1 ------------------------------------------------------------------------
2 r599 | lh3lh3 | 2010-06-13 21:41:11 -0400 (Sun, 13 Jun 2010) | 2 lines
4 M /trunk/samtools/bamtk.c
6 minor fix. No actual effect.
8 ------------------------------------------------------------------------
9 r598 | lh3lh3 | 2010-06-13 21:32:45 -0400 (Sun, 13 Jun 2010) | 2 lines
11 M /trunk/samtools/Makefile
13 added Makefile targets to compile shared/dynamic library
15 ------------------------------------------------------------------------
16 r596 | lh3lh3 | 2010-06-13 19:48:07 -0400 (Sun, 13 Jun 2010) | 3 lines
18 M /trunk/samtools/ChangeLog
19 M /trunk/samtools/bam_index.c
20 M /trunk/samtools/bamtk.c
22 * samtools-0.1.7-17 (r596)
23 * also keep the number of coor-less reads in the index file
25 ------------------------------------------------------------------------
26 r595 | lh3lh3 | 2010-06-13 18:54:26 -0400 (Sun, 13 Jun 2010) | 3 lines
28 M /trunk/samtools/bam_index.c
29 M /trunk/samtools/bamtk.c
31 * samtools-0.1.7-16 (r595)
32 * write additional information to bam index
34 ------------------------------------------------------------------------
35 r594 | lh3lh3 | 2010-06-13 17:29:52 -0400 (Sun, 13 Jun 2010) | 2 lines
37 M /trunk/samtools/bam_index.c
39 fixed a bug for unmapped sequences in indexing
41 ------------------------------------------------------------------------
42 r593 | lh3lh3 | 2010-06-12 18:11:32 -0400 (Sat, 12 Jun 2010) | 2 lines
44 M /trunk/samtools/bam.h
45 M /trunk/samtools/bam_index.c
46 M /trunk/samtools/bam_plcmd.c
47 M /trunk/samtools/samtools.1
51 ------------------------------------------------------------------------
52 r592 | lh3lh3 | 2010-06-12 18:02:38 -0400 (Sat, 12 Jun 2010) | 4 lines
54 M /trunk/samtools/ChangeLog
55 M /trunk/samtools/bam_aux.c
56 M /trunk/samtools/bam_index.c
57 M /trunk/samtools/bam_pileup.c
58 M /trunk/samtools/bam_plcmd.c
59 M /trunk/samtools/bamtk.c
61 * samtools-0.1.7-15 (r592)
62 * fixed a few minor memory leaks in the new pileup code
63 * improved the functionality of mpileup
65 ------------------------------------------------------------------------
66 r591 | lh3lh3 | 2010-06-12 14:09:22 -0400 (Sat, 12 Jun 2010) | 3 lines
68 M /trunk/samtools/bam.h
69 M /trunk/samtools/bam_pileup.c
70 M /trunk/samtools/bam_plcmd.c
71 M /trunk/samtools/bamtk.c
73 * samtools-0.1.7-14 (r591)
74 * elementary multi-way pileup. More testing and more functionality to be done.
76 ------------------------------------------------------------------------
77 r590 | lh3lh3 | 2010-06-12 01:00:24 -0400 (Sat, 12 Jun 2010) | 3 lines
79 M /trunk/samtools/bam.h
80 M /trunk/samtools/bam_pileup.c
81 M /trunk/samtools/bamtk.c
83 * samtools-0.1.7-13 (r590)
84 * added mpileup APIs. No compiling errors, but not tested at all. It is late.
86 ------------------------------------------------------------------------
87 r589 | lh3lh3 | 2010-06-11 22:37:09 -0400 (Fri, 11 Jun 2010) | 3 lines
89 M /trunk/samtools/bam.h
90 M /trunk/samtools/bam_pileup.c
91 M /trunk/samtools/bamtk.c
93 * samtools-0.1.7-12 (r589)
94 * added iterator-like APIs for pileup
96 ------------------------------------------------------------------------
97 r588 | lh3lh3 | 2010-06-11 17:41:13 -0400 (Fri, 11 Jun 2010) | 3 lines
99 M /trunk/samtools/bam_index.c
100 M /trunk/samtools/bamtk.c
102 * samtools-0.1.7-11 (r588)
103 * ported a few improvements from tabix back to samtools
105 ------------------------------------------------------------------------
106 r587 | lh3lh3 | 2010-06-11 17:33:16 -0400 (Fri, 11 Jun 2010) | 3 lines
108 M /trunk/samtools/bam.h
109 M /trunk/samtools/bam_index.c
110 M /trunk/samtools/bamtk.c
112 * samtools-0.1.7-10 (r587)
113 * added iterator interface for bam_fetch (ported back from tabix)
115 ------------------------------------------------------------------------
116 r586 | lh3lh3 | 2010-06-11 13:23:53 -0400 (Fri, 11 Jun 2010) | 3 lines
118 M /trunk/samtools/Makefile
119 A /trunk/samtools/bam_reheader.c
120 M /trunk/samtools/bamtk.c
121 M /trunk/samtools/bgzf.c
123 * samtools-0.1.7-9 (r586)
124 * added "reheader" to replace the BAM header
126 ------------------------------------------------------------------------
127 r585 | lh3lh3 | 2010-06-11 12:22:06 -0400 (Fri, 11 Jun 2010) | 3 lines
129 M /trunk/samtools/bam.c
130 M /trunk/samtools/bamtk.c
131 M /trunk/samtools/kstring.h
133 * samtools-0.1.7-8 (r585)
136 ------------------------------------------------------------------------
137 r584 | lh3lh3 | 2010-06-11 12:00:41 -0400 (Fri, 11 Jun 2010) | 4 lines
139 M /trunk/samtools/bam.c
140 M /trunk/samtools/bamtk.c
141 M /trunk/samtools/bgzf.c
142 M /trunk/samtools/bgzf.h
143 M /trunk/samtools/kstring.h
144 M /trunk/samtools/misc/wgsim_eval.pl
146 * samtools-0.1.7-7 (r584)
147 * ported tabix BGZF to samtools
148 * flush BGZF after writing the BAM header and between alignment boundaries
150 ------------------------------------------------------------------------
151 r583 | petulda | 2010-06-11 11:58:20 -0400 (Fri, 11 Jun 2010) | 1 line
153 A /trunk/samtools/misc/varfilter.py
155 Initial release on behalf of Aylwyn Scally
156 ------------------------------------------------------------------------
157 r561 | petulda | 2010-05-07 08:41:56 -0400 (Fri, 07 May 2010) | 1 line
159 M /trunk/samtools/samtools.1
161 Added a note about the indels coordinates
162 ------------------------------------------------------------------------
163 r551 | petulda | 2010-04-23 09:42:13 -0400 (Fri, 23 Apr 2010) | 1 line
165 M /trunk/samtools/misc/sam2vcf.pl
167 Added the possibility to print or not to print the reference allele
168 ------------------------------------------------------------------------
169 r546 | petulda | 2010-04-15 04:33:55 -0400 (Thu, 15 Apr 2010) | 1 line
171 M /trunk/samtools/sam_header.c
173 More descriptive message for space separated tags
174 ------------------------------------------------------------------------
175 r545 | petulda | 2010-04-14 11:44:50 -0400 (Wed, 14 Apr 2010) | 1 line
177 M /trunk/samtools/misc/sam2vcf.pl
179 Speedup with -i, no need to query the reference all the time
180 ------------------------------------------------------------------------
181 r541 | petulda | 2010-03-15 10:03:51 -0400 (Mon, 15 Mar 2010) | 1 line
183 M /trunk/samtools/sam_header.c
185 Fixed the order of sequences in the header
186 ------------------------------------------------------------------------
187 r540 | petulda | 2010-03-04 06:28:35 -0500 (Thu, 04 Mar 2010) | 1 line
189 M /trunk/samtools/misc/sam2vcf.pl
191 Added possibility to select indels only and fixed a bug in reporting homozygous indels.
192 ------------------------------------------------------------------------
193 r539 | jmarshall | 2010-02-27 06:48:17 -0500 (Sat, 27 Feb 2010) | 4 lines
195 M /trunk/samtools/bam.c
197 Improve the invalid 'BAM\1' magic number error message, and also print it
198 when no bytes can be read from the alleged BAM file, e.g., in the common
199 user error case when a SAM file has accidentally been supplied.
201 ------------------------------------------------------------------------
202 r538 | petulda | 2010-02-26 10:51:40 -0500 (Fri, 26 Feb 2010) | 1 line
204 M /trunk/samtools/AUTHORS
205 M /trunk/samtools/bam.h
206 M /trunk/samtools/bam_import.c
207 M /trunk/samtools/sam_header.c
209 Improved efficiency of header parsing
210 ------------------------------------------------------------------------
211 r537 | lh3lh3 | 2010-02-23 21:08:48 -0500 (Tue, 23 Feb 2010) | 3 lines
213 M /trunk/samtools/misc/export2sam.pl
215 Updated export2sam.pl by Chris Saunders from Illumina.
218 ------------------------------------------------------------------------
219 r536 | petulda | 2010-02-17 08:32:53 -0500 (Wed, 17 Feb 2010) | 1 line
221 M /trunk/samtools/misc/samtools.pl
223 Fixed filtering of SNPs near indels. Added min indel and SNP quality filter.
224 ------------------------------------------------------------------------
225 r535 | petulda | 2010-02-12 04:52:37 -0500 (Fri, 12 Feb 2010) | 1 line
227 M /trunk/samtools/misc/sam2vcf.pl
229 Print an error for pileups in simple format
230 ------------------------------------------------------------------------
231 r534 | lh3lh3 | 2010-02-11 14:01:41 -0500 (Thu, 11 Feb 2010) | 2 lines
233 M /trunk/samtools/bam_plcmd.c
235 added a hidden option in pileup to output the base position (for Erin)
237 ------------------------------------------------------------------------
238 r533 | petulda | 2010-02-09 10:12:14 -0500 (Tue, 09 Feb 2010) | 1 line
240 M /trunk/samtools/misc/sam2vcf.pl
242 Added possibility to specify a custom column title for the data column
243 ------------------------------------------------------------------------
244 r532 | petulda | 2010-02-09 09:46:09 -0500 (Tue, 09 Feb 2010) | 1 line
246 M /trunk/samtools/bam_plcmd.c
248 Added the -d option to limit maximum depth for indels.
249 ------------------------------------------------------------------------
250 r531 | petulda | 2010-02-03 07:57:27 -0500 (Wed, 03 Feb 2010) | 1 line
252 M /trunk/samtools/misc/sam2vcf.pl
255 ------------------------------------------------------------------------
256 r530 | lh3lh3 | 2010-02-01 09:13:19 -0500 (Mon, 01 Feb 2010) | 3 lines
258 M /trunk/samtools/ChangeLog
259 M /trunk/samtools/bam_plcmd.c
260 M /trunk/samtools/bamtk.c
261 M /trunk/samtools/misc/samtools.pl
262 M /trunk/samtools/misc/wgsim.c
265 * fixed a bug in faidx
267 ------------------------------------------------------------------------
268 r529 | jmarshall | 2010-01-11 18:51:49 -0500 (Mon, 11 Jan 2010) | 2 lines
270 M /trunk/samtools/faidx.c
272 Put the right filename in the error message.
274 ------------------------------------------------------------------------
275 r528 | lh3lh3 | 2009-12-14 11:26:47 -0500 (Mon, 14 Dec 2009) | 3 lines
277 M /trunk/samtools/bam_plcmd.c
278 M /trunk/samtools/bamtk.c
280 * samtools-0.1.7-5 (r528)
281 * further add new consensus generation strategy
283 ------------------------------------------------------------------------
284 r527 | petulda | 2009-12-11 12:31:05 -0500 (Fri, 11 Dec 2009) | 1 line
286 M /trunk/samtools/knetfile.c
288 Fixed a bug in knet_seek
289 ------------------------------------------------------------------------
290 r526 | petulda | 2009-12-11 07:51:18 -0500 (Fri, 11 Dec 2009) | 1 line
292 M /trunk/samtools/misc/sam2vcf.pl
294 Small fix in VCF format: dot for the empty INFO field
295 ------------------------------------------------------------------------
296 r525 | petulda | 2009-12-11 04:36:18 -0500 (Fri, 11 Dec 2009) | 1 line
298 M /trunk/samtools/sam_header.c
300 Allow tabs in the CO header field
301 ------------------------------------------------------------------------
302 r524 | jmarshall | 2009-12-10 10:03:58 -0500 (Thu, 10 Dec 2009) | 3 lines
304 M /trunk/samtools/Makefile
305 M /trunk/samtools/Makefile.mingw
307 Depend on libbam.a rather than the phony target, so that samtools is not
308 unnecessarily rebuilt every time. Also clean bgzip.
310 ------------------------------------------------------------------------
311 r523 | jmarshall | 2009-12-10 09:45:32 -0500 (Thu, 10 Dec 2009) | 4 lines
313 M /trunk/samtools/Makefile
314 M /trunk/samtools/Makefile.mingw
316 Fix a bug in compiling bgzip: this also needs knetfile.o when _USE_KNETFILE
317 is defined. Also introduce $(KNETFILE_O) which can be set to empty to
318 facilitate non-knet builds.
320 ------------------------------------------------------------------------
321 r522 | lh3lh3 | 2009-12-01 13:02:36 -0500 (Tue, 01 Dec 2009) | 4 lines
323 M /trunk/samtools/bamtk.c
324 M /trunk/samtools/sam_view.c
326 * samtools-0.1.7-4 (r522)
327 * fixed a bug in "view -r"
328 * added a new option "view -R" to read required read groups from a file
330 ------------------------------------------------------------------------
331 r521 | lh3lh3 | 2009-12-01 10:00:12 -0500 (Tue, 01 Dec 2009) | 3 lines
333 M /trunk/samtools/bam_md.c
334 M /trunk/samtools/bamtk.c
336 * samtools-0.1.7-3 (r521)
337 * calmd: optionally mask matching bases as N
339 ------------------------------------------------------------------------
340 r520 | lh3lh3 | 2009-12-01 09:37:17 -0500 (Tue, 01 Dec 2009) | 4 lines
342 M /trunk/samtools/bam_plcmd.c
343 M /trunk/samtools/bamtk.c
344 M /trunk/samtools/misc/samtools.pl
346 * samtools-0.1.7-2 (r520)
347 * fixed a few issues with compilation in Windows (on behalf of John)
348 * choose a random base as the consensus (for population genetics studies)
350 ------------------------------------------------------------------------
351 r519 | jmarshall | 2009-11-30 10:53:02 -0500 (Mon, 30 Nov 2009) | 6 lines
353 M /trunk/samtools/Makefile
355 Put libraries at the end, so they can resolve references from libbam.a
356 as well, even with old-fashioned linkers.
358 Also use libbam.a explicitly rather than "-L. -lbam" to ensure that we get
359 the freshly built library, not some other libbam.a lying around the system.
361 ------------------------------------------------------------------------
362 r518 | jmarshall | 2009-11-30 08:44:56 -0500 (Mon, 30 Nov 2009) | 2 lines
364 M /trunk/samtools/Makefile
365 M /trunk/samtools/misc/Makefile
367 Also clean *.exe (for Cygwin users using this makefile).
369 ------------------------------------------------------------------------
370 r517 | jmarshall | 2009-11-30 07:09:04 -0500 (Mon, 30 Nov 2009) | 2 lines
372 M /trunk/samtools/bam_index.c
374 Index files should be opened in binary mode, not text mode.
376 ------------------------------------------------------------------------
377 r516 | lh3lh3 | 2009-11-27 15:18:59 -0500 (Fri, 27 Nov 2009) | 2 lines
379 A /trunk/samtools/examples/bam2bed.c
381 another example program
383 ------------------------------------------------------------------------
384 r515 | lh3lh3 | 2009-11-27 10:44:56 -0500 (Fri, 27 Nov 2009) | 3 lines
386 M /trunk/samtools/bam_import.c
387 M /trunk/samtools/bamtk.c
388 M /trunk/samtools/misc/wgsim_eval.pl
389 M /trunk/samtools/sam.c
391 * samtools-0.1.7-1 (r515)
392 * report an error when .fai contains duplicated names, instead of segfault
394 ------------------------------------------------------------------------
395 r514 | jmarshall | 2009-11-24 09:45:35 -0500 (Tue, 24 Nov 2009) | 2 lines
397 M /trunk/samtools/bam.c
399 Format 'c'-encoded auxiliary fields correctly, as *signed* integers.
401 ------------------------------------------------------------------------
402 r513 | lh3lh3 | 2009-11-16 10:13:07 -0500 (Mon, 16 Nov 2009) | 2 lines
404 M /trunk/samtools/Makefile.mingw
406 Update Makefile.mingw for the same reason
408 ------------------------------------------------------------------------
409 r512 | lh3lh3 | 2009-11-16 10:00:08 -0500 (Mon, 16 Nov 2009) | 2 lines
411 M /trunk/samtools/Makefile
413 Fixed a bug in compiling razip
415 ------------------------------------------------------------------------
416 r510 | lh3lh3 | 2009-11-10 10:55:41 -0500 (Tue, 10 Nov 2009) | 2 lines
418 M /trunk/samtools/ChangeLog
419 M /trunk/samtools/NEWS
420 M /trunk/samtools/bamtk.c
421 M /trunk/samtools/samtools.1
423 Release samtools-0.1.7 (r510)
425 ------------------------------------------------------------------------
426 r509 | lh3lh3 | 2009-11-06 09:17:09 -0500 (Fri, 06 Nov 2009) | 3 lines
428 M /trunk/samtools/bam_plcmd.c
429 M /trunk/samtools/bamtk.c
431 * samtools-0.1.6-22 (r509)
432 * forget to fix a similar problem in glfgen
434 ------------------------------------------------------------------------
435 r508 | lh3lh3 | 2009-11-06 09:06:40 -0500 (Fri, 06 Nov 2009) | 3 lines
437 M /trunk/samtools/bam_maqcns.c
438 M /trunk/samtools/bam_plcmd.c
439 M /trunk/samtools/bamtk.c
440 M /trunk/samtools/sam_view.c
442 * samtools-0.1.6-21 (r508)
443 * fixed a potential bug in the indel caller towards the end of a chromosome
445 ------------------------------------------------------------------------
446 r494 | lh3lh3 | 2009-10-26 11:38:00 -0400 (Mon, 26 Oct 2009) | 3 lines
448 M /trunk/samtools/bamtk.c
449 M /trunk/samtools/sam_view.c
451 * samtools-0.1.6-19 (r494)
452 * allow to convert Illumina quality (64 based) to the BAM quality
454 ------------------------------------------------------------------------
455 r493 | lh3lh3 | 2009-10-26 10:24:39 -0400 (Mon, 26 Oct 2009) | 4 lines
457 M /trunk/samtools/Makefile
458 M /trunk/samtools/bam.c
459 M /trunk/samtools/bam_import.c
460 M /trunk/samtools/bamtk.c
461 M /trunk/samtools/sam.c
462 M /trunk/samtools/sam_header.c
464 * samtools-0.1.6-18 (r493)
465 * fixed the bugs due to improperly incorporating Petr's header parser
466 * a little code clean up in sam_header.c
468 ------------------------------------------------------------------------
469 r492 | petulda | 2009-10-24 09:43:25 -0400 (Sat, 24 Oct 2009) | 1 line
471 M /trunk/samtools/sam_header.c
473 Added sam_header_line_free call for sam_header_parse2
474 ------------------------------------------------------------------------
475 r491 | lh3lh3 | 2009-10-24 00:50:16 -0400 (Sat, 24 Oct 2009) | 3 lines
477 M /trunk/samtools/sam_view.c
482 ------------------------------------------------------------------------
483 r490 | lh3lh3 | 2009-10-24 00:45:12 -0400 (Sat, 24 Oct 2009) | 4 lines
485 M /trunk/samtools/bam.c
486 M /trunk/samtools/bam.h
487 M /trunk/samtools/bam_import.c
488 M /trunk/samtools/sam.c
491 * improved the interface a bit
494 ------------------------------------------------------------------------
495 r489 | lh3lh3 | 2009-10-24 00:41:50 -0400 (Sat, 24 Oct 2009) | 3 lines
497 M /trunk/samtools/bam_import.c
498 M /trunk/samtools/sam_header.c
499 M /trunk/samtools/sam_header.h
501 * BUGGY VERSION. Please NOT use it.
