1 ------------------------------------------------------------------------
2 r828 | lh3lh3 | 2010-11-16 20:48:49 -0500 (Tue, 16 Nov 2010) | 2 lines
4 M /trunk/samtools/bamtk.c
6 update version information: samtools-0.1.9-20 (r828)
8 ------------------------------------------------------------------------
9 r827 | lh3lh3 | 2010-11-16 15:32:50 -0500 (Tue, 16 Nov 2010) | 2 lines
11 M /trunk/samtools/bcftools/call1.c
13 bcftools: allow to skip indels
15 ------------------------------------------------------------------------
16 r826 | lh3lh3 | 2010-11-16 14:11:58 -0500 (Tue, 16 Nov 2010) | 2 lines
18 M /trunk/samtools/bam_md.c
20 remove ZQ if both BQ and ZQ are present
22 ------------------------------------------------------------------------
23 r825 | lh3lh3 | 2010-11-16 13:51:33 -0500 (Tue, 16 Nov 2010) | 3 lines
25 M /trunk/samtools/bam2bcf_indel.c
26 M /trunk/samtools/bam_md.c
27 M /trunk/samtools/bamtk.c
28 M /trunk/samtools/samtools.1
30 * samtools-0.1.9-18 (r825)
31 * change the behaviour of calmd such that by default it does not change the base quality
33 ------------------------------------------------------------------------
34 r824 | lh3lh3 | 2010-11-15 23:31:53 -0500 (Mon, 15 Nov 2010) | 4 lines
36 M /trunk/samtools/bam_plcmd.c
37 M /trunk/samtools/bamtk.c
38 M /trunk/samtools/bcftools/call1.c
39 M /trunk/samtools/samtools.1
41 * samtools-0.1.9-17 (r824)
42 * added command line options to change the default parameters in indel calling
45 ------------------------------------------------------------------------
46 r823 | lh3lh3 | 2010-11-15 12:20:13 -0500 (Mon, 15 Nov 2010) | 3 lines
48 M /trunk/samtools/bam2bcf_indel.c
49 M /trunk/samtools/bam_md.c
50 M /trunk/samtools/bamtk.c
53 * the BQ tag is now 64 shifted, not 33 shifted
55 ------------------------------------------------------------------------
56 r822 | lh3lh3 | 2010-11-15 00:30:18 -0500 (Mon, 15 Nov 2010) | 3 lines
58 M /trunk/samtools/bam2bcf.c
59 M /trunk/samtools/bam2bcf.h
60 M /trunk/samtools/bamtk.c
61 M /trunk/samtools/bcftools/vcfutils.pl
62 M /trunk/samtools/misc/samtools.pl
64 * samtools-0.1.9-16 (r822)
65 * keep the raw depth because in indel calling, DP4 may be way off the true depth
67 ------------------------------------------------------------------------
68 r821 | lh3lh3 | 2010-11-13 01:18:31 -0500 (Sat, 13 Nov 2010) | 4 lines
70 M /trunk/samtools/bam_md.c
71 M /trunk/samtools/bamtk.c
73 * samtools-0.1.9-15 (r821)
75 * skip realignment if BQ is present
77 ------------------------------------------------------------------------
78 r820 | lh3lh3 | 2010-11-13 01:08:26 -0500 (Sat, 13 Nov 2010) | 3 lines
80 M /trunk/samtools/bam2bcf_indel.c
81 M /trunk/samtools/bamtk.c
83 * samtools-0.1.9-14 (r820)
84 * penalize reads with excessive differences in indel calling
86 ------------------------------------------------------------------------
87 r819 | lh3lh3 | 2010-11-12 21:36:27 -0500 (Fri, 12 Nov 2010) | 3 lines
89 M /trunk/samtools/bam_maqcns.c
90 M /trunk/samtools/bamtk.c
92 * samtools-0.1.9-13 (r819)
93 * fixed a bug in pileup given refskip
95 ------------------------------------------------------------------------
96 r818 | lh3lh3 | 2010-11-12 13:04:53 -0500 (Fri, 12 Nov 2010) | 3 lines
98 M /trunk/samtools/bam2bcf_indel.c
99 M /trunk/samtools/bamtk.c
102 * for indel calling, do two rounds of probabilistic realignments
104 ------------------------------------------------------------------------
105 r817 | lh3lh3 | 2010-11-11 20:04:07 -0500 (Thu, 11 Nov 2010) | 3 lines
107 M /trunk/samtools/bam2bcf_indel.c
108 M /trunk/samtools/bamtk.c
109 M /trunk/samtools/bcftools/vcfutils.pl
111 * samtools-0.1.19-11 (r817)
112 * only initiate indel calling when 0.2% of reads contain a gap
114 ------------------------------------------------------------------------
115 r816 | lh3lh3 | 2010-11-11 01:22:59 -0500 (Thu, 11 Nov 2010) | 7 lines
117 M /trunk/samtools/bam2bcf_indel.c
118 M /trunk/samtools/bamtk.c
120 * samtools-0.1.9-10 (r816)
122 * I know why the forward method fails. it is because of zero base
123 qualities. when that is fixed, the forward method seems to give
124 better results than Viterbi, as it should be. I am tired...
127 ------------------------------------------------------------------------
128 r815 | lh3lh3 | 2010-11-11 00:57:15 -0500 (Thu, 11 Nov 2010) | 2 lines
130 M /trunk/samtools/ChangeLog
131 M /trunk/samtools/bam2bcf_indel.c
133 effectively revert to the viterbi version. The forward realignment gives too many false positives.
135 ------------------------------------------------------------------------
136 r814 | lh3lh3 | 2010-11-11 00:18:02 -0500 (Thu, 11 Nov 2010) | 4 lines
138 M /trunk/samtools/bam2bcf_indel.c
139 M /trunk/samtools/bam_md.c
140 M /trunk/samtools/bam_plcmd.c
141 M /trunk/samtools/bamtk.c
143 * samtools-0.1.9-9 (r810)
144 * use forward, instead of viterbi, for realignment
145 * realignment is now quality aware
147 ------------------------------------------------------------------------
148 r813 | lh3lh3 | 2010-11-10 22:45:24 -0500 (Wed, 10 Nov 2010) | 2 lines
150 M /trunk/samtools/bam2bcf_indel.c
151 M /trunk/samtools/kprobaln.c
152 M /trunk/samtools/kprobaln.h
154 * prepare to replace kaln with kprobaln in realignment
156 ------------------------------------------------------------------------
157 r812 | lh3lh3 | 2010-11-10 17:28:50 -0500 (Wed, 10 Nov 2010) | 2 lines
159 M /trunk/samtools/bcftools/bcf.c
163 ------------------------------------------------------------------------
164 r811 | lh3lh3 | 2010-11-10 16:54:46 -0500 (Wed, 10 Nov 2010) | 2 lines
166 M /trunk/samtools/bcftools/bcf.c
167 M /trunk/samtools/bcftools/bcf.h
169 use zlib for direct reading when BCF_LITE is in use
171 ------------------------------------------------------------------------
172 r810 | lh3lh3 | 2010-11-10 16:32:13 -0500 (Wed, 10 Nov 2010) | 3 lines
174 M /trunk/samtools/bam2bcf_indel.c
176 * do not use reads containing too many mismatches for indel calling
177 * fixed a trivial bug in case of multi-allelic indels
179 ------------------------------------------------------------------------
180 r809 | lh3lh3 | 2010-11-10 13:23:02 -0500 (Wed, 10 Nov 2010) | 3 lines
182 M /trunk/samtools/bam2bcf.c
183 M /trunk/samtools/bam2bcf_indel.c
184 M /trunk/samtools/bam_plcmd.c
185 M /trunk/samtools/bamtk.c
187 * samtools-0.1.9-8 (r809)
188 * fixed a bug in the indel caller
190 ------------------------------------------------------------------------
191 r808 | lh3lh3 | 2010-11-10 12:24:10 -0500 (Wed, 10 Nov 2010) | 2 lines
193 M /trunk/samtools/Makefile
195 minor change to makefile
197 ------------------------------------------------------------------------
198 r807 | lh3lh3 | 2010-11-10 12:10:21 -0500 (Wed, 10 Nov 2010) | 4 lines
200 M /trunk/samtools/Makefile
201 M /trunk/samtools/bam2bcf.h
202 M /trunk/samtools/bam2bcf_indel.c
203 M /trunk/samtools/bam_plcmd.c
204 M /trunk/samtools/bamtk.c
205 M /trunk/samtools/bcftools/vcfutils.pl
207 * samtools-0.1.9-8 (r807)
208 * collect indel candidates only from specified platforms (@RG-PL)
209 * merge varFilter and filter4vcf in vcfutils.pl
211 ------------------------------------------------------------------------
212 r806 | lh3lh3 | 2010-11-09 22:05:46 -0500 (Tue, 09 Nov 2010) | 2 lines
214 M /trunk/samtools/bcftools/call1.c
215 M /trunk/samtools/bcftools/prob1.c
216 M /trunk/samtools/bcftools/prob1.h
218 bcftools: compute equal-tail (Bayesian) credible interval
220 ------------------------------------------------------------------------
221 r805 | lh3lh3 | 2010-11-09 16:28:39 -0500 (Tue, 09 Nov 2010) | 2 lines
223 M /trunk/samtools/bcftools/vcfutils.pl
225 added a double-hit filter to avoid overestimated indel likelihood
227 ------------------------------------------------------------------------
228 r804 | lh3lh3 | 2010-11-09 14:12:06 -0500 (Tue, 09 Nov 2010) | 3 lines
230 M /trunk/samtools/bam2bcf_indel.c
231 M /trunk/samtools/bamtk.c
233 * samtools-0.1.9-7 (r804)
234 * fixed a bug in the gap caller
236 ------------------------------------------------------------------------
237 r803 | lh3lh3 | 2010-11-09 10:45:33 -0500 (Tue, 09 Nov 2010) | 4 lines
239 M /trunk/samtools/bam2bcf.c
240 M /trunk/samtools/bam2bcf_indel.c
241 M /trunk/samtools/bamtk.c
242 M /trunk/samtools/bcftools/bcf.c
243 M /trunk/samtools/bcftools/bcf.h
244 M /trunk/samtools/bcftools/prob1.c
246 * samtools-0.1.9-6 (r803)
247 * mpileup: apply homopolymer correction when calculating GL, instead of before
248 * bcftools: apply a different prior to indels
250 ------------------------------------------------------------------------
251 r802 | lh3lh3 | 2010-11-08 23:53:15 -0500 (Mon, 08 Nov 2010) | 3 lines
253 M /trunk/samtools/bam2bcf.c
254 M /trunk/samtools/bamtk.c
256 * samtools-0.1.9-5 (r802)
257 * relax tandem penalty. this will be made a command-line option in future.
259 ------------------------------------------------------------------------
260 r801 | lh3lh3 | 2010-11-08 23:35:52 -0500 (Mon, 08 Nov 2010) | 3 lines
262 M /trunk/samtools/bam2bcf.c
263 M /trunk/samtools/bamtk.c
265 * samtools-0.1.9-4 (r801)
266 * fixed a minor issue in printing indel VCF
268 ------------------------------------------------------------------------
269 r800 | lh3lh3 | 2010-11-08 15:28:14 -0500 (Mon, 08 Nov 2010) | 2 lines
271 M /trunk/samtools/bam2bcf_indel.c
272 M /trunk/samtools/bcftools/vcfutils.pl
274 fixed another silly bug in mpileup's indel caller
276 ------------------------------------------------------------------------
277 r799 | lh3lh3 | 2010-11-08 14:28:27 -0500 (Mon, 08 Nov 2010) | 2 lines
279 M /trunk/samtools/bam2bcf.c
281 fixed a silly bug in the indel caller
283 ------------------------------------------------------------------------
284 r798 | lh3lh3 | 2010-11-08 14:07:33 -0500 (Mon, 08 Nov 2010) | 2 lines
286 M /trunk/samtools/ChangeLog
287 M /trunk/samtools/sam_view.c
288 M /trunk/samtools/samtools.1
290 Incorporate patches by Marcel Martin for read counting.
292 ------------------------------------------------------------------------
293 r797 | lh3lh3 | 2010-11-08 13:39:52 -0500 (Mon, 08 Nov 2010) | 3 lines
295 M /trunk/samtools/bam2bcf.c
296 M /trunk/samtools/bam2bcf.h
297 M /trunk/samtools/bam2bcf_indel.c
298 M /trunk/samtools/bam_plcmd.c
299 M /trunk/samtools/bamtk.c
301 * samtools-0.1.9-2 (r797)
302 * mpileup: indel calling seems to be working
304 ------------------------------------------------------------------------
305 r796 | lh3lh3 | 2010-11-08 10:54:46 -0500 (Mon, 08 Nov 2010) | 2 lines
307 M /trunk/samtools/bam2bcf.c
308 M /trunk/samtools/bam2bcf.h
309 M /trunk/samtools/bam2bcf_indel.c
310 M /trunk/samtools/bam_plcmd.c
311 M /trunk/samtools/kaln.c
313 indel calling is apparently working, but more information needs to be collected
315 ------------------------------------------------------------------------
316 r795 | lh3lh3 | 2010-11-08 00:39:18 -0500 (Mon, 08 Nov 2010) | 2 lines
318 M /trunk/samtools/bam2bcf.c
319 M /trunk/samtools/bam2bcf_indel.c
321 fixed a few bugs in the indel caller. Probably there are more.
323 ------------------------------------------------------------------------
324 r794 | lh3lh3 | 2010-11-07 22:23:16 -0500 (Sun, 07 Nov 2010) | 2 lines
326 M /trunk/samtools/Makefile
327 M /trunk/samtools/bam.h
328 M /trunk/samtools/bam2bcf.c
329 M /trunk/samtools/bam2bcf.h
330 A /trunk/samtools/bam2bcf_indel.c
331 M /trunk/samtools/bam_plcmd.c
332 M /trunk/samtools/kaln.c
333 M /trunk/samtools/kaln.h
335 prepare for the indel caller. It is not ready yet.
337 ------------------------------------------------------------------------
338 r793 | lh3lh3 | 2010-11-05 11:28:23 -0400 (Fri, 05 Nov 2010) | 2 lines
340 M /trunk/samtools/bam2bcf.c
341 M /trunk/samtools/bam2bcf.h
342 M /trunk/samtools/bam_plcmd.c
344 Revert to r790. The recent changes are not good...
346 ------------------------------------------------------------------------
347 r792 | lh3lh3 | 2010-11-05 00:19:14 -0400 (Fri, 05 Nov 2010) | 6 lines
349 M /trunk/samtools/bam2bcf.c
350 M /trunk/samtools/bam2bcf.h
351 M /trunk/samtools/bam_plcmd.c
353 * this revision is UNSTABLE
355 * indel caller seems working, but it is very insensitive and has
356 several things I do not quite understand.
359 ------------------------------------------------------------------------
360 r791 | lh3lh3 | 2010-11-04 22:58:43 -0400 (Thu, 04 Nov 2010) | 2 lines
362 M /trunk/samtools/bam2bcf.c
363 M /trunk/samtools/bam2bcf.h
364 M /trunk/samtools/bam_plcmd.c
366 for backup. no effective changes
368 ------------------------------------------------------------------------
369 r790 | lh3lh3 | 2010-11-03 15:51:24 -0400 (Wed, 03 Nov 2010) | 2 lines
371 M /trunk/samtools/bcftools/vcfutils.pl
372 M /trunk/samtools/kprobaln.c
374 fixed a minor problem in the example coming with kprobaln.c
376 ------------------------------------------------------------------------
377 r789 | lh3lh3 | 2010-11-02 15:41:27 -0400 (Tue, 02 Nov 2010) | 4 lines
379 M /trunk/samtools/Makefile
380 M /trunk/samtools/bam_md.c
381 M /trunk/samtools/kaln.c
382 M /trunk/samtools/kaln.h
383 A /trunk/samtools/kprobaln.c
384 A /trunk/samtools/kprobaln.h
386 Separate kaln and kprobaln as I am preparing further changes. At
387 present, the results should be identical to the previous.
390 ------------------------------------------------------------------------
391 r788 | petulda | 2010-11-02 12:19:04 -0400 (Tue, 02 Nov 2010) | 1 line
393 M /trunk/samtools/bam_plcmd.c
395 Added -b option: read file names from a file
396 ------------------------------------------------------------------------
397 r787 | lh3lh3 | 2010-10-29 23:17:22 -0400 (Fri, 29 Oct 2010) | 7 lines
399 M /trunk/samtools/bam.h
400 M /trunk/samtools/bam_pileup.c
401 M /trunk/samtools/bam_plcmd.c
402 M /trunk/samtools/bamtk.c
404 * samtools-0.1.9-2 (r787)
406 * Allow to set a maximum per-sample depth to reduce memory. However,
407 BAQ computation is still applied to every read. The speed is not
411 ------------------------------------------------------------------------
412 r786 | lh3lh3 | 2010-10-29 12:10:40 -0400 (Fri, 29 Oct 2010) | 3 lines
414 M /trunk/samtools/bam2bcf.c
415 M /trunk/samtools/bam2bcf.h
416 M /trunk/samtools/bam_plcmd.c
417 M /trunk/samtools/bamtk.c
418 M /trunk/samtools/bcftools/bcf.c
419 M /trunk/samtools/bcftools/vcf.c
421 * samtools-0.1.9-1 (r786)
422 * samtools: optionally perform exact test for each sample
424 ------------------------------------------------------------------------
425 r785 | lh3lh3 | 2010-10-29 09:42:25 -0400 (Fri, 29 Oct 2010) | 2 lines
427 M /trunk/samtools/bam2bcf.c
428 M /trunk/samtools/bam2bcf.h
429 M /trunk/samtools/bam_plcmd.c
430 M /trunk/samtools/bcftools/bcf.c
432 Optionally output "DP", the individual read depth
434 ------------------------------------------------------------------------
435 r784 | lh3lh3 | 2010-10-27 23:10:27 -0400 (Wed, 27 Oct 2010) | 2 lines
437 M /trunk/samtools/samtools.1
439 acknowledge Petr and John who have greatly contributed to the project.
441 ------------------------------------------------------------------------
442 r783 | lh3lh3 | 2010-10-27 22:47:47 -0400 (Wed, 27 Oct 2010) | 2 lines
444 M /trunk/samtools/ChangeLog
445 M /trunk/samtools/NEWS
446 M /trunk/samtools/bamtk.c
447 M /trunk/samtools/samtools.1
449 Release samtools-0.1.9 (r783)
451 ------------------------------------------------------------------------
452 r782 | lh3lh3 | 2010-10-27 19:58:54 -0400 (Wed, 27 Oct 2010) | 2 lines
454 M /trunk/samtools/bam_plcmd.c
456 fixed a silly bug in pileup
458 ------------------------------------------------------------------------
459 r781 | lh3lh3 | 2010-10-27 14:39:48 -0400 (Wed, 27 Oct 2010) | 5 lines
461 M /trunk/samtools/ChangeLog
462 M /trunk/samtools/bam_plcmd.c
463 M /trunk/samtools/bam_sort.c
464 M /trunk/samtools/bamtk.c
465 M /trunk/samtools/samtools.1
467 * samtools-0.1.8-22 (r781)
468 * made BAQ the default behavior of mpileup
470 * in merge, force to exit given inconsistent header when "-R" is not in use.
472 ------------------------------------------------------------------------
473 r780 | lh3lh3 | 2010-10-27 11:01:11 -0400 (Wed, 27 Oct 2010) | 3 lines
475 M /trunk/samtools/bam.h
476 M /trunk/samtools/bam_plcmd.c
477 M /trunk/samtools/bamtk.c
479 * samtools-0.1.8-21 (r780)
480 * minor speedup to pileup
482 ------------------------------------------------------------------------
483 r779 | lh3lh3 | 2010-10-27 09:58:56 -0400 (Wed, 27 Oct 2010) | 2 lines
485 M /trunk/samtools/bam_pileup.c
486 M /trunk/samtools/bam_plcmd.c
487 M /trunk/samtools/examples/toy.sam
489 improve pileup a little bit
491 ------------------------------------------------------------------------
492 r778 | lh3lh3 | 2010-10-27 00:14:43 -0400 (Wed, 27 Oct 2010) | 3 lines
494 M /trunk/samtools/bam.h
495 M /trunk/samtools/bam_pileup.c
496 M /trunk/samtools/bam_plcmd.c
497 M /trunk/samtools/bam_tview.c
498 M /trunk/samtools/bamtk.c
500 * samtools-0.1.8-20 (r778)
501 * speed up pileup, although I do not know how much is the improvement
503 ------------------------------------------------------------------------
504 r777 | lh3lh3 | 2010-10-26 17:26:04 -0400 (Tue, 26 Oct 2010) | 3 lines
506 M /trunk/samtools/bam_maqcns.c
507 M /trunk/samtools/bam_maqcns.h
508 M /trunk/samtools/bam_plcmd.c
509 M /trunk/samtools/bamtk.c
510 M /trunk/samtools/examples/Makefile
512 * samtools-0.1.8-19 (r777)
513 * integrate mpileup features to pileup: min_baseQ, capQ, prob_realn, paired-only and biased prior
515 ------------------------------------------------------------------------
516 r776 | lh3lh3 | 2010-10-26 15:27:46 -0400 (Tue, 26 Oct 2010) | 2 lines
518 M /trunk/samtools/bam_md.c
520 remove local realignment (probabilistic realignment is still there)
522 ------------------------------------------------------------------------
523 r774 | jmarshall | 2010-10-21 06:52:38 -0400 (Thu, 21 Oct 2010) | 3 lines
525 M /trunk/samtools/sam_view.c
527 Add the relevant filename or region to error messages, and cause a failure
528 exit status where appropriate. Based on a patch provided by Marcel Martin.
530 ------------------------------------------------------------------------
531 r773 | lh3lh3 | 2010-10-19 19:44:31 -0400 (Tue, 19 Oct 2010) | 3 lines
533 M /trunk/samtools/examples/toy.sam
534 M /trunk/samtools/kaln.c
536 * Minor code changes. No real effect.
537 * change quality to 30 in toy.sam
539 ------------------------------------------------------------------------
540 r772 | lh3lh3 | 2010-10-18 23:40:13 -0400 (Mon, 18 Oct 2010) | 2 lines
542 M /trunk/samtools/examples/toy.fa
543 M /trunk/samtools/examples/toy.sam
545 added another toy example
547 ------------------------------------------------------------------------
548 r771 | lh3lh3 | 2010-10-13 23:32:12 -0400 (Wed, 13 Oct 2010) | 2 lines
550 M /trunk/samtools/bcftools/call1.c
551 M /trunk/samtools/bcftools/ld.c
552 M /trunk/samtools/bcftools/vcfutils.pl
554 improve the LD statistics
556 ------------------------------------------------------------------------
557 r770 | lh3lh3 | 2010-10-12 23:49:26 -0400 (Tue, 12 Oct 2010) | 3 lines
559 M /trunk/samtools/bcftools/call1.c
560 M /trunk/samtools/bcftools/vcfutils.pl
562 * a minor fix to the -L option
563 * add ldstats to vcfutils.pl
565 ------------------------------------------------------------------------
566 r769 | lh3lh3 | 2010-10-12 15:51:57 -0400 (Tue, 12 Oct 2010) | 2 lines
568 M /trunk/samtools/bcftools/bcf.c
572 ------------------------------------------------------------------------
573 r768 | lh3lh3 | 2010-10-12 15:49:06 -0400 (Tue, 12 Oct 2010) | 2 lines
575 M /trunk/samtools/bcftools/Makefile
576 A /trunk/samtools/bcftools/ld.c
578 forget to add the key file
580 ------------------------------------------------------------------------
581 r767 | lh3lh3 | 2010-10-12 15:48:46 -0400 (Tue, 12 Oct 2010) | 4 lines
583 M /trunk/samtools/bcftools/Makefile
584 M /trunk/samtools/bcftools/bcf.c
585 M /trunk/samtools/bcftools/bcf.h
586 M /trunk/samtools/bcftools/call1.c
587 M /trunk/samtools/bcftools/prob1.c
588 M /trunk/samtools/bcftools/vcfutils.pl
590 * vcfutils.pl: fixed a typo in help message
591 * added APIs: bcf_append_info() and bcf_cpy()
592 * calculate adjacent LD
594 ------------------------------------------------------------------------
595 r766 | lh3lh3 | 2010-10-11 11:06:40 -0400 (Mon, 11 Oct 2010) | 2 lines
597 M /trunk/samtools/bcftools/vcfutils.pl
599 added filter for samtools/bcftools genetated VCFs
601 ------------------------------------------------------------------------
602 r765 | lh3lh3 | 2010-10-05 14:05:18 -0400 (Tue, 05 Oct 2010) | 3 lines
604 M /trunk/samtools/bcftools/vcfutils.pl
605 M /trunk/samtools/kaln.c
607 * removed a comment line in kaln.c
608 * vcfutils.pl fillac works when GT is not the first field
610 ------------------------------------------------------------------------
611 r764 | petulda | 2010-10-05 08:59:36 -0400 (Tue, 05 Oct 2010) | 1 line
613 A /trunk/samtools/bcftools/bcf-fix.pl
615 Convert VCF output of "bcftools view -bgcv" to a valid VCF file
616 ------------------------------------------------------------------------
617 r763 | lh3lh3 | 2010-10-02 22:51:03 -0400 (Sat, 02 Oct 2010) | 4 lines
619 M /trunk/samtools/bam_plcmd.c
620 M /trunk/samtools/bamtk.c
621 A /trunk/samtools/bcftools/bcftools.1
622 M /trunk/samtools/bcftools/call1.c
623 M /trunk/samtools/samtools.1
625 * samtools-0.1.8-18 (r763)
626 * added bcftools manual page
627 * minor fix to mpileup and view command lines
629 ------------------------------------------------------------------------
630 r762 | lh3lh3 | 2010-10-02 21:46:25 -0400 (Sat, 02 Oct 2010) | 3 lines
632 M /trunk/samtools/bcftools/bcf.c
633 M /trunk/samtools/bcftools/call1.c
634 M /trunk/samtools/bcftools/vcfutils.pl
636 * vcfutils.pl qstats: calculate marginal ts/tv
637 * allow to call genotypes at variant sites
639 ------------------------------------------------------------------------
640 r761 | lh3lh3 | 2010-10-01 00:29:55 -0400 (Fri, 01 Oct 2010) | 3 lines
642 M /trunk/samtools/kaln.c
643 M /trunk/samtools/misc/HmmGlocal.java
645 I am changing the gap open probability back to 0.001. It seems that
646 being conservative here is a good thing...
648 ------------------------------------------------------------------------
649 r760 | lh3lh3 | 2010-10-01 00:11:27 -0400 (Fri, 01 Oct 2010) | 5 lines
651 M /trunk/samtools/bamtk.c
652 M /trunk/samtools/kaln.c
653 A /trunk/samtools/misc/HmmGlocal.java
655 * samtools-0.1.8-17 (r760)
656 * the default gap open penalty is too small (a typo)
657 * added comments on hmm_realn
658 * Java implementation
660 ------------------------------------------------------------------------
661 r759 | lh3lh3 | 2010-09-30 10:12:54 -0400 (Thu, 30 Sep 2010) | 2 lines
663 M /trunk/samtools/bamtk.c
665 mark samtools-0.1.8-16 (r759)
667 ------------------------------------------------------------------------
668 r758 | lh3lh3 | 2010-09-30 10:12:02 -0400 (Thu, 30 Sep 2010) | 2 lines
670 M /trunk/samtools/kaln.c
672 round to the nearest integer
674 ------------------------------------------------------------------------
675 r757 | lh3lh3 | 2010-09-28 17:16:43 -0400 (Tue, 28 Sep 2010) | 4 lines
677 M /trunk/samtools/kaln.c
679 I was trying to accelerate ka_prob_glocal() as this will be the
680 bottleneck. After an hour, the only gain is to change division to
681 multiplication. OK. I will stop.
