1 ------------------------------------------------------------------------
2 r529 | jmarshall | 2010-01-11 18:51:49 -0500 (Mon, 11 Jan 2010) | 2 lines
4 M /trunk/samtools/faidx.c
6 Put the right filename in the error message.
8 ------------------------------------------------------------------------
9 r528 | lh3lh3 | 2009-12-14 11:26:47 -0500 (Mon, 14 Dec 2009) | 3 lines
11 M /trunk/samtools/bam_plcmd.c
12 M /trunk/samtools/bamtk.c
14 * samtools-0.1.7-5 (r528)
15 * further add new consensus generation strategy
17 ------------------------------------------------------------------------
18 r527 | petulda | 2009-12-11 12:31:05 -0500 (Fri, 11 Dec 2009) | 1 line
20 M /trunk/samtools/knetfile.c
22 Fixed a bug in knet_seek
23 ------------------------------------------------------------------------
24 r526 | petulda | 2009-12-11 07:51:18 -0500 (Fri, 11 Dec 2009) | 1 line
26 M /trunk/samtools/misc/sam2vcf.pl
28 Small fix in VCF format: dot for the empty INFO field
29 ------------------------------------------------------------------------
30 r525 | petulda | 2009-12-11 04:36:18 -0500 (Fri, 11 Dec 2009) | 1 line
32 M /trunk/samtools/sam_header.c
34 Allow tabs in the CO header field
35 ------------------------------------------------------------------------
36 r524 | jmarshall | 2009-12-10 10:03:58 -0500 (Thu, 10 Dec 2009) | 3 lines
38 M /trunk/samtools/Makefile
39 M /trunk/samtools/Makefile.mingw
41 Depend on libbam.a rather than the phony target, so that samtools is not
42 unnecessarily rebuilt every time. Also clean bgzip.
44 ------------------------------------------------------------------------
45 r523 | jmarshall | 2009-12-10 09:45:32 -0500 (Thu, 10 Dec 2009) | 4 lines
47 M /trunk/samtools/Makefile
48 M /trunk/samtools/Makefile.mingw
50 Fix a bug in compiling bgzip: this also needs knetfile.o when _USE_KNETFILE
51 is defined. Also introduce $(KNETFILE_O) which can be set to empty to
52 facilitate non-knet builds.
54 ------------------------------------------------------------------------
55 r522 | lh3lh3 | 2009-12-01 13:02:36 -0500 (Tue, 01 Dec 2009) | 4 lines
57 M /trunk/samtools/bamtk.c
58 M /trunk/samtools/sam_view.c
60 * samtools-0.1.7-4 (r522)
61 * fixed a bug in "view -r"
62 * added a new option "view -R" to read required read groups from a file
64 ------------------------------------------------------------------------
65 r521 | lh3lh3 | 2009-12-01 10:00:12 -0500 (Tue, 01 Dec 2009) | 3 lines
67 M /trunk/samtools/bam_md.c
68 M /trunk/samtools/bamtk.c
70 * samtools-0.1.7-3 (r521)
71 * calmd: optionally mask matching bases as N
73 ------------------------------------------------------------------------
74 r520 | lh3lh3 | 2009-12-01 09:37:17 -0500 (Tue, 01 Dec 2009) | 4 lines
76 M /trunk/samtools/bam_plcmd.c
77 M /trunk/samtools/bamtk.c
78 M /trunk/samtools/misc/samtools.pl
80 * samtools-0.1.7-2 (r520)
81 * fixed a few issues with compilation in Windows (on behalf of John)
82 * choose a random base as the consensus (for population genetics studies)
84 ------------------------------------------------------------------------
85 r519 | jmarshall | 2009-11-30 10:53:02 -0500 (Mon, 30 Nov 2009) | 6 lines
87 M /trunk/samtools/Makefile
89 Put libraries at the end, so they can resolve references from libbam.a
90 as well, even with old-fashioned linkers.
92 Also use libbam.a explicitly rather than "-L. -lbam" to ensure that we get
93 the freshly built library, not some other libbam.a lying around the system.
95 ------------------------------------------------------------------------
96 r518 | jmarshall | 2009-11-30 08:44:56 -0500 (Mon, 30 Nov 2009) | 2 lines
98 M /trunk/samtools/Makefile
99 M /trunk/samtools/misc/Makefile
101 Also clean *.exe (for Cygwin users using this makefile).
103 ------------------------------------------------------------------------
104 r517 | jmarshall | 2009-11-30 07:09:04 -0500 (Mon, 30 Nov 2009) | 2 lines
106 M /trunk/samtools/bam_index.c
108 Index files should be opened in binary mode, not text mode.
110 ------------------------------------------------------------------------
111 r516 | lh3lh3 | 2009-11-27 15:18:59 -0500 (Fri, 27 Nov 2009) | 2 lines
113 A /trunk/samtools/examples/bam2bed.c
115 another example program
117 ------------------------------------------------------------------------
118 r515 | lh3lh3 | 2009-11-27 10:44:56 -0500 (Fri, 27 Nov 2009) | 3 lines
120 M /trunk/samtools/bam_import.c
121 M /trunk/samtools/bamtk.c
122 M /trunk/samtools/misc/wgsim_eval.pl
123 M /trunk/samtools/sam.c
125 * samtools-0.1.7-1 (r515)
126 * report an error when .fai contains duplicated names, instead of segfault
128 ------------------------------------------------------------------------
129 r514 | jmarshall | 2009-11-24 09:45:35 -0500 (Tue, 24 Nov 2009) | 2 lines
131 M /trunk/samtools/bam.c
133 Format 'c'-encoded auxiliary fields correctly, as *signed* integers.
135 ------------------------------------------------------------------------
136 r513 | lh3lh3 | 2009-11-16 10:13:07 -0500 (Mon, 16 Nov 2009) | 2 lines
138 M /trunk/samtools/Makefile.mingw
140 Update Makefile.mingw for the same reason
142 ------------------------------------------------------------------------
143 r512 | lh3lh3 | 2009-11-16 10:00:08 -0500 (Mon, 16 Nov 2009) | 2 lines
145 M /trunk/samtools/Makefile
147 Fixed a bug in compiling razip
149 ------------------------------------------------------------------------
150 r510 | lh3lh3 | 2009-11-10 10:55:41 -0500 (Tue, 10 Nov 2009) | 2 lines
152 M /trunk/samtools/ChangeLog
153 M /trunk/samtools/NEWS
154 M /trunk/samtools/bamtk.c
155 M /trunk/samtools/samtools.1
157 Release samtools-0.1.7 (r510)
159 ------------------------------------------------------------------------
160 r509 | lh3lh3 | 2009-11-06 09:17:09 -0500 (Fri, 06 Nov 2009) | 3 lines
162 M /trunk/samtools/bam_plcmd.c
163 M /trunk/samtools/bamtk.c
165 * samtools-0.1.6-22 (r509)
166 * forget to fix a similar problem in glfgen
168 ------------------------------------------------------------------------
169 r508 | lh3lh3 | 2009-11-06 09:06:40 -0500 (Fri, 06 Nov 2009) | 3 lines
171 M /trunk/samtools/bam_maqcns.c
172 M /trunk/samtools/bam_plcmd.c
173 M /trunk/samtools/bamtk.c
174 M /trunk/samtools/sam_view.c
176 * samtools-0.1.6-21 (r508)
177 * fixed a potential bug in the indel caller towards the end of a chromosome
179 ------------------------------------------------------------------------
180 r494 | lh3lh3 | 2009-10-26 11:38:00 -0400 (Mon, 26 Oct 2009) | 3 lines
182 M /trunk/samtools/bamtk.c
183 M /trunk/samtools/sam_view.c
185 * samtools-0.1.6-19 (r494)
186 * allow to convert Illumina quality (64 based) to the BAM quality
188 ------------------------------------------------------------------------
189 r493 | lh3lh3 | 2009-10-26 10:24:39 -0400 (Mon, 26 Oct 2009) | 4 lines
191 M /trunk/samtools/Makefile
192 M /trunk/samtools/bam.c
193 M /trunk/samtools/bam_import.c
194 M /trunk/samtools/bamtk.c
195 M /trunk/samtools/sam.c
196 M /trunk/samtools/sam_header.c
198 * samtools-0.1.6-18 (r493)
199 * fixed the bugs due to improperly incorporating Petr's header parser
200 * a little code clean up in sam_header.c
202 ------------------------------------------------------------------------
203 r492 | petulda | 2009-10-24 09:43:25 -0400 (Sat, 24 Oct 2009) | 1 line
205 M /trunk/samtools/sam_header.c
207 Added sam_header_line_free call for sam_header_parse2
208 ------------------------------------------------------------------------
209 r491 | lh3lh3 | 2009-10-24 00:50:16 -0400 (Sat, 24 Oct 2009) | 3 lines
211 M /trunk/samtools/sam_view.c
216 ------------------------------------------------------------------------
217 r490 | lh3lh3 | 2009-10-24 00:45:12 -0400 (Sat, 24 Oct 2009) | 4 lines
219 M /trunk/samtools/bam.c
220 M /trunk/samtools/bam.h
221 M /trunk/samtools/bam_import.c
222 M /trunk/samtools/sam.c
225 * improved the interface a bit
228 ------------------------------------------------------------------------
229 r489 | lh3lh3 | 2009-10-24 00:41:50 -0400 (Sat, 24 Oct 2009) | 3 lines
231 M /trunk/samtools/bam_import.c
232 M /trunk/samtools/sam_header.c
233 M /trunk/samtools/sam_header.h
235 * BUGGY VERSION. Please NOT use it.
236 * Fixed a minor bug, but the major bug is still there.
238 ------------------------------------------------------------------------
239 r488 | lh3lh3 | 2009-10-24 00:17:10 -0400 (Sat, 24 Oct 2009) | 3 lines
241 M /trunk/samtools/Makefile
242 M /trunk/samtools/bam.c
243 M /trunk/samtools/bam.h
244 M /trunk/samtools/bam_aux.c
245 M /trunk/samtools/bam_import.c
246 M /trunk/samtools/bam_rmdup.c
247 M /trunk/samtools/bam_rmdupse.c
248 M /trunk/samtools/kaln.c
249 M /trunk/samtools/sam.c
250 M /trunk/samtools/sam_header.c
251 M /trunk/samtools/sam_header.h
252 M /trunk/samtools/sam_view.c
254 * This revision is SERIOUSLY BUGGY. Please NOT use it.
255 * Start to incorporate header parsing from Petr Danecek
257 ------------------------------------------------------------------------
258 r487 | petulda | 2009-10-23 11:44:32 -0400 (Fri, 23 Oct 2009) | 1 line
260 M /trunk/samtools/sam_header.c
261 M /trunk/samtools/sam_header.h
263 Now possible to merge multiple HeaderDict dictionaries
264 ------------------------------------------------------------------------
265 r486 | petulda | 2009-10-22 11:46:58 -0400 (Thu, 22 Oct 2009) | 1 line
267 M /trunk/samtools/sam_header.c
270 ------------------------------------------------------------------------
271 r485 | petulda | 2009-10-22 11:41:56 -0400 (Thu, 22 Oct 2009) | 1 line
273 A /trunk/samtools/sam_header.c
274 A /trunk/samtools/sam_header.h
277 ------------------------------------------------------------------------
278 r484 | lh3lh3 | 2009-10-19 14:31:32 -0400 (Mon, 19 Oct 2009) | 5 lines
280 M /trunk/samtools/bam_import.c
281 M /trunk/samtools/bam_rmdupse.c
282 M /trunk/samtools/bamtk.c
283 M /trunk/samtools/examples/Makefile
285 * samtools-0.1.6-17 (r484)
286 * fixed a memory leak in rmdupse
287 * fixed a bug in parsing @RG header lines
288 * test rmdup in examples/
290 ------------------------------------------------------------------------
291 r483 | lh3lh3 | 2009-10-19 13:22:48 -0400 (Mon, 19 Oct 2009) | 4 lines
293 M /trunk/samtools/bam_rmdup.c
294 M /trunk/samtools/bam_rmdupse.c
295 M /trunk/samtools/bamtk.c
297 * samtools-0.1.6-16 (r483)
298 * unify the interface of rmdup and rmdupse
299 * a new bug found in rg2lib(). Have not been fixed yet.
301 ------------------------------------------------------------------------
302 r482 | lh3lh3 | 2009-10-19 13:03:34 -0400 (Mon, 19 Oct 2009) | 4 lines
304 M /trunk/samtools/bam.h
305 M /trunk/samtools/bam_rmdup.c
306 M /trunk/samtools/bam_rmdupse.c
307 M /trunk/samtools/bamtk.c
308 A /trunk/samtools/klist.h
310 * samtools-0.1.6-15 (r482)
312 * rmdupse is now library aware
314 ------------------------------------------------------------------------
315 r481 | lh3lh3 | 2009-10-18 00:07:21 -0400 (Sun, 18 Oct 2009) | 3 lines
317 M /trunk/samtools/bam_rmdup.c
318 M /trunk/samtools/bamtk.c
320 * samtools-0.1.6-14 (r480)
321 * rmdup is now RG aware
323 ------------------------------------------------------------------------
324 r480 | lh3lh3 | 2009-10-17 22:05:20 -0400 (Sat, 17 Oct 2009) | 2 lines
326 M /trunk/samtools/misc/samtools.pl
328 added a small unitity to parse SRA XML files
330 ------------------------------------------------------------------------
331 r479 | lh3lh3 | 2009-10-17 20:57:26 -0400 (Sat, 17 Oct 2009) | 3 lines
333 M /trunk/samtools/bam_maqcns.c
334 M /trunk/samtools/bam_maqcns.h
335 M /trunk/samtools/bam_plcmd.c
336 M /trunk/samtools/bam_sort.c
337 M /trunk/samtools/bamtk.c
339 * samtools-0.1.6-13 (r479)
340 * merge: optionally use file names as RG tags
342 ------------------------------------------------------------------------
343 r478 | lh3lh3 | 2009-10-14 14:18:12 -0400 (Wed, 14 Oct 2009) | 3 lines
345 M /trunk/samtools/bam.c
346 M /trunk/samtools/bam.h
347 M /trunk/samtools/bam_maqcns.c
348 M /trunk/samtools/bamtk.c
349 M /trunk/samtools/kaln.c
351 * samtools-0.1.6-12 (r478)
352 * fixed a bug in the indel caller
354 ------------------------------------------------------------------------
355 r477 | lh3lh3 | 2009-10-10 06:12:26 -0400 (Sat, 10 Oct 2009) | 3 lines
357 M /trunk/samtools/bam_index.c
358 M /trunk/samtools/bamtk.c
360 * samtools-0.1.6-11 (r477)
361 * fixed a bug due to recent change in bam_index.c (thank Nicole Washington for the patch)
363 ------------------------------------------------------------------------
364 r476 | petulda | 2009-10-09 11:45:36 -0400 (Fri, 09 Oct 2009) | 1 line
366 A /trunk/samtools/misc/sam2vcf.pl
368 Added the sam2vcf.pl script.
369 ------------------------------------------------------------------------
370 r475 | lh3lh3 | 2009-10-08 10:19:16 -0400 (Thu, 08 Oct 2009) | 2 lines
372 M /trunk/samtools/Makefile
373 M /trunk/samtools/bam.c
374 M /trunk/samtools/bam.h
375 M /trunk/samtools/bam_maqcns.c
376 M /trunk/samtools/bamtk.c
377 A /trunk/samtools/kaln.c
378 A /trunk/samtools/kaln.h
380 Unfinished modification. Please do not use this revision...
382 ------------------------------------------------------------------------
383 r474 | petulda | 2009-10-08 06:39:54 -0400 (Thu, 08 Oct 2009) | 1 line
385 M /trunk/samtools/knetfile.c
387 Removed the offending knet_seek message.
388 ------------------------------------------------------------------------
389 r473 | petulda | 2009-10-06 09:26:35 -0400 (Tue, 06 Oct 2009) | 1 line
391 M /trunk/samtools/knetfile.c
392 M /trunk/samtools/razf.c
394 Bug fix - faidx on RAZF compressed files now working.
395 ------------------------------------------------------------------------
396 r472 | lh3lh3 | 2009-10-02 08:42:57 -0400 (Fri, 02 Oct 2009) | 2 lines
398 M /trunk/samtools/samtools.1
400 Clarify the meaning of a region like "chr2:1,000,000".
402 ------------------------------------------------------------------------
403 r471 | lh3lh3 | 2009-10-02 05:42:19 -0400 (Fri, 02 Oct 2009) | 2 lines
405 M /trunk/samtools/misc/novo2sam.pl
407 Fixed minor bugs in novo2sam.pl (on behalf of Ken Chen and Colin Hercus)
409 ------------------------------------------------------------------------
410 r470 | lh3lh3 | 2009-09-29 15:01:27 -0400 (Tue, 29 Sep 2009) | 3 lines
412 M /trunk/samtools/Makefile.mingw
413 M /trunk/samtools/bamtk.c
414 M /trunk/samtools/knetfile.c
415 M /trunk/samtools/knetfile.h
417 * samtools-0.1.6-9 (r470)
418 * make knetfile.c compatible with MinGW (thank Martin Morgan for the patch)
420 ------------------------------------------------------------------------
421 r469 | lh3lh3 | 2009-09-29 08:07:44 -0400 (Tue, 29 Sep 2009) | 3 lines
423 M /trunk/samtools/bam_index.c
424 M /trunk/samtools/bamtk.c
426 * samtools-0.1.6-9 (r469)
427 * refactor bam_fetch() for Python binding. On behalf of Leo Goodstadt.
