1 ------------------------------------------------------------------------
2 r780 | lh3lh3 | 2010-10-27 11:01:11 -0400 (Wed, 27 Oct 2010) | 3 lines
4 M /trunk/samtools/bam.h
5 M /trunk/samtools/bam_plcmd.c
6 M /trunk/samtools/bamtk.c
8 * samtools-0.1.8-21 (r780)
9 * minor speedup to pileup
11 ------------------------------------------------------------------------
12 r779 | lh3lh3 | 2010-10-27 09:58:56 -0400 (Wed, 27 Oct 2010) | 2 lines
14 M /trunk/samtools/bam_pileup.c
15 M /trunk/samtools/bam_plcmd.c
16 M /trunk/samtools/examples/toy.sam
18 improve pileup a little bit
20 ------------------------------------------------------------------------
21 r778 | lh3lh3 | 2010-10-27 00:14:43 -0400 (Wed, 27 Oct 2010) | 3 lines
23 M /trunk/samtools/bam.h
24 M /trunk/samtools/bam_pileup.c
25 M /trunk/samtools/bam_plcmd.c
26 M /trunk/samtools/bam_tview.c
27 M /trunk/samtools/bamtk.c
29 * samtools-0.1.8-20 (r778)
30 * speed up pileup, although I do not know how much is the improvement
32 ------------------------------------------------------------------------
33 r777 | lh3lh3 | 2010-10-26 17:26:04 -0400 (Tue, 26 Oct 2010) | 3 lines
35 M /trunk/samtools/bam_maqcns.c
36 M /trunk/samtools/bam_maqcns.h
37 M /trunk/samtools/bam_plcmd.c
38 M /trunk/samtools/bamtk.c
39 M /trunk/samtools/examples/Makefile
41 * samtools-0.1.8-19 (r777)
42 * integrate mpileup features to pileup: min_baseQ, capQ, prob_realn, paired-only and biased prior
44 ------------------------------------------------------------------------
45 r776 | lh3lh3 | 2010-10-26 15:27:46 -0400 (Tue, 26 Oct 2010) | 2 lines
47 M /trunk/samtools/bam_md.c
49 remove local realignment (probabilistic realignment is still there)
51 ------------------------------------------------------------------------
52 r774 | jmarshall | 2010-10-21 06:52:38 -0400 (Thu, 21 Oct 2010) | 3 lines
54 M /trunk/samtools/sam_view.c
56 Add the relevant filename or region to error messages, and cause a failure
57 exit status where appropriate. Based on a patch provided by Marcel Martin.
59 ------------------------------------------------------------------------
60 r773 | lh3lh3 | 2010-10-19 19:44:31 -0400 (Tue, 19 Oct 2010) | 3 lines
62 M /trunk/samtools/examples/toy.sam
63 M /trunk/samtools/kaln.c
65 * Minor code changes. No real effect.
66 * change quality to 30 in toy.sam
68 ------------------------------------------------------------------------
69 r772 | lh3lh3 | 2010-10-18 23:40:13 -0400 (Mon, 18 Oct 2010) | 2 lines
71 M /trunk/samtools/examples/toy.fa
72 M /trunk/samtools/examples/toy.sam
74 added another toy example
76 ------------------------------------------------------------------------
77 r771 | lh3lh3 | 2010-10-13 23:32:12 -0400 (Wed, 13 Oct 2010) | 2 lines
79 M /trunk/samtools/bcftools/call1.c
80 M /trunk/samtools/bcftools/ld.c
81 M /trunk/samtools/bcftools/vcfutils.pl
83 improve the LD statistics
85 ------------------------------------------------------------------------
86 r770 | lh3lh3 | 2010-10-12 23:49:26 -0400 (Tue, 12 Oct 2010) | 3 lines
88 M /trunk/samtools/bcftools/call1.c
89 M /trunk/samtools/bcftools/vcfutils.pl
91 * a minor fix to the -L option
92 * add ldstats to vcfutils.pl
94 ------------------------------------------------------------------------
95 r769 | lh3lh3 | 2010-10-12 15:51:57 -0400 (Tue, 12 Oct 2010) | 2 lines
97 M /trunk/samtools/bcftools/bcf.c
101 ------------------------------------------------------------------------
102 r768 | lh3lh3 | 2010-10-12 15:49:06 -0400 (Tue, 12 Oct 2010) | 2 lines
104 M /trunk/samtools/bcftools/Makefile
105 A /trunk/samtools/bcftools/ld.c
107 forget to add the key file
109 ------------------------------------------------------------------------
110 r767 | lh3lh3 | 2010-10-12 15:48:46 -0400 (Tue, 12 Oct 2010) | 4 lines
112 M /trunk/samtools/bcftools/Makefile
113 M /trunk/samtools/bcftools/bcf.c
114 M /trunk/samtools/bcftools/bcf.h
115 M /trunk/samtools/bcftools/call1.c
116 M /trunk/samtools/bcftools/prob1.c
117 M /trunk/samtools/bcftools/vcfutils.pl
119 * vcfutils.pl: fixed a typo in help message
120 * added APIs: bcf_append_info() and bcf_cpy()
121 * calculate adjacent LD
123 ------------------------------------------------------------------------
124 r766 | lh3lh3 | 2010-10-11 11:06:40 -0400 (Mon, 11 Oct 2010) | 2 lines
126 M /trunk/samtools/bcftools/vcfutils.pl
128 added filter for samtools/bcftools genetated VCFs
130 ------------------------------------------------------------------------
131 r765 | lh3lh3 | 2010-10-05 14:05:18 -0400 (Tue, 05 Oct 2010) | 3 lines
133 M /trunk/samtools/bcftools/vcfutils.pl
134 M /trunk/samtools/kaln.c
136 * removed a comment line in kaln.c
137 * vcfutils.pl fillac works when GT is not the first field
139 ------------------------------------------------------------------------
140 r764 | petulda | 2010-10-05 08:59:36 -0400 (Tue, 05 Oct 2010) | 1 line
142 A /trunk/samtools/bcftools/bcf-fix.pl
144 Convert VCF output of "bcftools view -bgcv" to a valid VCF file
145 ------------------------------------------------------------------------
146 r763 | lh3lh3 | 2010-10-02 22:51:03 -0400 (Sat, 02 Oct 2010) | 4 lines
148 M /trunk/samtools/bam_plcmd.c
149 M /trunk/samtools/bamtk.c
150 A /trunk/samtools/bcftools/bcftools.1
151 M /trunk/samtools/bcftools/call1.c
152 M /trunk/samtools/samtools.1
154 * samtools-0.1.8-18 (r763)
155 * added bcftools manual page
156 * minor fix to mpileup and view command lines
158 ------------------------------------------------------------------------
159 r762 | lh3lh3 | 2010-10-02 21:46:25 -0400 (Sat, 02 Oct 2010) | 3 lines
161 M /trunk/samtools/bcftools/bcf.c
162 M /trunk/samtools/bcftools/call1.c
163 M /trunk/samtools/bcftools/vcfutils.pl
165 * vcfutils.pl qstats: calculate marginal ts/tv
166 * allow to call genotypes at variant sites
168 ------------------------------------------------------------------------
169 r761 | lh3lh3 | 2010-10-01 00:29:55 -0400 (Fri, 01 Oct 2010) | 3 lines
171 M /trunk/samtools/kaln.c
172 M /trunk/samtools/misc/HmmGlocal.java
174 I am changing the gap open probability back to 0.001. It seems that
175 being conservative here is a good thing...
177 ------------------------------------------------------------------------
178 r760 | lh3lh3 | 2010-10-01 00:11:27 -0400 (Fri, 01 Oct 2010) | 5 lines
180 M /trunk/samtools/bamtk.c
181 M /trunk/samtools/kaln.c
182 A /trunk/samtools/misc/HmmGlocal.java
184 * samtools-0.1.8-17 (r760)
185 * the default gap open penalty is too small (a typo)
186 * added comments on hmm_realn
187 * Java implementation
189 ------------------------------------------------------------------------
190 r759 | lh3lh3 | 2010-09-30 10:12:54 -0400 (Thu, 30 Sep 2010) | 2 lines
192 M /trunk/samtools/bamtk.c
194 mark samtools-0.1.8-16 (r759)
196 ------------------------------------------------------------------------
197 r758 | lh3lh3 | 2010-09-30 10:12:02 -0400 (Thu, 30 Sep 2010) | 2 lines
199 M /trunk/samtools/kaln.c
201 round to the nearest integer
203 ------------------------------------------------------------------------
204 r757 | lh3lh3 | 2010-09-28 17:16:43 -0400 (Tue, 28 Sep 2010) | 4 lines
206 M /trunk/samtools/kaln.c
208 I was trying to accelerate ka_prob_glocal() as this will be the
209 bottleneck. After an hour, the only gain is to change division to
210 multiplication. OK. I will stop.
212 ------------------------------------------------------------------------
213 r756 | lh3lh3 | 2010-09-28 16:57:49 -0400 (Tue, 28 Sep 2010) | 2 lines
215 M /trunk/samtools/kaln.c
217 this is interesting. multiplication is much faster than division, at least on my Mac
219 ------------------------------------------------------------------------
220 r755 | lh3lh3 | 2010-09-28 16:19:13 -0400 (Tue, 28 Sep 2010) | 2 lines
222 M /trunk/samtools/kaln.c
226 ------------------------------------------------------------------------
227 r754 | lh3lh3 | 2010-09-28 15:44:16 -0400 (Tue, 28 Sep 2010) | 2 lines
229 M /trunk/samtools/bam_md.c
230 M /trunk/samtools/bam_plcmd.c
231 M /trunk/samtools/kaln.c
233 prob_realn() seems working!
235 ------------------------------------------------------------------------
236 r753 | lh3lh3 | 2010-09-28 12:48:23 -0400 (Tue, 28 Sep 2010) | 2 lines
238 M /trunk/samtools/kaln.c
242 ------------------------------------------------------------------------
243 r752 | lh3lh3 | 2010-09-28 12:47:41 -0400 (Tue, 28 Sep 2010) | 2 lines
245 M /trunk/samtools/kaln.c
246 M /trunk/samtools/kaln.h
248 Convert phredQ to probabilities
250 ------------------------------------------------------------------------
251 r751 | lh3lh3 | 2010-09-28 12:32:08 -0400 (Tue, 28 Sep 2010) | 2 lines
253 M /trunk/samtools/kaln.c
254 M /trunk/samtools/kaln.h
256 Implement the glocal HMM; discard the extention HMM
258 ------------------------------------------------------------------------
259 r750 | lh3lh3 | 2010-09-28 00:06:11 -0400 (Tue, 28 Sep 2010) | 2 lines
261 M /trunk/samtools/kaln.c
263 improve numerical stability
265 ------------------------------------------------------------------------
266 r749 | lh3lh3 | 2010-09-27 23:27:54 -0400 (Mon, 27 Sep 2010) | 2 lines
268 M /trunk/samtools/kaln.c
272 ------------------------------------------------------------------------
273 r748 | lh3lh3 | 2010-09-27 23:17:16 -0400 (Mon, 27 Sep 2010) | 2 lines
275 M /trunk/samtools/kaln.c
277 fixed a bug in banded DP
279 ------------------------------------------------------------------------
280 r747 | lh3lh3 | 2010-09-27 23:05:12 -0400 (Mon, 27 Sep 2010) | 3 lines
282 M /trunk/samtools/kaln.c
284 * fixed that weird issue.
285 * the banded version is NOT working
287 ------------------------------------------------------------------------
288 r746 | lh3lh3 | 2010-09-27 22:57:05 -0400 (Mon, 27 Sep 2010) | 2 lines
290 M /trunk/samtools/kaln.c
292 More comments. This version seems working, but something is a little weird...
294 ------------------------------------------------------------------------
295 r745 | lh3lh3 | 2010-09-27 17:21:40 -0400 (Mon, 27 Sep 2010) | 6 lines
297 M /trunk/samtools/kaln.c
299 A little code cleanup. Now the forward and backback algorithms give
300 nearly identical P(x), which means both are close to the correct
301 forms. However, I have only tested on toy examples. Minor errors in
302 the implementation may not be obvious.
305 ------------------------------------------------------------------------
306 r744 | lh3lh3 | 2010-09-27 16:55:15 -0400 (Mon, 27 Sep 2010) | 2 lines
308 M /trunk/samtools/bam_plcmd.c
309 M /trunk/samtools/bam_sort.c
310 M /trunk/samtools/kaln.c
311 M /trunk/samtools/kaln.h
315 ------------------------------------------------------------------------
316 r743 | jmarshall | 2010-09-27 08:19:06 -0400 (Mon, 27 Sep 2010) | 6 lines
318 M /trunk/samtools/bam_sort.c
320 Abort if merge -h's INH.SAM cannot be opened, just as we abort
321 if any of the IN#.BAM input files cannot be opened.
323 Also propagate any error indication returned by bam_merge_core()
324 to samtools merge's exit status.
326 ------------------------------------------------------------------------
327 r741 | jmarshall | 2010-09-24 11:08:24 -0400 (Fri, 24 Sep 2010) | 5 lines
329 M /trunk/samtools/bam_index.c
331 Use bam_validate1() to detect garbage records in the event of a corrupt
332 BAI index file that causes a bam_seek() to an invalid position. At most
333 one record (namely, the bam_iter_read terminator) is tested per bam_fetch()
334 call, so the cost is insignificant in the normal case.
336 ------------------------------------------------------------------------
337 r740 | jmarshall | 2010-09-24 11:00:19 -0400 (Fri, 24 Sep 2010) | 2 lines
339 M /trunk/samtools/bam.c
340 M /trunk/samtools/bam.h
344 ------------------------------------------------------------------------
345 r739 | lh3lh3 | 2010-09-22 12:07:50 -0400 (Wed, 22 Sep 2010) | 3 lines
347 M /trunk/samtools/bam_md.c
348 M /trunk/samtools/bamtk.c
350 * samtools-0.1.8-15 (r379)
351 * allow to change capQ parameter in calmd
353 ------------------------------------------------------------------------
354 r738 | jmarshall | 2010-09-22 11:15:33 -0400 (Wed, 22 Sep 2010) | 13 lines
356 M /trunk/samtools/bam_index.c
357 M /trunk/samtools/sam_view.c
359 When bam_read1() returns an error (return value <= -2), propagate that error
360 to bam_iter_read()'s own return value. Similarly, also propagate it up to
361 bam_fetch()'s return value. Previously bam_fetch() always returned 0, and
362 callers ignored its return value anyway. With this change, 0 continues to
363 indicate success, while <= -2 (which can be written as < 0, as -1 is never
364 returned) indicates corrupted input.
366 bam_iter_read() ought also to propagate errors returned by bam_seek().
368 main_samview() can now print an error message and fail when bam_fetch()
369 detects that a .bai index file is corrupted or otherwise does not correspond
370 to the .bam file it is being used with.
372 ------------------------------------------------------------------------
373 r737 | jmarshall | 2010-09-22 10:47:42 -0400 (Wed, 22 Sep 2010) | 3 lines
375 M /trunk/samtools/bam_index.c
377 0 is a successful return value from bam_read1(). (In practice, it never
378 returns 0 anyway; but all the other callers treat 0 as successful.)
380 ------------------------------------------------------------------------
381 r736 | lh3lh3 | 2010-09-20 17:43:08 -0400 (Mon, 20 Sep 2010) | 2 lines
383 M /trunk/samtools/bam.h
384 M /trunk/samtools/bam_index.c
385 M /trunk/samtools/bam_sort.c
387 * merge files region-by-region. work on small examples but more tests are needed.
389 ------------------------------------------------------------------------
390 r735 | lh3lh3 | 2010-09-20 16:56:24 -0400 (Mon, 20 Sep 2010) | 2 lines
392 M /trunk/samtools/bcftools/vcfutils.pl
394 improve qstats by checking the alleles as well
396 ------------------------------------------------------------------------
397 r734 | lh3lh3 | 2010-09-17 18:12:13 -0400 (Fri, 17 Sep 2010) | 2 lines
399 M /trunk/samtools/bcftools/vcfutils.pl
401 convert UCSC SNP SQL dump to VCF
403 ------------------------------------------------------------------------
404 r733 | lh3lh3 | 2010-09-17 13:02:11 -0400 (Fri, 17 Sep 2010) | 2 lines
406 M /trunk/samtools/bcftools/vcfutils.pl
410 ------------------------------------------------------------------------
411 r732 | lh3lh3 | 2010-09-17 10:11:37 -0400 (Fri, 17 Sep 2010) | 3 lines
413 M /trunk/samtools/bcftools/Makefile
414 M /trunk/samtools/bcftools/bcf.c
415 M /trunk/samtools/bcftools/bcf.h
416 M /trunk/samtools/bcftools/vcf.c
419 * VCF->BCF is not possible without knowing the sequence dictionary before hand...
421 ------------------------------------------------------------------------
422 r731 | lh3lh3 | 2010-09-17 09:15:53 -0400 (Fri, 17 Sep 2010) | 2 lines
424 M /trunk/samtools/bam2bcf.c
425 M /trunk/samtools/bcftools/bcf.c
426 M /trunk/samtools/bcftools/bcf.h
427 M /trunk/samtools/bcftools/bcfutils.c
428 M /trunk/samtools/bcftools/call1.c
429 M /trunk/samtools/bcftools/vcf.c
431 * put n_smpl to "bcf1_t" to simplify API a little
433 ------------------------------------------------------------------------
434 r730 | lh3lh3 | 2010-09-16 21:36:01 -0400 (Thu, 16 Sep 2010) | 2 lines
436 M /trunk/samtools/bcftools/bcf.h
437 M /trunk/samtools/bcftools/call1.c
438 M /trunk/samtools/bcftools/index.c
440 fixed a bug in indexing
442 ------------------------------------------------------------------------
443 r729 | lh3lh3 | 2010-09-16 16:54:48 -0400 (Thu, 16 Sep 2010) | 3 lines
445 M /trunk/samtools/bam.c
446 M /trunk/samtools/bam_md.c
447 M /trunk/samtools/bam_pileup.c
449 * fixed a bug in capQ
450 * valgrind identifies a use of uninitialised value, but I have not fixed it.
452 ------------------------------------------------------------------------
453 r728 | lh3lh3 | 2010-09-16 15:03:59 -0400 (Thu, 16 Sep 2010) | 3 lines
455 M /trunk/samtools/bgzip.c
456 M /trunk/samtools/razip.c
458 * fixed a bug in razip: -c will delete the input file
459 * copy tabix/bgzip to here
461 ------------------------------------------------------------------------
462 r727 | lh3lh3 | 2010-09-16 13:45:49 -0400 (Thu, 16 Sep 2010) | 3 lines
464 M /trunk/samtools/bam_md.c
465 M /trunk/samtools/bam_plcmd.c
466 M /trunk/samtools/bamtk.c
468 * samtools-0.1.8-14 (r727)
469 * allow to change the capQ parameter at the command line
471 ------------------------------------------------------------------------
472 r726 | lh3lh3 | 2010-09-16 13:38:43 -0400 (Thu, 16 Sep 2010) | 4 lines
474 M /trunk/samtools/bam_md.c
475 M /trunk/samtools/bam_plcmd.c
476 M /trunk/samtools/bcftools/vcfutils.pl
477 M /trunk/samtools/misc/samtools.pl
479 * added varFilter to vcfutils.pl
480 * reimplement realn(). now it performs a local alignment
481 * added cap_mapQ() to cap mapping quality when there are many substitutions
483 ------------------------------------------------------------------------
484 r724 | lh3lh3 | 2010-09-15 00:18:31 -0400 (Wed, 15 Sep 2010) | 2 lines
486 M /trunk/samtools/bcftools/Makefile
487 A /trunk/samtools/bcftools/bcf2qcall.c
488 M /trunk/samtools/bcftools/call1.c
490 * convert BCF to QCALL input
492 ------------------------------------------------------------------------
493 r723 | lh3lh3 | 2010-09-14 22:41:50 -0400 (Tue, 14 Sep 2010) | 2 lines
495 M /trunk/samtools/bam_md.c
497 dynamic band width in realignment
499 ------------------------------------------------------------------------
500 r722 | lh3lh3 | 2010-09-14 22:05:32 -0400 (Tue, 14 Sep 2010) | 2 lines
502 M /trunk/samtools/bam_md.c
503 M /trunk/samtools/bam_plcmd.c
505 fixed a bug in realignment
507 ------------------------------------------------------------------------
508 r721 | lh3lh3 | 2010-09-14 20:54:09 -0400 (Tue, 14 Sep 2010) | 2 lines
510 M /trunk/samtools/bcftools/prob1.c
514 ------------------------------------------------------------------------
515 r720 | lh3lh3 | 2010-09-14 19:25:10 -0400 (Tue, 14 Sep 2010) | 2 lines
517 M /trunk/samtools/Makefile
518 M /trunk/samtools/bam_maqcns.c
519 M /trunk/samtools/bam_md.c
521 fixed a bug in realignment
523 ------------------------------------------------------------------------
524 r719 | lh3lh3 | 2010-09-14 19:18:24 -0400 (Tue, 14 Sep 2010) | 2 lines
526 M /trunk/samtools/bam_plcmd.c
528 minor changes. It is BUGGY now!
530 ------------------------------------------------------------------------
531 r718 | lh3lh3 | 2010-09-14 16:32:33 -0400 (Tue, 14 Sep 2010) | 4 lines
533 M /trunk/samtools/bam_md.c
534 M /trunk/samtools/bam_pileup.c
535 M /trunk/samtools/kaln.c
536 M /trunk/samtools/kaln.h
538 * aggressive gapped aligner is implemented in calmd.
539 * distinguish gap_open and gap_end_open in banded alignment
540 * make tview accepts alignment with heading and tailing D
542 ------------------------------------------------------------------------
543 r717 | jmarshall | 2010-09-14 09:04:28 -0400 (Tue, 14 Sep 2010) | 2 lines
547 Add svn:ignore properties for generated files that don't appear in "make all".
549 ------------------------------------------------------------------------
550 r716 | jmarshall | 2010-09-13 08:37:53 -0400 (Mon, 13 Sep 2010) | 3 lines
553 M /trunk/samtools/bcftools
554 M /trunk/samtools/misc
556 Add svn:ignore properties listing the generated files.
557 (Except for *.o, which we'll assume is in global-ignores.)
559 ------------------------------------------------------------------------
560 r715 | lh3lh3 | 2010-09-08 12:53:55 -0400 (Wed, 08 Sep 2010) | 5 lines
562 M /trunk/samtools/bamtk.c
563 M /trunk/samtools/bcftools/call1.c
564 M /trunk/samtools/bcftools/prob1.c
565 M /trunk/samtools/sample.c
566 M /trunk/samtools/sample.h
568 * samtools-0.1.8-13 (r715)
569 * fixed a bug in identifying SM across files
570 * bcftools: estimate heterozygosity
571 * bcftools: allow to skip sites without reference bases
573 ------------------------------------------------------------------------
574 r713 | lh3lh3 | 2010-09-03 17:19:12 -0400 (Fri, 03 Sep 2010) | 2 lines
576 M /trunk/samtools/bcftools/Makefile
577 M /trunk/samtools/bcftools/call1.c
578 M /trunk/samtools/bcftools/prob1.c
579 M /trunk/samtools/bcftools/prob1.h
581 quite a lot changes to the contrast caller, but I still feel something is missing...
583 ------------------------------------------------------------------------
584 r711 | lh3lh3 | 2010-09-03 00:30:48 -0400 (Fri, 03 Sep 2010) | 4 lines
586 M /trunk/samtools/bcftools/Makefile
587 M /trunk/samtools/bcftools/call1.c
588 M /trunk/samtools/bcftools/prob1.c
589 M /trunk/samtools/bcftools/vcfutils.pl
591 * changed 3.434 to 4.343 (typo!)
