1 ------------------------------------------------------------------------
2 r462 | lh3lh3 | 2009-09-16 09:51:07 +0100 (Wed, 16 Sep 2009) | 3 lines
4 M /trunk/samtools/bamtk.c
5 M /trunk/samtools/faidx.c
6 M /trunk/samtools/knetfile.c
7 M /trunk/samtools/knetfile.h
8 M /trunk/samtools/razf.c
9 M /trunk/samtools/razf.h
11 * samtools-0.1.6-5 (r462)
12 * Added knetfile support in razf and faidx (on behalf of Petr Danecek)
14 ------------------------------------------------------------------------
15 r460 | lh3lh3 | 2009-09-09 12:06:22 +0100 (Wed, 09 Sep 2009) | 2 lines
17 M /trunk/samtools/samtools.1
19 fixed a formatting issue
21 ------------------------------------------------------------------------
22 r459 | lh3lh3 | 2009-09-08 23:14:08 +0100 (Tue, 08 Sep 2009) | 3 lines
24 M /trunk/samtools/bam_sort.c
25 M /trunk/samtools/bamtk.c
27 * samtools-0.1.6-4 (r459)
28 * make sort output the result to stdout when -o is in use
30 ------------------------------------------------------------------------
31 r458 | lh3lh3 | 2009-09-07 10:10:28 +0100 (Mon, 07 Sep 2009) | 4 lines
33 M /trunk/samtools/bamtk.c
34 M /trunk/samtools/faidx.c
35 M /trunk/samtools/faidx.h
36 M /trunk/samtools/samtools.1
38 * samtools-0.1.6-2 (r458)
39 * added more interface to faidx (by Nils)
40 * updated documentation
42 ------------------------------------------------------------------------
43 r457 | lh3lh3 | 2009-09-05 21:12:04 +0100 (Sat, 05 Sep 2009) | 3 lines
45 M /trunk/samtools/bam_sort.c
46 M /trunk/samtools/bamtk.c
48 * samtools-0.1.6-2 (r457)
49 * get rid of three assert() in bam_sort.c
51 ------------------------------------------------------------------------
52 r456 | jmarshall | 2009-09-04 17:46:25 +0100 (Fri, 04 Sep 2009) | 3 lines
54 M /trunk/samtools/razf.c
56 Return NULL from _razf_open() (and hence razf_open()/razf_open2())
57 when opening the file fails.
59 ------------------------------------------------------------------------
60 r453 | lh3lh3 | 2009-09-02 13:56:33 +0100 (Wed, 02 Sep 2009) | 2 lines
62 M /trunk/samtools/ChangeLog
63 M /trunk/samtools/NEWS
64 M /trunk/samtools/bamtk.c
65 M /trunk/samtools/samtools.1
66 D /trunk/samtools/source.dot
68 Release samtools-0.1.6
70 ------------------------------------------------------------------------
71 r451 | lh3lh3 | 2009-09-02 10:44:48 +0100 (Wed, 02 Sep 2009) | 4 lines
73 M /trunk/samtools/bam_md.c
74 M /trunk/samtools/bam_rmdup.c
75 M /trunk/samtools/bam_rmdupse.c
76 M /trunk/samtools/bam_sort.c
77 M /trunk/samtools/bamtk.c
78 M /trunk/samtools/samtools.1
80 * samtools-0.1.5-34 (r451)
81 * applied the patch by John
82 * improved the help message a little bit
84 ------------------------------------------------------------------------
85 r450 | lh3lh3 | 2009-09-02 09:55:55 +0100 (Wed, 02 Sep 2009) | 3 lines
87 M /trunk/samtools/bam_color.c
88 M /trunk/samtools/bamtk.c
90 * samtools-0.1.5-33 (r450)
91 * fixed a bug in bam_color.c (on behalf of Nils Homer)
93 ------------------------------------------------------------------------
94 r449 | lh3lh3 | 2009-08-29 20:36:41 +0100 (Sat, 29 Aug 2009) | 4 lines
96 M /trunk/samtools/bam_import.c
97 M /trunk/samtools/bam_md.c
98 M /trunk/samtools/bamtk.c
99 M /trunk/samtools/misc/samtools.pl
101 * samtools-0.1.5-32 (r449)
102 * fillmd: fixed a bug in modifying MD/NM tags
103 * in import, give a warning if the read is aligned but there is no CIGAR.
105 ------------------------------------------------------------------------
106 r448 | lh3lh3 | 2009-08-19 09:44:28 +0100 (Wed, 19 Aug 2009) | 3 lines
108 M /trunk/samtools/ChangeLog
109 M /trunk/samtools/bam_pileup.c
110 M /trunk/samtools/bamtk.c
111 M /trunk/samtools/misc/wgsim_eval.pl
113 * samtools-0.1.5-31 (r448)
114 * fixed an issue when the last CIGAR is I or D
116 ------------------------------------------------------------------------
117 r447 | lh3lh3 | 2009-08-17 09:34:57 +0100 (Mon, 17 Aug 2009) | 3 lines
119 M /trunk/samtools/bam_aux.c
120 M /trunk/samtools/bamtk.c
122 * samtools-0.1.5-30 (r447)
123 * fixed a bug in bam_aux_get(): 'A' is not checked
125 ------------------------------------------------------------------------
126 r446 | lh3lh3 | 2009-08-17 09:33:17 +0100 (Mon, 17 Aug 2009) | 2 lines
128 M /trunk/samtools/bam_aux.c
129 M /trunk/samtools/bamtk.c
133 ------------------------------------------------------------------------
134 r444 | lh3lh3 | 2009-08-11 10:02:36 +0100 (Tue, 11 Aug 2009) | 3 lines
136 M /trunk/samtools/bam_sort.c
137 M /trunk/samtools/bamtk.c
139 * samtools-0.1.5-28 (r444)
142 ------------------------------------------------------------------------
143 r443 | lh3lh3 | 2009-08-11 09:29:11 +0100 (Tue, 11 Aug 2009) | 4 lines
145 M /trunk/samtools/bam.c
146 M /trunk/samtools/bam_import.c
147 M /trunk/samtools/bamtk.c
149 * samtools-0.1.5-27 (r443)
150 * SEQ and QUAL can be "*"
151 * parse CIGAR "=" and "X" as "M"
153 ------------------------------------------------------------------------
154 r442 | lh3lh3 | 2009-08-07 21:56:38 +0100 (Fri, 07 Aug 2009) | 4 lines
156 M /trunk/samtools/bam_pileup.c
157 M /trunk/samtools/bamtk.c
158 M /trunk/samtools/misc/md5.c
159 M /trunk/samtools/misc/md5.h
160 M /trunk/samtools/misc/md5fa.c
162 * samtools-0.1.5-26 (r442)
163 * replace RSA Inc md5.* with ones under permissive lincense
164 * fixed a bug in detecting unsorted bam in pileup
166 ------------------------------------------------------------------------
167 r441 | bhandsaker | 2009-08-05 14:41:28 +0100 (Wed, 05 Aug 2009) | 2 lines
169 M /trunk/samtools/bgzf.c
170 M /trunk/samtools/bgzf.h
171 M /trunk/samtools/bgzip.c
173 Change copyright notices now that MIT has approved open source distribution.
175 ------------------------------------------------------------------------
176 r440 | lh3lh3 | 2009-08-05 10:44:24 +0100 (Wed, 05 Aug 2009) | 3 lines
178 M /trunk/samtools/bam_stat.c
179 M /trunk/samtools/bamtk.c
181 * samtools-0.1.5-25 (r436)
182 * in flagstats, do not report singletons if both ends are unmapped
184 ------------------------------------------------------------------------
185 r439 | lh3lh3 | 2009-08-04 22:16:51 +0100 (Tue, 04 Aug 2009) | 2 lines
187 M /trunk/samtools/misc/maq2sam.c
189 fixed a SERIOUS bug in setting 0x20 flag
191 ------------------------------------------------------------------------
192 r438 | lh3lh3 | 2009-08-04 21:50:43 +0100 (Tue, 04 Aug 2009) | 2 lines
194 M /trunk/samtools/misc/samtools.pl
196 fixed two minor bugs (suggested by Tim M Storm)
198 ------------------------------------------------------------------------
199 r437 | lh3lh3 | 2009-08-04 09:13:24 +0100 (Tue, 04 Aug 2009) | 3 lines
201 M /trunk/samtools/bamtk.c
202 M /trunk/samtools/misc/samtools.pl
203 M /trunk/samtools/sam_view.c
205 * samtools-0.1.5-24 (r435)
208 ------------------------------------------------------------------------
209 r434 | lh3lh3 | 2009-08-03 10:40:42 +0100 (Mon, 03 Aug 2009) | 3 lines
211 M /trunk/samtools/bam_tview.c
212 M /trunk/samtools/bamtk.c
214 * samtools-0.1.5-23 (r434)
215 * in tview, press 'r' to show read names rather than sequences
217 ------------------------------------------------------------------------
218 r433 | lh3lh3 | 2009-08-02 19:13:35 +0100 (Sun, 02 Aug 2009) | 3 lines
220 M /trunk/samtools/knetfile.c
222 * tried to fixed the buggy FTP random access in Windows. FAILED.
223 * anyway, MinGW seems to have problem with "%lld".
225 ------------------------------------------------------------------------
226 r432 | lh3lh3 | 2009-08-02 00:32:07 +0100 (Sun, 02 Aug 2009) | 5 lines
228 M /trunk/samtools/Makefile.mingw
229 M /trunk/samtools/bamtk.c
230 M /trunk/samtools/faidx.c
231 M /trunk/samtools/razf.c
232 A /trunk/samtools/win32/libcurses.a
233 A /trunk/samtools/win32/xcurses.h
235 * samtools-0.1.5-22 (r432)
236 * faidx: fixed compitability issue with _WIN32
237 * razf: fixed potential compitability issue with _WIN32
238 * PDCurses support in Windows
240 ------------------------------------------------------------------------
241 r431 | lh3lh3 | 2009-08-01 23:34:54 +0100 (Sat, 01 Aug 2009) | 2 lines
243 M /trunk/samtools/win32/libz.a
245 replace the GnuWin32 version of libz.a with my own build with MinGW.
247 ------------------------------------------------------------------------
248 r430 | lh3lh3 | 2009-08-01 23:21:07 +0100 (Sat, 01 Aug 2009) | 2 lines
250 M /trunk/samtools/knetfile.c
254 ------------------------------------------------------------------------
255 r429 | lh3lh3 | 2009-08-01 22:41:19 +0100 (Sat, 01 Aug 2009) | 3 lines
257 M /trunk/samtools/Makefile.mingw
258 M /trunk/samtools/bamtk.c
259 M /trunk/samtools/knetfile.c
260 M /trunk/samtools/knetfile.h
262 * samtools-0.1.5-21 (r428)
263 * knetfile.c is now compatible with mingw-winsock
265 ------------------------------------------------------------------------
266 r428 | lh3lh3 | 2009-08-01 00:39:07 +0100 (Sat, 01 Aug 2009) | 2 lines
268 M /trunk/samtools/Makefile.mingw
270 simplify MinGW Makefile
272 ------------------------------------------------------------------------
273 r427 | lh3lh3 | 2009-08-01 00:30:54 +0100 (Sat, 01 Aug 2009) | 5 lines
275 A /trunk/samtools/Makefile.mingw
276 M /trunk/samtools/bam_import.c
277 M /trunk/samtools/bamtk.c
278 A /trunk/samtools/win32
279 A /trunk/samtools/win32/libz.a
280 A /trunk/samtools/win32/zconf.h
281 A /trunk/samtools/win32/zlib.h
283 * samtools-0.1.5-20 (r427)
284 * MinGW support. At least SAM<->BAM conversion is working. Other
285 functionality are not tested at the moment.
286 * zlib headers and Windows version of libz.a are included in win32/
288 ------------------------------------------------------------------------
289 r426 | lh3lh3 | 2009-07-31 23:32:09 +0100 (Fri, 31 Jul 2009) | 3 lines
291 M /trunk/samtools/bamtk.c
292 M /trunk/samtools/sam_view.c
294 * samtools-0.1.5-19 (r426)
295 * fixed a bug caused by recent modifications. Sorry.
297 ------------------------------------------------------------------------
298 r425 | lh3lh3 | 2009-07-31 23:23:51 +0100 (Fri, 31 Jul 2009) | 2 lines
300 M /trunk/samtools/bgzf.c
302 compatible with Windows binary files
304 ------------------------------------------------------------------------
305 r424 | lh3lh3 | 2009-07-31 10:19:59 +0100 (Fri, 31 Jul 2009) | 5 lines
307 M /trunk/samtools/bam_maqcns.c
308 M /trunk/samtools/bam_maqcns.h
309 M /trunk/samtools/bam_plcmd.c
310 M /trunk/samtools/bam_tview.c
311 M /trunk/samtools/bamtk.c
312 M /trunk/samtools/misc/samtools.pl
314 * samtools-0.1.5-18 (r423)
315 * output additional information in pileup indel lines, for the purepose
316 of debugging at the moment
317 * in tview, optionally allow to treat reference skip as deletion
319 ------------------------------------------------------------------------
320 r423 | lh3lh3 | 2009-07-30 22:00:36 +0100 (Thu, 30 Jul 2009) | 2 lines
322 A /trunk/samtools/misc/psl2sam.pl
324 convert BLAT psl to SAM.
326 ------------------------------------------------------------------------
327 r422 | lh3lh3 | 2009-07-30 11:24:39 +0100 (Thu, 30 Jul 2009) | 6 lines
329 M /trunk/samtools/ChangeLog
330 M /trunk/samtools/bam.c
331 M /trunk/samtools/bamtk.c
332 M /trunk/samtools/bgzf.c
333 M /trunk/samtools/bgzf.h
334 M /trunk/samtools/knetfile.c
335 M /trunk/samtools/sam.c
336 M /trunk/samtools/sam_view.c
338 * samtools-0.1.5-17 (r422)
339 * fixed a but in knetfile.c when seek type is not SEEK_SET
340 * write an empty BGZF block to every BGZF file
341 * check BGZF EOF marker in bam_header_read()
344 ------------------------------------------------------------------------
345 r421 | lh3lh3 | 2009-07-30 10:03:39 +0100 (Thu, 30 Jul 2009) | 3 lines
347 M /trunk/samtools/bam_import.c
348 M /trunk/samtools/bam_plcmd.c
349 M /trunk/samtools/bamtk.c
350 M /trunk/samtools/misc/samtools.pl
351 M /trunk/samtools/sam.c
352 M /trunk/samtools/sam.h
353 M /trunk/samtools/sam_view.c
355 * samtools-0.1.5-16 (r421)
356 * in view and pileup, load header from FASTA index if the input is SAM.
