1 ------------------------------------------------------------------------
2 r896 | lh3lh3 | 2011-01-06 10:52:15 -0500 (Thu, 06 Jan 2011) | 3 lines
4 M /trunk/samtools/bam_plcmd.c
5 M /trunk/samtools/bamtk.c
6 M /trunk/samtools/bcftools/bcf.h
7 M /trunk/samtools/bcftools/bcfutils.c
8 M /trunk/samtools/bcftools/call1.c
10 * samtools-0.1.12-10 (r896)
11 * allow to exclude read groups in mpileup
13 ------------------------------------------------------------------------
14 r895 | lh3lh3 | 2011-01-04 11:31:29 -0500 (Tue, 04 Jan 2011) | 2 lines
16 M /trunk/samtools/bcftools/bcf.tex
18 sorry. It is SP not ST
20 ------------------------------------------------------------------------
21 r894 | lh3lh3 | 2011-01-04 11:29:06 -0500 (Tue, 04 Jan 2011) | 2 lines
23 M /trunk/samtools/bcftools/bcf.tex
27 ------------------------------------------------------------------------
28 r893 | petulda | 2011-01-04 06:55:56 -0500 (Tue, 04 Jan 2011) | 1 line
30 M /trunk/samtools/bcftools/call1.c
32 Fixed a typo in read_samples
33 ------------------------------------------------------------------------
34 r892 | jmarshall | 2010-12-28 08:06:49 -0500 (Tue, 28 Dec 2010) | 9 lines
36 M /trunk/samtools/Makefile
37 M /trunk/samtools/bcftools/Makefile
38 M /trunk/samtools/examples/Makefile
40 System libraries go *after* user libraries in link commands, because
41 the user libraries may themselves have dependencies that are satisfied
42 by the system libraries. It's not rocket science!
44 This makes a difference with some linkers; or with -static or --as-needed.
46 The examples/Makefile fix is from Charles Plessy.
47 See also http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=606004
49 ------------------------------------------------------------------------
50 r891 | lh3lh3 | 2010-12-21 12:16:33 -0500 (Tue, 21 Dec 2010) | 3 lines
52 M /trunk/samtools/bamtk.c
53 M /trunk/samtools/bcftools/bcf.h
54 M /trunk/samtools/bcftools/bcfutils.c
55 M /trunk/samtools/bcftools/call1.c
57 * samtools-0.1.12-9 (r891)
58 * allow to call SNPs from a subset of samples
60 ------------------------------------------------------------------------
61 r889 | lh3lh3 | 2010-12-15 11:28:16 -0500 (Wed, 15 Dec 2010) | 3 lines
63 M /trunk/samtools/bam2bcf.c
64 M /trunk/samtools/bamtk.c
66 * samtools-0.1.12-12 (r889)
67 * set mapQ as 20 if it equals 255
69 ------------------------------------------------------------------------
70 r888 | lh3lh3 | 2010-12-14 22:41:09 -0500 (Tue, 14 Dec 2010) | 2 lines
72 M /trunk/samtools/bam_plcmd.c
73 M /trunk/samtools/bamtk.c
75 When -B is applied to mpileup, still use paired reads only unless -A is flagged.
77 ------------------------------------------------------------------------
78 r887 | lh3lh3 | 2010-12-14 22:37:05 -0500 (Tue, 14 Dec 2010) | 3 lines
80 M /trunk/samtools/bam_md.c
81 M /trunk/samtools/bam_plcmd.c
82 M /trunk/samtools/bamtk.c
84 * samtools-0.1.12-6 (r887)
85 * added a hidden option -E to mpileup/calmd. -E triggers an alternative way to apply BAQ.
87 ------------------------------------------------------------------------
88 r886 | lh3lh3 | 2010-12-14 12:51:03 -0500 (Tue, 14 Dec 2010) | 2 lines
90 M /trunk/samtools/bam2bcf_indel.c
91 M /trunk/samtools/bamtk.c
93 (Arguably) improved the indel caller a tiny bit for lowCov data.
95 ------------------------------------------------------------------------
96 r885 | petulda | 2010-12-14 04:55:46 -0500 (Tue, 14 Dec 2010) | 1 line
98 M /trunk/samtools/bcftools/call1.c
100 Fixed the VCF header to pass validation
101 ------------------------------------------------------------------------
102 r884 | lh3lh3 | 2010-12-12 23:02:19 -0500 (Sun, 12 Dec 2010) | 3 lines
104 M /trunk/samtools/bam2bcf_indel.c
105 M /trunk/samtools/bamtk.c
106 M /trunk/samtools/bcftools/vcfutils.pl
108 * samtools-0.1.12-4 (r884)
109 * fixed a long-existing flaw in the INDEL calling model
111 ------------------------------------------------------------------------
112 r883 | lh3lh3 | 2010-12-11 20:05:42 -0500 (Sat, 11 Dec 2010) | 2 lines
114 M /trunk/samtools/bcftools/bcfutils.c
115 M /trunk/samtools/bcftools/call1.c
116 M /trunk/samtools/bcftools/vcfutils.pl
118 compute max SP and max GQ from sample genotypes
120 ------------------------------------------------------------------------
121 r880 | lh3lh3 | 2010-12-10 10:50:54 -0500 (Fri, 10 Dec 2010) | 2 lines
123 D /trunk/samtools/bcftools/bcf-fix.pl
125 drop bcf-fix.pl as it is redundant by the latest changes
127 ------------------------------------------------------------------------
128 r879 | lh3lh3 | 2010-12-10 10:50:29 -0500 (Fri, 10 Dec 2010) | 3 lines
130 M /trunk/samtools/bcftools/call1.c
131 M /trunk/samtools/bcftools/vcf.c
133 * fixed a minor issue in printing VCFs
134 * write bcftools specific INFO and FORMAT in the header
136 ------------------------------------------------------------------------
137 r878 | lh3lh3 | 2010-12-10 10:09:14 -0500 (Fri, 10 Dec 2010) | 2 lines
139 M /trunk/samtools/bamtk.c
140 M /trunk/samtools/bcftools/bcfutils.c
141 M /trunk/samtools/bcftools/call1.c
143 Make sure that the GT genotype field is the first
145 ------------------------------------------------------------------------
146 r877 | lh3lh3 | 2010-12-08 17:27:05 -0500 (Wed, 08 Dec 2010) | 7 lines
148 M /trunk/samtools/bam2bcf.c
149 M /trunk/samtools/bam2bcf.h
150 M /trunk/samtools/bam2bcf_indel.c
151 M /trunk/samtools/bam_plcmd.c
152 M /trunk/samtools/bamtk.c
154 * samtools-0.1.12-2 (r877)
156 * allow to fine control the selection of indel candidates. The current
157 setting is okay for lowCov and highCov with ~100 samples, but it
158 skips too many indels for highCov with >250 samples.
161 ------------------------------------------------------------------------
162 r874 | lh3lh3 | 2010-12-07 22:40:35 -0500 (Tue, 07 Dec 2010) | 2 lines
164 M /trunk/samtools/bam_plcmd.c
168 ------------------------------------------------------------------------
169 r873 | lh3lh3 | 2010-12-07 22:39:57 -0500 (Tue, 07 Dec 2010) | 3 lines
171 M /trunk/samtools/bam_plcmd.c
172 M /trunk/samtools/bamtk.c
174 * samtools-0.1.12-1 (r873)
175 * added a switch to allow anomalous read pairs in calling
177 ------------------------------------------------------------------------
178 r872 | lh3lh3 | 2010-12-07 14:43:54 -0500 (Tue, 07 Dec 2010) | 2 lines
180 M /trunk/samtools/bcftools/vcfutils.pl
182 fixed a bug in vcf2fq
184 ------------------------------------------------------------------------
185 r869 | lh3lh3 | 2010-12-05 01:18:06 -0500 (Sun, 05 Dec 2010) | 2 lines
187 M /trunk/samtools/bamtk.c
189 added a warning for the Windows version
191 ------------------------------------------------------------------------
192 r868 | lh3lh3 | 2010-12-05 01:05:51 -0500 (Sun, 05 Dec 2010) | 4 lines
194 M /trunk/samtools/bcftools/call1.c
196 In ksprintf(), change "%lf" and "%lg" to "%f" and "%g", respectively.
197 According to the manual page, this change is valid. However, MinGW seems
198 to interpret "%lf" as "%Lf".
200 ------------------------------------------------------------------------
201 r867 | lh3lh3 | 2010-12-05 00:35:43 -0500 (Sun, 05 Dec 2010) | 2 lines
203 M /trunk/samtools/Makefile.mingw
204 M /trunk/samtools/bam_aux.c
206 bring back the windows support
208 ------------------------------------------------------------------------
209 r866 | lh3lh3 | 2010-12-04 23:33:51 -0500 (Sat, 04 Dec 2010) | 2 lines
211 M /trunk/samtools/bam_reheader.c
212 M /trunk/samtools/bcftools/vcfutils.pl
214 Fixed a compiling error when knetfile is not used.
216 ------------------------------------------------------------------------
217 r865 | lh3lh3 | 2010-12-04 00:13:22 -0500 (Sat, 04 Dec 2010) | 2 lines
219 M /trunk/samtools/bcftools/vcfutils.pl
223 ------------------------------------------------------------------------
224 r864 | lh3lh3 | 2010-12-03 17:12:30 -0500 (Fri, 03 Dec 2010) | 3 lines
226 M /trunk/samtools/bcftools/call1.c
227 M /trunk/samtools/bcftools/prob1.c
228 M /trunk/samtools/bcftools/prob1.h
230 * remove "-f". Instead always compute consensus quality
231 * increase the upper limit of quality
233 ------------------------------------------------------------------------
234 r863 | lh3lh3 | 2010-12-03 15:28:15 -0500 (Fri, 03 Dec 2010) | 2 lines
236 M /trunk/samtools/bcftools/bcf.c
238 more informative error message
240 ------------------------------------------------------------------------
241 r862 | lh3lh3 | 2010-12-02 16:16:08 -0500 (Thu, 02 Dec 2010) | 2 lines
243 M /trunk/samtools/NEWS
244 M /trunk/samtools/bamtk.c
246 Release samtools-0.1.12a
248 ------------------------------------------------------------------------
249 r861 | lh3lh3 | 2010-12-02 15:55:06 -0500 (Thu, 02 Dec 2010) | 2 lines
251 M /trunk/samtools/bcftools/call1.c
253 a possible fix to DP4=0,0,0,0; have not tested, but should have no side-effect
255 ------------------------------------------------------------------------
256 r859 | lh3lh3 | 2010-12-02 11:39:57 -0500 (Thu, 02 Dec 2010) | 2 lines
258 M /trunk/samtools/NEWS
259 M /trunk/samtools/bam_index.c
260 M /trunk/samtools/bamtk.c
261 M /trunk/samtools/samtools.1
263 Release samtools-0.1.12
265 ------------------------------------------------------------------------
266 r858 | lh3lh3 | 2010-12-02 11:24:41 -0500 (Thu, 02 Dec 2010) | 4 lines
268 M /trunk/samtools/bam_plcmd.c
269 M /trunk/samtools/bamtk.c
270 M /trunk/samtools/bcftools/bcf.c
272 * samtools-0.1.11-1 (r858)
273 * fixed a bug in mpileup which causes segfaults
274 * bcftools: do not segfault when BCF contains errors
276 ------------------------------------------------------------------------
277 r857 | lh3lh3 | 2010-11-30 23:52:50 -0500 (Tue, 30 Nov 2010) | 2 lines
279 M /trunk/samtools/bam_index.c
281 fixed a memory leak in bam_fetch()
283 ------------------------------------------------------------------------
284 r856 | lh3lh3 | 2010-11-26 00:07:31 -0500 (Fri, 26 Nov 2010) | 3 lines
286 M /trunk/samtools/bam2bcf_indel.c
287 M /trunk/samtools/bcftools/vcfutils.pl
289 * fixed a memory violation
290 * added splitchr to vcfutils.pl
292 ------------------------------------------------------------------------
293 r854 | lh3lh3 | 2010-11-23 09:05:08 -0500 (Tue, 23 Nov 2010) | 2 lines
295 M /trunk/samtools/bcftools/ld.c
297 fixed a typo/bug in r^2 computation
299 ------------------------------------------------------------------------
300 r852 | lh3lh3 | 2010-11-21 22:20:20 -0500 (Sun, 21 Nov 2010) | 2 lines
302 M /trunk/samtools/bamtk.c
304 forget to change the version information
306 ------------------------------------------------------------------------
307 r851 | lh3lh3 | 2010-11-21 22:16:52 -0500 (Sun, 21 Nov 2010) | 2 lines
309 M /trunk/samtools/ChangeLog
310 M /trunk/samtools/NEWS
311 M /trunk/samtools/bcftools/bcftools.1
312 M /trunk/samtools/samtools.1
314 Release samtools-0.1.11
316 ------------------------------------------------------------------------
317 r844 | lh3lh3 | 2010-11-19 23:16:08 -0500 (Fri, 19 Nov 2010) | 3 lines
319 M /trunk/samtools/bamtk.c
320 M /trunk/samtools/bcftools/call1.c
321 M /trunk/samtools/bcftools/prob1.c
322 M /trunk/samtools/bcftools/prob1.h
324 * samtools-0.1.10-9 (r844)
325 * added the "folded" or reference-free mode for variant calling
327 ------------------------------------------------------------------------
328 r843 | lh3lh3 | 2010-11-19 22:26:36 -0500 (Fri, 19 Nov 2010) | 2 lines
330 M /trunk/samtools/NEWS
331 M /trunk/samtools/bam_sort.c
333 In merging, if -R is specified, do not abort if the sequence dictionary is different.
335 ------------------------------------------------------------------------
336 r842 | jmarshall | 2010-11-19 21:24:28 -0500 (Fri, 19 Nov 2010) | 5 lines
338 M /trunk/samtools/bam_sort.c
340 When merging BAM headers, compare the list of target reference sequences
341 strictly (and fail/abort if there is a mismatch), but allow one list to be a
342 prefix of the other. (i.e., check that the lists are identical up until the
343 shorter runs out, and add the excess targets from the longer to the output.)
345 ------------------------------------------------------------------------
346 r841 | lh3lh3 | 2010-11-19 14:49:27 -0500 (Fri, 19 Nov 2010) | 4 lines
348 M /trunk/samtools/bam_index.c
349 M /trunk/samtools/bam_pileup.c
350 M /trunk/samtools/bamtk.c
352 * samtools-0.1.10 (r841)
353 * fixed a bug in pileup when the first CIGAR operation is D
354 * fixed a bug in view with range query
356 ------------------------------------------------------------------------
357 r840 | lh3lh3 | 2010-11-19 13:45:51 -0500 (Fri, 19 Nov 2010) | 10 lines
359 M /trunk/samtools/ChangeLog
360 M /trunk/samtools/bam2bcf.c
361 M /trunk/samtools/bam2bcf.h
362 M /trunk/samtools/bam2bcf_indel.c
363 M /trunk/samtools/bam_plcmd.c
364 M /trunk/samtools/bamtk.c
366 * samtools-0.1.10-4 (r840)
368 * drop the MNP caller. It is slow while does not diliver too much
369 benefit. Possibly I will work on it in future given more time.
371 * there is a segfault in pileup
373 * someone has reported segfault from view/index/sort
376 ------------------------------------------------------------------------
377 r839 | lh3lh3 | 2010-11-18 17:30:11 -0500 (Thu, 18 Nov 2010) | 9 lines
379 M /trunk/samtools/bam2bcf.h
380 M /trunk/samtools/bam2bcf_indel.c
381 M /trunk/samtools/bamtk.c
383 * samtools-0.1.10-6 (r839)
385 * call MNPs without realignment because it seems to me that it is not
386 worthwhile to significantly slow down SNP calling.
388 * the result looks quite different from the previous version. I have
392 ------------------------------------------------------------------------
393 r838 | lh3lh3 | 2010-11-18 11:26:09 -0500 (Thu, 18 Nov 2010) | 2 lines
395 M /trunk/samtools/knetfile.c
397 Apply a patch by Rob Davis, which improves fault detection.
399 ------------------------------------------------------------------------
400 r836 | lh3lh3 | 2010-11-18 11:09:23 -0500 (Thu, 18 Nov 2010) | 3 lines
402 M /trunk/samtools/bam2bcf_indel.c
403 M /trunk/samtools/bamtk.c
406 * initiate MNP realignment when the MNP has at least 0.2% frequency (otherwise too slow)
408 ------------------------------------------------------------------------
409 r835 | lh3lh3 | 2010-11-18 00:25:13 -0500 (Thu, 18 Nov 2010) | 3 lines
411 M /trunk/samtools/bcftools/vcfutils.pl
413 * modify the filtering rule: also filter SNPs around filtered indels
416 ------------------------------------------------------------------------
417 r834 | lh3lh3 | 2010-11-17 23:13:52 -0500 (Wed, 17 Nov 2010) | 4 lines
419 M /trunk/samtools/bam2bcf.c
420 M /trunk/samtools/bam2bcf_indel.c
421 M /trunk/samtools/bamtk.c
423 * samtools-0.1.10-4 (r834)
424 * fixed a silly bug in printing MNP
425 * restrict to at most 1 alternative allele
427 ------------------------------------------------------------------------
428 r833 | lh3lh3 | 2010-11-17 21:58:58 -0500 (Wed, 17 Nov 2010) | 2 lines
430 M /trunk/samtools/bam2bcf.c
431 M /trunk/samtools/bamtk.c
433 fixed a bug in printing MNPs
435 ------------------------------------------------------------------------
436 r832 | lh3lh3 | 2010-11-17 21:47:20 -0500 (Wed, 17 Nov 2010) | 2 lines
438 M /trunk/samtools/bam2bcf_indel.c
439 M /trunk/samtools/bamtk.c
441 minor change to how seqQ is applied
443 ------------------------------------------------------------------------
444 r831 | lh3lh3 | 2010-11-17 21:41:12 -0500 (Wed, 17 Nov 2010) | 3 lines
446 M /trunk/samtools/bam2bcf.c
447 M /trunk/samtools/bam2bcf.h
448 M /trunk/samtools/bam2bcf_indel.c
449 M /trunk/samtools/bam_plcmd.c
450 M /trunk/samtools/bamtk.c
452 * samtools-0.1.10 (r831)
455 ------------------------------------------------------------------------
456 r829 | lh3lh3 | 2010-11-16 23:14:15 -0500 (Tue, 16 Nov 2010) | 2 lines
458 M /trunk/samtools/ChangeLog
459 M /trunk/samtools/NEWS
460 M /trunk/samtools/bamtk.c
462 Release samtools-0.1.10 (r829)
464 ------------------------------------------------------------------------
465 r828 | lh3lh3 | 2010-11-16 20:48:49 -0500 (Tue, 16 Nov 2010) | 2 lines
467 M /trunk/samtools/bamtk.c
469 update version information: samtools-0.1.9-20 (r828)
471 ------------------------------------------------------------------------
472 r827 | lh3lh3 | 2010-11-16 15:32:50 -0500 (Tue, 16 Nov 2010) | 2 lines
474 M /trunk/samtools/bcftools/call1.c
476 bcftools: allow to skip indels
478 ------------------------------------------------------------------------
479 r826 | lh3lh3 | 2010-11-16 14:11:58 -0500 (Tue, 16 Nov 2010) | 2 lines
481 M /trunk/samtools/bam_md.c
483 remove ZQ if both BQ and ZQ are present
485 ------------------------------------------------------------------------
486 r825 | lh3lh3 | 2010-11-16 13:51:33 -0500 (Tue, 16 Nov 2010) | 3 lines
488 M /trunk/samtools/bam2bcf_indel.c
489 M /trunk/samtools/bam_md.c
490 M /trunk/samtools/bamtk.c
491 M /trunk/samtools/samtools.1
493 * samtools-0.1.9-18 (r825)
494 * change the behaviour of calmd such that by default it does not change the base quality
496 ------------------------------------------------------------------------
497 r824 | lh3lh3 | 2010-11-15 23:31:53 -0500 (Mon, 15 Nov 2010) | 4 lines
499 M /trunk/samtools/bam_plcmd.c
500 M /trunk/samtools/bamtk.c
501 M /trunk/samtools/bcftools/call1.c
502 M /trunk/samtools/samtools.1
504 * samtools-0.1.9-17 (r824)
505 * added command line options to change the default parameters in indel calling
508 ------------------------------------------------------------------------
509 r823 | lh3lh3 | 2010-11-15 12:20:13 -0500 (Mon, 15 Nov 2010) | 3 lines
511 M /trunk/samtools/bam2bcf_indel.c
512 M /trunk/samtools/bam_md.c
513 M /trunk/samtools/bamtk.c
515 * samtools-0.1.9-r823
516 * the BQ tag is now 64 shifted, not 33 shifted
518 ------------------------------------------------------------------------
519 r822 | lh3lh3 | 2010-11-15 00:30:18 -0500 (Mon, 15 Nov 2010) | 3 lines
521 M /trunk/samtools/bam2bcf.c
522 M /trunk/samtools/bam2bcf.h
523 M /trunk/samtools/bamtk.c
524 M /trunk/samtools/bcftools/vcfutils.pl
525 M /trunk/samtools/misc/samtools.pl
527 * samtools-0.1.9-16 (r822)
528 * keep the raw depth because in indel calling, DP4 may be way off the true depth
530 ------------------------------------------------------------------------
531 r821 | lh3lh3 | 2010-11-13 01:18:31 -0500 (Sat, 13 Nov 2010) | 4 lines
533 M /trunk/samtools/bam_md.c
534 M /trunk/samtools/bamtk.c
536 * samtools-0.1.9-15 (r821)
538 * skip realignment if BQ is present
540 ------------------------------------------------------------------------
541 r820 | lh3lh3 | 2010-11-13 01:08:26 -0500 (Sat, 13 Nov 2010) | 3 lines
543 M /trunk/samtools/bam2bcf_indel.c
544 M /trunk/samtools/bamtk.c
546 * samtools-0.1.9-14 (r820)
547 * penalize reads with excessive differences in indel calling
549 ------------------------------------------------------------------------
550 r819 | lh3lh3 | 2010-11-12 21:36:27 -0500 (Fri, 12 Nov 2010) | 3 lines
552 M /trunk/samtools/bam_maqcns.c
553 M /trunk/samtools/bamtk.c
555 * samtools-0.1.9-13 (r819)
556 * fixed a bug in pileup given refskip
558 ------------------------------------------------------------------------
559 r818 | lh3lh3 | 2010-11-12 13:04:53 -0500 (Fri, 12 Nov 2010) | 3 lines
561 M /trunk/samtools/bam2bcf_indel.c
562 M /trunk/samtools/bamtk.c
565 * for indel calling, do two rounds of probabilistic realignments
567 ------------------------------------------------------------------------
568 r817 | lh3lh3 | 2010-11-11 20:04:07 -0500 (Thu, 11 Nov 2010) | 3 lines
570 M /trunk/samtools/bam2bcf_indel.c
571 M /trunk/samtools/bamtk.c
572 M /trunk/samtools/bcftools/vcfutils.pl
574 * samtools-0.1.19-11 (r817)
575 * only initiate indel calling when 0.2% of reads contain a gap
577 ------------------------------------------------------------------------
578 r816 | lh3lh3 | 2010-11-11 01:22:59 -0500 (Thu, 11 Nov 2010) | 7 lines
580 M /trunk/samtools/bam2bcf_indel.c
581 M /trunk/samtools/bamtk.c
583 * samtools-0.1.9-10 (r816)
585 * I know why the forward method fails. it is because of zero base
586 qualities. when that is fixed, the forward method seems to give
587 better results than Viterbi, as it should be. I am tired...
590 ------------------------------------------------------------------------
591 r815 | lh3lh3 | 2010-11-11 00:57:15 -0500 (Thu, 11 Nov 2010) | 2 lines
593 M /trunk/samtools/ChangeLog
594 M /trunk/samtools/bam2bcf_indel.c
596 effectively revert to the viterbi version. The forward realignment gives too many false positives.
598 ------------------------------------------------------------------------
599 r814 | lh3lh3 | 2010-11-11 00:18:02 -0500 (Thu, 11 Nov 2010) | 4 lines
601 M /trunk/samtools/bam2bcf_indel.c
602 M /trunk/samtools/bam_md.c
603 M /trunk/samtools/bam_plcmd.c
604 M /trunk/samtools/bamtk.c
606 * samtools-0.1.9-9 (r810)
607 * use forward, instead of viterbi, for realignment
608 * realignment is now quality aware
610 ------------------------------------------------------------------------
611 r813 | lh3lh3 | 2010-11-10 22:45:24 -0500 (Wed, 10 Nov 2010) | 2 lines
613 M /trunk/samtools/bam2bcf_indel.c
614 M /trunk/samtools/kprobaln.c
615 M /trunk/samtools/kprobaln.h
617 * prepare to replace kaln with kprobaln in realignment
619 ------------------------------------------------------------------------
620 r812 | lh3lh3 | 2010-11-10 17:28:50 -0500 (Wed, 10 Nov 2010) | 2 lines
622 M /trunk/samtools/bcftools/bcf.c
626 ------------------------------------------------------------------------
627 r811 | lh3lh3 | 2010-11-10 16:54:46 -0500 (Wed, 10 Nov 2010) | 2 lines
629 M /trunk/samtools/bcftools/bcf.c
630 M /trunk/samtools/bcftools/bcf.h
632 use zlib for direct reading when BCF_LITE is in use
634 ------------------------------------------------------------------------
635 r810 | lh3lh3 | 2010-11-10 16:32:13 -0500 (Wed, 10 Nov 2010) | 3 lines
637 M /trunk/samtools/bam2bcf_indel.c
639 * do not use reads containing too many mismatches for indel calling
640 * fixed a trivial bug in case of multi-allelic indels
642 ------------------------------------------------------------------------
643 r809 | lh3lh3 | 2010-11-10 13:23:02 -0500 (Wed, 10 Nov 2010) | 3 lines
645 M /trunk/samtools/bam2bcf.c
646 M /trunk/samtools/bam2bcf_indel.c
647 M /trunk/samtools/bam_plcmd.c
648 M /trunk/samtools/bamtk.c
650 * samtools-0.1.9-8 (r809)
651 * fixed a bug in the indel caller
653 ------------------------------------------------------------------------
654 r808 | lh3lh3 | 2010-11-10 12:24:10 -0500 (Wed, 10 Nov 2010) | 2 lines
656 M /trunk/samtools/Makefile
658 minor change to makefile
660 ------------------------------------------------------------------------
661 r807 | lh3lh3 | 2010-11-10 12:10:21 -0500 (Wed, 10 Nov 2010) | 4 lines
663 M /trunk/samtools/Makefile
664 M /trunk/samtools/bam2bcf.h
665 M /trunk/samtools/bam2bcf_indel.c
666 M /trunk/samtools/bam_plcmd.c
667 M /trunk/samtools/bamtk.c
668 M /trunk/samtools/bcftools/vcfutils.pl
670 * samtools-0.1.9-8 (r807)
671 * collect indel candidates only from specified platforms (@RG-PL)
672 * merge varFilter and filter4vcf in vcfutils.pl
674 ------------------------------------------------------------------------
675 r806 | lh3lh3 | 2010-11-09 22:05:46 -0500 (Tue, 09 Nov 2010) | 2 lines
677 M /trunk/samtools/bcftools/call1.c
678 M /trunk/samtools/bcftools/prob1.c
679 M /trunk/samtools/bcftools/prob1.h
681 bcftools: compute equal-tail (Bayesian) credible interval
683 ------------------------------------------------------------------------
684 r805 | lh3lh3 | 2010-11-09 16:28:39 -0500 (Tue, 09 Nov 2010) | 2 lines
686 M /trunk/samtools/bcftools/vcfutils.pl
688 added a double-hit filter to avoid overestimated indel likelihood
690 ------------------------------------------------------------------------
691 r804 | lh3lh3 | 2010-11-09 14:12:06 -0500 (Tue, 09 Nov 2010) | 3 lines
693 M /trunk/samtools/bam2bcf_indel.c
694 M /trunk/samtools/bamtk.c
696 * samtools-0.1.9-7 (r804)
697 * fixed a bug in the gap caller
699 ------------------------------------------------------------------------
700 r803 | lh3lh3 | 2010-11-09 10:45:33 -0500 (Tue, 09 Nov 2010) | 4 lines
702 M /trunk/samtools/bam2bcf.c
703 M /trunk/samtools/bam2bcf_indel.c
704 M /trunk/samtools/bamtk.c
705 M /trunk/samtools/bcftools/bcf.c
706 M /trunk/samtools/bcftools/bcf.h
707 M /trunk/samtools/bcftools/prob1.c
709 * samtools-0.1.9-6 (r803)
710 * mpileup: apply homopolymer correction when calculating GL, instead of before
711 * bcftools: apply a different prior to indels
713 ------------------------------------------------------------------------
714 r802 | lh3lh3 | 2010-11-08 23:53:15 -0500 (Mon, 08 Nov 2010) | 3 lines
716 M /trunk/samtools/bam2bcf.c
717 M /trunk/samtools/bamtk.c
719 * samtools-0.1.9-5 (r802)
720 * relax tandem penalty. this will be made a command-line option in future.
