1 ------------------------------------------------------------------------
2 r844 | lh3lh3 | 2010-11-19 23:16:08 -0500 (Fri, 19 Nov 2010) | 3 lines
4 M /trunk/samtools/bamtk.c
5 M /trunk/samtools/bcftools/call1.c
6 M /trunk/samtools/bcftools/prob1.c
7 M /trunk/samtools/bcftools/prob1.h
9 * samtools-0.1.10-9 (r844)
10 * added the "folded" or reference-free mode for variant calling
12 ------------------------------------------------------------------------
13 r843 | lh3lh3 | 2010-11-19 22:26:36 -0500 (Fri, 19 Nov 2010) | 2 lines
15 M /trunk/samtools/NEWS
16 M /trunk/samtools/bam_sort.c
18 In merging, if -R is specified, do not abort if the sequence dictionary is different.
20 ------------------------------------------------------------------------
21 r842 | jmarshall | 2010-11-19 21:24:28 -0500 (Fri, 19 Nov 2010) | 5 lines
23 M /trunk/samtools/bam_sort.c
25 When merging BAM headers, compare the list of target reference sequences
26 strictly (and fail/abort if there is a mismatch), but allow one list to be a
27 prefix of the other. (i.e., check that the lists are identical up until the
28 shorter runs out, and add the excess targets from the longer to the output.)
30 ------------------------------------------------------------------------
31 r841 | lh3lh3 | 2010-11-19 14:49:27 -0500 (Fri, 19 Nov 2010) | 4 lines
33 M /trunk/samtools/bam_index.c
34 M /trunk/samtools/bam_pileup.c
35 M /trunk/samtools/bamtk.c
37 * samtools-0.1.10 (r841)
38 * fixed a bug in pileup when the first CIGAR operation is D
39 * fixed a bug in view with range query
41 ------------------------------------------------------------------------
42 r840 | lh3lh3 | 2010-11-19 13:45:51 -0500 (Fri, 19 Nov 2010) | 10 lines
44 M /trunk/samtools/ChangeLog
45 M /trunk/samtools/bam2bcf.c
46 M /trunk/samtools/bam2bcf.h
47 M /trunk/samtools/bam2bcf_indel.c
48 M /trunk/samtools/bam_plcmd.c
49 M /trunk/samtools/bamtk.c
51 * samtools-0.1.10-4 (r840)
53 * drop the MNP caller. It is slow while does not diliver too much
54 benefit. Possibly I will work on it in future given more time.
56 * there is a segfault in pileup
58 * someone has reported segfault from view/index/sort
61 ------------------------------------------------------------------------
62 r839 | lh3lh3 | 2010-11-18 17:30:11 -0500 (Thu, 18 Nov 2010) | 9 lines
64 M /trunk/samtools/bam2bcf.h
65 M /trunk/samtools/bam2bcf_indel.c
66 M /trunk/samtools/bamtk.c
68 * samtools-0.1.10-6 (r839)
70 * call MNPs without realignment because it seems to me that it is not
71 worthwhile to significantly slow down SNP calling.
73 * the result looks quite different from the previous version. I have
77 ------------------------------------------------------------------------
78 r838 | lh3lh3 | 2010-11-18 11:26:09 -0500 (Thu, 18 Nov 2010) | 2 lines
80 M /trunk/samtools/knetfile.c
82 Apply a patch by Rob Davis, which improves fault detection.
84 ------------------------------------------------------------------------
85 r836 | lh3lh3 | 2010-11-18 11:09:23 -0500 (Thu, 18 Nov 2010) | 3 lines
87 M /trunk/samtools/bam2bcf_indel.c
88 M /trunk/samtools/bamtk.c
91 * initiate MNP realignment when the MNP has at least 0.2% frequency (otherwise too slow)
93 ------------------------------------------------------------------------
94 r835 | lh3lh3 | 2010-11-18 00:25:13 -0500 (Thu, 18 Nov 2010) | 3 lines
96 M /trunk/samtools/bcftools/vcfutils.pl
98 * modify the filtering rule: also filter SNPs around filtered indels
101 ------------------------------------------------------------------------
102 r834 | lh3lh3 | 2010-11-17 23:13:52 -0500 (Wed, 17 Nov 2010) | 4 lines
104 M /trunk/samtools/bam2bcf.c
105 M /trunk/samtools/bam2bcf_indel.c
106 M /trunk/samtools/bamtk.c
108 * samtools-0.1.10-4 (r834)
109 * fixed a silly bug in printing MNP
110 * restrict to at most 1 alternative allele
112 ------------------------------------------------------------------------
113 r833 | lh3lh3 | 2010-11-17 21:58:58 -0500 (Wed, 17 Nov 2010) | 2 lines
115 M /trunk/samtools/bam2bcf.c
116 M /trunk/samtools/bamtk.c
118 fixed a bug in printing MNPs
120 ------------------------------------------------------------------------
121 r832 | lh3lh3 | 2010-11-17 21:47:20 -0500 (Wed, 17 Nov 2010) | 2 lines
123 M /trunk/samtools/bam2bcf_indel.c
124 M /trunk/samtools/bamtk.c
126 minor change to how seqQ is applied
128 ------------------------------------------------------------------------
129 r831 | lh3lh3 | 2010-11-17 21:41:12 -0500 (Wed, 17 Nov 2010) | 3 lines
131 M /trunk/samtools/bam2bcf.c
132 M /trunk/samtools/bam2bcf.h
133 M /trunk/samtools/bam2bcf_indel.c
134 M /trunk/samtools/bam_plcmd.c
135 M /trunk/samtools/bamtk.c
137 * samtools-0.1.10 (r831)
140 ------------------------------------------------------------------------
141 r829 | lh3lh3 | 2010-11-16 23:14:15 -0500 (Tue, 16 Nov 2010) | 2 lines
143 M /trunk/samtools/ChangeLog
144 M /trunk/samtools/NEWS
145 M /trunk/samtools/bamtk.c
147 Release samtools-0.1.10 (r829)
149 ------------------------------------------------------------------------
150 r828 | lh3lh3 | 2010-11-16 20:48:49 -0500 (Tue, 16 Nov 2010) | 2 lines
152 M /trunk/samtools/bamtk.c
154 update version information: samtools-0.1.9-20 (r828)
156 ------------------------------------------------------------------------
157 r827 | lh3lh3 | 2010-11-16 15:32:50 -0500 (Tue, 16 Nov 2010) | 2 lines
159 M /trunk/samtools/bcftools/call1.c
161 bcftools: allow to skip indels
163 ------------------------------------------------------------------------
164 r826 | lh3lh3 | 2010-11-16 14:11:58 -0500 (Tue, 16 Nov 2010) | 2 lines
166 M /trunk/samtools/bam_md.c
168 remove ZQ if both BQ and ZQ are present
170 ------------------------------------------------------------------------
171 r825 | lh3lh3 | 2010-11-16 13:51:33 -0500 (Tue, 16 Nov 2010) | 3 lines
173 M /trunk/samtools/bam2bcf_indel.c
174 M /trunk/samtools/bam_md.c
175 M /trunk/samtools/bamtk.c
176 M /trunk/samtools/samtools.1
178 * samtools-0.1.9-18 (r825)
179 * change the behaviour of calmd such that by default it does not change the base quality
181 ------------------------------------------------------------------------
182 r824 | lh3lh3 | 2010-11-15 23:31:53 -0500 (Mon, 15 Nov 2010) | 4 lines
184 M /trunk/samtools/bam_plcmd.c
185 M /trunk/samtools/bamtk.c
186 M /trunk/samtools/bcftools/call1.c
187 M /trunk/samtools/samtools.1
189 * samtools-0.1.9-17 (r824)
190 * added command line options to change the default parameters in indel calling
193 ------------------------------------------------------------------------
194 r823 | lh3lh3 | 2010-11-15 12:20:13 -0500 (Mon, 15 Nov 2010) | 3 lines
196 M /trunk/samtools/bam2bcf_indel.c
197 M /trunk/samtools/bam_md.c
198 M /trunk/samtools/bamtk.c
200 * samtools-0.1.9-r823
201 * the BQ tag is now 64 shifted, not 33 shifted
203 ------------------------------------------------------------------------
204 r822 | lh3lh3 | 2010-11-15 00:30:18 -0500 (Mon, 15 Nov 2010) | 3 lines
206 M /trunk/samtools/bam2bcf.c
207 M /trunk/samtools/bam2bcf.h
208 M /trunk/samtools/bamtk.c
209 M /trunk/samtools/bcftools/vcfutils.pl
210 M /trunk/samtools/misc/samtools.pl
212 * samtools-0.1.9-16 (r822)
213 * keep the raw depth because in indel calling, DP4 may be way off the true depth
215 ------------------------------------------------------------------------
216 r821 | lh3lh3 | 2010-11-13 01:18:31 -0500 (Sat, 13 Nov 2010) | 4 lines
218 M /trunk/samtools/bam_md.c
219 M /trunk/samtools/bamtk.c
221 * samtools-0.1.9-15 (r821)
223 * skip realignment if BQ is present
225 ------------------------------------------------------------------------
226 r820 | lh3lh3 | 2010-11-13 01:08:26 -0500 (Sat, 13 Nov 2010) | 3 lines
228 M /trunk/samtools/bam2bcf_indel.c
229 M /trunk/samtools/bamtk.c
231 * samtools-0.1.9-14 (r820)
232 * penalize reads with excessive differences in indel calling
234 ------------------------------------------------------------------------
235 r819 | lh3lh3 | 2010-11-12 21:36:27 -0500 (Fri, 12 Nov 2010) | 3 lines
237 M /trunk/samtools/bam_maqcns.c
238 M /trunk/samtools/bamtk.c
240 * samtools-0.1.9-13 (r819)
241 * fixed a bug in pileup given refskip
243 ------------------------------------------------------------------------
244 r818 | lh3lh3 | 2010-11-12 13:04:53 -0500 (Fri, 12 Nov 2010) | 3 lines
246 M /trunk/samtools/bam2bcf_indel.c
247 M /trunk/samtools/bamtk.c
250 * for indel calling, do two rounds of probabilistic realignments
252 ------------------------------------------------------------------------
253 r817 | lh3lh3 | 2010-11-11 20:04:07 -0500 (Thu, 11 Nov 2010) | 3 lines
255 M /trunk/samtools/bam2bcf_indel.c
256 M /trunk/samtools/bamtk.c
257 M /trunk/samtools/bcftools/vcfutils.pl
259 * samtools-0.1.19-11 (r817)
260 * only initiate indel calling when 0.2% of reads contain a gap
262 ------------------------------------------------------------------------
263 r816 | lh3lh3 | 2010-11-11 01:22:59 -0500 (Thu, 11 Nov 2010) | 7 lines
265 M /trunk/samtools/bam2bcf_indel.c
266 M /trunk/samtools/bamtk.c
268 * samtools-0.1.9-10 (r816)
270 * I know why the forward method fails. it is because of zero base
271 qualities. when that is fixed, the forward method seems to give
272 better results than Viterbi, as it should be. I am tired...
275 ------------------------------------------------------------------------
276 r815 | lh3lh3 | 2010-11-11 00:57:15 -0500 (Thu, 11 Nov 2010) | 2 lines
278 M /trunk/samtools/ChangeLog
279 M /trunk/samtools/bam2bcf_indel.c
281 effectively revert to the viterbi version. The forward realignment gives too many false positives.
283 ------------------------------------------------------------------------
284 r814 | lh3lh3 | 2010-11-11 00:18:02 -0500 (Thu, 11 Nov 2010) | 4 lines
286 M /trunk/samtools/bam2bcf_indel.c
287 M /trunk/samtools/bam_md.c
288 M /trunk/samtools/bam_plcmd.c
289 M /trunk/samtools/bamtk.c
291 * samtools-0.1.9-9 (r810)
292 * use forward, instead of viterbi, for realignment
293 * realignment is now quality aware
295 ------------------------------------------------------------------------
296 r813 | lh3lh3 | 2010-11-10 22:45:24 -0500 (Wed, 10 Nov 2010) | 2 lines
298 M /trunk/samtools/bam2bcf_indel.c
299 M /trunk/samtools/kprobaln.c
300 M /trunk/samtools/kprobaln.h
302 * prepare to replace kaln with kprobaln in realignment
304 ------------------------------------------------------------------------
305 r812 | lh3lh3 | 2010-11-10 17:28:50 -0500 (Wed, 10 Nov 2010) | 2 lines
307 M /trunk/samtools/bcftools/bcf.c
311 ------------------------------------------------------------------------
312 r811 | lh3lh3 | 2010-11-10 16:54:46 -0500 (Wed, 10 Nov 2010) | 2 lines
314 M /trunk/samtools/bcftools/bcf.c
315 M /trunk/samtools/bcftools/bcf.h
317 use zlib for direct reading when BCF_LITE is in use
319 ------------------------------------------------------------------------
320 r810 | lh3lh3 | 2010-11-10 16:32:13 -0500 (Wed, 10 Nov 2010) | 3 lines
322 M /trunk/samtools/bam2bcf_indel.c
324 * do not use reads containing too many mismatches for indel calling
325 * fixed a trivial bug in case of multi-allelic indels
327 ------------------------------------------------------------------------
328 r809 | lh3lh3 | 2010-11-10 13:23:02 -0500 (Wed, 10 Nov 2010) | 3 lines
330 M /trunk/samtools/bam2bcf.c
331 M /trunk/samtools/bam2bcf_indel.c
332 M /trunk/samtools/bam_plcmd.c
333 M /trunk/samtools/bamtk.c
335 * samtools-0.1.9-8 (r809)
336 * fixed a bug in the indel caller
338 ------------------------------------------------------------------------
339 r808 | lh3lh3 | 2010-11-10 12:24:10 -0500 (Wed, 10 Nov 2010) | 2 lines
341 M /trunk/samtools/Makefile
343 minor change to makefile
345 ------------------------------------------------------------------------
346 r807 | lh3lh3 | 2010-11-10 12:10:21 -0500 (Wed, 10 Nov 2010) | 4 lines
348 M /trunk/samtools/Makefile
349 M /trunk/samtools/bam2bcf.h
350 M /trunk/samtools/bam2bcf_indel.c
351 M /trunk/samtools/bam_plcmd.c
352 M /trunk/samtools/bamtk.c
353 M /trunk/samtools/bcftools/vcfutils.pl
355 * samtools-0.1.9-8 (r807)
356 * collect indel candidates only from specified platforms (@RG-PL)
357 * merge varFilter and filter4vcf in vcfutils.pl
359 ------------------------------------------------------------------------
360 r806 | lh3lh3 | 2010-11-09 22:05:46 -0500 (Tue, 09 Nov 2010) | 2 lines
362 M /trunk/samtools/bcftools/call1.c
363 M /trunk/samtools/bcftools/prob1.c
364 M /trunk/samtools/bcftools/prob1.h
366 bcftools: compute equal-tail (Bayesian) credible interval
368 ------------------------------------------------------------------------
369 r805 | lh3lh3 | 2010-11-09 16:28:39 -0500 (Tue, 09 Nov 2010) | 2 lines
371 M /trunk/samtools/bcftools/vcfutils.pl
373 added a double-hit filter to avoid overestimated indel likelihood
375 ------------------------------------------------------------------------
376 r804 | lh3lh3 | 2010-11-09 14:12:06 -0500 (Tue, 09 Nov 2010) | 3 lines
378 M /trunk/samtools/bam2bcf_indel.c
379 M /trunk/samtools/bamtk.c
381 * samtools-0.1.9-7 (r804)
382 * fixed a bug in the gap caller
384 ------------------------------------------------------------------------
385 r803 | lh3lh3 | 2010-11-09 10:45:33 -0500 (Tue, 09 Nov 2010) | 4 lines
387 M /trunk/samtools/bam2bcf.c
388 M /trunk/samtools/bam2bcf_indel.c
389 M /trunk/samtools/bamtk.c
390 M /trunk/samtools/bcftools/bcf.c
391 M /trunk/samtools/bcftools/bcf.h
392 M /trunk/samtools/bcftools/prob1.c
394 * samtools-0.1.9-6 (r803)
395 * mpileup: apply homopolymer correction when calculating GL, instead of before
396 * bcftools: apply a different prior to indels
398 ------------------------------------------------------------------------
399 r802 | lh3lh3 | 2010-11-08 23:53:15 -0500 (Mon, 08 Nov 2010) | 3 lines
401 M /trunk/samtools/bam2bcf.c
402 M /trunk/samtools/bamtk.c
404 * samtools-0.1.9-5 (r802)
405 * relax tandem penalty. this will be made a command-line option in future.
407 ------------------------------------------------------------------------
408 r801 | lh3lh3 | 2010-11-08 23:35:52 -0500 (Mon, 08 Nov 2010) | 3 lines
410 M /trunk/samtools/bam2bcf.c
411 M /trunk/samtools/bamtk.c
413 * samtools-0.1.9-4 (r801)
414 * fixed a minor issue in printing indel VCF
416 ------------------------------------------------------------------------
417 r800 | lh3lh3 | 2010-11-08 15:28:14 -0500 (Mon, 08 Nov 2010) | 2 lines
419 M /trunk/samtools/bam2bcf_indel.c
420 M /trunk/samtools/bcftools/vcfutils.pl
422 fixed another silly bug in mpileup's indel caller
424 ------------------------------------------------------------------------
425 r799 | lh3lh3 | 2010-11-08 14:28:27 -0500 (Mon, 08 Nov 2010) | 2 lines
427 M /trunk/samtools/bam2bcf.c
429 fixed a silly bug in the indel caller
431 ------------------------------------------------------------------------
432 r798 | lh3lh3 | 2010-11-08 14:07:33 -0500 (Mon, 08 Nov 2010) | 2 lines
434 M /trunk/samtools/ChangeLog
435 M /trunk/samtools/sam_view.c
436 M /trunk/samtools/samtools.1
438 Incorporate patches by Marcel Martin for read counting.
440 ------------------------------------------------------------------------
441 r797 | lh3lh3 | 2010-11-08 13:39:52 -0500 (Mon, 08 Nov 2010) | 3 lines
443 M /trunk/samtools/bam2bcf.c
444 M /trunk/samtools/bam2bcf.h
445 M /trunk/samtools/bam2bcf_indel.c
446 M /trunk/samtools/bam_plcmd.c
447 M /trunk/samtools/bamtk.c
449 * samtools-0.1.9-2 (r797)
450 * mpileup: indel calling seems to be working
452 ------------------------------------------------------------------------
453 r796 | lh3lh3 | 2010-11-08 10:54:46 -0500 (Mon, 08 Nov 2010) | 2 lines
455 M /trunk/samtools/bam2bcf.c
456 M /trunk/samtools/bam2bcf.h
457 M /trunk/samtools/bam2bcf_indel.c
458 M /trunk/samtools/bam_plcmd.c
459 M /trunk/samtools/kaln.c
461 indel calling is apparently working, but more information needs to be collected
463 ------------------------------------------------------------------------
464 r795 | lh3lh3 | 2010-11-08 00:39:18 -0500 (Mon, 08 Nov 2010) | 2 lines
466 M /trunk/samtools/bam2bcf.c
467 M /trunk/samtools/bam2bcf_indel.c
469 fixed a few bugs in the indel caller. Probably there are more.
471 ------------------------------------------------------------------------
472 r794 | lh3lh3 | 2010-11-07 22:23:16 -0500 (Sun, 07 Nov 2010) | 2 lines
474 M /trunk/samtools/Makefile
475 M /trunk/samtools/bam.h
476 M /trunk/samtools/bam2bcf.c
477 M /trunk/samtools/bam2bcf.h
478 A /trunk/samtools/bam2bcf_indel.c
479 M /trunk/samtools/bam_plcmd.c
480 M /trunk/samtools/kaln.c
481 M /trunk/samtools/kaln.h
483 prepare for the indel caller. It is not ready yet.
485 ------------------------------------------------------------------------
486 r793 | lh3lh3 | 2010-11-05 11:28:23 -0400 (Fri, 05 Nov 2010) | 2 lines
488 M /trunk/samtools/bam2bcf.c
489 M /trunk/samtools/bam2bcf.h
490 M /trunk/samtools/bam_plcmd.c
492 Revert to r790. The recent changes are not good...
494 ------------------------------------------------------------------------
495 r792 | lh3lh3 | 2010-11-05 00:19:14 -0400 (Fri, 05 Nov 2010) | 6 lines
497 M /trunk/samtools/bam2bcf.c
498 M /trunk/samtools/bam2bcf.h
499 M /trunk/samtools/bam_plcmd.c
501 * this revision is UNSTABLE
503 * indel caller seems working, but it is very insensitive and has
504 several things I do not quite understand.
507 ------------------------------------------------------------------------
508 r791 | lh3lh3 | 2010-11-04 22:58:43 -0400 (Thu, 04 Nov 2010) | 2 lines
510 M /trunk/samtools/bam2bcf.c
511 M /trunk/samtools/bam2bcf.h
512 M /trunk/samtools/bam_plcmd.c
514 for backup. no effective changes
516 ------------------------------------------------------------------------
517 r790 | lh3lh3 | 2010-11-03 15:51:24 -0400 (Wed, 03 Nov 2010) | 2 lines
519 M /trunk/samtools/bcftools/vcfutils.pl
520 M /trunk/samtools/kprobaln.c
522 fixed a minor problem in the example coming with kprobaln.c
524 ------------------------------------------------------------------------
525 r789 | lh3lh3 | 2010-11-02 15:41:27 -0400 (Tue, 02 Nov 2010) | 4 lines
527 M /trunk/samtools/Makefile
528 M /trunk/samtools/bam_md.c
529 M /trunk/samtools/kaln.c
530 M /trunk/samtools/kaln.h
531 A /trunk/samtools/kprobaln.c
532 A /trunk/samtools/kprobaln.h
534 Separate kaln and kprobaln as I am preparing further changes. At
535 present, the results should be identical to the previous.
538 ------------------------------------------------------------------------
539 r788 | petulda | 2010-11-02 12:19:04 -0400 (Tue, 02 Nov 2010) | 1 line
541 M /trunk/samtools/bam_plcmd.c
543 Added -b option: read file names from a file
544 ------------------------------------------------------------------------
545 r787 | lh3lh3 | 2010-10-29 23:17:22 -0400 (Fri, 29 Oct 2010) | 7 lines
547 M /trunk/samtools/bam.h
548 M /trunk/samtools/bam_pileup.c
549 M /trunk/samtools/bam_plcmd.c
550 M /trunk/samtools/bamtk.c
552 * samtools-0.1.9-2 (r787)
554 * Allow to set a maximum per-sample depth to reduce memory. However,
555 BAQ computation is still applied to every read. The speed is not
559 ------------------------------------------------------------------------
560 r786 | lh3lh3 | 2010-10-29 12:10:40 -0400 (Fri, 29 Oct 2010) | 3 lines
562 M /trunk/samtools/bam2bcf.c
563 M /trunk/samtools/bam2bcf.h
564 M /trunk/samtools/bam_plcmd.c
565 M /trunk/samtools/bamtk.c
566 M /trunk/samtools/bcftools/bcf.c
567 M /trunk/samtools/bcftools/vcf.c
569 * samtools-0.1.9-1 (r786)
570 * samtools: optionally perform exact test for each sample
572 ------------------------------------------------------------------------
573 r785 | lh3lh3 | 2010-10-29 09:42:25 -0400 (Fri, 29 Oct 2010) | 2 lines
575 M /trunk/samtools/bam2bcf.c
576 M /trunk/samtools/bam2bcf.h
577 M /trunk/samtools/bam_plcmd.c
578 M /trunk/samtools/bcftools/bcf.c
580 Optionally output "DP", the individual read depth
582 ------------------------------------------------------------------------
583 r784 | lh3lh3 | 2010-10-27 23:10:27 -0400 (Wed, 27 Oct 2010) | 2 lines
585 M /trunk/samtools/samtools.1
587 acknowledge Petr and John who have greatly contributed to the project.
589 ------------------------------------------------------------------------
590 r783 | lh3lh3 | 2010-10-27 22:47:47 -0400 (Wed, 27 Oct 2010) | 2 lines
592 M /trunk/samtools/ChangeLog
593 M /trunk/samtools/NEWS
594 M /trunk/samtools/bamtk.c
595 M /trunk/samtools/samtools.1
597 Release samtools-0.1.9 (r783)
599 ------------------------------------------------------------------------
600 r782 | lh3lh3 | 2010-10-27 19:58:54 -0400 (Wed, 27 Oct 2010) | 2 lines
602 M /trunk/samtools/bam_plcmd.c
604 fixed a silly bug in pileup
606 ------------------------------------------------------------------------
607 r781 | lh3lh3 | 2010-10-27 14:39:48 -0400 (Wed, 27 Oct 2010) | 5 lines
609 M /trunk/samtools/ChangeLog
610 M /trunk/samtools/bam_plcmd.c
611 M /trunk/samtools/bam_sort.c
612 M /trunk/samtools/bamtk.c
613 M /trunk/samtools/samtools.1
615 * samtools-0.1.8-22 (r781)
616 * made BAQ the default behavior of mpileup
618 * in merge, force to exit given inconsistent header when "-R" is not in use.
620 ------------------------------------------------------------------------
621 r780 | lh3lh3 | 2010-10-27 11:01:11 -0400 (Wed, 27 Oct 2010) | 3 lines
623 M /trunk/samtools/bam.h
624 M /trunk/samtools/bam_plcmd.c
625 M /trunk/samtools/bamtk.c
627 * samtools-0.1.8-21 (r780)
628 * minor speedup to pileup
630 ------------------------------------------------------------------------
631 r779 | lh3lh3 | 2010-10-27 09:58:56 -0400 (Wed, 27 Oct 2010) | 2 lines
633 M /trunk/samtools/bam_pileup.c
634 M /trunk/samtools/bam_plcmd.c
635 M /trunk/samtools/examples/toy.sam
637 improve pileup a little bit
639 ------------------------------------------------------------------------
640 r778 | lh3lh3 | 2010-10-27 00:14:43 -0400 (Wed, 27 Oct 2010) | 3 lines
642 M /trunk/samtools/bam.h
643 M /trunk/samtools/bam_pileup.c
644 M /trunk/samtools/bam_plcmd.c
645 M /trunk/samtools/bam_tview.c
646 M /trunk/samtools/bamtk.c
648 * samtools-0.1.8-20 (r778)
649 * speed up pileup, although I do not know how much is the improvement
651 ------------------------------------------------------------------------
652 r777 | lh3lh3 | 2010-10-26 17:26:04 -0400 (Tue, 26 Oct 2010) | 3 lines
654 M /trunk/samtools/bam_maqcns.c
655 M /trunk/samtools/bam_maqcns.h
656 M /trunk/samtools/bam_plcmd.c
657 M /trunk/samtools/bamtk.c
658 M /trunk/samtools/examples/Makefile
660 * samtools-0.1.8-19 (r777)
661 * integrate mpileup features to pileup: min_baseQ, capQ, prob_realn, paired-only and biased prior
663 ------------------------------------------------------------------------
664 r776 | lh3lh3 | 2010-10-26 15:27:46 -0400 (Tue, 26 Oct 2010) | 2 lines
666 M /trunk/samtools/bam_md.c
668 remove local realignment (probabilistic realignment is still there)
670 ------------------------------------------------------------------------
671 r774 | jmarshall | 2010-10-21 06:52:38 -0400 (Thu, 21 Oct 2010) | 3 lines
673 M /trunk/samtools/sam_view.c
675 Add the relevant filename or region to error messages, and cause a failure
676 exit status where appropriate. Based on a patch provided by Marcel Martin.
678 ------------------------------------------------------------------------
679 r773 | lh3lh3 | 2010-10-19 19:44:31 -0400 (Tue, 19 Oct 2010) | 3 lines
681 M /trunk/samtools/examples/toy.sam
682 M /trunk/samtools/kaln.c
684 * Minor code changes. No real effect.
