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comparison pyPRADA_1.2/tools/bwa-0.5.7-mh/ChangeLog @ 0:acc2ca1a3ba4

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date Thu, 20 Feb 2014 00:44:58 -0500
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1 ------------------------------------------------------------------------
2 r1309 | lh3 | 2010-02-26 21:42:22 -0500 (Fri, 26 Feb 2010) | 4 lines
3 Changed paths:
4 M /branches/prog/bwa/bwape.c
5 M /branches/prog/bwa/bwtaln.c
6 M /branches/prog/bwa/main.c
7
8 * bwa-0.5.6-2 (r1309)
9 * fixed an unfixed bug (by Carol Scott)
10 * fixed some tiny formatting
11
12 ------------------------------------------------------------------------
13 r1305 | lh3 | 2010-02-25 13:47:58 -0500 (Thu, 25 Feb 2010) | 3 lines
14 Changed paths:
15 M /branches/prog/bwa/bwape.c
16 M /branches/prog/bwa/bwase.c
17 M /branches/prog/bwa/bwtaln.c
18 M /branches/prog/bwa/bwtsw2_main.c
19 M /branches/prog/bwa/main.c
20
21 * bwa-0.5.6-1 (r1304)
22 * optionally write output to a file (by Tim Fennel)
23
24 ------------------------------------------------------------------------
25 r1303 | lh3 | 2010-02-10 23:43:48 -0500 (Wed, 10 Feb 2010) | 2 lines
26 Changed paths:
27 M /branches/prog/bwa/ChangeLog
28 M /branches/prog/bwa/NEWS
29 M /branches/prog/bwa/bwa.1
30 M /branches/prog/bwa/bwtsw2_main.c
31 M /branches/prog/bwa/main.c
32
33 Release bwa-0.5.6
34
35 ------------------------------------------------------------------------
36 r1302 | lh3 | 2010-02-10 11:11:49 -0500 (Wed, 10 Feb 2010) | 3 lines
37 Changed paths:
38 M /branches/prog/bwa/ChangeLog
39 M /branches/prog/bwa/NEWS
40 M /branches/prog/bwa/bwape.c
41 M /branches/prog/bwa/bwtaln.h
42 M /branches/prog/bwa/main.c
43
44 * bwa-0.5.5-10 (r1302)
45 * improve max insert size estimate (method suggested by Gerton Lunter)
46
47 ------------------------------------------------------------------------
48 r1301 | lh3 | 2010-02-09 16:15:28 -0500 (Tue, 09 Feb 2010) | 5 lines
49 Changed paths:
50 M /branches/prog/bwa/bwape.c
51 M /branches/prog/bwa/bwase.c
52 M /branches/prog/bwa/main.c
53
54 * bwa-0.5.5-9 (r1301)
55 * improve mapping quality calculation for abnomalous pairs
56 * fixed a bug in multiple hits
57 * SOLiD multiple hits should work now
58
59 ------------------------------------------------------------------------
60 r1300 | lh3 | 2010-02-09 12:50:02 -0500 (Tue, 09 Feb 2010) | 3 lines
61 Changed paths:
62 M /branches/prog/bwa/bwape.c
63 M /branches/prog/bwa/main.c
64
65 * bwa-0.5.5-8 (r1300)
66 * output kurtosis
67
68 ------------------------------------------------------------------------
69 r1299 | lh3 | 2010-02-09 12:33:34 -0500 (Tue, 09 Feb 2010) | 5 lines
70 Changed paths:
71 M /branches/prog/bwa/bwape.c
72 M /branches/prog/bwa/main.c
73
74 * bwa-0.5.5-7 (r1299)
75 * calculate skewness in sampe
76 * increase min_len in SW to 20
77 * perform more SW to fix discordant pairs
78
79 ------------------------------------------------------------------------
80 r1298 | lh3 | 2010-02-08 12:40:31 -0500 (Mon, 08 Feb 2010) | 3 lines
81 Changed paths:
82 M /branches/prog/bwa/bwape.c
83 M /branches/prog/bwa/bwase.c
84 M /branches/prog/bwa/bwtaln.c
85 M /branches/prog/bwa/bwtaln.h
86 M /branches/prog/bwa/cs2nt.c
87 M /branches/prog/bwa/main.c
88 M /branches/prog/bwa/stdaln.h
89
90 * bwa-0.5.5-6 (r1297)
91 * prepare to replace all 16-bit CIGAR (patches by Rodrigo Goya)
92
93 ------------------------------------------------------------------------
94 r1297 | lh3 | 2010-02-05 22:26:11 -0500 (Fri, 05 Feb 2010) | 2 lines
95 Changed paths:
96 M /branches/prog/bwa/solid2fastq.pl
97
98 the old fix seems not working!
99
100 ------------------------------------------------------------------------
101 r1296 | lh3 | 2010-02-05 21:51:03 -0500 (Fri, 05 Feb 2010) | 3 lines
102 Changed paths:
103 M /branches/prog/bwa/bwa.1
104 M /branches/prog/bwa/bwape.c
105 M /branches/prog/bwa/main.c
106
107 * bwa-0.5.5-5 (r1296)
108 * fixed a minor issue that the lower bound of insert size is not correctly set.
109
110 ------------------------------------------------------------------------
111 r1295 | lh3 | 2010-02-05 21:01:10 -0500 (Fri, 05 Feb 2010) | 5 lines
112 Changed paths:
113 M /branches/prog/bwa/bwape.c
114 M /branches/prog/bwa/bwase.c
115 M /branches/prog/bwa/bwaseqio.c
116 M /branches/prog/bwa/main.c
117
118 * bwa-0.5.5-4 (r1295)
119 * fixed a memory leak
120 * change the behaviour of -n (samse and sampe)
121 * change the default of -n
122
123 ------------------------------------------------------------------------
124 r1294 | lh3 | 2010-02-05 17:24:06 -0500 (Fri, 05 Feb 2010) | 3 lines
125 Changed paths:
126 M /branches/prog/bwa/bwape.c
127 M /branches/prog/bwa/bwase.c
128 M /branches/prog/bwa/bwaseqio.c
129 M /branches/prog/bwa/bwtaln.h
130 M /branches/prog/bwa/main.c
131
132 * bwa-0.5.5-3 (r1294)
133 * improved multi-hit report
134
135 ------------------------------------------------------------------------
136 r1293 | lh3 | 2010-02-05 12:57:38 -0500 (Fri, 05 Feb 2010) | 5 lines
137 Changed paths:
138 M /branches/prog/bwa/bwape.c
139 M /branches/prog/bwa/bwase.c
140 M /branches/prog/bwa/cs2nt.c
141 M /branches/prog/bwa/main.c
142 M /branches/prog/bwa/solid2fastq.pl
143
144 * bwa-0.5.5-2 (r1293)
145 * bugfix: truncated quality string
146 * bugfix: quality -1 in solid->fastq conversion
147 * bugfix: color reads on the reverse strand is not complemented
148
149 ------------------------------------------------------------------------
150 r1279 | lh3 | 2009-11-23 22:42:34 -0500 (Mon, 23 Nov 2009) | 3 lines
151 Changed paths:
152 M /branches/prog/bwa/bntseq.c
153 M /branches/prog/bwa/bntseq.h
154 M /branches/prog/bwa/bwase.c
155 A /branches/prog/bwa/bwase.h
156 M /branches/prog/bwa/bwtaln.c
157 M /branches/prog/bwa/bwtaln.h
158 M /branches/prog/bwa/bwtsw2_aux.c
159 M /branches/prog/bwa/main.c
160
161 * bwa-0.5.5-1 (r1279)
162 * incorporate changes from Matt Hanna for Java bindings.
163
164 ------------------------------------------------------------------------
165 r1275 | lh3 | 2009-11-10 22:13:10 -0500 (Tue, 10 Nov 2009) | 2 lines
166 Changed paths:
167 M /branches/prog/bwa/ChangeLog
168
169 update ChangeLog
170
171 ------------------------------------------------------------------------
172 r1273 | lh3 | 2009-11-10 22:08:16 -0500 (Tue, 10 Nov 2009) | 2 lines
173 Changed paths:
174 M /branches/prog/bwa/NEWS
175 M /branches/prog/bwa/bwa.1
176 M /branches/prog/bwa/main.c
177 A /branches/prog/bwa/qualfa2fq.pl
178
179 Release bwa-0.5.5 (r1273)
180
181 ------------------------------------------------------------------------
182 r1272 | lh3 | 2009-11-10 22:02:50 -0500 (Tue, 10 Nov 2009) | 3 lines
183 Changed paths:
184 M /branches/prog/bwa/bwape.c
185 M /branches/prog/bwa/main.c
186
187 * bwa-0.5.4-3 (r1272)
188 * fixed another typo which may lead to incorrect single-end mapping quality
189
190 ------------------------------------------------------------------------
191 r1271 | lh3 | 2009-11-10 21:59:47 -0500 (Tue, 10 Nov 2009) | 4 lines
192 Changed paths:
193 M /branches/prog/bwa/bwtaln.c
194 M /branches/prog/bwa/main.c
195
196 * bwa-0.5.4-2 (r1271)
197 * fixed a serious typo/bug which does not hurt if we allow one gap open
198 and work with <200bp reads, but causes segfault for long reads.
199
200 ------------------------------------------------------------------------
201 r1270 | lh3 | 2009-11-09 23:12:42 -0500 (Mon, 09 Nov 2009) | 3 lines
202 Changed paths:
203 M /branches/prog/bwa/cs2nt.c
204 M /branches/prog/bwa/main.c
205
206 * bwa-0.5.4-1 (r1270)
207 * fixed a bug in color alignment
208
209 ------------------------------------------------------------------------
210 r1245 | lh3 | 2009-10-09 07:42:52 -0400 (Fri, 09 Oct 2009) | 2 lines
211 Changed paths:
212 M /branches/prog/bwa/ChangeLog
213 M /branches/prog/bwa/NEWS
214 M /branches/prog/bwa/bwa.1
215 M /branches/prog/bwa/bwape.c
216 M /branches/prog/bwa/bwase.c
217 M /branches/prog/bwa/bwaseqio.c
218 M /branches/prog/bwa/main.c
219
220 Release bwa-0.5.4
221
222 ------------------------------------------------------------------------
223 r1244 | lh3 | 2009-10-09 05:53:52 -0400 (Fri, 09 Oct 2009) | 5 lines
224 Changed paths:
225 M /branches/prog/bwa/ChangeLog
226 M /branches/prog/bwa/bwape.c
227 M /branches/prog/bwa/bwase.c
228 M /branches/prog/bwa/bwaseqio.c
229 M /branches/prog/bwa/bwtaln.h
230 M /branches/prog/bwa/main.c
231 M /branches/prog/bwa/stdaln.c
232
233 * bwa-0.5.3-4 (r1244)
234 * output the clipped length in XC:i: tag
235 * skip mate alignment when stdaln is buggy
236 * fixed a bug in NM:i: tag
237
238 ------------------------------------------------------------------------
239 r1243 | lh3 | 2009-10-07 08:15:04 -0400 (Wed, 07 Oct 2009) | 3 lines
240 Changed paths:
241 M /branches/prog/bwa/bwape.c
242 M /branches/prog/bwa/main.c
243
244 * bwa-0.5.3-3 (r1243)
245 * sampe: fixed a bug when a read sequence is identical its reverse complement.
246
247 ------------------------------------------------------------------------
248 r1242 | lh3 | 2009-10-07 07:49:13 -0400 (Wed, 07 Oct 2009) | 4 lines
249 Changed paths:
250 M /branches/prog/bwa/bntseq.c
251 M /branches/prog/bwa/bwape.c
252 M /branches/prog/bwa/bwtaln.c
253 M /branches/prog/bwa/bwtaln.h
254 M /branches/prog/bwa/main.c
255
256 * bwa-0.5.3-2 (r1242)
257 * sampe: optionall preload the full index into memory
258 * aln: change the default seed length to 32bp
259
260 ------------------------------------------------------------------------
261 r1238 | lh3 | 2009-09-26 18:38:15 -0400 (Sat, 26 Sep 2009) | 2 lines
262 Changed paths:
263 M /branches/prog/bwa/khash.h
264
265 Improve portability of khash.h
266
267 ------------------------------------------------------------------------
268 r1228 | lh3 | 2009-09-15 09:20:22 -0400 (Tue, 15 Sep 2009) | 2 lines
269 Changed paths:
270 M /branches/prog/bwa/main.c
271
272 fixed a typo
273
274 ------------------------------------------------------------------------
275 r1227 | lh3 | 2009-09-15 09:19:35 -0400 (Tue, 15 Sep 2009) | 3 lines
276 Changed paths:
277 M /branches/prog/bwa/bwtsw2.h
278 M /branches/prog/bwa/bwtsw2_aux.c
279 M /branches/prog/bwa/bwtsw2_main.c
280 M /branches/prog/bwa/main.c
281
282 * bwa-0.5.3-1 (r1226)
283 * in dBWT-SW, optionall use hard clipping instead of soft clipping
284
285 ------------------------------------------------------------------------
286 r1225 | lh3 | 2009-09-15 08:32:30 -0400 (Tue, 15 Sep 2009) | 2 lines
287 Changed paths:
288 M /branches/prog/bwa/NEWS
289 M /branches/prog/bwa/bwase.c
290 M /branches/prog/bwa/main.c
291
292 Release bwa-0.5.3 (r1225)
293
294 ------------------------------------------------------------------------
295 r1223 | lh3 | 2009-09-13 07:30:41 -0400 (Sun, 13 Sep 2009) | 2 lines
296 Changed paths:
297 M /branches/prog/bwa/ChangeLog
298 M /branches/prog/bwa/NEWS
299 M /branches/prog/bwa/bwa.1
300 M /branches/prog/bwa/main.c
301
302 Release bwa-0.5.2
303
304 ------------------------------------------------------------------------
305 r1222 | lh3 | 2009-09-11 09:11:39 -0400 (Fri, 11 Sep 2009) | 3 lines
306 Changed paths:
307 M /branches/prog/bwa/bwtaln.c
308 M /branches/prog/bwa/main.c
309
310 * bwa-0.5.1-5 (r1222)
311 * fixed a typo. No real change
312
313 ------------------------------------------------------------------------
314 r1221 | lh3 | 2009-09-11 09:09:44 -0400 (Fri, 11 Sep 2009) | 3 lines
315 Changed paths:
316 M /branches/prog/bwa/bwa.1
317 M /branches/prog/bwa/bwape.c
318 M /branches/prog/bwa/bwase.c
319 M /branches/prog/bwa/bwaseqio.c
320 M /branches/prog/bwa/bwtaln.c
321 M /branches/prog/bwa/bwtaln.h
322 M /branches/prog/bwa/main.c
323
324 * bwa-0.5.1-4 (r1221)
325 * trim reads before alignment
326
327 ------------------------------------------------------------------------
328 r1216 | lh3 | 2009-09-08 17:50:15 -0400 (Tue, 08 Sep 2009) | 4 lines
329 Changed paths:
330 M /branches/prog/bwa/bwape.c
331 M /branches/prog/bwa/bwase.c
332 M /branches/prog/bwa/bwtaln.h
333 M /branches/prog/bwa/main.c
334
335 * bwa-0.5.1-3 (r1216)
336 * fixed a bug about NM tags for gapped alignment
337 * print SAM header
338
339 ------------------------------------------------------------------------
340 r1215 | lh3 | 2009-09-08 17:14:42 -0400 (Tue, 08 Sep 2009) | 3 lines
341 Changed paths:
342 M /branches/prog/bwa/bwtaln.c
343 M /branches/prog/bwa/main.c
344
345 * bwa-0.5.1-2 (r1215)
346 * fixed a bug when read lengths vary (by John Marshall)
347
348 ------------------------------------------------------------------------
349 r1213 | lh3 | 2009-09-06 18:58:15 -0400 (Sun, 06 Sep 2009) | 3 lines
350 Changed paths:
351 M /branches/prog/bwa/bwtsw2_aux.c
352 M /branches/prog/bwa/main.c
353
354 * bwa-0.5.1-1 (r1213)
355 * change default -T to 30
356
357 ------------------------------------------------------------------------
358 r1209 | lh3 | 2009-09-02 06:06:02 -0400 (Wed, 02 Sep 2009) | 2 lines
359 Changed paths:
360 M /branches/prog/bwa/NEWS
361 M /branches/prog/bwa/bwa.1
362 M /branches/prog/bwa/main.c
363
364 Release bwa-0.5.1
365
366 ------------------------------------------------------------------------
367 r1208 | lh3 | 2009-09-02 05:56:33 -0400 (Wed, 02 Sep 2009) | 2 lines
368 Changed paths:
369 M /branches/prog/bwa/ChangeLog
370
371 * ChangeLog
372
373 ------------------------------------------------------------------------
374 r1206 | lh3 | 2009-08-30 18:27:30 -0400 (Sun, 30 Aug 2009) | 3 lines
375 Changed paths:
376 M /branches/prog/bwa/bwtsw2_aux.c
377 M /branches/prog/bwa/main.c
378
379 * bwa-0.5.0-6 (r1206)
380 * fixed two bugs caused by previous modification
381
382 ------------------------------------------------------------------------
383 r1205 | lh3 | 2009-08-30 17:28:36 -0400 (Sun, 30 Aug 2009) | 4 lines
384 Changed paths:
385 M /branches/prog/bwa/ChangeLog
386 M /branches/prog/bwa/bwtsw2_aux.c
387 M /branches/prog/bwa/main.c
388
389 * bwa-0.5.0-4 (r1205)
390 * reduce false coordinates and CIGAR when a query bridges two reference
391 sequences, although some very rare cases may fail bwa.
392
393 ------------------------------------------------------------------------
394 r1204 | lh3 | 2009-08-30 06:06:16 -0400 (Sun, 30 Aug 2009) | 3 lines
395 Changed paths:
396 M /branches/prog/bwa/bwtsw2_aux.c
397 M /branches/prog/bwa/bwtsw2_core.c
398 M /branches/prog/bwa/main.c
399
400 * bwa-0.5.0-3 (r1204)
401 * choose one repetitive hit to extend
402
403 ------------------------------------------------------------------------
404 r1203 | lh3 | 2009-08-29 18:11:51 -0400 (Sat, 29 Aug 2009) | 4 lines
405 Changed paths:
406 M /branches/prog/bwa/bwase.c
407 M /branches/prog/bwa/bwtsw2_aux.c
408 M /branches/prog/bwa/main.c
409
410 * bwa-0.5.0-2 (r1203)
411 * dBWT-SW: change a parameter in calculating mapping quality
412 * fixed a bug in samse
413
414 ------------------------------------------------------------------------
415 r1202 | lh3 | 2009-08-28 19:48:41 -0400 (Fri, 28 Aug 2009) | 4 lines
416 Changed paths:
417 M /branches/prog/bwa/bwtsw2_aux.c
418 M /branches/prog/bwa/main.c
419
420 * bwa-0.5.0-1 (r1202)
421 * change default band width to 50
422 * improve mapping quality a bit
423
424 ------------------------------------------------------------------------
425 r1200 | lh3 | 2009-08-20 06:21:24 -0400 (Thu, 20 Aug 2009) | 2 lines
426 Changed paths:
427 M /branches/prog/bwa/NEWS
428 M /branches/prog/bwa/main.c
429
430 Release bwa-0.5.0 (r1200)
431
432 ------------------------------------------------------------------------
433 r1199 | lh3 | 2009-08-20 04:49:15 -0400 (Thu, 20 Aug 2009) | 2 lines
434 Changed paths:
435 M /branches/prog/bwa/ChangeLog
436 M /branches/prog/bwa/bwa.1
437
438 Updated ChangeLog and the manual
439
440 ------------------------------------------------------------------------
441 r1198 | lh3 | 2009-08-19 11:09:15 -0400 (Wed, 19 Aug 2009) | 3 lines
442 Changed paths:
443 M /branches/prog/bwa/bwtsw2_aux.c
444 M /branches/prog/bwa/bwtsw2_core.c
445 M /branches/prog/bwa/main.c
446
447 * bwa-0.4.9-36 (r1198)
448 * simplify duphits removal. The accuracy is changed a tiny bit, sometimes better, sometimes worse.