502 * Fixed a minor bug, but the major bug is still there.
504 ------------------------------------------------------------------------
505 r488 | lh3lh3 | 2009-10-24 00:17:10 -0400 (Sat, 24 Oct 2009) | 3 lines
507 M /trunk/samtools/Makefile
508 M /trunk/samtools/bam.c
509 M /trunk/samtools/bam.h
510 M /trunk/samtools/bam_aux.c
511 M /trunk/samtools/bam_import.c
512 M /trunk/samtools/bam_rmdup.c
513 M /trunk/samtools/bam_rmdupse.c
514 M /trunk/samtools/kaln.c
515 M /trunk/samtools/sam.c
516 M /trunk/samtools/sam_header.c
517 M /trunk/samtools/sam_header.h
518 M /trunk/samtools/sam_view.c
520 * This revision is SERIOUSLY BUGGY. Please NOT use it.
521 * Start to incorporate header parsing from Petr Danecek
523 ------------------------------------------------------------------------
524 r487 | petulda | 2009-10-23 11:44:32 -0400 (Fri, 23 Oct 2009) | 1 line
526 M /trunk/samtools/sam_header.c
527 M /trunk/samtools/sam_header.h
529 Now possible to merge multiple HeaderDict dictionaries
530 ------------------------------------------------------------------------
531 r486 | petulda | 2009-10-22 11:46:58 -0400 (Thu, 22 Oct 2009) | 1 line
533 M /trunk/samtools/sam_header.c
536 ------------------------------------------------------------------------
537 r485 | petulda | 2009-10-22 11:41:56 -0400 (Thu, 22 Oct 2009) | 1 line
539 A /trunk/samtools/sam_header.c
540 A /trunk/samtools/sam_header.h
543 ------------------------------------------------------------------------
544 r484 | lh3lh3 | 2009-10-19 14:31:32 -0400 (Mon, 19 Oct 2009) | 5 lines
546 M /trunk/samtools/bam_import.c
547 M /trunk/samtools/bam_rmdupse.c
548 M /trunk/samtools/bamtk.c
549 M /trunk/samtools/examples/Makefile
551 * samtools-0.1.6-17 (r484)
552 * fixed a memory leak in rmdupse
553 * fixed a bug in parsing @RG header lines
554 * test rmdup in examples/
556 ------------------------------------------------------------------------
557 r483 | lh3lh3 | 2009-10-19 13:22:48 -0400 (Mon, 19 Oct 2009) | 4 lines
559 M /trunk/samtools/bam_rmdup.c
560 M /trunk/samtools/bam_rmdupse.c
561 M /trunk/samtools/bamtk.c
563 * samtools-0.1.6-16 (r483)
564 * unify the interface of rmdup and rmdupse
565 * a new bug found in rg2lib(). Have not been fixed yet.
567 ------------------------------------------------------------------------
568 r482 | lh3lh3 | 2009-10-19 13:03:34 -0400 (Mon, 19 Oct 2009) | 4 lines
570 M /trunk/samtools/bam.h
571 M /trunk/samtools/bam_rmdup.c
572 M /trunk/samtools/bam_rmdupse.c
573 M /trunk/samtools/bamtk.c
574 A /trunk/samtools/klist.h
576 * samtools-0.1.6-15 (r482)
578 * rmdupse is now library aware
580 ------------------------------------------------------------------------
581 r481 | lh3lh3 | 2009-10-18 00:07:21 -0400 (Sun, 18 Oct 2009) | 3 lines
583 M /trunk/samtools/bam_rmdup.c
584 M /trunk/samtools/bamtk.c
586 * samtools-0.1.6-14 (r480)
587 * rmdup is now RG aware
589 ------------------------------------------------------------------------
590 r480 | lh3lh3 | 2009-10-17 22:05:20 -0400 (Sat, 17 Oct 2009) | 2 lines
592 M /trunk/samtools/misc/samtools.pl
594 added a small unitity to parse SRA XML files
596 ------------------------------------------------------------------------
597 r479 | lh3lh3 | 2009-10-17 20:57:26 -0400 (Sat, 17 Oct 2009) | 3 lines
599 M /trunk/samtools/bam_maqcns.c
600 M /trunk/samtools/bam_maqcns.h
601 M /trunk/samtools/bam_plcmd.c
602 M /trunk/samtools/bam_sort.c
603 M /trunk/samtools/bamtk.c
605 * samtools-0.1.6-13 (r479)
606 * merge: optionally use file names as RG tags
608 ------------------------------------------------------------------------
609 r478 | lh3lh3 | 2009-10-14 14:18:12 -0400 (Wed, 14 Oct 2009) | 3 lines
611 M /trunk/samtools/bam.c
612 M /trunk/samtools/bam.h
613 M /trunk/samtools/bam_maqcns.c
614 M /trunk/samtools/bamtk.c
615 M /trunk/samtools/kaln.c
617 * samtools-0.1.6-12 (r478)
618 * fixed a bug in the indel caller
620 ------------------------------------------------------------------------
621 r477 | lh3lh3 | 2009-10-10 06:12:26 -0400 (Sat, 10 Oct 2009) | 3 lines
623 M /trunk/samtools/bam_index.c
624 M /trunk/samtools/bamtk.c
626 * samtools-0.1.6-11 (r477)
627 * fixed a bug due to recent change in bam_index.c (thank Nicole Washington for the patch)
629 ------------------------------------------------------------------------
630 r476 | petulda | 2009-10-09 11:45:36 -0400 (Fri, 09 Oct 2009) | 1 line
632 A /trunk/samtools/misc/sam2vcf.pl
634 Added the sam2vcf.pl script.
635 ------------------------------------------------------------------------
636 r475 | lh3lh3 | 2009-10-08 10:19:16 -0400 (Thu, 08 Oct 2009) | 2 lines
638 M /trunk/samtools/Makefile
639 M /trunk/samtools/bam.c
640 M /trunk/samtools/bam.h
641 M /trunk/samtools/bam_maqcns.c
642 M /trunk/samtools/bamtk.c
643 A /trunk/samtools/kaln.c
644 A /trunk/samtools/kaln.h
646 Unfinished modification. Please do not use this revision...
648 ------------------------------------------------------------------------
649 r474 | petulda | 2009-10-08 06:39:54 -0400 (Thu, 08 Oct 2009) | 1 line
651 M /trunk/samtools/knetfile.c
653 Removed the offending knet_seek message.
654 ------------------------------------------------------------------------
655 r473 | petulda | 2009-10-06 09:26:35 -0400 (Tue, 06 Oct 2009) | 1 line
657 M /trunk/samtools/knetfile.c
658 M /trunk/samtools/razf.c
660 Bug fix - faidx on RAZF compressed files now working.
661 ------------------------------------------------------------------------
662 r472 | lh3lh3 | 2009-10-02 08:42:57 -0400 (Fri, 02 Oct 2009) | 2 lines
664 M /trunk/samtools/samtools.1
666 Clarify the meaning of a region like "chr2:1,000,000".
668 ------------------------------------------------------------------------
669 r471 | lh3lh3 | 2009-10-02 05:42:19 -0400 (Fri, 02 Oct 2009) | 2 lines
671 M /trunk/samtools/misc/novo2sam.pl
673 Fixed minor bugs in novo2sam.pl (on behalf of Ken Chen and Colin Hercus)
675 ------------------------------------------------------------------------
676 r470 | lh3lh3 | 2009-09-29 15:01:27 -0400 (Tue, 29 Sep 2009) | 3 lines
678 M /trunk/samtools/Makefile.mingw
679 M /trunk/samtools/bamtk.c
680 M /trunk/samtools/knetfile.c
681 M /trunk/samtools/knetfile.h
683 * samtools-0.1.6-9 (r470)
684 * make knetfile.c compatible with MinGW (thank Martin Morgan for the patch)
686 ------------------------------------------------------------------------
687 r469 | lh3lh3 | 2009-09-29 08:07:44 -0400 (Tue, 29 Sep 2009) | 3 lines
689 M /trunk/samtools/bam_index.c
690 M /trunk/samtools/bamtk.c
692 * samtools-0.1.6-9 (r469)
693 * refactor bam_fetch() for Python binding. On behalf of Leo Goodstadt.
695 ------------------------------------------------------------------------
696 r468 | lh3lh3 | 2009-09-28 05:18:29 -0400 (Mon, 28 Sep 2009) | 3 lines
698 M /trunk/samtools/bam_sort.c
699 M /trunk/samtools/bamtk.c
700 M /trunk/samtools/misc/samtools.pl
702 * samtools-0.1.6-7 (r468)
705 ------------------------------------------------------------------------
706 r467 | petulda | 2009-09-28 04:51:29 -0400 (Mon, 28 Sep 2009) | 1 line
708 M /trunk/samtools/bgzf.c
709 M /trunk/samtools/bgzip.c
710 M /trunk/samtools/razf.c
711 M /trunk/samtools/razip.c
713 Changed the mode for newly created files to 0666. This allows less strict permissions with umask properly set (e.g. 0002 vs. 0022).
714 ------------------------------------------------------------------------
715 r466 | lh3lh3 | 2009-09-24 06:29:19 -0400 (Thu, 24 Sep 2009) | 3 lines
717 M /trunk/samtools/ChangeLog
718 M /trunk/samtools/bam_md.c
719 M /trunk/samtools/bamtk.c
721 * samtools-0.1.6-6 (r466)
722 * do not crash calmd when some sequences are absent from the reference.
724 ------------------------------------------------------------------------
725 r464 | jmarshall | 2009-09-23 06:14:32 -0400 (Wed, 23 Sep 2009) | 3 lines
727 M /trunk/samtools/bam.c
728 M /trunk/samtools/knetfile.c
730 Suppress bgzf_check_EOF() messages when reading from a pipe, as there is
731 no way to seek on a pipe and the messages always appear.
733 ------------------------------------------------------------------------
734 r463 | petulda | 2009-09-16 07:05:41 -0400 (Wed, 16 Sep 2009) | 1 line
736 M /trunk/samtools/knetfile.c
737 M /trunk/samtools/razf.c
739 A bug fix, "samtools view" is now working again.
740 ------------------------------------------------------------------------
741 r462 | lh3lh3 | 2009-09-16 04:51:07 -0400 (Wed, 16 Sep 2009) | 3 lines
743 M /trunk/samtools/bamtk.c
744 M /trunk/samtools/faidx.c
745 M /trunk/samtools/knetfile.c
746 M /trunk/samtools/knetfile.h
747 M /trunk/samtools/razf.c
748 M /trunk/samtools/razf.h
750 * samtools-0.1.6-5 (r462)
751 * Added knetfile support in razf and faidx (on behalf of Petr Danecek)
753 ------------------------------------------------------------------------
754 r460 | lh3lh3 | 2009-09-09 07:06:22 -0400 (Wed, 09 Sep 2009) | 2 lines
756 M /trunk/samtools/samtools.1
758 fixed a formatting issue
760 ------------------------------------------------------------------------
761 r459 | lh3lh3 | 2009-09-08 18:14:08 -0400 (Tue, 08 Sep 2009) | 3 lines
763 M /trunk/samtools/bam_sort.c
764 M /trunk/samtools/bamtk.c
766 * samtools-0.1.6-4 (r459)
767 * make sort output the result to stdout when -o is in use
769 ------------------------------------------------------------------------
770 r458 | lh3lh3 | 2009-09-07 05:10:28 -0400 (Mon, 07 Sep 2009) | 4 lines
772 M /trunk/samtools/bamtk.c
773 M /trunk/samtools/faidx.c
774 M /trunk/samtools/faidx.h
775 M /trunk/samtools/samtools.1
777 * samtools-0.1.6-2 (r458)
778 * added more interface to faidx (by Nils)
779 * updated documentation
781 ------------------------------------------------------------------------
782 r457 | lh3lh3 | 2009-09-05 16:12:04 -0400 (Sat, 05 Sep 2009) | 3 lines
784 M /trunk/samtools/bam_sort.c
785 M /trunk/samtools/bamtk.c
787 * samtools-0.1.6-2 (r457)
788 * get rid of three assert() in bam_sort.c
790 ------------------------------------------------------------------------
791 r456 | jmarshall | 2009-09-04 12:46:25 -0400 (Fri, 04 Sep 2009) | 3 lines
793 M /trunk/samtools/razf.c
795 Return NULL from _razf_open() (and hence razf_open()/razf_open2())
796 when opening the file fails.
798 ------------------------------------------------------------------------
799 r453 | lh3lh3 | 2009-09-02 08:56:33 -0400 (Wed, 02 Sep 2009) | 2 lines
801 M /trunk/samtools/ChangeLog
802 M /trunk/samtools/NEWS
803 M /trunk/samtools/bamtk.c
804 M /trunk/samtools/samtools.1
805 D /trunk/samtools/source.dot
807 Release samtools-0.1.6
809 ------------------------------------------------------------------------
810 r451 | lh3lh3 | 2009-09-02 05:44:48 -0400 (Wed, 02 Sep 2009) | 4 lines
812 M /trunk/samtools/bam_md.c
813 M /trunk/samtools/bam_rmdup.c
814 M /trunk/samtools/bam_rmdupse.c
815 M /trunk/samtools/bam_sort.c
816 M /trunk/samtools/bamtk.c
817 M /trunk/samtools/samtools.1
819 * samtools-0.1.5-34 (r451)
820 * applied the patch by John
821 * improved the help message a little bit
823 ------------------------------------------------------------------------
824 r450 | lh3lh3 | 2009-09-02 04:55:55 -0400 (Wed, 02 Sep 2009) | 3 lines
826 M /trunk/samtools/bam_color.c
827 M /trunk/samtools/bamtk.c
829 * samtools-0.1.5-33 (r450)
830 * fixed a bug in bam_color.c (on behalf of Nils Homer)
832 ------------------------------------------------------------------------
833 r449 | lh3lh3 | 2009-08-29 15:36:41 -0400 (Sat, 29 Aug 2009) | 4 lines
835 M /trunk/samtools/bam_import.c
836 M /trunk/samtools/bam_md.c
837 M /trunk/samtools/bamtk.c
838 M /trunk/samtools/misc/samtools.pl
840 * samtools-0.1.5-32 (r449)
841 * fillmd: fixed a bug in modifying MD/NM tags
842 * in import, give a warning if the read is aligned but there is no CIGAR.
