1 ------------------------------------------------------------------------
2 r421 | lh3lh3 | 2009-07-30 10:03:39 +0100 (Thu, 30 Jul 2009) | 3 lines
4 M /trunk/samtools/bam_import.c
5 M /trunk/samtools/bam_plcmd.c
6 M /trunk/samtools/bamtk.c
7 M /trunk/samtools/misc/samtools.pl
8 M /trunk/samtools/sam.c
9 M /trunk/samtools/sam.h
10 M /trunk/samtools/sam_view.c
12 * samtools-0.1.5-16 (r421)
13 * in view and pileup, load header from FASTA index if the input is SAM.
15 ------------------------------------------------------------------------
16 r420 | lh3lh3 | 2009-07-29 09:18:55 +0100 (Wed, 29 Jul 2009) | 2 lines
18 M /trunk/samtools/misc/maq2sam.c
20 do not set "read 1" if reads are not mapped in the PE mode of maq
22 ------------------------------------------------------------------------
23 r419 | lh3lh3 | 2009-07-28 09:52:33 +0100 (Tue, 28 Jul 2009) | 5 lines
25 M /trunk/samtools/bam_import.c
26 M /trunk/samtools/bamtk.c
27 M /trunk/samtools/misc/samtools.pl
28 M /trunk/samtools/misc/wgsim_eval.pl
30 * samtools-0.1.5-15 (r419)
31 * in sam_open(), return NULL when the file cannot be opened.
32 * make wgsim_eval.pl more robust to imperfect SAM
33 * add "unique" command to samtools.pl
35 ------------------------------------------------------------------------
36 r418 | lh3lh3 | 2009-07-24 14:04:19 +0100 (Fri, 24 Jul 2009) | 2 lines
38 M /trunk/samtools/misc/wgsim_eval.pl
40 skip @header lines in SAM
42 ------------------------------------------------------------------------
43 r417 | lh3lh3 | 2009-07-24 12:42:38 +0100 (Fri, 24 Jul 2009) | 3 lines
45 M /trunk/samtools/bamtk.c
46 M /trunk/samtools/sam_view.c
48 * samtools-0.1.5-14 (r417)
49 * more help in "samtools view" due to the recent changes.
51 ------------------------------------------------------------------------
52 r416 | lh3lh3 | 2009-07-24 12:34:30 +0100 (Fri, 24 Jul 2009) | 3 lines
54 M /trunk/samtools/bam.c
55 M /trunk/samtools/bam.h
56 M /trunk/samtools/bam_import.c
57 M /trunk/samtools/bamtk.c
58 M /trunk/samtools/sam.c
59 M /trunk/samtools/sam.h
60 M /trunk/samtools/sam_view.c
62 * samtools-0.1.5-17 (r416)
63 * support import/export SAM with string tags
65 ------------------------------------------------------------------------
66 r415 | lh3lh3 | 2009-07-24 11:39:26 +0100 (Fri, 24 Jul 2009) | 3 lines
68 M /trunk/samtools/bam.c
69 M /trunk/samtools/bam.h
70 M /trunk/samtools/bam_import.c
71 M /trunk/samtools/bamtk.c
72 M /trunk/samtools/sam.c
73 M /trunk/samtools/sam.h
74 M /trunk/samtools/sam_view.c
76 * samtools-0.1.5-12 (r415)
77 * FLAG now can be in HEX
79 ------------------------------------------------------------------------
80 r414 | lh3lh3 | 2009-07-22 22:03:49 +0100 (Wed, 22 Jul 2009) | 2 lines
82 M /trunk/samtools/kstring.h
84 fixed a compiling error (thank Ken for fixing it)
86 ------------------------------------------------------------------------
87 r412 | lh3lh3 | 2009-07-21 22:19:40 +0100 (Tue, 21 Jul 2009) | 2 lines
89 M /trunk/samtools/kstring.c
90 M /trunk/samtools/kstring.h
92 Implemented Boyer-Moore search in the kstring library.
94 ------------------------------------------------------------------------
95 r409 | lh3lh3 | 2009-07-17 17:10:20 +0100 (Fri, 17 Jul 2009) | 2 lines
97 M /trunk/samtools/bam_index.c
99 do not include knetfile.h when _USE_KNETFILE is not defined
101 ------------------------------------------------------------------------
102 r408 | lh3lh3 | 2009-07-17 15:29:21 +0100 (Fri, 17 Jul 2009) | 5 lines
104 M /trunk/samtools/bam_md.c
105 M /trunk/samtools/bam_tview.c
106 M /trunk/samtools/bamtk.c
107 M /trunk/samtools/bgzf.c
109 * samtools-0.1.5-11 (r408)
110 * force to overwirte existing MD if it is different from the one calculated
112 * bgzf.c: improved the compatibility with Windows headers
114 ------------------------------------------------------------------------
115 r407 | lh3lh3 | 2009-07-17 14:46:56 +0100 (Fri, 17 Jul 2009) | 5 lines
117 M /trunk/samtools/bam.h
118 M /trunk/samtools/bam_aux.c
119 M /trunk/samtools/bam_md.c
120 M /trunk/samtools/bamtk.c
121 M /trunk/samtools/sam.h
123 * samtools-0.1.5-10 (r407)
124 * implemented bam_aux_del() to remove a tag
125 * fillmd: generate the NM tag
126 * fillmd: cmd interface improvement
128 ------------------------------------------------------------------------
129 r406 | lh3lh3 | 2009-07-16 23:30:40 +0100 (Thu, 16 Jul 2009) | 2 lines
131 M /trunk/samtools/Makefile
133 Sorry. The old Makefile is for PDCurses...
135 ------------------------------------------------------------------------
136 r405 | lh3lh3 | 2009-07-16 23:30:11 +0100 (Thu, 16 Jul 2009) | 3 lines
138 M /trunk/samtools/Makefile
139 M /trunk/samtools/bam_tview.c
140 M /trunk/samtools/bamtk.c
142 * samtools-0.1.5-9 (r405)
143 * improved the compatibility with PDCurses a little bit
145 ------------------------------------------------------------------------
146 r404 | lh3lh3 | 2009-07-16 23:23:52 +0100 (Thu, 16 Jul 2009) | 3 lines
148 M /trunk/samtools/Makefile
149 M /trunk/samtools/bam_tview.c
150 M /trunk/samtools/bamtk.c
152 * samtools-0.1.5-8 (r404)
153 * compatible with PDCurses
155 ------------------------------------------------------------------------
156 r403 | lh3lh3 | 2009-07-16 22:39:39 +0100 (Thu, 16 Jul 2009) | 3 lines
158 M /trunk/samtools/bamtk.c
159 M /trunk/samtools/kseq.h
161 * samtools-0.1.5-7 (r403)
162 * fixed a bug in kseq.h for binary files (text files are fine)
164 ------------------------------------------------------------------------
165 r402 | lh3lh3 | 2009-07-16 11:49:53 +0100 (Thu, 16 Jul 2009) | 4 lines
167 M /trunk/samtools/bam_import.c
168 M /trunk/samtools/bam_index.c
169 M /trunk/samtools/bamtk.c
170 M /trunk/samtools/bgzf.c
172 * samtools-0.1.5-6 (r402)
173 * fixed compiling error when "-D_USE_NETFILE" is not applied
174 * improve portability to MinGW
176 ------------------------------------------------------------------------
177 r398 | lh3lh3 | 2009-07-13 10:21:36 +0100 (Mon, 13 Jul 2009) | 3 lines
179 A /trunk/bam-lite/bam.h (from /trunk/samtools/bam.h:395)
180 A /trunk/bam-lite/bam_lite.c (from /trunk/samtools/bam_lite.c:395)
181 D /trunk/samtools/bam_lite.c
183 * move bam_lite.c to bam-lite
184 * copy bam.h to bam-lite
186 ------------------------------------------------------------------------
187 r395 | lh3lh3 | 2009-07-13 10:12:57 +0100 (Mon, 13 Jul 2009) | 3 lines
189 M /trunk/samtools/bam.h
190 M /trunk/samtools/bam_lite.c
191 M /trunk/samtools/bam_lpileup.c
192 M /trunk/samtools/bam_pileup.c
193 M /trunk/samtools/bamtk.c
195 * samtools-0.1.5-5 (r395)
196 * added bam_pileup_file() and removed bam_lpileup_file()
198 ------------------------------------------------------------------------
199 r394 | lh3lh3 | 2009-07-13 00:35:10 +0100 (Mon, 13 Jul 2009) | 3 lines
201 M /trunk/samtools/bamtk.c
202 M /trunk/samtools/knetfile.c
203 M /trunk/samtools/knetfile.h
205 * samtools-0.1.5-4 (r394)
206 * http_proxy support in knetfile library (check http_proxy ENV)
208 ------------------------------------------------------------------------
209 r393 | lh3lh3 | 2009-07-12 23:57:07 +0100 (Sun, 12 Jul 2009) | 5 lines
211 M /trunk/samtools/bam_index.c
212 M /trunk/samtools/bam_tview.c
213 M /trunk/samtools/bamtk.c
214 M /trunk/samtools/knetfile.c
215 M /trunk/samtools/knetfile.h
217 * samtools-0.1.5-3 (r393)
218 * knetfile now supports HTTP (no proxy at the moment)
219 * fixed a potential issue in knetfile on opening ordinary file, although I have
220 not seen the sideeffect so far.