449
450 ------------------------------------------------------------------------
451 r1197 | lh3 | 2009-08-19 08:15:05 -0400 (Wed, 19 Aug 2009) | 3 lines
452 Changed paths:
453 M /branches/prog/bwa/Makefile
454 M /branches/prog/bwa/bwtsw2_aux.c
455 A /branches/prog/bwa/bwtsw2_chain.c
456 M /branches/prog/bwa/main.c
457
458 * bwa-0.4.9-35 (r1197)
459 * further heuristic acceleration for long queries
460
461 ------------------------------------------------------------------------
462 r1196 | lh3 | 2009-08-18 06:54:03 -0400 (Tue, 18 Aug 2009) | 4 lines
463 Changed paths:
464 M /branches/prog/bwa/bwa.1
465 M /branches/prog/bwa/bwtsw2_aux.c
466 M /branches/prog/bwa/main.c
467
468 * bwa-0.4.9-34 (r1196)
469 * updated the manual page
470 * output base quality if the input is fastq
471
472 ------------------------------------------------------------------------
473 r1195 | lh3 | 2009-08-18 06:23:00 -0400 (Tue, 18 Aug 2009) | 4 lines
474 Changed paths:
475 M /branches/prog/bwa/bwase.c
476 M /branches/prog/bwa/bwtsw2_main.c
477 M /branches/prog/bwa/main.c
478 M /branches/prog/bwa/simple_dp.c
479
480 * bwa-0.4.9-33 (r1191)
481 * fixed a bug in sampe/samse when gaps occur to the 5'-end in SW alignment
482 * in dbwtsw adjust -T and -c according to -a
483
484 ------------------------------------------------------------------------
485 r1192 | lh3 | 2009-08-13 05:37:28 -0400 (Thu, 13 Aug 2009) | 2 lines
486 Changed paths:
487 M /branches/prog/bwa/bwa.1
488
489 update manual
490
491 ------------------------------------------------------------------------
492 r1191 | lh3 | 2009-08-12 19:40:51 -0400 (Wed, 12 Aug 2009) | 2 lines
493 Changed paths:
494 M /branches/prog/bwa/bwa.1
495 M /branches/prog/bwa/bwtsw2_main.c
496
497 update documentation
498
499 ------------------------------------------------------------------------
500 r1190 | lh3 | 2009-08-12 08:56:10 -0400 (Wed, 12 Aug 2009) | 3 lines
501 Changed paths:
502 M /branches/prog/bwa/bwtsw2_main.c
503 M /branches/prog/bwa/main.c
504
505 * bwa-0.4.9-32 (r1190)
506 * only help messages are changed
507
508 ------------------------------------------------------------------------
509 r1189 | lh3 | 2009-08-11 09:28:55 -0400 (Tue, 11 Aug 2009) | 4 lines
510 Changed paths:
511 M /branches/prog/bwa/bwase.c
512 M /branches/prog/bwa/bwtsw2.h
513 M /branches/prog/bwa/bwtsw2_aux.c
514 M /branches/prog/bwa/bwtsw2_core.c
515 M /branches/prog/bwa/main.c
516
517 * bwa-0.4.9-31 (r1189)
518 * in bwape/bwase, print CIGAR "*" if the read is unmapped
519 * improved the calculation of mapping quality
520
521 ------------------------------------------------------------------------
522 r1181 | lh3 | 2009-08-03 12:09:41 -0400 (Mon, 03 Aug 2009) | 2 lines
523 Changed paths:
524 M /branches/prog/bwa/bwtsw2_aux.c
525
526 fflush()
527
528 ------------------------------------------------------------------------
529 r1180 | lh3 | 2009-08-03 12:08:46 -0400 (Mon, 03 Aug 2009) | 4 lines
530 Changed paths:
531 M /branches/prog/bwa/bwtsw2_aux.c
532 M /branches/prog/bwa/main.c
533
534 * bwa-0.4.9-30 (r1180)
535 * fixed a memory problem
536 * multi-threading sometimes does not work...
537
538 ------------------------------------------------------------------------
539 r1179 | lh3 | 2009-08-03 11:04:39 -0400 (Mon, 03 Aug 2009) | 3 lines
540 Changed paths:
541 M /branches/prog/bwa/Makefile
542 M /branches/prog/bwa/bwtsw2.h
543 M /branches/prog/bwa/bwtsw2_aux.c
544 M /branches/prog/bwa/bwtsw2_main.c
545 M /branches/prog/bwa/main.c
546
547 * bwa-0.4.9-29 (r1179)
548 * preliminary mutli-threading support in dbwtsw
549
550 ------------------------------------------------------------------------
551 r1178 | lh3 | 2009-08-03 09:14:54 -0400 (Mon, 03 Aug 2009) | 3 lines
552 Changed paths:
553 M /branches/prog/bwa/bwtsw2_aux.c
554 M /branches/prog/bwa/bwtsw2_main.c
555 M /branches/prog/bwa/main.c
556
557 * bwa-0.4.9-28 (r1178)
558 * fixed a bug in printing repetitive hits
559
560 ------------------------------------------------------------------------
561 r1177 | lh3 | 2009-08-03 05:03:42 -0400 (Mon, 03 Aug 2009) | 3 lines
562 Changed paths:
563 M /branches/prog/bwa/bwtsw2_core.c
564 M /branches/prog/bwa/main.c
565
566 * bwa-0.4.9-27 (r1177)
567 * bwtsw2: fixed a hidden memory leak
568
569 ------------------------------------------------------------------------
570 r1176 | lh3 | 2009-07-31 10:58:24 -0400 (Fri, 31 Jul 2009) | 3 lines
571 Changed paths:
572 M /branches/prog/bwa/bwtsw2_aux.c
573 M /branches/prog/bwa/bwtsw2_main.c
574 M /branches/prog/bwa/main.c
575
576 * bwa-0.4.9-26
577 * change the way mapping quality is calculated
578
579 ------------------------------------------------------------------------
580 r1175 | lh3 | 2009-07-31 09:15:54 -0400 (Fri, 31 Jul 2009) | 4 lines
581 Changed paths:
582 M /branches/prog/bwa/bwtsw2.h
583 M /branches/prog/bwa/bwtsw2_aux.c
584 M /branches/prog/bwa/bwtsw2_core.c
585 M /branches/prog/bwa/bwtsw2_main.c
586 M /branches/prog/bwa/main.c
587
588 * bwa-0.4.9-25
589 * code clean up
590 * automatically adjust ->t and ->is_rev based on input
591
592 ------------------------------------------------------------------------
593 r1174 | lh3 | 2009-07-30 08:50:25 -0400 (Thu, 30 Jul 2009) | 3 lines
594 Changed paths:
595 M /branches/prog/bwa/bwtsw2_aux.c
596 M /branches/prog/bwa/main.c
597
598 * bwa-0.4.9-24
599 * fixed a bug in printing the hits
600
601 ------------------------------------------------------------------------
602 r1173 | lh3 | 2009-07-29 18:32:43 -0400 (Wed, 29 Jul 2009) | 4 lines
603 Changed paths:
604 M /branches/prog/bwa/bwtsw2.h
605 M /branches/prog/bwa/bwtsw2_aux.c
606 M /branches/prog/bwa/bwtsw2_main.c
607 M /branches/prog/bwa/main.c
608
609 * bwa-0.4.9-23
610 * allow to skip reverse alignment
611 * increase opt->t to 37
612
613 ------------------------------------------------------------------------
614 r1172 | lh3 | 2009-07-29 17:22:39 -0400 (Wed, 29 Jul 2009) | 3 lines
615 Changed paths:
616 M /branches/prog/bwa/bwtsw2_aux.c
617 M /branches/prog/bwa/bwtsw2_main.c
618 M /branches/prog/bwa/main.c
619
620 * bwa-0.4.9-22
621 * report if the hit is found in both directions
622
623 ------------------------------------------------------------------------
624 r1171 | lh3 | 2009-07-29 17:12:02 -0400 (Wed, 29 Jul 2009) | 3 lines
625 Changed paths:
626 M /branches/prog/bwa/bwtsw2.h
627 M /branches/prog/bwa/bwtsw2_aux.c
628 M /branches/prog/bwa/bwtsw2_main.c
629 M /branches/prog/bwa/main.c
630
631 * bwa-0.4.9-21
632 * dbwtsw: map to both forward and reverse BWT to reduce false alignment
633
634 ------------------------------------------------------------------------
635 r1170 | lh3 | 2009-07-29 15:25:14 -0400 (Wed, 29 Jul 2009) | 2 lines
636 Changed paths:
637 M /branches/prog/bwa/bwtsw2_core.c
638 M /branches/prog/bwa/main.c
639
640 save hits before cut_tail()
641
642 ------------------------------------------------------------------------
643 r1169 | lh3 | 2009-07-29 08:06:01 -0400 (Wed, 29 Jul 2009) | 3 lines
644 Changed paths:
645 M /branches/prog/bwa/bwtsw2.h
646 M /branches/prog/bwa/bwtsw2_aux.c
647 M /branches/prog/bwa/bwtsw2_core.c
648 M /branches/prog/bwa/main.c
649 M /branches/prog/bwa/stdaln.c
650 M /branches/prog/bwa/stdaln.h
651
652 * bwa-0.4.9-19
653 * use a global memory pool to reduce the CPU time spent on malloc/free().
654
655 ------------------------------------------------------------------------
656 r1168 | lh3 | 2009-07-29 06:13:29 -0400 (Wed, 29 Jul 2009) | 5 lines
657 Changed paths:
658 M /branches/prog/bwa/bwtsw2.h
659 M /branches/prog/bwa/bwtsw2_aux.c
660 M /branches/prog/bwa/bwtsw2_core.c
661 M /branches/prog/bwa/bwtsw2_main.c
662 M /branches/prog/bwa/main.c
663
664 * bwa-0.4.9-18
665 * reduce unnecessary extension to the 5'-end
666 * allow to use different interval size for the 2 rounds
667 * change default parameters
668
669 ------------------------------------------------------------------------
670 r1167 | lh3 | 2009-07-28 19:06:17 -0400 (Tue, 28 Jul 2009) | 3 lines
671 Changed paths:
672 M /branches/prog/bwa/bwtsw2_core.c
673 M /branches/prog/bwa/main.c
674
675 * bwa-0.4.9-17
676 * dbwtsw: fixed THE memory leak.
677
678 ------------------------------------------------------------------------
679 r1166 | lh3 | 2009-07-28 16:31:41 -0400 (Tue, 28 Jul 2009) | 5 lines
680 Changed paths:
681 M /branches/prog/bwa/bwtsw2_aux.c
682 M /branches/prog/bwa/bwtsw2_core.c
683 M /branches/prog/bwa/bwtsw2_main.c
684 M /branches/prog/bwa/main.c
685 M /branches/prog/bwa/stdaln.c
686
687 * bwa-0.4.9-16
688 * fixed a memory leak
689 * a small memory leak still occurs to bwtsw2_core(). I will work on that later.
690 * changed the default parameters
691
692 ------------------------------------------------------------------------
693 r1165 | lh3 | 2009-07-28 10:15:40 -0400 (Tue, 28 Jul 2009) | 4 lines
694 Changed paths:
695 M /branches/prog/bwa/bwtsw2_aux.c
696 M /branches/prog/bwa/bwtsw2_core.c
697 M /branches/prog/bwa/main.c
698 M /branches/prog/bwa/stdaln.c
699
700 * bwa-0.4.9-15
701 * generate CIGAR right before output. This saves unnecessary computation.
702 * this version may be buggy as I have not tested it.
703
704 ------------------------------------------------------------------------
705 r1164 | lh3 | 2009-07-28 09:04:14 -0400 (Tue, 28 Jul 2009) | 11 lines
706 Changed paths:
707 M /branches/prog/bwa/bwtsw2.h
708 M /branches/prog/bwa/bwtsw2_aux.c
709 M /branches/prog/bwa/bwtsw2_core.c
710 M /branches/prog/bwa/main.c
711 M /branches/prog/bwa/stdaln.c
712 M /branches/prog/bwa/stdaln.h
713
714 * bwa-0.4.9-14
715
716 * deplete unique hits in dbwtsw and postprocess them with standard sw
717
718 * in principle, this stratgy should be faster and more accurate, but I
719 have not tested this point. I may switch back to the old method if
720 this does not work.
721
722 * the code looks quite nasty now. it needs clean up...
723
724
725 ------------------------------------------------------------------------
726 r1163 | lh3 | 2009-07-27 17:41:10 -0400 (Mon, 27 Jul 2009) | 2 lines
727 Changed paths:
728 M /branches/prog/bwa/bwtsw2_aux.c
729
730 change a default parameter
731
732 ------------------------------------------------------------------------
733 r1162 | lh3 | 2009-07-27 17:04:35 -0400 (Mon, 27 Jul 2009) | 3 lines
734 Changed paths:
735 M /branches/prog/bwa/bwtsw2.h
736 M /branches/prog/bwa/bwtsw2_aux.c
737 M /branches/prog/bwa/bwtsw2_core.c
738 M /branches/prog/bwa/bwtsw2_main.c
739 M /branches/prog/bwa/main.c
740
741 * bwa-0.4.9-13
742 * dbwtsw: switch between small and large Z-best
743
744 ------------------------------------------------------------------------
745 r1161 | lh3 | 2009-07-27 12:17:41 -0400 (Mon, 27 Jul 2009) | 4 lines
746 Changed paths:
747 M /branches/prog/bwa/bwtsw2_aux.c
748 M /branches/prog/bwa/bwtsw2_core.c
749 M /branches/prog/bwa/main.c
750
751 * bwa-0.4.9-12
752 * changed the default -z to 100
753 * heuristically speed up alignments for polyA reads
754
755 ------------------------------------------------------------------------
756 r1160 | lh3 | 2009-07-27 07:50:57 -0400 (Mon, 27 Jul 2009) | 6 lines
757 Changed paths:
758 M /branches/prog/bwa/bwtsw2.h
759 M /branches/prog/bwa/bwtsw2_aux.c
760 M /branches/prog/bwa/bwtsw2_core.c
761 M /branches/prog/bwa/main.c
762
763 * bwa-0.4.9-11
764
765 * dbwtsw potentially generates less false alignments, although in
766 practice, the modification brings no improvement.
767
768
769 ------------------------------------------------------------------------
770 r1159 | lh3 | 2009-07-27 04:37:02 -0400 (Mon, 27 Jul 2009) | 4 lines
771 Changed paths:
772 M /branches/prog/bwa/bwase.c
773 M /branches/prog/bwa/bwtsw2_aux.c
774 M /branches/prog/bwa/bwtsw2_core.c
775 M /branches/prog/bwa/main.c
776
777 * bwa-0.4.9-10
778 * disabled debugging code
779 * add "BAM_FMU" if both ends are unmapped
780
781 ------------------------------------------------------------------------
782 r1158 | lh3 | 2009-07-24 09:36:52 -0400 (Fri, 24 Jul 2009) | 2 lines
783 Changed paths:
784 M /branches/prog/bwa/main.c
785
786 nothing, really
787
788 ------------------------------------------------------------------------
789 r1157 | lh3 | 2009-07-24 09:05:44 -0400 (Fri, 24 Jul 2009) | 3 lines
790 Changed paths:
791 M /branches/prog/bwa/bwtsw2_aux.c
792 M /branches/prog/bwa/bwtsw2_core.c
793 M /branches/prog/bwa/main.c
794
795 * bwa-0.4.9-9
796 * bwtsw2: generate SAM output
797
798 ------------------------------------------------------------------------
799 r1156 | lh3 | 2009-07-24 05:42:47 -0400 (Fri, 24 Jul 2009) | 6 lines
800 Changed paths:
801 M /branches/prog/bwa/bwape.c
802 M /branches/prog/bwa/main.c
803
804 * bwa-0.4.9-8
805
806 * fixed a weird deadloop which only happens to icc -O3. Thanks John
807 Marshall for the fix.
808
809
810 ------------------------------------------------------------------------
811 r1155 | lh3 | 2009-07-24 05:28:40 -0400 (Fri, 24 Jul 2009) | 8 lines
812 Changed paths:
813 M /branches/prog/bwa/bwtsw2_aux.c
814 M /branches/prog/bwa/bwtsw2_core.c
815 M /branches/prog/bwa/main.c
816
817 * bwa-0.4.9-7
818
819 * fixed a typo in bwtsw2 alignment. Now score from the standard SW
820 seems to agree with score from bwtsw2, except that in reporting
821 alignments, bwtsw2 may report non-optimal segments. This is expected,
822 though. I will improve in future.
823
824
825 ------------------------------------------------------------------------
826 r1154 | lh3 | 2009-07-23 17:40:20 -0400 (Thu, 23 Jul 2009) | 3 lines
827 Changed paths:
828 M /branches/prog/bwa/stdaln.c
829 M /branches/prog/bwa/stdaln.h
830
831 * aln_left_core() seems to work properly
832 * aln_local_core() has a bug... AN EVER EXISTING BUG!!!!!!!!!!!
833
834 ------------------------------------------------------------------------
835 r1153 | lh3 | 2009-07-23 17:06:09 -0400 (Thu, 23 Jul 2009) | 2 lines
836 Changed paths:
837 M /branches/prog/bwa/stdaln.c
838
839 removed debugging code...
840
841 ------------------------------------------------------------------------
842 r1152 | lh3 | 2009-07-23 17:01:00 -0400 (Thu, 23 Jul 2009) | 3 lines
843 Changed paths:
844 M /branches/prog/bwa/stdaln.c
845
846 * radical changes failed...
847 * fixed a bug
848
849 ------------------------------------------------------------------------
850 r1151 | lh3 | 2009-07-23 14:46:35 -0400 (Thu, 23 Jul 2009) | 2 lines
851 Changed paths:
852 M /branches/prog/bwa/stdaln.c
853
854 temporary changes. Will apply some radical changes to this file...
855
856 ------------------------------------------------------------------------
857 r1150 | lh3 | 2009-07-23 10:09:56 -0400 (Thu, 23 Jul 2009) | 2 lines
858 Changed paths:
859 M /branches/prog/bwa/bwtsw2_aux.c
860 M /branches/prog/bwa/bwtsw2_main.c
861 M /branches/prog/bwa/stdaln.c
862
863 fixed a long-existing bug in Smith-Waterman alignment
864
865 ------------------------------------------------------------------------
866 r1149 | lh3 | 2009-07-23 08:50:52 -0400 (Thu, 23 Jul 2009) | 3 lines
867 Changed paths:
868 M /branches/prog/bwa/bwtsw2.h
869 M /branches/prog/bwa/bwtsw2_aux.c
870 M /branches/prog/bwa/bwtsw2_main.c
871 M /branches/prog/bwa/main.c
872 M /branches/prog/bwa/simple_dp.c
873 M /branches/prog/bwa/stdaln.c
874 M /branches/prog/bwa/stdaln.h
875
876 * bwa-0.4.9-6
877 * unexplained inconsistency still occurs, but the results largely look reasonable.
