1 ------------------------------------------------------------------------
2 r451 | lh3lh3 | 2009-09-02 10:44:48 +0100 (Wed, 02 Sep 2009) | 4 lines
4 M /trunk/samtools/bam_md.c
5 M /trunk/samtools/bam_rmdup.c
6 M /trunk/samtools/bam_rmdupse.c
7 M /trunk/samtools/bam_sort.c
8 M /trunk/samtools/bamtk.c
9 M /trunk/samtools/samtools.1
11 * samtools-0.1.5-34 (r451)
12 * applied the patch by John
13 * improved the help message a little bit
15 ------------------------------------------------------------------------
16 r450 | lh3lh3 | 2009-09-02 09:55:55 +0100 (Wed, 02 Sep 2009) | 3 lines
18 M /trunk/samtools/bam_color.c
19 M /trunk/samtools/bamtk.c
21 * samtools-0.1.5-33 (r450)
22 * fixed a bug in bam_color.c (on behalf of Nils Homer)
24 ------------------------------------------------------------------------
25 r449 | lh3lh3 | 2009-08-29 20:36:41 +0100 (Sat, 29 Aug 2009) | 4 lines
27 M /trunk/samtools/bam_import.c
28 M /trunk/samtools/bam_md.c
29 M /trunk/samtools/bamtk.c
30 M /trunk/samtools/misc/samtools.pl
32 * samtools-0.1.5-32 (r449)
33 * fillmd: fixed a bug in modifying MD/NM tags
34 * in import, give a warning if the read is aligned but there is no CIGAR.
36 ------------------------------------------------------------------------
37 r448 | lh3lh3 | 2009-08-19 09:44:28 +0100 (Wed, 19 Aug 2009) | 3 lines
39 M /trunk/samtools/ChangeLog
40 M /trunk/samtools/bam_pileup.c
41 M /trunk/samtools/bamtk.c
42 M /trunk/samtools/misc/wgsim_eval.pl
44 * samtools-0.1.5-31 (r448)
45 * fixed an issue when the last CIGAR is I or D
47 ------------------------------------------------------------------------
48 r447 | lh3lh3 | 2009-08-17 09:34:57 +0100 (Mon, 17 Aug 2009) | 3 lines
50 M /trunk/samtools/bam_aux.c
51 M /trunk/samtools/bamtk.c
53 * samtools-0.1.5-30 (r447)
54 * fixed a bug in bam_aux_get(): 'A' is not checked
56 ------------------------------------------------------------------------
57 r446 | lh3lh3 | 2009-08-17 09:33:17 +0100 (Mon, 17 Aug 2009) | 2 lines
59 M /trunk/samtools/bam_aux.c
60 M /trunk/samtools/bamtk.c
64 ------------------------------------------------------------------------
65 r444 | lh3lh3 | 2009-08-11 10:02:36 +0100 (Tue, 11 Aug 2009) | 3 lines
67 M /trunk/samtools/bam_sort.c
68 M /trunk/samtools/bamtk.c
70 * samtools-0.1.5-28 (r444)
73 ------------------------------------------------------------------------
74 r443 | lh3lh3 | 2009-08-11 09:29:11 +0100 (Tue, 11 Aug 2009) | 4 lines
76 M /trunk/samtools/bam.c
77 M /trunk/samtools/bam_import.c
78 M /trunk/samtools/bamtk.c
80 * samtools-0.1.5-27 (r443)
81 * SEQ and QUAL can be "*"
82 * parse CIGAR "=" and "X" as "M"
84 ------------------------------------------------------------------------
85 r442 | lh3lh3 | 2009-08-07 21:56:38 +0100 (Fri, 07 Aug 2009) | 4 lines
87 M /trunk/samtools/bam_pileup.c
88 M /trunk/samtools/bamtk.c
89 M /trunk/samtools/misc/md5.c
90 M /trunk/samtools/misc/md5.h
91 M /trunk/samtools/misc/md5fa.c
93 * samtools-0.1.5-26 (r442)
94 * replace RSA Inc md5.* with ones under permissive lincense
95 * fixed a bug in detecting unsorted bam in pileup
97 ------------------------------------------------------------------------
98 r441 | bhandsaker | 2009-08-05 14:41:28 +0100 (Wed, 05 Aug 2009) | 2 lines
100 M /trunk/samtools/bgzf.c
101 M /trunk/samtools/bgzf.h
102 M /trunk/samtools/bgzip.c
104 Change copyright notices now that MIT has approved open source distribution.
106 ------------------------------------------------------------------------
107 r440 | lh3lh3 | 2009-08-05 10:44:24 +0100 (Wed, 05 Aug 2009) | 3 lines
109 M /trunk/samtools/bam_stat.c
110 M /trunk/samtools/bamtk.c
112 * samtools-0.1.5-25 (r436)
113 * in flagstats, do not report singletons if both ends are unmapped
115 ------------------------------------------------------------------------
116 r439 | lh3lh3 | 2009-08-04 22:16:51 +0100 (Tue, 04 Aug 2009) | 2 lines
118 M /trunk/samtools/misc/maq2sam.c
120 fixed a SERIOUS bug in setting 0x20 flag
122 ------------------------------------------------------------------------
123 r438 | lh3lh3 | 2009-08-04 21:50:43 +0100 (Tue, 04 Aug 2009) | 2 lines
125 M /trunk/samtools/misc/samtools.pl
127 fixed two minor bugs (suggested by Tim M Storm)
129 ------------------------------------------------------------------------
130 r437 | lh3lh3 | 2009-08-04 09:13:24 +0100 (Tue, 04 Aug 2009) | 3 lines
132 M /trunk/samtools/bamtk.c
133 M /trunk/samtools/misc/samtools.pl
134 M /trunk/samtools/sam_view.c
136 * samtools-0.1.5-24 (r435)
139 ------------------------------------------------------------------------
140 r434 | lh3lh3 | 2009-08-03 10:40:42 +0100 (Mon, 03 Aug 2009) | 3 lines
142 M /trunk/samtools/bam_tview.c
143 M /trunk/samtools/bamtk.c
145 * samtools-0.1.5-23 (r434)
146 * in tview, press 'r' to show read names rather than sequences
148 ------------------------------------------------------------------------
149 r433 | lh3lh3 | 2009-08-02 19:13:35 +0100 (Sun, 02 Aug 2009) | 3 lines
151 M /trunk/samtools/knetfile.c
153 * tried to fixed the buggy FTP random access in Windows. FAILED.
154 * anyway, MinGW seems to have problem with "%lld".
156 ------------------------------------------------------------------------
157 r432 | lh3lh3 | 2009-08-02 00:32:07 +0100 (Sun, 02 Aug 2009) | 5 lines
159 M /trunk/samtools/Makefile.mingw
160 M /trunk/samtools/bamtk.c
161 M /trunk/samtools/faidx.c
162 M /trunk/samtools/razf.c
163 A /trunk/samtools/win32/libcurses.a
164 A /trunk/samtools/win32/xcurses.h
166 * samtools-0.1.5-22 (r432)
167 * faidx: fixed compitability issue with _WIN32
168 * razf: fixed potential compitability issue with _WIN32
169 * PDCurses support in Windows
171 ------------------------------------------------------------------------
172 r431 | lh3lh3 | 2009-08-01 23:34:54 +0100 (Sat, 01 Aug 2009) | 2 lines
174 M /trunk/samtools/win32/libz.a
176 replace the GnuWin32 version of libz.a with my own build with MinGW.
178 ------------------------------------------------------------------------
179 r430 | lh3lh3 | 2009-08-01 23:21:07 +0100 (Sat, 01 Aug 2009) | 2 lines
181 M /trunk/samtools/knetfile.c
185 ------------------------------------------------------------------------
186 r429 | lh3lh3 | 2009-08-01 22:41:19 +0100 (Sat, 01 Aug 2009) | 3 lines
188 M /trunk/samtools/Makefile.mingw
189 M /trunk/samtools/bamtk.c
190 M /trunk/samtools/knetfile.c
191 M /trunk/samtools/knetfile.h
193 * samtools-0.1.5-21 (r428)
194 * knetfile.c is now compatible with mingw-winsock
196 ------------------------------------------------------------------------
197 r428 | lh3lh3 | 2009-08-01 00:39:07 +0100 (Sat, 01 Aug 2009) | 2 lines
199 M /trunk/samtools/Makefile.mingw
201 simplify MinGW Makefile
203 ------------------------------------------------------------------------
204 r427 | lh3lh3 | 2009-08-01 00:30:54 +0100 (Sat, 01 Aug 2009) | 5 lines
206 A /trunk/samtools/Makefile.mingw
207 M /trunk/samtools/bam_import.c
208 M /trunk/samtools/bamtk.c
209 A /trunk/samtools/win32
210 A /trunk/samtools/win32/libz.a
211 A /trunk/samtools/win32/zconf.h
212 A /trunk/samtools/win32/zlib.h
214 * samtools-0.1.5-20 (r427)
215 * MinGW support. At least SAM<->BAM conversion is working. Other
216 functionality are not tested at the moment.
217 * zlib headers and Windows version of libz.a are included in win32/
219 ------------------------------------------------------------------------
220 r426 | lh3lh3 | 2009-07-31 23:32:09 +0100 (Fri, 31 Jul 2009) | 3 lines
222 M /trunk/samtools/bamtk.c
223 M /trunk/samtools/sam_view.c
225 * samtools-0.1.5-19 (r426)
226 * fixed a bug caused by recent modifications. Sorry.
228 ------------------------------------------------------------------------
229 r425 | lh3lh3 | 2009-07-31 23:23:51 +0100 (Fri, 31 Jul 2009) | 2 lines
231 M /trunk/samtools/bgzf.c
233 compatible with Windows binary files
235 ------------------------------------------------------------------------
236 r424 | lh3lh3 | 2009-07-31 10:19:59 +0100 (Fri, 31 Jul 2009) | 5 lines
238 M /trunk/samtools/bam_maqcns.c
239 M /trunk/samtools/bam_maqcns.h
240 M /trunk/samtools/bam_plcmd.c
241 M /trunk/samtools/bam_tview.c
242 M /trunk/samtools/bamtk.c
243 M /trunk/samtools/misc/samtools.pl
245 * samtools-0.1.5-18 (r423)
246 * output additional information in pileup indel lines, for the purepose
247 of debugging at the moment
248 * in tview, optionally allow to treat reference skip as deletion
250 ------------------------------------------------------------------------
251 r423 | lh3lh3 | 2009-07-30 22:00:36 +0100 (Thu, 30 Jul 2009) | 2 lines
253 A /trunk/samtools/misc/psl2sam.pl
255 convert BLAT psl to SAM.
257 ------------------------------------------------------------------------
258 r422 | lh3lh3 | 2009-07-30 11:24:39 +0100 (Thu, 30 Jul 2009) | 6 lines
260 M /trunk/samtools/ChangeLog
261 M /trunk/samtools/bam.c
262 M /trunk/samtools/bamtk.c
263 M /trunk/samtools/bgzf.c
264 M /trunk/samtools/bgzf.h
265 M /trunk/samtools/knetfile.c
266 M /trunk/samtools/sam.c
267 M /trunk/samtools/sam_view.c
269 * samtools-0.1.5-17 (r422)
270 * fixed a but in knetfile.c when seek type is not SEEK_SET
271 * write an empty BGZF block to every BGZF file
272 * check BGZF EOF marker in bam_header_read()
275 ------------------------------------------------------------------------
276 r421 | lh3lh3 | 2009-07-30 10:03:39 +0100 (Thu, 30 Jul 2009) | 3 lines
278 M /trunk/samtools/bam_import.c
279 M /trunk/samtools/bam_plcmd.c
280 M /trunk/samtools/bamtk.c
281 M /trunk/samtools/misc/samtools.pl
282 M /trunk/samtools/sam.c
283 M /trunk/samtools/sam.h
284 M /trunk/samtools/sam_view.c
286 * samtools-0.1.5-16 (r421)
287 * in view and pileup, load header from FASTA index if the input is SAM.
289 ------------------------------------------------------------------------
290 r420 | lh3lh3 | 2009-07-29 09:18:55 +0100 (Wed, 29 Jul 2009) | 2 lines
292 M /trunk/samtools/misc/maq2sam.c
294 do not set "read 1" if reads are not mapped in the PE mode of maq
296 ------------------------------------------------------------------------
297 r419 | lh3lh3 | 2009-07-28 09:52:33 +0100 (Tue, 28 Jul 2009) | 5 lines
299 M /trunk/samtools/bam_import.c
300 M /trunk/samtools/bamtk.c
301 M /trunk/samtools/misc/samtools.pl
302 M /trunk/samtools/misc/wgsim_eval.pl
304 * samtools-0.1.5-15 (r419)
305 * in sam_open(), return NULL when the file cannot be opened.
306 * make wgsim_eval.pl more robust to imperfect SAM
307 * add "unique" command to samtools.pl
309 ------------------------------------------------------------------------
310 r418 | lh3lh3 | 2009-07-24 14:04:19 +0100 (Fri, 24 Jul 2009) | 2 lines
312 M /trunk/samtools/misc/wgsim_eval.pl
314 skip @header lines in SAM
316 ------------------------------------------------------------------------
317 r417 | lh3lh3 | 2009-07-24 12:42:38 +0100 (Fri, 24 Jul 2009) | 3 lines
319 M /trunk/samtools/bamtk.c
320 M /trunk/samtools/sam_view.c
322 * samtools-0.1.5-14 (r417)
323 * more help in "samtools view" due to the recent changes.