429 ------------------------------------------------------------------------
430 r468 | lh3lh3 | 2009-09-28 05:18:29 -0400 (Mon, 28 Sep 2009) | 3 lines
432 M /trunk/samtools/bam_sort.c
433 M /trunk/samtools/bamtk.c
434 M /trunk/samtools/misc/samtools.pl
436 * samtools-0.1.6-7 (r468)
439 ------------------------------------------------------------------------
440 r467 | petulda | 2009-09-28 04:51:29 -0400 (Mon, 28 Sep 2009) | 1 line
442 M /trunk/samtools/bgzf.c
443 M /trunk/samtools/bgzip.c
444 M /trunk/samtools/razf.c
445 M /trunk/samtools/razip.c
447 Changed the mode for newly created files to 0666. This allows less strict permissions with umask properly set (e.g. 0002 vs. 0022).
448 ------------------------------------------------------------------------
449 r466 | lh3lh3 | 2009-09-24 06:29:19 -0400 (Thu, 24 Sep 2009) | 3 lines
451 M /trunk/samtools/ChangeLog
452 M /trunk/samtools/bam_md.c
453 M /trunk/samtools/bamtk.c
455 * samtools-0.1.6-6 (r466)
456 * do not crash calmd when some sequences are absent from the reference.
458 ------------------------------------------------------------------------
459 r464 | jmarshall | 2009-09-23 06:14:32 -0400 (Wed, 23 Sep 2009) | 3 lines
461 M /trunk/samtools/bam.c
462 M /trunk/samtools/knetfile.c
464 Suppress bgzf_check_EOF() messages when reading from a pipe, as there is
465 no way to seek on a pipe and the messages always appear.
467 ------------------------------------------------------------------------
468 r463 | petulda | 2009-09-16 07:05:41 -0400 (Wed, 16 Sep 2009) | 1 line
470 M /trunk/samtools/knetfile.c
471 M /trunk/samtools/razf.c
473 A bug fix, "samtools view" is now working again.
474 ------------------------------------------------------------------------
475 r462 | lh3lh3 | 2009-09-16 04:51:07 -0400 (Wed, 16 Sep 2009) | 3 lines
477 M /trunk/samtools/bamtk.c
478 M /trunk/samtools/faidx.c
479 M /trunk/samtools/knetfile.c
480 M /trunk/samtools/knetfile.h
481 M /trunk/samtools/razf.c
482 M /trunk/samtools/razf.h
484 * samtools-0.1.6-5 (r462)
485 * Added knetfile support in razf and faidx (on behalf of Petr Danecek)
487 ------------------------------------------------------------------------
488 r460 | lh3lh3 | 2009-09-09 07:06:22 -0400 (Wed, 09 Sep 2009) | 2 lines
490 M /trunk/samtools/samtools.1
492 fixed a formatting issue
494 ------------------------------------------------------------------------
495 r459 | lh3lh3 | 2009-09-08 18:14:08 -0400 (Tue, 08 Sep 2009) | 3 lines
497 M /trunk/samtools/bam_sort.c
498 M /trunk/samtools/bamtk.c
500 * samtools-0.1.6-4 (r459)
501 * make sort output the result to stdout when -o is in use
503 ------------------------------------------------------------------------
504 r458 | lh3lh3 | 2009-09-07 05:10:28 -0400 (Mon, 07 Sep 2009) | 4 lines
506 M /trunk/samtools/bamtk.c
507 M /trunk/samtools/faidx.c
508 M /trunk/samtools/faidx.h
509 M /trunk/samtools/samtools.1
511 * samtools-0.1.6-2 (r458)
512 * added more interface to faidx (by Nils)
513 * updated documentation
515 ------------------------------------------------------------------------
516 r457 | lh3lh3 | 2009-09-05 16:12:04 -0400 (Sat, 05 Sep 2009) | 3 lines
518 M /trunk/samtools/bam_sort.c
519 M /trunk/samtools/bamtk.c
521 * samtools-0.1.6-2 (r457)
522 * get rid of three assert() in bam_sort.c
524 ------------------------------------------------------------------------
525 r456 | jmarshall | 2009-09-04 12:46:25 -0400 (Fri, 04 Sep 2009) | 3 lines
527 M /trunk/samtools/razf.c
529 Return NULL from _razf_open() (and hence razf_open()/razf_open2())
530 when opening the file fails.
532 ------------------------------------------------------------------------
533 r453 | lh3lh3 | 2009-09-02 08:56:33 -0400 (Wed, 02 Sep 2009) | 2 lines
535 M /trunk/samtools/ChangeLog
536 M /trunk/samtools/NEWS
537 M /trunk/samtools/bamtk.c
538 M /trunk/samtools/samtools.1
539 D /trunk/samtools/source.dot
541 Release samtools-0.1.6
543 ------------------------------------------------------------------------
544 r451 | lh3lh3 | 2009-09-02 05:44:48 -0400 (Wed, 02 Sep 2009) | 4 lines
546 M /trunk/samtools/bam_md.c
547 M /trunk/samtools/bam_rmdup.c
548 M /trunk/samtools/bam_rmdupse.c
549 M /trunk/samtools/bam_sort.c
550 M /trunk/samtools/bamtk.c
551 M /trunk/samtools/samtools.1
553 * samtools-0.1.5-34 (r451)
554 * applied the patch by John
555 * improved the help message a little bit
557 ------------------------------------------------------------------------
558 r450 | lh3lh3 | 2009-09-02 04:55:55 -0400 (Wed, 02 Sep 2009) | 3 lines
560 M /trunk/samtools/bam_color.c
561 M /trunk/samtools/bamtk.c
563 * samtools-0.1.5-33 (r450)
564 * fixed a bug in bam_color.c (on behalf of Nils Homer)
566 ------------------------------------------------------------------------
567 r449 | lh3lh3 | 2009-08-29 15:36:41 -0400 (Sat, 29 Aug 2009) | 4 lines
569 M /trunk/samtools/bam_import.c
570 M /trunk/samtools/bam_md.c
571 M /trunk/samtools/bamtk.c
572 M /trunk/samtools/misc/samtools.pl
574 * samtools-0.1.5-32 (r449)
575 * fillmd: fixed a bug in modifying MD/NM tags
576 * in import, give a warning if the read is aligned but there is no CIGAR.
578 ------------------------------------------------------------------------
579 r448 | lh3lh3 | 2009-08-19 04:44:28 -0400 (Wed, 19 Aug 2009) | 3 lines
581 M /trunk/samtools/ChangeLog
582 M /trunk/samtools/bam_pileup.c
583 M /trunk/samtools/bamtk.c
584 M /trunk/samtools/misc/wgsim_eval.pl
586 * samtools-0.1.5-31 (r448)
587 * fixed an issue when the last CIGAR is I or D
589 ------------------------------------------------------------------------
590 r447 | lh3lh3 | 2009-08-17 04:34:57 -0400 (Mon, 17 Aug 2009) | 3 lines
592 M /trunk/samtools/bam_aux.c
593 M /trunk/samtools/bamtk.c
595 * samtools-0.1.5-30 (r447)
596 * fixed a bug in bam_aux_get(): 'A' is not checked
598 ------------------------------------------------------------------------
599 r446 | lh3lh3 | 2009-08-17 04:33:17 -0400 (Mon, 17 Aug 2009) | 2 lines
601 M /trunk/samtools/bam_aux.c
602 M /trunk/samtools/bamtk.c
606 ------------------------------------------------------------------------
607 r444 | lh3lh3 | 2009-08-11 05:02:36 -0400 (Tue, 11 Aug 2009) | 3 lines
609 M /trunk/samtools/bam_sort.c
610 M /trunk/samtools/bamtk.c
612 * samtools-0.1.5-28 (r444)
615 ------------------------------------------------------------------------
616 r443 | lh3lh3 | 2009-08-11 04:29:11 -0400 (Tue, 11 Aug 2009) | 4 lines
618 M /trunk/samtools/bam.c
619 M /trunk/samtools/bam_import.c
620 M /trunk/samtools/bamtk.c
622 * samtools-0.1.5-27 (r443)
623 * SEQ and QUAL can be "*"
624 * parse CIGAR "=" and "X" as "M"
626 ------------------------------------------------------------------------
627 r442 | lh3lh3 | 2009-08-07 16:56:38 -0400 (Fri, 07 Aug 2009) | 4 lines
629 M /trunk/samtools/bam_pileup.c
630 M /trunk/samtools/bamtk.c
631 M /trunk/samtools/misc/md5.c
632 M /trunk/samtools/misc/md5.h
633 M /trunk/samtools/misc/md5fa.c
635 * samtools-0.1.5-26 (r442)
636 * replace RSA Inc md5.* with ones under permissive lincense
637 * fixed a bug in detecting unsorted bam in pileup
639 ------------------------------------------------------------------------
640 r441 | bhandsaker | 2009-08-05 09:41:28 -0400 (Wed, 05 Aug 2009) | 2 lines
642 M /trunk/samtools/bgzf.c
643 M /trunk/samtools/bgzf.h
644 M /trunk/samtools/bgzip.c
646 Change copyright notices now that MIT has approved open source distribution.
648 ------------------------------------------------------------------------
649 r440 | lh3lh3 | 2009-08-05 05:44:24 -0400 (Wed, 05 Aug 2009) | 3 lines
651 M /trunk/samtools/bam_stat.c
652 M /trunk/samtools/bamtk.c
654 * samtools-0.1.5-25 (r436)
655 * in flagstats, do not report singletons if both ends are unmapped
657 ------------------------------------------------------------------------
658 r439 | lh3lh3 | 2009-08-04 17:16:51 -0400 (Tue, 04 Aug 2009) | 2 lines
660 M /trunk/samtools/misc/maq2sam.c
662 fixed a SERIOUS bug in setting 0x20 flag
664 ------------------------------------------------------------------------
665 r438 | lh3lh3 | 2009-08-04 16:50:43 -0400 (Tue, 04 Aug 2009) | 2 lines
667 M /trunk/samtools/misc/samtools.pl
669 fixed two minor bugs (suggested by Tim M Storm)
671 ------------------------------------------------------------------------
672 r437 | lh3lh3 | 2009-08-04 04:13:24 -0400 (Tue, 04 Aug 2009) | 3 lines
674 M /trunk/samtools/bamtk.c
675 M /trunk/samtools/misc/samtools.pl
676 M /trunk/samtools/sam_view.c
678 * samtools-0.1.5-24 (r435)
681 ------------------------------------------------------------------------
682 r434 | lh3lh3 | 2009-08-03 05:40:42 -0400 (Mon, 03 Aug 2009) | 3 lines
684 M /trunk/samtools/bam_tview.c
685 M /trunk/samtools/bamtk.c
687 * samtools-0.1.5-23 (r434)
688 * in tview, press 'r' to show read names rather than sequences
690 ------------------------------------------------------------------------
691 r433 | lh3lh3 | 2009-08-02 14:13:35 -0400 (Sun, 02 Aug 2009) | 3 lines
693 M /trunk/samtools/knetfile.c
695 * tried to fixed the buggy FTP random access in Windows. FAILED.
696 * anyway, MinGW seems to have problem with "%lld".
698 ------------------------------------------------------------------------
699 r432 | lh3lh3 | 2009-08-01 19:32:07 -0400 (Sat, 01 Aug 2009) | 5 lines
701 M /trunk/samtools/Makefile.mingw
702 M /trunk/samtools/bamtk.c
703 M /trunk/samtools/faidx.c
704 M /trunk/samtools/razf.c
705 A /trunk/samtools/win32/libcurses.a
706 A /trunk/samtools/win32/xcurses.h
708 * samtools-0.1.5-22 (r432)
709 * faidx: fixed compitability issue with _WIN32
710 * razf: fixed potential compitability issue with _WIN32
711 * PDCurses support in Windows
713 ------------------------------------------------------------------------
714 r431 | lh3lh3 | 2009-08-01 18:34:54 -0400 (Sat, 01 Aug 2009) | 2 lines
716 M /trunk/samtools/win32/libz.a
718 replace the GnuWin32 version of libz.a with my own build with MinGW.
720 ------------------------------------------------------------------------
721 r430 | lh3lh3 | 2009-08-01 18:21:07 -0400 (Sat, 01 Aug 2009) | 2 lines
723 M /trunk/samtools/knetfile.c
727 ------------------------------------------------------------------------
728 r429 | lh3lh3 | 2009-08-01 17:41:19 -0400 (Sat, 01 Aug 2009) | 3 lines
730 M /trunk/samtools/Makefile.mingw
731 M /trunk/samtools/bamtk.c
732 M /trunk/samtools/knetfile.c
733 M /trunk/samtools/knetfile.h
735 * samtools-0.1.5-21 (r428)
736 * knetfile.c is now compatible with mingw-winsock
738 ------------------------------------------------------------------------
739 r428 | lh3lh3 | 2009-07-31 19:39:07 -0400 (Fri, 31 Jul 2009) | 2 lines
741 M /trunk/samtools/Makefile.mingw
743 simplify MinGW Makefile
745 ------------------------------------------------------------------------
746 r427 | lh3lh3 | 2009-07-31 19:30:54 -0400 (Fri, 31 Jul 2009) | 5 lines
748 A /trunk/samtools/Makefile.mingw
749 M /trunk/samtools/bam_import.c
750 M /trunk/samtools/bamtk.c
751 A /trunk/samtools/win32
752 A /trunk/samtools/win32/libz.a
753 A /trunk/samtools/win32/zconf.h
754 A /trunk/samtools/win32/zlib.h
756 * samtools-0.1.5-20 (r427)
757 * MinGW support. At least SAM<->BAM conversion is working. Other
758 functionality are not tested at the moment.
759 * zlib headers and Windows version of libz.a are included in win32/
761 ------------------------------------------------------------------------
762 r426 | lh3lh3 | 2009-07-31 18:32:09 -0400 (Fri, 31 Jul 2009) | 3 lines
764 M /trunk/samtools/bamtk.c
765 M /trunk/samtools/sam_view.c
767 * samtools-0.1.5-19 (r426)
768 * fixed a bug caused by recent modifications. Sorry.
770 ------------------------------------------------------------------------
771 r425 | lh3lh3 | 2009-07-31 18:23:51 -0400 (Fri, 31 Jul 2009) | 2 lines
773 M /trunk/samtools/bgzf.c
775 compatible with Windows binary files
777 ------------------------------------------------------------------------
778 r424 | lh3lh3 | 2009-07-31 05:19:59 -0400 (Fri, 31 Jul 2009) | 5 lines
780 M /trunk/samtools/bam_maqcns.c
781 M /trunk/samtools/bam_maqcns.h
782 M /trunk/samtools/bam_plcmd.c
783 M /trunk/samtools/bam_tview.c
784 M /trunk/samtools/bamtk.c
785 M /trunk/samtools/misc/samtools.pl
787 * samtools-0.1.5-18 (r423)
788 * output additional information in pileup indel lines, for the purepose
789 of debugging at the moment
790 * in tview, optionally allow to treat reference skip as deletion
792 ------------------------------------------------------------------------
793 r423 | lh3lh3 | 2009-07-30 17:00:36 -0400 (Thu, 30 Jul 2009) | 2 lines
795 A /trunk/samtools/misc/psl2sam.pl
797 convert BLAT psl to SAM.