878
879 ------------------------------------------------------------------------
880 r1148 | lh3 | 2009-07-23 08:07:29 -0400 (Thu, 23 Jul 2009) | 2 lines
881 Changed paths:
882 M /branches/prog/bwa/stdaln.c
883
884 half DP
885
886 ------------------------------------------------------------------------
887 r1147 | lh3 | 2009-07-22 08:03:06 -0400 (Wed, 22 Jul 2009) | 2 lines
888 Changed paths:
889 M /branches/prog/bwa/bwtsw2.h
890 M /branches/prog/bwa/bwtsw2_aux.c
891 M /branches/prog/bwa/bwtsw2_core.c
892 M /branches/prog/bwa/bwtsw2_main.c
893
894 a bit code clean up
895
896 ------------------------------------------------------------------------
897 r1145 | lh3 | 2009-07-21 15:52:05 -0400 (Tue, 21 Jul 2009) | 4 lines
898 Changed paths:
899 M /branches/prog/bwa/bwtsw2_aux.c
900 M /branches/prog/bwa/bwtsw2_core.c
901 M /branches/prog/bwa/main.c
902
903 * bwa-0.4.9-5
904 * fixed a bug in determining sub-optimal hits
905 * removed some debugging codes
906
907 ------------------------------------------------------------------------
908 r1144 | lh3 | 2009-07-21 10:17:29 -0400 (Tue, 21 Jul 2009) | 4 lines
909 Changed paths:
910 M /branches/prog/bwa/bwtsw2.h
911 M /branches/prog/bwa/bwtsw2_aux.c
912 M /branches/prog/bwa/bwtsw2_core.c
913 M /branches/prog/bwa/bwtsw2_main.c
914 M /branches/prog/bwa/main.c
915
916 * bwa-0.4.9-4
917 * better cmd interface
918 * faster speed
919
920 ------------------------------------------------------------------------
921 r1143 | lh3 | 2009-07-20 16:38:18 -0400 (Mon, 20 Jul 2009) | 3 lines
922 Changed paths:
923 M /branches/prog/bwa/bwtsw2.h
924 M /branches/prog/bwa/bwtsw2_aux.c
925 M /branches/prog/bwa/bwtsw2_core.c
926 M /branches/prog/bwa/bwtsw2_main.c
927 M /branches/prog/bwa/main.c
928
929 bwtsw2 (dBWT-SW) is working apparently...
930
931
932 ------------------------------------------------------------------------
933 r1139 | lh3 | 2009-07-15 05:52:18 -0400 (Wed, 15 Jul 2009) | 4 lines
934 Changed paths:
935 M /branches/prog/bwa/bwtsw2_core.c
936 M /branches/prog/bwa/main.c
937
938 * bwa-0.4.9-2
939 * bwtsw2: change cut_tail() such that it is faster but more likely to
940 miss true hits
941
942 ------------------------------------------------------------------------
943 r1138 | lh3 | 2009-07-15 05:18:42 -0400 (Wed, 15 Jul 2009) | 3 lines
944 Changed paths:
945 M /branches/prog/bwa/Makefile
946 A /branches/prog/bwa/bwt_lite.c
947 A /branches/prog/bwa/bwt_lite.h
948 A /branches/prog/bwa/bwtsw2.h
949 A /branches/prog/bwa/bwtsw2_aux.c
950 A /branches/prog/bwa/bwtsw2_core.c
951 A /branches/prog/bwa/bwtsw2_main.c
952 M /branches/prog/bwa/main.c
953 M /branches/prog/bwa/main.h
954
955 * bwa-0.4.9-1
956 * added back bwtsw2
957
958 ------------------------------------------------------------------------
959 r1075 | lh3 | 2009-05-19 05:14:50 -0400 (Tue, 19 May 2009) | 2 lines
960 Changed paths:
961 M /branches/prog/bwa/NEWS
962 M /branches/prog/bwa/bwase.c
963 M /branches/prog/bwa/main.c
964
965 Release bwa-0.4.9
966
967 ------------------------------------------------------------------------
968 r1073 | lh3 | 2009-05-18 17:13:19 -0400 (Mon, 18 May 2009) | 2 lines
969 Changed paths:
970 M /branches/prog/bwa/NEWS
971 M /branches/prog/bwa/bwa.1
972 M /branches/prog/bwa/main.c
973
974 Release bwa-0.4.8
975
976 ------------------------------------------------------------------------
977 r1069 | lh3 | 2009-05-14 09:54:54 -0400 (Thu, 14 May 2009) | 3 lines
978 Changed paths:
979 M /branches/prog/bwa/bwtaln.c
980 M /branches/prog/bwa/main.c
981
982 * bwa-0.4.7-2
983 * change the default of "aln -R" to 30
984
985 ------------------------------------------------------------------------
986 r1068 | lh3 | 2009-05-14 09:27:55 -0400 (Thu, 14 May 2009) | 3 lines
987 Changed paths:
988 M /branches/prog/bwa/bwape.c
989 M /branches/prog/bwa/bwase.c
990 M /branches/prog/bwa/bwtaln.c
991 M /branches/prog/bwa/bwtaln.h
992 M /branches/prog/bwa/bwtgap.c
993 M /branches/prog/bwa/main.c
994
995 * bwa-0.4.7-1
996 * search for suboptimal hits if the top hit is not so repetitive
997
998 ------------------------------------------------------------------------
999 r1066 | lh3 | 2009-05-12 15:31:31 -0400 (Tue, 12 May 2009) | 2 lines
1000 Changed paths:
1001 M /branches/prog/bwa/ChangeLog
1002 M /branches/prog/bwa/NEWS
1003 M /branches/prog/bwa/bwase.c
1004 M /branches/prog/bwa/main.c
1005
1006 Release bwa-0.4.7
1007
1008 ------------------------------------------------------------------------
1009 r1065 | lh3 | 2009-05-12 15:20:40 -0400 (Tue, 12 May 2009) | 3 lines
1010 Changed paths:
1011 M /branches/prog/bwa/bwape.c
1012 M /branches/prog/bwa/bwase.c
1013 M /branches/prog/bwa/main.c
1014
1015 * bwa-0.4.6-9
1016 * fixed compiling errors on some Linux machines
1017
1018 ------------------------------------------------------------------------
1019 r1064 | lh3 | 2009-05-12 07:30:46 -0400 (Tue, 12 May 2009) | 3 lines
1020 Changed paths:
1021 M /branches/prog/bwa/bwtaln.c
1022 M /branches/prog/bwa/main.c
1023
1024 * bwa-0.4.6-8
1025 * avoid compilation error on some systems.
1026
1027 ------------------------------------------------------------------------
1028 r1035 | lh3 | 2009-05-09 05:41:33 -0400 (Sat, 09 May 2009) | 4 lines
1029 Changed paths:
1030 M /branches/prog/bwa/bwape.c
1031 M /branches/prog/bwa/bwase.c
1032 M /branches/prog/bwa/main.c
1033
1034 * bwa-0.4.6-7
1035 * fixed an integer overflow caused by previous modifications
1036 * made insert size estimation more robust
1037
1038 ------------------------------------------------------------------------
1039 r1008 | lh3 | 2009-04-29 05:41:58 -0400 (Wed, 29 Apr 2009) | 4 lines
1040 Changed paths:
1041 M /branches/prog/bwa/bwase.c
1042 M /branches/prog/bwa/main.c
1043
1044 * bwa-0.4.6-5
1045 * fixed a integer overflow problem which may cause seg fault in very rare cases
1046 * made XN tags more accurate
1047
1048 ------------------------------------------------------------------------
1049 r1005 | lh3 | 2009-04-27 07:37:23 -0400 (Mon, 27 Apr 2009) | 4 lines
1050 Changed paths:
1051 M /branches/prog/bwa/bwape.c
1052 M /branches/prog/bwa/main.c
1053 M /branches/prog/bwa/simple_dp.c
1054 M /branches/prog/bwa/stdaln.c
1055 M /branches/prog/bwa/stdaln.h
1056
1057 * bwa-0.4.6-4
1058 * heuristic rules to detect suboptimal alignment
1059 * stdsw: support double-strand and protein alignment
1060
1061 ------------------------------------------------------------------------
1062 r1003 | lh3 | 2009-04-26 12:48:19 -0400 (Sun, 26 Apr 2009) | 4 lines
1063 Changed paths:
1064 M /branches/prog/bwa/main.c
1065 M /branches/prog/bwa/simple_dp.c
1066 M /branches/prog/bwa/stdaln.c
1067 M /branches/prog/bwa/stdaln.h
1068
1069 * bwa-0.4.6-2
1070 * improve the functionality of stdsw
1071 * allow to add a threshold on SW alignment. Hope this does not incur new bugs...
1072
1073 ------------------------------------------------------------------------
1074 r1002 | lh3 | 2009-04-22 03:56:15 -0400 (Wed, 22 Apr 2009) | 3 lines
1075 Changed paths:
1076 M /branches/prog/bwa/bwa.1
1077 M /branches/prog/bwa/bwape.c
1078 M /branches/prog/bwa/bwase.c
1079 M /branches/prog/bwa/bwtaln.h
1080 M /branches/prog/bwa/main.c
1081
1082 * bwa-0.4.6-1
1083 * output SM and AM tag
1084
1085 ------------------------------------------------------------------------
1086 r914 | lh3 | 2009-03-09 17:53:50 -0400 (Mon, 09 Mar 2009) | 2 lines
1087 Changed paths:
1088 M /branches/prog/bwa/ChangeLog
1089 M /branches/prog/bwa/NEWS
1090 M /branches/prog/bwa/main.c
1091
1092 Release bwa-0.4.6
1093
1094 ------------------------------------------------------------------------
1095 r913 | lh3 | 2009-03-09 17:23:24 -0400 (Mon, 09 Mar 2009) | 4 lines
1096 Changed paths:
1097 M /branches/prog/bwa/bwa.1
1098 M /branches/prog/bwa/bwape.c
1099 A /branches/prog/bwa/solid2fastq.pl
1100
1101 * added notes to bwa
1102 * added a script to convert SOLiD reads
1103 * updated documentations
1104
1105 ------------------------------------------------------------------------
1106 r912 | lh3 | 2009-03-09 16:57:05 -0400 (Mon, 09 Mar 2009) | 2 lines
1107 Changed paths:
1108 M /branches/prog/bwa/ChangeLog
1109 M /branches/prog/bwa/kstring.c
1110 M /branches/prog/bwa/main.c
1111
1112 fixed a bug in kstring
1113
1114 ------------------------------------------------------------------------
1115 r881 | lh3 | 2009-03-02 15:36:06 -0500 (Mon, 02 Mar 2009) | 3 lines
1116 Changed paths:
1117 M /branches/prog/bwa/bwtmisc.c
1118 M /branches/prog/bwa/main.c
1119
1120 * bwa-0.4.5-7
1121 * fixed a bug in pac2cspac
1122
1123 ------------------------------------------------------------------------
1124 r880 | lh3 | 2009-03-01 16:34:08 -0500 (Sun, 01 Mar 2009) | 2 lines
1125 Changed paths:
1126 M /branches/prog/bwa/Makefile
1127
1128 disable debugging
1129
1130 ------------------------------------------------------------------------
1131 r879 | lh3 | 2009-03-01 16:28:04 -0500 (Sun, 01 Mar 2009) | 3 lines
1132 Changed paths:
1133 M /branches/prog/bwa/bwase.c
1134 M /branches/prog/bwa/cs2nt.c
1135 M /branches/prog/bwa/main.c
1136
1137 * bwa-0.4.5-6
1138 * fixed problems with coordinates for color gapped alignment
1139
1140 ------------------------------------------------------------------------
1141 r878 | lh3 | 2009-03-01 13:43:09 -0500 (Sun, 01 Mar 2009) | 3 lines
1142 Changed paths:
1143 M /branches/prog/bwa/bwase.c
1144 M /branches/prog/bwa/cs2nt.c
1145 M /branches/prog/bwa/main.c
1146
1147 * bwa-0.4.5-5
1148 * added support for gapped color alignment
1149
1150 ------------------------------------------------------------------------
1151 r877 | lh3 | 2009-03-01 10:27:52 -0500 (Sun, 01 Mar 2009) | 2 lines
1152 Changed paths:
1153 M /branches/prog/bwa/Makefile
1154 M /branches/prog/bwa/bwape.c
1155 M /branches/prog/bwa/bwase.c
1156 M /branches/prog/bwa/bwtaln.h
1157 M /branches/prog/bwa/cs2nt.c
1158 M /branches/prog/bwa/main.c
1159
1160 * convert cs read to nt read (for ungapped alignment only)
1161
1162 ------------------------------------------------------------------------
1163 r860 | lh3 | 2009-02-27 08:58:39 -0500 (Fri, 27 Feb 2009) | 2 lines
1164 Changed paths:
1165 M /branches/prog/bwa/Makefile
1166 M /branches/prog/bwa/bwase.c
1167 A /branches/prog/bwa/cs2nt.c
1168
1169 prepare to implement cs->nt conversion (have not yet...)
1170
1171 ------------------------------------------------------------------------
1172 r859 | lh3 | 2009-02-27 07:00:03 -0500 (Fri, 27 Feb 2009) | 3 lines
1173 Changed paths:
1174 M /branches/prog/bwa/bntseq.c
1175 M /branches/prog/bwa/bntseq.h
1176 M /branches/prog/bwa/bwtindex.c
1177 M /branches/prog/bwa/bwtmisc.c
1178 M /branches/prog/bwa/main.c
1179 M /branches/prog/bwa/main.h
1180
1181 * bwa-0.4.5-3
1182 * generate color index from nucleotide fasta reference
1183
1184 ------------------------------------------------------------------------
1185 r857 | lh3 | 2009-02-26 10:22:58 -0500 (Thu, 26 Feb 2009) | 4 lines
1186 Changed paths:
1187 M /branches/prog/bwa/bwape.c
1188 M /branches/prog/bwa/main.c
1189
1190 * bwa-0.4.5-2
1191 * improved mapping quality a bit if one end falls in a tandem repeat
1192 but the mate is unique.
1193
1194 ------------------------------------------------------------------------
1195 r856 | lh3 | 2009-02-26 10:02:29 -0500 (Thu, 26 Feb 2009) | 3 lines
1196 Changed paths:
1197 M /branches/prog/bwa/bwape.c
1198 M /branches/prog/bwa/bwtaln.h
1199 M /branches/prog/bwa/main.c
1200
1201 * bwa-0.4.5-1
1202 * make bwa work for SOLiD reads
1203
1204 ------------------------------------------------------------------------
1205 r828 | lh3 | 2009-02-18 17:36:41 -0500 (Wed, 18 Feb 2009) | 2 lines
1206 Changed paths:
1207 M /branches/prog/bwa/ChangeLog
1208 M /branches/prog/bwa/NEWS
1209 M /branches/prog/bwa/bwa.1
1210 M /branches/prog/bwa/main.c
1211
1212 Release bwa-0.4.5
1213
1214 ------------------------------------------------------------------------
1215 r827 | lh3 | 2009-02-18 16:48:48 -0500 (Wed, 18 Feb 2009) | 3 lines
1216 Changed paths:
1217 M /branches/prog/bwa/main.c
1218 M /branches/prog/bwa/stdaln.c
1219 M /branches/prog/bwa/stdaln.h
1220
1221 * bwa-0.4.4-6
1222 * fixed a bug in SW alignment when no residue matches
1223
1224 ------------------------------------------------------------------------
1225 r824 | lh3 | 2009-02-17 05:33:07 -0500 (Tue, 17 Feb 2009) | 3 lines
1226 Changed paths:
1227 M /branches/prog/bwa/bwape.c
1228 M /branches/prog/bwa/main.c
1229
1230 * bwa-0.4.4-5
1231 * fixed that bounary bug
1232
1233 ------------------------------------------------------------------------
1234 r823 | lh3 | 2009-02-17 04:54:18 -0500 (Tue, 17 Feb 2009) | 2 lines
1235 Changed paths:
1236 M /branches/prog/bwa/ChangeLog
1237 M /branches/prog/bwa/bwape.c
1238
1239 just change some logging information
1240
1241 ------------------------------------------------------------------------
1242 r822 | lh3 | 2009-02-17 04:20:39 -0500 (Tue, 17 Feb 2009) | 2 lines
1243 Changed paths:
1244 M /branches/prog/bwa/bwa.1
1245
1246 update manual
1247
1248 ------------------------------------------------------------------------
1249 r821 | lh3 | 2009-02-17 04:11:14 -0500 (Tue, 17 Feb 2009) | 3 lines
1250 Changed paths:
1251 M /branches/prog/bwa/bwape.c
1252 M /branches/prog/bwa/bwase.c
1253 M /branches/prog/bwa/main.c
1254
1255 * bwa-0.4.4-4
1256 * fixed a bug on boundary check in pair_sw
1257
1258 ------------------------------------------------------------------------
1259 r820 | lh3 | 2009-02-16 17:43:37 -0500 (Mon, 16 Feb 2009) | 3 lines
1260 Changed paths:
1261 M /branches/prog/bwa/bwtaln.c
1262 M /branches/prog/bwa/main.c
1263
1264 * bwa-0.4.4-3
1265 * allow to change mismatch penalty
1266
1267 ------------------------------------------------------------------------
1268 r819 | lh3 | 2009-02-16 17:40:28 -0500 (Mon, 16 Feb 2009) | 4 lines
1269 Changed paths:
1270 M /branches/prog/bwa/bwtaln.c
1271 M /branches/prog/bwa/main.c
1272
1273 * bwa-0.4.4-2
1274 * remove timer
1275 * allow to change default gapo and gape penalty at the command line
1276
1277 ------------------------------------------------------------------------
1278 r818 | lh3 | 2009-02-16 09:30:51 -0500 (Mon, 16 Feb 2009) | 2 lines
1279 Changed paths:
1280 M /branches/prog/bwa/bwa.1
1281
1282 update benchmark
1283
1284 ------------------------------------------------------------------------
1285 r817 | lh3 | 2009-02-16 08:44:40 -0500 (Mon, 16 Feb 2009) | 4 lines
1286 Changed paths:
1287 M /branches/prog/bwa/bwape.c
1288 M /branches/prog/bwa/bwtaln.c
1289 M /branches/prog/bwa/kvec.h
1290 M /branches/prog/bwa/main.c
1291
1292 * bwa-0.4.4-1
1293 * automatically detect insert size
1294 * use insert size in pairing. This may potentially improve accuracy (untested!)