325 ------------------------------------------------------------------------
326 r416 | lh3lh3 | 2009-07-24 12:34:30 +0100 (Fri, 24 Jul 2009) | 3 lines
328 M /trunk/samtools/bam.c
329 M /trunk/samtools/bam.h
330 M /trunk/samtools/bam_import.c
331 M /trunk/samtools/bamtk.c
332 M /trunk/samtools/sam.c
333 M /trunk/samtools/sam.h
334 M /trunk/samtools/sam_view.c
336 * samtools-0.1.5-17 (r416)
337 * support import/export SAM with string tags
339 ------------------------------------------------------------------------
340 r415 | lh3lh3 | 2009-07-24 11:39:26 +0100 (Fri, 24 Jul 2009) | 3 lines
342 M /trunk/samtools/bam.c
343 M /trunk/samtools/bam.h
344 M /trunk/samtools/bam_import.c
345 M /trunk/samtools/bamtk.c
346 M /trunk/samtools/sam.c
347 M /trunk/samtools/sam.h
348 M /trunk/samtools/sam_view.c
350 * samtools-0.1.5-12 (r415)
351 * FLAG now can be in HEX
353 ------------------------------------------------------------------------
354 r414 | lh3lh3 | 2009-07-22 22:03:49 +0100 (Wed, 22 Jul 2009) | 2 lines
356 M /trunk/samtools/kstring.h
358 fixed a compiling error (thank Ken for fixing it)
360 ------------------------------------------------------------------------
361 r412 | lh3lh3 | 2009-07-21 22:19:40 +0100 (Tue, 21 Jul 2009) | 2 lines
363 M /trunk/samtools/kstring.c
364 M /trunk/samtools/kstring.h
366 Implemented Boyer-Moore search in the kstring library.
368 ------------------------------------------------------------------------
369 r409 | lh3lh3 | 2009-07-17 17:10:20 +0100 (Fri, 17 Jul 2009) | 2 lines
371 M /trunk/samtools/bam_index.c
373 do not include knetfile.h when _USE_KNETFILE is not defined
375 ------------------------------------------------------------------------
376 r408 | lh3lh3 | 2009-07-17 15:29:21 +0100 (Fri, 17 Jul 2009) | 5 lines
378 M /trunk/samtools/bam_md.c
379 M /trunk/samtools/bam_tview.c
380 M /trunk/samtools/bamtk.c
381 M /trunk/samtools/bgzf.c
383 * samtools-0.1.5-11 (r408)
384 * force to overwirte existing MD if it is different from the one calculated
386 * bgzf.c: improved the compatibility with Windows headers
388 ------------------------------------------------------------------------
389 r407 | lh3lh3 | 2009-07-17 14:46:56 +0100 (Fri, 17 Jul 2009) | 5 lines
391 M /trunk/samtools/bam.h
392 M /trunk/samtools/bam_aux.c
393 M /trunk/samtools/bam_md.c
394 M /trunk/samtools/bamtk.c
395 M /trunk/samtools/sam.h
397 * samtools-0.1.5-10 (r407)
398 * implemented bam_aux_del() to remove a tag
399 * fillmd: generate the NM tag
400 * fillmd: cmd interface improvement
402 ------------------------------------------------------------------------
403 r406 | lh3lh3 | 2009-07-16 23:30:40 +0100 (Thu, 16 Jul 2009) | 2 lines
405 M /trunk/samtools/Makefile
407 Sorry. The old Makefile is for PDCurses...
409 ------------------------------------------------------------------------
410 r405 | lh3lh3 | 2009-07-16 23:30:11 +0100 (Thu, 16 Jul 2009) | 3 lines
412 M /trunk/samtools/Makefile
413 M /trunk/samtools/bam_tview.c
414 M /trunk/samtools/bamtk.c
416 * samtools-0.1.5-9 (r405)
417 * improved the compatibility with PDCurses a little bit
419 ------------------------------------------------------------------------
420 r404 | lh3lh3 | 2009-07-16 23:23:52 +0100 (Thu, 16 Jul 2009) | 3 lines
422 M /trunk/samtools/Makefile
423 M /trunk/samtools/bam_tview.c
424 M /trunk/samtools/bamtk.c
426 * samtools-0.1.5-8 (r404)
427 * compatible with PDCurses
429 ------------------------------------------------------------------------
430 r403 | lh3lh3 | 2009-07-16 22:39:39 +0100 (Thu, 16 Jul 2009) | 3 lines
432 M /trunk/samtools/bamtk.c
433 M /trunk/samtools/kseq.h
435 * samtools-0.1.5-7 (r403)
436 * fixed a bug in kseq.h for binary files (text files are fine)
438 ------------------------------------------------------------------------
439 r402 | lh3lh3 | 2009-07-16 11:49:53 +0100 (Thu, 16 Jul 2009) | 4 lines
441 M /trunk/samtools/bam_import.c
442 M /trunk/samtools/bam_index.c
443 M /trunk/samtools/bamtk.c
444 M /trunk/samtools/bgzf.c
446 * samtools-0.1.5-6 (r402)
447 * fixed compiling error when "-D_USE_NETFILE" is not applied
448 * improve portability to MinGW
450 ------------------------------------------------------------------------
451 r398 | lh3lh3 | 2009-07-13 10:21:36 +0100 (Mon, 13 Jul 2009) | 3 lines
453 A /trunk/bam-lite/bam.h (from /trunk/samtools/bam.h:395)
454 A /trunk/bam-lite/bam_lite.c (from /trunk/samtools/bam_lite.c:395)
455 D /trunk/samtools/bam_lite.c
457 * move bam_lite.c to bam-lite
458 * copy bam.h to bam-lite
460 ------------------------------------------------------------------------
461 r395 | lh3lh3 | 2009-07-13 10:12:57 +0100 (Mon, 13 Jul 2009) | 3 lines
463 M /trunk/samtools/bam.h
464 M /trunk/samtools/bam_lite.c
465 M /trunk/samtools/bam_lpileup.c
466 M /trunk/samtools/bam_pileup.c
467 M /trunk/samtools/bamtk.c
469 * samtools-0.1.5-5 (r395)
470 * added bam_pileup_file() and removed bam_lpileup_file()
472 ------------------------------------------------------------------------
473 r394 | lh3lh3 | 2009-07-13 00:35:10 +0100 (Mon, 13 Jul 2009) | 3 lines
475 M /trunk/samtools/bamtk.c
476 M /trunk/samtools/knetfile.c
477 M /trunk/samtools/knetfile.h
479 * samtools-0.1.5-4 (r394)
480 * http_proxy support in knetfile library (check http_proxy ENV)
482 ------------------------------------------------------------------------
483 r393 | lh3lh3 | 2009-07-12 23:57:07 +0100 (Sun, 12 Jul 2009) | 5 lines
485 M /trunk/samtools/bam_index.c
486 M /trunk/samtools/bam_tview.c
487 M /trunk/samtools/bamtk.c
488 M /trunk/samtools/knetfile.c
489 M /trunk/samtools/knetfile.h
491 * samtools-0.1.5-3 (r393)
492 * knetfile now supports HTTP (no proxy at the moment)
493 * fixed a potential issue in knetfile on opening ordinary file, although I have
494 not seen the sideeffect so far.
496 ------------------------------------------------------------------------
497 r392 | lh3lh3 | 2009-07-12 18:50:55 +0100 (Sun, 12 Jul 2009) | 2 lines
499 M /trunk/samtools/samtools.1
501 Remove the warning in tview
503 ------------------------------------------------------------------------
504 r391 | lh3lh3 | 2009-07-12 18:42:43 +0100 (Sun, 12 Jul 2009) | 3 lines
506 M /trunk/samtools/bam_tview.c
507 M /trunk/samtools/bamtk.c
509 * samtools-0.1.5-2 (r391)
510 * do not show a blank screen when no reads mapped
512 ------------------------------------------------------------------------
513 r390 | lh3lh3 | 2009-07-09 14:01:42 +0100 (Thu, 09 Jul 2009) | 4 lines
515 M /trunk/samtools/bam.h
516 A /trunk/samtools/bam_lite.c
517 M /trunk/samtools/bamtk.c
519 * samtools-0.1.5-1 (r390)
520 * removed useless _IOLIB in bam.h. This should cause no change at all.
521 * added bam_lite.c for light-weight BAM reading
523 ------------------------------------------------------------------------
524 r385 | lh3lh3 | 2009-07-07 16:53:29 +0100 (Tue, 07 Jul 2009) | 2 lines
526 M /trunk/samtools/bamtk.c
527 M /trunk/samtools/knetfile.c
529 Release samtools-0.1.5c (fixed a bug in piping)
531 ------------------------------------------------------------------------
532 r383 | lh3lh3 | 2009-07-07 11:39:55 +0100 (Tue, 07 Jul 2009) | 2 lines
534 M /trunk/samtools/bamtk.c
535 M /trunk/samtools/sam.c
537 Release samtools-0.1.5b (BUG! so embarrassing!)
539 ------------------------------------------------------------------------
540 r381 | lh3lh3 | 2009-07-07 11:20:06 +0100 (Tue, 07 Jul 2009) | 2 lines
542 M /trunk/samtools/Makefile
543 M /trunk/samtools/bam.h
544 M /trunk/samtools/bam_aux.c
545 M /trunk/samtools/bamtk.c
547 Release samtools-0.1.5a (for compatibility with Bio::DB::Sam)
549 ------------------------------------------------------------------------
550 r373 | lh3lh3 | 2009-07-07 10:26:57 +0100 (Tue, 07 Jul 2009) | 2 lines
552 M /trunk/samtools/ChangeLog
553 M /trunk/samtools/NEWS
554 M /trunk/samtools/bamtk.c
555 M /trunk/samtools/samtools.1
557 Release samtools-0.1.5
559 ------------------------------------------------------------------------
560 r372 | lh3lh3 | 2009-07-07 09:49:27 +0100 (Tue, 07 Jul 2009) | 3 lines
562 M /trunk/samtools/bamtk.c
563 M /trunk/samtools/sam.c
565 * samtools-0.1.4-23 (r372)
566 * keep header text if "view -t" is used (by Gerton)
568 ------------------------------------------------------------------------
569 r371 | lh3lh3 | 2009-07-07 01:13:32 +0100 (Tue, 07 Jul 2009) | 2 lines
571 M /trunk/samtools/samtools.1
575 ------------------------------------------------------------------------
576 r370 | bhandsaker | 2009-07-02 22:24:34 +0100 (Thu, 02 Jul 2009) | 2 lines
578 M /trunk/samtools/Makefile
580 Introduced LIBPATH variable so this could be overridden to allow samtools to build correct at the Broad.
582 ------------------------------------------------------------------------
583 r369 | lh3lh3 | 2009-07-02 13:36:53 +0100 (Thu, 02 Jul 2009) | 4 lines
585 M /trunk/samtools/ChangeLog
586 M /trunk/samtools/bam_aux.c
587 M /trunk/samtools/bam_plcmd.c
588 M /trunk/samtools/bamtk.c
590 * samtools-0.1.4-22 (r369)
591 * in pileup, optionally print E2 and U2
592 * remove the debugging code in bam_aux_get() (Drat!)
594 ------------------------------------------------------------------------
595 r368 | lh3lh3 | 2009-07-02 11:32:26 +0100 (Thu, 02 Jul 2009) | 6 lines
597 M /trunk/samtools/bam.c
598 M /trunk/samtools/bam.h
599 M /trunk/samtools/bam_aux.c
600 M /trunk/samtools/bam_index.c
601 M /trunk/samtools/bam_lpileup.c
602 M /trunk/samtools/bam_md.c
603 M /trunk/samtools/bam_pileup.c
604 M /trunk/samtools/bam_rmdup.c
605 M /trunk/samtools/bam_stat.c
606 M /trunk/samtools/bam_tview.c
607 M /trunk/samtools/bamtk.c
608 M /trunk/samtools/faidx.c
609 M /trunk/samtools/faidx.h
610 M /trunk/samtools/glf.c
612 * samtools-0.1.4-21 (r368)
613 * propagate errors rather than exit or complain assertion failure. Assertion
614 should be only used for checking internal bugs, but not for external input
615 inconsistency. I was just a bit lazy.
616 * small memory leak may be present on failure, though
618 ------------------------------------------------------------------------
619 r367 | lh3lh3 | 2009-06-30 16:18:42 +0100 (Tue, 30 Jun 2009) | 2 lines
621 M /trunk/samtools/knetfile.c
623 reduce the chance of blocking in FTP connection
625 ------------------------------------------------------------------------
626 r366 | lh3lh3 | 2009-06-30 15:35:21 +0100 (Tue, 30 Jun 2009) | 2 lines
628 M /trunk/samtools/knetfile.c
630 minor changes to knetfile: invalid fd equals -1 rather than 0
632 ------------------------------------------------------------------------
633 r365 | lh3lh3 | 2009-06-30 14:04:30 +0100 (Tue, 30 Jun 2009) | 3 lines
635 M /trunk/samtools/bam_index.c
636 M /trunk/samtools/bamtk.c
637 M /trunk/samtools/knetfile.c
638 M /trunk/samtools/knetfile.h
640 * samtools-0.1.4-20 (r365)
641 * download the BAM index file if it is not found in the current working directory.