222 ------------------------------------------------------------------------
223 r392 | lh3lh3 | 2009-07-12 18:50:55 +0100 (Sun, 12 Jul 2009) | 2 lines
225 M /trunk/samtools/samtools.1
227 Remove the warning in tview
229 ------------------------------------------------------------------------
230 r391 | lh3lh3 | 2009-07-12 18:42:43 +0100 (Sun, 12 Jul 2009) | 3 lines
232 M /trunk/samtools/bam_tview.c
233 M /trunk/samtools/bamtk.c
235 * samtools-0.1.5-2 (r391)
236 * do not show a blank screen when no reads mapped
238 ------------------------------------------------------------------------
239 r390 | lh3lh3 | 2009-07-09 14:01:42 +0100 (Thu, 09 Jul 2009) | 4 lines
241 M /trunk/samtools/bam.h
242 A /trunk/samtools/bam_lite.c
243 M /trunk/samtools/bamtk.c
245 * samtools-0.1.5-1 (r390)
246 * removed useless _IOLIB in bam.h. This should cause no change at all.
247 * added bam_lite.c for light-weight BAM reading
249 ------------------------------------------------------------------------
250 r385 | lh3lh3 | 2009-07-07 16:53:29 +0100 (Tue, 07 Jul 2009) | 2 lines
252 M /trunk/samtools/bamtk.c
253 M /trunk/samtools/knetfile.c
255 Release samtools-0.1.5c (fixed a bug in piping)
257 ------------------------------------------------------------------------
258 r383 | lh3lh3 | 2009-07-07 11:39:55 +0100 (Tue, 07 Jul 2009) | 2 lines
260 M /trunk/samtools/bamtk.c
261 M /trunk/samtools/sam.c
263 Release samtools-0.1.5b (BUG! so embarrassing!)
265 ------------------------------------------------------------------------
266 r381 | lh3lh3 | 2009-07-07 11:20:06 +0100 (Tue, 07 Jul 2009) | 2 lines
268 M /trunk/samtools/Makefile
269 M /trunk/samtools/bam.h
270 M /trunk/samtools/bam_aux.c
271 M /trunk/samtools/bamtk.c
273 Release samtools-0.1.5a (for compatibility with Bio::DB::Sam)
275 ------------------------------------------------------------------------
276 r373 | lh3lh3 | 2009-07-07 10:26:57 +0100 (Tue, 07 Jul 2009) | 2 lines
278 M /trunk/samtools/ChangeLog
279 M /trunk/samtools/NEWS
280 M /trunk/samtools/bamtk.c
281 M /trunk/samtools/samtools.1
283 Release samtools-0.1.5
285 ------------------------------------------------------------------------
286 r372 | lh3lh3 | 2009-07-07 09:49:27 +0100 (Tue, 07 Jul 2009) | 3 lines
288 M /trunk/samtools/bamtk.c
289 M /trunk/samtools/sam.c
291 * samtools-0.1.4-23 (r372)
292 * keep header text if "view -t" is used (by Gerton)
294 ------------------------------------------------------------------------
295 r371 | lh3lh3 | 2009-07-07 01:13:32 +0100 (Tue, 07 Jul 2009) | 2 lines
297 M /trunk/samtools/samtools.1
301 ------------------------------------------------------------------------
302 r370 | bhandsaker | 2009-07-02 22:24:34 +0100 (Thu, 02 Jul 2009) | 2 lines
304 M /trunk/samtools/Makefile
306 Introduced LIBPATH variable so this could be overridden to allow samtools to build correct at the Broad.
308 ------------------------------------------------------------------------
309 r369 | lh3lh3 | 2009-07-02 13:36:53 +0100 (Thu, 02 Jul 2009) | 4 lines
311 M /trunk/samtools/ChangeLog
312 M /trunk/samtools/bam_aux.c
313 M /trunk/samtools/bam_plcmd.c
314 M /trunk/samtools/bamtk.c
316 * samtools-0.1.4-22 (r369)
317 * in pileup, optionally print E2 and U2
318 * remove the debugging code in bam_aux_get() (Drat!)
320 ------------------------------------------------------------------------
321 r368 | lh3lh3 | 2009-07-02 11:32:26 +0100 (Thu, 02 Jul 2009) | 6 lines
323 M /trunk/samtools/bam.c
324 M /trunk/samtools/bam.h
325 M /trunk/samtools/bam_aux.c
326 M /trunk/samtools/bam_index.c
327 M /trunk/samtools/bam_lpileup.c
328 M /trunk/samtools/bam_md.c
329 M /trunk/samtools/bam_pileup.c
330 M /trunk/samtools/bam_rmdup.c
331 M /trunk/samtools/bam_stat.c
332 M /trunk/samtools/bam_tview.c
333 M /trunk/samtools/bamtk.c
334 M /trunk/samtools/faidx.c
335 M /trunk/samtools/faidx.h
336 M /trunk/samtools/glf.c
338 * samtools-0.1.4-21 (r368)
339 * propagate errors rather than exit or complain assertion failure. Assertion
340 should be only used for checking internal bugs, but not for external input
341 inconsistency. I was just a bit lazy.
342 * small memory leak may be present on failure, though
344 ------------------------------------------------------------------------
345 r367 | lh3lh3 | 2009-06-30 16:18:42 +0100 (Tue, 30 Jun 2009) | 2 lines
347 M /trunk/samtools/knetfile.c
349 reduce the chance of blocking in FTP connection
351 ------------------------------------------------------------------------
352 r366 | lh3lh3 | 2009-06-30 15:35:21 +0100 (Tue, 30 Jun 2009) | 2 lines
354 M /trunk/samtools/knetfile.c
356 minor changes to knetfile: invalid fd equals -1 rather than 0
358 ------------------------------------------------------------------------
359 r365 | lh3lh3 | 2009-06-30 14:04:30 +0100 (Tue, 30 Jun 2009) | 3 lines
361 M /trunk/samtools/bam_index.c
362 M /trunk/samtools/bamtk.c
363 M /trunk/samtools/knetfile.c
364 M /trunk/samtools/knetfile.h
366 * samtools-0.1.4-20 (r365)
367 * download the BAM index file if it is not found in the current working directory.
