Mercurial > repos > ashvark > qiime_1_8_0
comparison bwa-0.6.2/ChangeLog @ 0:dd1186b11b3b draft
Uploaded BWA
author | ashvark |
---|---|
date | Fri, 18 Jul 2014 07:55:14 -0400 (2014-07-18) |
parents | |
children |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:dd1186b11b3b |
---|---|
1 ------------------------------------------------------------------------ | |
2 r1605 | lh3 | 2010-12-29 20:20:20 -0500 (Wed, 29 Dec 2010) | 3 lines | |
3 Changed paths: | |
4 M /branches/prog/bwa/bwtsw2_aux.c | |
5 M /branches/prog/bwa/main.c | |
6 | |
7 * bwa-0.5.9rc1-2 (r1605) | |
8 * fixed a typo/bug in bwasw | |
9 | |
10 ------------------------------------------------------------------------ | |
11 r1587 | lh3 | 2010-12-21 18:48:30 -0500 (Tue, 21 Dec 2010) | 2 lines | |
12 Changed paths: | |
13 M /branches/prog/bwa/bwa.1 | |
14 | |
15 a typo in the manual | |
16 | |
17 ------------------------------------------------------------------------ | |
18 r1586 | lh3 | 2010-12-21 18:47:48 -0500 (Tue, 21 Dec 2010) | 3 lines | |
19 Changed paths: | |
20 M /branches/prog/bwa/bwape.c | |
21 M /branches/prog/bwa/bwase.c | |
22 M /branches/prog/bwa/bwtaln.c | |
23 M /branches/prog/bwa/bwtsw2_main.c | |
24 M /branches/prog/bwa/main.c | |
25 M /branches/prog/bwa/utils.c | |
26 M /branches/prog/bwa/utils.h | |
27 | |
28 * bwa-0.5.9rc1-1 (r1586) | |
29 * a few patches by John | |
30 | |
31 ------------------------------------------------------------------------ | |
32 r1562 | lh3 | 2010-12-10 01:02:06 -0500 (Fri, 10 Dec 2010) | 2 lines | |
33 Changed paths: | |
34 M /branches/prog/bwa/bwa.1 | |
35 M /branches/prog/bwa/bwape.c | |
36 M /branches/prog/bwa/bwase.c | |
37 | |
38 documentation on specifying @RG | |
39 | |
40 ------------------------------------------------------------------------ | |
41 r1561 | lh3 | 2010-12-10 00:45:40 -0500 (Fri, 10 Dec 2010) | 2 lines | |
42 Changed paths: | |
43 M /branches/prog/bwa/ChangeLog | |
44 M /branches/prog/bwa/NEWS | |
45 M /branches/prog/bwa/bwa.1 | |
46 M /branches/prog/bwa/main.c | |
47 | |
48 Release bwa-0.5.9rc1 (r1561) | |
49 | |
50 ------------------------------------------------------------------------ | |
51 r1560 | lh3 | 2010-12-10 00:29:08 -0500 (Fri, 10 Dec 2010) | 3 lines | |
52 Changed paths: | |
53 M /branches/prog/bwa/bwaseqio.c | |
54 M /branches/prog/bwa/main.c | |
55 | |
56 * fixed a small memory leak caused by the BAM reader | |
57 * fixed a memory violation, also in the BAM reader | |
58 | |
59 ------------------------------------------------------------------------ | |
60 r1559 | lh3 | 2010-12-10 00:10:48 -0500 (Fri, 10 Dec 2010) | 2 lines | |
61 Changed paths: | |
62 M /branches/prog/bwa/ChangeLog | |
63 M /branches/prog/bwa/Makefile | |
64 | |
65 change Makefile gcc options | |
66 | |
67 ------------------------------------------------------------------------ | |
68 r1558 | lh3 | 2010-12-10 00:09:22 -0500 (Fri, 10 Dec 2010) | 4 lines | |
69 Changed paths: | |
70 M /branches/prog/bwa/bwtsw2_aux.c | |
71 M /branches/prog/bwa/bwtsw2_core.c | |
72 M /branches/prog/bwa/main.c | |
73 | |
74 * bwa-0.5.8-6 (r1557) | |
75 * added a little more comments to BWA-SW | |
76 * randomly choosing a mapping if there are more than one | |
77 | |
78 ------------------------------------------------------------------------ | |
79 r1557 | lh3 | 2010-12-09 21:58:00 -0500 (Thu, 09 Dec 2010) | 2 lines | |
80 Changed paths: | |
81 M /branches/prog/bwa/Makefile | |
82 M /branches/prog/bwa/bwtsw2_aux.c | |
83 | |
84 sometimes unmapped reads may not be printed... | |
85 | |
86 ------------------------------------------------------------------------ | |
87 r1556 | lh3 | 2010-12-09 21:50:26 -0500 (Thu, 09 Dec 2010) | 2 lines | |
88 Changed paths: | |
89 M /branches/prog/bwa/Makefile | |
90 M /branches/prog/bwa/bwtsw2_aux.c | |
91 | |
92 print unmapped reads | |
93 | |
94 ------------------------------------------------------------------------ | |
95 r1555 | lh3 | 2010-12-09 21:17:20 -0500 (Thu, 09 Dec 2010) | 3 lines | |
96 Changed paths: | |
97 M /branches/prog/bwa/ChangeLog | |
98 M /branches/prog/bwa/bwa.1 | |
99 M /branches/prog/bwa/bwtaln.c | |
100 M /branches/prog/bwa/main.c | |
101 | |
102 * bwa-0.5.8-5 (r1555) | |
103 * BAM input documentation | |
104 | |
105 ------------------------------------------------------------------------ | |
106 r1544 | lh3 | 2010-11-23 11:01:41 -0500 (Tue, 23 Nov 2010) | 3 lines | |
107 Changed paths: | |
108 M /branches/prog/bwa/bwape.c | |
109 M /branches/prog/bwa/bwase.c | |
110 M /branches/prog/bwa/main.c | |
111 | |
112 * bwa-0.5.8-4 (r1544) | |
113 * supporting adding RG tags and RG lines | |
114 | |
115 ------------------------------------------------------------------------ | |
116 r1543 | lh3 | 2010-11-23 00:16:40 -0500 (Tue, 23 Nov 2010) | 3 lines | |
117 Changed paths: | |
118 M /branches/prog/bwa/bwtaln.c | |
119 M /branches/prog/bwa/main.c | |
120 | |
121 * bwa-0.5.8-3 (r1543) | |
122 * fixed a memory leak | |
123 | |
124 ------------------------------------------------------------------------ | |
125 r1542 | lh3 | 2010-11-22 23:50:56 -0500 (Mon, 22 Nov 2010) | 3 lines | |
126 Changed paths: | |
127 M /branches/prog/bwa/bwase.c | |
128 M /branches/prog/bwa/main.c | |
129 | |
130 * bwa-0.5.8-2 (r1542) | |
131 * fixed a long existing bug in random placement of reads | |
132 | |
133 ------------------------------------------------------------------------ | |
134 r1541 | lh3 | 2010-11-22 23:27:29 -0500 (Mon, 22 Nov 2010) | 2 lines | |
135 Changed paths: | |
136 M /branches/prog/bwa/Makefile | |
137 A /branches/prog/bwa/bamlite.c | |
138 A /branches/prog/bwa/bamlite.h | |
139 M /branches/prog/bwa/bwape.c | |
140 M /branches/prog/bwa/bwase.c | |
141 M /branches/prog/bwa/bwaseqio.c | |
142 M /branches/prog/bwa/bwtaln.c | |
143 M /branches/prog/bwa/bwtaln.h | |
144 M /branches/prog/bwa/main.c | |
145 | |
146 preliminary BAM input support | |
147 | |
148 ------------------------------------------------------------------------ | |
149 r1537 | lh3 | 2010-10-16 23:46:20 -0400 (Sat, 16 Oct 2010) | 2 lines | |
150 Changed paths: | |
151 M /branches/prog/bwa/ChangeLog | |
152 M /branches/prog/bwa/bwa.1 | |
153 | |
154 change version number and ChangeLog | |
155 | |
156 ------------------------------------------------------------------------ | |
157 r1536 | lh3 | 2010-10-16 23:35:10 -0400 (Sat, 16 Oct 2010) | 3 lines | |
158 Changed paths: | |
159 M /branches/prog/bwa/bwape.c | |
160 M /branches/prog/bwa/main.c | |
161 M /branches/prog/bwa/stdaln.c | |
162 | |
163 * fixed a bug in the scoring matrix | |
164 * release bwa-0.5.8c (r1536) | |
165 | |
166 ------------------------------------------------------------------------ | |
167 r1451 | lh3 | 2010-06-15 09:43:52 -0400 (Tue, 15 Jun 2010) | 2 lines | |
168 Changed paths: | |
169 M /branches/prog/bwa/bwa.1 | |
170 | |
171 version change | |
172 | |
173 ------------------------------------------------------------------------ | |
174 r1450 | lh3 | 2010-06-15 09:42:21 -0400 (Tue, 15 Jun 2010) | 3 lines | |
175 Changed paths: | |
176 M /branches/prog/bwa/main.c | |
177 M /branches/prog/bwa/stdaln.c | |
178 | |
179 * bwa-0.5.8b (r1450) | |
180 * fixed a bug in scoring matrix | |
181 | |
182 ------------------------------------------------------------------------ | |
183 r1445 | lh3 | 2010-06-11 08:58:33 -0400 (Fri, 11 Jun 2010) | 2 lines | |
184 Changed paths: | |
185 M /branches/prog/bwa/bwa.1 | |
186 M /branches/prog/bwa/bwape.c | |
187 | |
188 fixed a serious bug | |
189 | |
190 ------------------------------------------------------------------------ | |
191 r1442 | lh3 | 2010-06-08 10:22:14 -0400 (Tue, 08 Jun 2010) | 2 lines | |
192 Changed paths: | |
193 M /branches/prog/bwa/ChangeLog | |
194 M /branches/prog/bwa/NEWS | |
195 M /branches/prog/bwa/main.c | |
196 | |
197 Release bwa-0.5.8 (r1442) | |
198 | |
199 ------------------------------------------------------------------------ | |
200 r1440 | lh3 | 2010-05-19 13:43:50 -0400 (Wed, 19 May 2010) | 3 lines | |
201 Changed paths: | |
202 M /branches/prog/bwa/bwtsw2_core.c | |
203 M /branches/prog/bwa/main.c | |
204 | |
205 * bwa-r1440 | |
206 * sorry, forget to remove a debugging line | |
207 | |
208 ------------------------------------------------------------------------ | |
209 r1439 | lh3 | 2010-05-19 13:43:08 -0400 (Wed, 19 May 2010) | 4 lines | |
210 Changed paths: | |
211 M /branches/prog/bwa/bwape.c | |
212 M /branches/prog/bwa/bwtsw2_core.c | |
213 M /branches/prog/bwa/main.c | |
214 | |
215 * bwa-r1439 | |
216 * fixed a bug in bwasw caused by a recent modification | |
217 * throwing insane insert size when estimating isize | |
218 | |
219 ------------------------------------------------------------------------ | |
220 r1425 | lh3 | 2010-04-29 15:15:23 -0400 (Thu, 29 Apr 2010) | 10 lines | |
221 Changed paths: | |
222 M /branches/prog/bwa/bwtsw2_core.c | |
223 M /branches/prog/bwa/bwtsw2_main.c | |
224 M /branches/prog/bwa/main.c | |
225 | |
226 * bwa-0.5.7-7 (r1425) | |
227 * fixed a minor bug in bwasw command-line parsing | |
228 * When band-width is not large enough, bwasw may find two highly | |
229 overlapping but not completely overlapping alignments. The old | |
230 version will filter out one of them, which leads to false | |
231 negatives. The current outputs both. This solution is obviously not | |
232 ideal. The ideal one would be to increase the band-width and redo the | |
233 alignment. | |
234 | |
235 | |
236 ------------------------------------------------------------------------ | |
237 r1399 | lh3 | 2010-04-16 09:20:49 -0400 (Fri, 16 Apr 2010) | 3 lines | |
238 Changed paths: | |
239 M /branches/prog/bwa/ChangeLog | |
240 M /branches/prog/bwa/bwase.c | |
241 M /branches/prog/bwa/main.c | |
242 | |
243 * bwa-0.5.7-6 (r1399) | |
244 * fixed a typo/bug (by Vaughn Iverson) | |
245 | |
246 ------------------------------------------------------------------------ | |
247 r1329 | lh3 | 2010-03-19 23:32:46 -0400 (Fri, 19 Mar 2010) | 2 lines | |
248 Changed paths: | |
249 M /branches/prog/bwa/bwape.c | |
250 M /branches/prog/bwa/main.c | |
251 | |
252 small correction | |
253 | |
254 ------------------------------------------------------------------------ | |
255 r1328 | lh3 | 2010-03-19 23:28:44 -0400 (Fri, 19 Mar 2010) | 3 lines | |
256 Changed paths: | |
257 M /branches/prog/bwa/bwape.c | |
258 M /branches/prog/bwa/main.c | |
259 | |
260 * bwa-0.5.7-4 (r1328) | |
261 * automatically adjust ap_prior based on alignment | |
262 | |
263 ------------------------------------------------------------------------ | |
264 r1327 | lh3 | 2010-03-19 23:02:40 -0400 (Fri, 19 Mar 2010) | 3 lines | |
265 Changed paths: | |
266 M /branches/prog/bwa/bwape.c | |
267 M /branches/prog/bwa/main.c | |
268 M /branches/prog/bwa/stdaln.c | |
269 M /branches/prog/bwa/stdaln.h | |
270 | |
271 * bwa-0.5.7-3 (r1327) | |
272 * evaluate hits obtained from SW alignment in a more proper way. | |
273 | |
274 ------------------------------------------------------------------------ | |
275 r1320 | lh3 | 2010-03-17 15:13:22 -0400 (Wed, 17 Mar 2010) | 2 lines | |
276 Changed paths: | |
277 M /branches/prog/bwa/bwape.c | |
278 | |
279 fixed a potential out-of-boundary error. Need more testing. | |
280 | |
281 ------------------------------------------------------------------------ | |
282 r1319 | lh3 | 2010-03-14 22:44:46 -0400 (Sun, 14 Mar 2010) | 2 lines | |
283 Changed paths: | |
284 M /branches/prog/bwa/bwape.c | |
285 | |
286 insert size is `weird' if the 3rd quatile larger than 100,000bp | |
287 | |
288 ------------------------------------------------------------------------ | |
289 r1318 | lh3 | 2010-03-14 22:37:35 -0400 (Sun, 14 Mar 2010) | 3 lines | |
290 Changed paths: | |
291 M /branches/prog/bwa/bwape.c | |
292 M /branches/prog/bwa/bwtaln.h | |
293 M /branches/prog/bwa/main.c | |
294 | |
295 * bwa-0.5.7-2 (r1318) | |
296 * in sampe, allow to disable insert size estimate | |
297 | |
298 ------------------------------------------------------------------------ | |
299 r1317 | lh3 | 2010-03-14 22:14:14 -0400 (Sun, 14 Mar 2010) | 5 lines | |
300 Changed paths: | |
301 M /branches/prog/bwa/bwape.c | |
302 M /branches/prog/bwa/bwase.c | |
303 M /branches/prog/bwa/main.c | |
304 M /branches/prog/bwa/solid2fastq.pl | |
305 | |
306 * bwa-0.5.7-1 (r1317) | |
307 * fixed a potential bug in solid2fastq.pl | |
308 * fixed a bug in calculating mapping quality (by Rodrigo Goya) | |
309 * fixed a very rare bug (if ever occur) about pairing | |
310 | |
311 ------------------------------------------------------------------------ | |
312 r1310 | lh3 | 2010-03-01 10:35:45 -0500 (Mon, 01 Mar 2010) | 2 lines | |
313 Changed paths: | |
314 M /branches/prog/bwa/ChangeLog | |
315 M /branches/prog/bwa/NEWS | |
316 M /branches/prog/bwa/main.c | |
317 | |
318 Release bwa-0.5.7 | |
319 | |
320 ------------------------------------------------------------------------ | |
321 r1309 | lh3 | 2010-02-26 21:42:22 -0500 (Fri, 26 Feb 2010) | 4 lines | |
322 Changed paths: | |
323 M /branches/prog/bwa/bwape.c | |
324 M /branches/prog/bwa/bwtaln.c | |
325 M /branches/prog/bwa/main.c | |
326 | |
327 * bwa-0.5.6-2 (r1309) | |
328 * fixed an unfixed bug (by Carol Scott) | |
329 * fixed some tiny formatting | |
330 | |
331 ------------------------------------------------------------------------ | |
332 r1305 | lh3 | 2010-02-25 13:47:58 -0500 (Thu, 25 Feb 2010) | 3 lines | |
333 Changed paths: | |
334 M /branches/prog/bwa/bwape.c | |
335 M /branches/prog/bwa/bwase.c | |
336 M /branches/prog/bwa/bwtaln.c | |
337 M /branches/prog/bwa/bwtsw2_main.c | |
338 M /branches/prog/bwa/main.c | |
339 | |
340 * bwa-0.5.6-1 (r1304) | |
341 * optionally write output to a file (by Tim Fennel) | |
342 | |
343 ------------------------------------------------------------------------ | |
344 r1303 | lh3 | 2010-02-10 23:43:48 -0500 (Wed, 10 Feb 2010) | 2 lines | |
345 Changed paths: | |
346 M /branches/prog/bwa/ChangeLog | |
347 M /branches/prog/bwa/NEWS | |
348 M /branches/prog/bwa/bwa.1 | |
349 M /branches/prog/bwa/bwtsw2_main.c | |
350 M /branches/prog/bwa/main.c | |
351 | |
352 Release bwa-0.5.6 | |
353 | |
354 ------------------------------------------------------------------------ | |
355 r1302 | lh3 | 2010-02-10 11:11:49 -0500 (Wed, 10 Feb 2010) | 3 lines | |
356 Changed paths: | |
357 M /branches/prog/bwa/ChangeLog | |
358 M /branches/prog/bwa/NEWS | |
359 M /branches/prog/bwa/bwape.c | |
360 M /branches/prog/bwa/bwtaln.h | |
361 M /branches/prog/bwa/main.c | |
362 | |
363 * bwa-0.5.5-10 (r1302) | |
364 * improve max insert size estimate (method suggested by Gerton Lunter) | |
365 | |
366 ------------------------------------------------------------------------ | |
367 r1301 | lh3 | 2010-02-09 16:15:28 -0500 (Tue, 09 Feb 2010) | 5 lines | |
368 Changed paths: | |
369 M /branches/prog/bwa/bwape.c | |
370 M /branches/prog/bwa/bwase.c | |
371 M /branches/prog/bwa/main.c | |
372 | |
373 * bwa-0.5.5-9 (r1301) | |
374 * improve mapping quality calculation for abnomalous pairs | |
375 * fixed a bug in multiple hits | |
376 * SOLiD multiple hits should work now | |
377 | |
378 ------------------------------------------------------------------------ | |
379 r1300 | lh3 | 2010-02-09 12:50:02 -0500 (Tue, 09 Feb 2010) | 3 lines | |
380 Changed paths: | |
381 M /branches/prog/bwa/bwape.c | |
382 M /branches/prog/bwa/main.c | |
383 | |
384 * bwa-0.5.5-8 (r1300) | |
385 * output kurtosis | |
386 | |
387 ------------------------------------------------------------------------ | |
388 r1299 | lh3 | 2010-02-09 12:33:34 -0500 (Tue, 09 Feb 2010) | 5 lines | |
389 Changed paths: | |
390 M /branches/prog/bwa/bwape.c | |
391 M /branches/prog/bwa/main.c | |
392 | |
393 * bwa-0.5.5-7 (r1299) | |
394 * calculate skewness in sampe | |
395 * increase min_len in SW to 20 | |
396 * perform more SW to fix discordant pairs | |
397 | |
398 ------------------------------------------------------------------------ | |
399 r1298 | lh3 | 2010-02-08 12:40:31 -0500 (Mon, 08 Feb 2010) | 3 lines | |
400 Changed paths: | |
401 M /branches/prog/bwa/bwape.c | |
402 M /branches/prog/bwa/bwase.c | |
403 M /branches/prog/bwa/bwtaln.c | |
404 M /branches/prog/bwa/bwtaln.h | |
405 M /branches/prog/bwa/cs2nt.c | |
406 M /branches/prog/bwa/main.c | |
407 M /branches/prog/bwa/stdaln.h | |
408 | |
409 * bwa-0.5.5-6 (r1297) | |
410 * prepare to replace all 16-bit CIGAR (patches by Rodrigo Goya) | |
411 | |
412 ------------------------------------------------------------------------ | |
413 r1297 | lh3 | 2010-02-05 22:26:11 -0500 (Fri, 05 Feb 2010) | 2 lines | |
414 Changed paths: | |
415 M /branches/prog/bwa/solid2fastq.pl | |
416 | |
417 the old fix seems not working! | |
418 | |
419 ------------------------------------------------------------------------ | |
420 r1296 | lh3 | 2010-02-05 21:51:03 -0500 (Fri, 05 Feb 2010) | 3 lines | |
421 Changed paths: | |
422 M /branches/prog/bwa/bwa.1 | |
423 M /branches/prog/bwa/bwape.c | |
424 M /branches/prog/bwa/main.c | |
425 | |
426 * bwa-0.5.5-5 (r1296) | |
427 * fixed a minor issue that the lower bound of insert size is not correctly set. | |
428 | |
429 ------------------------------------------------------------------------ | |
430 r1295 | lh3 | 2010-02-05 21:01:10 -0500 (Fri, 05 Feb 2010) | 5 lines | |
431 Changed paths: | |
432 M /branches/prog/bwa/bwape.c | |
433 M /branches/prog/bwa/bwase.c | |
434 M /branches/prog/bwa/bwaseqio.c | |
435 M /branches/prog/bwa/main.c | |
436 | |
437 * bwa-0.5.5-4 (r1295) | |
438 * fixed a memory leak | |
439 * change the behaviour of -n (samse and sampe) | |
440 * change the default of -n | |
441 | |
442 ------------------------------------------------------------------------ | |
443 r1294 | lh3 | 2010-02-05 17:24:06 -0500 (Fri, 05 Feb 2010) | 3 lines | |
444 Changed paths: | |
445 M /branches/prog/bwa/bwape.c | |
446 M /branches/prog/bwa/bwase.c | |
447 M /branches/prog/bwa/bwaseqio.c | |
448 M /branches/prog/bwa/bwtaln.h | |
449 M /branches/prog/bwa/main.c | |
450 | |
451 * bwa-0.5.5-3 (r1294) | |
452 * improved multi-hit report | |
453 | |
454 ------------------------------------------------------------------------ | |
455 r1293 | lh3 | 2010-02-05 12:57:38 -0500 (Fri, 05 Feb 2010) | 5 lines | |
456 Changed paths: | |
457 M /branches/prog/bwa/bwape.c | |
458 M /branches/prog/bwa/bwase.c | |
459 M /branches/prog/bwa/cs2nt.c | |
460 M /branches/prog/bwa/main.c | |
461 M /branches/prog/bwa/solid2fastq.pl | |
462 | |
463 * bwa-0.5.5-2 (r1293) | |
464 * bugfix: truncated quality string | |
465 * bugfix: quality -1 in solid->fastq conversion | |
466 * bugfix: color reads on the reverse strand is not complemented | |
467 | |
468 ------------------------------------------------------------------------ | |
469 r1279 | lh3 | 2009-11-23 22:42:34 -0500 (Mon, 23 Nov 2009) | 3 lines | |
470 Changed paths: | |
471 M /branches/prog/bwa/bntseq.c | |
472 M /branches/prog/bwa/bntseq.h | |
473 M /branches/prog/bwa/bwase.c | |
474 A /branches/prog/bwa/bwase.h | |
475 M /branches/prog/bwa/bwtaln.c | |
476 M /branches/prog/bwa/bwtaln.h | |
477 M /branches/prog/bwa/bwtsw2_aux.c | |
478 M /branches/prog/bwa/main.c | |
479 | |
480 * bwa-0.5.5-1 (r1279) | |
481 * incorporate changes from Matt Hanna for Java bindings. | |
482 | |
