1 ------------------------------------------------------------------------
2 r797 | lh3lh3 | 2010-11-08 13:39:52 -0500 (Mon, 08 Nov 2010) | 3 lines
4 M /trunk/samtools/bam2bcf.c
5 M /trunk/samtools/bam2bcf.h
6 M /trunk/samtools/bam2bcf_indel.c
7 M /trunk/samtools/bam_plcmd.c
8 M /trunk/samtools/bamtk.c
10 * samtools-0.1.9-2 (r797)
11 * mpileup: indel calling seems to be working
13 ------------------------------------------------------------------------
14 r796 | lh3lh3 | 2010-11-08 10:54:46 -0500 (Mon, 08 Nov 2010) | 2 lines
16 M /trunk/samtools/bam2bcf.c
17 M /trunk/samtools/bam2bcf.h
18 M /trunk/samtools/bam2bcf_indel.c
19 M /trunk/samtools/bam_plcmd.c
20 M /trunk/samtools/kaln.c
22 indel calling is apparently working, but more information needs to be collected
24 ------------------------------------------------------------------------
25 r795 | lh3lh3 | 2010-11-08 00:39:18 -0500 (Mon, 08 Nov 2010) | 2 lines
27 M /trunk/samtools/bam2bcf.c
28 M /trunk/samtools/bam2bcf_indel.c
30 fixed a few bugs in the indel caller. Probably there are more.
32 ------------------------------------------------------------------------
33 r794 | lh3lh3 | 2010-11-07 22:23:16 -0500 (Sun, 07 Nov 2010) | 2 lines
35 M /trunk/samtools/Makefile
36 M /trunk/samtools/bam.h
37 M /trunk/samtools/bam2bcf.c
38 M /trunk/samtools/bam2bcf.h
39 A /trunk/samtools/bam2bcf_indel.c
40 M /trunk/samtools/bam_plcmd.c
41 M /trunk/samtools/kaln.c
42 M /trunk/samtools/kaln.h
44 prepare for the indel caller. It is not ready yet.
46 ------------------------------------------------------------------------
47 r793 | lh3lh3 | 2010-11-05 11:28:23 -0400 (Fri, 05 Nov 2010) | 2 lines
49 M /trunk/samtools/bam2bcf.c
50 M /trunk/samtools/bam2bcf.h
51 M /trunk/samtools/bam_plcmd.c
53 Revert to r790. The recent changes are not good...
55 ------------------------------------------------------------------------
56 r792 | lh3lh3 | 2010-11-05 00:19:14 -0400 (Fri, 05 Nov 2010) | 6 lines
58 M /trunk/samtools/bam2bcf.c
59 M /trunk/samtools/bam2bcf.h
60 M /trunk/samtools/bam_plcmd.c
62 * this revision is UNSTABLE
64 * indel caller seems working, but it is very insensitive and has
65 several things I do not quite understand.
68 ------------------------------------------------------------------------
69 r791 | lh3lh3 | 2010-11-04 22:58:43 -0400 (Thu, 04 Nov 2010) | 2 lines
71 M /trunk/samtools/bam2bcf.c
72 M /trunk/samtools/bam2bcf.h
73 M /trunk/samtools/bam_plcmd.c
75 for backup. no effective changes
77 ------------------------------------------------------------------------
78 r790 | lh3lh3 | 2010-11-03 15:51:24 -0400 (Wed, 03 Nov 2010) | 2 lines
80 M /trunk/samtools/bcftools/vcfutils.pl
81 M /trunk/samtools/kprobaln.c
83 fixed a minor problem in the example coming with kprobaln.c
85 ------------------------------------------------------------------------
86 r789 | lh3lh3 | 2010-11-02 15:41:27 -0400 (Tue, 02 Nov 2010) | 4 lines
88 M /trunk/samtools/Makefile
89 M /trunk/samtools/bam_md.c
90 M /trunk/samtools/kaln.c
91 M /trunk/samtools/kaln.h
92 A /trunk/samtools/kprobaln.c
93 A /trunk/samtools/kprobaln.h
95 Separate kaln and kprobaln as I am preparing further changes. At
96 present, the results should be identical to the previous.
99 ------------------------------------------------------------------------
100 r788 | petulda | 2010-11-02 12:19:04 -0400 (Tue, 02 Nov 2010) | 1 line
102 M /trunk/samtools/bam_plcmd.c
104 Added -b option: read file names from a file
105 ------------------------------------------------------------------------
106 r787 | lh3lh3 | 2010-10-29 23:17:22 -0400 (Fri, 29 Oct 2010) | 7 lines
108 M /trunk/samtools/bam.h
109 M /trunk/samtools/bam_pileup.c
110 M /trunk/samtools/bam_plcmd.c
111 M /trunk/samtools/bamtk.c
113 * samtools-0.1.9-2 (r787)
115 * Allow to set a maximum per-sample depth to reduce memory. However,
116 BAQ computation is still applied to every read. The speed is not
120 ------------------------------------------------------------------------
121 r786 | lh3lh3 | 2010-10-29 12:10:40 -0400 (Fri, 29 Oct 2010) | 3 lines
123 M /trunk/samtools/bam2bcf.c
124 M /trunk/samtools/bam2bcf.h
125 M /trunk/samtools/bam_plcmd.c
126 M /trunk/samtools/bamtk.c
127 M /trunk/samtools/bcftools/bcf.c
128 M /trunk/samtools/bcftools/vcf.c
130 * samtools-0.1.9-1 (r786)
131 * samtools: optionally perform exact test for each sample
133 ------------------------------------------------------------------------
134 r785 | lh3lh3 | 2010-10-29 09:42:25 -0400 (Fri, 29 Oct 2010) | 2 lines
136 M /trunk/samtools/bam2bcf.c
137 M /trunk/samtools/bam2bcf.h
138 M /trunk/samtools/bam_plcmd.c
139 M /trunk/samtools/bcftools/bcf.c
141 Optionally output "DP", the individual read depth
143 ------------------------------------------------------------------------
144 r784 | lh3lh3 | 2010-10-27 23:10:27 -0400 (Wed, 27 Oct 2010) | 2 lines
146 M /trunk/samtools/samtools.1
148 acknowledge Petr and John who have greatly contributed to the project.
150 ------------------------------------------------------------------------
151 r783 | lh3lh3 | 2010-10-27 22:47:47 -0400 (Wed, 27 Oct 2010) | 2 lines
153 M /trunk/samtools/ChangeLog
154 M /trunk/samtools/NEWS
155 M /trunk/samtools/bamtk.c
156 M /trunk/samtools/samtools.1
158 Release samtools-0.1.9 (r783)
160 ------------------------------------------------------------------------
161 r782 | lh3lh3 | 2010-10-27 19:58:54 -0400 (Wed, 27 Oct 2010) | 2 lines
163 M /trunk/samtools/bam_plcmd.c
165 fixed a silly bug in pileup
167 ------------------------------------------------------------------------
168 r781 | lh3lh3 | 2010-10-27 14:39:48 -0400 (Wed, 27 Oct 2010) | 5 lines
170 M /trunk/samtools/ChangeLog
171 M /trunk/samtools/bam_plcmd.c
172 M /trunk/samtools/bam_sort.c
173 M /trunk/samtools/bamtk.c
174 M /trunk/samtools/samtools.1
176 * samtools-0.1.8-22 (r781)
177 * made BAQ the default behavior of mpileup
179 * in merge, force to exit given inconsistent header when "-R" is not in use.
181 ------------------------------------------------------------------------
182 r780 | lh3lh3 | 2010-10-27 11:01:11 -0400 (Wed, 27 Oct 2010) | 3 lines
184 M /trunk/samtools/bam.h
185 M /trunk/samtools/bam_plcmd.c
186 M /trunk/samtools/bamtk.c
188 * samtools-0.1.8-21 (r780)
189 * minor speedup to pileup
191 ------------------------------------------------------------------------
192 r779 | lh3lh3 | 2010-10-27 09:58:56 -0400 (Wed, 27 Oct 2010) | 2 lines
194 M /trunk/samtools/bam_pileup.c
195 M /trunk/samtools/bam_plcmd.c
196 M /trunk/samtools/examples/toy.sam
198 improve pileup a little bit
200 ------------------------------------------------------------------------
201 r778 | lh3lh3 | 2010-10-27 00:14:43 -0400 (Wed, 27 Oct 2010) | 3 lines
203 M /trunk/samtools/bam.h
204 M /trunk/samtools/bam_pileup.c
205 M /trunk/samtools/bam_plcmd.c
206 M /trunk/samtools/bam_tview.c
207 M /trunk/samtools/bamtk.c
209 * samtools-0.1.8-20 (r778)
210 * speed up pileup, although I do not know how much is the improvement
212 ------------------------------------------------------------------------
213 r777 | lh3lh3 | 2010-10-26 17:26:04 -0400 (Tue, 26 Oct 2010) | 3 lines
215 M /trunk/samtools/bam_maqcns.c
216 M /trunk/samtools/bam_maqcns.h
217 M /trunk/samtools/bam_plcmd.c
218 M /trunk/samtools/bamtk.c
219 M /trunk/samtools/examples/Makefile
221 * samtools-0.1.8-19 (r777)
222 * integrate mpileup features to pileup: min_baseQ, capQ, prob_realn, paired-only and biased prior
224 ------------------------------------------------------------------------
225 r776 | lh3lh3 | 2010-10-26 15:27:46 -0400 (Tue, 26 Oct 2010) | 2 lines
227 M /trunk/samtools/bam_md.c
229 remove local realignment (probabilistic realignment is still there)
231 ------------------------------------------------------------------------
232 r774 | jmarshall | 2010-10-21 06:52:38 -0400 (Thu, 21 Oct 2010) | 3 lines
234 M /trunk/samtools/sam_view.c
236 Add the relevant filename or region to error messages, and cause a failure
237 exit status where appropriate. Based on a patch provided by Marcel Martin.
239 ------------------------------------------------------------------------
240 r773 | lh3lh3 | 2010-10-19 19:44:31 -0400 (Tue, 19 Oct 2010) | 3 lines
242 M /trunk/samtools/examples/toy.sam
243 M /trunk/samtools/kaln.c
245 * Minor code changes. No real effect.
246 * change quality to 30 in toy.sam
248 ------------------------------------------------------------------------
249 r772 | lh3lh3 | 2010-10-18 23:40:13 -0400 (Mon, 18 Oct 2010) | 2 lines
251 M /trunk/samtools/examples/toy.fa
252 M /trunk/samtools/examples/toy.sam
254 added another toy example
256 ------------------------------------------------------------------------
257 r771 | lh3lh3 | 2010-10-13 23:32:12 -0400 (Wed, 13 Oct 2010) | 2 lines
259 M /trunk/samtools/bcftools/call1.c
260 M /trunk/samtools/bcftools/ld.c
261 M /trunk/samtools/bcftools/vcfutils.pl
263 improve the LD statistics
265 ------------------------------------------------------------------------
266 r770 | lh3lh3 | 2010-10-12 23:49:26 -0400 (Tue, 12 Oct 2010) | 3 lines
268 M /trunk/samtools/bcftools/call1.c
269 M /trunk/samtools/bcftools/vcfutils.pl
271 * a minor fix to the -L option
272 * add ldstats to vcfutils.pl
274 ------------------------------------------------------------------------
275 r769 | lh3lh3 | 2010-10-12 15:51:57 -0400 (Tue, 12 Oct 2010) | 2 lines
277 M /trunk/samtools/bcftools/bcf.c
281 ------------------------------------------------------------------------
282 r768 | lh3lh3 | 2010-10-12 15:49:06 -0400 (Tue, 12 Oct 2010) | 2 lines
284 M /trunk/samtools/bcftools/Makefile
285 A /trunk/samtools/bcftools/ld.c
287 forget to add the key file
289 ------------------------------------------------------------------------
290 r767 | lh3lh3 | 2010-10-12 15:48:46 -0400 (Tue, 12 Oct 2010) | 4 lines
292 M /trunk/samtools/bcftools/Makefile
293 M /trunk/samtools/bcftools/bcf.c
294 M /trunk/samtools/bcftools/bcf.h
295 M /trunk/samtools/bcftools/call1.c
296 M /trunk/samtools/bcftools/prob1.c
297 M /trunk/samtools/bcftools/vcfutils.pl
299 * vcfutils.pl: fixed a typo in help message
300 * added APIs: bcf_append_info() and bcf_cpy()
301 * calculate adjacent LD
303 ------------------------------------------------------------------------
304 r766 | lh3lh3 | 2010-10-11 11:06:40 -0400 (Mon, 11 Oct 2010) | 2 lines
306 M /trunk/samtools/bcftools/vcfutils.pl
308 added filter for samtools/bcftools genetated VCFs
310 ------------------------------------------------------------------------
311 r765 | lh3lh3 | 2010-10-05 14:05:18 -0400 (Tue, 05 Oct 2010) | 3 lines
313 M /trunk/samtools/bcftools/vcfutils.pl
314 M /trunk/samtools/kaln.c
316 * removed a comment line in kaln.c
317 * vcfutils.pl fillac works when GT is not the first field
319 ------------------------------------------------------------------------
320 r764 | petulda | 2010-10-05 08:59:36 -0400 (Tue, 05 Oct 2010) | 1 line
322 A /trunk/samtools/bcftools/bcf-fix.pl
324 Convert VCF output of "bcftools view -bgcv" to a valid VCF file
325 ------------------------------------------------------------------------
326 r763 | lh3lh3 | 2010-10-02 22:51:03 -0400 (Sat, 02 Oct 2010) | 4 lines
328 M /trunk/samtools/bam_plcmd.c
329 M /trunk/samtools/bamtk.c
330 A /trunk/samtools/bcftools/bcftools.1
331 M /trunk/samtools/bcftools/call1.c
332 M /trunk/samtools/samtools.1
334 * samtools-0.1.8-18 (r763)
335 * added bcftools manual page
336 * minor fix to mpileup and view command lines
338 ------------------------------------------------------------------------
339 r762 | lh3lh3 | 2010-10-02 21:46:25 -0400 (Sat, 02 Oct 2010) | 3 lines
341 M /trunk/samtools/bcftools/bcf.c
342 M /trunk/samtools/bcftools/call1.c
343 M /trunk/samtools/bcftools/vcfutils.pl
345 * vcfutils.pl qstats: calculate marginal ts/tv
346 * allow to call genotypes at variant sites
348 ------------------------------------------------------------------------
349 r761 | lh3lh3 | 2010-10-01 00:29:55 -0400 (Fri, 01 Oct 2010) | 3 lines
351 M /trunk/samtools/kaln.c
352 M /trunk/samtools/misc/HmmGlocal.java
354 I am changing the gap open probability back to 0.001. It seems that
355 being conservative here is a good thing...
357 ------------------------------------------------------------------------
358 r760 | lh3lh3 | 2010-10-01 00:11:27 -0400 (Fri, 01 Oct 2010) | 5 lines
360 M /trunk/samtools/bamtk.c
361 M /trunk/samtools/kaln.c
362 A /trunk/samtools/misc/HmmGlocal.java
364 * samtools-0.1.8-17 (r760)
365 * the default gap open penalty is too small (a typo)
366 * added comments on hmm_realn
367 * Java implementation
369 ------------------------------------------------------------------------
370 r759 | lh3lh3 | 2010-09-30 10:12:54 -0400 (Thu, 30 Sep 2010) | 2 lines
372 M /trunk/samtools/bamtk.c
374 mark samtools-0.1.8-16 (r759)
376 ------------------------------------------------------------------------
377 r758 | lh3lh3 | 2010-09-30 10:12:02 -0400 (Thu, 30 Sep 2010) | 2 lines
379 M /trunk/samtools/kaln.c
381 round to the nearest integer
383 ------------------------------------------------------------------------
384 r757 | lh3lh3 | 2010-09-28 17:16:43 -0400 (Tue, 28 Sep 2010) | 4 lines
386 M /trunk/samtools/kaln.c
388 I was trying to accelerate ka_prob_glocal() as this will be the
389 bottleneck. After an hour, the only gain is to change division to
390 multiplication. OK. I will stop.
392 ------------------------------------------------------------------------
393 r756 | lh3lh3 | 2010-09-28 16:57:49 -0400 (Tue, 28 Sep 2010) | 2 lines
395 M /trunk/samtools/kaln.c
397 this is interesting. multiplication is much faster than division, at least on my Mac
399 ------------------------------------------------------------------------
400 r755 | lh3lh3 | 2010-09-28 16:19:13 -0400 (Tue, 28 Sep 2010) | 2 lines
402 M /trunk/samtools/kaln.c
406 ------------------------------------------------------------------------
407 r754 | lh3lh3 | 2010-09-28 15:44:16 -0400 (Tue, 28 Sep 2010) | 2 lines
409 M /trunk/samtools/bam_md.c
410 M /trunk/samtools/bam_plcmd.c
411 M /trunk/samtools/kaln.c
413 prob_realn() seems working!
415 ------------------------------------------------------------------------
416 r753 | lh3lh3 | 2010-09-28 12:48:23 -0400 (Tue, 28 Sep 2010) | 2 lines
418 M /trunk/samtools/kaln.c
422 ------------------------------------------------------------------------
423 r752 | lh3lh3 | 2010-09-28 12:47:41 -0400 (Tue, 28 Sep 2010) | 2 lines
425 M /trunk/samtools/kaln.c
426 M /trunk/samtools/kaln.h
428 Convert phredQ to probabilities
430 ------------------------------------------------------------------------
431 r751 | lh3lh3 | 2010-09-28 12:32:08 -0400 (Tue, 28 Sep 2010) | 2 lines
433 M /trunk/samtools/kaln.c
434 M /trunk/samtools/kaln.h
436 Implement the glocal HMM; discard the extention HMM
438 ------------------------------------------------------------------------
439 r750 | lh3lh3 | 2010-09-28 00:06:11 -0400 (Tue, 28 Sep 2010) | 2 lines
441 M /trunk/samtools/kaln.c
443 improve numerical stability
445 ------------------------------------------------------------------------
446 r749 | lh3lh3 | 2010-09-27 23:27:54 -0400 (Mon, 27 Sep 2010) | 2 lines
448 M /trunk/samtools/kaln.c
452 ------------------------------------------------------------------------
453 r748 | lh3lh3 | 2010-09-27 23:17:16 -0400 (Mon, 27 Sep 2010) | 2 lines
455 M /trunk/samtools/kaln.c
457 fixed a bug in banded DP
459 ------------------------------------------------------------------------
460 r747 | lh3lh3 | 2010-09-27 23:05:12 -0400 (Mon, 27 Sep 2010) | 3 lines
462 M /trunk/samtools/kaln.c
464 * fixed that weird issue.
465 * the banded version is NOT working
467 ------------------------------------------------------------------------
468 r746 | lh3lh3 | 2010-09-27 22:57:05 -0400 (Mon, 27 Sep 2010) | 2 lines
470 M /trunk/samtools/kaln.c
472 More comments. This version seems working, but something is a little weird...
474 ------------------------------------------------------------------------
475 r745 | lh3lh3 | 2010-09-27 17:21:40 -0400 (Mon, 27 Sep 2010) | 6 lines
477 M /trunk/samtools/kaln.c
479 A little code cleanup. Now the forward and backback algorithms give
480 nearly identical P(x), which means both are close to the correct
481 forms. However, I have only tested on toy examples. Minor errors in
482 the implementation may not be obvious.
485 ------------------------------------------------------------------------
486 r744 | lh3lh3 | 2010-09-27 16:55:15 -0400 (Mon, 27 Sep 2010) | 2 lines
488 M /trunk/samtools/bam_plcmd.c
489 M /trunk/samtools/bam_sort.c
490 M /trunk/samtools/kaln.c
491 M /trunk/samtools/kaln.h
495 ------------------------------------------------------------------------
496 r743 | jmarshall | 2010-09-27 08:19:06 -0400 (Mon, 27 Sep 2010) | 6 lines
498 M /trunk/samtools/bam_sort.c
500 Abort if merge -h's INH.SAM cannot be opened, just as we abort
501 if any of the IN#.BAM input files cannot be opened.
503 Also propagate any error indication returned by bam_merge_core()
504 to samtools merge's exit status.
506 ------------------------------------------------------------------------
507 r741 | jmarshall | 2010-09-24 11:08:24 -0400 (Fri, 24 Sep 2010) | 5 lines
509 M /trunk/samtools/bam_index.c
511 Use bam_validate1() to detect garbage records in the event of a corrupt
512 BAI index file that causes a bam_seek() to an invalid position. At most
513 one record (namely, the bam_iter_read terminator) is tested per bam_fetch()
514 call, so the cost is insignificant in the normal case.
516 ------------------------------------------------------------------------
517 r740 | jmarshall | 2010-09-24 11:00:19 -0400 (Fri, 24 Sep 2010) | 2 lines
519 M /trunk/samtools/bam.c
520 M /trunk/samtools/bam.h
524 ------------------------------------------------------------------------
525 r739 | lh3lh3 | 2010-09-22 12:07:50 -0400 (Wed, 22 Sep 2010) | 3 lines
527 M /trunk/samtools/bam_md.c
528 M /trunk/samtools/bamtk.c
530 * samtools-0.1.8-15 (r379)
531 * allow to change capQ parameter in calmd
533 ------------------------------------------------------------------------
534 r738 | jmarshall | 2010-09-22 11:15:33 -0400 (Wed, 22 Sep 2010) | 13 lines
536 M /trunk/samtools/bam_index.c
537 M /trunk/samtools/sam_view.c
539 When bam_read1() returns an error (return value <= -2), propagate that error
540 to bam_iter_read()'s own return value. Similarly, also propagate it up to
541 bam_fetch()'s return value. Previously bam_fetch() always returned 0, and
542 callers ignored its return value anyway. With this change, 0 continues to
543 indicate success, while <= -2 (which can be written as < 0, as -1 is never
544 returned) indicates corrupted input.
546 bam_iter_read() ought also to propagate errors returned by bam_seek().
548 main_samview() can now print an error message and fail when bam_fetch()
549 detects that a .bai index file is corrupted or otherwise does not correspond
550 to the .bam file it is being used with.
552 ------------------------------------------------------------------------
553 r737 | jmarshall | 2010-09-22 10:47:42 -0400 (Wed, 22 Sep 2010) | 3 lines
555 M /trunk/samtools/bam_index.c
557 0 is a successful return value from bam_read1(). (In practice, it never
558 returns 0 anyway; but all the other callers treat 0 as successful.)
560 ------------------------------------------------------------------------
561 r736 | lh3lh3 | 2010-09-20 17:43:08 -0400 (Mon, 20 Sep 2010) | 2 lines
563 M /trunk/samtools/bam.h
564 M /trunk/samtools/bam_index.c
565 M /trunk/samtools/bam_sort.c
567 * merge files region-by-region. work on small examples but more tests are needed.
569 ------------------------------------------------------------------------
570 r735 | lh3lh3 | 2010-09-20 16:56:24 -0400 (Mon, 20 Sep 2010) | 2 lines
572 M /trunk/samtools/bcftools/vcfutils.pl
574 improve qstats by checking the alleles as well
576 ------------------------------------------------------------------------
577 r734 | lh3lh3 | 2010-09-17 18:12:13 -0400 (Fri, 17 Sep 2010) | 2 lines
579 M /trunk/samtools/bcftools/vcfutils.pl
581 convert UCSC SNP SQL dump to VCF
583 ------------------------------------------------------------------------
584 r733 | lh3lh3 | 2010-09-17 13:02:11 -0400 (Fri, 17 Sep 2010) | 2 lines
586 M /trunk/samtools/bcftools/vcfutils.pl
590 ------------------------------------------------------------------------
591 r732 | lh3lh3 | 2010-09-17 10:11:37 -0400 (Fri, 17 Sep 2010) | 3 lines
593 M /trunk/samtools/bcftools/Makefile
594 M /trunk/samtools/bcftools/bcf.c
595 M /trunk/samtools/bcftools/bcf.h
596 M /trunk/samtools/bcftools/vcf.c
599 * VCF->BCF is not possible without knowing the sequence dictionary before hand...
601 ------------------------------------------------------------------------
602 r731 | lh3lh3 | 2010-09-17 09:15:53 -0400 (Fri, 17 Sep 2010) | 2 lines
604 M /trunk/samtools/bam2bcf.c
605 M /trunk/samtools/bcftools/bcf.c
606 M /trunk/samtools/bcftools/bcf.h
607 M /trunk/samtools/bcftools/bcfutils.c
608 M /trunk/samtools/bcftools/call1.c
609 M /trunk/samtools/bcftools/vcf.c
611 * put n_smpl to "bcf1_t" to simplify API a little
613 ------------------------------------------------------------------------
614 r730 | lh3lh3 | 2010-09-16 21:36:01 -0400 (Thu, 16 Sep 2010) | 2 lines
616 M /trunk/samtools/bcftools/bcf.h
617 M /trunk/samtools/bcftools/call1.c
618 M /trunk/samtools/bcftools/index.c
620 fixed a bug in indexing
622 ------------------------------------------------------------------------
623 r729 | lh3lh3 | 2010-09-16 16:54:48 -0400 (Thu, 16 Sep 2010) | 3 lines
625 M /trunk/samtools/bam.c
626 M /trunk/samtools/bam_md.c
627 M /trunk/samtools/bam_pileup.c
629 * fixed a bug in capQ
630 * valgrind identifies a use of uninitialised value, but I have not fixed it.