722 ------------------------------------------------------------------------
723 r801 | lh3lh3 | 2010-11-08 23:35:52 -0500 (Mon, 08 Nov 2010) | 3 lines
725 M /trunk/samtools/bam2bcf.c
726 M /trunk/samtools/bamtk.c
728 * samtools-0.1.9-4 (r801)
729 * fixed a minor issue in printing indel VCF
731 ------------------------------------------------------------------------
732 r800 | lh3lh3 | 2010-11-08 15:28:14 -0500 (Mon, 08 Nov 2010) | 2 lines
734 M /trunk/samtools/bam2bcf_indel.c
735 M /trunk/samtools/bcftools/vcfutils.pl
737 fixed another silly bug in mpileup's indel caller
739 ------------------------------------------------------------------------
740 r799 | lh3lh3 | 2010-11-08 14:28:27 -0500 (Mon, 08 Nov 2010) | 2 lines
742 M /trunk/samtools/bam2bcf.c
744 fixed a silly bug in the indel caller
746 ------------------------------------------------------------------------
747 r798 | lh3lh3 | 2010-11-08 14:07:33 -0500 (Mon, 08 Nov 2010) | 2 lines
749 M /trunk/samtools/ChangeLog
750 M /trunk/samtools/sam_view.c
751 M /trunk/samtools/samtools.1
753 Incorporate patches by Marcel Martin for read counting.
755 ------------------------------------------------------------------------
756 r797 | lh3lh3 | 2010-11-08 13:39:52 -0500 (Mon, 08 Nov 2010) | 3 lines
758 M /trunk/samtools/bam2bcf.c
759 M /trunk/samtools/bam2bcf.h
760 M /trunk/samtools/bam2bcf_indel.c
761 M /trunk/samtools/bam_plcmd.c
762 M /trunk/samtools/bamtk.c
764 * samtools-0.1.9-2 (r797)
765 * mpileup: indel calling seems to be working
767 ------------------------------------------------------------------------
768 r796 | lh3lh3 | 2010-11-08 10:54:46 -0500 (Mon, 08 Nov 2010) | 2 lines
770 M /trunk/samtools/bam2bcf.c
771 M /trunk/samtools/bam2bcf.h
772 M /trunk/samtools/bam2bcf_indel.c
773 M /trunk/samtools/bam_plcmd.c
774 M /trunk/samtools/kaln.c
776 indel calling is apparently working, but more information needs to be collected
778 ------------------------------------------------------------------------
779 r795 | lh3lh3 | 2010-11-08 00:39:18 -0500 (Mon, 08 Nov 2010) | 2 lines
781 M /trunk/samtools/bam2bcf.c
782 M /trunk/samtools/bam2bcf_indel.c
784 fixed a few bugs in the indel caller. Probably there are more.
786 ------------------------------------------------------------------------
787 r794 | lh3lh3 | 2010-11-07 22:23:16 -0500 (Sun, 07 Nov 2010) | 2 lines
789 M /trunk/samtools/Makefile
790 M /trunk/samtools/bam.h
791 M /trunk/samtools/bam2bcf.c
792 M /trunk/samtools/bam2bcf.h
793 A /trunk/samtools/bam2bcf_indel.c
794 M /trunk/samtools/bam_plcmd.c
795 M /trunk/samtools/kaln.c
796 M /trunk/samtools/kaln.h
798 prepare for the indel caller. It is not ready yet.
800 ------------------------------------------------------------------------
801 r793 | lh3lh3 | 2010-11-05 11:28:23 -0400 (Fri, 05 Nov 2010) | 2 lines
803 M /trunk/samtools/bam2bcf.c
804 M /trunk/samtools/bam2bcf.h
805 M /trunk/samtools/bam_plcmd.c
807 Revert to r790. The recent changes are not good...
809 ------------------------------------------------------------------------
810 r792 | lh3lh3 | 2010-11-05 00:19:14 -0400 (Fri, 05 Nov 2010) | 6 lines
812 M /trunk/samtools/bam2bcf.c
813 M /trunk/samtools/bam2bcf.h
814 M /trunk/samtools/bam_plcmd.c
816 * this revision is UNSTABLE
818 * indel caller seems working, but it is very insensitive and has
819 several things I do not quite understand.
822 ------------------------------------------------------------------------
823 r791 | lh3lh3 | 2010-11-04 22:58:43 -0400 (Thu, 04 Nov 2010) | 2 lines
825 M /trunk/samtools/bam2bcf.c
826 M /trunk/samtools/bam2bcf.h
827 M /trunk/samtools/bam_plcmd.c
829 for backup. no effective changes
831 ------------------------------------------------------------------------
832 r790 | lh3lh3 | 2010-11-03 15:51:24 -0400 (Wed, 03 Nov 2010) | 2 lines
834 M /trunk/samtools/bcftools/vcfutils.pl
835 M /trunk/samtools/kprobaln.c
837 fixed a minor problem in the example coming with kprobaln.c
839 ------------------------------------------------------------------------
840 r789 | lh3lh3 | 2010-11-02 15:41:27 -0400 (Tue, 02 Nov 2010) | 4 lines
842 M /trunk/samtools/Makefile
843 M /trunk/samtools/bam_md.c
844 M /trunk/samtools/kaln.c
845 M /trunk/samtools/kaln.h
846 A /trunk/samtools/kprobaln.c
847 A /trunk/samtools/kprobaln.h
849 Separate kaln and kprobaln as I am preparing further changes. At
850 present, the results should be identical to the previous.
853 ------------------------------------------------------------------------
854 r788 | petulda | 2010-11-02 12:19:04 -0400 (Tue, 02 Nov 2010) | 1 line
856 M /trunk/samtools/bam_plcmd.c
858 Added -b option: read file names from a file
859 ------------------------------------------------------------------------
860 r787 | lh3lh3 | 2010-10-29 23:17:22 -0400 (Fri, 29 Oct 2010) | 7 lines
862 M /trunk/samtools/bam.h
863 M /trunk/samtools/bam_pileup.c
864 M /trunk/samtools/bam_plcmd.c
865 M /trunk/samtools/bamtk.c
867 * samtools-0.1.9-2 (r787)
869 * Allow to set a maximum per-sample depth to reduce memory. However,
870 BAQ computation is still applied to every read. The speed is not
874 ------------------------------------------------------------------------
875 r786 | lh3lh3 | 2010-10-29 12:10:40 -0400 (Fri, 29 Oct 2010) | 3 lines
877 M /trunk/samtools/bam2bcf.c
878 M /trunk/samtools/bam2bcf.h
879 M /trunk/samtools/bam_plcmd.c
880 M /trunk/samtools/bamtk.c
881 M /trunk/samtools/bcftools/bcf.c
882 M /trunk/samtools/bcftools/vcf.c
884 * samtools-0.1.9-1 (r786)
885 * samtools: optionally perform exact test for each sample
887 ------------------------------------------------------------------------
888 r785 | lh3lh3 | 2010-10-29 09:42:25 -0400 (Fri, 29 Oct 2010) | 2 lines
890 M /trunk/samtools/bam2bcf.c
891 M /trunk/samtools/bam2bcf.h
892 M /trunk/samtools/bam_plcmd.c
893 M /trunk/samtools/bcftools/bcf.c
895 Optionally output "DP", the individual read depth
897 ------------------------------------------------------------------------
898 r784 | lh3lh3 | 2010-10-27 23:10:27 -0400 (Wed, 27 Oct 2010) | 2 lines
900 M /trunk/samtools/samtools.1
902 acknowledge Petr and John who have greatly contributed to the project.
904 ------------------------------------------------------------------------
905 r783 | lh3lh3 | 2010-10-27 22:47:47 -0400 (Wed, 27 Oct 2010) | 2 lines
907 M /trunk/samtools/ChangeLog
908 M /trunk/samtools/NEWS
909 M /trunk/samtools/bamtk.c
910 M /trunk/samtools/samtools.1
912 Release samtools-0.1.9 (r783)
914 ------------------------------------------------------------------------
915 r782 | lh3lh3 | 2010-10-27 19:58:54 -0400 (Wed, 27 Oct 2010) | 2 lines
917 M /trunk/samtools/bam_plcmd.c
919 fixed a silly bug in pileup
921 ------------------------------------------------------------------------
922 r781 | lh3lh3 | 2010-10-27 14:39:48 -0400 (Wed, 27 Oct 2010) | 5 lines
924 M /trunk/samtools/ChangeLog
925 M /trunk/samtools/bam_plcmd.c
926 M /trunk/samtools/bam_sort.c
927 M /trunk/samtools/bamtk.c
928 M /trunk/samtools/samtools.1
930 * samtools-0.1.8-22 (r781)
931 * made BAQ the default behavior of mpileup
933 * in merge, force to exit given inconsistent header when "-R" is not in use.
935 ------------------------------------------------------------------------
936 r780 | lh3lh3 | 2010-10-27 11:01:11 -0400 (Wed, 27 Oct 2010) | 3 lines
938 M /trunk/samtools/bam.h
939 M /trunk/samtools/bam_plcmd.c
940 M /trunk/samtools/bamtk.c
942 * samtools-0.1.8-21 (r780)
943 * minor speedup to pileup
945 ------------------------------------------------------------------------
946 r779 | lh3lh3 | 2010-10-27 09:58:56 -0400 (Wed, 27 Oct 2010) | 2 lines
948 M /trunk/samtools/bam_pileup.c
949 M /trunk/samtools/bam_plcmd.c
950 M /trunk/samtools/examples/toy.sam
952 improve pileup a little bit
954 ------------------------------------------------------------------------
955 r778 | lh3lh3 | 2010-10-27 00:14:43 -0400 (Wed, 27 Oct 2010) | 3 lines
957 M /trunk/samtools/bam.h
958 M /trunk/samtools/bam_pileup.c
959 M /trunk/samtools/bam_plcmd.c
960 M /trunk/samtools/bam_tview.c
961 M /trunk/samtools/bamtk.c
963 * samtools-0.1.8-20 (r778)
964 * speed up pileup, although I do not know how much is the improvement
966 ------------------------------------------------------------------------
967 r777 | lh3lh3 | 2010-10-26 17:26:04 -0400 (Tue, 26 Oct 2010) | 3 lines
969 M /trunk/samtools/bam_maqcns.c
970 M /trunk/samtools/bam_maqcns.h
971 M /trunk/samtools/bam_plcmd.c
972 M /trunk/samtools/bamtk.c
973 M /trunk/samtools/examples/Makefile
975 * samtools-0.1.8-19 (r777)
976 * integrate mpileup features to pileup: min_baseQ, capQ, prob_realn, paired-only and biased prior
978 ------------------------------------------------------------------------
979 r776 | lh3lh3 | 2010-10-26 15:27:46 -0400 (Tue, 26 Oct 2010) | 2 lines
981 M /trunk/samtools/bam_md.c
983 remove local realignment (probabilistic realignment is still there)
985 ------------------------------------------------------------------------
986 r774 | jmarshall | 2010-10-21 06:52:38 -0400 (Thu, 21 Oct 2010) | 3 lines
988 M /trunk/samtools/sam_view.c
990 Add the relevant filename or region to error messages, and cause a failure
991 exit status where appropriate. Based on a patch provided by Marcel Martin.
993 ------------------------------------------------------------------------
994 r773 | lh3lh3 | 2010-10-19 19:44:31 -0400 (Tue, 19 Oct 2010) | 3 lines
996 M /trunk/samtools/examples/toy.sam
997 M /trunk/samtools/kaln.c
999 * Minor code changes. No real effect.
1000 * change quality to 30 in toy.sam
1002 ------------------------------------------------------------------------
1003 r772 | lh3lh3 | 2010-10-18 23:40:13 -0400 (Mon, 18 Oct 2010) | 2 lines
1005 M /trunk/samtools/examples/toy.fa
1006 M /trunk/samtools/examples/toy.sam
1008 added another toy example
1010 ------------------------------------------------------------------------
1011 r771 | lh3lh3 | 2010-10-13 23:32:12 -0400 (Wed, 13 Oct 2010) | 2 lines
1013 M /trunk/samtools/bcftools/call1.c
1014 M /trunk/samtools/bcftools/ld.c
1015 M /trunk/samtools/bcftools/vcfutils.pl
1017 improve the LD statistics
1019 ------------------------------------------------------------------------
1020 r770 | lh3lh3 | 2010-10-12 23:49:26 -0400 (Tue, 12 Oct 2010) | 3 lines
1022 M /trunk/samtools/bcftools/call1.c
1023 M /trunk/samtools/bcftools/vcfutils.pl
1025 * a minor fix to the -L option
1026 * add ldstats to vcfutils.pl
1028 ------------------------------------------------------------------------
1029 r769 | lh3lh3 | 2010-10-12 15:51:57 -0400 (Tue, 12 Oct 2010) | 2 lines
1031 M /trunk/samtools/bcftools/bcf.c
1035 ------------------------------------------------------------------------
1036 r768 | lh3lh3 | 2010-10-12 15:49:06 -0400 (Tue, 12 Oct 2010) | 2 lines
1038 M /trunk/samtools/bcftools/Makefile
1039 A /trunk/samtools/bcftools/ld.c
1041 forget to add the key file
1043 ------------------------------------------------------------------------
1044 r767 | lh3lh3 | 2010-10-12 15:48:46 -0400 (Tue, 12 Oct 2010) | 4 lines
1046 M /trunk/samtools/bcftools/Makefile
1047 M /trunk/samtools/bcftools/bcf.c
1048 M /trunk/samtools/bcftools/bcf.h
1049 M /trunk/samtools/bcftools/call1.c
1050 M /trunk/samtools/bcftools/prob1.c
1051 M /trunk/samtools/bcftools/vcfutils.pl
1053 * vcfutils.pl: fixed a typo in help message
1054 * added APIs: bcf_append_info() and bcf_cpy()
1055 * calculate adjacent LD
1057 ------------------------------------------------------------------------
1058 r766 | lh3lh3 | 2010-10-11 11:06:40 -0400 (Mon, 11 Oct 2010) | 2 lines
1060 M /trunk/samtools/bcftools/vcfutils.pl
1062 added filter for samtools/bcftools genetated VCFs
1064 ------------------------------------------------------------------------
1065 r765 | lh3lh3 | 2010-10-05 14:05:18 -0400 (Tue, 05 Oct 2010) | 3 lines
1067 M /trunk/samtools/bcftools/vcfutils.pl
1068 M /trunk/samtools/kaln.c
1070 * removed a comment line in kaln.c
1071 * vcfutils.pl fillac works when GT is not the first field
1073 ------------------------------------------------------------------------
1074 r764 | petulda | 2010-10-05 08:59:36 -0400 (Tue, 05 Oct 2010) | 1 line
1076 A /trunk/samtools/bcftools/bcf-fix.pl
1078 Convert VCF output of "bcftools view -bgcv" to a valid VCF file
1079 ------------------------------------------------------------------------
1080 r763 | lh3lh3 | 2010-10-02 22:51:03 -0400 (Sat, 02 Oct 2010) | 4 lines
1082 M /trunk/samtools/bam_plcmd.c
1083 M /trunk/samtools/bamtk.c
1084 A /trunk/samtools/bcftools/bcftools.1
1085 M /trunk/samtools/bcftools/call1.c
1086 M /trunk/samtools/samtools.1
1088 * samtools-0.1.8-18 (r763)
1089 * added bcftools manual page
1090 * minor fix to mpileup and view command lines
1092 ------------------------------------------------------------------------
1093 r762 | lh3lh3 | 2010-10-02 21:46:25 -0400 (Sat, 02 Oct 2010) | 3 lines
1095 M /trunk/samtools/bcftools/bcf.c
1096 M /trunk/samtools/bcftools/call1.c
1097 M /trunk/samtools/bcftools/vcfutils.pl
1099 * vcfutils.pl qstats: calculate marginal ts/tv
1100 * allow to call genotypes at variant sites
1102 ------------------------------------------------------------------------
1103 r761 | lh3lh3 | 2010-10-01 00:29:55 -0400 (Fri, 01 Oct 2010) | 3 lines
1105 M /trunk/samtools/kaln.c
1106 M /trunk/samtools/misc/HmmGlocal.java
1108 I am changing the gap open probability back to 0.001. It seems that
1109 being conservative here is a good thing...
1111 ------------------------------------------------------------------------
1112 r760 | lh3lh3 | 2010-10-01 00:11:27 -0400 (Fri, 01 Oct 2010) | 5 lines
1114 M /trunk/samtools/bamtk.c
1115 M /trunk/samtools/kaln.c
1116 A /trunk/samtools/misc/HmmGlocal.java
1118 * samtools-0.1.8-17 (r760)
1119 * the default gap open penalty is too small (a typo)
1120 * added comments on hmm_realn
1121 * Java implementation
1123 ------------------------------------------------------------------------
1124 r759 | lh3lh3 | 2010-09-30 10:12:54 -0400 (Thu, 30 Sep 2010) | 2 lines
1126 M /trunk/samtools/bamtk.c
1128 mark samtools-0.1.8-16 (r759)
1130 ------------------------------------------------------------------------
1131 r758 | lh3lh3 | 2010-09-30 10:12:02 -0400 (Thu, 30 Sep 2010) | 2 lines
1133 M /trunk/samtools/kaln.c
1135 round to the nearest integer
1137 ------------------------------------------------------------------------
1138 r757 | lh3lh3 | 2010-09-28 17:16:43 -0400 (Tue, 28 Sep 2010) | 4 lines
1140 M /trunk/samtools/kaln.c
1142 I was trying to accelerate ka_prob_glocal() as this will be the
1143 bottleneck. After an hour, the only gain is to change division to
1144 multiplication. OK. I will stop.
1146 ------------------------------------------------------------------------
1147 r756 | lh3lh3 | 2010-09-28 16:57:49 -0400 (Tue, 28 Sep 2010) | 2 lines
1149 M /trunk/samtools/kaln.c
1151 this is interesting. multiplication is much faster than division, at least on my Mac
1153 ------------------------------------------------------------------------
1154 r755 | lh3lh3 | 2010-09-28 16:19:13 -0400 (Tue, 28 Sep 2010) | 2 lines
1156 M /trunk/samtools/kaln.c
1160 ------------------------------------------------------------------------
1161 r754 | lh3lh3 | 2010-09-28 15:44:16 -0400 (Tue, 28 Sep 2010) | 2 lines
1163 M /trunk/samtools/bam_md.c
1164 M /trunk/samtools/bam_plcmd.c
1165 M /trunk/samtools/kaln.c
1167 prob_realn() seems working!
1169 ------------------------------------------------------------------------
1170 r753 | lh3lh3 | 2010-09-28 12:48:23 -0400 (Tue, 28 Sep 2010) | 2 lines
1172 M /trunk/samtools/kaln.c
1176 ------------------------------------------------------------------------
1177 r752 | lh3lh3 | 2010-09-28 12:47:41 -0400 (Tue, 28 Sep 2010) | 2 lines
1179 M /trunk/samtools/kaln.c
1180 M /trunk/samtools/kaln.h
1182 Convert phredQ to probabilities
1184 ------------------------------------------------------------------------
1185 r751 | lh3lh3 | 2010-09-28 12:32:08 -0400 (Tue, 28 Sep 2010) | 2 lines
1187 M /trunk/samtools/kaln.c
1188 M /trunk/samtools/kaln.h
1190 Implement the glocal HMM; discard the extention HMM
1192 ------------------------------------------------------------------------
1193 r750 | lh3lh3 | 2010-09-28 00:06:11 -0400 (Tue, 28 Sep 2010) | 2 lines
1195 M /trunk/samtools/kaln.c
1197 improve numerical stability
1199 ------------------------------------------------------------------------
1200 r749 | lh3lh3 | 2010-09-27 23:27:54 -0400 (Mon, 27 Sep 2010) | 2 lines
1202 M /trunk/samtools/kaln.c
1206 ------------------------------------------------------------------------
1207 r748 | lh3lh3 | 2010-09-27 23:17:16 -0400 (Mon, 27 Sep 2010) | 2 lines
1209 M /trunk/samtools/kaln.c
1211 fixed a bug in banded DP
1213 ------------------------------------------------------------------------
1214 r747 | lh3lh3 | 2010-09-27 23:05:12 -0400 (Mon, 27 Sep 2010) | 3 lines
1216 M /trunk/samtools/kaln.c
1218 * fixed that weird issue.
1219 * the banded version is NOT working
1221 ------------------------------------------------------------------------
1222 r746 | lh3lh3 | 2010-09-27 22:57:05 -0400 (Mon, 27 Sep 2010) | 2 lines
1224 M /trunk/samtools/kaln.c
1226 More comments. This version seems working, but something is a little weird...
1228 ------------------------------------------------------------------------
1229 r745 | lh3lh3 | 2010-09-27 17:21:40 -0400 (Mon, 27 Sep 2010) | 6 lines
1231 M /trunk/samtools/kaln.c
1233 A little code cleanup. Now the forward and backback algorithms give
1234 nearly identical P(x), which means both are close to the correct
1235 forms. However, I have only tested on toy examples. Minor errors in
1236 the implementation may not be obvious.
1239 ------------------------------------------------------------------------
1240 r744 | lh3lh3 | 2010-09-27 16:55:15 -0400 (Mon, 27 Sep 2010) | 2 lines
1242 M /trunk/samtools/bam_plcmd.c
1243 M /trunk/samtools/bam_sort.c
1244 M /trunk/samtools/kaln.c
1245 M /trunk/samtools/kaln.h
1249 ------------------------------------------------------------------------
1250 r743 | jmarshall | 2010-09-27 08:19:06 -0400 (Mon, 27 Sep 2010) | 6 lines
1252 M /trunk/samtools/bam_sort.c
1254 Abort if merge -h's INH.SAM cannot be opened, just as we abort
1255 if any of the IN#.BAM input files cannot be opened.
1257 Also propagate any error indication returned by bam_merge_core()
1258 to samtools merge's exit status.
1260 ------------------------------------------------------------------------
1261 r741 | jmarshall | 2010-09-24 11:08:24 -0400 (Fri, 24 Sep 2010) | 5 lines
1263 M /trunk/samtools/bam_index.c
1265 Use bam_validate1() to detect garbage records in the event of a corrupt
1266 BAI index file that causes a bam_seek() to an invalid position. At most
1267 one record (namely, the bam_iter_read terminator) is tested per bam_fetch()
1268 call, so the cost is insignificant in the normal case.
1270 ------------------------------------------------------------------------
1271 r740 | jmarshall | 2010-09-24 11:00:19 -0400 (Fri, 24 Sep 2010) | 2 lines
1273 M /trunk/samtools/bam.c
1274 M /trunk/samtools/bam.h
1276 Add bam_validate1().
1278 ------------------------------------------------------------------------
1279 r739 | lh3lh3 | 2010-09-22 12:07:50 -0400 (Wed, 22 Sep 2010) | 3 lines
1281 M /trunk/samtools/bam_md.c
1282 M /trunk/samtools/bamtk.c
1284 * samtools-0.1.8-15 (r379)
1285 * allow to change capQ parameter in calmd
1287 ------------------------------------------------------------------------
1288 r738 | jmarshall | 2010-09-22 11:15:33 -0400 (Wed, 22 Sep 2010) | 13 lines
1290 M /trunk/samtools/bam_index.c
1291 M /trunk/samtools/sam_view.c
1293 When bam_read1() returns an error (return value <= -2), propagate that error
1294 to bam_iter_read()'s own return value. Similarly, also propagate it up to
1295 bam_fetch()'s return value. Previously bam_fetch() always returned 0, and
1296 callers ignored its return value anyway. With this change, 0 continues to
1297 indicate success, while <= -2 (which can be written as < 0, as -1 is never
1298 returned) indicates corrupted input.
1300 bam_iter_read() ought also to propagate errors returned by bam_seek().
1302 main_samview() can now print an error message and fail when bam_fetch()
1303 detects that a .bai index file is corrupted or otherwise does not correspond
1304 to the .bam file it is being used with.
1306 ------------------------------------------------------------------------
1307 r737 | jmarshall | 2010-09-22 10:47:42 -0400 (Wed, 22 Sep 2010) | 3 lines
1309 M /trunk/samtools/bam_index.c
1311 0 is a successful return value from bam_read1(). (In practice, it never
1312 returns 0 anyway; but all the other callers treat 0 as successful.)
1314 ------------------------------------------------------------------------
1315 r736 | lh3lh3 | 2010-09-20 17:43:08 -0400 (Mon, 20 Sep 2010) | 2 lines
1317 M /trunk/samtools/bam.h
1318 M /trunk/samtools/bam_index.c
1319 M /trunk/samtools/bam_sort.c
1321 * merge files region-by-region. work on small examples but more tests are needed.
1323 ------------------------------------------------------------------------
1324 r735 | lh3lh3 | 2010-09-20 16:56:24 -0400 (Mon, 20 Sep 2010) | 2 lines
1326 M /trunk/samtools/bcftools/vcfutils.pl
1328 improve qstats by checking the alleles as well
1330 ------------------------------------------------------------------------
1331 r734 | lh3lh3 | 2010-09-17 18:12:13 -0400 (Fri, 17 Sep 2010) | 2 lines
1333 M /trunk/samtools/bcftools/vcfutils.pl
1335 convert UCSC SNP SQL dump to VCF
1337 ------------------------------------------------------------------------
1338 r733 | lh3lh3 | 2010-09-17 13:02:11 -0400 (Fri, 17 Sep 2010) | 2 lines
1340 M /trunk/samtools/bcftools/vcfutils.pl
1342 hapmap2vcf convertor
1344 ------------------------------------------------------------------------
1345 r732 | lh3lh3 | 2010-09-17 10:11:37 -0400 (Fri, 17 Sep 2010) | 3 lines
1347 M /trunk/samtools/bcftools/Makefile
1348 M /trunk/samtools/bcftools/bcf.c
1349 M /trunk/samtools/bcftools/bcf.h
1350 M /trunk/samtools/bcftools/vcf.c
1353 * VCF->BCF is not possible without knowing the sequence dictionary before hand...
1355 ------------------------------------------------------------------------
1356 r731 | lh3lh3 | 2010-09-17 09:15:53 -0400 (Fri, 17 Sep 2010) | 2 lines
1358 M /trunk/samtools/bam2bcf.c
1359 M /trunk/samtools/bcftools/bcf.c
1360 M /trunk/samtools/bcftools/bcf.h
1361 M /trunk/samtools/bcftools/bcfutils.c
1362 M /trunk/samtools/bcftools/call1.c
1363 M /trunk/samtools/bcftools/vcf.c
1365 * put n_smpl to "bcf1_t" to simplify API a little
1367 ------------------------------------------------------------------------
1368 r730 | lh3lh3 | 2010-09-16 21:36:01 -0400 (Thu, 16 Sep 2010) | 2 lines
1370 M /trunk/samtools/bcftools/bcf.h
1371 M /trunk/samtools/bcftools/call1.c
1372 M /trunk/samtools/bcftools/index.c
1374 fixed a bug in indexing
1376 ------------------------------------------------------------------------
1377 r729 | lh3lh3 | 2010-09-16 16:54:48 -0400 (Thu, 16 Sep 2010) | 3 lines
1379 M /trunk/samtools/bam.c
1380 M /trunk/samtools/bam_md.c
1381 M /trunk/samtools/bam_pileup.c
1383 * fixed a bug in capQ
1384 * valgrind identifies a use of uninitialised value, but I have not fixed it.
1386 ------------------------------------------------------------------------
1387 r728 | lh3lh3 | 2010-09-16 15:03:59 -0400 (Thu, 16 Sep 2010) | 3 lines
1389 M /trunk/samtools/bgzip.c
1390 M /trunk/samtools/razip.c
1392 * fixed a bug in razip: -c will delete the input file
1393 * copy tabix/bgzip to here
1395 ------------------------------------------------------------------------
1396 r727 | lh3lh3 | 2010-09-16 13:45:49 -0400 (Thu, 16 Sep 2010) | 3 lines
1398 M /trunk/samtools/bam_md.c
1399 M /trunk/samtools/bam_plcmd.c
1400 M /trunk/samtools/bamtk.c
1402 * samtools-0.1.8-14 (r727)
1403 * allow to change the capQ parameter at the command line
1405 ------------------------------------------------------------------------
1406 r726 | lh3lh3 | 2010-09-16 13:38:43 -0400 (Thu, 16 Sep 2010) | 4 lines
1408 M /trunk/samtools/bam_md.c
1409 M /trunk/samtools/bam_plcmd.c
1410 M /trunk/samtools/bcftools/vcfutils.pl
1411 M /trunk/samtools/misc/samtools.pl
1413 * added varFilter to vcfutils.pl
1414 * reimplement realn(). now it performs a local alignment
1415 * added cap_mapQ() to cap mapping quality when there are many substitutions
1417 ------------------------------------------------------------------------
1418 r724 | lh3lh3 | 2010-09-15 00:18:31 -0400 (Wed, 15 Sep 2010) | 2 lines
1420 M /trunk/samtools/bcftools/Makefile
1421 A /trunk/samtools/bcftools/bcf2qcall.c
1422 M /trunk/samtools/bcftools/call1.c
1424 * convert BCF to QCALL input
1426 ------------------------------------------------------------------------
1427 r723 | lh3lh3 | 2010-09-14 22:41:50 -0400 (Tue, 14 Sep 2010) | 2 lines
1429 M /trunk/samtools/bam_md.c
1431 dynamic band width in realignment
1433 ------------------------------------------------------------------------
1434 r722 | lh3lh3 | 2010-09-14 22:05:32 -0400 (Tue, 14 Sep 2010) | 2 lines
1436 M /trunk/samtools/bam_md.c
1437 M /trunk/samtools/bam_plcmd.c
1439 fixed a bug in realignment
1441 ------------------------------------------------------------------------
1442 r721 | lh3lh3 | 2010-09-14 20:54:09 -0400 (Tue, 14 Sep 2010) | 2 lines
1444 M /trunk/samtools/bcftools/prob1.c
1448 ------------------------------------------------------------------------
1449 r720 | lh3lh3 | 2010-09-14 19:25:10 -0400 (Tue, 14 Sep 2010) | 2 lines
1451 M /trunk/samtools/Makefile
1452 M /trunk/samtools/bam_maqcns.c
1453 M /trunk/samtools/bam_md.c
1455 fixed a bug in realignment
1457 ------------------------------------------------------------------------
1458 r719 | lh3lh3 | 2010-09-14 19:18:24 -0400 (Tue, 14 Sep 2010) | 2 lines
1460 M /trunk/samtools/bam_plcmd.c
1462 minor changes. It is BUGGY now!
1464 ------------------------------------------------------------------------
1465 r718 | lh3lh3 | 2010-09-14 16:32:33 -0400 (Tue, 14 Sep 2010) | 4 lines
1467 M /trunk/samtools/bam_md.c
1468 M /trunk/samtools/bam_pileup.c
1469 M /trunk/samtools/kaln.c
1470 M /trunk/samtools/kaln.h
1472 * aggressive gapped aligner is implemented in calmd.
