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comparison bwa-0.6.2/ChangeLog @ 0:dd1186b11b3b draft

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author ashvark
date Fri, 18 Jul 2014 07:55:14 -0400
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-1:000000000000 0:dd1186b11b3b
1 ------------------------------------------------------------------------
2 r1605 | lh3 | 2010-12-29 20:20:20 -0500 (Wed, 29 Dec 2010) | 3 lines
3 Changed paths:
4 M /branches/prog/bwa/bwtsw2_aux.c
5 M /branches/prog/bwa/main.c
6
7 * bwa-0.5.9rc1-2 (r1605)
8 * fixed a typo/bug in bwasw
9
10 ------------------------------------------------------------------------
11 r1587 | lh3 | 2010-12-21 18:48:30 -0500 (Tue, 21 Dec 2010) | 2 lines
12 Changed paths:
13 M /branches/prog/bwa/bwa.1
14
15 a typo in the manual
16
17 ------------------------------------------------------------------------
18 r1586 | lh3 | 2010-12-21 18:47:48 -0500 (Tue, 21 Dec 2010) | 3 lines
19 Changed paths:
20 M /branches/prog/bwa/bwape.c
21 M /branches/prog/bwa/bwase.c
22 M /branches/prog/bwa/bwtaln.c
23 M /branches/prog/bwa/bwtsw2_main.c
24 M /branches/prog/bwa/main.c
25 M /branches/prog/bwa/utils.c
26 M /branches/prog/bwa/utils.h
27
28 * bwa-0.5.9rc1-1 (r1586)
29 * a few patches by John
30
31 ------------------------------------------------------------------------
32 r1562 | lh3 | 2010-12-10 01:02:06 -0500 (Fri, 10 Dec 2010) | 2 lines
33 Changed paths:
34 M /branches/prog/bwa/bwa.1
35 M /branches/prog/bwa/bwape.c
36 M /branches/prog/bwa/bwase.c
37
38 documentation on specifying @RG
39
40 ------------------------------------------------------------------------
41 r1561 | lh3 | 2010-12-10 00:45:40 -0500 (Fri, 10 Dec 2010) | 2 lines
42 Changed paths:
43 M /branches/prog/bwa/ChangeLog
44 M /branches/prog/bwa/NEWS
45 M /branches/prog/bwa/bwa.1
46 M /branches/prog/bwa/main.c
47
48 Release bwa-0.5.9rc1 (r1561)
49
50 ------------------------------------------------------------------------
51 r1560 | lh3 | 2010-12-10 00:29:08 -0500 (Fri, 10 Dec 2010) | 3 lines
52 Changed paths:
53 M /branches/prog/bwa/bwaseqio.c
54 M /branches/prog/bwa/main.c
55
56 * fixed a small memory leak caused by the BAM reader
57 * fixed a memory violation, also in the BAM reader
58
59 ------------------------------------------------------------------------
60 r1559 | lh3 | 2010-12-10 00:10:48 -0500 (Fri, 10 Dec 2010) | 2 lines
61 Changed paths:
62 M /branches/prog/bwa/ChangeLog
63 M /branches/prog/bwa/Makefile
64
65 change Makefile gcc options
66
67 ------------------------------------------------------------------------
68 r1558 | lh3 | 2010-12-10 00:09:22 -0500 (Fri, 10 Dec 2010) | 4 lines
69 Changed paths:
70 M /branches/prog/bwa/bwtsw2_aux.c
71 M /branches/prog/bwa/bwtsw2_core.c
72 M /branches/prog/bwa/main.c
73
74 * bwa-0.5.8-6 (r1557)
75 * added a little more comments to BWA-SW
76 * randomly choosing a mapping if there are more than one
77
78 ------------------------------------------------------------------------
79 r1557 | lh3 | 2010-12-09 21:58:00 -0500 (Thu, 09 Dec 2010) | 2 lines
80 Changed paths:
81 M /branches/prog/bwa/Makefile
82 M /branches/prog/bwa/bwtsw2_aux.c
83
84 sometimes unmapped reads may not be printed...
85
86 ------------------------------------------------------------------------
87 r1556 | lh3 | 2010-12-09 21:50:26 -0500 (Thu, 09 Dec 2010) | 2 lines
88 Changed paths:
89 M /branches/prog/bwa/Makefile
90 M /branches/prog/bwa/bwtsw2_aux.c
91
92 print unmapped reads
93
94 ------------------------------------------------------------------------
95 r1555 | lh3 | 2010-12-09 21:17:20 -0500 (Thu, 09 Dec 2010) | 3 lines
96 Changed paths:
97 M /branches/prog/bwa/ChangeLog
98 M /branches/prog/bwa/bwa.1
99 M /branches/prog/bwa/bwtaln.c
100 M /branches/prog/bwa/main.c
101
102 * bwa-0.5.8-5 (r1555)
103 * BAM input documentation
104
105 ------------------------------------------------------------------------
106 r1544 | lh3 | 2010-11-23 11:01:41 -0500 (Tue, 23 Nov 2010) | 3 lines
107 Changed paths:
108 M /branches/prog/bwa/bwape.c
109 M /branches/prog/bwa/bwase.c
110 M /branches/prog/bwa/main.c
111
112 * bwa-0.5.8-4 (r1544)
113 * supporting adding RG tags and RG lines
114
115 ------------------------------------------------------------------------
116 r1543 | lh3 | 2010-11-23 00:16:40 -0500 (Tue, 23 Nov 2010) | 3 lines
117 Changed paths:
118 M /branches/prog/bwa/bwtaln.c
119 M /branches/prog/bwa/main.c
120
121 * bwa-0.5.8-3 (r1543)
122 * fixed a memory leak
123
124 ------------------------------------------------------------------------
125 r1542 | lh3 | 2010-11-22 23:50:56 -0500 (Mon, 22 Nov 2010) | 3 lines
126 Changed paths:
127 M /branches/prog/bwa/bwase.c
128 M /branches/prog/bwa/main.c
129
130 * bwa-0.5.8-2 (r1542)
131 * fixed a long existing bug in random placement of reads
132
133 ------------------------------------------------------------------------
134 r1541 | lh3 | 2010-11-22 23:27:29 -0500 (Mon, 22 Nov 2010) | 2 lines
135 Changed paths:
136 M /branches/prog/bwa/Makefile
137 A /branches/prog/bwa/bamlite.c
138 A /branches/prog/bwa/bamlite.h
139 M /branches/prog/bwa/bwape.c
140 M /branches/prog/bwa/bwase.c
141 M /branches/prog/bwa/bwaseqio.c
142 M /branches/prog/bwa/bwtaln.c
143 M /branches/prog/bwa/bwtaln.h
144 M /branches/prog/bwa/main.c
145
146 preliminary BAM input support
147
148 ------------------------------------------------------------------------
149 r1537 | lh3 | 2010-10-16 23:46:20 -0400 (Sat, 16 Oct 2010) | 2 lines
150 Changed paths:
151 M /branches/prog/bwa/ChangeLog
152 M /branches/prog/bwa/bwa.1
153
154 change version number and ChangeLog
155
156 ------------------------------------------------------------------------
157 r1536 | lh3 | 2010-10-16 23:35:10 -0400 (Sat, 16 Oct 2010) | 3 lines
158 Changed paths:
159 M /branches/prog/bwa/bwape.c
160 M /branches/prog/bwa/main.c
161 M /branches/prog/bwa/stdaln.c
162
163 * fixed a bug in the scoring matrix
164 * release bwa-0.5.8c (r1536)
165
166 ------------------------------------------------------------------------
167 r1451 | lh3 | 2010-06-15 09:43:52 -0400 (Tue, 15 Jun 2010) | 2 lines
168 Changed paths:
169 M /branches/prog/bwa/bwa.1
170
171 version change
172
173 ------------------------------------------------------------------------
