1 ------------------------------------------------------------------------
2 r612 | lh3lh3 | 2010-07-11 21:08:56 -0400 (Sun, 11 Jul 2010) | 2 lines
4 M /trunk/samtools/knetfile.c
6 fixed a compiling issue for Windows
8 ------------------------------------------------------------------------
9 r611 | lh3lh3 | 2010-07-11 20:59:15 -0400 (Sun, 11 Jul 2010) | 2 lines
11 M /trunk/samtools/bam_sort.c
13 fixed a bug in sorting when output to stdout (by Peter Chines)
15 ------------------------------------------------------------------------
16 r610 | lh3lh3 | 2010-07-09 17:05:10 -0400 (Fri, 09 Jul 2010) | 2 lines
18 M /trunk/samtools/NEWS
19 M /trunk/samtools/bam_plcmd.c
21 change the command line option of pileup
23 ------------------------------------------------------------------------
24 r609 | lh3lh3 | 2010-07-09 00:39:34 -0400 (Fri, 09 Jul 2010) | 2 lines
26 M /trunk/samtools/bam_pileup.c
27 A /trunk/samtools/examples/toy.fa
28 A /trunk/samtools/examples/toy.sam
30 make pileup work with CIGAR with I/D at the beginning or in the end
32 ------------------------------------------------------------------------
33 r608 | lh3lh3 | 2010-07-08 22:36:12 -0400 (Thu, 08 Jul 2010) | 3 lines
35 M /trunk/samtools/bam_maqcns.c
36 M /trunk/samtools/bam_maqcns.h
37 M /trunk/samtools/bam_plcmd.c
38 M /trunk/samtools/bam_tview.c
40 * make tview more friendly
41 * a temporary remedy for an issue in indel calling
43 ------------------------------------------------------------------------
44 r607 | lh3lh3 | 2010-07-08 14:43:52 -0400 (Thu, 08 Jul 2010) | 4 lines
46 M /trunk/samtools/bam_maqcns.c
47 M /trunk/samtools/bam_plcmd.c
48 M /trunk/samtools/bamtk.c
51 * improved the genotype accuracy for indels
52 * use the SOAPsnp model for SNP calling by default.
54 ------------------------------------------------------------------------
55 r606 | lh3lh3 | 2010-07-08 01:05:19 -0400 (Thu, 08 Jul 2010) | 2 lines
57 M /trunk/samtools/misc/Makefile
59 removed a debugging example
61 ------------------------------------------------------------------------
62 r605 | lh3lh3 | 2010-07-08 01:04:09 -0400 (Thu, 08 Jul 2010) | 4 lines
64 M /trunk/samtools/bam_maqcns.c
65 M /trunk/samtools/bamtk.c
67 * samtools-.1.7-18 (r605)
68 * fixed an issue when a deletion and mismatch occur at the same time
69 and the base quality is higher than 40 (if -I40).
71 ------------------------------------------------------------------------
72 r604 | lh3lh3 | 2010-07-02 19:32:24 -0400 (Fri, 02 Jul 2010) | 2 lines
74 M /trunk/samtools/bam.h
75 M /trunk/samtools/bam_index.c
76 M /trunk/samtools/misc/Makefile
78 fixed a minor bug in idxstats
80 ------------------------------------------------------------------------
81 r601 | lh3lh3 | 2010-06-16 09:03:59 -0400 (Wed, 16 Jun 2010) | 2 lines
83 M /trunk/samtools/bam_index.c
85 fixed a minor bug in indexing
87 ------------------------------------------------------------------------
88 r600 | lh3lh3 | 2010-06-15 10:17:53 -0400 (Tue, 15 Jun 2010) | 2 lines
90 M /trunk/samtools/ChangeLog
91 M /trunk/samtools/bam.c
93 change printf() to puts in exporting
95 ------------------------------------------------------------------------
96 r599 | lh3lh3 | 2010-06-13 21:41:11 -0400 (Sun, 13 Jun 2010) | 2 lines
98 M /trunk/samtools/bamtk.c
100 minor fix. No actual effect.
102 ------------------------------------------------------------------------
103 r598 | lh3lh3 | 2010-06-13 21:32:45 -0400 (Sun, 13 Jun 2010) | 2 lines
105 M /trunk/samtools/Makefile
107 added Makefile targets to compile shared/dynamic library
109 ------------------------------------------------------------------------
110 r596 | lh3lh3 | 2010-06-13 19:48:07 -0400 (Sun, 13 Jun 2010) | 3 lines
112 M /trunk/samtools/ChangeLog
113 M /trunk/samtools/bam_index.c
114 M /trunk/samtools/bamtk.c
116 * samtools-0.1.7-17 (r596)
117 * also keep the number of coor-less reads in the index file
119 ------------------------------------------------------------------------
120 r595 | lh3lh3 | 2010-06-13 18:54:26 -0400 (Sun, 13 Jun 2010) | 3 lines
122 M /trunk/samtools/bam_index.c
123 M /trunk/samtools/bamtk.c
125 * samtools-0.1.7-16 (r595)
126 * write additional information to bam index
128 ------------------------------------------------------------------------
129 r594 | lh3lh3 | 2010-06-13 17:29:52 -0400 (Sun, 13 Jun 2010) | 2 lines
131 M /trunk/samtools/bam_index.c
133 fixed a bug for unmapped sequences in indexing
135 ------------------------------------------------------------------------
136 r593 | lh3lh3 | 2010-06-12 18:11:32 -0400 (Sat, 12 Jun 2010) | 2 lines
138 M /trunk/samtools/bam.h
139 M /trunk/samtools/bam_index.c
140 M /trunk/samtools/bam_plcmd.c
141 M /trunk/samtools/samtools.1
145 ------------------------------------------------------------------------
146 r592 | lh3lh3 | 2010-06-12 18:02:38 -0400 (Sat, 12 Jun 2010) | 4 lines
148 M /trunk/samtools/ChangeLog
149 M /trunk/samtools/bam_aux.c
150 M /trunk/samtools/bam_index.c
151 M /trunk/samtools/bam_pileup.c
152 M /trunk/samtools/bam_plcmd.c
153 M /trunk/samtools/bamtk.c
155 * samtools-0.1.7-15 (r592)
156 * fixed a few minor memory leaks in the new pileup code
157 * improved the functionality of mpileup
159 ------------------------------------------------------------------------
160 r591 | lh3lh3 | 2010-06-12 14:09:22 -0400 (Sat, 12 Jun 2010) | 3 lines
162 M /trunk/samtools/bam.h
163 M /trunk/samtools/bam_pileup.c
164 M /trunk/samtools/bam_plcmd.c
165 M /trunk/samtools/bamtk.c
167 * samtools-0.1.7-14 (r591)
168 * elementary multi-way pileup. More testing and more functionality to be done.
170 ------------------------------------------------------------------------
171 r590 | lh3lh3 | 2010-06-12 01:00:24 -0400 (Sat, 12 Jun 2010) | 3 lines
173 M /trunk/samtools/bam.h
174 M /trunk/samtools/bam_pileup.c
175 M /trunk/samtools/bamtk.c
177 * samtools-0.1.7-13 (r590)
178 * added mpileup APIs. No compiling errors, but not tested at all. It is late.
180 ------------------------------------------------------------------------
181 r589 | lh3lh3 | 2010-06-11 22:37:09 -0400 (Fri, 11 Jun 2010) | 3 lines
183 M /trunk/samtools/bam.h
184 M /trunk/samtools/bam_pileup.c
185 M /trunk/samtools/bamtk.c
187 * samtools-0.1.7-12 (r589)
188 * added iterator-like APIs for pileup
190 ------------------------------------------------------------------------
191 r588 | lh3lh3 | 2010-06-11 17:41:13 -0400 (Fri, 11 Jun 2010) | 3 lines
193 M /trunk/samtools/bam_index.c
194 M /trunk/samtools/bamtk.c
196 * samtools-0.1.7-11 (r588)
197 * ported a few improvements from tabix back to samtools
199 ------------------------------------------------------------------------
200 r587 | lh3lh3 | 2010-06-11 17:33:16 -0400 (Fri, 11 Jun 2010) | 3 lines
202 M /trunk/samtools/bam.h
203 M /trunk/samtools/bam_index.c
204 M /trunk/samtools/bamtk.c
206 * samtools-0.1.7-10 (r587)
207 * added iterator interface for bam_fetch (ported back from tabix)
209 ------------------------------------------------------------------------
210 r586 | lh3lh3 | 2010-06-11 13:23:53 -0400 (Fri, 11 Jun 2010) | 3 lines
212 M /trunk/samtools/Makefile
213 A /trunk/samtools/bam_reheader.c
214 M /trunk/samtools/bamtk.c
215 M /trunk/samtools/bgzf.c
217 * samtools-0.1.7-9 (r586)
218 * added "reheader" to replace the BAM header
220 ------------------------------------------------------------------------
221 r585 | lh3lh3 | 2010-06-11 12:22:06 -0400 (Fri, 11 Jun 2010) | 3 lines
223 M /trunk/samtools/bam.c
224 M /trunk/samtools/bamtk.c
225 M /trunk/samtools/kstring.h
227 * samtools-0.1.7-8 (r585)
230 ------------------------------------------------------------------------
231 r584 | lh3lh3 | 2010-06-11 12:00:41 -0400 (Fri, 11 Jun 2010) | 4 lines
233 M /trunk/samtools/bam.c
234 M /trunk/samtools/bamtk.c
235 M /trunk/samtools/bgzf.c
236 M /trunk/samtools/bgzf.h
237 M /trunk/samtools/kstring.h
238 M /trunk/samtools/misc/wgsim_eval.pl
240 * samtools-0.1.7-7 (r584)
241 * ported tabix BGZF to samtools
242 * flush BGZF after writing the BAM header and between alignment boundaries
244 ------------------------------------------------------------------------
245 r583 | petulda | 2010-06-11 11:58:20 -0400 (Fri, 11 Jun 2010) | 1 line
247 A /trunk/samtools/misc/varfilter.py
249 Initial release on behalf of Aylwyn Scally
250 ------------------------------------------------------------------------
251 r561 | petulda | 2010-05-07 08:41:56 -0400 (Fri, 07 May 2010) | 1 line
253 M /trunk/samtools/samtools.1
255 Added a note about the indels coordinates
256 ------------------------------------------------------------------------
257 r551 | petulda | 2010-04-23 09:42:13 -0400 (Fri, 23 Apr 2010) | 1 line
259 M /trunk/samtools/misc/sam2vcf.pl
261 Added the possibility to print or not to print the reference allele
262 ------------------------------------------------------------------------
263 r546 | petulda | 2010-04-15 04:33:55 -0400 (Thu, 15 Apr 2010) | 1 line
265 M /trunk/samtools/sam_header.c
267 More descriptive message for space separated tags
268 ------------------------------------------------------------------------
269 r545 | petulda | 2010-04-14 11:44:50 -0400 (Wed, 14 Apr 2010) | 1 line
271 M /trunk/samtools/misc/sam2vcf.pl
273 Speedup with -i, no need to query the reference all the time
274 ------------------------------------------------------------------------
275 r541 | petulda | 2010-03-15 10:03:51 -0400 (Mon, 15 Mar 2010) | 1 line
277 M /trunk/samtools/sam_header.c
279 Fixed the order of sequences in the header
280 ------------------------------------------------------------------------
281 r540 | petulda | 2010-03-04 06:28:35 -0500 (Thu, 04 Mar 2010) | 1 line
283 M /trunk/samtools/misc/sam2vcf.pl
285 Added possibility to select indels only and fixed a bug in reporting homozygous indels.
286 ------------------------------------------------------------------------
287 r539 | jmarshall | 2010-02-27 06:48:17 -0500 (Sat, 27 Feb 2010) | 4 lines
289 M /trunk/samtools/bam.c
291 Improve the invalid 'BAM\1' magic number error message, and also print it
292 when no bytes can be read from the alleged BAM file, e.g., in the common
293 user error case when a SAM file has accidentally been supplied.
295 ------------------------------------------------------------------------
296 r538 | petulda | 2010-02-26 10:51:40 -0500 (Fri, 26 Feb 2010) | 1 line
298 M /trunk/samtools/AUTHORS
299 M /trunk/samtools/bam.h
300 M /trunk/samtools/bam_import.c
301 M /trunk/samtools/sam_header.c
303 Improved efficiency of header parsing
304 ------------------------------------------------------------------------
305 r537 | lh3lh3 | 2010-02-23 21:08:48 -0500 (Tue, 23 Feb 2010) | 3 lines
307 M /trunk/samtools/misc/export2sam.pl
309 Updated export2sam.pl by Chris Saunders from Illumina.
312 ------------------------------------------------------------------------
313 r536 | petulda | 2010-02-17 08:32:53 -0500 (Wed, 17 Feb 2010) | 1 line
315 M /trunk/samtools/misc/samtools.pl
317 Fixed filtering of SNPs near indels. Added min indel and SNP quality filter.
318 ------------------------------------------------------------------------
319 r535 | petulda | 2010-02-12 04:52:37 -0500 (Fri, 12 Feb 2010) | 1 line
321 M /trunk/samtools/misc/sam2vcf.pl
323 Print an error for pileups in simple format
324 ------------------------------------------------------------------------
325 r534 | lh3lh3 | 2010-02-11 14:01:41 -0500 (Thu, 11 Feb 2010) | 2 lines
327 M /trunk/samtools/bam_plcmd.c
329 added a hidden option in pileup to output the base position (for Erin)
331 ------------------------------------------------------------------------
332 r533 | petulda | 2010-02-09 10:12:14 -0500 (Tue, 09 Feb 2010) | 1 line
334 M /trunk/samtools/misc/sam2vcf.pl
336 Added possibility to specify a custom column title for the data column
337 ------------------------------------------------------------------------
338 r532 | petulda | 2010-02-09 09:46:09 -0500 (Tue, 09 Feb 2010) | 1 line
340 M /trunk/samtools/bam_plcmd.c
342 Added the -d option to limit maximum depth for indels.
343 ------------------------------------------------------------------------
344 r531 | petulda | 2010-02-03 07:57:27 -0500 (Wed, 03 Feb 2010) | 1 line
346 M /trunk/samtools/misc/sam2vcf.pl
349 ------------------------------------------------------------------------
350 r530 | lh3lh3 | 2010-02-01 09:13:19 -0500 (Mon, 01 Feb 2010) | 3 lines
352 M /trunk/samtools/ChangeLog
353 M /trunk/samtools/bam_plcmd.c
354 M /trunk/samtools/bamtk.c
355 M /trunk/samtools/misc/samtools.pl
356 M /trunk/samtools/misc/wgsim.c
359 * fixed a bug in faidx
361 ------------------------------------------------------------------------
362 r529 | jmarshall | 2010-01-11 18:51:49 -0500 (Mon, 11 Jan 2010) | 2 lines
364 M /trunk/samtools/faidx.c
366 Put the right filename in the error message.
368 ------------------------------------------------------------------------
369 r528 | lh3lh3 | 2009-12-14 11:26:47 -0500 (Mon, 14 Dec 2009) | 3 lines
371 M /trunk/samtools/bam_plcmd.c
372 M /trunk/samtools/bamtk.c
374 * samtools-0.1.7-5 (r528)
375 * further add new consensus generation strategy
377 ------------------------------------------------------------------------
378 r527 | petulda | 2009-12-11 12:31:05 -0500 (Fri, 11 Dec 2009) | 1 line
380 M /trunk/samtools/knetfile.c
382 Fixed a bug in knet_seek
383 ------------------------------------------------------------------------
384 r526 | petulda | 2009-12-11 07:51:18 -0500 (Fri, 11 Dec 2009) | 1 line
386 M /trunk/samtools/misc/sam2vcf.pl
388 Small fix in VCF format: dot for the empty INFO field
389 ------------------------------------------------------------------------
390 r525 | petulda | 2009-12-11 04:36:18 -0500 (Fri, 11 Dec 2009) | 1 line
392 M /trunk/samtools/sam_header.c
394 Allow tabs in the CO header field
395 ------------------------------------------------------------------------
396 r524 | jmarshall | 2009-12-10 10:03:58 -0500 (Thu, 10 Dec 2009) | 3 lines
398 M /trunk/samtools/Makefile
399 M /trunk/samtools/Makefile.mingw
401 Depend on libbam.a rather than the phony target, so that samtools is not
402 unnecessarily rebuilt every time. Also clean bgzip.
404 ------------------------------------------------------------------------
405 r523 | jmarshall | 2009-12-10 09:45:32 -0500 (Thu, 10 Dec 2009) | 4 lines
407 M /trunk/samtools/Makefile
408 M /trunk/samtools/Makefile.mingw
410 Fix a bug in compiling bgzip: this also needs knetfile.o when _USE_KNETFILE
411 is defined. Also introduce $(KNETFILE_O) which can be set to empty to
412 facilitate non-knet builds.
414 ------------------------------------------------------------------------
415 r522 | lh3lh3 | 2009-12-01 13:02:36 -0500 (Tue, 01 Dec 2009) | 4 lines
417 M /trunk/samtools/bamtk.c
418 M /trunk/samtools/sam_view.c
420 * samtools-0.1.7-4 (r522)
421 * fixed a bug in "view -r"
422 * added a new option "view -R" to read required read groups from a file
424 ------------------------------------------------------------------------
425 r521 | lh3lh3 | 2009-12-01 10:00:12 -0500 (Tue, 01 Dec 2009) | 3 lines
427 M /trunk/samtools/bam_md.c
428 M /trunk/samtools/bamtk.c
430 * samtools-0.1.7-3 (r521)
431 * calmd: optionally mask matching bases as N
433 ------------------------------------------------------------------------
434 r520 | lh3lh3 | 2009-12-01 09:37:17 -0500 (Tue, 01 Dec 2009) | 4 lines
436 M /trunk/samtools/bam_plcmd.c
437 M /trunk/samtools/bamtk.c
438 M /trunk/samtools/misc/samtools.pl
440 * samtools-0.1.7-2 (r520)
441 * fixed a few issues with compilation in Windows (on behalf of John)
442 * choose a random base as the consensus (for population genetics studies)
444 ------------------------------------------------------------------------
445 r519 | jmarshall | 2009-11-30 10:53:02 -0500 (Mon, 30 Nov 2009) | 6 lines
447 M /trunk/samtools/Makefile
449 Put libraries at the end, so they can resolve references from libbam.a
450 as well, even with old-fashioned linkers.