483 ------------------------------------------------------------------------ | |
484 r1275 | lh3 | 2009-11-10 22:13:10 -0500 (Tue, 10 Nov 2009) | 2 lines | |
485 Changed paths: | |
486 M /branches/prog/bwa/ChangeLog | |
487 | |
488 update ChangeLog | |
489 | |
490 ------------------------------------------------------------------------ | |
491 r1273 | lh3 | 2009-11-10 22:08:16 -0500 (Tue, 10 Nov 2009) | 2 lines | |
492 Changed paths: | |
493 M /branches/prog/bwa/NEWS | |
494 M /branches/prog/bwa/bwa.1 | |
495 M /branches/prog/bwa/main.c | |
496 A /branches/prog/bwa/qualfa2fq.pl | |
497 | |
498 Release bwa-0.5.5 (r1273) | |
499 | |
500 ------------------------------------------------------------------------ | |
501 r1272 | lh3 | 2009-11-10 22:02:50 -0500 (Tue, 10 Nov 2009) | 3 lines | |
502 Changed paths: | |
503 M /branches/prog/bwa/bwape.c | |
504 M /branches/prog/bwa/main.c | |
505 | |
506 * bwa-0.5.4-3 (r1272) | |
507 * fixed another typo which may lead to incorrect single-end mapping quality | |
508 | |
509 ------------------------------------------------------------------------ | |
510 r1271 | lh3 | 2009-11-10 21:59:47 -0500 (Tue, 10 Nov 2009) | 4 lines | |
511 Changed paths: | |
512 M /branches/prog/bwa/bwtaln.c | |
513 M /branches/prog/bwa/main.c | |
514 | |
515 * bwa-0.5.4-2 (r1271) | |
516 * fixed a serious typo/bug which does not hurt if we allow one gap open | |
517 and work with <200bp reads, but causes segfault for long reads. | |
518 | |
519 ------------------------------------------------------------------------ | |
520 r1270 | lh3 | 2009-11-09 23:12:42 -0500 (Mon, 09 Nov 2009) | 3 lines | |
521 Changed paths: | |
522 M /branches/prog/bwa/cs2nt.c | |
523 M /branches/prog/bwa/main.c | |
524 | |
525 * bwa-0.5.4-1 (r1270) | |
526 * fixed a bug in color alignment | |
527 | |
528 ------------------------------------------------------------------------ | |
529 r1245 | lh3 | 2009-10-09 07:42:52 -0400 (Fri, 09 Oct 2009) | 2 lines | |
530 Changed paths: | |
531 M /branches/prog/bwa/ChangeLog | |
532 M /branches/prog/bwa/NEWS | |
533 M /branches/prog/bwa/bwa.1 | |
534 M /branches/prog/bwa/bwape.c | |
535 M /branches/prog/bwa/bwase.c | |
536 M /branches/prog/bwa/bwaseqio.c | |
537 M /branches/prog/bwa/main.c | |
538 | |
539 Release bwa-0.5.4 | |
540 | |
541 ------------------------------------------------------------------------ | |
542 r1244 | lh3 | 2009-10-09 05:53:52 -0400 (Fri, 09 Oct 2009) | 5 lines | |
543 Changed paths: | |
544 M /branches/prog/bwa/ChangeLog | |
545 M /branches/prog/bwa/bwape.c | |
546 M /branches/prog/bwa/bwase.c | |
547 M /branches/prog/bwa/bwaseqio.c | |
548 M /branches/prog/bwa/bwtaln.h | |
549 M /branches/prog/bwa/main.c | |
550 M /branches/prog/bwa/stdaln.c | |
551 | |
552 * bwa-0.5.3-4 (r1244) | |
553 * output the clipped length in XC:i: tag | |
554 * skip mate alignment when stdaln is buggy | |
555 * fixed a bug in NM:i: tag | |
556 | |
557 ------------------------------------------------------------------------ | |
558 r1243 | lh3 | 2009-10-07 08:15:04 -0400 (Wed, 07 Oct 2009) | 3 lines | |
559 Changed paths: | |
560 M /branches/prog/bwa/bwape.c | |
561 M /branches/prog/bwa/main.c | |
562 | |
563 * bwa-0.5.3-3 (r1243) | |
564 * sampe: fixed a bug when a read sequence is identical its reverse complement. | |
565 | |
566 ------------------------------------------------------------------------ | |
567 r1242 | lh3 | 2009-10-07 07:49:13 -0400 (Wed, 07 Oct 2009) | 4 lines | |
568 Changed paths: | |
569 M /branches/prog/bwa/bntseq.c | |
570 M /branches/prog/bwa/bwape.c | |
571 M /branches/prog/bwa/bwtaln.c | |
572 M /branches/prog/bwa/bwtaln.h | |
573 M /branches/prog/bwa/main.c | |
574 | |
575 * bwa-0.5.3-2 (r1242) | |
576 * sampe: optionall preload the full index into memory | |
577 * aln: change the default seed length to 32bp | |
578 | |
579 ------------------------------------------------------------------------ | |
580 r1238 | lh3 | 2009-09-26 18:38:15 -0400 (Sat, 26 Sep 2009) | 2 lines | |
581 Changed paths: | |
582 M /branches/prog/bwa/khash.h | |
583 | |
584 Improve portability of khash.h | |
585 | |
586 ------------------------------------------------------------------------ | |
587 r1228 | lh3 | 2009-09-15 09:20:22 -0400 (Tue, 15 Sep 2009) | 2 lines | |
588 Changed paths: | |
589 M /branches/prog/bwa/main.c | |
590 | |
591 fixed a typo | |
592 | |
593 ------------------------------------------------------------------------ | |
594 r1227 | lh3 | 2009-09-15 09:19:35 -0400 (Tue, 15 Sep 2009) | 3 lines | |
595 Changed paths: | |
596 M /branches/prog/bwa/bwtsw2.h | |
597 M /branches/prog/bwa/bwtsw2_aux.c | |
598 M /branches/prog/bwa/bwtsw2_main.c | |
599 M /branches/prog/bwa/main.c | |
600 | |
601 * bwa-0.5.3-1 (r1226) | |
602 * in dBWT-SW, optionall use hard clipping instead of soft clipping | |
603 | |
604 ------------------------------------------------------------------------ | |
605 r1225 | lh3 | 2009-09-15 08:32:30 -0400 (Tue, 15 Sep 2009) | 2 lines | |
606 Changed paths: | |
607 M /branches/prog/bwa/NEWS | |
608 M /branches/prog/bwa/bwase.c | |
609 M /branches/prog/bwa/main.c | |
610 | |
611 Release bwa-0.5.3 (r1225) | |
612 | |
613 ------------------------------------------------------------------------ | |
614 r1223 | lh3 | 2009-09-13 07:30:41 -0400 (Sun, 13 Sep 2009) | 2 lines | |
615 Changed paths: | |
616 M /branches/prog/bwa/ChangeLog | |
617 M /branches/prog/bwa/NEWS | |
618 M /branches/prog/bwa/bwa.1 | |
619 M /branches/prog/bwa/main.c | |
620 | |
621 Release bwa-0.5.2 | |
622 | |
623 ------------------------------------------------------------------------ | |
624 r1222 | lh3 | 2009-09-11 09:11:39 -0400 (Fri, 11 Sep 2009) | 3 lines | |
625 Changed paths: | |
626 M /branches/prog/bwa/bwtaln.c | |
627 M /branches/prog/bwa/main.c | |
628 | |
629 * bwa-0.5.1-5 (r1222) | |
630 * fixed a typo. No real change | |
631 | |
632 ------------------------------------------------------------------------ | |
633 r1221 | lh3 | 2009-09-11 09:09:44 -0400 (Fri, 11 Sep 2009) | 3 lines | |
634 Changed paths: | |
635 M /branches/prog/bwa/bwa.1 | |
636 M /branches/prog/bwa/bwape.c | |
637 M /branches/prog/bwa/bwase.c | |
638 M /branches/prog/bwa/bwaseqio.c | |
639 M /branches/prog/bwa/bwtaln.c | |
640 M /branches/prog/bwa/bwtaln.h | |
641 M /branches/prog/bwa/main.c | |
642 | |
643 * bwa-0.5.1-4 (r1221) | |
644 * trim reads before alignment | |
645 | |
646 ------------------------------------------------------------------------ | |
647 r1216 | lh3 | 2009-09-08 17:50:15 -0400 (Tue, 08 Sep 2009) | 4 lines | |
648 Changed paths: | |
649 M /branches/prog/bwa/bwape.c | |
650 M /branches/prog/bwa/bwase.c | |
651 M /branches/prog/bwa/bwtaln.h | |
652 M /branches/prog/bwa/main.c | |
653 | |
654 * bwa-0.5.1-3 (r1216) | |
655 * fixed a bug about NM tags for gapped alignment | |
656 * print SAM header | |
657 | |
658 ------------------------------------------------------------------------ | |
659 r1215 | lh3 | 2009-09-08 17:14:42 -0400 (Tue, 08 Sep 2009) | 3 lines | |
660 Changed paths: | |
661 M /branches/prog/bwa/bwtaln.c | |
662 M /branches/prog/bwa/main.c | |
663 | |
664 * bwa-0.5.1-2 (r1215) | |
665 * fixed a bug when read lengths vary (by John Marshall) | |
666 | |
667 ------------------------------------------------------------------------ | |
668 r1213 | lh3 | 2009-09-06 18:58:15 -0400 (Sun, 06 Sep 2009) | 3 lines | |
669 Changed paths: | |
670 M /branches/prog/bwa/bwtsw2_aux.c | |
671 M /branches/prog/bwa/main.c | |
672 | |
673 * bwa-0.5.1-1 (r1213) | |
674 * change default -T to 30 | |
675 | |
676 ------------------------------------------------------------------------ | |
677 r1209 | lh3 | 2009-09-02 06:06:02 -0400 (Wed, 02 Sep 2009) | 2 lines | |
678 Changed paths: | |
679 M /branches/prog/bwa/NEWS | |
680 M /branches/prog/bwa/bwa.1 | |
681 M /branches/prog/bwa/main.c | |
682 | |
683 Release bwa-0.5.1 | |
684 | |
685 ------------------------------------------------------------------------ | |
686 r1208 | lh3 | 2009-09-02 05:56:33 -0400 (Wed, 02 Sep 2009) | 2 lines | |
687 Changed paths: | |
688 M /branches/prog/bwa/ChangeLog | |
689 | |
690 * ChangeLog | |
691 | |
692 ------------------------------------------------------------------------ | |
693 r1206 | lh3 | 2009-08-30 18:27:30 -0400 (Sun, 30 Aug 2009) | 3 lines | |
694 Changed paths: | |
695 M /branches/prog/bwa/bwtsw2_aux.c | |
696 M /branches/prog/bwa/main.c | |
697 | |
698 * bwa-0.5.0-6 (r1206) | |
699 * fixed two bugs caused by previous modification | |
700 | |
701 ------------------------------------------------------------------------ | |
702 r1205 | lh3 | 2009-08-30 17:28:36 -0400 (Sun, 30 Aug 2009) | 4 lines | |
703 Changed paths: | |
704 M /branches/prog/bwa/ChangeLog | |
705 M /branches/prog/bwa/bwtsw2_aux.c | |
706 M /branches/prog/bwa/main.c | |
707 | |
708 * bwa-0.5.0-4 (r1205) | |
709 * reduce false coordinates and CIGAR when a query bridges two reference | |
710 sequences, although some very rare cases may fail bwa. | |
711 | |
712 ------------------------------------------------------------------------ | |
713 r1204 | lh3 | 2009-08-30 06:06:16 -0400 (Sun, 30 Aug 2009) | 3 lines | |
714 Changed paths: | |
715 M /branches/prog/bwa/bwtsw2_aux.c | |
716 M /branches/prog/bwa/bwtsw2_core.c | |
717 M /branches/prog/bwa/main.c | |
718 | |
719 * bwa-0.5.0-3 (r1204) | |
720 * choose one repetitive hit to extend | |
721 | |
722 ------------------------------------------------------------------------ | |
723 r1203 | lh3 | 2009-08-29 18:11:51 -0400 (Sat, 29 Aug 2009) | 4 lines | |
724 Changed paths: | |
725 M /branches/prog/bwa/bwase.c | |
726 M /branches/prog/bwa/bwtsw2_aux.c | |
727 M /branches/prog/bwa/main.c | |
728 | |
729 * bwa-0.5.0-2 (r1203) | |
730 * dBWT-SW: change a parameter in calculating mapping quality | |
731 * fixed a bug in samse | |
732 | |
733 ------------------------------------------------------------------------ | |
734 r1202 | lh3 | 2009-08-28 19:48:41 -0400 (Fri, 28 Aug 2009) | 4 lines | |
735 Changed paths: | |
736 M /branches/prog/bwa/bwtsw2_aux.c | |
737 M /branches/prog/bwa/main.c | |
738 | |
739 * bwa-0.5.0-1 (r1202) | |
740 * change default band width to 50 | |
741 * improve mapping quality a bit | |
742 | |
743 ------------------------------------------------------------------------ | |
744 r1200 | lh3 | 2009-08-20 06:21:24 -0400 (Thu, 20 Aug 2009) | 2 lines | |
745 Changed paths: | |
746 M /branches/prog/bwa/NEWS | |
747 M /branches/prog/bwa/main.c | |
748 | |
749 Release bwa-0.5.0 (r1200) | |
750 | |
751 ------------------------------------------------------------------------ | |
752 r1199 | lh3 | 2009-08-20 04:49:15 -0400 (Thu, 20 Aug 2009) | 2 lines | |
753 Changed paths: | |
754 M /branches/prog/bwa/ChangeLog | |
755 M /branches/prog/bwa/bwa.1 | |
756 | |
757 Updated ChangeLog and the manual | |
758 | |
759 ------------------------------------------------------------------------ | |
760 r1198 | lh3 | 2009-08-19 11:09:15 -0400 (Wed, 19 Aug 2009) | 3 lines | |
761 Changed paths: | |
762 M /branches/prog/bwa/bwtsw2_aux.c | |
763 M /branches/prog/bwa/bwtsw2_core.c | |
764 M /branches/prog/bwa/main.c | |
765 | |
766 * bwa-0.4.9-36 (r1198) | |
767 * simplify duphits removal. The accuracy is changed a tiny bit, sometimes better, sometimes worse. | |
768 | |
769 ------------------------------------------------------------------------ | |
770 r1197 | lh3 | 2009-08-19 08:15:05 -0400 (Wed, 19 Aug 2009) | 3 lines | |
771 Changed paths: | |
772 M /branches/prog/bwa/Makefile | |
773 M /branches/prog/bwa/bwtsw2_aux.c | |
774 A /branches/prog/bwa/bwtsw2_chain.c | |
775 M /branches/prog/bwa/main.c | |
776 | |
777 * bwa-0.4.9-35 (r1197) | |
778 * further heuristic acceleration for long queries | |
779 | |
780 ------------------------------------------------------------------------ | |
781 r1196 | lh3 | 2009-08-18 06:54:03 -0400 (Tue, 18 Aug 2009) | 4 lines | |
782 Changed paths: | |
783 M /branches/prog/bwa/bwa.1 | |
784 M /branches/prog/bwa/bwtsw2_aux.c | |
785 M /branches/prog/bwa/main.c | |
786 | |
787 * bwa-0.4.9-34 (r1196) | |
788 * updated the manual page | |
789 * output base quality if the input is fastq | |
790 | |
791 ------------------------------------------------------------------------ | |
792 r1195 | lh3 | 2009-08-18 06:23:00 -0400 (Tue, 18 Aug 2009) | 4 lines | |
793 Changed paths: | |
794 M /branches/prog/bwa/bwase.c | |
795 M /branches/prog/bwa/bwtsw2_main.c | |
796 M /branches/prog/bwa/main.c | |
797 M /branches/prog/bwa/simple_dp.c | |
798 | |
799 * bwa-0.4.9-33 (r1191) | |
800 * fixed a bug in sampe/samse when gaps occur to the 5'-end in SW alignment | |
801 * in dbwtsw adjust -T and -c according to -a | |
802 | |
803 ------------------------------------------------------------------------ | |
804 r1192 | lh3 | 2009-08-13 05:37:28 -0400 (Thu, 13 Aug 2009) | 2 lines | |
805 Changed paths: | |
806 M /branches/prog/bwa/bwa.1 | |
807 | |
808 update manual | |
809 | |
810 ------------------------------------------------------------------------ | |
811 r1191 | lh3 | 2009-08-12 19:40:51 -0400 (Wed, 12 Aug 2009) | 2 lines | |
812 Changed paths: | |
813 M /branches/prog/bwa/bwa.1 | |
814 M /branches/prog/bwa/bwtsw2_main.c | |
815 | |
816 update documentation | |
817 | |
818 ------------------------------------------------------------------------ | |
819 r1190 | lh3 | 2009-08-12 08:56:10 -0400 (Wed, 12 Aug 2009) | 3 lines | |
820 Changed paths: | |
821 M /branches/prog/bwa/bwtsw2_main.c | |
822 M /branches/prog/bwa/main.c | |
823 | |
824 * bwa-0.4.9-32 (r1190) | |
825 * only help messages are changed | |
826 | |
827 ------------------------------------------------------------------------ | |
828 r1189 | lh3 | 2009-08-11 09:28:55 -0400 (Tue, 11 Aug 2009) | 4 lines | |
829 Changed paths: | |
830 M /branches/prog/bwa/bwase.c | |
831 M /branches/prog/bwa/bwtsw2.h | |
832 M /branches/prog/bwa/bwtsw2_aux.c | |
833 M /branches/prog/bwa/bwtsw2_core.c | |
834 M /branches/prog/bwa/main.c | |
835 | |
836 * bwa-0.4.9-31 (r1189) | |
837 * in bwape/bwase, print CIGAR "*" if the read is unmapped | |
838 * improved the calculation of mapping quality | |
839 | |
840 ------------------------------------------------------------------------ | |
841 r1181 | lh3 | 2009-08-03 12:09:41 -0400 (Mon, 03 Aug 2009) | 2 lines | |
842 Changed paths: | |
843 M /branches/prog/bwa/bwtsw2_aux.c | |
844 | |
845 fflush() | |
846 | |
847 ------------------------------------------------------------------------ | |
848 r1180 | lh3 | 2009-08-03 12:08:46 -0400 (Mon, 03 Aug 2009) | 4 lines | |
849 Changed paths: | |
850 M /branches/prog/bwa/bwtsw2_aux.c | |
851 M /branches/prog/bwa/main.c | |
852 | |
853 * bwa-0.4.9-30 (r1180) | |
854 * fixed a memory problem | |
855 * multi-threading sometimes does not work... | |
856 | |
857 ------------------------------------------------------------------------ | |
858 r1179 | lh3 | 2009-08-03 11:04:39 -0400 (Mon, 03 Aug 2009) | 3 lines | |
859 Changed paths: | |
860 M /branches/prog/bwa/Makefile | |
861 M /branches/prog/bwa/bwtsw2.h | |
862 M /branches/prog/bwa/bwtsw2_aux.c | |
863 M /branches/prog/bwa/bwtsw2_main.c | |
864 M /branches/prog/bwa/main.c | |
865 | |
866 * bwa-0.4.9-29 (r1179) | |
867 * preliminary mutli-threading support in dbwtsw | |
868 | |
869 ------------------------------------------------------------------------ | |
870 r1178 | lh3 | 2009-08-03 09:14:54 -0400 (Mon, 03 Aug 2009) | 3 lines | |
871 Changed paths: | |
872 M /branches/prog/bwa/bwtsw2_aux.c | |
873 M /branches/prog/bwa/bwtsw2_main.c | |
874 M /branches/prog/bwa/main.c | |
875 | |
876 * bwa-0.4.9-28 (r1178) | |
877 * fixed a bug in printing repetitive hits | |
878 | |
879 ------------------------------------------------------------------------ | |
880 r1177 | lh3 | 2009-08-03 05:03:42 -0400 (Mon, 03 Aug 2009) | 3 lines | |
881 Changed paths: | |
882 M /branches/prog/bwa/bwtsw2_core.c | |
883 M /branches/prog/bwa/main.c | |
884 | |
885 * bwa-0.4.9-27 (r1177) | |
886 * bwtsw2: fixed a hidden memory leak | |
887 | |
888 ------------------------------------------------------------------------ | |
889 r1176 | lh3 | 2009-07-31 10:58:24 -0400 (Fri, 31 Jul 2009) | 3 lines | |
890 Changed paths: | |
891 M /branches/prog/bwa/bwtsw2_aux.c | |
892 M /branches/prog/bwa/bwtsw2_main.c | |
893 M /branches/prog/bwa/main.c | |
894 | |
895 * bwa-0.4.9-26 | |
896 * change the way mapping quality is calculated | |
897 | |
898 ------------------------------------------------------------------------ | |
899 r1175 | lh3 | 2009-07-31 09:15:54 -0400 (Fri, 31 Jul 2009) | 4 lines | |
900 Changed paths: | |
901 M /branches/prog/bwa/bwtsw2.h | |
902 M /branches/prog/bwa/bwtsw2_aux.c | |
903 M /branches/prog/bwa/bwtsw2_core.c | |
904 M /branches/prog/bwa/bwtsw2_main.c | |
905 M /branches/prog/bwa/main.c | |
906 | |
907 * bwa-0.4.9-25 | |
908 * code clean up | |
909 * automatically adjust ->t and ->is_rev based on input | |
910 | |
911 ------------------------------------------------------------------------ | |
912 r1174 | lh3 | 2009-07-30 08:50:25 -0400 (Thu, 30 Jul 2009) | 3 lines | |
913 Changed paths: | |
914 M /branches/prog/bwa/bwtsw2_aux.c | |
915 M /branches/prog/bwa/main.c | |
916 | |
917 * bwa-0.4.9-24 | |
918 * fixed a bug in printing the hits | |
919 | |
920 ------------------------------------------------------------------------ | |
921 r1173 | lh3 | 2009-07-29 18:32:43 -0400 (Wed, 29 Jul 2009) | 4 lines | |
922 Changed paths: | |
923 M /branches/prog/bwa/bwtsw2.h | |
924 M /branches/prog/bwa/bwtsw2_aux.c | |
925 M /branches/prog/bwa/bwtsw2_main.c | |
926 M /branches/prog/bwa/main.c | |
927 | |
928 * bwa-0.4.9-23 | |
929 * allow to skip reverse alignment | |
930 * increase opt->t to 37 | |
931 | |
932 ------------------------------------------------------------------------ | |
933 r1172 | lh3 | 2009-07-29 17:22:39 -0400 (Wed, 29 Jul 2009) | 3 lines | |
934 Changed paths: | |
935 M /branches/prog/bwa/bwtsw2_aux.c | |
936 M /branches/prog/bwa/bwtsw2_main.c | |
937 M /branches/prog/bwa/main.c | |
938 | |
939 * bwa-0.4.9-22 | |
940 * report if the hit is found in both directions | |
941 | |
942 ------------------------------------------------------------------------ | |
943 r1171 | lh3 | 2009-07-29 17:12:02 -0400 (Wed, 29 Jul 2009) | 3 lines | |
944 Changed paths: | |
945 M /branches/prog/bwa/bwtsw2.h | |
946 M /branches/prog/bwa/bwtsw2_aux.c | |
947 M /branches/prog/bwa/bwtsw2_main.c | |
948 M /branches/prog/bwa/main.c | |
949 | |
950 * bwa-0.4.9-21 | |
951 * dbwtsw: map to both forward and reverse BWT to reduce false alignment | |
952 | |
953 ------------------------------------------------------------------------ | |
954 r1170 | lh3 | 2009-07-29 15:25:14 -0400 (Wed, 29 Jul 2009) | 2 lines | |
955 Changed paths: | |
956 M /branches/prog/bwa/bwtsw2_core.c | |
957 M /branches/prog/bwa/main.c | |
958 | |
959 save hits before cut_tail() | |
960 | |
961 ------------------------------------------------------------------------ | |
962 r1169 | lh3 | 2009-07-29 08:06:01 -0400 (Wed, 29 Jul 2009) | 3 lines | |
963 Changed paths: | |
964 M /branches/prog/bwa/bwtsw2.h | |
965 M /branches/prog/bwa/bwtsw2_aux.c | |
966 M /branches/prog/bwa/bwtsw2_core.c | |
967 M /branches/prog/bwa/main.c | |
968 M /branches/prog/bwa/stdaln.c | |
969 M /branches/prog/bwa/stdaln.h | |
970 | |
971 * bwa-0.4.9-19 | |
