1 ------------------------------------------------------------------------
2 r782 | lh3lh3 | 2010-10-27 19:58:54 -0400 (Wed, 27 Oct 2010) | 2 lines
4 M /trunk/samtools/bam_plcmd.c
6 fixed a silly bug in pileup
8 ------------------------------------------------------------------------
9 r781 | lh3lh3 | 2010-10-27 14:39:48 -0400 (Wed, 27 Oct 2010) | 5 lines
11 M /trunk/samtools/ChangeLog
12 M /trunk/samtools/bam_plcmd.c
13 M /trunk/samtools/bam_sort.c
14 M /trunk/samtools/bamtk.c
15 M /trunk/samtools/samtools.1
17 * samtools-0.1.8-22 (r781)
18 * made BAQ the default behavior of mpileup
20 * in merge, force to exit given inconsistent header when "-R" is not in use.
22 ------------------------------------------------------------------------
23 r780 | lh3lh3 | 2010-10-27 11:01:11 -0400 (Wed, 27 Oct 2010) | 3 lines
25 M /trunk/samtools/bam.h
26 M /trunk/samtools/bam_plcmd.c
27 M /trunk/samtools/bamtk.c
29 * samtools-0.1.8-21 (r780)
30 * minor speedup to pileup
32 ------------------------------------------------------------------------
33 r779 | lh3lh3 | 2010-10-27 09:58:56 -0400 (Wed, 27 Oct 2010) | 2 lines
35 M /trunk/samtools/bam_pileup.c
36 M /trunk/samtools/bam_plcmd.c
37 M /trunk/samtools/examples/toy.sam
39 improve pileup a little bit
41 ------------------------------------------------------------------------
42 r778 | lh3lh3 | 2010-10-27 00:14:43 -0400 (Wed, 27 Oct 2010) | 3 lines
44 M /trunk/samtools/bam.h
45 M /trunk/samtools/bam_pileup.c
46 M /trunk/samtools/bam_plcmd.c
47 M /trunk/samtools/bam_tview.c
48 M /trunk/samtools/bamtk.c
50 * samtools-0.1.8-20 (r778)
51 * speed up pileup, although I do not know how much is the improvement
53 ------------------------------------------------------------------------
54 r777 | lh3lh3 | 2010-10-26 17:26:04 -0400 (Tue, 26 Oct 2010) | 3 lines
56 M /trunk/samtools/bam_maqcns.c
57 M /trunk/samtools/bam_maqcns.h
58 M /trunk/samtools/bam_plcmd.c
59 M /trunk/samtools/bamtk.c
60 M /trunk/samtools/examples/Makefile
62 * samtools-0.1.8-19 (r777)
63 * integrate mpileup features to pileup: min_baseQ, capQ, prob_realn, paired-only and biased prior
65 ------------------------------------------------------------------------
66 r776 | lh3lh3 | 2010-10-26 15:27:46 -0400 (Tue, 26 Oct 2010) | 2 lines
68 M /trunk/samtools/bam_md.c
70 remove local realignment (probabilistic realignment is still there)
72 ------------------------------------------------------------------------
73 r774 | jmarshall | 2010-10-21 06:52:38 -0400 (Thu, 21 Oct 2010) | 3 lines
75 M /trunk/samtools/sam_view.c
77 Add the relevant filename or region to error messages, and cause a failure
78 exit status where appropriate. Based on a patch provided by Marcel Martin.
80 ------------------------------------------------------------------------
81 r773 | lh3lh3 | 2010-10-19 19:44:31 -0400 (Tue, 19 Oct 2010) | 3 lines
83 M /trunk/samtools/examples/toy.sam
84 M /trunk/samtools/kaln.c
86 * Minor code changes. No real effect.
87 * change quality to 30 in toy.sam
89 ------------------------------------------------------------------------
90 r772 | lh3lh3 | 2010-10-18 23:40:13 -0400 (Mon, 18 Oct 2010) | 2 lines
92 M /trunk/samtools/examples/toy.fa
93 M /trunk/samtools/examples/toy.sam
95 added another toy example
97 ------------------------------------------------------------------------
98 r771 | lh3lh3 | 2010-10-13 23:32:12 -0400 (Wed, 13 Oct 2010) | 2 lines
100 M /trunk/samtools/bcftools/call1.c
101 M /trunk/samtools/bcftools/ld.c
102 M /trunk/samtools/bcftools/vcfutils.pl
104 improve the LD statistics
106 ------------------------------------------------------------------------
107 r770 | lh3lh3 | 2010-10-12 23:49:26 -0400 (Tue, 12 Oct 2010) | 3 lines
109 M /trunk/samtools/bcftools/call1.c
110 M /trunk/samtools/bcftools/vcfutils.pl
112 * a minor fix to the -L option
113 * add ldstats to vcfutils.pl
115 ------------------------------------------------------------------------
116 r769 | lh3lh3 | 2010-10-12 15:51:57 -0400 (Tue, 12 Oct 2010) | 2 lines
118 M /trunk/samtools/bcftools/bcf.c
122 ------------------------------------------------------------------------
123 r768 | lh3lh3 | 2010-10-12 15:49:06 -0400 (Tue, 12 Oct 2010) | 2 lines
125 M /trunk/samtools/bcftools/Makefile
126 A /trunk/samtools/bcftools/ld.c
128 forget to add the key file
130 ------------------------------------------------------------------------
131 r767 | lh3lh3 | 2010-10-12 15:48:46 -0400 (Tue, 12 Oct 2010) | 4 lines
133 M /trunk/samtools/bcftools/Makefile
134 M /trunk/samtools/bcftools/bcf.c
135 M /trunk/samtools/bcftools/bcf.h
136 M /trunk/samtools/bcftools/call1.c
137 M /trunk/samtools/bcftools/prob1.c
138 M /trunk/samtools/bcftools/vcfutils.pl
140 * vcfutils.pl: fixed a typo in help message
141 * added APIs: bcf_append_info() and bcf_cpy()
142 * calculate adjacent LD
144 ------------------------------------------------------------------------
145 r766 | lh3lh3 | 2010-10-11 11:06:40 -0400 (Mon, 11 Oct 2010) | 2 lines
147 M /trunk/samtools/bcftools/vcfutils.pl
149 added filter for samtools/bcftools genetated VCFs
151 ------------------------------------------------------------------------
152 r765 | lh3lh3 | 2010-10-05 14:05:18 -0400 (Tue, 05 Oct 2010) | 3 lines
154 M /trunk/samtools/bcftools/vcfutils.pl
155 M /trunk/samtools/kaln.c
157 * removed a comment line in kaln.c
158 * vcfutils.pl fillac works when GT is not the first field
160 ------------------------------------------------------------------------
161 r764 | petulda | 2010-10-05 08:59:36 -0400 (Tue, 05 Oct 2010) | 1 line
163 A /trunk/samtools/bcftools/bcf-fix.pl
165 Convert VCF output of "bcftools view -bgcv" to a valid VCF file
166 ------------------------------------------------------------------------
167 r763 | lh3lh3 | 2010-10-02 22:51:03 -0400 (Sat, 02 Oct 2010) | 4 lines
169 M /trunk/samtools/bam_plcmd.c
170 M /trunk/samtools/bamtk.c
171 A /trunk/samtools/bcftools/bcftools.1
172 M /trunk/samtools/bcftools/call1.c
173 M /trunk/samtools/samtools.1
175 * samtools-0.1.8-18 (r763)
176 * added bcftools manual page
177 * minor fix to mpileup and view command lines
179 ------------------------------------------------------------------------
180 r762 | lh3lh3 | 2010-10-02 21:46:25 -0400 (Sat, 02 Oct 2010) | 3 lines
182 M /trunk/samtools/bcftools/bcf.c
183 M /trunk/samtools/bcftools/call1.c
184 M /trunk/samtools/bcftools/vcfutils.pl
186 * vcfutils.pl qstats: calculate marginal ts/tv
187 * allow to call genotypes at variant sites
189 ------------------------------------------------------------------------
190 r761 | lh3lh3 | 2010-10-01 00:29:55 -0400 (Fri, 01 Oct 2010) | 3 lines
192 M /trunk/samtools/kaln.c
193 M /trunk/samtools/misc/HmmGlocal.java
195 I am changing the gap open probability back to 0.001. It seems that
196 being conservative here is a good thing...
198 ------------------------------------------------------------------------
199 r760 | lh3lh3 | 2010-10-01 00:11:27 -0400 (Fri, 01 Oct 2010) | 5 lines
201 M /trunk/samtools/bamtk.c
202 M /trunk/samtools/kaln.c
203 A /trunk/samtools/misc/HmmGlocal.java
205 * samtools-0.1.8-17 (r760)
206 * the default gap open penalty is too small (a typo)
207 * added comments on hmm_realn
208 * Java implementation
210 ------------------------------------------------------------------------
211 r759 | lh3lh3 | 2010-09-30 10:12:54 -0400 (Thu, 30 Sep 2010) | 2 lines
213 M /trunk/samtools/bamtk.c
215 mark samtools-0.1.8-16 (r759)
217 ------------------------------------------------------------------------
218 r758 | lh3lh3 | 2010-09-30 10:12:02 -0400 (Thu, 30 Sep 2010) | 2 lines
220 M /trunk/samtools/kaln.c
222 round to the nearest integer
224 ------------------------------------------------------------------------
225 r757 | lh3lh3 | 2010-09-28 17:16:43 -0400 (Tue, 28 Sep 2010) | 4 lines
227 M /trunk/samtools/kaln.c
229 I was trying to accelerate ka_prob_glocal() as this will be the
230 bottleneck. After an hour, the only gain is to change division to
231 multiplication. OK. I will stop.
233 ------------------------------------------------------------------------
234 r756 | lh3lh3 | 2010-09-28 16:57:49 -0400 (Tue, 28 Sep 2010) | 2 lines
236 M /trunk/samtools/kaln.c
238 this is interesting. multiplication is much faster than division, at least on my Mac
240 ------------------------------------------------------------------------
241 r755 | lh3lh3 | 2010-09-28 16:19:13 -0400 (Tue, 28 Sep 2010) | 2 lines
243 M /trunk/samtools/kaln.c
247 ------------------------------------------------------------------------
248 r754 | lh3lh3 | 2010-09-28 15:44:16 -0400 (Tue, 28 Sep 2010) | 2 lines
250 M /trunk/samtools/bam_md.c
251 M /trunk/samtools/bam_plcmd.c
252 M /trunk/samtools/kaln.c
254 prob_realn() seems working!
256 ------------------------------------------------------------------------
257 r753 | lh3lh3 | 2010-09-28 12:48:23 -0400 (Tue, 28 Sep 2010) | 2 lines
259 M /trunk/samtools/kaln.c
263 ------------------------------------------------------------------------
264 r752 | lh3lh3 | 2010-09-28 12:47:41 -0400 (Tue, 28 Sep 2010) | 2 lines
266 M /trunk/samtools/kaln.c
267 M /trunk/samtools/kaln.h
269 Convert phredQ to probabilities
271 ------------------------------------------------------------------------
272 r751 | lh3lh3 | 2010-09-28 12:32:08 -0400 (Tue, 28 Sep 2010) | 2 lines
274 M /trunk/samtools/kaln.c
275 M /trunk/samtools/kaln.h
277 Implement the glocal HMM; discard the extention HMM
279 ------------------------------------------------------------------------
280 r750 | lh3lh3 | 2010-09-28 00:06:11 -0400 (Tue, 28 Sep 2010) | 2 lines
282 M /trunk/samtools/kaln.c
284 improve numerical stability
286 ------------------------------------------------------------------------
287 r749 | lh3lh3 | 2010-09-27 23:27:54 -0400 (Mon, 27 Sep 2010) | 2 lines
289 M /trunk/samtools/kaln.c
293 ------------------------------------------------------------------------
294 r748 | lh3lh3 | 2010-09-27 23:17:16 -0400 (Mon, 27 Sep 2010) | 2 lines
296 M /trunk/samtools/kaln.c
298 fixed a bug in banded DP
300 ------------------------------------------------------------------------
301 r747 | lh3lh3 | 2010-09-27 23:05:12 -0400 (Mon, 27 Sep 2010) | 3 lines
303 M /trunk/samtools/kaln.c
305 * fixed that weird issue.
306 * the banded version is NOT working
308 ------------------------------------------------------------------------
309 r746 | lh3lh3 | 2010-09-27 22:57:05 -0400 (Mon, 27 Sep 2010) | 2 lines
311 M /trunk/samtools/kaln.c
313 More comments. This version seems working, but something is a little weird...
315 ------------------------------------------------------------------------
316 r745 | lh3lh3 | 2010-09-27 17:21:40 -0400 (Mon, 27 Sep 2010) | 6 lines
318 M /trunk/samtools/kaln.c
320 A little code cleanup. Now the forward and backback algorithms give
321 nearly identical P(x), which means both are close to the correct
322 forms. However, I have only tested on toy examples. Minor errors in
323 the implementation may not be obvious.
326 ------------------------------------------------------------------------
327 r744 | lh3lh3 | 2010-09-27 16:55:15 -0400 (Mon, 27 Sep 2010) | 2 lines
329 M /trunk/samtools/bam_plcmd.c
330 M /trunk/samtools/bam_sort.c
331 M /trunk/samtools/kaln.c
332 M /trunk/samtools/kaln.h
336 ------------------------------------------------------------------------
337 r743 | jmarshall | 2010-09-27 08:19:06 -0400 (Mon, 27 Sep 2010) | 6 lines
339 M /trunk/samtools/bam_sort.c
341 Abort if merge -h's INH.SAM cannot be opened, just as we abort
342 if any of the IN#.BAM input files cannot be opened.
344 Also propagate any error indication returned by bam_merge_core()
345 to samtools merge's exit status.
347 ------------------------------------------------------------------------
348 r741 | jmarshall | 2010-09-24 11:08:24 -0400 (Fri, 24 Sep 2010) | 5 lines
350 M /trunk/samtools/bam_index.c
352 Use bam_validate1() to detect garbage records in the event of a corrupt
353 BAI index file that causes a bam_seek() to an invalid position. At most
354 one record (namely, the bam_iter_read terminator) is tested per bam_fetch()
355 call, so the cost is insignificant in the normal case.
357 ------------------------------------------------------------------------
358 r740 | jmarshall | 2010-09-24 11:00:19 -0400 (Fri, 24 Sep 2010) | 2 lines
360 M /trunk/samtools/bam.c
361 M /trunk/samtools/bam.h
365 ------------------------------------------------------------------------
366 r739 | lh3lh3 | 2010-09-22 12:07:50 -0400 (Wed, 22 Sep 2010) | 3 lines
368 M /trunk/samtools/bam_md.c
369 M /trunk/samtools/bamtk.c
371 * samtools-0.1.8-15 (r379)
372 * allow to change capQ parameter in calmd
374 ------------------------------------------------------------------------
375 r738 | jmarshall | 2010-09-22 11:15:33 -0400 (Wed, 22 Sep 2010) | 13 lines
377 M /trunk/samtools/bam_index.c
378 M /trunk/samtools/sam_view.c
380 When bam_read1() returns an error (return value <= -2), propagate that error
381 to bam_iter_read()'s own return value. Similarly, also propagate it up to
382 bam_fetch()'s return value. Previously bam_fetch() always returned 0, and
383 callers ignored its return value anyway. With this change, 0 continues to
384 indicate success, while <= -2 (which can be written as < 0, as -1 is never
385 returned) indicates corrupted input.
387 bam_iter_read() ought also to propagate errors returned by bam_seek().
389 main_samview() can now print an error message and fail when bam_fetch()
390 detects that a .bai index file is corrupted or otherwise does not correspond
391 to the .bam file it is being used with.
393 ------------------------------------------------------------------------
394 r737 | jmarshall | 2010-09-22 10:47:42 -0400 (Wed, 22 Sep 2010) | 3 lines
396 M /trunk/samtools/bam_index.c
398 0 is a successful return value from bam_read1(). (In practice, it never
399 returns 0 anyway; but all the other callers treat 0 as successful.)
401 ------------------------------------------------------------------------
402 r736 | lh3lh3 | 2010-09-20 17:43:08 -0400 (Mon, 20 Sep 2010) | 2 lines
404 M /trunk/samtools/bam.h
405 M /trunk/samtools/bam_index.c
406 M /trunk/samtools/bam_sort.c
408 * merge files region-by-region. work on small examples but more tests are needed.
410 ------------------------------------------------------------------------
411 r735 | lh3lh3 | 2010-09-20 16:56:24 -0400 (Mon, 20 Sep 2010) | 2 lines
413 M /trunk/samtools/bcftools/vcfutils.pl
415 improve qstats by checking the alleles as well
417 ------------------------------------------------------------------------
418 r734 | lh3lh3 | 2010-09-17 18:12:13 -0400 (Fri, 17 Sep 2010) | 2 lines
420 M /trunk/samtools/bcftools/vcfutils.pl
422 convert UCSC SNP SQL dump to VCF
424 ------------------------------------------------------------------------
425 r733 | lh3lh3 | 2010-09-17 13:02:11 -0400 (Fri, 17 Sep 2010) | 2 lines
427 M /trunk/samtools/bcftools/vcfutils.pl
431 ------------------------------------------------------------------------
432 r732 | lh3lh3 | 2010-09-17 10:11:37 -0400 (Fri, 17 Sep 2010) | 3 lines
434 M /trunk/samtools/bcftools/Makefile
435 M /trunk/samtools/bcftools/bcf.c
436 M /trunk/samtools/bcftools/bcf.h
437 M /trunk/samtools/bcftools/vcf.c
440 * VCF->BCF is not possible without knowing the sequence dictionary before hand...
442 ------------------------------------------------------------------------
443 r731 | lh3lh3 | 2010-09-17 09:15:53 -0400 (Fri, 17 Sep 2010) | 2 lines
445 M /trunk/samtools/bam2bcf.c
446 M /trunk/samtools/bcftools/bcf.c
447 M /trunk/samtools/bcftools/bcf.h
448 M /trunk/samtools/bcftools/bcfutils.c
449 M /trunk/samtools/bcftools/call1.c
450 M /trunk/samtools/bcftools/vcf.c
452 * put n_smpl to "bcf1_t" to simplify API a little
454 ------------------------------------------------------------------------
455 r730 | lh3lh3 | 2010-09-16 21:36:01 -0400 (Thu, 16 Sep 2010) | 2 lines
457 M /trunk/samtools/bcftools/bcf.h
458 M /trunk/samtools/bcftools/call1.c
459 M /trunk/samtools/bcftools/index.c
461 fixed a bug in indexing
463 ------------------------------------------------------------------------
464 r729 | lh3lh3 | 2010-09-16 16:54:48 -0400 (Thu, 16 Sep 2010) | 3 lines
466 M /trunk/samtools/bam.c
467 M /trunk/samtools/bam_md.c
468 M /trunk/samtools/bam_pileup.c
470 * fixed a bug in capQ
471 * valgrind identifies a use of uninitialised value, but I have not fixed it.
473 ------------------------------------------------------------------------
474 r728 | lh3lh3 | 2010-09-16 15:03:59 -0400 (Thu, 16 Sep 2010) | 3 lines
476 M /trunk/samtools/bgzip.c
477 M /trunk/samtools/razip.c
479 * fixed a bug in razip: -c will delete the input file
480 * copy tabix/bgzip to here
482 ------------------------------------------------------------------------
483 r727 | lh3lh3 | 2010-09-16 13:45:49 -0400 (Thu, 16 Sep 2010) | 3 lines
485 M /trunk/samtools/bam_md.c
486 M /trunk/samtools/bam_plcmd.c
487 M /trunk/samtools/bamtk.c
489 * samtools-0.1.8-14 (r727)
490 * allow to change the capQ parameter at the command line
492 ------------------------------------------------------------------------
493 r726 | lh3lh3 | 2010-09-16 13:38:43 -0400 (Thu, 16 Sep 2010) | 4 lines
495 M /trunk/samtools/bam_md.c
496 M /trunk/samtools/bam_plcmd.c
497 M /trunk/samtools/bcftools/vcfutils.pl
498 M /trunk/samtools/misc/samtools.pl
500 * added varFilter to vcfutils.pl
501 * reimplement realn(). now it performs a local alignment
502 * added cap_mapQ() to cap mapping quality when there are many substitutions
504 ------------------------------------------------------------------------
505 r724 | lh3lh3 | 2010-09-15 00:18:31 -0400 (Wed, 15 Sep 2010) | 2 lines
507 M /trunk/samtools/bcftools/Makefile
508 A /trunk/samtools/bcftools/bcf2qcall.c
509 M /trunk/samtools/bcftools/call1.c
511 * convert BCF to QCALL input
513 ------------------------------------------------------------------------
514 r723 | lh3lh3 | 2010-09-14 22:41:50 -0400 (Tue, 14 Sep 2010) | 2 lines
516 M /trunk/samtools/bam_md.c
518 dynamic band width in realignment
520 ------------------------------------------------------------------------
521 r722 | lh3lh3 | 2010-09-14 22:05:32 -0400 (Tue, 14 Sep 2010) | 2 lines
523 M /trunk/samtools/bam_md.c
524 M /trunk/samtools/bam_plcmd.c
526 fixed a bug in realignment
528 ------------------------------------------------------------------------
529 r721 | lh3lh3 | 2010-09-14 20:54:09 -0400 (Tue, 14 Sep 2010) | 2 lines
531 M /trunk/samtools/bcftools/prob1.c
535 ------------------------------------------------------------------------
536 r720 | lh3lh3 | 2010-09-14 19:25:10 -0400 (Tue, 14 Sep 2010) | 2 lines
538 M /trunk/samtools/Makefile
539 M /trunk/samtools/bam_maqcns.c
540 M /trunk/samtools/bam_md.c
542 fixed a bug in realignment
544 ------------------------------------------------------------------------
545 r719 | lh3lh3 | 2010-09-14 19:18:24 -0400 (Tue, 14 Sep 2010) | 2 lines
547 M /trunk/samtools/bam_plcmd.c
549 minor changes. It is BUGGY now!
551 ------------------------------------------------------------------------
552 r718 | lh3lh3 | 2010-09-14 16:32:33 -0400 (Tue, 14 Sep 2010) | 4 lines
554 M /trunk/samtools/bam_md.c
555 M /trunk/samtools/bam_pileup.c
556 M /trunk/samtools/kaln.c
557 M /trunk/samtools/kaln.h
559 * aggressive gapped aligner is implemented in calmd.
560 * distinguish gap_open and gap_end_open in banded alignment
561 * make tview accepts alignment with heading and tailing D
563 ------------------------------------------------------------------------
564 r717 | jmarshall | 2010-09-14 09:04:28 -0400 (Tue, 14 Sep 2010) | 2 lines
568 Add svn:ignore properties for generated files that don't appear in "make all".
570 ------------------------------------------------------------------------
571 r716 | jmarshall | 2010-09-13 08:37:53 -0400 (Mon, 13 Sep 2010) | 3 lines
574 M /trunk/samtools/bcftools
575 M /trunk/samtools/misc
577 Add svn:ignore properties listing the generated files.
578 (Except for *.o, which we'll assume is in global-ignores.)
580 ------------------------------------------------------------------------
581 r715 | lh3lh3 | 2010-09-08 12:53:55 -0400 (Wed, 08 Sep 2010) | 5 lines
583 M /trunk/samtools/bamtk.c
584 M /trunk/samtools/bcftools/call1.c
585 M /trunk/samtools/bcftools/prob1.c
586 M /trunk/samtools/sample.c
587 M /trunk/samtools/sample.h
589 * samtools-0.1.8-13 (r715)
590 * fixed a bug in identifying SM across files
591 * bcftools: estimate heterozygosity
592 * bcftools: allow to skip sites without reference bases
594 ------------------------------------------------------------------------
595 r713 | lh3lh3 | 2010-09-03 17:19:12 -0400 (Fri, 03 Sep 2010) | 2 lines
597 M /trunk/samtools/bcftools/Makefile
598 M /trunk/samtools/bcftools/call1.c
599 M /trunk/samtools/bcftools/prob1.c
600 M /trunk/samtools/bcftools/prob1.h
602 quite a lot changes to the contrast caller, but I still feel something is missing...
604 ------------------------------------------------------------------------
605 r711 | lh3lh3 | 2010-09-03 00:30:48 -0400 (Fri, 03 Sep 2010) | 4 lines
607 M /trunk/samtools/bcftools/Makefile
608 M /trunk/samtools/bcftools/call1.c
609 M /trunk/samtools/bcftools/prob1.c
610 M /trunk/samtools/bcftools/vcfutils.pl
612 * changed 3.434 to 4.343 (typo!)