592 * fixed a bug in the contrast caller
593 * calculate heterozygosity
595 ------------------------------------------------------------------------
596 r710 | lh3lh3 | 2010-09-01 23:24:47 -0400 (Wed, 01 Sep 2010) | 2 lines
598 M /trunk/samtools/bcftools/bcf.h
599 M /trunk/samtools/bcftools/bcfutils.c
600 M /trunk/samtools/bcftools/call1.c
602 SNP calling from the GL field
604 ------------------------------------------------------------------------
605 r709 | lh3lh3 | 2010-09-01 18:52:30 -0400 (Wed, 01 Sep 2010) | 2 lines
607 M /trunk/samtools/bcftools/vcf.c
609 fixed another problem
611 ------------------------------------------------------------------------
612 r708 | lh3lh3 | 2010-09-01 18:31:17 -0400 (Wed, 01 Sep 2010) | 3 lines
614 M /trunk/samtools/bcftools/bcf.c
615 M /trunk/samtools/bcftools/vcf.c
617 * fixed bugs in parsing VCF
618 * parser now works with GT/GQ/DP/PL/GL
620 ------------------------------------------------------------------------
621 r707 | lh3lh3 | 2010-09-01 15:28:29 -0400 (Wed, 01 Sep 2010) | 2 lines
623 M /trunk/samtools/bcftools/Makefile
624 M /trunk/samtools/bcftools/prob1.c
626 Do not compile _BCF_QUAD by default
628 ------------------------------------------------------------------------
629 r706 | lh3lh3 | 2010-09-01 15:21:41 -0400 (Wed, 01 Sep 2010) | 2 lines
631 M /trunk/samtools/bcftools/bcf.c
632 M /trunk/samtools/bcftools/bcf.h
633 M /trunk/samtools/bcftools/bcfutils.c
634 M /trunk/samtools/bcftools/call1.c
636 Write the correct ALT and PL in the SNP calling mode.
638 ------------------------------------------------------------------------
639 r705 | lh3lh3 | 2010-09-01 12:50:33 -0400 (Wed, 01 Sep 2010) | 2 lines
641 M /trunk/samtools/bcftools/vcfutils.pl
643 more commands for my own uses
645 ------------------------------------------------------------------------
646 r704 | lh3lh3 | 2010-09-01 09:26:10 -0400 (Wed, 01 Sep 2010) | 2 lines
648 A /trunk/samtools/bcftools/vcfutils.pl
650 Utilities for processing VCF
652 ------------------------------------------------------------------------
653 r703 | lh3lh3 | 2010-08-31 16:44:57 -0400 (Tue, 31 Aug 2010) | 2 lines
655 M /trunk/samtools/bcftools/Makefile
656 M /trunk/samtools/bcftools/call1.c
657 M /trunk/samtools/bcftools/prob1.c
658 M /trunk/samtools/bcftools/prob1.h
660 preliminary contrast variant caller
662 ------------------------------------------------------------------------
663 r702 | lh3lh3 | 2010-08-31 12:28:39 -0400 (Tue, 31 Aug 2010) | 2 lines
665 M /trunk/samtools/bcftools/call1.c
666 M /trunk/samtools/bcftools/prob1.c
667 M /trunk/samtools/bcftools/prob1.h
669 z' and z'' can be calculated
671 ------------------------------------------------------------------------
672 r701 | lh3lh3 | 2010-08-31 10:20:57 -0400 (Tue, 31 Aug 2010) | 3 lines
674 M /trunk/samtools/bcftools/Makefile
675 A /trunk/samtools/bcftools/call1.c (from /trunk/samtools/bcftools/vcfout.c:699)
676 M /trunk/samtools/bcftools/prob1.c
677 D /trunk/samtools/bcftools/vcfout.c
679 * rename vcfout.c as call1.c
680 * prepare to add two-sample comparison
682 ------------------------------------------------------------------------
683 r699 | lh3lh3 | 2010-08-24 15:28:16 -0400 (Tue, 24 Aug 2010) | 2 lines
685 M /trunk/samtools/bcftools/vcfout.c
687 fixed a bug in calculating the t statistics
689 ------------------------------------------------------------------------
690 r698 | lh3lh3 | 2010-08-24 14:05:50 -0400 (Tue, 24 Aug 2010) | 3 lines
692 M /trunk/samtools/bam2bcf.c
693 M /trunk/samtools/bam2bcf.h
694 M /trunk/samtools/bamtk.c
695 M /trunk/samtools/bcftools/kfunc.c
696 M /trunk/samtools/bcftools/vcfout.c
698 * samtools-0.1.8-13 (r698)
699 * perform one-tailed t-test for baseQ, mapQ and endDist
701 ------------------------------------------------------------------------
702 r697 | lh3lh3 | 2010-08-24 12:30:13 -0400 (Tue, 24 Aug 2010) | 2 lines
704 M /trunk/samtools/bcftools/kfunc.c
706 added regularized incomplete beta function
708 ------------------------------------------------------------------------
709 r695 | lh3lh3 | 2010-08-23 17:36:17 -0400 (Mon, 23 Aug 2010) | 2 lines
711 M /trunk/samtools/bam_maqcns.c
712 M /trunk/samtools/bam_plcmd.c
714 change the default correlation coefficient
716 ------------------------------------------------------------------------
717 r694 | lh3lh3 | 2010-08-23 14:46:52 -0400 (Mon, 23 Aug 2010) | 2 lines
719 M /trunk/samtools/bcftools/bcf.c
720 M /trunk/samtools/bcftools/vcfout.c
722 print QUAL as floating numbers
724 ------------------------------------------------------------------------
725 r693 | lh3lh3 | 2010-08-23 14:06:07 -0400 (Mon, 23 Aug 2010) | 3 lines
727 M /trunk/samtools/Makefile
728 M /trunk/samtools/bam_plcmd.c
729 M /trunk/samtools/bamtk.c
730 M /trunk/samtools/examples/Makefile
731 A /trunk/samtools/sample.c
732 A /trunk/samtools/sample.h
734 * samtools-0.1.8-12 (r692)
735 * group data by samples in "mpileup -g"
737 ------------------------------------------------------------------------
738 r692 | lh3lh3 | 2010-08-23 10:58:53 -0400 (Mon, 23 Aug 2010) | 2 lines
740 M /trunk/samtools/Makefile
741 D /trunk/samtools/bam_mcns.c
742 D /trunk/samtools/bam_mcns.h
743 M /trunk/samtools/bam_plcmd.c
745 remove VCF output in mpileup
747 ------------------------------------------------------------------------
748 r691 | lh3lh3 | 2010-08-23 10:48:20 -0400 (Mon, 23 Aug 2010) | 3 lines
750 M /trunk/samtools/bam2bcf.c
751 M /trunk/samtools/bam2bcf.h
753 * use the revised MAQ error model for mpileup
754 * prepare to remove the independent model from mpileup
756 ------------------------------------------------------------------------
757 r690 | lh3lh3 | 2010-08-20 15:46:40 -0400 (Fri, 20 Aug 2010) | 2 lines
759 M /trunk/samtools/Makefile
760 M /trunk/samtools/bam_maqcns.c
761 M /trunk/samtools/bam_maqcns.h
762 M /trunk/samtools/bam_plcmd.c
763 A /trunk/samtools/errmod.c
764 A /trunk/samtools/errmod.h
765 M /trunk/samtools/ksort.h
767 added revised MAQ error model
769 ------------------------------------------------------------------------
770 r689 | lh3lh3 | 2010-08-18 09:55:20 -0400 (Wed, 18 Aug 2010) | 2 lines
772 M /trunk/samtools/bcftools/prob1.c
773 M /trunk/samtools/bcftools/prob1.h
774 M /trunk/samtools/bcftools/vcfout.c
776 allow to read the prior from the error output. EM iteration is working.
778 ------------------------------------------------------------------------
779 r688 | lh3lh3 | 2010-08-17 12:12:20 -0400 (Tue, 17 Aug 2010) | 3 lines
781 M /trunk/samtools/bcftools/main.c
782 M /trunk/samtools/bcftools/vcf.c
784 * write a little more VCF header
787 ------------------------------------------------------------------------
788 r687 | lh3lh3 | 2010-08-16 20:53:16 -0400 (Mon, 16 Aug 2010) | 2 lines
790 M /trunk/samtools/bcftools/bcf.c
791 M /trunk/samtools/bcftools/bcf.h
792 M /trunk/samtools/bcftools/bcf.tex
796 ------------------------------------------------------------------------
797 r686 | lh3lh3 | 2010-08-14 00:11:13 -0400 (Sat, 14 Aug 2010) | 2 lines
799 M /trunk/samtools/bcftools/bcf.c
800 M /trunk/samtools/bcftools/prob1.c
802 faster for large sample size (in principle)
804 ------------------------------------------------------------------------
805 r685 | lh3lh3 | 2010-08-13 23:28:31 -0400 (Fri, 13 Aug 2010) | 4 lines
807 M /trunk/samtools/bcftools/prob1.c
809 * a numerically stable method to calculate z_{jk}
810 * currently slower than the old method but will be important for large sample size
811 * in principle, we can speed up for large n, but have not tried
813 ------------------------------------------------------------------------
814 r684 | lh3lh3 | 2010-08-11 21:58:31 -0400 (Wed, 11 Aug 2010) | 2 lines
816 M /trunk/samtools/bcftools/vcfout.c
818 fixed an issue in parsing integer
820 ------------------------------------------------------------------------
821 r683 | lh3lh3 | 2010-08-09 13:05:07 -0400 (Mon, 09 Aug 2010) | 2 lines
823 M /trunk/samtools/bcftools/bcf.c
825 do not print refname if file is converted from VCF
827 ------------------------------------------------------------------------
828 r682 | lh3lh3 | 2010-08-09 12:59:47 -0400 (Mon, 09 Aug 2010) | 3 lines
830 M /trunk/samtools/bcftools/vcf.c
833 * fixed a bug in parsing VCF
835 ------------------------------------------------------------------------
836 r681 | lh3lh3 | 2010-08-09 12:49:23 -0400 (Mon, 09 Aug 2010) | 4 lines
838 M /trunk/samtools/bcftools/bcf.c
839 M /trunk/samtools/bcftools/bcf.h
840 M /trunk/samtools/bcftools/bcfutils.c
841 M /trunk/samtools/bcftools/main.c
842 M /trunk/samtools/bcftools/vcf.c
843 M /trunk/samtools/bcftools/vcfout.c
844 M /trunk/samtools/bgzf.c
845 M /trunk/samtools/kstring.c
847 * fixed a bug in kstrtok@kstring.c
848 * preliminary VCF parser (not parse everything for now)
849 * improved view interface
851 ------------------------------------------------------------------------
852 r680 | lh3lh3 | 2010-08-09 10:43:13 -0400 (Mon, 09 Aug 2010) | 4 lines
854 M /trunk/samtools/bcftools/bcf.c
855 M /trunk/samtools/bcftools/bcf.h
856 M /trunk/samtools/bcftools/vcfout.c
857 M /trunk/samtools/kstring.c
858 M /trunk/samtools/kstring.h
860 * improved kstring (added kstrtok)
861 * removed the limit on the format string length in bcftools
862 * use kstrtok to parse format which fixed a bug in the old code
864 ------------------------------------------------------------------------
865 r679 | lh3lh3 | 2010-08-09 01:12:05 -0400 (Mon, 09 Aug 2010) | 2 lines
867 A /trunk/samtools/bcftools/README
868 M /trunk/samtools/bcftools/vcfout.c
872 ------------------------------------------------------------------------
873 r678 | lh3lh3 | 2010-08-09 00:01:52 -0400 (Mon, 09 Aug 2010) | 2 lines
875 M /trunk/samtools/bcftools/vcfout.c
877 perform single-tail test for ED4
879 ------------------------------------------------------------------------
880 r677 | lh3lh3 | 2010-08-08 23:48:35 -0400 (Sun, 08 Aug 2010) | 2 lines
882 M /trunk/samtools/bcftools/Makefile
883 M /trunk/samtools/bcftools/kfunc.c
884 M /trunk/samtools/bcftools/vcfout.c
886 * test depth, end distance and HWE
888 ------------------------------------------------------------------------
889 r676 | lh3lh3 | 2010-08-08 02:04:15 -0400 (Sun, 08 Aug 2010) | 2 lines
891 M /trunk/samtools/bcftools/kfunc.c
893 reimplement incomplete gamma functions. no copy-paste
895 ------------------------------------------------------------------------
896 r675 | lh3lh3 | 2010-08-06 22:42:54 -0400 (Fri, 06 Aug 2010) | 3 lines
898 M /trunk/samtools/bam2bcf.c
899 M /trunk/samtools/bam2bcf.h
900 M /trunk/samtools/bcftools/fet.c
901 M /trunk/samtools/bcftools/prob1.c
902 M /trunk/samtools/bcftools/prob1.h
903 M /trunk/samtools/bcftools/vcfout.c
905 * bcftools: add HWE (no testing for now)
906 * record end dist in a 2x2 table, not avg, std any more
908 ------------------------------------------------------------------------
909 r674 | lh3lh3 | 2010-08-06 17:30:16 -0400 (Fri, 06 Aug 2010) | 3 lines
911 A /trunk/samtools/bcftools/kfunc.c
913 * Special functions: log(gamma()), erfc(), P(a,x) (incomplete gamma)
914 * Not using Numerical Recipe due to licensing issues
916 ------------------------------------------------------------------------
917 r673 | lh3lh3 | 2010-08-05 23:46:53 -0400 (Thu, 05 Aug 2010) | 2 lines
919 A /trunk/samtools/bcftools/fet.c
923 ------------------------------------------------------------------------
924 r672 | lh3lh3 | 2010-08-05 21:48:33 -0400 (Thu, 05 Aug 2010) | 3 lines
926 M /trunk/samtools/bam2bcf.c
927 M /trunk/samtools/bam2bcf.h
928 M /trunk/samtools/bamtk.c
929 M /trunk/samtools/examples/Makefile
931 * samtools-0.1.8-11 (r672)
932 * collect more stats for allele balance test in bcftools (not yet)
934 ------------------------------------------------------------------------
935 r671 | lh3lh3 | 2010-08-05 16:17:58 -0400 (Thu, 05 Aug 2010) | 3 lines
937 M /trunk/samtools/bam_plcmd.c
938 M /trunk/samtools/bcftools/bcf.c
939 M /trunk/samtools/bcftools/main.c
941 * the code base is stablized again.
942 * I will delay the vcf parser, which is quite complicated but with little value for now
944 ------------------------------------------------------------------------
945 r670 | lh3lh3 | 2010-08-05 16:03:23 -0400 (Thu, 05 Aug 2010) | 2 lines
947 M /trunk/samtools/examples/Makefile
951 ------------------------------------------------------------------------
952 r669 | lh3lh3 | 2010-08-05 16:03:08 -0400 (Thu, 05 Aug 2010) | 2 lines
954 M /trunk/samtools/bcftools/vcf.c
956 unfinished vcf parser
958 ------------------------------------------------------------------------
959 r668 | lh3lh3 | 2010-08-05 15:46:40 -0400 (Thu, 05 Aug 2010) | 3 lines
961 M /trunk/samtools/bcftools/Makefile
962 M /trunk/samtools/bcftools/bcf.c
963 M /trunk/samtools/bcftools/bcf.h
964 M /trunk/samtools/bcftools/bcfutils.c
965 M /trunk/samtools/bcftools/index.c
966 M /trunk/samtools/bcftools/main.c
967 A /trunk/samtools/bcftools/vcf.c
968 M /trunk/samtools/bcftools/vcfout.c
970 * added prelimiary VCF parser (not finished)
971 * change struct a bit
973 ------------------------------------------------------------------------
974 r667 | lh3lh3 | 2010-08-03 22:35:27 -0400 (Tue, 03 Aug 2010) | 3 lines
976 M /trunk/samtools/bam2bcf.c
977 M /trunk/samtools/bam2bcf.h
978 M /trunk/samtools/bam_plcmd.c
979 M /trunk/samtools/bcftools/bcf.c
981 * allow to set min base q
982 * fixed a bug in mpileup -u
984 ------------------------------------------------------------------------
985 r666 | lh3lh3 | 2010-08-03 22:08:44 -0400 (Tue, 03 Aug 2010) | 2 lines
987 A /trunk/samtools/bcftools/bcf.tex
991 ------------------------------------------------------------------------
992 r665 | lh3lh3 | 2010-08-03 21:18:57 -0400 (Tue, 03 Aug 2010) | 2 lines
994 M /trunk/samtools/examples/Makefile
998 ------------------------------------------------------------------------
999 r664 | lh3lh3 | 2010-08-03 21:13:00 -0400 (Tue, 03 Aug 2010) | 2 lines
1001 M /trunk/samtools/Makefile
1002 M /trunk/samtools/bam2bcf.c
1003 M /trunk/samtools/bam2bcf.h
1004 M /trunk/samtools/bcftools/Makefile
1006 fixed compilation error
1008 ------------------------------------------------------------------------
1009 r662 | lh3lh3 | 2010-08-03 21:04:00 -0400 (Tue, 03 Aug 2010) | 2 lines
1011 M /trunk/samtools/Makefile
1012 D /trunk/samtools/bcf.c
1013 D /trunk/samtools/bcf.h
1014 A /trunk/samtools/bcftools
1015 A /trunk/samtools/bcftools/Makefile
1016 A /trunk/samtools/bcftools/bcf.c
1017 A /trunk/samtools/bcftools/bcf.h
1018 A /trunk/samtools/bcftools/bcfutils.c
1019 A /trunk/samtools/bcftools/index.c
1020 A /trunk/samtools/bcftools/main.c
1021 A /trunk/samtools/bcftools/prob1.c
1022 A /trunk/samtools/bcftools/prob1.h
1023 A /trunk/samtools/bcftools/vcfout.c
1025 move bcftools to samtools
1027 ------------------------------------------------------------------------
1028 r660 | lh3lh3 | 2010-08-03 15:58:32 -0400 (Tue, 03 Aug 2010) | 2 lines
1030 M /trunk/samtools/bam2bcf.c
1032 fixed another minor bug
1034 ------------------------------------------------------------------------
1035 r658 | lh3lh3 | 2010-08-03 15:06:45 -0400 (Tue, 03 Aug 2010) | 3 lines
1037 M /trunk/samtools/bamtk.c
1038 M /trunk/samtools/bcf.c
1040 * samtools-0.1.8-10 (r658)
1041 * fixed a bug in bam2bcf when the reference is N
1043 ------------------------------------------------------------------------
1044 r657 | lh3lh3 | 2010-08-03 14:50:23 -0400 (Tue, 03 Aug 2010) | 3 lines
1046 M /trunk/samtools/bam2bcf.c
1047 M /trunk/samtools/bam2bcf.h
1050 * treat ambiguous ref base as the fifth base
1052 ------------------------------------------------------------------------
1053 r654 | lh3lh3 | 2010-08-02 17:38:27 -0400 (Mon, 02 Aug 2010) | 2 lines
1055 M /trunk/bcftools/bcf.c
1056 M /trunk/samtools/bcf.c
1058 missing a column in VCF output...
1060 ------------------------------------------------------------------------
1061 r653 | lh3lh3 | 2010-08-02 17:31:33 -0400 (Mon, 02 Aug 2010) | 2 lines
1063 M /trunk/samtools/bcf.c
1067 ------------------------------------------------------------------------
1068 r651 | lh3lh3 | 2010-08-02 17:27:31 -0400 (Mon, 02 Aug 2010) | 2 lines
1070 M /trunk/samtools/bcf.c
1072 fixed a bug in bcf reader
1074 ------------------------------------------------------------------------
1075 r650 | lh3lh3 | 2010-08-02 17:00:41 -0400 (Mon, 02 Aug 2010) | 2 lines
1077 M /trunk/samtools/bam2bcf.c
1081 ------------------------------------------------------------------------
1082 r649 | lh3lh3 | 2010-08-02 16:49:35 -0400 (Mon, 02 Aug 2010) | 3 lines
1084 M /trunk/samtools/Makefile
1085 M /trunk/samtools/bam2bcf.c
1086 M /trunk/samtools/bam2bcf.h
1087 M /trunk/samtools/bamtk.c
1089 * samtools-0.1.8-9 (r649)
1090 * lossless representation of PL in BCF output
1092 ------------------------------------------------------------------------
1093 r648 | lh3lh3 | 2010-08-02 16:07:25 -0400 (Mon, 02 Aug 2010) | 2 lines
1095 M /trunk/samtools/Makefile
1096 A /trunk/samtools/bam2bcf.c
1097 A /trunk/samtools/bam2bcf.h
1098 M /trunk/samtools/bam_plcmd.c
1099 A /trunk/samtools/bcf.c
1100 A /trunk/samtools/bcf.h
1104 ------------------------------------------------------------------------
1105 r644 | lh3lh3 | 2010-07-28 11:59:19 -0400 (Wed, 28 Jul 2010) | 5 lines
1107 M /trunk/samtools/bam_mcns.c
1108 M /trunk/samtools/bamtk.c
1110 * samtools-0.1.8-8 (r644)
1111 * mpileup becomes a little stable again
1112 * the method is slightly different, but is more theoretically correct
1113 * snp calling is O(n^2) instead of O(n^3)
1115 ------------------------------------------------------------------------
1116 r643 | lh3lh3 | 2010-07-28 11:54:15 -0400 (Wed, 28 Jul 2010) | 3 lines
1118 M /trunk/samtools/bam_mcns.c
1120 * fixed a STUPID bug, which cost me a lot of time.
1121 * I am going to clean up mcns a little bit
1123 ------------------------------------------------------------------------
1124 r642 | lh3lh3 | 2010-07-27 23:23:07 -0400 (Tue, 27 Jul 2010) | 2 lines
1126 M /trunk/samtools/bam_mcns.c
1127 M /trunk/samtools/bam_mcns.h
1128 M /trunk/samtools/bam_plcmd.c
1130 supposedly this is THE correct implementation, but more testing is needed
1132 ------------------------------------------------------------------------
1133 r641 | lh3lh3 | 2010-07-27 22:43:39 -0400 (Tue, 27 Jul 2010) | 2 lines
1135 M /trunk/samtools/bam_mcns.c
1137 NOT ready yet. Going to make further changes...
1139 ------------------------------------------------------------------------
1140 r639 | lh3lh3 | 2010-07-25 22:18:38 -0400 (Sun, 25 Jul 2010) | 3 lines
1142 M /trunk/samtools/bam_mcns.c
1143 M /trunk/samtools/bam_plcmd.c
1144 M /trunk/samtools/bamtk.c
1146 * samtools-0.1.8-7 (r639)
1147 * fixed the reference allele assignment
1149 ------------------------------------------------------------------------
1150 r638 | lh3lh3 | 2010-07-25 12:01:26 -0400 (Sun, 25 Jul 2010) | 5 lines
1152 M /trunk/samtools/bam_mcns.c
1153 M /trunk/samtools/bam_mcns.h
1154 M /trunk/samtools/bam_plcmd.c
1155 M /trunk/samtools/bamtk.c
1157 * samtools-0.1.8-6 (r638)
1158 * skip isnan/isinf in case of float underflow
1159 * added the flat prior
1160 * fixed an issue where there are no reads supporting the reference
1162 ------------------------------------------------------------------------
1163 r637 | lh3lh3 | 2010-07-24 14:16:27 -0400 (Sat, 24 Jul 2010) | 2 lines
1165 M /trunk/samtools/bam_plcmd.c
1169 ------------------------------------------------------------------------
1170 r636 | lh3lh3 | 2010-07-24 14:07:27 -0400 (Sat, 24 Jul 2010) | 2 lines
1172 M /trunk/samtools/bam_mcns.c
1173 M /trunk/samtools/bam_mcns.h
1174 M /trunk/samtools/bam_plcmd.c
1175 M /trunk/samtools/bamtk.c
1179 ------------------------------------------------------------------------
1180 r635 | lh3lh3 | 2010-07-24 01:49:49 -0400 (Sat, 24 Jul 2010) | 2 lines
1182 M /trunk/samtools/bam_mcns.c
1183 M /trunk/samtools/bam_mcns.h
1184 M /trunk/samtools/bam_plcmd.c
1186 posterior expectation FINALLY working. I am so tired...
1188 ------------------------------------------------------------------------
1189 r633 | lh3lh3 | 2010-07-23 13:50:48 -0400 (Fri, 23 Jul 2010) | 2 lines
1191 M /trunk/samtools/bam_plcmd.c
1193 another minor fix to mpileup
1195 ------------------------------------------------------------------------
1196 r632 | lh3lh3 | 2010-07-23 13:43:31 -0400 (Fri, 23 Jul 2010) | 2 lines
1198 M /trunk/samtools/bam_plcmd.c
1200 added the format column
1202 ------------------------------------------------------------------------
1203 r631 | lh3lh3 | 2010-07-23 13:25:44 -0400 (Fri, 23 Jul 2010) | 2 lines
1205 M /trunk/samtools/bam_mcns.c
1206 M /trunk/samtools/bam_mcns.h
1207 M /trunk/samtools/bam_plcmd.c
1208 M /trunk/samtools/bamtk.c
1210 added an alternative prior
1212 ------------------------------------------------------------------------
1213 r628 | lh3lh3 | 2010-07-23 11:48:51 -0400 (Fri, 23 Jul 2010) | 2 lines
1215 M /trunk/samtools/bam_mcns.c
1216 M /trunk/samtools/bam_mcns.h
1217 M /trunk/samtools/bam_plcmd.c
1219 calculate posterior allele frequency
1221 ------------------------------------------------------------------------
1222 r627 | lh3lh3 | 2010-07-22 21:39:13 -0400 (Thu, 22 Jul 2010) | 3 lines
1224 M /trunk/samtools/bam_mcns.c
1225 M /trunk/samtools/bam_plcmd.c
1226 M /trunk/samtools/bamtk.c
1228 * samtools-0.1.8-3 (r627)
1229 * multi-sample snp calling appears to work. More tests needed.
1231 ------------------------------------------------------------------------
1232 r626 | lh3lh3 | 2010-07-22 16:37:56 -0400 (Thu, 22 Jul 2010) | 3 lines
1234 M /trunk/samtools/bam_mcns.c
1235 M /trunk/samtools/bam_mcns.h
1236 M /trunk/samtools/bam_plcmd.c
1237 M /trunk/samtools/bam_tview.c
1239 * preliminary multisample SNP caller.