683 ------------------------------------------------------------------------
684 r756 | lh3lh3 | 2010-09-28 16:57:49 -0400 (Tue, 28 Sep 2010) | 2 lines
686 M /trunk/samtools/kaln.c
688 this is interesting. multiplication is much faster than division, at least on my Mac
690 ------------------------------------------------------------------------
691 r755 | lh3lh3 | 2010-09-28 16:19:13 -0400 (Tue, 28 Sep 2010) | 2 lines
693 M /trunk/samtools/kaln.c
697 ------------------------------------------------------------------------
698 r754 | lh3lh3 | 2010-09-28 15:44:16 -0400 (Tue, 28 Sep 2010) | 2 lines
700 M /trunk/samtools/bam_md.c
701 M /trunk/samtools/bam_plcmd.c
702 M /trunk/samtools/kaln.c
704 prob_realn() seems working!
706 ------------------------------------------------------------------------
707 r753 | lh3lh3 | 2010-09-28 12:48:23 -0400 (Tue, 28 Sep 2010) | 2 lines
709 M /trunk/samtools/kaln.c
713 ------------------------------------------------------------------------
714 r752 | lh3lh3 | 2010-09-28 12:47:41 -0400 (Tue, 28 Sep 2010) | 2 lines
716 M /trunk/samtools/kaln.c
717 M /trunk/samtools/kaln.h
719 Convert phredQ to probabilities
721 ------------------------------------------------------------------------
722 r751 | lh3lh3 | 2010-09-28 12:32:08 -0400 (Tue, 28 Sep 2010) | 2 lines
724 M /trunk/samtools/kaln.c
725 M /trunk/samtools/kaln.h
727 Implement the glocal HMM; discard the extention HMM
729 ------------------------------------------------------------------------
730 r750 | lh3lh3 | 2010-09-28 00:06:11 -0400 (Tue, 28 Sep 2010) | 2 lines
732 M /trunk/samtools/kaln.c
734 improve numerical stability
736 ------------------------------------------------------------------------
737 r749 | lh3lh3 | 2010-09-27 23:27:54 -0400 (Mon, 27 Sep 2010) | 2 lines
739 M /trunk/samtools/kaln.c
743 ------------------------------------------------------------------------
744 r748 | lh3lh3 | 2010-09-27 23:17:16 -0400 (Mon, 27 Sep 2010) | 2 lines
746 M /trunk/samtools/kaln.c
748 fixed a bug in banded DP
750 ------------------------------------------------------------------------
751 r747 | lh3lh3 | 2010-09-27 23:05:12 -0400 (Mon, 27 Sep 2010) | 3 lines
753 M /trunk/samtools/kaln.c
755 * fixed that weird issue.
756 * the banded version is NOT working
758 ------------------------------------------------------------------------
759 r746 | lh3lh3 | 2010-09-27 22:57:05 -0400 (Mon, 27 Sep 2010) | 2 lines
761 M /trunk/samtools/kaln.c
763 More comments. This version seems working, but something is a little weird...
765 ------------------------------------------------------------------------
766 r745 | lh3lh3 | 2010-09-27 17:21:40 -0400 (Mon, 27 Sep 2010) | 6 lines
768 M /trunk/samtools/kaln.c
770 A little code cleanup. Now the forward and backback algorithms give
771 nearly identical P(x), which means both are close to the correct
772 forms. However, I have only tested on toy examples. Minor errors in
773 the implementation may not be obvious.
776 ------------------------------------------------------------------------
777 r744 | lh3lh3 | 2010-09-27 16:55:15 -0400 (Mon, 27 Sep 2010) | 2 lines
779 M /trunk/samtools/bam_plcmd.c
780 M /trunk/samtools/bam_sort.c
781 M /trunk/samtools/kaln.c
782 M /trunk/samtools/kaln.h
786 ------------------------------------------------------------------------
787 r743 | jmarshall | 2010-09-27 08:19:06 -0400 (Mon, 27 Sep 2010) | 6 lines
789 M /trunk/samtools/bam_sort.c
791 Abort if merge -h's INH.SAM cannot be opened, just as we abort
792 if any of the IN#.BAM input files cannot be opened.
794 Also propagate any error indication returned by bam_merge_core()
795 to samtools merge's exit status.
797 ------------------------------------------------------------------------
798 r741 | jmarshall | 2010-09-24 11:08:24 -0400 (Fri, 24 Sep 2010) | 5 lines
800 M /trunk/samtools/bam_index.c
802 Use bam_validate1() to detect garbage records in the event of a corrupt
803 BAI index file that causes a bam_seek() to an invalid position. At most
804 one record (namely, the bam_iter_read terminator) is tested per bam_fetch()
805 call, so the cost is insignificant in the normal case.
807 ------------------------------------------------------------------------
808 r740 | jmarshall | 2010-09-24 11:00:19 -0400 (Fri, 24 Sep 2010) | 2 lines
810 M /trunk/samtools/bam.c
811 M /trunk/samtools/bam.h
815 ------------------------------------------------------------------------
816 r739 | lh3lh3 | 2010-09-22 12:07:50 -0400 (Wed, 22 Sep 2010) | 3 lines
818 M /trunk/samtools/bam_md.c
819 M /trunk/samtools/bamtk.c
821 * samtools-0.1.8-15 (r379)
822 * allow to change capQ parameter in calmd
824 ------------------------------------------------------------------------
825 r738 | jmarshall | 2010-09-22 11:15:33 -0400 (Wed, 22 Sep 2010) | 13 lines
827 M /trunk/samtools/bam_index.c
828 M /trunk/samtools/sam_view.c
830 When bam_read1() returns an error (return value <= -2), propagate that error
831 to bam_iter_read()'s own return value. Similarly, also propagate it up to
832 bam_fetch()'s return value. Previously bam_fetch() always returned 0, and
833 callers ignored its return value anyway. With this change, 0 continues to
834 indicate success, while <= -2 (which can be written as < 0, as -1 is never
835 returned) indicates corrupted input.
837 bam_iter_read() ought also to propagate errors returned by bam_seek().
839 main_samview() can now print an error message and fail when bam_fetch()
840 detects that a .bai index file is corrupted or otherwise does not correspond
841 to the .bam file it is being used with.
843 ------------------------------------------------------------------------
844 r737 | jmarshall | 2010-09-22 10:47:42 -0400 (Wed, 22 Sep 2010) | 3 lines
846 M /trunk/samtools/bam_index.c
848 0 is a successful return value from bam_read1(). (In practice, it never
849 returns 0 anyway; but all the other callers treat 0 as successful.)
851 ------------------------------------------------------------------------
852 r736 | lh3lh3 | 2010-09-20 17:43:08 -0400 (Mon, 20 Sep 2010) | 2 lines
854 M /trunk/samtools/bam.h
855 M /trunk/samtools/bam_index.c
856 M /trunk/samtools/bam_sort.c
858 * merge files region-by-region. work on small examples but more tests are needed.
860 ------------------------------------------------------------------------
861 r735 | lh3lh3 | 2010-09-20 16:56:24 -0400 (Mon, 20 Sep 2010) | 2 lines
863 M /trunk/samtools/bcftools/vcfutils.pl
865 improve qstats by checking the alleles as well
867 ------------------------------------------------------------------------
868 r734 | lh3lh3 | 2010-09-17 18:12:13 -0400 (Fri, 17 Sep 2010) | 2 lines
870 M /trunk/samtools/bcftools/vcfutils.pl
872 convert UCSC SNP SQL dump to VCF
874 ------------------------------------------------------------------------
875 r733 | lh3lh3 | 2010-09-17 13:02:11 -0400 (Fri, 17 Sep 2010) | 2 lines
877 M /trunk/samtools/bcftools/vcfutils.pl
881 ------------------------------------------------------------------------
882 r732 | lh3lh3 | 2010-09-17 10:11:37 -0400 (Fri, 17 Sep 2010) | 3 lines
884 M /trunk/samtools/bcftools/Makefile
885 M /trunk/samtools/bcftools/bcf.c
886 M /trunk/samtools/bcftools/bcf.h
887 M /trunk/samtools/bcftools/vcf.c
890 * VCF->BCF is not possible without knowing the sequence dictionary before hand...
892 ------------------------------------------------------------------------
893 r731 | lh3lh3 | 2010-09-17 09:15:53 -0400 (Fri, 17 Sep 2010) | 2 lines
895 M /trunk/samtools/bam2bcf.c
896 M /trunk/samtools/bcftools/bcf.c
897 M /trunk/samtools/bcftools/bcf.h
898 M /trunk/samtools/bcftools/bcfutils.c
899 M /trunk/samtools/bcftools/call1.c
900 M /trunk/samtools/bcftools/vcf.c
902 * put n_smpl to "bcf1_t" to simplify API a little
904 ------------------------------------------------------------------------
905 r730 | lh3lh3 | 2010-09-16 21:36:01 -0400 (Thu, 16 Sep 2010) | 2 lines
907 M /trunk/samtools/bcftools/bcf.h
908 M /trunk/samtools/bcftools/call1.c
909 M /trunk/samtools/bcftools/index.c
911 fixed a bug in indexing
913 ------------------------------------------------------------------------
914 r729 | lh3lh3 | 2010-09-16 16:54:48 -0400 (Thu, 16 Sep 2010) | 3 lines
916 M /trunk/samtools/bam.c
917 M /trunk/samtools/bam_md.c
918 M /trunk/samtools/bam_pileup.c
920 * fixed a bug in capQ
921 * valgrind identifies a use of uninitialised value, but I have not fixed it.
923 ------------------------------------------------------------------------
924 r728 | lh3lh3 | 2010-09-16 15:03:59 -0400 (Thu, 16 Sep 2010) | 3 lines
926 M /trunk/samtools/bgzip.c
927 M /trunk/samtools/razip.c
929 * fixed a bug in razip: -c will delete the input file
930 * copy tabix/bgzip to here
932 ------------------------------------------------------------------------
933 r727 | lh3lh3 | 2010-09-16 13:45:49 -0400 (Thu, 16 Sep 2010) | 3 lines
935 M /trunk/samtools/bam_md.c
936 M /trunk/samtools/bam_plcmd.c
937 M /trunk/samtools/bamtk.c
939 * samtools-0.1.8-14 (r727)
940 * allow to change the capQ parameter at the command line
942 ------------------------------------------------------------------------
943 r726 | lh3lh3 | 2010-09-16 13:38:43 -0400 (Thu, 16 Sep 2010) | 4 lines
945 M /trunk/samtools/bam_md.c
946 M /trunk/samtools/bam_plcmd.c
947 M /trunk/samtools/bcftools/vcfutils.pl
948 M /trunk/samtools/misc/samtools.pl
950 * added varFilter to vcfutils.pl
951 * reimplement realn(). now it performs a local alignment
952 * added cap_mapQ() to cap mapping quality when there are many substitutions
954 ------------------------------------------------------------------------
955 r724 | lh3lh3 | 2010-09-15 00:18:31 -0400 (Wed, 15 Sep 2010) | 2 lines
957 M /trunk/samtools/bcftools/Makefile
958 A /trunk/samtools/bcftools/bcf2qcall.c
959 M /trunk/samtools/bcftools/call1.c
961 * convert BCF to QCALL input
963 ------------------------------------------------------------------------
964 r723 | lh3lh3 | 2010-09-14 22:41:50 -0400 (Tue, 14 Sep 2010) | 2 lines
966 M /trunk/samtools/bam_md.c
968 dynamic band width in realignment
970 ------------------------------------------------------------------------
971 r722 | lh3lh3 | 2010-09-14 22:05:32 -0400 (Tue, 14 Sep 2010) | 2 lines
973 M /trunk/samtools/bam_md.c
974 M /trunk/samtools/bam_plcmd.c
976 fixed a bug in realignment
978 ------------------------------------------------------------------------
979 r721 | lh3lh3 | 2010-09-14 20:54:09 -0400 (Tue, 14 Sep 2010) | 2 lines
981 M /trunk/samtools/bcftools/prob1.c
985 ------------------------------------------------------------------------
986 r720 | lh3lh3 | 2010-09-14 19:25:10 -0400 (Tue, 14 Sep 2010) | 2 lines
988 M /trunk/samtools/Makefile
989 M /trunk/samtools/bam_maqcns.c
990 M /trunk/samtools/bam_md.c
992 fixed a bug in realignment
994 ------------------------------------------------------------------------
995 r719 | lh3lh3 | 2010-09-14 19:18:24 -0400 (Tue, 14 Sep 2010) | 2 lines
997 M /trunk/samtools/bam_plcmd.c
999 minor changes. It is BUGGY now!
1001 ------------------------------------------------------------------------
1002 r718 | lh3lh3 | 2010-09-14 16:32:33 -0400 (Tue, 14 Sep 2010) | 4 lines
1004 M /trunk/samtools/bam_md.c
1005 M /trunk/samtools/bam_pileup.c
1006 M /trunk/samtools/kaln.c
1007 M /trunk/samtools/kaln.h
1009 * aggressive gapped aligner is implemented in calmd.
1010 * distinguish gap_open and gap_end_open in banded alignment
1011 * make tview accepts alignment with heading and tailing D
1013 ------------------------------------------------------------------------
1014 r717 | jmarshall | 2010-09-14 09:04:28 -0400 (Tue, 14 Sep 2010) | 2 lines
1018 Add svn:ignore properties for generated files that don't appear in "make all".
1020 ------------------------------------------------------------------------
1021 r716 | jmarshall | 2010-09-13 08:37:53 -0400 (Mon, 13 Sep 2010) | 3 lines
1024 M /trunk/samtools/bcftools
1025 M /trunk/samtools/misc
1027 Add svn:ignore properties listing the generated files.
1028 (Except for *.o, which we'll assume is in global-ignores.)
1030 ------------------------------------------------------------------------
1031 r715 | lh3lh3 | 2010-09-08 12:53:55 -0400 (Wed, 08 Sep 2010) | 5 lines
1033 M /trunk/samtools/bamtk.c
1034 M /trunk/samtools/bcftools/call1.c
1035 M /trunk/samtools/bcftools/prob1.c
1036 M /trunk/samtools/sample.c
1037 M /trunk/samtools/sample.h
1039 * samtools-0.1.8-13 (r715)
1040 * fixed a bug in identifying SM across files
1041 * bcftools: estimate heterozygosity
1042 * bcftools: allow to skip sites without reference bases
1044 ------------------------------------------------------------------------
1045 r713 | lh3lh3 | 2010-09-03 17:19:12 -0400 (Fri, 03 Sep 2010) | 2 lines
1047 M /trunk/samtools/bcftools/Makefile
1048 M /trunk/samtools/bcftools/call1.c
1049 M /trunk/samtools/bcftools/prob1.c
1050 M /trunk/samtools/bcftools/prob1.h
1052 quite a lot changes to the contrast caller, but I still feel something is missing...
1054 ------------------------------------------------------------------------
1055 r711 | lh3lh3 | 2010-09-03 00:30:48 -0400 (Fri, 03 Sep 2010) | 4 lines
1057 M /trunk/samtools/bcftools/Makefile
1058 M /trunk/samtools/bcftools/call1.c
1059 M /trunk/samtools/bcftools/prob1.c
1060 M /trunk/samtools/bcftools/vcfutils.pl
1062 * changed 3.434 to 4.343 (typo!)
1063 * fixed a bug in the contrast caller
1064 * calculate heterozygosity
1066 ------------------------------------------------------------------------
1067 r710 | lh3lh3 | 2010-09-01 23:24:47 -0400 (Wed, 01 Sep 2010) | 2 lines
1069 M /trunk/samtools/bcftools/bcf.h
1070 M /trunk/samtools/bcftools/bcfutils.c
1071 M /trunk/samtools/bcftools/call1.c
1073 SNP calling from the GL field
1075 ------------------------------------------------------------------------
1076 r709 | lh3lh3 | 2010-09-01 18:52:30 -0400 (Wed, 01 Sep 2010) | 2 lines
1078 M /trunk/samtools/bcftools/vcf.c
1080 fixed another problem
1082 ------------------------------------------------------------------------
1083 r708 | lh3lh3 | 2010-09-01 18:31:17 -0400 (Wed, 01 Sep 2010) | 3 lines
1085 M /trunk/samtools/bcftools/bcf.c
1086 M /trunk/samtools/bcftools/vcf.c
1088 * fixed bugs in parsing VCF
1089 * parser now works with GT/GQ/DP/PL/GL
1091 ------------------------------------------------------------------------
1092 r707 | lh3lh3 | 2010-09-01 15:28:29 -0400 (Wed, 01 Sep 2010) | 2 lines
1094 M /trunk/samtools/bcftools/Makefile
1095 M /trunk/samtools/bcftools/prob1.c
1097 Do not compile _BCF_QUAD by default
1099 ------------------------------------------------------------------------
1100 r706 | lh3lh3 | 2010-09-01 15:21:41 -0400 (Wed, 01 Sep 2010) | 2 lines
1102 M /trunk/samtools/bcftools/bcf.c
1103 M /trunk/samtools/bcftools/bcf.h
1104 M /trunk/samtools/bcftools/bcfutils.c
1105 M /trunk/samtools/bcftools/call1.c
1107 Write the correct ALT and PL in the SNP calling mode.
1109 ------------------------------------------------------------------------
1110 r705 | lh3lh3 | 2010-09-01 12:50:33 -0400 (Wed, 01 Sep 2010) | 2 lines
1112 M /trunk/samtools/bcftools/vcfutils.pl
1114 more commands for my own uses
1116 ------------------------------------------------------------------------
1117 r704 | lh3lh3 | 2010-09-01 09:26:10 -0400 (Wed, 01 Sep 2010) | 2 lines
1119 A /trunk/samtools/bcftools/vcfutils.pl
1121 Utilities for processing VCF
1123 ------------------------------------------------------------------------
1124 r703 | lh3lh3 | 2010-08-31 16:44:57 -0400 (Tue, 31 Aug 2010) | 2 lines
1126 M /trunk/samtools/bcftools/Makefile
1127 M /trunk/samtools/bcftools/call1.c
1128 M /trunk/samtools/bcftools/prob1.c
1129 M /trunk/samtools/bcftools/prob1.h
1131 preliminary contrast variant caller
1133 ------------------------------------------------------------------------
1134 r702 | lh3lh3 | 2010-08-31 12:28:39 -0400 (Tue, 31 Aug 2010) | 2 lines
1136 M /trunk/samtools/bcftools/call1.c
1137 M /trunk/samtools/bcftools/prob1.c
1138 M /trunk/samtools/bcftools/prob1.h
1140 z' and z'' can be calculated
1142 ------------------------------------------------------------------------
1143 r701 | lh3lh3 | 2010-08-31 10:20:57 -0400 (Tue, 31 Aug 2010) | 3 lines
1145 M /trunk/samtools/bcftools/Makefile
1146 A /trunk/samtools/bcftools/call1.c (from /trunk/samtools/bcftools/vcfout.c:699)
1147 M /trunk/samtools/bcftools/prob1.c
1148 D /trunk/samtools/bcftools/vcfout.c
1150 * rename vcfout.c as call1.c
1151 * prepare to add two-sample comparison
1153 ------------------------------------------------------------------------
1154 r699 | lh3lh3 | 2010-08-24 15:28:16 -0400 (Tue, 24 Aug 2010) | 2 lines
1156 M /trunk/samtools/bcftools/vcfout.c
1158 fixed a bug in calculating the t statistics
1160 ------------------------------------------------------------------------
1161 r698 | lh3lh3 | 2010-08-24 14:05:50 -0400 (Tue, 24 Aug 2010) | 3 lines
1163 M /trunk/samtools/bam2bcf.c
1164 M /trunk/samtools/bam2bcf.h
1165 M /trunk/samtools/bamtk.c
1166 M /trunk/samtools/bcftools/kfunc.c
1167 M /trunk/samtools/bcftools/vcfout.c
1169 * samtools-0.1.8-13 (r698)
1170 * perform one-tailed t-test for baseQ, mapQ and endDist
1172 ------------------------------------------------------------------------
1173 r697 | lh3lh3 | 2010-08-24 12:30:13 -0400 (Tue, 24 Aug 2010) | 2 lines
1175 M /trunk/samtools/bcftools/kfunc.c
1177 added regularized incomplete beta function
1179 ------------------------------------------------------------------------
1180 r695 | lh3lh3 | 2010-08-23 17:36:17 -0400 (Mon, 23 Aug 2010) | 2 lines
1182 M /trunk/samtools/bam_maqcns.c
1183 M /trunk/samtools/bam_plcmd.c
1185 change the default correlation coefficient
1187 ------------------------------------------------------------------------
1188 r694 | lh3lh3 | 2010-08-23 14:46:52 -0400 (Mon, 23 Aug 2010) | 2 lines
1190 M /trunk/samtools/bcftools/bcf.c
1191 M /trunk/samtools/bcftools/vcfout.c
1193 print QUAL as floating numbers
1195 ------------------------------------------------------------------------
1196 r693 | lh3lh3 | 2010-08-23 14:06:07 -0400 (Mon, 23 Aug 2010) | 3 lines
1198 M /trunk/samtools/Makefile
1199 M /trunk/samtools/bam_plcmd.c
1200 M /trunk/samtools/bamtk.c
1201 M /trunk/samtools/examples/Makefile
1202 A /trunk/samtools/sample.c
1203 A /trunk/samtools/sample.h
1205 * samtools-0.1.8-12 (r692)
1206 * group data by samples in "mpileup -g"
1208 ------------------------------------------------------------------------
1209 r692 | lh3lh3 | 2010-08-23 10:58:53 -0400 (Mon, 23 Aug 2010) | 2 lines
1211 M /trunk/samtools/Makefile
1212 D /trunk/samtools/bam_mcns.c
1213 D /trunk/samtools/bam_mcns.h
1214 M /trunk/samtools/bam_plcmd.c
1216 remove VCF output in mpileup
1218 ------------------------------------------------------------------------
1219 r691 | lh3lh3 | 2010-08-23 10:48:20 -0400 (Mon, 23 Aug 2010) | 3 lines
1221 M /trunk/samtools/bam2bcf.c
1222 M /trunk/samtools/bam2bcf.h
1224 * use the revised MAQ error model for mpileup
1225 * prepare to remove the independent model from mpileup
1227 ------------------------------------------------------------------------
1228 r690 | lh3lh3 | 2010-08-20 15:46:40 -0400 (Fri, 20 Aug 2010) | 2 lines
1230 M /trunk/samtools/Makefile
1231 M /trunk/samtools/bam_maqcns.c
1232 M /trunk/samtools/bam_maqcns.h
1233 M /trunk/samtools/bam_plcmd.c
1234 A /trunk/samtools/errmod.c
1235 A /trunk/samtools/errmod.h
1236 M /trunk/samtools/ksort.h
1238 added revised MAQ error model
1240 ------------------------------------------------------------------------
1241 r689 | lh3lh3 | 2010-08-18 09:55:20 -0400 (Wed, 18 Aug 2010) | 2 lines
1243 M /trunk/samtools/bcftools/prob1.c
1244 M /trunk/samtools/bcftools/prob1.h
1245 M /trunk/samtools/bcftools/vcfout.c
1247 allow to read the prior from the error output. EM iteration is working.
1249 ------------------------------------------------------------------------
1250 r688 | lh3lh3 | 2010-08-17 12:12:20 -0400 (Tue, 17 Aug 2010) | 3 lines
1252 M /trunk/samtools/bcftools/main.c
1253 M /trunk/samtools/bcftools/vcf.c
1255 * write a little more VCF header
1258 ------------------------------------------------------------------------
1259 r687 | lh3lh3 | 2010-08-16 20:53:16 -0400 (Mon, 16 Aug 2010) | 2 lines
1261 M /trunk/samtools/bcftools/bcf.c
1262 M /trunk/samtools/bcftools/bcf.h
1263 M /trunk/samtools/bcftools/bcf.tex
1267 ------------------------------------------------------------------------
1268 r686 | lh3lh3 | 2010-08-14 00:11:13 -0400 (Sat, 14 Aug 2010) | 2 lines
1270 M /trunk/samtools/bcftools/bcf.c
1271 M /trunk/samtools/bcftools/prob1.c
1273 faster for large sample size (in principle)
1275 ------------------------------------------------------------------------
1276 r685 | lh3lh3 | 2010-08-13 23:28:31 -0400 (Fri, 13 Aug 2010) | 4 lines
1278 M /trunk/samtools/bcftools/prob1.c
1280 * a numerically stable method to calculate z_{jk}
1281 * currently slower than the old method but will be important for large sample size
1282 * in principle, we can speed up for large n, but have not tried
1284 ------------------------------------------------------------------------
1285 r684 | lh3lh3 | 2010-08-11 21:58:31 -0400 (Wed, 11 Aug 2010) | 2 lines
1287 M /trunk/samtools/bcftools/vcfout.c
1289 fixed an issue in parsing integer
1291 ------------------------------------------------------------------------
1292 r683 | lh3lh3 | 2010-08-09 13:05:07 -0400 (Mon, 09 Aug 2010) | 2 lines
1294 M /trunk/samtools/bcftools/bcf.c
1296 do not print refname if file is converted from VCF
1298 ------------------------------------------------------------------------
1299 r682 | lh3lh3 | 2010-08-09 12:59:47 -0400 (Mon, 09 Aug 2010) | 3 lines
1301 M /trunk/samtools/bcftools/vcf.c
1304 * fixed a bug in parsing VCF
1306 ------------------------------------------------------------------------
1307 r681 | lh3lh3 | 2010-08-09 12:49:23 -0400 (Mon, 09 Aug 2010) | 4 lines
1309 M /trunk/samtools/bcftools/bcf.c
1310 M /trunk/samtools/bcftools/bcf.h
1311 M /trunk/samtools/bcftools/bcfutils.c
1312 M /trunk/samtools/bcftools/main.c
1313 M /trunk/samtools/bcftools/vcf.c
1314 M /trunk/samtools/bcftools/vcfout.c
1315 M /trunk/samtools/bgzf.c
1316 M /trunk/samtools/kstring.c
1318 * fixed a bug in kstrtok@kstring.c
1319 * preliminary VCF parser (not parse everything for now)
1320 * improved view interface
1322 ------------------------------------------------------------------------
1323 r680 | lh3lh3 | 2010-08-09 10:43:13 -0400 (Mon, 09 Aug 2010) | 4 lines
1325 M /trunk/samtools/bcftools/bcf.c
1326 M /trunk/samtools/bcftools/bcf.h
1327 M /trunk/samtools/bcftools/vcfout.c
1328 M /trunk/samtools/kstring.c
1329 M /trunk/samtools/kstring.h
1331 * improved kstring (added kstrtok)
1332 * removed the limit on the format string length in bcftools
1333 * use kstrtok to parse format which fixed a bug in the old code
1335 ------------------------------------------------------------------------
1336 r679 | lh3lh3 | 2010-08-09 01:12:05 -0400 (Mon, 09 Aug 2010) | 2 lines
1338 A /trunk/samtools/bcftools/README
1339 M /trunk/samtools/bcftools/vcfout.c
1343 ------------------------------------------------------------------------
1344 r678 | lh3lh3 | 2010-08-09 00:01:52 -0400 (Mon, 09 Aug 2010) | 2 lines
1346 M /trunk/samtools/bcftools/vcfout.c
1348 perform single-tail test for ED4
1350 ------------------------------------------------------------------------
1351 r677 | lh3lh3 | 2010-08-08 23:48:35 -0400 (Sun, 08 Aug 2010) | 2 lines
1353 M /trunk/samtools/bcftools/Makefile
1354 M /trunk/samtools/bcftools/kfunc.c
1355 M /trunk/samtools/bcftools/vcfout.c
1357 * test depth, end distance and HWE
1359 ------------------------------------------------------------------------
1360 r676 | lh3lh3 | 2010-08-08 02:04:15 -0400 (Sun, 08 Aug 2010) | 2 lines
1362 M /trunk/samtools/bcftools/kfunc.c
1364 reimplement incomplete gamma functions. no copy-paste
1366 ------------------------------------------------------------------------
1367 r675 | lh3lh3 | 2010-08-06 22:42:54 -0400 (Fri, 06 Aug 2010) | 3 lines
1369 M /trunk/samtools/bam2bcf.c
1370 M /trunk/samtools/bam2bcf.h
1371 M /trunk/samtools/bcftools/fet.c
1372 M /trunk/samtools/bcftools/prob1.c
1373 M /trunk/samtools/bcftools/prob1.h
1374 M /trunk/samtools/bcftools/vcfout.c
1376 * bcftools: add HWE (no testing for now)
1377 * record end dist in a 2x2 table, not avg, std any more
1379 ------------------------------------------------------------------------
1380 r674 | lh3lh3 | 2010-08-06 17:30:16 -0400 (Fri, 06 Aug 2010) | 3 lines
1382 A /trunk/samtools/bcftools/kfunc.c
1384 * Special functions: log(gamma()), erfc(), P(a,x) (incomplete gamma)
1385 * Not using Numerical Recipe due to licensing issues
1387 ------------------------------------------------------------------------
1388 r673 | lh3lh3 | 2010-08-05 23:46:53 -0400 (Thu, 05 Aug 2010) | 2 lines
1390 A /trunk/samtools/bcftools/fet.c
1394 ------------------------------------------------------------------------
1395 r672 | lh3lh3 | 2010-08-05 21:48:33 -0400 (Thu, 05 Aug 2010) | 3 lines
1397 M /trunk/samtools/bam2bcf.c
1398 M /trunk/samtools/bam2bcf.h
1399 M /trunk/samtools/bamtk.c
1400 M /trunk/samtools/examples/Makefile
1402 * samtools-0.1.8-11 (r672)
1403 * collect more stats for allele balance test in bcftools (not yet)
1405 ------------------------------------------------------------------------
1406 r671 | lh3lh3 | 2010-08-05 16:17:58 -0400 (Thu, 05 Aug 2010) | 3 lines
1408 M /trunk/samtools/bam_plcmd.c
1409 M /trunk/samtools/bcftools/bcf.c
1410 M /trunk/samtools/bcftools/main.c
1412 * the code base is stablized again.