972 * use a global memory pool to reduce the CPU time spent on malloc/free(). | |
973 | |
974 ------------------------------------------------------------------------ | |
975 r1168 | lh3 | 2009-07-29 06:13:29 -0400 (Wed, 29 Jul 2009) | 5 lines | |
976 Changed paths: | |
977 M /branches/prog/bwa/bwtsw2.h | |
978 M /branches/prog/bwa/bwtsw2_aux.c | |
979 M /branches/prog/bwa/bwtsw2_core.c | |
980 M /branches/prog/bwa/bwtsw2_main.c | |
981 M /branches/prog/bwa/main.c | |
982 | |
983 * bwa-0.4.9-18 | |
984 * reduce unnecessary extension to the 5'-end | |
985 * allow to use different interval size for the 2 rounds | |
986 * change default parameters | |
987 | |
988 ------------------------------------------------------------------------ | |
989 r1167 | lh3 | 2009-07-28 19:06:17 -0400 (Tue, 28 Jul 2009) | 3 lines | |
990 Changed paths: | |
991 M /branches/prog/bwa/bwtsw2_core.c | |
992 M /branches/prog/bwa/main.c | |
993 | |
994 * bwa-0.4.9-17 | |
995 * dbwtsw: fixed THE memory leak. | |
996 | |
997 ------------------------------------------------------------------------ | |
998 r1166 | lh3 | 2009-07-28 16:31:41 -0400 (Tue, 28 Jul 2009) | 5 lines | |
999 Changed paths: | |
1000 M /branches/prog/bwa/bwtsw2_aux.c | |
1001 M /branches/prog/bwa/bwtsw2_core.c | |
1002 M /branches/prog/bwa/bwtsw2_main.c | |
1003 M /branches/prog/bwa/main.c | |
1004 M /branches/prog/bwa/stdaln.c | |
1005 | |
1006 * bwa-0.4.9-16 | |
1007 * fixed a memory leak | |
1008 * a small memory leak still occurs to bwtsw2_core(). I will work on that later. | |
1009 * changed the default parameters | |
1010 | |
1011 ------------------------------------------------------------------------ | |
1012 r1165 | lh3 | 2009-07-28 10:15:40 -0400 (Tue, 28 Jul 2009) | 4 lines | |
1013 Changed paths: | |
1014 M /branches/prog/bwa/bwtsw2_aux.c | |
1015 M /branches/prog/bwa/bwtsw2_core.c | |
1016 M /branches/prog/bwa/main.c | |
1017 M /branches/prog/bwa/stdaln.c | |
1018 | |
1019 * bwa-0.4.9-15 | |
1020 * generate CIGAR right before output. This saves unnecessary computation. | |
1021 * this version may be buggy as I have not tested it. | |
1022 | |
1023 ------------------------------------------------------------------------ | |
1024 r1164 | lh3 | 2009-07-28 09:04:14 -0400 (Tue, 28 Jul 2009) | 11 lines | |
1025 Changed paths: | |
1026 M /branches/prog/bwa/bwtsw2.h | |
1027 M /branches/prog/bwa/bwtsw2_aux.c | |
1028 M /branches/prog/bwa/bwtsw2_core.c | |
1029 M /branches/prog/bwa/main.c | |
1030 M /branches/prog/bwa/stdaln.c | |
1031 M /branches/prog/bwa/stdaln.h | |
1032 | |
1033 * bwa-0.4.9-14 | |
1034 | |
1035 * deplete unique hits in dbwtsw and postprocess them with standard sw | |
1036 | |
1037 * in principle, this stratgy should be faster and more accurate, but I | |
1038 have not tested this point. I may switch back to the old method if | |
1039 this does not work. | |
1040 | |
1041 * the code looks quite nasty now. it needs clean up... | |
1042 | |
1043 | |
1044 ------------------------------------------------------------------------ | |
1045 r1163 | lh3 | 2009-07-27 17:41:10 -0400 (Mon, 27 Jul 2009) | 2 lines | |
1046 Changed paths: | |
1047 M /branches/prog/bwa/bwtsw2_aux.c | |
1048 | |
1049 change a default parameter | |
1050 | |
1051 ------------------------------------------------------------------------ | |
1052 r1162 | lh3 | 2009-07-27 17:04:35 -0400 (Mon, 27 Jul 2009) | 3 lines | |
1053 Changed paths: | |
1054 M /branches/prog/bwa/bwtsw2.h | |
1055 M /branches/prog/bwa/bwtsw2_aux.c | |
1056 M /branches/prog/bwa/bwtsw2_core.c | |
1057 M /branches/prog/bwa/bwtsw2_main.c | |
1058 M /branches/prog/bwa/main.c | |
1059 | |
1060 * bwa-0.4.9-13 | |
1061 * dbwtsw: switch between small and large Z-best | |
1062 | |
1063 ------------------------------------------------------------------------ | |
1064 r1161 | lh3 | 2009-07-27 12:17:41 -0400 (Mon, 27 Jul 2009) | 4 lines | |
1065 Changed paths: | |
1066 M /branches/prog/bwa/bwtsw2_aux.c | |
1067 M /branches/prog/bwa/bwtsw2_core.c | |
1068 M /branches/prog/bwa/main.c | |
1069 | |
1070 * bwa-0.4.9-12 | |
1071 * changed the default -z to 100 | |
1072 * heuristically speed up alignments for polyA reads | |
1073 | |
1074 ------------------------------------------------------------------------ | |
1075 r1160 | lh3 | 2009-07-27 07:50:57 -0400 (Mon, 27 Jul 2009) | 6 lines | |
1076 Changed paths: | |
1077 M /branches/prog/bwa/bwtsw2.h | |
1078 M /branches/prog/bwa/bwtsw2_aux.c | |
1079 M /branches/prog/bwa/bwtsw2_core.c | |
1080 M /branches/prog/bwa/main.c | |
1081 | |
1082 * bwa-0.4.9-11 | |
1083 | |
1084 * dbwtsw potentially generates less false alignments, although in | |
1085 practice, the modification brings no improvement. | |
1086 | |
1087 | |
1088 ------------------------------------------------------------------------ | |
1089 r1159 | lh3 | 2009-07-27 04:37:02 -0400 (Mon, 27 Jul 2009) | 4 lines | |
1090 Changed paths: | |
1091 M /branches/prog/bwa/bwase.c | |
1092 M /branches/prog/bwa/bwtsw2_aux.c | |
1093 M /branches/prog/bwa/bwtsw2_core.c | |
1094 M /branches/prog/bwa/main.c | |
1095 | |
1096 * bwa-0.4.9-10 | |
1097 * disabled debugging code | |
1098 * add "BAM_FMU" if both ends are unmapped | |
1099 | |
1100 ------------------------------------------------------------------------ | |
1101 r1158 | lh3 | 2009-07-24 09:36:52 -0400 (Fri, 24 Jul 2009) | 2 lines | |
1102 Changed paths: | |
1103 M /branches/prog/bwa/main.c | |
1104 | |
1105 nothing, really | |
1106 | |
1107 ------------------------------------------------------------------------ | |
1108 r1157 | lh3 | 2009-07-24 09:05:44 -0400 (Fri, 24 Jul 2009) | 3 lines | |
1109 Changed paths: | |
1110 M /branches/prog/bwa/bwtsw2_aux.c | |
1111 M /branches/prog/bwa/bwtsw2_core.c | |
1112 M /branches/prog/bwa/main.c | |
1113 | |
1114 * bwa-0.4.9-9 | |
1115 * bwtsw2: generate SAM output | |
1116 | |
1117 ------------------------------------------------------------------------ | |
1118 r1156 | lh3 | 2009-07-24 05:42:47 -0400 (Fri, 24 Jul 2009) | 6 lines | |
1119 Changed paths: | |
1120 M /branches/prog/bwa/bwape.c | |
1121 M /branches/prog/bwa/main.c | |
1122 | |
1123 * bwa-0.4.9-8 | |
1124 | |
1125 * fixed a weird deadloop which only happens to icc -O3. Thanks John | |
1126 Marshall for the fix. | |
1127 | |
1128 | |
1129 ------------------------------------------------------------------------ | |
1130 r1155 | lh3 | 2009-07-24 05:28:40 -0400 (Fri, 24 Jul 2009) | 8 lines | |
1131 Changed paths: | |
1132 M /branches/prog/bwa/bwtsw2_aux.c | |
1133 M /branches/prog/bwa/bwtsw2_core.c | |
1134 M /branches/prog/bwa/main.c | |
1135 | |
1136 * bwa-0.4.9-7 | |
1137 | |
1138 * fixed a typo in bwtsw2 alignment. Now score from the standard SW | |
1139 seems to agree with score from bwtsw2, except that in reporting | |
1140 alignments, bwtsw2 may report non-optimal segments. This is expected, | |
1141 though. I will improve in future. | |
1142 | |
1143 | |
1144 ------------------------------------------------------------------------ | |
1145 r1154 | lh3 | 2009-07-23 17:40:20 -0400 (Thu, 23 Jul 2009) | 3 lines | |
1146 Changed paths: | |
1147 M /branches/prog/bwa/stdaln.c | |
1148 M /branches/prog/bwa/stdaln.h | |
1149 | |
1150 * aln_left_core() seems to work properly | |
1151 * aln_local_core() has a bug... AN EVER EXISTING BUG!!!!!!!!!!! | |
1152 | |
1153 ------------------------------------------------------------------------ | |
1154 r1153 | lh3 | 2009-07-23 17:06:09 -0400 (Thu, 23 Jul 2009) | 2 lines | |
1155 Changed paths: | |
1156 M /branches/prog/bwa/stdaln.c | |
1157 | |
1158 removed debugging code... | |
1159 | |
1160 ------------------------------------------------------------------------ | |
1161 r1152 | lh3 | 2009-07-23 17:01:00 -0400 (Thu, 23 Jul 2009) | 3 lines | |
1162 Changed paths: | |
1163 M /branches/prog/bwa/stdaln.c | |
1164 | |
1165 * radical changes failed... | |
1166 * fixed a bug | |
1167 | |
1168 ------------------------------------------------------------------------ | |
1169 r1151 | lh3 | 2009-07-23 14:46:35 -0400 (Thu, 23 Jul 2009) | 2 lines | |
1170 Changed paths: | |
1171 M /branches/prog/bwa/stdaln.c | |
1172 | |
1173 temporary changes. Will apply some radical changes to this file... | |
1174 | |
1175 ------------------------------------------------------------------------ | |
1176 r1150 | lh3 | 2009-07-23 10:09:56 -0400 (Thu, 23 Jul 2009) | 2 lines | |
1177 Changed paths: | |
1178 M /branches/prog/bwa/bwtsw2_aux.c | |
1179 M /branches/prog/bwa/bwtsw2_main.c | |
1180 M /branches/prog/bwa/stdaln.c | |
1181 | |
1182 fixed a long-existing bug in Smith-Waterman alignment | |
1183 | |
1184 ------------------------------------------------------------------------ | |
1185 r1149 | lh3 | 2009-07-23 08:50:52 -0400 (Thu, 23 Jul 2009) | 3 lines | |
1186 Changed paths: | |
1187 M /branches/prog/bwa/bwtsw2.h | |
1188 M /branches/prog/bwa/bwtsw2_aux.c | |
1189 M /branches/prog/bwa/bwtsw2_main.c | |
1190 M /branches/prog/bwa/main.c | |
1191 M /branches/prog/bwa/simple_dp.c | |
1192 M /branches/prog/bwa/stdaln.c | |
1193 M /branches/prog/bwa/stdaln.h | |
1194 | |
1195 * bwa-0.4.9-6 | |
1196 * unexplained inconsistency still occurs, but the results largely look reasonable. | |
1197 | |
1198 ------------------------------------------------------------------------ | |
1199 r1148 | lh3 | 2009-07-23 08:07:29 -0400 (Thu, 23 Jul 2009) | 2 lines | |
1200 Changed paths: | |
1201 M /branches/prog/bwa/stdaln.c | |
1202 | |
1203 half DP | |
1204 | |
1205 ------------------------------------------------------------------------ | |
1206 r1147 | lh3 | 2009-07-22 08:03:06 -0400 (Wed, 22 Jul 2009) | 2 lines | |
1207 Changed paths: | |
1208 M /branches/prog/bwa/bwtsw2.h | |
1209 M /branches/prog/bwa/bwtsw2_aux.c | |
1210 M /branches/prog/bwa/bwtsw2_core.c | |
1211 M /branches/prog/bwa/bwtsw2_main.c | |
1212 | |
1213 a bit code clean up | |
1214 | |
1215 ------------------------------------------------------------------------ | |
1216 r1145 | lh3 | 2009-07-21 15:52:05 -0400 (Tue, 21 Jul 2009) | 4 lines | |
1217 Changed paths: | |
1218 M /branches/prog/bwa/bwtsw2_aux.c | |
1219 M /branches/prog/bwa/bwtsw2_core.c | |
1220 M /branches/prog/bwa/main.c | |
1221 | |
1222 * bwa-0.4.9-5 | |
1223 * fixed a bug in determining sub-optimal hits | |
1224 * removed some debugging codes | |
1225 | |
1226 ------------------------------------------------------------------------ | |
1227 r1144 | lh3 | 2009-07-21 10:17:29 -0400 (Tue, 21 Jul 2009) | 4 lines | |
1228 Changed paths: | |
1229 M /branches/prog/bwa/bwtsw2.h | |
1230 M /branches/prog/bwa/bwtsw2_aux.c | |
1231 M /branches/prog/bwa/bwtsw2_core.c | |
1232 M /branches/prog/bwa/bwtsw2_main.c | |
1233 M /branches/prog/bwa/main.c | |
1234 | |
1235 * bwa-0.4.9-4 | |
1236 * better cmd interface | |
1237 * faster speed | |
1238 | |
1239 ------------------------------------------------------------------------ | |
1240 r1143 | lh3 | 2009-07-20 16:38:18 -0400 (Mon, 20 Jul 2009) | 3 lines | |
1241 Changed paths: | |
1242 M /branches/prog/bwa/bwtsw2.h | |
1243 M /branches/prog/bwa/bwtsw2_aux.c | |
1244 M /branches/prog/bwa/bwtsw2_core.c | |
1245 M /branches/prog/bwa/bwtsw2_main.c | |
1246 M /branches/prog/bwa/main.c | |
1247 | |
1248 bwtsw2 (dBWT-SW) is working apparently... | |
1249 | |
1250 | |
1251 ------------------------------------------------------------------------ | |
1252 r1139 | lh3 | 2009-07-15 05:52:18 -0400 (Wed, 15 Jul 2009) | 4 lines | |
1253 Changed paths: | |
1254 M /branches/prog/bwa/bwtsw2_core.c | |
1255 M /branches/prog/bwa/main.c | |
1256 | |
1257 * bwa-0.4.9-2 | |
1258 * bwtsw2: change cut_tail() such that it is faster but more likely to | |
1259 miss true hits | |
1260 | |
1261 ------------------------------------------------------------------------ | |
1262 r1138 | lh3 | 2009-07-15 05:18:42 -0400 (Wed, 15 Jul 2009) | 3 lines | |
1263 Changed paths: | |
1264 M /branches/prog/bwa/Makefile | |
1265 A /branches/prog/bwa/bwt_lite.c | |
1266 A /branches/prog/bwa/bwt_lite.h | |
1267 A /branches/prog/bwa/bwtsw2.h | |
1268 A /branches/prog/bwa/bwtsw2_aux.c | |
1269 A /branches/prog/bwa/bwtsw2_core.c | |
1270 A /branches/prog/bwa/bwtsw2_main.c | |
1271 M /branches/prog/bwa/main.c | |
1272 M /branches/prog/bwa/main.h | |
1273 | |
1274 * bwa-0.4.9-1 | |
1275 * added back bwtsw2 | |
1276 | |
1277 ------------------------------------------------------------------------ | |
1278 r1075 | lh3 | 2009-05-19 05:14:50 -0400 (Tue, 19 May 2009) | 2 lines | |
1279 Changed paths: | |
1280 M /branches/prog/bwa/NEWS | |
1281 M /branches/prog/bwa/bwase.c | |
1282 M /branches/prog/bwa/main.c | |
1283 | |
1284 Release bwa-0.4.9 | |
1285 | |
1286 ------------------------------------------------------------------------ | |
1287 r1073 | lh3 | 2009-05-18 17:13:19 -0400 (Mon, 18 May 2009) | 2 lines | |
1288 Changed paths: | |
1289 M /branches/prog/bwa/NEWS | |
1290 M /branches/prog/bwa/bwa.1 | |
1291 M /branches/prog/bwa/main.c | |
1292 | |
1293 Release bwa-0.4.8 | |
1294 | |
1295 ------------------------------------------------------------------------ | |
1296 r1069 | lh3 | 2009-05-14 09:54:54 -0400 (Thu, 14 May 2009) | 3 lines | |
1297 Changed paths: | |
1298 M /branches/prog/bwa/bwtaln.c | |
1299 M /branches/prog/bwa/main.c | |
1300 | |
1301 * bwa-0.4.7-2 | |
1302 * change the default of "aln -R" to 30 | |
1303 | |
1304 ------------------------------------------------------------------------ | |
1305 r1068 | lh3 | 2009-05-14 09:27:55 -0400 (Thu, 14 May 2009) | 3 lines | |
1306 Changed paths: | |
1307 M /branches/prog/bwa/bwape.c | |
1308 M /branches/prog/bwa/bwase.c | |
1309 M /branches/prog/bwa/bwtaln.c | |
1310 M /branches/prog/bwa/bwtaln.h | |
1311 M /branches/prog/bwa/bwtgap.c | |
1312 M /branches/prog/bwa/main.c | |
1313 | |
1314 * bwa-0.4.7-1 | |
1315 * search for suboptimal hits if the top hit is not so repetitive | |
1316 | |
1317 ------------------------------------------------------------------------ | |
1318 r1066 | lh3 | 2009-05-12 15:31:31 -0400 (Tue, 12 May 2009) | 2 lines | |
1319 Changed paths: | |
1320 M /branches/prog/bwa/ChangeLog | |
1321 M /branches/prog/bwa/NEWS | |
1322 M /branches/prog/bwa/bwase.c | |
1323 M /branches/prog/bwa/main.c | |
1324 | |
1325 Release bwa-0.4.7 | |
1326 | |
1327 ------------------------------------------------------------------------ | |
1328 r1065 | lh3 | 2009-05-12 15:20:40 -0400 (Tue, 12 May 2009) | 3 lines | |
1329 Changed paths: | |
1330 M /branches/prog/bwa/bwape.c | |
1331 M /branches/prog/bwa/bwase.c | |
1332 M /branches/prog/bwa/main.c | |
1333 | |
1334 * bwa-0.4.6-9 | |
1335 * fixed compiling errors on some Linux machines | |
1336 | |
1337 ------------------------------------------------------------------------ | |
1338 r1064 | lh3 | 2009-05-12 07:30:46 -0400 (Tue, 12 May 2009) | 3 lines | |
1339 Changed paths: | |
1340 M /branches/prog/bwa/bwtaln.c | |
1341 M /branches/prog/bwa/main.c | |
1342 | |
1343 * bwa-0.4.6-8 | |
1344 * avoid compilation error on some systems. | |
1345 | |
1346 ------------------------------------------------------------------------ | |
1347 r1035 | lh3 | 2009-05-09 05:41:33 -0400 (Sat, 09 May 2009) | 4 lines | |
1348 Changed paths: | |
1349 M /branches/prog/bwa/bwape.c | |
1350 M /branches/prog/bwa/bwase.c | |
1351 M /branches/prog/bwa/main.c | |
1352 | |
1353 * bwa-0.4.6-7 | |
1354 * fixed an integer overflow caused by previous modifications | |
1355 * made insert size estimation more robust | |
1356 | |
1357 ------------------------------------------------------------------------ | |
1358 r1008 | lh3 | 2009-04-29 05:41:58 -0400 (Wed, 29 Apr 2009) | 4 lines | |
1359 Changed paths: | |
1360 M /branches/prog/bwa/bwase.c | |
1361 M /branches/prog/bwa/main.c | |
1362 | |
1363 * bwa-0.4.6-5 | |
1364 * fixed a integer overflow problem which may cause seg fault in very rare cases | |
1365 * made XN tags more accurate | |
1366 | |
1367 ------------------------------------------------------------------------ | |
1368 r1005 | lh3 | 2009-04-27 07:37:23 -0400 (Mon, 27 Apr 2009) | 4 lines | |
1369 Changed paths: | |
1370 M /branches/prog/bwa/bwape.c | |
1371 M /branches/prog/bwa/main.c | |
1372 M /branches/prog/bwa/simple_dp.c | |
1373 M /branches/prog/bwa/stdaln.c | |
1374 M /branches/prog/bwa/stdaln.h | |
1375 | |
1376 * bwa-0.4.6-4 | |
1377 * heuristic rules to detect suboptimal alignment | |
1378 * stdsw: support double-strand and protein alignment | |
1379 | |
1380 ------------------------------------------------------------------------ | |
1381 r1003 | lh3 | 2009-04-26 12:48:19 -0400 (Sun, 26 Apr 2009) | 4 lines | |
1382 Changed paths: | |
1383 M /branches/prog/bwa/main.c | |
1384 M /branches/prog/bwa/simple_dp.c | |
1385 M /branches/prog/bwa/stdaln.c | |
1386 M /branches/prog/bwa/stdaln.h | |
1387 | |
1388 * bwa-0.4.6-2 | |
1389 * improve the functionality of stdsw | |
1390 * allow to add a threshold on SW alignment. Hope this does not incur new bugs... | |
1391 | |
1392 ------------------------------------------------------------------------ | |
1393 r1002 | lh3 | 2009-04-22 03:56:15 -0400 (Wed, 22 Apr 2009) | 3 lines | |
1394 Changed paths: | |
1395 M /branches/prog/bwa/bwa.1 | |
1396 M /branches/prog/bwa/bwape.c | |
1397 M /branches/prog/bwa/bwase.c | |
1398 M /branches/prog/bwa/bwtaln.h | |
1399 M /branches/prog/bwa/main.c | |
1400 | |
1401 * bwa-0.4.6-1 | |
1402 * output SM and AM tag | |
1403 | |
1404 ------------------------------------------------------------------------ | |
1405 r914 | lh3 | 2009-03-09 17:53:50 -0400 (Mon, 09 Mar 2009) | 2 lines | |
1406 Changed paths: | |
1407 M /branches/prog/bwa/ChangeLog | |
1408 M /branches/prog/bwa/NEWS | |
1409 M /branches/prog/bwa/main.c | |
1410 | |
1411 Release bwa-0.4.6 | |
1412 | |
1413 ------------------------------------------------------------------------ | |
1414 r913 | lh3 | 2009-03-09 17:23:24 -0400 (Mon, 09 Mar 2009) | 4 lines | |
1415 Changed paths: | |
1416 M /branches/prog/bwa/bwa.1 | |
1417 M /branches/prog/bwa/bwape.c | |
1418 A /branches/prog/bwa/solid2fastq.pl | |
1419 | |
1420 * added notes to bwa | |
1421 * added a script to convert SOLiD reads | |
1422 * updated documentations | |
1423 | |
1424 ------------------------------------------------------------------------ | |
1425 r912 | lh3 | 2009-03-09 16:57:05 -0400 (Mon, 09 Mar 2009) | 2 lines | |
1426 Changed paths: | |
1427 M /branches/prog/bwa/ChangeLog | |
1428 M /branches/prog/bwa/kstring.c | |
1429 M /branches/prog/bwa/main.c | |
1430 | |
1431 fixed a bug in kstring | |
1432 | |
1433 ------------------------------------------------------------------------ | |
1434 r881 | lh3 | 2009-03-02 15:36:06 -0500 (Mon, 02 Mar 2009) | 3 lines | |
1435 Changed paths: | |
1436 M /branches/prog/bwa/bwtmisc.c | |
1437 M /branches/prog/bwa/main.c | |
1438 | |
1439 * bwa-0.4.5-7 | |
1440 * fixed a bug in pac2cspac | |
1441 | |
1442 ------------------------------------------------------------------------ | |
1443 r880 | lh3 | 2009-03-01 16:34:08 -0500 (Sun, 01 Mar 2009) | 2 lines | |
1444 Changed paths: | |
1445 M /branches/prog/bwa/Makefile | |
1446 | |
1447 disable debugging | |
1448 | |
1449 ------------------------------------------------------------------------ | |
1450 r879 | lh3 | 2009-03-01 16:28:04 -0500 (Sun, 01 Mar 2009) | 3 lines | |
1451 Changed paths: | |
1452 M /branches/prog/bwa/bwase.c | |