632 ------------------------------------------------------------------------
633 r728 | lh3lh3 | 2010-09-16 15:03:59 -0400 (Thu, 16 Sep 2010) | 3 lines
635 M /trunk/samtools/bgzip.c
636 M /trunk/samtools/razip.c
638 * fixed a bug in razip: -c will delete the input file
639 * copy tabix/bgzip to here
641 ------------------------------------------------------------------------
642 r727 | lh3lh3 | 2010-09-16 13:45:49 -0400 (Thu, 16 Sep 2010) | 3 lines
644 M /trunk/samtools/bam_md.c
645 M /trunk/samtools/bam_plcmd.c
646 M /trunk/samtools/bamtk.c
648 * samtools-0.1.8-14 (r727)
649 * allow to change the capQ parameter at the command line
651 ------------------------------------------------------------------------
652 r726 | lh3lh3 | 2010-09-16 13:38:43 -0400 (Thu, 16 Sep 2010) | 4 lines
654 M /trunk/samtools/bam_md.c
655 M /trunk/samtools/bam_plcmd.c
656 M /trunk/samtools/bcftools/vcfutils.pl
657 M /trunk/samtools/misc/samtools.pl
659 * added varFilter to vcfutils.pl
660 * reimplement realn(). now it performs a local alignment
661 * added cap_mapQ() to cap mapping quality when there are many substitutions
663 ------------------------------------------------------------------------
664 r724 | lh3lh3 | 2010-09-15 00:18:31 -0400 (Wed, 15 Sep 2010) | 2 lines
666 M /trunk/samtools/bcftools/Makefile
667 A /trunk/samtools/bcftools/bcf2qcall.c
668 M /trunk/samtools/bcftools/call1.c
670 * convert BCF to QCALL input
672 ------------------------------------------------------------------------
673 r723 | lh3lh3 | 2010-09-14 22:41:50 -0400 (Tue, 14 Sep 2010) | 2 lines
675 M /trunk/samtools/bam_md.c
677 dynamic band width in realignment
679 ------------------------------------------------------------------------
680 r722 | lh3lh3 | 2010-09-14 22:05:32 -0400 (Tue, 14 Sep 2010) | 2 lines
682 M /trunk/samtools/bam_md.c
683 M /trunk/samtools/bam_plcmd.c
685 fixed a bug in realignment
687 ------------------------------------------------------------------------
688 r721 | lh3lh3 | 2010-09-14 20:54:09 -0400 (Tue, 14 Sep 2010) | 2 lines
690 M /trunk/samtools/bcftools/prob1.c
694 ------------------------------------------------------------------------
695 r720 | lh3lh3 | 2010-09-14 19:25:10 -0400 (Tue, 14 Sep 2010) | 2 lines
697 M /trunk/samtools/Makefile
698 M /trunk/samtools/bam_maqcns.c
699 M /trunk/samtools/bam_md.c
701 fixed a bug in realignment
703 ------------------------------------------------------------------------
704 r719 | lh3lh3 | 2010-09-14 19:18:24 -0400 (Tue, 14 Sep 2010) | 2 lines
706 M /trunk/samtools/bam_plcmd.c
708 minor changes. It is BUGGY now!
710 ------------------------------------------------------------------------
711 r718 | lh3lh3 | 2010-09-14 16:32:33 -0400 (Tue, 14 Sep 2010) | 4 lines
713 M /trunk/samtools/bam_md.c
714 M /trunk/samtools/bam_pileup.c
715 M /trunk/samtools/kaln.c
716 M /trunk/samtools/kaln.h
718 * aggressive gapped aligner is implemented in calmd.
719 * distinguish gap_open and gap_end_open in banded alignment
720 * make tview accepts alignment with heading and tailing D
722 ------------------------------------------------------------------------
723 r717 | jmarshall | 2010-09-14 09:04:28 -0400 (Tue, 14 Sep 2010) | 2 lines
727 Add svn:ignore properties for generated files that don't appear in "make all".
729 ------------------------------------------------------------------------
730 r716 | jmarshall | 2010-09-13 08:37:53 -0400 (Mon, 13 Sep 2010) | 3 lines
733 M /trunk/samtools/bcftools
734 M /trunk/samtools/misc
736 Add svn:ignore properties listing the generated files.
737 (Except for *.o, which we'll assume is in global-ignores.)
739 ------------------------------------------------------------------------
740 r715 | lh3lh3 | 2010-09-08 12:53:55 -0400 (Wed, 08 Sep 2010) | 5 lines
742 M /trunk/samtools/bamtk.c
743 M /trunk/samtools/bcftools/call1.c
744 M /trunk/samtools/bcftools/prob1.c
745 M /trunk/samtools/sample.c
746 M /trunk/samtools/sample.h
748 * samtools-0.1.8-13 (r715)
749 * fixed a bug in identifying SM across files
750 * bcftools: estimate heterozygosity
751 * bcftools: allow to skip sites without reference bases
753 ------------------------------------------------------------------------
754 r713 | lh3lh3 | 2010-09-03 17:19:12 -0400 (Fri, 03 Sep 2010) | 2 lines
756 M /trunk/samtools/bcftools/Makefile
757 M /trunk/samtools/bcftools/call1.c
758 M /trunk/samtools/bcftools/prob1.c
759 M /trunk/samtools/bcftools/prob1.h
761 quite a lot changes to the contrast caller, but I still feel something is missing...
763 ------------------------------------------------------------------------
764 r711 | lh3lh3 | 2010-09-03 00:30:48 -0400 (Fri, 03 Sep 2010) | 4 lines
766 M /trunk/samtools/bcftools/Makefile
767 M /trunk/samtools/bcftools/call1.c
768 M /trunk/samtools/bcftools/prob1.c
769 M /trunk/samtools/bcftools/vcfutils.pl
771 * changed 3.434 to 4.343 (typo!)
772 * fixed a bug in the contrast caller
773 * calculate heterozygosity
775 ------------------------------------------------------------------------
776 r710 | lh3lh3 | 2010-09-01 23:24:47 -0400 (Wed, 01 Sep 2010) | 2 lines
778 M /trunk/samtools/bcftools/bcf.h
779 M /trunk/samtools/bcftools/bcfutils.c
780 M /trunk/samtools/bcftools/call1.c
782 SNP calling from the GL field
784 ------------------------------------------------------------------------
785 r709 | lh3lh3 | 2010-09-01 18:52:30 -0400 (Wed, 01 Sep 2010) | 2 lines
787 M /trunk/samtools/bcftools/vcf.c
789 fixed another problem
791 ------------------------------------------------------------------------
792 r708 | lh3lh3 | 2010-09-01 18:31:17 -0400 (Wed, 01 Sep 2010) | 3 lines
794 M /trunk/samtools/bcftools/bcf.c
795 M /trunk/samtools/bcftools/vcf.c
797 * fixed bugs in parsing VCF
798 * parser now works with GT/GQ/DP/PL/GL
800 ------------------------------------------------------------------------
801 r707 | lh3lh3 | 2010-09-01 15:28:29 -0400 (Wed, 01 Sep 2010) | 2 lines
803 M /trunk/samtools/bcftools/Makefile
804 M /trunk/samtools/bcftools/prob1.c
806 Do not compile _BCF_QUAD by default
808 ------------------------------------------------------------------------
809 r706 | lh3lh3 | 2010-09-01 15:21:41 -0400 (Wed, 01 Sep 2010) | 2 lines
811 M /trunk/samtools/bcftools/bcf.c
812 M /trunk/samtools/bcftools/bcf.h
813 M /trunk/samtools/bcftools/bcfutils.c
814 M /trunk/samtools/bcftools/call1.c
816 Write the correct ALT and PL in the SNP calling mode.
818 ------------------------------------------------------------------------
819 r705 | lh3lh3 | 2010-09-01 12:50:33 -0400 (Wed, 01 Sep 2010) | 2 lines
821 M /trunk/samtools/bcftools/vcfutils.pl
823 more commands for my own uses
825 ------------------------------------------------------------------------
826 r704 | lh3lh3 | 2010-09-01 09:26:10 -0400 (Wed, 01 Sep 2010) | 2 lines
828 A /trunk/samtools/bcftools/vcfutils.pl
830 Utilities for processing VCF
832 ------------------------------------------------------------------------
833 r703 | lh3lh3 | 2010-08-31 16:44:57 -0400 (Tue, 31 Aug 2010) | 2 lines
835 M /trunk/samtools/bcftools/Makefile
836 M /trunk/samtools/bcftools/call1.c
837 M /trunk/samtools/bcftools/prob1.c
838 M /trunk/samtools/bcftools/prob1.h
840 preliminary contrast variant caller
842 ------------------------------------------------------------------------
843 r702 | lh3lh3 | 2010-08-31 12:28:39 -0400 (Tue, 31 Aug 2010) | 2 lines
845 M /trunk/samtools/bcftools/call1.c
846 M /trunk/samtools/bcftools/prob1.c
847 M /trunk/samtools/bcftools/prob1.h
849 z' and z'' can be calculated
851 ------------------------------------------------------------------------
852 r701 | lh3lh3 | 2010-08-31 10:20:57 -0400 (Tue, 31 Aug 2010) | 3 lines
854 M /trunk/samtools/bcftools/Makefile
855 A /trunk/samtools/bcftools/call1.c (from /trunk/samtools/bcftools/vcfout.c:699)
856 M /trunk/samtools/bcftools/prob1.c
857 D /trunk/samtools/bcftools/vcfout.c
859 * rename vcfout.c as call1.c
860 * prepare to add two-sample comparison
862 ------------------------------------------------------------------------
863 r699 | lh3lh3 | 2010-08-24 15:28:16 -0400 (Tue, 24 Aug 2010) | 2 lines
865 M /trunk/samtools/bcftools/vcfout.c
867 fixed a bug in calculating the t statistics
869 ------------------------------------------------------------------------
870 r698 | lh3lh3 | 2010-08-24 14:05:50 -0400 (Tue, 24 Aug 2010) | 3 lines
872 M /trunk/samtools/bam2bcf.c
873 M /trunk/samtools/bam2bcf.h
874 M /trunk/samtools/bamtk.c
875 M /trunk/samtools/bcftools/kfunc.c
876 M /trunk/samtools/bcftools/vcfout.c
878 * samtools-0.1.8-13 (r698)
879 * perform one-tailed t-test for baseQ, mapQ and endDist
881 ------------------------------------------------------------------------
882 r697 | lh3lh3 | 2010-08-24 12:30:13 -0400 (Tue, 24 Aug 2010) | 2 lines
884 M /trunk/samtools/bcftools/kfunc.c
886 added regularized incomplete beta function
888 ------------------------------------------------------------------------
889 r695 | lh3lh3 | 2010-08-23 17:36:17 -0400 (Mon, 23 Aug 2010) | 2 lines
891 M /trunk/samtools/bam_maqcns.c
892 M /trunk/samtools/bam_plcmd.c
894 change the default correlation coefficient
896 ------------------------------------------------------------------------
897 r694 | lh3lh3 | 2010-08-23 14:46:52 -0400 (Mon, 23 Aug 2010) | 2 lines
899 M /trunk/samtools/bcftools/bcf.c
900 M /trunk/samtools/bcftools/vcfout.c
902 print QUAL as floating numbers
904 ------------------------------------------------------------------------
905 r693 | lh3lh3 | 2010-08-23 14:06:07 -0400 (Mon, 23 Aug 2010) | 3 lines
907 M /trunk/samtools/Makefile
908 M /trunk/samtools/bam_plcmd.c
909 M /trunk/samtools/bamtk.c
910 M /trunk/samtools/examples/Makefile
911 A /trunk/samtools/sample.c
912 A /trunk/samtools/sample.h
914 * samtools-0.1.8-12 (r692)
915 * group data by samples in "mpileup -g"
917 ------------------------------------------------------------------------
918 r692 | lh3lh3 | 2010-08-23 10:58:53 -0400 (Mon, 23 Aug 2010) | 2 lines
920 M /trunk/samtools/Makefile
921 D /trunk/samtools/bam_mcns.c
922 D /trunk/samtools/bam_mcns.h
923 M /trunk/samtools/bam_plcmd.c
925 remove VCF output in mpileup
927 ------------------------------------------------------------------------
928 r691 | lh3lh3 | 2010-08-23 10:48:20 -0400 (Mon, 23 Aug 2010) | 3 lines
930 M /trunk/samtools/bam2bcf.c
931 M /trunk/samtools/bam2bcf.h
933 * use the revised MAQ error model for mpileup
934 * prepare to remove the independent model from mpileup
936 ------------------------------------------------------------------------
937 r690 | lh3lh3 | 2010-08-20 15:46:40 -0400 (Fri, 20 Aug 2010) | 2 lines
939 M /trunk/samtools/Makefile
940 M /trunk/samtools/bam_maqcns.c
941 M /trunk/samtools/bam_maqcns.h
942 M /trunk/samtools/bam_plcmd.c
943 A /trunk/samtools/errmod.c
944 A /trunk/samtools/errmod.h
945 M /trunk/samtools/ksort.h
947 added revised MAQ error model
949 ------------------------------------------------------------------------
950 r689 | lh3lh3 | 2010-08-18 09:55:20 -0400 (Wed, 18 Aug 2010) | 2 lines
952 M /trunk/samtools/bcftools/prob1.c
953 M /trunk/samtools/bcftools/prob1.h
954 M /trunk/samtools/bcftools/vcfout.c
956 allow to read the prior from the error output. EM iteration is working.
958 ------------------------------------------------------------------------
959 r688 | lh3lh3 | 2010-08-17 12:12:20 -0400 (Tue, 17 Aug 2010) | 3 lines
961 M /trunk/samtools/bcftools/main.c
962 M /trunk/samtools/bcftools/vcf.c
964 * write a little more VCF header
967 ------------------------------------------------------------------------
968 r687 | lh3lh3 | 2010-08-16 20:53:16 -0400 (Mon, 16 Aug 2010) | 2 lines
970 M /trunk/samtools/bcftools/bcf.c
971 M /trunk/samtools/bcftools/bcf.h
972 M /trunk/samtools/bcftools/bcf.tex
976 ------------------------------------------------------------------------
977 r686 | lh3lh3 | 2010-08-14 00:11:13 -0400 (Sat, 14 Aug 2010) | 2 lines
979 M /trunk/samtools/bcftools/bcf.c
980 M /trunk/samtools/bcftools/prob1.c
982 faster for large sample size (in principle)
984 ------------------------------------------------------------------------
985 r685 | lh3lh3 | 2010-08-13 23:28:31 -0400 (Fri, 13 Aug 2010) | 4 lines
987 M /trunk/samtools/bcftools/prob1.c
989 * a numerically stable method to calculate z_{jk}
990 * currently slower than the old method but will be important for large sample size
991 * in principle, we can speed up for large n, but have not tried
993 ------------------------------------------------------------------------
994 r684 | lh3lh3 | 2010-08-11 21:58:31 -0400 (Wed, 11 Aug 2010) | 2 lines
996 M /trunk/samtools/bcftools/vcfout.c
998 fixed an issue in parsing integer
1000 ------------------------------------------------------------------------
1001 r683 | lh3lh3 | 2010-08-09 13:05:07 -0400 (Mon, 09 Aug 2010) | 2 lines
1003 M /trunk/samtools/bcftools/bcf.c
1005 do not print refname if file is converted from VCF
1007 ------------------------------------------------------------------------
1008 r682 | lh3lh3 | 2010-08-09 12:59:47 -0400 (Mon, 09 Aug 2010) | 3 lines
1010 M /trunk/samtools/bcftools/vcf.c
1013 * fixed a bug in parsing VCF
1015 ------------------------------------------------------------------------
1016 r681 | lh3lh3 | 2010-08-09 12:49:23 -0400 (Mon, 09 Aug 2010) | 4 lines
1018 M /trunk/samtools/bcftools/bcf.c
1019 M /trunk/samtools/bcftools/bcf.h
1020 M /trunk/samtools/bcftools/bcfutils.c
1021 M /trunk/samtools/bcftools/main.c
1022 M /trunk/samtools/bcftools/vcf.c
1023 M /trunk/samtools/bcftools/vcfout.c
1024 M /trunk/samtools/bgzf.c
1025 M /trunk/samtools/kstring.c
1027 * fixed a bug in kstrtok@kstring.c
1028 * preliminary VCF parser (not parse everything for now)
1029 * improved view interface
1031 ------------------------------------------------------------------------
1032 r680 | lh3lh3 | 2010-08-09 10:43:13 -0400 (Mon, 09 Aug 2010) | 4 lines
1034 M /trunk/samtools/bcftools/bcf.c
1035 M /trunk/samtools/bcftools/bcf.h
1036 M /trunk/samtools/bcftools/vcfout.c
1037 M /trunk/samtools/kstring.c
1038 M /trunk/samtools/kstring.h
1040 * improved kstring (added kstrtok)
1041 * removed the limit on the format string length in bcftools
1042 * use kstrtok to parse format which fixed a bug in the old code
1044 ------------------------------------------------------------------------
1045 r679 | lh3lh3 | 2010-08-09 01:12:05 -0400 (Mon, 09 Aug 2010) | 2 lines
1047 A /trunk/samtools/bcftools/README
1048 M /trunk/samtools/bcftools/vcfout.c
1052 ------------------------------------------------------------------------
1053 r678 | lh3lh3 | 2010-08-09 00:01:52 -0400 (Mon, 09 Aug 2010) | 2 lines
1055 M /trunk/samtools/bcftools/vcfout.c
1057 perform single-tail test for ED4
1059 ------------------------------------------------------------------------
1060 r677 | lh3lh3 | 2010-08-08 23:48:35 -0400 (Sun, 08 Aug 2010) | 2 lines
1062 M /trunk/samtools/bcftools/Makefile
1063 M /trunk/samtools/bcftools/kfunc.c
1064 M /trunk/samtools/bcftools/vcfout.c
1066 * test depth, end distance and HWE
1068 ------------------------------------------------------------------------
1069 r676 | lh3lh3 | 2010-08-08 02:04:15 -0400 (Sun, 08 Aug 2010) | 2 lines
1071 M /trunk/samtools/bcftools/kfunc.c
1073 reimplement incomplete gamma functions. no copy-paste
1075 ------------------------------------------------------------------------
1076 r675 | lh3lh3 | 2010-08-06 22:42:54 -0400 (Fri, 06 Aug 2010) | 3 lines
1078 M /trunk/samtools/bam2bcf.c
1079 M /trunk/samtools/bam2bcf.h
1080 M /trunk/samtools/bcftools/fet.c
1081 M /trunk/samtools/bcftools/prob1.c
1082 M /trunk/samtools/bcftools/prob1.h
1083 M /trunk/samtools/bcftools/vcfout.c
1085 * bcftools: add HWE (no testing for now)
1086 * record end dist in a 2x2 table, not avg, std any more
1088 ------------------------------------------------------------------------
1089 r674 | lh3lh3 | 2010-08-06 17:30:16 -0400 (Fri, 06 Aug 2010) | 3 lines
1091 A /trunk/samtools/bcftools/kfunc.c
1093 * Special functions: log(gamma()), erfc(), P(a,x) (incomplete gamma)
1094 * Not using Numerical Recipe due to licensing issues
1096 ------------------------------------------------------------------------
1097 r673 | lh3lh3 | 2010-08-05 23:46:53 -0400 (Thu, 05 Aug 2010) | 2 lines
1099 A /trunk/samtools/bcftools/fet.c
1103 ------------------------------------------------------------------------
1104 r672 | lh3lh3 | 2010-08-05 21:48:33 -0400 (Thu, 05 Aug 2010) | 3 lines
1106 M /trunk/samtools/bam2bcf.c
1107 M /trunk/samtools/bam2bcf.h
1108 M /trunk/samtools/bamtk.c
1109 M /trunk/samtools/examples/Makefile
1111 * samtools-0.1.8-11 (r672)
1112 * collect more stats for allele balance test in bcftools (not yet)
1114 ------------------------------------------------------------------------
1115 r671 | lh3lh3 | 2010-08-05 16:17:58 -0400 (Thu, 05 Aug 2010) | 3 lines
1117 M /trunk/samtools/bam_plcmd.c
1118 M /trunk/samtools/bcftools/bcf.c
1119 M /trunk/samtools/bcftools/main.c
1121 * the code base is stablized again.
1122 * I will delay the vcf parser, which is quite complicated but with little value for now
1124 ------------------------------------------------------------------------
1125 r670 | lh3lh3 | 2010-08-05 16:03:23 -0400 (Thu, 05 Aug 2010) | 2 lines
1127 M /trunk/samtools/examples/Makefile
1131 ------------------------------------------------------------------------
1132 r669 | lh3lh3 | 2010-08-05 16:03:08 -0400 (Thu, 05 Aug 2010) | 2 lines
1134 M /trunk/samtools/bcftools/vcf.c
1136 unfinished vcf parser
1138 ------------------------------------------------------------------------
1139 r668 | lh3lh3 | 2010-08-05 15:46:40 -0400 (Thu, 05 Aug 2010) | 3 lines
1141 M /trunk/samtools/bcftools/Makefile
1142 M /trunk/samtools/bcftools/bcf.c
1143 M /trunk/samtools/bcftools/bcf.h
1144 M /trunk/samtools/bcftools/bcfutils.c
1145 M /trunk/samtools/bcftools/index.c
1146 M /trunk/samtools/bcftools/main.c
1147 A /trunk/samtools/bcftools/vcf.c
1148 M /trunk/samtools/bcftools/vcfout.c
1150 * added prelimiary VCF parser (not finished)
1151 * change struct a bit
1153 ------------------------------------------------------------------------
1154 r667 | lh3lh3 | 2010-08-03 22:35:27 -0400 (Tue, 03 Aug 2010) | 3 lines
1156 M /trunk/samtools/bam2bcf.c
1157 M /trunk/samtools/bam2bcf.h
1158 M /trunk/samtools/bam_plcmd.c
1159 M /trunk/samtools/bcftools/bcf.c
1161 * allow to set min base q
1162 * fixed a bug in mpileup -u
1164 ------------------------------------------------------------------------
1165 r666 | lh3lh3 | 2010-08-03 22:08:44 -0400 (Tue, 03 Aug 2010) | 2 lines
1167 A /trunk/samtools/bcftools/bcf.tex
1171 ------------------------------------------------------------------------
1172 r665 | lh3lh3 | 2010-08-03 21:18:57 -0400 (Tue, 03 Aug 2010) | 2 lines
1174 M /trunk/samtools/examples/Makefile
1178 ------------------------------------------------------------------------
1179 r664 | lh3lh3 | 2010-08-03 21:13:00 -0400 (Tue, 03 Aug 2010) | 2 lines
1181 M /trunk/samtools/Makefile
1182 M /trunk/samtools/bam2bcf.c
1183 M /trunk/samtools/bam2bcf.h
1184 M /trunk/samtools/bcftools/Makefile
1186 fixed compilation error
1188 ------------------------------------------------------------------------
1189 r662 | lh3lh3 | 2010-08-03 21:04:00 -0400 (Tue, 03 Aug 2010) | 2 lines
1191 M /trunk/samtools/Makefile
1192 D /trunk/samtools/bcf.c
1193 D /trunk/samtools/bcf.h
1194 A /trunk/samtools/bcftools
1195 A /trunk/samtools/bcftools/Makefile
1196 A /trunk/samtools/bcftools/bcf.c
1197 A /trunk/samtools/bcftools/bcf.h
1198 A /trunk/samtools/bcftools/bcfutils.c
1199 A /trunk/samtools/bcftools/index.c
1200 A /trunk/samtools/bcftools/main.c
1201 A /trunk/samtools/bcftools/prob1.c
1202 A /trunk/samtools/bcftools/prob1.h
1203 A /trunk/samtools/bcftools/vcfout.c
1205 move bcftools to samtools
1207 ------------------------------------------------------------------------
1208 r660 | lh3lh3 | 2010-08-03 15:58:32 -0400 (Tue, 03 Aug 2010) | 2 lines
1210 M /trunk/samtools/bam2bcf.c
1212 fixed another minor bug
1214 ------------------------------------------------------------------------
1215 r658 | lh3lh3 | 2010-08-03 15:06:45 -0400 (Tue, 03 Aug 2010) | 3 lines
1217 M /trunk/samtools/bamtk.c
1218 M /trunk/samtools/bcf.c
1220 * samtools-0.1.8-10 (r658)
1221 * fixed a bug in bam2bcf when the reference is N
1223 ------------------------------------------------------------------------
1224 r657 | lh3lh3 | 2010-08-03 14:50:23 -0400 (Tue, 03 Aug 2010) | 3 lines
1226 M /trunk/samtools/bam2bcf.c
1227 M /trunk/samtools/bam2bcf.h
1230 * treat ambiguous ref base as the fifth base
1232 ------------------------------------------------------------------------
1233 r654 | lh3lh3 | 2010-08-02 17:38:27 -0400 (Mon, 02 Aug 2010) | 2 lines
1235 M /trunk/bcftools/bcf.c
1236 M /trunk/samtools/bcf.c
1238 missing a column in VCF output...
1240 ------------------------------------------------------------------------
1241 r653 | lh3lh3 | 2010-08-02 17:31:33 -0400 (Mon, 02 Aug 2010) | 2 lines
1243 M /trunk/samtools/bcf.c
1247 ------------------------------------------------------------------------
1248 r651 | lh3lh3 | 2010-08-02 17:27:31 -0400 (Mon, 02 Aug 2010) | 2 lines
1250 M /trunk/samtools/bcf.c
1252 fixed a bug in bcf reader
1254 ------------------------------------------------------------------------
1255 r650 | lh3lh3 | 2010-08-02 17:00:41 -0400 (Mon, 02 Aug 2010) | 2 lines
1257 M /trunk/samtools/bam2bcf.c
1261 ------------------------------------------------------------------------
1262 r649 | lh3lh3 | 2010-08-02 16:49:35 -0400 (Mon, 02 Aug 2010) | 3 lines
1264 M /trunk/samtools/Makefile
1265 M /trunk/samtools/bam2bcf.c
1266 M /trunk/samtools/bam2bcf.h
1267 M /trunk/samtools/bamtk.c
1269 * samtools-0.1.8-9 (r649)
1270 * lossless representation of PL in BCF output
1272 ------------------------------------------------------------------------
1273 r648 | lh3lh3 | 2010-08-02 16:07:25 -0400 (Mon, 02 Aug 2010) | 2 lines
1275 M /trunk/samtools/Makefile
1276 A /trunk/samtools/bam2bcf.c
1277 A /trunk/samtools/bam2bcf.h
1278 M /trunk/samtools/bam_plcmd.c
1279 A /trunk/samtools/bcf.c
1280 A /trunk/samtools/bcf.h
1284 ------------------------------------------------------------------------
1285 r644 | lh3lh3 | 2010-07-28 11:59:19 -0400 (Wed, 28 Jul 2010) | 5 lines
1287 M /trunk/samtools/bam_mcns.c
1288 M /trunk/samtools/bamtk.c
1290 * samtools-0.1.8-8 (r644)
1291 * mpileup becomes a little stable again
1292 * the method is slightly different, but is more theoretically correct
1293 * snp calling is O(n^2) instead of O(n^3)
1295 ------------------------------------------------------------------------
1296 r643 | lh3lh3 | 2010-07-28 11:54:15 -0400 (Wed, 28 Jul 2010) | 3 lines
1298 M /trunk/samtools/bam_mcns.c
1300 * fixed a STUPID bug, which cost me a lot of time.