1295
1296 ------------------------------------------------------------------------
1297 r814 | lh3 | 2009-02-15 11:10:23 -0500 (Sun, 15 Feb 2009) | 2 lines
1298 Changed paths:
1299 M /branches/prog/bwa/ChangeLog
1300 M /branches/prog/bwa/NEWS
1301 M /branches/prog/bwa/main.c
1302
1303 Release bwa-0.4.4
1304
1305 ------------------------------------------------------------------------
1306 r813 | lh3 | 2009-02-15 10:22:50 -0500 (Sun, 15 Feb 2009) | 3 lines
1307 Changed paths:
1308 M /branches/prog/bwa/bwa.1
1309 M /branches/prog/bwa/bwase.c
1310 M /branches/prog/bwa/main.c
1311
1312 * bwa-0.4.3-5
1313 * impose boundary check in refine_gapped
1314
1315 ------------------------------------------------------------------------
1316 r811 | lh3 | 2009-02-14 09:46:13 -0500 (Sat, 14 Feb 2009) | 3 lines
1317 Changed paths:
1318 M /branches/prog/bwa/bwase.c
1319 M /branches/prog/bwa/main.c
1320
1321 * bwa-0.4.3-4
1322 * change MD tag to match the latest SAM specification
1323
1324 ------------------------------------------------------------------------
1325 r810 | lh3 | 2009-02-13 04:46:04 -0500 (Fri, 13 Feb 2009) | 2 lines
1326 Changed paths:
1327 M /branches/prog/bwa/ChangeLog
1328
1329 update ChangeLog
1330
1331 ------------------------------------------------------------------------
1332 r799 | lh3 | 2009-02-05 12:01:17 -0500 (Thu, 05 Feb 2009) | 2 lines
1333 Changed paths:
1334 M /branches/prog/bwa/bwase.c
1335 M /branches/prog/bwa/main.c
1336
1337 change MD tag to meet the latest SAM specification
1338
1339 ------------------------------------------------------------------------
1340 r796 | lh3 | 2009-02-05 08:35:13 -0500 (Thu, 05 Feb 2009) | 3 lines
1341 Changed paths:
1342 M /branches/prog/bwa/bntseq.c
1343 M /branches/prog/bwa/bwase.c
1344 M /branches/prog/bwa/main.c
1345
1346 * bwa-0.4.3-2
1347 * fixed a bug on counting 'N'
1348
1349 ------------------------------------------------------------------------
1350 r795 | lh3 | 2009-02-05 07:41:27 -0500 (Thu, 05 Feb 2009) | 4 lines
1351 Changed paths:
1352 M /branches/prog/bwa/bwa.1
1353 M /branches/prog/bwa/bwape.c
1354 M /branches/prog/bwa/main.c
1355
1356 * bwa-0.4.3-1
1357 * fixed potential boundary problems
1358 * update benchmark result
1359
1360 ------------------------------------------------------------------------
1361 r791 | lh3 | 2009-01-25 05:20:47 -0500 (Sun, 25 Jan 2009) | 2 lines
1362 Changed paths:
1363 M /branches/prog/bwa/bwa.1
1364
1365 update some numbers
1366
1367 ------------------------------------------------------------------------
1368 r790 | lh3 | 2009-01-24 15:13:03 -0500 (Sat, 24 Jan 2009) | 2 lines
1369 Changed paths:
1370 M /branches/prog/bwa/bwa.1
1371
1372 update benchmark
1373
1374 ------------------------------------------------------------------------
1375 r789 | lh3 | 2009-01-22 10:18:44 -0500 (Thu, 22 Jan 2009) | 2 lines
1376 Changed paths:
1377 M /branches/prog/bwa/bwtindex.c
1378
1379 a warning message for index
1380
1381 ------------------------------------------------------------------------
1382 r788 | lh3 | 2009-01-22 09:54:06 -0500 (Thu, 22 Jan 2009) | 2 lines
1383 Changed paths:
1384 M /branches/prog/bwa/main.c
1385
1386 forget to change release number
1387
1388 ------------------------------------------------------------------------
1389 r786 | lh3 | 2009-01-22 06:27:39 -0500 (Thu, 22 Jan 2009) | 2 lines
1390 Changed paths:
1391 M /branches/prog/bwa/NEWS
1392
1393 Release bwa-0.4.3
1394
1395 ------------------------------------------------------------------------
1396 r785 | lh3 | 2009-01-22 06:27:16 -0500 (Thu, 22 Jan 2009) | 2 lines
1397 Changed paths:
1398 M /branches/prog/bwa/ChangeLog
1399 M /branches/prog/bwa/NEWS
1400
1401 Release bwa-0.4.3
1402
1403 ------------------------------------------------------------------------
1404 r784 | lh3 | 2009-01-22 06:19:59 -0500 (Thu, 22 Jan 2009) | 4 lines
1405 Changed paths:
1406 M /branches/prog/bwa/bwa.1
1407 M /branches/prog/bwa/bwase.c
1408 M /branches/prog/bwa/main.c
1409
1410 * bwa-0.4.2-10
1411 * update documentation
1412 * fixed a bug on generating MD tags for SW alignment
1413
1414 ------------------------------------------------------------------------
1415 r782 | lh3 | 2009-01-19 12:08:38 -0500 (Mon, 19 Jan 2009) | 3 lines
1416 Changed paths:
1417 M /branches/prog/bwa/bwase.c
1418 M /branches/prog/bwa/main.c
1419
1420 * bwa-0.4.2-9
1421 * fixed a bug in samse -n...
1422
1423 ------------------------------------------------------------------------
1424 r781 | lh3 | 2009-01-19 11:26:37 -0500 (Mon, 19 Jan 2009) | 3 lines
1425 Changed paths:
1426 M /branches/prog/bwa/bwtaln.c
1427 M /branches/prog/bwa/main.c
1428
1429 * bwa-0.4.2-8
1430 * given -N, the previous version would stop if the top hit is a repeat. Now changed.
1431
1432 ------------------------------------------------------------------------
1433 r780 | lh3 | 2009-01-19 11:20:18 -0500 (Mon, 19 Jan 2009) | 4 lines
1434 Changed paths:
1435 M /branches/prog/bwa/bwape.c
1436 M /branches/prog/bwa/bwase.c
1437 M /branches/prog/bwa/bwtaln.c
1438 M /branches/prog/bwa/bwtaln.h
1439 M /branches/prog/bwa/bwtgap.c
1440 M /branches/prog/bwa/main.c
1441
1442 * bwa-0.4.2-7
1443 * use a bit-wise flag to replace some member variables in the option struct
1444 * allow to switch off the iterative strategy
1445
1446 ------------------------------------------------------------------------
1447 r779 | lh3 | 2009-01-19 10:45:57 -0500 (Mon, 19 Jan 2009) | 3 lines
1448 Changed paths:
1449 M /branches/prog/bwa/bwa.1
1450 M /branches/prog/bwa/bwase.c
1451 M /branches/prog/bwa/main.c
1452
1453 * bwa-0.4.2-6
1454 * allow to dump multiple hits from samse, in another format, though
1455
1456 ------------------------------------------------------------------------
1457 r778 | lh3 | 2009-01-19 06:24:29 -0500 (Mon, 19 Jan 2009) | 5 lines
1458 Changed paths:
1459 M /branches/prog/bwa/Makefile
1460 M /branches/prog/bwa/bwape.c
1461 M /branches/prog/bwa/bwase.c
1462 M /branches/prog/bwa/bwaseqio.c
1463 M /branches/prog/bwa/bwtaln.h
1464 M /branches/prog/bwa/kseq.h
1465 A /branches/prog/bwa/kstring.c
1466 A /branches/prog/bwa/kstring.h
1467 M /branches/prog/bwa/main.c
1468 M /branches/prog/bwa/simple_dp.c
1469
1470 * bwa-0.4.2-5
1471 * update kseq.h to the latest version
1472 * generate MD tag
1473 * print mate coordinate if only one end is unmapped
1474
1475 ------------------------------------------------------------------------
1476 r775 | lh3 | 2009-01-18 05:40:35 -0500 (Sun, 18 Jan 2009) | 3 lines
1477 Changed paths:
1478 M /branches/prog/bwa/bwase.c
1479 M /branches/prog/bwa/main.c
1480
1481 * bwa-0.4.2-4
1482 * fixed a bug for SAM format
1483
1484 ------------------------------------------------------------------------
1485 r774 | lh3 | 2009-01-17 13:48:52 -0500 (Sat, 17 Jan 2009) | 4 lines
1486 Changed paths:
1487 M /branches/prog/bwa/bwtaln.c
1488 M /branches/prog/bwa/main.c
1489
1490 * bwa-0.4.2-3
1491 * change default fnr to 0.04
1492 * print max_diff for valid fnr
1493
1494 ------------------------------------------------------------------------
1495 r773 | lh3 | 2009-01-17 05:54:37 -0500 (Sat, 17 Jan 2009) | 3 lines
1496 Changed paths:
1497 M /branches/prog/bwa/bwape.c
1498 M /branches/prog/bwa/bwase.c
1499 M /branches/prog/bwa/bwtaln.c
1500 M /branches/prog/bwa/bwtaln.h
1501 M /branches/prog/bwa/main.c
1502
1503 * bwa-0.4.2-2
1504 * automatically choose max_diff
1505
1506 ------------------------------------------------------------------------
1507 r772 | lh3 | 2009-01-16 18:16:14 -0500 (Fri, 16 Jan 2009) | 3 lines
1508 Changed paths:
1509 M /branches/prog/bwa/bwaseqio.c
1510 M /branches/prog/bwa/bwt.c
1511 M /branches/prog/bwa/bwtaln.c
1512 M /branches/prog/bwa/bwtaln.h
1513 M /branches/prog/bwa/bwtgap.c
1514 M /branches/prog/bwa/main.c
1515
1516 * bwa-0.4.2-1
1517 * take N as a mismatch
1518
1519 ------------------------------------------------------------------------
1520 r768 | lh3 | 2009-01-09 11:57:23 -0500 (Fri, 09 Jan 2009) | 2 lines
1521 Changed paths:
1522 M /branches/prog/bwa/ChangeLog
1523 M /branches/prog/bwa/NEWS
1524 M /branches/prog/bwa/bntseq.c
1525 M /branches/prog/bwa/main.c
1526
1527 Release bwa-0.4.2
1528
1529 ------------------------------------------------------------------------
1530 r759 | lh3 | 2009-01-07 09:55:43 -0500 (Wed, 07 Jan 2009) | 2 lines
1531 Changed paths:
1532 M /branches/prog/bwa/ChangeLog
1533 M /branches/prog/bwa/NEWS
1534 M /branches/prog/bwa/bwa.1
1535 M /branches/prog/bwa/bwape.c
1536 M /branches/prog/bwa/bwtaln.h
1537 M /branches/prog/bwa/main.c
1538
1539 Release bwa-0.4.1
1540
1541 ------------------------------------------------------------------------
1542 r758 | lh3 | 2009-01-07 05:36:06 -0500 (Wed, 07 Jan 2009) | 3 lines
1543 Changed paths:
1544 M /branches/prog/bwa/bwape.c
1545 M /branches/prog/bwa/bwase.c
1546 M /branches/prog/bwa/bwtaln.h
1547 M /branches/prog/bwa/main.c
1548
1549 * bwa-0.4.0-2
1550 * make mate_sw fully working
1551
1552 ------------------------------------------------------------------------
1553 r757 | lh3 | 2009-01-06 18:04:29 -0500 (Tue, 06 Jan 2009) | 5 lines
1554 Changed paths:
1555 M /branches/prog/bwa/bwape.c
1556 M /branches/prog/bwa/bwase.c
1557 M /branches/prog/bwa/bwaseqio.c
1558 M /branches/prog/bwa/bwtaln.h
1559 M /branches/prog/bwa/main.c
1560
1561 * bwa-0.4.0-1
1562 * do SW alignment for unmapped mate. It is working.
1563 * I still need to do some extra work for SW alignment, but it is too late
1564 and I am getting tired... I will do tomorrow.
1565
1566 ------------------------------------------------------------------------
1567 r755 | lh3 | 2009-01-06 10:23:29 -0500 (Tue, 06 Jan 2009) | 2 lines
1568 Changed paths:
1569 M /branches/prog/bwa/ChangeLog
1570 M /branches/prog/bwa/NEWS
1571 M /branches/prog/bwa/bwa.1
1572 M /branches/prog/bwa/main.c
1573
1574 Release bwa-0.4.0
1575
1576 ------------------------------------------------------------------------
1577 r754 | lh3 | 2009-01-06 07:45:02 -0500 (Tue, 06 Jan 2009) | 3 lines
1578 Changed paths:
1579 M /branches/prog/bwa/bwtaln.c
1580 M /branches/prog/bwa/bwtgap.c
1581 M /branches/prog/bwa/bwtgap.h
1582 M /branches/prog/bwa/main.c
1583
1584 * bwa-0.3.0-12
1585 * better lock
1586
1587 ------------------------------------------------------------------------
1588 r753 | lh3 | 2009-01-06 06:17:21 -0500 (Tue, 06 Jan 2009) | 5 lines
1589 Changed paths:
1590 M /branches/prog/bwa/Makefile
1591 M /branches/prog/bwa/bwaseqio.c
1592 M /branches/prog/bwa/bwtaln.c
1593 M /branches/prog/bwa/bwtaln.h
1594 M /branches/prog/bwa/bwtgap.c
1595 M /branches/prog/bwa/main.c
1596
1597 * bwa-0.3.0-11
1598 * fixed a small memory leak in bwa_seq_close()
1599 * fixed "uninitialized memory" from bwt_aln1_t
1600 * multithreading for "aln" command
1601
1602 ------------------------------------------------------------------------
1603 r752 | lh3 | 2009-01-05 17:34:13 -0500 (Mon, 05 Jan 2009) | 3 lines
1604 Changed paths:
1605 M /branches/prog/bwa/Makefile
1606 D /branches/prog/bwa/bwt2fmv.c
1607 M /branches/prog/bwa/bwt_gen/bwt_gen.c
1608 A /branches/prog/bwa/bwtmisc.c (from /branches/prog/bwa/pac2bwt.c:748)
1609 M /branches/prog/bwa/main.c
1610 M /branches/prog/bwa/main.h
1611 D /branches/prog/bwa/pac2bwt.c
1612
1613 * bwa-0.3.0-10
1614 * a little bit code clean up
1615
1616 ------------------------------------------------------------------------
1617 r751 | lh3 | 2009-01-05 17:19:04 -0500 (Mon, 05 Jan 2009) | 3 lines
1618 Changed paths:
1619 M /branches/prog/bwa/bwt.c
1620 M /branches/prog/bwa/main.c
1621
1622 * bwa-0.3.0-9
1623 * use 64-bit integer to speed up Occ calculate, although just a little bit
1624
1625 ------------------------------------------------------------------------
1626 r750 | lh3 | 2009-01-05 16:44:26 -0500 (Mon, 05 Jan 2009) | 3 lines
1627 Changed paths:
1628 M /branches/prog/bwa/bwt.c
1629 M /branches/prog/bwa/main.c
1630
1631 * bwa-0.3.0-8
1632 * a little bit code cleanup
1633
1634 ------------------------------------------------------------------------
1635 r749 | lh3 | 2009-01-05 16:37:28 -0500 (Mon, 05 Jan 2009) | 3 lines
1636 Changed paths:
1637 M /branches/prog/bwa/bwt.c
1638 M /branches/prog/bwa/main.c
1639
1640 * bwa-0.1.0-7
1641 * accelerate Occ calculation
1642
1643 ------------------------------------------------------------------------
1644 r748 | lh3 | 2009-01-05 16:12:28 -0500 (Mon, 05 Jan 2009) | 4 lines
1645 Changed paths:
1646 M /branches/prog/bwa/bwape.c
1647 M /branches/prog/bwa/bwase.c
1648 M /branches/prog/bwa/bwt.c
1649 M /branches/prog/bwa/bwt.h
1650 M /branches/prog/bwa/bwt2fmv.c
1651 M /branches/prog/bwa/bwtaln.c
1652 M /branches/prog/bwa/bwtindex.c
1653 M /branches/prog/bwa/bwtio.c
1654 M /branches/prog/bwa/main.c
1655 M /branches/prog/bwa/main.h
1656 M /branches/prog/bwa/pac2bwt.c
1657
1658 * bwa-0.3.0-6
1659 * put occ table along with bwt to save another cache miss
1660 * this version is already faster than the previous and I can still improve it...
1661
1662 ------------------------------------------------------------------------
1663 r747 | lh3 | 2009-01-05 10:16:18 -0500 (Mon, 05 Jan 2009) | 5 lines
1664 Changed paths:
1665 M /branches/prog/bwa/bwt.c
1666 M /branches/prog/bwa/bwt.h
1667 M /branches/prog/bwa/bwtio.c
1668 M /branches/prog/bwa/main.c
1669
1670 * bwa-0.3.0-5
1671 * remove occ_major to save a cache miss; however, OCC_INTERVAL has to be
1672 increased to keep the same memory. As a result, the speed is a little
1673 slower in fact.
1674
1675 ------------------------------------------------------------------------
1676 r746 | lh3 | 2009-01-05 09:50:53 -0500 (Mon, 05 Jan 2009) | 3 lines
1677 Changed paths:
1678 M /branches/prog/bwa/bwt.c
1679 M /branches/prog/bwa/main.c
1680
1681 * bwa-0.3.0-4
1682 * added back optimization codes (it is a pain...)
1683
1684 ------------------------------------------------------------------------
1685 r745 | lh3 | 2009-01-05 08:23:00 -0500 (Mon, 05 Jan 2009) | 3 lines
1686 Changed paths:
1687 M /branches/prog/bwa/bwt.c
1688 M /branches/prog/bwa/bwtaln.c
1689 M /branches/prog/bwa/main.c
1690
1691 * bwa-0.3.0-3
1692 * faster bit operations
1693
1694 ------------------------------------------------------------------------
1695 r744 | lh3 | 2009-01-05 05:58:46 -0500 (Mon, 05 Jan 2009) | 4 lines
1696 Changed paths:
1697 M /branches/prog/bwa/bwt.c
1698 M /branches/prog/bwa/main.c
1699
1700 * bwa-0.3.0-2
1701 * removed optimization codes again...
1702 * use a new method to count the bits
1703
1704 ------------------------------------------------------------------------
1705 r743 | lh3 | 2009-01-04 17:18:38 -0500 (Sun, 04 Jan 2009) | 5 lines
1706 Changed paths:
1707 M /branches/prog/bwa/bwa.1
1708 M /branches/prog/bwa/bwt.c
1709 M /branches/prog/bwa/bwtaln.c
1710 M /branches/prog/bwa/bwtaln.h
1711 M /branches/prog/bwa/bwtgap.c
1712 M /branches/prog/bwa/main.c
1713
1714 * bwa-0.3.0-1
1715 * added back the optimization codes
1716 * added a new option to aln: max_entries, although this is disabled by default
1717 * updated benchmark
1718
1719 ------------------------------------------------------------------------
1720 r742 | lh3 | 2009-01-04 07:56:12 -0500 (Sun, 04 Jan 2009) | 2 lines
1721 Changed paths:
1722 M /branches/prog/bwa/bwa.1
1723
1724 add URL
1725
1726 ------------------------------------------------------------------------
1727 r740 | lh3 | 2009-01-04 07:39:43 -0500 (Sun, 04 Jan 2009) | 2 lines
1728 Changed paths:
1729 M /branches/prog/bwa/ChangeLog
1730 M /branches/prog/bwa/NEWS
1731 M /branches/prog/bwa/bwa.1
1732 M /branches/prog/bwa/main.c
1733
1734 Release bwa-0.3.0
1735
1736 ------------------------------------------------------------------------
1737 r739 | lh3 | 2009-01-04 06:55:06 -0500 (Sun, 04 Jan 2009) | 2 lines
1738 Changed paths:
1739 A /branches/prog/bwa/COPYING
1740 M /branches/prog/bwa/ChangeLog
1741 M /branches/prog/bwa/bntseq.c
1742 M /branches/prog/bwa/bntseq.h
1743 M /branches/prog/bwa/bwa.1
1744 M /branches/prog/bwa/bwt.c
1745 M /branches/prog/bwa/bwt.h
1746 M /branches/prog/bwa/bwtindex.c
1747 M /branches/prog/bwa/utils.c
1748 M /branches/prog/bwa/utils.h
1749
1750 added licensing information
1751
1752 ------------------------------------------------------------------------
1753 r738 | lh3 | 2009-01-04 06:18:25 -0500 (Sun, 04 Jan 2009) | 4 lines
1754 Changed paths:
1755 M /branches/prog/bwa/bwa.1
1756 M /branches/prog/bwa/bwape.c
1757 M /branches/prog/bwa/main.c
1758
1759 * bwa-0.2.0-31
1760 * better mapping quality
1761 * update benchmark
1762
1763 ------------------------------------------------------------------------
1764 r737 | lh3 | 2009-01-03 16:00:58 -0500 (Sat, 03 Jan 2009) | 2 lines
1765 Changed paths:
1766 M /branches/prog/bwa/ChangeLog
1767 M /branches/prog/bwa/bwa.1
1768
1769 update documentation
1770
1771 ------------------------------------------------------------------------
1772 r736 | lh3 | 2009-01-02 10:26:38 -0500 (Fri, 02 Jan 2009) | 2 lines
1773 Changed paths:
1774 M /branches/prog/bwa/bwa.1
1775
1776 update documentation
1777
1778 ------------------------------------------------------------------------
1779 r735 | lh3 | 2009-01-02 07:10:20 -0500 (Fri, 02 Jan 2009) | 4 lines
1780 Changed paths:
1781 M /branches/prog/bwa/bwa.1
1782 M /branches/prog/bwa/bwape.c
1783 M /branches/prog/bwa/bwtaln.c
1784 M /branches/prog/bwa/main.c
1785
1786 * bwa-0.2.0-30
1787 * reduce memory a little bit
1788 * update documentation
1789
1790 ------------------------------------------------------------------------
1791 r734 | lh3 | 2009-01-01 13:45:45 -0500 (Thu, 01 Jan 2009) | 8 lines
1792 Changed paths:
1793 M /branches/prog/bwa/bwa.1
1794 M /branches/prog/bwa/bwape.c
1795 M /branches/prog/bwa/bwase.c
1796 M /branches/prog/bwa/bwtaln.c
1797 M /branches/prog/bwa/bwtaln.h
1798 M /branches/prog/bwa/bwtgap.c
1799 M /branches/prog/bwa/main.c
1800
1801 * bwa-0.2.0-29
1802 * sampe: removed -O option; changed default -o to 100000
1803 * sampe: fixed a bug in calculating paired mapping quality
1804 * aln: added an option to search for suboptimal hits even if the best is a repeat.