174 r1450 | lh3 | 2010-06-15 09:42:21 -0400 (Tue, 15 Jun 2010) | 3 lines
175 Changed paths:
176 M /branches/prog/bwa/main.c
177 M /branches/prog/bwa/stdaln.c
178
179 * bwa-0.5.8b (r1450)
180 * fixed a bug in scoring matrix
181
182 ------------------------------------------------------------------------
183 r1445 | lh3 | 2010-06-11 08:58:33 -0400 (Fri, 11 Jun 2010) | 2 lines
184 Changed paths:
185 M /branches/prog/bwa/bwa.1
186 M /branches/prog/bwa/bwape.c
187
188 fixed a serious bug
189
190 ------------------------------------------------------------------------
191 r1442 | lh3 | 2010-06-08 10:22:14 -0400 (Tue, 08 Jun 2010) | 2 lines
192 Changed paths:
193 M /branches/prog/bwa/ChangeLog
194 M /branches/prog/bwa/NEWS
195 M /branches/prog/bwa/main.c
196
197 Release bwa-0.5.8 (r1442)
198
199 ------------------------------------------------------------------------
200 r1440 | lh3 | 2010-05-19 13:43:50 -0400 (Wed, 19 May 2010) | 3 lines
201 Changed paths:
202 M /branches/prog/bwa/bwtsw2_core.c
203 M /branches/prog/bwa/main.c
204
205 * bwa-r1440
206 * sorry, forget to remove a debugging line
207
208 ------------------------------------------------------------------------
209 r1439 | lh3 | 2010-05-19 13:43:08 -0400 (Wed, 19 May 2010) | 4 lines
210 Changed paths:
211 M /branches/prog/bwa/bwape.c
212 M /branches/prog/bwa/bwtsw2_core.c
213 M /branches/prog/bwa/main.c
214
215 * bwa-r1439
216 * fixed a bug in bwasw caused by a recent modification
217 * throwing insane insert size when estimating isize
218
219 ------------------------------------------------------------------------
220 r1425 | lh3 | 2010-04-29 15:15:23 -0400 (Thu, 29 Apr 2010) | 10 lines
221 Changed paths:
222 M /branches/prog/bwa/bwtsw2_core.c
223 M /branches/prog/bwa/bwtsw2_main.c
224 M /branches/prog/bwa/main.c
225
226 * bwa-0.5.7-7 (r1425)
227 * fixed a minor bug in bwasw command-line parsing
228 * When band-width is not large enough, bwasw may find two highly
229 overlapping but not completely overlapping alignments. The old
230 version will filter out one of them, which leads to false
231 negatives. The current outputs both. This solution is obviously not
232 ideal. The ideal one would be to increase the band-width and redo the
233 alignment.
234
235
236 ------------------------------------------------------------------------
237 r1399 | lh3 | 2010-04-16 09:20:49 -0400 (Fri, 16 Apr 2010) | 3 lines
238 Changed paths:
239 M /branches/prog/bwa/ChangeLog
240 M /branches/prog/bwa/bwase.c
241 M /branches/prog/bwa/main.c
242
243 * bwa-0.5.7-6 (r1399)
244 * fixed a typo/bug (by Vaughn Iverson)
245
246 ------------------------------------------------------------------------
247 r1329 | lh3 | 2010-03-19 23:32:46 -0400 (Fri, 19 Mar 2010) | 2 lines
248 Changed paths:
249 M /branches/prog/bwa/bwape.c
250 M /branches/prog/bwa/main.c
251
252 small correction
253
254 ------------------------------------------------------------------------
255 r1328 | lh3 | 2010-03-19 23:28:44 -0400 (Fri, 19 Mar 2010) | 3 lines
256 Changed paths:
257 M /branches/prog/bwa/bwape.c
258 M /branches/prog/bwa/main.c
259
260 * bwa-0.5.7-4 (r1328)
261 * automatically adjust ap_prior based on alignment
262
263 ------------------------------------------------------------------------
264 r1327 | lh3 | 2010-03-19 23:02:40 -0400 (Fri, 19 Mar 2010) | 3 lines
265 Changed paths:
266 M /branches/prog/bwa/bwape.c
267 M /branches/prog/bwa/main.c
268 M /branches/prog/bwa/stdaln.c
269 M /branches/prog/bwa/stdaln.h
270
271 * bwa-0.5.7-3 (r1327)
272 * evaluate hits obtained from SW alignment in a more proper way.
273
274 ------------------------------------------------------------------------
275 r1320 | lh3 | 2010-03-17 15:13:22 -0400 (Wed, 17 Mar 2010) | 2 lines
276 Changed paths:
277 M /branches/prog/bwa/bwape.c
278
279 fixed a potential out-of-boundary error. Need more testing.
280
281 ------------------------------------------------------------------------
282 r1319 | lh3 | 2010-03-14 22:44:46 -0400 (Sun, 14 Mar 2010) | 2 lines
283 Changed paths:
284 M /branches/prog/bwa/bwape.c
285
286 insert size is `weird' if the 3rd quatile larger than 100,000bp
287
288 ------------------------------------------------------------------------
289 r1318 | lh3 | 2010-03-14 22:37:35 -0400 (Sun, 14 Mar 2010) | 3 lines
290 Changed paths:
291 M /branches/prog/bwa/bwape.c
292 M /branches/prog/bwa/bwtaln.h
293 M /branches/prog/bwa/main.c
294
295 * bwa-0.5.7-2 (r1318)
296 * in sampe, allow to disable insert size estimate
297
298 ------------------------------------------------------------------------
299 r1317 | lh3 | 2010-03-14 22:14:14 -0400 (Sun, 14 Mar 2010) | 5 lines
300 Changed paths:
301 M /branches/prog/bwa/bwape.c
302 M /branches/prog/bwa/bwase.c
303 M /branches/prog/bwa/main.c
304 M /branches/prog/bwa/solid2fastq.pl
305
306 * bwa-0.5.7-1 (r1317)
307 * fixed a potential bug in solid2fastq.pl
308 * fixed a bug in calculating mapping quality (by Rodrigo Goya)
309 * fixed a very rare bug (if ever occur) about pairing
310
311 ------------------------------------------------------------------------
312 r1310 | lh3 | 2010-03-01 10:35:45 -0500 (Mon, 01 Mar 2010) | 2 lines
313 Changed paths:
314 M /branches/prog/bwa/ChangeLog
315 M /branches/prog/bwa/NEWS
316 M /branches/prog/bwa/main.c
317
318 Release bwa-0.5.7
319
320 ------------------------------------------------------------------------
321 r1309 | lh3 | 2010-02-26 21:42:22 -0500 (Fri, 26 Feb 2010) | 4 lines
322 Changed paths:
323 M /branches/prog/bwa/bwape.c
324 M /branches/prog/bwa/bwtaln.c
325 M /branches/prog/bwa/main.c
326
327 * bwa-0.5.6-2 (r1309)
328 * fixed an unfixed bug (by Carol Scott)
329 * fixed some tiny formatting
330
331 ------------------------------------------------------------------------
332 r1305 | lh3 | 2010-02-25 13:47:58 -0500 (Thu, 25 Feb 2010) | 3 lines
333 Changed paths:
334 M /branches/prog/bwa/bwape.c
335 M /branches/prog/bwa/bwase.c
336 M /branches/prog/bwa/bwtaln.c
337 M /branches/prog/bwa/bwtsw2_main.c
338 M /branches/prog/bwa/main.c
339
340 * bwa-0.5.6-1 (r1304)
341 * optionally write output to a file (by Tim Fennel)
342
343 ------------------------------------------------------------------------