1301 * I am going to clean up mcns a little bit
1303 ------------------------------------------------------------------------
1304 r642 | lh3lh3 | 2010-07-27 23:23:07 -0400 (Tue, 27 Jul 2010) | 2 lines
1306 M /trunk/samtools/bam_mcns.c
1307 M /trunk/samtools/bam_mcns.h
1308 M /trunk/samtools/bam_plcmd.c
1310 supposedly this is THE correct implementation, but more testing is needed
1312 ------------------------------------------------------------------------
1313 r641 | lh3lh3 | 2010-07-27 22:43:39 -0400 (Tue, 27 Jul 2010) | 2 lines
1315 M /trunk/samtools/bam_mcns.c
1317 NOT ready yet. Going to make further changes...
1319 ------------------------------------------------------------------------
1320 r639 | lh3lh3 | 2010-07-25 22:18:38 -0400 (Sun, 25 Jul 2010) | 3 lines
1322 M /trunk/samtools/bam_mcns.c
1323 M /trunk/samtools/bam_plcmd.c
1324 M /trunk/samtools/bamtk.c
1326 * samtools-0.1.8-7 (r639)
1327 * fixed the reference allele assignment
1329 ------------------------------------------------------------------------
1330 r638 | lh3lh3 | 2010-07-25 12:01:26 -0400 (Sun, 25 Jul 2010) | 5 lines
1332 M /trunk/samtools/bam_mcns.c
1333 M /trunk/samtools/bam_mcns.h
1334 M /trunk/samtools/bam_plcmd.c
1335 M /trunk/samtools/bamtk.c
1337 * samtools-0.1.8-6 (r638)
1338 * skip isnan/isinf in case of float underflow
1339 * added the flat prior
1340 * fixed an issue where there are no reads supporting the reference
1342 ------------------------------------------------------------------------
1343 r637 | lh3lh3 | 2010-07-24 14:16:27 -0400 (Sat, 24 Jul 2010) | 2 lines
1345 M /trunk/samtools/bam_plcmd.c
1349 ------------------------------------------------------------------------
1350 r636 | lh3lh3 | 2010-07-24 14:07:27 -0400 (Sat, 24 Jul 2010) | 2 lines
1352 M /trunk/samtools/bam_mcns.c
1353 M /trunk/samtools/bam_mcns.h
1354 M /trunk/samtools/bam_plcmd.c
1355 M /trunk/samtools/bamtk.c
1359 ------------------------------------------------------------------------
1360 r635 | lh3lh3 | 2010-07-24 01:49:49 -0400 (Sat, 24 Jul 2010) | 2 lines
1362 M /trunk/samtools/bam_mcns.c
1363 M /trunk/samtools/bam_mcns.h
1364 M /trunk/samtools/bam_plcmd.c
1366 posterior expectation FINALLY working. I am so tired...
1368 ------------------------------------------------------------------------
1369 r633 | lh3lh3 | 2010-07-23 13:50:48 -0400 (Fri, 23 Jul 2010) | 2 lines
1371 M /trunk/samtools/bam_plcmd.c
1373 another minor fix to mpileup
1375 ------------------------------------------------------------------------
1376 r632 | lh3lh3 | 2010-07-23 13:43:31 -0400 (Fri, 23 Jul 2010) | 2 lines
1378 M /trunk/samtools/bam_plcmd.c
1380 added the format column
1382 ------------------------------------------------------------------------
1383 r631 | lh3lh3 | 2010-07-23 13:25:44 -0400 (Fri, 23 Jul 2010) | 2 lines
1385 M /trunk/samtools/bam_mcns.c
1386 M /trunk/samtools/bam_mcns.h
1387 M /trunk/samtools/bam_plcmd.c
1388 M /trunk/samtools/bamtk.c
1390 added an alternative prior
1392 ------------------------------------------------------------------------
1393 r628 | lh3lh3 | 2010-07-23 11:48:51 -0400 (Fri, 23 Jul 2010) | 2 lines
1395 M /trunk/samtools/bam_mcns.c
1396 M /trunk/samtools/bam_mcns.h
1397 M /trunk/samtools/bam_plcmd.c
1399 calculate posterior allele frequency
1401 ------------------------------------------------------------------------
1402 r627 | lh3lh3 | 2010-07-22 21:39:13 -0400 (Thu, 22 Jul 2010) | 3 lines
1404 M /trunk/samtools/bam_mcns.c
1405 M /trunk/samtools/bam_plcmd.c
1406 M /trunk/samtools/bamtk.c
1408 * samtools-0.1.8-3 (r627)
1409 * multi-sample snp calling appears to work. More tests needed.
1411 ------------------------------------------------------------------------
1412 r626 | lh3lh3 | 2010-07-22 16:37:56 -0400 (Thu, 22 Jul 2010) | 3 lines
1414 M /trunk/samtools/bam_mcns.c
1415 M /trunk/samtools/bam_mcns.h
1416 M /trunk/samtools/bam_plcmd.c
1417 M /trunk/samtools/bam_tview.c
1419 * preliminary multisample SNP caller.
1420 * something looks not so right, but it largely works
1422 ------------------------------------------------------------------------
1423 r617 | lh3lh3 | 2010-07-14 16:26:27 -0400 (Wed, 14 Jul 2010) | 3 lines
1425 M /trunk/samtools/bam_mcns.c
1426 M /trunk/samtools/bam_plcmd.c
1427 M /trunk/samtools/bamtk.c
1429 * samtools-0.1.8-2 (r617)
1430 * allele frequency calculation apparently works...
1432 ------------------------------------------------------------------------
1433 r616 | lh3lh3 | 2010-07-14 13:33:51 -0400 (Wed, 14 Jul 2010) | 3 lines
1435 M /trunk/samtools/Makefile
1436 A /trunk/samtools/bam_mcns.c
1437 A /trunk/samtools/bam_mcns.h
1438 M /trunk/samtools/bam_plcmd.c
1440 * added mutli-sample framework. It is not working, yet.
1441 * improved the mpileup interface
1443 ------------------------------------------------------------------------
1444 r615 | lh3lh3 | 2010-07-13 14:50:12 -0400 (Tue, 13 Jul 2010) | 3 lines
1446 M /trunk/samtools/bam_plcmd.c
1447 M /trunk/samtools/bamtk.c
1448 M /trunk/samtools/misc/Makefile
1450 * samtools-0.1.8-1 (r615)
1451 * allow to get mpileup at required sites
1453 ------------------------------------------------------------------------
1454 r613 | lh3lh3 | 2010-07-11 22:40:56 -0400 (Sun, 11 Jul 2010) | 2 lines
1456 M /trunk/samtools/ChangeLog
1457 M /trunk/samtools/NEWS
1458 M /trunk/samtools/bam_plcmd.c
1459 M /trunk/samtools/bamtk.c
1460 M /trunk/samtools/samtools.1
1462 Release samtools-0.1.8
1464 ------------------------------------------------------------------------
1465 r612 | lh3lh3 | 2010-07-11 21:08:56 -0400 (Sun, 11 Jul 2010) | 2 lines
1467 M /trunk/samtools/knetfile.c
1469 fixed a compiling issue for Windows
1471 ------------------------------------------------------------------------
1472 r611 | lh3lh3 | 2010-07-11 20:59:15 -0400 (Sun, 11 Jul 2010) | 2 lines
1474 M /trunk/samtools/bam_sort.c
1476 fixed a bug in sorting when output to stdout (by Peter Chines)
1478 ------------------------------------------------------------------------
1479 r610 | lh3lh3 | 2010-07-09 17:05:10 -0400 (Fri, 09 Jul 2010) | 2 lines
1481 M /trunk/samtools/NEWS
1482 M /trunk/samtools/bam_plcmd.c
1484 change the command line option of pileup
1486 ------------------------------------------------------------------------
1487 r609 | lh3lh3 | 2010-07-09 00:39:34 -0400 (Fri, 09 Jul 2010) | 2 lines
1489 M /trunk/samtools/bam_pileup.c
1490 A /trunk/samtools/examples/toy.fa
1491 A /trunk/samtools/examples/toy.sam
1493 make pileup work with CIGAR with I/D at the beginning or in the end
1495 ------------------------------------------------------------------------
1496 r608 | lh3lh3 | 2010-07-08 22:36:12 -0400 (Thu, 08 Jul 2010) | 3 lines
1498 M /trunk/samtools/bam_maqcns.c
1499 M /trunk/samtools/bam_maqcns.h
1500 M /trunk/samtools/bam_plcmd.c
1501 M /trunk/samtools/bam_tview.c
1503 * make tview more friendly
1504 * a temporary remedy for an issue in indel calling
1506 ------------------------------------------------------------------------
1507 r607 | lh3lh3 | 2010-07-08 14:43:52 -0400 (Thu, 08 Jul 2010) | 4 lines
1509 M /trunk/samtools/bam_maqcns.c
1510 M /trunk/samtools/bam_plcmd.c
1511 M /trunk/samtools/bamtk.c
1513 * samtools-0.1.7-r607
1514 * improved the genotype accuracy for indels
1515 * use the SOAPsnp model for SNP calling by default.
1517 ------------------------------------------------------------------------
1518 r606 | lh3lh3 | 2010-07-08 01:05:19 -0400 (Thu, 08 Jul 2010) | 2 lines
1520 M /trunk/samtools/misc/Makefile
1522 removed a debugging example
1524 ------------------------------------------------------------------------
1525 r605 | lh3lh3 | 2010-07-08 01:04:09 -0400 (Thu, 08 Jul 2010) | 4 lines
1527 M /trunk/samtools/bam_maqcns.c
1528 M /trunk/samtools/bamtk.c
1530 * samtools-.1.7-18 (r605)
1531 * fixed an issue when a deletion and mismatch occur at the same time
1532 and the base quality is higher than 40 (if -I40).
1534 ------------------------------------------------------------------------
1535 r604 | lh3lh3 | 2010-07-02 19:32:24 -0400 (Fri, 02 Jul 2010) | 2 lines
1537 M /trunk/samtools/bam.h
1538 M /trunk/samtools/bam_index.c
1539 M /trunk/samtools/misc/Makefile
1541 fixed a minor bug in idxstats
1543 ------------------------------------------------------------------------
1544 r601 | lh3lh3 | 2010-06-16 09:03:59 -0400 (Wed, 16 Jun 2010) | 2 lines
1546 M /trunk/samtools/bam_index.c
1548 fixed a minor bug in indexing
1550 ------------------------------------------------------------------------
1551 r600 | lh3lh3 | 2010-06-15 10:17:53 -0400 (Tue, 15 Jun 2010) | 2 lines
1553 M /trunk/samtools/ChangeLog
1554 M /trunk/samtools/bam.c
1556 change printf() to puts in exporting
1558 ------------------------------------------------------------------------
1559 r599 | lh3lh3 | 2010-06-13 21:41:11 -0400 (Sun, 13 Jun 2010) | 2 lines
1561 M /trunk/samtools/bamtk.c
1563 minor fix. No actual effect.
1565 ------------------------------------------------------------------------
1566 r598 | lh3lh3 | 2010-06-13 21:32:45 -0400 (Sun, 13 Jun 2010) | 2 lines
1568 M /trunk/samtools/Makefile
1570 added Makefile targets to compile shared/dynamic library
1572 ------------------------------------------------------------------------
1573 r596 | lh3lh3 | 2010-06-13 19:48:07 -0400 (Sun, 13 Jun 2010) | 3 lines
1575 M /trunk/samtools/ChangeLog
1576 M /trunk/samtools/bam_index.c
1577 M /trunk/samtools/bamtk.c
1579 * samtools-0.1.7-17 (r596)
1580 * also keep the number of coor-less reads in the index file
1582 ------------------------------------------------------------------------
1583 r595 | lh3lh3 | 2010-06-13 18:54:26 -0400 (Sun, 13 Jun 2010) | 3 lines
1585 M /trunk/samtools/bam_index.c
1586 M /trunk/samtools/bamtk.c
1588 * samtools-0.1.7-16 (r595)
1589 * write additional information to bam index
1591 ------------------------------------------------------------------------
1592 r594 | lh3lh3 | 2010-06-13 17:29:52 -0400 (Sun, 13 Jun 2010) | 2 lines
1594 M /trunk/samtools/bam_index.c
1596 fixed a bug for unmapped sequences in indexing
1598 ------------------------------------------------------------------------
1599 r593 | lh3lh3 | 2010-06-12 18:11:32 -0400 (Sat, 12 Jun 2010) | 2 lines
1601 M /trunk/samtools/bam.h
1602 M /trunk/samtools/bam_index.c
1603 M /trunk/samtools/bam_plcmd.c
1604 M /trunk/samtools/samtools.1
1606 rename iterf as iter
1608 ------------------------------------------------------------------------
1609 r592 | lh3lh3 | 2010-06-12 18:02:38 -0400 (Sat, 12 Jun 2010) | 4 lines
1611 M /trunk/samtools/ChangeLog
1612 M /trunk/samtools/bam_aux.c
1613 M /trunk/samtools/bam_index.c
1614 M /trunk/samtools/bam_pileup.c
1615 M /trunk/samtools/bam_plcmd.c
1616 M /trunk/samtools/bamtk.c
1618 * samtools-0.1.7-15 (r592)
1619 * fixed a few minor memory leaks in the new pileup code
1620 * improved the functionality of mpileup
1622 ------------------------------------------------------------------------
1623 r591 | lh3lh3 | 2010-06-12 14:09:22 -0400 (Sat, 12 Jun 2010) | 3 lines
1625 M /trunk/samtools/bam.h
1626 M /trunk/samtools/bam_pileup.c
1627 M /trunk/samtools/bam_plcmd.c
1628 M /trunk/samtools/bamtk.c
1630 * samtools-0.1.7-14 (r591)
1631 * elementary multi-way pileup. More testing and more functionality to be done.
1633 ------------------------------------------------------------------------
1634 r590 | lh3lh3 | 2010-06-12 01:00:24 -0400 (Sat, 12 Jun 2010) | 3 lines
1636 M /trunk/samtools/bam.h
1637 M /trunk/samtools/bam_pileup.c
1638 M /trunk/samtools/bamtk.c
1640 * samtools-0.1.7-13 (r590)
1641 * added mpileup APIs. No compiling errors, but not tested at all. It is late.
1643 ------------------------------------------------------------------------
1644 r589 | lh3lh3 | 2010-06-11 22:37:09 -0400 (Fri, 11 Jun 2010) | 3 lines
1646 M /trunk/samtools/bam.h
1647 M /trunk/samtools/bam_pileup.c
1648 M /trunk/samtools/bamtk.c
1650 * samtools-0.1.7-12 (r589)
1651 * added iterator-like APIs for pileup
1653 ------------------------------------------------------------------------
1654 r588 | lh3lh3 | 2010-06-11 17:41:13 -0400 (Fri, 11 Jun 2010) | 3 lines
1656 M /trunk/samtools/bam_index.c
1657 M /trunk/samtools/bamtk.c
1659 * samtools-0.1.7-11 (r588)
1660 * ported a few improvements from tabix back to samtools
1662 ------------------------------------------------------------------------
1663 r587 | lh3lh3 | 2010-06-11 17:33:16 -0400 (Fri, 11 Jun 2010) | 3 lines
1665 M /trunk/samtools/bam.h
1666 M /trunk/samtools/bam_index.c
1667 M /trunk/samtools/bamtk.c
1669 * samtools-0.1.7-10 (r587)
1670 * added iterator interface for bam_fetch (ported back from tabix)
1672 ------------------------------------------------------------------------
1673 r586 | lh3lh3 | 2010-06-11 13:23:53 -0400 (Fri, 11 Jun 2010) | 3 lines
1675 M /trunk/samtools/Makefile
1676 A /trunk/samtools/bam_reheader.c
1677 M /trunk/samtools/bamtk.c
1678 M /trunk/samtools/bgzf.c
1680 * samtools-0.1.7-9 (r586)
1681 * added "reheader" to replace the BAM header
1683 ------------------------------------------------------------------------
1684 r585 | lh3lh3 | 2010-06-11 12:22:06 -0400 (Fri, 11 Jun 2010) | 3 lines
1686 M /trunk/samtools/bam.c
1687 M /trunk/samtools/bamtk.c
1688 M /trunk/samtools/kstring.h
1690 * samtools-0.1.7-8 (r585)
1693 ------------------------------------------------------------------------
1694 r584 | lh3lh3 | 2010-06-11 12:00:41 -0400 (Fri, 11 Jun 2010) | 4 lines
1696 M /trunk/samtools/bam.c
1697 M /trunk/samtools/bamtk.c
1698 M /trunk/samtools/bgzf.c
1699 M /trunk/samtools/bgzf.h
1700 M /trunk/samtools/kstring.h
1701 M /trunk/samtools/misc/wgsim_eval.pl
1703 * samtools-0.1.7-7 (r584)
1704 * ported tabix BGZF to samtools
1705 * flush BGZF after writing the BAM header and between alignment boundaries
1707 ------------------------------------------------------------------------
1708 r583 | petulda | 2010-06-11 11:58:20 -0400 (Fri, 11 Jun 2010) | 1 line
1710 A /trunk/samtools/misc/varfilter.py
1712 Initial release on behalf of Aylwyn Scally
1713 ------------------------------------------------------------------------
1714 r561 | petulda | 2010-05-07 08:41:56 -0400 (Fri, 07 May 2010) | 1 line
1716 M /trunk/samtools/samtools.1
1718 Added a note about the indels coordinates
1719 ------------------------------------------------------------------------
1720 r551 | petulda | 2010-04-23 09:42:13 -0400 (Fri, 23 Apr 2010) | 1 line
1722 M /trunk/samtools/misc/sam2vcf.pl
1724 Added the possibility to print or not to print the reference allele
1725 ------------------------------------------------------------------------
1726 r546 | petulda | 2010-04-15 04:33:55 -0400 (Thu, 15 Apr 2010) | 1 line
1728 M /trunk/samtools/sam_header.c
1730 More descriptive message for space separated tags
1731 ------------------------------------------------------------------------
1732 r545 | petulda | 2010-04-14 11:44:50 -0400 (Wed, 14 Apr 2010) | 1 line
1734 M /trunk/samtools/misc/sam2vcf.pl
1736 Speedup with -i, no need to query the reference all the time
1737 ------------------------------------------------------------------------
1738 r541 | petulda | 2010-03-15 10:03:51 -0400 (Mon, 15 Mar 2010) | 1 line
1740 M /trunk/samtools/sam_header.c
1742 Fixed the order of sequences in the header
1743 ------------------------------------------------------------------------
1744 r540 | petulda | 2010-03-04 06:28:35 -0500 (Thu, 04 Mar 2010) | 1 line
1746 M /trunk/samtools/misc/sam2vcf.pl
1748 Added possibility to select indels only and fixed a bug in reporting homozygous indels.
1749 ------------------------------------------------------------------------
1750 r539 | jmarshall | 2010-02-27 06:48:17 -0500 (Sat, 27 Feb 2010) | 4 lines
1752 M /trunk/samtools/bam.c
1754 Improve the invalid 'BAM\1' magic number error message, and also print it
1755 when no bytes can be read from the alleged BAM file, e.g., in the common
1756 user error case when a SAM file has accidentally been supplied.
1758 ------------------------------------------------------------------------
1759 r538 | petulda | 2010-02-26 10:51:40 -0500 (Fri, 26 Feb 2010) | 1 line
1761 M /trunk/samtools/AUTHORS
1762 M /trunk/samtools/bam.h
1763 M /trunk/samtools/bam_import.c
1764 M /trunk/samtools/sam_header.c
1766 Improved efficiency of header parsing
1767 ------------------------------------------------------------------------
1768 r537 | lh3lh3 | 2010-02-23 21:08:48 -0500 (Tue, 23 Feb 2010) | 3 lines
1770 M /trunk/samtools/misc/export2sam.pl
1772 Updated export2sam.pl by Chris Saunders from Illumina.
1775 ------------------------------------------------------------------------
1776 r536 | petulda | 2010-02-17 08:32:53 -0500 (Wed, 17 Feb 2010) | 1 line
1778 M /trunk/samtools/misc/samtools.pl
1780 Fixed filtering of SNPs near indels. Added min indel and SNP quality filter.
1781 ------------------------------------------------------------------------
1782 r535 | petulda | 2010-02-12 04:52:37 -0500 (Fri, 12 Feb 2010) | 1 line
1784 M /trunk/samtools/misc/sam2vcf.pl
1786 Print an error for pileups in simple format
1787 ------------------------------------------------------------------------
1788 r534 | lh3lh3 | 2010-02-11 14:01:41 -0500 (Thu, 11 Feb 2010) | 2 lines
1790 M /trunk/samtools/bam_plcmd.c
1792 added a hidden option in pileup to output the base position (for Erin)
1794 ------------------------------------------------------------------------
1795 r533 | petulda | 2010-02-09 10:12:14 -0500 (Tue, 09 Feb 2010) | 1 line
1797 M /trunk/samtools/misc/sam2vcf.pl
1799 Added possibility to specify a custom column title for the data column
1800 ------------------------------------------------------------------------
1801 r532 | petulda | 2010-02-09 09:46:09 -0500 (Tue, 09 Feb 2010) | 1 line
1803 M /trunk/samtools/bam_plcmd.c
1805 Added the -d option to limit maximum depth for indels.
1806 ------------------------------------------------------------------------
1807 r531 | petulda | 2010-02-03 07:57:27 -0500 (Wed, 03 Feb 2010) | 1 line
1809 M /trunk/samtools/misc/sam2vcf.pl
1812 ------------------------------------------------------------------------
1813 r530 | lh3lh3 | 2010-02-01 09:13:19 -0500 (Mon, 01 Feb 2010) | 3 lines
1815 M /trunk/samtools/ChangeLog
1816 M /trunk/samtools/bam_plcmd.c
1817 M /trunk/samtools/bamtk.c
1818 M /trunk/samtools/misc/samtools.pl
1819 M /trunk/samtools/misc/wgsim.c
1822 * fixed a bug in faidx
1824 ------------------------------------------------------------------------
1825 r529 | jmarshall | 2010-01-11 18:51:49 -0500 (Mon, 11 Jan 2010) | 2 lines
1827 M /trunk/samtools/faidx.c
1829 Put the right filename in the error message.
1831 ------------------------------------------------------------------------
1832 r528 | lh3lh3 | 2009-12-14 11:26:47 -0500 (Mon, 14 Dec 2009) | 3 lines
1834 M /trunk/samtools/bam_plcmd.c
1835 M /trunk/samtools/bamtk.c
1837 * samtools-0.1.7-5 (r528)
1838 * further add new consensus generation strategy
1840 ------------------------------------------------------------------------
1841 r527 | petulda | 2009-12-11 12:31:05 -0500 (Fri, 11 Dec 2009) | 1 line
1843 M /trunk/samtools/knetfile.c
1845 Fixed a bug in knet_seek
1846 ------------------------------------------------------------------------
1847 r526 | petulda | 2009-12-11 07:51:18 -0500 (Fri, 11 Dec 2009) | 1 line
1849 M /trunk/samtools/misc/sam2vcf.pl
1851 Small fix in VCF format: dot for the empty INFO field
1852 ------------------------------------------------------------------------
1853 r525 | petulda | 2009-12-11 04:36:18 -0500 (Fri, 11 Dec 2009) | 1 line
1855 M /trunk/samtools/sam_header.c
1857 Allow tabs in the CO header field
1858 ------------------------------------------------------------------------
1859 r524 | jmarshall | 2009-12-10 10:03:58 -0500 (Thu, 10 Dec 2009) | 3 lines
1861 M /trunk/samtools/Makefile
1862 M /trunk/samtools/Makefile.mingw
1864 Depend on libbam.a rather than the phony target, so that samtools is not
1865 unnecessarily rebuilt every time. Also clean bgzip.
1867 ------------------------------------------------------------------------
1868 r523 | jmarshall | 2009-12-10 09:45:32 -0500 (Thu, 10 Dec 2009) | 4 lines
1870 M /trunk/samtools/Makefile
1871 M /trunk/samtools/Makefile.mingw
1873 Fix a bug in compiling bgzip: this also needs knetfile.o when _USE_KNETFILE
1874 is defined. Also introduce $(KNETFILE_O) which can be set to empty to
1875 facilitate non-knet builds.
1877 ------------------------------------------------------------------------
1878 r522 | lh3lh3 | 2009-12-01 13:02:36 -0500 (Tue, 01 Dec 2009) | 4 lines
1880 M /trunk/samtools/bamtk.c
1881 M /trunk/samtools/sam_view.c
1883 * samtools-0.1.7-4 (r522)
1884 * fixed a bug in "view -r"
1885 * added a new option "view -R" to read required read groups from a file
1887 ------------------------------------------------------------------------
1888 r521 | lh3lh3 | 2009-12-01 10:00:12 -0500 (Tue, 01 Dec 2009) | 3 lines
1890 M /trunk/samtools/bam_md.c
1891 M /trunk/samtools/bamtk.c
1893 * samtools-0.1.7-3 (r521)
1894 * calmd: optionally mask matching bases as N
1896 ------------------------------------------------------------------------
1897 r520 | lh3lh3 | 2009-12-01 09:37:17 -0500 (Tue, 01 Dec 2009) | 4 lines
1899 M /trunk/samtools/bam_plcmd.c
1900 M /trunk/samtools/bamtk.c
1901 M /trunk/samtools/misc/samtools.pl
1903 * samtools-0.1.7-2 (r520)
1904 * fixed a few issues with compilation in Windows (on behalf of John)
1905 * choose a random base as the consensus (for population genetics studies)
1907 ------------------------------------------------------------------------
1908 r519 | jmarshall | 2009-11-30 10:53:02 -0500 (Mon, 30 Nov 2009) | 6 lines
1910 M /trunk/samtools/Makefile
1912 Put libraries at the end, so they can resolve references from libbam.a
1913 as well, even with old-fashioned linkers.
