1------------------------------------------------------------------------
2r1605 | lh3 | 2010-12-29 20:20:20 -0500 (Wed, 29 Dec 2010) | 3 lines
3Changed 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------------------------------------------------------------------------
11r1587 | lh3 | 2010-12-21 18:48:30 -0500 (Tue, 21 Dec 2010) | 2 lines
12Changed paths:
13   M /branches/prog/bwa/bwa.1
14
15a typo in the manual
16
17------------------------------------------------------------------------
18r1586 | lh3 | 2010-12-21 18:47:48 -0500 (Tue, 21 Dec 2010) | 3 lines
19Changed 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------------------------------------------------------------------------
32r1562 | lh3 | 2010-12-10 01:02:06 -0500 (Fri, 10 Dec 2010) | 2 lines
33Changed paths:
34   M /branches/prog/bwa/bwa.1
35   M /branches/prog/bwa/bwape.c
36   M /branches/prog/bwa/bwase.c
37
38documentation on specifying @RG
39
40------------------------------------------------------------------------
41r1561 | lh3 | 2010-12-10 00:45:40 -0500 (Fri, 10 Dec 2010) | 2 lines
42Changed 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
48Release bwa-0.5.9rc1 (r1561)
49
50------------------------------------------------------------------------
51r1560 | lh3 | 2010-12-10 00:29:08 -0500 (Fri, 10 Dec 2010) | 3 lines
52Changed 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------------------------------------------------------------------------
60r1559 | lh3 | 2010-12-10 00:10:48 -0500 (Fri, 10 Dec 2010) | 2 lines
61Changed paths:
62   M /branches/prog/bwa/ChangeLog
63   M /branches/prog/bwa/Makefile
64
65change Makefile gcc options
66
67------------------------------------------------------------------------
68r1558 | lh3 | 2010-12-10 00:09:22 -0500 (Fri, 10 Dec 2010) | 4 lines
69Changed 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------------------------------------------------------------------------
79r1557 | lh3 | 2010-12-09 21:58:00 -0500 (Thu, 09 Dec 2010) | 2 lines
80Changed paths:
81   M /branches/prog/bwa/Makefile
82   M /branches/prog/bwa/bwtsw2_aux.c
83
84sometimes unmapped reads may not be printed...
85
86------------------------------------------------------------------------
87r1556 | lh3 | 2010-12-09 21:50:26 -0500 (Thu, 09 Dec 2010) | 2 lines
88Changed paths:
89   M /branches/prog/bwa/Makefile
90   M /branches/prog/bwa/bwtsw2_aux.c
91
92print unmapped reads
93
94------------------------------------------------------------------------
95r1555 | lh3 | 2010-12-09 21:17:20 -0500 (Thu, 09 Dec 2010) | 3 lines
96Changed 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------------------------------------------------------------------------
106r1544 | lh3 | 2010-11-23 11:01:41 -0500 (Tue, 23 Nov 2010) | 3 lines
107Changed 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------------------------------------------------------------------------
116r1543 | lh3 | 2010-11-23 00:16:40 -0500 (Tue, 23 Nov 2010) | 3 lines
117Changed 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------------------------------------------------------------------------
125r1542 | lh3 | 2010-11-22 23:50:56 -0500 (Mon, 22 Nov 2010) | 3 lines
126Changed 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------------------------------------------------------------------------
134r1541 | lh3 | 2010-11-22 23:27:29 -0500 (Mon, 22 Nov 2010) | 2 lines
135Changed 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
146preliminary BAM input support
147
148------------------------------------------------------------------------
149r1537 | lh3 | 2010-10-16 23:46:20 -0400 (Sat, 16 Oct 2010) | 2 lines
150Changed paths:
151   M /branches/prog/bwa/ChangeLog
152   M /branches/prog/bwa/bwa.1
153
154change version number and ChangeLog
155
156------------------------------------------------------------------------
157r1536 | lh3 | 2010-10-16 23:35:10 -0400 (Sat, 16 Oct 2010) | 3 lines
158Changed 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------------------------------------------------------------------------
167r1451 | lh3 | 2010-06-15 09:43:52 -0400 (Tue, 15 Jun 2010) | 2 lines
168Changed paths:
169   M /branches/prog/bwa/bwa.1
170
171version change
172
173------------------------------------------------------------------------
174r1450 | lh3 | 2010-06-15 09:42:21 -0400 (Tue, 15 Jun 2010) | 3 lines
175Changed 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------------------------------------------------------------------------
183r1445 | lh3 | 2010-06-11 08:58:33 -0400 (Fri, 11 Jun 2010) | 2 lines
184Changed paths:
185   M /branches/prog/bwa/bwa.1
186   M /branches/prog/bwa/bwape.c
187
188fixed a serious bug
189
190------------------------------------------------------------------------
191r1442 | lh3 | 2010-06-08 10:22:14 -0400 (Tue, 08 Jun 2010) | 2 lines
192Changed paths:
193   M /branches/prog/bwa/ChangeLog
194   M /branches/prog/bwa/NEWS
195   M /branches/prog/bwa/main.c
196
197Release bwa-0.5.8 (r1442)
198
199------------------------------------------------------------------------
200r1440 | lh3 | 2010-05-19 13:43:50 -0400 (Wed, 19 May 2010) | 3 lines
201Changed 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------------------------------------------------------------------------
209r1439 | lh3 | 2010-05-19 13:43:08 -0400 (Wed, 19 May 2010) | 4 lines
210Changed 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------------------------------------------------------------------------
220r1425 | lh3 | 2010-04-29 15:15:23 -0400 (Thu, 29 Apr 2010) | 10 lines
221Changed 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------------------------------------------------------------------------
237r1399 | lh3 | 2010-04-16 09:20:49 -0400 (Fri, 16 Apr 2010) | 3 lines
238Changed 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------------------------------------------------------------------------
247r1329 | lh3 | 2010-03-19 23:32:46 -0400 (Fri, 19 Mar 2010) | 2 lines
248Changed paths:
249   M /branches/prog/bwa/bwape.c
250   M /branches/prog/bwa/main.c
251
252small correction
253
254------------------------------------------------------------------------
255r1328 | lh3 | 2010-03-19 23:28:44 -0400 (Fri, 19 Mar 2010) | 3 lines
256Changed 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------------------------------------------------------------------------
264r1327 | lh3 | 2010-03-19 23:02:40 -0400 (Fri, 19 Mar 2010) | 3 lines
265Changed 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------------------------------------------------------------------------
275r1320 | lh3 | 2010-03-17 15:13:22 -0400 (Wed, 17 Mar 2010) | 2 lines
276Changed paths:
277   M /branches/prog/bwa/bwape.c
278
279fixed a potential out-of-boundary error. Need more testing.
280
281------------------------------------------------------------------------
282r1319 | lh3 | 2010-03-14 22:44:46 -0400 (Sun, 14 Mar 2010) | 2 lines
283Changed paths:
284   M /branches/prog/bwa/bwape.c
285
286insert size is `weird' if the 3rd quatile larger than 100,000bp
287
288------------------------------------------------------------------------
289r1318 | lh3 | 2010-03-14 22:37:35 -0400 (Sun, 14 Mar 2010) | 3 lines
290Changed 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------------------------------------------------------------------------
299r1317 | lh3 | 2010-03-14 22:14:14 -0400 (Sun, 14 Mar 2010) | 5 lines
300Changed 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------------------------------------------------------------------------
312r1310 | lh3 | 2010-03-01 10:35:45 -0500 (Mon, 01 Mar 2010) | 2 lines
313Changed paths:
314   M /branches/prog/bwa/ChangeLog
315   M /branches/prog/bwa/NEWS
316   M /branches/prog/bwa/main.c
317
318Release bwa-0.5.7
319
320------------------------------------------------------------------------
321r1309 | lh3 | 2010-02-26 21:42:22 -0500 (Fri, 26 Feb 2010) | 4 lines
322Changed 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------------------------------------------------------------------------
332r1305 | lh3 | 2010-02-25 13:47:58 -0500 (Thu, 25 Feb 2010) | 3 lines
333Changed 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------------------------------------------------------------------------
344r1303 | lh3 | 2010-02-10 23:43:48 -0500 (Wed, 10 Feb 2010) | 2 lines
345Changed 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
352Release bwa-0.5.6
353
354------------------------------------------------------------------------
355r1302 | lh3 | 2010-02-10 11:11:49 -0500 (Wed, 10 Feb 2010) | 3 lines
356Changed 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------------------------------------------------------------------------
367r1301 | lh3 | 2010-02-09 16:15:28 -0500 (Tue, 09 Feb 2010) | 5 lines
368Changed 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------------------------------------------------------------------------
379r1300 | lh3 | 2010-02-09 12:50:02 -0500 (Tue, 09 Feb 2010) | 3 lines
380Changed 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------------------------------------------------------------------------
388r1299 | lh3 | 2010-02-09 12:33:34 -0500 (Tue, 09 Feb 2010) | 5 lines
389Changed 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------------------------------------------------------------------------
399r1298 | lh3 | 2010-02-08 12:40:31 -0500 (Mon, 08 Feb 2010) | 3 lines
400Changed 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------------------------------------------------------------------------
413r1297 | lh3 | 2010-02-05 22:26:11 -0500 (Fri, 05 Feb 2010) | 2 lines
414Changed paths:
415   M /branches/prog/bwa/solid2fastq.pl
416
417the old fix seems not working!