1240 * something looks not so right, but it largely works
1242 ------------------------------------------------------------------------
1243 r617 | lh3lh3 | 2010-07-14 16:26:27 -0400 (Wed, 14 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-0.1.8-2 (r617)
1250 * allele frequency calculation apparently works...
1252 ------------------------------------------------------------------------
1253 r616 | lh3lh3 | 2010-07-14 13:33:51 -0400 (Wed, 14 Jul 2010) | 3 lines
1255 M /trunk/samtools/Makefile
1256 A /trunk/samtools/bam_mcns.c
1257 A /trunk/samtools/bam_mcns.h
1258 M /trunk/samtools/bam_plcmd.c
1260 * added mutli-sample framework. It is not working, yet.
1261 * improved the mpileup interface
1263 ------------------------------------------------------------------------
1264 r615 | lh3lh3 | 2010-07-13 14:50:12 -0400 (Tue, 13 Jul 2010) | 3 lines
1266 M /trunk/samtools/bam_plcmd.c
1267 M /trunk/samtools/bamtk.c
1268 M /trunk/samtools/misc/Makefile
1270 * samtools-0.1.8-1 (r615)
1271 * allow to get mpileup at required sites
1273 ------------------------------------------------------------------------
1274 r613 | lh3lh3 | 2010-07-11 22:40:56 -0400 (Sun, 11 Jul 2010) | 2 lines
1276 M /trunk/samtools/ChangeLog
1277 M /trunk/samtools/NEWS
1278 M /trunk/samtools/bam_plcmd.c
1279 M /trunk/samtools/bamtk.c
1280 M /trunk/samtools/samtools.1
1282 Release samtools-0.1.8
1284 ------------------------------------------------------------------------
1285 r612 | lh3lh3 | 2010-07-11 21:08:56 -0400 (Sun, 11 Jul 2010) | 2 lines
1287 M /trunk/samtools/knetfile.c
1289 fixed a compiling issue for Windows
1291 ------------------------------------------------------------------------
1292 r611 | lh3lh3 | 2010-07-11 20:59:15 -0400 (Sun, 11 Jul 2010) | 2 lines
1294 M /trunk/samtools/bam_sort.c
1296 fixed a bug in sorting when output to stdout (by Peter Chines)
1298 ------------------------------------------------------------------------
1299 r610 | lh3lh3 | 2010-07-09 17:05:10 -0400 (Fri, 09 Jul 2010) | 2 lines
1301 M /trunk/samtools/NEWS
1302 M /trunk/samtools/bam_plcmd.c
1304 change the command line option of pileup
1306 ------------------------------------------------------------------------
1307 r609 | lh3lh3 | 2010-07-09 00:39:34 -0400 (Fri, 09 Jul 2010) | 2 lines
1309 M /trunk/samtools/bam_pileup.c
1310 A /trunk/samtools/examples/toy.fa
1311 A /trunk/samtools/examples/toy.sam
1313 make pileup work with CIGAR with I/D at the beginning or in the end
1315 ------------------------------------------------------------------------
1316 r608 | lh3lh3 | 2010-07-08 22:36:12 -0400 (Thu, 08 Jul 2010) | 3 lines
1318 M /trunk/samtools/bam_maqcns.c
1319 M /trunk/samtools/bam_maqcns.h
1320 M /trunk/samtools/bam_plcmd.c
1321 M /trunk/samtools/bam_tview.c
1323 * make tview more friendly
1324 * a temporary remedy for an issue in indel calling
1326 ------------------------------------------------------------------------
1327 r607 | lh3lh3 | 2010-07-08 14:43:52 -0400 (Thu, 08 Jul 2010) | 4 lines
1329 M /trunk/samtools/bam_maqcns.c
1330 M /trunk/samtools/bam_plcmd.c
1331 M /trunk/samtools/bamtk.c
1333 * samtools-0.1.7-r607
1334 * improved the genotype accuracy for indels
1335 * use the SOAPsnp model for SNP calling by default.
1337 ------------------------------------------------------------------------
1338 r606 | lh3lh3 | 2010-07-08 01:05:19 -0400 (Thu, 08 Jul 2010) | 2 lines
1340 M /trunk/samtools/misc/Makefile
1342 removed a debugging example
1344 ------------------------------------------------------------------------
1345 r605 | lh3lh3 | 2010-07-08 01:04:09 -0400 (Thu, 08 Jul 2010) | 4 lines
1347 M /trunk/samtools/bam_maqcns.c
1348 M /trunk/samtools/bamtk.c
1350 * samtools-.1.7-18 (r605)
1351 * fixed an issue when a deletion and mismatch occur at the same time
1352 and the base quality is higher than 40 (if -I40).
1354 ------------------------------------------------------------------------
1355 r604 | lh3lh3 | 2010-07-02 19:32:24 -0400 (Fri, 02 Jul 2010) | 2 lines
1357 M /trunk/samtools/bam.h
1358 M /trunk/samtools/bam_index.c
1359 M /trunk/samtools/misc/Makefile
1361 fixed a minor bug in idxstats
1363 ------------------------------------------------------------------------
1364 r601 | lh3lh3 | 2010-06-16 09:03:59 -0400 (Wed, 16 Jun 2010) | 2 lines
1366 M /trunk/samtools/bam_index.c
1368 fixed a minor bug in indexing
1370 ------------------------------------------------------------------------
1371 r600 | lh3lh3 | 2010-06-15 10:17:53 -0400 (Tue, 15 Jun 2010) | 2 lines
1373 M /trunk/samtools/ChangeLog
1374 M /trunk/samtools/bam.c
1376 change printf() to puts in exporting
1378 ------------------------------------------------------------------------
1379 r599 | lh3lh3 | 2010-06-13 21:41:11 -0400 (Sun, 13 Jun 2010) | 2 lines
1381 M /trunk/samtools/bamtk.c
1383 minor fix. No actual effect.
1385 ------------------------------------------------------------------------
1386 r598 | lh3lh3 | 2010-06-13 21:32:45 -0400 (Sun, 13 Jun 2010) | 2 lines
1388 M /trunk/samtools/Makefile
1390 added Makefile targets to compile shared/dynamic library
1392 ------------------------------------------------------------------------
1393 r596 | lh3lh3 | 2010-06-13 19:48:07 -0400 (Sun, 13 Jun 2010) | 3 lines
1395 M /trunk/samtools/ChangeLog
1396 M /trunk/samtools/bam_index.c
1397 M /trunk/samtools/bamtk.c
1399 * samtools-0.1.7-17 (r596)
1400 * also keep the number of coor-less reads in the index file
1402 ------------------------------------------------------------------------
1403 r595 | lh3lh3 | 2010-06-13 18:54:26 -0400 (Sun, 13 Jun 2010) | 3 lines
1405 M /trunk/samtools/bam_index.c
1406 M /trunk/samtools/bamtk.c
1408 * samtools-0.1.7-16 (r595)
1409 * write additional information to bam index
1411 ------------------------------------------------------------------------
1412 r594 | lh3lh3 | 2010-06-13 17:29:52 -0400 (Sun, 13 Jun 2010) | 2 lines
1414 M /trunk/samtools/bam_index.c
1416 fixed a bug for unmapped sequences in indexing
1418 ------------------------------------------------------------------------
1419 r593 | lh3lh3 | 2010-06-12 18:11:32 -0400 (Sat, 12 Jun 2010) | 2 lines
1421 M /trunk/samtools/bam.h
1422 M /trunk/samtools/bam_index.c
1423 M /trunk/samtools/bam_plcmd.c
1424 M /trunk/samtools/samtools.1
1426 rename iterf as iter
1428 ------------------------------------------------------------------------
1429 r592 | lh3lh3 | 2010-06-12 18:02:38 -0400 (Sat, 12 Jun 2010) | 4 lines
1431 M /trunk/samtools/ChangeLog
1432 M /trunk/samtools/bam_aux.c
1433 M /trunk/samtools/bam_index.c
1434 M /trunk/samtools/bam_pileup.c
1435 M /trunk/samtools/bam_plcmd.c
1436 M /trunk/samtools/bamtk.c
1438 * samtools-0.1.7-15 (r592)
1439 * fixed a few minor memory leaks in the new pileup code
1440 * improved the functionality of mpileup
1442 ------------------------------------------------------------------------
1443 r591 | lh3lh3 | 2010-06-12 14:09:22 -0400 (Sat, 12 Jun 2010) | 3 lines
1445 M /trunk/samtools/bam.h
1446 M /trunk/samtools/bam_pileup.c
1447 M /trunk/samtools/bam_plcmd.c
1448 M /trunk/samtools/bamtk.c
1450 * samtools-0.1.7-14 (r591)
1451 * elementary multi-way pileup. More testing and more functionality to be done.
1453 ------------------------------------------------------------------------
1454 r590 | lh3lh3 | 2010-06-12 01:00:24 -0400 (Sat, 12 Jun 2010) | 3 lines
1456 M /trunk/samtools/bam.h
1457 M /trunk/samtools/bam_pileup.c
1458 M /trunk/samtools/bamtk.c
1460 * samtools-0.1.7-13 (r590)
1461 * added mpileup APIs. No compiling errors, but not tested at all. It is late.
1463 ------------------------------------------------------------------------
1464 r589 | lh3lh3 | 2010-06-11 22:37:09 -0400 (Fri, 11 Jun 2010) | 3 lines
1466 M /trunk/samtools/bam.h
1467 M /trunk/samtools/bam_pileup.c
1468 M /trunk/samtools/bamtk.c
1470 * samtools-0.1.7-12 (r589)
1471 * added iterator-like APIs for pileup
1473 ------------------------------------------------------------------------
1474 r588 | lh3lh3 | 2010-06-11 17:41:13 -0400 (Fri, 11 Jun 2010) | 3 lines
1476 M /trunk/samtools/bam_index.c
1477 M /trunk/samtools/bamtk.c
1479 * samtools-0.1.7-11 (r588)
1480 * ported a few improvements from tabix back to samtools
1482 ------------------------------------------------------------------------
1483 r587 | lh3lh3 | 2010-06-11 17:33:16 -0400 (Fri, 11 Jun 2010) | 3 lines
1485 M /trunk/samtools/bam.h
1486 M /trunk/samtools/bam_index.c
1487 M /trunk/samtools/bamtk.c
1489 * samtools-0.1.7-10 (r587)
1490 * added iterator interface for bam_fetch (ported back from tabix)
1492 ------------------------------------------------------------------------
1493 r586 | lh3lh3 | 2010-06-11 13:23:53 -0400 (Fri, 11 Jun 2010) | 3 lines
1495 M /trunk/samtools/Makefile
1496 A /trunk/samtools/bam_reheader.c
1497 M /trunk/samtools/bamtk.c
1498 M /trunk/samtools/bgzf.c
1500 * samtools-0.1.7-9 (r586)
1501 * added "reheader" to replace the BAM header
1503 ------------------------------------------------------------------------
1504 r585 | lh3lh3 | 2010-06-11 12:22:06 -0400 (Fri, 11 Jun 2010) | 3 lines
1506 M /trunk/samtools/bam.c
1507 M /trunk/samtools/bamtk.c
1508 M /trunk/samtools/kstring.h
1510 * samtools-0.1.7-8 (r585)
1513 ------------------------------------------------------------------------
1514 r584 | lh3lh3 | 2010-06-11 12:00:41 -0400 (Fri, 11 Jun 2010) | 4 lines
1516 M /trunk/samtools/bam.c
1517 M /trunk/samtools/bamtk.c
1518 M /trunk/samtools/bgzf.c
1519 M /trunk/samtools/bgzf.h
1520 M /trunk/samtools/kstring.h
1521 M /trunk/samtools/misc/wgsim_eval.pl
1523 * samtools-0.1.7-7 (r584)
1524 * ported tabix BGZF to samtools
1525 * flush BGZF after writing the BAM header and between alignment boundaries
1527 ------------------------------------------------------------------------
1528 r583 | petulda | 2010-06-11 11:58:20 -0400 (Fri, 11 Jun 2010) | 1 line
1530 A /trunk/samtools/misc/varfilter.py
1532 Initial release on behalf of Aylwyn Scally
1533 ------------------------------------------------------------------------
1534 r561 | petulda | 2010-05-07 08:41:56 -0400 (Fri, 07 May 2010) | 1 line
1536 M /trunk/samtools/samtools.1
1538 Added a note about the indels coordinates
1539 ------------------------------------------------------------------------
1540 r551 | petulda | 2010-04-23 09:42:13 -0400 (Fri, 23 Apr 2010) | 1 line
1542 M /trunk/samtools/misc/sam2vcf.pl
1544 Added the possibility to print or not to print the reference allele
1545 ------------------------------------------------------------------------
1546 r546 | petulda | 2010-04-15 04:33:55 -0400 (Thu, 15 Apr 2010) | 1 line
1548 M /trunk/samtools/sam_header.c
1550 More descriptive message for space separated tags
1551 ------------------------------------------------------------------------
1552 r545 | petulda | 2010-04-14 11:44:50 -0400 (Wed, 14 Apr 2010) | 1 line
1554 M /trunk/samtools/misc/sam2vcf.pl
1556 Speedup with -i, no need to query the reference all the time
1557 ------------------------------------------------------------------------
1558 r541 | petulda | 2010-03-15 10:03:51 -0400 (Mon, 15 Mar 2010) | 1 line
1560 M /trunk/samtools/sam_header.c
1562 Fixed the order of sequences in the header
1563 ------------------------------------------------------------------------
1564 r540 | petulda | 2010-03-04 06:28:35 -0500 (Thu, 04 Mar 2010) | 1 line
1566 M /trunk/samtools/misc/sam2vcf.pl
1568 Added possibility to select indels only and fixed a bug in reporting homozygous indels.
1569 ------------------------------------------------------------------------
1570 r539 | jmarshall | 2010-02-27 06:48:17 -0500 (Sat, 27 Feb 2010) | 4 lines
1572 M /trunk/samtools/bam.c
1574 Improve the invalid 'BAM\1' magic number error message, and also print it
1575 when no bytes can be read from the alleged BAM file, e.g., in the common
1576 user error case when a SAM file has accidentally been supplied.
1578 ------------------------------------------------------------------------
1579 r538 | petulda | 2010-02-26 10:51:40 -0500 (Fri, 26 Feb 2010) | 1 line
1581 M /trunk/samtools/AUTHORS
1582 M /trunk/samtools/bam.h
1583 M /trunk/samtools/bam_import.c
1584 M /trunk/samtools/sam_header.c
1586 Improved efficiency of header parsing
1587 ------------------------------------------------------------------------
1588 r537 | lh3lh3 | 2010-02-23 21:08:48 -0500 (Tue, 23 Feb 2010) | 3 lines
1590 M /trunk/samtools/misc/export2sam.pl
1592 Updated export2sam.pl by Chris Saunders from Illumina.
1595 ------------------------------------------------------------------------
1596 r536 | petulda | 2010-02-17 08:32:53 -0500 (Wed, 17 Feb 2010) | 1 line
1598 M /trunk/samtools/misc/samtools.pl
1600 Fixed filtering of SNPs near indels. Added min indel and SNP quality filter.
1601 ------------------------------------------------------------------------
1602 r535 | petulda | 2010-02-12 04:52:37 -0500 (Fri, 12 Feb 2010) | 1 line
1604 M /trunk/samtools/misc/sam2vcf.pl
1606 Print an error for pileups in simple format
1607 ------------------------------------------------------------------------
1608 r534 | lh3lh3 | 2010-02-11 14:01:41 -0500 (Thu, 11 Feb 2010) | 2 lines
1610 M /trunk/samtools/bam_plcmd.c
1612 added a hidden option in pileup to output the base position (for Erin)
1614 ------------------------------------------------------------------------
1615 r533 | petulda | 2010-02-09 10:12:14 -0500 (Tue, 09 Feb 2010) | 1 line
1617 M /trunk/samtools/misc/sam2vcf.pl
1619 Added possibility to specify a custom column title for the data column
1620 ------------------------------------------------------------------------
1621 r532 | petulda | 2010-02-09 09:46:09 -0500 (Tue, 09 Feb 2010) | 1 line
1623 M /trunk/samtools/bam_plcmd.c
1625 Added the -d option to limit maximum depth for indels.
1626 ------------------------------------------------------------------------
1627 r531 | petulda | 2010-02-03 07:57:27 -0500 (Wed, 03 Feb 2010) | 1 line
1629 M /trunk/samtools/misc/sam2vcf.pl
1632 ------------------------------------------------------------------------
1633 r530 | lh3lh3 | 2010-02-01 09:13:19 -0500 (Mon, 01 Feb 2010) | 3 lines
1635 M /trunk/samtools/ChangeLog
1636 M /trunk/samtools/bam_plcmd.c
1637 M /trunk/samtools/bamtk.c
1638 M /trunk/samtools/misc/samtools.pl
1639 M /trunk/samtools/misc/wgsim.c
1642 * fixed a bug in faidx
1644 ------------------------------------------------------------------------
1645 r529 | jmarshall | 2010-01-11 18:51:49 -0500 (Mon, 11 Jan 2010) | 2 lines
1647 M /trunk/samtools/faidx.c
1649 Put the right filename in the error message.
1651 ------------------------------------------------------------------------
1652 r528 | lh3lh3 | 2009-12-14 11:26:47 -0500 (Mon, 14 Dec 2009) | 3 lines
1654 M /trunk/samtools/bam_plcmd.c
1655 M /trunk/samtools/bamtk.c
1657 * samtools-0.1.7-5 (r528)
1658 * further add new consensus generation strategy
1660 ------------------------------------------------------------------------
1661 r527 | petulda | 2009-12-11 12:31:05 -0500 (Fri, 11 Dec 2009) | 1 line
1663 M /trunk/samtools/knetfile.c
1665 Fixed a bug in knet_seek
1666 ------------------------------------------------------------------------
1667 r526 | petulda | 2009-12-11 07:51:18 -0500 (Fri, 11 Dec 2009) | 1 line
1669 M /trunk/samtools/misc/sam2vcf.pl
1671 Small fix in VCF format: dot for the empty INFO field
1672 ------------------------------------------------------------------------
1673 r525 | petulda | 2009-12-11 04:36:18 -0500 (Fri, 11 Dec 2009) | 1 line
1675 M /trunk/samtools/sam_header.c
1677 Allow tabs in the CO header field
1678 ------------------------------------------------------------------------
1679 r524 | jmarshall | 2009-12-10 10:03:58 -0500 (Thu, 10 Dec 2009) | 3 lines
1681 M /trunk/samtools/Makefile
1682 M /trunk/samtools/Makefile.mingw
1684 Depend on libbam.a rather than the phony target, so that samtools is not
1685 unnecessarily rebuilt every time. Also clean bgzip.
1687 ------------------------------------------------------------------------
1688 r523 | jmarshall | 2009-12-10 09:45:32 -0500 (Thu, 10 Dec 2009) | 4 lines
1690 M /trunk/samtools/Makefile
1691 M /trunk/samtools/Makefile.mingw
1693 Fix a bug in compiling bgzip: this also needs knetfile.o when _USE_KNETFILE
1694 is defined. Also introduce $(KNETFILE_O) which can be set to empty to
1695 facilitate non-knet builds.
1697 ------------------------------------------------------------------------
1698 r522 | lh3lh3 | 2009-12-01 13:02:36 -0500 (Tue, 01 Dec 2009) | 4 lines
1700 M /trunk/samtools/bamtk.c
1701 M /trunk/samtools/sam_view.c
1703 * samtools-0.1.7-4 (r522)
1704 * fixed a bug in "view -r"
1705 * added a new option "view -R" to read required read groups from a file
1707 ------------------------------------------------------------------------
1708 r521 | lh3lh3 | 2009-12-01 10:00:12 -0500 (Tue, 01 Dec 2009) | 3 lines
1710 M /trunk/samtools/bam_md.c
1711 M /trunk/samtools/bamtk.c
1713 * samtools-0.1.7-3 (r521)
1714 * calmd: optionally mask matching bases as N
1716 ------------------------------------------------------------------------
1717 r520 | lh3lh3 | 2009-12-01 09:37:17 -0500 (Tue, 01 Dec 2009) | 4 lines
1719 M /trunk/samtools/bam_plcmd.c
1720 M /trunk/samtools/bamtk.c
1721 M /trunk/samtools/misc/samtools.pl
1723 * samtools-0.1.7-2 (r520)
1724 * fixed a few issues with compilation in Windows (on behalf of John)
1725 * choose a random base as the consensus (for population genetics studies)
1727 ------------------------------------------------------------------------
1728 r519 | jmarshall | 2009-11-30 10:53:02 -0500 (Mon, 30 Nov 2009) | 6 lines
1730 M /trunk/samtools/Makefile
1732 Put libraries at the end, so they can resolve references from libbam.a
1733 as well, even with old-fashioned linkers.
1735 Also use libbam.a explicitly rather than "-L. -lbam" to ensure that we get
1736 the freshly built library, not some other libbam.a lying around the system.
1738 ------------------------------------------------------------------------
1739 r518 | jmarshall | 2009-11-30 08:44:56 -0500 (Mon, 30 Nov 2009) | 2 lines
1741 M /trunk/samtools/Makefile
1742 M /trunk/samtools/misc/Makefile
1744 Also clean *.exe (for Cygwin users using this makefile).
1746 ------------------------------------------------------------------------
1747 r517 | jmarshall | 2009-11-30 07:09:04 -0500 (Mon, 30 Nov 2009) | 2 lines
1749 M /trunk/samtools/bam_index.c
1751 Index files should be opened in binary mode, not text mode.
1753 ------------------------------------------------------------------------
1754 r516 | lh3lh3 | 2009-11-27 15:18:59 -0500 (Fri, 27 Nov 2009) | 2 lines
1756 A /trunk/samtools/examples/bam2bed.c
1758 another example program
1760 ------------------------------------------------------------------------
1761 r515 | lh3lh3 | 2009-11-27 10:44:56 -0500 (Fri, 27 Nov 2009) | 3 lines
1763 M /trunk/samtools/bam_import.c
1764 M /trunk/samtools/bamtk.c
1765 M /trunk/samtools/misc/wgsim_eval.pl
1766 M /trunk/samtools/sam.c
1768 * samtools-0.1.7-1 (r515)
1769 * report an error when .fai contains duplicated names, instead of segfault
1771 ------------------------------------------------------------------------
1772 r514 | jmarshall | 2009-11-24 09:45:35 -0500 (Tue, 24 Nov 2009) | 2 lines
1774 M /trunk/samtools/bam.c
1776 Format 'c'-encoded auxiliary fields correctly, as *signed* integers.
1778 ------------------------------------------------------------------------
1779 r513 | lh3lh3 | 2009-11-16 10:13:07 -0500 (Mon, 16 Nov 2009) | 2 lines
1781 M /trunk/samtools/Makefile.mingw
1783 Update Makefile.mingw for the same reason
1785 ------------------------------------------------------------------------
1786 r512 | lh3lh3 | 2009-11-16 10:00:08 -0500 (Mon, 16 Nov 2009) | 2 lines
1788 M /trunk/samtools/Makefile
1790 Fixed a bug in compiling razip
1792 ------------------------------------------------------------------------
1793 r510 | lh3lh3 | 2009-11-10 10:55:41 -0500 (Tue, 10 Nov 2009) | 2 lines
1795 M /trunk/samtools/ChangeLog
1796 M /trunk/samtools/NEWS
1797 M /trunk/samtools/bamtk.c
1798 M /trunk/samtools/samtools.1
1800 Release samtools-0.1.7 (r510)
1802 ------------------------------------------------------------------------
1803 r509 | lh3lh3 | 2009-11-06 09:17:09 -0500 (Fri, 06 Nov 2009) | 3 lines
1805 M /trunk/samtools/bam_plcmd.c
1806 M /trunk/samtools/bamtk.c
1808 * samtools-0.1.6-22 (r509)
1809 * forget to fix a similar problem in glfgen
1811 ------------------------------------------------------------------------
1812 r508 | lh3lh3 | 2009-11-06 09:06:40 -0500 (Fri, 06 Nov 2009) | 3 lines
1814 M /trunk/samtools/bam_maqcns.c
1815 M /trunk/samtools/bam_plcmd.c
1816 M /trunk/samtools/bamtk.c
1817 M /trunk/samtools/sam_view.c
1819 * samtools-0.1.6-21 (r508)
1820 * fixed a potential bug in the indel caller towards the end of a chromosome
1822 ------------------------------------------------------------------------
1823 r494 | lh3lh3 | 2009-10-26 11:38:00 -0400 (Mon, 26 Oct 2009) | 3 lines
1825 M /trunk/samtools/bamtk.c
1826 M /trunk/samtools/sam_view.c
1828 * samtools-0.1.6-19 (r494)
1829 * allow to convert Illumina quality (64 based) to the BAM quality
1831 ------------------------------------------------------------------------
1832 r493 | lh3lh3 | 2009-10-26 10:24:39 -0400 (Mon, 26 Oct 2009) | 4 lines
1834 M /trunk/samtools/Makefile
1835 M /trunk/samtools/bam.c
1836 M /trunk/samtools/bam_import.c
1837 M /trunk/samtools/bamtk.c
1838 M /trunk/samtools/sam.c
1839 M /trunk/samtools/sam_header.c
1841 * samtools-0.1.6-18 (r493)
1842 * fixed the bugs due to improperly incorporating Petr's header parser
1843 * a little code clean up in sam_header.c
1845 ------------------------------------------------------------------------
1846 r492 | petulda | 2009-10-24 09:43:25 -0400 (Sat, 24 Oct 2009) | 1 line
1848 M /trunk/samtools/sam_header.c
1850 Added sam_header_line_free call for sam_header_parse2
1851 ------------------------------------------------------------------------
1852 r491 | lh3lh3 | 2009-10-24 00:50:16 -0400 (Sat, 24 Oct 2009) | 3 lines
1854 M /trunk/samtools/sam_view.c
1859 ------------------------------------------------------------------------
1860 r490 | lh3lh3 | 2009-10-24 00:45:12 -0400 (Sat, 24 Oct 2009) | 4 lines
1862 M /trunk/samtools/bam.c
1863 M /trunk/samtools/bam.h
1864 M /trunk/samtools/bam_import.c
1865 M /trunk/samtools/sam.c
1868 * improved the interface a bit
1871 ------------------------------------------------------------------------
1872 r489 | lh3lh3 | 2009-10-24 00:41:50 -0400 (Sat, 24 Oct 2009) | 3 lines
1874 M /trunk/samtools/bam_import.c
1875 M /trunk/samtools/sam_header.c
1876 M /trunk/samtools/sam_header.h
1878 * BUGGY VERSION. Please NOT use it.