1413 * I will delay the vcf parser, which is quite complicated but with little value for now
1415 ------------------------------------------------------------------------
1416 r670 | lh3lh3 | 2010-08-05 16:03:23 -0400 (Thu, 05 Aug 2010) | 2 lines
1418 M /trunk/samtools/examples/Makefile
1422 ------------------------------------------------------------------------
1423 r669 | lh3lh3 | 2010-08-05 16:03:08 -0400 (Thu, 05 Aug 2010) | 2 lines
1425 M /trunk/samtools/bcftools/vcf.c
1427 unfinished vcf parser
1429 ------------------------------------------------------------------------
1430 r668 | lh3lh3 | 2010-08-05 15:46:40 -0400 (Thu, 05 Aug 2010) | 3 lines
1432 M /trunk/samtools/bcftools/Makefile
1433 M /trunk/samtools/bcftools/bcf.c
1434 M /trunk/samtools/bcftools/bcf.h
1435 M /trunk/samtools/bcftools/bcfutils.c
1436 M /trunk/samtools/bcftools/index.c
1437 M /trunk/samtools/bcftools/main.c
1438 A /trunk/samtools/bcftools/vcf.c
1439 M /trunk/samtools/bcftools/vcfout.c
1441 * added prelimiary VCF parser (not finished)
1442 * change struct a bit
1444 ------------------------------------------------------------------------
1445 r667 | lh3lh3 | 2010-08-03 22:35:27 -0400 (Tue, 03 Aug 2010) | 3 lines
1447 M /trunk/samtools/bam2bcf.c
1448 M /trunk/samtools/bam2bcf.h
1449 M /trunk/samtools/bam_plcmd.c
1450 M /trunk/samtools/bcftools/bcf.c
1452 * allow to set min base q
1453 * fixed a bug in mpileup -u
1455 ------------------------------------------------------------------------
1456 r666 | lh3lh3 | 2010-08-03 22:08:44 -0400 (Tue, 03 Aug 2010) | 2 lines
1458 A /trunk/samtools/bcftools/bcf.tex
1462 ------------------------------------------------------------------------
1463 r665 | lh3lh3 | 2010-08-03 21:18:57 -0400 (Tue, 03 Aug 2010) | 2 lines
1465 M /trunk/samtools/examples/Makefile
1469 ------------------------------------------------------------------------
1470 r664 | lh3lh3 | 2010-08-03 21:13:00 -0400 (Tue, 03 Aug 2010) | 2 lines
1472 M /trunk/samtools/Makefile
1473 M /trunk/samtools/bam2bcf.c
1474 M /trunk/samtools/bam2bcf.h
1475 M /trunk/samtools/bcftools/Makefile
1477 fixed compilation error
1479 ------------------------------------------------------------------------
1480 r662 | lh3lh3 | 2010-08-03 21:04:00 -0400 (Tue, 03 Aug 2010) | 2 lines
1482 M /trunk/samtools/Makefile
1483 D /trunk/samtools/bcf.c
1484 D /trunk/samtools/bcf.h
1485 A /trunk/samtools/bcftools
1486 A /trunk/samtools/bcftools/Makefile
1487 A /trunk/samtools/bcftools/bcf.c
1488 A /trunk/samtools/bcftools/bcf.h
1489 A /trunk/samtools/bcftools/bcfutils.c
1490 A /trunk/samtools/bcftools/index.c
1491 A /trunk/samtools/bcftools/main.c
1492 A /trunk/samtools/bcftools/prob1.c
1493 A /trunk/samtools/bcftools/prob1.h
1494 A /trunk/samtools/bcftools/vcfout.c
1496 move bcftools to samtools
1498 ------------------------------------------------------------------------
1499 r660 | lh3lh3 | 2010-08-03 15:58:32 -0400 (Tue, 03 Aug 2010) | 2 lines
1501 M /trunk/samtools/bam2bcf.c
1503 fixed another minor bug
1505 ------------------------------------------------------------------------
1506 r658 | lh3lh3 | 2010-08-03 15:06:45 -0400 (Tue, 03 Aug 2010) | 3 lines
1508 M /trunk/samtools/bamtk.c
1509 M /trunk/samtools/bcf.c
1511 * samtools-0.1.8-10 (r658)
1512 * fixed a bug in bam2bcf when the reference is N
1514 ------------------------------------------------------------------------
1515 r657 | lh3lh3 | 2010-08-03 14:50:23 -0400 (Tue, 03 Aug 2010) | 3 lines
1517 M /trunk/samtools/bam2bcf.c
1518 M /trunk/samtools/bam2bcf.h
1521 * treat ambiguous ref base as the fifth base
1523 ------------------------------------------------------------------------
1524 r654 | lh3lh3 | 2010-08-02 17:38:27 -0400 (Mon, 02 Aug 2010) | 2 lines
1526 M /trunk/bcftools/bcf.c
1527 M /trunk/samtools/bcf.c
1529 missing a column in VCF output...
1531 ------------------------------------------------------------------------
1532 r653 | lh3lh3 | 2010-08-02 17:31:33 -0400 (Mon, 02 Aug 2010) | 2 lines
1534 M /trunk/samtools/bcf.c
1538 ------------------------------------------------------------------------
1539 r651 | lh3lh3 | 2010-08-02 17:27:31 -0400 (Mon, 02 Aug 2010) | 2 lines
1541 M /trunk/samtools/bcf.c
1543 fixed a bug in bcf reader
1545 ------------------------------------------------------------------------
1546 r650 | lh3lh3 | 2010-08-02 17:00:41 -0400 (Mon, 02 Aug 2010) | 2 lines
1548 M /trunk/samtools/bam2bcf.c
1552 ------------------------------------------------------------------------
1553 r649 | lh3lh3 | 2010-08-02 16:49:35 -0400 (Mon, 02 Aug 2010) | 3 lines
1555 M /trunk/samtools/Makefile
1556 M /trunk/samtools/bam2bcf.c
1557 M /trunk/samtools/bam2bcf.h
1558 M /trunk/samtools/bamtk.c
1560 * samtools-0.1.8-9 (r649)
1561 * lossless representation of PL in BCF output
1563 ------------------------------------------------------------------------
1564 r648 | lh3lh3 | 2010-08-02 16:07:25 -0400 (Mon, 02 Aug 2010) | 2 lines
1566 M /trunk/samtools/Makefile
1567 A /trunk/samtools/bam2bcf.c
1568 A /trunk/samtools/bam2bcf.h
1569 M /trunk/samtools/bam_plcmd.c
1570 A /trunk/samtools/bcf.c
1571 A /trunk/samtools/bcf.h
1575 ------------------------------------------------------------------------
1576 r644 | lh3lh3 | 2010-07-28 11:59:19 -0400 (Wed, 28 Jul 2010) | 5 lines
1578 M /trunk/samtools/bam_mcns.c
1579 M /trunk/samtools/bamtk.c
1581 * samtools-0.1.8-8 (r644)
1582 * mpileup becomes a little stable again
1583 * the method is slightly different, but is more theoretically correct
1584 * snp calling is O(n^2) instead of O(n^3)
1586 ------------------------------------------------------------------------
1587 r643 | lh3lh3 | 2010-07-28 11:54:15 -0400 (Wed, 28 Jul 2010) | 3 lines
1589 M /trunk/samtools/bam_mcns.c
1591 * fixed a STUPID bug, which cost me a lot of time.
1592 * I am going to clean up mcns a little bit
1594 ------------------------------------------------------------------------
1595 r642 | lh3lh3 | 2010-07-27 23:23:07 -0400 (Tue, 27 Jul 2010) | 2 lines
1597 M /trunk/samtools/bam_mcns.c
1598 M /trunk/samtools/bam_mcns.h
1599 M /trunk/samtools/bam_plcmd.c
1601 supposedly this is THE correct implementation, but more testing is needed
1603 ------------------------------------------------------------------------
1604 r641 | lh3lh3 | 2010-07-27 22:43:39 -0400 (Tue, 27 Jul 2010) | 2 lines
1606 M /trunk/samtools/bam_mcns.c
1608 NOT ready yet. Going to make further changes...
1610 ------------------------------------------------------------------------
1611 r639 | lh3lh3 | 2010-07-25 22:18:38 -0400 (Sun, 25 Jul 2010) | 3 lines
1613 M /trunk/samtools/bam_mcns.c
1614 M /trunk/samtools/bam_plcmd.c
1615 M /trunk/samtools/bamtk.c
1617 * samtools-0.1.8-7 (r639)
1618 * fixed the reference allele assignment
1620 ------------------------------------------------------------------------
1621 r638 | lh3lh3 | 2010-07-25 12:01:26 -0400 (Sun, 25 Jul 2010) | 5 lines
1623 M /trunk/samtools/bam_mcns.c
1624 M /trunk/samtools/bam_mcns.h
1625 M /trunk/samtools/bam_plcmd.c
1626 M /trunk/samtools/bamtk.c
1628 * samtools-0.1.8-6 (r638)
1629 * skip isnan/isinf in case of float underflow
1630 * added the flat prior
1631 * fixed an issue where there are no reads supporting the reference
1633 ------------------------------------------------------------------------
1634 r637 | lh3lh3 | 2010-07-24 14:16:27 -0400 (Sat, 24 Jul 2010) | 2 lines
1636 M /trunk/samtools/bam_plcmd.c
1640 ------------------------------------------------------------------------
1641 r636 | lh3lh3 | 2010-07-24 14:07:27 -0400 (Sat, 24 Jul 2010) | 2 lines
1643 M /trunk/samtools/bam_mcns.c
1644 M /trunk/samtools/bam_mcns.h
1645 M /trunk/samtools/bam_plcmd.c
1646 M /trunk/samtools/bamtk.c
1650 ------------------------------------------------------------------------
1651 r635 | lh3lh3 | 2010-07-24 01:49:49 -0400 (Sat, 24 Jul 2010) | 2 lines
1653 M /trunk/samtools/bam_mcns.c
1654 M /trunk/samtools/bam_mcns.h
1655 M /trunk/samtools/bam_plcmd.c
1657 posterior expectation FINALLY working. I am so tired...
1659 ------------------------------------------------------------------------
1660 r633 | lh3lh3 | 2010-07-23 13:50:48 -0400 (Fri, 23 Jul 2010) | 2 lines
1662 M /trunk/samtools/bam_plcmd.c
1664 another minor fix to mpileup
1666 ------------------------------------------------------------------------
1667 r632 | lh3lh3 | 2010-07-23 13:43:31 -0400 (Fri, 23 Jul 2010) | 2 lines
1669 M /trunk/samtools/bam_plcmd.c
1671 added the format column
1673 ------------------------------------------------------------------------
1674 r631 | lh3lh3 | 2010-07-23 13:25:44 -0400 (Fri, 23 Jul 2010) | 2 lines
1676 M /trunk/samtools/bam_mcns.c
1677 M /trunk/samtools/bam_mcns.h
1678 M /trunk/samtools/bam_plcmd.c
1679 M /trunk/samtools/bamtk.c
1681 added an alternative prior
1683 ------------------------------------------------------------------------
1684 r628 | lh3lh3 | 2010-07-23 11:48:51 -0400 (Fri, 23 Jul 2010) | 2 lines
1686 M /trunk/samtools/bam_mcns.c
1687 M /trunk/samtools/bam_mcns.h
1688 M /trunk/samtools/bam_plcmd.c
1690 calculate posterior allele frequency
1692 ------------------------------------------------------------------------
1693 r627 | lh3lh3 | 2010-07-22 21:39:13 -0400 (Thu, 22 Jul 2010) | 3 lines
1695 M /trunk/samtools/bam_mcns.c
1696 M /trunk/samtools/bam_plcmd.c
1697 M /trunk/samtools/bamtk.c
1699 * samtools-0.1.8-3 (r627)
1700 * multi-sample snp calling appears to work. More tests needed.
1702 ------------------------------------------------------------------------
1703 r626 | lh3lh3 | 2010-07-22 16:37:56 -0400 (Thu, 22 Jul 2010) | 3 lines
1705 M /trunk/samtools/bam_mcns.c
1706 M /trunk/samtools/bam_mcns.h
1707 M /trunk/samtools/bam_plcmd.c
1708 M /trunk/samtools/bam_tview.c
1710 * preliminary multisample SNP caller.
1711 * something looks not so right, but it largely works
1713 ------------------------------------------------------------------------
1714 r617 | lh3lh3 | 2010-07-14 16:26:27 -0400 (Wed, 14 Jul 2010) | 3 lines
1716 M /trunk/samtools/bam_mcns.c
1717 M /trunk/samtools/bam_plcmd.c
1718 M /trunk/samtools/bamtk.c
1720 * samtools-0.1.8-2 (r617)
1721 * allele frequency calculation apparently works...
1723 ------------------------------------------------------------------------
1724 r616 | lh3lh3 | 2010-07-14 13:33:51 -0400 (Wed, 14 Jul 2010) | 3 lines
1726 M /trunk/samtools/Makefile
1727 A /trunk/samtools/bam_mcns.c
1728 A /trunk/samtools/bam_mcns.h
1729 M /trunk/samtools/bam_plcmd.c
1731 * added mutli-sample framework. It is not working, yet.
1732 * improved the mpileup interface
1734 ------------------------------------------------------------------------
1735 r615 | lh3lh3 | 2010-07-13 14:50:12 -0400 (Tue, 13 Jul 2010) | 3 lines
1737 M /trunk/samtools/bam_plcmd.c
1738 M /trunk/samtools/bamtk.c
1739 M /trunk/samtools/misc/Makefile
1741 * samtools-0.1.8-1 (r615)
1742 * allow to get mpileup at required sites
1744 ------------------------------------------------------------------------
1745 r613 | lh3lh3 | 2010-07-11 22:40:56 -0400 (Sun, 11 Jul 2010) | 2 lines
1747 M /trunk/samtools/ChangeLog
1748 M /trunk/samtools/NEWS
1749 M /trunk/samtools/bam_plcmd.c
1750 M /trunk/samtools/bamtk.c
1751 M /trunk/samtools/samtools.1
1753 Release samtools-0.1.8
1755 ------------------------------------------------------------------------
1756 r612 | lh3lh3 | 2010-07-11 21:08:56 -0400 (Sun, 11 Jul 2010) | 2 lines
1758 M /trunk/samtools/knetfile.c
1760 fixed a compiling issue for Windows
1762 ------------------------------------------------------------------------
1763 r611 | lh3lh3 | 2010-07-11 20:59:15 -0400 (Sun, 11 Jul 2010) | 2 lines
1765 M /trunk/samtools/bam_sort.c
1767 fixed a bug in sorting when output to stdout (by Peter Chines)
1769 ------------------------------------------------------------------------
1770 r610 | lh3lh3 | 2010-07-09 17:05:10 -0400 (Fri, 09 Jul 2010) | 2 lines
1772 M /trunk/samtools/NEWS
1773 M /trunk/samtools/bam_plcmd.c
1775 change the command line option of pileup
1777 ------------------------------------------------------------------------
1778 r609 | lh3lh3 | 2010-07-09 00:39:34 -0400 (Fri, 09 Jul 2010) | 2 lines
1780 M /trunk/samtools/bam_pileup.c
1781 A /trunk/samtools/examples/toy.fa
1782 A /trunk/samtools/examples/toy.sam
1784 make pileup work with CIGAR with I/D at the beginning or in the end
1786 ------------------------------------------------------------------------
1787 r608 | lh3lh3 | 2010-07-08 22:36:12 -0400 (Thu, 08 Jul 2010) | 3 lines
1789 M /trunk/samtools/bam_maqcns.c
1790 M /trunk/samtools/bam_maqcns.h
1791 M /trunk/samtools/bam_plcmd.c
1792 M /trunk/samtools/bam_tview.c
1794 * make tview more friendly
1795 * a temporary remedy for an issue in indel calling
1797 ------------------------------------------------------------------------
1798 r607 | lh3lh3 | 2010-07-08 14:43:52 -0400 (Thu, 08 Jul 2010) | 4 lines
1800 M /trunk/samtools/bam_maqcns.c
1801 M /trunk/samtools/bam_plcmd.c
1802 M /trunk/samtools/bamtk.c
1804 * samtools-0.1.7-r607
1805 * improved the genotype accuracy for indels
1806 * use the SOAPsnp model for SNP calling by default.
1808 ------------------------------------------------------------------------
1809 r606 | lh3lh3 | 2010-07-08 01:05:19 -0400 (Thu, 08 Jul 2010) | 2 lines
1811 M /trunk/samtools/misc/Makefile
1813 removed a debugging example
1815 ------------------------------------------------------------------------
1816 r605 | lh3lh3 | 2010-07-08 01:04:09 -0400 (Thu, 08 Jul 2010) | 4 lines
1818 M /trunk/samtools/bam_maqcns.c
1819 M /trunk/samtools/bamtk.c
1821 * samtools-.1.7-18 (r605)
1822 * fixed an issue when a deletion and mismatch occur at the same time
1823 and the base quality is higher than 40 (if -I40).
1825 ------------------------------------------------------------------------
1826 r604 | lh3lh3 | 2010-07-02 19:32:24 -0400 (Fri, 02 Jul 2010) | 2 lines
1828 M /trunk/samtools/bam.h
1829 M /trunk/samtools/bam_index.c
1830 M /trunk/samtools/misc/Makefile
1832 fixed a minor bug in idxstats
1834 ------------------------------------------------------------------------
1835 r601 | lh3lh3 | 2010-06-16 09:03:59 -0400 (Wed, 16 Jun 2010) | 2 lines
1837 M /trunk/samtools/bam_index.c
1839 fixed a minor bug in indexing
1841 ------------------------------------------------------------------------
1842 r600 | lh3lh3 | 2010-06-15 10:17:53 -0400 (Tue, 15 Jun 2010) | 2 lines
1844 M /trunk/samtools/ChangeLog
1845 M /trunk/samtools/bam.c
1847 change printf() to puts in exporting
1849 ------------------------------------------------------------------------
1850 r599 | lh3lh3 | 2010-06-13 21:41:11 -0400 (Sun, 13 Jun 2010) | 2 lines
1852 M /trunk/samtools/bamtk.c
1854 minor fix. No actual effect.
1856 ------------------------------------------------------------------------
1857 r598 | lh3lh3 | 2010-06-13 21:32:45 -0400 (Sun, 13 Jun 2010) | 2 lines
1859 M /trunk/samtools/Makefile
1861 added Makefile targets to compile shared/dynamic library
1863 ------------------------------------------------------------------------
1864 r596 | lh3lh3 | 2010-06-13 19:48:07 -0400 (Sun, 13 Jun 2010) | 3 lines
1866 M /trunk/samtools/ChangeLog
1867 M /trunk/samtools/bam_index.c
1868 M /trunk/samtools/bamtk.c
1870 * samtools-0.1.7-17 (r596)
1871 * also keep the number of coor-less reads in the index file
1873 ------------------------------------------------------------------------
1874 r595 | lh3lh3 | 2010-06-13 18:54:26 -0400 (Sun, 13 Jun 2010) | 3 lines
1876 M /trunk/samtools/bam_index.c
1877 M /trunk/samtools/bamtk.c
1879 * samtools-0.1.7-16 (r595)
1880 * write additional information to bam index
1882 ------------------------------------------------------------------------
1883 r594 | lh3lh3 | 2010-06-13 17:29:52 -0400 (Sun, 13 Jun 2010) | 2 lines
1885 M /trunk/samtools/bam_index.c
1887 fixed a bug for unmapped sequences in indexing
1889 ------------------------------------------------------------------------
1890 r593 | lh3lh3 | 2010-06-12 18:11:32 -0400 (Sat, 12 Jun 2010) | 2 lines
1892 M /trunk/samtools/bam.h
1893 M /trunk/samtools/bam_index.c
1894 M /trunk/samtools/bam_plcmd.c
1895 M /trunk/samtools/samtools.1
1897 rename iterf as iter
1899 ------------------------------------------------------------------------
1900 r592 | lh3lh3 | 2010-06-12 18:02:38 -0400 (Sat, 12 Jun 2010) | 4 lines
1902 M /trunk/samtools/ChangeLog
1903 M /trunk/samtools/bam_aux.c
1904 M /trunk/samtools/bam_index.c
1905 M /trunk/samtools/bam_pileup.c
1906 M /trunk/samtools/bam_plcmd.c
1907 M /trunk/samtools/bamtk.c
1909 * samtools-0.1.7-15 (r592)
1910 * fixed a few minor memory leaks in the new pileup code
1911 * improved the functionality of mpileup
1913 ------------------------------------------------------------------------
1914 r591 | lh3lh3 | 2010-06-12 14:09:22 -0400 (Sat, 12 Jun 2010) | 3 lines
1916 M /trunk/samtools/bam.h
1917 M /trunk/samtools/bam_pileup.c
1918 M /trunk/samtools/bam_plcmd.c
1919 M /trunk/samtools/bamtk.c
1921 * samtools-0.1.7-14 (r591)
1922 * elementary multi-way pileup. More testing and more functionality to be done.
1924 ------------------------------------------------------------------------
1925 r590 | lh3lh3 | 2010-06-12 01:00:24 -0400 (Sat, 12 Jun 2010) | 3 lines
1927 M /trunk/samtools/bam.h
1928 M /trunk/samtools/bam_pileup.c
1929 M /trunk/samtools/bamtk.c
1931 * samtools-0.1.7-13 (r590)
1932 * added mpileup APIs. No compiling errors, but not tested at all. It is late.
1934 ------------------------------------------------------------------------
1935 r589 | lh3lh3 | 2010-06-11 22:37:09 -0400 (Fri, 11 Jun 2010) | 3 lines
1937 M /trunk/samtools/bam.h
1938 M /trunk/samtools/bam_pileup.c
1939 M /trunk/samtools/bamtk.c
1941 * samtools-0.1.7-12 (r589)
1942 * added iterator-like APIs for pileup
1944 ------------------------------------------------------------------------
1945 r588 | lh3lh3 | 2010-06-11 17:41:13 -0400 (Fri, 11 Jun 2010) | 3 lines
1947 M /trunk/samtools/bam_index.c
1948 M /trunk/samtools/bamtk.c
1950 * samtools-0.1.7-11 (r588)
1951 * ported a few improvements from tabix back to samtools
1953 ------------------------------------------------------------------------
1954 r587 | lh3lh3 | 2010-06-11 17:33:16 -0400 (Fri, 11 Jun 2010) | 3 lines
1956 M /trunk/samtools/bam.h
1957 M /trunk/samtools/bam_index.c
1958 M /trunk/samtools/bamtk.c
1960 * samtools-0.1.7-10 (r587)
1961 * added iterator interface for bam_fetch (ported back from tabix)
1963 ------------------------------------------------------------------------
1964 r586 | lh3lh3 | 2010-06-11 13:23:53 -0400 (Fri, 11 Jun 2010) | 3 lines
1966 M /trunk/samtools/Makefile
1967 A /trunk/samtools/bam_reheader.c
1968 M /trunk/samtools/bamtk.c
1969 M /trunk/samtools/bgzf.c
1971 * samtools-0.1.7-9 (r586)
1972 * added "reheader" to replace the BAM header
1974 ------------------------------------------------------------------------
1975 r585 | lh3lh3 | 2010-06-11 12:22:06 -0400 (Fri, 11 Jun 2010) | 3 lines
1977 M /trunk/samtools/bam.c
1978 M /trunk/samtools/bamtk.c
1979 M /trunk/samtools/kstring.h
1981 * samtools-0.1.7-8 (r585)
1984 ------------------------------------------------------------------------
1985 r584 | lh3lh3 | 2010-06-11 12:00:41 -0400 (Fri, 11 Jun 2010) | 4 lines
1987 M /trunk/samtools/bam.c
1988 M /trunk/samtools/bamtk.c
1989 M /trunk/samtools/bgzf.c
1990 M /trunk/samtools/bgzf.h
1991 M /trunk/samtools/kstring.h
1992 M /trunk/samtools/misc/wgsim_eval.pl
1994 * samtools-0.1.7-7 (r584)
1995 * ported tabix BGZF to samtools
1996 * flush BGZF after writing the BAM header and between alignment boundaries
1998 ------------------------------------------------------------------------
1999 r583 | petulda | 2010-06-11 11:58:20 -0400 (Fri, 11 Jun 2010) | 1 line
2001 A /trunk/samtools/misc/varfilter.py
2003 Initial release on behalf of Aylwyn Scally
2004 ------------------------------------------------------------------------
2005 r561 | petulda | 2010-05-07 08:41:56 -0400 (Fri, 07 May 2010) | 1 line
2007 M /trunk/samtools/samtools.1
2009 Added a note about the indels coordinates
2010 ------------------------------------------------------------------------
2011 r551 | petulda | 2010-04-23 09:42:13 -0400 (Fri, 23 Apr 2010) | 1 line
2013 M /trunk/samtools/misc/sam2vcf.pl
2015 Added the possibility to print or not to print the reference allele
2016 ------------------------------------------------------------------------
2017 r546 | petulda | 2010-04-15 04:33:55 -0400 (Thu, 15 Apr 2010) | 1 line
2019 M /trunk/samtools/sam_header.c
2021 More descriptive message for space separated tags
2022 ------------------------------------------------------------------------
2023 r545 | petulda | 2010-04-14 11:44:50 -0400 (Wed, 14 Apr 2010) | 1 line
2025 M /trunk/samtools/misc/sam2vcf.pl
2027 Speedup with -i, no need to query the reference all the time
2028 ------------------------------------------------------------------------
2029 r541 | petulda | 2010-03-15 10:03:51 -0400 (Mon, 15 Mar 2010) | 1 line
2031 M /trunk/samtools/sam_header.c
2033 Fixed the order of sequences in the header
2034 ------------------------------------------------------------------------
2035 r540 | petulda | 2010-03-04 06:28:35 -0500 (Thu, 04 Mar 2010) | 1 line
2037 M /trunk/samtools/misc/sam2vcf.pl
2039 Added possibility to select indels only and fixed a bug in reporting homozygous indels.
2040 ------------------------------------------------------------------------
2041 r539 | jmarshall | 2010-02-27 06:48:17 -0500 (Sat, 27 Feb 2010) | 4 lines
2043 M /trunk/samtools/bam.c
2045 Improve the invalid 'BAM\1' magic number error message, and also print it
2046 when no bytes can be read from the alleged BAM file, e.g., in the common
2047 user error case when a SAM file has accidentally been supplied.