418
419------------------------------------------------------------------------
420r1296 | lh3 | 2010-02-05 21:51:03 -0500 (Fri, 05 Feb 2010) | 3 lines
421Changed 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------------------------------------------------------------------------
430r1295 | lh3 | 2010-02-05 21:01:10 -0500 (Fri, 05 Feb 2010) | 5 lines
431Changed 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------------------------------------------------------------------------
443r1294 | lh3 | 2010-02-05 17:24:06 -0500 (Fri, 05 Feb 2010) | 3 lines
444Changed 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------------------------------------------------------------------------
455r1293 | lh3 | 2010-02-05 12:57:38 -0500 (Fri, 05 Feb 2010) | 5 lines
456Changed 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------------------------------------------------------------------------
469r1279 | lh3 | 2009-11-23 22:42:34 -0500 (Mon, 23 Nov 2009) | 3 lines
470Changed 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------------------------------------------------------------------------
484r1275 | lh3 | 2009-11-10 22:13:10 -0500 (Tue, 10 Nov 2009) | 2 lines
485Changed paths:
486   M /branches/prog/bwa/ChangeLog
487
488update ChangeLog
489
490------------------------------------------------------------------------
491r1273 | lh3 | 2009-11-10 22:08:16 -0500 (Tue, 10 Nov 2009) | 2 lines
492Changed 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
498Release bwa-0.5.5 (r1273)
499
500------------------------------------------------------------------------
501r1272 | lh3 | 2009-11-10 22:02:50 -0500 (Tue, 10 Nov 2009) | 3 lines
502Changed 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------------------------------------------------------------------------
510r1271 | lh3 | 2009-11-10 21:59:47 -0500 (Tue, 10 Nov 2009) | 4 lines
511Changed 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------------------------------------------------------------------------
520r1270 | lh3 | 2009-11-09 23:12:42 -0500 (Mon, 09 Nov 2009) | 3 lines
521Changed 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------------------------------------------------------------------------
529r1245 | lh3 | 2009-10-09 07:42:52 -0400 (Fri, 09 Oct 2009) | 2 lines
530Changed 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
539Release bwa-0.5.4
540
541------------------------------------------------------------------------
542r1244 | lh3 | 2009-10-09 05:53:52 -0400 (Fri, 09 Oct 2009) | 5 lines
543Changed 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------------------------------------------------------------------------
558r1243 | lh3 | 2009-10-07 08:15:04 -0400 (Wed, 07 Oct 2009) | 3 lines
559Changed 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------------------------------------------------------------------------
567r1242 | lh3 | 2009-10-07 07:49:13 -0400 (Wed, 07 Oct 2009) | 4 lines
568Changed 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------------------------------------------------------------------------
580r1238 | lh3 | 2009-09-26 18:38:15 -0400 (Sat, 26 Sep 2009) | 2 lines
581Changed paths:
582   M /branches/prog/bwa/khash.h
583
584Improve portability of khash.h
585
586------------------------------------------------------------------------
587r1228 | lh3 | 2009-09-15 09:20:22 -0400 (Tue, 15 Sep 2009) | 2 lines
588Changed paths:
589   M /branches/prog/bwa/main.c
590
591fixed a typo
592
593------------------------------------------------------------------------
594r1227 | lh3 | 2009-09-15 09:19:35 -0400 (Tue, 15 Sep 2009) | 3 lines
595Changed 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------------------------------------------------------------------------
605r1225 | lh3 | 2009-09-15 08:32:30 -0400 (Tue, 15 Sep 2009) | 2 lines
606Changed paths:
607   M /branches/prog/bwa/NEWS
608   M /branches/prog/bwa/bwase.c
609   M /branches/prog/bwa/main.c
610
611Release bwa-0.5.3 (r1225)
612
613------------------------------------------------------------------------
614r1223 | lh3 | 2009-09-13 07:30:41 -0400 (Sun, 13 Sep 2009) | 2 lines
615Changed 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
621Release bwa-0.5.2
622
623------------------------------------------------------------------------
624r1222 | lh3 | 2009-09-11 09:11:39 -0400 (Fri, 11 Sep 2009) | 3 lines
625Changed 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------------------------------------------------------------------------
633r1221 | lh3 | 2009-09-11 09:09:44 -0400 (Fri, 11 Sep 2009) | 3 lines
634Changed 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------------------------------------------------------------------------
647r1216 | lh3 | 2009-09-08 17:50:15 -0400 (Tue, 08 Sep 2009) | 4 lines
648Changed 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------------------------------------------------------------------------
659r1215 | lh3 | 2009-09-08 17:14:42 -0400 (Tue, 08 Sep 2009) | 3 lines
660Changed 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------------------------------------------------------------------------
668r1213 | lh3 | 2009-09-06 18:58:15 -0400 (Sun, 06 Sep 2009) | 3 lines
669Changed 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------------------------------------------------------------------------
677r1209 | lh3 | 2009-09-02 06:06:02 -0400 (Wed, 02 Sep 2009) | 2 lines
678Changed paths:
679   M /branches/prog/bwa/NEWS
680   M /branches/prog/bwa/bwa.1
681   M /branches/prog/bwa/main.c
682
683Release bwa-0.5.1
684
685------------------------------------------------------------------------
686r1208 | lh3 | 2009-09-02 05:56:33 -0400 (Wed, 02 Sep 2009) | 2 lines
687Changed paths:
688   M /branches/prog/bwa/ChangeLog
689
690 * ChangeLog
691
692------------------------------------------------------------------------
693r1206 | lh3 | 2009-08-30 18:27:30 -0400 (Sun, 30 Aug 2009) | 3 lines
694Changed 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------------------------------------------------------------------------
702r1205 | lh3 | 2009-08-30 17:28:36 -0400 (Sun, 30 Aug 2009) | 4 lines
703Changed 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------------------------------------------------------------------------
713r1204 | lh3 | 2009-08-30 06:06:16 -0400 (Sun, 30 Aug 2009) | 3 lines
714Changed 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------------------------------------------------------------------------
723r1203 | lh3 | 2009-08-29 18:11:51 -0400 (Sat, 29 Aug 2009) | 4 lines
724Changed 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------------------------------------------------------------------------
734r1202 | lh3 | 2009-08-28 19:48:41 -0400 (Fri, 28 Aug 2009) | 4 lines
735Changed 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------------------------------------------------------------------------
744r1200 | lh3 | 2009-08-20 06:21:24 -0400 (Thu, 20 Aug 2009) | 2 lines
745Changed paths:
746   M /branches/prog/bwa/NEWS
747   M /branches/prog/bwa/main.c
748
749Release bwa-0.5.0 (r1200)
750
751------------------------------------------------------------------------
752r1199 | lh3 | 2009-08-20 04:49:15 -0400 (Thu, 20 Aug 2009) | 2 lines
753Changed paths:
754   M /branches/prog/bwa/ChangeLog
755   M /branches/prog/bwa/bwa.1
756
757Updated ChangeLog and the manual
758
759------------------------------------------------------------------------
760r1198 | lh3 | 2009-08-19 11:09:15 -0400 (Wed, 19 Aug 2009) | 3 lines
761Changed 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------------------------------------------------------------------------
770r1197 | lh3 | 2009-08-19 08:15:05 -0400 (Wed, 19 Aug 2009) | 3 lines
771Changed 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------------------------------------------------------------------------
781r1196 | lh3 | 2009-08-18 06:54:03 -0400 (Tue, 18 Aug 2009) | 4 lines
782Changed 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------------------------------------------------------------------------
792r1195 | lh3 | 2009-08-18 06:23:00 -0400 (Tue, 18 Aug 2009) | 4 lines
793Changed 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------------------------------------------------------------------------
804r1192 | lh3 | 2009-08-13 05:37:28 -0400 (Thu, 13 Aug 2009) | 2 lines
805Changed paths:
806   M /branches/prog/bwa/bwa.1
807
808update manual
809
810------------------------------------------------------------------------
811r1191 | lh3 | 2009-08-12 19:40:51 -0400 (Wed, 12 Aug 2009) | 2 lines
812Changed paths:
813   M /branches/prog/bwa/bwa.1
814   M /branches/prog/bwa/bwtsw2_main.c
815
816update documentation
817
818------------------------------------------------------------------------
819r1190 | lh3 | 2009-08-12 08:56:10 -0400 (Wed, 12 Aug 2009) | 3 lines
820Changed 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------------------------------------------------------------------------
828r1189 | lh3 | 2009-08-11 09:28:55 -0400 (Tue, 11 Aug 2009) | 4 lines
829Changed 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------------------------------------------------------------------------
841r1181 | lh3 | 2009-08-03 12:09:41 -0400 (Mon, 03 Aug 2009) | 2 lines
842Changed paths:
843   M /branches/prog/bwa/bwtsw2_aux.c
844
845fflush()
846
847------------------------------------------------------------------------
848r1180 | lh3 | 2009-08-03 12:08:46 -0400 (Mon, 03 Aug 2009) | 4 lines
849Changed 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------------------------------------------------------------------------
858r1179 | lh3 | 2009-08-03 11:04:39 -0400 (Mon, 03 Aug 2009) | 3 lines
859Changed 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------------------------------------------------------------------------
870r1178 | lh3 | 2009-08-03 09:14:54 -0400 (Mon, 03 Aug 2009) | 3 lines
871Changed 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------------------------------------------------------------------------
880r1177 | lh3 | 2009-08-03 05:03:42 -0400 (Mon, 03 Aug 2009) | 3 lines
881Changed 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------------------------------------------------------------------------
889r1176 | lh3 | 2009-07-31 10:58:24 -0400 (Fri, 31 Jul 2009) | 3 lines
890Changed 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------------------------------------------------------------------------
899r1175 | lh3 | 2009-07-31 09:15:54 -0400 (Fri, 31 Jul 2009) | 4 lines
900Changed 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------------------------------------------------------------------------
912r1174 | lh3 | 2009-07-30 08:50:25 -0400 (Thu, 30 Jul 2009) | 3 lines
913Changed 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------------------------------------------------------------------------
921r1173 | lh3 | 2009-07-29 18:32:43 -0400 (Wed, 29 Jul 2009) | 4 lines
922Changed 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------------------------------------------------------------------------
933r1172 | lh3 | 2009-07-29 17:22:39 -0400 (Wed, 29 Jul 2009) | 3 lines
934Changed 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------------------------------------------------------------------------
943r1171 | lh3 | 2009-07-29 17:12:02 -0400 (Wed, 29 Jul 2009) | 3 lines
944Changed 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------------------------------------------------------------------------