685 * change quality to 30 in toy.sam
687 ------------------------------------------------------------------------
688 r772 | lh3lh3 | 2010-10-18 23:40:13 -0400 (Mon, 18 Oct 2010) | 2 lines
690 M /trunk/samtools/examples/toy.fa
691 M /trunk/samtools/examples/toy.sam
693 added another toy example
695 ------------------------------------------------------------------------
696 r771 | lh3lh3 | 2010-10-13 23:32:12 -0400 (Wed, 13 Oct 2010) | 2 lines
698 M /trunk/samtools/bcftools/call1.c
699 M /trunk/samtools/bcftools/ld.c
700 M /trunk/samtools/bcftools/vcfutils.pl
702 improve the LD statistics
704 ------------------------------------------------------------------------
705 r770 | lh3lh3 | 2010-10-12 23:49:26 -0400 (Tue, 12 Oct 2010) | 3 lines
707 M /trunk/samtools/bcftools/call1.c
708 M /trunk/samtools/bcftools/vcfutils.pl
710 * a minor fix to the -L option
711 * add ldstats to vcfutils.pl
713 ------------------------------------------------------------------------
714 r769 | lh3lh3 | 2010-10-12 15:51:57 -0400 (Tue, 12 Oct 2010) | 2 lines
716 M /trunk/samtools/bcftools/bcf.c
720 ------------------------------------------------------------------------
721 r768 | lh3lh3 | 2010-10-12 15:49:06 -0400 (Tue, 12 Oct 2010) | 2 lines
723 M /trunk/samtools/bcftools/Makefile
724 A /trunk/samtools/bcftools/ld.c
726 forget to add the key file
728 ------------------------------------------------------------------------
729 r767 | lh3lh3 | 2010-10-12 15:48:46 -0400 (Tue, 12 Oct 2010) | 4 lines
731 M /trunk/samtools/bcftools/Makefile
732 M /trunk/samtools/bcftools/bcf.c
733 M /trunk/samtools/bcftools/bcf.h
734 M /trunk/samtools/bcftools/call1.c
735 M /trunk/samtools/bcftools/prob1.c
736 M /trunk/samtools/bcftools/vcfutils.pl
738 * vcfutils.pl: fixed a typo in help message
739 * added APIs: bcf_append_info() and bcf_cpy()
740 * calculate adjacent LD
742 ------------------------------------------------------------------------
743 r766 | lh3lh3 | 2010-10-11 11:06:40 -0400 (Mon, 11 Oct 2010) | 2 lines
745 M /trunk/samtools/bcftools/vcfutils.pl
747 added filter for samtools/bcftools genetated VCFs
749 ------------------------------------------------------------------------
750 r765 | lh3lh3 | 2010-10-05 14:05:18 -0400 (Tue, 05 Oct 2010) | 3 lines
752 M /trunk/samtools/bcftools/vcfutils.pl
753 M /trunk/samtools/kaln.c
755 * removed a comment line in kaln.c
756 * vcfutils.pl fillac works when GT is not the first field
758 ------------------------------------------------------------------------
759 r764 | petulda | 2010-10-05 08:59:36 -0400 (Tue, 05 Oct 2010) | 1 line
761 A /trunk/samtools/bcftools/bcf-fix.pl
763 Convert VCF output of "bcftools view -bgcv" to a valid VCF file
764 ------------------------------------------------------------------------
765 r763 | lh3lh3 | 2010-10-02 22:51:03 -0400 (Sat, 02 Oct 2010) | 4 lines
767 M /trunk/samtools/bam_plcmd.c
768 M /trunk/samtools/bamtk.c
769 A /trunk/samtools/bcftools/bcftools.1
770 M /trunk/samtools/bcftools/call1.c
771 M /trunk/samtools/samtools.1
773 * samtools-0.1.8-18 (r763)
774 * added bcftools manual page
775 * minor fix to mpileup and view command lines
777 ------------------------------------------------------------------------
778 r762 | lh3lh3 | 2010-10-02 21:46:25 -0400 (Sat, 02 Oct 2010) | 3 lines
780 M /trunk/samtools/bcftools/bcf.c
781 M /trunk/samtools/bcftools/call1.c
782 M /trunk/samtools/bcftools/vcfutils.pl
784 * vcfutils.pl qstats: calculate marginal ts/tv
785 * allow to call genotypes at variant sites
787 ------------------------------------------------------------------------
788 r761 | lh3lh3 | 2010-10-01 00:29:55 -0400 (Fri, 01 Oct 2010) | 3 lines
790 M /trunk/samtools/kaln.c
791 M /trunk/samtools/misc/HmmGlocal.java
793 I am changing the gap open probability back to 0.001. It seems that
794 being conservative here is a good thing...
796 ------------------------------------------------------------------------
797 r760 | lh3lh3 | 2010-10-01 00:11:27 -0400 (Fri, 01 Oct 2010) | 5 lines
799 M /trunk/samtools/bamtk.c
800 M /trunk/samtools/kaln.c
801 A /trunk/samtools/misc/HmmGlocal.java
803 * samtools-0.1.8-17 (r760)
804 * the default gap open penalty is too small (a typo)
805 * added comments on hmm_realn
806 * Java implementation
808 ------------------------------------------------------------------------
809 r759 | lh3lh3 | 2010-09-30 10:12:54 -0400 (Thu, 30 Sep 2010) | 2 lines
811 M /trunk/samtools/bamtk.c
813 mark samtools-0.1.8-16 (r759)
815 ------------------------------------------------------------------------
816 r758 | lh3lh3 | 2010-09-30 10:12:02 -0400 (Thu, 30 Sep 2010) | 2 lines
818 M /trunk/samtools/kaln.c
820 round to the nearest integer
822 ------------------------------------------------------------------------
823 r757 | lh3lh3 | 2010-09-28 17:16:43 -0400 (Tue, 28 Sep 2010) | 4 lines
825 M /trunk/samtools/kaln.c
827 I was trying to accelerate ka_prob_glocal() as this will be the
828 bottleneck. After an hour, the only gain is to change division to
829 multiplication. OK. I will stop.
831 ------------------------------------------------------------------------
832 r756 | lh3lh3 | 2010-09-28 16:57:49 -0400 (Tue, 28 Sep 2010) | 2 lines
834 M /trunk/samtools/kaln.c
836 this is interesting. multiplication is much faster than division, at least on my Mac
838 ------------------------------------------------------------------------
839 r755 | lh3lh3 | 2010-09-28 16:19:13 -0400 (Tue, 28 Sep 2010) | 2 lines
841 M /trunk/samtools/kaln.c
845 ------------------------------------------------------------------------
846 r754 | lh3lh3 | 2010-09-28 15:44:16 -0400 (Tue, 28 Sep 2010) | 2 lines
848 M /trunk/samtools/bam_md.c
849 M /trunk/samtools/bam_plcmd.c
850 M /trunk/samtools/kaln.c
852 prob_realn() seems working!
854 ------------------------------------------------------------------------
855 r753 | lh3lh3 | 2010-09-28 12:48:23 -0400 (Tue, 28 Sep 2010) | 2 lines
857 M /trunk/samtools/kaln.c
861 ------------------------------------------------------------------------
862 r752 | lh3lh3 | 2010-09-28 12:47:41 -0400 (Tue, 28 Sep 2010) | 2 lines
864 M /trunk/samtools/kaln.c
865 M /trunk/samtools/kaln.h
867 Convert phredQ to probabilities
869 ------------------------------------------------------------------------
870 r751 | lh3lh3 | 2010-09-28 12:32:08 -0400 (Tue, 28 Sep 2010) | 2 lines
872 M /trunk/samtools/kaln.c
873 M /trunk/samtools/kaln.h
875 Implement the glocal HMM; discard the extention HMM
877 ------------------------------------------------------------------------
878 r750 | lh3lh3 | 2010-09-28 00:06:11 -0400 (Tue, 28 Sep 2010) | 2 lines
880 M /trunk/samtools/kaln.c
882 improve numerical stability
884 ------------------------------------------------------------------------
885 r749 | lh3lh3 | 2010-09-27 23:27:54 -0400 (Mon, 27 Sep 2010) | 2 lines
887 M /trunk/samtools/kaln.c
891 ------------------------------------------------------------------------
892 r748 | lh3lh3 | 2010-09-27 23:17:16 -0400 (Mon, 27 Sep 2010) | 2 lines
894 M /trunk/samtools/kaln.c
896 fixed a bug in banded DP
898 ------------------------------------------------------------------------
899 r747 | lh3lh3 | 2010-09-27 23:05:12 -0400 (Mon, 27 Sep 2010) | 3 lines
901 M /trunk/samtools/kaln.c
903 * fixed that weird issue.
904 * the banded version is NOT working
906 ------------------------------------------------------------------------
907 r746 | lh3lh3 | 2010-09-27 22:57:05 -0400 (Mon, 27 Sep 2010) | 2 lines
909 M /trunk/samtools/kaln.c
911 More comments. This version seems working, but something is a little weird...
913 ------------------------------------------------------------------------
914 r745 | lh3lh3 | 2010-09-27 17:21:40 -0400 (Mon, 27 Sep 2010) | 6 lines
916 M /trunk/samtools/kaln.c
918 A little code cleanup. Now the forward and backback algorithms give
919 nearly identical P(x), which means both are close to the correct
920 forms. However, I have only tested on toy examples. Minor errors in
921 the implementation may not be obvious.
924 ------------------------------------------------------------------------
925 r744 | lh3lh3 | 2010-09-27 16:55:15 -0400 (Mon, 27 Sep 2010) | 2 lines
927 M /trunk/samtools/bam_plcmd.c
928 M /trunk/samtools/bam_sort.c
929 M /trunk/samtools/kaln.c
930 M /trunk/samtools/kaln.h
934 ------------------------------------------------------------------------
935 r743 | jmarshall | 2010-09-27 08:19:06 -0400 (Mon, 27 Sep 2010) | 6 lines
937 M /trunk/samtools/bam_sort.c
939 Abort if merge -h's INH.SAM cannot be opened, just as we abort
940 if any of the IN#.BAM input files cannot be opened.
942 Also propagate any error indication returned by bam_merge_core()
943 to samtools merge's exit status.
945 ------------------------------------------------------------------------
946 r741 | jmarshall | 2010-09-24 11:08:24 -0400 (Fri, 24 Sep 2010) | 5 lines
948 M /trunk/samtools/bam_index.c
950 Use bam_validate1() to detect garbage records in the event of a corrupt
951 BAI index file that causes a bam_seek() to an invalid position. At most
952 one record (namely, the bam_iter_read terminator) is tested per bam_fetch()
953 call, so the cost is insignificant in the normal case.
955 ------------------------------------------------------------------------
956 r740 | jmarshall | 2010-09-24 11:00:19 -0400 (Fri, 24 Sep 2010) | 2 lines
958 M /trunk/samtools/bam.c
959 M /trunk/samtools/bam.h
963 ------------------------------------------------------------------------
964 r739 | lh3lh3 | 2010-09-22 12:07:50 -0400 (Wed, 22 Sep 2010) | 3 lines
966 M /trunk/samtools/bam_md.c
967 M /trunk/samtools/bamtk.c
969 * samtools-0.1.8-15 (r379)
970 * allow to change capQ parameter in calmd
972 ------------------------------------------------------------------------
973 r738 | jmarshall | 2010-09-22 11:15:33 -0400 (Wed, 22 Sep 2010) | 13 lines
975 M /trunk/samtools/bam_index.c
976 M /trunk/samtools/sam_view.c
978 When bam_read1() returns an error (return value <= -2), propagate that error
979 to bam_iter_read()'s own return value. Similarly, also propagate it up to
980 bam_fetch()'s return value. Previously bam_fetch() always returned 0, and
981 callers ignored its return value anyway. With this change, 0 continues to
982 indicate success, while <= -2 (which can be written as < 0, as -1 is never
983 returned) indicates corrupted input.
985 bam_iter_read() ought also to propagate errors returned by bam_seek().
987 main_samview() can now print an error message and fail when bam_fetch()
988 detects that a .bai index file is corrupted or otherwise does not correspond
989 to the .bam file it is being used with.
991 ------------------------------------------------------------------------
992 r737 | jmarshall | 2010-09-22 10:47:42 -0400 (Wed, 22 Sep 2010) | 3 lines
994 M /trunk/samtools/bam_index.c
996 0 is a successful return value from bam_read1(). (In practice, it never
997 returns 0 anyway; but all the other callers treat 0 as successful.)
999 ------------------------------------------------------------------------
1000 r736 | lh3lh3 | 2010-09-20 17:43:08 -0400 (Mon, 20 Sep 2010) | 2 lines
1002 M /trunk/samtools/bam.h
1003 M /trunk/samtools/bam_index.c
1004 M /trunk/samtools/bam_sort.c
1006 * merge files region-by-region. work on small examples but more tests are needed.
1008 ------------------------------------------------------------------------
1009 r735 | lh3lh3 | 2010-09-20 16:56:24 -0400 (Mon, 20 Sep 2010) | 2 lines
1011 M /trunk/samtools/bcftools/vcfutils.pl
1013 improve qstats by checking the alleles as well
1015 ------------------------------------------------------------------------
1016 r734 | lh3lh3 | 2010-09-17 18:12:13 -0400 (Fri, 17 Sep 2010) | 2 lines
1018 M /trunk/samtools/bcftools/vcfutils.pl
1020 convert UCSC SNP SQL dump to VCF
1022 ------------------------------------------------------------------------
1023 r733 | lh3lh3 | 2010-09-17 13:02:11 -0400 (Fri, 17 Sep 2010) | 2 lines
1025 M /trunk/samtools/bcftools/vcfutils.pl
1027 hapmap2vcf convertor
1029 ------------------------------------------------------------------------
1030 r732 | lh3lh3 | 2010-09-17 10:11:37 -0400 (Fri, 17 Sep 2010) | 3 lines
1032 M /trunk/samtools/bcftools/Makefile
1033 M /trunk/samtools/bcftools/bcf.c
1034 M /trunk/samtools/bcftools/bcf.h
1035 M /trunk/samtools/bcftools/vcf.c
1038 * VCF->BCF is not possible without knowing the sequence dictionary before hand...
1040 ------------------------------------------------------------------------
1041 r731 | lh3lh3 | 2010-09-17 09:15:53 -0400 (Fri, 17 Sep 2010) | 2 lines
1043 M /trunk/samtools/bam2bcf.c
1044 M /trunk/samtools/bcftools/bcf.c
1045 M /trunk/samtools/bcftools/bcf.h
1046 M /trunk/samtools/bcftools/bcfutils.c
1047 M /trunk/samtools/bcftools/call1.c
1048 M /trunk/samtools/bcftools/vcf.c
1050 * put n_smpl to "bcf1_t" to simplify API a little
1052 ------------------------------------------------------------------------
1053 r730 | lh3lh3 | 2010-09-16 21:36:01 -0400 (Thu, 16 Sep 2010) | 2 lines
1055 M /trunk/samtools/bcftools/bcf.h
1056 M /trunk/samtools/bcftools/call1.c
1057 M /trunk/samtools/bcftools/index.c
1059 fixed a bug in indexing
1061 ------------------------------------------------------------------------
1062 r729 | lh3lh3 | 2010-09-16 16:54:48 -0400 (Thu, 16 Sep 2010) | 3 lines
1064 M /trunk/samtools/bam.c
1065 M /trunk/samtools/bam_md.c
1066 M /trunk/samtools/bam_pileup.c
1068 * fixed a bug in capQ
1069 * valgrind identifies a use of uninitialised value, but I have not fixed it.
1071 ------------------------------------------------------------------------
1072 r728 | lh3lh3 | 2010-09-16 15:03:59 -0400 (Thu, 16 Sep 2010) | 3 lines
1074 M /trunk/samtools/bgzip.c
1075 M /trunk/samtools/razip.c
1077 * fixed a bug in razip: -c will delete the input file
1078 * copy tabix/bgzip to here
1080 ------------------------------------------------------------------------
1081 r727 | lh3lh3 | 2010-09-16 13:45:49 -0400 (Thu, 16 Sep 2010) | 3 lines
1083 M /trunk/samtools/bam_md.c
1084 M /trunk/samtools/bam_plcmd.c
1085 M /trunk/samtools/bamtk.c
1087 * samtools-0.1.8-14 (r727)
1088 * allow to change the capQ parameter at the command line
1090 ------------------------------------------------------------------------
1091 r726 | lh3lh3 | 2010-09-16 13:38:43 -0400 (Thu, 16 Sep 2010) | 4 lines
1093 M /trunk/samtools/bam_md.c
1094 M /trunk/samtools/bam_plcmd.c
1095 M /trunk/samtools/bcftools/vcfutils.pl
1096 M /trunk/samtools/misc/samtools.pl
1098 * added varFilter to vcfutils.pl
1099 * reimplement realn(). now it performs a local alignment
1100 * added cap_mapQ() to cap mapping quality when there are many substitutions
1102 ------------------------------------------------------------------------
1103 r724 | lh3lh3 | 2010-09-15 00:18:31 -0400 (Wed, 15 Sep 2010) | 2 lines
1105 M /trunk/samtools/bcftools/Makefile
1106 A /trunk/samtools/bcftools/bcf2qcall.c
1107 M /trunk/samtools/bcftools/call1.c
1109 * convert BCF to QCALL input
1111 ------------------------------------------------------------------------
1112 r723 | lh3lh3 | 2010-09-14 22:41:50 -0400 (Tue, 14 Sep 2010) | 2 lines
1114 M /trunk/samtools/bam_md.c
1116 dynamic band width in realignment
1118 ------------------------------------------------------------------------
1119 r722 | lh3lh3 | 2010-09-14 22:05:32 -0400 (Tue, 14 Sep 2010) | 2 lines
1121 M /trunk/samtools/bam_md.c
1122 M /trunk/samtools/bam_plcmd.c
1124 fixed a bug in realignment
1126 ------------------------------------------------------------------------
1127 r721 | lh3lh3 | 2010-09-14 20:54:09 -0400 (Tue, 14 Sep 2010) | 2 lines
1129 M /trunk/samtools/bcftools/prob1.c
1133 ------------------------------------------------------------------------
1134 r720 | lh3lh3 | 2010-09-14 19:25:10 -0400 (Tue, 14 Sep 2010) | 2 lines
1136 M /trunk/samtools/Makefile
1137 M /trunk/samtools/bam_maqcns.c
1138 M /trunk/samtools/bam_md.c
1140 fixed a bug in realignment
1142 ------------------------------------------------------------------------
1143 r719 | lh3lh3 | 2010-09-14 19:18:24 -0400 (Tue, 14 Sep 2010) | 2 lines
1145 M /trunk/samtools/bam_plcmd.c
1147 minor changes. It is BUGGY now!
1149 ------------------------------------------------------------------------
1150 r718 | lh3lh3 | 2010-09-14 16:32:33 -0400 (Tue, 14 Sep 2010) | 4 lines
1152 M /trunk/samtools/bam_md.c
1153 M /trunk/samtools/bam_pileup.c
1154 M /trunk/samtools/kaln.c
1155 M /trunk/samtools/kaln.h
1157 * aggressive gapped aligner is implemented in calmd.
1158 * distinguish gap_open and gap_end_open in banded alignment
1159 * make tview accepts alignment with heading and tailing D
1161 ------------------------------------------------------------------------
1162 r717 | jmarshall | 2010-09-14 09:04:28 -0400 (Tue, 14 Sep 2010) | 2 lines
1166 Add svn:ignore properties for generated files that don't appear in "make all".
1168 ------------------------------------------------------------------------
1169 r716 | jmarshall | 2010-09-13 08:37:53 -0400 (Mon, 13 Sep 2010) | 3 lines
1172 M /trunk/samtools/bcftools
1173 M /trunk/samtools/misc
1175 Add svn:ignore properties listing the generated files.
1176 (Except for *.o, which we'll assume is in global-ignores.)
1178 ------------------------------------------------------------------------
1179 r715 | lh3lh3 | 2010-09-08 12:53:55 -0400 (Wed, 08 Sep 2010) | 5 lines
1181 M /trunk/samtools/bamtk.c
1182 M /trunk/samtools/bcftools/call1.c
1183 M /trunk/samtools/bcftools/prob1.c
1184 M /trunk/samtools/sample.c
1185 M /trunk/samtools/sample.h
1187 * samtools-0.1.8-13 (r715)
1188 * fixed a bug in identifying SM across files
1189 * bcftools: estimate heterozygosity
1190 * bcftools: allow to skip sites without reference bases
1192 ------------------------------------------------------------------------
1193 r713 | lh3lh3 | 2010-09-03 17:19:12 -0400 (Fri, 03 Sep 2010) | 2 lines
1195 M /trunk/samtools/bcftools/Makefile
1196 M /trunk/samtools/bcftools/call1.c
1197 M /trunk/samtools/bcftools/prob1.c
1198 M /trunk/samtools/bcftools/prob1.h
1200 quite a lot changes to the contrast caller, but I still feel something is missing...
1202 ------------------------------------------------------------------------
1203 r711 | lh3lh3 | 2010-09-03 00:30:48 -0400 (Fri, 03 Sep 2010) | 4 lines
1205 M /trunk/samtools/bcftools/Makefile
1206 M /trunk/samtools/bcftools/call1.c
1207 M /trunk/samtools/bcftools/prob1.c
1208 M /trunk/samtools/bcftools/vcfutils.pl
1210 * changed 3.434 to 4.343 (typo!)
1211 * fixed a bug in the contrast caller
1212 * calculate heterozygosity
1214 ------------------------------------------------------------------------
1215 r710 | lh3lh3 | 2010-09-01 23:24:47 -0400 (Wed, 01 Sep 2010) | 2 lines
1217 M /trunk/samtools/bcftools/bcf.h
1218 M /trunk/samtools/bcftools/bcfutils.c
1219 M /trunk/samtools/bcftools/call1.c
1221 SNP calling from the GL field
1223 ------------------------------------------------------------------------
1224 r709 | lh3lh3 | 2010-09-01 18:52:30 -0400 (Wed, 01 Sep 2010) | 2 lines
1226 M /trunk/samtools/bcftools/vcf.c
1228 fixed another problem
1230 ------------------------------------------------------------------------
1231 r708 | lh3lh3 | 2010-09-01 18:31:17 -0400 (Wed, 01 Sep 2010) | 3 lines
1233 M /trunk/samtools/bcftools/bcf.c
1234 M /trunk/samtools/bcftools/vcf.c
1236 * fixed bugs in parsing VCF
1237 * parser now works with GT/GQ/DP/PL/GL
1239 ------------------------------------------------------------------------
1240 r707 | lh3lh3 | 2010-09-01 15:28:29 -0400 (Wed, 01 Sep 2010) | 2 lines
1242 M /trunk/samtools/bcftools/Makefile
1243 M /trunk/samtools/bcftools/prob1.c
1245 Do not compile _BCF_QUAD by default
1247 ------------------------------------------------------------------------
1248 r706 | lh3lh3 | 2010-09-01 15:21:41 -0400 (Wed, 01 Sep 2010) | 2 lines
1250 M /trunk/samtools/bcftools/bcf.c
1251 M /trunk/samtools/bcftools/bcf.h
1252 M /trunk/samtools/bcftools/bcfutils.c
1253 M /trunk/samtools/bcftools/call1.c
1255 Write the correct ALT and PL in the SNP calling mode.
1257 ------------------------------------------------------------------------
1258 r705 | lh3lh3 | 2010-09-01 12:50:33 -0400 (Wed, 01 Sep 2010) | 2 lines
1260 M /trunk/samtools/bcftools/vcfutils.pl
1262 more commands for my own uses
1264 ------------------------------------------------------------------------
1265 r704 | lh3lh3 | 2010-09-01 09:26:10 -0400 (Wed, 01 Sep 2010) | 2 lines
1267 A /trunk/samtools/bcftools/vcfutils.pl
1269 Utilities for processing VCF
1271 ------------------------------------------------------------------------
1272 r703 | lh3lh3 | 2010-08-31 16:44:57 -0400 (Tue, 31 Aug 2010) | 2 lines
1274 M /trunk/samtools/bcftools/Makefile
1275 M /trunk/samtools/bcftools/call1.c
1276 M /trunk/samtools/bcftools/prob1.c
1277 M /trunk/samtools/bcftools/prob1.h
1279 preliminary contrast variant caller
1281 ------------------------------------------------------------------------
1282 r702 | lh3lh3 | 2010-08-31 12:28:39 -0400 (Tue, 31 Aug 2010) | 2 lines
1284 M /trunk/samtools/bcftools/call1.c
1285 M /trunk/samtools/bcftools/prob1.c
1286 M /trunk/samtools/bcftools/prob1.h
1288 z' and z'' can be calculated
1290 ------------------------------------------------------------------------
1291 r701 | lh3lh3 | 2010-08-31 10:20:57 -0400 (Tue, 31 Aug 2010) | 3 lines
1293 M /trunk/samtools/bcftools/Makefile
1294 A /trunk/samtools/bcftools/call1.c (from /trunk/samtools/bcftools/vcfout.c:699)
1295 M /trunk/samtools/bcftools/prob1.c
1296 D /trunk/samtools/bcftools/vcfout.c
1298 * rename vcfout.c as call1.c
1299 * prepare to add two-sample comparison
1301 ------------------------------------------------------------------------
1302 r699 | lh3lh3 | 2010-08-24 15:28:16 -0400 (Tue, 24 Aug 2010) | 2 lines
1304 M /trunk/samtools/bcftools/vcfout.c
1306 fixed a bug in calculating the t statistics
1308 ------------------------------------------------------------------------
1309 r698 | lh3lh3 | 2010-08-24 14:05:50 -0400 (Tue, 24 Aug 2010) | 3 lines
1311 M /trunk/samtools/bam2bcf.c
1312 M /trunk/samtools/bam2bcf.h
1313 M /trunk/samtools/bamtk.c
1314 M /trunk/samtools/bcftools/kfunc.c
1315 M /trunk/samtools/bcftools/vcfout.c
1317 * samtools-0.1.8-13 (r698)
1318 * perform one-tailed t-test for baseQ, mapQ and endDist
1320 ------------------------------------------------------------------------
1321 r697 | lh3lh3 | 2010-08-24 12:30:13 -0400 (Tue, 24 Aug 2010) | 2 lines
1323 M /trunk/samtools/bcftools/kfunc.c
1325 added regularized incomplete beta function
1327 ------------------------------------------------------------------------
1328 r695 | lh3lh3 | 2010-08-23 17:36:17 -0400 (Mon, 23 Aug 2010) | 2 lines
1330 M /trunk/samtools/bam_maqcns.c
1331 M /trunk/samtools/bam_plcmd.c
1333 change the default correlation coefficient
1335 ------------------------------------------------------------------------
1336 r694 | lh3lh3 | 2010-08-23 14:46:52 -0400 (Mon, 23 Aug 2010) | 2 lines
1338 M /trunk/samtools/bcftools/bcf.c
1339 M /trunk/samtools/bcftools/vcfout.c
1341 print QUAL as floating numbers
1343 ------------------------------------------------------------------------
1344 r693 | lh3lh3 | 2010-08-23 14:06:07 -0400 (Mon, 23 Aug 2010) | 3 lines
1346 M /trunk/samtools/Makefile
1347 M /trunk/samtools/bam_plcmd.c
1348 M /trunk/samtools/bamtk.c
1349 M /trunk/samtools/examples/Makefile
1350 A /trunk/samtools/sample.c
1351 A /trunk/samtools/sample.h
1353 * samtools-0.1.8-12 (r692)
1354 * group data by samples in "mpileup -g"
1356 ------------------------------------------------------------------------
1357 r692 | lh3lh3 | 2010-08-23 10:58:53 -0400 (Mon, 23 Aug 2010) | 2 lines
1359 M /trunk/samtools/Makefile
1360 D /trunk/samtools/bam_mcns.c
1361 D /trunk/samtools/bam_mcns.h
1362 M /trunk/samtools/bam_plcmd.c
1364 remove VCF output in mpileup
1366 ------------------------------------------------------------------------
1367 r691 | lh3lh3 | 2010-08-23 10:48:20 -0400 (Mon, 23 Aug 2010) | 3 lines
1369 M /trunk/samtools/bam2bcf.c
1370 M /trunk/samtools/bam2bcf.h
1372 * use the revised MAQ error model for mpileup
1373 * prepare to remove the independent model from mpileup
1375 ------------------------------------------------------------------------
1376 r690 | lh3lh3 | 2010-08-20 15:46:40 -0400 (Fri, 20 Aug 2010) | 2 lines
1378 M /trunk/samtools/Makefile
1379 M /trunk/samtools/bam_maqcns.c
1380 M /trunk/samtools/bam_maqcns.h
1381 M /trunk/samtools/bam_plcmd.c
1382 A /trunk/samtools/errmod.c
1383 A /trunk/samtools/errmod.h
1384 M /trunk/samtools/ksort.h
1386 added revised MAQ error model
1388 ------------------------------------------------------------------------
1389 r689 | lh3lh3 | 2010-08-18 09:55:20 -0400 (Wed, 18 Aug 2010) | 2 lines
1391 M /trunk/samtools/bcftools/prob1.c
1392 M /trunk/samtools/bcftools/prob1.h
1393 M /trunk/samtools/bcftools/vcfout.c
1395 allow to read the prior from the error output. EM iteration is working.
