1 ------------------------------------------------------------------------
2 r509 | lh3lh3 | 2009-11-06 09:17:09 -0500 (Fri, 06 Nov 2009) | 3 lines
4 M /trunk/samtools/bam_plcmd.c
5 M /trunk/samtools/bamtk.c
7 * samtools-0.1.6-22 (r509)
8 * forget to fix a similar problem in glfgen
10 ------------------------------------------------------------------------
11 r508 | lh3lh3 | 2009-11-06 09:06:40 -0500 (Fri, 06 Nov 2009) | 3 lines
13 M /trunk/samtools/bam_maqcns.c
14 M /trunk/samtools/bam_plcmd.c
15 M /trunk/samtools/bamtk.c
16 M /trunk/samtools/sam_view.c
18 * samtools-0.1.6-21 (r508)
19 * fixed a potential bug in the indel caller towards the end of a chromosome
21 ------------------------------------------------------------------------
22 r494 | lh3lh3 | 2009-10-26 11:38:00 -0400 (Mon, 26 Oct 2009) | 3 lines
24 M /trunk/samtools/bamtk.c
25 M /trunk/samtools/sam_view.c
27 * samtools-0.1.6-19 (r494)
28 * allow to convert Illumina quality (64 based) to the BAM quality
30 ------------------------------------------------------------------------
31 r493 | lh3lh3 | 2009-10-26 10:24:39 -0400 (Mon, 26 Oct 2009) | 4 lines
33 M /trunk/samtools/Makefile
34 M /trunk/samtools/bam.c
35 M /trunk/samtools/bam_import.c
36 M /trunk/samtools/bamtk.c
37 M /trunk/samtools/sam.c
38 M /trunk/samtools/sam_header.c
40 * samtools-0.1.6-18 (r493)
41 * fixed the bugs due to improperly incorporating Petr's header parser
42 * a little code clean up in sam_header.c
44 ------------------------------------------------------------------------
45 r492 | petulda | 2009-10-24 09:43:25 -0400 (Sat, 24 Oct 2009) | 1 line
47 M /trunk/samtools/sam_header.c
49 Added sam_header_line_free call for sam_header_parse2
50 ------------------------------------------------------------------------
51 r491 | lh3lh3 | 2009-10-24 00:50:16 -0400 (Sat, 24 Oct 2009) | 3 lines
53 M /trunk/samtools/sam_view.c
58 ------------------------------------------------------------------------
59 r490 | lh3lh3 | 2009-10-24 00:45:12 -0400 (Sat, 24 Oct 2009) | 4 lines
61 M /trunk/samtools/bam.c
62 M /trunk/samtools/bam.h
63 M /trunk/samtools/bam_import.c
64 M /trunk/samtools/sam.c
67 * improved the interface a bit
70 ------------------------------------------------------------------------
71 r489 | lh3lh3 | 2009-10-24 00:41:50 -0400 (Sat, 24 Oct 2009) | 3 lines
73 M /trunk/samtools/bam_import.c
74 M /trunk/samtools/sam_header.c
75 M /trunk/samtools/sam_header.h
77 * BUGGY VERSION. Please NOT use it.
78 * Fixed a minor bug, but the major bug is still there.
80 ------------------------------------------------------------------------
81 r488 | lh3lh3 | 2009-10-24 00:17:10 -0400 (Sat, 24 Oct 2009) | 3 lines
83 M /trunk/samtools/Makefile
84 M /trunk/samtools/bam.c
85 M /trunk/samtools/bam.h
86 M /trunk/samtools/bam_aux.c
87 M /trunk/samtools/bam_import.c
88 M /trunk/samtools/bam_rmdup.c
89 M /trunk/samtools/bam_rmdupse.c
90 M /trunk/samtools/kaln.c
91 M /trunk/samtools/sam.c
92 M /trunk/samtools/sam_header.c
93 M /trunk/samtools/sam_header.h
94 M /trunk/samtools/sam_view.c
96 * This revision is SERIOUSLY BUGGY. Please NOT use it.
97 * Start to incorporate header parsing from Petr Danecek
99 ------------------------------------------------------------------------
100 r487 | petulda | 2009-10-23 11:44:32 -0400 (Fri, 23 Oct 2009) | 1 line
102 M /trunk/samtools/sam_header.c
103 M /trunk/samtools/sam_header.h
105 Now possible to merge multiple HeaderDict dictionaries
106 ------------------------------------------------------------------------
107 r486 | petulda | 2009-10-22 11:46:58 -0400 (Thu, 22 Oct 2009) | 1 line
109 M /trunk/samtools/sam_header.c
112 ------------------------------------------------------------------------
113 r485 | petulda | 2009-10-22 11:41:56 -0400 (Thu, 22 Oct 2009) | 1 line
115 A /trunk/samtools/sam_header.c
116 A /trunk/samtools/sam_header.h
119 ------------------------------------------------------------------------
120 r484 | lh3lh3 | 2009-10-19 14:31:32 -0400 (Mon, 19 Oct 2009) | 5 lines
122 M /trunk/samtools/bam_import.c
123 M /trunk/samtools/bam_rmdupse.c
124 M /trunk/samtools/bamtk.c
125 M /trunk/samtools/examples/Makefile
127 * samtools-0.1.6-17 (r484)
128 * fixed a memory leak in rmdupse
129 * fixed a bug in parsing @RG header lines
130 * test rmdup in examples/
132 ------------------------------------------------------------------------
133 r483 | lh3lh3 | 2009-10-19 13:22:48 -0400 (Mon, 19 Oct 2009) | 4 lines
135 M /trunk/samtools/bam_rmdup.c
136 M /trunk/samtools/bam_rmdupse.c
137 M /trunk/samtools/bamtk.c
139 * samtools-0.1.6-16 (r483)
140 * unify the interface of rmdup and rmdupse
141 * a new bug found in rg2lib(). Have not been fixed yet.
143 ------------------------------------------------------------------------
144 r482 | lh3lh3 | 2009-10-19 13:03:34 -0400 (Mon, 19 Oct 2009) | 4 lines
146 M /trunk/samtools/bam.h
147 M /trunk/samtools/bam_rmdup.c
148 M /trunk/samtools/bam_rmdupse.c
149 M /trunk/samtools/bamtk.c
150 A /trunk/samtools/klist.h
152 * samtools-0.1.6-15 (r482)
154 * rmdupse is now library aware
156 ------------------------------------------------------------------------
157 r481 | lh3lh3 | 2009-10-18 00:07:21 -0400 (Sun, 18 Oct 2009) | 3 lines
159 M /trunk/samtools/bam_rmdup.c
160 M /trunk/samtools/bamtk.c
162 * samtools-0.1.6-14 (r480)
163 * rmdup is now RG aware
165 ------------------------------------------------------------------------
166 r480 | lh3lh3 | 2009-10-17 22:05:20 -0400 (Sat, 17 Oct 2009) | 2 lines
168 M /trunk/samtools/misc/samtools.pl
170 added a small unitity to parse SRA XML files
172 ------------------------------------------------------------------------
173 r479 | lh3lh3 | 2009-10-17 20:57:26 -0400 (Sat, 17 Oct 2009) | 3 lines
175 M /trunk/samtools/bam_maqcns.c
176 M /trunk/samtools/bam_maqcns.h
177 M /trunk/samtools/bam_plcmd.c
178 M /trunk/samtools/bam_sort.c
179 M /trunk/samtools/bamtk.c
181 * samtools-0.1.6-13 (r479)
182 * merge: optionally use file names as RG tags
184 ------------------------------------------------------------------------
185 r478 | lh3lh3 | 2009-10-14 14:18:12 -0400 (Wed, 14 Oct 2009) | 3 lines
187 M /trunk/samtools/bam.c
188 M /trunk/samtools/bam.h
189 M /trunk/samtools/bam_maqcns.c
190 M /trunk/samtools/bamtk.c
191 M /trunk/samtools/kaln.c
193 * samtools-0.1.6-12 (r478)
194 * fixed a bug in the indel caller
196 ------------------------------------------------------------------------
197 r477 | lh3lh3 | 2009-10-10 06:12:26 -0400 (Sat, 10 Oct 2009) | 3 lines
199 M /trunk/samtools/bam_index.c
200 M /trunk/samtools/bamtk.c
202 * samtools-0.1.6-11 (r477)
203 * fixed a bug due to recent change in bam_index.c (thank Nicole Washington for the patch)
205 ------------------------------------------------------------------------
206 r476 | petulda | 2009-10-09 11:45:36 -0400 (Fri, 09 Oct 2009) | 1 line
208 A /trunk/samtools/misc/sam2vcf.pl
210 Added the sam2vcf.pl script.
211 ------------------------------------------------------------------------
212 r475 | lh3lh3 | 2009-10-08 10:19:16 -0400 (Thu, 08 Oct 2009) | 2 lines
214 M /trunk/samtools/Makefile
215 M /trunk/samtools/bam.c
216 M /trunk/samtools/bam.h
217 M /trunk/samtools/bam_maqcns.c
218 M /trunk/samtools/bamtk.c
219 A /trunk/samtools/kaln.c
220 A /trunk/samtools/kaln.h
222 Unfinished modification. Please do not use this revision...
224 ------------------------------------------------------------------------
225 r474 | petulda | 2009-10-08 06:39:54 -0400 (Thu, 08 Oct 2009) | 1 line
227 M /trunk/samtools/knetfile.c
229 Removed the offending knet_seek message.
230 ------------------------------------------------------------------------
231 r473 | petulda | 2009-10-06 09:26:35 -0400 (Tue, 06 Oct 2009) | 1 line
233 M /trunk/samtools/knetfile.c
234 M /trunk/samtools/razf.c
236 Bug fix - faidx on RAZF compressed files now working.
237 ------------------------------------------------------------------------
238 r472 | lh3lh3 | 2009-10-02 08:42:57 -0400 (Fri, 02 Oct 2009) | 2 lines
240 M /trunk/samtools/samtools.1
242 Clarify the meaning of a region like "chr2:1,000,000".
244 ------------------------------------------------------------------------
245 r471 | lh3lh3 | 2009-10-02 05:42:19 -0400 (Fri, 02 Oct 2009) | 2 lines
247 M /trunk/samtools/misc/novo2sam.pl
249 Fixed minor bugs in novo2sam.pl (on behalf of Ken Chen and Colin Hercus)
251 ------------------------------------------------------------------------
252 r470 | lh3lh3 | 2009-09-29 15:01:27 -0400 (Tue, 29 Sep 2009) | 3 lines
254 M /trunk/samtools/Makefile.mingw
255 M /trunk/samtools/bamtk.c
256 M /trunk/samtools/knetfile.c
257 M /trunk/samtools/knetfile.h
259 * samtools-0.1.6-9 (r470)
260 * make knetfile.c compatible with MinGW (thank Martin Morgan for the patch)
262 ------------------------------------------------------------------------
263 r469 | lh3lh3 | 2009-09-29 08:07:44 -0400 (Tue, 29 Sep 2009) | 3 lines
265 M /trunk/samtools/bam_index.c
266 M /trunk/samtools/bamtk.c
268 * samtools-0.1.6-9 (r469)
269 * refactor bam_fetch() for Python binding. On behalf of Leo Goodstadt.
271 ------------------------------------------------------------------------
272 r468 | lh3lh3 | 2009-09-28 05:18:29 -0400 (Mon, 28 Sep 2009) | 3 lines
274 M /trunk/samtools/bam_sort.c
275 M /trunk/samtools/bamtk.c
276 M /trunk/samtools/misc/samtools.pl
278 * samtools-0.1.6-7 (r468)
281 ------------------------------------------------------------------------
282 r467 | petulda | 2009-09-28 04:51:29 -0400 (Mon, 28 Sep 2009) | 1 line
284 M /trunk/samtools/bgzf.c
285 M /trunk/samtools/bgzip.c
286 M /trunk/samtools/razf.c
287 M /trunk/samtools/razip.c
289 Changed the mode for newly created files to 0666. This allows less strict permissions with umask properly set (e.g. 0002 vs. 0022).
290 ------------------------------------------------------------------------
291 r466 | lh3lh3 | 2009-09-24 06:29:19 -0400 (Thu, 24 Sep 2009) | 3 lines
293 M /trunk/samtools/ChangeLog
294 M /trunk/samtools/bam_md.c
295 M /trunk/samtools/bamtk.c
297 * samtools-0.1.6-6 (r466)
298 * do not crash calmd when some sequences are absent from the reference.
300 ------------------------------------------------------------------------
301 r464 | jmarshall | 2009-09-23 06:14:32 -0400 (Wed, 23 Sep 2009) | 3 lines
303 M /trunk/samtools/bam.c
304 M /trunk/samtools/knetfile.c
306 Suppress bgzf_check_EOF() messages when reading from a pipe, as there is
307 no way to seek on a pipe and the messages always appear.
309 ------------------------------------------------------------------------
310 r463 | petulda | 2009-09-16 07:05:41 -0400 (Wed, 16 Sep 2009) | 1 line
312 M /trunk/samtools/knetfile.c
313 M /trunk/samtools/razf.c
315 A bug fix, "samtools view" is now working again.
316 ------------------------------------------------------------------------
317 r462 | lh3lh3 | 2009-09-16 04:51:07 -0400 (Wed, 16 Sep 2009) | 3 lines
319 M /trunk/samtools/bamtk.c
320 M /trunk/samtools/faidx.c
321 M /trunk/samtools/knetfile.c
322 M /trunk/samtools/knetfile.h
323 M /trunk/samtools/razf.c
324 M /trunk/samtools/razf.h
326 * samtools-0.1.6-5 (r462)
327 * Added knetfile support in razf and faidx (on behalf of Petr Danecek)
329 ------------------------------------------------------------------------
330 r460 | lh3lh3 | 2009-09-09 07:06:22 -0400 (Wed, 09 Sep 2009) | 2 lines
332 M /trunk/samtools/samtools.1
334 fixed a formatting issue
336 ------------------------------------------------------------------------
337 r459 | lh3lh3 | 2009-09-08 18:14:08 -0400 (Tue, 08 Sep 2009) | 3 lines
339 M /trunk/samtools/bam_sort.c
340 M /trunk/samtools/bamtk.c
342 * samtools-0.1.6-4 (r459)
343 * make sort output the result to stdout when -o is in use
345 ------------------------------------------------------------------------
346 r458 | lh3lh3 | 2009-09-07 05:10:28 -0400 (Mon, 07 Sep 2009) | 4 lines
348 M /trunk/samtools/bamtk.c
349 M /trunk/samtools/faidx.c
350 M /trunk/samtools/faidx.h
351 M /trunk/samtools/samtools.1
353 * samtools-0.1.6-2 (r458)
354 * added more interface to faidx (by Nils)
355 * updated documentation
357 ------------------------------------------------------------------------
358 r457 | lh3lh3 | 2009-09-05 16:12:04 -0400 (Sat, 05 Sep 2009) | 3 lines
360 M /trunk/samtools/bam_sort.c
361 M /trunk/samtools/bamtk.c
363 * samtools-0.1.6-2 (r457)
364 * get rid of three assert() in bam_sort.c
366 ------------------------------------------------------------------------
367 r456 | jmarshall | 2009-09-04 12:46:25 -0400 (Fri, 04 Sep 2009) | 3 lines
369 M /trunk/samtools/razf.c
371 Return NULL from _razf_open() (and hence razf_open()/razf_open2())
372 when opening the file fails.