954r1170 | lh3 | 2009-07-29 15:25:14 -0400 (Wed, 29 Jul 2009) | 2 lines
955Changed paths:
956   M /branches/prog/bwa/bwtsw2_core.c
957   M /branches/prog/bwa/main.c
958
959save hits before cut_tail()
960
961------------------------------------------------------------------------
962r1169 | lh3 | 2009-07-29 08:06:01 -0400 (Wed, 29 Jul 2009) | 3 lines
963Changed 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------------------------------------------------------------------------
975r1168 | lh3 | 2009-07-29 06:13:29 -0400 (Wed, 29 Jul 2009) | 5 lines
976Changed 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------------------------------------------------------------------------
989r1167 | lh3 | 2009-07-28 19:06:17 -0400 (Tue, 28 Jul 2009) | 3 lines
990Changed 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------------------------------------------------------------------------
998r1166 | lh3 | 2009-07-28 16:31:41 -0400 (Tue, 28 Jul 2009) | 5 lines
999Changed 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------------------------------------------------------------------------
1012r1165 | lh3 | 2009-07-28 10:15:40 -0400 (Tue, 28 Jul 2009) | 4 lines
1013Changed 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------------------------------------------------------------------------
1024r1164 | lh3 | 2009-07-28 09:04:14 -0400 (Tue, 28 Jul 2009) | 11 lines
1025Changed 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------------------------------------------------------------------------
1045r1163 | lh3 | 2009-07-27 17:41:10 -0400 (Mon, 27 Jul 2009) | 2 lines
1046Changed paths:
1047   M /branches/prog/bwa/bwtsw2_aux.c
1048
1049change a default parameter
1050
1051------------------------------------------------------------------------
1052r1162 | lh3 | 2009-07-27 17:04:35 -0400 (Mon, 27 Jul 2009) | 3 lines
1053Changed 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------------------------------------------------------------------------
1064r1161 | lh3 | 2009-07-27 12:17:41 -0400 (Mon, 27 Jul 2009) | 4 lines
1065Changed 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------------------------------------------------------------------------
1075r1160 | lh3 | 2009-07-27 07:50:57 -0400 (Mon, 27 Jul 2009) | 6 lines
1076Changed 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------------------------------------------------------------------------
1089r1159 | lh3 | 2009-07-27 04:37:02 -0400 (Mon, 27 Jul 2009) | 4 lines
1090Changed 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------------------------------------------------------------------------
1101r1158 | lh3 | 2009-07-24 09:36:52 -0400 (Fri, 24 Jul 2009) | 2 lines
1102Changed paths:
1103   M /branches/prog/bwa/main.c
1104
1105nothing, really
1106
1107------------------------------------------------------------------------
1108r1157 | lh3 | 2009-07-24 09:05:44 -0400 (Fri, 24 Jul 2009) | 3 lines
1109Changed 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------------------------------------------------------------------------
1118r1156 | lh3 | 2009-07-24 05:42:47 -0400 (Fri, 24 Jul 2009) | 6 lines
1119Changed 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------------------------------------------------------------------------
1130r1155 | lh3 | 2009-07-24 05:28:40 -0400 (Fri, 24 Jul 2009) | 8 lines
1131Changed 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------------------------------------------------------------------------
1145r1154 | lh3 | 2009-07-23 17:40:20 -0400 (Thu, 23 Jul 2009) | 3 lines
1146Changed 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------------------------------------------------------------------------
1154r1153 | lh3 | 2009-07-23 17:06:09 -0400 (Thu, 23 Jul 2009) | 2 lines
1155Changed paths:
1156   M /branches/prog/bwa/stdaln.c
1157
1158removed debugging code...
1159
1160------------------------------------------------------------------------
1161r1152 | lh3 | 2009-07-23 17:01:00 -0400 (Thu, 23 Jul 2009) | 3 lines
1162Changed paths:
1163   M /branches/prog/bwa/stdaln.c
1164
1165 * radical changes failed...
1166 * fixed a bug
1167
1168------------------------------------------------------------------------
1169r1151 | lh3 | 2009-07-23 14:46:35 -0400 (Thu, 23 Jul 2009) | 2 lines
1170Changed paths:
1171   M /branches/prog/bwa/stdaln.c
1172
1173temporary changes. Will apply some radical changes to this file...
1174
1175------------------------------------------------------------------------
1176r1150 | lh3 | 2009-07-23 10:09:56 -0400 (Thu, 23 Jul 2009) | 2 lines
1177Changed 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
1182fixed a long-existing bug in Smith-Waterman alignment
1183
1184------------------------------------------------------------------------
1185r1149 | lh3 | 2009-07-23 08:50:52 -0400 (Thu, 23 Jul 2009) | 3 lines
1186Changed 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------------------------------------------------------------------------
1199r1148 | lh3 | 2009-07-23 08:07:29 -0400 (Thu, 23 Jul 2009) | 2 lines
1200Changed paths:
1201   M /branches/prog/bwa/stdaln.c
1202
1203half DP
1204
1205------------------------------------------------------------------------
1206r1147 | lh3 | 2009-07-22 08:03:06 -0400 (Wed, 22 Jul 2009) | 2 lines
1207Changed 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
1213a bit code clean up
1214
1215------------------------------------------------------------------------
1216r1145 | lh3 | 2009-07-21 15:52:05 -0400 (Tue, 21 Jul 2009) | 4 lines
1217Changed 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------------------------------------------------------------------------
1227r1144 | lh3 | 2009-07-21 10:17:29 -0400 (Tue, 21 Jul 2009) | 4 lines
1228Changed 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------------------------------------------------------------------------
1240r1143 | lh3 | 2009-07-20 16:38:18 -0400 (Mon, 20 Jul 2009) | 3 lines
1241Changed 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
1248bwtsw2 (dBWT-SW) is working apparently...
1249
1250
1251------------------------------------------------------------------------
1252r1139 | lh3 | 2009-07-15 05:52:18 -0400 (Wed, 15 Jul 2009) | 4 lines
1253Changed 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------------------------------------------------------------------------
1262r1138 | lh3 | 2009-07-15 05:18:42 -0400 (Wed, 15 Jul 2009) | 3 lines
1263Changed 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------------------------------------------------------------------------
1278r1075 | lh3 | 2009-05-19 05:14:50 -0400 (Tue, 19 May 2009) | 2 lines
1279Changed paths:
1280   M /branches/prog/bwa/NEWS
1281   M /branches/prog/bwa/bwase.c
1282   M /branches/prog/bwa/main.c
1283
1284Release bwa-0.4.9
1285
1286------------------------------------------------------------------------
1287r1073 | lh3 | 2009-05-18 17:13:19 -0400 (Mon, 18 May 2009) | 2 lines
1288Changed paths:
1289   M /branches/prog/bwa/NEWS
1290   M /branches/prog/bwa/bwa.1
1291   M /branches/prog/bwa/main.c
1292
1293Release bwa-0.4.8
1294
1295------------------------------------------------------------------------
1296r1069 | lh3 | 2009-05-14 09:54:54 -0400 (Thu, 14 May 2009) | 3 lines
1297Changed 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------------------------------------------------------------------------
1305r1068 | lh3 | 2009-05-14 09:27:55 -0400 (Thu, 14 May 2009) | 3 lines
1306Changed 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------------------------------------------------------------------------
1318r1066 | lh3 | 2009-05-12 15:31:31 -0400 (Tue, 12 May 2009) | 2 lines
1319Changed 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
1325Release bwa-0.4.7
1326
1327------------------------------------------------------------------------
1328r1065 | lh3 | 2009-05-12 15:20:40 -0400 (Tue, 12 May 2009) | 3 lines
1329Changed 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------------------------------------------------------------------------
1338r1064 | lh3 | 2009-05-12 07:30:46 -0400 (Tue, 12 May 2009) | 3 lines
1339Changed 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------------------------------------------------------------------------
1347r1035 | lh3 | 2009-05-09 05:41:33 -0400 (Sat, 09 May 2009) | 4 lines
1348Changed 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------------------------------------------------------------------------
1358r1008 | lh3 | 2009-04-29 05:41:58 -0400 (Wed, 29 Apr 2009) | 4 lines
1359Changed 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------------------------------------------------------------------------
1368r1005 | lh3 | 2009-04-27 07:37:23 -0400 (Mon, 27 Apr 2009) | 4 lines
1369Changed 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------------------------------------------------------------------------
1381r1003 | lh3 | 2009-04-26 12:48:19 -0400 (Sun, 26 Apr 2009) | 4 lines
1382Changed 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------------------------------------------------------------------------
1393r1002 | lh3 | 2009-04-22 03:56:15 -0400 (Wed, 22 Apr 2009) | 3 lines
1394Changed 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------------------------------------------------------------------------
1405r914 | lh3 | 2009-03-09 17:53:50 -0400 (Mon, 09 Mar 2009) | 2 lines
1406Changed paths:
1407   M /branches/prog/bwa/ChangeLog
1408   M /branches/prog/bwa/NEWS
1409   M /branches/prog/bwa/main.c
1410
1411Release bwa-0.4.6
1412
1413------------------------------------------------------------------------
1414r913 | lh3 | 2009-03-09 17:23:24 -0400 (Mon, 09 Mar 2009) | 4 lines
1415Changed 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------------------------------------------------------------------------
1425r912 | lh3 | 2009-03-09 16:57:05 -0400 (Mon, 09 Mar 2009) | 2 lines
1426Changed paths:
1427   M /branches/prog/bwa/ChangeLog
1428   M /branches/prog/bwa/kstring.c
1429   M /branches/prog/bwa/main.c
1430
1431fixed a bug in kstring
1432
1433------------------------------------------------------------------------
1434r881 | lh3 | 2009-03-02 15:36:06 -0500 (Mon, 02 Mar 2009) | 3 lines
1435Changed 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------------------------------------------------------------------------
1443r880 | lh3 | 2009-03-01 16:34:08 -0500 (Sun, 01 Mar 2009) | 2 lines
1444Changed paths:
1445   M /branches/prog/bwa/Makefile
1446
1447disable debugging
1448
1449------------------------------------------------------------------------
1450r879 | lh3 | 2009-03-01 16:28:04 -0500 (Sun, 01 Mar 2009) | 3 lines
1451Changed 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------------------------------------------------------------------------
1460r878 | lh3 | 2009-03-01 13:43:09 -0500 (Sun, 01 Mar 2009) | 3 lines
1461Changed 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------------------------------------------------------------------------
1470r877 | lh3 | 2009-03-01 10:27:52 -0500 (Sun, 01 Mar 2009) | 2 lines
1471Changed 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------------------------------------------------------------------------
1482r860 | lh3 | 2009-02-27 08:58:39 -0500 (Fri, 27 Feb 2009) | 2 lines
1483Changed paths:
1484   M /branches/prog/bwa/Makefile
1485   M /branches/prog/bwa/bwase.c
1486   A /branches/prog/bwa/cs2nt.c
1487
1488prepare to implement cs->nt conversion (have not yet...)