452 Also use libbam.a explicitly rather than "-L. -lbam" to ensure that we get
453 the freshly built library, not some other libbam.a lying around the system.
455 ------------------------------------------------------------------------
456 r518 | jmarshall | 2009-11-30 08:44:56 -0500 (Mon, 30 Nov 2009) | 2 lines
458 M /trunk/samtools/Makefile
459 M /trunk/samtools/misc/Makefile
461 Also clean *.exe (for Cygwin users using this makefile).
463 ------------------------------------------------------------------------
464 r517 | jmarshall | 2009-11-30 07:09:04 -0500 (Mon, 30 Nov 2009) | 2 lines
466 M /trunk/samtools/bam_index.c
468 Index files should be opened in binary mode, not text mode.
470 ------------------------------------------------------------------------
471 r516 | lh3lh3 | 2009-11-27 15:18:59 -0500 (Fri, 27 Nov 2009) | 2 lines
473 A /trunk/samtools/examples/bam2bed.c
475 another example program
477 ------------------------------------------------------------------------
478 r515 | lh3lh3 | 2009-11-27 10:44:56 -0500 (Fri, 27 Nov 2009) | 3 lines
480 M /trunk/samtools/bam_import.c
481 M /trunk/samtools/bamtk.c
482 M /trunk/samtools/misc/wgsim_eval.pl
483 M /trunk/samtools/sam.c
485 * samtools-0.1.7-1 (r515)
486 * report an error when .fai contains duplicated names, instead of segfault
488 ------------------------------------------------------------------------
489 r514 | jmarshall | 2009-11-24 09:45:35 -0500 (Tue, 24 Nov 2009) | 2 lines
491 M /trunk/samtools/bam.c
493 Format 'c'-encoded auxiliary fields correctly, as *signed* integers.
495 ------------------------------------------------------------------------
496 r513 | lh3lh3 | 2009-11-16 10:13:07 -0500 (Mon, 16 Nov 2009) | 2 lines
498 M /trunk/samtools/Makefile.mingw
500 Update Makefile.mingw for the same reason
502 ------------------------------------------------------------------------
503 r512 | lh3lh3 | 2009-11-16 10:00:08 -0500 (Mon, 16 Nov 2009) | 2 lines
505 M /trunk/samtools/Makefile
507 Fixed a bug in compiling razip
509 ------------------------------------------------------------------------
510 r510 | lh3lh3 | 2009-11-10 10:55:41 -0500 (Tue, 10 Nov 2009) | 2 lines
512 M /trunk/samtools/ChangeLog
513 M /trunk/samtools/NEWS
514 M /trunk/samtools/bamtk.c
515 M /trunk/samtools/samtools.1
517 Release samtools-0.1.7 (r510)
519 ------------------------------------------------------------------------
520 r509 | lh3lh3 | 2009-11-06 09:17:09 -0500 (Fri, 06 Nov 2009) | 3 lines
522 M /trunk/samtools/bam_plcmd.c
523 M /trunk/samtools/bamtk.c
525 * samtools-0.1.6-22 (r509)
526 * forget to fix a similar problem in glfgen
528 ------------------------------------------------------------------------
529 r508 | lh3lh3 | 2009-11-06 09:06:40 -0500 (Fri, 06 Nov 2009) | 3 lines
531 M /trunk/samtools/bam_maqcns.c
532 M /trunk/samtools/bam_plcmd.c
533 M /trunk/samtools/bamtk.c
534 M /trunk/samtools/sam_view.c
536 * samtools-0.1.6-21 (r508)
537 * fixed a potential bug in the indel caller towards the end of a chromosome
539 ------------------------------------------------------------------------
540 r494 | lh3lh3 | 2009-10-26 11:38:00 -0400 (Mon, 26 Oct 2009) | 3 lines
542 M /trunk/samtools/bamtk.c
543 M /trunk/samtools/sam_view.c
545 * samtools-0.1.6-19 (r494)
546 * allow to convert Illumina quality (64 based) to the BAM quality
548 ------------------------------------------------------------------------
549 r493 | lh3lh3 | 2009-10-26 10:24:39 -0400 (Mon, 26 Oct 2009) | 4 lines
551 M /trunk/samtools/Makefile
552 M /trunk/samtools/bam.c
553 M /trunk/samtools/bam_import.c
554 M /trunk/samtools/bamtk.c
555 M /trunk/samtools/sam.c
556 M /trunk/samtools/sam_header.c
558 * samtools-0.1.6-18 (r493)
559 * fixed the bugs due to improperly incorporating Petr's header parser
560 * a little code clean up in sam_header.c
562 ------------------------------------------------------------------------
563 r492 | petulda | 2009-10-24 09:43:25 -0400 (Sat, 24 Oct 2009) | 1 line
565 M /trunk/samtools/sam_header.c
567 Added sam_header_line_free call for sam_header_parse2
568 ------------------------------------------------------------------------
569 r491 | lh3lh3 | 2009-10-24 00:50:16 -0400 (Sat, 24 Oct 2009) | 3 lines
571 M /trunk/samtools/sam_view.c
576 ------------------------------------------------------------------------
577 r490 | lh3lh3 | 2009-10-24 00:45:12 -0400 (Sat, 24 Oct 2009) | 4 lines
579 M /trunk/samtools/bam.c
580 M /trunk/samtools/bam.h
581 M /trunk/samtools/bam_import.c
582 M /trunk/samtools/sam.c
585 * improved the interface a bit
588 ------------------------------------------------------------------------
589 r489 | lh3lh3 | 2009-10-24 00:41:50 -0400 (Sat, 24 Oct 2009) | 3 lines
591 M /trunk/samtools/bam_import.c
592 M /trunk/samtools/sam_header.c
593 M /trunk/samtools/sam_header.h
595 * BUGGY VERSION. Please NOT use it.
596 * Fixed a minor bug, but the major bug is still there.
598 ------------------------------------------------------------------------
599 r488 | lh3lh3 | 2009-10-24 00:17:10 -0400 (Sat, 24 Oct 2009) | 3 lines
601 M /trunk/samtools/Makefile
602 M /trunk/samtools/bam.c
603 M /trunk/samtools/bam.h
604 M /trunk/samtools/bam_aux.c
605 M /trunk/samtools/bam_import.c
606 M /trunk/samtools/bam_rmdup.c
607 M /trunk/samtools/bam_rmdupse.c
608 M /trunk/samtools/kaln.c
609 M /trunk/samtools/sam.c
610 M /trunk/samtools/sam_header.c
611 M /trunk/samtools/sam_header.h
612 M /trunk/samtools/sam_view.c
614 * This revision is SERIOUSLY BUGGY. Please NOT use it.
615 * Start to incorporate header parsing from Petr Danecek
617 ------------------------------------------------------------------------
618 r487 | petulda | 2009-10-23 11:44:32 -0400 (Fri, 23 Oct 2009) | 1 line
620 M /trunk/samtools/sam_header.c
621 M /trunk/samtools/sam_header.h
623 Now possible to merge multiple HeaderDict dictionaries
624 ------------------------------------------------------------------------
625 r486 | petulda | 2009-10-22 11:46:58 -0400 (Thu, 22 Oct 2009) | 1 line
627 M /trunk/samtools/sam_header.c
630 ------------------------------------------------------------------------
631 r485 | petulda | 2009-10-22 11:41:56 -0400 (Thu, 22 Oct 2009) | 1 line
633 A /trunk/samtools/sam_header.c
634 A /trunk/samtools/sam_header.h
637 ------------------------------------------------------------------------
638 r484 | lh3lh3 | 2009-10-19 14:31:32 -0400 (Mon, 19 Oct 2009) | 5 lines
640 M /trunk/samtools/bam_import.c
641 M /trunk/samtools/bam_rmdupse.c
642 M /trunk/samtools/bamtk.c
643 M /trunk/samtools/examples/Makefile
645 * samtools-0.1.6-17 (r484)
646 * fixed a memory leak in rmdupse
647 * fixed a bug in parsing @RG header lines
648 * test rmdup in examples/
650 ------------------------------------------------------------------------
651 r483 | lh3lh3 | 2009-10-19 13:22:48 -0400 (Mon, 19 Oct 2009) | 4 lines
653 M /trunk/samtools/bam_rmdup.c
654 M /trunk/samtools/bam_rmdupse.c
655 M /trunk/samtools/bamtk.c
657 * samtools-0.1.6-16 (r483)
658 * unify the interface of rmdup and rmdupse
659 * a new bug found in rg2lib(). Have not been fixed yet.
661 ------------------------------------------------------------------------
662 r482 | lh3lh3 | 2009-10-19 13:03:34 -0400 (Mon, 19 Oct 2009) | 4 lines
664 M /trunk/samtools/bam.h
665 M /trunk/samtools/bam_rmdup.c
666 M /trunk/samtools/bam_rmdupse.c
667 M /trunk/samtools/bamtk.c
668 A /trunk/samtools/klist.h
670 * samtools-0.1.6-15 (r482)
672 * rmdupse is now library aware
674 ------------------------------------------------------------------------
675 r481 | lh3lh3 | 2009-10-18 00:07:21 -0400 (Sun, 18 Oct 2009) | 3 lines
677 M /trunk/samtools/bam_rmdup.c
678 M /trunk/samtools/bamtk.c
680 * samtools-0.1.6-14 (r480)
681 * rmdup is now RG aware
683 ------------------------------------------------------------------------
684 r480 | lh3lh3 | 2009-10-17 22:05:20 -0400 (Sat, 17 Oct 2009) | 2 lines
686 M /trunk/samtools/misc/samtools.pl
688 added a small unitity to parse SRA XML files
690 ------------------------------------------------------------------------
691 r479 | lh3lh3 | 2009-10-17 20:57:26 -0400 (Sat, 17 Oct 2009) | 3 lines
693 M /trunk/samtools/bam_maqcns.c
694 M /trunk/samtools/bam_maqcns.h
695 M /trunk/samtools/bam_plcmd.c
696 M /trunk/samtools/bam_sort.c
697 M /trunk/samtools/bamtk.c
699 * samtools-0.1.6-13 (r479)
700 * merge: optionally use file names as RG tags
702 ------------------------------------------------------------------------
703 r478 | lh3lh3 | 2009-10-14 14:18:12 -0400 (Wed, 14 Oct 2009) | 3 lines
705 M /trunk/samtools/bam.c
706 M /trunk/samtools/bam.h
707 M /trunk/samtools/bam_maqcns.c
708 M /trunk/samtools/bamtk.c
709 M /trunk/samtools/kaln.c
711 * samtools-0.1.6-12 (r478)
712 * fixed a bug in the indel caller
714 ------------------------------------------------------------------------
715 r477 | lh3lh3 | 2009-10-10 06:12:26 -0400 (Sat, 10 Oct 2009) | 3 lines
717 M /trunk/samtools/bam_index.c
718 M /trunk/samtools/bamtk.c
720 * samtools-0.1.6-11 (r477)
721 * fixed a bug due to recent change in bam_index.c (thank Nicole Washington for the patch)
723 ------------------------------------------------------------------------
724 r476 | petulda | 2009-10-09 11:45:36 -0400 (Fri, 09 Oct 2009) | 1 line
726 A /trunk/samtools/misc/sam2vcf.pl
728 Added the sam2vcf.pl script.
729 ------------------------------------------------------------------------
730 r475 | lh3lh3 | 2009-10-08 10:19:16 -0400 (Thu, 08 Oct 2009) | 2 lines
732 M /trunk/samtools/Makefile
733 M /trunk/samtools/bam.c
734 M /trunk/samtools/bam.h
735 M /trunk/samtools/bam_maqcns.c
736 M /trunk/samtools/bamtk.c
737 A /trunk/samtools/kaln.c
738 A /trunk/samtools/kaln.h
740 Unfinished modification. Please do not use this revision...
742 ------------------------------------------------------------------------
743 r474 | petulda | 2009-10-08 06:39:54 -0400 (Thu, 08 Oct 2009) | 1 line
745 M /trunk/samtools/knetfile.c
747 Removed the offending knet_seek message.
748 ------------------------------------------------------------------------
749 r473 | petulda | 2009-10-06 09:26:35 -0400 (Tue, 06 Oct 2009) | 1 line
751 M /trunk/samtools/knetfile.c
752 M /trunk/samtools/razf.c
754 Bug fix - faidx on RAZF compressed files now working.
755 ------------------------------------------------------------------------
756 r472 | lh3lh3 | 2009-10-02 08:42:57 -0400 (Fri, 02 Oct 2009) | 2 lines
758 M /trunk/samtools/samtools.1
760 Clarify the meaning of a region like "chr2:1,000,000".
762 ------------------------------------------------------------------------
763 r471 | lh3lh3 | 2009-10-02 05:42:19 -0400 (Fri, 02 Oct 2009) | 2 lines
765 M /trunk/samtools/misc/novo2sam.pl
767 Fixed minor bugs in novo2sam.pl (on behalf of Ken Chen and Colin Hercus)
769 ------------------------------------------------------------------------
770 r470 | lh3lh3 | 2009-09-29 15:01:27 -0400 (Tue, 29 Sep 2009) | 3 lines
772 M /trunk/samtools/Makefile.mingw
773 M /trunk/samtools/bamtk.c
774 M /trunk/samtools/knetfile.c
775 M /trunk/samtools/knetfile.h
777 * samtools-0.1.6-9 (r470)
778 * make knetfile.c compatible with MinGW (thank Martin Morgan for the patch)
780 ------------------------------------------------------------------------
781 r469 | lh3lh3 | 2009-09-29 08:07:44 -0400 (Tue, 29 Sep 2009) | 3 lines
783 M /trunk/samtools/bam_index.c
784 M /trunk/samtools/bamtk.c
786 * samtools-0.1.6-9 (r469)
787 * refactor bam_fetch() for Python binding. On behalf of Leo Goodstadt.
789 ------------------------------------------------------------------------
790 r468 | lh3lh3 | 2009-09-28 05:18:29 -0400 (Mon, 28 Sep 2009) | 3 lines
792 M /trunk/samtools/bam_sort.c
793 M /trunk/samtools/bamtk.c
794 M /trunk/samtools/misc/samtools.pl
796 * samtools-0.1.6-7 (r468)
799 ------------------------------------------------------------------------
800 r467 | petulda | 2009-09-28 04:51:29 -0400 (Mon, 28 Sep 2009) | 1 line
802 M /trunk/samtools/bgzf.c
803 M /trunk/samtools/bgzip.c
804 M /trunk/samtools/razf.c
805 M /trunk/samtools/razip.c
807 Changed the mode for newly created files to 0666. This allows less strict permissions with umask properly set (e.g. 0002 vs. 0022).
808 ------------------------------------------------------------------------
809 r466 | lh3lh3 | 2009-09-24 06:29:19 -0400 (Thu, 24 Sep 2009) | 3 lines
811 M /trunk/samtools/ChangeLog
812 M /trunk/samtools/bam_md.c
813 M /trunk/samtools/bamtk.c
815 * samtools-0.1.6-6 (r466)
816 * do not crash calmd when some sequences are absent from the reference.
818 ------------------------------------------------------------------------
819 r464 | jmarshall | 2009-09-23 06:14:32 -0400 (Wed, 23 Sep 2009) | 3 lines
821 M /trunk/samtools/bam.c
822 M /trunk/samtools/knetfile.c
824 Suppress bgzf_check_EOF() messages when reading from a pipe, as there is
825 no way to seek on a pipe and the messages always appear.
827 ------------------------------------------------------------------------
828 r463 | petulda | 2009-09-16 07:05:41 -0400 (Wed, 16 Sep 2009) | 1 line
830 M /trunk/samtools/knetfile.c
831 M /trunk/samtools/razf.c
833 A bug fix, "samtools view" is now working again.
834 ------------------------------------------------------------------------
835 r462 | lh3lh3 | 2009-09-16 04:51:07 -0400 (Wed, 16 Sep 2009) | 3 lines
837 M /trunk/samtools/bamtk.c
838 M /trunk/samtools/faidx.c
839 M /trunk/samtools/knetfile.c
840 M /trunk/samtools/knetfile.h
841 M /trunk/samtools/razf.c
842 M /trunk/samtools/razf.h
844 * samtools-0.1.6-5 (r462)
845 * Added knetfile support in razf and faidx (on behalf of Petr Danecek)
847 ------------------------------------------------------------------------
848 r460 | lh3lh3 | 2009-09-09 07:06:22 -0400 (Wed, 09 Sep 2009) | 2 lines
850 M /trunk/samtools/samtools.1
852 fixed a formatting issue
854 ------------------------------------------------------------------------
855 r459 | lh3lh3 | 2009-09-08 18:14:08 -0400 (Tue, 08 Sep 2009) | 3 lines
857 M /trunk/samtools/bam_sort.c
858 M /trunk/samtools/bamtk.c
860 * samtools-0.1.6-4 (r459)
861 * make sort output the result to stdout when -o is in use
863 ------------------------------------------------------------------------
864 r458 | lh3lh3 | 2009-09-07 05:10:28 -0400 (Mon, 07 Sep 2009) | 4 lines
866 M /trunk/samtools/bamtk.c
867 M /trunk/samtools/faidx.c
868 M /trunk/samtools/faidx.h
869 M /trunk/samtools/samtools.1
871 * samtools-0.1.6-2 (r458)
872 * added more interface to faidx (by Nils)
873 * updated documentation
875 ------------------------------------------------------------------------
876 r457 | lh3lh3 | 2009-09-05 16:12:04 -0400 (Sat, 05 Sep 2009) | 3 lines
878 M /trunk/samtools/bam_sort.c
879 M /trunk/samtools/bamtk.c
881 * samtools-0.1.6-2 (r457)
882 * get rid of three assert() in bam_sort.c
884 ------------------------------------------------------------------------
885 r456 | jmarshall | 2009-09-04 12:46:25 -0400 (Fri, 04 Sep 2009) | 3 lines
887 M /trunk/samtools/razf.c
889 Return NULL from _razf_open() (and hence razf_open()/razf_open2())
890 when opening the file fails.