1473 * distinguish gap_open and gap_end_open in banded alignment
1474 * make tview accepts alignment with heading and tailing D
1476 ------------------------------------------------------------------------
1477 r717 | jmarshall | 2010-09-14 09:04:28 -0400 (Tue, 14 Sep 2010) | 2 lines
1481 Add svn:ignore properties for generated files that don't appear in "make all".
1483 ------------------------------------------------------------------------
1484 r716 | jmarshall | 2010-09-13 08:37:53 -0400 (Mon, 13 Sep 2010) | 3 lines
1487 M /trunk/samtools/bcftools
1488 M /trunk/samtools/misc
1490 Add svn:ignore properties listing the generated files.
1491 (Except for *.o, which we'll assume is in global-ignores.)
1493 ------------------------------------------------------------------------
1494 r715 | lh3lh3 | 2010-09-08 12:53:55 -0400 (Wed, 08 Sep 2010) | 5 lines
1496 M /trunk/samtools/bamtk.c
1497 M /trunk/samtools/bcftools/call1.c
1498 M /trunk/samtools/bcftools/prob1.c
1499 M /trunk/samtools/sample.c
1500 M /trunk/samtools/sample.h
1502 * samtools-0.1.8-13 (r715)
1503 * fixed a bug in identifying SM across files
1504 * bcftools: estimate heterozygosity
1505 * bcftools: allow to skip sites without reference bases
1507 ------------------------------------------------------------------------
1508 r713 | lh3lh3 | 2010-09-03 17:19:12 -0400 (Fri, 03 Sep 2010) | 2 lines
1510 M /trunk/samtools/bcftools/Makefile
1511 M /trunk/samtools/bcftools/call1.c
1512 M /trunk/samtools/bcftools/prob1.c
1513 M /trunk/samtools/bcftools/prob1.h
1515 quite a lot changes to the contrast caller, but I still feel something is missing...
1517 ------------------------------------------------------------------------
1518 r711 | lh3lh3 | 2010-09-03 00:30:48 -0400 (Fri, 03 Sep 2010) | 4 lines
1520 M /trunk/samtools/bcftools/Makefile
1521 M /trunk/samtools/bcftools/call1.c
1522 M /trunk/samtools/bcftools/prob1.c
1523 M /trunk/samtools/bcftools/vcfutils.pl
1525 * changed 3.434 to 4.343 (typo!)
1526 * fixed a bug in the contrast caller
1527 * calculate heterozygosity
1529 ------------------------------------------------------------------------
1530 r710 | lh3lh3 | 2010-09-01 23:24:47 -0400 (Wed, 01 Sep 2010) | 2 lines
1532 M /trunk/samtools/bcftools/bcf.h
1533 M /trunk/samtools/bcftools/bcfutils.c
1534 M /trunk/samtools/bcftools/call1.c
1536 SNP calling from the GL field
1538 ------------------------------------------------------------------------
1539 r709 | lh3lh3 | 2010-09-01 18:52:30 -0400 (Wed, 01 Sep 2010) | 2 lines
1541 M /trunk/samtools/bcftools/vcf.c
1543 fixed another problem
1545 ------------------------------------------------------------------------
1546 r708 | lh3lh3 | 2010-09-01 18:31:17 -0400 (Wed, 01 Sep 2010) | 3 lines
1548 M /trunk/samtools/bcftools/bcf.c
1549 M /trunk/samtools/bcftools/vcf.c
1551 * fixed bugs in parsing VCF
1552 * parser now works with GT/GQ/DP/PL/GL
1554 ------------------------------------------------------------------------
1555 r707 | lh3lh3 | 2010-09-01 15:28:29 -0400 (Wed, 01 Sep 2010) | 2 lines
1557 M /trunk/samtools/bcftools/Makefile
1558 M /trunk/samtools/bcftools/prob1.c
1560 Do not compile _BCF_QUAD by default
1562 ------------------------------------------------------------------------
1563 r706 | lh3lh3 | 2010-09-01 15:21:41 -0400 (Wed, 01 Sep 2010) | 2 lines
1565 M /trunk/samtools/bcftools/bcf.c
1566 M /trunk/samtools/bcftools/bcf.h
1567 M /trunk/samtools/bcftools/bcfutils.c
1568 M /trunk/samtools/bcftools/call1.c
1570 Write the correct ALT and PL in the SNP calling mode.
1572 ------------------------------------------------------------------------
1573 r705 | lh3lh3 | 2010-09-01 12:50:33 -0400 (Wed, 01 Sep 2010) | 2 lines
1575 M /trunk/samtools/bcftools/vcfutils.pl
1577 more commands for my own uses
1579 ------------------------------------------------------------------------
1580 r704 | lh3lh3 | 2010-09-01 09:26:10 -0400 (Wed, 01 Sep 2010) | 2 lines
1582 A /trunk/samtools/bcftools/vcfutils.pl
1584 Utilities for processing VCF
1586 ------------------------------------------------------------------------
1587 r703 | lh3lh3 | 2010-08-31 16:44:57 -0400 (Tue, 31 Aug 2010) | 2 lines
1589 M /trunk/samtools/bcftools/Makefile
1590 M /trunk/samtools/bcftools/call1.c
1591 M /trunk/samtools/bcftools/prob1.c
1592 M /trunk/samtools/bcftools/prob1.h
1594 preliminary contrast variant caller
1596 ------------------------------------------------------------------------
1597 r702 | lh3lh3 | 2010-08-31 12:28:39 -0400 (Tue, 31 Aug 2010) | 2 lines
1599 M /trunk/samtools/bcftools/call1.c
1600 M /trunk/samtools/bcftools/prob1.c
1601 M /trunk/samtools/bcftools/prob1.h
1603 z' and z'' can be calculated
1605 ------------------------------------------------------------------------
1606 r701 | lh3lh3 | 2010-08-31 10:20:57 -0400 (Tue, 31 Aug 2010) | 3 lines
1608 M /trunk/samtools/bcftools/Makefile
1609 A /trunk/samtools/bcftools/call1.c (from /trunk/samtools/bcftools/vcfout.c:699)
1610 M /trunk/samtools/bcftools/prob1.c
1611 D /trunk/samtools/bcftools/vcfout.c
1613 * rename vcfout.c as call1.c
1614 * prepare to add two-sample comparison
1616 ------------------------------------------------------------------------
1617 r699 | lh3lh3 | 2010-08-24 15:28:16 -0400 (Tue, 24 Aug 2010) | 2 lines
1619 M /trunk/samtools/bcftools/vcfout.c
1621 fixed a bug in calculating the t statistics
1623 ------------------------------------------------------------------------
1624 r698 | lh3lh3 | 2010-08-24 14:05:50 -0400 (Tue, 24 Aug 2010) | 3 lines
1626 M /trunk/samtools/bam2bcf.c
1627 M /trunk/samtools/bam2bcf.h
1628 M /trunk/samtools/bamtk.c
1629 M /trunk/samtools/bcftools/kfunc.c
1630 M /trunk/samtools/bcftools/vcfout.c
1632 * samtools-0.1.8-13 (r698)
1633 * perform one-tailed t-test for baseQ, mapQ and endDist
1635 ------------------------------------------------------------------------
1636 r697 | lh3lh3 | 2010-08-24 12:30:13 -0400 (Tue, 24 Aug 2010) | 2 lines
1638 M /trunk/samtools/bcftools/kfunc.c
1640 added regularized incomplete beta function
1642 ------------------------------------------------------------------------
1643 r695 | lh3lh3 | 2010-08-23 17:36:17 -0400 (Mon, 23 Aug 2010) | 2 lines
1645 M /trunk/samtools/bam_maqcns.c
1646 M /trunk/samtools/bam_plcmd.c
1648 change the default correlation coefficient
1650 ------------------------------------------------------------------------
1651 r694 | lh3lh3 | 2010-08-23 14:46:52 -0400 (Mon, 23 Aug 2010) | 2 lines
1653 M /trunk/samtools/bcftools/bcf.c
1654 M /trunk/samtools/bcftools/vcfout.c
1656 print QUAL as floating numbers
1658 ------------------------------------------------------------------------
1659 r693 | lh3lh3 | 2010-08-23 14:06:07 -0400 (Mon, 23 Aug 2010) | 3 lines
1661 M /trunk/samtools/Makefile
1662 M /trunk/samtools/bam_plcmd.c
1663 M /trunk/samtools/bamtk.c
1664 M /trunk/samtools/examples/Makefile
1665 A /trunk/samtools/sample.c
1666 A /trunk/samtools/sample.h
1668 * samtools-0.1.8-12 (r692)
1669 * group data by samples in "mpileup -g"
1671 ------------------------------------------------------------------------
1672 r692 | lh3lh3 | 2010-08-23 10:58:53 -0400 (Mon, 23 Aug 2010) | 2 lines
1674 M /trunk/samtools/Makefile
1675 D /trunk/samtools/bam_mcns.c
1676 D /trunk/samtools/bam_mcns.h
1677 M /trunk/samtools/bam_plcmd.c
1679 remove VCF output in mpileup
1681 ------------------------------------------------------------------------
1682 r691 | lh3lh3 | 2010-08-23 10:48:20 -0400 (Mon, 23 Aug 2010) | 3 lines
1684 M /trunk/samtools/bam2bcf.c
1685 M /trunk/samtools/bam2bcf.h
1687 * use the revised MAQ error model for mpileup
1688 * prepare to remove the independent model from mpileup
1690 ------------------------------------------------------------------------
1691 r690 | lh3lh3 | 2010-08-20 15:46:40 -0400 (Fri, 20 Aug 2010) | 2 lines
1693 M /trunk/samtools/Makefile
1694 M /trunk/samtools/bam_maqcns.c
1695 M /trunk/samtools/bam_maqcns.h
1696 M /trunk/samtools/bam_plcmd.c
1697 A /trunk/samtools/errmod.c
1698 A /trunk/samtools/errmod.h
1699 M /trunk/samtools/ksort.h
1701 added revised MAQ error model
1703 ------------------------------------------------------------------------
1704 r689 | lh3lh3 | 2010-08-18 09:55:20 -0400 (Wed, 18 Aug 2010) | 2 lines
1706 M /trunk/samtools/bcftools/prob1.c
1707 M /trunk/samtools/bcftools/prob1.h
1708 M /trunk/samtools/bcftools/vcfout.c
1710 allow to read the prior from the error output. EM iteration is working.
1712 ------------------------------------------------------------------------
1713 r688 | lh3lh3 | 2010-08-17 12:12:20 -0400 (Tue, 17 Aug 2010) | 3 lines
1715 M /trunk/samtools/bcftools/main.c
1716 M /trunk/samtools/bcftools/vcf.c
1718 * write a little more VCF header
1721 ------------------------------------------------------------------------
1722 r687 | lh3lh3 | 2010-08-16 20:53:16 -0400 (Mon, 16 Aug 2010) | 2 lines
1724 M /trunk/samtools/bcftools/bcf.c
1725 M /trunk/samtools/bcftools/bcf.h
1726 M /trunk/samtools/bcftools/bcf.tex
1730 ------------------------------------------------------------------------
1731 r686 | lh3lh3 | 2010-08-14 00:11:13 -0400 (Sat, 14 Aug 2010) | 2 lines
1733 M /trunk/samtools/bcftools/bcf.c
1734 M /trunk/samtools/bcftools/prob1.c
1736 faster for large sample size (in principle)
1738 ------------------------------------------------------------------------
1739 r685 | lh3lh3 | 2010-08-13 23:28:31 -0400 (Fri, 13 Aug 2010) | 4 lines
1741 M /trunk/samtools/bcftools/prob1.c
1743 * a numerically stable method to calculate z_{jk}
1744 * currently slower than the old method but will be important for large sample size
1745 * in principle, we can speed up for large n, but have not tried
1747 ------------------------------------------------------------------------
1748 r684 | lh3lh3 | 2010-08-11 21:58:31 -0400 (Wed, 11 Aug 2010) | 2 lines
1750 M /trunk/samtools/bcftools/vcfout.c
1752 fixed an issue in parsing integer
1754 ------------------------------------------------------------------------
1755 r683 | lh3lh3 | 2010-08-09 13:05:07 -0400 (Mon, 09 Aug 2010) | 2 lines
1757 M /trunk/samtools/bcftools/bcf.c
1759 do not print refname if file is converted from VCF
1761 ------------------------------------------------------------------------
1762 r682 | lh3lh3 | 2010-08-09 12:59:47 -0400 (Mon, 09 Aug 2010) | 3 lines
1764 M /trunk/samtools/bcftools/vcf.c
1767 * fixed a bug in parsing VCF
1769 ------------------------------------------------------------------------
1770 r681 | lh3lh3 | 2010-08-09 12:49:23 -0400 (Mon, 09 Aug 2010) | 4 lines
1772 M /trunk/samtools/bcftools/bcf.c
1773 M /trunk/samtools/bcftools/bcf.h
1774 M /trunk/samtools/bcftools/bcfutils.c
1775 M /trunk/samtools/bcftools/main.c
1776 M /trunk/samtools/bcftools/vcf.c
1777 M /trunk/samtools/bcftools/vcfout.c
1778 M /trunk/samtools/bgzf.c
1779 M /trunk/samtools/kstring.c
1781 * fixed a bug in kstrtok@kstring.c
1782 * preliminary VCF parser (not parse everything for now)
1783 * improved view interface
1785 ------------------------------------------------------------------------
1786 r680 | lh3lh3 | 2010-08-09 10:43:13 -0400 (Mon, 09 Aug 2010) | 4 lines
1788 M /trunk/samtools/bcftools/bcf.c
1789 M /trunk/samtools/bcftools/bcf.h
1790 M /trunk/samtools/bcftools/vcfout.c
1791 M /trunk/samtools/kstring.c
1792 M /trunk/samtools/kstring.h
1794 * improved kstring (added kstrtok)
1795 * removed the limit on the format string length in bcftools
1796 * use kstrtok to parse format which fixed a bug in the old code
1798 ------------------------------------------------------------------------
1799 r679 | lh3lh3 | 2010-08-09 01:12:05 -0400 (Mon, 09 Aug 2010) | 2 lines
1801 A /trunk/samtools/bcftools/README
1802 M /trunk/samtools/bcftools/vcfout.c
1806 ------------------------------------------------------------------------
1807 r678 | lh3lh3 | 2010-08-09 00:01:52 -0400 (Mon, 09 Aug 2010) | 2 lines
1809 M /trunk/samtools/bcftools/vcfout.c
1811 perform single-tail test for ED4
1813 ------------------------------------------------------------------------
1814 r677 | lh3lh3 | 2010-08-08 23:48:35 -0400 (Sun, 08 Aug 2010) | 2 lines
1816 M /trunk/samtools/bcftools/Makefile
1817 M /trunk/samtools/bcftools/kfunc.c
1818 M /trunk/samtools/bcftools/vcfout.c
1820 * test depth, end distance and HWE
1822 ------------------------------------------------------------------------
1823 r676 | lh3lh3 | 2010-08-08 02:04:15 -0400 (Sun, 08 Aug 2010) | 2 lines
1825 M /trunk/samtools/bcftools/kfunc.c
1827 reimplement incomplete gamma functions. no copy-paste
1829 ------------------------------------------------------------------------
1830 r675 | lh3lh3 | 2010-08-06 22:42:54 -0400 (Fri, 06 Aug 2010) | 3 lines
1832 M /trunk/samtools/bam2bcf.c
1833 M /trunk/samtools/bam2bcf.h
1834 M /trunk/samtools/bcftools/fet.c
1835 M /trunk/samtools/bcftools/prob1.c
1836 M /trunk/samtools/bcftools/prob1.h
1837 M /trunk/samtools/bcftools/vcfout.c
1839 * bcftools: add HWE (no testing for now)
1840 * record end dist in a 2x2 table, not avg, std any more
1842 ------------------------------------------------------------------------
1843 r674 | lh3lh3 | 2010-08-06 17:30:16 -0400 (Fri, 06 Aug 2010) | 3 lines
1845 A /trunk/samtools/bcftools/kfunc.c
1847 * Special functions: log(gamma()), erfc(), P(a,x) (incomplete gamma)
1848 * Not using Numerical Recipe due to licensing issues
1850 ------------------------------------------------------------------------
1851 r673 | lh3lh3 | 2010-08-05 23:46:53 -0400 (Thu, 05 Aug 2010) | 2 lines
1853 A /trunk/samtools/bcftools/fet.c
1857 ------------------------------------------------------------------------
1858 r672 | lh3lh3 | 2010-08-05 21:48:33 -0400 (Thu, 05 Aug 2010) | 3 lines
1860 M /trunk/samtools/bam2bcf.c
1861 M /trunk/samtools/bam2bcf.h
1862 M /trunk/samtools/bamtk.c
1863 M /trunk/samtools/examples/Makefile
1865 * samtools-0.1.8-11 (r672)
1866 * collect more stats for allele balance test in bcftools (not yet)
1868 ------------------------------------------------------------------------
1869 r671 | lh3lh3 | 2010-08-05 16:17:58 -0400 (Thu, 05 Aug 2010) | 3 lines
1871 M /trunk/samtools/bam_plcmd.c
1872 M /trunk/samtools/bcftools/bcf.c
1873 M /trunk/samtools/bcftools/main.c
1875 * the code base is stablized again.
1876 * I will delay the vcf parser, which is quite complicated but with little value for now
1878 ------------------------------------------------------------------------
1879 r670 | lh3lh3 | 2010-08-05 16:03:23 -0400 (Thu, 05 Aug 2010) | 2 lines
1881 M /trunk/samtools/examples/Makefile
1885 ------------------------------------------------------------------------
1886 r669 | lh3lh3 | 2010-08-05 16:03:08 -0400 (Thu, 05 Aug 2010) | 2 lines
1888 M /trunk/samtools/bcftools/vcf.c
1890 unfinished vcf parser
1892 ------------------------------------------------------------------------
1893 r668 | lh3lh3 | 2010-08-05 15:46:40 -0400 (Thu, 05 Aug 2010) | 3 lines
1895 M /trunk/samtools/bcftools/Makefile
1896 M /trunk/samtools/bcftools/bcf.c
1897 M /trunk/samtools/bcftools/bcf.h
1898 M /trunk/samtools/bcftools/bcfutils.c
1899 M /trunk/samtools/bcftools/index.c
1900 M /trunk/samtools/bcftools/main.c
1901 A /trunk/samtools/bcftools/vcf.c
1902 M /trunk/samtools/bcftools/vcfout.c
1904 * added prelimiary VCF parser (not finished)
1905 * change struct a bit
1907 ------------------------------------------------------------------------
1908 r667 | lh3lh3 | 2010-08-03 22:35:27 -0400 (Tue, 03 Aug 2010) | 3 lines
1910 M /trunk/samtools/bam2bcf.c
1911 M /trunk/samtools/bam2bcf.h
1912 M /trunk/samtools/bam_plcmd.c
1913 M /trunk/samtools/bcftools/bcf.c
1915 * allow to set min base q
1916 * fixed a bug in mpileup -u
1918 ------------------------------------------------------------------------
1919 r666 | lh3lh3 | 2010-08-03 22:08:44 -0400 (Tue, 03 Aug 2010) | 2 lines
1921 A /trunk/samtools/bcftools/bcf.tex
1925 ------------------------------------------------------------------------
1926 r665 | lh3lh3 | 2010-08-03 21:18:57 -0400 (Tue, 03 Aug 2010) | 2 lines
1928 M /trunk/samtools/examples/Makefile
1932 ------------------------------------------------------------------------
1933 r664 | lh3lh3 | 2010-08-03 21:13:00 -0400 (Tue, 03 Aug 2010) | 2 lines
1935 M /trunk/samtools/Makefile
1936 M /trunk/samtools/bam2bcf.c
1937 M /trunk/samtools/bam2bcf.h
1938 M /trunk/samtools/bcftools/Makefile
1940 fixed compilation error
1942 ------------------------------------------------------------------------
1943 r662 | lh3lh3 | 2010-08-03 21:04:00 -0400 (Tue, 03 Aug 2010) | 2 lines
1945 M /trunk/samtools/Makefile
1946 D /trunk/samtools/bcf.c
1947 D /trunk/samtools/bcf.h
1948 A /trunk/samtools/bcftools
1949 A /trunk/samtools/bcftools/Makefile
1950 A /trunk/samtools/bcftools/bcf.c
1951 A /trunk/samtools/bcftools/bcf.h
1952 A /trunk/samtools/bcftools/bcfutils.c
1953 A /trunk/samtools/bcftools/index.c
1954 A /trunk/samtools/bcftools/main.c
1955 A /trunk/samtools/bcftools/prob1.c
1956 A /trunk/samtools/bcftools/prob1.h
1957 A /trunk/samtools/bcftools/vcfout.c
1959 move bcftools to samtools
1961 ------------------------------------------------------------------------
1962 r660 | lh3lh3 | 2010-08-03 15:58:32 -0400 (Tue, 03 Aug 2010) | 2 lines
1964 M /trunk/samtools/bam2bcf.c
1966 fixed another minor bug
1968 ------------------------------------------------------------------------
1969 r658 | lh3lh3 | 2010-08-03 15:06:45 -0400 (Tue, 03 Aug 2010) | 3 lines
1971 M /trunk/samtools/bamtk.c
1972 M /trunk/samtools/bcf.c
1974 * samtools-0.1.8-10 (r658)
1975 * fixed a bug in bam2bcf when the reference is N
1977 ------------------------------------------------------------------------
1978 r657 | lh3lh3 | 2010-08-03 14:50:23 -0400 (Tue, 03 Aug 2010) | 3 lines
1980 M /trunk/samtools/bam2bcf.c
1981 M /trunk/samtools/bam2bcf.h
1984 * treat ambiguous ref base as the fifth base
1986 ------------------------------------------------------------------------
1987 r654 | lh3lh3 | 2010-08-02 17:38:27 -0400 (Mon, 02 Aug 2010) | 2 lines
1989 M /trunk/bcftools/bcf.c
1990 M /trunk/samtools/bcf.c
1992 missing a column in VCF output...
1994 ------------------------------------------------------------------------
1995 r653 | lh3lh3 | 2010-08-02 17:31:33 -0400 (Mon, 02 Aug 2010) | 2 lines
1997 M /trunk/samtools/bcf.c
2001 ------------------------------------------------------------------------
2002 r651 | lh3lh3 | 2010-08-02 17:27:31 -0400 (Mon, 02 Aug 2010) | 2 lines
2004 M /trunk/samtools/bcf.c
2006 fixed a bug in bcf reader
2008 ------------------------------------------------------------------------
2009 r650 | lh3lh3 | 2010-08-02 17:00:41 -0400 (Mon, 02 Aug 2010) | 2 lines
2011 M /trunk/samtools/bam2bcf.c
2015 ------------------------------------------------------------------------
2016 r649 | lh3lh3 | 2010-08-02 16:49:35 -0400 (Mon, 02 Aug 2010) | 3 lines
2018 M /trunk/samtools/Makefile
2019 M /trunk/samtools/bam2bcf.c
2020 M /trunk/samtools/bam2bcf.h
2021 M /trunk/samtools/bamtk.c
2023 * samtools-0.1.8-9 (r649)
2024 * lossless representation of PL in BCF output
2026 ------------------------------------------------------------------------
2027 r648 | lh3lh3 | 2010-08-02 16:07:25 -0400 (Mon, 02 Aug 2010) | 2 lines
2029 M /trunk/samtools/Makefile
2030 A /trunk/samtools/bam2bcf.c
2031 A /trunk/samtools/bam2bcf.h
2032 M /trunk/samtools/bam_plcmd.c
2033 A /trunk/samtools/bcf.c
2034 A /trunk/samtools/bcf.h
2038 ------------------------------------------------------------------------
2039 r644 | lh3lh3 | 2010-07-28 11:59:19 -0400 (Wed, 28 Jul 2010) | 5 lines
2041 M /trunk/samtools/bam_mcns.c
2042 M /trunk/samtools/bamtk.c
2044 * samtools-0.1.8-8 (r644)
2045 * mpileup becomes a little stable again
2046 * the method is slightly different, but is more theoretically correct
2047 * snp calling is O(n^2) instead of O(n^3)
2049 ------------------------------------------------------------------------
2050 r643 | lh3lh3 | 2010-07-28 11:54:15 -0400 (Wed, 28 Jul 2010) | 3 lines
2052 M /trunk/samtools/bam_mcns.c
2054 * fixed a STUPID bug, which cost me a lot of time.
2055 * I am going to clean up mcns a little bit
2057 ------------------------------------------------------------------------
2058 r642 | lh3lh3 | 2010-07-27 23:23:07 -0400 (Tue, 27 Jul 2010) | 2 lines
2060 M /trunk/samtools/bam_mcns.c
2061 M /trunk/samtools/bam_mcns.h
2062 M /trunk/samtools/bam_plcmd.c
2064 supposedly this is THE correct implementation, but more testing is needed
2066 ------------------------------------------------------------------------
2067 r641 | lh3lh3 | 2010-07-27 22:43:39 -0400 (Tue, 27 Jul 2010) | 2 lines
2069 M /trunk/samtools/bam_mcns.c
2071 NOT ready yet. Going to make further changes...
2073 ------------------------------------------------------------------------
2074 r639 | lh3lh3 | 2010-07-25 22:18:38 -0400 (Sun, 25 Jul 2010) | 3 lines
2076 M /trunk/samtools/bam_mcns.c
2077 M /trunk/samtools/bam_plcmd.c
2078 M /trunk/samtools/bamtk.c
2080 * samtools-0.1.8-7 (r639)
2081 * fixed the reference allele assignment
2083 ------------------------------------------------------------------------
2084 r638 | lh3lh3 | 2010-07-25 12:01:26 -0400 (Sun, 25 Jul 2010) | 5 lines
2086 M /trunk/samtools/bam_mcns.c
2087 M /trunk/samtools/bam_mcns.h
2088 M /trunk/samtools/bam_plcmd.c
2089 M /trunk/samtools/bamtk.c
2091 * samtools-0.1.8-6 (r638)
2092 * skip isnan/isinf in case of float underflow
2093 * added the flat prior
2094 * fixed an issue where there are no reads supporting the reference
2096 ------------------------------------------------------------------------
2097 r637 | lh3lh3 | 2010-07-24 14:16:27 -0400 (Sat, 24 Jul 2010) | 2 lines
2099 M /trunk/samtools/bam_plcmd.c
2103 ------------------------------------------------------------------------
2104 r636 | lh3lh3 | 2010-07-24 14:07:27 -0400 (Sat, 24 Jul 2010) | 2 lines
2106 M /trunk/samtools/bam_mcns.c
2107 M /trunk/samtools/bam_mcns.h
2108 M /trunk/samtools/bam_plcmd.c
2109 M /trunk/samtools/bamtk.c
2113 ------------------------------------------------------------------------
2114 r635 | lh3lh3 | 2010-07-24 01:49:49 -0400 (Sat, 24 Jul 2010) | 2 lines
2116 M /trunk/samtools/bam_mcns.c
2117 M /trunk/samtools/bam_mcns.h
2118 M /trunk/samtools/bam_plcmd.c
2120 posterior expectation FINALLY working. I am so tired...
2122 ------------------------------------------------------------------------
2123 r633 | lh3lh3 | 2010-07-23 13:50:48 -0400 (Fri, 23 Jul 2010) | 2 lines
2125 M /trunk/samtools/bam_plcmd.c
2127 another minor fix to mpileup
2129 ------------------------------------------------------------------------
2130 r632 | lh3lh3 | 2010-07-23 13:43:31 -0400 (Fri, 23 Jul 2010) | 2 lines
2132 M /trunk/samtools/bam_plcmd.c
2134 added the format column
2136 ------------------------------------------------------------------------
2137 r631 | lh3lh3 | 2010-07-23 13:25:44 -0400 (Fri, 23 Jul 2010) | 2 lines
2139 M /trunk/samtools/bam_mcns.c
2140 M /trunk/samtools/bam_mcns.h
2141 M /trunk/samtools/bam_plcmd.c
2142 M /trunk/samtools/bamtk.c
2144 added an alternative prior
2146 ------------------------------------------------------------------------
2147 r628 | lh3lh3 | 2010-07-23 11:48:51 -0400 (Fri, 23 Jul 2010) | 2 lines
2149 M /trunk/samtools/bam_mcns.c
2150 M /trunk/samtools/bam_mcns.h
2151 M /trunk/samtools/bam_plcmd.c
2153 calculate posterior allele frequency
2155 ------------------------------------------------------------------------
2156 r627 | lh3lh3 | 2010-07-22 21:39:13 -0400 (Thu, 22 Jul 2010) | 3 lines
2158 M /trunk/samtools/bam_mcns.c
2159 M /trunk/samtools/bam_plcmd.c
2160 M /trunk/samtools/bamtk.c
2162 * samtools-0.1.8-3 (r627)
2163 * multi-sample snp calling appears to work. More tests needed.
2165 ------------------------------------------------------------------------
2166 r626 | lh3lh3 | 2010-07-22 16:37:56 -0400 (Thu, 22 Jul 2010) | 3 lines
2168 M /trunk/samtools/bam_mcns.c
2169 M /trunk/samtools/bam_mcns.h
2170 M /trunk/samtools/bam_plcmd.c
2171 M /trunk/samtools/bam_tview.c
2173 * preliminary multisample SNP caller.
2174 * something looks not so right, but it largely works
2176 ------------------------------------------------------------------------
2177 r617 | lh3lh3 | 2010-07-14 16:26:27 -0400 (Wed, 14 Jul 2010) | 3 lines
2179 M /trunk/samtools/bam_mcns.c
2180 M /trunk/samtools/bam_plcmd.c
2181 M /trunk/samtools/bamtk.c
2183 * samtools-0.1.8-2 (r617)
2184 * allele frequency calculation apparently works...
