1 ------------------------------------------------------------------------
2 r839 | lh3lh3 | 2010-11-18 17:30:11 -0500 (Thu, 18 Nov 2010) | 9 lines
4 M /trunk/samtools/bam2bcf.h
5 M /trunk/samtools/bam2bcf_indel.c
6 M /trunk/samtools/bamtk.c
8 * samtools-0.1.10-6 (r839)
10 * call MNPs without realignment because it seems to me that it is not
11 worthwhile to significantly slow down SNP calling.
13 * the result looks quite different from the previous version. I have
17 ------------------------------------------------------------------------
18 r838 | lh3lh3 | 2010-11-18 11:26:09 -0500 (Thu, 18 Nov 2010) | 2 lines
20 M /trunk/samtools/knetfile.c
22 Apply a patch by Rob Davis, which improves fault detection.
24 ------------------------------------------------------------------------
25 r836 | lh3lh3 | 2010-11-18 11:09:23 -0500 (Thu, 18 Nov 2010) | 3 lines
27 M /trunk/samtools/bam2bcf_indel.c
28 M /trunk/samtools/bamtk.c
31 * initiate MNP realignment when the MNP has at least 0.2% frequency (otherwise too slow)
33 ------------------------------------------------------------------------
34 r835 | lh3lh3 | 2010-11-18 00:25:13 -0500 (Thu, 18 Nov 2010) | 3 lines
36 M /trunk/samtools/bcftools/vcfutils.pl
38 * modify the filtering rule: also filter SNPs around filtered indels
41 ------------------------------------------------------------------------
42 r834 | lh3lh3 | 2010-11-17 23:13:52 -0500 (Wed, 17 Nov 2010) | 4 lines
44 M /trunk/samtools/bam2bcf.c
45 M /trunk/samtools/bam2bcf_indel.c
46 M /trunk/samtools/bamtk.c
48 * samtools-0.1.10-4 (r834)
49 * fixed a silly bug in printing MNP
50 * restrict to at most 1 alternative allele
52 ------------------------------------------------------------------------
53 r833 | lh3lh3 | 2010-11-17 21:58:58 -0500 (Wed, 17 Nov 2010) | 2 lines
55 M /trunk/samtools/bam2bcf.c
56 M /trunk/samtools/bamtk.c
58 fixed a bug in printing MNPs
60 ------------------------------------------------------------------------
61 r832 | lh3lh3 | 2010-11-17 21:47:20 -0500 (Wed, 17 Nov 2010) | 2 lines
63 M /trunk/samtools/bam2bcf_indel.c
64 M /trunk/samtools/bamtk.c
66 minor change to how seqQ is applied
68 ------------------------------------------------------------------------
69 r831 | lh3lh3 | 2010-11-17 21:41:12 -0500 (Wed, 17 Nov 2010) | 3 lines
71 M /trunk/samtools/bam2bcf.c
72 M /trunk/samtools/bam2bcf.h
73 M /trunk/samtools/bam2bcf_indel.c
74 M /trunk/samtools/bam_plcmd.c
75 M /trunk/samtools/bamtk.c
77 * samtools-0.1.10 (r831)
80 ------------------------------------------------------------------------
81 r829 | lh3lh3 | 2010-11-16 23:14:15 -0500 (Tue, 16 Nov 2010) | 2 lines
83 M /trunk/samtools/ChangeLog
84 M /trunk/samtools/NEWS
85 M /trunk/samtools/bamtk.c
87 Release samtools-0.1.10 (r829)
89 ------------------------------------------------------------------------
90 r828 | lh3lh3 | 2010-11-16 20:48:49 -0500 (Tue, 16 Nov 2010) | 2 lines
92 M /trunk/samtools/bamtk.c
94 update version information: samtools-0.1.9-20 (r828)
96 ------------------------------------------------------------------------
97 r827 | lh3lh3 | 2010-11-16 15:32:50 -0500 (Tue, 16 Nov 2010) | 2 lines
99 M /trunk/samtools/bcftools/call1.c
101 bcftools: allow to skip indels
103 ------------------------------------------------------------------------
104 r826 | lh3lh3 | 2010-11-16 14:11:58 -0500 (Tue, 16 Nov 2010) | 2 lines
106 M /trunk/samtools/bam_md.c
108 remove ZQ if both BQ and ZQ are present
110 ------------------------------------------------------------------------
111 r825 | lh3lh3 | 2010-11-16 13:51:33 -0500 (Tue, 16 Nov 2010) | 3 lines
113 M /trunk/samtools/bam2bcf_indel.c
114 M /trunk/samtools/bam_md.c
115 M /trunk/samtools/bamtk.c
116 M /trunk/samtools/samtools.1
118 * samtools-0.1.9-18 (r825)
119 * change the behaviour of calmd such that by default it does not change the base quality
121 ------------------------------------------------------------------------
122 r824 | lh3lh3 | 2010-11-15 23:31:53 -0500 (Mon, 15 Nov 2010) | 4 lines
124 M /trunk/samtools/bam_plcmd.c
125 M /trunk/samtools/bamtk.c
126 M /trunk/samtools/bcftools/call1.c
127 M /trunk/samtools/samtools.1
129 * samtools-0.1.9-17 (r824)
130 * added command line options to change the default parameters in indel calling
133 ------------------------------------------------------------------------
134 r823 | lh3lh3 | 2010-11-15 12:20:13 -0500 (Mon, 15 Nov 2010) | 3 lines
136 M /trunk/samtools/bam2bcf_indel.c
137 M /trunk/samtools/bam_md.c
138 M /trunk/samtools/bamtk.c
140 * samtools-0.1.9-r823
141 * the BQ tag is now 64 shifted, not 33 shifted
143 ------------------------------------------------------------------------
144 r822 | lh3lh3 | 2010-11-15 00:30:18 -0500 (Mon, 15 Nov 2010) | 3 lines
146 M /trunk/samtools/bam2bcf.c
147 M /trunk/samtools/bam2bcf.h
148 M /trunk/samtools/bamtk.c
149 M /trunk/samtools/bcftools/vcfutils.pl
150 M /trunk/samtools/misc/samtools.pl
152 * samtools-0.1.9-16 (r822)
153 * keep the raw depth because in indel calling, DP4 may be way off the true depth
155 ------------------------------------------------------------------------
156 r821 | lh3lh3 | 2010-11-13 01:18:31 -0500 (Sat, 13 Nov 2010) | 4 lines
158 M /trunk/samtools/bam_md.c
159 M /trunk/samtools/bamtk.c
161 * samtools-0.1.9-15 (r821)
163 * skip realignment if BQ is present
165 ------------------------------------------------------------------------
166 r820 | lh3lh3 | 2010-11-13 01:08:26 -0500 (Sat, 13 Nov 2010) | 3 lines
168 M /trunk/samtools/bam2bcf_indel.c
169 M /trunk/samtools/bamtk.c
171 * samtools-0.1.9-14 (r820)
172 * penalize reads with excessive differences in indel calling
174 ------------------------------------------------------------------------
175 r819 | lh3lh3 | 2010-11-12 21:36:27 -0500 (Fri, 12 Nov 2010) | 3 lines
177 M /trunk/samtools/bam_maqcns.c
178 M /trunk/samtools/bamtk.c
180 * samtools-0.1.9-13 (r819)
181 * fixed a bug in pileup given refskip
183 ------------------------------------------------------------------------
184 r818 | lh3lh3 | 2010-11-12 13:04:53 -0500 (Fri, 12 Nov 2010) | 3 lines
186 M /trunk/samtools/bam2bcf_indel.c
187 M /trunk/samtools/bamtk.c
190 * for indel calling, do two rounds of probabilistic realignments
192 ------------------------------------------------------------------------
193 r817 | lh3lh3 | 2010-11-11 20:04:07 -0500 (Thu, 11 Nov 2010) | 3 lines
195 M /trunk/samtools/bam2bcf_indel.c
196 M /trunk/samtools/bamtk.c
197 M /trunk/samtools/bcftools/vcfutils.pl
199 * samtools-0.1.19-11 (r817)
200 * only initiate indel calling when 0.2% of reads contain a gap
202 ------------------------------------------------------------------------
203 r816 | lh3lh3 | 2010-11-11 01:22:59 -0500 (Thu, 11 Nov 2010) | 7 lines
205 M /trunk/samtools/bam2bcf_indel.c
206 M /trunk/samtools/bamtk.c
208 * samtools-0.1.9-10 (r816)
210 * I know why the forward method fails. it is because of zero base
211 qualities. when that is fixed, the forward method seems to give
212 better results than Viterbi, as it should be. I am tired...
215 ------------------------------------------------------------------------
216 r815 | lh3lh3 | 2010-11-11 00:57:15 -0500 (Thu, 11 Nov 2010) | 2 lines
218 M /trunk/samtools/ChangeLog
219 M /trunk/samtools/bam2bcf_indel.c
221 effectively revert to the viterbi version. The forward realignment gives too many false positives.
223 ------------------------------------------------------------------------
224 r814 | lh3lh3 | 2010-11-11 00:18:02 -0500 (Thu, 11 Nov 2010) | 4 lines
226 M /trunk/samtools/bam2bcf_indel.c
227 M /trunk/samtools/bam_md.c
228 M /trunk/samtools/bam_plcmd.c
229 M /trunk/samtools/bamtk.c
231 * samtools-0.1.9-9 (r810)
232 * use forward, instead of viterbi, for realignment
233 * realignment is now quality aware
235 ------------------------------------------------------------------------
236 r813 | lh3lh3 | 2010-11-10 22:45:24 -0500 (Wed, 10 Nov 2010) | 2 lines
238 M /trunk/samtools/bam2bcf_indel.c
239 M /trunk/samtools/kprobaln.c
240 M /trunk/samtools/kprobaln.h
242 * prepare to replace kaln with kprobaln in realignment
244 ------------------------------------------------------------------------
245 r812 | lh3lh3 | 2010-11-10 17:28:50 -0500 (Wed, 10 Nov 2010) | 2 lines
247 M /trunk/samtools/bcftools/bcf.c
251 ------------------------------------------------------------------------
252 r811 | lh3lh3 | 2010-11-10 16:54:46 -0500 (Wed, 10 Nov 2010) | 2 lines
254 M /trunk/samtools/bcftools/bcf.c
255 M /trunk/samtools/bcftools/bcf.h
257 use zlib for direct reading when BCF_LITE is in use
259 ------------------------------------------------------------------------
260 r810 | lh3lh3 | 2010-11-10 16:32:13 -0500 (Wed, 10 Nov 2010) | 3 lines
262 M /trunk/samtools/bam2bcf_indel.c
264 * do not use reads containing too many mismatches for indel calling
265 * fixed a trivial bug in case of multi-allelic indels
267 ------------------------------------------------------------------------
268 r809 | lh3lh3 | 2010-11-10 13:23:02 -0500 (Wed, 10 Nov 2010) | 3 lines
270 M /trunk/samtools/bam2bcf.c
271 M /trunk/samtools/bam2bcf_indel.c
272 M /trunk/samtools/bam_plcmd.c
273 M /trunk/samtools/bamtk.c
275 * samtools-0.1.9-8 (r809)
276 * fixed a bug in the indel caller
278 ------------------------------------------------------------------------
279 r808 | lh3lh3 | 2010-11-10 12:24:10 -0500 (Wed, 10 Nov 2010) | 2 lines
281 M /trunk/samtools/Makefile
283 minor change to makefile
285 ------------------------------------------------------------------------
286 r807 | lh3lh3 | 2010-11-10 12:10:21 -0500 (Wed, 10 Nov 2010) | 4 lines
288 M /trunk/samtools/Makefile
289 M /trunk/samtools/bam2bcf.h
290 M /trunk/samtools/bam2bcf_indel.c
291 M /trunk/samtools/bam_plcmd.c
292 M /trunk/samtools/bamtk.c
293 M /trunk/samtools/bcftools/vcfutils.pl
295 * samtools-0.1.9-8 (r807)
296 * collect indel candidates only from specified platforms (@RG-PL)
297 * merge varFilter and filter4vcf in vcfutils.pl
299 ------------------------------------------------------------------------
300 r806 | lh3lh3 | 2010-11-09 22:05:46 -0500 (Tue, 09 Nov 2010) | 2 lines
302 M /trunk/samtools/bcftools/call1.c
303 M /trunk/samtools/bcftools/prob1.c
304 M /trunk/samtools/bcftools/prob1.h
306 bcftools: compute equal-tail (Bayesian) credible interval
308 ------------------------------------------------------------------------
309 r805 | lh3lh3 | 2010-11-09 16:28:39 -0500 (Tue, 09 Nov 2010) | 2 lines
311 M /trunk/samtools/bcftools/vcfutils.pl
313 added a double-hit filter to avoid overestimated indel likelihood
315 ------------------------------------------------------------------------
316 r804 | lh3lh3 | 2010-11-09 14:12:06 -0500 (Tue, 09 Nov 2010) | 3 lines
318 M /trunk/samtools/bam2bcf_indel.c
319 M /trunk/samtools/bamtk.c
321 * samtools-0.1.9-7 (r804)
322 * fixed a bug in the gap caller
324 ------------------------------------------------------------------------
325 r803 | lh3lh3 | 2010-11-09 10:45:33 -0500 (Tue, 09 Nov 2010) | 4 lines
327 M /trunk/samtools/bam2bcf.c
328 M /trunk/samtools/bam2bcf_indel.c
329 M /trunk/samtools/bamtk.c
330 M /trunk/samtools/bcftools/bcf.c
331 M /trunk/samtools/bcftools/bcf.h
332 M /trunk/samtools/bcftools/prob1.c
334 * samtools-0.1.9-6 (r803)
335 * mpileup: apply homopolymer correction when calculating GL, instead of before
336 * bcftools: apply a different prior to indels
338 ------------------------------------------------------------------------
339 r802 | lh3lh3 | 2010-11-08 23:53:15 -0500 (Mon, 08 Nov 2010) | 3 lines
341 M /trunk/samtools/bam2bcf.c
342 M /trunk/samtools/bamtk.c
344 * samtools-0.1.9-5 (r802)
345 * relax tandem penalty. this will be made a command-line option in future.
347 ------------------------------------------------------------------------
348 r801 | lh3lh3 | 2010-11-08 23:35:52 -0500 (Mon, 08 Nov 2010) | 3 lines
350 M /trunk/samtools/bam2bcf.c
351 M /trunk/samtools/bamtk.c
353 * samtools-0.1.9-4 (r801)
354 * fixed a minor issue in printing indel VCF
356 ------------------------------------------------------------------------
357 r800 | lh3lh3 | 2010-11-08 15:28:14 -0500 (Mon, 08 Nov 2010) | 2 lines
359 M /trunk/samtools/bam2bcf_indel.c
360 M /trunk/samtools/bcftools/vcfutils.pl
362 fixed another silly bug in mpileup's indel caller
364 ------------------------------------------------------------------------
365 r799 | lh3lh3 | 2010-11-08 14:28:27 -0500 (Mon, 08 Nov 2010) | 2 lines
367 M /trunk/samtools/bam2bcf.c
369 fixed a silly bug in the indel caller
371 ------------------------------------------------------------------------
372 r798 | lh3lh3 | 2010-11-08 14:07:33 -0500 (Mon, 08 Nov 2010) | 2 lines
374 M /trunk/samtools/ChangeLog
375 M /trunk/samtools/sam_view.c
376 M /trunk/samtools/samtools.1
378 Incorporate patches by Marcel Martin for read counting.
380 ------------------------------------------------------------------------
381 r797 | lh3lh3 | 2010-11-08 13:39:52 -0500 (Mon, 08 Nov 2010) | 3 lines
383 M /trunk/samtools/bam2bcf.c
384 M /trunk/samtools/bam2bcf.h
385 M /trunk/samtools/bam2bcf_indel.c
386 M /trunk/samtools/bam_plcmd.c
387 M /trunk/samtools/bamtk.c
389 * samtools-0.1.9-2 (r797)
390 * mpileup: indel calling seems to be working
392 ------------------------------------------------------------------------
393 r796 | lh3lh3 | 2010-11-08 10:54:46 -0500 (Mon, 08 Nov 2010) | 2 lines
395 M /trunk/samtools/bam2bcf.c
396 M /trunk/samtools/bam2bcf.h
397 M /trunk/samtools/bam2bcf_indel.c
398 M /trunk/samtools/bam_plcmd.c
399 M /trunk/samtools/kaln.c
401 indel calling is apparently working, but more information needs to be collected
403 ------------------------------------------------------------------------
404 r795 | lh3lh3 | 2010-11-08 00:39:18 -0500 (Mon, 08 Nov 2010) | 2 lines
406 M /trunk/samtools/bam2bcf.c
407 M /trunk/samtools/bam2bcf_indel.c
409 fixed a few bugs in the indel caller. Probably there are more.
411 ------------------------------------------------------------------------
412 r794 | lh3lh3 | 2010-11-07 22:23:16 -0500 (Sun, 07 Nov 2010) | 2 lines
414 M /trunk/samtools/Makefile
415 M /trunk/samtools/bam.h
416 M /trunk/samtools/bam2bcf.c
417 M /trunk/samtools/bam2bcf.h
418 A /trunk/samtools/bam2bcf_indel.c
419 M /trunk/samtools/bam_plcmd.c
420 M /trunk/samtools/kaln.c
421 M /trunk/samtools/kaln.h
423 prepare for the indel caller. It is not ready yet.
425 ------------------------------------------------------------------------
426 r793 | lh3lh3 | 2010-11-05 11:28:23 -0400 (Fri, 05 Nov 2010) | 2 lines
428 M /trunk/samtools/bam2bcf.c
429 M /trunk/samtools/bam2bcf.h
430 M /trunk/samtools/bam_plcmd.c
432 Revert to r790. The recent changes are not good...
434 ------------------------------------------------------------------------
435 r792 | lh3lh3 | 2010-11-05 00:19:14 -0400 (Fri, 05 Nov 2010) | 6 lines
437 M /trunk/samtools/bam2bcf.c
438 M /trunk/samtools/bam2bcf.h
439 M /trunk/samtools/bam_plcmd.c
441 * this revision is UNSTABLE
443 * indel caller seems working, but it is very insensitive and has
444 several things I do not quite understand.
447 ------------------------------------------------------------------------
448 r791 | lh3lh3 | 2010-11-04 22:58:43 -0400 (Thu, 04 Nov 2010) | 2 lines
450 M /trunk/samtools/bam2bcf.c
451 M /trunk/samtools/bam2bcf.h
452 M /trunk/samtools/bam_plcmd.c
454 for backup. no effective changes
456 ------------------------------------------------------------------------
457 r790 | lh3lh3 | 2010-11-03 15:51:24 -0400 (Wed, 03 Nov 2010) | 2 lines
459 M /trunk/samtools/bcftools/vcfutils.pl
460 M /trunk/samtools/kprobaln.c
462 fixed a minor problem in the example coming with kprobaln.c
464 ------------------------------------------------------------------------
465 r789 | lh3lh3 | 2010-11-02 15:41:27 -0400 (Tue, 02 Nov 2010) | 4 lines
467 M /trunk/samtools/Makefile
468 M /trunk/samtools/bam_md.c
469 M /trunk/samtools/kaln.c
470 M /trunk/samtools/kaln.h
471 A /trunk/samtools/kprobaln.c
472 A /trunk/samtools/kprobaln.h
474 Separate kaln and kprobaln as I am preparing further changes. At
475 present, the results should be identical to the previous.
478 ------------------------------------------------------------------------
479 r788 | petulda | 2010-11-02 12:19:04 -0400 (Tue, 02 Nov 2010) | 1 line
481 M /trunk/samtools/bam_plcmd.c
483 Added -b option: read file names from a file
484 ------------------------------------------------------------------------
485 r787 | lh3lh3 | 2010-10-29 23:17:22 -0400 (Fri, 29 Oct 2010) | 7 lines
487 M /trunk/samtools/bam.h
488 M /trunk/samtools/bam_pileup.c
489 M /trunk/samtools/bam_plcmd.c
490 M /trunk/samtools/bamtk.c
492 * samtools-0.1.9-2 (r787)
494 * Allow to set a maximum per-sample depth to reduce memory. However,
495 BAQ computation is still applied to every read. The speed is not
499 ------------------------------------------------------------------------
500 r786 | lh3lh3 | 2010-10-29 12:10:40 -0400 (Fri, 29 Oct 2010) | 3 lines
502 M /trunk/samtools/bam2bcf.c
503 M /trunk/samtools/bam2bcf.h
504 M /trunk/samtools/bam_plcmd.c
505 M /trunk/samtools/bamtk.c
506 M /trunk/samtools/bcftools/bcf.c
507 M /trunk/samtools/bcftools/vcf.c
509 * samtools-0.1.9-1 (r786)
510 * samtools: optionally perform exact test for each sample
512 ------------------------------------------------------------------------
513 r785 | lh3lh3 | 2010-10-29 09:42:25 -0400 (Fri, 29 Oct 2010) | 2 lines
515 M /trunk/samtools/bam2bcf.c
516 M /trunk/samtools/bam2bcf.h
517 M /trunk/samtools/bam_plcmd.c
518 M /trunk/samtools/bcftools/bcf.c
520 Optionally output "DP", the individual read depth
522 ------------------------------------------------------------------------
523 r784 | lh3lh3 | 2010-10-27 23:10:27 -0400 (Wed, 27 Oct 2010) | 2 lines
525 M /trunk/samtools/samtools.1
527 acknowledge Petr and John who have greatly contributed to the project.
529 ------------------------------------------------------------------------
530 r783 | lh3lh3 | 2010-10-27 22:47:47 -0400 (Wed, 27 Oct 2010) | 2 lines
532 M /trunk/samtools/ChangeLog
533 M /trunk/samtools/NEWS
534 M /trunk/samtools/bamtk.c
535 M /trunk/samtools/samtools.1
537 Release samtools-0.1.9 (r783)
539 ------------------------------------------------------------------------
540 r782 | lh3lh3 | 2010-10-27 19:58:54 -0400 (Wed, 27 Oct 2010) | 2 lines
542 M /trunk/samtools/bam_plcmd.c
544 fixed a silly bug in pileup
546 ------------------------------------------------------------------------
547 r781 | lh3lh3 | 2010-10-27 14:39:48 -0400 (Wed, 27 Oct 2010) | 5 lines
549 M /trunk/samtools/ChangeLog
550 M /trunk/samtools/bam_plcmd.c
551 M /trunk/samtools/bam_sort.c
552 M /trunk/samtools/bamtk.c
553 M /trunk/samtools/samtools.1
555 * samtools-0.1.8-22 (r781)
556 * made BAQ the default behavior of mpileup
558 * in merge, force to exit given inconsistent header when "-R" is not in use.
560 ------------------------------------------------------------------------
561 r780 | lh3lh3 | 2010-10-27 11:01:11 -0400 (Wed, 27 Oct 2010) | 3 lines
563 M /trunk/samtools/bam.h
564 M /trunk/samtools/bam_plcmd.c
565 M /trunk/samtools/bamtk.c
567 * samtools-0.1.8-21 (r780)
568 * minor speedup to pileup
570 ------------------------------------------------------------------------
571 r779 | lh3lh3 | 2010-10-27 09:58:56 -0400 (Wed, 27 Oct 2010) | 2 lines
573 M /trunk/samtools/bam_pileup.c
574 M /trunk/samtools/bam_plcmd.c
575 M /trunk/samtools/examples/toy.sam
577 improve pileup a little bit
579 ------------------------------------------------------------------------
580 r778 | lh3lh3 | 2010-10-27 00:14:43 -0400 (Wed, 27 Oct 2010) | 3 lines
582 M /trunk/samtools/bam.h
583 M /trunk/samtools/bam_pileup.c
584 M /trunk/samtools/bam_plcmd.c
585 M /trunk/samtools/bam_tview.c
586 M /trunk/samtools/bamtk.c
588 * samtools-0.1.8-20 (r778)
589 * speed up pileup, although I do not know how much is the improvement
591 ------------------------------------------------------------------------
592 r777 | lh3lh3 | 2010-10-26 17:26:04 -0400 (Tue, 26 Oct 2010) | 3 lines
594 M /trunk/samtools/bam_maqcns.c
595 M /trunk/samtools/bam_maqcns.h
596 M /trunk/samtools/bam_plcmd.c
597 M /trunk/samtools/bamtk.c
598 M /trunk/samtools/examples/Makefile
600 * samtools-0.1.8-19 (r777)
601 * integrate mpileup features to pileup: min_baseQ, capQ, prob_realn, paired-only and biased prior
603 ------------------------------------------------------------------------
604 r776 | lh3lh3 | 2010-10-26 15:27:46 -0400 (Tue, 26 Oct 2010) | 2 lines
606 M /trunk/samtools/bam_md.c
608 remove local realignment (probabilistic realignment is still there)
610 ------------------------------------------------------------------------
611 r774 | jmarshall | 2010-10-21 06:52:38 -0400 (Thu, 21 Oct 2010) | 3 lines
613 M /trunk/samtools/sam_view.c
615 Add the relevant filename or region to error messages, and cause a failure
616 exit status where appropriate. Based on a patch provided by Marcel Martin.
618 ------------------------------------------------------------------------
619 r773 | lh3lh3 | 2010-10-19 19:44:31 -0400 (Tue, 19 Oct 2010) | 3 lines
621 M /trunk/samtools/examples/toy.sam
622 M /trunk/samtools/kaln.c
624 * Minor code changes. No real effect.
625 * change quality to 30 in toy.sam
627 ------------------------------------------------------------------------
628 r772 | lh3lh3 | 2010-10-18 23:40:13 -0400 (Mon, 18 Oct 2010) | 2 lines
630 M /trunk/samtools/examples/toy.fa
631 M /trunk/samtools/examples/toy.sam
633 added another toy example
635 ------------------------------------------------------------------------
636 r771 | lh3lh3 | 2010-10-13 23:32:12 -0400 (Wed, 13 Oct 2010) | 2 lines
638 M /trunk/samtools/bcftools/call1.c
639 M /trunk/samtools/bcftools/ld.c
640 M /trunk/samtools/bcftools/vcfutils.pl
642 improve the LD statistics
644 ------------------------------------------------------------------------
645 r770 | lh3lh3 | 2010-10-12 23:49:26 -0400 (Tue, 12 Oct 2010) | 3 lines
647 M /trunk/samtools/bcftools/call1.c
648 M /trunk/samtools/bcftools/vcfutils.pl
650 * a minor fix to the -L option
651 * add ldstats to vcfutils.pl
653 ------------------------------------------------------------------------
654 r769 | lh3lh3 | 2010-10-12 15:51:57 -0400 (Tue, 12 Oct 2010) | 2 lines
656 M /trunk/samtools/bcftools/bcf.c
660 ------------------------------------------------------------------------
661 r768 | lh3lh3 | 2010-10-12 15:49:06 -0400 (Tue, 12 Oct 2010) | 2 lines
663 M /trunk/samtools/bcftools/Makefile
664 A /trunk/samtools/bcftools/ld.c
666 forget to add the key file
668 ------------------------------------------------------------------------
669 r767 | lh3lh3 | 2010-10-12 15:48:46 -0400 (Tue, 12 Oct 2010) | 4 lines
671 M /trunk/samtools/bcftools/Makefile
672 M /trunk/samtools/bcftools/bcf.c
673 M /trunk/samtools/bcftools/bcf.h
674 M /trunk/samtools/bcftools/call1.c
675 M /trunk/samtools/bcftools/prob1.c
676 M /trunk/samtools/bcftools/vcfutils.pl
678 * vcfutils.pl: fixed a typo in help message
679 * added APIs: bcf_append_info() and bcf_cpy()
680 * calculate adjacent LD
682 ------------------------------------------------------------------------
683 r766 | lh3lh3 | 2010-10-11 11:06:40 -0400 (Mon, 11 Oct 2010) | 2 lines
685 M /trunk/samtools/bcftools/vcfutils.pl
687 added filter for samtools/bcftools genetated VCFs
689 ------------------------------------------------------------------------
690 r765 | lh3lh3 | 2010-10-05 14:05:18 -0400 (Tue, 05 Oct 2010) | 3 lines
692 M /trunk/samtools/bcftools/vcfutils.pl
693 M /trunk/samtools/kaln.c
695 * removed a comment line in kaln.c
696 * vcfutils.pl fillac works when GT is not the first field
698 ------------------------------------------------------------------------
699 r764 | petulda | 2010-10-05 08:59:36 -0400 (Tue, 05 Oct 2010) | 1 line
701 A /trunk/samtools/bcftools/bcf-fix.pl
703 Convert VCF output of "bcftools view -bgcv" to a valid VCF file
704 ------------------------------------------------------------------------
705 r763 | lh3lh3 | 2010-10-02 22:51:03 -0400 (Sat, 02 Oct 2010) | 4 lines
707 M /trunk/samtools/bam_plcmd.c
708 M /trunk/samtools/bamtk.c
709 A /trunk/samtools/bcftools/bcftools.1
710 M /trunk/samtools/bcftools/call1.c
711 M /trunk/samtools/samtools.1
713 * samtools-0.1.8-18 (r763)
714 * added bcftools manual page
715 * minor fix to mpileup and view command lines
717 ------------------------------------------------------------------------
718 r762 | lh3lh3 | 2010-10-02 21:46:25 -0400 (Sat, 02 Oct 2010) | 3 lines
720 M /trunk/samtools/bcftools/bcf.c
721 M /trunk/samtools/bcftools/call1.c
722 M /trunk/samtools/bcftools/vcfutils.pl
724 * vcfutils.pl qstats: calculate marginal ts/tv
725 * allow to call genotypes at variant sites
727 ------------------------------------------------------------------------
728 r761 | lh3lh3 | 2010-10-01 00:29:55 -0400 (Fri, 01 Oct 2010) | 3 lines
730 M /trunk/samtools/kaln.c
731 M /trunk/samtools/misc/HmmGlocal.java
733 I am changing the gap open probability back to 0.001. It seems that
734 being conservative here is a good thing...