892 ------------------------------------------------------------------------
893 r453 | lh3lh3 | 2009-09-02 08:56:33 -0400 (Wed, 02 Sep 2009) | 2 lines
895 M /trunk/samtools/ChangeLog
896 M /trunk/samtools/NEWS
897 M /trunk/samtools/bamtk.c
898 M /trunk/samtools/samtools.1
899 D /trunk/samtools/source.dot
901 Release samtools-0.1.6
903 ------------------------------------------------------------------------
904 r451 | lh3lh3 | 2009-09-02 05:44:48 -0400 (Wed, 02 Sep 2009) | 4 lines
906 M /trunk/samtools/bam_md.c
907 M /trunk/samtools/bam_rmdup.c
908 M /trunk/samtools/bam_rmdupse.c
909 M /trunk/samtools/bam_sort.c
910 M /trunk/samtools/bamtk.c
911 M /trunk/samtools/samtools.1
913 * samtools-0.1.5-34 (r451)
914 * applied the patch by John
915 * improved the help message a little bit
917 ------------------------------------------------------------------------
918 r450 | lh3lh3 | 2009-09-02 04:55:55 -0400 (Wed, 02 Sep 2009) | 3 lines
920 M /trunk/samtools/bam_color.c
921 M /trunk/samtools/bamtk.c
923 * samtools-0.1.5-33 (r450)
924 * fixed a bug in bam_color.c (on behalf of Nils Homer)
926 ------------------------------------------------------------------------
927 r449 | lh3lh3 | 2009-08-29 15:36:41 -0400 (Sat, 29 Aug 2009) | 4 lines
929 M /trunk/samtools/bam_import.c
930 M /trunk/samtools/bam_md.c
931 M /trunk/samtools/bamtk.c
932 M /trunk/samtools/misc/samtools.pl
934 * samtools-0.1.5-32 (r449)
935 * fillmd: fixed a bug in modifying MD/NM tags
936 * in import, give a warning if the read is aligned but there is no CIGAR.
938 ------------------------------------------------------------------------
939 r448 | lh3lh3 | 2009-08-19 04:44:28 -0400 (Wed, 19 Aug 2009) | 3 lines
941 M /trunk/samtools/ChangeLog
942 M /trunk/samtools/bam_pileup.c
943 M /trunk/samtools/bamtk.c
944 M /trunk/samtools/misc/wgsim_eval.pl
946 * samtools-0.1.5-31 (r448)
947 * fixed an issue when the last CIGAR is I or D
949 ------------------------------------------------------------------------
950 r447 | lh3lh3 | 2009-08-17 04:34:57 -0400 (Mon, 17 Aug 2009) | 3 lines
952 M /trunk/samtools/bam_aux.c
953 M /trunk/samtools/bamtk.c
955 * samtools-0.1.5-30 (r447)
956 * fixed a bug in bam_aux_get(): 'A' is not checked
958 ------------------------------------------------------------------------
959 r446 | lh3lh3 | 2009-08-17 04:33:17 -0400 (Mon, 17 Aug 2009) | 2 lines
961 M /trunk/samtools/bam_aux.c
962 M /trunk/samtools/bamtk.c
966 ------------------------------------------------------------------------
967 r444 | lh3lh3 | 2009-08-11 05:02:36 -0400 (Tue, 11 Aug 2009) | 3 lines
969 M /trunk/samtools/bam_sort.c
970 M /trunk/samtools/bamtk.c
972 * samtools-0.1.5-28 (r444)
975 ------------------------------------------------------------------------
976 r443 | lh3lh3 | 2009-08-11 04:29:11 -0400 (Tue, 11 Aug 2009) | 4 lines
978 M /trunk/samtools/bam.c
979 M /trunk/samtools/bam_import.c
980 M /trunk/samtools/bamtk.c
982 * samtools-0.1.5-27 (r443)
983 * SEQ and QUAL can be "*"
984 * parse CIGAR "=" and "X" as "M"
986 ------------------------------------------------------------------------
987 r442 | lh3lh3 | 2009-08-07 16:56:38 -0400 (Fri, 07 Aug 2009) | 4 lines
989 M /trunk/samtools/bam_pileup.c
990 M /trunk/samtools/bamtk.c
991 M /trunk/samtools/misc/md5.c
992 M /trunk/samtools/misc/md5.h
993 M /trunk/samtools/misc/md5fa.c
995 * samtools-0.1.5-26 (r442)
996 * replace RSA Inc md5.* with ones under permissive lincense
997 * fixed a bug in detecting unsorted bam in pileup
999 ------------------------------------------------------------------------
1000 r441 | bhandsaker | 2009-08-05 09:41:28 -0400 (Wed, 05 Aug 2009) | 2 lines
1002 M /trunk/samtools/bgzf.c
1003 M /trunk/samtools/bgzf.h
1004 M /trunk/samtools/bgzip.c
1006 Change copyright notices now that MIT has approved open source distribution.
1008 ------------------------------------------------------------------------
1009 r440 | lh3lh3 | 2009-08-05 05:44:24 -0400 (Wed, 05 Aug 2009) | 3 lines
1011 M /trunk/samtools/bam_stat.c
1012 M /trunk/samtools/bamtk.c
1014 * samtools-0.1.5-25 (r436)
1015 * in flagstats, do not report singletons if both ends are unmapped
1017 ------------------------------------------------------------------------
1018 r439 | lh3lh3 | 2009-08-04 17:16:51 -0400 (Tue, 04 Aug 2009) | 2 lines
1020 M /trunk/samtools/misc/maq2sam.c
1022 fixed a SERIOUS bug in setting 0x20 flag
1024 ------------------------------------------------------------------------
1025 r438 | lh3lh3 | 2009-08-04 16:50:43 -0400 (Tue, 04 Aug 2009) | 2 lines
1027 M /trunk/samtools/misc/samtools.pl
1029 fixed two minor bugs (suggested by Tim M Storm)
1031 ------------------------------------------------------------------------
1032 r437 | lh3lh3 | 2009-08-04 04:13:24 -0400 (Tue, 04 Aug 2009) | 3 lines
1034 M /trunk/samtools/bamtk.c
1035 M /trunk/samtools/misc/samtools.pl
1036 M /trunk/samtools/sam_view.c
1038 * samtools-0.1.5-24 (r435)
1041 ------------------------------------------------------------------------
1042 r434 | lh3lh3 | 2009-08-03 05:40:42 -0400 (Mon, 03 Aug 2009) | 3 lines
1044 M /trunk/samtools/bam_tview.c
1045 M /trunk/samtools/bamtk.c
1047 * samtools-0.1.5-23 (r434)
1048 * in tview, press 'r' to show read names rather than sequences
1050 ------------------------------------------------------------------------
1051 r433 | lh3lh3 | 2009-08-02 14:13:35 -0400 (Sun, 02 Aug 2009) | 3 lines
1053 M /trunk/samtools/knetfile.c
1055 * tried to fixed the buggy FTP random access in Windows. FAILED.
1056 * anyway, MinGW seems to have problem with "%lld".
1058 ------------------------------------------------------------------------
1059 r432 | lh3lh3 | 2009-08-01 19:32:07 -0400 (Sat, 01 Aug 2009) | 5 lines
1061 M /trunk/samtools/Makefile.mingw
1062 M /trunk/samtools/bamtk.c
1063 M /trunk/samtools/faidx.c
1064 M /trunk/samtools/razf.c
1065 A /trunk/samtools/win32/libcurses.a
1066 A /trunk/samtools/win32/xcurses.h
1068 * samtools-0.1.5-22 (r432)
1069 * faidx: fixed compitability issue with _WIN32
1070 * razf: fixed potential compitability issue with _WIN32
1071 * PDCurses support in Windows
1073 ------------------------------------------------------------------------
1074 r431 | lh3lh3 | 2009-08-01 18:34:54 -0400 (Sat, 01 Aug 2009) | 2 lines
1076 M /trunk/samtools/win32/libz.a
1078 replace the GnuWin32 version of libz.a with my own build with MinGW.
1080 ------------------------------------------------------------------------
1081 r430 | lh3lh3 | 2009-08-01 18:21:07 -0400 (Sat, 01 Aug 2009) | 2 lines
1083 M /trunk/samtools/knetfile.c
1087 ------------------------------------------------------------------------
1088 r429 | lh3lh3 | 2009-08-01 17:41:19 -0400 (Sat, 01 Aug 2009) | 3 lines
1090 M /trunk/samtools/Makefile.mingw
1091 M /trunk/samtools/bamtk.c
1092 M /trunk/samtools/knetfile.c
1093 M /trunk/samtools/knetfile.h
1095 * samtools-0.1.5-21 (r428)
1096 * knetfile.c is now compatible with mingw-winsock
1098 ------------------------------------------------------------------------
1099 r428 | lh3lh3 | 2009-07-31 19:39:07 -0400 (Fri, 31 Jul 2009) | 2 lines
1101 M /trunk/samtools/Makefile.mingw
1103 simplify MinGW Makefile
1105 ------------------------------------------------------------------------
1106 r427 | lh3lh3 | 2009-07-31 19:30:54 -0400 (Fri, 31 Jul 2009) | 5 lines
1108 A /trunk/samtools/Makefile.mingw
1109 M /trunk/samtools/bam_import.c
1110 M /trunk/samtools/bamtk.c
1111 A /trunk/samtools/win32
1112 A /trunk/samtools/win32/libz.a
1113 A /trunk/samtools/win32/zconf.h
1114 A /trunk/samtools/win32/zlib.h
1116 * samtools-0.1.5-20 (r427)
1117 * MinGW support. At least SAM<->BAM conversion is working. Other
1118 functionality are not tested at the moment.
1119 * zlib headers and Windows version of libz.a are included in win32/
1121 ------------------------------------------------------------------------
1122 r426 | lh3lh3 | 2009-07-31 18:32:09 -0400 (Fri, 31 Jul 2009) | 3 lines
1124 M /trunk/samtools/bamtk.c
1125 M /trunk/samtools/sam_view.c
1127 * samtools-0.1.5-19 (r426)
1128 * fixed a bug caused by recent modifications. Sorry.
1130 ------------------------------------------------------------------------
1131 r425 | lh3lh3 | 2009-07-31 18:23:51 -0400 (Fri, 31 Jul 2009) | 2 lines
1133 M /trunk/samtools/bgzf.c
1135 compatible with Windows binary files
1137 ------------------------------------------------------------------------
1138 r424 | lh3lh3 | 2009-07-31 05:19:59 -0400 (Fri, 31 Jul 2009) | 5 lines
1140 M /trunk/samtools/bam_maqcns.c
1141 M /trunk/samtools/bam_maqcns.h
1142 M /trunk/samtools/bam_plcmd.c
1143 M /trunk/samtools/bam_tview.c
1144 M /trunk/samtools/bamtk.c
1145 M /trunk/samtools/misc/samtools.pl
1147 * samtools-0.1.5-18 (r423)
1148 * output additional information in pileup indel lines, for the purepose
1149 of debugging at the moment
1150 * in tview, optionally allow to treat reference skip as deletion
1152 ------------------------------------------------------------------------
1153 r423 | lh3lh3 | 2009-07-30 17:00:36 -0400 (Thu, 30 Jul 2009) | 2 lines
1155 A /trunk/samtools/misc/psl2sam.pl
1157 convert BLAT psl to SAM.
1159 ------------------------------------------------------------------------
1160 r422 | lh3lh3 | 2009-07-30 06:24:39 -0400 (Thu, 30 Jul 2009) | 6 lines
1162 M /trunk/samtools/ChangeLog
1163 M /trunk/samtools/bam.c
1164 M /trunk/samtools/bamtk.c
1165 M /trunk/samtools/bgzf.c
1166 M /trunk/samtools/bgzf.h
1167 M /trunk/samtools/knetfile.c
1168 M /trunk/samtools/sam.c
1169 M /trunk/samtools/sam_view.c
1171 * samtools-0.1.5-17 (r422)
1172 * fixed a but in knetfile.c when seek type is not SEEK_SET
1173 * write an empty BGZF block to every BGZF file
1174 * check BGZF EOF marker in bam_header_read()
1177 ------------------------------------------------------------------------
1178 r421 | lh3lh3 | 2009-07-30 05:03:39 -0400 (Thu, 30 Jul 2009) | 3 lines
1180 M /trunk/samtools/bam_import.c
1181 M /trunk/samtools/bam_plcmd.c
1182 M /trunk/samtools/bamtk.c
1183 M /trunk/samtools/misc/samtools.pl
1184 M /trunk/samtools/sam.c
1185 M /trunk/samtools/sam.h
1186 M /trunk/samtools/sam_view.c
1188 * samtools-0.1.5-16 (r421)
1189 * in view and pileup, load header from FASTA index if the input is SAM.
1191 ------------------------------------------------------------------------
1192 r420 | lh3lh3 | 2009-07-29 04:18:55 -0400 (Wed, 29 Jul 2009) | 2 lines
1194 M /trunk/samtools/misc/maq2sam.c
1196 do not set "read 1" if reads are not mapped in the PE mode of maq
1198 ------------------------------------------------------------------------
1199 r419 | lh3lh3 | 2009-07-28 04:52:33 -0400 (Tue, 28 Jul 2009) | 5 lines
1201 M /trunk/samtools/bam_import.c
1202 M /trunk/samtools/bamtk.c
1203 M /trunk/samtools/misc/samtools.pl
1204 M /trunk/samtools/misc/wgsim_eval.pl
1206 * samtools-0.1.5-15 (r419)
1207 * in sam_open(), return NULL when the file cannot be opened.
1208 * make wgsim_eval.pl more robust to imperfect SAM
1209 * add "unique" command to samtools.pl
1211 ------------------------------------------------------------------------
1212 r418 | lh3lh3 | 2009-07-24 09:04:19 -0400 (Fri, 24 Jul 2009) | 2 lines
1214 M /trunk/samtools/misc/wgsim_eval.pl
1216 skip @header lines in SAM
1218 ------------------------------------------------------------------------
1219 r417 | lh3lh3 | 2009-07-24 07:42:38 -0400 (Fri, 24 Jul 2009) | 3 lines
1221 M /trunk/samtools/bamtk.c
1222 M /trunk/samtools/sam_view.c
1224 * samtools-0.1.5-14 (r417)
1225 * more help in "samtools view" due to the recent changes.
1227 ------------------------------------------------------------------------
1228 r416 | lh3lh3 | 2009-07-24 07:34:30 -0400 (Fri, 24 Jul 2009) | 3 lines
1230 M /trunk/samtools/bam.c
1231 M /trunk/samtools/bam.h
1232 M /trunk/samtools/bam_import.c
1233 M /trunk/samtools/bamtk.c
1234 M /trunk/samtools/sam.c
1235 M /trunk/samtools/sam.h
1236 M /trunk/samtools/sam_view.c
1238 * samtools-0.1.5-17 (r416)
1239 * support import/export SAM with string tags
1241 ------------------------------------------------------------------------
1242 r415 | lh3lh3 | 2009-07-24 06:39:26 -0400 (Fri, 24 Jul 2009) | 3 lines
1244 M /trunk/samtools/bam.c
1245 M /trunk/samtools/bam.h
1246 M /trunk/samtools/bam_import.c
1247 M /trunk/samtools/bamtk.c
1248 M /trunk/samtools/sam.c
1249 M /trunk/samtools/sam.h
1250 M /trunk/samtools/sam_view.c
1252 * samtools-0.1.5-12 (r415)
1253 * FLAG now can be in HEX
1255 ------------------------------------------------------------------------
1256 r414 | lh3lh3 | 2009-07-22 17:03:49 -0400 (Wed, 22 Jul 2009) | 2 lines
1258 M /trunk/samtools/kstring.h
1260 fixed a compiling error (thank Ken for fixing it)
1262 ------------------------------------------------------------------------
1263 r412 | lh3lh3 | 2009-07-21 17:19:40 -0400 (Tue, 21 Jul 2009) | 2 lines
1265 M /trunk/samtools/kstring.c
1266 M /trunk/samtools/kstring.h
1268 Implemented Boyer-Moore search in the kstring library.
1270 ------------------------------------------------------------------------
1271 r409 | lh3lh3 | 2009-07-17 12:10:20 -0400 (Fri, 17 Jul 2009) | 2 lines
1273 M /trunk/samtools/bam_index.c
1275 do not include knetfile.h when _USE_KNETFILE is not defined
1277 ------------------------------------------------------------------------
1278 r408 | lh3lh3 | 2009-07-17 10:29:21 -0400 (Fri, 17 Jul 2009) | 5 lines
1280 M /trunk/samtools/bam_md.c
1281 M /trunk/samtools/bam_tview.c
1282 M /trunk/samtools/bamtk.c
1283 M /trunk/samtools/bgzf.c
1285 * samtools-0.1.5-11 (r408)
1286 * force to overwirte existing MD if it is different from the one calculated
1288 * bgzf.c: improved the compatibility with Windows headers
1290 ------------------------------------------------------------------------
1291 r407 | lh3lh3 | 2009-07-17 09:46:56 -0400 (Fri, 17 Jul 2009) | 5 lines
1293 M /trunk/samtools/bam.h
1294 M /trunk/samtools/bam_aux.c
1295 M /trunk/samtools/bam_md.c
1296 M /trunk/samtools/bamtk.c
1297 M /trunk/samtools/sam.h
1299 * samtools-0.1.5-10 (r407)
1300 * implemented bam_aux_del() to remove a tag
1301 * fillmd: generate the NM tag
1302 * fillmd: cmd interface improvement
1304 ------------------------------------------------------------------------
1305 r406 | lh3lh3 | 2009-07-16 18:30:40 -0400 (Thu, 16 Jul 2009) | 2 lines
1307 M /trunk/samtools/Makefile
1309 Sorry. The old Makefile is for PDCurses...
1311 ------------------------------------------------------------------------
1312 r405 | lh3lh3 | 2009-07-16 18:30:11 -0400 (Thu, 16 Jul 2009) | 3 lines
1314 M /trunk/samtools/Makefile
1315 M /trunk/samtools/bam_tview.c
1316 M /trunk/samtools/bamtk.c
1318 * samtools-0.1.5-9 (r405)
1319 * improved the compatibility with PDCurses a little bit
1321 ------------------------------------------------------------------------
1322 r404 | lh3lh3 | 2009-07-16 18:23:52 -0400 (Thu, 16 Jul 2009) | 3 lines
1324 M /trunk/samtools/Makefile
1325 M /trunk/samtools/bam_tview.c
1326 M /trunk/samtools/bamtk.c
1328 * samtools-0.1.5-8 (r404)
1329 * compatible with PDCurses
1331 ------------------------------------------------------------------------
1332 r403 | lh3lh3 | 2009-07-16 17:39:39 -0400 (Thu, 16 Jul 2009) | 3 lines
1334 M /trunk/samtools/bamtk.c
1335 M /trunk/samtools/kseq.h
1337 * samtools-0.1.5-7 (r403)
1338 * fixed a bug in kseq.h for binary files (text files are fine)
1340 ------------------------------------------------------------------------
1341 r402 | lh3lh3 | 2009-07-16 06:49:53 -0400 (Thu, 16 Jul 2009) | 4 lines
1343 M /trunk/samtools/bam_import.c
1344 M /trunk/samtools/bam_index.c
1345 M /trunk/samtools/bamtk.c
1346 M /trunk/samtools/bgzf.c
1348 * samtools-0.1.5-6 (r402)
1349 * fixed compiling error when "-D_USE_NETFILE" is not applied
1350 * improve portability to MinGW
1352 ------------------------------------------------------------------------
1353 r398 | lh3lh3 | 2009-07-13 05:21:36 -0400 (Mon, 13 Jul 2009) | 3 lines
1355 A /trunk/bam-lite/bam.h (from /trunk/samtools/bam.h:395)
1356 A /trunk/bam-lite/bam_lite.c (from /trunk/samtools/bam_lite.c:395)
1357 D /trunk/samtools/bam_lite.c
1359 * move bam_lite.c to bam-lite
1360 * copy bam.h to bam-lite
1362 ------------------------------------------------------------------------
1363 r395 | lh3lh3 | 2009-07-13 05:12:57 -0400 (Mon, 13 Jul 2009) | 3 lines
1365 M /trunk/samtools/bam.h
1366 M /trunk/samtools/bam_lite.c
1367 M /trunk/samtools/bam_lpileup.c
1368 M /trunk/samtools/bam_pileup.c
1369 M /trunk/samtools/bamtk.c
1371 * samtools-0.1.5-5 (r395)
1372 * added bam_pileup_file() and removed bam_lpileup_file()
1374 ------------------------------------------------------------------------
1375 r394 | lh3lh3 | 2009-07-12 19:35:10 -0400 (Sun, 12 Jul 2009) | 3 lines
1377 M /trunk/samtools/bamtk.c
1378 M /trunk/samtools/knetfile.c
1379 M /trunk/samtools/knetfile.h
1381 * samtools-0.1.5-4 (r394)
1382 * http_proxy support in knetfile library (check http_proxy ENV)
1384 ------------------------------------------------------------------------
1385 r393 | lh3lh3 | 2009-07-12 18:57:07 -0400 (Sun, 12 Jul 2009) | 5 lines
1387 M /trunk/samtools/bam_index.c
1388 M /trunk/samtools/bam_tview.c
1389 M /trunk/samtools/bamtk.c
1390 M /trunk/samtools/knetfile.c
1391 M /trunk/samtools/knetfile.h
1393 * samtools-0.1.5-3 (r393)
1394 * knetfile now supports HTTP (no proxy at the moment)
1395 * fixed a potential issue in knetfile on opening ordinary file, although I have
1396 not seen the sideeffect so far.