369 ------------------------------------------------------------------------
370 r364 | lh3lh3 | 2009-06-30 12:39:07 +0100 (Tue, 30 Jun 2009) | 3 lines
372 M /trunk/samtools/bamtk.c
373 M /trunk/samtools/knetfile.c
375 * samtools-0.1.4-19 (r364)
376 * knetfile: report error when the file is not present on FTP
378 ------------------------------------------------------------------------
379 r363 | lh3lh3 | 2009-06-29 23:23:32 +0100 (Mon, 29 Jun 2009) | 4 lines
381 M /trunk/samtools/bam_tview.c
382 M /trunk/samtools/bamtk.c
383 M /trunk/samtools/bgzf.c
384 M /trunk/samtools/bgzf.h
385 M /trunk/samtools/knetfile.c
386 M /trunk/samtools/knetfile.h
388 * samtools-0.1.4-18 (r363)
389 * knetfile: do not trigger network communication in FTP seek (lazy seek)
390 * bgzf: cache recent blocks (disabled by default)
392 ------------------------------------------------------------------------
393 r362 | lh3lh3 | 2009-06-25 21:04:34 +0100 (Thu, 25 Jun 2009) | 2 lines
395 M /trunk/samtools/bgzf.c
399 ------------------------------------------------------------------------
400 r361 | lh3lh3 | 2009-06-25 21:03:10 +0100 (Thu, 25 Jun 2009) | 3 lines
402 M /trunk/samtools/bam_index.c
403 M /trunk/samtools/bamtk.c
405 * samtools-0.1.4-17 (r361)
406 * if a file is given on FTP, search locally for the BAM index
408 ------------------------------------------------------------------------
409 r360 | lh3lh3 | 2009-06-25 20:44:52 +0100 (Thu, 25 Jun 2009) | 5 lines
411 M /trunk/samtools/Makefile
412 M /trunk/samtools/bam_import.c
413 M /trunk/samtools/bam_index.c
414 M /trunk/samtools/bamtk.c
415 M /trunk/samtools/bgzf.c
416 M /trunk/samtools/bgzf.h
417 M /trunk/samtools/knetfile.c
418 M /trunk/samtools/knetfile.h
420 * samtools-0.1.4-16 (r360)
421 * report more information in index when the input is not sorted
422 * change the behaviour of knet_seek() such that it returns 0 on success
423 * support knetfile library in BGZF
425 ------------------------------------------------------------------------
426 r359 | lh3lh3 | 2009-06-25 17:10:55 +0100 (Thu, 25 Jun 2009) | 2 lines
428 M /trunk/samtools/knetfile.c
429 M /trunk/samtools/knetfile.h
431 fixed bugs in knetfile.*
433 ------------------------------------------------------------------------
434 r358 | lh3lh3 | 2009-06-25 13:53:19 +0100 (Thu, 25 Jun 2009) | 2 lines
436 A /trunk/samtools/knetfile.h
438 this is the header file
440 ------------------------------------------------------------------------
441 r357 | lh3lh3 | 2009-06-25 13:52:03 +0100 (Thu, 25 Jun 2009) | 3 lines
443 A /trunk/samtools/knetfile.c
446 * preliminary version
448 ------------------------------------------------------------------------
449 r354 | lh3lh3 | 2009-06-24 14:02:25 +0100 (Wed, 24 Jun 2009) | 3 lines
451 M /trunk/samtools/bam.c
452 M /trunk/samtools/bamtk.c
454 * samtools-0.1.4-15 (r354)
455 * fixed a memory leak in bam_view1(), although samtools is not using this routine.
457 ------------------------------------------------------------------------
458 r351 | lh3lh3 | 2009-06-18 00:16:26 +0100 (Thu, 18 Jun 2009) | 4 lines
460 M /trunk/samtools/bamtk.c
461 M /trunk/samtools/faidx.c
463 * samtools-0.1.4-13 (r351)
464 * make faidx more tolerant to empty lines right before or after > lines
465 * hope this does not introduce new bugs...
467 ------------------------------------------------------------------------
468 r350 | lh3lh3 | 2009-06-16 14:37:01 +0100 (Tue, 16 Jun 2009) | 3 lines
470 M /trunk/samtools/bam_plcmd.c
471 M /trunk/samtools/bamtk.c
473 * samtools-0.1.4-13 (r350)
474 * fixed a small memory leak in pileup, caused by recent modifications
476 ------------------------------------------------------------------------
477 r347 | lh3lh3 | 2009-06-13 21:20:49 +0100 (Sat, 13 Jun 2009) | 3 lines
479 M /trunk/samtools/bam_plcmd.c
480 M /trunk/samtools/bamtk.c
481 M /trunk/samtools/sam_view.c
483 * samtools-0.1.4-12 (r347)
484 * added `-S' to pileup, similar to `view -S'
486 ------------------------------------------------------------------------
487 r346 | lh3lh3 | 2009-06-13 17:52:31 +0100 (Sat, 13 Jun 2009) | 3 lines
489 M /trunk/samtools/Makefile
490 M /trunk/samtools/bamtk.c
491 M /trunk/samtools/sam_view.c
492 M /trunk/samtools/samtools.1
494 * samtools-0.1.4-11 (r346)
495 * allow to select a read group at view command-line
497 ------------------------------------------------------------------------
498 r344 | lh3lh3 | 2009-06-13 14:06:24 +0100 (Sat, 13 Jun 2009) | 2 lines
500 M /trunk/samtools/examples/calDepth.c
504 ------------------------------------------------------------------------
505 r343 | lh3lh3 | 2009-06-13 14:01:22 +0100 (Sat, 13 Jun 2009) | 2 lines
507 M /trunk/samtools/examples/calDepth.c
511 ------------------------------------------------------------------------
512 r342 | lh3lh3 | 2009-06-13 13:58:48 +0100 (Sat, 13 Jun 2009) | 2 lines
514 M /trunk/samtools/examples/Makefile
515 A /trunk/samtools/examples/calDepth.c
517 added an example of calculating read depth
519 ------------------------------------------------------------------------
520 r341 | lh3lh3 | 2009-06-13 13:00:08 +0100 (Sat, 13 Jun 2009) | 6 lines
522 M /trunk/samtools/Makefile
523 M /trunk/samtools/bam.h
524 M /trunk/samtools/bam_aux.c
525 A /trunk/samtools/bam_color.c
526 M /trunk/samtools/bam_plcmd.c
527 M /trunk/samtools/bam_sort.c
528 M /trunk/samtools/bam_tview.c
529 M /trunk/samtools/bamtk.c
530 M /trunk/samtools/sam.c
531 M /trunk/samtools/sam.h
533 * samtools-0.1.4-10 (r341)
534 * only include key APIs in libbam.a
535 * move color-specific routines to bam_color.c
536 * update documentations
537 * remove the support of -q in pileup
539 ------------------------------------------------------------------------
540 r340 | lh3lh3 | 2009-06-13 11:17:14 +0100 (Sat, 13 Jun 2009) | 6 lines
542 M /trunk/samtools/INSTALL
543 M /trunk/samtools/Makefile
544 M /trunk/samtools/bam_aux.c
545 M /trunk/samtools/bam_import.c
546 M /trunk/samtools/bam_tview.c
547 M /trunk/samtools/bamtk.c
548 M /trunk/samtools/razf.c
549 M /trunk/samtools/sam_view.c
551 * samtools-0.1.4-9 (r340)
552 * added a warning to razf.c if zlib<1.2.2.1
553 * fixed a compilation warning
554 * fixed a segfault caused by @RG parsing
555 * detect NCURSES in bam_tview.c
557 ------------------------------------------------------------------------
558 r339 | lh3lh3 | 2009-06-13 10:35:19 +0100 (Sat, 13 Jun 2009) | 2 lines
560 M /trunk/samtools/INSTALL
564 ------------------------------------------------------------------------
565 r338 | lh3lh3 | 2009-06-13 00:15:24 +0100 (Sat, 13 Jun 2009) | 4 lines
567 M /trunk/samtools/bam.c
568 M /trunk/samtools/bam.h
569 M /trunk/samtools/bam_aux.c
570 M /trunk/samtools/bam_import.c
571 M /trunk/samtools/bamtk.c
572 M /trunk/samtools/kstring.h
573 M /trunk/samtools/sam.c
574 M /trunk/samtools/sam_view.c
576 * samtools-0.1.4-8 (r338)
577 * parse the @RG header lines and allow to choose library at the "samtools view"
580 ------------------------------------------------------------------------
581 r337 | lh3lh3 | 2009-06-12 21:25:50 +0100 (Fri, 12 Jun 2009) | 4 lines
583 M /trunk/samtools/bamtk.c
584 M /trunk/samtools/bgzf.c
585 M /trunk/samtools/bgzf.h
586 M /trunk/samtools/sam.c
587 M /trunk/samtools/sam_view.c
589 * samtools-0.1.4-7 (r337)
590 * bgzf.c: support mode string "wu": uncompressed output
591 * "samtools view" support "-u" command-line option
593 ------------------------------------------------------------------------
594 r336 | lh3lh3 | 2009-06-12 17:20:12 +0100 (Fri, 12 Jun 2009) | 5 lines
596 M /trunk/samtools/Makefile
597 M /trunk/samtools/misc/Makefile
598 M /trunk/samtools/razf.c
599 M /trunk/samtools/razf.h
600 M /trunk/samtools/razip.c
602 * no changes to samtools itself
603 * remove zlib source codes
604 * make RAZF reading compatible with old version of zlib
605 * on old version of zlib, writing is not available
607 ------------------------------------------------------------------------
608 r335 | lh3lh3 | 2009-06-12 16:47:33 +0100 (Fri, 12 Jun 2009) | 2 lines
610 D /trunk/samtools/zlib
612 remove zlib for simplification...