2186 ------------------------------------------------------------------------
2187 r616 | lh3lh3 | 2010-07-14 13:33:51 -0400 (Wed, 14 Jul 2010) | 3 lines
2189 M /trunk/samtools/Makefile
2190 A /trunk/samtools/bam_mcns.c
2191 A /trunk/samtools/bam_mcns.h
2192 M /trunk/samtools/bam_plcmd.c
2194 * added mutli-sample framework. It is not working, yet.
2195 * improved the mpileup interface
2197 ------------------------------------------------------------------------
2198 r615 | lh3lh3 | 2010-07-13 14:50:12 -0400 (Tue, 13 Jul 2010) | 3 lines
2200 M /trunk/samtools/bam_plcmd.c
2201 M /trunk/samtools/bamtk.c
2202 M /trunk/samtools/misc/Makefile
2204 * samtools-0.1.8-1 (r615)
2205 * allow to get mpileup at required sites
2207 ------------------------------------------------------------------------
2208 r613 | lh3lh3 | 2010-07-11 22:40:56 -0400 (Sun, 11 Jul 2010) | 2 lines
2210 M /trunk/samtools/ChangeLog
2211 M /trunk/samtools/NEWS
2212 M /trunk/samtools/bam_plcmd.c
2213 M /trunk/samtools/bamtk.c
2214 M /trunk/samtools/samtools.1
2216 Release samtools-0.1.8
2218 ------------------------------------------------------------------------
2219 r612 | lh3lh3 | 2010-07-11 21:08:56 -0400 (Sun, 11 Jul 2010) | 2 lines
2221 M /trunk/samtools/knetfile.c
2223 fixed a compiling issue for Windows
2225 ------------------------------------------------------------------------
2226 r611 | lh3lh3 | 2010-07-11 20:59:15 -0400 (Sun, 11 Jul 2010) | 2 lines
2228 M /trunk/samtools/bam_sort.c
2230 fixed a bug in sorting when output to stdout (by Peter Chines)
2232 ------------------------------------------------------------------------
2233 r610 | lh3lh3 | 2010-07-09 17:05:10 -0400 (Fri, 09 Jul 2010) | 2 lines
2235 M /trunk/samtools/NEWS
2236 M /trunk/samtools/bam_plcmd.c
2238 change the command line option of pileup
2240 ------------------------------------------------------------------------
2241 r609 | lh3lh3 | 2010-07-09 00:39:34 -0400 (Fri, 09 Jul 2010) | 2 lines
2243 M /trunk/samtools/bam_pileup.c
2244 A /trunk/samtools/examples/toy.fa
2245 A /trunk/samtools/examples/toy.sam
2247 make pileup work with CIGAR with I/D at the beginning or in the end
2249 ------------------------------------------------------------------------
2250 r608 | lh3lh3 | 2010-07-08 22:36:12 -0400 (Thu, 08 Jul 2010) | 3 lines
2252 M /trunk/samtools/bam_maqcns.c
2253 M /trunk/samtools/bam_maqcns.h
2254 M /trunk/samtools/bam_plcmd.c
2255 M /trunk/samtools/bam_tview.c
2257 * make tview more friendly
2258 * a temporary remedy for an issue in indel calling
2260 ------------------------------------------------------------------------
2261 r607 | lh3lh3 | 2010-07-08 14:43:52 -0400 (Thu, 08 Jul 2010) | 4 lines
2263 M /trunk/samtools/bam_maqcns.c
2264 M /trunk/samtools/bam_plcmd.c
2265 M /trunk/samtools/bamtk.c
2267 * samtools-0.1.7-r607
2268 * improved the genotype accuracy for indels
2269 * use the SOAPsnp model for SNP calling by default.
2271 ------------------------------------------------------------------------
2272 r606 | lh3lh3 | 2010-07-08 01:05:19 -0400 (Thu, 08 Jul 2010) | 2 lines
2274 M /trunk/samtools/misc/Makefile
2276 removed a debugging example
2278 ------------------------------------------------------------------------
2279 r605 | lh3lh3 | 2010-07-08 01:04:09 -0400 (Thu, 08 Jul 2010) | 4 lines
2281 M /trunk/samtools/bam_maqcns.c
2282 M /trunk/samtools/bamtk.c
2284 * samtools-.1.7-18 (r605)
2285 * fixed an issue when a deletion and mismatch occur at the same time
2286 and the base quality is higher than 40 (if -I40).
2288 ------------------------------------------------------------------------
2289 r604 | lh3lh3 | 2010-07-02 19:32:24 -0400 (Fri, 02 Jul 2010) | 2 lines
2291 M /trunk/samtools/bam.h
2292 M /trunk/samtools/bam_index.c
2293 M /trunk/samtools/misc/Makefile
2295 fixed a minor bug in idxstats
2297 ------------------------------------------------------------------------
2298 r601 | lh3lh3 | 2010-06-16 09:03:59 -0400 (Wed, 16 Jun 2010) | 2 lines
2300 M /trunk/samtools/bam_index.c
2302 fixed a minor bug in indexing
2304 ------------------------------------------------------------------------
2305 r600 | lh3lh3 | 2010-06-15 10:17:53 -0400 (Tue, 15 Jun 2010) | 2 lines
2307 M /trunk/samtools/ChangeLog
2308 M /trunk/samtools/bam.c
2310 change printf() to puts in exporting
2312 ------------------------------------------------------------------------
2313 r599 | lh3lh3 | 2010-06-13 21:41:11 -0400 (Sun, 13 Jun 2010) | 2 lines
2315 M /trunk/samtools/bamtk.c
2317 minor fix. No actual effect.
2319 ------------------------------------------------------------------------
2320 r598 | lh3lh3 | 2010-06-13 21:32:45 -0400 (Sun, 13 Jun 2010) | 2 lines
2322 M /trunk/samtools/Makefile
2324 added Makefile targets to compile shared/dynamic library
2326 ------------------------------------------------------------------------
2327 r596 | lh3lh3 | 2010-06-13 19:48:07 -0400 (Sun, 13 Jun 2010) | 3 lines
2329 M /trunk/samtools/ChangeLog
2330 M /trunk/samtools/bam_index.c
2331 M /trunk/samtools/bamtk.c
2333 * samtools-0.1.7-17 (r596)
2334 * also keep the number of coor-less reads in the index file
2336 ------------------------------------------------------------------------
2337 r595 | lh3lh3 | 2010-06-13 18:54:26 -0400 (Sun, 13 Jun 2010) | 3 lines
2339 M /trunk/samtools/bam_index.c
2340 M /trunk/samtools/bamtk.c
2342 * samtools-0.1.7-16 (r595)
2343 * write additional information to bam index
2345 ------------------------------------------------------------------------
2346 r594 | lh3lh3 | 2010-06-13 17:29:52 -0400 (Sun, 13 Jun 2010) | 2 lines
2348 M /trunk/samtools/bam_index.c
2350 fixed a bug for unmapped sequences in indexing
2352 ------------------------------------------------------------------------
2353 r593 | lh3lh3 | 2010-06-12 18:11:32 -0400 (Sat, 12 Jun 2010) | 2 lines
2355 M /trunk/samtools/bam.h
2356 M /trunk/samtools/bam_index.c
2357 M /trunk/samtools/bam_plcmd.c
2358 M /trunk/samtools/samtools.1
2360 rename iterf as iter
2362 ------------------------------------------------------------------------
2363 r592 | lh3lh3 | 2010-06-12 18:02:38 -0400 (Sat, 12 Jun 2010) | 4 lines
2365 M /trunk/samtools/ChangeLog
2366 M /trunk/samtools/bam_aux.c
2367 M /trunk/samtools/bam_index.c
2368 M /trunk/samtools/bam_pileup.c
2369 M /trunk/samtools/bam_plcmd.c
2370 M /trunk/samtools/bamtk.c
2372 * samtools-0.1.7-15 (r592)
2373 * fixed a few minor memory leaks in the new pileup code
2374 * improved the functionality of mpileup
2376 ------------------------------------------------------------------------
2377 r591 | lh3lh3 | 2010-06-12 14:09:22 -0400 (Sat, 12 Jun 2010) | 3 lines
2379 M /trunk/samtools/bam.h
2380 M /trunk/samtools/bam_pileup.c
2381 M /trunk/samtools/bam_plcmd.c
2382 M /trunk/samtools/bamtk.c
2384 * samtools-0.1.7-14 (r591)
2385 * elementary multi-way pileup. More testing and more functionality to be done.
2387 ------------------------------------------------------------------------
2388 r590 | lh3lh3 | 2010-06-12 01:00:24 -0400 (Sat, 12 Jun 2010) | 3 lines
2390 M /trunk/samtools/bam.h
2391 M /trunk/samtools/bam_pileup.c
2392 M /trunk/samtools/bamtk.c
2394 * samtools-0.1.7-13 (r590)
2395 * added mpileup APIs. No compiling errors, but not tested at all. It is late.
2397 ------------------------------------------------------------------------
2398 r589 | lh3lh3 | 2010-06-11 22:37:09 -0400 (Fri, 11 Jun 2010) | 3 lines
2400 M /trunk/samtools/bam.h
2401 M /trunk/samtools/bam_pileup.c
2402 M /trunk/samtools/bamtk.c
2404 * samtools-0.1.7-12 (r589)
2405 * added iterator-like APIs for pileup
2407 ------------------------------------------------------------------------
2408 r588 | lh3lh3 | 2010-06-11 17:41:13 -0400 (Fri, 11 Jun 2010) | 3 lines
2410 M /trunk/samtools/bam_index.c
2411 M /trunk/samtools/bamtk.c
2413 * samtools-0.1.7-11 (r588)
2414 * ported a few improvements from tabix back to samtools
2416 ------------------------------------------------------------------------
2417 r587 | lh3lh3 | 2010-06-11 17:33:16 -0400 (Fri, 11 Jun 2010) | 3 lines
2419 M /trunk/samtools/bam.h
2420 M /trunk/samtools/bam_index.c
2421 M /trunk/samtools/bamtk.c
2423 * samtools-0.1.7-10 (r587)
2424 * added iterator interface for bam_fetch (ported back from tabix)
2426 ------------------------------------------------------------------------
2427 r586 | lh3lh3 | 2010-06-11 13:23:53 -0400 (Fri, 11 Jun 2010) | 3 lines
2429 M /trunk/samtools/Makefile
2430 A /trunk/samtools/bam_reheader.c
2431 M /trunk/samtools/bamtk.c
2432 M /trunk/samtools/bgzf.c
2434 * samtools-0.1.7-9 (r586)
2435 * added "reheader" to replace the BAM header
2437 ------------------------------------------------------------------------
2438 r585 | lh3lh3 | 2010-06-11 12:22:06 -0400 (Fri, 11 Jun 2010) | 3 lines
2440 M /trunk/samtools/bam.c
2441 M /trunk/samtools/bamtk.c
2442 M /trunk/samtools/kstring.h
2444 * samtools-0.1.7-8 (r585)
2447 ------------------------------------------------------------------------
2448 r584 | lh3lh3 | 2010-06-11 12:00:41 -0400 (Fri, 11 Jun 2010) | 4 lines
2450 M /trunk/samtools/bam.c
2451 M /trunk/samtools/bamtk.c
2452 M /trunk/samtools/bgzf.c
2453 M /trunk/samtools/bgzf.h
2454 M /trunk/samtools/kstring.h
2455 M /trunk/samtools/misc/wgsim_eval.pl
2457 * samtools-0.1.7-7 (r584)
2458 * ported tabix BGZF to samtools
2459 * flush BGZF after writing the BAM header and between alignment boundaries
2461 ------------------------------------------------------------------------
2462 r583 | petulda | 2010-06-11 11:58:20 -0400 (Fri, 11 Jun 2010) | 1 line
2464 A /trunk/samtools/misc/varfilter.py
2466 Initial release on behalf of Aylwyn Scally
2467 ------------------------------------------------------------------------
2468 r561 | petulda | 2010-05-07 08:41:56 -0400 (Fri, 07 May 2010) | 1 line
2470 M /trunk/samtools/samtools.1
2472 Added a note about the indels coordinates
2473 ------------------------------------------------------------------------
2474 r551 | petulda | 2010-04-23 09:42:13 -0400 (Fri, 23 Apr 2010) | 1 line
2476 M /trunk/samtools/misc/sam2vcf.pl
2478 Added the possibility to print or not to print the reference allele
2479 ------------------------------------------------------------------------
2480 r546 | petulda | 2010-04-15 04:33:55 -0400 (Thu, 15 Apr 2010) | 1 line
2482 M /trunk/samtools/sam_header.c
2484 More descriptive message for space separated tags
2485 ------------------------------------------------------------------------
2486 r545 | petulda | 2010-04-14 11:44:50 -0400 (Wed, 14 Apr 2010) | 1 line
2488 M /trunk/samtools/misc/sam2vcf.pl
2490 Speedup with -i, no need to query the reference all the time
2491 ------------------------------------------------------------------------
2492 r541 | petulda | 2010-03-15 10:03:51 -0400 (Mon, 15 Mar 2010) | 1 line
2494 M /trunk/samtools/sam_header.c
2496 Fixed the order of sequences in the header
2497 ------------------------------------------------------------------------
2498 r540 | petulda | 2010-03-04 06:28:35 -0500 (Thu, 04 Mar 2010) | 1 line
2500 M /trunk/samtools/misc/sam2vcf.pl
2502 Added possibility to select indels only and fixed a bug in reporting homozygous indels.
2503 ------------------------------------------------------------------------
2504 r539 | jmarshall | 2010-02-27 06:48:17 -0500 (Sat, 27 Feb 2010) | 4 lines
2506 M /trunk/samtools/bam.c
2508 Improve the invalid 'BAM\1' magic number error message, and also print it
2509 when no bytes can be read from the alleged BAM file, e.g., in the common
2510 user error case when a SAM file has accidentally been supplied.
2512 ------------------------------------------------------------------------
2513 r538 | petulda | 2010-02-26 10:51:40 -0500 (Fri, 26 Feb 2010) | 1 line
2515 M /trunk/samtools/AUTHORS
2516 M /trunk/samtools/bam.h
2517 M /trunk/samtools/bam_import.c
2518 M /trunk/samtools/sam_header.c
2520 Improved efficiency of header parsing
2521 ------------------------------------------------------------------------
2522 r537 | lh3lh3 | 2010-02-23 21:08:48 -0500 (Tue, 23 Feb 2010) | 3 lines
2524 M /trunk/samtools/misc/export2sam.pl
2526 Updated export2sam.pl by Chris Saunders from Illumina.
2529 ------------------------------------------------------------------------
2530 r536 | petulda | 2010-02-17 08:32:53 -0500 (Wed, 17 Feb 2010) | 1 line
2532 M /trunk/samtools/misc/samtools.pl
2534 Fixed filtering of SNPs near indels. Added min indel and SNP quality filter.
2535 ------------------------------------------------------------------------
2536 r535 | petulda | 2010-02-12 04:52:37 -0500 (Fri, 12 Feb 2010) | 1 line
2538 M /trunk/samtools/misc/sam2vcf.pl
2540 Print an error for pileups in simple format
2541 ------------------------------------------------------------------------
2542 r534 | lh3lh3 | 2010-02-11 14:01:41 -0500 (Thu, 11 Feb 2010) | 2 lines
2544 M /trunk/samtools/bam_plcmd.c
2546 added a hidden option in pileup to output the base position (for Erin)
2548 ------------------------------------------------------------------------
2549 r533 | petulda | 2010-02-09 10:12:14 -0500 (Tue, 09 Feb 2010) | 1 line
2551 M /trunk/samtools/misc/sam2vcf.pl
2553 Added possibility to specify a custom column title for the data column
2554 ------------------------------------------------------------------------
2555 r532 | petulda | 2010-02-09 09:46:09 -0500 (Tue, 09 Feb 2010) | 1 line
2557 M /trunk/samtools/bam_plcmd.c
2559 Added the -d option to limit maximum depth for indels.
2560 ------------------------------------------------------------------------
2561 r531 | petulda | 2010-02-03 07:57:27 -0500 (Wed, 03 Feb 2010) | 1 line
2563 M /trunk/samtools/misc/sam2vcf.pl
2566 ------------------------------------------------------------------------
2567 r530 | lh3lh3 | 2010-02-01 09:13:19 -0500 (Mon, 01 Feb 2010) | 3 lines
2569 M /trunk/samtools/ChangeLog
2570 M /trunk/samtools/bam_plcmd.c
2571 M /trunk/samtools/bamtk.c
2572 M /trunk/samtools/misc/samtools.pl
2573 M /trunk/samtools/misc/wgsim.c
2576 * fixed a bug in faidx
2578 ------------------------------------------------------------------------
2579 r529 | jmarshall | 2010-01-11 18:51:49 -0500 (Mon, 11 Jan 2010) | 2 lines
2581 M /trunk/samtools/faidx.c
2583 Put the right filename in the error message.
2585 ------------------------------------------------------------------------
2586 r528 | lh3lh3 | 2009-12-14 11:26:47 -0500 (Mon, 14 Dec 2009) | 3 lines
2588 M /trunk/samtools/bam_plcmd.c
2589 M /trunk/samtools/bamtk.c
2591 * samtools-0.1.7-5 (r528)
2592 * further add new consensus generation strategy
2594 ------------------------------------------------------------------------
2595 r527 | petulda | 2009-12-11 12:31:05 -0500 (Fri, 11 Dec 2009) | 1 line
2597 M /trunk/samtools/knetfile.c
2599 Fixed a bug in knet_seek
2600 ------------------------------------------------------------------------
2601 r526 | petulda | 2009-12-11 07:51:18 -0500 (Fri, 11 Dec 2009) | 1 line
2603 M /trunk/samtools/misc/sam2vcf.pl
2605 Small fix in VCF format: dot for the empty INFO field
2606 ------------------------------------------------------------------------
2607 r525 | petulda | 2009-12-11 04:36:18 -0500 (Fri, 11 Dec 2009) | 1 line
2609 M /trunk/samtools/sam_header.c
2611 Allow tabs in the CO header field
2612 ------------------------------------------------------------------------
2613 r524 | jmarshall | 2009-12-10 10:03:58 -0500 (Thu, 10 Dec 2009) | 3 lines
2615 M /trunk/samtools/Makefile
2616 M /trunk/samtools/Makefile.mingw
2618 Depend on libbam.a rather than the phony target, so that samtools is not
2619 unnecessarily rebuilt every time. Also clean bgzip.
2621 ------------------------------------------------------------------------
2622 r523 | jmarshall | 2009-12-10 09:45:32 -0500 (Thu, 10 Dec 2009) | 4 lines
2624 M /trunk/samtools/Makefile
2625 M /trunk/samtools/Makefile.mingw
2627 Fix a bug in compiling bgzip: this also needs knetfile.o when _USE_KNETFILE
2628 is defined. Also introduce $(KNETFILE_O) which can be set to empty to
2629 facilitate non-knet builds.
2631 ------------------------------------------------------------------------
2632 r522 | lh3lh3 | 2009-12-01 13:02:36 -0500 (Tue, 01 Dec 2009) | 4 lines
2634 M /trunk/samtools/bamtk.c
2635 M /trunk/samtools/sam_view.c
2637 * samtools-0.1.7-4 (r522)
2638 * fixed a bug in "view -r"
2639 * added a new option "view -R" to read required read groups from a file
2641 ------------------------------------------------------------------------
2642 r521 | lh3lh3 | 2009-12-01 10:00:12 -0500 (Tue, 01 Dec 2009) | 3 lines
2644 M /trunk/samtools/bam_md.c
2645 M /trunk/samtools/bamtk.c
2647 * samtools-0.1.7-3 (r521)
2648 * calmd: optionally mask matching bases as N
2650 ------------------------------------------------------------------------
2651 r520 | lh3lh3 | 2009-12-01 09:37:17 -0500 (Tue, 01 Dec 2009) | 4 lines
2653 M /trunk/samtools/bam_plcmd.c
2654 M /trunk/samtools/bamtk.c
2655 M /trunk/samtools/misc/samtools.pl
2657 * samtools-0.1.7-2 (r520)
2658 * fixed a few issues with compilation in Windows (on behalf of John)
2659 * choose a random base as the consensus (for population genetics studies)
2661 ------------------------------------------------------------------------
2662 r519 | jmarshall | 2009-11-30 10:53:02 -0500 (Mon, 30 Nov 2009) | 6 lines
2664 M /trunk/samtools/Makefile
2666 Put libraries at the end, so they can resolve references from libbam.a
2667 as well, even with old-fashioned linkers.
2669 Also use libbam.a explicitly rather than "-L. -lbam" to ensure that we get
2670 the freshly built library, not some other libbam.a lying around the system.
2672 ------------------------------------------------------------------------
2673 r518 | jmarshall | 2009-11-30 08:44:56 -0500 (Mon, 30 Nov 2009) | 2 lines
2675 M /trunk/samtools/Makefile
2676 M /trunk/samtools/misc/Makefile
2678 Also clean *.exe (for Cygwin users using this makefile).
2680 ------------------------------------------------------------------------
2681 r517 | jmarshall | 2009-11-30 07:09:04 -0500 (Mon, 30 Nov 2009) | 2 lines
2683 M /trunk/samtools/bam_index.c
2685 Index files should be opened in binary mode, not text mode.
2687 ------------------------------------------------------------------------
2688 r516 | lh3lh3 | 2009-11-27 15:18:59 -0500 (Fri, 27 Nov 2009) | 2 lines
2690 A /trunk/samtools/examples/bam2bed.c
2692 another example program
2694 ------------------------------------------------------------------------
2695 r515 | lh3lh3 | 2009-11-27 10:44:56 -0500 (Fri, 27 Nov 2009) | 3 lines
2697 M /trunk/samtools/bam_import.c
2698 M /trunk/samtools/bamtk.c
2699 M /trunk/samtools/misc/wgsim_eval.pl
2700 M /trunk/samtools/sam.c
2702 * samtools-0.1.7-1 (r515)
2703 * report an error when .fai contains duplicated names, instead of segfault
2705 ------------------------------------------------------------------------
2706 r514 | jmarshall | 2009-11-24 09:45:35 -0500 (Tue, 24 Nov 2009) | 2 lines
2708 M /trunk/samtools/bam.c
2710 Format 'c'-encoded auxiliary fields correctly, as *signed* integers.
2712 ------------------------------------------------------------------------
2713 r513 | lh3lh3 | 2009-11-16 10:13:07 -0500 (Mon, 16 Nov 2009) | 2 lines
2715 M /trunk/samtools/Makefile.mingw
2717 Update Makefile.mingw for the same reason
2719 ------------------------------------------------------------------------
2720 r512 | lh3lh3 | 2009-11-16 10:00:08 -0500 (Mon, 16 Nov 2009) | 2 lines
2722 M /trunk/samtools/Makefile
2724 Fixed a bug in compiling razip
2726 ------------------------------------------------------------------------
2727 r510 | lh3lh3 | 2009-11-10 10:55:41 -0500 (Tue, 10 Nov 2009) | 2 lines
2729 M /trunk/samtools/ChangeLog
2730 M /trunk/samtools/NEWS
2731 M /trunk/samtools/bamtk.c
2732 M /trunk/samtools/samtools.1
2734 Release samtools-0.1.7 (r510)
2736 ------------------------------------------------------------------------
2737 r509 | lh3lh3 | 2009-11-06 09:17:09 -0500 (Fri, 06 Nov 2009) | 3 lines
2739 M /trunk/samtools/bam_plcmd.c
2740 M /trunk/samtools/bamtk.c
2742 * samtools-0.1.6-22 (r509)
2743 * forget to fix a similar problem in glfgen
2745 ------------------------------------------------------------------------
2746 r508 | lh3lh3 | 2009-11-06 09:06:40 -0500 (Fri, 06 Nov 2009) | 3 lines
2748 M /trunk/samtools/bam_maqcns.c
2749 M /trunk/samtools/bam_plcmd.c
2750 M /trunk/samtools/bamtk.c
2751 M /trunk/samtools/sam_view.c
2753 * samtools-0.1.6-21 (r508)
2754 * fixed a potential bug in the indel caller towards the end of a chromosome
2756 ------------------------------------------------------------------------
2757 r494 | lh3lh3 | 2009-10-26 11:38:00 -0400 (Mon, 26 Oct 2009) | 3 lines
2759 M /trunk/samtools/bamtk.c
2760 M /trunk/samtools/sam_view.c
2762 * samtools-0.1.6-19 (r494)
2763 * allow to convert Illumina quality (64 based) to the BAM quality
2765 ------------------------------------------------------------------------
2766 r493 | lh3lh3 | 2009-10-26 10:24:39 -0400 (Mon, 26 Oct 2009) | 4 lines
2768 M /trunk/samtools/Makefile
2769 M /trunk/samtools/bam.c
2770 M /trunk/samtools/bam_import.c
2771 M /trunk/samtools/bamtk.c
2772 M /trunk/samtools/sam.c
2773 M /trunk/samtools/sam_header.c
2775 * samtools-0.1.6-18 (r493)
2776 * fixed the bugs due to improperly incorporating Petr's header parser
2777 * a little code clean up in sam_header.c
2779 ------------------------------------------------------------------------
2780 r492 | petulda | 2009-10-24 09:43:25 -0400 (Sat, 24 Oct 2009) | 1 line
2782 M /trunk/samtools/sam_header.c
2784 Added sam_header_line_free call for sam_header_parse2
2785 ------------------------------------------------------------------------
2786 r491 | lh3lh3 | 2009-10-24 00:50:16 -0400 (Sat, 24 Oct 2009) | 3 lines
2788 M /trunk/samtools/sam_view.c
2793 ------------------------------------------------------------------------
2794 r490 | lh3lh3 | 2009-10-24 00:45:12 -0400 (Sat, 24 Oct 2009) | 4 lines
2796 M /trunk/samtools/bam.c
2797 M /trunk/samtools/bam.h
2798 M /trunk/samtools/bam_import.c
2799 M /trunk/samtools/sam.c
2802 * improved the interface a bit
2805 ------------------------------------------------------------------------
2806 r489 | lh3lh3 | 2009-10-24 00:41:50 -0400 (Sat, 24 Oct 2009) | 3 lines
2808 M /trunk/samtools/bam_import.c
2809 M /trunk/samtools/sam_header.c
2810 M /trunk/samtools/sam_header.h
2812 * BUGGY VERSION. Please NOT use it.
2813 * Fixed a minor bug, but the major bug is still there.
2815 ------------------------------------------------------------------------
2816 r488 | lh3lh3 | 2009-10-24 00:17:10 -0400 (Sat, 24 Oct 2009) | 3 lines
2818 M /trunk/samtools/Makefile
2819 M /trunk/samtools/bam.c
2820 M /trunk/samtools/bam.h
2821 M /trunk/samtools/bam_aux.c
2822 M /trunk/samtools/bam_import.c
2823 M /trunk/samtools/bam_rmdup.c
2824 M /trunk/samtools/bam_rmdupse.c
2825 M /trunk/samtools/kaln.c
2826 M /trunk/samtools/sam.c
2827 M /trunk/samtools/sam_header.c
2828 M /trunk/samtools/sam_header.h
2829 M /trunk/samtools/sam_view.c
2831 * This revision is SERIOUSLY BUGGY. Please NOT use it.
2832 * Start to incorporate header parsing from Petr Danecek
2834 ------------------------------------------------------------------------
2835 r487 | petulda | 2009-10-23 11:44:32 -0400 (Fri, 23 Oct 2009) | 1 line
2837 M /trunk/samtools/sam_header.c
2838 M /trunk/samtools/sam_header.h
2840 Now possible to merge multiple HeaderDict dictionaries
2841 ------------------------------------------------------------------------
2842 r486 | petulda | 2009-10-22 11:46:58 -0400 (Thu, 22 Oct 2009) | 1 line
2844 M /trunk/samtools/sam_header.c
2847 ------------------------------------------------------------------------
2848 r485 | petulda | 2009-10-22 11:41:56 -0400 (Thu, 22 Oct 2009) | 1 line
2850 A /trunk/samtools/sam_header.c
2851 A /trunk/samtools/sam_header.h
2854 ------------------------------------------------------------------------
2855 r484 | lh3lh3 | 2009-10-19 14:31:32 -0400 (Mon, 19 Oct 2009) | 5 lines
2857 M /trunk/samtools/bam_import.c
2858 M /trunk/samtools/bam_rmdupse.c
2859 M /trunk/samtools/bamtk.c
2860 M /trunk/samtools/examples/Makefile
2862 * samtools-0.1.6-17 (r484)
2863 * fixed a memory leak in rmdupse
2864 * fixed a bug in parsing @RG header lines
2865 * test rmdup in examples/
2867 ------------------------------------------------------------------------
2868 r483 | lh3lh3 | 2009-10-19 13:22:48 -0400 (Mon, 19 Oct 2009) | 4 lines
2870 M /trunk/samtools/bam_rmdup.c
2871 M /trunk/samtools/bam_rmdupse.c
2872 M /trunk/samtools/bamtk.c
2874 * samtools-0.1.6-16 (r483)
2875 * unify the interface of rmdup and rmdupse
2876 * a new bug found in rg2lib(). Have not been fixed yet.