1879 * Fixed a minor bug, but the major bug is still there.
1881 ------------------------------------------------------------------------
1882 r488 | lh3lh3 | 2009-10-24 00:17:10 -0400 (Sat, 24 Oct 2009) | 3 lines
1884 M /trunk/samtools/Makefile
1885 M /trunk/samtools/bam.c
1886 M /trunk/samtools/bam.h
1887 M /trunk/samtools/bam_aux.c
1888 M /trunk/samtools/bam_import.c
1889 M /trunk/samtools/bam_rmdup.c
1890 M /trunk/samtools/bam_rmdupse.c
1891 M /trunk/samtools/kaln.c
1892 M /trunk/samtools/sam.c
1893 M /trunk/samtools/sam_header.c
1894 M /trunk/samtools/sam_header.h
1895 M /trunk/samtools/sam_view.c
1897 * This revision is SERIOUSLY BUGGY. Please NOT use it.
1898 * Start to incorporate header parsing from Petr Danecek
1900 ------------------------------------------------------------------------
1901 r487 | petulda | 2009-10-23 11:44:32 -0400 (Fri, 23 Oct 2009) | 1 line
1903 M /trunk/samtools/sam_header.c
1904 M /trunk/samtools/sam_header.h
1906 Now possible to merge multiple HeaderDict dictionaries
1907 ------------------------------------------------------------------------
1908 r486 | petulda | 2009-10-22 11:46:58 -0400 (Thu, 22 Oct 2009) | 1 line
1910 M /trunk/samtools/sam_header.c
1913 ------------------------------------------------------------------------
1914 r485 | petulda | 2009-10-22 11:41:56 -0400 (Thu, 22 Oct 2009) | 1 line
1916 A /trunk/samtools/sam_header.c
1917 A /trunk/samtools/sam_header.h
1920 ------------------------------------------------------------------------
1921 r484 | lh3lh3 | 2009-10-19 14:31:32 -0400 (Mon, 19 Oct 2009) | 5 lines
1923 M /trunk/samtools/bam_import.c
1924 M /trunk/samtools/bam_rmdupse.c
1925 M /trunk/samtools/bamtk.c
1926 M /trunk/samtools/examples/Makefile
1928 * samtools-0.1.6-17 (r484)
1929 * fixed a memory leak in rmdupse
1930 * fixed a bug in parsing @RG header lines
1931 * test rmdup in examples/
1933 ------------------------------------------------------------------------
1934 r483 | lh3lh3 | 2009-10-19 13:22:48 -0400 (Mon, 19 Oct 2009) | 4 lines
1936 M /trunk/samtools/bam_rmdup.c
1937 M /trunk/samtools/bam_rmdupse.c
1938 M /trunk/samtools/bamtk.c
1940 * samtools-0.1.6-16 (r483)
1941 * unify the interface of rmdup and rmdupse
1942 * a new bug found in rg2lib(). Have not been fixed yet.
1944 ------------------------------------------------------------------------
1945 r482 | lh3lh3 | 2009-10-19 13:03:34 -0400 (Mon, 19 Oct 2009) | 4 lines
1947 M /trunk/samtools/bam.h
1948 M /trunk/samtools/bam_rmdup.c
1949 M /trunk/samtools/bam_rmdupse.c
1950 M /trunk/samtools/bamtk.c
1951 A /trunk/samtools/klist.h
1953 * samtools-0.1.6-15 (r482)
1955 * rmdupse is now library aware
1957 ------------------------------------------------------------------------
1958 r481 | lh3lh3 | 2009-10-18 00:07:21 -0400 (Sun, 18 Oct 2009) | 3 lines
1960 M /trunk/samtools/bam_rmdup.c
1961 M /trunk/samtools/bamtk.c
1963 * samtools-0.1.6-14 (r480)
1964 * rmdup is now RG aware
1966 ------------------------------------------------------------------------
1967 r480 | lh3lh3 | 2009-10-17 22:05:20 -0400 (Sat, 17 Oct 2009) | 2 lines
1969 M /trunk/samtools/misc/samtools.pl
1971 added a small unitity to parse SRA XML files
1973 ------------------------------------------------------------------------
1974 r479 | lh3lh3 | 2009-10-17 20:57:26 -0400 (Sat, 17 Oct 2009) | 3 lines
1976 M /trunk/samtools/bam_maqcns.c
1977 M /trunk/samtools/bam_maqcns.h
1978 M /trunk/samtools/bam_plcmd.c
1979 M /trunk/samtools/bam_sort.c
1980 M /trunk/samtools/bamtk.c
1982 * samtools-0.1.6-13 (r479)
1983 * merge: optionally use file names as RG tags
1985 ------------------------------------------------------------------------
1986 r478 | lh3lh3 | 2009-10-14 14:18:12 -0400 (Wed, 14 Oct 2009) | 3 lines
1988 M /trunk/samtools/bam.c
1989 M /trunk/samtools/bam.h
1990 M /trunk/samtools/bam_maqcns.c
1991 M /trunk/samtools/bamtk.c
1992 M /trunk/samtools/kaln.c
1994 * samtools-0.1.6-12 (r478)
1995 * fixed a bug in the indel caller
1997 ------------------------------------------------------------------------
1998 r477 | lh3lh3 | 2009-10-10 06:12:26 -0400 (Sat, 10 Oct 2009) | 3 lines
2000 M /trunk/samtools/bam_index.c
2001 M /trunk/samtools/bamtk.c
2003 * samtools-0.1.6-11 (r477)
2004 * fixed a bug due to recent change in bam_index.c (thank Nicole Washington for the patch)
2006 ------------------------------------------------------------------------
2007 r476 | petulda | 2009-10-09 11:45:36 -0400 (Fri, 09 Oct 2009) | 1 line
2009 A /trunk/samtools/misc/sam2vcf.pl
2011 Added the sam2vcf.pl script.
2012 ------------------------------------------------------------------------
2013 r475 | lh3lh3 | 2009-10-08 10:19:16 -0400 (Thu, 08 Oct 2009) | 2 lines
2015 M /trunk/samtools/Makefile
2016 M /trunk/samtools/bam.c
2017 M /trunk/samtools/bam.h
2018 M /trunk/samtools/bam_maqcns.c
2019 M /trunk/samtools/bamtk.c
2020 A /trunk/samtools/kaln.c
2021 A /trunk/samtools/kaln.h
2023 Unfinished modification. Please do not use this revision...
2025 ------------------------------------------------------------------------
2026 r474 | petulda | 2009-10-08 06:39:54 -0400 (Thu, 08 Oct 2009) | 1 line
2028 M /trunk/samtools/knetfile.c
2030 Removed the offending knet_seek message.
2031 ------------------------------------------------------------------------
2032 r473 | petulda | 2009-10-06 09:26:35 -0400 (Tue, 06 Oct 2009) | 1 line
2034 M /trunk/samtools/knetfile.c
2035 M /trunk/samtools/razf.c
2037 Bug fix - faidx on RAZF compressed files now working.
2038 ------------------------------------------------------------------------
2039 r472 | lh3lh3 | 2009-10-02 08:42:57 -0400 (Fri, 02 Oct 2009) | 2 lines
2041 M /trunk/samtools/samtools.1
2043 Clarify the meaning of a region like "chr2:1,000,000".
2045 ------------------------------------------------------------------------
2046 r471 | lh3lh3 | 2009-10-02 05:42:19 -0400 (Fri, 02 Oct 2009) | 2 lines
2048 M /trunk/samtools/misc/novo2sam.pl
2050 Fixed minor bugs in novo2sam.pl (on behalf of Ken Chen and Colin Hercus)
2052 ------------------------------------------------------------------------
2053 r470 | lh3lh3 | 2009-09-29 15:01:27 -0400 (Tue, 29 Sep 2009) | 3 lines
2055 M /trunk/samtools/Makefile.mingw
2056 M /trunk/samtools/bamtk.c
2057 M /trunk/samtools/knetfile.c
2058 M /trunk/samtools/knetfile.h
2060 * samtools-0.1.6-9 (r470)
2061 * make knetfile.c compatible with MinGW (thank Martin Morgan for the patch)
2063 ------------------------------------------------------------------------
2064 r469 | lh3lh3 | 2009-09-29 08:07:44 -0400 (Tue, 29 Sep 2009) | 3 lines
2066 M /trunk/samtools/bam_index.c
2067 M /trunk/samtools/bamtk.c
2069 * samtools-0.1.6-9 (r469)
2070 * refactor bam_fetch() for Python binding. On behalf of Leo Goodstadt.
2072 ------------------------------------------------------------------------
2073 r468 | lh3lh3 | 2009-09-28 05:18:29 -0400 (Mon, 28 Sep 2009) | 3 lines
2075 M /trunk/samtools/bam_sort.c
2076 M /trunk/samtools/bamtk.c
2077 M /trunk/samtools/misc/samtools.pl
2079 * samtools-0.1.6-7 (r468)
2082 ------------------------------------------------------------------------
2083 r467 | petulda | 2009-09-28 04:51:29 -0400 (Mon, 28 Sep 2009) | 1 line
2085 M /trunk/samtools/bgzf.c
2086 M /trunk/samtools/bgzip.c
2087 M /trunk/samtools/razf.c
2088 M /trunk/samtools/razip.c
2090 Changed the mode for newly created files to 0666. This allows less strict permissions with umask properly set (e.g. 0002 vs. 0022).
2091 ------------------------------------------------------------------------
2092 r466 | lh3lh3 | 2009-09-24 06:29:19 -0400 (Thu, 24 Sep 2009) | 3 lines
2094 M /trunk/samtools/ChangeLog
2095 M /trunk/samtools/bam_md.c
2096 M /trunk/samtools/bamtk.c
2098 * samtools-0.1.6-6 (r466)
2099 * do not crash calmd when some sequences are absent from the reference.
2101 ------------------------------------------------------------------------
2102 r464 | jmarshall | 2009-09-23 06:14:32 -0400 (Wed, 23 Sep 2009) | 3 lines
2104 M /trunk/samtools/bam.c
2105 M /trunk/samtools/knetfile.c
2107 Suppress bgzf_check_EOF() messages when reading from a pipe, as there is
2108 no way to seek on a pipe and the messages always appear.
2110 ------------------------------------------------------------------------
2111 r463 | petulda | 2009-09-16 07:05:41 -0400 (Wed, 16 Sep 2009) | 1 line
2113 M /trunk/samtools/knetfile.c
2114 M /trunk/samtools/razf.c
2116 A bug fix, "samtools view" is now working again.
2117 ------------------------------------------------------------------------
2118 r462 | lh3lh3 | 2009-09-16 04:51:07 -0400 (Wed, 16 Sep 2009) | 3 lines
2120 M /trunk/samtools/bamtk.c
2121 M /trunk/samtools/faidx.c
2122 M /trunk/samtools/knetfile.c
2123 M /trunk/samtools/knetfile.h
2124 M /trunk/samtools/razf.c
2125 M /trunk/samtools/razf.h
2127 * samtools-0.1.6-5 (r462)
2128 * Added knetfile support in razf and faidx (on behalf of Petr Danecek)
2130 ------------------------------------------------------------------------
2131 r460 | lh3lh3 | 2009-09-09 07:06:22 -0400 (Wed, 09 Sep 2009) | 2 lines
2133 M /trunk/samtools/samtools.1
2135 fixed a formatting issue
2137 ------------------------------------------------------------------------
2138 r459 | lh3lh3 | 2009-09-08 18:14:08 -0400 (Tue, 08 Sep 2009) | 3 lines
2140 M /trunk/samtools/bam_sort.c
2141 M /trunk/samtools/bamtk.c
2143 * samtools-0.1.6-4 (r459)
2144 * make sort output the result to stdout when -o is in use
2146 ------------------------------------------------------------------------
2147 r458 | lh3lh3 | 2009-09-07 05:10:28 -0400 (Mon, 07 Sep 2009) | 4 lines
2149 M /trunk/samtools/bamtk.c
2150 M /trunk/samtools/faidx.c
2151 M /trunk/samtools/faidx.h
2152 M /trunk/samtools/samtools.1
2154 * samtools-0.1.6-2 (r458)
2155 * added more interface to faidx (by Nils)
2156 * updated documentation
2158 ------------------------------------------------------------------------
2159 r457 | lh3lh3 | 2009-09-05 16:12:04 -0400 (Sat, 05 Sep 2009) | 3 lines
2161 M /trunk/samtools/bam_sort.c
2162 M /trunk/samtools/bamtk.c
2164 * samtools-0.1.6-2 (r457)
2165 * get rid of three assert() in bam_sort.c
2167 ------------------------------------------------------------------------
2168 r456 | jmarshall | 2009-09-04 12:46:25 -0400 (Fri, 04 Sep 2009) | 3 lines
2170 M /trunk/samtools/razf.c
2172 Return NULL from _razf_open() (and hence razf_open()/razf_open2())
2173 when opening the file fails.
2175 ------------------------------------------------------------------------
2176 r453 | lh3lh3 | 2009-09-02 08:56:33 -0400 (Wed, 02 Sep 2009) | 2 lines
2178 M /trunk/samtools/ChangeLog
2179 M /trunk/samtools/NEWS
2180 M /trunk/samtools/bamtk.c
2181 M /trunk/samtools/samtools.1
2182 D /trunk/samtools/source.dot
2184 Release samtools-0.1.6
2186 ------------------------------------------------------------------------
2187 r451 | lh3lh3 | 2009-09-02 05:44:48 -0400 (Wed, 02 Sep 2009) | 4 lines
2189 M /trunk/samtools/bam_md.c
2190 M /trunk/samtools/bam_rmdup.c
2191 M /trunk/samtools/bam_rmdupse.c
2192 M /trunk/samtools/bam_sort.c
2193 M /trunk/samtools/bamtk.c
2194 M /trunk/samtools/samtools.1
2196 * samtools-0.1.5-34 (r451)
2197 * applied the patch by John
2198 * improved the help message a little bit
2200 ------------------------------------------------------------------------
2201 r450 | lh3lh3 | 2009-09-02 04:55:55 -0400 (Wed, 02 Sep 2009) | 3 lines
2203 M /trunk/samtools/bam_color.c
2204 M /trunk/samtools/bamtk.c
2206 * samtools-0.1.5-33 (r450)
2207 * fixed a bug in bam_color.c (on behalf of Nils Homer)
2209 ------------------------------------------------------------------------
2210 r449 | lh3lh3 | 2009-08-29 15:36:41 -0400 (Sat, 29 Aug 2009) | 4 lines
2212 M /trunk/samtools/bam_import.c
2213 M /trunk/samtools/bam_md.c
2214 M /trunk/samtools/bamtk.c
2215 M /trunk/samtools/misc/samtools.pl
2217 * samtools-0.1.5-32 (r449)
2218 * fillmd: fixed a bug in modifying MD/NM tags
2219 * in import, give a warning if the read is aligned but there is no CIGAR.
2221 ------------------------------------------------------------------------
2222 r448 | lh3lh3 | 2009-08-19 04:44:28 -0400 (Wed, 19 Aug 2009) | 3 lines
2224 M /trunk/samtools/ChangeLog
2225 M /trunk/samtools/bam_pileup.c
2226 M /trunk/samtools/bamtk.c
2227 M /trunk/samtools/misc/wgsim_eval.pl
2229 * samtools-0.1.5-31 (r448)
2230 * fixed an issue when the last CIGAR is I or D
2232 ------------------------------------------------------------------------
2233 r447 | lh3lh3 | 2009-08-17 04:34:57 -0400 (Mon, 17 Aug 2009) | 3 lines
2235 M /trunk/samtools/bam_aux.c
2236 M /trunk/samtools/bamtk.c
2238 * samtools-0.1.5-30 (r447)
2239 * fixed a bug in bam_aux_get(): 'A' is not checked
2241 ------------------------------------------------------------------------
2242 r446 | lh3lh3 | 2009-08-17 04:33:17 -0400 (Mon, 17 Aug 2009) | 2 lines
2244 M /trunk/samtools/bam_aux.c
2245 M /trunk/samtools/bamtk.c
2249 ------------------------------------------------------------------------
2250 r444 | lh3lh3 | 2009-08-11 05:02:36 -0400 (Tue, 11 Aug 2009) | 3 lines
2252 M /trunk/samtools/bam_sort.c
2253 M /trunk/samtools/bamtk.c
2255 * samtools-0.1.5-28 (r444)
2258 ------------------------------------------------------------------------
2259 r443 | lh3lh3 | 2009-08-11 04:29:11 -0400 (Tue, 11 Aug 2009) | 4 lines
2261 M /trunk/samtools/bam.c
2262 M /trunk/samtools/bam_import.c
2263 M /trunk/samtools/bamtk.c
2265 * samtools-0.1.5-27 (r443)
2266 * SEQ and QUAL can be "*"
2267 * parse CIGAR "=" and "X" as "M"
2269 ------------------------------------------------------------------------
2270 r442 | lh3lh3 | 2009-08-07 16:56:38 -0400 (Fri, 07 Aug 2009) | 4 lines
2272 M /trunk/samtools/bam_pileup.c
2273 M /trunk/samtools/bamtk.c
2274 M /trunk/samtools/misc/md5.c
2275 M /trunk/samtools/misc/md5.h
2276 M /trunk/samtools/misc/md5fa.c
2278 * samtools-0.1.5-26 (r442)
2279 * replace RSA Inc md5.* with ones under permissive lincense
2280 * fixed a bug in detecting unsorted bam in pileup
2282 ------------------------------------------------------------------------
2283 r441 | bhandsaker | 2009-08-05 09:41:28 -0400 (Wed, 05 Aug 2009) | 2 lines
2285 M /trunk/samtools/bgzf.c
2286 M /trunk/samtools/bgzf.h
2287 M /trunk/samtools/bgzip.c
2289 Change copyright notices now that MIT has approved open source distribution.
2291 ------------------------------------------------------------------------
2292 r440 | lh3lh3 | 2009-08-05 05:44:24 -0400 (Wed, 05 Aug 2009) | 3 lines
2294 M /trunk/samtools/bam_stat.c
2295 M /trunk/samtools/bamtk.c
2297 * samtools-0.1.5-25 (r436)
2298 * in flagstats, do not report singletons if both ends are unmapped
2300 ------------------------------------------------------------------------
2301 r439 | lh3lh3 | 2009-08-04 17:16:51 -0400 (Tue, 04 Aug 2009) | 2 lines
2303 M /trunk/samtools/misc/maq2sam.c
2305 fixed a SERIOUS bug in setting 0x20 flag
2307 ------------------------------------------------------------------------
2308 r438 | lh3lh3 | 2009-08-04 16:50:43 -0400 (Tue, 04 Aug 2009) | 2 lines
2310 M /trunk/samtools/misc/samtools.pl
2312 fixed two minor bugs (suggested by Tim M Storm)
2314 ------------------------------------------------------------------------
2315 r437 | lh3lh3 | 2009-08-04 04:13:24 -0400 (Tue, 04 Aug 2009) | 3 lines
2317 M /trunk/samtools/bamtk.c
2318 M /trunk/samtools/misc/samtools.pl
2319 M /trunk/samtools/sam_view.c
2321 * samtools-0.1.5-24 (r435)
2324 ------------------------------------------------------------------------
2325 r434 | lh3lh3 | 2009-08-03 05:40:42 -0400 (Mon, 03 Aug 2009) | 3 lines
2327 M /trunk/samtools/bam_tview.c
2328 M /trunk/samtools/bamtk.c
2330 * samtools-0.1.5-23 (r434)
2331 * in tview, press 'r' to show read names rather than sequences
2333 ------------------------------------------------------------------------
2334 r433 | lh3lh3 | 2009-08-02 14:13:35 -0400 (Sun, 02 Aug 2009) | 3 lines
2336 M /trunk/samtools/knetfile.c
2338 * tried to fixed the buggy FTP random access in Windows. FAILED.
2339 * anyway, MinGW seems to have problem with "%lld".
2341 ------------------------------------------------------------------------
2342 r432 | lh3lh3 | 2009-08-01 19:32:07 -0400 (Sat, 01 Aug 2009) | 5 lines
2344 M /trunk/samtools/Makefile.mingw
2345 M /trunk/samtools/bamtk.c
2346 M /trunk/samtools/faidx.c
2347 M /trunk/samtools/razf.c
2348 A /trunk/samtools/win32/libcurses.a
2349 A /trunk/samtools/win32/xcurses.h
2351 * samtools-0.1.5-22 (r432)
2352 * faidx: fixed compitability issue with _WIN32
2353 * razf: fixed potential compitability issue with _WIN32
2354 * PDCurses support in Windows
2356 ------------------------------------------------------------------------
2357 r431 | lh3lh3 | 2009-08-01 18:34:54 -0400 (Sat, 01 Aug 2009) | 2 lines
2359 M /trunk/samtools/win32/libz.a
2361 replace the GnuWin32 version of libz.a with my own build with MinGW.
2363 ------------------------------------------------------------------------
2364 r430 | lh3lh3 | 2009-08-01 18:21:07 -0400 (Sat, 01 Aug 2009) | 2 lines
2366 M /trunk/samtools/knetfile.c
2370 ------------------------------------------------------------------------
2371 r429 | lh3lh3 | 2009-08-01 17:41:19 -0400 (Sat, 01 Aug 2009) | 3 lines
2373 M /trunk/samtools/Makefile.mingw
2374 M /trunk/samtools/bamtk.c
2375 M /trunk/samtools/knetfile.c
2376 M /trunk/samtools/knetfile.h
2378 * samtools-0.1.5-21 (r428)
2379 * knetfile.c is now compatible with mingw-winsock
2381 ------------------------------------------------------------------------
2382 r428 | lh3lh3 | 2009-07-31 19:39:07 -0400 (Fri, 31 Jul 2009) | 2 lines
2384 M /trunk/samtools/Makefile.mingw
2386 simplify MinGW Makefile
2388 ------------------------------------------------------------------------
2389 r427 | lh3lh3 | 2009-07-31 19:30:54 -0400 (Fri, 31 Jul 2009) | 5 lines
2391 A /trunk/samtools/Makefile.mingw
2392 M /trunk/samtools/bam_import.c
2393 M /trunk/samtools/bamtk.c
2394 A /trunk/samtools/win32
2395 A /trunk/samtools/win32/libz.a
2396 A /trunk/samtools/win32/zconf.h
2397 A /trunk/samtools/win32/zlib.h
2399 * samtools-0.1.5-20 (r427)
2400 * MinGW support. At least SAM<->BAM conversion is working. Other
2401 functionality are not tested at the moment.
2402 * zlib headers and Windows version of libz.a are included in win32/
2404 ------------------------------------------------------------------------
2405 r426 | lh3lh3 | 2009-07-31 18:32:09 -0400 (Fri, 31 Jul 2009) | 3 lines
2407 M /trunk/samtools/bamtk.c
2408 M /trunk/samtools/sam_view.c
2410 * samtools-0.1.5-19 (r426)
2411 * fixed a bug caused by recent modifications. Sorry.