1915 Also use libbam.a explicitly rather than "-L. -lbam" to ensure that we get
1916 the freshly built library, not some other libbam.a lying around the system.
1918 ------------------------------------------------------------------------
1919 r518 | jmarshall | 2009-11-30 08:44:56 -0500 (Mon, 30 Nov 2009) | 2 lines
1921 M /trunk/samtools/Makefile
1922 M /trunk/samtools/misc/Makefile
1924 Also clean *.exe (for Cygwin users using this makefile).
1926 ------------------------------------------------------------------------
1927 r517 | jmarshall | 2009-11-30 07:09:04 -0500 (Mon, 30 Nov 2009) | 2 lines
1929 M /trunk/samtools/bam_index.c
1931 Index files should be opened in binary mode, not text mode.
1933 ------------------------------------------------------------------------
1934 r516 | lh3lh3 | 2009-11-27 15:18:59 -0500 (Fri, 27 Nov 2009) | 2 lines
1936 A /trunk/samtools/examples/bam2bed.c
1938 another example program
1940 ------------------------------------------------------------------------
1941 r515 | lh3lh3 | 2009-11-27 10:44:56 -0500 (Fri, 27 Nov 2009) | 3 lines
1943 M /trunk/samtools/bam_import.c
1944 M /trunk/samtools/bamtk.c
1945 M /trunk/samtools/misc/wgsim_eval.pl
1946 M /trunk/samtools/sam.c
1948 * samtools-0.1.7-1 (r515)
1949 * report an error when .fai contains duplicated names, instead of segfault
1951 ------------------------------------------------------------------------
1952 r514 | jmarshall | 2009-11-24 09:45:35 -0500 (Tue, 24 Nov 2009) | 2 lines
1954 M /trunk/samtools/bam.c
1956 Format 'c'-encoded auxiliary fields correctly, as *signed* integers.
1958 ------------------------------------------------------------------------
1959 r513 | lh3lh3 | 2009-11-16 10:13:07 -0500 (Mon, 16 Nov 2009) | 2 lines
1961 M /trunk/samtools/Makefile.mingw
1963 Update Makefile.mingw for the same reason
1965 ------------------------------------------------------------------------
1966 r512 | lh3lh3 | 2009-11-16 10:00:08 -0500 (Mon, 16 Nov 2009) | 2 lines
1968 M /trunk/samtools/Makefile
1970 Fixed a bug in compiling razip
1972 ------------------------------------------------------------------------
1973 r510 | lh3lh3 | 2009-11-10 10:55:41 -0500 (Tue, 10 Nov 2009) | 2 lines
1975 M /trunk/samtools/ChangeLog
1976 M /trunk/samtools/NEWS
1977 M /trunk/samtools/bamtk.c
1978 M /trunk/samtools/samtools.1
1980 Release samtools-0.1.7 (r510)
1982 ------------------------------------------------------------------------
1983 r509 | lh3lh3 | 2009-11-06 09:17:09 -0500 (Fri, 06 Nov 2009) | 3 lines
1985 M /trunk/samtools/bam_plcmd.c
1986 M /trunk/samtools/bamtk.c
1988 * samtools-0.1.6-22 (r509)
1989 * forget to fix a similar problem in glfgen
1991 ------------------------------------------------------------------------
1992 r508 | lh3lh3 | 2009-11-06 09:06:40 -0500 (Fri, 06 Nov 2009) | 3 lines
1994 M /trunk/samtools/bam_maqcns.c
1995 M /trunk/samtools/bam_plcmd.c
1996 M /trunk/samtools/bamtk.c
1997 M /trunk/samtools/sam_view.c
1999 * samtools-0.1.6-21 (r508)
2000 * fixed a potential bug in the indel caller towards the end of a chromosome
2002 ------------------------------------------------------------------------
2003 r494 | lh3lh3 | 2009-10-26 11:38:00 -0400 (Mon, 26 Oct 2009) | 3 lines
2005 M /trunk/samtools/bamtk.c
2006 M /trunk/samtools/sam_view.c
2008 * samtools-0.1.6-19 (r494)
2009 * allow to convert Illumina quality (64 based) to the BAM quality
2011 ------------------------------------------------------------------------
2012 r493 | lh3lh3 | 2009-10-26 10:24:39 -0400 (Mon, 26 Oct 2009) | 4 lines
2014 M /trunk/samtools/Makefile
2015 M /trunk/samtools/bam.c
2016 M /trunk/samtools/bam_import.c
2017 M /trunk/samtools/bamtk.c
2018 M /trunk/samtools/sam.c
2019 M /trunk/samtools/sam_header.c
2021 * samtools-0.1.6-18 (r493)
2022 * fixed the bugs due to improperly incorporating Petr's header parser
2023 * a little code clean up in sam_header.c
2025 ------------------------------------------------------------------------
2026 r492 | petulda | 2009-10-24 09:43:25 -0400 (Sat, 24 Oct 2009) | 1 line
2028 M /trunk/samtools/sam_header.c
2030 Added sam_header_line_free call for sam_header_parse2
2031 ------------------------------------------------------------------------
2032 r491 | lh3lh3 | 2009-10-24 00:50:16 -0400 (Sat, 24 Oct 2009) | 3 lines
2034 M /trunk/samtools/sam_view.c
2039 ------------------------------------------------------------------------
2040 r490 | lh3lh3 | 2009-10-24 00:45:12 -0400 (Sat, 24 Oct 2009) | 4 lines
2042 M /trunk/samtools/bam.c
2043 M /trunk/samtools/bam.h
2044 M /trunk/samtools/bam_import.c
2045 M /trunk/samtools/sam.c
2048 * improved the interface a bit
2051 ------------------------------------------------------------------------
2052 r489 | lh3lh3 | 2009-10-24 00:41:50 -0400 (Sat, 24 Oct 2009) | 3 lines
2054 M /trunk/samtools/bam_import.c
2055 M /trunk/samtools/sam_header.c
2056 M /trunk/samtools/sam_header.h
2058 * BUGGY VERSION. Please NOT use it.
2059 * Fixed a minor bug, but the major bug is still there.
2061 ------------------------------------------------------------------------
2062 r488 | lh3lh3 | 2009-10-24 00:17:10 -0400 (Sat, 24 Oct 2009) | 3 lines
2064 M /trunk/samtools/Makefile
2065 M /trunk/samtools/bam.c
2066 M /trunk/samtools/bam.h
2067 M /trunk/samtools/bam_aux.c
2068 M /trunk/samtools/bam_import.c
2069 M /trunk/samtools/bam_rmdup.c
2070 M /trunk/samtools/bam_rmdupse.c
2071 M /trunk/samtools/kaln.c
2072 M /trunk/samtools/sam.c
2073 M /trunk/samtools/sam_header.c
2074 M /trunk/samtools/sam_header.h
2075 M /trunk/samtools/sam_view.c
2077 * This revision is SERIOUSLY BUGGY. Please NOT use it.
2078 * Start to incorporate header parsing from Petr Danecek
2080 ------------------------------------------------------------------------
2081 r487 | petulda | 2009-10-23 11:44:32 -0400 (Fri, 23 Oct 2009) | 1 line
2083 M /trunk/samtools/sam_header.c
2084 M /trunk/samtools/sam_header.h
2086 Now possible to merge multiple HeaderDict dictionaries
2087 ------------------------------------------------------------------------
2088 r486 | petulda | 2009-10-22 11:46:58 -0400 (Thu, 22 Oct 2009) | 1 line
2090 M /trunk/samtools/sam_header.c
2093 ------------------------------------------------------------------------
2094 r485 | petulda | 2009-10-22 11:41:56 -0400 (Thu, 22 Oct 2009) | 1 line
2096 A /trunk/samtools/sam_header.c
2097 A /trunk/samtools/sam_header.h
2100 ------------------------------------------------------------------------
2101 r484 | lh3lh3 | 2009-10-19 14:31:32 -0400 (Mon, 19 Oct 2009) | 5 lines
2103 M /trunk/samtools/bam_import.c
2104 M /trunk/samtools/bam_rmdupse.c
2105 M /trunk/samtools/bamtk.c
2106 M /trunk/samtools/examples/Makefile
2108 * samtools-0.1.6-17 (r484)
2109 * fixed a memory leak in rmdupse
2110 * fixed a bug in parsing @RG header lines
2111 * test rmdup in examples/
2113 ------------------------------------------------------------------------
2114 r483 | lh3lh3 | 2009-10-19 13:22:48 -0400 (Mon, 19 Oct 2009) | 4 lines
2116 M /trunk/samtools/bam_rmdup.c
2117 M /trunk/samtools/bam_rmdupse.c
2118 M /trunk/samtools/bamtk.c
2120 * samtools-0.1.6-16 (r483)
2121 * unify the interface of rmdup and rmdupse
2122 * a new bug found in rg2lib(). Have not been fixed yet.
2124 ------------------------------------------------------------------------
2125 r482 | lh3lh3 | 2009-10-19 13:03:34 -0400 (Mon, 19 Oct 2009) | 4 lines
2127 M /trunk/samtools/bam.h
2128 M /trunk/samtools/bam_rmdup.c
2129 M /trunk/samtools/bam_rmdupse.c
2130 M /trunk/samtools/bamtk.c
2131 A /trunk/samtools/klist.h
2133 * samtools-0.1.6-15 (r482)
2135 * rmdupse is now library aware
2137 ------------------------------------------------------------------------
2138 r481 | lh3lh3 | 2009-10-18 00:07:21 -0400 (Sun, 18 Oct 2009) | 3 lines
2140 M /trunk/samtools/bam_rmdup.c
2141 M /trunk/samtools/bamtk.c
2143 * samtools-0.1.6-14 (r480)
2144 * rmdup is now RG aware
2146 ------------------------------------------------------------------------
2147 r480 | lh3lh3 | 2009-10-17 22:05:20 -0400 (Sat, 17 Oct 2009) | 2 lines
2149 M /trunk/samtools/misc/samtools.pl
2151 added a small unitity to parse SRA XML files
2153 ------------------------------------------------------------------------
2154 r479 | lh3lh3 | 2009-10-17 20:57:26 -0400 (Sat, 17 Oct 2009) | 3 lines
2156 M /trunk/samtools/bam_maqcns.c
2157 M /trunk/samtools/bam_maqcns.h
2158 M /trunk/samtools/bam_plcmd.c
2159 M /trunk/samtools/bam_sort.c
2160 M /trunk/samtools/bamtk.c
2162 * samtools-0.1.6-13 (r479)
2163 * merge: optionally use file names as RG tags
2165 ------------------------------------------------------------------------
2166 r478 | lh3lh3 | 2009-10-14 14:18:12 -0400 (Wed, 14 Oct 2009) | 3 lines
2168 M /trunk/samtools/bam.c
2169 M /trunk/samtools/bam.h
2170 M /trunk/samtools/bam_maqcns.c
2171 M /trunk/samtools/bamtk.c
2172 M /trunk/samtools/kaln.c
2174 * samtools-0.1.6-12 (r478)
2175 * fixed a bug in the indel caller
2177 ------------------------------------------------------------------------
2178 r477 | lh3lh3 | 2009-10-10 06:12:26 -0400 (Sat, 10 Oct 2009) | 3 lines
2180 M /trunk/samtools/bam_index.c
2181 M /trunk/samtools/bamtk.c
2183 * samtools-0.1.6-11 (r477)
2184 * fixed a bug due to recent change in bam_index.c (thank Nicole Washington for the patch)
2186 ------------------------------------------------------------------------
2187 r476 | petulda | 2009-10-09 11:45:36 -0400 (Fri, 09 Oct 2009) | 1 line
2189 A /trunk/samtools/misc/sam2vcf.pl
2191 Added the sam2vcf.pl script.
2192 ------------------------------------------------------------------------
2193 r475 | lh3lh3 | 2009-10-08 10:19:16 -0400 (Thu, 08 Oct 2009) | 2 lines
2195 M /trunk/samtools/Makefile
2196 M /trunk/samtools/bam.c
2197 M /trunk/samtools/bam.h
2198 M /trunk/samtools/bam_maqcns.c
2199 M /trunk/samtools/bamtk.c
2200 A /trunk/samtools/kaln.c
2201 A /trunk/samtools/kaln.h
2203 Unfinished modification. Please do not use this revision...
2205 ------------------------------------------------------------------------
2206 r474 | petulda | 2009-10-08 06:39:54 -0400 (Thu, 08 Oct 2009) | 1 line
2208 M /trunk/samtools/knetfile.c
2210 Removed the offending knet_seek message.
2211 ------------------------------------------------------------------------
2212 r473 | petulda | 2009-10-06 09:26:35 -0400 (Tue, 06 Oct 2009) | 1 line
2214 M /trunk/samtools/knetfile.c
2215 M /trunk/samtools/razf.c
2217 Bug fix - faidx on RAZF compressed files now working.
2218 ------------------------------------------------------------------------
2219 r472 | lh3lh3 | 2009-10-02 08:42:57 -0400 (Fri, 02 Oct 2009) | 2 lines
2221 M /trunk/samtools/samtools.1
2223 Clarify the meaning of a region like "chr2:1,000,000".
2225 ------------------------------------------------------------------------
2226 r471 | lh3lh3 | 2009-10-02 05:42:19 -0400 (Fri, 02 Oct 2009) | 2 lines
2228 M /trunk/samtools/misc/novo2sam.pl
2230 Fixed minor bugs in novo2sam.pl (on behalf of Ken Chen and Colin Hercus)
2232 ------------------------------------------------------------------------
2233 r470 | lh3lh3 | 2009-09-29 15:01:27 -0400 (Tue, 29 Sep 2009) | 3 lines
2235 M /trunk/samtools/Makefile.mingw
2236 M /trunk/samtools/bamtk.c
2237 M /trunk/samtools/knetfile.c
2238 M /trunk/samtools/knetfile.h
2240 * samtools-0.1.6-9 (r470)
2241 * make knetfile.c compatible with MinGW (thank Martin Morgan for the patch)
2243 ------------------------------------------------------------------------
2244 r469 | lh3lh3 | 2009-09-29 08:07:44 -0400 (Tue, 29 Sep 2009) | 3 lines
2246 M /trunk/samtools/bam_index.c
2247 M /trunk/samtools/bamtk.c
2249 * samtools-0.1.6-9 (r469)
2250 * refactor bam_fetch() for Python binding. On behalf of Leo Goodstadt.
2252 ------------------------------------------------------------------------
2253 r468 | lh3lh3 | 2009-09-28 05:18:29 -0400 (Mon, 28 Sep 2009) | 3 lines
2255 M /trunk/samtools/bam_sort.c
2256 M /trunk/samtools/bamtk.c
2257 M /trunk/samtools/misc/samtools.pl
2259 * samtools-0.1.6-7 (r468)
2262 ------------------------------------------------------------------------
2263 r467 | petulda | 2009-09-28 04:51:29 -0400 (Mon, 28 Sep 2009) | 1 line
2265 M /trunk/samtools/bgzf.c
2266 M /trunk/samtools/bgzip.c
2267 M /trunk/samtools/razf.c
2268 M /trunk/samtools/razip.c
2270 Changed the mode for newly created files to 0666. This allows less strict permissions with umask properly set (e.g. 0002 vs. 0022).
2271 ------------------------------------------------------------------------
2272 r466 | lh3lh3 | 2009-09-24 06:29:19 -0400 (Thu, 24 Sep 2009) | 3 lines
2274 M /trunk/samtools/ChangeLog
2275 M /trunk/samtools/bam_md.c
2276 M /trunk/samtools/bamtk.c
2278 * samtools-0.1.6-6 (r466)
2279 * do not crash calmd when some sequences are absent from the reference.
2281 ------------------------------------------------------------------------
2282 r464 | jmarshall | 2009-09-23 06:14:32 -0400 (Wed, 23 Sep 2009) | 3 lines
2284 M /trunk/samtools/bam.c
2285 M /trunk/samtools/knetfile.c
2287 Suppress bgzf_check_EOF() messages when reading from a pipe, as there is
2288 no way to seek on a pipe and the messages always appear.
2290 ------------------------------------------------------------------------
2291 r463 | petulda | 2009-09-16 07:05:41 -0400 (Wed, 16 Sep 2009) | 1 line
2293 M /trunk/samtools/knetfile.c
2294 M /trunk/samtools/razf.c
2296 A bug fix, "samtools view" is now working again.
2297 ------------------------------------------------------------------------
2298 r462 | lh3lh3 | 2009-09-16 04:51:07 -0400 (Wed, 16 Sep 2009) | 3 lines
2300 M /trunk/samtools/bamtk.c
2301 M /trunk/samtools/faidx.c
2302 M /trunk/samtools/knetfile.c
2303 M /trunk/samtools/knetfile.h
2304 M /trunk/samtools/razf.c
2305 M /trunk/samtools/razf.h
2307 * samtools-0.1.6-5 (r462)
2308 * Added knetfile support in razf and faidx (on behalf of Petr Danecek)
2310 ------------------------------------------------------------------------
2311 r460 | lh3lh3 | 2009-09-09 07:06:22 -0400 (Wed, 09 Sep 2009) | 2 lines
2313 M /trunk/samtools/samtools.1
2315 fixed a formatting issue
2317 ------------------------------------------------------------------------
2318 r459 | lh3lh3 | 2009-09-08 18:14:08 -0400 (Tue, 08 Sep 2009) | 3 lines
2320 M /trunk/samtools/bam_sort.c
2321 M /trunk/samtools/bamtk.c
2323 * samtools-0.1.6-4 (r459)
2324 * make sort output the result to stdout when -o is in use
2326 ------------------------------------------------------------------------
2327 r458 | lh3lh3 | 2009-09-07 05:10:28 -0400 (Mon, 07 Sep 2009) | 4 lines
2329 M /trunk/samtools/bamtk.c
2330 M /trunk/samtools/faidx.c
2331 M /trunk/samtools/faidx.h
2332 M /trunk/samtools/samtools.1
2334 * samtools-0.1.6-2 (r458)
2335 * added more interface to faidx (by Nils)
2336 * updated documentation
2338 ------------------------------------------------------------------------
2339 r457 | lh3lh3 | 2009-09-05 16:12:04 -0400 (Sat, 05 Sep 2009) | 3 lines
2341 M /trunk/samtools/bam_sort.c
2342 M /trunk/samtools/bamtk.c
2344 * samtools-0.1.6-2 (r457)
2345 * get rid of three assert() in bam_sort.c
2347 ------------------------------------------------------------------------
2348 r456 | jmarshall | 2009-09-04 12:46:25 -0400 (Fri, 04 Sep 2009) | 3 lines
2350 M /trunk/samtools/razf.c
2352 Return NULL from _razf_open() (and hence razf_open()/razf_open2())
2353 when opening the file fails.
2355 ------------------------------------------------------------------------
2356 r453 | lh3lh3 | 2009-09-02 08:56:33 -0400 (Wed, 02 Sep 2009) | 2 lines
2358 M /trunk/samtools/ChangeLog
2359 M /trunk/samtools/NEWS
2360 M /trunk/samtools/bamtk.c
2361 M /trunk/samtools/samtools.1
2362 D /trunk/samtools/source.dot
2364 Release samtools-0.1.6
2366 ------------------------------------------------------------------------
2367 r451 | lh3lh3 | 2009-09-02 05:44:48 -0400 (Wed, 02 Sep 2009) | 4 lines
2369 M /trunk/samtools/bam_md.c
2370 M /trunk/samtools/bam_rmdup.c
2371 M /trunk/samtools/bam_rmdupse.c
2372 M /trunk/samtools/bam_sort.c
2373 M /trunk/samtools/bamtk.c
2374 M /trunk/samtools/samtools.1
2376 * samtools-0.1.5-34 (r451)
2377 * applied the patch by John
2378 * improved the help message a little bit
2380 ------------------------------------------------------------------------
2381 r450 | lh3lh3 | 2009-09-02 04:55:55 -0400 (Wed, 02 Sep 2009) | 3 lines
2383 M /trunk/samtools/bam_color.c
2384 M /trunk/samtools/bamtk.c
2386 * samtools-0.1.5-33 (r450)
2387 * fixed a bug in bam_color.c (on behalf of Nils Homer)
2389 ------------------------------------------------------------------------
2390 r449 | lh3lh3 | 2009-08-29 15:36:41 -0400 (Sat, 29 Aug 2009) | 4 lines
2392 M /trunk/samtools/bam_import.c
2393 M /trunk/samtools/bam_md.c
2394 M /trunk/samtools/bamtk.c
2395 M /trunk/samtools/misc/samtools.pl
2397 * samtools-0.1.5-32 (r449)
2398 * fillmd: fixed a bug in modifying MD/NM tags
2399 * in import, give a warning if the read is aligned but there is no CIGAR.
2401 ------------------------------------------------------------------------
2402 r448 | lh3lh3 | 2009-08-19 04:44:28 -0400 (Wed, 19 Aug 2009) | 3 lines
2404 M /trunk/samtools/ChangeLog
2405 M /trunk/samtools/bam_pileup.c
2406 M /trunk/samtools/bamtk.c
2407 M /trunk/samtools/misc/wgsim_eval.pl
2409 * samtools-0.1.5-31 (r448)
2410 * fixed an issue when the last CIGAR is I or D
2412 ------------------------------------------------------------------------
2413 r447 | lh3lh3 | 2009-08-17 04:34:57 -0400 (Mon, 17 Aug 2009) | 3 lines
2415 M /trunk/samtools/bam_aux.c
2416 M /trunk/samtools/bamtk.c
2418 * samtools-0.1.5-30 (r447)
2419 * fixed a bug in bam_aux_get(): 'A' is not checked
2421 ------------------------------------------------------------------------
2422 r446 | lh3lh3 | 2009-08-17 04:33:17 -0400 (Mon, 17 Aug 2009) | 2 lines
2424 M /trunk/samtools/bam_aux.c
2425 M /trunk/samtools/bamtk.c
2429 ------------------------------------------------------------------------
2430 r444 | lh3lh3 | 2009-08-11 05:02:36 -0400 (Tue, 11 Aug 2009) | 3 lines
2432 M /trunk/samtools/bam_sort.c
2433 M /trunk/samtools/bamtk.c
2435 * samtools-0.1.5-28 (r444)
2438 ------------------------------------------------------------------------
2439 r443 | lh3lh3 | 2009-08-11 04:29:11 -0400 (Tue, 11 Aug 2009) | 4 lines
2441 M /trunk/samtools/bam.c
2442 M /trunk/samtools/bam_import.c
2443 M /trunk/samtools/bamtk.c
2445 * samtools-0.1.5-27 (r443)
2446 * SEQ and QUAL can be "*"
2447 * parse CIGAR "=" and "X" as "M"
2449 ------------------------------------------------------------------------
2450 r442 | lh3lh3 | 2009-08-07 16:56:38 -0400 (Fri, 07 Aug 2009) | 4 lines
2452 M /trunk/samtools/bam_pileup.c
2453 M /trunk/samtools/bamtk.c
2454 M /trunk/samtools/misc/md5.c
2455 M /trunk/samtools/misc/md5.h
2456 M /trunk/samtools/misc/md5fa.c
2458 * samtools-0.1.5-26 (r442)
2459 * replace RSA Inc md5.* with ones under permissive lincense
2460 * fixed a bug in detecting unsorted bam in pileup
2462 ------------------------------------------------------------------------
2463 r441 | bhandsaker | 2009-08-05 09:41:28 -0400 (Wed, 05 Aug 2009) | 2 lines
2465 M /trunk/samtools/bgzf.c
2466 M /trunk/samtools/bgzf.h
2467 M /trunk/samtools/bgzip.c
2469 Change copyright notices now that MIT has approved open source distribution.
2471 ------------------------------------------------------------------------
2472 r440 | lh3lh3 | 2009-08-05 05:44:24 -0400 (Wed, 05 Aug 2009) | 3 lines
2474 M /trunk/samtools/bam_stat.c
2475 M /trunk/samtools/bamtk.c
2477 * samtools-0.1.5-25 (r436)
2478 * in flagstats, do not report singletons if both ends are unmapped
2480 ------------------------------------------------------------------------
2481 r439 | lh3lh3 | 2009-08-04 17:16:51 -0400 (Tue, 04 Aug 2009) | 2 lines
2483 M /trunk/samtools/misc/maq2sam.c
2485 fixed a SERIOUS bug in setting 0x20 flag
2487 ------------------------------------------------------------------------
2488 r438 | lh3lh3 | 2009-08-04 16:50:43 -0400 (Tue, 04 Aug 2009) | 2 lines
2490 M /trunk/samtools/misc/samtools.pl
2492 fixed two minor bugs (suggested by Tim M Storm)
2494 ------------------------------------------------------------------------
2495 r437 | lh3lh3 | 2009-08-04 04:13:24 -0400 (Tue, 04 Aug 2009) | 3 lines
2497 M /trunk/samtools/bamtk.c
2498 M /trunk/samtools/misc/samtools.pl
2499 M /trunk/samtools/sam_view.c
2501 * samtools-0.1.5-24 (r435)
2504 ------------------------------------------------------------------------
2505 r434 | lh3lh3 | 2009-08-03 05:40:42 -0400 (Mon, 03 Aug 2009) | 3 lines
2507 M /trunk/samtools/bam_tview.c
2508 M /trunk/samtools/bamtk.c
2510 * samtools-0.1.5-23 (r434)
2511 * in tview, press 'r' to show read names rather than sequences
2513 ------------------------------------------------------------------------
2514 r433 | lh3lh3 | 2009-08-02 14:13:35 -0400 (Sun, 02 Aug 2009) | 3 lines
2516 M /trunk/samtools/knetfile.c
2518 * tried to fixed the buggy FTP random access in Windows. FAILED.