344 r1303 | lh3 | 2010-02-10 23:43:48 -0500 (Wed, 10 Feb 2010) | 2 lines
345 Changed paths:
346 M /branches/prog/bwa/ChangeLog
347 M /branches/prog/bwa/NEWS
348 M /branches/prog/bwa/bwa.1
349 M /branches/prog/bwa/bwtsw2_main.c
350 M /branches/prog/bwa/main.c
351
352 Release bwa-0.5.6
353
354 ------------------------------------------------------------------------
355 r1302 | lh3 | 2010-02-10 11:11:49 -0500 (Wed, 10 Feb 2010) | 3 lines
356 Changed paths:
357 M /branches/prog/bwa/ChangeLog
358 M /branches/prog/bwa/NEWS
359 M /branches/prog/bwa/bwape.c
360 M /branches/prog/bwa/bwtaln.h
361 M /branches/prog/bwa/main.c
362
363 * bwa-0.5.5-10 (r1302)
364 * improve max insert size estimate (method suggested by Gerton Lunter)
365
366 ------------------------------------------------------------------------
367 r1301 | lh3 | 2010-02-09 16:15:28 -0500 (Tue, 09 Feb 2010) | 5 lines
368 Changed paths:
369 M /branches/prog/bwa/bwape.c
370 M /branches/prog/bwa/bwase.c
371 M /branches/prog/bwa/main.c
372
373 * bwa-0.5.5-9 (r1301)
374 * improve mapping quality calculation for abnomalous pairs
375 * fixed a bug in multiple hits
376 * SOLiD multiple hits should work now
377
378 ------------------------------------------------------------------------
379 r1300 | lh3 | 2010-02-09 12:50:02 -0500 (Tue, 09 Feb 2010) | 3 lines
380 Changed paths:
381 M /branches/prog/bwa/bwape.c
382 M /branches/prog/bwa/main.c
383
384 * bwa-0.5.5-8 (r1300)
385 * output kurtosis
386
387 ------------------------------------------------------------------------
388 r1299 | lh3 | 2010-02-09 12:33:34 -0500 (Tue, 09 Feb 2010) | 5 lines
389 Changed paths:
390 M /branches/prog/bwa/bwape.c
391 M /branches/prog/bwa/main.c
392
393 * bwa-0.5.5-7 (r1299)
394 * calculate skewness in sampe
395 * increase min_len in SW to 20
396 * perform more SW to fix discordant pairs
397
398 ------------------------------------------------------------------------
399 r1298 | lh3 | 2010-02-08 12:40:31 -0500 (Mon, 08 Feb 2010) | 3 lines
400 Changed paths:
401 M /branches/prog/bwa/bwape.c
402 M /branches/prog/bwa/bwase.c
403 M /branches/prog/bwa/bwtaln.c
404 M /branches/prog/bwa/bwtaln.h
405 M /branches/prog/bwa/cs2nt.c
406 M /branches/prog/bwa/main.c
407 M /branches/prog/bwa/stdaln.h
408
409 * bwa-0.5.5-6 (r1297)
410 * prepare to replace all 16-bit CIGAR (patches by Rodrigo Goya)
411
412 ------------------------------------------------------------------------
413 r1297 | lh3 | 2010-02-05 22:26:11 -0500 (Fri, 05 Feb 2010) | 2 lines
414 Changed paths:
415 M /branches/prog/bwa/solid2fastq.pl
416
417 the old fix seems not working!
418
419 ------------------------------------------------------------------------
420 r1296 | lh3 | 2010-02-05 21:51:03 -0500 (Fri, 05 Feb 2010) | 3 lines
421 Changed paths:
422 M /branches/prog/bwa/bwa.1
423 M /branches/prog/bwa/bwape.c
424 M /branches/prog/bwa/main.c
425
426 * bwa-0.5.5-5 (r1296)
427 * fixed a minor issue that the lower bound of insert size is not correctly set.
428
429 ------------------------------------------------------------------------
430 r1295 | lh3 | 2010-02-05 21:01:10 -0500 (Fri, 05 Feb 2010) | 5 lines
431 Changed paths:
432 M /branches/prog/bwa/bwape.c
433 M /branches/prog/bwa/bwase.c
434 M /branches/prog/bwa/bwaseqio.c
435 M /branches/prog/bwa/main.c
436
437 * bwa-0.5.5-4 (r1295)
438 * fixed a memory leak
439 * change the behaviour of -n (samse and sampe)
440 * change the default of -n
441
442 ------------------------------------------------------------------------
443 r1294 | lh3 | 2010-02-05 17:24:06 -0500 (Fri, 05 Feb 2010) | 3 lines
444 Changed paths:
445 M /branches/prog/bwa/bwape.c
446 M /branches/prog/bwa/bwase.c
447 M /branches/prog/bwa/bwaseqio.c
448 M /branches/prog/bwa/bwtaln.h
449 M /branches/prog/bwa/main.c
450
451 * bwa-0.5.5-3 (r1294)
452 * improved multi-hit report
453
454 ------------------------------------------------------------------------
455 r1293 | lh3 | 2010-02-05 12:57:38 -0500 (Fri, 05 Feb 2010) | 5 lines
456 Changed paths:
457 M /branches/prog/bwa/bwape.c
458 M /branches/prog/bwa/bwase.c
459 M /branches/prog/bwa/cs2nt.c
460 M /branches/prog/bwa/main.c
461 M /branches/prog/bwa/solid2fastq.pl
462
463 * bwa-0.5.5-2 (r1293)
464 * bugfix: truncated quality string
465 * bugfix: quality -1 in solid->fastq conversion
466 * bugfix: color reads on the reverse strand is not complemented
467
468 ------------------------------------------------------------------------
469 r1279 | lh3 | 2009-11-23 22:42:34 -0500 (Mon, 23 Nov 2009) | 3 lines
470 Changed paths:
471 M /branches/prog/bwa/bntseq.c
472 M /branches/prog/bwa/bntseq.h
473 M /branches/prog/bwa/bwase.c
474 A /branches/prog/bwa/bwase.h
475 M /branches/prog/bwa/bwtaln.c
476 M /branches/prog/bwa/bwtaln.h
477 M /branches/prog/bwa/bwtsw2_aux.c
478 M /branches/prog/bwa/main.c
479
480 * bwa-0.5.5-1 (r1279)
481 * incorporate changes from Matt Hanna for Java bindings.
482
483 ------------------------------------------------------------------------
484 r1275 | lh3 | 2009-11-10 22:13:10 -0500 (Tue, 10 Nov 2009) | 2 lines
485 Changed paths:
486 M /branches/prog/bwa/ChangeLog
487
488 update ChangeLog
489
490 ------------------------------------------------------------------------
491 r1273 | lh3 | 2009-11-10 22:08:16 -0500 (Tue, 10 Nov 2009) | 2 lines
492 Changed paths:
493 M /branches/prog/bwa/NEWS
494 M /branches/prog/bwa/bwa.1
495 M /branches/prog/bwa/main.c
496 A /branches/prog/bwa/qualfa2fq.pl
497
498 Release bwa-0.5.5 (r1273)
499
500 ------------------------------------------------------------------------
501 r1272 | lh3 | 2009-11-10 22:02:50 -0500 (Tue, 10 Nov 2009) | 3 lines
502 Changed paths:
503 M /branches/prog/bwa/bwape.c
504 M /branches/prog/bwa/main.c
505
506 * bwa-0.5.4-3 (r1272)
507 * fixed another typo which may lead to incorrect single-end mapping quality
508
509 ------------------------------------------------------------------------
510 r1271 | lh3 | 2009-11-10 21:59:47 -0500 (Tue, 10 Nov 2009) | 4 lines
511 Changed paths:
512 M /branches/prog/bwa/bwtaln.c
513 M /branches/prog/bwa/main.c
514
515 * bwa-0.5.4-2 (r1271)
516 * fixed a serious typo/bug which does not hurt if we allow one gap open
517 and work with <200bp reads, but causes segfault for long reads.