2413 ------------------------------------------------------------------------
2414 r425 | lh3lh3 | 2009-07-31 18:23:51 -0400 (Fri, 31 Jul 2009) | 2 lines
2416 M /trunk/samtools/bgzf.c
2418 compatible with Windows binary files
2420 ------------------------------------------------------------------------
2421 r424 | lh3lh3 | 2009-07-31 05:19:59 -0400 (Fri, 31 Jul 2009) | 5 lines
2423 M /trunk/samtools/bam_maqcns.c
2424 M /trunk/samtools/bam_maqcns.h
2425 M /trunk/samtools/bam_plcmd.c
2426 M /trunk/samtools/bam_tview.c
2427 M /trunk/samtools/bamtk.c
2428 M /trunk/samtools/misc/samtools.pl
2430 * samtools-0.1.5-18 (r423)
2431 * output additional information in pileup indel lines, for the purepose
2432 of debugging at the moment
2433 * in tview, optionally allow to treat reference skip as deletion
2435 ------------------------------------------------------------------------
2436 r423 | lh3lh3 | 2009-07-30 17:00:36 -0400 (Thu, 30 Jul 2009) | 2 lines
2438 A /trunk/samtools/misc/psl2sam.pl
2440 convert BLAT psl to SAM.
2442 ------------------------------------------------------------------------
2443 r422 | lh3lh3 | 2009-07-30 06:24:39 -0400 (Thu, 30 Jul 2009) | 6 lines
2445 M /trunk/samtools/ChangeLog
2446 M /trunk/samtools/bam.c
2447 M /trunk/samtools/bamtk.c
2448 M /trunk/samtools/bgzf.c
2449 M /trunk/samtools/bgzf.h
2450 M /trunk/samtools/knetfile.c
2451 M /trunk/samtools/sam.c
2452 M /trunk/samtools/sam_view.c
2454 * samtools-0.1.5-17 (r422)
2455 * fixed a but in knetfile.c when seek type is not SEEK_SET
2456 * write an empty BGZF block to every BGZF file
2457 * check BGZF EOF marker in bam_header_read()
2460 ------------------------------------------------------------------------
2461 r421 | lh3lh3 | 2009-07-30 05:03:39 -0400 (Thu, 30 Jul 2009) | 3 lines
2463 M /trunk/samtools/bam_import.c
2464 M /trunk/samtools/bam_plcmd.c
2465 M /trunk/samtools/bamtk.c
2466 M /trunk/samtools/misc/samtools.pl
2467 M /trunk/samtools/sam.c
2468 M /trunk/samtools/sam.h
2469 M /trunk/samtools/sam_view.c
2471 * samtools-0.1.5-16 (r421)
2472 * in view and pileup, load header from FASTA index if the input is SAM.
2474 ------------------------------------------------------------------------
2475 r420 | lh3lh3 | 2009-07-29 04:18:55 -0400 (Wed, 29 Jul 2009) | 2 lines
2477 M /trunk/samtools/misc/maq2sam.c
2479 do not set "read 1" if reads are not mapped in the PE mode of maq
2481 ------------------------------------------------------------------------
2482 r419 | lh3lh3 | 2009-07-28 04:52:33 -0400 (Tue, 28 Jul 2009) | 5 lines
2484 M /trunk/samtools/bam_import.c
2485 M /trunk/samtools/bamtk.c
2486 M /trunk/samtools/misc/samtools.pl
2487 M /trunk/samtools/misc/wgsim_eval.pl
2489 * samtools-0.1.5-15 (r419)
2490 * in sam_open(), return NULL when the file cannot be opened.
2491 * make wgsim_eval.pl more robust to imperfect SAM
2492 * add "unique" command to samtools.pl
2494 ------------------------------------------------------------------------
2495 r418 | lh3lh3 | 2009-07-24 09:04:19 -0400 (Fri, 24 Jul 2009) | 2 lines
2497 M /trunk/samtools/misc/wgsim_eval.pl
2499 skip @header lines in SAM
2501 ------------------------------------------------------------------------
2502 r417 | lh3lh3 | 2009-07-24 07:42:38 -0400 (Fri, 24 Jul 2009) | 3 lines
2504 M /trunk/samtools/bamtk.c
2505 M /trunk/samtools/sam_view.c
2507 * samtools-0.1.5-14 (r417)
2508 * more help in "samtools view" due to the recent changes.
2510 ------------------------------------------------------------------------
2511 r416 | lh3lh3 | 2009-07-24 07:34:30 -0400 (Fri, 24 Jul 2009) | 3 lines
2513 M /trunk/samtools/bam.c
2514 M /trunk/samtools/bam.h
2515 M /trunk/samtools/bam_import.c
2516 M /trunk/samtools/bamtk.c
2517 M /trunk/samtools/sam.c
2518 M /trunk/samtools/sam.h
2519 M /trunk/samtools/sam_view.c
2521 * samtools-0.1.5-17 (r416)
2522 * support import/export SAM with string tags
2524 ------------------------------------------------------------------------
2525 r415 | lh3lh3 | 2009-07-24 06:39:26 -0400 (Fri, 24 Jul 2009) | 3 lines
2527 M /trunk/samtools/bam.c
2528 M /trunk/samtools/bam.h
2529 M /trunk/samtools/bam_import.c
2530 M /trunk/samtools/bamtk.c
2531 M /trunk/samtools/sam.c
2532 M /trunk/samtools/sam.h
2533 M /trunk/samtools/sam_view.c
2535 * samtools-0.1.5-12 (r415)
2536 * FLAG now can be in HEX
2538 ------------------------------------------------------------------------
2539 r414 | lh3lh3 | 2009-07-22 17:03:49 -0400 (Wed, 22 Jul 2009) | 2 lines
2541 M /trunk/samtools/kstring.h
2543 fixed a compiling error (thank Ken for fixing it)
2545 ------------------------------------------------------------------------
2546 r412 | lh3lh3 | 2009-07-21 17:19:40 -0400 (Tue, 21 Jul 2009) | 2 lines
2548 M /trunk/samtools/kstring.c
2549 M /trunk/samtools/kstring.h
2551 Implemented Boyer-Moore search in the kstring library.
2553 ------------------------------------------------------------------------
2554 r409 | lh3lh3 | 2009-07-17 12:10:20 -0400 (Fri, 17 Jul 2009) | 2 lines
2556 M /trunk/samtools/bam_index.c
2558 do not include knetfile.h when _USE_KNETFILE is not defined
2560 ------------------------------------------------------------------------
2561 r408 | lh3lh3 | 2009-07-17 10:29:21 -0400 (Fri, 17 Jul 2009) | 5 lines
2563 M /trunk/samtools/bam_md.c
2564 M /trunk/samtools/bam_tview.c
2565 M /trunk/samtools/bamtk.c
2566 M /trunk/samtools/bgzf.c
2568 * samtools-0.1.5-11 (r408)
2569 * force to overwirte existing MD if it is different from the one calculated
2571 * bgzf.c: improved the compatibility with Windows headers
2573 ------------------------------------------------------------------------
2574 r407 | lh3lh3 | 2009-07-17 09:46:56 -0400 (Fri, 17 Jul 2009) | 5 lines
2576 M /trunk/samtools/bam.h
2577 M /trunk/samtools/bam_aux.c
2578 M /trunk/samtools/bam_md.c
2579 M /trunk/samtools/bamtk.c
2580 M /trunk/samtools/sam.h
2582 * samtools-0.1.5-10 (r407)
2583 * implemented bam_aux_del() to remove a tag
2584 * fillmd: generate the NM tag
2585 * fillmd: cmd interface improvement
2587 ------------------------------------------------------------------------
2588 r406 | lh3lh3 | 2009-07-16 18:30:40 -0400 (Thu, 16 Jul 2009) | 2 lines
2590 M /trunk/samtools/Makefile
2592 Sorry. The old Makefile is for PDCurses...
2594 ------------------------------------------------------------------------
2595 r405 | lh3lh3 | 2009-07-16 18:30:11 -0400 (Thu, 16 Jul 2009) | 3 lines
2597 M /trunk/samtools/Makefile
2598 M /trunk/samtools/bam_tview.c
2599 M /trunk/samtools/bamtk.c
2601 * samtools-0.1.5-9 (r405)
2602 * improved the compatibility with PDCurses a little bit
2604 ------------------------------------------------------------------------
2605 r404 | lh3lh3 | 2009-07-16 18:23:52 -0400 (Thu, 16 Jul 2009) | 3 lines
2607 M /trunk/samtools/Makefile
2608 M /trunk/samtools/bam_tview.c
2609 M /trunk/samtools/bamtk.c
2611 * samtools-0.1.5-8 (r404)
2612 * compatible with PDCurses
2614 ------------------------------------------------------------------------
2615 r403 | lh3lh3 | 2009-07-16 17:39:39 -0400 (Thu, 16 Jul 2009) | 3 lines
2617 M /trunk/samtools/bamtk.c
2618 M /trunk/samtools/kseq.h
2620 * samtools-0.1.5-7 (r403)
2621 * fixed a bug in kseq.h for binary files (text files are fine)
2623 ------------------------------------------------------------------------
2624 r402 | lh3lh3 | 2009-07-16 06:49:53 -0400 (Thu, 16 Jul 2009) | 4 lines
2626 M /trunk/samtools/bam_import.c
2627 M /trunk/samtools/bam_index.c
2628 M /trunk/samtools/bamtk.c
2629 M /trunk/samtools/bgzf.c
2631 * samtools-0.1.5-6 (r402)
2632 * fixed compiling error when "-D_USE_NETFILE" is not applied
2633 * improve portability to MinGW
2635 ------------------------------------------------------------------------
2636 r398 | lh3lh3 | 2009-07-13 05:21:36 -0400 (Mon, 13 Jul 2009) | 3 lines
2638 A /trunk/bam-lite/bam.h (from /trunk/samtools/bam.h:395)
2639 A /trunk/bam-lite/bam_lite.c (from /trunk/samtools/bam_lite.c:395)
2640 D /trunk/samtools/bam_lite.c
2642 * move bam_lite.c to bam-lite
2643 * copy bam.h to bam-lite
2645 ------------------------------------------------------------------------
2646 r395 | lh3lh3 | 2009-07-13 05:12:57 -0400 (Mon, 13 Jul 2009) | 3 lines
2648 M /trunk/samtools/bam.h
2649 M /trunk/samtools/bam_lite.c
2650 M /trunk/samtools/bam_lpileup.c
2651 M /trunk/samtools/bam_pileup.c
2652 M /trunk/samtools/bamtk.c
2654 * samtools-0.1.5-5 (r395)
2655 * added bam_pileup_file() and removed bam_lpileup_file()
2657 ------------------------------------------------------------------------
2658 r394 | lh3lh3 | 2009-07-12 19:35:10 -0400 (Sun, 12 Jul 2009) | 3 lines
2660 M /trunk/samtools/bamtk.c
2661 M /trunk/samtools/knetfile.c
2662 M /trunk/samtools/knetfile.h
2664 * samtools-0.1.5-4 (r394)
2665 * http_proxy support in knetfile library (check http_proxy ENV)
2667 ------------------------------------------------------------------------
2668 r393 | lh3lh3 | 2009-07-12 18:57:07 -0400 (Sun, 12 Jul 2009) | 5 lines
2670 M /trunk/samtools/bam_index.c
2671 M /trunk/samtools/bam_tview.c
2672 M /trunk/samtools/bamtk.c
2673 M /trunk/samtools/knetfile.c
2674 M /trunk/samtools/knetfile.h
2676 * samtools-0.1.5-3 (r393)
2677 * knetfile now supports HTTP (no proxy at the moment)
2678 * fixed a potential issue in knetfile on opening ordinary file, although I have
2679 not seen the sideeffect so far.
2681 ------------------------------------------------------------------------
2682 r392 | lh3lh3 | 2009-07-12 13:50:55 -0400 (Sun, 12 Jul 2009) | 2 lines
2684 M /trunk/samtools/samtools.1
2686 Remove the warning in tview
2688 ------------------------------------------------------------------------
2689 r391 | lh3lh3 | 2009-07-12 13:42:43 -0400 (Sun, 12 Jul 2009) | 3 lines
2691 M /trunk/samtools/bam_tview.c
2692 M /trunk/samtools/bamtk.c
2694 * samtools-0.1.5-2 (r391)
2695 * do not show a blank screen when no reads mapped
2697 ------------------------------------------------------------------------
2698 r390 | lh3lh3 | 2009-07-09 09:01:42 -0400 (Thu, 09 Jul 2009) | 4 lines
2700 M /trunk/samtools/bam.h
2701 A /trunk/samtools/bam_lite.c
2702 M /trunk/samtools/bamtk.c
2704 * samtools-0.1.5-1 (r390)
2705 * removed useless _IOLIB in bam.h. This should cause no change at all.
2706 * added bam_lite.c for light-weight BAM reading
2708 ------------------------------------------------------------------------
2709 r385 | lh3lh3 | 2009-07-07 11:53:29 -0400 (Tue, 07 Jul 2009) | 2 lines
2711 M /trunk/samtools/bamtk.c
2712 M /trunk/samtools/knetfile.c
2714 Release samtools-0.1.5c (fixed a bug in piping)
2716 ------------------------------------------------------------------------
2717 r383 | lh3lh3 | 2009-07-07 06:39:55 -0400 (Tue, 07 Jul 2009) | 2 lines
2719 M /trunk/samtools/bamtk.c
2720 M /trunk/samtools/sam.c
2722 Release samtools-0.1.5b (BUG! so embarrassing!)
2724 ------------------------------------------------------------------------
2725 r381 | lh3lh3 | 2009-07-07 06:20:06 -0400 (Tue, 07 Jul 2009) | 2 lines
2727 M /trunk/samtools/Makefile
2728 M /trunk/samtools/bam.h
2729 M /trunk/samtools/bam_aux.c
2730 M /trunk/samtools/bamtk.c
2732 Release samtools-0.1.5a (for compatibility with Bio::DB::Sam)
2734 ------------------------------------------------------------------------
2735 r373 | lh3lh3 | 2009-07-07 05:26:57 -0400 (Tue, 07 Jul 2009) | 2 lines
2737 M /trunk/samtools/ChangeLog
2738 M /trunk/samtools/NEWS
2739 M /trunk/samtools/bamtk.c
2740 M /trunk/samtools/samtools.1
2742 Release samtools-0.1.5
2744 ------------------------------------------------------------------------
2745 r372 | lh3lh3 | 2009-07-07 04:49:27 -0400 (Tue, 07 Jul 2009) | 3 lines
2747 M /trunk/samtools/bamtk.c
2748 M /trunk/samtools/sam.c
2750 * samtools-0.1.4-23 (r372)
2751 * keep header text if "view -t" is used (by Gerton)
2753 ------------------------------------------------------------------------
2754 r371 | lh3lh3 | 2009-07-06 20:13:32 -0400 (Mon, 06 Jul 2009) | 2 lines
2756 M /trunk/samtools/samtools.1
2758 update documentation
2760 ------------------------------------------------------------------------
2761 r370 | bhandsaker | 2009-07-02 17:24:34 -0400 (Thu, 02 Jul 2009) | 2 lines
2763 M /trunk/samtools/Makefile
2765 Introduced LIBPATH variable so this could be overridden to allow samtools to build correct at the Broad.
2767 ------------------------------------------------------------------------
2768 r369 | lh3lh3 | 2009-07-02 08:36:53 -0400 (Thu, 02 Jul 2009) | 4 lines
2770 M /trunk/samtools/ChangeLog
2771 M /trunk/samtools/bam_aux.c
2772 M /trunk/samtools/bam_plcmd.c
2773 M /trunk/samtools/bamtk.c
2775 * samtools-0.1.4-22 (r369)
2776 * in pileup, optionally print E2 and U2
2777 * remove the debugging code in bam_aux_get() (Drat!)
2779 ------------------------------------------------------------------------
2780 r368 | lh3lh3 | 2009-07-02 06:32:26 -0400 (Thu, 02 Jul 2009) | 6 lines
2782 M /trunk/samtools/bam.c
2783 M /trunk/samtools/bam.h
2784 M /trunk/samtools/bam_aux.c
2785 M /trunk/samtools/bam_index.c
2786 M /trunk/samtools/bam_lpileup.c
2787 M /trunk/samtools/bam_md.c
2788 M /trunk/samtools/bam_pileup.c
2789 M /trunk/samtools/bam_rmdup.c
2790 M /trunk/samtools/bam_stat.c
2791 M /trunk/samtools/bam_tview.c
2792 M /trunk/samtools/bamtk.c
2793 M /trunk/samtools/faidx.c
2794 M /trunk/samtools/faidx.h
2795 M /trunk/samtools/glf.c
2797 * samtools-0.1.4-21 (r368)
2798 * propagate errors rather than exit or complain assertion failure. Assertion
2799 should be only used for checking internal bugs, but not for external input
2800 inconsistency. I was just a bit lazy.
2801 * small memory leak may be present on failure, though
2803 ------------------------------------------------------------------------
2804 r367 | lh3lh3 | 2009-06-30 11:18:42 -0400 (Tue, 30 Jun 2009) | 2 lines
2806 M /trunk/samtools/knetfile.c
2808 reduce the chance of blocking in FTP connection
2810 ------------------------------------------------------------------------
2811 r366 | lh3lh3 | 2009-06-30 10:35:21 -0400 (Tue, 30 Jun 2009) | 2 lines
2813 M /trunk/samtools/knetfile.c
2815 minor changes to knetfile: invalid fd equals -1 rather than 0
2817 ------------------------------------------------------------------------
2818 r365 | lh3lh3 | 2009-06-30 09:04:30 -0400 (Tue, 30 Jun 2009) | 3 lines
2820 M /trunk/samtools/bam_index.c
2821 M /trunk/samtools/bamtk.c
2822 M /trunk/samtools/knetfile.c
2823 M /trunk/samtools/knetfile.h
2825 * samtools-0.1.4-20 (r365)
2826 * download the BAM index file if it is not found in the current working directory.
2828 ------------------------------------------------------------------------
2829 r364 | lh3lh3 | 2009-06-30 07:39:07 -0400 (Tue, 30 Jun 2009) | 3 lines
2831 M /trunk/samtools/bamtk.c
2832 M /trunk/samtools/knetfile.c
2834 * samtools-0.1.4-19 (r364)
2835 * knetfile: report error when the file is not present on FTP
2837 ------------------------------------------------------------------------
2838 r363 | lh3lh3 | 2009-06-29 18:23:32 -0400 (Mon, 29 Jun 2009) | 4 lines
2840 M /trunk/samtools/bam_tview.c
2841 M /trunk/samtools/bamtk.c
2842 M /trunk/samtools/bgzf.c
2843 M /trunk/samtools/bgzf.h
2844 M /trunk/samtools/knetfile.c
2845 M /trunk/samtools/knetfile.h
2847 * samtools-0.1.4-18 (r363)
2848 * knetfile: do not trigger network communication in FTP seek (lazy seek)
2849 * bgzf: cache recent blocks (disabled by default)
2851 ------------------------------------------------------------------------
2852 r362 | lh3lh3 | 2009-06-25 16:04:34 -0400 (Thu, 25 Jun 2009) | 2 lines
2854 M /trunk/samtools/bgzf.c
2858 ------------------------------------------------------------------------
2859 r361 | lh3lh3 | 2009-06-25 16:03:10 -0400 (Thu, 25 Jun 2009) | 3 lines
2861 M /trunk/samtools/bam_index.c
2862 M /trunk/samtools/bamtk.c
2864 * samtools-0.1.4-17 (r361)
2865 * if a file is given on FTP, search locally for the BAM index
2867 ------------------------------------------------------------------------
2868 r360 | lh3lh3 | 2009-06-25 15:44:52 -0400 (Thu, 25 Jun 2009) | 5 lines
2870 M /trunk/samtools/Makefile
2871 M /trunk/samtools/bam_import.c
2872 M /trunk/samtools/bam_index.c
2873 M /trunk/samtools/bamtk.c
2874 M /trunk/samtools/bgzf.c
2875 M /trunk/samtools/bgzf.h
2876 M /trunk/samtools/knetfile.c
2877 M /trunk/samtools/knetfile.h
2879 * samtools-0.1.4-16 (r360)
2880 * report more information in index when the input is not sorted
2881 * change the behaviour of knet_seek() such that it returns 0 on success
2882 * support knetfile library in BGZF
2884 ------------------------------------------------------------------------
2885 r359 | lh3lh3 | 2009-06-25 12:10:55 -0400 (Thu, 25 Jun 2009) | 2 lines
2887 M /trunk/samtools/knetfile.c
2888 M /trunk/samtools/knetfile.h
2890 fixed bugs in knetfile.*
2892 ------------------------------------------------------------------------
2893 r358 | lh3lh3 | 2009-06-25 08:53:19 -0400 (Thu, 25 Jun 2009) | 2 lines
2895 A /trunk/samtools/knetfile.h
2897 this is the header file
2899 ------------------------------------------------------------------------
2900 r357 | lh3lh3 | 2009-06-25 08:52:03 -0400 (Thu, 25 Jun 2009) | 3 lines
2902 A /trunk/samtools/knetfile.c
2904 * open a file at FTP
2905 * preliminary version
2907 ------------------------------------------------------------------------
2908 r354 | lh3lh3 | 2009-06-24 09:02:25 -0400 (Wed, 24 Jun 2009) | 3 lines
2910 M /trunk/samtools/bam.c
2911 M /trunk/samtools/bamtk.c
2913 * samtools-0.1.4-15 (r354)
2914 * fixed a memory leak in bam_view1(), although samtools is not using this routine.
2916 ------------------------------------------------------------------------
2917 r351 | lh3lh3 | 2009-06-17 19:16:26 -0400 (Wed, 17 Jun 2009) | 4 lines
2919 M /trunk/samtools/bamtk.c
2920 M /trunk/samtools/faidx.c
2922 * samtools-0.1.4-13 (r351)
2923 * make faidx more tolerant to empty lines right before or after > lines
2924 * hope this does not introduce new bugs...
2926 ------------------------------------------------------------------------
2927 r350 | lh3lh3 | 2009-06-16 09:37:01 -0400 (Tue, 16 Jun 2009) | 3 lines
2929 M /trunk/samtools/bam_plcmd.c
2930 M /trunk/samtools/bamtk.c
2932 * samtools-0.1.4-13 (r350)
2933 * fixed a small memory leak in pileup, caused by recent modifications
2935 ------------------------------------------------------------------------
2936 r347 | lh3lh3 | 2009-06-13 16:20:49 -0400 (Sat, 13 Jun 2009) | 3 lines
2938 M /trunk/samtools/bam_plcmd.c
2939 M /trunk/samtools/bamtk.c
2940 M /trunk/samtools/sam_view.c
2942 * samtools-0.1.4-12 (r347)
2943 * added `-S' to pileup, similar to `view -S'
2945 ------------------------------------------------------------------------
2946 r346 | lh3lh3 | 2009-06-13 12:52:31 -0400 (Sat, 13 Jun 2009) | 3 lines
2948 M /trunk/samtools/Makefile
2949 M /trunk/samtools/bamtk.c
2950 M /trunk/samtools/sam_view.c
2951 M /trunk/samtools/samtools.1
2953 * samtools-0.1.4-11 (r346)
2954 * allow to select a read group at view command-line
2956 ------------------------------------------------------------------------
2957 r344 | lh3lh3 | 2009-06-13 09:06:24 -0400 (Sat, 13 Jun 2009) | 2 lines
2959 M /trunk/samtools/examples/calDepth.c
2963 ------------------------------------------------------------------------
2964 r343 | lh3lh3 | 2009-06-13 09:01:22 -0400 (Sat, 13 Jun 2009) | 2 lines
2966 M /trunk/samtools/examples/calDepth.c
2970 ------------------------------------------------------------------------
2971 r342 | lh3lh3 | 2009-06-13 08:58:48 -0400 (Sat, 13 Jun 2009) | 2 lines
2973 M /trunk/samtools/examples/Makefile
2974 A /trunk/samtools/examples/calDepth.c
2976 added an example of calculating read depth
2978 ------------------------------------------------------------------------
2979 r341 | lh3lh3 | 2009-06-13 08:00:08 -0400 (Sat, 13 Jun 2009) | 6 lines
2981 M /trunk/samtools/Makefile
2982 M /trunk/samtools/bam.h
2983 M /trunk/samtools/bam_aux.c
2984 A /trunk/samtools/bam_color.c
2985 M /trunk/samtools/bam_plcmd.c
2986 M /trunk/samtools/bam_sort.c
2987 M /trunk/samtools/bam_tview.c
2988 M /trunk/samtools/bamtk.c
2989 M /trunk/samtools/sam.c
2990 M /trunk/samtools/sam.h
2992 * samtools-0.1.4-10 (r341)
2993 * only include key APIs in libbam.a
2994 * move color-specific routines to bam_color.c
2995 * update documentations
2996 * remove the support of -q in pileup
2998 ------------------------------------------------------------------------
2999 r340 | lh3lh3 | 2009-06-13 06:17:14 -0400 (Sat, 13 Jun 2009) | 6 lines
3001 M /trunk/samtools/INSTALL
3002 M /trunk/samtools/Makefile
3003 M /trunk/samtools/bam_aux.c
3004 M /trunk/samtools/bam_import.c
3005 M /trunk/samtools/bam_tview.c
3006 M /trunk/samtools/bamtk.c
3007 M /trunk/samtools/razf.c
3008 M /trunk/samtools/sam_view.c
3010 * samtools-0.1.4-9 (r340)
3011 * added a warning to razf.c if zlib<1.2.2.1
3012 * fixed a compilation warning
3013 * fixed a segfault caused by @RG parsing
3014 * detect NCURSES in bam_tview.c
3016 ------------------------------------------------------------------------
3017 r339 | lh3lh3 | 2009-06-13 05:35:19 -0400 (Sat, 13 Jun 2009) | 2 lines
3019 M /trunk/samtools/INSTALL
3023 ------------------------------------------------------------------------
3024 r338 | lh3lh3 | 2009-06-12 19:15:24 -0400 (Fri, 12 Jun 2009) | 4 lines
3026 M /trunk/samtools/bam.c
3027 M /trunk/samtools/bam.h
3028 M /trunk/samtools/bam_aux.c
3029 M /trunk/samtools/bam_import.c
3030 M /trunk/samtools/bamtk.c
3031 M /trunk/samtools/kstring.h
3032 M /trunk/samtools/sam.c
3033 M /trunk/samtools/sam_view.c
3035 * samtools-0.1.4-8 (r338)
3036 * parse the @RG header lines and allow to choose library at the "samtools view"
3039 ------------------------------------------------------------------------
3040 r337 | lh3lh3 | 2009-06-12 16:25:50 -0400 (Fri, 12 Jun 2009) | 4 lines
3042 M /trunk/samtools/bamtk.c
3043 M /trunk/samtools/bgzf.c
3044 M /trunk/samtools/bgzf.h
3045 M /trunk/samtools/sam.c
3046 M /trunk/samtools/sam_view.c
3048 * samtools-0.1.4-7 (r337)
3049 * bgzf.c: support mode string "wu": uncompressed output
3050 * "samtools view" support "-u" command-line option
3052 ------------------------------------------------------------------------
3053 r336 | lh3lh3 | 2009-06-12 12:20:12 -0400 (Fri, 12 Jun 2009) | 5 lines
3055 M /trunk/samtools/Makefile
3056 M /trunk/samtools/misc/Makefile
3057 M /trunk/samtools/razf.c
3058 M /trunk/samtools/razf.h
3059 M /trunk/samtools/razip.c
3061 * no changes to samtools itself
3062 * remove zlib source codes
3063 * make RAZF reading compatible with old version of zlib
3064 * on old version of zlib, writing is not available
3066 ------------------------------------------------------------------------
3067 r335 | lh3lh3 | 2009-06-12 11:47:33 -0400 (Fri, 12 Jun 2009) | 2 lines
3069 D /trunk/samtools/zlib
3071 remove zlib for simplification...