614 ------------------------------------------------------------------------
615 r334 | lh3lh3 | 2009-06-12 15:43:36 +0100 (Fri, 12 Jun 2009) | 5 lines
617 M /trunk/samtools/bam.h
618 M /trunk/samtools/bam_aux.c
619 M /trunk/samtools/bamtk.c
621 * samtools-0.1.4-6 (r334)
622 * do not export bam_aux_get_core() for Bio::DB::Sam because it has already
623 been implemented in that.
624 * this version works with the latest Bio::DB::Sam (20090612)
626 ------------------------------------------------------------------------
627 r333 | lh3lh3 | 2009-06-12 15:33:42 +0100 (Fri, 12 Jun 2009) | 2 lines
629 M /trunk/samtools/ChangeLog
633 ------------------------------------------------------------------------
634 r332 | lh3lh3 | 2009-06-12 15:21:21 +0100 (Fri, 12 Jun 2009) | 2 lines
636 M /trunk/samtools/AUTHORS
637 M /trunk/samtools/Makefile
638 M /trunk/samtools/misc/Makefile
640 fixed minor things in Makefile
642 ------------------------------------------------------------------------
643 r331 | lh3lh3 | 2009-06-12 15:07:05 +0100 (Fri, 12 Jun 2009) | 4 lines
645 M /trunk/samtools/bamtk.c
647 * samtools-0.1.4-5 (r3310
648 * no change to samtools itself. Version number is increased to reflect the
649 changes in the Makefile building system.
651 ------------------------------------------------------------------------
652 r330 | lh3lh3 | 2009-06-12 15:03:38 +0100 (Fri, 12 Jun 2009) | 2 lines
654 M /trunk/samtools/AUTHORS
655 D /trunk/samtools/README
657 update information...
659 ------------------------------------------------------------------------
660 r329 | lh3lh3 | 2009-06-12 14:52:21 +0100 (Fri, 12 Jun 2009) | 3 lines
662 M /trunk/samtools/misc/novo2sam.pl
664 * updated novoalign converter by Colin Hercus et al.
665 * this version works with indels
667 ------------------------------------------------------------------------
668 r328 | lh3lh3 | 2009-06-12 14:50:53 +0100 (Fri, 12 Jun 2009) | 3 lines
670 M /trunk/samtools/INSTALL
671 M /trunk/samtools/Makefile
672 M /trunk/samtools/misc/Makefile
673 M /trunk/samtools/zlib/Makefile
676 * update INSTALL instruction
678 ------------------------------------------------------------------------
679 r327 | lh3lh3 | 2009-06-12 14:18:29 +0100 (Fri, 12 Jun 2009) | 4 lines
681 A /trunk/samtools/Makefile (from /trunk/samtools/Makefile.generic:325)
682 D /trunk/samtools/Makefile.am
683 D /trunk/samtools/Makefile.generic
684 D /trunk/samtools/Makefile.lite
685 D /trunk/samtools/autogen.sh
686 D /trunk/samtools/cleanup.sh
687 D /trunk/samtools/configure.ac
688 A /trunk/samtools/misc/Makefile (from /trunk/samtools/misc/Makefile.generic:305)
689 D /trunk/samtools/misc/Makefile.am
690 D /trunk/samtools/misc/Makefile.generic
691 M /trunk/samtools/razf.c
692 A /trunk/samtools/zlib
693 A /trunk/samtools/zlib/Makefile
694 A /trunk/samtools/zlib/adler32.c
695 A /trunk/samtools/zlib/compress.c
696 A /trunk/samtools/zlib/crc32.c
697 A /trunk/samtools/zlib/crc32.h
698 A /trunk/samtools/zlib/deflate.c
699 A /trunk/samtools/zlib/deflate.h
700 A /trunk/samtools/zlib/gzio.c
701 A /trunk/samtools/zlib/infback.c
702 A /trunk/samtools/zlib/inffast.c
703 A /trunk/samtools/zlib/inffast.h
704 A /trunk/samtools/zlib/inffixed.h
705 A /trunk/samtools/zlib/inflate.c
706 A /trunk/samtools/zlib/inflate.h
707 A /trunk/samtools/zlib/inftrees.c
708 A /trunk/samtools/zlib/inftrees.h
709 A /trunk/samtools/zlib/trees.c
710 A /trunk/samtools/zlib/trees.h
711 A /trunk/samtools/zlib/uncompr.c
712 A /trunk/samtools/zlib/zconf.h
713 A /trunk/samtools/zlib/zlib.h
714 A /trunk/samtools/zlib/zutil.c
715 A /trunk/samtools/zlib/zutil.h
716 D /trunk/samtools/zutil.h
718 * added zlib-1.2.3 as razip requires that
719 * prepare to changed back to the Makefile building system
720 * unfinished! (will be soon)
722 ------------------------------------------------------------------------
723 r326 | lh3lh3 | 2009-06-12 14:12:03 +0100 (Fri, 12 Jun 2009) | 2 lines
725 M /trunk/samtools/misc/samtools.pl
729 ------------------------------------------------------------------------
730 r325 | lh3lh3 | 2009-06-10 16:27:59 +0100 (Wed, 10 Jun 2009) | 3 lines
732 M /trunk/samtools/bam_maqcns.c
733 M /trunk/samtools/bamtk.c
735 * samtools-0.1.4-4 (r325)
736 * further avoid wrong consensus calls in repetitive regions.
738 ------------------------------------------------------------------------
739 r324 | lh3lh3 | 2009-06-10 15:56:17 +0100 (Wed, 10 Jun 2009) | 4 lines
741 M /trunk/samtools/bam_maqcns.c
742 M /trunk/samtools/bam_plcmd.c
743 M /trunk/samtools/bamtk.c
744 M /trunk/samtools/sam.c
745 M /trunk/samtools/sam.h
747 * samtools-0.1.4-3 (r324)
748 * make maqcns generate the correct call in repetitive regions.