736 ------------------------------------------------------------------------
737 r760 | lh3lh3 | 2010-10-01 00:11:27 -0400 (Fri, 01 Oct 2010) | 5 lines
739 M /trunk/samtools/bamtk.c
740 M /trunk/samtools/kaln.c
741 A /trunk/samtools/misc/HmmGlocal.java
743 * samtools-0.1.8-17 (r760)
744 * the default gap open penalty is too small (a typo)
745 * added comments on hmm_realn
746 * Java implementation
748 ------------------------------------------------------------------------
749 r759 | lh3lh3 | 2010-09-30 10:12:54 -0400 (Thu, 30 Sep 2010) | 2 lines
751 M /trunk/samtools/bamtk.c
753 mark samtools-0.1.8-16 (r759)
755 ------------------------------------------------------------------------
756 r758 | lh3lh3 | 2010-09-30 10:12:02 -0400 (Thu, 30 Sep 2010) | 2 lines
758 M /trunk/samtools/kaln.c
760 round to the nearest integer
762 ------------------------------------------------------------------------
763 r757 | lh3lh3 | 2010-09-28 17:16:43 -0400 (Tue, 28 Sep 2010) | 4 lines
765 M /trunk/samtools/kaln.c
767 I was trying to accelerate ka_prob_glocal() as this will be the
768 bottleneck. After an hour, the only gain is to change division to
769 multiplication. OK. I will stop.
771 ------------------------------------------------------------------------
772 r756 | lh3lh3 | 2010-09-28 16:57:49 -0400 (Tue, 28 Sep 2010) | 2 lines
774 M /trunk/samtools/kaln.c
776 this is interesting. multiplication is much faster than division, at least on my Mac
778 ------------------------------------------------------------------------
779 r755 | lh3lh3 | 2010-09-28 16:19:13 -0400 (Tue, 28 Sep 2010) | 2 lines
781 M /trunk/samtools/kaln.c
785 ------------------------------------------------------------------------
786 r754 | lh3lh3 | 2010-09-28 15:44:16 -0400 (Tue, 28 Sep 2010) | 2 lines
788 M /trunk/samtools/bam_md.c
789 M /trunk/samtools/bam_plcmd.c
790 M /trunk/samtools/kaln.c
792 prob_realn() seems working!
794 ------------------------------------------------------------------------
795 r753 | lh3lh3 | 2010-09-28 12:48:23 -0400 (Tue, 28 Sep 2010) | 2 lines
797 M /trunk/samtools/kaln.c
801 ------------------------------------------------------------------------
802 r752 | lh3lh3 | 2010-09-28 12:47:41 -0400 (Tue, 28 Sep 2010) | 2 lines
804 M /trunk/samtools/kaln.c
805 M /trunk/samtools/kaln.h
807 Convert phredQ to probabilities
809 ------------------------------------------------------------------------
810 r751 | lh3lh3 | 2010-09-28 12:32:08 -0400 (Tue, 28 Sep 2010) | 2 lines
812 M /trunk/samtools/kaln.c
813 M /trunk/samtools/kaln.h
815 Implement the glocal HMM; discard the extention HMM
817 ------------------------------------------------------------------------
818 r750 | lh3lh3 | 2010-09-28 00:06:11 -0400 (Tue, 28 Sep 2010) | 2 lines
820 M /trunk/samtools/kaln.c
822 improve numerical stability
824 ------------------------------------------------------------------------
825 r749 | lh3lh3 | 2010-09-27 23:27:54 -0400 (Mon, 27 Sep 2010) | 2 lines
827 M /trunk/samtools/kaln.c
831 ------------------------------------------------------------------------
832 r748 | lh3lh3 | 2010-09-27 23:17:16 -0400 (Mon, 27 Sep 2010) | 2 lines
834 M /trunk/samtools/kaln.c
836 fixed a bug in banded DP
838 ------------------------------------------------------------------------
839 r747 | lh3lh3 | 2010-09-27 23:05:12 -0400 (Mon, 27 Sep 2010) | 3 lines
841 M /trunk/samtools/kaln.c
843 * fixed that weird issue.
844 * the banded version is NOT working
846 ------------------------------------------------------------------------
847 r746 | lh3lh3 | 2010-09-27 22:57:05 -0400 (Mon, 27 Sep 2010) | 2 lines
849 M /trunk/samtools/kaln.c
851 More comments. This version seems working, but something is a little weird...
853 ------------------------------------------------------------------------
854 r745 | lh3lh3 | 2010-09-27 17:21:40 -0400 (Mon, 27 Sep 2010) | 6 lines
856 M /trunk/samtools/kaln.c
858 A little code cleanup. Now the forward and backback algorithms give
859 nearly identical P(x), which means both are close to the correct
860 forms. However, I have only tested on toy examples. Minor errors in
861 the implementation may not be obvious.
864 ------------------------------------------------------------------------
865 r744 | lh3lh3 | 2010-09-27 16:55:15 -0400 (Mon, 27 Sep 2010) | 2 lines
867 M /trunk/samtools/bam_plcmd.c
868 M /trunk/samtools/bam_sort.c
869 M /trunk/samtools/kaln.c
870 M /trunk/samtools/kaln.h
874 ------------------------------------------------------------------------
875 r743 | jmarshall | 2010-09-27 08:19:06 -0400 (Mon, 27 Sep 2010) | 6 lines
877 M /trunk/samtools/bam_sort.c
879 Abort if merge -h's INH.SAM cannot be opened, just as we abort
880 if any of the IN#.BAM input files cannot be opened.
882 Also propagate any error indication returned by bam_merge_core()
883 to samtools merge's exit status.
885 ------------------------------------------------------------------------
886 r741 | jmarshall | 2010-09-24 11:08:24 -0400 (Fri, 24 Sep 2010) | 5 lines
888 M /trunk/samtools/bam_index.c
890 Use bam_validate1() to detect garbage records in the event of a corrupt
891 BAI index file that causes a bam_seek() to an invalid position. At most
892 one record (namely, the bam_iter_read terminator) is tested per bam_fetch()
893 call, so the cost is insignificant in the normal case.
895 ------------------------------------------------------------------------
896 r740 | jmarshall | 2010-09-24 11:00:19 -0400 (Fri, 24 Sep 2010) | 2 lines
898 M /trunk/samtools/bam.c
899 M /trunk/samtools/bam.h
903 ------------------------------------------------------------------------
904 r739 | lh3lh3 | 2010-09-22 12:07:50 -0400 (Wed, 22 Sep 2010) | 3 lines
906 M /trunk/samtools/bam_md.c
907 M /trunk/samtools/bamtk.c
909 * samtools-0.1.8-15 (r379)
910 * allow to change capQ parameter in calmd
912 ------------------------------------------------------------------------
913 r738 | jmarshall | 2010-09-22 11:15:33 -0400 (Wed, 22 Sep 2010) | 13 lines
915 M /trunk/samtools/bam_index.c
916 M /trunk/samtools/sam_view.c
918 When bam_read1() returns an error (return value <= -2), propagate that error
919 to bam_iter_read()'s own return value. Similarly, also propagate it up to
920 bam_fetch()'s return value. Previously bam_fetch() always returned 0, and
921 callers ignored its return value anyway. With this change, 0 continues to
922 indicate success, while <= -2 (which can be written as < 0, as -1 is never
923 returned) indicates corrupted input.
925 bam_iter_read() ought also to propagate errors returned by bam_seek().
927 main_samview() can now print an error message and fail when bam_fetch()
928 detects that a .bai index file is corrupted or otherwise does not correspond
929 to the .bam file it is being used with.
931 ------------------------------------------------------------------------
932 r737 | jmarshall | 2010-09-22 10:47:42 -0400 (Wed, 22 Sep 2010) | 3 lines
934 M /trunk/samtools/bam_index.c
936 0 is a successful return value from bam_read1(). (In practice, it never
937 returns 0 anyway; but all the other callers treat 0 as successful.)
939 ------------------------------------------------------------------------
940 r736 | lh3lh3 | 2010-09-20 17:43:08 -0400 (Mon, 20 Sep 2010) | 2 lines
942 M /trunk/samtools/bam.h
943 M /trunk/samtools/bam_index.c
944 M /trunk/samtools/bam_sort.c
946 * merge files region-by-region. work on small examples but more tests are needed.
948 ------------------------------------------------------------------------
949 r735 | lh3lh3 | 2010-09-20 16:56:24 -0400 (Mon, 20 Sep 2010) | 2 lines
951 M /trunk/samtools/bcftools/vcfutils.pl
953 improve qstats by checking the alleles as well
955 ------------------------------------------------------------------------
956 r734 | lh3lh3 | 2010-09-17 18:12:13 -0400 (Fri, 17 Sep 2010) | 2 lines
958 M /trunk/samtools/bcftools/vcfutils.pl
960 convert UCSC SNP SQL dump to VCF
962 ------------------------------------------------------------------------
963 r733 | lh3lh3 | 2010-09-17 13:02:11 -0400 (Fri, 17 Sep 2010) | 2 lines
965 M /trunk/samtools/bcftools/vcfutils.pl
969 ------------------------------------------------------------------------
970 r732 | lh3lh3 | 2010-09-17 10:11:37 -0400 (Fri, 17 Sep 2010) | 3 lines
972 M /trunk/samtools/bcftools/Makefile
973 M /trunk/samtools/bcftools/bcf.c
974 M /trunk/samtools/bcftools/bcf.h
975 M /trunk/samtools/bcftools/vcf.c
978 * VCF->BCF is not possible without knowing the sequence dictionary before hand...
980 ------------------------------------------------------------------------
981 r731 | lh3lh3 | 2010-09-17 09:15:53 -0400 (Fri, 17 Sep 2010) | 2 lines
983 M /trunk/samtools/bam2bcf.c
984 M /trunk/samtools/bcftools/bcf.c
985 M /trunk/samtools/bcftools/bcf.h
986 M /trunk/samtools/bcftools/bcfutils.c
987 M /trunk/samtools/bcftools/call1.c
988 M /trunk/samtools/bcftools/vcf.c
990 * put n_smpl to "bcf1_t" to simplify API a little
992 ------------------------------------------------------------------------
993 r730 | lh3lh3 | 2010-09-16 21:36:01 -0400 (Thu, 16 Sep 2010) | 2 lines
995 M /trunk/samtools/bcftools/bcf.h
996 M /trunk/samtools/bcftools/call1.c
997 M /trunk/samtools/bcftools/index.c
999 fixed a bug in indexing
1001 ------------------------------------------------------------------------
1002 r729 | lh3lh3 | 2010-09-16 16:54:48 -0400 (Thu, 16 Sep 2010) | 3 lines
1004 M /trunk/samtools/bam.c
1005 M /trunk/samtools/bam_md.c
1006 M /trunk/samtools/bam_pileup.c
1008 * fixed a bug in capQ
1009 * valgrind identifies a use of uninitialised value, but I have not fixed it.
1011 ------------------------------------------------------------------------
1012 r728 | lh3lh3 | 2010-09-16 15:03:59 -0400 (Thu, 16 Sep 2010) | 3 lines
1014 M /trunk/samtools/bgzip.c
1015 M /trunk/samtools/razip.c
1017 * fixed a bug in razip: -c will delete the input file
1018 * copy tabix/bgzip to here
1020 ------------------------------------------------------------------------
1021 r727 | lh3lh3 | 2010-09-16 13:45:49 -0400 (Thu, 16 Sep 2010) | 3 lines
1023 M /trunk/samtools/bam_md.c
1024 M /trunk/samtools/bam_plcmd.c
1025 M /trunk/samtools/bamtk.c
1027 * samtools-0.1.8-14 (r727)
1028 * allow to change the capQ parameter at the command line
1030 ------------------------------------------------------------------------
1031 r726 | lh3lh3 | 2010-09-16 13:38:43 -0400 (Thu, 16 Sep 2010) | 4 lines
1033 M /trunk/samtools/bam_md.c
1034 M /trunk/samtools/bam_plcmd.c
1035 M /trunk/samtools/bcftools/vcfutils.pl
1036 M /trunk/samtools/misc/samtools.pl
1038 * added varFilter to vcfutils.pl
1039 * reimplement realn(). now it performs a local alignment
1040 * added cap_mapQ() to cap mapping quality when there are many substitutions
1042 ------------------------------------------------------------------------
1043 r724 | lh3lh3 | 2010-09-15 00:18:31 -0400 (Wed, 15 Sep 2010) | 2 lines
1045 M /trunk/samtools/bcftools/Makefile
1046 A /trunk/samtools/bcftools/bcf2qcall.c
1047 M /trunk/samtools/bcftools/call1.c
1049 * convert BCF to QCALL input
1051 ------------------------------------------------------------------------
1052 r723 | lh3lh3 | 2010-09-14 22:41:50 -0400 (Tue, 14 Sep 2010) | 2 lines
1054 M /trunk/samtools/bam_md.c
1056 dynamic band width in realignment
1058 ------------------------------------------------------------------------
1059 r722 | lh3lh3 | 2010-09-14 22:05:32 -0400 (Tue, 14 Sep 2010) | 2 lines
1061 M /trunk/samtools/bam_md.c
1062 M /trunk/samtools/bam_plcmd.c
1064 fixed a bug in realignment
1066 ------------------------------------------------------------------------
1067 r721 | lh3lh3 | 2010-09-14 20:54:09 -0400 (Tue, 14 Sep 2010) | 2 lines
1069 M /trunk/samtools/bcftools/prob1.c
1073 ------------------------------------------------------------------------
1074 r720 | lh3lh3 | 2010-09-14 19:25:10 -0400 (Tue, 14 Sep 2010) | 2 lines
1076 M /trunk/samtools/Makefile
1077 M /trunk/samtools/bam_maqcns.c
1078 M /trunk/samtools/bam_md.c
1080 fixed a bug in realignment
1082 ------------------------------------------------------------------------
1083 r719 | lh3lh3 | 2010-09-14 19:18:24 -0400 (Tue, 14 Sep 2010) | 2 lines
1085 M /trunk/samtools/bam_plcmd.c
1087 minor changes. It is BUGGY now!
1089 ------------------------------------------------------------------------
1090 r718 | lh3lh3 | 2010-09-14 16:32:33 -0400 (Tue, 14 Sep 2010) | 4 lines
1092 M /trunk/samtools/bam_md.c
1093 M /trunk/samtools/bam_pileup.c
1094 M /trunk/samtools/kaln.c
1095 M /trunk/samtools/kaln.h
1097 * aggressive gapped aligner is implemented in calmd.
1098 * distinguish gap_open and gap_end_open in banded alignment
1099 * make tview accepts alignment with heading and tailing D
1101 ------------------------------------------------------------------------
1102 r717 | jmarshall | 2010-09-14 09:04:28 -0400 (Tue, 14 Sep 2010) | 2 lines
1106 Add svn:ignore properties for generated files that don't appear in "make all".
1108 ------------------------------------------------------------------------
1109 r716 | jmarshall | 2010-09-13 08:37:53 -0400 (Mon, 13 Sep 2010) | 3 lines
1112 M /trunk/samtools/bcftools
1113 M /trunk/samtools/misc
1115 Add svn:ignore properties listing the generated files.
1116 (Except for *.o, which we'll assume is in global-ignores.)
1118 ------------------------------------------------------------------------
1119 r715 | lh3lh3 | 2010-09-08 12:53:55 -0400 (Wed, 08 Sep 2010) | 5 lines
1121 M /trunk/samtools/bamtk.c
1122 M /trunk/samtools/bcftools/call1.c
1123 M /trunk/samtools/bcftools/prob1.c
1124 M /trunk/samtools/sample.c
1125 M /trunk/samtools/sample.h
1127 * samtools-0.1.8-13 (r715)
1128 * fixed a bug in identifying SM across files
1129 * bcftools: estimate heterozygosity
1130 * bcftools: allow to skip sites without reference bases
1132 ------------------------------------------------------------------------
1133 r713 | lh3lh3 | 2010-09-03 17:19:12 -0400 (Fri, 03 Sep 2010) | 2 lines
1135 M /trunk/samtools/bcftools/Makefile
1136 M /trunk/samtools/bcftools/call1.c
1137 M /trunk/samtools/bcftools/prob1.c
1138 M /trunk/samtools/bcftools/prob1.h
1140 quite a lot changes to the contrast caller, but I still feel something is missing...
1142 ------------------------------------------------------------------------
1143 r711 | lh3lh3 | 2010-09-03 00:30:48 -0400 (Fri, 03 Sep 2010) | 4 lines
1145 M /trunk/samtools/bcftools/Makefile
1146 M /trunk/samtools/bcftools/call1.c
1147 M /trunk/samtools/bcftools/prob1.c
1148 M /trunk/samtools/bcftools/vcfutils.pl
1150 * changed 3.434 to 4.343 (typo!)
1151 * fixed a bug in the contrast caller
1152 * calculate heterozygosity
1154 ------------------------------------------------------------------------
1155 r710 | lh3lh3 | 2010-09-01 23:24:47 -0400 (Wed, 01 Sep 2010) | 2 lines
1157 M /trunk/samtools/bcftools/bcf.h
1158 M /trunk/samtools/bcftools/bcfutils.c
1159 M /trunk/samtools/bcftools/call1.c
1161 SNP calling from the GL field
1163 ------------------------------------------------------------------------
1164 r709 | lh3lh3 | 2010-09-01 18:52:30 -0400 (Wed, 01 Sep 2010) | 2 lines
1166 M /trunk/samtools/bcftools/vcf.c
1168 fixed another problem
1170 ------------------------------------------------------------------------
1171 r708 | lh3lh3 | 2010-09-01 18:31:17 -0400 (Wed, 01 Sep 2010) | 3 lines
1173 M /trunk/samtools/bcftools/bcf.c
1174 M /trunk/samtools/bcftools/vcf.c
1176 * fixed bugs in parsing VCF
1177 * parser now works with GT/GQ/DP/PL/GL
1179 ------------------------------------------------------------------------
1180 r707 | lh3lh3 | 2010-09-01 15:28:29 -0400 (Wed, 01 Sep 2010) | 2 lines
1182 M /trunk/samtools/bcftools/Makefile
1183 M /trunk/samtools/bcftools/prob1.c
1185 Do not compile _BCF_QUAD by default
1187 ------------------------------------------------------------------------
1188 r706 | lh3lh3 | 2010-09-01 15:21:41 -0400 (Wed, 01 Sep 2010) | 2 lines
1190 M /trunk/samtools/bcftools/bcf.c
1191 M /trunk/samtools/bcftools/bcf.h
1192 M /trunk/samtools/bcftools/bcfutils.c
1193 M /trunk/samtools/bcftools/call1.c
1195 Write the correct ALT and PL in the SNP calling mode.
1197 ------------------------------------------------------------------------
1198 r705 | lh3lh3 | 2010-09-01 12:50:33 -0400 (Wed, 01 Sep 2010) | 2 lines
1200 M /trunk/samtools/bcftools/vcfutils.pl
1202 more commands for my own uses
1204 ------------------------------------------------------------------------
1205 r704 | lh3lh3 | 2010-09-01 09:26:10 -0400 (Wed, 01 Sep 2010) | 2 lines
1207 A /trunk/samtools/bcftools/vcfutils.pl
1209 Utilities for processing VCF
1211 ------------------------------------------------------------------------
1212 r703 | lh3lh3 | 2010-08-31 16:44:57 -0400 (Tue, 31 Aug 2010) | 2 lines
1214 M /trunk/samtools/bcftools/Makefile
1215 M /trunk/samtools/bcftools/call1.c
1216 M /trunk/samtools/bcftools/prob1.c
1217 M /trunk/samtools/bcftools/prob1.h
1219 preliminary contrast variant caller
1221 ------------------------------------------------------------------------
1222 r702 | lh3lh3 | 2010-08-31 12:28:39 -0400 (Tue, 31 Aug 2010) | 2 lines
1224 M /trunk/samtools/bcftools/call1.c
1225 M /trunk/samtools/bcftools/prob1.c
1226 M /trunk/samtools/bcftools/prob1.h
1228 z' and z'' can be calculated
1230 ------------------------------------------------------------------------
1231 r701 | lh3lh3 | 2010-08-31 10:20:57 -0400 (Tue, 31 Aug 2010) | 3 lines
1233 M /trunk/samtools/bcftools/Makefile
1234 A /trunk/samtools/bcftools/call1.c (from /trunk/samtools/bcftools/vcfout.c:699)
1235 M /trunk/samtools/bcftools/prob1.c
1236 D /trunk/samtools/bcftools/vcfout.c
1238 * rename vcfout.c as call1.c
1239 * prepare to add two-sample comparison
1241 ------------------------------------------------------------------------
1242 r699 | lh3lh3 | 2010-08-24 15:28:16 -0400 (Tue, 24 Aug 2010) | 2 lines
1244 M /trunk/samtools/bcftools/vcfout.c
1246 fixed a bug in calculating the t statistics
1248 ------------------------------------------------------------------------
1249 r698 | lh3lh3 | 2010-08-24 14:05:50 -0400 (Tue, 24 Aug 2010) | 3 lines
1251 M /trunk/samtools/bam2bcf.c
1252 M /trunk/samtools/bam2bcf.h
1253 M /trunk/samtools/bamtk.c
1254 M /trunk/samtools/bcftools/kfunc.c
1255 M /trunk/samtools/bcftools/vcfout.c
1257 * samtools-0.1.8-13 (r698)
1258 * perform one-tailed t-test for baseQ, mapQ and endDist
1260 ------------------------------------------------------------------------
1261 r697 | lh3lh3 | 2010-08-24 12:30:13 -0400 (Tue, 24 Aug 2010) | 2 lines
1263 M /trunk/samtools/bcftools/kfunc.c
1265 added regularized incomplete beta function
1267 ------------------------------------------------------------------------
1268 r695 | lh3lh3 | 2010-08-23 17:36:17 -0400 (Mon, 23 Aug 2010) | 2 lines
1270 M /trunk/samtools/bam_maqcns.c
1271 M /trunk/samtools/bam_plcmd.c
1273 change the default correlation coefficient
1275 ------------------------------------------------------------------------
1276 r694 | lh3lh3 | 2010-08-23 14:46:52 -0400 (Mon, 23 Aug 2010) | 2 lines
1278 M /trunk/samtools/bcftools/bcf.c
1279 M /trunk/samtools/bcftools/vcfout.c
1281 print QUAL as floating numbers
1283 ------------------------------------------------------------------------
1284 r693 | lh3lh3 | 2010-08-23 14:06:07 -0400 (Mon, 23 Aug 2010) | 3 lines
1286 M /trunk/samtools/Makefile
1287 M /trunk/samtools/bam_plcmd.c
1288 M /trunk/samtools/bamtk.c
1289 M /trunk/samtools/examples/Makefile
1290 A /trunk/samtools/sample.c
1291 A /trunk/samtools/sample.h
1293 * samtools-0.1.8-12 (r692)
1294 * group data by samples in "mpileup -g"
1296 ------------------------------------------------------------------------
1297 r692 | lh3lh3 | 2010-08-23 10:58:53 -0400 (Mon, 23 Aug 2010) | 2 lines
1299 M /trunk/samtools/Makefile
1300 D /trunk/samtools/bam_mcns.c
1301 D /trunk/samtools/bam_mcns.h
1302 M /trunk/samtools/bam_plcmd.c
1304 remove VCF output in mpileup
1306 ------------------------------------------------------------------------
1307 r691 | lh3lh3 | 2010-08-23 10:48:20 -0400 (Mon, 23 Aug 2010) | 3 lines
1309 M /trunk/samtools/bam2bcf.c
1310 M /trunk/samtools/bam2bcf.h
1312 * use the revised MAQ error model for mpileup
1313 * prepare to remove the independent model from mpileup
1315 ------------------------------------------------------------------------
1316 r690 | lh3lh3 | 2010-08-20 15:46:40 -0400 (Fri, 20 Aug 2010) | 2 lines
1318 M /trunk/samtools/Makefile
1319 M /trunk/samtools/bam_maqcns.c
1320 M /trunk/samtools/bam_maqcns.h
1321 M /trunk/samtools/bam_plcmd.c
1322 A /trunk/samtools/errmod.c
1323 A /trunk/samtools/errmod.h
1324 M /trunk/samtools/ksort.h
1326 added revised MAQ error model
1328 ------------------------------------------------------------------------
1329 r689 | lh3lh3 | 2010-08-18 09:55:20 -0400 (Wed, 18 Aug 2010) | 2 lines
1331 M /trunk/samtools/bcftools/prob1.c
1332 M /trunk/samtools/bcftools/prob1.h
1333 M /trunk/samtools/bcftools/vcfout.c
1335 allow to read the prior from the error output. EM iteration is working.