1805 This option will make sampe MUCH SLOWER.
1806 * sampe: set isize as zero if mapped to two different chr
1807 * update manual (unfinished)
1808
1809 ------------------------------------------------------------------------
1810 r733 | lh3 | 2009-01-01 11:01:20 -0500 (Thu, 01 Jan 2009) | 3 lines
1811 Changed paths:
1812 M /branches/prog/bwa/bwape.c
1813 M /branches/prog/bwa/main.c
1814
1815 * bwa-0.2.0-28
1816 * fixed a bug in calculating paired mapping quality
1817
1818 ------------------------------------------------------------------------
1819 r732 | lh3 | 2009-01-01 09:27:46 -0500 (Thu, 01 Jan 2009) | 3 lines
1820 Changed paths:
1821 M /branches/prog/bwa/bwape.c
1822 A /branches/prog/bwa/khash.h (from /branches/prog/sclib/khash/khash.h:675)
1823 M /branches/prog/bwa/main.c
1824
1825 * bwa-0.2.0-27
1826 * accelerate sampe by storing visited large intervals
1827
1828 ------------------------------------------------------------------------
1829 r731 | lh3 | 2009-01-01 06:51:21 -0500 (Thu, 01 Jan 2009) | 3 lines
1830 Changed paths:
1831 M /branches/prog/bwa/bwt.c
1832 M /branches/prog/bwa/main.c
1833
1834 * bwa-0.2.0-26
1835 * remove the optimation codes
1836
1837 ------------------------------------------------------------------------
1838 r730 | lh3 | 2009-01-01 06:48:59 -0500 (Thu, 01 Jan 2009) | 4 lines
1839 Changed paths:
1840 M /branches/prog/bwa/bwt.c
1841 M /branches/prog/bwa/main.c
1842
1843 * bwa-0.2.0-25
1844 * accelerate OCC calculation by ~7%. However, it seems not worth doing
1845 this by complicate the codes. I will change back later.
1846
1847 ------------------------------------------------------------------------
1848 r729 | lh3 | 2008-12-31 16:43:56 -0500 (Wed, 31 Dec 2008) | 6 lines
1849 Changed paths:
1850 M /branches/prog/bwa/bntseq.c
1851 M /branches/prog/bwa/bwape.c
1852 M /branches/prog/bwa/bwase.c
1853 M /branches/prog/bwa/main.c
1854
1855 * bwa-0.2.0-24
1856 * change command "sai2sam_pe" to "sampe"
1857 * print usage for sampe command
1858 * in sampe: change default max_occ to 1000
1859 * fixed a few compiling warnings in bntseq.c
1860
1861 ------------------------------------------------------------------------
1862 r728 | lh3 | 2008-12-27 07:14:59 -0500 (Sat, 27 Dec 2008) | 3 lines
1863 Changed paths:
1864 M /branches/prog/bwa/bwape.c
1865 M /branches/prog/bwa/bwase.c
1866 M /branches/prog/bwa/main.c
1867
1868 * bwa-0.2.0-22
1869 * mating information can be printed to SAM
1870
1871 ------------------------------------------------------------------------
1872 r727 | lh3 | 2008-12-26 18:10:59 -0500 (Fri, 26 Dec 2008) | 4 lines
1873 Changed paths:
1874 M /branches/prog/bwa/bwape.c
1875 M /branches/prog/bwa/bwase.c
1876 M /branches/prog/bwa/bwaseqio.c
1877 M /branches/prog/bwa/bwtaln.c
1878 M /branches/prog/bwa/bwtaln.h
1879 M /branches/prog/bwa/main.c
1880
1881 * bwa-0.2.0-21
1882 * implement pairing (still UNFINISHED)
1883 * output all reads even if full of N
1884
1885 ------------------------------------------------------------------------
1886 r726 | lh3 | 2008-12-26 13:31:27 -0500 (Fri, 26 Dec 2008) | 5 lines
1887 Changed paths:
1888 M /branches/prog/bwa/Makefile
1889 A /branches/prog/bwa/bwape.c
1890 M /branches/prog/bwa/bwase.c
1891 M /branches/prog/bwa/bwt2fmv.c
1892 M /branches/prog/bwa/bwtaln.c
1893 M /branches/prog/bwa/bwtaln.h
1894 M /branches/prog/bwa/bwtgap.c
1895 M /branches/prog/bwa/main.c
1896 M /branches/prog/bwa/main.h
1897
1898 * bwa-0.2.0-20
1899 * remove "-t" from aln cmd
1900 * code clean up: move some functions in bwt2fmv.c to other source files
1901 * added sai2sam_pe cmd: *UNFINISHED*
1902
1903 ------------------------------------------------------------------------
1904 r725 | lh3 | 2008-12-26 07:04:11 -0500 (Fri, 26 Dec 2008) | 3 lines
1905 Changed paths:
1906 M /branches/prog/bwa/Makefile
1907 A /branches/prog/bwa/bwase.c
1908 A /branches/prog/bwa/bwaseqio.c
1909 M /branches/prog/bwa/bwt2fmv.c
1910 M /branches/prog/bwa/bwtaln.c
1911 M /branches/prog/bwa/bwtaln.h
1912 M /branches/prog/bwa/bwtgap.c
1913 M /branches/prog/bwa/kseq.h
1914 A /branches/prog/bwa/ksort.h (from /branches/prog/sclib/ksort/ksort.h:712)
1915 A /branches/prog/bwa/kvec.h (from /branches/prog/sclib/kvec/kvec.h:537)
1916 M /branches/prog/bwa/main.c
1917
1918 * bwa-0.2.0-19
1919 * considerable code cleanup; no actual changes
1920
1921 ------------------------------------------------------------------------
1922 r724 | lh3 | 2008-12-25 11:32:11 -0500 (Thu, 25 Dec 2008) | 3 lines
1923 Changed paths:
1924 M /branches/prog/bwa/bwtaln.c
1925 M /branches/prog/bwa/bwtaln.h
1926 M /branches/prog/bwa/main.c
1927
1928 * bwa-0.2.0-18
1929 * generate SAM output
1930
1931 ------------------------------------------------------------------------
1932 r723 | lh3 | 2008-12-25 10:48:31 -0500 (Thu, 25 Dec 2008) | 4 lines
1933 Changed paths:
1934 M /branches/prog/bwa/bwt2fmv.c
1935 M /branches/prog/bwa/bwtaln.c
1936 M /branches/prog/bwa/main.c
1937 M /branches/prog/bwa/main.h
1938
1939 * bwa-0.2.0-17
1940 * remove bwtsw2 related codes
1941 * separate searching for SA interval from generating alignments
1942
1943 ------------------------------------------------------------------------
1944 r722 | lh3 | 2008-12-25 08:57:13 -0500 (Thu, 25 Dec 2008) | 3 lines
1945 Changed paths:
1946 M /branches/prog/bwa/Makefile
1947 M /branches/prog/bwa/bwt2fmv.c
1948 D /branches/prog/bwa/bwt_lite.c
1949 D /branches/prog/bwa/bwt_lite.h
1950 M /branches/prog/bwa/bwtgap.c
1951 D /branches/prog/bwa/bwtsw2.h
1952 D /branches/prog/bwa/bwtsw2_aux.c
1953 D /branches/prog/bwa/bwtsw2_core.c
1954 D /branches/prog/bwa/bwtsw2_main.c
1955 D /branches/prog/bwa/khash.h
1956 D /branches/prog/bwa/ksort.h
1957 D /branches/prog/bwa/kvec.h
1958 M /branches/prog/bwa/main.c
1959
1960 * added interface to "aln -t"
1961 * remove bwtsw2 related codes
1962
1963 ------------------------------------------------------------------------
1964 r666 | lh3 | 2008-11-18 18:34:29 -0500 (Tue, 18 Nov 2008) | 4 lines
1965 Changed paths:
1966 M /branches/prog/bwa/bwt2fmv.c
1967 M /branches/prog/bwa/bwtaln.c
1968 M /branches/prog/bwa/bwtaln.h
1969 M /branches/prog/bwa/main.c
1970
1971 * bwa-0.2.0-16
1972 * allow to set max mismatches based on read length, but I do not know
1973 whether this really works
1974
1975 ------------------------------------------------------------------------
1976 r665 | lh3 | 2008-11-18 08:34:03 -0500 (Tue, 18 Nov 2008) | 3 lines
1977 Changed paths:
1978 M /branches/prog/bwa/bwtaln.c
1979 M /branches/prog/bwa/main.c
1980
1981 * bwa-0.2.0-15
1982 * fixed a bug in sequence parser.
1983
1984 ------------------------------------------------------------------------
1985 r612 | lh3 | 2008-10-28 06:50:53 -0400 (Tue, 28 Oct 2008) | 3 lines
1986 Changed paths:
1987 M /branches/prog/bwa/bntseq.c
1988 M /branches/prog/bwa/bwtindex.c
1989 M /branches/prog/bwa/main.c
1990 M /branches/prog/bwa/utils.c
1991
1992 * bwa-0.2.0-14
1993 * fixed a bug caused by the change of the FASTA/Q parser
1994
1995 ------------------------------------------------------------------------
1996 r611 | lh3 | 2008-10-28 06:24:56 -0400 (Tue, 28 Oct 2008) | 2 lines
1997 Changed paths:
1998 M /branches/prog/bwa/Makefile
1999 M /branches/prog/bwa/bntseq.c
2000 M /branches/prog/bwa/bntseq.h
2001 M /branches/prog/bwa/bwtaln.c
2002 M /branches/prog/bwa/bwtsw2_core.c
2003 A /branches/prog/bwa/kseq.h
2004 D /branches/prog/bwa/seq.c
2005 D /branches/prog/bwa/seq.h
2006 M /branches/prog/bwa/simple_dp.c
2007 M /branches/prog/bwa/utils.c
2008 M /branches/prog/bwa/utils.h
2009
2010 replace seq.* with kseq.h
2011
2012 ------------------------------------------------------------------------
2013 r610 | lh3 | 2008-10-27 13:00:04 -0400 (Mon, 27 Oct 2008) | 3 lines
2014 Changed paths:
2015 M /branches/prog/bwa/bwtsw2.h
2016 M /branches/prog/bwa/bwtsw2_aux.c
2017 M /branches/prog/bwa/bwtsw2_core.c
2018 M /branches/prog/bwa/main.c
2019
2020 * bwa-0.2.0-13
2021 * make bwtsw2 output sub-optimal hits. not completed
2022
2023 ------------------------------------------------------------------------
2024 r609 | lh3 | 2008-10-24 16:52:00 -0400 (Fri, 24 Oct 2008) | 2 lines
2025 Changed paths:
2026 M /branches/prog/bwa/kvec.h
2027
2028 little...
2029
2030 ------------------------------------------------------------------------
2031 r532 | lh3 | 2008-09-19 05:28:45 -0400 (Fri, 19 Sep 2008) | 2 lines
2032 Changed paths:
2033 M /branches/prog/bwa/bwtsw2_core.c
2034 M /branches/prog/bwa/khash.h
2035
2036 improve interface of khash
2037
2038 ------------------------------------------------------------------------
2039 r531 | lh3 | 2008-09-18 06:52:59 -0400 (Thu, 18 Sep 2008) | 2 lines
2040 Changed paths:
2041 M /branches/prog/bwa/bwtsw2_core.c
2042
2043 improve minor things, which make bwtsw2 slower, but should miss less true hits
2044
2045 ------------------------------------------------------------------------
2046 r530 | lh3 | 2008-09-17 18:19:26 -0400 (Wed, 17 Sep 2008) | 3 lines
2047 Changed paths:
2048 M /branches/prog/bwa/bwtsw2_core.c
2049
2050 * fixed a bug in calculating ->D
2051 * enforce band-width checking
2052
2053 ------------------------------------------------------------------------
2054 r529 | lh3 | 2008-09-17 18:06:49 -0400 (Wed, 17 Sep 2008) | 2 lines
2055 Changed paths:
2056 M /branches/prog/bwa/bwtsw2_core.c
2057
2058 delete a line of code that is never visited
2059
2060 ------------------------------------------------------------------------
2061 r528 | lh3 | 2008-09-17 17:58:51 -0400 (Wed, 17 Sep 2008) | 2 lines
2062 Changed paths:
2063 M /branches/prog/bwa/bwtsw2_core.c
2064
2065 a bit code clean up
2066
2067 ------------------------------------------------------------------------
2068 r527 | lh3 | 2008-09-17 10:55:45 -0400 (Wed, 17 Sep 2008) | 3 lines
2069 Changed paths:
2070 M /branches/prog/bwa/bwtsw2_core.c
2071 M /branches/prog/bwa/bwtsw2_main.c
2072 M /branches/prog/bwa/main.c
2073
2074 * bwa-0.2.0-12
2075 * max-depth can be set, although it does not help the speed at all
2076
2077 ------------------------------------------------------------------------
2078 r526 | lh3 | 2008-09-16 17:59:36 -0400 (Tue, 16 Sep 2008) | 2 lines
2079 Changed paths:
2080 M /branches/prog/bwa/bwtsw2_core.c
2081
2082 cut_tail after remove duplicate
2083
2084 ------------------------------------------------------------------------
2085 r525 | lh3 | 2008-09-16 17:56:11 -0400 (Tue, 16 Sep 2008) | 3 lines
2086 Changed paths:
2087 M /branches/prog/bwa/bwtsw2.h
2088 M /branches/prog/bwa/bwtsw2_aux.c
2089 M /branches/prog/bwa/bwtsw2_core.c
2090 M /branches/prog/bwa/bwtsw2_main.c
2091 M /branches/prog/bwa/khash.h
2092 M /branches/prog/bwa/main.c
2093
2094 * bwa-0.2.0-11
2095 * improved cut_tail()
2096
2097 ------------------------------------------------------------------------
2098 r524 | lh3 | 2008-09-15 16:53:22 -0400 (Mon, 15 Sep 2008) | 3 lines
2099 Changed paths:
2100 M /branches/prog/bwa/bwtsw2_aux.c
2101 M /branches/prog/bwa/bwtsw2_core.c
2102 M /branches/prog/bwa/bwtsw2_main.c
2103 M /branches/prog/bwa/main.c
2104
2105 * bwa-0.2.0-10
2106 * fixed a bug in cut_tail()
2107
2108 ------------------------------------------------------------------------
2109 r518 | lh3 | 2008-09-15 04:35:59 -0400 (Mon, 15 Sep 2008) | 2 lines
2110 Changed paths:
2111 M /branches/prog/bwa/bwtsw2_core.c
2112
2113 a bit code clean up
2114
2115 ------------------------------------------------------------------------
2116 r517 | lh3 | 2008-09-14 18:18:11 -0400 (Sun, 14 Sep 2008) | 2 lines
2117 Changed paths:
2118 M /branches/prog/bwa/bwtsw2_core.c
2119
2120 improve speed (<1%)
2121
2122 ------------------------------------------------------------------------
2123 r516 | lh3 | 2008-09-14 18:08:55 -0400 (Sun, 14 Sep 2008) | 3 lines
2124 Changed paths:
2125 M /branches/prog/bwa/bwtsw2_core.c
2126
2127 * fixed two potential bugs, although I have not seen their effects
2128 * improve speed a bit (<2%)
2129
2130 ------------------------------------------------------------------------
2131 r515 | lh3 | 2008-09-14 17:26:49 -0400 (Sun, 14 Sep 2008) | 2 lines
2132 Changed paths:
2133 M /branches/prog/bwa/bwtsw2_core.c
2134 M /branches/prog/bwa/bwtsw2_main.c
2135
2136 nothing, really
2137
2138 ------------------------------------------------------------------------
2139 r514 | lh3 | 2008-09-14 17:10:13 -0400 (Sun, 14 Sep 2008) | 2 lines
2140 Changed paths:
2141 M /branches/prog/bwa/bwtsw2_core.c
2142
2143 disable X-drop, which has to be reimplemented in the current algorithm
2144
2145 ------------------------------------------------------------------------
2146 r513 | lh3 | 2008-09-14 16:49:42 -0400 (Sun, 14 Sep 2008) | 4 lines
2147 Changed paths:
2148 M /branches/prog/bwa/bwt_lite.c
2149 M /branches/prog/bwa/bwt_lite.h
2150 M /branches/prog/bwa/bwtsw2_core.c
2151 M /branches/prog/bwa/bwtsw2_main.c
2152
2153 * temporarily disable cut_tail()
2154 * calculate SA in bwt_lite.c
2155 * fixed a bug in reversing the sequence
2156
2157 ------------------------------------------------------------------------
2158 r512 | lh3 | 2008-09-13 17:35:40 -0400 (Sat, 13 Sep 2008) | 2 lines
2159 Changed paths:
2160 M /branches/prog/bwa/bwtsw2.h
2161 M /branches/prog/bwa/bwtsw2_aux.c
2162 M /branches/prog/bwa/bwtsw2_core.c
2163 M /branches/prog/bwa/bwtsw2_main.c
2164 A /branches/prog/bwa/ksort.h
2165
2166 n-best method
2167
2168 ------------------------------------------------------------------------
2169 r507 | lh3 | 2008-09-13 09:06:54 -0400 (Sat, 13 Sep 2008) | 2 lines
2170 Changed paths:
2171 M /branches/prog/bwa/Makefile
2172 M /branches/prog/bwa/bwtsw2_core.c
2173
2174 give correct result again
2175
2176 ------------------------------------------------------------------------
2177 r506 | lh3 | 2008-09-13 08:12:07 -0400 (Sat, 13 Sep 2008) | 2 lines
2178 Changed paths:
2179 M /branches/prog/bwa/bwtsw2_core.c
2180
2181 I think I know the reason. It needs more work...
2182
2183 ------------------------------------------------------------------------
2184 r505 | lh3 | 2008-09-13 06:20:43 -0400 (Sat, 13 Sep 2008) | 2 lines
2185 Changed paths:
2186 M /branches/prog/bwa/Makefile
2187 M /branches/prog/bwa/bwtsw2_core.c
2188
2189 fixed another bug, but still have
2190
2191 ------------------------------------------------------------------------
2192 r504 | lh3 | 2008-09-12 18:13:37 -0400 (Fri, 12 Sep 2008) | 2 lines
2193 Changed paths:
2194 M /branches/prog/bwa/bwtsw2_core.c
2195
2196 fixed another bug
2197
2198 ------------------------------------------------------------------------
2199 r503 | lh3 | 2008-09-12 17:15:56 -0400 (Fri, 12 Sep 2008) | 3 lines
2200 Changed paths:
2201 M /branches/prog/bwa/bwtsw2_core.c
2202 M /branches/prog/bwa/khash.h
2203
2204 * do not segfault, but the result is WRONG!