613 * fixed a bug in the contrast caller
614 * calculate heterozygosity
616 ------------------------------------------------------------------------
617 r710 | lh3lh3 | 2010-09-01 23:24:47 -0400 (Wed, 01 Sep 2010) | 2 lines
619 M /trunk/samtools/bcftools/bcf.h
620 M /trunk/samtools/bcftools/bcfutils.c
621 M /trunk/samtools/bcftools/call1.c
623 SNP calling from the GL field
625 ------------------------------------------------------------------------
626 r709 | lh3lh3 | 2010-09-01 18:52:30 -0400 (Wed, 01 Sep 2010) | 2 lines
628 M /trunk/samtools/bcftools/vcf.c
630 fixed another problem
632 ------------------------------------------------------------------------
633 r708 | lh3lh3 | 2010-09-01 18:31:17 -0400 (Wed, 01 Sep 2010) | 3 lines
635 M /trunk/samtools/bcftools/bcf.c
636 M /trunk/samtools/bcftools/vcf.c
638 * fixed bugs in parsing VCF
639 * parser now works with GT/GQ/DP/PL/GL
641 ------------------------------------------------------------------------
642 r707 | lh3lh3 | 2010-09-01 15:28:29 -0400 (Wed, 01 Sep 2010) | 2 lines
644 M /trunk/samtools/bcftools/Makefile
645 M /trunk/samtools/bcftools/prob1.c
647 Do not compile _BCF_QUAD by default
649 ------------------------------------------------------------------------
650 r706 | lh3lh3 | 2010-09-01 15:21:41 -0400 (Wed, 01 Sep 2010) | 2 lines
652 M /trunk/samtools/bcftools/bcf.c
653 M /trunk/samtools/bcftools/bcf.h
654 M /trunk/samtools/bcftools/bcfutils.c
655 M /trunk/samtools/bcftools/call1.c
657 Write the correct ALT and PL in the SNP calling mode.
659 ------------------------------------------------------------------------
660 r705 | lh3lh3 | 2010-09-01 12:50:33 -0400 (Wed, 01 Sep 2010) | 2 lines
662 M /trunk/samtools/bcftools/vcfutils.pl
664 more commands for my own uses
666 ------------------------------------------------------------------------
667 r704 | lh3lh3 | 2010-09-01 09:26:10 -0400 (Wed, 01 Sep 2010) | 2 lines
669 A /trunk/samtools/bcftools/vcfutils.pl
671 Utilities for processing VCF
673 ------------------------------------------------------------------------
674 r703 | lh3lh3 | 2010-08-31 16:44:57 -0400 (Tue, 31 Aug 2010) | 2 lines
676 M /trunk/samtools/bcftools/Makefile
677 M /trunk/samtools/bcftools/call1.c
678 M /trunk/samtools/bcftools/prob1.c
679 M /trunk/samtools/bcftools/prob1.h
681 preliminary contrast variant caller
683 ------------------------------------------------------------------------
684 r702 | lh3lh3 | 2010-08-31 12:28:39 -0400 (Tue, 31 Aug 2010) | 2 lines
686 M /trunk/samtools/bcftools/call1.c
687 M /trunk/samtools/bcftools/prob1.c
688 M /trunk/samtools/bcftools/prob1.h
690 z' and z'' can be calculated
692 ------------------------------------------------------------------------
693 r701 | lh3lh3 | 2010-08-31 10:20:57 -0400 (Tue, 31 Aug 2010) | 3 lines
695 M /trunk/samtools/bcftools/Makefile
696 A /trunk/samtools/bcftools/call1.c (from /trunk/samtools/bcftools/vcfout.c:699)
697 M /trunk/samtools/bcftools/prob1.c
698 D /trunk/samtools/bcftools/vcfout.c
700 * rename vcfout.c as call1.c
701 * prepare to add two-sample comparison
703 ------------------------------------------------------------------------
704 r699 | lh3lh3 | 2010-08-24 15:28:16 -0400 (Tue, 24 Aug 2010) | 2 lines
706 M /trunk/samtools/bcftools/vcfout.c
708 fixed a bug in calculating the t statistics
710 ------------------------------------------------------------------------
711 r698 | lh3lh3 | 2010-08-24 14:05:50 -0400 (Tue, 24 Aug 2010) | 3 lines
713 M /trunk/samtools/bam2bcf.c
714 M /trunk/samtools/bam2bcf.h
715 M /trunk/samtools/bamtk.c
716 M /trunk/samtools/bcftools/kfunc.c
717 M /trunk/samtools/bcftools/vcfout.c
719 * samtools-0.1.8-13 (r698)
720 * perform one-tailed t-test for baseQ, mapQ and endDist
722 ------------------------------------------------------------------------
723 r697 | lh3lh3 | 2010-08-24 12:30:13 -0400 (Tue, 24 Aug 2010) | 2 lines
725 M /trunk/samtools/bcftools/kfunc.c
727 added regularized incomplete beta function
729 ------------------------------------------------------------------------
730 r695 | lh3lh3 | 2010-08-23 17:36:17 -0400 (Mon, 23 Aug 2010) | 2 lines
732 M /trunk/samtools/bam_maqcns.c
733 M /trunk/samtools/bam_plcmd.c
735 change the default correlation coefficient
737 ------------------------------------------------------------------------
738 r694 | lh3lh3 | 2010-08-23 14:46:52 -0400 (Mon, 23 Aug 2010) | 2 lines
740 M /trunk/samtools/bcftools/bcf.c
741 M /trunk/samtools/bcftools/vcfout.c
743 print QUAL as floating numbers
745 ------------------------------------------------------------------------
746 r693 | lh3lh3 | 2010-08-23 14:06:07 -0400 (Mon, 23 Aug 2010) | 3 lines
748 M /trunk/samtools/Makefile
749 M /trunk/samtools/bam_plcmd.c
750 M /trunk/samtools/bamtk.c
751 M /trunk/samtools/examples/Makefile
752 A /trunk/samtools/sample.c
753 A /trunk/samtools/sample.h
755 * samtools-0.1.8-12 (r692)
756 * group data by samples in "mpileup -g"
758 ------------------------------------------------------------------------
759 r692 | lh3lh3 | 2010-08-23 10:58:53 -0400 (Mon, 23 Aug 2010) | 2 lines
761 M /trunk/samtools/Makefile
762 D /trunk/samtools/bam_mcns.c
763 D /trunk/samtools/bam_mcns.h
764 M /trunk/samtools/bam_plcmd.c
766 remove VCF output in mpileup
768 ------------------------------------------------------------------------
769 r691 | lh3lh3 | 2010-08-23 10:48:20 -0400 (Mon, 23 Aug 2010) | 3 lines
771 M /trunk/samtools/bam2bcf.c
772 M /trunk/samtools/bam2bcf.h
774 * use the revised MAQ error model for mpileup
775 * prepare to remove the independent model from mpileup
777 ------------------------------------------------------------------------
778 r690 | lh3lh3 | 2010-08-20 15:46:40 -0400 (Fri, 20 Aug 2010) | 2 lines
780 M /trunk/samtools/Makefile
781 M /trunk/samtools/bam_maqcns.c
782 M /trunk/samtools/bam_maqcns.h
783 M /trunk/samtools/bam_plcmd.c
784 A /trunk/samtools/errmod.c
785 A /trunk/samtools/errmod.h
786 M /trunk/samtools/ksort.h
788 added revised MAQ error model
790 ------------------------------------------------------------------------
791 r689 | lh3lh3 | 2010-08-18 09:55:20 -0400 (Wed, 18 Aug 2010) | 2 lines
793 M /trunk/samtools/bcftools/prob1.c
794 M /trunk/samtools/bcftools/prob1.h
795 M /trunk/samtools/bcftools/vcfout.c
797 allow to read the prior from the error output. EM iteration is working.
799 ------------------------------------------------------------------------
800 r688 | lh3lh3 | 2010-08-17 12:12:20 -0400 (Tue, 17 Aug 2010) | 3 lines
802 M /trunk/samtools/bcftools/main.c
803 M /trunk/samtools/bcftools/vcf.c
805 * write a little more VCF header
808 ------------------------------------------------------------------------
809 r687 | lh3lh3 | 2010-08-16 20:53:16 -0400 (Mon, 16 Aug 2010) | 2 lines
811 M /trunk/samtools/bcftools/bcf.c
812 M /trunk/samtools/bcftools/bcf.h
813 M /trunk/samtools/bcftools/bcf.tex
817 ------------------------------------------------------------------------
818 r686 | lh3lh3 | 2010-08-14 00:11:13 -0400 (Sat, 14 Aug 2010) | 2 lines
820 M /trunk/samtools/bcftools/bcf.c
821 M /trunk/samtools/bcftools/prob1.c
823 faster for large sample size (in principle)
825 ------------------------------------------------------------------------
826 r685 | lh3lh3 | 2010-08-13 23:28:31 -0400 (Fri, 13 Aug 2010) | 4 lines
828 M /trunk/samtools/bcftools/prob1.c
830 * a numerically stable method to calculate z_{jk}
831 * currently slower than the old method but will be important for large sample size
832 * in principle, we can speed up for large n, but have not tried
834 ------------------------------------------------------------------------
835 r684 | lh3lh3 | 2010-08-11 21:58:31 -0400 (Wed, 11 Aug 2010) | 2 lines
837 M /trunk/samtools/bcftools/vcfout.c
839 fixed an issue in parsing integer
841 ------------------------------------------------------------------------
842 r683 | lh3lh3 | 2010-08-09 13:05:07 -0400 (Mon, 09 Aug 2010) | 2 lines
844 M /trunk/samtools/bcftools/bcf.c
846 do not print refname if file is converted from VCF
848 ------------------------------------------------------------------------
849 r682 | lh3lh3 | 2010-08-09 12:59:47 -0400 (Mon, 09 Aug 2010) | 3 lines
851 M /trunk/samtools/bcftools/vcf.c
854 * fixed a bug in parsing VCF
856 ------------------------------------------------------------------------
857 r681 | lh3lh3 | 2010-08-09 12:49:23 -0400 (Mon, 09 Aug 2010) | 4 lines
859 M /trunk/samtools/bcftools/bcf.c
860 M /trunk/samtools/bcftools/bcf.h
861 M /trunk/samtools/bcftools/bcfutils.c
862 M /trunk/samtools/bcftools/main.c
863 M /trunk/samtools/bcftools/vcf.c
864 M /trunk/samtools/bcftools/vcfout.c
865 M /trunk/samtools/bgzf.c
866 M /trunk/samtools/kstring.c
868 * fixed a bug in kstrtok@kstring.c
869 * preliminary VCF parser (not parse everything for now)
870 * improved view interface
872 ------------------------------------------------------------------------
873 r680 | lh3lh3 | 2010-08-09 10:43:13 -0400 (Mon, 09 Aug 2010) | 4 lines
875 M /trunk/samtools/bcftools/bcf.c
876 M /trunk/samtools/bcftools/bcf.h
877 M /trunk/samtools/bcftools/vcfout.c
878 M /trunk/samtools/kstring.c
879 M /trunk/samtools/kstring.h
881 * improved kstring (added kstrtok)
882 * removed the limit on the format string length in bcftools
883 * use kstrtok to parse format which fixed a bug in the old code
885 ------------------------------------------------------------------------
886 r679 | lh3lh3 | 2010-08-09 01:12:05 -0400 (Mon, 09 Aug 2010) | 2 lines
888 A /trunk/samtools/bcftools/README
889 M /trunk/samtools/bcftools/vcfout.c
893 ------------------------------------------------------------------------
894 r678 | lh3lh3 | 2010-08-09 00:01:52 -0400 (Mon, 09 Aug 2010) | 2 lines
896 M /trunk/samtools/bcftools/vcfout.c
898 perform single-tail test for ED4
900 ------------------------------------------------------------------------
901 r677 | lh3lh3 | 2010-08-08 23:48:35 -0400 (Sun, 08 Aug 2010) | 2 lines
903 M /trunk/samtools/bcftools/Makefile
904 M /trunk/samtools/bcftools/kfunc.c
905 M /trunk/samtools/bcftools/vcfout.c
907 * test depth, end distance and HWE
909 ------------------------------------------------------------------------
910 r676 | lh3lh3 | 2010-08-08 02:04:15 -0400 (Sun, 08 Aug 2010) | 2 lines
912 M /trunk/samtools/bcftools/kfunc.c
914 reimplement incomplete gamma functions. no copy-paste
916 ------------------------------------------------------------------------
917 r675 | lh3lh3 | 2010-08-06 22:42:54 -0400 (Fri, 06 Aug 2010) | 3 lines
919 M /trunk/samtools/bam2bcf.c
920 M /trunk/samtools/bam2bcf.h
921 M /trunk/samtools/bcftools/fet.c
922 M /trunk/samtools/bcftools/prob1.c
923 M /trunk/samtools/bcftools/prob1.h
924 M /trunk/samtools/bcftools/vcfout.c
926 * bcftools: add HWE (no testing for now)
927 * record end dist in a 2x2 table, not avg, std any more
929 ------------------------------------------------------------------------
930 r674 | lh3lh3 | 2010-08-06 17:30:16 -0400 (Fri, 06 Aug 2010) | 3 lines
932 A /trunk/samtools/bcftools/kfunc.c
934 * Special functions: log(gamma()), erfc(), P(a,x) (incomplete gamma)
935 * Not using Numerical Recipe due to licensing issues
937 ------------------------------------------------------------------------
938 r673 | lh3lh3 | 2010-08-05 23:46:53 -0400 (Thu, 05 Aug 2010) | 2 lines
940 A /trunk/samtools/bcftools/fet.c
944 ------------------------------------------------------------------------
945 r672 | lh3lh3 | 2010-08-05 21:48:33 -0400 (Thu, 05 Aug 2010) | 3 lines
947 M /trunk/samtools/bam2bcf.c
948 M /trunk/samtools/bam2bcf.h
949 M /trunk/samtools/bamtk.c
950 M /trunk/samtools/examples/Makefile
952 * samtools-0.1.8-11 (r672)
953 * collect more stats for allele balance test in bcftools (not yet)
955 ------------------------------------------------------------------------
956 r671 | lh3lh3 | 2010-08-05 16:17:58 -0400 (Thu, 05 Aug 2010) | 3 lines
958 M /trunk/samtools/bam_plcmd.c
959 M /trunk/samtools/bcftools/bcf.c
960 M /trunk/samtools/bcftools/main.c
962 * the code base is stablized again.
963 * I will delay the vcf parser, which is quite complicated but with little value for now
965 ------------------------------------------------------------------------
966 r670 | lh3lh3 | 2010-08-05 16:03:23 -0400 (Thu, 05 Aug 2010) | 2 lines
968 M /trunk/samtools/examples/Makefile
972 ------------------------------------------------------------------------
973 r669 | lh3lh3 | 2010-08-05 16:03:08 -0400 (Thu, 05 Aug 2010) | 2 lines
975 M /trunk/samtools/bcftools/vcf.c
977 unfinished vcf parser
979 ------------------------------------------------------------------------
980 r668 | lh3lh3 | 2010-08-05 15:46:40 -0400 (Thu, 05 Aug 2010) | 3 lines
982 M /trunk/samtools/bcftools/Makefile
983 M /trunk/samtools/bcftools/bcf.c
984 M /trunk/samtools/bcftools/bcf.h
985 M /trunk/samtools/bcftools/bcfutils.c
986 M /trunk/samtools/bcftools/index.c
987 M /trunk/samtools/bcftools/main.c
988 A /trunk/samtools/bcftools/vcf.c
989 M /trunk/samtools/bcftools/vcfout.c
991 * added prelimiary VCF parser (not finished)
992 * change struct a bit
994 ------------------------------------------------------------------------
995 r667 | lh3lh3 | 2010-08-03 22:35:27 -0400 (Tue, 03 Aug 2010) | 3 lines
997 M /trunk/samtools/bam2bcf.c
998 M /trunk/samtools/bam2bcf.h
999 M /trunk/samtools/bam_plcmd.c
1000 M /trunk/samtools/bcftools/bcf.c
1002 * allow to set min base q
1003 * fixed a bug in mpileup -u
1005 ------------------------------------------------------------------------
1006 r666 | lh3lh3 | 2010-08-03 22:08:44 -0400 (Tue, 03 Aug 2010) | 2 lines
1008 A /trunk/samtools/bcftools/bcf.tex
1012 ------------------------------------------------------------------------
1013 r665 | lh3lh3 | 2010-08-03 21:18:57 -0400 (Tue, 03 Aug 2010) | 2 lines
1015 M /trunk/samtools/examples/Makefile
1019 ------------------------------------------------------------------------
1020 r664 | lh3lh3 | 2010-08-03 21:13:00 -0400 (Tue, 03 Aug 2010) | 2 lines
1022 M /trunk/samtools/Makefile
1023 M /trunk/samtools/bam2bcf.c
1024 M /trunk/samtools/bam2bcf.h
1025 M /trunk/samtools/bcftools/Makefile
1027 fixed compilation error
1029 ------------------------------------------------------------------------
1030 r662 | lh3lh3 | 2010-08-03 21:04:00 -0400 (Tue, 03 Aug 2010) | 2 lines
1032 M /trunk/samtools/Makefile
1033 D /trunk/samtools/bcf.c
1034 D /trunk/samtools/bcf.h
1035 A /trunk/samtools/bcftools
1036 A /trunk/samtools/bcftools/Makefile
1037 A /trunk/samtools/bcftools/bcf.c
1038 A /trunk/samtools/bcftools/bcf.h
1039 A /trunk/samtools/bcftools/bcfutils.c
1040 A /trunk/samtools/bcftools/index.c
1041 A /trunk/samtools/bcftools/main.c
1042 A /trunk/samtools/bcftools/prob1.c
1043 A /trunk/samtools/bcftools/prob1.h
1044 A /trunk/samtools/bcftools/vcfout.c
1046 move bcftools to samtools
1048 ------------------------------------------------------------------------
1049 r660 | lh3lh3 | 2010-08-03 15:58:32 -0400 (Tue, 03 Aug 2010) | 2 lines
1051 M /trunk/samtools/bam2bcf.c
1053 fixed another minor bug
1055 ------------------------------------------------------------------------
1056 r658 | lh3lh3 | 2010-08-03 15:06:45 -0400 (Tue, 03 Aug 2010) | 3 lines
1058 M /trunk/samtools/bamtk.c
1059 M /trunk/samtools/bcf.c
1061 * samtools-0.1.8-10 (r658)
1062 * fixed a bug in bam2bcf when the reference is N
1064 ------------------------------------------------------------------------
1065 r657 | lh3lh3 | 2010-08-03 14:50:23 -0400 (Tue, 03 Aug 2010) | 3 lines
1067 M /trunk/samtools/bam2bcf.c
1068 M /trunk/samtools/bam2bcf.h
1071 * treat ambiguous ref base as the fifth base
1073 ------------------------------------------------------------------------
1074 r654 | lh3lh3 | 2010-08-02 17:38:27 -0400 (Mon, 02 Aug 2010) | 2 lines
1076 M /trunk/bcftools/bcf.c
1077 M /trunk/samtools/bcf.c
1079 missing a column in VCF output...
1081 ------------------------------------------------------------------------
1082 r653 | lh3lh3 | 2010-08-02 17:31:33 -0400 (Mon, 02 Aug 2010) | 2 lines
1084 M /trunk/samtools/bcf.c
1088 ------------------------------------------------------------------------
1089 r651 | lh3lh3 | 2010-08-02 17:27:31 -0400 (Mon, 02 Aug 2010) | 2 lines
1091 M /trunk/samtools/bcf.c
1093 fixed a bug in bcf reader
1095 ------------------------------------------------------------------------
1096 r650 | lh3lh3 | 2010-08-02 17:00:41 -0400 (Mon, 02 Aug 2010) | 2 lines
1098 M /trunk/samtools/bam2bcf.c
1102 ------------------------------------------------------------------------
1103 r649 | lh3lh3 | 2010-08-02 16:49:35 -0400 (Mon, 02 Aug 2010) | 3 lines
1105 M /trunk/samtools/Makefile
1106 M /trunk/samtools/bam2bcf.c
1107 M /trunk/samtools/bam2bcf.h
1108 M /trunk/samtools/bamtk.c
1110 * samtools-0.1.8-9 (r649)
1111 * lossless representation of PL in BCF output
1113 ------------------------------------------------------------------------
1114 r648 | lh3lh3 | 2010-08-02 16:07:25 -0400 (Mon, 02 Aug 2010) | 2 lines
1116 M /trunk/samtools/Makefile
1117 A /trunk/samtools/bam2bcf.c
1118 A /trunk/samtools/bam2bcf.h
1119 M /trunk/samtools/bam_plcmd.c
1120 A /trunk/samtools/bcf.c
1121 A /trunk/samtools/bcf.h
1125 ------------------------------------------------------------------------
1126 r644 | lh3lh3 | 2010-07-28 11:59:19 -0400 (Wed, 28 Jul 2010) | 5 lines
1128 M /trunk/samtools/bam_mcns.c
1129 M /trunk/samtools/bamtk.c
1131 * samtools-0.1.8-8 (r644)
1132 * mpileup becomes a little stable again
1133 * the method is slightly different, but is more theoretically correct
1134 * snp calling is O(n^2) instead of O(n^3)
1136 ------------------------------------------------------------------------
1137 r643 | lh3lh3 | 2010-07-28 11:54:15 -0400 (Wed, 28 Jul 2010) | 3 lines
1139 M /trunk/samtools/bam_mcns.c
1141 * fixed a STUPID bug, which cost me a lot of time.
1142 * I am going to clean up mcns a little bit
1144 ------------------------------------------------------------------------
1145 r642 | lh3lh3 | 2010-07-27 23:23:07 -0400 (Tue, 27 Jul 2010) | 2 lines
1147 M /trunk/samtools/bam_mcns.c
1148 M /trunk/samtools/bam_mcns.h
1149 M /trunk/samtools/bam_plcmd.c
1151 supposedly this is THE correct implementation, but more testing is needed
1153 ------------------------------------------------------------------------
1154 r641 | lh3lh3 | 2010-07-27 22:43:39 -0400 (Tue, 27 Jul 2010) | 2 lines
1156 M /trunk/samtools/bam_mcns.c
1158 NOT ready yet. Going to make further changes...
1160 ------------------------------------------------------------------------
1161 r639 | lh3lh3 | 2010-07-25 22:18:38 -0400 (Sun, 25 Jul 2010) | 3 lines
1163 M /trunk/samtools/bam_mcns.c
1164 M /trunk/samtools/bam_plcmd.c
1165 M /trunk/samtools/bamtk.c
1167 * samtools-0.1.8-7 (r639)
1168 * fixed the reference allele assignment
1170 ------------------------------------------------------------------------
1171 r638 | lh3lh3 | 2010-07-25 12:01:26 -0400 (Sun, 25 Jul 2010) | 5 lines
1173 M /trunk/samtools/bam_mcns.c
1174 M /trunk/samtools/bam_mcns.h
1175 M /trunk/samtools/bam_plcmd.c
1176 M /trunk/samtools/bamtk.c
1178 * samtools-0.1.8-6 (r638)
1179 * skip isnan/isinf in case of float underflow
1180 * added the flat prior
1181 * fixed an issue where there are no reads supporting the reference
1183 ------------------------------------------------------------------------
1184 r637 | lh3lh3 | 2010-07-24 14:16:27 -0400 (Sat, 24 Jul 2010) | 2 lines
1186 M /trunk/samtools/bam_plcmd.c
1190 ------------------------------------------------------------------------
1191 r636 | lh3lh3 | 2010-07-24 14:07:27 -0400 (Sat, 24 Jul 2010) | 2 lines
1193 M /trunk/samtools/bam_mcns.c
1194 M /trunk/samtools/bam_mcns.h
1195 M /trunk/samtools/bam_plcmd.c
1196 M /trunk/samtools/bamtk.c
1200 ------------------------------------------------------------------------
1201 r635 | lh3lh3 | 2010-07-24 01:49:49 -0400 (Sat, 24 Jul 2010) | 2 lines
1203 M /trunk/samtools/bam_mcns.c
1204 M /trunk/samtools/bam_mcns.h
1205 M /trunk/samtools/bam_plcmd.c
1207 posterior expectation FINALLY working. I am so tired...
1209 ------------------------------------------------------------------------
1210 r633 | lh3lh3 | 2010-07-23 13:50:48 -0400 (Fri, 23 Jul 2010) | 2 lines
1212 M /trunk/samtools/bam_plcmd.c
1214 another minor fix to mpileup
1216 ------------------------------------------------------------------------
1217 r632 | lh3lh3 | 2010-07-23 13:43:31 -0400 (Fri, 23 Jul 2010) | 2 lines
1219 M /trunk/samtools/bam_plcmd.c
1221 added the format column
1223 ------------------------------------------------------------------------
1224 r631 | lh3lh3 | 2010-07-23 13:25:44 -0400 (Fri, 23 Jul 2010) | 2 lines
1226 M /trunk/samtools/bam_mcns.c
1227 M /trunk/samtools/bam_mcns.h
1228 M /trunk/samtools/bam_plcmd.c
1229 M /trunk/samtools/bamtk.c
1231 added an alternative prior
1233 ------------------------------------------------------------------------
1234 r628 | lh3lh3 | 2010-07-23 11:48:51 -0400 (Fri, 23 Jul 2010) | 2 lines
1236 M /trunk/samtools/bam_mcns.c
1237 M /trunk/samtools/bam_mcns.h
1238 M /trunk/samtools/bam_plcmd.c
1240 calculate posterior allele frequency
1242 ------------------------------------------------------------------------
1243 r627 | lh3lh3 | 2010-07-22 21:39:13 -0400 (Thu, 22 Jul 2010) | 3 lines
1245 M /trunk/samtools/bam_mcns.c
1246 M /trunk/samtools/bam_plcmd.c
1247 M /trunk/samtools/bamtk.c
1249 * samtools-0.1.8-3 (r627)
1250 * multi-sample snp calling appears to work. More tests needed.