374 ------------------------------------------------------------------------
375 r453 | lh3lh3 | 2009-09-02 08:56:33 -0400 (Wed, 02 Sep 2009) | 2 lines
377 M /trunk/samtools/ChangeLog
378 M /trunk/samtools/NEWS
379 M /trunk/samtools/bamtk.c
380 M /trunk/samtools/samtools.1
381 D /trunk/samtools/source.dot
383 Release samtools-0.1.6
385 ------------------------------------------------------------------------
386 r451 | lh3lh3 | 2009-09-02 05:44:48 -0400 (Wed, 02 Sep 2009) | 4 lines
388 M /trunk/samtools/bam_md.c
389 M /trunk/samtools/bam_rmdup.c
390 M /trunk/samtools/bam_rmdupse.c
391 M /trunk/samtools/bam_sort.c
392 M /trunk/samtools/bamtk.c
393 M /trunk/samtools/samtools.1
395 * samtools-0.1.5-34 (r451)
396 * applied the patch by John
397 * improved the help message a little bit
399 ------------------------------------------------------------------------
400 r450 | lh3lh3 | 2009-09-02 04:55:55 -0400 (Wed, 02 Sep 2009) | 3 lines
402 M /trunk/samtools/bam_color.c
403 M /trunk/samtools/bamtk.c
405 * samtools-0.1.5-33 (r450)
406 * fixed a bug in bam_color.c (on behalf of Nils Homer)
408 ------------------------------------------------------------------------
409 r449 | lh3lh3 | 2009-08-29 15:36:41 -0400 (Sat, 29 Aug 2009) | 4 lines
411 M /trunk/samtools/bam_import.c
412 M /trunk/samtools/bam_md.c
413 M /trunk/samtools/bamtk.c
414 M /trunk/samtools/misc/samtools.pl
416 * samtools-0.1.5-32 (r449)
417 * fillmd: fixed a bug in modifying MD/NM tags
418 * in import, give a warning if the read is aligned but there is no CIGAR.
420 ------------------------------------------------------------------------
421 r448 | lh3lh3 | 2009-08-19 04:44:28 -0400 (Wed, 19 Aug 2009) | 3 lines
423 M /trunk/samtools/ChangeLog
424 M /trunk/samtools/bam_pileup.c
425 M /trunk/samtools/bamtk.c
426 M /trunk/samtools/misc/wgsim_eval.pl
428 * samtools-0.1.5-31 (r448)
429 * fixed an issue when the last CIGAR is I or D
431 ------------------------------------------------------------------------
432 r447 | lh3lh3 | 2009-08-17 04:34:57 -0400 (Mon, 17 Aug 2009) | 3 lines
434 M /trunk/samtools/bam_aux.c
435 M /trunk/samtools/bamtk.c
437 * samtools-0.1.5-30 (r447)
438 * fixed a bug in bam_aux_get(): 'A' is not checked
440 ------------------------------------------------------------------------
441 r446 | lh3lh3 | 2009-08-17 04:33:17 -0400 (Mon, 17 Aug 2009) | 2 lines
443 M /trunk/samtools/bam_aux.c
444 M /trunk/samtools/bamtk.c
448 ------------------------------------------------------------------------
449 r444 | lh3lh3 | 2009-08-11 05:02:36 -0400 (Tue, 11 Aug 2009) | 3 lines
451 M /trunk/samtools/bam_sort.c
452 M /trunk/samtools/bamtk.c
454 * samtools-0.1.5-28 (r444)
457 ------------------------------------------------------------------------
458 r443 | lh3lh3 | 2009-08-11 04:29:11 -0400 (Tue, 11 Aug 2009) | 4 lines
460 M /trunk/samtools/bam.c
461 M /trunk/samtools/bam_import.c
462 M /trunk/samtools/bamtk.c
464 * samtools-0.1.5-27 (r443)
465 * SEQ and QUAL can be "*"
466 * parse CIGAR "=" and "X" as "M"
468 ------------------------------------------------------------------------
469 r442 | lh3lh3 | 2009-08-07 16:56:38 -0400 (Fri, 07 Aug 2009) | 4 lines
471 M /trunk/samtools/bam_pileup.c
472 M /trunk/samtools/bamtk.c
473 M /trunk/samtools/misc/md5.c
474 M /trunk/samtools/misc/md5.h
475 M /trunk/samtools/misc/md5fa.c
477 * samtools-0.1.5-26 (r442)
478 * replace RSA Inc md5.* with ones under permissive lincense
479 * fixed a bug in detecting unsorted bam in pileup
481 ------------------------------------------------------------------------
482 r441 | bhandsaker | 2009-08-05 09:41:28 -0400 (Wed, 05 Aug 2009) | 2 lines
484 M /trunk/samtools/bgzf.c
485 M /trunk/samtools/bgzf.h
486 M /trunk/samtools/bgzip.c
488 Change copyright notices now that MIT has approved open source distribution.
490 ------------------------------------------------------------------------
491 r440 | lh3lh3 | 2009-08-05 05:44:24 -0400 (Wed, 05 Aug 2009) | 3 lines
493 M /trunk/samtools/bam_stat.c
494 M /trunk/samtools/bamtk.c
496 * samtools-0.1.5-25 (r436)
497 * in flagstats, do not report singletons if both ends are unmapped
499 ------------------------------------------------------------------------
500 r439 | lh3lh3 | 2009-08-04 17:16:51 -0400 (Tue, 04 Aug 2009) | 2 lines
502 M /trunk/samtools/misc/maq2sam.c
504 fixed a SERIOUS bug in setting 0x20 flag
506 ------------------------------------------------------------------------
507 r438 | lh3lh3 | 2009-08-04 16:50:43 -0400 (Tue, 04 Aug 2009) | 2 lines
509 M /trunk/samtools/misc/samtools.pl
511 fixed two minor bugs (suggested by Tim M Storm)
513 ------------------------------------------------------------------------
514 r437 | lh3lh3 | 2009-08-04 04:13:24 -0400 (Tue, 04 Aug 2009) | 3 lines
516 M /trunk/samtools/bamtk.c
517 M /trunk/samtools/misc/samtools.pl
518 M /trunk/samtools/sam_view.c
520 * samtools-0.1.5-24 (r435)
523 ------------------------------------------------------------------------
524 r434 | lh3lh3 | 2009-08-03 05:40:42 -0400 (Mon, 03 Aug 2009) | 3 lines
526 M /trunk/samtools/bam_tview.c
527 M /trunk/samtools/bamtk.c
529 * samtools-0.1.5-23 (r434)
530 * in tview, press 'r' to show read names rather than sequences
532 ------------------------------------------------------------------------
533 r433 | lh3lh3 | 2009-08-02 14:13:35 -0400 (Sun, 02 Aug 2009) | 3 lines
535 M /trunk/samtools/knetfile.c
537 * tried to fixed the buggy FTP random access in Windows. FAILED.
538 * anyway, MinGW seems to have problem with "%lld".
540 ------------------------------------------------------------------------
541 r432 | lh3lh3 | 2009-08-01 19:32:07 -0400 (Sat, 01 Aug 2009) | 5 lines
543 M /trunk/samtools/Makefile.mingw
544 M /trunk/samtools/bamtk.c
545 M /trunk/samtools/faidx.c
546 M /trunk/samtools/razf.c
547 A /trunk/samtools/win32/libcurses.a
548 A /trunk/samtools/win32/xcurses.h
550 * samtools-0.1.5-22 (r432)
551 * faidx: fixed compitability issue with _WIN32
552 * razf: fixed potential compitability issue with _WIN32
553 * PDCurses support in Windows
555 ------------------------------------------------------------------------
556 r431 | lh3lh3 | 2009-08-01 18:34:54 -0400 (Sat, 01 Aug 2009) | 2 lines
558 M /trunk/samtools/win32/libz.a
560 replace the GnuWin32 version of libz.a with my own build with MinGW.
562 ------------------------------------------------------------------------
563 r430 | lh3lh3 | 2009-08-01 18:21:07 -0400 (Sat, 01 Aug 2009) | 2 lines
565 M /trunk/samtools/knetfile.c
569 ------------------------------------------------------------------------
570 r429 | lh3lh3 | 2009-08-01 17:41:19 -0400 (Sat, 01 Aug 2009) | 3 lines
572 M /trunk/samtools/Makefile.mingw
573 M /trunk/samtools/bamtk.c
574 M /trunk/samtools/knetfile.c
575 M /trunk/samtools/knetfile.h
577 * samtools-0.1.5-21 (r428)
578 * knetfile.c is now compatible with mingw-winsock
580 ------------------------------------------------------------------------
581 r428 | lh3lh3 | 2009-07-31 19:39:07 -0400 (Fri, 31 Jul 2009) | 2 lines
583 M /trunk/samtools/Makefile.mingw
585 simplify MinGW Makefile
587 ------------------------------------------------------------------------
588 r427 | lh3lh3 | 2009-07-31 19:30:54 -0400 (Fri, 31 Jul 2009) | 5 lines
590 A /trunk/samtools/Makefile.mingw
591 M /trunk/samtools/bam_import.c
592 M /trunk/samtools/bamtk.c
593 A /trunk/samtools/win32
594 A /trunk/samtools/win32/libz.a
595 A /trunk/samtools/win32/zconf.h
596 A /trunk/samtools/win32/zlib.h
598 * samtools-0.1.5-20 (r427)
599 * MinGW support. At least SAM<->BAM conversion is working. Other
600 functionality are not tested at the moment.
601 * zlib headers and Windows version of libz.a are included in win32/
603 ------------------------------------------------------------------------
604 r426 | lh3lh3 | 2009-07-31 18:32:09 -0400 (Fri, 31 Jul 2009) | 3 lines
606 M /trunk/samtools/bamtk.c
607 M /trunk/samtools/sam_view.c
609 * samtools-0.1.5-19 (r426)
610 * fixed a bug caused by recent modifications. Sorry.
612 ------------------------------------------------------------------------
613 r425 | lh3lh3 | 2009-07-31 18:23:51 -0400 (Fri, 31 Jul 2009) | 2 lines
615 M /trunk/samtools/bgzf.c
617 compatible with Windows binary files
619 ------------------------------------------------------------------------
620 r424 | lh3lh3 | 2009-07-31 05:19:59 -0400 (Fri, 31 Jul 2009) | 5 lines
622 M /trunk/samtools/bam_maqcns.c
623 M /trunk/samtools/bam_maqcns.h
624 M /trunk/samtools/bam_plcmd.c
625 M /trunk/samtools/bam_tview.c
626 M /trunk/samtools/bamtk.c
627 M /trunk/samtools/misc/samtools.pl
629 * samtools-0.1.5-18 (r423)
630 * output additional information in pileup indel lines, for the purepose
631 of debugging at the moment
632 * in tview, optionally allow to treat reference skip as deletion
634 ------------------------------------------------------------------------
635 r423 | lh3lh3 | 2009-07-30 17:00:36 -0400 (Thu, 30 Jul 2009) | 2 lines
637 A /trunk/samtools/misc/psl2sam.pl
639 convert BLAT psl to SAM.
641 ------------------------------------------------------------------------
642 r422 | lh3lh3 | 2009-07-30 06:24:39 -0400 (Thu, 30 Jul 2009) | 6 lines
644 M /trunk/samtools/ChangeLog
645 M /trunk/samtools/bam.c
646 M /trunk/samtools/bamtk.c
647 M /trunk/samtools/bgzf.c
648 M /trunk/samtools/bgzf.h
649 M /trunk/samtools/knetfile.c
650 M /trunk/samtools/sam.c
651 M /trunk/samtools/sam_view.c
653 * samtools-0.1.5-17 (r422)
654 * fixed a but in knetfile.c when seek type is not SEEK_SET
655 * write an empty BGZF block to every BGZF file
656 * check BGZF EOF marker in bam_header_read()
659 ------------------------------------------------------------------------
660 r421 | lh3lh3 | 2009-07-30 05:03:39 -0400 (Thu, 30 Jul 2009) | 3 lines
662 M /trunk/samtools/bam_import.c
663 M /trunk/samtools/bam_plcmd.c
664 M /trunk/samtools/bamtk.c
665 M /trunk/samtools/misc/samtools.pl
666 M /trunk/samtools/sam.c
667 M /trunk/samtools/sam.h
668 M /trunk/samtools/sam_view.c
670 * samtools-0.1.5-16 (r421)
671 * in view and pileup, load header from FASTA index if the input is SAM.
673 ------------------------------------------------------------------------
674 r420 | lh3lh3 | 2009-07-29 04:18:55 -0400 (Wed, 29 Jul 2009) | 2 lines
676 M /trunk/samtools/misc/maq2sam.c
678 do not set "read 1" if reads are not mapped in the PE mode of maq
680 ------------------------------------------------------------------------
681 r419 | lh3lh3 | 2009-07-28 04:52:33 -0400 (Tue, 28 Jul 2009) | 5 lines
683 M /trunk/samtools/bam_import.c
684 M /trunk/samtools/bamtk.c
685 M /trunk/samtools/misc/samtools.pl
686 M /trunk/samtools/misc/wgsim_eval.pl
688 * samtools-0.1.5-15 (r419)
689 * in sam_open(), return NULL when the file cannot be opened.
690 * make wgsim_eval.pl more robust to imperfect SAM
691 * add "unique" command to samtools.pl
693 ------------------------------------------------------------------------
694 r418 | lh3lh3 | 2009-07-24 09:04:19 -0400 (Fri, 24 Jul 2009) | 2 lines
696 M /trunk/samtools/misc/wgsim_eval.pl
698 skip @header lines in SAM
700 ------------------------------------------------------------------------
701 r417 | lh3lh3 | 2009-07-24 07:42:38 -0400 (Fri, 24 Jul 2009) | 3 lines
703 M /trunk/samtools/bamtk.c
704 M /trunk/samtools/sam_view.c
706 * samtools-0.1.5-14 (r417)
707 * more help in "samtools view" due to the recent changes.