2049 ------------------------------------------------------------------------
2050 r538 | petulda | 2010-02-26 10:51:40 -0500 (Fri, 26 Feb 2010) | 1 line
2052 M /trunk/samtools/AUTHORS
2053 M /trunk/samtools/bam.h
2054 M /trunk/samtools/bam_import.c
2055 M /trunk/samtools/sam_header.c
2057 Improved efficiency of header parsing
2058 ------------------------------------------------------------------------
2059 r537 | lh3lh3 | 2010-02-23 21:08:48 -0500 (Tue, 23 Feb 2010) | 3 lines
2061 M /trunk/samtools/misc/export2sam.pl
2063 Updated export2sam.pl by Chris Saunders from Illumina.
2066 ------------------------------------------------------------------------
2067 r536 | petulda | 2010-02-17 08:32:53 -0500 (Wed, 17 Feb 2010) | 1 line
2069 M /trunk/samtools/misc/samtools.pl
2071 Fixed filtering of SNPs near indels. Added min indel and SNP quality filter.
2072 ------------------------------------------------------------------------
2073 r535 | petulda | 2010-02-12 04:52:37 -0500 (Fri, 12 Feb 2010) | 1 line
2075 M /trunk/samtools/misc/sam2vcf.pl
2077 Print an error for pileups in simple format
2078 ------------------------------------------------------------------------
2079 r534 | lh3lh3 | 2010-02-11 14:01:41 -0500 (Thu, 11 Feb 2010) | 2 lines
2081 M /trunk/samtools/bam_plcmd.c
2083 added a hidden option in pileup to output the base position (for Erin)
2085 ------------------------------------------------------------------------
2086 r533 | petulda | 2010-02-09 10:12:14 -0500 (Tue, 09 Feb 2010) | 1 line
2088 M /trunk/samtools/misc/sam2vcf.pl
2090 Added possibility to specify a custom column title for the data column
2091 ------------------------------------------------------------------------
2092 r532 | petulda | 2010-02-09 09:46:09 -0500 (Tue, 09 Feb 2010) | 1 line
2094 M /trunk/samtools/bam_plcmd.c
2096 Added the -d option to limit maximum depth for indels.
2097 ------------------------------------------------------------------------
2098 r531 | petulda | 2010-02-03 07:57:27 -0500 (Wed, 03 Feb 2010) | 1 line
2100 M /trunk/samtools/misc/sam2vcf.pl
2103 ------------------------------------------------------------------------
2104 r530 | lh3lh3 | 2010-02-01 09:13:19 -0500 (Mon, 01 Feb 2010) | 3 lines
2106 M /trunk/samtools/ChangeLog
2107 M /trunk/samtools/bam_plcmd.c
2108 M /trunk/samtools/bamtk.c
2109 M /trunk/samtools/misc/samtools.pl
2110 M /trunk/samtools/misc/wgsim.c
2113 * fixed a bug in faidx
2115 ------------------------------------------------------------------------
2116 r529 | jmarshall | 2010-01-11 18:51:49 -0500 (Mon, 11 Jan 2010) | 2 lines
2118 M /trunk/samtools/faidx.c
2120 Put the right filename in the error message.
2122 ------------------------------------------------------------------------
2123 r528 | lh3lh3 | 2009-12-14 11:26:47 -0500 (Mon, 14 Dec 2009) | 3 lines
2125 M /trunk/samtools/bam_plcmd.c
2126 M /trunk/samtools/bamtk.c
2128 * samtools-0.1.7-5 (r528)
2129 * further add new consensus generation strategy
2131 ------------------------------------------------------------------------
2132 r527 | petulda | 2009-12-11 12:31:05 -0500 (Fri, 11 Dec 2009) | 1 line
2134 M /trunk/samtools/knetfile.c
2136 Fixed a bug in knet_seek
2137 ------------------------------------------------------------------------
2138 r526 | petulda | 2009-12-11 07:51:18 -0500 (Fri, 11 Dec 2009) | 1 line
2140 M /trunk/samtools/misc/sam2vcf.pl
2142 Small fix in VCF format: dot for the empty INFO field
2143 ------------------------------------------------------------------------
2144 r525 | petulda | 2009-12-11 04:36:18 -0500 (Fri, 11 Dec 2009) | 1 line
2146 M /trunk/samtools/sam_header.c
2148 Allow tabs in the CO header field
2149 ------------------------------------------------------------------------
2150 r524 | jmarshall | 2009-12-10 10:03:58 -0500 (Thu, 10 Dec 2009) | 3 lines
2152 M /trunk/samtools/Makefile
2153 M /trunk/samtools/Makefile.mingw
2155 Depend on libbam.a rather than the phony target, so that samtools is not
2156 unnecessarily rebuilt every time. Also clean bgzip.
2158 ------------------------------------------------------------------------
2159 r523 | jmarshall | 2009-12-10 09:45:32 -0500 (Thu, 10 Dec 2009) | 4 lines
2161 M /trunk/samtools/Makefile
2162 M /trunk/samtools/Makefile.mingw
2164 Fix a bug in compiling bgzip: this also needs knetfile.o when _USE_KNETFILE
2165 is defined. Also introduce $(KNETFILE_O) which can be set to empty to
2166 facilitate non-knet builds.
2168 ------------------------------------------------------------------------
2169 r522 | lh3lh3 | 2009-12-01 13:02:36 -0500 (Tue, 01 Dec 2009) | 4 lines
2171 M /trunk/samtools/bamtk.c
2172 M /trunk/samtools/sam_view.c
2174 * samtools-0.1.7-4 (r522)
2175 * fixed a bug in "view -r"
2176 * added a new option "view -R" to read required read groups from a file
2178 ------------------------------------------------------------------------
2179 r521 | lh3lh3 | 2009-12-01 10:00:12 -0500 (Tue, 01 Dec 2009) | 3 lines
2181 M /trunk/samtools/bam_md.c
2182 M /trunk/samtools/bamtk.c
2184 * samtools-0.1.7-3 (r521)
2185 * calmd: optionally mask matching bases as N
2187 ------------------------------------------------------------------------
2188 r520 | lh3lh3 | 2009-12-01 09:37:17 -0500 (Tue, 01 Dec 2009) | 4 lines
2190 M /trunk/samtools/bam_plcmd.c
2191 M /trunk/samtools/bamtk.c
2192 M /trunk/samtools/misc/samtools.pl
2194 * samtools-0.1.7-2 (r520)
2195 * fixed a few issues with compilation in Windows (on behalf of John)
2196 * choose a random base as the consensus (for population genetics studies)
2198 ------------------------------------------------------------------------
2199 r519 | jmarshall | 2009-11-30 10:53:02 -0500 (Mon, 30 Nov 2009) | 6 lines
2201 M /trunk/samtools/Makefile
2203 Put libraries at the end, so they can resolve references from libbam.a
2204 as well, even with old-fashioned linkers.
2206 Also use libbam.a explicitly rather than "-L. -lbam" to ensure that we get
2207 the freshly built library, not some other libbam.a lying around the system.
2209 ------------------------------------------------------------------------
2210 r518 | jmarshall | 2009-11-30 08:44:56 -0500 (Mon, 30 Nov 2009) | 2 lines
2212 M /trunk/samtools/Makefile
2213 M /trunk/samtools/misc/Makefile
2215 Also clean *.exe (for Cygwin users using this makefile).
2217 ------------------------------------------------------------------------
2218 r517 | jmarshall | 2009-11-30 07:09:04 -0500 (Mon, 30 Nov 2009) | 2 lines
2220 M /trunk/samtools/bam_index.c
2222 Index files should be opened in binary mode, not text mode.
2224 ------------------------------------------------------------------------
2225 r516 | lh3lh3 | 2009-11-27 15:18:59 -0500 (Fri, 27 Nov 2009) | 2 lines
2227 A /trunk/samtools/examples/bam2bed.c
2229 another example program
2231 ------------------------------------------------------------------------
2232 r515 | lh3lh3 | 2009-11-27 10:44:56 -0500 (Fri, 27 Nov 2009) | 3 lines
2234 M /trunk/samtools/bam_import.c
2235 M /trunk/samtools/bamtk.c
2236 M /trunk/samtools/misc/wgsim_eval.pl
2237 M /trunk/samtools/sam.c
2239 * samtools-0.1.7-1 (r515)
2240 * report an error when .fai contains duplicated names, instead of segfault
2242 ------------------------------------------------------------------------
2243 r514 | jmarshall | 2009-11-24 09:45:35 -0500 (Tue, 24 Nov 2009) | 2 lines
2245 M /trunk/samtools/bam.c
2247 Format 'c'-encoded auxiliary fields correctly, as *signed* integers.
2249 ------------------------------------------------------------------------
2250 r513 | lh3lh3 | 2009-11-16 10:13:07 -0500 (Mon, 16 Nov 2009) | 2 lines
2252 M /trunk/samtools/Makefile.mingw
2254 Update Makefile.mingw for the same reason
2256 ------------------------------------------------------------------------
2257 r512 | lh3lh3 | 2009-11-16 10:00:08 -0500 (Mon, 16 Nov 2009) | 2 lines
2259 M /trunk/samtools/Makefile
2261 Fixed a bug in compiling razip
2263 ------------------------------------------------------------------------
2264 r510 | lh3lh3 | 2009-11-10 10:55:41 -0500 (Tue, 10 Nov 2009) | 2 lines
2266 M /trunk/samtools/ChangeLog
2267 M /trunk/samtools/NEWS
2268 M /trunk/samtools/bamtk.c
2269 M /trunk/samtools/samtools.1
2271 Release samtools-0.1.7 (r510)
2273 ------------------------------------------------------------------------
2274 r509 | lh3lh3 | 2009-11-06 09:17:09 -0500 (Fri, 06 Nov 2009) | 3 lines
2276 M /trunk/samtools/bam_plcmd.c
2277 M /trunk/samtools/bamtk.c
2279 * samtools-0.1.6-22 (r509)
2280 * forget to fix a similar problem in glfgen
2282 ------------------------------------------------------------------------
2283 r508 | lh3lh3 | 2009-11-06 09:06:40 -0500 (Fri, 06 Nov 2009) | 3 lines
2285 M /trunk/samtools/bam_maqcns.c
2286 M /trunk/samtools/bam_plcmd.c
2287 M /trunk/samtools/bamtk.c
2288 M /trunk/samtools/sam_view.c
2290 * samtools-0.1.6-21 (r508)
2291 * fixed a potential bug in the indel caller towards the end of a chromosome
2293 ------------------------------------------------------------------------
2294 r494 | lh3lh3 | 2009-10-26 11:38:00 -0400 (Mon, 26 Oct 2009) | 3 lines
2296 M /trunk/samtools/bamtk.c
2297 M /trunk/samtools/sam_view.c
2299 * samtools-0.1.6-19 (r494)
2300 * allow to convert Illumina quality (64 based) to the BAM quality
2302 ------------------------------------------------------------------------
2303 r493 | lh3lh3 | 2009-10-26 10:24:39 -0400 (Mon, 26 Oct 2009) | 4 lines
2305 M /trunk/samtools/Makefile
2306 M /trunk/samtools/bam.c
2307 M /trunk/samtools/bam_import.c
2308 M /trunk/samtools/bamtk.c
2309 M /trunk/samtools/sam.c
2310 M /trunk/samtools/sam_header.c
2312 * samtools-0.1.6-18 (r493)
2313 * fixed the bugs due to improperly incorporating Petr's header parser
2314 * a little code clean up in sam_header.c
2316 ------------------------------------------------------------------------
2317 r492 | petulda | 2009-10-24 09:43:25 -0400 (Sat, 24 Oct 2009) | 1 line
2319 M /trunk/samtools/sam_header.c
2321 Added sam_header_line_free call for sam_header_parse2
2322 ------------------------------------------------------------------------
2323 r491 | lh3lh3 | 2009-10-24 00:50:16 -0400 (Sat, 24 Oct 2009) | 3 lines
2325 M /trunk/samtools/sam_view.c
2330 ------------------------------------------------------------------------
2331 r490 | lh3lh3 | 2009-10-24 00:45:12 -0400 (Sat, 24 Oct 2009) | 4 lines
2333 M /trunk/samtools/bam.c
2334 M /trunk/samtools/bam.h
2335 M /trunk/samtools/bam_import.c
2336 M /trunk/samtools/sam.c
2339 * improved the interface a bit
2342 ------------------------------------------------------------------------
2343 r489 | lh3lh3 | 2009-10-24 00:41:50 -0400 (Sat, 24 Oct 2009) | 3 lines
2345 M /trunk/samtools/bam_import.c
2346 M /trunk/samtools/sam_header.c
2347 M /trunk/samtools/sam_header.h
2349 * BUGGY VERSION. Please NOT use it.
2350 * Fixed a minor bug, but the major bug is still there.
2352 ------------------------------------------------------------------------
2353 r488 | lh3lh3 | 2009-10-24 00:17:10 -0400 (Sat, 24 Oct 2009) | 3 lines
2355 M /trunk/samtools/Makefile
2356 M /trunk/samtools/bam.c
2357 M /trunk/samtools/bam.h
2358 M /trunk/samtools/bam_aux.c
2359 M /trunk/samtools/bam_import.c
2360 M /trunk/samtools/bam_rmdup.c
2361 M /trunk/samtools/bam_rmdupse.c
2362 M /trunk/samtools/kaln.c
2363 M /trunk/samtools/sam.c
2364 M /trunk/samtools/sam_header.c
2365 M /trunk/samtools/sam_header.h
2366 M /trunk/samtools/sam_view.c
2368 * This revision is SERIOUSLY BUGGY. Please NOT use it.
2369 * Start to incorporate header parsing from Petr Danecek
2371 ------------------------------------------------------------------------
2372 r487 | petulda | 2009-10-23 11:44:32 -0400 (Fri, 23 Oct 2009) | 1 line
2374 M /trunk/samtools/sam_header.c
2375 M /trunk/samtools/sam_header.h
2377 Now possible to merge multiple HeaderDict dictionaries
2378 ------------------------------------------------------------------------
2379 r486 | petulda | 2009-10-22 11:46:58 -0400 (Thu, 22 Oct 2009) | 1 line
2381 M /trunk/samtools/sam_header.c
2384 ------------------------------------------------------------------------
2385 r485 | petulda | 2009-10-22 11:41:56 -0400 (Thu, 22 Oct 2009) | 1 line
2387 A /trunk/samtools/sam_header.c
2388 A /trunk/samtools/sam_header.h
2391 ------------------------------------------------------------------------
2392 r484 | lh3lh3 | 2009-10-19 14:31:32 -0400 (Mon, 19 Oct 2009) | 5 lines
2394 M /trunk/samtools/bam_import.c
2395 M /trunk/samtools/bam_rmdupse.c
2396 M /trunk/samtools/bamtk.c
2397 M /trunk/samtools/examples/Makefile
2399 * samtools-0.1.6-17 (r484)
2400 * fixed a memory leak in rmdupse
2401 * fixed a bug in parsing @RG header lines
2402 * test rmdup in examples/
2404 ------------------------------------------------------------------------
2405 r483 | lh3lh3 | 2009-10-19 13:22:48 -0400 (Mon, 19 Oct 2009) | 4 lines
2407 M /trunk/samtools/bam_rmdup.c
2408 M /trunk/samtools/bam_rmdupse.c
2409 M /trunk/samtools/bamtk.c
2411 * samtools-0.1.6-16 (r483)
2412 * unify the interface of rmdup and rmdupse
2413 * a new bug found in rg2lib(). Have not been fixed yet.
2415 ------------------------------------------------------------------------
2416 r482 | lh3lh3 | 2009-10-19 13:03:34 -0400 (Mon, 19 Oct 2009) | 4 lines
2418 M /trunk/samtools/bam.h
2419 M /trunk/samtools/bam_rmdup.c
2420 M /trunk/samtools/bam_rmdupse.c
2421 M /trunk/samtools/bamtk.c
2422 A /trunk/samtools/klist.h
2424 * samtools-0.1.6-15 (r482)
2426 * rmdupse is now library aware
2428 ------------------------------------------------------------------------
2429 r481 | lh3lh3 | 2009-10-18 00:07:21 -0400 (Sun, 18 Oct 2009) | 3 lines
2431 M /trunk/samtools/bam_rmdup.c
2432 M /trunk/samtools/bamtk.c
2434 * samtools-0.1.6-14 (r480)
2435 * rmdup is now RG aware
2437 ------------------------------------------------------------------------
2438 r480 | lh3lh3 | 2009-10-17 22:05:20 -0400 (Sat, 17 Oct 2009) | 2 lines
2440 M /trunk/samtools/misc/samtools.pl
2442 added a small unitity to parse SRA XML files
2444 ------------------------------------------------------------------------
2445 r479 | lh3lh3 | 2009-10-17 20:57:26 -0400 (Sat, 17 Oct 2009) | 3 lines
2447 M /trunk/samtools/bam_maqcns.c
2448 M /trunk/samtools/bam_maqcns.h
2449 M /trunk/samtools/bam_plcmd.c
2450 M /trunk/samtools/bam_sort.c
2451 M /trunk/samtools/bamtk.c
2453 * samtools-0.1.6-13 (r479)
2454 * merge: optionally use file names as RG tags
2456 ------------------------------------------------------------------------
2457 r478 | lh3lh3 | 2009-10-14 14:18:12 -0400 (Wed, 14 Oct 2009) | 3 lines
2459 M /trunk/samtools/bam.c
2460 M /trunk/samtools/bam.h
2461 M /trunk/samtools/bam_maqcns.c
2462 M /trunk/samtools/bamtk.c
2463 M /trunk/samtools/kaln.c
2465 * samtools-0.1.6-12 (r478)
2466 * fixed a bug in the indel caller
2468 ------------------------------------------------------------------------
2469 r477 | lh3lh3 | 2009-10-10 06:12:26 -0400 (Sat, 10 Oct 2009) | 3 lines
2471 M /trunk/samtools/bam_index.c
2472 M /trunk/samtools/bamtk.c
2474 * samtools-0.1.6-11 (r477)
2475 * fixed a bug due to recent change in bam_index.c (thank Nicole Washington for the patch)
2477 ------------------------------------------------------------------------
2478 r476 | petulda | 2009-10-09 11:45:36 -0400 (Fri, 09 Oct 2009) | 1 line
2480 A /trunk/samtools/misc/sam2vcf.pl
2482 Added the sam2vcf.pl script.
2483 ------------------------------------------------------------------------
2484 r475 | lh3lh3 | 2009-10-08 10:19:16 -0400 (Thu, 08 Oct 2009) | 2 lines
2486 M /trunk/samtools/Makefile
2487 M /trunk/samtools/bam.c
2488 M /trunk/samtools/bam.h
2489 M /trunk/samtools/bam_maqcns.c
2490 M /trunk/samtools/bamtk.c
2491 A /trunk/samtools/kaln.c
2492 A /trunk/samtools/kaln.h
2494 Unfinished modification. Please do not use this revision...
2496 ------------------------------------------------------------------------
2497 r474 | petulda | 2009-10-08 06:39:54 -0400 (Thu, 08 Oct 2009) | 1 line
2499 M /trunk/samtools/knetfile.c
2501 Removed the offending knet_seek message.
2502 ------------------------------------------------------------------------
2503 r473 | petulda | 2009-10-06 09:26:35 -0400 (Tue, 06 Oct 2009) | 1 line
2505 M /trunk/samtools/knetfile.c
2506 M /trunk/samtools/razf.c
2508 Bug fix - faidx on RAZF compressed files now working.
2509 ------------------------------------------------------------------------
2510 r472 | lh3lh3 | 2009-10-02 08:42:57 -0400 (Fri, 02 Oct 2009) | 2 lines
2512 M /trunk/samtools/samtools.1
2514 Clarify the meaning of a region like "chr2:1,000,000".
2516 ------------------------------------------------------------------------
2517 r471 | lh3lh3 | 2009-10-02 05:42:19 -0400 (Fri, 02 Oct 2009) | 2 lines
2519 M /trunk/samtools/misc/novo2sam.pl
2521 Fixed minor bugs in novo2sam.pl (on behalf of Ken Chen and Colin Hercus)
2523 ------------------------------------------------------------------------
2524 r470 | lh3lh3 | 2009-09-29 15:01:27 -0400 (Tue, 29 Sep 2009) | 3 lines
2526 M /trunk/samtools/Makefile.mingw
2527 M /trunk/samtools/bamtk.c
2528 M /trunk/samtools/knetfile.c
2529 M /trunk/samtools/knetfile.h
2531 * samtools-0.1.6-9 (r470)
2532 * make knetfile.c compatible with MinGW (thank Martin Morgan for the patch)
2534 ------------------------------------------------------------------------
2535 r469 | lh3lh3 | 2009-09-29 08:07:44 -0400 (Tue, 29 Sep 2009) | 3 lines
2537 M /trunk/samtools/bam_index.c
2538 M /trunk/samtools/bamtk.c
2540 * samtools-0.1.6-9 (r469)
2541 * refactor bam_fetch() for Python binding. On behalf of Leo Goodstadt.
2543 ------------------------------------------------------------------------
2544 r468 | lh3lh3 | 2009-09-28 05:18:29 -0400 (Mon, 28 Sep 2009) | 3 lines
2546 M /trunk/samtools/bam_sort.c
2547 M /trunk/samtools/bamtk.c
2548 M /trunk/samtools/misc/samtools.pl
2550 * samtools-0.1.6-7 (r468)
2553 ------------------------------------------------------------------------
2554 r467 | petulda | 2009-09-28 04:51:29 -0400 (Mon, 28 Sep 2009) | 1 line
2556 M /trunk/samtools/bgzf.c
2557 M /trunk/samtools/bgzip.c
2558 M /trunk/samtools/razf.c
2559 M /trunk/samtools/razip.c
2561 Changed the mode for newly created files to 0666. This allows less strict permissions with umask properly set (e.g. 0002 vs. 0022).
2562 ------------------------------------------------------------------------
2563 r466 | lh3lh3 | 2009-09-24 06:29:19 -0400 (Thu, 24 Sep 2009) | 3 lines
2565 M /trunk/samtools/ChangeLog
2566 M /trunk/samtools/bam_md.c
2567 M /trunk/samtools/bamtk.c
2569 * samtools-0.1.6-6 (r466)
2570 * do not crash calmd when some sequences are absent from the reference.
2572 ------------------------------------------------------------------------
2573 r464 | jmarshall | 2009-09-23 06:14:32 -0400 (Wed, 23 Sep 2009) | 3 lines
2575 M /trunk/samtools/bam.c
2576 M /trunk/samtools/knetfile.c
2578 Suppress bgzf_check_EOF() messages when reading from a pipe, as there is
2579 no way to seek on a pipe and the messages always appear.
2581 ------------------------------------------------------------------------
2582 r463 | petulda | 2009-09-16 07:05:41 -0400 (Wed, 16 Sep 2009) | 1 line
2584 M /trunk/samtools/knetfile.c
2585 M /trunk/samtools/razf.c
2587 A bug fix, "samtools view" is now working again.
2588 ------------------------------------------------------------------------
2589 r462 | lh3lh3 | 2009-09-16 04:51:07 -0400 (Wed, 16 Sep 2009) | 3 lines
2591 M /trunk/samtools/bamtk.c
2592 M /trunk/samtools/faidx.c
2593 M /trunk/samtools/knetfile.c
2594 M /trunk/samtools/knetfile.h
2595 M /trunk/samtools/razf.c
2596 M /trunk/samtools/razf.h
2598 * samtools-0.1.6-5 (r462)
2599 * Added knetfile support in razf and faidx (on behalf of Petr Danecek)
2601 ------------------------------------------------------------------------
2602 r460 | lh3lh3 | 2009-09-09 07:06:22 -0400 (Wed, 09 Sep 2009) | 2 lines
2604 M /trunk/samtools/samtools.1
2606 fixed a formatting issue
2608 ------------------------------------------------------------------------
2609 r459 | lh3lh3 | 2009-09-08 18:14:08 -0400 (Tue, 08 Sep 2009) | 3 lines
2611 M /trunk/samtools/bam_sort.c
2612 M /trunk/samtools/bamtk.c
2614 * samtools-0.1.6-4 (r459)
2615 * make sort output the result to stdout when -o is in use
2617 ------------------------------------------------------------------------
2618 r458 | lh3lh3 | 2009-09-07 05:10:28 -0400 (Mon, 07 Sep 2009) | 4 lines
2620 M /trunk/samtools/bamtk.c
2621 M /trunk/samtools/faidx.c
2622 M /trunk/samtools/faidx.h
2623 M /trunk/samtools/samtools.1
2625 * samtools-0.1.6-2 (r458)
2626 * added more interface to faidx (by Nils)
2627 * updated documentation
2629 ------------------------------------------------------------------------
2630 r457 | lh3lh3 | 2009-09-05 16:12:04 -0400 (Sat, 05 Sep 2009) | 3 lines
2632 M /trunk/samtools/bam_sort.c
2633 M /trunk/samtools/bamtk.c
2635 * samtools-0.1.6-2 (r457)
2636 * get rid of three assert() in bam_sort.c
2638 ------------------------------------------------------------------------
2639 r456 | jmarshall | 2009-09-04 12:46:25 -0400 (Fri, 04 Sep 2009) | 3 lines
2641 M /trunk/samtools/razf.c
2643 Return NULL from _razf_open() (and hence razf_open()/razf_open2())
2644 when opening the file fails.