844 ------------------------------------------------------------------------
845 r448 | lh3lh3 | 2009-08-19 04:44:28 -0400 (Wed, 19 Aug 2009) | 3 lines
847 M /trunk/samtools/ChangeLog
848 M /trunk/samtools/bam_pileup.c
849 M /trunk/samtools/bamtk.c
850 M /trunk/samtools/misc/wgsim_eval.pl
852 * samtools-0.1.5-31 (r448)
853 * fixed an issue when the last CIGAR is I or D
855 ------------------------------------------------------------------------
856 r447 | lh3lh3 | 2009-08-17 04:34:57 -0400 (Mon, 17 Aug 2009) | 3 lines
858 M /trunk/samtools/bam_aux.c
859 M /trunk/samtools/bamtk.c
861 * samtools-0.1.5-30 (r447)
862 * fixed a bug in bam_aux_get(): 'A' is not checked
864 ------------------------------------------------------------------------
865 r446 | lh3lh3 | 2009-08-17 04:33:17 -0400 (Mon, 17 Aug 2009) | 2 lines
867 M /trunk/samtools/bam_aux.c
868 M /trunk/samtools/bamtk.c
872 ------------------------------------------------------------------------
873 r444 | lh3lh3 | 2009-08-11 05:02:36 -0400 (Tue, 11 Aug 2009) | 3 lines
875 M /trunk/samtools/bam_sort.c
876 M /trunk/samtools/bamtk.c
878 * samtools-0.1.5-28 (r444)
881 ------------------------------------------------------------------------
882 r443 | lh3lh3 | 2009-08-11 04:29:11 -0400 (Tue, 11 Aug 2009) | 4 lines
884 M /trunk/samtools/bam.c
885 M /trunk/samtools/bam_import.c
886 M /trunk/samtools/bamtk.c
888 * samtools-0.1.5-27 (r443)
889 * SEQ and QUAL can be "*"
890 * parse CIGAR "=" and "X" as "M"
892 ------------------------------------------------------------------------
893 r442 | lh3lh3 | 2009-08-07 16:56:38 -0400 (Fri, 07 Aug 2009) | 4 lines
895 M /trunk/samtools/bam_pileup.c
896 M /trunk/samtools/bamtk.c
897 M /trunk/samtools/misc/md5.c
898 M /trunk/samtools/misc/md5.h
899 M /trunk/samtools/misc/md5fa.c
901 * samtools-0.1.5-26 (r442)
902 * replace RSA Inc md5.* with ones under permissive lincense
903 * fixed a bug in detecting unsorted bam in pileup
905 ------------------------------------------------------------------------
906 r441 | bhandsaker | 2009-08-05 09:41:28 -0400 (Wed, 05 Aug 2009) | 2 lines
908 M /trunk/samtools/bgzf.c
909 M /trunk/samtools/bgzf.h
910 M /trunk/samtools/bgzip.c
912 Change copyright notices now that MIT has approved open source distribution.
914 ------------------------------------------------------------------------
915 r440 | lh3lh3 | 2009-08-05 05:44:24 -0400 (Wed, 05 Aug 2009) | 3 lines
917 M /trunk/samtools/bam_stat.c
918 M /trunk/samtools/bamtk.c
920 * samtools-0.1.5-25 (r436)
921 * in flagstats, do not report singletons if both ends are unmapped
923 ------------------------------------------------------------------------
924 r439 | lh3lh3 | 2009-08-04 17:16:51 -0400 (Tue, 04 Aug 2009) | 2 lines
926 M /trunk/samtools/misc/maq2sam.c
928 fixed a SERIOUS bug in setting 0x20 flag
930 ------------------------------------------------------------------------
931 r438 | lh3lh3 | 2009-08-04 16:50:43 -0400 (Tue, 04 Aug 2009) | 2 lines
933 M /trunk/samtools/misc/samtools.pl
935 fixed two minor bugs (suggested by Tim M Storm)
937 ------------------------------------------------------------------------
938 r437 | lh3lh3 | 2009-08-04 04:13:24 -0400 (Tue, 04 Aug 2009) | 3 lines
940 M /trunk/samtools/bamtk.c
941 M /trunk/samtools/misc/samtools.pl
942 M /trunk/samtools/sam_view.c
944 * samtools-0.1.5-24 (r435)
947 ------------------------------------------------------------------------
948 r434 | lh3lh3 | 2009-08-03 05:40:42 -0400 (Mon, 03 Aug 2009) | 3 lines
950 M /trunk/samtools/bam_tview.c
951 M /trunk/samtools/bamtk.c
953 * samtools-0.1.5-23 (r434)
954 * in tview, press 'r' to show read names rather than sequences
956 ------------------------------------------------------------------------
957 r433 | lh3lh3 | 2009-08-02 14:13:35 -0400 (Sun, 02 Aug 2009) | 3 lines
959 M /trunk/samtools/knetfile.c
961 * tried to fixed the buggy FTP random access in Windows. FAILED.
962 * anyway, MinGW seems to have problem with "%lld".
964 ------------------------------------------------------------------------
965 r432 | lh3lh3 | 2009-08-01 19:32:07 -0400 (Sat, 01 Aug 2009) | 5 lines
967 M /trunk/samtools/Makefile.mingw
968 M /trunk/samtools/bamtk.c
969 M /trunk/samtools/faidx.c
970 M /trunk/samtools/razf.c
971 A /trunk/samtools/win32/libcurses.a
972 A /trunk/samtools/win32/xcurses.h
974 * samtools-0.1.5-22 (r432)
975 * faidx: fixed compitability issue with _WIN32
976 * razf: fixed potential compitability issue with _WIN32
977 * PDCurses support in Windows
979 ------------------------------------------------------------------------
980 r431 | lh3lh3 | 2009-08-01 18:34:54 -0400 (Sat, 01 Aug 2009) | 2 lines
982 M /trunk/samtools/win32/libz.a
984 replace the GnuWin32 version of libz.a with my own build with MinGW.
986 ------------------------------------------------------------------------
987 r430 | lh3lh3 | 2009-08-01 18:21:07 -0400 (Sat, 01 Aug 2009) | 2 lines
989 M /trunk/samtools/knetfile.c
993 ------------------------------------------------------------------------
994 r429 | lh3lh3 | 2009-08-01 17:41:19 -0400 (Sat, 01 Aug 2009) | 3 lines
996 M /trunk/samtools/Makefile.mingw
997 M /trunk/samtools/bamtk.c
998 M /trunk/samtools/knetfile.c
999 M /trunk/samtools/knetfile.h
1001 * samtools-0.1.5-21 (r428)
1002 * knetfile.c is now compatible with mingw-winsock
1004 ------------------------------------------------------------------------
1005 r428 | lh3lh3 | 2009-07-31 19:39:07 -0400 (Fri, 31 Jul 2009) | 2 lines
1007 M /trunk/samtools/Makefile.mingw
1009 simplify MinGW Makefile
1011 ------------------------------------------------------------------------
1012 r427 | lh3lh3 | 2009-07-31 19:30:54 -0400 (Fri, 31 Jul 2009) | 5 lines
1014 A /trunk/samtools/Makefile.mingw
1015 M /trunk/samtools/bam_import.c
1016 M /trunk/samtools/bamtk.c
1017 A /trunk/samtools/win32
1018 A /trunk/samtools/win32/libz.a
1019 A /trunk/samtools/win32/zconf.h
1020 A /trunk/samtools/win32/zlib.h
1022 * samtools-0.1.5-20 (r427)
1023 * MinGW support. At least SAM<->BAM conversion is working. Other
1024 functionality are not tested at the moment.
1025 * zlib headers and Windows version of libz.a are included in win32/
1027 ------------------------------------------------------------------------
1028 r426 | lh3lh3 | 2009-07-31 18:32:09 -0400 (Fri, 31 Jul 2009) | 3 lines
1030 M /trunk/samtools/bamtk.c
1031 M /trunk/samtools/sam_view.c
1033 * samtools-0.1.5-19 (r426)
1034 * fixed a bug caused by recent modifications. Sorry.
1036 ------------------------------------------------------------------------
1037 r425 | lh3lh3 | 2009-07-31 18:23:51 -0400 (Fri, 31 Jul 2009) | 2 lines
1039 M /trunk/samtools/bgzf.c
1041 compatible with Windows binary files
1043 ------------------------------------------------------------------------
1044 r424 | lh3lh3 | 2009-07-31 05:19:59 -0400 (Fri, 31 Jul 2009) | 5 lines
1046 M /trunk/samtools/bam_maqcns.c
1047 M /trunk/samtools/bam_maqcns.h
1048 M /trunk/samtools/bam_plcmd.c
1049 M /trunk/samtools/bam_tview.c
1050 M /trunk/samtools/bamtk.c
1051 M /trunk/samtools/misc/samtools.pl
1053 * samtools-0.1.5-18 (r423)
1054 * output additional information in pileup indel lines, for the purepose
1055 of debugging at the moment
1056 * in tview, optionally allow to treat reference skip as deletion
1058 ------------------------------------------------------------------------
1059 r423 | lh3lh3 | 2009-07-30 17:00:36 -0400 (Thu, 30 Jul 2009) | 2 lines
1061 A /trunk/samtools/misc/psl2sam.pl
1063 convert BLAT psl to SAM.
1065 ------------------------------------------------------------------------
1066 r422 | lh3lh3 | 2009-07-30 06:24:39 -0400 (Thu, 30 Jul 2009) | 6 lines
1068 M /trunk/samtools/ChangeLog
1069 M /trunk/samtools/bam.c
1070 M /trunk/samtools/bamtk.c
1071 M /trunk/samtools/bgzf.c
1072 M /trunk/samtools/bgzf.h
1073 M /trunk/samtools/knetfile.c
1074 M /trunk/samtools/sam.c
1075 M /trunk/samtools/sam_view.c
1077 * samtools-0.1.5-17 (r422)
1078 * fixed a but in knetfile.c when seek type is not SEEK_SET
1079 * write an empty BGZF block to every BGZF file
1080 * check BGZF EOF marker in bam_header_read()
1083 ------------------------------------------------------------------------
1084 r421 | lh3lh3 | 2009-07-30 05:03:39 -0400 (Thu, 30 Jul 2009) | 3 lines
1086 M /trunk/samtools/bam_import.c
1087 M /trunk/samtools/bam_plcmd.c
1088 M /trunk/samtools/bamtk.c
1089 M /trunk/samtools/misc/samtools.pl
1090 M /trunk/samtools/sam.c
1091 M /trunk/samtools/sam.h
1092 M /trunk/samtools/sam_view.c
1094 * samtools-0.1.5-16 (r421)
1095 * in view and pileup, load header from FASTA index if the input is SAM.
1097 ------------------------------------------------------------------------
1098 r420 | lh3lh3 | 2009-07-29 04:18:55 -0400 (Wed, 29 Jul 2009) | 2 lines
1100 M /trunk/samtools/misc/maq2sam.c
1102 do not set "read 1" if reads are not mapped in the PE mode of maq
1104 ------------------------------------------------------------------------
1105 r419 | lh3lh3 | 2009-07-28 04:52:33 -0400 (Tue, 28 Jul 2009) | 5 lines
1107 M /trunk/samtools/bam_import.c
1108 M /trunk/samtools/bamtk.c
1109 M /trunk/samtools/misc/samtools.pl
1110 M /trunk/samtools/misc/wgsim_eval.pl
1112 * samtools-0.1.5-15 (r419)
1113 * in sam_open(), return NULL when the file cannot be opened.
1114 * make wgsim_eval.pl more robust to imperfect SAM
1115 * add "unique" command to samtools.pl
1117 ------------------------------------------------------------------------
1118 r418 | lh3lh3 | 2009-07-24 09:04:19 -0400 (Fri, 24 Jul 2009) | 2 lines
1120 M /trunk/samtools/misc/wgsim_eval.pl
1122 skip @header lines in SAM
1124 ------------------------------------------------------------------------
1125 r417 | lh3lh3 | 2009-07-24 07:42:38 -0400 (Fri, 24 Jul 2009) | 3 lines
1127 M /trunk/samtools/bamtk.c
1128 M /trunk/samtools/sam_view.c
1130 * samtools-0.1.5-14 (r417)
1131 * more help in "samtools view" due to the recent changes.
1133 ------------------------------------------------------------------------
1134 r416 | lh3lh3 | 2009-07-24 07:34:30 -0400 (Fri, 24 Jul 2009) | 3 lines
1136 M /trunk/samtools/bam.c
1137 M /trunk/samtools/bam.h
1138 M /trunk/samtools/bam_import.c
1139 M /trunk/samtools/bamtk.c
1140 M /trunk/samtools/sam.c
1141 M /trunk/samtools/sam.h
1142 M /trunk/samtools/sam_view.c
1144 * samtools-0.1.5-17 (r416)
1145 * support import/export SAM with string tags
1147 ------------------------------------------------------------------------
1148 r415 | lh3lh3 | 2009-07-24 06:39:26 -0400 (Fri, 24 Jul 2009) | 3 lines
1150 M /trunk/samtools/bam.c
1151 M /trunk/samtools/bam.h
1152 M /trunk/samtools/bam_import.c
1153 M /trunk/samtools/bamtk.c
1154 M /trunk/samtools/sam.c
1155 M /trunk/samtools/sam.h
1156 M /trunk/samtools/sam_view.c
1158 * samtools-0.1.5-12 (r415)
1159 * FLAG now can be in HEX
1161 ------------------------------------------------------------------------
1162 r414 | lh3lh3 | 2009-07-22 17:03:49 -0400 (Wed, 22 Jul 2009) | 2 lines
1164 M /trunk/samtools/kstring.h
1166 fixed a compiling error (thank Ken for fixing it)
1168 ------------------------------------------------------------------------
1169 r412 | lh3lh3 | 2009-07-21 17:19:40 -0400 (Tue, 21 Jul 2009) | 2 lines
1171 M /trunk/samtools/kstring.c
1172 M /trunk/samtools/kstring.h
1174 Implemented Boyer-Moore search in the kstring library.
1176 ------------------------------------------------------------------------
1177 r409 | lh3lh3 | 2009-07-17 12:10:20 -0400 (Fri, 17 Jul 2009) | 2 lines
1179 M /trunk/samtools/bam_index.c
1181 do not include knetfile.h when _USE_KNETFILE is not defined
1183 ------------------------------------------------------------------------
1184 r408 | lh3lh3 | 2009-07-17 10:29:21 -0400 (Fri, 17 Jul 2009) | 5 lines
1186 M /trunk/samtools/bam_md.c
1187 M /trunk/samtools/bam_tview.c
1188 M /trunk/samtools/bamtk.c
1189 M /trunk/samtools/bgzf.c
1191 * samtools-0.1.5-11 (r408)
1192 * force to overwirte existing MD if it is different from the one calculated
1194 * bgzf.c: improved the compatibility with Windows headers
1196 ------------------------------------------------------------------------
1197 r407 | lh3lh3 | 2009-07-17 09:46:56 -0400 (Fri, 17 Jul 2009) | 5 lines
1199 M /trunk/samtools/bam.h
1200 M /trunk/samtools/bam_aux.c
1201 M /trunk/samtools/bam_md.c
1202 M /trunk/samtools/bamtk.c
1203 M /trunk/samtools/sam.h
1205 * samtools-0.1.5-10 (r407)
1206 * implemented bam_aux_del() to remove a tag
1207 * fillmd: generate the NM tag
1208 * fillmd: cmd interface improvement
1210 ------------------------------------------------------------------------
1211 r406 | lh3lh3 | 2009-07-16 18:30:40 -0400 (Thu, 16 Jul 2009) | 2 lines
1213 M /trunk/samtools/Makefile
1215 Sorry. The old Makefile is for PDCurses...
1217 ------------------------------------------------------------------------
1218 r405 | lh3lh3 | 2009-07-16 18:30:11 -0400 (Thu, 16 Jul 2009) | 3 lines
1220 M /trunk/samtools/Makefile
1221 M /trunk/samtools/bam_tview.c
1222 M /trunk/samtools/bamtk.c
1224 * samtools-0.1.5-9 (r405)
1225 * improved the compatibility with PDCurses a little bit
1227 ------------------------------------------------------------------------
1228 r404 | lh3lh3 | 2009-07-16 18:23:52 -0400 (Thu, 16 Jul 2009) | 3 lines
1230 M /trunk/samtools/Makefile
1231 M /trunk/samtools/bam_tview.c
1232 M /trunk/samtools/bamtk.c
1234 * samtools-0.1.5-8 (r404)
1235 * compatible with PDCurses
1237 ------------------------------------------------------------------------
1238 r403 | lh3lh3 | 2009-07-16 17:39:39 -0400 (Thu, 16 Jul 2009) | 3 lines
1240 M /trunk/samtools/bamtk.c
1241 M /trunk/samtools/kseq.h
1243 * samtools-0.1.5-7 (r403)
1244 * fixed a bug in kseq.h for binary files (text files are fine)
1246 ------------------------------------------------------------------------
1247 r402 | lh3lh3 | 2009-07-16 06:49:53 -0400 (Thu, 16 Jul 2009) | 4 lines
1249 M /trunk/samtools/bam_import.c
1250 M /trunk/samtools/bam_index.c
1251 M /trunk/samtools/bamtk.c
1252 M /trunk/samtools/bgzf.c
1254 * samtools-0.1.5-6 (r402)
1255 * fixed compiling error when "-D_USE_NETFILE" is not applied
1256 * improve portability to MinGW
1258 ------------------------------------------------------------------------
1259 r398 | lh3lh3 | 2009-07-13 05:21:36 -0400 (Mon, 13 Jul 2009) | 3 lines
1261 A /trunk/bam-lite/bam.h (from /trunk/samtools/bam.h:395)
1262 A /trunk/bam-lite/bam_lite.c (from /trunk/samtools/bam_lite.c:395)
1263 D /trunk/samtools/bam_lite.c
1265 * move bam_lite.c to bam-lite
1266 * copy bam.h to bam-lite
1268 ------------------------------------------------------------------------
1269 r395 | lh3lh3 | 2009-07-13 05:12:57 -0400 (Mon, 13 Jul 2009) | 3 lines
1271 M /trunk/samtools/bam.h
1272 M /trunk/samtools/bam_lite.c
1273 M /trunk/samtools/bam_lpileup.c
1274 M /trunk/samtools/bam_pileup.c
1275 M /trunk/samtools/bamtk.c
1277 * samtools-0.1.5-5 (r395)
1278 * added bam_pileup_file() and removed bam_lpileup_file()
1280 ------------------------------------------------------------------------
1281 r394 | lh3lh3 | 2009-07-12 19:35:10 -0400 (Sun, 12 Jul 2009) | 3 lines
1283 M /trunk/samtools/bamtk.c
1284 M /trunk/samtools/knetfile.c
1285 M /trunk/samtools/knetfile.h
1287 * samtools-0.1.5-4 (r394)
1288 * http_proxy support in knetfile library (check http_proxy ENV)
1290 ------------------------------------------------------------------------
1291 r393 | lh3lh3 | 2009-07-12 18:57:07 -0400 (Sun, 12 Jul 2009) | 5 lines
1293 M /trunk/samtools/bam_index.c
1294 M /trunk/samtools/bam_tview.c
1295 M /trunk/samtools/bamtk.c
1296 M /trunk/samtools/knetfile.c
1297 M /trunk/samtools/knetfile.h
1299 * samtools-0.1.5-3 (r393)
1300 * knetfile now supports HTTP (no proxy at the moment)
1301 * fixed a potential issue in knetfile on opening ordinary file, although I have
1302 not seen the sideeffect so far.