749 * allow filtering on mapQ at the pileup command line
751 ------------------------------------------------------------------------
752 r323 | lh3lh3 | 2009-06-10 10:04:21 +0100 (Wed, 10 Jun 2009) | 3 lines
754 M /trunk/samtools/misc/samtools.pl
756 * samtools.pl-0.3.2 (r322)
757 * indels and SNPs use different mapping quality threshold
759 ------------------------------------------------------------------------
760 r322 | lh3lh3 | 2009-06-10 10:03:22 +0100 (Wed, 10 Jun 2009) | 2 lines
762 M /trunk/samtools/misc/export2sam.pl
766 ------------------------------------------------------------------------
767 r321 | lh3lh3 | 2009-06-09 09:21:48 +0100 (Tue, 09 Jun 2009) | 2 lines
769 M /trunk/samtools/misc/samtools.pl
771 just typo. no real change
773 ------------------------------------------------------------------------
774 r320 | lh3lh3 | 2009-06-08 14:32:51 +0100 (Mon, 08 Jun 2009) | 2 lines
776 M /trunk/samtools/misc/samtools.pl
778 a little bit code cleanup
780 ------------------------------------------------------------------------
781 r319 | lh3lh3 | 2009-06-08 14:22:33 +0100 (Mon, 08 Jun 2009) | 4 lines
783 M /trunk/samtools/misc/samtools.pl
786 * change default parameters
787 * optionally print filtered variants
789 ------------------------------------------------------------------------
790 r318 | lh3lh3 | 2009-06-08 14:14:26 +0100 (Mon, 08 Jun 2009) | 3 lines
792 M /trunk/samtools/misc/samtools.pl
795 * combine snpFilter and indelFilter
797 ------------------------------------------------------------------------
798 r317 | lh3lh3 | 2009-06-08 11:31:42 +0100 (Mon, 08 Jun 2009) | 3 lines
800 M /trunk/samtools/misc/samtools.pl
803 * change a default parameter
805 ------------------------------------------------------------------------
806 r316 | lh3lh3 | 2009-06-08 11:11:06 +0100 (Mon, 08 Jun 2009) | 5 lines
808 M /trunk/samtools/bam_maqcns.c
809 M /trunk/samtools/bam_maqcns.h
810 M /trunk/samtools/bam_plcmd.c
811 M /trunk/samtools/bamtk.c
812 M /trunk/samtools/sam.c
814 * samtools-0.1.4-2 (r316)
815 * pileup: cap mapping quality at 60 (by default)
816 * pileup: always calculate RMS mapq
817 * pileup: allow to output variant sites only
819 ------------------------------------------------------------------------
820 r312 | lh3lh3 | 2009-06-04 13:01:10 +0100 (Thu, 04 Jun 2009) | 3 lines
822 M /trunk/samtools/misc/samtools.pl
827 ------------------------------------------------------------------------
828 r311 | lh3lh3 | 2009-06-03 09:40:40 +0100 (Wed, 03 Jun 2009) | 2 lines
830 M /trunk/samtools/misc/samtools.pl
832 * in snpFilter, suppress non-SNP sites
834 ------------------------------------------------------------------------
835 r310 | lh3lh3 | 2009-06-01 14:35:13 +0100 (Mon, 01 Jun 2009) | 3 lines
837 M /trunk/samtools/misc/samtools.pl
842 ------------------------------------------------------------------------
843 r309 | lh3lh3 | 2009-06-01 14:04:39 +0100 (Mon, 01 Jun 2009) | 3 lines
845 M /trunk/samtools/misc/samtools.pl
850 ------------------------------------------------------------------------
851 r306 | lh3lh3 | 2009-05-28 11:49:35 +0100 (Thu, 28 May 2009) | 3 lines
853 M /trunk/samtools/bgzf.c
855 * minor changes to bgzf: return NULL if fd == -1
856 * suggested by {kdj,jm18}@sanger.ac.uk
858 ------------------------------------------------------------------------
859 r305 | lh3lh3 | 2009-05-28 11:16:08 +0100 (Thu, 28 May 2009) | 2 lines
861 A /trunk/samtools/misc/interpolate_sam.pl
863 Script for paired-end pileup, contributed by Stephen Montgomery.
865 ------------------------------------------------------------------------
866 r304 | lh3lh3 | 2009-05-28 11:08:49 +0100 (Thu, 28 May 2009) | 3 lines
868 M /trunk/samtools/bamtk.c
869 M /trunk/samtools/sam.c
871 * samtools-0.1.4-1 (r304)
872 * fixed a minor bug in printing headers
874 ------------------------------------------------------------------------
875 r297 | lh3lh3 | 2009-05-21 16:06:16 +0100 (Thu, 21 May 2009) | 2 lines
877 M /trunk/samtools/ChangeLog
878 M /trunk/samtools/NEWS
879 M /trunk/samtools/bam_plcmd.c
880 M /trunk/samtools/bamtk.c
881 M /trunk/samtools/misc/maq2sam.c
882 M /trunk/samtools/samtools.1
884 Release samtools-0.1.4
886 ------------------------------------------------------------------------
887 r296 | lh3lh3 | 2009-05-21 12:53:14 +0100 (Thu, 21 May 2009) | 3 lines
889 M /trunk/samtools/bam_maqcns.c
890 M /trunk/samtools/bamtk.c
892 * samtools-0.1.3-24 (r296)
893 * another similar bug in the indel caller
895 ------------------------------------------------------------------------
896 r295 | lh3lh3 | 2009-05-21 12:50:28 +0100 (Thu, 21 May 2009) | 3 lines
898 M /trunk/samtools/bam_maqcns.c
899 M /trunk/samtools/bamtk.c
901 * samtools-0.1.3-23 (r295)
902 * fixed a critical bug in the indel caller
904 ------------------------------------------------------------------------
905 r294 | lh3lh3 | 2009-05-20 13:00:20 +0100 (Wed, 20 May 2009) | 2 lines
907 M /trunk/samtools/bam_stat.c
909 added a missing header file
911 ------------------------------------------------------------------------
912 r293 | lh3lh3 | 2009-05-19 23:44:25 +0100 (Tue, 19 May 2009) | 3 lines
914 M /trunk/samtools/bam_tview.c
915 M /trunk/samtools/bamtk.c
917 * samtools-0.1.3-22 (r293)
918 * open tview in the dot-view mode by default
920 ------------------------------------------------------------------------
921 r292 | lh3lh3 | 2009-05-18 21:01:23 +0100 (Mon, 18 May 2009) | 6 lines
923 M /trunk/samtools/samtools.1
925 Added a note to the manual. Currently SAMtools used unaligned words in
926 several places. Although this does not cause bus errors to me, it may
927 affect portability. Please see the "Bus error" wiki page for more
928 information. Also thank James Bonfields for pointing this out.
931 ------------------------------------------------------------------------
932 r286 | lh3lh3 | 2009-05-14 15:23:13 +0100 (Thu, 14 May 2009) | 3 lines
934 M /trunk/samtools/bam.h
935 M /trunk/samtools/bam_aux.c
936 M /trunk/samtools/bamtk.c
938 * samtools-0.1.3-21 (286)
939 * declare bam_aux_get_core() in bam.h
941 ------------------------------------------------------------------------
942 r276 | lh3lh3 | 2009-05-13 10:07:55 +0100 (Wed, 13 May 2009) | 5 lines
944 M /trunk/samtools/bam.h
945 M /trunk/samtools/bam_index.c
946 M /trunk/samtools/bamtk.c
948 * samtools-0.1.3-20 (r276)
949 * remove bam1_t::hash again. We need to modify the Perl API anyway to
950 make it work with the latest SVN.