1398 ------------------------------------------------------------------------
1399 r392 | lh3lh3 | 2009-07-12 13:50:55 -0400 (Sun, 12 Jul 2009) | 2 lines
1401 M /trunk/samtools/samtools.1
1403 Remove the warning in tview
1405 ------------------------------------------------------------------------
1406 r391 | lh3lh3 | 2009-07-12 13:42:43 -0400 (Sun, 12 Jul 2009) | 3 lines
1408 M /trunk/samtools/bam_tview.c
1409 M /trunk/samtools/bamtk.c
1411 * samtools-0.1.5-2 (r391)
1412 * do not show a blank screen when no reads mapped
1414 ------------------------------------------------------------------------
1415 r390 | lh3lh3 | 2009-07-09 09:01:42 -0400 (Thu, 09 Jul 2009) | 4 lines
1417 M /trunk/samtools/bam.h
1418 A /trunk/samtools/bam_lite.c
1419 M /trunk/samtools/bamtk.c
1421 * samtools-0.1.5-1 (r390)
1422 * removed useless _IOLIB in bam.h. This should cause no change at all.
1423 * added bam_lite.c for light-weight BAM reading
1425 ------------------------------------------------------------------------
1426 r385 | lh3lh3 | 2009-07-07 11:53:29 -0400 (Tue, 07 Jul 2009) | 2 lines
1428 M /trunk/samtools/bamtk.c
1429 M /trunk/samtools/knetfile.c
1431 Release samtools-0.1.5c (fixed a bug in piping)
1433 ------------------------------------------------------------------------
1434 r383 | lh3lh3 | 2009-07-07 06:39:55 -0400 (Tue, 07 Jul 2009) | 2 lines
1436 M /trunk/samtools/bamtk.c
1437 M /trunk/samtools/sam.c
1439 Release samtools-0.1.5b (BUG! so embarrassing!)
1441 ------------------------------------------------------------------------
1442 r381 | lh3lh3 | 2009-07-07 06:20:06 -0400 (Tue, 07 Jul 2009) | 2 lines
1444 M /trunk/samtools/Makefile
1445 M /trunk/samtools/bam.h
1446 M /trunk/samtools/bam_aux.c
1447 M /trunk/samtools/bamtk.c
1449 Release samtools-0.1.5a (for compatibility with Bio::DB::Sam)
1451 ------------------------------------------------------------------------
1452 r373 | lh3lh3 | 2009-07-07 05:26:57 -0400 (Tue, 07 Jul 2009) | 2 lines
1454 M /trunk/samtools/ChangeLog
1455 M /trunk/samtools/NEWS
1456 M /trunk/samtools/bamtk.c
1457 M /trunk/samtools/samtools.1
1459 Release samtools-0.1.5
1461 ------------------------------------------------------------------------
1462 r372 | lh3lh3 | 2009-07-07 04:49:27 -0400 (Tue, 07 Jul 2009) | 3 lines
1464 M /trunk/samtools/bamtk.c
1465 M /trunk/samtools/sam.c
1467 * samtools-0.1.4-23 (r372)
1468 * keep header text if "view -t" is used (by Gerton)
1470 ------------------------------------------------------------------------
1471 r371 | lh3lh3 | 2009-07-06 20:13:32 -0400 (Mon, 06 Jul 2009) | 2 lines
1473 M /trunk/samtools/samtools.1
1475 update documentation
1477 ------------------------------------------------------------------------
1478 r370 | bhandsaker | 2009-07-02 17:24:34 -0400 (Thu, 02 Jul 2009) | 2 lines
1480 M /trunk/samtools/Makefile
1482 Introduced LIBPATH variable so this could be overridden to allow samtools to build correct at the Broad.
1484 ------------------------------------------------------------------------
1485 r369 | lh3lh3 | 2009-07-02 08:36:53 -0400 (Thu, 02 Jul 2009) | 4 lines
1487 M /trunk/samtools/ChangeLog
1488 M /trunk/samtools/bam_aux.c
1489 M /trunk/samtools/bam_plcmd.c
1490 M /trunk/samtools/bamtk.c
1492 * samtools-0.1.4-22 (r369)
1493 * in pileup, optionally print E2 and U2
1494 * remove the debugging code in bam_aux_get() (Drat!)
1496 ------------------------------------------------------------------------
1497 r368 | lh3lh3 | 2009-07-02 06:32:26 -0400 (Thu, 02 Jul 2009) | 6 lines
1499 M /trunk/samtools/bam.c
1500 M /trunk/samtools/bam.h
1501 M /trunk/samtools/bam_aux.c
1502 M /trunk/samtools/bam_index.c
1503 M /trunk/samtools/bam_lpileup.c
1504 M /trunk/samtools/bam_md.c
1505 M /trunk/samtools/bam_pileup.c
1506 M /trunk/samtools/bam_rmdup.c
1507 M /trunk/samtools/bam_stat.c
1508 M /trunk/samtools/bam_tview.c
1509 M /trunk/samtools/bamtk.c
1510 M /trunk/samtools/faidx.c
1511 M /trunk/samtools/faidx.h
1512 M /trunk/samtools/glf.c
1514 * samtools-0.1.4-21 (r368)
1515 * propagate errors rather than exit or complain assertion failure. Assertion
1516 should be only used for checking internal bugs, but not for external input
1517 inconsistency. I was just a bit lazy.
1518 * small memory leak may be present on failure, though
1520 ------------------------------------------------------------------------
1521 r367 | lh3lh3 | 2009-06-30 11:18:42 -0400 (Tue, 30 Jun 2009) | 2 lines
1523 M /trunk/samtools/knetfile.c
1525 reduce the chance of blocking in FTP connection
1527 ------------------------------------------------------------------------
1528 r366 | lh3lh3 | 2009-06-30 10:35:21 -0400 (Tue, 30 Jun 2009) | 2 lines
1530 M /trunk/samtools/knetfile.c
1532 minor changes to knetfile: invalid fd equals -1 rather than 0
1534 ------------------------------------------------------------------------
1535 r365 | lh3lh3 | 2009-06-30 09:04:30 -0400 (Tue, 30 Jun 2009) | 3 lines
1537 M /trunk/samtools/bam_index.c
1538 M /trunk/samtools/bamtk.c
1539 M /trunk/samtools/knetfile.c
1540 M /trunk/samtools/knetfile.h
1542 * samtools-0.1.4-20 (r365)
1543 * download the BAM index file if it is not found in the current working directory.
1545 ------------------------------------------------------------------------
1546 r364 | lh3lh3 | 2009-06-30 07:39:07 -0400 (Tue, 30 Jun 2009) | 3 lines
1548 M /trunk/samtools/bamtk.c
1549 M /trunk/samtools/knetfile.c
1551 * samtools-0.1.4-19 (r364)
1552 * knetfile: report error when the file is not present on FTP
1554 ------------------------------------------------------------------------
1555 r363 | lh3lh3 | 2009-06-29 18:23:32 -0400 (Mon, 29 Jun 2009) | 4 lines
1557 M /trunk/samtools/bam_tview.c
1558 M /trunk/samtools/bamtk.c
1559 M /trunk/samtools/bgzf.c
1560 M /trunk/samtools/bgzf.h
1561 M /trunk/samtools/knetfile.c
1562 M /trunk/samtools/knetfile.h
1564 * samtools-0.1.4-18 (r363)
1565 * knetfile: do not trigger network communication in FTP seek (lazy seek)
1566 * bgzf: cache recent blocks (disabled by default)
1568 ------------------------------------------------------------------------
1569 r362 | lh3lh3 | 2009-06-25 16:04:34 -0400 (Thu, 25 Jun 2009) | 2 lines
1571 M /trunk/samtools/bgzf.c
1575 ------------------------------------------------------------------------
1576 r361 | lh3lh3 | 2009-06-25 16:03:10 -0400 (Thu, 25 Jun 2009) | 3 lines
1578 M /trunk/samtools/bam_index.c
1579 M /trunk/samtools/bamtk.c
1581 * samtools-0.1.4-17 (r361)
1582 * if a file is given on FTP, search locally for the BAM index
1584 ------------------------------------------------------------------------
1585 r360 | lh3lh3 | 2009-06-25 15:44:52 -0400 (Thu, 25 Jun 2009) | 5 lines
1587 M /trunk/samtools/Makefile
1588 M /trunk/samtools/bam_import.c
1589 M /trunk/samtools/bam_index.c
1590 M /trunk/samtools/bamtk.c
1591 M /trunk/samtools/bgzf.c
1592 M /trunk/samtools/bgzf.h
1593 M /trunk/samtools/knetfile.c
1594 M /trunk/samtools/knetfile.h
1596 * samtools-0.1.4-16 (r360)
1597 * report more information in index when the input is not sorted
1598 * change the behaviour of knet_seek() such that it returns 0 on success
1599 * support knetfile library in BGZF
1601 ------------------------------------------------------------------------
1602 r359 | lh3lh3 | 2009-06-25 12:10:55 -0400 (Thu, 25 Jun 2009) | 2 lines
1604 M /trunk/samtools/knetfile.c
1605 M /trunk/samtools/knetfile.h
1607 fixed bugs in knetfile.*
1609 ------------------------------------------------------------------------
1610 r358 | lh3lh3 | 2009-06-25 08:53:19 -0400 (Thu, 25 Jun 2009) | 2 lines
1612 A /trunk/samtools/knetfile.h
1614 this is the header file
1616 ------------------------------------------------------------------------
1617 r357 | lh3lh3 | 2009-06-25 08:52:03 -0400 (Thu, 25 Jun 2009) | 3 lines
1619 A /trunk/samtools/knetfile.c
1621 * open a file at FTP
1622 * preliminary version
1624 ------------------------------------------------------------------------
1625 r354 | lh3lh3 | 2009-06-24 09:02:25 -0400 (Wed, 24 Jun 2009) | 3 lines
1627 M /trunk/samtools/bam.c
1628 M /trunk/samtools/bamtk.c
1630 * samtools-0.1.4-15 (r354)
1631 * fixed a memory leak in bam_view1(), although samtools is not using this routine.
1633 ------------------------------------------------------------------------
1634 r351 | lh3lh3 | 2009-06-17 19:16:26 -0400 (Wed, 17 Jun 2009) | 4 lines
1636 M /trunk/samtools/bamtk.c
1637 M /trunk/samtools/faidx.c
1639 * samtools-0.1.4-13 (r351)
1640 * make faidx more tolerant to empty lines right before or after > lines
1641 * hope this does not introduce new bugs...
1643 ------------------------------------------------------------------------
1644 r350 | lh3lh3 | 2009-06-16 09:37:01 -0400 (Tue, 16 Jun 2009) | 3 lines
1646 M /trunk/samtools/bam_plcmd.c
1647 M /trunk/samtools/bamtk.c
1649 * samtools-0.1.4-13 (r350)
1650 * fixed a small memory leak in pileup, caused by recent modifications
1652 ------------------------------------------------------------------------
1653 r347 | lh3lh3 | 2009-06-13 16:20:49 -0400 (Sat, 13 Jun 2009) | 3 lines
1655 M /trunk/samtools/bam_plcmd.c
1656 M /trunk/samtools/bamtk.c
1657 M /trunk/samtools/sam_view.c
1659 * samtools-0.1.4-12 (r347)
1660 * added `-S' to pileup, similar to `view -S'
1662 ------------------------------------------------------------------------
1663 r346 | lh3lh3 | 2009-06-13 12:52:31 -0400 (Sat, 13 Jun 2009) | 3 lines
1665 M /trunk/samtools/Makefile
1666 M /trunk/samtools/bamtk.c
1667 M /trunk/samtools/sam_view.c
1668 M /trunk/samtools/samtools.1
1670 * samtools-0.1.4-11 (r346)
1671 * allow to select a read group at view command-line
1673 ------------------------------------------------------------------------
1674 r344 | lh3lh3 | 2009-06-13 09:06:24 -0400 (Sat, 13 Jun 2009) | 2 lines
1676 M /trunk/samtools/examples/calDepth.c
1680 ------------------------------------------------------------------------
1681 r343 | lh3lh3 | 2009-06-13 09:01:22 -0400 (Sat, 13 Jun 2009) | 2 lines
1683 M /trunk/samtools/examples/calDepth.c
1687 ------------------------------------------------------------------------
1688 r342 | lh3lh3 | 2009-06-13 08:58:48 -0400 (Sat, 13 Jun 2009) | 2 lines
1690 M /trunk/samtools/examples/Makefile
1691 A /trunk/samtools/examples/calDepth.c
1693 added an example of calculating read depth
1695 ------------------------------------------------------------------------
1696 r341 | lh3lh3 | 2009-06-13 08:00:08 -0400 (Sat, 13 Jun 2009) | 6 lines
1698 M /trunk/samtools/Makefile
1699 M /trunk/samtools/bam.h
1700 M /trunk/samtools/bam_aux.c
1701 A /trunk/samtools/bam_color.c
1702 M /trunk/samtools/bam_plcmd.c
1703 M /trunk/samtools/bam_sort.c
1704 M /trunk/samtools/bam_tview.c
1705 M /trunk/samtools/bamtk.c
1706 M /trunk/samtools/sam.c
1707 M /trunk/samtools/sam.h
1709 * samtools-0.1.4-10 (r341)
1710 * only include key APIs in libbam.a
1711 * move color-specific routines to bam_color.c
1712 * update documentations
1713 * remove the support of -q in pileup
1715 ------------------------------------------------------------------------
1716 r340 | lh3lh3 | 2009-06-13 06:17:14 -0400 (Sat, 13 Jun 2009) | 6 lines
1718 M /trunk/samtools/INSTALL
1719 M /trunk/samtools/Makefile
1720 M /trunk/samtools/bam_aux.c
1721 M /trunk/samtools/bam_import.c
1722 M /trunk/samtools/bam_tview.c
1723 M /trunk/samtools/bamtk.c
1724 M /trunk/samtools/razf.c
1725 M /trunk/samtools/sam_view.c
1727 * samtools-0.1.4-9 (r340)
1728 * added a warning to razf.c if zlib<1.2.2.1
1729 * fixed a compilation warning
1730 * fixed a segfault caused by @RG parsing
1731 * detect NCURSES in bam_tview.c
1733 ------------------------------------------------------------------------
1734 r339 | lh3lh3 | 2009-06-13 05:35:19 -0400 (Sat, 13 Jun 2009) | 2 lines
1736 M /trunk/samtools/INSTALL
1740 ------------------------------------------------------------------------
1741 r338 | lh3lh3 | 2009-06-12 19:15:24 -0400 (Fri, 12 Jun 2009) | 4 lines
1743 M /trunk/samtools/bam.c
1744 M /trunk/samtools/bam.h
1745 M /trunk/samtools/bam_aux.c
1746 M /trunk/samtools/bam_import.c
1747 M /trunk/samtools/bamtk.c
1748 M /trunk/samtools/kstring.h
1749 M /trunk/samtools/sam.c
1750 M /trunk/samtools/sam_view.c
1752 * samtools-0.1.4-8 (r338)
1753 * parse the @RG header lines and allow to choose library at the "samtools view"
1756 ------------------------------------------------------------------------
1757 r337 | lh3lh3 | 2009-06-12 16:25:50 -0400 (Fri, 12 Jun 2009) | 4 lines
1759 M /trunk/samtools/bamtk.c
1760 M /trunk/samtools/bgzf.c
1761 M /trunk/samtools/bgzf.h
1762 M /trunk/samtools/sam.c
1763 M /trunk/samtools/sam_view.c
1765 * samtools-0.1.4-7 (r337)
1766 * bgzf.c: support mode string "wu": uncompressed output
1767 * "samtools view" support "-u" command-line option
1769 ------------------------------------------------------------------------
1770 r336 | lh3lh3 | 2009-06-12 12:20:12 -0400 (Fri, 12 Jun 2009) | 5 lines
1772 M /trunk/samtools/Makefile
1773 M /trunk/samtools/misc/Makefile
1774 M /trunk/samtools/razf.c
1775 M /trunk/samtools/razf.h
1776 M /trunk/samtools/razip.c
1778 * no changes to samtools itself
1779 * remove zlib source codes
1780 * make RAZF reading compatible with old version of zlib
1781 * on old version of zlib, writing is not available
1783 ------------------------------------------------------------------------
1784 r335 | lh3lh3 | 2009-06-12 11:47:33 -0400 (Fri, 12 Jun 2009) | 2 lines
1786 D /trunk/samtools/zlib
1788 remove zlib for simplification...