643 ------------------------------------------------------------------------
644 r364 | lh3lh3 | 2009-06-30 12:39:07 +0100 (Tue, 30 Jun 2009) | 3 lines
646 M /trunk/samtools/bamtk.c
647 M /trunk/samtools/knetfile.c
649 * samtools-0.1.4-19 (r364)
650 * knetfile: report error when the file is not present on FTP
652 ------------------------------------------------------------------------
653 r363 | lh3lh3 | 2009-06-29 23:23:32 +0100 (Mon, 29 Jun 2009) | 4 lines
655 M /trunk/samtools/bam_tview.c
656 M /trunk/samtools/bamtk.c
657 M /trunk/samtools/bgzf.c
658 M /trunk/samtools/bgzf.h
659 M /trunk/samtools/knetfile.c
660 M /trunk/samtools/knetfile.h
662 * samtools-0.1.4-18 (r363)
663 * knetfile: do not trigger network communication in FTP seek (lazy seek)
664 * bgzf: cache recent blocks (disabled by default)
666 ------------------------------------------------------------------------
667 r362 | lh3lh3 | 2009-06-25 21:04:34 +0100 (Thu, 25 Jun 2009) | 2 lines
669 M /trunk/samtools/bgzf.c
673 ------------------------------------------------------------------------
674 r361 | lh3lh3 | 2009-06-25 21:03:10 +0100 (Thu, 25 Jun 2009) | 3 lines
676 M /trunk/samtools/bam_index.c
677 M /trunk/samtools/bamtk.c
679 * samtools-0.1.4-17 (r361)
680 * if a file is given on FTP, search locally for the BAM index
682 ------------------------------------------------------------------------
683 r360 | lh3lh3 | 2009-06-25 20:44:52 +0100 (Thu, 25 Jun 2009) | 5 lines
685 M /trunk/samtools/Makefile
686 M /trunk/samtools/bam_import.c
687 M /trunk/samtools/bam_index.c
688 M /trunk/samtools/bamtk.c
689 M /trunk/samtools/bgzf.c
690 M /trunk/samtools/bgzf.h
691 M /trunk/samtools/knetfile.c
692 M /trunk/samtools/knetfile.h
694 * samtools-0.1.4-16 (r360)
695 * report more information in index when the input is not sorted
696 * change the behaviour of knet_seek() such that it returns 0 on success
697 * support knetfile library in BGZF
699 ------------------------------------------------------------------------
700 r359 | lh3lh3 | 2009-06-25 17:10:55 +0100 (Thu, 25 Jun 2009) | 2 lines
702 M /trunk/samtools/knetfile.c
703 M /trunk/samtools/knetfile.h
705 fixed bugs in knetfile.*
707 ------------------------------------------------------------------------
708 r358 | lh3lh3 | 2009-06-25 13:53:19 +0100 (Thu, 25 Jun 2009) | 2 lines
710 A /trunk/samtools/knetfile.h
712 this is the header file
714 ------------------------------------------------------------------------
715 r357 | lh3lh3 | 2009-06-25 13:52:03 +0100 (Thu, 25 Jun 2009) | 3 lines
717 A /trunk/samtools/knetfile.c
720 * preliminary version
722 ------------------------------------------------------------------------
723 r354 | lh3lh3 | 2009-06-24 14:02:25 +0100 (Wed, 24 Jun 2009) | 3 lines
725 M /trunk/samtools/bam.c
726 M /trunk/samtools/bamtk.c
728 * samtools-0.1.4-15 (r354)
729 * fixed a memory leak in bam_view1(), although samtools is not using this routine.
731 ------------------------------------------------------------------------
732 r351 | lh3lh3 | 2009-06-18 00:16:26 +0100 (Thu, 18 Jun 2009) | 4 lines
734 M /trunk/samtools/bamtk.c
735 M /trunk/samtools/faidx.c
737 * samtools-0.1.4-13 (r351)
738 * make faidx more tolerant to empty lines right before or after > lines
739 * hope this does not introduce new bugs...
741 ------------------------------------------------------------------------
742 r350 | lh3lh3 | 2009-06-16 14:37:01 +0100 (Tue, 16 Jun 2009) | 3 lines
744 M /trunk/samtools/bam_plcmd.c
745 M /trunk/samtools/bamtk.c
747 * samtools-0.1.4-13 (r350)
748 * fixed a small memory leak in pileup, caused by recent modifications
750 ------------------------------------------------------------------------
751 r347 | lh3lh3 | 2009-06-13 21:20:49 +0100 (Sat, 13 Jun 2009) | 3 lines
753 M /trunk/samtools/bam_plcmd.c
754 M /trunk/samtools/bamtk.c
755 M /trunk/samtools/sam_view.c
757 * samtools-0.1.4-12 (r347)
758 * added `-S' to pileup, similar to `view -S'
760 ------------------------------------------------------------------------
761 r346 | lh3lh3 | 2009-06-13 17:52:31 +0100 (Sat, 13 Jun 2009) | 3 lines
763 M /trunk/samtools/Makefile
764 M /trunk/samtools/bamtk.c
765 M /trunk/samtools/sam_view.c
766 M /trunk/samtools/samtools.1
768 * samtools-0.1.4-11 (r346)
769 * allow to select a read group at view command-line
771 ------------------------------------------------------------------------
772 r344 | lh3lh3 | 2009-06-13 14:06:24 +0100 (Sat, 13 Jun 2009) | 2 lines
774 M /trunk/samtools/examples/calDepth.c
778 ------------------------------------------------------------------------
779 r343 | lh3lh3 | 2009-06-13 14:01:22 +0100 (Sat, 13 Jun 2009) | 2 lines
781 M /trunk/samtools/examples/calDepth.c
785 ------------------------------------------------------------------------
786 r342 | lh3lh3 | 2009-06-13 13:58:48 +0100 (Sat, 13 Jun 2009) | 2 lines
788 M /trunk/samtools/examples/Makefile
789 A /trunk/samtools/examples/calDepth.c
791 added an example of calculating read depth
793 ------------------------------------------------------------------------
794 r341 | lh3lh3 | 2009-06-13 13:00:08 +0100 (Sat, 13 Jun 2009) | 6 lines
796 M /trunk/samtools/Makefile
797 M /trunk/samtools/bam.h
798 M /trunk/samtools/bam_aux.c
799 A /trunk/samtools/bam_color.c
800 M /trunk/samtools/bam_plcmd.c
801 M /trunk/samtools/bam_sort.c
802 M /trunk/samtools/bam_tview.c
803 M /trunk/samtools/bamtk.c
804 M /trunk/samtools/sam.c
805 M /trunk/samtools/sam.h
807 * samtools-0.1.4-10 (r341)
808 * only include key APIs in libbam.a
809 * move color-specific routines to bam_color.c
810 * update documentations
811 * remove the support of -q in pileup
813 ------------------------------------------------------------------------
814 r340 | lh3lh3 | 2009-06-13 11:17:14 +0100 (Sat, 13 Jun 2009) | 6 lines
816 M /trunk/samtools/INSTALL
817 M /trunk/samtools/Makefile
818 M /trunk/samtools/bam_aux.c
819 M /trunk/samtools/bam_import.c
820 M /trunk/samtools/bam_tview.c
821 M /trunk/samtools/bamtk.c
822 M /trunk/samtools/razf.c
823 M /trunk/samtools/sam_view.c
825 * samtools-0.1.4-9 (r340)
826 * added a warning to razf.c if zlib<1.2.2.1
827 * fixed a compilation warning
828 * fixed a segfault caused by @RG parsing
829 * detect NCURSES in bam_tview.c
831 ------------------------------------------------------------------------
832 r339 | lh3lh3 | 2009-06-13 10:35:19 +0100 (Sat, 13 Jun 2009) | 2 lines
834 M /trunk/samtools/INSTALL
838 ------------------------------------------------------------------------
839 r338 | lh3lh3 | 2009-06-13 00:15:24 +0100 (Sat, 13 Jun 2009) | 4 lines
841 M /trunk/samtools/bam.c
842 M /trunk/samtools/bam.h
843 M /trunk/samtools/bam_aux.c
844 M /trunk/samtools/bam_import.c
845 M /trunk/samtools/bamtk.c
846 M /trunk/samtools/kstring.h
847 M /trunk/samtools/sam.c
848 M /trunk/samtools/sam_view.c
850 * samtools-0.1.4-8 (r338)
851 * parse the @RG header lines and allow to choose library at the "samtools view"
854 ------------------------------------------------------------------------
855 r337 | lh3lh3 | 2009-06-12 21:25:50 +0100 (Fri, 12 Jun 2009) | 4 lines
857 M /trunk/samtools/bamtk.c
858 M /trunk/samtools/bgzf.c
859 M /trunk/samtools/bgzf.h
860 M /trunk/samtools/sam.c
861 M /trunk/samtools/sam_view.c
863 * samtools-0.1.4-7 (r337)
864 * bgzf.c: support mode string "wu": uncompressed output
865 * "samtools view" support "-u" command-line option
867 ------------------------------------------------------------------------
868 r336 | lh3lh3 | 2009-06-12 17:20:12 +0100 (Fri, 12 Jun 2009) | 5 lines
870 M /trunk/samtools/Makefile
871 M /trunk/samtools/misc/Makefile
872 M /trunk/samtools/razf.c
873 M /trunk/samtools/razf.h
874 M /trunk/samtools/razip.c
876 * no changes to samtools itself
877 * remove zlib source codes
878 * make RAZF reading compatible with old version of zlib
879 * on old version of zlib, writing is not available
881 ------------------------------------------------------------------------
882 r335 | lh3lh3 | 2009-06-12 16:47:33 +0100 (Fri, 12 Jun 2009) | 2 lines
884 D /trunk/samtools/zlib
886 remove zlib for simplification...
888 ------------------------------------------------------------------------
889 r334 | lh3lh3 | 2009-06-12 15:43:36 +0100 (Fri, 12 Jun 2009) | 5 lines
891 M /trunk/samtools/bam.h
892 M /trunk/samtools/bam_aux.c
893 M /trunk/samtools/bamtk.c
895 * samtools-0.1.4-6 (r334)
896 * do not export bam_aux_get_core() for Bio::DB::Sam because it has already
897 been implemented in that.
898 * this version works with the latest Bio::DB::Sam (20090612)
900 ------------------------------------------------------------------------
901 r333 | lh3lh3 | 2009-06-12 15:33:42 +0100 (Fri, 12 Jun 2009) | 2 lines
903 M /trunk/samtools/ChangeLog
907 ------------------------------------------------------------------------
908 r332 | lh3lh3 | 2009-06-12 15:21:21 +0100 (Fri, 12 Jun 2009) | 2 lines
910 M /trunk/samtools/AUTHORS
911 M /trunk/samtools/Makefile
912 M /trunk/samtools/misc/Makefile
914 fixed minor things in Makefile
916 ------------------------------------------------------------------------
917 r331 | lh3lh3 | 2009-06-12 15:07:05 +0100 (Fri, 12 Jun 2009) | 4 lines
919 M /trunk/samtools/bamtk.c
921 * samtools-0.1.4-5 (r3310
922 * no change to samtools itself. Version number is increased to reflect the
923 changes in the Makefile building system.
925 ------------------------------------------------------------------------
926 r330 | lh3lh3 | 2009-06-12 15:03:38 +0100 (Fri, 12 Jun 2009) | 2 lines
928 M /trunk/samtools/AUTHORS
929 D /trunk/samtools/README
931 update information...
933 ------------------------------------------------------------------------
934 r329 | lh3lh3 | 2009-06-12 14:52:21 +0100 (Fri, 12 Jun 2009) | 3 lines
936 M /trunk/samtools/misc/novo2sam.pl
938 * updated novoalign converter by Colin Hercus et al.
939 * this version works with indels
941 ------------------------------------------------------------------------
942 r328 | lh3lh3 | 2009-06-12 14:50:53 +0100 (Fri, 12 Jun 2009) | 3 lines
944 M /trunk/samtools/INSTALL
945 M /trunk/samtools/Makefile
946 M /trunk/samtools/misc/Makefile
947 M /trunk/samtools/zlib/Makefile
950 * update INSTALL instruction
952 ------------------------------------------------------------------------
953 r327 | lh3lh3 | 2009-06-12 14:18:29 +0100 (Fri, 12 Jun 2009) | 4 lines
955 A /trunk/samtools/Makefile (from /trunk/samtools/Makefile.generic:325)
956 D /trunk/samtools/Makefile.am
957 D /trunk/samtools/Makefile.generic
958 D /trunk/samtools/Makefile.lite
959 D /trunk/samtools/autogen.sh
960 D /trunk/samtools/cleanup.sh
961 D /trunk/samtools/configure.ac
962 A /trunk/samtools/misc/Makefile (from /trunk/samtools/misc/Makefile.generic:305)
963 D /trunk/samtools/misc/Makefile.am
964 D /trunk/samtools/misc/Makefile.generic
965 M /trunk/samtools/razf.c
966 A /trunk/samtools/zlib
967 A /trunk/samtools/zlib/Makefile
968 A /trunk/samtools/zlib/adler32.c
969 A /trunk/samtools/zlib/compress.c
970 A /trunk/samtools/zlib/crc32.c
971 A /trunk/samtools/zlib/crc32.h
972 A /trunk/samtools/zlib/deflate.c
973 A /trunk/samtools/zlib/deflate.h
974 A /trunk/samtools/zlib/gzio.c
975 A /trunk/samtools/zlib/infback.c
976 A /trunk/samtools/zlib/inffast.c
977 A /trunk/samtools/zlib/inffast.h
978 A /trunk/samtools/zlib/inffixed.h
979 A /trunk/samtools/zlib/inflate.c
980 A /trunk/samtools/zlib/inflate.h
981 A /trunk/samtools/zlib/inftrees.c
982 A /trunk/samtools/zlib/inftrees.h
983 A /trunk/samtools/zlib/trees.c
984 A /trunk/samtools/zlib/trees.h
985 A /trunk/samtools/zlib/uncompr.c
986 A /trunk/samtools/zlib/zconf.h
987 A /trunk/samtools/zlib/zlib.h
988 A /trunk/samtools/zlib/zutil.c
989 A /trunk/samtools/zlib/zutil.h
990 D /trunk/samtools/zutil.h
992 * added zlib-1.2.3 as razip requires that
993 * prepare to changed back to the Makefile building system
994 * unfinished! (will be soon)
996 ------------------------------------------------------------------------
997 r326 | lh3lh3 | 2009-06-12 14:12:03 +0100 (Fri, 12 Jun 2009) | 2 lines
999 M /trunk/samtools/misc/samtools.pl
1003 ------------------------------------------------------------------------
1004 r325 | lh3lh3 | 2009-06-10 16:27:59 +0100 (Wed, 10 Jun 2009) | 3 lines
1006 M /trunk/samtools/bam_maqcns.c
1007 M /trunk/samtools/bamtk.c
1009 * samtools-0.1.4-4 (r325)
1010 * further avoid wrong consensus calls in repetitive regions.