358 ------------------------------------------------------------------------
359 r420 | lh3lh3 | 2009-07-29 09:18:55 +0100 (Wed, 29 Jul 2009) | 2 lines
361 M /trunk/samtools/misc/maq2sam.c
363 do not set "read 1" if reads are not mapped in the PE mode of maq
365 ------------------------------------------------------------------------
366 r419 | lh3lh3 | 2009-07-28 09:52:33 +0100 (Tue, 28 Jul 2009) | 5 lines
368 M /trunk/samtools/bam_import.c
369 M /trunk/samtools/bamtk.c
370 M /trunk/samtools/misc/samtools.pl
371 M /trunk/samtools/misc/wgsim_eval.pl
373 * samtools-0.1.5-15 (r419)
374 * in sam_open(), return NULL when the file cannot be opened.
375 * make wgsim_eval.pl more robust to imperfect SAM
376 * add "unique" command to samtools.pl
378 ------------------------------------------------------------------------
379 r418 | lh3lh3 | 2009-07-24 14:04:19 +0100 (Fri, 24 Jul 2009) | 2 lines
381 M /trunk/samtools/misc/wgsim_eval.pl
383 skip @header lines in SAM
385 ------------------------------------------------------------------------
386 r417 | lh3lh3 | 2009-07-24 12:42:38 +0100 (Fri, 24 Jul 2009) | 3 lines
388 M /trunk/samtools/bamtk.c
389 M /trunk/samtools/sam_view.c
391 * samtools-0.1.5-14 (r417)
392 * more help in "samtools view" due to the recent changes.
394 ------------------------------------------------------------------------
395 r416 | lh3lh3 | 2009-07-24 12:34:30 +0100 (Fri, 24 Jul 2009) | 3 lines
397 M /trunk/samtools/bam.c
398 M /trunk/samtools/bam.h
399 M /trunk/samtools/bam_import.c
400 M /trunk/samtools/bamtk.c
401 M /trunk/samtools/sam.c
402 M /trunk/samtools/sam.h
403 M /trunk/samtools/sam_view.c
405 * samtools-0.1.5-17 (r416)
406 * support import/export SAM with string tags
408 ------------------------------------------------------------------------
409 r415 | lh3lh3 | 2009-07-24 11:39:26 +0100 (Fri, 24 Jul 2009) | 3 lines
411 M /trunk/samtools/bam.c
412 M /trunk/samtools/bam.h
413 M /trunk/samtools/bam_import.c
414 M /trunk/samtools/bamtk.c
415 M /trunk/samtools/sam.c
416 M /trunk/samtools/sam.h
417 M /trunk/samtools/sam_view.c
419 * samtools-0.1.5-12 (r415)
420 * FLAG now can be in HEX
422 ------------------------------------------------------------------------
423 r414 | lh3lh3 | 2009-07-22 22:03:49 +0100 (Wed, 22 Jul 2009) | 2 lines
425 M /trunk/samtools/kstring.h
427 fixed a compiling error (thank Ken for fixing it)
429 ------------------------------------------------------------------------
430 r412 | lh3lh3 | 2009-07-21 22:19:40 +0100 (Tue, 21 Jul 2009) | 2 lines
432 M /trunk/samtools/kstring.c
433 M /trunk/samtools/kstring.h
435 Implemented Boyer-Moore search in the kstring library.
437 ------------------------------------------------------------------------
438 r409 | lh3lh3 | 2009-07-17 17:10:20 +0100 (Fri, 17 Jul 2009) | 2 lines
440 M /trunk/samtools/bam_index.c
442 do not include knetfile.h when _USE_KNETFILE is not defined
444 ------------------------------------------------------------------------
445 r408 | lh3lh3 | 2009-07-17 15:29:21 +0100 (Fri, 17 Jul 2009) | 5 lines
447 M /trunk/samtools/bam_md.c
448 M /trunk/samtools/bam_tview.c
449 M /trunk/samtools/bamtk.c
450 M /trunk/samtools/bgzf.c
452 * samtools-0.1.5-11 (r408)
453 * force to overwirte existing MD if it is different from the one calculated
455 * bgzf.c: improved the compatibility with Windows headers
457 ------------------------------------------------------------------------
458 r407 | lh3lh3 | 2009-07-17 14:46:56 +0100 (Fri, 17 Jul 2009) | 5 lines
460 M /trunk/samtools/bam.h
461 M /trunk/samtools/bam_aux.c
462 M /trunk/samtools/bam_md.c
463 M /trunk/samtools/bamtk.c
464 M /trunk/samtools/sam.h
466 * samtools-0.1.5-10 (r407)
467 * implemented bam_aux_del() to remove a tag
468 * fillmd: generate the NM tag
469 * fillmd: cmd interface improvement
471 ------------------------------------------------------------------------
472 r406 | lh3lh3 | 2009-07-16 23:30:40 +0100 (Thu, 16 Jul 2009) | 2 lines
474 M /trunk/samtools/Makefile
476 Sorry. The old Makefile is for PDCurses...
478 ------------------------------------------------------------------------
479 r405 | lh3lh3 | 2009-07-16 23:30:11 +0100 (Thu, 16 Jul 2009) | 3 lines
481 M /trunk/samtools/Makefile
482 M /trunk/samtools/bam_tview.c
483 M /trunk/samtools/bamtk.c
485 * samtools-0.1.5-9 (r405)
486 * improved the compatibility with PDCurses a little bit
488 ------------------------------------------------------------------------
489 r404 | lh3lh3 | 2009-07-16 23:23:52 +0100 (Thu, 16 Jul 2009) | 3 lines
491 M /trunk/samtools/Makefile
492 M /trunk/samtools/bam_tview.c
493 M /trunk/samtools/bamtk.c
495 * samtools-0.1.5-8 (r404)
496 * compatible with PDCurses
498 ------------------------------------------------------------------------
499 r403 | lh3lh3 | 2009-07-16 22:39:39 +0100 (Thu, 16 Jul 2009) | 3 lines
501 M /trunk/samtools/bamtk.c
502 M /trunk/samtools/kseq.h
504 * samtools-0.1.5-7 (r403)
505 * fixed a bug in kseq.h for binary files (text files are fine)
507 ------------------------------------------------------------------------
508 r402 | lh3lh3 | 2009-07-16 11:49:53 +0100 (Thu, 16 Jul 2009) | 4 lines
510 M /trunk/samtools/bam_import.c
511 M /trunk/samtools/bam_index.c
512 M /trunk/samtools/bamtk.c
513 M /trunk/samtools/bgzf.c
515 * samtools-0.1.5-6 (r402)
516 * fixed compiling error when "-D_USE_NETFILE" is not applied
517 * improve portability to MinGW
519 ------------------------------------------------------------------------
520 r398 | lh3lh3 | 2009-07-13 10:21:36 +0100 (Mon, 13 Jul 2009) | 3 lines
522 A /trunk/bam-lite/bam.h (from /trunk/samtools/bam.h:395)
523 A /trunk/bam-lite/bam_lite.c (from /trunk/samtools/bam_lite.c:395)
524 D /trunk/samtools/bam_lite.c
526 * move bam_lite.c to bam-lite
527 * copy bam.h to bam-lite
529 ------------------------------------------------------------------------
530 r395 | lh3lh3 | 2009-07-13 10:12:57 +0100 (Mon, 13 Jul 2009) | 3 lines
532 M /trunk/samtools/bam.h
533 M /trunk/samtools/bam_lite.c
534 M /trunk/samtools/bam_lpileup.c
535 M /trunk/samtools/bam_pileup.c
536 M /trunk/samtools/bamtk.c
538 * samtools-0.1.5-5 (r395)
539 * added bam_pileup_file() and removed bam_lpileup_file()
541 ------------------------------------------------------------------------
542 r394 | lh3lh3 | 2009-07-13 00:35:10 +0100 (Mon, 13 Jul 2009) | 3 lines
544 M /trunk/samtools/bamtk.c
545 M /trunk/samtools/knetfile.c
546 M /trunk/samtools/knetfile.h
548 * samtools-0.1.5-4 (r394)
549 * http_proxy support in knetfile library (check http_proxy ENV)
551 ------------------------------------------------------------------------
552 r393 | lh3lh3 | 2009-07-12 23:57:07 +0100 (Sun, 12 Jul 2009) | 5 lines
554 M /trunk/samtools/bam_index.c
555 M /trunk/samtools/bam_tview.c
556 M /trunk/samtools/bamtk.c
557 M /trunk/samtools/knetfile.c
558 M /trunk/samtools/knetfile.h
560 * samtools-0.1.5-3 (r393)
561 * knetfile now supports HTTP (no proxy at the moment)
562 * fixed a potential issue in knetfile on opening ordinary file, although I have
563 not seen the sideeffect so far.
565 ------------------------------------------------------------------------
566 r392 | lh3lh3 | 2009-07-12 18:50:55 +0100 (Sun, 12 Jul 2009) | 2 lines
568 M /trunk/samtools/samtools.1
570 Remove the warning in tview
572 ------------------------------------------------------------------------
573 r391 | lh3lh3 | 2009-07-12 18:42:43 +0100 (Sun, 12 Jul 2009) | 3 lines
575 M /trunk/samtools/bam_tview.c
576 M /trunk/samtools/bamtk.c
578 * samtools-0.1.5-2 (r391)
579 * do not show a blank screen when no reads mapped
581 ------------------------------------------------------------------------
582 r390 | lh3lh3 | 2009-07-09 14:01:42 +0100 (Thu, 09 Jul 2009) | 4 lines
584 M /trunk/samtools/bam.h
585 A /trunk/samtools/bam_lite.c
586 M /trunk/samtools/bamtk.c
588 * samtools-0.1.5-1 (r390)
589 * removed useless _IOLIB in bam.h. This should cause no change at all.
590 * added bam_lite.c for light-weight BAM reading
592 ------------------------------------------------------------------------
593 r385 | lh3lh3 | 2009-07-07 16:53:29 +0100 (Tue, 07 Jul 2009) | 2 lines
595 M /trunk/samtools/bamtk.c
596 M /trunk/samtools/knetfile.c
598 Release samtools-0.1.5c (fixed a bug in piping)
600 ------------------------------------------------------------------------
601 r383 | lh3lh3 | 2009-07-07 11:39:55 +0100 (Tue, 07 Jul 2009) | 2 lines
603 M /trunk/samtools/bamtk.c
604 M /trunk/samtools/sam.c
606 Release samtools-0.1.5b (BUG! so embarrassing!)
608 ------------------------------------------------------------------------
609 r381 | lh3lh3 | 2009-07-07 11:20:06 +0100 (Tue, 07 Jul 2009) | 2 lines
611 M /trunk/samtools/Makefile
612 M /trunk/samtools/bam.h
613 M /trunk/samtools/bam_aux.c
614 M /trunk/samtools/bamtk.c
616 Release samtools-0.1.5a (for compatibility with Bio::DB::Sam)
618 ------------------------------------------------------------------------
619 r373 | lh3lh3 | 2009-07-07 10:26:57 +0100 (Tue, 07 Jul 2009) | 2 lines
621 M /trunk/samtools/ChangeLog
622 M /trunk/samtools/NEWS
623 M /trunk/samtools/bamtk.c
624 M /trunk/samtools/samtools.1
626 Release samtools-0.1.5
628 ------------------------------------------------------------------------
629 r372 | lh3lh3 | 2009-07-07 09:49:27 +0100 (Tue, 07 Jul 2009) | 3 lines
631 M /trunk/samtools/bamtk.c
632 M /trunk/samtools/sam.c
634 * samtools-0.1.4-23 (r372)
635 * keep header text if "view -t" is used (by Gerton)
637 ------------------------------------------------------------------------
638 r371 | lh3lh3 | 2009-07-07 01:13:32 +0100 (Tue, 07 Jul 2009) | 2 lines
640 M /trunk/samtools/samtools.1
644 ------------------------------------------------------------------------
645 r370 | bhandsaker | 2009-07-02 22:24:34 +0100 (Thu, 02 Jul 2009) | 2 lines
647 M /trunk/samtools/Makefile
649 Introduced LIBPATH variable so this could be overridden to allow samtools to build correct at the Broad.
651 ------------------------------------------------------------------------
652 r369 | lh3lh3 | 2009-07-02 13:36:53 +0100 (Thu, 02 Jul 2009) | 4 lines
654 M /trunk/samtools/ChangeLog
655 M /trunk/samtools/bam_aux.c
656 M /trunk/samtools/bam_plcmd.c
657 M /trunk/samtools/bamtk.c
659 * samtools-0.1.4-22 (r369)
660 * in pileup, optionally print E2 and U2
661 * remove the debugging code in bam_aux_get() (Drat!)
663 ------------------------------------------------------------------------
664 r368 | lh3lh3 | 2009-07-02 11:32:26 +0100 (Thu, 02 Jul 2009) | 6 lines
666 M /trunk/samtools/bam.c
667 M /trunk/samtools/bam.h
668 M /trunk/samtools/bam_aux.c
669 M /trunk/samtools/bam_index.c
670 M /trunk/samtools/bam_lpileup.c
671 M /trunk/samtools/bam_md.c
672 M /trunk/samtools/bam_pileup.c
673 M /trunk/samtools/bam_rmdup.c
674 M /trunk/samtools/bam_stat.c
675 M /trunk/samtools/bam_tview.c
676 M /trunk/samtools/bamtk.c
677 M /trunk/samtools/faidx.c
678 M /trunk/samtools/faidx.h
679 M /trunk/samtools/glf.c
681 * samtools-0.1.4-21 (r368)
682 * propagate errors rather than exit or complain assertion failure. Assertion
683 should be only used for checking internal bugs, but not for external input
684 inconsistency. I was just a bit lazy.