1489
1490------------------------------------------------------------------------
1491r859 | lh3 | 2009-02-27 07:00:03 -0500 (Fri, 27 Feb 2009) | 3 lines
1492Changed 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------------------------------------------------------------------------
1504r857 | lh3 | 2009-02-26 10:22:58 -0500 (Thu, 26 Feb 2009) | 4 lines
1505Changed 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------------------------------------------------------------------------
1514r856 | lh3 | 2009-02-26 10:02:29 -0500 (Thu, 26 Feb 2009) | 3 lines
1515Changed 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------------------------------------------------------------------------
1524r828 | lh3 | 2009-02-18 17:36:41 -0500 (Wed, 18 Feb 2009) | 2 lines
1525Changed 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
1531Release bwa-0.4.5
1532
1533------------------------------------------------------------------------
1534r827 | lh3 | 2009-02-18 16:48:48 -0500 (Wed, 18 Feb 2009) | 3 lines
1535Changed 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------------------------------------------------------------------------
1544r824 | lh3 | 2009-02-17 05:33:07 -0500 (Tue, 17 Feb 2009) | 3 lines
1545Changed 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------------------------------------------------------------------------
1553r823 | lh3 | 2009-02-17 04:54:18 -0500 (Tue, 17 Feb 2009) | 2 lines
1554Changed paths:
1555   M /branches/prog/bwa/ChangeLog
1556   M /branches/prog/bwa/bwape.c
1557
1558just change some logging information
1559
1560------------------------------------------------------------------------
1561r822 | lh3 | 2009-02-17 04:20:39 -0500 (Tue, 17 Feb 2009) | 2 lines
1562Changed paths:
1563   M /branches/prog/bwa/bwa.1
1564
1565update manual
1566
1567------------------------------------------------------------------------
1568r821 | lh3 | 2009-02-17 04:11:14 -0500 (Tue, 17 Feb 2009) | 3 lines
1569Changed 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------------------------------------------------------------------------
1578r820 | lh3 | 2009-02-16 17:43:37 -0500 (Mon, 16 Feb 2009) | 3 lines
1579Changed 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------------------------------------------------------------------------
1587r819 | lh3 | 2009-02-16 17:40:28 -0500 (Mon, 16 Feb 2009) | 4 lines
1588Changed 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------------------------------------------------------------------------
1597r818 | lh3 | 2009-02-16 09:30:51 -0500 (Mon, 16 Feb 2009) | 2 lines
1598Changed paths:
1599   M /branches/prog/bwa/bwa.1
1600
1601update benchmark
1602
1603------------------------------------------------------------------------
1604r817 | lh3 | 2009-02-16 08:44:40 -0500 (Mon, 16 Feb 2009) | 4 lines
1605Changed 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------------------------------------------------------------------------
1616r814 | lh3 | 2009-02-15 11:10:23 -0500 (Sun, 15 Feb 2009) | 2 lines
1617Changed paths:
1618   M /branches/prog/bwa/ChangeLog
1619   M /branches/prog/bwa/NEWS
1620   M /branches/prog/bwa/main.c
1621
1622Release bwa-0.4.4
1623
1624------------------------------------------------------------------------
1625r813 | lh3 | 2009-02-15 10:22:50 -0500 (Sun, 15 Feb 2009) | 3 lines
1626Changed 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------------------------------------------------------------------------
1635r811 | lh3 | 2009-02-14 09:46:13 -0500 (Sat, 14 Feb 2009) | 3 lines
1636Changed 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------------------------------------------------------------------------
1644r810 | lh3 | 2009-02-13 04:46:04 -0500 (Fri, 13 Feb 2009) | 2 lines
1645Changed paths:
1646   M /branches/prog/bwa/ChangeLog
1647
1648update ChangeLog
1649
1650------------------------------------------------------------------------
1651r799 | lh3 | 2009-02-05 12:01:17 -0500 (Thu, 05 Feb 2009) | 2 lines
1652Changed paths:
1653   M /branches/prog/bwa/bwase.c
1654   M /branches/prog/bwa/main.c
1655
1656change MD tag to meet the latest SAM specification
1657
1658------------------------------------------------------------------------
1659r796 | lh3 | 2009-02-05 08:35:13 -0500 (Thu, 05 Feb 2009) | 3 lines
1660Changed 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------------------------------------------------------------------------
1669r795 | lh3 | 2009-02-05 07:41:27 -0500 (Thu, 05 Feb 2009) | 4 lines
1670Changed 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------------------------------------------------------------------------
1680r791 | lh3 | 2009-01-25 05:20:47 -0500 (Sun, 25 Jan 2009) | 2 lines
1681Changed paths:
1682   M /branches/prog/bwa/bwa.1
1683
1684update some numbers
1685
1686------------------------------------------------------------------------
1687r790 | lh3 | 2009-01-24 15:13:03 -0500 (Sat, 24 Jan 2009) | 2 lines
1688Changed paths:
1689   M /branches/prog/bwa/bwa.1
1690
1691update benchmark
1692
1693------------------------------------------------------------------------
1694r789 | lh3 | 2009-01-22 10:18:44 -0500 (Thu, 22 Jan 2009) | 2 lines
1695Changed paths:
1696   M /branches/prog/bwa/bwtindex.c
1697
1698a warning message for index
1699
1700------------------------------------------------------------------------
1701r788 | lh3 | 2009-01-22 09:54:06 -0500 (Thu, 22 Jan 2009) | 2 lines
1702Changed paths:
1703   M /branches/prog/bwa/main.c
1704
1705forget to change release number
1706
1707------------------------------------------------------------------------
1708r786 | lh3 | 2009-01-22 06:27:39 -0500 (Thu, 22 Jan 2009) | 2 lines
1709Changed paths:
1710   M /branches/prog/bwa/NEWS
1711
1712Release bwa-0.4.3
1713
1714------------------------------------------------------------------------
1715r785 | lh3 | 2009-01-22 06:27:16 -0500 (Thu, 22 Jan 2009) | 2 lines
1716Changed paths:
1717   M /branches/prog/bwa/ChangeLog
1718   M /branches/prog/bwa/NEWS
1719
1720Release bwa-0.4.3
1721
1722------------------------------------------------------------------------
1723r784 | lh3 | 2009-01-22 06:19:59 -0500 (Thu, 22 Jan 2009) | 4 lines
1724Changed 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------------------------------------------------------------------------
1734r782 | lh3 | 2009-01-19 12:08:38 -0500 (Mon, 19 Jan 2009) | 3 lines
1735Changed 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------------------------------------------------------------------------
1743r781 | lh3 | 2009-01-19 11:26:37 -0500 (Mon, 19 Jan 2009) | 3 lines
1744Changed 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------------------------------------------------------------------------
1752r780 | lh3 | 2009-01-19 11:20:18 -0500 (Mon, 19 Jan 2009) | 4 lines
1753Changed 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------------------------------------------------------------------------
1766r779 | lh3 | 2009-01-19 10:45:57 -0500 (Mon, 19 Jan 2009) | 3 lines
1767Changed 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------------------------------------------------------------------------
1776r778 | lh3 | 2009-01-19 06:24:29 -0500 (Mon, 19 Jan 2009) | 5 lines
1777Changed 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------------------------------------------------------------------------
1795r775 | lh3 | 2009-01-18 05:40:35 -0500 (Sun, 18 Jan 2009) | 3 lines
1796Changed 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------------------------------------------------------------------------
1804r774 | lh3 | 2009-01-17 13:48:52 -0500 (Sat, 17 Jan 2009) | 4 lines
1805Changed 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------------------------------------------------------------------------
1814r773 | lh3 | 2009-01-17 05:54:37 -0500 (Sat, 17 Jan 2009) | 3 lines
1815Changed 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------------------------------------------------------------------------
1826r772 | lh3 | 2009-01-16 18:16:14 -0500 (Fri, 16 Jan 2009) | 3 lines
1827Changed 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------------------------------------------------------------------------
1839r768 | lh3 | 2009-01-09 11:57:23 -0500 (Fri, 09 Jan 2009) | 2 lines
1840Changed 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
1846Release bwa-0.4.2
1847
1848------------------------------------------------------------------------
1849r759 | lh3 | 2009-01-07 09:55:43 -0500 (Wed, 07 Jan 2009) | 2 lines
1850Changed 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
1858Release bwa-0.4.1
1859
1860------------------------------------------------------------------------
1861r758 | lh3 | 2009-01-07 05:36:06 -0500 (Wed, 07 Jan 2009) | 3 lines
1862Changed 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------------------------------------------------------------------------
1872r757 | lh3 | 2009-01-06 18:04:29 -0500 (Tue, 06 Jan 2009) | 5 lines
1873Changed 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------------------------------------------------------------------------
1886r755 | lh3 | 2009-01-06 10:23:29 -0500 (Tue, 06 Jan 2009) | 2 lines
1887Changed 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
1893Release bwa-0.4.0
1894
1895------------------------------------------------------------------------
1896r754 | lh3 | 2009-01-06 07:45:02 -0500 (Tue, 06 Jan 2009) | 3 lines
1897Changed 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------------------------------------------------------------------------
1907r753 | lh3 | 2009-01-06 06:17:21 -0500 (Tue, 06 Jan 2009) | 5 lines
1908Changed 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------------------------------------------------------------------------
1922r752 | lh3 | 2009-01-05 17:34:13 -0500 (Mon, 05 Jan 2009) | 3 lines
1923Changed 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------------------------------------------------------------------------
1936r751 | lh3 | 2009-01-05 17:19:04 -0500 (Mon, 05 Jan 2009) | 3 lines
1937Changed 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------------------------------------------------------------------------
1945r750 | lh3 | 2009-01-05 16:44:26 -0500 (Mon, 05 Jan 2009) | 3 lines
1946Changed 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------------------------------------------------------------------------
1954r749 | lh3 | 2009-01-05 16:37:28 -0500 (Mon, 05 Jan 2009) | 3 lines
1955Changed 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------------------------------------------------------------------------
1963r748 | lh3 | 2009-01-05 16:12:28 -0500 (Mon, 05 Jan 2009) | 4 lines
1964Changed 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------------------------------------------------------------------------
1982r747 | lh3 | 2009-01-05 10:16:18 -0500 (Mon, 05 Jan 2009) | 5 lines
1983Changed 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------------------------------------------------------------------------