1304 ------------------------------------------------------------------------
1305 r392 | lh3lh3 | 2009-07-12 13:50:55 -0400 (Sun, 12 Jul 2009) | 2 lines
1307 M /trunk/samtools/samtools.1
1309 Remove the warning in tview
1311 ------------------------------------------------------------------------
1312 r391 | lh3lh3 | 2009-07-12 13:42:43 -0400 (Sun, 12 Jul 2009) | 3 lines
1314 M /trunk/samtools/bam_tview.c
1315 M /trunk/samtools/bamtk.c
1317 * samtools-0.1.5-2 (r391)
1318 * do not show a blank screen when no reads mapped
1320 ------------------------------------------------------------------------
1321 r390 | lh3lh3 | 2009-07-09 09:01:42 -0400 (Thu, 09 Jul 2009) | 4 lines
1323 M /trunk/samtools/bam.h
1324 A /trunk/samtools/bam_lite.c
1325 M /trunk/samtools/bamtk.c
1327 * samtools-0.1.5-1 (r390)
1328 * removed useless _IOLIB in bam.h. This should cause no change at all.
1329 * added bam_lite.c for light-weight BAM reading
1331 ------------------------------------------------------------------------
1332 r385 | lh3lh3 | 2009-07-07 11:53:29 -0400 (Tue, 07 Jul 2009) | 2 lines
1334 M /trunk/samtools/bamtk.c
1335 M /trunk/samtools/knetfile.c
1337 Release samtools-0.1.5c (fixed a bug in piping)
1339 ------------------------------------------------------------------------
1340 r383 | lh3lh3 | 2009-07-07 06:39:55 -0400 (Tue, 07 Jul 2009) | 2 lines
1342 M /trunk/samtools/bamtk.c
1343 M /trunk/samtools/sam.c
1345 Release samtools-0.1.5b (BUG! so embarrassing!)
1347 ------------------------------------------------------------------------
1348 r381 | lh3lh3 | 2009-07-07 06:20:06 -0400 (Tue, 07 Jul 2009) | 2 lines
1350 M /trunk/samtools/Makefile
1351 M /trunk/samtools/bam.h
1352 M /trunk/samtools/bam_aux.c
1353 M /trunk/samtools/bamtk.c
1355 Release samtools-0.1.5a (for compatibility with Bio::DB::Sam)
1357 ------------------------------------------------------------------------
1358 r373 | lh3lh3 | 2009-07-07 05:26:57 -0400 (Tue, 07 Jul 2009) | 2 lines
1360 M /trunk/samtools/ChangeLog
1361 M /trunk/samtools/NEWS
1362 M /trunk/samtools/bamtk.c
1363 M /trunk/samtools/samtools.1
1365 Release samtools-0.1.5
1367 ------------------------------------------------------------------------
1368 r372 | lh3lh3 | 2009-07-07 04:49:27 -0400 (Tue, 07 Jul 2009) | 3 lines
1370 M /trunk/samtools/bamtk.c
1371 M /trunk/samtools/sam.c
1373 * samtools-0.1.4-23 (r372)
1374 * keep header text if "view -t" is used (by Gerton)
1376 ------------------------------------------------------------------------
1377 r371 | lh3lh3 | 2009-07-06 20:13:32 -0400 (Mon, 06 Jul 2009) | 2 lines
1379 M /trunk/samtools/samtools.1
1381 update documentation
1383 ------------------------------------------------------------------------
1384 r370 | bhandsaker | 2009-07-02 17:24:34 -0400 (Thu, 02 Jul 2009) | 2 lines
1386 M /trunk/samtools/Makefile
1388 Introduced LIBPATH variable so this could be overridden to allow samtools to build correct at the Broad.
1390 ------------------------------------------------------------------------
1391 r369 | lh3lh3 | 2009-07-02 08:36:53 -0400 (Thu, 02 Jul 2009) | 4 lines
1393 M /trunk/samtools/ChangeLog
1394 M /trunk/samtools/bam_aux.c
1395 M /trunk/samtools/bam_plcmd.c
1396 M /trunk/samtools/bamtk.c
1398 * samtools-0.1.4-22 (r369)
1399 * in pileup, optionally print E2 and U2
1400 * remove the debugging code in bam_aux_get() (Drat!)
1402 ------------------------------------------------------------------------
1403 r368 | lh3lh3 | 2009-07-02 06:32:26 -0400 (Thu, 02 Jul 2009) | 6 lines
1405 M /trunk/samtools/bam.c
1406 M /trunk/samtools/bam.h
1407 M /trunk/samtools/bam_aux.c
1408 M /trunk/samtools/bam_index.c
1409 M /trunk/samtools/bam_lpileup.c
1410 M /trunk/samtools/bam_md.c
1411 M /trunk/samtools/bam_pileup.c
1412 M /trunk/samtools/bam_rmdup.c
1413 M /trunk/samtools/bam_stat.c
1414 M /trunk/samtools/bam_tview.c
1415 M /trunk/samtools/bamtk.c
1416 M /trunk/samtools/faidx.c
1417 M /trunk/samtools/faidx.h
1418 M /trunk/samtools/glf.c
1420 * samtools-0.1.4-21 (r368)
1421 * propagate errors rather than exit or complain assertion failure. Assertion
1422 should be only used for checking internal bugs, but not for external input
1423 inconsistency. I was just a bit lazy.
1424 * small memory leak may be present on failure, though
1426 ------------------------------------------------------------------------
1427 r367 | lh3lh3 | 2009-06-30 11:18:42 -0400 (Tue, 30 Jun 2009) | 2 lines
1429 M /trunk/samtools/knetfile.c
1431 reduce the chance of blocking in FTP connection
1433 ------------------------------------------------------------------------
1434 r366 | lh3lh3 | 2009-06-30 10:35:21 -0400 (Tue, 30 Jun 2009) | 2 lines
1436 M /trunk/samtools/knetfile.c
1438 minor changes to knetfile: invalid fd equals -1 rather than 0
1440 ------------------------------------------------------------------------
1441 r365 | lh3lh3 | 2009-06-30 09:04:30 -0400 (Tue, 30 Jun 2009) | 3 lines
1443 M /trunk/samtools/bam_index.c
1444 M /trunk/samtools/bamtk.c
1445 M /trunk/samtools/knetfile.c
1446 M /trunk/samtools/knetfile.h
1448 * samtools-0.1.4-20 (r365)
1449 * download the BAM index file if it is not found in the current working directory.
1451 ------------------------------------------------------------------------
1452 r364 | lh3lh3 | 2009-06-30 07:39:07 -0400 (Tue, 30 Jun 2009) | 3 lines
1454 M /trunk/samtools/bamtk.c
1455 M /trunk/samtools/knetfile.c
1457 * samtools-0.1.4-19 (r364)
1458 * knetfile: report error when the file is not present on FTP
1460 ------------------------------------------------------------------------
1461 r363 | lh3lh3 | 2009-06-29 18:23:32 -0400 (Mon, 29 Jun 2009) | 4 lines
1463 M /trunk/samtools/bam_tview.c
1464 M /trunk/samtools/bamtk.c
1465 M /trunk/samtools/bgzf.c
1466 M /trunk/samtools/bgzf.h
1467 M /trunk/samtools/knetfile.c
1468 M /trunk/samtools/knetfile.h
1470 * samtools-0.1.4-18 (r363)
1471 * knetfile: do not trigger network communication in FTP seek (lazy seek)
1472 * bgzf: cache recent blocks (disabled by default)
1474 ------------------------------------------------------------------------
1475 r362 | lh3lh3 | 2009-06-25 16:04:34 -0400 (Thu, 25 Jun 2009) | 2 lines
1477 M /trunk/samtools/bgzf.c
1481 ------------------------------------------------------------------------
1482 r361 | lh3lh3 | 2009-06-25 16:03:10 -0400 (Thu, 25 Jun 2009) | 3 lines
1484 M /trunk/samtools/bam_index.c
1485 M /trunk/samtools/bamtk.c
1487 * samtools-0.1.4-17 (r361)
1488 * if a file is given on FTP, search locally for the BAM index
1490 ------------------------------------------------------------------------
1491 r360 | lh3lh3 | 2009-06-25 15:44:52 -0400 (Thu, 25 Jun 2009) | 5 lines
1493 M /trunk/samtools/Makefile
1494 M /trunk/samtools/bam_import.c
1495 M /trunk/samtools/bam_index.c
1496 M /trunk/samtools/bamtk.c
1497 M /trunk/samtools/bgzf.c
1498 M /trunk/samtools/bgzf.h
1499 M /trunk/samtools/knetfile.c
1500 M /trunk/samtools/knetfile.h
1502 * samtools-0.1.4-16 (r360)
1503 * report more information in index when the input is not sorted
1504 * change the behaviour of knet_seek() such that it returns 0 on success
1505 * support knetfile library in BGZF
1507 ------------------------------------------------------------------------
1508 r359 | lh3lh3 | 2009-06-25 12:10:55 -0400 (Thu, 25 Jun 2009) | 2 lines
1510 M /trunk/samtools/knetfile.c
1511 M /trunk/samtools/knetfile.h
1513 fixed bugs in knetfile.*
1515 ------------------------------------------------------------------------
1516 r358 | lh3lh3 | 2009-06-25 08:53:19 -0400 (Thu, 25 Jun 2009) | 2 lines
1518 A /trunk/samtools/knetfile.h
1520 this is the header file
1522 ------------------------------------------------------------------------
1523 r357 | lh3lh3 | 2009-06-25 08:52:03 -0400 (Thu, 25 Jun 2009) | 3 lines
1525 A /trunk/samtools/knetfile.c
1527 * open a file at FTP
1528 * preliminary version
1530 ------------------------------------------------------------------------
1531 r354 | lh3lh3 | 2009-06-24 09:02:25 -0400 (Wed, 24 Jun 2009) | 3 lines
1533 M /trunk/samtools/bam.c
1534 M /trunk/samtools/bamtk.c
1536 * samtools-0.1.4-15 (r354)
1537 * fixed a memory leak in bam_view1(), although samtools is not using this routine.
1539 ------------------------------------------------------------------------
1540 r351 | lh3lh3 | 2009-06-17 19:16:26 -0400 (Wed, 17 Jun 2009) | 4 lines
1542 M /trunk/samtools/bamtk.c
1543 M /trunk/samtools/faidx.c
1545 * samtools-0.1.4-13 (r351)
1546 * make faidx more tolerant to empty lines right before or after > lines
1547 * hope this does not introduce new bugs...
1549 ------------------------------------------------------------------------
1550 r350 | lh3lh3 | 2009-06-16 09:37:01 -0400 (Tue, 16 Jun 2009) | 3 lines
1552 M /trunk/samtools/bam_plcmd.c
1553 M /trunk/samtools/bamtk.c
1555 * samtools-0.1.4-13 (r350)
1556 * fixed a small memory leak in pileup, caused by recent modifications
1558 ------------------------------------------------------------------------
1559 r347 | lh3lh3 | 2009-06-13 16:20:49 -0400 (Sat, 13 Jun 2009) | 3 lines
1561 M /trunk/samtools/bam_plcmd.c
1562 M /trunk/samtools/bamtk.c
1563 M /trunk/samtools/sam_view.c
1565 * samtools-0.1.4-12 (r347)
1566 * added `-S' to pileup, similar to `view -S'
1568 ------------------------------------------------------------------------
1569 r346 | lh3lh3 | 2009-06-13 12:52:31 -0400 (Sat, 13 Jun 2009) | 3 lines
1571 M /trunk/samtools/Makefile
1572 M /trunk/samtools/bamtk.c
1573 M /trunk/samtools/sam_view.c
1574 M /trunk/samtools/samtools.1
1576 * samtools-0.1.4-11 (r346)
1577 * allow to select a read group at view command-line
1579 ------------------------------------------------------------------------
1580 r344 | lh3lh3 | 2009-06-13 09:06:24 -0400 (Sat, 13 Jun 2009) | 2 lines
1582 M /trunk/samtools/examples/calDepth.c
1586 ------------------------------------------------------------------------
1587 r343 | lh3lh3 | 2009-06-13 09:01:22 -0400 (Sat, 13 Jun 2009) | 2 lines
1589 M /trunk/samtools/examples/calDepth.c
1593 ------------------------------------------------------------------------
1594 r342 | lh3lh3 | 2009-06-13 08:58:48 -0400 (Sat, 13 Jun 2009) | 2 lines
1596 M /trunk/samtools/examples/Makefile
1597 A /trunk/samtools/examples/calDepth.c
1599 added an example of calculating read depth
1601 ------------------------------------------------------------------------
1602 r341 | lh3lh3 | 2009-06-13 08:00:08 -0400 (Sat, 13 Jun 2009) | 6 lines
1604 M /trunk/samtools/Makefile
1605 M /trunk/samtools/bam.h
1606 M /trunk/samtools/bam_aux.c
1607 A /trunk/samtools/bam_color.c
1608 M /trunk/samtools/bam_plcmd.c
1609 M /trunk/samtools/bam_sort.c
1610 M /trunk/samtools/bam_tview.c
1611 M /trunk/samtools/bamtk.c
1612 M /trunk/samtools/sam.c
1613 M /trunk/samtools/sam.h
1615 * samtools-0.1.4-10 (r341)
1616 * only include key APIs in libbam.a
1617 * move color-specific routines to bam_color.c
1618 * update documentations
1619 * remove the support of -q in pileup
1621 ------------------------------------------------------------------------
1622 r340 | lh3lh3 | 2009-06-13 06:17:14 -0400 (Sat, 13 Jun 2009) | 6 lines
1624 M /trunk/samtools/INSTALL
1625 M /trunk/samtools/Makefile
1626 M /trunk/samtools/bam_aux.c
1627 M /trunk/samtools/bam_import.c
1628 M /trunk/samtools/bam_tview.c
1629 M /trunk/samtools/bamtk.c
1630 M /trunk/samtools/razf.c
1631 M /trunk/samtools/sam_view.c
1633 * samtools-0.1.4-9 (r340)
1634 * added a warning to razf.c if zlib<1.2.2.1
1635 * fixed a compilation warning
1636 * fixed a segfault caused by @RG parsing
1637 * detect NCURSES in bam_tview.c
1639 ------------------------------------------------------------------------
1640 r339 | lh3lh3 | 2009-06-13 05:35:19 -0400 (Sat, 13 Jun 2009) | 2 lines
1642 M /trunk/samtools/INSTALL
1646 ------------------------------------------------------------------------
1647 r338 | lh3lh3 | 2009-06-12 19:15:24 -0400 (Fri, 12 Jun 2009) | 4 lines
1649 M /trunk/samtools/bam.c
1650 M /trunk/samtools/bam.h
1651 M /trunk/samtools/bam_aux.c
1652 M /trunk/samtools/bam_import.c
1653 M /trunk/samtools/bamtk.c
1654 M /trunk/samtools/kstring.h
1655 M /trunk/samtools/sam.c
1656 M /trunk/samtools/sam_view.c
1658 * samtools-0.1.4-8 (r338)
1659 * parse the @RG header lines and allow to choose library at the "samtools view"
1662 ------------------------------------------------------------------------
1663 r337 | lh3lh3 | 2009-06-12 16:25:50 -0400 (Fri, 12 Jun 2009) | 4 lines
1665 M /trunk/samtools/bamtk.c
1666 M /trunk/samtools/bgzf.c
1667 M /trunk/samtools/bgzf.h
1668 M /trunk/samtools/sam.c
1669 M /trunk/samtools/sam_view.c
1671 * samtools-0.1.4-7 (r337)
1672 * bgzf.c: support mode string "wu": uncompressed output
1673 * "samtools view" support "-u" command-line option
1675 ------------------------------------------------------------------------
1676 r336 | lh3lh3 | 2009-06-12 12:20:12 -0400 (Fri, 12 Jun 2009) | 5 lines
1678 M /trunk/samtools/Makefile
1679 M /trunk/samtools/misc/Makefile
1680 M /trunk/samtools/razf.c
1681 M /trunk/samtools/razf.h
1682 M /trunk/samtools/razip.c
1684 * no changes to samtools itself
1685 * remove zlib source codes
1686 * make RAZF reading compatible with old version of zlib
1687 * on old version of zlib, writing is not available
1689 ------------------------------------------------------------------------
1690 r335 | lh3lh3 | 2009-06-12 11:47:33 -0400 (Fri, 12 Jun 2009) | 2 lines
1692 D /trunk/samtools/zlib
1694 remove zlib for simplification...
1696 ------------------------------------------------------------------------
1697 r334 | lh3lh3 | 2009-06-12 10:43:36 -0400 (Fri, 12 Jun 2009) | 5 lines
1699 M /trunk/samtools/bam.h
1700 M /trunk/samtools/bam_aux.c
1701 M /trunk/samtools/bamtk.c
1703 * samtools-0.1.4-6 (r334)
1704 * do not export bam_aux_get_core() for Bio::DB::Sam because it has already
1705 been implemented in that.
1706 * this version works with the latest Bio::DB::Sam (20090612)
1708 ------------------------------------------------------------------------
1709 r333 | lh3lh3 | 2009-06-12 10:33:42 -0400 (Fri, 12 Jun 2009) | 2 lines
1711 M /trunk/samtools/ChangeLog
1715 ------------------------------------------------------------------------
1716 r332 | lh3lh3 | 2009-06-12 10:21:21 -0400 (Fri, 12 Jun 2009) | 2 lines
1718 M /trunk/samtools/AUTHORS
1719 M /trunk/samtools/Makefile
1720 M /trunk/samtools/misc/Makefile
1722 fixed minor things in Makefile
1724 ------------------------------------------------------------------------
1725 r331 | lh3lh3 | 2009-06-12 10:07:05 -0400 (Fri, 12 Jun 2009) | 4 lines
1727 M /trunk/samtools/bamtk.c
1729 * samtools-0.1.4-5 (r3310
1730 * no change to samtools itself. Version number is increased to reflect the
1731 changes in the Makefile building system.