1012 ------------------------------------------------------------------------
1013 r324 | lh3lh3 | 2009-06-10 15:56:17 +0100 (Wed, 10 Jun 2009) | 4 lines
1015 M /trunk/samtools/bam_maqcns.c
1016 M /trunk/samtools/bam_plcmd.c
1017 M /trunk/samtools/bamtk.c
1018 M /trunk/samtools/sam.c
1019 M /trunk/samtools/sam.h
1021 * samtools-0.1.4-3 (r324)
1022 * make maqcns generate the correct call in repetitive regions.
1023 * allow filtering on mapQ at the pileup command line
1025 ------------------------------------------------------------------------
1026 r323 | lh3lh3 | 2009-06-10 10:04:21 +0100 (Wed, 10 Jun 2009) | 3 lines
1028 M /trunk/samtools/misc/samtools.pl
1030 * samtools.pl-0.3.2 (r322)
1031 * indels and SNPs use different mapping quality threshold
1033 ------------------------------------------------------------------------
1034 r322 | lh3lh3 | 2009-06-10 10:03:22 +0100 (Wed, 10 Jun 2009) | 2 lines
1036 M /trunk/samtools/misc/export2sam.pl
1040 ------------------------------------------------------------------------
1041 r321 | lh3lh3 | 2009-06-09 09:21:48 +0100 (Tue, 09 Jun 2009) | 2 lines
1043 M /trunk/samtools/misc/samtools.pl
1045 just typo. no real change
1047 ------------------------------------------------------------------------
1048 r320 | lh3lh3 | 2009-06-08 14:32:51 +0100 (Mon, 08 Jun 2009) | 2 lines
1050 M /trunk/samtools/misc/samtools.pl
1052 a little bit code cleanup
1054 ------------------------------------------------------------------------
1055 r319 | lh3lh3 | 2009-06-08 14:22:33 +0100 (Mon, 08 Jun 2009) | 4 lines
1057 M /trunk/samtools/misc/samtools.pl
1060 * change default parameters
1061 * optionally print filtered variants
1063 ------------------------------------------------------------------------
1064 r318 | lh3lh3 | 2009-06-08 14:14:26 +0100 (Mon, 08 Jun 2009) | 3 lines
1066 M /trunk/samtools/misc/samtools.pl
1069 * combine snpFilter and indelFilter
1071 ------------------------------------------------------------------------
1072 r317 | lh3lh3 | 2009-06-08 11:31:42 +0100 (Mon, 08 Jun 2009) | 3 lines
1074 M /trunk/samtools/misc/samtools.pl
1077 * change a default parameter
1079 ------------------------------------------------------------------------
1080 r316 | lh3lh3 | 2009-06-08 11:11:06 +0100 (Mon, 08 Jun 2009) | 5 lines
1082 M /trunk/samtools/bam_maqcns.c
1083 M /trunk/samtools/bam_maqcns.h
1084 M /trunk/samtools/bam_plcmd.c
1085 M /trunk/samtools/bamtk.c
1086 M /trunk/samtools/sam.c
1088 * samtools-0.1.4-2 (r316)
1089 * pileup: cap mapping quality at 60 (by default)
1090 * pileup: always calculate RMS mapq
1091 * pileup: allow to output variant sites only
1093 ------------------------------------------------------------------------
1094 r312 | lh3lh3 | 2009-06-04 13:01:10 +0100 (Thu, 04 Jun 2009) | 3 lines
1096 M /trunk/samtools/misc/samtools.pl
1101 ------------------------------------------------------------------------
1102 r311 | lh3lh3 | 2009-06-03 09:40:40 +0100 (Wed, 03 Jun 2009) | 2 lines
1104 M /trunk/samtools/misc/samtools.pl
1106 * in snpFilter, suppress non-SNP sites
1108 ------------------------------------------------------------------------
1109 r310 | lh3lh3 | 2009-06-01 14:35:13 +0100 (Mon, 01 Jun 2009) | 3 lines
1111 M /trunk/samtools/misc/samtools.pl
1116 ------------------------------------------------------------------------
1117 r309 | lh3lh3 | 2009-06-01 14:04:39 +0100 (Mon, 01 Jun 2009) | 3 lines
1119 M /trunk/samtools/misc/samtools.pl
1124 ------------------------------------------------------------------------
1125 r306 | lh3lh3 | 2009-05-28 11:49:35 +0100 (Thu, 28 May 2009) | 3 lines
1127 M /trunk/samtools/bgzf.c
1129 * minor changes to bgzf: return NULL if fd == -1
1130 * suggested by {kdj,jm18}@sanger.ac.uk
1132 ------------------------------------------------------------------------
1133 r305 | lh3lh3 | 2009-05-28 11:16:08 +0100 (Thu, 28 May 2009) | 2 lines
1135 A /trunk/samtools/misc/interpolate_sam.pl
1137 Script for paired-end pileup, contributed by Stephen Montgomery.
1139 ------------------------------------------------------------------------
1140 r304 | lh3lh3 | 2009-05-28 11:08:49 +0100 (Thu, 28 May 2009) | 3 lines
1142 M /trunk/samtools/bamtk.c
1143 M /trunk/samtools/sam.c
1145 * samtools-0.1.4-1 (r304)
1146 * fixed a minor bug in printing headers
1148 ------------------------------------------------------------------------
1149 r297 | lh3lh3 | 2009-05-21 16:06:16 +0100 (Thu, 21 May 2009) | 2 lines
1151 M /trunk/samtools/ChangeLog
1152 M /trunk/samtools/NEWS
1153 M /trunk/samtools/bam_plcmd.c
1154 M /trunk/samtools/bamtk.c
1155 M /trunk/samtools/misc/maq2sam.c
1156 M /trunk/samtools/samtools.1
1158 Release samtools-0.1.4
1160 ------------------------------------------------------------------------
1161 r296 | lh3lh3 | 2009-05-21 12:53:14 +0100 (Thu, 21 May 2009) | 3 lines
1163 M /trunk/samtools/bam_maqcns.c
1164 M /trunk/samtools/bamtk.c
1166 * samtools-0.1.3-24 (r296)
1167 * another similar bug in the indel caller
1169 ------------------------------------------------------------------------
1170 r295 | lh3lh3 | 2009-05-21 12:50:28 +0100 (Thu, 21 May 2009) | 3 lines
1172 M /trunk/samtools/bam_maqcns.c
1173 M /trunk/samtools/bamtk.c
1175 * samtools-0.1.3-23 (r295)
1176 * fixed a critical bug in the indel caller
1178 ------------------------------------------------------------------------
1179 r294 | lh3lh3 | 2009-05-20 13:00:20 +0100 (Wed, 20 May 2009) | 2 lines
1181 M /trunk/samtools/bam_stat.c
1183 added a missing header file
1185 ------------------------------------------------------------------------
1186 r293 | lh3lh3 | 2009-05-19 23:44:25 +0100 (Tue, 19 May 2009) | 3 lines
1188 M /trunk/samtools/bam_tview.c
1189 M /trunk/samtools/bamtk.c
1191 * samtools-0.1.3-22 (r293)
1192 * open tview in the dot-view mode by default
1194 ------------------------------------------------------------------------
1195 r292 | lh3lh3 | 2009-05-18 21:01:23 +0100 (Mon, 18 May 2009) | 6 lines
1197 M /trunk/samtools/samtools.1
1199 Added a note to the manual. Currently SAMtools used unaligned words in
1200 several places. Although this does not cause bus errors to me, it may
1201 affect portability. Please see the "Bus error" wiki page for more
1202 information. Also thank James Bonfields for pointing this out.
1205 ------------------------------------------------------------------------
1206 r286 | lh3lh3 | 2009-05-14 15:23:13 +0100 (Thu, 14 May 2009) | 3 lines
1208 M /trunk/samtools/bam.h
1209 M /trunk/samtools/bam_aux.c
1210 M /trunk/samtools/bamtk.c
1212 * samtools-0.1.3-21 (286)
1213 * declare bam_aux_get_core() in bam.h
1215 ------------------------------------------------------------------------
1216 r276 | lh3lh3 | 2009-05-13 10:07:55 +0100 (Wed, 13 May 2009) | 5 lines
1218 M /trunk/samtools/bam.h
1219 M /trunk/samtools/bam_index.c
1220 M /trunk/samtools/bamtk.c
1222 * samtools-0.1.3-20 (r276)
1223 * remove bam1_t::hash again. We need to modify the Perl API anyway to
1224 make it work with the latest SVN.
1225 * As is suggested by Tim, scan "{base}.bai" and "{base}.bam.bai" for index
1227 ------------------------------------------------------------------------
1228 r275 | lh3lh3 | 2009-05-12 21:14:10 +0100 (Tue, 12 May 2009) | 4 lines
1230 M /trunk/samtools/ChangeLog
1231 M /trunk/samtools/bam.h
1232 M /trunk/samtools/bamtk.c
1234 * samtools-0.1.3-19 (r275)
1235 * a minor change to the bam1_t struct: added back "void *hash" for the
1236 backward compatibility with Bio::DB::Sam
1238 ------------------------------------------------------------------------
1239 r273 | lh3lh3 | 2009-05-12 14:28:39 +0100 (Tue, 12 May 2009) | 3 lines
1241 M /trunk/samtools/bam_rmdupse.c
1242 M /trunk/samtools/bamtk.c
1244 * samtools-0.1.3-18 (r273)
1245 * rmdupse: do not remove unmapped reads
1247 ------------------------------------------------------------------------
1248 r272 | lh3lh3 | 2009-05-12 14:20:00 +0100 (Tue, 12 May 2009) | 2 lines
1250 M /trunk/samtools/bam_rmdupse.c
1252 change a parameter. It does nothing
1254 ------------------------------------------------------------------------
1255 r271 | lh3lh3 | 2009-05-12 14:17:58 +0100 (Tue, 12 May 2009) | 3 lines
1257 M /trunk/samtools/Makefile.am
1258 M /trunk/samtools/Makefile.generic
1259 M /trunk/samtools/Makefile.lite
1260 A /trunk/samtools/bam_rmdupse.c
1261 M /trunk/samtools/bamtk.c
1262 M /trunk/samtools/configure.ac
1264 * samtools-0.1.3-17 (r271)
1265 * added 'rmdupse' command
1267 ------------------------------------------------------------------------
1268 r267 | lh3lh3 | 2009-05-05 22:31:41 +0100 (Tue, 05 May 2009) | 3 lines
1270 M /trunk/samtools/bamtk.c
1271 M /trunk/samtools/sam_view.c
1273 * samtools-0.1.3-16 (r267)
1274 * in sam_view.c, changed g_flag_on based on the suggestion by Angie Hinrichs
1276 ------------------------------------------------------------------------
1277 r266 | lh3lh3 | 2009-05-05 22:23:27 +0100 (Tue, 05 May 2009) | 3 lines
1279 M /trunk/samtools/bam_import.c
1280 M /trunk/samtools/bamtk.c
1282 * samtools-0.1.3-15 (r266)
1283 * report an error if a non-* reference is present while @SQ is absent
1285 ------------------------------------------------------------------------
1286 r265 | lh3lh3 | 2009-05-05 22:09:00 +0100 (Tue, 05 May 2009) | 3 lines
1288 M /trunk/samtools/bam.h
1289 M /trunk/samtools/bam_import.c
1290 M /trunk/samtools/bamtk.c
1291 M /trunk/samtools/sam.c
1292 M /trunk/samtools/sam_view.c
1294 * samtools-0.1.3-14 (r262)
1295 * make samopen() recognize @SQ header lines
1297 ------------------------------------------------------------------------
1298 r261 | lh3lh3 | 2009-05-05 15:10:30 +0100 (Tue, 05 May 2009) | 3 lines
1300 M /trunk/samtools/bam_plcmd.c
1301 M /trunk/samtools/bamtk.c
1302 M /trunk/samtools/bgzf.c
1303 M /trunk/samtools/sam.c
1304 M /trunk/samtools/sam_view.c
1306 * samtools-0.1.3-13 (r260)
1307 * report error for file I/O error
1309 ------------------------------------------------------------------------
1310 r260 | lh3lh3 | 2009-05-05 15:01:16 +0100 (Tue, 05 May 2009) | 2 lines
1312 M /trunk/samtools/Makefile.am
1316 ------------------------------------------------------------------------
1317 r259 | lh3lh3 | 2009-05-05 14:52:25 +0100 (Tue, 05 May 2009) | 3 lines
1319 M /trunk/samtools/bam.h
1320 M /trunk/samtools/bam_pileup.c
1321 M /trunk/samtools/bam_plcmd.c
1322 M /trunk/samtools/bamtk.c
1323 M /trunk/samtools/sam.c
1324 M /trunk/samtools/sam.h
1326 * samtools-0.1.3-12 (r259)
1327 * use the new I/O interface in pileup
1329 ------------------------------------------------------------------------
1330 r258 | lh3lh3 | 2009-05-05 14:33:22 +0100 (Tue, 05 May 2009) | 3 lines
1332 M /trunk/samtools/Makefile.generic
1333 M /trunk/samtools/Makefile.lite
1334 M /trunk/samtools/bam.c
1335 M /trunk/samtools/bam.h
1336 M /trunk/samtools/bam_import.c
1337 M /trunk/samtools/bamtk.c
1338 A /trunk/samtools/sam.c
1339 A /trunk/samtools/sam.h
1340 A /trunk/samtools/sam_view.c
1342 * samtools-0.1.3-11 (r258)
1343 * unify the interface to BAM and SAM I/O
1345 ------------------------------------------------------------------------
1346 r257 | lh3lh3 | 2009-05-05 09:53:35 +0100 (Tue, 05 May 2009) | 3 lines
1348 M /trunk/samtools/Makefile.lite