1995r746 | lh3 | 2009-01-05 09:50:53 -0500 (Mon, 05 Jan 2009) | 3 lines
1996Changed 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------------------------------------------------------------------------
2004r745 | lh3 | 2009-01-05 08:23:00 -0500 (Mon, 05 Jan 2009) | 3 lines
2005Changed 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------------------------------------------------------------------------
2014r744 | lh3 | 2009-01-05 05:58:46 -0500 (Mon, 05 Jan 2009) | 4 lines
2015Changed 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------------------------------------------------------------------------
2024r743 | lh3 | 2009-01-04 17:18:38 -0500 (Sun, 04 Jan 2009) | 5 lines
2025Changed 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------------------------------------------------------------------------
2039r742 | lh3 | 2009-01-04 07:56:12 -0500 (Sun, 04 Jan 2009) | 2 lines
2040Changed paths:
2041   M /branches/prog/bwa/bwa.1
2042
2043add URL
2044
2045------------------------------------------------------------------------
2046r740 | lh3 | 2009-01-04 07:39:43 -0500 (Sun, 04 Jan 2009) | 2 lines
2047Changed 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
2053Release bwa-0.3.0
2054
2055------------------------------------------------------------------------
2056r739 | lh3 | 2009-01-04 06:55:06 -0500 (Sun, 04 Jan 2009) | 2 lines
2057Changed 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
2069added licensing information
2070
2071------------------------------------------------------------------------
2072r738 | lh3 | 2009-01-04 06:18:25 -0500 (Sun, 04 Jan 2009) | 4 lines
2073Changed 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------------------------------------------------------------------------
2083r737 | lh3 | 2009-01-03 16:00:58 -0500 (Sat, 03 Jan 2009) | 2 lines
2084Changed paths:
2085   M /branches/prog/bwa/ChangeLog
2086   M /branches/prog/bwa/bwa.1
2087
2088update documentation
2089
2090------------------------------------------------------------------------
2091r736 | lh3 | 2009-01-02 10:26:38 -0500 (Fri, 02 Jan 2009) | 2 lines
2092Changed paths:
2093   M /branches/prog/bwa/bwa.1
2094
2095update documentation
2096
2097------------------------------------------------------------------------
2098r735 | lh3 | 2009-01-02 07:10:20 -0500 (Fri, 02 Jan 2009) | 4 lines
2099Changed 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------------------------------------------------------------------------
2110r734 | lh3 | 2009-01-01 13:45:45 -0500 (Thu, 01 Jan 2009) | 8 lines
2111Changed 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------------------------------------------------------------------------
2129r733 | lh3 | 2009-01-01 11:01:20 -0500 (Thu, 01 Jan 2009) | 3 lines
2130Changed 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------------------------------------------------------------------------
2138r732 | lh3 | 2009-01-01 09:27:46 -0500 (Thu, 01 Jan 2009) | 3 lines
2139Changed 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------------------------------------------------------------------------
2148r731 | lh3 | 2009-01-01 06:51:21 -0500 (Thu, 01 Jan 2009) | 3 lines
2149Changed 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------------------------------------------------------------------------
2157r730 | lh3 | 2009-01-01 06:48:59 -0500 (Thu, 01 Jan 2009) | 4 lines
2158Changed 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------------------------------------------------------------------------
2167r729 | lh3 | 2008-12-31 16:43:56 -0500 (Wed, 31 Dec 2008) | 6 lines
2168Changed 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------------------------------------------------------------------------
2181r728 | lh3 | 2008-12-27 07:14:59 -0500 (Sat, 27 Dec 2008) | 3 lines
2182Changed 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------------------------------------------------------------------------
2191r727 | lh3 | 2008-12-26 18:10:59 -0500 (Fri, 26 Dec 2008) | 4 lines
2192Changed 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------------------------------------------------------------------------
2205r726 | lh3 | 2008-12-26 13:31:27 -0500 (Fri, 26 Dec 2008) | 5 lines
2206Changed 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------------------------------------------------------------------------
2223r725 | lh3 | 2008-12-26 07:04:11 -0500 (Fri, 26 Dec 2008) | 3 lines
2224Changed 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------------------------------------------------------------------------
2241r724 | lh3 | 2008-12-25 11:32:11 -0500 (Thu, 25 Dec 2008) | 3 lines
2242Changed 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------------------------------------------------------------------------
2251r723 | lh3 | 2008-12-25 10:48:31 -0500 (Thu, 25 Dec 2008) | 4 lines
2252Changed 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------------------------------------------------------------------------
2263r722 | lh3 | 2008-12-25 08:57:13 -0500 (Thu, 25 Dec 2008) | 3 lines
2264Changed 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------------------------------------------------------------------------
2283r666 | lh3 | 2008-11-18 18:34:29 -0500 (Tue, 18 Nov 2008) | 4 lines
2284Changed 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------------------------------------------------------------------------
2295r665 | lh3 | 2008-11-18 08:34:03 -0500 (Tue, 18 Nov 2008) | 3 lines
2296Changed 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------------------------------------------------------------------------
2304r612 | lh3 | 2008-10-28 06:50:53 -0400 (Tue, 28 Oct 2008) | 3 lines
2305Changed 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------------------------------------------------------------------------
2315r611 | lh3 | 2008-10-28 06:24:56 -0400 (Tue, 28 Oct 2008) | 2 lines
2316Changed 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
2329replace seq.* with kseq.h
2330
2331------------------------------------------------------------------------
2332r610 | lh3 | 2008-10-27 13:00:04 -0400 (Mon, 27 Oct 2008) | 3 lines
2333Changed 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------------------------------------------------------------------------
2343r609 | lh3 | 2008-10-24 16:52:00 -0400 (Fri, 24 Oct 2008) | 2 lines
2344Changed paths:
2345   M /branches/prog/bwa/kvec.h
2346
2347little...
2348
2349------------------------------------------------------------------------
2350r532 | lh3 | 2008-09-19 05:28:45 -0400 (Fri, 19 Sep 2008) | 2 lines
2351Changed paths:
2352   M /branches/prog/bwa/bwtsw2_core.c
2353   M /branches/prog/bwa/khash.h
2354
2355improve interface of khash
2356
2357------------------------------------------------------------------------
2358r531 | lh3 | 2008-09-18 06:52:59 -0400 (Thu, 18 Sep 2008) | 2 lines
2359Changed paths:
2360   M /branches/prog/bwa/bwtsw2_core.c
2361
2362improve minor things, which make bwtsw2 slower, but should miss less true hits
2363
2364------------------------------------------------------------------------
2365r530 | lh3 | 2008-09-17 18:19:26 -0400 (Wed, 17 Sep 2008) | 3 lines
2366Changed paths:
2367   M /branches/prog/bwa/bwtsw2_core.c
2368
2369 * fixed a bug in calculating ->D
2370 * enforce band-width checking
2371
2372------------------------------------------------------------------------
2373r529 | lh3 | 2008-09-17 18:06:49 -0400 (Wed, 17 Sep 2008) | 2 lines
2374Changed paths:
2375   M /branches/prog/bwa/bwtsw2_core.c
2376
2377delete a line of code that is never visited
2378
2379------------------------------------------------------------------------
2380r528 | lh3 | 2008-09-17 17:58:51 -0400 (Wed, 17 Sep 2008) | 2 lines
2381Changed paths:
2382   M /branches/prog/bwa/bwtsw2_core.c
2383
2384a bit code clean up
2385
2386------------------------------------------------------------------------
2387r527 | lh3 | 2008-09-17 10:55:45 -0400 (Wed, 17 Sep 2008) | 3 lines
2388Changed 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------------------------------------------------------------------------
2397r526 | lh3 | 2008-09-16 17:59:36 -0400 (Tue, 16 Sep 2008) | 2 lines
2398Changed paths:
2399   M /branches/prog/bwa/bwtsw2_core.c
2400
2401cut_tail after remove duplicate
2402
2403------------------------------------------------------------------------
2404r525 | lh3 | 2008-09-16 17:56:11 -0400 (Tue, 16 Sep 2008) | 3 lines
2405Changed 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------------------------------------------------------------------------
2417r524 | lh3 | 2008-09-15 16:53:22 -0400 (Mon, 15 Sep 2008) | 3 lines
2418Changed 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------------------------------------------------------------------------
2428r518 | lh3 | 2008-09-15 04:35:59 -0400 (Mon, 15 Sep 2008) | 2 lines
2429Changed paths:
2430   M /branches/prog/bwa/bwtsw2_core.c
2431
2432a bit code clean up
2433
2434------------------------------------------------------------------------
2435r517 | lh3 | 2008-09-14 18:18:11 -0400 (Sun, 14 Sep 2008) | 2 lines
2436Changed paths:
2437   M /branches/prog/bwa/bwtsw2_core.c
2438
2439improve speed (<1%)
2440
2441------------------------------------------------------------------------
2442r516 | lh3 | 2008-09-14 18:08:55 -0400 (Sun, 14 Sep 2008) | 3 lines
2443Changed 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------------------------------------------------------------------------
2450r515 | lh3 | 2008-09-14 17:26:49 -0400 (Sun, 14 Sep 2008) | 2 lines
2451Changed paths:
2452   M /branches/prog/bwa/bwtsw2_core.c
2453   M /branches/prog/bwa/bwtsw2_main.c
2454
2455nothing, really
2456
2457------------------------------------------------------------------------
2458r514 | lh3 | 2008-09-14 17:10:13 -0400 (Sun, 14 Sep 2008) | 2 lines
2459Changed paths:
2460   M /branches/prog/bwa/bwtsw2_core.c
2461
2462disable X-drop, which has to be reimplemented in the current algorithm
2463
2464------------------------------------------------------------------------
2465r513 | lh3 | 2008-09-14 16:49:42 -0400 (Sun, 14 Sep 2008) | 4 lines
2466Changed 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------------------------------------------------------------------------
2477r512 | lh3 | 2008-09-13 17:35:40 -0400 (Sat, 13 Sep 2008) | 2 lines
2478Changed 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
2485n-best method
2486
2487------------------------------------------------------------------------
2488r507 | lh3 | 2008-09-13 09:06:54 -0400 (Sat, 13 Sep 2008) | 2 lines
2489Changed paths:
2490   M /branches/prog/bwa/Makefile
2491   M /branches/prog/bwa/bwtsw2_core.c
2492
2493give correct result again
2494
2495------------------------------------------------------------------------
2496r506 | lh3 | 2008-09-13 08:12:07 -0400 (Sat, 13 Sep 2008) | 2 lines
2497Changed paths:
2498   M /branches/prog/bwa/bwtsw2_core.c
2499
2500I think I know the reason. It needs more work...