685 * small memory leak may be present on failure, though
687 ------------------------------------------------------------------------
688 r367 | lh3lh3 | 2009-06-30 16:18:42 +0100 (Tue, 30 Jun 2009) | 2 lines
690 M /trunk/samtools/knetfile.c
692 reduce the chance of blocking in FTP connection
694 ------------------------------------------------------------------------
695 r366 | lh3lh3 | 2009-06-30 15:35:21 +0100 (Tue, 30 Jun 2009) | 2 lines
697 M /trunk/samtools/knetfile.c
699 minor changes to knetfile: invalid fd equals -1 rather than 0
701 ------------------------------------------------------------------------
702 r365 | lh3lh3 | 2009-06-30 14:04:30 +0100 (Tue, 30 Jun 2009) | 3 lines
704 M /trunk/samtools/bam_index.c
705 M /trunk/samtools/bamtk.c
706 M /trunk/samtools/knetfile.c
707 M /trunk/samtools/knetfile.h
709 * samtools-0.1.4-20 (r365)
710 * download the BAM index file if it is not found in the current working directory.
712 ------------------------------------------------------------------------
713 r364 | lh3lh3 | 2009-06-30 12:39:07 +0100 (Tue, 30 Jun 2009) | 3 lines
715 M /trunk/samtools/bamtk.c
716 M /trunk/samtools/knetfile.c
718 * samtools-0.1.4-19 (r364)
719 * knetfile: report error when the file is not present on FTP
721 ------------------------------------------------------------------------
722 r363 | lh3lh3 | 2009-06-29 23:23:32 +0100 (Mon, 29 Jun 2009) | 4 lines
724 M /trunk/samtools/bam_tview.c
725 M /trunk/samtools/bamtk.c
726 M /trunk/samtools/bgzf.c
727 M /trunk/samtools/bgzf.h
728 M /trunk/samtools/knetfile.c
729 M /trunk/samtools/knetfile.h
731 * samtools-0.1.4-18 (r363)
732 * knetfile: do not trigger network communication in FTP seek (lazy seek)
733 * bgzf: cache recent blocks (disabled by default)
735 ------------------------------------------------------------------------
736 r362 | lh3lh3 | 2009-06-25 21:04:34 +0100 (Thu, 25 Jun 2009) | 2 lines
738 M /trunk/samtools/bgzf.c
742 ------------------------------------------------------------------------
743 r361 | lh3lh3 | 2009-06-25 21:03:10 +0100 (Thu, 25 Jun 2009) | 3 lines
745 M /trunk/samtools/bam_index.c
746 M /trunk/samtools/bamtk.c
748 * samtools-0.1.4-17 (r361)
749 * if a file is given on FTP, search locally for the BAM index
751 ------------------------------------------------------------------------
752 r360 | lh3lh3 | 2009-06-25 20:44:52 +0100 (Thu, 25 Jun 2009) | 5 lines
754 M /trunk/samtools/Makefile
755 M /trunk/samtools/bam_import.c
756 M /trunk/samtools/bam_index.c
757 M /trunk/samtools/bamtk.c
758 M /trunk/samtools/bgzf.c
759 M /trunk/samtools/bgzf.h
760 M /trunk/samtools/knetfile.c
761 M /trunk/samtools/knetfile.h
763 * samtools-0.1.4-16 (r360)
764 * report more information in index when the input is not sorted
765 * change the behaviour of knet_seek() such that it returns 0 on success
766 * support knetfile library in BGZF
768 ------------------------------------------------------------------------
769 r359 | lh3lh3 | 2009-06-25 17:10:55 +0100 (Thu, 25 Jun 2009) | 2 lines
771 M /trunk/samtools/knetfile.c
772 M /trunk/samtools/knetfile.h
774 fixed bugs in knetfile.*
776 ------------------------------------------------------------------------
777 r358 | lh3lh3 | 2009-06-25 13:53:19 +0100 (Thu, 25 Jun 2009) | 2 lines
779 A /trunk/samtools/knetfile.h
781 this is the header file
783 ------------------------------------------------------------------------
784 r357 | lh3lh3 | 2009-06-25 13:52:03 +0100 (Thu, 25 Jun 2009) | 3 lines
786 A /trunk/samtools/knetfile.c
789 * preliminary version
791 ------------------------------------------------------------------------
792 r354 | lh3lh3 | 2009-06-24 14:02:25 +0100 (Wed, 24 Jun 2009) | 3 lines
794 M /trunk/samtools/bam.c
795 M /trunk/samtools/bamtk.c
797 * samtools-0.1.4-15 (r354)
798 * fixed a memory leak in bam_view1(), although samtools is not using this routine.
800 ------------------------------------------------------------------------
801 r351 | lh3lh3 | 2009-06-18 00:16:26 +0100 (Thu, 18 Jun 2009) | 4 lines
803 M /trunk/samtools/bamtk.c
804 M /trunk/samtools/faidx.c
806 * samtools-0.1.4-13 (r351)
807 * make faidx more tolerant to empty lines right before or after > lines
808 * hope this does not introduce new bugs...
810 ------------------------------------------------------------------------
811 r350 | lh3lh3 | 2009-06-16 14:37:01 +0100 (Tue, 16 Jun 2009) | 3 lines
813 M /trunk/samtools/bam_plcmd.c
814 M /trunk/samtools/bamtk.c
816 * samtools-0.1.4-13 (r350)
817 * fixed a small memory leak in pileup, caused by recent modifications
819 ------------------------------------------------------------------------
820 r347 | lh3lh3 | 2009-06-13 21:20:49 +0100 (Sat, 13 Jun 2009) | 3 lines
822 M /trunk/samtools/bam_plcmd.c
823 M /trunk/samtools/bamtk.c
824 M /trunk/samtools/sam_view.c
826 * samtools-0.1.4-12 (r347)
827 * added `-S' to pileup, similar to `view -S'
829 ------------------------------------------------------------------------
830 r346 | lh3lh3 | 2009-06-13 17:52:31 +0100 (Sat, 13 Jun 2009) | 3 lines
832 M /trunk/samtools/Makefile
833 M /trunk/samtools/bamtk.c
834 M /trunk/samtools/sam_view.c
835 M /trunk/samtools/samtools.1
837 * samtools-0.1.4-11 (r346)
838 * allow to select a read group at view command-line
840 ------------------------------------------------------------------------
841 r344 | lh3lh3 | 2009-06-13 14:06:24 +0100 (Sat, 13 Jun 2009) | 2 lines
843 M /trunk/samtools/examples/calDepth.c
847 ------------------------------------------------------------------------
848 r343 | lh3lh3 | 2009-06-13 14:01:22 +0100 (Sat, 13 Jun 2009) | 2 lines
850 M /trunk/samtools/examples/calDepth.c
854 ------------------------------------------------------------------------
855 r342 | lh3lh3 | 2009-06-13 13:58:48 +0100 (Sat, 13 Jun 2009) | 2 lines
857 M /trunk/samtools/examples/Makefile
858 A /trunk/samtools/examples/calDepth.c
860 added an example of calculating read depth
862 ------------------------------------------------------------------------
863 r341 | lh3lh3 | 2009-06-13 13:00:08 +0100 (Sat, 13 Jun 2009) | 6 lines
865 M /trunk/samtools/Makefile
866 M /trunk/samtools/bam.h
867 M /trunk/samtools/bam_aux.c
868 A /trunk/samtools/bam_color.c
869 M /trunk/samtools/bam_plcmd.c
870 M /trunk/samtools/bam_sort.c
871 M /trunk/samtools/bam_tview.c
872 M /trunk/samtools/bamtk.c
873 M /trunk/samtools/sam.c
874 M /trunk/samtools/sam.h
876 * samtools-0.1.4-10 (r341)
877 * only include key APIs in libbam.a
878 * move color-specific routines to bam_color.c
879 * update documentations
880 * remove the support of -q in pileup
882 ------------------------------------------------------------------------
883 r340 | lh3lh3 | 2009-06-13 11:17:14 +0100 (Sat, 13 Jun 2009) | 6 lines
885 M /trunk/samtools/INSTALL
886 M /trunk/samtools/Makefile
887 M /trunk/samtools/bam_aux.c
888 M /trunk/samtools/bam_import.c
889 M /trunk/samtools/bam_tview.c
890 M /trunk/samtools/bamtk.c
891 M /trunk/samtools/razf.c
892 M /trunk/samtools/sam_view.c
894 * samtools-0.1.4-9 (r340)
895 * added a warning to razf.c if zlib<1.2.2.1
896 * fixed a compilation warning
897 * fixed a segfault caused by @RG parsing
898 * detect NCURSES in bam_tview.c
900 ------------------------------------------------------------------------
901 r339 | lh3lh3 | 2009-06-13 10:35:19 +0100 (Sat, 13 Jun 2009) | 2 lines
903 M /trunk/samtools/INSTALL
907 ------------------------------------------------------------------------
908 r338 | lh3lh3 | 2009-06-13 00:15:24 +0100 (Sat, 13 Jun 2009) | 4 lines
910 M /trunk/samtools/bam.c
911 M /trunk/samtools/bam.h
912 M /trunk/samtools/bam_aux.c
913 M /trunk/samtools/bam_import.c
914 M /trunk/samtools/bamtk.c
915 M /trunk/samtools/kstring.h
916 M /trunk/samtools/sam.c
917 M /trunk/samtools/sam_view.c
919 * samtools-0.1.4-8 (r338)
920 * parse the @RG header lines and allow to choose library at the "samtools view"
923 ------------------------------------------------------------------------
924 r337 | lh3lh3 | 2009-06-12 21:25:50 +0100 (Fri, 12 Jun 2009) | 4 lines
926 M /trunk/samtools/bamtk.c
927 M /trunk/samtools/bgzf.c
928 M /trunk/samtools/bgzf.h
929 M /trunk/samtools/sam.c
930 M /trunk/samtools/sam_view.c
932 * samtools-0.1.4-7 (r337)
933 * bgzf.c: support mode string "wu": uncompressed output
934 * "samtools view" support "-u" command-line option
936 ------------------------------------------------------------------------
937 r336 | lh3lh3 | 2009-06-12 17:20:12 +0100 (Fri, 12 Jun 2009) | 5 lines
939 M /trunk/samtools/Makefile
940 M /trunk/samtools/misc/Makefile
941 M /trunk/samtools/razf.c
942 M /trunk/samtools/razf.h
943 M /trunk/samtools/razip.c
945 * no changes to samtools itself
946 * remove zlib source codes
947 * make RAZF reading compatible with old version of zlib
948 * on old version of zlib, writing is not available
950 ------------------------------------------------------------------------
951 r335 | lh3lh3 | 2009-06-12 16:47:33 +0100 (Fri, 12 Jun 2009) | 2 lines
953 D /trunk/samtools/zlib
955 remove zlib for simplification...
957 ------------------------------------------------------------------------
958 r334 | lh3lh3 | 2009-06-12 15:43:36 +0100 (Fri, 12 Jun 2009) | 5 lines
960 M /trunk/samtools/bam.h
961 M /trunk/samtools/bam_aux.c
962 M /trunk/samtools/bamtk.c
964 * samtools-0.1.4-6 (r334)
965 * do not export bam_aux_get_core() for Bio::DB::Sam because it has already
966 been implemented in that.
967 * this version works with the latest Bio::DB::Sam (20090612)
969 ------------------------------------------------------------------------
970 r333 | lh3lh3 | 2009-06-12 15:33:42 +0100 (Fri, 12 Jun 2009) | 2 lines
972 M /trunk/samtools/ChangeLog
976 ------------------------------------------------------------------------
977 r332 | lh3lh3 | 2009-06-12 15:21:21 +0100 (Fri, 12 Jun 2009) | 2 lines
979 M /trunk/samtools/AUTHORS
980 M /trunk/samtools/Makefile
981 M /trunk/samtools/misc/Makefile
983 fixed minor things in Makefile
985 ------------------------------------------------------------------------
986 r331 | lh3lh3 | 2009-06-12 15:07:05 +0100 (Fri, 12 Jun 2009) | 4 lines
988 M /trunk/samtools/bamtk.c
990 * samtools-0.1.4-5 (r3310
991 * no change to samtools itself. Version number is increased to reflect the
992 changes in the Makefile building system.
994 ------------------------------------------------------------------------
995 r330 | lh3lh3 | 2009-06-12 15:03:38 +0100 (Fri, 12 Jun 2009) | 2 lines
997 M /trunk/samtools/AUTHORS
998 D /trunk/samtools/README
1000 update information...
1002 ------------------------------------------------------------------------
1003 r329 | lh3lh3 | 2009-06-12 14:52:21 +0100 (Fri, 12 Jun 2009) | 3 lines
1005 M /trunk/samtools/misc/novo2sam.pl
1007 * updated novoalign converter by Colin Hercus et al.