3073 ------------------------------------------------------------------------
3074 r334 | lh3lh3 | 2009-06-12 10:43:36 -0400 (Fri, 12 Jun 2009) | 5 lines
3076 M /trunk/samtools/bam.h
3077 M /trunk/samtools/bam_aux.c
3078 M /trunk/samtools/bamtk.c
3080 * samtools-0.1.4-6 (r334)
3081 * do not export bam_aux_get_core() for Bio::DB::Sam because it has already
3082 been implemented in that.
3083 * this version works with the latest Bio::DB::Sam (20090612)
3085 ------------------------------------------------------------------------
3086 r333 | lh3lh3 | 2009-06-12 10:33:42 -0400 (Fri, 12 Jun 2009) | 2 lines
3088 M /trunk/samtools/ChangeLog
3092 ------------------------------------------------------------------------
3093 r332 | lh3lh3 | 2009-06-12 10:21:21 -0400 (Fri, 12 Jun 2009) | 2 lines
3095 M /trunk/samtools/AUTHORS
3096 M /trunk/samtools/Makefile
3097 M /trunk/samtools/misc/Makefile
3099 fixed minor things in Makefile
3101 ------------------------------------------------------------------------
3102 r331 | lh3lh3 | 2009-06-12 10:07:05 -0400 (Fri, 12 Jun 2009) | 4 lines
3104 M /trunk/samtools/bamtk.c
3106 * samtools-0.1.4-5 (r3310
3107 * no change to samtools itself. Version number is increased to reflect the
3108 changes in the Makefile building system.
3110 ------------------------------------------------------------------------
3111 r330 | lh3lh3 | 2009-06-12 10:03:38 -0400 (Fri, 12 Jun 2009) | 2 lines
3113 M /trunk/samtools/AUTHORS
3114 D /trunk/samtools/README
3116 update information...
3118 ------------------------------------------------------------------------
3119 r329 | lh3lh3 | 2009-06-12 09:52:21 -0400 (Fri, 12 Jun 2009) | 3 lines
3121 M /trunk/samtools/misc/novo2sam.pl
3123 * updated novoalign converter by Colin Hercus et al.
3124 * this version works with indels
3126 ------------------------------------------------------------------------
3127 r328 | lh3lh3 | 2009-06-12 09:50:53 -0400 (Fri, 12 Jun 2009) | 3 lines
3129 M /trunk/samtools/INSTALL
3130 M /trunk/samtools/Makefile
3131 M /trunk/samtools/misc/Makefile
3132 M /trunk/samtools/zlib/Makefile
3135 * update INSTALL instruction
3137 ------------------------------------------------------------------------
3138 r327 | lh3lh3 | 2009-06-12 09:18:29 -0400 (Fri, 12 Jun 2009) | 4 lines
3140 A /trunk/samtools/Makefile (from /trunk/samtools/Makefile.generic:325)
3141 D /trunk/samtools/Makefile.am
3142 D /trunk/samtools/Makefile.generic
3143 D /trunk/samtools/Makefile.lite
3144 D /trunk/samtools/autogen.sh
3145 D /trunk/samtools/cleanup.sh
3146 D /trunk/samtools/configure.ac
3147 A /trunk/samtools/misc/Makefile (from /trunk/samtools/misc/Makefile.generic:305)
3148 D /trunk/samtools/misc/Makefile.am
3149 D /trunk/samtools/misc/Makefile.generic
3150 M /trunk/samtools/razf.c
3151 A /trunk/samtools/zlib
3152 A /trunk/samtools/zlib/Makefile
3153 A /trunk/samtools/zlib/adler32.c
3154 A /trunk/samtools/zlib/compress.c
3155 A /trunk/samtools/zlib/crc32.c
3156 A /trunk/samtools/zlib/crc32.h
3157 A /trunk/samtools/zlib/deflate.c
3158 A /trunk/samtools/zlib/deflate.h
3159 A /trunk/samtools/zlib/gzio.c
3160 A /trunk/samtools/zlib/infback.c
3161 A /trunk/samtools/zlib/inffast.c
3162 A /trunk/samtools/zlib/inffast.h
3163 A /trunk/samtools/zlib/inffixed.h
3164 A /trunk/samtools/zlib/inflate.c
3165 A /trunk/samtools/zlib/inflate.h
3166 A /trunk/samtools/zlib/inftrees.c
3167 A /trunk/samtools/zlib/inftrees.h
3168 A /trunk/samtools/zlib/trees.c
3169 A /trunk/samtools/zlib/trees.h
3170 A /trunk/samtools/zlib/uncompr.c
3171 A /trunk/samtools/zlib/zconf.h
3172 A /trunk/samtools/zlib/zlib.h
3173 A /trunk/samtools/zlib/zutil.c
3174 A /trunk/samtools/zlib/zutil.h
3175 D /trunk/samtools/zutil.h
3177 * added zlib-1.2.3 as razip requires that
3178 * prepare to changed back to the Makefile building system
3179 * unfinished! (will be soon)
3181 ------------------------------------------------------------------------
3182 r326 | lh3lh3 | 2009-06-12 09:12:03 -0400 (Fri, 12 Jun 2009) | 2 lines
3184 M /trunk/samtools/misc/samtools.pl
3188 ------------------------------------------------------------------------
3189 r325 | lh3lh3 | 2009-06-10 11:27:59 -0400 (Wed, 10 Jun 2009) | 3 lines
3191 M /trunk/samtools/bam_maqcns.c
3192 M /trunk/samtools/bamtk.c
3194 * samtools-0.1.4-4 (r325)
3195 * further avoid wrong consensus calls in repetitive regions.
3197 ------------------------------------------------------------------------
3198 r324 | lh3lh3 | 2009-06-10 10:56:17 -0400 (Wed, 10 Jun 2009) | 4 lines
3200 M /trunk/samtools/bam_maqcns.c
3201 M /trunk/samtools/bam_plcmd.c
3202 M /trunk/samtools/bamtk.c
3203 M /trunk/samtools/sam.c
3204 M /trunk/samtools/sam.h
3206 * samtools-0.1.4-3 (r324)
3207 * make maqcns generate the correct call in repetitive regions.
3208 * allow filtering on mapQ at the pileup command line
3210 ------------------------------------------------------------------------
3211 r323 | lh3lh3 | 2009-06-10 05:04:21 -0400 (Wed, 10 Jun 2009) | 3 lines
3213 M /trunk/samtools/misc/samtools.pl
3215 * samtools.pl-0.3.2 (r322)
3216 * indels and SNPs use different mapping quality threshold
3218 ------------------------------------------------------------------------
3219 r322 | lh3lh3 | 2009-06-10 05:03:22 -0400 (Wed, 10 Jun 2009) | 2 lines
3221 M /trunk/samtools/misc/export2sam.pl
3225 ------------------------------------------------------------------------
3226 r321 | lh3lh3 | 2009-06-09 04:21:48 -0400 (Tue, 09 Jun 2009) | 2 lines
3228 M /trunk/samtools/misc/samtools.pl
3230 just typo. no real change
3232 ------------------------------------------------------------------------
3233 r320 | lh3lh3 | 2009-06-08 09:32:51 -0400 (Mon, 08 Jun 2009) | 2 lines
3235 M /trunk/samtools/misc/samtools.pl
3237 a little bit code cleanup
3239 ------------------------------------------------------------------------
3240 r319 | lh3lh3 | 2009-06-08 09:22:33 -0400 (Mon, 08 Jun 2009) | 4 lines
3242 M /trunk/samtools/misc/samtools.pl
3245 * change default parameters
3246 * optionally print filtered variants
3248 ------------------------------------------------------------------------
3249 r318 | lh3lh3 | 2009-06-08 09:14:26 -0400 (Mon, 08 Jun 2009) | 3 lines
3251 M /trunk/samtools/misc/samtools.pl
3254 * combine snpFilter and indelFilter
3256 ------------------------------------------------------------------------
3257 r317 | lh3lh3 | 2009-06-08 06:31:42 -0400 (Mon, 08 Jun 2009) | 3 lines
3259 M /trunk/samtools/misc/samtools.pl
3262 * change a default parameter
3264 ------------------------------------------------------------------------
3265 r316 | lh3lh3 | 2009-06-08 06:11:06 -0400 (Mon, 08 Jun 2009) | 5 lines
3267 M /trunk/samtools/bam_maqcns.c
3268 M /trunk/samtools/bam_maqcns.h
3269 M /trunk/samtools/bam_plcmd.c
3270 M /trunk/samtools/bamtk.c
3271 M /trunk/samtools/sam.c
3273 * samtools-0.1.4-2 (r316)
3274 * pileup: cap mapping quality at 60 (by default)
3275 * pileup: always calculate RMS mapq
3276 * pileup: allow to output variant sites only
3278 ------------------------------------------------------------------------
3279 r312 | lh3lh3 | 2009-06-04 08:01:10 -0400 (Thu, 04 Jun 2009) | 3 lines
3281 M /trunk/samtools/misc/samtools.pl
3286 ------------------------------------------------------------------------
3287 r311 | lh3lh3 | 2009-06-03 04:40:40 -0400 (Wed, 03 Jun 2009) | 2 lines
3289 M /trunk/samtools/misc/samtools.pl
3291 * in snpFilter, suppress non-SNP sites
3293 ------------------------------------------------------------------------
3294 r310 | lh3lh3 | 2009-06-01 09:35:13 -0400 (Mon, 01 Jun 2009) | 3 lines
3296 M /trunk/samtools/misc/samtools.pl
3301 ------------------------------------------------------------------------
3302 r309 | lh3lh3 | 2009-06-01 09:04:39 -0400 (Mon, 01 Jun 2009) | 3 lines
3304 M /trunk/samtools/misc/samtools.pl
3309 ------------------------------------------------------------------------
3310 r306 | lh3lh3 | 2009-05-28 06:49:35 -0400 (Thu, 28 May 2009) | 3 lines
3312 M /trunk/samtools/bgzf.c
3314 * minor changes to bgzf: return NULL if fd == -1
3315 * suggested by {kdj,jm18}@sanger.ac.uk
3317 ------------------------------------------------------------------------
3318 r305 | lh3lh3 | 2009-05-28 06:16:08 -0400 (Thu, 28 May 2009) | 2 lines
3320 A /trunk/samtools/misc/interpolate_sam.pl
3322 Script for paired-end pileup, contributed by Stephen Montgomery.
3324 ------------------------------------------------------------------------
3325 r304 | lh3lh3 | 2009-05-28 06:08:49 -0400 (Thu, 28 May 2009) | 3 lines
3327 M /trunk/samtools/bamtk.c
3328 M /trunk/samtools/sam.c
3330 * samtools-0.1.4-1 (r304)
3331 * fixed a minor bug in printing headers
3333 ------------------------------------------------------------------------
3334 r297 | lh3lh3 | 2009-05-21 11:06:16 -0400 (Thu, 21 May 2009) | 2 lines
3336 M /trunk/samtools/ChangeLog
3337 M /trunk/samtools/NEWS
3338 M /trunk/samtools/bam_plcmd.c
3339 M /trunk/samtools/bamtk.c
3340 M /trunk/samtools/misc/maq2sam.c
3341 M /trunk/samtools/samtools.1
3343 Release samtools-0.1.4
3345 ------------------------------------------------------------------------
3346 r296 | lh3lh3 | 2009-05-21 07:53:14 -0400 (Thu, 21 May 2009) | 3 lines
3348 M /trunk/samtools/bam_maqcns.c
3349 M /trunk/samtools/bamtk.c
3351 * samtools-0.1.3-24 (r296)
3352 * another similar bug in the indel caller
3354 ------------------------------------------------------------------------
3355 r295 | lh3lh3 | 2009-05-21 07:50:28 -0400 (Thu, 21 May 2009) | 3 lines
3357 M /trunk/samtools/bam_maqcns.c
3358 M /trunk/samtools/bamtk.c
3360 * samtools-0.1.3-23 (r295)
3361 * fixed a critical bug in the indel caller
3363 ------------------------------------------------------------------------
3364 r294 | lh3lh3 | 2009-05-20 08:00:20 -0400 (Wed, 20 May 2009) | 2 lines
3366 M /trunk/samtools/bam_stat.c
3368 added a missing header file
3370 ------------------------------------------------------------------------
3371 r293 | lh3lh3 | 2009-05-19 18:44:25 -0400 (Tue, 19 May 2009) | 3 lines
3373 M /trunk/samtools/bam_tview.c
3374 M /trunk/samtools/bamtk.c
3376 * samtools-0.1.3-22 (r293)
3377 * open tview in the dot-view mode by default
3379 ------------------------------------------------------------------------
3380 r292 | lh3lh3 | 2009-05-18 16:01:23 -0400 (Mon, 18 May 2009) | 6 lines
3382 M /trunk/samtools/samtools.1
3384 Added a note to the manual. Currently SAMtools used unaligned words in
3385 several places. Although this does not cause bus errors to me, it may
3386 affect portability. Please see the "Bus error" wiki page for more
3387 information. Also thank James Bonfields for pointing this out.
3390 ------------------------------------------------------------------------
3391 r286 | lh3lh3 | 2009-05-14 10:23:13 -0400 (Thu, 14 May 2009) | 3 lines
3393 M /trunk/samtools/bam.h
3394 M /trunk/samtools/bam_aux.c
3395 M /trunk/samtools/bamtk.c
3397 * samtools-0.1.3-21 (286)
3398 * declare bam_aux_get_core() in bam.h
3400 ------------------------------------------------------------------------
3401 r276 | lh3lh3 | 2009-05-13 05:07:55 -0400 (Wed, 13 May 2009) | 5 lines
3403 M /trunk/samtools/bam.h
3404 M /trunk/samtools/bam_index.c
3405 M /trunk/samtools/bamtk.c
3407 * samtools-0.1.3-20 (r276)
3408 * remove bam1_t::hash again. We need to modify the Perl API anyway to
3409 make it work with the latest SVN.
3410 * As is suggested by Tim, scan "{base}.bai" and "{base}.bam.bai" for index
3412 ------------------------------------------------------------------------
3413 r275 | lh3lh3 | 2009-05-12 16:14:10 -0400 (Tue, 12 May 2009) | 4 lines
3415 M /trunk/samtools/ChangeLog
3416 M /trunk/samtools/bam.h
3417 M /trunk/samtools/bamtk.c
3419 * samtools-0.1.3-19 (r275)
3420 * a minor change to the bam1_t struct: added back "void *hash" for the
3421 backward compatibility with Bio::DB::Sam
3423 ------------------------------------------------------------------------
3424 r273 | lh3lh3 | 2009-05-12 09:28:39 -0400 (Tue, 12 May 2009) | 3 lines
3426 M /trunk/samtools/bam_rmdupse.c
3427 M /trunk/samtools/bamtk.c
3429 * samtools-0.1.3-18 (r273)
3430 * rmdupse: do not remove unmapped reads
3432 ------------------------------------------------------------------------
3433 r272 | lh3lh3 | 2009-05-12 09:20:00 -0400 (Tue, 12 May 2009) | 2 lines
3435 M /trunk/samtools/bam_rmdupse.c
3437 change a parameter. It does nothing
3439 ------------------------------------------------------------------------
3440 r271 | lh3lh3 | 2009-05-12 09:17:58 -0400 (Tue, 12 May 2009) | 3 lines
3442 M /trunk/samtools/Makefile.am
3443 M /trunk/samtools/Makefile.generic
3444 M /trunk/samtools/Makefile.lite
3445 A /trunk/samtools/bam_rmdupse.c
3446 M /trunk/samtools/bamtk.c
3447 M /trunk/samtools/configure.ac
3449 * samtools-0.1.3-17 (r271)
3450 * added 'rmdupse' command
3452 ------------------------------------------------------------------------
3453 r267 | lh3lh3 | 2009-05-05 17:31:41 -0400 (Tue, 05 May 2009) | 3 lines
3455 M /trunk/samtools/bamtk.c
3456 M /trunk/samtools/sam_view.c
3458 * samtools-0.1.3-16 (r267)
3459 * in sam_view.c, changed g_flag_on based on the suggestion by Angie Hinrichs
3461 ------------------------------------------------------------------------
3462 r266 | lh3lh3 | 2009-05-05 17:23:27 -0400 (Tue, 05 May 2009) | 3 lines
3464 M /trunk/samtools/bam_import.c
3465 M /trunk/samtools/bamtk.c
3467 * samtools-0.1.3-15 (r266)
3468 * report an error if a non-* reference is present while @SQ is absent
3470 ------------------------------------------------------------------------
3471 r265 | lh3lh3 | 2009-05-05 17:09:00 -0400 (Tue, 05 May 2009) | 3 lines
3473 M /trunk/samtools/bam.h
3474 M /trunk/samtools/bam_import.c
3475 M /trunk/samtools/bamtk.c
3476 M /trunk/samtools/sam.c
3477 M /trunk/samtools/sam_view.c
3479 * samtools-0.1.3-14 (r262)
3480 * make samopen() recognize @SQ header lines
3482 ------------------------------------------------------------------------
3483 r261 | lh3lh3 | 2009-05-05 10:10:30 -0400 (Tue, 05 May 2009) | 3 lines
3485 M /trunk/samtools/bam_plcmd.c
3486 M /trunk/samtools/bamtk.c
3487 M /trunk/samtools/bgzf.c
3488 M /trunk/samtools/sam.c
3489 M /trunk/samtools/sam_view.c
3491 * samtools-0.1.3-13 (r260)
3492 * report error for file I/O error
3494 ------------------------------------------------------------------------
3495 r260 | lh3lh3 | 2009-05-05 10:01:16 -0400 (Tue, 05 May 2009) | 2 lines
3497 M /trunk/samtools/Makefile.am
3501 ------------------------------------------------------------------------
3502 r259 | lh3lh3 | 2009-05-05 09:52:25 -0400 (Tue, 05 May 2009) | 3 lines
3504 M /trunk/samtools/bam.h
3505 M /trunk/samtools/bam_pileup.c
3506 M /trunk/samtools/bam_plcmd.c
3507 M /trunk/samtools/bamtk.c
3508 M /trunk/samtools/sam.c
3509 M /trunk/samtools/sam.h
3511 * samtools-0.1.3-12 (r259)
3512 * use the new I/O interface in pileup
3514 ------------------------------------------------------------------------
3515 r258 | lh3lh3 | 2009-05-05 09:33:22 -0400 (Tue, 05 May 2009) | 3 lines
3517 M /trunk/samtools/Makefile.generic
3518 M /trunk/samtools/Makefile.lite
3519 M /trunk/samtools/bam.c
3520 M /trunk/samtools/bam.h
3521 M /trunk/samtools/bam_import.c
3522 M /trunk/samtools/bamtk.c
3523 A /trunk/samtools/sam.c
3524 A /trunk/samtools/sam.h
3525 A /trunk/samtools/sam_view.c
3527 * samtools-0.1.3-11 (r258)
3528 * unify the interface to BAM and SAM I/O
3530 ------------------------------------------------------------------------
3531 r257 | lh3lh3 | 2009-05-05 04:53:35 -0400 (Tue, 05 May 2009) | 3 lines