2878 ------------------------------------------------------------------------
2879 r482 | lh3lh3 | 2009-10-19 13:03:34 -0400 (Mon, 19 Oct 2009) | 4 lines
2881 M /trunk/samtools/bam.h
2882 M /trunk/samtools/bam_rmdup.c
2883 M /trunk/samtools/bam_rmdupse.c
2884 M /trunk/samtools/bamtk.c
2885 A /trunk/samtools/klist.h
2887 * samtools-0.1.6-15 (r482)
2889 * rmdupse is now library aware
2891 ------------------------------------------------------------------------
2892 r481 | lh3lh3 | 2009-10-18 00:07:21 -0400 (Sun, 18 Oct 2009) | 3 lines
2894 M /trunk/samtools/bam_rmdup.c
2895 M /trunk/samtools/bamtk.c
2897 * samtools-0.1.6-14 (r480)
2898 * rmdup is now RG aware
2900 ------------------------------------------------------------------------
2901 r480 | lh3lh3 | 2009-10-17 22:05:20 -0400 (Sat, 17 Oct 2009) | 2 lines
2903 M /trunk/samtools/misc/samtools.pl
2905 added a small unitity to parse SRA XML files
2907 ------------------------------------------------------------------------
2908 r479 | lh3lh3 | 2009-10-17 20:57:26 -0400 (Sat, 17 Oct 2009) | 3 lines
2910 M /trunk/samtools/bam_maqcns.c
2911 M /trunk/samtools/bam_maqcns.h
2912 M /trunk/samtools/bam_plcmd.c
2913 M /trunk/samtools/bam_sort.c
2914 M /trunk/samtools/bamtk.c
2916 * samtools-0.1.6-13 (r479)
2917 * merge: optionally use file names as RG tags
2919 ------------------------------------------------------------------------
2920 r478 | lh3lh3 | 2009-10-14 14:18:12 -0400 (Wed, 14 Oct 2009) | 3 lines
2922 M /trunk/samtools/bam.c
2923 M /trunk/samtools/bam.h
2924 M /trunk/samtools/bam_maqcns.c
2925 M /trunk/samtools/bamtk.c
2926 M /trunk/samtools/kaln.c
2928 * samtools-0.1.6-12 (r478)
2929 * fixed a bug in the indel caller
2931 ------------------------------------------------------------------------
2932 r477 | lh3lh3 | 2009-10-10 06:12:26 -0400 (Sat, 10 Oct 2009) | 3 lines
2934 M /trunk/samtools/bam_index.c
2935 M /trunk/samtools/bamtk.c
2937 * samtools-0.1.6-11 (r477)
2938 * fixed a bug due to recent change in bam_index.c (thank Nicole Washington for the patch)
2940 ------------------------------------------------------------------------
2941 r476 | petulda | 2009-10-09 11:45:36 -0400 (Fri, 09 Oct 2009) | 1 line
2943 A /trunk/samtools/misc/sam2vcf.pl
2945 Added the sam2vcf.pl script.
2946 ------------------------------------------------------------------------
2947 r475 | lh3lh3 | 2009-10-08 10:19:16 -0400 (Thu, 08 Oct 2009) | 2 lines
2949 M /trunk/samtools/Makefile
2950 M /trunk/samtools/bam.c
2951 M /trunk/samtools/bam.h
2952 M /trunk/samtools/bam_maqcns.c
2953 M /trunk/samtools/bamtk.c
2954 A /trunk/samtools/kaln.c
2955 A /trunk/samtools/kaln.h
2957 Unfinished modification. Please do not use this revision...
2959 ------------------------------------------------------------------------
2960 r474 | petulda | 2009-10-08 06:39:54 -0400 (Thu, 08 Oct 2009) | 1 line
2962 M /trunk/samtools/knetfile.c
2964 Removed the offending knet_seek message.
2965 ------------------------------------------------------------------------
2966 r473 | petulda | 2009-10-06 09:26:35 -0400 (Tue, 06 Oct 2009) | 1 line
2968 M /trunk/samtools/knetfile.c
2969 M /trunk/samtools/razf.c
2971 Bug fix - faidx on RAZF compressed files now working.
2972 ------------------------------------------------------------------------
2973 r472 | lh3lh3 | 2009-10-02 08:42:57 -0400 (Fri, 02 Oct 2009) | 2 lines
2975 M /trunk/samtools/samtools.1
2977 Clarify the meaning of a region like "chr2:1,000,000".
2979 ------------------------------------------------------------------------
2980 r471 | lh3lh3 | 2009-10-02 05:42:19 -0400 (Fri, 02 Oct 2009) | 2 lines
2982 M /trunk/samtools/misc/novo2sam.pl
2984 Fixed minor bugs in novo2sam.pl (on behalf of Ken Chen and Colin Hercus)
2986 ------------------------------------------------------------------------
2987 r470 | lh3lh3 | 2009-09-29 15:01:27 -0400 (Tue, 29 Sep 2009) | 3 lines
2989 M /trunk/samtools/Makefile.mingw
2990 M /trunk/samtools/bamtk.c
2991 M /trunk/samtools/knetfile.c
2992 M /trunk/samtools/knetfile.h
2994 * samtools-0.1.6-9 (r470)
2995 * make knetfile.c compatible with MinGW (thank Martin Morgan for the patch)
2997 ------------------------------------------------------------------------
2998 r469 | lh3lh3 | 2009-09-29 08:07:44 -0400 (Tue, 29 Sep 2009) | 3 lines
3000 M /trunk/samtools/bam_index.c
3001 M /trunk/samtools/bamtk.c
3003 * samtools-0.1.6-9 (r469)
3004 * refactor bam_fetch() for Python binding. On behalf of Leo Goodstadt.
3006 ------------------------------------------------------------------------
3007 r468 | lh3lh3 | 2009-09-28 05:18:29 -0400 (Mon, 28 Sep 2009) | 3 lines
3009 M /trunk/samtools/bam_sort.c
3010 M /trunk/samtools/bamtk.c
3011 M /trunk/samtools/misc/samtools.pl
3013 * samtools-0.1.6-7 (r468)
3016 ------------------------------------------------------------------------
3017 r467 | petulda | 2009-09-28 04:51:29 -0400 (Mon, 28 Sep 2009) | 1 line
3019 M /trunk/samtools/bgzf.c
3020 M /trunk/samtools/bgzip.c
3021 M /trunk/samtools/razf.c
3022 M /trunk/samtools/razip.c
3024 Changed the mode for newly created files to 0666. This allows less strict permissions with umask properly set (e.g. 0002 vs. 0022).
3025 ------------------------------------------------------------------------
3026 r466 | lh3lh3 | 2009-09-24 06:29:19 -0400 (Thu, 24 Sep 2009) | 3 lines
3028 M /trunk/samtools/ChangeLog
3029 M /trunk/samtools/bam_md.c
3030 M /trunk/samtools/bamtk.c
3032 * samtools-0.1.6-6 (r466)
3033 * do not crash calmd when some sequences are absent from the reference.
3035 ------------------------------------------------------------------------
3036 r464 | jmarshall | 2009-09-23 06:14:32 -0400 (Wed, 23 Sep 2009) | 3 lines
3038 M /trunk/samtools/bam.c
3039 M /trunk/samtools/knetfile.c
3041 Suppress bgzf_check_EOF() messages when reading from a pipe, as there is
3042 no way to seek on a pipe and the messages always appear.
3044 ------------------------------------------------------------------------
3045 r463 | petulda | 2009-09-16 07:05:41 -0400 (Wed, 16 Sep 2009) | 1 line
3047 M /trunk/samtools/knetfile.c
3048 M /trunk/samtools/razf.c
3050 A bug fix, "samtools view" is now working again.
3051 ------------------------------------------------------------------------
3052 r462 | lh3lh3 | 2009-09-16 04:51:07 -0400 (Wed, 16 Sep 2009) | 3 lines
3054 M /trunk/samtools/bamtk.c
3055 M /trunk/samtools/faidx.c
3056 M /trunk/samtools/knetfile.c
3057 M /trunk/samtools/knetfile.h
3058 M /trunk/samtools/razf.c
3059 M /trunk/samtools/razf.h
3061 * samtools-0.1.6-5 (r462)
3062 * Added knetfile support in razf and faidx (on behalf of Petr Danecek)
3064 ------------------------------------------------------------------------
3065 r460 | lh3lh3 | 2009-09-09 07:06:22 -0400 (Wed, 09 Sep 2009) | 2 lines
3067 M /trunk/samtools/samtools.1
3069 fixed a formatting issue
3071 ------------------------------------------------------------------------
3072 r459 | lh3lh3 | 2009-09-08 18:14:08 -0400 (Tue, 08 Sep 2009) | 3 lines
3074 M /trunk/samtools/bam_sort.c
3075 M /trunk/samtools/bamtk.c
3077 * samtools-0.1.6-4 (r459)
3078 * make sort output the result to stdout when -o is in use
3080 ------------------------------------------------------------------------
3081 r458 | lh3lh3 | 2009-09-07 05:10:28 -0400 (Mon, 07 Sep 2009) | 4 lines
3083 M /trunk/samtools/bamtk.c
3084 M /trunk/samtools/faidx.c
3085 M /trunk/samtools/faidx.h
3086 M /trunk/samtools/samtools.1
3088 * samtools-0.1.6-2 (r458)
3089 * added more interface to faidx (by Nils)
3090 * updated documentation
3092 ------------------------------------------------------------------------
3093 r457 | lh3lh3 | 2009-09-05 16:12:04 -0400 (Sat, 05 Sep 2009) | 3 lines
3095 M /trunk/samtools/bam_sort.c
3096 M /trunk/samtools/bamtk.c
3098 * samtools-0.1.6-2 (r457)
3099 * get rid of three assert() in bam_sort.c
3101 ------------------------------------------------------------------------
3102 r456 | jmarshall | 2009-09-04 12:46:25 -0400 (Fri, 04 Sep 2009) | 3 lines
3104 M /trunk/samtools/razf.c
3106 Return NULL from _razf_open() (and hence razf_open()/razf_open2())
3107 when opening the file fails.
3109 ------------------------------------------------------------------------
3110 r453 | lh3lh3 | 2009-09-02 08:56:33 -0400 (Wed, 02 Sep 2009) | 2 lines
3112 M /trunk/samtools/ChangeLog
3113 M /trunk/samtools/NEWS
3114 M /trunk/samtools/bamtk.c
3115 M /trunk/samtools/samtools.1
3116 D /trunk/samtools/source.dot
3118 Release samtools-0.1.6
3120 ------------------------------------------------------------------------
3121 r451 | lh3lh3 | 2009-09-02 05:44:48 -0400 (Wed, 02 Sep 2009) | 4 lines
3123 M /trunk/samtools/bam_md.c
3124 M /trunk/samtools/bam_rmdup.c
3125 M /trunk/samtools/bam_rmdupse.c
3126 M /trunk/samtools/bam_sort.c
3127 M /trunk/samtools/bamtk.c
3128 M /trunk/samtools/samtools.1
3130 * samtools-0.1.5-34 (r451)
3131 * applied the patch by John
3132 * improved the help message a little bit
3134 ------------------------------------------------------------------------
3135 r450 | lh3lh3 | 2009-09-02 04:55:55 -0400 (Wed, 02 Sep 2009) | 3 lines
3137 M /trunk/samtools/bam_color.c
3138 M /trunk/samtools/bamtk.c
3140 * samtools-0.1.5-33 (r450)
3141 * fixed a bug in bam_color.c (on behalf of Nils Homer)
3143 ------------------------------------------------------------------------
3144 r449 | lh3lh3 | 2009-08-29 15:36:41 -0400 (Sat, 29 Aug 2009) | 4 lines
3146 M /trunk/samtools/bam_import.c
3147 M /trunk/samtools/bam_md.c
3148 M /trunk/samtools/bamtk.c
3149 M /trunk/samtools/misc/samtools.pl
3151 * samtools-0.1.5-32 (r449)
3152 * fillmd: fixed a bug in modifying MD/NM tags
3153 * in import, give a warning if the read is aligned but there is no CIGAR.
3155 ------------------------------------------------------------------------
3156 r448 | lh3lh3 | 2009-08-19 04:44:28 -0400 (Wed, 19 Aug 2009) | 3 lines
3158 M /trunk/samtools/ChangeLog
3159 M /trunk/samtools/bam_pileup.c
3160 M /trunk/samtools/bamtk.c
3161 M /trunk/samtools/misc/wgsim_eval.pl
3163 * samtools-0.1.5-31 (r448)
3164 * fixed an issue when the last CIGAR is I or D
3166 ------------------------------------------------------------------------
3167 r447 | lh3lh3 | 2009-08-17 04:34:57 -0400 (Mon, 17 Aug 2009) | 3 lines
3169 M /trunk/samtools/bam_aux.c
3170 M /trunk/samtools/bamtk.c
3172 * samtools-0.1.5-30 (r447)
3173 * fixed a bug in bam_aux_get(): 'A' is not checked
3175 ------------------------------------------------------------------------
3176 r446 | lh3lh3 | 2009-08-17 04:33:17 -0400 (Mon, 17 Aug 2009) | 2 lines
3178 M /trunk/samtools/bam_aux.c
3179 M /trunk/samtools/bamtk.c
3183 ------------------------------------------------------------------------
3184 r444 | lh3lh3 | 2009-08-11 05:02:36 -0400 (Tue, 11 Aug 2009) | 3 lines
3186 M /trunk/samtools/bam_sort.c
3187 M /trunk/samtools/bamtk.c
3189 * samtools-0.1.5-28 (r444)
3192 ------------------------------------------------------------------------
3193 r443 | lh3lh3 | 2009-08-11 04:29:11 -0400 (Tue, 11 Aug 2009) | 4 lines
3195 M /trunk/samtools/bam.c
3196 M /trunk/samtools/bam_import.c
3197 M /trunk/samtools/bamtk.c
3199 * samtools-0.1.5-27 (r443)
3200 * SEQ and QUAL can be "*"
3201 * parse CIGAR "=" and "X" as "M"
3203 ------------------------------------------------------------------------
3204 r442 | lh3lh3 | 2009-08-07 16:56:38 -0400 (Fri, 07 Aug 2009) | 4 lines
3206 M /trunk/samtools/bam_pileup.c
3207 M /trunk/samtools/bamtk.c
3208 M /trunk/samtools/misc/md5.c
3209 M /trunk/samtools/misc/md5.h
3210 M /trunk/samtools/misc/md5fa.c
3212 * samtools-0.1.5-26 (r442)
3213 * replace RSA Inc md5.* with ones under permissive lincense
3214 * fixed a bug in detecting unsorted bam in pileup
3216 ------------------------------------------------------------------------
3217 r441 | bhandsaker | 2009-08-05 09:41:28 -0400 (Wed, 05 Aug 2009) | 2 lines
3219 M /trunk/samtools/bgzf.c
3220 M /trunk/samtools/bgzf.h
3221 M /trunk/samtools/bgzip.c
3223 Change copyright notices now that MIT has approved open source distribution.
3225 ------------------------------------------------------------------------
3226 r440 | lh3lh3 | 2009-08-05 05:44:24 -0400 (Wed, 05 Aug 2009) | 3 lines
3228 M /trunk/samtools/bam_stat.c
3229 M /trunk/samtools/bamtk.c
3231 * samtools-0.1.5-25 (r436)
3232 * in flagstats, do not report singletons if both ends are unmapped
3234 ------------------------------------------------------------------------
3235 r439 | lh3lh3 | 2009-08-04 17:16:51 -0400 (Tue, 04 Aug 2009) | 2 lines
3237 M /trunk/samtools/misc/maq2sam.c
3239 fixed a SERIOUS bug in setting 0x20 flag
3241 ------------------------------------------------------------------------
3242 r438 | lh3lh3 | 2009-08-04 16:50:43 -0400 (Tue, 04 Aug 2009) | 2 lines
3244 M /trunk/samtools/misc/samtools.pl
3246 fixed two minor bugs (suggested by Tim M Storm)
3248 ------------------------------------------------------------------------
3249 r437 | lh3lh3 | 2009-08-04 04:13:24 -0400 (Tue, 04 Aug 2009) | 3 lines
3251 M /trunk/samtools/bamtk.c
3252 M /trunk/samtools/misc/samtools.pl
3253 M /trunk/samtools/sam_view.c
3255 * samtools-0.1.5-24 (r435)
3258 ------------------------------------------------------------------------
3259 r434 | lh3lh3 | 2009-08-03 05:40:42 -0400 (Mon, 03 Aug 2009) | 3 lines
3261 M /trunk/samtools/bam_tview.c
3262 M /trunk/samtools/bamtk.c
3264 * samtools-0.1.5-23 (r434)
3265 * in tview, press 'r' to show read names rather than sequences
3267 ------------------------------------------------------------------------
3268 r433 | lh3lh3 | 2009-08-02 14:13:35 -0400 (Sun, 02 Aug 2009) | 3 lines
3270 M /trunk/samtools/knetfile.c
3272 * tried to fixed the buggy FTP random access in Windows. FAILED.
3273 * anyway, MinGW seems to have problem with "%lld".
3275 ------------------------------------------------------------------------
3276 r432 | lh3lh3 | 2009-08-01 19:32:07 -0400 (Sat, 01 Aug 2009) | 5 lines
3278 M /trunk/samtools/Makefile.mingw
3279 M /trunk/samtools/bamtk.c
3280 M /trunk/samtools/faidx.c
3281 M /trunk/samtools/razf.c
3282 A /trunk/samtools/win32/libcurses.a
3283 A /trunk/samtools/win32/xcurses.h
3285 * samtools-0.1.5-22 (r432)
3286 * faidx: fixed compitability issue with _WIN32
3287 * razf: fixed potential compitability issue with _WIN32
3288 * PDCurses support in Windows
3290 ------------------------------------------------------------------------
3291 r431 | lh3lh3 | 2009-08-01 18:34:54 -0400 (Sat, 01 Aug 2009) | 2 lines
3293 M /trunk/samtools/win32/libz.a
3295 replace the GnuWin32 version of libz.a with my own build with MinGW.
3297 ------------------------------------------------------------------------
3298 r430 | lh3lh3 | 2009-08-01 18:21:07 -0400 (Sat, 01 Aug 2009) | 2 lines
3300 M /trunk/samtools/knetfile.c
3304 ------------------------------------------------------------------------
3305 r429 | lh3lh3 | 2009-08-01 17:41:19 -0400 (Sat, 01 Aug 2009) | 3 lines
3307 M /trunk/samtools/Makefile.mingw
3308 M /trunk/samtools/bamtk.c
3309 M /trunk/samtools/knetfile.c
3310 M /trunk/samtools/knetfile.h
3312 * samtools-0.1.5-21 (r428)
3313 * knetfile.c is now compatible with mingw-winsock
3315 ------------------------------------------------------------------------
3316 r428 | lh3lh3 | 2009-07-31 19:39:07 -0400 (Fri, 31 Jul 2009) | 2 lines
3318 M /trunk/samtools/Makefile.mingw
3320 simplify MinGW Makefile
3322 ------------------------------------------------------------------------
3323 r427 | lh3lh3 | 2009-07-31 19:30:54 -0400 (Fri, 31 Jul 2009) | 5 lines
3325 A /trunk/samtools/Makefile.mingw
3326 M /trunk/samtools/bam_import.c
3327 M /trunk/samtools/bamtk.c
3328 A /trunk/samtools/win32
3329 A /trunk/samtools/win32/libz.a
3330 A /trunk/samtools/win32/zconf.h
3331 A /trunk/samtools/win32/zlib.h
3333 * samtools-0.1.5-20 (r427)
3334 * MinGW support. At least SAM<->BAM conversion is working. Other
3335 functionality are not tested at the moment.
3336 * zlib headers and Windows version of libz.a are included in win32/
3338 ------------------------------------------------------------------------
3339 r426 | lh3lh3 | 2009-07-31 18:32:09 -0400 (Fri, 31 Jul 2009) | 3 lines
3341 M /trunk/samtools/bamtk.c
3342 M /trunk/samtools/sam_view.c
3344 * samtools-0.1.5-19 (r426)
3345 * fixed a bug caused by recent modifications. Sorry.
3347 ------------------------------------------------------------------------
3348 r425 | lh3lh3 | 2009-07-31 18:23:51 -0400 (Fri, 31 Jul 2009) | 2 lines
3350 M /trunk/samtools/bgzf.c
3352 compatible with Windows binary files
3354 ------------------------------------------------------------------------
3355 r424 | lh3lh3 | 2009-07-31 05:19:59 -0400 (Fri, 31 Jul 2009) | 5 lines
3357 M /trunk/samtools/bam_maqcns.c
3358 M /trunk/samtools/bam_maqcns.h
3359 M /trunk/samtools/bam_plcmd.c
3360 M /trunk/samtools/bam_tview.c
3361 M /trunk/samtools/bamtk.c
3362 M /trunk/samtools/misc/samtools.pl
3364 * samtools-0.1.5-18 (r423)
3365 * output additional information in pileup indel lines, for the purepose
3366 of debugging at the moment
3367 * in tview, optionally allow to treat reference skip as deletion
3369 ------------------------------------------------------------------------
3370 r423 | lh3lh3 | 2009-07-30 17:00:36 -0400 (Thu, 30 Jul 2009) | 2 lines
3372 A /trunk/samtools/misc/psl2sam.pl
3374 convert BLAT psl to SAM.
3376 ------------------------------------------------------------------------
3377 r422 | lh3lh3 | 2009-07-30 06:24:39 -0400 (Thu, 30 Jul 2009) | 6 lines
3379 M /trunk/samtools/ChangeLog
3380 M /trunk/samtools/bam.c
3381 M /trunk/samtools/bamtk.c
3382 M /trunk/samtools/bgzf.c
3383 M /trunk/samtools/bgzf.h
3384 M /trunk/samtools/knetfile.c
3385 M /trunk/samtools/sam.c
3386 M /trunk/samtools/sam_view.c
3388 * samtools-0.1.5-17 (r422)
3389 * fixed a but in knetfile.c when seek type is not SEEK_SET
3390 * write an empty BGZF block to every BGZF file
3391 * check BGZF EOF marker in bam_header_read()
3394 ------------------------------------------------------------------------
3395 r421 | lh3lh3 | 2009-07-30 05:03:39 -0400 (Thu, 30 Jul 2009) | 3 lines
3397 M /trunk/samtools/bam_import.c
3398 M /trunk/samtools/bam_plcmd.c
3399 M /trunk/samtools/bamtk.c
3400 M /trunk/samtools/misc/samtools.pl
3401 M /trunk/samtools/sam.c
3402 M /trunk/samtools/sam.h
3403 M /trunk/samtools/sam_view.c
3405 * samtools-0.1.5-16 (r421)
3406 * in view and pileup, load header from FASTA index if the input is SAM.
3408 ------------------------------------------------------------------------
3409 r420 | lh3lh3 | 2009-07-29 04:18:55 -0400 (Wed, 29 Jul 2009) | 2 lines
3411 M /trunk/samtools/misc/maq2sam.c
3413 do not set "read 1" if reads are not mapped in the PE mode of maq
3415 ------------------------------------------------------------------------
3416 r419 | lh3lh3 | 2009-07-28 04:52:33 -0400 (Tue, 28 Jul 2009) | 5 lines
3418 M /trunk/samtools/bam_import.c
3419 M /trunk/samtools/bamtk.c
3420 M /trunk/samtools/misc/samtools.pl
3421 M /trunk/samtools/misc/wgsim_eval.pl
3423 * samtools-0.1.5-15 (r419)
3424 * in sam_open(), return NULL when the file cannot be opened.
3425 * make wgsim_eval.pl more robust to imperfect SAM
3426 * add "unique" command to samtools.pl
3428 ------------------------------------------------------------------------
3429 r418 | lh3lh3 | 2009-07-24 09:04:19 -0400 (Fri, 24 Jul 2009) | 2 lines
3431 M /trunk/samtools/misc/wgsim_eval.pl
3433 skip @header lines in SAM
3435 ------------------------------------------------------------------------
3436 r417 | lh3lh3 | 2009-07-24 07:42:38 -0400 (Fri, 24 Jul 2009) | 3 lines
3438 M /trunk/samtools/bamtk.c
3439 M /trunk/samtools/sam_view.c
3441 * samtools-0.1.5-14 (r417)
3442 * more help in "samtools view" due to the recent changes.
3444 ------------------------------------------------------------------------
3445 r416 | lh3lh3 | 2009-07-24 07:34:30 -0400 (Fri, 24 Jul 2009) | 3 lines
3447 M /trunk/samtools/bam.c
3448 M /trunk/samtools/bam.h
3449 M /trunk/samtools/bam_import.c
3450 M /trunk/samtools/bamtk.c
3451 M /trunk/samtools/sam.c
3452 M /trunk/samtools/sam.h
3453 M /trunk/samtools/sam_view.c
3455 * samtools-0.1.5-17 (r416)
3456 * support import/export SAM with string tags
3458 ------------------------------------------------------------------------
3459 r415 | lh3lh3 | 2009-07-24 06:39:26 -0400 (Fri, 24 Jul 2009) | 3 lines
3461 M /trunk/samtools/bam.c
3462 M /trunk/samtools/bam.h
3463 M /trunk/samtools/bam_import.c
3464 M /trunk/samtools/bamtk.c
3465 M /trunk/samtools/sam.c
3466 M /trunk/samtools/sam.h
3467 M /trunk/samtools/sam_view.c
3469 * samtools-0.1.5-12 (r415)
3470 * FLAG now can be in HEX
3472 ------------------------------------------------------------------------
3473 r414 | lh3lh3 | 2009-07-22 17:03:49 -0400 (Wed, 22 Jul 2009) | 2 lines
3475 M /trunk/samtools/kstring.h
3477 fixed a compiling error (thank Ken for fixing it)
3479 ------------------------------------------------------------------------
3480 r412 | lh3lh3 | 2009-07-21 17:19:40 -0400 (Tue, 21 Jul 2009) | 2 lines
3482 M /trunk/samtools/kstring.c
3483 M /trunk/samtools/kstring.h
3485 Implemented Boyer-Moore search in the kstring library.
3487 ------------------------------------------------------------------------
3488 r409 | lh3lh3 | 2009-07-17 12:10:20 -0400 (Fri, 17 Jul 2009) | 2 lines
3490 M /trunk/samtools/bam_index.c
3492 do not include knetfile.h when _USE_KNETFILE is not defined
3494 ------------------------------------------------------------------------
3495 r408 | lh3lh3 | 2009-07-17 10:29:21 -0400 (Fri, 17 Jul 2009) | 5 lines
3497 M /trunk/samtools/bam_md.c
3498 M /trunk/samtools/bam_tview.c
3499 M /trunk/samtools/bamtk.c
3500 M /trunk/samtools/bgzf.c
3502 * samtools-0.1.5-11 (r408)
3503 * force to overwirte existing MD if it is different from the one calculated
3505 * bgzf.c: improved the compatibility with Windows headers
3507 ------------------------------------------------------------------------
3508 r407 | lh3lh3 | 2009-07-17 09:46:56 -0400 (Fri, 17 Jul 2009) | 5 lines
3510 M /trunk/samtools/bam.h
3511 M /trunk/samtools/bam_aux.c
3512 M /trunk/samtools/bam_md.c
3513 M /trunk/samtools/bamtk.c
3514 M /trunk/samtools/sam.h
3516 * samtools-0.1.5-10 (r407)
3517 * implemented bam_aux_del() to remove a tag
3518 * fillmd: generate the NM tag
3519 * fillmd: cmd interface improvement
3521 ------------------------------------------------------------------------
3522 r406 | lh3lh3 | 2009-07-16 18:30:40 -0400 (Thu, 16 Jul 2009) | 2 lines
3524 M /trunk/samtools/Makefile
3526 Sorry. The old Makefile is for PDCurses...
3528 ------------------------------------------------------------------------
3529 r405 | lh3lh3 | 2009-07-16 18:30:11 -0400 (Thu, 16 Jul 2009) | 3 lines
3531 M /trunk/samtools/Makefile
3532 M /trunk/samtools/bam_tview.c
3533 M /trunk/samtools/bamtk.c
3535 * samtools-0.1.5-9 (r405)
3536 * improved the compatibility with PDCurses a little bit
3538 ------------------------------------------------------------------------
3539 r404 | lh3lh3 | 2009-07-16 18:23:52 -0400 (Thu, 16 Jul 2009) | 3 lines
3541 M /trunk/samtools/Makefile
3542 M /trunk/samtools/bam_tview.c
3543 M /trunk/samtools/bamtk.c
3545 * samtools-0.1.5-8 (r404)
3546 * compatible with PDCurses
3548 ------------------------------------------------------------------------
3549 r403 | lh3lh3 | 2009-07-16 17:39:39 -0400 (Thu, 16 Jul 2009) | 3 lines
3551 M /trunk/samtools/bamtk.c
3552 M /trunk/samtools/kseq.h
3554 * samtools-0.1.5-7 (r403)
3555 * fixed a bug in kseq.h for binary files (text files are fine)
3557 ------------------------------------------------------------------------
3558 r402 | lh3lh3 | 2009-07-16 06:49:53 -0400 (Thu, 16 Jul 2009) | 4 lines
3560 M /trunk/samtools/bam_import.c
3561 M /trunk/samtools/bam_index.c
3562 M /trunk/samtools/bamtk.c
3563 M /trunk/samtools/bgzf.c
3565 * samtools-0.1.5-6 (r402)
3566 * fixed compiling error when "-D_USE_NETFILE" is not applied
3567 * improve portability to MinGW
3569 ------------------------------------------------------------------------
3570 r398 | lh3lh3 | 2009-07-13 05:21:36 -0400 (Mon, 13 Jul 2009) | 3 lines
3572 A /trunk/bam-lite/bam.h (from /trunk/samtools/bam.h:395)
3573 A /trunk/bam-lite/bam_lite.c (from /trunk/samtools/bam_lite.c:395)
3574 D /trunk/samtools/bam_lite.c
3576 * move bam_lite.c to bam-lite
3577 * copy bam.h to bam-lite
3579 ------------------------------------------------------------------------
3580 r395 | lh3lh3 | 2009-07-13 05:12:57 -0400 (Mon, 13 Jul 2009) | 3 lines
3582 M /trunk/samtools/bam.h
3583 M /trunk/samtools/bam_lite.c
3584 M /trunk/samtools/bam_lpileup.c
3585 M /trunk/samtools/bam_pileup.c
3586 M /trunk/samtools/bamtk.c
3588 * samtools-0.1.5-5 (r395)
3589 * added bam_pileup_file() and removed bam_lpileup_file()
3591 ------------------------------------------------------------------------
3592 r394 | lh3lh3 | 2009-07-12 19:35:10 -0400 (Sun, 12 Jul 2009) | 3 lines
3594 M /trunk/samtools/bamtk.c
3595 M /trunk/samtools/knetfile.c
3596 M /trunk/samtools/knetfile.h
3598 * samtools-0.1.5-4 (r394)
3599 * http_proxy support in knetfile library (check http_proxy ENV)
3601 ------------------------------------------------------------------------
3602 r393 | lh3lh3 | 2009-07-12 18:57:07 -0400 (Sun, 12 Jul 2009) | 5 lines
3604 M /trunk/samtools/bam_index.c
3605 M /trunk/samtools/bam_tview.c
3606 M /trunk/samtools/bamtk.c
3607 M /trunk/samtools/knetfile.c
3608 M /trunk/samtools/knetfile.h
3610 * samtools-0.1.5-3 (r393)
3611 * knetfile now supports HTTP (no proxy at the moment)
3612 * fixed a potential issue in knetfile on opening ordinary file, although I have
3613 not seen the sideeffect so far.