1453 M /branches/prog/bwa/cs2nt.c | |
1454 M /branches/prog/bwa/main.c | |
1455 | |
1456 * bwa-0.4.5-6 | |
1457 * fixed problems with coordinates for color gapped alignment | |
1458 | |
1459 ------------------------------------------------------------------------ | |
1460 r878 | lh3 | 2009-03-01 13:43:09 -0500 (Sun, 01 Mar 2009) | 3 lines | |
1461 Changed paths: | |
1462 M /branches/prog/bwa/bwase.c | |
1463 M /branches/prog/bwa/cs2nt.c | |
1464 M /branches/prog/bwa/main.c | |
1465 | |
1466 * bwa-0.4.5-5 | |
1467 * added support for gapped color alignment | |
1468 | |
1469 ------------------------------------------------------------------------ | |
1470 r877 | lh3 | 2009-03-01 10:27:52 -0500 (Sun, 01 Mar 2009) | 2 lines | |
1471 Changed paths: | |
1472 M /branches/prog/bwa/Makefile | |
1473 M /branches/prog/bwa/bwape.c | |
1474 M /branches/prog/bwa/bwase.c | |
1475 M /branches/prog/bwa/bwtaln.h | |
1476 M /branches/prog/bwa/cs2nt.c | |
1477 M /branches/prog/bwa/main.c | |
1478 | |
1479 * convert cs read to nt read (for ungapped alignment only) | |
1480 | |
1481 ------------------------------------------------------------------------ | |
1482 r860 | lh3 | 2009-02-27 08:58:39 -0500 (Fri, 27 Feb 2009) | 2 lines | |
1483 Changed paths: | |
1484 M /branches/prog/bwa/Makefile | |
1485 M /branches/prog/bwa/bwase.c | |
1486 A /branches/prog/bwa/cs2nt.c | |
1487 | |
1488 prepare to implement cs->nt conversion (have not yet...) | |
1489 | |
1490 ------------------------------------------------------------------------ | |
1491 r859 | lh3 | 2009-02-27 07:00:03 -0500 (Fri, 27 Feb 2009) | 3 lines | |
1492 Changed paths: | |
1493 M /branches/prog/bwa/bntseq.c | |
1494 M /branches/prog/bwa/bntseq.h | |
1495 M /branches/prog/bwa/bwtindex.c | |
1496 M /branches/prog/bwa/bwtmisc.c | |
1497 M /branches/prog/bwa/main.c | |
1498 M /branches/prog/bwa/main.h | |
1499 | |
1500 * bwa-0.4.5-3 | |
1501 * generate color index from nucleotide fasta reference | |
1502 | |
1503 ------------------------------------------------------------------------ | |
1504 r857 | lh3 | 2009-02-26 10:22:58 -0500 (Thu, 26 Feb 2009) | 4 lines | |
1505 Changed paths: | |
1506 M /branches/prog/bwa/bwape.c | |
1507 M /branches/prog/bwa/main.c | |
1508 | |
1509 * bwa-0.4.5-2 | |
1510 * improved mapping quality a bit if one end falls in a tandem repeat | |
1511 but the mate is unique. | |
1512 | |
1513 ------------------------------------------------------------------------ | |
1514 r856 | lh3 | 2009-02-26 10:02:29 -0500 (Thu, 26 Feb 2009) | 3 lines | |
1515 Changed paths: | |
1516 M /branches/prog/bwa/bwape.c | |
1517 M /branches/prog/bwa/bwtaln.h | |
1518 M /branches/prog/bwa/main.c | |
1519 | |
1520 * bwa-0.4.5-1 | |
1521 * make bwa work for SOLiD reads | |
1522 | |
1523 ------------------------------------------------------------------------ | |
1524 r828 | lh3 | 2009-02-18 17:36:41 -0500 (Wed, 18 Feb 2009) | 2 lines | |
1525 Changed paths: | |
1526 M /branches/prog/bwa/ChangeLog | |
1527 M /branches/prog/bwa/NEWS | |
1528 M /branches/prog/bwa/bwa.1 | |
1529 M /branches/prog/bwa/main.c | |
1530 | |
1531 Release bwa-0.4.5 | |
1532 | |
1533 ------------------------------------------------------------------------ | |
1534 r827 | lh3 | 2009-02-18 16:48:48 -0500 (Wed, 18 Feb 2009) | 3 lines | |
1535 Changed paths: | |
1536 M /branches/prog/bwa/main.c | |
1537 M /branches/prog/bwa/stdaln.c | |
1538 M /branches/prog/bwa/stdaln.h | |
1539 | |
1540 * bwa-0.4.4-6 | |
1541 * fixed a bug in SW alignment when no residue matches | |
1542 | |
1543 ------------------------------------------------------------------------ | |
1544 r824 | lh3 | 2009-02-17 05:33:07 -0500 (Tue, 17 Feb 2009) | 3 lines | |
1545 Changed paths: | |
1546 M /branches/prog/bwa/bwape.c | |
1547 M /branches/prog/bwa/main.c | |
1548 | |
1549 * bwa-0.4.4-5 | |
1550 * fixed that bounary bug | |
1551 | |
1552 ------------------------------------------------------------------------ | |
1553 r823 | lh3 | 2009-02-17 04:54:18 -0500 (Tue, 17 Feb 2009) | 2 lines | |
1554 Changed paths: | |
1555 M /branches/prog/bwa/ChangeLog | |
1556 M /branches/prog/bwa/bwape.c | |
1557 | |
1558 just change some logging information | |
1559 | |
1560 ------------------------------------------------------------------------ | |
1561 r822 | lh3 | 2009-02-17 04:20:39 -0500 (Tue, 17 Feb 2009) | 2 lines | |
1562 Changed paths: | |
1563 M /branches/prog/bwa/bwa.1 | |
1564 | |
1565 update manual | |
1566 | |
1567 ------------------------------------------------------------------------ | |
1568 r821 | lh3 | 2009-02-17 04:11:14 -0500 (Tue, 17 Feb 2009) | 3 lines | |
1569 Changed paths: | |
1570 M /branches/prog/bwa/bwape.c | |
1571 M /branches/prog/bwa/bwase.c | |
1572 M /branches/prog/bwa/main.c | |
1573 | |
1574 * bwa-0.4.4-4 | |
1575 * fixed a bug on boundary check in pair_sw | |
1576 | |
1577 ------------------------------------------------------------------------ | |
1578 r820 | lh3 | 2009-02-16 17:43:37 -0500 (Mon, 16 Feb 2009) | 3 lines | |
1579 Changed paths: | |
1580 M /branches/prog/bwa/bwtaln.c | |
1581 M /branches/prog/bwa/main.c | |
1582 | |
1583 * bwa-0.4.4-3 | |
1584 * allow to change mismatch penalty | |
1585 | |
1586 ------------------------------------------------------------------------ | |
1587 r819 | lh3 | 2009-02-16 17:40:28 -0500 (Mon, 16 Feb 2009) | 4 lines | |
1588 Changed paths: | |
1589 M /branches/prog/bwa/bwtaln.c | |
1590 M /branches/prog/bwa/main.c | |
1591 | |
1592 * bwa-0.4.4-2 | |
1593 * remove timer | |
1594 * allow to change default gapo and gape penalty at the command line | |
1595 | |
1596 ------------------------------------------------------------------------ | |
1597 r818 | lh3 | 2009-02-16 09:30:51 -0500 (Mon, 16 Feb 2009) | 2 lines | |
1598 Changed paths: | |
1599 M /branches/prog/bwa/bwa.1 | |
1600 | |
1601 update benchmark | |
1602 | |
1603 ------------------------------------------------------------------------ | |
1604 r817 | lh3 | 2009-02-16 08:44:40 -0500 (Mon, 16 Feb 2009) | 4 lines | |
1605 Changed paths: | |
1606 M /branches/prog/bwa/bwape.c | |
1607 M /branches/prog/bwa/bwtaln.c | |
1608 M /branches/prog/bwa/kvec.h | |
1609 M /branches/prog/bwa/main.c | |
1610 | |
1611 * bwa-0.4.4-1 | |
1612 * automatically detect insert size | |
1613 * use insert size in pairing. This may potentially improve accuracy (untested!) | |
1614 | |
1615 ------------------------------------------------------------------------ | |
1616 r814 | lh3 | 2009-02-15 11:10:23 -0500 (Sun, 15 Feb 2009) | 2 lines | |
1617 Changed paths: | |
1618 M /branches/prog/bwa/ChangeLog | |
1619 M /branches/prog/bwa/NEWS | |
1620 M /branches/prog/bwa/main.c | |
1621 | |
1622 Release bwa-0.4.4 | |
1623 | |
1624 ------------------------------------------------------------------------ | |
1625 r813 | lh3 | 2009-02-15 10:22:50 -0500 (Sun, 15 Feb 2009) | 3 lines | |
1626 Changed paths: | |
1627 M /branches/prog/bwa/bwa.1 | |
1628 M /branches/prog/bwa/bwase.c | |
1629 M /branches/prog/bwa/main.c | |
1630 | |
1631 * bwa-0.4.3-5 | |
1632 * impose boundary check in refine_gapped | |
1633 | |
1634 ------------------------------------------------------------------------ | |
1635 r811 | lh3 | 2009-02-14 09:46:13 -0500 (Sat, 14 Feb 2009) | 3 lines | |
1636 Changed paths: | |
1637 M /branches/prog/bwa/bwase.c | |
1638 M /branches/prog/bwa/main.c | |
1639 | |
1640 * bwa-0.4.3-4 | |
1641 * change MD tag to match the latest SAM specification | |
1642 | |
1643 ------------------------------------------------------------------------ | |
1644 r810 | lh3 | 2009-02-13 04:46:04 -0500 (Fri, 13 Feb 2009) | 2 lines | |
1645 Changed paths: | |
1646 M /branches/prog/bwa/ChangeLog | |
1647 | |
1648 update ChangeLog | |
1649 | |
1650 ------------------------------------------------------------------------ | |
1651 r799 | lh3 | 2009-02-05 12:01:17 -0500 (Thu, 05 Feb 2009) | 2 lines | |
1652 Changed paths: | |
1653 M /branches/prog/bwa/bwase.c | |
1654 M /branches/prog/bwa/main.c | |
1655 | |
1656 change MD tag to meet the latest SAM specification | |
1657 | |
1658 ------------------------------------------------------------------------ | |
1659 r796 | lh3 | 2009-02-05 08:35:13 -0500 (Thu, 05 Feb 2009) | 3 lines | |
1660 Changed paths: | |
1661 M /branches/prog/bwa/bntseq.c | |
1662 M /branches/prog/bwa/bwase.c | |
1663 M /branches/prog/bwa/main.c | |
1664 | |
1665 * bwa-0.4.3-2 | |
1666 * fixed a bug on counting 'N' | |
1667 | |
1668 ------------------------------------------------------------------------ | |
1669 r795 | lh3 | 2009-02-05 07:41:27 -0500 (Thu, 05 Feb 2009) | 4 lines | |
1670 Changed paths: | |
1671 M /branches/prog/bwa/bwa.1 | |
1672 M /branches/prog/bwa/bwape.c | |
1673 M /branches/prog/bwa/main.c | |
1674 | |
1675 * bwa-0.4.3-1 | |
1676 * fixed potential boundary problems | |
1677 * update benchmark result | |
1678 | |
1679 ------------------------------------------------------------------------ | |
1680 r791 | lh3 | 2009-01-25 05:20:47 -0500 (Sun, 25 Jan 2009) | 2 lines | |
1681 Changed paths: | |
1682 M /branches/prog/bwa/bwa.1 | |
1683 | |
1684 update some numbers | |
1685 | |
1686 ------------------------------------------------------------------------ | |
1687 r790 | lh3 | 2009-01-24 15:13:03 -0500 (Sat, 24 Jan 2009) | 2 lines | |
1688 Changed paths: | |
1689 M /branches/prog/bwa/bwa.1 | |
1690 | |
1691 update benchmark | |
1692 | |
1693 ------------------------------------------------------------------------ | |
1694 r789 | lh3 | 2009-01-22 10:18:44 -0500 (Thu, 22 Jan 2009) | 2 lines | |
1695 Changed paths: | |
1696 M /branches/prog/bwa/bwtindex.c | |
1697 | |
1698 a warning message for index | |
1699 | |
1700 ------------------------------------------------------------------------ | |
1701 r788 | lh3 | 2009-01-22 09:54:06 -0500 (Thu, 22 Jan 2009) | 2 lines | |
1702 Changed paths: | |
1703 M /branches/prog/bwa/main.c | |
1704 | |
1705 forget to change release number | |
1706 | |
1707 ------------------------------------------------------------------------ | |
1708 r786 | lh3 | 2009-01-22 06:27:39 -0500 (Thu, 22 Jan 2009) | 2 lines | |
1709 Changed paths: | |
1710 M /branches/prog/bwa/NEWS | |
1711 | |
1712 Release bwa-0.4.3 | |
1713 | |
1714 ------------------------------------------------------------------------ | |
1715 r785 | lh3 | 2009-01-22 06:27:16 -0500 (Thu, 22 Jan 2009) | 2 lines | |
1716 Changed paths: | |
1717 M /branches/prog/bwa/ChangeLog | |
1718 M /branches/prog/bwa/NEWS | |
1719 | |
1720 Release bwa-0.4.3 | |
1721 | |
1722 ------------------------------------------------------------------------ | |
1723 r784 | lh3 | 2009-01-22 06:19:59 -0500 (Thu, 22 Jan 2009) | 4 lines | |
1724 Changed paths: | |
1725 M /branches/prog/bwa/bwa.1 | |
1726 M /branches/prog/bwa/bwase.c | |
1727 M /branches/prog/bwa/main.c | |
1728 | |
1729 * bwa-0.4.2-10 | |
1730 * update documentation | |
1731 * fixed a bug on generating MD tags for SW alignment | |
1732 | |
1733 ------------------------------------------------------------------------ | |
1734 r782 | lh3 | 2009-01-19 12:08:38 -0500 (Mon, 19 Jan 2009) | 3 lines | |
1735 Changed paths: | |
1736 M /branches/prog/bwa/bwase.c | |
1737 M /branches/prog/bwa/main.c | |
1738 | |
1739 * bwa-0.4.2-9 | |
1740 * fixed a bug in samse -n... | |
1741 | |
1742 ------------------------------------------------------------------------ | |
1743 r781 | lh3 | 2009-01-19 11:26:37 -0500 (Mon, 19 Jan 2009) | 3 lines | |
1744 Changed paths: | |
1745 M /branches/prog/bwa/bwtaln.c | |
1746 M /branches/prog/bwa/main.c | |
1747 | |
1748 * bwa-0.4.2-8 | |
1749 * given -N, the previous version would stop if the top hit is a repeat. Now changed. | |
1750 | |
1751 ------------------------------------------------------------------------ | |
1752 r780 | lh3 | 2009-01-19 11:20:18 -0500 (Mon, 19 Jan 2009) | 4 lines | |
1753 Changed paths: | |
1754 M /branches/prog/bwa/bwape.c | |
1755 M /branches/prog/bwa/bwase.c | |
1756 M /branches/prog/bwa/bwtaln.c | |
1757 M /branches/prog/bwa/bwtaln.h | |
1758 M /branches/prog/bwa/bwtgap.c | |
1759 M /branches/prog/bwa/main.c | |
1760 | |
1761 * bwa-0.4.2-7 | |
1762 * use a bit-wise flag to replace some member variables in the option struct | |
1763 * allow to switch off the iterative strategy | |
1764 | |
1765 ------------------------------------------------------------------------ | |
1766 r779 | lh3 | 2009-01-19 10:45:57 -0500 (Mon, 19 Jan 2009) | 3 lines | |
1767 Changed paths: | |
1768 M /branches/prog/bwa/bwa.1 | |
1769 M /branches/prog/bwa/bwase.c | |
1770 M /branches/prog/bwa/main.c | |
1771 | |
1772 * bwa-0.4.2-6 | |
1773 * allow to dump multiple hits from samse, in another format, though | |
1774 | |
1775 ------------------------------------------------------------------------ | |
1776 r778 | lh3 | 2009-01-19 06:24:29 -0500 (Mon, 19 Jan 2009) | 5 lines | |
1777 Changed paths: | |
1778 M /branches/prog/bwa/Makefile | |
1779 M /branches/prog/bwa/bwape.c | |
1780 M /branches/prog/bwa/bwase.c | |
1781 M /branches/prog/bwa/bwaseqio.c | |
1782 M /branches/prog/bwa/bwtaln.h | |
1783 M /branches/prog/bwa/kseq.h | |
1784 A /branches/prog/bwa/kstring.c | |
1785 A /branches/prog/bwa/kstring.h | |
1786 M /branches/prog/bwa/main.c | |
1787 M /branches/prog/bwa/simple_dp.c | |
1788 | |
1789 * bwa-0.4.2-5 | |
1790 * update kseq.h to the latest version | |
1791 * generate MD tag | |
1792 * print mate coordinate if only one end is unmapped | |
1793 | |
1794 ------------------------------------------------------------------------ | |
1795 r775 | lh3 | 2009-01-18 05:40:35 -0500 (Sun, 18 Jan 2009) | 3 lines | |
1796 Changed paths: | |
1797 M /branches/prog/bwa/bwase.c | |
1798 M /branches/prog/bwa/main.c | |
1799 | |
1800 * bwa-0.4.2-4 | |
1801 * fixed a bug for SAM format | |
1802 | |
1803 ------------------------------------------------------------------------ | |
1804 r774 | lh3 | 2009-01-17 13:48:52 -0500 (Sat, 17 Jan 2009) | 4 lines | |
1805 Changed paths: | |
1806 M /branches/prog/bwa/bwtaln.c | |
1807 M /branches/prog/bwa/main.c | |
1808 | |
1809 * bwa-0.4.2-3 | |
1810 * change default fnr to 0.04 | |
1811 * print max_diff for valid fnr | |
1812 | |
1813 ------------------------------------------------------------------------ | |
1814 r773 | lh3 | 2009-01-17 05:54:37 -0500 (Sat, 17 Jan 2009) | 3 lines | |
1815 Changed paths: | |
1816 M /branches/prog/bwa/bwape.c | |
1817 M /branches/prog/bwa/bwase.c | |
1818 M /branches/prog/bwa/bwtaln.c | |
1819 M /branches/prog/bwa/bwtaln.h | |
1820 M /branches/prog/bwa/main.c | |
1821 | |
1822 * bwa-0.4.2-2 | |
1823 * automatically choose max_diff | |
1824 | |
1825 ------------------------------------------------------------------------ | |
1826 r772 | lh3 | 2009-01-16 18:16:14 -0500 (Fri, 16 Jan 2009) | 3 lines | |
1827 Changed paths: | |
1828 M /branches/prog/bwa/bwaseqio.c | |
1829 M /branches/prog/bwa/bwt.c | |
1830 M /branches/prog/bwa/bwtaln.c | |
1831 M /branches/prog/bwa/bwtaln.h | |
1832 M /branches/prog/bwa/bwtgap.c | |
1833 M /branches/prog/bwa/main.c | |
1834 | |
1835 * bwa-0.4.2-1 | |
1836 * take N as a mismatch | |
1837 | |
1838 ------------------------------------------------------------------------ | |
1839 r768 | lh3 | 2009-01-09 11:57:23 -0500 (Fri, 09 Jan 2009) | 2 lines | |
1840 Changed paths: | |
1841 M /branches/prog/bwa/ChangeLog | |
1842 M /branches/prog/bwa/NEWS | |
1843 M /branches/prog/bwa/bntseq.c | |
1844 M /branches/prog/bwa/main.c | |
1845 | |
1846 Release bwa-0.4.2 | |
1847 | |
1848 ------------------------------------------------------------------------ | |
1849 r759 | lh3 | 2009-01-07 09:55:43 -0500 (Wed, 07 Jan 2009) | 2 lines | |
1850 Changed paths: | |
1851 M /branches/prog/bwa/ChangeLog | |
1852 M /branches/prog/bwa/NEWS | |
1853 M /branches/prog/bwa/bwa.1 | |
1854 M /branches/prog/bwa/bwape.c | |
1855 M /branches/prog/bwa/bwtaln.h | |
1856 M /branches/prog/bwa/main.c | |
1857 | |
1858 Release bwa-0.4.1 | |
1859 | |
1860 ------------------------------------------------------------------------ | |
1861 r758 | lh3 | 2009-01-07 05:36:06 -0500 (Wed, 07 Jan 2009) | 3 lines | |
1862 Changed paths: | |
1863 M /branches/prog/bwa/bwape.c | |
1864 M /branches/prog/bwa/bwase.c | |
1865 M /branches/prog/bwa/bwtaln.h | |
1866 M /branches/prog/bwa/main.c | |
1867 | |
1868 * bwa-0.4.0-2 | |
1869 * make mate_sw fully working | |
1870 | |
1871 ------------------------------------------------------------------------ | |
1872 r757 | lh3 | 2009-01-06 18:04:29 -0500 (Tue, 06 Jan 2009) | 5 lines | |
1873 Changed paths: | |
1874 M /branches/prog/bwa/bwape.c | |
1875 M /branches/prog/bwa/bwase.c | |
1876 M /branches/prog/bwa/bwaseqio.c | |
1877 M /branches/prog/bwa/bwtaln.h | |
1878 M /branches/prog/bwa/main.c | |
1879 | |
1880 * bwa-0.4.0-1 | |
1881 * do SW alignment for unmapped mate. It is working. | |
1882 * I still need to do some extra work for SW alignment, but it is too late | |
1883 and I am getting tired... I will do tomorrow. | |
1884 | |
1885 ------------------------------------------------------------------------ | |
1886 r755 | lh3 | 2009-01-06 10:23:29 -0500 (Tue, 06 Jan 2009) | 2 lines | |
1887 Changed paths: | |
1888 M /branches/prog/bwa/ChangeLog | |
1889 M /branches/prog/bwa/NEWS | |
1890 M /branches/prog/bwa/bwa.1 | |
1891 M /branches/prog/bwa/main.c | |
1892 | |
1893 Release bwa-0.4.0 | |
1894 | |
1895 ------------------------------------------------------------------------ | |
1896 r754 | lh3 | 2009-01-06 07:45:02 -0500 (Tue, 06 Jan 2009) | 3 lines | |
1897 Changed paths: | |
1898 M /branches/prog/bwa/bwtaln.c | |
1899 M /branches/prog/bwa/bwtgap.c | |
1900 M /branches/prog/bwa/bwtgap.h | |
1901 M /branches/prog/bwa/main.c | |
1902 | |
1903 * bwa-0.3.0-12 | |
1904 * better lock | |
1905 | |
1906 ------------------------------------------------------------------------ | |
1907 r753 | lh3 | 2009-01-06 06:17:21 -0500 (Tue, 06 Jan 2009) | 5 lines | |
1908 Changed paths: | |
1909 M /branches/prog/bwa/Makefile | |
1910 M /branches/prog/bwa/bwaseqio.c | |
1911 M /branches/prog/bwa/bwtaln.c | |
1912 M /branches/prog/bwa/bwtaln.h | |
1913 M /branches/prog/bwa/bwtgap.c | |
1914 M /branches/prog/bwa/main.c | |
1915 | |
1916 * bwa-0.3.0-11 | |
1917 * fixed a small memory leak in bwa_seq_close() | |
1918 * fixed "uninitialized memory" from bwt_aln1_t | |
1919 * multithreading for "aln" command | |
1920 | |
1921 ------------------------------------------------------------------------ | |
1922 r752 | lh3 | 2009-01-05 17:34:13 -0500 (Mon, 05 Jan 2009) | 3 lines | |
1923 Changed paths: | |
1924 M /branches/prog/bwa/Makefile | |
1925 D /branches/prog/bwa/bwt2fmv.c | |
1926 M /branches/prog/bwa/bwt_gen/bwt_gen.c | |
1927 A /branches/prog/bwa/bwtmisc.c (from /branches/prog/bwa/pac2bwt.c:748) | |
1928 M /branches/prog/bwa/main.c | |
1929 M /branches/prog/bwa/main.h | |
1930 D /branches/prog/bwa/pac2bwt.c | |
1931 | |
1932 * bwa-0.3.0-10 | |
1933 * a little bit code clean up | |
1934 | |
1935 ------------------------------------------------------------------------ | |
1936 r751 | lh3 | 2009-01-05 17:19:04 -0500 (Mon, 05 Jan 2009) | 3 lines | |
1937 Changed paths: | |
1938 M /branches/prog/bwa/bwt.c | |
1939 M /branches/prog/bwa/main.c | |
1940 | |
1941 * bwa-0.3.0-9 | |
1942 * use 64-bit integer to speed up Occ calculate, although just a little bit | |