2205 * prepare to remove bsw2_connectivity_check()
2206
2207 ------------------------------------------------------------------------
2208 r502 | lh3 | 2008-09-12 15:52:41 -0400 (Fri, 12 Sep 2008) | 2 lines
2209 Changed paths:
2210 M /branches/prog/bwa/bwtsw2_core.c
2211 M /branches/prog/bwa/kvec.h
2212
2213 more revisions
2214
2215 ------------------------------------------------------------------------
2216 r501 | lh3 | 2008-09-11 18:06:15 -0400 (Thu, 11 Sep 2008) | 2 lines
2217 Changed paths:
2218 M /branches/prog/bwa/bwtsw2_core.c
2219
2220 further simply codes with kvec.h
2221
2222 ------------------------------------------------------------------------
2223 r500 | lh3 | 2008-09-11 17:42:15 -0400 (Thu, 11 Sep 2008) | 2 lines
2224 Changed paths:
2225 M /branches/prog/bwa/bwtsw2_core.c
2226
2227 part of revisions... have not finished
2228
2229 ------------------------------------------------------------------------
2230 r499 | lh3 | 2008-09-11 17:24:15 -0400 (Thu, 11 Sep 2008) | 2 lines
2231 Changed paths:
2232 M /branches/prog/bwa/bwtsw2.h
2233 M /branches/prog/bwa/bwtsw2_core.c
2234 M /branches/prog/bwa/bwtsw2_main.c
2235 M /branches/prog/bwa/khash.h
2236 A /branches/prog/bwa/kvec.h
2237
2238 prepare for abrupt change
2239
2240 ------------------------------------------------------------------------
2241 r496 | lh3 | 2008-09-11 10:34:38 -0400 (Thu, 11 Sep 2008) | 2 lines
2242 Changed paths:
2243 M /branches/prog/bwa/bwtsw2_core.c
2244
2245 fixed a bug; now "bwtsw2 -d" is useless
2246
2247 ------------------------------------------------------------------------
2248 r495 | lh3 | 2008-09-11 09:22:03 -0400 (Thu, 11 Sep 2008) | 2 lines
2249 Changed paths:
2250 M /branches/prog/bwa/bwtsw2_core.c
2251 M /branches/prog/bwa/simple_dp.c
2252 M /branches/prog/bwa/stdaln.c
2253 M /branches/prog/bwa/stdaln.h
2254
2255 improve speed a little bit
2256
2257 ------------------------------------------------------------------------
2258 r494 | lh3 | 2008-09-11 08:28:08 -0400 (Thu, 11 Sep 2008) | 2 lines
2259 Changed paths:
2260 M /branches/prog/bwa/bwtsw2_core.c
2261
2262 remove debug codes
2263
2264 ------------------------------------------------------------------------
2265 r493 | lh3 | 2008-09-11 07:49:53 -0400 (Thu, 11 Sep 2008) | 3 lines
2266 Changed paths:
2267 M /branches/prog/bwa/bwtsw2_core.c
2268
2269 * improve the speed a little bit (<5%)
2270 * prepare to remove BSW_DEBUG
2271
2272 ------------------------------------------------------------------------
2273 r492 | lh3 | 2008-09-11 06:15:56 -0400 (Thu, 11 Sep 2008) | 4 lines
2274 Changed paths:
2275 M /branches/prog/bwa/bwtsw2.h
2276 M /branches/prog/bwa/bwtsw2_aux.c
2277 M /branches/prog/bwa/bwtsw2_core.c
2278 M /branches/prog/bwa/bwtsw2_main.c
2279 M /branches/prog/bwa/main.c
2280
2281 * bwa-0.2.0-9
2282 * support reverse strand
2283 * fixed a bug that causes missing hits
2284
2285 ------------------------------------------------------------------------
2286 r491 | lh3 | 2008-09-11 05:46:16 -0400 (Thu, 11 Sep 2008) | 3 lines
2287 Changed paths:
2288 M /branches/prog/bwa/bwtsw2_core.c
2289 M /branches/prog/bwa/main.c
2290
2291 * bwa-0.2.0-8
2292 * better progress report
2293
2294 ------------------------------------------------------------------------
2295 r490 | lh3 | 2008-09-10 17:04:49 -0400 (Wed, 10 Sep 2008) | 4 lines
2296 Changed paths:
2297 M /branches/prog/bwa/bwtsw2.h
2298 M /branches/prog/bwa/bwtsw2_aux.c
2299 M /branches/prog/bwa/bwtsw2_core.c
2300 M /branches/prog/bwa/bwtsw2_main.c
2301 M /branches/prog/bwa/main.c
2302
2303 * bwa-0.2.0-7
2304 * avoid some missing hits
2305 * add maximum depth
2306
2307 ------------------------------------------------------------------------
2308 r489 | lh3 | 2008-09-10 11:51:13 -0400 (Wed, 10 Sep 2008) | 4 lines
2309 Changed paths:
2310 M /branches/prog/bwa/bwtsw2_core.c
2311 M /branches/prog/bwa/main.c
2312
2313 * bwa-0.2.0-6
2314 * bwtsw2 works although on the forward strand only for now
2315 * better progress information
2316
2317 ------------------------------------------------------------------------
2318 r488 | lh3 | 2008-09-10 10:21:53 -0400 (Wed, 10 Sep 2008) | 3 lines
2319 Changed paths:
2320 M /branches/prog/bwa/bwtsw2_core.c
2321
2322 * implement memory pool
2323 * avoid some rehashing
2324
2325 ------------------------------------------------------------------------
2326 r487 | lh3 | 2008-09-10 09:23:38 -0400 (Wed, 10 Sep 2008) | 3 lines
2327 Changed paths:
2328 M /branches/prog/bwa/bwtsw2.h
2329 M /branches/prog/bwa/bwtsw2_aux.c
2330 M /branches/prog/bwa/bwtsw2_main.c
2331
2332 * fixed a memory leak
2333 * prepare to implement mempool
2334
2335 ------------------------------------------------------------------------
2336 r486 | lh3 | 2008-09-10 09:10:09 -0400 (Wed, 10 Sep 2008) | 4 lines
2337 Changed paths:
2338 M /branches/prog/bwa/bwtsw2.h
2339 M /branches/prog/bwa/bwtsw2_aux.c
2340 M /branches/prog/bwa/bwtsw2_core.c
2341 M /branches/prog/bwa/bwtsw2_main.c
2342 M /branches/prog/bwa/khash.h
2343
2344 * add X-dropoff
2345 * remove duplicated results
2346 * switch to simple stack
2347
2348 ------------------------------------------------------------------------
2349 r485 | lh3 | 2008-09-10 06:31:20 -0400 (Wed, 10 Sep 2008) | 3 lines
2350 Changed paths:
2351 M /branches/prog/bwa/bwtsw2.h
2352 M /branches/prog/bwa/bwtsw2_aux.c
2353 M /branches/prog/bwa/bwtsw2_core.c
2354 M /branches/prog/bwa/bwtsw2_main.c
2355
2356 * check whether t-node has been visited
2357 * prepare to remove two-level stack
2358
2359 ------------------------------------------------------------------------
2360 r484 | lh3 | 2008-09-10 05:00:57 -0400 (Wed, 10 Sep 2008) | 2 lines
2361 Changed paths:
2362 A /branches/prog/bwa/khash.h
2363
2364 khash library
2365
2366 ------------------------------------------------------------------------
2367 r483 | lh3 | 2008-09-10 04:22:53 -0400 (Wed, 10 Sep 2008) | 2 lines
2368 Changed paths:
2369 M /branches/prog/bwa/bwtsw2_core.c
2370
2371 add inline
2372
2373 ------------------------------------------------------------------------
2374 r482 | lh3 | 2008-09-09 16:34:57 -0400 (Tue, 09 Sep 2008) | 2 lines
2375 Changed paths:
2376 M /branches/prog/bwa/Makefile
2377 M /branches/prog/bwa/bwtsw2_aux.c
2378 M /branches/prog/bwa/bwtsw2_core.c
2379
2380 improve speed
2381
2382 ------------------------------------------------------------------------
2383 r481 | lh3 | 2008-09-09 13:13:00 -0400 (Tue, 09 Sep 2008) | 4 lines
2384 Changed paths:
2385 M /branches/prog/bwa/bwtsw2_core.c
2386
2387 Use a 128bit hash table to keep all (tk,tl,qk,ql). This is slow. Just
2388 keep a copy in case I may need this in future.
2389
2390
2391 ------------------------------------------------------------------------
2392 r480 | lh3 | 2008-09-09 12:53:32 -0400 (Tue, 09 Sep 2008) | 2 lines
2393 Changed paths:
2394 M /branches/prog/bwa/bwtsw2.h
2395 M /branches/prog/bwa/bwtsw2_core.c
2396
2397 * no principal modification
2398
2399 ------------------------------------------------------------------------
2400 r479 | lh3 | 2008-09-09 11:01:45 -0400 (Tue, 09 Sep 2008) | 4 lines
2401 Changed paths:
2402 M /branches/prog/bwa/Makefile
2403 M /branches/prog/bwa/bwtsw2_core.c
2404
2405 * fixed a bug which may cause duplicated matching
2406 * accelerate the speed a bit, although using hash in avoiding duplications
2407 slows the speed down in the end
2408
2409 ------------------------------------------------------------------------
2410 r474 | lh3 | 2008-09-03 17:22:57 -0400 (Wed, 03 Sep 2008) | 4 lines
2411 Changed paths:
2412 M /branches/prog/bwa/Makefile
2413 M /branches/prog/bwa/bwtsw2.h
2414 M /branches/prog/bwa/bwtsw2_aux.c
2415 M /branches/prog/bwa/bwtsw2_core.c
2416 M /branches/prog/bwa/bwtsw2_main.c
2417 M /branches/prog/bwa/main.c
2418
2419 * bwa-0.2.0-5
2420 * indel seems to work on toy example
2421 * add band
2422
2423 ------------------------------------------------------------------------
2424 r469 | lh3 | 2008-09-01 09:18:45 -0400 (Mon, 01 Sep 2008) | 3 lines
2425 Changed paths:
2426 M /branches/prog/bwa/ChangeLog
2427 M /branches/prog/bwa/Makefile
2428 M /branches/prog/bwa/bwt_lite.c
2429 M /branches/prog/bwa/bwt_lite.h
2430 M /branches/prog/bwa/bwtgap.c
2431 M /branches/prog/bwa/bwtsw2.h
2432 A /branches/prog/bwa/bwtsw2_aux.c
2433 M /branches/prog/bwa/bwtsw2_core.c
2434 M /branches/prog/bwa/bwtsw2_main.c
2435 M /branches/prog/bwa/is.c
2436 M /branches/prog/bwa/main.c
2437 M /branches/prog/bwa/main.h
2438 M /branches/prog/bwa/simple_dp.c
2439
2440 * bwa-0.2.0-4
2441 * updated bwtsw2, which seems to work properly on toy examples
2442
2443 ------------------------------------------------------------------------
2444 r447 | lh3 | 2008-08-27 10:05:09 -0400 (Wed, 27 Aug 2008) | 3 lines
2445 Changed paths:
2446 M /branches/prog/bwa/bwt2fmv.c
2447 M /branches/prog/bwa/bwtaln.c
2448 M /branches/prog/bwa/bwtaln.h
2449 M /branches/prog/bwa/bwtgap.c
2450 M /branches/prog/bwa/main.c
2451
2452 * bwa-0.2.0-3
2453 * tune for longer gaps, but it does not really work with kilo-bp gaps...
2454
2455 ------------------------------------------------------------------------
2456 r446 | lh3 | 2008-08-26 13:30:41 -0400 (Tue, 26 Aug 2008) | 3 lines
2457 Changed paths:
2458 M /branches/prog/bwa/bwt2fmv.c
2459 M /branches/prog/bwa/bwtaln.c
2460 M /branches/prog/bwa/bwtaln.h
2461 M /branches/prog/bwa/bwtgap.c
2462 M /branches/prog/bwa/main.c
2463
2464 * bwa-0.2.0-2
2465 * changed the way to extend long deletions. Now use max_del_occ.
2466
2467 ------------------------------------------------------------------------
2468 r445 | lh3 | 2008-08-26 13:05:58 -0400 (Tue, 26 Aug 2008) | 2 lines
2469 Changed paths:
2470 M /branches/prog/bwa/bwt_lite.c
2471 M /branches/prog/bwa/bwt_lite.h
2472
2473 updated from bwtsw2_lite
2474
2475 ------------------------------------------------------------------------
2476 r436 | lh3 | 2008-08-23 12:28:44 -0400 (Sat, 23 Aug 2008) | 4 lines
2477 Changed paths:
2478 M /branches/prog/bwa/Makefile
2479 M /branches/prog/bwa/bwt.h
2480 A /branches/prog/bwa/bwt_lite.c
2481 A /branches/prog/bwa/bwt_lite.h
2482 A /branches/prog/bwa/bwtsw2.h
2483 A /branches/prog/bwa/bwtsw2_core.c
2484 A /branches/prog/bwa/bwtsw2_main.c
2485 M /branches/prog/bwa/main.c
2486
2487 * bwa-0.2.0-1
2488 * add bwt_lite: a light-weighted version of bwt (NOT TESTED!)
2489 * add core codes for bwtsw2: NOT TESTED!!!
2490
2491 ------------------------------------------------------------------------
2492 r427 | lh3 | 2008-08-15 05:38:12 -0400 (Fri, 15 Aug 2008) | 2 lines
2493 Changed paths:
2494 M /branches/prog/bwa/ChangeLog
2495 M /branches/prog/bwa/NEWS
2496 M /branches/prog/bwa/bwa.1
2497 M /branches/prog/bwa/bwtaln.c
2498 M /branches/prog/bwa/main.c
2499
2500 Release bwa-0.2.0
2501
2502 ------------------------------------------------------------------------
2503 r426 | lh3 | 2008-08-14 11:26:19 -0400 (Thu, 14 Aug 2008) | 4 lines
2504 Changed paths:
2505 M /branches/prog/bwa/bwt2fmv.c
2506 M /branches/prog/bwa/bwtaln.c
2507 M /branches/prog/bwa/bwtaln.h
2508 M /branches/prog/bwa/main.c
2509
2510 * bwa-0.1.6-7
2511 * change default seed length to 31
2512 * add incomplete support to color sequences (not tested yet!)
2513
2514 ------------------------------------------------------------------------
2515 r425 | lh3 | 2008-08-14 06:23:11 -0400 (Thu, 14 Aug 2008) | 3 lines
2516 Changed paths:
2517 M /branches/prog/bwa/bwtaln.c
2518 M /branches/prog/bwa/main.c
2519
2520 * bwa-0.1.6-6
2521 * change default seed length to 33bp
2522
2523 ------------------------------------------------------------------------
2524 r424 | lh3 | 2008-08-14 05:55:33 -0400 (Thu, 14 Aug 2008) | 6 lines
2525 Changed paths:
2526 M /branches/prog/bwa/bwtaln.c
2527 M /branches/prog/bwa/bwtgap.c
2528 M /branches/prog/bwa/main.c
2529
2530 * bwa-0.1.6-5
2531 * fixed a bug that may miss true alignments. this bugs exists in most
2532 early versions.
2533 * fixed a bug that yields wrong coordinates for reads mapped on the forward
2534 strands with gaps.
2535
2536 ------------------------------------------------------------------------
2537 r423 | lh3 | 2008-08-14 04:07:28 -0400 (Thu, 14 Aug 2008) | 2 lines
2538 Changed paths:
2539 D /branches/prog/bwa/Makefile.div
2540
2541 useless
2542
2543 ------------------------------------------------------------------------
2544 r422 | lh3 | 2008-08-13 19:21:14 -0400 (Wed, 13 Aug 2008) | 4 lines
2545 Changed paths:
2546 M /branches/prog/bwa/bwtaln.c
2547 M /branches/prog/bwa/main.c
2548
2549 * bwa-0.1.6-4
2550 * fixed one bug
2551 * there is another one...
2552
2553 ------------------------------------------------------------------------
2554 r421 | lh3 | 2008-08-13 18:23:33 -0400 (Wed, 13 Aug 2008) | 3 lines
2555 Changed paths:
2556 M /branches/prog/bwa/bwtaln.c
2557 M /branches/prog/bwa/bwtaln.h
2558 M /branches/prog/bwa/bwtgap.c
2559 M /branches/prog/bwa/bwtgap.h
2560 M /branches/prog/bwa/bwtindex.c
2561 M /branches/prog/bwa/main.c
2562
2563 * bwa-0.1.6-3
2564 * almost there, but not quite right
2565
2566 ------------------------------------------------------------------------
2567 r419 | lh3 | 2008-08-13 17:27:02 -0400 (Wed, 13 Aug 2008) | 3 lines
2568 Changed paths:
2569 M /branches/prog/bwa/bwtaln.c
2570 M /branches/prog/bwa/bwtaln.h
2571 M /branches/prog/bwa/bwtgap.c
2572 M /branches/prog/bwa/bwtgap.h
2573 M /branches/prog/bwa/main.c
2574
2575 * improve the seeding method
2576 * prepare to load two BWTs into memory. A BIG change!
2577
2578 ------------------------------------------------------------------------
2579 r418 | lh3 | 2008-08-13 10:56:54 -0400 (Wed, 13 Aug 2008) | 3 lines
2580 Changed paths:
2581 M /branches/prog/bwa/bwt2fmv.c
2582 M /branches/prog/bwa/bwtaln.c
2583 M /branches/prog/bwa/bwtaln.h
2584 M /branches/prog/bwa/bwtgap.c
2585 M /branches/prog/bwa/bwtgap.h
2586 M /branches/prog/bwa/main.c
2587
2588 * added seeding
2589 * unfinished yet
2590
2591 ------------------------------------------------------------------------
2592 r413 | lh3 | 2008-08-08 11:48:35 -0400 (Fri, 08 Aug 2008) | 2 lines
2593 Changed paths:
2594 M /branches/prog/bwa/ChangeLog
2595 M /branches/prog/bwa/NEWS
2596 M /branches/prog/bwa/main.c
2597
2598 Release bwa-0.1.6
2599
2600 ------------------------------------------------------------------------
2601 r410 | lh3 | 2008-08-06 15:48:22 -0400 (Wed, 06 Aug 2008) | 2 lines
2602 Changed paths:
2603 M /branches/prog/bwa/simple_dp.c
2604
2605 sw: output alignment score
2606
2607 ------------------------------------------------------------------------
2608 r407 | lh3 | 2008-08-04 10:01:20 -0400 (Mon, 04 Aug 2008) | 4 lines
2609 Changed paths:
2610 M /branches/prog/bwa/Makefile
2611 M /branches/prog/bwa/main.c
2612 M /branches/prog/bwa/main.h
2613 A /branches/prog/bwa/simple_dp.c
2614 M /branches/prog/bwa/stdaln.c
2615 M /branches/prog/bwa/stdaln.h
2616
2617 * bwa-0.1.5-3
2618 * added a simple interface to SW/NW alignment
2619 * stdaln-0.9.8 (see header for more details)
2620
2621 ------------------------------------------------------------------------
2622 r406 | lh3 | 2008-08-01 19:21:59 -0400 (Fri, 01 Aug 2008) | 3 lines
2623 Changed paths:
2624 M /branches/prog/bwa/Makefile
2625 M /branches/prog/bwa/bwtaln.c
2626 M /branches/prog/bwa/bwtaln.h
2627 M /branches/prog/bwa/main.c
2628 A /branches/prog/bwa/stdaln.c
2629 A /branches/prog/bwa/stdaln.h
2630
2631 * bwa-0.1.5-2
2632 * give accurate gap positions
2633
2634 ------------------------------------------------------------------------
2635 r405 | lh3 | 2008-08-01 19:06:19 -0400 (Fri, 01 Aug 2008) | 2 lines
2636 Changed paths:
2637 M /branches/prog/bwa/Makefile
2638 M /branches/prog/bwa/bwtaln.c
2639 M /branches/prog/bwa/bwtaln.h
2640
2641 unfinished, but I am tired...
2642
2643 ------------------------------------------------------------------------
2644 r401 | lh3 | 2008-07-30 05:59:24 -0400 (Wed, 30 Jul 2008) | 4 lines
2645 Changed paths:
2646 M /branches/prog/bwa/bntseq.c
2647 M /branches/prog/bwa/main.c
2648
2649 * bwa-0.1.5-1
2650 * fixed a potential bug which may produce an alignment in N regions,
2651 although extremely rare.