518
519 ------------------------------------------------------------------------
520 r1270 | lh3 | 2009-11-09 23:12:42 -0500 (Mon, 09 Nov 2009) | 3 lines
521 Changed paths:
522 M /branches/prog/bwa/cs2nt.c
523 M /branches/prog/bwa/main.c
524
525 * bwa-0.5.4-1 (r1270)
526 * fixed a bug in color alignment
527
528 ------------------------------------------------------------------------
529 r1245 | lh3 | 2009-10-09 07:42:52 -0400 (Fri, 09 Oct 2009) | 2 lines
530 Changed paths:
531 M /branches/prog/bwa/ChangeLog
532 M /branches/prog/bwa/NEWS
533 M /branches/prog/bwa/bwa.1
534 M /branches/prog/bwa/bwape.c
535 M /branches/prog/bwa/bwase.c
536 M /branches/prog/bwa/bwaseqio.c
537 M /branches/prog/bwa/main.c
538
539 Release bwa-0.5.4
540
541 ------------------------------------------------------------------------
542 r1244 | lh3 | 2009-10-09 05:53:52 -0400 (Fri, 09 Oct 2009) | 5 lines
543 Changed paths:
544 M /branches/prog/bwa/ChangeLog
545 M /branches/prog/bwa/bwape.c
546 M /branches/prog/bwa/bwase.c
547 M /branches/prog/bwa/bwaseqio.c
548 M /branches/prog/bwa/bwtaln.h
549 M /branches/prog/bwa/main.c
550 M /branches/prog/bwa/stdaln.c
551
552 * bwa-0.5.3-4 (r1244)
553 * output the clipped length in XC:i: tag
554 * skip mate alignment when stdaln is buggy
555 * fixed a bug in NM:i: tag
556
557 ------------------------------------------------------------------------
558 r1243 | lh3 | 2009-10-07 08:15:04 -0400 (Wed, 07 Oct 2009) | 3 lines
559 Changed paths:
560 M /branches/prog/bwa/bwape.c
561 M /branches/prog/bwa/main.c
562
563 * bwa-0.5.3-3 (r1243)
564 * sampe: fixed a bug when a read sequence is identical its reverse complement.
565
566 ------------------------------------------------------------------------
567 r1242 | lh3 | 2009-10-07 07:49:13 -0400 (Wed, 07 Oct 2009) | 4 lines
568 Changed paths:
569 M /branches/prog/bwa/bntseq.c
570 M /branches/prog/bwa/bwape.c
571 M /branches/prog/bwa/bwtaln.c
572 M /branches/prog/bwa/bwtaln.h
573 M /branches/prog/bwa/main.c
574
575 * bwa-0.5.3-2 (r1242)
576 * sampe: optionall preload the full index into memory
577 * aln: change the default seed length to 32bp
578
579 ------------------------------------------------------------------------
580 r1238 | lh3 | 2009-09-26 18:38:15 -0400 (Sat, 26 Sep 2009) | 2 lines
581 Changed paths:
582 M /branches/prog/bwa/khash.h
583
584 Improve portability of khash.h
585
586 ------------------------------------------------------------------------
587 r1228 | lh3 | 2009-09-15 09:20:22 -0400 (Tue, 15 Sep 2009) | 2 lines
588 Changed paths:
589 M /branches/prog/bwa/main.c
590
591 fixed a typo
592
593 ------------------------------------------------------------------------
594 r1227 | lh3 | 2009-09-15 09:19:35 -0400 (Tue, 15 Sep 2009) | 3 lines
595 Changed paths:
596 M /branches/prog/bwa/bwtsw2.h
597 M /branches/prog/bwa/bwtsw2_aux.c
598 M /branches/prog/bwa/bwtsw2_main.c
599 M /branches/prog/bwa/main.c
600
601 * bwa-0.5.3-1 (r1226)
602 * in dBWT-SW, optionall use hard clipping instead of soft clipping
603
604 ------------------------------------------------------------------------
605 r1225 | lh3 | 2009-09-15 08:32:30 -0400 (Tue, 15 Sep 2009) | 2 lines
606 Changed paths:
607 M /branches/prog/bwa/NEWS
608 M /branches/prog/bwa/bwase.c
609 M /branches/prog/bwa/main.c
610
611 Release bwa-0.5.3 (r1225)
612
613 ------------------------------------------------------------------------
614 r1223 | lh3 | 2009-09-13 07:30:41 -0400 (Sun, 13 Sep 2009) | 2 lines
615 Changed paths:
616 M /branches/prog/bwa/ChangeLog
617 M /branches/prog/bwa/NEWS
618 M /branches/prog/bwa/bwa.1
619 M /branches/prog/bwa/main.c
620
621 Release bwa-0.5.2
622
623 ------------------------------------------------------------------------
624 r1222 | lh3 | 2009-09-11 09:11:39 -0400 (Fri, 11 Sep 2009) | 3 lines
625 Changed paths:
626 M /branches/prog/bwa/bwtaln.c
627 M /branches/prog/bwa/main.c
628
629 * bwa-0.5.1-5 (r1222)
630 * fixed a typo. No real change
631
632 ------------------------------------------------------------------------
633 r1221 | lh3 | 2009-09-11 09:09:44 -0400 (Fri, 11 Sep 2009) | 3 lines
634 Changed paths:
635 M /branches/prog/bwa/bwa.1
636 M /branches/prog/bwa/bwape.c
637 M /branches/prog/bwa/bwase.c
638 M /branches/prog/bwa/bwaseqio.c
639 M /branches/prog/bwa/bwtaln.c
640 M /branches/prog/bwa/bwtaln.h
641 M /branches/prog/bwa/main.c
642
643 * bwa-0.5.1-4 (r1221)
644 * trim reads before alignment
645
646 ------------------------------------------------------------------------
647 r1216 | lh3 | 2009-09-08 17:50:15 -0400 (Tue, 08 Sep 2009) | 4 lines
648 Changed paths:
649 M /branches/prog/bwa/bwape.c
650 M /branches/prog/bwa/bwase.c
651 M /branches/prog/bwa/bwtaln.h
652 M /branches/prog/bwa/main.c
653
654 * bwa-0.5.1-3 (r1216)
655 * fixed a bug about NM tags for gapped alignment
656 * print SAM header
657
658 ------------------------------------------------------------------------
659 r1215 | lh3 | 2009-09-08 17:14:42 -0400 (Tue, 08 Sep 2009) | 3 lines
660 Changed paths:
661 M /branches/prog/bwa/bwtaln.c
662 M /branches/prog/bwa/main.c
663
664 * bwa-0.5.1-2 (r1215)
665 * fixed a bug when read lengths vary (by John Marshall)
666
667 ------------------------------------------------------------------------
668 r1213 | lh3 | 2009-09-06 18:58:15 -0400 (Sun, 06 Sep 2009) | 3 lines
669 Changed paths:
670 M /branches/prog/bwa/bwtsw2_aux.c
671 M /branches/prog/bwa/main.c
672
673 * bwa-0.5.1-1 (r1213)
674 * change default -T to 30
675
676 ------------------------------------------------------------------------
677 r1209 | lh3 | 2009-09-02 06:06:02 -0400 (Wed, 02 Sep 2009) | 2 lines
678 Changed paths:
679 M /branches/prog/bwa/NEWS
680 M /branches/prog/bwa/bwa.1
681 M /branches/prog/bwa/main.c
682
683 Release bwa-0.5.1
684
685 ------------------------------------------------------------------------
686 r1208 | lh3 | 2009-09-02 05:56:33 -0400 (Wed, 02 Sep 2009) | 2 lines
687 Changed paths:
688 M /branches/prog/bwa/ChangeLog
689
690 * ChangeLog
691
692 ------------------------------------------------------------------------
693 r1206 | lh3 | 2009-08-30 18:27:30 -0400 (Sun, 30 Aug 2009) | 3 lines
694 Changed paths:
695 M /branches/prog/bwa/bwtsw2_aux.c
696 M /branches/prog/bwa/main.c
697
698 * bwa-0.5.0-6 (r1206)
699 * fixed two bugs caused by previous modification
700
701 ------------------------------------------------------------------------
702 r1205 | lh3 | 2009-08-30 17:28:36 -0400 (Sun, 30 Aug 2009) | 4 lines
703 Changed paths:
704 M /branches/prog/bwa/ChangeLog
705 M /branches/prog/bwa/bwtsw2_aux.c
706 M /branches/prog/bwa/main.c
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 ------------------------------------------------------------------------
713 r1204 | lh3 | 2009-08-30 06:06:16 -0400 (Sun, 30 Aug 2009) | 3 lines
714 Changed paths:
715 M /branches/prog/bwa/bwtsw2_aux.c
716 M /branches/prog/bwa/bwtsw2_core.c
717 M /branches/prog/bwa/main.c
718
719 * bwa-0.5.0-3 (r1204)
720 * choose one repetitive hit to extend
721
722 ------------------------------------------------------------------------
723 r1203 | lh3 | 2009-08-29 18:11:51 -0400 (Sat, 29 Aug 2009) | 4 lines
724 Changed paths:
725 M /branches/prog/bwa/bwase.c
726 M /branches/prog/bwa/bwtsw2_aux.c
727 M /branches/prog/bwa/main.c
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 ------------------------------------------------------------------------