2646 ------------------------------------------------------------------------
2647 r453 | lh3lh3 | 2009-09-02 08:56:33 -0400 (Wed, 02 Sep 2009) | 2 lines
2649 M /trunk/samtools/ChangeLog
2650 M /trunk/samtools/NEWS
2651 M /trunk/samtools/bamtk.c
2652 M /trunk/samtools/samtools.1
2653 D /trunk/samtools/source.dot
2655 Release samtools-0.1.6
2657 ------------------------------------------------------------------------
2658 r451 | lh3lh3 | 2009-09-02 05:44:48 -0400 (Wed, 02 Sep 2009) | 4 lines
2660 M /trunk/samtools/bam_md.c
2661 M /trunk/samtools/bam_rmdup.c
2662 M /trunk/samtools/bam_rmdupse.c
2663 M /trunk/samtools/bam_sort.c
2664 M /trunk/samtools/bamtk.c
2665 M /trunk/samtools/samtools.1
2667 * samtools-0.1.5-34 (r451)
2668 * applied the patch by John
2669 * improved the help message a little bit
2671 ------------------------------------------------------------------------
2672 r450 | lh3lh3 | 2009-09-02 04:55:55 -0400 (Wed, 02 Sep 2009) | 3 lines
2674 M /trunk/samtools/bam_color.c
2675 M /trunk/samtools/bamtk.c
2677 * samtools-0.1.5-33 (r450)
2678 * fixed a bug in bam_color.c (on behalf of Nils Homer)
2680 ------------------------------------------------------------------------
2681 r449 | lh3lh3 | 2009-08-29 15:36:41 -0400 (Sat, 29 Aug 2009) | 4 lines
2683 M /trunk/samtools/bam_import.c
2684 M /trunk/samtools/bam_md.c
2685 M /trunk/samtools/bamtk.c
2686 M /trunk/samtools/misc/samtools.pl
2688 * samtools-0.1.5-32 (r449)
2689 * fillmd: fixed a bug in modifying MD/NM tags
2690 * in import, give a warning if the read is aligned but there is no CIGAR.
2692 ------------------------------------------------------------------------
2693 r448 | lh3lh3 | 2009-08-19 04:44:28 -0400 (Wed, 19 Aug 2009) | 3 lines
2695 M /trunk/samtools/ChangeLog
2696 M /trunk/samtools/bam_pileup.c
2697 M /trunk/samtools/bamtk.c
2698 M /trunk/samtools/misc/wgsim_eval.pl
2700 * samtools-0.1.5-31 (r448)
2701 * fixed an issue when the last CIGAR is I or D
2703 ------------------------------------------------------------------------
2704 r447 | lh3lh3 | 2009-08-17 04:34:57 -0400 (Mon, 17 Aug 2009) | 3 lines
2706 M /trunk/samtools/bam_aux.c
2707 M /trunk/samtools/bamtk.c
2709 * samtools-0.1.5-30 (r447)
2710 * fixed a bug in bam_aux_get(): 'A' is not checked
2712 ------------------------------------------------------------------------
2713 r446 | lh3lh3 | 2009-08-17 04:33:17 -0400 (Mon, 17 Aug 2009) | 2 lines
2715 M /trunk/samtools/bam_aux.c
2716 M /trunk/samtools/bamtk.c
2720 ------------------------------------------------------------------------
2721 r444 | lh3lh3 | 2009-08-11 05:02:36 -0400 (Tue, 11 Aug 2009) | 3 lines
2723 M /trunk/samtools/bam_sort.c
2724 M /trunk/samtools/bamtk.c
2726 * samtools-0.1.5-28 (r444)
2729 ------------------------------------------------------------------------
2730 r443 | lh3lh3 | 2009-08-11 04:29:11 -0400 (Tue, 11 Aug 2009) | 4 lines
2732 M /trunk/samtools/bam.c
2733 M /trunk/samtools/bam_import.c
2734 M /trunk/samtools/bamtk.c
2736 * samtools-0.1.5-27 (r443)
2737 * SEQ and QUAL can be "*"
2738 * parse CIGAR "=" and "X" as "M"
2740 ------------------------------------------------------------------------
2741 r442 | lh3lh3 | 2009-08-07 16:56:38 -0400 (Fri, 07 Aug 2009) | 4 lines
2743 M /trunk/samtools/bam_pileup.c
2744 M /trunk/samtools/bamtk.c
2745 M /trunk/samtools/misc/md5.c
2746 M /trunk/samtools/misc/md5.h
2747 M /trunk/samtools/misc/md5fa.c
2749 * samtools-0.1.5-26 (r442)
2750 * replace RSA Inc md5.* with ones under permissive lincense
2751 * fixed a bug in detecting unsorted bam in pileup
2753 ------------------------------------------------------------------------
2754 r441 | bhandsaker | 2009-08-05 09:41:28 -0400 (Wed, 05 Aug 2009) | 2 lines
2756 M /trunk/samtools/bgzf.c
2757 M /trunk/samtools/bgzf.h
2758 M /trunk/samtools/bgzip.c
2760 Change copyright notices now that MIT has approved open source distribution.
2762 ------------------------------------------------------------------------
2763 r440 | lh3lh3 | 2009-08-05 05:44:24 -0400 (Wed, 05 Aug 2009) | 3 lines
2765 M /trunk/samtools/bam_stat.c
2766 M /trunk/samtools/bamtk.c
2768 * samtools-0.1.5-25 (r436)
2769 * in flagstats, do not report singletons if both ends are unmapped
2771 ------------------------------------------------------------------------
2772 r439 | lh3lh3 | 2009-08-04 17:16:51 -0400 (Tue, 04 Aug 2009) | 2 lines
2774 M /trunk/samtools/misc/maq2sam.c
2776 fixed a SERIOUS bug in setting 0x20 flag
2778 ------------------------------------------------------------------------
2779 r438 | lh3lh3 | 2009-08-04 16:50:43 -0400 (Tue, 04 Aug 2009) | 2 lines
2781 M /trunk/samtools/misc/samtools.pl
2783 fixed two minor bugs (suggested by Tim M Storm)
2785 ------------------------------------------------------------------------
2786 r437 | lh3lh3 | 2009-08-04 04:13:24 -0400 (Tue, 04 Aug 2009) | 3 lines
2788 M /trunk/samtools/bamtk.c
2789 M /trunk/samtools/misc/samtools.pl
2790 M /trunk/samtools/sam_view.c
2792 * samtools-0.1.5-24 (r435)
2795 ------------------------------------------------------------------------
2796 r434 | lh3lh3 | 2009-08-03 05:40:42 -0400 (Mon, 03 Aug 2009) | 3 lines
2798 M /trunk/samtools/bam_tview.c
2799 M /trunk/samtools/bamtk.c
2801 * samtools-0.1.5-23 (r434)
2802 * in tview, press 'r' to show read names rather than sequences
2804 ------------------------------------------------------------------------
2805 r433 | lh3lh3 | 2009-08-02 14:13:35 -0400 (Sun, 02 Aug 2009) | 3 lines
2807 M /trunk/samtools/knetfile.c
2809 * tried to fixed the buggy FTP random access in Windows. FAILED.
2810 * anyway, MinGW seems to have problem with "%lld".
2812 ------------------------------------------------------------------------
2813 r432 | lh3lh3 | 2009-08-01 19:32:07 -0400 (Sat, 01 Aug 2009) | 5 lines
2815 M /trunk/samtools/Makefile.mingw
2816 M /trunk/samtools/bamtk.c
2817 M /trunk/samtools/faidx.c
2818 M /trunk/samtools/razf.c
2819 A /trunk/samtools/win32/libcurses.a
2820 A /trunk/samtools/win32/xcurses.h
2822 * samtools-0.1.5-22 (r432)
2823 * faidx: fixed compitability issue with _WIN32
2824 * razf: fixed potential compitability issue with _WIN32
2825 * PDCurses support in Windows
2827 ------------------------------------------------------------------------
2828 r431 | lh3lh3 | 2009-08-01 18:34:54 -0400 (Sat, 01 Aug 2009) | 2 lines
2830 M /trunk/samtools/win32/libz.a
2832 replace the GnuWin32 version of libz.a with my own build with MinGW.
2834 ------------------------------------------------------------------------
2835 r430 | lh3lh3 | 2009-08-01 18:21:07 -0400 (Sat, 01 Aug 2009) | 2 lines
2837 M /trunk/samtools/knetfile.c
2841 ------------------------------------------------------------------------
2842 r429 | lh3lh3 | 2009-08-01 17:41:19 -0400 (Sat, 01 Aug 2009) | 3 lines
2844 M /trunk/samtools/Makefile.mingw
2845 M /trunk/samtools/bamtk.c
2846 M /trunk/samtools/knetfile.c
2847 M /trunk/samtools/knetfile.h
2849 * samtools-0.1.5-21 (r428)
2850 * knetfile.c is now compatible with mingw-winsock
2852 ------------------------------------------------------------------------
2853 r428 | lh3lh3 | 2009-07-31 19:39:07 -0400 (Fri, 31 Jul 2009) | 2 lines
2855 M /trunk/samtools/Makefile.mingw
2857 simplify MinGW Makefile
2859 ------------------------------------------------------------------------
2860 r427 | lh3lh3 | 2009-07-31 19:30:54 -0400 (Fri, 31 Jul 2009) | 5 lines
2862 A /trunk/samtools/Makefile.mingw
2863 M /trunk/samtools/bam_import.c
2864 M /trunk/samtools/bamtk.c
2865 A /trunk/samtools/win32
2866 A /trunk/samtools/win32/libz.a
2867 A /trunk/samtools/win32/zconf.h
2868 A /trunk/samtools/win32/zlib.h
2870 * samtools-0.1.5-20 (r427)
2871 * MinGW support. At least SAM<->BAM conversion is working. Other
2872 functionality are not tested at the moment.
2873 * zlib headers and Windows version of libz.a are included in win32/
2875 ------------------------------------------------------------------------
2876 r426 | lh3lh3 | 2009-07-31 18:32:09 -0400 (Fri, 31 Jul 2009) | 3 lines
2878 M /trunk/samtools/bamtk.c
2879 M /trunk/samtools/sam_view.c
2881 * samtools-0.1.5-19 (r426)
2882 * fixed a bug caused by recent modifications. Sorry.
2884 ------------------------------------------------------------------------
2885 r425 | lh3lh3 | 2009-07-31 18:23:51 -0400 (Fri, 31 Jul 2009) | 2 lines
2887 M /trunk/samtools/bgzf.c
2889 compatible with Windows binary files
2891 ------------------------------------------------------------------------
2892 r424 | lh3lh3 | 2009-07-31 05:19:59 -0400 (Fri, 31 Jul 2009) | 5 lines
2894 M /trunk/samtools/bam_maqcns.c
2895 M /trunk/samtools/bam_maqcns.h
2896 M /trunk/samtools/bam_plcmd.c
2897 M /trunk/samtools/bam_tview.c
2898 M /trunk/samtools/bamtk.c
2899 M /trunk/samtools/misc/samtools.pl
2901 * samtools-0.1.5-18 (r423)
2902 * output additional information in pileup indel lines, for the purepose
2903 of debugging at the moment
2904 * in tview, optionally allow to treat reference skip as deletion
2906 ------------------------------------------------------------------------
2907 r423 | lh3lh3 | 2009-07-30 17:00:36 -0400 (Thu, 30 Jul 2009) | 2 lines
2909 A /trunk/samtools/misc/psl2sam.pl
2911 convert BLAT psl to SAM.
2913 ------------------------------------------------------------------------
2914 r422 | lh3lh3 | 2009-07-30 06:24:39 -0400 (Thu, 30 Jul 2009) | 6 lines
2916 M /trunk/samtools/ChangeLog
2917 M /trunk/samtools/bam.c
2918 M /trunk/samtools/bamtk.c
2919 M /trunk/samtools/bgzf.c
2920 M /trunk/samtools/bgzf.h
2921 M /trunk/samtools/knetfile.c
2922 M /trunk/samtools/sam.c
2923 M /trunk/samtools/sam_view.c
2925 * samtools-0.1.5-17 (r422)
2926 * fixed a but in knetfile.c when seek type is not SEEK_SET
2927 * write an empty BGZF block to every BGZF file
2928 * check BGZF EOF marker in bam_header_read()
2931 ------------------------------------------------------------------------
2932 r421 | lh3lh3 | 2009-07-30 05:03:39 -0400 (Thu, 30 Jul 2009) | 3 lines
2934 M /trunk/samtools/bam_import.c
2935 M /trunk/samtools/bam_plcmd.c
2936 M /trunk/samtools/bamtk.c
2937 M /trunk/samtools/misc/samtools.pl
2938 M /trunk/samtools/sam.c
2939 M /trunk/samtools/sam.h
2940 M /trunk/samtools/sam_view.c
2942 * samtools-0.1.5-16 (r421)
2943 * in view and pileup, load header from FASTA index if the input is SAM.
2945 ------------------------------------------------------------------------
2946 r420 | lh3lh3 | 2009-07-29 04:18:55 -0400 (Wed, 29 Jul 2009) | 2 lines
2948 M /trunk/samtools/misc/maq2sam.c
2950 do not set "read 1" if reads are not mapped in the PE mode of maq
2952 ------------------------------------------------------------------------
2953 r419 | lh3lh3 | 2009-07-28 04:52:33 -0400 (Tue, 28 Jul 2009) | 5 lines
2955 M /trunk/samtools/bam_import.c
2956 M /trunk/samtools/bamtk.c
2957 M /trunk/samtools/misc/samtools.pl
2958 M /trunk/samtools/misc/wgsim_eval.pl
2960 * samtools-0.1.5-15 (r419)
2961 * in sam_open(), return NULL when the file cannot be opened.
2962 * make wgsim_eval.pl more robust to imperfect SAM
2963 * add "unique" command to samtools.pl
2965 ------------------------------------------------------------------------
2966 r418 | lh3lh3 | 2009-07-24 09:04:19 -0400 (Fri, 24 Jul 2009) | 2 lines
2968 M /trunk/samtools/misc/wgsim_eval.pl
2970 skip @header lines in SAM
2972 ------------------------------------------------------------------------
2973 r417 | lh3lh3 | 2009-07-24 07:42:38 -0400 (Fri, 24 Jul 2009) | 3 lines
2975 M /trunk/samtools/bamtk.c
2976 M /trunk/samtools/sam_view.c
2978 * samtools-0.1.5-14 (r417)
2979 * more help in "samtools view" due to the recent changes.
2981 ------------------------------------------------------------------------
2982 r416 | lh3lh3 | 2009-07-24 07:34:30 -0400 (Fri, 24 Jul 2009) | 3 lines
2984 M /trunk/samtools/bam.c
2985 M /trunk/samtools/bam.h
2986 M /trunk/samtools/bam_import.c
2987 M /trunk/samtools/bamtk.c
2988 M /trunk/samtools/sam.c
2989 M /trunk/samtools/sam.h
2990 M /trunk/samtools/sam_view.c
2992 * samtools-0.1.5-17 (r416)
2993 * support import/export SAM with string tags
2995 ------------------------------------------------------------------------
2996 r415 | lh3lh3 | 2009-07-24 06:39:26 -0400 (Fri, 24 Jul 2009) | 3 lines
2998 M /trunk/samtools/bam.c
2999 M /trunk/samtools/bam.h
3000 M /trunk/samtools/bam_import.c
3001 M /trunk/samtools/bamtk.c
3002 M /trunk/samtools/sam.c
3003 M /trunk/samtools/sam.h
3004 M /trunk/samtools/sam_view.c
3006 * samtools-0.1.5-12 (r415)
3007 * FLAG now can be in HEX
3009 ------------------------------------------------------------------------
3010 r414 | lh3lh3 | 2009-07-22 17:03:49 -0400 (Wed, 22 Jul 2009) | 2 lines
3012 M /trunk/samtools/kstring.h
3014 fixed a compiling error (thank Ken for fixing it)
3016 ------------------------------------------------------------------------
3017 r412 | lh3lh3 | 2009-07-21 17:19:40 -0400 (Tue, 21 Jul 2009) | 2 lines
3019 M /trunk/samtools/kstring.c
3020 M /trunk/samtools/kstring.h
3022 Implemented Boyer-Moore search in the kstring library.
3024 ------------------------------------------------------------------------
3025 r409 | lh3lh3 | 2009-07-17 12:10:20 -0400 (Fri, 17 Jul 2009) | 2 lines
3027 M /trunk/samtools/bam_index.c
3029 do not include knetfile.h when _USE_KNETFILE is not defined
3031 ------------------------------------------------------------------------
3032 r408 | lh3lh3 | 2009-07-17 10:29:21 -0400 (Fri, 17 Jul 2009) | 5 lines
3034 M /trunk/samtools/bam_md.c
3035 M /trunk/samtools/bam_tview.c
3036 M /trunk/samtools/bamtk.c
3037 M /trunk/samtools/bgzf.c
3039 * samtools-0.1.5-11 (r408)
3040 * force to overwirte existing MD if it is different from the one calculated
3042 * bgzf.c: improved the compatibility with Windows headers
3044 ------------------------------------------------------------------------
3045 r407 | lh3lh3 | 2009-07-17 09:46:56 -0400 (Fri, 17 Jul 2009) | 5 lines
3047 M /trunk/samtools/bam.h
3048 M /trunk/samtools/bam_aux.c
3049 M /trunk/samtools/bam_md.c
3050 M /trunk/samtools/bamtk.c
3051 M /trunk/samtools/sam.h
3053 * samtools-0.1.5-10 (r407)
3054 * implemented bam_aux_del() to remove a tag
3055 * fillmd: generate the NM tag
3056 * fillmd: cmd interface improvement
3058 ------------------------------------------------------------------------
3059 r406 | lh3lh3 | 2009-07-16 18:30:40 -0400 (Thu, 16 Jul 2009) | 2 lines
3061 M /trunk/samtools/Makefile
3063 Sorry. The old Makefile is for PDCurses...
3065 ------------------------------------------------------------------------
3066 r405 | lh3lh3 | 2009-07-16 18:30:11 -0400 (Thu, 16 Jul 2009) | 3 lines
3068 M /trunk/samtools/Makefile
3069 M /trunk/samtools/bam_tview.c
3070 M /trunk/samtools/bamtk.c
3072 * samtools-0.1.5-9 (r405)
3073 * improved the compatibility with PDCurses a little bit
3075 ------------------------------------------------------------------------
3076 r404 | lh3lh3 | 2009-07-16 18:23:52 -0400 (Thu, 16 Jul 2009) | 3 lines
3078 M /trunk/samtools/Makefile
3079 M /trunk/samtools/bam_tview.c
3080 M /trunk/samtools/bamtk.c
3082 * samtools-0.1.5-8 (r404)
3083 * compatible with PDCurses
3085 ------------------------------------------------------------------------
3086 r403 | lh3lh3 | 2009-07-16 17:39:39 -0400 (Thu, 16 Jul 2009) | 3 lines
3088 M /trunk/samtools/bamtk.c
3089 M /trunk/samtools/kseq.h
3091 * samtools-0.1.5-7 (r403)
3092 * fixed a bug in kseq.h for binary files (text files are fine)
3094 ------------------------------------------------------------------------
3095 r402 | lh3lh3 | 2009-07-16 06:49:53 -0400 (Thu, 16 Jul 2009) | 4 lines
3097 M /trunk/samtools/bam_import.c
3098 M /trunk/samtools/bam_index.c
3099 M /trunk/samtools/bamtk.c
3100 M /trunk/samtools/bgzf.c
3102 * samtools-0.1.5-6 (r402)
3103 * fixed compiling error when "-D_USE_NETFILE" is not applied
3104 * improve portability to MinGW
3106 ------------------------------------------------------------------------
3107 r398 | lh3lh3 | 2009-07-13 05:21:36 -0400 (Mon, 13 Jul 2009) | 3 lines
3109 A /trunk/bam-lite/bam.h (from /trunk/samtools/bam.h:395)
3110 A /trunk/bam-lite/bam_lite.c (from /trunk/samtools/bam_lite.c:395)
3111 D /trunk/samtools/bam_lite.c
3113 * move bam_lite.c to bam-lite
3114 * copy bam.h to bam-lite
3116 ------------------------------------------------------------------------
3117 r395 | lh3lh3 | 2009-07-13 05:12:57 -0400 (Mon, 13 Jul 2009) | 3 lines
3119 M /trunk/samtools/bam.h
3120 M /trunk/samtools/bam_lite.c
3121 M /trunk/samtools/bam_lpileup.c
3122 M /trunk/samtools/bam_pileup.c
3123 M /trunk/samtools/bamtk.c
3125 * samtools-0.1.5-5 (r395)
3126 * added bam_pileup_file() and removed bam_lpileup_file()
3128 ------------------------------------------------------------------------
3129 r394 | lh3lh3 | 2009-07-12 19:35:10 -0400 (Sun, 12 Jul 2009) | 3 lines
3131 M /trunk/samtools/bamtk.c
3132 M /trunk/samtools/knetfile.c
3133 M /trunk/samtools/knetfile.h
3135 * samtools-0.1.5-4 (r394)
3136 * http_proxy support in knetfile library (check http_proxy ENV)
3138 ------------------------------------------------------------------------
3139 r393 | lh3lh3 | 2009-07-12 18:57:07 -0400 (Sun, 12 Jul 2009) | 5 lines
3141 M /trunk/samtools/bam_index.c
3142 M /trunk/samtools/bam_tview.c
3143 M /trunk/samtools/bamtk.c
3144 M /trunk/samtools/knetfile.c
3145 M /trunk/samtools/knetfile.h
3147 * samtools-0.1.5-3 (r393)
3148 * knetfile now supports HTTP (no proxy at the moment)
3149 * fixed a potential issue in knetfile on opening ordinary file, although I have
3150 not seen the sideeffect so far.
3152 ------------------------------------------------------------------------
3153 r392 | lh3lh3 | 2009-07-12 13:50:55 -0400 (Sun, 12 Jul 2009) | 2 lines
3155 M /trunk/samtools/samtools.1
3157 Remove the warning in tview
3159 ------------------------------------------------------------------------
3160 r391 | lh3lh3 | 2009-07-12 13:42:43 -0400 (Sun, 12 Jul 2009) | 3 lines
3162 M /trunk/samtools/bam_tview.c
3163 M /trunk/samtools/bamtk.c
3165 * samtools-0.1.5-2 (r391)
3166 * do not show a blank screen when no reads mapped
3168 ------------------------------------------------------------------------
3169 r390 | lh3lh3 | 2009-07-09 09:01:42 -0400 (Thu, 09 Jul 2009) | 4 lines
3171 M /trunk/samtools/bam.h
3172 A /trunk/samtools/bam_lite.c
3173 M /trunk/samtools/bamtk.c
3175 * samtools-0.1.5-1 (r390)
3176 * removed useless _IOLIB in bam.h. This should cause no change at all.
3177 * added bam_lite.c for light-weight BAM reading
3179 ------------------------------------------------------------------------
3180 r385 | lh3lh3 | 2009-07-07 11:53:29 -0400 (Tue, 07 Jul 2009) | 2 lines
3182 M /trunk/samtools/bamtk.c
3183 M /trunk/samtools/knetfile.c
3185 Release samtools-0.1.5c (fixed a bug in piping)
3187 ------------------------------------------------------------------------
3188 r383 | lh3lh3 | 2009-07-07 06:39:55 -0400 (Tue, 07 Jul 2009) | 2 lines
3190 M /trunk/samtools/bamtk.c
3191 M /trunk/samtools/sam.c
3193 Release samtools-0.1.5b (BUG! so embarrassing!)
3195 ------------------------------------------------------------------------
3196 r381 | lh3lh3 | 2009-07-07 06:20:06 -0400 (Tue, 07 Jul 2009) | 2 lines
3198 M /trunk/samtools/Makefile
3199 M /trunk/samtools/bam.h
3200 M /trunk/samtools/bam_aux.c
3201 M /trunk/samtools/bamtk.c
3203 Release samtools-0.1.5a (for compatibility with Bio::DB::Sam)
3205 ------------------------------------------------------------------------
3206 r373 | lh3lh3 | 2009-07-07 05:26:57 -0400 (Tue, 07 Jul 2009) | 2 lines
3208 M /trunk/samtools/ChangeLog
3209 M /trunk/samtools/NEWS
3210 M /trunk/samtools/bamtk.c
3211 M /trunk/samtools/samtools.1
3213 Release samtools-0.1.5
3215 ------------------------------------------------------------------------
3216 r372 | lh3lh3 | 2009-07-07 04:49:27 -0400 (Tue, 07 Jul 2009) | 3 lines
3218 M /trunk/samtools/bamtk.c
3219 M /trunk/samtools/sam.c
3221 * samtools-0.1.4-23 (r372)
3222 * keep header text if "view -t" is used (by Gerton)
3224 ------------------------------------------------------------------------
3225 r371 | lh3lh3 | 2009-07-06 20:13:32 -0400 (Mon, 06 Jul 2009) | 2 lines
3227 M /trunk/samtools/samtools.1
3229 update documentation
3231 ------------------------------------------------------------------------
3232 r370 | bhandsaker | 2009-07-02 17:24:34 -0400 (Thu, 02 Jul 2009) | 2 lines
3234 M /trunk/samtools/Makefile
3236 Introduced LIBPATH variable so this could be overridden to allow samtools to build correct at the Broad.
3238 ------------------------------------------------------------------------
3239 r369 | lh3lh3 | 2009-07-02 08:36:53 -0400 (Thu, 02 Jul 2009) | 4 lines
3241 M /trunk/samtools/ChangeLog
3242 M /trunk/samtools/bam_aux.c
3243 M /trunk/samtools/bam_plcmd.c
3244 M /trunk/samtools/bamtk.c
3246 * samtools-0.1.4-22 (r369)
3247 * in pileup, optionally print E2 and U2
3248 * remove the debugging code in bam_aux_get() (Drat!)
3250 ------------------------------------------------------------------------
3251 r368 | lh3lh3 | 2009-07-02 06:32:26 -0400 (Thu, 02 Jul 2009) | 6 lines
3253 M /trunk/samtools/bam.c
3254 M /trunk/samtools/bam.h
3255 M /trunk/samtools/bam_aux.c
3256 M /trunk/samtools/bam_index.c
3257 M /trunk/samtools/bam_lpileup.c
3258 M /trunk/samtools/bam_md.c
3259 M /trunk/samtools/bam_pileup.c
3260 M /trunk/samtools/bam_rmdup.c
3261 M /trunk/samtools/bam_stat.c
3262 M /trunk/samtools/bam_tview.c
3263 M /trunk/samtools/bamtk.c
3264 M /trunk/samtools/faidx.c
3265 M /trunk/samtools/faidx.h
3266 M /trunk/samtools/glf.c
3268 * samtools-0.1.4-21 (r368)
3269 * propagate errors rather than exit or complain assertion failure. Assertion
3270 should be only used for checking internal bugs, but not for external input
3271 inconsistency. I was just a bit lazy.
3272 * small memory leak may be present on failure, though
3274 ------------------------------------------------------------------------
3275 r367 | lh3lh3 | 2009-06-30 11:18:42 -0400 (Tue, 30 Jun 2009) | 2 lines
3277 M /trunk/samtools/knetfile.c
3279 reduce the chance of blocking in FTP connection
3281 ------------------------------------------------------------------------
3282 r366 | lh3lh3 | 2009-06-30 10:35:21 -0400 (Tue, 30 Jun 2009) | 2 lines
3284 M /trunk/samtools/knetfile.c
3286 minor changes to knetfile: invalid fd equals -1 rather than 0
3288 ------------------------------------------------------------------------
3289 r365 | lh3lh3 | 2009-06-30 09:04:30 -0400 (Tue, 30 Jun 2009) | 3 lines
3291 M /trunk/samtools/bam_index.c
3292 M /trunk/samtools/bamtk.c
3293 M /trunk/samtools/knetfile.c
3294 M /trunk/samtools/knetfile.h
3296 * samtools-0.1.4-20 (r365)
3297 * download the BAM index file if it is not found in the current working directory.