1252 ------------------------------------------------------------------------
1253 r626 | lh3lh3 | 2010-07-22 16:37:56 -0400 (Thu, 22 Jul 2010) | 3 lines
1255 M /trunk/samtools/bam_mcns.c
1256 M /trunk/samtools/bam_mcns.h
1257 M /trunk/samtools/bam_plcmd.c
1258 M /trunk/samtools/bam_tview.c
1260 * preliminary multisample SNP caller.
1261 * something looks not so right, but it largely works
1263 ------------------------------------------------------------------------
1264 r617 | lh3lh3 | 2010-07-14 16:26:27 -0400 (Wed, 14 Jul 2010) | 3 lines
1266 M /trunk/samtools/bam_mcns.c
1267 M /trunk/samtools/bam_plcmd.c
1268 M /trunk/samtools/bamtk.c
1270 * samtools-0.1.8-2 (r617)
1271 * allele frequency calculation apparently works...
1273 ------------------------------------------------------------------------
1274 r616 | lh3lh3 | 2010-07-14 13:33:51 -0400 (Wed, 14 Jul 2010) | 3 lines
1276 M /trunk/samtools/Makefile
1277 A /trunk/samtools/bam_mcns.c
1278 A /trunk/samtools/bam_mcns.h
1279 M /trunk/samtools/bam_plcmd.c
1281 * added mutli-sample framework. It is not working, yet.
1282 * improved the mpileup interface
1284 ------------------------------------------------------------------------
1285 r615 | lh3lh3 | 2010-07-13 14:50:12 -0400 (Tue, 13 Jul 2010) | 3 lines
1287 M /trunk/samtools/bam_plcmd.c
1288 M /trunk/samtools/bamtk.c
1289 M /trunk/samtools/misc/Makefile
1291 * samtools-0.1.8-1 (r615)
1292 * allow to get mpileup at required sites
1294 ------------------------------------------------------------------------
1295 r613 | lh3lh3 | 2010-07-11 22:40:56 -0400 (Sun, 11 Jul 2010) | 2 lines
1297 M /trunk/samtools/ChangeLog
1298 M /trunk/samtools/NEWS
1299 M /trunk/samtools/bam_plcmd.c
1300 M /trunk/samtools/bamtk.c
1301 M /trunk/samtools/samtools.1
1303 Release samtools-0.1.8
1305 ------------------------------------------------------------------------
1306 r612 | lh3lh3 | 2010-07-11 21:08:56 -0400 (Sun, 11 Jul 2010) | 2 lines
1308 M /trunk/samtools/knetfile.c
1310 fixed a compiling issue for Windows
1312 ------------------------------------------------------------------------
1313 r611 | lh3lh3 | 2010-07-11 20:59:15 -0400 (Sun, 11 Jul 2010) | 2 lines
1315 M /trunk/samtools/bam_sort.c
1317 fixed a bug in sorting when output to stdout (by Peter Chines)
1319 ------------------------------------------------------------------------
1320 r610 | lh3lh3 | 2010-07-09 17:05:10 -0400 (Fri, 09 Jul 2010) | 2 lines
1322 M /trunk/samtools/NEWS
1323 M /trunk/samtools/bam_plcmd.c
1325 change the command line option of pileup
1327 ------------------------------------------------------------------------
1328 r609 | lh3lh3 | 2010-07-09 00:39:34 -0400 (Fri, 09 Jul 2010) | 2 lines
1330 M /trunk/samtools/bam_pileup.c
1331 A /trunk/samtools/examples/toy.fa
1332 A /trunk/samtools/examples/toy.sam
1334 make pileup work with CIGAR with I/D at the beginning or in the end
1336 ------------------------------------------------------------------------
1337 r608 | lh3lh3 | 2010-07-08 22:36:12 -0400 (Thu, 08 Jul 2010) | 3 lines
1339 M /trunk/samtools/bam_maqcns.c
1340 M /trunk/samtools/bam_maqcns.h
1341 M /trunk/samtools/bam_plcmd.c
1342 M /trunk/samtools/bam_tview.c
1344 * make tview more friendly
1345 * a temporary remedy for an issue in indel calling
1347 ------------------------------------------------------------------------
1348 r607 | lh3lh3 | 2010-07-08 14:43:52 -0400 (Thu, 08 Jul 2010) | 4 lines
1350 M /trunk/samtools/bam_maqcns.c
1351 M /trunk/samtools/bam_plcmd.c
1352 M /trunk/samtools/bamtk.c
1354 * samtools-0.1.7-r607
1355 * improved the genotype accuracy for indels
1356 * use the SOAPsnp model for SNP calling by default.
1358 ------------------------------------------------------------------------
1359 r606 | lh3lh3 | 2010-07-08 01:05:19 -0400 (Thu, 08 Jul 2010) | 2 lines
1361 M /trunk/samtools/misc/Makefile
1363 removed a debugging example
1365 ------------------------------------------------------------------------
1366 r605 | lh3lh3 | 2010-07-08 01:04:09 -0400 (Thu, 08 Jul 2010) | 4 lines
1368 M /trunk/samtools/bam_maqcns.c
1369 M /trunk/samtools/bamtk.c
1371 * samtools-.1.7-18 (r605)
1372 * fixed an issue when a deletion and mismatch occur at the same time
1373 and the base quality is higher than 40 (if -I40).
1375 ------------------------------------------------------------------------
1376 r604 | lh3lh3 | 2010-07-02 19:32:24 -0400 (Fri, 02 Jul 2010) | 2 lines
1378 M /trunk/samtools/bam.h
1379 M /trunk/samtools/bam_index.c
1380 M /trunk/samtools/misc/Makefile
1382 fixed a minor bug in idxstats
1384 ------------------------------------------------------------------------
1385 r601 | lh3lh3 | 2010-06-16 09:03:59 -0400 (Wed, 16 Jun 2010) | 2 lines
1387 M /trunk/samtools/bam_index.c
1389 fixed a minor bug in indexing
1391 ------------------------------------------------------------------------
1392 r600 | lh3lh3 | 2010-06-15 10:17:53 -0400 (Tue, 15 Jun 2010) | 2 lines
1394 M /trunk/samtools/ChangeLog
1395 M /trunk/samtools/bam.c
1397 change printf() to puts in exporting
1399 ------------------------------------------------------------------------
1400 r599 | lh3lh3 | 2010-06-13 21:41:11 -0400 (Sun, 13 Jun 2010) | 2 lines
1402 M /trunk/samtools/bamtk.c
1404 minor fix. No actual effect.
1406 ------------------------------------------------------------------------
1407 r598 | lh3lh3 | 2010-06-13 21:32:45 -0400 (Sun, 13 Jun 2010) | 2 lines
1409 M /trunk/samtools/Makefile
1411 added Makefile targets to compile shared/dynamic library
1413 ------------------------------------------------------------------------
1414 r596 | lh3lh3 | 2010-06-13 19:48:07 -0400 (Sun, 13 Jun 2010) | 3 lines
1416 M /trunk/samtools/ChangeLog
1417 M /trunk/samtools/bam_index.c
1418 M /trunk/samtools/bamtk.c
1420 * samtools-0.1.7-17 (r596)
1421 * also keep the number of coor-less reads in the index file
1423 ------------------------------------------------------------------------
1424 r595 | lh3lh3 | 2010-06-13 18:54:26 -0400 (Sun, 13 Jun 2010) | 3 lines
1426 M /trunk/samtools/bam_index.c
1427 M /trunk/samtools/bamtk.c
1429 * samtools-0.1.7-16 (r595)
1430 * write additional information to bam index
1432 ------------------------------------------------------------------------
1433 r594 | lh3lh3 | 2010-06-13 17:29:52 -0400 (Sun, 13 Jun 2010) | 2 lines
1435 M /trunk/samtools/bam_index.c
1437 fixed a bug for unmapped sequences in indexing
1439 ------------------------------------------------------------------------
1440 r593 | lh3lh3 | 2010-06-12 18:11:32 -0400 (Sat, 12 Jun 2010) | 2 lines
1442 M /trunk/samtools/bam.h
1443 M /trunk/samtools/bam_index.c
1444 M /trunk/samtools/bam_plcmd.c
1445 M /trunk/samtools/samtools.1
1447 rename iterf as iter
1449 ------------------------------------------------------------------------
1450 r592 | lh3lh3 | 2010-06-12 18:02:38 -0400 (Sat, 12 Jun 2010) | 4 lines
1452 M /trunk/samtools/ChangeLog
1453 M /trunk/samtools/bam_aux.c
1454 M /trunk/samtools/bam_index.c
1455 M /trunk/samtools/bam_pileup.c
1456 M /trunk/samtools/bam_plcmd.c
1457 M /trunk/samtools/bamtk.c
1459 * samtools-0.1.7-15 (r592)
1460 * fixed a few minor memory leaks in the new pileup code
1461 * improved the functionality of mpileup
1463 ------------------------------------------------------------------------
1464 r591 | lh3lh3 | 2010-06-12 14:09:22 -0400 (Sat, 12 Jun 2010) | 3 lines
1466 M /trunk/samtools/bam.h
1467 M /trunk/samtools/bam_pileup.c
1468 M /trunk/samtools/bam_plcmd.c
1469 M /trunk/samtools/bamtk.c
1471 * samtools-0.1.7-14 (r591)
1472 * elementary multi-way pileup. More testing and more functionality to be done.
1474 ------------------------------------------------------------------------
1475 r590 | lh3lh3 | 2010-06-12 01:00:24 -0400 (Sat, 12 Jun 2010) | 3 lines
1477 M /trunk/samtools/bam.h
1478 M /trunk/samtools/bam_pileup.c
1479 M /trunk/samtools/bamtk.c
1481 * samtools-0.1.7-13 (r590)
1482 * added mpileup APIs. No compiling errors, but not tested at all. It is late.
1484 ------------------------------------------------------------------------
1485 r589 | lh3lh3 | 2010-06-11 22:37:09 -0400 (Fri, 11 Jun 2010) | 3 lines
1487 M /trunk/samtools/bam.h
1488 M /trunk/samtools/bam_pileup.c
1489 M /trunk/samtools/bamtk.c
1491 * samtools-0.1.7-12 (r589)
1492 * added iterator-like APIs for pileup
1494 ------------------------------------------------------------------------
1495 r588 | lh3lh3 | 2010-06-11 17:41:13 -0400 (Fri, 11 Jun 2010) | 3 lines
1497 M /trunk/samtools/bam_index.c
1498 M /trunk/samtools/bamtk.c
1500 * samtools-0.1.7-11 (r588)
1501 * ported a few improvements from tabix back to samtools
1503 ------------------------------------------------------------------------
1504 r587 | lh3lh3 | 2010-06-11 17:33:16 -0400 (Fri, 11 Jun 2010) | 3 lines
1506 M /trunk/samtools/bam.h
1507 M /trunk/samtools/bam_index.c
1508 M /trunk/samtools/bamtk.c
1510 * samtools-0.1.7-10 (r587)
1511 * added iterator interface for bam_fetch (ported back from tabix)
1513 ------------------------------------------------------------------------
1514 r586 | lh3lh3 | 2010-06-11 13:23:53 -0400 (Fri, 11 Jun 2010) | 3 lines
1516 M /trunk/samtools/Makefile
1517 A /trunk/samtools/bam_reheader.c
1518 M /trunk/samtools/bamtk.c
1519 M /trunk/samtools/bgzf.c
1521 * samtools-0.1.7-9 (r586)
1522 * added "reheader" to replace the BAM header
1524 ------------------------------------------------------------------------
1525 r585 | lh3lh3 | 2010-06-11 12:22:06 -0400 (Fri, 11 Jun 2010) | 3 lines
1527 M /trunk/samtools/bam.c
1528 M /trunk/samtools/bamtk.c
1529 M /trunk/samtools/kstring.h
1531 * samtools-0.1.7-8 (r585)
1534 ------------------------------------------------------------------------
1535 r584 | lh3lh3 | 2010-06-11 12:00:41 -0400 (Fri, 11 Jun 2010) | 4 lines
1537 M /trunk/samtools/bam.c
1538 M /trunk/samtools/bamtk.c
1539 M /trunk/samtools/bgzf.c
1540 M /trunk/samtools/bgzf.h
1541 M /trunk/samtools/kstring.h
1542 M /trunk/samtools/misc/wgsim_eval.pl
1544 * samtools-0.1.7-7 (r584)
1545 * ported tabix BGZF to samtools
1546 * flush BGZF after writing the BAM header and between alignment boundaries
1548 ------------------------------------------------------------------------
1549 r583 | petulda | 2010-06-11 11:58:20 -0400 (Fri, 11 Jun 2010) | 1 line
1551 A /trunk/samtools/misc/varfilter.py
1553 Initial release on behalf of Aylwyn Scally
1554 ------------------------------------------------------------------------
1555 r561 | petulda | 2010-05-07 08:41:56 -0400 (Fri, 07 May 2010) | 1 line
1557 M /trunk/samtools/samtools.1
1559 Added a note about the indels coordinates
1560 ------------------------------------------------------------------------
1561 r551 | petulda | 2010-04-23 09:42:13 -0400 (Fri, 23 Apr 2010) | 1 line
1563 M /trunk/samtools/misc/sam2vcf.pl
1565 Added the possibility to print or not to print the reference allele
1566 ------------------------------------------------------------------------
1567 r546 | petulda | 2010-04-15 04:33:55 -0400 (Thu, 15 Apr 2010) | 1 line
1569 M /trunk/samtools/sam_header.c
1571 More descriptive message for space separated tags
1572 ------------------------------------------------------------------------
1573 r545 | petulda | 2010-04-14 11:44:50 -0400 (Wed, 14 Apr 2010) | 1 line
1575 M /trunk/samtools/misc/sam2vcf.pl
1577 Speedup with -i, no need to query the reference all the time
1578 ------------------------------------------------------------------------
1579 r541 | petulda | 2010-03-15 10:03:51 -0400 (Mon, 15 Mar 2010) | 1 line
1581 M /trunk/samtools/sam_header.c
1583 Fixed the order of sequences in the header
1584 ------------------------------------------------------------------------
1585 r540 | petulda | 2010-03-04 06:28:35 -0500 (Thu, 04 Mar 2010) | 1 line
1587 M /trunk/samtools/misc/sam2vcf.pl
1589 Added possibility to select indels only and fixed a bug in reporting homozygous indels.
1590 ------------------------------------------------------------------------
1591 r539 | jmarshall | 2010-02-27 06:48:17 -0500 (Sat, 27 Feb 2010) | 4 lines
1593 M /trunk/samtools/bam.c
1595 Improve the invalid 'BAM\1' magic number error message, and also print it
1596 when no bytes can be read from the alleged BAM file, e.g., in the common
1597 user error case when a SAM file has accidentally been supplied.
1599 ------------------------------------------------------------------------
1600 r538 | petulda | 2010-02-26 10:51:40 -0500 (Fri, 26 Feb 2010) | 1 line
1602 M /trunk/samtools/AUTHORS
1603 M /trunk/samtools/bam.h
1604 M /trunk/samtools/bam_import.c
1605 M /trunk/samtools/sam_header.c
1607 Improved efficiency of header parsing
1608 ------------------------------------------------------------------------
1609 r537 | lh3lh3 | 2010-02-23 21:08:48 -0500 (Tue, 23 Feb 2010) | 3 lines
1611 M /trunk/samtools/misc/export2sam.pl
1613 Updated export2sam.pl by Chris Saunders from Illumina.
1616 ------------------------------------------------------------------------
1617 r536 | petulda | 2010-02-17 08:32:53 -0500 (Wed, 17 Feb 2010) | 1 line
1619 M /trunk/samtools/misc/samtools.pl
1621 Fixed filtering of SNPs near indels. Added min indel and SNP quality filter.
1622 ------------------------------------------------------------------------
1623 r535 | petulda | 2010-02-12 04:52:37 -0500 (Fri, 12 Feb 2010) | 1 line
1625 M /trunk/samtools/misc/sam2vcf.pl
1627 Print an error for pileups in simple format
1628 ------------------------------------------------------------------------
1629 r534 | lh3lh3 | 2010-02-11 14:01:41 -0500 (Thu, 11 Feb 2010) | 2 lines
1631 M /trunk/samtools/bam_plcmd.c
1633 added a hidden option in pileup to output the base position (for Erin)
1635 ------------------------------------------------------------------------
1636 r533 | petulda | 2010-02-09 10:12:14 -0500 (Tue, 09 Feb 2010) | 1 line
1638 M /trunk/samtools/misc/sam2vcf.pl
1640 Added possibility to specify a custom column title for the data column
1641 ------------------------------------------------------------------------
1642 r532 | petulda | 2010-02-09 09:46:09 -0500 (Tue, 09 Feb 2010) | 1 line
1644 M /trunk/samtools/bam_plcmd.c
1646 Added the -d option to limit maximum depth for indels.
1647 ------------------------------------------------------------------------
1648 r531 | petulda | 2010-02-03 07:57:27 -0500 (Wed, 03 Feb 2010) | 1 line
1650 M /trunk/samtools/misc/sam2vcf.pl
1653 ------------------------------------------------------------------------
1654 r530 | lh3lh3 | 2010-02-01 09:13:19 -0500 (Mon, 01 Feb 2010) | 3 lines
1656 M /trunk/samtools/ChangeLog
1657 M /trunk/samtools/bam_plcmd.c
1658 M /trunk/samtools/bamtk.c
1659 M /trunk/samtools/misc/samtools.pl
1660 M /trunk/samtools/misc/wgsim.c
1663 * fixed a bug in faidx
1665 ------------------------------------------------------------------------
1666 r529 | jmarshall | 2010-01-11 18:51:49 -0500 (Mon, 11 Jan 2010) | 2 lines
1668 M /trunk/samtools/faidx.c
1670 Put the right filename in the error message.
1672 ------------------------------------------------------------------------
1673 r528 | lh3lh3 | 2009-12-14 11:26:47 -0500 (Mon, 14 Dec 2009) | 3 lines
1675 M /trunk/samtools/bam_plcmd.c
1676 M /trunk/samtools/bamtk.c
1678 * samtools-0.1.7-5 (r528)
1679 * further add new consensus generation strategy
1681 ------------------------------------------------------------------------
1682 r527 | petulda | 2009-12-11 12:31:05 -0500 (Fri, 11 Dec 2009) | 1 line
1684 M /trunk/samtools/knetfile.c
1686 Fixed a bug in knet_seek
1687 ------------------------------------------------------------------------
1688 r526 | petulda | 2009-12-11 07:51:18 -0500 (Fri, 11 Dec 2009) | 1 line
1690 M /trunk/samtools/misc/sam2vcf.pl
1692 Small fix in VCF format: dot for the empty INFO field
1693 ------------------------------------------------------------------------
1694 r525 | petulda | 2009-12-11 04:36:18 -0500 (Fri, 11 Dec 2009) | 1 line
1696 M /trunk/samtools/sam_header.c
1698 Allow tabs in the CO header field
1699 ------------------------------------------------------------------------
1700 r524 | jmarshall | 2009-12-10 10:03:58 -0500 (Thu, 10 Dec 2009) | 3 lines
1702 M /trunk/samtools/Makefile
1703 M /trunk/samtools/Makefile.mingw
1705 Depend on libbam.a rather than the phony target, so that samtools is not
1706 unnecessarily rebuilt every time. Also clean bgzip.
1708 ------------------------------------------------------------------------
1709 r523 | jmarshall | 2009-12-10 09:45:32 -0500 (Thu, 10 Dec 2009) | 4 lines
1711 M /trunk/samtools/Makefile
1712 M /trunk/samtools/Makefile.mingw
1714 Fix a bug in compiling bgzip: this also needs knetfile.o when _USE_KNETFILE
1715 is defined. Also introduce $(KNETFILE_O) which can be set to empty to
1716 facilitate non-knet builds.
1718 ------------------------------------------------------------------------
1719 r522 | lh3lh3 | 2009-12-01 13:02:36 -0500 (Tue, 01 Dec 2009) | 4 lines
1721 M /trunk/samtools/bamtk.c
1722 M /trunk/samtools/sam_view.c
1724 * samtools-0.1.7-4 (r522)
1725 * fixed a bug in "view -r"
1726 * added a new option "view -R" to read required read groups from a file
1728 ------------------------------------------------------------------------
1729 r521 | lh3lh3 | 2009-12-01 10:00:12 -0500 (Tue, 01 Dec 2009) | 3 lines
1731 M /trunk/samtools/bam_md.c
1732 M /trunk/samtools/bamtk.c
1734 * samtools-0.1.7-3 (r521)
1735 * calmd: optionally mask matching bases as N
1737 ------------------------------------------------------------------------
1738 r520 | lh3lh3 | 2009-12-01 09:37:17 -0500 (Tue, 01 Dec 2009) | 4 lines
1740 M /trunk/samtools/bam_plcmd.c
1741 M /trunk/samtools/bamtk.c
1742 M /trunk/samtools/misc/samtools.pl
1744 * samtools-0.1.7-2 (r520)
1745 * fixed a few issues with compilation in Windows (on behalf of John)
1746 * choose a random base as the consensus (for population genetics studies)
1748 ------------------------------------------------------------------------
1749 r519 | jmarshall | 2009-11-30 10:53:02 -0500 (Mon, 30 Nov 2009) | 6 lines
1751 M /trunk/samtools/Makefile
1753 Put libraries at the end, so they can resolve references from libbam.a
1754 as well, even with old-fashioned linkers.
1756 Also use libbam.a explicitly rather than "-L. -lbam" to ensure that we get
1757 the freshly built library, not some other libbam.a lying around the system.
1759 ------------------------------------------------------------------------
1760 r518 | jmarshall | 2009-11-30 08:44:56 -0500 (Mon, 30 Nov 2009) | 2 lines
1762 M /trunk/samtools/Makefile
1763 M /trunk/samtools/misc/Makefile
1765 Also clean *.exe (for Cygwin users using this makefile).
1767 ------------------------------------------------------------------------
1768 r517 | jmarshall | 2009-11-30 07:09:04 -0500 (Mon, 30 Nov 2009) | 2 lines
1770 M /trunk/samtools/bam_index.c
1772 Index files should be opened in binary mode, not text mode.
1774 ------------------------------------------------------------------------
1775 r516 | lh3lh3 | 2009-11-27 15:18:59 -0500 (Fri, 27 Nov 2009) | 2 lines
1777 A /trunk/samtools/examples/bam2bed.c
1779 another example program
1781 ------------------------------------------------------------------------
1782 r515 | lh3lh3 | 2009-11-27 10:44:56 -0500 (Fri, 27 Nov 2009) | 3 lines
1784 M /trunk/samtools/bam_import.c
1785 M /trunk/samtools/bamtk.c
1786 M /trunk/samtools/misc/wgsim_eval.pl
1787 M /trunk/samtools/sam.c
1789 * samtools-0.1.7-1 (r515)
1790 * report an error when .fai contains duplicated names, instead of segfault
1792 ------------------------------------------------------------------------
1793 r514 | jmarshall | 2009-11-24 09:45:35 -0500 (Tue, 24 Nov 2009) | 2 lines
1795 M /trunk/samtools/bam.c
1797 Format 'c'-encoded auxiliary fields correctly, as *signed* integers.
1799 ------------------------------------------------------------------------
1800 r513 | lh3lh3 | 2009-11-16 10:13:07 -0500 (Mon, 16 Nov 2009) | 2 lines
1802 M /trunk/samtools/Makefile.mingw
1804 Update Makefile.mingw for the same reason
1806 ------------------------------------------------------------------------
1807 r512 | lh3lh3 | 2009-11-16 10:00:08 -0500 (Mon, 16 Nov 2009) | 2 lines
1809 M /trunk/samtools/Makefile
1811 Fixed a bug in compiling razip
1813 ------------------------------------------------------------------------
1814 r510 | lh3lh3 | 2009-11-10 10:55:41 -0500 (Tue, 10 Nov 2009) | 2 lines
1816 M /trunk/samtools/ChangeLog
1817 M /trunk/samtools/NEWS
1818 M /trunk/samtools/bamtk.c
1819 M /trunk/samtools/samtools.1
1821 Release samtools-0.1.7 (r510)
1823 ------------------------------------------------------------------------
1824 r509 | lh3lh3 | 2009-11-06 09:17:09 -0500 (Fri, 06 Nov 2009) | 3 lines
1826 M /trunk/samtools/bam_plcmd.c
1827 M /trunk/samtools/bamtk.c
1829 * samtools-0.1.6-22 (r509)
1830 * forget to fix a similar problem in glfgen
1832 ------------------------------------------------------------------------
1833 r508 | lh3lh3 | 2009-11-06 09:06:40 -0500 (Fri, 06 Nov 2009) | 3 lines
1835 M /trunk/samtools/bam_maqcns.c
1836 M /trunk/samtools/bam_plcmd.c
1837 M /trunk/samtools/bamtk.c
1838 M /trunk/samtools/sam_view.c
1840 * samtools-0.1.6-21 (r508)
1841 * fixed a potential bug in the indel caller towards the end of a chromosome
1843 ------------------------------------------------------------------------
1844 r494 | lh3lh3 | 2009-10-26 11:38:00 -0400 (Mon, 26 Oct 2009) | 3 lines
1846 M /trunk/samtools/bamtk.c
1847 M /trunk/samtools/sam_view.c
1849 * samtools-0.1.6-19 (r494)
1850 * allow to convert Illumina quality (64 based) to the BAM quality
1852 ------------------------------------------------------------------------
1853 r493 | lh3lh3 | 2009-10-26 10:24:39 -0400 (Mon, 26 Oct 2009) | 4 lines
1855 M /trunk/samtools/Makefile
1856 M /trunk/samtools/bam.c
1857 M /trunk/samtools/bam_import.c
1858 M /trunk/samtools/bamtk.c
1859 M /trunk/samtools/sam.c
1860 M /trunk/samtools/sam_header.c
1862 * samtools-0.1.6-18 (r493)
1863 * fixed the bugs due to improperly incorporating Petr's header parser
1864 * a little code clean up in sam_header.c
1866 ------------------------------------------------------------------------
1867 r492 | petulda | 2009-10-24 09:43:25 -0400 (Sat, 24 Oct 2009) | 1 line
1869 M /trunk/samtools/sam_header.c
1871 Added sam_header_line_free call for sam_header_parse2
1872 ------------------------------------------------------------------------
1873 r491 | lh3lh3 | 2009-10-24 00:50:16 -0400 (Sat, 24 Oct 2009) | 3 lines
1875 M /trunk/samtools/sam_view.c
1880 ------------------------------------------------------------------------
1881 r490 | lh3lh3 | 2009-10-24 00:45:12 -0400 (Sat, 24 Oct 2009) | 4 lines
1883 M /trunk/samtools/bam.c
1884 M /trunk/samtools/bam.h
1885 M /trunk/samtools/bam_import.c
1886 M /trunk/samtools/sam.c
1889 * improved the interface a bit
1892 ------------------------------------------------------------------------
1893 r489 | lh3lh3 | 2009-10-24 00:41:50 -0400 (Sat, 24 Oct 2009) | 3 lines
1895 M /trunk/samtools/bam_import.c
1896 M /trunk/samtools/sam_header.c
1897 M /trunk/samtools/sam_header.h
1899 * BUGGY VERSION. Please NOT use it.