2519 * anyway, MinGW seems to have problem with "%lld".
2521 ------------------------------------------------------------------------
2522 r432 | lh3lh3 | 2009-08-01 19:32:07 -0400 (Sat, 01 Aug 2009) | 5 lines
2524 M /trunk/samtools/Makefile.mingw
2525 M /trunk/samtools/bamtk.c
2526 M /trunk/samtools/faidx.c
2527 M /trunk/samtools/razf.c
2528 A /trunk/samtools/win32/libcurses.a
2529 A /trunk/samtools/win32/xcurses.h
2531 * samtools-0.1.5-22 (r432)
2532 * faidx: fixed compitability issue with _WIN32
2533 * razf: fixed potential compitability issue with _WIN32
2534 * PDCurses support in Windows
2536 ------------------------------------------------------------------------
2537 r431 | lh3lh3 | 2009-08-01 18:34:54 -0400 (Sat, 01 Aug 2009) | 2 lines
2539 M /trunk/samtools/win32/libz.a
2541 replace the GnuWin32 version of libz.a with my own build with MinGW.
2543 ------------------------------------------------------------------------
2544 r430 | lh3lh3 | 2009-08-01 18:21:07 -0400 (Sat, 01 Aug 2009) | 2 lines
2546 M /trunk/samtools/knetfile.c
2550 ------------------------------------------------------------------------
2551 r429 | lh3lh3 | 2009-08-01 17:41:19 -0400 (Sat, 01 Aug 2009) | 3 lines
2553 M /trunk/samtools/Makefile.mingw
2554 M /trunk/samtools/bamtk.c
2555 M /trunk/samtools/knetfile.c
2556 M /trunk/samtools/knetfile.h
2558 * samtools-0.1.5-21 (r428)
2559 * knetfile.c is now compatible with mingw-winsock
2561 ------------------------------------------------------------------------
2562 r428 | lh3lh3 | 2009-07-31 19:39:07 -0400 (Fri, 31 Jul 2009) | 2 lines
2564 M /trunk/samtools/Makefile.mingw
2566 simplify MinGW Makefile
2568 ------------------------------------------------------------------------
2569 r427 | lh3lh3 | 2009-07-31 19:30:54 -0400 (Fri, 31 Jul 2009) | 5 lines
2571 A /trunk/samtools/Makefile.mingw
2572 M /trunk/samtools/bam_import.c
2573 M /trunk/samtools/bamtk.c
2574 A /trunk/samtools/win32
2575 A /trunk/samtools/win32/libz.a
2576 A /trunk/samtools/win32/zconf.h
2577 A /trunk/samtools/win32/zlib.h
2579 * samtools-0.1.5-20 (r427)
2580 * MinGW support. At least SAM<->BAM conversion is working. Other
2581 functionality are not tested at the moment.
2582 * zlib headers and Windows version of libz.a are included in win32/
2584 ------------------------------------------------------------------------
2585 r426 | lh3lh3 | 2009-07-31 18:32:09 -0400 (Fri, 31 Jul 2009) | 3 lines
2587 M /trunk/samtools/bamtk.c
2588 M /trunk/samtools/sam_view.c
2590 * samtools-0.1.5-19 (r426)
2591 * fixed a bug caused by recent modifications. Sorry.
2593 ------------------------------------------------------------------------
2594 r425 | lh3lh3 | 2009-07-31 18:23:51 -0400 (Fri, 31 Jul 2009) | 2 lines
2596 M /trunk/samtools/bgzf.c
2598 compatible with Windows binary files
2600 ------------------------------------------------------------------------
2601 r424 | lh3lh3 | 2009-07-31 05:19:59 -0400 (Fri, 31 Jul 2009) | 5 lines
2603 M /trunk/samtools/bam_maqcns.c
2604 M /trunk/samtools/bam_maqcns.h
2605 M /trunk/samtools/bam_plcmd.c
2606 M /trunk/samtools/bam_tview.c
2607 M /trunk/samtools/bamtk.c
2608 M /trunk/samtools/misc/samtools.pl
2610 * samtools-0.1.5-18 (r423)
2611 * output additional information in pileup indel lines, for the purepose
2612 of debugging at the moment
2613 * in tview, optionally allow to treat reference skip as deletion
2615 ------------------------------------------------------------------------
2616 r423 | lh3lh3 | 2009-07-30 17:00:36 -0400 (Thu, 30 Jul 2009) | 2 lines
2618 A /trunk/samtools/misc/psl2sam.pl
2620 convert BLAT psl to SAM.
2622 ------------------------------------------------------------------------
2623 r422 | lh3lh3 | 2009-07-30 06:24:39 -0400 (Thu, 30 Jul 2009) | 6 lines
2625 M /trunk/samtools/ChangeLog
2626 M /trunk/samtools/bam.c
2627 M /trunk/samtools/bamtk.c
2628 M /trunk/samtools/bgzf.c
2629 M /trunk/samtools/bgzf.h
2630 M /trunk/samtools/knetfile.c
2631 M /trunk/samtools/sam.c
2632 M /trunk/samtools/sam_view.c
2634 * samtools-0.1.5-17 (r422)
2635 * fixed a but in knetfile.c when seek type is not SEEK_SET
2636 * write an empty BGZF block to every BGZF file
2637 * check BGZF EOF marker in bam_header_read()
2640 ------------------------------------------------------------------------
2641 r421 | lh3lh3 | 2009-07-30 05:03:39 -0400 (Thu, 30 Jul 2009) | 3 lines
2643 M /trunk/samtools/bam_import.c
2644 M /trunk/samtools/bam_plcmd.c
2645 M /trunk/samtools/bamtk.c
2646 M /trunk/samtools/misc/samtools.pl
2647 M /trunk/samtools/sam.c
2648 M /trunk/samtools/sam.h
2649 M /trunk/samtools/sam_view.c
2651 * samtools-0.1.5-16 (r421)
2652 * in view and pileup, load header from FASTA index if the input is SAM.
2654 ------------------------------------------------------------------------
2655 r420 | lh3lh3 | 2009-07-29 04:18:55 -0400 (Wed, 29 Jul 2009) | 2 lines
2657 M /trunk/samtools/misc/maq2sam.c
2659 do not set "read 1" if reads are not mapped in the PE mode of maq
2661 ------------------------------------------------------------------------
2662 r419 | lh3lh3 | 2009-07-28 04:52:33 -0400 (Tue, 28 Jul 2009) | 5 lines
2664 M /trunk/samtools/bam_import.c
2665 M /trunk/samtools/bamtk.c
2666 M /trunk/samtools/misc/samtools.pl
2667 M /trunk/samtools/misc/wgsim_eval.pl
2669 * samtools-0.1.5-15 (r419)
2670 * in sam_open(), return NULL when the file cannot be opened.
2671 * make wgsim_eval.pl more robust to imperfect SAM
2672 * add "unique" command to samtools.pl
2674 ------------------------------------------------------------------------
2675 r418 | lh3lh3 | 2009-07-24 09:04:19 -0400 (Fri, 24 Jul 2009) | 2 lines
2677 M /trunk/samtools/misc/wgsim_eval.pl
2679 skip @header lines in SAM
2681 ------------------------------------------------------------------------
2682 r417 | lh3lh3 | 2009-07-24 07:42:38 -0400 (Fri, 24 Jul 2009) | 3 lines
2684 M /trunk/samtools/bamtk.c
2685 M /trunk/samtools/sam_view.c
2687 * samtools-0.1.5-14 (r417)
2688 * more help in "samtools view" due to the recent changes.
2690 ------------------------------------------------------------------------
2691 r416 | lh3lh3 | 2009-07-24 07:34:30 -0400 (Fri, 24 Jul 2009) | 3 lines
2693 M /trunk/samtools/bam.c
2694 M /trunk/samtools/bam.h
2695 M /trunk/samtools/bam_import.c
2696 M /trunk/samtools/bamtk.c
2697 M /trunk/samtools/sam.c
2698 M /trunk/samtools/sam.h
2699 M /trunk/samtools/sam_view.c
2701 * samtools-0.1.5-17 (r416)
2702 * support import/export SAM with string tags
2704 ------------------------------------------------------------------------
2705 r415 | lh3lh3 | 2009-07-24 06:39:26 -0400 (Fri, 24 Jul 2009) | 3 lines
2707 M /trunk/samtools/bam.c
2708 M /trunk/samtools/bam.h
2709 M /trunk/samtools/bam_import.c
2710 M /trunk/samtools/bamtk.c
2711 M /trunk/samtools/sam.c
2712 M /trunk/samtools/sam.h
2713 M /trunk/samtools/sam_view.c
2715 * samtools-0.1.5-12 (r415)
2716 * FLAG now can be in HEX
2718 ------------------------------------------------------------------------
2719 r414 | lh3lh3 | 2009-07-22 17:03:49 -0400 (Wed, 22 Jul 2009) | 2 lines
2721 M /trunk/samtools/kstring.h
2723 fixed a compiling error (thank Ken for fixing it)
2725 ------------------------------------------------------------------------
2726 r412 | lh3lh3 | 2009-07-21 17:19:40 -0400 (Tue, 21 Jul 2009) | 2 lines
2728 M /trunk/samtools/kstring.c
2729 M /trunk/samtools/kstring.h
2731 Implemented Boyer-Moore search in the kstring library.
2733 ------------------------------------------------------------------------
2734 r409 | lh3lh3 | 2009-07-17 12:10:20 -0400 (Fri, 17 Jul 2009) | 2 lines
2736 M /trunk/samtools/bam_index.c
2738 do not include knetfile.h when _USE_KNETFILE is not defined
2740 ------------------------------------------------------------------------
2741 r408 | lh3lh3 | 2009-07-17 10:29:21 -0400 (Fri, 17 Jul 2009) | 5 lines
2743 M /trunk/samtools/bam_md.c
2744 M /trunk/samtools/bam_tview.c
2745 M /trunk/samtools/bamtk.c
2746 M /trunk/samtools/bgzf.c
2748 * samtools-0.1.5-11 (r408)
2749 * force to overwirte existing MD if it is different from the one calculated
2751 * bgzf.c: improved the compatibility with Windows headers
2753 ------------------------------------------------------------------------
2754 r407 | lh3lh3 | 2009-07-17 09:46:56 -0400 (Fri, 17 Jul 2009) | 5 lines
2756 M /trunk/samtools/bam.h
2757 M /trunk/samtools/bam_aux.c
2758 M /trunk/samtools/bam_md.c
2759 M /trunk/samtools/bamtk.c
2760 M /trunk/samtools/sam.h
2762 * samtools-0.1.5-10 (r407)
2763 * implemented bam_aux_del() to remove a tag
2764 * fillmd: generate the NM tag
2765 * fillmd: cmd interface improvement
2767 ------------------------------------------------------------------------
2768 r406 | lh3lh3 | 2009-07-16 18:30:40 -0400 (Thu, 16 Jul 2009) | 2 lines
2770 M /trunk/samtools/Makefile
2772 Sorry. The old Makefile is for PDCurses...
2774 ------------------------------------------------------------------------
2775 r405 | lh3lh3 | 2009-07-16 18:30:11 -0400 (Thu, 16 Jul 2009) | 3 lines
2777 M /trunk/samtools/Makefile
2778 M /trunk/samtools/bam_tview.c
2779 M /trunk/samtools/bamtk.c
2781 * samtools-0.1.5-9 (r405)
2782 * improved the compatibility with PDCurses a little bit
2784 ------------------------------------------------------------------------
2785 r404 | lh3lh3 | 2009-07-16 18:23:52 -0400 (Thu, 16 Jul 2009) | 3 lines
2787 M /trunk/samtools/Makefile
2788 M /trunk/samtools/bam_tview.c
2789 M /trunk/samtools/bamtk.c
2791 * samtools-0.1.5-8 (r404)
2792 * compatible with PDCurses
2794 ------------------------------------------------------------------------
2795 r403 | lh3lh3 | 2009-07-16 17:39:39 -0400 (Thu, 16 Jul 2009) | 3 lines
2797 M /trunk/samtools/bamtk.c
2798 M /trunk/samtools/kseq.h
2800 * samtools-0.1.5-7 (r403)
2801 * fixed a bug in kseq.h for binary files (text files are fine)
2803 ------------------------------------------------------------------------
2804 r402 | lh3lh3 | 2009-07-16 06:49:53 -0400 (Thu, 16 Jul 2009) | 4 lines
2806 M /trunk/samtools/bam_import.c
2807 M /trunk/samtools/bam_index.c
2808 M /trunk/samtools/bamtk.c
2809 M /trunk/samtools/bgzf.c
2811 * samtools-0.1.5-6 (r402)
2812 * fixed compiling error when "-D_USE_NETFILE" is not applied
2813 * improve portability to MinGW
2815 ------------------------------------------------------------------------
2816 r398 | lh3lh3 | 2009-07-13 05:21:36 -0400 (Mon, 13 Jul 2009) | 3 lines
2818 A /trunk/bam-lite/bam.h (from /trunk/samtools/bam.h:395)
2819 A /trunk/bam-lite/bam_lite.c (from /trunk/samtools/bam_lite.c:395)
2820 D /trunk/samtools/bam_lite.c
2822 * move bam_lite.c to bam-lite
2823 * copy bam.h to bam-lite
2825 ------------------------------------------------------------------------
2826 r395 | lh3lh3 | 2009-07-13 05:12:57 -0400 (Mon, 13 Jul 2009) | 3 lines
2828 M /trunk/samtools/bam.h
2829 M /trunk/samtools/bam_lite.c
2830 M /trunk/samtools/bam_lpileup.c
2831 M /trunk/samtools/bam_pileup.c
2832 M /trunk/samtools/bamtk.c
2834 * samtools-0.1.5-5 (r395)
2835 * added bam_pileup_file() and removed bam_lpileup_file()
2837 ------------------------------------------------------------------------
2838 r394 | lh3lh3 | 2009-07-12 19:35:10 -0400 (Sun, 12 Jul 2009) | 3 lines
2840 M /trunk/samtools/bamtk.c
2841 M /trunk/samtools/knetfile.c
2842 M /trunk/samtools/knetfile.h
2844 * samtools-0.1.5-4 (r394)
2845 * http_proxy support in knetfile library (check http_proxy ENV)
2847 ------------------------------------------------------------------------
2848 r393 | lh3lh3 | 2009-07-12 18:57:07 -0400 (Sun, 12 Jul 2009) | 5 lines
2850 M /trunk/samtools/bam_index.c
2851 M /trunk/samtools/bam_tview.c
2852 M /trunk/samtools/bamtk.c
2853 M /trunk/samtools/knetfile.c
2854 M /trunk/samtools/knetfile.h
2856 * samtools-0.1.5-3 (r393)
2857 * knetfile now supports HTTP (no proxy at the moment)
2858 * fixed a potential issue in knetfile on opening ordinary file, although I have
2859 not seen the sideeffect so far.
2861 ------------------------------------------------------------------------
2862 r392 | lh3lh3 | 2009-07-12 13:50:55 -0400 (Sun, 12 Jul 2009) | 2 lines
2864 M /trunk/samtools/samtools.1
2866 Remove the warning in tview
2868 ------------------------------------------------------------------------
2869 r391 | lh3lh3 | 2009-07-12 13:42:43 -0400 (Sun, 12 Jul 2009) | 3 lines
2871 M /trunk/samtools/bam_tview.c
2872 M /trunk/samtools/bamtk.c
2874 * samtools-0.1.5-2 (r391)
2875 * do not show a blank screen when no reads mapped
2877 ------------------------------------------------------------------------
2878 r390 | lh3lh3 | 2009-07-09 09:01:42 -0400 (Thu, 09 Jul 2009) | 4 lines
2880 M /trunk/samtools/bam.h
2881 A /trunk/samtools/bam_lite.c
2882 M /trunk/samtools/bamtk.c
2884 * samtools-0.1.5-1 (r390)
2885 * removed useless _IOLIB in bam.h. This should cause no change at all.
2886 * added bam_lite.c for light-weight BAM reading
2888 ------------------------------------------------------------------------
2889 r385 | lh3lh3 | 2009-07-07 11:53:29 -0400 (Tue, 07 Jul 2009) | 2 lines
2891 M /trunk/samtools/bamtk.c
2892 M /trunk/samtools/knetfile.c
2894 Release samtools-0.1.5c (fixed a bug in piping)
2896 ------------------------------------------------------------------------
2897 r383 | lh3lh3 | 2009-07-07 06:39:55 -0400 (Tue, 07 Jul 2009) | 2 lines
2899 M /trunk/samtools/bamtk.c
2900 M /trunk/samtools/sam.c
2902 Release samtools-0.1.5b (BUG! so embarrassing!)
2904 ------------------------------------------------------------------------
2905 r381 | lh3lh3 | 2009-07-07 06:20:06 -0400 (Tue, 07 Jul 2009) | 2 lines
2907 M /trunk/samtools/Makefile
2908 M /trunk/samtools/bam.h
2909 M /trunk/samtools/bam_aux.c
2910 M /trunk/samtools/bamtk.c
2912 Release samtools-0.1.5a (for compatibility with Bio::DB::Sam)
2914 ------------------------------------------------------------------------
2915 r373 | lh3lh3 | 2009-07-07 05:26:57 -0400 (Tue, 07 Jul 2009) | 2 lines
2917 M /trunk/samtools/ChangeLog
2918 M /trunk/samtools/NEWS
2919 M /trunk/samtools/bamtk.c
2920 M /trunk/samtools/samtools.1
2922 Release samtools-0.1.5
2924 ------------------------------------------------------------------------
2925 r372 | lh3lh3 | 2009-07-07 04:49:27 -0400 (Tue, 07 Jul 2009) | 3 lines
2927 M /trunk/samtools/bamtk.c
2928 M /trunk/samtools/sam.c
2930 * samtools-0.1.4-23 (r372)
2931 * keep header text if "view -t" is used (by Gerton)
2933 ------------------------------------------------------------------------
2934 r371 | lh3lh3 | 2009-07-06 20:13:32 -0400 (Mon, 06 Jul 2009) | 2 lines
2936 M /trunk/samtools/samtools.1
2938 update documentation
2940 ------------------------------------------------------------------------
2941 r370 | bhandsaker | 2009-07-02 17:24:34 -0400 (Thu, 02 Jul 2009) | 2 lines
2943 M /trunk/samtools/Makefile
2945 Introduced LIBPATH variable so this could be overridden to allow samtools to build correct at the Broad.
2947 ------------------------------------------------------------------------
2948 r369 | lh3lh3 | 2009-07-02 08:36:53 -0400 (Thu, 02 Jul 2009) | 4 lines
2950 M /trunk/samtools/ChangeLog
2951 M /trunk/samtools/bam_aux.c
2952 M /trunk/samtools/bam_plcmd.c
2953 M /trunk/samtools/bamtk.c
2955 * samtools-0.1.4-22 (r369)
2956 * in pileup, optionally print E2 and U2
2957 * remove the debugging code in bam_aux_get() (Drat!)
2959 ------------------------------------------------------------------------
2960 r368 | lh3lh3 | 2009-07-02 06:32:26 -0400 (Thu, 02 Jul 2009) | 6 lines
2962 M /trunk/samtools/bam.c
2963 M /trunk/samtools/bam.h
2964 M /trunk/samtools/bam_aux.c
2965 M /trunk/samtools/bam_index.c
2966 M /trunk/samtools/bam_lpileup.c
2967 M /trunk/samtools/bam_md.c
2968 M /trunk/samtools/bam_pileup.c
2969 M /trunk/samtools/bam_rmdup.c
2970 M /trunk/samtools/bam_stat.c
2971 M /trunk/samtools/bam_tview.c
2972 M /trunk/samtools/bamtk.c
2973 M /trunk/samtools/faidx.c
2974 M /trunk/samtools/faidx.h
2975 M /trunk/samtools/glf.c
2977 * samtools-0.1.4-21 (r368)
2978 * propagate errors rather than exit or complain assertion failure. Assertion
2979 should be only used for checking internal bugs, but not for external input
2980 inconsistency. I was just a bit lazy.
2981 * small memory leak may be present on failure, though
2983 ------------------------------------------------------------------------
2984 r367 | lh3lh3 | 2009-06-30 11:18:42 -0400 (Tue, 30 Jun 2009) | 2 lines
2986 M /trunk/samtools/knetfile.c
2988 reduce the chance of blocking in FTP connection
2990 ------------------------------------------------------------------------
2991 r366 | lh3lh3 | 2009-06-30 10:35:21 -0400 (Tue, 30 Jun 2009) | 2 lines
2993 M /trunk/samtools/knetfile.c
2995 minor changes to knetfile: invalid fd equals -1 rather than 0
2997 ------------------------------------------------------------------------
2998 r365 | lh3lh3 | 2009-06-30 09:04:30 -0400 (Tue, 30 Jun 2009) | 3 lines
3000 M /trunk/samtools/bam_index.c
3001 M /trunk/samtools/bamtk.c
3002 M /trunk/samtools/knetfile.c
3003 M /trunk/samtools/knetfile.h
3005 * samtools-0.1.4-20 (r365)
3006 * download the BAM index file if it is not found in the current working directory.
3008 ------------------------------------------------------------------------
3009 r364 | lh3lh3 | 2009-06-30 07:39:07 -0400 (Tue, 30 Jun 2009) | 3 lines
3011 M /trunk/samtools/bamtk.c
3012 M /trunk/samtools/knetfile.c
3014 * samtools-0.1.4-19 (r364)
3015 * knetfile: report error when the file is not present on FTP
3017 ------------------------------------------------------------------------
3018 r363 | lh3lh3 | 2009-06-29 18:23:32 -0400 (Mon, 29 Jun 2009) | 4 lines
3020 M /trunk/samtools/bam_tview.c
3021 M /trunk/samtools/bamtk.c
3022 M /trunk/samtools/bgzf.c
3023 M /trunk/samtools/bgzf.h
3024 M /trunk/samtools/knetfile.c
3025 M /trunk/samtools/knetfile.h
3027 * samtools-0.1.4-18 (r363)
3028 * knetfile: do not trigger network communication in FTP seek (lazy seek)
3029 * bgzf: cache recent blocks (disabled by default)
3031 ------------------------------------------------------------------------
3032 r362 | lh3lh3 | 2009-06-25 16:04:34 -0400 (Thu, 25 Jun 2009) | 2 lines
3034 M /trunk/samtools/bgzf.c
3038 ------------------------------------------------------------------------
3039 r361 | lh3lh3 | 2009-06-25 16:03:10 -0400 (Thu, 25 Jun 2009) | 3 lines
3041 M /trunk/samtools/bam_index.c
3042 M /trunk/samtools/bamtk.c
3044 * samtools-0.1.4-17 (r361)
3045 * if a file is given on FTP, search locally for the BAM index
3047 ------------------------------------------------------------------------
3048 r360 | lh3lh3 | 2009-06-25 15:44:52 -0400 (Thu, 25 Jun 2009) | 5 lines
3050 M /trunk/samtools/Makefile
3051 M /trunk/samtools/bam_import.c
3052 M /trunk/samtools/bam_index.c
3053 M /trunk/samtools/bamtk.c
3054 M /trunk/samtools/bgzf.c
3055 M /trunk/samtools/bgzf.h
3056 M /trunk/samtools/knetfile.c
3057 M /trunk/samtools/knetfile.h
3059 * samtools-0.1.4-16 (r360)
3060 * report more information in index when the input is not sorted
3061 * change the behaviour of knet_seek() such that it returns 0 on success
3062 * support knetfile library in BGZF
3064 ------------------------------------------------------------------------
3065 r359 | lh3lh3 | 2009-06-25 12:10:55 -0400 (Thu, 25 Jun 2009) | 2 lines
3067 M /trunk/samtools/knetfile.c
3068 M /trunk/samtools/knetfile.h
3070 fixed bugs in knetfile.*
3072 ------------------------------------------------------------------------
3073 r358 | lh3lh3 | 2009-06-25 08:53:19 -0400 (Thu, 25 Jun 2009) | 2 lines
3075 A /trunk/samtools/knetfile.h
3077 this is the header file
3079 ------------------------------------------------------------------------
3080 r357 | lh3lh3 | 2009-06-25 08:52:03 -0400 (Thu, 25 Jun 2009) | 3 lines
3082 A /trunk/samtools/knetfile.c
3084 * open a file at FTP
3085 * preliminary version
3087 ------------------------------------------------------------------------
3088 r354 | lh3lh3 | 2009-06-24 09:02:25 -0400 (Wed, 24 Jun 2009) | 3 lines
3090 M /trunk/samtools/bam.c
3091 M /trunk/samtools/bamtk.c
3093 * samtools-0.1.4-15 (r354)
3094 * fixed a memory leak in bam_view1(), although samtools is not using this routine.
3096 ------------------------------------------------------------------------
3097 r351 | lh3lh3 | 2009-06-17 19:16:26 -0400 (Wed, 17 Jun 2009) | 4 lines
3099 M /trunk/samtools/bamtk.c
3100 M /trunk/samtools/faidx.c
3102 * samtools-0.1.4-13 (r351)
3103 * make faidx more tolerant to empty lines right before or after > lines
3104 * hope this does not introduce new bugs...