1733 ------------------------------------------------------------------------
1734 r330 | lh3lh3 | 2009-06-12 10:03:38 -0400 (Fri, 12 Jun 2009) | 2 lines
1736 M /trunk/samtools/AUTHORS
1737 D /trunk/samtools/README
1739 update information...
1741 ------------------------------------------------------------------------
1742 r329 | lh3lh3 | 2009-06-12 09:52:21 -0400 (Fri, 12 Jun 2009) | 3 lines
1744 M /trunk/samtools/misc/novo2sam.pl
1746 * updated novoalign converter by Colin Hercus et al.
1747 * this version works with indels
1749 ------------------------------------------------------------------------
1750 r328 | lh3lh3 | 2009-06-12 09:50:53 -0400 (Fri, 12 Jun 2009) | 3 lines
1752 M /trunk/samtools/INSTALL
1753 M /trunk/samtools/Makefile
1754 M /trunk/samtools/misc/Makefile
1755 M /trunk/samtools/zlib/Makefile
1758 * update INSTALL instruction
1760 ------------------------------------------------------------------------
1761 r327 | lh3lh3 | 2009-06-12 09:18:29 -0400 (Fri, 12 Jun 2009) | 4 lines
1763 A /trunk/samtools/Makefile (from /trunk/samtools/Makefile.generic:325)
1764 D /trunk/samtools/Makefile.am
1765 D /trunk/samtools/Makefile.generic
1766 D /trunk/samtools/Makefile.lite
1767 D /trunk/samtools/autogen.sh
1768 D /trunk/samtools/cleanup.sh
1769 D /trunk/samtools/configure.ac
1770 A /trunk/samtools/misc/Makefile (from /trunk/samtools/misc/Makefile.generic:305)
1771 D /trunk/samtools/misc/Makefile.am
1772 D /trunk/samtools/misc/Makefile.generic
1773 M /trunk/samtools/razf.c
1774 A /trunk/samtools/zlib
1775 A /trunk/samtools/zlib/Makefile
1776 A /trunk/samtools/zlib/adler32.c
1777 A /trunk/samtools/zlib/compress.c
1778 A /trunk/samtools/zlib/crc32.c
1779 A /trunk/samtools/zlib/crc32.h
1780 A /trunk/samtools/zlib/deflate.c
1781 A /trunk/samtools/zlib/deflate.h
1782 A /trunk/samtools/zlib/gzio.c
1783 A /trunk/samtools/zlib/infback.c
1784 A /trunk/samtools/zlib/inffast.c
1785 A /trunk/samtools/zlib/inffast.h
1786 A /trunk/samtools/zlib/inffixed.h
1787 A /trunk/samtools/zlib/inflate.c
1788 A /trunk/samtools/zlib/inflate.h
1789 A /trunk/samtools/zlib/inftrees.c
1790 A /trunk/samtools/zlib/inftrees.h
1791 A /trunk/samtools/zlib/trees.c
1792 A /trunk/samtools/zlib/trees.h
1793 A /trunk/samtools/zlib/uncompr.c
1794 A /trunk/samtools/zlib/zconf.h
1795 A /trunk/samtools/zlib/zlib.h
1796 A /trunk/samtools/zlib/zutil.c
1797 A /trunk/samtools/zlib/zutil.h
1798 D /trunk/samtools/zutil.h
1800 * added zlib-1.2.3 as razip requires that
1801 * prepare to changed back to the Makefile building system
1802 * unfinished! (will be soon)
1804 ------------------------------------------------------------------------
1805 r326 | lh3lh3 | 2009-06-12 09:12:03 -0400 (Fri, 12 Jun 2009) | 2 lines
1807 M /trunk/samtools/misc/samtools.pl
1811 ------------------------------------------------------------------------
1812 r325 | lh3lh3 | 2009-06-10 11:27:59 -0400 (Wed, 10 Jun 2009) | 3 lines
1814 M /trunk/samtools/bam_maqcns.c
1815 M /trunk/samtools/bamtk.c
1817 * samtools-0.1.4-4 (r325)
1818 * further avoid wrong consensus calls in repetitive regions.
1820 ------------------------------------------------------------------------
1821 r324 | lh3lh3 | 2009-06-10 10:56:17 -0400 (Wed, 10 Jun 2009) | 4 lines
1823 M /trunk/samtools/bam_maqcns.c
1824 M /trunk/samtools/bam_plcmd.c
1825 M /trunk/samtools/bamtk.c
1826 M /trunk/samtools/sam.c
1827 M /trunk/samtools/sam.h
1829 * samtools-0.1.4-3 (r324)
1830 * make maqcns generate the correct call in repetitive regions.
1831 * allow filtering on mapQ at the pileup command line
1833 ------------------------------------------------------------------------
1834 r323 | lh3lh3 | 2009-06-10 05:04:21 -0400 (Wed, 10 Jun 2009) | 3 lines
1836 M /trunk/samtools/misc/samtools.pl
1838 * samtools.pl-0.3.2 (r322)
1839 * indels and SNPs use different mapping quality threshold
1841 ------------------------------------------------------------------------
1842 r322 | lh3lh3 | 2009-06-10 05:03:22 -0400 (Wed, 10 Jun 2009) | 2 lines
1844 M /trunk/samtools/misc/export2sam.pl
1848 ------------------------------------------------------------------------
1849 r321 | lh3lh3 | 2009-06-09 04:21:48 -0400 (Tue, 09 Jun 2009) | 2 lines
1851 M /trunk/samtools/misc/samtools.pl
1853 just typo. no real change
1855 ------------------------------------------------------------------------
1856 r320 | lh3lh3 | 2009-06-08 09:32:51 -0400 (Mon, 08 Jun 2009) | 2 lines
1858 M /trunk/samtools/misc/samtools.pl
1860 a little bit code cleanup
1862 ------------------------------------------------------------------------
1863 r319 | lh3lh3 | 2009-06-08 09:22:33 -0400 (Mon, 08 Jun 2009) | 4 lines
1865 M /trunk/samtools/misc/samtools.pl
1868 * change default parameters
1869 * optionally print filtered variants
1871 ------------------------------------------------------------------------
1872 r318 | lh3lh3 | 2009-06-08 09:14:26 -0400 (Mon, 08 Jun 2009) | 3 lines
1874 M /trunk/samtools/misc/samtools.pl
1877 * combine snpFilter and indelFilter
1879 ------------------------------------------------------------------------
1880 r317 | lh3lh3 | 2009-06-08 06:31:42 -0400 (Mon, 08 Jun 2009) | 3 lines
1882 M /trunk/samtools/misc/samtools.pl
1885 * change a default parameter
1887 ------------------------------------------------------------------------
1888 r316 | lh3lh3 | 2009-06-08 06:11:06 -0400 (Mon, 08 Jun 2009) | 5 lines
1890 M /trunk/samtools/bam_maqcns.c
1891 M /trunk/samtools/bam_maqcns.h
1892 M /trunk/samtools/bam_plcmd.c
1893 M /trunk/samtools/bamtk.c
1894 M /trunk/samtools/sam.c
1896 * samtools-0.1.4-2 (r316)
1897 * pileup: cap mapping quality at 60 (by default)
1898 * pileup: always calculate RMS mapq
1899 * pileup: allow to output variant sites only
1901 ------------------------------------------------------------------------
1902 r312 | lh3lh3 | 2009-06-04 08:01:10 -0400 (Thu, 04 Jun 2009) | 3 lines
1904 M /trunk/samtools/misc/samtools.pl
1909 ------------------------------------------------------------------------
1910 r311 | lh3lh3 | 2009-06-03 04:40:40 -0400 (Wed, 03 Jun 2009) | 2 lines
1912 M /trunk/samtools/misc/samtools.pl
1914 * in snpFilter, suppress non-SNP sites
1916 ------------------------------------------------------------------------
1917 r310 | lh3lh3 | 2009-06-01 09:35:13 -0400 (Mon, 01 Jun 2009) | 3 lines
1919 M /trunk/samtools/misc/samtools.pl
1924 ------------------------------------------------------------------------
1925 r309 | lh3lh3 | 2009-06-01 09:04:39 -0400 (Mon, 01 Jun 2009) | 3 lines
1927 M /trunk/samtools/misc/samtools.pl
1932 ------------------------------------------------------------------------
1933 r306 | lh3lh3 | 2009-05-28 06:49:35 -0400 (Thu, 28 May 2009) | 3 lines
1935 M /trunk/samtools/bgzf.c
1937 * minor changes to bgzf: return NULL if fd == -1
1938 * suggested by {kdj,jm18}@sanger.ac.uk
1940 ------------------------------------------------------------------------
1941 r305 | lh3lh3 | 2009-05-28 06:16:08 -0400 (Thu, 28 May 2009) | 2 lines
1943 A /trunk/samtools/misc/interpolate_sam.pl
1945 Script for paired-end pileup, contributed by Stephen Montgomery.
1947 ------------------------------------------------------------------------
1948 r304 | lh3lh3 | 2009-05-28 06:08:49 -0400 (Thu, 28 May 2009) | 3 lines
1950 M /trunk/samtools/bamtk.c
1951 M /trunk/samtools/sam.c
1953 * samtools-0.1.4-1 (r304)
1954 * fixed a minor bug in printing headers
1956 ------------------------------------------------------------------------
1957 r297 | lh3lh3 | 2009-05-21 11:06:16 -0400 (Thu, 21 May 2009) | 2 lines
1959 M /trunk/samtools/ChangeLog
1960 M /trunk/samtools/NEWS
1961 M /trunk/samtools/bam_plcmd.c
1962 M /trunk/samtools/bamtk.c
1963 M /trunk/samtools/misc/maq2sam.c
1964 M /trunk/samtools/samtools.1
1966 Release samtools-0.1.4
1968 ------------------------------------------------------------------------
1969 r296 | lh3lh3 | 2009-05-21 07:53:14 -0400 (Thu, 21 May 2009) | 3 lines
1971 M /trunk/samtools/bam_maqcns.c
1972 M /trunk/samtools/bamtk.c
1974 * samtools-0.1.3-24 (r296)
1975 * another similar bug in the indel caller
1977 ------------------------------------------------------------------------
1978 r295 | lh3lh3 | 2009-05-21 07:50:28 -0400 (Thu, 21 May 2009) | 3 lines
1980 M /trunk/samtools/bam_maqcns.c
1981 M /trunk/samtools/bamtk.c
1983 * samtools-0.1.3-23 (r295)
1984 * fixed a critical bug in the indel caller
1986 ------------------------------------------------------------------------
1987 r294 | lh3lh3 | 2009-05-20 08:00:20 -0400 (Wed, 20 May 2009) | 2 lines
1989 M /trunk/samtools/bam_stat.c
1991 added a missing header file
1993 ------------------------------------------------------------------------
1994 r293 | lh3lh3 | 2009-05-19 18:44:25 -0400 (Tue, 19 May 2009) | 3 lines
1996 M /trunk/samtools/bam_tview.c
1997 M /trunk/samtools/bamtk.c
1999 * samtools-0.1.3-22 (r293)
2000 * open tview in the dot-view mode by default
2002 ------------------------------------------------------------------------
2003 r292 | lh3lh3 | 2009-05-18 16:01:23 -0400 (Mon, 18 May 2009) | 6 lines
2005 M /trunk/samtools/samtools.1
2007 Added a note to the manual. Currently SAMtools used unaligned words in
2008 several places. Although this does not cause bus errors to me, it may
2009 affect portability. Please see the "Bus error" wiki page for more
2010 information. Also thank James Bonfields for pointing this out.
2013 ------------------------------------------------------------------------
2014 r286 | lh3lh3 | 2009-05-14 10:23:13 -0400 (Thu, 14 May 2009) | 3 lines
2016 M /trunk/samtools/bam.h
2017 M /trunk/samtools/bam_aux.c
2018 M /trunk/samtools/bamtk.c
2020 * samtools-0.1.3-21 (286)
2021 * declare bam_aux_get_core() in bam.h
2023 ------------------------------------------------------------------------
2024 r276 | lh3lh3 | 2009-05-13 05:07:55 -0400 (Wed, 13 May 2009) | 5 lines
2026 M /trunk/samtools/bam.h
2027 M /trunk/samtools/bam_index.c
2028 M /trunk/samtools/bamtk.c
2030 * samtools-0.1.3-20 (r276)
2031 * remove bam1_t::hash again. We need to modify the Perl API anyway to
2032 make it work with the latest SVN.