1900 * Fixed a minor bug, but the major bug is still there.
1902 ------------------------------------------------------------------------
1903 r488 | lh3lh3 | 2009-10-24 00:17:10 -0400 (Sat, 24 Oct 2009) | 3 lines
1905 M /trunk/samtools/Makefile
1906 M /trunk/samtools/bam.c
1907 M /trunk/samtools/bam.h
1908 M /trunk/samtools/bam_aux.c
1909 M /trunk/samtools/bam_import.c
1910 M /trunk/samtools/bam_rmdup.c
1911 M /trunk/samtools/bam_rmdupse.c
1912 M /trunk/samtools/kaln.c
1913 M /trunk/samtools/sam.c
1914 M /trunk/samtools/sam_header.c
1915 M /trunk/samtools/sam_header.h
1916 M /trunk/samtools/sam_view.c
1918 * This revision is SERIOUSLY BUGGY. Please NOT use it.
1919 * Start to incorporate header parsing from Petr Danecek
1921 ------------------------------------------------------------------------
1922 r487 | petulda | 2009-10-23 11:44:32 -0400 (Fri, 23 Oct 2009) | 1 line
1924 M /trunk/samtools/sam_header.c
1925 M /trunk/samtools/sam_header.h
1927 Now possible to merge multiple HeaderDict dictionaries
1928 ------------------------------------------------------------------------
1929 r486 | petulda | 2009-10-22 11:46:58 -0400 (Thu, 22 Oct 2009) | 1 line
1931 M /trunk/samtools/sam_header.c
1934 ------------------------------------------------------------------------
1935 r485 | petulda | 2009-10-22 11:41:56 -0400 (Thu, 22 Oct 2009) | 1 line
1937 A /trunk/samtools/sam_header.c
1938 A /trunk/samtools/sam_header.h
1941 ------------------------------------------------------------------------
1942 r484 | lh3lh3 | 2009-10-19 14:31:32 -0400 (Mon, 19 Oct 2009) | 5 lines
1944 M /trunk/samtools/bam_import.c
1945 M /trunk/samtools/bam_rmdupse.c
1946 M /trunk/samtools/bamtk.c
1947 M /trunk/samtools/examples/Makefile
1949 * samtools-0.1.6-17 (r484)
1950 * fixed a memory leak in rmdupse
1951 * fixed a bug in parsing @RG header lines
1952 * test rmdup in examples/
1954 ------------------------------------------------------------------------
1955 r483 | lh3lh3 | 2009-10-19 13:22:48 -0400 (Mon, 19 Oct 2009) | 4 lines
1957 M /trunk/samtools/bam_rmdup.c
1958 M /trunk/samtools/bam_rmdupse.c
1959 M /trunk/samtools/bamtk.c
1961 * samtools-0.1.6-16 (r483)
1962 * unify the interface of rmdup and rmdupse
1963 * a new bug found in rg2lib(). Have not been fixed yet.
1965 ------------------------------------------------------------------------
1966 r482 | lh3lh3 | 2009-10-19 13:03:34 -0400 (Mon, 19 Oct 2009) | 4 lines
1968 M /trunk/samtools/bam.h
1969 M /trunk/samtools/bam_rmdup.c
1970 M /trunk/samtools/bam_rmdupse.c
1971 M /trunk/samtools/bamtk.c
1972 A /trunk/samtools/klist.h
1974 * samtools-0.1.6-15 (r482)
1976 * rmdupse is now library aware
1978 ------------------------------------------------------------------------
1979 r481 | lh3lh3 | 2009-10-18 00:07:21 -0400 (Sun, 18 Oct 2009) | 3 lines
1981 M /trunk/samtools/bam_rmdup.c
1982 M /trunk/samtools/bamtk.c
1984 * samtools-0.1.6-14 (r480)
1985 * rmdup is now RG aware
1987 ------------------------------------------------------------------------
1988 r480 | lh3lh3 | 2009-10-17 22:05:20 -0400 (Sat, 17 Oct 2009) | 2 lines
1990 M /trunk/samtools/misc/samtools.pl
1992 added a small unitity to parse SRA XML files
1994 ------------------------------------------------------------------------
1995 r479 | lh3lh3 | 2009-10-17 20:57:26 -0400 (Sat, 17 Oct 2009) | 3 lines
1997 M /trunk/samtools/bam_maqcns.c
1998 M /trunk/samtools/bam_maqcns.h
1999 M /trunk/samtools/bam_plcmd.c
2000 M /trunk/samtools/bam_sort.c
2001 M /trunk/samtools/bamtk.c
2003 * samtools-0.1.6-13 (r479)
2004 * merge: optionally use file names as RG tags
2006 ------------------------------------------------------------------------
2007 r478 | lh3lh3 | 2009-10-14 14:18:12 -0400 (Wed, 14 Oct 2009) | 3 lines
2009 M /trunk/samtools/bam.c
2010 M /trunk/samtools/bam.h
2011 M /trunk/samtools/bam_maqcns.c
2012 M /trunk/samtools/bamtk.c
2013 M /trunk/samtools/kaln.c
2015 * samtools-0.1.6-12 (r478)
2016 * fixed a bug in the indel caller
2018 ------------------------------------------------------------------------
2019 r477 | lh3lh3 | 2009-10-10 06:12:26 -0400 (Sat, 10 Oct 2009) | 3 lines
2021 M /trunk/samtools/bam_index.c
2022 M /trunk/samtools/bamtk.c
2024 * samtools-0.1.6-11 (r477)
2025 * fixed a bug due to recent change in bam_index.c (thank Nicole Washington for the patch)
2027 ------------------------------------------------------------------------
2028 r476 | petulda | 2009-10-09 11:45:36 -0400 (Fri, 09 Oct 2009) | 1 line
2030 A /trunk/samtools/misc/sam2vcf.pl
2032 Added the sam2vcf.pl script.
2033 ------------------------------------------------------------------------
2034 r475 | lh3lh3 | 2009-10-08 10:19:16 -0400 (Thu, 08 Oct 2009) | 2 lines
2036 M /trunk/samtools/Makefile
2037 M /trunk/samtools/bam.c
2038 M /trunk/samtools/bam.h
2039 M /trunk/samtools/bam_maqcns.c
2040 M /trunk/samtools/bamtk.c
2041 A /trunk/samtools/kaln.c
2042 A /trunk/samtools/kaln.h
2044 Unfinished modification. Please do not use this revision...
2046 ------------------------------------------------------------------------
2047 r474 | petulda | 2009-10-08 06:39:54 -0400 (Thu, 08 Oct 2009) | 1 line
2049 M /trunk/samtools/knetfile.c
2051 Removed the offending knet_seek message.
2052 ------------------------------------------------------------------------
2053 r473 | petulda | 2009-10-06 09:26:35 -0400 (Tue, 06 Oct 2009) | 1 line
2055 M /trunk/samtools/knetfile.c
2056 M /trunk/samtools/razf.c
2058 Bug fix - faidx on RAZF compressed files now working.
2059 ------------------------------------------------------------------------
2060 r472 | lh3lh3 | 2009-10-02 08:42:57 -0400 (Fri, 02 Oct 2009) | 2 lines
2062 M /trunk/samtools/samtools.1
2064 Clarify the meaning of a region like "chr2:1,000,000".
2066 ------------------------------------------------------------------------
2067 r471 | lh3lh3 | 2009-10-02 05:42:19 -0400 (Fri, 02 Oct 2009) | 2 lines
2069 M /trunk/samtools/misc/novo2sam.pl
2071 Fixed minor bugs in novo2sam.pl (on behalf of Ken Chen and Colin Hercus)
2073 ------------------------------------------------------------------------
2074 r470 | lh3lh3 | 2009-09-29 15:01:27 -0400 (Tue, 29 Sep 2009) | 3 lines
2076 M /trunk/samtools/Makefile.mingw
2077 M /trunk/samtools/bamtk.c
2078 M /trunk/samtools/knetfile.c
2079 M /trunk/samtools/knetfile.h
2081 * samtools-0.1.6-9 (r470)
2082 * make knetfile.c compatible with MinGW (thank Martin Morgan for the patch)
2084 ------------------------------------------------------------------------
2085 r469 | lh3lh3 | 2009-09-29 08:07:44 -0400 (Tue, 29 Sep 2009) | 3 lines
2087 M /trunk/samtools/bam_index.c
2088 M /trunk/samtools/bamtk.c
2090 * samtools-0.1.6-9 (r469)
2091 * refactor bam_fetch() for Python binding. On behalf of Leo Goodstadt.
2093 ------------------------------------------------------------------------
2094 r468 | lh3lh3 | 2009-09-28 05:18:29 -0400 (Mon, 28 Sep 2009) | 3 lines
2096 M /trunk/samtools/bam_sort.c
2097 M /trunk/samtools/bamtk.c
2098 M /trunk/samtools/misc/samtools.pl
2100 * samtools-0.1.6-7 (r468)
2103 ------------------------------------------------------------------------
2104 r467 | petulda | 2009-09-28 04:51:29 -0400 (Mon, 28 Sep 2009) | 1 line
2106 M /trunk/samtools/bgzf.c
2107 M /trunk/samtools/bgzip.c
2108 M /trunk/samtools/razf.c
2109 M /trunk/samtools/razip.c
2111 Changed the mode for newly created files to 0666. This allows less strict permissions with umask properly set (e.g. 0002 vs. 0022).
2112 ------------------------------------------------------------------------
2113 r466 | lh3lh3 | 2009-09-24 06:29:19 -0400 (Thu, 24 Sep 2009) | 3 lines
2115 M /trunk/samtools/ChangeLog
2116 M /trunk/samtools/bam_md.c
2117 M /trunk/samtools/bamtk.c
2119 * samtools-0.1.6-6 (r466)
2120 * do not crash calmd when some sequences are absent from the reference.
2122 ------------------------------------------------------------------------
2123 r464 | jmarshall | 2009-09-23 06:14:32 -0400 (Wed, 23 Sep 2009) | 3 lines
2125 M /trunk/samtools/bam.c
2126 M /trunk/samtools/knetfile.c
2128 Suppress bgzf_check_EOF() messages when reading from a pipe, as there is
2129 no way to seek on a pipe and the messages always appear.
2131 ------------------------------------------------------------------------
2132 r463 | petulda | 2009-09-16 07:05:41 -0400 (Wed, 16 Sep 2009) | 1 line
2134 M /trunk/samtools/knetfile.c
2135 M /trunk/samtools/razf.c
2137 A bug fix, "samtools view" is now working again.
2138 ------------------------------------------------------------------------
2139 r462 | lh3lh3 | 2009-09-16 04:51:07 -0400 (Wed, 16 Sep 2009) | 3 lines
2141 M /trunk/samtools/bamtk.c
2142 M /trunk/samtools/faidx.c
2143 M /trunk/samtools/knetfile.c
2144 M /trunk/samtools/knetfile.h
2145 M /trunk/samtools/razf.c
2146 M /trunk/samtools/razf.h
2148 * samtools-0.1.6-5 (r462)
2149 * Added knetfile support in razf and faidx (on behalf of Petr Danecek)
2151 ------------------------------------------------------------------------
2152 r460 | lh3lh3 | 2009-09-09 07:06:22 -0400 (Wed, 09 Sep 2009) | 2 lines
2154 M /trunk/samtools/samtools.1
2156 fixed a formatting issue
2158 ------------------------------------------------------------------------
2159 r459 | lh3lh3 | 2009-09-08 18:14:08 -0400 (Tue, 08 Sep 2009) | 3 lines
2161 M /trunk/samtools/bam_sort.c
2162 M /trunk/samtools/bamtk.c
2164 * samtools-0.1.6-4 (r459)
2165 * make sort output the result to stdout when -o is in use
2167 ------------------------------------------------------------------------
2168 r458 | lh3lh3 | 2009-09-07 05:10:28 -0400 (Mon, 07 Sep 2009) | 4 lines
2170 M /trunk/samtools/bamtk.c
2171 M /trunk/samtools/faidx.c
2172 M /trunk/samtools/faidx.h
2173 M /trunk/samtools/samtools.1
2175 * samtools-0.1.6-2 (r458)
2176 * added more interface to faidx (by Nils)
2177 * updated documentation
2179 ------------------------------------------------------------------------
2180 r457 | lh3lh3 | 2009-09-05 16:12:04 -0400 (Sat, 05 Sep 2009) | 3 lines
2182 M /trunk/samtools/bam_sort.c
2183 M /trunk/samtools/bamtk.c
2185 * samtools-0.1.6-2 (r457)
2186 * get rid of three assert() in bam_sort.c
2188 ------------------------------------------------------------------------
2189 r456 | jmarshall | 2009-09-04 12:46:25 -0400 (Fri, 04 Sep 2009) | 3 lines
2191 M /trunk/samtools/razf.c
2193 Return NULL from _razf_open() (and hence razf_open()/razf_open2())
2194 when opening the file fails.
2196 ------------------------------------------------------------------------
2197 r453 | lh3lh3 | 2009-09-02 08:56:33 -0400 (Wed, 02 Sep 2009) | 2 lines
2199 M /trunk/samtools/ChangeLog
2200 M /trunk/samtools/NEWS
2201 M /trunk/samtools/bamtk.c
2202 M /trunk/samtools/samtools.1
2203 D /trunk/samtools/source.dot
2205 Release samtools-0.1.6
2207 ------------------------------------------------------------------------
2208 r451 | lh3lh3 | 2009-09-02 05:44:48 -0400 (Wed, 02 Sep 2009) | 4 lines
2210 M /trunk/samtools/bam_md.c
2211 M /trunk/samtools/bam_rmdup.c
2212 M /trunk/samtools/bam_rmdupse.c
2213 M /trunk/samtools/bam_sort.c
2214 M /trunk/samtools/bamtk.c
2215 M /trunk/samtools/samtools.1
2217 * samtools-0.1.5-34 (r451)
2218 * applied the patch by John
2219 * improved the help message a little bit
2221 ------------------------------------------------------------------------
2222 r450 | lh3lh3 | 2009-09-02 04:55:55 -0400 (Wed, 02 Sep 2009) | 3 lines
2224 M /trunk/samtools/bam_color.c
2225 M /trunk/samtools/bamtk.c
2227 * samtools-0.1.5-33 (r450)
2228 * fixed a bug in bam_color.c (on behalf of Nils Homer)
2230 ------------------------------------------------------------------------
2231 r449 | lh3lh3 | 2009-08-29 15:36:41 -0400 (Sat, 29 Aug 2009) | 4 lines
2233 M /trunk/samtools/bam_import.c
2234 M /trunk/samtools/bam_md.c
2235 M /trunk/samtools/bamtk.c
2236 M /trunk/samtools/misc/samtools.pl
2238 * samtools-0.1.5-32 (r449)
2239 * fillmd: fixed a bug in modifying MD/NM tags
2240 * in import, give a warning if the read is aligned but there is no CIGAR.
2242 ------------------------------------------------------------------------
2243 r448 | lh3lh3 | 2009-08-19 04:44:28 -0400 (Wed, 19 Aug 2009) | 3 lines
2245 M /trunk/samtools/ChangeLog
2246 M /trunk/samtools/bam_pileup.c
2247 M /trunk/samtools/bamtk.c
2248 M /trunk/samtools/misc/wgsim_eval.pl
2250 * samtools-0.1.5-31 (r448)
2251 * fixed an issue when the last CIGAR is I or D
2253 ------------------------------------------------------------------------
2254 r447 | lh3lh3 | 2009-08-17 04:34:57 -0400 (Mon, 17 Aug 2009) | 3 lines
2256 M /trunk/samtools/bam_aux.c
2257 M /trunk/samtools/bamtk.c
2259 * samtools-0.1.5-30 (r447)
2260 * fixed a bug in bam_aux_get(): 'A' is not checked
2262 ------------------------------------------------------------------------
2263 r446 | lh3lh3 | 2009-08-17 04:33:17 -0400 (Mon, 17 Aug 2009) | 2 lines
2265 M /trunk/samtools/bam_aux.c
2266 M /trunk/samtools/bamtk.c
2270 ------------------------------------------------------------------------
2271 r444 | lh3lh3 | 2009-08-11 05:02:36 -0400 (Tue, 11 Aug 2009) | 3 lines
2273 M /trunk/samtools/bam_sort.c
2274 M /trunk/samtools/bamtk.c
2276 * samtools-0.1.5-28 (r444)
2279 ------------------------------------------------------------------------
2280 r443 | lh3lh3 | 2009-08-11 04:29:11 -0400 (Tue, 11 Aug 2009) | 4 lines
2282 M /trunk/samtools/bam.c
2283 M /trunk/samtools/bam_import.c
2284 M /trunk/samtools/bamtk.c
2286 * samtools-0.1.5-27 (r443)
2287 * SEQ and QUAL can be "*"
2288 * parse CIGAR "=" and "X" as "M"
2290 ------------------------------------------------------------------------
2291 r442 | lh3lh3 | 2009-08-07 16:56:38 -0400 (Fri, 07 Aug 2009) | 4 lines
2293 M /trunk/samtools/bam_pileup.c
2294 M /trunk/samtools/bamtk.c
2295 M /trunk/samtools/misc/md5.c
2296 M /trunk/samtools/misc/md5.h
2297 M /trunk/samtools/misc/md5fa.c
2299 * samtools-0.1.5-26 (r442)
2300 * replace RSA Inc md5.* with ones under permissive lincense
2301 * fixed a bug in detecting unsorted bam in pileup
2303 ------------------------------------------------------------------------
2304 r441 | bhandsaker | 2009-08-05 09:41:28 -0400 (Wed, 05 Aug 2009) | 2 lines
2306 M /trunk/samtools/bgzf.c
2307 M /trunk/samtools/bgzf.h
2308 M /trunk/samtools/bgzip.c
2310 Change copyright notices now that MIT has approved open source distribution.
2312 ------------------------------------------------------------------------
2313 r440 | lh3lh3 | 2009-08-05 05:44:24 -0400 (Wed, 05 Aug 2009) | 3 lines
2315 M /trunk/samtools/bam_stat.c
2316 M /trunk/samtools/bamtk.c
2318 * samtools-0.1.5-25 (r436)
2319 * in flagstats, do not report singletons if both ends are unmapped
2321 ------------------------------------------------------------------------
2322 r439 | lh3lh3 | 2009-08-04 17:16:51 -0400 (Tue, 04 Aug 2009) | 2 lines
2324 M /trunk/samtools/misc/maq2sam.c
2326 fixed a SERIOUS bug in setting 0x20 flag
2328 ------------------------------------------------------------------------
2329 r438 | lh3lh3 | 2009-08-04 16:50:43 -0400 (Tue, 04 Aug 2009) | 2 lines
2331 M /trunk/samtools/misc/samtools.pl
2333 fixed two minor bugs (suggested by Tim M Storm)
2335 ------------------------------------------------------------------------
2336 r437 | lh3lh3 | 2009-08-04 04:13:24 -0400 (Tue, 04 Aug 2009) | 3 lines
2338 M /trunk/samtools/bamtk.c
2339 M /trunk/samtools/misc/samtools.pl
2340 M /trunk/samtools/sam_view.c
2342 * samtools-0.1.5-24 (r435)
2345 ------------------------------------------------------------------------
2346 r434 | lh3lh3 | 2009-08-03 05:40:42 -0400 (Mon, 03 Aug 2009) | 3 lines
2348 M /trunk/samtools/bam_tview.c
2349 M /trunk/samtools/bamtk.c
2351 * samtools-0.1.5-23 (r434)
2352 * in tview, press 'r' to show read names rather than sequences
2354 ------------------------------------------------------------------------
2355 r433 | lh3lh3 | 2009-08-02 14:13:35 -0400 (Sun, 02 Aug 2009) | 3 lines
2357 M /trunk/samtools/knetfile.c
2359 * tried to fixed the buggy FTP random access in Windows. FAILED.
2360 * anyway, MinGW seems to have problem with "%lld".
2362 ------------------------------------------------------------------------
2363 r432 | lh3lh3 | 2009-08-01 19:32:07 -0400 (Sat, 01 Aug 2009) | 5 lines
2365 M /trunk/samtools/Makefile.mingw
2366 M /trunk/samtools/bamtk.c
2367 M /trunk/samtools/faidx.c
2368 M /trunk/samtools/razf.c
2369 A /trunk/samtools/win32/libcurses.a
2370 A /trunk/samtools/win32/xcurses.h
2372 * samtools-0.1.5-22 (r432)
2373 * faidx: fixed compitability issue with _WIN32
2374 * razf: fixed potential compitability issue with _WIN32
2375 * PDCurses support in Windows
2377 ------------------------------------------------------------------------
2378 r431 | lh3lh3 | 2009-08-01 18:34:54 -0400 (Sat, 01 Aug 2009) | 2 lines
2380 M /trunk/samtools/win32/libz.a
2382 replace the GnuWin32 version of libz.a with my own build with MinGW.
2384 ------------------------------------------------------------------------
2385 r430 | lh3lh3 | 2009-08-01 18:21:07 -0400 (Sat, 01 Aug 2009) | 2 lines
2387 M /trunk/samtools/knetfile.c
2391 ------------------------------------------------------------------------
2392 r429 | lh3lh3 | 2009-08-01 17:41:19 -0400 (Sat, 01 Aug 2009) | 3 lines
2394 M /trunk/samtools/Makefile.mingw
2395 M /trunk/samtools/bamtk.c
2396 M /trunk/samtools/knetfile.c
2397 M /trunk/samtools/knetfile.h
2399 * samtools-0.1.5-21 (r428)
2400 * knetfile.c is now compatible with mingw-winsock
2402 ------------------------------------------------------------------------
2403 r428 | lh3lh3 | 2009-07-31 19:39:07 -0400 (Fri, 31 Jul 2009) | 2 lines
2405 M /trunk/samtools/Makefile.mingw
2407 simplify MinGW Makefile
2409 ------------------------------------------------------------------------
2410 r427 | lh3lh3 | 2009-07-31 19:30:54 -0400 (Fri, 31 Jul 2009) | 5 lines
2412 A /trunk/samtools/Makefile.mingw
2413 M /trunk/samtools/bam_import.c
2414 M /trunk/samtools/bamtk.c
2415 A /trunk/samtools/win32
2416 A /trunk/samtools/win32/libz.a
2417 A /trunk/samtools/win32/zconf.h
2418 A /trunk/samtools/win32/zlib.h
2420 * samtools-0.1.5-20 (r427)
2421 * MinGW support. At least SAM<->BAM conversion is working. Other
2422 functionality are not tested at the moment.
2423 * zlib headers and Windows version of libz.a are included in win32/
2425 ------------------------------------------------------------------------
2426 r426 | lh3lh3 | 2009-07-31 18:32:09 -0400 (Fri, 31 Jul 2009) | 3 lines
2428 M /trunk/samtools/bamtk.c
2429 M /trunk/samtools/sam_view.c
2431 * samtools-0.1.5-19 (r426)
2432 * fixed a bug caused by recent modifications. Sorry.