1397 ------------------------------------------------------------------------
1398 r688 | lh3lh3 | 2010-08-17 12:12:20 -0400 (Tue, 17 Aug 2010) | 3 lines
1400 M /trunk/samtools/bcftools/main.c
1401 M /trunk/samtools/bcftools/vcf.c
1403 * write a little more VCF header
1406 ------------------------------------------------------------------------
1407 r687 | lh3lh3 | 2010-08-16 20:53:16 -0400 (Mon, 16 Aug 2010) | 2 lines
1409 M /trunk/samtools/bcftools/bcf.c
1410 M /trunk/samtools/bcftools/bcf.h
1411 M /trunk/samtools/bcftools/bcf.tex
1415 ------------------------------------------------------------------------
1416 r686 | lh3lh3 | 2010-08-14 00:11:13 -0400 (Sat, 14 Aug 2010) | 2 lines
1418 M /trunk/samtools/bcftools/bcf.c
1419 M /trunk/samtools/bcftools/prob1.c
1421 faster for large sample size (in principle)
1423 ------------------------------------------------------------------------
1424 r685 | lh3lh3 | 2010-08-13 23:28:31 -0400 (Fri, 13 Aug 2010) | 4 lines
1426 M /trunk/samtools/bcftools/prob1.c
1428 * a numerically stable method to calculate z_{jk}
1429 * currently slower than the old method but will be important for large sample size
1430 * in principle, we can speed up for large n, but have not tried
1432 ------------------------------------------------------------------------
1433 r684 | lh3lh3 | 2010-08-11 21:58:31 -0400 (Wed, 11 Aug 2010) | 2 lines
1435 M /trunk/samtools/bcftools/vcfout.c
1437 fixed an issue in parsing integer
1439 ------------------------------------------------------------------------
1440 r683 | lh3lh3 | 2010-08-09 13:05:07 -0400 (Mon, 09 Aug 2010) | 2 lines
1442 M /trunk/samtools/bcftools/bcf.c
1444 do not print refname if file is converted from VCF
1446 ------------------------------------------------------------------------
1447 r682 | lh3lh3 | 2010-08-09 12:59:47 -0400 (Mon, 09 Aug 2010) | 3 lines
1449 M /trunk/samtools/bcftools/vcf.c
1452 * fixed a bug in parsing VCF
1454 ------------------------------------------------------------------------
1455 r681 | lh3lh3 | 2010-08-09 12:49:23 -0400 (Mon, 09 Aug 2010) | 4 lines
1457 M /trunk/samtools/bcftools/bcf.c
1458 M /trunk/samtools/bcftools/bcf.h
1459 M /trunk/samtools/bcftools/bcfutils.c
1460 M /trunk/samtools/bcftools/main.c
1461 M /trunk/samtools/bcftools/vcf.c
1462 M /trunk/samtools/bcftools/vcfout.c
1463 M /trunk/samtools/bgzf.c
1464 M /trunk/samtools/kstring.c
1466 * fixed a bug in kstrtok@kstring.c
1467 * preliminary VCF parser (not parse everything for now)
1468 * improved view interface
1470 ------------------------------------------------------------------------
1471 r680 | lh3lh3 | 2010-08-09 10:43:13 -0400 (Mon, 09 Aug 2010) | 4 lines
1473 M /trunk/samtools/bcftools/bcf.c
1474 M /trunk/samtools/bcftools/bcf.h
1475 M /trunk/samtools/bcftools/vcfout.c
1476 M /trunk/samtools/kstring.c
1477 M /trunk/samtools/kstring.h
1479 * improved kstring (added kstrtok)
1480 * removed the limit on the format string length in bcftools
1481 * use kstrtok to parse format which fixed a bug in the old code
1483 ------------------------------------------------------------------------
1484 r679 | lh3lh3 | 2010-08-09 01:12:05 -0400 (Mon, 09 Aug 2010) | 2 lines
1486 A /trunk/samtools/bcftools/README
1487 M /trunk/samtools/bcftools/vcfout.c
1491 ------------------------------------------------------------------------
1492 r678 | lh3lh3 | 2010-08-09 00:01:52 -0400 (Mon, 09 Aug 2010) | 2 lines
1494 M /trunk/samtools/bcftools/vcfout.c
1496 perform single-tail test for ED4
1498 ------------------------------------------------------------------------
1499 r677 | lh3lh3 | 2010-08-08 23:48:35 -0400 (Sun, 08 Aug 2010) | 2 lines
1501 M /trunk/samtools/bcftools/Makefile
1502 M /trunk/samtools/bcftools/kfunc.c
1503 M /trunk/samtools/bcftools/vcfout.c
1505 * test depth, end distance and HWE
1507 ------------------------------------------------------------------------
1508 r676 | lh3lh3 | 2010-08-08 02:04:15 -0400 (Sun, 08 Aug 2010) | 2 lines
1510 M /trunk/samtools/bcftools/kfunc.c
1512 reimplement incomplete gamma functions. no copy-paste
1514 ------------------------------------------------------------------------
1515 r675 | lh3lh3 | 2010-08-06 22:42:54 -0400 (Fri, 06 Aug 2010) | 3 lines
1517 M /trunk/samtools/bam2bcf.c
1518 M /trunk/samtools/bam2bcf.h
1519 M /trunk/samtools/bcftools/fet.c
1520 M /trunk/samtools/bcftools/prob1.c
1521 M /trunk/samtools/bcftools/prob1.h
1522 M /trunk/samtools/bcftools/vcfout.c
1524 * bcftools: add HWE (no testing for now)
1525 * record end dist in a 2x2 table, not avg, std any more
1527 ------------------------------------------------------------------------
1528 r674 | lh3lh3 | 2010-08-06 17:30:16 -0400 (Fri, 06 Aug 2010) | 3 lines
1530 A /trunk/samtools/bcftools/kfunc.c
1532 * Special functions: log(gamma()), erfc(), P(a,x) (incomplete gamma)
1533 * Not using Numerical Recipe due to licensing issues
1535 ------------------------------------------------------------------------
1536 r673 | lh3lh3 | 2010-08-05 23:46:53 -0400 (Thu, 05 Aug 2010) | 2 lines
1538 A /trunk/samtools/bcftools/fet.c
1542 ------------------------------------------------------------------------
1543 r672 | lh3lh3 | 2010-08-05 21:48:33 -0400 (Thu, 05 Aug 2010) | 3 lines
1545 M /trunk/samtools/bam2bcf.c
1546 M /trunk/samtools/bam2bcf.h
1547 M /trunk/samtools/bamtk.c
1548 M /trunk/samtools/examples/Makefile
1550 * samtools-0.1.8-11 (r672)
1551 * collect more stats for allele balance test in bcftools (not yet)
1553 ------------------------------------------------------------------------
1554 r671 | lh3lh3 | 2010-08-05 16:17:58 -0400 (Thu, 05 Aug 2010) | 3 lines
1556 M /trunk/samtools/bam_plcmd.c
1557 M /trunk/samtools/bcftools/bcf.c
1558 M /trunk/samtools/bcftools/main.c
1560 * the code base is stablized again.
1561 * I will delay the vcf parser, which is quite complicated but with little value for now
1563 ------------------------------------------------------------------------
1564 r670 | lh3lh3 | 2010-08-05 16:03:23 -0400 (Thu, 05 Aug 2010) | 2 lines
1566 M /trunk/samtools/examples/Makefile
1570 ------------------------------------------------------------------------
1571 r669 | lh3lh3 | 2010-08-05 16:03:08 -0400 (Thu, 05 Aug 2010) | 2 lines
1573 M /trunk/samtools/bcftools/vcf.c
1575 unfinished vcf parser
1577 ------------------------------------------------------------------------
1578 r668 | lh3lh3 | 2010-08-05 15:46:40 -0400 (Thu, 05 Aug 2010) | 3 lines
1580 M /trunk/samtools/bcftools/Makefile
1581 M /trunk/samtools/bcftools/bcf.c
1582 M /trunk/samtools/bcftools/bcf.h
1583 M /trunk/samtools/bcftools/bcfutils.c
1584 M /trunk/samtools/bcftools/index.c
1585 M /trunk/samtools/bcftools/main.c
1586 A /trunk/samtools/bcftools/vcf.c
1587 M /trunk/samtools/bcftools/vcfout.c
1589 * added prelimiary VCF parser (not finished)
1590 * change struct a bit
1592 ------------------------------------------------------------------------
1593 r667 | lh3lh3 | 2010-08-03 22:35:27 -0400 (Tue, 03 Aug 2010) | 3 lines
1595 M /trunk/samtools/bam2bcf.c
1596 M /trunk/samtools/bam2bcf.h
1597 M /trunk/samtools/bam_plcmd.c
1598 M /trunk/samtools/bcftools/bcf.c
1600 * allow to set min base q
1601 * fixed a bug in mpileup -u
1603 ------------------------------------------------------------------------
1604 r666 | lh3lh3 | 2010-08-03 22:08:44 -0400 (Tue, 03 Aug 2010) | 2 lines
1606 A /trunk/samtools/bcftools/bcf.tex
1610 ------------------------------------------------------------------------
1611 r665 | lh3lh3 | 2010-08-03 21:18:57 -0400 (Tue, 03 Aug 2010) | 2 lines
1613 M /trunk/samtools/examples/Makefile
1617 ------------------------------------------------------------------------
1618 r664 | lh3lh3 | 2010-08-03 21:13:00 -0400 (Tue, 03 Aug 2010) | 2 lines
1620 M /trunk/samtools/Makefile
1621 M /trunk/samtools/bam2bcf.c
1622 M /trunk/samtools/bam2bcf.h
1623 M /trunk/samtools/bcftools/Makefile
1625 fixed compilation error
1627 ------------------------------------------------------------------------
1628 r662 | lh3lh3 | 2010-08-03 21:04:00 -0400 (Tue, 03 Aug 2010) | 2 lines
1630 M /trunk/samtools/Makefile
1631 D /trunk/samtools/bcf.c
1632 D /trunk/samtools/bcf.h
1633 A /trunk/samtools/bcftools
1634 A /trunk/samtools/bcftools/Makefile
1635 A /trunk/samtools/bcftools/bcf.c
1636 A /trunk/samtools/bcftools/bcf.h
1637 A /trunk/samtools/bcftools/bcfutils.c
1638 A /trunk/samtools/bcftools/index.c
1639 A /trunk/samtools/bcftools/main.c
1640 A /trunk/samtools/bcftools/prob1.c
1641 A /trunk/samtools/bcftools/prob1.h
1642 A /trunk/samtools/bcftools/vcfout.c
1644 move bcftools to samtools
1646 ------------------------------------------------------------------------
1647 r660 | lh3lh3 | 2010-08-03 15:58:32 -0400 (Tue, 03 Aug 2010) | 2 lines
1649 M /trunk/samtools/bam2bcf.c
1651 fixed another minor bug
1653 ------------------------------------------------------------------------
1654 r658 | lh3lh3 | 2010-08-03 15:06:45 -0400 (Tue, 03 Aug 2010) | 3 lines
1656 M /trunk/samtools/bamtk.c
1657 M /trunk/samtools/bcf.c
1659 * samtools-0.1.8-10 (r658)
1660 * fixed a bug in bam2bcf when the reference is N
1662 ------------------------------------------------------------------------
1663 r657 | lh3lh3 | 2010-08-03 14:50:23 -0400 (Tue, 03 Aug 2010) | 3 lines
1665 M /trunk/samtools/bam2bcf.c
1666 M /trunk/samtools/bam2bcf.h
1669 * treat ambiguous ref base as the fifth base
1671 ------------------------------------------------------------------------
1672 r654 | lh3lh3 | 2010-08-02 17:38:27 -0400 (Mon, 02 Aug 2010) | 2 lines
1674 M /trunk/bcftools/bcf.c
1675 M /trunk/samtools/bcf.c
1677 missing a column in VCF output...
1679 ------------------------------------------------------------------------
1680 r653 | lh3lh3 | 2010-08-02 17:31:33 -0400 (Mon, 02 Aug 2010) | 2 lines
1682 M /trunk/samtools/bcf.c
1686 ------------------------------------------------------------------------
1687 r651 | lh3lh3 | 2010-08-02 17:27:31 -0400 (Mon, 02 Aug 2010) | 2 lines
1689 M /trunk/samtools/bcf.c
1691 fixed a bug in bcf reader
1693 ------------------------------------------------------------------------
1694 r650 | lh3lh3 | 2010-08-02 17:00:41 -0400 (Mon, 02 Aug 2010) | 2 lines
1696 M /trunk/samtools/bam2bcf.c
1700 ------------------------------------------------------------------------
1701 r649 | lh3lh3 | 2010-08-02 16:49:35 -0400 (Mon, 02 Aug 2010) | 3 lines
1703 M /trunk/samtools/Makefile
1704 M /trunk/samtools/bam2bcf.c
1705 M /trunk/samtools/bam2bcf.h
1706 M /trunk/samtools/bamtk.c
1708 * samtools-0.1.8-9 (r649)
1709 * lossless representation of PL in BCF output
1711 ------------------------------------------------------------------------
1712 r648 | lh3lh3 | 2010-08-02 16:07:25 -0400 (Mon, 02 Aug 2010) | 2 lines
1714 M /trunk/samtools/Makefile
1715 A /trunk/samtools/bam2bcf.c
1716 A /trunk/samtools/bam2bcf.h
1717 M /trunk/samtools/bam_plcmd.c
1718 A /trunk/samtools/bcf.c
1719 A /trunk/samtools/bcf.h
1723 ------------------------------------------------------------------------
1724 r644 | lh3lh3 | 2010-07-28 11:59:19 -0400 (Wed, 28 Jul 2010) | 5 lines
1726 M /trunk/samtools/bam_mcns.c
1727 M /trunk/samtools/bamtk.c
1729 * samtools-0.1.8-8 (r644)
1730 * mpileup becomes a little stable again
1731 * the method is slightly different, but is more theoretically correct
1732 * snp calling is O(n^2) instead of O(n^3)
1734 ------------------------------------------------------------------------
1735 r643 | lh3lh3 | 2010-07-28 11:54:15 -0400 (Wed, 28 Jul 2010) | 3 lines
1737 M /trunk/samtools/bam_mcns.c
1739 * fixed a STUPID bug, which cost me a lot of time.
1740 * I am going to clean up mcns a little bit
1742 ------------------------------------------------------------------------
1743 r642 | lh3lh3 | 2010-07-27 23:23:07 -0400 (Tue, 27 Jul 2010) | 2 lines
1745 M /trunk/samtools/bam_mcns.c
1746 M /trunk/samtools/bam_mcns.h
1747 M /trunk/samtools/bam_plcmd.c
1749 supposedly this is THE correct implementation, but more testing is needed
1751 ------------------------------------------------------------------------
1752 r641 | lh3lh3 | 2010-07-27 22:43:39 -0400 (Tue, 27 Jul 2010) | 2 lines
1754 M /trunk/samtools/bam_mcns.c
1756 NOT ready yet. Going to make further changes...
1758 ------------------------------------------------------------------------
1759 r639 | lh3lh3 | 2010-07-25 22:18:38 -0400 (Sun, 25 Jul 2010) | 3 lines
1761 M /trunk/samtools/bam_mcns.c
1762 M /trunk/samtools/bam_plcmd.c
1763 M /trunk/samtools/bamtk.c
1765 * samtools-0.1.8-7 (r639)
1766 * fixed the reference allele assignment
1768 ------------------------------------------------------------------------
1769 r638 | lh3lh3 | 2010-07-25 12:01:26 -0400 (Sun, 25 Jul 2010) | 5 lines
1771 M /trunk/samtools/bam_mcns.c
1772 M /trunk/samtools/bam_mcns.h
1773 M /trunk/samtools/bam_plcmd.c
1774 M /trunk/samtools/bamtk.c
1776 * samtools-0.1.8-6 (r638)
1777 * skip isnan/isinf in case of float underflow
1778 * added the flat prior
1779 * fixed an issue where there are no reads supporting the reference
1781 ------------------------------------------------------------------------
1782 r637 | lh3lh3 | 2010-07-24 14:16:27 -0400 (Sat, 24 Jul 2010) | 2 lines
1784 M /trunk/samtools/bam_plcmd.c
1788 ------------------------------------------------------------------------
1789 r636 | lh3lh3 | 2010-07-24 14:07:27 -0400 (Sat, 24 Jul 2010) | 2 lines
1791 M /trunk/samtools/bam_mcns.c
1792 M /trunk/samtools/bam_mcns.h
1793 M /trunk/samtools/bam_plcmd.c
1794 M /trunk/samtools/bamtk.c
1798 ------------------------------------------------------------------------
1799 r635 | lh3lh3 | 2010-07-24 01:49:49 -0400 (Sat, 24 Jul 2010) | 2 lines
1801 M /trunk/samtools/bam_mcns.c
1802 M /trunk/samtools/bam_mcns.h
1803 M /trunk/samtools/bam_plcmd.c
1805 posterior expectation FINALLY working. I am so tired...
1807 ------------------------------------------------------------------------
1808 r633 | lh3lh3 | 2010-07-23 13:50:48 -0400 (Fri, 23 Jul 2010) | 2 lines
1810 M /trunk/samtools/bam_plcmd.c
1812 another minor fix to mpileup
1814 ------------------------------------------------------------------------
1815 r632 | lh3lh3 | 2010-07-23 13:43:31 -0400 (Fri, 23 Jul 2010) | 2 lines
1817 M /trunk/samtools/bam_plcmd.c
1819 added the format column
1821 ------------------------------------------------------------------------
1822 r631 | lh3lh3 | 2010-07-23 13:25:44 -0400 (Fri, 23 Jul 2010) | 2 lines
1824 M /trunk/samtools/bam_mcns.c
1825 M /trunk/samtools/bam_mcns.h
1826 M /trunk/samtools/bam_plcmd.c
1827 M /trunk/samtools/bamtk.c
1829 added an alternative prior
1831 ------------------------------------------------------------------------
1832 r628 | lh3lh3 | 2010-07-23 11:48:51 -0400 (Fri, 23 Jul 2010) | 2 lines
1834 M /trunk/samtools/bam_mcns.c
1835 M /trunk/samtools/bam_mcns.h
1836 M /trunk/samtools/bam_plcmd.c
1838 calculate posterior allele frequency
1840 ------------------------------------------------------------------------
1841 r627 | lh3lh3 | 2010-07-22 21:39:13 -0400 (Thu, 22 Jul 2010) | 3 lines
1843 M /trunk/samtools/bam_mcns.c
1844 M /trunk/samtools/bam_plcmd.c
1845 M /trunk/samtools/bamtk.c
1847 * samtools-0.1.8-3 (r627)
1848 * multi-sample snp calling appears to work. More tests needed.
1850 ------------------------------------------------------------------------
1851 r626 | lh3lh3 | 2010-07-22 16:37:56 -0400 (Thu, 22 Jul 2010) | 3 lines
1853 M /trunk/samtools/bam_mcns.c
1854 M /trunk/samtools/bam_mcns.h
1855 M /trunk/samtools/bam_plcmd.c
1856 M /trunk/samtools/bam_tview.c
1858 * preliminary multisample SNP caller.
1859 * something looks not so right, but it largely works
1861 ------------------------------------------------------------------------
1862 r617 | lh3lh3 | 2010-07-14 16:26:27 -0400 (Wed, 14 Jul 2010) | 3 lines
1864 M /trunk/samtools/bam_mcns.c
1865 M /trunk/samtools/bam_plcmd.c
1866 M /trunk/samtools/bamtk.c
1868 * samtools-0.1.8-2 (r617)
1869 * allele frequency calculation apparently works...
1871 ------------------------------------------------------------------------
1872 r616 | lh3lh3 | 2010-07-14 13:33:51 -0400 (Wed, 14 Jul 2010) | 3 lines
1874 M /trunk/samtools/Makefile
1875 A /trunk/samtools/bam_mcns.c
1876 A /trunk/samtools/bam_mcns.h
1877 M /trunk/samtools/bam_plcmd.c
1879 * added mutli-sample framework. It is not working, yet.
1880 * improved the mpileup interface
1882 ------------------------------------------------------------------------
1883 r615 | lh3lh3 | 2010-07-13 14:50:12 -0400 (Tue, 13 Jul 2010) | 3 lines
1885 M /trunk/samtools/bam_plcmd.c
1886 M /trunk/samtools/bamtk.c
1887 M /trunk/samtools/misc/Makefile
1889 * samtools-0.1.8-1 (r615)
1890 * allow to get mpileup at required sites
1892 ------------------------------------------------------------------------
1893 r613 | lh3lh3 | 2010-07-11 22:40:56 -0400 (Sun, 11 Jul 2010) | 2 lines
1895 M /trunk/samtools/ChangeLog
1896 M /trunk/samtools/NEWS
1897 M /trunk/samtools/bam_plcmd.c
1898 M /trunk/samtools/bamtk.c
1899 M /trunk/samtools/samtools.1
1901 Release samtools-0.1.8
1903 ------------------------------------------------------------------------
1904 r612 | lh3lh3 | 2010-07-11 21:08:56 -0400 (Sun, 11 Jul 2010) | 2 lines
1906 M /trunk/samtools/knetfile.c
1908 fixed a compiling issue for Windows
1910 ------------------------------------------------------------------------
1911 r611 | lh3lh3 | 2010-07-11 20:59:15 -0400 (Sun, 11 Jul 2010) | 2 lines
1913 M /trunk/samtools/bam_sort.c
1915 fixed a bug in sorting when output to stdout (by Peter Chines)
1917 ------------------------------------------------------------------------
1918 r610 | lh3lh3 | 2010-07-09 17:05:10 -0400 (Fri, 09 Jul 2010) | 2 lines
1920 M /trunk/samtools/NEWS
1921 M /trunk/samtools/bam_plcmd.c
1923 change the command line option of pileup
1925 ------------------------------------------------------------------------
1926 r609 | lh3lh3 | 2010-07-09 00:39:34 -0400 (Fri, 09 Jul 2010) | 2 lines
1928 M /trunk/samtools/bam_pileup.c
1929 A /trunk/samtools/examples/toy.fa
1930 A /trunk/samtools/examples/toy.sam
1932 make pileup work with CIGAR with I/D at the beginning or in the end
1934 ------------------------------------------------------------------------
1935 r608 | lh3lh3 | 2010-07-08 22:36:12 -0400 (Thu, 08 Jul 2010) | 3 lines
1937 M /trunk/samtools/bam_maqcns.c
1938 M /trunk/samtools/bam_maqcns.h
1939 M /trunk/samtools/bam_plcmd.c
1940 M /trunk/samtools/bam_tview.c
1942 * make tview more friendly
1943 * a temporary remedy for an issue in indel calling
1945 ------------------------------------------------------------------------
1946 r607 | lh3lh3 | 2010-07-08 14:43:52 -0400 (Thu, 08 Jul 2010) | 4 lines
1948 M /trunk/samtools/bam_maqcns.c
1949 M /trunk/samtools/bam_plcmd.c
1950 M /trunk/samtools/bamtk.c
1952 * samtools-0.1.7-r607
1953 * improved the genotype accuracy for indels
1954 * use the SOAPsnp model for SNP calling by default.
1956 ------------------------------------------------------------------------
1957 r606 | lh3lh3 | 2010-07-08 01:05:19 -0400 (Thu, 08 Jul 2010) | 2 lines
1959 M /trunk/samtools/misc/Makefile
1961 removed a debugging example
1963 ------------------------------------------------------------------------
1964 r605 | lh3lh3 | 2010-07-08 01:04:09 -0400 (Thu, 08 Jul 2010) | 4 lines
1966 M /trunk/samtools/bam_maqcns.c
1967 M /trunk/samtools/bamtk.c
1969 * samtools-.1.7-18 (r605)
1970 * fixed an issue when a deletion and mismatch occur at the same time
1971 and the base quality is higher than 40 (if -I40).
1973 ------------------------------------------------------------------------
1974 r604 | lh3lh3 | 2010-07-02 19:32:24 -0400 (Fri, 02 Jul 2010) | 2 lines
1976 M /trunk/samtools/bam.h
1977 M /trunk/samtools/bam_index.c
1978 M /trunk/samtools/misc/Makefile
1980 fixed a minor bug in idxstats
1982 ------------------------------------------------------------------------
1983 r601 | lh3lh3 | 2010-06-16 09:03:59 -0400 (Wed, 16 Jun 2010) | 2 lines
1985 M /trunk/samtools/bam_index.c
1987 fixed a minor bug in indexing
1989 ------------------------------------------------------------------------
1990 r600 | lh3lh3 | 2010-06-15 10:17:53 -0400 (Tue, 15 Jun 2010) | 2 lines
1992 M /trunk/samtools/ChangeLog
1993 M /trunk/samtools/bam.c
1995 change printf() to puts in exporting
1997 ------------------------------------------------------------------------
1998 r599 | lh3lh3 | 2010-06-13 21:41:11 -0400 (Sun, 13 Jun 2010) | 2 lines
2000 M /trunk/samtools/bamtk.c
2002 minor fix. No actual effect.
2004 ------------------------------------------------------------------------
2005 r598 | lh3lh3 | 2010-06-13 21:32:45 -0400 (Sun, 13 Jun 2010) | 2 lines
2007 M /trunk/samtools/Makefile
2009 added Makefile targets to compile shared/dynamic library
2011 ------------------------------------------------------------------------
2012 r596 | lh3lh3 | 2010-06-13 19:48:07 -0400 (Sun, 13 Jun 2010) | 3 lines
2014 M /trunk/samtools/ChangeLog
2015 M /trunk/samtools/bam_index.c
2016 M /trunk/samtools/bamtk.c
2018 * samtools-0.1.7-17 (r596)
2019 * also keep the number of coor-less reads in the index file
2021 ------------------------------------------------------------------------
2022 r595 | lh3lh3 | 2010-06-13 18:54:26 -0400 (Sun, 13 Jun 2010) | 3 lines
2024 M /trunk/samtools/bam_index.c
2025 M /trunk/samtools/bamtk.c
2027 * samtools-0.1.7-16 (r595)
2028 * write additional information to bam index
2030 ------------------------------------------------------------------------
2031 r594 | lh3lh3 | 2010-06-13 17:29:52 -0400 (Sun, 13 Jun 2010) | 2 lines
2033 M /trunk/samtools/bam_index.c
2035 fixed a bug for unmapped sequences in indexing
2037 ------------------------------------------------------------------------
2038 r593 | lh3lh3 | 2010-06-12 18:11:32 -0400 (Sat, 12 Jun 2010) | 2 lines
2040 M /trunk/samtools/bam.h
2041 M /trunk/samtools/bam_index.c
2042 M /trunk/samtools/bam_plcmd.c
2043 M /trunk/samtools/samtools.1
2045 rename iterf as iter
2047 ------------------------------------------------------------------------
2048 r592 | lh3lh3 | 2010-06-12 18:02:38 -0400 (Sat, 12 Jun 2010) | 4 lines
2050 M /trunk/samtools/ChangeLog
2051 M /trunk/samtools/bam_aux.c
2052 M /trunk/samtools/bam_index.c
2053 M /trunk/samtools/bam_pileup.c
2054 M /trunk/samtools/bam_plcmd.c
2055 M /trunk/samtools/bamtk.c
2057 * samtools-0.1.7-15 (r592)
2058 * fixed a few minor memory leaks in the new pileup code
2059 * improved the functionality of mpileup
2061 ------------------------------------------------------------------------
2062 r591 | lh3lh3 | 2010-06-12 14:09:22 -0400 (Sat, 12 Jun 2010) | 3 lines
2064 M /trunk/samtools/bam.h
2065 M /trunk/samtools/bam_pileup.c
2066 M /trunk/samtools/bam_plcmd.c
2067 M /trunk/samtools/bamtk.c
2069 * samtools-0.1.7-14 (r591)
2070 * elementary multi-way pileup. More testing and more functionality to be done.