2033 * As is suggested by Tim, scan "{base}.bai" and "{base}.bam.bai" for index
2035 ------------------------------------------------------------------------
2036 r275 | lh3lh3 | 2009-05-12 16:14:10 -0400 (Tue, 12 May 2009) | 4 lines
2038 M /trunk/samtools/ChangeLog
2039 M /trunk/samtools/bam.h
2040 M /trunk/samtools/bamtk.c
2042 * samtools-0.1.3-19 (r275)
2043 * a minor change to the bam1_t struct: added back "void *hash" for the
2044 backward compatibility with Bio::DB::Sam
2046 ------------------------------------------------------------------------
2047 r273 | lh3lh3 | 2009-05-12 09:28:39 -0400 (Tue, 12 May 2009) | 3 lines
2049 M /trunk/samtools/bam_rmdupse.c
2050 M /trunk/samtools/bamtk.c
2052 * samtools-0.1.3-18 (r273)
2053 * rmdupse: do not remove unmapped reads
2055 ------------------------------------------------------------------------
2056 r272 | lh3lh3 | 2009-05-12 09:20:00 -0400 (Tue, 12 May 2009) | 2 lines
2058 M /trunk/samtools/bam_rmdupse.c
2060 change a parameter. It does nothing
2062 ------------------------------------------------------------------------
2063 r271 | lh3lh3 | 2009-05-12 09:17:58 -0400 (Tue, 12 May 2009) | 3 lines
2065 M /trunk/samtools/Makefile.am
2066 M /trunk/samtools/Makefile.generic
2067 M /trunk/samtools/Makefile.lite
2068 A /trunk/samtools/bam_rmdupse.c
2069 M /trunk/samtools/bamtk.c
2070 M /trunk/samtools/configure.ac
2072 * samtools-0.1.3-17 (r271)
2073 * added 'rmdupse' command
2075 ------------------------------------------------------------------------
2076 r267 | lh3lh3 | 2009-05-05 17:31:41 -0400 (Tue, 05 May 2009) | 3 lines
2078 M /trunk/samtools/bamtk.c
2079 M /trunk/samtools/sam_view.c
2081 * samtools-0.1.3-16 (r267)
2082 * in sam_view.c, changed g_flag_on based on the suggestion by Angie Hinrichs
2084 ------------------------------------------------------------------------
2085 r266 | lh3lh3 | 2009-05-05 17:23:27 -0400 (Tue, 05 May 2009) | 3 lines
2087 M /trunk/samtools/bam_import.c
2088 M /trunk/samtools/bamtk.c
2090 * samtools-0.1.3-15 (r266)
2091 * report an error if a non-* reference is present while @SQ is absent
2093 ------------------------------------------------------------------------
2094 r265 | lh3lh3 | 2009-05-05 17:09:00 -0400 (Tue, 05 May 2009) | 3 lines
2096 M /trunk/samtools/bam.h
2097 M /trunk/samtools/bam_import.c
2098 M /trunk/samtools/bamtk.c
2099 M /trunk/samtools/sam.c
2100 M /trunk/samtools/sam_view.c
2102 * samtools-0.1.3-14 (r262)
2103 * make samopen() recognize @SQ header lines
2105 ------------------------------------------------------------------------
2106 r261 | lh3lh3 | 2009-05-05 10:10:30 -0400 (Tue, 05 May 2009) | 3 lines
2108 M /trunk/samtools/bam_plcmd.c
2109 M /trunk/samtools/bamtk.c
2110 M /trunk/samtools/bgzf.c
2111 M /trunk/samtools/sam.c
2112 M /trunk/samtools/sam_view.c
2114 * samtools-0.1.3-13 (r260)
2115 * report error for file I/O error
2117 ------------------------------------------------------------------------
2118 r260 | lh3lh3 | 2009-05-05 10:01:16 -0400 (Tue, 05 May 2009) | 2 lines
2120 M /trunk/samtools/Makefile.am
2124 ------------------------------------------------------------------------
2125 r259 | lh3lh3 | 2009-05-05 09:52:25 -0400 (Tue, 05 May 2009) | 3 lines
2127 M /trunk/samtools/bam.h
2128 M /trunk/samtools/bam_pileup.c
2129 M /trunk/samtools/bam_plcmd.c
2130 M /trunk/samtools/bamtk.c
2131 M /trunk/samtools/sam.c
2132 M /trunk/samtools/sam.h
2134 * samtools-0.1.3-12 (r259)
2135 * use the new I/O interface in pileup
2137 ------------------------------------------------------------------------
2138 r258 | lh3lh3 | 2009-05-05 09:33:22 -0400 (Tue, 05 May 2009) | 3 lines
2140 M /trunk/samtools/Makefile.generic
2141 M /trunk/samtools/Makefile.lite
2142 M /trunk/samtools/bam.c
2143 M /trunk/samtools/bam.h
2144 M /trunk/samtools/bam_import.c
2145 M /trunk/samtools/bamtk.c
2146 A /trunk/samtools/sam.c
2147 A /trunk/samtools/sam.h
2148 A /trunk/samtools/sam_view.c
2150 * samtools-0.1.3-11 (r258)
2151 * unify the interface to BAM and SAM I/O
2153 ------------------------------------------------------------------------
2154 r257 | lh3lh3 | 2009-05-05 04:53:35 -0400 (Tue, 05 May 2009) | 3 lines
2156 M /trunk/samtools/Makefile.lite
2157 M /trunk/samtools/bam_plcmd.c
2158 M /trunk/samtools/bamtk.c
2160 * samtools-0.1.3-10 (r257)
2161 * allow hex with "pileup -m"
2163 ------------------------------------------------------------------------
2164 r256 | lh3lh3 | 2009-05-04 14:16:50 -0400 (Mon, 04 May 2009) | 4 lines
2166 M /trunk/samtools/bam_lpileup.c
2167 M /trunk/samtools/bamtk.c
2169 * samtools-0.1.3-9 (r256)
2170 * fixed a bug in bam_lpileup.c
2171 * I do not know if this also fixes the bug causing assertion failure in the tview
2173 ------------------------------------------------------------------------
2174 r251 | lh3lh3 | 2009-04-28 08:53:23 -0400 (Tue, 28 Apr 2009) | 3 lines
2176 M /trunk/samtools/bam_pileup.c
2177 M /trunk/samtools/bamtk.c
2179 * samtools-0.1.3-8 (r251)
2180 * fixed a bug when there are reads without coordinates
2182 ------------------------------------------------------------------------
2183 r250 | lh3lh3 | 2009-04-28 08:43:33 -0400 (Tue, 28 Apr 2009) | 2 lines
2185 A /trunk/samtools/AUTHORS
2186 A /trunk/samtools/README
2187 M /trunk/samtools/cleanup.sh
2191 ------------------------------------------------------------------------
2192 r249 | lh3lh3 | 2009-04-28 08:37:16 -0400 (Tue, 28 Apr 2009) | 2 lines
2194 M /trunk/samtools/Makefile.generic
2195 M /trunk/samtools/Makefile.lite
2196 M /trunk/samtools/configure.ac
2197 M /trunk/samtools/misc/Makefile.generic
2199 improve large file support in compilation
2201 ------------------------------------------------------------------------
2202 r248 | lh3lh3 | 2009-04-28 08:33:24 -0400 (Tue, 28 Apr 2009) | 2 lines
2204 M /trunk/samtools/INSTALL
2208 ------------------------------------------------------------------------
2209 r247 | lh3lh3 | 2009-04-28 08:28:50 -0400 (Tue, 28 Apr 2009) | 2 lines
2211 M /trunk/samtools/Makefile.am
2212 M /trunk/samtools/autogen.sh
2213 M /trunk/samtools/cleanup.sh
2214 M /trunk/samtools/configure.ac
2215 A /trunk/samtools/misc/Makefile.am
2217 fixed various issues about the GNU building scripts
2219 ------------------------------------------------------------------------
2220 r246 | lh3lh3 | 2009-04-28 08:10:23 -0400 (Tue, 28 Apr 2009) | 4 lines
2222 M /trunk/samtools/ChangeLog
2223 D /trunk/samtools/Makefile
2224 A /trunk/samtools/Makefile.am
2225 A /trunk/samtools/Makefile.generic
2226 A /trunk/samtools/autogen.sh
2227 M /trunk/samtools/bam.h
2228 M /trunk/samtools/bam_aux.c
2229 M /trunk/samtools/bam_tview.c
2230 M /trunk/samtools/bamtk.c
2231 A /trunk/samtools/cleanup.sh
2232 A /trunk/samtools/configure.ac
2233 D /trunk/samtools/misc/Makefile
2234 A /trunk/samtools/misc/Makefile.generic (from /trunk/samtools/misc/Makefile:245)
2236 * samtools-0.1.3-7 (r246)
2237 * incorporated revisions from Nils Homer
2238 * enhanced support of displaying color-space reads
2240 ------------------------------------------------------------------------
2241 r244 | lh3lh3 | 2009-04-25 06:49:40 -0400 (Sat, 25 Apr 2009) | 3 lines
2243 M /trunk/samtools/bam_md.c
2244 M /trunk/samtools/bamtk.c
2246 * samtools-0.1.3-6 (r244)
2247 * fixed segfault for unmapped reads
2249 ------------------------------------------------------------------------
2250 r243 | lh3lh3 | 2009-04-24 16:27:26 -0400 (Fri, 24 Apr 2009) | 5 lines
2252 M /trunk/samtools/bam.h
2253 M /trunk/samtools/bam_maqcns.c
2254 M /trunk/samtools/bam_md.c
2255 M /trunk/samtools/bamtk.c
2257 * samtools-0.1.3-5 (r243)
2258 * fixed a long existing bug which may cause memory leak
2260 * consensus calling now works with "=", but indel calling not
2262 ------------------------------------------------------------------------
2263 r242 | lh3lh3 | 2009-04-24 15:44:46 -0400 (Fri, 24 Apr 2009) | 3 lines
2265 M /trunk/samtools/bam_md.c
2266 M /trunk/samtools/bamtk.c
2268 * samtools-0.1.3-4 (r242)
2269 * fixed a memory leak
2271 ------------------------------------------------------------------------
2272 r240 | lh3lh3 | 2009-04-24 11:40:18 -0400 (Fri, 24 Apr 2009) | 5 lines
2274 M /trunk/samtools/Makefile
2275 M /trunk/samtools/Makefile.lite
2276 M /trunk/samtools/bam.h
2277 M /trunk/samtools/bam_aux.c
2278 A /trunk/samtools/bam_md.c
2279 M /trunk/samtools/bam_plcmd.c
2280 M /trunk/samtools/bamtk.c
2282 * samtools-0.1.3-3 (r240)
2284 * generate "=" bases
2285 * the plain pileup now support "=" bases, but consensus calling and glfgen may fail
2287 ------------------------------------------------------------------------
2288 r239 | lh3lh3 | 2009-04-24 07:08:20 -0400 (Fri, 24 Apr 2009) | 5 lines
2290 M /trunk/samtools/bam.h
2291 M /trunk/samtools/bam_aux.c
2292 M /trunk/samtools/bamtk.c
2294 * samtools-0.1.3-2 (r239)
2295 * fixed bugs in bam_aux.c (these functions nevered used by samtools)
2296 * removed bam_aux_init()/bam_aux_destroy()
2297 * added tagview for testing bam_aux
2299 ------------------------------------------------------------------------
2300 r235 | lh3lh3 | 2009-04-21 18:17:39 -0400 (Tue, 21 Apr 2009) | 3 lines
2302 M /trunk/samtools/bam_pileup.c
2303 M /trunk/samtools/bamtk.c
2306 * fixed a bug in pileup: the first read in a chromosome may not be printed
2308 ------------------------------------------------------------------------
2309 r232 | lh3lh3 | 2009-04-16 10:25:43 -0400 (Thu, 16 Apr 2009) | 2 lines
2311 M /trunk/samtools/Makefile.lite
2313 a missing file in Makefile.lite
2315 ------------------------------------------------------------------------
2316 r227 | lh3lh3 | 2009-04-15 17:02:53 -0400 (Wed, 15 Apr 2009) | 2 lines
2318 M /trunk/samtools/NEWS
2319 M /trunk/samtools/bamtk.c
2321 Release samtools-0.1.3
2323 ------------------------------------------------------------------------
2324 r223 | lh3lh3 | 2009-04-15 09:31:32 -0400 (Wed, 15 Apr 2009) | 3 lines
2326 M /trunk/samtools/bam_plcmd.c
2327 M /trunk/samtools/bamtk.c
2330 * make samtools more robust to weird input such as empty file
2332 ------------------------------------------------------------------------
2333 r222 | lh3lh3 | 2009-04-15 09:05:33 -0400 (Wed, 15 Apr 2009) | 2 lines
2335 M /trunk/samtools/ChangeLog
2336 M /trunk/samtools/NEWS
2337 M /trunk/samtools/samtools.1
2339 prepare for release 0.1.3
2341 ------------------------------------------------------------------------
2342 r221 | lh3lh3 | 2009-04-15 08:32:14 -0400 (Wed, 15 Apr 2009) | 2 lines
2344 A /trunk/samtools/misc/blast2sam.pl
2346 convert NCBI-BLASTN to SAM
2348 ------------------------------------------------------------------------
2349 r220 | lh3lh3 | 2009-04-15 08:18:19 -0400 (Wed, 15 Apr 2009) | 3 lines
2351 M /trunk/samtools/bam_lpileup.c
2352 M /trunk/samtools/bamtk.c
2355 * fixed a small memory leak in tview
2357 ------------------------------------------------------------------------
2358 r219 | lh3lh3 | 2009-04-15 08:00:08 -0400 (Wed, 15 Apr 2009) | 3 lines
2360 M /trunk/samtools/bam_rmdup.c
2361 M /trunk/samtools/bamtk.c
2364 * fixed a bug in rmdup when there are unmapped reads
2366 ------------------------------------------------------------------------
2367 r218 | lh3lh3 | 2009-04-14 17:28:58 -0400 (Tue, 14 Apr 2009) | 2 lines
2369 M /trunk/samtools/ChangeLog
2370 M /trunk/samtools/NEWS
2372 proposed NEWS for the new release (have not yet)
2374 ------------------------------------------------------------------------
2375 r216 | lh3lh3 | 2009-04-14 17:10:46 -0400 (Tue, 14 Apr 2009) | 4 lines
2377 M /trunk/samtools/misc/samtools.pl
2380 * improve indelFilter to avoid filtering true indels. The new filter relies
2381 on the new pileup indel line implemented in samtools-0.1.2-25
2383 ------------------------------------------------------------------------
2384 r215 | lh3lh3 | 2009-04-14 17:04:19 -0400 (Tue, 14 Apr 2009) | 4 lines
2386 M /trunk/samtools/bam_maqcns.c
2387 M /trunk/samtools/bam_plcmd.c
2388 M /trunk/samtools/bamtk.c
2389 M /trunk/samtools/samtools.1
2392 * change the pileup indel line to shows the number of alignments actually
2395 ------------------------------------------------------------------------
2396 r211 | lh3lh3 | 2009-04-13 07:07:13 -0400 (Mon, 13 Apr 2009) | 2 lines
2398 M /trunk/samtools/ChangeLog
2400 update ChangeLog from "svn log"
2402 ------------------------------------------------------------------------
2403 r210 | lh3lh3 | 2009-04-12 15:57:05 -0400 (Sun, 12 Apr 2009) | 4 lines
2405 M /trunk/samtools/bam.c
2406 M /trunk/samtools/bam_import.c
2407 M /trunk/samtools/bam_sort.c
2408 M /trunk/samtools/bamtk.c
2409 M /trunk/samtools/kseq.h
2412 * in merge, gives a warning rather than error if the target sequence length is different
2413 * allow empty header
2415 ------------------------------------------------------------------------
2416 r209 | lh3lh3 | 2009-04-12 15:32:44 -0400 (Sun, 12 Apr 2009) | 3 lines
2418 M /trunk/samtools/bam.c
2419 M /trunk/samtools/bam_import.c
2420 M /trunk/samtools/bamtk.c
2423 * recognize '*' at the QUAL field
2425 ------------------------------------------------------------------------
2426 r208 | lh3lh3 | 2009-04-12 15:08:02 -0400 (Sun, 12 Apr 2009) | 3 lines
2428 M /trunk/samtools/bam_import.c
2429 M /trunk/samtools/bamtk.c
2430 M /trunk/samtools/kseq.h
2433 * the field separater is TAB only, now
2435 ------------------------------------------------------------------------
2436 r207 | lh3lh3 | 2009-04-08 10:18:03 -0400 (Wed, 08 Apr 2009) | 2 lines
2438 M /trunk/samtools/examples/ex1.sam.gz
2440 * fixed the problem in the example alignment due to the bug in fixmate
2442 ------------------------------------------------------------------------
2443 r206 | lh3lh3 | 2009-04-08 10:15:05 -0400 (Wed, 08 Apr 2009) | 3 lines
2445 M /trunk/samtools/bam_mate.c
2446 M /trunk/samtools/bamtk.c
2447 M /trunk/samtools/misc/soap2sam.pl
2450 * fixed a nasty bug in `fixmate'
2452 ------------------------------------------------------------------------
2453 r205 | lh3lh3 | 2009-04-08 05:57:08 -0400 (Wed, 08 Apr 2009) | 2 lines
2455 M /trunk/samtools/misc/bowtie2sam.pl
2456 M /trunk/samtools/misc/soap2sam.pl
2457 M /trunk/samtools/misc/wgsim_eval.pl
2459 make the script robust to the bugs in SOAP-2.1.7
2461 ------------------------------------------------------------------------
2462 r200 | lh3lh3 | 2009-04-02 10:14:56 -0400 (Thu, 02 Apr 2009) | 3 lines
2464 M /trunk/samtools/bam_stat.c
2465 M /trunk/samtools/bamtk.c
2468 * check if file is truncated in flagstat
2470 ------------------------------------------------------------------------
2471 r199 | lh3lh3 | 2009-04-02 10:09:10 -0400 (Thu, 02 Apr 2009) | 3 lines
2473 M /trunk/samtools/bamtk.c
2476 * print the header if requested
2478 ------------------------------------------------------------------------
2479 r193 | lh3lh3 | 2009-03-27 11:09:50 -0400 (Fri, 27 Mar 2009) | 3 lines
2481 M /trunk/samtools/bam_plcmd.c
2482 M /trunk/samtools/bamtk.c
2485 * fixed a minor bug reported by Nils Homer
2487 ------------------------------------------------------------------------
2488 r185 | lh3lh3 | 2009-03-24 07:50:32 -0400 (Tue, 24 Mar 2009) | 2 lines
2490 A /trunk/samtools/Makefile (from /trunk/samtools/Makefile.std:184)
2491 D /trunk/samtools/Makefile.std
2492 A /trunk/samtools/misc/Makefile (from /trunk/samtools/misc/Makefile.std:184)
2493 D /trunk/samtools/misc/Makefile.std
2495 rename Makefile.std as Makefile. GNU building systerm is not ready and may take some time...
2497 ------------------------------------------------------------------------
2498 r184 | lh3lh3 | 2009-03-24 06:36:38 -0400 (Tue, 24 Mar 2009) | 4 lines
2500 D /trunk/samtools/Makefile
2501 A /trunk/samtools/Makefile.std (from /trunk/samtools/Makefile:183)
2502 M /trunk/samtools/bam_sort.c
2503 M /trunk/samtools/bam_tview.c
2504 M /trunk/samtools/bamtk.c
2505 D /trunk/samtools/misc/Makefile
2506 A /trunk/samtools/misc/Makefile.std (from /trunk/samtools/misc/Makefile:182)
2507 M /trunk/samtools/samtools.1
2510 * incorporating Nils' changes
2511 * rename Makefile to Makefile.std and prepare to add the GNU building systerms (also by Nils)
2513 ------------------------------------------------------------------------
2514 r183 | lh3lh3 | 2009-03-24 06:30:23 -0400 (Tue, 24 Mar 2009) | 4 lines
2516 M /trunk/samtools/Makefile
2517 M /trunk/samtools/bam_import.c
2518 M /trunk/samtools/bam_maqcns.c
2519 M /trunk/samtools/bam_maqcns.h
2520 M /trunk/samtools/bam_plcmd.c
2521 M /trunk/samtools/bamtk.c
2522 M /trunk/samtools/kseq.h
2523 A /trunk/samtools/kstring.c
2524 A /trunk/samtools/kstring.h
2527 * made pileup take a list of proposed indels. An insertion is N at the moment.
2528 * added my kstring library for a bit complex parsing of the position list.
2530 ------------------------------------------------------------------------
2531 r169 | lh3lh3 | 2009-03-12 09:40:14 -0400 (Thu, 12 Mar 2009) | 3 lines
2533 M /trunk/samtools/misc/soap2sam.pl
2536 * more robust to truncated soap output
2538 ------------------------------------------------------------------------
2539 r168 | lh3lh3 | 2009-03-11 06:49:00 -0400 (Wed, 11 Mar 2009) | 2 lines
2541 M /trunk/samtools/Makefile.lite
2543 added bam_stat.o to Makefile.lite
2545 ------------------------------------------------------------------------
2546 r167 | lh3lh3 | 2009-03-10 18:11:31 -0400 (Tue, 10 Mar 2009) | 3 lines
2548 M /trunk/samtools/bam_maqcns.c
2549 M /trunk/samtools/bamtk.c
2552 * generate RMS of mapQ instead of max mapQ
2554 ------------------------------------------------------------------------
2555 r166 | lh3lh3 | 2009-03-10 18:06:45 -0400 (Tue, 10 Mar 2009) | 3 lines
2557 M /trunk/samtools/bam_plcmd.c
2558 M /trunk/samtools/bamtk.c
2559 M /trunk/samtools/glf.c
2560 M /trunk/samtools/glf.h
2561 M /trunk/samtools/misc/Makefile
2566 ------------------------------------------------------------------------
2567 r159 | lh3lh3 | 2009-03-03 06:26:08 -0500 (Tue, 03 Mar 2009) | 3 lines
2569 M /trunk/samtools/bam_plcmd.c
2570 M /trunk/samtools/bamtk.c
2573 * fixed a minor bug in displaying pileup
2575 ------------------------------------------------------------------------
2576 r158 | lh3lh3 | 2009-03-03 06:24:16 -0500 (Tue, 03 Mar 2009) | 3 lines
2578 M /trunk/samtools/ChangeLog
2579 M /trunk/samtools/bamtk.c
2582 * optionally print SAM header
2584 ------------------------------------------------------------------------
2585 r153 | lh3lh3 | 2009-03-02 05:45:28 -0500 (Mon, 02 Mar 2009) | 3 lines
2587 M /trunk/samtools/bamtk.c
2588 M /trunk/samtools/glf.c
2591 * use "GLF\3" as the magic for GLFv3 files
2593 ------------------------------------------------------------------------
2594 r152 | lh3lh3 | 2009-03-02 05:39:09 -0500 (Mon, 02 Mar 2009) | 5 lines
2596 M /trunk/samtools/Makefile
2597 M /trunk/samtools/bam_import.c
2598 M /trunk/samtools/bam_index.c
2599 M /trunk/samtools/bam_plcmd.c
2600 M /trunk/samtools/bamtk.c
2601 M /trunk/samtools/glf.c
2602 M /trunk/samtools/glf.h
2605 * fixed a bug in import: core.bin is undefined for unmapped reads
2606 * this bug can be alleviated (not completely solved) in bam_index.c
2607 * update to GLFv3: pos is changed to offset for better compression
2609 ------------------------------------------------------------------------
2610 r151 | lh3lh3 | 2009-03-01 10:18:43 -0500 (Sun, 01 Mar 2009) | 3 lines
2612 M /trunk/samtools/misc/wgsim.c
2615 * fixed a bug in simulating indels
2617 ------------------------------------------------------------------------
2618 r145 | lh3lh3 | 2009-02-26 14:43:57 -0500 (Thu, 26 Feb 2009) | 4 lines
2620 M /trunk/samtools/misc/wgsim.c
2623 * allow to print mismatch information as fastq comment. MAQ does
2624 not like long read names.