1349 M /trunk/samtools/bam_plcmd.c
1350 M /trunk/samtools/bamtk.c
1352 * samtools-0.1.3-10 (r257)
1353 * allow hex with "pileup -m"
1355 ------------------------------------------------------------------------
1356 r256 | lh3lh3 | 2009-05-04 19:16:50 +0100 (Mon, 04 May 2009) | 4 lines
1358 M /trunk/samtools/bam_lpileup.c
1359 M /trunk/samtools/bamtk.c
1361 * samtools-0.1.3-9 (r256)
1362 * fixed a bug in bam_lpileup.c
1363 * I do not know if this also fixes the bug causing assertion failure in the tview
1365 ------------------------------------------------------------------------
1366 r251 | lh3lh3 | 2009-04-28 13:53:23 +0100 (Tue, 28 Apr 2009) | 3 lines
1368 M /trunk/samtools/bam_pileup.c
1369 M /trunk/samtools/bamtk.c
1371 * samtools-0.1.3-8 (r251)
1372 * fixed a bug when there are reads without coordinates
1374 ------------------------------------------------------------------------
1375 r250 | lh3lh3 | 2009-04-28 13:43:33 +0100 (Tue, 28 Apr 2009) | 2 lines
1377 A /trunk/samtools/AUTHORS
1378 A /trunk/samtools/README
1379 M /trunk/samtools/cleanup.sh
1383 ------------------------------------------------------------------------
1384 r249 | lh3lh3 | 2009-04-28 13:37:16 +0100 (Tue, 28 Apr 2009) | 2 lines
1386 M /trunk/samtools/Makefile.generic
1387 M /trunk/samtools/Makefile.lite
1388 M /trunk/samtools/configure.ac
1389 M /trunk/samtools/misc/Makefile.generic
1391 improve large file support in compilation
1393 ------------------------------------------------------------------------
1394 r248 | lh3lh3 | 2009-04-28 13:33:24 +0100 (Tue, 28 Apr 2009) | 2 lines
1396 M /trunk/samtools/INSTALL
1400 ------------------------------------------------------------------------
1401 r247 | lh3lh3 | 2009-04-28 13:28:50 +0100 (Tue, 28 Apr 2009) | 2 lines
1403 M /trunk/samtools/Makefile.am
1404 M /trunk/samtools/autogen.sh
1405 M /trunk/samtools/cleanup.sh
1406 M /trunk/samtools/configure.ac
1407 A /trunk/samtools/misc/Makefile.am
1409 fixed various issues about the GNU building scripts
1411 ------------------------------------------------------------------------
1412 r246 | lh3lh3 | 2009-04-28 13:10:23 +0100 (Tue, 28 Apr 2009) | 4 lines
1414 M /trunk/samtools/ChangeLog
1415 D /trunk/samtools/Makefile
1416 A /trunk/samtools/Makefile.am
1417 A /trunk/samtools/Makefile.generic
1418 A /trunk/samtools/autogen.sh
1419 M /trunk/samtools/bam.h
1420 M /trunk/samtools/bam_aux.c
1421 M /trunk/samtools/bam_tview.c
1422 M /trunk/samtools/bamtk.c
1423 A /trunk/samtools/cleanup.sh
1424 A /trunk/samtools/configure.ac
1425 D /trunk/samtools/misc/Makefile
1426 A /trunk/samtools/misc/Makefile.generic (from /trunk/samtools/misc/Makefile:245)
1428 * samtools-0.1.3-7 (r246)
1429 * incorporated revisions from Nils Homer
1430 * enhanced support of displaying color-space reads
1432 ------------------------------------------------------------------------
1433 r244 | lh3lh3 | 2009-04-25 11:49:40 +0100 (Sat, 25 Apr 2009) | 3 lines
1435 M /trunk/samtools/bam_md.c
1436 M /trunk/samtools/bamtk.c
1438 * samtools-0.1.3-6 (r244)
1439 * fixed segfault for unmapped reads
1441 ------------------------------------------------------------------------
1442 r243 | lh3lh3 | 2009-04-24 21:27:26 +0100 (Fri, 24 Apr 2009) | 5 lines
1444 M /trunk/samtools/bam.h
1445 M /trunk/samtools/bam_maqcns.c
1446 M /trunk/samtools/bam_md.c
1447 M /trunk/samtools/bamtk.c
1449 * samtools-0.1.3-5 (r243)
1450 * fixed a long existing bug which may cause memory leak
1452 * consensus calling now works with "=", but indel calling not
1454 ------------------------------------------------------------------------
1455 r242 | lh3lh3 | 2009-04-24 20:44:46 +0100 (Fri, 24 Apr 2009) | 3 lines
1457 M /trunk/samtools/bam_md.c
1458 M /trunk/samtools/bamtk.c
1460 * samtools-0.1.3-4 (r242)
1461 * fixed a memory leak
1463 ------------------------------------------------------------------------
1464 r240 | lh3lh3 | 2009-04-24 16:40:18 +0100 (Fri, 24 Apr 2009) | 5 lines
1466 M /trunk/samtools/Makefile
1467 M /trunk/samtools/Makefile.lite
1468 M /trunk/samtools/bam.h
1469 M /trunk/samtools/bam_aux.c
1470 A /trunk/samtools/bam_md.c
1471 M /trunk/samtools/bam_plcmd.c
1472 M /trunk/samtools/bamtk.c
1474 * samtools-0.1.3-3 (r240)
1476 * generate "=" bases
1477 * the plain pileup now support "=" bases, but consensus calling and glfgen may fail
1479 ------------------------------------------------------------------------
1480 r239 | lh3lh3 | 2009-04-24 12:08:20 +0100 (Fri, 24 Apr 2009) | 5 lines
1482 M /trunk/samtools/bam.h
1483 M /trunk/samtools/bam_aux.c
1484 M /trunk/samtools/bamtk.c
1486 * samtools-0.1.3-2 (r239)
1487 * fixed bugs in bam_aux.c (these functions nevered used by samtools)
1488 * removed bam_aux_init()/bam_aux_destroy()
1489 * added tagview for testing bam_aux
1491 ------------------------------------------------------------------------
1492 r235 | lh3lh3 | 2009-04-21 23:17:39 +0100 (Tue, 21 Apr 2009) | 3 lines
1494 M /trunk/samtools/bam_pileup.c
1495 M /trunk/samtools/bamtk.c
1498 * fixed a bug in pileup: the first read in a chromosome may not be printed
1500 ------------------------------------------------------------------------
1501 r232 | lh3lh3 | 2009-04-16 15:25:43 +0100 (Thu, 16 Apr 2009) | 2 lines
1503 M /trunk/samtools/Makefile.lite
1505 a missing file in Makefile.lite
1507 ------------------------------------------------------------------------
1508 r227 | lh3lh3 | 2009-04-15 22:02:53 +0100 (Wed, 15 Apr 2009) | 2 lines
1510 M /trunk/samtools/NEWS
1511 M /trunk/samtools/bamtk.c
1513 Release samtools-0.1.3
1515 ------------------------------------------------------------------------
1516 r223 | lh3lh3 | 2009-04-15 14:31:32 +0100 (Wed, 15 Apr 2009) | 3 lines
1518 M /trunk/samtools/bam_plcmd.c
1519 M /trunk/samtools/bamtk.c
1522 * make samtools more robust to weird input such as empty file
1524 ------------------------------------------------------------------------
1525 r222 | lh3lh3 | 2009-04-15 14:05:33 +0100 (Wed, 15 Apr 2009) | 2 lines
1527 M /trunk/samtools/ChangeLog
1528 M /trunk/samtools/NEWS
1529 M /trunk/samtools/samtools.1
1531 prepare for release 0.1.3
1533 ------------------------------------------------------------------------
1534 r221 | lh3lh3 | 2009-04-15 13:32:14 +0100 (Wed, 15 Apr 2009) | 2 lines
1536 A /trunk/samtools/misc/blast2sam.pl
1538 convert NCBI-BLASTN to SAM
1540 ------------------------------------------------------------------------
1541 r220 | lh3lh3 | 2009-04-15 13:18:19 +0100 (Wed, 15 Apr 2009) | 3 lines
1543 M /trunk/samtools/bam_lpileup.c
1544 M /trunk/samtools/bamtk.c
1547 * fixed a small memory leak in tview
1549 ------------------------------------------------------------------------
1550 r219 | lh3lh3 | 2009-04-15 13:00:08 +0100 (Wed, 15 Apr 2009) | 3 lines
1552 M /trunk/samtools/bam_rmdup.c
1553 M /trunk/samtools/bamtk.c
1556 * fixed a bug in rmdup when there are unmapped reads
1558 ------------------------------------------------------------------------
1559 r218 | lh3lh3 | 2009-04-14 22:28:58 +0100 (Tue, 14 Apr 2009) | 2 lines
1561 M /trunk/samtools/ChangeLog
1562 M /trunk/samtools/NEWS
1564 proposed NEWS for the new release (have not yet)
1566 ------------------------------------------------------------------------
1567 r216 | lh3lh3 | 2009-04-14 22:10:46 +0100 (Tue, 14 Apr 2009) | 4 lines
1569 M /trunk/samtools/misc/samtools.pl
1572 * improve indelFilter to avoid filtering true indels. The new filter relies
1573 on the new pileup indel line implemented in samtools-0.1.2-25
1575 ------------------------------------------------------------------------
1576 r215 | lh3lh3 | 2009-04-14 22:04:19 +0100 (Tue, 14 Apr 2009) | 4 lines
1578 M /trunk/samtools/bam_maqcns.c
1579 M /trunk/samtools/bam_plcmd.c
1580 M /trunk/samtools/bamtk.c
1581 M /trunk/samtools/samtools.1
1584 * change the pileup indel line to shows the number of alignments actually
1587 ------------------------------------------------------------------------
1588 r211 | lh3lh3 | 2009-04-13 12:07:13 +0100 (Mon, 13 Apr 2009) | 2 lines
1590 M /trunk/samtools/ChangeLog
1592 update ChangeLog from "svn log"
1594 ------------------------------------------------------------------------
1595 r210 | lh3lh3 | 2009-04-12 20:57:05 +0100 (Sun, 12 Apr 2009) | 4 lines
1597 M /trunk/samtools/bam.c
1598 M /trunk/samtools/bam_import.c
1599 M /trunk/samtools/bam_sort.c
1600 M /trunk/samtools/bamtk.c
1601 M /trunk/samtools/kseq.h
1604 * in merge, gives a warning rather than error if the target sequence length is different
1605 * allow empty header
1607 ------------------------------------------------------------------------
1608 r209 | lh3lh3 | 2009-04-12 20:32:44 +0100 (Sun, 12 Apr 2009) | 3 lines
1610 M /trunk/samtools/bam.c
1611 M /trunk/samtools/bam_import.c
1612 M /trunk/samtools/bamtk.c
1615 * recognize '*' at the QUAL field
1617 ------------------------------------------------------------------------
1618 r208 | lh3lh3 | 2009-04-12 20:08:02 +0100 (Sun, 12 Apr 2009) | 3 lines
1620 M /trunk/samtools/bam_import.c
1621 M /trunk/samtools/bamtk.c
1622 M /trunk/samtools/kseq.h
1625 * the field separater is TAB only, now
1627 ------------------------------------------------------------------------
1628 r207 | lh3lh3 | 2009-04-08 15:18:03 +0100 (Wed, 08 Apr 2009) | 2 lines
1630 M /trunk/samtools/examples/ex1.sam.gz
1632 * fixed the problem in the example alignment due to the bug in fixmate
1634 ------------------------------------------------------------------------
1635 r206 | lh3lh3 | 2009-04-08 15:15:05 +0100 (Wed, 08 Apr 2009) | 3 lines
1637 M /trunk/samtools/bam_mate.c
1638 M /trunk/samtools/bamtk.c
1639 M /trunk/samtools/misc/soap2sam.pl
1642 * fixed a nasty bug in `fixmate'
1644 ------------------------------------------------------------------------
1645 r205 | lh3lh3 | 2009-04-08 10:57:08 +0100 (Wed, 08 Apr 2009) | 2 lines
1647 M /trunk/samtools/misc/bowtie2sam.pl
1648 M /trunk/samtools/misc/soap2sam.pl
1649 M /trunk/samtools/misc/wgsim_eval.pl
1651 make the script robust to the bugs in SOAP-2.1.7
1653 ------------------------------------------------------------------------
1654 r200 | lh3lh3 | 2009-04-02 15:14:56 +0100 (Thu, 02 Apr 2009) | 3 lines
1656 M /trunk/samtools/bam_stat.c
1657 M /trunk/samtools/bamtk.c
1660 * check if file is truncated in flagstat
1662 ------------------------------------------------------------------------
1663 r199 | lh3lh3 | 2009-04-02 15:09:10 +0100 (Thu, 02 Apr 2009) | 3 lines
1665 M /trunk/samtools/bamtk.c
1668 * print the header if requested
1670 ------------------------------------------------------------------------
1671 r193 | lh3lh3 | 2009-03-27 15:09:50 +0000 (Fri, 27 Mar 2009) | 3 lines
1673 M /trunk/samtools/bam_plcmd.c
1674 M /trunk/samtools/bamtk.c
1677 * fixed a minor bug reported by Nils Homer
1679 ------------------------------------------------------------------------
1680 r185 | lh3lh3 | 2009-03-24 11:50:32 +0000 (Tue, 24 Mar 2009) | 2 lines
1682 A /trunk/samtools/Makefile (from /trunk/samtools/Makefile.std:184)
1683 D /trunk/samtools/Makefile.std
1684 A /trunk/samtools/misc/Makefile (from /trunk/samtools/misc/Makefile.std:184)
1685 D /trunk/samtools/misc/Makefile.std
1687 rename Makefile.std as Makefile. GNU building systerm is not ready and may take some time...