3533 M /trunk/samtools/Makefile.lite
3534 M /trunk/samtools/bam_plcmd.c
3535 M /trunk/samtools/bamtk.c
3537 * samtools-0.1.3-10 (r257)
3538 * allow hex with "pileup -m"
3540 ------------------------------------------------------------------------
3541 r256 | lh3lh3 | 2009-05-04 14:16:50 -0400 (Mon, 04 May 2009) | 4 lines
3543 M /trunk/samtools/bam_lpileup.c
3544 M /trunk/samtools/bamtk.c
3546 * samtools-0.1.3-9 (r256)
3547 * fixed a bug in bam_lpileup.c
3548 * I do not know if this also fixes the bug causing assertion failure in the tview
3550 ------------------------------------------------------------------------
3551 r251 | lh3lh3 | 2009-04-28 08:53:23 -0400 (Tue, 28 Apr 2009) | 3 lines
3553 M /trunk/samtools/bam_pileup.c
3554 M /trunk/samtools/bamtk.c
3556 * samtools-0.1.3-8 (r251)
3557 * fixed a bug when there are reads without coordinates
3559 ------------------------------------------------------------------------
3560 r250 | lh3lh3 | 2009-04-28 08:43:33 -0400 (Tue, 28 Apr 2009) | 2 lines
3562 A /trunk/samtools/AUTHORS
3563 A /trunk/samtools/README
3564 M /trunk/samtools/cleanup.sh
3568 ------------------------------------------------------------------------
3569 r249 | lh3lh3 | 2009-04-28 08:37:16 -0400 (Tue, 28 Apr 2009) | 2 lines
3571 M /trunk/samtools/Makefile.generic
3572 M /trunk/samtools/Makefile.lite
3573 M /trunk/samtools/configure.ac
3574 M /trunk/samtools/misc/Makefile.generic
3576 improve large file support in compilation
3578 ------------------------------------------------------------------------
3579 r248 | lh3lh3 | 2009-04-28 08:33:24 -0400 (Tue, 28 Apr 2009) | 2 lines
3581 M /trunk/samtools/INSTALL
3585 ------------------------------------------------------------------------
3586 r247 | lh3lh3 | 2009-04-28 08:28:50 -0400 (Tue, 28 Apr 2009) | 2 lines
3588 M /trunk/samtools/Makefile.am
3589 M /trunk/samtools/autogen.sh
3590 M /trunk/samtools/cleanup.sh
3591 M /trunk/samtools/configure.ac
3592 A /trunk/samtools/misc/Makefile.am
3594 fixed various issues about the GNU building scripts
3596 ------------------------------------------------------------------------
3597 r246 | lh3lh3 | 2009-04-28 08:10:23 -0400 (Tue, 28 Apr 2009) | 4 lines
3599 M /trunk/samtools/ChangeLog
3600 D /trunk/samtools/Makefile
3601 A /trunk/samtools/Makefile.am
3602 A /trunk/samtools/Makefile.generic
3603 A /trunk/samtools/autogen.sh
3604 M /trunk/samtools/bam.h
3605 M /trunk/samtools/bam_aux.c
3606 M /trunk/samtools/bam_tview.c
3607 M /trunk/samtools/bamtk.c
3608 A /trunk/samtools/cleanup.sh
3609 A /trunk/samtools/configure.ac
3610 D /trunk/samtools/misc/Makefile
3611 A /trunk/samtools/misc/Makefile.generic (from /trunk/samtools/misc/Makefile:245)
3613 * samtools-0.1.3-7 (r246)
3614 * incorporated revisions from Nils Homer
3615 * enhanced support of displaying color-space reads
3617 ------------------------------------------------------------------------
3618 r244 | lh3lh3 | 2009-04-25 06:49:40 -0400 (Sat, 25 Apr 2009) | 3 lines
3620 M /trunk/samtools/bam_md.c
3621 M /trunk/samtools/bamtk.c
3623 * samtools-0.1.3-6 (r244)
3624 * fixed segfault for unmapped reads
3626 ------------------------------------------------------------------------
3627 r243 | lh3lh3 | 2009-04-24 16:27:26 -0400 (Fri, 24 Apr 2009) | 5 lines
3629 M /trunk/samtools/bam.h
3630 M /trunk/samtools/bam_maqcns.c
3631 M /trunk/samtools/bam_md.c
3632 M /trunk/samtools/bamtk.c
3634 * samtools-0.1.3-5 (r243)
3635 * fixed a long existing bug which may cause memory leak
3637 * consensus calling now works with "=", but indel calling not
3639 ------------------------------------------------------------------------
3640 r242 | lh3lh3 | 2009-04-24 15:44:46 -0400 (Fri, 24 Apr 2009) | 3 lines
3642 M /trunk/samtools/bam_md.c
3643 M /trunk/samtools/bamtk.c
3645 * samtools-0.1.3-4 (r242)
3646 * fixed a memory leak
3648 ------------------------------------------------------------------------
3649 r240 | lh3lh3 | 2009-04-24 11:40:18 -0400 (Fri, 24 Apr 2009) | 5 lines
3651 M /trunk/samtools/Makefile
3652 M /trunk/samtools/Makefile.lite
3653 M /trunk/samtools/bam.h
3654 M /trunk/samtools/bam_aux.c
3655 A /trunk/samtools/bam_md.c
3656 M /trunk/samtools/bam_plcmd.c
3657 M /trunk/samtools/bamtk.c
3659 * samtools-0.1.3-3 (r240)
3661 * generate "=" bases
3662 * the plain pileup now support "=" bases, but consensus calling and glfgen may fail
3664 ------------------------------------------------------------------------
3665 r239 | lh3lh3 | 2009-04-24 07:08:20 -0400 (Fri, 24 Apr 2009) | 5 lines
3667 M /trunk/samtools/bam.h
3668 M /trunk/samtools/bam_aux.c
3669 M /trunk/samtools/bamtk.c
3671 * samtools-0.1.3-2 (r239)
3672 * fixed bugs in bam_aux.c (these functions nevered used by samtools)
3673 * removed bam_aux_init()/bam_aux_destroy()
3674 * added tagview for testing bam_aux
3676 ------------------------------------------------------------------------
3677 r235 | lh3lh3 | 2009-04-21 18:17:39 -0400 (Tue, 21 Apr 2009) | 3 lines
3679 M /trunk/samtools/bam_pileup.c
3680 M /trunk/samtools/bamtk.c
3683 * fixed a bug in pileup: the first read in a chromosome may not be printed
3685 ------------------------------------------------------------------------
3686 r232 | lh3lh3 | 2009-04-16 10:25:43 -0400 (Thu, 16 Apr 2009) | 2 lines
3688 M /trunk/samtools/Makefile.lite
3690 a missing file in Makefile.lite
3692 ------------------------------------------------------------------------
3693 r227 | lh3lh3 | 2009-04-15 17:02:53 -0400 (Wed, 15 Apr 2009) | 2 lines
3695 M /trunk/samtools/NEWS
3696 M /trunk/samtools/bamtk.c
3698 Release samtools-0.1.3
3700 ------------------------------------------------------------------------
3701 r223 | lh3lh3 | 2009-04-15 09:31:32 -0400 (Wed, 15 Apr 2009) | 3 lines
3703 M /trunk/samtools/bam_plcmd.c
3704 M /trunk/samtools/bamtk.c
3707 * make samtools more robust to weird input such as empty file
3709 ------------------------------------------------------------------------
3710 r222 | lh3lh3 | 2009-04-15 09:05:33 -0400 (Wed, 15 Apr 2009) | 2 lines
3712 M /trunk/samtools/ChangeLog
3713 M /trunk/samtools/NEWS
3714 M /trunk/samtools/samtools.1
3716 prepare for release 0.1.3
3718 ------------------------------------------------------------------------
3719 r221 | lh3lh3 | 2009-04-15 08:32:14 -0400 (Wed, 15 Apr 2009) | 2 lines
3721 A /trunk/samtools/misc/blast2sam.pl
3723 convert NCBI-BLASTN to SAM
3725 ------------------------------------------------------------------------
3726 r220 | lh3lh3 | 2009-04-15 08:18:19 -0400 (Wed, 15 Apr 2009) | 3 lines
3728 M /trunk/samtools/bam_lpileup.c
3729 M /trunk/samtools/bamtk.c
3732 * fixed a small memory leak in tview
3734 ------------------------------------------------------------------------
3735 r219 | lh3lh3 | 2009-04-15 08:00:08 -0400 (Wed, 15 Apr 2009) | 3 lines
3737 M /trunk/samtools/bam_rmdup.c
3738 M /trunk/samtools/bamtk.c
3741 * fixed a bug in rmdup when there are unmapped reads
3743 ------------------------------------------------------------------------
3744 r218 | lh3lh3 | 2009-04-14 17:28:58 -0400 (Tue, 14 Apr 2009) | 2 lines
3746 M /trunk/samtools/ChangeLog
3747 M /trunk/samtools/NEWS
3749 proposed NEWS for the new release (have not yet)
3751 ------------------------------------------------------------------------
3752 r216 | lh3lh3 | 2009-04-14 17:10:46 -0400 (Tue, 14 Apr 2009) | 4 lines
3754 M /trunk/samtools/misc/samtools.pl
3757 * improve indelFilter to avoid filtering true indels. The new filter relies
3758 on the new pileup indel line implemented in samtools-0.1.2-25
3760 ------------------------------------------------------------------------
3761 r215 | lh3lh3 | 2009-04-14 17:04:19 -0400 (Tue, 14 Apr 2009) | 4 lines
3763 M /trunk/samtools/bam_maqcns.c
3764 M /trunk/samtools/bam_plcmd.c
3765 M /trunk/samtools/bamtk.c
3766 M /trunk/samtools/samtools.1
3769 * change the pileup indel line to shows the number of alignments actually
3772 ------------------------------------------------------------------------
3773 r211 | lh3lh3 | 2009-04-13 07:07:13 -0400 (Mon, 13 Apr 2009) | 2 lines
3775 M /trunk/samtools/ChangeLog
3777 update ChangeLog from "svn log"
3779 ------------------------------------------------------------------------
3780 r210 | lh3lh3 | 2009-04-12 15:57:05 -0400 (Sun, 12 Apr 2009) | 4 lines
3782 M /trunk/samtools/bam.c
3783 M /trunk/samtools/bam_import.c
3784 M /trunk/samtools/bam_sort.c
3785 M /trunk/samtools/bamtk.c
3786 M /trunk/samtools/kseq.h
3789 * in merge, gives a warning rather than error if the target sequence length is different
3790 * allow empty header
3792 ------------------------------------------------------------------------
3793 r209 | lh3lh3 | 2009-04-12 15:32:44 -0400 (Sun, 12 Apr 2009) | 3 lines
3795 M /trunk/samtools/bam.c
3796 M /trunk/samtools/bam_import.c
3797 M /trunk/samtools/bamtk.c
3800 * recognize '*' at the QUAL field
3802 ------------------------------------------------------------------------
3803 r208 | lh3lh3 | 2009-04-12 15:08:02 -0400 (Sun, 12 Apr 2009) | 3 lines
3805 M /trunk/samtools/bam_import.c
3806 M /trunk/samtools/bamtk.c
3807 M /trunk/samtools/kseq.h
3810 * the field separater is TAB only, now
3812 ------------------------------------------------------------------------
3813 r207 | lh3lh3 | 2009-04-08 10:18:03 -0400 (Wed, 08 Apr 2009) | 2 lines
3815 M /trunk/samtools/examples/ex1.sam.gz
3817 * fixed the problem in the example alignment due to the bug in fixmate
3819 ------------------------------------------------------------------------
3820 r206 | lh3lh3 | 2009-04-08 10:15:05 -0400 (Wed, 08 Apr 2009) | 3 lines
3822 M /trunk/samtools/bam_mate.c
3823 M /trunk/samtools/bamtk.c
3824 M /trunk/samtools/misc/soap2sam.pl
3827 * fixed a nasty bug in `fixmate'
3829 ------------------------------------------------------------------------
3830 r205 | lh3lh3 | 2009-04-08 05:57:08 -0400 (Wed, 08 Apr 2009) | 2 lines
3832 M /trunk/samtools/misc/bowtie2sam.pl
3833 M /trunk/samtools/misc/soap2sam.pl
3834 M /trunk/samtools/misc/wgsim_eval.pl
3836 make the script robust to the bugs in SOAP-2.1.7
3838 ------------------------------------------------------------------------
3839 r200 | lh3lh3 | 2009-04-02 10:14:56 -0400 (Thu, 02 Apr 2009) | 3 lines
3841 M /trunk/samtools/bam_stat.c
3842 M /trunk/samtools/bamtk.c
3845 * check if file is truncated in flagstat
3847 ------------------------------------------------------------------------
3848 r199 | lh3lh3 | 2009-04-02 10:09:10 -0400 (Thu, 02 Apr 2009) | 3 lines
3850 M /trunk/samtools/bamtk.c
3853 * print the header if requested
3855 ------------------------------------------------------------------------
3856 r193 | lh3lh3 | 2009-03-27 11:09:50 -0400 (Fri, 27 Mar 2009) | 3 lines
3858 M /trunk/samtools/bam_plcmd.c
3859 M /trunk/samtools/bamtk.c
3862 * fixed a minor bug reported by Nils Homer
3864 ------------------------------------------------------------------------
3865 r185 | lh3lh3 | 2009-03-24 07:50:32 -0400 (Tue, 24 Mar 2009) | 2 lines
3867 A /trunk/samtools/Makefile (from /trunk/samtools/Makefile.std:184)
3868 D /trunk/samtools/Makefile.std
3869 A /trunk/samtools/misc/Makefile (from /trunk/samtools/misc/Makefile.std:184)
3870 D /trunk/samtools/misc/Makefile.std
3872 rename Makefile.std as Makefile. GNU building systerm is not ready and may take some time...
3874 ------------------------------------------------------------------------
3875 r184 | lh3lh3 | 2009-03-24 06:36:38 -0400 (Tue, 24 Mar 2009) | 4 lines
3877 D /trunk/samtools/Makefile
3878 A /trunk/samtools/Makefile.std (from /trunk/samtools/Makefile:183)
3879 M /trunk/samtools/bam_sort.c
3880 M /trunk/samtools/bam_tview.c
3881 M /trunk/samtools/bamtk.c
3882 D /trunk/samtools/misc/Makefile
3883 A /trunk/samtools/misc/Makefile.std (from /trunk/samtools/misc/Makefile:182)
3884 M /trunk/samtools/samtools.1
3887 * incorporating Nils' changes
3888 * rename Makefile to Makefile.std and prepare to add the GNU building systerms (also by Nils)
3890 ------------------------------------------------------------------------
3891 r183 | lh3lh3 | 2009-03-24 06:30:23 -0400 (Tue, 24 Mar 2009) | 4 lines
3893 M /trunk/samtools/Makefile
3894 M /trunk/samtools/bam_import.c
3895 M /trunk/samtools/bam_maqcns.c
3896 M /trunk/samtools/bam_maqcns.h
3897 M /trunk/samtools/bam_plcmd.c
3898 M /trunk/samtools/bamtk.c
3899 M /trunk/samtools/kseq.h
3900 A /trunk/samtools/kstring.c
3901 A /trunk/samtools/kstring.h
3904 * made pileup take a list of proposed indels. An insertion is N at the moment.
3905 * added my kstring library for a bit complex parsing of the position list.
3907 ------------------------------------------------------------------------
3908 r169 | lh3lh3 | 2009-03-12 09:40:14 -0400 (Thu, 12 Mar 2009) | 3 lines
3910 M /trunk/samtools/misc/soap2sam.pl
3913 * more robust to truncated soap output
3915 ------------------------------------------------------------------------
3916 r168 | lh3lh3 | 2009-03-11 06:49:00 -0400 (Wed, 11 Mar 2009) | 2 lines
3918 M /trunk/samtools/Makefile.lite
3920 added bam_stat.o to Makefile.lite
3922 ------------------------------------------------------------------------
3923 r167 | lh3lh3 | 2009-03-10 18:11:31 -0400 (Tue, 10 Mar 2009) | 3 lines
3925 M /trunk/samtools/bam_maqcns.c
3926 M /trunk/samtools/bamtk.c
3929 * generate RMS of mapQ instead of max mapQ
3931 ------------------------------------------------------------------------
3932 r166 | lh3lh3 | 2009-03-10 18:06:45 -0400 (Tue, 10 Mar 2009) | 3 lines
3934 M /trunk/samtools/bam_plcmd.c
3935 M /trunk/samtools/bamtk.c
3936 M /trunk/samtools/glf.c
3937 M /trunk/samtools/glf.h
3938 M /trunk/samtools/misc/Makefile
3943 ------------------------------------------------------------------------
3944 r159 | lh3lh3 | 2009-03-03 06:26:08 -0500 (Tue, 03 Mar 2009) | 3 lines
3946 M /trunk/samtools/bam_plcmd.c
3947 M /trunk/samtools/bamtk.c
3950 * fixed a minor bug in displaying pileup
3952 ------------------------------------------------------------------------
3953 r158 | lh3lh3 | 2009-03-03 06:24:16 -0500 (Tue, 03 Mar 2009) | 3 lines
3955 M /trunk/samtools/ChangeLog
3956 M /trunk/samtools/bamtk.c
3959 * optionally print SAM header
3961 ------------------------------------------------------------------------
3962 r153 | lh3lh3 | 2009-03-02 05:45:28 -0500 (Mon, 02 Mar 2009) | 3 lines
3964 M /trunk/samtools/bamtk.c
3965 M /trunk/samtools/glf.c
3968 * use "GLF\3" as the magic for GLFv3 files
3970 ------------------------------------------------------------------------
3971 r152 | lh3lh3 | 2009-03-02 05:39:09 -0500 (Mon, 02 Mar 2009) | 5 lines
3973 M /trunk/samtools/Makefile
3974 M /trunk/samtools/bam_import.c
3975 M /trunk/samtools/bam_index.c
3976 M /trunk/samtools/bam_plcmd.c
3977 M /trunk/samtools/bamtk.c
3978 M /trunk/samtools/glf.c
3979 M /trunk/samtools/glf.h
3982 * fixed a bug in import: core.bin is undefined for unmapped reads
3983 * this bug can be alleviated (not completely solved) in bam_index.c
3984 * update to GLFv3: pos is changed to offset for better compression
3986 ------------------------------------------------------------------------
3987 r151 | lh3lh3 | 2009-03-01 10:18:43 -0500 (Sun, 01 Mar 2009) | 3 lines
3989 M /trunk/samtools/misc/wgsim.c
3992 * fixed a bug in simulating indels
3994 ------------------------------------------------------------------------
3995 r145 | lh3lh3 | 2009-02-26 14:43:57 -0500 (Thu, 26 Feb 2009) | 4 lines
3997 M /trunk/samtools/misc/wgsim.c
4000 * allow to print mismatch information as fastq comment. MAQ does
4001 not like long read names.