3299 ------------------------------------------------------------------------
3300 r364 | lh3lh3 | 2009-06-30 07:39:07 -0400 (Tue, 30 Jun 2009) | 3 lines
3302 M /trunk/samtools/bamtk.c
3303 M /trunk/samtools/knetfile.c
3305 * samtools-0.1.4-19 (r364)
3306 * knetfile: report error when the file is not present on FTP
3308 ------------------------------------------------------------------------
3309 r363 | lh3lh3 | 2009-06-29 18:23:32 -0400 (Mon, 29 Jun 2009) | 4 lines
3311 M /trunk/samtools/bam_tview.c
3312 M /trunk/samtools/bamtk.c
3313 M /trunk/samtools/bgzf.c
3314 M /trunk/samtools/bgzf.h
3315 M /trunk/samtools/knetfile.c
3316 M /trunk/samtools/knetfile.h
3318 * samtools-0.1.4-18 (r363)
3319 * knetfile: do not trigger network communication in FTP seek (lazy seek)
3320 * bgzf: cache recent blocks (disabled by default)
3322 ------------------------------------------------------------------------
3323 r362 | lh3lh3 | 2009-06-25 16:04:34 -0400 (Thu, 25 Jun 2009) | 2 lines
3325 M /trunk/samtools/bgzf.c
3329 ------------------------------------------------------------------------
3330 r361 | lh3lh3 | 2009-06-25 16:03:10 -0400 (Thu, 25 Jun 2009) | 3 lines
3332 M /trunk/samtools/bam_index.c
3333 M /trunk/samtools/bamtk.c
3335 * samtools-0.1.4-17 (r361)
3336 * if a file is given on FTP, search locally for the BAM index
3338 ------------------------------------------------------------------------
3339 r360 | lh3lh3 | 2009-06-25 15:44:52 -0400 (Thu, 25 Jun 2009) | 5 lines
3341 M /trunk/samtools/Makefile
3342 M /trunk/samtools/bam_import.c
3343 M /trunk/samtools/bam_index.c
3344 M /trunk/samtools/bamtk.c
3345 M /trunk/samtools/bgzf.c
3346 M /trunk/samtools/bgzf.h
3347 M /trunk/samtools/knetfile.c
3348 M /trunk/samtools/knetfile.h
3350 * samtools-0.1.4-16 (r360)
3351 * report more information in index when the input is not sorted
3352 * change the behaviour of knet_seek() such that it returns 0 on success
3353 * support knetfile library in BGZF
3355 ------------------------------------------------------------------------
3356 r359 | lh3lh3 | 2009-06-25 12:10:55 -0400 (Thu, 25 Jun 2009) | 2 lines
3358 M /trunk/samtools/knetfile.c
3359 M /trunk/samtools/knetfile.h
3361 fixed bugs in knetfile.*
3363 ------------------------------------------------------------------------
3364 r358 | lh3lh3 | 2009-06-25 08:53:19 -0400 (Thu, 25 Jun 2009) | 2 lines
3366 A /trunk/samtools/knetfile.h
3368 this is the header file
3370 ------------------------------------------------------------------------
3371 r357 | lh3lh3 | 2009-06-25 08:52:03 -0400 (Thu, 25 Jun 2009) | 3 lines
3373 A /trunk/samtools/knetfile.c
3375 * open a file at FTP
3376 * preliminary version
3378 ------------------------------------------------------------------------
3379 r354 | lh3lh3 | 2009-06-24 09:02:25 -0400 (Wed, 24 Jun 2009) | 3 lines
3381 M /trunk/samtools/bam.c
3382 M /trunk/samtools/bamtk.c
3384 * samtools-0.1.4-15 (r354)
3385 * fixed a memory leak in bam_view1(), although samtools is not using this routine.
3387 ------------------------------------------------------------------------
3388 r351 | lh3lh3 | 2009-06-17 19:16:26 -0400 (Wed, 17 Jun 2009) | 4 lines
3390 M /trunk/samtools/bamtk.c
3391 M /trunk/samtools/faidx.c
3393 * samtools-0.1.4-13 (r351)
3394 * make faidx more tolerant to empty lines right before or after > lines
3395 * hope this does not introduce new bugs...
3397 ------------------------------------------------------------------------
3398 r350 | lh3lh3 | 2009-06-16 09:37:01 -0400 (Tue, 16 Jun 2009) | 3 lines
3400 M /trunk/samtools/bam_plcmd.c
3401 M /trunk/samtools/bamtk.c
3403 * samtools-0.1.4-13 (r350)
3404 * fixed a small memory leak in pileup, caused by recent modifications
3406 ------------------------------------------------------------------------
3407 r347 | lh3lh3 | 2009-06-13 16:20:49 -0400 (Sat, 13 Jun 2009) | 3 lines
3409 M /trunk/samtools/bam_plcmd.c
3410 M /trunk/samtools/bamtk.c
3411 M /trunk/samtools/sam_view.c
3413 * samtools-0.1.4-12 (r347)
3414 * added `-S' to pileup, similar to `view -S'
3416 ------------------------------------------------------------------------
3417 r346 | lh3lh3 | 2009-06-13 12:52:31 -0400 (Sat, 13 Jun 2009) | 3 lines
3419 M /trunk/samtools/Makefile
3420 M /trunk/samtools/bamtk.c
3421 M /trunk/samtools/sam_view.c
3422 M /trunk/samtools/samtools.1
3424 * samtools-0.1.4-11 (r346)
3425 * allow to select a read group at view command-line
3427 ------------------------------------------------------------------------
3428 r344 | lh3lh3 | 2009-06-13 09:06:24 -0400 (Sat, 13 Jun 2009) | 2 lines
3430 M /trunk/samtools/examples/calDepth.c
3434 ------------------------------------------------------------------------
3435 r343 | lh3lh3 | 2009-06-13 09:01:22 -0400 (Sat, 13 Jun 2009) | 2 lines
3437 M /trunk/samtools/examples/calDepth.c
3441 ------------------------------------------------------------------------
3442 r342 | lh3lh3 | 2009-06-13 08:58:48 -0400 (Sat, 13 Jun 2009) | 2 lines
3444 M /trunk/samtools/examples/Makefile
3445 A /trunk/samtools/examples/calDepth.c
3447 added an example of calculating read depth
3449 ------------------------------------------------------------------------
3450 r341 | lh3lh3 | 2009-06-13 08:00:08 -0400 (Sat, 13 Jun 2009) | 6 lines
3452 M /trunk/samtools/Makefile
3453 M /trunk/samtools/bam.h
3454 M /trunk/samtools/bam_aux.c
3455 A /trunk/samtools/bam_color.c
3456 M /trunk/samtools/bam_plcmd.c
3457 M /trunk/samtools/bam_sort.c
3458 M /trunk/samtools/bam_tview.c
3459 M /trunk/samtools/bamtk.c
3460 M /trunk/samtools/sam.c
3461 M /trunk/samtools/sam.h
3463 * samtools-0.1.4-10 (r341)
3464 * only include key APIs in libbam.a
3465 * move color-specific routines to bam_color.c
3466 * update documentations
3467 * remove the support of -q in pileup
3469 ------------------------------------------------------------------------
3470 r340 | lh3lh3 | 2009-06-13 06:17:14 -0400 (Sat, 13 Jun 2009) | 6 lines
3472 M /trunk/samtools/INSTALL
3473 M /trunk/samtools/Makefile
3474 M /trunk/samtools/bam_aux.c
3475 M /trunk/samtools/bam_import.c
3476 M /trunk/samtools/bam_tview.c
3477 M /trunk/samtools/bamtk.c
3478 M /trunk/samtools/razf.c
3479 M /trunk/samtools/sam_view.c
3481 * samtools-0.1.4-9 (r340)
3482 * added a warning to razf.c if zlib<1.2.2.1
3483 * fixed a compilation warning
3484 * fixed a segfault caused by @RG parsing
3485 * detect NCURSES in bam_tview.c
3487 ------------------------------------------------------------------------
3488 r339 | lh3lh3 | 2009-06-13 05:35:19 -0400 (Sat, 13 Jun 2009) | 2 lines
3490 M /trunk/samtools/INSTALL
3494 ------------------------------------------------------------------------
3495 r338 | lh3lh3 | 2009-06-12 19:15:24 -0400 (Fri, 12 Jun 2009) | 4 lines
3497 M /trunk/samtools/bam.c
3498 M /trunk/samtools/bam.h
3499 M /trunk/samtools/bam_aux.c
3500 M /trunk/samtools/bam_import.c
3501 M /trunk/samtools/bamtk.c
3502 M /trunk/samtools/kstring.h
3503 M /trunk/samtools/sam.c
3504 M /trunk/samtools/sam_view.c
3506 * samtools-0.1.4-8 (r338)
3507 * parse the @RG header lines and allow to choose library at the "samtools view"
3510 ------------------------------------------------------------------------
3511 r337 | lh3lh3 | 2009-06-12 16:25:50 -0400 (Fri, 12 Jun 2009) | 4 lines
3513 M /trunk/samtools/bamtk.c
3514 M /trunk/samtools/bgzf.c
3515 M /trunk/samtools/bgzf.h
3516 M /trunk/samtools/sam.c
3517 M /trunk/samtools/sam_view.c
3519 * samtools-0.1.4-7 (r337)
3520 * bgzf.c: support mode string "wu": uncompressed output
3521 * "samtools view" support "-u" command-line option
3523 ------------------------------------------------------------------------
3524 r336 | lh3lh3 | 2009-06-12 12:20:12 -0400 (Fri, 12 Jun 2009) | 5 lines
3526 M /trunk/samtools/Makefile
3527 M /trunk/samtools/misc/Makefile
3528 M /trunk/samtools/razf.c
3529 M /trunk/samtools/razf.h
3530 M /trunk/samtools/razip.c
3532 * no changes to samtools itself
3533 * remove zlib source codes
3534 * make RAZF reading compatible with old version of zlib
3535 * on old version of zlib, writing is not available
3537 ------------------------------------------------------------------------
3538 r335 | lh3lh3 | 2009-06-12 11:47:33 -0400 (Fri, 12 Jun 2009) | 2 lines
3540 D /trunk/samtools/zlib
3542 remove zlib for simplification...
3544 ------------------------------------------------------------------------
3545 r334 | lh3lh3 | 2009-06-12 10:43:36 -0400 (Fri, 12 Jun 2009) | 5 lines
3547 M /trunk/samtools/bam.h
3548 M /trunk/samtools/bam_aux.c
3549 M /trunk/samtools/bamtk.c
3551 * samtools-0.1.4-6 (r334)
3552 * do not export bam_aux_get_core() for Bio::DB::Sam because it has already
3553 been implemented in that.
3554 * this version works with the latest Bio::DB::Sam (20090612)
3556 ------------------------------------------------------------------------
3557 r333 | lh3lh3 | 2009-06-12 10:33:42 -0400 (Fri, 12 Jun 2009) | 2 lines
3559 M /trunk/samtools/ChangeLog
3563 ------------------------------------------------------------------------
3564 r332 | lh3lh3 | 2009-06-12 10:21:21 -0400 (Fri, 12 Jun 2009) | 2 lines
3566 M /trunk/samtools/AUTHORS
3567 M /trunk/samtools/Makefile
3568 M /trunk/samtools/misc/Makefile
3570 fixed minor things in Makefile
3572 ------------------------------------------------------------------------
3573 r331 | lh3lh3 | 2009-06-12 10:07:05 -0400 (Fri, 12 Jun 2009) | 4 lines
3575 M /trunk/samtools/bamtk.c
3577 * samtools-0.1.4-5 (r3310
3578 * no change to samtools itself. Version number is increased to reflect the
3579 changes in the Makefile building system.
3581 ------------------------------------------------------------------------
3582 r330 | lh3lh3 | 2009-06-12 10:03:38 -0400 (Fri, 12 Jun 2009) | 2 lines
3584 M /trunk/samtools/AUTHORS
3585 D /trunk/samtools/README
3587 update information...
3589 ------------------------------------------------------------------------
3590 r329 | lh3lh3 | 2009-06-12 09:52:21 -0400 (Fri, 12 Jun 2009) | 3 lines
3592 M /trunk/samtools/misc/novo2sam.pl
3594 * updated novoalign converter by Colin Hercus et al.
3595 * this version works with indels
3597 ------------------------------------------------------------------------
3598 r328 | lh3lh3 | 2009-06-12 09:50:53 -0400 (Fri, 12 Jun 2009) | 3 lines
3600 M /trunk/samtools/INSTALL
3601 M /trunk/samtools/Makefile
3602 M /trunk/samtools/misc/Makefile
3603 M /trunk/samtools/zlib/Makefile
3606 * update INSTALL instruction
3608 ------------------------------------------------------------------------
3609 r327 | lh3lh3 | 2009-06-12 09:18:29 -0400 (Fri, 12 Jun 2009) | 4 lines
3611 A /trunk/samtools/Makefile (from /trunk/samtools/Makefile.generic:325)
3612 D /trunk/samtools/Makefile.am
3613 D /trunk/samtools/Makefile.generic
3614 D /trunk/samtools/Makefile.lite
3615 D /trunk/samtools/autogen.sh
3616 D /trunk/samtools/cleanup.sh
3617 D /trunk/samtools/configure.ac
3618 A /trunk/samtools/misc/Makefile (from /trunk/samtools/misc/Makefile.generic:305)
3619 D /trunk/samtools/misc/Makefile.am
3620 D /trunk/samtools/misc/Makefile.generic
3621 M /trunk/samtools/razf.c
3622 A /trunk/samtools/zlib
3623 A /trunk/samtools/zlib/Makefile
3624 A /trunk/samtools/zlib/adler32.c
3625 A /trunk/samtools/zlib/compress.c
3626 A /trunk/samtools/zlib/crc32.c
3627 A /trunk/samtools/zlib/crc32.h
3628 A /trunk/samtools/zlib/deflate.c
3629 A /trunk/samtools/zlib/deflate.h
3630 A /trunk/samtools/zlib/gzio.c
3631 A /trunk/samtools/zlib/infback.c
3632 A /trunk/samtools/zlib/inffast.c
3633 A /trunk/samtools/zlib/inffast.h
3634 A /trunk/samtools/zlib/inffixed.h
3635 A /trunk/samtools/zlib/inflate.c
3636 A /trunk/samtools/zlib/inflate.h
3637 A /trunk/samtools/zlib/inftrees.c
3638 A /trunk/samtools/zlib/inftrees.h
3639 A /trunk/samtools/zlib/trees.c
3640 A /trunk/samtools/zlib/trees.h
3641 A /trunk/samtools/zlib/uncompr.c
3642 A /trunk/samtools/zlib/zconf.h
3643 A /trunk/samtools/zlib/zlib.h
3644 A /trunk/samtools/zlib/zutil.c
3645 A /trunk/samtools/zlib/zutil.h
3646 D /trunk/samtools/zutil.h
3648 * added zlib-1.2.3 as razip requires that
3649 * prepare to changed back to the Makefile building system
3650 * unfinished! (will be soon)
3652 ------------------------------------------------------------------------
3653 r326 | lh3lh3 | 2009-06-12 09:12:03 -0400 (Fri, 12 Jun 2009) | 2 lines
3655 M /trunk/samtools/misc/samtools.pl
3659 ------------------------------------------------------------------------
3660 r325 | lh3lh3 | 2009-06-10 11:27:59 -0400 (Wed, 10 Jun 2009) | 3 lines
3662 M /trunk/samtools/bam_maqcns.c
3663 M /trunk/samtools/bamtk.c
3665 * samtools-0.1.4-4 (r325)
3666 * further avoid wrong consensus calls in repetitive regions.
3668 ------------------------------------------------------------------------
3669 r324 | lh3lh3 | 2009-06-10 10:56:17 -0400 (Wed, 10 Jun 2009) | 4 lines
3671 M /trunk/samtools/bam_maqcns.c
3672 M /trunk/samtools/bam_plcmd.c
3673 M /trunk/samtools/bamtk.c
3674 M /trunk/samtools/sam.c
3675 M /trunk/samtools/sam.h
3677 * samtools-0.1.4-3 (r324)
3678 * make maqcns generate the correct call in repetitive regions.
3679 * allow filtering on mapQ at the pileup command line
3681 ------------------------------------------------------------------------
3682 r323 | lh3lh3 | 2009-06-10 05:04:21 -0400 (Wed, 10 Jun 2009) | 3 lines
3684 M /trunk/samtools/misc/samtools.pl
3686 * samtools.pl-0.3.2 (r322)
3687 * indels and SNPs use different mapping quality threshold
3689 ------------------------------------------------------------------------
3690 r322 | lh3lh3 | 2009-06-10 05:03:22 -0400 (Wed, 10 Jun 2009) | 2 lines
3692 M /trunk/samtools/misc/export2sam.pl
3696 ------------------------------------------------------------------------
3697 r321 | lh3lh3 | 2009-06-09 04:21:48 -0400 (Tue, 09 Jun 2009) | 2 lines
3699 M /trunk/samtools/misc/samtools.pl
3701 just typo. no real change
3703 ------------------------------------------------------------------------
3704 r320 | lh3lh3 | 2009-06-08 09:32:51 -0400 (Mon, 08 Jun 2009) | 2 lines
3706 M /trunk/samtools/misc/samtools.pl
3708 a little bit code cleanup
3710 ------------------------------------------------------------------------
3711 r319 | lh3lh3 | 2009-06-08 09:22:33 -0400 (Mon, 08 Jun 2009) | 4 lines
3713 M /trunk/samtools/misc/samtools.pl
3716 * change default parameters
3717 * optionally print filtered variants
3719 ------------------------------------------------------------------------
3720 r318 | lh3lh3 | 2009-06-08 09:14:26 -0400 (Mon, 08 Jun 2009) | 3 lines
3722 M /trunk/samtools/misc/samtools.pl
3725 * combine snpFilter and indelFilter
3727 ------------------------------------------------------------------------
3728 r317 | lh3lh3 | 2009-06-08 06:31:42 -0400 (Mon, 08 Jun 2009) | 3 lines
3730 M /trunk/samtools/misc/samtools.pl
3733 * change a default parameter
3735 ------------------------------------------------------------------------
3736 r316 | lh3lh3 | 2009-06-08 06:11:06 -0400 (Mon, 08 Jun 2009) | 5 lines
3738 M /trunk/samtools/bam_maqcns.c
3739 M /trunk/samtools/bam_maqcns.h
3740 M /trunk/samtools/bam_plcmd.c
3741 M /trunk/samtools/bamtk.c
3742 M /trunk/samtools/sam.c
3744 * samtools-0.1.4-2 (r316)
3745 * pileup: cap mapping quality at 60 (by default)
3746 * pileup: always calculate RMS mapq
3747 * pileup: allow to output variant sites only
3749 ------------------------------------------------------------------------
3750 r312 | lh3lh3 | 2009-06-04 08:01:10 -0400 (Thu, 04 Jun 2009) | 3 lines
3752 M /trunk/samtools/misc/samtools.pl
3757 ------------------------------------------------------------------------
3758 r311 | lh3lh3 | 2009-06-03 04:40:40 -0400 (Wed, 03 Jun 2009) | 2 lines
3760 M /trunk/samtools/misc/samtools.pl
3762 * in snpFilter, suppress non-SNP sites
3764 ------------------------------------------------------------------------
3765 r310 | lh3lh3 | 2009-06-01 09:35:13 -0400 (Mon, 01 Jun 2009) | 3 lines
3767 M /trunk/samtools/misc/samtools.pl
3772 ------------------------------------------------------------------------
3773 r309 | lh3lh3 | 2009-06-01 09:04:39 -0400 (Mon, 01 Jun 2009) | 3 lines
3775 M /trunk/samtools/misc/samtools.pl
3780 ------------------------------------------------------------------------
3781 r306 | lh3lh3 | 2009-05-28 06:49:35 -0400 (Thu, 28 May 2009) | 3 lines
3783 M /trunk/samtools/bgzf.c
3785 * minor changes to bgzf: return NULL if fd == -1
3786 * suggested by {kdj,jm18}@sanger.ac.uk
3788 ------------------------------------------------------------------------
3789 r305 | lh3lh3 | 2009-05-28 06:16:08 -0400 (Thu, 28 May 2009) | 2 lines
3791 A /trunk/samtools/misc/interpolate_sam.pl
3793 Script for paired-end pileup, contributed by Stephen Montgomery.
3795 ------------------------------------------------------------------------
3796 r304 | lh3lh3 | 2009-05-28 06:08:49 -0400 (Thu, 28 May 2009) | 3 lines
3798 M /trunk/samtools/bamtk.c
3799 M /trunk/samtools/sam.c
3801 * samtools-0.1.4-1 (r304)
3802 * fixed a minor bug in printing headers
3804 ------------------------------------------------------------------------
3805 r297 | lh3lh3 | 2009-05-21 11:06:16 -0400 (Thu, 21 May 2009) | 2 lines
3807 M /trunk/samtools/ChangeLog
3808 M /trunk/samtools/NEWS
3809 M /trunk/samtools/bam_plcmd.c
3810 M /trunk/samtools/bamtk.c
3811 M /trunk/samtools/misc/maq2sam.c
3812 M /trunk/samtools/samtools.1
3814 Release samtools-0.1.4
3816 ------------------------------------------------------------------------
3817 r296 | lh3lh3 | 2009-05-21 07:53:14 -0400 (Thu, 21 May 2009) | 3 lines
3819 M /trunk/samtools/bam_maqcns.c
3820 M /trunk/samtools/bamtk.c
3822 * samtools-0.1.3-24 (r296)
3823 * another similar bug in the indel caller
3825 ------------------------------------------------------------------------
3826 r295 | lh3lh3 | 2009-05-21 07:50:28 -0400 (Thu, 21 May 2009) | 3 lines
3828 M /trunk/samtools/bam_maqcns.c
3829 M /trunk/samtools/bamtk.c
3831 * samtools-0.1.3-23 (r295)
3832 * fixed a critical bug in the indel caller
3834 ------------------------------------------------------------------------
3835 r294 | lh3lh3 | 2009-05-20 08:00:20 -0400 (Wed, 20 May 2009) | 2 lines
3837 M /trunk/samtools/bam_stat.c
3839 added a missing header file
3841 ------------------------------------------------------------------------
3842 r293 | lh3lh3 | 2009-05-19 18:44:25 -0400 (Tue, 19 May 2009) | 3 lines
3844 M /trunk/samtools/bam_tview.c
3845 M /trunk/samtools/bamtk.c
3847 * samtools-0.1.3-22 (r293)
3848 * open tview in the dot-view mode by default
3850 ------------------------------------------------------------------------
3851 r292 | lh3lh3 | 2009-05-18 16:01:23 -0400 (Mon, 18 May 2009) | 6 lines
3853 M /trunk/samtools/samtools.1
3855 Added a note to the manual. Currently SAMtools used unaligned words in
3856 several places. Although this does not cause bus errors to me, it may
3857 affect portability. Please see the "Bus error" wiki page for more
3858 information. Also thank James Bonfields for pointing this out.
3861 ------------------------------------------------------------------------
3862 r286 | lh3lh3 | 2009-05-14 10:23:13 -0400 (Thu, 14 May 2009) | 3 lines
3864 M /trunk/samtools/bam.h
3865 M /trunk/samtools/bam_aux.c
3866 M /trunk/samtools/bamtk.c
3868 * samtools-0.1.3-21 (286)
3869 * declare bam_aux_get_core() in bam.h
3871 ------------------------------------------------------------------------
3872 r276 | lh3lh3 | 2009-05-13 05:07:55 -0400 (Wed, 13 May 2009) | 5 lines
3874 M /trunk/samtools/bam.h
3875 M /trunk/samtools/bam_index.c
3876 M /trunk/samtools/bamtk.c
3878 * samtools-0.1.3-20 (r276)
3879 * remove bam1_t::hash again. We need to modify the Perl API anyway to
3880 make it work with the latest SVN.