799 ------------------------------------------------------------------------
800 r422 | lh3lh3 | 2009-07-30 06:24:39 -0400 (Thu, 30 Jul 2009) | 6 lines
802 M /trunk/samtools/ChangeLog
803 M /trunk/samtools/bam.c
804 M /trunk/samtools/bamtk.c
805 M /trunk/samtools/bgzf.c
806 M /trunk/samtools/bgzf.h
807 M /trunk/samtools/knetfile.c
808 M /trunk/samtools/sam.c
809 M /trunk/samtools/sam_view.c
811 * samtools-0.1.5-17 (r422)
812 * fixed a but in knetfile.c when seek type is not SEEK_SET
813 * write an empty BGZF block to every BGZF file
814 * check BGZF EOF marker in bam_header_read()
817 ------------------------------------------------------------------------
818 r421 | lh3lh3 | 2009-07-30 05:03:39 -0400 (Thu, 30 Jul 2009) | 3 lines
820 M /trunk/samtools/bam_import.c
821 M /trunk/samtools/bam_plcmd.c
822 M /trunk/samtools/bamtk.c
823 M /trunk/samtools/misc/samtools.pl
824 M /trunk/samtools/sam.c
825 M /trunk/samtools/sam.h
826 M /trunk/samtools/sam_view.c
828 * samtools-0.1.5-16 (r421)
829 * in view and pileup, load header from FASTA index if the input is SAM.
831 ------------------------------------------------------------------------
832 r420 | lh3lh3 | 2009-07-29 04:18:55 -0400 (Wed, 29 Jul 2009) | 2 lines
834 M /trunk/samtools/misc/maq2sam.c
836 do not set "read 1" if reads are not mapped in the PE mode of maq
838 ------------------------------------------------------------------------
839 r419 | lh3lh3 | 2009-07-28 04:52:33 -0400 (Tue, 28 Jul 2009) | 5 lines
841 M /trunk/samtools/bam_import.c
842 M /trunk/samtools/bamtk.c
843 M /trunk/samtools/misc/samtools.pl
844 M /trunk/samtools/misc/wgsim_eval.pl
846 * samtools-0.1.5-15 (r419)
847 * in sam_open(), return NULL when the file cannot be opened.
848 * make wgsim_eval.pl more robust to imperfect SAM
849 * add "unique" command to samtools.pl
851 ------------------------------------------------------------------------
852 r418 | lh3lh3 | 2009-07-24 09:04:19 -0400 (Fri, 24 Jul 2009) | 2 lines
854 M /trunk/samtools/misc/wgsim_eval.pl
856 skip @header lines in SAM
858 ------------------------------------------------------------------------
859 r417 | lh3lh3 | 2009-07-24 07:42:38 -0400 (Fri, 24 Jul 2009) | 3 lines
861 M /trunk/samtools/bamtk.c
862 M /trunk/samtools/sam_view.c
864 * samtools-0.1.5-14 (r417)
865 * more help in "samtools view" due to the recent changes.
867 ------------------------------------------------------------------------
868 r416 | lh3lh3 | 2009-07-24 07:34:30 -0400 (Fri, 24 Jul 2009) | 3 lines
870 M /trunk/samtools/bam.c
871 M /trunk/samtools/bam.h
872 M /trunk/samtools/bam_import.c
873 M /trunk/samtools/bamtk.c
874 M /trunk/samtools/sam.c
875 M /trunk/samtools/sam.h
876 M /trunk/samtools/sam_view.c
878 * samtools-0.1.5-17 (r416)
879 * support import/export SAM with string tags
881 ------------------------------------------------------------------------
882 r415 | lh3lh3 | 2009-07-24 06:39:26 -0400 (Fri, 24 Jul 2009) | 3 lines
884 M /trunk/samtools/bam.c
885 M /trunk/samtools/bam.h
886 M /trunk/samtools/bam_import.c
887 M /trunk/samtools/bamtk.c
888 M /trunk/samtools/sam.c
889 M /trunk/samtools/sam.h
890 M /trunk/samtools/sam_view.c
892 * samtools-0.1.5-12 (r415)
893 * FLAG now can be in HEX
895 ------------------------------------------------------------------------
896 r414 | lh3lh3 | 2009-07-22 17:03:49 -0400 (Wed, 22 Jul 2009) | 2 lines
898 M /trunk/samtools/kstring.h
900 fixed a compiling error (thank Ken for fixing it)
902 ------------------------------------------------------------------------
903 r412 | lh3lh3 | 2009-07-21 17:19:40 -0400 (Tue, 21 Jul 2009) | 2 lines
905 M /trunk/samtools/kstring.c
906 M /trunk/samtools/kstring.h
908 Implemented Boyer-Moore search in the kstring library.
910 ------------------------------------------------------------------------
911 r409 | lh3lh3 | 2009-07-17 12:10:20 -0400 (Fri, 17 Jul 2009) | 2 lines
913 M /trunk/samtools/bam_index.c
915 do not include knetfile.h when _USE_KNETFILE is not defined
917 ------------------------------------------------------------------------
918 r408 | lh3lh3 | 2009-07-17 10:29:21 -0400 (Fri, 17 Jul 2009) | 5 lines
920 M /trunk/samtools/bam_md.c
921 M /trunk/samtools/bam_tview.c
922 M /trunk/samtools/bamtk.c
923 M /trunk/samtools/bgzf.c
925 * samtools-0.1.5-11 (r408)
926 * force to overwirte existing MD if it is different from the one calculated
928 * bgzf.c: improved the compatibility with Windows headers
930 ------------------------------------------------------------------------
931 r407 | lh3lh3 | 2009-07-17 09:46:56 -0400 (Fri, 17 Jul 2009) | 5 lines
933 M /trunk/samtools/bam.h
934 M /trunk/samtools/bam_aux.c
935 M /trunk/samtools/bam_md.c
936 M /trunk/samtools/bamtk.c
937 M /trunk/samtools/sam.h
939 * samtools-0.1.5-10 (r407)
940 * implemented bam_aux_del() to remove a tag
941 * fillmd: generate the NM tag
942 * fillmd: cmd interface improvement
944 ------------------------------------------------------------------------
945 r406 | lh3lh3 | 2009-07-16 18:30:40 -0400 (Thu, 16 Jul 2009) | 2 lines
947 M /trunk/samtools/Makefile
949 Sorry. The old Makefile is for PDCurses...
951 ------------------------------------------------------------------------
952 r405 | lh3lh3 | 2009-07-16 18:30:11 -0400 (Thu, 16 Jul 2009) | 3 lines
954 M /trunk/samtools/Makefile
955 M /trunk/samtools/bam_tview.c
956 M /trunk/samtools/bamtk.c
958 * samtools-0.1.5-9 (r405)
959 * improved the compatibility with PDCurses a little bit
961 ------------------------------------------------------------------------
962 r404 | lh3lh3 | 2009-07-16 18:23:52 -0400 (Thu, 16 Jul 2009) | 3 lines
964 M /trunk/samtools/Makefile
965 M /trunk/samtools/bam_tview.c
966 M /trunk/samtools/bamtk.c
968 * samtools-0.1.5-8 (r404)
969 * compatible with PDCurses
971 ------------------------------------------------------------------------
972 r403 | lh3lh3 | 2009-07-16 17:39:39 -0400 (Thu, 16 Jul 2009) | 3 lines
974 M /trunk/samtools/bamtk.c
975 M /trunk/samtools/kseq.h
977 * samtools-0.1.5-7 (r403)
978 * fixed a bug in kseq.h for binary files (text files are fine)
980 ------------------------------------------------------------------------
981 r402 | lh3lh3 | 2009-07-16 06:49:53 -0400 (Thu, 16 Jul 2009) | 4 lines
983 M /trunk/samtools/bam_import.c
984 M /trunk/samtools/bam_index.c
985 M /trunk/samtools/bamtk.c
986 M /trunk/samtools/bgzf.c
988 * samtools-0.1.5-6 (r402)
989 * fixed compiling error when "-D_USE_NETFILE" is not applied
990 * improve portability to MinGW
992 ------------------------------------------------------------------------
993 r398 | lh3lh3 | 2009-07-13 05:21:36 -0400 (Mon, 13 Jul 2009) | 3 lines
995 A /trunk/bam-lite/bam.h (from /trunk/samtools/bam.h:395)
996 A /trunk/bam-lite/bam_lite.c (from /trunk/samtools/bam_lite.c:395)
997 D /trunk/samtools/bam_lite.c
999 * move bam_lite.c to bam-lite
1000 * copy bam.h to bam-lite
1002 ------------------------------------------------------------------------
1003 r395 | lh3lh3 | 2009-07-13 05:12:57 -0400 (Mon, 13 Jul 2009) | 3 lines
1005 M /trunk/samtools/bam.h
1006 M /trunk/samtools/bam_lite.c
1007 M /trunk/samtools/bam_lpileup.c
1008 M /trunk/samtools/bam_pileup.c
1009 M /trunk/samtools/bamtk.c
1011 * samtools-0.1.5-5 (r395)
1012 * added bam_pileup_file() and removed bam_lpileup_file()
1014 ------------------------------------------------------------------------
1015 r394 | lh3lh3 | 2009-07-12 19:35:10 -0400 (Sun, 12 Jul 2009) | 3 lines
1017 M /trunk/samtools/bamtk.c
1018 M /trunk/samtools/knetfile.c
1019 M /trunk/samtools/knetfile.h
1021 * samtools-0.1.5-4 (r394)
1022 * http_proxy support in knetfile library (check http_proxy ENV)
1024 ------------------------------------------------------------------------
1025 r393 | lh3lh3 | 2009-07-12 18:57:07 -0400 (Sun, 12 Jul 2009) | 5 lines
1027 M /trunk/samtools/bam_index.c
1028 M /trunk/samtools/bam_tview.c
1029 M /trunk/samtools/bamtk.c
1030 M /trunk/samtools/knetfile.c
1031 M /trunk/samtools/knetfile.h
1033 * samtools-0.1.5-3 (r393)
1034 * knetfile now supports HTTP (no proxy at the moment)
1035 * fixed a potential issue in knetfile on opening ordinary file, although I have
1036 not seen the sideeffect so far.
1038 ------------------------------------------------------------------------
1039 r392 | lh3lh3 | 2009-07-12 13:50:55 -0400 (Sun, 12 Jul 2009) | 2 lines
1041 M /trunk/samtools/samtools.1
1043 Remove the warning in tview
1045 ------------------------------------------------------------------------
1046 r391 | lh3lh3 | 2009-07-12 13:42:43 -0400 (Sun, 12 Jul 2009) | 3 lines
1048 M /trunk/samtools/bam_tview.c
1049 M /trunk/samtools/bamtk.c
1051 * samtools-0.1.5-2 (r391)
1052 * do not show a blank screen when no reads mapped
1054 ------------------------------------------------------------------------
1055 r390 | lh3lh3 | 2009-07-09 09:01:42 -0400 (Thu, 09 Jul 2009) | 4 lines
1057 M /trunk/samtools/bam.h
1058 A /trunk/samtools/bam_lite.c
1059 M /trunk/samtools/bamtk.c
1061 * samtools-0.1.5-1 (r390)
1062 * removed useless _IOLIB in bam.h. This should cause no change at all.
1063 * added bam_lite.c for light-weight BAM reading
1065 ------------------------------------------------------------------------
1066 r385 | lh3lh3 | 2009-07-07 11:53:29 -0400 (Tue, 07 Jul 2009) | 2 lines
1068 M /trunk/samtools/bamtk.c
1069 M /trunk/samtools/knetfile.c
1071 Release samtools-0.1.5c (fixed a bug in piping)
1073 ------------------------------------------------------------------------
1074 r383 | lh3lh3 | 2009-07-07 06:39:55 -0400 (Tue, 07 Jul 2009) | 2 lines
1076 M /trunk/samtools/bamtk.c
1077 M /trunk/samtools/sam.c
1079 Release samtools-0.1.5b (BUG! so embarrassing!)
1081 ------------------------------------------------------------------------
1082 r381 | lh3lh3 | 2009-07-07 06:20:06 -0400 (Tue, 07 Jul 2009) | 2 lines
1084 M /trunk/samtools/Makefile
1085 M /trunk/samtools/bam.h
1086 M /trunk/samtools/bam_aux.c
1087 M /trunk/samtools/bamtk.c
1089 Release samtools-0.1.5a (for compatibility with Bio::DB::Sam)
1091 ------------------------------------------------------------------------
1092 r373 | lh3lh3 | 2009-07-07 05:26:57 -0400 (Tue, 07 Jul 2009) | 2 lines
1094 M /trunk/samtools/ChangeLog
1095 M /trunk/samtools/NEWS
1096 M /trunk/samtools/bamtk.c
1097 M /trunk/samtools/samtools.1
1099 Release samtools-0.1.5
1101 ------------------------------------------------------------------------
1102 r372 | lh3lh3 | 2009-07-07 04:49:27 -0400 (Tue, 07 Jul 2009) | 3 lines
1104 M /trunk/samtools/bamtk.c
1105 M /trunk/samtools/sam.c
1107 * samtools-0.1.4-23 (r372)
1108 * keep header text if "view -t" is used (by Gerton)
1110 ------------------------------------------------------------------------
1111 r371 | lh3lh3 | 2009-07-06 20:13:32 -0400 (Mon, 06 Jul 2009) | 2 lines
1113 M /trunk/samtools/samtools.1
1115 update documentation
1117 ------------------------------------------------------------------------
1118 r370 | bhandsaker | 2009-07-02 17:24:34 -0400 (Thu, 02 Jul 2009) | 2 lines
1120 M /trunk/samtools/Makefile
1122 Introduced LIBPATH variable so this could be overridden to allow samtools to build correct at the Broad.
1124 ------------------------------------------------------------------------
1125 r369 | lh3lh3 | 2009-07-02 08:36:53 -0400 (Thu, 02 Jul 2009) | 4 lines
1127 M /trunk/samtools/ChangeLog
1128 M /trunk/samtools/bam_aux.c
1129 M /trunk/samtools/bam_plcmd.c
1130 M /trunk/samtools/bamtk.c
1132 * samtools-0.1.4-22 (r369)
1133 * in pileup, optionally print E2 and U2
1134 * remove the debugging code in bam_aux_get() (Drat!)
1136 ------------------------------------------------------------------------
1137 r368 | lh3lh3 | 2009-07-02 06:32:26 -0400 (Thu, 02 Jul 2009) | 6 lines
1139 M /trunk/samtools/bam.c
1140 M /trunk/samtools/bam.h
1141 M /trunk/samtools/bam_aux.c
1142 M /trunk/samtools/bam_index.c
1143 M /trunk/samtools/bam_lpileup.c
1144 M /trunk/samtools/bam_md.c
1145 M /trunk/samtools/bam_pileup.c
1146 M /trunk/samtools/bam_rmdup.c
1147 M /trunk/samtools/bam_stat.c
1148 M /trunk/samtools/bam_tview.c
1149 M /trunk/samtools/bamtk.c
1150 M /trunk/samtools/faidx.c
1151 M /trunk/samtools/faidx.h
1152 M /trunk/samtools/glf.c
1154 * samtools-0.1.4-21 (r368)
1155 * propagate errors rather than exit or complain assertion failure. Assertion
1156 should be only used for checking internal bugs, but not for external input
1157 inconsistency. I was just a bit lazy.
1158 * small memory leak may be present on failure, though
1160 ------------------------------------------------------------------------
1161 r367 | lh3lh3 | 2009-06-30 11:18:42 -0400 (Tue, 30 Jun 2009) | 2 lines
1163 M /trunk/samtools/knetfile.c
1165 reduce the chance of blocking in FTP connection
1167 ------------------------------------------------------------------------
1168 r366 | lh3lh3 | 2009-06-30 10:35:21 -0400 (Tue, 30 Jun 2009) | 2 lines
1170 M /trunk/samtools/knetfile.c
1172 minor changes to knetfile: invalid fd equals -1 rather than 0
1174 ------------------------------------------------------------------------
1175 r365 | lh3lh3 | 2009-06-30 09:04:30 -0400 (Tue, 30 Jun 2009) | 3 lines
1177 M /trunk/samtools/bam_index.c
1178 M /trunk/samtools/bamtk.c
1179 M /trunk/samtools/knetfile.c
1180 M /trunk/samtools/knetfile.h
1182 * samtools-0.1.4-20 (r365)
1183 * download the BAM index file if it is not found in the current working directory.
