1225) | |
304 | |
305 | |
306 | |
307 Beta Release 0.5.2 (13 September, 2009) | |
308 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
309 | |
310 Notable changes in bwa-short: | |
311 | |
312 * Optionally trim reads before alignment. See the manual page on `aln | |
313 -q' for detailed description. | |
314 | |
315 * Fixed a bug in calculating the NM tag for a gapped alignment. | |
316 | |
317 * Fixed a bug given a mixture of reads with some longer than the seed | |
318 length and some shorter. | |
319 | |
320 * Print SAM header. | |
321 | |
322 Notable changes in dBWT-SW: | |
323 | |
324 * Changed the default value of -T to 30. As a result, the accuracy is a | |
325 little higher for short reads at the cost of speed. | |
326 | |
327 (0.5.2: 13 September 2009, r1223) | |
328 | |
329 | |
330 | |
331 Beta Release 0.5.1 (2 September, 2009) | |
332 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
333 | |
334 Notable changes in the short read alignment component: | |
335 | |
336 * Fixed a bug in samse: do not write mate coordinates. | |
337 | |
338 Notable changes in dBWT-SW: | |
339 | |
340 * Randomly choose one alignment if the read is a repetitive. | |
341 | |
342 * Fixed a flaw when a read is mapped across two adjacent reference | |
343 sequences. However, wrong alignment reports may still occur rarely in | |
344 this case. | |
345 | |
346 * Changed the default band width to 50. The speed is slower due to this | |
347 change. | |
348 | |
349 * Improved the mapping quality a little given long query sequences. | |
350 | |
351 (0.5.1: 2 September 2009, r1209) | |
352 | |
353 | |
354 | |
355 Beta Release 0.5.0 (20 August, 2009) | |
356 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
357 | |
358 This release implements a novel algorithm, dBWT-SW, specifically | |
359 designed for long reads. It is 10-50 times faster than SSAHA2, depending | |
360 on the characteristics of the input data, and achieves comparable | |
361 alignment accuracy while allowing chimera detection. In comparison to | |
362 BLAT, dBWT-SW is several times faster and much more accurate especially | |
363 when the error rate is high. Please read the manual page for more | |
364 information. | |
365 | |
366 The dBWT-SW algorithm is kind of developed for future sequencing | |
367 technologies which produce much longer reads with a little higher error | |
368 rate. It is still at its early development stage. Some features are | |
369 missing and it may be buggy although I have evaluated on several | |
370 simulated and real data sets. But following the "release early" | |
371 paradigm, I would like the users to try it first. | |
372 | |
373 Other notable changes in BWA are: | |
374 | |
375 * Fixed a rare bug in the Smith-Waterman alignment module. | |
376 | |
377 * Fixed a rare bug about the wrong alignment coordinate when a read is | |
378 poorly aligned. | |
379 | |
380 * Fixed a bug in generating the "mate-unmap" SAM tag when both ends in | |
381 a pair are unmapped. | |
382 | |
383 (0.5.0: 20 August 2009, r1200) | |
384 | |
385 | |
386 | |
387 Beta Release 0.4.9 (19 May, 2009) | |
388 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
389 | |
390 Interestingly, the integer overflow bug claimed to be fixed in 0.4.7 has | |
391 not in fact. Now I have fixed the bug. Sorry for this and thank Quan | |
392 Long for pointing out the bug (again). | |
393 | |
394 (0.4.9: 19 May 2009, r1075) | |
395 | |
396 | |
397 | |
398 Beta Release 0.4.8 (18 May, 2009) | |
399 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
400 | |
401 One change to "aln -R". Now by default, if there are no more than `-R' | |
402 equally best hits, bwa will search for suboptimal hits. This change | |
403 affects the ability in finding SNPs in segmental duplications. | |
404 | |
405 I have not tested this option thoroughly, but this simple change is less | |
406 likely to cause new bugs. Hope I am right. | |
407 | |
408 (0.4.8: 18 May 2009, r1073) | |
409 | |
410 | |
411 | |
412 Beta Release 0.4.7 (12 May, 2009) | |
413 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
414 | |
415 Notable changes: | |
416 | |
417 * Output SM (single-end mapping quality) and AM (smaller mapping | |
418 quality among the two ends) tag from sam output. | |
419 | |
420 * Improved the functionality of stdsw. | |
421 | |
422 * Made the XN tag more accurate. | |
423 | |
424 * Fixed a very rare segfault caused by integer overflow. | |
425 | |
426 * Improve the insert size estimation. | |
427 | |
428 * Fixed compiling errors for some Linux systems. | |
429 | |
430 (0.4.7: 12 May 2009, r1066) | |
431 | |
432 | |
433 | |
434 Beta Release 0.4.6 (9 March, 2009) | |
435 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
436 | |
437 This release improves the SOLiD support. First, a script for converting | |
438 SOLiD raw data is provided. This script is adapted from solid2fastq.pl | |
439 in the MAQ package. Second, a nucleotide reference file can be directly | |
440 used with `bwa index'. Third, SOLiD paired-end support is | |
441 completed. Fourth, color-space reads will be converted to nucleotides | |
442 when SAM output is generated. Color errors are corrected in this | |
443 process. Please note that like MAQ, BWA cannot make use of the primer | |
444 base and the first color. | |
445 | |
446 In addition, the calculation of mapping quality is also improved a | |
447 little bit, although end-users may barely observe the difference. | |
448 | |
449 (0.4.6: 9 March 2009, r915) | |
450 | |
451 | |
452 | |
453 Beta Release 0.4.5 (18 Feburary, 2009) | |
454 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
455 | |
456 Not much happened, but I think it would be good to let the users use the | |
457 latest version. | |
458 | |
459 Notable changes (Thank Bob Handsaker for catching the two bugs): | |
460 | |
461 * Improved bounary check. Previous version may still give incorrect | |
462 alignment coordinates in rare cases. | |
463 | |
464 * Fixed a bug in SW alignment when no residue matches. This only | |
465 affects the `sampe' command. | |
466 | |
467 * Robustly estimate insert size without setting the maximum on the | |
468 command line. Since this release `sampe -a' only has an effect if | |
469 there are not enough good pairs to infer the insert size | |
470 distribution. | |
471 | |
472 * Reduced false PE alignments a little bit by using the inferred insert | |
473 size distribution. This fix may be more important for long insert | |
474 size libraries. | |
475 | |
476 (0.4.5: 18 Feburary 2009, r829) | |
477 | |
478 | |
479 | |
480 Beta Release 0.4.4 (15 Feburary, 2009) | |
481 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
482 | |
483 This is mainly a bug fix release. Notable changes are: | |
484 | |
485 * Imposed boundary check for extracting subsequence from the | |
486 genome. Previously this causes memory problem in rare cases. | |
487 | |
488 * Fixed a bug in failing to find whether an alignment overlapping with | |
489 N on the genome. | |
490 | |
491 * Changed MD tag to meet the latest SAM specification. | |
492 | |
493 (0.4.4: 15 Feburary 2009, r815) | |
494 | |
495 | |
496 | |
497 Beta Release 0.4.3 (22 January, 2009) | |
498 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
499 | |
500 Notable changes: | |
501 | |
502 * Treat an ambiguous base N as a mismatch. Previous versions will not | |
503 map reads containing any N. | |
504 | |
505 * Automatically choose the maximum allowed number of differences. This | |
506 is important when reads of different lengths are mixed together. | |
507 | |
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) | |
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 |