1337 ------------------------------------------------------------------------
1338 r688 | lh3lh3 | 2010-08-17 12:12:20 -0400 (Tue, 17 Aug 2010) | 3 lines
1340 M /trunk/samtools/bcftools/main.c
1341 M /trunk/samtools/bcftools/vcf.c
1343 * write a little more VCF header
1346 ------------------------------------------------------------------------
1347 r687 | lh3lh3 | 2010-08-16 20:53:16 -0400 (Mon, 16 Aug 2010) | 2 lines
1349 M /trunk/samtools/bcftools/bcf.c
1350 M /trunk/samtools/bcftools/bcf.h
1351 M /trunk/samtools/bcftools/bcf.tex
1355 ------------------------------------------------------------------------
1356 r686 | lh3lh3 | 2010-08-14 00:11:13 -0400 (Sat, 14 Aug 2010) | 2 lines
1358 M /trunk/samtools/bcftools/bcf.c
1359 M /trunk/samtools/bcftools/prob1.c
1361 faster for large sample size (in principle)
1363 ------------------------------------------------------------------------
1364 r685 | lh3lh3 | 2010-08-13 23:28:31 -0400 (Fri, 13 Aug 2010) | 4 lines
1366 M /trunk/samtools/bcftools/prob1.c
1368 * a numerically stable method to calculate z_{jk}
1369 * currently slower than the old method but will be important for large sample size
1370 * in principle, we can speed up for large n, but have not tried
1372 ------------------------------------------------------------------------
1373 r684 | lh3lh3 | 2010-08-11 21:58:31 -0400 (Wed, 11 Aug 2010) | 2 lines
1375 M /trunk/samtools/bcftools/vcfout.c
1377 fixed an issue in parsing integer
1379 ------------------------------------------------------------------------
1380 r683 | lh3lh3 | 2010-08-09 13:05:07 -0400 (Mon, 09 Aug 2010) | 2 lines
1382 M /trunk/samtools/bcftools/bcf.c
1384 do not print refname if file is converted from VCF
1386 ------------------------------------------------------------------------
1387 r682 | lh3lh3 | 2010-08-09 12:59:47 -0400 (Mon, 09 Aug 2010) | 3 lines
1389 M /trunk/samtools/bcftools/vcf.c
1392 * fixed a bug in parsing VCF
1394 ------------------------------------------------------------------------
1395 r681 | lh3lh3 | 2010-08-09 12:49:23 -0400 (Mon, 09 Aug 2010) | 4 lines
1397 M /trunk/samtools/bcftools/bcf.c
1398 M /trunk/samtools/bcftools/bcf.h
1399 M /trunk/samtools/bcftools/bcfutils.c
1400 M /trunk/samtools/bcftools/main.c
1401 M /trunk/samtools/bcftools/vcf.c
1402 M /trunk/samtools/bcftools/vcfout.c
1403 M /trunk/samtools/bgzf.c
1404 M /trunk/samtools/kstring.c
1406 * fixed a bug in kstrtok@kstring.c
1407 * preliminary VCF parser (not parse everything for now)
1408 * improved view interface
1410 ------------------------------------------------------------------------
1411 r680 | lh3lh3 | 2010-08-09 10:43:13 -0400 (Mon, 09 Aug 2010) | 4 lines
1413 M /trunk/samtools/bcftools/bcf.c
1414 M /trunk/samtools/bcftools/bcf.h
1415 M /trunk/samtools/bcftools/vcfout.c
1416 M /trunk/samtools/kstring.c
1417 M /trunk/samtools/kstring.h
1419 * improved kstring (added kstrtok)
1420 * removed the limit on the format string length in bcftools
1421 * use kstrtok to parse format which fixed a bug in the old code
1423 ------------------------------------------------------------------------
1424 r679 | lh3lh3 | 2010-08-09 01:12:05 -0400 (Mon, 09 Aug 2010) | 2 lines
1426 A /trunk/samtools/bcftools/README
1427 M /trunk/samtools/bcftools/vcfout.c
1431 ------------------------------------------------------------------------
1432 r678 | lh3lh3 | 2010-08-09 00:01:52 -0400 (Mon, 09 Aug 2010) | 2 lines
1434 M /trunk/samtools/bcftools/vcfout.c
1436 perform single-tail test for ED4
1438 ------------------------------------------------------------------------
1439 r677 | lh3lh3 | 2010-08-08 23:48:35 -0400 (Sun, 08 Aug 2010) | 2 lines
1441 M /trunk/samtools/bcftools/Makefile
1442 M /trunk/samtools/bcftools/kfunc.c
1443 M /trunk/samtools/bcftools/vcfout.c
1445 * test depth, end distance and HWE
1447 ------------------------------------------------------------------------
1448 r676 | lh3lh3 | 2010-08-08 02:04:15 -0400 (Sun, 08 Aug 2010) | 2 lines
1450 M /trunk/samtools/bcftools/kfunc.c
1452 reimplement incomplete gamma functions. no copy-paste
1454 ------------------------------------------------------------------------
1455 r675 | lh3lh3 | 2010-08-06 22:42:54 -0400 (Fri, 06 Aug 2010) | 3 lines
1457 M /trunk/samtools/bam2bcf.c
1458 M /trunk/samtools/bam2bcf.h
1459 M /trunk/samtools/bcftools/fet.c
1460 M /trunk/samtools/bcftools/prob1.c
1461 M /trunk/samtools/bcftools/prob1.h
1462 M /trunk/samtools/bcftools/vcfout.c
1464 * bcftools: add HWE (no testing for now)
1465 * record end dist in a 2x2 table, not avg, std any more
1467 ------------------------------------------------------------------------
1468 r674 | lh3lh3 | 2010-08-06 17:30:16 -0400 (Fri, 06 Aug 2010) | 3 lines
1470 A /trunk/samtools/bcftools/kfunc.c
1472 * Special functions: log(gamma()), erfc(), P(a,x) (incomplete gamma)
1473 * Not using Numerical Recipe due to licensing issues
1475 ------------------------------------------------------------------------
1476 r673 | lh3lh3 | 2010-08-05 23:46:53 -0400 (Thu, 05 Aug 2010) | 2 lines
1478 A /trunk/samtools/bcftools/fet.c
1482 ------------------------------------------------------------------------
1483 r672 | lh3lh3 | 2010-08-05 21:48:33 -0400 (Thu, 05 Aug 2010) | 3 lines
1485 M /trunk/samtools/bam2bcf.c
1486 M /trunk/samtools/bam2bcf.h
1487 M /trunk/samtools/bamtk.c
1488 M /trunk/samtools/examples/Makefile
1490 * samtools-0.1.8-11 (r672)
1491 * collect more stats for allele balance test in bcftools (not yet)
1493 ------------------------------------------------------------------------
1494 r671 | lh3lh3 | 2010-08-05 16:17:58 -0400 (Thu, 05 Aug 2010) | 3 lines
1496 M /trunk/samtools/bam_plcmd.c
1497 M /trunk/samtools/bcftools/bcf.c
1498 M /trunk/samtools/bcftools/main.c
1500 * the code base is stablized again.
1501 * I will delay the vcf parser, which is quite complicated but with little value for now
1503 ------------------------------------------------------------------------
1504 r670 | lh3lh3 | 2010-08-05 16:03:23 -0400 (Thu, 05 Aug 2010) | 2 lines
1506 M /trunk/samtools/examples/Makefile
1510 ------------------------------------------------------------------------
1511 r669 | lh3lh3 | 2010-08-05 16:03:08 -0400 (Thu, 05 Aug 2010) | 2 lines
1513 M /trunk/samtools/bcftools/vcf.c
1515 unfinished vcf parser
1517 ------------------------------------------------------------------------
1518 r668 | lh3lh3 | 2010-08-05 15:46:40 -0400 (Thu, 05 Aug 2010) | 3 lines
1520 M /trunk/samtools/bcftools/Makefile
1521 M /trunk/samtools/bcftools/bcf.c
1522 M /trunk/samtools/bcftools/bcf.h
1523 M /trunk/samtools/bcftools/bcfutils.c
1524 M /trunk/samtools/bcftools/index.c
1525 M /trunk/samtools/bcftools/main.c
1526 A /trunk/samtools/bcftools/vcf.c
1527 M /trunk/samtools/bcftools/vcfout.c
1529 * added prelimiary VCF parser (not finished)
1530 * change struct a bit
1532 ------------------------------------------------------------------------
1533 r667 | lh3lh3 | 2010-08-03 22:35:27 -0400 (Tue, 03 Aug 2010) | 3 lines
1535 M /trunk/samtools/bam2bcf.c
1536 M /trunk/samtools/bam2bcf.h
1537 M /trunk/samtools/bam_plcmd.c
1538 M /trunk/samtools/bcftools/bcf.c
1540 * allow to set min base q
1541 * fixed a bug in mpileup -u
1543 ------------------------------------------------------------------------
1544 r666 | lh3lh3 | 2010-08-03 22:08:44 -0400 (Tue, 03 Aug 2010) | 2 lines
1546 A /trunk/samtools/bcftools/bcf.tex
1550 ------------------------------------------------------------------------
1551 r665 | lh3lh3 | 2010-08-03 21:18:57 -0400 (Tue, 03 Aug 2010) | 2 lines
1553 M /trunk/samtools/examples/Makefile
1557 ------------------------------------------------------------------------
1558 r664 | lh3lh3 | 2010-08-03 21:13:00 -0400 (Tue, 03 Aug 2010) | 2 lines
1560 M /trunk/samtools/Makefile
1561 M /trunk/samtools/bam2bcf.c
1562 M /trunk/samtools/bam2bcf.h
1563 M /trunk/samtools/bcftools/Makefile
1565 fixed compilation error
1567 ------------------------------------------------------------------------
1568 r662 | lh3lh3 | 2010-08-03 21:04:00 -0400 (Tue, 03 Aug 2010) | 2 lines
1570 M /trunk/samtools/Makefile
1571 D /trunk/samtools/bcf.c
1572 D /trunk/samtools/bcf.h
1573 A /trunk/samtools/bcftools
1574 A /trunk/samtools/bcftools/Makefile
1575 A /trunk/samtools/bcftools/bcf.c
1576 A /trunk/samtools/bcftools/bcf.h
1577 A /trunk/samtools/bcftools/bcfutils.c
1578 A /trunk/samtools/bcftools/index.c
1579 A /trunk/samtools/bcftools/main.c
1580 A /trunk/samtools/bcftools/prob1.c
1581 A /trunk/samtools/bcftools/prob1.h
1582 A /trunk/samtools/bcftools/vcfout.c
1584 move bcftools to samtools
1586 ------------------------------------------------------------------------
1587 r660 | lh3lh3 | 2010-08-03 15:58:32 -0400 (Tue, 03 Aug 2010) | 2 lines
1589 M /trunk/samtools/bam2bcf.c
1591 fixed another minor bug
1593 ------------------------------------------------------------------------
1594 r658 | lh3lh3 | 2010-08-03 15:06:45 -0400 (Tue, 03 Aug 2010) | 3 lines
1596 M /trunk/samtools/bamtk.c
1597 M /trunk/samtools/bcf.c
1599 * samtools-0.1.8-10 (r658)
1600 * fixed a bug in bam2bcf when the reference is N
1602 ------------------------------------------------------------------------
1603 r657 | lh3lh3 | 2010-08-03 14:50:23 -0400 (Tue, 03 Aug 2010) | 3 lines
1605 M /trunk/samtools/bam2bcf.c
1606 M /trunk/samtools/bam2bcf.h
1609 * treat ambiguous ref base as the fifth base
1611 ------------------------------------------------------------------------
1612 r654 | lh3lh3 | 2010-08-02 17:38:27 -0400 (Mon, 02 Aug 2010) | 2 lines
1614 M /trunk/bcftools/bcf.c
1615 M /trunk/samtools/bcf.c
1617 missing a column in VCF output...
1619 ------------------------------------------------------------------------
1620 r653 | lh3lh3 | 2010-08-02 17:31:33 -0400 (Mon, 02 Aug 2010) | 2 lines
1622 M /trunk/samtools/bcf.c
1626 ------------------------------------------------------------------------
1627 r651 | lh3lh3 | 2010-08-02 17:27:31 -0400 (Mon, 02 Aug 2010) | 2 lines
1629 M /trunk/samtools/bcf.c
1631 fixed a bug in bcf reader
1633 ------------------------------------------------------------------------
1634 r650 | lh3lh3 | 2010-08-02 17:00:41 -0400 (Mon, 02 Aug 2010) | 2 lines
1636 M /trunk/samtools/bam2bcf.c
1640 ------------------------------------------------------------------------
1641 r649 | lh3lh3 | 2010-08-02 16:49:35 -0400 (Mon, 02 Aug 2010) | 3 lines
1643 M /trunk/samtools/Makefile
1644 M /trunk/samtools/bam2bcf.c
1645 M /trunk/samtools/bam2bcf.h
1646 M /trunk/samtools/bamtk.c
1648 * samtools-0.1.8-9 (r649)
1649 * lossless representation of PL in BCF output
1651 ------------------------------------------------------------------------
1652 r648 | lh3lh3 | 2010-08-02 16:07:25 -0400 (Mon, 02 Aug 2010) | 2 lines
1654 M /trunk/samtools/Makefile
1655 A /trunk/samtools/bam2bcf.c
1656 A /trunk/samtools/bam2bcf.h
1657 M /trunk/samtools/bam_plcmd.c
1658 A /trunk/samtools/bcf.c
1659 A /trunk/samtools/bcf.h
1663 ------------------------------------------------------------------------
1664 r644 | lh3lh3 | 2010-07-28 11:59:19 -0400 (Wed, 28 Jul 2010) | 5 lines
1666 M /trunk/samtools/bam_mcns.c
1667 M /trunk/samtools/bamtk.c
1669 * samtools-0.1.8-8 (r644)
1670 * mpileup becomes a little stable again
1671 * the method is slightly different, but is more theoretically correct
1672 * snp calling is O(n^2) instead of O(n^3)
1674 ------------------------------------------------------------------------
1675 r643 | lh3lh3 | 2010-07-28 11:54:15 -0400 (Wed, 28 Jul 2010) | 3 lines
1677 M /trunk/samtools/bam_mcns.c
1679 * fixed a STUPID bug, which cost me a lot of time.
1680 * I am going to clean up mcns a little bit
1682 ------------------------------------------------------------------------
1683 r642 | lh3lh3 | 2010-07-27 23:23:07 -0400 (Tue, 27 Jul 2010) | 2 lines
1685 M /trunk/samtools/bam_mcns.c
1686 M /trunk/samtools/bam_mcns.h
1687 M /trunk/samtools/bam_plcmd.c
1689 supposedly this is THE correct implementation, but more testing is needed
1691 ------------------------------------------------------------------------
1692 r641 | lh3lh3 | 2010-07-27 22:43:39 -0400 (Tue, 27 Jul 2010) | 2 lines
1694 M /trunk/samtools/bam_mcns.c
1696 NOT ready yet. Going to make further changes...
1698 ------------------------------------------------------------------------
1699 r639 | lh3lh3 | 2010-07-25 22:18:38 -0400 (Sun, 25 Jul 2010) | 3 lines
1701 M /trunk/samtools/bam_mcns.c
1702 M /trunk/samtools/bam_plcmd.c
1703 M /trunk/samtools/bamtk.c
1705 * samtools-0.1.8-7 (r639)
1706 * fixed the reference allele assignment
1708 ------------------------------------------------------------------------
1709 r638 | lh3lh3 | 2010-07-25 12:01:26 -0400 (Sun, 25 Jul 2010) | 5 lines
1711 M /trunk/samtools/bam_mcns.c
1712 M /trunk/samtools/bam_mcns.h
1713 M /trunk/samtools/bam_plcmd.c
1714 M /trunk/samtools/bamtk.c
1716 * samtools-0.1.8-6 (r638)
1717 * skip isnan/isinf in case of float underflow
1718 * added the flat prior
1719 * fixed an issue where there are no reads supporting the reference
1721 ------------------------------------------------------------------------
1722 r637 | lh3lh3 | 2010-07-24 14:16:27 -0400 (Sat, 24 Jul 2010) | 2 lines
1724 M /trunk/samtools/bam_plcmd.c
1728 ------------------------------------------------------------------------
1729 r636 | lh3lh3 | 2010-07-24 14:07:27 -0400 (Sat, 24 Jul 2010) | 2 lines
1731 M /trunk/samtools/bam_mcns.c
1732 M /trunk/samtools/bam_mcns.h
1733 M /trunk/samtools/bam_plcmd.c
1734 M /trunk/samtools/bamtk.c
1738 ------------------------------------------------------------------------
1739 r635 | lh3lh3 | 2010-07-24 01:49:49 -0400 (Sat, 24 Jul 2010) | 2 lines
1741 M /trunk/samtools/bam_mcns.c
1742 M /trunk/samtools/bam_mcns.h
1743 M /trunk/samtools/bam_plcmd.c
1745 posterior expectation FINALLY working. I am so tired...
1747 ------------------------------------------------------------------------
1748 r633 | lh3lh3 | 2010-07-23 13:50:48 -0400 (Fri, 23 Jul 2010) | 2 lines
1750 M /trunk/samtools/bam_plcmd.c
1752 another minor fix to mpileup
1754 ------------------------------------------------------------------------
1755 r632 | lh3lh3 | 2010-07-23 13:43:31 -0400 (Fri, 23 Jul 2010) | 2 lines
1757 M /trunk/samtools/bam_plcmd.c
1759 added the format column
1761 ------------------------------------------------------------------------
1762 r631 | lh3lh3 | 2010-07-23 13:25:44 -0400 (Fri, 23 Jul 2010) | 2 lines
1764 M /trunk/samtools/bam_mcns.c
1765 M /trunk/samtools/bam_mcns.h
1766 M /trunk/samtools/bam_plcmd.c
1767 M /trunk/samtools/bamtk.c
1769 added an alternative prior
1771 ------------------------------------------------------------------------
1772 r628 | lh3lh3 | 2010-07-23 11:48:51 -0400 (Fri, 23 Jul 2010) | 2 lines
1774 M /trunk/samtools/bam_mcns.c
1775 M /trunk/samtools/bam_mcns.h
1776 M /trunk/samtools/bam_plcmd.c
1778 calculate posterior allele frequency
1780 ------------------------------------------------------------------------
1781 r627 | lh3lh3 | 2010-07-22 21:39:13 -0400 (Thu, 22 Jul 2010) | 3 lines
1783 M /trunk/samtools/bam_mcns.c
1784 M /trunk/samtools/bam_plcmd.c
1785 M /trunk/samtools/bamtk.c
1787 * samtools-0.1.8-3 (r627)
1788 * multi-sample snp calling appears to work. More tests needed.
1790 ------------------------------------------------------------------------
1791 r626 | lh3lh3 | 2010-07-22 16:37:56 -0400 (Thu, 22 Jul 2010) | 3 lines
1793 M /trunk/samtools/bam_mcns.c
1794 M /trunk/samtools/bam_mcns.h
1795 M /trunk/samtools/bam_plcmd.c
1796 M /trunk/samtools/bam_tview.c
1798 * preliminary multisample SNP caller.
1799 * something looks not so right, but it largely works
1801 ------------------------------------------------------------------------
1802 r617 | lh3lh3 | 2010-07-14 16:26:27 -0400 (Wed, 14 Jul 2010) | 3 lines
1804 M /trunk/samtools/bam_mcns.c
1805 M /trunk/samtools/bam_plcmd.c
1806 M /trunk/samtools/bamtk.c
1808 * samtools-0.1.8-2 (r617)
1809 * allele frequency calculation apparently works...
1811 ------------------------------------------------------------------------
1812 r616 | lh3lh3 | 2010-07-14 13:33:51 -0400 (Wed, 14 Jul 2010) | 3 lines
1814 M /trunk/samtools/Makefile
1815 A /trunk/samtools/bam_mcns.c
1816 A /trunk/samtools/bam_mcns.h
1817 M /trunk/samtools/bam_plcmd.c
1819 * added mutli-sample framework. It is not working, yet.
1820 * improved the mpileup interface
1822 ------------------------------------------------------------------------
1823 r615 | lh3lh3 | 2010-07-13 14:50:12 -0400 (Tue, 13 Jul 2010) | 3 lines
1825 M /trunk/samtools/bam_plcmd.c
1826 M /trunk/samtools/bamtk.c
1827 M /trunk/samtools/misc/Makefile
1829 * samtools-0.1.8-1 (r615)
1830 * allow to get mpileup at required sites
1832 ------------------------------------------------------------------------
1833 r613 | lh3lh3 | 2010-07-11 22:40:56 -0400 (Sun, 11 Jul 2010) | 2 lines
1835 M /trunk/samtools/ChangeLog
1836 M /trunk/samtools/NEWS
1837 M /trunk/samtools/bam_plcmd.c
1838 M /trunk/samtools/bamtk.c
1839 M /trunk/samtools/samtools.1
1841 Release samtools-0.1.8
1843 ------------------------------------------------------------------------
1844 r612 | lh3lh3 | 2010-07-11 21:08:56 -0400 (Sun, 11 Jul 2010) | 2 lines
1846 M /trunk/samtools/knetfile.c
1848 fixed a compiling issue for Windows
1850 ------------------------------------------------------------------------
1851 r611 | lh3lh3 | 2010-07-11 20:59:15 -0400 (Sun, 11 Jul 2010) | 2 lines
1853 M /trunk/samtools/bam_sort.c
1855 fixed a bug in sorting when output to stdout (by Peter Chines)
1857 ------------------------------------------------------------------------
1858 r610 | lh3lh3 | 2010-07-09 17:05:10 -0400 (Fri, 09 Jul 2010) | 2 lines
1860 M /trunk/samtools/NEWS
1861 M /trunk/samtools/bam_plcmd.c
1863 change the command line option of pileup
1865 ------------------------------------------------------------------------
1866 r609 | lh3lh3 | 2010-07-09 00:39:34 -0400 (Fri, 09 Jul 2010) | 2 lines
1868 M /trunk/samtools/bam_pileup.c
1869 A /trunk/samtools/examples/toy.fa
1870 A /trunk/samtools/examples/toy.sam
1872 make pileup work with CIGAR with I/D at the beginning or in the end
1874 ------------------------------------------------------------------------
1875 r608 | lh3lh3 | 2010-07-08 22:36:12 -0400 (Thu, 08 Jul 2010) | 3 lines
1877 M /trunk/samtools/bam_maqcns.c
1878 M /trunk/samtools/bam_maqcns.h
1879 M /trunk/samtools/bam_plcmd.c
1880 M /trunk/samtools/bam_tview.c
1882 * make tview more friendly
1883 * a temporary remedy for an issue in indel calling
1885 ------------------------------------------------------------------------
1886 r607 | lh3lh3 | 2010-07-08 14:43:52 -0400 (Thu, 08 Jul 2010) | 4 lines
1888 M /trunk/samtools/bam_maqcns.c
1889 M /trunk/samtools/bam_plcmd.c
1890 M /trunk/samtools/bamtk.c
1892 * samtools-0.1.7-r607
1893 * improved the genotype accuracy for indels
1894 * use the SOAPsnp model for SNP calling by default.
1896 ------------------------------------------------------------------------
1897 r606 | lh3lh3 | 2010-07-08 01:05:19 -0400 (Thu, 08 Jul 2010) | 2 lines
1899 M /trunk/samtools/misc/Makefile
1901 removed a debugging example
1903 ------------------------------------------------------------------------
1904 r605 | lh3lh3 | 2010-07-08 01:04:09 -0400 (Thu, 08 Jul 2010) | 4 lines
1906 M /trunk/samtools/bam_maqcns.c
1907 M /trunk/samtools/bamtk.c
1909 * samtools-.1.7-18 (r605)
1910 * fixed an issue when a deletion and mismatch occur at the same time
1911 and the base quality is higher than 40 (if -I40).
1913 ------------------------------------------------------------------------
1914 r604 | lh3lh3 | 2010-07-02 19:32:24 -0400 (Fri, 02 Jul 2010) | 2 lines
1916 M /trunk/samtools/bam.h
1917 M /trunk/samtools/bam_index.c
1918 M /trunk/samtools/misc/Makefile
1920 fixed a minor bug in idxstats
1922 ------------------------------------------------------------------------
1923 r601 | lh3lh3 | 2010-06-16 09:03:59 -0400 (Wed, 16 Jun 2010) | 2 lines
1925 M /trunk/samtools/bam_index.c
1927 fixed a minor bug in indexing
1929 ------------------------------------------------------------------------
1930 r600 | lh3lh3 | 2010-06-15 10:17:53 -0400 (Tue, 15 Jun 2010) | 2 lines
1932 M /trunk/samtools/ChangeLog
1933 M /trunk/samtools/bam.c
1935 change printf() to puts in exporting
1937 ------------------------------------------------------------------------
1938 r599 | lh3lh3 | 2010-06-13 21:41:11 -0400 (Sun, 13 Jun 2010) | 2 lines
1940 M /trunk/samtools/bamtk.c
1942 minor fix. No actual effect.
1944 ------------------------------------------------------------------------
1945 r598 | lh3lh3 | 2010-06-13 21:32:45 -0400 (Sun, 13 Jun 2010) | 2 lines
1947 M /trunk/samtools/Makefile
1949 added Makefile targets to compile shared/dynamic library
1951 ------------------------------------------------------------------------
1952 r596 | lh3lh3 | 2010-06-13 19:48:07 -0400 (Sun, 13 Jun 2010) | 3 lines
1954 M /trunk/samtools/ChangeLog
1955 M /trunk/samtools/bam_index.c
1956 M /trunk/samtools/bamtk.c
1958 * samtools-0.1.7-17 (r596)
1959 * also keep the number of coor-less reads in the index file
1961 ------------------------------------------------------------------------
1962 r595 | lh3lh3 | 2010-06-13 18:54:26 -0400 (Sun, 13 Jun 2010) | 3 lines
1964 M /trunk/samtools/bam_index.c
1965 M /trunk/samtools/bamtk.c
1967 * samtools-0.1.7-16 (r595)
1968 * write additional information to bam index
1970 ------------------------------------------------------------------------
1971 r594 | lh3lh3 | 2010-06-13 17:29:52 -0400 (Sun, 13 Jun 2010) | 2 lines
1973 M /trunk/samtools/bam_index.c
1975 fixed a bug for unmapped sequences in indexing
1977 ------------------------------------------------------------------------
1978 r593 | lh3lh3 | 2010-06-12 18:11:32 -0400 (Sat, 12 Jun 2010) | 2 lines
1980 M /trunk/samtools/bam.h
1981 M /trunk/samtools/bam_index.c
1982 M /trunk/samtools/bam_plcmd.c
1983 M /trunk/samtools/samtools.1
1985 rename iterf as iter
1987 ------------------------------------------------------------------------
1988 r592 | lh3lh3 | 2010-06-12 18:02:38 -0400 (Sat, 12 Jun 2010) | 4 lines
1990 M /trunk/samtools/ChangeLog
1991 M /trunk/samtools/bam_aux.c
1992 M /trunk/samtools/bam_index.c
1993 M /trunk/samtools/bam_pileup.c
1994 M /trunk/samtools/bam_plcmd.c
1995 M /trunk/samtools/bamtk.c
1997 * samtools-0.1.7-15 (r592)
1998 * fixed a few minor memory leaks in the new pileup code
1999 * improved the functionality of mpileup
2001 ------------------------------------------------------------------------
2002 r591 | lh3lh3 | 2010-06-12 14:09:22 -0400 (Sat, 12 Jun 2010) | 3 lines
2004 M /trunk/samtools/bam.h
2005 M /trunk/samtools/bam_pileup.c
2006 M /trunk/samtools/bam_plcmd.c
2007 M /trunk/samtools/bamtk.c
2009 * samtools-0.1.7-14 (r591)
2010 * elementary multi-way pileup. More testing and more functionality to be done.
2012 ------------------------------------------------------------------------
2013 r590 | lh3lh3 | 2010-06-12 01:00:24 -0400 (Sat, 12 Jun 2010) | 3 lines
2015 M /trunk/samtools/bam.h
2016 M /trunk/samtools/bam_pileup.c
2017 M /trunk/samtools/bamtk.c
2019 * samtools-0.1.7-13 (r590)
2020 * added mpileup APIs. No compiling errors, but not tested at all. It is late.