1790 ------------------------------------------------------------------------
1791 r334 | lh3lh3 | 2009-06-12 10:43:36 -0400 (Fri, 12 Jun 2009) | 5 lines
1793 M /trunk/samtools/bam.h
1794 M /trunk/samtools/bam_aux.c
1795 M /trunk/samtools/bamtk.c
1797 * samtools-0.1.4-6 (r334)
1798 * do not export bam_aux_get_core() for Bio::DB::Sam because it has already
1799 been implemented in that.
1800 * this version works with the latest Bio::DB::Sam (20090612)
1802 ------------------------------------------------------------------------
1803 r333 | lh3lh3 | 2009-06-12 10:33:42 -0400 (Fri, 12 Jun 2009) | 2 lines
1805 M /trunk/samtools/ChangeLog
1809 ------------------------------------------------------------------------
1810 r332 | lh3lh3 | 2009-06-12 10:21:21 -0400 (Fri, 12 Jun 2009) | 2 lines
1812 M /trunk/samtools/AUTHORS
1813 M /trunk/samtools/Makefile
1814 M /trunk/samtools/misc/Makefile
1816 fixed minor things in Makefile
1818 ------------------------------------------------------------------------
1819 r331 | lh3lh3 | 2009-06-12 10:07:05 -0400 (Fri, 12 Jun 2009) | 4 lines
1821 M /trunk/samtools/bamtk.c
1823 * samtools-0.1.4-5 (r3310
1824 * no change to samtools itself. Version number is increased to reflect the
1825 changes in the Makefile building system.
1827 ------------------------------------------------------------------------
1828 r330 | lh3lh3 | 2009-06-12 10:03:38 -0400 (Fri, 12 Jun 2009) | 2 lines
1830 M /trunk/samtools/AUTHORS
1831 D /trunk/samtools/README
1833 update information...
1835 ------------------------------------------------------------------------
1836 r329 | lh3lh3 | 2009-06-12 09:52:21 -0400 (Fri, 12 Jun 2009) | 3 lines
1838 M /trunk/samtools/misc/novo2sam.pl
1840 * updated novoalign converter by Colin Hercus et al.
1841 * this version works with indels
1843 ------------------------------------------------------------------------
1844 r328 | lh3lh3 | 2009-06-12 09:50:53 -0400 (Fri, 12 Jun 2009) | 3 lines
1846 M /trunk/samtools/INSTALL
1847 M /trunk/samtools/Makefile
1848 M /trunk/samtools/misc/Makefile
1849 M /trunk/samtools/zlib/Makefile
1852 * update INSTALL instruction
1854 ------------------------------------------------------------------------
1855 r327 | lh3lh3 | 2009-06-12 09:18:29 -0400 (Fri, 12 Jun 2009) | 4 lines
1857 A /trunk/samtools/Makefile (from /trunk/samtools/Makefile.generic:325)
1858 D /trunk/samtools/Makefile.am
1859 D /trunk/samtools/Makefile.generic
1860 D /trunk/samtools/Makefile.lite
1861 D /trunk/samtools/autogen.sh
1862 D /trunk/samtools/cleanup.sh
1863 D /trunk/samtools/configure.ac
1864 A /trunk/samtools/misc/Makefile (from /trunk/samtools/misc/Makefile.generic:305)
1865 D /trunk/samtools/misc/Makefile.am
1866 D /trunk/samtools/misc/Makefile.generic
1867 M /trunk/samtools/razf.c
1868 A /trunk/samtools/zlib
1869 A /trunk/samtools/zlib/Makefile
1870 A /trunk/samtools/zlib/adler32.c
1871 A /trunk/samtools/zlib/compress.c
1872 A /trunk/samtools/zlib/crc32.c
1873 A /trunk/samtools/zlib/crc32.h
1874 A /trunk/samtools/zlib/deflate.c
1875 A /trunk/samtools/zlib/deflate.h
1876 A /trunk/samtools/zlib/gzio.c
1877 A /trunk/samtools/zlib/infback.c
1878 A /trunk/samtools/zlib/inffast.c
1879 A /trunk/samtools/zlib/inffast.h
1880 A /trunk/samtools/zlib/inffixed.h
1881 A /trunk/samtools/zlib/inflate.c
1882 A /trunk/samtools/zlib/inflate.h
1883 A /trunk/samtools/zlib/inftrees.c
1884 A /trunk/samtools/zlib/inftrees.h
1885 A /trunk/samtools/zlib/trees.c
1886 A /trunk/samtools/zlib/trees.h
1887 A /trunk/samtools/zlib/uncompr.c
1888 A /trunk/samtools/zlib/zconf.h
1889 A /trunk/samtools/zlib/zlib.h
1890 A /trunk/samtools/zlib/zutil.c
1891 A /trunk/samtools/zlib/zutil.h
1892 D /trunk/samtools/zutil.h
1894 * added zlib-1.2.3 as razip requires that
1895 * prepare to changed back to the Makefile building system
1896 * unfinished! (will be soon)
1898 ------------------------------------------------------------------------
1899 r326 | lh3lh3 | 2009-06-12 09:12:03 -0400 (Fri, 12 Jun 2009) | 2 lines
1901 M /trunk/samtools/misc/samtools.pl
1905 ------------------------------------------------------------------------
1906 r325 | lh3lh3 | 2009-06-10 11:27:59 -0400 (Wed, 10 Jun 2009) | 3 lines
1908 M /trunk/samtools/bam_maqcns.c
1909 M /trunk/samtools/bamtk.c
1911 * samtools-0.1.4-4 (r325)
1912 * further avoid wrong consensus calls in repetitive regions.
1914 ------------------------------------------------------------------------
1915 r324 | lh3lh3 | 2009-06-10 10:56:17 -0400 (Wed, 10 Jun 2009) | 4 lines
1917 M /trunk/samtools/bam_maqcns.c
1918 M /trunk/samtools/bam_plcmd.c
1919 M /trunk/samtools/bamtk.c
1920 M /trunk/samtools/sam.c
1921 M /trunk/samtools/sam.h
1923 * samtools-0.1.4-3 (r324)
1924 * make maqcns generate the correct call in repetitive regions.
1925 * allow filtering on mapQ at the pileup command line
1927 ------------------------------------------------------------------------
1928 r323 | lh3lh3 | 2009-06-10 05:04:21 -0400 (Wed, 10 Jun 2009) | 3 lines
1930 M /trunk/samtools/misc/samtools.pl
1932 * samtools.pl-0.3.2 (r322)
1933 * indels and SNPs use different mapping quality threshold
1935 ------------------------------------------------------------------------
1936 r322 | lh3lh3 | 2009-06-10 05:03:22 -0400 (Wed, 10 Jun 2009) | 2 lines
1938 M /trunk/samtools/misc/export2sam.pl
1942 ------------------------------------------------------------------------
1943 r321 | lh3lh3 | 2009-06-09 04:21:48 -0400 (Tue, 09 Jun 2009) | 2 lines
1945 M /trunk/samtools/misc/samtools.pl
1947 just typo. no real change
1949 ------------------------------------------------------------------------
1950 r320 | lh3lh3 | 2009-06-08 09:32:51 -0400 (Mon, 08 Jun 2009) | 2 lines
1952 M /trunk/samtools/misc/samtools.pl
1954 a little bit code cleanup
1956 ------------------------------------------------------------------------
1957 r319 | lh3lh3 | 2009-06-08 09:22:33 -0400 (Mon, 08 Jun 2009) | 4 lines
1959 M /trunk/samtools/misc/samtools.pl
1962 * change default parameters
1963 * optionally print filtered variants
1965 ------------------------------------------------------------------------
1966 r318 | lh3lh3 | 2009-06-08 09:14:26 -0400 (Mon, 08 Jun 2009) | 3 lines
1968 M /trunk/samtools/misc/samtools.pl
1971 * combine snpFilter and indelFilter
1973 ------------------------------------------------------------------------
1974 r317 | lh3lh3 | 2009-06-08 06:31:42 -0400 (Mon, 08 Jun 2009) | 3 lines
1976 M /trunk/samtools/misc/samtools.pl
1979 * change a default parameter
1981 ------------------------------------------------------------------------
1982 r316 | lh3lh3 | 2009-06-08 06:11:06 -0400 (Mon, 08 Jun 2009) | 5 lines
1984 M /trunk/samtools/bam_maqcns.c
1985 M /trunk/samtools/bam_maqcns.h
1986 M /trunk/samtools/bam_plcmd.c
1987 M /trunk/samtools/bamtk.c
1988 M /trunk/samtools/sam.c
1990 * samtools-0.1.4-2 (r316)
1991 * pileup: cap mapping quality at 60 (by default)
1992 * pileup: always calculate RMS mapq
1993 * pileup: allow to output variant sites only
1995 ------------------------------------------------------------------------
1996 r312 | lh3lh3 | 2009-06-04 08:01:10 -0400 (Thu, 04 Jun 2009) | 3 lines
1998 M /trunk/samtools/misc/samtools.pl
2003 ------------------------------------------------------------------------
2004 r311 | lh3lh3 | 2009-06-03 04:40:40 -0400 (Wed, 03 Jun 2009) | 2 lines
2006 M /trunk/samtools/misc/samtools.pl
2008 * in snpFilter, suppress non-SNP sites
2010 ------------------------------------------------------------------------
2011 r310 | lh3lh3 | 2009-06-01 09:35:13 -0400 (Mon, 01 Jun 2009) | 3 lines
2013 M /trunk/samtools/misc/samtools.pl
2018 ------------------------------------------------------------------------
2019 r309 | lh3lh3 | 2009-06-01 09:04:39 -0400 (Mon, 01 Jun 2009) | 3 lines
2021 M /trunk/samtools/misc/samtools.pl
2026 ------------------------------------------------------------------------
2027 r306 | lh3lh3 | 2009-05-28 06:49:35 -0400 (Thu, 28 May 2009) | 3 lines
2029 M /trunk/samtools/bgzf.c
2031 * minor changes to bgzf: return NULL if fd == -1
2032 * suggested by {kdj,jm18}@sanger.ac.uk
2034 ------------------------------------------------------------------------
2035 r305 | lh3lh3 | 2009-05-28 06:16:08 -0400 (Thu, 28 May 2009) | 2 lines
2037 A /trunk/samtools/misc/interpolate_sam.pl
2039 Script for paired-end pileup, contributed by Stephen Montgomery.
2041 ------------------------------------------------------------------------
2042 r304 | lh3lh3 | 2009-05-28 06:08:49 -0400 (Thu, 28 May 2009) | 3 lines
2044 M /trunk/samtools/bamtk.c
2045 M /trunk/samtools/sam.c
2047 * samtools-0.1.4-1 (r304)
2048 * fixed a minor bug in printing headers
2050 ------------------------------------------------------------------------
2051 r297 | lh3lh3 | 2009-05-21 11:06:16 -0400 (Thu, 21 May 2009) | 2 lines
2053 M /trunk/samtools/ChangeLog
2054 M /trunk/samtools/NEWS
2055 M /trunk/samtools/bam_plcmd.c
2056 M /trunk/samtools/bamtk.c
2057 M /trunk/samtools/misc/maq2sam.c
2058 M /trunk/samtools/samtools.1
2060 Release samtools-0.1.4
2062 ------------------------------------------------------------------------
2063 r296 | lh3lh3 | 2009-05-21 07:53:14 -0400 (Thu, 21 May 2009) | 3 lines
2065 M /trunk/samtools/bam_maqcns.c
2066 M /trunk/samtools/bamtk.c
2068 * samtools-0.1.3-24 (r296)
2069 * another similar bug in the indel caller
2071 ------------------------------------------------------------------------
2072 r295 | lh3lh3 | 2009-05-21 07:50:28 -0400 (Thu, 21 May 2009) | 3 lines
2074 M /trunk/samtools/bam_maqcns.c
2075 M /trunk/samtools/bamtk.c
2077 * samtools-0.1.3-23 (r295)
2078 * fixed a critical bug in the indel caller
2080 ------------------------------------------------------------------------
2081 r294 | lh3lh3 | 2009-05-20 08:00:20 -0400 (Wed, 20 May 2009) | 2 lines
2083 M /trunk/samtools/bam_stat.c
2085 added a missing header file
2087 ------------------------------------------------------------------------
2088 r293 | lh3lh3 | 2009-05-19 18:44:25 -0400 (Tue, 19 May 2009) | 3 lines
2090 M /trunk/samtools/bam_tview.c
2091 M /trunk/samtools/bamtk.c
2093 * samtools-0.1.3-22 (r293)
2094 * open tview in the dot-view mode by default
2096 ------------------------------------------------------------------------
2097 r292 | lh3lh3 | 2009-05-18 16:01:23 -0400 (Mon, 18 May 2009) | 6 lines
2099 M /trunk/samtools/samtools.1
2101 Added a note to the manual. Currently SAMtools used unaligned words in
2102 several places. Although this does not cause bus errors to me, it may
2103 affect portability. Please see the "Bus error" wiki page for more
2104 information. Also thank James Bonfields for pointing this out.
2107 ------------------------------------------------------------------------
2108 r286 | lh3lh3 | 2009-05-14 10:23:13 -0400 (Thu, 14 May 2009) | 3 lines
2110 M /trunk/samtools/bam.h
2111 M /trunk/samtools/bam_aux.c
2112 M /trunk/samtools/bamtk.c
2114 * samtools-0.1.3-21 (286)
2115 * declare bam_aux_get_core() in bam.h
2117 ------------------------------------------------------------------------
2118 r276 | lh3lh3 | 2009-05-13 05:07:55 -0400 (Wed, 13 May 2009) | 5 lines
2120 M /trunk/samtools/bam.h
2121 M /trunk/samtools/bam_index.c
2122 M /trunk/samtools/bamtk.c
2124 * samtools-0.1.3-20 (r276)
2125 * remove bam1_t::hash again. We need to modify the Perl API anyway to
2126 make it work with the latest SVN.