709 ------------------------------------------------------------------------
710 r416 | lh3lh3 | 2009-07-24 07:34:30 -0400 (Fri, 24 Jul 2009) | 3 lines
712 M /trunk/samtools/bam.c
713 M /trunk/samtools/bam.h
714 M /trunk/samtools/bam_import.c
715 M /trunk/samtools/bamtk.c
716 M /trunk/samtools/sam.c
717 M /trunk/samtools/sam.h
718 M /trunk/samtools/sam_view.c
720 * samtools-0.1.5-17 (r416)
721 * support import/export SAM with string tags
723 ------------------------------------------------------------------------
724 r415 | lh3lh3 | 2009-07-24 06:39:26 -0400 (Fri, 24 Jul 2009) | 3 lines
726 M /trunk/samtools/bam.c
727 M /trunk/samtools/bam.h
728 M /trunk/samtools/bam_import.c
729 M /trunk/samtools/bamtk.c
730 M /trunk/samtools/sam.c
731 M /trunk/samtools/sam.h
732 M /trunk/samtools/sam_view.c
734 * samtools-0.1.5-12 (r415)
735 * FLAG now can be in HEX
737 ------------------------------------------------------------------------
738 r414 | lh3lh3 | 2009-07-22 17:03:49 -0400 (Wed, 22 Jul 2009) | 2 lines
740 M /trunk/samtools/kstring.h
742 fixed a compiling error (thank Ken for fixing it)
744 ------------------------------------------------------------------------
745 r412 | lh3lh3 | 2009-07-21 17:19:40 -0400 (Tue, 21 Jul 2009) | 2 lines
747 M /trunk/samtools/kstring.c
748 M /trunk/samtools/kstring.h
750 Implemented Boyer-Moore search in the kstring library.
752 ------------------------------------------------------------------------
753 r409 | lh3lh3 | 2009-07-17 12:10:20 -0400 (Fri, 17 Jul 2009) | 2 lines
755 M /trunk/samtools/bam_index.c
757 do not include knetfile.h when _USE_KNETFILE is not defined
759 ------------------------------------------------------------------------
760 r408 | lh3lh3 | 2009-07-17 10:29:21 -0400 (Fri, 17 Jul 2009) | 5 lines
762 M /trunk/samtools/bam_md.c
763 M /trunk/samtools/bam_tview.c
764 M /trunk/samtools/bamtk.c
765 M /trunk/samtools/bgzf.c
767 * samtools-0.1.5-11 (r408)
768 * force to overwirte existing MD if it is different from the one calculated
770 * bgzf.c: improved the compatibility with Windows headers
772 ------------------------------------------------------------------------
773 r407 | lh3lh3 | 2009-07-17 09:46:56 -0400 (Fri, 17 Jul 2009) | 5 lines
775 M /trunk/samtools/bam.h
776 M /trunk/samtools/bam_aux.c
777 M /trunk/samtools/bam_md.c
778 M /trunk/samtools/bamtk.c
779 M /trunk/samtools/sam.h
781 * samtools-0.1.5-10 (r407)
782 * implemented bam_aux_del() to remove a tag
783 * fillmd: generate the NM tag
784 * fillmd: cmd interface improvement
786 ------------------------------------------------------------------------
787 r406 | lh3lh3 | 2009-07-16 18:30:40 -0400 (Thu, 16 Jul 2009) | 2 lines
789 M /trunk/samtools/Makefile
791 Sorry. The old Makefile is for PDCurses...
793 ------------------------------------------------------------------------
794 r405 | lh3lh3 | 2009-07-16 18:30:11 -0400 (Thu, 16 Jul 2009) | 3 lines
796 M /trunk/samtools/Makefile
797 M /trunk/samtools/bam_tview.c
798 M /trunk/samtools/bamtk.c
800 * samtools-0.1.5-9 (r405)
801 * improved the compatibility with PDCurses a little bit
803 ------------------------------------------------------------------------
804 r404 | lh3lh3 | 2009-07-16 18:23:52 -0400 (Thu, 16 Jul 2009) | 3 lines
806 M /trunk/samtools/Makefile
807 M /trunk/samtools/bam_tview.c
808 M /trunk/samtools/bamtk.c
810 * samtools-0.1.5-8 (r404)
811 * compatible with PDCurses
813 ------------------------------------------------------------------------
814 r403 | lh3lh3 | 2009-07-16 17:39:39 -0400 (Thu, 16 Jul 2009) | 3 lines
816 M /trunk/samtools/bamtk.c
817 M /trunk/samtools/kseq.h
819 * samtools-0.1.5-7 (r403)
820 * fixed a bug in kseq.h for binary files (text files are fine)
822 ------------------------------------------------------------------------
823 r402 | lh3lh3 | 2009-07-16 06:49:53 -0400 (Thu, 16 Jul 2009) | 4 lines
825 M /trunk/samtools/bam_import.c
826 M /trunk/samtools/bam_index.c
827 M /trunk/samtools/bamtk.c
828 M /trunk/samtools/bgzf.c
830 * samtools-0.1.5-6 (r402)
831 * fixed compiling error when "-D_USE_NETFILE" is not applied
832 * improve portability to MinGW
834 ------------------------------------------------------------------------
835 r398 | lh3lh3 | 2009-07-13 05:21:36 -0400 (Mon, 13 Jul 2009) | 3 lines
837 A /trunk/bam-lite/bam.h (from /trunk/samtools/bam.h:395)
838 A /trunk/bam-lite/bam_lite.c (from /trunk/samtools/bam_lite.c:395)
839 D /trunk/samtools/bam_lite.c
841 * move bam_lite.c to bam-lite
842 * copy bam.h to bam-lite
844 ------------------------------------------------------------------------
845 r395 | lh3lh3 | 2009-07-13 05:12:57 -0400 (Mon, 13 Jul 2009) | 3 lines
847 M /trunk/samtools/bam.h
848 M /trunk/samtools/bam_lite.c
849 M /trunk/samtools/bam_lpileup.c
850 M /trunk/samtools/bam_pileup.c
851 M /trunk/samtools/bamtk.c
853 * samtools-0.1.5-5 (r395)
854 * added bam_pileup_file() and removed bam_lpileup_file()
856 ------------------------------------------------------------------------
857 r394 | lh3lh3 | 2009-07-12 19:35:10 -0400 (Sun, 12 Jul 2009) | 3 lines
859 M /trunk/samtools/bamtk.c
860 M /trunk/samtools/knetfile.c
861 M /trunk/samtools/knetfile.h
863 * samtools-0.1.5-4 (r394)
864 * http_proxy support in knetfile library (check http_proxy ENV)
866 ------------------------------------------------------------------------
867 r393 | lh3lh3 | 2009-07-12 18:57:07 -0400 (Sun, 12 Jul 2009) | 5 lines
869 M /trunk/samtools/bam_index.c
870 M /trunk/samtools/bam_tview.c
871 M /trunk/samtools/bamtk.c
872 M /trunk/samtools/knetfile.c
873 M /trunk/samtools/knetfile.h
875 * samtools-0.1.5-3 (r393)
876 * knetfile now supports HTTP (no proxy at the moment)
877 * fixed a potential issue in knetfile on opening ordinary file, although I have
878 not seen the sideeffect so far.
880 ------------------------------------------------------------------------
881 r392 | lh3lh3 | 2009-07-12 13:50:55 -0400 (Sun, 12 Jul 2009) | 2 lines
883 M /trunk/samtools/samtools.1
885 Remove the warning in tview
887 ------------------------------------------------------------------------
888 r391 | lh3lh3 | 2009-07-12 13:42:43 -0400 (Sun, 12 Jul 2009) | 3 lines
890 M /trunk/samtools/bam_tview.c
891 M /trunk/samtools/bamtk.c
893 * samtools-0.1.5-2 (r391)
894 * do not show a blank screen when no reads mapped
896 ------------------------------------------------------------------------
897 r390 | lh3lh3 | 2009-07-09 09:01:42 -0400 (Thu, 09 Jul 2009) | 4 lines
899 M /trunk/samtools/bam.h
900 A /trunk/samtools/bam_lite.c
901 M /trunk/samtools/bamtk.c
903 * samtools-0.1.5-1 (r390)
904 * removed useless _IOLIB in bam.h. This should cause no change at all.
905 * added bam_lite.c for light-weight BAM reading
907 ------------------------------------------------------------------------
908 r385 | lh3lh3 | 2009-07-07 11:53:29 -0400 (Tue, 07 Jul 2009) | 2 lines
910 M /trunk/samtools/bamtk.c
911 M /trunk/samtools/knetfile.c
913 Release samtools-0.1.5c (fixed a bug in piping)
915 ------------------------------------------------------------------------
916 r383 | lh3lh3 | 2009-07-07 06:39:55 -0400 (Tue, 07 Jul 2009) | 2 lines
918 M /trunk/samtools/bamtk.c
919 M /trunk/samtools/sam.c
921 Release samtools-0.1.5b (BUG! so embarrassing!)
923 ------------------------------------------------------------------------
924 r381 | lh3lh3 | 2009-07-07 06:20:06 -0400 (Tue, 07 Jul 2009) | 2 lines
926 M /trunk/samtools/Makefile
927 M /trunk/samtools/bam.h
928 M /trunk/samtools/bam_aux.c
929 M /trunk/samtools/bamtk.c
931 Release samtools-0.1.5a (for compatibility with Bio::DB::Sam)
933 ------------------------------------------------------------------------
934 r373 | lh3lh3 | 2009-07-07 05:26:57 -0400 (Tue, 07 Jul 2009) | 2 lines
936 M /trunk/samtools/ChangeLog
937 M /trunk/samtools/NEWS
938 M /trunk/samtools/bamtk.c
939 M /trunk/samtools/samtools.1
941 Release samtools-0.1.5
943 ------------------------------------------------------------------------
944 r372 | lh3lh3 | 2009-07-07 04:49:27 -0400 (Tue, 07 Jul 2009) | 3 lines
946 M /trunk/samtools/bamtk.c
947 M /trunk/samtools/sam.c
949 * samtools-0.1.4-23 (r372)
950 * keep header text if "view -t" is used (by Gerton)
952 ------------------------------------------------------------------------
953 r371 | lh3lh3 | 2009-07-06 20:13:32 -0400 (Mon, 06 Jul 2009) | 2 lines
955 M /trunk/samtools/samtools.1
959 ------------------------------------------------------------------------
960 r370 | bhandsaker | 2009-07-02 17:24:34 -0400 (Thu, 02 Jul 2009) | 2 lines
962 M /trunk/samtools/Makefile
964 Introduced LIBPATH variable so this could be overridden to allow samtools to build correct at the Broad.
966 ------------------------------------------------------------------------
967 r369 | lh3lh3 | 2009-07-02 08:36:53 -0400 (Thu, 02 Jul 2009) | 4 lines
969 M /trunk/samtools/ChangeLog
970 M /trunk/samtools/bam_aux.c
971 M /trunk/samtools/bam_plcmd.c
972 M /trunk/samtools/bamtk.c
974 * samtools-0.1.4-22 (r369)
975 * in pileup, optionally print E2 and U2
976 * remove the debugging code in bam_aux_get() (Drat!)
978 ------------------------------------------------------------------------
979 r368 | lh3lh3 | 2009-07-02 06:32:26 -0400 (Thu, 02 Jul 2009) | 6 lines
981 M /trunk/samtools/bam.c
982 M /trunk/samtools/bam.h
983 M /trunk/samtools/bam_aux.c
984 M /trunk/samtools/bam_index.c
985 M /trunk/samtools/bam_lpileup.c
986 M /trunk/samtools/bam_md.c
987 M /trunk/samtools/bam_pileup.c
988 M /trunk/samtools/bam_rmdup.c
989 M /trunk/samtools/bam_stat.c
990 M /trunk/samtools/bam_tview.c
991 M /trunk/samtools/bamtk.c
992 M /trunk/samtools/faidx.c
993 M /trunk/samtools/faidx.h
994 M /trunk/samtools/glf.c
996 * samtools-0.1.4-21 (r368)
997 * propagate errors rather than exit or complain assertion failure. Assertion
998 should be only used for checking internal bugs, but not for external input
999 inconsistency. I was just a bit lazy.
1000 * small memory leak may be present on failure, though
1002 ------------------------------------------------------------------------
1003 r367 | lh3lh3 | 2009-06-30 11:18:42 -0400 (Tue, 30 Jun 2009) | 2 lines
1005 M /trunk/samtools/knetfile.c
1007 reduce the chance of blocking in FTP connection
1009 ------------------------------------------------------------------------
1010 r366 | lh3lh3 | 2009-06-30 10:35:21 -0400 (Tue, 30 Jun 2009) | 2 lines
1012 M /trunk/samtools/knetfile.c
1014 minor changes to knetfile: invalid fd equals -1 rather than 0
1016 ------------------------------------------------------------------------
1017 r365 | lh3lh3 | 2009-06-30 09:04:30 -0400 (Tue, 30 Jun 2009) | 3 lines
1019 M /trunk/samtools/bam_index.c
1020 M /trunk/samtools/bamtk.c
1021 M /trunk/samtools/knetfile.c
1022 M /trunk/samtools/knetfile.h
1024 * samtools-0.1.4-20 (r365)
1025 * download the BAM index file if it is not found in the current working directory.
1027 ------------------------------------------------------------------------
1028 r364 | lh3lh3 | 2009-06-30 07:39:07 -0400 (Tue, 30 Jun 2009) | 3 lines
1030 M /trunk/samtools/bamtk.c
1031 M /trunk/samtools/knetfile.c
1033 * samtools-0.1.4-19 (r364)
1034 * knetfile: report error when the file is not present on FTP
1036 ------------------------------------------------------------------------
1037 r363 | lh3lh3 | 2009-06-29 18:23:32 -0400 (Mon, 29 Jun 2009) | 4 lines
1039 M /trunk/samtools/bam_tview.c
1040 M /trunk/samtools/bamtk.c
1041 M /trunk/samtools/bgzf.c
1042 M /trunk/samtools/bgzf.h
1043 M /trunk/samtools/knetfile.c
1044 M /trunk/samtools/knetfile.h
1046 * samtools-0.1.4-18 (r363)
1047 * knetfile: do not trigger network communication in FTP seek (lazy seek)
1048 * bgzf: cache recent blocks (disabled by default)
1050 ------------------------------------------------------------------------
1051 r362 | lh3lh3 | 2009-06-25 16:04:34 -0400 (Thu, 25 Jun 2009) | 2 lines
1053 M /trunk/samtools/bgzf.c
1057 ------------------------------------------------------------------------
1058 r361 | lh3lh3 | 2009-06-25 16:03:10 -0400 (Thu, 25 Jun 2009) | 3 lines
1060 M /trunk/samtools/bam_index.c
1061 M /trunk/samtools/bamtk.c
1063 * samtools-0.1.4-17 (r361)
1064 * if a file is given on FTP, search locally for the BAM index
1066 ------------------------------------------------------------------------
1067 r360 | lh3lh3 | 2009-06-25 15:44:52 -0400 (Thu, 25 Jun 2009) | 5 lines
1069 M /trunk/samtools/Makefile
1070 M /trunk/samtools/bam_import.c
1071 M /trunk/samtools/bam_index.c
1072 M /trunk/samtools/bamtk.c
1073 M /trunk/samtools/bgzf.c
1074 M /trunk/samtools/bgzf.h
1075 M /trunk/samtools/knetfile.c
1076 M /trunk/samtools/knetfile.h
1078 * samtools-0.1.4-16 (r360)
1079 * report more information in index when the input is not sorted
1080 * change the behaviour of knet_seek() such that it returns 0 on success
1081 * support knetfile library in BGZF
1083 ------------------------------------------------------------------------
1084 r359 | lh3lh3 | 2009-06-25 12:10:55 -0400 (Thu, 25 Jun 2009) | 2 lines
1086 M /trunk/samtools/knetfile.c
1087 M /trunk/samtools/knetfile.h
1089 fixed bugs in knetfile.*
1091 ------------------------------------------------------------------------
1092 r358 | lh3lh3 | 2009-06-25 08:53:19 -0400 (Thu, 25 Jun 2009) | 2 lines
1094 A /trunk/samtools/knetfile.h
1096 this is the header file
1098 ------------------------------------------------------------------------
1099 r357 | lh3lh3 | 2009-06-25 08:52:03 -0400 (Thu, 25 Jun 2009) | 3 lines
1101 A /trunk/samtools/knetfile.c
1103 * open a file at FTP
1104 * preliminary version
1106 ------------------------------------------------------------------------
1107 r354 | lh3lh3 | 2009-06-24 09:02:25 -0400 (Wed, 24 Jun 2009) | 3 lines
1109 M /trunk/samtools/bam.c
1110 M /trunk/samtools/bamtk.c
1112 * samtools-0.1.4-15 (r354)
1113 * fixed a memory leak in bam_view1(), although samtools is not using this routine.
1115 ------------------------------------------------------------------------
1116 r351 | lh3lh3 | 2009-06-17 19:16:26 -0400 (Wed, 17 Jun 2009) | 4 lines
1118 M /trunk/samtools/bamtk.c
1119 M /trunk/samtools/faidx.c
1121 * samtools-0.1.4-13 (r351)
1122 * make faidx more tolerant to empty lines right before or after > lines
1123 * hope this does not introduce new bugs...