1185 ------------------------------------------------------------------------
1186 r364 | lh3lh3 | 2009-06-30 07:39:07 -0400 (Tue, 30 Jun 2009) | 3 lines
1188 M /trunk/samtools/bamtk.c
1189 M /trunk/samtools/knetfile.c
1191 * samtools-0.1.4-19 (r364)
1192 * knetfile: report error when the file is not present on FTP
1194 ------------------------------------------------------------------------
1195 r363 | lh3lh3 | 2009-06-29 18:23:32 -0400 (Mon, 29 Jun 2009) | 4 lines
1197 M /trunk/samtools/bam_tview.c
1198 M /trunk/samtools/bamtk.c
1199 M /trunk/samtools/bgzf.c
1200 M /trunk/samtools/bgzf.h
1201 M /trunk/samtools/knetfile.c
1202 M /trunk/samtools/knetfile.h
1204 * samtools-0.1.4-18 (r363)
1205 * knetfile: do not trigger network communication in FTP seek (lazy seek)
1206 * bgzf: cache recent blocks (disabled by default)
1208 ------------------------------------------------------------------------
1209 r362 | lh3lh3 | 2009-06-25 16:04:34 -0400 (Thu, 25 Jun 2009) | 2 lines
1211 M /trunk/samtools/bgzf.c
1215 ------------------------------------------------------------------------
1216 r361 | lh3lh3 | 2009-06-25 16:03:10 -0400 (Thu, 25 Jun 2009) | 3 lines
1218 M /trunk/samtools/bam_index.c
1219 M /trunk/samtools/bamtk.c
1221 * samtools-0.1.4-17 (r361)
1222 * if a file is given on FTP, search locally for the BAM index
1224 ------------------------------------------------------------------------
1225 r360 | lh3lh3 | 2009-06-25 15:44:52 -0400 (Thu, 25 Jun 2009) | 5 lines
1227 M /trunk/samtools/Makefile
1228 M /trunk/samtools/bam_import.c
1229 M /trunk/samtools/bam_index.c
1230 M /trunk/samtools/bamtk.c
1231 M /trunk/samtools/bgzf.c
1232 M /trunk/samtools/bgzf.h
1233 M /trunk/samtools/knetfile.c
1234 M /trunk/samtools/knetfile.h
1236 * samtools-0.1.4-16 (r360)
1237 * report more information in index when the input is not sorted
1238 * change the behaviour of knet_seek() such that it returns 0 on success
1239 * support knetfile library in BGZF
1241 ------------------------------------------------------------------------
1242 r359 | lh3lh3 | 2009-06-25 12:10:55 -0400 (Thu, 25 Jun 2009) | 2 lines
1244 M /trunk/samtools/knetfile.c
1245 M /trunk/samtools/knetfile.h
1247 fixed bugs in knetfile.*
1249 ------------------------------------------------------------------------
1250 r358 | lh3lh3 | 2009-06-25 08:53:19 -0400 (Thu, 25 Jun 2009) | 2 lines
1252 A /trunk/samtools/knetfile.h
1254 this is the header file
1256 ------------------------------------------------------------------------
1257 r357 | lh3lh3 | 2009-06-25 08:52:03 -0400 (Thu, 25 Jun 2009) | 3 lines
1259 A /trunk/samtools/knetfile.c
1261 * open a file at FTP
1262 * preliminary version
1264 ------------------------------------------------------------------------
1265 r354 | lh3lh3 | 2009-06-24 09:02:25 -0400 (Wed, 24 Jun 2009) | 3 lines
1267 M /trunk/samtools/bam.c
1268 M /trunk/samtools/bamtk.c
1270 * samtools-0.1.4-15 (r354)
1271 * fixed a memory leak in bam_view1(), although samtools is not using this routine.
1273 ------------------------------------------------------------------------
1274 r351 | lh3lh3 | 2009-06-17 19:16:26 -0400 (Wed, 17 Jun 2009) | 4 lines
1276 M /trunk/samtools/bamtk.c
1277 M /trunk/samtools/faidx.c
1279 * samtools-0.1.4-13 (r351)
1280 * make faidx more tolerant to empty lines right before or after > lines
1281 * hope this does not introduce new bugs...
1283 ------------------------------------------------------------------------
1284 r350 | lh3lh3 | 2009-06-16 09:37:01 -0400 (Tue, 16 Jun 2009) | 3 lines
1286 M /trunk/samtools/bam_plcmd.c
1287 M /trunk/samtools/bamtk.c
1289 * samtools-0.1.4-13 (r350)
1290 * fixed a small memory leak in pileup, caused by recent modifications
1292 ------------------------------------------------------------------------
1293 r347 | lh3lh3 | 2009-06-13 16:20:49 -0400 (Sat, 13 Jun 2009) | 3 lines
1295 M /trunk/samtools/bam_plcmd.c
1296 M /trunk/samtools/bamtk.c
1297 M /trunk/samtools/sam_view.c
1299 * samtools-0.1.4-12 (r347)
1300 * added `-S' to pileup, similar to `view -S'
1302 ------------------------------------------------------------------------
1303 r346 | lh3lh3 | 2009-06-13 12:52:31 -0400 (Sat, 13 Jun 2009) | 3 lines
1305 M /trunk/samtools/Makefile
1306 M /trunk/samtools/bamtk.c
1307 M /trunk/samtools/sam_view.c
1308 M /trunk/samtools/samtools.1
1310 * samtools-0.1.4-11 (r346)
1311 * allow to select a read group at view command-line
1313 ------------------------------------------------------------------------
1314 r344 | lh3lh3 | 2009-06-13 09:06:24 -0400 (Sat, 13 Jun 2009) | 2 lines
1316 M /trunk/samtools/examples/calDepth.c
1320 ------------------------------------------------------------------------
1321 r343 | lh3lh3 | 2009-06-13 09:01:22 -0400 (Sat, 13 Jun 2009) | 2 lines
1323 M /trunk/samtools/examples/calDepth.c
1327 ------------------------------------------------------------------------
1328 r342 | lh3lh3 | 2009-06-13 08:58:48 -0400 (Sat, 13 Jun 2009) | 2 lines
1330 M /trunk/samtools/examples/Makefile
1331 A /trunk/samtools/examples/calDepth.c
1333 added an example of calculating read depth
1335 ------------------------------------------------------------------------
1336 r341 | lh3lh3 | 2009-06-13 08:00:08 -0400 (Sat, 13 Jun 2009) | 6 lines
1338 M /trunk/samtools/Makefile
1339 M /trunk/samtools/bam.h
1340 M /trunk/samtools/bam_aux.c
1341 A /trunk/samtools/bam_color.c
1342 M /trunk/samtools/bam_plcmd.c
1343 M /trunk/samtools/bam_sort.c
1344 M /trunk/samtools/bam_tview.c
1345 M /trunk/samtools/bamtk.c
1346 M /trunk/samtools/sam.c
1347 M /trunk/samtools/sam.h
1349 * samtools-0.1.4-10 (r341)
1350 * only include key APIs in libbam.a
1351 * move color-specific routines to bam_color.c
1352 * update documentations
1353 * remove the support of -q in pileup
1355 ------------------------------------------------------------------------
1356 r340 | lh3lh3 | 2009-06-13 06:17:14 -0400 (Sat, 13 Jun 2009) | 6 lines
1358 M /trunk/samtools/INSTALL
1359 M /trunk/samtools/Makefile
1360 M /trunk/samtools/bam_aux.c
1361 M /trunk/samtools/bam_import.c
1362 M /trunk/samtools/bam_tview.c
1363 M /trunk/samtools/bamtk.c
1364 M /trunk/samtools/razf.c
1365 M /trunk/samtools/sam_view.c
1367 * samtools-0.1.4-9 (r340)
1368 * added a warning to razf.c if zlib<1.2.2.1
1369 * fixed a compilation warning
1370 * fixed a segfault caused by @RG parsing
1371 * detect NCURSES in bam_tview.c
1373 ------------------------------------------------------------------------
1374 r339 | lh3lh3 | 2009-06-13 05:35:19 -0400 (Sat, 13 Jun 2009) | 2 lines
1376 M /trunk/samtools/INSTALL
1380 ------------------------------------------------------------------------
1381 r338 | lh3lh3 | 2009-06-12 19:15:24 -0400 (Fri, 12 Jun 2009) | 4 lines
1383 M /trunk/samtools/bam.c
1384 M /trunk/samtools/bam.h
1385 M /trunk/samtools/bam_aux.c
1386 M /trunk/samtools/bam_import.c
1387 M /trunk/samtools/bamtk.c
1388 M /trunk/samtools/kstring.h
1389 M /trunk/samtools/sam.c
1390 M /trunk/samtools/sam_view.c
1392 * samtools-0.1.4-8 (r338)
1393 * parse the @RG header lines and allow to choose library at the "samtools view"
1396 ------------------------------------------------------------------------
1397 r337 | lh3lh3 | 2009-06-12 16:25:50 -0400 (Fri, 12 Jun 2009) | 4 lines
1399 M /trunk/samtools/bamtk.c
1400 M /trunk/samtools/bgzf.c
1401 M /trunk/samtools/bgzf.h
1402 M /trunk/samtools/sam.c
1403 M /trunk/samtools/sam_view.c
1405 * samtools-0.1.4-7 (r337)
1406 * bgzf.c: support mode string "wu": uncompressed output
1407 * "samtools view" support "-u" command-line option
1409 ------------------------------------------------------------------------
1410 r336 | lh3lh3 | 2009-06-12 12:20:12 -0400 (Fri, 12 Jun 2009) | 5 lines
1412 M /trunk/samtools/Makefile
1413 M /trunk/samtools/misc/Makefile
1414 M /trunk/samtools/razf.c
1415 M /trunk/samtools/razf.h
1416 M /trunk/samtools/razip.c
1418 * no changes to samtools itself
1419 * remove zlib source codes
1420 * make RAZF reading compatible with old version of zlib
1421 * on old version of zlib, writing is not available
1423 ------------------------------------------------------------------------
1424 r335 | lh3lh3 | 2009-06-12 11:47:33 -0400 (Fri, 12 Jun 2009) | 2 lines
1426 D /trunk/samtools/zlib
1428 remove zlib for simplification...
1430 ------------------------------------------------------------------------
1431 r334 | lh3lh3 | 2009-06-12 10:43:36 -0400 (Fri, 12 Jun 2009) | 5 lines
1433 M /trunk/samtools/bam.h
1434 M /trunk/samtools/bam_aux.c
1435 M /trunk/samtools/bamtk.c
1437 * samtools-0.1.4-6 (r334)
1438 * do not export bam_aux_get_core() for Bio::DB::Sam because it has already
1439 been implemented in that.
1440 * this version works with the latest Bio::DB::Sam (20090612)
1442 ------------------------------------------------------------------------
1443 r333 | lh3lh3 | 2009-06-12 10:33:42 -0400 (Fri, 12 Jun 2009) | 2 lines
1445 M /trunk/samtools/ChangeLog
1449 ------------------------------------------------------------------------
1450 r332 | lh3lh3 | 2009-06-12 10:21:21 -0400 (Fri, 12 Jun 2009) | 2 lines
1452 M /trunk/samtools/AUTHORS
1453 M /trunk/samtools/Makefile
1454 M /trunk/samtools/misc/Makefile
1456 fixed minor things in Makefile
1458 ------------------------------------------------------------------------
1459 r331 | lh3lh3 | 2009-06-12 10:07:05 -0400 (Fri, 12 Jun 2009) | 4 lines
1461 M /trunk/samtools/bamtk.c
1463 * samtools-0.1.4-5 (r3310
1464 * no change to samtools itself. Version number is increased to reflect the
1465 changes in the Makefile building system.
1467 ------------------------------------------------------------------------
1468 r330 | lh3lh3 | 2009-06-12 10:03:38 -0400 (Fri, 12 Jun 2009) | 2 lines
1470 M /trunk/samtools/AUTHORS
1471 D /trunk/samtools/README
1473 update information...
1475 ------------------------------------------------------------------------
1476 r329 | lh3lh3 | 2009-06-12 09:52:21 -0400 (Fri, 12 Jun 2009) | 3 lines
1478 M /trunk/samtools/misc/novo2sam.pl
1480 * updated novoalign converter by Colin Hercus et al.
1481 * this version works with indels
1483 ------------------------------------------------------------------------
1484 r328 | lh3lh3 | 2009-06-12 09:50:53 -0400 (Fri, 12 Jun 2009) | 3 lines
1486 M /trunk/samtools/INSTALL
1487 M /trunk/samtools/Makefile
1488 M /trunk/samtools/misc/Makefile
1489 M /trunk/samtools/zlib/Makefile
1492 * update INSTALL instruction
1494 ------------------------------------------------------------------------
1495 r327 | lh3lh3 | 2009-06-12 09:18:29 -0400 (Fri, 12 Jun 2009) | 4 lines
1497 A /trunk/samtools/Makefile (from /trunk/samtools/Makefile.generic:325)
1498 D /trunk/samtools/Makefile.am
1499 D /trunk/samtools/Makefile.generic
1500 D /trunk/samtools/Makefile.lite
1501 D /trunk/samtools/autogen.sh
1502 D /trunk/samtools/cleanup.sh
1503 D /trunk/samtools/configure.ac
1504 A /trunk/samtools/misc/Makefile (from /trunk/samtools/misc/Makefile.generic:305)
1505 D /trunk/samtools/misc/Makefile.am
1506 D /trunk/samtools/misc/Makefile.generic
1507 M /trunk/samtools/razf.c
1508 A /trunk/samtools/zlib
1509 A /trunk/samtools/zlib/Makefile
1510 A /trunk/samtools/zlib/adler32.c
1511 A /trunk/samtools/zlib/compress.c
1512 A /trunk/samtools/zlib/crc32.c
1513 A /trunk/samtools/zlib/crc32.h
1514 A /trunk/samtools/zlib/deflate.c
1515 A /trunk/samtools/zlib/deflate.h
1516 A /trunk/samtools/zlib/gzio.c
1517 A /trunk/samtools/zlib/infback.c
1518 A /trunk/samtools/zlib/inffast.c
1519 A /trunk/samtools/zlib/inffast.h
1520 A /trunk/samtools/zlib/inffixed.h
1521 A /trunk/samtools/zlib/inflate.c
1522 A /trunk/samtools/zlib/inflate.h
1523 A /trunk/samtools/zlib/inftrees.c
1524 A /trunk/samtools/zlib/inftrees.h
1525 A /trunk/samtools/zlib/trees.c
1526 A /trunk/samtools/zlib/trees.h
1527 A /trunk/samtools/zlib/uncompr.c
1528 A /trunk/samtools/zlib/zconf.h
1529 A /trunk/samtools/zlib/zlib.h
1530 A /trunk/samtools/zlib/zutil.c
1531 A /trunk/samtools/zlib/zutil.h
1532 D /trunk/samtools/zutil.h
1534 * added zlib-1.2.3 as razip requires that
1535 * prepare to changed back to the Makefile building system
1536 * unfinished! (will be soon)
1538 ------------------------------------------------------------------------
1539 r326 | lh3lh3 | 2009-06-12 09:12:03 -0400 (Fri, 12 Jun 2009) | 2 lines
1541 M /trunk/samtools/misc/samtools.pl
1545 ------------------------------------------------------------------------
1546 r325 | lh3lh3 | 2009-06-10 11:27:59 -0400 (Wed, 10 Jun 2009) | 3 lines
1548 M /trunk/samtools/bam_maqcns.c
1549 M /trunk/samtools/bamtk.c
1551 * samtools-0.1.4-4 (r325)
1552 * further avoid wrong consensus calls in repetitive regions.
1554 ------------------------------------------------------------------------
1555 r324 | lh3lh3 | 2009-06-10 10:56:17 -0400 (Wed, 10 Jun 2009) | 4 lines
1557 M /trunk/samtools/bam_maqcns.c
1558 M /trunk/samtools/bam_plcmd.c
1559 M /trunk/samtools/bamtk.c
1560 M /trunk/samtools/sam.c
1561 M /trunk/samtools/sam.h
1563 * samtools-0.1.4-3 (r324)
1564 * make maqcns generate the correct call in repetitive regions.