2127 * As is suggested by Tim, scan "{base}.bai" and "{base}.bam.bai" for index
2129 ------------------------------------------------------------------------
2130 r275 | lh3lh3 | 2009-05-12 16:14:10 -0400 (Tue, 12 May 2009) | 4 lines
2132 M /trunk/samtools/ChangeLog
2133 M /trunk/samtools/bam.h
2134 M /trunk/samtools/bamtk.c
2136 * samtools-0.1.3-19 (r275)
2137 * a minor change to the bam1_t struct: added back "void *hash" for the
2138 backward compatibility with Bio::DB::Sam
2140 ------------------------------------------------------------------------
2141 r273 | lh3lh3 | 2009-05-12 09:28:39 -0400 (Tue, 12 May 2009) | 3 lines
2143 M /trunk/samtools/bam_rmdupse.c
2144 M /trunk/samtools/bamtk.c
2146 * samtools-0.1.3-18 (r273)
2147 * rmdupse: do not remove unmapped reads
2149 ------------------------------------------------------------------------
2150 r272 | lh3lh3 | 2009-05-12 09:20:00 -0400 (Tue, 12 May 2009) | 2 lines
2152 M /trunk/samtools/bam_rmdupse.c
2154 change a parameter. It does nothing
2156 ------------------------------------------------------------------------
2157 r271 | lh3lh3 | 2009-05-12 09:17:58 -0400 (Tue, 12 May 2009) | 3 lines
2159 M /trunk/samtools/Makefile.am
2160 M /trunk/samtools/Makefile.generic
2161 M /trunk/samtools/Makefile.lite
2162 A /trunk/samtools/bam_rmdupse.c
2163 M /trunk/samtools/bamtk.c
2164 M /trunk/samtools/configure.ac
2166 * samtools-0.1.3-17 (r271)
2167 * added 'rmdupse' command
2169 ------------------------------------------------------------------------
2170 r267 | lh3lh3 | 2009-05-05 17:31:41 -0400 (Tue, 05 May 2009) | 3 lines
2172 M /trunk/samtools/bamtk.c
2173 M /trunk/samtools/sam_view.c
2175 * samtools-0.1.3-16 (r267)
2176 * in sam_view.c, changed g_flag_on based on the suggestion by Angie Hinrichs
2178 ------------------------------------------------------------------------
2179 r266 | lh3lh3 | 2009-05-05 17:23:27 -0400 (Tue, 05 May 2009) | 3 lines
2181 M /trunk/samtools/bam_import.c
2182 M /trunk/samtools/bamtk.c
2184 * samtools-0.1.3-15 (r266)
2185 * report an error if a non-* reference is present while @SQ is absent
2187 ------------------------------------------------------------------------
2188 r265 | lh3lh3 | 2009-05-05 17:09:00 -0400 (Tue, 05 May 2009) | 3 lines
2190 M /trunk/samtools/bam.h
2191 M /trunk/samtools/bam_import.c
2192 M /trunk/samtools/bamtk.c
2193 M /trunk/samtools/sam.c
2194 M /trunk/samtools/sam_view.c
2196 * samtools-0.1.3-14 (r262)
2197 * make samopen() recognize @SQ header lines
2199 ------------------------------------------------------------------------
2200 r261 | lh3lh3 | 2009-05-05 10:10:30 -0400 (Tue, 05 May 2009) | 3 lines
2202 M /trunk/samtools/bam_plcmd.c
2203 M /trunk/samtools/bamtk.c
2204 M /trunk/samtools/bgzf.c
2205 M /trunk/samtools/sam.c
2206 M /trunk/samtools/sam_view.c
2208 * samtools-0.1.3-13 (r260)
2209 * report error for file I/O error
2211 ------------------------------------------------------------------------
2212 r260 | lh3lh3 | 2009-05-05 10:01:16 -0400 (Tue, 05 May 2009) | 2 lines
2214 M /trunk/samtools/Makefile.am
2218 ------------------------------------------------------------------------
2219 r259 | lh3lh3 | 2009-05-05 09:52:25 -0400 (Tue, 05 May 2009) | 3 lines
2221 M /trunk/samtools/bam.h
2222 M /trunk/samtools/bam_pileup.c
2223 M /trunk/samtools/bam_plcmd.c
2224 M /trunk/samtools/bamtk.c
2225 M /trunk/samtools/sam.c
2226 M /trunk/samtools/sam.h
2228 * samtools-0.1.3-12 (r259)
2229 * use the new I/O interface in pileup
2231 ------------------------------------------------------------------------
2232 r258 | lh3lh3 | 2009-05-05 09:33:22 -0400 (Tue, 05 May 2009) | 3 lines
2234 M /trunk/samtools/Makefile.generic
2235 M /trunk/samtools/Makefile.lite
2236 M /trunk/samtools/bam.c
2237 M /trunk/samtools/bam.h
2238 M /trunk/samtools/bam_import.c
2239 M /trunk/samtools/bamtk.c
2240 A /trunk/samtools/sam.c
2241 A /trunk/samtools/sam.h
2242 A /trunk/samtools/sam_view.c
2244 * samtools-0.1.3-11 (r258)
2245 * unify the interface to BAM and SAM I/O
2247 ------------------------------------------------------------------------
2248 r257 | lh3lh3 | 2009-05-05 04:53:35 -0400 (Tue, 05 May 2009) | 3 lines
2250 M /trunk/samtools/Makefile.lite
2251 M /trunk/samtools/bam_plcmd.c
2252 M /trunk/samtools/bamtk.c
2254 * samtools-0.1.3-10 (r257)
2255 * allow hex with "pileup -m"
2257 ------------------------------------------------------------------------
2258 r256 | lh3lh3 | 2009-05-04 14:16:50 -0400 (Mon, 04 May 2009) | 4 lines
2260 M /trunk/samtools/bam_lpileup.c
2261 M /trunk/samtools/bamtk.c
2263 * samtools-0.1.3-9 (r256)
2264 * fixed a bug in bam_lpileup.c
2265 * I do not know if this also fixes the bug causing assertion failure in the tview
2267 ------------------------------------------------------------------------
2268 r251 | lh3lh3 | 2009-04-28 08:53:23 -0400 (Tue, 28 Apr 2009) | 3 lines
2270 M /trunk/samtools/bam_pileup.c
2271 M /trunk/samtools/bamtk.c
2273 * samtools-0.1.3-8 (r251)
2274 * fixed a bug when there are reads without coordinates
2276 ------------------------------------------------------------------------
2277 r250 | lh3lh3 | 2009-04-28 08:43:33 -0400 (Tue, 28 Apr 2009) | 2 lines
2279 A /trunk/samtools/AUTHORS
2280 A /trunk/samtools/README
2281 M /trunk/samtools/cleanup.sh
2285 ------------------------------------------------------------------------
2286 r249 | lh3lh3 | 2009-04-28 08:37:16 -0400 (Tue, 28 Apr 2009) | 2 lines
2288 M /trunk/samtools/Makefile.generic
2289 M /trunk/samtools/Makefile.lite
2290 M /trunk/samtools/configure.ac
2291 M /trunk/samtools/misc/Makefile.generic
2293 improve large file support in compilation
2295 ------------------------------------------------------------------------
2296 r248 | lh3lh3 | 2009-04-28 08:33:24 -0400 (Tue, 28 Apr 2009) | 2 lines
2298 M /trunk/samtools/INSTALL
2302 ------------------------------------------------------------------------
2303 r247 | lh3lh3 | 2009-04-28 08:28:50 -0400 (Tue, 28 Apr 2009) | 2 lines
2305 M /trunk/samtools/Makefile.am
2306 M /trunk/samtools/autogen.sh
2307 M /trunk/samtools/cleanup.sh
2308 M /trunk/samtools/configure.ac
2309 A /trunk/samtools/misc/Makefile.am
2311 fixed various issues about the GNU building scripts
2313 ------------------------------------------------------------------------
2314 r246 | lh3lh3 | 2009-04-28 08:10:23 -0400 (Tue, 28 Apr 2009) | 4 lines
2316 M /trunk/samtools/ChangeLog
2317 D /trunk/samtools/Makefile
2318 A /trunk/samtools/Makefile.am
2319 A /trunk/samtools/Makefile.generic
2320 A /trunk/samtools/autogen.sh
2321 M /trunk/samtools/bam.h
2322 M /trunk/samtools/bam_aux.c
2323 M /trunk/samtools/bam_tview.c
2324 M /trunk/samtools/bamtk.c
2325 A /trunk/samtools/cleanup.sh
2326 A /trunk/samtools/configure.ac
2327 D /trunk/samtools/misc/Makefile
2328 A /trunk/samtools/misc/Makefile.generic (from /trunk/samtools/misc/Makefile:245)
2330 * samtools-0.1.3-7 (r246)
2331 * incorporated revisions from Nils Homer
2332 * enhanced support of displaying color-space reads
2334 ------------------------------------------------------------------------
2335 r244 | lh3lh3 | 2009-04-25 06:49:40 -0400 (Sat, 25 Apr 2009) | 3 lines
2337 M /trunk/samtools/bam_md.c
2338 M /trunk/samtools/bamtk.c
2340 * samtools-0.1.3-6 (r244)
2341 * fixed segfault for unmapped reads
2343 ------------------------------------------------------------------------
2344 r243 | lh3lh3 | 2009-04-24 16:27:26 -0400 (Fri, 24 Apr 2009) | 5 lines
2346 M /trunk/samtools/bam.h
2347 M /trunk/samtools/bam_maqcns.c
2348 M /trunk/samtools/bam_md.c
2349 M /trunk/samtools/bamtk.c
2351 * samtools-0.1.3-5 (r243)
2352 * fixed a long existing bug which may cause memory leak
2354 * consensus calling now works with "=", but indel calling not
2356 ------------------------------------------------------------------------
2357 r242 | lh3lh3 | 2009-04-24 15:44:46 -0400 (Fri, 24 Apr 2009) | 3 lines
2359 M /trunk/samtools/bam_md.c
2360 M /trunk/samtools/bamtk.c
2362 * samtools-0.1.3-4 (r242)
2363 * fixed a memory leak
2365 ------------------------------------------------------------------------
2366 r240 | lh3lh3 | 2009-04-24 11:40:18 -0400 (Fri, 24 Apr 2009) | 5 lines
2368 M /trunk/samtools/Makefile
2369 M /trunk/samtools/Makefile.lite
2370 M /trunk/samtools/bam.h
2371 M /trunk/samtools/bam_aux.c
2372 A /trunk/samtools/bam_md.c
2373 M /trunk/samtools/bam_plcmd.c
2374 M /trunk/samtools/bamtk.c
2376 * samtools-0.1.3-3 (r240)
2378 * generate "=" bases
2379 * the plain pileup now support "=" bases, but consensus calling and glfgen may fail
2381 ------------------------------------------------------------------------
2382 r239 | lh3lh3 | 2009-04-24 07:08:20 -0400 (Fri, 24 Apr 2009) | 5 lines
2384 M /trunk/samtools/bam.h
2385 M /trunk/samtools/bam_aux.c
2386 M /trunk/samtools/bamtk.c
2388 * samtools-0.1.3-2 (r239)
2389 * fixed bugs in bam_aux.c (these functions nevered used by samtools)
2390 * removed bam_aux_init()/bam_aux_destroy()
2391 * added tagview for testing bam_aux
2393 ------------------------------------------------------------------------
2394 r235 | lh3lh3 | 2009-04-21 18:17:39 -0400 (Tue, 21 Apr 2009) | 3 lines
2396 M /trunk/samtools/bam_pileup.c
2397 M /trunk/samtools/bamtk.c
2400 * fixed a bug in pileup: the first read in a chromosome may not be printed
2402 ------------------------------------------------------------------------
2403 r232 | lh3lh3 | 2009-04-16 10:25:43 -0400 (Thu, 16 Apr 2009) | 2 lines
2405 M /trunk/samtools/Makefile.lite
2407 a missing file in Makefile.lite
2409 ------------------------------------------------------------------------
2410 r227 | lh3lh3 | 2009-04-15 17:02:53 -0400 (Wed, 15 Apr 2009) | 2 lines
2412 M /trunk/samtools/NEWS
2413 M /trunk/samtools/bamtk.c
2415 Release samtools-0.1.3
2417 ------------------------------------------------------------------------
2418 r223 | lh3lh3 | 2009-04-15 09:31:32 -0400 (Wed, 15 Apr 2009) | 3 lines
2420 M /trunk/samtools/bam_plcmd.c
2421 M /trunk/samtools/bamtk.c
2424 * make samtools more robust to weird input such as empty file
2426 ------------------------------------------------------------------------
2427 r222 | lh3lh3 | 2009-04-15 09:05:33 -0400 (Wed, 15 Apr 2009) | 2 lines
2429 M /trunk/samtools/ChangeLog
2430 M /trunk/samtools/NEWS
2431 M /trunk/samtools/samtools.1
2433 prepare for release 0.1.3
2435 ------------------------------------------------------------------------
2436 r221 | lh3lh3 | 2009-04-15 08:32:14 -0400 (Wed, 15 Apr 2009) | 2 lines
2438 A /trunk/samtools/misc/blast2sam.pl
2440 convert NCBI-BLASTN to SAM
2442 ------------------------------------------------------------------------
2443 r220 | lh3lh3 | 2009-04-15 08:18:19 -0400 (Wed, 15 Apr 2009) | 3 lines
2445 M /trunk/samtools/bam_lpileup.c
2446 M /trunk/samtools/bamtk.c
2449 * fixed a small memory leak in tview
2451 ------------------------------------------------------------------------
2452 r219 | lh3lh3 | 2009-04-15 08:00:08 -0400 (Wed, 15 Apr 2009) | 3 lines
2454 M /trunk/samtools/bam_rmdup.c
2455 M /trunk/samtools/bamtk.c
2458 * fixed a bug in rmdup when there are unmapped reads
2460 ------------------------------------------------------------------------
2461 r218 | lh3lh3 | 2009-04-14 17:28:58 -0400 (Tue, 14 Apr 2009) | 2 lines
2463 M /trunk/samtools/ChangeLog
2464 M /trunk/samtools/NEWS
2466 proposed NEWS for the new release (have not yet)
2468 ------------------------------------------------------------------------
2469 r216 | lh3lh3 | 2009-04-14 17:10:46 -0400 (Tue, 14 Apr 2009) | 4 lines
2471 M /trunk/samtools/misc/samtools.pl
2474 * improve indelFilter to avoid filtering true indels. The new filter relies
2475 on the new pileup indel line implemented in samtools-0.1.2-25
2477 ------------------------------------------------------------------------
2478 r215 | lh3lh3 | 2009-04-14 17:04:19 -0400 (Tue, 14 Apr 2009) | 4 lines
2480 M /trunk/samtools/bam_maqcns.c
2481 M /trunk/samtools/bam_plcmd.c
2482 M /trunk/samtools/bamtk.c
2483 M /trunk/samtools/samtools.1
2486 * change the pileup indel line to shows the number of alignments actually
2489 ------------------------------------------------------------------------
2490 r211 | lh3lh3 | 2009-04-13 07:07:13 -0400 (Mon, 13 Apr 2009) | 2 lines
2492 M /trunk/samtools/ChangeLog
2494 update ChangeLog from "svn log"
2496 ------------------------------------------------------------------------
2497 r210 | lh3lh3 | 2009-04-12 15:57:05 -0400 (Sun, 12 Apr 2009) | 4 lines
2499 M /trunk/samtools/bam.c
2500 M /trunk/samtools/bam_import.c
2501 M /trunk/samtools/bam_sort.c
2502 M /trunk/samtools/bamtk.c
2503 M /trunk/samtools/kseq.h
2506 * in merge, gives a warning rather than error if the target sequence length is different
2507 * allow empty header
2509 ------------------------------------------------------------------------
2510 r209 | lh3lh3 | 2009-04-12 15:32:44 -0400 (Sun, 12 Apr 2009) | 3 lines
2512 M /trunk/samtools/bam.c
2513 M /trunk/samtools/bam_import.c
2514 M /trunk/samtools/bamtk.c
2517 * recognize '*' at the QUAL field
2519 ------------------------------------------------------------------------
2520 r208 | lh3lh3 | 2009-04-12 15:08:02 -0400 (Sun, 12 Apr 2009) | 3 lines
2522 M /trunk/samtools/bam_import.c
2523 M /trunk/samtools/bamtk.c
2524 M /trunk/samtools/kseq.h
2527 * the field separater is TAB only, now
2529 ------------------------------------------------------------------------
2530 r207 | lh3lh3 | 2009-04-08 10:18:03 -0400 (Wed, 08 Apr 2009) | 2 lines
2532 M /trunk/samtools/examples/ex1.sam.gz
2534 * fixed the problem in the example alignment due to the bug in fixmate
2536 ------------------------------------------------------------------------
2537 r206 | lh3lh3 | 2009-04-08 10:15:05 -0400 (Wed, 08 Apr 2009) | 3 lines
2539 M /trunk/samtools/bam_mate.c
2540 M /trunk/samtools/bamtk.c
2541 M /trunk/samtools/misc/soap2sam.pl
2544 * fixed a nasty bug in `fixmate'
2546 ------------------------------------------------------------------------
2547 r205 | lh3lh3 | 2009-04-08 05:57:08 -0400 (Wed, 08 Apr 2009) | 2 lines
2549 M /trunk/samtools/misc/bowtie2sam.pl
2550 M /trunk/samtools/misc/soap2sam.pl
2551 M /trunk/samtools/misc/wgsim_eval.pl
2553 make the script robust to the bugs in SOAP-2.1.7
2555 ------------------------------------------------------------------------
2556 r200 | lh3lh3 | 2009-04-02 10:14:56 -0400 (Thu, 02 Apr 2009) | 3 lines
2558 M /trunk/samtools/bam_stat.c
2559 M /trunk/samtools/bamtk.c
2562 * check if file is truncated in flagstat
2564 ------------------------------------------------------------------------
2565 r199 | lh3lh3 | 2009-04-02 10:09:10 -0400 (Thu, 02 Apr 2009) | 3 lines
2567 M /trunk/samtools/bamtk.c
2570 * print the header if requested
2572 ------------------------------------------------------------------------
2573 r193 | lh3lh3 | 2009-03-27 11:09:50 -0400 (Fri, 27 Mar 2009) | 3 lines
2575 M /trunk/samtools/bam_plcmd.c
2576 M /trunk/samtools/bamtk.c
2579 * fixed a minor bug reported by Nils Homer
2581 ------------------------------------------------------------------------
2582 r185 | lh3lh3 | 2009-03-24 07:50:32 -0400 (Tue, 24 Mar 2009) | 2 lines
2584 A /trunk/samtools/Makefile (from /trunk/samtools/Makefile.std:184)
2585 D /trunk/samtools/Makefile.std
2586 A /trunk/samtools/misc/Makefile (from /trunk/samtools/misc/Makefile.std:184)
2587 D /trunk/samtools/misc/Makefile.std
2589 rename Makefile.std as Makefile. GNU building systerm is not ready and may take some time...
2591 ------------------------------------------------------------------------
2592 r184 | lh3lh3 | 2009-03-24 06:36:38 -0400 (Tue, 24 Mar 2009) | 4 lines
2594 D /trunk/samtools/Makefile
2595 A /trunk/samtools/Makefile.std (from /trunk/samtools/Makefile:183)
2596 M /trunk/samtools/bam_sort.c
2597 M /trunk/samtools/bam_tview.c
2598 M /trunk/samtools/bamtk.c
2599 D /trunk/samtools/misc/Makefile
2600 A /trunk/samtools/misc/Makefile.std (from /trunk/samtools/misc/Makefile:182)
2601 M /trunk/samtools/samtools.1
2604 * incorporating Nils' changes
2605 * rename Makefile to Makefile.std and prepare to add the GNU building systerms (also by Nils)
2607 ------------------------------------------------------------------------
2608 r183 | lh3lh3 | 2009-03-24 06:30:23 -0400 (Tue, 24 Mar 2009) | 4 lines
2610 M /trunk/samtools/Makefile
2611 M /trunk/samtools/bam_import.c
2612 M /trunk/samtools/bam_maqcns.c
2613 M /trunk/samtools/bam_maqcns.h
2614 M /trunk/samtools/bam_plcmd.c
2615 M /trunk/samtools/bamtk.c
2616 M /trunk/samtools/kseq.h
2617 A /trunk/samtools/kstring.c
2618 A /trunk/samtools/kstring.h
2621 * made pileup take a list of proposed indels. An insertion is N at the moment.
2622 * added my kstring library for a bit complex parsing of the position list.
2624 ------------------------------------------------------------------------
2625 r169 | lh3lh3 | 2009-03-12 09:40:14 -0400 (Thu, 12 Mar 2009) | 3 lines
2627 M /trunk/samtools/misc/soap2sam.pl
2630 * more robust to truncated soap output
2632 ------------------------------------------------------------------------
2633 r168 | lh3lh3 | 2009-03-11 06:49:00 -0400 (Wed, 11 Mar 2009) | 2 lines
2635 M /trunk/samtools/Makefile.lite
2637 added bam_stat.o to Makefile.lite
2639 ------------------------------------------------------------------------
2640 r167 | lh3lh3 | 2009-03-10 18:11:31 -0400 (Tue, 10 Mar 2009) | 3 lines
2642 M /trunk/samtools/bam_maqcns.c
2643 M /trunk/samtools/bamtk.c
2646 * generate RMS of mapQ instead of max mapQ
2648 ------------------------------------------------------------------------
2649 r166 | lh3lh3 | 2009-03-10 18:06:45 -0400 (Tue, 10 Mar 2009) | 3 lines
2651 M /trunk/samtools/bam_plcmd.c
2652 M /trunk/samtools/bamtk.c
2653 M /trunk/samtools/glf.c
2654 M /trunk/samtools/glf.h
2655 M /trunk/samtools/misc/Makefile
2660 ------------------------------------------------------------------------
2661 r159 | lh3lh3 | 2009-03-03 06:26:08 -0500 (Tue, 03 Mar 2009) | 3 lines
2663 M /trunk/samtools/bam_plcmd.c
2664 M /trunk/samtools/bamtk.c
2667 * fixed a minor bug in displaying pileup
2669 ------------------------------------------------------------------------
2670 r158 | lh3lh3 | 2009-03-03 06:24:16 -0500 (Tue, 03 Mar 2009) | 3 lines
2672 M /trunk/samtools/ChangeLog
2673 M /trunk/samtools/bamtk.c
2676 * optionally print SAM header
2678 ------------------------------------------------------------------------
2679 r153 | lh3lh3 | 2009-03-02 05:45:28 -0500 (Mon, 02 Mar 2009) | 3 lines
2681 M /trunk/samtools/bamtk.c
2682 M /trunk/samtools/glf.c
2685 * use "GLF\3" as the magic for GLFv3 files
2687 ------------------------------------------------------------------------
2688 r152 | lh3lh3 | 2009-03-02 05:39:09 -0500 (Mon, 02 Mar 2009) | 5 lines
2690 M /trunk/samtools/Makefile
2691 M /trunk/samtools/bam_import.c
2692 M /trunk/samtools/bam_index.c
2693 M /trunk/samtools/bam_plcmd.c
2694 M /trunk/samtools/bamtk.c
2695 M /trunk/samtools/glf.c
2696 M /trunk/samtools/glf.h
2699 * fixed a bug in import: core.bin is undefined for unmapped reads
2700 * this bug can be alleviated (not completely solved) in bam_index.c
2701 * update to GLFv3: pos is changed to offset for better compression
2703 ------------------------------------------------------------------------
2704 r151 | lh3lh3 | 2009-03-01 10:18:43 -0500 (Sun, 01 Mar 2009) | 3 lines
2706 M /trunk/samtools/misc/wgsim.c
2709 * fixed a bug in simulating indels
2711 ------------------------------------------------------------------------
2712 r145 | lh3lh3 | 2009-02-26 14:43:57 -0500 (Thu, 26 Feb 2009) | 4 lines
2714 M /trunk/samtools/misc/wgsim.c
2717 * allow to print mismatch information as fastq comment. MAQ does
2718 not like long read names.