2434 ------------------------------------------------------------------------
2435 r425 | lh3lh3 | 2009-07-31 18:23:51 -0400 (Fri, 31 Jul 2009) | 2 lines
2437 M /trunk/samtools/bgzf.c
2439 compatible with Windows binary files
2441 ------------------------------------------------------------------------
2442 r424 | lh3lh3 | 2009-07-31 05:19:59 -0400 (Fri, 31 Jul 2009) | 5 lines
2444 M /trunk/samtools/bam_maqcns.c
2445 M /trunk/samtools/bam_maqcns.h
2446 M /trunk/samtools/bam_plcmd.c
2447 M /trunk/samtools/bam_tview.c
2448 M /trunk/samtools/bamtk.c
2449 M /trunk/samtools/misc/samtools.pl
2451 * samtools-0.1.5-18 (r423)
2452 * output additional information in pileup indel lines, for the purepose
2453 of debugging at the moment
2454 * in tview, optionally allow to treat reference skip as deletion
2456 ------------------------------------------------------------------------
2457 r423 | lh3lh3 | 2009-07-30 17:00:36 -0400 (Thu, 30 Jul 2009) | 2 lines
2459 A /trunk/samtools/misc/psl2sam.pl
2461 convert BLAT psl to SAM.
2463 ------------------------------------------------------------------------
2464 r422 | lh3lh3 | 2009-07-30 06:24:39 -0400 (Thu, 30 Jul 2009) | 6 lines
2466 M /trunk/samtools/ChangeLog
2467 M /trunk/samtools/bam.c
2468 M /trunk/samtools/bamtk.c
2469 M /trunk/samtools/bgzf.c
2470 M /trunk/samtools/bgzf.h
2471 M /trunk/samtools/knetfile.c
2472 M /trunk/samtools/sam.c
2473 M /trunk/samtools/sam_view.c
2475 * samtools-0.1.5-17 (r422)
2476 * fixed a but in knetfile.c when seek type is not SEEK_SET
2477 * write an empty BGZF block to every BGZF file
2478 * check BGZF EOF marker in bam_header_read()
2481 ------------------------------------------------------------------------
2482 r421 | lh3lh3 | 2009-07-30 05:03:39 -0400 (Thu, 30 Jul 2009) | 3 lines
2484 M /trunk/samtools/bam_import.c
2485 M /trunk/samtools/bam_plcmd.c
2486 M /trunk/samtools/bamtk.c
2487 M /trunk/samtools/misc/samtools.pl
2488 M /trunk/samtools/sam.c
2489 M /trunk/samtools/sam.h
2490 M /trunk/samtools/sam_view.c
2492 * samtools-0.1.5-16 (r421)
2493 * in view and pileup, load header from FASTA index if the input is SAM.
2495 ------------------------------------------------------------------------
2496 r420 | lh3lh3 | 2009-07-29 04:18:55 -0400 (Wed, 29 Jul 2009) | 2 lines
2498 M /trunk/samtools/misc/maq2sam.c
2500 do not set "read 1" if reads are not mapped in the PE mode of maq
2502 ------------------------------------------------------------------------
2503 r419 | lh3lh3 | 2009-07-28 04:52:33 -0400 (Tue, 28 Jul 2009) | 5 lines
2505 M /trunk/samtools/bam_import.c
2506 M /trunk/samtools/bamtk.c
2507 M /trunk/samtools/misc/samtools.pl
2508 M /trunk/samtools/misc/wgsim_eval.pl
2510 * samtools-0.1.5-15 (r419)
2511 * in sam_open(), return NULL when the file cannot be opened.
2512 * make wgsim_eval.pl more robust to imperfect SAM
2513 * add "unique" command to samtools.pl
2515 ------------------------------------------------------------------------
2516 r418 | lh3lh3 | 2009-07-24 09:04:19 -0400 (Fri, 24 Jul 2009) | 2 lines
2518 M /trunk/samtools/misc/wgsim_eval.pl
2520 skip @header lines in SAM
2522 ------------------------------------------------------------------------
2523 r417 | lh3lh3 | 2009-07-24 07:42:38 -0400 (Fri, 24 Jul 2009) | 3 lines
2525 M /trunk/samtools/bamtk.c
2526 M /trunk/samtools/sam_view.c
2528 * samtools-0.1.5-14 (r417)
2529 * more help in "samtools view" due to the recent changes.
2531 ------------------------------------------------------------------------
2532 r416 | lh3lh3 | 2009-07-24 07:34:30 -0400 (Fri, 24 Jul 2009) | 3 lines
2534 M /trunk/samtools/bam.c
2535 M /trunk/samtools/bam.h
2536 M /trunk/samtools/bam_import.c
2537 M /trunk/samtools/bamtk.c
2538 M /trunk/samtools/sam.c
2539 M /trunk/samtools/sam.h
2540 M /trunk/samtools/sam_view.c
2542 * samtools-0.1.5-17 (r416)
2543 * support import/export SAM with string tags
2545 ------------------------------------------------------------------------
2546 r415 | lh3lh3 | 2009-07-24 06:39:26 -0400 (Fri, 24 Jul 2009) | 3 lines
2548 M /trunk/samtools/bam.c
2549 M /trunk/samtools/bam.h
2550 M /trunk/samtools/bam_import.c
2551 M /trunk/samtools/bamtk.c
2552 M /trunk/samtools/sam.c
2553 M /trunk/samtools/sam.h
2554 M /trunk/samtools/sam_view.c
2556 * samtools-0.1.5-12 (r415)
2557 * FLAG now can be in HEX
2559 ------------------------------------------------------------------------
2560 r414 | lh3lh3 | 2009-07-22 17:03:49 -0400 (Wed, 22 Jul 2009) | 2 lines
2562 M /trunk/samtools/kstring.h
2564 fixed a compiling error (thank Ken for fixing it)
2566 ------------------------------------------------------------------------
2567 r412 | lh3lh3 | 2009-07-21 17:19:40 -0400 (Tue, 21 Jul 2009) | 2 lines
2569 M /trunk/samtools/kstring.c
2570 M /trunk/samtools/kstring.h
2572 Implemented Boyer-Moore search in the kstring library.
2574 ------------------------------------------------------------------------
2575 r409 | lh3lh3 | 2009-07-17 12:10:20 -0400 (Fri, 17 Jul 2009) | 2 lines
2577 M /trunk/samtools/bam_index.c
2579 do not include knetfile.h when _USE_KNETFILE is not defined
2581 ------------------------------------------------------------------------
2582 r408 | lh3lh3 | 2009-07-17 10:29:21 -0400 (Fri, 17 Jul 2009) | 5 lines
2584 M /trunk/samtools/bam_md.c
2585 M /trunk/samtools/bam_tview.c
2586 M /trunk/samtools/bamtk.c
2587 M /trunk/samtools/bgzf.c
2589 * samtools-0.1.5-11 (r408)
2590 * force to overwirte existing MD if it is different from the one calculated
2592 * bgzf.c: improved the compatibility with Windows headers
2594 ------------------------------------------------------------------------
2595 r407 | lh3lh3 | 2009-07-17 09:46:56 -0400 (Fri, 17 Jul 2009) | 5 lines
2597 M /trunk/samtools/bam.h
2598 M /trunk/samtools/bam_aux.c
2599 M /trunk/samtools/bam_md.c
2600 M /trunk/samtools/bamtk.c
2601 M /trunk/samtools/sam.h
2603 * samtools-0.1.5-10 (r407)
2604 * implemented bam_aux_del() to remove a tag
2605 * fillmd: generate the NM tag
2606 * fillmd: cmd interface improvement
2608 ------------------------------------------------------------------------
2609 r406 | lh3lh3 | 2009-07-16 18:30:40 -0400 (Thu, 16 Jul 2009) | 2 lines
2611 M /trunk/samtools/Makefile
2613 Sorry. The old Makefile is for PDCurses...
2615 ------------------------------------------------------------------------
2616 r405 | lh3lh3 | 2009-07-16 18:30:11 -0400 (Thu, 16 Jul 2009) | 3 lines
2618 M /trunk/samtools/Makefile
2619 M /trunk/samtools/bam_tview.c
2620 M /trunk/samtools/bamtk.c
2622 * samtools-0.1.5-9 (r405)
2623 * improved the compatibility with PDCurses a little bit
2625 ------------------------------------------------------------------------
2626 r404 | lh3lh3 | 2009-07-16 18:23:52 -0400 (Thu, 16 Jul 2009) | 3 lines
2628 M /trunk/samtools/Makefile
2629 M /trunk/samtools/bam_tview.c
2630 M /trunk/samtools/bamtk.c
2632 * samtools-0.1.5-8 (r404)
2633 * compatible with PDCurses
2635 ------------------------------------------------------------------------
2636 r403 | lh3lh3 | 2009-07-16 17:39:39 -0400 (Thu, 16 Jul 2009) | 3 lines
2638 M /trunk/samtools/bamtk.c
2639 M /trunk/samtools/kseq.h
2641 * samtools-0.1.5-7 (r403)
2642 * fixed a bug in kseq.h for binary files (text files are fine)
2644 ------------------------------------------------------------------------
2645 r402 | lh3lh3 | 2009-07-16 06:49:53 -0400 (Thu, 16 Jul 2009) | 4 lines
2647 M /trunk/samtools/bam_import.c
2648 M /trunk/samtools/bam_index.c
2649 M /trunk/samtools/bamtk.c
2650 M /trunk/samtools/bgzf.c
2652 * samtools-0.1.5-6 (r402)
2653 * fixed compiling error when "-D_USE_NETFILE" is not applied
2654 * improve portability to MinGW
2656 ------------------------------------------------------------------------
2657 r398 | lh3lh3 | 2009-07-13 05:21:36 -0400 (Mon, 13 Jul 2009) | 3 lines
2659 A /trunk/bam-lite/bam.h (from /trunk/samtools/bam.h:395)
2660 A /trunk/bam-lite/bam_lite.c (from /trunk/samtools/bam_lite.c:395)
2661 D /trunk/samtools/bam_lite.c
2663 * move bam_lite.c to bam-lite
2664 * copy bam.h to bam-lite
2666 ------------------------------------------------------------------------
2667 r395 | lh3lh3 | 2009-07-13 05:12:57 -0400 (Mon, 13 Jul 2009) | 3 lines
2669 M /trunk/samtools/bam.h
2670 M /trunk/samtools/bam_lite.c
2671 M /trunk/samtools/bam_lpileup.c
2672 M /trunk/samtools/bam_pileup.c
2673 M /trunk/samtools/bamtk.c
2675 * samtools-0.1.5-5 (r395)
2676 * added bam_pileup_file() and removed bam_lpileup_file()
2678 ------------------------------------------------------------------------
2679 r394 | lh3lh3 | 2009-07-12 19:35:10 -0400 (Sun, 12 Jul 2009) | 3 lines
2681 M /trunk/samtools/bamtk.c
2682 M /trunk/samtools/knetfile.c
2683 M /trunk/samtools/knetfile.h
2685 * samtools-0.1.5-4 (r394)
2686 * http_proxy support in knetfile library (check http_proxy ENV)
2688 ------------------------------------------------------------------------
2689 r393 | lh3lh3 | 2009-07-12 18:57:07 -0400 (Sun, 12 Jul 2009) | 5 lines
2691 M /trunk/samtools/bam_index.c
2692 M /trunk/samtools/bam_tview.c
2693 M /trunk/samtools/bamtk.c
2694 M /trunk/samtools/knetfile.c
2695 M /trunk/samtools/knetfile.h
2697 * samtools-0.1.5-3 (r393)
2698 * knetfile now supports HTTP (no proxy at the moment)
2699 * fixed a potential issue in knetfile on opening ordinary file, although I have
2700 not seen the sideeffect so far.
2702 ------------------------------------------------------------------------
2703 r392 | lh3lh3 | 2009-07-12 13:50:55 -0400 (Sun, 12 Jul 2009) | 2 lines
2705 M /trunk/samtools/samtools.1
2707 Remove the warning in tview
2709 ------------------------------------------------------------------------
2710 r391 | lh3lh3 | 2009-07-12 13:42:43 -0400 (Sun, 12 Jul 2009) | 3 lines
2712 M /trunk/samtools/bam_tview.c
2713 M /trunk/samtools/bamtk.c
2715 * samtools-0.1.5-2 (r391)
2716 * do not show a blank screen when no reads mapped
2718 ------------------------------------------------------------------------
2719 r390 | lh3lh3 | 2009-07-09 09:01:42 -0400 (Thu, 09 Jul 2009) | 4 lines
2721 M /trunk/samtools/bam.h
2722 A /trunk/samtools/bam_lite.c
2723 M /trunk/samtools/bamtk.c
2725 * samtools-0.1.5-1 (r390)
2726 * removed useless _IOLIB in bam.h. This should cause no change at all.
2727 * added bam_lite.c for light-weight BAM reading
2729 ------------------------------------------------------------------------
2730 r385 | lh3lh3 | 2009-07-07 11:53:29 -0400 (Tue, 07 Jul 2009) | 2 lines
2732 M /trunk/samtools/bamtk.c
2733 M /trunk/samtools/knetfile.c
2735 Release samtools-0.1.5c (fixed a bug in piping)
2737 ------------------------------------------------------------------------
2738 r383 | lh3lh3 | 2009-07-07 06:39:55 -0400 (Tue, 07 Jul 2009) | 2 lines
2740 M /trunk/samtools/bamtk.c
2741 M /trunk/samtools/sam.c
2743 Release samtools-0.1.5b (BUG! so embarrassing!)
2745 ------------------------------------------------------------------------
2746 r381 | lh3lh3 | 2009-07-07 06:20:06 -0400 (Tue, 07 Jul 2009) | 2 lines
2748 M /trunk/samtools/Makefile
2749 M /trunk/samtools/bam.h
2750 M /trunk/samtools/bam_aux.c
2751 M /trunk/samtools/bamtk.c
2753 Release samtools-0.1.5a (for compatibility with Bio::DB::Sam)
2755 ------------------------------------------------------------------------
2756 r373 | lh3lh3 | 2009-07-07 05:26:57 -0400 (Tue, 07 Jul 2009) | 2 lines
2758 M /trunk/samtools/ChangeLog
2759 M /trunk/samtools/NEWS
2760 M /trunk/samtools/bamtk.c
2761 M /trunk/samtools/samtools.1
2763 Release samtools-0.1.5
2765 ------------------------------------------------------------------------
2766 r372 | lh3lh3 | 2009-07-07 04:49:27 -0400 (Tue, 07 Jul 2009) | 3 lines
2768 M /trunk/samtools/bamtk.c
2769 M /trunk/samtools/sam.c
2771 * samtools-0.1.4-23 (r372)
2772 * keep header text if "view -t" is used (by Gerton)
2774 ------------------------------------------------------------------------
2775 r371 | lh3lh3 | 2009-07-06 20:13:32 -0400 (Mon, 06 Jul 2009) | 2 lines
2777 M /trunk/samtools/samtools.1
2779 update documentation
2781 ------------------------------------------------------------------------
2782 r370 | bhandsaker | 2009-07-02 17:24:34 -0400 (Thu, 02 Jul 2009) | 2 lines
2784 M /trunk/samtools/Makefile
2786 Introduced LIBPATH variable so this could be overridden to allow samtools to build correct at the Broad.
2788 ------------------------------------------------------------------------
2789 r369 | lh3lh3 | 2009-07-02 08:36:53 -0400 (Thu, 02 Jul 2009) | 4 lines
2791 M /trunk/samtools/ChangeLog
2792 M /trunk/samtools/bam_aux.c
2793 M /trunk/samtools/bam_plcmd.c
2794 M /trunk/samtools/bamtk.c
2796 * samtools-0.1.4-22 (r369)
2797 * in pileup, optionally print E2 and U2
2798 * remove the debugging code in bam_aux_get() (Drat!)
2800 ------------------------------------------------------------------------
2801 r368 | lh3lh3 | 2009-07-02 06:32:26 -0400 (Thu, 02 Jul 2009) | 6 lines
2803 M /trunk/samtools/bam.c
2804 M /trunk/samtools/bam.h
2805 M /trunk/samtools/bam_aux.c
2806 M /trunk/samtools/bam_index.c
2807 M /trunk/samtools/bam_lpileup.c
2808 M /trunk/samtools/bam_md.c
2809 M /trunk/samtools/bam_pileup.c
2810 M /trunk/samtools/bam_rmdup.c
2811 M /trunk/samtools/bam_stat.c
2812 M /trunk/samtools/bam_tview.c
2813 M /trunk/samtools/bamtk.c
2814 M /trunk/samtools/faidx.c
2815 M /trunk/samtools/faidx.h
2816 M /trunk/samtools/glf.c
2818 * samtools-0.1.4-21 (r368)
2819 * propagate errors rather than exit or complain assertion failure. Assertion
2820 should be only used for checking internal bugs, but not for external input
2821 inconsistency. I was just a bit lazy.
2822 * small memory leak may be present on failure, though
2824 ------------------------------------------------------------------------
2825 r367 | lh3lh3 | 2009-06-30 11:18:42 -0400 (Tue, 30 Jun 2009) | 2 lines
2827 M /trunk/samtools/knetfile.c
2829 reduce the chance of blocking in FTP connection
2831 ------------------------------------------------------------------------
2832 r366 | lh3lh3 | 2009-06-30 10:35:21 -0400 (Tue, 30 Jun 2009) | 2 lines
2834 M /trunk/samtools/knetfile.c
2836 minor changes to knetfile: invalid fd equals -1 rather than 0
2838 ------------------------------------------------------------------------
2839 r365 | lh3lh3 | 2009-06-30 09:04:30 -0400 (Tue, 30 Jun 2009) | 3 lines
2841 M /trunk/samtools/bam_index.c
2842 M /trunk/samtools/bamtk.c
2843 M /trunk/samtools/knetfile.c
2844 M /trunk/samtools/knetfile.h
2846 * samtools-0.1.4-20 (r365)
2847 * download the BAM index file if it is not found in the current working directory.
2849 ------------------------------------------------------------------------
2850 r364 | lh3lh3 | 2009-06-30 07:39:07 -0400 (Tue, 30 Jun 2009) | 3 lines
2852 M /trunk/samtools/bamtk.c
2853 M /trunk/samtools/knetfile.c
2855 * samtools-0.1.4-19 (r364)
2856 * knetfile: report error when the file is not present on FTP
2858 ------------------------------------------------------------------------
2859 r363 | lh3lh3 | 2009-06-29 18:23:32 -0400 (Mon, 29 Jun 2009) | 4 lines
2861 M /trunk/samtools/bam_tview.c
2862 M /trunk/samtools/bamtk.c
2863 M /trunk/samtools/bgzf.c
2864 M /trunk/samtools/bgzf.h
2865 M /trunk/samtools/knetfile.c
2866 M /trunk/samtools/knetfile.h
2868 * samtools-0.1.4-18 (r363)
2869 * knetfile: do not trigger network communication in FTP seek (lazy seek)
2870 * bgzf: cache recent blocks (disabled by default)
2872 ------------------------------------------------------------------------
2873 r362 | lh3lh3 | 2009-06-25 16:04:34 -0400 (Thu, 25 Jun 2009) | 2 lines
2875 M /trunk/samtools/bgzf.c
2879 ------------------------------------------------------------------------
2880 r361 | lh3lh3 | 2009-06-25 16:03:10 -0400 (Thu, 25 Jun 2009) | 3 lines
2882 M /trunk/samtools/bam_index.c
2883 M /trunk/samtools/bamtk.c
2885 * samtools-0.1.4-17 (r361)
2886 * if a file is given on FTP, search locally for the BAM index
2888 ------------------------------------------------------------------------
2889 r360 | lh3lh3 | 2009-06-25 15:44:52 -0400 (Thu, 25 Jun 2009) | 5 lines
2891 M /trunk/samtools/Makefile
2892 M /trunk/samtools/bam_import.c
2893 M /trunk/samtools/bam_index.c
2894 M /trunk/samtools/bamtk.c
2895 M /trunk/samtools/bgzf.c
2896 M /trunk/samtools/bgzf.h
2897 M /trunk/samtools/knetfile.c
2898 M /trunk/samtools/knetfile.h
2900 * samtools-0.1.4-16 (r360)
2901 * report more information in index when the input is not sorted
2902 * change the behaviour of knet_seek() such that it returns 0 on success
2903 * support knetfile library in BGZF
2905 ------------------------------------------------------------------------
2906 r359 | lh3lh3 | 2009-06-25 12:10:55 -0400 (Thu, 25 Jun 2009) | 2 lines
2908 M /trunk/samtools/knetfile.c
2909 M /trunk/samtools/knetfile.h
2911 fixed bugs in knetfile.*
2913 ------------------------------------------------------------------------
2914 r358 | lh3lh3 | 2009-06-25 08:53:19 -0400 (Thu, 25 Jun 2009) | 2 lines
2916 A /trunk/samtools/knetfile.h
2918 this is the header file
2920 ------------------------------------------------------------------------
2921 r357 | lh3lh3 | 2009-06-25 08:52:03 -0400 (Thu, 25 Jun 2009) | 3 lines
2923 A /trunk/samtools/knetfile.c
2925 * open a file at FTP
2926 * preliminary version
2928 ------------------------------------------------------------------------
2929 r354 | lh3lh3 | 2009-06-24 09:02:25 -0400 (Wed, 24 Jun 2009) | 3 lines
2931 M /trunk/samtools/bam.c
2932 M /trunk/samtools/bamtk.c
2934 * samtools-0.1.4-15 (r354)
2935 * fixed a memory leak in bam_view1(), although samtools is not using this routine.
2937 ------------------------------------------------------------------------
2938 r351 | lh3lh3 | 2009-06-17 19:16:26 -0400 (Wed, 17 Jun 2009) | 4 lines
2940 M /trunk/samtools/bamtk.c
2941 M /trunk/samtools/faidx.c
2943 * samtools-0.1.4-13 (r351)
2944 * make faidx more tolerant to empty lines right before or after > lines
2945 * hope this does not introduce new bugs...
2947 ------------------------------------------------------------------------
2948 r350 | lh3lh3 | 2009-06-16 09:37:01 -0400 (Tue, 16 Jun 2009) | 3 lines
2950 M /trunk/samtools/bam_plcmd.c
2951 M /trunk/samtools/bamtk.c
2953 * samtools-0.1.4-13 (r350)
2954 * fixed a small memory leak in pileup, caused by recent modifications
2956 ------------------------------------------------------------------------
2957 r347 | lh3lh3 | 2009-06-13 16:20:49 -0400 (Sat, 13 Jun 2009) | 3 lines
2959 M /trunk/samtools/bam_plcmd.c
2960 M /trunk/samtools/bamtk.c
2961 M /trunk/samtools/sam_view.c
2963 * samtools-0.1.4-12 (r347)
2964 * added `-S' to pileup, similar to `view -S'
2966 ------------------------------------------------------------------------
2967 r346 | lh3lh3 | 2009-06-13 12:52:31 -0400 (Sat, 13 Jun 2009) | 3 lines
2969 M /trunk/samtools/Makefile
2970 M /trunk/samtools/bamtk.c
2971 M /trunk/samtools/sam_view.c
2972 M /trunk/samtools/samtools.1
2974 * samtools-0.1.4-11 (r346)
2975 * allow to select a read group at view command-line
2977 ------------------------------------------------------------------------
2978 r344 | lh3lh3 | 2009-06-13 09:06:24 -0400 (Sat, 13 Jun 2009) | 2 lines
2980 M /trunk/samtools/examples/calDepth.c
2984 ------------------------------------------------------------------------
2985 r343 | lh3lh3 | 2009-06-13 09:01:22 -0400 (Sat, 13 Jun 2009) | 2 lines
2987 M /trunk/samtools/examples/calDepth.c
2991 ------------------------------------------------------------------------
2992 r342 | lh3lh3 | 2009-06-13 08:58:48 -0400 (Sat, 13 Jun 2009) | 2 lines
2994 M /trunk/samtools/examples/Makefile
2995 A /trunk/samtools/examples/calDepth.c
2997 added an example of calculating read depth
2999 ------------------------------------------------------------------------
3000 r341 | lh3lh3 | 2009-06-13 08:00:08 -0400 (Sat, 13 Jun 2009) | 6 lines
3002 M /trunk/samtools/Makefile
3003 M /trunk/samtools/bam.h
3004 M /trunk/samtools/bam_aux.c
3005 A /trunk/samtools/bam_color.c
3006 M /trunk/samtools/bam_plcmd.c
3007 M /trunk/samtools/bam_sort.c
3008 M /trunk/samtools/bam_tview.c
3009 M /trunk/samtools/bamtk.c
3010 M /trunk/samtools/sam.c
3011 M /trunk/samtools/sam.h
3013 * samtools-0.1.4-10 (r341)
3014 * only include key APIs in libbam.a
3015 * move color-specific routines to bam_color.c
3016 * update documentations
3017 * remove the support of -q in pileup
3019 ------------------------------------------------------------------------
3020 r340 | lh3lh3 | 2009-06-13 06:17:14 -0400 (Sat, 13 Jun 2009) | 6 lines
3022 M /trunk/samtools/INSTALL
3023 M /trunk/samtools/Makefile
3024 M /trunk/samtools/bam_aux.c
3025 M /trunk/samtools/bam_import.c
3026 M /trunk/samtools/bam_tview.c
3027 M /trunk/samtools/bamtk.c
3028 M /trunk/samtools/razf.c
3029 M /trunk/samtools/sam_view.c
3031 * samtools-0.1.4-9 (r340)
3032 * added a warning to razf.c if zlib<1.2.2.1
3033 * fixed a compilation warning
3034 * fixed a segfault caused by @RG parsing
3035 * detect NCURSES in bam_tview.c
3037 ------------------------------------------------------------------------
3038 r339 | lh3lh3 | 2009-06-13 05:35:19 -0400 (Sat, 13 Jun 2009) | 2 lines
3040 M /trunk/samtools/INSTALL
3044 ------------------------------------------------------------------------
3045 r338 | lh3lh3 | 2009-06-12 19:15:24 -0400 (Fri, 12 Jun 2009) | 4 lines
3047 M /trunk/samtools/bam.c
3048 M /trunk/samtools/bam.h
3049 M /trunk/samtools/bam_aux.c
3050 M /trunk/samtools/bam_import.c
3051 M /trunk/samtools/bamtk.c
3052 M /trunk/samtools/kstring.h
3053 M /trunk/samtools/sam.c
3054 M /trunk/samtools/sam_view.c
3056 * samtools-0.1.4-8 (r338)
3057 * parse the @RG header lines and allow to choose library at the "samtools view"
3060 ------------------------------------------------------------------------
3061 r337 | lh3lh3 | 2009-06-12 16:25:50 -0400 (Fri, 12 Jun 2009) | 4 lines
3063 M /trunk/samtools/bamtk.c
3064 M /trunk/samtools/bgzf.c
3065 M /trunk/samtools/bgzf.h
3066 M /trunk/samtools/sam.c
3067 M /trunk/samtools/sam_view.c
3069 * samtools-0.1.4-7 (r337)
3070 * bgzf.c: support mode string "wu": uncompressed output
3071 * "samtools view" support "-u" command-line option
3073 ------------------------------------------------------------------------
3074 r336 | lh3lh3 | 2009-06-12 12:20:12 -0400 (Fri, 12 Jun 2009) | 5 lines
3076 M /trunk/samtools/Makefile
3077 M /trunk/samtools/misc/Makefile
3078 M /trunk/samtools/razf.c
3079 M /trunk/samtools/razf.h
3080 M /trunk/samtools/razip.c
3082 * no changes to samtools itself
3083 * remove zlib source codes
3084 * make RAZF reading compatible with old version of zlib
3085 * on old version of zlib, writing is not available
3087 ------------------------------------------------------------------------
3088 r335 | lh3lh3 | 2009-06-12 11:47:33 -0400 (Fri, 12 Jun 2009) | 2 lines
3090 D /trunk/samtools/zlib
3092 remove zlib for simplification...