1008 * this version works with indels
1010 ------------------------------------------------------------------------
1011 r328 | lh3lh3 | 2009-06-12 14:50:53 +0100 (Fri, 12 Jun 2009) | 3 lines
1013 M /trunk/samtools/INSTALL
1014 M /trunk/samtools/Makefile
1015 M /trunk/samtools/misc/Makefile
1016 M /trunk/samtools/zlib/Makefile
1019 * update INSTALL instruction
1021 ------------------------------------------------------------------------
1022 r327 | lh3lh3 | 2009-06-12 14:18:29 +0100 (Fri, 12 Jun 2009) | 4 lines
1024 A /trunk/samtools/Makefile (from /trunk/samtools/Makefile.generic:325)
1025 D /trunk/samtools/Makefile.am
1026 D /trunk/samtools/Makefile.generic
1027 D /trunk/samtools/Makefile.lite
1028 D /trunk/samtools/autogen.sh
1029 D /trunk/samtools/cleanup.sh
1030 D /trunk/samtools/configure.ac
1031 A /trunk/samtools/misc/Makefile (from /trunk/samtools/misc/Makefile.generic:305)
1032 D /trunk/samtools/misc/Makefile.am
1033 D /trunk/samtools/misc/Makefile.generic
1034 M /trunk/samtools/razf.c
1035 A /trunk/samtools/zlib
1036 A /trunk/samtools/zlib/Makefile
1037 A /trunk/samtools/zlib/adler32.c
1038 A /trunk/samtools/zlib/compress.c
1039 A /trunk/samtools/zlib/crc32.c
1040 A /trunk/samtools/zlib/crc32.h
1041 A /trunk/samtools/zlib/deflate.c
1042 A /trunk/samtools/zlib/deflate.h
1043 A /trunk/samtools/zlib/gzio.c
1044 A /trunk/samtools/zlib/infback.c
1045 A /trunk/samtools/zlib/inffast.c
1046 A /trunk/samtools/zlib/inffast.h
1047 A /trunk/samtools/zlib/inffixed.h
1048 A /trunk/samtools/zlib/inflate.c
1049 A /trunk/samtools/zlib/inflate.h
1050 A /trunk/samtools/zlib/inftrees.c
1051 A /trunk/samtools/zlib/inftrees.h
1052 A /trunk/samtools/zlib/trees.c
1053 A /trunk/samtools/zlib/trees.h
1054 A /trunk/samtools/zlib/uncompr.c
1055 A /trunk/samtools/zlib/zconf.h
1056 A /trunk/samtools/zlib/zlib.h
1057 A /trunk/samtools/zlib/zutil.c
1058 A /trunk/samtools/zlib/zutil.h
1059 D /trunk/samtools/zutil.h
1061 * added zlib-1.2.3 as razip requires that
1062 * prepare to changed back to the Makefile building system
1063 * unfinished! (will be soon)
1065 ------------------------------------------------------------------------
1066 r326 | lh3lh3 | 2009-06-12 14:12:03 +0100 (Fri, 12 Jun 2009) | 2 lines
1068 M /trunk/samtools/misc/samtools.pl
1072 ------------------------------------------------------------------------
1073 r325 | lh3lh3 | 2009-06-10 16:27:59 +0100 (Wed, 10 Jun 2009) | 3 lines
1075 M /trunk/samtools/bam_maqcns.c
1076 M /trunk/samtools/bamtk.c
1078 * samtools-0.1.4-4 (r325)
1079 * further avoid wrong consensus calls in repetitive regions.
1081 ------------------------------------------------------------------------
1082 r324 | lh3lh3 | 2009-06-10 15:56:17 +0100 (Wed, 10 Jun 2009) | 4 lines
1084 M /trunk/samtools/bam_maqcns.c
1085 M /trunk/samtools/bam_plcmd.c
1086 M /trunk/samtools/bamtk.c
1087 M /trunk/samtools/sam.c
1088 M /trunk/samtools/sam.h
1090 * samtools-0.1.4-3 (r324)
1091 * make maqcns generate the correct call in repetitive regions.
1092 * allow filtering on mapQ at the pileup command line
1094 ------------------------------------------------------------------------
1095 r323 | lh3lh3 | 2009-06-10 10:04:21 +0100 (Wed, 10 Jun 2009) | 3 lines
1097 M /trunk/samtools/misc/samtools.pl
1099 * samtools.pl-0.3.2 (r322)
1100 * indels and SNPs use different mapping quality threshold
1102 ------------------------------------------------------------------------
1103 r322 | lh3lh3 | 2009-06-10 10:03:22 +0100 (Wed, 10 Jun 2009) | 2 lines
1105 M /trunk/samtools/misc/export2sam.pl
1109 ------------------------------------------------------------------------
1110 r321 | lh3lh3 | 2009-06-09 09:21:48 +0100 (Tue, 09 Jun 2009) | 2 lines
1112 M /trunk/samtools/misc/samtools.pl
1114 just typo. no real change
1116 ------------------------------------------------------------------------
1117 r320 | lh3lh3 | 2009-06-08 14:32:51 +0100 (Mon, 08 Jun 2009) | 2 lines
1119 M /trunk/samtools/misc/samtools.pl
1121 a little bit code cleanup
1123 ------------------------------------------------------------------------
1124 r319 | lh3lh3 | 2009-06-08 14:22:33 +0100 (Mon, 08 Jun 2009) | 4 lines
1126 M /trunk/samtools/misc/samtools.pl
1129 * change default parameters
1130 * optionally print filtered variants
1132 ------------------------------------------------------------------------
1133 r318 | lh3lh3 | 2009-06-08 14:14:26 +0100 (Mon, 08 Jun 2009) | 3 lines
1135 M /trunk/samtools/misc/samtools.pl
1138 * combine snpFilter and indelFilter
1140 ------------------------------------------------------------------------
1141 r317 | lh3lh3 | 2009-06-08 11:31:42 +0100 (Mon, 08 Jun 2009) | 3 lines
1143 M /trunk/samtools/misc/samtools.pl
1146 * change a default parameter
1148 ------------------------------------------------------------------------
1149 r316 | lh3lh3 | 2009-06-08 11:11:06 +0100 (Mon, 08 Jun 2009) | 5 lines
1151 M /trunk/samtools/bam_maqcns.c
1152 M /trunk/samtools/bam_maqcns.h
1153 M /trunk/samtools/bam_plcmd.c
1154 M /trunk/samtools/bamtk.c
1155 M /trunk/samtools/sam.c
1157 * samtools-0.1.4-2 (r316)
1158 * pileup: cap mapping quality at 60 (by default)
1159 * pileup: always calculate RMS mapq
1160 * pileup: allow to output variant sites only
1162 ------------------------------------------------------------------------
1163 r312 | lh3lh3 | 2009-06-04 13:01:10 +0100 (Thu, 04 Jun 2009) | 3 lines
1165 M /trunk/samtools/misc/samtools.pl
1170 ------------------------------------------------------------------------
1171 r311 | lh3lh3 | 2009-06-03 09:40:40 +0100 (Wed, 03 Jun 2009) | 2 lines
1173 M /trunk/samtools/misc/samtools.pl
1175 * in snpFilter, suppress non-SNP sites
1177 ------------------------------------------------------------------------
1178 r310 | lh3lh3 | 2009-06-01 14:35:13 +0100 (Mon, 01 Jun 2009) | 3 lines
1180 M /trunk/samtools/misc/samtools.pl
1185 ------------------------------------------------------------------------
1186 r309 | lh3lh3 | 2009-06-01 14:04:39 +0100 (Mon, 01 Jun 2009) | 3 lines
1188 M /trunk/samtools/misc/samtools.pl
1193 ------------------------------------------------------------------------
1194 r306 | lh3lh3 | 2009-05-28 11:49:35 +0100 (Thu, 28 May 2009) | 3 lines
1196 M /trunk/samtools/bgzf.c
1198 * minor changes to bgzf: return NULL if fd == -1
1199 * suggested by {kdj,jm18}@sanger.ac.uk
1201 ------------------------------------------------------------------------
1202 r305 | lh3lh3 | 2009-05-28 11:16:08 +0100 (Thu, 28 May 2009) | 2 lines
1204 A /trunk/samtools/misc/interpolate_sam.pl
1206 Script for paired-end pileup, contributed by Stephen Montgomery.
1208 ------------------------------------------------------------------------
1209 r304 | lh3lh3 | 2009-05-28 11:08:49 +0100 (Thu, 28 May 2009) | 3 lines
1211 M /trunk/samtools/bamtk.c
1212 M /trunk/samtools/sam.c
1214 * samtools-0.1.4-1 (r304)
1215 * fixed a minor bug in printing headers
1217 ------------------------------------------------------------------------
1218 r297 | lh3lh3 | 2009-05-21 16:06:16 +0100 (Thu, 21 May 2009) | 2 lines
1220 M /trunk/samtools/ChangeLog
1221 M /trunk/samtools/NEWS
1222 M /trunk/samtools/bam_plcmd.c
1223 M /trunk/samtools/bamtk.c
1224 M /trunk/samtools/misc/maq2sam.c
1225 M /trunk/samtools/samtools.1
1227 Release samtools-0.1.4
1229 ------------------------------------------------------------------------
1230 r296 | lh3lh3 | 2009-05-21 12:53:14 +0100 (Thu, 21 May 2009) | 3 lines
1232 M /trunk/samtools/bam_maqcns.c
1233 M /trunk/samtools/bamtk.c
1235 * samtools-0.1.3-24 (r296)
1236 * another similar bug in the indel caller
1238 ------------------------------------------------------------------------
1239 r295 | lh3lh3 | 2009-05-21 12:50:28 +0100 (Thu, 21 May 2009) | 3 lines
1241 M /trunk/samtools/bam_maqcns.c
1242 M /trunk/samtools/bamtk.c
1244 * samtools-0.1.3-23 (r295)
1245 * fixed a critical bug in the indel caller
1247 ------------------------------------------------------------------------
1248 r294 | lh3lh3 | 2009-05-20 13:00:20 +0100 (Wed, 20 May 2009) | 2 lines
1250 M /trunk/samtools/bam_stat.c
1252 added a missing header file
1254 ------------------------------------------------------------------------
1255 r293 | lh3lh3 | 2009-05-19 23:44:25 +0100 (Tue, 19 May 2009) | 3 lines
1257 M /trunk/samtools/bam_tview.c
1258 M /trunk/samtools/bamtk.c
1260 * samtools-0.1.3-22 (r293)
1261 * open tview in the dot-view mode by default
1263 ------------------------------------------------------------------------
1264 r292 | lh3lh3 | 2009-05-18 21:01:23 +0100 (Mon, 18 May 2009) | 6 lines
1266 M /trunk/samtools/samtools.1
1268 Added a note to the manual. Currently SAMtools used unaligned words in
1269 several places. Although this does not cause bus errors to me, it may
1270 affect portability. Please see the "Bus error" wiki page for more
1271 information. Also thank James Bonfields for pointing this out.
1274 ------------------------------------------------------------------------
1275 r286 | lh3lh3 | 2009-05-14 15:23:13 +0100 (Thu, 14 May 2009) | 3 lines
1277 M /trunk/samtools/bam.h
1278 M /trunk/samtools/bam_aux.c
1279 M /trunk/samtools/bamtk.c
1281 * samtools-0.1.3-21 (286)
1282 * declare bam_aux_get_core() in bam.h
1284 ------------------------------------------------------------------------
1285 r276 | lh3lh3 | 2009-05-13 10:07:55 +0100 (Wed, 13 May 2009) | 5 lines
1287 M /trunk/samtools/bam.h
1288 M /trunk/samtools/bam_index.c
1289 M /trunk/samtools/bamtk.c
1291 * samtools-0.1.3-20 (r276)
1292 * remove bam1_t::hash again. We need to modify the Perl API anyway to
1293 make it work with the latest SVN.