2720 ------------------------------------------------------------------------
2721 r141 | lh3lh3 | 2009-02-26 09:53:03 -0500 (Thu, 26 Feb 2009) | 6 lines
2723 M /trunk/samtools/ChangeLog
2724 M /trunk/samtools/misc/wgsim.c
2725 M /trunk/samtools/misc/wgsim_eval.pl
2728 * fixed a bug about color read coordinates
2729 * fixed a bug in read names
2730 * wgsim_eval.pl-0.1.3
2731 * make the script work with color reads
2733 ------------------------------------------------------------------------
2734 r140 | lh3lh3 | 2009-02-26 09:02:57 -0500 (Thu, 26 Feb 2009) | 2 lines
2736 M /trunk/samtools/misc/Makefile
2737 M /trunk/samtools/misc/wgsim.c
2739 * wgsim: added a note
2741 ------------------------------------------------------------------------
2742 r139 | lh3lh3 | 2009-02-26 06:39:08 -0500 (Thu, 26 Feb 2009) | 7 lines
2744 M /trunk/samtools/misc/wgsim.c
2745 M /trunk/samtools/misc/wgsim_eval.pl
2748 * considerable code clean up
2749 * print number of substitutions/indels/errors on each read
2750 * potentially support SOLiD simulation, though not tested at the moment
2751 * wgsim_eval.pl-0.1.2
2752 * change in accordant with wgsim
2754 ------------------------------------------------------------------------
2755 r129 | lh3lh3 | 2009-02-18 17:23:27 -0500 (Wed, 18 Feb 2009) | 3 lines
2757 M /trunk/samtools/bam_index.c
2758 M /trunk/samtools/bamtk.c
2761 * fixed a bug in bam_fetch, caused by completely contained adjacent chunks
2763 ------------------------------------------------------------------------
2764 r128 | bhandsaker | 2009-02-18 14:06:57 -0500 (Wed, 18 Feb 2009) | 2 lines
2766 M /trunk/samtools/bamtk.c
2768 Fix annoying segv when invalid region specified.
2770 ------------------------------------------------------------------------
2771 r127 | lh3lh3 | 2009-02-17 05:49:55 -0500 (Tue, 17 Feb 2009) | 2 lines
2773 D /trunk/samtools/misc/indel_filter.pl
2774 A /trunk/samtools/misc/samtools.pl
2776 * move indel_filter.pl to samtools.pl
2778 ------------------------------------------------------------------------
2779 r126 | lh3lh3 | 2009-02-14 16:22:30 -0500 (Sat, 14 Feb 2009) | 3 lines
2781 M /trunk/samtools/bam_mate.c
2782 M /trunk/samtools/bamtk.c
2785 * fixed a bug in fixmate: SE reads are flagged as BAM_FMUNMAP
2787 ------------------------------------------------------------------------
2788 r125 | lh3lh3 | 2009-02-13 04:54:45 -0500 (Fri, 13 Feb 2009) | 3 lines
2790 M /trunk/samtools/bam_stat.c
2791 M /trunk/samtools/bamtk.c
2794 * fixed a minor bug in flagstat
2796 ------------------------------------------------------------------------
2797 r124 | lh3lh3 | 2009-02-12 06:15:32 -0500 (Thu, 12 Feb 2009) | 3 lines
2799 M /trunk/samtools/bam_maqcns.c
2800 M /trunk/samtools/bamtk.c
2801 M /trunk/samtools/misc/indel_filter.pl
2804 * improve indel caller by setting maximum window size
2806 ------------------------------------------------------------------------
2807 r123 | lh3lh3 | 2009-02-12 05:30:29 -0500 (Thu, 12 Feb 2009) | 2 lines
2809 M /trunk/samtools/bam_plcmd.c
2810 M /trunk/samtools/bamtk.c
2812 * output max mapping quality in indel line
2814 ------------------------------------------------------------------------
2815 r122 | lh3lh3 | 2009-02-11 05:59:10 -0500 (Wed, 11 Feb 2009) | 2 lines
2817 M /trunk/samtools/misc/maq2sam.c
2819 fixed a bug in generating tag AM
2821 ------------------------------------------------------------------------
2822 r121 | lh3lh3 | 2009-02-03 05:43:11 -0500 (Tue, 03 Feb 2009) | 2 lines
2824 M /trunk/samtools/bam_index.c
2825 M /trunk/samtools/bamtk.c
2827 fixed a potential memory problem in indexing
2829 ------------------------------------------------------------------------
2830 r120 | bhandsaker | 2009-02-02 10:52:52 -0500 (Mon, 02 Feb 2009) | 2 lines
2832 M /trunk/samtools/Makefile
2834 Pass LIBS to recursive targets to facilitate building at Broad.
2836 ------------------------------------------------------------------------
2837 r119 | lh3lh3 | 2009-02-02 05:12:15 -0500 (Mon, 02 Feb 2009) | 4 lines
2839 M /trunk/samtools/ChangeLog
2840 M /trunk/samtools/bam_plcmd.c
2841 M /trunk/samtools/bam_stat.c
2842 M /trunk/samtools/bamtk.c
2845 * fixed a bug in generating GLFv2 for indels
2846 * improve flagstat report a little bit
2848 ------------------------------------------------------------------------
2849 r118 | lh3lh3 | 2009-01-29 07:33:23 -0500 (Thu, 29 Jan 2009) | 3 lines
2851 M /trunk/samtools/Makefile
2852 A /trunk/samtools/bam_stat.c
2853 M /trunk/samtools/bamtk.c
2856 * added flagstat command
2858 ------------------------------------------------------------------------
2859 r116 | lh3lh3 | 2009-01-28 08:31:12 -0500 (Wed, 28 Jan 2009) | 2 lines
2861 M /trunk/samtools/ChangeLog
2862 M /trunk/samtools/NEWS
2863 M /trunk/samtools/bamtk.c
2864 M /trunk/samtools/samtools.1
2866 Release SAMtools-0.1.2
2868 ------------------------------------------------------------------------
2869 r115 | lh3lh3 | 2009-01-28 07:54:08 -0500 (Wed, 28 Jan 2009) | 2 lines
2871 A /trunk/samtools/misc/indel_filter.pl
2873 Script for filtering indel results
2875 ------------------------------------------------------------------------
2876 r114 | lh3lh3 | 2009-01-25 06:45:37 -0500 (Sun, 25 Jan 2009) | 2 lines
2878 A /trunk/samtools/misc/zoom2sam.pl
2882 ------------------------------------------------------------------------
2883 r113 | lh3lh3 | 2009-01-24 09:25:07 -0500 (Sat, 24 Jan 2009) | 2 lines
2885 A /trunk/samtools/misc/novo2sam.pl
2887 add a script to convert novo alignment to SAM
2889 ------------------------------------------------------------------------
2890 r112 | lh3lh3 | 2009-01-23 15:57:39 -0500 (Fri, 23 Jan 2009) | 2 lines
2892 M /trunk/samtools/ChangeLog
2893 M /trunk/samtools/ChangeLog.old
2894 M /trunk/samtools/samtools.1
2896 update documentation and ChangeLog
2898 ------------------------------------------------------------------------
2899 r111 | lh3lh3 | 2009-01-23 14:22:59 -0500 (Fri, 23 Jan 2009) | 3 lines
2901 M /trunk/samtools/bam_sort.c
2902 M /trunk/samtools/bamtk.c
2905 * fixed a bug in "merge" command line
2907 ------------------------------------------------------------------------
2908 r110 | lh3lh3 | 2009-01-22 10:36:48 -0500 (Thu, 22 Jan 2009) | 3 lines
2910 M /trunk/samtools/misc/Makefile
2911 A /trunk/samtools/misc/bowtie2sam.pl (from /branches/dev/samtools/misc/bowtie2sam.pl:108)
2912 M /trunk/samtools/misc/export2sam.pl
2913 A /trunk/samtools/misc/soap2sam.pl (from /branches/dev/samtools/misc/soap2sam.pl:108)
2914 A /trunk/samtools/misc/wgsim.c (from /branches/dev/samtools/misc/wgsim.c:108)
2915 A /trunk/samtools/misc/wgsim_eval.pl (from /branches/dev/samtools/misc/wgsim_eval.pl:108)
2917 * merge from branches/dev/
2918 * all future development will happen here
2920 ------------------------------------------------------------------------
2921 r109 | lh3lh3 | 2009-01-22 10:14:27 -0500 (Thu, 22 Jan 2009) | 3 lines
2923 M /trunk/samtools/COPYING
2924 M /trunk/samtools/ChangeLog
2925 A /trunk/samtools/INSTALL (from /branches/dev/samtools/INSTALL:108)
2926 M /trunk/samtools/Makefile
2927 A /trunk/samtools/Makefile.lite (from /branches/dev/samtools/Makefile.lite:108)
2928 M /trunk/samtools/bam.c
2929 M /trunk/samtools/bam.h
2930 M /trunk/samtools/bam_import.c
2931 M /trunk/samtools/bam_index.c
2932 M /trunk/samtools/bam_lpileup.c
2933 M /trunk/samtools/bam_maqcns.c
2934 M /trunk/samtools/bam_maqcns.h
2935 A /trunk/samtools/bam_mate.c (from /branches/dev/samtools/bam_mate.c:108)
2936 M /trunk/samtools/bam_pileup.c
2937 M /trunk/samtools/bam_plcmd.c
2938 A /trunk/samtools/bam_rmdup.c (from /branches/dev/samtools/bam_rmdup.c:108)
2939 M /trunk/samtools/bam_sort.c
2940 M /trunk/samtools/bamtk.c
2941 M /trunk/samtools/bgzf.h
2942 M /trunk/samtools/examples/00README.txt
2943 A /trunk/samtools/examples/Makefile (from /branches/dev/samtools/examples/Makefile:108)
2944 D /trunk/samtools/examples/ex1.fa.fai
2945 M /trunk/samtools/examples/ex1.sam.gz
2946 M /trunk/samtools/faidx.c
2947 A /trunk/samtools/glf.c (from /branches/dev/samtools/glf.c:108)
2948 M /trunk/samtools/glf.h
2949 M /trunk/samtools/misc/Makefile
2950 M /trunk/samtools/misc/maq2sam.c
2951 M /trunk/samtools/razf.c
2952 M /trunk/samtools/source.dot
2954 * Merge from branches/dev/
2955 * all future development will happen here at trunk/
2957 ------------------------------------------------------------------------
2958 r79 | bhandsaker | 2009-01-07 16:42:15 -0500 (Wed, 07 Jan 2009) | 2 lines
2960 M /trunk/samtools/bam_maqcns.c
2961 M /trunk/samtools/bam_tview.c
2963 Fix problem with compiling without curses.
2965 ------------------------------------------------------------------------
2966 r63 | lh3lh3 | 2008-12-22 10:58:02 -0500 (Mon, 22 Dec 2008) | 2 lines
2968 A /trunk/samtools (from /branches/dev/samtools:62)
2972 ------------------------------------------------------------------------
2973 r62 | lh3lh3 | 2008-12-22 10:55:13 -0500 (Mon, 22 Dec 2008) | 2 lines
2975 A /branches/dev/samtools/NEWS
2976 M /branches/dev/samtools/bamtk.c
2977 M /branches/dev/samtools/samtools.1
2979 Release samtools-0.1.1
2981 ------------------------------------------------------------------------
2982 r61 | lh3lh3 | 2008-12-22 10:46:08 -0500 (Mon, 22 Dec 2008) | 10 lines
2984 M /branches/dev/samtools/bam_aux.c
2985 M /branches/dev/samtools/bam_index.c
2986 M /branches/dev/samtools/bam_plcmd.c
2987 M /branches/dev/samtools/bam_tview.c
2988 M /branches/dev/samtools/bamtk.c
2989 M /branches/dev/samtools/razf.c
2990 M /branches/dev/samtools/samtools.1
2993 * fixed a bug in razf.c: reset z_eof when razf_seek() is called
2994 * fixed a memory leak in parsing a region
2995 * changed pileup a little bit when -s is in use: output ^ and $
2996 * when a bam is not indexed, output more meaningful error message
2997 * fixed a bug in indexing for small alignment
2998 * fixed a bug in the viewer when we come to the end of a reference file
2999 * updated documentation
3000 * prepare to release 0.1.1
3002 ------------------------------------------------------------------------
3003 r60 | lh3lh3 | 2008-12-22 10:10:16 -0500 (Mon, 22 Dec 2008) | 2 lines
3005 A /branches/dev/samtools/examples
3006 A /branches/dev/samtools/examples/00README.txt
3007 A /branches/dev/samtools/examples/ex1.fa
3008 A /branches/dev/samtools/examples/ex1.fa.fai
3009 A /branches/dev/samtools/examples/ex1.sam.gz
3013 ------------------------------------------------------------------------
3014 r59 | lh3lh3 | 2008-12-22 04:38:15 -0500 (Mon, 22 Dec 2008) | 2 lines
3016 M /branches/dev/samtools/ChangeLog
3020 ------------------------------------------------------------------------
3021 r58 | lh3lh3 | 2008-12-20 18:06:00 -0500 (Sat, 20 Dec 2008) | 3 lines
3023 M /branches/dev/samtools/misc/export2sam.pl
3026 * fixed several bugs
3028 ------------------------------------------------------------------------
3029 r57 | lh3lh3 | 2008-12-20 10:44:20 -0500 (Sat, 20 Dec 2008) | 2 lines
3031 A /branches/dev/samtools/misc/export2sam.pl
3033 convert Export format to SAM; not thoroughly tested
3035 ------------------------------------------------------------------------
3036 r56 | lh3lh3 | 2008-12-19 17:13:28 -0500 (Fri, 19 Dec 2008) | 6 lines
3038 M /branches/dev/samtools/bam_import.c
3039 M /branches/dev/samtools/bam_plcmd.c
3040 M /branches/dev/samtools/bam_tview.c
3041 M /branches/dev/samtools/bamtk.c
3042 A /branches/dev/samtools/source.dot
3045 * pileup: generate maq-like simple output
3046 * pileup: allow to output pileup at required sites
3047 * source.dot: source file relationship graph
3048 * tview: fixed a minor bug
3050 ------------------------------------------------------------------------
3051 r55 | lh3lh3 | 2008-12-19 15:10:26 -0500 (Fri, 19 Dec 2008) | 2 lines
3053 D /branches/dev/samtools/misc/all2sam.pl
3057 ------------------------------------------------------------------------
3058 r54 | lh3lh3 | 2008-12-16 17:34:25 -0500 (Tue, 16 Dec 2008) | 2 lines
3060 A /branches/dev/samtools/COPYING
3061 M /branches/dev/samtools/bam.h
3062 M /branches/dev/samtools/faidx.h
3063 M /branches/dev/samtools/khash.h
3064 M /branches/dev/samtools/kseq.h
3065 M /branches/dev/samtools/ksort.h
3066 M /branches/dev/samtools/samtools.1
3068 Added copyright information and a bit more documentation. No code change.
3070 ------------------------------------------------------------------------
3071 r53 | lh3lh3 | 2008-12-16 08:40:18 -0500 (Tue, 16 Dec 2008) | 3 lines
3073 M /branches/dev/samtools/bam.c
3074 M /branches/dev/samtools/bam.h
3075 M /branches/dev/samtools/bam_index.c
3076 M /branches/dev/samtools/bam_maqcns.c
3077 M /branches/dev/samtools/bamtk.c
3080 * improved efficiency of the indel caller for spliced alignments
3082 ------------------------------------------------------------------------
3083 r52 | lh3lh3 | 2008-12-16 05:28:20 -0500 (Tue, 16 Dec 2008) | 3 lines
3085 M /branches/dev/samtools/bam.c
3086 M /branches/dev/samtools/bam.h
3087 M /branches/dev/samtools/bam_aux.c
3088 M /branches/dev/samtools/bam_index.c
3089 M /branches/dev/samtools/bamtk.c
3092 * a bit code cleanup: reduce the dependency between source files
3094 ------------------------------------------------------------------------
3095 r51 | lh3lh3 | 2008-12-15 09:29:32 -0500 (Mon, 15 Dec 2008) | 3 lines
3097 M /branches/dev/samtools/bam_maqcns.c
3098 M /branches/dev/samtools/bam_plcmd.c
3099 M /branches/dev/samtools/bamtk.c
3102 * fixed a memory leak
3104 ------------------------------------------------------------------------
3105 r50 | lh3lh3 | 2008-12-15 09:00:13 -0500 (Mon, 15 Dec 2008) | 2 lines
3107 M /branches/dev/samtools/ChangeLog
3108 M /branches/dev/samtools/bam.h
3109 M /branches/dev/samtools/samtools.1
3111 update documentation, ChangeLog and a comment
3113 ------------------------------------------------------------------------
3114 r49 | lh3lh3 | 2008-12-15 08:36:43 -0500 (Mon, 15 Dec 2008) | 6 lines
3116 M /branches/dev/samtools/Makefile
3117 M /branches/dev/samtools/bam.h
3118 M /branches/dev/samtools/bam_maqcns.c
3119 M /branches/dev/samtools/bam_maqcns.h
3120 M /branches/dev/samtools/bam_pileup.c
3121 A /branches/dev/samtools/bam_plcmd.c
3122 M /branches/dev/samtools/bamtk.c
3123 M /branches/dev/samtools/samtools.1
3126 * moved pileup command to a separate source file
3127 * added indel caller
3128 * added bam_cal_segend(). (NOT WORKING for spliced alignment!!!)