1565 * allow filtering on mapQ at the pileup command line
1567 ------------------------------------------------------------------------
1568 r323 | lh3lh3 | 2009-06-10 05:04:21 -0400 (Wed, 10 Jun 2009) | 3 lines
1570 M /trunk/samtools/misc/samtools.pl
1572 * samtools.pl-0.3.2 (r322)
1573 * indels and SNPs use different mapping quality threshold
1575 ------------------------------------------------------------------------
1576 r322 | lh3lh3 | 2009-06-10 05:03:22 -0400 (Wed, 10 Jun 2009) | 2 lines
1578 M /trunk/samtools/misc/export2sam.pl
1582 ------------------------------------------------------------------------
1583 r321 | lh3lh3 | 2009-06-09 04:21:48 -0400 (Tue, 09 Jun 2009) | 2 lines
1585 M /trunk/samtools/misc/samtools.pl
1587 just typo. no real change
1589 ------------------------------------------------------------------------
1590 r320 | lh3lh3 | 2009-06-08 09:32:51 -0400 (Mon, 08 Jun 2009) | 2 lines
1592 M /trunk/samtools/misc/samtools.pl
1594 a little bit code cleanup
1596 ------------------------------------------------------------------------
1597 r319 | lh3lh3 | 2009-06-08 09:22:33 -0400 (Mon, 08 Jun 2009) | 4 lines
1599 M /trunk/samtools/misc/samtools.pl
1602 * change default parameters
1603 * optionally print filtered variants
1605 ------------------------------------------------------------------------
1606 r318 | lh3lh3 | 2009-06-08 09:14:26 -0400 (Mon, 08 Jun 2009) | 3 lines
1608 M /trunk/samtools/misc/samtools.pl
1611 * combine snpFilter and indelFilter
1613 ------------------------------------------------------------------------
1614 r317 | lh3lh3 | 2009-06-08 06:31:42 -0400 (Mon, 08 Jun 2009) | 3 lines
1616 M /trunk/samtools/misc/samtools.pl
1619 * change a default parameter
1621 ------------------------------------------------------------------------
1622 r316 | lh3lh3 | 2009-06-08 06:11:06 -0400 (Mon, 08 Jun 2009) | 5 lines
1624 M /trunk/samtools/bam_maqcns.c
1625 M /trunk/samtools/bam_maqcns.h
1626 M /trunk/samtools/bam_plcmd.c
1627 M /trunk/samtools/bamtk.c
1628 M /trunk/samtools/sam.c
1630 * samtools-0.1.4-2 (r316)
1631 * pileup: cap mapping quality at 60 (by default)
1632 * pileup: always calculate RMS mapq
1633 * pileup: allow to output variant sites only
1635 ------------------------------------------------------------------------
1636 r312 | lh3lh3 | 2009-06-04 08:01:10 -0400 (Thu, 04 Jun 2009) | 3 lines
1638 M /trunk/samtools/misc/samtools.pl
1643 ------------------------------------------------------------------------
1644 r311 | lh3lh3 | 2009-06-03 04:40:40 -0400 (Wed, 03 Jun 2009) | 2 lines
1646 M /trunk/samtools/misc/samtools.pl
1648 * in snpFilter, suppress non-SNP sites
1650 ------------------------------------------------------------------------
1651 r310 | lh3lh3 | 2009-06-01 09:35:13 -0400 (Mon, 01 Jun 2009) | 3 lines
1653 M /trunk/samtools/misc/samtools.pl
1658 ------------------------------------------------------------------------
1659 r309 | lh3lh3 | 2009-06-01 09:04:39 -0400 (Mon, 01 Jun 2009) | 3 lines
1661 M /trunk/samtools/misc/samtools.pl
1666 ------------------------------------------------------------------------
1667 r306 | lh3lh3 | 2009-05-28 06:49:35 -0400 (Thu, 28 May 2009) | 3 lines
1669 M /trunk/samtools/bgzf.c
1671 * minor changes to bgzf: return NULL if fd == -1
1672 * suggested by {kdj,jm18}@sanger.ac.uk
1674 ------------------------------------------------------------------------
1675 r305 | lh3lh3 | 2009-05-28 06:16:08 -0400 (Thu, 28 May 2009) | 2 lines
1677 A /trunk/samtools/misc/interpolate_sam.pl
1679 Script for paired-end pileup, contributed by Stephen Montgomery.
1681 ------------------------------------------------------------------------
1682 r304 | lh3lh3 | 2009-05-28 06:08:49 -0400 (Thu, 28 May 2009) | 3 lines
1684 M /trunk/samtools/bamtk.c
1685 M /trunk/samtools/sam.c
1687 * samtools-0.1.4-1 (r304)
1688 * fixed a minor bug in printing headers
1690 ------------------------------------------------------------------------
1691 r297 | lh3lh3 | 2009-05-21 11:06:16 -0400 (Thu, 21 May 2009) | 2 lines
1693 M /trunk/samtools/ChangeLog
1694 M /trunk/samtools/NEWS
1695 M /trunk/samtools/bam_plcmd.c
1696 M /trunk/samtools/bamtk.c
1697 M /trunk/samtools/misc/maq2sam.c
1698 M /trunk/samtools/samtools.1
1700 Release samtools-0.1.4
1702 ------------------------------------------------------------------------
1703 r296 | lh3lh3 | 2009-05-21 07:53:14 -0400 (Thu, 21 May 2009) | 3 lines
1705 M /trunk/samtools/bam_maqcns.c
1706 M /trunk/samtools/bamtk.c
1708 * samtools-0.1.3-24 (r296)
1709 * another similar bug in the indel caller
1711 ------------------------------------------------------------------------
1712 r295 | lh3lh3 | 2009-05-21 07:50:28 -0400 (Thu, 21 May 2009) | 3 lines
1714 M /trunk/samtools/bam_maqcns.c
1715 M /trunk/samtools/bamtk.c
1717 * samtools-0.1.3-23 (r295)
1718 * fixed a critical bug in the indel caller
1720 ------------------------------------------------------------------------
1721 r294 | lh3lh3 | 2009-05-20 08:00:20 -0400 (Wed, 20 May 2009) | 2 lines
1723 M /trunk/samtools/bam_stat.c
1725 added a missing header file
1727 ------------------------------------------------------------------------
1728 r293 | lh3lh3 | 2009-05-19 18:44:25 -0400 (Tue, 19 May 2009) | 3 lines
1730 M /trunk/samtools/bam_tview.c
1731 M /trunk/samtools/bamtk.c
1733 * samtools-0.1.3-22 (r293)
1734 * open tview in the dot-view mode by default
1736 ------------------------------------------------------------------------
1737 r292 | lh3lh3 | 2009-05-18 16:01:23 -0400 (Mon, 18 May 2009) | 6 lines
1739 M /trunk/samtools/samtools.1
1741 Added a note to the manual. Currently SAMtools used unaligned words in
1742 several places. Although this does not cause bus errors to me, it may
1743 affect portability. Please see the "Bus error" wiki page for more
1744 information. Also thank James Bonfields for pointing this out.
1747 ------------------------------------------------------------------------
1748 r286 | lh3lh3 | 2009-05-14 10:23:13 -0400 (Thu, 14 May 2009) | 3 lines
1750 M /trunk/samtools/bam.h
1751 M /trunk/samtools/bam_aux.c
1752 M /trunk/samtools/bamtk.c
1754 * samtools-0.1.3-21 (286)
1755 * declare bam_aux_get_core() in bam.h
1757 ------------------------------------------------------------------------
1758 r276 | lh3lh3 | 2009-05-13 05:07:55 -0400 (Wed, 13 May 2009) | 5 lines
1760 M /trunk/samtools/bam.h
1761 M /trunk/samtools/bam_index.c
1762 M /trunk/samtools/bamtk.c
1764 * samtools-0.1.3-20 (r276)
1765 * remove bam1_t::hash again. We need to modify the Perl API anyway to
1766 make it work with the latest SVN.
1767 * As is suggested by Tim, scan "{base}.bai" and "{base}.bam.bai" for index
1769 ------------------------------------------------------------------------
1770 r275 | lh3lh3 | 2009-05-12 16:14:10 -0400 (Tue, 12 May 2009) | 4 lines
1772 M /trunk/samtools/ChangeLog
1773 M /trunk/samtools/bam.h
1774 M /trunk/samtools/bamtk.c
1776 * samtools-0.1.3-19 (r275)
1777 * a minor change to the bam1_t struct: added back "void *hash" for the
1778 backward compatibility with Bio::DB::Sam
1780 ------------------------------------------------------------------------
1781 r273 | lh3lh3 | 2009-05-12 09:28:39 -0400 (Tue, 12 May 2009) | 3 lines
1783 M /trunk/samtools/bam_rmdupse.c
1784 M /trunk/samtools/bamtk.c
1786 * samtools-0.1.3-18 (r273)
1787 * rmdupse: do not remove unmapped reads
1789 ------------------------------------------------------------------------
1790 r272 | lh3lh3 | 2009-05-12 09:20:00 -0400 (Tue, 12 May 2009) | 2 lines
1792 M /trunk/samtools/bam_rmdupse.c
1794 change a parameter. It does nothing
1796 ------------------------------------------------------------------------
1797 r271 | lh3lh3 | 2009-05-12 09:17:58 -0400 (Tue, 12 May 2009) | 3 lines
1799 M /trunk/samtools/Makefile.am
1800 M /trunk/samtools/Makefile.generic
1801 M /trunk/samtools/Makefile.lite
1802 A /trunk/samtools/bam_rmdupse.c
1803 M /trunk/samtools/bamtk.c
1804 M /trunk/samtools/configure.ac
1806 * samtools-0.1.3-17 (r271)
1807 * added 'rmdupse' command
1809 ------------------------------------------------------------------------
1810 r267 | lh3lh3 | 2009-05-05 17:31:41 -0400 (Tue, 05 May 2009) | 3 lines
1812 M /trunk/samtools/bamtk.c
1813 M /trunk/samtools/sam_view.c
1815 * samtools-0.1.3-16 (r267)
1816 * in sam_view.c, changed g_flag_on based on the suggestion by Angie Hinrichs
1818 ------------------------------------------------------------------------
1819 r266 | lh3lh3 | 2009-05-05 17:23:27 -0400 (Tue, 05 May 2009) | 3 lines
1821 M /trunk/samtools/bam_import.c
1822 M /trunk/samtools/bamtk.c
1824 * samtools-0.1.3-15 (r266)
1825 * report an error if a non-* reference is present while @SQ is absent
1827 ------------------------------------------------------------------------
1828 r265 | lh3lh3 | 2009-05-05 17:09:00 -0400 (Tue, 05 May 2009) | 3 lines
1830 M /trunk/samtools/bam.h
1831 M /trunk/samtools/bam_import.c
1832 M /trunk/samtools/bamtk.c
1833 M /trunk/samtools/sam.c
1834 M /trunk/samtools/sam_view.c
1836 * samtools-0.1.3-14 (r262)
1837 * make samopen() recognize @SQ header lines
1839 ------------------------------------------------------------------------
1840 r261 | lh3lh3 | 2009-05-05 10:10:30 -0400 (Tue, 05 May 2009) | 3 lines
1842 M /trunk/samtools/bam_plcmd.c
1843 M /trunk/samtools/bamtk.c
1844 M /trunk/samtools/bgzf.c
1845 M /trunk/samtools/sam.c
1846 M /trunk/samtools/sam_view.c
1848 * samtools-0.1.3-13 (r260)
1849 * report error for file I/O error
1851 ------------------------------------------------------------------------
1852 r260 | lh3lh3 | 2009-05-05 10:01:16 -0400 (Tue, 05 May 2009) | 2 lines
1854 M /trunk/samtools/Makefile.am
1858 ------------------------------------------------------------------------
1859 r259 | lh3lh3 | 2009-05-05 09:52:25 -0400 (Tue, 05 May 2009) | 3 lines
1861 M /trunk/samtools/bam.h
1862 M /trunk/samtools/bam_pileup.c
1863 M /trunk/samtools/bam_plcmd.c
1864 M /trunk/samtools/bamtk.c
1865 M /trunk/samtools/sam.c
1866 M /trunk/samtools/sam.h
1868 * samtools-0.1.3-12 (r259)
1869 * use the new I/O interface in pileup
1871 ------------------------------------------------------------------------
1872 r258 | lh3lh3 | 2009-05-05 09:33:22 -0400 (Tue, 05 May 2009) | 3 lines
1874 M /trunk/samtools/Makefile.generic
1875 M /trunk/samtools/Makefile.lite
1876 M /trunk/samtools/bam.c
1877 M /trunk/samtools/bam.h
1878 M /trunk/samtools/bam_import.c
1879 M /trunk/samtools/bamtk.c
1880 A /trunk/samtools/sam.c
1881 A /trunk/samtools/sam.h
1882 A /trunk/samtools/sam_view.c
1884 * samtools-0.1.3-11 (r258)
1885 * unify the interface to BAM and SAM I/O
1887 ------------------------------------------------------------------------
1888 r257 | lh3lh3 | 2009-05-05 04:53:35 -0400 (Tue, 05 May 2009) | 3 lines
1890 M /trunk/samtools/Makefile.lite
1891 M /trunk/samtools/bam_plcmd.c
1892 M /trunk/samtools/bamtk.c
1894 * samtools-0.1.3-10 (r257)
1895 * allow hex with "pileup -m"
1897 ------------------------------------------------------------------------
1898 r256 | lh3lh3 | 2009-05-04 14:16:50 -0400 (Mon, 04 May 2009) | 4 lines
1900 M /trunk/samtools/bam_lpileup.c
1901 M /trunk/samtools/bamtk.c
1903 * samtools-0.1.3-9 (r256)
1904 * fixed a bug in bam_lpileup.c
1905 * I do not know if this also fixes the bug causing assertion failure in the tview
1907 ------------------------------------------------------------------------
1908 r251 | lh3lh3 | 2009-04-28 08:53:23 -0400 (Tue, 28 Apr 2009) | 3 lines
1910 M /trunk/samtools/bam_pileup.c
1911 M /trunk/samtools/bamtk.c
1913 * samtools-0.1.3-8 (r251)
1914 * fixed a bug when there are reads without coordinates
1916 ------------------------------------------------------------------------
1917 r250 | lh3lh3 | 2009-04-28 08:43:33 -0400 (Tue, 28 Apr 2009) | 2 lines
1919 A /trunk/samtools/AUTHORS
1920 A /trunk/samtools/README
1921 M /trunk/samtools/cleanup.sh
1925 ------------------------------------------------------------------------
1926 r249 | lh3lh3 | 2009-04-28 08:37:16 -0400 (Tue, 28 Apr 2009) | 2 lines
1928 M /trunk/samtools/Makefile.generic
1929 M /trunk/samtools/Makefile.lite
1930 M /trunk/samtools/configure.ac
1931 M /trunk/samtools/misc/Makefile.generic
1933 improve large file support in compilation
1935 ------------------------------------------------------------------------
1936 r248 | lh3lh3 | 2009-04-28 08:33:24 -0400 (Tue, 28 Apr 2009) | 2 lines
1938 M /trunk/samtools/INSTALL
1942 ------------------------------------------------------------------------
1943 r247 | lh3lh3 | 2009-04-28 08:28:50 -0400 (Tue, 28 Apr 2009) | 2 lines
1945 M /trunk/samtools/Makefile.am
1946 M /trunk/samtools/autogen.sh
1947 M /trunk/samtools/cleanup.sh
1948 M /trunk/samtools/configure.ac
1949 A /trunk/samtools/misc/Makefile.am
1951 fixed various issues about the GNU building scripts
1953 ------------------------------------------------------------------------
1954 r246 | lh3lh3 | 2009-04-28 08:10:23 -0400 (Tue, 28 Apr 2009) | 4 lines
1956 M /trunk/samtools/ChangeLog
1957 D /trunk/samtools/Makefile
1958 A /trunk/samtools/Makefile.am
1959 A /trunk/samtools/Makefile.generic
1960 A /trunk/samtools/autogen.sh