3106 ------------------------------------------------------------------------
3107 r350 | lh3lh3 | 2009-06-16 09:37:01 -0400 (Tue, 16 Jun 2009) | 3 lines
3109 M /trunk/samtools/bam_plcmd.c
3110 M /trunk/samtools/bamtk.c
3112 * samtools-0.1.4-13 (r350)
3113 * fixed a small memory leak in pileup, caused by recent modifications
3115 ------------------------------------------------------------------------
3116 r347 | lh3lh3 | 2009-06-13 16:20:49 -0400 (Sat, 13 Jun 2009) | 3 lines
3118 M /trunk/samtools/bam_plcmd.c
3119 M /trunk/samtools/bamtk.c
3120 M /trunk/samtools/sam_view.c
3122 * samtools-0.1.4-12 (r347)
3123 * added `-S' to pileup, similar to `view -S'
3125 ------------------------------------------------------------------------
3126 r346 | lh3lh3 | 2009-06-13 12:52:31 -0400 (Sat, 13 Jun 2009) | 3 lines
3128 M /trunk/samtools/Makefile
3129 M /trunk/samtools/bamtk.c
3130 M /trunk/samtools/sam_view.c
3131 M /trunk/samtools/samtools.1
3133 * samtools-0.1.4-11 (r346)
3134 * allow to select a read group at view command-line
3136 ------------------------------------------------------------------------
3137 r344 | lh3lh3 | 2009-06-13 09:06:24 -0400 (Sat, 13 Jun 2009) | 2 lines
3139 M /trunk/samtools/examples/calDepth.c
3143 ------------------------------------------------------------------------
3144 r343 | lh3lh3 | 2009-06-13 09:01:22 -0400 (Sat, 13 Jun 2009) | 2 lines
3146 M /trunk/samtools/examples/calDepth.c
3150 ------------------------------------------------------------------------
3151 r342 | lh3lh3 | 2009-06-13 08:58:48 -0400 (Sat, 13 Jun 2009) | 2 lines
3153 M /trunk/samtools/examples/Makefile
3154 A /trunk/samtools/examples/calDepth.c
3156 added an example of calculating read depth
3158 ------------------------------------------------------------------------
3159 r341 | lh3lh3 | 2009-06-13 08:00:08 -0400 (Sat, 13 Jun 2009) | 6 lines
3161 M /trunk/samtools/Makefile
3162 M /trunk/samtools/bam.h
3163 M /trunk/samtools/bam_aux.c
3164 A /trunk/samtools/bam_color.c
3165 M /trunk/samtools/bam_plcmd.c
3166 M /trunk/samtools/bam_sort.c
3167 M /trunk/samtools/bam_tview.c
3168 M /trunk/samtools/bamtk.c
3169 M /trunk/samtools/sam.c
3170 M /trunk/samtools/sam.h
3172 * samtools-0.1.4-10 (r341)
3173 * only include key APIs in libbam.a
3174 * move color-specific routines to bam_color.c
3175 * update documentations
3176 * remove the support of -q in pileup
3178 ------------------------------------------------------------------------
3179 r340 | lh3lh3 | 2009-06-13 06:17:14 -0400 (Sat, 13 Jun 2009) | 6 lines
3181 M /trunk/samtools/INSTALL
3182 M /trunk/samtools/Makefile
3183 M /trunk/samtools/bam_aux.c
3184 M /trunk/samtools/bam_import.c
3185 M /trunk/samtools/bam_tview.c
3186 M /trunk/samtools/bamtk.c
3187 M /trunk/samtools/razf.c
3188 M /trunk/samtools/sam_view.c
3190 * samtools-0.1.4-9 (r340)
3191 * added a warning to razf.c if zlib<1.2.2.1
3192 * fixed a compilation warning
3193 * fixed a segfault caused by @RG parsing
3194 * detect NCURSES in bam_tview.c
3196 ------------------------------------------------------------------------
3197 r339 | lh3lh3 | 2009-06-13 05:35:19 -0400 (Sat, 13 Jun 2009) | 2 lines
3199 M /trunk/samtools/INSTALL
3203 ------------------------------------------------------------------------
3204 r338 | lh3lh3 | 2009-06-12 19:15:24 -0400 (Fri, 12 Jun 2009) | 4 lines
3206 M /trunk/samtools/bam.c
3207 M /trunk/samtools/bam.h
3208 M /trunk/samtools/bam_aux.c
3209 M /trunk/samtools/bam_import.c
3210 M /trunk/samtools/bamtk.c
3211 M /trunk/samtools/kstring.h
3212 M /trunk/samtools/sam.c
3213 M /trunk/samtools/sam_view.c
3215 * samtools-0.1.4-8 (r338)
3216 * parse the @RG header lines and allow to choose library at the "samtools view"
3219 ------------------------------------------------------------------------
3220 r337 | lh3lh3 | 2009-06-12 16:25:50 -0400 (Fri, 12 Jun 2009) | 4 lines
3222 M /trunk/samtools/bamtk.c
3223 M /trunk/samtools/bgzf.c
3224 M /trunk/samtools/bgzf.h
3225 M /trunk/samtools/sam.c
3226 M /trunk/samtools/sam_view.c
3228 * samtools-0.1.4-7 (r337)
3229 * bgzf.c: support mode string "wu": uncompressed output
3230 * "samtools view" support "-u" command-line option
3232 ------------------------------------------------------------------------
3233 r336 | lh3lh3 | 2009-06-12 12:20:12 -0400 (Fri, 12 Jun 2009) | 5 lines
3235 M /trunk/samtools/Makefile
3236 M /trunk/samtools/misc/Makefile
3237 M /trunk/samtools/razf.c
3238 M /trunk/samtools/razf.h
3239 M /trunk/samtools/razip.c
3241 * no changes to samtools itself
3242 * remove zlib source codes
3243 * make RAZF reading compatible with old version of zlib
3244 * on old version of zlib, writing is not available
3246 ------------------------------------------------------------------------
3247 r335 | lh3lh3 | 2009-06-12 11:47:33 -0400 (Fri, 12 Jun 2009) | 2 lines
3249 D /trunk/samtools/zlib
3251 remove zlib for simplification...
3253 ------------------------------------------------------------------------
3254 r334 | lh3lh3 | 2009-06-12 10:43:36 -0400 (Fri, 12 Jun 2009) | 5 lines
3256 M /trunk/samtools/bam.h
3257 M /trunk/samtools/bam_aux.c
3258 M /trunk/samtools/bamtk.c
3260 * samtools-0.1.4-6 (r334)
3261 * do not export bam_aux_get_core() for Bio::DB::Sam because it has already
3262 been implemented in that.
3263 * this version works with the latest Bio::DB::Sam (20090612)
3265 ------------------------------------------------------------------------
3266 r333 | lh3lh3 | 2009-06-12 10:33:42 -0400 (Fri, 12 Jun 2009) | 2 lines
3268 M /trunk/samtools/ChangeLog
3272 ------------------------------------------------------------------------
3273 r332 | lh3lh3 | 2009-06-12 10:21:21 -0400 (Fri, 12 Jun 2009) | 2 lines
3275 M /trunk/samtools/AUTHORS
3276 M /trunk/samtools/Makefile
3277 M /trunk/samtools/misc/Makefile
3279 fixed minor things in Makefile
3281 ------------------------------------------------------------------------
3282 r331 | lh3lh3 | 2009-06-12 10:07:05 -0400 (Fri, 12 Jun 2009) | 4 lines
3284 M /trunk/samtools/bamtk.c
3286 * samtools-0.1.4-5 (r3310
3287 * no change to samtools itself. Version number is increased to reflect the
3288 changes in the Makefile building system.
3290 ------------------------------------------------------------------------
3291 r330 | lh3lh3 | 2009-06-12 10:03:38 -0400 (Fri, 12 Jun 2009) | 2 lines
3293 M /trunk/samtools/AUTHORS
3294 D /trunk/samtools/README
3296 update information...
3298 ------------------------------------------------------------------------
3299 r329 | lh3lh3 | 2009-06-12 09:52:21 -0400 (Fri, 12 Jun 2009) | 3 lines
3301 M /trunk/samtools/misc/novo2sam.pl
3303 * updated novoalign converter by Colin Hercus et al.
3304 * this version works with indels
3306 ------------------------------------------------------------------------
3307 r328 | lh3lh3 | 2009-06-12 09:50:53 -0400 (Fri, 12 Jun 2009) | 3 lines
3309 M /trunk/samtools/INSTALL
3310 M /trunk/samtools/Makefile
3311 M /trunk/samtools/misc/Makefile
3312 M /trunk/samtools/zlib/Makefile
3315 * update INSTALL instruction
3317 ------------------------------------------------------------------------
3318 r327 | lh3lh3 | 2009-06-12 09:18:29 -0400 (Fri, 12 Jun 2009) | 4 lines
3320 A /trunk/samtools/Makefile (from /trunk/samtools/Makefile.generic:325)
3321 D /trunk/samtools/Makefile.am
3322 D /trunk/samtools/Makefile.generic
3323 D /trunk/samtools/Makefile.lite
3324 D /trunk/samtools/autogen.sh
3325 D /trunk/samtools/cleanup.sh
3326 D /trunk/samtools/configure.ac
3327 A /trunk/samtools/misc/Makefile (from /trunk/samtools/misc/Makefile.generic:305)
3328 D /trunk/samtools/misc/Makefile.am
3329 D /trunk/samtools/misc/Makefile.generic
3330 M /trunk/samtools/razf.c
3331 A /trunk/samtools/zlib
3332 A /trunk/samtools/zlib/Makefile
3333 A /trunk/samtools/zlib/adler32.c
3334 A /trunk/samtools/zlib/compress.c
3335 A /trunk/samtools/zlib/crc32.c
3336 A /trunk/samtools/zlib/crc32.h
3337 A /trunk/samtools/zlib/deflate.c
3338 A /trunk/samtools/zlib/deflate.h
3339 A /trunk/samtools/zlib/gzio.c
3340 A /trunk/samtools/zlib/infback.c
3341 A /trunk/samtools/zlib/inffast.c
3342 A /trunk/samtools/zlib/inffast.h
3343 A /trunk/samtools/zlib/inffixed.h
3344 A /trunk/samtools/zlib/inflate.c
3345 A /trunk/samtools/zlib/inflate.h
3346 A /trunk/samtools/zlib/inftrees.c
3347 A /trunk/samtools/zlib/inftrees.h
3348 A /trunk/samtools/zlib/trees.c
3349 A /trunk/samtools/zlib/trees.h
3350 A /trunk/samtools/zlib/uncompr.c
3351 A /trunk/samtools/zlib/zconf.h
3352 A /trunk/samtools/zlib/zlib.h
3353 A /trunk/samtools/zlib/zutil.c
3354 A /trunk/samtools/zlib/zutil.h
3355 D /trunk/samtools/zutil.h
3357 * added zlib-1.2.3 as razip requires that
3358 * prepare to changed back to the Makefile building system
3359 * unfinished! (will be soon)
3361 ------------------------------------------------------------------------
3362 r326 | lh3lh3 | 2009-06-12 09:12:03 -0400 (Fri, 12 Jun 2009) | 2 lines
3364 M /trunk/samtools/misc/samtools.pl
3368 ------------------------------------------------------------------------
3369 r325 | lh3lh3 | 2009-06-10 11:27:59 -0400 (Wed, 10 Jun 2009) | 3 lines
3371 M /trunk/samtools/bam_maqcns.c
3372 M /trunk/samtools/bamtk.c
3374 * samtools-0.1.4-4 (r325)
3375 * further avoid wrong consensus calls in repetitive regions.
3377 ------------------------------------------------------------------------
3378 r324 | lh3lh3 | 2009-06-10 10:56:17 -0400 (Wed, 10 Jun 2009) | 4 lines
3380 M /trunk/samtools/bam_maqcns.c
3381 M /trunk/samtools/bam_plcmd.c
3382 M /trunk/samtools/bamtk.c
3383 M /trunk/samtools/sam.c
3384 M /trunk/samtools/sam.h
3386 * samtools-0.1.4-3 (r324)
3387 * make maqcns generate the correct call in repetitive regions.
3388 * allow filtering on mapQ at the pileup command line
3390 ------------------------------------------------------------------------
3391 r323 | lh3lh3 | 2009-06-10 05:04:21 -0400 (Wed, 10 Jun 2009) | 3 lines
3393 M /trunk/samtools/misc/samtools.pl
3395 * samtools.pl-0.3.2 (r322)
3396 * indels and SNPs use different mapping quality threshold
3398 ------------------------------------------------------------------------
3399 r322 | lh3lh3 | 2009-06-10 05:03:22 -0400 (Wed, 10 Jun 2009) | 2 lines
3401 M /trunk/samtools/misc/export2sam.pl
3405 ------------------------------------------------------------------------
3406 r321 | lh3lh3 | 2009-06-09 04:21:48 -0400 (Tue, 09 Jun 2009) | 2 lines
3408 M /trunk/samtools/misc/samtools.pl
3410 just typo. no real change
3412 ------------------------------------------------------------------------
3413 r320 | lh3lh3 | 2009-06-08 09:32:51 -0400 (Mon, 08 Jun 2009) | 2 lines
3415 M /trunk/samtools/misc/samtools.pl
3417 a little bit code cleanup
3419 ------------------------------------------------------------------------
3420 r319 | lh3lh3 | 2009-06-08 09:22:33 -0400 (Mon, 08 Jun 2009) | 4 lines
3422 M /trunk/samtools/misc/samtools.pl
3425 * change default parameters
3426 * optionally print filtered variants
3428 ------------------------------------------------------------------------
3429 r318 | lh3lh3 | 2009-06-08 09:14:26 -0400 (Mon, 08 Jun 2009) | 3 lines
3431 M /trunk/samtools/misc/samtools.pl
3434 * combine snpFilter and indelFilter
3436 ------------------------------------------------------------------------
3437 r317 | lh3lh3 | 2009-06-08 06:31:42 -0400 (Mon, 08 Jun 2009) | 3 lines
3439 M /trunk/samtools/misc/samtools.pl
3442 * change a default parameter
3444 ------------------------------------------------------------------------
3445 r316 | lh3lh3 | 2009-06-08 06:11:06 -0400 (Mon, 08 Jun 2009) | 5 lines
3447 M /trunk/samtools/bam_maqcns.c
3448 M /trunk/samtools/bam_maqcns.h
3449 M /trunk/samtools/bam_plcmd.c
3450 M /trunk/samtools/bamtk.c
3451 M /trunk/samtools/sam.c
3453 * samtools-0.1.4-2 (r316)
3454 * pileup: cap mapping quality at 60 (by default)
3455 * pileup: always calculate RMS mapq
3456 * pileup: allow to output variant sites only
3458 ------------------------------------------------------------------------
3459 r312 | lh3lh3 | 2009-06-04 08:01:10 -0400 (Thu, 04 Jun 2009) | 3 lines
3461 M /trunk/samtools/misc/samtools.pl
3466 ------------------------------------------------------------------------
3467 r311 | lh3lh3 | 2009-06-03 04:40:40 -0400 (Wed, 03 Jun 2009) | 2 lines
3469 M /trunk/samtools/misc/samtools.pl
3471 * in snpFilter, suppress non-SNP sites
3473 ------------------------------------------------------------------------
3474 r310 | lh3lh3 | 2009-06-01 09:35:13 -0400 (Mon, 01 Jun 2009) | 3 lines
3476 M /trunk/samtools/misc/samtools.pl
3481 ------------------------------------------------------------------------
3482 r309 | lh3lh3 | 2009-06-01 09:04:39 -0400 (Mon, 01 Jun 2009) | 3 lines
3484 M /trunk/samtools/misc/samtools.pl
3489 ------------------------------------------------------------------------
3490 r306 | lh3lh3 | 2009-05-28 06:49:35 -0400 (Thu, 28 May 2009) | 3 lines
3492 M /trunk/samtools/bgzf.c
3494 * minor changes to bgzf: return NULL if fd == -1
3495 * suggested by {kdj,jm18}@sanger.ac.uk
3497 ------------------------------------------------------------------------
3498 r305 | lh3lh3 | 2009-05-28 06:16:08 -0400 (Thu, 28 May 2009) | 2 lines
3500 A /trunk/samtools/misc/interpolate_sam.pl
3502 Script for paired-end pileup, contributed by Stephen Montgomery.
3504 ------------------------------------------------------------------------
3505 r304 | lh3lh3 | 2009-05-28 06:08:49 -0400 (Thu, 28 May 2009) | 3 lines
3507 M /trunk/samtools/bamtk.c
3508 M /trunk/samtools/sam.c
3510 * samtools-0.1.4-1 (r304)
3511 * fixed a minor bug in printing headers
3513 ------------------------------------------------------------------------
3514 r297 | lh3lh3 | 2009-05-21 11:06:16 -0400 (Thu, 21 May 2009) | 2 lines
3516 M /trunk/samtools/ChangeLog
3517 M /trunk/samtools/NEWS
3518 M /trunk/samtools/bam_plcmd.c
3519 M /trunk/samtools/bamtk.c
3520 M /trunk/samtools/misc/maq2sam.c
3521 M /trunk/samtools/samtools.1
3523 Release samtools-0.1.4
3525 ------------------------------------------------------------------------
3526 r296 | lh3lh3 | 2009-05-21 07:53:14 -0400 (Thu, 21 May 2009) | 3 lines
3528 M /trunk/samtools/bam_maqcns.c
3529 M /trunk/samtools/bamtk.c
3531 * samtools-0.1.3-24 (r296)
3532 * another similar bug in the indel caller
3534 ------------------------------------------------------------------------
3535 r295 | lh3lh3 | 2009-05-21 07:50:28 -0400 (Thu, 21 May 2009) | 3 lines
3537 M /trunk/samtools/bam_maqcns.c
3538 M /trunk/samtools/bamtk.c
3540 * samtools-0.1.3-23 (r295)
3541 * fixed a critical bug in the indel caller
3543 ------------------------------------------------------------------------
3544 r294 | lh3lh3 | 2009-05-20 08:00:20 -0400 (Wed, 20 May 2009) | 2 lines
3546 M /trunk/samtools/bam_stat.c
3548 added a missing header file
3550 ------------------------------------------------------------------------
3551 r293 | lh3lh3 | 2009-05-19 18:44:25 -0400 (Tue, 19 May 2009) | 3 lines
3553 M /trunk/samtools/bam_tview.c
3554 M /trunk/samtools/bamtk.c
3556 * samtools-0.1.3-22 (r293)
3557 * open tview in the dot-view mode by default
3559 ------------------------------------------------------------------------
3560 r292 | lh3lh3 | 2009-05-18 16:01:23 -0400 (Mon, 18 May 2009) | 6 lines
3562 M /trunk/samtools/samtools.1
3564 Added a note to the manual. Currently SAMtools used unaligned words in
3565 several places. Although this does not cause bus errors to me, it may
3566 affect portability. Please see the "Bus error" wiki page for more
3567 information. Also thank James Bonfields for pointing this out.
3570 ------------------------------------------------------------------------
3571 r286 | lh3lh3 | 2009-05-14 10:23:13 -0400 (Thu, 14 May 2009) | 3 lines
3573 M /trunk/samtools/bam.h
3574 M /trunk/samtools/bam_aux.c
3575 M /trunk/samtools/bamtk.c
3577 * samtools-0.1.3-21 (286)
3578 * declare bam_aux_get_core() in bam.h
3580 ------------------------------------------------------------------------
3581 r276 | lh3lh3 | 2009-05-13 05:07:55 -0400 (Wed, 13 May 2009) | 5 lines
3583 M /trunk/samtools/bam.h
3584 M /trunk/samtools/bam_index.c
3585 M /trunk/samtools/bamtk.c
3587 * samtools-0.1.3-20 (r276)
3588 * remove bam1_t::hash again. We need to modify the Perl API anyway to
3589 make it work with the latest SVN.