2626 ------------------------------------------------------------------------
2627 r141 | lh3lh3 | 2009-02-26 09:53:03 -0500 (Thu, 26 Feb 2009) | 6 lines
2629 M /trunk/samtools/ChangeLog
2630 M /trunk/samtools/misc/wgsim.c
2631 M /trunk/samtools/misc/wgsim_eval.pl
2634 * fixed a bug about color read coordinates
2635 * fixed a bug in read names
2636 * wgsim_eval.pl-0.1.3
2637 * make the script work with color reads
2639 ------------------------------------------------------------------------
2640 r140 | lh3lh3 | 2009-02-26 09:02:57 -0500 (Thu, 26 Feb 2009) | 2 lines
2642 M /trunk/samtools/misc/Makefile
2643 M /trunk/samtools/misc/wgsim.c
2645 * wgsim: added a note
2647 ------------------------------------------------------------------------
2648 r139 | lh3lh3 | 2009-02-26 06:39:08 -0500 (Thu, 26 Feb 2009) | 7 lines
2650 M /trunk/samtools/misc/wgsim.c
2651 M /trunk/samtools/misc/wgsim_eval.pl
2654 * considerable code clean up
2655 * print number of substitutions/indels/errors on each read
2656 * potentially support SOLiD simulation, though not tested at the moment
2657 * wgsim_eval.pl-0.1.2
2658 * change in accordant with wgsim
2660 ------------------------------------------------------------------------
2661 r129 | lh3lh3 | 2009-02-18 17:23:27 -0500 (Wed, 18 Feb 2009) | 3 lines
2663 M /trunk/samtools/bam_index.c
2664 M /trunk/samtools/bamtk.c
2667 * fixed a bug in bam_fetch, caused by completely contained adjacent chunks
2669 ------------------------------------------------------------------------
2670 r128 | bhandsaker | 2009-02-18 14:06:57 -0500 (Wed, 18 Feb 2009) | 2 lines
2672 M /trunk/samtools/bamtk.c
2674 Fix annoying segv when invalid region specified.
2676 ------------------------------------------------------------------------
2677 r127 | lh3lh3 | 2009-02-17 05:49:55 -0500 (Tue, 17 Feb 2009) | 2 lines
2679 D /trunk/samtools/misc/indel_filter.pl
2680 A /trunk/samtools/misc/samtools.pl
2682 * move indel_filter.pl to samtools.pl
2684 ------------------------------------------------------------------------
2685 r126 | lh3lh3 | 2009-02-14 16:22:30 -0500 (Sat, 14 Feb 2009) | 3 lines
2687 M /trunk/samtools/bam_mate.c
2688 M /trunk/samtools/bamtk.c
2691 * fixed a bug in fixmate: SE reads are flagged as BAM_FMUNMAP
2693 ------------------------------------------------------------------------
2694 r125 | lh3lh3 | 2009-02-13 04:54:45 -0500 (Fri, 13 Feb 2009) | 3 lines
2696 M /trunk/samtools/bam_stat.c
2697 M /trunk/samtools/bamtk.c
2700 * fixed a minor bug in flagstat
2702 ------------------------------------------------------------------------
2703 r124 | lh3lh3 | 2009-02-12 06:15:32 -0500 (Thu, 12 Feb 2009) | 3 lines
2705 M /trunk/samtools/bam_maqcns.c
2706 M /trunk/samtools/bamtk.c
2707 M /trunk/samtools/misc/indel_filter.pl
2710 * improve indel caller by setting maximum window size
2712 ------------------------------------------------------------------------
2713 r123 | lh3lh3 | 2009-02-12 05:30:29 -0500 (Thu, 12 Feb 2009) | 2 lines
2715 M /trunk/samtools/bam_plcmd.c
2716 M /trunk/samtools/bamtk.c
2718 * output max mapping quality in indel line
2720 ------------------------------------------------------------------------
2721 r122 | lh3lh3 | 2009-02-11 05:59:10 -0500 (Wed, 11 Feb 2009) | 2 lines
2723 M /trunk/samtools/misc/maq2sam.c
2725 fixed a bug in generating tag AM
2727 ------------------------------------------------------------------------
2728 r121 | lh3lh3 | 2009-02-03 05:43:11 -0500 (Tue, 03 Feb 2009) | 2 lines
2730 M /trunk/samtools/bam_index.c
2731 M /trunk/samtools/bamtk.c
2733 fixed a potential memory problem in indexing
2735 ------------------------------------------------------------------------
2736 r120 | bhandsaker | 2009-02-02 10:52:52 -0500 (Mon, 02 Feb 2009) | 2 lines
2738 M /trunk/samtools/Makefile
2740 Pass LIBS to recursive targets to facilitate building at Broad.
2742 ------------------------------------------------------------------------
2743 r119 | lh3lh3 | 2009-02-02 05:12:15 -0500 (Mon, 02 Feb 2009) | 4 lines
2745 M /trunk/samtools/ChangeLog
2746 M /trunk/samtools/bam_plcmd.c
2747 M /trunk/samtools/bam_stat.c
2748 M /trunk/samtools/bamtk.c
2751 * fixed a bug in generating GLFv2 for indels
2752 * improve flagstat report a little bit
2754 ------------------------------------------------------------------------
2755 r118 | lh3lh3 | 2009-01-29 07:33:23 -0500 (Thu, 29 Jan 2009) | 3 lines
2757 M /trunk/samtools/Makefile
2758 A /trunk/samtools/bam_stat.c
2759 M /trunk/samtools/bamtk.c
2762 * added flagstat command
2764 ------------------------------------------------------------------------
2765 r116 | lh3lh3 | 2009-01-28 08:31:12 -0500 (Wed, 28 Jan 2009) | 2 lines
2767 M /trunk/samtools/ChangeLog
2768 M /trunk/samtools/NEWS
2769 M /trunk/samtools/bamtk.c
2770 M /trunk/samtools/samtools.1
2772 Release SAMtools-0.1.2
2774 ------------------------------------------------------------------------
2775 r115 | lh3lh3 | 2009-01-28 07:54:08 -0500 (Wed, 28 Jan 2009) | 2 lines
2777 A /trunk/samtools/misc/indel_filter.pl
2779 Script for filtering indel results
2781 ------------------------------------------------------------------------
2782 r114 | lh3lh3 | 2009-01-25 06:45:37 -0500 (Sun, 25 Jan 2009) | 2 lines
2784 A /trunk/samtools/misc/zoom2sam.pl
2788 ------------------------------------------------------------------------
2789 r113 | lh3lh3 | 2009-01-24 09:25:07 -0500 (Sat, 24 Jan 2009) | 2 lines
2791 A /trunk/samtools/misc/novo2sam.pl
2793 add a script to convert novo alignment to SAM
2795 ------------------------------------------------------------------------
2796 r112 | lh3lh3 | 2009-01-23 15:57:39 -0500 (Fri, 23 Jan 2009) | 2 lines
2798 M /trunk/samtools/ChangeLog
2799 M /trunk/samtools/ChangeLog.old
2800 M /trunk/samtools/samtools.1
2802 update documentation and ChangeLog
2804 ------------------------------------------------------------------------
2805 r111 | lh3lh3 | 2009-01-23 14:22:59 -0500 (Fri, 23 Jan 2009) | 3 lines
2807 M /trunk/samtools/bam_sort.c
2808 M /trunk/samtools/bamtk.c
2811 * fixed a bug in "merge" command line
2813 ------------------------------------------------------------------------
2814 r110 | lh3lh3 | 2009-01-22 10:36:48 -0500 (Thu, 22 Jan 2009) | 3 lines
2816 M /trunk/samtools/misc/Makefile
2817 A /trunk/samtools/misc/bowtie2sam.pl (from /branches/dev/samtools/misc/bowtie2sam.pl:108)
2818 M /trunk/samtools/misc/export2sam.pl
2819 A /trunk/samtools/misc/soap2sam.pl (from /branches/dev/samtools/misc/soap2sam.pl:108)
2820 A /trunk/samtools/misc/wgsim.c (from /branches/dev/samtools/misc/wgsim.c:108)
2821 A /trunk/samtools/misc/wgsim_eval.pl (from /branches/dev/samtools/misc/wgsim_eval.pl:108)
2823 * merge from branches/dev/
2824 * all future development will happen here
2826 ------------------------------------------------------------------------
2827 r109 | lh3lh3 | 2009-01-22 10:14:27 -0500 (Thu, 22 Jan 2009) | 3 lines
2829 M /trunk/samtools/COPYING
2830 M /trunk/samtools/ChangeLog
2831 A /trunk/samtools/INSTALL (from /branches/dev/samtools/INSTALL:108)
2832 M /trunk/samtools/Makefile
2833 A /trunk/samtools/Makefile.lite (from /branches/dev/samtools/Makefile.lite:108)
2834 M /trunk/samtools/bam.c
2835 M /trunk/samtools/bam.h
2836 M /trunk/samtools/bam_import.c
2837 M /trunk/samtools/bam_index.c
2838 M /trunk/samtools/bam_lpileup.c
2839 M /trunk/samtools/bam_maqcns.c
2840 M /trunk/samtools/bam_maqcns.h
2841 A /trunk/samtools/bam_mate.c (from /branches/dev/samtools/bam_mate.c:108)
2842 M /trunk/samtools/bam_pileup.c
2843 M /trunk/samtools/bam_plcmd.c
2844 A /trunk/samtools/bam_rmdup.c (from /branches/dev/samtools/bam_rmdup.c:108)
2845 M /trunk/samtools/bam_sort.c
2846 M /trunk/samtools/bamtk.c
2847 M /trunk/samtools/bgzf.h
2848 M /trunk/samtools/examples/00README.txt
2849 A /trunk/samtools/examples/Makefile (from /branches/dev/samtools/examples/Makefile:108)
2850 D /trunk/samtools/examples/ex1.fa.fai
2851 M /trunk/samtools/examples/ex1.sam.gz
2852 M /trunk/samtools/faidx.c
2853 A /trunk/samtools/glf.c (from /branches/dev/samtools/glf.c:108)
2854 M /trunk/samtools/glf.h
2855 M /trunk/samtools/misc/Makefile
2856 M /trunk/samtools/misc/maq2sam.c
2857 M /trunk/samtools/razf.c
2858 M /trunk/samtools/source.dot
2860 * Merge from branches/dev/
2861 * all future development will happen here at trunk/
2863 ------------------------------------------------------------------------
2864 r79 | bhandsaker | 2009-01-07 16:42:15 -0500 (Wed, 07 Jan 2009) | 2 lines
2866 M /trunk/samtools/bam_maqcns.c
2867 M /trunk/samtools/bam_tview.c
2869 Fix problem with compiling without curses.
2871 ------------------------------------------------------------------------
2872 r63 | lh3lh3 | 2008-12-22 10:58:02 -0500 (Mon, 22 Dec 2008) | 2 lines
2874 A /trunk/samtools (from /branches/dev/samtools:62)
2878 ------------------------------------------------------------------------
2879 r62 | lh3lh3 | 2008-12-22 10:55:13 -0500 (Mon, 22 Dec 2008) | 2 lines
2881 A /branches/dev/samtools/NEWS
2882 M /branches/dev/samtools/bamtk.c
2883 M /branches/dev/samtools/samtools.1
2885 Release samtools-0.1.1
2887 ------------------------------------------------------------------------
2888 r61 | lh3lh3 | 2008-12-22 10:46:08 -0500 (Mon, 22 Dec 2008) | 10 lines
2890 M /branches/dev/samtools/bam_aux.c
2891 M /branches/dev/samtools/bam_index.c
2892 M /branches/dev/samtools/bam_plcmd.c
2893 M /branches/dev/samtools/bam_tview.c
2894 M /branches/dev/samtools/bamtk.c
2895 M /branches/dev/samtools/razf.c
2896 M /branches/dev/samtools/samtools.1
2899 * fixed a bug in razf.c: reset z_eof when razf_seek() is called
2900 * fixed a memory leak in parsing a region
2901 * changed pileup a little bit when -s is in use: output ^ and $
2902 * when a bam is not indexed, output more meaningful error message
2903 * fixed a bug in indexing for small alignment
2904 * fixed a bug in the viewer when we come to the end of a reference file
2905 * updated documentation
2906 * prepare to release 0.1.1
2908 ------------------------------------------------------------------------
2909 r60 | lh3lh3 | 2008-12-22 10:10:16 -0500 (Mon, 22 Dec 2008) | 2 lines
2911 A /branches/dev/samtools/examples
2912 A /branches/dev/samtools/examples/00README.txt
2913 A /branches/dev/samtools/examples/ex1.fa
2914 A /branches/dev/samtools/examples/ex1.fa.fai
2915 A /branches/dev/samtools/examples/ex1.sam.gz
2919 ------------------------------------------------------------------------
2920 r59 | lh3lh3 | 2008-12-22 04:38:15 -0500 (Mon, 22 Dec 2008) | 2 lines
2922 M /branches/dev/samtools/ChangeLog
2926 ------------------------------------------------------------------------
2927 r58 | lh3lh3 | 2008-12-20 18:06:00 -0500 (Sat, 20 Dec 2008) | 3 lines
2929 M /branches/dev/samtools/misc/export2sam.pl
2932 * fixed several bugs
2934 ------------------------------------------------------------------------
2935 r57 | lh3lh3 | 2008-12-20 10:44:20 -0500 (Sat, 20 Dec 2008) | 2 lines
2937 A /branches/dev/samtools/misc/export2sam.pl
2939 convert Export format to SAM; not thoroughly tested
2941 ------------------------------------------------------------------------
2942 r56 | lh3lh3 | 2008-12-19 17:13:28 -0500 (Fri, 19 Dec 2008) | 6 lines
2944 M /branches/dev/samtools/bam_import.c
2945 M /branches/dev/samtools/bam_plcmd.c
2946 M /branches/dev/samtools/bam_tview.c
2947 M /branches/dev/samtools/bamtk.c
2948 A /branches/dev/samtools/source.dot
2951 * pileup: generate maq-like simple output
2952 * pileup: allow to output pileup at required sites
2953 * source.dot: source file relationship graph
2954 * tview: fixed a minor bug
2956 ------------------------------------------------------------------------
2957 r55 | lh3lh3 | 2008-12-19 15:10:26 -0500 (Fri, 19 Dec 2008) | 2 lines
2959 D /branches/dev/samtools/misc/all2sam.pl
2963 ------------------------------------------------------------------------
2964 r54 | lh3lh3 | 2008-12-16 17:34:25 -0500 (Tue, 16 Dec 2008) | 2 lines
2966 A /branches/dev/samtools/COPYING
2967 M /branches/dev/samtools/bam.h
2968 M /branches/dev/samtools/faidx.h
2969 M /branches/dev/samtools/khash.h
2970 M /branches/dev/samtools/kseq.h
2971 M /branches/dev/samtools/ksort.h
2972 M /branches/dev/samtools/samtools.1
2974 Added copyright information and a bit more documentation. No code change.
2976 ------------------------------------------------------------------------
2977 r53 | lh3lh3 | 2008-12-16 08:40:18 -0500 (Tue, 16 Dec 2008) | 3 lines
2979 M /branches/dev/samtools/bam.c
2980 M /branches/dev/samtools/bam.h
2981 M /branches/dev/samtools/bam_index.c
2982 M /branches/dev/samtools/bam_maqcns.c
2983 M /branches/dev/samtools/bamtk.c
2986 * improved efficiency of the indel caller for spliced alignments
2988 ------------------------------------------------------------------------
2989 r52 | lh3lh3 | 2008-12-16 05:28:20 -0500 (Tue, 16 Dec 2008) | 3 lines
2991 M /branches/dev/samtools/bam.c
2992 M /branches/dev/samtools/bam.h
2993 M /branches/dev/samtools/bam_aux.c
2994 M /branches/dev/samtools/bam_index.c
2995 M /branches/dev/samtools/bamtk.c
2998 * a bit code cleanup: reduce the dependency between source files
3000 ------------------------------------------------------------------------
3001 r51 | lh3lh3 | 2008-12-15 09:29:32 -0500 (Mon, 15 Dec 2008) | 3 lines
3003 M /branches/dev/samtools/bam_maqcns.c
3004 M /branches/dev/samtools/bam_plcmd.c
3005 M /branches/dev/samtools/bamtk.c
3008 * fixed a memory leak
3010 ------------------------------------------------------------------------
3011 r50 | lh3lh3 | 2008-12-15 09:00:13 -0500 (Mon, 15 Dec 2008) | 2 lines
3013 M /branches/dev/samtools/ChangeLog
3014 M /branches/dev/samtools/bam.h
3015 M /branches/dev/samtools/samtools.1
3017 update documentation, ChangeLog and a comment
3019 ------------------------------------------------------------------------
3020 r49 | lh3lh3 | 2008-12-15 08:36:43 -0500 (Mon, 15 Dec 2008) | 6 lines
3022 M /branches/dev/samtools/Makefile
3023 M /branches/dev/samtools/bam.h
3024 M /branches/dev/samtools/bam_maqcns.c
3025 M /branches/dev/samtools/bam_maqcns.h
3026 M /branches/dev/samtools/bam_pileup.c
3027 A /branches/dev/samtools/bam_plcmd.c
3028 M /branches/dev/samtools/bamtk.c
3029 M /branches/dev/samtools/samtools.1
3032 * moved pileup command to a separate source file
3033 * added indel caller
3034 * added bam_cal_segend(). (NOT WORKING for spliced alignment!!!)