1961 M /trunk/samtools/bam.h
1962 M /trunk/samtools/bam_aux.c
1963 M /trunk/samtools/bam_tview.c
1964 M /trunk/samtools/bamtk.c
1965 A /trunk/samtools/cleanup.sh
1966 A /trunk/samtools/configure.ac
1967 D /trunk/samtools/misc/Makefile
1968 A /trunk/samtools/misc/Makefile.generic (from /trunk/samtools/misc/Makefile:245)
1970 * samtools-0.1.3-7 (r246)
1971 * incorporated revisions from Nils Homer
1972 * enhanced support of displaying color-space reads
1974 ------------------------------------------------------------------------
1975 r244 | lh3lh3 | 2009-04-25 06:49:40 -0400 (Sat, 25 Apr 2009) | 3 lines
1977 M /trunk/samtools/bam_md.c
1978 M /trunk/samtools/bamtk.c
1980 * samtools-0.1.3-6 (r244)
1981 * fixed segfault for unmapped reads
1983 ------------------------------------------------------------------------
1984 r243 | lh3lh3 | 2009-04-24 16:27:26 -0400 (Fri, 24 Apr 2009) | 5 lines
1986 M /trunk/samtools/bam.h
1987 M /trunk/samtools/bam_maqcns.c
1988 M /trunk/samtools/bam_md.c
1989 M /trunk/samtools/bamtk.c
1991 * samtools-0.1.3-5 (r243)
1992 * fixed a long existing bug which may cause memory leak
1994 * consensus calling now works with "=", but indel calling not
1996 ------------------------------------------------------------------------
1997 r242 | lh3lh3 | 2009-04-24 15:44:46 -0400 (Fri, 24 Apr 2009) | 3 lines
1999 M /trunk/samtools/bam_md.c
2000 M /trunk/samtools/bamtk.c
2002 * samtools-0.1.3-4 (r242)
2003 * fixed a memory leak
2005 ------------------------------------------------------------------------
2006 r240 | lh3lh3 | 2009-04-24 11:40:18 -0400 (Fri, 24 Apr 2009) | 5 lines
2008 M /trunk/samtools/Makefile
2009 M /trunk/samtools/Makefile.lite
2010 M /trunk/samtools/bam.h
2011 M /trunk/samtools/bam_aux.c
2012 A /trunk/samtools/bam_md.c
2013 M /trunk/samtools/bam_plcmd.c
2014 M /trunk/samtools/bamtk.c
2016 * samtools-0.1.3-3 (r240)
2018 * generate "=" bases
2019 * the plain pileup now support "=" bases, but consensus calling and glfgen may fail
2021 ------------------------------------------------------------------------
2022 r239 | lh3lh3 | 2009-04-24 07:08:20 -0400 (Fri, 24 Apr 2009) | 5 lines
2024 M /trunk/samtools/bam.h
2025 M /trunk/samtools/bam_aux.c
2026 M /trunk/samtools/bamtk.c
2028 * samtools-0.1.3-2 (r239)
2029 * fixed bugs in bam_aux.c (these functions nevered used by samtools)
2030 * removed bam_aux_init()/bam_aux_destroy()
2031 * added tagview for testing bam_aux
2033 ------------------------------------------------------------------------
2034 r235 | lh3lh3 | 2009-04-21 18:17:39 -0400 (Tue, 21 Apr 2009) | 3 lines
2036 M /trunk/samtools/bam_pileup.c
2037 M /trunk/samtools/bamtk.c
2040 * fixed a bug in pileup: the first read in a chromosome may not be printed
2042 ------------------------------------------------------------------------
2043 r232 | lh3lh3 | 2009-04-16 10:25:43 -0400 (Thu, 16 Apr 2009) | 2 lines
2045 M /trunk/samtools/Makefile.lite
2047 a missing file in Makefile.lite
2049 ------------------------------------------------------------------------
2050 r227 | lh3lh3 | 2009-04-15 17:02:53 -0400 (Wed, 15 Apr 2009) | 2 lines
2052 M /trunk/samtools/NEWS
2053 M /trunk/samtools/bamtk.c
2055 Release samtools-0.1.3
2057 ------------------------------------------------------------------------
2058 r223 | lh3lh3 | 2009-04-15 09:31:32 -0400 (Wed, 15 Apr 2009) | 3 lines
2060 M /trunk/samtools/bam_plcmd.c
2061 M /trunk/samtools/bamtk.c
2064 * make samtools more robust to weird input such as empty file
2066 ------------------------------------------------------------------------
2067 r222 | lh3lh3 | 2009-04-15 09:05:33 -0400 (Wed, 15 Apr 2009) | 2 lines
2069 M /trunk/samtools/ChangeLog
2070 M /trunk/samtools/NEWS
2071 M /trunk/samtools/samtools.1
2073 prepare for release 0.1.3
2075 ------------------------------------------------------------------------
2076 r221 | lh3lh3 | 2009-04-15 08:32:14 -0400 (Wed, 15 Apr 2009) | 2 lines
2078 A /trunk/samtools/misc/blast2sam.pl
2080 convert NCBI-BLASTN to SAM
2082 ------------------------------------------------------------------------
2083 r220 | lh3lh3 | 2009-04-15 08:18:19 -0400 (Wed, 15 Apr 2009) | 3 lines
2085 M /trunk/samtools/bam_lpileup.c
2086 M /trunk/samtools/bamtk.c
2089 * fixed a small memory leak in tview
2091 ------------------------------------------------------------------------
2092 r219 | lh3lh3 | 2009-04-15 08:00:08 -0400 (Wed, 15 Apr 2009) | 3 lines
2094 M /trunk/samtools/bam_rmdup.c
2095 M /trunk/samtools/bamtk.c
2098 * fixed a bug in rmdup when there are unmapped reads
2100 ------------------------------------------------------------------------
2101 r218 | lh3lh3 | 2009-04-14 17:28:58 -0400 (Tue, 14 Apr 2009) | 2 lines
2103 M /trunk/samtools/ChangeLog
2104 M /trunk/samtools/NEWS
2106 proposed NEWS for the new release (have not yet)
2108 ------------------------------------------------------------------------
2109 r216 | lh3lh3 | 2009-04-14 17:10:46 -0400 (Tue, 14 Apr 2009) | 4 lines
2111 M /trunk/samtools/misc/samtools.pl
2114 * improve indelFilter to avoid filtering true indels. The new filter relies
2115 on the new pileup indel line implemented in samtools-0.1.2-25
2117 ------------------------------------------------------------------------
2118 r215 | lh3lh3 | 2009-04-14 17:04:19 -0400 (Tue, 14 Apr 2009) | 4 lines
2120 M /trunk/samtools/bam_maqcns.c
2121 M /trunk/samtools/bam_plcmd.c
2122 M /trunk/samtools/bamtk.c
2123 M /trunk/samtools/samtools.1
2126 * change the pileup indel line to shows the number of alignments actually
2129 ------------------------------------------------------------------------
2130 r211 | lh3lh3 | 2009-04-13 07:07:13 -0400 (Mon, 13 Apr 2009) | 2 lines
2132 M /trunk/samtools/ChangeLog
2134 update ChangeLog from "svn log"
2136 ------------------------------------------------------------------------
2137 r210 | lh3lh3 | 2009-04-12 15:57:05 -0400 (Sun, 12 Apr 2009) | 4 lines
2139 M /trunk/samtools/bam.c
2140 M /trunk/samtools/bam_import.c
2141 M /trunk/samtools/bam_sort.c
2142 M /trunk/samtools/bamtk.c
2143 M /trunk/samtools/kseq.h
2146 * in merge, gives a warning rather than error if the target sequence length is different
2147 * allow empty header
2149 ------------------------------------------------------------------------
2150 r209 | lh3lh3 | 2009-04-12 15:32:44 -0400 (Sun, 12 Apr 2009) | 3 lines
2152 M /trunk/samtools/bam.c
2153 M /trunk/samtools/bam_import.c
2154 M /trunk/samtools/bamtk.c
2157 * recognize '*' at the QUAL field
2159 ------------------------------------------------------------------------
2160 r208 | lh3lh3 | 2009-04-12 15:08:02 -0400 (Sun, 12 Apr 2009) | 3 lines
2162 M /trunk/samtools/bam_import.c
2163 M /trunk/samtools/bamtk.c
2164 M /trunk/samtools/kseq.h
2167 * the field separater is TAB only, now
2169 ------------------------------------------------------------------------
2170 r207 | lh3lh3 | 2009-04-08 10:18:03 -0400 (Wed, 08 Apr 2009) | 2 lines
2172 M /trunk/samtools/examples/ex1.sam.gz
2174 * fixed the problem in the example alignment due to the bug in fixmate
2176 ------------------------------------------------------------------------
2177 r206 | lh3lh3 | 2009-04-08 10:15:05 -0400 (Wed, 08 Apr 2009) | 3 lines
2179 M /trunk/samtools/bam_mate.c
2180 M /trunk/samtools/bamtk.c
2181 M /trunk/samtools/misc/soap2sam.pl
2184 * fixed a nasty bug in `fixmate'
2186 ------------------------------------------------------------------------
2187 r205 | lh3lh3 | 2009-04-08 05:57:08 -0400 (Wed, 08 Apr 2009) | 2 lines
2189 M /trunk/samtools/misc/bowtie2sam.pl
2190 M /trunk/samtools/misc/soap2sam.pl
2191 M /trunk/samtools/misc/wgsim_eval.pl
2193 make the script robust to the bugs in SOAP-2.1.7
2195 ------------------------------------------------------------------------
2196 r200 | lh3lh3 | 2009-04-02 10:14:56 -0400 (Thu, 02 Apr 2009) | 3 lines
2198 M /trunk/samtools/bam_stat.c
2199 M /trunk/samtools/bamtk.c
2202 * check if file is truncated in flagstat
2204 ------------------------------------------------------------------------
2205 r199 | lh3lh3 | 2009-04-02 10:09:10 -0400 (Thu, 02 Apr 2009) | 3 lines
2207 M /trunk/samtools/bamtk.c
2210 * print the header if requested
2212 ------------------------------------------------------------------------
2213 r193 | lh3lh3 | 2009-03-27 11:09:50 -0400 (Fri, 27 Mar 2009) | 3 lines
2215 M /trunk/samtools/bam_plcmd.c
2216 M /trunk/samtools/bamtk.c
2219 * fixed a minor bug reported by Nils Homer
2221 ------------------------------------------------------------------------
2222 r185 | lh3lh3 | 2009-03-24 07:50:32 -0400 (Tue, 24 Mar 2009) | 2 lines
2224 A /trunk/samtools/Makefile (from /trunk/samtools/Makefile.std:184)
2225 D /trunk/samtools/Makefile.std
2226 A /trunk/samtools/misc/Makefile (from /trunk/samtools/misc/Makefile.std:184)
2227 D /trunk/samtools/misc/Makefile.std
2229 rename Makefile.std as Makefile. GNU building systerm is not ready and may take some time...
2231 ------------------------------------------------------------------------
2232 r184 | lh3lh3 | 2009-03-24 06:36:38 -0400 (Tue, 24 Mar 2009) | 4 lines
2234 D /trunk/samtools/Makefile
2235 A /trunk/samtools/Makefile.std (from /trunk/samtools/Makefile:183)
2236 M /trunk/samtools/bam_sort.c
2237 M /trunk/samtools/bam_tview.c
2238 M /trunk/samtools/bamtk.c
2239 D /trunk/samtools/misc/Makefile
2240 A /trunk/samtools/misc/Makefile.std (from /trunk/samtools/misc/Makefile:182)
2241 M /trunk/samtools/samtools.1
2244 * incorporating Nils' changes
2245 * rename Makefile to Makefile.std and prepare to add the GNU building systerms (also by Nils)
2247 ------------------------------------------------------------------------
2248 r183 | lh3lh3 | 2009-03-24 06:30:23 -0400 (Tue, 24 Mar 2009) | 4 lines
2250 M /trunk/samtools/Makefile
2251 M /trunk/samtools/bam_import.c
2252 M /trunk/samtools/bam_maqcns.c
2253 M /trunk/samtools/bam_maqcns.h
2254 M /trunk/samtools/bam_plcmd.c
2255 M /trunk/samtools/bamtk.c
2256 M /trunk/samtools/kseq.h
2257 A /trunk/samtools/kstring.c
2258 A /trunk/samtools/kstring.h
2261 * made pileup take a list of proposed indels. An insertion is N at the moment.
2262 * added my kstring library for a bit complex parsing of the position list.
2264 ------------------------------------------------------------------------
2265 r169 | lh3lh3 | 2009-03-12 09:40:14 -0400 (Thu, 12 Mar 2009) | 3 lines
2267 M /trunk/samtools/misc/soap2sam.pl
2270 * more robust to truncated soap output
2272 ------------------------------------------------------------------------
2273 r168 | lh3lh3 | 2009-03-11 06:49:00 -0400 (Wed, 11 Mar 2009) | 2 lines
2275 M /trunk/samtools/Makefile.lite
2277 added bam_stat.o to Makefile.lite
2279 ------------------------------------------------------------------------
2280 r167 | lh3lh3 | 2009-03-10 18:11:31 -0400 (Tue, 10 Mar 2009) | 3 lines
2282 M /trunk/samtools/bam_maqcns.c
2283 M /trunk/samtools/bamtk.c
2286 * generate RMS of mapQ instead of max mapQ
2288 ------------------------------------------------------------------------
2289 r166 | lh3lh3 | 2009-03-10 18:06:45 -0400 (Tue, 10 Mar 2009) | 3 lines
2291 M /trunk/samtools/bam_plcmd.c
2292 M /trunk/samtools/bamtk.c
2293 M /trunk/samtools/glf.c
2294 M /trunk/samtools/glf.h
2295 M /trunk/samtools/misc/Makefile
2300 ------------------------------------------------------------------------
2301 r159 | lh3lh3 | 2009-03-03 06:26:08 -0500 (Tue, 03 Mar 2009) | 3 lines
2303 M /trunk/samtools/bam_plcmd.c
2304 M /trunk/samtools/bamtk.c
2307 * fixed a minor bug in displaying pileup
2309 ------------------------------------------------------------------------
2310 r158 | lh3lh3 | 2009-03-03 06:24:16 -0500 (Tue, 03 Mar 2009) | 3 lines
2312 M /trunk/samtools/ChangeLog
2313 M /trunk/samtools/bamtk.c
2316 * optionally print SAM header
2318 ------------------------------------------------------------------------
2319 r153 | lh3lh3 | 2009-03-02 05:45:28 -0500 (Mon, 02 Mar 2009) | 3 lines
2321 M /trunk/samtools/bamtk.c
2322 M /trunk/samtools/glf.c
2325 * use "GLF\3" as the magic for GLFv3 files
2327 ------------------------------------------------------------------------
2328 r152 | lh3lh3 | 2009-03-02 05:39:09 -0500 (Mon, 02 Mar 2009) | 5 lines
2330 M /trunk/samtools/Makefile
2331 M /trunk/samtools/bam_import.c
2332 M /trunk/samtools/bam_index.c
2333 M /trunk/samtools/bam_plcmd.c
2334 M /trunk/samtools/bamtk.c
2335 M /trunk/samtools/glf.c
2336 M /trunk/samtools/glf.h
2339 * fixed a bug in import: core.bin is undefined for unmapped reads
2340 * this bug can be alleviated (not completely solved) in bam_index.c
2341 * update to GLFv3: pos is changed to offset for better compression
2343 ------------------------------------------------------------------------
2344 r151 | lh3lh3 | 2009-03-01 10:18:43 -0500 (Sun, 01 Mar 2009) | 3 lines
2346 M /trunk/samtools/misc/wgsim.c
2349 * fixed a bug in simulating indels
2351 ------------------------------------------------------------------------
2352 r145 | lh3lh3 | 2009-02-26 14:43:57 -0500 (Thu, 26 Feb 2009) | 4 lines
2354 M /trunk/samtools/misc/wgsim.c
2357 * allow to print mismatch information as fastq comment. MAQ does
2358 not like long read names.