4003 ------------------------------------------------------------------------
4004 r141 | lh3lh3 | 2009-02-26 09:53:03 -0500 (Thu, 26 Feb 2009) | 6 lines
4006 M /trunk/samtools/ChangeLog
4007 M /trunk/samtools/misc/wgsim.c
4008 M /trunk/samtools/misc/wgsim_eval.pl
4011 * fixed a bug about color read coordinates
4012 * fixed a bug in read names
4013 * wgsim_eval.pl-0.1.3
4014 * make the script work with color reads
4016 ------------------------------------------------------------------------
4017 r140 | lh3lh3 | 2009-02-26 09:02:57 -0500 (Thu, 26 Feb 2009) | 2 lines
4019 M /trunk/samtools/misc/Makefile
4020 M /trunk/samtools/misc/wgsim.c
4022 * wgsim: added a note
4024 ------------------------------------------------------------------------
4025 r139 | lh3lh3 | 2009-02-26 06:39:08 -0500 (Thu, 26 Feb 2009) | 7 lines
4027 M /trunk/samtools/misc/wgsim.c
4028 M /trunk/samtools/misc/wgsim_eval.pl
4031 * considerable code clean up
4032 * print number of substitutions/indels/errors on each read
4033 * potentially support SOLiD simulation, though not tested at the moment
4034 * wgsim_eval.pl-0.1.2
4035 * change in accordant with wgsim
4037 ------------------------------------------------------------------------
4038 r129 | lh3lh3 | 2009-02-18 17:23:27 -0500 (Wed, 18 Feb 2009) | 3 lines
4040 M /trunk/samtools/bam_index.c
4041 M /trunk/samtools/bamtk.c
4044 * fixed a bug in bam_fetch, caused by completely contained adjacent chunks
4046 ------------------------------------------------------------------------
4047 r128 | bhandsaker | 2009-02-18 14:06:57 -0500 (Wed, 18 Feb 2009) | 2 lines
4049 M /trunk/samtools/bamtk.c
4051 Fix annoying segv when invalid region specified.
4053 ------------------------------------------------------------------------
4054 r127 | lh3lh3 | 2009-02-17 05:49:55 -0500 (Tue, 17 Feb 2009) | 2 lines
4056 D /trunk/samtools/misc/indel_filter.pl
4057 A /trunk/samtools/misc/samtools.pl
4059 * move indel_filter.pl to samtools.pl
4061 ------------------------------------------------------------------------
4062 r126 | lh3lh3 | 2009-02-14 16:22:30 -0500 (Sat, 14 Feb 2009) | 3 lines
4064 M /trunk/samtools/bam_mate.c
4065 M /trunk/samtools/bamtk.c
4068 * fixed a bug in fixmate: SE reads are flagged as BAM_FMUNMAP
4070 ------------------------------------------------------------------------
4071 r125 | lh3lh3 | 2009-02-13 04:54:45 -0500 (Fri, 13 Feb 2009) | 3 lines
4073 M /trunk/samtools/bam_stat.c
4074 M /trunk/samtools/bamtk.c
4077 * fixed a minor bug in flagstat
4079 ------------------------------------------------------------------------
4080 r124 | lh3lh3 | 2009-02-12 06:15:32 -0500 (Thu, 12 Feb 2009) | 3 lines
4082 M /trunk/samtools/bam_maqcns.c
4083 M /trunk/samtools/bamtk.c
4084 M /trunk/samtools/misc/indel_filter.pl
4087 * improve indel caller by setting maximum window size
4089 ------------------------------------------------------------------------
4090 r123 | lh3lh3 | 2009-02-12 05:30:29 -0500 (Thu, 12 Feb 2009) | 2 lines
4092 M /trunk/samtools/bam_plcmd.c
4093 M /trunk/samtools/bamtk.c
4095 * output max mapping quality in indel line
4097 ------------------------------------------------------------------------
4098 r122 | lh3lh3 | 2009-02-11 05:59:10 -0500 (Wed, 11 Feb 2009) | 2 lines
4100 M /trunk/samtools/misc/maq2sam.c
4102 fixed a bug in generating tag AM
4104 ------------------------------------------------------------------------
4105 r121 | lh3lh3 | 2009-02-03 05:43:11 -0500 (Tue, 03 Feb 2009) | 2 lines
4107 M /trunk/samtools/bam_index.c
4108 M /trunk/samtools/bamtk.c
4110 fixed a potential memory problem in indexing
4112 ------------------------------------------------------------------------
4113 r120 | bhandsaker | 2009-02-02 10:52:52 -0500 (Mon, 02 Feb 2009) | 2 lines
4115 M /trunk/samtools/Makefile
4117 Pass LIBS to recursive targets to facilitate building at Broad.
4119 ------------------------------------------------------------------------
4120 r119 | lh3lh3 | 2009-02-02 05:12:15 -0500 (Mon, 02 Feb 2009) | 4 lines
4122 M /trunk/samtools/ChangeLog
4123 M /trunk/samtools/bam_plcmd.c
4124 M /trunk/samtools/bam_stat.c
4125 M /trunk/samtools/bamtk.c
4128 * fixed a bug in generating GLFv2 for indels
4129 * improve flagstat report a little bit
4131 ------------------------------------------------------------------------
4132 r118 | lh3lh3 | 2009-01-29 07:33:23 -0500 (Thu, 29 Jan 2009) | 3 lines
4134 M /trunk/samtools/Makefile
4135 A /trunk/samtools/bam_stat.c
4136 M /trunk/samtools/bamtk.c
4139 * added flagstat command
4141 ------------------------------------------------------------------------
4142 r116 | lh3lh3 | 2009-01-28 08:31:12 -0500 (Wed, 28 Jan 2009) | 2 lines
4144 M /trunk/samtools/ChangeLog
4145 M /trunk/samtools/NEWS
4146 M /trunk/samtools/bamtk.c
4147 M /trunk/samtools/samtools.1
4149 Release SAMtools-0.1.2
4151 ------------------------------------------------------------------------
4152 r115 | lh3lh3 | 2009-01-28 07:54:08 -0500 (Wed, 28 Jan 2009) | 2 lines
4154 A /trunk/samtools/misc/indel_filter.pl
4156 Script for filtering indel results
4158 ------------------------------------------------------------------------
4159 r114 | lh3lh3 | 2009-01-25 06:45:37 -0500 (Sun, 25 Jan 2009) | 2 lines
4161 A /trunk/samtools/misc/zoom2sam.pl
4165 ------------------------------------------------------------------------
4166 r113 | lh3lh3 | 2009-01-24 09:25:07 -0500 (Sat, 24 Jan 2009) | 2 lines
4168 A /trunk/samtools/misc/novo2sam.pl
4170 add a script to convert novo alignment to SAM
4172 ------------------------------------------------------------------------
4173 r112 | lh3lh3 | 2009-01-23 15:57:39 -0500 (Fri, 23 Jan 2009) | 2 lines
4175 M /trunk/samtools/ChangeLog
4176 M /trunk/samtools/ChangeLog.old
4177 M /trunk/samtools/samtools.1
4179 update documentation and ChangeLog
4181 ------------------------------------------------------------------------
4182 r111 | lh3lh3 | 2009-01-23 14:22:59 -0500 (Fri, 23 Jan 2009) | 3 lines
4184 M /trunk/samtools/bam_sort.c
4185 M /trunk/samtools/bamtk.c
4188 * fixed a bug in "merge" command line
4190 ------------------------------------------------------------------------
4191 r110 | lh3lh3 | 2009-01-22 10:36:48 -0500 (Thu, 22 Jan 2009) | 3 lines
4193 M /trunk/samtools/misc/Makefile
4194 A /trunk/samtools/misc/bowtie2sam.pl (from /branches/dev/samtools/misc/bowtie2sam.pl:108)
4195 M /trunk/samtools/misc/export2sam.pl
4196 A /trunk/samtools/misc/soap2sam.pl (from /branches/dev/samtools/misc/soap2sam.pl:108)
4197 A /trunk/samtools/misc/wgsim.c (from /branches/dev/samtools/misc/wgsim.c:108)
4198 A /trunk/samtools/misc/wgsim_eval.pl (from /branches/dev/samtools/misc/wgsim_eval.pl:108)
4200 * merge from branches/dev/
4201 * all future development will happen here
4203 ------------------------------------------------------------------------
4204 r109 | lh3lh3 | 2009-01-22 10:14:27 -0500 (Thu, 22 Jan 2009) | 3 lines
4206 M /trunk/samtools/COPYING
4207 M /trunk/samtools/ChangeLog
4208 A /trunk/samtools/INSTALL (from /branches/dev/samtools/INSTALL:108)
4209 M /trunk/samtools/Makefile
4210 A /trunk/samtools/Makefile.lite (from /branches/dev/samtools/Makefile.lite:108)
4211 M /trunk/samtools/bam.c
4212 M /trunk/samtools/bam.h
4213 M /trunk/samtools/bam_import.c
4214 M /trunk/samtools/bam_index.c
4215 M /trunk/samtools/bam_lpileup.c
4216 M /trunk/samtools/bam_maqcns.c
4217 M /trunk/samtools/bam_maqcns.h
4218 A /trunk/samtools/bam_mate.c (from /branches/dev/samtools/bam_mate.c:108)
4219 M /trunk/samtools/bam_pileup.c
4220 M /trunk/samtools/bam_plcmd.c
4221 A /trunk/samtools/bam_rmdup.c (from /branches/dev/samtools/bam_rmdup.c:108)
4222 M /trunk/samtools/bam_sort.c
4223 M /trunk/samtools/bamtk.c
4224 M /trunk/samtools/bgzf.h
4225 M /trunk/samtools/examples/00README.txt
4226 A /trunk/samtools/examples/Makefile (from /branches/dev/samtools/examples/Makefile:108)
4227 D /trunk/samtools/examples/ex1.fa.fai
4228 M /trunk/samtools/examples/ex1.sam.gz
4229 M /trunk/samtools/faidx.c
4230 A /trunk/samtools/glf.c (from /branches/dev/samtools/glf.c:108)
4231 M /trunk/samtools/glf.h
4232 M /trunk/samtools/misc/Makefile
4233 M /trunk/samtools/misc/maq2sam.c
4234 M /trunk/samtools/razf.c
4235 M /trunk/samtools/source.dot
4237 * Merge from branches/dev/
4238 * all future development will happen here at trunk/
4240 ------------------------------------------------------------------------
4241 r79 | bhandsaker | 2009-01-07 16:42:15 -0500 (Wed, 07 Jan 2009) | 2 lines
4243 M /trunk/samtools/bam_maqcns.c
4244 M /trunk/samtools/bam_tview.c
4246 Fix problem with compiling without curses.
4248 ------------------------------------------------------------------------
4249 r63 | lh3lh3 | 2008-12-22 10:58:02 -0500 (Mon, 22 Dec 2008) | 2 lines
4251 A /trunk/samtools (from /branches/dev/samtools:62)
4255 ------------------------------------------------------------------------
4256 r62 | lh3lh3 | 2008-12-22 10:55:13 -0500 (Mon, 22 Dec 2008) | 2 lines
4258 A /branches/dev/samtools/NEWS
4259 M /branches/dev/samtools/bamtk.c
4260 M /branches/dev/samtools/samtools.1
4262 Release samtools-0.1.1
4264 ------------------------------------------------------------------------
4265 r61 | lh3lh3 | 2008-12-22 10:46:08 -0500 (Mon, 22 Dec 2008) | 10 lines
4267 M /branches/dev/samtools/bam_aux.c
4268 M /branches/dev/samtools/bam_index.c
4269 M /branches/dev/samtools/bam_plcmd.c
4270 M /branches/dev/samtools/bam_tview.c
4271 M /branches/dev/samtools/bamtk.c
4272 M /branches/dev/samtools/razf.c
4273 M /branches/dev/samtools/samtools.1
4276 * fixed a bug in razf.c: reset z_eof when razf_seek() is called
4277 * fixed a memory leak in parsing a region
4278 * changed pileup a little bit when -s is in use: output ^ and $
4279 * when a bam is not indexed, output more meaningful error message
4280 * fixed a bug in indexing for small alignment
4281 * fixed a bug in the viewer when we come to the end of a reference file
4282 * updated documentation
4283 * prepare to release 0.1.1
4285 ------------------------------------------------------------------------
4286 r60 | lh3lh3 | 2008-12-22 10:10:16 -0500 (Mon, 22 Dec 2008) | 2 lines
4288 A /branches/dev/samtools/examples
4289 A /branches/dev/samtools/examples/00README.txt
4290 A /branches/dev/samtools/examples/ex1.fa
4291 A /branches/dev/samtools/examples/ex1.fa.fai
4292 A /branches/dev/samtools/examples/ex1.sam.gz
4296 ------------------------------------------------------------------------
4297 r59 | lh3lh3 | 2008-12-22 04:38:15 -0500 (Mon, 22 Dec 2008) | 2 lines
4299 M /branches/dev/samtools/ChangeLog
4303 ------------------------------------------------------------------------
4304 r58 | lh3lh3 | 2008-12-20 18:06:00 -0500 (Sat, 20 Dec 2008) | 3 lines
4306 M /branches/dev/samtools/misc/export2sam.pl
4309 * fixed several bugs
4311 ------------------------------------------------------------------------
4312 r57 | lh3lh3 | 2008-12-20 10:44:20 -0500 (Sat, 20 Dec 2008) | 2 lines
4314 A /branches/dev/samtools/misc/export2sam.pl
4316 convert Export format to SAM; not thoroughly tested
4318 ------------------------------------------------------------------------
4319 r56 | lh3lh3 | 2008-12-19 17:13:28 -0500 (Fri, 19 Dec 2008) | 6 lines
4321 M /branches/dev/samtools/bam_import.c
4322 M /branches/dev/samtools/bam_plcmd.c
4323 M /branches/dev/samtools/bam_tview.c
4324 M /branches/dev/samtools/bamtk.c
4325 A /branches/dev/samtools/source.dot
4328 * pileup: generate maq-like simple output
4329 * pileup: allow to output pileup at required sites
4330 * source.dot: source file relationship graph
4331 * tview: fixed a minor bug
4333 ------------------------------------------------------------------------
4334 r55 | lh3lh3 | 2008-12-19 15:10:26 -0500 (Fri, 19 Dec 2008) | 2 lines
4336 D /branches/dev/samtools/misc/all2sam.pl
4340 ------------------------------------------------------------------------
4341 r54 | lh3lh3 | 2008-12-16 17:34:25 -0500 (Tue, 16 Dec 2008) | 2 lines
4343 A /branches/dev/samtools/COPYING
4344 M /branches/dev/samtools/bam.h
4345 M /branches/dev/samtools/faidx.h
4346 M /branches/dev/samtools/khash.h
4347 M /branches/dev/samtools/kseq.h
4348 M /branches/dev/samtools/ksort.h
4349 M /branches/dev/samtools/samtools.1
4351 Added copyright information and a bit more documentation. No code change.
4353 ------------------------------------------------------------------------
4354 r53 | lh3lh3 | 2008-12-16 08:40:18 -0500 (Tue, 16 Dec 2008) | 3 lines
4356 M /branches/dev/samtools/bam.c
4357 M /branches/dev/samtools/bam.h
4358 M /branches/dev/samtools/bam_index.c
4359 M /branches/dev/samtools/bam_maqcns.c
4360 M /branches/dev/samtools/bamtk.c
4363 * improved efficiency of the indel caller for spliced alignments
4365 ------------------------------------------------------------------------
4366 r52 | lh3lh3 | 2008-12-16 05:28:20 -0500 (Tue, 16 Dec 2008) | 3 lines
4368 M /branches/dev/samtools/bam.c
4369 M /branches/dev/samtools/bam.h
4370 M /branches/dev/samtools/bam_aux.c
4371 M /branches/dev/samtools/bam_index.c
4372 M /branches/dev/samtools/bamtk.c
4375 * a bit code cleanup: reduce the dependency between source files
4377 ------------------------------------------------------------------------
4378 r51 | lh3lh3 | 2008-12-15 09:29:32 -0500 (Mon, 15 Dec 2008) | 3 lines
4380 M /branches/dev/samtools/bam_maqcns.c
4381 M /branches/dev/samtools/bam_plcmd.c
4382 M /branches/dev/samtools/bamtk.c
4385 * fixed a memory leak
4387 ------------------------------------------------------------------------
4388 r50 | lh3lh3 | 2008-12-15 09:00:13 -0500 (Mon, 15 Dec 2008) | 2 lines
4390 M /branches/dev/samtools/ChangeLog
4391 M /branches/dev/samtools/bam.h
4392 M /branches/dev/samtools/samtools.1
4394 update documentation, ChangeLog and a comment
4396 ------------------------------------------------------------------------
4397 r49 | lh3lh3 | 2008-12-15 08:36:43 -0500 (Mon, 15 Dec 2008) | 6 lines
4399 M /branches/dev/samtools/Makefile
4400 M /branches/dev/samtools/bam.h
4401 M /branches/dev/samtools/bam_maqcns.c
4402 M /branches/dev/samtools/bam_maqcns.h
4403 M /branches/dev/samtools/bam_pileup.c
4404 A /branches/dev/samtools/bam_plcmd.c
4405 M /branches/dev/samtools/bamtk.c
4406 M /branches/dev/samtools/samtools.1
4409 * moved pileup command to a separate source file
4410 * added indel caller
4411 * added bam_cal_segend(). (NOT WORKING for spliced alignment!!!)
4412 * updated documentation
4414 ------------------------------------------------------------------------
4415 r48 | lh3lh3 | 2008-12-12 08:55:36 -0500 (Fri, 12 Dec 2008) | 3 lines
4417 M /branches/dev/samtools/bam_maqcns.c
4418 M /branches/dev/samtools/bamtk.c
4421 * fixed another bug in maqcns when there is a nearby deletion
4423 ------------------------------------------------------------------------
4424 r47 | lh3lh3 | 2008-12-12 08:42:16 -0500 (Fri, 12 Dec 2008) | 5 lines
4426 M /branches/dev/samtools/bam_maqcns.c
4427 M /branches/dev/samtools/bam_pileup.c
4428 M /branches/dev/samtools/bamtk.c
4431 * pileup: outputing consensus is now optional
4432 * fixed a bug in glfgen. This bug also exists in maq's glfgen. However,
4433 I am not quite sure why the previous version may have problem.
4435 ------------------------------------------------------------------------
4436 r46 | lh3lh3 | 2008-12-12 06:44:56 -0500 (Fri, 12 Dec 2008) | 6 lines
4438 M /branches/dev/samtools/bam_pileup.c
4439 M /branches/dev/samtools/bamtk.c
4442 * add maq consensus to pileup. However, I will move this part to a new
4443 command as strictly speaking, consensus callin is not part of pileup,
4444 and imposing it would make it harder to generate for other language
4447 ------------------------------------------------------------------------
4448 r45 | bhandsaker | 2008-12-11 15:43:56 -0500 (Thu, 11 Dec 2008) | 2 lines
4450 M /branches/dev/samtools/bgzf.c
4452 Fix bug in tell() after reads that consume to the exact end of a block.
4454 ------------------------------------------------------------------------
4455 r44 | lh3lh3 | 2008-12-11 04:36:53 -0500 (Thu, 11 Dec 2008) | 2 lines
4457 M /branches/dev/samtools/samtools.1
4461 ------------------------------------------------------------------------
4462 r43 | lh3lh3 | 2008-12-11 04:25:36 -0500 (Thu, 11 Dec 2008) | 4 lines
4464 M /branches/dev/samtools/bam_import.c
4465 M /branches/dev/samtools/bamtk.c
4468 * fixed a bug in parser when there is auxiliary fields
4469 * made the parser a bit more robust
4471 ------------------------------------------------------------------------
4472 r42 | lh3lh3 | 2008-12-10 09:57:29 -0500 (Wed, 10 Dec 2008) | 5 lines
4474 M /branches/dev/samtools/bam_index.c
4475 M /branches/dev/samtools/bamtk.c
4476 M /branches/dev/samtools/bgzf.c
4479 * fixed a bug in bgzf (only reading is affected)
4480 * fixed a typo in bam_index.c
4481 * in bam_index.c, check potential bugs in the underlying I/O library
4483 ------------------------------------------------------------------------
4484 r41 | lh3lh3 | 2008-12-10 07:53:08 -0500 (Wed, 10 Dec 2008) | 2 lines
4486 M /branches/dev/samtools/samtools.1
4490 ------------------------------------------------------------------------
4491 r40 | lh3lh3 | 2008-12-10 06:52:10 -0500 (Wed, 10 Dec 2008) | 5 lines
4493 M /branches/dev/samtools/bam.h
4494 M /branches/dev/samtools/bam_pileup.c
4495 M /branches/dev/samtools/bamtk.c
4498 * tried to make pileup work with clipping (previously not), though NOT tested
4499 * removed -v from pileup
4500 * made pileup take the reference sequence
4502 ------------------------------------------------------------------------
4503 r39 | lh3lh3 | 2008-12-09 06:59:28 -0500 (Tue, 09 Dec 2008) | 4 lines
4505 M /branches/dev/samtools/bam_import.c
4506 M /branches/dev/samtools/bamtk.c
4507 M /branches/dev/samtools/samtools.1
4510 * in parser, recognize "=", rather than ",", as a match
4511 * in parser, correctl parse "=" at the MRNM field.
4513 ------------------------------------------------------------------------
4514 r38 | lh3lh3 | 2008-12-09 06:39:07 -0500 (Tue, 09 Dec 2008) | 2 lines
4516 M /branches/dev/samtools/misc/maq2sam.c
4518 fixed a bug in handling maq flag 64 and 192
4520 ------------------------------------------------------------------------
4521 r37 | lh3lh3 | 2008-12-09 04:53:46 -0500 (Tue, 09 Dec 2008) | 2 lines
4523 M /branches/dev/samtools/misc/md5fa.c
4525 also calculate unordered md5sum check
4527 ------------------------------------------------------------------------
4528 r36 | lh3lh3 | 2008-12-09 04:46:21 -0500 (Tue, 09 Dec 2008) | 2 lines
4530 M /branches/dev/samtools/misc/md5fa.c
4532 fixed a minor bug when there are space in the sequence
4534 ------------------------------------------------------------------------
4535 r35 | lh3lh3 | 2008-12-09 04:40:45 -0500 (Tue, 09 Dec 2008) | 2 lines
4537 M /branches/dev/samtools/misc/md5fa.c
4539 fixed a potential memory leak
4541 ------------------------------------------------------------------------
4542 r34 | lh3lh3 | 2008-12-08 09:52:17 -0500 (Mon, 08 Dec 2008) | 2 lines
4544 M /branches/dev/samtools/bam_import.c
4545 M /branches/dev/samtools/bam_index.c
4546 M /branches/dev/samtools/bamtk.c
4548 * fixed a bug in import: bin is wrongly calculated
4550 ------------------------------------------------------------------------
4551 r33 | lh3lh3 | 2008-12-08 09:08:01 -0500 (Mon, 08 Dec 2008) | 2 lines
4553 M /branches/dev/samtools/misc/all2sam.pl
4557 ------------------------------------------------------------------------
4558 r32 | lh3lh3 | 2008-12-08 07:56:02 -0500 (Mon, 08 Dec 2008) | 3 lines
4560 M /branches/dev/samtools/Makefile
4561 M /branches/dev/samtools/kseq.h
4562 M /branches/dev/samtools/misc/Makefile
4563 A /branches/dev/samtools/misc/md5.c
4564 A /branches/dev/samtools/misc/md5.h
4565 A /branches/dev/samtools/misc/md5fa.c
4567 * fixed two warnings in kseq.h
4568 * added md5sum utilities
4570 ------------------------------------------------------------------------
4571 r31 | lh3lh3 | 2008-12-08 06:35:29 -0500 (Mon, 08 Dec 2008) | 5 lines
4573 M /branches/dev/samtools/Makefile
4574 M /branches/dev/samtools/bam_import.c
4575 M /branches/dev/samtools/bamtk.c
4576 A /branches/dev/samtools/kseq.h
4577 D /branches/dev/samtools/kstream.h
4580 * replace kstream with kseq. kseq is a superset of kstream. I need the
4581 extra functions in kseq.h.
4582 * also compile stand-alone faidx
4584 ------------------------------------------------------------------------
4585 r30 | lh3lh3 | 2008-12-08 06:17:04 -0500 (Mon, 08 Dec 2008) | 3 lines
4587 M /branches/dev/samtools/bam.h
4588 M /branches/dev/samtools/bam_sort.c
4589 M /branches/dev/samtools/bamtk.c
4592 * sorting by read names is available
4594 ------------------------------------------------------------------------
4595 r29 | lh3lh3 | 2008-12-08 05:29:02 -0500 (Mon, 08 Dec 2008) | 3 lines
4597 M /branches/dev/samtools/bam.c
4598 M /branches/dev/samtools/bam.h
4599 M /branches/dev/samtools/bam_import.c
4600 M /branches/dev/samtools/bam_maqcns.c
4601 M /branches/dev/samtools/bam_pileup.c
4602 M /branches/dev/samtools/bam_sort.c
4603 M /branches/dev/samtools/bam_tview.c
4604 M /branches/dev/samtools/bamtk.c
4605 M /branches/dev/samtools/misc/maq2sam.c
4608 * format change to meet the latest specification
4610 ------------------------------------------------------------------------
4611 r28 | lh3lh3 | 2008-12-04 11:09:21 -0500 (Thu, 04 Dec 2008) | 3 lines
4613 M /branches/dev/samtools/bam_maqcns.c
4614 M /branches/dev/samtools/misc/maq2sam.c
4616 * minor change in maqcns: special care when n==0
4617 * change maq2sam to meet the latest specification
4619 ------------------------------------------------------------------------
4620 r27 | lh3lh3 | 2008-12-04 10:55:44 -0500 (Thu, 04 Dec 2008) | 2 lines
4622 M /branches/dev/samtools/razf.c
4623 M /branches/dev/samtools/razf.h
4625 considerable code clean up in razf
4627 ------------------------------------------------------------------------
4628 r26 | lh3lh3 | 2008-12-04 10:08:18 -0500 (Thu, 04 Dec 2008) | 2 lines
4630 M /branches/dev/samtools/ChangeLog
4631 M /branches/dev/samtools/Makefile
4632 M /branches/dev/samtools/faidx.c
4634 make RAZF optional in faidx.c
4636 ------------------------------------------------------------------------
4637 r25 | lh3lh3 | 2008-12-01 10:27:22 -0500 (Mon, 01 Dec 2008) | 3 lines
4639 M /branches/dev/samtools/Makefile
4640 M /branches/dev/samtools/bam.h
4641 M /branches/dev/samtools/bam_aux.c
4642 M /branches/dev/samtools/bamtk.c
4643 M /branches/dev/samtools/samtools.1
4646 * added routines for retrieving aux data, NOT TESTED YET!
4648 ------------------------------------------------------------------------
4649 r24 | lh3lh3 | 2008-12-01 09:29:43 -0500 (Mon, 01 Dec 2008) | 5 lines
4651 M /branches/dev/samtools/bam.c
4652 M /branches/dev/samtools/bam_import.c
4653 M /branches/dev/samtools/bam_maqcns.c
4654 M /branches/dev/samtools/bamtk.c
4655 M /branches/dev/samtools/bgzf.c
4656 M /branches/dev/samtools/samtools.1
4659 * bgzf: fixed a potential integer overflow on 32-it machines
4660 * maqcns: set the minimum combined quality as 0
4661 * supporting hex strings
4663 ------------------------------------------------------------------------
4664 r23 | lh3lh3 | 2008-11-27 12:14:37 -0500 (Thu, 27 Nov 2008) | 3 lines
4666 M /branches/dev/samtools/bam_maqcns.c
4667 M /branches/dev/samtools/bamtk.c
4670 * fixed the bug in maqcns
4672 ------------------------------------------------------------------------
4673 r22 | lh3lh3 | 2008-11-27 12:08:11 -0500 (Thu, 27 Nov 2008) | 3 lines
4675 M /branches/dev/samtools/Makefile
4676 M /branches/dev/samtools/bam.h
4677 A /branches/dev/samtools/bam_maqcns.c
4678 A /branches/dev/samtools/bam_maqcns.h
4679 M /branches/dev/samtools/bam_tview.c
4680 M /branches/dev/samtools/bamtk.c
4681 A /branches/dev/samtools/glf.h
4684 * add MAQ consensus caller, currently BUGGY!
4686 ------------------------------------------------------------------------
4687 r21 | lh3lh3 | 2008-11-27 08:51:28 -0500 (Thu, 27 Nov 2008) | 4 lines
4689 M /branches/dev/samtools/bam_pileup.c
4690 M /branches/dev/samtools/bam_tview.c
4691 M /branches/dev/samtools/bamtk.c
4694 * tview: display padded alignment (but not P operation)
4695 * better coordinates and reference sequence
4697 ------------------------------------------------------------------------
4698 r19 | lh3lh3 | 2008-11-27 04:26:05 -0500 (Thu, 27 Nov 2008) | 2 lines
4700 A /branches/dev/samtools/ChangeLog
4704 ------------------------------------------------------------------------
4705 r18 | lh3lh3 | 2008-11-27 04:24:45 -0500 (Thu, 27 Nov 2008) | 3 lines
4707 D /branches/dev/samtools/ChangeLog
4708 A /branches/dev/samtools/ChangeLog.old (from /branches/dev/samtools/ChangeLog:6)
4710 Rename ChangeLog to ChangeLog.old. This old ChangeLog is generated from
4711 the log of my personal SVN repository.
4713 ------------------------------------------------------------------------
4714 r17 | lh3lh3 | 2008-11-27 04:22:55 -0500 (Thu, 27 Nov 2008) | 6 lines
4716 M /branches/dev/samtools/Makefile
4717 M /branches/dev/samtools/bamtk.c
4718 M /branches/dev/samtools/bgzf.c
4721 * declare fseeko and ftello as some Linux may not do this by default and
4722 missing these declarations will make bgzf buggy
4723 * get rid of some harmless warings
4724 * use BGZF by default, now
4726 ------------------------------------------------------------------------
4727 r16 | lh3lh3 | 2008-11-26 16:19:11 -0500 (Wed, 26 Nov 2008) | 4 lines
4729 M /branches/dev/samtools/bam_index.c
4730 M /branches/dev/samtools/bamtk.c
4731 M /branches/dev/samtools/razf.c
4734 * fixed a bug in razf_read()
4735 * give more warnings when the file is truncated (or due to bugs in I/O library)
4737 ------------------------------------------------------------------------
4738 r15 | lh3lh3 | 2008-11-26 15:41:39 -0500 (Wed, 26 Nov 2008) | 2 lines
4740 M /branches/dev/samtools/bgzf.c
4742 fixed a bug in bgzf.c at the end of the file
4744 ------------------------------------------------------------------------
4745 r14 | lh3lh3 | 2008-11-26 12:05:18 -0500 (Wed, 26 Nov 2008) | 4 lines
4747 M /branches/dev/samtools/bamtk.c
4750 * a lot happened to RAZF, although samtools itself is untouched. Better
4751 also update the version number anyway to avoid confusion
4753 ------------------------------------------------------------------------
4754 r13 | lh3lh3 | 2008-11-26 12:03:48 -0500 (Wed, 26 Nov 2008) | 2 lines
4756 M /branches/dev/samtools/razf.c
4758 a change from Jue, but I think it should not matter
4760 ------------------------------------------------------------------------
4761 r12 | lh3lh3 | 2008-11-26 11:48:14 -0500 (Wed, 26 Nov 2008) | 3 lines
4763 M /branches/dev/samtools/razf.c
4765 fixed a potential bug in razf. However, it seems still buggy, just
4766 rarely happens, very rarely.
4768 ------------------------------------------------------------------------
4769 r11 | lh3lh3 | 2008-11-26 09:02:56 -0500 (Wed, 26 Nov 2008) | 2 lines
4771 M /branches/dev/samtools/razf.c
4773 fixed a bug in razf, with the help of Jue
4775 ------------------------------------------------------------------------
4776 r10 | lh3lh3 | 2008-11-26 06:55:32 -0500 (Wed, 26 Nov 2008) | 2 lines
4778 M /branches/dev/samtools/bam_index.c
4782 ------------------------------------------------------------------------
4783 r9 | lh3lh3 | 2008-11-26 06:37:05 -0500 (Wed, 26 Nov 2008) | 2 lines
4785 M /branches/dev/samtools/Makefile
4786 M /branches/dev/samtools/bam.h
4787 M /branches/dev/samtools/razf.c
4788 M /branches/dev/samtools/razf.h
4790 * Jue has updated razf to realize Bob's scheme
4792 ------------------------------------------------------------------------
4793 r7 | lh3lh3 | 2008-11-25 15:37:37 -0500 (Tue, 25 Nov 2008) | 2 lines
4795 A /branches/dev/samtools/samtools.1
4799 ------------------------------------------------------------------------
4800 r6 | lh3lh3 | 2008-11-25 15:37:16 -0500 (Tue, 25 Nov 2008) | 3 lines
4802 A /branches/dev/samtools/ChangeLog
4803 A /branches/dev/samtools/Makefile
4804 A /branches/dev/samtools/bam.c
4805 A /branches/dev/samtools/bam.h
4806 A /branches/dev/samtools/bam_aux.c
4807 A /branches/dev/samtools/bam_endian.h
4808 A /branches/dev/samtools/bam_import.c
4809 A /branches/dev/samtools/bam_index.c
4810 A /branches/dev/samtools/bam_lpileup.c
4811 A /branches/dev/samtools/bam_pileup.c
4812 A /branches/dev/samtools/bam_sort.c
4813 A /branches/dev/samtools/bam_tview.c
4814 A /branches/dev/samtools/bamtk.c
4815 A /branches/dev/samtools/bgzf.c
4816 A /branches/dev/samtools/bgzf.h
4817 A /branches/dev/samtools/bgzip.c
4818 A /branches/dev/samtools/faidx.c
4819 A /branches/dev/samtools/faidx.h
4820 A /branches/dev/samtools/khash.h
4821 A /branches/dev/samtools/ksort.h
4822 A /branches/dev/samtools/kstream.h
4823 A /branches/dev/samtools/misc
4824 A /branches/dev/samtools/misc/Makefile
4825 A /branches/dev/samtools/misc/all2sam.pl
4826 A /branches/dev/samtools/misc/maq2sam.c
4827 A /branches/dev/samtools/razf.c
4828 A /branches/dev/samtools/razf.h
4829 A /branches/dev/samtools/razip.c
4830 A /branches/dev/samtools/zutil.h
4832 The initial version of samtools, replicated from my local SVN repository.
4833 The current version is: 0.1.0-42. All future development will happen here.
4835 ------------------------------------------------------------------------
4836 r5 | lh3lh3 | 2008-11-25 15:30:49 -0500 (Tue, 25 Nov 2008) | 2 lines
4838 A /branches/dev/samtools
4840 samtools (C version)
4842 ------------------------------------------------------------------------