1689 ------------------------------------------------------------------------
1690 r184 | lh3lh3 | 2009-03-24 10:36:38 +0000 (Tue, 24 Mar 2009) | 4 lines
1692 D /trunk/samtools/Makefile
1693 A /trunk/samtools/Makefile.std (from /trunk/samtools/Makefile:183)
1694 M /trunk/samtools/bam_sort.c
1695 M /trunk/samtools/bam_tview.c
1696 M /trunk/samtools/bamtk.c
1697 D /trunk/samtools/misc/Makefile
1698 A /trunk/samtools/misc/Makefile.std (from /trunk/samtools/misc/Makefile:182)
1699 M /trunk/samtools/samtools.1
1702 * incorporating Nils' changes
1703 * rename Makefile to Makefile.std and prepare to add the GNU building systerms (also by Nils)
1705 ------------------------------------------------------------------------
1706 r183 | lh3lh3 | 2009-03-24 10:30:23 +0000 (Tue, 24 Mar 2009) | 4 lines
1708 M /trunk/samtools/Makefile
1709 M /trunk/samtools/bam_import.c
1710 M /trunk/samtools/bam_maqcns.c
1711 M /trunk/samtools/bam_maqcns.h
1712 M /trunk/samtools/bam_plcmd.c
1713 M /trunk/samtools/bamtk.c
1714 M /trunk/samtools/kseq.h
1715 A /trunk/samtools/kstring.c
1716 A /trunk/samtools/kstring.h
1719 * made pileup take a list of proposed indels. An insertion is N at the moment.
1720 * added my kstring library for a bit complex parsing of the position list.
1722 ------------------------------------------------------------------------
1723 r169 | lh3lh3 | 2009-03-12 13:40:14 +0000 (Thu, 12 Mar 2009) | 3 lines
1725 M /trunk/samtools/misc/soap2sam.pl
1728 * more robust to truncated soap output
1730 ------------------------------------------------------------------------
1731 r168 | lh3lh3 | 2009-03-11 10:49:00 +0000 (Wed, 11 Mar 2009) | 2 lines
1733 M /trunk/samtools/Makefile.lite
1735 added bam_stat.o to Makefile.lite
1737 ------------------------------------------------------------------------
1738 r167 | lh3lh3 | 2009-03-10 22:11:31 +0000 (Tue, 10 Mar 2009) | 3 lines
1740 M /trunk/samtools/bam_maqcns.c
1741 M /trunk/samtools/bamtk.c
1744 * generate RMS of mapQ instead of max mapQ
1746 ------------------------------------------------------------------------
1747 r166 | lh3lh3 | 2009-03-10 22:06:45 +0000 (Tue, 10 Mar 2009) | 3 lines
1749 M /trunk/samtools/bam_plcmd.c
1750 M /trunk/samtools/bamtk.c
1751 M /trunk/samtools/glf.c
1752 M /trunk/samtools/glf.h
1753 M /trunk/samtools/misc/Makefile
1758 ------------------------------------------------------------------------
1759 r159 | lh3lh3 | 2009-03-03 11:26:08 +0000 (Tue, 03 Mar 2009) | 3 lines
1761 M /trunk/samtools/bam_plcmd.c
1762 M /trunk/samtools/bamtk.c
1765 * fixed a minor bug in displaying pileup
1767 ------------------------------------------------------------------------
1768 r158 | lh3lh3 | 2009-03-03 11:24:16 +0000 (Tue, 03 Mar 2009) | 3 lines
1770 M /trunk/samtools/ChangeLog
1771 M /trunk/samtools/bamtk.c
1774 * optionally print SAM header
1776 ------------------------------------------------------------------------
1777 r153 | lh3lh3 | 2009-03-02 10:45:28 +0000 (Mon, 02 Mar 2009) | 3 lines
1779 M /trunk/samtools/bamtk.c
1780 M /trunk/samtools/glf.c
1783 * use "GLF\3" as the magic for GLFv3 files
1785 ------------------------------------------------------------------------
1786 r152 | lh3lh3 | 2009-03-02 10:39:09 +0000 (Mon, 02 Mar 2009) | 5 lines
1788 M /trunk/samtools/Makefile
1789 M /trunk/samtools/bam_import.c
1790 M /trunk/samtools/bam_index.c
1791 M /trunk/samtools/bam_plcmd.c
1792 M /trunk/samtools/bamtk.c
1793 M /trunk/samtools/glf.c
1794 M /trunk/samtools/glf.h
1797 * fixed a bug in import: core.bin is undefined for unmapped reads
1798 * this bug can be alleviated (not completely solved) in bam_index.c
1799 * update to GLFv3: pos is changed to offset for better compression
1801 ------------------------------------------------------------------------
1802 r151 | lh3lh3 | 2009-03-01 15:18:43 +0000 (Sun, 01 Mar 2009) | 3 lines
1804 M /trunk/samtools/misc/wgsim.c
1807 * fixed a bug in simulating indels
1809 ------------------------------------------------------------------------
1810 r145 | lh3lh3 | 2009-02-26 19:43:57 +0000 (Thu, 26 Feb 2009) | 4 lines
1812 M /trunk/samtools/misc/wgsim.c
1815 * allow to print mismatch information as fastq comment. MAQ does
1816 not like long read names.