1294 * As is suggested by Tim, scan "{base}.bai" and "{base}.bam.bai" for index
1296 ------------------------------------------------------------------------
1297 r275 | lh3lh3 | 2009-05-12 21:14:10 +0100 (Tue, 12 May 2009) | 4 lines
1299 M /trunk/samtools/ChangeLog
1300 M /trunk/samtools/bam.h
1301 M /trunk/samtools/bamtk.c
1303 * samtools-0.1.3-19 (r275)
1304 * a minor change to the bam1_t struct: added back "void *hash" for the
1305 backward compatibility with Bio::DB::Sam
1307 ------------------------------------------------------------------------
1308 r273 | lh3lh3 | 2009-05-12 14:28:39 +0100 (Tue, 12 May 2009) | 3 lines
1310 M /trunk/samtools/bam_rmdupse.c
1311 M /trunk/samtools/bamtk.c
1313 * samtools-0.1.3-18 (r273)
1314 * rmdupse: do not remove unmapped reads
1316 ------------------------------------------------------------------------
1317 r272 | lh3lh3 | 2009-05-12 14:20:00 +0100 (Tue, 12 May 2009) | 2 lines
1319 M /trunk/samtools/bam_rmdupse.c
1321 change a parameter. It does nothing
1323 ------------------------------------------------------------------------
1324 r271 | lh3lh3 | 2009-05-12 14:17:58 +0100 (Tue, 12 May 2009) | 3 lines
1326 M /trunk/samtools/Makefile.am
1327 M /trunk/samtools/Makefile.generic
1328 M /trunk/samtools/Makefile.lite
1329 A /trunk/samtools/bam_rmdupse.c
1330 M /trunk/samtools/bamtk.c
1331 M /trunk/samtools/configure.ac
1333 * samtools-0.1.3-17 (r271)
1334 * added 'rmdupse' command
1336 ------------------------------------------------------------------------
1337 r267 | lh3lh3 | 2009-05-05 22:31:41 +0100 (Tue, 05 May 2009) | 3 lines
1339 M /trunk/samtools/bamtk.c
1340 M /trunk/samtools/sam_view.c
1342 * samtools-0.1.3-16 (r267)
1343 * in sam_view.c, changed g_flag_on based on the suggestion by Angie Hinrichs
1345 ------------------------------------------------------------------------
1346 r266 | lh3lh3 | 2009-05-05 22:23:27 +0100 (Tue, 05 May 2009) | 3 lines
1348 M /trunk/samtools/bam_import.c
1349 M /trunk/samtools/bamtk.c
1351 * samtools-0.1.3-15 (r266)
1352 * report an error if a non-* reference is present while @SQ is absent
1354 ------------------------------------------------------------------------
1355 r265 | lh3lh3 | 2009-05-05 22:09:00 +0100 (Tue, 05 May 2009) | 3 lines
1357 M /trunk/samtools/bam.h
1358 M /trunk/samtools/bam_import.c
1359 M /trunk/samtools/bamtk.c
1360 M /trunk/samtools/sam.c
1361 M /trunk/samtools/sam_view.c
1363 * samtools-0.1.3-14 (r262)
1364 * make samopen() recognize @SQ header lines
1366 ------------------------------------------------------------------------
1367 r261 | lh3lh3 | 2009-05-05 15:10:30 +0100 (Tue, 05 May 2009) | 3 lines
1369 M /trunk/samtools/bam_plcmd.c
1370 M /trunk/samtools/bamtk.c
1371 M /trunk/samtools/bgzf.c
1372 M /trunk/samtools/sam.c
1373 M /trunk/samtools/sam_view.c
1375 * samtools-0.1.3-13 (r260)
1376 * report error for file I/O error
1378 ------------------------------------------------------------------------
1379 r260 | lh3lh3 | 2009-05-05 15:01:16 +0100 (Tue, 05 May 2009) | 2 lines
1381 M /trunk/samtools/Makefile.am
1385 ------------------------------------------------------------------------
1386 r259 | lh3lh3 | 2009-05-05 14:52:25 +0100 (Tue, 05 May 2009) | 3 lines
1388 M /trunk/samtools/bam.h
1389 M /trunk/samtools/bam_pileup.c
1390 M /trunk/samtools/bam_plcmd.c
1391 M /trunk/samtools/bamtk.c
1392 M /trunk/samtools/sam.c
1393 M /trunk/samtools/sam.h
1395 * samtools-0.1.3-12 (r259)
1396 * use the new I/O interface in pileup
1398 ------------------------------------------------------------------------
1399 r258 | lh3lh3 | 2009-05-05 14:33:22 +0100 (Tue, 05 May 2009) | 3 lines
1401 M /trunk/samtools/Makefile.generic
1402 M /trunk/samtools/Makefile.lite
1403 M /trunk/samtools/bam.c
1404 M /trunk/samtools/bam.h
1405 M /trunk/samtools/bam_import.c
1406 M /trunk/samtools/bamtk.c
1407 A /trunk/samtools/sam.c
1408 A /trunk/samtools/sam.h
1409 A /trunk/samtools/sam_view.c
1411 * samtools-0.1.3-11 (r258)
1412 * unify the interface to BAM and SAM I/O
1414 ------------------------------------------------------------------------
1415 r257 | lh3lh3 | 2009-05-05 09:53:35 +0100 (Tue, 05 May 2009) | 3 lines
1417 M /trunk/samtools/Makefile.lite
1418 M /trunk/samtools/bam_plcmd.c
1419 M /trunk/samtools/bamtk.c
1421 * samtools-0.1.3-10 (r257)
1422 * allow hex with "pileup -m"
1424 ------------------------------------------------------------------------
1425 r256 | lh3lh3 | 2009-05-04 19:16:50 +0100 (Mon, 04 May 2009) | 4 lines
1427 M /trunk/samtools/bam_lpileup.c
1428 M /trunk/samtools/bamtk.c
1430 * samtools-0.1.3-9 (r256)
1431 * fixed a bug in bam_lpileup.c
1432 * I do not know if this also fixes the bug causing assertion failure in the tview
1434 ------------------------------------------------------------------------
1435 r251 | lh3lh3 | 2009-04-28 13:53:23 +0100 (Tue, 28 Apr 2009) | 3 lines
1437 M /trunk/samtools/bam_pileup.c
1438 M /trunk/samtools/bamtk.c
1440 * samtools-0.1.3-8 (r251)
1441 * fixed a bug when there are reads without coordinates
1443 ------------------------------------------------------------------------
1444 r250 | lh3lh3 | 2009-04-28 13:43:33 +0100 (Tue, 28 Apr 2009) | 2 lines
1446 A /trunk/samtools/AUTHORS
1447 A /trunk/samtools/README
1448 M /trunk/samtools/cleanup.sh
1452 ------------------------------------------------------------------------
1453 r249 | lh3lh3 | 2009-04-28 13:37:16 +0100 (Tue, 28 Apr 2009) | 2 lines
1455 M /trunk/samtools/Makefile.generic
1456 M /trunk/samtools/Makefile.lite
1457 M /trunk/samtools/configure.ac
1458 M /trunk/samtools/misc/Makefile.generic
1460 improve large file support in compilation
1462 ------------------------------------------------------------------------
1463 r248 | lh3lh3 | 2009-04-28 13:33:24 +0100 (Tue, 28 Apr 2009) | 2 lines
1465 M /trunk/samtools/INSTALL
1469 ------------------------------------------------------------------------
1470 r247 | lh3lh3 | 2009-04-28 13:28:50 +0100 (Tue, 28 Apr 2009) | 2 lines
1472 M /trunk/samtools/Makefile.am
1473 M /trunk/samtools/autogen.sh
1474 M /trunk/samtools/cleanup.sh
1475 M /trunk/samtools/configure.ac
1476 A /trunk/samtools/misc/Makefile.am
1478 fixed various issues about the GNU building scripts
1480 ------------------------------------------------------------------------
1481 r246 | lh3lh3 | 2009-04-28 13:10:23 +0100 (Tue, 28 Apr 2009) | 4 lines
1483 M /trunk/samtools/ChangeLog
1484 D /trunk/samtools/Makefile
1485 A /trunk/samtools/Makefile.am
1486 A /trunk/samtools/Makefile.generic
1487 A /trunk/samtools/autogen.sh
1488 M /trunk/samtools/bam.h
1489 M /trunk/samtools/bam_aux.c
1490 M /trunk/samtools/bam_tview.c
1491 M /trunk/samtools/bamtk.c
1492 A /trunk/samtools/cleanup.sh
1493 A /trunk/samtools/configure.ac
1494 D /trunk/samtools/misc/Makefile
1495 A /trunk/samtools/misc/Makefile.generic (from /trunk/samtools/misc/Makefile:245)
1497 * samtools-0.1.3-7 (r246)
1498 * incorporated revisions from Nils Homer
1499 * enhanced support of displaying color-space reads
1501 ------------------------------------------------------------------------
1502 r244 | lh3lh3 | 2009-04-25 11:49:40 +0100 (Sat, 25 Apr 2009) | 3 lines
1504 M /trunk/samtools/bam_md.c
1505 M /trunk/samtools/bamtk.c
1507 * samtools-0.1.3-6 (r244)
1508 * fixed segfault for unmapped reads
1510 ------------------------------------------------------------------------
1511 r243 | lh3lh3 | 2009-04-24 21:27:26 +0100 (Fri, 24 Apr 2009) | 5 lines
1513 M /trunk/samtools/bam.h
1514 M /trunk/samtools/bam_maqcns.c
1515 M /trunk/samtools/bam_md.c
1516 M /trunk/samtools/bamtk.c
1518 * samtools-0.1.3-5 (r243)
1519 * fixed a long existing bug which may cause memory leak
1521 * consensus calling now works with "=", but indel calling not
1523 ------------------------------------------------------------------------
1524 r242 | lh3lh3 | 2009-04-24 20:44:46 +0100 (Fri, 24 Apr 2009) | 3 lines
1526 M /trunk/samtools/bam_md.c
1527 M /trunk/samtools/bamtk.c
1529 * samtools-0.1.3-4 (r242)
1530 * fixed a memory leak
1532 ------------------------------------------------------------------------
1533 r240 | lh3lh3 | 2009-04-24 16:40:18 +0100 (Fri, 24 Apr 2009) | 5 lines
1535 M /trunk/samtools/Makefile
1536 M /trunk/samtools/Makefile.lite
1537 M /trunk/samtools/bam.h
1538 M /trunk/samtools/bam_aux.c
1539 A /trunk/samtools/bam_md.c
1540 M /trunk/samtools/bam_plcmd.c
1541 M /trunk/samtools/bamtk.c
1543 * samtools-0.1.3-3 (r240)
1545 * generate "=" bases
1546 * the plain pileup now support "=" bases, but consensus calling and glfgen may fail
1548 ------------------------------------------------------------------------
1549 r239 | lh3lh3 | 2009-04-24 12:08:20 +0100 (Fri, 24 Apr 2009) | 5 lines
1551 M /trunk/samtools/bam.h
1552 M /trunk/samtools/bam_aux.c
1553 M /trunk/samtools/bamtk.c
1555 * samtools-0.1.3-2 (r239)
1556 * fixed bugs in bam_aux.c (these functions nevered used by samtools)
1557 * removed bam_aux_init()/bam_aux_destroy()
1558 * added tagview for testing bam_aux
1560 ------------------------------------------------------------------------
1561 r235 | lh3lh3 | 2009-04-21 23:17:39 +0100 (Tue, 21 Apr 2009) | 3 lines
1563 M /trunk/samtools/bam_pileup.c
1564 M /trunk/samtools/bamtk.c
1567 * fixed a bug in pileup: the first read in a chromosome may not be printed
1569 ------------------------------------------------------------------------
1570 r232 | lh3lh3 | 2009-04-16 15:25:43 +0100 (Thu, 16 Apr 2009) | 2 lines
1572 M /trunk/samtools/Makefile.lite
1574 a missing file in Makefile.lite
1576 ------------------------------------------------------------------------
1577 r227 | lh3lh3 | 2009-04-15 22:02:53 +0100 (Wed, 15 Apr 2009) | 2 lines
1579 M /trunk/samtools/NEWS
1580 M /trunk/samtools/bamtk.c
1582 Release samtools-0.1.3
1584 ------------------------------------------------------------------------
1585 r223 | lh3lh3 | 2009-04-15 14:31:32 +0100 (Wed, 15 Apr 2009) | 3 lines
1587 M /trunk/samtools/bam_plcmd.c
1588 M /trunk/samtools/bamtk.c
1591 * make samtools more robust to weird input such as empty file
1593 ------------------------------------------------------------------------
1594 r222 | lh3lh3 | 2009-04-15 14:05:33 +0100 (Wed, 15 Apr 2009) | 2 lines
1596 M /trunk/samtools/ChangeLog
1597 M /trunk/samtools/NEWS
1598 M /trunk/samtools/samtools.1
1600 prepare for release 0.1.3
1602 ------------------------------------------------------------------------
1603 r221 | lh3lh3 | 2009-04-15 13:32:14 +0100 (Wed, 15 Apr 2009) | 2 lines
1605 A /trunk/samtools/misc/blast2sam.pl
1607 convert NCBI-BLASTN to SAM
1609 ------------------------------------------------------------------------
1610 r220 | lh3lh3 | 2009-04-15 13:18:19 +0100 (Wed, 15 Apr 2009) | 3 lines
1612 M /trunk/samtools/bam_lpileup.c
1613 M /trunk/samtools/bamtk.c
1616 * fixed a small memory leak in tview
1618 ------------------------------------------------------------------------
1619 r219 | lh3lh3 | 2009-04-15 13:00:08 +0100 (Wed, 15 Apr 2009) | 3 lines
1621 M /trunk/samtools/bam_rmdup.c
1622 M /trunk/samtools/bamtk.c
1625 * fixed a bug in rmdup when there are unmapped reads
1627 ------------------------------------------------------------------------
1628 r218 | lh3lh3 | 2009-04-14 22:28:58 +0100 (Tue, 14 Apr 2009) | 2 lines
1630 M /trunk/samtools/ChangeLog
1631 M /trunk/samtools/NEWS
1633 proposed NEWS for the new release (have not yet)
1635 ------------------------------------------------------------------------
1636 r216 | lh3lh3 | 2009-04-14 22:10:46 +0100 (Tue, 14 Apr 2009) | 4 lines
1638 M /trunk/samtools/misc/samtools.pl
1641 * improve indelFilter to avoid filtering true indels. The new filter relies
1642 on the new pileup indel line implemented in samtools-0.1.2-25
1644 ------------------------------------------------------------------------
1645 r215 | lh3lh3 | 2009-04-14 22:04:19 +0100 (Tue, 14 Apr 2009) | 4 lines
1647 M /trunk/samtools/bam_maqcns.c
1648 M /trunk/samtools/bam_plcmd.c
1649 M /trunk/samtools/bamtk.c
1650 M /trunk/samtools/samtools.1
1653 * change the pileup indel line to shows the number of alignments actually
1656 ------------------------------------------------------------------------
1657 r211 | lh3lh3 | 2009-04-13 12:07:13 +0100 (Mon, 13 Apr 2009) | 2 lines
1659 M /trunk/samtools/ChangeLog
1661 update ChangeLog from "svn log"
1663 ------------------------------------------------------------------------
1664 r210 | lh3lh3 | 2009-04-12 20:57:05 +0100 (Sun, 12 Apr 2009) | 4 lines
1666 M /trunk/samtools/bam.c
1667 M /trunk/samtools/bam_import.c
1668 M /trunk/samtools/bam_sort.c
1669 M /trunk/samtools/bamtk.c
1670 M /trunk/samtools/kseq.h
1673 * in merge, gives a warning rather than error if the target sequence length is different
1674 * allow empty header
1676 ------------------------------------------------------------------------
1677 r209 | lh3lh3 | 2009-04-12 20:32:44 +0100 (Sun, 12 Apr 2009) | 3 lines
1679 M /trunk/samtools/bam.c
1680 M /trunk/samtools/bam_import.c
1681 M /trunk/samtools/bamtk.c
1684 * recognize '*' at the QUAL field
1686 ------------------------------------------------------------------------
1687 r208 | lh3lh3 | 2009-04-12 20:08:02 +0100 (Sun, 12 Apr 2009) | 3 lines
1689 M /trunk/samtools/bam_import.c
1690 M /trunk/samtools/bamtk.c
1691 M /trunk/samtools/kseq.h
1694 * the field separater is TAB only, now
1696 ------------------------------------------------------------------------
1697 r207 | lh3lh3 | 2009-04-08 15:18:03 +0100 (Wed, 08 Apr 2009) | 2 lines
1699 M /trunk/samtools/examples/ex1.sam.gz
1701 * fixed the problem in the example alignment due to the bug in fixmate
1703 ------------------------------------------------------------------------
1704 r206 | lh3lh3 | 2009-04-08 15:15:05 +0100 (Wed, 08 Apr 2009) | 3 lines
1706 M /trunk/samtools/bam_mate.c
1707 M /trunk/samtools/bamtk.c
1708 M /trunk/samtools/misc/soap2sam.pl
1711 * fixed a nasty bug in `fixmate'
1713 ------------------------------------------------------------------------
1714 r205 | lh3lh3 | 2009-04-08 10:57:08 +0100 (Wed, 08 Apr 2009) | 2 lines
1716 M /trunk/samtools/misc/bowtie2sam.pl
1717 M /trunk/samtools/misc/soap2sam.pl
1718 M /trunk/samtools/misc/wgsim_eval.pl
1720 make the script robust to the bugs in SOAP-2.1.7
1722 ------------------------------------------------------------------------
1723 r200 | lh3lh3 | 2009-04-02 15:14:56 +0100 (Thu, 02 Apr 2009) | 3 lines
1725 M /trunk/samtools/bam_stat.c
1726 M /trunk/samtools/bamtk.c
1729 * check if file is truncated in flagstat
1731 ------------------------------------------------------------------------
1732 r199 | lh3lh3 | 2009-04-02 15:09:10 +0100 (Thu, 02 Apr 2009) | 3 lines
1734 M /trunk/samtools/bamtk.c
1737 * print the header if requested
1739 ------------------------------------------------------------------------
1740 r193 | lh3lh3 | 2009-03-27 15:09:50 +0000 (Fri, 27 Mar 2009) | 3 lines
1742 M /trunk/samtools/bam_plcmd.c
1743 M /trunk/samtools/bamtk.c
1746 * fixed a minor bug reported by Nils Homer
1748 ------------------------------------------------------------------------
1749 r185 | lh3lh3 | 2009-03-24 11:50:32 +0000 (Tue, 24 Mar 2009) | 2 lines
1751 A /trunk/samtools/Makefile (from /trunk/samtools/Makefile.std:184)
1752 D /trunk/samtools/Makefile.std
1753 A /trunk/samtools/misc/Makefile (from /trunk/samtools/misc/Makefile.std:184)
1754 D /trunk/samtools/misc/Makefile.std
1756 rename Makefile.std as Makefile. GNU building systerm is not ready and may take some time...