951 * As is suggested by Tim, scan "{base}.bai" and "{base}.bam.bai" for index
953 ------------------------------------------------------------------------
954 r275 | lh3lh3 | 2009-05-12 21:14:10 +0100 (Tue, 12 May 2009) | 4 lines
956 M /trunk/samtools/ChangeLog
957 M /trunk/samtools/bam.h
958 M /trunk/samtools/bamtk.c
960 * samtools-0.1.3-19 (r275)
961 * a minor change to the bam1_t struct: added back "void *hash" for the
962 backward compatibility with Bio::DB::Sam
964 ------------------------------------------------------------------------
965 r273 | lh3lh3 | 2009-05-12 14:28:39 +0100 (Tue, 12 May 2009) | 3 lines
967 M /trunk/samtools/bam_rmdupse.c
968 M /trunk/samtools/bamtk.c
970 * samtools-0.1.3-18 (r273)
971 * rmdupse: do not remove unmapped reads
973 ------------------------------------------------------------------------
974 r272 | lh3lh3 | 2009-05-12 14:20:00 +0100 (Tue, 12 May 2009) | 2 lines
976 M /trunk/samtools/bam_rmdupse.c
978 change a parameter. It does nothing
980 ------------------------------------------------------------------------
981 r271 | lh3lh3 | 2009-05-12 14:17:58 +0100 (Tue, 12 May 2009) | 3 lines
983 M /trunk/samtools/Makefile.am
984 M /trunk/samtools/Makefile.generic
985 M /trunk/samtools/Makefile.lite
986 A /trunk/samtools/bam_rmdupse.c
987 M /trunk/samtools/bamtk.c
988 M /trunk/samtools/configure.ac
990 * samtools-0.1.3-17 (r271)
991 * added 'rmdupse' command
993 ------------------------------------------------------------------------
994 r267 | lh3lh3 | 2009-05-05 22:31:41 +0100 (Tue, 05 May 2009) | 3 lines
996 M /trunk/samtools/bamtk.c
997 M /trunk/samtools/sam_view.c
999 * samtools-0.1.3-16 (r267)
1000 * in sam_view.c, changed g_flag_on based on the suggestion by Angie Hinrichs
1002 ------------------------------------------------------------------------
1003 r266 | lh3lh3 | 2009-05-05 22:23:27 +0100 (Tue, 05 May 2009) | 3 lines
1005 M /trunk/samtools/bam_import.c
1006 M /trunk/samtools/bamtk.c
1008 * samtools-0.1.3-15 (r266)
1009 * report an error if a non-* reference is present while @SQ is absent
1011 ------------------------------------------------------------------------
1012 r265 | lh3lh3 | 2009-05-05 22:09:00 +0100 (Tue, 05 May 2009) | 3 lines
1014 M /trunk/samtools/bam.h
1015 M /trunk/samtools/bam_import.c
1016 M /trunk/samtools/bamtk.c
1017 M /trunk/samtools/sam.c
1018 M /trunk/samtools/sam_view.c
1020 * samtools-0.1.3-14 (r262)
1021 * make samopen() recognize @SQ header lines
1023 ------------------------------------------------------------------------
1024 r261 | lh3lh3 | 2009-05-05 15:10:30 +0100 (Tue, 05 May 2009) | 3 lines
1026 M /trunk/samtools/bam_plcmd.c
1027 M /trunk/samtools/bamtk.c
1028 M /trunk/samtools/bgzf.c
1029 M /trunk/samtools/sam.c
1030 M /trunk/samtools/sam_view.c
1032 * samtools-0.1.3-13 (r260)
1033 * report error for file I/O error
1035 ------------------------------------------------------------------------
1036 r260 | lh3lh3 | 2009-05-05 15:01:16 +0100 (Tue, 05 May 2009) | 2 lines
1038 M /trunk/samtools/Makefile.am
1042 ------------------------------------------------------------------------
1043 r259 | lh3lh3 | 2009-05-05 14:52:25 +0100 (Tue, 05 May 2009) | 3 lines
1045 M /trunk/samtools/bam.h
1046 M /trunk/samtools/bam_pileup.c
1047 M /trunk/samtools/bam_plcmd.c
1048 M /trunk/samtools/bamtk.c
1049 M /trunk/samtools/sam.c
1050 M /trunk/samtools/sam.h
1052 * samtools-0.1.3-12 (r259)
1053 * use the new I/O interface in pileup
1055 ------------------------------------------------------------------------
1056 r258 | lh3lh3 | 2009-05-05 14:33:22 +0100 (Tue, 05 May 2009) | 3 lines
1058 M /trunk/samtools/Makefile.generic
1059 M /trunk/samtools/Makefile.lite
1060 M /trunk/samtools/bam.c
1061 M /trunk/samtools/bam.h
1062 M /trunk/samtools/bam_import.c
1063 M /trunk/samtools/bamtk.c
1064 A /trunk/samtools/sam.c
1065 A /trunk/samtools/sam.h
1066 A /trunk/samtools/sam_view.c
1068 * samtools-0.1.3-11 (r258)
1069 * unify the interface to BAM and SAM I/O
1071 ------------------------------------------------------------------------
1072 r257 | lh3lh3 | 2009-05-05 09:53:35 +0100 (Tue, 05 May 2009) | 3 lines
1074 M /trunk/samtools/Makefile.lite
1075 M /trunk/samtools/bam_plcmd.c
1076 M /trunk/samtools/bamtk.c
1078 * samtools-0.1.3-10 (r257)
1079 * allow hex with "pileup -m"
1081 ------------------------------------------------------------------------
1082 r256 | lh3lh3 | 2009-05-04 19:16:50 +0100 (Mon, 04 May 2009) | 4 lines
1084 M /trunk/samtools/bam_lpileup.c
1085 M /trunk/samtools/bamtk.c
1087 * samtools-0.1.3-9 (r256)
1088 * fixed a bug in bam_lpileup.c
1089 * I do not know if this also fixes the bug causing assertion failure in the tview
1091 ------------------------------------------------------------------------
1092 r251 | lh3lh3 | 2009-04-28 13:53:23 +0100 (Tue, 28 Apr 2009) | 3 lines
1094 M /trunk/samtools/bam_pileup.c
1095 M /trunk/samtools/bamtk.c
1097 * samtools-0.1.3-8 (r251)
1098 * fixed a bug when there are reads without coordinates
1100 ------------------------------------------------------------------------
1101 r250 | lh3lh3 | 2009-04-28 13:43:33 +0100 (Tue, 28 Apr 2009) | 2 lines
1103 A /trunk/samtools/AUTHORS
1104 A /trunk/samtools/README
1105 M /trunk/samtools/cleanup.sh
1109 ------------------------------------------------------------------------
1110 r249 | lh3lh3 | 2009-04-28 13:37:16 +0100 (Tue, 28 Apr 2009) | 2 lines
1112 M /trunk/samtools/Makefile.generic
1113 M /trunk/samtools/Makefile.lite
1114 M /trunk/samtools/configure.ac
1115 M /trunk/samtools/misc/Makefile.generic
1117 improve large file support in compilation
1119 ------------------------------------------------------------------------
1120 r248 | lh3lh3 | 2009-04-28 13:33:24 +0100 (Tue, 28 Apr 2009) | 2 lines
1122 M /trunk/samtools/INSTALL
1126 ------------------------------------------------------------------------
1127 r247 | lh3lh3 | 2009-04-28 13:28:50 +0100 (Tue, 28 Apr 2009) | 2 lines
1129 M /trunk/samtools/Makefile.am
1130 M /trunk/samtools/autogen.sh
1131 M /trunk/samtools/cleanup.sh
1132 M /trunk/samtools/configure.ac
1133 A /trunk/samtools/misc/Makefile.am
1135 fixed various issues about the GNU building scripts
1137 ------------------------------------------------------------------------
1138 r246 | lh3lh3 | 2009-04-28 13:10:23 +0100 (Tue, 28 Apr 2009) | 4 lines
1140 M /trunk/samtools/ChangeLog
1141 D /trunk/samtools/Makefile
1142 A /trunk/samtools/Makefile.am
1143 A /trunk/samtools/Makefile.generic
1144 A /trunk/samtools/autogen.sh
1145 M /trunk/samtools/bam.h
1146 M /trunk/samtools/bam_aux.c
1147 M /trunk/samtools/bam_tview.c
1148 M /trunk/samtools/bamtk.c
1149 A /trunk/samtools/cleanup.sh
1150 A /trunk/samtools/configure.ac
1151 D /trunk/samtools/misc/Makefile
1152 A /trunk/samtools/misc/Makefile.generic (from /trunk/samtools/misc/Makefile:245)
1154 * samtools-0.1.3-7 (r246)
1155 * incorporated revisions from Nils Homer
1156 * enhanced support of displaying color-space reads
1158 ------------------------------------------------------------------------
1159 r244 | lh3lh3 | 2009-04-25 11:49:40 +0100 (Sat, 25 Apr 2009) | 3 lines
1161 M /trunk/samtools/bam_md.c
1162 M /trunk/samtools/bamtk.c
1164 * samtools-0.1.3-6 (r244)
1165 * fixed segfault for unmapped reads
1167 ------------------------------------------------------------------------
1168 r243 | lh3lh3 | 2009-04-24 21:27:26 +0100 (Fri, 24 Apr 2009) | 5 lines
1170 M /trunk/samtools/bam.h
1171 M /trunk/samtools/bam_maqcns.c
1172 M /trunk/samtools/bam_md.c
1173 M /trunk/samtools/bamtk.c
1175 * samtools-0.1.3-5 (r243)
1176 * fixed a long existing bug which may cause memory leak
1178 * consensus calling now works with "=", but indel calling not