1818 ------------------------------------------------------------------------
1819 r141 | lh3lh3 | 2009-02-26 14:53:03 +0000 (Thu, 26 Feb 2009) | 6 lines
1821 M /trunk/samtools/ChangeLog
1822 M /trunk/samtools/misc/wgsim.c
1823 M /trunk/samtools/misc/wgsim_eval.pl
1826 * fixed a bug about color read coordinates
1827 * fixed a bug in read names
1828 * wgsim_eval.pl-0.1.3
1829 * make the script work with color reads
1831 ------------------------------------------------------------------------
1832 r140 | lh3lh3 | 2009-02-26 14:02:57 +0000 (Thu, 26 Feb 2009) | 2 lines
1834 M /trunk/samtools/misc/Makefile
1835 M /trunk/samtools/misc/wgsim.c
1837 * wgsim: added a note
1839 ------------------------------------------------------------------------
1840 r139 | lh3lh3 | 2009-02-26 11:39:08 +0000 (Thu, 26 Feb 2009) | 7 lines
1842 M /trunk/samtools/misc/wgsim.c
1843 M /trunk/samtools/misc/wgsim_eval.pl
1846 * considerable code clean up
1847 * print number of substitutions/indels/errors on each read
1848 * potentially support SOLiD simulation, though not tested at the moment
1849 * wgsim_eval.pl-0.1.2
1850 * change in accordant with wgsim
1852 ------------------------------------------------------------------------
1853 r129 | lh3lh3 | 2009-02-18 22:23:27 +0000 (Wed, 18 Feb 2009) | 3 lines
1855 M /trunk/samtools/bam_index.c
1856 M /trunk/samtools/bamtk.c
1859 * fixed a bug in bam_fetch, caused by completely contained adjacent chunks
1861 ------------------------------------------------------------------------
1862 r128 | bhandsaker | 2009-02-18 19:06:57 +0000 (Wed, 18 Feb 2009) | 2 lines
1864 M /trunk/samtools/bamtk.c
1866 Fix annoying segv when invalid region specified.
1868 ------------------------------------------------------------------------
1869 r127 | lh3lh3 | 2009-02-17 10:49:55 +0000 (Tue, 17 Feb 2009) | 2 lines
1871 D /trunk/samtools/misc/indel_filter.pl
1872 A /trunk/samtools/misc/samtools.pl
1874 * move indel_filter.pl to samtools.pl
1876 ------------------------------------------------------------------------
1877 r126 | lh3lh3 | 2009-02-14 21:22:30 +0000 (Sat, 14 Feb 2009) | 3 lines
1879 M /trunk/samtools/bam_mate.c
1880 M /trunk/samtools/bamtk.c
1883 * fixed a bug in fixmate: SE reads are flagged as BAM_FMUNMAP
1885 ------------------------------------------------------------------------
1886 r125 | lh3lh3 | 2009-02-13 09:54:45 +0000 (Fri, 13 Feb 2009) | 3 lines
1888 M /trunk/samtools/bam_stat.c
1889 M /trunk/samtools/bamtk.c
1892 * fixed a minor bug in flagstat
1894 ------------------------------------------------------------------------
1895 r124 | lh3lh3 | 2009-02-12 11:15:32 +0000 (Thu, 12 Feb 2009) | 3 lines
1897 M /trunk/samtools/bam_maqcns.c
1898 M /trunk/samtools/bamtk.c
1899 M /trunk/samtools/misc/indel_filter.pl
1902 * improve indel caller by setting maximum window size
1904 ------------------------------------------------------------------------
1905 r123 | lh3lh3 | 2009-02-12 10:30:29 +0000 (Thu, 12 Feb 2009) | 2 lines
1907 M /trunk/samtools/bam_plcmd.c
1908 M /trunk/samtools/bamtk.c
1910 * output max mapping quality in indel line
1912 ------------------------------------------------------------------------
1913 r122 | lh3lh3 | 2009-02-11 10:59:10 +0000 (Wed, 11 Feb 2009) | 2 lines
1915 M /trunk/samtools/misc/maq2sam.c
1917 fixed a bug in generating tag AM
1919 ------------------------------------------------------------------------
1920 r121 | lh3lh3 | 2009-02-03 10:43:11 +0000 (Tue, 03 Feb 2009) | 2 lines
1922 M /trunk/samtools/bam_index.c
1923 M /trunk/samtools/bamtk.c
1925 fixed a potential memory problem in indexing
1927 ------------------------------------------------------------------------
1928 r120 | bhandsaker | 2009-02-02 15:52:52 +0000 (Mon, 02 Feb 2009) | 2 lines
1930 M /trunk/samtools/Makefile
1932 Pass LIBS to recursive targets to facilitate building at Broad.
1934 ------------------------------------------------------------------------
1935 r119 | lh3lh3 | 2009-02-02 10:12:15 +0000 (Mon, 02 Feb 2009) | 4 lines
1937 M /trunk/samtools/ChangeLog
1938 M /trunk/samtools/bam_plcmd.c
1939 M /trunk/samtools/bam_stat.c
1940 M /trunk/samtools/bamtk.c
1943 * fixed a bug in generating GLFv2 for indels
1944 * improve flagstat report a little bit
1946 ------------------------------------------------------------------------
1947 r118 | lh3lh3 | 2009-01-29 12:33:23 +0000 (Thu, 29 Jan 2009) | 3 lines
1949 M /trunk/samtools/Makefile
1950 A /trunk/samtools/bam_stat.c
1951 M /trunk/samtools/bamtk.c
1954 * added flagstat command
1956 ------------------------------------------------------------------------
1957 r116 | lh3lh3 | 2009-01-28 13:31:12 +0000 (Wed, 28 Jan 2009) | 2 lines
1959 M /trunk/samtools/ChangeLog
1960 M /trunk/samtools/NEWS
1961 M /trunk/samtools/bamtk.c
1962 M /trunk/samtools/samtools.1
1964 Release SAMtools-0.1.2
1966 ------------------------------------------------------------------------
1967 r115 | lh3lh3 | 2009-01-28 12:54:08 +0000 (Wed, 28 Jan 2009) | 2 lines
1969 A /trunk/samtools/misc/indel_filter.pl
1971 Script for filtering indel results
1973 ------------------------------------------------------------------------
1974 r114 | lh3lh3 | 2009-01-25 11:45:37 +0000 (Sun, 25 Jan 2009) | 2 lines
1976 A /trunk/samtools/misc/zoom2sam.pl
1980 ------------------------------------------------------------------------
1981 r113 | lh3lh3 | 2009-01-24 14:25:07 +0000 (Sat, 24 Jan 2009) | 2 lines
1983 A /trunk/samtools/misc/novo2sam.pl
1985 add a script to convert novo alignment to SAM
1987 ------------------------------------------------------------------------
1988 r112 | lh3lh3 | 2009-01-23 20:57:39 +0000 (Fri, 23 Jan 2009) | 2 lines
1990 M /trunk/samtools/ChangeLog
1991 M /trunk/samtools/ChangeLog.old
1992 M /trunk/samtools/samtools.1
1994 update documentation and ChangeLog
1996 ------------------------------------------------------------------------
1997 r111 | lh3lh3 | 2009-01-23 19:22:59 +0000 (Fri, 23 Jan 2009) | 3 lines
1999 M /trunk/samtools/bam_sort.c
2000 M /trunk/samtools/bamtk.c
2003 * fixed a bug in "merge" command line
2005 ------------------------------------------------------------------------
2006 r110 | lh3lh3 | 2009-01-22 15:36:48 +0000 (Thu, 22 Jan 2009) | 3 lines
2008 M /trunk/samtools/misc/Makefile
2009 A /trunk/samtools/misc/bowtie2sam.pl (from /branches/dev/samtools/misc/bowtie2sam.pl:108)
2010 M /trunk/samtools/misc/export2sam.pl
2011 A /trunk/samtools/misc/soap2sam.pl (from /branches/dev/samtools/misc/soap2sam.pl:108)
2012 A /trunk/samtools/misc/wgsim.c (from /branches/dev/samtools/misc/wgsim.c:108)
2013 A /trunk/samtools/misc/wgsim_eval.pl (from /branches/dev/samtools/misc/wgsim_eval.pl:108)
2015 * merge from branches/dev/
2016 * all future development will happen here
2018 ------------------------------------------------------------------------
2019 r109 | lh3lh3 | 2009-01-22 15:14:27 +0000 (Thu, 22 Jan 2009) | 3 lines
2021 M /trunk/samtools/COPYING
2022 M /trunk/samtools/ChangeLog
2023 A /trunk/samtools/INSTALL (from /branches/dev/samtools/INSTALL:108)
2024 M /trunk/samtools/Makefile
2025 A /trunk/samtools/Makefile.lite (from /branches/dev/samtools/Makefile.lite:108)
2026 M /trunk/samtools/bam.c
2027 M /trunk/samtools/bam.h
2028 M /trunk/samtools/bam_import.c
2029 M /trunk/samtools/bam_index.c
2030 M /trunk/samtools/bam_lpileup.c
2031 M /trunk/samtools/bam_maqcns.c
2032 M /trunk/samtools/bam_maqcns.h
2033 A /trunk/samtools/bam_mate.c (from /branches/dev/samtools/bam_mate.c:108)
2034 M /trunk/samtools/bam_pileup.c
2035 M /trunk/samtools/bam_plcmd.c
2036 A /trunk/samtools/bam_rmdup.c (from /branches/dev/samtools/bam_rmdup.c:108)
2037 M /trunk/samtools/bam_sort.c
2038 M /trunk/samtools/bamtk.c
2039 M /trunk/samtools/bgzf.h
2040 M /trunk/samtools/examples/00README.txt
2041 A /trunk/samtools/examples/Makefile (from /branches/dev/samtools/examples/Makefile:108)
2042 D /trunk/samtools/examples/ex1.fa.fai
2043 M /trunk/samtools/examples/ex1.sam.gz
2044 M /trunk/samtools/faidx.c
2045 A /trunk/samtools/glf.c (from /branches/dev/samtools/glf.c:108)
2046 M /trunk/samtools/glf.h
2047 M /trunk/samtools/misc/Makefile
2048 M /trunk/samtools/misc/maq2sam.c
2049 M /trunk/samtools/razf.c
2050 M /trunk/samtools/source.dot
2052 * Merge from branches/dev/
2053 * all future development will happen here at trunk/
2055 ------------------------------------------------------------------------
2056 r79 | bhandsaker | 2009-01-07 21:42:15 +0000 (Wed, 07 Jan 2009) | 2 lines
2058 M /trunk/samtools/bam_maqcns.c
2059 M /trunk/samtools/bam_tview.c
2061 Fix problem with compiling without curses.
2063 ------------------------------------------------------------------------
2064 r63 | lh3lh3 | 2008-12-22 15:58:02 +0000 (Mon, 22 Dec 2008) | 2 lines
2066 A /trunk/samtools (from /branches/dev/samtools:62)
2070 ------------------------------------------------------------------------
2071 r62 | lh3lh3 | 2008-12-22 15:55:13 +0000 (Mon, 22 Dec 2008) | 2 lines
2073 A /branches/dev/samtools/NEWS
2074 M /branches/dev/samtools/bamtk.c
2075 M /branches/dev/samtools/samtools.1
2077 Release samtools-0.1.1
2079 ------------------------------------------------------------------------
2080 r61 | lh3lh3 | 2008-12-22 15:46:08 +0000 (Mon, 22 Dec 2008) | 10 lines
2082 M /branches/dev/samtools/bam_aux.c
2083 M /branches/dev/samtools/bam_index.c
2084 M /branches/dev/samtools/bam_plcmd.c
2085 M /branches/dev/samtools/bam_tview.c
2086 M /branches/dev/samtools/bamtk.c
2087 M /branches/dev/samtools/razf.c
2088 M /branches/dev/samtools/samtools.1
2091 * fixed a bug in razf.c: reset z_eof when razf_seek() is called
2092 * fixed a memory leak in parsing a region
2093 * changed pileup a little bit when -s is in use: output ^ and $
2094 * when a bam is not indexed, output more meaningful error message
2095 * fixed a bug in indexing for small alignment
2096 * fixed a bug in the viewer when we come to the end of a reference file
2097 * updated documentation
2098 * prepare to release 0.1.1
2100 ------------------------------------------------------------------------
2101 r60 | lh3lh3 | 2008-12-22 15:10:16 +0000 (Mon, 22 Dec 2008) | 2 lines
2103 A /branches/dev/samtools/examples
2104 A /branches/dev/samtools/examples/00README.txt
2105 A /branches/dev/samtools/examples/ex1.fa
2106 A /branches/dev/samtools/examples/ex1.fa.fai
2107 A /branches/dev/samtools/examples/ex1.sam.gz
2111 ------------------------------------------------------------------------
2112 r59 | lh3lh3 | 2008-12-22 09:38:15 +0000 (Mon, 22 Dec 2008) | 2 lines
2114 M /branches/dev/samtools/ChangeLog
2118 ------------------------------------------------------------------------
2119 r58 | lh3lh3 | 2008-12-20 23:06:00 +0000 (Sat, 20 Dec 2008) | 3 lines
2121 M /branches/dev/samtools/misc/export2sam.pl
2124 * fixed several bugs
2126 ------------------------------------------------------------------------
2127 r57 | lh3lh3 | 2008-12-20 15:44:20 +0000 (Sat, 20 Dec 2008) | 2 lines
2129 A /branches/dev/samtools/misc/export2sam.pl
2131 convert Export format to SAM; not thoroughly tested
2133 ------------------------------------------------------------------------
2134 r56 | lh3lh3 | 2008-12-19 22:13:28 +0000 (Fri, 19 Dec 2008) | 6 lines
2136 M /branches/dev/samtools/bam_import.c
2137 M /branches/dev/samtools/bam_plcmd.c
2138 M /branches/dev/samtools/bam_tview.c
2139 M /branches/dev/samtools/bamtk.c
2140 A /branches/dev/samtools/source.dot
2143 * pileup: generate maq-like simple output
2144 * pileup: allow to output pileup at required sites
2145 * source.dot: source file relationship graph
2146 * tview: fixed a minor bug
2148 ------------------------------------------------------------------------
2149 r55 | lh3lh3 | 2008-12-19 20:10:26 +0000 (Fri, 19 Dec 2008) | 2 lines
2151 D /branches/dev/samtools/misc/all2sam.pl
2155 ------------------------------------------------------------------------
2156 r54 | lh3lh3 | 2008-12-16 22:34:25 +0000 (Tue, 16 Dec 2008) | 2 lines
2158 A /branches/dev/samtools/COPYING
2159 M /branches/dev/samtools/bam.h
2160 M /branches/dev/samtools/faidx.h
2161 M /branches/dev/samtools/khash.h
2162 M /branches/dev/samtools/kseq.h
2163 M /branches/dev/samtools/ksort.h
2164 M /branches/dev/samtools/samtools.1
2166 Added copyright information and a bit more documentation. No code change.
2168 ------------------------------------------------------------------------
2169 r53 | lh3lh3 | 2008-12-16 13:40:18 +0000 (Tue, 16 Dec 2008) | 3 lines
2171 M /branches/dev/samtools/bam.c
2172 M /branches/dev/samtools/bam.h
2173 M /branches/dev/samtools/bam_index.c
2174 M /branches/dev/samtools/bam_maqcns.c
2175 M /branches/dev/samtools/bamtk.c
2178 * improved efficiency of the indel caller for spliced alignments
2180 ------------------------------------------------------------------------
2181 r52 | lh3lh3 | 2008-12-16 10:28:20 +0000 (Tue, 16 Dec 2008) | 3 lines
2183 M /branches/dev/samtools/bam.c
2184 M /branches/dev/samtools/bam.h
2185 M /branches/dev/samtools/bam_aux.c
2186 M /branches/dev/samtools/bam_index.c
2187 M /branches/dev/samtools/bamtk.c
2190 * a bit code cleanup: reduce the dependency between source files
2192 ------------------------------------------------------------------------
2193 r51 | lh3lh3 | 2008-12-15 14:29:32 +0000 (Mon, 15 Dec 2008) | 3 lines
2195 M /branches/dev/samtools/bam_maqcns.c
2196 M /branches/dev/samtools/bam_plcmd.c
2197 M /branches/dev/samtools/bamtk.c
2200 * fixed a memory leak
2202 ------------------------------------------------------------------------
2203 r50 | lh3lh3 | 2008-12-15 14:00:13 +0000 (Mon, 15 Dec 2008) | 2 lines
2205 M /branches/dev/samtools/ChangeLog
2206 M /branches/dev/samtools/bam.h
2207 M /branches/dev/samtools/samtools.1
2209 update documentation, ChangeLog and a comment
2211 ------------------------------------------------------------------------
2212 r49 | lh3lh3 | 2008-12-15 13:36:43 +0000 (Mon, 15 Dec 2008) | 6 lines
2214 M /branches/dev/samtools/Makefile
2215 M /branches/dev/samtools/bam.h
2216 M /branches/dev/samtools/bam_maqcns.c
2217 M /branches/dev/samtools/bam_maqcns.h
2218 M /branches/dev/samtools/bam_pileup.c
2219 A /branches/dev/samtools/bam_plcmd.c
2220 M /branches/dev/samtools/bamtk.c
2221 M /branches/dev/samtools/samtools.1
2224 * moved pileup command to a separate source file
2225 * added indel caller
2226 * added bam_cal_segend(). (NOT WORKING for spliced alignment!!!)
2227 * updated documentation
2229 ------------------------------------------------------------------------
2230 r48 | lh3lh3 | 2008-12-12 13:55:36 +0000 (Fri, 12 Dec 2008) | 3 lines
2232 M /branches/dev/samtools/bam_maqcns.c
2233 M /branches/dev/samtools/bamtk.c
2236 * fixed another bug in maqcns when there is a nearby deletion
2238 ------------------------------------------------------------------------
2239 r47 | lh3lh3 | 2008-12-12 13:42:16 +0000 (Fri, 12 Dec 2008) | 5 lines
2241 M /branches/dev/samtools/bam_maqcns.c
2242 M /branches/dev/samtools/bam_pileup.c
2243 M /branches/dev/samtools/bamtk.c
2246 * pileup: outputing consensus is now optional
2247 * fixed a bug in glfgen. This bug also exists in maq's glfgen. However,
2248 I am not quite sure why the previous version may have problem.
2250 ------------------------------------------------------------------------
2251 r46 | lh3lh3 | 2008-12-12 11:44:56 +0000 (Fri, 12 Dec 2008) | 6 lines
2253 M /branches/dev/samtools/bam_pileup.c
2254 M /branches/dev/samtools/bamtk.c
2257 * add maq consensus to pileup. However, I will move this part to a new
2258 command as strictly speaking, consensus callin is not part of pileup,
2259 and imposing it would make it harder to generate for other language
2262 ------------------------------------------------------------------------
2263 r45 | bhandsaker | 2008-12-11 20:43:56 +0000 (Thu, 11 Dec 2008) | 2 lines
2265 M /branches/dev/samtools/bgzf.c
2267 Fix bug in tell() after reads that consume to the exact end of a block.
2269 ------------------------------------------------------------------------
2270 r44 | lh3lh3 | 2008-12-11 09:36:53 +0000 (Thu, 11 Dec 2008) | 2 lines
2272 M /branches/dev/samtools/samtools.1
2276 ------------------------------------------------------------------------
2277 r43 | lh3lh3 | 2008-12-11 09:25:36 +0000 (Thu, 11 Dec 2008) | 4 lines
2279 M /branches/dev/samtools/bam_import.c
2280 M /branches/dev/samtools/bamtk.c
2283 * fixed a bug in parser when there is auxiliary fields
2284 * made the parser a bit more robust
2286 ------------------------------------------------------------------------
2287 r42 | lh3lh3 | 2008-12-10 14:57:29 +0000 (Wed, 10 Dec 2008) | 5 lines
2289 M /branches/dev/samtools/bam_index.c
2290 M /branches/dev/samtools/bamtk.c
2291 M /branches/dev/samtools/bgzf.c
2294 * fixed a bug in bgzf (only reading is affected)
2295 * fixed a typo in bam_index.c
2296 * in bam_index.c, check potential bugs in the underlying I/O library
2298 ------------------------------------------------------------------------
2299 r41 | lh3lh3 | 2008-12-10 12:53:08 +0000 (Wed, 10 Dec 2008) | 2 lines
2301 M /branches/dev/samtools/samtools.1
2305 ------------------------------------------------------------------------
2306 r40 | lh3lh3 | 2008-12-10 11:52:10 +0000 (Wed, 10 Dec 2008) | 5 lines
2308 M /branches/dev/samtools/bam.h
2309 M /branches/dev/samtools/bam_pileup.c
2310 M /branches/dev/samtools/bamtk.c
2313 * tried to make pileup work with clipping (previously not), though NOT tested
2314 * removed -v from pileup
2315 * made pileup take the reference sequence
2317 ------------------------------------------------------------------------
2318 r39 | lh3lh3 | 2008-12-09 11:59:28 +0000 (Tue, 09 Dec 2008) | 4 lines
2320 M /branches/dev/samtools/bam_import.c
2321 M /branches/dev/samtools/bamtk.c
2322 M /branches/dev/samtools/samtools.1
2325 * in parser, recognize "=", rather than ",", as a match
2326 * in parser, correctl parse "=" at the MRNM field.