734 r1202 | lh3 | 2009-08-28 19:48:41 -0400 (Fri, 28 Aug 2009) | 4 lines
735 Changed paths:
736 M /branches/prog/bwa/bwtsw2_aux.c
737 M /branches/prog/bwa/main.c
738
739 * bwa-0.5.0-1 (r1202)
740 * change default band width to 50
741 * improve mapping quality a bit
742
743 ------------------------------------------------------------------------
744 r1200 | lh3 | 2009-08-20 06:21:24 -0400 (Thu, 20 Aug 2009) | 2 lines
745 Changed paths:
746 M /branches/prog/bwa/NEWS
747 M /branches/prog/bwa/main.c
748
749 Release bwa-0.5.0 (r1200)
750
751 ------------------------------------------------------------------------
752 r1199 | lh3 | 2009-08-20 04:49:15 -0400 (Thu, 20 Aug 2009) | 2 lines
753 Changed paths:
754 M /branches/prog/bwa/ChangeLog
755 M /branches/prog/bwa/bwa.1
756
757 Updated ChangeLog and the manual
758
759 ------------------------------------------------------------------------
760 r1198 | lh3 | 2009-08-19 11:09:15 -0400 (Wed, 19 Aug 2009) | 3 lines
761 Changed paths:
762 M /branches/prog/bwa/bwtsw2_aux.c
763 M /branches/prog/bwa/bwtsw2_core.c
764 M /branches/prog/bwa/main.c
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 ------------------------------------------------------------------------
770 r1197 | lh3 | 2009-08-19 08:15:05 -0400 (Wed, 19 Aug 2009) | 3 lines
771 Changed paths:
772 M /branches/prog/bwa/Makefile
773 M /branches/prog/bwa/bwtsw2_aux.c
774 A /branches/prog/bwa/bwtsw2_chain.c
775 M /branches/prog/bwa/main.c
776
777 * bwa-0.4.9-35 (r1197)
778 * further heuristic acceleration for long queries
779
780 ------------------------------------------------------------------------
781 r1196 | lh3 | 2009-08-18 06:54:03 -0400 (Tue, 18 Aug 2009) | 4 lines
782 Changed paths:
783 M /branches/prog/bwa/bwa.1
784 M /branches/prog/bwa/bwtsw2_aux.c
785 M /branches/prog/bwa/main.c
786
787 * bwa-0.4.9-34 (r1196)
788 * updated the manual page
789 * output base quality if the input is fastq
790
791 ------------------------------------------------------------------------
792 r1195 | lh3 | 2009-08-18 06:23:00 -0400 (Tue, 18 Aug 2009) | 4 lines
793 Changed paths:
794 M /branches/prog/bwa/bwase.c
795 M /branches/prog/bwa/bwtsw2_main.c
796 M /branches/prog/bwa/main.c
797 M /branches/prog/bwa/simple_dp.c
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 ------------------------------------------------------------------------
804 r1192 | lh3 | 2009-08-13 05:37:28 -0400 (Thu, 13 Aug 2009) | 2 lines
805 Changed paths:
806 M /branches/prog/bwa/bwa.1
807
808 update manual
809
810 ------------------------------------------------------------------------
811 r1191 | lh3 | 2009-08-12 19:40:51 -0400 (Wed, 12 Aug 2009) | 2 lines
812 Changed paths:
813 M /branches/prog/bwa/bwa.1
814 M /branches/prog/bwa/bwtsw2_main.c
815
816 update documentation
817
818 ------------------------------------------------------------------------
819 r1190 | lh3 | 2009-08-12 08:56:10 -0400 (Wed, 12 Aug 2009) | 3 lines
820 Changed paths:
821 M /branches/prog/bwa/bwtsw2_main.c
822 M /branches/prog/bwa/main.c
823
824 * bwa-0.4.9-32 (r1190)
825 * only help messages are changed
826
827 ------------------------------------------------------------------------
828 r1189 | lh3 | 2009-08-11 09:28:55 -0400 (Tue, 11 Aug 2009) | 4 lines
829 Changed paths:
830 M /branches/prog/bwa/bwase.c
831 M /branches/prog/bwa/bwtsw2.h
832 M /branches/prog/bwa/bwtsw2_aux.c
833 M /branches/prog/bwa/bwtsw2_core.c
834 M /branches/prog/bwa/main.c
835
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
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:
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
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
924 M /branches/prog/bwa/bwtsw2_aux.c
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
955 Changed paths:
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:
964 M /branches/prog/bwa/bwtsw2.h
965 M /branches/prog/bwa/bwtsw2_aux.c
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
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
1246 M /branches/prog/bwa/main.c
1247
1248 bwtsw2 (dBWT-SW) is working apparently...
1249
1250
1251 ------------------------------------------------------------------------
1252 r1139 | lh3 | 2009-07-15 05:52:18 -0400 (Wed, 15 Jul 2009) | 4 lines
1253 Changed paths:
1254 M /branches/prog/bwa/bwtsw2_core.c
1255 M /branches/prog/bwa/main.c
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
1261 ------------------------------------------------------------------------
1262 r1138 | lh3 | 2009-07-15 05:18:42 -0400 (Wed, 15 Jul 2009) | 3 lines
1263 Changed paths:
1264 M /branches/prog/bwa/Makefile
1265 A /branches/prog/bwa/bwt_lite.c
1266 A /branches/prog/bwa/bwt_lite.h
1267 A /branches/prog/bwa/bwtsw2.h
1268 A /branches/prog/bwa/bwtsw2_aux.c
1269 A /branches/prog/bwa/bwtsw2_core.c
1270 A /branches/prog/bwa/bwtsw2_main.c
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 ------------------------------------------------------------------------
1278 r1075 | lh3 | 2009-05-19 05:14:50 -0400 (Tue, 19 May 2009) | 2 lines
1279 Changed paths:
1280 M /branches/prog/bwa/NEWS
1281 M /branches/prog/bwa/bwase.c
1282 M /branches/prog/bwa/main.c
1283
1284 Release bwa-0.4.9
1285
1286 ------------------------------------------------------------------------
1287 r1073 | lh3 | 2009-05-18 17:13:19 -0400 (Mon, 18 May 2009) | 2 lines
1288 Changed paths:
1289 M /branches/prog/bwa/NEWS
1290 M /branches/prog/bwa/bwa.1
1291 M /branches/prog/bwa/main.c
1292
1293 Release bwa-0.4.8
1294
1295 ------------------------------------------------------------------------
1296 r1069 | lh3 | 2009-05-14 09:54:54 -0400 (Thu, 14 May 2009) | 3 lines
1297 Changed paths:
1298 M /branches/prog/bwa/bwtaln.c
1299 M /branches/prog/bwa/main.c
1300
1301 * bwa-0.4.7-2
1302 * change the default of "aln -R" to 30
1303
1304 ------------------------------------------------------------------------
1305 r1068 | lh3 | 2009-05-14 09:27:55 -0400 (Thu, 14 May 2009) | 3 lines
1306 Changed paths:
1307 M /branches/prog/bwa/bwape.c
1308 M /branches/prog/bwa/bwase.c
1309 M /branches/prog/bwa/bwtaln.c
1310 M /branches/prog/bwa/bwtaln.h
1311 M /branches/prog/bwa/bwtgap.c
1312 M /branches/prog/bwa/main.c
1313
1314 * bwa-0.4.7-1
1315 * search for suboptimal hits if the top hit is not so repetitive
1316
1317 ------------------------------------------------------------------------
1318 r1066 | lh3 | 2009-05-12 15:31:31 -0400 (Tue, 12 May 2009) | 2 lines
1319 Changed paths:
1320 M /branches/prog/bwa/ChangeLog
1321 M /branches/prog/bwa/NEWS
1322 M /branches/prog/bwa/bwase.c
1323 M /branches/prog/bwa/main.c
1324
1325 Release bwa-0.4.7
1326
1327 ------------------------------------------------------------------------
1328 r1065 | lh3 | 2009-05-12 15:20:40 -0400 (Tue, 12 May 2009) | 3 lines
1329 Changed paths:
1330 M /branches/prog/bwa/bwape.c
1331 M /branches/prog/bwa/bwase.c
1332 M /branches/prog/bwa/main.c
1333
1334 * bwa-0.4.6-9
1335 * fixed compiling errors on some Linux machines
1336
1337 ------------------------------------------------------------------------
1338 r1064 | lh3 | 2009-05-12 07:30:46 -0400 (Tue, 12 May 2009) | 3 lines
1339 Changed paths:
1340 M /branches/prog/bwa/bwtaln.c
1341 M /branches/prog/bwa/main.c
1342
1343 * bwa-0.4.6-8
1344 * avoid compilation error on some systems.