1943 | |
1944 ------------------------------------------------------------------------ | |
1945 r750 | lh3 | 2009-01-05 16:44:26 -0500 (Mon, 05 Jan 2009) | 3 lines | |
1946 Changed paths: | |
1947 M /branches/prog/bwa/bwt.c | |
1948 M /branches/prog/bwa/main.c | |
1949 | |
1950 * bwa-0.3.0-8 | |
1951 * a little bit code cleanup | |
1952 | |
1953 ------------------------------------------------------------------------ | |
1954 r749 | lh3 | 2009-01-05 16:37:28 -0500 (Mon, 05 Jan 2009) | 3 lines | |
1955 Changed paths: | |
1956 M /branches/prog/bwa/bwt.c | |
1957 M /branches/prog/bwa/main.c | |
1958 | |
1959 * bwa-0.1.0-7 | |
1960 * accelerate Occ calculation | |
1961 | |
1962 ------------------------------------------------------------------------ | |
1963 r748 | lh3 | 2009-01-05 16:12:28 -0500 (Mon, 05 Jan 2009) | 4 lines | |
1964 Changed paths: | |
1965 M /branches/prog/bwa/bwape.c | |
1966 M /branches/prog/bwa/bwase.c | |
1967 M /branches/prog/bwa/bwt.c | |
1968 M /branches/prog/bwa/bwt.h | |
1969 M /branches/prog/bwa/bwt2fmv.c | |
1970 M /branches/prog/bwa/bwtaln.c | |
1971 M /branches/prog/bwa/bwtindex.c | |
1972 M /branches/prog/bwa/bwtio.c | |
1973 M /branches/prog/bwa/main.c | |
1974 M /branches/prog/bwa/main.h | |
1975 M /branches/prog/bwa/pac2bwt.c | |
1976 | |
1977 * bwa-0.3.0-6 | |
1978 * put occ table along with bwt to save another cache miss | |
1979 * this version is already faster than the previous and I can still improve it... | |
1980 | |
1981 ------------------------------------------------------------------------ | |
1982 r747 | lh3 | 2009-01-05 10:16:18 -0500 (Mon, 05 Jan 2009) | 5 lines | |
1983 Changed paths: | |
1984 M /branches/prog/bwa/bwt.c | |
1985 M /branches/prog/bwa/bwt.h | |
1986 M /branches/prog/bwa/bwtio.c | |
1987 M /branches/prog/bwa/main.c | |
1988 | |
1989 * bwa-0.3.0-5 | |
1990 * remove occ_major to save a cache miss; however, OCC_INTERVAL has to be | |
1991 increased to keep the same memory. As a result, the speed is a little | |
1992 slower in fact. | |
1993 | |
1994 ------------------------------------------------------------------------ | |
1995 r746 | lh3 | 2009-01-05 09:50:53 -0500 (Mon, 05 Jan 2009) | 3 lines | |
1996 Changed paths: | |
1997 M /branches/prog/bwa/bwt.c | |
1998 M /branches/prog/bwa/main.c | |
1999 | |
2000 * bwa-0.3.0-4 | |
2001 * added back optimization codes (it is a pain...) | |
2002 | |
2003 ------------------------------------------------------------------------ | |
2004 r745 | lh3 | 2009-01-05 08:23:00 -0500 (Mon, 05 Jan 2009) | 3 lines | |
2005 Changed paths: | |
2006 M /branches/prog/bwa/bwt.c | |
2007 M /branches/prog/bwa/bwtaln.c | |
2008 M /branches/prog/bwa/main.c | |
2009 | |
2010 * bwa-0.3.0-3 | |
2011 * faster bit operations | |
2012 | |
2013 ------------------------------------------------------------------------ | |
2014 r744 | lh3 | 2009-01-05 05:58:46 -0500 (Mon, 05 Jan 2009) | 4 lines | |
2015 Changed paths: | |
2016 M /branches/prog/bwa/bwt.c | |
2017 M /branches/prog/bwa/main.c | |
2018 | |
2019 * bwa-0.3.0-2 | |
2020 * removed optimization codes again... | |
2021 * use a new method to count the bits | |
2022 | |
2023 ------------------------------------------------------------------------ | |
2024 r743 | lh3 | 2009-01-04 17:18:38 -0500 (Sun, 04 Jan 2009) | 5 lines | |
2025 Changed paths: | |
2026 M /branches/prog/bwa/bwa.1 | |
2027 M /branches/prog/bwa/bwt.c | |
2028 M /branches/prog/bwa/bwtaln.c | |
2029 M /branches/prog/bwa/bwtaln.h | |
2030 M /branches/prog/bwa/bwtgap.c | |
2031 M /branches/prog/bwa/main.c | |
2032 | |
2033 * bwa-0.3.0-1 | |
2034 * added back the optimization codes | |
2035 * added a new option to aln: max_entries, although this is disabled by default | |
2036 * updated benchmark | |
2037 | |
2038 ------------------------------------------------------------------------ | |
2039 r742 | lh3 | 2009-01-04 07:56:12 -0500 (Sun, 04 Jan 2009) | 2 lines | |
2040 Changed paths: | |
2041 M /branches/prog/bwa/bwa.1 | |
2042 | |
2043 add URL | |
2044 | |
2045 ------------------------------------------------------------------------ | |
2046 r740 | lh3 | 2009-01-04 07:39:43 -0500 (Sun, 04 Jan 2009) | 2 lines | |
2047 Changed paths: | |
2048 M /branches/prog/bwa/ChangeLog | |
2049 M /branches/prog/bwa/NEWS | |
2050 M /branches/prog/bwa/bwa.1 | |
2051 M /branches/prog/bwa/main.c | |
2052 | |
2053 Release bwa-0.3.0 | |
2054 | |
2055 ------------------------------------------------------------------------ | |
2056 r739 | lh3 | 2009-01-04 06:55:06 -0500 (Sun, 04 Jan 2009) | 2 lines | |
2057 Changed paths: | |
2058 A /branches/prog/bwa/COPYING | |
2059 M /branches/prog/bwa/ChangeLog | |
2060 M /branches/prog/bwa/bntseq.c | |
2061 M /branches/prog/bwa/bntseq.h | |
2062 M /branches/prog/bwa/bwa.1 | |
2063 M /branches/prog/bwa/bwt.c | |
2064 M /branches/prog/bwa/bwt.h | |
2065 M /branches/prog/bwa/bwtindex.c | |
2066 M /branches/prog/bwa/utils.c | |
2067 M /branches/prog/bwa/utils.h | |
2068 | |
2069 added licensing information | |
2070 | |
2071 ------------------------------------------------------------------------ | |
2072 r738 | lh3 | 2009-01-04 06:18:25 -0500 (Sun, 04 Jan 2009) | 4 lines | |
2073 Changed paths: | |
2074 M /branches/prog/bwa/bwa.1 | |
2075 M /branches/prog/bwa/bwape.c | |
2076 M /branches/prog/bwa/main.c | |
2077 | |
2078 * bwa-0.2.0-31 | |
2079 * better mapping quality | |
2080 * update benchmark | |
2081 | |
2082 ------------------------------------------------------------------------ | |
2083 r737 | lh3 | 2009-01-03 16:00:58 -0500 (Sat, 03 Jan 2009) | 2 lines | |
2084 Changed paths: | |
2085 M /branches/prog/bwa/ChangeLog | |
2086 M /branches/prog/bwa/bwa.1 | |
2087 | |
2088 update documentation | |
2089 | |
2090 ------------------------------------------------------------------------ | |
2091 r736 | lh3 | 2009-01-02 10:26:38 -0500 (Fri, 02 Jan 2009) | 2 lines | |
2092 Changed paths: | |
2093 M /branches/prog/bwa/bwa.1 | |
2094 | |
2095 update documentation | |
2096 | |
2097 ------------------------------------------------------------------------ | |
2098 r735 | lh3 | 2009-01-02 07:10:20 -0500 (Fri, 02 Jan 2009) | 4 lines | |
2099 Changed paths: | |
2100 M /branches/prog/bwa/bwa.1 | |
2101 M /branches/prog/bwa/bwape.c | |
2102 M /branches/prog/bwa/bwtaln.c | |
2103 M /branches/prog/bwa/main.c | |
2104 | |
2105 * bwa-0.2.0-30 | |
2106 * reduce memory a little bit | |
2107 * update documentation | |
2108 | |
2109 ------------------------------------------------------------------------ | |
2110 r734 | lh3 | 2009-01-01 13:45:45 -0500 (Thu, 01 Jan 2009) | 8 lines | |
2111 Changed paths: | |
2112 M /branches/prog/bwa/bwa.1 | |
2113 M /branches/prog/bwa/bwape.c | |
2114 M /branches/prog/bwa/bwase.c | |
2115 M /branches/prog/bwa/bwtaln.c | |
2116 M /branches/prog/bwa/bwtaln.h | |
2117 M /branches/prog/bwa/bwtgap.c | |
2118 M /branches/prog/bwa/main.c | |
2119 | |
2120 * bwa-0.2.0-29 | |
2121 * sampe: removed -O option; changed default -o to 100000 | |
2122 * sampe: fixed a bug in calculating paired mapping quality | |
2123 * aln: added an option to search for suboptimal hits even if the best is a repeat. | |
2124 This option will make sampe MUCH SLOWER. | |
2125 * sampe: set isize as zero if mapped to two different chr | |
2126 * update manual (unfinished) | |
2127 | |
2128 ------------------------------------------------------------------------ | |
2129 r733 | lh3 | 2009-01-01 11:01:20 -0500 (Thu, 01 Jan 2009) | 3 lines | |
2130 Changed paths: | |
2131 M /branches/prog/bwa/bwape.c | |
2132 M /branches/prog/bwa/main.c | |
2133 | |
2134 * bwa-0.2.0-28 | |
2135 * fixed a bug in calculating paired mapping quality | |
2136 | |
2137 ------------------------------------------------------------------------ | |
2138 r732 | lh3 | 2009-01-01 09:27:46 -0500 (Thu, 01 Jan 2009) | 3 lines | |
2139 Changed paths: | |
2140 M /branches/prog/bwa/bwape.c | |
2141 A /branches/prog/bwa/khash.h (from /branches/prog/sclib/khash/khash.h:675) | |
2142 M /branches/prog/bwa/main.c | |
2143 | |
2144 * bwa-0.2.0-27 | |
2145 * accelerate sampe by storing visited large intervals | |
2146 | |
2147 ------------------------------------------------------------------------ | |
2148 r731 | lh3 | 2009-01-01 06:51:21 -0500 (Thu, 01 Jan 2009) | 3 lines | |
2149 Changed paths: | |
2150 M /branches/prog/bwa/bwt.c | |
2151 M /branches/prog/bwa/main.c | |
2152 | |
2153 * bwa-0.2.0-26 | |
2154 * remove the optimation codes | |
2155 | |
2156 ------------------------------------------------------------------------ | |
2157 r730 | lh3 | 2009-01-01 06:48:59 -0500 (Thu, 01 Jan 2009) | 4 lines | |
2158 Changed paths: | |
2159 M /branches/prog/bwa/bwt.c | |
2160 M /branches/prog/bwa/main.c | |
2161 | |
2162 * bwa-0.2.0-25 | |
2163 * accelerate OCC calculation by ~7%. However, it seems not worth doing | |
2164 this by complicate the codes. I will change back later. | |
2165 | |
2166 ------------------------------------------------------------------------ | |
2167 r729 | lh3 | 2008-12-31 16:43:56 -0500 (Wed, 31 Dec 2008) | 6 lines | |
2168 Changed paths: | |
2169 M /branches/prog/bwa/bntseq.c | |
2170 M /branches/prog/bwa/bwape.c | |
2171 M /branches/prog/bwa/bwase.c | |
2172 M /branches/prog/bwa/main.c | |
2173 | |
2174 * bwa-0.2.0-24 | |
2175 * change command "sai2sam_pe" to "sampe" | |
2176 * print usage for sampe command | |
2177 * in sampe: change default max_occ to 1000 | |
2178 * fixed a few compiling warnings in bntseq.c | |
2179 | |
2180 ------------------------------------------------------------------------ | |
2181 r728 | lh3 | 2008-12-27 07:14:59 -0500 (Sat, 27 Dec 2008) | 3 lines | |
2182 Changed paths: | |
2183 M /branches/prog/bwa/bwape.c | |
2184 M /branches/prog/bwa/bwase.c | |
2185 M /branches/prog/bwa/main.c | |
2186 | |
2187 * bwa-0.2.0-22 | |
2188 * mating information can be printed to SAM | |
2189 | |
2190 ------------------------------------------------------------------------ | |
2191 r727 | lh3 | 2008-12-26 18:10:59 -0500 (Fri, 26 Dec 2008) | 4 lines | |
2192 Changed paths: | |
2193 M /branches/prog/bwa/bwape.c | |
2194 M /branches/prog/bwa/bwase.c | |
2195 M /branches/prog/bwa/bwaseqio.c | |
2196 M /branches/prog/bwa/bwtaln.c | |
2197 M /branches/prog/bwa/bwtaln.h | |
2198 M /branches/prog/bwa/main.c | |
2199 | |
2200 * bwa-0.2.0-21 | |
2201 * implement pairing (still UNFINISHED) | |
2202 * output all reads even if full of N | |
2203 | |
2204 ------------------------------------------------------------------------ | |
2205 r726 | lh3 | 2008-12-26 13:31:27 -0500 (Fri, 26 Dec 2008) | 5 lines | |
2206 Changed paths: | |
2207 M /branches/prog/bwa/Makefile | |
2208 A /branches/prog/bwa/bwape.c | |
2209 M /branches/prog/bwa/bwase.c | |
2210 M /branches/prog/bwa/bwt2fmv.c | |
2211 M /branches/prog/bwa/bwtaln.c | |
2212 M /branches/prog/bwa/bwtaln.h | |
2213 M /branches/prog/bwa/bwtgap.c | |
2214 M /branches/prog/bwa/main.c | |
2215 M /branches/prog/bwa/main.h | |
2216 | |
2217 * bwa-0.2.0-20 | |
2218 * remove "-t" from aln cmd | |
2219 * code clean up: move some functions in bwt2fmv.c to other source files | |
2220 * added sai2sam_pe cmd: *UNFINISHED* | |
2221 | |
2222 ------------------------------------------------------------------------ | |
2223 r725 | lh3 | 2008-12-26 07:04:11 -0500 (Fri, 26 Dec 2008) | 3 lines | |
2224 Changed paths: | |
2225 M /branches/prog/bwa/Makefile | |
2226 A /branches/prog/bwa/bwase.c | |
2227 A /branches/prog/bwa/bwaseqio.c | |
2228 M /branches/prog/bwa/bwt2fmv.c | |
2229 M /branches/prog/bwa/bwtaln.c | |
2230 M /branches/prog/bwa/bwtaln.h | |
2231 M /branches/prog/bwa/bwtgap.c | |
2232 M /branches/prog/bwa/kseq.h | |
2233 A /branches/prog/bwa/ksort.h (from /branches/prog/sclib/ksort/ksort.h:712) | |
2234 A /branches/prog/bwa/kvec.h (from /branches/prog/sclib/kvec/kvec.h:537) | |
2235 M /branches/prog/bwa/main.c | |
2236 | |
2237 * bwa-0.2.0-19 | |
2238 * considerable code cleanup; no actual changes | |
2239 | |
2240 ------------------------------------------------------------------------ | |
2241 r724 | lh3 | 2008-12-25 11:32:11 -0500 (Thu, 25 Dec 2008) | 3 lines | |
2242 Changed paths: | |
2243 M /branches/prog/bwa/bwtaln.c | |
2244 M /branches/prog/bwa/bwtaln.h | |
2245 M /branches/prog/bwa/main.c | |
2246 | |
2247 * bwa-0.2.0-18 | |
2248 * generate SAM output | |
2249 | |
2250 ------------------------------------------------------------------------ | |
2251 r723 | lh3 | 2008-12-25 10:48:31 -0500 (Thu, 25 Dec 2008) | 4 lines | |
2252 Changed paths: | |
2253 M /branches/prog/bwa/bwt2fmv.c | |
2254 M /branches/prog/bwa/bwtaln.c | |
2255 M /branches/prog/bwa/main.c | |
2256 M /branches/prog/bwa/main.h | |
2257 | |
2258 * bwa-0.2.0-17 | |
2259 * remove bwtsw2 related codes | |
2260 * separate searching for SA interval from generating alignments | |
2261 | |
2262 ------------------------------------------------------------------------ | |
2263 r722 | lh3 | 2008-12-25 08:57:13 -0500 (Thu, 25 Dec 2008) | 3 lines | |
2264 Changed paths: | |
2265 M /branches/prog/bwa/Makefile | |
2266 M /branches/prog/bwa/bwt2fmv.c | |
2267 D /branches/prog/bwa/bwt_lite.c | |
2268 D /branches/prog/bwa/bwt_lite.h | |
2269 M /branches/prog/bwa/bwtgap.c | |
2270 D /branches/prog/bwa/bwtsw2.h | |
2271 D /branches/prog/bwa/bwtsw2_aux.c | |
2272 D /branches/prog/bwa/bwtsw2_core.c | |
2273 D /branches/prog/bwa/bwtsw2_main.c | |
2274 D /branches/prog/bwa/khash.h | |
2275 D /branches/prog/bwa/ksort.h | |
2276 D /branches/prog/bwa/kvec.h | |
2277 M /branches/prog/bwa/main.c | |
2278 | |
2279 * added interface to "aln -t" | |
2280 * remove bwtsw2 related codes | |
2281 | |
2282 ------------------------------------------------------------------------ | |
2283 r666 | lh3 | 2008-11-18 18:34:29 -0500 (Tue, 18 Nov 2008) | 4 lines | |
2284 Changed paths: | |
2285 M /branches/prog/bwa/bwt2fmv.c | |
2286 M /branches/prog/bwa/bwtaln.c | |
2287 M /branches/prog/bwa/bwtaln.h | |
2288 M /branches/prog/bwa/main.c | |
2289 | |
2290 * bwa-0.2.0-16 | |
2291 * allow to set max mismatches based on read length, but I do not know | |
2292 whether this really works | |
2293 | |
2294 ------------------------------------------------------------------------ | |
2295 r665 | lh3 | 2008-11-18 08:34:03 -0500 (Tue, 18 Nov 2008) | 3 lines | |
2296 Changed paths: | |
2297 M /branches/prog/bwa/bwtaln.c | |
2298 M /branches/prog/bwa/main.c | |
2299 | |
2300 * bwa-0.2.0-15 | |
2301 * fixed a bug in sequence parser. | |
2302 | |
2303 ------------------------------------------------------------------------ | |
2304 r612 | lh3 | 2008-10-28 06:50:53 -0400 (Tue, 28 Oct 2008) | 3 lines | |
2305 Changed paths: | |
2306 M /branches/prog/bwa/bntseq.c | |
2307 M /branches/prog/bwa/bwtindex.c | |
2308 M /branches/prog/bwa/main.c | |
2309 M /branches/prog/bwa/utils.c | |
2310 | |
2311 * bwa-0.2.0-14 | |
2312 * fixed a bug caused by the change of the FASTA/Q parser | |
2313 | |
2314 ------------------------------------------------------------------------ | |
2315 r611 | lh3 | 2008-10-28 06:24:56 -0400 (Tue, 28 Oct 2008) | 2 lines | |
2316 Changed paths: | |
2317 M /branches/prog/bwa/Makefile | |
2318 M /branches/prog/bwa/bntseq.c | |
2319 M /branches/prog/bwa/bntseq.h | |
2320 M /branches/prog/bwa/bwtaln.c | |
2321 M /branches/prog/bwa/bwtsw2_core.c | |
2322 A /branches/prog/bwa/kseq.h | |
2323 D /branches/prog/bwa/seq.c | |
2324 D /branches/prog/bwa/seq.h | |
2325 M /branches/prog/bwa/simple_dp.c | |
2326 M /branches/prog/bwa/utils.c | |
2327 M /branches/prog/bwa/utils.h | |
2328 | |
2329 replace seq.* with kseq.h | |
2330 | |
2331 ------------------------------------------------------------------------ | |
2332 r610 | lh3 | 2008-10-27 13:00:04 -0400 (Mon, 27 Oct 2008) | 3 lines | |
2333 Changed paths: | |
2334 M /branches/prog/bwa/bwtsw2.h | |
2335 M /branches/prog/bwa/bwtsw2_aux.c | |
2336 M /branches/prog/bwa/bwtsw2_core.c | |
2337 M /branches/prog/bwa/main.c | |
2338 | |
2339 * bwa-0.2.0-13 | |
2340 * make bwtsw2 output sub-optimal hits. not completed | |
2341 | |
2342 ------------------------------------------------------------------------ | |
2343 r609 | lh3 | 2008-10-24 16:52:00 -0400 (Fri, 24 Oct 2008) | 2 lines | |
2344 Changed paths: | |
2345 M /branches/prog/bwa/kvec.h | |
2346 | |
2347 little... | |
2348 | |
2349 ------------------------------------------------------------------------ | |
2350 r532 | lh3 | 2008-09-19 05:28:45 -0400 (Fri, 19 Sep 2008) | 2 lines | |
2351 Changed paths: | |
2352 M /branches/prog/bwa/bwtsw2_core.c | |
2353 M /branches/prog/bwa/khash.h | |
2354 | |
2355 improve interface of khash | |
2356 | |
2357 ------------------------------------------------------------------------ | |
2358 r531 | lh3 | 2008-09-18 06:52:59 -0400 (Thu, 18 Sep 2008) | 2 lines | |
2359 Changed paths: | |
2360 M /branches/prog/bwa/bwtsw2_core.c | |
2361 | |
2362 improve minor things, which make bwtsw2 slower, but should miss less true hits | |
2363 | |
2364 ------------------------------------------------------------------------ | |
2365 r530 | lh3 | 2008-09-17 18:19:26 -0400 (Wed, 17 Sep 2008) | 3 lines | |
2366 Changed paths: | |
2367 M /branches/prog/bwa/bwtsw2_core.c | |
2368 | |
2369 * fixed a bug in calculating ->D | |
2370 * enforce band-width checking | |
2371 | |
2372 ------------------------------------------------------------------------ | |
2373 r529 | lh3 | 2008-09-17 18:06:49 -0400 (Wed, 17 Sep 2008) | 2 lines | |
2374 Changed paths: | |
2375 M /branches/prog/bwa/bwtsw2_core.c | |
2376 | |
2377 delete a line of code that is never visited | |
2378 | |
2379 ------------------------------------------------------------------------ | |
2380 r528 | lh3 | 2008-09-17 17:58:51 -0400 (Wed, 17 Sep 2008) | 2 lines | |
2381 Changed paths: | |
2382 M /branches/prog/bwa/bwtsw2_core.c | |
2383 | |
2384 a bit code clean up | |
2385 | |
2386 ------------------------------------------------------------------------ | |
2387 r527 | lh3 | 2008-09-17 10:55:45 -0400 (Wed, 17 Sep 2008) | 3 lines | |
2388 Changed paths: | |
2389 M /branches/prog/bwa/bwtsw2_core.c | |
2390 M /branches/prog/bwa/bwtsw2_main.c | |
2391 M /branches/prog/bwa/main.c | |
2392 | |
2393 * bwa-0.2.0-12 | |
2394 * max-depth can be set, although it does not help the speed at all | |
2395 | |
2396 ------------------------------------------------------------------------ | |
2397 r526 | lh3 | 2008-09-16 17:59:36 -0400 (Tue, 16 Sep 2008) | 2 lines | |
2398 Changed paths: | |
2399 M /branches/prog/bwa/bwtsw2_core.c | |
2400 | |
2401 cut_tail after remove duplicate | |
2402 | |
2403 ------------------------------------------------------------------------ | |
2404 r525 | lh3 | 2008-09-16 17:56:11 -0400 (Tue, 16 Sep 2008) | 3 lines | |
2405 Changed paths: | |
2406 M /branches/prog/bwa/bwtsw2.h | |
2407 M /branches/prog/bwa/bwtsw2_aux.c | |
2408 M /branches/prog/bwa/bwtsw2_core.c | |
2409 M /branches/prog/bwa/bwtsw2_main.c | |
2410 M /branches/prog/bwa/khash.h | |
2411 M /branches/prog/bwa/main.c | |
2412 | |
2413 * bwa-0.2.0-11 | |
2414 * improved cut_tail() | |
2415 | |
2416 ------------------------------------------------------------------------ | |
2417 r524 | lh3 | 2008-09-15 16:53:22 -0400 (Mon, 15 Sep 2008) | 3 lines | |
2418 Changed paths: | |
2419 M /branches/prog/bwa/bwtsw2_aux.c | |
2420 M /branches/prog/bwa/bwtsw2_core.c | |