2022 ------------------------------------------------------------------------
2023 r589 | lh3lh3 | 2010-06-11 22:37:09 -0400 (Fri, 11 Jun 2010) | 3 lines
2025 M /trunk/samtools/bam.h
2026 M /trunk/samtools/bam_pileup.c
2027 M /trunk/samtools/bamtk.c
2029 * samtools-0.1.7-12 (r589)
2030 * added iterator-like APIs for pileup
2032 ------------------------------------------------------------------------
2033 r588 | lh3lh3 | 2010-06-11 17:41:13 -0400 (Fri, 11 Jun 2010) | 3 lines
2035 M /trunk/samtools/bam_index.c
2036 M /trunk/samtools/bamtk.c
2038 * samtools-0.1.7-11 (r588)
2039 * ported a few improvements from tabix back to samtools
2041 ------------------------------------------------------------------------
2042 r587 | lh3lh3 | 2010-06-11 17:33:16 -0400 (Fri, 11 Jun 2010) | 3 lines
2044 M /trunk/samtools/bam.h
2045 M /trunk/samtools/bam_index.c
2046 M /trunk/samtools/bamtk.c
2048 * samtools-0.1.7-10 (r587)
2049 * added iterator interface for bam_fetch (ported back from tabix)
2051 ------------------------------------------------------------------------
2052 r586 | lh3lh3 | 2010-06-11 13:23:53 -0400 (Fri, 11 Jun 2010) | 3 lines
2054 M /trunk/samtools/Makefile
2055 A /trunk/samtools/bam_reheader.c
2056 M /trunk/samtools/bamtk.c
2057 M /trunk/samtools/bgzf.c
2059 * samtools-0.1.7-9 (r586)
2060 * added "reheader" to replace the BAM header
2062 ------------------------------------------------------------------------
2063 r585 | lh3lh3 | 2010-06-11 12:22:06 -0400 (Fri, 11 Jun 2010) | 3 lines
2065 M /trunk/samtools/bam.c
2066 M /trunk/samtools/bamtk.c
2067 M /trunk/samtools/kstring.h
2069 * samtools-0.1.7-8 (r585)
2072 ------------------------------------------------------------------------
2073 r584 | lh3lh3 | 2010-06-11 12:00:41 -0400 (Fri, 11 Jun 2010) | 4 lines
2075 M /trunk/samtools/bam.c
2076 M /trunk/samtools/bamtk.c
2077 M /trunk/samtools/bgzf.c
2078 M /trunk/samtools/bgzf.h
2079 M /trunk/samtools/kstring.h
2080 M /trunk/samtools/misc/wgsim_eval.pl
2082 * samtools-0.1.7-7 (r584)
2083 * ported tabix BGZF to samtools
2084 * flush BGZF after writing the BAM header and between alignment boundaries
2086 ------------------------------------------------------------------------
2087 r583 | petulda | 2010-06-11 11:58:20 -0400 (Fri, 11 Jun 2010) | 1 line
2089 A /trunk/samtools/misc/varfilter.py
2091 Initial release on behalf of Aylwyn Scally
2092 ------------------------------------------------------------------------
2093 r561 | petulda | 2010-05-07 08:41:56 -0400 (Fri, 07 May 2010) | 1 line
2095 M /trunk/samtools/samtools.1
2097 Added a note about the indels coordinates
2098 ------------------------------------------------------------------------
2099 r551 | petulda | 2010-04-23 09:42:13 -0400 (Fri, 23 Apr 2010) | 1 line
2101 M /trunk/samtools/misc/sam2vcf.pl
2103 Added the possibility to print or not to print the reference allele
2104 ------------------------------------------------------------------------
2105 r546 | petulda | 2010-04-15 04:33:55 -0400 (Thu, 15 Apr 2010) | 1 line
2107 M /trunk/samtools/sam_header.c
2109 More descriptive message for space separated tags
2110 ------------------------------------------------------------------------
2111 r545 | petulda | 2010-04-14 11:44:50 -0400 (Wed, 14 Apr 2010) | 1 line
2113 M /trunk/samtools/misc/sam2vcf.pl
2115 Speedup with -i, no need to query the reference all the time
2116 ------------------------------------------------------------------------
2117 r541 | petulda | 2010-03-15 10:03:51 -0400 (Mon, 15 Mar 2010) | 1 line
2119 M /trunk/samtools/sam_header.c
2121 Fixed the order of sequences in the header
2122 ------------------------------------------------------------------------
2123 r540 | petulda | 2010-03-04 06:28:35 -0500 (Thu, 04 Mar 2010) | 1 line
2125 M /trunk/samtools/misc/sam2vcf.pl
2127 Added possibility to select indels only and fixed a bug in reporting homozygous indels.
2128 ------------------------------------------------------------------------
2129 r539 | jmarshall | 2010-02-27 06:48:17 -0500 (Sat, 27 Feb 2010) | 4 lines
2131 M /trunk/samtools/bam.c
2133 Improve the invalid 'BAM\1' magic number error message, and also print it
2134 when no bytes can be read from the alleged BAM file, e.g., in the common
2135 user error case when a SAM file has accidentally been supplied.
2137 ------------------------------------------------------------------------
2138 r538 | petulda | 2010-02-26 10:51:40 -0500 (Fri, 26 Feb 2010) | 1 line
2140 M /trunk/samtools/AUTHORS
2141 M /trunk/samtools/bam.h
2142 M /trunk/samtools/bam_import.c
2143 M /trunk/samtools/sam_header.c
2145 Improved efficiency of header parsing
2146 ------------------------------------------------------------------------
2147 r537 | lh3lh3 | 2010-02-23 21:08:48 -0500 (Tue, 23 Feb 2010) | 3 lines
2149 M /trunk/samtools/misc/export2sam.pl
2151 Updated export2sam.pl by Chris Saunders from Illumina.
2154 ------------------------------------------------------------------------
2155 r536 | petulda | 2010-02-17 08:32:53 -0500 (Wed, 17 Feb 2010) | 1 line
2157 M /trunk/samtools/misc/samtools.pl
2159 Fixed filtering of SNPs near indels. Added min indel and SNP quality filter.
2160 ------------------------------------------------------------------------
2161 r535 | petulda | 2010-02-12 04:52:37 -0500 (Fri, 12 Feb 2010) | 1 line
2163 M /trunk/samtools/misc/sam2vcf.pl
2165 Print an error for pileups in simple format
2166 ------------------------------------------------------------------------
2167 r534 | lh3lh3 | 2010-02-11 14:01:41 -0500 (Thu, 11 Feb 2010) | 2 lines
2169 M /trunk/samtools/bam_plcmd.c
2171 added a hidden option in pileup to output the base position (for Erin)
2173 ------------------------------------------------------------------------
2174 r533 | petulda | 2010-02-09 10:12:14 -0500 (Tue, 09 Feb 2010) | 1 line
2176 M /trunk/samtools/misc/sam2vcf.pl
2178 Added possibility to specify a custom column title for the data column
2179 ------------------------------------------------------------------------
2180 r532 | petulda | 2010-02-09 09:46:09 -0500 (Tue, 09 Feb 2010) | 1 line
2182 M /trunk/samtools/bam_plcmd.c
2184 Added the -d option to limit maximum depth for indels.
2185 ------------------------------------------------------------------------
2186 r531 | petulda | 2010-02-03 07:57:27 -0500 (Wed, 03 Feb 2010) | 1 line
2188 M /trunk/samtools/misc/sam2vcf.pl
2191 ------------------------------------------------------------------------
2192 r530 | lh3lh3 | 2010-02-01 09:13:19 -0500 (Mon, 01 Feb 2010) | 3 lines
2194 M /trunk/samtools/ChangeLog
2195 M /trunk/samtools/bam_plcmd.c
2196 M /trunk/samtools/bamtk.c
2197 M /trunk/samtools/misc/samtools.pl
2198 M /trunk/samtools/misc/wgsim.c
2201 * fixed a bug in faidx
2203 ------------------------------------------------------------------------
2204 r529 | jmarshall | 2010-01-11 18:51:49 -0500 (Mon, 11 Jan 2010) | 2 lines
2206 M /trunk/samtools/faidx.c
2208 Put the right filename in the error message.
2210 ------------------------------------------------------------------------
2211 r528 | lh3lh3 | 2009-12-14 11:26:47 -0500 (Mon, 14 Dec 2009) | 3 lines
2213 M /trunk/samtools/bam_plcmd.c
2214 M /trunk/samtools/bamtk.c
2216 * samtools-0.1.7-5 (r528)
2217 * further add new consensus generation strategy
2219 ------------------------------------------------------------------------
2220 r527 | petulda | 2009-12-11 12:31:05 -0500 (Fri, 11 Dec 2009) | 1 line
2222 M /trunk/samtools/knetfile.c
2224 Fixed a bug in knet_seek
2225 ------------------------------------------------------------------------
2226 r526 | petulda | 2009-12-11 07:51:18 -0500 (Fri, 11 Dec 2009) | 1 line
2228 M /trunk/samtools/misc/sam2vcf.pl
2230 Small fix in VCF format: dot for the empty INFO field
2231 ------------------------------------------------------------------------
2232 r525 | petulda | 2009-12-11 04:36:18 -0500 (Fri, 11 Dec 2009) | 1 line
2234 M /trunk/samtools/sam_header.c
2236 Allow tabs in the CO header field
2237 ------------------------------------------------------------------------
2238 r524 | jmarshall | 2009-12-10 10:03:58 -0500 (Thu, 10 Dec 2009) | 3 lines
2240 M /trunk/samtools/Makefile
2241 M /trunk/samtools/Makefile.mingw
2243 Depend on libbam.a rather than the phony target, so that samtools is not
2244 unnecessarily rebuilt every time. Also clean bgzip.
2246 ------------------------------------------------------------------------
2247 r523 | jmarshall | 2009-12-10 09:45:32 -0500 (Thu, 10 Dec 2009) | 4 lines
2249 M /trunk/samtools/Makefile
2250 M /trunk/samtools/Makefile.mingw
2252 Fix a bug in compiling bgzip: this also needs knetfile.o when _USE_KNETFILE
2253 is defined. Also introduce $(KNETFILE_O) which can be set to empty to
2254 facilitate non-knet builds.
2256 ------------------------------------------------------------------------
2257 r522 | lh3lh3 | 2009-12-01 13:02:36 -0500 (Tue, 01 Dec 2009) | 4 lines
2259 M /trunk/samtools/bamtk.c
2260 M /trunk/samtools/sam_view.c
2262 * samtools-0.1.7-4 (r522)
2263 * fixed a bug in "view -r"
2264 * added a new option "view -R" to read required read groups from a file
2266 ------------------------------------------------------------------------
2267 r521 | lh3lh3 | 2009-12-01 10:00:12 -0500 (Tue, 01 Dec 2009) | 3 lines
2269 M /trunk/samtools/bam_md.c
2270 M /trunk/samtools/bamtk.c
2272 * samtools-0.1.7-3 (r521)
2273 * calmd: optionally mask matching bases as N
2275 ------------------------------------------------------------------------
2276 r520 | lh3lh3 | 2009-12-01 09:37:17 -0500 (Tue, 01 Dec 2009) | 4 lines
2278 M /trunk/samtools/bam_plcmd.c
2279 M /trunk/samtools/bamtk.c
2280 M /trunk/samtools/misc/samtools.pl
2282 * samtools-0.1.7-2 (r520)
2283 * fixed a few issues with compilation in Windows (on behalf of John)
2284 * choose a random base as the consensus (for population genetics studies)
2286 ------------------------------------------------------------------------
2287 r519 | jmarshall | 2009-11-30 10:53:02 -0500 (Mon, 30 Nov 2009) | 6 lines
2289 M /trunk/samtools/Makefile
2291 Put libraries at the end, so they can resolve references from libbam.a
2292 as well, even with old-fashioned linkers.
2294 Also use libbam.a explicitly rather than "-L. -lbam" to ensure that we get
2295 the freshly built library, not some other libbam.a lying around the system.
2297 ------------------------------------------------------------------------
2298 r518 | jmarshall | 2009-11-30 08:44:56 -0500 (Mon, 30 Nov 2009) | 2 lines
2300 M /trunk/samtools/Makefile
2301 M /trunk/samtools/misc/Makefile
2303 Also clean *.exe (for Cygwin users using this makefile).
2305 ------------------------------------------------------------------------
2306 r517 | jmarshall | 2009-11-30 07:09:04 -0500 (Mon, 30 Nov 2009) | 2 lines
2308 M /trunk/samtools/bam_index.c
2310 Index files should be opened in binary mode, not text mode.
2312 ------------------------------------------------------------------------
2313 r516 | lh3lh3 | 2009-11-27 15:18:59 -0500 (Fri, 27 Nov 2009) | 2 lines
2315 A /trunk/samtools/examples/bam2bed.c
2317 another example program
2319 ------------------------------------------------------------------------
2320 r515 | lh3lh3 | 2009-11-27 10:44:56 -0500 (Fri, 27 Nov 2009) | 3 lines
2322 M /trunk/samtools/bam_import.c
2323 M /trunk/samtools/bamtk.c
2324 M /trunk/samtools/misc/wgsim_eval.pl
2325 M /trunk/samtools/sam.c
2327 * samtools-0.1.7-1 (r515)
2328 * report an error when .fai contains duplicated names, instead of segfault
2330 ------------------------------------------------------------------------
2331 r514 | jmarshall | 2009-11-24 09:45:35 -0500 (Tue, 24 Nov 2009) | 2 lines
2333 M /trunk/samtools/bam.c
2335 Format 'c'-encoded auxiliary fields correctly, as *signed* integers.
2337 ------------------------------------------------------------------------
2338 r513 | lh3lh3 | 2009-11-16 10:13:07 -0500 (Mon, 16 Nov 2009) | 2 lines
2340 M /trunk/samtools/Makefile.mingw
2342 Update Makefile.mingw for the same reason
2344 ------------------------------------------------------------------------
2345 r512 | lh3lh3 | 2009-11-16 10:00:08 -0500 (Mon, 16 Nov 2009) | 2 lines
2347 M /trunk/samtools/Makefile
2349 Fixed a bug in compiling razip
2351 ------------------------------------------------------------------------
2352 r510 | lh3lh3 | 2009-11-10 10:55:41 -0500 (Tue, 10 Nov 2009) | 2 lines
2354 M /trunk/samtools/ChangeLog
2355 M /trunk/samtools/NEWS
2356 M /trunk/samtools/bamtk.c
2357 M /trunk/samtools/samtools.1
2359 Release samtools-0.1.7 (r510)
2361 ------------------------------------------------------------------------
2362 r509 | lh3lh3 | 2009-11-06 09:17:09 -0500 (Fri, 06 Nov 2009) | 3 lines
2364 M /trunk/samtools/bam_plcmd.c
2365 M /trunk/samtools/bamtk.c
2367 * samtools-0.1.6-22 (r509)
2368 * forget to fix a similar problem in glfgen
2370 ------------------------------------------------------------------------
2371 r508 | lh3lh3 | 2009-11-06 09:06:40 -0500 (Fri, 06 Nov 2009) | 3 lines
2373 M /trunk/samtools/bam_maqcns.c
2374 M /trunk/samtools/bam_plcmd.c
2375 M /trunk/samtools/bamtk.c
2376 M /trunk/samtools/sam_view.c
2378 * samtools-0.1.6-21 (r508)
2379 * fixed a potential bug in the indel caller towards the end of a chromosome
2381 ------------------------------------------------------------------------
2382 r494 | lh3lh3 | 2009-10-26 11:38:00 -0400 (Mon, 26 Oct 2009) | 3 lines
2384 M /trunk/samtools/bamtk.c
2385 M /trunk/samtools/sam_view.c
2387 * samtools-0.1.6-19 (r494)
2388 * allow to convert Illumina quality (64 based) to the BAM quality
2390 ------------------------------------------------------------------------
2391 r493 | lh3lh3 | 2009-10-26 10:24:39 -0400 (Mon, 26 Oct 2009) | 4 lines
2393 M /trunk/samtools/Makefile
2394 M /trunk/samtools/bam.c
2395 M /trunk/samtools/bam_import.c
2396 M /trunk/samtools/bamtk.c
2397 M /trunk/samtools/sam.c
2398 M /trunk/samtools/sam_header.c
2400 * samtools-0.1.6-18 (r493)
2401 * fixed the bugs due to improperly incorporating Petr's header parser
2402 * a little code clean up in sam_header.c
2404 ------------------------------------------------------------------------
2405 r492 | petulda | 2009-10-24 09:43:25 -0400 (Sat, 24 Oct 2009) | 1 line
2407 M /trunk/samtools/sam_header.c
2409 Added sam_header_line_free call for sam_header_parse2
2410 ------------------------------------------------------------------------
2411 r491 | lh3lh3 | 2009-10-24 00:50:16 -0400 (Sat, 24 Oct 2009) | 3 lines
2413 M /trunk/samtools/sam_view.c
2418 ------------------------------------------------------------------------
2419 r490 | lh3lh3 | 2009-10-24 00:45:12 -0400 (Sat, 24 Oct 2009) | 4 lines
2421 M /trunk/samtools/bam.c
2422 M /trunk/samtools/bam.h
2423 M /trunk/samtools/bam_import.c
2424 M /trunk/samtools/sam.c
2427 * improved the interface a bit
2430 ------------------------------------------------------------------------
2431 r489 | lh3lh3 | 2009-10-24 00:41:50 -0400 (Sat, 24 Oct 2009) | 3 lines
2433 M /trunk/samtools/bam_import.c
2434 M /trunk/samtools/sam_header.c
2435 M /trunk/samtools/sam_header.h
2437 * BUGGY VERSION. Please NOT use it.
2438 * Fixed a minor bug, but the major bug is still there.
2440 ------------------------------------------------------------------------
2441 r488 | lh3lh3 | 2009-10-24 00:17:10 -0400 (Sat, 24 Oct 2009) | 3 lines
2443 M /trunk/samtools/Makefile
2444 M /trunk/samtools/bam.c
2445 M /trunk/samtools/bam.h
2446 M /trunk/samtools/bam_aux.c
2447 M /trunk/samtools/bam_import.c
2448 M /trunk/samtools/bam_rmdup.c
2449 M /trunk/samtools/bam_rmdupse.c
2450 M /trunk/samtools/kaln.c
2451 M /trunk/samtools/sam.c
2452 M /trunk/samtools/sam_header.c
2453 M /trunk/samtools/sam_header.h
2454 M /trunk/samtools/sam_view.c
2456 * This revision is SERIOUSLY BUGGY. Please NOT use it.
2457 * Start to incorporate header parsing from Petr Danecek
2459 ------------------------------------------------------------------------
2460 r487 | petulda | 2009-10-23 11:44:32 -0400 (Fri, 23 Oct 2009) | 1 line
2462 M /trunk/samtools/sam_header.c
2463 M /trunk/samtools/sam_header.h
2465 Now possible to merge multiple HeaderDict dictionaries
2466 ------------------------------------------------------------------------
2467 r486 | petulda | 2009-10-22 11:46:58 -0400 (Thu, 22 Oct 2009) | 1 line
2469 M /trunk/samtools/sam_header.c
2472 ------------------------------------------------------------------------
2473 r485 | petulda | 2009-10-22 11:41:56 -0400 (Thu, 22 Oct 2009) | 1 line
2475 A /trunk/samtools/sam_header.c
2476 A /trunk/samtools/sam_header.h
2479 ------------------------------------------------------------------------
2480 r484 | lh3lh3 | 2009-10-19 14:31:32 -0400 (Mon, 19 Oct 2009) | 5 lines
2482 M /trunk/samtools/bam_import.c
2483 M /trunk/samtools/bam_rmdupse.c
2484 M /trunk/samtools/bamtk.c
2485 M /trunk/samtools/examples/Makefile
2487 * samtools-0.1.6-17 (r484)
2488 * fixed a memory leak in rmdupse
2489 * fixed a bug in parsing @RG header lines
2490 * test rmdup in examples/
2492 ------------------------------------------------------------------------
2493 r483 | lh3lh3 | 2009-10-19 13:22:48 -0400 (Mon, 19 Oct 2009) | 4 lines
2495 M /trunk/samtools/bam_rmdup.c
2496 M /trunk/samtools/bam_rmdupse.c
2497 M /trunk/samtools/bamtk.c
2499 * samtools-0.1.6-16 (r483)
2500 * unify the interface of rmdup and rmdupse
2501 * a new bug found in rg2lib(). Have not been fixed yet.
2503 ------------------------------------------------------------------------
2504 r482 | lh3lh3 | 2009-10-19 13:03:34 -0400 (Mon, 19 Oct 2009) | 4 lines
2506 M /trunk/samtools/bam.h
2507 M /trunk/samtools/bam_rmdup.c
2508 M /trunk/samtools/bam_rmdupse.c
2509 M /trunk/samtools/bamtk.c
2510 A /trunk/samtools/klist.h
2512 * samtools-0.1.6-15 (r482)
2514 * rmdupse is now library aware
2516 ------------------------------------------------------------------------
2517 r481 | lh3lh3 | 2009-10-18 00:07:21 -0400 (Sun, 18 Oct 2009) | 3 lines
2519 M /trunk/samtools/bam_rmdup.c
2520 M /trunk/samtools/bamtk.c
2522 * samtools-0.1.6-14 (r480)
2523 * rmdup is now RG aware
2525 ------------------------------------------------------------------------
2526 r480 | lh3lh3 | 2009-10-17 22:05:20 -0400 (Sat, 17 Oct 2009) | 2 lines
2528 M /trunk/samtools/misc/samtools.pl
2530 added a small unitity to parse SRA XML files
2532 ------------------------------------------------------------------------
2533 r479 | lh3lh3 | 2009-10-17 20:57:26 -0400 (Sat, 17 Oct 2009) | 3 lines
2535 M /trunk/samtools/bam_maqcns.c
2536 M /trunk/samtools/bam_maqcns.h
2537 M /trunk/samtools/bam_plcmd.c
2538 M /trunk/samtools/bam_sort.c
2539 M /trunk/samtools/bamtk.c
2541 * samtools-0.1.6-13 (r479)
2542 * merge: optionally use file names as RG tags
2544 ------------------------------------------------------------------------
2545 r478 | lh3lh3 | 2009-10-14 14:18:12 -0400 (Wed, 14 Oct 2009) | 3 lines
2547 M /trunk/samtools/bam.c
2548 M /trunk/samtools/bam.h
2549 M /trunk/samtools/bam_maqcns.c
2550 M /trunk/samtools/bamtk.c
2551 M /trunk/samtools/kaln.c
2553 * samtools-0.1.6-12 (r478)
2554 * fixed a bug in the indel caller
2556 ------------------------------------------------------------------------
2557 r477 | lh3lh3 | 2009-10-10 06:12:26 -0400 (Sat, 10 Oct 2009) | 3 lines
2559 M /trunk/samtools/bam_index.c
2560 M /trunk/samtools/bamtk.c
2562 * samtools-0.1.6-11 (r477)
2563 * fixed a bug due to recent change in bam_index.c (thank Nicole Washington for the patch)
2565 ------------------------------------------------------------------------
2566 r476 | petulda | 2009-10-09 11:45:36 -0400 (Fri, 09 Oct 2009) | 1 line
2568 A /trunk/samtools/misc/sam2vcf.pl
2570 Added the sam2vcf.pl script.
2571 ------------------------------------------------------------------------
2572 r475 | lh3lh3 | 2009-10-08 10:19:16 -0400 (Thu, 08 Oct 2009) | 2 lines
2574 M /trunk/samtools/Makefile
2575 M /trunk/samtools/bam.c
2576 M /trunk/samtools/bam.h
2577 M /trunk/samtools/bam_maqcns.c
2578 M /trunk/samtools/bamtk.c
2579 A /trunk/samtools/kaln.c
2580 A /trunk/samtools/kaln.h
2582 Unfinished modification. Please do not use this revision...
2584 ------------------------------------------------------------------------
2585 r474 | petulda | 2009-10-08 06:39:54 -0400 (Thu, 08 Oct 2009) | 1 line
2587 M /trunk/samtools/knetfile.c
2589 Removed the offending knet_seek message.
2590 ------------------------------------------------------------------------
2591 r473 | petulda | 2009-10-06 09:26:35 -0400 (Tue, 06 Oct 2009) | 1 line
2593 M /trunk/samtools/knetfile.c
2594 M /trunk/samtools/razf.c
2596 Bug fix - faidx on RAZF compressed files now working.
2597 ------------------------------------------------------------------------
2598 r472 | lh3lh3 | 2009-10-02 08:42:57 -0400 (Fri, 02 Oct 2009) | 2 lines
2600 M /trunk/samtools/samtools.1
2602 Clarify the meaning of a region like "chr2:1,000,000".
2604 ------------------------------------------------------------------------
2605 r471 | lh3lh3 | 2009-10-02 05:42:19 -0400 (Fri, 02 Oct 2009) | 2 lines
2607 M /trunk/samtools/misc/novo2sam.pl
2609 Fixed minor bugs in novo2sam.pl (on behalf of Ken Chen and Colin Hercus)
2611 ------------------------------------------------------------------------
2612 r470 | lh3lh3 | 2009-09-29 15:01:27 -0400 (Tue, 29 Sep 2009) | 3 lines
2614 M /trunk/samtools/Makefile.mingw
2615 M /trunk/samtools/bamtk.c
2616 M /trunk/samtools/knetfile.c
2617 M /trunk/samtools/knetfile.h
2619 * samtools-0.1.6-9 (r470)
2620 * make knetfile.c compatible with MinGW (thank Martin Morgan for the patch)
2622 ------------------------------------------------------------------------
2623 r469 | lh3lh3 | 2009-09-29 08:07:44 -0400 (Tue, 29 Sep 2009) | 3 lines
2625 M /trunk/samtools/bam_index.c
2626 M /trunk/samtools/bamtk.c
2628 * samtools-0.1.6-9 (r469)
2629 * refactor bam_fetch() for Python binding. On behalf of Leo Goodstadt.
2631 ------------------------------------------------------------------------
2632 r468 | lh3lh3 | 2009-09-28 05:18:29 -0400 (Mon, 28 Sep 2009) | 3 lines
2634 M /trunk/samtools/bam_sort.c
2635 M /trunk/samtools/bamtk.c
2636 M /trunk/samtools/misc/samtools.pl
2638 * samtools-0.1.6-7 (r468)
2641 ------------------------------------------------------------------------
2642 r467 | petulda | 2009-09-28 04:51:29 -0400 (Mon, 28 Sep 2009) | 1 line
2644 M /trunk/samtools/bgzf.c
2645 M /trunk/samtools/bgzip.c
2646 M /trunk/samtools/razf.c
2647 M /trunk/samtools/razip.c
2649 Changed the mode for newly created files to 0666. This allows less strict permissions with umask properly set (e.g. 0002 vs. 0022).
2650 ------------------------------------------------------------------------
2651 r466 | lh3lh3 | 2009-09-24 06:29:19 -0400 (Thu, 24 Sep 2009) | 3 lines
2653 M /trunk/samtools/ChangeLog
2654 M /trunk/samtools/bam_md.c
2655 M /trunk/samtools/bamtk.c
2657 * samtools-0.1.6-6 (r466)
2658 * do not crash calmd when some sequences are absent from the reference.
2660 ------------------------------------------------------------------------
2661 r464 | jmarshall | 2009-09-23 06:14:32 -0400 (Wed, 23 Sep 2009) | 3 lines
2663 M /trunk/samtools/bam.c
2664 M /trunk/samtools/knetfile.c
2666 Suppress bgzf_check_EOF() messages when reading from a pipe, as there is
2667 no way to seek on a pipe and the messages always appear.
2669 ------------------------------------------------------------------------
2670 r463 | petulda | 2009-09-16 07:05:41 -0400 (Wed, 16 Sep 2009) | 1 line
2672 M /trunk/samtools/knetfile.c
2673 M /trunk/samtools/razf.c
2675 A bug fix, "samtools view" is now working again.
2676 ------------------------------------------------------------------------
2677 r462 | lh3lh3 | 2009-09-16 04:51:07 -0400 (Wed, 16 Sep 2009) | 3 lines
2679 M /trunk/samtools/bamtk.c
2680 M /trunk/samtools/faidx.c
2681 M /trunk/samtools/knetfile.c
2682 M /trunk/samtools/knetfile.h
2683 M /trunk/samtools/razf.c
2684 M /trunk/samtools/razf.h
2686 * samtools-0.1.6-5 (r462)
2687 * Added knetfile support in razf and faidx (on behalf of Petr Danecek)
2689 ------------------------------------------------------------------------
2690 r460 | lh3lh3 | 2009-09-09 07:06:22 -0400 (Wed, 09 Sep 2009) | 2 lines
2692 M /trunk/samtools/samtools.1
2694 fixed a formatting issue
2696 ------------------------------------------------------------------------
2697 r459 | lh3lh3 | 2009-09-08 18:14:08 -0400 (Tue, 08 Sep 2009) | 3 lines
2699 M /trunk/samtools/bam_sort.c
2700 M /trunk/samtools/bamtk.c
2702 * samtools-0.1.6-4 (r459)
2703 * make sort output the result to stdout when -o is in use
2705 ------------------------------------------------------------------------
2706 r458 | lh3lh3 | 2009-09-07 05:10:28 -0400 (Mon, 07 Sep 2009) | 4 lines
2708 M /trunk/samtools/bamtk.c
2709 M /trunk/samtools/faidx.c
2710 M /trunk/samtools/faidx.h
2711 M /trunk/samtools/samtools.1
2713 * samtools-0.1.6-2 (r458)
2714 * added more interface to faidx (by Nils)
2715 * updated documentation
2717 ------------------------------------------------------------------------
2718 r457 | lh3lh3 | 2009-09-05 16:12:04 -0400 (Sat, 05 Sep 2009) | 3 lines
2720 M /trunk/samtools/bam_sort.c
2721 M /trunk/samtools/bamtk.c
2723 * samtools-0.1.6-2 (r457)
2724 * get rid of three assert() in bam_sort.c
2726 ------------------------------------------------------------------------
2727 r456 | jmarshall | 2009-09-04 12:46:25 -0400 (Fri, 04 Sep 2009) | 3 lines
2729 M /trunk/samtools/razf.c
2731 Return NULL from _razf_open() (and hence razf_open()/razf_open2())
2732 when opening the file fails.