2501
2502------------------------------------------------------------------------
2503r505 | lh3 | 2008-09-13 06:20:43 -0400 (Sat, 13 Sep 2008) | 2 lines
2504Changed paths:
2505   M /branches/prog/bwa/Makefile
2506   M /branches/prog/bwa/bwtsw2_core.c
2507
2508fixed another bug, but still have
2509
2510------------------------------------------------------------------------
2511r504 | lh3 | 2008-09-12 18:13:37 -0400 (Fri, 12 Sep 2008) | 2 lines
2512Changed paths:
2513   M /branches/prog/bwa/bwtsw2_core.c
2514
2515fixed another bug
2516
2517------------------------------------------------------------------------
2518r503 | lh3 | 2008-09-12 17:15:56 -0400 (Fri, 12 Sep 2008) | 3 lines
2519Changed 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------------------------------------------------------------------------
2527r502 | lh3 | 2008-09-12 15:52:41 -0400 (Fri, 12 Sep 2008) | 2 lines
2528Changed paths:
2529   M /branches/prog/bwa/bwtsw2_core.c
2530   M /branches/prog/bwa/kvec.h
2531
2532more revisions
2533
2534------------------------------------------------------------------------
2535r501 | lh3 | 2008-09-11 18:06:15 -0400 (Thu, 11 Sep 2008) | 2 lines
2536Changed paths:
2537   M /branches/prog/bwa/bwtsw2_core.c
2538
2539further simply codes with kvec.h
2540
2541------------------------------------------------------------------------
2542r500 | lh3 | 2008-09-11 17:42:15 -0400 (Thu, 11 Sep 2008) | 2 lines
2543Changed paths:
2544   M /branches/prog/bwa/bwtsw2_core.c
2545
2546part of revisions... have not finished
2547
2548------------------------------------------------------------------------
2549r499 | lh3 | 2008-09-11 17:24:15 -0400 (Thu, 11 Sep 2008) | 2 lines
2550Changed 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
2557prepare for abrupt change
2558
2559------------------------------------------------------------------------
2560r496 | lh3 | 2008-09-11 10:34:38 -0400 (Thu, 11 Sep 2008) | 2 lines
2561Changed paths:
2562   M /branches/prog/bwa/bwtsw2_core.c
2563
2564fixed a bug; now "bwtsw2 -d" is useless
2565
2566------------------------------------------------------------------------
2567r495 | lh3 | 2008-09-11 09:22:03 -0400 (Thu, 11 Sep 2008) | 2 lines
2568Changed 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
2574improve speed a little bit
2575
2576------------------------------------------------------------------------
2577r494 | lh3 | 2008-09-11 08:28:08 -0400 (Thu, 11 Sep 2008) | 2 lines
2578Changed paths:
2579   M /branches/prog/bwa/bwtsw2_core.c
2580
2581remove debug codes
2582
2583------------------------------------------------------------------------
2584r493 | lh3 | 2008-09-11 07:49:53 -0400 (Thu, 11 Sep 2008) | 3 lines
2585Changed 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------------------------------------------------------------------------
2592r492 | lh3 | 2008-09-11 06:15:56 -0400 (Thu, 11 Sep 2008) | 4 lines
2593Changed 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------------------------------------------------------------------------
2605r491 | lh3 | 2008-09-11 05:46:16 -0400 (Thu, 11 Sep 2008) | 3 lines
2606Changed 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------------------------------------------------------------------------
2614r490 | lh3 | 2008-09-10 17:04:49 -0400 (Wed, 10 Sep 2008) | 4 lines
2615Changed 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------------------------------------------------------------------------
2627r489 | lh3 | 2008-09-10 11:51:13 -0400 (Wed, 10 Sep 2008) | 4 lines
2628Changed 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------------------------------------------------------------------------
2637r488 | lh3 | 2008-09-10 10:21:53 -0400 (Wed, 10 Sep 2008) | 3 lines
2638Changed paths:
2639   M /branches/prog/bwa/bwtsw2_core.c
2640
2641 * implement memory pool
2642 * avoid some rehashing
2643
2644------------------------------------------------------------------------
2645r487 | lh3 | 2008-09-10 09:23:38 -0400 (Wed, 10 Sep 2008) | 3 lines
2646Changed 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------------------------------------------------------------------------
2655r486 | lh3 | 2008-09-10 09:10:09 -0400 (Wed, 10 Sep 2008) | 4 lines
2656Changed 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------------------------------------------------------------------------
2668r485 | lh3 | 2008-09-10 06:31:20 -0400 (Wed, 10 Sep 2008) | 3 lines
2669Changed 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------------------------------------------------------------------------
2679r484 | lh3 | 2008-09-10 05:00:57 -0400 (Wed, 10 Sep 2008) | 2 lines
2680Changed paths:
2681   A /branches/prog/bwa/khash.h
2682
2683khash library
2684
2685------------------------------------------------------------------------
2686r483 | lh3 | 2008-09-10 04:22:53 -0400 (Wed, 10 Sep 2008) | 2 lines
2687Changed paths:
2688   M /branches/prog/bwa/bwtsw2_core.c
2689
2690add inline
2691
2692------------------------------------------------------------------------
2693r482 | lh3 | 2008-09-09 16:34:57 -0400 (Tue, 09 Sep 2008) | 2 lines
2694Changed paths:
2695   M /branches/prog/bwa/Makefile
2696   M /branches/prog/bwa/bwtsw2_aux.c
2697   M /branches/prog/bwa/bwtsw2_core.c
2698
2699improve speed
2700
2701------------------------------------------------------------------------
2702r481 | lh3 | 2008-09-09 13:13:00 -0400 (Tue, 09 Sep 2008) | 4 lines
2703Changed paths:
2704   M /branches/prog/bwa/bwtsw2_core.c
2705
2706Use a 128bit hash table to keep all (tk,tl,qk,ql). This is slow. Just
2707keep a copy in case I may need this in future.
2708
2709
2710------------------------------------------------------------------------
2711r480 | lh3 | 2008-09-09 12:53:32 -0400 (Tue, 09 Sep 2008) | 2 lines
2712Changed paths:
2713   M /branches/prog/bwa/bwtsw2.h
2714   M /branches/prog/bwa/bwtsw2_core.c
2715
2716 * no principal modification
2717
2718------------------------------------------------------------------------
2719r479 | lh3 | 2008-09-09 11:01:45 -0400 (Tue, 09 Sep 2008) | 4 lines
2720Changed 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------------------------------------------------------------------------
2729r474 | lh3 | 2008-09-03 17:22:57 -0400 (Wed, 03 Sep 2008) | 4 lines
2730Changed 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------------------------------------------------------------------------
2743r469 | lh3 | 2008-09-01 09:18:45 -0400 (Mon, 01 Sep 2008) | 3 lines
2744Changed 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------------------------------------------------------------------------
2763r447 | lh3 | 2008-08-27 10:05:09 -0400 (Wed, 27 Aug 2008) | 3 lines
2764Changed 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------------------------------------------------------------------------
2775r446 | lh3 | 2008-08-26 13:30:41 -0400 (Tue, 26 Aug 2008) | 3 lines
2776Changed 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------------------------------------------------------------------------
2787r445 | lh3 | 2008-08-26 13:05:58 -0400 (Tue, 26 Aug 2008) | 2 lines
2788Changed paths:
2789   M /branches/prog/bwa/bwt_lite.c
2790   M /branches/prog/bwa/bwt_lite.h
2791
2792updated from bwtsw2_lite
2793
2794------------------------------------------------------------------------
2795r436 | lh3 | 2008-08-23 12:28:44 -0400 (Sat, 23 Aug 2008) | 4 lines
2796Changed 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------------------------------------------------------------------------
2811r427 | lh3 | 2008-08-15 05:38:12 -0400 (Fri, 15 Aug 2008) | 2 lines
2812Changed 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
2819Release bwa-0.2.0
2820
2821------------------------------------------------------------------------
2822r426 | lh3 | 2008-08-14 11:26:19 -0400 (Thu, 14 Aug 2008) | 4 lines
2823Changed 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------------------------------------------------------------------------
2834r425 | lh3 | 2008-08-14 06:23:11 -0400 (Thu, 14 Aug 2008) | 3 lines
2835Changed 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------------------------------------------------------------------------
2843r424 | lh3 | 2008-08-14 05:55:33 -0400 (Thu, 14 Aug 2008) | 6 lines
2844Changed 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------------------------------------------------------------------------
2856r423 | lh3 | 2008-08-14 04:07:28 -0400 (Thu, 14 Aug 2008) | 2 lines
2857Changed paths:
2858   D /branches/prog/bwa/Makefile.div
2859
2860useless
2861
2862------------------------------------------------------------------------
2863r422 | lh3 | 2008-08-13 19:21:14 -0400 (Wed, 13 Aug 2008) | 4 lines
2864Changed 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------------------------------------------------------------------------
2873r421 | lh3 | 2008-08-13 18:23:33 -0400 (Wed, 13 Aug 2008) | 3 lines
2874Changed 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------------------------------------------------------------------------
2886r419 | lh3 | 2008-08-13 17:27:02 -0400 (Wed, 13 Aug 2008) | 3 lines
2887Changed 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------------------------------------------------------------------------
2898r418 | lh3 | 2008-08-13 10:56:54 -0400 (Wed, 13 Aug 2008) | 3 lines
2899Changed 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------------------------------------------------------------------------
2911r413 | lh3 | 2008-08-08 11:48:35 -0400 (Fri, 08 Aug 2008) | 2 lines
2912Changed paths:
2913   M /branches/prog/bwa/ChangeLog
2914   M /branches/prog/bwa/NEWS
2915   M /branches/prog/bwa/main.c
2916
2917Release bwa-0.1.6
2918
2919------------------------------------------------------------------------
2920r410 | lh3 | 2008-08-06 15:48:22 -0400 (Wed, 06 Aug 2008) | 2 lines
2921Changed paths:
2922   M /branches/prog/bwa/simple_dp.c
2923
2924sw: output alignment score
2925
2926------------------------------------------------------------------------
2927r407 | lh3 | 2008-08-04 10:01:20 -0400 (Mon, 04 Aug 2008) | 4 lines
2928Changed 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------------------------------------------------------------------------
2941r406 | lh3 | 2008-08-01 19:21:59 -0400 (Fri, 01 Aug 2008) | 3 lines
2942Changed 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------------------------------------------------------------------------
2954r405 | lh3 | 2008-08-01 19:06:19 -0400 (Fri, 01 Aug 2008) | 2 lines
2955Changed paths:
2956   M /branches/prog/bwa/Makefile
2957   M /branches/prog/bwa/bwtaln.c
2958   M /branches/prog/bwa/bwtaln.h
2959
2960unfinished, but I am tired...