1758 ------------------------------------------------------------------------
1759 r184 | lh3lh3 | 2009-03-24 10:36:38 +0000 (Tue, 24 Mar 2009) | 4 lines
1761 D /trunk/samtools/Makefile
1762 A /trunk/samtools/Makefile.std (from /trunk/samtools/Makefile:183)
1763 M /trunk/samtools/bam_sort.c
1764 M /trunk/samtools/bam_tview.c
1765 M /trunk/samtools/bamtk.c
1766 D /trunk/samtools/misc/Makefile
1767 A /trunk/samtools/misc/Makefile.std (from /trunk/samtools/misc/Makefile:182)
1768 M /trunk/samtools/samtools.1
1771 * incorporating Nils' changes
1772 * rename Makefile to Makefile.std and prepare to add the GNU building systerms (also by Nils)
1774 ------------------------------------------------------------------------
1775 r183 | lh3lh3 | 2009-03-24 10:30:23 +0000 (Tue, 24 Mar 2009) | 4 lines
1777 M /trunk/samtools/Makefile
1778 M /trunk/samtools/bam_import.c
1779 M /trunk/samtools/bam_maqcns.c
1780 M /trunk/samtools/bam_maqcns.h
1781 M /trunk/samtools/bam_plcmd.c
1782 M /trunk/samtools/bamtk.c
1783 M /trunk/samtools/kseq.h
1784 A /trunk/samtools/kstring.c
1785 A /trunk/samtools/kstring.h
1788 * made pileup take a list of proposed indels. An insertion is N at the moment.
1789 * added my kstring library for a bit complex parsing of the position list.
1791 ------------------------------------------------------------------------
1792 r169 | lh3lh3 | 2009-03-12 13:40:14 +0000 (Thu, 12 Mar 2009) | 3 lines
1794 M /trunk/samtools/misc/soap2sam.pl
1797 * more robust to truncated soap output
1799 ------------------------------------------------------------------------
1800 r168 | lh3lh3 | 2009-03-11 10:49:00 +0000 (Wed, 11 Mar 2009) | 2 lines
1802 M /trunk/samtools/Makefile.lite
1804 added bam_stat.o to Makefile.lite
1806 ------------------------------------------------------------------------
1807 r167 | lh3lh3 | 2009-03-10 22:11:31 +0000 (Tue, 10 Mar 2009) | 3 lines
1809 M /trunk/samtools/bam_maqcns.c
1810 M /trunk/samtools/bamtk.c
1813 * generate RMS of mapQ instead of max mapQ
1815 ------------------------------------------------------------------------
1816 r166 | lh3lh3 | 2009-03-10 22:06:45 +0000 (Tue, 10 Mar 2009) | 3 lines
1818 M /trunk/samtools/bam_plcmd.c
1819 M /trunk/samtools/bamtk.c
1820 M /trunk/samtools/glf.c
1821 M /trunk/samtools/glf.h
1822 M /trunk/samtools/misc/Makefile
1827 ------------------------------------------------------------------------
1828 r159 | lh3lh3 | 2009-03-03 11:26:08 +0000 (Tue, 03 Mar 2009) | 3 lines
1830 M /trunk/samtools/bam_plcmd.c
1831 M /trunk/samtools/bamtk.c
1834 * fixed a minor bug in displaying pileup
1836 ------------------------------------------------------------------------
1837 r158 | lh3lh3 | 2009-03-03 11:24:16 +0000 (Tue, 03 Mar 2009) | 3 lines
1839 M /trunk/samtools/ChangeLog
1840 M /trunk/samtools/bamtk.c
1843 * optionally print SAM header
1845 ------------------------------------------------------------------------
1846 r153 | lh3lh3 | 2009-03-02 10:45:28 +0000 (Mon, 02 Mar 2009) | 3 lines
1848 M /trunk/samtools/bamtk.c
1849 M /trunk/samtools/glf.c
1852 * use "GLF\3" as the magic for GLFv3 files
1854 ------------------------------------------------------------------------
1855 r152 | lh3lh3 | 2009-03-02 10:39:09 +0000 (Mon, 02 Mar 2009) | 5 lines
1857 M /trunk/samtools/Makefile
1858 M /trunk/samtools/bam_import.c
1859 M /trunk/samtools/bam_index.c
1860 M /trunk/samtools/bam_plcmd.c
1861 M /trunk/samtools/bamtk.c
1862 M /trunk/samtools/glf.c
1863 M /trunk/samtools/glf.h
1866 * fixed a bug in import: core.bin is undefined for unmapped reads
1867 * this bug can be alleviated (not completely solved) in bam_index.c
1868 * update to GLFv3: pos is changed to offset for better compression
1870 ------------------------------------------------------------------------
1871 r151 | lh3lh3 | 2009-03-01 15:18:43 +0000 (Sun, 01 Mar 2009) | 3 lines
1873 M /trunk/samtools/misc/wgsim.c
1876 * fixed a bug in simulating indels
1878 ------------------------------------------------------------------------
1879 r145 | lh3lh3 | 2009-02-26 19:43:57 +0000 (Thu, 26 Feb 2009) | 4 lines
1881 M /trunk/samtools/misc/wgsim.c
1884 * allow to print mismatch information as fastq comment. MAQ does
1885 not like long read names.