2734 ------------------------------------------------------------------------
2735 r453 | lh3lh3 | 2009-09-02 08:56:33 -0400 (Wed, 02 Sep 2009) | 2 lines
2737 M /trunk/samtools/ChangeLog
2738 M /trunk/samtools/NEWS
2739 M /trunk/samtools/bamtk.c
2740 M /trunk/samtools/samtools.1
2741 D /trunk/samtools/source.dot
2743 Release samtools-0.1.6
2745 ------------------------------------------------------------------------
2746 r451 | lh3lh3 | 2009-09-02 05:44:48 -0400 (Wed, 02 Sep 2009) | 4 lines
2748 M /trunk/samtools/bam_md.c
2749 M /trunk/samtools/bam_rmdup.c
2750 M /trunk/samtools/bam_rmdupse.c
2751 M /trunk/samtools/bam_sort.c
2752 M /trunk/samtools/bamtk.c
2753 M /trunk/samtools/samtools.1
2755 * samtools-0.1.5-34 (r451)
2756 * applied the patch by John
2757 * improved the help message a little bit
2759 ------------------------------------------------------------------------
2760 r450 | lh3lh3 | 2009-09-02 04:55:55 -0400 (Wed, 02 Sep 2009) | 3 lines
2762 M /trunk/samtools/bam_color.c
2763 M /trunk/samtools/bamtk.c
2765 * samtools-0.1.5-33 (r450)
2766 * fixed a bug in bam_color.c (on behalf of Nils Homer)
2768 ------------------------------------------------------------------------
2769 r449 | lh3lh3 | 2009-08-29 15:36:41 -0400 (Sat, 29 Aug 2009) | 4 lines
2771 M /trunk/samtools/bam_import.c
2772 M /trunk/samtools/bam_md.c
2773 M /trunk/samtools/bamtk.c
2774 M /trunk/samtools/misc/samtools.pl
2776 * samtools-0.1.5-32 (r449)
2777 * fillmd: fixed a bug in modifying MD/NM tags
2778 * in import, give a warning if the read is aligned but there is no CIGAR.
2780 ------------------------------------------------------------------------
2781 r448 | lh3lh3 | 2009-08-19 04:44:28 -0400 (Wed, 19 Aug 2009) | 3 lines
2783 M /trunk/samtools/ChangeLog
2784 M /trunk/samtools/bam_pileup.c
2785 M /trunk/samtools/bamtk.c
2786 M /trunk/samtools/misc/wgsim_eval.pl
2788 * samtools-0.1.5-31 (r448)
2789 * fixed an issue when the last CIGAR is I or D
2791 ------------------------------------------------------------------------
2792 r447 | lh3lh3 | 2009-08-17 04:34:57 -0400 (Mon, 17 Aug 2009) | 3 lines
2794 M /trunk/samtools/bam_aux.c
2795 M /trunk/samtools/bamtk.c
2797 * samtools-0.1.5-30 (r447)
2798 * fixed a bug in bam_aux_get(): 'A' is not checked
2800 ------------------------------------------------------------------------
2801 r446 | lh3lh3 | 2009-08-17 04:33:17 -0400 (Mon, 17 Aug 2009) | 2 lines
2803 M /trunk/samtools/bam_aux.c
2804 M /trunk/samtools/bamtk.c
2808 ------------------------------------------------------------------------
2809 r444 | lh3lh3 | 2009-08-11 05:02:36 -0400 (Tue, 11 Aug 2009) | 3 lines
2811 M /trunk/samtools/bam_sort.c
2812 M /trunk/samtools/bamtk.c
2814 * samtools-0.1.5-28 (r444)
2817 ------------------------------------------------------------------------
2818 r443 | lh3lh3 | 2009-08-11 04:29:11 -0400 (Tue, 11 Aug 2009) | 4 lines
2820 M /trunk/samtools/bam.c
2821 M /trunk/samtools/bam_import.c
2822 M /trunk/samtools/bamtk.c
2824 * samtools-0.1.5-27 (r443)
2825 * SEQ and QUAL can be "*"
2826 * parse CIGAR "=" and "X" as "M"
2828 ------------------------------------------------------------------------
2829 r442 | lh3lh3 | 2009-08-07 16:56:38 -0400 (Fri, 07 Aug 2009) | 4 lines
2831 M /trunk/samtools/bam_pileup.c
2832 M /trunk/samtools/bamtk.c
2833 M /trunk/samtools/misc/md5.c
2834 M /trunk/samtools/misc/md5.h
2835 M /trunk/samtools/misc/md5fa.c
2837 * samtools-0.1.5-26 (r442)
2838 * replace RSA Inc md5.* with ones under permissive lincense
2839 * fixed a bug in detecting unsorted bam in pileup
2841 ------------------------------------------------------------------------
2842 r441 | bhandsaker | 2009-08-05 09:41:28 -0400 (Wed, 05 Aug 2009) | 2 lines
2844 M /trunk/samtools/bgzf.c
2845 M /trunk/samtools/bgzf.h
2846 M /trunk/samtools/bgzip.c
2848 Change copyright notices now that MIT has approved open source distribution.
2850 ------------------------------------------------------------------------
2851 r440 | lh3lh3 | 2009-08-05 05:44:24 -0400 (Wed, 05 Aug 2009) | 3 lines
2853 M /trunk/samtools/bam_stat.c
2854 M /trunk/samtools/bamtk.c
2856 * samtools-0.1.5-25 (r436)
2857 * in flagstats, do not report singletons if both ends are unmapped
2859 ------------------------------------------------------------------------
2860 r439 | lh3lh3 | 2009-08-04 17:16:51 -0400 (Tue, 04 Aug 2009) | 2 lines
2862 M /trunk/samtools/misc/maq2sam.c
2864 fixed a SERIOUS bug in setting 0x20 flag
2866 ------------------------------------------------------------------------
2867 r438 | lh3lh3 | 2009-08-04 16:50:43 -0400 (Tue, 04 Aug 2009) | 2 lines
2869 M /trunk/samtools/misc/samtools.pl
2871 fixed two minor bugs (suggested by Tim M Storm)
2873 ------------------------------------------------------------------------
2874 r437 | lh3lh3 | 2009-08-04 04:13:24 -0400 (Tue, 04 Aug 2009) | 3 lines
2876 M /trunk/samtools/bamtk.c
2877 M /trunk/samtools/misc/samtools.pl
2878 M /trunk/samtools/sam_view.c
2880 * samtools-0.1.5-24 (r435)
2883 ------------------------------------------------------------------------
2884 r434 | lh3lh3 | 2009-08-03 05:40:42 -0400 (Mon, 03 Aug 2009) | 3 lines
2886 M /trunk/samtools/bam_tview.c
2887 M /trunk/samtools/bamtk.c
2889 * samtools-0.1.5-23 (r434)
2890 * in tview, press 'r' to show read names rather than sequences
2892 ------------------------------------------------------------------------
2893 r433 | lh3lh3 | 2009-08-02 14:13:35 -0400 (Sun, 02 Aug 2009) | 3 lines
2895 M /trunk/samtools/knetfile.c
2897 * tried to fixed the buggy FTP random access in Windows. FAILED.
2898 * anyway, MinGW seems to have problem with "%lld".
2900 ------------------------------------------------------------------------
2901 r432 | lh3lh3 | 2009-08-01 19:32:07 -0400 (Sat, 01 Aug 2009) | 5 lines
2903 M /trunk/samtools/Makefile.mingw
2904 M /trunk/samtools/bamtk.c
2905 M /trunk/samtools/faidx.c
2906 M /trunk/samtools/razf.c
2907 A /trunk/samtools/win32/libcurses.a
2908 A /trunk/samtools/win32/xcurses.h
2910 * samtools-0.1.5-22 (r432)
2911 * faidx: fixed compitability issue with _WIN32
2912 * razf: fixed potential compitability issue with _WIN32
2913 * PDCurses support in Windows
2915 ------------------------------------------------------------------------
2916 r431 | lh3lh3 | 2009-08-01 18:34:54 -0400 (Sat, 01 Aug 2009) | 2 lines
2918 M /trunk/samtools/win32/libz.a
2920 replace the GnuWin32 version of libz.a with my own build with MinGW.
2922 ------------------------------------------------------------------------
2923 r430 | lh3lh3 | 2009-08-01 18:21:07 -0400 (Sat, 01 Aug 2009) | 2 lines
2925 M /trunk/samtools/knetfile.c
2929 ------------------------------------------------------------------------
2930 r429 | lh3lh3 | 2009-08-01 17:41:19 -0400 (Sat, 01 Aug 2009) | 3 lines
2932 M /trunk/samtools/Makefile.mingw
2933 M /trunk/samtools/bamtk.c
2934 M /trunk/samtools/knetfile.c
2935 M /trunk/samtools/knetfile.h
2937 * samtools-0.1.5-21 (r428)
2938 * knetfile.c is now compatible with mingw-winsock
2940 ------------------------------------------------------------------------
2941 r428 | lh3lh3 | 2009-07-31 19:39:07 -0400 (Fri, 31 Jul 2009) | 2 lines
2943 M /trunk/samtools/Makefile.mingw
2945 simplify MinGW Makefile
2947 ------------------------------------------------------------------------
2948 r427 | lh3lh3 | 2009-07-31 19:30:54 -0400 (Fri, 31 Jul 2009) | 5 lines
2950 A /trunk/samtools/Makefile.mingw
2951 M /trunk/samtools/bam_import.c
2952 M /trunk/samtools/bamtk.c
2953 A /trunk/samtools/win32
2954 A /trunk/samtools/win32/libz.a
2955 A /trunk/samtools/win32/zconf.h
2956 A /trunk/samtools/win32/zlib.h
2958 * samtools-0.1.5-20 (r427)
2959 * MinGW support. At least SAM<->BAM conversion is working. Other
2960 functionality are not tested at the moment.
2961 * zlib headers and Windows version of libz.a are included in win32/
2963 ------------------------------------------------------------------------
2964 r426 | lh3lh3 | 2009-07-31 18:32:09 -0400 (Fri, 31 Jul 2009) | 3 lines
2966 M /trunk/samtools/bamtk.c
2967 M /trunk/samtools/sam_view.c
2969 * samtools-0.1.5-19 (r426)
2970 * fixed a bug caused by recent modifications. Sorry.
2972 ------------------------------------------------------------------------
2973 r425 | lh3lh3 | 2009-07-31 18:23:51 -0400 (Fri, 31 Jul 2009) | 2 lines
2975 M /trunk/samtools/bgzf.c
2977 compatible with Windows binary files
2979 ------------------------------------------------------------------------
2980 r424 | lh3lh3 | 2009-07-31 05:19:59 -0400 (Fri, 31 Jul 2009) | 5 lines
2982 M /trunk/samtools/bam_maqcns.c
2983 M /trunk/samtools/bam_maqcns.h
2984 M /trunk/samtools/bam_plcmd.c
2985 M /trunk/samtools/bam_tview.c
2986 M /trunk/samtools/bamtk.c
2987 M /trunk/samtools/misc/samtools.pl
2989 * samtools-0.1.5-18 (r423)
2990 * output additional information in pileup indel lines, for the purepose
2991 of debugging at the moment
2992 * in tview, optionally allow to treat reference skip as deletion
2994 ------------------------------------------------------------------------
2995 r423 | lh3lh3 | 2009-07-30 17:00:36 -0400 (Thu, 30 Jul 2009) | 2 lines
2997 A /trunk/samtools/misc/psl2sam.pl
2999 convert BLAT psl to SAM.
3001 ------------------------------------------------------------------------
3002 r422 | lh3lh3 | 2009-07-30 06:24:39 -0400 (Thu, 30 Jul 2009) | 6 lines
3004 M /trunk/samtools/ChangeLog
3005 M /trunk/samtools/bam.c
3006 M /trunk/samtools/bamtk.c
3007 M /trunk/samtools/bgzf.c
3008 M /trunk/samtools/bgzf.h
3009 M /trunk/samtools/knetfile.c
3010 M /trunk/samtools/sam.c
3011 M /trunk/samtools/sam_view.c
3013 * samtools-0.1.5-17 (r422)
3014 * fixed a but in knetfile.c when seek type is not SEEK_SET
3015 * write an empty BGZF block to every BGZF file
3016 * check BGZF EOF marker in bam_header_read()
3019 ------------------------------------------------------------------------
3020 r421 | lh3lh3 | 2009-07-30 05:03:39 -0400 (Thu, 30 Jul 2009) | 3 lines
3022 M /trunk/samtools/bam_import.c
3023 M /trunk/samtools/bam_plcmd.c
3024 M /trunk/samtools/bamtk.c
3025 M /trunk/samtools/misc/samtools.pl
3026 M /trunk/samtools/sam.c
3027 M /trunk/samtools/sam.h
3028 M /trunk/samtools/sam_view.c
3030 * samtools-0.1.5-16 (r421)
3031 * in view and pileup, load header from FASTA index if the input is SAM.
3033 ------------------------------------------------------------------------
3034 r420 | lh3lh3 | 2009-07-29 04:18:55 -0400 (Wed, 29 Jul 2009) | 2 lines
3036 M /trunk/samtools/misc/maq2sam.c
3038 do not set "read 1" if reads are not mapped in the PE mode of maq
3040 ------------------------------------------------------------------------
3041 r419 | lh3lh3 | 2009-07-28 04:52:33 -0400 (Tue, 28 Jul 2009) | 5 lines
3043 M /trunk/samtools/bam_import.c
3044 M /trunk/samtools/bamtk.c
3045 M /trunk/samtools/misc/samtools.pl
3046 M /trunk/samtools/misc/wgsim_eval.pl
3048 * samtools-0.1.5-15 (r419)
3049 * in sam_open(), return NULL when the file cannot be opened.
3050 * make wgsim_eval.pl more robust to imperfect SAM
3051 * add "unique" command to samtools.pl
3053 ------------------------------------------------------------------------
3054 r418 | lh3lh3 | 2009-07-24 09:04:19 -0400 (Fri, 24 Jul 2009) | 2 lines
3056 M /trunk/samtools/misc/wgsim_eval.pl
3058 skip @header lines in SAM
3060 ------------------------------------------------------------------------
3061 r417 | lh3lh3 | 2009-07-24 07:42:38 -0400 (Fri, 24 Jul 2009) | 3 lines
3063 M /trunk/samtools/bamtk.c
3064 M /trunk/samtools/sam_view.c
3066 * samtools-0.1.5-14 (r417)
3067 * more help in "samtools view" due to the recent changes.
3069 ------------------------------------------------------------------------
3070 r416 | lh3lh3 | 2009-07-24 07:34:30 -0400 (Fri, 24 Jul 2009) | 3 lines
3072 M /trunk/samtools/bam.c
3073 M /trunk/samtools/bam.h
3074 M /trunk/samtools/bam_import.c
3075 M /trunk/samtools/bamtk.c
3076 M /trunk/samtools/sam.c
3077 M /trunk/samtools/sam.h
3078 M /trunk/samtools/sam_view.c
3080 * samtools-0.1.5-17 (r416)
3081 * support import/export SAM with string tags
3083 ------------------------------------------------------------------------
3084 r415 | lh3lh3 | 2009-07-24 06:39:26 -0400 (Fri, 24 Jul 2009) | 3 lines
3086 M /trunk/samtools/bam.c
3087 M /trunk/samtools/bam.h
3088 M /trunk/samtools/bam_import.c
3089 M /trunk/samtools/bamtk.c
3090 M /trunk/samtools/sam.c
3091 M /trunk/samtools/sam.h
3092 M /trunk/samtools/sam_view.c
3094 * samtools-0.1.5-12 (r415)
3095 * FLAG now can be in HEX
3097 ------------------------------------------------------------------------
3098 r414 | lh3lh3 | 2009-07-22 17:03:49 -0400 (Wed, 22 Jul 2009) | 2 lines
3100 M /trunk/samtools/kstring.h
3102 fixed a compiling error (thank Ken for fixing it)
3104 ------------------------------------------------------------------------
3105 r412 | lh3lh3 | 2009-07-21 17:19:40 -0400 (Tue, 21 Jul 2009) | 2 lines
3107 M /trunk/samtools/kstring.c
3108 M /trunk/samtools/kstring.h
3110 Implemented Boyer-Moore search in the kstring library.
3112 ------------------------------------------------------------------------
3113 r409 | lh3lh3 | 2009-07-17 12:10:20 -0400 (Fri, 17 Jul 2009) | 2 lines
3115 M /trunk/samtools/bam_index.c
3117 do not include knetfile.h when _USE_KNETFILE is not defined
3119 ------------------------------------------------------------------------
3120 r408 | lh3lh3 | 2009-07-17 10:29:21 -0400 (Fri, 17 Jul 2009) | 5 lines
3122 M /trunk/samtools/bam_md.c
3123 M /trunk/samtools/bam_tview.c
3124 M /trunk/samtools/bamtk.c
3125 M /trunk/samtools/bgzf.c
3127 * samtools-0.1.5-11 (r408)
3128 * force to overwirte existing MD if it is different from the one calculated
3130 * bgzf.c: improved the compatibility with Windows headers
3132 ------------------------------------------------------------------------
3133 r407 | lh3lh3 | 2009-07-17 09:46:56 -0400 (Fri, 17 Jul 2009) | 5 lines
3135 M /trunk/samtools/bam.h
3136 M /trunk/samtools/bam_aux.c
3137 M /trunk/samtools/bam_md.c
3138 M /trunk/samtools/bamtk.c
3139 M /trunk/samtools/sam.h
3141 * samtools-0.1.5-10 (r407)
3142 * implemented bam_aux_del() to remove a tag
3143 * fillmd: generate the NM tag
3144 * fillmd: cmd interface improvement
3146 ------------------------------------------------------------------------
3147 r406 | lh3lh3 | 2009-07-16 18:30:40 -0400 (Thu, 16 Jul 2009) | 2 lines
3149 M /trunk/samtools/Makefile
3151 Sorry. The old Makefile is for PDCurses...
3153 ------------------------------------------------------------------------
3154 r405 | lh3lh3 | 2009-07-16 18:30:11 -0400 (Thu, 16 Jul 2009) | 3 lines
3156 M /trunk/samtools/Makefile
3157 M /trunk/samtools/bam_tview.c
3158 M /trunk/samtools/bamtk.c
3160 * samtools-0.1.5-9 (r405)
3161 * improved the compatibility with PDCurses a little bit
3163 ------------------------------------------------------------------------
3164 r404 | lh3lh3 | 2009-07-16 18:23:52 -0400 (Thu, 16 Jul 2009) | 3 lines
3166 M /trunk/samtools/Makefile
3167 M /trunk/samtools/bam_tview.c
3168 M /trunk/samtools/bamtk.c
3170 * samtools-0.1.5-8 (r404)
3171 * compatible with PDCurses
3173 ------------------------------------------------------------------------
3174 r403 | lh3lh3 | 2009-07-16 17:39:39 -0400 (Thu, 16 Jul 2009) | 3 lines
3176 M /trunk/samtools/bamtk.c
3177 M /trunk/samtools/kseq.h
3179 * samtools-0.1.5-7 (r403)
3180 * fixed a bug in kseq.h for binary files (text files are fine)
3182 ------------------------------------------------------------------------
3183 r402 | lh3lh3 | 2009-07-16 06:49:53 -0400 (Thu, 16 Jul 2009) | 4 lines
3185 M /trunk/samtools/bam_import.c
3186 M /trunk/samtools/bam_index.c
3187 M /trunk/samtools/bamtk.c
3188 M /trunk/samtools/bgzf.c
3190 * samtools-0.1.5-6 (r402)
3191 * fixed compiling error when "-D_USE_NETFILE" is not applied
3192 * improve portability to MinGW
3194 ------------------------------------------------------------------------
3195 r398 | lh3lh3 | 2009-07-13 05:21:36 -0400 (Mon, 13 Jul 2009) | 3 lines
3197 A /trunk/bam-lite/bam.h (from /trunk/samtools/bam.h:395)
3198 A /trunk/bam-lite/bam_lite.c (from /trunk/samtools/bam_lite.c:395)
3199 D /trunk/samtools/bam_lite.c
3201 * move bam_lite.c to bam-lite
3202 * copy bam.h to bam-lite
3204 ------------------------------------------------------------------------
3205 r395 | lh3lh3 | 2009-07-13 05:12:57 -0400 (Mon, 13 Jul 2009) | 3 lines
3207 M /trunk/samtools/bam.h
3208 M /trunk/samtools/bam_lite.c
3209 M /trunk/samtools/bam_lpileup.c
3210 M /trunk/samtools/bam_pileup.c
3211 M /trunk/samtools/bamtk.c
3213 * samtools-0.1.5-5 (r395)
3214 * added bam_pileup_file() and removed bam_lpileup_file()
3216 ------------------------------------------------------------------------
3217 r394 | lh3lh3 | 2009-07-12 19:35:10 -0400 (Sun, 12 Jul 2009) | 3 lines
3219 M /trunk/samtools/bamtk.c
3220 M /trunk/samtools/knetfile.c
3221 M /trunk/samtools/knetfile.h
3223 * samtools-0.1.5-4 (r394)
3224 * http_proxy support in knetfile library (check http_proxy ENV)
3226 ------------------------------------------------------------------------
3227 r393 | lh3lh3 | 2009-07-12 18:57:07 -0400 (Sun, 12 Jul 2009) | 5 lines
3229 M /trunk/samtools/bam_index.c
3230 M /trunk/samtools/bam_tview.c
3231 M /trunk/samtools/bamtk.c
3232 M /trunk/samtools/knetfile.c
3233 M /trunk/samtools/knetfile.h
3235 * samtools-0.1.5-3 (r393)
3236 * knetfile now supports HTTP (no proxy at the moment)
3237 * fixed a potential issue in knetfile on opening ordinary file, although I have
3238 not seen the sideeffect so far.
3240 ------------------------------------------------------------------------
3241 r392 | lh3lh3 | 2009-07-12 13:50:55 -0400 (Sun, 12 Jul 2009) | 2 lines
3243 M /trunk/samtools/samtools.1
3245 Remove the warning in tview
3247 ------------------------------------------------------------------------
3248 r391 | lh3lh3 | 2009-07-12 13:42:43 -0400 (Sun, 12 Jul 2009) | 3 lines
3250 M /trunk/samtools/bam_tview.c
3251 M /trunk/samtools/bamtk.c
3253 * samtools-0.1.5-2 (r391)
3254 * do not show a blank screen when no reads mapped
3256 ------------------------------------------------------------------------
3257 r390 | lh3lh3 | 2009-07-09 09:01:42 -0400 (Thu, 09 Jul 2009) | 4 lines
3259 M /trunk/samtools/bam.h
3260 A /trunk/samtools/bam_lite.c
3261 M /trunk/samtools/bamtk.c
3263 * samtools-0.1.5-1 (r390)
3264 * removed useless _IOLIB in bam.h. This should cause no change at all.
3265 * added bam_lite.c for light-weight BAM reading
3267 ------------------------------------------------------------------------
3268 r385 | lh3lh3 | 2009-07-07 11:53:29 -0400 (Tue, 07 Jul 2009) | 2 lines
3270 M /trunk/samtools/bamtk.c
3271 M /trunk/samtools/knetfile.c
3273 Release samtools-0.1.5c (fixed a bug in piping)
3275 ------------------------------------------------------------------------
3276 r383 | lh3lh3 | 2009-07-07 06:39:55 -0400 (Tue, 07 Jul 2009) | 2 lines
3278 M /trunk/samtools/bamtk.c
3279 M /trunk/samtools/sam.c
3281 Release samtools-0.1.5b (BUG! so embarrassing!)
3283 ------------------------------------------------------------------------
3284 r381 | lh3lh3 | 2009-07-07 06:20:06 -0400 (Tue, 07 Jul 2009) | 2 lines
3286 M /trunk/samtools/Makefile
3287 M /trunk/samtools/bam.h
3288 M /trunk/samtools/bam_aux.c
3289 M /trunk/samtools/bamtk.c
3291 Release samtools-0.1.5a (for compatibility with Bio::DB::Sam)
3293 ------------------------------------------------------------------------
3294 r373 | lh3lh3 | 2009-07-07 05:26:57 -0400 (Tue, 07 Jul 2009) | 2 lines
3296 M /trunk/samtools/ChangeLog
3297 M /trunk/samtools/NEWS
3298 M /trunk/samtools/bamtk.c
3299 M /trunk/samtools/samtools.1
3301 Release samtools-0.1.5
3303 ------------------------------------------------------------------------
3304 r372 | lh3lh3 | 2009-07-07 04:49:27 -0400 (Tue, 07 Jul 2009) | 3 lines
3306 M /trunk/samtools/bamtk.c
3307 M /trunk/samtools/sam.c
3309 * samtools-0.1.4-23 (r372)
3310 * keep header text if "view -t" is used (by Gerton)
3312 ------------------------------------------------------------------------
3313 r371 | lh3lh3 | 2009-07-06 20:13:32 -0400 (Mon, 06 Jul 2009) | 2 lines
3315 M /trunk/samtools/samtools.1
3317 update documentation
3319 ------------------------------------------------------------------------
3320 r370 | bhandsaker | 2009-07-02 17:24:34 -0400 (Thu, 02 Jul 2009) | 2 lines
3322 M /trunk/samtools/Makefile
3324 Introduced LIBPATH variable so this could be overridden to allow samtools to build correct at the Broad.
3326 ------------------------------------------------------------------------
3327 r369 | lh3lh3 | 2009-07-02 08:36:53 -0400 (Thu, 02 Jul 2009) | 4 lines
3329 M /trunk/samtools/ChangeLog
3330 M /trunk/samtools/bam_aux.c
3331 M /trunk/samtools/bam_plcmd.c
3332 M /trunk/samtools/bamtk.c
3334 * samtools-0.1.4-22 (r369)
3335 * in pileup, optionally print E2 and U2
3336 * remove the debugging code in bam_aux_get() (Drat!)
3338 ------------------------------------------------------------------------
3339 r368 | lh3lh3 | 2009-07-02 06:32:26 -0400 (Thu, 02 Jul 2009) | 6 lines
3341 M /trunk/samtools/bam.c
3342 M /trunk/samtools/bam.h
3343 M /trunk/samtools/bam_aux.c
3344 M /trunk/samtools/bam_index.c
3345 M /trunk/samtools/bam_lpileup.c
3346 M /trunk/samtools/bam_md.c
3347 M /trunk/samtools/bam_pileup.c
3348 M /trunk/samtools/bam_rmdup.c
3349 M /trunk/samtools/bam_stat.c
3350 M /trunk/samtools/bam_tview.c
3351 M /trunk/samtools/bamtk.c
3352 M /trunk/samtools/faidx.c
3353 M /trunk/samtools/faidx.h
3354 M /trunk/samtools/glf.c
3356 * samtools-0.1.4-21 (r368)
3357 * propagate errors rather than exit or complain assertion failure. Assertion
3358 should be only used for checking internal bugs, but not for external input
3359 inconsistency. I was just a bit lazy.