3590 * As is suggested by Tim, scan "{base}.bai" and "{base}.bam.bai" for index
3592 ------------------------------------------------------------------------
3593 r275 | lh3lh3 | 2009-05-12 16:14:10 -0400 (Tue, 12 May 2009) | 4 lines
3595 M /trunk/samtools/ChangeLog
3596 M /trunk/samtools/bam.h
3597 M /trunk/samtools/bamtk.c
3599 * samtools-0.1.3-19 (r275)
3600 * a minor change to the bam1_t struct: added back "void *hash" for the
3601 backward compatibility with Bio::DB::Sam
3603 ------------------------------------------------------------------------
3604 r273 | lh3lh3 | 2009-05-12 09:28:39 -0400 (Tue, 12 May 2009) | 3 lines
3606 M /trunk/samtools/bam_rmdupse.c
3607 M /trunk/samtools/bamtk.c
3609 * samtools-0.1.3-18 (r273)
3610 * rmdupse: do not remove unmapped reads
3612 ------------------------------------------------------------------------
3613 r272 | lh3lh3 | 2009-05-12 09:20:00 -0400 (Tue, 12 May 2009) | 2 lines
3615 M /trunk/samtools/bam_rmdupse.c
3617 change a parameter. It does nothing
3619 ------------------------------------------------------------------------
3620 r271 | lh3lh3 | 2009-05-12 09:17:58 -0400 (Tue, 12 May 2009) | 3 lines
3622 M /trunk/samtools/Makefile.am
3623 M /trunk/samtools/Makefile.generic
3624 M /trunk/samtools/Makefile.lite
3625 A /trunk/samtools/bam_rmdupse.c
3626 M /trunk/samtools/bamtk.c
3627 M /trunk/samtools/configure.ac
3629 * samtools-0.1.3-17 (r271)
3630 * added 'rmdupse' command
3632 ------------------------------------------------------------------------
3633 r267 | lh3lh3 | 2009-05-05 17:31:41 -0400 (Tue, 05 May 2009) | 3 lines
3635 M /trunk/samtools/bamtk.c
3636 M /trunk/samtools/sam_view.c
3638 * samtools-0.1.3-16 (r267)
3639 * in sam_view.c, changed g_flag_on based on the suggestion by Angie Hinrichs
3641 ------------------------------------------------------------------------
3642 r266 | lh3lh3 | 2009-05-05 17:23:27 -0400 (Tue, 05 May 2009) | 3 lines
3644 M /trunk/samtools/bam_import.c
3645 M /trunk/samtools/bamtk.c
3647 * samtools-0.1.3-15 (r266)
3648 * report an error if a non-* reference is present while @SQ is absent
3650 ------------------------------------------------------------------------
3651 r265 | lh3lh3 | 2009-05-05 17:09:00 -0400 (Tue, 05 May 2009) | 3 lines
3653 M /trunk/samtools/bam.h
3654 M /trunk/samtools/bam_import.c
3655 M /trunk/samtools/bamtk.c
3656 M /trunk/samtools/sam.c
3657 M /trunk/samtools/sam_view.c
3659 * samtools-0.1.3-14 (r262)
3660 * make samopen() recognize @SQ header lines
3662 ------------------------------------------------------------------------
3663 r261 | lh3lh3 | 2009-05-05 10:10:30 -0400 (Tue, 05 May 2009) | 3 lines
3665 M /trunk/samtools/bam_plcmd.c
3666 M /trunk/samtools/bamtk.c
3667 M /trunk/samtools/bgzf.c
3668 M /trunk/samtools/sam.c
3669 M /trunk/samtools/sam_view.c
3671 * samtools-0.1.3-13 (r260)
3672 * report error for file I/O error
3674 ------------------------------------------------------------------------
3675 r260 | lh3lh3 | 2009-05-05 10:01:16 -0400 (Tue, 05 May 2009) | 2 lines
3677 M /trunk/samtools/Makefile.am
3681 ------------------------------------------------------------------------
3682 r259 | lh3lh3 | 2009-05-05 09:52:25 -0400 (Tue, 05 May 2009) | 3 lines
3684 M /trunk/samtools/bam.h
3685 M /trunk/samtools/bam_pileup.c
3686 M /trunk/samtools/bam_plcmd.c
3687 M /trunk/samtools/bamtk.c
3688 M /trunk/samtools/sam.c
3689 M /trunk/samtools/sam.h
3691 * samtools-0.1.3-12 (r259)
3692 * use the new I/O interface in pileup
3694 ------------------------------------------------------------------------
3695 r258 | lh3lh3 | 2009-05-05 09:33:22 -0400 (Tue, 05 May 2009) | 3 lines
3697 M /trunk/samtools/Makefile.generic
3698 M /trunk/samtools/Makefile.lite
3699 M /trunk/samtools/bam.c
3700 M /trunk/samtools/bam.h
3701 M /trunk/samtools/bam_import.c
3702 M /trunk/samtools/bamtk.c
3703 A /trunk/samtools/sam.c
3704 A /trunk/samtools/sam.h
3705 A /trunk/samtools/sam_view.c
3707 * samtools-0.1.3-11 (r258)
3708 * unify the interface to BAM and SAM I/O
3710 ------------------------------------------------------------------------
3711 r257 | lh3lh3 | 2009-05-05 04:53:35 -0400 (Tue, 05 May 2009) | 3 lines
3713 M /trunk/samtools/Makefile.lite
3714 M /trunk/samtools/bam_plcmd.c
3715 M /trunk/samtools/bamtk.c
3717 * samtools-0.1.3-10 (r257)
3718 * allow hex with "pileup -m"
3720 ------------------------------------------------------------------------
3721 r256 | lh3lh3 | 2009-05-04 14:16:50 -0400 (Mon, 04 May 2009) | 4 lines
3723 M /trunk/samtools/bam_lpileup.c
3724 M /trunk/samtools/bamtk.c
3726 * samtools-0.1.3-9 (r256)
3727 * fixed a bug in bam_lpileup.c
3728 * I do not know if this also fixes the bug causing assertion failure in the tview
3730 ------------------------------------------------------------------------
3731 r251 | lh3lh3 | 2009-04-28 08:53:23 -0400 (Tue, 28 Apr 2009) | 3 lines
3733 M /trunk/samtools/bam_pileup.c
3734 M /trunk/samtools/bamtk.c
3736 * samtools-0.1.3-8 (r251)
3737 * fixed a bug when there are reads without coordinates
3739 ------------------------------------------------------------------------
3740 r250 | lh3lh3 | 2009-04-28 08:43:33 -0400 (Tue, 28 Apr 2009) | 2 lines
3742 A /trunk/samtools/AUTHORS
3743 A /trunk/samtools/README
3744 M /trunk/samtools/cleanup.sh
3748 ------------------------------------------------------------------------
3749 r249 | lh3lh3 | 2009-04-28 08:37:16 -0400 (Tue, 28 Apr 2009) | 2 lines
3751 M /trunk/samtools/Makefile.generic
3752 M /trunk/samtools/Makefile.lite
3753 M /trunk/samtools/configure.ac
3754 M /trunk/samtools/misc/Makefile.generic
3756 improve large file support in compilation
3758 ------------------------------------------------------------------------
3759 r248 | lh3lh3 | 2009-04-28 08:33:24 -0400 (Tue, 28 Apr 2009) | 2 lines
3761 M /trunk/samtools/INSTALL
3765 ------------------------------------------------------------------------
3766 r247 | lh3lh3 | 2009-04-28 08:28:50 -0400 (Tue, 28 Apr 2009) | 2 lines
3768 M /trunk/samtools/Makefile.am
3769 M /trunk/samtools/autogen.sh
3770 M /trunk/samtools/cleanup.sh
3771 M /trunk/samtools/configure.ac
3772 A /trunk/samtools/misc/Makefile.am
3774 fixed various issues about the GNU building scripts
3776 ------------------------------------------------------------------------
3777 r246 | lh3lh3 | 2009-04-28 08:10:23 -0400 (Tue, 28 Apr 2009) | 4 lines
3779 M /trunk/samtools/ChangeLog
3780 D /trunk/samtools/Makefile
3781 A /trunk/samtools/Makefile.am
3782 A /trunk/samtools/Makefile.generic
3783 A /trunk/samtools/autogen.sh
3784 M /trunk/samtools/bam.h
3785 M /trunk/samtools/bam_aux.c
3786 M /trunk/samtools/bam_tview.c
3787 M /trunk/samtools/bamtk.c
3788 A /trunk/samtools/cleanup.sh
3789 A /trunk/samtools/configure.ac
3790 D /trunk/samtools/misc/Makefile
3791 A /trunk/samtools/misc/Makefile.generic (from /trunk/samtools/misc/Makefile:245)
3793 * samtools-0.1.3-7 (r246)
3794 * incorporated revisions from Nils Homer
3795 * enhanced support of displaying color-space reads
3797 ------------------------------------------------------------------------
3798 r244 | lh3lh3 | 2009-04-25 06:49:40 -0400 (Sat, 25 Apr 2009) | 3 lines
3800 M /trunk/samtools/bam_md.c
3801 M /trunk/samtools/bamtk.c
3803 * samtools-0.1.3-6 (r244)
3804 * fixed segfault for unmapped reads
3806 ------------------------------------------------------------------------
3807 r243 | lh3lh3 | 2009-04-24 16:27:26 -0400 (Fri, 24 Apr 2009) | 5 lines
3809 M /trunk/samtools/bam.h
3810 M /trunk/samtools/bam_maqcns.c
3811 M /trunk/samtools/bam_md.c
3812 M /trunk/samtools/bamtk.c
3814 * samtools-0.1.3-5 (r243)
3815 * fixed a long existing bug which may cause memory leak
3817 * consensus calling now works with "=", but indel calling not
3819 ------------------------------------------------------------------------
3820 r242 | lh3lh3 | 2009-04-24 15:44:46 -0400 (Fri, 24 Apr 2009) | 3 lines
3822 M /trunk/samtools/bam_md.c
3823 M /trunk/samtools/bamtk.c
3825 * samtools-0.1.3-4 (r242)
3826 * fixed a memory leak
3828 ------------------------------------------------------------------------
3829 r240 | lh3lh3 | 2009-04-24 11:40:18 -0400 (Fri, 24 Apr 2009) | 5 lines
3831 M /trunk/samtools/Makefile
3832 M /trunk/samtools/Makefile.lite
3833 M /trunk/samtools/bam.h
3834 M /trunk/samtools/bam_aux.c
3835 A /trunk/samtools/bam_md.c
3836 M /trunk/samtools/bam_plcmd.c
3837 M /trunk/samtools/bamtk.c
3839 * samtools-0.1.3-3 (r240)
3841 * generate "=" bases
3842 * the plain pileup now support "=" bases, but consensus calling and glfgen may fail
3844 ------------------------------------------------------------------------
3845 r239 | lh3lh3 | 2009-04-24 07:08:20 -0400 (Fri, 24 Apr 2009) | 5 lines
3847 M /trunk/samtools/bam.h
3848 M /trunk/samtools/bam_aux.c
3849 M /trunk/samtools/bamtk.c
3851 * samtools-0.1.3-2 (r239)
3852 * fixed bugs in bam_aux.c (these functions nevered used by samtools)
3853 * removed bam_aux_init()/bam_aux_destroy()
3854 * added tagview for testing bam_aux
3856 ------------------------------------------------------------------------
3857 r235 | lh3lh3 | 2009-04-21 18:17:39 -0400 (Tue, 21 Apr 2009) | 3 lines
3859 M /trunk/samtools/bam_pileup.c
3860 M /trunk/samtools/bamtk.c
3863 * fixed a bug in pileup: the first read in a chromosome may not be printed
3865 ------------------------------------------------------------------------
3866 r232 | lh3lh3 | 2009-04-16 10:25:43 -0400 (Thu, 16 Apr 2009) | 2 lines
3868 M /trunk/samtools/Makefile.lite
3870 a missing file in Makefile.lite
3872 ------------------------------------------------------------------------
3873 r227 | lh3lh3 | 2009-04-15 17:02:53 -0400 (Wed, 15 Apr 2009) | 2 lines
3875 M /trunk/samtools/NEWS
3876 M /trunk/samtools/bamtk.c
3878 Release samtools-0.1.3
3880 ------------------------------------------------------------------------
3881 r223 | lh3lh3 | 2009-04-15 09:31:32 -0400 (Wed, 15 Apr 2009) | 3 lines
3883 M /trunk/samtools/bam_plcmd.c
3884 M /trunk/samtools/bamtk.c
3887 * make samtools more robust to weird input such as empty file
3889 ------------------------------------------------------------------------
3890 r222 | lh3lh3 | 2009-04-15 09:05:33 -0400 (Wed, 15 Apr 2009) | 2 lines
3892 M /trunk/samtools/ChangeLog
3893 M /trunk/samtools/NEWS
3894 M /trunk/samtools/samtools.1
3896 prepare for release 0.1.3
3898 ------------------------------------------------------------------------
3899 r221 | lh3lh3 | 2009-04-15 08:32:14 -0400 (Wed, 15 Apr 2009) | 2 lines
3901 A /trunk/samtools/misc/blast2sam.pl
3903 convert NCBI-BLASTN to SAM
3905 ------------------------------------------------------------------------
3906 r220 | lh3lh3 | 2009-04-15 08:18:19 -0400 (Wed, 15 Apr 2009) | 3 lines
3908 M /trunk/samtools/bam_lpileup.c
3909 M /trunk/samtools/bamtk.c
3912 * fixed a small memory leak in tview
3914 ------------------------------------------------------------------------
3915 r219 | lh3lh3 | 2009-04-15 08:00:08 -0400 (Wed, 15 Apr 2009) | 3 lines
3917 M /trunk/samtools/bam_rmdup.c
3918 M /trunk/samtools/bamtk.c
3921 * fixed a bug in rmdup when there are unmapped reads
3923 ------------------------------------------------------------------------
3924 r218 | lh3lh3 | 2009-04-14 17:28:58 -0400 (Tue, 14 Apr 2009) | 2 lines
3926 M /trunk/samtools/ChangeLog
3927 M /trunk/samtools/NEWS
3929 proposed NEWS for the new release (have not yet)
3931 ------------------------------------------------------------------------
3932 r216 | lh3lh3 | 2009-04-14 17:10:46 -0400 (Tue, 14 Apr 2009) | 4 lines
3934 M /trunk/samtools/misc/samtools.pl
3937 * improve indelFilter to avoid filtering true indels. The new filter relies
3938 on the new pileup indel line implemented in samtools-0.1.2-25
3940 ------------------------------------------------------------------------
3941 r215 | lh3lh3 | 2009-04-14 17:04:19 -0400 (Tue, 14 Apr 2009) | 4 lines
3943 M /trunk/samtools/bam_maqcns.c
3944 M /trunk/samtools/bam_plcmd.c
3945 M /trunk/samtools/bamtk.c
3946 M /trunk/samtools/samtools.1
3949 * change the pileup indel line to shows the number of alignments actually
3952 ------------------------------------------------------------------------
3953 r211 | lh3lh3 | 2009-04-13 07:07:13 -0400 (Mon, 13 Apr 2009) | 2 lines
3955 M /trunk/samtools/ChangeLog
3957 update ChangeLog from "svn log"
3959 ------------------------------------------------------------------------
3960 r210 | lh3lh3 | 2009-04-12 15:57:05 -0400 (Sun, 12 Apr 2009) | 4 lines
3962 M /trunk/samtools/bam.c
3963 M /trunk/samtools/bam_import.c
3964 M /trunk/samtools/bam_sort.c
3965 M /trunk/samtools/bamtk.c
3966 M /trunk/samtools/kseq.h
3969 * in merge, gives a warning rather than error if the target sequence length is different
3970 * allow empty header
3972 ------------------------------------------------------------------------
3973 r209 | lh3lh3 | 2009-04-12 15:32:44 -0400 (Sun, 12 Apr 2009) | 3 lines
3975 M /trunk/samtools/bam.c
3976 M /trunk/samtools/bam_import.c
3977 M /trunk/samtools/bamtk.c
3980 * recognize '*' at the QUAL field
3982 ------------------------------------------------------------------------
3983 r208 | lh3lh3 | 2009-04-12 15:08:02 -0400 (Sun, 12 Apr 2009) | 3 lines
3985 M /trunk/samtools/bam_import.c
3986 M /trunk/samtools/bamtk.c
3987 M /trunk/samtools/kseq.h
3990 * the field separater is TAB only, now
3992 ------------------------------------------------------------------------
3993 r207 | lh3lh3 | 2009-04-08 10:18:03 -0400 (Wed, 08 Apr 2009) | 2 lines
3995 M /trunk/samtools/examples/ex1.sam.gz
3997 * fixed the problem in the example alignment due to the bug in fixmate
3999 ------------------------------------------------------------------------
4000 r206 | lh3lh3 | 2009-04-08 10:15:05 -0400 (Wed, 08 Apr 2009) | 3 lines
4002 M /trunk/samtools/bam_mate.c
4003 M /trunk/samtools/bamtk.c
4004 M /trunk/samtools/misc/soap2sam.pl
4007 * fixed a nasty bug in `fixmate'
4009 ------------------------------------------------------------------------
4010 r205 | lh3lh3 | 2009-04-08 05:57:08 -0400 (Wed, 08 Apr 2009) | 2 lines
4012 M /trunk/samtools/misc/bowtie2sam.pl
4013 M /trunk/samtools/misc/soap2sam.pl
4014 M /trunk/samtools/misc/wgsim_eval.pl
4016 make the script robust to the bugs in SOAP-2.1.7
4018 ------------------------------------------------------------------------
4019 r200 | lh3lh3 | 2009-04-02 10:14:56 -0400 (Thu, 02 Apr 2009) | 3 lines
4021 M /trunk/samtools/bam_stat.c
4022 M /trunk/samtools/bamtk.c
4025 * check if file is truncated in flagstat
4027 ------------------------------------------------------------------------
4028 r199 | lh3lh3 | 2009-04-02 10:09:10 -0400 (Thu, 02 Apr 2009) | 3 lines
4030 M /trunk/samtools/bamtk.c
4033 * print the header if requested
4035 ------------------------------------------------------------------------
4036 r193 | lh3lh3 | 2009-03-27 11:09:50 -0400 (Fri, 27 Mar 2009) | 3 lines
4038 M /trunk/samtools/bam_plcmd.c
4039 M /trunk/samtools/bamtk.c
4042 * fixed a minor bug reported by Nils Homer
4044 ------------------------------------------------------------------------
4045 r185 | lh3lh3 | 2009-03-24 07:50:32 -0400 (Tue, 24 Mar 2009) | 2 lines
4047 A /trunk/samtools/Makefile (from /trunk/samtools/Makefile.std:184)
4048 D /trunk/samtools/Makefile.std
4049 A /trunk/samtools/misc/Makefile (from /trunk/samtools/misc/Makefile.std:184)
4050 D /trunk/samtools/misc/Makefile.std
4052 rename Makefile.std as Makefile. GNU building systerm is not ready and may take some time...
4054 ------------------------------------------------------------------------
4055 r184 | lh3lh3 | 2009-03-24 06:36:38 -0400 (Tue, 24 Mar 2009) | 4 lines
4057 D /trunk/samtools/Makefile
4058 A /trunk/samtools/Makefile.std (from /trunk/samtools/Makefile:183)
4059 M /trunk/samtools/bam_sort.c
4060 M /trunk/samtools/bam_tview.c
4061 M /trunk/samtools/bamtk.c
4062 D /trunk/samtools/misc/Makefile
4063 A /trunk/samtools/misc/Makefile.std (from /trunk/samtools/misc/Makefile:182)
4064 M /trunk/samtools/samtools.1
4067 * incorporating Nils' changes
4068 * rename Makefile to Makefile.std and prepare to add the GNU building systerms (also by Nils)
4070 ------------------------------------------------------------------------
4071 r183 | lh3lh3 | 2009-03-24 06:30:23 -0400 (Tue, 24 Mar 2009) | 4 lines
4073 M /trunk/samtools/Makefile
4074 M /trunk/samtools/bam_import.c
4075 M /trunk/samtools/bam_maqcns.c
4076 M /trunk/samtools/bam_maqcns.h
4077 M /trunk/samtools/bam_plcmd.c
4078 M /trunk/samtools/bamtk.c
4079 M /trunk/samtools/kseq.h
4080 A /trunk/samtools/kstring.c
4081 A /trunk/samtools/kstring.h
4084 * made pileup take a list of proposed indels. An insertion is N at the moment.
4085 * added my kstring library for a bit complex parsing of the position list.
4087 ------------------------------------------------------------------------
4088 r169 | lh3lh3 | 2009-03-12 09:40:14 -0400 (Thu, 12 Mar 2009) | 3 lines
4090 M /trunk/samtools/misc/soap2sam.pl
4093 * more robust to truncated soap output
4095 ------------------------------------------------------------------------
4096 r168 | lh3lh3 | 2009-03-11 06:49:00 -0400 (Wed, 11 Mar 2009) | 2 lines
4098 M /trunk/samtools/Makefile.lite
4100 added bam_stat.o to Makefile.lite
4102 ------------------------------------------------------------------------
4103 r167 | lh3lh3 | 2009-03-10 18:11:31 -0400 (Tue, 10 Mar 2009) | 3 lines
4105 M /trunk/samtools/bam_maqcns.c
4106 M /trunk/samtools/bamtk.c
4109 * generate RMS of mapQ instead of max mapQ
4111 ------------------------------------------------------------------------
4112 r166 | lh3lh3 | 2009-03-10 18:06:45 -0400 (Tue, 10 Mar 2009) | 3 lines
4114 M /trunk/samtools/bam_plcmd.c
4115 M /trunk/samtools/bamtk.c
4116 M /trunk/samtools/glf.c
4117 M /trunk/samtools/glf.h
4118 M /trunk/samtools/misc/Makefile
4123 ------------------------------------------------------------------------
4124 r159 | lh3lh3 | 2009-03-03 06:26:08 -0500 (Tue, 03 Mar 2009) | 3 lines
4126 M /trunk/samtools/bam_plcmd.c
4127 M /trunk/samtools/bamtk.c
4130 * fixed a minor bug in displaying pileup
4132 ------------------------------------------------------------------------
4133 r158 | lh3lh3 | 2009-03-03 06:24:16 -0500 (Tue, 03 Mar 2009) | 3 lines
4135 M /trunk/samtools/ChangeLog
4136 M /trunk/samtools/bamtk.c
4139 * optionally print SAM header
4141 ------------------------------------------------------------------------
4142 r153 | lh3lh3 | 2009-03-02 05:45:28 -0500 (Mon, 02 Mar 2009) | 3 lines
4144 M /trunk/samtools/bamtk.c
4145 M /trunk/samtools/glf.c
4148 * use "GLF\3" as the magic for GLFv3 files
4150 ------------------------------------------------------------------------
4151 r152 | lh3lh3 | 2009-03-02 05:39:09 -0500 (Mon, 02 Mar 2009) | 5 lines
4153 M /trunk/samtools/Makefile
4154 M /trunk/samtools/bam_import.c
4155 M /trunk/samtools/bam_index.c
4156 M /trunk/samtools/bam_plcmd.c
4157 M /trunk/samtools/bamtk.c
4158 M /trunk/samtools/glf.c
4159 M /trunk/samtools/glf.h
4162 * fixed a bug in import: core.bin is undefined for unmapped reads
4163 * this bug can be alleviated (not completely solved) in bam_index.c
4164 * update to GLFv3: pos is changed to offset for better compression
4166 ------------------------------------------------------------------------
4167 r151 | lh3lh3 | 2009-03-01 10:18:43 -0500 (Sun, 01 Mar 2009) | 3 lines
4169 M /trunk/samtools/misc/wgsim.c
4172 * fixed a bug in simulating indels
4174 ------------------------------------------------------------------------
4175 r145 | lh3lh3 | 2009-02-26 14:43:57 -0500 (Thu, 26 Feb 2009) | 4 lines
4177 M /trunk/samtools/misc/wgsim.c
4180 * allow to print mismatch information as fastq comment. MAQ does
4181 not like long read names.