1345
1346 ------------------------------------------------------------------------
1347 r1035 | lh3 | 2009-05-09 05:41:33 -0400 (Sat, 09 May 2009) | 4 lines
1348 Changed paths:
1349 M /branches/prog/bwa/bwape.c
1350 M /branches/prog/bwa/bwase.c
1351 M /branches/prog/bwa/main.c
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 ------------------------------------------------------------------------
1358 r1008 | lh3 | 2009-04-29 05:41:58 -0400 (Wed, 29 Apr 2009) | 4 lines
1359 Changed paths:
1360 M /branches/prog/bwa/bwase.c
1361 M /branches/prog/bwa/main.c
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
1369 Changed paths:
1370 M /branches/prog/bwa/bwape.c
1371 M /branches/prog/bwa/main.c
1372 M /branches/prog/bwa/simple_dp.c
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
1382 Changed paths:
1383 M /branches/prog/bwa/main.c
1384 M /branches/prog/bwa/simple_dp.c
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
1394 Changed paths:
1395 M /branches/prog/bwa/bwa.1
1396 M /branches/prog/bwa/bwape.c
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:
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:
1416 M /branches/prog/bwa/bwa.1
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
1426 Changed paths:
1427 M /branches/prog/bwa/ChangeLog
1428 M /branches/prog/bwa/kstring.c
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
1435 Changed paths:
1436 M /branches/prog/bwa/bwtmisc.c
1437 M /branches/prog/bwa/main.c
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
1444 Changed paths:
1445 M /branches/prog/bwa/Makefile
1446
1447 disable debugging
1448
1449 ------------------------------------------------------------------------
1450 r879 | lh3 | 2009-03-01 16:28:04 -0500 (Sun, 01 Mar 2009) | 3 lines
1451 Changed paths:
1452 M /branches/prog/bwa/bwase.c
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
1461 Changed paths:
1462 M /branches/prog/bwa/bwase.c
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
1473 M /branches/prog/bwa/bwape.c
1474 M /branches/prog/bwa/bwase.c
1475 M /branches/prog/bwa/bwtaln.h
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
1483 Changed paths:
1484 M /branches/prog/bwa/Makefile
1485 M /branches/prog/bwa/bwase.c
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
1492 Changed paths:
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
1505 Changed paths:
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:
1516 M /branches/prog/bwa/bwape.c
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
1535 Changed paths:
1536 M /branches/prog/bwa/main.c
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
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
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
1660 Changed paths:
1661 M /branches/prog/bwa/bntseq.c
1662 M /branches/prog/bwa/bwase.c
1663 M /branches/prog/bwa/main.c
1664
1665 * bwa-0.4.3-2
1666 * fixed a bug on counting 'N'
1667
1668 ------------------------------------------------------------------------
1669 r795 | lh3 | 2009-02-05 07:41:27 -0500 (Thu, 05 Feb 2009) | 4 lines
1670 Changed paths:
1671 M /branches/prog/bwa/bwa.1
1672 M /branches/prog/bwa/bwape.c
1673 M /branches/prog/bwa/main.c
1674
1675 * bwa-0.4.3-1
1676 * fixed potential boundary problems
1677 * update benchmark result
1678
1679 ------------------------------------------------------------------------
1680 r791 | lh3 | 2009-01-25 05:20:47 -0500 (Sun, 25 Jan 2009) | 2 lines
1681 Changed paths:
1682 M /branches/prog/bwa/bwa.1
1683
1684 update some numbers
1685
1686 ------------------------------------------------------------------------
1687 r790 | lh3 | 2009-01-24 15:13:03 -0500 (Sat, 24 Jan 2009) | 2 lines
1688 Changed paths:
1689 M /branches/prog/bwa/bwa.1
1690
1691 update benchmark
1692
1693 ------------------------------------------------------------------------
1694 r789 | lh3 | 2009-01-22 10:18:44 -0500 (Thu, 22 Jan 2009) | 2 lines
1695 Changed paths:
1696 M /branches/prog/bwa/bwtindex.c
1697
1698 a warning message for index
1699
1700 ------------------------------------------------------------------------
1701 r788 | lh3 | 2009-01-22 09:54:06 -0500 (Thu, 22 Jan 2009) | 2 lines
1702 Changed paths:
1703 M /branches/prog/bwa/main.c
1704
1705 forget to change release number
1706
1707 ------------------------------------------------------------------------
1708 r786 | lh3 | 2009-01-22 06:27:39 -0500 (Thu, 22 Jan 2009) | 2 lines
1709 Changed paths:
1710 M /branches/prog/bwa/NEWS
1711
1712 Release bwa-0.4.3
1713
1714 ------------------------------------------------------------------------
1715 r785 | lh3 | 2009-01-22 06:27:16 -0500 (Thu, 22 Jan 2009) | 2 lines
1716 Changed paths:
1717 M /branches/prog/bwa/ChangeLog
1718 M /branches/prog/bwa/NEWS
1719
1720 Release bwa-0.4.3
1721
1722 ------------------------------------------------------------------------
1723 r784 | lh3 | 2009-01-22 06:19:59 -0500 (Thu, 22 Jan 2009) | 4 lines
1724 Changed paths:
1725 M /branches/prog/bwa/bwa.1
1726 M /branches/prog/bwa/bwase.c
1727 M /branches/prog/bwa/main.c
1728
1729 * bwa-0.4.2-10
1730 * update documentation
1731 * fixed a bug on generating MD tags for SW alignment
1732
1733 ------------------------------------------------------------------------
1734 r782 | lh3 | 2009-01-19 12:08:38 -0500 (Mon, 19 Jan 2009) | 3 lines
1735 Changed paths:
1736 M /branches/prog/bwa/bwase.c
1737 M /branches/prog/bwa/main.c
1738
1739 * bwa-0.4.2-9
1740 * fixed a bug in samse -n...
1741
1742 ------------------------------------------------------------------------
1743 r781 | lh3 | 2009-01-19 11:26:37 -0500 (Mon, 19 Jan 2009) | 3 lines
1744 Changed paths:
1745 M /branches/prog/bwa/bwtaln.c
1746 M /branches/prog/bwa/main.c
1747
1748 * bwa-0.4.2-8
1749 * given -N, the previous version would stop if the top hit is a repeat. Now changed.