2360 ------------------------------------------------------------------------
2361 r141 | lh3lh3 | 2009-02-26 09:53:03 -0500 (Thu, 26 Feb 2009) | 6 lines
2363 M /trunk/samtools/ChangeLog
2364 M /trunk/samtools/misc/wgsim.c
2365 M /trunk/samtools/misc/wgsim_eval.pl
2368 * fixed a bug about color read coordinates
2369 * fixed a bug in read names
2370 * wgsim_eval.pl-0.1.3
2371 * make the script work with color reads
2373 ------------------------------------------------------------------------
2374 r140 | lh3lh3 | 2009-02-26 09:02:57 -0500 (Thu, 26 Feb 2009) | 2 lines
2376 M /trunk/samtools/misc/Makefile
2377 M /trunk/samtools/misc/wgsim.c
2379 * wgsim: added a note
2381 ------------------------------------------------------------------------
2382 r139 | lh3lh3 | 2009-02-26 06:39:08 -0500 (Thu, 26 Feb 2009) | 7 lines
2384 M /trunk/samtools/misc/wgsim.c
2385 M /trunk/samtools/misc/wgsim_eval.pl
2388 * considerable code clean up
2389 * print number of substitutions/indels/errors on each read
2390 * potentially support SOLiD simulation, though not tested at the moment
2391 * wgsim_eval.pl-0.1.2
2392 * change in accordant with wgsim
2394 ------------------------------------------------------------------------
2395 r129 | lh3lh3 | 2009-02-18 17:23:27 -0500 (Wed, 18 Feb 2009) | 3 lines
2397 M /trunk/samtools/bam_index.c
2398 M /trunk/samtools/bamtk.c
2401 * fixed a bug in bam_fetch, caused by completely contained adjacent chunks
2403 ------------------------------------------------------------------------
2404 r128 | bhandsaker | 2009-02-18 14:06:57 -0500 (Wed, 18 Feb 2009) | 2 lines
2406 M /trunk/samtools/bamtk.c
2408 Fix annoying segv when invalid region specified.
2410 ------------------------------------------------------------------------
2411 r127 | lh3lh3 | 2009-02-17 05:49:55 -0500 (Tue, 17 Feb 2009) | 2 lines
2413 D /trunk/samtools/misc/indel_filter.pl
2414 A /trunk/samtools/misc/samtools.pl
2416 * move indel_filter.pl to samtools.pl
2418 ------------------------------------------------------------------------
2419 r126 | lh3lh3 | 2009-02-14 16:22:30 -0500 (Sat, 14 Feb 2009) | 3 lines
2421 M /trunk/samtools/bam_mate.c
2422 M /trunk/samtools/bamtk.c
2425 * fixed a bug in fixmate: SE reads are flagged as BAM_FMUNMAP
2427 ------------------------------------------------------------------------
2428 r125 | lh3lh3 | 2009-02-13 04:54:45 -0500 (Fri, 13 Feb 2009) | 3 lines
2430 M /trunk/samtools/bam_stat.c
2431 M /trunk/samtools/bamtk.c
2434 * fixed a minor bug in flagstat
2436 ------------------------------------------------------------------------
2437 r124 | lh3lh3 | 2009-02-12 06:15:32 -0500 (Thu, 12 Feb 2009) | 3 lines
2439 M /trunk/samtools/bam_maqcns.c
2440 M /trunk/samtools/bamtk.c
2441 M /trunk/samtools/misc/indel_filter.pl
2444 * improve indel caller by setting maximum window size
2446 ------------------------------------------------------------------------
2447 r123 | lh3lh3 | 2009-02-12 05:30:29 -0500 (Thu, 12 Feb 2009) | 2 lines
2449 M /trunk/samtools/bam_plcmd.c
2450 M /trunk/samtools/bamtk.c
2452 * output max mapping quality in indel line
2454 ------------------------------------------------------------------------
2455 r122 | lh3lh3 | 2009-02-11 05:59:10 -0500 (Wed, 11 Feb 2009) | 2 lines
2457 M /trunk/samtools/misc/maq2sam.c
2459 fixed a bug in generating tag AM
2461 ------------------------------------------------------------------------
2462 r121 | lh3lh3 | 2009-02-03 05:43:11 -0500 (Tue, 03 Feb 2009) | 2 lines
2464 M /trunk/samtools/bam_index.c
2465 M /trunk/samtools/bamtk.c
2467 fixed a potential memory problem in indexing
2469 ------------------------------------------------------------------------
2470 r120 | bhandsaker | 2009-02-02 10:52:52 -0500 (Mon, 02 Feb 2009) | 2 lines
2472 M /trunk/samtools/Makefile
2474 Pass LIBS to recursive targets to facilitate building at Broad.
2476 ------------------------------------------------------------------------
2477 r119 | lh3lh3 | 2009-02-02 05:12:15 -0500 (Mon, 02 Feb 2009) | 4 lines
2479 M /trunk/samtools/ChangeLog
2480 M /trunk/samtools/bam_plcmd.c
2481 M /trunk/samtools/bam_stat.c
2482 M /trunk/samtools/bamtk.c
2485 * fixed a bug in generating GLFv2 for indels
2486 * improve flagstat report a little bit
2488 ------------------------------------------------------------------------
2489 r118 | lh3lh3 | 2009-01-29 07:33:23 -0500 (Thu, 29 Jan 2009) | 3 lines
2491 M /trunk/samtools/Makefile
2492 A /trunk/samtools/bam_stat.c
2493 M /trunk/samtools/bamtk.c
2496 * added flagstat command
2498 ------------------------------------------------------------------------
2499 r116 | lh3lh3 | 2009-01-28 08:31:12 -0500 (Wed, 28 Jan 2009) | 2 lines
2501 M /trunk/samtools/ChangeLog
2502 M /trunk/samtools/NEWS
2503 M /trunk/samtools/bamtk.c
2504 M /trunk/samtools/samtools.1
2506 Release SAMtools-0.1.2
2508 ------------------------------------------------------------------------
2509 r115 | lh3lh3 | 2009-01-28 07:54:08 -0500 (Wed, 28 Jan 2009) | 2 lines
2511 A /trunk/samtools/misc/indel_filter.pl
2513 Script for filtering indel results
2515 ------------------------------------------------------------------------
2516 r114 | lh3lh3 | 2009-01-25 06:45:37 -0500 (Sun, 25 Jan 2009) | 2 lines
2518 A /trunk/samtools/misc/zoom2sam.pl
2522 ------------------------------------------------------------------------
2523 r113 | lh3lh3 | 2009-01-24 09:25:07 -0500 (Sat, 24 Jan 2009) | 2 lines
2525 A /trunk/samtools/misc/novo2sam.pl
2527 add a script to convert novo alignment to SAM
2529 ------------------------------------------------------------------------
2530 r112 | lh3lh3 | 2009-01-23 15:57:39 -0500 (Fri, 23 Jan 2009) | 2 lines
2532 M /trunk/samtools/ChangeLog
2533 M /trunk/samtools/ChangeLog.old
2534 M /trunk/samtools/samtools.1
2536 update documentation and ChangeLog
2538 ------------------------------------------------------------------------
2539 r111 | lh3lh3 | 2009-01-23 14:22:59 -0500 (Fri, 23 Jan 2009) | 3 lines
2541 M /trunk/samtools/bam_sort.c
2542 M /trunk/samtools/bamtk.c
2545 * fixed a bug in "merge" command line
2547 ------------------------------------------------------------------------
2548 r110 | lh3lh3 | 2009-01-22 10:36:48 -0500 (Thu, 22 Jan 2009) | 3 lines
2550 M /trunk/samtools/misc/Makefile
2551 A /trunk/samtools/misc/bowtie2sam.pl (from /branches/dev/samtools/misc/bowtie2sam.pl:108)
2552 M /trunk/samtools/misc/export2sam.pl
2553 A /trunk/samtools/misc/soap2sam.pl (from /branches/dev/samtools/misc/soap2sam.pl:108)
2554 A /trunk/samtools/misc/wgsim.c (from /branches/dev/samtools/misc/wgsim.c:108)
2555 A /trunk/samtools/misc/wgsim_eval.pl (from /branches/dev/samtools/misc/wgsim_eval.pl:108)
2557 * merge from branches/dev/
2558 * all future development will happen here
2560 ------------------------------------------------------------------------
2561 r109 | lh3lh3 | 2009-01-22 10:14:27 -0500 (Thu, 22 Jan 2009) | 3 lines
2563 M /trunk/samtools/COPYING
2564 M /trunk/samtools/ChangeLog
2565 A /trunk/samtools/INSTALL (from /branches/dev/samtools/INSTALL:108)
2566 M /trunk/samtools/Makefile
2567 A /trunk/samtools/Makefile.lite (from /branches/dev/samtools/Makefile.lite:108)
2568 M /trunk/samtools/bam.c
2569 M /trunk/samtools/bam.h
2570 M /trunk/samtools/bam_import.c
2571 M /trunk/samtools/bam_index.c
2572 M /trunk/samtools/bam_lpileup.c
2573 M /trunk/samtools/bam_maqcns.c
2574 M /trunk/samtools/bam_maqcns.h
2575 A /trunk/samtools/bam_mate.c (from /branches/dev/samtools/bam_mate.c:108)
2576 M /trunk/samtools/bam_pileup.c
2577 M /trunk/samtools/bam_plcmd.c
2578 A /trunk/samtools/bam_rmdup.c (from /branches/dev/samtools/bam_rmdup.c:108)
2579 M /trunk/samtools/bam_sort.c
2580 M /trunk/samtools/bamtk.c
2581 M /trunk/samtools/bgzf.h
2582 M /trunk/samtools/examples/00README.txt
2583 A /trunk/samtools/examples/Makefile (from /branches/dev/samtools/examples/Makefile:108)
2584 D /trunk/samtools/examples/ex1.fa.fai
2585 M /trunk/samtools/examples/ex1.sam.gz
2586 M /trunk/samtools/faidx.c
2587 A /trunk/samtools/glf.c (from /branches/dev/samtools/glf.c:108)
2588 M /trunk/samtools/glf.h
2589 M /trunk/samtools/misc/Makefile
2590 M /trunk/samtools/misc/maq2sam.c
2591 M /trunk/samtools/razf.c
2592 M /trunk/samtools/source.dot
2594 * Merge from branches/dev/
2595 * all future development will happen here at trunk/
2597 ------------------------------------------------------------------------
2598 r79 | bhandsaker | 2009-01-07 16:42:15 -0500 (Wed, 07 Jan 2009) | 2 lines
2600 M /trunk/samtools/bam_maqcns.c
2601 M /trunk/samtools/bam_tview.c
2603 Fix problem with compiling without curses.
2605 ------------------------------------------------------------------------
2606 r63 | lh3lh3 | 2008-12-22 10:58:02 -0500 (Mon, 22 Dec 2008) | 2 lines
2608 A /trunk/samtools (from /branches/dev/samtools:62)
2612 ------------------------------------------------------------------------
2613 r62 | lh3lh3 | 2008-12-22 10:55:13 -0500 (Mon, 22 Dec 2008) | 2 lines
2615 A /branches/dev/samtools/NEWS
2616 M /branches/dev/samtools/bamtk.c
2617 M /branches/dev/samtools/samtools.1
2619 Release samtools-0.1.1
2621 ------------------------------------------------------------------------
2622 r61 | lh3lh3 | 2008-12-22 10:46:08 -0500 (Mon, 22 Dec 2008) | 10 lines
2624 M /branches/dev/samtools/bam_aux.c
2625 M /branches/dev/samtools/bam_index.c
2626 M /branches/dev/samtools/bam_plcmd.c
2627 M /branches/dev/samtools/bam_tview.c
2628 M /branches/dev/samtools/bamtk.c
2629 M /branches/dev/samtools/razf.c
2630 M /branches/dev/samtools/samtools.1
2633 * fixed a bug in razf.c: reset z_eof when razf_seek() is called
2634 * fixed a memory leak in parsing a region
2635 * changed pileup a little bit when -s is in use: output ^ and $
2636 * when a bam is not indexed, output more meaningful error message
2637 * fixed a bug in indexing for small alignment
2638 * fixed a bug in the viewer when we come to the end of a reference file
2639 * updated documentation
2640 * prepare to release 0.1.1
2642 ------------------------------------------------------------------------
2643 r60 | lh3lh3 | 2008-12-22 10:10:16 -0500 (Mon, 22 Dec 2008) | 2 lines
2645 A /branches/dev/samtools/examples
2646 A /branches/dev/samtools/examples/00README.txt
2647 A /branches/dev/samtools/examples/ex1.fa
2648 A /branches/dev/samtools/examples/ex1.fa.fai
2649 A /branches/dev/samtools/examples/ex1.sam.gz
2653 ------------------------------------------------------------------------
2654 r59 | lh3lh3 | 2008-12-22 04:38:15 -0500 (Mon, 22 Dec 2008) | 2 lines
2656 M /branches/dev/samtools/ChangeLog
2660 ------------------------------------------------------------------------
2661 r58 | lh3lh3 | 2008-12-20 18:06:00 -0500 (Sat, 20 Dec 2008) | 3 lines
2663 M /branches/dev/samtools/misc/export2sam.pl
2666 * fixed several bugs
2668 ------------------------------------------------------------------------
2669 r57 | lh3lh3 | 2008-12-20 10:44:20 -0500 (Sat, 20 Dec 2008) | 2 lines
2671 A /branches/dev/samtools/misc/export2sam.pl
2673 convert Export format to SAM; not thoroughly tested
2675 ------------------------------------------------------------------------
2676 r56 | lh3lh3 | 2008-12-19 17:13:28 -0500 (Fri, 19 Dec 2008) | 6 lines
2678 M /branches/dev/samtools/bam_import.c
2679 M /branches/dev/samtools/bam_plcmd.c
2680 M /branches/dev/samtools/bam_tview.c
2681 M /branches/dev/samtools/bamtk.c
2682 A /branches/dev/samtools/source.dot
2685 * pileup: generate maq-like simple output
2686 * pileup: allow to output pileup at required sites
2687 * source.dot: source file relationship graph
2688 * tview: fixed a minor bug
2690 ------------------------------------------------------------------------
2691 r55 | lh3lh3 | 2008-12-19 15:10:26 -0500 (Fri, 19 Dec 2008) | 2 lines
2693 D /branches/dev/samtools/misc/all2sam.pl
2697 ------------------------------------------------------------------------
2698 r54 | lh3lh3 | 2008-12-16 17:34:25 -0500 (Tue, 16 Dec 2008) | 2 lines
2700 A /branches/dev/samtools/COPYING
2701 M /branches/dev/samtools/bam.h
2702 M /branches/dev/samtools/faidx.h
2703 M /branches/dev/samtools/khash.h
2704 M /branches/dev/samtools/kseq.h
2705 M /branches/dev/samtools/ksort.h
2706 M /branches/dev/samtools/samtools.1
2708 Added copyright information and a bit more documentation. No code change.
2710 ------------------------------------------------------------------------
2711 r53 | lh3lh3 | 2008-12-16 08:40:18 -0500 (Tue, 16 Dec 2008) | 3 lines
2713 M /branches/dev/samtools/bam.c
2714 M /branches/dev/samtools/bam.h
2715 M /branches/dev/samtools/bam_index.c
2716 M /branches/dev/samtools/bam_maqcns.c
2717 M /branches/dev/samtools/bamtk.c
2720 * improved efficiency of the indel caller for spliced alignments
2722 ------------------------------------------------------------------------
2723 r52 | lh3lh3 | 2008-12-16 05:28:20 -0500 (Tue, 16 Dec 2008) | 3 lines
2725 M /branches/dev/samtools/bam.c
2726 M /branches/dev/samtools/bam.h
2727 M /branches/dev/samtools/bam_aux.c
2728 M /branches/dev/samtools/bam_index.c
2729 M /branches/dev/samtools/bamtk.c
2732 * a bit code cleanup: reduce the dependency between source files
2734 ------------------------------------------------------------------------
2735 r51 | lh3lh3 | 2008-12-15 09:29:32 -0500 (Mon, 15 Dec 2008) | 3 lines
2737 M /branches/dev/samtools/bam_maqcns.c
2738 M /branches/dev/samtools/bam_plcmd.c
2739 M /branches/dev/samtools/bamtk.c
2742 * fixed a memory leak
2744 ------------------------------------------------------------------------
2745 r50 | lh3lh3 | 2008-12-15 09:00:13 -0500 (Mon, 15 Dec 2008) | 2 lines
2747 M /branches/dev/samtools/ChangeLog
2748 M /branches/dev/samtools/bam.h
2749 M /branches/dev/samtools/samtools.1
2751 update documentation, ChangeLog and a comment
2753 ------------------------------------------------------------------------
2754 r49 | lh3lh3 | 2008-12-15 08:36:43 -0500 (Mon, 15 Dec 2008) | 6 lines
2756 M /branches/dev/samtools/Makefile
2757 M /branches/dev/samtools/bam.h
2758 M /branches/dev/samtools/bam_maqcns.c
2759 M /branches/dev/samtools/bam_maqcns.h
2760 M /branches/dev/samtools/bam_pileup.c
2761 A /branches/dev/samtools/bam_plcmd.c
2762 M /branches/dev/samtools/bamtk.c
2763 M /branches/dev/samtools/samtools.1
2766 * moved pileup command to a separate source file
2767 * added indel caller
2768 * added bam_cal_segend(). (NOT WORKING for spliced alignment!!!)