2421 M /branches/prog/bwa/bwtsw2_main.c | |
2422 M /branches/prog/bwa/main.c | |
2423 | |
2424 * bwa-0.2.0-10 | |
2425 * fixed a bug in cut_tail() | |
2426 | |
2427 ------------------------------------------------------------------------ | |
2428 r518 | lh3 | 2008-09-15 04:35:59 -0400 (Mon, 15 Sep 2008) | 2 lines | |
2429 Changed paths: | |
2430 M /branches/prog/bwa/bwtsw2_core.c | |
2431 | |
2432 a bit code clean up | |
2433 | |
2434 ------------------------------------------------------------------------ | |
2435 r517 | lh3 | 2008-09-14 18:18:11 -0400 (Sun, 14 Sep 2008) | 2 lines | |
2436 Changed paths: | |
2437 M /branches/prog/bwa/bwtsw2_core.c | |
2438 | |
2439 improve speed (<1%) | |
2440 | |
2441 ------------------------------------------------------------------------ | |
2442 r516 | lh3 | 2008-09-14 18:08:55 -0400 (Sun, 14 Sep 2008) | 3 lines | |
2443 Changed paths: | |
2444 M /branches/prog/bwa/bwtsw2_core.c | |
2445 | |
2446 * fixed two potential bugs, although I have not seen their effects | |
2447 * improve speed a bit (<2%) | |
2448 | |
2449 ------------------------------------------------------------------------ | |
2450 r515 | lh3 | 2008-09-14 17:26:49 -0400 (Sun, 14 Sep 2008) | 2 lines | |
2451 Changed paths: | |
2452 M /branches/prog/bwa/bwtsw2_core.c | |
2453 M /branches/prog/bwa/bwtsw2_main.c | |
2454 | |
2455 nothing, really | |
2456 | |
2457 ------------------------------------------------------------------------ | |
2458 r514 | lh3 | 2008-09-14 17:10:13 -0400 (Sun, 14 Sep 2008) | 2 lines | |
2459 Changed paths: | |
2460 M /branches/prog/bwa/bwtsw2_core.c | |
2461 | |
2462 disable X-drop, which has to be reimplemented in the current algorithm | |
2463 | |
2464 ------------------------------------------------------------------------ | |
2465 r513 | lh3 | 2008-09-14 16:49:42 -0400 (Sun, 14 Sep 2008) | 4 lines | |
2466 Changed paths: | |
2467 M /branches/prog/bwa/bwt_lite.c | |
2468 M /branches/prog/bwa/bwt_lite.h | |
2469 M /branches/prog/bwa/bwtsw2_core.c | |
2470 M /branches/prog/bwa/bwtsw2_main.c | |
2471 | |
2472 * temporarily disable cut_tail() | |
2473 * calculate SA in bwt_lite.c | |
2474 * fixed a bug in reversing the sequence | |
2475 | |
2476 ------------------------------------------------------------------------ | |
2477 r512 | lh3 | 2008-09-13 17:35:40 -0400 (Sat, 13 Sep 2008) | 2 lines | |
2478 Changed paths: | |
2479 M /branches/prog/bwa/bwtsw2.h | |
2480 M /branches/prog/bwa/bwtsw2_aux.c | |
2481 M /branches/prog/bwa/bwtsw2_core.c | |
2482 M /branches/prog/bwa/bwtsw2_main.c | |
2483 A /branches/prog/bwa/ksort.h | |
2484 | |
2485 n-best method | |
2486 | |
2487 ------------------------------------------------------------------------ | |
2488 r507 | lh3 | 2008-09-13 09:06:54 -0400 (Sat, 13 Sep 2008) | 2 lines | |
2489 Changed paths: | |
2490 M /branches/prog/bwa/Makefile | |
2491 M /branches/prog/bwa/bwtsw2_core.c | |
2492 | |
2493 give correct result again | |
2494 | |
2495 ------------------------------------------------------------------------ | |
2496 r506 | lh3 | 2008-09-13 08:12:07 -0400 (Sat, 13 Sep 2008) | 2 lines | |
2497 Changed paths: | |
2498 M /branches/prog/bwa/bwtsw2_core.c | |
2499 | |
2500 I think I know the reason. It needs more work... | |
2501 | |
2502 ------------------------------------------------------------------------ | |
2503 r505 | lh3 | 2008-09-13 06:20:43 -0400 (Sat, 13 Sep 2008) | 2 lines | |
2504 Changed paths: | |
2505 M /branches/prog/bwa/Makefile | |
2506 M /branches/prog/bwa/bwtsw2_core.c | |
2507 | |
2508 fixed another bug, but still have | |
2509 | |
2510 ------------------------------------------------------------------------ | |
2511 r504 | lh3 | 2008-09-12 18:13:37 -0400 (Fri, 12 Sep 2008) | 2 lines | |
2512 Changed paths: | |
2513 M /branches/prog/bwa/bwtsw2_core.c | |
2514 | |
2515 fixed another bug | |
2516 | |
2517 ------------------------------------------------------------------------ | |
2518 r503 | lh3 | 2008-09-12 17:15:56 -0400 (Fri, 12 Sep 2008) | 3 lines | |
2519 Changed paths: | |
2520 M /branches/prog/bwa/bwtsw2_core.c | |
2521 M /branches/prog/bwa/khash.h | |
2522 | |
2523 * do not segfault, but the result is WRONG! | |
2524 * prepare to remove bsw2_connectivity_check() | |
2525 | |
2526 ------------------------------------------------------------------------ | |
2527 r502 | lh3 | 2008-09-12 15:52:41 -0400 (Fri, 12 Sep 2008) | 2 lines | |
2528 Changed paths: | |
2529 M /branches/prog/bwa/bwtsw2_core.c | |
2530 M /branches/prog/bwa/kvec.h | |
2531 | |
2532 more revisions | |
2533 | |
2534 ------------------------------------------------------------------------ | |
2535 r501 | lh3 | 2008-09-11 18:06:15 -0400 (Thu, 11 Sep 2008) | 2 lines | |
2536 Changed paths: | |
2537 M /branches/prog/bwa/bwtsw2_core.c | |
2538 | |
2539 further simply codes with kvec.h | |
2540 | |
2541 ------------------------------------------------------------------------ | |
2542 r500 | lh3 | 2008-09-11 17:42:15 -0400 (Thu, 11 Sep 2008) | 2 lines | |
2543 Changed paths: | |
2544 M /branches/prog/bwa/bwtsw2_core.c | |
2545 | |
2546 part of revisions... have not finished | |
2547 | |
2548 ------------------------------------------------------------------------ | |
2549 r499 | lh3 | 2008-09-11 17:24:15 -0400 (Thu, 11 Sep 2008) | 2 lines | |
2550 Changed paths: | |
2551 M /branches/prog/bwa/bwtsw2.h | |
2552 M /branches/prog/bwa/bwtsw2_core.c | |
2553 M /branches/prog/bwa/bwtsw2_main.c | |
2554 M /branches/prog/bwa/khash.h | |
2555 A /branches/prog/bwa/kvec.h | |
2556 | |
2557 prepare for abrupt change | |
2558 | |
2559 ------------------------------------------------------------------------ | |
2560 r496 | lh3 | 2008-09-11 10:34:38 -0400 (Thu, 11 Sep 2008) | 2 lines | |
2561 Changed paths: | |
2562 M /branches/prog/bwa/bwtsw2_core.c | |
2563 | |
2564 fixed a bug; now "bwtsw2 -d" is useless | |
2565 | |
2566 ------------------------------------------------------------------------ | |
2567 r495 | lh3 | 2008-09-11 09:22:03 -0400 (Thu, 11 Sep 2008) | 2 lines | |
2568 Changed paths: | |
2569 M /branches/prog/bwa/bwtsw2_core.c | |
2570 M /branches/prog/bwa/simple_dp.c | |
2571 M /branches/prog/bwa/stdaln.c | |
2572 M /branches/prog/bwa/stdaln.h | |
2573 | |
2574 improve speed a little bit | |
2575 | |
2576 ------------------------------------------------------------------------ | |
2577 r494 | lh3 | 2008-09-11 08:28:08 -0400 (Thu, 11 Sep 2008) | 2 lines | |
2578 Changed paths: | |
2579 M /branches/prog/bwa/bwtsw2_core.c | |
2580 | |
2581 remove debug codes | |
2582 | |
2583 ------------------------------------------------------------------------ | |
2584 r493 | lh3 | 2008-09-11 07:49:53 -0400 (Thu, 11 Sep 2008) | 3 lines | |
2585 Changed paths: | |
2586 M /branches/prog/bwa/bwtsw2_core.c | |
2587 | |
2588 * improve the speed a little bit (<5%) | |
2589 * prepare to remove BSW_DEBUG | |
2590 | |
2591 ------------------------------------------------------------------------ | |
2592 r492 | lh3 | 2008-09-11 06:15:56 -0400 (Thu, 11 Sep 2008) | 4 lines | |
2593 Changed paths: | |
2594 M /branches/prog/bwa/bwtsw2.h | |
2595 M /branches/prog/bwa/bwtsw2_aux.c | |
2596 M /branches/prog/bwa/bwtsw2_core.c | |
2597 M /branches/prog/bwa/bwtsw2_main.c | |
2598 M /branches/prog/bwa/main.c | |
2599 | |
2600 * bwa-0.2.0-9 | |
2601 * support reverse strand | |
2602 * fixed a bug that causes missing hits | |
2603 | |
2604 ------------------------------------------------------------------------ | |
2605 r491 | lh3 | 2008-09-11 05:46:16 -0400 (Thu, 11 Sep 2008) | 3 lines | |
2606 Changed paths: | |
2607 M /branches/prog/bwa/bwtsw2_core.c | |
2608 M /branches/prog/bwa/main.c | |
2609 | |
2610 * bwa-0.2.0-8 | |
2611 * better progress report | |
2612 | |
2613 ------------------------------------------------------------------------ | |
2614 r490 | lh3 | 2008-09-10 17:04:49 -0400 (Wed, 10 Sep 2008) | 4 lines | |
2615 Changed paths: | |
2616 M /branches/prog/bwa/bwtsw2.h | |
2617 M /branches/prog/bwa/bwtsw2_aux.c | |
2618 M /branches/prog/bwa/bwtsw2_core.c | |
2619 M /branches/prog/bwa/bwtsw2_main.c | |
2620 M /branches/prog/bwa/main.c | |
2621 | |
2622 * bwa-0.2.0-7 | |
2623 * avoid some missing hits | |
2624 * add maximum depth | |
2625 | |
2626 ------------------------------------------------------------------------ | |
2627 r489 | lh3 | 2008-09-10 11:51:13 -0400 (Wed, 10 Sep 2008) | 4 lines | |
2628 Changed paths: | |
2629 M /branches/prog/bwa/bwtsw2_core.c | |
2630 M /branches/prog/bwa/main.c | |
2631 | |
2632 * bwa-0.2.0-6 | |
2633 * bwtsw2 works although on the forward strand only for now | |
2634 * better progress information | |
2635 | |
2636 ------------------------------------------------------------------------ | |
2637 r488 | lh3 | 2008-09-10 10:21:53 -0400 (Wed, 10 Sep 2008) | 3 lines | |
2638 Changed paths: | |
2639 M /branches/prog/bwa/bwtsw2_core.c | |
2640 | |
2641 * implement memory pool | |
2642 * avoid some rehashing | |
2643 | |
2644 ------------------------------------------------------------------------ | |
2645 r487 | lh3 | 2008-09-10 09:23:38 -0400 (Wed, 10 Sep 2008) | 3 lines | |
2646 Changed paths: | |
2647 M /branches/prog/bwa/bwtsw2.h | |
2648 M /branches/prog/bwa/bwtsw2_aux.c | |
2649 M /branches/prog/bwa/bwtsw2_main.c | |
2650 | |
2651 * fixed a memory leak | |
2652 * prepare to implement mempool | |
2653 | |
2654 ------------------------------------------------------------------------ | |
2655 r486 | lh3 | 2008-09-10 09:10:09 -0400 (Wed, 10 Sep 2008) | 4 lines | |
2656 Changed paths: | |
2657 M /branches/prog/bwa/bwtsw2.h | |
2658 M /branches/prog/bwa/bwtsw2_aux.c | |
2659 M /branches/prog/bwa/bwtsw2_core.c | |
2660 M /branches/prog/bwa/bwtsw2_main.c | |
2661 M /branches/prog/bwa/khash.h | |
2662 | |
2663 * add X-dropoff | |
2664 * remove duplicated results | |
2665 * switch to simple stack | |
2666 | |
2667 ------------------------------------------------------------------------ | |
2668 r485 | lh3 | 2008-09-10 06:31:20 -0400 (Wed, 10 Sep 2008) | 3 lines | |
2669 Changed paths: | |
2670 M /branches/prog/bwa/bwtsw2.h | |
2671 M /branches/prog/bwa/bwtsw2_aux.c | |
2672 M /branches/prog/bwa/bwtsw2_core.c | |
2673 M /branches/prog/bwa/bwtsw2_main.c | |
2674 | |
2675 * check whether t-node has been visited | |
2676 * prepare to remove two-level stack | |
2677 | |
2678 ------------------------------------------------------------------------ | |
2679 r484 | lh3 | 2008-09-10 05:00:57 -0400 (Wed, 10 Sep 2008) | 2 lines | |
2680 Changed paths: | |
2681 A /branches/prog/bwa/khash.h | |
2682 | |
2683 khash library | |
2684 | |
2685 ------------------------------------------------------------------------ | |
2686 r483 | lh3 | 2008-09-10 04:22:53 -0400 (Wed, 10 Sep 2008) | 2 lines | |
2687 Changed paths: | |
2688 M /branches/prog/bwa/bwtsw2_core.c | |
2689 | |
2690 add inline | |
2691 | |
2692 ------------------------------------------------------------------------ | |
2693 r482 | lh3 | 2008-09-09 16:34:57 -0400 (Tue, 09 Sep 2008) | 2 lines | |
2694 Changed paths: | |
2695 M /branches/prog/bwa/Makefile | |
2696 M /branches/prog/bwa/bwtsw2_aux.c | |
2697 M /branches/prog/bwa/bwtsw2_core.c | |
2698 | |
2699 improve speed | |
2700 | |
2701 ------------------------------------------------------------------------ | |
2702 r481 | lh3 | 2008-09-09 13:13:00 -0400 (Tue, 09 Sep 2008) | 4 lines | |
2703 Changed paths: | |
2704 M /branches/prog/bwa/bwtsw2_core.c | |
2705 | |
2706 Use a 128bit hash table to keep all (tk,tl,qk,ql). This is slow. Just | |
2707 keep a copy in case I may need this in future. | |
2708 | |
2709 | |
2710 ------------------------------------------------------------------------ | |
2711 r480 | lh3 | 2008-09-09 12:53:32 -0400 (Tue, 09 Sep 2008) | 2 lines | |
2712 Changed paths: | |
2713 M /branches/prog/bwa/bwtsw2.h | |
2714 M /branches/prog/bwa/bwtsw2_core.c | |
2715 | |
2716 * no principal modification | |
2717 | |
2718 ------------------------------------------------------------------------ | |
2719 r479 | lh3 | 2008-09-09 11:01:45 -0400 (Tue, 09 Sep 2008) | 4 lines | |
2720 Changed paths: | |
2721 M /branches/prog/bwa/Makefile | |
2722 M /branches/prog/bwa/bwtsw2_core.c | |
2723 | |
2724 * fixed a bug which may cause duplicated matching | |
2725 * accelerate the speed a bit, although using hash in avoiding duplications | |
2726 slows the speed down in the end | |
2727 | |
2728 ------------------------------------------------------------------------ | |
2729 r474 | lh3 | 2008-09-03 17:22:57 -0400 (Wed, 03 Sep 2008) | 4 lines | |
2730 Changed paths: | |
2731 M /branches/prog/bwa/Makefile | |
2732 M /branches/prog/bwa/bwtsw2.h | |
2733 M /branches/prog/bwa/bwtsw2_aux.c | |
2734 M /branches/prog/bwa/bwtsw2_core.c | |
2735 M /branches/prog/bwa/bwtsw2_main.c | |
2736 M /branches/prog/bwa/main.c | |
2737 | |
2738 * bwa-0.2.0-5 | |
2739 * indel seems to work on toy example | |
2740 * add band | |
2741 | |
2742 ------------------------------------------------------------------------ | |
2743 r469 | lh3 | 2008-09-01 09:18:45 -0400 (Mon, 01 Sep 2008) | 3 lines | |
2744 Changed paths: | |
2745 M /branches/prog/bwa/ChangeLog | |
2746 M /branches/prog/bwa/Makefile | |
2747 M /branches/prog/bwa/bwt_lite.c | |
2748 M /branches/prog/bwa/bwt_lite.h | |
2749 M /branches/prog/bwa/bwtgap.c | |
2750 M /branches/prog/bwa/bwtsw2.h | |
2751 A /branches/prog/bwa/bwtsw2_aux.c | |
2752 M /branches/prog/bwa/bwtsw2_core.c | |
2753 M /branches/prog/bwa/bwtsw2_main.c | |
2754 M /branches/prog/bwa/is.c | |
2755 M /branches/prog/bwa/main.c | |
2756 M /branches/prog/bwa/main.h | |
2757 M /branches/prog/bwa/simple_dp.c | |
2758 | |
2759 * bwa-0.2.0-4 | |
2760 * updated bwtsw2, which seems to work properly on toy examples | |
2761 | |
2762 ------------------------------------------------------------------------ | |
2763 r447 | lh3 | 2008-08-27 10:05:09 -0400 (Wed, 27 Aug 2008) | 3 lines | |
2764 Changed paths: | |
2765 M /branches/prog/bwa/bwt2fmv.c | |
2766 M /branches/prog/bwa/bwtaln.c | |
2767 M /branches/prog/bwa/bwtaln.h | |
2768 M /branches/prog/bwa/bwtgap.c | |
2769 M /branches/prog/bwa/main.c | |
2770 | |
2771 * bwa-0.2.0-3 | |
2772 * tune for longer gaps, but it does not really work with kilo-bp gaps... | |
2773 | |
2774 ------------------------------------------------------------------------ | |
2775 r446 | lh3 | 2008-08-26 13:30:41 -0400 (Tue, 26 Aug 2008) | 3 lines | |
2776 Changed paths: | |
2777 M /branches/prog/bwa/bwt2fmv.c | |
2778 M /branches/prog/bwa/bwtaln.c | |
2779 M /branches/prog/bwa/bwtaln.h | |
2780 M /branches/prog/bwa/bwtgap.c | |
2781 M /branches/prog/bwa/main.c | |
2782 | |
2783 * bwa-0.2.0-2 | |
2784 * changed the way to extend long deletions. Now use max_del_occ. | |
2785 | |
2786 ------------------------------------------------------------------------ | |
2787 r445 | lh3 | 2008-08-26 13:05:58 -0400 (Tue, 26 Aug 2008) | 2 lines | |
2788 Changed paths: | |
2789 M /branches/prog/bwa/bwt_lite.c | |
2790 M /branches/prog/bwa/bwt_lite.h | |
2791 | |
2792 updated from bwtsw2_lite | |
2793 | |
2794 ------------------------------------------------------------------------ | |
2795 r436 | lh3 | 2008-08-23 12:28:44 -0400 (Sat, 23 Aug 2008) | 4 lines | |
2796 Changed paths: | |
2797 M /branches/prog/bwa/Makefile | |
2798 M /branches/prog/bwa/bwt.h | |
2799 A /branches/prog/bwa/bwt_lite.c | |
2800 A /branches/prog/bwa/bwt_lite.h | |
2801 A /branches/prog/bwa/bwtsw2.h | |
2802 A /branches/prog/bwa/bwtsw2_core.c | |
2803 A /branches/prog/bwa/bwtsw2_main.c | |
2804 M /branches/prog/bwa/main.c | |
2805 | |
2806 * bwa-0.2.0-1 | |
2807 * add bwt_lite: a light-weighted version of bwt (NOT TESTED!) | |
2808 * add core codes for bwtsw2: NOT TESTED!!! | |
2809 | |
2810 ------------------------------------------------------------------------ | |
2811 r427 | lh3 | 2008-08-15 05:38:12 -0400 (Fri, 15 Aug 2008) | 2 lines | |
2812 Changed paths: | |
2813 M /branches/prog/bwa/ChangeLog | |
2814 M /branches/prog/bwa/NEWS | |
2815 M /branches/prog/bwa/bwa.1 | |
2816 M /branches/prog/bwa/bwtaln.c | |
2817 M /branches/prog/bwa/main.c | |
2818 | |
2819 Release bwa-0.2.0 | |
2820 | |
2821 ------------------------------------------------------------------------ | |
2822 r426 | lh3 | 2008-08-14 11:26:19 -0400 (Thu, 14 Aug 2008) | 4 lines | |
2823 Changed paths: | |
2824 M /branches/prog/bwa/bwt2fmv.c | |
2825 M /branches/prog/bwa/bwtaln.c | |
2826 M /branches/prog/bwa/bwtaln.h | |
2827 M /branches/prog/bwa/main.c | |
2828 | |
2829 * bwa-0.1.6-7 | |
2830 * change default seed length to 31 | |
2831 * add incomplete support to color sequences (not tested yet!) | |
2832 | |
2833 ------------------------------------------------------------------------ | |
2834 r425 | lh3 | 2008-08-14 06:23:11 -0400 (Thu, 14 Aug 2008) | 3 lines | |
2835 Changed paths: | |
2836 M /branches/prog/bwa/bwtaln.c | |
2837 M /branches/prog/bwa/main.c | |
2838 | |
2839 * bwa-0.1.6-6 | |
2840 * change default seed length to 33bp | |
2841 | |
2842 ------------------------------------------------------------------------ | |
2843 r424 | lh3 | 2008-08-14 05:55:33 -0400 (Thu, 14 Aug 2008) | 6 lines | |
2844 Changed paths: | |
2845 M /branches/prog/bwa/bwtaln.c | |
2846 M /branches/prog/bwa/bwtgap.c | |
2847 M /branches/prog/bwa/main.c | |
2848 | |
2849 * bwa-0.1.6-5 | |
2850 * fixed a bug that may miss true alignments. this bugs exists in most | |
2851 early versions. | |
2852 * fixed a bug that yields wrong coordinates for reads mapped on the forward | |
2853 strands with gaps. | |
2854 | |
2855 ------------------------------------------------------------------------ | |
2856 r423 | lh3 | 2008-08-14 04:07:28 -0400 (Thu, 14 Aug 2008) | 2 lines | |
2857 Changed paths: | |
2858 D /branches/prog/bwa/Makefile.div | |
2859 | |
2860 useless | |
2861 | |
2862 ------------------------------------------------------------------------ | |
2863 r422 | lh3 | 2008-08-13 19:21:14 -0400 (Wed, 13 Aug 2008) | 4 lines | |
2864 Changed paths: | |
2865 M /branches/prog/bwa/bwtaln.c | |
2866 M /branches/prog/bwa/main.c | |
2867 | |
2868 * bwa-0.1.6-4 | |
2869 * fixed one bug | |
2870 * there is another one... | |
2871 | |
2872 ------------------------------------------------------------------------ | |
2873 r421 | lh3 | 2008-08-13 18:23:33 -0400 (Wed, 13 Aug 2008) | 3 lines | |
2874 Changed paths: | |
2875 M /branches/prog/bwa/bwtaln.c | |
2876 M /branches/prog/bwa/bwtaln.h | |
2877 M /branches/prog/bwa/bwtgap.c | |
2878 M /branches/prog/bwa/bwtgap.h | |
2879 M /branches/prog/bwa/bwtindex.c | |
2880 M /branches/prog/bwa/main.c | |
2881 | |
2882 * bwa-0.1.6-3 | |
2883 * almost there, but not quite right | |
2884 | |
2885 ------------------------------------------------------------------------ | |
2886 r419 | lh3 | 2008-08-13 17:27:02 -0400 (Wed, 13 Aug 2008) | 3 lines | |
2887 Changed paths: | |
2888 M /branches/prog/bwa/bwtaln.c | |
2889 M /branches/prog/bwa/bwtaln.h | |
2890 M /branches/prog/bwa/bwtgap.c | |
2891 M /branches/prog/bwa/bwtgap.h | |
2892 M /branches/prog/bwa/main.c | |
2893 | |
2894 * improve the seeding method | |
2895 * prepare to load two BWTs into memory. A BIG change! | |
2896 | |
2897 ------------------------------------------------------------------------ | |
2898 r418 | lh3 | 2008-08-13 10:56:54 -0400 (Wed, 13 Aug 2008) | 3 lines | |
2899 Changed paths: | |