1750
1751 ------------------------------------------------------------------------
1752 r780 | lh3 | 2009-01-19 11:20:18 -0500 (Mon, 19 Jan 2009) | 4 lines
1753 Changed paths:
1754 M /branches/prog/bwa/bwape.c
1755 M /branches/prog/bwa/bwase.c
1756 M /branches/prog/bwa/bwtaln.c
1757 M /branches/prog/bwa/bwtaln.h
1758 M /branches/prog/bwa/bwtgap.c
1759 M /branches/prog/bwa/main.c
1760
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
1764
1765 ------------------------------------------------------------------------
1766 r779 | lh3 | 2009-01-19 10:45:57 -0500 (Mon, 19 Jan 2009) | 3 lines
1767 Changed paths:
1768 M /branches/prog/bwa/bwa.1
1769 M /branches/prog/bwa/bwase.c
1770 M /branches/prog/bwa/main.c
1771
1772 * bwa-0.4.2-6
1773 * allow to dump multiple hits from samse, in another format, though
1774
1775 ------------------------------------------------------------------------
1776 r778 | lh3 | 2009-01-19 06:24:29 -0500 (Mon, 19 Jan 2009) | 5 lines
1777 Changed paths:
1778 M /branches/prog/bwa/Makefile
1779 M /branches/prog/bwa/bwape.c
1780 M /branches/prog/bwa/bwase.c
1781 M /branches/prog/bwa/bwaseqio.c
1782 M /branches/prog/bwa/bwtaln.h
1783 M /branches/prog/bwa/kseq.h
1784 A /branches/prog/bwa/kstring.c
1785 A /branches/prog/bwa/kstring.h
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
1796 Changed paths:
1797 M /branches/prog/bwa/bwase.c
1798 M /branches/prog/bwa/main.c
1799
1800 * bwa-0.4.2-4
1801 * fixed a bug for SAM format
1802
1803 ------------------------------------------------------------------------
1804 r774 | lh3 | 2009-01-17 13:48:52 -0500 (Sat, 17 Jan 2009) | 4 lines
1805 Changed paths:
1806 M /branches/prog/bwa/bwtaln.c
1807 M /branches/prog/bwa/main.c
1808
1809 * bwa-0.4.2-3
1810 * change default fnr to 0.04
1811 * print max_diff for valid fnr
1812
1813 ------------------------------------------------------------------------
1814 r773 | lh3 | 2009-01-17 05:54:37 -0500 (Sat, 17 Jan 2009) | 3 lines
1815 Changed paths:
1816 M /branches/prog/bwa/bwape.c
1817 M /branches/prog/bwa/bwase.c
1818 M /branches/prog/bwa/bwtaln.c
1819 M /branches/prog/bwa/bwtaln.h
1820 M /branches/prog/bwa/main.c
1821
1822 * bwa-0.4.2-2
1823 * automatically choose max_diff
1824
1825 ------------------------------------------------------------------------
1826 r772 | lh3 | 2009-01-16 18:16:14 -0500 (Fri, 16 Jan 2009) | 3 lines
1827 Changed paths:
1828 M /branches/prog/bwa/bwaseqio.c
1829 M /branches/prog/bwa/bwt.c
1830 M /branches/prog/bwa/bwtaln.c
1831 M /branches/prog/bwa/bwtaln.h
1832 M /branches/prog/bwa/bwtgap.c
1833 M /branches/prog/bwa/main.c
1834
1835 * bwa-0.4.2-1
1836 * take N as a mismatch
1837
1838 ------------------------------------------------------------------------
1839 r768 | lh3 | 2009-01-09 11:57:23 -0500 (Fri, 09 Jan 2009) | 2 lines
1840 Changed paths:
1841 M /branches/prog/bwa/ChangeLog
1842 M /branches/prog/bwa/NEWS
1843 M /branches/prog/bwa/bntseq.c
1844 M /branches/prog/bwa/main.c
1845
1846 Release bwa-0.4.2
1847
1848 ------------------------------------------------------------------------
1849 r759 | lh3 | 2009-01-07 09:55:43 -0500 (Wed, 07 Jan 2009) | 2 lines
1850 Changed paths:
1851 M /branches/prog/bwa/ChangeLog
1852 M /branches/prog/bwa/NEWS
1853 M /branches/prog/bwa/bwa.1
1854 M /branches/prog/bwa/bwape.c
1855 M /branches/prog/bwa/bwtaln.h
1856 M /branches/prog/bwa/main.c
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
1862 Changed paths:
1863 M /branches/prog/bwa/bwape.c
1864 M /branches/prog/bwa/bwase.c
1865 M /branches/prog/bwa/bwtaln.h
1866 M /branches/prog/bwa/main.c
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
1873 Changed paths:
1874 M /branches/prog/bwa/bwape.c
1875 M /branches/prog/bwa/bwase.c
1876 M /branches/prog/bwa/bwaseqio.c
1877 M /branches/prog/bwa/bwtaln.h
1878 M /branches/prog/bwa/main.c
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 ------------------------------------------------------------------------
1886 r755 | lh3 | 2009-01-06 10:23:29 -0500 (Tue, 06 Jan 2009) | 2 lines
1887 Changed paths:
1888 M /branches/prog/bwa/ChangeLog
1889 M /branches/prog/bwa/NEWS
1890 M /branches/prog/bwa/bwa.1
1891 M /branches/prog/bwa/main.c
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
1897 Changed paths:
1898 M /branches/prog/bwa/bwtaln.c
1899 M /branches/prog/bwa/bwtgap.c
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
1908 Changed paths:
1909 M /branches/prog/bwa/Makefile
1910 M /branches/prog/bwa/bwaseqio.c
1911 M /branches/prog/bwa/bwtaln.c
1912 M /branches/prog/bwa/bwtaln.h
1913 M /branches/prog/bwa/bwtgap.c
1914 M /branches/prog/bwa/main.c
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
1923 Changed paths:
1924 M /branches/prog/bwa/Makefile
1925 D /branches/prog/bwa/bwt2fmv.c
1926 M /branches/prog/bwa/bwt_gen/bwt_gen.c
1927 A /branches/prog/bwa/bwtmisc.c (from /branches/prog/bwa/pac2bwt.c:748)
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
1937 Changed paths:
1938 M /branches/prog/bwa/bwt.c
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:
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
1955 Changed paths:
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
1964 Changed paths:
1965 M /branches/prog/bwa/bwape.c
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
2068
2069 added licensing information
2070
2071 ------------------------------------------------------------------------
2072 r738 | lh3 | 2009-01-04 06:18:25 -0500 (Sun, 04 Jan 2009) | 4 lines
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
2082 ------------------------------------------------------------------------
2083 r737 | lh3 | 2009-01-03 16:00:58 -0500 (Sat, 03 Jan 2009) | 2 lines
2084 Changed paths:
2085 M /branches/prog/bwa/ChangeLog
2086 M /branches/prog/bwa/bwa.1
2087
2088 update documentation
2089
2090 ------------------------------------------------------------------------
2091 r736 | lh3 | 2009-01-02 10:26:38 -0500 (Fri, 02 Jan 2009) | 2 lines
2092 Changed paths:
2093 M /branches/prog/bwa/bwa.1
2094
2095 update documentation
2096
2097 ------------------------------------------------------------------------
2098 r735 | lh3 | 2009-01-02 07:10:20 -0500 (Fri, 02 Jan 2009) | 4 lines
2099 Changed paths:
2100 M /branches/prog/bwa/bwa.1
2101 M /branches/prog/bwa/bwape.c
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
2111 Changed paths:
2112 M /branches/prog/bwa/bwa.1
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
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
2130 Changed paths:
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
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
2149 Changed paths:
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:
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:
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:
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
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
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
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 ------------------------------------------------------------------------
3679 r309 | lh3 | 2008-05-28 11:39:37 -0400 (Wed, 28 May 2008) | 2 lines
3680 Changed paths:
3681 M /branches/prog/bwa/bwt.c
3682 M /branches/prog/bwa/bwt2fmv.c
3683
3684 fix a bug
3685
3686 ------------------------------------------------------------------------
3687 r308 | lh3 | 2008-05-28 09:56:16 -0400 (Wed, 28 May 2008) | 4 lines
3688 Changed paths:
3689 M /branches/prog/bwa/bwt.c
3690 M /branches/prog/bwa/bwt2fmv.c
3691
3692 add heuristics to improve the speed, but I have not tested whether the
3693 results are correct or not.