3094 ------------------------------------------------------------------------
3095 r334 | lh3lh3 | 2009-06-12 10:43:36 -0400 (Fri, 12 Jun 2009) | 5 lines
3097 M /trunk/samtools/bam.h
3098 M /trunk/samtools/bam_aux.c
3099 M /trunk/samtools/bamtk.c
3101 * samtools-0.1.4-6 (r334)
3102 * do not export bam_aux_get_core() for Bio::DB::Sam because it has already
3103 been implemented in that.
3104 * this version works with the latest Bio::DB::Sam (20090612)
3106 ------------------------------------------------------------------------
3107 r333 | lh3lh3 | 2009-06-12 10:33:42 -0400 (Fri, 12 Jun 2009) | 2 lines
3109 M /trunk/samtools/ChangeLog
3113 ------------------------------------------------------------------------
3114 r332 | lh3lh3 | 2009-06-12 10:21:21 -0400 (Fri, 12 Jun 2009) | 2 lines
3116 M /trunk/samtools/AUTHORS
3117 M /trunk/samtools/Makefile
3118 M /trunk/samtools/misc/Makefile
3120 fixed minor things in Makefile
3122 ------------------------------------------------------------------------
3123 r331 | lh3lh3 | 2009-06-12 10:07:05 -0400 (Fri, 12 Jun 2009) | 4 lines
3125 M /trunk/samtools/bamtk.c
3127 * samtools-0.1.4-5 (r3310
3128 * no change to samtools itself. Version number is increased to reflect the
3129 changes in the Makefile building system.
3131 ------------------------------------------------------------------------
3132 r330 | lh3lh3 | 2009-06-12 10:03:38 -0400 (Fri, 12 Jun 2009) | 2 lines
3134 M /trunk/samtools/AUTHORS
3135 D /trunk/samtools/README
3137 update information...
3139 ------------------------------------------------------------------------
3140 r329 | lh3lh3 | 2009-06-12 09:52:21 -0400 (Fri, 12 Jun 2009) | 3 lines
3142 M /trunk/samtools/misc/novo2sam.pl
3144 * updated novoalign converter by Colin Hercus et al.
3145 * this version works with indels
3147 ------------------------------------------------------------------------
3148 r328 | lh3lh3 | 2009-06-12 09:50:53 -0400 (Fri, 12 Jun 2009) | 3 lines
3150 M /trunk/samtools/INSTALL
3151 M /trunk/samtools/Makefile
3152 M /trunk/samtools/misc/Makefile
3153 M /trunk/samtools/zlib/Makefile
3156 * update INSTALL instruction
3158 ------------------------------------------------------------------------
3159 r327 | lh3lh3 | 2009-06-12 09:18:29 -0400 (Fri, 12 Jun 2009) | 4 lines
3161 A /trunk/samtools/Makefile (from /trunk/samtools/Makefile.generic:325)
3162 D /trunk/samtools/Makefile.am
3163 D /trunk/samtools/Makefile.generic
3164 D /trunk/samtools/Makefile.lite
3165 D /trunk/samtools/autogen.sh
3166 D /trunk/samtools/cleanup.sh
3167 D /trunk/samtools/configure.ac
3168 A /trunk/samtools/misc/Makefile (from /trunk/samtools/misc/Makefile.generic:305)
3169 D /trunk/samtools/misc/Makefile.am
3170 D /trunk/samtools/misc/Makefile.generic
3171 M /trunk/samtools/razf.c
3172 A /trunk/samtools/zlib
3173 A /trunk/samtools/zlib/Makefile
3174 A /trunk/samtools/zlib/adler32.c
3175 A /trunk/samtools/zlib/compress.c
3176 A /trunk/samtools/zlib/crc32.c
3177 A /trunk/samtools/zlib/crc32.h
3178 A /trunk/samtools/zlib/deflate.c
3179 A /trunk/samtools/zlib/deflate.h
3180 A /trunk/samtools/zlib/gzio.c
3181 A /trunk/samtools/zlib/infback.c
3182 A /trunk/samtools/zlib/inffast.c
3183 A /trunk/samtools/zlib/inffast.h
3184 A /trunk/samtools/zlib/inffixed.h
3185 A /trunk/samtools/zlib/inflate.c
3186 A /trunk/samtools/zlib/inflate.h
3187 A /trunk/samtools/zlib/inftrees.c
3188 A /trunk/samtools/zlib/inftrees.h
3189 A /trunk/samtools/zlib/trees.c
3190 A /trunk/samtools/zlib/trees.h
3191 A /trunk/samtools/zlib/uncompr.c
3192 A /trunk/samtools/zlib/zconf.h
3193 A /trunk/samtools/zlib/zlib.h
3194 A /trunk/samtools/zlib/zutil.c
3195 A /trunk/samtools/zlib/zutil.h
3196 D /trunk/samtools/zutil.h
3198 * added zlib-1.2.3 as razip requires that
3199 * prepare to changed back to the Makefile building system
3200 * unfinished! (will be soon)
3202 ------------------------------------------------------------------------
3203 r326 | lh3lh3 | 2009-06-12 09:12:03 -0400 (Fri, 12 Jun 2009) | 2 lines
3205 M /trunk/samtools/misc/samtools.pl
3209 ------------------------------------------------------------------------
3210 r325 | lh3lh3 | 2009-06-10 11:27:59 -0400 (Wed, 10 Jun 2009) | 3 lines
3212 M /trunk/samtools/bam_maqcns.c
3213 M /trunk/samtools/bamtk.c
3215 * samtools-0.1.4-4 (r325)
3216 * further avoid wrong consensus calls in repetitive regions.
3218 ------------------------------------------------------------------------
3219 r324 | lh3lh3 | 2009-06-10 10:56:17 -0400 (Wed, 10 Jun 2009) | 4 lines
3221 M /trunk/samtools/bam_maqcns.c
3222 M /trunk/samtools/bam_plcmd.c
3223 M /trunk/samtools/bamtk.c
3224 M /trunk/samtools/sam.c
3225 M /trunk/samtools/sam.h
3227 * samtools-0.1.4-3 (r324)
3228 * make maqcns generate the correct call in repetitive regions.
3229 * allow filtering on mapQ at the pileup command line
3231 ------------------------------------------------------------------------
3232 r323 | lh3lh3 | 2009-06-10 05:04:21 -0400 (Wed, 10 Jun 2009) | 3 lines
3234 M /trunk/samtools/misc/samtools.pl
3236 * samtools.pl-0.3.2 (r322)
3237 * indels and SNPs use different mapping quality threshold
3239 ------------------------------------------------------------------------
3240 r322 | lh3lh3 | 2009-06-10 05:03:22 -0400 (Wed, 10 Jun 2009) | 2 lines
3242 M /trunk/samtools/misc/export2sam.pl
3246 ------------------------------------------------------------------------
3247 r321 | lh3lh3 | 2009-06-09 04:21:48 -0400 (Tue, 09 Jun 2009) | 2 lines
3249 M /trunk/samtools/misc/samtools.pl
3251 just typo. no real change
3253 ------------------------------------------------------------------------
3254 r320 | lh3lh3 | 2009-06-08 09:32:51 -0400 (Mon, 08 Jun 2009) | 2 lines
3256 M /trunk/samtools/misc/samtools.pl
3258 a little bit code cleanup
3260 ------------------------------------------------------------------------
3261 r319 | lh3lh3 | 2009-06-08 09:22:33 -0400 (Mon, 08 Jun 2009) | 4 lines
3263 M /trunk/samtools/misc/samtools.pl
3266 * change default parameters
3267 * optionally print filtered variants
3269 ------------------------------------------------------------------------
3270 r318 | lh3lh3 | 2009-06-08 09:14:26 -0400 (Mon, 08 Jun 2009) | 3 lines
3272 M /trunk/samtools/misc/samtools.pl
3275 * combine snpFilter and indelFilter
3277 ------------------------------------------------------------------------
3278 r317 | lh3lh3 | 2009-06-08 06:31:42 -0400 (Mon, 08 Jun 2009) | 3 lines
3280 M /trunk/samtools/misc/samtools.pl
3283 * change a default parameter
3285 ------------------------------------------------------------------------
3286 r316 | lh3lh3 | 2009-06-08 06:11:06 -0400 (Mon, 08 Jun 2009) | 5 lines
3288 M /trunk/samtools/bam_maqcns.c
3289 M /trunk/samtools/bam_maqcns.h
3290 M /trunk/samtools/bam_plcmd.c
3291 M /trunk/samtools/bamtk.c
3292 M /trunk/samtools/sam.c
3294 * samtools-0.1.4-2 (r316)
3295 * pileup: cap mapping quality at 60 (by default)
3296 * pileup: always calculate RMS mapq
3297 * pileup: allow to output variant sites only
3299 ------------------------------------------------------------------------
3300 r312 | lh3lh3 | 2009-06-04 08:01:10 -0400 (Thu, 04 Jun 2009) | 3 lines
3302 M /trunk/samtools/misc/samtools.pl
3307 ------------------------------------------------------------------------
3308 r311 | lh3lh3 | 2009-06-03 04:40:40 -0400 (Wed, 03 Jun 2009) | 2 lines
3310 M /trunk/samtools/misc/samtools.pl
3312 * in snpFilter, suppress non-SNP sites
3314 ------------------------------------------------------------------------
3315 r310 | lh3lh3 | 2009-06-01 09:35:13 -0400 (Mon, 01 Jun 2009) | 3 lines
3317 M /trunk/samtools/misc/samtools.pl
3322 ------------------------------------------------------------------------
3323 r309 | lh3lh3 | 2009-06-01 09:04:39 -0400 (Mon, 01 Jun 2009) | 3 lines
3325 M /trunk/samtools/misc/samtools.pl
3330 ------------------------------------------------------------------------
3331 r306 | lh3lh3 | 2009-05-28 06:49:35 -0400 (Thu, 28 May 2009) | 3 lines
3333 M /trunk/samtools/bgzf.c
3335 * minor changes to bgzf: return NULL if fd == -1
3336 * suggested by {kdj,jm18}@sanger.ac.uk
3338 ------------------------------------------------------------------------
3339 r305 | lh3lh3 | 2009-05-28 06:16:08 -0400 (Thu, 28 May 2009) | 2 lines
3341 A /trunk/samtools/misc/interpolate_sam.pl
3343 Script for paired-end pileup, contributed by Stephen Montgomery.
3345 ------------------------------------------------------------------------
3346 r304 | lh3lh3 | 2009-05-28 06:08:49 -0400 (Thu, 28 May 2009) | 3 lines
3348 M /trunk/samtools/bamtk.c
3349 M /trunk/samtools/sam.c
3351 * samtools-0.1.4-1 (r304)
3352 * fixed a minor bug in printing headers
3354 ------------------------------------------------------------------------
3355 r297 | lh3lh3 | 2009-05-21 11:06:16 -0400 (Thu, 21 May 2009) | 2 lines
3357 M /trunk/samtools/ChangeLog
3358 M /trunk/samtools/NEWS
3359 M /trunk/samtools/bam_plcmd.c
3360 M /trunk/samtools/bamtk.c
3361 M /trunk/samtools/misc/maq2sam.c
3362 M /trunk/samtools/samtools.1
3364 Release samtools-0.1.4
3366 ------------------------------------------------------------------------
3367 r296 | lh3lh3 | 2009-05-21 07:53:14 -0400 (Thu, 21 May 2009) | 3 lines
3369 M /trunk/samtools/bam_maqcns.c
3370 M /trunk/samtools/bamtk.c
3372 * samtools-0.1.3-24 (r296)
3373 * another similar bug in the indel caller
3375 ------------------------------------------------------------------------
3376 r295 | lh3lh3 | 2009-05-21 07:50:28 -0400 (Thu, 21 May 2009) | 3 lines
3378 M /trunk/samtools/bam_maqcns.c
3379 M /trunk/samtools/bamtk.c
3381 * samtools-0.1.3-23 (r295)
3382 * fixed a critical bug in the indel caller
3384 ------------------------------------------------------------------------
3385 r294 | lh3lh3 | 2009-05-20 08:00:20 -0400 (Wed, 20 May 2009) | 2 lines
3387 M /trunk/samtools/bam_stat.c
3389 added a missing header file
3391 ------------------------------------------------------------------------
3392 r293 | lh3lh3 | 2009-05-19 18:44:25 -0400 (Tue, 19 May 2009) | 3 lines
3394 M /trunk/samtools/bam_tview.c
3395 M /trunk/samtools/bamtk.c
3397 * samtools-0.1.3-22 (r293)
3398 * open tview in the dot-view mode by default
3400 ------------------------------------------------------------------------
3401 r292 | lh3lh3 | 2009-05-18 16:01:23 -0400 (Mon, 18 May 2009) | 6 lines
3403 M /trunk/samtools/samtools.1
3405 Added a note to the manual. Currently SAMtools used unaligned words in
3406 several places. Although this does not cause bus errors to me, it may
3407 affect portability. Please see the "Bus error" wiki page for more
3408 information. Also thank James Bonfields for pointing this out.
3411 ------------------------------------------------------------------------
3412 r286 | lh3lh3 | 2009-05-14 10:23:13 -0400 (Thu, 14 May 2009) | 3 lines
3414 M /trunk/samtools/bam.h
3415 M /trunk/samtools/bam_aux.c
3416 M /trunk/samtools/bamtk.c
3418 * samtools-0.1.3-21 (286)
3419 * declare bam_aux_get_core() in bam.h
3421 ------------------------------------------------------------------------
3422 r276 | lh3lh3 | 2009-05-13 05:07:55 -0400 (Wed, 13 May 2009) | 5 lines
3424 M /trunk/samtools/bam.h
3425 M /trunk/samtools/bam_index.c
3426 M /trunk/samtools/bamtk.c
3428 * samtools-0.1.3-20 (r276)
3429 * remove bam1_t::hash again. We need to modify the Perl API anyway to
3430 make it work with the latest SVN.
3431 * As is suggested by Tim, scan "{base}.bai" and "{base}.bam.bai" for index
3433 ------------------------------------------------------------------------
3434 r275 | lh3lh3 | 2009-05-12 16:14:10 -0400 (Tue, 12 May 2009) | 4 lines
3436 M /trunk/samtools/ChangeLog
3437 M /trunk/samtools/bam.h
3438 M /trunk/samtools/bamtk.c
3440 * samtools-0.1.3-19 (r275)
3441 * a minor change to the bam1_t struct: added back "void *hash" for the
3442 backward compatibility with Bio::DB::Sam
3444 ------------------------------------------------------------------------
3445 r273 | lh3lh3 | 2009-05-12 09:28:39 -0400 (Tue, 12 May 2009) | 3 lines
3447 M /trunk/samtools/bam_rmdupse.c
3448 M /trunk/samtools/bamtk.c
3450 * samtools-0.1.3-18 (r273)
3451 * rmdupse: do not remove unmapped reads
3453 ------------------------------------------------------------------------
3454 r272 | lh3lh3 | 2009-05-12 09:20:00 -0400 (Tue, 12 May 2009) | 2 lines
3456 M /trunk/samtools/bam_rmdupse.c
3458 change a parameter. It does nothing
3460 ------------------------------------------------------------------------
3461 r271 | lh3lh3 | 2009-05-12 09:17:58 -0400 (Tue, 12 May 2009) | 3 lines
3463 M /trunk/samtools/Makefile.am
3464 M /trunk/samtools/Makefile.generic
3465 M /trunk/samtools/Makefile.lite
3466 A /trunk/samtools/bam_rmdupse.c
3467 M /trunk/samtools/bamtk.c
3468 M /trunk/samtools/configure.ac
3470 * samtools-0.1.3-17 (r271)
3471 * added 'rmdupse' command
3473 ------------------------------------------------------------------------
3474 r267 | lh3lh3 | 2009-05-05 17:31:41 -0400 (Tue, 05 May 2009) | 3 lines
3476 M /trunk/samtools/bamtk.c
3477 M /trunk/samtools/sam_view.c
3479 * samtools-0.1.3-16 (r267)
3480 * in sam_view.c, changed g_flag_on based on the suggestion by Angie Hinrichs
3482 ------------------------------------------------------------------------
3483 r266 | lh3lh3 | 2009-05-05 17:23:27 -0400 (Tue, 05 May 2009) | 3 lines
3485 M /trunk/samtools/bam_import.c
3486 M /trunk/samtools/bamtk.c
3488 * samtools-0.1.3-15 (r266)
3489 * report an error if a non-* reference is present while @SQ is absent
3491 ------------------------------------------------------------------------
3492 r265 | lh3lh3 | 2009-05-05 17:09:00 -0400 (Tue, 05 May 2009) | 3 lines
3494 M /trunk/samtools/bam.h
3495 M /trunk/samtools/bam_import.c
3496 M /trunk/samtools/bamtk.c
3497 M /trunk/samtools/sam.c
3498 M /trunk/samtools/sam_view.c
3500 * samtools-0.1.3-14 (r262)
3501 * make samopen() recognize @SQ header lines
3503 ------------------------------------------------------------------------
3504 r261 | lh3lh3 | 2009-05-05 10:10:30 -0400 (Tue, 05 May 2009) | 3 lines
3506 M /trunk/samtools/bam_plcmd.c
3507 M /trunk/samtools/bamtk.c
3508 M /trunk/samtools/bgzf.c
3509 M /trunk/samtools/sam.c
3510 M /trunk/samtools/sam_view.c
3512 * samtools-0.1.3-13 (r260)
3513 * report error for file I/O error
3515 ------------------------------------------------------------------------
3516 r260 | lh3lh3 | 2009-05-05 10:01:16 -0400 (Tue, 05 May 2009) | 2 lines
3518 M /trunk/samtools/Makefile.am
3522 ------------------------------------------------------------------------
3523 r259 | lh3lh3 | 2009-05-05 09:52:25 -0400 (Tue, 05 May 2009) | 3 lines
3525 M /trunk/samtools/bam.h
3526 M /trunk/samtools/bam_pileup.c
3527 M /trunk/samtools/bam_plcmd.c
3528 M /trunk/samtools/bamtk.c
3529 M /trunk/samtools/sam.c
3530 M /trunk/samtools/sam.h
3532 * samtools-0.1.3-12 (r259)
3533 * use the new I/O interface in pileup
3535 ------------------------------------------------------------------------
3536 r258 | lh3lh3 | 2009-05-05 09:33:22 -0400 (Tue, 05 May 2009) | 3 lines
3538 M /trunk/samtools/Makefile.generic
3539 M /trunk/samtools/Makefile.lite
3540 M /trunk/samtools/bam.c
3541 M /trunk/samtools/bam.h
3542 M /trunk/samtools/bam_import.c
3543 M /trunk/samtools/bamtk.c
3544 A /trunk/samtools/sam.c
3545 A /trunk/samtools/sam.h
3546 A /trunk/samtools/sam_view.c
3548 * samtools-0.1.3-11 (r258)
3549 * unify the interface to BAM and SAM I/O
3551 ------------------------------------------------------------------------
3552 r257 | lh3lh3 | 2009-05-05 04:53:35 -0400 (Tue, 05 May 2009) | 3 lines