3360 * small memory leak may be present on failure, though
3362 ------------------------------------------------------------------------
3363 r367 | lh3lh3 | 2009-06-30 11:18:42 -0400 (Tue, 30 Jun 2009) | 2 lines
3365 M /trunk/samtools/knetfile.c
3367 reduce the chance of blocking in FTP connection
3369 ------------------------------------------------------------------------
3370 r366 | lh3lh3 | 2009-06-30 10:35:21 -0400 (Tue, 30 Jun 2009) | 2 lines
3372 M /trunk/samtools/knetfile.c
3374 minor changes to knetfile: invalid fd equals -1 rather than 0
3376 ------------------------------------------------------------------------
3377 r365 | lh3lh3 | 2009-06-30 09:04:30 -0400 (Tue, 30 Jun 2009) | 3 lines
3379 M /trunk/samtools/bam_index.c
3380 M /trunk/samtools/bamtk.c
3381 M /trunk/samtools/knetfile.c
3382 M /trunk/samtools/knetfile.h
3384 * samtools-0.1.4-20 (r365)
3385 * download the BAM index file if it is not found in the current working directory.
3387 ------------------------------------------------------------------------
3388 r364 | lh3lh3 | 2009-06-30 07:39:07 -0400 (Tue, 30 Jun 2009) | 3 lines
3390 M /trunk/samtools/bamtk.c
3391 M /trunk/samtools/knetfile.c
3393 * samtools-0.1.4-19 (r364)
3394 * knetfile: report error when the file is not present on FTP
3396 ------------------------------------------------------------------------
3397 r363 | lh3lh3 | 2009-06-29 18:23:32 -0400 (Mon, 29 Jun 2009) | 4 lines
3399 M /trunk/samtools/bam_tview.c
3400 M /trunk/samtools/bamtk.c
3401 M /trunk/samtools/bgzf.c
3402 M /trunk/samtools/bgzf.h
3403 M /trunk/samtools/knetfile.c
3404 M /trunk/samtools/knetfile.h
3406 * samtools-0.1.4-18 (r363)
3407 * knetfile: do not trigger network communication in FTP seek (lazy seek)
3408 * bgzf: cache recent blocks (disabled by default)
3410 ------------------------------------------------------------------------
3411 r362 | lh3lh3 | 2009-06-25 16:04:34 -0400 (Thu, 25 Jun 2009) | 2 lines
3413 M /trunk/samtools/bgzf.c
3417 ------------------------------------------------------------------------
3418 r361 | lh3lh3 | 2009-06-25 16:03:10 -0400 (Thu, 25 Jun 2009) | 3 lines
3420 M /trunk/samtools/bam_index.c
3421 M /trunk/samtools/bamtk.c
3423 * samtools-0.1.4-17 (r361)
3424 * if a file is given on FTP, search locally for the BAM index
3426 ------------------------------------------------------------------------
3427 r360 | lh3lh3 | 2009-06-25 15:44:52 -0400 (Thu, 25 Jun 2009) | 5 lines
3429 M /trunk/samtools/Makefile
3430 M /trunk/samtools/bam_import.c
3431 M /trunk/samtools/bam_index.c
3432 M /trunk/samtools/bamtk.c
3433 M /trunk/samtools/bgzf.c
3434 M /trunk/samtools/bgzf.h
3435 M /trunk/samtools/knetfile.c
3436 M /trunk/samtools/knetfile.h
3438 * samtools-0.1.4-16 (r360)
3439 * report more information in index when the input is not sorted
3440 * change the behaviour of knet_seek() such that it returns 0 on success
3441 * support knetfile library in BGZF
3443 ------------------------------------------------------------------------
3444 r359 | lh3lh3 | 2009-06-25 12:10:55 -0400 (Thu, 25 Jun 2009) | 2 lines
3446 M /trunk/samtools/knetfile.c
3447 M /trunk/samtools/knetfile.h
3449 fixed bugs in knetfile.*
3451 ------------------------------------------------------------------------
3452 r358 | lh3lh3 | 2009-06-25 08:53:19 -0400 (Thu, 25 Jun 2009) | 2 lines
3454 A /trunk/samtools/knetfile.h
3456 this is the header file
3458 ------------------------------------------------------------------------
3459 r357 | lh3lh3 | 2009-06-25 08:52:03 -0400 (Thu, 25 Jun 2009) | 3 lines
3461 A /trunk/samtools/knetfile.c
3463 * open a file at FTP
3464 * preliminary version
3466 ------------------------------------------------------------------------
3467 r354 | lh3lh3 | 2009-06-24 09:02:25 -0400 (Wed, 24 Jun 2009) | 3 lines
3469 M /trunk/samtools/bam.c
3470 M /trunk/samtools/bamtk.c
3472 * samtools-0.1.4-15 (r354)
3473 * fixed a memory leak in bam_view1(), although samtools is not using this routine.
3475 ------------------------------------------------------------------------
3476 r351 | lh3lh3 | 2009-06-17 19:16:26 -0400 (Wed, 17 Jun 2009) | 4 lines
3478 M /trunk/samtools/bamtk.c
3479 M /trunk/samtools/faidx.c
3481 * samtools-0.1.4-13 (r351)
3482 * make faidx more tolerant to empty lines right before or after > lines
3483 * hope this does not introduce new bugs...
3485 ------------------------------------------------------------------------
3486 r350 | lh3lh3 | 2009-06-16 09:37:01 -0400 (Tue, 16 Jun 2009) | 3 lines
3488 M /trunk/samtools/bam_plcmd.c
3489 M /trunk/samtools/bamtk.c
3491 * samtools-0.1.4-13 (r350)
3492 * fixed a small memory leak in pileup, caused by recent modifications
3494 ------------------------------------------------------------------------
3495 r347 | lh3lh3 | 2009-06-13 16:20:49 -0400 (Sat, 13 Jun 2009) | 3 lines
3497 M /trunk/samtools/bam_plcmd.c
3498 M /trunk/samtools/bamtk.c
3499 M /trunk/samtools/sam_view.c
3501 * samtools-0.1.4-12 (r347)
3502 * added `-S' to pileup, similar to `view -S'
3504 ------------------------------------------------------------------------
3505 r346 | lh3lh3 | 2009-06-13 12:52:31 -0400 (Sat, 13 Jun 2009) | 3 lines
3507 M /trunk/samtools/Makefile
3508 M /trunk/samtools/bamtk.c
3509 M /trunk/samtools/sam_view.c
3510 M /trunk/samtools/samtools.1
3512 * samtools-0.1.4-11 (r346)
3513 * allow to select a read group at view command-line
3515 ------------------------------------------------------------------------
3516 r344 | lh3lh3 | 2009-06-13 09:06:24 -0400 (Sat, 13 Jun 2009) | 2 lines
3518 M /trunk/samtools/examples/calDepth.c
3522 ------------------------------------------------------------------------
3523 r343 | lh3lh3 | 2009-06-13 09:01:22 -0400 (Sat, 13 Jun 2009) | 2 lines
3525 M /trunk/samtools/examples/calDepth.c
3529 ------------------------------------------------------------------------
3530 r342 | lh3lh3 | 2009-06-13 08:58:48 -0400 (Sat, 13 Jun 2009) | 2 lines
3532 M /trunk/samtools/examples/Makefile
3533 A /trunk/samtools/examples/calDepth.c
3535 added an example of calculating read depth
3537 ------------------------------------------------------------------------
3538 r341 | lh3lh3 | 2009-06-13 08:00:08 -0400 (Sat, 13 Jun 2009) | 6 lines
3540 M /trunk/samtools/Makefile
3541 M /trunk/samtools/bam.h
3542 M /trunk/samtools/bam_aux.c
3543 A /trunk/samtools/bam_color.c
3544 M /trunk/samtools/bam_plcmd.c
3545 M /trunk/samtools/bam_sort.c
3546 M /trunk/samtools/bam_tview.c
3547 M /trunk/samtools/bamtk.c
3548 M /trunk/samtools/sam.c
3549 M /trunk/samtools/sam.h
3551 * samtools-0.1.4-10 (r341)
3552 * only include key APIs in libbam.a
3553 * move color-specific routines to bam_color.c
3554 * update documentations
3555 * remove the support of -q in pileup
3557 ------------------------------------------------------------------------
3558 r340 | lh3lh3 | 2009-06-13 06:17:14 -0400 (Sat, 13 Jun 2009) | 6 lines
3560 M /trunk/samtools/INSTALL
3561 M /trunk/samtools/Makefile
3562 M /trunk/samtools/bam_aux.c
3563 M /trunk/samtools/bam_import.c
3564 M /trunk/samtools/bam_tview.c
3565 M /trunk/samtools/bamtk.c
3566 M /trunk/samtools/razf.c
3567 M /trunk/samtools/sam_view.c
3569 * samtools-0.1.4-9 (r340)
3570 * added a warning to razf.c if zlib<1.2.2.1
3571 * fixed a compilation warning
3572 * fixed a segfault caused by @RG parsing
3573 * detect NCURSES in bam_tview.c
3575 ------------------------------------------------------------------------
3576 r339 | lh3lh3 | 2009-06-13 05:35:19 -0400 (Sat, 13 Jun 2009) | 2 lines
3578 M /trunk/samtools/INSTALL
3582 ------------------------------------------------------------------------
3583 r338 | lh3lh3 | 2009-06-12 19:15:24 -0400 (Fri, 12 Jun 2009) | 4 lines
3585 M /trunk/samtools/bam.c
3586 M /trunk/samtools/bam.h
3587 M /trunk/samtools/bam_aux.c
3588 M /trunk/samtools/bam_import.c
3589 M /trunk/samtools/bamtk.c
3590 M /trunk/samtools/kstring.h
3591 M /trunk/samtools/sam.c
3592 M /trunk/samtools/sam_view.c
3594 * samtools-0.1.4-8 (r338)
3595 * parse the @RG header lines and allow to choose library at the "samtools view"
3598 ------------------------------------------------------------------------
3599 r337 | lh3lh3 | 2009-06-12 16:25:50 -0400 (Fri, 12 Jun 2009) | 4 lines
3601 M /trunk/samtools/bamtk.c
3602 M /trunk/samtools/bgzf.c
3603 M /trunk/samtools/bgzf.h
3604 M /trunk/samtools/sam.c
3605 M /trunk/samtools/sam_view.c
3607 * samtools-0.1.4-7 (r337)
3608 * bgzf.c: support mode string "wu": uncompressed output
3609 * "samtools view" support "-u" command-line option
3611 ------------------------------------------------------------------------
3612 r336 | lh3lh3 | 2009-06-12 12:20:12 -0400 (Fri, 12 Jun 2009) | 5 lines
3614 M /trunk/samtools/Makefile
3615 M /trunk/samtools/misc/Makefile
3616 M /trunk/samtools/razf.c
3617 M /trunk/samtools/razf.h
3618 M /trunk/samtools/razip.c
3620 * no changes to samtools itself
3621 * remove zlib source codes
3622 * make RAZF reading compatible with old version of zlib
3623 * on old version of zlib, writing is not available
3625 ------------------------------------------------------------------------
3626 r335 | lh3lh3 | 2009-06-12 11:47:33 -0400 (Fri, 12 Jun 2009) | 2 lines
3628 D /trunk/samtools/zlib
3630 remove zlib for simplification...
3632 ------------------------------------------------------------------------
3633 r334 | lh3lh3 | 2009-06-12 10:43:36 -0400 (Fri, 12 Jun 2009) | 5 lines
3635 M /trunk/samtools/bam.h
3636 M /trunk/samtools/bam_aux.c
3637 M /trunk/samtools/bamtk.c
3639 * samtools-0.1.4-6 (r334)
3640 * do not export bam_aux_get_core() for Bio::DB::Sam because it has already
3641 been implemented in that.
3642 * this version works with the latest Bio::DB::Sam (20090612)
3644 ------------------------------------------------------------------------
3645 r333 | lh3lh3 | 2009-06-12 10:33:42 -0400 (Fri, 12 Jun 2009) | 2 lines
3647 M /trunk/samtools/ChangeLog
3651 ------------------------------------------------------------------------
3652 r332 | lh3lh3 | 2009-06-12 10:21:21 -0400 (Fri, 12 Jun 2009) | 2 lines
3654 M /trunk/samtools/AUTHORS
3655 M /trunk/samtools/Makefile
3656 M /trunk/samtools/misc/Makefile
3658 fixed minor things in Makefile
3660 ------------------------------------------------------------------------
3661 r331 | lh3lh3 | 2009-06-12 10:07:05 -0400 (Fri, 12 Jun 2009) | 4 lines
3663 M /trunk/samtools/bamtk.c
3665 * samtools-0.1.4-5 (r3310
3666 * no change to samtools itself. Version number is increased to reflect the
3667 changes in the Makefile building system.
3669 ------------------------------------------------------------------------
3670 r330 | lh3lh3 | 2009-06-12 10:03:38 -0400 (Fri, 12 Jun 2009) | 2 lines
3672 M /trunk/samtools/AUTHORS
3673 D /trunk/samtools/README
3675 update information...
3677 ------------------------------------------------------------------------
3678 r329 | lh3lh3 | 2009-06-12 09:52:21 -0400 (Fri, 12 Jun 2009) | 3 lines
3680 M /trunk/samtools/misc/novo2sam.pl
3682 * updated novoalign converter by Colin Hercus et al.
3683 * this version works with indels
3685 ------------------------------------------------------------------------
3686 r328 | lh3lh3 | 2009-06-12 09:50:53 -0400 (Fri, 12 Jun 2009) | 3 lines
3688 M /trunk/samtools/INSTALL
3689 M /trunk/samtools/Makefile
3690 M /trunk/samtools/misc/Makefile
3691 M /trunk/samtools/zlib/Makefile
3694 * update INSTALL instruction
3696 ------------------------------------------------------------------------
3697 r327 | lh3lh3 | 2009-06-12 09:18:29 -0400 (Fri, 12 Jun 2009) | 4 lines
3699 A /trunk/samtools/Makefile (from /trunk/samtools/Makefile.generic:325)
3700 D /trunk/samtools/Makefile.am
3701 D /trunk/samtools/Makefile.generic
3702 D /trunk/samtools/Makefile.lite
3703 D /trunk/samtools/autogen.sh
3704 D /trunk/samtools/cleanup.sh
3705 D /trunk/samtools/configure.ac
3706 A /trunk/samtools/misc/Makefile (from /trunk/samtools/misc/Makefile.generic:305)
3707 D /trunk/samtools/misc/Makefile.am
3708 D /trunk/samtools/misc/Makefile.generic
3709 M /trunk/samtools/razf.c
3710 A /trunk/samtools/zlib
3711 A /trunk/samtools/zlib/Makefile
3712 A /trunk/samtools/zlib/adler32.c
3713 A /trunk/samtools/zlib/compress.c
3714 A /trunk/samtools/zlib/crc32.c
3715 A /trunk/samtools/zlib/crc32.h
3716 A /trunk/samtools/zlib/deflate.c
3717 A /trunk/samtools/zlib/deflate.h
3718 A /trunk/samtools/zlib/gzio.c
3719 A /trunk/samtools/zlib/infback.c
3720 A /trunk/samtools/zlib/inffast.c
3721 A /trunk/samtools/zlib/inffast.h
3722 A /trunk/samtools/zlib/inffixed.h
3723 A /trunk/samtools/zlib/inflate.c
3724 A /trunk/samtools/zlib/inflate.h
3725 A /trunk/samtools/zlib/inftrees.c
3726 A /trunk/samtools/zlib/inftrees.h
3727 A /trunk/samtools/zlib/trees.c
3728 A /trunk/samtools/zlib/trees.h
3729 A /trunk/samtools/zlib/uncompr.c
3730 A /trunk/samtools/zlib/zconf.h
3731 A /trunk/samtools/zlib/zlib.h
3732 A /trunk/samtools/zlib/zutil.c
3733 A /trunk/samtools/zlib/zutil.h
3734 D /trunk/samtools/zutil.h
3736 * added zlib-1.2.3 as razip requires that
3737 * prepare to changed back to the Makefile building system
3738 * unfinished! (will be soon)
3740 ------------------------------------------------------------------------
3741 r326 | lh3lh3 | 2009-06-12 09:12:03 -0400 (Fri, 12 Jun 2009) | 2 lines
3743 M /trunk/samtools/misc/samtools.pl
3747 ------------------------------------------------------------------------
3748 r325 | lh3lh3 | 2009-06-10 11:27:59 -0400 (Wed, 10 Jun 2009) | 3 lines
3750 M /trunk/samtools/bam_maqcns.c
3751 M /trunk/samtools/bamtk.c
3753 * samtools-0.1.4-4 (r325)
3754 * further avoid wrong consensus calls in repetitive regions.
3756 ------------------------------------------------------------------------
3757 r324 | lh3lh3 | 2009-06-10 10:56:17 -0400 (Wed, 10 Jun 2009) | 4 lines
3759 M /trunk/samtools/bam_maqcns.c
3760 M /trunk/samtools/bam_plcmd.c
3761 M /trunk/samtools/bamtk.c
3762 M /trunk/samtools/sam.c
3763 M /trunk/samtools/sam.h
3765 * samtools-0.1.4-3 (r324)
3766 * make maqcns generate the correct call in repetitive regions.
3767 * allow filtering on mapQ at the pileup command line
3769 ------------------------------------------------------------------------
3770 r323 | lh3lh3 | 2009-06-10 05:04:21 -0400 (Wed, 10 Jun 2009) | 3 lines
3772 M /trunk/samtools/misc/samtools.pl
3774 * samtools.pl-0.3.2 (r322)
3775 * indels and SNPs use different mapping quality threshold
3777 ------------------------------------------------------------------------
3778 r322 | lh3lh3 | 2009-06-10 05:03:22 -0400 (Wed, 10 Jun 2009) | 2 lines
3780 M /trunk/samtools/misc/export2sam.pl
3784 ------------------------------------------------------------------------
3785 r321 | lh3lh3 | 2009-06-09 04:21:48 -0400 (Tue, 09 Jun 2009) | 2 lines
3787 M /trunk/samtools/misc/samtools.pl
3789 just typo. no real change
3791 ------------------------------------------------------------------------
3792 r320 | lh3lh3 | 2009-06-08 09:32:51 -0400 (Mon, 08 Jun 2009) | 2 lines
3794 M /trunk/samtools/misc/samtools.pl
3796 a little bit code cleanup
3798 ------------------------------------------------------------------------
3799 r319 | lh3lh3 | 2009-06-08 09:22:33 -0400 (Mon, 08 Jun 2009) | 4 lines
3801 M /trunk/samtools/misc/samtools.pl
3804 * change default parameters
3805 * optionally print filtered variants
3807 ------------------------------------------------------------------------
3808 r318 | lh3lh3 | 2009-06-08 09:14:26 -0400 (Mon, 08 Jun 2009) | 3 lines
3810 M /trunk/samtools/misc/samtools.pl
3813 * combine snpFilter and indelFilter
3815 ------------------------------------------------------------------------
3816 r317 | lh3lh3 | 2009-06-08 06:31:42 -0400 (Mon, 08 Jun 2009) | 3 lines
3818 M /trunk/samtools/misc/samtools.pl
3821 * change a default parameter
3823 ------------------------------------------------------------------------
3824 r316 | lh3lh3 | 2009-06-08 06:11:06 -0400 (Mon, 08 Jun 2009) | 5 lines
3826 M /trunk/samtools/bam_maqcns.c
3827 M /trunk/samtools/bam_maqcns.h
3828 M /trunk/samtools/bam_plcmd.c
3829 M /trunk/samtools/bamtk.c
3830 M /trunk/samtools/sam.c
3832 * samtools-0.1.4-2 (r316)
3833 * pileup: cap mapping quality at 60 (by default)
3834 * pileup: always calculate RMS mapq
3835 * pileup: allow to output variant sites only
3837 ------------------------------------------------------------------------
3838 r312 | lh3lh3 | 2009-06-04 08:01:10 -0400 (Thu, 04 Jun 2009) | 3 lines
3840 M /trunk/samtools/misc/samtools.pl
3845 ------------------------------------------------------------------------
3846 r311 | lh3lh3 | 2009-06-03 04:40:40 -0400 (Wed, 03 Jun 2009) | 2 lines
3848 M /trunk/samtools/misc/samtools.pl
3850 * in snpFilter, suppress non-SNP sites
3852 ------------------------------------------------------------------------
3853 r310 | lh3lh3 | 2009-06-01 09:35:13 -0400 (Mon, 01 Jun 2009) | 3 lines
3855 M /trunk/samtools/misc/samtools.pl
3860 ------------------------------------------------------------------------
3861 r309 | lh3lh3 | 2009-06-01 09:04:39 -0400 (Mon, 01 Jun 2009) | 3 lines
3863 M /trunk/samtools/misc/samtools.pl
3868 ------------------------------------------------------------------------
3869 r306 | lh3lh3 | 2009-05-28 06:49:35 -0400 (Thu, 28 May 2009) | 3 lines
3871 M /trunk/samtools/bgzf.c
3873 * minor changes to bgzf: return NULL if fd == -1
3874 * suggested by {kdj,jm18}@sanger.ac.uk
3876 ------------------------------------------------------------------------
3877 r305 | lh3lh3 | 2009-05-28 06:16:08 -0400 (Thu, 28 May 2009) | 2 lines
3879 A /trunk/samtools/misc/interpolate_sam.pl
3881 Script for paired-end pileup, contributed by Stephen Montgomery.
3883 ------------------------------------------------------------------------
3884 r304 | lh3lh3 | 2009-05-28 06:08:49 -0400 (Thu, 28 May 2009) | 3 lines
3886 M /trunk/samtools/bamtk.c
3887 M /trunk/samtools/sam.c
3889 * samtools-0.1.4-1 (r304)
3890 * fixed a minor bug in printing headers
3892 ------------------------------------------------------------------------
3893 r297 | lh3lh3 | 2009-05-21 11:06:16 -0400 (Thu, 21 May 2009) | 2 lines
3895 M /trunk/samtools/ChangeLog
3896 M /trunk/samtools/NEWS
3897 M /trunk/samtools/bam_plcmd.c
3898 M /trunk/samtools/bamtk.c
3899 M /trunk/samtools/misc/maq2sam.c
3900 M /trunk/samtools/samtools.1
3902 Release samtools-0.1.4
3904 ------------------------------------------------------------------------
3905 r296 | lh3lh3 | 2009-05-21 07:53:14 -0400 (Thu, 21 May 2009) | 3 lines
3907 M /trunk/samtools/bam_maqcns.c
3908 M /trunk/samtools/bamtk.c
3910 * samtools-0.1.3-24 (r296)
3911 * another similar bug in the indel caller
3913 ------------------------------------------------------------------------
3914 r295 | lh3lh3 | 2009-05-21 07:50:28 -0400 (Thu, 21 May 2009) | 3 lines
3916 M /trunk/samtools/bam_maqcns.c
3917 M /trunk/samtools/bamtk.c
3919 * samtools-0.1.3-23 (r295)
3920 * fixed a critical bug in the indel caller
3922 ------------------------------------------------------------------------
3923 r294 | lh3lh3 | 2009-05-20 08:00:20 -0400 (Wed, 20 May 2009) | 2 lines
3925 M /trunk/samtools/bam_stat.c
3927 added a missing header file
3929 ------------------------------------------------------------------------
3930 r293 | lh3lh3 | 2009-05-19 18:44:25 -0400 (Tue, 19 May 2009) | 3 lines
3932 M /trunk/samtools/bam_tview.c
3933 M /trunk/samtools/bamtk.c
3935 * samtools-0.1.3-22 (r293)
3936 * open tview in the dot-view mode by default
3938 ------------------------------------------------------------------------
3939 r292 | lh3lh3 | 2009-05-18 16:01:23 -0400 (Mon, 18 May 2009) | 6 lines
3941 M /trunk/samtools/samtools.1
3943 Added a note to the manual. Currently SAMtools used unaligned words in
3944 several places. Although this does not cause bus errors to me, it may
3945 affect portability. Please see the "Bus error" wiki page for more
3946 information. Also thank James Bonfields for pointing this out.
3949 ------------------------------------------------------------------------
3950 r286 | lh3lh3 | 2009-05-14 10:23:13 -0400 (Thu, 14 May 2009) | 3 lines
3952 M /trunk/samtools/bam.h
3953 M /trunk/samtools/bam_aux.c
3954 M /trunk/samtools/bamtk.c
3956 * samtools-0.1.3-21 (286)
3957 * declare bam_aux_get_core() in bam.h
3959 ------------------------------------------------------------------------
3960 r276 | lh3lh3 | 2009-05-13 05:07:55 -0400 (Wed, 13 May 2009) | 5 lines
3962 M /trunk/samtools/bam.h
3963 M /trunk/samtools/bam_index.c
3964 M /trunk/samtools/bamtk.c
3966 * samtools-0.1.3-20 (r276)
3967 * remove bam1_t::hash again. We need to modify the Perl API anyway to
3968 make it work with the latest SVN.