3881 * As is suggested by Tim, scan "{base}.bai" and "{base}.bam.bai" for index
3883 ------------------------------------------------------------------------
3884 r275 | lh3lh3 | 2009-05-12 16:14:10 -0400 (Tue, 12 May 2009) | 4 lines
3886 M /trunk/samtools/ChangeLog
3887 M /trunk/samtools/bam.h
3888 M /trunk/samtools/bamtk.c
3890 * samtools-0.1.3-19 (r275)
3891 * a minor change to the bam1_t struct: added back "void *hash" for the
3892 backward compatibility with Bio::DB::Sam
3894 ------------------------------------------------------------------------
3895 r273 | lh3lh3 | 2009-05-12 09:28:39 -0400 (Tue, 12 May 2009) | 3 lines
3897 M /trunk/samtools/bam_rmdupse.c
3898 M /trunk/samtools/bamtk.c
3900 * samtools-0.1.3-18 (r273)
3901 * rmdupse: do not remove unmapped reads
3903 ------------------------------------------------------------------------
3904 r272 | lh3lh3 | 2009-05-12 09:20:00 -0400 (Tue, 12 May 2009) | 2 lines
3906 M /trunk/samtools/bam_rmdupse.c
3908 change a parameter. It does nothing
3910 ------------------------------------------------------------------------
3911 r271 | lh3lh3 | 2009-05-12 09:17:58 -0400 (Tue, 12 May 2009) | 3 lines
3913 M /trunk/samtools/Makefile.am
3914 M /trunk/samtools/Makefile.generic
3915 M /trunk/samtools/Makefile.lite
3916 A /trunk/samtools/bam_rmdupse.c
3917 M /trunk/samtools/bamtk.c
3918 M /trunk/samtools/configure.ac
3920 * samtools-0.1.3-17 (r271)
3921 * added 'rmdupse' command
3923 ------------------------------------------------------------------------
3924 r267 | lh3lh3 | 2009-05-05 17:31:41 -0400 (Tue, 05 May 2009) | 3 lines
3926 M /trunk/samtools/bamtk.c
3927 M /trunk/samtools/sam_view.c
3929 * samtools-0.1.3-16 (r267)
3930 * in sam_view.c, changed g_flag_on based on the suggestion by Angie Hinrichs
3932 ------------------------------------------------------------------------
3933 r266 | lh3lh3 | 2009-05-05 17:23:27 -0400 (Tue, 05 May 2009) | 3 lines
3935 M /trunk/samtools/bam_import.c
3936 M /trunk/samtools/bamtk.c
3938 * samtools-0.1.3-15 (r266)
3939 * report an error if a non-* reference is present while @SQ is absent
3941 ------------------------------------------------------------------------
3942 r265 | lh3lh3 | 2009-05-05 17:09:00 -0400 (Tue, 05 May 2009) | 3 lines
3944 M /trunk/samtools/bam.h
3945 M /trunk/samtools/bam_import.c
3946 M /trunk/samtools/bamtk.c
3947 M /trunk/samtools/sam.c
3948 M /trunk/samtools/sam_view.c
3950 * samtools-0.1.3-14 (r262)
3951 * make samopen() recognize @SQ header lines
3953 ------------------------------------------------------------------------
3954 r261 | lh3lh3 | 2009-05-05 10:10:30 -0400 (Tue, 05 May 2009) | 3 lines
3956 M /trunk/samtools/bam_plcmd.c
3957 M /trunk/samtools/bamtk.c
3958 M /trunk/samtools/bgzf.c
3959 M /trunk/samtools/sam.c
3960 M /trunk/samtools/sam_view.c
3962 * samtools-0.1.3-13 (r260)
3963 * report error for file I/O error
3965 ------------------------------------------------------------------------
3966 r260 | lh3lh3 | 2009-05-05 10:01:16 -0400 (Tue, 05 May 2009) | 2 lines
3968 M /trunk/samtools/Makefile.am
3972 ------------------------------------------------------------------------
3973 r259 | lh3lh3 | 2009-05-05 09:52:25 -0400 (Tue, 05 May 2009) | 3 lines
3975 M /trunk/samtools/bam.h
3976 M /trunk/samtools/bam_pileup.c
3977 M /trunk/samtools/bam_plcmd.c
3978 M /trunk/samtools/bamtk.c
3979 M /trunk/samtools/sam.c
3980 M /trunk/samtools/sam.h
3982 * samtools-0.1.3-12 (r259)
3983 * use the new I/O interface in pileup
3985 ------------------------------------------------------------------------
3986 r258 | lh3lh3 | 2009-05-05 09:33:22 -0400 (Tue, 05 May 2009) | 3 lines
3988 M /trunk/samtools/Makefile.generic
3989 M /trunk/samtools/Makefile.lite
3990 M /trunk/samtools/bam.c
3991 M /trunk/samtools/bam.h
3992 M /trunk/samtools/bam_import.c
3993 M /trunk/samtools/bamtk.c
3994 A /trunk/samtools/sam.c
3995 A /trunk/samtools/sam.h
3996 A /trunk/samtools/sam_view.c
3998 * samtools-0.1.3-11 (r258)
3999 * unify the interface to BAM and SAM I/O
4001 ------------------------------------------------------------------------
4002 r257 | lh3lh3 | 2009-05-05 04:53:35 -0400 (Tue, 05 May 2009) | 3 lines
4004 M /trunk/samtools/Makefile.lite
4005 M /trunk/samtools/bam_plcmd.c
4006 M /trunk/samtools/bamtk.c
4008 * samtools-0.1.3-10 (r257)
4009 * allow hex with "pileup -m"
4011 ------------------------------------------------------------------------
4012 r256 | lh3lh3 | 2009-05-04 14:16:50 -0400 (Mon, 04 May 2009) | 4 lines
4014 M /trunk/samtools/bam_lpileup.c
4015 M /trunk/samtools/bamtk.c
4017 * samtools-0.1.3-9 (r256)
4018 * fixed a bug in bam_lpileup.c
4019 * I do not know if this also fixes the bug causing assertion failure in the tview
4021 ------------------------------------------------------------------------
4022 r251 | lh3lh3 | 2009-04-28 08:53:23 -0400 (Tue, 28 Apr 2009) | 3 lines
4024 M /trunk/samtools/bam_pileup.c
4025 M /trunk/samtools/bamtk.c
4027 * samtools-0.1.3-8 (r251)
4028 * fixed a bug when there are reads without coordinates
4030 ------------------------------------------------------------------------
4031 r250 | lh3lh3 | 2009-04-28 08:43:33 -0400 (Tue, 28 Apr 2009) | 2 lines
4033 A /trunk/samtools/AUTHORS
4034 A /trunk/samtools/README
4035 M /trunk/samtools/cleanup.sh
4039 ------------------------------------------------------------------------
4040 r249 | lh3lh3 | 2009-04-28 08:37:16 -0400 (Tue, 28 Apr 2009) | 2 lines
4042 M /trunk/samtools/Makefile.generic
4043 M /trunk/samtools/Makefile.lite
4044 M /trunk/samtools/configure.ac
4045 M /trunk/samtools/misc/Makefile.generic
4047 improve large file support in compilation
4049 ------------------------------------------------------------------------
4050 r248 | lh3lh3 | 2009-04-28 08:33:24 -0400 (Tue, 28 Apr 2009) | 2 lines
4052 M /trunk/samtools/INSTALL
4056 ------------------------------------------------------------------------
4057 r247 | lh3lh3 | 2009-04-28 08:28:50 -0400 (Tue, 28 Apr 2009) | 2 lines
4059 M /trunk/samtools/Makefile.am
4060 M /trunk/samtools/autogen.sh
4061 M /trunk/samtools/cleanup.sh
4062 M /trunk/samtools/configure.ac
4063 A /trunk/samtools/misc/Makefile.am
4065 fixed various issues about the GNU building scripts
4067 ------------------------------------------------------------------------
4068 r246 | lh3lh3 | 2009-04-28 08:10:23 -0400 (Tue, 28 Apr 2009) | 4 lines
4070 M /trunk/samtools/ChangeLog
4071 D /trunk/samtools/Makefile
4072 A /trunk/samtools/Makefile.am
4073 A /trunk/samtools/Makefile.generic
4074 A /trunk/samtools/autogen.sh
4075 M /trunk/samtools/bam.h
4076 M /trunk/samtools/bam_aux.c
4077 M /trunk/samtools/bam_tview.c
4078 M /trunk/samtools/bamtk.c
4079 A /trunk/samtools/cleanup.sh
4080 A /trunk/samtools/configure.ac
4081 D /trunk/samtools/misc/Makefile
4082 A /trunk/samtools/misc/Makefile.generic (from /trunk/samtools/misc/Makefile:245)
4084 * samtools-0.1.3-7 (r246)
4085 * incorporated revisions from Nils Homer
4086 * enhanced support of displaying color-space reads
4088 ------------------------------------------------------------------------
4089 r244 | lh3lh3 | 2009-04-25 06:49:40 -0400 (Sat, 25 Apr 2009) | 3 lines
4091 M /trunk/samtools/bam_md.c
4092 M /trunk/samtools/bamtk.c
4094 * samtools-0.1.3-6 (r244)
4095 * fixed segfault for unmapped reads
4097 ------------------------------------------------------------------------
4098 r243 | lh3lh3 | 2009-04-24 16:27:26 -0400 (Fri, 24 Apr 2009) | 5 lines
4100 M /trunk/samtools/bam.h
4101 M /trunk/samtools/bam_maqcns.c
4102 M /trunk/samtools/bam_md.c
4103 M /trunk/samtools/bamtk.c
4105 * samtools-0.1.3-5 (r243)
4106 * fixed a long existing bug which may cause memory leak
4108 * consensus calling now works with "=", but indel calling not
4110 ------------------------------------------------------------------------
4111 r242 | lh3lh3 | 2009-04-24 15:44:46 -0400 (Fri, 24 Apr 2009) | 3 lines
4113 M /trunk/samtools/bam_md.c
4114 M /trunk/samtools/bamtk.c
4116 * samtools-0.1.3-4 (r242)
4117 * fixed a memory leak
4119 ------------------------------------------------------------------------
4120 r240 | lh3lh3 | 2009-04-24 11:40:18 -0400 (Fri, 24 Apr 2009) | 5 lines
4122 M /trunk/samtools/Makefile
4123 M /trunk/samtools/Makefile.lite
4124 M /trunk/samtools/bam.h
4125 M /trunk/samtools/bam_aux.c
4126 A /trunk/samtools/bam_md.c
4127 M /trunk/samtools/bam_plcmd.c
4128 M /trunk/samtools/bamtk.c
4130 * samtools-0.1.3-3 (r240)
4132 * generate "=" bases
4133 * the plain pileup now support "=" bases, but consensus calling and glfgen may fail
4135 ------------------------------------------------------------------------
4136 r239 | lh3lh3 | 2009-04-24 07:08:20 -0400 (Fri, 24 Apr 2009) | 5 lines
4138 M /trunk/samtools/bam.h
4139 M /trunk/samtools/bam_aux.c
4140 M /trunk/samtools/bamtk.c
4142 * samtools-0.1.3-2 (r239)
4143 * fixed bugs in bam_aux.c (these functions nevered used by samtools)
4144 * removed bam_aux_init()/bam_aux_destroy()
4145 * added tagview for testing bam_aux
4147 ------------------------------------------------------------------------
4148 r235 | lh3lh3 | 2009-04-21 18:17:39 -0400 (Tue, 21 Apr 2009) | 3 lines
4150 M /trunk/samtools/bam_pileup.c
4151 M /trunk/samtools/bamtk.c
4154 * fixed a bug in pileup: the first read in a chromosome may not be printed
4156 ------------------------------------------------------------------------
4157 r232 | lh3lh3 | 2009-04-16 10:25:43 -0400 (Thu, 16 Apr 2009) | 2 lines
4159 M /trunk/samtools/Makefile.lite
4161 a missing file in Makefile.lite
4163 ------------------------------------------------------------------------
4164 r227 | lh3lh3 | 2009-04-15 17:02:53 -0400 (Wed, 15 Apr 2009) | 2 lines
4166 M /trunk/samtools/NEWS
4167 M /trunk/samtools/bamtk.c
4169 Release samtools-0.1.3
4171 ------------------------------------------------------------------------
4172 r223 | lh3lh3 | 2009-04-15 09:31:32 -0400 (Wed, 15 Apr 2009) | 3 lines
4174 M /trunk/samtools/bam_plcmd.c
4175 M /trunk/samtools/bamtk.c
4178 * make samtools more robust to weird input such as empty file
4180 ------------------------------------------------------------------------
4181 r222 | lh3lh3 | 2009-04-15 09:05:33 -0400 (Wed, 15 Apr 2009) | 2 lines
4183 M /trunk/samtools/ChangeLog
4184 M /trunk/samtools/NEWS
4185 M /trunk/samtools/samtools.1
4187 prepare for release 0.1.3
4189 ------------------------------------------------------------------------
4190 r221 | lh3lh3 | 2009-04-15 08:32:14 -0400 (Wed, 15 Apr 2009) | 2 lines
4192 A /trunk/samtools/misc/blast2sam.pl
4194 convert NCBI-BLASTN to SAM
4196 ------------------------------------------------------------------------
4197 r220 | lh3lh3 | 2009-04-15 08:18:19 -0400 (Wed, 15 Apr 2009) | 3 lines
4199 M /trunk/samtools/bam_lpileup.c
4200 M /trunk/samtools/bamtk.c
4203 * fixed a small memory leak in tview
4205 ------------------------------------------------------------------------
4206 r219 | lh3lh3 | 2009-04-15 08:00:08 -0400 (Wed, 15 Apr 2009) | 3 lines
4208 M /trunk/samtools/bam_rmdup.c
4209 M /trunk/samtools/bamtk.c
4212 * fixed a bug in rmdup when there are unmapped reads
4214 ------------------------------------------------------------------------
4215 r218 | lh3lh3 | 2009-04-14 17:28:58 -0400 (Tue, 14 Apr 2009) | 2 lines
4217 M /trunk/samtools/ChangeLog
4218 M /trunk/samtools/NEWS
4220 proposed NEWS for the new release (have not yet)
4222 ------------------------------------------------------------------------
4223 r216 | lh3lh3 | 2009-04-14 17:10:46 -0400 (Tue, 14 Apr 2009) | 4 lines
4225 M /trunk/samtools/misc/samtools.pl
4228 * improve indelFilter to avoid filtering true indels. The new filter relies
4229 on the new pileup indel line implemented in samtools-0.1.2-25
4231 ------------------------------------------------------------------------
4232 r215 | lh3lh3 | 2009-04-14 17:04:19 -0400 (Tue, 14 Apr 2009) | 4 lines
4234 M /trunk/samtools/bam_maqcns.c
4235 M /trunk/samtools/bam_plcmd.c
4236 M /trunk/samtools/bamtk.c
4237 M /trunk/samtools/samtools.1
4240 * change the pileup indel line to shows the number of alignments actually
4243 ------------------------------------------------------------------------
4244 r211 | lh3lh3 | 2009-04-13 07:07:13 -0400 (Mon, 13 Apr 2009) | 2 lines
4246 M /trunk/samtools/ChangeLog
4248 update ChangeLog from "svn log"
4250 ------------------------------------------------------------------------
4251 r210 | lh3lh3 | 2009-04-12 15:57:05 -0400 (Sun, 12 Apr 2009) | 4 lines
4253 M /trunk/samtools/bam.c
4254 M /trunk/samtools/bam_import.c
4255 M /trunk/samtools/bam_sort.c
4256 M /trunk/samtools/bamtk.c
4257 M /trunk/samtools/kseq.h
4260 * in merge, gives a warning rather than error if the target sequence length is different
4261 * allow empty header
4263 ------------------------------------------------------------------------
4264 r209 | lh3lh3 | 2009-04-12 15:32:44 -0400 (Sun, 12 Apr 2009) | 3 lines
4266 M /trunk/samtools/bam.c
4267 M /trunk/samtools/bam_import.c
4268 M /trunk/samtools/bamtk.c
4271 * recognize '*' at the QUAL field
4273 ------------------------------------------------------------------------
4274 r208 | lh3lh3 | 2009-04-12 15:08:02 -0400 (Sun, 12 Apr 2009) | 3 lines
4276 M /trunk/samtools/bam_import.c
4277 M /trunk/samtools/bamtk.c
4278 M /trunk/samtools/kseq.h
4281 * the field separater is TAB only, now
4283 ------------------------------------------------------------------------
4284 r207 | lh3lh3 | 2009-04-08 10:18:03 -0400 (Wed, 08 Apr 2009) | 2 lines
4286 M /trunk/samtools/examples/ex1.sam.gz
4288 * fixed the problem in the example alignment due to the bug in fixmate
4290 ------------------------------------------------------------------------
4291 r206 | lh3lh3 | 2009-04-08 10:15:05 -0400 (Wed, 08 Apr 2009) | 3 lines
4293 M /trunk/samtools/bam_mate.c
4294 M /trunk/samtools/bamtk.c
4295 M /trunk/samtools/misc/soap2sam.pl
4298 * fixed a nasty bug in `fixmate'
4300 ------------------------------------------------------------------------
4301 r205 | lh3lh3 | 2009-04-08 05:57:08 -0400 (Wed, 08 Apr 2009) | 2 lines
4303 M /trunk/samtools/misc/bowtie2sam.pl
4304 M /trunk/samtools/misc/soap2sam.pl
4305 M /trunk/samtools/misc/wgsim_eval.pl
4307 make the script robust to the bugs in SOAP-2.1.7
4309 ------------------------------------------------------------------------
4310 r200 | lh3lh3 | 2009-04-02 10:14:56 -0400 (Thu, 02 Apr 2009) | 3 lines
4312 M /trunk/samtools/bam_stat.c
4313 M /trunk/samtools/bamtk.c
4316 * check if file is truncated in flagstat
4318 ------------------------------------------------------------------------
4319 r199 | lh3lh3 | 2009-04-02 10:09:10 -0400 (Thu, 02 Apr 2009) | 3 lines
4321 M /trunk/samtools/bamtk.c
4324 * print the header if requested
4326 ------------------------------------------------------------------------
4327 r193 | lh3lh3 | 2009-03-27 11:09:50 -0400 (Fri, 27 Mar 2009) | 3 lines
4329 M /trunk/samtools/bam_plcmd.c
4330 M /trunk/samtools/bamtk.c
4333 * fixed a minor bug reported by Nils Homer
4335 ------------------------------------------------------------------------
4336 r185 | lh3lh3 | 2009-03-24 07:50:32 -0400 (Tue, 24 Mar 2009) | 2 lines
4338 A /trunk/samtools/Makefile (from /trunk/samtools/Makefile.std:184)
4339 D /trunk/samtools/Makefile.std
4340 A /trunk/samtools/misc/Makefile (from /trunk/samtools/misc/Makefile.std:184)
4341 D /trunk/samtools/misc/Makefile.std
4343 rename Makefile.std as Makefile. GNU building systerm is not ready and may take some time...
4345 ------------------------------------------------------------------------
4346 r184 | lh3lh3 | 2009-03-24 06:36:38 -0400 (Tue, 24 Mar 2009) | 4 lines
4348 D /trunk/samtools/Makefile
4349 A /trunk/samtools/Makefile.std (from /trunk/samtools/Makefile:183)
4350 M /trunk/samtools/bam_sort.c
4351 M /trunk/samtools/bam_tview.c
4352 M /trunk/samtools/bamtk.c
4353 D /trunk/samtools/misc/Makefile
4354 A /trunk/samtools/misc/Makefile.std (from /trunk/samtools/misc/Makefile:182)
4355 M /trunk/samtools/samtools.1
4358 * incorporating Nils' changes
4359 * rename Makefile to Makefile.std and prepare to add the GNU building systerms (also by Nils)
4361 ------------------------------------------------------------------------
4362 r183 | lh3lh3 | 2009-03-24 06:30:23 -0400 (Tue, 24 Mar 2009) | 4 lines
4364 M /trunk/samtools/Makefile
4365 M /trunk/samtools/bam_import.c
4366 M /trunk/samtools/bam_maqcns.c
4367 M /trunk/samtools/bam_maqcns.h
4368 M /trunk/samtools/bam_plcmd.c
4369 M /trunk/samtools/bamtk.c
4370 M /trunk/samtools/kseq.h
4371 A /trunk/samtools/kstring.c
4372 A /trunk/samtools/kstring.h
4375 * made pileup take a list of proposed indels. An insertion is N at the moment.
4376 * added my kstring library for a bit complex parsing of the position list.
4378 ------------------------------------------------------------------------
4379 r169 | lh3lh3 | 2009-03-12 09:40:14 -0400 (Thu, 12 Mar 2009) | 3 lines
4381 M /trunk/samtools/misc/soap2sam.pl
4384 * more robust to truncated soap output
4386 ------------------------------------------------------------------------
4387 r168 | lh3lh3 | 2009-03-11 06:49:00 -0400 (Wed, 11 Mar 2009) | 2 lines
4389 M /trunk/samtools/Makefile.lite
4391 added bam_stat.o to Makefile.lite
4393 ------------------------------------------------------------------------
4394 r167 | lh3lh3 | 2009-03-10 18:11:31 -0400 (Tue, 10 Mar 2009) | 3 lines
4396 M /trunk/samtools/bam_maqcns.c
4397 M /trunk/samtools/bamtk.c
4400 * generate RMS of mapQ instead of max mapQ
4402 ------------------------------------------------------------------------
4403 r166 | lh3lh3 | 2009-03-10 18:06:45 -0400 (Tue, 10 Mar 2009) | 3 lines
4405 M /trunk/samtools/bam_plcmd.c
4406 M /trunk/samtools/bamtk.c
4407 M /trunk/samtools/glf.c
4408 M /trunk/samtools/glf.h
4409 M /trunk/samtools/misc/Makefile
4414 ------------------------------------------------------------------------
4415 r159 | lh3lh3 | 2009-03-03 06:26:08 -0500 (Tue, 03 Mar 2009) | 3 lines
4417 M /trunk/samtools/bam_plcmd.c
4418 M /trunk/samtools/bamtk.c
4421 * fixed a minor bug in displaying pileup
4423 ------------------------------------------------------------------------
4424 r158 | lh3lh3 | 2009-03-03 06:24:16 -0500 (Tue, 03 Mar 2009) | 3 lines
4426 M /trunk/samtools/ChangeLog
4427 M /trunk/samtools/bamtk.c
4430 * optionally print SAM header
4432 ------------------------------------------------------------------------
4433 r153 | lh3lh3 | 2009-03-02 05:45:28 -0500 (Mon, 02 Mar 2009) | 3 lines
4435 M /trunk/samtools/bamtk.c
4436 M /trunk/samtools/glf.c
4439 * use "GLF\3" as the magic for GLFv3 files
4441 ------------------------------------------------------------------------
4442 r152 | lh3lh3 | 2009-03-02 05:39:09 -0500 (Mon, 02 Mar 2009) | 5 lines
4444 M /trunk/samtools/Makefile
4445 M /trunk/samtools/bam_import.c
4446 M /trunk/samtools/bam_index.c
4447 M /trunk/samtools/bam_plcmd.c
4448 M /trunk/samtools/bamtk.c
4449 M /trunk/samtools/glf.c
4450 M /trunk/samtools/glf.h
4453 * fixed a bug in import: core.bin is undefined for unmapped reads
4454 * this bug can be alleviated (not completely solved) in bam_index.c
4455 * update to GLFv3: pos is changed to offset for better compression
4457 ------------------------------------------------------------------------
4458 r151 | lh3lh3 | 2009-03-01 10:18:43 -0500 (Sun, 01 Mar 2009) | 3 lines
4460 M /trunk/samtools/misc/wgsim.c
4463 * fixed a bug in simulating indels
4465 ------------------------------------------------------------------------
4466 r145 | lh3lh3 | 2009-02-26 14:43:57 -0500 (Thu, 26 Feb 2009) | 4 lines
4468 M /trunk/samtools/misc/wgsim.c
4471 * allow to print mismatch information as fastq comment. MAQ does
4472 not like long read names.