2072 ------------------------------------------------------------------------
2073 r590 | lh3lh3 | 2010-06-12 01:00:24 -0400 (Sat, 12 Jun 2010) | 3 lines
2075 M /trunk/samtools/bam.h
2076 M /trunk/samtools/bam_pileup.c
2077 M /trunk/samtools/bamtk.c
2079 * samtools-0.1.7-13 (r590)
2080 * added mpileup APIs. No compiling errors, but not tested at all. It is late.
2082 ------------------------------------------------------------------------
2083 r589 | lh3lh3 | 2010-06-11 22:37:09 -0400 (Fri, 11 Jun 2010) | 3 lines
2085 M /trunk/samtools/bam.h
2086 M /trunk/samtools/bam_pileup.c
2087 M /trunk/samtools/bamtk.c
2089 * samtools-0.1.7-12 (r589)
2090 * added iterator-like APIs for pileup
2092 ------------------------------------------------------------------------
2093 r588 | lh3lh3 | 2010-06-11 17:41:13 -0400 (Fri, 11 Jun 2010) | 3 lines
2095 M /trunk/samtools/bam_index.c
2096 M /trunk/samtools/bamtk.c
2098 * samtools-0.1.7-11 (r588)
2099 * ported a few improvements from tabix back to samtools
2101 ------------------------------------------------------------------------
2102 r587 | lh3lh3 | 2010-06-11 17:33:16 -0400 (Fri, 11 Jun 2010) | 3 lines
2104 M /trunk/samtools/bam.h
2105 M /trunk/samtools/bam_index.c
2106 M /trunk/samtools/bamtk.c
2108 * samtools-0.1.7-10 (r587)
2109 * added iterator interface for bam_fetch (ported back from tabix)
2111 ------------------------------------------------------------------------
2112 r586 | lh3lh3 | 2010-06-11 13:23:53 -0400 (Fri, 11 Jun 2010) | 3 lines
2114 M /trunk/samtools/Makefile
2115 A /trunk/samtools/bam_reheader.c
2116 M /trunk/samtools/bamtk.c
2117 M /trunk/samtools/bgzf.c
2119 * samtools-0.1.7-9 (r586)
2120 * added "reheader" to replace the BAM header
2122 ------------------------------------------------------------------------
2123 r585 | lh3lh3 | 2010-06-11 12:22:06 -0400 (Fri, 11 Jun 2010) | 3 lines
2125 M /trunk/samtools/bam.c
2126 M /trunk/samtools/bamtk.c
2127 M /trunk/samtools/kstring.h
2129 * samtools-0.1.7-8 (r585)
2132 ------------------------------------------------------------------------
2133 r584 | lh3lh3 | 2010-06-11 12:00:41 -0400 (Fri, 11 Jun 2010) | 4 lines
2135 M /trunk/samtools/bam.c
2136 M /trunk/samtools/bamtk.c
2137 M /trunk/samtools/bgzf.c
2138 M /trunk/samtools/bgzf.h
2139 M /trunk/samtools/kstring.h
2140 M /trunk/samtools/misc/wgsim_eval.pl
2142 * samtools-0.1.7-7 (r584)
2143 * ported tabix BGZF to samtools
2144 * flush BGZF after writing the BAM header and between alignment boundaries
2146 ------------------------------------------------------------------------
2147 r583 | petulda | 2010-06-11 11:58:20 -0400 (Fri, 11 Jun 2010) | 1 line
2149 A /trunk/samtools/misc/varfilter.py
2151 Initial release on behalf of Aylwyn Scally
2152 ------------------------------------------------------------------------
2153 r561 | petulda | 2010-05-07 08:41:56 -0400 (Fri, 07 May 2010) | 1 line
2155 M /trunk/samtools/samtools.1
2157 Added a note about the indels coordinates
2158 ------------------------------------------------------------------------
2159 r551 | petulda | 2010-04-23 09:42:13 -0400 (Fri, 23 Apr 2010) | 1 line
2161 M /trunk/samtools/misc/sam2vcf.pl
2163 Added the possibility to print or not to print the reference allele
2164 ------------------------------------------------------------------------
2165 r546 | petulda | 2010-04-15 04:33:55 -0400 (Thu, 15 Apr 2010) | 1 line
2167 M /trunk/samtools/sam_header.c
2169 More descriptive message for space separated tags
2170 ------------------------------------------------------------------------
2171 r545 | petulda | 2010-04-14 11:44:50 -0400 (Wed, 14 Apr 2010) | 1 line
2173 M /trunk/samtools/misc/sam2vcf.pl
2175 Speedup with -i, no need to query the reference all the time
2176 ------------------------------------------------------------------------
2177 r541 | petulda | 2010-03-15 10:03:51 -0400 (Mon, 15 Mar 2010) | 1 line
2179 M /trunk/samtools/sam_header.c
2181 Fixed the order of sequences in the header
2182 ------------------------------------------------------------------------
2183 r540 | petulda | 2010-03-04 06:28:35 -0500 (Thu, 04 Mar 2010) | 1 line
2185 M /trunk/samtools/misc/sam2vcf.pl
2187 Added possibility to select indels only and fixed a bug in reporting homozygous indels.
2188 ------------------------------------------------------------------------
2189 r539 | jmarshall | 2010-02-27 06:48:17 -0500 (Sat, 27 Feb 2010) | 4 lines
2191 M /trunk/samtools/bam.c
2193 Improve the invalid 'BAM\1' magic number error message, and also print it
2194 when no bytes can be read from the alleged BAM file, e.g., in the common
2195 user error case when a SAM file has accidentally been supplied.
2197 ------------------------------------------------------------------------
2198 r538 | petulda | 2010-02-26 10:51:40 -0500 (Fri, 26 Feb 2010) | 1 line
2200 M /trunk/samtools/AUTHORS
2201 M /trunk/samtools/bam.h
2202 M /trunk/samtools/bam_import.c
2203 M /trunk/samtools/sam_header.c
2205 Improved efficiency of header parsing
2206 ------------------------------------------------------------------------
2207 r537 | lh3lh3 | 2010-02-23 21:08:48 -0500 (Tue, 23 Feb 2010) | 3 lines
2209 M /trunk/samtools/misc/export2sam.pl
2211 Updated export2sam.pl by Chris Saunders from Illumina.
2214 ------------------------------------------------------------------------
2215 r536 | petulda | 2010-02-17 08:32:53 -0500 (Wed, 17 Feb 2010) | 1 line
2217 M /trunk/samtools/misc/samtools.pl
2219 Fixed filtering of SNPs near indels. Added min indel and SNP quality filter.
2220 ------------------------------------------------------------------------
2221 r535 | petulda | 2010-02-12 04:52:37 -0500 (Fri, 12 Feb 2010) | 1 line
2223 M /trunk/samtools/misc/sam2vcf.pl
2225 Print an error for pileups in simple format
2226 ------------------------------------------------------------------------
2227 r534 | lh3lh3 | 2010-02-11 14:01:41 -0500 (Thu, 11 Feb 2010) | 2 lines
2229 M /trunk/samtools/bam_plcmd.c
2231 added a hidden option in pileup to output the base position (for Erin)
2233 ------------------------------------------------------------------------
2234 r533 | petulda | 2010-02-09 10:12:14 -0500 (Tue, 09 Feb 2010) | 1 line
2236 M /trunk/samtools/misc/sam2vcf.pl
2238 Added possibility to specify a custom column title for the data column
2239 ------------------------------------------------------------------------
2240 r532 | petulda | 2010-02-09 09:46:09 -0500 (Tue, 09 Feb 2010) | 1 line
2242 M /trunk/samtools/bam_plcmd.c
2244 Added the -d option to limit maximum depth for indels.
2245 ------------------------------------------------------------------------
2246 r531 | petulda | 2010-02-03 07:57:27 -0500 (Wed, 03 Feb 2010) | 1 line
2248 M /trunk/samtools/misc/sam2vcf.pl
2251 ------------------------------------------------------------------------
2252 r530 | lh3lh3 | 2010-02-01 09:13:19 -0500 (Mon, 01 Feb 2010) | 3 lines
2254 M /trunk/samtools/ChangeLog
2255 M /trunk/samtools/bam_plcmd.c
2256 M /trunk/samtools/bamtk.c
2257 M /trunk/samtools/misc/samtools.pl
2258 M /trunk/samtools/misc/wgsim.c
2261 * fixed a bug in faidx
2263 ------------------------------------------------------------------------
2264 r529 | jmarshall | 2010-01-11 18:51:49 -0500 (Mon, 11 Jan 2010) | 2 lines
2266 M /trunk/samtools/faidx.c
2268 Put the right filename in the error message.
2270 ------------------------------------------------------------------------
2271 r528 | lh3lh3 | 2009-12-14 11:26:47 -0500 (Mon, 14 Dec 2009) | 3 lines
2273 M /trunk/samtools/bam_plcmd.c
2274 M /trunk/samtools/bamtk.c
2276 * samtools-0.1.7-5 (r528)
2277 * further add new consensus generation strategy
2279 ------------------------------------------------------------------------
2280 r527 | petulda | 2009-12-11 12:31:05 -0500 (Fri, 11 Dec 2009) | 1 line
2282 M /trunk/samtools/knetfile.c
2284 Fixed a bug in knet_seek
2285 ------------------------------------------------------------------------
2286 r526 | petulda | 2009-12-11 07:51:18 -0500 (Fri, 11 Dec 2009) | 1 line
2288 M /trunk/samtools/misc/sam2vcf.pl
2290 Small fix in VCF format: dot for the empty INFO field
2291 ------------------------------------------------------------------------
2292 r525 | petulda | 2009-12-11 04:36:18 -0500 (Fri, 11 Dec 2009) | 1 line
2294 M /trunk/samtools/sam_header.c
2296 Allow tabs in the CO header field
2297 ------------------------------------------------------------------------
2298 r524 | jmarshall | 2009-12-10 10:03:58 -0500 (Thu, 10 Dec 2009) | 3 lines
2300 M /trunk/samtools/Makefile
2301 M /trunk/samtools/Makefile.mingw
2303 Depend on libbam.a rather than the phony target, so that samtools is not
2304 unnecessarily rebuilt every time. Also clean bgzip.
2306 ------------------------------------------------------------------------
2307 r523 | jmarshall | 2009-12-10 09:45:32 -0500 (Thu, 10 Dec 2009) | 4 lines
2309 M /trunk/samtools/Makefile
2310 M /trunk/samtools/Makefile.mingw
2312 Fix a bug in compiling bgzip: this also needs knetfile.o when _USE_KNETFILE
2313 is defined. Also introduce $(KNETFILE_O) which can be set to empty to
2314 facilitate non-knet builds.
2316 ------------------------------------------------------------------------
2317 r522 | lh3lh3 | 2009-12-01 13:02:36 -0500 (Tue, 01 Dec 2009) | 4 lines
2319 M /trunk/samtools/bamtk.c
2320 M /trunk/samtools/sam_view.c
2322 * samtools-0.1.7-4 (r522)
2323 * fixed a bug in "view -r"
2324 * added a new option "view -R" to read required read groups from a file
2326 ------------------------------------------------------------------------
2327 r521 | lh3lh3 | 2009-12-01 10:00:12 -0500 (Tue, 01 Dec 2009) | 3 lines
2329 M /trunk/samtools/bam_md.c
2330 M /trunk/samtools/bamtk.c
2332 * samtools-0.1.7-3 (r521)
2333 * calmd: optionally mask matching bases as N
2335 ------------------------------------------------------------------------
2336 r520 | lh3lh3 | 2009-12-01 09:37:17 -0500 (Tue, 01 Dec 2009) | 4 lines
2338 M /trunk/samtools/bam_plcmd.c
2339 M /trunk/samtools/bamtk.c
2340 M /trunk/samtools/misc/samtools.pl
2342 * samtools-0.1.7-2 (r520)
2343 * fixed a few issues with compilation in Windows (on behalf of John)
2344 * choose a random base as the consensus (for population genetics studies)
2346 ------------------------------------------------------------------------
2347 r519 | jmarshall | 2009-11-30 10:53:02 -0500 (Mon, 30 Nov 2009) | 6 lines
2349 M /trunk/samtools/Makefile
2351 Put libraries at the end, so they can resolve references from libbam.a
2352 as well, even with old-fashioned linkers.
2354 Also use libbam.a explicitly rather than "-L. -lbam" to ensure that we get
2355 the freshly built library, not some other libbam.a lying around the system.
2357 ------------------------------------------------------------------------
2358 r518 | jmarshall | 2009-11-30 08:44:56 -0500 (Mon, 30 Nov 2009) | 2 lines
2360 M /trunk/samtools/Makefile
2361 M /trunk/samtools/misc/Makefile
2363 Also clean *.exe (for Cygwin users using this makefile).
2365 ------------------------------------------------------------------------
2366 r517 | jmarshall | 2009-11-30 07:09:04 -0500 (Mon, 30 Nov 2009) | 2 lines
2368 M /trunk/samtools/bam_index.c
2370 Index files should be opened in binary mode, not text mode.
2372 ------------------------------------------------------------------------
2373 r516 | lh3lh3 | 2009-11-27 15:18:59 -0500 (Fri, 27 Nov 2009) | 2 lines
2375 A /trunk/samtools/examples/bam2bed.c
2377 another example program
2379 ------------------------------------------------------------------------
2380 r515 | lh3lh3 | 2009-11-27 10:44:56 -0500 (Fri, 27 Nov 2009) | 3 lines
2382 M /trunk/samtools/bam_import.c
2383 M /trunk/samtools/bamtk.c
2384 M /trunk/samtools/misc/wgsim_eval.pl
2385 M /trunk/samtools/sam.c
2387 * samtools-0.1.7-1 (r515)
2388 * report an error when .fai contains duplicated names, instead of segfault
2390 ------------------------------------------------------------------------
2391 r514 | jmarshall | 2009-11-24 09:45:35 -0500 (Tue, 24 Nov 2009) | 2 lines
2393 M /trunk/samtools/bam.c
2395 Format 'c'-encoded auxiliary fields correctly, as *signed* integers.
2397 ------------------------------------------------------------------------
2398 r513 | lh3lh3 | 2009-11-16 10:13:07 -0500 (Mon, 16 Nov 2009) | 2 lines
2400 M /trunk/samtools/Makefile.mingw
2402 Update Makefile.mingw for the same reason
2404 ------------------------------------------------------------------------
2405 r512 | lh3lh3 | 2009-11-16 10:00:08 -0500 (Mon, 16 Nov 2009) | 2 lines
2407 M /trunk/samtools/Makefile
2409 Fixed a bug in compiling razip
2411 ------------------------------------------------------------------------
2412 r510 | lh3lh3 | 2009-11-10 10:55:41 -0500 (Tue, 10 Nov 2009) | 2 lines
2414 M /trunk/samtools/ChangeLog
2415 M /trunk/samtools/NEWS
2416 M /trunk/samtools/bamtk.c
2417 M /trunk/samtools/samtools.1
2419 Release samtools-0.1.7 (r510)
2421 ------------------------------------------------------------------------
2422 r509 | lh3lh3 | 2009-11-06 09:17:09 -0500 (Fri, 06 Nov 2009) | 3 lines
2424 M /trunk/samtools/bam_plcmd.c
2425 M /trunk/samtools/bamtk.c
2427 * samtools-0.1.6-22 (r509)
2428 * forget to fix a similar problem in glfgen
2430 ------------------------------------------------------------------------
2431 r508 | lh3lh3 | 2009-11-06 09:06:40 -0500 (Fri, 06 Nov 2009) | 3 lines
2433 M /trunk/samtools/bam_maqcns.c
2434 M /trunk/samtools/bam_plcmd.c
2435 M /trunk/samtools/bamtk.c
2436 M /trunk/samtools/sam_view.c
2438 * samtools-0.1.6-21 (r508)
2439 * fixed a potential bug in the indel caller towards the end of a chromosome
2441 ------------------------------------------------------------------------
2442 r494 | lh3lh3 | 2009-10-26 11:38:00 -0400 (Mon, 26 Oct 2009) | 3 lines
2444 M /trunk/samtools/bamtk.c
2445 M /trunk/samtools/sam_view.c
2447 * samtools-0.1.6-19 (r494)
2448 * allow to convert Illumina quality (64 based) to the BAM quality
2450 ------------------------------------------------------------------------
2451 r493 | lh3lh3 | 2009-10-26 10:24:39 -0400 (Mon, 26 Oct 2009) | 4 lines
2453 M /trunk/samtools/Makefile
2454 M /trunk/samtools/bam.c
2455 M /trunk/samtools/bam_import.c
2456 M /trunk/samtools/bamtk.c
2457 M /trunk/samtools/sam.c
2458 M /trunk/samtools/sam_header.c
2460 * samtools-0.1.6-18 (r493)
2461 * fixed the bugs due to improperly incorporating Petr's header parser
2462 * a little code clean up in sam_header.c
2464 ------------------------------------------------------------------------
2465 r492 | petulda | 2009-10-24 09:43:25 -0400 (Sat, 24 Oct 2009) | 1 line
2467 M /trunk/samtools/sam_header.c
2469 Added sam_header_line_free call for sam_header_parse2
2470 ------------------------------------------------------------------------
2471 r491 | lh3lh3 | 2009-10-24 00:50:16 -0400 (Sat, 24 Oct 2009) | 3 lines
2473 M /trunk/samtools/sam_view.c
2478 ------------------------------------------------------------------------
2479 r490 | lh3lh3 | 2009-10-24 00:45:12 -0400 (Sat, 24 Oct 2009) | 4 lines
2481 M /trunk/samtools/bam.c
2482 M /trunk/samtools/bam.h
2483 M /trunk/samtools/bam_import.c
2484 M /trunk/samtools/sam.c
2487 * improved the interface a bit
2490 ------------------------------------------------------------------------
2491 r489 | lh3lh3 | 2009-10-24 00:41:50 -0400 (Sat, 24 Oct 2009) | 3 lines
2493 M /trunk/samtools/bam_import.c
2494 M /trunk/samtools/sam_header.c
2495 M /trunk/samtools/sam_header.h
2497 * BUGGY VERSION. Please NOT use it.
2498 * Fixed a minor bug, but the major bug is still there.
2500 ------------------------------------------------------------------------
2501 r488 | lh3lh3 | 2009-10-24 00:17:10 -0400 (Sat, 24 Oct 2009) | 3 lines
2503 M /trunk/samtools/Makefile
2504 M /trunk/samtools/bam.c
2505 M /trunk/samtools/bam.h
2506 M /trunk/samtools/bam_aux.c
2507 M /trunk/samtools/bam_import.c
2508 M /trunk/samtools/bam_rmdup.c
2509 M /trunk/samtools/bam_rmdupse.c
2510 M /trunk/samtools/kaln.c
2511 M /trunk/samtools/sam.c
2512 M /trunk/samtools/sam_header.c
2513 M /trunk/samtools/sam_header.h
2514 M /trunk/samtools/sam_view.c
2516 * This revision is SERIOUSLY BUGGY. Please NOT use it.
2517 * Start to incorporate header parsing from Petr Danecek
2519 ------------------------------------------------------------------------
2520 r487 | petulda | 2009-10-23 11:44:32 -0400 (Fri, 23 Oct 2009) | 1 line
2522 M /trunk/samtools/sam_header.c
2523 M /trunk/samtools/sam_header.h
2525 Now possible to merge multiple HeaderDict dictionaries
2526 ------------------------------------------------------------------------
2527 r486 | petulda | 2009-10-22 11:46:58 -0400 (Thu, 22 Oct 2009) | 1 line
2529 M /trunk/samtools/sam_header.c
2532 ------------------------------------------------------------------------
2533 r485 | petulda | 2009-10-22 11:41:56 -0400 (Thu, 22 Oct 2009) | 1 line
2535 A /trunk/samtools/sam_header.c
2536 A /trunk/samtools/sam_header.h
2539 ------------------------------------------------------------------------
2540 r484 | lh3lh3 | 2009-10-19 14:31:32 -0400 (Mon, 19 Oct 2009) | 5 lines
2542 M /trunk/samtools/bam_import.c
2543 M /trunk/samtools/bam_rmdupse.c
2544 M /trunk/samtools/bamtk.c
2545 M /trunk/samtools/examples/Makefile
2547 * samtools-0.1.6-17 (r484)
2548 * fixed a memory leak in rmdupse
2549 * fixed a bug in parsing @RG header lines
2550 * test rmdup in examples/
2552 ------------------------------------------------------------------------
2553 r483 | lh3lh3 | 2009-10-19 13:22:48 -0400 (Mon, 19 Oct 2009) | 4 lines
2555 M /trunk/samtools/bam_rmdup.c
2556 M /trunk/samtools/bam_rmdupse.c
2557 M /trunk/samtools/bamtk.c
2559 * samtools-0.1.6-16 (r483)
2560 * unify the interface of rmdup and rmdupse
2561 * a new bug found in rg2lib(). Have not been fixed yet.
2563 ------------------------------------------------------------------------
2564 r482 | lh3lh3 | 2009-10-19 13:03:34 -0400 (Mon, 19 Oct 2009) | 4 lines
2566 M /trunk/samtools/bam.h
2567 M /trunk/samtools/bam_rmdup.c
2568 M /trunk/samtools/bam_rmdupse.c
2569 M /trunk/samtools/bamtk.c
2570 A /trunk/samtools/klist.h
2572 * samtools-0.1.6-15 (r482)
2574 * rmdupse is now library aware
2576 ------------------------------------------------------------------------
2577 r481 | lh3lh3 | 2009-10-18 00:07:21 -0400 (Sun, 18 Oct 2009) | 3 lines
2579 M /trunk/samtools/bam_rmdup.c
2580 M /trunk/samtools/bamtk.c
2582 * samtools-0.1.6-14 (r480)
2583 * rmdup is now RG aware
2585 ------------------------------------------------------------------------
2586 r480 | lh3lh3 | 2009-10-17 22:05:20 -0400 (Sat, 17 Oct 2009) | 2 lines
2588 M /trunk/samtools/misc/samtools.pl
2590 added a small unitity to parse SRA XML files
2592 ------------------------------------------------------------------------
2593 r479 | lh3lh3 | 2009-10-17 20:57:26 -0400 (Sat, 17 Oct 2009) | 3 lines
2595 M /trunk/samtools/bam_maqcns.c
2596 M /trunk/samtools/bam_maqcns.h
2597 M /trunk/samtools/bam_plcmd.c
2598 M /trunk/samtools/bam_sort.c
2599 M /trunk/samtools/bamtk.c
2601 * samtools-0.1.6-13 (r479)
2602 * merge: optionally use file names as RG tags
2604 ------------------------------------------------------------------------
2605 r478 | lh3lh3 | 2009-10-14 14:18:12 -0400 (Wed, 14 Oct 2009) | 3 lines
2607 M /trunk/samtools/bam.c
2608 M /trunk/samtools/bam.h
2609 M /trunk/samtools/bam_maqcns.c
2610 M /trunk/samtools/bamtk.c
2611 M /trunk/samtools/kaln.c
2613 * samtools-0.1.6-12 (r478)
2614 * fixed a bug in the indel caller
2616 ------------------------------------------------------------------------
2617 r477 | lh3lh3 | 2009-10-10 06:12:26 -0400 (Sat, 10 Oct 2009) | 3 lines
2619 M /trunk/samtools/bam_index.c
2620 M /trunk/samtools/bamtk.c
2622 * samtools-0.1.6-11 (r477)
2623 * fixed a bug due to recent change in bam_index.c (thank Nicole Washington for the patch)
2625 ------------------------------------------------------------------------
2626 r476 | petulda | 2009-10-09 11:45:36 -0400 (Fri, 09 Oct 2009) | 1 line
2628 A /trunk/samtools/misc/sam2vcf.pl
2630 Added the sam2vcf.pl script.
2631 ------------------------------------------------------------------------
2632 r475 | lh3lh3 | 2009-10-08 10:19:16 -0400 (Thu, 08 Oct 2009) | 2 lines
2634 M /trunk/samtools/Makefile
2635 M /trunk/samtools/bam.c
2636 M /trunk/samtools/bam.h
2637 M /trunk/samtools/bam_maqcns.c
2638 M /trunk/samtools/bamtk.c
2639 A /trunk/samtools/kaln.c
2640 A /trunk/samtools/kaln.h
2642 Unfinished modification. Please do not use this revision...
2644 ------------------------------------------------------------------------
2645 r474 | petulda | 2009-10-08 06:39:54 -0400 (Thu, 08 Oct 2009) | 1 line
2647 M /trunk/samtools/knetfile.c
2649 Removed the offending knet_seek message.
2650 ------------------------------------------------------------------------
2651 r473 | petulda | 2009-10-06 09:26:35 -0400 (Tue, 06 Oct 2009) | 1 line
2653 M /trunk/samtools/knetfile.c
2654 M /trunk/samtools/razf.c
2656 Bug fix - faidx on RAZF compressed files now working.
2657 ------------------------------------------------------------------------
2658 r472 | lh3lh3 | 2009-10-02 08:42:57 -0400 (Fri, 02 Oct 2009) | 2 lines
2660 M /trunk/samtools/samtools.1
2662 Clarify the meaning of a region like "chr2:1,000,000".
2664 ------------------------------------------------------------------------
2665 r471 | lh3lh3 | 2009-10-02 05:42:19 -0400 (Fri, 02 Oct 2009) | 2 lines
2667 M /trunk/samtools/misc/novo2sam.pl
2669 Fixed minor bugs in novo2sam.pl (on behalf of Ken Chen and Colin Hercus)
2671 ------------------------------------------------------------------------
2672 r470 | lh3lh3 | 2009-09-29 15:01:27 -0400 (Tue, 29 Sep 2009) | 3 lines
2674 M /trunk/samtools/Makefile.mingw
2675 M /trunk/samtools/bamtk.c
2676 M /trunk/samtools/knetfile.c
2677 M /trunk/samtools/knetfile.h
2679 * samtools-0.1.6-9 (r470)
2680 * make knetfile.c compatible with MinGW (thank Martin Morgan for the patch)
2682 ------------------------------------------------------------------------
2683 r469 | lh3lh3 | 2009-09-29 08:07:44 -0400 (Tue, 29 Sep 2009) | 3 lines
2685 M /trunk/samtools/bam_index.c
2686 M /trunk/samtools/bamtk.c
2688 * samtools-0.1.6-9 (r469)
2689 * refactor bam_fetch() for Python binding. On behalf of Leo Goodstadt.
2691 ------------------------------------------------------------------------
2692 r468 | lh3lh3 | 2009-09-28 05:18:29 -0400 (Mon, 28 Sep 2009) | 3 lines
2694 M /trunk/samtools/bam_sort.c
2695 M /trunk/samtools/bamtk.c
2696 M /trunk/samtools/misc/samtools.pl
2698 * samtools-0.1.6-7 (r468)
2701 ------------------------------------------------------------------------
2702 r467 | petulda | 2009-09-28 04:51:29 -0400 (Mon, 28 Sep 2009) | 1 line
2704 M /trunk/samtools/bgzf.c
2705 M /trunk/samtools/bgzip.c
2706 M /trunk/samtools/razf.c
2707 M /trunk/samtools/razip.c
2709 Changed the mode for newly created files to 0666. This allows less strict permissions with umask properly set (e.g. 0002 vs. 0022).
2710 ------------------------------------------------------------------------
2711 r466 | lh3lh3 | 2009-09-24 06:29:19 -0400 (Thu, 24 Sep 2009) | 3 lines
2713 M /trunk/samtools/ChangeLog
2714 M /trunk/samtools/bam_md.c
2715 M /trunk/samtools/bamtk.c
2717 * samtools-0.1.6-6 (r466)
2718 * do not crash calmd when some sequences are absent from the reference.
2720 ------------------------------------------------------------------------
2721 r464 | jmarshall | 2009-09-23 06:14:32 -0400 (Wed, 23 Sep 2009) | 3 lines
2723 M /trunk/samtools/bam.c
2724 M /trunk/samtools/knetfile.c
2726 Suppress bgzf_check_EOF() messages when reading from a pipe, as there is
2727 no way to seek on a pipe and the messages always appear.