1125 ------------------------------------------------------------------------
1126 r350 | lh3lh3 | 2009-06-16 09:37:01 -0400 (Tue, 16 Jun 2009) | 3 lines
1128 M /trunk/samtools/bam_plcmd.c
1129 M /trunk/samtools/bamtk.c
1131 * samtools-0.1.4-13 (r350)
1132 * fixed a small memory leak in pileup, caused by recent modifications
1134 ------------------------------------------------------------------------
1135 r347 | lh3lh3 | 2009-06-13 16:20:49 -0400 (Sat, 13 Jun 2009) | 3 lines
1137 M /trunk/samtools/bam_plcmd.c
1138 M /trunk/samtools/bamtk.c
1139 M /trunk/samtools/sam_view.c
1141 * samtools-0.1.4-12 (r347)
1142 * added `-S' to pileup, similar to `view -S'
1144 ------------------------------------------------------------------------
1145 r346 | lh3lh3 | 2009-06-13 12:52:31 -0400 (Sat, 13 Jun 2009) | 3 lines
1147 M /trunk/samtools/Makefile
1148 M /trunk/samtools/bamtk.c
1149 M /trunk/samtools/sam_view.c
1150 M /trunk/samtools/samtools.1
1152 * samtools-0.1.4-11 (r346)
1153 * allow to select a read group at view command-line
1155 ------------------------------------------------------------------------
1156 r344 | lh3lh3 | 2009-06-13 09:06:24 -0400 (Sat, 13 Jun 2009) | 2 lines
1158 M /trunk/samtools/examples/calDepth.c
1162 ------------------------------------------------------------------------
1163 r343 | lh3lh3 | 2009-06-13 09:01:22 -0400 (Sat, 13 Jun 2009) | 2 lines
1165 M /trunk/samtools/examples/calDepth.c
1169 ------------------------------------------------------------------------
1170 r342 | lh3lh3 | 2009-06-13 08:58:48 -0400 (Sat, 13 Jun 2009) | 2 lines
1172 M /trunk/samtools/examples/Makefile
1173 A /trunk/samtools/examples/calDepth.c
1175 added an example of calculating read depth
1177 ------------------------------------------------------------------------
1178 r341 | lh3lh3 | 2009-06-13 08:00:08 -0400 (Sat, 13 Jun 2009) | 6 lines
1180 M /trunk/samtools/Makefile
1181 M /trunk/samtools/bam.h
1182 M /trunk/samtools/bam_aux.c
1183 A /trunk/samtools/bam_color.c
1184 M /trunk/samtools/bam_plcmd.c
1185 M /trunk/samtools/bam_sort.c
1186 M /trunk/samtools/bam_tview.c
1187 M /trunk/samtools/bamtk.c
1188 M /trunk/samtools/sam.c
1189 M /trunk/samtools/sam.h
1191 * samtools-0.1.4-10 (r341)
1192 * only include key APIs in libbam.a
1193 * move color-specific routines to bam_color.c
1194 * update documentations
1195 * remove the support of -q in pileup
1197 ------------------------------------------------------------------------
1198 r340 | lh3lh3 | 2009-06-13 06:17:14 -0400 (Sat, 13 Jun 2009) | 6 lines
1200 M /trunk/samtools/INSTALL
1201 M /trunk/samtools/Makefile
1202 M /trunk/samtools/bam_aux.c
1203 M /trunk/samtools/bam_import.c
1204 M /trunk/samtools/bam_tview.c
1205 M /trunk/samtools/bamtk.c
1206 M /trunk/samtools/razf.c
1207 M /trunk/samtools/sam_view.c
1209 * samtools-0.1.4-9 (r340)
1210 * added a warning to razf.c if zlib<1.2.2.1
1211 * fixed a compilation warning
1212 * fixed a segfault caused by @RG parsing
1213 * detect NCURSES in bam_tview.c
1215 ------------------------------------------------------------------------
1216 r339 | lh3lh3 | 2009-06-13 05:35:19 -0400 (Sat, 13 Jun 2009) | 2 lines
1218 M /trunk/samtools/INSTALL
1222 ------------------------------------------------------------------------
1223 r338 | lh3lh3 | 2009-06-12 19:15:24 -0400 (Fri, 12 Jun 2009) | 4 lines
1225 M /trunk/samtools/bam.c
1226 M /trunk/samtools/bam.h
1227 M /trunk/samtools/bam_aux.c
1228 M /trunk/samtools/bam_import.c
1229 M /trunk/samtools/bamtk.c
1230 M /trunk/samtools/kstring.h
1231 M /trunk/samtools/sam.c
1232 M /trunk/samtools/sam_view.c
1234 * samtools-0.1.4-8 (r338)
1235 * parse the @RG header lines and allow to choose library at the "samtools view"
1238 ------------------------------------------------------------------------
1239 r337 | lh3lh3 | 2009-06-12 16:25:50 -0400 (Fri, 12 Jun 2009) | 4 lines
1241 M /trunk/samtools/bamtk.c
1242 M /trunk/samtools/bgzf.c
1243 M /trunk/samtools/bgzf.h
1244 M /trunk/samtools/sam.c
1245 M /trunk/samtools/sam_view.c
1247 * samtools-0.1.4-7 (r337)
1248 * bgzf.c: support mode string "wu": uncompressed output
1249 * "samtools view" support "-u" command-line option
1251 ------------------------------------------------------------------------
1252 r336 | lh3lh3 | 2009-06-12 12:20:12 -0400 (Fri, 12 Jun 2009) | 5 lines
1254 M /trunk/samtools/Makefile
1255 M /trunk/samtools/misc/Makefile
1256 M /trunk/samtools/razf.c
1257 M /trunk/samtools/razf.h
1258 M /trunk/samtools/razip.c
1260 * no changes to samtools itself
1261 * remove zlib source codes
1262 * make RAZF reading compatible with old version of zlib
1263 * on old version of zlib, writing is not available
1265 ------------------------------------------------------------------------
1266 r335 | lh3lh3 | 2009-06-12 11:47:33 -0400 (Fri, 12 Jun 2009) | 2 lines
1268 D /trunk/samtools/zlib
1270 remove zlib for simplification...
1272 ------------------------------------------------------------------------
1273 r334 | lh3lh3 | 2009-06-12 10:43:36 -0400 (Fri, 12 Jun 2009) | 5 lines
1275 M /trunk/samtools/bam.h
1276 M /trunk/samtools/bam_aux.c
1277 M /trunk/samtools/bamtk.c
1279 * samtools-0.1.4-6 (r334)
1280 * do not export bam_aux_get_core() for Bio::DB::Sam because it has already
1281 been implemented in that.
1282 * this version works with the latest Bio::DB::Sam (20090612)
1284 ------------------------------------------------------------------------
1285 r333 | lh3lh3 | 2009-06-12 10:33:42 -0400 (Fri, 12 Jun 2009) | 2 lines
1287 M /trunk/samtools/ChangeLog
1291 ------------------------------------------------------------------------
1292 r332 | lh3lh3 | 2009-06-12 10:21:21 -0400 (Fri, 12 Jun 2009) | 2 lines
1294 M /trunk/samtools/AUTHORS
1295 M /trunk/samtools/Makefile
1296 M /trunk/samtools/misc/Makefile
1298 fixed minor things in Makefile
1300 ------------------------------------------------------------------------
1301 r331 | lh3lh3 | 2009-06-12 10:07:05 -0400 (Fri, 12 Jun 2009) | 4 lines
1303 M /trunk/samtools/bamtk.c
1305 * samtools-0.1.4-5 (r3310
1306 * no change to samtools itself. Version number is increased to reflect the
1307 changes in the Makefile building system.
1309 ------------------------------------------------------------------------
1310 r330 | lh3lh3 | 2009-06-12 10:03:38 -0400 (Fri, 12 Jun 2009) | 2 lines
1312 M /trunk/samtools/AUTHORS
1313 D /trunk/samtools/README
1315 update information...
1317 ------------------------------------------------------------------------
1318 r329 | lh3lh3 | 2009-06-12 09:52:21 -0400 (Fri, 12 Jun 2009) | 3 lines
1320 M /trunk/samtools/misc/novo2sam.pl
1322 * updated novoalign converter by Colin Hercus et al.
1323 * this version works with indels
1325 ------------------------------------------------------------------------
1326 r328 | lh3lh3 | 2009-06-12 09:50:53 -0400 (Fri, 12 Jun 2009) | 3 lines
1328 M /trunk/samtools/INSTALL
1329 M /trunk/samtools/Makefile
1330 M /trunk/samtools/misc/Makefile
1331 M /trunk/samtools/zlib/Makefile
1334 * update INSTALL instruction
1336 ------------------------------------------------------------------------
1337 r327 | lh3lh3 | 2009-06-12 09:18:29 -0400 (Fri, 12 Jun 2009) | 4 lines
1339 A /trunk/samtools/Makefile (from /trunk/samtools/Makefile.generic:325)
1340 D /trunk/samtools/Makefile.am
1341 D /trunk/samtools/Makefile.generic
1342 D /trunk/samtools/Makefile.lite
1343 D /trunk/samtools/autogen.sh
1344 D /trunk/samtools/cleanup.sh
1345 D /trunk/samtools/configure.ac
1346 A /trunk/samtools/misc/Makefile (from /trunk/samtools/misc/Makefile.generic:305)
1347 D /trunk/samtools/misc/Makefile.am
1348 D /trunk/samtools/misc/Makefile.generic
1349 M /trunk/samtools/razf.c
1350 A /trunk/samtools/zlib
1351 A /trunk/samtools/zlib/Makefile
1352 A /trunk/samtools/zlib/adler32.c
1353 A /trunk/samtools/zlib/compress.c
1354 A /trunk/samtools/zlib/crc32.c
1355 A /trunk/samtools/zlib/crc32.h
1356 A /trunk/samtools/zlib/deflate.c
1357 A /trunk/samtools/zlib/deflate.h
1358 A /trunk/samtools/zlib/gzio.c
1359 A /trunk/samtools/zlib/infback.c
1360 A /trunk/samtools/zlib/inffast.c
1361 A /trunk/samtools/zlib/inffast.h
1362 A /trunk/samtools/zlib/inffixed.h
1363 A /trunk/samtools/zlib/inflate.c
1364 A /trunk/samtools/zlib/inflate.h
1365 A /trunk/samtools/zlib/inftrees.c
1366 A /trunk/samtools/zlib/inftrees.h
1367 A /trunk/samtools/zlib/trees.c
1368 A /trunk/samtools/zlib/trees.h
1369 A /trunk/samtools/zlib/uncompr.c
1370 A /trunk/samtools/zlib/zconf.h
1371 A /trunk/samtools/zlib/zlib.h
1372 A /trunk/samtools/zlib/zutil.c
1373 A /trunk/samtools/zlib/zutil.h
1374 D /trunk/samtools/zutil.h
1376 * added zlib-1.2.3 as razip requires that
1377 * prepare to changed back to the Makefile building system
1378 * unfinished! (will be soon)
1380 ------------------------------------------------------------------------
1381 r326 | lh3lh3 | 2009-06-12 09:12:03 -0400 (Fri, 12 Jun 2009) | 2 lines
1383 M /trunk/samtools/misc/samtools.pl
1387 ------------------------------------------------------------------------
1388 r325 | lh3lh3 | 2009-06-10 11:27:59 -0400 (Wed, 10 Jun 2009) | 3 lines
1390 M /trunk/samtools/bam_maqcns.c
1391 M /trunk/samtools/bamtk.c
1393 * samtools-0.1.4-4 (r325)
1394 * further avoid wrong consensus calls in repetitive regions.
1396 ------------------------------------------------------------------------
1397 r324 | lh3lh3 | 2009-06-10 10:56:17 -0400 (Wed, 10 Jun 2009) | 4 lines
1399 M /trunk/samtools/bam_maqcns.c
1400 M /trunk/samtools/bam_plcmd.c
1401 M /trunk/samtools/bamtk.c
1402 M /trunk/samtools/sam.c
1403 M /trunk/samtools/sam.h
1405 * samtools-0.1.4-3 (r324)
1406 * make maqcns generate the correct call in repetitive regions.
1407 * allow filtering on mapQ at the pileup command line
1409 ------------------------------------------------------------------------
1410 r323 | lh3lh3 | 2009-06-10 05:04:21 -0400 (Wed, 10 Jun 2009) | 3 lines
1412 M /trunk/samtools/misc/samtools.pl
1414 * samtools.pl-0.3.2 (r322)
1415 * indels and SNPs use different mapping quality threshold
1417 ------------------------------------------------------------------------
1418 r322 | lh3lh3 | 2009-06-10 05:03:22 -0400 (Wed, 10 Jun 2009) | 2 lines
1420 M /trunk/samtools/misc/export2sam.pl
1424 ------------------------------------------------------------------------
1425 r321 | lh3lh3 | 2009-06-09 04:21:48 -0400 (Tue, 09 Jun 2009) | 2 lines
1427 M /trunk/samtools/misc/samtools.pl
1429 just typo. no real change
1431 ------------------------------------------------------------------------
1432 r320 | lh3lh3 | 2009-06-08 09:32:51 -0400 (Mon, 08 Jun 2009) | 2 lines
1434 M /trunk/samtools/misc/samtools.pl
1436 a little bit code cleanup
1438 ------------------------------------------------------------------------
1439 r319 | lh3lh3 | 2009-06-08 09:22:33 -0400 (Mon, 08 Jun 2009) | 4 lines
1441 M /trunk/samtools/misc/samtools.pl
1444 * change default parameters
1445 * optionally print filtered variants
1447 ------------------------------------------------------------------------
1448 r318 | lh3lh3 | 2009-06-08 09:14:26 -0400 (Mon, 08 Jun 2009) | 3 lines
1450 M /trunk/samtools/misc/samtools.pl
1453 * combine snpFilter and indelFilter
1455 ------------------------------------------------------------------------
1456 r317 | lh3lh3 | 2009-06-08 06:31:42 -0400 (Mon, 08 Jun 2009) | 3 lines
1458 M /trunk/samtools/misc/samtools.pl
1461 * change a default parameter
1463 ------------------------------------------------------------------------
1464 r316 | lh3lh3 | 2009-06-08 06:11:06 -0400 (Mon, 08 Jun 2009) | 5 lines
1466 M /trunk/samtools/bam_maqcns.c
1467 M /trunk/samtools/bam_maqcns.h
1468 M /trunk/samtools/bam_plcmd.c
1469 M /trunk/samtools/bamtk.c
1470 M /trunk/samtools/sam.c
1472 * samtools-0.1.4-2 (r316)
1473 * pileup: cap mapping quality at 60 (by default)