3554 M /trunk/samtools/Makefile.lite
3555 M /trunk/samtools/bam_plcmd.c
3556 M /trunk/samtools/bamtk.c
3558 * samtools-0.1.3-10 (r257)
3559 * allow hex with "pileup -m"
3561 ------------------------------------------------------------------------
3562 r256 | lh3lh3 | 2009-05-04 14:16:50 -0400 (Mon, 04 May 2009) | 4 lines
3564 M /trunk/samtools/bam_lpileup.c
3565 M /trunk/samtools/bamtk.c
3567 * samtools-0.1.3-9 (r256)
3568 * fixed a bug in bam_lpileup.c
3569 * I do not know if this also fixes the bug causing assertion failure in the tview
3571 ------------------------------------------------------------------------
3572 r251 | lh3lh3 | 2009-04-28 08:53:23 -0400 (Tue, 28 Apr 2009) | 3 lines
3574 M /trunk/samtools/bam_pileup.c
3575 M /trunk/samtools/bamtk.c
3577 * samtools-0.1.3-8 (r251)
3578 * fixed a bug when there are reads without coordinates
3580 ------------------------------------------------------------------------
3581 r250 | lh3lh3 | 2009-04-28 08:43:33 -0400 (Tue, 28 Apr 2009) | 2 lines
3583 A /trunk/samtools/AUTHORS
3584 A /trunk/samtools/README
3585 M /trunk/samtools/cleanup.sh
3589 ------------------------------------------------------------------------
3590 r249 | lh3lh3 | 2009-04-28 08:37:16 -0400 (Tue, 28 Apr 2009) | 2 lines
3592 M /trunk/samtools/Makefile.generic
3593 M /trunk/samtools/Makefile.lite
3594 M /trunk/samtools/configure.ac
3595 M /trunk/samtools/misc/Makefile.generic
3597 improve large file support in compilation
3599 ------------------------------------------------------------------------
3600 r248 | lh3lh3 | 2009-04-28 08:33:24 -0400 (Tue, 28 Apr 2009) | 2 lines
3602 M /trunk/samtools/INSTALL
3606 ------------------------------------------------------------------------
3607 r247 | lh3lh3 | 2009-04-28 08:28:50 -0400 (Tue, 28 Apr 2009) | 2 lines
3609 M /trunk/samtools/Makefile.am
3610 M /trunk/samtools/autogen.sh
3611 M /trunk/samtools/cleanup.sh
3612 M /trunk/samtools/configure.ac
3613 A /trunk/samtools/misc/Makefile.am
3615 fixed various issues about the GNU building scripts
3617 ------------------------------------------------------------------------
3618 r246 | lh3lh3 | 2009-04-28 08:10:23 -0400 (Tue, 28 Apr 2009) | 4 lines
3620 M /trunk/samtools/ChangeLog
3621 D /trunk/samtools/Makefile
3622 A /trunk/samtools/Makefile.am
3623 A /trunk/samtools/Makefile.generic
3624 A /trunk/samtools/autogen.sh
3625 M /trunk/samtools/bam.h
3626 M /trunk/samtools/bam_aux.c
3627 M /trunk/samtools/bam_tview.c
3628 M /trunk/samtools/bamtk.c
3629 A /trunk/samtools/cleanup.sh
3630 A /trunk/samtools/configure.ac
3631 D /trunk/samtools/misc/Makefile
3632 A /trunk/samtools/misc/Makefile.generic (from /trunk/samtools/misc/Makefile:245)
3634 * samtools-0.1.3-7 (r246)
3635 * incorporated revisions from Nils Homer
3636 * enhanced support of displaying color-space reads
3638 ------------------------------------------------------------------------
3639 r244 | lh3lh3 | 2009-04-25 06:49:40 -0400 (Sat, 25 Apr 2009) | 3 lines
3641 M /trunk/samtools/bam_md.c
3642 M /trunk/samtools/bamtk.c
3644 * samtools-0.1.3-6 (r244)
3645 * fixed segfault for unmapped reads
3647 ------------------------------------------------------------------------
3648 r243 | lh3lh3 | 2009-04-24 16:27:26 -0400 (Fri, 24 Apr 2009) | 5 lines
3650 M /trunk/samtools/bam.h
3651 M /trunk/samtools/bam_maqcns.c
3652 M /trunk/samtools/bam_md.c
3653 M /trunk/samtools/bamtk.c
3655 * samtools-0.1.3-5 (r243)
3656 * fixed a long existing bug which may cause memory leak
3658 * consensus calling now works with "=", but indel calling not
3660 ------------------------------------------------------------------------
3661 r242 | lh3lh3 | 2009-04-24 15:44:46 -0400 (Fri, 24 Apr 2009) | 3 lines
3663 M /trunk/samtools/bam_md.c
3664 M /trunk/samtools/bamtk.c
3666 * samtools-0.1.3-4 (r242)
3667 * fixed a memory leak
3669 ------------------------------------------------------------------------
3670 r240 | lh3lh3 | 2009-04-24 11:40:18 -0400 (Fri, 24 Apr 2009) | 5 lines
3672 M /trunk/samtools/Makefile
3673 M /trunk/samtools/Makefile.lite
3674 M /trunk/samtools/bam.h
3675 M /trunk/samtools/bam_aux.c
3676 A /trunk/samtools/bam_md.c
3677 M /trunk/samtools/bam_plcmd.c
3678 M /trunk/samtools/bamtk.c
3680 * samtools-0.1.3-3 (r240)
3682 * generate "=" bases
3683 * the plain pileup now support "=" bases, but consensus calling and glfgen may fail
3685 ------------------------------------------------------------------------
3686 r239 | lh3lh3 | 2009-04-24 07:08:20 -0400 (Fri, 24 Apr 2009) | 5 lines
3688 M /trunk/samtools/bam.h
3689 M /trunk/samtools/bam_aux.c
3690 M /trunk/samtools/bamtk.c
3692 * samtools-0.1.3-2 (r239)
3693 * fixed bugs in bam_aux.c (these functions nevered used by samtools)
3694 * removed bam_aux_init()/bam_aux_destroy()
3695 * added tagview for testing bam_aux
3697 ------------------------------------------------------------------------
3698 r235 | lh3lh3 | 2009-04-21 18:17:39 -0400 (Tue, 21 Apr 2009) | 3 lines
3700 M /trunk/samtools/bam_pileup.c
3701 M /trunk/samtools/bamtk.c
3704 * fixed a bug in pileup: the first read in a chromosome may not be printed
3706 ------------------------------------------------------------------------
3707 r232 | lh3lh3 | 2009-04-16 10:25:43 -0400 (Thu, 16 Apr 2009) | 2 lines
3709 M /trunk/samtools/Makefile.lite
3711 a missing file in Makefile.lite
3713 ------------------------------------------------------------------------
3714 r227 | lh3lh3 | 2009-04-15 17:02:53 -0400 (Wed, 15 Apr 2009) | 2 lines
3716 M /trunk/samtools/NEWS
3717 M /trunk/samtools/bamtk.c
3719 Release samtools-0.1.3
3721 ------------------------------------------------------------------------
3722 r223 | lh3lh3 | 2009-04-15 09:31:32 -0400 (Wed, 15 Apr 2009) | 3 lines
3724 M /trunk/samtools/bam_plcmd.c
3725 M /trunk/samtools/bamtk.c
3728 * make samtools more robust to weird input such as empty file
3730 ------------------------------------------------------------------------
3731 r222 | lh3lh3 | 2009-04-15 09:05:33 -0400 (Wed, 15 Apr 2009) | 2 lines
3733 M /trunk/samtools/ChangeLog
3734 M /trunk/samtools/NEWS
3735 M /trunk/samtools/samtools.1
3737 prepare for release 0.1.3
3739 ------------------------------------------------------------------------
3740 r221 | lh3lh3 | 2009-04-15 08:32:14 -0400 (Wed, 15 Apr 2009) | 2 lines
3742 A /trunk/samtools/misc/blast2sam.pl
3744 convert NCBI-BLASTN to SAM
3746 ------------------------------------------------------------------------
3747 r220 | lh3lh3 | 2009-04-15 08:18:19 -0400 (Wed, 15 Apr 2009) | 3 lines
3749 M /trunk/samtools/bam_lpileup.c
3750 M /trunk/samtools/bamtk.c
3753 * fixed a small memory leak in tview
3755 ------------------------------------------------------------------------
3756 r219 | lh3lh3 | 2009-04-15 08:00:08 -0400 (Wed, 15 Apr 2009) | 3 lines
3758 M /trunk/samtools/bam_rmdup.c
3759 M /trunk/samtools/bamtk.c
3762 * fixed a bug in rmdup when there are unmapped reads
3764 ------------------------------------------------------------------------
3765 r218 | lh3lh3 | 2009-04-14 17:28:58 -0400 (Tue, 14 Apr 2009) | 2 lines
3767 M /trunk/samtools/ChangeLog
3768 M /trunk/samtools/NEWS
3770 proposed NEWS for the new release (have not yet)
3772 ------------------------------------------------------------------------
3773 r216 | lh3lh3 | 2009-04-14 17:10:46 -0400 (Tue, 14 Apr 2009) | 4 lines
3775 M /trunk/samtools/misc/samtools.pl
3778 * improve indelFilter to avoid filtering true indels. The new filter relies
3779 on the new pileup indel line implemented in samtools-0.1.2-25
3781 ------------------------------------------------------------------------
3782 r215 | lh3lh3 | 2009-04-14 17:04:19 -0400 (Tue, 14 Apr 2009) | 4 lines
3784 M /trunk/samtools/bam_maqcns.c
3785 M /trunk/samtools/bam_plcmd.c
3786 M /trunk/samtools/bamtk.c
3787 M /trunk/samtools/samtools.1
3790 * change the pileup indel line to shows the number of alignments actually
3793 ------------------------------------------------------------------------
3794 r211 | lh3lh3 | 2009-04-13 07:07:13 -0400 (Mon, 13 Apr 2009) | 2 lines
3796 M /trunk/samtools/ChangeLog
3798 update ChangeLog from "svn log"
3800 ------------------------------------------------------------------------
3801 r210 | lh3lh3 | 2009-04-12 15:57:05 -0400 (Sun, 12 Apr 2009) | 4 lines
3803 M /trunk/samtools/bam.c
3804 M /trunk/samtools/bam_import.c
3805 M /trunk/samtools/bam_sort.c
3806 M /trunk/samtools/bamtk.c
3807 M /trunk/samtools/kseq.h
3810 * in merge, gives a warning rather than error if the target sequence length is different
3811 * allow empty header
3813 ------------------------------------------------------------------------
3814 r209 | lh3lh3 | 2009-04-12 15:32:44 -0400 (Sun, 12 Apr 2009) | 3 lines
3816 M /trunk/samtools/bam.c
3817 M /trunk/samtools/bam_import.c
3818 M /trunk/samtools/bamtk.c
3821 * recognize '*' at the QUAL field
3823 ------------------------------------------------------------------------
3824 r208 | lh3lh3 | 2009-04-12 15:08:02 -0400 (Sun, 12 Apr 2009) | 3 lines
3826 M /trunk/samtools/bam_import.c
3827 M /trunk/samtools/bamtk.c
3828 M /trunk/samtools/kseq.h
3831 * the field separater is TAB only, now
3833 ------------------------------------------------------------------------
3834 r207 | lh3lh3 | 2009-04-08 10:18:03 -0400 (Wed, 08 Apr 2009) | 2 lines
3836 M /trunk/samtools/examples/ex1.sam.gz
3838 * fixed the problem in the example alignment due to the bug in fixmate
3840 ------------------------------------------------------------------------
3841 r206 | lh3lh3 | 2009-04-08 10:15:05 -0400 (Wed, 08 Apr 2009) | 3 lines
3843 M /trunk/samtools/bam_mate.c
3844 M /trunk/samtools/bamtk.c
3845 M /trunk/samtools/misc/soap2sam.pl
3848 * fixed a nasty bug in `fixmate'
3850 ------------------------------------------------------------------------
3851 r205 | lh3lh3 | 2009-04-08 05:57:08 -0400 (Wed, 08 Apr 2009) | 2 lines
3853 M /trunk/samtools/misc/bowtie2sam.pl
3854 M /trunk/samtools/misc/soap2sam.pl
3855 M /trunk/samtools/misc/wgsim_eval.pl
3857 make the script robust to the bugs in SOAP-2.1.7
3859 ------------------------------------------------------------------------
3860 r200 | lh3lh3 | 2009-04-02 10:14:56 -0400 (Thu, 02 Apr 2009) | 3 lines
3862 M /trunk/samtools/bam_stat.c
3863 M /trunk/samtools/bamtk.c
3866 * check if file is truncated in flagstat
3868 ------------------------------------------------------------------------
3869 r199 | lh3lh3 | 2009-04-02 10:09:10 -0400 (Thu, 02 Apr 2009) | 3 lines
3871 M /trunk/samtools/bamtk.c
3874 * print the header if requested
3876 ------------------------------------------------------------------------
3877 r193 | lh3lh3 | 2009-03-27 11:09:50 -0400 (Fri, 27 Mar 2009) | 3 lines
3879 M /trunk/samtools/bam_plcmd.c
3880 M /trunk/samtools/bamtk.c
3883 * fixed a minor bug reported by Nils Homer
3885 ------------------------------------------------------------------------
3886 r185 | lh3lh3 | 2009-03-24 07:50:32 -0400 (Tue, 24 Mar 2009) | 2 lines
3888 A /trunk/samtools/Makefile (from /trunk/samtools/Makefile.std:184)
3889 D /trunk/samtools/Makefile.std
3890 A /trunk/samtools/misc/Makefile (from /trunk/samtools/misc/Makefile.std:184)
3891 D /trunk/samtools/misc/Makefile.std
3893 rename Makefile.std as Makefile. GNU building systerm is not ready and may take some time...
3895 ------------------------------------------------------------------------
3896 r184 | lh3lh3 | 2009-03-24 06:36:38 -0400 (Tue, 24 Mar 2009) | 4 lines
3898 D /trunk/samtools/Makefile
3899 A /trunk/samtools/Makefile.std (from /trunk/samtools/Makefile:183)
3900 M /trunk/samtools/bam_sort.c
3901 M /trunk/samtools/bam_tview.c
3902 M /trunk/samtools/bamtk.c
3903 D /trunk/samtools/misc/Makefile
3904 A /trunk/samtools/misc/Makefile.std (from /trunk/samtools/misc/Makefile:182)
3905 M /trunk/samtools/samtools.1
3908 * incorporating Nils' changes
3909 * rename Makefile to Makefile.std and prepare to add the GNU building systerms (also by Nils)
3911 ------------------------------------------------------------------------
3912 r183 | lh3lh3 | 2009-03-24 06:30:23 -0400 (Tue, 24 Mar 2009) | 4 lines
3914 M /trunk/samtools/Makefile
3915 M /trunk/samtools/bam_import.c
3916 M /trunk/samtools/bam_maqcns.c
3917 M /trunk/samtools/bam_maqcns.h
3918 M /trunk/samtools/bam_plcmd.c
3919 M /trunk/samtools/bamtk.c
3920 M /trunk/samtools/kseq.h
3921 A /trunk/samtools/kstring.c
3922 A /trunk/samtools/kstring.h
3925 * made pileup take a list of proposed indels. An insertion is N at the moment.
3926 * added my kstring library for a bit complex parsing of the position list.
3928 ------------------------------------------------------------------------
3929 r169 | lh3lh3 | 2009-03-12 09:40:14 -0400 (Thu, 12 Mar 2009) | 3 lines
3931 M /trunk/samtools/misc/soap2sam.pl
3934 * more robust to truncated soap output
3936 ------------------------------------------------------------------------
3937 r168 | lh3lh3 | 2009-03-11 06:49:00 -0400 (Wed, 11 Mar 2009) | 2 lines
3939 M /trunk/samtools/Makefile.lite
3941 added bam_stat.o to Makefile.lite
3943 ------------------------------------------------------------------------
3944 r167 | lh3lh3 | 2009-03-10 18:11:31 -0400 (Tue, 10 Mar 2009) | 3 lines
3946 M /trunk/samtools/bam_maqcns.c
3947 M /trunk/samtools/bamtk.c
3950 * generate RMS of mapQ instead of max mapQ
3952 ------------------------------------------------------------------------
3953 r166 | lh3lh3 | 2009-03-10 18:06:45 -0400 (Tue, 10 Mar 2009) | 3 lines
3955 M /trunk/samtools/bam_plcmd.c
3956 M /trunk/samtools/bamtk.c
3957 M /trunk/samtools/glf.c
3958 M /trunk/samtools/glf.h
3959 M /trunk/samtools/misc/Makefile
3964 ------------------------------------------------------------------------
3965 r159 | lh3lh3 | 2009-03-03 06:26:08 -0500 (Tue, 03 Mar 2009) | 3 lines
3967 M /trunk/samtools/bam_plcmd.c
3968 M /trunk/samtools/bamtk.c
3971 * fixed a minor bug in displaying pileup
3973 ------------------------------------------------------------------------
3974 r158 | lh3lh3 | 2009-03-03 06:24:16 -0500 (Tue, 03 Mar 2009) | 3 lines
3976 M /trunk/samtools/ChangeLog
3977 M /trunk/samtools/bamtk.c
3980 * optionally print SAM header
3982 ------------------------------------------------------------------------
3983 r153 | lh3lh3 | 2009-03-02 05:45:28 -0500 (Mon, 02 Mar 2009) | 3 lines
3985 M /trunk/samtools/bamtk.c
3986 M /trunk/samtools/glf.c
3989 * use "GLF\3" as the magic for GLFv3 files
3991 ------------------------------------------------------------------------
3992 r152 | lh3lh3 | 2009-03-02 05:39:09 -0500 (Mon, 02 Mar 2009) | 5 lines
3994 M /trunk/samtools/Makefile
3995 M /trunk/samtools/bam_import.c
3996 M /trunk/samtools/bam_index.c
3997 M /trunk/samtools/bam_plcmd.c
3998 M /trunk/samtools/bamtk.c
3999 M /trunk/samtools/glf.c
4000 M /trunk/samtools/glf.h
4003 * fixed a bug in import: core.bin is undefined for unmapped reads
4004 * this bug can be alleviated (not completely solved) in bam_index.c
4005 * update to GLFv3: pos is changed to offset for better compression
4007 ------------------------------------------------------------------------
4008 r151 | lh3lh3 | 2009-03-01 10:18:43 -0500 (Sun, 01 Mar 2009) | 3 lines
4010 M /trunk/samtools/misc/wgsim.c
4013 * fixed a bug in simulating indels
4015 ------------------------------------------------------------------------
4016 r145 | lh3lh3 | 2009-02-26 14:43:57 -0500 (Thu, 26 Feb 2009) | 4 lines
4018 M /trunk/samtools/misc/wgsim.c
4021 * allow to print mismatch information as fastq comment. MAQ does
4022 not like long read names.