1887 ------------------------------------------------------------------------
1888 r141 | lh3lh3 | 2009-02-26 14:53:03 +0000 (Thu, 26 Feb 2009) | 6 lines
1890 M /trunk/samtools/ChangeLog
1891 M /trunk/samtools/misc/wgsim.c
1892 M /trunk/samtools/misc/wgsim_eval.pl
1895 * fixed a bug about color read coordinates
1896 * fixed a bug in read names
1897 * wgsim_eval.pl-0.1.3
1898 * make the script work with color reads
1900 ------------------------------------------------------------------------
1901 r140 | lh3lh3 | 2009-02-26 14:02:57 +0000 (Thu, 26 Feb 2009) | 2 lines
1903 M /trunk/samtools/misc/Makefile
1904 M /trunk/samtools/misc/wgsim.c
1906 * wgsim: added a note
1908 ------------------------------------------------------------------------
1909 r139 | lh3lh3 | 2009-02-26 11:39:08 +0000 (Thu, 26 Feb 2009) | 7 lines
1911 M /trunk/samtools/misc/wgsim.c
1912 M /trunk/samtools/misc/wgsim_eval.pl
1915 * considerable code clean up
1916 * print number of substitutions/indels/errors on each read
1917 * potentially support SOLiD simulation, though not tested at the moment
1918 * wgsim_eval.pl-0.1.2
1919 * change in accordant with wgsim
1921 ------------------------------------------------------------------------
1922 r129 | lh3lh3 | 2009-02-18 22:23:27 +0000 (Wed, 18 Feb 2009) | 3 lines
1924 M /trunk/samtools/bam_index.c
1925 M /trunk/samtools/bamtk.c
1928 * fixed a bug in bam_fetch, caused by completely contained adjacent chunks
1930 ------------------------------------------------------------------------
1931 r128 | bhandsaker | 2009-02-18 19:06:57 +0000 (Wed, 18 Feb 2009) | 2 lines
1933 M /trunk/samtools/bamtk.c
1935 Fix annoying segv when invalid region specified.
1937 ------------------------------------------------------------------------
1938 r127 | lh3lh3 | 2009-02-17 10:49:55 +0000 (Tue, 17 Feb 2009) | 2 lines
1940 D /trunk/samtools/misc/indel_filter.pl
1941 A /trunk/samtools/misc/samtools.pl
1943 * move indel_filter.pl to samtools.pl
1945 ------------------------------------------------------------------------
1946 r126 | lh3lh3 | 2009-02-14 21:22:30 +0000 (Sat, 14 Feb 2009) | 3 lines
1948 M /trunk/samtools/bam_mate.c
1949 M /trunk/samtools/bamtk.c
1952 * fixed a bug in fixmate: SE reads are flagged as BAM_FMUNMAP
1954 ------------------------------------------------------------------------
1955 r125 | lh3lh3 | 2009-02-13 09:54:45 +0000 (Fri, 13 Feb 2009) | 3 lines
1957 M /trunk/samtools/bam_stat.c
1958 M /trunk/samtools/bamtk.c
1961 * fixed a minor bug in flagstat
1963 ------------------------------------------------------------------------
1964 r124 | lh3lh3 | 2009-02-12 11:15:32 +0000 (Thu, 12 Feb 2009) | 3 lines
1966 M /trunk/samtools/bam_maqcns.c
1967 M /trunk/samtools/bamtk.c
1968 M /trunk/samtools/misc/indel_filter.pl
1971 * improve indel caller by setting maximum window size
1973 ------------------------------------------------------------------------
1974 r123 | lh3lh3 | 2009-02-12 10:30:29 +0000 (Thu, 12 Feb 2009) | 2 lines
1976 M /trunk/samtools/bam_plcmd.c
1977 M /trunk/samtools/bamtk.c
1979 * output max mapping quality in indel line
1981 ------------------------------------------------------------------------
1982 r122 | lh3lh3 | 2009-02-11 10:59:10 +0000 (Wed, 11 Feb 2009) | 2 lines
1984 M /trunk/samtools/misc/maq2sam.c
1986 fixed a bug in generating tag AM
1988 ------------------------------------------------------------------------
1989 r121 | lh3lh3 | 2009-02-03 10:43:11 +0000 (Tue, 03 Feb 2009) | 2 lines
1991 M /trunk/samtools/bam_index.c
1992 M /trunk/samtools/bamtk.c
1994 fixed a potential memory problem in indexing
1996 ------------------------------------------------------------------------
1997 r120 | bhandsaker | 2009-02-02 15:52:52 +0000 (Mon, 02 Feb 2009) | 2 lines
1999 M /trunk/samtools/Makefile
2001 Pass LIBS to recursive targets to facilitate building at Broad.
2003 ------------------------------------------------------------------------
2004 r119 | lh3lh3 | 2009-02-02 10:12:15 +0000 (Mon, 02 Feb 2009) | 4 lines
2006 M /trunk/samtools/ChangeLog
2007 M /trunk/samtools/bam_plcmd.c
2008 M /trunk/samtools/bam_stat.c
2009 M /trunk/samtools/bamtk.c
2012 * fixed a bug in generating GLFv2 for indels
2013 * improve flagstat report a little bit
2015 ------------------------------------------------------------------------
2016 r118 | lh3lh3 | 2009-01-29 12:33:23 +0000 (Thu, 29 Jan 2009) | 3 lines
2018 M /trunk/samtools/Makefile
2019 A /trunk/samtools/bam_stat.c
2020 M /trunk/samtools/bamtk.c
2023 * added flagstat command
2025 ------------------------------------------------------------------------
2026 r116 | lh3lh3 | 2009-01-28 13:31:12 +0000 (Wed, 28 Jan 2009) | 2 lines
2028 M /trunk/samtools/ChangeLog
2029 M /trunk/samtools/NEWS
2030 M /trunk/samtools/bamtk.c
2031 M /trunk/samtools/samtools.1
2033 Release SAMtools-0.1.2
2035 ------------------------------------------------------------------------
2036 r115 | lh3lh3 | 2009-01-28 12:54:08 +0000 (Wed, 28 Jan 2009) | 2 lines
2038 A /trunk/samtools/misc/indel_filter.pl
2040 Script for filtering indel results
2042 ------------------------------------------------------------------------
2043 r114 | lh3lh3 | 2009-01-25 11:45:37 +0000 (Sun, 25 Jan 2009) | 2 lines
2045 A /trunk/samtools/misc/zoom2sam.pl
2049 ------------------------------------------------------------------------
2050 r113 | lh3lh3 | 2009-01-24 14:25:07 +0000 (Sat, 24 Jan 2009) | 2 lines
2052 A /trunk/samtools/misc/novo2sam.pl
2054 add a script to convert novo alignment to SAM
2056 ------------------------------------------------------------------------
2057 r112 | lh3lh3 | 2009-01-23 20:57:39 +0000 (Fri, 23 Jan 2009) | 2 lines
2059 M /trunk/samtools/ChangeLog
2060 M /trunk/samtools/ChangeLog.old
2061 M /trunk/samtools/samtools.1
2063 update documentation and ChangeLog
2065 ------------------------------------------------------------------------
2066 r111 | lh3lh3 | 2009-01-23 19:22:59 +0000 (Fri, 23 Jan 2009) | 3 lines
2068 M /trunk/samtools/bam_sort.c
2069 M /trunk/samtools/bamtk.c
2072 * fixed a bug in "merge" command line
2074 ------------------------------------------------------------------------
2075 r110 | lh3lh3 | 2009-01-22 15:36:48 +0000 (Thu, 22 Jan 2009) | 3 lines
2077 M /trunk/samtools/misc/Makefile
2078 A /trunk/samtools/misc/bowtie2sam.pl (from /branches/dev/samtools/misc/bowtie2sam.pl:108)
2079 M /trunk/samtools/misc/export2sam.pl
2080 A /trunk/samtools/misc/soap2sam.pl (from /branches/dev/samtools/misc/soap2sam.pl:108)
2081 A /trunk/samtools/misc/wgsim.c (from /branches/dev/samtools/misc/wgsim.c:108)
2082 A /trunk/samtools/misc/wgsim_eval.pl (from /branches/dev/samtools/misc/wgsim_eval.pl:108)
2084 * merge from branches/dev/
2085 * all future development will happen here
2087 ------------------------------------------------------------------------
2088 r109 | lh3lh3 | 2009-01-22 15:14:27 +0000 (Thu, 22 Jan 2009) | 3 lines
2090 M /trunk/samtools/COPYING
2091 M /trunk/samtools/ChangeLog
2092 A /trunk/samtools/INSTALL (from /branches/dev/samtools/INSTALL:108)
2093 M /trunk/samtools/Makefile
2094 A /trunk/samtools/Makefile.lite (from /branches/dev/samtools/Makefile.lite:108)
2095 M /trunk/samtools/bam.c
2096 M /trunk/samtools/bam.h
2097 M /trunk/samtools/bam_import.c
2098 M /trunk/samtools/bam_index.c
2099 M /trunk/samtools/bam_lpileup.c
2100 M /trunk/samtools/bam_maqcns.c
2101 M /trunk/samtools/bam_maqcns.h
2102 A /trunk/samtools/bam_mate.c (from /branches/dev/samtools/bam_mate.c:108)
2103 M /trunk/samtools/bam_pileup.c
2104 M /trunk/samtools/bam_plcmd.c
2105 A /trunk/samtools/bam_rmdup.c (from /branches/dev/samtools/bam_rmdup.c:108)
2106 M /trunk/samtools/bam_sort.c
2107 M /trunk/samtools/bamtk.c
2108 M /trunk/samtools/bgzf.h
2109 M /trunk/samtools/examples/00README.txt
2110 A /trunk/samtools/examples/Makefile (from /branches/dev/samtools/examples/Makefile:108)
2111 D /trunk/samtools/examples/ex1.fa.fai
2112 M /trunk/samtools/examples/ex1.sam.gz
2113 M /trunk/samtools/faidx.c
2114 A /trunk/samtools/glf.c (from /branches/dev/samtools/glf.c:108)
2115 M /trunk/samtools/glf.h
2116 M /trunk/samtools/misc/Makefile
2117 M /trunk/samtools/misc/maq2sam.c
2118 M /trunk/samtools/razf.c
2119 M /trunk/samtools/source.dot
2121 * Merge from branches/dev/
2122 * all future development will happen here at trunk/
2124 ------------------------------------------------------------------------
2125 r79 | bhandsaker | 2009-01-07 21:42:15 +0000 (Wed, 07 Jan 2009) | 2 lines
2127 M /trunk/samtools/bam_maqcns.c
2128 M /trunk/samtools/bam_tview.c
2130 Fix problem with compiling without curses.
2132 ------------------------------------------------------------------------
2133 r63 | lh3lh3 | 2008-12-22 15:58:02 +0000 (Mon, 22 Dec 2008) | 2 lines
2135 A /trunk/samtools (from /branches/dev/samtools:62)
2139 ------------------------------------------------------------------------
2140 r62 | lh3lh3 | 2008-12-22 15:55:13 +0000 (Mon, 22 Dec 2008) | 2 lines
2142 A /branches/dev/samtools/NEWS
2143 M /branches/dev/samtools/bamtk.c
2144 M /branches/dev/samtools/samtools.1
2146 Release samtools-0.1.1
2148 ------------------------------------------------------------------------
2149 r61 | lh3lh3 | 2008-12-22 15:46:08 +0000 (Mon, 22 Dec 2008) | 10 lines
2151 M /branches/dev/samtools/bam_aux.c
2152 M /branches/dev/samtools/bam_index.c
2153 M /branches/dev/samtools/bam_plcmd.c
2154 M /branches/dev/samtools/bam_tview.c
2155 M /branches/dev/samtools/bamtk.c
2156 M /branches/dev/samtools/razf.c
2157 M /branches/dev/samtools/samtools.1
2160 * fixed a bug in razf.c: reset z_eof when razf_seek() is called
2161 * fixed a memory leak in parsing a region
2162 * changed pileup a little bit when -s is in use: output ^ and $
2163 * when a bam is not indexed, output more meaningful error message
2164 * fixed a bug in indexing for small alignment
2165 * fixed a bug in the viewer when we come to the end of a reference file
2166 * updated documentation
2167 * prepare to release 0.1.1
2169 ------------------------------------------------------------------------
2170 r60 | lh3lh3 | 2008-12-22 15:10:16 +0000 (Mon, 22 Dec 2008) | 2 lines
2172 A /branches/dev/samtools/examples
2173 A /branches/dev/samtools/examples/00README.txt
2174 A /branches/dev/samtools/examples/ex1.fa
2175 A /branches/dev/samtools/examples/ex1.fa.fai
2176 A /branches/dev/samtools/examples/ex1.sam.gz
2180 ------------------------------------------------------------------------
2181 r59 | lh3lh3 | 2008-12-22 09:38:15 +0000 (Mon, 22 Dec 2008) | 2 lines
2183 M /branches/dev/samtools/ChangeLog
2187 ------------------------------------------------------------------------
2188 r58 | lh3lh3 | 2008-12-20 23:06:00 +0000 (Sat, 20 Dec 2008) | 3 lines
2190 M /branches/dev/samtools/misc/export2sam.pl
2193 * fixed several bugs
2195 ------------------------------------------------------------------------
2196 r57 | lh3lh3 | 2008-12-20 15:44:20 +0000 (Sat, 20 Dec 2008) | 2 lines
2198 A /branches/dev/samtools/misc/export2sam.pl
2200 convert Export format to SAM; not thoroughly tested
2202 ------------------------------------------------------------------------
2203 r56 | lh3lh3 | 2008-12-19 22:13:28 +0000 (Fri, 19 Dec 2008) | 6 lines
2205 M /branches/dev/samtools/bam_import.c
2206 M /branches/dev/samtools/bam_plcmd.c
2207 M /branches/dev/samtools/bam_tview.c
2208 M /branches/dev/samtools/bamtk.c
2209 A /branches/dev/samtools/source.dot
2212 * pileup: generate maq-like simple output
2213 * pileup: allow to output pileup at required sites
2214 * source.dot: source file relationship graph
2215 * tview: fixed a minor bug
2217 ------------------------------------------------------------------------
2218 r55 | lh3lh3 | 2008-12-19 20:10:26 +0000 (Fri, 19 Dec 2008) | 2 lines
2220 D /branches/dev/samtools/misc/all2sam.pl
2224 ------------------------------------------------------------------------
2225 r54 | lh3lh3 | 2008-12-16 22:34:25 +0000 (Tue, 16 Dec 2008) | 2 lines
2227 A /branches/dev/samtools/COPYING
2228 M /branches/dev/samtools/bam.h
2229 M /branches/dev/samtools/faidx.h
2230 M /branches/dev/samtools/khash.h
2231 M /branches/dev/samtools/kseq.h
2232 M /branches/dev/samtools/ksort.h
2233 M /branches/dev/samtools/samtools.1
2235 Added copyright information and a bit more documentation. No code change.
2237 ------------------------------------------------------------------------
2238 r53 | lh3lh3 | 2008-12-16 13:40:18 +0000 (Tue, 16 Dec 2008) | 3 lines
2240 M /branches/dev/samtools/bam.c
2241 M /branches/dev/samtools/bam.h
2242 M /branches/dev/samtools/bam_index.c
2243 M /branches/dev/samtools/bam_maqcns.c
2244 M /branches/dev/samtools/bamtk.c
2247 * improved efficiency of the indel caller for spliced alignments
2249 ------------------------------------------------------------------------
2250 r52 | lh3lh3 | 2008-12-16 10:28:20 +0000 (Tue, 16 Dec 2008) | 3 lines
2252 M /branches/dev/samtools/bam.c
2253 M /branches/dev/samtools/bam.h
2254 M /branches/dev/samtools/bam_aux.c
2255 M /branches/dev/samtools/bam_index.c
2256 M /branches/dev/samtools/bamtk.c
2259 * a bit code cleanup: reduce the dependency between source files
2261 ------------------------------------------------------------------------
2262 r51 | lh3lh3 | 2008-12-15 14:29:32 +0000 (Mon, 15 Dec 2008) | 3 lines
2264 M /branches/dev/samtools/bam_maqcns.c
2265 M /branches/dev/samtools/bam_plcmd.c
2266 M /branches/dev/samtools/bamtk.c
2269 * fixed a memory leak
2271 ------------------------------------------------------------------------
2272 r50 | lh3lh3 | 2008-12-15 14:00:13 +0000 (Mon, 15 Dec 2008) | 2 lines
2274 M /branches/dev/samtools/ChangeLog
2275 M /branches/dev/samtools/bam.h
2276 M /branches/dev/samtools/samtools.1
2278 update documentation, ChangeLog and a comment
2280 ------------------------------------------------------------------------
2281 r49 | lh3lh3 | 2008-12-15 13:36:43 +0000 (Mon, 15 Dec 2008) | 6 lines
2283 M /branches/dev/samtools/Makefile
2284 M /branches/dev/samtools/bam.h
2285 M /branches/dev/samtools/bam_maqcns.c
2286 M /branches/dev/samtools/bam_maqcns.h
2287 M /branches/dev/samtools/bam_pileup.c
2288 A /branches/dev/samtools/bam_plcmd.c
2289 M /branches/dev/samtools/bamtk.c
2290 M /branches/dev/samtools/samtools.1
2293 * moved pileup command to a separate source file
2294 * added indel caller
2295 * added bam_cal_segend(). (NOT WORKING for spliced alignment!!!)
2296 * updated documentation
2298 ------------------------------------------------------------------------
2299 r48 | lh3lh3 | 2008-12-12 13:55:36 +0000 (Fri, 12 Dec 2008) | 3 lines
2301 M /branches/dev/samtools/bam_maqcns.c
2302 M /branches/dev/samtools/bamtk.c
2305 * fixed another bug in maqcns when there is a nearby deletion
2307 ------------------------------------------------------------------------
2308 r47 | lh3lh3 | 2008-12-12 13:42:16 +0000 (Fri, 12 Dec 2008) | 5 lines
2310 M /branches/dev/samtools/bam_maqcns.c
2311 M /branches/dev/samtools/bam_pileup.c
2312 M /branches/dev/samtools/bamtk.c
2315 * pileup: outputing consensus is now optional
2316 * fixed a bug in glfgen. This bug also exists in maq's glfgen. However,
2317 I am not quite sure why the previous version may have problem.
2319 ------------------------------------------------------------------------
2320 r46 | lh3lh3 | 2008-12-12 11:44:56 +0000 (Fri, 12 Dec 2008) | 6 lines
2322 M /branches/dev/samtools/bam_pileup.c
2323 M /branches/dev/samtools/bamtk.c
2326 * add maq consensus to pileup. However, I will move this part to a new
2327 command as strictly speaking, consensus callin is not part of pileup,
2328 and imposing it would make it harder to generate for other language
2331 ------------------------------------------------------------------------
2332 r45 | bhandsaker | 2008-12-11 20:43:56 +0000 (Thu, 11 Dec 2008) | 2 lines
2334 M /branches/dev/samtools/bgzf.c
2336 Fix bug in tell() after reads that consume to the exact end of a block.
2338 ------------------------------------------------------------------------
2339 r44 | lh3lh3 | 2008-12-11 09:36:53 +0000 (Thu, 11 Dec 2008) | 2 lines
2341 M /branches/dev/samtools/samtools.1
2345 ------------------------------------------------------------------------
2346 r43 | lh3lh3 | 2008-12-11 09:25:36 +0000 (Thu, 11 Dec 2008) | 4 lines
2348 M /branches/dev/samtools/bam_import.c
2349 M /branches/dev/samtools/bamtk.c
2352 * fixed a bug in parser when there is auxiliary fields
2353 * made the parser a bit more robust
2355 ------------------------------------------------------------------------
2356 r42 | lh3lh3 | 2008-12-10 14:57:29 +0000 (Wed, 10 Dec 2008) | 5 lines
2358 M /branches/dev/samtools/bam_index.c
2359 M /branches/dev/samtools/bamtk.c
2360 M /branches/dev/samtools/bgzf.c
2363 * fixed a bug in bgzf (only reading is affected)
2364 * fixed a typo in bam_index.c
2365 * in bam_index.c, check potential bugs in the underlying I/O library
2367 ------------------------------------------------------------------------
2368 r41 | lh3lh3 | 2008-12-10 12:53:08 +0000 (Wed, 10 Dec 2008) | 2 lines
2370 M /branches/dev/samtools/samtools.1
2374 ------------------------------------------------------------------------
2375 r40 | lh3lh3 | 2008-12-10 11:52:10 +0000 (Wed, 10 Dec 2008) | 5 lines
2377 M /branches/dev/samtools/bam.h
2378 M /branches/dev/samtools/bam_pileup.c
2379 M /branches/dev/samtools/bamtk.c
2382 * tried to make pileup work with clipping (previously not), though NOT tested
2383 * removed -v from pileup
2384 * made pileup take the reference sequence
2386 ------------------------------------------------------------------------
2387 r39 | lh3lh3 | 2008-12-09 11:59:28 +0000 (Tue, 09 Dec 2008) | 4 lines
2389 M /branches/dev/samtools/bam_import.c
2390 M /branches/dev/samtools/bamtk.c
2391 M /branches/dev/samtools/samtools.1
2394 * in parser, recognize "=", rather than ",", as a match
2395 * in parser, correctl parse "=" at the MRNM field.