2769 * updated documentation
2771 ------------------------------------------------------------------------
2772 r48 | lh3lh3 | 2008-12-12 08:55:36 -0500 (Fri, 12 Dec 2008) | 3 lines
2774 M /branches/dev/samtools/bam_maqcns.c
2775 M /branches/dev/samtools/bamtk.c
2778 * fixed another bug in maqcns when there is a nearby deletion
2780 ------------------------------------------------------------------------
2781 r47 | lh3lh3 | 2008-12-12 08:42:16 -0500 (Fri, 12 Dec 2008) | 5 lines
2783 M /branches/dev/samtools/bam_maqcns.c
2784 M /branches/dev/samtools/bam_pileup.c
2785 M /branches/dev/samtools/bamtk.c
2788 * pileup: outputing consensus is now optional
2789 * fixed a bug in glfgen. This bug also exists in maq's glfgen. However,
2790 I am not quite sure why the previous version may have problem.
2792 ------------------------------------------------------------------------
2793 r46 | lh3lh3 | 2008-12-12 06:44:56 -0500 (Fri, 12 Dec 2008) | 6 lines
2795 M /branches/dev/samtools/bam_pileup.c
2796 M /branches/dev/samtools/bamtk.c
2799 * add maq consensus to pileup. However, I will move this part to a new
2800 command as strictly speaking, consensus callin is not part of pileup,
2801 and imposing it would make it harder to generate for other language
2804 ------------------------------------------------------------------------
2805 r45 | bhandsaker | 2008-12-11 15:43:56 -0500 (Thu, 11 Dec 2008) | 2 lines
2807 M /branches/dev/samtools/bgzf.c
2809 Fix bug in tell() after reads that consume to the exact end of a block.
2811 ------------------------------------------------------------------------
2812 r44 | lh3lh3 | 2008-12-11 04:36:53 -0500 (Thu, 11 Dec 2008) | 2 lines
2814 M /branches/dev/samtools/samtools.1
2818 ------------------------------------------------------------------------
2819 r43 | lh3lh3 | 2008-12-11 04:25:36 -0500 (Thu, 11 Dec 2008) | 4 lines
2821 M /branches/dev/samtools/bam_import.c
2822 M /branches/dev/samtools/bamtk.c
2825 * fixed a bug in parser when there is auxiliary fields
2826 * made the parser a bit more robust
2828 ------------------------------------------------------------------------
2829 r42 | lh3lh3 | 2008-12-10 09:57:29 -0500 (Wed, 10 Dec 2008) | 5 lines
2831 M /branches/dev/samtools/bam_index.c
2832 M /branches/dev/samtools/bamtk.c
2833 M /branches/dev/samtools/bgzf.c
2836 * fixed a bug in bgzf (only reading is affected)
2837 * fixed a typo in bam_index.c
2838 * in bam_index.c, check potential bugs in the underlying I/O library
2840 ------------------------------------------------------------------------
2841 r41 | lh3lh3 | 2008-12-10 07:53:08 -0500 (Wed, 10 Dec 2008) | 2 lines
2843 M /branches/dev/samtools/samtools.1
2847 ------------------------------------------------------------------------
2848 r40 | lh3lh3 | 2008-12-10 06:52:10 -0500 (Wed, 10 Dec 2008) | 5 lines
2850 M /branches/dev/samtools/bam.h
2851 M /branches/dev/samtools/bam_pileup.c
2852 M /branches/dev/samtools/bamtk.c
2855 * tried to make pileup work with clipping (previously not), though NOT tested
2856 * removed -v from pileup
2857 * made pileup take the reference sequence
2859 ------------------------------------------------------------------------
2860 r39 | lh3lh3 | 2008-12-09 06:59:28 -0500 (Tue, 09 Dec 2008) | 4 lines
2862 M /branches/dev/samtools/bam_import.c
2863 M /branches/dev/samtools/bamtk.c
2864 M /branches/dev/samtools/samtools.1
2867 * in parser, recognize "=", rather than ",", as a match
2868 * in parser, correctl parse "=" at the MRNM field.
2870 ------------------------------------------------------------------------
2871 r38 | lh3lh3 | 2008-12-09 06:39:07 -0500 (Tue, 09 Dec 2008) | 2 lines
2873 M /branches/dev/samtools/misc/maq2sam.c
2875 fixed a bug in handling maq flag 64 and 192
2877 ------------------------------------------------------------------------
2878 r37 | lh3lh3 | 2008-12-09 04:53:46 -0500 (Tue, 09 Dec 2008) | 2 lines
2880 M /branches/dev/samtools/misc/md5fa.c
2882 also calculate unordered md5sum check
2884 ------------------------------------------------------------------------
2885 r36 | lh3lh3 | 2008-12-09 04:46:21 -0500 (Tue, 09 Dec 2008) | 2 lines
2887 M /branches/dev/samtools/misc/md5fa.c
2889 fixed a minor bug when there are space in the sequence
2891 ------------------------------------------------------------------------
2892 r35 | lh3lh3 | 2008-12-09 04:40:45 -0500 (Tue, 09 Dec 2008) | 2 lines
2894 M /branches/dev/samtools/misc/md5fa.c
2896 fixed a potential memory leak
2898 ------------------------------------------------------------------------
2899 r34 | lh3lh3 | 2008-12-08 09:52:17 -0500 (Mon, 08 Dec 2008) | 2 lines
2901 M /branches/dev/samtools/bam_import.c
2902 M /branches/dev/samtools/bam_index.c
2903 M /branches/dev/samtools/bamtk.c
2905 * fixed a bug in import: bin is wrongly calculated
2907 ------------------------------------------------------------------------
2908 r33 | lh3lh3 | 2008-12-08 09:08:01 -0500 (Mon, 08 Dec 2008) | 2 lines
2910 M /branches/dev/samtools/misc/all2sam.pl
2914 ------------------------------------------------------------------------
2915 r32 | lh3lh3 | 2008-12-08 07:56:02 -0500 (Mon, 08 Dec 2008) | 3 lines
2917 M /branches/dev/samtools/Makefile
2918 M /branches/dev/samtools/kseq.h
2919 M /branches/dev/samtools/misc/Makefile
2920 A /branches/dev/samtools/misc/md5.c
2921 A /branches/dev/samtools/misc/md5.h
2922 A /branches/dev/samtools/misc/md5fa.c
2924 * fixed two warnings in kseq.h
2925 * added md5sum utilities
2927 ------------------------------------------------------------------------
2928 r31 | lh3lh3 | 2008-12-08 06:35:29 -0500 (Mon, 08 Dec 2008) | 5 lines
2930 M /branches/dev/samtools/Makefile
2931 M /branches/dev/samtools/bam_import.c
2932 M /branches/dev/samtools/bamtk.c
2933 A /branches/dev/samtools/kseq.h
2934 D /branches/dev/samtools/kstream.h
2937 * replace kstream with kseq. kseq is a superset of kstream. I need the
2938 extra functions in kseq.h.
2939 * also compile stand-alone faidx
2941 ------------------------------------------------------------------------
2942 r30 | lh3lh3 | 2008-12-08 06:17:04 -0500 (Mon, 08 Dec 2008) | 3 lines
2944 M /branches/dev/samtools/bam.h
2945 M /branches/dev/samtools/bam_sort.c
2946 M /branches/dev/samtools/bamtk.c
2949 * sorting by read names is available
2951 ------------------------------------------------------------------------
2952 r29 | lh3lh3 | 2008-12-08 05:29:02 -0500 (Mon, 08 Dec 2008) | 3 lines
2954 M /branches/dev/samtools/bam.c
2955 M /branches/dev/samtools/bam.h
2956 M /branches/dev/samtools/bam_import.c
2957 M /branches/dev/samtools/bam_maqcns.c
2958 M /branches/dev/samtools/bam_pileup.c
2959 M /branches/dev/samtools/bam_sort.c
2960 M /branches/dev/samtools/bam_tview.c
2961 M /branches/dev/samtools/bamtk.c
2962 M /branches/dev/samtools/misc/maq2sam.c
2965 * format change to meet the latest specification
2967 ------------------------------------------------------------------------
2968 r28 | lh3lh3 | 2008-12-04 11:09:21 -0500 (Thu, 04 Dec 2008) | 3 lines
2970 M /branches/dev/samtools/bam_maqcns.c
2971 M /branches/dev/samtools/misc/maq2sam.c
2973 * minor change in maqcns: special care when n==0
2974 * change maq2sam to meet the latest specification
2976 ------------------------------------------------------------------------
2977 r27 | lh3lh3 | 2008-12-04 10:55:44 -0500 (Thu, 04 Dec 2008) | 2 lines
2979 M /branches/dev/samtools/razf.c
2980 M /branches/dev/samtools/razf.h
2982 considerable code clean up in razf
2984 ------------------------------------------------------------------------
2985 r26 | lh3lh3 | 2008-12-04 10:08:18 -0500 (Thu, 04 Dec 2008) | 2 lines
2987 M /branches/dev/samtools/ChangeLog
2988 M /branches/dev/samtools/Makefile
2989 M /branches/dev/samtools/faidx.c
2991 make RAZF optional in faidx.c
2993 ------------------------------------------------------------------------
2994 r25 | lh3lh3 | 2008-12-01 10:27:22 -0500 (Mon, 01 Dec 2008) | 3 lines
2996 M /branches/dev/samtools/Makefile
2997 M /branches/dev/samtools/bam.h
2998 M /branches/dev/samtools/bam_aux.c
2999 M /branches/dev/samtools/bamtk.c
3000 M /branches/dev/samtools/samtools.1
3003 * added routines for retrieving aux data, NOT TESTED YET!
3005 ------------------------------------------------------------------------
3006 r24 | lh3lh3 | 2008-12-01 09:29:43 -0500 (Mon, 01 Dec 2008) | 5 lines
3008 M /branches/dev/samtools/bam.c
3009 M /branches/dev/samtools/bam_import.c
3010 M /branches/dev/samtools/bam_maqcns.c
3011 M /branches/dev/samtools/bamtk.c
3012 M /branches/dev/samtools/bgzf.c
3013 M /branches/dev/samtools/samtools.1
3016 * bgzf: fixed a potential integer overflow on 32-it machines
3017 * maqcns: set the minimum combined quality as 0
3018 * supporting hex strings
3020 ------------------------------------------------------------------------
3021 r23 | lh3lh3 | 2008-11-27 12:14:37 -0500 (Thu, 27 Nov 2008) | 3 lines
3023 M /branches/dev/samtools/bam_maqcns.c
3024 M /branches/dev/samtools/bamtk.c
3027 * fixed the bug in maqcns
3029 ------------------------------------------------------------------------
3030 r22 | lh3lh3 | 2008-11-27 12:08:11 -0500 (Thu, 27 Nov 2008) | 3 lines
3032 M /branches/dev/samtools/Makefile
3033 M /branches/dev/samtools/bam.h
3034 A /branches/dev/samtools/bam_maqcns.c
3035 A /branches/dev/samtools/bam_maqcns.h
3036 M /branches/dev/samtools/bam_tview.c
3037 M /branches/dev/samtools/bamtk.c
3038 A /branches/dev/samtools/glf.h
3041 * add MAQ consensus caller, currently BUGGY!
3043 ------------------------------------------------------------------------
3044 r21 | lh3lh3 | 2008-11-27 08:51:28 -0500 (Thu, 27 Nov 2008) | 4 lines
3046 M /branches/dev/samtools/bam_pileup.c
3047 M /branches/dev/samtools/bam_tview.c
3048 M /branches/dev/samtools/bamtk.c
3051 * tview: display padded alignment (but not P operation)
3052 * better coordinates and reference sequence
3054 ------------------------------------------------------------------------
3055 r19 | lh3lh3 | 2008-11-27 04:26:05 -0500 (Thu, 27 Nov 2008) | 2 lines
3057 A /branches/dev/samtools/ChangeLog
3061 ------------------------------------------------------------------------
3062 r18 | lh3lh3 | 2008-11-27 04:24:45 -0500 (Thu, 27 Nov 2008) | 3 lines
3064 D /branches/dev/samtools/ChangeLog
3065 A /branches/dev/samtools/ChangeLog.old (from /branches/dev/samtools/ChangeLog:6)
3067 Rename ChangeLog to ChangeLog.old. This old ChangeLog is generated from
3068 the log of my personal SVN repository.
3070 ------------------------------------------------------------------------
3071 r17 | lh3lh3 | 2008-11-27 04:22:55 -0500 (Thu, 27 Nov 2008) | 6 lines
3073 M /branches/dev/samtools/Makefile
3074 M /branches/dev/samtools/bamtk.c
3075 M /branches/dev/samtools/bgzf.c
3078 * declare fseeko and ftello as some Linux may not do this by default and
3079 missing these declarations will make bgzf buggy
3080 * get rid of some harmless warings
3081 * use BGZF by default, now
3083 ------------------------------------------------------------------------
3084 r16 | lh3lh3 | 2008-11-26 16:19:11 -0500 (Wed, 26 Nov 2008) | 4 lines
3086 M /branches/dev/samtools/bam_index.c
3087 M /branches/dev/samtools/bamtk.c
3088 M /branches/dev/samtools/razf.c
3091 * fixed a bug in razf_read()
3092 * give more warnings when the file is truncated (or due to bugs in I/O library)
3094 ------------------------------------------------------------------------
3095 r15 | lh3lh3 | 2008-11-26 15:41:39 -0500 (Wed, 26 Nov 2008) | 2 lines
3097 M /branches/dev/samtools/bgzf.c
3099 fixed a bug in bgzf.c at the end of the file
3101 ------------------------------------------------------------------------
3102 r14 | lh3lh3 | 2008-11-26 12:05:18 -0500 (Wed, 26 Nov 2008) | 4 lines
3104 M /branches/dev/samtools/bamtk.c
3107 * a lot happened to RAZF, although samtools itself is untouched. Better
3108 also update the version number anyway to avoid confusion
3110 ------------------------------------------------------------------------
3111 r13 | lh3lh3 | 2008-11-26 12:03:48 -0500 (Wed, 26 Nov 2008) | 2 lines
3113 M /branches/dev/samtools/razf.c
3115 a change from Jue, but I think it should not matter
3117 ------------------------------------------------------------------------
3118 r12 | lh3lh3 | 2008-11-26 11:48:14 -0500 (Wed, 26 Nov 2008) | 3 lines
3120 M /branches/dev/samtools/razf.c
3122 fixed a potential bug in razf. However, it seems still buggy, just
3123 rarely happens, very rarely.
3125 ------------------------------------------------------------------------
3126 r11 | lh3lh3 | 2008-11-26 09:02:56 -0500 (Wed, 26 Nov 2008) | 2 lines
3128 M /branches/dev/samtools/razf.c
3130 fixed a bug in razf, with the help of Jue
3132 ------------------------------------------------------------------------
3133 r10 | lh3lh3 | 2008-11-26 06:55:32 -0500 (Wed, 26 Nov 2008) | 2 lines
3135 M /branches/dev/samtools/bam_index.c
3139 ------------------------------------------------------------------------
3140 r9 | lh3lh3 | 2008-11-26 06:37:05 -0500 (Wed, 26 Nov 2008) | 2 lines
3142 M /branches/dev/samtools/Makefile
3143 M /branches/dev/samtools/bam.h
3144 M /branches/dev/samtools/razf.c
3145 M /branches/dev/samtools/razf.h
3147 * Jue has updated razf to realize Bob's scheme
3149 ------------------------------------------------------------------------
3150 r7 | lh3lh3 | 2008-11-25 15:37:37 -0500 (Tue, 25 Nov 2008) | 2 lines
3152 A /branches/dev/samtools/samtools.1
3156 ------------------------------------------------------------------------
3157 r6 | lh3lh3 | 2008-11-25 15:37:16 -0500 (Tue, 25 Nov 2008) | 3 lines
3159 A /branches/dev/samtools/ChangeLog
3160 A /branches/dev/samtools/Makefile
3161 A /branches/dev/samtools/bam.c
3162 A /branches/dev/samtools/bam.h
3163 A /branches/dev/samtools/bam_aux.c
3164 A /branches/dev/samtools/bam_endian.h
3165 A /branches/dev/samtools/bam_import.c
3166 A /branches/dev/samtools/bam_index.c
3167 A /branches/dev/samtools/bam_lpileup.c
3168 A /branches/dev/samtools/bam_pileup.c
3169 A /branches/dev/samtools/bam_sort.c
3170 A /branches/dev/samtools/bam_tview.c
3171 A /branches/dev/samtools/bamtk.c
3172 A /branches/dev/samtools/bgzf.c
3173 A /branches/dev/samtools/bgzf.h
3174 A /branches/dev/samtools/bgzip.c
3175 A /branches/dev/samtools/faidx.c
3176 A /branches/dev/samtools/faidx.h
3177 A /branches/dev/samtools/khash.h
3178 A /branches/dev/samtools/ksort.h
3179 A /branches/dev/samtools/kstream.h
3180 A /branches/dev/samtools/misc
3181 A /branches/dev/samtools/misc/Makefile
3182 A /branches/dev/samtools/misc/all2sam.pl
3183 A /branches/dev/samtools/misc/maq2sam.c
3184 A /branches/dev/samtools/razf.c
3185 A /branches/dev/samtools/razf.h
3186 A /branches/dev/samtools/razip.c
3187 A /branches/dev/samtools/zutil.h
3189 The initial version of samtools, replicated from my local SVN repository.
3190 The current version is: 0.1.0-42. All future development will happen here.
3192 ------------------------------------------------------------------------
3193 r5 | lh3lh3 | 2008-11-25 15:30:49 -0500 (Tue, 25 Nov 2008) | 2 lines
3195 A /branches/dev/samtools
3197 samtools (C version)
3199 ------------------------------------------------------------------------