2328 ------------------------------------------------------------------------
2329 r38 | lh3lh3 | 2008-12-09 11:39:07 +0000 (Tue, 09 Dec 2008) | 2 lines
2331 M /branches/dev/samtools/misc/maq2sam.c
2333 fixed a bug in handling maq flag 64 and 192
2335 ------------------------------------------------------------------------
2336 r37 | lh3lh3 | 2008-12-09 09:53:46 +0000 (Tue, 09 Dec 2008) | 2 lines
2338 M /branches/dev/samtools/misc/md5fa.c
2340 also calculate unordered md5sum check
2342 ------------------------------------------------------------------------
2343 r36 | lh3lh3 | 2008-12-09 09:46:21 +0000 (Tue, 09 Dec 2008) | 2 lines
2345 M /branches/dev/samtools/misc/md5fa.c
2347 fixed a minor bug when there are space in the sequence
2349 ------------------------------------------------------------------------
2350 r35 | lh3lh3 | 2008-12-09 09:40:45 +0000 (Tue, 09 Dec 2008) | 2 lines
2352 M /branches/dev/samtools/misc/md5fa.c
2354 fixed a potential memory leak
2356 ------------------------------------------------------------------------
2357 r34 | lh3lh3 | 2008-12-08 14:52:17 +0000 (Mon, 08 Dec 2008) | 2 lines
2359 M /branches/dev/samtools/bam_import.c
2360 M /branches/dev/samtools/bam_index.c
2361 M /branches/dev/samtools/bamtk.c
2363 * fixed a bug in import: bin is wrongly calculated
2365 ------------------------------------------------------------------------
2366 r33 | lh3lh3 | 2008-12-08 14:08:01 +0000 (Mon, 08 Dec 2008) | 2 lines
2368 M /branches/dev/samtools/misc/all2sam.pl
2372 ------------------------------------------------------------------------
2373 r32 | lh3lh3 | 2008-12-08 12:56:02 +0000 (Mon, 08 Dec 2008) | 3 lines
2375 M /branches/dev/samtools/Makefile
2376 M /branches/dev/samtools/kseq.h
2377 M /branches/dev/samtools/misc/Makefile
2378 A /branches/dev/samtools/misc/md5.c
2379 A /branches/dev/samtools/misc/md5.h
2380 A /branches/dev/samtools/misc/md5fa.c
2382 * fixed two warnings in kseq.h
2383 * added md5sum utilities
2385 ------------------------------------------------------------------------
2386 r31 | lh3lh3 | 2008-12-08 11:35:29 +0000 (Mon, 08 Dec 2008) | 5 lines
2388 M /branches/dev/samtools/Makefile
2389 M /branches/dev/samtools/bam_import.c
2390 M /branches/dev/samtools/bamtk.c
2391 A /branches/dev/samtools/kseq.h
2392 D /branches/dev/samtools/kstream.h
2395 * replace kstream with kseq. kseq is a superset of kstream. I need the
2396 extra functions in kseq.h.
2397 * also compile stand-alone faidx
2399 ------------------------------------------------------------------------
2400 r30 | lh3lh3 | 2008-12-08 11:17:04 +0000 (Mon, 08 Dec 2008) | 3 lines
2402 M /branches/dev/samtools/bam.h
2403 M /branches/dev/samtools/bam_sort.c
2404 M /branches/dev/samtools/bamtk.c
2407 * sorting by read names is available
2409 ------------------------------------------------------------------------
2410 r29 | lh3lh3 | 2008-12-08 10:29:02 +0000 (Mon, 08 Dec 2008) | 3 lines
2412 M /branches/dev/samtools/bam.c
2413 M /branches/dev/samtools/bam.h
2414 M /branches/dev/samtools/bam_import.c
2415 M /branches/dev/samtools/bam_maqcns.c
2416 M /branches/dev/samtools/bam_pileup.c
2417 M /branches/dev/samtools/bam_sort.c
2418 M /branches/dev/samtools/bam_tview.c
2419 M /branches/dev/samtools/bamtk.c
2420 M /branches/dev/samtools/misc/maq2sam.c
2423 * format change to meet the latest specification
2425 ------------------------------------------------------------------------
2426 r28 | lh3lh3 | 2008-12-04 16:09:21 +0000 (Thu, 04 Dec 2008) | 3 lines
2428 M /branches/dev/samtools/bam_maqcns.c
2429 M /branches/dev/samtools/misc/maq2sam.c
2431 * minor change in maqcns: special care when n==0
2432 * change maq2sam to meet the latest specification
2434 ------------------------------------------------------------------------
2435 r27 | lh3lh3 | 2008-12-04 15:55:44 +0000 (Thu, 04 Dec 2008) | 2 lines
2437 M /branches/dev/samtools/razf.c
2438 M /branches/dev/samtools/razf.h
2440 considerable code clean up in razf
2442 ------------------------------------------------------------------------
2443 r26 | lh3lh3 | 2008-12-04 15:08:18 +0000 (Thu, 04 Dec 2008) | 2 lines
2445 M /branches/dev/samtools/ChangeLog
2446 M /branches/dev/samtools/Makefile
2447 M /branches/dev/samtools/faidx.c
2449 make RAZF optional in faidx.c
2451 ------------------------------------------------------------------------
2452 r25 | lh3lh3 | 2008-12-01 15:27:22 +0000 (Mon, 01 Dec 2008) | 3 lines
2454 M /branches/dev/samtools/Makefile
2455 M /branches/dev/samtools/bam.h
2456 M /branches/dev/samtools/bam_aux.c
2457 M /branches/dev/samtools/bamtk.c
2458 M /branches/dev/samtools/samtools.1
2461 * added routines for retrieving aux data, NOT TESTED YET!
2463 ------------------------------------------------------------------------
2464 r24 | lh3lh3 | 2008-12-01 14:29:43 +0000 (Mon, 01 Dec 2008) | 5 lines
2466 M /branches/dev/samtools/bam.c
2467 M /branches/dev/samtools/bam_import.c
2468 M /branches/dev/samtools/bam_maqcns.c
2469 M /branches/dev/samtools/bamtk.c
2470 M /branches/dev/samtools/bgzf.c
2471 M /branches/dev/samtools/samtools.1
2474 * bgzf: fixed a potential integer overflow on 32-it machines
2475 * maqcns: set the minimum combined quality as 0
2476 * supporting hex strings
2478 ------------------------------------------------------------------------
2479 r23 | lh3lh3 | 2008-11-27 17:14:37 +0000 (Thu, 27 Nov 2008) | 3 lines
2481 M /branches/dev/samtools/bam_maqcns.c
2482 M /branches/dev/samtools/bamtk.c
2485 * fixed the bug in maqcns
2487 ------------------------------------------------------------------------
2488 r22 | lh3lh3 | 2008-11-27 17:08:11 +0000 (Thu, 27 Nov 2008) | 3 lines
2490 M /branches/dev/samtools/Makefile
2491 M /branches/dev/samtools/bam.h
2492 A /branches/dev/samtools/bam_maqcns.c
2493 A /branches/dev/samtools/bam_maqcns.h
2494 M /branches/dev/samtools/bam_tview.c
2495 M /branches/dev/samtools/bamtk.c
2496 A /branches/dev/samtools/glf.h
2499 * add MAQ consensus caller, currently BUGGY!
2501 ------------------------------------------------------------------------
2502 r21 | lh3lh3 | 2008-11-27 13:51:28 +0000 (Thu, 27 Nov 2008) | 4 lines
2504 M /branches/dev/samtools/bam_pileup.c
2505 M /branches/dev/samtools/bam_tview.c
2506 M /branches/dev/samtools/bamtk.c
2509 * tview: display padded alignment (but not P operation)
2510 * better coordinates and reference sequence
2512 ------------------------------------------------------------------------
2513 r19 | lh3lh3 | 2008-11-27 09:26:05 +0000 (Thu, 27 Nov 2008) | 2 lines
2515 A /branches/dev/samtools/ChangeLog
2519 ------------------------------------------------------------------------
2520 r18 | lh3lh3 | 2008-11-27 09:24:45 +0000 (Thu, 27 Nov 2008) | 3 lines
2522 D /branches/dev/samtools/ChangeLog
2523 A /branches/dev/samtools/ChangeLog.old (from /branches/dev/samtools/ChangeLog:6)
2525 Rename ChangeLog to ChangeLog.old. This old ChangeLog is generated from
2526 the log of my personal SVN repository.
2528 ------------------------------------------------------------------------
2529 r17 | lh3lh3 | 2008-11-27 09:22:55 +0000 (Thu, 27 Nov 2008) | 6 lines
2531 M /branches/dev/samtools/Makefile
2532 M /branches/dev/samtools/bamtk.c
2533 M /branches/dev/samtools/bgzf.c
2536 * declare fseeko and ftello as some Linux may not do this by default and
2537 missing these declarations will make bgzf buggy
2538 * get rid of some harmless warings
2539 * use BGZF by default, now
2541 ------------------------------------------------------------------------
2542 r16 | lh3lh3 | 2008-11-26 21:19:11 +0000 (Wed, 26 Nov 2008) | 4 lines
2544 M /branches/dev/samtools/bam_index.c
2545 M /branches/dev/samtools/bamtk.c
2546 M /branches/dev/samtools/razf.c
2549 * fixed a bug in razf_read()
2550 * give more warnings when the file is truncated (or due to bugs in I/O library)
2552 ------------------------------------------------------------------------
2553 r15 | lh3lh3 | 2008-11-26 20:41:39 +0000 (Wed, 26 Nov 2008) | 2 lines
2555 M /branches/dev/samtools/bgzf.c
2557 fixed a bug in bgzf.c at the end of the file
2559 ------------------------------------------------------------------------
2560 r14 | lh3lh3 | 2008-11-26 17:05:18 +0000 (Wed, 26 Nov 2008) | 4 lines
2562 M /branches/dev/samtools/bamtk.c
2565 * a lot happened to RAZF, although samtools itself is untouched. Better
2566 also update the version number anyway to avoid confusion
2568 ------------------------------------------------------------------------
2569 r13 | lh3lh3 | 2008-11-26 17:03:48 +0000 (Wed, 26 Nov 2008) | 2 lines
2571 M /branches/dev/samtools/razf.c
2573 a change from Jue, but I think it should not matter
2575 ------------------------------------------------------------------------
2576 r12 | lh3lh3 | 2008-11-26 16:48:14 +0000 (Wed, 26 Nov 2008) | 3 lines
2578 M /branches/dev/samtools/razf.c
2580 fixed a potential bug in razf. However, it seems still buggy, just
2581 rarely happens, very rarely.
2583 ------------------------------------------------------------------------
2584 r11 | lh3lh3 | 2008-11-26 14:02:56 +0000 (Wed, 26 Nov 2008) | 2 lines
2586 M /branches/dev/samtools/razf.c
2588 fixed a bug in razf, with the help of Jue
2590 ------------------------------------------------------------------------
2591 r10 | lh3lh3 | 2008-11-26 11:55:32 +0000 (Wed, 26 Nov 2008) | 2 lines
2593 M /branches/dev/samtools/bam_index.c
2597 ------------------------------------------------------------------------
2598 r9 | lh3lh3 | 2008-11-26 11:37:05 +0000 (Wed, 26 Nov 2008) | 2 lines
2600 M /branches/dev/samtools/Makefile
2601 M /branches/dev/samtools/bam.h
2602 M /branches/dev/samtools/razf.c
2603 M /branches/dev/samtools/razf.h
2605 * Jue has updated razf to realize Bob's scheme
2607 ------------------------------------------------------------------------
2608 r7 | lh3lh3 | 2008-11-25 20:37:37 +0000 (Tue, 25 Nov 2008) | 2 lines
2610 A /branches/dev/samtools/samtools.1
2614 ------------------------------------------------------------------------
2615 r6 | lh3lh3 | 2008-11-25 20:37:16 +0000 (Tue, 25 Nov 2008) | 3 lines
2617 A /branches/dev/samtools/ChangeLog
2618 A /branches/dev/samtools/Makefile
2619 A /branches/dev/samtools/bam.c
2620 A /branches/dev/samtools/bam.h
2621 A /branches/dev/samtools/bam_aux.c
2622 A /branches/dev/samtools/bam_endian.h
2623 A /branches/dev/samtools/bam_import.c
2624 A /branches/dev/samtools/bam_index.c
2625 A /branches/dev/samtools/bam_lpileup.c
2626 A /branches/dev/samtools/bam_pileup.c
2627 A /branches/dev/samtools/bam_sort.c
2628 A /branches/dev/samtools/bam_tview.c
2629 A /branches/dev/samtools/bamtk.c
2630 A /branches/dev/samtools/bgzf.c
2631 A /branches/dev/samtools/bgzf.h
2632 A /branches/dev/samtools/bgzip.c
2633 A /branches/dev/samtools/faidx.c
2634 A /branches/dev/samtools/faidx.h
2635 A /branches/dev/samtools/khash.h
2636 A /branches/dev/samtools/ksort.h
2637 A /branches/dev/samtools/kstream.h
2638 A /branches/dev/samtools/misc
2639 A /branches/dev/samtools/misc/Makefile
2640 A /branches/dev/samtools/misc/all2sam.pl
2641 A /branches/dev/samtools/misc/maq2sam.c
2642 A /branches/dev/samtools/razf.c
2643 A /branches/dev/samtools/razf.h
2644 A /branches/dev/samtools/razip.c
2645 A /branches/dev/samtools/zutil.h
2647 The initial version of samtools, replicated from my local SVN repository.
2648 The current version is: 0.1.0-42. All future development will happen here.
2650 ------------------------------------------------------------------------
2651 r5 | lh3lh3 | 2008-11-25 20:30:49 +0000 (Tue, 25 Nov 2008) | 2 lines
2653 A /branches/dev/samtools
2655 samtools (C version)
2657 ------------------------------------------------------------------------