3615 ------------------------------------------------------------------------
3616 r392 | lh3lh3 | 2009-07-12 13:50:55 -0400 (Sun, 12 Jul 2009) | 2 lines
3618 M /trunk/samtools/samtools.1
3620 Remove the warning in tview
3622 ------------------------------------------------------------------------
3623 r391 | lh3lh3 | 2009-07-12 13:42:43 -0400 (Sun, 12 Jul 2009) | 3 lines
3625 M /trunk/samtools/bam_tview.c
3626 M /trunk/samtools/bamtk.c
3628 * samtools-0.1.5-2 (r391)
3629 * do not show a blank screen when no reads mapped
3631 ------------------------------------------------------------------------
3632 r390 | lh3lh3 | 2009-07-09 09:01:42 -0400 (Thu, 09 Jul 2009) | 4 lines
3634 M /trunk/samtools/bam.h
3635 A /trunk/samtools/bam_lite.c
3636 M /trunk/samtools/bamtk.c
3638 * samtools-0.1.5-1 (r390)
3639 * removed useless _IOLIB in bam.h. This should cause no change at all.
3640 * added bam_lite.c for light-weight BAM reading
3642 ------------------------------------------------------------------------
3643 r385 | lh3lh3 | 2009-07-07 11:53:29 -0400 (Tue, 07 Jul 2009) | 2 lines
3645 M /trunk/samtools/bamtk.c
3646 M /trunk/samtools/knetfile.c
3648 Release samtools-0.1.5c (fixed a bug in piping)
3650 ------------------------------------------------------------------------
3651 r383 | lh3lh3 | 2009-07-07 06:39:55 -0400 (Tue, 07 Jul 2009) | 2 lines
3653 M /trunk/samtools/bamtk.c
3654 M /trunk/samtools/sam.c
3656 Release samtools-0.1.5b (BUG! so embarrassing!)
3658 ------------------------------------------------------------------------
3659 r381 | lh3lh3 | 2009-07-07 06:20:06 -0400 (Tue, 07 Jul 2009) | 2 lines
3661 M /trunk/samtools/Makefile
3662 M /trunk/samtools/bam.h
3663 M /trunk/samtools/bam_aux.c
3664 M /trunk/samtools/bamtk.c
3666 Release samtools-0.1.5a (for compatibility with Bio::DB::Sam)
3668 ------------------------------------------------------------------------
3669 r373 | lh3lh3 | 2009-07-07 05:26:57 -0400 (Tue, 07 Jul 2009) | 2 lines
3671 M /trunk/samtools/ChangeLog
3672 M /trunk/samtools/NEWS
3673 M /trunk/samtools/bamtk.c
3674 M /trunk/samtools/samtools.1
3676 Release samtools-0.1.5
3678 ------------------------------------------------------------------------
3679 r372 | lh3lh3 | 2009-07-07 04:49:27 -0400 (Tue, 07 Jul 2009) | 3 lines
3681 M /trunk/samtools/bamtk.c
3682 M /trunk/samtools/sam.c
3684 * samtools-0.1.4-23 (r372)
3685 * keep header text if "view -t" is used (by Gerton)
3687 ------------------------------------------------------------------------
3688 r371 | lh3lh3 | 2009-07-06 20:13:32 -0400 (Mon, 06 Jul 2009) | 2 lines
3690 M /trunk/samtools/samtools.1
3692 update documentation
3694 ------------------------------------------------------------------------
3695 r370 | bhandsaker | 2009-07-02 17:24:34 -0400 (Thu, 02 Jul 2009) | 2 lines
3697 M /trunk/samtools/Makefile
3699 Introduced LIBPATH variable so this could be overridden to allow samtools to build correct at the Broad.
3701 ------------------------------------------------------------------------
3702 r369 | lh3lh3 | 2009-07-02 08:36:53 -0400 (Thu, 02 Jul 2009) | 4 lines
3704 M /trunk/samtools/ChangeLog
3705 M /trunk/samtools/bam_aux.c
3706 M /trunk/samtools/bam_plcmd.c
3707 M /trunk/samtools/bamtk.c
3709 * samtools-0.1.4-22 (r369)
3710 * in pileup, optionally print E2 and U2
3711 * remove the debugging code in bam_aux_get() (Drat!)
3713 ------------------------------------------------------------------------
3714 r368 | lh3lh3 | 2009-07-02 06:32:26 -0400 (Thu, 02 Jul 2009) | 6 lines
3716 M /trunk/samtools/bam.c
3717 M /trunk/samtools/bam.h
3718 M /trunk/samtools/bam_aux.c
3719 M /trunk/samtools/bam_index.c
3720 M /trunk/samtools/bam_lpileup.c
3721 M /trunk/samtools/bam_md.c
3722 M /trunk/samtools/bam_pileup.c
3723 M /trunk/samtools/bam_rmdup.c
3724 M /trunk/samtools/bam_stat.c
3725 M /trunk/samtools/bam_tview.c
3726 M /trunk/samtools/bamtk.c
3727 M /trunk/samtools/faidx.c
3728 M /trunk/samtools/faidx.h
3729 M /trunk/samtools/glf.c
3731 * samtools-0.1.4-21 (r368)
3732 * propagate errors rather than exit or complain assertion failure. Assertion
3733 should be only used for checking internal bugs, but not for external input
3734 inconsistency. I was just a bit lazy.
3735 * small memory leak may be present on failure, though
3737 ------------------------------------------------------------------------
3738 r367 | lh3lh3 | 2009-06-30 11:18:42 -0400 (Tue, 30 Jun 2009) | 2 lines
3740 M /trunk/samtools/knetfile.c
3742 reduce the chance of blocking in FTP connection
3744 ------------------------------------------------------------------------
3745 r366 | lh3lh3 | 2009-06-30 10:35:21 -0400 (Tue, 30 Jun 2009) | 2 lines
3747 M /trunk/samtools/knetfile.c
3749 minor changes to knetfile: invalid fd equals -1 rather than 0
3751 ------------------------------------------------------------------------
3752 r365 | lh3lh3 | 2009-06-30 09:04:30 -0400 (Tue, 30 Jun 2009) | 3 lines
3754 M /trunk/samtools/bam_index.c
3755 M /trunk/samtools/bamtk.c
3756 M /trunk/samtools/knetfile.c
3757 M /trunk/samtools/knetfile.h
3759 * samtools-0.1.4-20 (r365)
3760 * download the BAM index file if it is not found in the current working directory.
3762 ------------------------------------------------------------------------
3763 r364 | lh3lh3 | 2009-06-30 07:39:07 -0400 (Tue, 30 Jun 2009) | 3 lines
3765 M /trunk/samtools/bamtk.c
3766 M /trunk/samtools/knetfile.c
3768 * samtools-0.1.4-19 (r364)
3769 * knetfile: report error when the file is not present on FTP
3771 ------------------------------------------------------------------------
3772 r363 | lh3lh3 | 2009-06-29 18:23:32 -0400 (Mon, 29 Jun 2009) | 4 lines
3774 M /trunk/samtools/bam_tview.c
3775 M /trunk/samtools/bamtk.c
3776 M /trunk/samtools/bgzf.c
3777 M /trunk/samtools/bgzf.h
3778 M /trunk/samtools/knetfile.c
3779 M /trunk/samtools/knetfile.h
3781 * samtools-0.1.4-18 (r363)
3782 * knetfile: do not trigger network communication in FTP seek (lazy seek)
3783 * bgzf: cache recent blocks (disabled by default)
3785 ------------------------------------------------------------------------
3786 r362 | lh3lh3 | 2009-06-25 16:04:34 -0400 (Thu, 25 Jun 2009) | 2 lines
3788 M /trunk/samtools/bgzf.c
3792 ------------------------------------------------------------------------
3793 r361 | lh3lh3 | 2009-06-25 16:03:10 -0400 (Thu, 25 Jun 2009) | 3 lines
3795 M /trunk/samtools/bam_index.c
3796 M /trunk/samtools/bamtk.c
3798 * samtools-0.1.4-17 (r361)
3799 * if a file is given on FTP, search locally for the BAM index
3801 ------------------------------------------------------------------------
3802 r360 | lh3lh3 | 2009-06-25 15:44:52 -0400 (Thu, 25 Jun 2009) | 5 lines
3804 M /trunk/samtools/Makefile
3805 M /trunk/samtools/bam_import.c
3806 M /trunk/samtools/bam_index.c
3807 M /trunk/samtools/bamtk.c
3808 M /trunk/samtools/bgzf.c
3809 M /trunk/samtools/bgzf.h
3810 M /trunk/samtools/knetfile.c
3811 M /trunk/samtools/knetfile.h
3813 * samtools-0.1.4-16 (r360)
3814 * report more information in index when the input is not sorted
3815 * change the behaviour of knet_seek() such that it returns 0 on success
3816 * support knetfile library in BGZF
3818 ------------------------------------------------------------------------
3819 r359 | lh3lh3 | 2009-06-25 12:10:55 -0400 (Thu, 25 Jun 2009) | 2 lines
3821 M /trunk/samtools/knetfile.c
3822 M /trunk/samtools/knetfile.h
3824 fixed bugs in knetfile.*
3826 ------------------------------------------------------------------------
3827 r358 | lh3lh3 | 2009-06-25 08:53:19 -0400 (Thu, 25 Jun 2009) | 2 lines
3829 A /trunk/samtools/knetfile.h
3831 this is the header file
3833 ------------------------------------------------------------------------
3834 r357 | lh3lh3 | 2009-06-25 08:52:03 -0400 (Thu, 25 Jun 2009) | 3 lines
3836 A /trunk/samtools/knetfile.c
3838 * open a file at FTP
3839 * preliminary version
3841 ------------------------------------------------------------------------
3842 r354 | lh3lh3 | 2009-06-24 09:02:25 -0400 (Wed, 24 Jun 2009) | 3 lines
3844 M /trunk/samtools/bam.c
3845 M /trunk/samtools/bamtk.c
3847 * samtools-0.1.4-15 (r354)
3848 * fixed a memory leak in bam_view1(), although samtools is not using this routine.
3850 ------------------------------------------------------------------------
3851 r351 | lh3lh3 | 2009-06-17 19:16:26 -0400 (Wed, 17 Jun 2009) | 4 lines
3853 M /trunk/samtools/bamtk.c
3854 M /trunk/samtools/faidx.c
3856 * samtools-0.1.4-13 (r351)
3857 * make faidx more tolerant to empty lines right before or after > lines
3858 * hope this does not introduce new bugs...
3860 ------------------------------------------------------------------------
3861 r350 | lh3lh3 | 2009-06-16 09:37:01 -0400 (Tue, 16 Jun 2009) | 3 lines
3863 M /trunk/samtools/bam_plcmd.c
3864 M /trunk/samtools/bamtk.c
3866 * samtools-0.1.4-13 (r350)
3867 * fixed a small memory leak in pileup, caused by recent modifications
3869 ------------------------------------------------------------------------
3870 r347 | lh3lh3 | 2009-06-13 16:20:49 -0400 (Sat, 13 Jun 2009) | 3 lines
3872 M /trunk/samtools/bam_plcmd.c
3873 M /trunk/samtools/bamtk.c
3874 M /trunk/samtools/sam_view.c
3876 * samtools-0.1.4-12 (r347)
3877 * added `-S' to pileup, similar to `view -S'
3879 ------------------------------------------------------------------------
3880 r346 | lh3lh3 | 2009-06-13 12:52:31 -0400 (Sat, 13 Jun 2009) | 3 lines
3882 M /trunk/samtools/Makefile
3883 M /trunk/samtools/bamtk.c
3884 M /trunk/samtools/sam_view.c
3885 M /trunk/samtools/samtools.1
3887 * samtools-0.1.4-11 (r346)
3888 * allow to select a read group at view command-line
3890 ------------------------------------------------------------------------
3891 r344 | lh3lh3 | 2009-06-13 09:06:24 -0400 (Sat, 13 Jun 2009) | 2 lines
3893 M /trunk/samtools/examples/calDepth.c
3897 ------------------------------------------------------------------------
3898 r343 | lh3lh3 | 2009-06-13 09:01:22 -0400 (Sat, 13 Jun 2009) | 2 lines
3900 M /trunk/samtools/examples/calDepth.c
3904 ------------------------------------------------------------------------
3905 r342 | lh3lh3 | 2009-06-13 08:58:48 -0400 (Sat, 13 Jun 2009) | 2 lines
3907 M /trunk/samtools/examples/Makefile
3908 A /trunk/samtools/examples/calDepth.c
3910 added an example of calculating read depth
3912 ------------------------------------------------------------------------
3913 r341 | lh3lh3 | 2009-06-13 08:00:08 -0400 (Sat, 13 Jun 2009) | 6 lines
3915 M /trunk/samtools/Makefile
3916 M /trunk/samtools/bam.h
3917 M /trunk/samtools/bam_aux.c
3918 A /trunk/samtools/bam_color.c
3919 M /trunk/samtools/bam_plcmd.c
3920 M /trunk/samtools/bam_sort.c
3921 M /trunk/samtools/bam_tview.c
3922 M /trunk/samtools/bamtk.c
3923 M /trunk/samtools/sam.c
3924 M /trunk/samtools/sam.h
3926 * samtools-0.1.4-10 (r341)
3927 * only include key APIs in libbam.a
3928 * move color-specific routines to bam_color.c
3929 * update documentations
3930 * remove the support of -q in pileup
3932 ------------------------------------------------------------------------
3933 r340 | lh3lh3 | 2009-06-13 06:17:14 -0400 (Sat, 13 Jun 2009) | 6 lines
3935 M /trunk/samtools/INSTALL
3936 M /trunk/samtools/Makefile
3937 M /trunk/samtools/bam_aux.c
3938 M /trunk/samtools/bam_import.c
3939 M /trunk/samtools/bam_tview.c
3940 M /trunk/samtools/bamtk.c
3941 M /trunk/samtools/razf.c
3942 M /trunk/samtools/sam_view.c
3944 * samtools-0.1.4-9 (r340)
3945 * added a warning to razf.c if zlib<1.2.2.1
3946 * fixed a compilation warning
3947 * fixed a segfault caused by @RG parsing
3948 * detect NCURSES in bam_tview.c
3950 ------------------------------------------------------------------------
3951 r339 | lh3lh3 | 2009-06-13 05:35:19 -0400 (Sat, 13 Jun 2009) | 2 lines
3953 M /trunk/samtools/INSTALL
3957 ------------------------------------------------------------------------
3958 r338 | lh3lh3 | 2009-06-12 19:15:24 -0400 (Fri, 12 Jun 2009) | 4 lines
3960 M /trunk/samtools/bam.c
3961 M /trunk/samtools/bam.h
3962 M /trunk/samtools/bam_aux.c
3963 M /trunk/samtools/bam_import.c
3964 M /trunk/samtools/bamtk.c
3965 M /trunk/samtools/kstring.h
3966 M /trunk/samtools/sam.c
3967 M /trunk/samtools/sam_view.c
3969 * samtools-0.1.4-8 (r338)
3970 * parse the @RG header lines and allow to choose library at the "samtools view"
3973 ------------------------------------------------------------------------
3974 r337 | lh3lh3 | 2009-06-12 16:25:50 -0400 (Fri, 12 Jun 2009) | 4 lines
3976 M /trunk/samtools/bamtk.c
3977 M /trunk/samtools/bgzf.c
3978 M /trunk/samtools/bgzf.h
3979 M /trunk/samtools/sam.c
3980 M /trunk/samtools/sam_view.c
3982 * samtools-0.1.4-7 (r337)
3983 * bgzf.c: support mode string "wu": uncompressed output
3984 * "samtools view" support "-u" command-line option
3986 ------------------------------------------------------------------------
3987 r336 | lh3lh3 | 2009-06-12 12:20:12 -0400 (Fri, 12 Jun 2009) | 5 lines
3989 M /trunk/samtools/Makefile
3990 M /trunk/samtools/misc/Makefile
3991 M /trunk/samtools/razf.c
3992 M /trunk/samtools/razf.h
3993 M /trunk/samtools/razip.c
3995 * no changes to samtools itself
3996 * remove zlib source codes
3997 * make RAZF reading compatible with old version of zlib
3998 * on old version of zlib, writing is not available
4000 ------------------------------------------------------------------------
4001 r335 | lh3lh3 | 2009-06-12 11:47:33 -0400 (Fri, 12 Jun 2009) | 2 lines
4003 D /trunk/samtools/zlib
4005 remove zlib for simplification...
4007 ------------------------------------------------------------------------
4008 r334 | lh3lh3 | 2009-06-12 10:43:36 -0400 (Fri, 12 Jun 2009) | 5 lines
4010 M /trunk/samtools/bam.h
4011 M /trunk/samtools/bam_aux.c
4012 M /trunk/samtools/bamtk.c
4014 * samtools-0.1.4-6 (r334)
4015 * do not export bam_aux_get_core() for Bio::DB::Sam because it has already
4016 been implemented in that.
4017 * this version works with the latest Bio::DB::Sam (20090612)
4019 ------------------------------------------------------------------------
4020 r333 | lh3lh3 | 2009-06-12 10:33:42 -0400 (Fri, 12 Jun 2009) | 2 lines
4022 M /trunk/samtools/ChangeLog
4026 ------------------------------------------------------------------------
4027 r332 | lh3lh3 | 2009-06-12 10:21:21 -0400 (Fri, 12 Jun 2009) | 2 lines
4029 M /trunk/samtools/AUTHORS
4030 M /trunk/samtools/Makefile
4031 M /trunk/samtools/misc/Makefile
4033 fixed minor things in Makefile
4035 ------------------------------------------------------------------------
4036 r331 | lh3lh3 | 2009-06-12 10:07:05 -0400 (Fri, 12 Jun 2009) | 4 lines
4038 M /trunk/samtools/bamtk.c
4040 * samtools-0.1.4-5 (r3310
4041 * no change to samtools itself. Version number is increased to reflect the
4042 changes in the Makefile building system.
4044 ------------------------------------------------------------------------
4045 r330 | lh3lh3 | 2009-06-12 10:03:38 -0400 (Fri, 12 Jun 2009) | 2 lines
4047 M /trunk/samtools/AUTHORS
4048 D /trunk/samtools/README
4050 update information...
4052 ------------------------------------------------------------------------
4053 r329 | lh3lh3 | 2009-06-12 09:52:21 -0400 (Fri, 12 Jun 2009) | 3 lines
4055 M /trunk/samtools/misc/novo2sam.pl
4057 * updated novoalign converter by Colin Hercus et al.
4058 * this version works with indels
4060 ------------------------------------------------------------------------
4061 r328 | lh3lh3 | 2009-06-12 09:50:53 -0400 (Fri, 12 Jun 2009) | 3 lines
4063 M /trunk/samtools/INSTALL
4064 M /trunk/samtools/Makefile
4065 M /trunk/samtools/misc/Makefile
4066 M /trunk/samtools/zlib/Makefile
4069 * update INSTALL instruction
4071 ------------------------------------------------------------------------
4072 r327 | lh3lh3 | 2009-06-12 09:18:29 -0400 (Fri, 12 Jun 2009) | 4 lines
4074 A /trunk/samtools/Makefile (from /trunk/samtools/Makefile.generic:325)
4075 D /trunk/samtools/Makefile.am
4076 D /trunk/samtools/Makefile.generic
4077 D /trunk/samtools/Makefile.lite
4078 D /trunk/samtools/autogen.sh
4079 D /trunk/samtools/cleanup.sh
4080 D /trunk/samtools/configure.ac
4081 A /trunk/samtools/misc/Makefile (from /trunk/samtools/misc/Makefile.generic:305)
4082 D /trunk/samtools/misc/Makefile.am
4083 D /trunk/samtools/misc/Makefile.generic
4084 M /trunk/samtools/razf.c
4085 A /trunk/samtools/zlib
4086 A /trunk/samtools/zlib/Makefile
4087 A /trunk/samtools/zlib/adler32.c
4088 A /trunk/samtools/zlib/compress.c
4089 A /trunk/samtools/zlib/crc32.c
4090 A /trunk/samtools/zlib/crc32.h
4091 A /trunk/samtools/zlib/deflate.c
4092 A /trunk/samtools/zlib/deflate.h
4093 A /trunk/samtools/zlib/gzio.c
4094 A /trunk/samtools/zlib/infback.c
4095 A /trunk/samtools/zlib/inffast.c
4096 A /trunk/samtools/zlib/inffast.h
4097 A /trunk/samtools/zlib/inffixed.h
4098 A /trunk/samtools/zlib/inflate.c
4099 A /trunk/samtools/zlib/inflate.h
4100 A /trunk/samtools/zlib/inftrees.c
4101 A /trunk/samtools/zlib/inftrees.h
4102 A /trunk/samtools/zlib/trees.c
4103 A /trunk/samtools/zlib/trees.h
4104 A /trunk/samtools/zlib/uncompr.c
4105 A /trunk/samtools/zlib/zconf.h
4106 A /trunk/samtools/zlib/zlib.h
4107 A /trunk/samtools/zlib/zutil.c
4108 A /trunk/samtools/zlib/zutil.h
4109 D /trunk/samtools/zutil.h
4111 * added zlib-1.2.3 as razip requires that
4112 * prepare to changed back to the Makefile building system
4113 * unfinished! (will be soon)
4115 ------------------------------------------------------------------------
4116 r326 | lh3lh3 | 2009-06-12 09:12:03 -0400 (Fri, 12 Jun 2009) | 2 lines
4118 M /trunk/samtools/misc/samtools.pl
4122 ------------------------------------------------------------------------
4123 r325 | lh3lh3 | 2009-06-10 11:27:59 -0400 (Wed, 10 Jun 2009) | 3 lines
4125 M /trunk/samtools/bam_maqcns.c
4126 M /trunk/samtools/bamtk.c
4128 * samtools-0.1.4-4 (r325)
4129 * further avoid wrong consensus calls in repetitive regions.
4131 ------------------------------------------------------------------------
4132 r324 | lh3lh3 | 2009-06-10 10:56:17 -0400 (Wed, 10 Jun 2009) | 4 lines
4134 M /trunk/samtools/bam_maqcns.c
4135 M /trunk/samtools/bam_plcmd.c
4136 M /trunk/samtools/bamtk.c
4137 M /trunk/samtools/sam.c
4138 M /trunk/samtools/sam.h
4140 * samtools-0.1.4-3 (r324)
4141 * make maqcns generate the correct call in repetitive regions.
4142 * allow filtering on mapQ at the pileup command line
4144 ------------------------------------------------------------------------
4145 r323 | lh3lh3 | 2009-06-10 05:04:21 -0400 (Wed, 10 Jun 2009) | 3 lines
4147 M /trunk/samtools/misc/samtools.pl
4149 * samtools.pl-0.3.2 (r322)
4150 * indels and SNPs use different mapping quality threshold
4152 ------------------------------------------------------------------------
4153 r322 | lh3lh3 | 2009-06-10 05:03:22 -0400 (Wed, 10 Jun 2009) | 2 lines
4155 M /trunk/samtools/misc/export2sam.pl
4159 ------------------------------------------------------------------------
4160 r321 | lh3lh3 | 2009-06-09 04:21:48 -0400 (Tue, 09 Jun 2009) | 2 lines
4162 M /trunk/samtools/misc/samtools.pl
4164 just typo. no real change
4166 ------------------------------------------------------------------------
4167 r320 | lh3lh3 | 2009-06-08 09:32:51 -0400 (Mon, 08 Jun 2009) | 2 lines
4169 M /trunk/samtools/misc/samtools.pl
4171 a little bit code cleanup
4173 ------------------------------------------------------------------------
4174 r319 | lh3lh3 | 2009-06-08 09:22:33 -0400 (Mon, 08 Jun 2009) | 4 lines
4176 M /trunk/samtools/misc/samtools.pl
4179 * change default parameters
4180 * optionally print filtered variants
4182 ------------------------------------------------------------------------
4183 r318 | lh3lh3 | 2009-06-08 09:14:26 -0400 (Mon, 08 Jun 2009) | 3 lines
4185 M /trunk/samtools/misc/samtools.pl
4188 * combine snpFilter and indelFilter
4190 ------------------------------------------------------------------------
4191 r317 | lh3lh3 | 2009-06-08 06:31:42 -0400 (Mon, 08 Jun 2009) | 3 lines
4193 M /trunk/samtools/misc/samtools.pl
4196 * change a default parameter
4198 ------------------------------------------------------------------------
4199 r316 | lh3lh3 | 2009-06-08 06:11:06 -0400 (Mon, 08 Jun 2009) | 5 lines
4201 M /trunk/samtools/bam_maqcns.c
4202 M /trunk/samtools/bam_maqcns.h
4203 M /trunk/samtools/bam_plcmd.c
4204 M /trunk/samtools/bamtk.c
4205 M /trunk/samtools/sam.c
4207 * samtools-0.1.4-2 (r316)
4208 * pileup: cap mapping quality at 60 (by default)
4209 * pileup: always calculate RMS mapq
4210 * pileup: allow to output variant sites only
4212 ------------------------------------------------------------------------
4213 r312 | lh3lh3 | 2009-06-04 08:01:10 -0400 (Thu, 04 Jun 2009) | 3 lines
4215 M /trunk/samtools/misc/samtools.pl
4220 ------------------------------------------------------------------------
4221 r311 | lh3lh3 | 2009-06-03 04:40:40 -0400 (Wed, 03 Jun 2009) | 2 lines
4223 M /trunk/samtools/misc/samtools.pl
4225 * in snpFilter, suppress non-SNP sites
4227 ------------------------------------------------------------------------
4228 r310 | lh3lh3 | 2009-06-01 09:35:13 -0400 (Mon, 01 Jun 2009) | 3 lines
4230 M /trunk/samtools/misc/samtools.pl
4235 ------------------------------------------------------------------------
4236 r309 | lh3lh3 | 2009-06-01 09:04:39 -0400 (Mon, 01 Jun 2009) | 3 lines
4238 M /trunk/samtools/misc/samtools.pl
4243 ------------------------------------------------------------------------
4244 r306 | lh3lh3 | 2009-05-28 06:49:35 -0400 (Thu, 28 May 2009) | 3 lines
4246 M /trunk/samtools/bgzf.c
4248 * minor changes to bgzf: return NULL if fd == -1
4249 * suggested by {kdj,jm18}@sanger.ac.uk
4251 ------------------------------------------------------------------------
4252 r305 | lh3lh3 | 2009-05-28 06:16:08 -0400 (Thu, 28 May 2009) | 2 lines
4254 A /trunk/samtools/misc/interpolate_sam.pl
4256 Script for paired-end pileup, contributed by Stephen Montgomery.
4258 ------------------------------------------------------------------------
4259 r304 | lh3lh3 | 2009-05-28 06:08:49 -0400 (Thu, 28 May 2009) | 3 lines
4261 M /trunk/samtools/bamtk.c
4262 M /trunk/samtools/sam.c
4264 * samtools-0.1.4-1 (r304)
4265 * fixed a minor bug in printing headers
4267 ------------------------------------------------------------------------
4268 r297 | lh3lh3 | 2009-05-21 11:06:16 -0400 (Thu, 21 May 2009) | 2 lines
4270 M /trunk/samtools/ChangeLog
4271 M /trunk/samtools/NEWS
4272 M /trunk/samtools/bam_plcmd.c
4273 M /trunk/samtools/bamtk.c
4274 M /trunk/samtools/misc/maq2sam.c
4275 M /trunk/samtools/samtools.1
4277 Release samtools-0.1.4
4279 ------------------------------------------------------------------------
4280 r296 | lh3lh3 | 2009-05-21 07:53:14 -0400 (Thu, 21 May 2009) | 3 lines
4282 M /trunk/samtools/bam_maqcns.c
4283 M /trunk/samtools/bamtk.c
4285 * samtools-0.1.3-24 (r296)
4286 * another similar bug in the indel caller
4288 ------------------------------------------------------------------------
4289 r295 | lh3lh3 | 2009-05-21 07:50:28 -0400 (Thu, 21 May 2009) | 3 lines
4291 M /trunk/samtools/bam_maqcns.c
4292 M /trunk/samtools/bamtk.c
4294 * samtools-0.1.3-23 (r295)
4295 * fixed a critical bug in the indel caller
4297 ------------------------------------------------------------------------
4298 r294 | lh3lh3 | 2009-05-20 08:00:20 -0400 (Wed, 20 May 2009) | 2 lines
4300 M /trunk/samtools/bam_stat.c
4302 added a missing header file
4304 ------------------------------------------------------------------------
4305 r293 | lh3lh3 | 2009-05-19 18:44:25 -0400 (Tue, 19 May 2009) | 3 lines
4307 M /trunk/samtools/bam_tview.c
4308 M /trunk/samtools/bamtk.c
4310 * samtools-0.1.3-22 (r293)
4311 * open tview in the dot-view mode by default
4313 ------------------------------------------------------------------------
4314 r292 | lh3lh3 | 2009-05-18 16:01:23 -0400 (Mon, 18 May 2009) | 6 lines
4316 M /trunk/samtools/samtools.1
4318 Added a note to the manual. Currently SAMtools used unaligned words in
4319 several places. Although this does not cause bus errors to me, it may
4320 affect portability. Please see the "Bus error" wiki page for more
4321 information. Also thank James Bonfields for pointing this out.