2652
2653 ------------------------------------------------------------------------
2654 r399 | lh3 | 2008-07-27 11:41:52 -0400 (Sun, 27 Jul 2008) | 2 lines
2655 Changed paths:
2656 M /branches/prog/bwa/ChangeLog
2657 M /branches/prog/bwa/NEWS
2658 M /branches/prog/bwa/main.c
2659
2660 Release bwa-0.1.5
2661
2662 ------------------------------------------------------------------------
2663 r398 | lh3 | 2008-07-25 12:14:47 -0400 (Fri, 25 Jul 2008) | 2 lines
2664 Changed paths:
2665 M /branches/prog/bwa/bwa.1
2666
2667 update documentation
2668
2669 ------------------------------------------------------------------------
2670 r397 | lh3 | 2008-07-25 09:58:56 -0400 (Fri, 25 Jul 2008) | 2 lines
2671 Changed paths:
2672 M /branches/prog/bwa/bwt2fmv.c
2673 M /branches/prog/bwa/bwtaln.c
2674 M /branches/prog/bwa/main.c
2675
2676 *
2677
2678 ------------------------------------------------------------------------
2679 r396 | lh3 | 2008-07-25 06:42:01 -0400 (Fri, 25 Jul 2008) | 3 lines
2680 Changed paths:
2681 M /branches/prog/bwa/bwtaln.c
2682 M /branches/prog/bwa/main.c
2683
2684 * bwa-0.1.4-4
2685 * add timer for debugging
2686
2687 ------------------------------------------------------------------------
2688 r395 | lh3 | 2008-07-24 05:46:21 -0400 (Thu, 24 Jul 2008) | 4 lines
2689 Changed paths:
2690 M /branches/prog/bwa/bwtgap.c
2691 M /branches/prog/bwa/main.c
2692
2693 * bwa-0.1.4-3
2694 * fixed a bug in the previous code
2695 * this version gives identical result to bwa-0.1.4, just 10% faster
2696
2697 ------------------------------------------------------------------------
2698 r394 | lh3 | 2008-07-24 05:18:53 -0400 (Thu, 24 Jul 2008) | 4 lines
2699 Changed paths:
2700 M /branches/prog/bwa/bwtaln.c
2701 M /branches/prog/bwa/bwtgap.c
2702 M /branches/prog/bwa/bwtgap.h
2703 M /branches/prog/bwa/main.c
2704
2705 * bwa-0.1.4-2
2706 * further improve the speed
2707 * The result is slightly different from bwa-0.1.4 now. I need to check...
2708
2709 ------------------------------------------------------------------------
2710 r393 | lh3 | 2008-07-23 12:04:16 -0400 (Wed, 23 Jul 2008) | 2 lines
2711 Changed paths:
2712 M /branches/prog/bwa/bwt.c
2713
2714 comments only
2715
2716 ------------------------------------------------------------------------
2717 r392 | lh3 | 2008-07-23 10:34:03 -0400 (Wed, 23 Jul 2008) | 2 lines
2718 Changed paths:
2719 M /branches/prog/bwa/bwt.c
2720 M /branches/prog/bwa/main.c
2721
2722 further improve the speed in Occ functions
2723
2724 ------------------------------------------------------------------------
2725 r386 | lh3 | 2008-07-22 10:03:54 -0400 (Tue, 22 Jul 2008) | 2 lines
2726 Changed paths:
2727 M /branches/prog/bwa/NEWS
2728 M /branches/prog/bwa/main.c
2729
2730 Release bwa-0.1.4
2731
2732 ------------------------------------------------------------------------
2733 r385 | lh3 | 2008-07-22 09:44:50 -0400 (Tue, 22 Jul 2008) | 2 lines
2734 Changed paths:
2735 M /branches/prog/bwa/ChangeLog
2736 M /branches/prog/bwa/bwa.1
2737
2738 update documentation and ChangeLog
2739
2740 ------------------------------------------------------------------------
2741 r384 | lh3 | 2008-07-22 08:50:03 -0400 (Tue, 22 Jul 2008) | 4 lines
2742 Changed paths:
2743 M /branches/prog/bwa/Makefile
2744 M /branches/prog/bwa/bwt2fmv.c
2745 M /branches/prog/bwa/bwtaln.c
2746 M /branches/prog/bwa/bwtaln.h
2747 M /branches/prog/bwa/bwtgap.c
2748 M /branches/prog/bwa/main.c
2749
2750 * bwa-0.1.3-2
2751 * fixed the bug in the last modification
2752 * now the alignment should be more clearly defined
2753
2754 ------------------------------------------------------------------------
2755 r383 | lh3 | 2008-07-21 18:32:21 -0400 (Mon, 21 Jul 2008) | 4 lines
2756 Changed paths:
2757 M /branches/prog/bwa/bwt2fmv.c
2758 M /branches/prog/bwa/bwtaln.c
2759 M /branches/prog/bwa/bwtgap.c
2760 M /branches/prog/bwa/main.c
2761
2762 * bwa-0.1.3-1
2763 * this is a buggy verion!
2764 * i will fix the bug tomorrow. It is late...
2765
2766 ------------------------------------------------------------------------
2767 r381 | lh3 | 2008-07-21 06:45:32 -0400 (Mon, 21 Jul 2008) | 2 lines
2768 Changed paths:
2769 M /branches/prog/bwa/ChangeLog
2770 M /branches/prog/bwa/NEWS
2771 M /branches/prog/bwa/bwa.1
2772 M /branches/prog/bwa/main.c
2773
2774 Release bwa-0.1.3
2775
2776 ------------------------------------------------------------------------
2777 r380 | lh3 | 2008-07-21 06:07:43 -0400 (Mon, 21 Jul 2008) | 4 lines
2778 Changed paths:
2779 M /branches/prog/bwa/ChangeLog
2780 M /branches/prog/bwa/bwa.1
2781 M /branches/prog/bwa/bwt.c
2782 M /branches/prog/bwa/bwt2fmv.c
2783 M /branches/prog/bwa/main.c
2784
2785 * bwa-0.1.2-3
2786 * improve the speed for gcc on Intel Mac OS X, but not really on icc on Linux
2787 * aln: more command-line options
2788
2789 ------------------------------------------------------------------------
2790 r373 | lh3 | 2008-07-17 09:09:46 -0400 (Thu, 17 Jul 2008) | 4 lines
2791 Changed paths:
2792 M /branches/prog/bwa/bwt.c
2793 M /branches/prog/bwa/bwt.h
2794 M /branches/prog/bwa/bwtio.c
2795 M /branches/prog/bwa/main.c
2796
2797 * bwa-0.1.2-2
2798 * further improve the speed
2799 * this version gives exactly the same result as bwa-0.1.2
2800
2801 ------------------------------------------------------------------------
2802 r372 | lh3 | 2008-07-17 07:51:08 -0400 (Thu, 17 Jul 2008) | 3 lines
2803 Changed paths:
2804 M /branches/prog/bwa/bwt.c
2805 M /branches/prog/bwa/main.c
2806
2807 * bwa-0.1.2-1
2808 * speed up by about 5%
2809
2810 ------------------------------------------------------------------------
2811 r370 | lh3 | 2008-07-17 05:12:00 -0400 (Thu, 17 Jul 2008) | 2 lines
2812 Changed paths:
2813 M /branches/prog/bwa/NEWS
2814 M /branches/prog/bwa/bwa.1
2815 M /branches/prog/bwa/main.c
2816
2817 Release bwa-0.1.2
2818
2819 ------------------------------------------------------------------------
2820 r368 | lh3 | 2008-07-16 08:51:25 -0400 (Wed, 16 Jul 2008) | 4 lines
2821 Changed paths:
2822 M /branches/prog/bwa/Makefile
2823 D /branches/prog/bwa/bwt1away.c
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/bwtgap.c
2828 M /branches/prog/bwa/bwtgap.h
2829 D /branches/prog/bwa/bwttop2.c
2830 M /branches/prog/bwa/main.c
2831
2832 * bwa-0.1.1-9
2833 * some code cleanup
2834 * remove 1away and top2
2835
2836 ------------------------------------------------------------------------
2837 r367 | lh3 | 2008-07-16 08:24:34 -0400 (Wed, 16 Jul 2008) | 2 lines
2838 Changed paths:
2839 M /branches/prog/bwa/is.c
2840
2841 Yuta Mori's implementation of IS algorithm.
2842
2843 ------------------------------------------------------------------------
2844 r365 | lh3 | 2008-07-16 06:58:04 -0400 (Wed, 16 Jul 2008) | 6 lines
2845 Changed paths:
2846 M /branches/prog/bwa/bwtaln.c
2847 M /branches/prog/bwa/bwtgap.c
2848 M /branches/prog/bwa/bwtgap.h
2849 M /branches/prog/bwa/main.c
2850
2851 * bwa-0.1.1-8
2852 * improve gapped alignment
2853 * this version will miss more gapped alignments, but the speed is much faster
2854 * prepare to remove top2 and 1away algorithms
2855 * prepare to add SAIS algorithm for bwt construction
2856
2857 ------------------------------------------------------------------------
2858 r358 | lh3 | 2008-06-09 06:03:04 -0400 (Mon, 09 Jun 2008) | 4 lines
2859 Changed paths:
2860 M /branches/prog/bwa/bwt2fmv.c
2861 M /branches/prog/bwa/bwtgap.c
2862 M /branches/prog/bwa/main.c
2863
2864 * bwa-0.1.1-7
2865 * change END_SKIP from 3 to 5, but still gaps may be wrongly added
2866 * change default '-g' from 5 to 3
2867
2868 ------------------------------------------------------------------------
2869 r357 | lh3 | 2008-06-09 05:18:36 -0400 (Mon, 09 Jun 2008) | 3 lines
2870 Changed paths:
2871 M /branches/prog/bwa/bntseq.c
2872 M /branches/prog/bwa/bwt2fmv.c
2873 M /branches/prog/bwa/bwtgap.c
2874 M /branches/prog/bwa/main.c
2875
2876 * bwa-0.1.1-6
2877 * fix a bug in nested stack
2878
2879 ------------------------------------------------------------------------
2880 r356 | lh3 | 2008-06-08 18:43:13 -0400 (Sun, 08 Jun 2008) | 4 lines
2881 Changed paths:
2882 M /branches/prog/bwa/Makefile
2883 M /branches/prog/bwa/bwtaln.c
2884 M /branches/prog/bwa/bwtaln.h
2885 M /branches/prog/bwa/bwtgap.c
2886 A /branches/prog/bwa/bwtgap.h
2887 M /branches/prog/bwa/main.c
2888
2889 * bwa-0.1.1-5
2890 * replace heap with nested stacks
2891 * there are still obvious bugs...
2892
2893 ------------------------------------------------------------------------
2894 r355 | lh3 | 2008-06-08 17:13:44 -0400 (Sun, 08 Jun 2008) | 4 lines
2895 Changed paths:
2896 M /branches/prog/bwa/bwt2fmv.c
2897 M /branches/prog/bwa/bwtaln.c
2898 M /branches/prog/bwa/bwtaln.h
2899 M /branches/prog/bwa/bwtgap.c
2900 M /branches/prog/bwa/main.c
2901 M /branches/prog/bwa/main.h
2902
2903 * bwa-0.1.1-4
2904 * add interface to affine gap alignment
2905 * there are obvious bugs and I will fix them later
2906
2907 ------------------------------------------------------------------------
2908 r354 | lh3 | 2008-06-08 15:39:05 -0400 (Sun, 08 Jun 2008) | 3 lines
2909 Changed paths:
2910 M /branches/prog/bwa/bwtaln.c
2911 M /branches/prog/bwa/bwtaln.h
2912 M /branches/prog/bwa/bwtgap.c
2913 M /branches/prog/bwa/main.c
2914
2915 * bwa-0.1.1-3
2916 * affine gap seems to work, at least partially
2917
2918 ------------------------------------------------------------------------
2919 r353 | lh3 | 2008-06-08 09:27:18 -0400 (Sun, 08 Jun 2008) | 3 lines
2920 Changed paths:
2921 M /branches/prog/bwa/Makefile
2922 M /branches/prog/bwa/bwt2fmv.c
2923 M /branches/prog/bwa/bwtaln.c
2924 M /branches/prog/bwa/bwtaln.h
2925 A /branches/prog/bwa/bwtgap.c
2926 M /branches/prog/bwa/bwttop2.c
2927 M /branches/prog/bwa/main.c
2928
2929 * bwa-0.1.1-2
2930 * initial gapped alignment. not work at the moment
2931
2932 ------------------------------------------------------------------------
2933 r352 | lh3 | 2008-06-06 04:37:34 -0400 (Fri, 06 Jun 2008) | 3 lines
2934 Changed paths:
2935 M /branches/prog/bwa/bwttop2.c
2936 M /branches/prog/bwa/main.c
2937
2938 * bwa-0.1.1-1
2939 * ungap: remove a useless varible in top2_entry_t
2940
2941 ------------------------------------------------------------------------
2942 r348 | lh3 | 2008-06-03 09:04:12 -0400 (Tue, 03 Jun 2008) | 2 lines
2943 Changed paths:
2944 M /branches/prog/bwa/ChangeLog
2945 A /branches/prog/bwa/NEWS
2946 M /branches/prog/bwa/bwa.1
2947 M /branches/prog/bwa/main.c
2948
2949 Release bwa-0.1.1
2950
2951 ------------------------------------------------------------------------
2952 r347 | lh3 | 2008-06-03 05:45:08 -0400 (Tue, 03 Jun 2008) | 2 lines
2953 Changed paths:
2954 M /branches/prog/bwa/bwa.1
2955
2956 update documentation
2957
2958 ------------------------------------------------------------------------
2959 r346 | lh3 | 2008-06-02 18:59:50 -0400 (Mon, 02 Jun 2008) | 5 lines
2960 Changed paths:
2961 A /branches/prog/bwa/ChangeLog
2962 A /branches/prog/bwa/bwa.1
2963 M /branches/prog/bwa/bwtaln.c
2964 M /branches/prog/bwa/main.c
2965
2966 * bwa-0.1.0-11
2967 * improve approximating mapping qualities
2968 * add documentation
2969 * add ChangeLog
2970
2971 ------------------------------------------------------------------------
2972 r345 | lh3 | 2008-06-02 16:04:39 -0400 (Mon, 02 Jun 2008) | 3 lines
2973 Changed paths:
2974 M /branches/prog/bwa/bwtaln.c
2975 M /branches/prog/bwa/bwttop2.c
2976 M /branches/prog/bwa/main.c
2977
2978 * bwa-0.1.0-10
2979 * output a random position for repetitive reads
2980
2981 ------------------------------------------------------------------------
2982 r344 | lh3 | 2008-06-02 15:03:54 -0400 (Mon, 02 Jun 2008) | 4 lines
2983 Changed paths:
2984 M /branches/prog/bwa/bntseq.c
2985 M /branches/prog/bwa/bwtaln.c
2986 M /branches/prog/bwa/main.c
2987 M /branches/prog/bwa/pac2bwt.c
2988
2989 * bwa-0.1.0-9
2990 * fix memory leaks
2991 * fix a potential bug in coverting to the real coordinate
2992
2993 ------------------------------------------------------------------------
2994 r343 | lh3 | 2008-06-02 13:44:51 -0400 (Mon, 02 Jun 2008) | 5 lines
2995 Changed paths:
2996 M /branches/prog/bwa/Makefile.div
2997 M /branches/prog/bwa/bwt.c
2998 M /branches/prog/bwa/bwt.h
2999 M /branches/prog/bwa/bwt2fmv.c
3000 M /branches/prog/bwa/bwtaln.c
3001 M /branches/prog/bwa/bwttop2.c
3002 M /branches/prog/bwa/main.c
3003
3004 * bwa-0.1.0-8
3005 * fix a bug about strand
3006 * update Makefile.div
3007 * change top2b as the default method
3008
3009 ------------------------------------------------------------------------
3010 r342 | lh3 | 2008-06-02 11:23:26 -0400 (Mon, 02 Jun 2008) | 3 lines
3011 Changed paths:
3012 M /branches/prog/bwa/bwt.c
3013 M /branches/prog/bwa/bwt1away.c
3014 M /branches/prog/bwa/bwtaln.c
3015 M /branches/prog/bwa/main.c
3016
3017 * bwa-0.1.0-7
3018 * use bwt_2occ() and bwt_2occ4() in other functions
3019
3020 ------------------------------------------------------------------------
3021 r341 | lh3 | 2008-06-02 09:31:39 -0400 (Mon, 02 Jun 2008) | 3 lines
3022 Changed paths:
3023 M /branches/prog/bwa/bwttop2.c
3024 M /branches/prog/bwa/main.c
3025
3026 * bwa-0.1.0-6
3027 * fix a bug for missing hits
3028
3029 ------------------------------------------------------------------------
3030 r340 | lh3 | 2008-06-02 09:10:18 -0400 (Mon, 02 Jun 2008) | 3 lines
3031 Changed paths:
3032 M /branches/prog/bwa/bwttop2.c
3033 M /branches/prog/bwa/main.c
3034
3035 * bwa-0.1.0-5
3036 * accelerate comparisons in heap, a bit
3037
3038 ------------------------------------------------------------------------
3039 r339 | lh3 | 2008-06-02 08:41:31 -0400 (Mon, 02 Jun 2008) | 3 lines
3040 Changed paths:
3041 M /branches/prog/bwa/bwt.c
3042 M /branches/prog/bwa/bwt.h
3043 M /branches/prog/bwa/bwttop2.c
3044 M /branches/prog/bwa/main.c
3045
3046 * bwa-0.1.0-4
3047 * avoid marginal repeated calculation in occ
3048
3049 ------------------------------------------------------------------------
3050 r338 | lh3 | 2008-06-02 06:46:51 -0400 (Mon, 02 Jun 2008) | 5 lines
3051 Changed paths:
3052 M /branches/prog/bwa/Makefile
3053 M /branches/prog/bwa/bwt.c
3054 M /branches/prog/bwa/bwttop2.c
3055 M /branches/prog/bwa/main.c
3056
3057 * bwa-0.1.0-3
3058 * fix a bug caused by previours change
3059 * fix a bug in heap
3060 * order the heap by more criteria
3061
3062 ------------------------------------------------------------------------
3063 r337 | lh3 | 2008-06-01 19:11:15 -0400 (Sun, 01 Jun 2008) | 4 lines
3064 Changed paths:
3065 M /branches/prog/bwa/bwttop2.c
3066 M /branches/prog/bwa/main.c
3067
3068 * bwa-0.1.0-2
3069 * also sort sa range in heapsort, in attempt to improve cache performance.