1180 ------------------------------------------------------------------------
1181 r242 | lh3lh3 | 2009-04-24 20:44:46 +0100 (Fri, 24 Apr 2009) | 3 lines
1183 M /trunk/samtools/bam_md.c
1184 M /trunk/samtools/bamtk.c
1186 * samtools-0.1.3-4 (r242)
1187 * fixed a memory leak
1189 ------------------------------------------------------------------------
1190 r240 | lh3lh3 | 2009-04-24 16:40:18 +0100 (Fri, 24 Apr 2009) | 5 lines
1192 M /trunk/samtools/Makefile
1193 M /trunk/samtools/Makefile.lite
1194 M /trunk/samtools/bam.h
1195 M /trunk/samtools/bam_aux.c
1196 A /trunk/samtools/bam_md.c
1197 M /trunk/samtools/bam_plcmd.c
1198 M /trunk/samtools/bamtk.c
1200 * samtools-0.1.3-3 (r240)
1202 * generate "=" bases
1203 * the plain pileup now support "=" bases, but consensus calling and glfgen may fail
1205 ------------------------------------------------------------------------
1206 r239 | lh3lh3 | 2009-04-24 12:08:20 +0100 (Fri, 24 Apr 2009) | 5 lines
1208 M /trunk/samtools/bam.h
1209 M /trunk/samtools/bam_aux.c
1210 M /trunk/samtools/bamtk.c
1212 * samtools-0.1.3-2 (r239)
1213 * fixed bugs in bam_aux.c (these functions nevered used by samtools)
1214 * removed bam_aux_init()/bam_aux_destroy()
1215 * added tagview for testing bam_aux
1217 ------------------------------------------------------------------------
1218 r235 | lh3lh3 | 2009-04-21 23:17:39 +0100 (Tue, 21 Apr 2009) | 3 lines
1220 M /trunk/samtools/bam_pileup.c
1221 M /trunk/samtools/bamtk.c
1224 * fixed a bug in pileup: the first read in a chromosome may not be printed
1226 ------------------------------------------------------------------------
1227 r232 | lh3lh3 | 2009-04-16 15:25:43 +0100 (Thu, 16 Apr 2009) | 2 lines
1229 M /trunk/samtools/Makefile.lite
1231 a missing file in Makefile.lite
1233 ------------------------------------------------------------------------
1234 r227 | lh3lh3 | 2009-04-15 22:02:53 +0100 (Wed, 15 Apr 2009) | 2 lines
1236 M /trunk/samtools/NEWS
1237 M /trunk/samtools/bamtk.c
1239 Release samtools-0.1.3
1241 ------------------------------------------------------------------------
1242 r223 | lh3lh3 | 2009-04-15 14:31:32 +0100 (Wed, 15 Apr 2009) | 3 lines
1244 M /trunk/samtools/bam_plcmd.c
1245 M /trunk/samtools/bamtk.c
1248 * make samtools more robust to weird input such as empty file
1250 ------------------------------------------------------------------------
1251 r222 | lh3lh3 | 2009-04-15 14:05:33 +0100 (Wed, 15 Apr 2009) | 2 lines
1253 M /trunk/samtools/ChangeLog
1254 M /trunk/samtools/NEWS
1255 M /trunk/samtools/samtools.1
1257 prepare for release 0.1.3
1259 ------------------------------------------------------------------------
1260 r221 | lh3lh3 | 2009-04-15 13:32:14 +0100 (Wed, 15 Apr 2009) | 2 lines
1262 A /trunk/samtools/misc/blast2sam.pl
1264 convert NCBI-BLASTN to SAM
1266 ------------------------------------------------------------------------
1267 r220 | lh3lh3 | 2009-04-15 13:18:19 +0100 (Wed, 15 Apr 2009) | 3 lines
1269 M /trunk/samtools/bam_lpileup.c
1270 M /trunk/samtools/bamtk.c
1273 * fixed a small memory leak in tview
1275 ------------------------------------------------------------------------
1276 r219 | lh3lh3 | 2009-04-15 13:00:08 +0100 (Wed, 15 Apr 2009) | 3 lines
1278 M /trunk/samtools/bam_rmdup.c
1279 M /trunk/samtools/bamtk.c
1282 * fixed a bug in rmdup when there are unmapped reads
1284 ------------------------------------------------------------------------
1285 r218 | lh3lh3 | 2009-04-14 22:28:58 +0100 (Tue, 14 Apr 2009) | 2 lines
1287 M /trunk/samtools/ChangeLog
1288 M /trunk/samtools/NEWS
1290 proposed NEWS for the new release (have not yet)
1292 ------------------------------------------------------------------------
1293 r216 | lh3lh3 | 2009-04-14 22:10:46 +0100 (Tue, 14 Apr 2009) | 4 lines
1295 M /trunk/samtools/misc/samtools.pl
1298 * improve indelFilter to avoid filtering true indels. The new filter relies
1299 on the new pileup indel line implemented in samtools-0.1.2-25
1301 ------------------------------------------------------------------------
1302 r215 | lh3lh3 | 2009-04-14 22:04:19 +0100 (Tue, 14 Apr 2009) | 4 lines
1304 M /trunk/samtools/bam_maqcns.c
1305 M /trunk/samtools/bam_plcmd.c
1306 M /trunk/samtools/bamtk.c
1307 M /trunk/samtools/samtools.1
1310 * change the pileup indel line to shows the number of alignments actually
1313 ------------------------------------------------------------------------
1314 r211 | lh3lh3 | 2009-04-13 12:07:13 +0100 (Mon, 13 Apr 2009) | 2 lines
1316 M /trunk/samtools/ChangeLog
1318 update ChangeLog from "svn log"
1320 ------------------------------------------------------------------------
1321 r210 | lh3lh3 | 2009-04-12 20:57:05 +0100 (Sun, 12 Apr 2009) | 4 lines
1323 M /trunk/samtools/bam.c
1324 M /trunk/samtools/bam_import.c
1325 M /trunk/samtools/bam_sort.c
1326 M /trunk/samtools/bamtk.c
1327 M /trunk/samtools/kseq.h
1330 * in merge, gives a warning rather than error if the target sequence length is different
1331 * allow empty header
1333 ------------------------------------------------------------------------
1334 r209 | lh3lh3 | 2009-04-12 20:32:44 +0100 (Sun, 12 Apr 2009) | 3 lines
1336 M /trunk/samtools/bam.c
1337 M /trunk/samtools/bam_import.c
1338 M /trunk/samtools/bamtk.c
1341 * recognize '*' at the QUAL field
1343 ------------------------------------------------------------------------
1344 r208 | lh3lh3 | 2009-04-12 20:08:02 +0100 (Sun, 12 Apr 2009) | 3 lines
1346 M /trunk/samtools/bam_import.c
1347 M /trunk/samtools/bamtk.c
1348 M /trunk/samtools/kseq.h
1351 * the field separater is TAB only, now
1353 ------------------------------------------------------------------------
1354 r207 | lh3lh3 | 2009-04-08 15:18:03 +0100 (Wed, 08 Apr 2009) | 2 lines
1356 M /trunk/samtools/examples/ex1.sam.gz
1358 * fixed the problem in the example alignment due to the bug in fixmate
1360 ------------------------------------------------------------------------
1361 r206 | lh3lh3 | 2009-04-08 15:15:05 +0100 (Wed, 08 Apr 2009) | 3 lines
1363 M /trunk/samtools/bam_mate.c
1364 M /trunk/samtools/bamtk.c
1365 M /trunk/samtools/misc/soap2sam.pl
1368 * fixed a nasty bug in `fixmate'
1370 ------------------------------------------------------------------------
1371 r205 | lh3lh3 | 2009-04-08 10:57:08 +0100 (Wed, 08 Apr 2009) | 2 lines
1373 M /trunk/samtools/misc/bowtie2sam.pl
1374 M /trunk/samtools/misc/soap2sam.pl
1375 M /trunk/samtools/misc/wgsim_eval.pl
1377 make the script robust to the bugs in SOAP-2.1.7
1379 ------------------------------------------------------------------------
1380 r200 | lh3lh3 | 2009-04-02 15:14:56 +0100 (Thu, 02 Apr 2009) | 3 lines
1382 M /trunk/samtools/bam_stat.c
1383 M /trunk/samtools/bamtk.c
1386 * check if file is truncated in flagstat
1388 ------------------------------------------------------------------------
1389 r199 | lh3lh3 | 2009-04-02 15:09:10 +0100 (Thu, 02 Apr 2009) | 3 lines
1391 M /trunk/samtools/bamtk.c
1394 * print the header if requested
1396 ------------------------------------------------------------------------
1397 r193 | lh3lh3 | 2009-03-27 15:09:50 +0000 (Fri, 27 Mar 2009) | 3 lines
1399 M /trunk/samtools/bam_plcmd.c
1400 M /trunk/samtools/bamtk.c
1403 * fixed a minor bug reported by Nils Homer
1405 ------------------------------------------------------------------------
1406 r185 | lh3lh3 | 2009-03-24 11:50:32 +0000 (Tue, 24 Mar 2009) | 2 lines
1408 A /trunk/samtools/Makefile (from /trunk/samtools/Makefile.std:184)
1409 D /trunk/samtools/Makefile.std
1410 A /trunk/samtools/misc/Makefile (from /trunk/samtools/misc/Makefile.std:184)
1411 D /trunk/samtools/misc/Makefile.std
1413 rename Makefile.std as Makefile. GNU building systerm is not ready and may take some time...