2961
2962------------------------------------------------------------------------
2963r401 | lh3 | 2008-07-30 05:59:24 -0400 (Wed, 30 Jul 2008) | 4 lines
2964Changed 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------------------------------------------------------------------------
2973r399 | lh3 | 2008-07-27 11:41:52 -0400 (Sun, 27 Jul 2008) | 2 lines
2974Changed paths:
2975   M /branches/prog/bwa/ChangeLog
2976   M /branches/prog/bwa/NEWS
2977   M /branches/prog/bwa/main.c
2978
2979Release bwa-0.1.5
2980
2981------------------------------------------------------------------------
2982r398 | lh3 | 2008-07-25 12:14:47 -0400 (Fri, 25 Jul 2008) | 2 lines
2983Changed paths:
2984   M /branches/prog/bwa/bwa.1
2985
2986update documentation
2987
2988------------------------------------------------------------------------
2989r397 | lh3 | 2008-07-25 09:58:56 -0400 (Fri, 25 Jul 2008) | 2 lines
2990Changed 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------------------------------------------------------------------------
2998r396 | lh3 | 2008-07-25 06:42:01 -0400 (Fri, 25 Jul 2008) | 3 lines
2999Changed 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------------------------------------------------------------------------
3007r395 | lh3 | 2008-07-24 05:46:21 -0400 (Thu, 24 Jul 2008) | 4 lines
3008Changed 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------------------------------------------------------------------------
3017r394 | lh3 | 2008-07-24 05:18:53 -0400 (Thu, 24 Jul 2008) | 4 lines
3018Changed 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------------------------------------------------------------------------
3029r393 | lh3 | 2008-07-23 12:04:16 -0400 (Wed, 23 Jul 2008) | 2 lines
3030Changed paths:
3031   M /branches/prog/bwa/bwt.c
3032
3033comments only
3034
3035------------------------------------------------------------------------
3036r392 | lh3 | 2008-07-23 10:34:03 -0400 (Wed, 23 Jul 2008) | 2 lines
3037Changed paths:
3038   M /branches/prog/bwa/bwt.c
3039   M /branches/prog/bwa/main.c
3040
3041further improve the speed in Occ functions
3042
3043------------------------------------------------------------------------
3044r386 | lh3 | 2008-07-22 10:03:54 -0400 (Tue, 22 Jul 2008) | 2 lines
3045Changed paths:
3046   M /branches/prog/bwa/NEWS
3047   M /branches/prog/bwa/main.c
3048
3049Release bwa-0.1.4
3050
3051------------------------------------------------------------------------
3052r385 | lh3 | 2008-07-22 09:44:50 -0400 (Tue, 22 Jul 2008) | 2 lines
3053Changed paths:
3054   M /branches/prog/bwa/ChangeLog
3055   M /branches/prog/bwa/bwa.1
3056
3057update documentation and ChangeLog
3058
3059------------------------------------------------------------------------
3060r384 | lh3 | 2008-07-22 08:50:03 -0400 (Tue, 22 Jul 2008) | 4 lines
3061Changed 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------------------------------------------------------------------------
3074r383 | lh3 | 2008-07-21 18:32:21 -0400 (Mon, 21 Jul 2008) | 4 lines
3075Changed 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------------------------------------------------------------------------
3086r381 | lh3 | 2008-07-21 06:45:32 -0400 (Mon, 21 Jul 2008) | 2 lines
3087Changed 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
3093Release bwa-0.1.3
3094
3095------------------------------------------------------------------------
3096r380 | lh3 | 2008-07-21 06:07:43 -0400 (Mon, 21 Jul 2008) | 4 lines
3097Changed 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------------------------------------------------------------------------
3109r373 | lh3 | 2008-07-17 09:09:46 -0400 (Thu, 17 Jul 2008) | 4 lines
3110Changed 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------------------------------------------------------------------------
3121r372 | lh3 | 2008-07-17 07:51:08 -0400 (Thu, 17 Jul 2008) | 3 lines
3122Changed 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------------------------------------------------------------------------
3130r370 | lh3 | 2008-07-17 05:12:00 -0400 (Thu, 17 Jul 2008) | 2 lines
3131Changed paths:
3132   M /branches/prog/bwa/NEWS
3133   M /branches/prog/bwa/bwa.1
3134   M /branches/prog/bwa/main.c
3135
3136Release bwa-0.1.2
3137
3138------------------------------------------------------------------------
3139r368 | lh3 | 2008-07-16 08:51:25 -0400 (Wed, 16 Jul 2008) | 4 lines
3140Changed 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------------------------------------------------------------------------
3156r367 | lh3 | 2008-07-16 08:24:34 -0400 (Wed, 16 Jul 2008) | 2 lines
3157Changed paths:
3158   M /branches/prog/bwa/is.c
3159
3160Yuta Mori's implementation of IS algorithm.