3129 * updated documentation
3131 ------------------------------------------------------------------------
3132 r48 | lh3lh3 | 2008-12-12 08:55:36 -0500 (Fri, 12 Dec 2008) | 3 lines
3134 M /branches/dev/samtools/bam_maqcns.c
3135 M /branches/dev/samtools/bamtk.c
3138 * fixed another bug in maqcns when there is a nearby deletion
3140 ------------------------------------------------------------------------
3141 r47 | lh3lh3 | 2008-12-12 08:42:16 -0500 (Fri, 12 Dec 2008) | 5 lines
3143 M /branches/dev/samtools/bam_maqcns.c
3144 M /branches/dev/samtools/bam_pileup.c
3145 M /branches/dev/samtools/bamtk.c
3148 * pileup: outputing consensus is now optional
3149 * fixed a bug in glfgen. This bug also exists in maq's glfgen. However,
3150 I am not quite sure why the previous version may have problem.
3152 ------------------------------------------------------------------------
3153 r46 | lh3lh3 | 2008-12-12 06:44:56 -0500 (Fri, 12 Dec 2008) | 6 lines
3155 M /branches/dev/samtools/bam_pileup.c
3156 M /branches/dev/samtools/bamtk.c
3159 * add maq consensus to pileup. However, I will move this part to a new
3160 command as strictly speaking, consensus callin is not part of pileup,
3161 and imposing it would make it harder to generate for other language
3164 ------------------------------------------------------------------------
3165 r45 | bhandsaker | 2008-12-11 15:43:56 -0500 (Thu, 11 Dec 2008) | 2 lines
3167 M /branches/dev/samtools/bgzf.c
3169 Fix bug in tell() after reads that consume to the exact end of a block.
3171 ------------------------------------------------------------------------
3172 r44 | lh3lh3 | 2008-12-11 04:36:53 -0500 (Thu, 11 Dec 2008) | 2 lines
3174 M /branches/dev/samtools/samtools.1
3178 ------------------------------------------------------------------------
3179 r43 | lh3lh3 | 2008-12-11 04:25:36 -0500 (Thu, 11 Dec 2008) | 4 lines
3181 M /branches/dev/samtools/bam_import.c
3182 M /branches/dev/samtools/bamtk.c
3185 * fixed a bug in parser when there is auxiliary fields
3186 * made the parser a bit more robust
3188 ------------------------------------------------------------------------
3189 r42 | lh3lh3 | 2008-12-10 09:57:29 -0500 (Wed, 10 Dec 2008) | 5 lines
3191 M /branches/dev/samtools/bam_index.c
3192 M /branches/dev/samtools/bamtk.c
3193 M /branches/dev/samtools/bgzf.c
3196 * fixed a bug in bgzf (only reading is affected)
3197 * fixed a typo in bam_index.c
3198 * in bam_index.c, check potential bugs in the underlying I/O library
3200 ------------------------------------------------------------------------
3201 r41 | lh3lh3 | 2008-12-10 07:53:08 -0500 (Wed, 10 Dec 2008) | 2 lines
3203 M /branches/dev/samtools/samtools.1
3207 ------------------------------------------------------------------------
3208 r40 | lh3lh3 | 2008-12-10 06:52:10 -0500 (Wed, 10 Dec 2008) | 5 lines
3210 M /branches/dev/samtools/bam.h
3211 M /branches/dev/samtools/bam_pileup.c
3212 M /branches/dev/samtools/bamtk.c
3215 * tried to make pileup work with clipping (previously not), though NOT tested
3216 * removed -v from pileup
3217 * made pileup take the reference sequence
3219 ------------------------------------------------------------------------
3220 r39 | lh3lh3 | 2008-12-09 06:59:28 -0500 (Tue, 09 Dec 2008) | 4 lines
3222 M /branches/dev/samtools/bam_import.c
3223 M /branches/dev/samtools/bamtk.c
3224 M /branches/dev/samtools/samtools.1
3227 * in parser, recognize "=", rather than ",", as a match
3228 * in parser, correctl parse "=" at the MRNM field.
3230 ------------------------------------------------------------------------
3231 r38 | lh3lh3 | 2008-12-09 06:39:07 -0500 (Tue, 09 Dec 2008) | 2 lines
3233 M /branches/dev/samtools/misc/maq2sam.c
3235 fixed a bug in handling maq flag 64 and 192
3237 ------------------------------------------------------------------------
3238 r37 | lh3lh3 | 2008-12-09 04:53:46 -0500 (Tue, 09 Dec 2008) | 2 lines
3240 M /branches/dev/samtools/misc/md5fa.c
3242 also calculate unordered md5sum check
3244 ------------------------------------------------------------------------
3245 r36 | lh3lh3 | 2008-12-09 04:46:21 -0500 (Tue, 09 Dec 2008) | 2 lines
3247 M /branches/dev/samtools/misc/md5fa.c
3249 fixed a minor bug when there are space in the sequence
3251 ------------------------------------------------------------------------
3252 r35 | lh3lh3 | 2008-12-09 04:40:45 -0500 (Tue, 09 Dec 2008) | 2 lines
3254 M /branches/dev/samtools/misc/md5fa.c
3256 fixed a potential memory leak
3258 ------------------------------------------------------------------------
3259 r34 | lh3lh3 | 2008-12-08 09:52:17 -0500 (Mon, 08 Dec 2008) | 2 lines
3261 M /branches/dev/samtools/bam_import.c
3262 M /branches/dev/samtools/bam_index.c
3263 M /branches/dev/samtools/bamtk.c
3265 * fixed a bug in import: bin is wrongly calculated
3267 ------------------------------------------------------------------------
3268 r33 | lh3lh3 | 2008-12-08 09:08:01 -0500 (Mon, 08 Dec 2008) | 2 lines
3270 M /branches/dev/samtools/misc/all2sam.pl
3274 ------------------------------------------------------------------------
3275 r32 | lh3lh3 | 2008-12-08 07:56:02 -0500 (Mon, 08 Dec 2008) | 3 lines
3277 M /branches/dev/samtools/Makefile
3278 M /branches/dev/samtools/kseq.h
3279 M /branches/dev/samtools/misc/Makefile
3280 A /branches/dev/samtools/misc/md5.c
3281 A /branches/dev/samtools/misc/md5.h
3282 A /branches/dev/samtools/misc/md5fa.c
3284 * fixed two warnings in kseq.h
3285 * added md5sum utilities
3287 ------------------------------------------------------------------------
3288 r31 | lh3lh3 | 2008-12-08 06:35:29 -0500 (Mon, 08 Dec 2008) | 5 lines
3290 M /branches/dev/samtools/Makefile
3291 M /branches/dev/samtools/bam_import.c
3292 M /branches/dev/samtools/bamtk.c
3293 A /branches/dev/samtools/kseq.h
3294 D /branches/dev/samtools/kstream.h
3297 * replace kstream with kseq. kseq is a superset of kstream. I need the
3298 extra functions in kseq.h.
3299 * also compile stand-alone faidx
3301 ------------------------------------------------------------------------
3302 r30 | lh3lh3 | 2008-12-08 06:17:04 -0500 (Mon, 08 Dec 2008) | 3 lines
3304 M /branches/dev/samtools/bam.h
3305 M /branches/dev/samtools/bam_sort.c
3306 M /branches/dev/samtools/bamtk.c
3309 * sorting by read names is available
3311 ------------------------------------------------------------------------
3312 r29 | lh3lh3 | 2008-12-08 05:29:02 -0500 (Mon, 08 Dec 2008) | 3 lines
3314 M /branches/dev/samtools/bam.c
3315 M /branches/dev/samtools/bam.h
3316 M /branches/dev/samtools/bam_import.c
3317 M /branches/dev/samtools/bam_maqcns.c
3318 M /branches/dev/samtools/bam_pileup.c
3319 M /branches/dev/samtools/bam_sort.c
3320 M /branches/dev/samtools/bam_tview.c
3321 M /branches/dev/samtools/bamtk.c
3322 M /branches/dev/samtools/misc/maq2sam.c
3325 * format change to meet the latest specification
3327 ------------------------------------------------------------------------
3328 r28 | lh3lh3 | 2008-12-04 11:09:21 -0500 (Thu, 04 Dec 2008) | 3 lines
3330 M /branches/dev/samtools/bam_maqcns.c
3331 M /branches/dev/samtools/misc/maq2sam.c
3333 * minor change in maqcns: special care when n==0
3334 * change maq2sam to meet the latest specification
3336 ------------------------------------------------------------------------
3337 r27 | lh3lh3 | 2008-12-04 10:55:44 -0500 (Thu, 04 Dec 2008) | 2 lines
3339 M /branches/dev/samtools/razf.c
3340 M /branches/dev/samtools/razf.h
3342 considerable code clean up in razf
3344 ------------------------------------------------------------------------
3345 r26 | lh3lh3 | 2008-12-04 10:08:18 -0500 (Thu, 04 Dec 2008) | 2 lines
3347 M /branches/dev/samtools/ChangeLog
3348 M /branches/dev/samtools/Makefile
3349 M /branches/dev/samtools/faidx.c
3351 make RAZF optional in faidx.c
3353 ------------------------------------------------------------------------
3354 r25 | lh3lh3 | 2008-12-01 10:27:22 -0500 (Mon, 01 Dec 2008) | 3 lines
3356 M /branches/dev/samtools/Makefile
3357 M /branches/dev/samtools/bam.h
3358 M /branches/dev/samtools/bam_aux.c
3359 M /branches/dev/samtools/bamtk.c
3360 M /branches/dev/samtools/samtools.1
3363 * added routines for retrieving aux data, NOT TESTED YET!
3365 ------------------------------------------------------------------------
3366 r24 | lh3lh3 | 2008-12-01 09:29:43 -0500 (Mon, 01 Dec 2008) | 5 lines
3368 M /branches/dev/samtools/bam.c
3369 M /branches/dev/samtools/bam_import.c
3370 M /branches/dev/samtools/bam_maqcns.c
3371 M /branches/dev/samtools/bamtk.c
3372 M /branches/dev/samtools/bgzf.c
3373 M /branches/dev/samtools/samtools.1
3376 * bgzf: fixed a potential integer overflow on 32-it machines
3377 * maqcns: set the minimum combined quality as 0
3378 * supporting hex strings
3380 ------------------------------------------------------------------------
3381 r23 | lh3lh3 | 2008-11-27 12:14:37 -0500 (Thu, 27 Nov 2008) | 3 lines
3383 M /branches/dev/samtools/bam_maqcns.c
3384 M /branches/dev/samtools/bamtk.c
3387 * fixed the bug in maqcns
3389 ------------------------------------------------------------------------
3390 r22 | lh3lh3 | 2008-11-27 12:08:11 -0500 (Thu, 27 Nov 2008) | 3 lines
3392 M /branches/dev/samtools/Makefile
3393 M /branches/dev/samtools/bam.h
3394 A /branches/dev/samtools/bam_maqcns.c
3395 A /branches/dev/samtools/bam_maqcns.h
3396 M /branches/dev/samtools/bam_tview.c
3397 M /branches/dev/samtools/bamtk.c
3398 A /branches/dev/samtools/glf.h
3401 * add MAQ consensus caller, currently BUGGY!
3403 ------------------------------------------------------------------------
3404 r21 | lh3lh3 | 2008-11-27 08:51:28 -0500 (Thu, 27 Nov 2008) | 4 lines
3406 M /branches/dev/samtools/bam_pileup.c
3407 M /branches/dev/samtools/bam_tview.c
3408 M /branches/dev/samtools/bamtk.c
3411 * tview: display padded alignment (but not P operation)
3412 * better coordinates and reference sequence
3414 ------------------------------------------------------------------------
3415 r19 | lh3lh3 | 2008-11-27 04:26:05 -0500 (Thu, 27 Nov 2008) | 2 lines
3417 A /branches/dev/samtools/ChangeLog
3421 ------------------------------------------------------------------------
3422 r18 | lh3lh3 | 2008-11-27 04:24:45 -0500 (Thu, 27 Nov 2008) | 3 lines
3424 D /branches/dev/samtools/ChangeLog
3425 A /branches/dev/samtools/ChangeLog.old (from /branches/dev/samtools/ChangeLog:6)
3427 Rename ChangeLog to ChangeLog.old. This old ChangeLog is generated from
3428 the log of my personal SVN repository.
3430 ------------------------------------------------------------------------
3431 r17 | lh3lh3 | 2008-11-27 04:22:55 -0500 (Thu, 27 Nov 2008) | 6 lines
3433 M /branches/dev/samtools/Makefile
3434 M /branches/dev/samtools/bamtk.c
3435 M /branches/dev/samtools/bgzf.c
3438 * declare fseeko and ftello as some Linux may not do this by default and
3439 missing these declarations will make bgzf buggy
3440 * get rid of some harmless warings
3441 * use BGZF by default, now
3443 ------------------------------------------------------------------------
3444 r16 | lh3lh3 | 2008-11-26 16:19:11 -0500 (Wed, 26 Nov 2008) | 4 lines
3446 M /branches/dev/samtools/bam_index.c
3447 M /branches/dev/samtools/bamtk.c
3448 M /branches/dev/samtools/razf.c
3451 * fixed a bug in razf_read()
3452 * give more warnings when the file is truncated (or due to bugs in I/O library)
3454 ------------------------------------------------------------------------
3455 r15 | lh3lh3 | 2008-11-26 15:41:39 -0500 (Wed, 26 Nov 2008) | 2 lines
3457 M /branches/dev/samtools/bgzf.c
3459 fixed a bug in bgzf.c at the end of the file
3461 ------------------------------------------------------------------------
3462 r14 | lh3lh3 | 2008-11-26 12:05:18 -0500 (Wed, 26 Nov 2008) | 4 lines
3464 M /branches/dev/samtools/bamtk.c
3467 * a lot happened to RAZF, although samtools itself is untouched. Better
3468 also update the version number anyway to avoid confusion
3470 ------------------------------------------------------------------------
3471 r13 | lh3lh3 | 2008-11-26 12:03:48 -0500 (Wed, 26 Nov 2008) | 2 lines
3473 M /branches/dev/samtools/razf.c
3475 a change from Jue, but I think it should not matter
3477 ------------------------------------------------------------------------
3478 r12 | lh3lh3 | 2008-11-26 11:48:14 -0500 (Wed, 26 Nov 2008) | 3 lines
3480 M /branches/dev/samtools/razf.c
3482 fixed a potential bug in razf. However, it seems still buggy, just
3483 rarely happens, very rarely.
3485 ------------------------------------------------------------------------
3486 r11 | lh3lh3 | 2008-11-26 09:02:56 -0500 (Wed, 26 Nov 2008) | 2 lines
3488 M /branches/dev/samtools/razf.c
3490 fixed a bug in razf, with the help of Jue
3492 ------------------------------------------------------------------------
3493 r10 | lh3lh3 | 2008-11-26 06:55:32 -0500 (Wed, 26 Nov 2008) | 2 lines
3495 M /branches/dev/samtools/bam_index.c
3499 ------------------------------------------------------------------------
3500 r9 | lh3lh3 | 2008-11-26 06:37:05 -0500 (Wed, 26 Nov 2008) | 2 lines
3502 M /branches/dev/samtools/Makefile
3503 M /branches/dev/samtools/bam.h
3504 M /branches/dev/samtools/razf.c
3505 M /branches/dev/samtools/razf.h
3507 * Jue has updated razf to realize Bob's scheme
3509 ------------------------------------------------------------------------
3510 r7 | lh3lh3 | 2008-11-25 15:37:37 -0500 (Tue, 25 Nov 2008) | 2 lines
3512 A /branches/dev/samtools/samtools.1
3516 ------------------------------------------------------------------------
3517 r6 | lh3lh3 | 2008-11-25 15:37:16 -0500 (Tue, 25 Nov 2008) | 3 lines
3519 A /branches/dev/samtools/ChangeLog
3520 A /branches/dev/samtools/Makefile
3521 A /branches/dev/samtools/bam.c
3522 A /branches/dev/samtools/bam.h
3523 A /branches/dev/samtools/bam_aux.c
3524 A /branches/dev/samtools/bam_endian.h
3525 A /branches/dev/samtools/bam_import.c
3526 A /branches/dev/samtools/bam_index.c
3527 A /branches/dev/samtools/bam_lpileup.c
3528 A /branches/dev/samtools/bam_pileup.c
3529 A /branches/dev/samtools/bam_sort.c
3530 A /branches/dev/samtools/bam_tview.c
3531 A /branches/dev/samtools/bamtk.c
3532 A /branches/dev/samtools/bgzf.c
3533 A /branches/dev/samtools/bgzf.h
3534 A /branches/dev/samtools/bgzip.c
3535 A /branches/dev/samtools/faidx.c
3536 A /branches/dev/samtools/faidx.h
3537 A /branches/dev/samtools/khash.h
3538 A /branches/dev/samtools/ksort.h
3539 A /branches/dev/samtools/kstream.h
3540 A /branches/dev/samtools/misc
3541 A /branches/dev/samtools/misc/Makefile
3542 A /branches/dev/samtools/misc/all2sam.pl
3543 A /branches/dev/samtools/misc/maq2sam.c
3544 A /branches/dev/samtools/razf.c
3545 A /branches/dev/samtools/razf.h
3546 A /branches/dev/samtools/razip.c
3547 A /branches/dev/samtools/zutil.h
3549 The initial version of samtools, replicated from my local SVN repository.
3550 The current version is: 0.1.0-42. All future development will happen here.
3552 ------------------------------------------------------------------------
3553 r5 | lh3lh3 | 2008-11-25 15:30:49 -0500 (Tue, 25 Nov 2008) | 2 lines
3555 A /branches/dev/samtools
3557 samtools (C version)
3559 ------------------------------------------------------------------------