4324 ------------------------------------------------------------------------
4325 r286 | lh3lh3 | 2009-05-14 10:23:13 -0400 (Thu, 14 May 2009) | 3 lines
4327 M /trunk/samtools/bam.h
4328 M /trunk/samtools/bam_aux.c
4329 M /trunk/samtools/bamtk.c
4331 * samtools-0.1.3-21 (286)
4332 * declare bam_aux_get_core() in bam.h
4334 ------------------------------------------------------------------------
4335 r276 | lh3lh3 | 2009-05-13 05:07:55 -0400 (Wed, 13 May 2009) | 5 lines
4337 M /trunk/samtools/bam.h
4338 M /trunk/samtools/bam_index.c
4339 M /trunk/samtools/bamtk.c
4341 * samtools-0.1.3-20 (r276)
4342 * remove bam1_t::hash again. We need to modify the Perl API anyway to
4343 make it work with the latest SVN.
4344 * As is suggested by Tim, scan "{base}.bai" and "{base}.bam.bai" for index
4346 ------------------------------------------------------------------------
4347 r275 | lh3lh3 | 2009-05-12 16:14:10 -0400 (Tue, 12 May 2009) | 4 lines
4349 M /trunk/samtools/ChangeLog
4350 M /trunk/samtools/bam.h
4351 M /trunk/samtools/bamtk.c
4353 * samtools-0.1.3-19 (r275)
4354 * a minor change to the bam1_t struct: added back "void *hash" for the
4355 backward compatibility with Bio::DB::Sam
4357 ------------------------------------------------------------------------
4358 r273 | lh3lh3 | 2009-05-12 09:28:39 -0400 (Tue, 12 May 2009) | 3 lines
4360 M /trunk/samtools/bam_rmdupse.c
4361 M /trunk/samtools/bamtk.c
4363 * samtools-0.1.3-18 (r273)
4364 * rmdupse: do not remove unmapped reads
4366 ------------------------------------------------------------------------
4367 r272 | lh3lh3 | 2009-05-12 09:20:00 -0400 (Tue, 12 May 2009) | 2 lines
4369 M /trunk/samtools/bam_rmdupse.c
4371 change a parameter. It does nothing
4373 ------------------------------------------------------------------------
4374 r271 | lh3lh3 | 2009-05-12 09:17:58 -0400 (Tue, 12 May 2009) | 3 lines
4376 M /trunk/samtools/Makefile.am
4377 M /trunk/samtools/Makefile.generic
4378 M /trunk/samtools/Makefile.lite
4379 A /trunk/samtools/bam_rmdupse.c
4380 M /trunk/samtools/bamtk.c
4381 M /trunk/samtools/configure.ac
4383 * samtools-0.1.3-17 (r271)
4384 * added 'rmdupse' command
4386 ------------------------------------------------------------------------
4387 r267 | lh3lh3 | 2009-05-05 17:31:41 -0400 (Tue, 05 May 2009) | 3 lines
4389 M /trunk/samtools/bamtk.c
4390 M /trunk/samtools/sam_view.c
4392 * samtools-0.1.3-16 (r267)
4393 * in sam_view.c, changed g_flag_on based on the suggestion by Angie Hinrichs
4395 ------------------------------------------------------------------------
4396 r266 | lh3lh3 | 2009-05-05 17:23:27 -0400 (Tue, 05 May 2009) | 3 lines
4398 M /trunk/samtools/bam_import.c
4399 M /trunk/samtools/bamtk.c
4401 * samtools-0.1.3-15 (r266)
4402 * report an error if a non-* reference is present while @SQ is absent
4404 ------------------------------------------------------------------------
4405 r265 | lh3lh3 | 2009-05-05 17:09:00 -0400 (Tue, 05 May 2009) | 3 lines
4407 M /trunk/samtools/bam.h
4408 M /trunk/samtools/bam_import.c
4409 M /trunk/samtools/bamtk.c
4410 M /trunk/samtools/sam.c
4411 M /trunk/samtools/sam_view.c
4413 * samtools-0.1.3-14 (r262)
4414 * make samopen() recognize @SQ header lines
4416 ------------------------------------------------------------------------
4417 r261 | lh3lh3 | 2009-05-05 10:10:30 -0400 (Tue, 05 May 2009) | 3 lines
4419 M /trunk/samtools/bam_plcmd.c
4420 M /trunk/samtools/bamtk.c
4421 M /trunk/samtools/bgzf.c
4422 M /trunk/samtools/sam.c
4423 M /trunk/samtools/sam_view.c
4425 * samtools-0.1.3-13 (r260)
4426 * report error for file I/O error
4428 ------------------------------------------------------------------------
4429 r260 | lh3lh3 | 2009-05-05 10:01:16 -0400 (Tue, 05 May 2009) | 2 lines
4431 M /trunk/samtools/Makefile.am
4435 ------------------------------------------------------------------------
4436 r259 | lh3lh3 | 2009-05-05 09:52:25 -0400 (Tue, 05 May 2009) | 3 lines
4438 M /trunk/samtools/bam.h
4439 M /trunk/samtools/bam_pileup.c
4440 M /trunk/samtools/bam_plcmd.c
4441 M /trunk/samtools/bamtk.c
4442 M /trunk/samtools/sam.c
4443 M /trunk/samtools/sam.h
4445 * samtools-0.1.3-12 (r259)
4446 * use the new I/O interface in pileup
4448 ------------------------------------------------------------------------
4449 r258 | lh3lh3 | 2009-05-05 09:33:22 -0400 (Tue, 05 May 2009) | 3 lines
4451 M /trunk/samtools/Makefile.generic
4452 M /trunk/samtools/Makefile.lite
4453 M /trunk/samtools/bam.c
4454 M /trunk/samtools/bam.h
4455 M /trunk/samtools/bam_import.c
4456 M /trunk/samtools/bamtk.c
4457 A /trunk/samtools/sam.c
4458 A /trunk/samtools/sam.h
4459 A /trunk/samtools/sam_view.c
4461 * samtools-0.1.3-11 (r258)
4462 * unify the interface to BAM and SAM I/O
4464 ------------------------------------------------------------------------
4465 r257 | lh3lh3 | 2009-05-05 04:53:35 -0400 (Tue, 05 May 2009) | 3 lines
4467 M /trunk/samtools/Makefile.lite
4468 M /trunk/samtools/bam_plcmd.c
4469 M /trunk/samtools/bamtk.c
4471 * samtools-0.1.3-10 (r257)
4472 * allow hex with "pileup -m"
4474 ------------------------------------------------------------------------
4475 r256 | lh3lh3 | 2009-05-04 14:16:50 -0400 (Mon, 04 May 2009) | 4 lines
4477 M /trunk/samtools/bam_lpileup.c
4478 M /trunk/samtools/bamtk.c
4480 * samtools-0.1.3-9 (r256)
4481 * fixed a bug in bam_lpileup.c
4482 * I do not know if this also fixes the bug causing assertion failure in the tview
4484 ------------------------------------------------------------------------
4485 r251 | lh3lh3 | 2009-04-28 08:53:23 -0400 (Tue, 28 Apr 2009) | 3 lines
4487 M /trunk/samtools/bam_pileup.c
4488 M /trunk/samtools/bamtk.c
4490 * samtools-0.1.3-8 (r251)
4491 * fixed a bug when there are reads without coordinates
4493 ------------------------------------------------------------------------
4494 r250 | lh3lh3 | 2009-04-28 08:43:33 -0400 (Tue, 28 Apr 2009) | 2 lines
4496 A /trunk/samtools/AUTHORS
4497 A /trunk/samtools/README
4498 M /trunk/samtools/cleanup.sh
4502 ------------------------------------------------------------------------
4503 r249 | lh3lh3 | 2009-04-28 08:37:16 -0400 (Tue, 28 Apr 2009) | 2 lines
4505 M /trunk/samtools/Makefile.generic
4506 M /trunk/samtools/Makefile.lite
4507 M /trunk/samtools/configure.ac
4508 M /trunk/samtools/misc/Makefile.generic
4510 improve large file support in compilation
4512 ------------------------------------------------------------------------
4513 r248 | lh3lh3 | 2009-04-28 08:33:24 -0400 (Tue, 28 Apr 2009) | 2 lines
4515 M /trunk/samtools/INSTALL
4519 ------------------------------------------------------------------------
4520 r247 | lh3lh3 | 2009-04-28 08:28:50 -0400 (Tue, 28 Apr 2009) | 2 lines
4522 M /trunk/samtools/Makefile.am
4523 M /trunk/samtools/autogen.sh
4524 M /trunk/samtools/cleanup.sh
4525 M /trunk/samtools/configure.ac
4526 A /trunk/samtools/misc/Makefile.am
4528 fixed various issues about the GNU building scripts
4530 ------------------------------------------------------------------------
4531 r246 | lh3lh3 | 2009-04-28 08:10:23 -0400 (Tue, 28 Apr 2009) | 4 lines
4533 M /trunk/samtools/ChangeLog
4534 D /trunk/samtools/Makefile
4535 A /trunk/samtools/Makefile.am
4536 A /trunk/samtools/Makefile.generic
4537 A /trunk/samtools/autogen.sh
4538 M /trunk/samtools/bam.h
4539 M /trunk/samtools/bam_aux.c
4540 M /trunk/samtools/bam_tview.c
4541 M /trunk/samtools/bamtk.c
4542 A /trunk/samtools/cleanup.sh
4543 A /trunk/samtools/configure.ac
4544 D /trunk/samtools/misc/Makefile
4545 A /trunk/samtools/misc/Makefile.generic (from /trunk/samtools/misc/Makefile:245)
4547 * samtools-0.1.3-7 (r246)
4548 * incorporated revisions from Nils Homer
4549 * enhanced support of displaying color-space reads
4551 ------------------------------------------------------------------------
4552 r244 | lh3lh3 | 2009-04-25 06:49:40 -0400 (Sat, 25 Apr 2009) | 3 lines
4554 M /trunk/samtools/bam_md.c
4555 M /trunk/samtools/bamtk.c
4557 * samtools-0.1.3-6 (r244)
4558 * fixed segfault for unmapped reads
4560 ------------------------------------------------------------------------
4561 r243 | lh3lh3 | 2009-04-24 16:27:26 -0400 (Fri, 24 Apr 2009) | 5 lines
4563 M /trunk/samtools/bam.h
4564 M /trunk/samtools/bam_maqcns.c
4565 M /trunk/samtools/bam_md.c
4566 M /trunk/samtools/bamtk.c
4568 * samtools-0.1.3-5 (r243)
4569 * fixed a long existing bug which may cause memory leak
4571 * consensus calling now works with "=", but indel calling not
4573 ------------------------------------------------------------------------
4574 r242 | lh3lh3 | 2009-04-24 15:44:46 -0400 (Fri, 24 Apr 2009) | 3 lines
4576 M /trunk/samtools/bam_md.c
4577 M /trunk/samtools/bamtk.c
4579 * samtools-0.1.3-4 (r242)
4580 * fixed a memory leak
4582 ------------------------------------------------------------------------
4583 r240 | lh3lh3 | 2009-04-24 11:40:18 -0400 (Fri, 24 Apr 2009) | 5 lines
4585 M /trunk/samtools/Makefile
4586 M /trunk/samtools/Makefile.lite
4587 M /trunk/samtools/bam.h
4588 M /trunk/samtools/bam_aux.c
4589 A /trunk/samtools/bam_md.c
4590 M /trunk/samtools/bam_plcmd.c
4591 M /trunk/samtools/bamtk.c
4593 * samtools-0.1.3-3 (r240)
4595 * generate "=" bases
4596 * the plain pileup now support "=" bases, but consensus calling and glfgen may fail
4598 ------------------------------------------------------------------------
4599 r239 | lh3lh3 | 2009-04-24 07:08:20 -0400 (Fri, 24 Apr 2009) | 5 lines
4601 M /trunk/samtools/bam.h
4602 M /trunk/samtools/bam_aux.c
4603 M /trunk/samtools/bamtk.c
4605 * samtools-0.1.3-2 (r239)
4606 * fixed bugs in bam_aux.c (these functions nevered used by samtools)
4607 * removed bam_aux_init()/bam_aux_destroy()
4608 * added tagview for testing bam_aux
4610 ------------------------------------------------------------------------
4611 r235 | lh3lh3 | 2009-04-21 18:17:39 -0400 (Tue, 21 Apr 2009) | 3 lines
4613 M /trunk/samtools/bam_pileup.c
4614 M /trunk/samtools/bamtk.c
4617 * fixed a bug in pileup: the first read in a chromosome may not be printed
4619 ------------------------------------------------------------------------
4620 r232 | lh3lh3 | 2009-04-16 10:25:43 -0400 (Thu, 16 Apr 2009) | 2 lines
4622 M /trunk/samtools/Makefile.lite
4624 a missing file in Makefile.lite
4626 ------------------------------------------------------------------------
4627 r227 | lh3lh3 | 2009-04-15 17:02:53 -0400 (Wed, 15 Apr 2009) | 2 lines
4629 M /trunk/samtools/NEWS
4630 M /trunk/samtools/bamtk.c
4632 Release samtools-0.1.3
4634 ------------------------------------------------------------------------
4635 r223 | lh3lh3 | 2009-04-15 09:31:32 -0400 (Wed, 15 Apr 2009) | 3 lines
4637 M /trunk/samtools/bam_plcmd.c
4638 M /trunk/samtools/bamtk.c
4641 * make samtools more robust to weird input such as empty file
4643 ------------------------------------------------------------------------
4644 r222 | lh3lh3 | 2009-04-15 09:05:33 -0400 (Wed, 15 Apr 2009) | 2 lines
4646 M /trunk/samtools/ChangeLog
4647 M /trunk/samtools/NEWS
4648 M /trunk/samtools/samtools.1
4650 prepare for release 0.1.3
4652 ------------------------------------------------------------------------
4653 r221 | lh3lh3 | 2009-04-15 08:32:14 -0400 (Wed, 15 Apr 2009) | 2 lines
4655 A /trunk/samtools/misc/blast2sam.pl
4657 convert NCBI-BLASTN to SAM
4659 ------------------------------------------------------------------------
4660 r220 | lh3lh3 | 2009-04-15 08:18:19 -0400 (Wed, 15 Apr 2009) | 3 lines
4662 M /trunk/samtools/bam_lpileup.c
4663 M /trunk/samtools/bamtk.c
4666 * fixed a small memory leak in tview
4668 ------------------------------------------------------------------------
4669 r219 | lh3lh3 | 2009-04-15 08:00:08 -0400 (Wed, 15 Apr 2009) | 3 lines
4671 M /trunk/samtools/bam_rmdup.c
4672 M /trunk/samtools/bamtk.c
4675 * fixed a bug in rmdup when there are unmapped reads
4677 ------------------------------------------------------------------------
4678 r218 | lh3lh3 | 2009-04-14 17:28:58 -0400 (Tue, 14 Apr 2009) | 2 lines
4680 M /trunk/samtools/ChangeLog
4681 M /trunk/samtools/NEWS
4683 proposed NEWS for the new release (have not yet)
4685 ------------------------------------------------------------------------
4686 r216 | lh3lh3 | 2009-04-14 17:10:46 -0400 (Tue, 14 Apr 2009) | 4 lines
4688 M /trunk/samtools/misc/samtools.pl
4691 * improve indelFilter to avoid filtering true indels. The new filter relies
4692 on the new pileup indel line implemented in samtools-0.1.2-25
4694 ------------------------------------------------------------------------
4695 r215 | lh3lh3 | 2009-04-14 17:04:19 -0400 (Tue, 14 Apr 2009) | 4 lines
4697 M /trunk/samtools/bam_maqcns.c
4698 M /trunk/samtools/bam_plcmd.c
4699 M /trunk/samtools/bamtk.c
4700 M /trunk/samtools/samtools.1
4703 * change the pileup indel line to shows the number of alignments actually
4706 ------------------------------------------------------------------------
4707 r211 | lh3lh3 | 2009-04-13 07:07:13 -0400 (Mon, 13 Apr 2009) | 2 lines
4709 M /trunk/samtools/ChangeLog
4711 update ChangeLog from "svn log"
4713 ------------------------------------------------------------------------
4714 r210 | lh3lh3 | 2009-04-12 15:57:05 -0400 (Sun, 12 Apr 2009) | 4 lines
4716 M /trunk/samtools/bam.c
4717 M /trunk/samtools/bam_import.c
4718 M /trunk/samtools/bam_sort.c
4719 M /trunk/samtools/bamtk.c
4720 M /trunk/samtools/kseq.h
4723 * in merge, gives a warning rather than error if the target sequence length is different
4724 * allow empty header
4726 ------------------------------------------------------------------------
4727 r209 | lh3lh3 | 2009-04-12 15:32:44 -0400 (Sun, 12 Apr 2009) | 3 lines
4729 M /trunk/samtools/bam.c
4730 M /trunk/samtools/bam_import.c
4731 M /trunk/samtools/bamtk.c
4734 * recognize '*' at the QUAL field
4736 ------------------------------------------------------------------------
4737 r208 | lh3lh3 | 2009-04-12 15:08:02 -0400 (Sun, 12 Apr 2009) | 3 lines
4739 M /trunk/samtools/bam_import.c
4740 M /trunk/samtools/bamtk.c
4741 M /trunk/samtools/kseq.h
4744 * the field separater is TAB only, now
4746 ------------------------------------------------------------------------
4747 r207 | lh3lh3 | 2009-04-08 10:18:03 -0400 (Wed, 08 Apr 2009) | 2 lines
4749 M /trunk/samtools/examples/ex1.sam.gz
4751 * fixed the problem in the example alignment due to the bug in fixmate
4753 ------------------------------------------------------------------------
4754 r206 | lh3lh3 | 2009-04-08 10:15:05 -0400 (Wed, 08 Apr 2009) | 3 lines
4756 M /trunk/samtools/bam_mate.c
4757 M /trunk/samtools/bamtk.c
4758 M /trunk/samtools/misc/soap2sam.pl
4761 * fixed a nasty bug in `fixmate'
4763 ------------------------------------------------------------------------
4764 r205 | lh3lh3 | 2009-04-08 05:57:08 -0400 (Wed, 08 Apr 2009) | 2 lines
4766 M /trunk/samtools/misc/bowtie2sam.pl
4767 M /trunk/samtools/misc/soap2sam.pl
4768 M /trunk/samtools/misc/wgsim_eval.pl
4770 make the script robust to the bugs in SOAP-2.1.7
4772 ------------------------------------------------------------------------
4773 r200 | lh3lh3 | 2009-04-02 10:14:56 -0400 (Thu, 02 Apr 2009) | 3 lines
4775 M /trunk/samtools/bam_stat.c
4776 M /trunk/samtools/bamtk.c
4779 * check if file is truncated in flagstat
4781 ------------------------------------------------------------------------
4782 r199 | lh3lh3 | 2009-04-02 10:09:10 -0400 (Thu, 02 Apr 2009) | 3 lines
4784 M /trunk/samtools/bamtk.c
4787 * print the header if requested
4789 ------------------------------------------------------------------------
4790 r193 | lh3lh3 | 2009-03-27 11:09:50 -0400 (Fri, 27 Mar 2009) | 3 lines
4792 M /trunk/samtools/bam_plcmd.c
4793 M /trunk/samtools/bamtk.c
4796 * fixed a minor bug reported by Nils Homer
4798 ------------------------------------------------------------------------
4799 r185 | lh3lh3 | 2009-03-24 07:50:32 -0400 (Tue, 24 Mar 2009) | 2 lines
4801 A /trunk/samtools/Makefile (from /trunk/samtools/Makefile.std:184)
4802 D /trunk/samtools/Makefile.std
4803 A /trunk/samtools/misc/Makefile (from /trunk/samtools/misc/Makefile.std:184)
4804 D /trunk/samtools/misc/Makefile.std
4806 rename Makefile.std as Makefile. GNU building systerm is not ready and may take some time...
4808 ------------------------------------------------------------------------
4809 r184 | lh3lh3 | 2009-03-24 06:36:38 -0400 (Tue, 24 Mar 2009) | 4 lines
4811 D /trunk/samtools/Makefile
4812 A /trunk/samtools/Makefile.std (from /trunk/samtools/Makefile:183)
4813 M /trunk/samtools/bam_sort.c
4814 M /trunk/samtools/bam_tview.c
4815 M /trunk/samtools/bamtk.c
4816 D /trunk/samtools/misc/Makefile
4817 A /trunk/samtools/misc/Makefile.std (from /trunk/samtools/misc/Makefile:182)
4818 M /trunk/samtools/samtools.1
4821 * incorporating Nils' changes
4822 * rename Makefile to Makefile.std and prepare to add the GNU building systerms (also by Nils)
4824 ------------------------------------------------------------------------
4825 r183 | lh3lh3 | 2009-03-24 06:30:23 -0400 (Tue, 24 Mar 2009) | 4 lines
4827 M /trunk/samtools/Makefile
4828 M /trunk/samtools/bam_import.c
4829 M /trunk/samtools/bam_maqcns.c
4830 M /trunk/samtools/bam_maqcns.h
4831 M /trunk/samtools/bam_plcmd.c
4832 M /trunk/samtools/bamtk.c
4833 M /trunk/samtools/kseq.h
4834 A /trunk/samtools/kstring.c
4835 A /trunk/samtools/kstring.h
4838 * made pileup take a list of proposed indels. An insertion is N at the moment.
4839 * added my kstring library for a bit complex parsing of the position list.
4841 ------------------------------------------------------------------------
4842 r169 | lh3lh3 | 2009-03-12 09:40:14 -0400 (Thu, 12 Mar 2009) | 3 lines
4844 M /trunk/samtools/misc/soap2sam.pl
4847 * more robust to truncated soap output
4849 ------------------------------------------------------------------------
4850 r168 | lh3lh3 | 2009-03-11 06:49:00 -0400 (Wed, 11 Mar 2009) | 2 lines
4852 M /trunk/samtools/Makefile.lite
4854 added bam_stat.o to Makefile.lite
4856 ------------------------------------------------------------------------
4857 r167 | lh3lh3 | 2009-03-10 18:11:31 -0400 (Tue, 10 Mar 2009) | 3 lines
4859 M /trunk/samtools/bam_maqcns.c
4860 M /trunk/samtools/bamtk.c
4863 * generate RMS of mapQ instead of max mapQ
4865 ------------------------------------------------------------------------
4866 r166 | lh3lh3 | 2009-03-10 18:06:45 -0400 (Tue, 10 Mar 2009) | 3 lines
4868 M /trunk/samtools/bam_plcmd.c
4869 M /trunk/samtools/bamtk.c
4870 M /trunk/samtools/glf.c
4871 M /trunk/samtools/glf.h
4872 M /trunk/samtools/misc/Makefile
4877 ------------------------------------------------------------------------
4878 r159 | lh3lh3 | 2009-03-03 06:26:08 -0500 (Tue, 03 Mar 2009) | 3 lines
4880 M /trunk/samtools/bam_plcmd.c
4881 M /trunk/samtools/bamtk.c
4884 * fixed a minor bug in displaying pileup
4886 ------------------------------------------------------------------------
4887 r158 | lh3lh3 | 2009-03-03 06:24:16 -0500 (Tue, 03 Mar 2009) | 3 lines
4889 M /trunk/samtools/ChangeLog
4890 M /trunk/samtools/bamtk.c
4893 * optionally print SAM header
4895 ------------------------------------------------------------------------
4896 r153 | lh3lh3 | 2009-03-02 05:45:28 -0500 (Mon, 02 Mar 2009) | 3 lines
4898 M /trunk/samtools/bamtk.c
4899 M /trunk/samtools/glf.c
4902 * use "GLF\3" as the magic for GLFv3 files
4904 ------------------------------------------------------------------------
4905 r152 | lh3lh3 | 2009-03-02 05:39:09 -0500 (Mon, 02 Mar 2009) | 5 lines
4907 M /trunk/samtools/Makefile
4908 M /trunk/samtools/bam_import.c
4909 M /trunk/samtools/bam_index.c
4910 M /trunk/samtools/bam_plcmd.c
4911 M /trunk/samtools/bamtk.c
4912 M /trunk/samtools/glf.c
4913 M /trunk/samtools/glf.h
4916 * fixed a bug in import: core.bin is undefined for unmapped reads
4917 * this bug can be alleviated (not completely solved) in bam_index.c
4918 * update to GLFv3: pos is changed to offset for better compression
4920 ------------------------------------------------------------------------
4921 r151 | lh3lh3 | 2009-03-01 10:18:43 -0500 (Sun, 01 Mar 2009) | 3 lines
4923 M /trunk/samtools/misc/wgsim.c
4926 * fixed a bug in simulating indels
4928 ------------------------------------------------------------------------
4929 r145 | lh3lh3 | 2009-02-26 14:43:57 -0500 (Thu, 26 Feb 2009) | 4 lines
4931 M /trunk/samtools/misc/wgsim.c
4934 * allow to print mismatch information as fastq comment. MAQ does
4935 not like long read names.