4183 ------------------------------------------------------------------------
4184 r141 | lh3lh3 | 2009-02-26 09:53:03 -0500 (Thu, 26 Feb 2009) | 6 lines
4186 M /trunk/samtools/ChangeLog
4187 M /trunk/samtools/misc/wgsim.c
4188 M /trunk/samtools/misc/wgsim_eval.pl
4191 * fixed a bug about color read coordinates
4192 * fixed a bug in read names
4193 * wgsim_eval.pl-0.1.3
4194 * make the script work with color reads
4196 ------------------------------------------------------------------------
4197 r140 | lh3lh3 | 2009-02-26 09:02:57 -0500 (Thu, 26 Feb 2009) | 2 lines
4199 M /trunk/samtools/misc/Makefile
4200 M /trunk/samtools/misc/wgsim.c
4202 * wgsim: added a note
4204 ------------------------------------------------------------------------
4205 r139 | lh3lh3 | 2009-02-26 06:39:08 -0500 (Thu, 26 Feb 2009) | 7 lines
4207 M /trunk/samtools/misc/wgsim.c
4208 M /trunk/samtools/misc/wgsim_eval.pl
4211 * considerable code clean up
4212 * print number of substitutions/indels/errors on each read
4213 * potentially support SOLiD simulation, though not tested at the moment
4214 * wgsim_eval.pl-0.1.2
4215 * change in accordant with wgsim
4217 ------------------------------------------------------------------------
4218 r129 | lh3lh3 | 2009-02-18 17:23:27 -0500 (Wed, 18 Feb 2009) | 3 lines
4220 M /trunk/samtools/bam_index.c
4221 M /trunk/samtools/bamtk.c
4224 * fixed a bug in bam_fetch, caused by completely contained adjacent chunks
4226 ------------------------------------------------------------------------
4227 r128 | bhandsaker | 2009-02-18 14:06:57 -0500 (Wed, 18 Feb 2009) | 2 lines
4229 M /trunk/samtools/bamtk.c
4231 Fix annoying segv when invalid region specified.
4233 ------------------------------------------------------------------------
4234 r127 | lh3lh3 | 2009-02-17 05:49:55 -0500 (Tue, 17 Feb 2009) | 2 lines
4236 D /trunk/samtools/misc/indel_filter.pl
4237 A /trunk/samtools/misc/samtools.pl
4239 * move indel_filter.pl to samtools.pl
4241 ------------------------------------------------------------------------
4242 r126 | lh3lh3 | 2009-02-14 16:22:30 -0500 (Sat, 14 Feb 2009) | 3 lines
4244 M /trunk/samtools/bam_mate.c
4245 M /trunk/samtools/bamtk.c
4248 * fixed a bug in fixmate: SE reads are flagged as BAM_FMUNMAP
4250 ------------------------------------------------------------------------
4251 r125 | lh3lh3 | 2009-02-13 04:54:45 -0500 (Fri, 13 Feb 2009) | 3 lines
4253 M /trunk/samtools/bam_stat.c
4254 M /trunk/samtools/bamtk.c
4257 * fixed a minor bug in flagstat
4259 ------------------------------------------------------------------------
4260 r124 | lh3lh3 | 2009-02-12 06:15:32 -0500 (Thu, 12 Feb 2009) | 3 lines
4262 M /trunk/samtools/bam_maqcns.c
4263 M /trunk/samtools/bamtk.c
4264 M /trunk/samtools/misc/indel_filter.pl
4267 * improve indel caller by setting maximum window size
4269 ------------------------------------------------------------------------
4270 r123 | lh3lh3 | 2009-02-12 05:30:29 -0500 (Thu, 12 Feb 2009) | 2 lines
4272 M /trunk/samtools/bam_plcmd.c
4273 M /trunk/samtools/bamtk.c
4275 * output max mapping quality in indel line
4277 ------------------------------------------------------------------------
4278 r122 | lh3lh3 | 2009-02-11 05:59:10 -0500 (Wed, 11 Feb 2009) | 2 lines
4280 M /trunk/samtools/misc/maq2sam.c
4282 fixed a bug in generating tag AM
4284 ------------------------------------------------------------------------
4285 r121 | lh3lh3 | 2009-02-03 05:43:11 -0500 (Tue, 03 Feb 2009) | 2 lines
4287 M /trunk/samtools/bam_index.c
4288 M /trunk/samtools/bamtk.c
4290 fixed a potential memory problem in indexing
4292 ------------------------------------------------------------------------
4293 r120 | bhandsaker | 2009-02-02 10:52:52 -0500 (Mon, 02 Feb 2009) | 2 lines
4295 M /trunk/samtools/Makefile
4297 Pass LIBS to recursive targets to facilitate building at Broad.
4299 ------------------------------------------------------------------------
4300 r119 | lh3lh3 | 2009-02-02 05:12:15 -0500 (Mon, 02 Feb 2009) | 4 lines
4302 M /trunk/samtools/ChangeLog
4303 M /trunk/samtools/bam_plcmd.c
4304 M /trunk/samtools/bam_stat.c
4305 M /trunk/samtools/bamtk.c
4308 * fixed a bug in generating GLFv2 for indels
4309 * improve flagstat report a little bit
4311 ------------------------------------------------------------------------
4312 r118 | lh3lh3 | 2009-01-29 07:33:23 -0500 (Thu, 29 Jan 2009) | 3 lines
4314 M /trunk/samtools/Makefile
4315 A /trunk/samtools/bam_stat.c
4316 M /trunk/samtools/bamtk.c
4319 * added flagstat command
4321 ------------------------------------------------------------------------
4322 r116 | lh3lh3 | 2009-01-28 08:31:12 -0500 (Wed, 28 Jan 2009) | 2 lines
4324 M /trunk/samtools/ChangeLog
4325 M /trunk/samtools/NEWS
4326 M /trunk/samtools/bamtk.c
4327 M /trunk/samtools/samtools.1
4329 Release SAMtools-0.1.2
4331 ------------------------------------------------------------------------
4332 r115 | lh3lh3 | 2009-01-28 07:54:08 -0500 (Wed, 28 Jan 2009) | 2 lines
4334 A /trunk/samtools/misc/indel_filter.pl
4336 Script for filtering indel results
4338 ------------------------------------------------------------------------
4339 r114 | lh3lh3 | 2009-01-25 06:45:37 -0500 (Sun, 25 Jan 2009) | 2 lines
4341 A /trunk/samtools/misc/zoom2sam.pl
4345 ------------------------------------------------------------------------
4346 r113 | lh3lh3 | 2009-01-24 09:25:07 -0500 (Sat, 24 Jan 2009) | 2 lines
4348 A /trunk/samtools/misc/novo2sam.pl
4350 add a script to convert novo alignment to SAM
4352 ------------------------------------------------------------------------
4353 r112 | lh3lh3 | 2009-01-23 15:57:39 -0500 (Fri, 23 Jan 2009) | 2 lines
4355 M /trunk/samtools/ChangeLog
4356 M /trunk/samtools/ChangeLog.old
4357 M /trunk/samtools/samtools.1
4359 update documentation and ChangeLog
4361 ------------------------------------------------------------------------
4362 r111 | lh3lh3 | 2009-01-23 14:22:59 -0500 (Fri, 23 Jan 2009) | 3 lines
4364 M /trunk/samtools/bam_sort.c
4365 M /trunk/samtools/bamtk.c
4368 * fixed a bug in "merge" command line
4370 ------------------------------------------------------------------------
4371 r110 | lh3lh3 | 2009-01-22 10:36:48 -0500 (Thu, 22 Jan 2009) | 3 lines
4373 M /trunk/samtools/misc/Makefile
4374 A /trunk/samtools/misc/bowtie2sam.pl (from /branches/dev/samtools/misc/bowtie2sam.pl:108)
4375 M /trunk/samtools/misc/export2sam.pl
4376 A /trunk/samtools/misc/soap2sam.pl (from /branches/dev/samtools/misc/soap2sam.pl:108)
4377 A /trunk/samtools/misc/wgsim.c (from /branches/dev/samtools/misc/wgsim.c:108)
4378 A /trunk/samtools/misc/wgsim_eval.pl (from /branches/dev/samtools/misc/wgsim_eval.pl:108)
4380 * merge from branches/dev/
4381 * all future development will happen here
4383 ------------------------------------------------------------------------
4384 r109 | lh3lh3 | 2009-01-22 10:14:27 -0500 (Thu, 22 Jan 2009) | 3 lines
4386 M /trunk/samtools/COPYING
4387 M /trunk/samtools/ChangeLog
4388 A /trunk/samtools/INSTALL (from /branches/dev/samtools/INSTALL:108)
4389 M /trunk/samtools/Makefile
4390 A /trunk/samtools/Makefile.lite (from /branches/dev/samtools/Makefile.lite:108)
4391 M /trunk/samtools/bam.c
4392 M /trunk/samtools/bam.h
4393 M /trunk/samtools/bam_import.c
4394 M /trunk/samtools/bam_index.c
4395 M /trunk/samtools/bam_lpileup.c
4396 M /trunk/samtools/bam_maqcns.c
4397 M /trunk/samtools/bam_maqcns.h
4398 A /trunk/samtools/bam_mate.c (from /branches/dev/samtools/bam_mate.c:108)
4399 M /trunk/samtools/bam_pileup.c
4400 M /trunk/samtools/bam_plcmd.c
4401 A /trunk/samtools/bam_rmdup.c (from /branches/dev/samtools/bam_rmdup.c:108)
4402 M /trunk/samtools/bam_sort.c
4403 M /trunk/samtools/bamtk.c
4404 M /trunk/samtools/bgzf.h
4405 M /trunk/samtools/examples/00README.txt
4406 A /trunk/samtools/examples/Makefile (from /branches/dev/samtools/examples/Makefile:108)
4407 D /trunk/samtools/examples/ex1.fa.fai
4408 M /trunk/samtools/examples/ex1.sam.gz
4409 M /trunk/samtools/faidx.c
4410 A /trunk/samtools/glf.c (from /branches/dev/samtools/glf.c:108)
4411 M /trunk/samtools/glf.h
4412 M /trunk/samtools/misc/Makefile
4413 M /trunk/samtools/misc/maq2sam.c
4414 M /trunk/samtools/razf.c
4415 M /trunk/samtools/source.dot
4417 * Merge from branches/dev/
4418 * all future development will happen here at trunk/
4420 ------------------------------------------------------------------------
4421 r79 | bhandsaker | 2009-01-07 16:42:15 -0500 (Wed, 07 Jan 2009) | 2 lines
4423 M /trunk/samtools/bam_maqcns.c
4424 M /trunk/samtools/bam_tview.c
4426 Fix problem with compiling without curses.
4428 ------------------------------------------------------------------------
4429 r63 | lh3lh3 | 2008-12-22 10:58:02 -0500 (Mon, 22 Dec 2008) | 2 lines
4431 A /trunk/samtools (from /branches/dev/samtools:62)
4435 ------------------------------------------------------------------------
4436 r62 | lh3lh3 | 2008-12-22 10:55:13 -0500 (Mon, 22 Dec 2008) | 2 lines
4438 A /branches/dev/samtools/NEWS
4439 M /branches/dev/samtools/bamtk.c
4440 M /branches/dev/samtools/samtools.1
4442 Release samtools-0.1.1
4444 ------------------------------------------------------------------------
4445 r61 | lh3lh3 | 2008-12-22 10:46:08 -0500 (Mon, 22 Dec 2008) | 10 lines
4447 M /branches/dev/samtools/bam_aux.c
4448 M /branches/dev/samtools/bam_index.c
4449 M /branches/dev/samtools/bam_plcmd.c
4450 M /branches/dev/samtools/bam_tview.c
4451 M /branches/dev/samtools/bamtk.c
4452 M /branches/dev/samtools/razf.c
4453 M /branches/dev/samtools/samtools.1
4456 * fixed a bug in razf.c: reset z_eof when razf_seek() is called
4457 * fixed a memory leak in parsing a region
4458 * changed pileup a little bit when -s is in use: output ^ and $
4459 * when a bam is not indexed, output more meaningful error message
4460 * fixed a bug in indexing for small alignment
4461 * fixed a bug in the viewer when we come to the end of a reference file
4462 * updated documentation
4463 * prepare to release 0.1.1
4465 ------------------------------------------------------------------------
4466 r60 | lh3lh3 | 2008-12-22 10:10:16 -0500 (Mon, 22 Dec 2008) | 2 lines
4468 A /branches/dev/samtools/examples
4469 A /branches/dev/samtools/examples/00README.txt
4470 A /branches/dev/samtools/examples/ex1.fa
4471 A /branches/dev/samtools/examples/ex1.fa.fai
4472 A /branches/dev/samtools/examples/ex1.sam.gz
4476 ------------------------------------------------------------------------
4477 r59 | lh3lh3 | 2008-12-22 04:38:15 -0500 (Mon, 22 Dec 2008) | 2 lines
4479 M /branches/dev/samtools/ChangeLog
4483 ------------------------------------------------------------------------
4484 r58 | lh3lh3 | 2008-12-20 18:06:00 -0500 (Sat, 20 Dec 2008) | 3 lines
4486 M /branches/dev/samtools/misc/export2sam.pl
4489 * fixed several bugs
4491 ------------------------------------------------------------------------
4492 r57 | lh3lh3 | 2008-12-20 10:44:20 -0500 (Sat, 20 Dec 2008) | 2 lines
4494 A /branches/dev/samtools/misc/export2sam.pl
4496 convert Export format to SAM; not thoroughly tested
4498 ------------------------------------------------------------------------
4499 r56 | lh3lh3 | 2008-12-19 17:13:28 -0500 (Fri, 19 Dec 2008) | 6 lines
4501 M /branches/dev/samtools/bam_import.c
4502 M /branches/dev/samtools/bam_plcmd.c
4503 M /branches/dev/samtools/bam_tview.c
4504 M /branches/dev/samtools/bamtk.c
4505 A /branches/dev/samtools/source.dot
4508 * pileup: generate maq-like simple output
4509 * pileup: allow to output pileup at required sites
4510 * source.dot: source file relationship graph
4511 * tview: fixed a minor bug
4513 ------------------------------------------------------------------------
4514 r55 | lh3lh3 | 2008-12-19 15:10:26 -0500 (Fri, 19 Dec 2008) | 2 lines
4516 D /branches/dev/samtools/misc/all2sam.pl
4520 ------------------------------------------------------------------------
4521 r54 | lh3lh3 | 2008-12-16 17:34:25 -0500 (Tue, 16 Dec 2008) | 2 lines
4523 A /branches/dev/samtools/COPYING
4524 M /branches/dev/samtools/bam.h
4525 M /branches/dev/samtools/faidx.h
4526 M /branches/dev/samtools/khash.h
4527 M /branches/dev/samtools/kseq.h
4528 M /branches/dev/samtools/ksort.h
4529 M /branches/dev/samtools/samtools.1
4531 Added copyright information and a bit more documentation. No code change.
4533 ------------------------------------------------------------------------
4534 r53 | lh3lh3 | 2008-12-16 08:40:18 -0500 (Tue, 16 Dec 2008) | 3 lines
4536 M /branches/dev/samtools/bam.c
4537 M /branches/dev/samtools/bam.h
4538 M /branches/dev/samtools/bam_index.c
4539 M /branches/dev/samtools/bam_maqcns.c
4540 M /branches/dev/samtools/bamtk.c
4543 * improved efficiency of the indel caller for spliced alignments
4545 ------------------------------------------------------------------------
4546 r52 | lh3lh3 | 2008-12-16 05:28:20 -0500 (Tue, 16 Dec 2008) | 3 lines
4548 M /branches/dev/samtools/bam.c
4549 M /branches/dev/samtools/bam.h
4550 M /branches/dev/samtools/bam_aux.c
4551 M /branches/dev/samtools/bam_index.c
4552 M /branches/dev/samtools/bamtk.c
4555 * a bit code cleanup: reduce the dependency between source files
4557 ------------------------------------------------------------------------
4558 r51 | lh3lh3 | 2008-12-15 09:29:32 -0500 (Mon, 15 Dec 2008) | 3 lines
4560 M /branches/dev/samtools/bam_maqcns.c
4561 M /branches/dev/samtools/bam_plcmd.c
4562 M /branches/dev/samtools/bamtk.c
4565 * fixed a memory leak
4567 ------------------------------------------------------------------------
4568 r50 | lh3lh3 | 2008-12-15 09:00:13 -0500 (Mon, 15 Dec 2008) | 2 lines
4570 M /branches/dev/samtools/ChangeLog
4571 M /branches/dev/samtools/bam.h
4572 M /branches/dev/samtools/samtools.1
4574 update documentation, ChangeLog and a comment
4576 ------------------------------------------------------------------------
4577 r49 | lh3lh3 | 2008-12-15 08:36:43 -0500 (Mon, 15 Dec 2008) | 6 lines
4579 M /branches/dev/samtools/Makefile
4580 M /branches/dev/samtools/bam.h
4581 M /branches/dev/samtools/bam_maqcns.c
4582 M /branches/dev/samtools/bam_maqcns.h
4583 M /branches/dev/samtools/bam_pileup.c
4584 A /branches/dev/samtools/bam_plcmd.c
4585 M /branches/dev/samtools/bamtk.c
4586 M /branches/dev/samtools/samtools.1
4589 * moved pileup command to a separate source file
4590 * added indel caller
4591 * added bam_cal_segend(). (NOT WORKING for spliced alignment!!!)
4592 * updated documentation
4594 ------------------------------------------------------------------------
4595 r48 | lh3lh3 | 2008-12-12 08:55:36 -0500 (Fri, 12 Dec 2008) | 3 lines
4597 M /branches/dev/samtools/bam_maqcns.c
4598 M /branches/dev/samtools/bamtk.c
4601 * fixed another bug in maqcns when there is a nearby deletion
4603 ------------------------------------------------------------------------
4604 r47 | lh3lh3 | 2008-12-12 08:42:16 -0500 (Fri, 12 Dec 2008) | 5 lines
4606 M /branches/dev/samtools/bam_maqcns.c
4607 M /branches/dev/samtools/bam_pileup.c
4608 M /branches/dev/samtools/bamtk.c
4611 * pileup: outputing consensus is now optional
4612 * fixed a bug in glfgen. This bug also exists in maq's glfgen. However,
4613 I am not quite sure why the previous version may have problem.
4615 ------------------------------------------------------------------------
4616 r46 | lh3lh3 | 2008-12-12 06:44:56 -0500 (Fri, 12 Dec 2008) | 6 lines
4618 M /branches/dev/samtools/bam_pileup.c
4619 M /branches/dev/samtools/bamtk.c
4622 * add maq consensus to pileup. However, I will move this part to a new
4623 command as strictly speaking, consensus callin is not part of pileup,
4624 and imposing it would make it harder to generate for other language
4627 ------------------------------------------------------------------------
4628 r45 | bhandsaker | 2008-12-11 15:43:56 -0500 (Thu, 11 Dec 2008) | 2 lines
4630 M /branches/dev/samtools/bgzf.c
4632 Fix bug in tell() after reads that consume to the exact end of a block.
4634 ------------------------------------------------------------------------
4635 r44 | lh3lh3 | 2008-12-11 04:36:53 -0500 (Thu, 11 Dec 2008) | 2 lines
4637 M /branches/dev/samtools/samtools.1
4641 ------------------------------------------------------------------------
4642 r43 | lh3lh3 | 2008-12-11 04:25:36 -0500 (Thu, 11 Dec 2008) | 4 lines
4644 M /branches/dev/samtools/bam_import.c
4645 M /branches/dev/samtools/bamtk.c
4648 * fixed a bug in parser when there is auxiliary fields
4649 * made the parser a bit more robust
4651 ------------------------------------------------------------------------
4652 r42 | lh3lh3 | 2008-12-10 09:57:29 -0500 (Wed, 10 Dec 2008) | 5 lines
4654 M /branches/dev/samtools/bam_index.c
4655 M /branches/dev/samtools/bamtk.c
4656 M /branches/dev/samtools/bgzf.c
4659 * fixed a bug in bgzf (only reading is affected)
4660 * fixed a typo in bam_index.c
4661 * in bam_index.c, check potential bugs in the underlying I/O library
4663 ------------------------------------------------------------------------
4664 r41 | lh3lh3 | 2008-12-10 07:53:08 -0500 (Wed, 10 Dec 2008) | 2 lines
4666 M /branches/dev/samtools/samtools.1
4670 ------------------------------------------------------------------------
4671 r40 | lh3lh3 | 2008-12-10 06:52:10 -0500 (Wed, 10 Dec 2008) | 5 lines
4673 M /branches/dev/samtools/bam.h
4674 M /branches/dev/samtools/bam_pileup.c
4675 M /branches/dev/samtools/bamtk.c
4678 * tried to make pileup work with clipping (previously not), though NOT tested
4679 * removed -v from pileup
4680 * made pileup take the reference sequence
4682 ------------------------------------------------------------------------
4683 r39 | lh3lh3 | 2008-12-09 06:59:28 -0500 (Tue, 09 Dec 2008) | 4 lines
4685 M /branches/dev/samtools/bam_import.c
4686 M /branches/dev/samtools/bamtk.c
4687 M /branches/dev/samtools/samtools.1
4690 * in parser, recognize "=", rather than ",", as a match
4691 * in parser, correctl parse "=" at the MRNM field.
4693 ------------------------------------------------------------------------
4694 r38 | lh3lh3 | 2008-12-09 06:39:07 -0500 (Tue, 09 Dec 2008) | 2 lines
4696 M /branches/dev/samtools/misc/maq2sam.c
4698 fixed a bug in handling maq flag 64 and 192
4700 ------------------------------------------------------------------------
4701 r37 | lh3lh3 | 2008-12-09 04:53:46 -0500 (Tue, 09 Dec 2008) | 2 lines
4703 M /branches/dev/samtools/misc/md5fa.c
4705 also calculate unordered md5sum check
4707 ------------------------------------------------------------------------
4708 r36 | lh3lh3 | 2008-12-09 04:46:21 -0500 (Tue, 09 Dec 2008) | 2 lines
4710 M /branches/dev/samtools/misc/md5fa.c
4712 fixed a minor bug when there are space in the sequence
4714 ------------------------------------------------------------------------
4715 r35 | lh3lh3 | 2008-12-09 04:40:45 -0500 (Tue, 09 Dec 2008) | 2 lines
4717 M /branches/dev/samtools/misc/md5fa.c
4719 fixed a potential memory leak
4721 ------------------------------------------------------------------------
4722 r34 | lh3lh3 | 2008-12-08 09:52:17 -0500 (Mon, 08 Dec 2008) | 2 lines
4724 M /branches/dev/samtools/bam_import.c
4725 M /branches/dev/samtools/bam_index.c
4726 M /branches/dev/samtools/bamtk.c
4728 * fixed a bug in import: bin is wrongly calculated
4730 ------------------------------------------------------------------------
4731 r33 | lh3lh3 | 2008-12-08 09:08:01 -0500 (Mon, 08 Dec 2008) | 2 lines
4733 M /branches/dev/samtools/misc/all2sam.pl
4737 ------------------------------------------------------------------------
4738 r32 | lh3lh3 | 2008-12-08 07:56:02 -0500 (Mon, 08 Dec 2008) | 3 lines
4740 M /branches/dev/samtools/Makefile
4741 M /branches/dev/samtools/kseq.h
4742 M /branches/dev/samtools/misc/Makefile
4743 A /branches/dev/samtools/misc/md5.c
4744 A /branches/dev/samtools/misc/md5.h
4745 A /branches/dev/samtools/misc/md5fa.c
4747 * fixed two warnings in kseq.h
4748 * added md5sum utilities
4750 ------------------------------------------------------------------------
4751 r31 | lh3lh3 | 2008-12-08 06:35:29 -0500 (Mon, 08 Dec 2008) | 5 lines
4753 M /branches/dev/samtools/Makefile
4754 M /branches/dev/samtools/bam_import.c
4755 M /branches/dev/samtools/bamtk.c
4756 A /branches/dev/samtools/kseq.h
4757 D /branches/dev/samtools/kstream.h
4760 * replace kstream with kseq. kseq is a superset of kstream. I need the
4761 extra functions in kseq.h.
4762 * also compile stand-alone faidx
4764 ------------------------------------------------------------------------
4765 r30 | lh3lh3 | 2008-12-08 06:17:04 -0500 (Mon, 08 Dec 2008) | 3 lines
4767 M /branches/dev/samtools/bam.h
4768 M /branches/dev/samtools/bam_sort.c
4769 M /branches/dev/samtools/bamtk.c
4772 * sorting by read names is available
4774 ------------------------------------------------------------------------
4775 r29 | lh3lh3 | 2008-12-08 05:29:02 -0500 (Mon, 08 Dec 2008) | 3 lines
4777 M /branches/dev/samtools/bam.c
4778 M /branches/dev/samtools/bam.h
4779 M /branches/dev/samtools/bam_import.c
4780 M /branches/dev/samtools/bam_maqcns.c
4781 M /branches/dev/samtools/bam_pileup.c
4782 M /branches/dev/samtools/bam_sort.c
4783 M /branches/dev/samtools/bam_tview.c
4784 M /branches/dev/samtools/bamtk.c
4785 M /branches/dev/samtools/misc/maq2sam.c
4788 * format change to meet the latest specification
4790 ------------------------------------------------------------------------
4791 r28 | lh3lh3 | 2008-12-04 11:09:21 -0500 (Thu, 04 Dec 2008) | 3 lines
4793 M /branches/dev/samtools/bam_maqcns.c
4794 M /branches/dev/samtools/misc/maq2sam.c
4796 * minor change in maqcns: special care when n==0
4797 * change maq2sam to meet the latest specification
4799 ------------------------------------------------------------------------
4800 r27 | lh3lh3 | 2008-12-04 10:55:44 -0500 (Thu, 04 Dec 2008) | 2 lines
4802 M /branches/dev/samtools/razf.c
4803 M /branches/dev/samtools/razf.h
4805 considerable code clean up in razf
4807 ------------------------------------------------------------------------
4808 r26 | lh3lh3 | 2008-12-04 10:08:18 -0500 (Thu, 04 Dec 2008) | 2 lines
4810 M /branches/dev/samtools/ChangeLog
4811 M /branches/dev/samtools/Makefile
4812 M /branches/dev/samtools/faidx.c
4814 make RAZF optional in faidx.c
4816 ------------------------------------------------------------------------
4817 r25 | lh3lh3 | 2008-12-01 10:27:22 -0500 (Mon, 01 Dec 2008) | 3 lines
4819 M /branches/dev/samtools/Makefile
4820 M /branches/dev/samtools/bam.h
4821 M /branches/dev/samtools/bam_aux.c
4822 M /branches/dev/samtools/bamtk.c
4823 M /branches/dev/samtools/samtools.1
4826 * added routines for retrieving aux data, NOT TESTED YET!
4828 ------------------------------------------------------------------------
4829 r24 | lh3lh3 | 2008-12-01 09:29:43 -0500 (Mon, 01 Dec 2008) | 5 lines
4831 M /branches/dev/samtools/bam.c
4832 M /branches/dev/samtools/bam_import.c
4833 M /branches/dev/samtools/bam_maqcns.c
4834 M /branches/dev/samtools/bamtk.c
4835 M /branches/dev/samtools/bgzf.c
4836 M /branches/dev/samtools/samtools.1
4839 * bgzf: fixed a potential integer overflow on 32-it machines
4840 * maqcns: set the minimum combined quality as 0
4841 * supporting hex strings
4843 ------------------------------------------------------------------------
4844 r23 | lh3lh3 | 2008-11-27 12:14:37 -0500 (Thu, 27 Nov 2008) | 3 lines
4846 M /branches/dev/samtools/bam_maqcns.c
4847 M /branches/dev/samtools/bamtk.c
4850 * fixed the bug in maqcns
4852 ------------------------------------------------------------------------
4853 r22 | lh3lh3 | 2008-11-27 12:08:11 -0500 (Thu, 27 Nov 2008) | 3 lines
4855 M /branches/dev/samtools/Makefile
4856 M /branches/dev/samtools/bam.h
4857 A /branches/dev/samtools/bam_maqcns.c
4858 A /branches/dev/samtools/bam_maqcns.h
4859 M /branches/dev/samtools/bam_tview.c
4860 M /branches/dev/samtools/bamtk.c
4861 A /branches/dev/samtools/glf.h
4864 * add MAQ consensus caller, currently BUGGY!
4866 ------------------------------------------------------------------------
4867 r21 | lh3lh3 | 2008-11-27 08:51:28 -0500 (Thu, 27 Nov 2008) | 4 lines
4869 M /branches/dev/samtools/bam_pileup.c
4870 M /branches/dev/samtools/bam_tview.c
4871 M /branches/dev/samtools/bamtk.c
4874 * tview: display padded alignment (but not P operation)
4875 * better coordinates and reference sequence
4877 ------------------------------------------------------------------------
4878 r19 | lh3lh3 | 2008-11-27 04:26:05 -0500 (Thu, 27 Nov 2008) | 2 lines
4880 A /branches/dev/samtools/ChangeLog
4884 ------------------------------------------------------------------------
4885 r18 | lh3lh3 | 2008-11-27 04:24:45 -0500 (Thu, 27 Nov 2008) | 3 lines
4887 D /branches/dev/samtools/ChangeLog
4888 A /branches/dev/samtools/ChangeLog.old (from /branches/dev/samtools/ChangeLog:6)
4890 Rename ChangeLog to ChangeLog.old. This old ChangeLog is generated from
4891 the log of my personal SVN repository.
4893 ------------------------------------------------------------------------
4894 r17 | lh3lh3 | 2008-11-27 04:22:55 -0500 (Thu, 27 Nov 2008) | 6 lines
4896 M /branches/dev/samtools/Makefile
4897 M /branches/dev/samtools/bamtk.c
4898 M /branches/dev/samtools/bgzf.c
4901 * declare fseeko and ftello as some Linux may not do this by default and
4902 missing these declarations will make bgzf buggy
4903 * get rid of some harmless warings
4904 * use BGZF by default, now
4906 ------------------------------------------------------------------------
4907 r16 | lh3lh3 | 2008-11-26 16:19:11 -0500 (Wed, 26 Nov 2008) | 4 lines
4909 M /branches/dev/samtools/bam_index.c
4910 M /branches/dev/samtools/bamtk.c
4911 M /branches/dev/samtools/razf.c
4914 * fixed a bug in razf_read()
4915 * give more warnings when the file is truncated (or due to bugs in I/O library)
4917 ------------------------------------------------------------------------
4918 r15 | lh3lh3 | 2008-11-26 15:41:39 -0500 (Wed, 26 Nov 2008) | 2 lines
4920 M /branches/dev/samtools/bgzf.c
4922 fixed a bug in bgzf.c at the end of the file
4924 ------------------------------------------------------------------------
4925 r14 | lh3lh3 | 2008-11-26 12:05:18 -0500 (Wed, 26 Nov 2008) | 4 lines
4927 M /branches/dev/samtools/bamtk.c
4930 * a lot happened to RAZF, although samtools itself is untouched. Better
4931 also update the version number anyway to avoid confusion
4933 ------------------------------------------------------------------------
4934 r13 | lh3lh3 | 2008-11-26 12:03:48 -0500 (Wed, 26 Nov 2008) | 2 lines
4936 M /branches/dev/samtools/razf.c
4938 a change from Jue, but I think it should not matter
4940 ------------------------------------------------------------------------
4941 r12 | lh3lh3 | 2008-11-26 11:48:14 -0500 (Wed, 26 Nov 2008) | 3 lines
4943 M /branches/dev/samtools/razf.c
4945 fixed a potential bug in razf. However, it seems still buggy, just
4946 rarely happens, very rarely.
4948 ------------------------------------------------------------------------
4949 r11 | lh3lh3 | 2008-11-26 09:02:56 -0500 (Wed, 26 Nov 2008) | 2 lines
4951 M /branches/dev/samtools/razf.c
4953 fixed a bug in razf, with the help of Jue
4955 ------------------------------------------------------------------------
4956 r10 | lh3lh3 | 2008-11-26 06:55:32 -0500 (Wed, 26 Nov 2008) | 2 lines
4958 M /branches/dev/samtools/bam_index.c
4962 ------------------------------------------------------------------------
4963 r9 | lh3lh3 | 2008-11-26 06:37:05 -0500 (Wed, 26 Nov 2008) | 2 lines
4965 M /branches/dev/samtools/Makefile
4966 M /branches/dev/samtools/bam.h
4967 M /branches/dev/samtools/razf.c
4968 M /branches/dev/samtools/razf.h
4970 * Jue has updated razf to realize Bob's scheme
4972 ------------------------------------------------------------------------
4973 r7 | lh3lh3 | 2008-11-25 15:37:37 -0500 (Tue, 25 Nov 2008) | 2 lines
4975 A /branches/dev/samtools/samtools.1
4979 ------------------------------------------------------------------------
4980 r6 | lh3lh3 | 2008-11-25 15:37:16 -0500 (Tue, 25 Nov 2008) | 3 lines
4982 A /branches/dev/samtools/ChangeLog
4983 A /branches/dev/samtools/Makefile
4984 A /branches/dev/samtools/bam.c
4985 A /branches/dev/samtools/bam.h
4986 A /branches/dev/samtools/bam_aux.c
4987 A /branches/dev/samtools/bam_endian.h
4988 A /branches/dev/samtools/bam_import.c
4989 A /branches/dev/samtools/bam_index.c
4990 A /branches/dev/samtools/bam_lpileup.c
4991 A /branches/dev/samtools/bam_pileup.c
4992 A /branches/dev/samtools/bam_sort.c
4993 A /branches/dev/samtools/bam_tview.c
4994 A /branches/dev/samtools/bamtk.c
4995 A /branches/dev/samtools/bgzf.c
4996 A /branches/dev/samtools/bgzf.h
4997 A /branches/dev/samtools/bgzip.c
4998 A /branches/dev/samtools/faidx.c
4999 A /branches/dev/samtools/faidx.h
5000 A /branches/dev/samtools/khash.h
5001 A /branches/dev/samtools/ksort.h
5002 A /branches/dev/samtools/kstream.h
5003 A /branches/dev/samtools/misc
5004 A /branches/dev/samtools/misc/Makefile
5005 A /branches/dev/samtools/misc/all2sam.pl
5006 A /branches/dev/samtools/misc/maq2sam.c
5007 A /branches/dev/samtools/razf.c
5008 A /branches/dev/samtools/razf.h
5009 A /branches/dev/samtools/razip.c
5010 A /branches/dev/samtools/zutil.h
5012 The initial version of samtools, replicated from my local SVN repository.
5013 The current version is: 0.1.0-42. All future development will happen here.
5015 ------------------------------------------------------------------------
5016 r5 | lh3lh3 | 2008-11-25 15:30:49 -0500 (Tue, 25 Nov 2008) | 2 lines
5018 A /branches/dev/samtools
5020 samtools (C version)
5022 ------------------------------------------------------------------------