3070 Unfortunately, it does not work well at all.
3071
3072 ------------------------------------------------------------------------
3073 r336 | lh3 | 2008-06-01 17:45:23 -0400 (Sun, 01 Jun 2008) | 3 lines
3074 Changed paths:
3075 M /branches/prog/bwa/Makefile
3076 M /branches/prog/bwa/Makefile.div
3077 M /branches/prog/bwa/bntseq.c
3078 M /branches/prog/bwa/main.c
3079
3080 * 0.1.0-1
3081 * fix a bug in calculating the real coordinate
3082
3083 ------------------------------------------------------------------------
3084 r335 | lh3 | 2008-06-01 16:03:09 -0400 (Sun, 01 Jun 2008) | 2 lines
3085 Changed paths:
3086 M /branches/prog/bwa/Makefile
3087
3088 nothing, really
3089
3090 ------------------------------------------------------------------------
3091 r334 | lh3 | 2008-06-01 15:59:13 -0400 (Sun, 01 Jun 2008) | 2 lines
3092 Changed paths:
3093 M /branches/prog/bwa/Makefile
3094 A /branches/prog/bwa/Makefile.div
3095 M /branches/prog/bwa/bwtindex.c
3096 M /branches/prog/bwa/pac2bwt.c
3097
3098 use IS algorithm by default
3099
3100 ------------------------------------------------------------------------
3101 r333 | lh3 | 2008-06-01 15:05:15 -0400 (Sun, 01 Jun 2008) | 3 lines
3102 Changed paths:
3103 M /branches/prog/bwa/Makefile
3104 M /branches/prog/bwa/bwtindex.c
3105 M /branches/prog/bwa/is.c
3106 M /branches/prog/bwa/pac2bwt.c
3107
3108 * a bit code clean up in is.c
3109 * add IS algorithm for constructing BWT, albeit slower
3110
3111 ------------------------------------------------------------------------
3112 r332 | lh3 | 2008-06-01 13:23:08 -0400 (Sun, 01 Jun 2008) | 2 lines
3113 Changed paths:
3114 A /branches/prog/bwa/is.c
3115
3116 IS linear-time algorithm for constructing SA/BWT
3117
3118 ------------------------------------------------------------------------
3119 r331 | lh3 | 2008-06-01 10:35:26 -0400 (Sun, 01 Jun 2008) | 3 lines
3120 Changed paths:
3121 M /branches/prog/bwa/Makefile
3122 M /branches/prog/bwa/bntseq.c
3123 A /branches/prog/bwa/bwtindex.c
3124 M /branches/prog/bwa/main.c
3125 M /branches/prog/bwa/main.h
3126
3127 * fix a bug in generating .pac
3128 * index in one go
3129
3130 ------------------------------------------------------------------------
3131 r330 | lh3 | 2008-06-01 09:17:05 -0400 (Sun, 01 Jun 2008) | 2 lines
3132 Changed paths:
3133 M /branches/prog/bwa/bntseq.c
3134 M /branches/prog/bwa/bntseq.h
3135 M /branches/prog/bwa/bwtaln.c
3136 M /branches/prog/bwa/bwttop2.c
3137
3138 real coordinates can be ouput
3139
3140 ------------------------------------------------------------------------
3141 r329 | lh3 | 2008-05-31 19:21:02 -0400 (Sat, 31 May 2008) | 2 lines
3142 Changed paths:
3143 M /branches/prog/bwa/bwt2fmv.c
3144 M /branches/prog/bwa/bwtaln.h
3145 M /branches/prog/bwa/bwttop2.c
3146
3147 add top2e which is similar to 1away
3148
3149 ------------------------------------------------------------------------
3150 r328 | lh3 | 2008-05-31 18:46:12 -0400 (Sat, 31 May 2008) | 3 lines
3151 Changed paths:
3152 M /branches/prog/bwa/bwt2fmv.c
3153 M /branches/prog/bwa/bwtaln.c
3154 M /branches/prog/bwa/bwtaln.h
3155 M /branches/prog/bwa/bwttop2.c
3156 M /branches/prog/bwa/main.c
3157 M /branches/prog/bwa/main.h
3158
3159 * unified cmd-line interface for ungapped alignment
3160 * add two alternatives to top2 algorithm
3161
3162 ------------------------------------------------------------------------
3163 r327 | lh3 | 2008-05-31 18:14:46 -0400 (Sat, 31 May 2008) | 2 lines
3164 Changed paths:
3165 M /branches/prog/bwa/bwt2fmv.c
3166 M /branches/prog/bwa/bwtaln.c
3167 M /branches/prog/bwa/bwtaln.h
3168 M /branches/prog/bwa/main.c
3169 M /branches/prog/bwa/main.h
3170
3171 add cmd-line interface to alntop2
3172
3173 ------------------------------------------------------------------------
3174 r326 | lh3 | 2008-05-31 17:59:31 -0400 (Sat, 31 May 2008) | 2 lines
3175 Changed paths:
3176 M /branches/prog/bwa/Makefile
3177 M /branches/prog/bwa/bwt1away.c
3178 M /branches/prog/bwa/bwtaln.c
3179 M /branches/prog/bwa/bwtaln.h
3180 A /branches/prog/bwa/bwttop2.c
3181
3182 top2 algorithm seems to work. I need to change interface, though
3183
3184 ------------------------------------------------------------------------
3185 r325 | lh3 | 2008-05-31 15:11:49 -0400 (Sat, 31 May 2008) | 2 lines
3186 Changed paths:
3187 M /branches/prog/bwa/bwt1away.c
3188
3189 change the variable in the structure
3190
3191 ------------------------------------------------------------------------
3192 r324 | lh3 | 2008-05-31 14:52:13 -0400 (Sat, 31 May 2008) | 2 lines
3193 Changed paths:
3194 M /branches/prog/bwa/bwt1away.c
3195
3196 set a slightly better bound on the maximum allowed mismatches
3197
3198 ------------------------------------------------------------------------
3199 r323 | lh3 | 2008-05-30 18:40:21 -0400 (Fri, 30 May 2008) | 2 lines
3200 Changed paths:
3201 M /branches/prog/bwa/bwtaln.c
3202
3203 * output time statistics
3204
3205 ------------------------------------------------------------------------
3206 r322 | lh3 | 2008-05-30 17:58:25 -0400 (Fri, 30 May 2008) | 4 lines
3207 Changed paths:
3208 M /branches/prog/bwa/Makefile
3209 M /branches/prog/bwa/bwt.c
3210 M /branches/prog/bwa/bwt.h
3211 A /branches/prog/bwa/bwt1away.c
3212 M /branches/prog/bwa/bwtaln.c
3213 M /branches/prog/bwa/bwtaln.h
3214
3215 * presumably better way to make use of prefix. But for the moment I do
3216 not know whether it is correct or not.
3217 * a bit code clean up: separate alignment part
3218
3219 ------------------------------------------------------------------------
3220 r321 | lh3 | 2008-05-30 13:57:43 -0400 (Fri, 30 May 2008) | 3 lines
3221 Changed paths:
3222 M /branches/prog/bwa/Makefile
3223 M /branches/prog/bwa/bwt.c
3224 M /branches/prog/bwa/bwt.h
3225 M /branches/prog/bwa/bwt_gen/Makefile
3226 M /branches/prog/bwa/bwt_gen/bwt_gen.c
3227 M /branches/prog/bwa/bwtaln.c
3228 M /branches/prog/bwa/main.c
3229 M /branches/prog/bwa/main.h
3230 M /branches/prog/bwa/pac2bwt.c
3231
3232 * a bit code clean up
3233 * put bwt_gen in bwa
3234
3235 ------------------------------------------------------------------------
3236 r320 | lh3 | 2008-05-30 11:40:11 -0400 (Fri, 30 May 2008) | 4 lines
3237 Changed paths:
3238 M /branches/prog/bwa/bwt.c
3239 M /branches/prog/bwa/bwt2fmv.c
3240 M /branches/prog/bwa/bwtaln.c
3241 M /branches/prog/bwa/bwtaln.h
3242 M /branches/prog/bwa/bwtio.c
3243
3244 * improve cmd-line interface
3245 * fix a bug in loading .sa
3246 * change default sa interval to 32
3247
3248 ------------------------------------------------------------------------
3249 r319 | lh3 | 2008-05-30 10:31:37 -0400 (Fri, 30 May 2008) | 3 lines
3250 Changed paths:
3251 M /branches/prog/bwa/bwtaln.c
3252
3253 * fix memory leak (I know that. Just a bit lazy)
3254 * change to another method to do 1-away alignment
3255
3256 ------------------------------------------------------------------------
3257 r318 | lh3 | 2008-05-30 09:21:49 -0400 (Fri, 30 May 2008) | 2 lines
3258 Changed paths:
3259 M /branches/prog/bwa/bwt.c
3260 M /branches/prog/bwa/bwt.h
3261 M /branches/prog/bwa/bwt2fmv.c
3262 M /branches/prog/bwa/bwtaln.c
3263 M /branches/prog/bwa/bwtaln.h
3264 M /branches/prog/bwa/main.c
3265 M /branches/prog/bwa/main.h
3266
3267 best unique match is partially finished
3268
3269 ------------------------------------------------------------------------
3270 r317 | lh3 | 2008-05-30 06:33:28 -0400 (Fri, 30 May 2008) | 2 lines
3271 Changed paths:
3272 M /branches/prog/bwa/bwt.c
3273 M /branches/prog/bwa/bwt2fmv.c
3274 M /branches/prog/bwa/bwtaln.c
3275 M /branches/prog/bwa/bwtaln.h
3276 M /branches/prog/bwa/main.c
3277 M /branches/prog/bwa/main.h
3278
3279 remove "ungapped" command and related codes
3280
3281 ------------------------------------------------------------------------
3282 r316 | lh3 | 2008-05-30 06:05:20 -0400 (Fri, 30 May 2008) | 2 lines
3283 Changed paths:
3284 M /branches/prog/bwa/Makefile
3285 M /branches/prog/bwa/bwt.c
3286 M /branches/prog/bwa/bwtaln.c
3287 M /branches/prog/bwa/bwtaln.h
3288
3289 change variable name thick to width
3290
3291 ------------------------------------------------------------------------
3292 r315 | lh3 | 2008-05-29 19:06:13 -0400 (Thu, 29 May 2008) | 2 lines
3293 Changed paths:
3294 M /branches/prog/bwa/bntseq.c
3295 M /branches/prog/bwa/bwt.c
3296 M /branches/prog/bwa/bwt.h
3297 M /branches/prog/bwa/bwt2fmv.c
3298 M /branches/prog/bwa/bwtaln.c
3299 M /branches/prog/bwa/bwtaln.h
3300 M /branches/prog/bwa/bwtio.c
3301 M /branches/prog/bwa/main.c
3302 M /branches/prog/bwa/main.h
3303 M /branches/prog/bwa/pac2bwt.c
3304
3305 revised algorithm for ungapped alignment. the old one can still be used.
3306
3307 ------------------------------------------------------------------------
3308 r314 | lh3 | 2008-05-29 16:36:11 -0400 (Thu, 29 May 2008) | 2 lines
3309 Changed paths:
3310 M /branches/prog/bwa/bwt2fmv.c
3311 M /branches/prog/bwa/bwt_gen/bwt_gen.c
3312 M /branches/prog/bwa/bwtio.c
3313 M /branches/prog/bwa/pac2bwt.c
3314
3315 * make commands more independent, but ungapped does not work at the moment
3316
3317 ------------------------------------------------------------------------
3318 r313 | lh3 | 2008-05-29 15:56:14 -0400 (Thu, 29 May 2008) | 2 lines
3319 Changed paths:
3320 M /branches/prog/bwa/bwt_gen/bwt_gen.c
3321
3322 little...
3323
3324 ------------------------------------------------------------------------
3325 r312 | lh3 | 2008-05-29 15:54:01 -0400 (Thu, 29 May 2008) | 3 lines
3326 Changed paths:
3327 M /branches/prog/bwa/bwt_gen/bwt_gen.c
3328 M /branches/prog/bwa/bwt_gen/bwt_gen.h
3329
3330 * add CopyRight information from the original codes
3331 * do not dump .fmv files
3332
3333 ------------------------------------------------------------------------
3334 r311 | lh3 | 2008-05-29 15:44:36 -0400 (Thu, 29 May 2008) | 2 lines
3335 Changed paths:
3336 A /branches/prog/bwa/bwt_gen
3337 A /branches/prog/bwa/bwt_gen/Makefile
3338 A /branches/prog/bwa/bwt_gen/QSufSort.c
3339 A /branches/prog/bwa/bwt_gen/QSufSort.h
3340 A /branches/prog/bwa/bwt_gen/bwt_gen.c
3341 A /branches/prog/bwa/bwt_gen/bwt_gen.h
3342
3343 codes from BWT-SW, for building BWT from packed file
3344
3345 ------------------------------------------------------------------------
3346 r310 | lh3 | 2008-05-28 17:03:35 -0400 (Wed, 28 May 2008) | 4 lines
3347 Changed paths:
3348 M /branches/prog/bwa/bwt.c
3349 M /branches/prog/bwa/bwt.h
3350 M /branches/prog/bwa/bwt2fmv.c
3351 M /branches/prog/bwa/bwtio.c
3352 M /branches/prog/bwa/main.c
3353 M /branches/prog/bwa/main.h
3354
3355 * change OCC_INTERVAL to 0x40, which makes bwa twice as fast.
3356 * write Occ file as ".occ" as it is using a different interval from
3357 .fmv, the BWT-SW correspondance of .occ
3358
3359 ------------------------------------------------------------------------
3360 r309 | lh3 | 2008-05-28 11:39:37 -0400 (Wed, 28 May 2008) | 2 lines
3361 Changed paths:
3362 M /branches/prog/bwa/bwt.c
3363 M /branches/prog/bwa/bwt2fmv.c
3364
3365 fix a bug
3366
3367 ------------------------------------------------------------------------
3368 r308 | lh3 | 2008-05-28 09:56:16 -0400 (Wed, 28 May 2008) | 4 lines
3369 Changed paths:
3370 M /branches/prog/bwa/bwt.c
3371 M /branches/prog/bwa/bwt2fmv.c
3372
3373 add heuristics to improve the speed, but I have not tested whether the
3374 results are correct or not.
3375
3376
3377 ------------------------------------------------------------------------
3378 r307 | lh3 | 2008-05-28 06:31:34 -0400 (Wed, 28 May 2008) | 5 lines
3379 Changed paths:
3380 M /branches/prog/bwa/bwt.c
3381 M /branches/prog/bwa/bwt2fmv.c
3382 M /branches/prog/bwa/bwtaln.c
3383 M /branches/prog/bwa/bwtaln.h
3384 M /branches/prog/bwa/main.c
3385 M /branches/prog/bwa/main.h
3386
3387 * make ungapped alignment basically works...
3388 * but it is very slow in comparison to others...
3389 * also I need to improve the interface...
3390 * a lot of things to keep me busy today...
3391
3392 ------------------------------------------------------------------------
3393 r306 | lh3 | 2008-05-27 18:41:27 -0400 (Tue, 27 May 2008) | 3 lines
3394 Changed paths:
3395 M /branches/prog/bwa/bwt.c
3396 M /branches/prog/bwa/bwt.h
3397 M /branches/prog/bwa/bwtaln.c
3398
3399 * remove recursion
3400 * fixed a bug in bwt_occ()
3401
3402 ------------------------------------------------------------------------
3403 r305 | lh3 | 2008-05-27 16:59:44 -0400 (Tue, 27 May 2008) | 5 lines
3404 Changed paths:
3405 M /branches/prog/bwa/bwt.c
3406 M /branches/prog/bwa/bwt.h
3407 M /branches/prog/bwa/bwtaln.c
3408
3409 * bwa now tells whether a sequenced can be mapped with maximum allowed
3410 mismatches. ONLY ungapped.
3411 * this is a recursive version. I will remove recursion later.
3412
3413
3414 ------------------------------------------------------------------------
3415 r304 | lh3 | 2008-05-27 09:12:17 -0400 (Tue, 27 May 2008) | 3 lines
3416 Changed paths:
3417 M /branches/prog/bwa/Makefile
3418 M /branches/prog/bwa/bwt.c
3419 M /branches/prog/bwa/bwt.h
3420 M /branches/prog/bwa/bwt2fmv.c
3421 A /branches/prog/bwa/bwtaln.c
3422 A /branches/prog/bwa/bwtaln.h
3423 M /branches/prog/bwa/bwtio.c
3424 M /branches/prog/bwa/main.c
3425 M /branches/prog/bwa/main.h
3426 M /branches/prog/bwa/utils.c
3427
3428 * load .sa and .fmv files
3429 * exact alignment now works
3430
3431 ------------------------------------------------------------------------
3432 r303 | lh3 | 2008-05-27 06:33:38 -0400 (Tue, 27 May 2008) | 2 lines
3433 Changed paths:
3434 M /branches/prog/bwa/bntseq.c
3435 M /branches/prog/bwa/bwt.c
3436 M /branches/prog/bwa/bwtio.c
3437 M /branches/prog/bwa/utils.c
3438 M /branches/prog/bwa/utils.h
3439
3440 add xassert and fix a bug
3441
3442 ------------------------------------------------------------------------
3443 r302 | lh3 | 2008-05-27 06:23:20 -0400 (Tue, 27 May 2008) | 2 lines
3444 Changed paths:
3445 M /branches/prog/bwa/Makefile
3446 M /branches/prog/bwa/bntseq.c
3447 M /branches/prog/bwa/bwt.c
3448 M /branches/prog/bwa/bwtio.c
3449 A /branches/prog/bwa/utils.c
3450 A /branches/prog/bwa/utils.h
3451
3452 improve error message and error handling
3453
3454 ------------------------------------------------------------------------
3455 r301 | lh3 | 2008-05-27 05:37:51 -0400 (Tue, 27 May 2008) | 4 lines
3456 Changed paths:
3457 M /branches/prog/bwa/Makefile
3458 M /branches/prog/bwa/bwt.c
3459 M /branches/prog/bwa/bwt.h
3460 M /branches/prog/bwa/bwt2fmv.c
3461 A /branches/prog/bwa/bwtio.c
3462 M /branches/prog/bwa/main.c
3463 M /branches/prog/bwa/main.h
3464
3465 * move I/O codes to bwtio.c
3466 * SA can be dumped and interestingly, it is identical to BWTSW
3467 * now, .fmv is still different from BWTSW
3468
3469 ------------------------------------------------------------------------
3470 r299 | lh3 | 2008-05-26 18:07:44 -0400 (Mon, 26 May 2008) | 2 lines
3471 Changed paths:
3472 M /branches/prog/bwa/Makefile
3473 M /branches/prog/bwa/bwt.c
3474 M /branches/prog/bwa/bwt.h
3475 M /branches/prog/bwa/bwt2fmv.c
3476
3477 generate/retrieve SA and Occ
3478
3479 ------------------------------------------------------------------------
3480 r298 | lh3 | 2008-05-26 13:16:49 -0400 (Mon, 26 May 2008) | 3 lines
3481 Changed paths:
3482 M /branches/prog/bwa/bntseq.h
3483 M /branches/prog/bwa/bwt.c
3484 M /branches/prog/bwa/bwt.h
3485 M /branches/prog/bwa/bwt2fmv.c
3486
3487 * retrieve occ value at any position
3488 * move bwt_cal_occ() to bwt.c
3489
3490 ------------------------------------------------------------------------
3491 r297 | lh3 | 2008-05-25 17:43:58 -0400 (Sun, 25 May 2008) | 6 lines
3492 Changed paths:
3493 M /branches/prog/bwa/Makefile
3494 A /branches/prog/bwa/bwt.c
3495 A /branches/prog/bwa/bwt.h
3496 A /branches/prog/bwa/bwt2fmv.c
3497 M /branches/prog/bwa/main.c
3498 M /branches/prog/bwa/main.h
3499 M /branches/prog/bwa/pac2bwt.c
3500
3501 * add bwt2fmv. It works to some extend. However, I do not understand
3502 the purpose of some weird codes in BWT-SW. As a consequence, bwt2fmv
3503 could generate a file almost identical, but not exactly identical, to
3504 the .fmv file from BWT-SW.
3505
3506
3507 ------------------------------------------------------------------------
3508 r296 | lh3 | 2008-05-24 18:35:02 -0400 (Sat, 24 May 2008) | 5 lines
3509 Changed paths:
3510 M /branches/prog/bwa/Makefile
3511 M /branches/prog/bwa/bntseq.c
3512 M /branches/prog/bwa/bntseq.h
3513 M /branches/prog/bwa/main.c
3514 M /branches/prog/bwa/main.h
3515 A /branches/prog/bwa/pac2bwt.c
3516
3517 Burrows-Wheeler Transform now works. At least on one example, the
3518 current code generates the same BWT as BWT-SW. Kind of magical, I would
3519 say. :)
3520
3521
3522 ------------------------------------------------------------------------
3523 r295 | lh3 | 2008-05-24 11:25:31 -0400 (Sat, 24 May 2008) | 3 lines
3524 Changed paths:
3525 A /branches/prog/bwa/Makefile
3526 M /branches/prog/bwa/bntseq.c
3527 A /branches/prog/bwa/main.c
3528 A /branches/prog/bwa/main.h
3529
3530 * add Makefile and main.*
3531 * improve interface to fa2bns, a bit
3532
3533 ------------------------------------------------------------------------
3534 r293 | lh3 | 2008-05-24 10:57:03 -0400 (Sat, 24 May 2008) | 3 lines
3535 Changed paths:
3536 A /branches/prog/bwa
3537 A /branches/prog/bwa/bntseq.c
3538 A /branches/prog/bwa/bntseq.h
3539 A /branches/prog/bwa/seq.c
3540 A /branches/prog/bwa/seq.h
3541
3542 * Burrow-Wheeler Alignment
3543 * initial codes
3544
3545 ------------------------------------------------------------------------