1474 * pileup: always calculate RMS mapq
1475 * pileup: allow to output variant sites only
1477 ------------------------------------------------------------------------
1478 r312 | lh3lh3 | 2009-06-04 08:01:10 -0400 (Thu, 04 Jun 2009) | 3 lines
1480 M /trunk/samtools/misc/samtools.pl
1485 ------------------------------------------------------------------------
1486 r311 | lh3lh3 | 2009-06-03 04:40:40 -0400 (Wed, 03 Jun 2009) | 2 lines
1488 M /trunk/samtools/misc/samtools.pl
1490 * in snpFilter, suppress non-SNP sites
1492 ------------------------------------------------------------------------
1493 r310 | lh3lh3 | 2009-06-01 09:35:13 -0400 (Mon, 01 Jun 2009) | 3 lines
1495 M /trunk/samtools/misc/samtools.pl
1500 ------------------------------------------------------------------------
1501 r309 | lh3lh3 | 2009-06-01 09:04:39 -0400 (Mon, 01 Jun 2009) | 3 lines
1503 M /trunk/samtools/misc/samtools.pl
1508 ------------------------------------------------------------------------
1509 r306 | lh3lh3 | 2009-05-28 06:49:35 -0400 (Thu, 28 May 2009) | 3 lines
1511 M /trunk/samtools/bgzf.c
1513 * minor changes to bgzf: return NULL if fd == -1
1514 * suggested by {kdj,jm18}@sanger.ac.uk
1516 ------------------------------------------------------------------------
1517 r305 | lh3lh3 | 2009-05-28 06:16:08 -0400 (Thu, 28 May 2009) | 2 lines
1519 A /trunk/samtools/misc/interpolate_sam.pl
1521 Script for paired-end pileup, contributed by Stephen Montgomery.
1523 ------------------------------------------------------------------------
1524 r304 | lh3lh3 | 2009-05-28 06:08:49 -0400 (Thu, 28 May 2009) | 3 lines
1526 M /trunk/samtools/bamtk.c
1527 M /trunk/samtools/sam.c
1529 * samtools-0.1.4-1 (r304)
1530 * fixed a minor bug in printing headers
1532 ------------------------------------------------------------------------
1533 r297 | lh3lh3 | 2009-05-21 11:06:16 -0400 (Thu, 21 May 2009) | 2 lines
1535 M /trunk/samtools/ChangeLog
1536 M /trunk/samtools/NEWS
1537 M /trunk/samtools/bam_plcmd.c
1538 M /trunk/samtools/bamtk.c
1539 M /trunk/samtools/misc/maq2sam.c
1540 M /trunk/samtools/samtools.1
1542 Release samtools-0.1.4
1544 ------------------------------------------------------------------------
1545 r296 | lh3lh3 | 2009-05-21 07:53:14 -0400 (Thu, 21 May 2009) | 3 lines
1547 M /trunk/samtools/bam_maqcns.c
1548 M /trunk/samtools/bamtk.c
1550 * samtools-0.1.3-24 (r296)
1551 * another similar bug in the indel caller
1553 ------------------------------------------------------------------------
1554 r295 | lh3lh3 | 2009-05-21 07:50:28 -0400 (Thu, 21 May 2009) | 3 lines
1556 M /trunk/samtools/bam_maqcns.c
1557 M /trunk/samtools/bamtk.c
1559 * samtools-0.1.3-23 (r295)
1560 * fixed a critical bug in the indel caller
1562 ------------------------------------------------------------------------
1563 r294 | lh3lh3 | 2009-05-20 08:00:20 -0400 (Wed, 20 May 2009) | 2 lines
1565 M /trunk/samtools/bam_stat.c
1567 added a missing header file
1569 ------------------------------------------------------------------------
1570 r293 | lh3lh3 | 2009-05-19 18:44:25 -0400 (Tue, 19 May 2009) | 3 lines
1572 M /trunk/samtools/bam_tview.c
1573 M /trunk/samtools/bamtk.c
1575 * samtools-0.1.3-22 (r293)
1576 * open tview in the dot-view mode by default
1578 ------------------------------------------------------------------------
1579 r292 | lh3lh3 | 2009-05-18 16:01:23 -0400 (Mon, 18 May 2009) | 6 lines
1581 M /trunk/samtools/samtools.1
1583 Added a note to the manual. Currently SAMtools used unaligned words in
1584 several places. Although this does not cause bus errors to me, it may
1585 affect portability. Please see the "Bus error" wiki page for more
1586 information. Also thank James Bonfields for pointing this out.
1589 ------------------------------------------------------------------------
1590 r286 | lh3lh3 | 2009-05-14 10:23:13 -0400 (Thu, 14 May 2009) | 3 lines
1592 M /trunk/samtools/bam.h
1593 M /trunk/samtools/bam_aux.c
1594 M /trunk/samtools/bamtk.c
1596 * samtools-0.1.3-21 (286)
1597 * declare bam_aux_get_core() in bam.h
1599 ------------------------------------------------------------------------
1600 r276 | lh3lh3 | 2009-05-13 05:07:55 -0400 (Wed, 13 May 2009) | 5 lines
1602 M /trunk/samtools/bam.h
1603 M /trunk/samtools/bam_index.c
1604 M /trunk/samtools/bamtk.c
1606 * samtools-0.1.3-20 (r276)
1607 * remove bam1_t::hash again. We need to modify the Perl API anyway to
1608 make it work with the latest SVN.
1609 * As is suggested by Tim, scan "{base}.bai" and "{base}.bam.bai" for index
1611 ------------------------------------------------------------------------
1612 r275 | lh3lh3 | 2009-05-12 16:14:10 -0400 (Tue, 12 May 2009) | 4 lines
1614 M /trunk/samtools/ChangeLog
1615 M /trunk/samtools/bam.h
1616 M /trunk/samtools/bamtk.c
1618 * samtools-0.1.3-19 (r275)
1619 * a minor change to the bam1_t struct: added back "void *hash" for the
1620 backward compatibility with Bio::DB::Sam
1622 ------------------------------------------------------------------------
1623 r273 | lh3lh3 | 2009-05-12 09:28:39 -0400 (Tue, 12 May 2009) | 3 lines
1625 M /trunk/samtools/bam_rmdupse.c
1626 M /trunk/samtools/bamtk.c
1628 * samtools-0.1.3-18 (r273)
1629 * rmdupse: do not remove unmapped reads
1631 ------------------------------------------------------------------------
1632 r272 | lh3lh3 | 2009-05-12 09:20:00 -0400 (Tue, 12 May 2009) | 2 lines
1634 M /trunk/samtools/bam_rmdupse.c
1636 change a parameter. It does nothing
1638 ------------------------------------------------------------------------
1639 r271 | lh3lh3 | 2009-05-12 09:17:58 -0400 (Tue, 12 May 2009) | 3 lines
1641 M /trunk/samtools/Makefile.am
1642 M /trunk/samtools/Makefile.generic
1643 M /trunk/samtools/Makefile.lite
1644 A /trunk/samtools/bam_rmdupse.c
1645 M /trunk/samtools/bamtk.c
1646 M /trunk/samtools/configure.ac
1648 * samtools-0.1.3-17 (r271)
1649 * added 'rmdupse' command
1651 ------------------------------------------------------------------------
1652 r267 | lh3lh3 | 2009-05-05 17:31:41 -0400 (Tue, 05 May 2009) | 3 lines
1654 M /trunk/samtools/bamtk.c
1655 M /trunk/samtools/sam_view.c
1657 * samtools-0.1.3-16 (r267)
1658 * in sam_view.c, changed g_flag_on based on the suggestion by Angie Hinrichs
1660 ------------------------------------------------------------------------
1661 r266 | lh3lh3 | 2009-05-05 17:23:27 -0400 (Tue, 05 May 2009) | 3 lines
1663 M /trunk/samtools/bam_import.c
1664 M /trunk/samtools/bamtk.c
1666 * samtools-0.1.3-15 (r266)
1667 * report an error if a non-* reference is present while @SQ is absent
1669 ------------------------------------------------------------------------
1670 r265 | lh3lh3 | 2009-05-05 17:09:00 -0400 (Tue, 05 May 2009) | 3 lines
1672 M /trunk/samtools/bam.h
1673 M /trunk/samtools/bam_import.c
1674 M /trunk/samtools/bamtk.c
1675 M /trunk/samtools/sam.c
1676 M /trunk/samtools/sam_view.c
1678 * samtools-0.1.3-14 (r262)
1679 * make samopen() recognize @SQ header lines
1681 ------------------------------------------------------------------------
1682 r261 | lh3lh3 | 2009-05-05 10:10:30 -0400 (Tue, 05 May 2009) | 3 lines
1684 M /trunk/samtools/bam_plcmd.c
1685 M /trunk/samtools/bamtk.c
1686 M /trunk/samtools/bgzf.c
1687 M /trunk/samtools/sam.c
1688 M /trunk/samtools/sam_view.c
1690 * samtools-0.1.3-13 (r260)
1691 * report error for file I/O error
1693 ------------------------------------------------------------------------
1694 r260 | lh3lh3 | 2009-05-05 10:01:16 -0400 (Tue, 05 May 2009) | 2 lines
1696 M /trunk/samtools/Makefile.am
1700 ------------------------------------------------------------------------
1701 r259 | lh3lh3 | 2009-05-05 09:52:25 -0400 (Tue, 05 May 2009) | 3 lines
1703 M /trunk/samtools/bam.h
1704 M /trunk/samtools/bam_pileup.c
1705 M /trunk/samtools/bam_plcmd.c
1706 M /trunk/samtools/bamtk.c
1707 M /trunk/samtools/sam.c
1708 M /trunk/samtools/sam.h
1710 * samtools-0.1.3-12 (r259)
1711 * use the new I/O interface in pileup
1713 ------------------------------------------------------------------------
1714 r258 | lh3lh3 | 2009-05-05 09:33:22 -0400 (Tue, 05 May 2009) | 3 lines
1716 M /trunk/samtools/Makefile.generic
1717 M /trunk/samtools/Makefile.lite
1718 M /trunk/samtools/bam.c
1719 M /trunk/samtools/bam.h
1720 M /trunk/samtools/bam_import.c
1721 M /trunk/samtools/bamtk.c
1722 A /trunk/samtools/sam.c
1723 A /trunk/samtools/sam.h
1724 A /trunk/samtools/sam_view.c
1726 * samtools-0.1.3-11 (r258)
1727 * unify the interface to BAM and SAM I/O
1729 ------------------------------------------------------------------------
1730 r257 | lh3lh3 | 2009-05-05 04:53:35 -0400 (Tue, 05 May 2009) | 3 lines
1732 M /trunk/samtools/Makefile.lite
1733 M /trunk/samtools/bam_plcmd.c
1734 M /trunk/samtools/bamtk.c
1736 * samtools-0.1.3-10 (r257)
1737 * allow hex with "pileup -m"
1739 ------------------------------------------------------------------------
1740 r256 | lh3lh3 | 2009-05-04 14:16:50 -0400 (Mon, 04 May 2009) | 4 lines
1742 M /trunk/samtools/bam_lpileup.c
1743 M /trunk/samtools/bamtk.c
1745 * samtools-0.1.3-9 (r256)
1746 * fixed a bug in bam_lpileup.c
1747 * I do not know if this also fixes the bug causing assertion failure in the tview
1749 ------------------------------------------------------------------------
1750 r251 | lh3lh3 | 2009-04-28 08:53:23 -0400 (Tue, 28 Apr 2009) | 3 lines
1752 M /trunk/samtools/bam_pileup.c
1753 M /trunk/samtools/bamtk.c
1755 * samtools-0.1.3-8 (r251)
1756 * fixed a bug when there are reads without coordinates
1758 ------------------------------------------------------------------------
1759 r250 | lh3lh3 | 2009-04-28 08:43:33 -0400 (Tue, 28 Apr 2009) | 2 lines
1761 A /trunk/samtools/AUTHORS
1762 A /trunk/samtools/README
1763 M /trunk/samtools/cleanup.sh
1767 ------------------------------------------------------------------------
1768 r249 | lh3lh3 | 2009-04-28 08:37:16 -0400 (Tue, 28 Apr 2009) | 2 lines
1770 M /trunk/samtools/Makefile.generic
1771 M /trunk/samtools/Makefile.lite
1772 M /trunk/samtools/configure.ac
1773 M /trunk/samtools/misc/Makefile.generic
1775 improve large file support in compilation
1777 ------------------------------------------------------------------------
1778 r248 | lh3lh3 | 2009-04-28 08:33:24 -0400 (Tue, 28 Apr 2009) | 2 lines
1780 M /trunk/samtools/INSTALL
1784 ------------------------------------------------------------------------
1785 r247 | lh3lh3 | 2009-04-28 08:28:50 -0400 (Tue, 28 Apr 2009) | 2 lines
1787 M /trunk/samtools/Makefile.am
1788 M /trunk/samtools/autogen.sh
1789 M /trunk/samtools/cleanup.sh
1790 M /trunk/samtools/configure.ac
1791 A /trunk/samtools/misc/Makefile.am
1793 fixed various issues about the GNU building scripts
1795 ------------------------------------------------------------------------
1796 r246 | lh3lh3 | 2009-04-28 08:10:23 -0400 (Tue, 28 Apr 2009) | 4 lines
1798 M /trunk/samtools/ChangeLog
1799 D /trunk/samtools/Makefile
1800 A /trunk/samtools/Makefile.am
1801 A /trunk/samtools/Makefile.generic
1802 A /trunk/samtools/autogen.sh
1803 M /trunk/samtools/bam.h
1804 M /trunk/samtools/bam_aux.c
1805 M /trunk/samtools/bam_tview.c
1806 M /trunk/samtools/bamtk.c
1807 A /trunk/samtools/cleanup.sh
1808 A /trunk/samtools/configure.ac
1809 D /trunk/samtools/misc/Makefile
1810 A /trunk/samtools/misc/Makefile.generic (from /trunk/samtools/misc/Makefile:245)
1812 * samtools-0.1.3-7 (r246)
1813 * incorporated revisions from Nils Homer
1814 * enhanced support of displaying color-space reads
1816 ------------------------------------------------------------------------
1817 r244 | lh3lh3 | 2009-04-25 06:49:40 -0400 (Sat, 25 Apr 2009) | 3 lines
1819 M /trunk/samtools/bam_md.c
1820 M /trunk/samtools/bamtk.c
1822 * samtools-0.1.3-6 (r244)
1823 * fixed segfault for unmapped reads
1825 ------------------------------------------------------------------------
1826 r243 | lh3lh3 | 2009-04-24 16:27:26 -0400 (Fri, 24 Apr 2009) | 5 lines
1828 M /trunk/samtools/bam.h
1829 M /trunk/samtools/bam_maqcns.c
1830 M /trunk/samtools/bam_md.c
1831 M /trunk/samtools/bamtk.c
1833 * samtools-0.1.3-5 (r243)