2729 ------------------------------------------------------------------------
2730 r463 | petulda | 2009-09-16 07:05:41 -0400 (Wed, 16 Sep 2009) | 1 line
2732 M /trunk/samtools/knetfile.c
2733 M /trunk/samtools/razf.c
2735 A bug fix, "samtools view" is now working again.
2736 ------------------------------------------------------------------------
2737 r462 | lh3lh3 | 2009-09-16 04:51:07 -0400 (Wed, 16 Sep 2009) | 3 lines
2739 M /trunk/samtools/bamtk.c
2740 M /trunk/samtools/faidx.c
2741 M /trunk/samtools/knetfile.c
2742 M /trunk/samtools/knetfile.h
2743 M /trunk/samtools/razf.c
2744 M /trunk/samtools/razf.h
2746 * samtools-0.1.6-5 (r462)
2747 * Added knetfile support in razf and faidx (on behalf of Petr Danecek)
2749 ------------------------------------------------------------------------
2750 r460 | lh3lh3 | 2009-09-09 07:06:22 -0400 (Wed, 09 Sep 2009) | 2 lines
2752 M /trunk/samtools/samtools.1
2754 fixed a formatting issue
2756 ------------------------------------------------------------------------
2757 r459 | lh3lh3 | 2009-09-08 18:14:08 -0400 (Tue, 08 Sep 2009) | 3 lines
2759 M /trunk/samtools/bam_sort.c
2760 M /trunk/samtools/bamtk.c
2762 * samtools-0.1.6-4 (r459)
2763 * make sort output the result to stdout when -o is in use
2765 ------------------------------------------------------------------------
2766 r458 | lh3lh3 | 2009-09-07 05:10:28 -0400 (Mon, 07 Sep 2009) | 4 lines
2768 M /trunk/samtools/bamtk.c
2769 M /trunk/samtools/faidx.c
2770 M /trunk/samtools/faidx.h
2771 M /trunk/samtools/samtools.1
2773 * samtools-0.1.6-2 (r458)
2774 * added more interface to faidx (by Nils)
2775 * updated documentation
2777 ------------------------------------------------------------------------
2778 r457 | lh3lh3 | 2009-09-05 16:12:04 -0400 (Sat, 05 Sep 2009) | 3 lines
2780 M /trunk/samtools/bam_sort.c
2781 M /trunk/samtools/bamtk.c
2783 * samtools-0.1.6-2 (r457)
2784 * get rid of three assert() in bam_sort.c
2786 ------------------------------------------------------------------------
2787 r456 | jmarshall | 2009-09-04 12:46:25 -0400 (Fri, 04 Sep 2009) | 3 lines
2789 M /trunk/samtools/razf.c
2791 Return NULL from _razf_open() (and hence razf_open()/razf_open2())
2792 when opening the file fails.
2794 ------------------------------------------------------------------------
2795 r453 | lh3lh3 | 2009-09-02 08:56:33 -0400 (Wed, 02 Sep 2009) | 2 lines
2797 M /trunk/samtools/ChangeLog
2798 M /trunk/samtools/NEWS
2799 M /trunk/samtools/bamtk.c
2800 M /trunk/samtools/samtools.1
2801 D /trunk/samtools/source.dot
2803 Release samtools-0.1.6
2805 ------------------------------------------------------------------------
2806 r451 | lh3lh3 | 2009-09-02 05:44:48 -0400 (Wed, 02 Sep 2009) | 4 lines
2808 M /trunk/samtools/bam_md.c
2809 M /trunk/samtools/bam_rmdup.c
2810 M /trunk/samtools/bam_rmdupse.c
2811 M /trunk/samtools/bam_sort.c
2812 M /trunk/samtools/bamtk.c
2813 M /trunk/samtools/samtools.1
2815 * samtools-0.1.5-34 (r451)
2816 * applied the patch by John
2817 * improved the help message a little bit
2819 ------------------------------------------------------------------------
2820 r450 | lh3lh3 | 2009-09-02 04:55:55 -0400 (Wed, 02 Sep 2009) | 3 lines
2822 M /trunk/samtools/bam_color.c
2823 M /trunk/samtools/bamtk.c
2825 * samtools-0.1.5-33 (r450)
2826 * fixed a bug in bam_color.c (on behalf of Nils Homer)
2828 ------------------------------------------------------------------------
2829 r449 | lh3lh3 | 2009-08-29 15:36:41 -0400 (Sat, 29 Aug 2009) | 4 lines
2831 M /trunk/samtools/bam_import.c
2832 M /trunk/samtools/bam_md.c
2833 M /trunk/samtools/bamtk.c
2834 M /trunk/samtools/misc/samtools.pl
2836 * samtools-0.1.5-32 (r449)
2837 * fillmd: fixed a bug in modifying MD/NM tags
2838 * in import, give a warning if the read is aligned but there is no CIGAR.
2840 ------------------------------------------------------------------------
2841 r448 | lh3lh3 | 2009-08-19 04:44:28 -0400 (Wed, 19 Aug 2009) | 3 lines
2843 M /trunk/samtools/ChangeLog
2844 M /trunk/samtools/bam_pileup.c
2845 M /trunk/samtools/bamtk.c
2846 M /trunk/samtools/misc/wgsim_eval.pl
2848 * samtools-0.1.5-31 (r448)
2849 * fixed an issue when the last CIGAR is I or D
2851 ------------------------------------------------------------------------
2852 r447 | lh3lh3 | 2009-08-17 04:34:57 -0400 (Mon, 17 Aug 2009) | 3 lines
2854 M /trunk/samtools/bam_aux.c
2855 M /trunk/samtools/bamtk.c
2857 * samtools-0.1.5-30 (r447)
2858 * fixed a bug in bam_aux_get(): 'A' is not checked
2860 ------------------------------------------------------------------------
2861 r446 | lh3lh3 | 2009-08-17 04:33:17 -0400 (Mon, 17 Aug 2009) | 2 lines
2863 M /trunk/samtools/bam_aux.c
2864 M /trunk/samtools/bamtk.c
2868 ------------------------------------------------------------------------
2869 r444 | lh3lh3 | 2009-08-11 05:02:36 -0400 (Tue, 11 Aug 2009) | 3 lines
2871 M /trunk/samtools/bam_sort.c
2872 M /trunk/samtools/bamtk.c
2874 * samtools-0.1.5-28 (r444)
2877 ------------------------------------------------------------------------
2878 r443 | lh3lh3 | 2009-08-11 04:29:11 -0400 (Tue, 11 Aug 2009) | 4 lines
2880 M /trunk/samtools/bam.c
2881 M /trunk/samtools/bam_import.c
2882 M /trunk/samtools/bamtk.c
2884 * samtools-0.1.5-27 (r443)
2885 * SEQ and QUAL can be "*"
2886 * parse CIGAR "=" and "X" as "M"
2888 ------------------------------------------------------------------------
2889 r442 | lh3lh3 | 2009-08-07 16:56:38 -0400 (Fri, 07 Aug 2009) | 4 lines
2891 M /trunk/samtools/bam_pileup.c
2892 M /trunk/samtools/bamtk.c
2893 M /trunk/samtools/misc/md5.c
2894 M /trunk/samtools/misc/md5.h
2895 M /trunk/samtools/misc/md5fa.c
2897 * samtools-0.1.5-26 (r442)
2898 * replace RSA Inc md5.* with ones under permissive lincense
2899 * fixed a bug in detecting unsorted bam in pileup
2901 ------------------------------------------------------------------------
2902 r441 | bhandsaker | 2009-08-05 09:41:28 -0400 (Wed, 05 Aug 2009) | 2 lines
2904 M /trunk/samtools/bgzf.c
2905 M /trunk/samtools/bgzf.h
2906 M /trunk/samtools/bgzip.c
2908 Change copyright notices now that MIT has approved open source distribution.
2910 ------------------------------------------------------------------------
2911 r440 | lh3lh3 | 2009-08-05 05:44:24 -0400 (Wed, 05 Aug 2009) | 3 lines
2913 M /trunk/samtools/bam_stat.c
2914 M /trunk/samtools/bamtk.c
2916 * samtools-0.1.5-25 (r436)
2917 * in flagstats, do not report singletons if both ends are unmapped
2919 ------------------------------------------------------------------------
2920 r439 | lh3lh3 | 2009-08-04 17:16:51 -0400 (Tue, 04 Aug 2009) | 2 lines
2922 M /trunk/samtools/misc/maq2sam.c
2924 fixed a SERIOUS bug in setting 0x20 flag
2926 ------------------------------------------------------------------------
2927 r438 | lh3lh3 | 2009-08-04 16:50:43 -0400 (Tue, 04 Aug 2009) | 2 lines
2929 M /trunk/samtools/misc/samtools.pl
2931 fixed two minor bugs (suggested by Tim M Storm)
2933 ------------------------------------------------------------------------
2934 r437 | lh3lh3 | 2009-08-04 04:13:24 -0400 (Tue, 04 Aug 2009) | 3 lines
2936 M /trunk/samtools/bamtk.c
2937 M /trunk/samtools/misc/samtools.pl
2938 M /trunk/samtools/sam_view.c
2940 * samtools-0.1.5-24 (r435)
2943 ------------------------------------------------------------------------
2944 r434 | lh3lh3 | 2009-08-03 05:40:42 -0400 (Mon, 03 Aug 2009) | 3 lines
2946 M /trunk/samtools/bam_tview.c
2947 M /trunk/samtools/bamtk.c
2949 * samtools-0.1.5-23 (r434)
2950 * in tview, press 'r' to show read names rather than sequences
2952 ------------------------------------------------------------------------
2953 r433 | lh3lh3 | 2009-08-02 14:13:35 -0400 (Sun, 02 Aug 2009) | 3 lines
2955 M /trunk/samtools/knetfile.c
2957 * tried to fixed the buggy FTP random access in Windows. FAILED.
2958 * anyway, MinGW seems to have problem with "%lld".
2960 ------------------------------------------------------------------------
2961 r432 | lh3lh3 | 2009-08-01 19:32:07 -0400 (Sat, 01 Aug 2009) | 5 lines
2963 M /trunk/samtools/Makefile.mingw
2964 M /trunk/samtools/bamtk.c
2965 M /trunk/samtools/faidx.c
2966 M /trunk/samtools/razf.c
2967 A /trunk/samtools/win32/libcurses.a
2968 A /trunk/samtools/win32/xcurses.h
2970 * samtools-0.1.5-22 (r432)
2971 * faidx: fixed compitability issue with _WIN32
2972 * razf: fixed potential compitability issue with _WIN32
2973 * PDCurses support in Windows
2975 ------------------------------------------------------------------------
2976 r431 | lh3lh3 | 2009-08-01 18:34:54 -0400 (Sat, 01 Aug 2009) | 2 lines
2978 M /trunk/samtools/win32/libz.a
2980 replace the GnuWin32 version of libz.a with my own build with MinGW.
2982 ------------------------------------------------------------------------
2983 r430 | lh3lh3 | 2009-08-01 18:21:07 -0400 (Sat, 01 Aug 2009) | 2 lines
2985 M /trunk/samtools/knetfile.c
2989 ------------------------------------------------------------------------
2990 r429 | lh3lh3 | 2009-08-01 17:41:19 -0400 (Sat, 01 Aug 2009) | 3 lines
2992 M /trunk/samtools/Makefile.mingw
2993 M /trunk/samtools/bamtk.c
2994 M /trunk/samtools/knetfile.c
2995 M /trunk/samtools/knetfile.h
2997 * samtools-0.1.5-21 (r428)
2998 * knetfile.c is now compatible with mingw-winsock
3000 ------------------------------------------------------------------------
3001 r428 | lh3lh3 | 2009-07-31 19:39:07 -0400 (Fri, 31 Jul 2009) | 2 lines
3003 M /trunk/samtools/Makefile.mingw
3005 simplify MinGW Makefile
3007 ------------------------------------------------------------------------
3008 r427 | lh3lh3 | 2009-07-31 19:30:54 -0400 (Fri, 31 Jul 2009) | 5 lines
3010 A /trunk/samtools/Makefile.mingw
3011 M /trunk/samtools/bam_import.c
3012 M /trunk/samtools/bamtk.c
3013 A /trunk/samtools/win32
3014 A /trunk/samtools/win32/libz.a
3015 A /trunk/samtools/win32/zconf.h
3016 A /trunk/samtools/win32/zlib.h
3018 * samtools-0.1.5-20 (r427)
3019 * MinGW support. At least SAM<->BAM conversion is working. Other
3020 functionality are not tested at the moment.
3021 * zlib headers and Windows version of libz.a are included in win32/
3023 ------------------------------------------------------------------------
3024 r426 | lh3lh3 | 2009-07-31 18:32:09 -0400 (Fri, 31 Jul 2009) | 3 lines
3026 M /trunk/samtools/bamtk.c
3027 M /trunk/samtools/sam_view.c
3029 * samtools-0.1.5-19 (r426)
3030 * fixed a bug caused by recent modifications. Sorry.
3032 ------------------------------------------------------------------------
3033 r425 | lh3lh3 | 2009-07-31 18:23:51 -0400 (Fri, 31 Jul 2009) | 2 lines
3035 M /trunk/samtools/bgzf.c
3037 compatible with Windows binary files
3039 ------------------------------------------------------------------------
3040 r424 | lh3lh3 | 2009-07-31 05:19:59 -0400 (Fri, 31 Jul 2009) | 5 lines
3042 M /trunk/samtools/bam_maqcns.c
3043 M /trunk/samtools/bam_maqcns.h
3044 M /trunk/samtools/bam_plcmd.c
3045 M /trunk/samtools/bam_tview.c
3046 M /trunk/samtools/bamtk.c
3047 M /trunk/samtools/misc/samtools.pl
3049 * samtools-0.1.5-18 (r423)
3050 * output additional information in pileup indel lines, for the purepose
3051 of debugging at the moment
3052 * in tview, optionally allow to treat reference skip as deletion
3054 ------------------------------------------------------------------------
3055 r423 | lh3lh3 | 2009-07-30 17:00:36 -0400 (Thu, 30 Jul 2009) | 2 lines
3057 A /trunk/samtools/misc/psl2sam.pl
3059 convert BLAT psl to SAM.
3061 ------------------------------------------------------------------------
3062 r422 | lh3lh3 | 2009-07-30 06:24:39 -0400 (Thu, 30 Jul 2009) | 6 lines
3064 M /trunk/samtools/ChangeLog
3065 M /trunk/samtools/bam.c
3066 M /trunk/samtools/bamtk.c
3067 M /trunk/samtools/bgzf.c
3068 M /trunk/samtools/bgzf.h
3069 M /trunk/samtools/knetfile.c
3070 M /trunk/samtools/sam.c
3071 M /trunk/samtools/sam_view.c
3073 * samtools-0.1.5-17 (r422)
3074 * fixed a but in knetfile.c when seek type is not SEEK_SET
3075 * write an empty BGZF block to every BGZF file
3076 * check BGZF EOF marker in bam_header_read()
3079 ------------------------------------------------------------------------
3080 r421 | lh3lh3 | 2009-07-30 05:03:39 -0400 (Thu, 30 Jul 2009) | 3 lines
3082 M /trunk/samtools/bam_import.c
3083 M /trunk/samtools/bam_plcmd.c
3084 M /trunk/samtools/bamtk.c
3085 M /trunk/samtools/misc/samtools.pl
3086 M /trunk/samtools/sam.c
3087 M /trunk/samtools/sam.h
3088 M /trunk/samtools/sam_view.c
3090 * samtools-0.1.5-16 (r421)
3091 * in view and pileup, load header from FASTA index if the input is SAM.
3093 ------------------------------------------------------------------------
3094 r420 | lh3lh3 | 2009-07-29 04:18:55 -0400 (Wed, 29 Jul 2009) | 2 lines
3096 M /trunk/samtools/misc/maq2sam.c
3098 do not set "read 1" if reads are not mapped in the PE mode of maq
3100 ------------------------------------------------------------------------
3101 r419 | lh3lh3 | 2009-07-28 04:52:33 -0400 (Tue, 28 Jul 2009) | 5 lines
3103 M /trunk/samtools/bam_import.c
3104 M /trunk/samtools/bamtk.c
3105 M /trunk/samtools/misc/samtools.pl
3106 M /trunk/samtools/misc/wgsim_eval.pl
3108 * samtools-0.1.5-15 (r419)
3109 * in sam_open(), return NULL when the file cannot be opened.
3110 * make wgsim_eval.pl more robust to imperfect SAM
3111 * add "unique" command to samtools.pl
3113 ------------------------------------------------------------------------
3114 r418 | lh3lh3 | 2009-07-24 09:04:19 -0400 (Fri, 24 Jul 2009) | 2 lines
3116 M /trunk/samtools/misc/wgsim_eval.pl
3118 skip @header lines in SAM
3120 ------------------------------------------------------------------------
3121 r417 | lh3lh3 | 2009-07-24 07:42:38 -0400 (Fri, 24 Jul 2009) | 3 lines
3123 M /trunk/samtools/bamtk.c
3124 M /trunk/samtools/sam_view.c
3126 * samtools-0.1.5-14 (r417)
3127 * more help in "samtools view" due to the recent changes.
3129 ------------------------------------------------------------------------
3130 r416 | lh3lh3 | 2009-07-24 07:34:30 -0400 (Fri, 24 Jul 2009) | 3 lines
3132 M /trunk/samtools/bam.c
3133 M /trunk/samtools/bam.h
3134 M /trunk/samtools/bam_import.c
3135 M /trunk/samtools/bamtk.c
3136 M /trunk/samtools/sam.c
3137 M /trunk/samtools/sam.h
3138 M /trunk/samtools/sam_view.c
3140 * samtools-0.1.5-17 (r416)
3141 * support import/export SAM with string tags
3143 ------------------------------------------------------------------------
3144 r415 | lh3lh3 | 2009-07-24 06:39:26 -0400 (Fri, 24 Jul 2009) | 3 lines
3146 M /trunk/samtools/bam.c
3147 M /trunk/samtools/bam.h
3148 M /trunk/samtools/bam_import.c
3149 M /trunk/samtools/bamtk.c
3150 M /trunk/samtools/sam.c
3151 M /trunk/samtools/sam.h
3152 M /trunk/samtools/sam_view.c
3154 * samtools-0.1.5-12 (r415)
3155 * FLAG now can be in HEX
3157 ------------------------------------------------------------------------
3158 r414 | lh3lh3 | 2009-07-22 17:03:49 -0400 (Wed, 22 Jul 2009) | 2 lines
3160 M /trunk/samtools/kstring.h
3162 fixed a compiling error (thank Ken for fixing it)
3164 ------------------------------------------------------------------------
3165 r412 | lh3lh3 | 2009-07-21 17:19:40 -0400 (Tue, 21 Jul 2009) | 2 lines
3167 M /trunk/samtools/kstring.c
3168 M /trunk/samtools/kstring.h
3170 Implemented Boyer-Moore search in the kstring library.
3172 ------------------------------------------------------------------------
3173 r409 | lh3lh3 | 2009-07-17 12:10:20 -0400 (Fri, 17 Jul 2009) | 2 lines
3175 M /trunk/samtools/bam_index.c
3177 do not include knetfile.h when _USE_KNETFILE is not defined
3179 ------------------------------------------------------------------------
3180 r408 | lh3lh3 | 2009-07-17 10:29:21 -0400 (Fri, 17 Jul 2009) | 5 lines
3182 M /trunk/samtools/bam_md.c
3183 M /trunk/samtools/bam_tview.c
3184 M /trunk/samtools/bamtk.c
3185 M /trunk/samtools/bgzf.c
3187 * samtools-0.1.5-11 (r408)
3188 * force to overwirte existing MD if it is different from the one calculated
3190 * bgzf.c: improved the compatibility with Windows headers
3192 ------------------------------------------------------------------------
3193 r407 | lh3lh3 | 2009-07-17 09:46:56 -0400 (Fri, 17 Jul 2009) | 5 lines
3195 M /trunk/samtools/bam.h
3196 M /trunk/samtools/bam_aux.c
3197 M /trunk/samtools/bam_md.c
3198 M /trunk/samtools/bamtk.c
3199 M /trunk/samtools/sam.h
3201 * samtools-0.1.5-10 (r407)
3202 * implemented bam_aux_del() to remove a tag
3203 * fillmd: generate the NM tag
3204 * fillmd: cmd interface improvement
3206 ------------------------------------------------------------------------
3207 r406 | lh3lh3 | 2009-07-16 18:30:40 -0400 (Thu, 16 Jul 2009) | 2 lines
3209 M /trunk/samtools/Makefile
3211 Sorry. The old Makefile is for PDCurses...
3213 ------------------------------------------------------------------------
3214 r405 | lh3lh3 | 2009-07-16 18:30:11 -0400 (Thu, 16 Jul 2009) | 3 lines
3216 M /trunk/samtools/Makefile
3217 M /trunk/samtools/bam_tview.c
3218 M /trunk/samtools/bamtk.c
3220 * samtools-0.1.5-9 (r405)
3221 * improved the compatibility with PDCurses a little bit
3223 ------------------------------------------------------------------------
3224 r404 | lh3lh3 | 2009-07-16 18:23:52 -0400 (Thu, 16 Jul 2009) | 3 lines
3226 M /trunk/samtools/Makefile
3227 M /trunk/samtools/bam_tview.c
3228 M /trunk/samtools/bamtk.c
3230 * samtools-0.1.5-8 (r404)
3231 * compatible with PDCurses
3233 ------------------------------------------------------------------------
3234 r403 | lh3lh3 | 2009-07-16 17:39:39 -0400 (Thu, 16 Jul 2009) | 3 lines
3236 M /trunk/samtools/bamtk.c
3237 M /trunk/samtools/kseq.h
3239 * samtools-0.1.5-7 (r403)
3240 * fixed a bug in kseq.h for binary files (text files are fine)
3242 ------------------------------------------------------------------------
3243 r402 | lh3lh3 | 2009-07-16 06:49:53 -0400 (Thu, 16 Jul 2009) | 4 lines
3245 M /trunk/samtools/bam_import.c
3246 M /trunk/samtools/bam_index.c
3247 M /trunk/samtools/bamtk.c
3248 M /trunk/samtools/bgzf.c
3250 * samtools-0.1.5-6 (r402)
3251 * fixed compiling error when "-D_USE_NETFILE" is not applied
3252 * improve portability to MinGW
3254 ------------------------------------------------------------------------
3255 r398 | lh3lh3 | 2009-07-13 05:21:36 -0400 (Mon, 13 Jul 2009) | 3 lines
3257 A /trunk/bam-lite/bam.h (from /trunk/samtools/bam.h:395)
3258 A /trunk/bam-lite/bam_lite.c (from /trunk/samtools/bam_lite.c:395)
3259 D /trunk/samtools/bam_lite.c
3261 * move bam_lite.c to bam-lite
3262 * copy bam.h to bam-lite
3264 ------------------------------------------------------------------------
3265 r395 | lh3lh3 | 2009-07-13 05:12:57 -0400 (Mon, 13 Jul 2009) | 3 lines
3267 M /trunk/samtools/bam.h
3268 M /trunk/samtools/bam_lite.c
3269 M /trunk/samtools/bam_lpileup.c
3270 M /trunk/samtools/bam_pileup.c
3271 M /trunk/samtools/bamtk.c
3273 * samtools-0.1.5-5 (r395)
3274 * added bam_pileup_file() and removed bam_lpileup_file()
3276 ------------------------------------------------------------------------
3277 r394 | lh3lh3 | 2009-07-12 19:35:10 -0400 (Sun, 12 Jul 2009) | 3 lines
3279 M /trunk/samtools/bamtk.c
3280 M /trunk/samtools/knetfile.c
3281 M /trunk/samtools/knetfile.h
3283 * samtools-0.1.5-4 (r394)
3284 * http_proxy support in knetfile library (check http_proxy ENV)
3286 ------------------------------------------------------------------------
3287 r393 | lh3lh3 | 2009-07-12 18:57:07 -0400 (Sun, 12 Jul 2009) | 5 lines
3289 M /trunk/samtools/bam_index.c
3290 M /trunk/samtools/bam_tview.c
3291 M /trunk/samtools/bamtk.c
3292 M /trunk/samtools/knetfile.c
3293 M /trunk/samtools/knetfile.h
3295 * samtools-0.1.5-3 (r393)
3296 * knetfile now supports HTTP (no proxy at the moment)
3297 * fixed a potential issue in knetfile on opening ordinary file, although I have
3298 not seen the sideeffect so far.
3300 ------------------------------------------------------------------------
3301 r392 | lh3lh3 | 2009-07-12 13:50:55 -0400 (Sun, 12 Jul 2009) | 2 lines
3303 M /trunk/samtools/samtools.1
3305 Remove the warning in tview
3307 ------------------------------------------------------------------------
3308 r391 | lh3lh3 | 2009-07-12 13:42:43 -0400 (Sun, 12 Jul 2009) | 3 lines
3310 M /trunk/samtools/bam_tview.c
3311 M /trunk/samtools/bamtk.c
3313 * samtools-0.1.5-2 (r391)
3314 * do not show a blank screen when no reads mapped
3316 ------------------------------------------------------------------------
3317 r390 | lh3lh3 | 2009-07-09 09:01:42 -0400 (Thu, 09 Jul 2009) | 4 lines
3319 M /trunk/samtools/bam.h
3320 A /trunk/samtools/bam_lite.c
3321 M /trunk/samtools/bamtk.c
3323 * samtools-0.1.5-1 (r390)
3324 * removed useless _IOLIB in bam.h. This should cause no change at all.
3325 * added bam_lite.c for light-weight BAM reading
3327 ------------------------------------------------------------------------
3328 r385 | lh3lh3 | 2009-07-07 11:53:29 -0400 (Tue, 07 Jul 2009) | 2 lines
3330 M /trunk/samtools/bamtk.c
3331 M /trunk/samtools/knetfile.c
3333 Release samtools-0.1.5c (fixed a bug in piping)
3335 ------------------------------------------------------------------------
3336 r383 | lh3lh3 | 2009-07-07 06:39:55 -0400 (Tue, 07 Jul 2009) | 2 lines
3338 M /trunk/samtools/bamtk.c
3339 M /trunk/samtools/sam.c
3341 Release samtools-0.1.5b (BUG! so embarrassing!)
3343 ------------------------------------------------------------------------
3344 r381 | lh3lh3 | 2009-07-07 06:20:06 -0400 (Tue, 07 Jul 2009) | 2 lines
3346 M /trunk/samtools/Makefile
3347 M /trunk/samtools/bam.h
3348 M /trunk/samtools/bam_aux.c
3349 M /trunk/samtools/bamtk.c
3351 Release samtools-0.1.5a (for compatibility with Bio::DB::Sam)
3353 ------------------------------------------------------------------------
3354 r373 | lh3lh3 | 2009-07-07 05:26:57 -0400 (Tue, 07 Jul 2009) | 2 lines
3356 M /trunk/samtools/ChangeLog
3357 M /trunk/samtools/NEWS
3358 M /trunk/samtools/bamtk.c
3359 M /trunk/samtools/samtools.1
3361 Release samtools-0.1.5
3363 ------------------------------------------------------------------------
3364 r372 | lh3lh3 | 2009-07-07 04:49:27 -0400 (Tue, 07 Jul 2009) | 3 lines
3366 M /trunk/samtools/bamtk.c
3367 M /trunk/samtools/sam.c
3369 * samtools-0.1.4-23 (r372)
3370 * keep header text if "view -t" is used (by Gerton)
3372 ------------------------------------------------------------------------
3373 r371 | lh3lh3 | 2009-07-06 20:13:32 -0400 (Mon, 06 Jul 2009) | 2 lines
3375 M /trunk/samtools/samtools.1
3377 update documentation
3379 ------------------------------------------------------------------------
3380 r370 | bhandsaker | 2009-07-02 17:24:34 -0400 (Thu, 02 Jul 2009) | 2 lines
3382 M /trunk/samtools/Makefile
3384 Introduced LIBPATH variable so this could be overridden to allow samtools to build correct at the Broad.
3386 ------------------------------------------------------------------------
3387 r369 | lh3lh3 | 2009-07-02 08:36:53 -0400 (Thu, 02 Jul 2009) | 4 lines
3389 M /trunk/samtools/ChangeLog
3390 M /trunk/samtools/bam_aux.c
3391 M /trunk/samtools/bam_plcmd.c
3392 M /trunk/samtools/bamtk.c
3394 * samtools-0.1.4-22 (r369)
3395 * in pileup, optionally print E2 and U2
3396 * remove the debugging code in bam_aux_get() (Drat!)