2397 ------------------------------------------------------------------------
2398 r38 | lh3lh3 | 2008-12-09 11:39:07 +0000 (Tue, 09 Dec 2008) | 2 lines
2400 M /branches/dev/samtools/misc/maq2sam.c
2402 fixed a bug in handling maq flag 64 and 192
2404 ------------------------------------------------------------------------
2405 r37 | lh3lh3 | 2008-12-09 09:53:46 +0000 (Tue, 09 Dec 2008) | 2 lines
2407 M /branches/dev/samtools/misc/md5fa.c
2409 also calculate unordered md5sum check
2411 ------------------------------------------------------------------------
2412 r36 | lh3lh3 | 2008-12-09 09:46:21 +0000 (Tue, 09 Dec 2008) | 2 lines
2414 M /branches/dev/samtools/misc/md5fa.c
2416 fixed a minor bug when there are space in the sequence
2418 ------------------------------------------------------------------------
2419 r35 | lh3lh3 | 2008-12-09 09:40:45 +0000 (Tue, 09 Dec 2008) | 2 lines
2421 M /branches/dev/samtools/misc/md5fa.c
2423 fixed a potential memory leak
2425 ------------------------------------------------------------------------
2426 r34 | lh3lh3 | 2008-12-08 14:52:17 +0000 (Mon, 08 Dec 2008) | 2 lines
2428 M /branches/dev/samtools/bam_import.c
2429 M /branches/dev/samtools/bam_index.c
2430 M /branches/dev/samtools/bamtk.c
2432 * fixed a bug in import: bin is wrongly calculated
2434 ------------------------------------------------------------------------
2435 r33 | lh3lh3 | 2008-12-08 14:08:01 +0000 (Mon, 08 Dec 2008) | 2 lines
2437 M /branches/dev/samtools/misc/all2sam.pl
2441 ------------------------------------------------------------------------
2442 r32 | lh3lh3 | 2008-12-08 12:56:02 +0000 (Mon, 08 Dec 2008) | 3 lines
2444 M /branches/dev/samtools/Makefile
2445 M /branches/dev/samtools/kseq.h
2446 M /branches/dev/samtools/misc/Makefile
2447 A /branches/dev/samtools/misc/md5.c
2448 A /branches/dev/samtools/misc/md5.h
2449 A /branches/dev/samtools/misc/md5fa.c
2451 * fixed two warnings in kseq.h
2452 * added md5sum utilities
2454 ------------------------------------------------------------------------
2455 r31 | lh3lh3 | 2008-12-08 11:35:29 +0000 (Mon, 08 Dec 2008) | 5 lines
2457 M /branches/dev/samtools/Makefile
2458 M /branches/dev/samtools/bam_import.c
2459 M /branches/dev/samtools/bamtk.c
2460 A /branches/dev/samtools/kseq.h
2461 D /branches/dev/samtools/kstream.h
2464 * replace kstream with kseq. kseq is a superset of kstream. I need the
2465 extra functions in kseq.h.
2466 * also compile stand-alone faidx
2468 ------------------------------------------------------------------------
2469 r30 | lh3lh3 | 2008-12-08 11:17:04 +0000 (Mon, 08 Dec 2008) | 3 lines
2471 M /branches/dev/samtools/bam.h
2472 M /branches/dev/samtools/bam_sort.c
2473 M /branches/dev/samtools/bamtk.c
2476 * sorting by read names is available
2478 ------------------------------------------------------------------------
2479 r29 | lh3lh3 | 2008-12-08 10:29:02 +0000 (Mon, 08 Dec 2008) | 3 lines
2481 M /branches/dev/samtools/bam.c
2482 M /branches/dev/samtools/bam.h
2483 M /branches/dev/samtools/bam_import.c
2484 M /branches/dev/samtools/bam_maqcns.c
2485 M /branches/dev/samtools/bam_pileup.c
2486 M /branches/dev/samtools/bam_sort.c
2487 M /branches/dev/samtools/bam_tview.c
2488 M /branches/dev/samtools/bamtk.c
2489 M /branches/dev/samtools/misc/maq2sam.c
2492 * format change to meet the latest specification
2494 ------------------------------------------------------------------------
2495 r28 | lh3lh3 | 2008-12-04 16:09:21 +0000 (Thu, 04 Dec 2008) | 3 lines
2497 M /branches/dev/samtools/bam_maqcns.c
2498 M /branches/dev/samtools/misc/maq2sam.c
2500 * minor change in maqcns: special care when n==0
2501 * change maq2sam to meet the latest specification
2503 ------------------------------------------------------------------------
2504 r27 | lh3lh3 | 2008-12-04 15:55:44 +0000 (Thu, 04 Dec 2008) | 2 lines
2506 M /branches/dev/samtools/razf.c
2507 M /branches/dev/samtools/razf.h
2509 considerable code clean up in razf
2511 ------------------------------------------------------------------------
2512 r26 | lh3lh3 | 2008-12-04 15:08:18 +0000 (Thu, 04 Dec 2008) | 2 lines
2514 M /branches/dev/samtools/ChangeLog
2515 M /branches/dev/samtools/Makefile
2516 M /branches/dev/samtools/faidx.c
2518 make RAZF optional in faidx.c
2520 ------------------------------------------------------------------------
2521 r25 | lh3lh3 | 2008-12-01 15:27:22 +0000 (Mon, 01 Dec 2008) | 3 lines
2523 M /branches/dev/samtools/Makefile
2524 M /branches/dev/samtools/bam.h
2525 M /branches/dev/samtools/bam_aux.c
2526 M /branches/dev/samtools/bamtk.c
2527 M /branches/dev/samtools/samtools.1
2530 * added routines for retrieving aux data, NOT TESTED YET!
2532 ------------------------------------------------------------------------
2533 r24 | lh3lh3 | 2008-12-01 14:29:43 +0000 (Mon, 01 Dec 2008) | 5 lines
2535 M /branches/dev/samtools/bam.c
2536 M /branches/dev/samtools/bam_import.c
2537 M /branches/dev/samtools/bam_maqcns.c
2538 M /branches/dev/samtools/bamtk.c
2539 M /branches/dev/samtools/bgzf.c
2540 M /branches/dev/samtools/samtools.1
2543 * bgzf: fixed a potential integer overflow on 32-it machines
2544 * maqcns: set the minimum combined quality as 0
2545 * supporting hex strings
2547 ------------------------------------------------------------------------
2548 r23 | lh3lh3 | 2008-11-27 17:14:37 +0000 (Thu, 27 Nov 2008) | 3 lines
2550 M /branches/dev/samtools/bam_maqcns.c
2551 M /branches/dev/samtools/bamtk.c
2554 * fixed the bug in maqcns
2556 ------------------------------------------------------------------------
2557 r22 | lh3lh3 | 2008-11-27 17:08:11 +0000 (Thu, 27 Nov 2008) | 3 lines
2559 M /branches/dev/samtools/Makefile
2560 M /branches/dev/samtools/bam.h
2561 A /branches/dev/samtools/bam_maqcns.c
2562 A /branches/dev/samtools/bam_maqcns.h
2563 M /branches/dev/samtools/bam_tview.c
2564 M /branches/dev/samtools/bamtk.c
2565 A /branches/dev/samtools/glf.h
2568 * add MAQ consensus caller, currently BUGGY!
2570 ------------------------------------------------------------------------
2571 r21 | lh3lh3 | 2008-11-27 13:51:28 +0000 (Thu, 27 Nov 2008) | 4 lines
2573 M /branches/dev/samtools/bam_pileup.c
2574 M /branches/dev/samtools/bam_tview.c
2575 M /branches/dev/samtools/bamtk.c
2578 * tview: display padded alignment (but not P operation)
2579 * better coordinates and reference sequence
2581 ------------------------------------------------------------------------
2582 r19 | lh3lh3 | 2008-11-27 09:26:05 +0000 (Thu, 27 Nov 2008) | 2 lines
2584 A /branches/dev/samtools/ChangeLog
2588 ------------------------------------------------------------------------
2589 r18 | lh3lh3 | 2008-11-27 09:24:45 +0000 (Thu, 27 Nov 2008) | 3 lines
2591 D /branches/dev/samtools/ChangeLog
2592 A /branches/dev/samtools/ChangeLog.old (from /branches/dev/samtools/ChangeLog:6)
2594 Rename ChangeLog to ChangeLog.old. This old ChangeLog is generated from
2595 the log of my personal SVN repository.
2597 ------------------------------------------------------------------------
2598 r17 | lh3lh3 | 2008-11-27 09:22:55 +0000 (Thu, 27 Nov 2008) | 6 lines
2600 M /branches/dev/samtools/Makefile
2601 M /branches/dev/samtools/bamtk.c
2602 M /branches/dev/samtools/bgzf.c
2605 * declare fseeko and ftello as some Linux may not do this by default and
2606 missing these declarations will make bgzf buggy
2607 * get rid of some harmless warings
2608 * use BGZF by default, now
2610 ------------------------------------------------------------------------
2611 r16 | lh3lh3 | 2008-11-26 21:19:11 +0000 (Wed, 26 Nov 2008) | 4 lines
2613 M /branches/dev/samtools/bam_index.c
2614 M /branches/dev/samtools/bamtk.c
2615 M /branches/dev/samtools/razf.c
2618 * fixed a bug in razf_read()
2619 * give more warnings when the file is truncated (or due to bugs in I/O library)
2621 ------------------------------------------------------------------------
2622 r15 | lh3lh3 | 2008-11-26 20:41:39 +0000 (Wed, 26 Nov 2008) | 2 lines
2624 M /branches/dev/samtools/bgzf.c
2626 fixed a bug in bgzf.c at the end of the file
2628 ------------------------------------------------------------------------
2629 r14 | lh3lh3 | 2008-11-26 17:05:18 +0000 (Wed, 26 Nov 2008) | 4 lines
2631 M /branches/dev/samtools/bamtk.c
2634 * a lot happened to RAZF, although samtools itself is untouched. Better
2635 also update the version number anyway to avoid confusion
2637 ------------------------------------------------------------------------
2638 r13 | lh3lh3 | 2008-11-26 17:03:48 +0000 (Wed, 26 Nov 2008) | 2 lines
2640 M /branches/dev/samtools/razf.c
2642 a change from Jue, but I think it should not matter
2644 ------------------------------------------------------------------------
2645 r12 | lh3lh3 | 2008-11-26 16:48:14 +0000 (Wed, 26 Nov 2008) | 3 lines
2647 M /branches/dev/samtools/razf.c
2649 fixed a potential bug in razf. However, it seems still buggy, just
2650 rarely happens, very rarely.
2652 ------------------------------------------------------------------------
2653 r11 | lh3lh3 | 2008-11-26 14:02:56 +0000 (Wed, 26 Nov 2008) | 2 lines
2655 M /branches/dev/samtools/razf.c
2657 fixed a bug in razf, with the help of Jue
2659 ------------------------------------------------------------------------
2660 r10 | lh3lh3 | 2008-11-26 11:55:32 +0000 (Wed, 26 Nov 2008) | 2 lines
2662 M /branches/dev/samtools/bam_index.c
2666 ------------------------------------------------------------------------
2667 r9 | lh3lh3 | 2008-11-26 11:37:05 +0000 (Wed, 26 Nov 2008) | 2 lines
2669 M /branches/dev/samtools/Makefile
2670 M /branches/dev/samtools/bam.h
2671 M /branches/dev/samtools/razf.c
2672 M /branches/dev/samtools/razf.h
2674 * Jue has updated razf to realize Bob's scheme
2676 ------------------------------------------------------------------------
2677 r7 | lh3lh3 | 2008-11-25 20:37:37 +0000 (Tue, 25 Nov 2008) | 2 lines
2679 A /branches/dev/samtools/samtools.1
2683 ------------------------------------------------------------------------
2684 r6 | lh3lh3 | 2008-11-25 20:37:16 +0000 (Tue, 25 Nov 2008) | 3 lines
2686 A /branches/dev/samtools/ChangeLog
2687 A /branches/dev/samtools/Makefile
2688 A /branches/dev/samtools/bam.c
2689 A /branches/dev/samtools/bam.h
2690 A /branches/dev/samtools/bam_aux.c
2691 A /branches/dev/samtools/bam_endian.h
2692 A /branches/dev/samtools/bam_import.c
2693 A /branches/dev/samtools/bam_index.c
2694 A /branches/dev/samtools/bam_lpileup.c
2695 A /branches/dev/samtools/bam_pileup.c
2696 A /branches/dev/samtools/bam_sort.c
2697 A /branches/dev/samtools/bam_tview.c
2698 A /branches/dev/samtools/bamtk.c
2699 A /branches/dev/samtools/bgzf.c
2700 A /branches/dev/samtools/bgzf.h
2701 A /branches/dev/samtools/bgzip.c
2702 A /branches/dev/samtools/faidx.c
2703 A /branches/dev/samtools/faidx.h
2704 A /branches/dev/samtools/khash.h
2705 A /branches/dev/samtools/ksort.h
2706 A /branches/dev/samtools/kstream.h
2707 A /branches/dev/samtools/misc
2708 A /branches/dev/samtools/misc/Makefile
2709 A /branches/dev/samtools/misc/all2sam.pl
2710 A /branches/dev/samtools/misc/maq2sam.c
2711 A /branches/dev/samtools/razf.c
2712 A /branches/dev/samtools/razf.h
2713 A /branches/dev/samtools/razip.c
2714 A /branches/dev/samtools/zutil.h
2716 The initial version of samtools, replicated from my local SVN repository.
2717 The current version is: 0.1.0-42. All future development will happen here.
2719 ------------------------------------------------------------------------
2720 r5 | lh3lh3 | 2008-11-25 20:30:49 +0000 (Tue, 25 Nov 2008) | 2 lines
2722 A /branches/dev/samtools
2724 samtools (C version)
2726 ------------------------------------------------------------------------