4024 ------------------------------------------------------------------------
4025 r141 | lh3lh3 | 2009-02-26 09:53:03 -0500 (Thu, 26 Feb 2009) | 6 lines
4027 M /trunk/samtools/ChangeLog
4028 M /trunk/samtools/misc/wgsim.c
4029 M /trunk/samtools/misc/wgsim_eval.pl
4032 * fixed a bug about color read coordinates
4033 * fixed a bug in read names
4034 * wgsim_eval.pl-0.1.3
4035 * make the script work with color reads
4037 ------------------------------------------------------------------------
4038 r140 | lh3lh3 | 2009-02-26 09:02:57 -0500 (Thu, 26 Feb 2009) | 2 lines
4040 M /trunk/samtools/misc/Makefile
4041 M /trunk/samtools/misc/wgsim.c
4043 * wgsim: added a note
4045 ------------------------------------------------------------------------
4046 r139 | lh3lh3 | 2009-02-26 06:39:08 -0500 (Thu, 26 Feb 2009) | 7 lines
4048 M /trunk/samtools/misc/wgsim.c
4049 M /trunk/samtools/misc/wgsim_eval.pl
4052 * considerable code clean up
4053 * print number of substitutions/indels/errors on each read
4054 * potentially support SOLiD simulation, though not tested at the moment
4055 * wgsim_eval.pl-0.1.2
4056 * change in accordant with wgsim
4058 ------------------------------------------------------------------------
4059 r129 | lh3lh3 | 2009-02-18 17:23:27 -0500 (Wed, 18 Feb 2009) | 3 lines
4061 M /trunk/samtools/bam_index.c
4062 M /trunk/samtools/bamtk.c
4065 * fixed a bug in bam_fetch, caused by completely contained adjacent chunks
4067 ------------------------------------------------------------------------
4068 r128 | bhandsaker | 2009-02-18 14:06:57 -0500 (Wed, 18 Feb 2009) | 2 lines
4070 M /trunk/samtools/bamtk.c
4072 Fix annoying segv when invalid region specified.
4074 ------------------------------------------------------------------------
4075 r127 | lh3lh3 | 2009-02-17 05:49:55 -0500 (Tue, 17 Feb 2009) | 2 lines
4077 D /trunk/samtools/misc/indel_filter.pl
4078 A /trunk/samtools/misc/samtools.pl
4080 * move indel_filter.pl to samtools.pl
4082 ------------------------------------------------------------------------
4083 r126 | lh3lh3 | 2009-02-14 16:22:30 -0500 (Sat, 14 Feb 2009) | 3 lines
4085 M /trunk/samtools/bam_mate.c
4086 M /trunk/samtools/bamtk.c
4089 * fixed a bug in fixmate: SE reads are flagged as BAM_FMUNMAP
4091 ------------------------------------------------------------------------
4092 r125 | lh3lh3 | 2009-02-13 04:54:45 -0500 (Fri, 13 Feb 2009) | 3 lines
4094 M /trunk/samtools/bam_stat.c
4095 M /trunk/samtools/bamtk.c
4098 * fixed a minor bug in flagstat
4100 ------------------------------------------------------------------------
4101 r124 | lh3lh3 | 2009-02-12 06:15:32 -0500 (Thu, 12 Feb 2009) | 3 lines
4103 M /trunk/samtools/bam_maqcns.c
4104 M /trunk/samtools/bamtk.c
4105 M /trunk/samtools/misc/indel_filter.pl
4108 * improve indel caller by setting maximum window size
4110 ------------------------------------------------------------------------
4111 r123 | lh3lh3 | 2009-02-12 05:30:29 -0500 (Thu, 12 Feb 2009) | 2 lines
4113 M /trunk/samtools/bam_plcmd.c
4114 M /trunk/samtools/bamtk.c
4116 * output max mapping quality in indel line
4118 ------------------------------------------------------------------------
4119 r122 | lh3lh3 | 2009-02-11 05:59:10 -0500 (Wed, 11 Feb 2009) | 2 lines
4121 M /trunk/samtools/misc/maq2sam.c
4123 fixed a bug in generating tag AM
4125 ------------------------------------------------------------------------
4126 r121 | lh3lh3 | 2009-02-03 05:43:11 -0500 (Tue, 03 Feb 2009) | 2 lines
4128 M /trunk/samtools/bam_index.c
4129 M /trunk/samtools/bamtk.c
4131 fixed a potential memory problem in indexing
4133 ------------------------------------------------------------------------
4134 r120 | bhandsaker | 2009-02-02 10:52:52 -0500 (Mon, 02 Feb 2009) | 2 lines
4136 M /trunk/samtools/Makefile
4138 Pass LIBS to recursive targets to facilitate building at Broad.
4140 ------------------------------------------------------------------------
4141 r119 | lh3lh3 | 2009-02-02 05:12:15 -0500 (Mon, 02 Feb 2009) | 4 lines
4143 M /trunk/samtools/ChangeLog
4144 M /trunk/samtools/bam_plcmd.c
4145 M /trunk/samtools/bam_stat.c
4146 M /trunk/samtools/bamtk.c
4149 * fixed a bug in generating GLFv2 for indels
4150 * improve flagstat report a little bit
4152 ------------------------------------------------------------------------
4153 r118 | lh3lh3 | 2009-01-29 07:33:23 -0500 (Thu, 29 Jan 2009) | 3 lines
4155 M /trunk/samtools/Makefile
4156 A /trunk/samtools/bam_stat.c
4157 M /trunk/samtools/bamtk.c
4160 * added flagstat command
4162 ------------------------------------------------------------------------
4163 r116 | lh3lh3 | 2009-01-28 08:31:12 -0500 (Wed, 28 Jan 2009) | 2 lines
4165 M /trunk/samtools/ChangeLog
4166 M /trunk/samtools/NEWS
4167 M /trunk/samtools/bamtk.c
4168 M /trunk/samtools/samtools.1
4170 Release SAMtools-0.1.2
4172 ------------------------------------------------------------------------
4173 r115 | lh3lh3 | 2009-01-28 07:54:08 -0500 (Wed, 28 Jan 2009) | 2 lines
4175 A /trunk/samtools/misc/indel_filter.pl
4177 Script for filtering indel results
4179 ------------------------------------------------------------------------
4180 r114 | lh3lh3 | 2009-01-25 06:45:37 -0500 (Sun, 25 Jan 2009) | 2 lines
4182 A /trunk/samtools/misc/zoom2sam.pl
4186 ------------------------------------------------------------------------
4187 r113 | lh3lh3 | 2009-01-24 09:25:07 -0500 (Sat, 24 Jan 2009) | 2 lines
4189 A /trunk/samtools/misc/novo2sam.pl
4191 add a script to convert novo alignment to SAM
4193 ------------------------------------------------------------------------
4194 r112 | lh3lh3 | 2009-01-23 15:57:39 -0500 (Fri, 23 Jan 2009) | 2 lines
4196 M /trunk/samtools/ChangeLog
4197 M /trunk/samtools/ChangeLog.old
4198 M /trunk/samtools/samtools.1
4200 update documentation and ChangeLog
4202 ------------------------------------------------------------------------
4203 r111 | lh3lh3 | 2009-01-23 14:22:59 -0500 (Fri, 23 Jan 2009) | 3 lines
4205 M /trunk/samtools/bam_sort.c
4206 M /trunk/samtools/bamtk.c
4209 * fixed a bug in "merge" command line
4211 ------------------------------------------------------------------------
4212 r110 | lh3lh3 | 2009-01-22 10:36:48 -0500 (Thu, 22 Jan 2009) | 3 lines
4214 M /trunk/samtools/misc/Makefile
4215 A /trunk/samtools/misc/bowtie2sam.pl (from /branches/dev/samtools/misc/bowtie2sam.pl:108)
4216 M /trunk/samtools/misc/export2sam.pl
4217 A /trunk/samtools/misc/soap2sam.pl (from /branches/dev/samtools/misc/soap2sam.pl:108)
4218 A /trunk/samtools/misc/wgsim.c (from /branches/dev/samtools/misc/wgsim.c:108)
4219 A /trunk/samtools/misc/wgsim_eval.pl (from /branches/dev/samtools/misc/wgsim_eval.pl:108)
4221 * merge from branches/dev/
4222 * all future development will happen here
4224 ------------------------------------------------------------------------
4225 r109 | lh3lh3 | 2009-01-22 10:14:27 -0500 (Thu, 22 Jan 2009) | 3 lines
4227 M /trunk/samtools/COPYING
4228 M /trunk/samtools/ChangeLog
4229 A /trunk/samtools/INSTALL (from /branches/dev/samtools/INSTALL:108)
4230 M /trunk/samtools/Makefile
4231 A /trunk/samtools/Makefile.lite (from /branches/dev/samtools/Makefile.lite:108)
4232 M /trunk/samtools/bam.c
4233 M /trunk/samtools/bam.h
4234 M /trunk/samtools/bam_import.c
4235 M /trunk/samtools/bam_index.c
4236 M /trunk/samtools/bam_lpileup.c
4237 M /trunk/samtools/bam_maqcns.c
4238 M /trunk/samtools/bam_maqcns.h
4239 A /trunk/samtools/bam_mate.c (from /branches/dev/samtools/bam_mate.c:108)
4240 M /trunk/samtools/bam_pileup.c
4241 M /trunk/samtools/bam_plcmd.c
4242 A /trunk/samtools/bam_rmdup.c (from /branches/dev/samtools/bam_rmdup.c:108)
4243 M /trunk/samtools/bam_sort.c
4244 M /trunk/samtools/bamtk.c
4245 M /trunk/samtools/bgzf.h
4246 M /trunk/samtools/examples/00README.txt
4247 A /trunk/samtools/examples/Makefile (from /branches/dev/samtools/examples/Makefile:108)
4248 D /trunk/samtools/examples/ex1.fa.fai
4249 M /trunk/samtools/examples/ex1.sam.gz
4250 M /trunk/samtools/faidx.c
4251 A /trunk/samtools/glf.c (from /branches/dev/samtools/glf.c:108)
4252 M /trunk/samtools/glf.h
4253 M /trunk/samtools/misc/Makefile
4254 M /trunk/samtools/misc/maq2sam.c
4255 M /trunk/samtools/razf.c
4256 M /trunk/samtools/source.dot
4258 * Merge from branches/dev/
4259 * all future development will happen here at trunk/
4261 ------------------------------------------------------------------------
4262 r79 | bhandsaker | 2009-01-07 16:42:15 -0500 (Wed, 07 Jan 2009) | 2 lines
4264 M /trunk/samtools/bam_maqcns.c
4265 M /trunk/samtools/bam_tview.c
4267 Fix problem with compiling without curses.
4269 ------------------------------------------------------------------------
4270 r63 | lh3lh3 | 2008-12-22 10:58:02 -0500 (Mon, 22 Dec 2008) | 2 lines
4272 A /trunk/samtools (from /branches/dev/samtools:62)
4276 ------------------------------------------------------------------------
4277 r62 | lh3lh3 | 2008-12-22 10:55:13 -0500 (Mon, 22 Dec 2008) | 2 lines
4279 A /branches/dev/samtools/NEWS
4280 M /branches/dev/samtools/bamtk.c
4281 M /branches/dev/samtools/samtools.1
4283 Release samtools-0.1.1
4285 ------------------------------------------------------------------------
4286 r61 | lh3lh3 | 2008-12-22 10:46:08 -0500 (Mon, 22 Dec 2008) | 10 lines
4288 M /branches/dev/samtools/bam_aux.c
4289 M /branches/dev/samtools/bam_index.c
4290 M /branches/dev/samtools/bam_plcmd.c
4291 M /branches/dev/samtools/bam_tview.c
4292 M /branches/dev/samtools/bamtk.c
4293 M /branches/dev/samtools/razf.c
4294 M /branches/dev/samtools/samtools.1
4297 * fixed a bug in razf.c: reset z_eof when razf_seek() is called
4298 * fixed a memory leak in parsing a region
4299 * changed pileup a little bit when -s is in use: output ^ and $
4300 * when a bam is not indexed, output more meaningful error message
4301 * fixed a bug in indexing for small alignment
4302 * fixed a bug in the viewer when we come to the end of a reference file
4303 * updated documentation
4304 * prepare to release 0.1.1
4306 ------------------------------------------------------------------------
4307 r60 | lh3lh3 | 2008-12-22 10:10:16 -0500 (Mon, 22 Dec 2008) | 2 lines
4309 A /branches/dev/samtools/examples
4310 A /branches/dev/samtools/examples/00README.txt
4311 A /branches/dev/samtools/examples/ex1.fa
4312 A /branches/dev/samtools/examples/ex1.fa.fai
4313 A /branches/dev/samtools/examples/ex1.sam.gz
4317 ------------------------------------------------------------------------
4318 r59 | lh3lh3 | 2008-12-22 04:38:15 -0500 (Mon, 22 Dec 2008) | 2 lines
4320 M /branches/dev/samtools/ChangeLog
4324 ------------------------------------------------------------------------
4325 r58 | lh3lh3 | 2008-12-20 18:06:00 -0500 (Sat, 20 Dec 2008) | 3 lines
4327 M /branches/dev/samtools/misc/export2sam.pl
4330 * fixed several bugs
4332 ------------------------------------------------------------------------
4333 r57 | lh3lh3 | 2008-12-20 10:44:20 -0500 (Sat, 20 Dec 2008) | 2 lines
4335 A /branches/dev/samtools/misc/export2sam.pl
4337 convert Export format to SAM; not thoroughly tested
4339 ------------------------------------------------------------------------
4340 r56 | lh3lh3 | 2008-12-19 17:13:28 -0500 (Fri, 19 Dec 2008) | 6 lines
4342 M /branches/dev/samtools/bam_import.c
4343 M /branches/dev/samtools/bam_plcmd.c
4344 M /branches/dev/samtools/bam_tview.c
4345 M /branches/dev/samtools/bamtk.c
4346 A /branches/dev/samtools/source.dot
4349 * pileup: generate maq-like simple output
4350 * pileup: allow to output pileup at required sites
4351 * source.dot: source file relationship graph
4352 * tview: fixed a minor bug
4354 ------------------------------------------------------------------------
4355 r55 | lh3lh3 | 2008-12-19 15:10:26 -0500 (Fri, 19 Dec 2008) | 2 lines
4357 D /branches/dev/samtools/misc/all2sam.pl
4361 ------------------------------------------------------------------------
4362 r54 | lh3lh3 | 2008-12-16 17:34:25 -0500 (Tue, 16 Dec 2008) | 2 lines
4364 A /branches/dev/samtools/COPYING
4365 M /branches/dev/samtools/bam.h
4366 M /branches/dev/samtools/faidx.h
4367 M /branches/dev/samtools/khash.h
4368 M /branches/dev/samtools/kseq.h
4369 M /branches/dev/samtools/ksort.h
4370 M /branches/dev/samtools/samtools.1
4372 Added copyright information and a bit more documentation. No code change.
4374 ------------------------------------------------------------------------
4375 r53 | lh3lh3 | 2008-12-16 08:40:18 -0500 (Tue, 16 Dec 2008) | 3 lines
4377 M /branches/dev/samtools/bam.c
4378 M /branches/dev/samtools/bam.h
4379 M /branches/dev/samtools/bam_index.c
4380 M /branches/dev/samtools/bam_maqcns.c
4381 M /branches/dev/samtools/bamtk.c
4384 * improved efficiency of the indel caller for spliced alignments
4386 ------------------------------------------------------------------------
4387 r52 | lh3lh3 | 2008-12-16 05:28:20 -0500 (Tue, 16 Dec 2008) | 3 lines
4389 M /branches/dev/samtools/bam.c
4390 M /branches/dev/samtools/bam.h
4391 M /branches/dev/samtools/bam_aux.c
4392 M /branches/dev/samtools/bam_index.c
4393 M /branches/dev/samtools/bamtk.c
4396 * a bit code cleanup: reduce the dependency between source files
4398 ------------------------------------------------------------------------
4399 r51 | lh3lh3 | 2008-12-15 09:29:32 -0500 (Mon, 15 Dec 2008) | 3 lines
4401 M /branches/dev/samtools/bam_maqcns.c
4402 M /branches/dev/samtools/bam_plcmd.c
4403 M /branches/dev/samtools/bamtk.c
4406 * fixed a memory leak
4408 ------------------------------------------------------------------------
4409 r50 | lh3lh3 | 2008-12-15 09:00:13 -0500 (Mon, 15 Dec 2008) | 2 lines
4411 M /branches/dev/samtools/ChangeLog
4412 M /branches/dev/samtools/bam.h
4413 M /branches/dev/samtools/samtools.1
4415 update documentation, ChangeLog and a comment
4417 ------------------------------------------------------------------------
4418 r49 | lh3lh3 | 2008-12-15 08:36:43 -0500 (Mon, 15 Dec 2008) | 6 lines
4420 M /branches/dev/samtools/Makefile
4421 M /branches/dev/samtools/bam.h
4422 M /branches/dev/samtools/bam_maqcns.c
4423 M /branches/dev/samtools/bam_maqcns.h
4424 M /branches/dev/samtools/bam_pileup.c
4425 A /branches/dev/samtools/bam_plcmd.c
4426 M /branches/dev/samtools/bamtk.c
4427 M /branches/dev/samtools/samtools.1
4430 * moved pileup command to a separate source file
4431 * added indel caller
4432 * added bam_cal_segend(). (NOT WORKING for spliced alignment!!!)
4433 * updated documentation
4435 ------------------------------------------------------------------------
4436 r48 | lh3lh3 | 2008-12-12 08:55:36 -0500 (Fri, 12 Dec 2008) | 3 lines
4438 M /branches/dev/samtools/bam_maqcns.c
4439 M /branches/dev/samtools/bamtk.c
4442 * fixed another bug in maqcns when there is a nearby deletion
4444 ------------------------------------------------------------------------
4445 r47 | lh3lh3 | 2008-12-12 08:42:16 -0500 (Fri, 12 Dec 2008) | 5 lines
4447 M /branches/dev/samtools/bam_maqcns.c
4448 M /branches/dev/samtools/bam_pileup.c
4449 M /branches/dev/samtools/bamtk.c
4452 * pileup: outputing consensus is now optional
4453 * fixed a bug in glfgen. This bug also exists in maq's glfgen. However,
4454 I am not quite sure why the previous version may have problem.
4456 ------------------------------------------------------------------------
4457 r46 | lh3lh3 | 2008-12-12 06:44:56 -0500 (Fri, 12 Dec 2008) | 6 lines
4459 M /branches/dev/samtools/bam_pileup.c
4460 M /branches/dev/samtools/bamtk.c
4463 * add maq consensus to pileup. However, I will move this part to a new
4464 command as strictly speaking, consensus callin is not part of pileup,
4465 and imposing it would make it harder to generate for other language
4468 ------------------------------------------------------------------------
4469 r45 | bhandsaker | 2008-12-11 15:43:56 -0500 (Thu, 11 Dec 2008) | 2 lines
4471 M /branches/dev/samtools/bgzf.c
4473 Fix bug in tell() after reads that consume to the exact end of a block.
4475 ------------------------------------------------------------------------
4476 r44 | lh3lh3 | 2008-12-11 04:36:53 -0500 (Thu, 11 Dec 2008) | 2 lines
4478 M /branches/dev/samtools/samtools.1
4482 ------------------------------------------------------------------------
4483 r43 | lh3lh3 | 2008-12-11 04:25:36 -0500 (Thu, 11 Dec 2008) | 4 lines
4485 M /branches/dev/samtools/bam_import.c
4486 M /branches/dev/samtools/bamtk.c
4489 * fixed a bug in parser when there is auxiliary fields
4490 * made the parser a bit more robust
4492 ------------------------------------------------------------------------
4493 r42 | lh3lh3 | 2008-12-10 09:57:29 -0500 (Wed, 10 Dec 2008) | 5 lines
4495 M /branches/dev/samtools/bam_index.c
4496 M /branches/dev/samtools/bamtk.c
4497 M /branches/dev/samtools/bgzf.c
4500 * fixed a bug in bgzf (only reading is affected)
4501 * fixed a typo in bam_index.c
4502 * in bam_index.c, check potential bugs in the underlying I/O library
4504 ------------------------------------------------------------------------
4505 r41 | lh3lh3 | 2008-12-10 07:53:08 -0500 (Wed, 10 Dec 2008) | 2 lines
4507 M /branches/dev/samtools/samtools.1
4511 ------------------------------------------------------------------------
4512 r40 | lh3lh3 | 2008-12-10 06:52:10 -0500 (Wed, 10 Dec 2008) | 5 lines
4514 M /branches/dev/samtools/bam.h
4515 M /branches/dev/samtools/bam_pileup.c
4516 M /branches/dev/samtools/bamtk.c
4519 * tried to make pileup work with clipping (previously not), though NOT tested
4520 * removed -v from pileup
4521 * made pileup take the reference sequence
4523 ------------------------------------------------------------------------
4524 r39 | lh3lh3 | 2008-12-09 06:59:28 -0500 (Tue, 09 Dec 2008) | 4 lines
4526 M /branches/dev/samtools/bam_import.c
4527 M /branches/dev/samtools/bamtk.c
4528 M /branches/dev/samtools/samtools.1
4531 * in parser, recognize "=", rather than ",", as a match
4532 * in parser, correctl parse "=" at the MRNM field.
4534 ------------------------------------------------------------------------
4535 r38 | lh3lh3 | 2008-12-09 06:39:07 -0500 (Tue, 09 Dec 2008) | 2 lines
4537 M /branches/dev/samtools/misc/maq2sam.c
4539 fixed a bug in handling maq flag 64 and 192
4541 ------------------------------------------------------------------------
4542 r37 | lh3lh3 | 2008-12-09 04:53:46 -0500 (Tue, 09 Dec 2008) | 2 lines
4544 M /branches/dev/samtools/misc/md5fa.c
4546 also calculate unordered md5sum check
4548 ------------------------------------------------------------------------
4549 r36 | lh3lh3 | 2008-12-09 04:46:21 -0500 (Tue, 09 Dec 2008) | 2 lines
4551 M /branches/dev/samtools/misc/md5fa.c
4553 fixed a minor bug when there are space in the sequence
4555 ------------------------------------------------------------------------
4556 r35 | lh3lh3 | 2008-12-09 04:40:45 -0500 (Tue, 09 Dec 2008) | 2 lines
4558 M /branches/dev/samtools/misc/md5fa.c
4560 fixed a potential memory leak
4562 ------------------------------------------------------------------------
4563 r34 | lh3lh3 | 2008-12-08 09:52:17 -0500 (Mon, 08 Dec 2008) | 2 lines
4565 M /branches/dev/samtools/bam_import.c
4566 M /branches/dev/samtools/bam_index.c
4567 M /branches/dev/samtools/bamtk.c
4569 * fixed a bug in import: bin is wrongly calculated
4571 ------------------------------------------------------------------------
4572 r33 | lh3lh3 | 2008-12-08 09:08:01 -0500 (Mon, 08 Dec 2008) | 2 lines
4574 M /branches/dev/samtools/misc/all2sam.pl
4578 ------------------------------------------------------------------------
4579 r32 | lh3lh3 | 2008-12-08 07:56:02 -0500 (Mon, 08 Dec 2008) | 3 lines
4581 M /branches/dev/samtools/Makefile
4582 M /branches/dev/samtools/kseq.h
4583 M /branches/dev/samtools/misc/Makefile
4584 A /branches/dev/samtools/misc/md5.c
4585 A /branches/dev/samtools/misc/md5.h
4586 A /branches/dev/samtools/misc/md5fa.c
4588 * fixed two warnings in kseq.h
4589 * added md5sum utilities
4591 ------------------------------------------------------------------------
4592 r31 | lh3lh3 | 2008-12-08 06:35:29 -0500 (Mon, 08 Dec 2008) | 5 lines
4594 M /branches/dev/samtools/Makefile
4595 M /branches/dev/samtools/bam_import.c
4596 M /branches/dev/samtools/bamtk.c
4597 A /branches/dev/samtools/kseq.h
4598 D /branches/dev/samtools/kstream.h
4601 * replace kstream with kseq. kseq is a superset of kstream. I need the
4602 extra functions in kseq.h.
4603 * also compile stand-alone faidx
4605 ------------------------------------------------------------------------
4606 r30 | lh3lh3 | 2008-12-08 06:17:04 -0500 (Mon, 08 Dec 2008) | 3 lines
4608 M /branches/dev/samtools/bam.h
4609 M /branches/dev/samtools/bam_sort.c
4610 M /branches/dev/samtools/bamtk.c
4613 * sorting by read names is available
4615 ------------------------------------------------------------------------
4616 r29 | lh3lh3 | 2008-12-08 05:29:02 -0500 (Mon, 08 Dec 2008) | 3 lines
4618 M /branches/dev/samtools/bam.c
4619 M /branches/dev/samtools/bam.h
4620 M /branches/dev/samtools/bam_import.c
4621 M /branches/dev/samtools/bam_maqcns.c
4622 M /branches/dev/samtools/bam_pileup.c
4623 M /branches/dev/samtools/bam_sort.c
4624 M /branches/dev/samtools/bam_tview.c
4625 M /branches/dev/samtools/bamtk.c
4626 M /branches/dev/samtools/misc/maq2sam.c
4629 * format change to meet the latest specification
4631 ------------------------------------------------------------------------
4632 r28 | lh3lh3 | 2008-12-04 11:09:21 -0500 (Thu, 04 Dec 2008) | 3 lines
4634 M /branches/dev/samtools/bam_maqcns.c
4635 M /branches/dev/samtools/misc/maq2sam.c
4637 * minor change in maqcns: special care when n==0
4638 * change maq2sam to meet the latest specification
4640 ------------------------------------------------------------------------
4641 r27 | lh3lh3 | 2008-12-04 10:55:44 -0500 (Thu, 04 Dec 2008) | 2 lines
4643 M /branches/dev/samtools/razf.c
4644 M /branches/dev/samtools/razf.h
4646 considerable code clean up in razf
4648 ------------------------------------------------------------------------
4649 r26 | lh3lh3 | 2008-12-04 10:08:18 -0500 (Thu, 04 Dec 2008) | 2 lines
4651 M /branches/dev/samtools/ChangeLog
4652 M /branches/dev/samtools/Makefile
4653 M /branches/dev/samtools/faidx.c
4655 make RAZF optional in faidx.c
4657 ------------------------------------------------------------------------
4658 r25 | lh3lh3 | 2008-12-01 10:27:22 -0500 (Mon, 01 Dec 2008) | 3 lines
4660 M /branches/dev/samtools/Makefile
4661 M /branches/dev/samtools/bam.h
4662 M /branches/dev/samtools/bam_aux.c
4663 M /branches/dev/samtools/bamtk.c
4664 M /branches/dev/samtools/samtools.1
4667 * added routines for retrieving aux data, NOT TESTED YET!
4669 ------------------------------------------------------------------------
4670 r24 | lh3lh3 | 2008-12-01 09:29:43 -0500 (Mon, 01 Dec 2008) | 5 lines
4672 M /branches/dev/samtools/bam.c
4673 M /branches/dev/samtools/bam_import.c
4674 M /branches/dev/samtools/bam_maqcns.c
4675 M /branches/dev/samtools/bamtk.c
4676 M /branches/dev/samtools/bgzf.c
4677 M /branches/dev/samtools/samtools.1
4680 * bgzf: fixed a potential integer overflow on 32-it machines
4681 * maqcns: set the minimum combined quality as 0
4682 * supporting hex strings
4684 ------------------------------------------------------------------------
4685 r23 | lh3lh3 | 2008-11-27 12:14:37 -0500 (Thu, 27 Nov 2008) | 3 lines
4687 M /branches/dev/samtools/bam_maqcns.c
4688 M /branches/dev/samtools/bamtk.c
4691 * fixed the bug in maqcns
4693 ------------------------------------------------------------------------
4694 r22 | lh3lh3 | 2008-11-27 12:08:11 -0500 (Thu, 27 Nov 2008) | 3 lines
4696 M /branches/dev/samtools/Makefile
4697 M /branches/dev/samtools/bam.h
4698 A /branches/dev/samtools/bam_maqcns.c
4699 A /branches/dev/samtools/bam_maqcns.h
4700 M /branches/dev/samtools/bam_tview.c
4701 M /branches/dev/samtools/bamtk.c
4702 A /branches/dev/samtools/glf.h
4705 * add MAQ consensus caller, currently BUGGY!
4707 ------------------------------------------------------------------------
4708 r21 | lh3lh3 | 2008-11-27 08:51:28 -0500 (Thu, 27 Nov 2008) | 4 lines
4710 M /branches/dev/samtools/bam_pileup.c
4711 M /branches/dev/samtools/bam_tview.c
4712 M /branches/dev/samtools/bamtk.c
4715 * tview: display padded alignment (but not P operation)
4716 * better coordinates and reference sequence
4718 ------------------------------------------------------------------------
4719 r19 | lh3lh3 | 2008-11-27 04:26:05 -0500 (Thu, 27 Nov 2008) | 2 lines
4721 A /branches/dev/samtools/ChangeLog
4725 ------------------------------------------------------------------------
4726 r18 | lh3lh3 | 2008-11-27 04:24:45 -0500 (Thu, 27 Nov 2008) | 3 lines
4728 D /branches/dev/samtools/ChangeLog
4729 A /branches/dev/samtools/ChangeLog.old (from /branches/dev/samtools/ChangeLog:6)
4731 Rename ChangeLog to ChangeLog.old. This old ChangeLog is generated from
4732 the log of my personal SVN repository.
4734 ------------------------------------------------------------------------
4735 r17 | lh3lh3 | 2008-11-27 04:22:55 -0500 (Thu, 27 Nov 2008) | 6 lines
4737 M /branches/dev/samtools/Makefile
4738 M /branches/dev/samtools/bamtk.c
4739 M /branches/dev/samtools/bgzf.c
4742 * declare fseeko and ftello as some Linux may not do this by default and
4743 missing these declarations will make bgzf buggy
4744 * get rid of some harmless warings
4745 * use BGZF by default, now
4747 ------------------------------------------------------------------------
4748 r16 | lh3lh3 | 2008-11-26 16:19:11 -0500 (Wed, 26 Nov 2008) | 4 lines
4750 M /branches/dev/samtools/bam_index.c
4751 M /branches/dev/samtools/bamtk.c
4752 M /branches/dev/samtools/razf.c
4755 * fixed a bug in razf_read()
4756 * give more warnings when the file is truncated (or due to bugs in I/O library)
4758 ------------------------------------------------------------------------
4759 r15 | lh3lh3 | 2008-11-26 15:41:39 -0500 (Wed, 26 Nov 2008) | 2 lines
4761 M /branches/dev/samtools/bgzf.c
4763 fixed a bug in bgzf.c at the end of the file
4765 ------------------------------------------------------------------------
4766 r14 | lh3lh3 | 2008-11-26 12:05:18 -0500 (Wed, 26 Nov 2008) | 4 lines
4768 M /branches/dev/samtools/bamtk.c
4771 * a lot happened to RAZF, although samtools itself is untouched. Better
4772 also update the version number anyway to avoid confusion
4774 ------------------------------------------------------------------------
4775 r13 | lh3lh3 | 2008-11-26 12:03:48 -0500 (Wed, 26 Nov 2008) | 2 lines
4777 M /branches/dev/samtools/razf.c
4779 a change from Jue, but I think it should not matter
4781 ------------------------------------------------------------------------
4782 r12 | lh3lh3 | 2008-11-26 11:48:14 -0500 (Wed, 26 Nov 2008) | 3 lines
4784 M /branches/dev/samtools/razf.c
4786 fixed a potential bug in razf. However, it seems still buggy, just
4787 rarely happens, very rarely.
4789 ------------------------------------------------------------------------
4790 r11 | lh3lh3 | 2008-11-26 09:02:56 -0500 (Wed, 26 Nov 2008) | 2 lines
4792 M /branches/dev/samtools/razf.c
4794 fixed a bug in razf, with the help of Jue
4796 ------------------------------------------------------------------------
4797 r10 | lh3lh3 | 2008-11-26 06:55:32 -0500 (Wed, 26 Nov 2008) | 2 lines
4799 M /branches/dev/samtools/bam_index.c
4803 ------------------------------------------------------------------------
4804 r9 | lh3lh3 | 2008-11-26 06:37:05 -0500 (Wed, 26 Nov 2008) | 2 lines
4806 M /branches/dev/samtools/Makefile
4807 M /branches/dev/samtools/bam.h
4808 M /branches/dev/samtools/razf.c
4809 M /branches/dev/samtools/razf.h
4811 * Jue has updated razf to realize Bob's scheme
4813 ------------------------------------------------------------------------
4814 r7 | lh3lh3 | 2008-11-25 15:37:37 -0500 (Tue, 25 Nov 2008) | 2 lines
4816 A /branches/dev/samtools/samtools.1
4820 ------------------------------------------------------------------------
4821 r6 | lh3lh3 | 2008-11-25 15:37:16 -0500 (Tue, 25 Nov 2008) | 3 lines
4823 A /branches/dev/samtools/ChangeLog
4824 A /branches/dev/samtools/Makefile
4825 A /branches/dev/samtools/bam.c
4826 A /branches/dev/samtools/bam.h
4827 A /branches/dev/samtools/bam_aux.c
4828 A /branches/dev/samtools/bam_endian.h
4829 A /branches/dev/samtools/bam_import.c
4830 A /branches/dev/samtools/bam_index.c
4831 A /branches/dev/samtools/bam_lpileup.c
4832 A /branches/dev/samtools/bam_pileup.c
4833 A /branches/dev/samtools/bam_sort.c
4834 A /branches/dev/samtools/bam_tview.c
4835 A /branches/dev/samtools/bamtk.c
4836 A /branches/dev/samtools/bgzf.c
4837 A /branches/dev/samtools/bgzf.h
4838 A /branches/dev/samtools/bgzip.c
4839 A /branches/dev/samtools/faidx.c
4840 A /branches/dev/samtools/faidx.h
4841 A /branches/dev/samtools/khash.h
4842 A /branches/dev/samtools/ksort.h
4843 A /branches/dev/samtools/kstream.h
4844 A /branches/dev/samtools/misc
4845 A /branches/dev/samtools/misc/Makefile
4846 A /branches/dev/samtools/misc/all2sam.pl
4847 A /branches/dev/samtools/misc/maq2sam.c
4848 A /branches/dev/samtools/razf.c
4849 A /branches/dev/samtools/razf.h
4850 A /branches/dev/samtools/razip.c
4851 A /branches/dev/samtools/zutil.h
4853 The initial version of samtools, replicated from my local SVN repository.
4854 The current version is: 0.1.0-42. All future development will happen here.
4856 ------------------------------------------------------------------------
4857 r5 | lh3lh3 | 2008-11-25 15:30:49 -0500 (Tue, 25 Nov 2008) | 2 lines
4859 A /branches/dev/samtools
4861 samtools (C version)
4863 ------------------------------------------------------------------------