3398 ------------------------------------------------------------------------
3399 r368 | lh3lh3 | 2009-07-02 06:32:26 -0400 (Thu, 02 Jul 2009) | 6 lines
3401 M /trunk/samtools/bam.c
3402 M /trunk/samtools/bam.h
3403 M /trunk/samtools/bam_aux.c
3404 M /trunk/samtools/bam_index.c
3405 M /trunk/samtools/bam_lpileup.c
3406 M /trunk/samtools/bam_md.c
3407 M /trunk/samtools/bam_pileup.c
3408 M /trunk/samtools/bam_rmdup.c
3409 M /trunk/samtools/bam_stat.c
3410 M /trunk/samtools/bam_tview.c
3411 M /trunk/samtools/bamtk.c
3412 M /trunk/samtools/faidx.c
3413 M /trunk/samtools/faidx.h
3414 M /trunk/samtools/glf.c
3416 * samtools-0.1.4-21 (r368)
3417 * propagate errors rather than exit or complain assertion failure. Assertion
3418 should be only used for checking internal bugs, but not for external input
3419 inconsistency. I was just a bit lazy.
3420 * small memory leak may be present on failure, though
3422 ------------------------------------------------------------------------
3423 r367 | lh3lh3 | 2009-06-30 11:18:42 -0400 (Tue, 30 Jun 2009) | 2 lines
3425 M /trunk/samtools/knetfile.c
3427 reduce the chance of blocking in FTP connection
3429 ------------------------------------------------------------------------
3430 r366 | lh3lh3 | 2009-06-30 10:35:21 -0400 (Tue, 30 Jun 2009) | 2 lines
3432 M /trunk/samtools/knetfile.c
3434 minor changes to knetfile: invalid fd equals -1 rather than 0
3436 ------------------------------------------------------------------------
3437 r365 | lh3lh3 | 2009-06-30 09:04:30 -0400 (Tue, 30 Jun 2009) | 3 lines
3439 M /trunk/samtools/bam_index.c
3440 M /trunk/samtools/bamtk.c
3441 M /trunk/samtools/knetfile.c
3442 M /trunk/samtools/knetfile.h
3444 * samtools-0.1.4-20 (r365)
3445 * download the BAM index file if it is not found in the current working directory.
3447 ------------------------------------------------------------------------
3448 r364 | lh3lh3 | 2009-06-30 07:39:07 -0400 (Tue, 30 Jun 2009) | 3 lines
3450 M /trunk/samtools/bamtk.c
3451 M /trunk/samtools/knetfile.c
3453 * samtools-0.1.4-19 (r364)
3454 * knetfile: report error when the file is not present on FTP
3456 ------------------------------------------------------------------------
3457 r363 | lh3lh3 | 2009-06-29 18:23:32 -0400 (Mon, 29 Jun 2009) | 4 lines
3459 M /trunk/samtools/bam_tview.c
3460 M /trunk/samtools/bamtk.c
3461 M /trunk/samtools/bgzf.c
3462 M /trunk/samtools/bgzf.h
3463 M /trunk/samtools/knetfile.c
3464 M /trunk/samtools/knetfile.h
3466 * samtools-0.1.4-18 (r363)
3467 * knetfile: do not trigger network communication in FTP seek (lazy seek)
3468 * bgzf: cache recent blocks (disabled by default)
3470 ------------------------------------------------------------------------
3471 r362 | lh3lh3 | 2009-06-25 16:04:34 -0400 (Thu, 25 Jun 2009) | 2 lines
3473 M /trunk/samtools/bgzf.c
3477 ------------------------------------------------------------------------
3478 r361 | lh3lh3 | 2009-06-25 16:03:10 -0400 (Thu, 25 Jun 2009) | 3 lines
3480 M /trunk/samtools/bam_index.c
3481 M /trunk/samtools/bamtk.c
3483 * samtools-0.1.4-17 (r361)
3484 * if a file is given on FTP, search locally for the BAM index
3486 ------------------------------------------------------------------------
3487 r360 | lh3lh3 | 2009-06-25 15:44:52 -0400 (Thu, 25 Jun 2009) | 5 lines
3489 M /trunk/samtools/Makefile
3490 M /trunk/samtools/bam_import.c
3491 M /trunk/samtools/bam_index.c
3492 M /trunk/samtools/bamtk.c
3493 M /trunk/samtools/bgzf.c
3494 M /trunk/samtools/bgzf.h
3495 M /trunk/samtools/knetfile.c
3496 M /trunk/samtools/knetfile.h
3498 * samtools-0.1.4-16 (r360)
3499 * report more information in index when the input is not sorted
3500 * change the behaviour of knet_seek() such that it returns 0 on success
3501 * support knetfile library in BGZF
3503 ------------------------------------------------------------------------
3504 r359 | lh3lh3 | 2009-06-25 12:10:55 -0400 (Thu, 25 Jun 2009) | 2 lines
3506 M /trunk/samtools/knetfile.c
3507 M /trunk/samtools/knetfile.h
3509 fixed bugs in knetfile.*
3511 ------------------------------------------------------------------------
3512 r358 | lh3lh3 | 2009-06-25 08:53:19 -0400 (Thu, 25 Jun 2009) | 2 lines
3514 A /trunk/samtools/knetfile.h
3516 this is the header file
3518 ------------------------------------------------------------------------
3519 r357 | lh3lh3 | 2009-06-25 08:52:03 -0400 (Thu, 25 Jun 2009) | 3 lines
3521 A /trunk/samtools/knetfile.c
3523 * open a file at FTP
3524 * preliminary version
3526 ------------------------------------------------------------------------
3527 r354 | lh3lh3 | 2009-06-24 09:02:25 -0400 (Wed, 24 Jun 2009) | 3 lines
3529 M /trunk/samtools/bam.c
3530 M /trunk/samtools/bamtk.c
3532 * samtools-0.1.4-15 (r354)
3533 * fixed a memory leak in bam_view1(), although samtools is not using this routine.
3535 ------------------------------------------------------------------------
3536 r351 | lh3lh3 | 2009-06-17 19:16:26 -0400 (Wed, 17 Jun 2009) | 4 lines
3538 M /trunk/samtools/bamtk.c
3539 M /trunk/samtools/faidx.c
3541 * samtools-0.1.4-13 (r351)
3542 * make faidx more tolerant to empty lines right before or after > lines
3543 * hope this does not introduce new bugs...
3545 ------------------------------------------------------------------------
3546 r350 | lh3lh3 | 2009-06-16 09:37:01 -0400 (Tue, 16 Jun 2009) | 3 lines
3548 M /trunk/samtools/bam_plcmd.c
3549 M /trunk/samtools/bamtk.c
3551 * samtools-0.1.4-13 (r350)
3552 * fixed a small memory leak in pileup, caused by recent modifications
3554 ------------------------------------------------------------------------
3555 r347 | lh3lh3 | 2009-06-13 16:20:49 -0400 (Sat, 13 Jun 2009) | 3 lines
3557 M /trunk/samtools/bam_plcmd.c
3558 M /trunk/samtools/bamtk.c
3559 M /trunk/samtools/sam_view.c
3561 * samtools-0.1.4-12 (r347)
3562 * added `-S' to pileup, similar to `view -S'
3564 ------------------------------------------------------------------------
3565 r346 | lh3lh3 | 2009-06-13 12:52:31 -0400 (Sat, 13 Jun 2009) | 3 lines
3567 M /trunk/samtools/Makefile
3568 M /trunk/samtools/bamtk.c
3569 M /trunk/samtools/sam_view.c
3570 M /trunk/samtools/samtools.1
3572 * samtools-0.1.4-11 (r346)
3573 * allow to select a read group at view command-line
3575 ------------------------------------------------------------------------
3576 r344 | lh3lh3 | 2009-06-13 09:06:24 -0400 (Sat, 13 Jun 2009) | 2 lines
3578 M /trunk/samtools/examples/calDepth.c
3582 ------------------------------------------------------------------------
3583 r343 | lh3lh3 | 2009-06-13 09:01:22 -0400 (Sat, 13 Jun 2009) | 2 lines
3585 M /trunk/samtools/examples/calDepth.c
3589 ------------------------------------------------------------------------
3590 r342 | lh3lh3 | 2009-06-13 08:58:48 -0400 (Sat, 13 Jun 2009) | 2 lines
3592 M /trunk/samtools/examples/Makefile
3593 A /trunk/samtools/examples/calDepth.c
3595 added an example of calculating read depth
3597 ------------------------------------------------------------------------
3598 r341 | lh3lh3 | 2009-06-13 08:00:08 -0400 (Sat, 13 Jun 2009) | 6 lines
3600 M /trunk/samtools/Makefile
3601 M /trunk/samtools/bam.h
3602 M /trunk/samtools/bam_aux.c
3603 A /trunk/samtools/bam_color.c
3604 M /trunk/samtools/bam_plcmd.c
3605 M /trunk/samtools/bam_sort.c
3606 M /trunk/samtools/bam_tview.c
3607 M /trunk/samtools/bamtk.c
3608 M /trunk/samtools/sam.c
3609 M /trunk/samtools/sam.h
3611 * samtools-0.1.4-10 (r341)
3612 * only include key APIs in libbam.a
3613 * move color-specific routines to bam_color.c
3614 * update documentations
3615 * remove the support of -q in pileup
3617 ------------------------------------------------------------------------
3618 r340 | lh3lh3 | 2009-06-13 06:17:14 -0400 (Sat, 13 Jun 2009) | 6 lines
3620 M /trunk/samtools/INSTALL
3621 M /trunk/samtools/Makefile
3622 M /trunk/samtools/bam_aux.c
3623 M /trunk/samtools/bam_import.c
3624 M /trunk/samtools/bam_tview.c
3625 M /trunk/samtools/bamtk.c
3626 M /trunk/samtools/razf.c
3627 M /trunk/samtools/sam_view.c
3629 * samtools-0.1.4-9 (r340)
3630 * added a warning to razf.c if zlib<1.2.2.1
3631 * fixed a compilation warning
3632 * fixed a segfault caused by @RG parsing
3633 * detect NCURSES in bam_tview.c
3635 ------------------------------------------------------------------------
3636 r339 | lh3lh3 | 2009-06-13 05:35:19 -0400 (Sat, 13 Jun 2009) | 2 lines
3638 M /trunk/samtools/INSTALL
3642 ------------------------------------------------------------------------
3643 r338 | lh3lh3 | 2009-06-12 19:15:24 -0400 (Fri, 12 Jun 2009) | 4 lines
3645 M /trunk/samtools/bam.c
3646 M /trunk/samtools/bam.h
3647 M /trunk/samtools/bam_aux.c
3648 M /trunk/samtools/bam_import.c
3649 M /trunk/samtools/bamtk.c
3650 M /trunk/samtools/kstring.h
3651 M /trunk/samtools/sam.c
3652 M /trunk/samtools/sam_view.c
3654 * samtools-0.1.4-8 (r338)
3655 * parse the @RG header lines and allow to choose library at the "samtools view"
3658 ------------------------------------------------------------------------
3659 r337 | lh3lh3 | 2009-06-12 16:25:50 -0400 (Fri, 12 Jun 2009) | 4 lines
3661 M /trunk/samtools/bamtk.c
3662 M /trunk/samtools/bgzf.c
3663 M /trunk/samtools/bgzf.h
3664 M /trunk/samtools/sam.c
3665 M /trunk/samtools/sam_view.c
3667 * samtools-0.1.4-7 (r337)
3668 * bgzf.c: support mode string "wu": uncompressed output
3669 * "samtools view" support "-u" command-line option
3671 ------------------------------------------------------------------------
3672 r336 | lh3lh3 | 2009-06-12 12:20:12 -0400 (Fri, 12 Jun 2009) | 5 lines
3674 M /trunk/samtools/Makefile
3675 M /trunk/samtools/misc/Makefile
3676 M /trunk/samtools/razf.c
3677 M /trunk/samtools/razf.h
3678 M /trunk/samtools/razip.c
3680 * no changes to samtools itself
3681 * remove zlib source codes
3682 * make RAZF reading compatible with old version of zlib
3683 * on old version of zlib, writing is not available
3685 ------------------------------------------------------------------------
3686 r335 | lh3lh3 | 2009-06-12 11:47:33 -0400 (Fri, 12 Jun 2009) | 2 lines
3688 D /trunk/samtools/zlib
3690 remove zlib for simplification...
3692 ------------------------------------------------------------------------
3693 r334 | lh3lh3 | 2009-06-12 10:43:36 -0400 (Fri, 12 Jun 2009) | 5 lines
3695 M /trunk/samtools/bam.h
3696 M /trunk/samtools/bam_aux.c
3697 M /trunk/samtools/bamtk.c
3699 * samtools-0.1.4-6 (r334)
3700 * do not export bam_aux_get_core() for Bio::DB::Sam because it has already
3701 been implemented in that.
3702 * this version works with the latest Bio::DB::Sam (20090612)
3704 ------------------------------------------------------------------------
3705 r333 | lh3lh3 | 2009-06-12 10:33:42 -0400 (Fri, 12 Jun 2009) | 2 lines
3707 M /trunk/samtools/ChangeLog
3711 ------------------------------------------------------------------------
3712 r332 | lh3lh3 | 2009-06-12 10:21:21 -0400 (Fri, 12 Jun 2009) | 2 lines
3714 M /trunk/samtools/AUTHORS
3715 M /trunk/samtools/Makefile
3716 M /trunk/samtools/misc/Makefile
3718 fixed minor things in Makefile
3720 ------------------------------------------------------------------------
3721 r331 | lh3lh3 | 2009-06-12 10:07:05 -0400 (Fri, 12 Jun 2009) | 4 lines
3723 M /trunk/samtools/bamtk.c
3725 * samtools-0.1.4-5 (r3310
3726 * no change to samtools itself. Version number is increased to reflect the
3727 changes in the Makefile building system.
3729 ------------------------------------------------------------------------
3730 r330 | lh3lh3 | 2009-06-12 10:03:38 -0400 (Fri, 12 Jun 2009) | 2 lines
3732 M /trunk/samtools/AUTHORS
3733 D /trunk/samtools/README
3735 update information...
3737 ------------------------------------------------------------------------
3738 r329 | lh3lh3 | 2009-06-12 09:52:21 -0400 (Fri, 12 Jun 2009) | 3 lines
3740 M /trunk/samtools/misc/novo2sam.pl
3742 * updated novoalign converter by Colin Hercus et al.
3743 * this version works with indels
3745 ------------------------------------------------------------------------
3746 r328 | lh3lh3 | 2009-06-12 09:50:53 -0400 (Fri, 12 Jun 2009) | 3 lines
3748 M /trunk/samtools/INSTALL
3749 M /trunk/samtools/Makefile
3750 M /trunk/samtools/misc/Makefile
3751 M /trunk/samtools/zlib/Makefile
3754 * update INSTALL instruction
3756 ------------------------------------------------------------------------
3757 r327 | lh3lh3 | 2009-06-12 09:18:29 -0400 (Fri, 12 Jun 2009) | 4 lines
3759 A /trunk/samtools/Makefile (from /trunk/samtools/Makefile.generic:325)
3760 D /trunk/samtools/Makefile.am
3761 D /trunk/samtools/Makefile.generic
3762 D /trunk/samtools/Makefile.lite
3763 D /trunk/samtools/autogen.sh
3764 D /trunk/samtools/cleanup.sh
3765 D /trunk/samtools/configure.ac
3766 A /trunk/samtools/misc/Makefile (from /trunk/samtools/misc/Makefile.generic:305)
3767 D /trunk/samtools/misc/Makefile.am
3768 D /trunk/samtools/misc/Makefile.generic
3769 M /trunk/samtools/razf.c
3770 A /trunk/samtools/zlib
3771 A /trunk/samtools/zlib/Makefile
3772 A /trunk/samtools/zlib/adler32.c
3773 A /trunk/samtools/zlib/compress.c
3774 A /trunk/samtools/zlib/crc32.c
3775 A /trunk/samtools/zlib/crc32.h
3776 A /trunk/samtools/zlib/deflate.c
3777 A /trunk/samtools/zlib/deflate.h
3778 A /trunk/samtools/zlib/gzio.c
3779 A /trunk/samtools/zlib/infback.c
3780 A /trunk/samtools/zlib/inffast.c
3781 A /trunk/samtools/zlib/inffast.h
3782 A /trunk/samtools/zlib/inffixed.h
3783 A /trunk/samtools/zlib/inflate.c
3784 A /trunk/samtools/zlib/inflate.h
3785 A /trunk/samtools/zlib/inftrees.c
3786 A /trunk/samtools/zlib/inftrees.h
3787 A /trunk/samtools/zlib/trees.c
3788 A /trunk/samtools/zlib/trees.h
3789 A /trunk/samtools/zlib/uncompr.c
3790 A /trunk/samtools/zlib/zconf.h
3791 A /trunk/samtools/zlib/zlib.h
3792 A /trunk/samtools/zlib/zutil.c
3793 A /trunk/samtools/zlib/zutil.h
3794 D /trunk/samtools/zutil.h
3796 * added zlib-1.2.3 as razip requires that
3797 * prepare to changed back to the Makefile building system
3798 * unfinished! (will be soon)
3800 ------------------------------------------------------------------------
3801 r326 | lh3lh3 | 2009-06-12 09:12:03 -0400 (Fri, 12 Jun 2009) | 2 lines
3803 M /trunk/samtools/misc/samtools.pl
3807 ------------------------------------------------------------------------
3808 r325 | lh3lh3 | 2009-06-10 11:27:59 -0400 (Wed, 10 Jun 2009) | 3 lines
3810 M /trunk/samtools/bam_maqcns.c
3811 M /trunk/samtools/bamtk.c
3813 * samtools-0.1.4-4 (r325)
3814 * further avoid wrong consensus calls in repetitive regions.
3816 ------------------------------------------------------------------------
3817 r324 | lh3lh3 | 2009-06-10 10:56:17 -0400 (Wed, 10 Jun 2009) | 4 lines
3819 M /trunk/samtools/bam_maqcns.c
3820 M /trunk/samtools/bam_plcmd.c
3821 M /trunk/samtools/bamtk.c
3822 M /trunk/samtools/sam.c
3823 M /trunk/samtools/sam.h
3825 * samtools-0.1.4-3 (r324)
3826 * make maqcns generate the correct call in repetitive regions.
3827 * allow filtering on mapQ at the pileup command line
3829 ------------------------------------------------------------------------
3830 r323 | lh3lh3 | 2009-06-10 05:04:21 -0400 (Wed, 10 Jun 2009) | 3 lines
3832 M /trunk/samtools/misc/samtools.pl
3834 * samtools.pl-0.3.2 (r322)
3835 * indels and SNPs use different mapping quality threshold
3837 ------------------------------------------------------------------------
3838 r322 | lh3lh3 | 2009-06-10 05:03:22 -0400 (Wed, 10 Jun 2009) | 2 lines
3840 M /trunk/samtools/misc/export2sam.pl
3844 ------------------------------------------------------------------------
3845 r321 | lh3lh3 | 2009-06-09 04:21:48 -0400 (Tue, 09 Jun 2009) | 2 lines
3847 M /trunk/samtools/misc/samtools.pl
3849 just typo. no real change
3851 ------------------------------------------------------------------------
3852 r320 | lh3lh3 | 2009-06-08 09:32:51 -0400 (Mon, 08 Jun 2009) | 2 lines
3854 M /trunk/samtools/misc/samtools.pl
3856 a little bit code cleanup
3858 ------------------------------------------------------------------------
3859 r319 | lh3lh3 | 2009-06-08 09:22:33 -0400 (Mon, 08 Jun 2009) | 4 lines
3861 M /trunk/samtools/misc/samtools.pl
3864 * change default parameters
3865 * optionally print filtered variants
3867 ------------------------------------------------------------------------
3868 r318 | lh3lh3 | 2009-06-08 09:14:26 -0400 (Mon, 08 Jun 2009) | 3 lines
3870 M /trunk/samtools/misc/samtools.pl
3873 * combine snpFilter and indelFilter
3875 ------------------------------------------------------------------------
3876 r317 | lh3lh3 | 2009-06-08 06:31:42 -0400 (Mon, 08 Jun 2009) | 3 lines
3878 M /trunk/samtools/misc/samtools.pl
3881 * change a default parameter
3883 ------------------------------------------------------------------------
3884 r316 | lh3lh3 | 2009-06-08 06:11:06 -0400 (Mon, 08 Jun 2009) | 5 lines
3886 M /trunk/samtools/bam_maqcns.c
3887 M /trunk/samtools/bam_maqcns.h
3888 M /trunk/samtools/bam_plcmd.c
3889 M /trunk/samtools/bamtk.c
3890 M /trunk/samtools/sam.c
3892 * samtools-0.1.4-2 (r316)
3893 * pileup: cap mapping quality at 60 (by default)
3894 * pileup: always calculate RMS mapq
3895 * pileup: allow to output variant sites only
3897 ------------------------------------------------------------------------
3898 r312 | lh3lh3 | 2009-06-04 08:01:10 -0400 (Thu, 04 Jun 2009) | 3 lines
3900 M /trunk/samtools/misc/samtools.pl
3905 ------------------------------------------------------------------------
3906 r311 | lh3lh3 | 2009-06-03 04:40:40 -0400 (Wed, 03 Jun 2009) | 2 lines
3908 M /trunk/samtools/misc/samtools.pl
3910 * in snpFilter, suppress non-SNP sites
3912 ------------------------------------------------------------------------
3913 r310 | lh3lh3 | 2009-06-01 09:35:13 -0400 (Mon, 01 Jun 2009) | 3 lines
3915 M /trunk/samtools/misc/samtools.pl
3920 ------------------------------------------------------------------------
3921 r309 | lh3lh3 | 2009-06-01 09:04:39 -0400 (Mon, 01 Jun 2009) | 3 lines
3923 M /trunk/samtools/misc/samtools.pl
3928 ------------------------------------------------------------------------
3929 r306 | lh3lh3 | 2009-05-28 06:49:35 -0400 (Thu, 28 May 2009) | 3 lines
3931 M /trunk/samtools/bgzf.c
3933 * minor changes to bgzf: return NULL if fd == -1
3934 * suggested by {kdj,jm18}@sanger.ac.uk
3936 ------------------------------------------------------------------------
3937 r305 | lh3lh3 | 2009-05-28 06:16:08 -0400 (Thu, 28 May 2009) | 2 lines
3939 A /trunk/samtools/misc/interpolate_sam.pl
3941 Script for paired-end pileup, contributed by Stephen Montgomery.
3943 ------------------------------------------------------------------------
3944 r304 | lh3lh3 | 2009-05-28 06:08:49 -0400 (Thu, 28 May 2009) | 3 lines
3946 M /trunk/samtools/bamtk.c
3947 M /trunk/samtools/sam.c
3949 * samtools-0.1.4-1 (r304)
3950 * fixed a minor bug in printing headers
3952 ------------------------------------------------------------------------
3953 r297 | lh3lh3 | 2009-05-21 11:06:16 -0400 (Thu, 21 May 2009) | 2 lines
3955 M /trunk/samtools/ChangeLog
3956 M /trunk/samtools/NEWS
3957 M /trunk/samtools/bam_plcmd.c
3958 M /trunk/samtools/bamtk.c
3959 M /trunk/samtools/misc/maq2sam.c
3960 M /trunk/samtools/samtools.1
3962 Release samtools-0.1.4
3964 ------------------------------------------------------------------------
3965 r296 | lh3lh3 | 2009-05-21 07:53:14 -0400 (Thu, 21 May 2009) | 3 lines
3967 M /trunk/samtools/bam_maqcns.c
3968 M /trunk/samtools/bamtk.c
3970 * samtools-0.1.3-24 (r296)
3971 * another similar bug in the indel caller
3973 ------------------------------------------------------------------------
3974 r295 | lh3lh3 | 2009-05-21 07:50:28 -0400 (Thu, 21 May 2009) | 3 lines
3976 M /trunk/samtools/bam_maqcns.c
3977 M /trunk/samtools/bamtk.c
3979 * samtools-0.1.3-23 (r295)
3980 * fixed a critical bug in the indel caller
3982 ------------------------------------------------------------------------
3983 r294 | lh3lh3 | 2009-05-20 08:00:20 -0400 (Wed, 20 May 2009) | 2 lines
3985 M /trunk/samtools/bam_stat.c
3987 added a missing header file
3989 ------------------------------------------------------------------------
3990 r293 | lh3lh3 | 2009-05-19 18:44:25 -0400 (Tue, 19 May 2009) | 3 lines
3992 M /trunk/samtools/bam_tview.c
3993 M /trunk/samtools/bamtk.c
3995 * samtools-0.1.3-22 (r293)
3996 * open tview in the dot-view mode by default
3998 ------------------------------------------------------------------------
3999 r292 | lh3lh3 | 2009-05-18 16:01:23 -0400 (Mon, 18 May 2009) | 6 lines
4001 M /trunk/samtools/samtools.1
4003 Added a note to the manual. Currently SAMtools used unaligned words in
4004 several places. Although this does not cause bus errors to me, it may
4005 affect portability. Please see the "Bus error" wiki page for more
4006 information. Also thank James Bonfields for pointing this out.
4009 ------------------------------------------------------------------------
4010 r286 | lh3lh3 | 2009-05-14 10:23:13 -0400 (Thu, 14 May 2009) | 3 lines
4012 M /trunk/samtools/bam.h
4013 M /trunk/samtools/bam_aux.c
4014 M /trunk/samtools/bamtk.c
4016 * samtools-0.1.3-21 (286)
4017 * declare bam_aux_get_core() in bam.h
4019 ------------------------------------------------------------------------
4020 r276 | lh3lh3 | 2009-05-13 05:07:55 -0400 (Wed, 13 May 2009) | 5 lines
4022 M /trunk/samtools/bam.h
4023 M /trunk/samtools/bam_index.c
4024 M /trunk/samtools/bamtk.c
4026 * samtools-0.1.3-20 (r276)
4027 * remove bam1_t::hash again. We need to modify the Perl API anyway to
4028 make it work with the latest SVN.