4474 ------------------------------------------------------------------------
4475 r141 | lh3lh3 | 2009-02-26 09:53:03 -0500 (Thu, 26 Feb 2009) | 6 lines
4477 M /trunk/samtools/ChangeLog
4478 M /trunk/samtools/misc/wgsim.c
4479 M /trunk/samtools/misc/wgsim_eval.pl
4482 * fixed a bug about color read coordinates
4483 * fixed a bug in read names
4484 * wgsim_eval.pl-0.1.3
4485 * make the script work with color reads
4487 ------------------------------------------------------------------------
4488 r140 | lh3lh3 | 2009-02-26 09:02:57 -0500 (Thu, 26 Feb 2009) | 2 lines
4490 M /trunk/samtools/misc/Makefile
4491 M /trunk/samtools/misc/wgsim.c
4493 * wgsim: added a note
4495 ------------------------------------------------------------------------
4496 r139 | lh3lh3 | 2009-02-26 06:39:08 -0500 (Thu, 26 Feb 2009) | 7 lines
4498 M /trunk/samtools/misc/wgsim.c
4499 M /trunk/samtools/misc/wgsim_eval.pl
4502 * considerable code clean up
4503 * print number of substitutions/indels/errors on each read
4504 * potentially support SOLiD simulation, though not tested at the moment
4505 * wgsim_eval.pl-0.1.2
4506 * change in accordant with wgsim
4508 ------------------------------------------------------------------------
4509 r129 | lh3lh3 | 2009-02-18 17:23:27 -0500 (Wed, 18 Feb 2009) | 3 lines
4511 M /trunk/samtools/bam_index.c
4512 M /trunk/samtools/bamtk.c
4515 * fixed a bug in bam_fetch, caused by completely contained adjacent chunks
4517 ------------------------------------------------------------------------
4518 r128 | bhandsaker | 2009-02-18 14:06:57 -0500 (Wed, 18 Feb 2009) | 2 lines
4520 M /trunk/samtools/bamtk.c
4522 Fix annoying segv when invalid region specified.
4524 ------------------------------------------------------------------------
4525 r127 | lh3lh3 | 2009-02-17 05:49:55 -0500 (Tue, 17 Feb 2009) | 2 lines
4527 D /trunk/samtools/misc/indel_filter.pl
4528 A /trunk/samtools/misc/samtools.pl
4530 * move indel_filter.pl to samtools.pl
4532 ------------------------------------------------------------------------
4533 r126 | lh3lh3 | 2009-02-14 16:22:30 -0500 (Sat, 14 Feb 2009) | 3 lines
4535 M /trunk/samtools/bam_mate.c
4536 M /trunk/samtools/bamtk.c
4539 * fixed a bug in fixmate: SE reads are flagged as BAM_FMUNMAP
4541 ------------------------------------------------------------------------
4542 r125 | lh3lh3 | 2009-02-13 04:54:45 -0500 (Fri, 13 Feb 2009) | 3 lines
4544 M /trunk/samtools/bam_stat.c
4545 M /trunk/samtools/bamtk.c
4548 * fixed a minor bug in flagstat
4550 ------------------------------------------------------------------------
4551 r124 | lh3lh3 | 2009-02-12 06:15:32 -0500 (Thu, 12 Feb 2009) | 3 lines
4553 M /trunk/samtools/bam_maqcns.c
4554 M /trunk/samtools/bamtk.c
4555 M /trunk/samtools/misc/indel_filter.pl
4558 * improve indel caller by setting maximum window size
4560 ------------------------------------------------------------------------
4561 r123 | lh3lh3 | 2009-02-12 05:30:29 -0500 (Thu, 12 Feb 2009) | 2 lines
4563 M /trunk/samtools/bam_plcmd.c
4564 M /trunk/samtools/bamtk.c
4566 * output max mapping quality in indel line
4568 ------------------------------------------------------------------------
4569 r122 | lh3lh3 | 2009-02-11 05:59:10 -0500 (Wed, 11 Feb 2009) | 2 lines
4571 M /trunk/samtools/misc/maq2sam.c
4573 fixed a bug in generating tag AM
4575 ------------------------------------------------------------------------
4576 r121 | lh3lh3 | 2009-02-03 05:43:11 -0500 (Tue, 03 Feb 2009) | 2 lines
4578 M /trunk/samtools/bam_index.c
4579 M /trunk/samtools/bamtk.c
4581 fixed a potential memory problem in indexing
4583 ------------------------------------------------------------------------
4584 r120 | bhandsaker | 2009-02-02 10:52:52 -0500 (Mon, 02 Feb 2009) | 2 lines
4586 M /trunk/samtools/Makefile
4588 Pass LIBS to recursive targets to facilitate building at Broad.
4590 ------------------------------------------------------------------------
4591 r119 | lh3lh3 | 2009-02-02 05:12:15 -0500 (Mon, 02 Feb 2009) | 4 lines
4593 M /trunk/samtools/ChangeLog
4594 M /trunk/samtools/bam_plcmd.c
4595 M /trunk/samtools/bam_stat.c
4596 M /trunk/samtools/bamtk.c
4599 * fixed a bug in generating GLFv2 for indels
4600 * improve flagstat report a little bit
4602 ------------------------------------------------------------------------
4603 r118 | lh3lh3 | 2009-01-29 07:33:23 -0500 (Thu, 29 Jan 2009) | 3 lines
4605 M /trunk/samtools/Makefile
4606 A /trunk/samtools/bam_stat.c
4607 M /trunk/samtools/bamtk.c
4610 * added flagstat command
4612 ------------------------------------------------------------------------
4613 r116 | lh3lh3 | 2009-01-28 08:31:12 -0500 (Wed, 28 Jan 2009) | 2 lines
4615 M /trunk/samtools/ChangeLog
4616 M /trunk/samtools/NEWS
4617 M /trunk/samtools/bamtk.c
4618 M /trunk/samtools/samtools.1
4620 Release SAMtools-0.1.2
4622 ------------------------------------------------------------------------
4623 r115 | lh3lh3 | 2009-01-28 07:54:08 -0500 (Wed, 28 Jan 2009) | 2 lines
4625 A /trunk/samtools/misc/indel_filter.pl
4627 Script for filtering indel results
4629 ------------------------------------------------------------------------
4630 r114 | lh3lh3 | 2009-01-25 06:45:37 -0500 (Sun, 25 Jan 2009) | 2 lines
4632 A /trunk/samtools/misc/zoom2sam.pl
4636 ------------------------------------------------------------------------
4637 r113 | lh3lh3 | 2009-01-24 09:25:07 -0500 (Sat, 24 Jan 2009) | 2 lines
4639 A /trunk/samtools/misc/novo2sam.pl
4641 add a script to convert novo alignment to SAM
4643 ------------------------------------------------------------------------
4644 r112 | lh3lh3 | 2009-01-23 15:57:39 -0500 (Fri, 23 Jan 2009) | 2 lines
4646 M /trunk/samtools/ChangeLog
4647 M /trunk/samtools/ChangeLog.old
4648 M /trunk/samtools/samtools.1
4650 update documentation and ChangeLog
4652 ------------------------------------------------------------------------
4653 r111 | lh3lh3 | 2009-01-23 14:22:59 -0500 (Fri, 23 Jan 2009) | 3 lines
4655 M /trunk/samtools/bam_sort.c
4656 M /trunk/samtools/bamtk.c
4659 * fixed a bug in "merge" command line
4661 ------------------------------------------------------------------------
4662 r110 | lh3lh3 | 2009-01-22 10:36:48 -0500 (Thu, 22 Jan 2009) | 3 lines
4664 M /trunk/samtools/misc/Makefile
4665 A /trunk/samtools/misc/bowtie2sam.pl (from /branches/dev/samtools/misc/bowtie2sam.pl:108)
4666 M /trunk/samtools/misc/export2sam.pl
4667 A /trunk/samtools/misc/soap2sam.pl (from /branches/dev/samtools/misc/soap2sam.pl:108)
4668 A /trunk/samtools/misc/wgsim.c (from /branches/dev/samtools/misc/wgsim.c:108)
4669 A /trunk/samtools/misc/wgsim_eval.pl (from /branches/dev/samtools/misc/wgsim_eval.pl:108)
4671 * merge from branches/dev/
4672 * all future development will happen here
4674 ------------------------------------------------------------------------
4675 r109 | lh3lh3 | 2009-01-22 10:14:27 -0500 (Thu, 22 Jan 2009) | 3 lines
4677 M /trunk/samtools/COPYING
4678 M /trunk/samtools/ChangeLog
4679 A /trunk/samtools/INSTALL (from /branches/dev/samtools/INSTALL:108)
4680 M /trunk/samtools/Makefile
4681 A /trunk/samtools/Makefile.lite (from /branches/dev/samtools/Makefile.lite:108)
4682 M /trunk/samtools/bam.c
4683 M /trunk/samtools/bam.h
4684 M /trunk/samtools/bam_import.c
4685 M /trunk/samtools/bam_index.c
4686 M /trunk/samtools/bam_lpileup.c
4687 M /trunk/samtools/bam_maqcns.c
4688 M /trunk/samtools/bam_maqcns.h
4689 A /trunk/samtools/bam_mate.c (from /branches/dev/samtools/bam_mate.c:108)
4690 M /trunk/samtools/bam_pileup.c
4691 M /trunk/samtools/bam_plcmd.c
4692 A /trunk/samtools/bam_rmdup.c (from /branches/dev/samtools/bam_rmdup.c:108)
4693 M /trunk/samtools/bam_sort.c
4694 M /trunk/samtools/bamtk.c
4695 M /trunk/samtools/bgzf.h
4696 M /trunk/samtools/examples/00README.txt
4697 A /trunk/samtools/examples/Makefile (from /branches/dev/samtools/examples/Makefile:108)
4698 D /trunk/samtools/examples/ex1.fa.fai
4699 M /trunk/samtools/examples/ex1.sam.gz
4700 M /trunk/samtools/faidx.c
4701 A /trunk/samtools/glf.c (from /branches/dev/samtools/glf.c:108)
4702 M /trunk/samtools/glf.h
4703 M /trunk/samtools/misc/Makefile
4704 M /trunk/samtools/misc/maq2sam.c
4705 M /trunk/samtools/razf.c
4706 M /trunk/samtools/source.dot
4708 * Merge from branches/dev/
4709 * all future development will happen here at trunk/
4711 ------------------------------------------------------------------------
4712 r79 | bhandsaker | 2009-01-07 16:42:15 -0500 (Wed, 07 Jan 2009) | 2 lines
4714 M /trunk/samtools/bam_maqcns.c
4715 M /trunk/samtools/bam_tview.c
4717 Fix problem with compiling without curses.
4719 ------------------------------------------------------------------------
4720 r63 | lh3lh3 | 2008-12-22 10:58:02 -0500 (Mon, 22 Dec 2008) | 2 lines
4722 A /trunk/samtools (from /branches/dev/samtools:62)
4726 ------------------------------------------------------------------------
4727 r62 | lh3lh3 | 2008-12-22 10:55:13 -0500 (Mon, 22 Dec 2008) | 2 lines
4729 A /branches/dev/samtools/NEWS
4730 M /branches/dev/samtools/bamtk.c
4731 M /branches/dev/samtools/samtools.1
4733 Release samtools-0.1.1
4735 ------------------------------------------------------------------------
4736 r61 | lh3lh3 | 2008-12-22 10:46:08 -0500 (Mon, 22 Dec 2008) | 10 lines
4738 M /branches/dev/samtools/bam_aux.c
4739 M /branches/dev/samtools/bam_index.c
4740 M /branches/dev/samtools/bam_plcmd.c
4741 M /branches/dev/samtools/bam_tview.c
4742 M /branches/dev/samtools/bamtk.c
4743 M /branches/dev/samtools/razf.c
4744 M /branches/dev/samtools/samtools.1
4747 * fixed a bug in razf.c: reset z_eof when razf_seek() is called
4748 * fixed a memory leak in parsing a region
4749 * changed pileup a little bit when -s is in use: output ^ and $
4750 * when a bam is not indexed, output more meaningful error message
4751 * fixed a bug in indexing for small alignment
4752 * fixed a bug in the viewer when we come to the end of a reference file
4753 * updated documentation
4754 * prepare to release 0.1.1
4756 ------------------------------------------------------------------------
4757 r60 | lh3lh3 | 2008-12-22 10:10:16 -0500 (Mon, 22 Dec 2008) | 2 lines
4759 A /branches/dev/samtools/examples
4760 A /branches/dev/samtools/examples/00README.txt
4761 A /branches/dev/samtools/examples/ex1.fa
4762 A /branches/dev/samtools/examples/ex1.fa.fai
4763 A /branches/dev/samtools/examples/ex1.sam.gz
4767 ------------------------------------------------------------------------
4768 r59 | lh3lh3 | 2008-12-22 04:38:15 -0500 (Mon, 22 Dec 2008) | 2 lines
4770 M /branches/dev/samtools/ChangeLog
4774 ------------------------------------------------------------------------
4775 r58 | lh3lh3 | 2008-12-20 18:06:00 -0500 (Sat, 20 Dec 2008) | 3 lines
4777 M /branches/dev/samtools/misc/export2sam.pl
4780 * fixed several bugs
4782 ------------------------------------------------------------------------
4783 r57 | lh3lh3 | 2008-12-20 10:44:20 -0500 (Sat, 20 Dec 2008) | 2 lines
4785 A /branches/dev/samtools/misc/export2sam.pl
4787 convert Export format to SAM; not thoroughly tested
4789 ------------------------------------------------------------------------
4790 r56 | lh3lh3 | 2008-12-19 17:13:28 -0500 (Fri, 19 Dec 2008) | 6 lines
4792 M /branches/dev/samtools/bam_import.c
4793 M /branches/dev/samtools/bam_plcmd.c
4794 M /branches/dev/samtools/bam_tview.c
4795 M /branches/dev/samtools/bamtk.c
4796 A /branches/dev/samtools/source.dot
4799 * pileup: generate maq-like simple output
4800 * pileup: allow to output pileup at required sites
4801 * source.dot: source file relationship graph
4802 * tview: fixed a minor bug
4804 ------------------------------------------------------------------------
4805 r55 | lh3lh3 | 2008-12-19 15:10:26 -0500 (Fri, 19 Dec 2008) | 2 lines
4807 D /branches/dev/samtools/misc/all2sam.pl
4811 ------------------------------------------------------------------------
4812 r54 | lh3lh3 | 2008-12-16 17:34:25 -0500 (Tue, 16 Dec 2008) | 2 lines
4814 A /branches/dev/samtools/COPYING
4815 M /branches/dev/samtools/bam.h
4816 M /branches/dev/samtools/faidx.h
4817 M /branches/dev/samtools/khash.h
4818 M /branches/dev/samtools/kseq.h
4819 M /branches/dev/samtools/ksort.h
4820 M /branches/dev/samtools/samtools.1
4822 Added copyright information and a bit more documentation. No code change.
4824 ------------------------------------------------------------------------
4825 r53 | lh3lh3 | 2008-12-16 08:40:18 -0500 (Tue, 16 Dec 2008) | 3 lines
4827 M /branches/dev/samtools/bam.c
4828 M /branches/dev/samtools/bam.h
4829 M /branches/dev/samtools/bam_index.c
4830 M /branches/dev/samtools/bam_maqcns.c
4831 M /branches/dev/samtools/bamtk.c
4834 * improved efficiency of the indel caller for spliced alignments
4836 ------------------------------------------------------------------------
4837 r52 | lh3lh3 | 2008-12-16 05:28:20 -0500 (Tue, 16 Dec 2008) | 3 lines
4839 M /branches/dev/samtools/bam.c
4840 M /branches/dev/samtools/bam.h
4841 M /branches/dev/samtools/bam_aux.c
4842 M /branches/dev/samtools/bam_index.c
4843 M /branches/dev/samtools/bamtk.c
4846 * a bit code cleanup: reduce the dependency between source files
4848 ------------------------------------------------------------------------
4849 r51 | lh3lh3 | 2008-12-15 09:29:32 -0500 (Mon, 15 Dec 2008) | 3 lines
4851 M /branches/dev/samtools/bam_maqcns.c
4852 M /branches/dev/samtools/bam_plcmd.c
4853 M /branches/dev/samtools/bamtk.c
4856 * fixed a memory leak
4858 ------------------------------------------------------------------------
4859 r50 | lh3lh3 | 2008-12-15 09:00:13 -0500 (Mon, 15 Dec 2008) | 2 lines
4861 M /branches/dev/samtools/ChangeLog
4862 M /branches/dev/samtools/bam.h
4863 M /branches/dev/samtools/samtools.1
4865 update documentation, ChangeLog and a comment
4867 ------------------------------------------------------------------------
4868 r49 | lh3lh3 | 2008-12-15 08:36:43 -0500 (Mon, 15 Dec 2008) | 6 lines
4870 M /branches/dev/samtools/Makefile
4871 M /branches/dev/samtools/bam.h
4872 M /branches/dev/samtools/bam_maqcns.c
4873 M /branches/dev/samtools/bam_maqcns.h
4874 M /branches/dev/samtools/bam_pileup.c
4875 A /branches/dev/samtools/bam_plcmd.c
4876 M /branches/dev/samtools/bamtk.c
4877 M /branches/dev/samtools/samtools.1
4880 * moved pileup command to a separate source file
4881 * added indel caller
4882 * added bam_cal_segend(). (NOT WORKING for spliced alignment!!!)
4883 * updated documentation
4885 ------------------------------------------------------------------------
4886 r48 | lh3lh3 | 2008-12-12 08:55:36 -0500 (Fri, 12 Dec 2008) | 3 lines
4888 M /branches/dev/samtools/bam_maqcns.c
4889 M /branches/dev/samtools/bamtk.c
4892 * fixed another bug in maqcns when there is a nearby deletion
4894 ------------------------------------------------------------------------
4895 r47 | lh3lh3 | 2008-12-12 08:42:16 -0500 (Fri, 12 Dec 2008) | 5 lines
4897 M /branches/dev/samtools/bam_maqcns.c
4898 M /branches/dev/samtools/bam_pileup.c
4899 M /branches/dev/samtools/bamtk.c
4902 * pileup: outputing consensus is now optional
4903 * fixed a bug in glfgen. This bug also exists in maq's glfgen. However,
4904 I am not quite sure why the previous version may have problem.
4906 ------------------------------------------------------------------------
4907 r46 | lh3lh3 | 2008-12-12 06:44:56 -0500 (Fri, 12 Dec 2008) | 6 lines
4909 M /branches/dev/samtools/bam_pileup.c
4910 M /branches/dev/samtools/bamtk.c
4913 * add maq consensus to pileup. However, I will move this part to a new
4914 command as strictly speaking, consensus callin is not part of pileup,
4915 and imposing it would make it harder to generate for other language
4918 ------------------------------------------------------------------------
4919 r45 | bhandsaker | 2008-12-11 15:43:56 -0500 (Thu, 11 Dec 2008) | 2 lines
4921 M /branches/dev/samtools/bgzf.c
4923 Fix bug in tell() after reads that consume to the exact end of a block.
4925 ------------------------------------------------------------------------
4926 r44 | lh3lh3 | 2008-12-11 04:36:53 -0500 (Thu, 11 Dec 2008) | 2 lines
4928 M /branches/dev/samtools/samtools.1
4932 ------------------------------------------------------------------------
4933 r43 | lh3lh3 | 2008-12-11 04:25:36 -0500 (Thu, 11 Dec 2008) | 4 lines
4935 M /branches/dev/samtools/bam_import.c
4936 M /branches/dev/samtools/bamtk.c
4939 * fixed a bug in parser when there is auxiliary fields
4940 * made the parser a bit more robust
4942 ------------------------------------------------------------------------
4943 r42 | lh3lh3 | 2008-12-10 09:57:29 -0500 (Wed, 10 Dec 2008) | 5 lines
4945 M /branches/dev/samtools/bam_index.c
4946 M /branches/dev/samtools/bamtk.c
4947 M /branches/dev/samtools/bgzf.c
4950 * fixed a bug in bgzf (only reading is affected)
4951 * fixed a typo in bam_index.c
4952 * in bam_index.c, check potential bugs in the underlying I/O library
4954 ------------------------------------------------------------------------
4955 r41 | lh3lh3 | 2008-12-10 07:53:08 -0500 (Wed, 10 Dec 2008) | 2 lines
4957 M /branches/dev/samtools/samtools.1
4961 ------------------------------------------------------------------------
4962 r40 | lh3lh3 | 2008-12-10 06:52:10 -0500 (Wed, 10 Dec 2008) | 5 lines
4964 M /branches/dev/samtools/bam.h
4965 M /branches/dev/samtools/bam_pileup.c
4966 M /branches/dev/samtools/bamtk.c
4969 * tried to make pileup work with clipping (previously not), though NOT tested
4970 * removed -v from pileup
4971 * made pileup take the reference sequence
4973 ------------------------------------------------------------------------
4974 r39 | lh3lh3 | 2008-12-09 06:59:28 -0500 (Tue, 09 Dec 2008) | 4 lines
4976 M /branches/dev/samtools/bam_import.c
4977 M /branches/dev/samtools/bamtk.c
4978 M /branches/dev/samtools/samtools.1
4981 * in parser, recognize "=", rather than ",", as a match
4982 * in parser, correctl parse "=" at the MRNM field.
4984 ------------------------------------------------------------------------
4985 r38 | lh3lh3 | 2008-12-09 06:39:07 -0500 (Tue, 09 Dec 2008) | 2 lines
4987 M /branches/dev/samtools/misc/maq2sam.c
4989 fixed a bug in handling maq flag 64 and 192
4991 ------------------------------------------------------------------------
4992 r37 | lh3lh3 | 2008-12-09 04:53:46 -0500 (Tue, 09 Dec 2008) | 2 lines
4994 M /branches/dev/samtools/misc/md5fa.c
4996 also calculate unordered md5sum check
4998 ------------------------------------------------------------------------
4999 r36 | lh3lh3 | 2008-12-09 04:46:21 -0500 (Tue, 09 Dec 2008) | 2 lines
5001 M /branches/dev/samtools/misc/md5fa.c
5003 fixed a minor bug when there are space in the sequence
5005 ------------------------------------------------------------------------
5006 r35 | lh3lh3 | 2008-12-09 04:40:45 -0500 (Tue, 09 Dec 2008) | 2 lines
5008 M /branches/dev/samtools/misc/md5fa.c
5010 fixed a potential memory leak
5012 ------------------------------------------------------------------------
5013 r34 | lh3lh3 | 2008-12-08 09:52:17 -0500 (Mon, 08 Dec 2008) | 2 lines
5015 M /branches/dev/samtools/bam_import.c
5016 M /branches/dev/samtools/bam_index.c
5017 M /branches/dev/samtools/bamtk.c
5019 * fixed a bug in import: bin is wrongly calculated
5021 ------------------------------------------------------------------------
5022 r33 | lh3lh3 | 2008-12-08 09:08:01 -0500 (Mon, 08 Dec 2008) | 2 lines
5024 M /branches/dev/samtools/misc/all2sam.pl
5028 ------------------------------------------------------------------------
5029 r32 | lh3lh3 | 2008-12-08 07:56:02 -0500 (Mon, 08 Dec 2008) | 3 lines
5031 M /branches/dev/samtools/Makefile
5032 M /branches/dev/samtools/kseq.h
5033 M /branches/dev/samtools/misc/Makefile
5034 A /branches/dev/samtools/misc/md5.c
5035 A /branches/dev/samtools/misc/md5.h
5036 A /branches/dev/samtools/misc/md5fa.c
5038 * fixed two warnings in kseq.h
5039 * added md5sum utilities
5041 ------------------------------------------------------------------------
5042 r31 | lh3lh3 | 2008-12-08 06:35:29 -0500 (Mon, 08 Dec 2008) | 5 lines
5044 M /branches/dev/samtools/Makefile
5045 M /branches/dev/samtools/bam_import.c
5046 M /branches/dev/samtools/bamtk.c
5047 A /branches/dev/samtools/kseq.h
5048 D /branches/dev/samtools/kstream.h
5051 * replace kstream with kseq. kseq is a superset of kstream. I need the
5052 extra functions in kseq.h.
5053 * also compile stand-alone faidx
5055 ------------------------------------------------------------------------
5056 r30 | lh3lh3 | 2008-12-08 06:17:04 -0500 (Mon, 08 Dec 2008) | 3 lines
5058 M /branches/dev/samtools/bam.h
5059 M /branches/dev/samtools/bam_sort.c
5060 M /branches/dev/samtools/bamtk.c
5063 * sorting by read names is available
5065 ------------------------------------------------------------------------
5066 r29 | lh3lh3 | 2008-12-08 05:29:02 -0500 (Mon, 08 Dec 2008) | 3 lines
5068 M /branches/dev/samtools/bam.c
5069 M /branches/dev/samtools/bam.h
5070 M /branches/dev/samtools/bam_import.c
5071 M /branches/dev/samtools/bam_maqcns.c
5072 M /branches/dev/samtools/bam_pileup.c
5073 M /branches/dev/samtools/bam_sort.c
5074 M /branches/dev/samtools/bam_tview.c
5075 M /branches/dev/samtools/bamtk.c
5076 M /branches/dev/samtools/misc/maq2sam.c
5079 * format change to meet the latest specification
5081 ------------------------------------------------------------------------
5082 r28 | lh3lh3 | 2008-12-04 11:09:21 -0500 (Thu, 04 Dec 2008) | 3 lines
5084 M /branches/dev/samtools/bam_maqcns.c
5085 M /branches/dev/samtools/misc/maq2sam.c
5087 * minor change in maqcns: special care when n==0
5088 * change maq2sam to meet the latest specification
5090 ------------------------------------------------------------------------
5091 r27 | lh3lh3 | 2008-12-04 10:55:44 -0500 (Thu, 04 Dec 2008) | 2 lines
5093 M /branches/dev/samtools/razf.c
5094 M /branches/dev/samtools/razf.h
5096 considerable code clean up in razf
5098 ------------------------------------------------------------------------
5099 r26 | lh3lh3 | 2008-12-04 10:08:18 -0500 (Thu, 04 Dec 2008) | 2 lines
5101 M /branches/dev/samtools/ChangeLog
5102 M /branches/dev/samtools/Makefile
5103 M /branches/dev/samtools/faidx.c
5105 make RAZF optional in faidx.c
5107 ------------------------------------------------------------------------
5108 r25 | lh3lh3 | 2008-12-01 10:27:22 -0500 (Mon, 01 Dec 2008) | 3 lines
5110 M /branches/dev/samtools/Makefile
5111 M /branches/dev/samtools/bam.h
5112 M /branches/dev/samtools/bam_aux.c
5113 M /branches/dev/samtools/bamtk.c
5114 M /branches/dev/samtools/samtools.1
5117 * added routines for retrieving aux data, NOT TESTED YET!
5119 ------------------------------------------------------------------------
5120 r24 | lh3lh3 | 2008-12-01 09:29:43 -0500 (Mon, 01 Dec 2008) | 5 lines
5122 M /branches/dev/samtools/bam.c
5123 M /branches/dev/samtools/bam_import.c
5124 M /branches/dev/samtools/bam_maqcns.c
5125 M /branches/dev/samtools/bamtk.c
5126 M /branches/dev/samtools/bgzf.c
5127 M /branches/dev/samtools/samtools.1
5130 * bgzf: fixed a potential integer overflow on 32-it machines
5131 * maqcns: set the minimum combined quality as 0
5132 * supporting hex strings
5134 ------------------------------------------------------------------------
5135 r23 | lh3lh3 | 2008-11-27 12:14:37 -0500 (Thu, 27 Nov 2008) | 3 lines
5137 M /branches/dev/samtools/bam_maqcns.c
5138 M /branches/dev/samtools/bamtk.c
5141 * fixed the bug in maqcns
5143 ------------------------------------------------------------------------
5144 r22 | lh3lh3 | 2008-11-27 12:08:11 -0500 (Thu, 27 Nov 2008) | 3 lines
5146 M /branches/dev/samtools/Makefile
5147 M /branches/dev/samtools/bam.h
5148 A /branches/dev/samtools/bam_maqcns.c
5149 A /branches/dev/samtools/bam_maqcns.h
5150 M /branches/dev/samtools/bam_tview.c
5151 M /branches/dev/samtools/bamtk.c
5152 A /branches/dev/samtools/glf.h
5155 * add MAQ consensus caller, currently BUGGY!
5157 ------------------------------------------------------------------------
5158 r21 | lh3lh3 | 2008-11-27 08:51:28 -0500 (Thu, 27 Nov 2008) | 4 lines
5160 M /branches/dev/samtools/bam_pileup.c
5161 M /branches/dev/samtools/bam_tview.c
5162 M /branches/dev/samtools/bamtk.c
5165 * tview: display padded alignment (but not P operation)
5166 * better coordinates and reference sequence
5168 ------------------------------------------------------------------------
5169 r19 | lh3lh3 | 2008-11-27 04:26:05 -0500 (Thu, 27 Nov 2008) | 2 lines
5171 A /branches/dev/samtools/ChangeLog
5175 ------------------------------------------------------------------------
5176 r18 | lh3lh3 | 2008-11-27 04:24:45 -0500 (Thu, 27 Nov 2008) | 3 lines
5178 D /branches/dev/samtools/ChangeLog
5179 A /branches/dev/samtools/ChangeLog.old (from /branches/dev/samtools/ChangeLog:6)
5181 Rename ChangeLog to ChangeLog.old. This old ChangeLog is generated from
5182 the log of my personal SVN repository.
5184 ------------------------------------------------------------------------
5185 r17 | lh3lh3 | 2008-11-27 04:22:55 -0500 (Thu, 27 Nov 2008) | 6 lines
5187 M /branches/dev/samtools/Makefile
5188 M /branches/dev/samtools/bamtk.c
5189 M /branches/dev/samtools/bgzf.c
5192 * declare fseeko and ftello as some Linux may not do this by default and
5193 missing these declarations will make bgzf buggy
5194 * get rid of some harmless warings
5195 * use BGZF by default, now
5197 ------------------------------------------------------------------------
5198 r16 | lh3lh3 | 2008-11-26 16:19:11 -0500 (Wed, 26 Nov 2008) | 4 lines
5200 M /branches/dev/samtools/bam_index.c
5201 M /branches/dev/samtools/bamtk.c
5202 M /branches/dev/samtools/razf.c
5205 * fixed a bug in razf_read()
5206 * give more warnings when the file is truncated (or due to bugs in I/O library)
5208 ------------------------------------------------------------------------
5209 r15 | lh3lh3 | 2008-11-26 15:41:39 -0500 (Wed, 26 Nov 2008) | 2 lines
5211 M /branches/dev/samtools/bgzf.c
5213 fixed a bug in bgzf.c at the end of the file
5215 ------------------------------------------------------------------------
5216 r14 | lh3lh3 | 2008-11-26 12:05:18 -0500 (Wed, 26 Nov 2008) | 4 lines
5218 M /branches/dev/samtools/bamtk.c
5221 * a lot happened to RAZF, although samtools itself is untouched. Better
5222 also update the version number anyway to avoid confusion
5224 ------------------------------------------------------------------------
5225 r13 | lh3lh3 | 2008-11-26 12:03:48 -0500 (Wed, 26 Nov 2008) | 2 lines
5227 M /branches/dev/samtools/razf.c
5229 a change from Jue, but I think it should not matter
5231 ------------------------------------------------------------------------
5232 r12 | lh3lh3 | 2008-11-26 11:48:14 -0500 (Wed, 26 Nov 2008) | 3 lines
5234 M /branches/dev/samtools/razf.c
5236 fixed a potential bug in razf. However, it seems still buggy, just
5237 rarely happens, very rarely.
5239 ------------------------------------------------------------------------
5240 r11 | lh3lh3 | 2008-11-26 09:02:56 -0500 (Wed, 26 Nov 2008) | 2 lines
5242 M /branches/dev/samtools/razf.c
5244 fixed a bug in razf, with the help of Jue
5246 ------------------------------------------------------------------------
5247 r10 | lh3lh3 | 2008-11-26 06:55:32 -0500 (Wed, 26 Nov 2008) | 2 lines
5249 M /branches/dev/samtools/bam_index.c
5253 ------------------------------------------------------------------------
5254 r9 | lh3lh3 | 2008-11-26 06:37:05 -0500 (Wed, 26 Nov 2008) | 2 lines
5256 M /branches/dev/samtools/Makefile
5257 M /branches/dev/samtools/bam.h
5258 M /branches/dev/samtools/razf.c
5259 M /branches/dev/samtools/razf.h
5261 * Jue has updated razf to realize Bob's scheme
5263 ------------------------------------------------------------------------
5264 r7 | lh3lh3 | 2008-11-25 15:37:37 -0500 (Tue, 25 Nov 2008) | 2 lines
5266 A /branches/dev/samtools/samtools.1
5270 ------------------------------------------------------------------------
5271 r6 | lh3lh3 | 2008-11-25 15:37:16 -0500 (Tue, 25 Nov 2008) | 3 lines
5273 A /branches/dev/samtools/ChangeLog
5274 A /branches/dev/samtools/Makefile
5275 A /branches/dev/samtools/bam.c
5276 A /branches/dev/samtools/bam.h
5277 A /branches/dev/samtools/bam_aux.c
5278 A /branches/dev/samtools/bam_endian.h
5279 A /branches/dev/samtools/bam_import.c
5280 A /branches/dev/samtools/bam_index.c
5281 A /branches/dev/samtools/bam_lpileup.c
5282 A /branches/dev/samtools/bam_pileup.c
5283 A /branches/dev/samtools/bam_sort.c
5284 A /branches/dev/samtools/bam_tview.c
5285 A /branches/dev/samtools/bamtk.c
5286 A /branches/dev/samtools/bgzf.c
5287 A /branches/dev/samtools/bgzf.h
5288 A /branches/dev/samtools/bgzip.c
5289 A /branches/dev/samtools/faidx.c
5290 A /branches/dev/samtools/faidx.h
5291 A /branches/dev/samtools/khash.h
5292 A /branches/dev/samtools/ksort.h
5293 A /branches/dev/samtools/kstream.h
5294 A /branches/dev/samtools/misc
5295 A /branches/dev/samtools/misc/Makefile
5296 A /branches/dev/samtools/misc/all2sam.pl
5297 A /branches/dev/samtools/misc/maq2sam.c
5298 A /branches/dev/samtools/razf.c
5299 A /branches/dev/samtools/razf.h
5300 A /branches/dev/samtools/razip.c
5301 A /branches/dev/samtools/zutil.h
5303 The initial version of samtools, replicated from my local SVN repository.
5304 The current version is: 0.1.0-42. All future development will happen here.
5306 ------------------------------------------------------------------------
5307 r5 | lh3lh3 | 2008-11-25 15:30:49 -0500 (Tue, 25 Nov 2008) | 2 lines
5309 A /branches/dev/samtools
5311 samtools (C version)
5313 ------------------------------------------------------------------------