3161
3162------------------------------------------------------------------------
3163r365 | lh3 | 2008-07-16 06:58:04 -0400 (Wed, 16 Jul 2008) | 6 lines
3164Changed 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------------------------------------------------------------------------
3177r358 | lh3 | 2008-06-09 06:03:04 -0400 (Mon, 09 Jun 2008) | 4 lines
3178Changed 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------------------------------------------------------------------------
3188r357 | lh3 | 2008-06-09 05:18:36 -0400 (Mon, 09 Jun 2008) | 3 lines
3189Changed 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------------------------------------------------------------------------
3199r356 | lh3 | 2008-06-08 18:43:13 -0400 (Sun, 08 Jun 2008) | 4 lines
3200Changed 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------------------------------------------------------------------------
3213r355 | lh3 | 2008-06-08 17:13:44 -0400 (Sun, 08 Jun 2008) | 4 lines
3214Changed 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------------------------------------------------------------------------
3227r354 | lh3 | 2008-06-08 15:39:05 -0400 (Sun, 08 Jun 2008) | 3 lines
3228Changed 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------------------------------------------------------------------------
3238r353 | lh3 | 2008-06-08 09:27:18 -0400 (Sun, 08 Jun 2008) | 3 lines
3239Changed 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------------------------------------------------------------------------
3252r352 | lh3 | 2008-06-06 04:37:34 -0400 (Fri, 06 Jun 2008) | 3 lines
3253Changed 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------------------------------------------------------------------------
3261r348 | lh3 | 2008-06-03 09:04:12 -0400 (Tue, 03 Jun 2008) | 2 lines
3262Changed 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
3268Release bwa-0.1.1
3269
3270------------------------------------------------------------------------
3271r347 | lh3 | 2008-06-03 05:45:08 -0400 (Tue, 03 Jun 2008) | 2 lines
3272Changed paths:
3273   M /branches/prog/bwa/bwa.1
3274
3275update documentation
3276
3277------------------------------------------------------------------------
3278r346 | lh3 | 2008-06-02 18:59:50 -0400 (Mon, 02 Jun 2008) | 5 lines
3279Changed 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------------------------------------------------------------------------
3291r345 | lh3 | 2008-06-02 16:04:39 -0400 (Mon, 02 Jun 2008) | 3 lines
3292Changed 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------------------------------------------------------------------------
3301r344 | lh3 | 2008-06-02 15:03:54 -0400 (Mon, 02 Jun 2008) | 4 lines
3302Changed 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------------------------------------------------------------------------
3313r343 | lh3 | 2008-06-02 13:44:51 -0400 (Mon, 02 Jun 2008) | 5 lines
3314Changed 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------------------------------------------------------------------------
3329r342 | lh3 | 2008-06-02 11:23:26 -0400 (Mon, 02 Jun 2008) | 3 lines
3330Changed 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------------------------------------------------------------------------
3340r341 | lh3 | 2008-06-02 09:31:39 -0400 (Mon, 02 Jun 2008) | 3 lines
3341Changed 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------------------------------------------------------------------------
3349r340 | lh3 | 2008-06-02 09:10:18 -0400 (Mon, 02 Jun 2008) | 3 lines
3350Changed 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------------------------------------------------------------------------
3358r339 | lh3 | 2008-06-02 08:41:31 -0400 (Mon, 02 Jun 2008) | 3 lines
3359Changed 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------------------------------------------------------------------------
3369r338 | lh3 | 2008-06-02 06:46:51 -0400 (Mon, 02 Jun 2008) | 5 lines
3370Changed 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------------------------------------------------------------------------
3382r337 | lh3 | 2008-06-01 19:11:15 -0400 (Sun, 01 Jun 2008) | 4 lines
3383Changed 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------------------------------------------------------------------------
3392r336 | lh3 | 2008-06-01 17:45:23 -0400 (Sun, 01 Jun 2008) | 3 lines
3393Changed 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------------------------------------------------------------------------
3403r335 | lh3 | 2008-06-01 16:03:09 -0400 (Sun, 01 Jun 2008) | 2 lines
3404Changed paths:
3405   M /branches/prog/bwa/Makefile
3406
3407nothing, really
3408
3409------------------------------------------------------------------------
3410r334 | lh3 | 2008-06-01 15:59:13 -0400 (Sun, 01 Jun 2008) | 2 lines
3411Changed 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
3417use IS algorithm by default
3418
3419------------------------------------------------------------------------
3420r333 | lh3 | 2008-06-01 15:05:15 -0400 (Sun, 01 Jun 2008) | 3 lines
3421Changed 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------------------------------------------------------------------------
3431r332 | lh3 | 2008-06-01 13:23:08 -0400 (Sun, 01 Jun 2008) | 2 lines
3432Changed paths:
3433   A /branches/prog/bwa/is.c
3434
3435IS linear-time algorithm for constructing SA/BWT
3436
3437------------------------------------------------------------------------
3438r331 | lh3 | 2008-06-01 10:35:26 -0400 (Sun, 01 Jun 2008) | 3 lines
3439Changed 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------------------------------------------------------------------------
3450r330 | lh3 | 2008-06-01 09:17:05 -0400 (Sun, 01 Jun 2008) | 2 lines
3451Changed 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
3457real coordinates can be ouput
3458
3459------------------------------------------------------------------------
3460r329 | lh3 | 2008-05-31 19:21:02 -0400 (Sat, 31 May 2008) | 2 lines
3461Changed paths:
3462   M /branches/prog/bwa/bwt2fmv.c
3463   M /branches/prog/bwa/bwtaln.h
3464   M /branches/prog/bwa/bwttop2.c
3465
3466add top2e which is similar to 1away
3467
3468------------------------------------------------------------------------
3469r328 | lh3 | 2008-05-31 18:46:12 -0400 (Sat, 31 May 2008) | 3 lines
3470Changed 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------------------------------------------------------------------------
3482r327 | lh3 | 2008-05-31 18:14:46 -0400 (Sat, 31 May 2008) | 2 lines
3483Changed 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
3490add cmd-line interface to alntop2
3491
3492------------------------------------------------------------------------
3493r326 | lh3 | 2008-05-31 17:59:31 -0400 (Sat, 31 May 2008) | 2 lines
3494Changed 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
3501top2 algorithm seems to work. I need to change interface, though
3502
3503------------------------------------------------------------------------
3504r325 | lh3 | 2008-05-31 15:11:49 -0400 (Sat, 31 May 2008) | 2 lines
3505Changed paths:
3506   M /branches/prog/bwa/bwt1away.c
3507
3508change the variable in the structure
3509
3510------------------------------------------------------------------------
3511r324 | lh3 | 2008-05-31 14:52:13 -0400 (Sat, 31 May 2008) | 2 lines
3512Changed paths:
3513   M /branches/prog/bwa/bwt1away.c
3514
3515set a slightly better bound on the maximum allowed mismatches
3516
3517------------------------------------------------------------------------
3518r323 | lh3 | 2008-05-30 18:40:21 -0400 (Fri, 30 May 2008) | 2 lines
3519Changed paths:
3520   M /branches/prog/bwa/bwtaln.c
3521
3522 * output time statistics
3523
3524------------------------------------------------------------------------
3525r322 | lh3 | 2008-05-30 17:58:25 -0400 (Fri, 30 May 2008) | 4 lines
3526Changed 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------------------------------------------------------------------------
3539r321 | lh3 | 2008-05-30 13:57:43 -0400 (Fri, 30 May 2008) | 3 lines
3540Changed 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------------------------------------------------------------------------
3555r320 | lh3 | 2008-05-30 11:40:11 -0400 (Fri, 30 May 2008) | 4 lines
3556Changed 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------------------------------------------------------------------------
3568r319 | lh3 | 2008-05-30 10:31:37 -0400 (Fri, 30 May 2008) | 3 lines
3569Changed 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------------------------------------------------------------------------
3576r318 | lh3 | 2008-05-30 09:21:49 -0400 (Fri, 30 May 2008) | 2 lines
3577Changed 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
3586best unique match is partially finished
3587
3588------------------------------------------------------------------------
3589r317 | lh3 | 2008-05-30 06:33:28 -0400 (Fri, 30 May 2008) | 2 lines
3590Changed 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
3598remove "ungapped" command and related codes
3599
3600------------------------------------------------------------------------
3601r316 | lh3 | 2008-05-30 06:05:20 -0400 (Fri, 30 May 2008) | 2 lines
3602Changed 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
3608change variable name thick to width
3609
3610------------------------------------------------------------------------
3611r315 | lh3 | 2008-05-29 19:06:13 -0400 (Thu, 29 May 2008) | 2 lines
3612Changed 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
3624revised algorithm for ungapped alignment. the old one can still be used.
3625
3626------------------------------------------------------------------------
3627r314 | lh3 | 2008-05-29 16:36:11 -0400 (Thu, 29 May 2008) | 2 lines
3628Changed 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------------------------------------------------------------------------
3637r313 | lh3 | 2008-05-29 15:56:14 -0400 (Thu, 29 May 2008) | 2 lines
3638Changed paths:
3639   M /branches/prog/bwa/bwt_gen/bwt_gen.c
3640
3641little...
3642
3643------------------------------------------------------------------------
3644r312 | lh3 | 2008-05-29 15:54:01 -0400 (Thu, 29 May 2008) | 3 lines
3645Changed 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------------------------------------------------------------------------
3653r311 | lh3 | 2008-05-29 15:44:36 -0400 (Thu, 29 May 2008) | 2 lines
3654Changed 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
3662codes from BWT-SW, for building BWT from packed file
3663
3664------------------------------------------------------------------------
3665r310 | lh3 | 2008-05-28 17:03:35 -0400 (Wed, 28 May 2008) | 4 lines
3666Changed 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------------------------------------------------------------------------
3679r309 | lh3 | 2008-05-28 11:39:37 -0400 (Wed, 28 May 2008) | 2 lines
3680Changed paths:
3681   M /branches/prog/bwa/bwt.c
3682   M /branches/prog/bwa/bwt2fmv.c
3683
3684fix a bug
3685
3686------------------------------------------------------------------------
3687r308 | lh3 | 2008-05-28 09:56:16 -0400 (Wed, 28 May 2008) | 4 lines
3688Changed paths:
3689   M /branches/prog/bwa/bwt.c
3690   M /branches/prog/bwa/bwt2fmv.c
3691
3692add heuristics to improve the speed, but I have not tested whether the
3693results are correct or not.
3694
3695
3696------------------------------------------------------------------------
3697r307 | lh3 | 2008-05-28 06:31:34 -0400 (Wed, 28 May 2008) | 5 lines
3698Changed 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------------------------------------------------------------------------
3712r306 | lh3 | 2008-05-27 18:41:27 -0400 (Tue, 27 May 2008) | 3 lines
3713Changed 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------------------------------------------------------------------------
3722r305 | lh3 | 2008-05-27 16:59:44 -0400 (Tue, 27 May 2008) | 5 lines
3723Changed 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------------------------------------------------------------------------
3734r304 | lh3 | 2008-05-27 09:12:17 -0400 (Tue, 27 May 2008) | 3 lines
3735Changed 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------------------------------------------------------------------------
3751r303 | lh3 | 2008-05-27 06:33:38 -0400 (Tue, 27 May 2008) | 2 lines
3752Changed 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
3759add xassert and fix a bug
3760
3761------------------------------------------------------------------------
3762r302 | lh3 | 2008-05-27 06:23:20 -0400 (Tue, 27 May 2008) | 2 lines
3763Changed 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
3771improve error message and error handling
3772
3773------------------------------------------------------------------------
3774r301 | lh3 | 2008-05-27 05:37:51 -0400 (Tue, 27 May 2008) | 4 lines
3775Changed 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------------------------------------------------------------------------
3789r299 | lh3 | 2008-05-26 18:07:44 -0400 (Mon, 26 May 2008) | 2 lines
3790Changed 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
3796generate/retrieve SA and Occ
3797
3798------------------------------------------------------------------------
3799r298 | lh3 | 2008-05-26 13:16:49 -0400 (Mon, 26 May 2008) | 3 lines
3800Changed 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------------------------------------------------------------------------
3810r297 | lh3 | 2008-05-25 17:43:58 -0400 (Sun, 25 May 2008) | 6 lines
3811Changed 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------------------------------------------------------------------------
3827r296 | lh3 | 2008-05-24 18:35:02 -0400 (Sat, 24 May 2008) | 5 lines
3828Changed 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
3836Burrows-Wheeler Transform now works. At least on one example, the
3837current code generates the same BWT as BWT-SW. Kind of magical, I would
3838say. :)
3839
3840
3841------------------------------------------------------------------------
3842r295 | lh3 | 2008-05-24 11:25:31 -0400 (Sat, 24 May 2008) | 3 lines
3843Changed 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------------------------------------------------------------------------
3853r293 | lh3 | 2008-05-24 10:57:03 -0400 (Sat, 24 May 2008) | 3 lines
3854Changed 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------------------------------------------------------------------------
3865