1834 * fixed a long existing bug which may cause memory leak
1836 * consensus calling now works with "=", but indel calling not
1838 ------------------------------------------------------------------------
1839 r242 | lh3lh3 | 2009-04-24 15:44:46 -0400 (Fri, 24 Apr 2009) | 3 lines
1841 M /trunk/samtools/bam_md.c
1842 M /trunk/samtools/bamtk.c
1844 * samtools-0.1.3-4 (r242)
1845 * fixed a memory leak
1847 ------------------------------------------------------------------------
1848 r240 | lh3lh3 | 2009-04-24 11:40:18 -0400 (Fri, 24 Apr 2009) | 5 lines
1850 M /trunk/samtools/Makefile
1851 M /trunk/samtools/Makefile.lite
1852 M /trunk/samtools/bam.h
1853 M /trunk/samtools/bam_aux.c
1854 A /trunk/samtools/bam_md.c
1855 M /trunk/samtools/bam_plcmd.c
1856 M /trunk/samtools/bamtk.c
1858 * samtools-0.1.3-3 (r240)
1860 * generate "=" bases
1861 * the plain pileup now support "=" bases, but consensus calling and glfgen may fail
1863 ------------------------------------------------------------------------
1864 r239 | lh3lh3 | 2009-04-24 07:08:20 -0400 (Fri, 24 Apr 2009) | 5 lines
1866 M /trunk/samtools/bam.h
1867 M /trunk/samtools/bam_aux.c
1868 M /trunk/samtools/bamtk.c
1870 * samtools-0.1.3-2 (r239)
1871 * fixed bugs in bam_aux.c (these functions nevered used by samtools)
1872 * removed bam_aux_init()/bam_aux_destroy()
1873 * added tagview for testing bam_aux
1875 ------------------------------------------------------------------------
1876 r235 | lh3lh3 | 2009-04-21 18:17:39 -0400 (Tue, 21 Apr 2009) | 3 lines
1878 M /trunk/samtools/bam_pileup.c
1879 M /trunk/samtools/bamtk.c
1882 * fixed a bug in pileup: the first read in a chromosome may not be printed
1884 ------------------------------------------------------------------------
1885 r232 | lh3lh3 | 2009-04-16 10:25:43 -0400 (Thu, 16 Apr 2009) | 2 lines
1887 M /trunk/samtools/Makefile.lite
1889 a missing file in Makefile.lite
1891 ------------------------------------------------------------------------
1892 r227 | lh3lh3 | 2009-04-15 17:02:53 -0400 (Wed, 15 Apr 2009) | 2 lines
1894 M /trunk/samtools/NEWS
1895 M /trunk/samtools/bamtk.c
1897 Release samtools-0.1.3
1899 ------------------------------------------------------------------------
1900 r223 | lh3lh3 | 2009-04-15 09:31:32 -0400 (Wed, 15 Apr 2009) | 3 lines
1902 M /trunk/samtools/bam_plcmd.c
1903 M /trunk/samtools/bamtk.c
1906 * make samtools more robust to weird input such as empty file
1908 ------------------------------------------------------------------------
1909 r222 | lh3lh3 | 2009-04-15 09:05:33 -0400 (Wed, 15 Apr 2009) | 2 lines
1911 M /trunk/samtools/ChangeLog
1912 M /trunk/samtools/NEWS
1913 M /trunk/samtools/samtools.1
1915 prepare for release 0.1.3
1917 ------------------------------------------------------------------------
1918 r221 | lh3lh3 | 2009-04-15 08:32:14 -0400 (Wed, 15 Apr 2009) | 2 lines
1920 A /trunk/samtools/misc/blast2sam.pl
1922 convert NCBI-BLASTN to SAM
1924 ------------------------------------------------------------------------
1925 r220 | lh3lh3 | 2009-04-15 08:18:19 -0400 (Wed, 15 Apr 2009) | 3 lines
1927 M /trunk/samtools/bam_lpileup.c
1928 M /trunk/samtools/bamtk.c
1931 * fixed a small memory leak in tview
1933 ------------------------------------------------------------------------
1934 r219 | lh3lh3 | 2009-04-15 08:00:08 -0400 (Wed, 15 Apr 2009) | 3 lines
1936 M /trunk/samtools/bam_rmdup.c
1937 M /trunk/samtools/bamtk.c
1940 * fixed a bug in rmdup when there are unmapped reads
1942 ------------------------------------------------------------------------
1943 r218 | lh3lh3 | 2009-04-14 17:28:58 -0400 (Tue, 14 Apr 2009) | 2 lines
1945 M /trunk/samtools/ChangeLog
1946 M /trunk/samtools/NEWS
1948 proposed NEWS for the new release (have not yet)
1950 ------------------------------------------------------------------------
1951 r216 | lh3lh3 | 2009-04-14 17:10:46 -0400 (Tue, 14 Apr 2009) | 4 lines
1953 M /trunk/samtools/misc/samtools.pl
1956 * improve indelFilter to avoid filtering true indels. The new filter relies
1957 on the new pileup indel line implemented in samtools-0.1.2-25
1959 ------------------------------------------------------------------------
1960 r215 | lh3lh3 | 2009-04-14 17:04:19 -0400 (Tue, 14 Apr 2009) | 4 lines
1962 M /trunk/samtools/bam_maqcns.c
1963 M /trunk/samtools/bam_plcmd.c
1964 M /trunk/samtools/bamtk.c
1965 M /trunk/samtools/samtools.1
1968 * change the pileup indel line to shows the number of alignments actually
1971 ------------------------------------------------------------------------
1972 r211 | lh3lh3 | 2009-04-13 07:07:13 -0400 (Mon, 13 Apr 2009) | 2 lines
1974 M /trunk/samtools/ChangeLog
1976 update ChangeLog from "svn log"
1978 ------------------------------------------------------------------------
1979 r210 | lh3lh3 | 2009-04-12 15:57:05 -0400 (Sun, 12 Apr 2009) | 4 lines
1981 M /trunk/samtools/bam.c
1982 M /trunk/samtools/bam_import.c
1983 M /trunk/samtools/bam_sort.c
1984 M /trunk/samtools/bamtk.c
1985 M /trunk/samtools/kseq.h
1988 * in merge, gives a warning rather than error if the target sequence length is different
1989 * allow empty header
1991 ------------------------------------------------------------------------
1992 r209 | lh3lh3 | 2009-04-12 15:32:44 -0400 (Sun, 12 Apr 2009) | 3 lines
1994 M /trunk/samtools/bam.c
1995 M /trunk/samtools/bam_import.c
1996 M /trunk/samtools/bamtk.c
1999 * recognize '*' at the QUAL field
2001 ------------------------------------------------------------------------
2002 r208 | lh3lh3 | 2009-04-12 15:08:02 -0400 (Sun, 12 Apr 2009) | 3 lines
2004 M /trunk/samtools/bam_import.c
2005 M /trunk/samtools/bamtk.c
2006 M /trunk/samtools/kseq.h
2009 * the field separater is TAB only, now
2011 ------------------------------------------------------------------------
2012 r207 | lh3lh3 | 2009-04-08 10:18:03 -0400 (Wed, 08 Apr 2009) | 2 lines
2014 M /trunk/samtools/examples/ex1.sam.gz
2016 * fixed the problem in the example alignment due to the bug in fixmate
2018 ------------------------------------------------------------------------
2019 r206 | lh3lh3 | 2009-04-08 10:15:05 -0400 (Wed, 08 Apr 2009) | 3 lines
2021 M /trunk/samtools/bam_mate.c
2022 M /trunk/samtools/bamtk.c
2023 M /trunk/samtools/misc/soap2sam.pl
2026 * fixed a nasty bug in `fixmate'
2028 ------------------------------------------------------------------------
2029 r205 | lh3lh3 | 2009-04-08 05:57:08 -0400 (Wed, 08 Apr 2009) | 2 lines
2031 M /trunk/samtools/misc/bowtie2sam.pl
2032 M /trunk/samtools/misc/soap2sam.pl
2033 M /trunk/samtools/misc/wgsim_eval.pl
2035 make the script robust to the bugs in SOAP-2.1.7
2037 ------------------------------------------------------------------------
2038 r200 | lh3lh3 | 2009-04-02 10:14:56 -0400 (Thu, 02 Apr 2009) | 3 lines
2040 M /trunk/samtools/bam_stat.c
2041 M /trunk/samtools/bamtk.c
2044 * check if file is truncated in flagstat
2046 ------------------------------------------------------------------------
2047 r199 | lh3lh3 | 2009-04-02 10:09:10 -0400 (Thu, 02 Apr 2009) | 3 lines
2049 M /trunk/samtools/bamtk.c
2052 * print the header if requested
2054 ------------------------------------------------------------------------
2055 r193 | lh3lh3 | 2009-03-27 11:09:50 -0400 (Fri, 27 Mar 2009) | 3 lines
2057 M /trunk/samtools/bam_plcmd.c
2058 M /trunk/samtools/bamtk.c
2061 * fixed a minor bug reported by Nils Homer
2063 ------------------------------------------------------------------------
2064 r185 | lh3lh3 | 2009-03-24 07:50:32 -0400 (Tue, 24 Mar 2009) | 2 lines
2066 A /trunk/samtools/Makefile (from /trunk/samtools/Makefile.std:184)
2067 D /trunk/samtools/Makefile.std
2068 A /trunk/samtools/misc/Makefile (from /trunk/samtools/misc/Makefile.std:184)
2069 D /trunk/samtools/misc/Makefile.std
2071 rename Makefile.std as Makefile. GNU building systerm is not ready and may take some time...
2073 ------------------------------------------------------------------------
2074 r184 | lh3lh3 | 2009-03-24 06:36:38 -0400 (Tue, 24 Mar 2009) | 4 lines
2076 D /trunk/samtools/Makefile
2077 A /trunk/samtools/Makefile.std (from /trunk/samtools/Makefile:183)
2078 M /trunk/samtools/bam_sort.c
2079 M /trunk/samtools/bam_tview.c
2080 M /trunk/samtools/bamtk.c
2081 D /trunk/samtools/misc/Makefile
2082 A /trunk/samtools/misc/Makefile.std (from /trunk/samtools/misc/Makefile:182)
2083 M /trunk/samtools/samtools.1
2086 * incorporating Nils' changes
2087 * rename Makefile to Makefile.std and prepare to add the GNU building systerms (also by Nils)
2089 ------------------------------------------------------------------------
2090 r183 | lh3lh3 | 2009-03-24 06:30:23 -0400 (Tue, 24 Mar 2009) | 4 lines
2092 M /trunk/samtools/Makefile
2093 M /trunk/samtools/bam_import.c
2094 M /trunk/samtools/bam_maqcns.c
2095 M /trunk/samtools/bam_maqcns.h
2096 M /trunk/samtools/bam_plcmd.c
2097 M /trunk/samtools/bamtk.c
2098 M /trunk/samtools/kseq.h
2099 A /trunk/samtools/kstring.c
2100 A /trunk/samtools/kstring.h
2103 * made pileup take a list of proposed indels. An insertion is N at the moment.
2104 * added my kstring library for a bit complex parsing of the position list.
2106 ------------------------------------------------------------------------
2107 r169 | lh3lh3 | 2009-03-12 09:40:14 -0400 (Thu, 12 Mar 2009) | 3 lines
2109 M /trunk/samtools/misc/soap2sam.pl
2112 * more robust to truncated soap output
2114 ------------------------------------------------------------------------
2115 r168 | lh3lh3 | 2009-03-11 06:49:00 -0400 (Wed, 11 Mar 2009) | 2 lines
2117 M /trunk/samtools/Makefile.lite
2119 added bam_stat.o to Makefile.lite
2121 ------------------------------------------------------------------------
2122 r167 | lh3lh3 | 2009-03-10 18:11:31 -0400 (Tue, 10 Mar 2009) | 3 lines
2124 M /trunk/samtools/bam_maqcns.c
2125 M /trunk/samtools/bamtk.c
2128 * generate RMS of mapQ instead of max mapQ
2130 ------------------------------------------------------------------------
2131 r166 | lh3lh3 | 2009-03-10 18:06:45 -0400 (Tue, 10 Mar 2009) | 3 lines
2133 M /trunk/samtools/bam_plcmd.c
2134 M /trunk/samtools/bamtk.c
2135 M /trunk/samtools/glf.c
2136 M /trunk/samtools/glf.h
2137 M /trunk/samtools/misc/Makefile
2142 ------------------------------------------------------------------------
2143 r159 | lh3lh3 | 2009-03-03 06:26:08 -0500 (Tue, 03 Mar 2009) | 3 lines
2145 M /trunk/samtools/bam_plcmd.c
2146 M /trunk/samtools/bamtk.c
2149 * fixed a minor bug in displaying pileup
2151 ------------------------------------------------------------------------
2152 r158 | lh3lh3 | 2009-03-03 06:24:16 -0500 (Tue, 03 Mar 2009) | 3 lines
2154 M /trunk/samtools/ChangeLog
2155 M /trunk/samtools/bamtk.c
2158 * optionally print SAM header
2160 ------------------------------------------------------------------------
2161 r153 | lh3lh3 | 2009-03-02 05:45:28 -0500 (Mon, 02 Mar 2009) | 3 lines
2163 M /trunk/samtools/bamtk.c
2164 M /trunk/samtools/glf.c
2167 * use "GLF\3" as the magic for GLFv3 files
2169 ------------------------------------------------------------------------
2170 r152 | lh3lh3 | 2009-03-02 05:39:09 -0500 (Mon, 02 Mar 2009) | 5 lines
2172 M /trunk/samtools/Makefile
2173 M /trunk/samtools/bam_import.c
2174 M /trunk/samtools/bam_index.c
2175 M /trunk/samtools/bam_plcmd.c
2176 M /trunk/samtools/bamtk.c
2177 M /trunk/samtools/glf.c
2178 M /trunk/samtools/glf.h
2181 * fixed a bug in import: core.bin is undefined for unmapped reads
2182 * this bug can be alleviated (not completely solved) in bam_index.c
2183 * update to GLFv3: pos is changed to offset for better compression
2185 ------------------------------------------------------------------------
2186 r151 | lh3lh3 | 2009-03-01 10:18:43 -0500 (Sun, 01 Mar 2009) | 3 lines
2188 M /trunk/samtools/misc/wgsim.c
2191 * fixed a bug in simulating indels
2193 ------------------------------------------------------------------------
2194 r145 | lh3lh3 | 2009-02-26 14:43:57 -0500 (Thu, 26 Feb 2009) | 4 lines
2196 M /trunk/samtools/misc/wgsim.c
2199 * allow to print mismatch information as fastq comment. MAQ does
2200 not like long read names.