4029 * As is suggested by Tim, scan "{base}.bai" and "{base}.bam.bai" for index
4031 ------------------------------------------------------------------------
4032 r275 | lh3lh3 | 2009-05-12 16:14:10 -0400 (Tue, 12 May 2009) | 4 lines
4034 M /trunk/samtools/ChangeLog
4035 M /trunk/samtools/bam.h
4036 M /trunk/samtools/bamtk.c
4038 * samtools-0.1.3-19 (r275)
4039 * a minor change to the bam1_t struct: added back "void *hash" for the
4040 backward compatibility with Bio::DB::Sam
4042 ------------------------------------------------------------------------
4043 r273 | lh3lh3 | 2009-05-12 09:28:39 -0400 (Tue, 12 May 2009) | 3 lines
4045 M /trunk/samtools/bam_rmdupse.c
4046 M /trunk/samtools/bamtk.c
4048 * samtools-0.1.3-18 (r273)
4049 * rmdupse: do not remove unmapped reads
4051 ------------------------------------------------------------------------
4052 r272 | lh3lh3 | 2009-05-12 09:20:00 -0400 (Tue, 12 May 2009) | 2 lines
4054 M /trunk/samtools/bam_rmdupse.c
4056 change a parameter. It does nothing
4058 ------------------------------------------------------------------------
4059 r271 | lh3lh3 | 2009-05-12 09:17:58 -0400 (Tue, 12 May 2009) | 3 lines
4061 M /trunk/samtools/Makefile.am
4062 M /trunk/samtools/Makefile.generic
4063 M /trunk/samtools/Makefile.lite
4064 A /trunk/samtools/bam_rmdupse.c
4065 M /trunk/samtools/bamtk.c
4066 M /trunk/samtools/configure.ac
4068 * samtools-0.1.3-17 (r271)
4069 * added 'rmdupse' command
4071 ------------------------------------------------------------------------
4072 r267 | lh3lh3 | 2009-05-05 17:31:41 -0400 (Tue, 05 May 2009) | 3 lines
4074 M /trunk/samtools/bamtk.c
4075 M /trunk/samtools/sam_view.c
4077 * samtools-0.1.3-16 (r267)
4078 * in sam_view.c, changed g_flag_on based on the suggestion by Angie Hinrichs
4080 ------------------------------------------------------------------------
4081 r266 | lh3lh3 | 2009-05-05 17:23:27 -0400 (Tue, 05 May 2009) | 3 lines
4083 M /trunk/samtools/bam_import.c
4084 M /trunk/samtools/bamtk.c
4086 * samtools-0.1.3-15 (r266)
4087 * report an error if a non-* reference is present while @SQ is absent
4089 ------------------------------------------------------------------------
4090 r265 | lh3lh3 | 2009-05-05 17:09:00 -0400 (Tue, 05 May 2009) | 3 lines
4092 M /trunk/samtools/bam.h
4093 M /trunk/samtools/bam_import.c
4094 M /trunk/samtools/bamtk.c
4095 M /trunk/samtools/sam.c
4096 M /trunk/samtools/sam_view.c
4098 * samtools-0.1.3-14 (r262)
4099 * make samopen() recognize @SQ header lines
4101 ------------------------------------------------------------------------
4102 r261 | lh3lh3 | 2009-05-05 10:10:30 -0400 (Tue, 05 May 2009) | 3 lines
4104 M /trunk/samtools/bam_plcmd.c
4105 M /trunk/samtools/bamtk.c
4106 M /trunk/samtools/bgzf.c
4107 M /trunk/samtools/sam.c
4108 M /trunk/samtools/sam_view.c
4110 * samtools-0.1.3-13 (r260)
4111 * report error for file I/O error
4113 ------------------------------------------------------------------------
4114 r260 | lh3lh3 | 2009-05-05 10:01:16 -0400 (Tue, 05 May 2009) | 2 lines
4116 M /trunk/samtools/Makefile.am
4120 ------------------------------------------------------------------------
4121 r259 | lh3lh3 | 2009-05-05 09:52:25 -0400 (Tue, 05 May 2009) | 3 lines
4123 M /trunk/samtools/bam.h
4124 M /trunk/samtools/bam_pileup.c
4125 M /trunk/samtools/bam_plcmd.c
4126 M /trunk/samtools/bamtk.c
4127 M /trunk/samtools/sam.c
4128 M /trunk/samtools/sam.h
4130 * samtools-0.1.3-12 (r259)
4131 * use the new I/O interface in pileup
4133 ------------------------------------------------------------------------
4134 r258 | lh3lh3 | 2009-05-05 09:33:22 -0400 (Tue, 05 May 2009) | 3 lines
4136 M /trunk/samtools/Makefile.generic
4137 M /trunk/samtools/Makefile.lite
4138 M /trunk/samtools/bam.c
4139 M /trunk/samtools/bam.h
4140 M /trunk/samtools/bam_import.c
4141 M /trunk/samtools/bamtk.c
4142 A /trunk/samtools/sam.c
4143 A /trunk/samtools/sam.h
4144 A /trunk/samtools/sam_view.c
4146 * samtools-0.1.3-11 (r258)
4147 * unify the interface to BAM and SAM I/O
4149 ------------------------------------------------------------------------
4150 r257 | lh3lh3 | 2009-05-05 04:53:35 -0400 (Tue, 05 May 2009) | 3 lines
4152 M /trunk/samtools/Makefile.lite
4153 M /trunk/samtools/bam_plcmd.c
4154 M /trunk/samtools/bamtk.c
4156 * samtools-0.1.3-10 (r257)
4157 * allow hex with "pileup -m"
4159 ------------------------------------------------------------------------
4160 r256 | lh3lh3 | 2009-05-04 14:16:50 -0400 (Mon, 04 May 2009) | 4 lines
4162 M /trunk/samtools/bam_lpileup.c
4163 M /trunk/samtools/bamtk.c
4165 * samtools-0.1.3-9 (r256)
4166 * fixed a bug in bam_lpileup.c
4167 * I do not know if this also fixes the bug causing assertion failure in the tview
4169 ------------------------------------------------------------------------
4170 r251 | lh3lh3 | 2009-04-28 08:53:23 -0400 (Tue, 28 Apr 2009) | 3 lines
4172 M /trunk/samtools/bam_pileup.c
4173 M /trunk/samtools/bamtk.c
4175 * samtools-0.1.3-8 (r251)
4176 * fixed a bug when there are reads without coordinates
4178 ------------------------------------------------------------------------
4179 r250 | lh3lh3 | 2009-04-28 08:43:33 -0400 (Tue, 28 Apr 2009) | 2 lines
4181 A /trunk/samtools/AUTHORS
4182 A /trunk/samtools/README
4183 M /trunk/samtools/cleanup.sh
4187 ------------------------------------------------------------------------
4188 r249 | lh3lh3 | 2009-04-28 08:37:16 -0400 (Tue, 28 Apr 2009) | 2 lines
4190 M /trunk/samtools/Makefile.generic
4191 M /trunk/samtools/Makefile.lite
4192 M /trunk/samtools/configure.ac
4193 M /trunk/samtools/misc/Makefile.generic
4195 improve large file support in compilation
4197 ------------------------------------------------------------------------
4198 r248 | lh3lh3 | 2009-04-28 08:33:24 -0400 (Tue, 28 Apr 2009) | 2 lines
4200 M /trunk/samtools/INSTALL
4204 ------------------------------------------------------------------------
4205 r247 | lh3lh3 | 2009-04-28 08:28:50 -0400 (Tue, 28 Apr 2009) | 2 lines
4207 M /trunk/samtools/Makefile.am
4208 M /trunk/samtools/autogen.sh
4209 M /trunk/samtools/cleanup.sh
4210 M /trunk/samtools/configure.ac
4211 A /trunk/samtools/misc/Makefile.am
4213 fixed various issues about the GNU building scripts
4215 ------------------------------------------------------------------------
4216 r246 | lh3lh3 | 2009-04-28 08:10:23 -0400 (Tue, 28 Apr 2009) | 4 lines
4218 M /trunk/samtools/ChangeLog
4219 D /trunk/samtools/Makefile
4220 A /trunk/samtools/Makefile.am
4221 A /trunk/samtools/Makefile.generic
4222 A /trunk/samtools/autogen.sh
4223 M /trunk/samtools/bam.h
4224 M /trunk/samtools/bam_aux.c
4225 M /trunk/samtools/bam_tview.c
4226 M /trunk/samtools/bamtk.c
4227 A /trunk/samtools/cleanup.sh
4228 A /trunk/samtools/configure.ac
4229 D /trunk/samtools/misc/Makefile
4230 A /trunk/samtools/misc/Makefile.generic (from /trunk/samtools/misc/Makefile:245)
4232 * samtools-0.1.3-7 (r246)
4233 * incorporated revisions from Nils Homer
4234 * enhanced support of displaying color-space reads
4236 ------------------------------------------------------------------------
4237 r244 | lh3lh3 | 2009-04-25 06:49:40 -0400 (Sat, 25 Apr 2009) | 3 lines
4239 M /trunk/samtools/bam_md.c
4240 M /trunk/samtools/bamtk.c
4242 * samtools-0.1.3-6 (r244)
4243 * fixed segfault for unmapped reads
4245 ------------------------------------------------------------------------
4246 r243 | lh3lh3 | 2009-04-24 16:27:26 -0400 (Fri, 24 Apr 2009) | 5 lines
4248 M /trunk/samtools/bam.h
4249 M /trunk/samtools/bam_maqcns.c
4250 M /trunk/samtools/bam_md.c
4251 M /trunk/samtools/bamtk.c
4253 * samtools-0.1.3-5 (r243)
4254 * fixed a long existing bug which may cause memory leak
4256 * consensus calling now works with "=", but indel calling not
4258 ------------------------------------------------------------------------
4259 r242 | lh3lh3 | 2009-04-24 15:44:46 -0400 (Fri, 24 Apr 2009) | 3 lines
4261 M /trunk/samtools/bam_md.c
4262 M /trunk/samtools/bamtk.c
4264 * samtools-0.1.3-4 (r242)
4265 * fixed a memory leak
4267 ------------------------------------------------------------------------
4268 r240 | lh3lh3 | 2009-04-24 11:40:18 -0400 (Fri, 24 Apr 2009) | 5 lines
4270 M /trunk/samtools/Makefile
4271 M /trunk/samtools/Makefile.lite
4272 M /trunk/samtools/bam.h
4273 M /trunk/samtools/bam_aux.c
4274 A /trunk/samtools/bam_md.c
4275 M /trunk/samtools/bam_plcmd.c
4276 M /trunk/samtools/bamtk.c
4278 * samtools-0.1.3-3 (r240)
4280 * generate "=" bases
4281 * the plain pileup now support "=" bases, but consensus calling and glfgen may fail
4283 ------------------------------------------------------------------------
4284 r239 | lh3lh3 | 2009-04-24 07:08:20 -0400 (Fri, 24 Apr 2009) | 5 lines
4286 M /trunk/samtools/bam.h
4287 M /trunk/samtools/bam_aux.c
4288 M /trunk/samtools/bamtk.c
4290 * samtools-0.1.3-2 (r239)
4291 * fixed bugs in bam_aux.c (these functions nevered used by samtools)
4292 * removed bam_aux_init()/bam_aux_destroy()
4293 * added tagview for testing bam_aux
4295 ------------------------------------------------------------------------
4296 r235 | lh3lh3 | 2009-04-21 18:17:39 -0400 (Tue, 21 Apr 2009) | 3 lines
4298 M /trunk/samtools/bam_pileup.c
4299 M /trunk/samtools/bamtk.c
4302 * fixed a bug in pileup: the first read in a chromosome may not be printed
4304 ------------------------------------------------------------------------
4305 r232 | lh3lh3 | 2009-04-16 10:25:43 -0400 (Thu, 16 Apr 2009) | 2 lines
4307 M /trunk/samtools/Makefile.lite
4309 a missing file in Makefile.lite
4311 ------------------------------------------------------------------------
4312 r227 | lh3lh3 | 2009-04-15 17:02:53 -0400 (Wed, 15 Apr 2009) | 2 lines
4314 M /trunk/samtools/NEWS
4315 M /trunk/samtools/bamtk.c
4317 Release samtools-0.1.3
4319 ------------------------------------------------------------------------
4320 r223 | lh3lh3 | 2009-04-15 09:31:32 -0400 (Wed, 15 Apr 2009) | 3 lines
4322 M /trunk/samtools/bam_plcmd.c
4323 M /trunk/samtools/bamtk.c
4326 * make samtools more robust to weird input such as empty file
4328 ------------------------------------------------------------------------
4329 r222 | lh3lh3 | 2009-04-15 09:05:33 -0400 (Wed, 15 Apr 2009) | 2 lines
4331 M /trunk/samtools/ChangeLog
4332 M /trunk/samtools/NEWS
4333 M /trunk/samtools/samtools.1
4335 prepare for release 0.1.3
4337 ------------------------------------------------------------------------
4338 r221 | lh3lh3 | 2009-04-15 08:32:14 -0400 (Wed, 15 Apr 2009) | 2 lines
4340 A /trunk/samtools/misc/blast2sam.pl
4342 convert NCBI-BLASTN to SAM
4344 ------------------------------------------------------------------------
4345 r220 | lh3lh3 | 2009-04-15 08:18:19 -0400 (Wed, 15 Apr 2009) | 3 lines
4347 M /trunk/samtools/bam_lpileup.c
4348 M /trunk/samtools/bamtk.c
4351 * fixed a small memory leak in tview
4353 ------------------------------------------------------------------------
4354 r219 | lh3lh3 | 2009-04-15 08:00:08 -0400 (Wed, 15 Apr 2009) | 3 lines
4356 M /trunk/samtools/bam_rmdup.c
4357 M /trunk/samtools/bamtk.c
4360 * fixed a bug in rmdup when there are unmapped reads
4362 ------------------------------------------------------------------------
4363 r218 | lh3lh3 | 2009-04-14 17:28:58 -0400 (Tue, 14 Apr 2009) | 2 lines
4365 M /trunk/samtools/ChangeLog
4366 M /trunk/samtools/NEWS
4368 proposed NEWS for the new release (have not yet)
4370 ------------------------------------------------------------------------
4371 r216 | lh3lh3 | 2009-04-14 17:10:46 -0400 (Tue, 14 Apr 2009) | 4 lines
4373 M /trunk/samtools/misc/samtools.pl
4376 * improve indelFilter to avoid filtering true indels. The new filter relies
4377 on the new pileup indel line implemented in samtools-0.1.2-25
4379 ------------------------------------------------------------------------
4380 r215 | lh3lh3 | 2009-04-14 17:04:19 -0400 (Tue, 14 Apr 2009) | 4 lines
4382 M /trunk/samtools/bam_maqcns.c
4383 M /trunk/samtools/bam_plcmd.c
4384 M /trunk/samtools/bamtk.c
4385 M /trunk/samtools/samtools.1
4388 * change the pileup indel line to shows the number of alignments actually
4391 ------------------------------------------------------------------------
4392 r211 | lh3lh3 | 2009-04-13 07:07:13 -0400 (Mon, 13 Apr 2009) | 2 lines
4394 M /trunk/samtools/ChangeLog
4396 update ChangeLog from "svn log"
4398 ------------------------------------------------------------------------
4399 r210 | lh3lh3 | 2009-04-12 15:57:05 -0400 (Sun, 12 Apr 2009) | 4 lines
4401 M /trunk/samtools/bam.c
4402 M /trunk/samtools/bam_import.c
4403 M /trunk/samtools/bam_sort.c
4404 M /trunk/samtools/bamtk.c
4405 M /trunk/samtools/kseq.h
4408 * in merge, gives a warning rather than error if the target sequence length is different
4409 * allow empty header
4411 ------------------------------------------------------------------------
4412 r209 | lh3lh3 | 2009-04-12 15:32:44 -0400 (Sun, 12 Apr 2009) | 3 lines
4414 M /trunk/samtools/bam.c
4415 M /trunk/samtools/bam_import.c
4416 M /trunk/samtools/bamtk.c
4419 * recognize '*' at the QUAL field
4421 ------------------------------------------------------------------------
4422 r208 | lh3lh3 | 2009-04-12 15:08:02 -0400 (Sun, 12 Apr 2009) | 3 lines
4424 M /trunk/samtools/bam_import.c
4425 M /trunk/samtools/bamtk.c
4426 M /trunk/samtools/kseq.h
4429 * the field separater is TAB only, now
4431 ------------------------------------------------------------------------
4432 r207 | lh3lh3 | 2009-04-08 10:18:03 -0400 (Wed, 08 Apr 2009) | 2 lines
4434 M /trunk/samtools/examples/ex1.sam.gz
4436 * fixed the problem in the example alignment due to the bug in fixmate
4438 ------------------------------------------------------------------------
4439 r206 | lh3lh3 | 2009-04-08 10:15:05 -0400 (Wed, 08 Apr 2009) | 3 lines
4441 M /trunk/samtools/bam_mate.c
4442 M /trunk/samtools/bamtk.c
4443 M /trunk/samtools/misc/soap2sam.pl
4446 * fixed a nasty bug in `fixmate'
4448 ------------------------------------------------------------------------
4449 r205 | lh3lh3 | 2009-04-08 05:57:08 -0400 (Wed, 08 Apr 2009) | 2 lines
4451 M /trunk/samtools/misc/bowtie2sam.pl
4452 M /trunk/samtools/misc/soap2sam.pl
4453 M /trunk/samtools/misc/wgsim_eval.pl
4455 make the script robust to the bugs in SOAP-2.1.7
4457 ------------------------------------------------------------------------
4458 r200 | lh3lh3 | 2009-04-02 10:14:56 -0400 (Thu, 02 Apr 2009) | 3 lines
4460 M /trunk/samtools/bam_stat.c
4461 M /trunk/samtools/bamtk.c
4464 * check if file is truncated in flagstat
4466 ------------------------------------------------------------------------
4467 r199 | lh3lh3 | 2009-04-02 10:09:10 -0400 (Thu, 02 Apr 2009) | 3 lines
4469 M /trunk/samtools/bamtk.c
4472 * print the header if requested
4474 ------------------------------------------------------------------------
4475 r193 | lh3lh3 | 2009-03-27 11:09:50 -0400 (Fri, 27 Mar 2009) | 3 lines
4477 M /trunk/samtools/bam_plcmd.c
4478 M /trunk/samtools/bamtk.c
4481 * fixed a minor bug reported by Nils Homer
4483 ------------------------------------------------------------------------
4484 r185 | lh3lh3 | 2009-03-24 07:50:32 -0400 (Tue, 24 Mar 2009) | 2 lines
4486 A /trunk/samtools/Makefile (from /trunk/samtools/Makefile.std:184)
4487 D /trunk/samtools/Makefile.std
4488 A /trunk/samtools/misc/Makefile (from /trunk/samtools/misc/Makefile.std:184)
4489 D /trunk/samtools/misc/Makefile.std
4491 rename Makefile.std as Makefile. GNU building systerm is not ready and may take some time...
4493 ------------------------------------------------------------------------
4494 r184 | lh3lh3 | 2009-03-24 06:36:38 -0400 (Tue, 24 Mar 2009) | 4 lines
4496 D /trunk/samtools/Makefile
4497 A /trunk/samtools/Makefile.std (from /trunk/samtools/Makefile:183)
4498 M /trunk/samtools/bam_sort.c
4499 M /trunk/samtools/bam_tview.c
4500 M /trunk/samtools/bamtk.c
4501 D /trunk/samtools/misc/Makefile
4502 A /trunk/samtools/misc/Makefile.std (from /trunk/samtools/misc/Makefile:182)
4503 M /trunk/samtools/samtools.1
4506 * incorporating Nils' changes
4507 * rename Makefile to Makefile.std and prepare to add the GNU building systerms (also by Nils)
4509 ------------------------------------------------------------------------
4510 r183 | lh3lh3 | 2009-03-24 06:30:23 -0400 (Tue, 24 Mar 2009) | 4 lines
4512 M /trunk/samtools/Makefile
4513 M /trunk/samtools/bam_import.c
4514 M /trunk/samtools/bam_maqcns.c
4515 M /trunk/samtools/bam_maqcns.h
4516 M /trunk/samtools/bam_plcmd.c
4517 M /trunk/samtools/bamtk.c
4518 M /trunk/samtools/kseq.h
4519 A /trunk/samtools/kstring.c
4520 A /trunk/samtools/kstring.h
4523 * made pileup take a list of proposed indels. An insertion is N at the moment.
4524 * added my kstring library for a bit complex parsing of the position list.
4526 ------------------------------------------------------------------------
4527 r169 | lh3lh3 | 2009-03-12 09:40:14 -0400 (Thu, 12 Mar 2009) | 3 lines
4529 M /trunk/samtools/misc/soap2sam.pl
4532 * more robust to truncated soap output
4534 ------------------------------------------------------------------------
4535 r168 | lh3lh3 | 2009-03-11 06:49:00 -0400 (Wed, 11 Mar 2009) | 2 lines
4537 M /trunk/samtools/Makefile.lite
4539 added bam_stat.o to Makefile.lite
4541 ------------------------------------------------------------------------
4542 r167 | lh3lh3 | 2009-03-10 18:11:31 -0400 (Tue, 10 Mar 2009) | 3 lines
4544 M /trunk/samtools/bam_maqcns.c
4545 M /trunk/samtools/bamtk.c
4548 * generate RMS of mapQ instead of max mapQ
4550 ------------------------------------------------------------------------
4551 r166 | lh3lh3 | 2009-03-10 18:06:45 -0400 (Tue, 10 Mar 2009) | 3 lines
4553 M /trunk/samtools/bam_plcmd.c
4554 M /trunk/samtools/bamtk.c
4555 M /trunk/samtools/glf.c
4556 M /trunk/samtools/glf.h
4557 M /trunk/samtools/misc/Makefile
4562 ------------------------------------------------------------------------
4563 r159 | lh3lh3 | 2009-03-03 06:26:08 -0500 (Tue, 03 Mar 2009) | 3 lines
4565 M /trunk/samtools/bam_plcmd.c
4566 M /trunk/samtools/bamtk.c
4569 * fixed a minor bug in displaying pileup
4571 ------------------------------------------------------------------------
4572 r158 | lh3lh3 | 2009-03-03 06:24:16 -0500 (Tue, 03 Mar 2009) | 3 lines
4574 M /trunk/samtools/ChangeLog
4575 M /trunk/samtools/bamtk.c
4578 * optionally print SAM header
4580 ------------------------------------------------------------------------
4581 r153 | lh3lh3 | 2009-03-02 05:45:28 -0500 (Mon, 02 Mar 2009) | 3 lines
4583 M /trunk/samtools/bamtk.c
4584 M /trunk/samtools/glf.c
4587 * use "GLF\3" as the magic for GLFv3 files
4589 ------------------------------------------------------------------------
4590 r152 | lh3lh3 | 2009-03-02 05:39:09 -0500 (Mon, 02 Mar 2009) | 5 lines
4592 M /trunk/samtools/Makefile
4593 M /trunk/samtools/bam_import.c
4594 M /trunk/samtools/bam_index.c
4595 M /trunk/samtools/bam_plcmd.c
4596 M /trunk/samtools/bamtk.c
4597 M /trunk/samtools/glf.c
4598 M /trunk/samtools/glf.h
4601 * fixed a bug in import: core.bin is undefined for unmapped reads
4602 * this bug can be alleviated (not completely solved) in bam_index.c
4603 * update to GLFv3: pos is changed to offset for better compression
4605 ------------------------------------------------------------------------
4606 r151 | lh3lh3 | 2009-03-01 10:18:43 -0500 (Sun, 01 Mar 2009) | 3 lines
4608 M /trunk/samtools/misc/wgsim.c
4611 * fixed a bug in simulating indels
4613 ------------------------------------------------------------------------
4614 r145 | lh3lh3 | 2009-02-26 14:43:57 -0500 (Thu, 26 Feb 2009) | 4 lines
4616 M /trunk/samtools/misc/wgsim.c
4619 * allow to print mismatch information as fastq comment. MAQ does
4620 not like long read names.