2900 M /branches/prog/bwa/bwt2fmv.c | |
2901 M /branches/prog/bwa/bwtaln.c | |
2902 M /branches/prog/bwa/bwtaln.h | |
2903 M /branches/prog/bwa/bwtgap.c | |
2904 M /branches/prog/bwa/bwtgap.h | |
2905 M /branches/prog/bwa/main.c | |
2906 | |
2907 * added seeding | |
2908 * unfinished yet | |
2909 | |
2910 ------------------------------------------------------------------------ | |
2911 r413 | lh3 | 2008-08-08 11:48:35 -0400 (Fri, 08 Aug 2008) | 2 lines | |
2912 Changed paths: | |
2913 M /branches/prog/bwa/ChangeLog | |
2914 M /branches/prog/bwa/NEWS | |
2915 M /branches/prog/bwa/main.c | |
2916 | |
2917 Release bwa-0.1.6 | |
2918 | |
2919 ------------------------------------------------------------------------ | |
2920 r410 | lh3 | 2008-08-06 15:48:22 -0400 (Wed, 06 Aug 2008) | 2 lines | |
2921 Changed paths: | |
2922 M /branches/prog/bwa/simple_dp.c | |
2923 | |
2924 sw: output alignment score | |
2925 | |
2926 ------------------------------------------------------------------------ | |
2927 r407 | lh3 | 2008-08-04 10:01:20 -0400 (Mon, 04 Aug 2008) | 4 lines | |
2928 Changed paths: | |
2929 M /branches/prog/bwa/Makefile | |
2930 M /branches/prog/bwa/main.c | |
2931 M /branches/prog/bwa/main.h | |
2932 A /branches/prog/bwa/simple_dp.c | |
2933 M /branches/prog/bwa/stdaln.c | |
2934 M /branches/prog/bwa/stdaln.h | |
2935 | |
2936 * bwa-0.1.5-3 | |
2937 * added a simple interface to SW/NW alignment | |
2938 * stdaln-0.9.8 (see header for more details) | |
2939 | |
2940 ------------------------------------------------------------------------ | |
2941 r406 | lh3 | 2008-08-01 19:21:59 -0400 (Fri, 01 Aug 2008) | 3 lines | |
2942 Changed paths: | |
2943 M /branches/prog/bwa/Makefile | |
2944 M /branches/prog/bwa/bwtaln.c | |
2945 M /branches/prog/bwa/bwtaln.h | |
2946 M /branches/prog/bwa/main.c | |
2947 A /branches/prog/bwa/stdaln.c | |
2948 A /branches/prog/bwa/stdaln.h | |
2949 | |
2950 * bwa-0.1.5-2 | |
2951 * give accurate gap positions | |
2952 | |
2953 ------------------------------------------------------------------------ | |
2954 r405 | lh3 | 2008-08-01 19:06:19 -0400 (Fri, 01 Aug 2008) | 2 lines | |
2955 Changed paths: | |
2956 M /branches/prog/bwa/Makefile | |
2957 M /branches/prog/bwa/bwtaln.c | |
2958 M /branches/prog/bwa/bwtaln.h | |
2959 | |
2960 unfinished, but I am tired... | |
2961 | |
2962 ------------------------------------------------------------------------ | |
2963 r401 | lh3 | 2008-07-30 05:59:24 -0400 (Wed, 30 Jul 2008) | 4 lines | |
2964 Changed paths: | |
2965 M /branches/prog/bwa/bntseq.c | |
2966 M /branches/prog/bwa/main.c | |
2967 | |
2968 * bwa-0.1.5-1 | |
2969 * fixed a potential bug which may produce an alignment in N regions, | |
2970 although extremely rare. | |
2971 | |
2972 ------------------------------------------------------------------------ | |
2973 r399 | lh3 | 2008-07-27 11:41:52 -0400 (Sun, 27 Jul 2008) | 2 lines | |
2974 Changed paths: | |
2975 M /branches/prog/bwa/ChangeLog | |
2976 M /branches/prog/bwa/NEWS | |
2977 M /branches/prog/bwa/main.c | |
2978 | |
2979 Release bwa-0.1.5 | |
2980 | |
2981 ------------------------------------------------------------------------ | |
2982 r398 | lh3 | 2008-07-25 12:14:47 -0400 (Fri, 25 Jul 2008) | 2 lines | |
2983 Changed paths: | |
2984 M /branches/prog/bwa/bwa.1 | |
2985 | |
2986 update documentation | |
2987 | |
2988 ------------------------------------------------------------------------ | |
2989 r397 | lh3 | 2008-07-25 09:58:56 -0400 (Fri, 25 Jul 2008) | 2 lines | |
2990 Changed paths: | |
2991 M /branches/prog/bwa/bwt2fmv.c | |
2992 M /branches/prog/bwa/bwtaln.c | |
2993 M /branches/prog/bwa/main.c | |
2994 | |
2995 * | |
2996 | |
2997 ------------------------------------------------------------------------ | |
2998 r396 | lh3 | 2008-07-25 06:42:01 -0400 (Fri, 25 Jul 2008) | 3 lines | |
2999 Changed paths: | |
3000 M /branches/prog/bwa/bwtaln.c | |
3001 M /branches/prog/bwa/main.c | |
3002 | |
3003 * bwa-0.1.4-4 | |
3004 * add timer for debugging | |
3005 | |
3006 ------------------------------------------------------------------------ | |
3007 r395 | lh3 | 2008-07-24 05:46:21 -0400 (Thu, 24 Jul 2008) | 4 lines | |
3008 Changed paths: | |
3009 M /branches/prog/bwa/bwtgap.c | |
3010 M /branches/prog/bwa/main.c | |
3011 | |
3012 * bwa-0.1.4-3 | |
3013 * fixed a bug in the previous code | |
3014 * this version gives identical result to bwa-0.1.4, just 10% faster | |
3015 | |
3016 ------------------------------------------------------------------------ | |
3017 r394 | lh3 | 2008-07-24 05:18:53 -0400 (Thu, 24 Jul 2008) | 4 lines | |
3018 Changed paths: | |
3019 M /branches/prog/bwa/bwtaln.c | |
3020 M /branches/prog/bwa/bwtgap.c | |
3021 M /branches/prog/bwa/bwtgap.h | |
3022 M /branches/prog/bwa/main.c | |
3023 | |
3024 * bwa-0.1.4-2 | |
3025 * further improve the speed | |
3026 * The result is slightly different from bwa-0.1.4 now. I need to check... | |
3027 | |
3028 ------------------------------------------------------------------------ | |
3029 r393 | lh3 | 2008-07-23 12:04:16 -0400 (Wed, 23 Jul 2008) | 2 lines | |
3030 Changed paths: | |
3031 M /branches/prog/bwa/bwt.c | |
3032 | |
3033 comments only | |
3034 | |
3035 ------------------------------------------------------------------------ | |
3036 r392 | lh3 | 2008-07-23 10:34:03 -0400 (Wed, 23 Jul 2008) | 2 lines | |
3037 Changed paths: | |
3038 M /branches/prog/bwa/bwt.c | |
3039 M /branches/prog/bwa/main.c | |
3040 | |
3041 further improve the speed in Occ functions | |
3042 | |
3043 ------------------------------------------------------------------------ | |
3044 r386 | lh3 | 2008-07-22 10:03:54 -0400 (Tue, 22 Jul 2008) | 2 lines | |
3045 Changed paths: | |
3046 M /branches/prog/bwa/NEWS | |
3047 M /branches/prog/bwa/main.c | |
3048 | |
3049 Release bwa-0.1.4 | |
3050 | |
3051 ------------------------------------------------------------------------ | |
3052 r385 | lh3 | 2008-07-22 09:44:50 -0400 (Tue, 22 Jul 2008) | 2 lines | |
3053 Changed paths: | |
3054 M /branches/prog/bwa/ChangeLog | |
3055 M /branches/prog/bwa/bwa.1 | |
3056 | |
3057 update documentation and ChangeLog | |
3058 | |
3059 ------------------------------------------------------------------------ | |
3060 r384 | lh3 | 2008-07-22 08:50:03 -0400 (Tue, 22 Jul 2008) | 4 lines | |
3061 Changed paths: | |
3062 M /branches/prog/bwa/Makefile | |
3063 M /branches/prog/bwa/bwt2fmv.c | |
3064 M /branches/prog/bwa/bwtaln.c | |
3065 M /branches/prog/bwa/bwtaln.h | |
3066 M /branches/prog/bwa/bwtgap.c | |
3067 M /branches/prog/bwa/main.c | |
3068 | |
3069 * bwa-0.1.3-2 | |
3070 * fixed the bug in the last modification | |
3071 * now the alignment should be more clearly defined | |
3072 | |
3073 ------------------------------------------------------------------------ | |
3074 r383 | lh3 | 2008-07-21 18:32:21 -0400 (Mon, 21 Jul 2008) | 4 lines | |
3075 Changed paths: | |
3076 M /branches/prog/bwa/bwt2fmv.c | |
3077 M /branches/prog/bwa/bwtaln.c | |
3078 M /branches/prog/bwa/bwtgap.c | |
3079 M /branches/prog/bwa/main.c | |
3080 | |
3081 * bwa-0.1.3-1 | |
3082 * this is a buggy verion! | |
3083 * i will fix the bug tomorrow. It is late... | |
3084 | |
3085 ------------------------------------------------------------------------ | |
3086 r381 | lh3 | 2008-07-21 06:45:32 -0400 (Mon, 21 Jul 2008) | 2 lines | |
3087 Changed paths: | |
3088 M /branches/prog/bwa/ChangeLog | |
3089 M /branches/prog/bwa/NEWS | |
3090 M /branches/prog/bwa/bwa.1 | |
3091 M /branches/prog/bwa/main.c | |
3092 | |
3093 Release bwa-0.1.3 | |
3094 | |
3095 ------------------------------------------------------------------------ | |
3096 r380 | lh3 | 2008-07-21 06:07:43 -0400 (Mon, 21 Jul 2008) | 4 lines | |
3097 Changed paths: | |
3098 M /branches/prog/bwa/ChangeLog | |
3099 M /branches/prog/bwa/bwa.1 | |
3100 M /branches/prog/bwa/bwt.c | |
3101 M /branches/prog/bwa/bwt2fmv.c | |
3102 M /branches/prog/bwa/main.c | |
3103 | |
3104 * bwa-0.1.2-3 | |
3105 * improve the speed for gcc on Intel Mac OS X, but not really on icc on Linux | |
3106 * aln: more command-line options | |
3107 | |
3108 ------------------------------------------------------------------------ | |
3109 r373 | lh3 | 2008-07-17 09:09:46 -0400 (Thu, 17 Jul 2008) | 4 lines | |
3110 Changed paths: | |
3111 M /branches/prog/bwa/bwt.c | |
3112 M /branches/prog/bwa/bwt.h | |
3113 M /branches/prog/bwa/bwtio.c | |
3114 M /branches/prog/bwa/main.c | |
3115 | |
3116 * bwa-0.1.2-2 | |
3117 * further improve the speed | |
3118 * this version gives exactly the same result as bwa-0.1.2 | |
3119 | |
3120 ------------------------------------------------------------------------ | |
3121 r372 | lh3 | 2008-07-17 07:51:08 -0400 (Thu, 17 Jul 2008) | 3 lines | |
3122 Changed paths: | |
3123 M /branches/prog/bwa/bwt.c | |
3124 M /branches/prog/bwa/main.c | |
3125 | |
3126 * bwa-0.1.2-1 | |
3127 * speed up by about 5% | |
3128 | |
3129 ------------------------------------------------------------------------ | |
3130 r370 | lh3 | 2008-07-17 05:12:00 -0400 (Thu, 17 Jul 2008) | 2 lines | |
3131 Changed paths: | |
3132 M /branches/prog/bwa/NEWS | |
3133 M /branches/prog/bwa/bwa.1 | |
3134 M /branches/prog/bwa/main.c | |
3135 | |
3136 Release bwa-0.1.2 | |
3137 | |
3138 ------------------------------------------------------------------------ | |
3139 r368 | lh3 | 2008-07-16 08:51:25 -0400 (Wed, 16 Jul 2008) | 4 lines | |
3140 Changed paths: | |
3141 M /branches/prog/bwa/Makefile | |
3142 D /branches/prog/bwa/bwt1away.c | |
3143 M /branches/prog/bwa/bwt2fmv.c | |
3144 M /branches/prog/bwa/bwtaln.c | |
3145 M /branches/prog/bwa/bwtaln.h | |
3146 M /branches/prog/bwa/bwtgap.c | |
3147 M /branches/prog/bwa/bwtgap.h | |
3148 D /branches/prog/bwa/bwttop2.c | |
3149 M /branches/prog/bwa/main.c | |
3150 | |
3151 * bwa-0.1.1-9 | |
3152 * some code cleanup | |
3153 * remove 1away and top2 | |
3154 | |
3155 ------------------------------------------------------------------------ | |
3156 r367 | lh3 | 2008-07-16 08:24:34 -0400 (Wed, 16 Jul 2008) | 2 lines | |
3157 Changed paths: | |
3158 M /branches/prog/bwa/is.c | |
3159 | |
3160 Yuta Mori's implementation of IS algorithm. | |
3161 | |
3162 ------------------------------------------------------------------------ | |
3163 r365 | lh3 | 2008-07-16 06:58:04 -0400 (Wed, 16 Jul 2008) | 6 lines | |
3164 Changed paths: | |
3165 M /branches/prog/bwa/bwtaln.c | |
3166 M /branches/prog/bwa/bwtgap.c | |
3167 M /branches/prog/bwa/bwtgap.h | |
3168 M /branches/prog/bwa/main.c | |
3169 | |
3170 * bwa-0.1.1-8 | |
3171 * improve gapped alignment | |
3172 * this version will miss more gapped alignments, but the speed is much faster | |
3173 * prepare to remove top2 and 1away algorithms | |
3174 * prepare to add SAIS algorithm for bwt construction | |
3175 | |
3176 ------------------------------------------------------------------------ | |
3177 r358 | lh3 | 2008-06-09 06:03:04 -0400 (Mon, 09 Jun 2008) | 4 lines | |
3178 Changed paths: | |
3179 M /branches/prog/bwa/bwt2fmv.c | |
3180 M /branches/prog/bwa/bwtgap.c | |
3181 M /branches/prog/bwa/main.c | |
3182 | |
3183 * bwa-0.1.1-7 | |
3184 * change END_SKIP from 3 to 5, but still gaps may be wrongly added | |
3185 * change default '-g' from 5 to 3 | |
3186 | |
3187 ------------------------------------------------------------------------ | |
3188 r357 | lh3 | 2008-06-09 05:18:36 -0400 (Mon, 09 Jun 2008) | 3 lines | |
3189 Changed paths: | |
3190 M /branches/prog/bwa/bntseq.c | |
3191 M /branches/prog/bwa/bwt2fmv.c | |
3192 M /branches/prog/bwa/bwtgap.c | |
3193 M /branches/prog/bwa/main.c | |
3194 | |
3195 * bwa-0.1.1-6 | |
3196 * fix a bug in nested stack | |
3197 | |
3198 ------------------------------------------------------------------------ | |
3199 r356 | lh3 | 2008-06-08 18:43:13 -0400 (Sun, 08 Jun 2008) | 4 lines | |
3200 Changed paths: | |
3201 M /branches/prog/bwa/Makefile | |
3202 M /branches/prog/bwa/bwtaln.c | |
3203 M /branches/prog/bwa/bwtaln.h | |
3204 M /branches/prog/bwa/bwtgap.c | |
3205 A /branches/prog/bwa/bwtgap.h | |
3206 M /branches/prog/bwa/main.c | |
3207 | |
3208 * bwa-0.1.1-5 | |
3209 * replace heap with nested stacks | |
3210 * there are still obvious bugs... | |
3211 | |
3212 ------------------------------------------------------------------------ | |
3213 r355 | lh3 | 2008-06-08 17:13:44 -0400 (Sun, 08 Jun 2008) | 4 lines | |
3214 Changed paths: | |
3215 M /branches/prog/bwa/bwt2fmv.c | |
3216 M /branches/prog/bwa/bwtaln.c | |
3217 M /branches/prog/bwa/bwtaln.h | |
3218 M /branches/prog/bwa/bwtgap.c | |
3219 M /branches/prog/bwa/main.c | |
3220 M /branches/prog/bwa/main.h | |
3221 | |
3222 * bwa-0.1.1-4 | |
3223 * add interface to affine gap alignment | |
3224 * there are obvious bugs and I will fix them later | |
3225 | |
3226 ------------------------------------------------------------------------ | |
3227 r354 | lh3 | 2008-06-08 15:39:05 -0400 (Sun, 08 Jun 2008) | 3 lines | |
3228 Changed paths: | |
3229 M /branches/prog/bwa/bwtaln.c | |
3230 M /branches/prog/bwa/bwtaln.h | |
3231 M /branches/prog/bwa/bwtgap.c | |
3232 M /branches/prog/bwa/main.c | |
3233 | |
3234 * bwa-0.1.1-3 | |
3235 * affine gap seems to work, at least partially | |
3236 | |
3237 ------------------------------------------------------------------------ | |
3238 r353 | lh3 | 2008-06-08 09:27:18 -0400 (Sun, 08 Jun 2008) | 3 lines | |
3239 Changed paths: | |
3240 M /branches/prog/bwa/Makefile | |
3241 M /branches/prog/bwa/bwt2fmv.c | |
3242 M /branches/prog/bwa/bwtaln.c | |
3243 M /branches/prog/bwa/bwtaln.h | |
3244 A /branches/prog/bwa/bwtgap.c | |
3245 M /branches/prog/bwa/bwttop2.c | |
3246 M /branches/prog/bwa/main.c | |
3247 | |
3248 * bwa-0.1.1-2 | |
3249 * initial gapped alignment. not work at the moment | |
3250 | |
3251 ------------------------------------------------------------------------ | |
3252 r352 | lh3 | 2008-06-06 04:37:34 -0400 (Fri, 06 Jun 2008) | 3 lines | |
3253 Changed paths: | |
3254 M /branches/prog/bwa/bwttop2.c | |
3255 M /branches/prog/bwa/main.c | |
3256 | |
3257 * bwa-0.1.1-1 | |
3258 * ungap: remove a useless varible in top2_entry_t | |
3259 | |
3260 ------------------------------------------------------------------------ | |
3261 r348 | lh3 | 2008-06-03 09:04:12 -0400 (Tue, 03 Jun 2008) | 2 lines | |
3262 Changed paths: | |
3263 M /branches/prog/bwa/ChangeLog | |
3264 A /branches/prog/bwa/NEWS | |
3265 M /branches/prog/bwa/bwa.1 | |
3266 M /branches/prog/bwa/main.c | |
3267 | |
3268 Release bwa-0.1.1 | |
3269 | |
3270 ------------------------------------------------------------------------ | |
3271 r347 | lh3 | 2008-06-03 05:45:08 -0400 (Tue, 03 Jun 2008) | 2 lines | |
3272 Changed paths: | |
3273 M /branches/prog/bwa/bwa.1 | |
3274 | |
3275 update documentation | |
3276 | |
3277 ------------------------------------------------------------------------ | |
3278 r346 | lh3 | 2008-06-02 18:59:50 -0400 (Mon, 02 Jun 2008) | 5 lines | |
3279 Changed paths: | |
3280 A /branches/prog/bwa/ChangeLog | |
3281 A /branches/prog/bwa/bwa.1 | |
3282 M /branches/prog/bwa/bwtaln.c | |
3283 M /branches/prog/bwa/main.c | |
3284 | |
3285 * bwa-0.1.0-11 | |
3286 * improve approximating mapping qualities | |
3287 * add documentation | |
3288 * add ChangeLog | |
3289 | |
3290 ------------------------------------------------------------------------ | |
3291 r345 | lh3 | 2008-06-02 16:04:39 -0400 (Mon, 02 Jun 2008) | 3 lines | |
3292 Changed paths: | |
3293 M /branches/prog/bwa/bwtaln.c | |
3294 M /branches/prog/bwa/bwttop2.c | |
3295 M /branches/prog/bwa/main.c | |
3296 | |
3297 * bwa-0.1.0-10 | |
3298 * output a random position for repetitive reads | |
3299 | |
3300 ------------------------------------------------------------------------ | |
3301 r344 | lh3 | 2008-06-02 15:03:54 -0400 (Mon, 02 Jun 2008) | 4 lines | |
3302 Changed paths: | |
3303 M /branches/prog/bwa/bntseq.c | |
3304 M /branches/prog/bwa/bwtaln.c | |
3305 M /branches/prog/bwa/main.c | |
3306 M /branches/prog/bwa/pac2bwt.c | |
3307 | |
3308 * bwa-0.1.0-9 | |
3309 * fix memory leaks | |
3310 * fix a potential bug in coverting to the real coordinate | |
3311 | |
3312 ------------------------------------------------------------------------ | |
3313 r343 | lh3 | 2008-06-02 13:44:51 -0400 (Mon, 02 Jun 2008) | 5 lines | |
3314 Changed paths: | |
3315 M /branches/prog/bwa/Makefile.div | |
3316 M /branches/prog/bwa/bwt.c | |
3317 M /branches/prog/bwa/bwt.h | |
3318 M /branches/prog/bwa/bwt2fmv.c | |
3319 M /branches/prog/bwa/bwtaln.c | |
3320 M /branches/prog/bwa/bwttop2.c | |
3321 M /branches/prog/bwa/main.c | |
3322 | |
3323 * bwa-0.1.0-8 | |
3324 * fix a bug about strand | |
3325 * update Makefile.div | |
3326 * change top2b as the default method | |
3327 | |
3328 ------------------------------------------------------------------------ | |
3329 r342 | lh3 | 2008-06-02 11:23:26 -0400 (Mon, 02 Jun 2008) | 3 lines | |
3330 Changed paths: | |
3331 M /branches/prog/bwa/bwt.c | |
3332 M /branches/prog/bwa/bwt1away.c | |
3333 M /branches/prog/bwa/bwtaln.c | |
3334 M /branches/prog/bwa/main.c | |
3335 | |
3336 * bwa-0.1.0-7 | |
3337 * use bwt_2occ() and bwt_2occ4() in other functions | |
3338 | |
3339 ------------------------------------------------------------------------ | |
3340 r341 | lh3 | 2008-06-02 09:31:39 -0400 (Mon, 02 Jun 2008) | 3 lines | |
3341 Changed paths: | |
3342 M /branches/prog/bwa/bwttop2.c | |
3343 M /branches/prog/bwa/main.c | |
3344 | |
3345 * bwa-0.1.0-6 | |
3346 * fix a bug for missing hits | |
3347 | |
3348 ------------------------------------------------------------------------ | |
3349 r340 | lh3 | 2008-06-02 09:10:18 -0400 (Mon, 02 Jun 2008) | 3 lines | |
3350 Changed paths: | |
3351 M /branches/prog/bwa/bwttop2.c | |
3352 M /branches/prog/bwa/main.c | |
3353 | |
3354 * bwa-0.1.0-5 | |
3355 * accelerate comparisons in heap, a bit | |
3356 | |
3357 ------------------------------------------------------------------------ | |
3358 r339 | lh3 | 2008-06-02 08:41:31 -0400 (Mon, 02 Jun 2008) | 3 lines | |
3359 Changed paths: | |
3360 M /branches/prog/bwa/bwt.c | |
3361 M /branches/prog/bwa/bwt.h | |
3362 M /branches/prog/bwa/bwttop2.c | |
3363 M /branches/prog/bwa/main.c | |
3364 | |
3365 * bwa-0.1.0-4 | |
3366 * avoid marginal repeated calculation in occ | |
3367 | |
3368 ------------------------------------------------------------------------ | |
3369 r338 | lh3 | 2008-06-02 06:46:51 -0400 (Mon, 02 Jun 2008) | 5 lines | |
3370 Changed paths: | |
3371 M /branches/prog/bwa/Makefile | |
3372 M /branches/prog/bwa/bwt.c | |
3373 M /branches/prog/bwa/bwttop2.c | |
3374 M /branches/prog/bwa/main.c | |
3375 | |
3376 * bwa-0.1.0-3 | |
3377 * fix a bug caused by previours change | |
3378 * fix a bug in heap | |
3379 * order the heap by more criteria | |
3380 | |
3381 ------------------------------------------------------------------------ | |
3382 r337 | lh3 | 2008-06-01 19:11:15 -0400 (Sun, 01 Jun 2008) | 4 lines | |
3383 Changed paths: | |
3384 M /branches/prog/bwa/bwttop2.c | |
3385 M /branches/prog/bwa/main.c | |
3386 | |
3387 * bwa-0.1.0-2 | |
3388 * also sort sa range in heapsort, in attempt to improve cache performance. | |
3389 Unfortunately, it does not work well at all. | |
3390 | |
3391 ------------------------------------------------------------------------ | |