2202 ------------------------------------------------------------------------
2203 r141 | lh3lh3 | 2009-02-26 09:53:03 -0500 (Thu, 26 Feb 2009) | 6 lines
2205 M /trunk/samtools/ChangeLog
2206 M /trunk/samtools/misc/wgsim.c
2207 M /trunk/samtools/misc/wgsim_eval.pl
2210 * fixed a bug about color read coordinates
2211 * fixed a bug in read names
2212 * wgsim_eval.pl-0.1.3
2213 * make the script work with color reads
2215 ------------------------------------------------------------------------
2216 r140 | lh3lh3 | 2009-02-26 09:02:57 -0500 (Thu, 26 Feb 2009) | 2 lines
2218 M /trunk/samtools/misc/Makefile
2219 M /trunk/samtools/misc/wgsim.c
2221 * wgsim: added a note
2223 ------------------------------------------------------------------------
2224 r139 | lh3lh3 | 2009-02-26 06:39:08 -0500 (Thu, 26 Feb 2009) | 7 lines
2226 M /trunk/samtools/misc/wgsim.c
2227 M /trunk/samtools/misc/wgsim_eval.pl
2230 * considerable code clean up
2231 * print number of substitutions/indels/errors on each read
2232 * potentially support SOLiD simulation, though not tested at the moment
2233 * wgsim_eval.pl-0.1.2
2234 * change in accordant with wgsim
2236 ------------------------------------------------------------------------
2237 r129 | lh3lh3 | 2009-02-18 17:23:27 -0500 (Wed, 18 Feb 2009) | 3 lines
2239 M /trunk/samtools/bam_index.c
2240 M /trunk/samtools/bamtk.c
2243 * fixed a bug in bam_fetch, caused by completely contained adjacent chunks
2245 ------------------------------------------------------------------------
2246 r128 | bhandsaker | 2009-02-18 14:06:57 -0500 (Wed, 18 Feb 2009) | 2 lines
2248 M /trunk/samtools/bamtk.c
2250 Fix annoying segv when invalid region specified.
2252 ------------------------------------------------------------------------
2253 r127 | lh3lh3 | 2009-02-17 05:49:55 -0500 (Tue, 17 Feb 2009) | 2 lines
2255 D /trunk/samtools/misc/indel_filter.pl
2256 A /trunk/samtools/misc/samtools.pl
2258 * move indel_filter.pl to samtools.pl
2260 ------------------------------------------------------------------------
2261 r126 | lh3lh3 | 2009-02-14 16:22:30 -0500 (Sat, 14 Feb 2009) | 3 lines
2263 M /trunk/samtools/bam_mate.c
2264 M /trunk/samtools/bamtk.c
2267 * fixed a bug in fixmate: SE reads are flagged as BAM_FMUNMAP
2269 ------------------------------------------------------------------------
2270 r125 | lh3lh3 | 2009-02-13 04:54:45 -0500 (Fri, 13 Feb 2009) | 3 lines
2272 M /trunk/samtools/bam_stat.c
2273 M /trunk/samtools/bamtk.c
2276 * fixed a minor bug in flagstat
2278 ------------------------------------------------------------------------
2279 r124 | lh3lh3 | 2009-02-12 06:15:32 -0500 (Thu, 12 Feb 2009) | 3 lines
2281 M /trunk/samtools/bam_maqcns.c
2282 M /trunk/samtools/bamtk.c
2283 M /trunk/samtools/misc/indel_filter.pl
2286 * improve indel caller by setting maximum window size
2288 ------------------------------------------------------------------------
2289 r123 | lh3lh3 | 2009-02-12 05:30:29 -0500 (Thu, 12 Feb 2009) | 2 lines
2291 M /trunk/samtools/bam_plcmd.c
2292 M /trunk/samtools/bamtk.c
2294 * output max mapping quality in indel line
2296 ------------------------------------------------------------------------
2297 r122 | lh3lh3 | 2009-02-11 05:59:10 -0500 (Wed, 11 Feb 2009) | 2 lines
2299 M /trunk/samtools/misc/maq2sam.c
2301 fixed a bug in generating tag AM
2303 ------------------------------------------------------------------------
2304 r121 | lh3lh3 | 2009-02-03 05:43:11 -0500 (Tue, 03 Feb 2009) | 2 lines
2306 M /trunk/samtools/bam_index.c
2307 M /trunk/samtools/bamtk.c
2309 fixed a potential memory problem in indexing
2311 ------------------------------------------------------------------------
2312 r120 | bhandsaker | 2009-02-02 10:52:52 -0500 (Mon, 02 Feb 2009) | 2 lines
2314 M /trunk/samtools/Makefile
2316 Pass LIBS to recursive targets to facilitate building at Broad.
2318 ------------------------------------------------------------------------
2319 r119 | lh3lh3 | 2009-02-02 05:12:15 -0500 (Mon, 02 Feb 2009) | 4 lines
2321 M /trunk/samtools/ChangeLog
2322 M /trunk/samtools/bam_plcmd.c
2323 M /trunk/samtools/bam_stat.c
2324 M /trunk/samtools/bamtk.c
2327 * fixed a bug in generating GLFv2 for indels
2328 * improve flagstat report a little bit
2330 ------------------------------------------------------------------------
2331 r118 | lh3lh3 | 2009-01-29 07:33:23 -0500 (Thu, 29 Jan 2009) | 3 lines
2333 M /trunk/samtools/Makefile
2334 A /trunk/samtools/bam_stat.c
2335 M /trunk/samtools/bamtk.c
2338 * added flagstat command
2340 ------------------------------------------------------------------------
2341 r116 | lh3lh3 | 2009-01-28 08:31:12 -0500 (Wed, 28 Jan 2009) | 2 lines
2343 M /trunk/samtools/ChangeLog
2344 M /trunk/samtools/NEWS
2345 M /trunk/samtools/bamtk.c
2346 M /trunk/samtools/samtools.1
2348 Release SAMtools-0.1.2
2350 ------------------------------------------------------------------------
2351 r115 | lh3lh3 | 2009-01-28 07:54:08 -0500 (Wed, 28 Jan 2009) | 2 lines
2353 A /trunk/samtools/misc/indel_filter.pl
2355 Script for filtering indel results
2357 ------------------------------------------------------------------------
2358 r114 | lh3lh3 | 2009-01-25 06:45:37 -0500 (Sun, 25 Jan 2009) | 2 lines
2360 A /trunk/samtools/misc/zoom2sam.pl
2364 ------------------------------------------------------------------------
2365 r113 | lh3lh3 | 2009-01-24 09:25:07 -0500 (Sat, 24 Jan 2009) | 2 lines
2367 A /trunk/samtools/misc/novo2sam.pl
2369 add a script to convert novo alignment to SAM
2371 ------------------------------------------------------------------------
2372 r112 | lh3lh3 | 2009-01-23 15:57:39 -0500 (Fri, 23 Jan 2009) | 2 lines
2374 M /trunk/samtools/ChangeLog
2375 M /trunk/samtools/ChangeLog.old
2376 M /trunk/samtools/samtools.1
2378 update documentation and ChangeLog
2380 ------------------------------------------------------------------------
2381 r111 | lh3lh3 | 2009-01-23 14:22:59 -0500 (Fri, 23 Jan 2009) | 3 lines
2383 M /trunk/samtools/bam_sort.c
2384 M /trunk/samtools/bamtk.c
2387 * fixed a bug in "merge" command line
2389 ------------------------------------------------------------------------
2390 r110 | lh3lh3 | 2009-01-22 10:36:48 -0500 (Thu, 22 Jan 2009) | 3 lines
2392 M /trunk/samtools/misc/Makefile
2393 A /trunk/samtools/misc/bowtie2sam.pl (from /branches/dev/samtools/misc/bowtie2sam.pl:108)
2394 M /trunk/samtools/misc/export2sam.pl
2395 A /trunk/samtools/misc/soap2sam.pl (from /branches/dev/samtools/misc/soap2sam.pl:108)
2396 A /trunk/samtools/misc/wgsim.c (from /branches/dev/samtools/misc/wgsim.c:108)
2397 A /trunk/samtools/misc/wgsim_eval.pl (from /branches/dev/samtools/misc/wgsim_eval.pl:108)
2399 * merge from branches/dev/
2400 * all future development will happen here
2402 ------------------------------------------------------------------------
2403 r109 | lh3lh3 | 2009-01-22 10:14:27 -0500 (Thu, 22 Jan 2009) | 3 lines
2405 M /trunk/samtools/COPYING
2406 M /trunk/samtools/ChangeLog
2407 A /trunk/samtools/INSTALL (from /branches/dev/samtools/INSTALL:108)
2408 M /trunk/samtools/Makefile
2409 A /trunk/samtools/Makefile.lite (from /branches/dev/samtools/Makefile.lite:108)
2410 M /trunk/samtools/bam.c
2411 M /trunk/samtools/bam.h
2412 M /trunk/samtools/bam_import.c
2413 M /trunk/samtools/bam_index.c
2414 M /trunk/samtools/bam_lpileup.c
2415 M /trunk/samtools/bam_maqcns.c
2416 M /trunk/samtools/bam_maqcns.h
2417 A /trunk/samtools/bam_mate.c (from /branches/dev/samtools/bam_mate.c:108)
2418 M /trunk/samtools/bam_pileup.c
2419 M /trunk/samtools/bam_plcmd.c
2420 A /trunk/samtools/bam_rmdup.c (from /branches/dev/samtools/bam_rmdup.c:108)
2421 M /trunk/samtools/bam_sort.c
2422 M /trunk/samtools/bamtk.c
2423 M /trunk/samtools/bgzf.h
2424 M /trunk/samtools/examples/00README.txt
2425 A /trunk/samtools/examples/Makefile (from /branches/dev/samtools/examples/Makefile:108)
2426 D /trunk/samtools/examples/ex1.fa.fai
2427 M /trunk/samtools/examples/ex1.sam.gz
2428 M /trunk/samtools/faidx.c
2429 A /trunk/samtools/glf.c (from /branches/dev/samtools/glf.c:108)
2430 M /trunk/samtools/glf.h
2431 M /trunk/samtools/misc/Makefile
2432 M /trunk/samtools/misc/maq2sam.c
2433 M /trunk/samtools/razf.c
2434 M /trunk/samtools/source.dot
2436 * Merge from branches/dev/
2437 * all future development will happen here at trunk/
2439 ------------------------------------------------------------------------
2440 r79 | bhandsaker | 2009-01-07 16:42:15 -0500 (Wed, 07 Jan 2009) | 2 lines
2442 M /trunk/samtools/bam_maqcns.c
2443 M /trunk/samtools/bam_tview.c
2445 Fix problem with compiling without curses.
2447 ------------------------------------------------------------------------
2448 r63 | lh3lh3 | 2008-12-22 10:58:02 -0500 (Mon, 22 Dec 2008) | 2 lines
2450 A /trunk/samtools (from /branches/dev/samtools:62)
2454 ------------------------------------------------------------------------
2455 r62 | lh3lh3 | 2008-12-22 10:55:13 -0500 (Mon, 22 Dec 2008) | 2 lines
2457 A /branches/dev/samtools/NEWS
2458 M /branches/dev/samtools/bamtk.c
2459 M /branches/dev/samtools/samtools.1
2461 Release samtools-0.1.1
2463 ------------------------------------------------------------------------
2464 r61 | lh3lh3 | 2008-12-22 10:46:08 -0500 (Mon, 22 Dec 2008) | 10 lines
2466 M /branches/dev/samtools/bam_aux.c
2467 M /branches/dev/samtools/bam_index.c
2468 M /branches/dev/samtools/bam_plcmd.c
2469 M /branches/dev/samtools/bam_tview.c
2470 M /branches/dev/samtools/bamtk.c
2471 M /branches/dev/samtools/razf.c
2472 M /branches/dev/samtools/samtools.1
2475 * fixed a bug in razf.c: reset z_eof when razf_seek() is called
2476 * fixed a memory leak in parsing a region
2477 * changed pileup a little bit when -s is in use: output ^ and $
2478 * when a bam is not indexed, output more meaningful error message
2479 * fixed a bug in indexing for small alignment
2480 * fixed a bug in the viewer when we come to the end of a reference file
2481 * updated documentation
2482 * prepare to release 0.1.1
2484 ------------------------------------------------------------------------
2485 r60 | lh3lh3 | 2008-12-22 10:10:16 -0500 (Mon, 22 Dec 2008) | 2 lines
2487 A /branches/dev/samtools/examples
2488 A /branches/dev/samtools/examples/00README.txt
2489 A /branches/dev/samtools/examples/ex1.fa
2490 A /branches/dev/samtools/examples/ex1.fa.fai
2491 A /branches/dev/samtools/examples/ex1.sam.gz
2495 ------------------------------------------------------------------------
2496 r59 | lh3lh3 | 2008-12-22 04:38:15 -0500 (Mon, 22 Dec 2008) | 2 lines
2498 M /branches/dev/samtools/ChangeLog
2502 ------------------------------------------------------------------------
2503 r58 | lh3lh3 | 2008-12-20 18:06:00 -0500 (Sat, 20 Dec 2008) | 3 lines
2505 M /branches/dev/samtools/misc/export2sam.pl
2508 * fixed several bugs
2510 ------------------------------------------------------------------------
2511 r57 | lh3lh3 | 2008-12-20 10:44:20 -0500 (Sat, 20 Dec 2008) | 2 lines
2513 A /branches/dev/samtools/misc/export2sam.pl
2515 convert Export format to SAM; not thoroughly tested
2517 ------------------------------------------------------------------------
2518 r56 | lh3lh3 | 2008-12-19 17:13:28 -0500 (Fri, 19 Dec 2008) | 6 lines
2520 M /branches/dev/samtools/bam_import.c
2521 M /branches/dev/samtools/bam_plcmd.c
2522 M /branches/dev/samtools/bam_tview.c
2523 M /branches/dev/samtools/bamtk.c
2524 A /branches/dev/samtools/source.dot
2527 * pileup: generate maq-like simple output
2528 * pileup: allow to output pileup at required sites
2529 * source.dot: source file relationship graph
2530 * tview: fixed a minor bug
2532 ------------------------------------------------------------------------
2533 r55 | lh3lh3 | 2008-12-19 15:10:26 -0500 (Fri, 19 Dec 2008) | 2 lines
2535 D /branches/dev/samtools/misc/all2sam.pl
2539 ------------------------------------------------------------------------
2540 r54 | lh3lh3 | 2008-12-16 17:34:25 -0500 (Tue, 16 Dec 2008) | 2 lines
2542 A /branches/dev/samtools/COPYING
2543 M /branches/dev/samtools/bam.h
2544 M /branches/dev/samtools/faidx.h
2545 M /branches/dev/samtools/khash.h
2546 M /branches/dev/samtools/kseq.h
2547 M /branches/dev/samtools/ksort.h
2548 M /branches/dev/samtools/samtools.1
2550 Added copyright information and a bit more documentation. No code change.
2552 ------------------------------------------------------------------------
2553 r53 | lh3lh3 | 2008-12-16 08:40:18 -0500 (Tue, 16 Dec 2008) | 3 lines
2555 M /branches/dev/samtools/bam.c
2556 M /branches/dev/samtools/bam.h
2557 M /branches/dev/samtools/bam_index.c
2558 M /branches/dev/samtools/bam_maqcns.c
2559 M /branches/dev/samtools/bamtk.c
2562 * improved efficiency of the indel caller for spliced alignments
2564 ------------------------------------------------------------------------
2565 r52 | lh3lh3 | 2008-12-16 05:28:20 -0500 (Tue, 16 Dec 2008) | 3 lines
2567 M /branches/dev/samtools/bam.c
2568 M /branches/dev/samtools/bam.h
2569 M /branches/dev/samtools/bam_aux.c
2570 M /branches/dev/samtools/bam_index.c
2571 M /branches/dev/samtools/bamtk.c
2574 * a bit code cleanup: reduce the dependency between source files
2576 ------------------------------------------------------------------------
2577 r51 | lh3lh3 | 2008-12-15 09:29:32 -0500 (Mon, 15 Dec 2008) | 3 lines
2579 M /branches/dev/samtools/bam_maqcns.c
2580 M /branches/dev/samtools/bam_plcmd.c
2581 M /branches/dev/samtools/bamtk.c
2584 * fixed a memory leak
2586 ------------------------------------------------------------------------
2587 r50 | lh3lh3 | 2008-12-15 09:00:13 -0500 (Mon, 15 Dec 2008) | 2 lines
2589 M /branches/dev/samtools/ChangeLog
2590 M /branches/dev/samtools/bam.h
2591 M /branches/dev/samtools/samtools.1
2593 update documentation, ChangeLog and a comment
2595 ------------------------------------------------------------------------
2596 r49 | lh3lh3 | 2008-12-15 08:36:43 -0500 (Mon, 15 Dec 2008) | 6 lines
2598 M /branches/dev/samtools/Makefile
2599 M /branches/dev/samtools/bam.h
2600 M /branches/dev/samtools/bam_maqcns.c
2601 M /branches/dev/samtools/bam_maqcns.h
2602 M /branches/dev/samtools/bam_pileup.c
2603 A /branches/dev/samtools/bam_plcmd.c
2604 M /branches/dev/samtools/bamtk.c
2605 M /branches/dev/samtools/samtools.1
2608 * moved pileup command to a separate source file
2609 * added indel caller
2610 * added bam_cal_segend(). (NOT WORKING for spliced alignment!!!)
2611 * updated documentation
2613 ------------------------------------------------------------------------
2614 r48 | lh3lh3 | 2008-12-12 08:55:36 -0500 (Fri, 12 Dec 2008) | 3 lines
2616 M /branches/dev/samtools/bam_maqcns.c
2617 M /branches/dev/samtools/bamtk.c
2620 * fixed another bug in maqcns when there is a nearby deletion
2622 ------------------------------------------------------------------------
2623 r47 | lh3lh3 | 2008-12-12 08:42:16 -0500 (Fri, 12 Dec 2008) | 5 lines
2625 M /branches/dev/samtools/bam_maqcns.c
2626 M /branches/dev/samtools/bam_pileup.c
2627 M /branches/dev/samtools/bamtk.c
2630 * pileup: outputing consensus is now optional
2631 * fixed a bug in glfgen. This bug also exists in maq's glfgen. However,
2632 I am not quite sure why the previous version may have problem.
2634 ------------------------------------------------------------------------
2635 r46 | lh3lh3 | 2008-12-12 06:44:56 -0500 (Fri, 12 Dec 2008) | 6 lines
2637 M /branches/dev/samtools/bam_pileup.c
2638 M /branches/dev/samtools/bamtk.c
2641 * add maq consensus to pileup. However, I will move this part to a new
2642 command as strictly speaking, consensus callin is not part of pileup,
2643 and imposing it would make it harder to generate for other language
2646 ------------------------------------------------------------------------
2647 r45 | bhandsaker | 2008-12-11 15:43:56 -0500 (Thu, 11 Dec 2008) | 2 lines
2649 M /branches/dev/samtools/bgzf.c
2651 Fix bug in tell() after reads that consume to the exact end of a block.
2653 ------------------------------------------------------------------------
2654 r44 | lh3lh3 | 2008-12-11 04:36:53 -0500 (Thu, 11 Dec 2008) | 2 lines
2656 M /branches/dev/samtools/samtools.1
2660 ------------------------------------------------------------------------
2661 r43 | lh3lh3 | 2008-12-11 04:25:36 -0500 (Thu, 11 Dec 2008) | 4 lines
2663 M /branches/dev/samtools/bam_import.c
2664 M /branches/dev/samtools/bamtk.c
2667 * fixed a bug in parser when there is auxiliary fields
2668 * made the parser a bit more robust
2670 ------------------------------------------------------------------------
2671 r42 | lh3lh3 | 2008-12-10 09:57:29 -0500 (Wed, 10 Dec 2008) | 5 lines
2673 M /branches/dev/samtools/bam_index.c
2674 M /branches/dev/samtools/bamtk.c
2675 M /branches/dev/samtools/bgzf.c
2678 * fixed a bug in bgzf (only reading is affected)
2679 * fixed a typo in bam_index.c
2680 * in bam_index.c, check potential bugs in the underlying I/O library
2682 ------------------------------------------------------------------------
2683 r41 | lh3lh3 | 2008-12-10 07:53:08 -0500 (Wed, 10 Dec 2008) | 2 lines
2685 M /branches/dev/samtools/samtools.1
2689 ------------------------------------------------------------------------
2690 r40 | lh3lh3 | 2008-12-10 06:52:10 -0500 (Wed, 10 Dec 2008) | 5 lines
2692 M /branches/dev/samtools/bam.h
2693 M /branches/dev/samtools/bam_pileup.c
2694 M /branches/dev/samtools/bamtk.c
2697 * tried to make pileup work with clipping (previously not), though NOT tested
2698 * removed -v from pileup
2699 * made pileup take the reference sequence
2701 ------------------------------------------------------------------------
2702 r39 | lh3lh3 | 2008-12-09 06:59:28 -0500 (Tue, 09 Dec 2008) | 4 lines
2704 M /branches/dev/samtools/bam_import.c
2705 M /branches/dev/samtools/bamtk.c
2706 M /branches/dev/samtools/samtools.1
2709 * in parser, recognize "=", rather than ",", as a match
2710 * in parser, correctl parse "=" at the MRNM field.