3969 * As is suggested by Tim, scan "{base}.bai" and "{base}.bam.bai" for index
3971 ------------------------------------------------------------------------
3972 r275 | lh3lh3 | 2009-05-12 16:14:10 -0400 (Tue, 12 May 2009) | 4 lines
3974 M /trunk/samtools/ChangeLog
3975 M /trunk/samtools/bam.h
3976 M /trunk/samtools/bamtk.c
3978 * samtools-0.1.3-19 (r275)
3979 * a minor change to the bam1_t struct: added back "void *hash" for the
3980 backward compatibility with Bio::DB::Sam
3982 ------------------------------------------------------------------------
3983 r273 | lh3lh3 | 2009-05-12 09:28:39 -0400 (Tue, 12 May 2009) | 3 lines
3985 M /trunk/samtools/bam_rmdupse.c
3986 M /trunk/samtools/bamtk.c
3988 * samtools-0.1.3-18 (r273)
3989 * rmdupse: do not remove unmapped reads
3991 ------------------------------------------------------------------------
3992 r272 | lh3lh3 | 2009-05-12 09:20:00 -0400 (Tue, 12 May 2009) | 2 lines
3994 M /trunk/samtools/bam_rmdupse.c
3996 change a parameter. It does nothing
3998 ------------------------------------------------------------------------
3999 r271 | lh3lh3 | 2009-05-12 09:17:58 -0400 (Tue, 12 May 2009) | 3 lines
4001 M /trunk/samtools/Makefile.am
4002 M /trunk/samtools/Makefile.generic
4003 M /trunk/samtools/Makefile.lite
4004 A /trunk/samtools/bam_rmdupse.c
4005 M /trunk/samtools/bamtk.c
4006 M /trunk/samtools/configure.ac
4008 * samtools-0.1.3-17 (r271)
4009 * added 'rmdupse' command
4011 ------------------------------------------------------------------------
4012 r267 | lh3lh3 | 2009-05-05 17:31:41 -0400 (Tue, 05 May 2009) | 3 lines
4014 M /trunk/samtools/bamtk.c
4015 M /trunk/samtools/sam_view.c
4017 * samtools-0.1.3-16 (r267)
4018 * in sam_view.c, changed g_flag_on based on the suggestion by Angie Hinrichs
4020 ------------------------------------------------------------------------
4021 r266 | lh3lh3 | 2009-05-05 17:23:27 -0400 (Tue, 05 May 2009) | 3 lines
4023 M /trunk/samtools/bam_import.c
4024 M /trunk/samtools/bamtk.c
4026 * samtools-0.1.3-15 (r266)
4027 * report an error if a non-* reference is present while @SQ is absent
4029 ------------------------------------------------------------------------
4030 r265 | lh3lh3 | 2009-05-05 17:09:00 -0400 (Tue, 05 May 2009) | 3 lines
4032 M /trunk/samtools/bam.h
4033 M /trunk/samtools/bam_import.c
4034 M /trunk/samtools/bamtk.c
4035 M /trunk/samtools/sam.c
4036 M /trunk/samtools/sam_view.c
4038 * samtools-0.1.3-14 (r262)
4039 * make samopen() recognize @SQ header lines
4041 ------------------------------------------------------------------------
4042 r261 | lh3lh3 | 2009-05-05 10:10:30 -0400 (Tue, 05 May 2009) | 3 lines
4044 M /trunk/samtools/bam_plcmd.c
4045 M /trunk/samtools/bamtk.c
4046 M /trunk/samtools/bgzf.c
4047 M /trunk/samtools/sam.c
4048 M /trunk/samtools/sam_view.c
4050 * samtools-0.1.3-13 (r260)
4051 * report error for file I/O error
4053 ------------------------------------------------------------------------
4054 r260 | lh3lh3 | 2009-05-05 10:01:16 -0400 (Tue, 05 May 2009) | 2 lines
4056 M /trunk/samtools/Makefile.am
4060 ------------------------------------------------------------------------
4061 r259 | lh3lh3 | 2009-05-05 09:52:25 -0400 (Tue, 05 May 2009) | 3 lines
4063 M /trunk/samtools/bam.h
4064 M /trunk/samtools/bam_pileup.c
4065 M /trunk/samtools/bam_plcmd.c
4066 M /trunk/samtools/bamtk.c
4067 M /trunk/samtools/sam.c
4068 M /trunk/samtools/sam.h
4070 * samtools-0.1.3-12 (r259)
4071 * use the new I/O interface in pileup
4073 ------------------------------------------------------------------------
4074 r258 | lh3lh3 | 2009-05-05 09:33:22 -0400 (Tue, 05 May 2009) | 3 lines
4076 M /trunk/samtools/Makefile.generic
4077 M /trunk/samtools/Makefile.lite
4078 M /trunk/samtools/bam.c
4079 M /trunk/samtools/bam.h
4080 M /trunk/samtools/bam_import.c
4081 M /trunk/samtools/bamtk.c
4082 A /trunk/samtools/sam.c
4083 A /trunk/samtools/sam.h
4084 A /trunk/samtools/sam_view.c
4086 * samtools-0.1.3-11 (r258)
4087 * unify the interface to BAM and SAM I/O
4089 ------------------------------------------------------------------------
4090 r257 | lh3lh3 | 2009-05-05 04:53:35 -0400 (Tue, 05 May 2009) | 3 lines
4092 M /trunk/samtools/Makefile.lite
4093 M /trunk/samtools/bam_plcmd.c
4094 M /trunk/samtools/bamtk.c
4096 * samtools-0.1.3-10 (r257)
4097 * allow hex with "pileup -m"
4099 ------------------------------------------------------------------------
4100 r256 | lh3lh3 | 2009-05-04 14:16:50 -0400 (Mon, 04 May 2009) | 4 lines
4102 M /trunk/samtools/bam_lpileup.c
4103 M /trunk/samtools/bamtk.c
4105 * samtools-0.1.3-9 (r256)
4106 * fixed a bug in bam_lpileup.c
4107 * I do not know if this also fixes the bug causing assertion failure in the tview
4109 ------------------------------------------------------------------------
4110 r251 | lh3lh3 | 2009-04-28 08:53:23 -0400 (Tue, 28 Apr 2009) | 3 lines
4112 M /trunk/samtools/bam_pileup.c
4113 M /trunk/samtools/bamtk.c
4115 * samtools-0.1.3-8 (r251)
4116 * fixed a bug when there are reads without coordinates
4118 ------------------------------------------------------------------------
4119 r250 | lh3lh3 | 2009-04-28 08:43:33 -0400 (Tue, 28 Apr 2009) | 2 lines
4121 A /trunk/samtools/AUTHORS
4122 A /trunk/samtools/README
4123 M /trunk/samtools/cleanup.sh
4127 ------------------------------------------------------------------------
4128 r249 | lh3lh3 | 2009-04-28 08:37:16 -0400 (Tue, 28 Apr 2009) | 2 lines
4130 M /trunk/samtools/Makefile.generic
4131 M /trunk/samtools/Makefile.lite
4132 M /trunk/samtools/configure.ac
4133 M /trunk/samtools/misc/Makefile.generic
4135 improve large file support in compilation
4137 ------------------------------------------------------------------------
4138 r248 | lh3lh3 | 2009-04-28 08:33:24 -0400 (Tue, 28 Apr 2009) | 2 lines
4140 M /trunk/samtools/INSTALL
4144 ------------------------------------------------------------------------
4145 r247 | lh3lh3 | 2009-04-28 08:28:50 -0400 (Tue, 28 Apr 2009) | 2 lines
4147 M /trunk/samtools/Makefile.am
4148 M /trunk/samtools/autogen.sh
4149 M /trunk/samtools/cleanup.sh
4150 M /trunk/samtools/configure.ac
4151 A /trunk/samtools/misc/Makefile.am
4153 fixed various issues about the GNU building scripts
4155 ------------------------------------------------------------------------
4156 r246 | lh3lh3 | 2009-04-28 08:10:23 -0400 (Tue, 28 Apr 2009) | 4 lines
4158 M /trunk/samtools/ChangeLog
4159 D /trunk/samtools/Makefile
4160 A /trunk/samtools/Makefile.am
4161 A /trunk/samtools/Makefile.generic
4162 A /trunk/samtools/autogen.sh
4163 M /trunk/samtools/bam.h
4164 M /trunk/samtools/bam_aux.c
4165 M /trunk/samtools/bam_tview.c
4166 M /trunk/samtools/bamtk.c
4167 A /trunk/samtools/cleanup.sh
4168 A /trunk/samtools/configure.ac
4169 D /trunk/samtools/misc/Makefile
4170 A /trunk/samtools/misc/Makefile.generic (from /trunk/samtools/misc/Makefile:245)
4172 * samtools-0.1.3-7 (r246)
4173 * incorporated revisions from Nils Homer
4174 * enhanced support of displaying color-space reads
4176 ------------------------------------------------------------------------
4177 r244 | lh3lh3 | 2009-04-25 06:49:40 -0400 (Sat, 25 Apr 2009) | 3 lines
4179 M /trunk/samtools/bam_md.c
4180 M /trunk/samtools/bamtk.c
4182 * samtools-0.1.3-6 (r244)
4183 * fixed segfault for unmapped reads
4185 ------------------------------------------------------------------------
4186 r243 | lh3lh3 | 2009-04-24 16:27:26 -0400 (Fri, 24 Apr 2009) | 5 lines
4188 M /trunk/samtools/bam.h
4189 M /trunk/samtools/bam_maqcns.c
4190 M /trunk/samtools/bam_md.c
4191 M /trunk/samtools/bamtk.c
4193 * samtools-0.1.3-5 (r243)
4194 * fixed a long existing bug which may cause memory leak
4196 * consensus calling now works with "=", but indel calling not
4198 ------------------------------------------------------------------------
4199 r242 | lh3lh3 | 2009-04-24 15:44:46 -0400 (Fri, 24 Apr 2009) | 3 lines
4201 M /trunk/samtools/bam_md.c
4202 M /trunk/samtools/bamtk.c
4204 * samtools-0.1.3-4 (r242)
4205 * fixed a memory leak
4207 ------------------------------------------------------------------------
4208 r240 | lh3lh3 | 2009-04-24 11:40:18 -0400 (Fri, 24 Apr 2009) | 5 lines
4210 M /trunk/samtools/Makefile
4211 M /trunk/samtools/Makefile.lite
4212 M /trunk/samtools/bam.h
4213 M /trunk/samtools/bam_aux.c
4214 A /trunk/samtools/bam_md.c
4215 M /trunk/samtools/bam_plcmd.c
4216 M /trunk/samtools/bamtk.c
4218 * samtools-0.1.3-3 (r240)
4220 * generate "=" bases
4221 * the plain pileup now support "=" bases, but consensus calling and glfgen may fail
4223 ------------------------------------------------------------------------
4224 r239 | lh3lh3 | 2009-04-24 07:08:20 -0400 (Fri, 24 Apr 2009) | 5 lines
4226 M /trunk/samtools/bam.h
4227 M /trunk/samtools/bam_aux.c
4228 M /trunk/samtools/bamtk.c
4230 * samtools-0.1.3-2 (r239)
4231 * fixed bugs in bam_aux.c (these functions nevered used by samtools)
4232 * removed bam_aux_init()/bam_aux_destroy()
4233 * added tagview for testing bam_aux
4235 ------------------------------------------------------------------------
4236 r235 | lh3lh3 | 2009-04-21 18:17:39 -0400 (Tue, 21 Apr 2009) | 3 lines
4238 M /trunk/samtools/bam_pileup.c
4239 M /trunk/samtools/bamtk.c
4242 * fixed a bug in pileup: the first read in a chromosome may not be printed
4244 ------------------------------------------------------------------------
4245 r232 | lh3lh3 | 2009-04-16 10:25:43 -0400 (Thu, 16 Apr 2009) | 2 lines
4247 M /trunk/samtools/Makefile.lite
4249 a missing file in Makefile.lite
4251 ------------------------------------------------------------------------
4252 r227 | lh3lh3 | 2009-04-15 17:02:53 -0400 (Wed, 15 Apr 2009) | 2 lines
4254 M /trunk/samtools/NEWS
4255 M /trunk/samtools/bamtk.c
4257 Release samtools-0.1.3
4259 ------------------------------------------------------------------------
4260 r223 | lh3lh3 | 2009-04-15 09:31:32 -0400 (Wed, 15 Apr 2009) | 3 lines
4262 M /trunk/samtools/bam_plcmd.c
4263 M /trunk/samtools/bamtk.c
4266 * make samtools more robust to weird input such as empty file
4268 ------------------------------------------------------------------------
4269 r222 | lh3lh3 | 2009-04-15 09:05:33 -0400 (Wed, 15 Apr 2009) | 2 lines
4271 M /trunk/samtools/ChangeLog
4272 M /trunk/samtools/NEWS
4273 M /trunk/samtools/samtools.1
4275 prepare for release 0.1.3
4277 ------------------------------------------------------------------------
4278 r221 | lh3lh3 | 2009-04-15 08:32:14 -0400 (Wed, 15 Apr 2009) | 2 lines
4280 A /trunk/samtools/misc/blast2sam.pl
4282 convert NCBI-BLASTN to SAM
4284 ------------------------------------------------------------------------
4285 r220 | lh3lh3 | 2009-04-15 08:18:19 -0400 (Wed, 15 Apr 2009) | 3 lines
4287 M /trunk/samtools/bam_lpileup.c
4288 M /trunk/samtools/bamtk.c
4291 * fixed a small memory leak in tview
4293 ------------------------------------------------------------------------
4294 r219 | lh3lh3 | 2009-04-15 08:00:08 -0400 (Wed, 15 Apr 2009) | 3 lines
4296 M /trunk/samtools/bam_rmdup.c
4297 M /trunk/samtools/bamtk.c
4300 * fixed a bug in rmdup when there are unmapped reads
4302 ------------------------------------------------------------------------
4303 r218 | lh3lh3 | 2009-04-14 17:28:58 -0400 (Tue, 14 Apr 2009) | 2 lines
4305 M /trunk/samtools/ChangeLog
4306 M /trunk/samtools/NEWS
4308 proposed NEWS for the new release (have not yet)
4310 ------------------------------------------------------------------------
4311 r216 | lh3lh3 | 2009-04-14 17:10:46 -0400 (Tue, 14 Apr 2009) | 4 lines
4313 M /trunk/samtools/misc/samtools.pl
4316 * improve indelFilter to avoid filtering true indels. The new filter relies
4317 on the new pileup indel line implemented in samtools-0.1.2-25
4319 ------------------------------------------------------------------------
4320 r215 | lh3lh3 | 2009-04-14 17:04:19 -0400 (Tue, 14 Apr 2009) | 4 lines
4322 M /trunk/samtools/bam_maqcns.c
4323 M /trunk/samtools/bam_plcmd.c
4324 M /trunk/samtools/bamtk.c
4325 M /trunk/samtools/samtools.1
4328 * change the pileup indel line to shows the number of alignments actually
4331 ------------------------------------------------------------------------
4332 r211 | lh3lh3 | 2009-04-13 07:07:13 -0400 (Mon, 13 Apr 2009) | 2 lines
4334 M /trunk/samtools/ChangeLog
4336 update ChangeLog from "svn log"
4338 ------------------------------------------------------------------------
4339 r210 | lh3lh3 | 2009-04-12 15:57:05 -0400 (Sun, 12 Apr 2009) | 4 lines
4341 M /trunk/samtools/bam.c
4342 M /trunk/samtools/bam_import.c
4343 M /trunk/samtools/bam_sort.c
4344 M /trunk/samtools/bamtk.c
4345 M /trunk/samtools/kseq.h
4348 * in merge, gives a warning rather than error if the target sequence length is different
4349 * allow empty header
4351 ------------------------------------------------------------------------
4352 r209 | lh3lh3 | 2009-04-12 15:32:44 -0400 (Sun, 12 Apr 2009) | 3 lines
4354 M /trunk/samtools/bam.c
4355 M /trunk/samtools/bam_import.c
4356 M /trunk/samtools/bamtk.c
4359 * recognize '*' at the QUAL field
4361 ------------------------------------------------------------------------
4362 r208 | lh3lh3 | 2009-04-12 15:08:02 -0400 (Sun, 12 Apr 2009) | 3 lines
4364 M /trunk/samtools/bam_import.c
4365 M /trunk/samtools/bamtk.c
4366 M /trunk/samtools/kseq.h
4369 * the field separater is TAB only, now
4371 ------------------------------------------------------------------------
4372 r207 | lh3lh3 | 2009-04-08 10:18:03 -0400 (Wed, 08 Apr 2009) | 2 lines
4374 M /trunk/samtools/examples/ex1.sam.gz
4376 * fixed the problem in the example alignment due to the bug in fixmate
4378 ------------------------------------------------------------------------
4379 r206 | lh3lh3 | 2009-04-08 10:15:05 -0400 (Wed, 08 Apr 2009) | 3 lines
4381 M /trunk/samtools/bam_mate.c
4382 M /trunk/samtools/bamtk.c
4383 M /trunk/samtools/misc/soap2sam.pl
4386 * fixed a nasty bug in `fixmate'
4388 ------------------------------------------------------------------------
4389 r205 | lh3lh3 | 2009-04-08 05:57:08 -0400 (Wed, 08 Apr 2009) | 2 lines
4391 M /trunk/samtools/misc/bowtie2sam.pl
4392 M /trunk/samtools/misc/soap2sam.pl
4393 M /trunk/samtools/misc/wgsim_eval.pl
4395 make the script robust to the bugs in SOAP-2.1.7
4397 ------------------------------------------------------------------------
4398 r200 | lh3lh3 | 2009-04-02 10:14:56 -0400 (Thu, 02 Apr 2009) | 3 lines
4400 M /trunk/samtools/bam_stat.c
4401 M /trunk/samtools/bamtk.c
4404 * check if file is truncated in flagstat
4406 ------------------------------------------------------------------------
4407 r199 | lh3lh3 | 2009-04-02 10:09:10 -0400 (Thu, 02 Apr 2009) | 3 lines
4409 M /trunk/samtools/bamtk.c
4412 * print the header if requested
4414 ------------------------------------------------------------------------
4415 r193 | lh3lh3 | 2009-03-27 11:09:50 -0400 (Fri, 27 Mar 2009) | 3 lines
4417 M /trunk/samtools/bam_plcmd.c
4418 M /trunk/samtools/bamtk.c
4421 * fixed a minor bug reported by Nils Homer
4423 ------------------------------------------------------------------------
4424 r185 | lh3lh3 | 2009-03-24 07:50:32 -0400 (Tue, 24 Mar 2009) | 2 lines
4426 A /trunk/samtools/Makefile (from /trunk/samtools/Makefile.std:184)
4427 D /trunk/samtools/Makefile.std
4428 A /trunk/samtools/misc/Makefile (from /trunk/samtools/misc/Makefile.std:184)
4429 D /trunk/samtools/misc/Makefile.std
4431 rename Makefile.std as Makefile. GNU building systerm is not ready and may take some time...
4433 ------------------------------------------------------------------------
4434 r184 | lh3lh3 | 2009-03-24 06:36:38 -0400 (Tue, 24 Mar 2009) | 4 lines
4436 D /trunk/samtools/Makefile
4437 A /trunk/samtools/Makefile.std (from /trunk/samtools/Makefile:183)
4438 M /trunk/samtools/bam_sort.c
4439 M /trunk/samtools/bam_tview.c
4440 M /trunk/samtools/bamtk.c
4441 D /trunk/samtools/misc/Makefile
4442 A /trunk/samtools/misc/Makefile.std (from /trunk/samtools/misc/Makefile:182)
4443 M /trunk/samtools/samtools.1
4446 * incorporating Nils' changes
4447 * rename Makefile to Makefile.std and prepare to add the GNU building systerms (also by Nils)
4449 ------------------------------------------------------------------------
4450 r183 | lh3lh3 | 2009-03-24 06:30:23 -0400 (Tue, 24 Mar 2009) | 4 lines
4452 M /trunk/samtools/Makefile
4453 M /trunk/samtools/bam_import.c
4454 M /trunk/samtools/bam_maqcns.c
4455 M /trunk/samtools/bam_maqcns.h
4456 M /trunk/samtools/bam_plcmd.c
4457 M /trunk/samtools/bamtk.c
4458 M /trunk/samtools/kseq.h
4459 A /trunk/samtools/kstring.c
4460 A /trunk/samtools/kstring.h
4463 * made pileup take a list of proposed indels. An insertion is N at the moment.
4464 * added my kstring library for a bit complex parsing of the position list.
4466 ------------------------------------------------------------------------
4467 r169 | lh3lh3 | 2009-03-12 09:40:14 -0400 (Thu, 12 Mar 2009) | 3 lines
4469 M /trunk/samtools/misc/soap2sam.pl
4472 * more robust to truncated soap output
4474 ------------------------------------------------------------------------
4475 r168 | lh3lh3 | 2009-03-11 06:49:00 -0400 (Wed, 11 Mar 2009) | 2 lines
4477 M /trunk/samtools/Makefile.lite
4479 added bam_stat.o to Makefile.lite
4481 ------------------------------------------------------------------------
4482 r167 | lh3lh3 | 2009-03-10 18:11:31 -0400 (Tue, 10 Mar 2009) | 3 lines
4484 M /trunk/samtools/bam_maqcns.c
4485 M /trunk/samtools/bamtk.c
4488 * generate RMS of mapQ instead of max mapQ
4490 ------------------------------------------------------------------------
4491 r166 | lh3lh3 | 2009-03-10 18:06:45 -0400 (Tue, 10 Mar 2009) | 3 lines
4493 M /trunk/samtools/bam_plcmd.c
4494 M /trunk/samtools/bamtk.c
4495 M /trunk/samtools/glf.c
4496 M /trunk/samtools/glf.h
4497 M /trunk/samtools/misc/Makefile
4502 ------------------------------------------------------------------------
4503 r159 | lh3lh3 | 2009-03-03 06:26:08 -0500 (Tue, 03 Mar 2009) | 3 lines
4505 M /trunk/samtools/bam_plcmd.c
4506 M /trunk/samtools/bamtk.c
4509 * fixed a minor bug in displaying pileup
4511 ------------------------------------------------------------------------
4512 r158 | lh3lh3 | 2009-03-03 06:24:16 -0500 (Tue, 03 Mar 2009) | 3 lines
4514 M /trunk/samtools/ChangeLog
4515 M /trunk/samtools/bamtk.c
4518 * optionally print SAM header
4520 ------------------------------------------------------------------------
4521 r153 | lh3lh3 | 2009-03-02 05:45:28 -0500 (Mon, 02 Mar 2009) | 3 lines
4523 M /trunk/samtools/bamtk.c
4524 M /trunk/samtools/glf.c
4527 * use "GLF\3" as the magic for GLFv3 files
4529 ------------------------------------------------------------------------
4530 r152 | lh3lh3 | 2009-03-02 05:39:09 -0500 (Mon, 02 Mar 2009) | 5 lines
4532 M /trunk/samtools/Makefile
4533 M /trunk/samtools/bam_import.c
4534 M /trunk/samtools/bam_index.c
4535 M /trunk/samtools/bam_plcmd.c
4536 M /trunk/samtools/bamtk.c
4537 M /trunk/samtools/glf.c
4538 M /trunk/samtools/glf.h
4541 * fixed a bug in import: core.bin is undefined for unmapped reads
4542 * this bug can be alleviated (not completely solved) in bam_index.c
4543 * update to GLFv3: pos is changed to offset for better compression
4545 ------------------------------------------------------------------------
4546 r151 | lh3lh3 | 2009-03-01 10:18:43 -0500 (Sun, 01 Mar 2009) | 3 lines
4548 M /trunk/samtools/misc/wgsim.c
4551 * fixed a bug in simulating indels
4553 ------------------------------------------------------------------------
4554 r145 | lh3lh3 | 2009-02-26 14:43:57 -0500 (Thu, 26 Feb 2009) | 4 lines
4556 M /trunk/samtools/misc/wgsim.c
4559 * allow to print mismatch information as fastq comment. MAQ does
4560 not like long read names.