3035 * updated documentation
3037 ------------------------------------------------------------------------
3038 r48 | lh3lh3 | 2008-12-12 08:55:36 -0500 (Fri, 12 Dec 2008) | 3 lines
3040 M /branches/dev/samtools/bam_maqcns.c
3041 M /branches/dev/samtools/bamtk.c
3044 * fixed another bug in maqcns when there is a nearby deletion
3046 ------------------------------------------------------------------------
3047 r47 | lh3lh3 | 2008-12-12 08:42:16 -0500 (Fri, 12 Dec 2008) | 5 lines
3049 M /branches/dev/samtools/bam_maqcns.c
3050 M /branches/dev/samtools/bam_pileup.c
3051 M /branches/dev/samtools/bamtk.c
3054 * pileup: outputing consensus is now optional
3055 * fixed a bug in glfgen. This bug also exists in maq's glfgen. However,
3056 I am not quite sure why the previous version may have problem.
3058 ------------------------------------------------------------------------
3059 r46 | lh3lh3 | 2008-12-12 06:44:56 -0500 (Fri, 12 Dec 2008) | 6 lines
3061 M /branches/dev/samtools/bam_pileup.c
3062 M /branches/dev/samtools/bamtk.c
3065 * add maq consensus to pileup. However, I will move this part to a new
3066 command as strictly speaking, consensus callin is not part of pileup,
3067 and imposing it would make it harder to generate for other language
3070 ------------------------------------------------------------------------
3071 r45 | bhandsaker | 2008-12-11 15:43:56 -0500 (Thu, 11 Dec 2008) | 2 lines
3073 M /branches/dev/samtools/bgzf.c
3075 Fix bug in tell() after reads that consume to the exact end of a block.
3077 ------------------------------------------------------------------------
3078 r44 | lh3lh3 | 2008-12-11 04:36:53 -0500 (Thu, 11 Dec 2008) | 2 lines
3080 M /branches/dev/samtools/samtools.1
3084 ------------------------------------------------------------------------
3085 r43 | lh3lh3 | 2008-12-11 04:25:36 -0500 (Thu, 11 Dec 2008) | 4 lines
3087 M /branches/dev/samtools/bam_import.c
3088 M /branches/dev/samtools/bamtk.c
3091 * fixed a bug in parser when there is auxiliary fields
3092 * made the parser a bit more robust
3094 ------------------------------------------------------------------------
3095 r42 | lh3lh3 | 2008-12-10 09:57:29 -0500 (Wed, 10 Dec 2008) | 5 lines
3097 M /branches/dev/samtools/bam_index.c
3098 M /branches/dev/samtools/bamtk.c
3099 M /branches/dev/samtools/bgzf.c
3102 * fixed a bug in bgzf (only reading is affected)
3103 * fixed a typo in bam_index.c
3104 * in bam_index.c, check potential bugs in the underlying I/O library
3106 ------------------------------------------------------------------------
3107 r41 | lh3lh3 | 2008-12-10 07:53:08 -0500 (Wed, 10 Dec 2008) | 2 lines
3109 M /branches/dev/samtools/samtools.1
3113 ------------------------------------------------------------------------
3114 r40 | lh3lh3 | 2008-12-10 06:52:10 -0500 (Wed, 10 Dec 2008) | 5 lines
3116 M /branches/dev/samtools/bam.h
3117 M /branches/dev/samtools/bam_pileup.c
3118 M /branches/dev/samtools/bamtk.c
3121 * tried to make pileup work with clipping (previously not), though NOT tested
3122 * removed -v from pileup
3123 * made pileup take the reference sequence
3125 ------------------------------------------------------------------------
3126 r39 | lh3lh3 | 2008-12-09 06:59:28 -0500 (Tue, 09 Dec 2008) | 4 lines
3128 M /branches/dev/samtools/bam_import.c
3129 M /branches/dev/samtools/bamtk.c
3130 M /branches/dev/samtools/samtools.1
3133 * in parser, recognize "=", rather than ",", as a match
3134 * in parser, correctl parse "=" at the MRNM field.
3136 ------------------------------------------------------------------------
3137 r38 | lh3lh3 | 2008-12-09 06:39:07 -0500 (Tue, 09 Dec 2008) | 2 lines
3139 M /branches/dev/samtools/misc/maq2sam.c
3141 fixed a bug in handling maq flag 64 and 192
3143 ------------------------------------------------------------------------
3144 r37 | lh3lh3 | 2008-12-09 04:53:46 -0500 (Tue, 09 Dec 2008) | 2 lines
3146 M /branches/dev/samtools/misc/md5fa.c
3148 also calculate unordered md5sum check
3150 ------------------------------------------------------------------------
3151 r36 | lh3lh3 | 2008-12-09 04:46:21 -0500 (Tue, 09 Dec 2008) | 2 lines
3153 M /branches/dev/samtools/misc/md5fa.c
3155 fixed a minor bug when there are space in the sequence
3157 ------------------------------------------------------------------------
3158 r35 | lh3lh3 | 2008-12-09 04:40:45 -0500 (Tue, 09 Dec 2008) | 2 lines
3160 M /branches/dev/samtools/misc/md5fa.c
3162 fixed a potential memory leak
3164 ------------------------------------------------------------------------
3165 r34 | lh3lh3 | 2008-12-08 09:52:17 -0500 (Mon, 08 Dec 2008) | 2 lines
3167 M /branches/dev/samtools/bam_import.c
3168 M /branches/dev/samtools/bam_index.c
3169 M /branches/dev/samtools/bamtk.c
3171 * fixed a bug in import: bin is wrongly calculated
3173 ------------------------------------------------------------------------
3174 r33 | lh3lh3 | 2008-12-08 09:08:01 -0500 (Mon, 08 Dec 2008) | 2 lines
3176 M /branches/dev/samtools/misc/all2sam.pl
3180 ------------------------------------------------------------------------
3181 r32 | lh3lh3 | 2008-12-08 07:56:02 -0500 (Mon, 08 Dec 2008) | 3 lines
3183 M /branches/dev/samtools/Makefile
3184 M /branches/dev/samtools/kseq.h
3185 M /branches/dev/samtools/misc/Makefile
3186 A /branches/dev/samtools/misc/md5.c
3187 A /branches/dev/samtools/misc/md5.h
3188 A /branches/dev/samtools/misc/md5fa.c
3190 * fixed two warnings in kseq.h
3191 * added md5sum utilities
3193 ------------------------------------------------------------------------
3194 r31 | lh3lh3 | 2008-12-08 06:35:29 -0500 (Mon, 08 Dec 2008) | 5 lines
3196 M /branches/dev/samtools/Makefile
3197 M /branches/dev/samtools/bam_import.c
3198 M /branches/dev/samtools/bamtk.c
3199 A /branches/dev/samtools/kseq.h
3200 D /branches/dev/samtools/kstream.h
3203 * replace kstream with kseq. kseq is a superset of kstream. I need the
3204 extra functions in kseq.h.
3205 * also compile stand-alone faidx
3207 ------------------------------------------------------------------------
3208 r30 | lh3lh3 | 2008-12-08 06:17:04 -0500 (Mon, 08 Dec 2008) | 3 lines
3210 M /branches/dev/samtools/bam.h
3211 M /branches/dev/samtools/bam_sort.c
3212 M /branches/dev/samtools/bamtk.c
3215 * sorting by read names is available
3217 ------------------------------------------------------------------------
3218 r29 | lh3lh3 | 2008-12-08 05:29:02 -0500 (Mon, 08 Dec 2008) | 3 lines
3220 M /branches/dev/samtools/bam.c
3221 M /branches/dev/samtools/bam.h
3222 M /branches/dev/samtools/bam_import.c
3223 M /branches/dev/samtools/bam_maqcns.c
3224 M /branches/dev/samtools/bam_pileup.c
3225 M /branches/dev/samtools/bam_sort.c
3226 M /branches/dev/samtools/bam_tview.c
3227 M /branches/dev/samtools/bamtk.c
3228 M /branches/dev/samtools/misc/maq2sam.c
3231 * format change to meet the latest specification
3233 ------------------------------------------------------------------------
3234 r28 | lh3lh3 | 2008-12-04 11:09:21 -0500 (Thu, 04 Dec 2008) | 3 lines
3236 M /branches/dev/samtools/bam_maqcns.c
3237 M /branches/dev/samtools/misc/maq2sam.c
3239 * minor change in maqcns: special care when n==0
3240 * change maq2sam to meet the latest specification
3242 ------------------------------------------------------------------------
3243 r27 | lh3lh3 | 2008-12-04 10:55:44 -0500 (Thu, 04 Dec 2008) | 2 lines
3245 M /branches/dev/samtools/razf.c
3246 M /branches/dev/samtools/razf.h
3248 considerable code clean up in razf
3250 ------------------------------------------------------------------------
3251 r26 | lh3lh3 | 2008-12-04 10:08:18 -0500 (Thu, 04 Dec 2008) | 2 lines
3253 M /branches/dev/samtools/ChangeLog
3254 M /branches/dev/samtools/Makefile
3255 M /branches/dev/samtools/faidx.c
3257 make RAZF optional in faidx.c
3259 ------------------------------------------------------------------------
3260 r25 | lh3lh3 | 2008-12-01 10:27:22 -0500 (Mon, 01 Dec 2008) | 3 lines
3262 M /branches/dev/samtools/Makefile
3263 M /branches/dev/samtools/bam.h
3264 M /branches/dev/samtools/bam_aux.c
3265 M /branches/dev/samtools/bamtk.c
3266 M /branches/dev/samtools/samtools.1
3269 * added routines for retrieving aux data, NOT TESTED YET!
3271 ------------------------------------------------------------------------
3272 r24 | lh3lh3 | 2008-12-01 09:29:43 -0500 (Mon, 01 Dec 2008) | 5 lines
3274 M /branches/dev/samtools/bam.c
3275 M /branches/dev/samtools/bam_import.c
3276 M /branches/dev/samtools/bam_maqcns.c
3277 M /branches/dev/samtools/bamtk.c
3278 M /branches/dev/samtools/bgzf.c
3279 M /branches/dev/samtools/samtools.1
3282 * bgzf: fixed a potential integer overflow on 32-it machines
3283 * maqcns: set the minimum combined quality as 0
3284 * supporting hex strings
3286 ------------------------------------------------------------------------
3287 r23 | lh3lh3 | 2008-11-27 12:14:37 -0500 (Thu, 27 Nov 2008) | 3 lines
3289 M /branches/dev/samtools/bam_maqcns.c
3290 M /branches/dev/samtools/bamtk.c
3293 * fixed the bug in maqcns
3295 ------------------------------------------------------------------------
3296 r22 | lh3lh3 | 2008-11-27 12:08:11 -0500 (Thu, 27 Nov 2008) | 3 lines
3298 M /branches/dev/samtools/Makefile
3299 M /branches/dev/samtools/bam.h
3300 A /branches/dev/samtools/bam_maqcns.c
3301 A /branches/dev/samtools/bam_maqcns.h
3302 M /branches/dev/samtools/bam_tview.c
3303 M /branches/dev/samtools/bamtk.c
3304 A /branches/dev/samtools/glf.h
3307 * add MAQ consensus caller, currently BUGGY!
3309 ------------------------------------------------------------------------
3310 r21 | lh3lh3 | 2008-11-27 08:51:28 -0500 (Thu, 27 Nov 2008) | 4 lines
3312 M /branches/dev/samtools/bam_pileup.c
3313 M /branches/dev/samtools/bam_tview.c
3314 M /branches/dev/samtools/bamtk.c
3317 * tview: display padded alignment (but not P operation)
3318 * better coordinates and reference sequence
3320 ------------------------------------------------------------------------
3321 r19 | lh3lh3 | 2008-11-27 04:26:05 -0500 (Thu, 27 Nov 2008) | 2 lines
3323 A /branches/dev/samtools/ChangeLog
3327 ------------------------------------------------------------------------
3328 r18 | lh3lh3 | 2008-11-27 04:24:45 -0500 (Thu, 27 Nov 2008) | 3 lines
3330 D /branches/dev/samtools/ChangeLog
3331 A /branches/dev/samtools/ChangeLog.old (from /branches/dev/samtools/ChangeLog:6)
3333 Rename ChangeLog to ChangeLog.old. This old ChangeLog is generated from
3334 the log of my personal SVN repository.
3336 ------------------------------------------------------------------------
3337 r17 | lh3lh3 | 2008-11-27 04:22:55 -0500 (Thu, 27 Nov 2008) | 6 lines
3339 M /branches/dev/samtools/Makefile
3340 M /branches/dev/samtools/bamtk.c
3341 M /branches/dev/samtools/bgzf.c
3344 * declare fseeko and ftello as some Linux may not do this by default and
3345 missing these declarations will make bgzf buggy
3346 * get rid of some harmless warings
3347 * use BGZF by default, now
3349 ------------------------------------------------------------------------
3350 r16 | lh3lh3 | 2008-11-26 16:19:11 -0500 (Wed, 26 Nov 2008) | 4 lines
3352 M /branches/dev/samtools/bam_index.c
3353 M /branches/dev/samtools/bamtk.c
3354 M /branches/dev/samtools/razf.c
3357 * fixed a bug in razf_read()
3358 * give more warnings when the file is truncated (or due to bugs in I/O library)
3360 ------------------------------------------------------------------------
3361 r15 | lh3lh3 | 2008-11-26 15:41:39 -0500 (Wed, 26 Nov 2008) | 2 lines
3363 M /branches/dev/samtools/bgzf.c
3365 fixed a bug in bgzf.c at the end of the file
3367 ------------------------------------------------------------------------
3368 r14 | lh3lh3 | 2008-11-26 12:05:18 -0500 (Wed, 26 Nov 2008) | 4 lines
3370 M /branches/dev/samtools/bamtk.c
3373 * a lot happened to RAZF, although samtools itself is untouched. Better
3374 also update the version number anyway to avoid confusion
3376 ------------------------------------------------------------------------
3377 r13 | lh3lh3 | 2008-11-26 12:03:48 -0500 (Wed, 26 Nov 2008) | 2 lines
3379 M /branches/dev/samtools/razf.c
3381 a change from Jue, but I think it should not matter
3383 ------------------------------------------------------------------------
3384 r12 | lh3lh3 | 2008-11-26 11:48:14 -0500 (Wed, 26 Nov 2008) | 3 lines
3386 M /branches/dev/samtools/razf.c
3388 fixed a potential bug in razf. However, it seems still buggy, just
3389 rarely happens, very rarely.
3391 ------------------------------------------------------------------------
3392 r11 | lh3lh3 | 2008-11-26 09:02:56 -0500 (Wed, 26 Nov 2008) | 2 lines
3394 M /branches/dev/samtools/razf.c
3396 fixed a bug in razf, with the help of Jue
3398 ------------------------------------------------------------------------
3399 r10 | lh3lh3 | 2008-11-26 06:55:32 -0500 (Wed, 26 Nov 2008) | 2 lines
3401 M /branches/dev/samtools/bam_index.c
3405 ------------------------------------------------------------------------
3406 r9 | lh3lh3 | 2008-11-26 06:37:05 -0500 (Wed, 26 Nov 2008) | 2 lines
3408 M /branches/dev/samtools/Makefile
3409 M /branches/dev/samtools/bam.h
3410 M /branches/dev/samtools/razf.c
3411 M /branches/dev/samtools/razf.h
3413 * Jue has updated razf to realize Bob's scheme
3415 ------------------------------------------------------------------------
3416 r7 | lh3lh3 | 2008-11-25 15:37:37 -0500 (Tue, 25 Nov 2008) | 2 lines
3418 A /branches/dev/samtools/samtools.1
3422 ------------------------------------------------------------------------
3423 r6 | lh3lh3 | 2008-11-25 15:37:16 -0500 (Tue, 25 Nov 2008) | 3 lines
3425 A /branches/dev/samtools/ChangeLog
3426 A /branches/dev/samtools/Makefile
3427 A /branches/dev/samtools/bam.c
3428 A /branches/dev/samtools/bam.h
3429 A /branches/dev/samtools/bam_aux.c
3430 A /branches/dev/samtools/bam_endian.h
3431 A /branches/dev/samtools/bam_import.c
3432 A /branches/dev/samtools/bam_index.c
3433 A /branches/dev/samtools/bam_lpileup.c
3434 A /branches/dev/samtools/bam_pileup.c
3435 A /branches/dev/samtools/bam_sort.c
3436 A /branches/dev/samtools/bam_tview.c
3437 A /branches/dev/samtools/bamtk.c
3438 A /branches/dev/samtools/bgzf.c
3439 A /branches/dev/samtools/bgzf.h
3440 A /branches/dev/samtools/bgzip.c
3441 A /branches/dev/samtools/faidx.c
3442 A /branches/dev/samtools/faidx.h
3443 A /branches/dev/samtools/khash.h
3444 A /branches/dev/samtools/ksort.h
3445 A /branches/dev/samtools/kstream.h
3446 A /branches/dev/samtools/misc
3447 A /branches/dev/samtools/misc/Makefile
3448 A /branches/dev/samtools/misc/all2sam.pl
3449 A /branches/dev/samtools/misc/maq2sam.c
3450 A /branches/dev/samtools/razf.c
3451 A /branches/dev/samtools/razf.h
3452 A /branches/dev/samtools/razip.c
3453 A /branches/dev/samtools/zutil.h
3455 The initial version of samtools, replicated from my local SVN repository.
3456 The current version is: 0.1.0-42. All future development will happen here.
3458 ------------------------------------------------------------------------
3459 r5 | lh3lh3 | 2008-11-25 15:30:49 -0500 (Tue, 25 Nov 2008) | 2 lines
3461 A /branches/dev/samtools
3463 samtools (C version)
3465 ------------------------------------------------------------------------