2712 ------------------------------------------------------------------------
2713 r38 | lh3lh3 | 2008-12-09 06:39:07 -0500 (Tue, 09 Dec 2008) | 2 lines
2715 M /branches/dev/samtools/misc/maq2sam.c
2717 fixed a bug in handling maq flag 64 and 192
2719 ------------------------------------------------------------------------
2720 r37 | lh3lh3 | 2008-12-09 04:53:46 -0500 (Tue, 09 Dec 2008) | 2 lines
2722 M /branches/dev/samtools/misc/md5fa.c
2724 also calculate unordered md5sum check
2726 ------------------------------------------------------------------------
2727 r36 | lh3lh3 | 2008-12-09 04:46:21 -0500 (Tue, 09 Dec 2008) | 2 lines
2729 M /branches/dev/samtools/misc/md5fa.c
2731 fixed a minor bug when there are space in the sequence
2733 ------------------------------------------------------------------------
2734 r35 | lh3lh3 | 2008-12-09 04:40:45 -0500 (Tue, 09 Dec 2008) | 2 lines
2736 M /branches/dev/samtools/misc/md5fa.c
2738 fixed a potential memory leak
2740 ------------------------------------------------------------------------
2741 r34 | lh3lh3 | 2008-12-08 09:52:17 -0500 (Mon, 08 Dec 2008) | 2 lines
2743 M /branches/dev/samtools/bam_import.c
2744 M /branches/dev/samtools/bam_index.c
2745 M /branches/dev/samtools/bamtk.c
2747 * fixed a bug in import: bin is wrongly calculated
2749 ------------------------------------------------------------------------
2750 r33 | lh3lh3 | 2008-12-08 09:08:01 -0500 (Mon, 08 Dec 2008) | 2 lines
2752 M /branches/dev/samtools/misc/all2sam.pl
2756 ------------------------------------------------------------------------
2757 r32 | lh3lh3 | 2008-12-08 07:56:02 -0500 (Mon, 08 Dec 2008) | 3 lines
2759 M /branches/dev/samtools/Makefile
2760 M /branches/dev/samtools/kseq.h
2761 M /branches/dev/samtools/misc/Makefile
2762 A /branches/dev/samtools/misc/md5.c
2763 A /branches/dev/samtools/misc/md5.h
2764 A /branches/dev/samtools/misc/md5fa.c
2766 * fixed two warnings in kseq.h
2767 * added md5sum utilities
2769 ------------------------------------------------------------------------
2770 r31 | lh3lh3 | 2008-12-08 06:35:29 -0500 (Mon, 08 Dec 2008) | 5 lines
2772 M /branches/dev/samtools/Makefile
2773 M /branches/dev/samtools/bam_import.c
2774 M /branches/dev/samtools/bamtk.c
2775 A /branches/dev/samtools/kseq.h
2776 D /branches/dev/samtools/kstream.h
2779 * replace kstream with kseq. kseq is a superset of kstream. I need the
2780 extra functions in kseq.h.
2781 * also compile stand-alone faidx
2783 ------------------------------------------------------------------------
2784 r30 | lh3lh3 | 2008-12-08 06:17:04 -0500 (Mon, 08 Dec 2008) | 3 lines
2786 M /branches/dev/samtools/bam.h
2787 M /branches/dev/samtools/bam_sort.c
2788 M /branches/dev/samtools/bamtk.c
2791 * sorting by read names is available
2793 ------------------------------------------------------------------------
2794 r29 | lh3lh3 | 2008-12-08 05:29:02 -0500 (Mon, 08 Dec 2008) | 3 lines
2796 M /branches/dev/samtools/bam.c
2797 M /branches/dev/samtools/bam.h
2798 M /branches/dev/samtools/bam_import.c
2799 M /branches/dev/samtools/bam_maqcns.c
2800 M /branches/dev/samtools/bam_pileup.c
2801 M /branches/dev/samtools/bam_sort.c
2802 M /branches/dev/samtools/bam_tview.c
2803 M /branches/dev/samtools/bamtk.c
2804 M /branches/dev/samtools/misc/maq2sam.c
2807 * format change to meet the latest specification
2809 ------------------------------------------------------------------------
2810 r28 | lh3lh3 | 2008-12-04 11:09:21 -0500 (Thu, 04 Dec 2008) | 3 lines
2812 M /branches/dev/samtools/bam_maqcns.c
2813 M /branches/dev/samtools/misc/maq2sam.c
2815 * minor change in maqcns: special care when n==0
2816 * change maq2sam to meet the latest specification
2818 ------------------------------------------------------------------------
2819 r27 | lh3lh3 | 2008-12-04 10:55:44 -0500 (Thu, 04 Dec 2008) | 2 lines
2821 M /branches/dev/samtools/razf.c
2822 M /branches/dev/samtools/razf.h
2824 considerable code clean up in razf
2826 ------------------------------------------------------------------------
2827 r26 | lh3lh3 | 2008-12-04 10:08:18 -0500 (Thu, 04 Dec 2008) | 2 lines
2829 M /branches/dev/samtools/ChangeLog
2830 M /branches/dev/samtools/Makefile
2831 M /branches/dev/samtools/faidx.c
2833 make RAZF optional in faidx.c
2835 ------------------------------------------------------------------------
2836 r25 | lh3lh3 | 2008-12-01 10:27:22 -0500 (Mon, 01 Dec 2008) | 3 lines
2838 M /branches/dev/samtools/Makefile
2839 M /branches/dev/samtools/bam.h
2840 M /branches/dev/samtools/bam_aux.c
2841 M /branches/dev/samtools/bamtk.c
2842 M /branches/dev/samtools/samtools.1
2845 * added routines for retrieving aux data, NOT TESTED YET!
2847 ------------------------------------------------------------------------
2848 r24 | lh3lh3 | 2008-12-01 09:29:43 -0500 (Mon, 01 Dec 2008) | 5 lines
2850 M /branches/dev/samtools/bam.c
2851 M /branches/dev/samtools/bam_import.c
2852 M /branches/dev/samtools/bam_maqcns.c
2853 M /branches/dev/samtools/bamtk.c
2854 M /branches/dev/samtools/bgzf.c
2855 M /branches/dev/samtools/samtools.1
2858 * bgzf: fixed a potential integer overflow on 32-it machines
2859 * maqcns: set the minimum combined quality as 0
2860 * supporting hex strings
2862 ------------------------------------------------------------------------
2863 r23 | lh3lh3 | 2008-11-27 12:14:37 -0500 (Thu, 27 Nov 2008) | 3 lines
2865 M /branches/dev/samtools/bam_maqcns.c
2866 M /branches/dev/samtools/bamtk.c
2869 * fixed the bug in maqcns
2871 ------------------------------------------------------------------------
2872 r22 | lh3lh3 | 2008-11-27 12:08:11 -0500 (Thu, 27 Nov 2008) | 3 lines
2874 M /branches/dev/samtools/Makefile
2875 M /branches/dev/samtools/bam.h
2876 A /branches/dev/samtools/bam_maqcns.c
2877 A /branches/dev/samtools/bam_maqcns.h
2878 M /branches/dev/samtools/bam_tview.c
2879 M /branches/dev/samtools/bamtk.c
2880 A /branches/dev/samtools/glf.h
2883 * add MAQ consensus caller, currently BUGGY!
2885 ------------------------------------------------------------------------
2886 r21 | lh3lh3 | 2008-11-27 08:51:28 -0500 (Thu, 27 Nov 2008) | 4 lines
2888 M /branches/dev/samtools/bam_pileup.c
2889 M /branches/dev/samtools/bam_tview.c
2890 M /branches/dev/samtools/bamtk.c
2893 * tview: display padded alignment (but not P operation)
2894 * better coordinates and reference sequence
2896 ------------------------------------------------------------------------
2897 r19 | lh3lh3 | 2008-11-27 04:26:05 -0500 (Thu, 27 Nov 2008) | 2 lines
2899 A /branches/dev/samtools/ChangeLog
2903 ------------------------------------------------------------------------
2904 r18 | lh3lh3 | 2008-11-27 04:24:45 -0500 (Thu, 27 Nov 2008) | 3 lines
2906 D /branches/dev/samtools/ChangeLog
2907 A /branches/dev/samtools/ChangeLog.old (from /branches/dev/samtools/ChangeLog:6)
2909 Rename ChangeLog to ChangeLog.old. This old ChangeLog is generated from
2910 the log of my personal SVN repository.
2912 ------------------------------------------------------------------------
2913 r17 | lh3lh3 | 2008-11-27 04:22:55 -0500 (Thu, 27 Nov 2008) | 6 lines
2915 M /branches/dev/samtools/Makefile
2916 M /branches/dev/samtools/bamtk.c
2917 M /branches/dev/samtools/bgzf.c
2920 * declare fseeko and ftello as some Linux may not do this by default and
2921 missing these declarations will make bgzf buggy
2922 * get rid of some harmless warings
2923 * use BGZF by default, now
2925 ------------------------------------------------------------------------
2926 r16 | lh3lh3 | 2008-11-26 16:19:11 -0500 (Wed, 26 Nov 2008) | 4 lines
2928 M /branches/dev/samtools/bam_index.c
2929 M /branches/dev/samtools/bamtk.c
2930 M /branches/dev/samtools/razf.c
2933 * fixed a bug in razf_read()
2934 * give more warnings when the file is truncated (or due to bugs in I/O library)
2936 ------------------------------------------------------------------------
2937 r15 | lh3lh3 | 2008-11-26 15:41:39 -0500 (Wed, 26 Nov 2008) | 2 lines
2939 M /branches/dev/samtools/bgzf.c
2941 fixed a bug in bgzf.c at the end of the file
2943 ------------------------------------------------------------------------
2944 r14 | lh3lh3 | 2008-11-26 12:05:18 -0500 (Wed, 26 Nov 2008) | 4 lines
2946 M /branches/dev/samtools/bamtk.c
2949 * a lot happened to RAZF, although samtools itself is untouched. Better
2950 also update the version number anyway to avoid confusion
2952 ------------------------------------------------------------------------
2953 r13 | lh3lh3 | 2008-11-26 12:03:48 -0500 (Wed, 26 Nov 2008) | 2 lines
2955 M /branches/dev/samtools/razf.c
2957 a change from Jue, but I think it should not matter
2959 ------------------------------------------------------------------------
2960 r12 | lh3lh3 | 2008-11-26 11:48:14 -0500 (Wed, 26 Nov 2008) | 3 lines
2962 M /branches/dev/samtools/razf.c
2964 fixed a potential bug in razf. However, it seems still buggy, just
2965 rarely happens, very rarely.
2967 ------------------------------------------------------------------------
2968 r11 | lh3lh3 | 2008-11-26 09:02:56 -0500 (Wed, 26 Nov 2008) | 2 lines
2970 M /branches/dev/samtools/razf.c
2972 fixed a bug in razf, with the help of Jue
2974 ------------------------------------------------------------------------
2975 r10 | lh3lh3 | 2008-11-26 06:55:32 -0500 (Wed, 26 Nov 2008) | 2 lines
2977 M /branches/dev/samtools/bam_index.c
2981 ------------------------------------------------------------------------
2982 r9 | lh3lh3 | 2008-11-26 06:37:05 -0500 (Wed, 26 Nov 2008) | 2 lines
2984 M /branches/dev/samtools/Makefile
2985 M /branches/dev/samtools/bam.h
2986 M /branches/dev/samtools/razf.c
2987 M /branches/dev/samtools/razf.h
2989 * Jue has updated razf to realize Bob's scheme
2991 ------------------------------------------------------------------------
2992 r7 | lh3lh3 | 2008-11-25 15:37:37 -0500 (Tue, 25 Nov 2008) | 2 lines
2994 A /branches/dev/samtools/samtools.1
2998 ------------------------------------------------------------------------
2999 r6 | lh3lh3 | 2008-11-25 15:37:16 -0500 (Tue, 25 Nov 2008) | 3 lines
3001 A /branches/dev/samtools/ChangeLog
3002 A /branches/dev/samtools/Makefile
3003 A /branches/dev/samtools/bam.c
3004 A /branches/dev/samtools/bam.h
3005 A /branches/dev/samtools/bam_aux.c
3006 A /branches/dev/samtools/bam_endian.h
3007 A /branches/dev/samtools/bam_import.c
3008 A /branches/dev/samtools/bam_index.c
3009 A /branches/dev/samtools/bam_lpileup.c
3010 A /branches/dev/samtools/bam_pileup.c
3011 A /branches/dev/samtools/bam_sort.c
3012 A /branches/dev/samtools/bam_tview.c
3013 A /branches/dev/samtools/bamtk.c
3014 A /branches/dev/samtools/bgzf.c
3015 A /branches/dev/samtools/bgzf.h
3016 A /branches/dev/samtools/bgzip.c
3017 A /branches/dev/samtools/faidx.c
3018 A /branches/dev/samtools/faidx.h
3019 A /branches/dev/samtools/khash.h
3020 A /branches/dev/samtools/ksort.h
3021 A /branches/dev/samtools/kstream.h
3022 A /branches/dev/samtools/misc
3023 A /branches/dev/samtools/misc/Makefile
3024 A /branches/dev/samtools/misc/all2sam.pl
3025 A /branches/dev/samtools/misc/maq2sam.c
3026 A /branches/dev/samtools/razf.c
3027 A /branches/dev/samtools/razf.h
3028 A /branches/dev/samtools/razip.c
3029 A /branches/dev/samtools/zutil.h
3031 The initial version of samtools, replicated from my local SVN repository.
3032 The current version is: 0.1.0-42. All future development will happen here.
3034 ------------------------------------------------------------------------
3035 r5 | lh3lh3 | 2008-11-25 15:30:49 -0500 (Tue, 25 Nov 2008) | 2 lines
3037 A /branches/dev/samtools
3039 samtools (C version)
3041 ------------------------------------------------------------------------