4622 ------------------------------------------------------------------------
4623 r141 | lh3lh3 | 2009-02-26 09:53:03 -0500 (Thu, 26 Feb 2009) | 6 lines
4625 M /trunk/samtools/ChangeLog
4626 M /trunk/samtools/misc/wgsim.c
4627 M /trunk/samtools/misc/wgsim_eval.pl
4630 * fixed a bug about color read coordinates
4631 * fixed a bug in read names
4632 * wgsim_eval.pl-0.1.3
4633 * make the script work with color reads
4635 ------------------------------------------------------------------------
4636 r140 | lh3lh3 | 2009-02-26 09:02:57 -0500 (Thu, 26 Feb 2009) | 2 lines
4638 M /trunk/samtools/misc/Makefile
4639 M /trunk/samtools/misc/wgsim.c
4641 * wgsim: added a note
4643 ------------------------------------------------------------------------
4644 r139 | lh3lh3 | 2009-02-26 06:39:08 -0500 (Thu, 26 Feb 2009) | 7 lines
4646 M /trunk/samtools/misc/wgsim.c
4647 M /trunk/samtools/misc/wgsim_eval.pl
4650 * considerable code clean up
4651 * print number of substitutions/indels/errors on each read
4652 * potentially support SOLiD simulation, though not tested at the moment
4653 * wgsim_eval.pl-0.1.2
4654 * change in accordant with wgsim
4656 ------------------------------------------------------------------------
4657 r129 | lh3lh3 | 2009-02-18 17:23:27 -0500 (Wed, 18 Feb 2009) | 3 lines
4659 M /trunk/samtools/bam_index.c
4660 M /trunk/samtools/bamtk.c
4663 * fixed a bug in bam_fetch, caused by completely contained adjacent chunks
4665 ------------------------------------------------------------------------
4666 r128 | bhandsaker | 2009-02-18 14:06:57 -0500 (Wed, 18 Feb 2009) | 2 lines
4668 M /trunk/samtools/bamtk.c
4670 Fix annoying segv when invalid region specified.
4672 ------------------------------------------------------------------------
4673 r127 | lh3lh3 | 2009-02-17 05:49:55 -0500 (Tue, 17 Feb 2009) | 2 lines
4675 D /trunk/samtools/misc/indel_filter.pl
4676 A /trunk/samtools/misc/samtools.pl
4678 * move indel_filter.pl to samtools.pl
4680 ------------------------------------------------------------------------
4681 r126 | lh3lh3 | 2009-02-14 16:22:30 -0500 (Sat, 14 Feb 2009) | 3 lines
4683 M /trunk/samtools/bam_mate.c
4684 M /trunk/samtools/bamtk.c
4687 * fixed a bug in fixmate: SE reads are flagged as BAM_FMUNMAP
4689 ------------------------------------------------------------------------
4690 r125 | lh3lh3 | 2009-02-13 04:54:45 -0500 (Fri, 13 Feb 2009) | 3 lines
4692 M /trunk/samtools/bam_stat.c
4693 M /trunk/samtools/bamtk.c
4696 * fixed a minor bug in flagstat
4698 ------------------------------------------------------------------------
4699 r124 | lh3lh3 | 2009-02-12 06:15:32 -0500 (Thu, 12 Feb 2009) | 3 lines
4701 M /trunk/samtools/bam_maqcns.c
4702 M /trunk/samtools/bamtk.c
4703 M /trunk/samtools/misc/indel_filter.pl
4706 * improve indel caller by setting maximum window size
4708 ------------------------------------------------------------------------
4709 r123 | lh3lh3 | 2009-02-12 05:30:29 -0500 (Thu, 12 Feb 2009) | 2 lines
4711 M /trunk/samtools/bam_plcmd.c
4712 M /trunk/samtools/bamtk.c
4714 * output max mapping quality in indel line
4716 ------------------------------------------------------------------------
4717 r122 | lh3lh3 | 2009-02-11 05:59:10 -0500 (Wed, 11 Feb 2009) | 2 lines
4719 M /trunk/samtools/misc/maq2sam.c
4721 fixed a bug in generating tag AM
4723 ------------------------------------------------------------------------
4724 r121 | lh3lh3 | 2009-02-03 05:43:11 -0500 (Tue, 03 Feb 2009) | 2 lines
4726 M /trunk/samtools/bam_index.c
4727 M /trunk/samtools/bamtk.c
4729 fixed a potential memory problem in indexing
4731 ------------------------------------------------------------------------
4732 r120 | bhandsaker | 2009-02-02 10:52:52 -0500 (Mon, 02 Feb 2009) | 2 lines
4734 M /trunk/samtools/Makefile
4736 Pass LIBS to recursive targets to facilitate building at Broad.
4738 ------------------------------------------------------------------------
4739 r119 | lh3lh3 | 2009-02-02 05:12:15 -0500 (Mon, 02 Feb 2009) | 4 lines
4741 M /trunk/samtools/ChangeLog
4742 M /trunk/samtools/bam_plcmd.c
4743 M /trunk/samtools/bam_stat.c
4744 M /trunk/samtools/bamtk.c
4747 * fixed a bug in generating GLFv2 for indels
4748 * improve flagstat report a little bit
4750 ------------------------------------------------------------------------
4751 r118 | lh3lh3 | 2009-01-29 07:33:23 -0500 (Thu, 29 Jan 2009) | 3 lines
4753 M /trunk/samtools/Makefile
4754 A /trunk/samtools/bam_stat.c
4755 M /trunk/samtools/bamtk.c
4758 * added flagstat command
4760 ------------------------------------------------------------------------
4761 r116 | lh3lh3 | 2009-01-28 08:31:12 -0500 (Wed, 28 Jan 2009) | 2 lines
4763 M /trunk/samtools/ChangeLog
4764 M /trunk/samtools/NEWS
4765 M /trunk/samtools/bamtk.c
4766 M /trunk/samtools/samtools.1
4768 Release SAMtools-0.1.2
4770 ------------------------------------------------------------------------
4771 r115 | lh3lh3 | 2009-01-28 07:54:08 -0500 (Wed, 28 Jan 2009) | 2 lines
4773 A /trunk/samtools/misc/indel_filter.pl
4775 Script for filtering indel results
4777 ------------------------------------------------------------------------
4778 r114 | lh3lh3 | 2009-01-25 06:45:37 -0500 (Sun, 25 Jan 2009) | 2 lines
4780 A /trunk/samtools/misc/zoom2sam.pl
4784 ------------------------------------------------------------------------
4785 r113 | lh3lh3 | 2009-01-24 09:25:07 -0500 (Sat, 24 Jan 2009) | 2 lines
4787 A /trunk/samtools/misc/novo2sam.pl
4789 add a script to convert novo alignment to SAM
4791 ------------------------------------------------------------------------
4792 r112 | lh3lh3 | 2009-01-23 15:57:39 -0500 (Fri, 23 Jan 2009) | 2 lines
4794 M /trunk/samtools/ChangeLog
4795 M /trunk/samtools/ChangeLog.old
4796 M /trunk/samtools/samtools.1
4798 update documentation and ChangeLog
4800 ------------------------------------------------------------------------
4801 r111 | lh3lh3 | 2009-01-23 14:22:59 -0500 (Fri, 23 Jan 2009) | 3 lines
4803 M /trunk/samtools/bam_sort.c
4804 M /trunk/samtools/bamtk.c
4807 * fixed a bug in "merge" command line
4809 ------------------------------------------------------------------------
4810 r110 | lh3lh3 | 2009-01-22 10:36:48 -0500 (Thu, 22 Jan 2009) | 3 lines
4812 M /trunk/samtools/misc/Makefile
4813 A /trunk/samtools/misc/bowtie2sam.pl (from /branches/dev/samtools/misc/bowtie2sam.pl:108)
4814 M /trunk/samtools/misc/export2sam.pl
4815 A /trunk/samtools/misc/soap2sam.pl (from /branches/dev/samtools/misc/soap2sam.pl:108)
4816 A /trunk/samtools/misc/wgsim.c (from /branches/dev/samtools/misc/wgsim.c:108)
4817 A /trunk/samtools/misc/wgsim_eval.pl (from /branches/dev/samtools/misc/wgsim_eval.pl:108)
4819 * merge from branches/dev/
4820 * all future development will happen here
4822 ------------------------------------------------------------------------
4823 r109 | lh3lh3 | 2009-01-22 10:14:27 -0500 (Thu, 22 Jan 2009) | 3 lines
4825 M /trunk/samtools/COPYING
4826 M /trunk/samtools/ChangeLog
4827 A /trunk/samtools/INSTALL (from /branches/dev/samtools/INSTALL:108)
4828 M /trunk/samtools/Makefile
4829 A /trunk/samtools/Makefile.lite (from /branches/dev/samtools/Makefile.lite:108)
4830 M /trunk/samtools/bam.c
4831 M /trunk/samtools/bam.h
4832 M /trunk/samtools/bam_import.c
4833 M /trunk/samtools/bam_index.c
4834 M /trunk/samtools/bam_lpileup.c
4835 M /trunk/samtools/bam_maqcns.c
4836 M /trunk/samtools/bam_maqcns.h
4837 A /trunk/samtools/bam_mate.c (from /branches/dev/samtools/bam_mate.c:108)
4838 M /trunk/samtools/bam_pileup.c
4839 M /trunk/samtools/bam_plcmd.c
4840 A /trunk/samtools/bam_rmdup.c (from /branches/dev/samtools/bam_rmdup.c:108)
4841 M /trunk/samtools/bam_sort.c
4842 M /trunk/samtools/bamtk.c
4843 M /trunk/samtools/bgzf.h
4844 M /trunk/samtools/examples/00README.txt
4845 A /trunk/samtools/examples/Makefile (from /branches/dev/samtools/examples/Makefile:108)
4846 D /trunk/samtools/examples/ex1.fa.fai
4847 M /trunk/samtools/examples/ex1.sam.gz
4848 M /trunk/samtools/faidx.c
4849 A /trunk/samtools/glf.c (from /branches/dev/samtools/glf.c:108)
4850 M /trunk/samtools/glf.h
4851 M /trunk/samtools/misc/Makefile
4852 M /trunk/samtools/misc/maq2sam.c
4853 M /trunk/samtools/razf.c
4854 M /trunk/samtools/source.dot
4856 * Merge from branches/dev/
4857 * all future development will happen here at trunk/
4859 ------------------------------------------------------------------------
4860 r79 | bhandsaker | 2009-01-07 16:42:15 -0500 (Wed, 07 Jan 2009) | 2 lines
4862 M /trunk/samtools/bam_maqcns.c
4863 M /trunk/samtools/bam_tview.c
4865 Fix problem with compiling without curses.
4867 ------------------------------------------------------------------------
4868 r63 | lh3lh3 | 2008-12-22 10:58:02 -0500 (Mon, 22 Dec 2008) | 2 lines
4870 A /trunk/samtools (from /branches/dev/samtools:62)
4874 ------------------------------------------------------------------------
4875 r62 | lh3lh3 | 2008-12-22 10:55:13 -0500 (Mon, 22 Dec 2008) | 2 lines
4877 A /branches/dev/samtools/NEWS
4878 M /branches/dev/samtools/bamtk.c
4879 M /branches/dev/samtools/samtools.1
4881 Release samtools-0.1.1
4883 ------------------------------------------------------------------------
4884 r61 | lh3lh3 | 2008-12-22 10:46:08 -0500 (Mon, 22 Dec 2008) | 10 lines
4886 M /branches/dev/samtools/bam_aux.c
4887 M /branches/dev/samtools/bam_index.c
4888 M /branches/dev/samtools/bam_plcmd.c
4889 M /branches/dev/samtools/bam_tview.c
4890 M /branches/dev/samtools/bamtk.c
4891 M /branches/dev/samtools/razf.c
4892 M /branches/dev/samtools/samtools.1
4895 * fixed a bug in razf.c: reset z_eof when razf_seek() is called
4896 * fixed a memory leak in parsing a region
4897 * changed pileup a little bit when -s is in use: output ^ and $
4898 * when a bam is not indexed, output more meaningful error message
4899 * fixed a bug in indexing for small alignment
4900 * fixed a bug in the viewer when we come to the end of a reference file
4901 * updated documentation
4902 * prepare to release 0.1.1
4904 ------------------------------------------------------------------------
4905 r60 | lh3lh3 | 2008-12-22 10:10:16 -0500 (Mon, 22 Dec 2008) | 2 lines
4907 A /branches/dev/samtools/examples
4908 A /branches/dev/samtools/examples/00README.txt
4909 A /branches/dev/samtools/examples/ex1.fa
4910 A /branches/dev/samtools/examples/ex1.fa.fai
4911 A /branches/dev/samtools/examples/ex1.sam.gz
4915 ------------------------------------------------------------------------
4916 r59 | lh3lh3 | 2008-12-22 04:38:15 -0500 (Mon, 22 Dec 2008) | 2 lines
4918 M /branches/dev/samtools/ChangeLog
4922 ------------------------------------------------------------------------
4923 r58 | lh3lh3 | 2008-12-20 18:06:00 -0500 (Sat, 20 Dec 2008) | 3 lines
4925 M /branches/dev/samtools/misc/export2sam.pl
4928 * fixed several bugs
4930 ------------------------------------------------------------------------
4931 r57 | lh3lh3 | 2008-12-20 10:44:20 -0500 (Sat, 20 Dec 2008) | 2 lines
4933 A /branches/dev/samtools/misc/export2sam.pl
4935 convert Export format to SAM; not thoroughly tested
4937 ------------------------------------------------------------------------
4938 r56 | lh3lh3 | 2008-12-19 17:13:28 -0500 (Fri, 19 Dec 2008) | 6 lines
4940 M /branches/dev/samtools/bam_import.c
4941 M /branches/dev/samtools/bam_plcmd.c
4942 M /branches/dev/samtools/bam_tview.c
4943 M /branches/dev/samtools/bamtk.c
4944 A /branches/dev/samtools/source.dot
4947 * pileup: generate maq-like simple output
4948 * pileup: allow to output pileup at required sites
4949 * source.dot: source file relationship graph
4950 * tview: fixed a minor bug
4952 ------------------------------------------------------------------------
4953 r55 | lh3lh3 | 2008-12-19 15:10:26 -0500 (Fri, 19 Dec 2008) | 2 lines
4955 D /branches/dev/samtools/misc/all2sam.pl
4959 ------------------------------------------------------------------------
4960 r54 | lh3lh3 | 2008-12-16 17:34:25 -0500 (Tue, 16 Dec 2008) | 2 lines
4962 A /branches/dev/samtools/COPYING
4963 M /branches/dev/samtools/bam.h
4964 M /branches/dev/samtools/faidx.h
4965 M /branches/dev/samtools/khash.h
4966 M /branches/dev/samtools/kseq.h
4967 M /branches/dev/samtools/ksort.h
4968 M /branches/dev/samtools/samtools.1
4970 Added copyright information and a bit more documentation. No code change.
4972 ------------------------------------------------------------------------
4973 r53 | lh3lh3 | 2008-12-16 08:40:18 -0500 (Tue, 16 Dec 2008) | 3 lines
4975 M /branches/dev/samtools/bam.c
4976 M /branches/dev/samtools/bam.h
4977 M /branches/dev/samtools/bam_index.c
4978 M /branches/dev/samtools/bam_maqcns.c
4979 M /branches/dev/samtools/bamtk.c
4982 * improved efficiency of the indel caller for spliced alignments
4984 ------------------------------------------------------------------------
4985 r52 | lh3lh3 | 2008-12-16 05:28:20 -0500 (Tue, 16 Dec 2008) | 3 lines
4987 M /branches/dev/samtools/bam.c
4988 M /branches/dev/samtools/bam.h
4989 M /branches/dev/samtools/bam_aux.c
4990 M /branches/dev/samtools/bam_index.c
4991 M /branches/dev/samtools/bamtk.c
4994 * a bit code cleanup: reduce the dependency between source files
4996 ------------------------------------------------------------------------
4997 r51 | lh3lh3 | 2008-12-15 09:29:32 -0500 (Mon, 15 Dec 2008) | 3 lines
4999 M /branches/dev/samtools/bam_maqcns.c
5000 M /branches/dev/samtools/bam_plcmd.c
5001 M /branches/dev/samtools/bamtk.c
5004 * fixed a memory leak
5006 ------------------------------------------------------------------------
5007 r50 | lh3lh3 | 2008-12-15 09:00:13 -0500 (Mon, 15 Dec 2008) | 2 lines
5009 M /branches/dev/samtools/ChangeLog
5010 M /branches/dev/samtools/bam.h
5011 M /branches/dev/samtools/samtools.1
5013 update documentation, ChangeLog and a comment
5015 ------------------------------------------------------------------------
5016 r49 | lh3lh3 | 2008-12-15 08:36:43 -0500 (Mon, 15 Dec 2008) | 6 lines
5018 M /branches/dev/samtools/Makefile
5019 M /branches/dev/samtools/bam.h
5020 M /branches/dev/samtools/bam_maqcns.c
5021 M /branches/dev/samtools/bam_maqcns.h
5022 M /branches/dev/samtools/bam_pileup.c
5023 A /branches/dev/samtools/bam_plcmd.c
5024 M /branches/dev/samtools/bamtk.c
5025 M /branches/dev/samtools/samtools.1
5028 * moved pileup command to a separate source file
5029 * added indel caller
5030 * added bam_cal_segend(). (NOT WORKING for spliced alignment!!!)
5031 * updated documentation
5033 ------------------------------------------------------------------------
5034 r48 | lh3lh3 | 2008-12-12 08:55:36 -0500 (Fri, 12 Dec 2008) | 3 lines
5036 M /branches/dev/samtools/bam_maqcns.c
5037 M /branches/dev/samtools/bamtk.c
5040 * fixed another bug in maqcns when there is a nearby deletion
5042 ------------------------------------------------------------------------
5043 r47 | lh3lh3 | 2008-12-12 08:42:16 -0500 (Fri, 12 Dec 2008) | 5 lines
5045 M /branches/dev/samtools/bam_maqcns.c
5046 M /branches/dev/samtools/bam_pileup.c
5047 M /branches/dev/samtools/bamtk.c
5050 * pileup: outputing consensus is now optional
5051 * fixed a bug in glfgen. This bug also exists in maq's glfgen. However,
5052 I am not quite sure why the previous version may have problem.
5054 ------------------------------------------------------------------------
5055 r46 | lh3lh3 | 2008-12-12 06:44:56 -0500 (Fri, 12 Dec 2008) | 6 lines
5057 M /branches/dev/samtools/bam_pileup.c
5058 M /branches/dev/samtools/bamtk.c
5061 * add maq consensus to pileup. However, I will move this part to a new
5062 command as strictly speaking, consensus callin is not part of pileup,
5063 and imposing it would make it harder to generate for other language
5066 ------------------------------------------------------------------------
5067 r45 | bhandsaker | 2008-12-11 15:43:56 -0500 (Thu, 11 Dec 2008) | 2 lines
5069 M /branches/dev/samtools/bgzf.c
5071 Fix bug in tell() after reads that consume to the exact end of a block.
5073 ------------------------------------------------------------------------
5074 r44 | lh3lh3 | 2008-12-11 04:36:53 -0500 (Thu, 11 Dec 2008) | 2 lines
5076 M /branches/dev/samtools/samtools.1
5080 ------------------------------------------------------------------------
5081 r43 | lh3lh3 | 2008-12-11 04:25:36 -0500 (Thu, 11 Dec 2008) | 4 lines
5083 M /branches/dev/samtools/bam_import.c
5084 M /branches/dev/samtools/bamtk.c
5087 * fixed a bug in parser when there is auxiliary fields
5088 * made the parser a bit more robust
5090 ------------------------------------------------------------------------
5091 r42 | lh3lh3 | 2008-12-10 09:57:29 -0500 (Wed, 10 Dec 2008) | 5 lines
5093 M /branches/dev/samtools/bam_index.c
5094 M /branches/dev/samtools/bamtk.c
5095 M /branches/dev/samtools/bgzf.c
5098 * fixed a bug in bgzf (only reading is affected)
5099 * fixed a typo in bam_index.c
5100 * in bam_index.c, check potential bugs in the underlying I/O library
5102 ------------------------------------------------------------------------
5103 r41 | lh3lh3 | 2008-12-10 07:53:08 -0500 (Wed, 10 Dec 2008) | 2 lines
5105 M /branches/dev/samtools/samtools.1
5109 ------------------------------------------------------------------------
5110 r40 | lh3lh3 | 2008-12-10 06:52:10 -0500 (Wed, 10 Dec 2008) | 5 lines
5112 M /branches/dev/samtools/bam.h
5113 M /branches/dev/samtools/bam_pileup.c
5114 M /branches/dev/samtools/bamtk.c
5117 * tried to make pileup work with clipping (previously not), though NOT tested
5118 * removed -v from pileup
5119 * made pileup take the reference sequence
5121 ------------------------------------------------------------------------
5122 r39 | lh3lh3 | 2008-12-09 06:59:28 -0500 (Tue, 09 Dec 2008) | 4 lines
5124 M /branches/dev/samtools/bam_import.c
5125 M /branches/dev/samtools/bamtk.c
5126 M /branches/dev/samtools/samtools.1
5129 * in parser, recognize "=", rather than ",", as a match
5130 * in parser, correctl parse "=" at the MRNM field.
5132 ------------------------------------------------------------------------
5133 r38 | lh3lh3 | 2008-12-09 06:39:07 -0500 (Tue, 09 Dec 2008) | 2 lines
5135 M /branches/dev/samtools/misc/maq2sam.c
5137 fixed a bug in handling maq flag 64 and 192
5139 ------------------------------------------------------------------------
5140 r37 | lh3lh3 | 2008-12-09 04:53:46 -0500 (Tue, 09 Dec 2008) | 2 lines
5142 M /branches/dev/samtools/misc/md5fa.c
5144 also calculate unordered md5sum check
5146 ------------------------------------------------------------------------
5147 r36 | lh3lh3 | 2008-12-09 04:46:21 -0500 (Tue, 09 Dec 2008) | 2 lines
5149 M /branches/dev/samtools/misc/md5fa.c
5151 fixed a minor bug when there are space in the sequence
5153 ------------------------------------------------------------------------
5154 r35 | lh3lh3 | 2008-12-09 04:40:45 -0500 (Tue, 09 Dec 2008) | 2 lines
5156 M /branches/dev/samtools/misc/md5fa.c
5158 fixed a potential memory leak
5160 ------------------------------------------------------------------------
5161 r34 | lh3lh3 | 2008-12-08 09:52:17 -0500 (Mon, 08 Dec 2008) | 2 lines
5163 M /branches/dev/samtools/bam_import.c
5164 M /branches/dev/samtools/bam_index.c
5165 M /branches/dev/samtools/bamtk.c
5167 * fixed a bug in import: bin is wrongly calculated
5169 ------------------------------------------------------------------------
5170 r33 | lh3lh3 | 2008-12-08 09:08:01 -0500 (Mon, 08 Dec 2008) | 2 lines
5172 M /branches/dev/samtools/misc/all2sam.pl
5176 ------------------------------------------------------------------------
5177 r32 | lh3lh3 | 2008-12-08 07:56:02 -0500 (Mon, 08 Dec 2008) | 3 lines
5179 M /branches/dev/samtools/Makefile
5180 M /branches/dev/samtools/kseq.h
5181 M /branches/dev/samtools/misc/Makefile
5182 A /branches/dev/samtools/misc/md5.c
5183 A /branches/dev/samtools/misc/md5.h
5184 A /branches/dev/samtools/misc/md5fa.c
5186 * fixed two warnings in kseq.h
5187 * added md5sum utilities
5189 ------------------------------------------------------------------------
5190 r31 | lh3lh3 | 2008-12-08 06:35:29 -0500 (Mon, 08 Dec 2008) | 5 lines
5192 M /branches/dev/samtools/Makefile
5193 M /branches/dev/samtools/bam_import.c
5194 M /branches/dev/samtools/bamtk.c
5195 A /branches/dev/samtools/kseq.h
5196 D /branches/dev/samtools/kstream.h
5199 * replace kstream with kseq. kseq is a superset of kstream. I need the
5200 extra functions in kseq.h.
5201 * also compile stand-alone faidx
5203 ------------------------------------------------------------------------
5204 r30 | lh3lh3 | 2008-12-08 06:17:04 -0500 (Mon, 08 Dec 2008) | 3 lines
5206 M /branches/dev/samtools/bam.h
5207 M /branches/dev/samtools/bam_sort.c
5208 M /branches/dev/samtools/bamtk.c
5211 * sorting by read names is available
5213 ------------------------------------------------------------------------
5214 r29 | lh3lh3 | 2008-12-08 05:29:02 -0500 (Mon, 08 Dec 2008) | 3 lines
5216 M /branches/dev/samtools/bam.c
5217 M /branches/dev/samtools/bam.h
5218 M /branches/dev/samtools/bam_import.c
5219 M /branches/dev/samtools/bam_maqcns.c
5220 M /branches/dev/samtools/bam_pileup.c
5221 M /branches/dev/samtools/bam_sort.c
5222 M /branches/dev/samtools/bam_tview.c
5223 M /branches/dev/samtools/bamtk.c
5224 M /branches/dev/samtools/misc/maq2sam.c
5227 * format change to meet the latest specification
5229 ------------------------------------------------------------------------
5230 r28 | lh3lh3 | 2008-12-04 11:09:21 -0500 (Thu, 04 Dec 2008) | 3 lines
5232 M /branches/dev/samtools/bam_maqcns.c
5233 M /branches/dev/samtools/misc/maq2sam.c
5235 * minor change in maqcns: special care when n==0
5236 * change maq2sam to meet the latest specification
5238 ------------------------------------------------------------------------
5239 r27 | lh3lh3 | 2008-12-04 10:55:44 -0500 (Thu, 04 Dec 2008) | 2 lines
5241 M /branches/dev/samtools/razf.c
5242 M /branches/dev/samtools/razf.h
5244 considerable code clean up in razf
5246 ------------------------------------------------------------------------
5247 r26 | lh3lh3 | 2008-12-04 10:08:18 -0500 (Thu, 04 Dec 2008) | 2 lines
5249 M /branches/dev/samtools/ChangeLog
5250 M /branches/dev/samtools/Makefile
5251 M /branches/dev/samtools/faidx.c
5253 make RAZF optional in faidx.c
5255 ------------------------------------------------------------------------
5256 r25 | lh3lh3 | 2008-12-01 10:27:22 -0500 (Mon, 01 Dec 2008) | 3 lines
5258 M /branches/dev/samtools/Makefile
5259 M /branches/dev/samtools/bam.h
5260 M /branches/dev/samtools/bam_aux.c
5261 M /branches/dev/samtools/bamtk.c
5262 M /branches/dev/samtools/samtools.1
5265 * added routines for retrieving aux data, NOT TESTED YET!
5267 ------------------------------------------------------------------------
5268 r24 | lh3lh3 | 2008-12-01 09:29:43 -0500 (Mon, 01 Dec 2008) | 5 lines
5270 M /branches/dev/samtools/bam.c
5271 M /branches/dev/samtools/bam_import.c
5272 M /branches/dev/samtools/bam_maqcns.c
5273 M /branches/dev/samtools/bamtk.c
5274 M /branches/dev/samtools/bgzf.c
5275 M /branches/dev/samtools/samtools.1
5278 * bgzf: fixed a potential integer overflow on 32-it machines
5279 * maqcns: set the minimum combined quality as 0
5280 * supporting hex strings
5282 ------------------------------------------------------------------------
5283 r23 | lh3lh3 | 2008-11-27 12:14:37 -0500 (Thu, 27 Nov 2008) | 3 lines
5285 M /branches/dev/samtools/bam_maqcns.c
5286 M /branches/dev/samtools/bamtk.c
5289 * fixed the bug in maqcns
5291 ------------------------------------------------------------------------
5292 r22 | lh3lh3 | 2008-11-27 12:08:11 -0500 (Thu, 27 Nov 2008) | 3 lines
5294 M /branches/dev/samtools/Makefile
5295 M /branches/dev/samtools/bam.h
5296 A /branches/dev/samtools/bam_maqcns.c
5297 A /branches/dev/samtools/bam_maqcns.h
5298 M /branches/dev/samtools/bam_tview.c
5299 M /branches/dev/samtools/bamtk.c
5300 A /branches/dev/samtools/glf.h
5303 * add MAQ consensus caller, currently BUGGY!
5305 ------------------------------------------------------------------------
5306 r21 | lh3lh3 | 2008-11-27 08:51:28 -0500 (Thu, 27 Nov 2008) | 4 lines
5308 M /branches/dev/samtools/bam_pileup.c
5309 M /branches/dev/samtools/bam_tview.c
5310 M /branches/dev/samtools/bamtk.c
5313 * tview: display padded alignment (but not P operation)
5314 * better coordinates and reference sequence
5316 ------------------------------------------------------------------------
5317 r19 | lh3lh3 | 2008-11-27 04:26:05 -0500 (Thu, 27 Nov 2008) | 2 lines
5319 A /branches/dev/samtools/ChangeLog
5323 ------------------------------------------------------------------------
5324 r18 | lh3lh3 | 2008-11-27 04:24:45 -0500 (Thu, 27 Nov 2008) | 3 lines
5326 D /branches/dev/samtools/ChangeLog
5327 A /branches/dev/samtools/ChangeLog.old (from /branches/dev/samtools/ChangeLog:6)
5329 Rename ChangeLog to ChangeLog.old. This old ChangeLog is generated from
5330 the log of my personal SVN repository.
5332 ------------------------------------------------------------------------
5333 r17 | lh3lh3 | 2008-11-27 04:22:55 -0500 (Thu, 27 Nov 2008) | 6 lines
5335 M /branches/dev/samtools/Makefile
5336 M /branches/dev/samtools/bamtk.c
5337 M /branches/dev/samtools/bgzf.c
5340 * declare fseeko and ftello as some Linux may not do this by default and
5341 missing these declarations will make bgzf buggy
5342 * get rid of some harmless warings
5343 * use BGZF by default, now
5345 ------------------------------------------------------------------------
5346 r16 | lh3lh3 | 2008-11-26 16:19:11 -0500 (Wed, 26 Nov 2008) | 4 lines
5348 M /branches/dev/samtools/bam_index.c
5349 M /branches/dev/samtools/bamtk.c
5350 M /branches/dev/samtools/razf.c
5353 * fixed a bug in razf_read()
5354 * give more warnings when the file is truncated (or due to bugs in I/O library)
5356 ------------------------------------------------------------------------
5357 r15 | lh3lh3 | 2008-11-26 15:41:39 -0500 (Wed, 26 Nov 2008) | 2 lines
5359 M /branches/dev/samtools/bgzf.c
5361 fixed a bug in bgzf.c at the end of the file
5363 ------------------------------------------------------------------------
5364 r14 | lh3lh3 | 2008-11-26 12:05:18 -0500 (Wed, 26 Nov 2008) | 4 lines
5366 M /branches/dev/samtools/bamtk.c
5369 * a lot happened to RAZF, although samtools itself is untouched. Better
5370 also update the version number anyway to avoid confusion
5372 ------------------------------------------------------------------------
5373 r13 | lh3lh3 | 2008-11-26 12:03:48 -0500 (Wed, 26 Nov 2008) | 2 lines
5375 M /branches/dev/samtools/razf.c
5377 a change from Jue, but I think it should not matter
5379 ------------------------------------------------------------------------
5380 r12 | lh3lh3 | 2008-11-26 11:48:14 -0500 (Wed, 26 Nov 2008) | 3 lines
5382 M /branches/dev/samtools/razf.c
5384 fixed a potential bug in razf. However, it seems still buggy, just
5385 rarely happens, very rarely.
5387 ------------------------------------------------------------------------
5388 r11 | lh3lh3 | 2008-11-26 09:02:56 -0500 (Wed, 26 Nov 2008) | 2 lines
5390 M /branches/dev/samtools/razf.c
5392 fixed a bug in razf, with the help of Jue
5394 ------------------------------------------------------------------------
5395 r10 | lh3lh3 | 2008-11-26 06:55:32 -0500 (Wed, 26 Nov 2008) | 2 lines
5397 M /branches/dev/samtools/bam_index.c
5401 ------------------------------------------------------------------------
5402 r9 | lh3lh3 | 2008-11-26 06:37:05 -0500 (Wed, 26 Nov 2008) | 2 lines
5404 M /branches/dev/samtools/Makefile
5405 M /branches/dev/samtools/bam.h
5406 M /branches/dev/samtools/razf.c
5407 M /branches/dev/samtools/razf.h
5409 * Jue has updated razf to realize Bob's scheme
5411 ------------------------------------------------------------------------
5412 r7 | lh3lh3 | 2008-11-25 15:37:37 -0500 (Tue, 25 Nov 2008) | 2 lines
5414 A /branches/dev/samtools/samtools.1
5418 ------------------------------------------------------------------------
5419 r6 | lh3lh3 | 2008-11-25 15:37:16 -0500 (Tue, 25 Nov 2008) | 3 lines
5421 A /branches/dev/samtools/ChangeLog
5422 A /branches/dev/samtools/Makefile
5423 A /branches/dev/samtools/bam.c
5424 A /branches/dev/samtools/bam.h
5425 A /branches/dev/samtools/bam_aux.c
5426 A /branches/dev/samtools/bam_endian.h
5427 A /branches/dev/samtools/bam_import.c
5428 A /branches/dev/samtools/bam_index.c
5429 A /branches/dev/samtools/bam_lpileup.c
5430 A /branches/dev/samtools/bam_pileup.c
5431 A /branches/dev/samtools/bam_sort.c
5432 A /branches/dev/samtools/bam_tview.c
5433 A /branches/dev/samtools/bamtk.c
5434 A /branches/dev/samtools/bgzf.c
5435 A /branches/dev/samtools/bgzf.h
5436 A /branches/dev/samtools/bgzip.c
5437 A /branches/dev/samtools/faidx.c
5438 A /branches/dev/samtools/faidx.h
5439 A /branches/dev/samtools/khash.h
5440 A /branches/dev/samtools/ksort.h
5441 A /branches/dev/samtools/kstream.h
5442 A /branches/dev/samtools/misc
5443 A /branches/dev/samtools/misc/Makefile
5444 A /branches/dev/samtools/misc/all2sam.pl
5445 A /branches/dev/samtools/misc/maq2sam.c
5446 A /branches/dev/samtools/razf.c
5447 A /branches/dev/samtools/razf.h
5448 A /branches/dev/samtools/razip.c
5449 A /branches/dev/samtools/zutil.h
5451 The initial version of samtools, replicated from my local SVN repository.
5452 The current version is: 0.1.0-42. All future development will happen here.
5454 ------------------------------------------------------------------------
5455 r5 | lh3lh3 | 2008-11-25 15:30:49 -0500 (Tue, 25 Nov 2008) | 2 lines
5457 A /branches/dev/samtools
5459 samtools (C version)
5461 ------------------------------------------------------------------------