3694
3695
3696 ------------------------------------------------------------------------
3697 r307 | lh3 | 2008-05-28 06:31:34 -0400 (Wed, 28 May 2008) | 5 lines
3698 Changed paths:
3699 M /branches/prog/bwa/bwt.c
3700 M /branches/prog/bwa/bwt2fmv.c
3701 M /branches/prog/bwa/bwtaln.c
3702 M /branches/prog/bwa/bwtaln.h
3703 M /branches/prog/bwa/main.c
3704 M /branches/prog/bwa/main.h
3705
3706 * make ungapped alignment basically works...
3707 * but it is very slow in comparison to others...
3708 * also I need to improve the interface...
3709 * a lot of things to keep me busy today...
3710
3711 ------------------------------------------------------------------------
3712 r306 | lh3 | 2008-05-27 18:41:27 -0400 (Tue, 27 May 2008) | 3 lines
3713 Changed paths:
3714 M /branches/prog/bwa/bwt.c
3715 M /branches/prog/bwa/bwt.h
3716 M /branches/prog/bwa/bwtaln.c
3717
3718 * remove recursion
3719 * fixed a bug in bwt_occ()
3720
3721 ------------------------------------------------------------------------
3722 r305 | lh3 | 2008-05-27 16:59:44 -0400 (Tue, 27 May 2008) | 5 lines
3723 Changed paths:
3724 M /branches/prog/bwa/bwt.c
3725 M /branches/prog/bwa/bwt.h
3726 M /branches/prog/bwa/bwtaln.c
3727
3728 * bwa now tells whether a sequenced can be mapped with maximum allowed
3729 mismatches. ONLY ungapped.
3730 * this is a recursive version. I will remove recursion later.
3731
3732
3733 ------------------------------------------------------------------------
3734 r304 | lh3 | 2008-05-27 09:12:17 -0400 (Tue, 27 May 2008) | 3 lines
3735 Changed paths:
3736 M /branches/prog/bwa/Makefile
3737 M /branches/prog/bwa/bwt.c
3738 M /branches/prog/bwa/bwt.h
3739 M /branches/prog/bwa/bwt2fmv.c
3740 A /branches/prog/bwa/bwtaln.c
3741 A /branches/prog/bwa/bwtaln.h
3742 M /branches/prog/bwa/bwtio.c
3743 M /branches/prog/bwa/main.c
3744 M /branches/prog/bwa/main.h
3745 M /branches/prog/bwa/utils.c
3746
3747 * load .sa and .fmv files
3748 * exact alignment now works
3749
3750 ------------------------------------------------------------------------
3751 r303 | lh3 | 2008-05-27 06:33:38 -0400 (Tue, 27 May 2008) | 2 lines
3752 Changed paths:
3753 M /branches/prog/bwa/bntseq.c
3754 M /branches/prog/bwa/bwt.c
3755 M /branches/prog/bwa/bwtio.c
3756 M /branches/prog/bwa/utils.c
3757 M /branches/prog/bwa/utils.h
3758
3759 add xassert and fix a bug
3760
3761 ------------------------------------------------------------------------
3762 r302 | lh3 | 2008-05-27 06:23:20 -0400 (Tue, 27 May 2008) | 2 lines
3763 Changed paths:
3764 M /branches/prog/bwa/Makefile
3765 M /branches/prog/bwa/bntseq.c
3766 M /branches/prog/bwa/bwt.c
3767 M /branches/prog/bwa/bwtio.c
3768 A /branches/prog/bwa/utils.c
3769 A /branches/prog/bwa/utils.h
3770
3771 improve error message and error handling
3772
3773 ------------------------------------------------------------------------
3774 r301 | lh3 | 2008-05-27 05:37:51 -0400 (Tue, 27 May 2008) | 4 lines
3775 Changed paths:
3776 M /branches/prog/bwa/Makefile
3777 M /branches/prog/bwa/bwt.c
3778 M /branches/prog/bwa/bwt.h
3779 M /branches/prog/bwa/bwt2fmv.c
3780 A /branches/prog/bwa/bwtio.c
3781 M /branches/prog/bwa/main.c
3782 M /branches/prog/bwa/main.h
3783
3784 * move I/O codes to bwtio.c
3785 * SA can be dumped and interestingly, it is identical to BWTSW
3786 * now, .fmv is still different from BWTSW
3787
3788 ------------------------------------------------------------------------
3789 r299 | lh3 | 2008-05-26 18:07:44 -0400 (Mon, 26 May 2008) | 2 lines
3790 Changed paths:
3791 M /branches/prog/bwa/Makefile
3792 M /branches/prog/bwa/bwt.c
3793 M /branches/prog/bwa/bwt.h
3794 M /branches/prog/bwa/bwt2fmv.c
3795
3796 generate/retrieve SA and Occ
3797
3798 ------------------------------------------------------------------------
3799 r298 | lh3 | 2008-05-26 13:16:49 -0400 (Mon, 26 May 2008) | 3 lines
3800 Changed paths:
3801 M /branches/prog/bwa/bntseq.h
3802 M /branches/prog/bwa/bwt.c
3803 M /branches/prog/bwa/bwt.h
3804 M /branches/prog/bwa/bwt2fmv.c
3805
3806 * retrieve occ value at any position
3807 * move bwt_cal_occ() to bwt.c
3808
3809 ------------------------------------------------------------------------
3810 r297 | lh3 | 2008-05-25 17:43:58 -0400 (Sun, 25 May 2008) | 6 lines
3811 Changed paths:
3812 M /branches/prog/bwa/Makefile
3813 A /branches/prog/bwa/bwt.c
3814 A /branches/prog/bwa/bwt.h
3815 A /branches/prog/bwa/bwt2fmv.c
3816 M /branches/prog/bwa/main.c
3817 M /branches/prog/bwa/main.h
3818 M /branches/prog/bwa/pac2bwt.c
3819
3820 * add bwt2fmv. It works to some extend. However, I do not understand
3821 the purpose of some weird codes in BWT-SW. As a consequence, bwt2fmv
3822 could generate a file almost identical, but not exactly identical, to
3823 the .fmv file from BWT-SW.
3824
3825
3826 ------------------------------------------------------------------------
3827 r296 | lh3 | 2008-05-24 18:35:02 -0400 (Sat, 24 May 2008) | 5 lines
3828 Changed paths:
3829 M /branches/prog/bwa/Makefile
3830 M /branches/prog/bwa/bntseq.c
3831 M /branches/prog/bwa/bntseq.h
3832 M /branches/prog/bwa/main.c
3833 M /branches/prog/bwa/main.h
3834 A /branches/prog/bwa/pac2bwt.c
3835
3836 Burrows-Wheeler Transform now works. At least on one example, the
3837 current code generates the same BWT as BWT-SW. Kind of magical, I would
3838 say. :)
3839
3840
3841 ------------------------------------------------------------------------
3842 r295 | lh3 | 2008-05-24 11:25:31 -0400 (Sat, 24 May 2008) | 3 lines
3843 Changed paths:
3844 A /branches/prog/bwa/Makefile
3845 M /branches/prog/bwa/bntseq.c
3846 A /branches/prog/bwa/main.c
3847 A /branches/prog/bwa/main.h
3848
3849 * add Makefile and main.*
3850 * improve interface to fa2bns, a bit
3851
3852 ------------------------------------------------------------------------
3853 r293 | lh3 | 2008-05-24 10:57:03 -0400 (Sat, 24 May 2008) | 3 lines
3854 Changed paths:
3855 A /branches/prog/bwa
3856 A /branches/prog/bwa/bntseq.c
3857 A /branches/prog/bwa/bntseq.h
3858 A /branches/prog/bwa/seq.c
3859 A /branches/prog/bwa/seq.h
3860
3861 * Burrow-Wheeler Alignment
3862 * initial codes
3863
3864 ------------------------------------------------------------------------