4937 ------------------------------------------------------------------------
4938 r141 | lh3lh3 | 2009-02-26 09:53:03 -0500 (Thu, 26 Feb 2009) | 6 lines
4940 M /trunk/samtools/ChangeLog
4941 M /trunk/samtools/misc/wgsim.c
4942 M /trunk/samtools/misc/wgsim_eval.pl
4945 * fixed a bug about color read coordinates
4946 * fixed a bug in read names
4947 * wgsim_eval.pl-0.1.3
4948 * make the script work with color reads
4950 ------------------------------------------------------------------------
4951 r140 | lh3lh3 | 2009-02-26 09:02:57 -0500 (Thu, 26 Feb 2009) | 2 lines
4953 M /trunk/samtools/misc/Makefile
4954 M /trunk/samtools/misc/wgsim.c
4956 * wgsim: added a note
4958 ------------------------------------------------------------------------
4959 r139 | lh3lh3 | 2009-02-26 06:39:08 -0500 (Thu, 26 Feb 2009) | 7 lines
4961 M /trunk/samtools/misc/wgsim.c
4962 M /trunk/samtools/misc/wgsim_eval.pl
4965 * considerable code clean up
4966 * print number of substitutions/indels/errors on each read
4967 * potentially support SOLiD simulation, though not tested at the moment
4968 * wgsim_eval.pl-0.1.2
4969 * change in accordant with wgsim
4971 ------------------------------------------------------------------------
4972 r129 | lh3lh3 | 2009-02-18 17:23:27 -0500 (Wed, 18 Feb 2009) | 3 lines
4974 M /trunk/samtools/bam_index.c
4975 M /trunk/samtools/bamtk.c
4978 * fixed a bug in bam_fetch, caused by completely contained adjacent chunks
4980 ------------------------------------------------------------------------
4981 r128 | bhandsaker | 2009-02-18 14:06:57 -0500 (Wed, 18 Feb 2009) | 2 lines
4983 M /trunk/samtools/bamtk.c
4985 Fix annoying segv when invalid region specified.
4987 ------------------------------------------------------------------------
4988 r127 | lh3lh3 | 2009-02-17 05:49:55 -0500 (Tue, 17 Feb 2009) | 2 lines
4990 D /trunk/samtools/misc/indel_filter.pl
4991 A /trunk/samtools/misc/samtools.pl
4993 * move indel_filter.pl to samtools.pl
4995 ------------------------------------------------------------------------
4996 r126 | lh3lh3 | 2009-02-14 16:22:30 -0500 (Sat, 14 Feb 2009) | 3 lines
4998 M /trunk/samtools/bam_mate.c
4999 M /trunk/samtools/bamtk.c
5002 * fixed a bug in fixmate: SE reads are flagged as BAM_FMUNMAP
5004 ------------------------------------------------------------------------
5005 r125 | lh3lh3 | 2009-02-13 04:54:45 -0500 (Fri, 13 Feb 2009) | 3 lines
5007 M /trunk/samtools/bam_stat.c
5008 M /trunk/samtools/bamtk.c
5011 * fixed a minor bug in flagstat
5013 ------------------------------------------------------------------------
5014 r124 | lh3lh3 | 2009-02-12 06:15:32 -0500 (Thu, 12 Feb 2009) | 3 lines
5016 M /trunk/samtools/bam_maqcns.c
5017 M /trunk/samtools/bamtk.c
5018 M /trunk/samtools/misc/indel_filter.pl
5021 * improve indel caller by setting maximum window size
5023 ------------------------------------------------------------------------
5024 r123 | lh3lh3 | 2009-02-12 05:30:29 -0500 (Thu, 12 Feb 2009) | 2 lines
5026 M /trunk/samtools/bam_plcmd.c
5027 M /trunk/samtools/bamtk.c
5029 * output max mapping quality in indel line
5031 ------------------------------------------------------------------------
5032 r122 | lh3lh3 | 2009-02-11 05:59:10 -0500 (Wed, 11 Feb 2009) | 2 lines
5034 M /trunk/samtools/misc/maq2sam.c
5036 fixed a bug in generating tag AM
5038 ------------------------------------------------------------------------
5039 r121 | lh3lh3 | 2009-02-03 05:43:11 -0500 (Tue, 03 Feb 2009) | 2 lines
5041 M /trunk/samtools/bam_index.c
5042 M /trunk/samtools/bamtk.c
5044 fixed a potential memory problem in indexing
5046 ------------------------------------------------------------------------
5047 r120 | bhandsaker | 2009-02-02 10:52:52 -0500 (Mon, 02 Feb 2009) | 2 lines
5049 M /trunk/samtools/Makefile
5051 Pass LIBS to recursive targets to facilitate building at Broad.
5053 ------------------------------------------------------------------------
5054 r119 | lh3lh3 | 2009-02-02 05:12:15 -0500 (Mon, 02 Feb 2009) | 4 lines
5056 M /trunk/samtools/ChangeLog
5057 M /trunk/samtools/bam_plcmd.c
5058 M /trunk/samtools/bam_stat.c
5059 M /trunk/samtools/bamtk.c
5062 * fixed a bug in generating GLFv2 for indels
5063 * improve flagstat report a little bit
5065 ------------------------------------------------------------------------
5066 r118 | lh3lh3 | 2009-01-29 07:33:23 -0500 (Thu, 29 Jan 2009) | 3 lines
5068 M /trunk/samtools/Makefile
5069 A /trunk/samtools/bam_stat.c
5070 M /trunk/samtools/bamtk.c
5073 * added flagstat command
5075 ------------------------------------------------------------------------
5076 r116 | lh3lh3 | 2009-01-28 08:31:12 -0500 (Wed, 28 Jan 2009) | 2 lines
5078 M /trunk/samtools/ChangeLog
5079 M /trunk/samtools/NEWS
5080 M /trunk/samtools/bamtk.c
5081 M /trunk/samtools/samtools.1
5083 Release SAMtools-0.1.2
5085 ------------------------------------------------------------------------
5086 r115 | lh3lh3 | 2009-01-28 07:54:08 -0500 (Wed, 28 Jan 2009) | 2 lines
5088 A /trunk/samtools/misc/indel_filter.pl
5090 Script for filtering indel results
5092 ------------------------------------------------------------------------
5093 r114 | lh3lh3 | 2009-01-25 06:45:37 -0500 (Sun, 25 Jan 2009) | 2 lines
5095 A /trunk/samtools/misc/zoom2sam.pl
5099 ------------------------------------------------------------------------
5100 r113 | lh3lh3 | 2009-01-24 09:25:07 -0500 (Sat, 24 Jan 2009) | 2 lines
5102 A /trunk/samtools/misc/novo2sam.pl
5104 add a script to convert novo alignment to SAM
5106 ------------------------------------------------------------------------
5107 r112 | lh3lh3 | 2009-01-23 15:57:39 -0500 (Fri, 23 Jan 2009) | 2 lines
5109 M /trunk/samtools/ChangeLog
5110 M /trunk/samtools/ChangeLog.old
5111 M /trunk/samtools/samtools.1
5113 update documentation and ChangeLog
5115 ------------------------------------------------------------------------
5116 r111 | lh3lh3 | 2009-01-23 14:22:59 -0500 (Fri, 23 Jan 2009) | 3 lines
5118 M /trunk/samtools/bam_sort.c
5119 M /trunk/samtools/bamtk.c
5122 * fixed a bug in "merge" command line
5124 ------------------------------------------------------------------------
5125 r110 | lh3lh3 | 2009-01-22 10:36:48 -0500 (Thu, 22 Jan 2009) | 3 lines
5127 M /trunk/samtools/misc/Makefile
5128 A /trunk/samtools/misc/bowtie2sam.pl (from /branches/dev/samtools/misc/bowtie2sam.pl:108)
5129 M /trunk/samtools/misc/export2sam.pl
5130 A /trunk/samtools/misc/soap2sam.pl (from /branches/dev/samtools/misc/soap2sam.pl:108)
5131 A /trunk/samtools/misc/wgsim.c (from /branches/dev/samtools/misc/wgsim.c:108)
5132 A /trunk/samtools/misc/wgsim_eval.pl (from /branches/dev/samtools/misc/wgsim_eval.pl:108)
5134 * merge from branches/dev/
5135 * all future development will happen here
5137 ------------------------------------------------------------------------
5138 r109 | lh3lh3 | 2009-01-22 10:14:27 -0500 (Thu, 22 Jan 2009) | 3 lines
5140 M /trunk/samtools/COPYING
5141 M /trunk/samtools/ChangeLog
5142 A /trunk/samtools/INSTALL (from /branches/dev/samtools/INSTALL:108)
5143 M /trunk/samtools/Makefile
5144 A /trunk/samtools/Makefile.lite (from /branches/dev/samtools/Makefile.lite:108)
5145 M /trunk/samtools/bam.c
5146 M /trunk/samtools/bam.h
5147 M /trunk/samtools/bam_import.c
5148 M /trunk/samtools/bam_index.c
5149 M /trunk/samtools/bam_lpileup.c
5150 M /trunk/samtools/bam_maqcns.c
5151 M /trunk/samtools/bam_maqcns.h
5152 A /trunk/samtools/bam_mate.c (from /branches/dev/samtools/bam_mate.c:108)
5153 M /trunk/samtools/bam_pileup.c
5154 M /trunk/samtools/bam_plcmd.c
5155 A /trunk/samtools/bam_rmdup.c (from /branches/dev/samtools/bam_rmdup.c:108)
5156 M /trunk/samtools/bam_sort.c
5157 M /trunk/samtools/bamtk.c
5158 M /trunk/samtools/bgzf.h
5159 M /trunk/samtools/examples/00README.txt
5160 A /trunk/samtools/examples/Makefile (from /branches/dev/samtools/examples/Makefile:108)
5161 D /trunk/samtools/examples/ex1.fa.fai
5162 M /trunk/samtools/examples/ex1.sam.gz
5163 M /trunk/samtools/faidx.c
5164 A /trunk/samtools/glf.c (from /branches/dev/samtools/glf.c:108)
5165 M /trunk/samtools/glf.h
5166 M /trunk/samtools/misc/Makefile
5167 M /trunk/samtools/misc/maq2sam.c
5168 M /trunk/samtools/razf.c
5169 M /trunk/samtools/source.dot
5171 * Merge from branches/dev/
5172 * all future development will happen here at trunk/
5174 ------------------------------------------------------------------------
5175 r79 | bhandsaker | 2009-01-07 16:42:15 -0500 (Wed, 07 Jan 2009) | 2 lines
5177 M /trunk/samtools/bam_maqcns.c
5178 M /trunk/samtools/bam_tview.c
5180 Fix problem with compiling without curses.
5182 ------------------------------------------------------------------------
5183 r63 | lh3lh3 | 2008-12-22 10:58:02 -0500 (Mon, 22 Dec 2008) | 2 lines
5185 A /trunk/samtools (from /branches/dev/samtools:62)
5189 ------------------------------------------------------------------------
5190 r62 | lh3lh3 | 2008-12-22 10:55:13 -0500 (Mon, 22 Dec 2008) | 2 lines
5192 A /branches/dev/samtools/NEWS
5193 M /branches/dev/samtools/bamtk.c
5194 M /branches/dev/samtools/samtools.1
5196 Release samtools-0.1.1
5198 ------------------------------------------------------------------------
5199 r61 | lh3lh3 | 2008-12-22 10:46:08 -0500 (Mon, 22 Dec 2008) | 10 lines
5201 M /branches/dev/samtools/bam_aux.c
5202 M /branches/dev/samtools/bam_index.c
5203 M /branches/dev/samtools/bam_plcmd.c
5204 M /branches/dev/samtools/bam_tview.c
5205 M /branches/dev/samtools/bamtk.c
5206 M /branches/dev/samtools/razf.c
5207 M /branches/dev/samtools/samtools.1
5210 * fixed a bug in razf.c: reset z_eof when razf_seek() is called
5211 * fixed a memory leak in parsing a region
5212 * changed pileup a little bit when -s is in use: output ^ and $
5213 * when a bam is not indexed, output more meaningful error message
5214 * fixed a bug in indexing for small alignment
5215 * fixed a bug in the viewer when we come to the end of a reference file
5216 * updated documentation
5217 * prepare to release 0.1.1
5219 ------------------------------------------------------------------------
5220 r60 | lh3lh3 | 2008-12-22 10:10:16 -0500 (Mon, 22 Dec 2008) | 2 lines
5222 A /branches/dev/samtools/examples
5223 A /branches/dev/samtools/examples/00README.txt
5224 A /branches/dev/samtools/examples/ex1.fa
5225 A /branches/dev/samtools/examples/ex1.fa.fai
5226 A /branches/dev/samtools/examples/ex1.sam.gz
5230 ------------------------------------------------------------------------
5231 r59 | lh3lh3 | 2008-12-22 04:38:15 -0500 (Mon, 22 Dec 2008) | 2 lines
5233 M /branches/dev/samtools/ChangeLog
5237 ------------------------------------------------------------------------
5238 r58 | lh3lh3 | 2008-12-20 18:06:00 -0500 (Sat, 20 Dec 2008) | 3 lines
5240 M /branches/dev/samtools/misc/export2sam.pl
5243 * fixed several bugs
5245 ------------------------------------------------------------------------
5246 r57 | lh3lh3 | 2008-12-20 10:44:20 -0500 (Sat, 20 Dec 2008) | 2 lines
5248 A /branches/dev/samtools/misc/export2sam.pl
5250 convert Export format to SAM; not thoroughly tested
5252 ------------------------------------------------------------------------
5253 r56 | lh3lh3 | 2008-12-19 17:13:28 -0500 (Fri, 19 Dec 2008) | 6 lines
5255 M /branches/dev/samtools/bam_import.c
5256 M /branches/dev/samtools/bam_plcmd.c
5257 M /branches/dev/samtools/bam_tview.c
5258 M /branches/dev/samtools/bamtk.c
5259 A /branches/dev/samtools/source.dot
5262 * pileup: generate maq-like simple output
5263 * pileup: allow to output pileup at required sites
5264 * source.dot: source file relationship graph
5265 * tview: fixed a minor bug
5267 ------------------------------------------------------------------------
5268 r55 | lh3lh3 | 2008-12-19 15:10:26 -0500 (Fri, 19 Dec 2008) | 2 lines
5270 D /branches/dev/samtools/misc/all2sam.pl
5274 ------------------------------------------------------------------------
5275 r54 | lh3lh3 | 2008-12-16 17:34:25 -0500 (Tue, 16 Dec 2008) | 2 lines
5277 A /branches/dev/samtools/COPYING
5278 M /branches/dev/samtools/bam.h
5279 M /branches/dev/samtools/faidx.h
5280 M /branches/dev/samtools/khash.h
5281 M /branches/dev/samtools/kseq.h
5282 M /branches/dev/samtools/ksort.h
5283 M /branches/dev/samtools/samtools.1
5285 Added copyright information and a bit more documentation. No code change.
5287 ------------------------------------------------------------------------
5288 r53 | lh3lh3 | 2008-12-16 08:40:18 -0500 (Tue, 16 Dec 2008) | 3 lines
5290 M /branches/dev/samtools/bam.c
5291 M /branches/dev/samtools/bam.h
5292 M /branches/dev/samtools/bam_index.c
5293 M /branches/dev/samtools/bam_maqcns.c
5294 M /branches/dev/samtools/bamtk.c
5297 * improved efficiency of the indel caller for spliced alignments
5299 ------------------------------------------------------------------------
5300 r52 | lh3lh3 | 2008-12-16 05:28:20 -0500 (Tue, 16 Dec 2008) | 3 lines
5302 M /branches/dev/samtools/bam.c
5303 M /branches/dev/samtools/bam.h
5304 M /branches/dev/samtools/bam_aux.c
5305 M /branches/dev/samtools/bam_index.c
5306 M /branches/dev/samtools/bamtk.c
5309 * a bit code cleanup: reduce the dependency between source files
5311 ------------------------------------------------------------------------
5312 r51 | lh3lh3 | 2008-12-15 09:29:32 -0500 (Mon, 15 Dec 2008) | 3 lines
5314 M /branches/dev/samtools/bam_maqcns.c
5315 M /branches/dev/samtools/bam_plcmd.c
5316 M /branches/dev/samtools/bamtk.c
5319 * fixed a memory leak
5321 ------------------------------------------------------------------------
5322 r50 | lh3lh3 | 2008-12-15 09:00:13 -0500 (Mon, 15 Dec 2008) | 2 lines
5324 M /branches/dev/samtools/ChangeLog
5325 M /branches/dev/samtools/bam.h
5326 M /branches/dev/samtools/samtools.1
5328 update documentation, ChangeLog and a comment
5330 ------------------------------------------------------------------------
5331 r49 | lh3lh3 | 2008-12-15 08:36:43 -0500 (Mon, 15 Dec 2008) | 6 lines
5333 M /branches/dev/samtools/Makefile
5334 M /branches/dev/samtools/bam.h
5335 M /branches/dev/samtools/bam_maqcns.c
5336 M /branches/dev/samtools/bam_maqcns.h
5337 M /branches/dev/samtools/bam_pileup.c
5338 A /branches/dev/samtools/bam_plcmd.c
5339 M /branches/dev/samtools/bamtk.c
5340 M /branches/dev/samtools/samtools.1
5343 * moved pileup command to a separate source file
5344 * added indel caller
5345 * added bam_cal_segend(). (NOT WORKING for spliced alignment!!!)
5346 * updated documentation
5348 ------------------------------------------------------------------------
5349 r48 | lh3lh3 | 2008-12-12 08:55:36 -0500 (Fri, 12 Dec 2008) | 3 lines
5351 M /branches/dev/samtools/bam_maqcns.c
5352 M /branches/dev/samtools/bamtk.c
5355 * fixed another bug in maqcns when there is a nearby deletion
5357 ------------------------------------------------------------------------
5358 r47 | lh3lh3 | 2008-12-12 08:42:16 -0500 (Fri, 12 Dec 2008) | 5 lines
5360 M /branches/dev/samtools/bam_maqcns.c
5361 M /branches/dev/samtools/bam_pileup.c
5362 M /branches/dev/samtools/bamtk.c
5365 * pileup: outputing consensus is now optional
5366 * fixed a bug in glfgen. This bug also exists in maq's glfgen. However,
5367 I am not quite sure why the previous version may have problem.
5369 ------------------------------------------------------------------------
5370 r46 | lh3lh3 | 2008-12-12 06:44:56 -0500 (Fri, 12 Dec 2008) | 6 lines
5372 M /branches/dev/samtools/bam_pileup.c
5373 M /branches/dev/samtools/bamtk.c
5376 * add maq consensus to pileup. However, I will move this part to a new
5377 command as strictly speaking, consensus callin is not part of pileup,
5378 and imposing it would make it harder to generate for other language
5381 ------------------------------------------------------------------------
5382 r45 | bhandsaker | 2008-12-11 15:43:56 -0500 (Thu, 11 Dec 2008) | 2 lines
5384 M /branches/dev/samtools/bgzf.c
5386 Fix bug in tell() after reads that consume to the exact end of a block.
5388 ------------------------------------------------------------------------
5389 r44 | lh3lh3 | 2008-12-11 04:36:53 -0500 (Thu, 11 Dec 2008) | 2 lines
5391 M /branches/dev/samtools/samtools.1
5395 ------------------------------------------------------------------------
5396 r43 | lh3lh3 | 2008-12-11 04:25:36 -0500 (Thu, 11 Dec 2008) | 4 lines
5398 M /branches/dev/samtools/bam_import.c
5399 M /branches/dev/samtools/bamtk.c
5402 * fixed a bug in parser when there is auxiliary fields
5403 * made the parser a bit more robust
5405 ------------------------------------------------------------------------
5406 r42 | lh3lh3 | 2008-12-10 09:57:29 -0500 (Wed, 10 Dec 2008) | 5 lines
5408 M /branches/dev/samtools/bam_index.c
5409 M /branches/dev/samtools/bamtk.c
5410 M /branches/dev/samtools/bgzf.c
5413 * fixed a bug in bgzf (only reading is affected)
5414 * fixed a typo in bam_index.c
5415 * in bam_index.c, check potential bugs in the underlying I/O library
5417 ------------------------------------------------------------------------
5418 r41 | lh3lh3 | 2008-12-10 07:53:08 -0500 (Wed, 10 Dec 2008) | 2 lines
5420 M /branches/dev/samtools/samtools.1
5424 ------------------------------------------------------------------------
5425 r40 | lh3lh3 | 2008-12-10 06:52:10 -0500 (Wed, 10 Dec 2008) | 5 lines
5427 M /branches/dev/samtools/bam.h
5428 M /branches/dev/samtools/bam_pileup.c
5429 M /branches/dev/samtools/bamtk.c
5432 * tried to make pileup work with clipping (previously not), though NOT tested
5433 * removed -v from pileup
5434 * made pileup take the reference sequence
5436 ------------------------------------------------------------------------
5437 r39 | lh3lh3 | 2008-12-09 06:59:28 -0500 (Tue, 09 Dec 2008) | 4 lines
5439 M /branches/dev/samtools/bam_import.c
5440 M /branches/dev/samtools/bamtk.c
5441 M /branches/dev/samtools/samtools.1
5444 * in parser, recognize "=", rather than ",", as a match
5445 * in parser, correctl parse "=" at the MRNM field.
5447 ------------------------------------------------------------------------
5448 r38 | lh3lh3 | 2008-12-09 06:39:07 -0500 (Tue, 09 Dec 2008) | 2 lines
5450 M /branches/dev/samtools/misc/maq2sam.c
5452 fixed a bug in handling maq flag 64 and 192
5454 ------------------------------------------------------------------------
5455 r37 | lh3lh3 | 2008-12-09 04:53:46 -0500 (Tue, 09 Dec 2008) | 2 lines
5457 M /branches/dev/samtools/misc/md5fa.c
5459 also calculate unordered md5sum check
5461 ------------------------------------------------------------------------
5462 r36 | lh3lh3 | 2008-12-09 04:46:21 -0500 (Tue, 09 Dec 2008) | 2 lines
5464 M /branches/dev/samtools/misc/md5fa.c
5466 fixed a minor bug when there are space in the sequence
5468 ------------------------------------------------------------------------
5469 r35 | lh3lh3 | 2008-12-09 04:40:45 -0500 (Tue, 09 Dec 2008) | 2 lines
5471 M /branches/dev/samtools/misc/md5fa.c
5473 fixed a potential memory leak
5475 ------------------------------------------------------------------------
5476 r34 | lh3lh3 | 2008-12-08 09:52:17 -0500 (Mon, 08 Dec 2008) | 2 lines
5478 M /branches/dev/samtools/bam_import.c
5479 M /branches/dev/samtools/bam_index.c
5480 M /branches/dev/samtools/bamtk.c
5482 * fixed a bug in import: bin is wrongly calculated
5484 ------------------------------------------------------------------------
5485 r33 | lh3lh3 | 2008-12-08 09:08:01 -0500 (Mon, 08 Dec 2008) | 2 lines
5487 M /branches/dev/samtools/misc/all2sam.pl
5491 ------------------------------------------------------------------------
5492 r32 | lh3lh3 | 2008-12-08 07:56:02 -0500 (Mon, 08 Dec 2008) | 3 lines
5494 M /branches/dev/samtools/Makefile
5495 M /branches/dev/samtools/kseq.h
5496 M /branches/dev/samtools/misc/Makefile
5497 A /branches/dev/samtools/misc/md5.c
5498 A /branches/dev/samtools/misc/md5.h
5499 A /branches/dev/samtools/misc/md5fa.c
5501 * fixed two warnings in kseq.h
5502 * added md5sum utilities
5504 ------------------------------------------------------------------------
5505 r31 | lh3lh3 | 2008-12-08 06:35:29 -0500 (Mon, 08 Dec 2008) | 5 lines
5507 M /branches/dev/samtools/Makefile
5508 M /branches/dev/samtools/bam_import.c
5509 M /branches/dev/samtools/bamtk.c
5510 A /branches/dev/samtools/kseq.h
5511 D /branches/dev/samtools/kstream.h
5514 * replace kstream with kseq. kseq is a superset of kstream. I need the
5515 extra functions in kseq.h.
5516 * also compile stand-alone faidx
5518 ------------------------------------------------------------------------
5519 r30 | lh3lh3 | 2008-12-08 06:17:04 -0500 (Mon, 08 Dec 2008) | 3 lines
5521 M /branches/dev/samtools/bam.h
5522 M /branches/dev/samtools/bam_sort.c
5523 M /branches/dev/samtools/bamtk.c
5526 * sorting by read names is available
5528 ------------------------------------------------------------------------
5529 r29 | lh3lh3 | 2008-12-08 05:29:02 -0500 (Mon, 08 Dec 2008) | 3 lines
5531 M /branches/dev/samtools/bam.c
5532 M /branches/dev/samtools/bam.h
5533 M /branches/dev/samtools/bam_import.c
5534 M /branches/dev/samtools/bam_maqcns.c
5535 M /branches/dev/samtools/bam_pileup.c
5536 M /branches/dev/samtools/bam_sort.c
5537 M /branches/dev/samtools/bam_tview.c
5538 M /branches/dev/samtools/bamtk.c
5539 M /branches/dev/samtools/misc/maq2sam.c
5542 * format change to meet the latest specification
5544 ------------------------------------------------------------------------
5545 r28 | lh3lh3 | 2008-12-04 11:09:21 -0500 (Thu, 04 Dec 2008) | 3 lines
5547 M /branches/dev/samtools/bam_maqcns.c
5548 M /branches/dev/samtools/misc/maq2sam.c
5550 * minor change in maqcns: special care when n==0
5551 * change maq2sam to meet the latest specification
5553 ------------------------------------------------------------------------
5554 r27 | lh3lh3 | 2008-12-04 10:55:44 -0500 (Thu, 04 Dec 2008) | 2 lines
5556 M /branches/dev/samtools/razf.c
5557 M /branches/dev/samtools/razf.h
5559 considerable code clean up in razf
5561 ------------------------------------------------------------------------
5562 r26 | lh3lh3 | 2008-12-04 10:08:18 -0500 (Thu, 04 Dec 2008) | 2 lines
5564 M /branches/dev/samtools/ChangeLog
5565 M /branches/dev/samtools/Makefile
5566 M /branches/dev/samtools/faidx.c
5568 make RAZF optional in faidx.c
5570 ------------------------------------------------------------------------
5571 r25 | lh3lh3 | 2008-12-01 10:27:22 -0500 (Mon, 01 Dec 2008) | 3 lines
5573 M /branches/dev/samtools/Makefile
5574 M /branches/dev/samtools/bam.h
5575 M /branches/dev/samtools/bam_aux.c
5576 M /branches/dev/samtools/bamtk.c
5577 M /branches/dev/samtools/samtools.1
5580 * added routines for retrieving aux data, NOT TESTED YET!
5582 ------------------------------------------------------------------------
5583 r24 | lh3lh3 | 2008-12-01 09:29:43 -0500 (Mon, 01 Dec 2008) | 5 lines
5585 M /branches/dev/samtools/bam.c
5586 M /branches/dev/samtools/bam_import.c
5587 M /branches/dev/samtools/bam_maqcns.c
5588 M /branches/dev/samtools/bamtk.c
5589 M /branches/dev/samtools/bgzf.c
5590 M /branches/dev/samtools/samtools.1
5593 * bgzf: fixed a potential integer overflow on 32-it machines
5594 * maqcns: set the minimum combined quality as 0
5595 * supporting hex strings
5597 ------------------------------------------------------------------------
5598 r23 | lh3lh3 | 2008-11-27 12:14:37 -0500 (Thu, 27 Nov 2008) | 3 lines
5600 M /branches/dev/samtools/bam_maqcns.c
5601 M /branches/dev/samtools/bamtk.c
5604 * fixed the bug in maqcns
5606 ------------------------------------------------------------------------
5607 r22 | lh3lh3 | 2008-11-27 12:08:11 -0500 (Thu, 27 Nov 2008) | 3 lines
5609 M /branches/dev/samtools/Makefile
5610 M /branches/dev/samtools/bam.h
5611 A /branches/dev/samtools/bam_maqcns.c
5612 A /branches/dev/samtools/bam_maqcns.h
5613 M /branches/dev/samtools/bam_tview.c
5614 M /branches/dev/samtools/bamtk.c
5615 A /branches/dev/samtools/glf.h
5618 * add MAQ consensus caller, currently BUGGY!
5620 ------------------------------------------------------------------------
5621 r21 | lh3lh3 | 2008-11-27 08:51:28 -0500 (Thu, 27 Nov 2008) | 4 lines
5623 M /branches/dev/samtools/bam_pileup.c
5624 M /branches/dev/samtools/bam_tview.c
5625 M /branches/dev/samtools/bamtk.c
5628 * tview: display padded alignment (but not P operation)
5629 * better coordinates and reference sequence
5631 ------------------------------------------------------------------------
5632 r19 | lh3lh3 | 2008-11-27 04:26:05 -0500 (Thu, 27 Nov 2008) | 2 lines
5634 A /branches/dev/samtools/ChangeLog
5638 ------------------------------------------------------------------------
5639 r18 | lh3lh3 | 2008-11-27 04:24:45 -0500 (Thu, 27 Nov 2008) | 3 lines
5641 D /branches/dev/samtools/ChangeLog
5642 A /branches/dev/samtools/ChangeLog.old (from /branches/dev/samtools/ChangeLog:6)
5644 Rename ChangeLog to ChangeLog.old. This old ChangeLog is generated from
5645 the log of my personal SVN repository.
5647 ------------------------------------------------------------------------
5648 r17 | lh3lh3 | 2008-11-27 04:22:55 -0500 (Thu, 27 Nov 2008) | 6 lines
5650 M /branches/dev/samtools/Makefile
5651 M /branches/dev/samtools/bamtk.c
5652 M /branches/dev/samtools/bgzf.c
5655 * declare fseeko and ftello as some Linux may not do this by default and
5656 missing these declarations will make bgzf buggy
5657 * get rid of some harmless warings
5658 * use BGZF by default, now
5660 ------------------------------------------------------------------------
5661 r16 | lh3lh3 | 2008-11-26 16:19:11 -0500 (Wed, 26 Nov 2008) | 4 lines
5663 M /branches/dev/samtools/bam_index.c
5664 M /branches/dev/samtools/bamtk.c
5665 M /branches/dev/samtools/razf.c
5668 * fixed a bug in razf_read()
5669 * give more warnings when the file is truncated (or due to bugs in I/O library)
5671 ------------------------------------------------------------------------
5672 r15 | lh3lh3 | 2008-11-26 15:41:39 -0500 (Wed, 26 Nov 2008) | 2 lines
5674 M /branches/dev/samtools/bgzf.c
5676 fixed a bug in bgzf.c at the end of the file
5678 ------------------------------------------------------------------------
5679 r14 | lh3lh3 | 2008-11-26 12:05:18 -0500 (Wed, 26 Nov 2008) | 4 lines
5681 M /branches/dev/samtools/bamtk.c
5684 * a lot happened to RAZF, although samtools itself is untouched. Better
5685 also update the version number anyway to avoid confusion
5687 ------------------------------------------------------------------------
5688 r13 | lh3lh3 | 2008-11-26 12:03:48 -0500 (Wed, 26 Nov 2008) | 2 lines
5690 M /branches/dev/samtools/razf.c
5692 a change from Jue, but I think it should not matter
5694 ------------------------------------------------------------------------
5695 r12 | lh3lh3 | 2008-11-26 11:48:14 -0500 (Wed, 26 Nov 2008) | 3 lines
5697 M /branches/dev/samtools/razf.c
5699 fixed a potential bug in razf. However, it seems still buggy, just
5700 rarely happens, very rarely.
5702 ------------------------------------------------------------------------
5703 r11 | lh3lh3 | 2008-11-26 09:02:56 -0500 (Wed, 26 Nov 2008) | 2 lines
5705 M /branches/dev/samtools/razf.c
5707 fixed a bug in razf, with the help of Jue
5709 ------------------------------------------------------------------------
5710 r10 | lh3lh3 | 2008-11-26 06:55:32 -0500 (Wed, 26 Nov 2008) | 2 lines
5712 M /branches/dev/samtools/bam_index.c
5716 ------------------------------------------------------------------------
5717 r9 | lh3lh3 | 2008-11-26 06:37:05 -0500 (Wed, 26 Nov 2008) | 2 lines
5719 M /branches/dev/samtools/Makefile
5720 M /branches/dev/samtools/bam.h
5721 M /branches/dev/samtools/razf.c
5722 M /branches/dev/samtools/razf.h
5724 * Jue has updated razf to realize Bob's scheme
5726 ------------------------------------------------------------------------
5727 r7 | lh3lh3 | 2008-11-25 15:37:37 -0500 (Tue, 25 Nov 2008) | 2 lines
5729 A /branches/dev/samtools/samtools.1
5733 ------------------------------------------------------------------------
5734 r6 | lh3lh3 | 2008-11-25 15:37:16 -0500 (Tue, 25 Nov 2008) | 3 lines
5736 A /branches/dev/samtools/ChangeLog
5737 A /branches/dev/samtools/Makefile
5738 A /branches/dev/samtools/bam.c
5739 A /branches/dev/samtools/bam.h
5740 A /branches/dev/samtools/bam_aux.c
5741 A /branches/dev/samtools/bam_endian.h
5742 A /branches/dev/samtools/bam_import.c
5743 A /branches/dev/samtools/bam_index.c
5744 A /branches/dev/samtools/bam_lpileup.c
5745 A /branches/dev/samtools/bam_pileup.c
5746 A /branches/dev/samtools/bam_sort.c
5747 A /branches/dev/samtools/bam_tview.c
5748 A /branches/dev/samtools/bamtk.c
5749 A /branches/dev/samtools/bgzf.c
5750 A /branches/dev/samtools/bgzf.h
5751 A /branches/dev/samtools/bgzip.c
5752 A /branches/dev/samtools/faidx.c
5753 A /branches/dev/samtools/faidx.h
5754 A /branches/dev/samtools/khash.h
5755 A /branches/dev/samtools/ksort.h
5756 A /branches/dev/samtools/kstream.h
5757 A /branches/dev/samtools/misc
5758 A /branches/dev/samtools/misc/Makefile
5759 A /branches/dev/samtools/misc/all2sam.pl
5760 A /branches/dev/samtools/misc/maq2sam.c
5761 A /branches/dev/samtools/razf.c
5762 A /branches/dev/samtools/razf.h
5763 A /branches/dev/samtools/razip.c
5764 A /branches/dev/samtools/zutil.h
5766 The initial version of samtools, replicated from my local SVN repository.
5767 The current version is: 0.1.0-42. All future development will happen here.
5769 ------------------------------------------------------------------------
5770 r5 | lh3lh3 | 2008-11-25 15:30:49 -0500 (Tue, 25 Nov 2008) | 2 lines
5772 A /branches/dev/samtools
5774 samtools (C version)
5776 ------------------------------------------------------------------------