4562 ------------------------------------------------------------------------
4563 r141 | lh3lh3 | 2009-02-26 09:53:03 -0500 (Thu, 26 Feb 2009) | 6 lines
4565 M /trunk/samtools/ChangeLog
4566 M /trunk/samtools/misc/wgsim.c
4567 M /trunk/samtools/misc/wgsim_eval.pl
4570 * fixed a bug about color read coordinates
4571 * fixed a bug in read names
4572 * wgsim_eval.pl-0.1.3
4573 * make the script work with color reads
4575 ------------------------------------------------------------------------
4576 r140 | lh3lh3 | 2009-02-26 09:02:57 -0500 (Thu, 26 Feb 2009) | 2 lines
4578 M /trunk/samtools/misc/Makefile
4579 M /trunk/samtools/misc/wgsim.c
4581 * wgsim: added a note
4583 ------------------------------------------------------------------------
4584 r139 | lh3lh3 | 2009-02-26 06:39:08 -0500 (Thu, 26 Feb 2009) | 7 lines
4586 M /trunk/samtools/misc/wgsim.c
4587 M /trunk/samtools/misc/wgsim_eval.pl
4590 * considerable code clean up
4591 * print number of substitutions/indels/errors on each read
4592 * potentially support SOLiD simulation, though not tested at the moment
4593 * wgsim_eval.pl-0.1.2
4594 * change in accordant with wgsim
4596 ------------------------------------------------------------------------
4597 r129 | lh3lh3 | 2009-02-18 17:23:27 -0500 (Wed, 18 Feb 2009) | 3 lines
4599 M /trunk/samtools/bam_index.c
4600 M /trunk/samtools/bamtk.c
4603 * fixed a bug in bam_fetch, caused by completely contained adjacent chunks
4605 ------------------------------------------------------------------------
4606 r128 | bhandsaker | 2009-02-18 14:06:57 -0500 (Wed, 18 Feb 2009) | 2 lines
4608 M /trunk/samtools/bamtk.c
4610 Fix annoying segv when invalid region specified.
4612 ------------------------------------------------------------------------
4613 r127 | lh3lh3 | 2009-02-17 05:49:55 -0500 (Tue, 17 Feb 2009) | 2 lines
4615 D /trunk/samtools/misc/indel_filter.pl
4616 A /trunk/samtools/misc/samtools.pl
4618 * move indel_filter.pl to samtools.pl
4620 ------------------------------------------------------------------------
4621 r126 | lh3lh3 | 2009-02-14 16:22:30 -0500 (Sat, 14 Feb 2009) | 3 lines
4623 M /trunk/samtools/bam_mate.c
4624 M /trunk/samtools/bamtk.c
4627 * fixed a bug in fixmate: SE reads are flagged as BAM_FMUNMAP
4629 ------------------------------------------------------------------------
4630 r125 | lh3lh3 | 2009-02-13 04:54:45 -0500 (Fri, 13 Feb 2009) | 3 lines
4632 M /trunk/samtools/bam_stat.c
4633 M /trunk/samtools/bamtk.c
4636 * fixed a minor bug in flagstat
4638 ------------------------------------------------------------------------
4639 r124 | lh3lh3 | 2009-02-12 06:15:32 -0500 (Thu, 12 Feb 2009) | 3 lines
4641 M /trunk/samtools/bam_maqcns.c
4642 M /trunk/samtools/bamtk.c
4643 M /trunk/samtools/misc/indel_filter.pl
4646 * improve indel caller by setting maximum window size
4648 ------------------------------------------------------------------------
4649 r123 | lh3lh3 | 2009-02-12 05:30:29 -0500 (Thu, 12 Feb 2009) | 2 lines
4651 M /trunk/samtools/bam_plcmd.c
4652 M /trunk/samtools/bamtk.c
4654 * output max mapping quality in indel line
4656 ------------------------------------------------------------------------
4657 r122 | lh3lh3 | 2009-02-11 05:59:10 -0500 (Wed, 11 Feb 2009) | 2 lines
4659 M /trunk/samtools/misc/maq2sam.c
4661 fixed a bug in generating tag AM
4663 ------------------------------------------------------------------------
4664 r121 | lh3lh3 | 2009-02-03 05:43:11 -0500 (Tue, 03 Feb 2009) | 2 lines
4666 M /trunk/samtools/bam_index.c
4667 M /trunk/samtools/bamtk.c
4669 fixed a potential memory problem in indexing
4671 ------------------------------------------------------------------------
4672 r120 | bhandsaker | 2009-02-02 10:52:52 -0500 (Mon, 02 Feb 2009) | 2 lines
4674 M /trunk/samtools/Makefile
4676 Pass LIBS to recursive targets to facilitate building at Broad.
4678 ------------------------------------------------------------------------
4679 r119 | lh3lh3 | 2009-02-02 05:12:15 -0500 (Mon, 02 Feb 2009) | 4 lines
4681 M /trunk/samtools/ChangeLog
4682 M /trunk/samtools/bam_plcmd.c
4683 M /trunk/samtools/bam_stat.c
4684 M /trunk/samtools/bamtk.c
4687 * fixed a bug in generating GLFv2 for indels
4688 * improve flagstat report a little bit
4690 ------------------------------------------------------------------------
4691 r118 | lh3lh3 | 2009-01-29 07:33:23 -0500 (Thu, 29 Jan 2009) | 3 lines
4693 M /trunk/samtools/Makefile
4694 A /trunk/samtools/bam_stat.c
4695 M /trunk/samtools/bamtk.c
4698 * added flagstat command
4700 ------------------------------------------------------------------------
4701 r116 | lh3lh3 | 2009-01-28 08:31:12 -0500 (Wed, 28 Jan 2009) | 2 lines
4703 M /trunk/samtools/ChangeLog
4704 M /trunk/samtools/NEWS
4705 M /trunk/samtools/bamtk.c
4706 M /trunk/samtools/samtools.1
4708 Release SAMtools-0.1.2
4710 ------------------------------------------------------------------------
4711 r115 | lh3lh3 | 2009-01-28 07:54:08 -0500 (Wed, 28 Jan 2009) | 2 lines
4713 A /trunk/samtools/misc/indel_filter.pl
4715 Script for filtering indel results
4717 ------------------------------------------------------------------------
4718 r114 | lh3lh3 | 2009-01-25 06:45:37 -0500 (Sun, 25 Jan 2009) | 2 lines
4720 A /trunk/samtools/misc/zoom2sam.pl
4724 ------------------------------------------------------------------------
4725 r113 | lh3lh3 | 2009-01-24 09:25:07 -0500 (Sat, 24 Jan 2009) | 2 lines
4727 A /trunk/samtools/misc/novo2sam.pl
4729 add a script to convert novo alignment to SAM
4731 ------------------------------------------------------------------------
4732 r112 | lh3lh3 | 2009-01-23 15:57:39 -0500 (Fri, 23 Jan 2009) | 2 lines
4734 M /trunk/samtools/ChangeLog
4735 M /trunk/samtools/ChangeLog.old
4736 M /trunk/samtools/samtools.1
4738 update documentation and ChangeLog
4740 ------------------------------------------------------------------------
4741 r111 | lh3lh3 | 2009-01-23 14:22:59 -0500 (Fri, 23 Jan 2009) | 3 lines
4743 M /trunk/samtools/bam_sort.c
4744 M /trunk/samtools/bamtk.c
4747 * fixed a bug in "merge" command line
4749 ------------------------------------------------------------------------
4750 r110 | lh3lh3 | 2009-01-22 10:36:48 -0500 (Thu, 22 Jan 2009) | 3 lines
4752 M /trunk/samtools/misc/Makefile
4753 A /trunk/samtools/misc/bowtie2sam.pl (from /branches/dev/samtools/misc/bowtie2sam.pl:108)
4754 M /trunk/samtools/misc/export2sam.pl
4755 A /trunk/samtools/misc/soap2sam.pl (from /branches/dev/samtools/misc/soap2sam.pl:108)
4756 A /trunk/samtools/misc/wgsim.c (from /branches/dev/samtools/misc/wgsim.c:108)
4757 A /trunk/samtools/misc/wgsim_eval.pl (from /branches/dev/samtools/misc/wgsim_eval.pl:108)
4759 * merge from branches/dev/
4760 * all future development will happen here
4762 ------------------------------------------------------------------------
4763 r109 | lh3lh3 | 2009-01-22 10:14:27 -0500 (Thu, 22 Jan 2009) | 3 lines
4765 M /trunk/samtools/COPYING
4766 M /trunk/samtools/ChangeLog
4767 A /trunk/samtools/INSTALL (from /branches/dev/samtools/INSTALL:108)
4768 M /trunk/samtools/Makefile
4769 A /trunk/samtools/Makefile.lite (from /branches/dev/samtools/Makefile.lite:108)
4770 M /trunk/samtools/bam.c
4771 M /trunk/samtools/bam.h
4772 M /trunk/samtools/bam_import.c
4773 M /trunk/samtools/bam_index.c
4774 M /trunk/samtools/bam_lpileup.c
4775 M /trunk/samtools/bam_maqcns.c
4776 M /trunk/samtools/bam_maqcns.h
4777 A /trunk/samtools/bam_mate.c (from /branches/dev/samtools/bam_mate.c:108)
4778 M /trunk/samtools/bam_pileup.c
4779 M /trunk/samtools/bam_plcmd.c
4780 A /trunk/samtools/bam_rmdup.c (from /branches/dev/samtools/bam_rmdup.c:108)
4781 M /trunk/samtools/bam_sort.c
4782 M /trunk/samtools/bamtk.c
4783 M /trunk/samtools/bgzf.h
4784 M /trunk/samtools/examples/00README.txt
4785 A /trunk/samtools/examples/Makefile (from /branches/dev/samtools/examples/Makefile:108)
4786 D /trunk/samtools/examples/ex1.fa.fai
4787 M /trunk/samtools/examples/ex1.sam.gz
4788 M /trunk/samtools/faidx.c
4789 A /trunk/samtools/glf.c (from /branches/dev/samtools/glf.c:108)
4790 M /trunk/samtools/glf.h
4791 M /trunk/samtools/misc/Makefile
4792 M /trunk/samtools/misc/maq2sam.c
4793 M /trunk/samtools/razf.c
4794 M /trunk/samtools/source.dot
4796 * Merge from branches/dev/
4797 * all future development will happen here at trunk/
4799 ------------------------------------------------------------------------
4800 r79 | bhandsaker | 2009-01-07 16:42:15 -0500 (Wed, 07 Jan 2009) | 2 lines
4802 M /trunk/samtools/bam_maqcns.c
4803 M /trunk/samtools/bam_tview.c
4805 Fix problem with compiling without curses.
4807 ------------------------------------------------------------------------
4808 r63 | lh3lh3 | 2008-12-22 10:58:02 -0500 (Mon, 22 Dec 2008) | 2 lines
4810 A /trunk/samtools (from /branches/dev/samtools:62)
4814 ------------------------------------------------------------------------
4815 r62 | lh3lh3 | 2008-12-22 10:55:13 -0500 (Mon, 22 Dec 2008) | 2 lines
4817 A /branches/dev/samtools/NEWS
4818 M /branches/dev/samtools/bamtk.c
4819 M /branches/dev/samtools/samtools.1
4821 Release samtools-0.1.1
4823 ------------------------------------------------------------------------
4824 r61 | lh3lh3 | 2008-12-22 10:46:08 -0500 (Mon, 22 Dec 2008) | 10 lines
4826 M /branches/dev/samtools/bam_aux.c
4827 M /branches/dev/samtools/bam_index.c
4828 M /branches/dev/samtools/bam_plcmd.c
4829 M /branches/dev/samtools/bam_tview.c
4830 M /branches/dev/samtools/bamtk.c
4831 M /branches/dev/samtools/razf.c
4832 M /branches/dev/samtools/samtools.1
4835 * fixed a bug in razf.c: reset z_eof when razf_seek() is called
4836 * fixed a memory leak in parsing a region
4837 * changed pileup a little bit when -s is in use: output ^ and $
4838 * when a bam is not indexed, output more meaningful error message
4839 * fixed a bug in indexing for small alignment
4840 * fixed a bug in the viewer when we come to the end of a reference file
4841 * updated documentation
4842 * prepare to release 0.1.1
4844 ------------------------------------------------------------------------
4845 r60 | lh3lh3 | 2008-12-22 10:10:16 -0500 (Mon, 22 Dec 2008) | 2 lines
4847 A /branches/dev/samtools/examples
4848 A /branches/dev/samtools/examples/00README.txt
4849 A /branches/dev/samtools/examples/ex1.fa
4850 A /branches/dev/samtools/examples/ex1.fa.fai
4851 A /branches/dev/samtools/examples/ex1.sam.gz
4855 ------------------------------------------------------------------------
4856 r59 | lh3lh3 | 2008-12-22 04:38:15 -0500 (Mon, 22 Dec 2008) | 2 lines
4858 M /branches/dev/samtools/ChangeLog
4862 ------------------------------------------------------------------------
4863 r58 | lh3lh3 | 2008-12-20 18:06:00 -0500 (Sat, 20 Dec 2008) | 3 lines
4865 M /branches/dev/samtools/misc/export2sam.pl
4868 * fixed several bugs
4870 ------------------------------------------------------------------------
4871 r57 | lh3lh3 | 2008-12-20 10:44:20 -0500 (Sat, 20 Dec 2008) | 2 lines
4873 A /branches/dev/samtools/misc/export2sam.pl
4875 convert Export format to SAM; not thoroughly tested
4877 ------------------------------------------------------------------------
4878 r56 | lh3lh3 | 2008-12-19 17:13:28 -0500 (Fri, 19 Dec 2008) | 6 lines
4880 M /branches/dev/samtools/bam_import.c
4881 M /branches/dev/samtools/bam_plcmd.c
4882 M /branches/dev/samtools/bam_tview.c
4883 M /branches/dev/samtools/bamtk.c
4884 A /branches/dev/samtools/source.dot
4887 * pileup: generate maq-like simple output
4888 * pileup: allow to output pileup at required sites
4889 * source.dot: source file relationship graph
4890 * tview: fixed a minor bug
4892 ------------------------------------------------------------------------
4893 r55 | lh3lh3 | 2008-12-19 15:10:26 -0500 (Fri, 19 Dec 2008) | 2 lines
4895 D /branches/dev/samtools/misc/all2sam.pl
4899 ------------------------------------------------------------------------
4900 r54 | lh3lh3 | 2008-12-16 17:34:25 -0500 (Tue, 16 Dec 2008) | 2 lines
4902 A /branches/dev/samtools/COPYING
4903 M /branches/dev/samtools/bam.h
4904 M /branches/dev/samtools/faidx.h
4905 M /branches/dev/samtools/khash.h
4906 M /branches/dev/samtools/kseq.h
4907 M /branches/dev/samtools/ksort.h
4908 M /branches/dev/samtools/samtools.1
4910 Added copyright information and a bit more documentation. No code change.
4912 ------------------------------------------------------------------------
4913 r53 | lh3lh3 | 2008-12-16 08:40:18 -0500 (Tue, 16 Dec 2008) | 3 lines
4915 M /branches/dev/samtools/bam.c
4916 M /branches/dev/samtools/bam.h
4917 M /branches/dev/samtools/bam_index.c
4918 M /branches/dev/samtools/bam_maqcns.c
4919 M /branches/dev/samtools/bamtk.c
4922 * improved efficiency of the indel caller for spliced alignments
4924 ------------------------------------------------------------------------
4925 r52 | lh3lh3 | 2008-12-16 05:28:20 -0500 (Tue, 16 Dec 2008) | 3 lines
4927 M /branches/dev/samtools/bam.c
4928 M /branches/dev/samtools/bam.h
4929 M /branches/dev/samtools/bam_aux.c
4930 M /branches/dev/samtools/bam_index.c
4931 M /branches/dev/samtools/bamtk.c
4934 * a bit code cleanup: reduce the dependency between source files
4936 ------------------------------------------------------------------------
4937 r51 | lh3lh3 | 2008-12-15 09:29:32 -0500 (Mon, 15 Dec 2008) | 3 lines
4939 M /branches/dev/samtools/bam_maqcns.c
4940 M /branches/dev/samtools/bam_plcmd.c
4941 M /branches/dev/samtools/bamtk.c
4944 * fixed a memory leak
4946 ------------------------------------------------------------------------
4947 r50 | lh3lh3 | 2008-12-15 09:00:13 -0500 (Mon, 15 Dec 2008) | 2 lines
4949 M /branches/dev/samtools/ChangeLog
4950 M /branches/dev/samtools/bam.h
4951 M /branches/dev/samtools/samtools.1
4953 update documentation, ChangeLog and a comment
4955 ------------------------------------------------------------------------
4956 r49 | lh3lh3 | 2008-12-15 08:36:43 -0500 (Mon, 15 Dec 2008) | 6 lines
4958 M /branches/dev/samtools/Makefile
4959 M /branches/dev/samtools/bam.h
4960 M /branches/dev/samtools/bam_maqcns.c
4961 M /branches/dev/samtools/bam_maqcns.h
4962 M /branches/dev/samtools/bam_pileup.c
4963 A /branches/dev/samtools/bam_plcmd.c
4964 M /branches/dev/samtools/bamtk.c
4965 M /branches/dev/samtools/samtools.1
4968 * moved pileup command to a separate source file
4969 * added indel caller
4970 * added bam_cal_segend(). (NOT WORKING for spliced alignment!!!)
4971 * updated documentation
4973 ------------------------------------------------------------------------
4974 r48 | lh3lh3 | 2008-12-12 08:55:36 -0500 (Fri, 12 Dec 2008) | 3 lines
4976 M /branches/dev/samtools/bam_maqcns.c
4977 M /branches/dev/samtools/bamtk.c
4980 * fixed another bug in maqcns when there is a nearby deletion
4982 ------------------------------------------------------------------------
4983 r47 | lh3lh3 | 2008-12-12 08:42:16 -0500 (Fri, 12 Dec 2008) | 5 lines
4985 M /branches/dev/samtools/bam_maqcns.c
4986 M /branches/dev/samtools/bam_pileup.c
4987 M /branches/dev/samtools/bamtk.c
4990 * pileup: outputing consensus is now optional
4991 * fixed a bug in glfgen. This bug also exists in maq's glfgen. However,
4992 I am not quite sure why the previous version may have problem.
4994 ------------------------------------------------------------------------
4995 r46 | lh3lh3 | 2008-12-12 06:44:56 -0500 (Fri, 12 Dec 2008) | 6 lines
4997 M /branches/dev/samtools/bam_pileup.c
4998 M /branches/dev/samtools/bamtk.c
5001 * add maq consensus to pileup. However, I will move this part to a new
5002 command as strictly speaking, consensus callin is not part of pileup,
5003 and imposing it would make it harder to generate for other language
5006 ------------------------------------------------------------------------
5007 r45 | bhandsaker | 2008-12-11 15:43:56 -0500 (Thu, 11 Dec 2008) | 2 lines
5009 M /branches/dev/samtools/bgzf.c
5011 Fix bug in tell() after reads that consume to the exact end of a block.
5013 ------------------------------------------------------------------------
5014 r44 | lh3lh3 | 2008-12-11 04:36:53 -0500 (Thu, 11 Dec 2008) | 2 lines
5016 M /branches/dev/samtools/samtools.1
5020 ------------------------------------------------------------------------
5021 r43 | lh3lh3 | 2008-12-11 04:25:36 -0500 (Thu, 11 Dec 2008) | 4 lines
5023 M /branches/dev/samtools/bam_import.c
5024 M /branches/dev/samtools/bamtk.c
5027 * fixed a bug in parser when there is auxiliary fields
5028 * made the parser a bit more robust
5030 ------------------------------------------------------------------------
5031 r42 | lh3lh3 | 2008-12-10 09:57:29 -0500 (Wed, 10 Dec 2008) | 5 lines
5033 M /branches/dev/samtools/bam_index.c
5034 M /branches/dev/samtools/bamtk.c
5035 M /branches/dev/samtools/bgzf.c
5038 * fixed a bug in bgzf (only reading is affected)
5039 * fixed a typo in bam_index.c
5040 * in bam_index.c, check potential bugs in the underlying I/O library
5042 ------------------------------------------------------------------------
5043 r41 | lh3lh3 | 2008-12-10 07:53:08 -0500 (Wed, 10 Dec 2008) | 2 lines
5045 M /branches/dev/samtools/samtools.1
5049 ------------------------------------------------------------------------
5050 r40 | lh3lh3 | 2008-12-10 06:52:10 -0500 (Wed, 10 Dec 2008) | 5 lines
5052 M /branches/dev/samtools/bam.h
5053 M /branches/dev/samtools/bam_pileup.c
5054 M /branches/dev/samtools/bamtk.c
5057 * tried to make pileup work with clipping (previously not), though NOT tested
5058 * removed -v from pileup
5059 * made pileup take the reference sequence
5061 ------------------------------------------------------------------------
5062 r39 | lh3lh3 | 2008-12-09 06:59:28 -0500 (Tue, 09 Dec 2008) | 4 lines
5064 M /branches/dev/samtools/bam_import.c
5065 M /branches/dev/samtools/bamtk.c
5066 M /branches/dev/samtools/samtools.1
5069 * in parser, recognize "=", rather than ",", as a match
5070 * in parser, correctl parse "=" at the MRNM field.
5072 ------------------------------------------------------------------------
5073 r38 | lh3lh3 | 2008-12-09 06:39:07 -0500 (Tue, 09 Dec 2008) | 2 lines
5075 M /branches/dev/samtools/misc/maq2sam.c
5077 fixed a bug in handling maq flag 64 and 192
5079 ------------------------------------------------------------------------
5080 r37 | lh3lh3 | 2008-12-09 04:53:46 -0500 (Tue, 09 Dec 2008) | 2 lines
5082 M /branches/dev/samtools/misc/md5fa.c
5084 also calculate unordered md5sum check
5086 ------------------------------------------------------------------------
5087 r36 | lh3lh3 | 2008-12-09 04:46:21 -0500 (Tue, 09 Dec 2008) | 2 lines
5089 M /branches/dev/samtools/misc/md5fa.c
5091 fixed a minor bug when there are space in the sequence
5093 ------------------------------------------------------------------------
5094 r35 | lh3lh3 | 2008-12-09 04:40:45 -0500 (Tue, 09 Dec 2008) | 2 lines
5096 M /branches/dev/samtools/misc/md5fa.c
5098 fixed a potential memory leak
5100 ------------------------------------------------------------------------
5101 r34 | lh3lh3 | 2008-12-08 09:52:17 -0500 (Mon, 08 Dec 2008) | 2 lines
5103 M /branches/dev/samtools/bam_import.c
5104 M /branches/dev/samtools/bam_index.c
5105 M /branches/dev/samtools/bamtk.c
5107 * fixed a bug in import: bin is wrongly calculated
5109 ------------------------------------------------------------------------
5110 r33 | lh3lh3 | 2008-12-08 09:08:01 -0500 (Mon, 08 Dec 2008) | 2 lines
5112 M /branches/dev/samtools/misc/all2sam.pl
5116 ------------------------------------------------------------------------
5117 r32 | lh3lh3 | 2008-12-08 07:56:02 -0500 (Mon, 08 Dec 2008) | 3 lines
5119 M /branches/dev/samtools/Makefile
5120 M /branches/dev/samtools/kseq.h
5121 M /branches/dev/samtools/misc/Makefile
5122 A /branches/dev/samtools/misc/md5.c
5123 A /branches/dev/samtools/misc/md5.h
5124 A /branches/dev/samtools/misc/md5fa.c
5126 * fixed two warnings in kseq.h
5127 * added md5sum utilities
5129 ------------------------------------------------------------------------
5130 r31 | lh3lh3 | 2008-12-08 06:35:29 -0500 (Mon, 08 Dec 2008) | 5 lines
5132 M /branches/dev/samtools/Makefile
5133 M /branches/dev/samtools/bam_import.c
5134 M /branches/dev/samtools/bamtk.c
5135 A /branches/dev/samtools/kseq.h
5136 D /branches/dev/samtools/kstream.h
5139 * replace kstream with kseq. kseq is a superset of kstream. I need the
5140 extra functions in kseq.h.
5141 * also compile stand-alone faidx
5143 ------------------------------------------------------------------------
5144 r30 | lh3lh3 | 2008-12-08 06:17:04 -0500 (Mon, 08 Dec 2008) | 3 lines
5146 M /branches/dev/samtools/bam.h
5147 M /branches/dev/samtools/bam_sort.c
5148 M /branches/dev/samtools/bamtk.c
5151 * sorting by read names is available
5153 ------------------------------------------------------------------------
5154 r29 | lh3lh3 | 2008-12-08 05:29:02 -0500 (Mon, 08 Dec 2008) | 3 lines
5156 M /branches/dev/samtools/bam.c
5157 M /branches/dev/samtools/bam.h
5158 M /branches/dev/samtools/bam_import.c
5159 M /branches/dev/samtools/bam_maqcns.c
5160 M /branches/dev/samtools/bam_pileup.c
5161 M /branches/dev/samtools/bam_sort.c
5162 M /branches/dev/samtools/bam_tview.c
5163 M /branches/dev/samtools/bamtk.c
5164 M /branches/dev/samtools/misc/maq2sam.c
5167 * format change to meet the latest specification
5169 ------------------------------------------------------------------------
5170 r28 | lh3lh3 | 2008-12-04 11:09:21 -0500 (Thu, 04 Dec 2008) | 3 lines
5172 M /branches/dev/samtools/bam_maqcns.c
5173 M /branches/dev/samtools/misc/maq2sam.c
5175 * minor change in maqcns: special care when n==0
5176 * change maq2sam to meet the latest specification
5178 ------------------------------------------------------------------------
5179 r27 | lh3lh3 | 2008-12-04 10:55:44 -0500 (Thu, 04 Dec 2008) | 2 lines
5181 M /branches/dev/samtools/razf.c
5182 M /branches/dev/samtools/razf.h
5184 considerable code clean up in razf
5186 ------------------------------------------------------------------------
5187 r26 | lh3lh3 | 2008-12-04 10:08:18 -0500 (Thu, 04 Dec 2008) | 2 lines
5189 M /branches/dev/samtools/ChangeLog
5190 M /branches/dev/samtools/Makefile
5191 M /branches/dev/samtools/faidx.c
5193 make RAZF optional in faidx.c
5195 ------------------------------------------------------------------------
5196 r25 | lh3lh3 | 2008-12-01 10:27:22 -0500 (Mon, 01 Dec 2008) | 3 lines
5198 M /branches/dev/samtools/Makefile
5199 M /branches/dev/samtools/bam.h
5200 M /branches/dev/samtools/bam_aux.c
5201 M /branches/dev/samtools/bamtk.c
5202 M /branches/dev/samtools/samtools.1
5205 * added routines for retrieving aux data, NOT TESTED YET!
5207 ------------------------------------------------------------------------
5208 r24 | lh3lh3 | 2008-12-01 09:29:43 -0500 (Mon, 01 Dec 2008) | 5 lines
5210 M /branches/dev/samtools/bam.c
5211 M /branches/dev/samtools/bam_import.c
5212 M /branches/dev/samtools/bam_maqcns.c
5213 M /branches/dev/samtools/bamtk.c
5214 M /branches/dev/samtools/bgzf.c
5215 M /branches/dev/samtools/samtools.1
5218 * bgzf: fixed a potential integer overflow on 32-it machines
5219 * maqcns: set the minimum combined quality as 0
5220 * supporting hex strings
5222 ------------------------------------------------------------------------
5223 r23 | lh3lh3 | 2008-11-27 12:14:37 -0500 (Thu, 27 Nov 2008) | 3 lines
5225 M /branches/dev/samtools/bam_maqcns.c
5226 M /branches/dev/samtools/bamtk.c
5229 * fixed the bug in maqcns
5231 ------------------------------------------------------------------------
5232 r22 | lh3lh3 | 2008-11-27 12:08:11 -0500 (Thu, 27 Nov 2008) | 3 lines
5234 M /branches/dev/samtools/Makefile
5235 M /branches/dev/samtools/bam.h
5236 A /branches/dev/samtools/bam_maqcns.c
5237 A /branches/dev/samtools/bam_maqcns.h
5238 M /branches/dev/samtools/bam_tview.c
5239 M /branches/dev/samtools/bamtk.c
5240 A /branches/dev/samtools/glf.h
5243 * add MAQ consensus caller, currently BUGGY!
5245 ------------------------------------------------------------------------
5246 r21 | lh3lh3 | 2008-11-27 08:51:28 -0500 (Thu, 27 Nov 2008) | 4 lines
5248 M /branches/dev/samtools/bam_pileup.c
5249 M /branches/dev/samtools/bam_tview.c
5250 M /branches/dev/samtools/bamtk.c
5253 * tview: display padded alignment (but not P operation)
5254 * better coordinates and reference sequence
5256 ------------------------------------------------------------------------
5257 r19 | lh3lh3 | 2008-11-27 04:26:05 -0500 (Thu, 27 Nov 2008) | 2 lines
5259 A /branches/dev/samtools/ChangeLog
5263 ------------------------------------------------------------------------
5264 r18 | lh3lh3 | 2008-11-27 04:24:45 -0500 (Thu, 27 Nov 2008) | 3 lines
5266 D /branches/dev/samtools/ChangeLog
5267 A /branches/dev/samtools/ChangeLog.old (from /branches/dev/samtools/ChangeLog:6)
5269 Rename ChangeLog to ChangeLog.old. This old ChangeLog is generated from
5270 the log of my personal SVN repository.
5272 ------------------------------------------------------------------------
5273 r17 | lh3lh3 | 2008-11-27 04:22:55 -0500 (Thu, 27 Nov 2008) | 6 lines
5275 M /branches/dev/samtools/Makefile
5276 M /branches/dev/samtools/bamtk.c
5277 M /branches/dev/samtools/bgzf.c
5280 * declare fseeko and ftello as some Linux may not do this by default and
5281 missing these declarations will make bgzf buggy
5282 * get rid of some harmless warings
5283 * use BGZF by default, now
5285 ------------------------------------------------------------------------
5286 r16 | lh3lh3 | 2008-11-26 16:19:11 -0500 (Wed, 26 Nov 2008) | 4 lines
5288 M /branches/dev/samtools/bam_index.c
5289 M /branches/dev/samtools/bamtk.c
5290 M /branches/dev/samtools/razf.c
5293 * fixed a bug in razf_read()
5294 * give more warnings when the file is truncated (or due to bugs in I/O library)
5296 ------------------------------------------------------------------------
5297 r15 | lh3lh3 | 2008-11-26 15:41:39 -0500 (Wed, 26 Nov 2008) | 2 lines
5299 M /branches/dev/samtools/bgzf.c
5301 fixed a bug in bgzf.c at the end of the file
5303 ------------------------------------------------------------------------
5304 r14 | lh3lh3 | 2008-11-26 12:05:18 -0500 (Wed, 26 Nov 2008) | 4 lines
5306 M /branches/dev/samtools/bamtk.c
5309 * a lot happened to RAZF, although samtools itself is untouched. Better
5310 also update the version number anyway to avoid confusion
5312 ------------------------------------------------------------------------
5313 r13 | lh3lh3 | 2008-11-26 12:03:48 -0500 (Wed, 26 Nov 2008) | 2 lines
5315 M /branches/dev/samtools/razf.c
5317 a change from Jue, but I think it should not matter
5319 ------------------------------------------------------------------------
5320 r12 | lh3lh3 | 2008-11-26 11:48:14 -0500 (Wed, 26 Nov 2008) | 3 lines
5322 M /branches/dev/samtools/razf.c
5324 fixed a potential bug in razf. However, it seems still buggy, just
5325 rarely happens, very rarely.
5327 ------------------------------------------------------------------------
5328 r11 | lh3lh3 | 2008-11-26 09:02:56 -0500 (Wed, 26 Nov 2008) | 2 lines
5330 M /branches/dev/samtools/razf.c
5332 fixed a bug in razf, with the help of Jue
5334 ------------------------------------------------------------------------
5335 r10 | lh3lh3 | 2008-11-26 06:55:32 -0500 (Wed, 26 Nov 2008) | 2 lines
5337 M /branches/dev/samtools/bam_index.c
5341 ------------------------------------------------------------------------
5342 r9 | lh3lh3 | 2008-11-26 06:37:05 -0500 (Wed, 26 Nov 2008) | 2 lines
5344 M /branches/dev/samtools/Makefile
5345 M /branches/dev/samtools/bam.h
5346 M /branches/dev/samtools/razf.c
5347 M /branches/dev/samtools/razf.h
5349 * Jue has updated razf to realize Bob's scheme
5351 ------------------------------------------------------------------------
5352 r7 | lh3lh3 | 2008-11-25 15:37:37 -0500 (Tue, 25 Nov 2008) | 2 lines
5354 A /branches/dev/samtools/samtools.1
5358 ------------------------------------------------------------------------
5359 r6 | lh3lh3 | 2008-11-25 15:37:16 -0500 (Tue, 25 Nov 2008) | 3 lines
5361 A /branches/dev/samtools/ChangeLog
5362 A /branches/dev/samtools/Makefile
5363 A /branches/dev/samtools/bam.c
5364 A /branches/dev/samtools/bam.h
5365 A /branches/dev/samtools/bam_aux.c
5366 A /branches/dev/samtools/bam_endian.h
5367 A /branches/dev/samtools/bam_import.c
5368 A /branches/dev/samtools/bam_index.c
5369 A /branches/dev/samtools/bam_lpileup.c
5370 A /branches/dev/samtools/bam_pileup.c
5371 A /branches/dev/samtools/bam_sort.c
5372 A /branches/dev/samtools/bam_tview.c
5373 A /branches/dev/samtools/bamtk.c
5374 A /branches/dev/samtools/bgzf.c
5375 A /branches/dev/samtools/bgzf.h
5376 A /branches/dev/samtools/bgzip.c
5377 A /branches/dev/samtools/faidx.c
5378 A /branches/dev/samtools/faidx.h
5379 A /branches/dev/samtools/khash.h
5380 A /branches/dev/samtools/ksort.h
5381 A /branches/dev/samtools/kstream.h
5382 A /branches/dev/samtools/misc
5383 A /branches/dev/samtools/misc/Makefile
5384 A /branches/dev/samtools/misc/all2sam.pl
5385 A /branches/dev/samtools/misc/maq2sam.c
5386 A /branches/dev/samtools/razf.c
5387 A /branches/dev/samtools/razf.h
5388 A /branches/dev/samtools/razip.c
5389 A /branches/dev/samtools/zutil.h
5391 The initial version of samtools, replicated from my local SVN repository.
5392 The current version is: 0.1.0-42. All future development will happen here.
5394 ------------------------------------------------------------------------
5395 r5 | lh3lh3 | 2008-11-25 15:30:49 -0500 (Tue, 25 Nov 2008) | 2 lines
5397 A /branches/dev/samtools
5399 samtools (C version)
5401 ------------------------------------------------------------------------