3392 r336 | lh3 | 2008-06-01 17:45:23 -0400 (Sun, 01 Jun 2008) | 3 lines | |
3393 Changed paths: | |
3394 M /branches/prog/bwa/Makefile | |
3395 M /branches/prog/bwa/Makefile.div | |
3396 M /branches/prog/bwa/bntseq.c | |
3397 M /branches/prog/bwa/main.c | |
3398 | |
3399 * 0.1.0-1 | |
3400 * fix a bug in calculating the real coordinate | |
3401 | |
3402 ------------------------------------------------------------------------ | |
3403 r335 | lh3 | 2008-06-01 16:03:09 -0400 (Sun, 01 Jun 2008) | 2 lines | |
3404 Changed paths: | |
3405 M /branches/prog/bwa/Makefile | |
3406 | |
3407 nothing, really | |
3408 | |
3409 ------------------------------------------------------------------------ | |
3410 r334 | lh3 | 2008-06-01 15:59:13 -0400 (Sun, 01 Jun 2008) | 2 lines | |
3411 Changed paths: | |
3412 M /branches/prog/bwa/Makefile | |
3413 A /branches/prog/bwa/Makefile.div | |
3414 M /branches/prog/bwa/bwtindex.c | |
3415 M /branches/prog/bwa/pac2bwt.c | |
3416 | |
3417 use IS algorithm by default | |
3418 | |
3419 ------------------------------------------------------------------------ | |
3420 r333 | lh3 | 2008-06-01 15:05:15 -0400 (Sun, 01 Jun 2008) | 3 lines | |
3421 Changed paths: | |
3422 M /branches/prog/bwa/Makefile | |
3423 M /branches/prog/bwa/bwtindex.c | |
3424 M /branches/prog/bwa/is.c | |
3425 M /branches/prog/bwa/pac2bwt.c | |
3426 | |
3427 * a bit code clean up in is.c | |
3428 * add IS algorithm for constructing BWT, albeit slower | |
3429 | |
3430 ------------------------------------------------------------------------ | |
3431 r332 | lh3 | 2008-06-01 13:23:08 -0400 (Sun, 01 Jun 2008) | 2 lines | |
3432 Changed paths: | |
3433 A /branches/prog/bwa/is.c | |
3434 | |
3435 IS linear-time algorithm for constructing SA/BWT | |
3436 | |
3437 ------------------------------------------------------------------------ | |
3438 r331 | lh3 | 2008-06-01 10:35:26 -0400 (Sun, 01 Jun 2008) | 3 lines | |
3439 Changed paths: | |
3440 M /branches/prog/bwa/Makefile | |
3441 M /branches/prog/bwa/bntseq.c | |
3442 A /branches/prog/bwa/bwtindex.c | |
3443 M /branches/prog/bwa/main.c | |
3444 M /branches/prog/bwa/main.h | |
3445 | |
3446 * fix a bug in generating .pac | |
3447 * index in one go | |
3448 | |
3449 ------------------------------------------------------------------------ | |
3450 r330 | lh3 | 2008-06-01 09:17:05 -0400 (Sun, 01 Jun 2008) | 2 lines | |
3451 Changed paths: | |
3452 M /branches/prog/bwa/bntseq.c | |
3453 M /branches/prog/bwa/bntseq.h | |
3454 M /branches/prog/bwa/bwtaln.c | |
3455 M /branches/prog/bwa/bwttop2.c | |
3456 | |
3457 real coordinates can be ouput | |
3458 | |
3459 ------------------------------------------------------------------------ | |
3460 r329 | lh3 | 2008-05-31 19:21:02 -0400 (Sat, 31 May 2008) | 2 lines | |
3461 Changed paths: | |
3462 M /branches/prog/bwa/bwt2fmv.c | |
3463 M /branches/prog/bwa/bwtaln.h | |
3464 M /branches/prog/bwa/bwttop2.c | |
3465 | |
3466 add top2e which is similar to 1away | |
3467 | |
3468 ------------------------------------------------------------------------ | |
3469 r328 | lh3 | 2008-05-31 18:46:12 -0400 (Sat, 31 May 2008) | 3 lines | |
3470 Changed paths: | |
3471 M /branches/prog/bwa/bwt2fmv.c | |
3472 M /branches/prog/bwa/bwtaln.c | |
3473 M /branches/prog/bwa/bwtaln.h | |
3474 M /branches/prog/bwa/bwttop2.c | |
3475 M /branches/prog/bwa/main.c | |
3476 M /branches/prog/bwa/main.h | |
3477 | |
3478 * unified cmd-line interface for ungapped alignment | |
3479 * add two alternatives to top2 algorithm | |
3480 | |
3481 ------------------------------------------------------------------------ | |
3482 r327 | lh3 | 2008-05-31 18:14:46 -0400 (Sat, 31 May 2008) | 2 lines | |
3483 Changed paths: | |
3484 M /branches/prog/bwa/bwt2fmv.c | |
3485 M /branches/prog/bwa/bwtaln.c | |
3486 M /branches/prog/bwa/bwtaln.h | |
3487 M /branches/prog/bwa/main.c | |
3488 M /branches/prog/bwa/main.h | |
3489 | |
3490 add cmd-line interface to alntop2 | |
3491 | |
3492 ------------------------------------------------------------------------ | |
3493 r326 | lh3 | 2008-05-31 17:59:31 -0400 (Sat, 31 May 2008) | 2 lines | |
3494 Changed paths: | |
3495 M /branches/prog/bwa/Makefile | |
3496 M /branches/prog/bwa/bwt1away.c | |
3497 M /branches/prog/bwa/bwtaln.c | |
3498 M /branches/prog/bwa/bwtaln.h | |
3499 A /branches/prog/bwa/bwttop2.c | |
3500 | |
3501 top2 algorithm seems to work. I need to change interface, though | |
3502 | |
3503 ------------------------------------------------------------------------ | |
3504 r325 | lh3 | 2008-05-31 15:11:49 -0400 (Sat, 31 May 2008) | 2 lines | |
3505 Changed paths: | |
3506 M /branches/prog/bwa/bwt1away.c | |
3507 | |
3508 change the variable in the structure | |
3509 | |
3510 ------------------------------------------------------------------------ | |
3511 r324 | lh3 | 2008-05-31 14:52:13 -0400 (Sat, 31 May 2008) | 2 lines | |
3512 Changed paths: | |
3513 M /branches/prog/bwa/bwt1away.c | |
3514 | |
3515 set a slightly better bound on the maximum allowed mismatches | |
3516 | |
3517 ------------------------------------------------------------------------ | |
3518 r323 | lh3 | 2008-05-30 18:40:21 -0400 (Fri, 30 May 2008) | 2 lines | |
3519 Changed paths: | |
3520 M /branches/prog/bwa/bwtaln.c | |
3521 | |
3522 * output time statistics | |
3523 | |
3524 ------------------------------------------------------------------------ | |
3525 r322 | lh3 | 2008-05-30 17:58:25 -0400 (Fri, 30 May 2008) | 4 lines | |
3526 Changed paths: | |
3527 M /branches/prog/bwa/Makefile | |
3528 M /branches/prog/bwa/bwt.c | |
3529 M /branches/prog/bwa/bwt.h | |
3530 A /branches/prog/bwa/bwt1away.c | |
3531 M /branches/prog/bwa/bwtaln.c | |
3532 M /branches/prog/bwa/bwtaln.h | |
3533 | |
3534 * presumably better way to make use of prefix. But for the moment I do | |
3535 not know whether it is correct or not. | |
3536 * a bit code clean up: separate alignment part | |
3537 | |
3538 ------------------------------------------------------------------------ | |
3539 r321 | lh3 | 2008-05-30 13:57:43 -0400 (Fri, 30 May 2008) | 3 lines | |
3540 Changed paths: | |
3541 M /branches/prog/bwa/Makefile | |
3542 M /branches/prog/bwa/bwt.c | |
3543 M /branches/prog/bwa/bwt.h | |
3544 M /branches/prog/bwa/bwt_gen/Makefile | |
3545 M /branches/prog/bwa/bwt_gen/bwt_gen.c | |
3546 M /branches/prog/bwa/bwtaln.c | |
3547 M /branches/prog/bwa/main.c | |
3548 M /branches/prog/bwa/main.h | |
3549 M /branches/prog/bwa/pac2bwt.c | |
3550 | |
3551 * a bit code clean up | |
3552 * put bwt_gen in bwa | |
3553 | |
3554 ------------------------------------------------------------------------ | |
3555 r320 | lh3 | 2008-05-30 11:40:11 -0400 (Fri, 30 May 2008) | 4 lines | |
3556 Changed paths: | |
3557 M /branches/prog/bwa/bwt.c | |
3558 M /branches/prog/bwa/bwt2fmv.c | |
3559 M /branches/prog/bwa/bwtaln.c | |
3560 M /branches/prog/bwa/bwtaln.h | |
3561 M /branches/prog/bwa/bwtio.c | |
3562 | |
3563 * improve cmd-line interface | |
3564 * fix a bug in loading .sa | |
3565 * change default sa interval to 32 | |
3566 | |
3567 ------------------------------------------------------------------------ | |
3568 r319 | lh3 | 2008-05-30 10:31:37 -0400 (Fri, 30 May 2008) | 3 lines | |
3569 Changed paths: | |
3570 M /branches/prog/bwa/bwtaln.c | |
3571 | |
3572 * fix memory leak (I know that. Just a bit lazy) | |
3573 * change to another method to do 1-away alignment | |
3574 | |
3575 ------------------------------------------------------------------------ | |
3576 r318 | lh3 | 2008-05-30 09:21:49 -0400 (Fri, 30 May 2008) | 2 lines | |
3577 Changed paths: | |
3578 M /branches/prog/bwa/bwt.c | |
3579 M /branches/prog/bwa/bwt.h | |
3580 M /branches/prog/bwa/bwt2fmv.c | |
3581 M /branches/prog/bwa/bwtaln.c | |
3582 M /branches/prog/bwa/bwtaln.h | |
3583 M /branches/prog/bwa/main.c | |
3584 M /branches/prog/bwa/main.h | |
3585 | |
3586 best unique match is partially finished | |
3587 | |
3588 ------------------------------------------------------------------------ | |
3589 r317 | lh3 | 2008-05-30 06:33:28 -0400 (Fri, 30 May 2008) | 2 lines | |
3590 Changed paths: | |
3591 M /branches/prog/bwa/bwt.c | |
3592 M /branches/prog/bwa/bwt2fmv.c | |
3593 M /branches/prog/bwa/bwtaln.c | |
3594 M /branches/prog/bwa/bwtaln.h | |
3595 M /branches/prog/bwa/main.c | |
3596 M /branches/prog/bwa/main.h | |
3597 | |
3598 remove "ungapped" command and related codes | |
3599 | |
3600 ------------------------------------------------------------------------ | |
3601 r316 | lh3 | 2008-05-30 06:05:20 -0400 (Fri, 30 May 2008) | 2 lines | |
3602 Changed paths: | |
3603 M /branches/prog/bwa/Makefile | |
3604 M /branches/prog/bwa/bwt.c | |
3605 M /branches/prog/bwa/bwtaln.c | |
3606 M /branches/prog/bwa/bwtaln.h | |
3607 | |
3608 change variable name thick to width | |
3609 | |
3610 ------------------------------------------------------------------------ | |
3611 r315 | lh3 | 2008-05-29 19:06:13 -0400 (Thu, 29 May 2008) | 2 lines | |
3612 Changed paths: | |
3613 M /branches/prog/bwa/bntseq.c | |
3614 M /branches/prog/bwa/bwt.c | |
3615 M /branches/prog/bwa/bwt.h | |
3616 M /branches/prog/bwa/bwt2fmv.c | |
3617 M /branches/prog/bwa/bwtaln.c | |
3618 M /branches/prog/bwa/bwtaln.h | |
3619 M /branches/prog/bwa/bwtio.c | |
3620 M /branches/prog/bwa/main.c | |
3621 M /branches/prog/bwa/main.h | |
3622 M /branches/prog/bwa/pac2bwt.c | |
3623 | |
3624 revised algorithm for ungapped alignment. the old one can still be used. | |
3625 | |
3626 ------------------------------------------------------------------------ | |
3627 r314 | lh3 | 2008-05-29 16:36:11 -0400 (Thu, 29 May 2008) | 2 lines | |
3628 Changed paths: | |
3629 M /branches/prog/bwa/bwt2fmv.c | |
3630 M /branches/prog/bwa/bwt_gen/bwt_gen.c | |
3631 M /branches/prog/bwa/bwtio.c | |
3632 M /branches/prog/bwa/pac2bwt.c | |
3633 | |
3634 * make commands more independent, but ungapped does not work at the moment | |
3635 | |
3636 ------------------------------------------------------------------------ | |
3637 r313 | lh3 | 2008-05-29 15:56:14 -0400 (Thu, 29 May 2008) | 2 lines | |
3638 Changed paths: | |
3639 M /branches/prog/bwa/bwt_gen/bwt_gen.c | |
3640 | |
3641 little... | |
3642 | |
3643 ------------------------------------------------------------------------ | |
3644 r312 | lh3 | 2008-05-29 15:54:01 -0400 (Thu, 29 May 2008) | 3 lines | |
3645 Changed paths: | |
3646 M /branches/prog/bwa/bwt_gen/bwt_gen.c | |
3647 M /branches/prog/bwa/bwt_gen/bwt_gen.h | |
3648 | |
3649 * add CopyRight information from the original codes | |
3650 * do not dump .fmv files | |
3651 | |
3652 ------------------------------------------------------------------------ | |
3653 r311 | lh3 | 2008-05-29 15:44:36 -0400 (Thu, 29 May 2008) | 2 lines | |
3654 Changed paths: | |
3655 A /branches/prog/bwa/bwt_gen | |
3656 A /branches/prog/bwa/bwt_gen/Makefile | |
3657 A /branches/prog/bwa/bwt_gen/QSufSort.c | |
3658 A /branches/prog/bwa/bwt_gen/QSufSort.h | |
3659 A /branches/prog/bwa/bwt_gen/bwt_gen.c | |
3660 A /branches/prog/bwa/bwt_gen/bwt_gen.h | |
3661 | |
3662 codes from BWT-SW, for building BWT from packed file | |
3663 | |
3664 ------------------------------------------------------------------------ | |
3665 r310 | lh3 | 2008-05-28 17:03:35 -0400 (Wed, 28 May 2008) | 4 lines | |
3666 Changed paths: | |
3667 M /branches/prog/bwa/bwt.c | |
3668 M /branches/prog/bwa/bwt.h | |
3669 M /branches/prog/bwa/bwt2fmv.c | |
3670 M /branches/prog/bwa/bwtio.c | |
3671 M /branches/prog/bwa/main.c | |
3672 M /branches/prog/bwa/main.h | |
3673 | |
3674 * change OCC_INTERVAL to 0x40, which makes bwa twice as fast. | |
3675 * write Occ file as ".occ" as it is using a different interval from | |
3676 .fmv, the BWT-SW correspondance of .occ | |
3677 | |
3678 ------------------------------------------------------------------------ | |
3679 r309 | lh3 | 2008-05-28 11:39:37 -0400 (Wed, 28 May 2008) | 2 lines | |
3680 Changed paths: | |
3681 M /branches/prog/bwa/bwt.c | |
3682 M /branches/prog/bwa/bwt2fmv.c | |
3683 | |
3684 fix a bug | |
3685 | |
3686 ------------------------------------------------------------------------ | |
3687 r308 | lh3 | 2008-05-28 09:56:16 -0400 (Wed, 28 May 2008) | 4 lines | |
3688 Changed paths: | |
3689 M /branches/prog/bwa/bwt.c | |
3690 M /branches/prog/bwa/bwt2fmv.c | |
3691 | |
3692 add heuristics to improve the speed, but I have not tested whether the | |
3693 results are correct or not. | |
3694 | |
3695 | |
3696 ------------------------------------------------------------------------ | |
3697 r307 | lh3 | 2008-05-28 06:31:34 -0400 (Wed, 28 May 2008) | 5 lines | |
3698 Changed paths: | |
3699 M /branches/prog/bwa/bwt.c | |
3700 M /branches/prog/bwa/bwt2fmv.c | |
3701 M /branches/prog/bwa/bwtaln.c | |
3702 M /branches/prog/bwa/bwtaln.h | |
3703 M /branches/prog/bwa/main.c | |
3704 M /branches/prog/bwa/main.h | |
3705 | |
3706 * make ungapped alignment basically works... | |
3707 * but it is very slow in comparison to others... | |
3708 * also I need to improve the interface... | |
3709 * a lot of things to keep me busy today... | |
3710 | |
3711 ------------------------------------------------------------------------ | |
3712 r306 | lh3 | 2008-05-27 18:41:27 -0400 (Tue, 27 May 2008) | 3 lines | |
3713 Changed paths: | |
3714 M /branches/prog/bwa/bwt.c | |
3715 M /branches/prog/bwa/bwt.h | |
3716 M /branches/prog/bwa/bwtaln.c | |
3717 | |
3718 * remove recursion | |
3719 * fixed a bug in bwt_occ() | |
3720 | |
3721 ------------------------------------------------------------------------ | |
3722 r305 | lh3 | 2008-05-27 16:59:44 -0400 (Tue, 27 May 2008) | 5 lines | |
3723 Changed paths: | |
3724 M /branches/prog/bwa/bwt.c | |
3725 M /branches/prog/bwa/bwt.h | |
3726 M /branches/prog/bwa/bwtaln.c | |
3727 | |
3728 * bwa now tells whether a sequenced can be mapped with maximum allowed | |
3729 mismatches. ONLY ungapped. | |
3730 * this is a recursive version. I will remove recursion later. | |
3731 | |
3732 | |
3733 ------------------------------------------------------------------------ | |
3734 r304 | lh3 | 2008-05-27 09:12:17 -0400 (Tue, 27 May 2008) | 3 lines | |
3735 Changed paths: | |
3736 M /branches/prog/bwa/Makefile | |
3737 M /branches/prog/bwa/bwt.c | |
3738 M /branches/prog/bwa/bwt.h | |
3739 M /branches/prog/bwa/bwt2fmv.c | |
3740 A /branches/prog/bwa/bwtaln.c | |
3741 A /branches/prog/bwa/bwtaln.h | |
3742 M /branches/prog/bwa/bwtio.c | |
3743 M /branches/prog/bwa/main.c | |
3744 M /branches/prog/bwa/main.h | |
3745 M /branches/prog/bwa/utils.c | |
3746 | |
3747 * load .sa and .fmv files | |
3748 * exact alignment now works | |
3749 | |
3750 ------------------------------------------------------------------------ | |
3751 r303 | lh3 | 2008-05-27 06:33:38 -0400 (Tue, 27 May 2008) | 2 lines | |
3752 Changed paths: | |
3753 M /branches/prog/bwa/bntseq.c | |
3754 M /branches/prog/bwa/bwt.c | |
3755 M /branches/prog/bwa/bwtio.c | |
3756 M /branches/prog/bwa/utils.c | |
3757 M /branches/prog/bwa/utils.h | |
3758 | |
3759 add xassert and fix a bug | |
3760 | |
3761 ------------------------------------------------------------------------ | |
3762 r302 | lh3 | 2008-05-27 06:23:20 -0400 (Tue, 27 May 2008) | 2 lines | |
3763 Changed paths: | |
3764 M /branches/prog/bwa/Makefile | |
3765 M /branches/prog/bwa/bntseq.c | |
3766 M /branches/prog/bwa/bwt.c | |
3767 M /branches/prog/bwa/bwtio.c | |
3768 A /branches/prog/bwa/utils.c | |
3769 A /branches/prog/bwa/utils.h | |
3770 | |
3771 improve error message and error handling | |
3772 | |
3773 ------------------------------------------------------------------------ | |
3774 r301 | lh3 | 2008-05-27 05:37:51 -0400 (Tue, 27 May 2008) | 4 lines | |
3775 Changed paths: | |
3776 M /branches/prog/bwa/Makefile | |
3777 M /branches/prog/bwa/bwt.c | |
3778 M /branches/prog/bwa/bwt.h | |
3779 M /branches/prog/bwa/bwt2fmv.c | |
3780 A /branches/prog/bwa/bwtio.c | |
3781 M /branches/prog/bwa/main.c | |
3782 M /branches/prog/bwa/main.h | |
3783 | |
3784 * move I/O codes to bwtio.c | |
3785 * SA can be dumped and interestingly, it is identical to BWTSW | |
3786 * now, .fmv is still different from BWTSW | |
3787 | |
3788 ------------------------------------------------------------------------ | |
3789 r299 | lh3 | 2008-05-26 18:07:44 -0400 (Mon, 26 May 2008) | 2 lines | |
3790 Changed paths: | |
3791 M /branches/prog/bwa/Makefile | |
3792 M /branches/prog/bwa/bwt.c | |
3793 M /branches/prog/bwa/bwt.h | |
3794 M /branches/prog/bwa/bwt2fmv.c | |
3795 | |
3796 generate/retrieve SA and Occ | |
3797 | |
3798 ------------------------------------------------------------------------ | |
3799 r298 | lh3 | 2008-05-26 13:16:49 -0400 (Mon, 26 May 2008) | 3 lines | |
3800 Changed paths: | |
3801 M /branches/prog/bwa/bntseq.h | |
3802 M /branches/prog/bwa/bwt.c | |
3803 M /branches/prog/bwa/bwt.h | |
3804 M /branches/prog/bwa/bwt2fmv.c | |
3805 | |
3806 * retrieve occ value at any position | |
3807 * move bwt_cal_occ() to bwt.c | |
3808 | |
3809 ------------------------------------------------------------------------ | |
3810 r297 | lh3 | 2008-05-25 17:43:58 -0400 (Sun, 25 May 2008) | 6 lines | |
3811 Changed paths: | |
3812 M /branches/prog/bwa/Makefile | |
3813 A /branches/prog/bwa/bwt.c | |
3814 A /branches/prog/bwa/bwt.h | |
3815 A /branches/prog/bwa/bwt2fmv.c | |
3816 M /branches/prog/bwa/main.c | |
3817 M /branches/prog/bwa/main.h | |
3818 M /branches/prog/bwa/pac2bwt.c | |
3819 | |
3820 * add bwt2fmv. It works to some extend. However, I do not understand | |
3821 the purpose of some weird codes in BWT-SW. As a consequence, bwt2fmv | |
3822 could generate a file almost identical, but not exactly identical, to | |
3823 the .fmv file from BWT-SW. | |
3824 | |
3825 | |
3826 ------------------------------------------------------------------------ | |
3827 r296 | lh3 | 2008-05-24 18:35:02 -0400 (Sat, 24 May 2008) | 5 lines | |
3828 Changed paths: | |
3829 M /branches/prog/bwa/Makefile | |
3830 M /branches/prog/bwa/bntseq.c | |
3831 M /branches/prog/bwa/bntseq.h | |
3832 M /branches/prog/bwa/main.c | |
3833 M /branches/prog/bwa/main.h | |
3834 A /branches/prog/bwa/pac2bwt.c | |
3835 | |
3836 Burrows-Wheeler Transform now works. At least on one example, the | |
3837 current code generates the same BWT as BWT-SW. Kind of magical, I would | |
3838 say. :) | |
3839 | |
3840 | |
3841 ------------------------------------------------------------------------ | |
3842 r295 | lh3 | 2008-05-24 11:25:31 -0400 (Sat, 24 May 2008) | 3 lines | |
3843 Changed paths: | |
3844 A /branches/prog/bwa/Makefile | |
3845 M /branches/prog/bwa/bntseq.c | |
3846 A /branches/prog/bwa/main.c | |
3847 A /branches/prog/bwa/main.h | |
3848 | |
3849 * add Makefile and main.* | |
3850 * improve interface to fa2bns, a bit | |
3851 | |
3852 ------------------------------------------------------------------------ | |
3853 r293 | lh3 | 2008-05-24 10:57:03 -0400 (Sat, 24 May 2008) | 3 lines | |
3854 Changed paths: | |
3855 A /branches/prog/bwa | |
3856 A /branches/prog/bwa/bntseq.c | |
3857 A /branches/prog/bwa/bntseq.h | |
3858 A /branches/prog/bwa/seq.c | |
3859 A /branches/prog/bwa/seq.h | |
3860 | |
3861 * Burrow-Wheeler Alignment | |
3862 * initial codes | |
3863 | |
3864 ------------------------------------------------------------------------ |