1415 ------------------------------------------------------------------------
1416 r184 | lh3lh3 | 2009-03-24 10:36:38 +0000 (Tue, 24 Mar 2009) | 4 lines
1418 D /trunk/samtools/Makefile
1419 A /trunk/samtools/Makefile.std (from /trunk/samtools/Makefile:183)
1420 M /trunk/samtools/bam_sort.c
1421 M /trunk/samtools/bam_tview.c
1422 M /trunk/samtools/bamtk.c
1423 D /trunk/samtools/misc/Makefile
1424 A /trunk/samtools/misc/Makefile.std (from /trunk/samtools/misc/Makefile:182)
1425 M /trunk/samtools/samtools.1
1428 * incorporating Nils' changes
1429 * rename Makefile to Makefile.std and prepare to add the GNU building systerms (also by Nils)
1431 ------------------------------------------------------------------------
1432 r183 | lh3lh3 | 2009-03-24 10:30:23 +0000 (Tue, 24 Mar 2009) | 4 lines
1434 M /trunk/samtools/Makefile
1435 M /trunk/samtools/bam_import.c
1436 M /trunk/samtools/bam_maqcns.c
1437 M /trunk/samtools/bam_maqcns.h
1438 M /trunk/samtools/bam_plcmd.c
1439 M /trunk/samtools/bamtk.c
1440 M /trunk/samtools/kseq.h
1441 A /trunk/samtools/kstring.c
1442 A /trunk/samtools/kstring.h
1445 * made pileup take a list of proposed indels. An insertion is N at the moment.
1446 * added my kstring library for a bit complex parsing of the position list.
1448 ------------------------------------------------------------------------
1449 r169 | lh3lh3 | 2009-03-12 13:40:14 +0000 (Thu, 12 Mar 2009) | 3 lines
1451 M /trunk/samtools/misc/soap2sam.pl
1454 * more robust to truncated soap output
1456 ------------------------------------------------------------------------
1457 r168 | lh3lh3 | 2009-03-11 10:49:00 +0000 (Wed, 11 Mar 2009) | 2 lines
1459 M /trunk/samtools/Makefile.lite
1461 added bam_stat.o to Makefile.lite
1463 ------------------------------------------------------------------------
1464 r167 | lh3lh3 | 2009-03-10 22:11:31 +0000 (Tue, 10 Mar 2009) | 3 lines
1466 M /trunk/samtools/bam_maqcns.c
1467 M /trunk/samtools/bamtk.c
1470 * generate RMS of mapQ instead of max mapQ
1472 ------------------------------------------------------------------------
1473 r166 | lh3lh3 | 2009-03-10 22:06:45 +0000 (Tue, 10 Mar 2009) | 3 lines
1475 M /trunk/samtools/bam_plcmd.c
1476 M /trunk/samtools/bamtk.c
1477 M /trunk/samtools/glf.c
1478 M /trunk/samtools/glf.h
1479 M /trunk/samtools/misc/Makefile
1484 ------------------------------------------------------------------------
1485 r159 | lh3lh3 | 2009-03-03 11:26:08 +0000 (Tue, 03 Mar 2009) | 3 lines
1487 M /trunk/samtools/bam_plcmd.c
1488 M /trunk/samtools/bamtk.c
1491 * fixed a minor bug in displaying pileup
1493 ------------------------------------------------------------------------
1494 r158 | lh3lh3 | 2009-03-03 11:24:16 +0000 (Tue, 03 Mar 2009) | 3 lines
1496 M /trunk/samtools/ChangeLog
1497 M /trunk/samtools/bamtk.c
1500 * optionally print SAM header
1502 ------------------------------------------------------------------------
1503 r153 | lh3lh3 | 2009-03-02 10:45:28 +0000 (Mon, 02 Mar 2009) | 3 lines
1505 M /trunk/samtools/bamtk.c
1506 M /trunk/samtools/glf.c
1509 * use "GLF\3" as the magic for GLFv3 files
1511 ------------------------------------------------------------------------
1512 r152 | lh3lh3 | 2009-03-02 10:39:09 +0000 (Mon, 02 Mar 2009) | 5 lines
1514 M /trunk/samtools/Makefile
1515 M /trunk/samtools/bam_import.c
1516 M /trunk/samtools/bam_index.c
1517 M /trunk/samtools/bam_plcmd.c
1518 M /trunk/samtools/bamtk.c
1519 M /trunk/samtools/glf.c
1520 M /trunk/samtools/glf.h
1523 * fixed a bug in import: core.bin is undefined for unmapped reads
1524 * this bug can be alleviated (not completely solved) in bam_index.c
1525 * update to GLFv3: pos is changed to offset for better compression
1527 ------------------------------------------------------------------------
1528 r151 | lh3lh3 | 2009-03-01 15:18:43 +0000 (Sun, 01 Mar 2009) | 3 lines
1530 M /trunk/samtools/misc/wgsim.c
1533 * fixed a bug in simulating indels
1535 ------------------------------------------------------------------------
1536 r145 | lh3lh3 | 2009-02-26 19:43:57 +0000 (Thu, 26 Feb 2009) | 4 lines
1538 M /trunk/samtools/misc/wgsim.c
1541 * allow to print mismatch information as fastq comment. MAQ does
1542 not like long read names.
1544 ------------------------------------------------------------------------
1545 r141 | lh3lh3 | 2009-02-26 14:53:03 +0000 (Thu, 26 Feb 2009) | 6 lines
1547 M /trunk/samtools/ChangeLog
1548 M /trunk/samtools/misc/wgsim.c
1549 M /trunk/samtools/misc/wgsim_eval.pl
1552 * fixed a bug about color read coordinates
1553 * fixed a bug in read names
1554 * wgsim_eval.pl-0.1.3
1555 * make the script work with color reads
1557 ------------------------------------------------------------------------
1558 r140 | lh3lh3 | 2009-02-26 14:02:57 +0000 (Thu, 26 Feb 2009) | 2 lines
1560 M /trunk/samtools/misc/Makefile
1561 M /trunk/samtools/misc/wgsim.c
1563 * wgsim: added a note
1565 ------------------------------------------------------------------------
1566 r139 | lh3lh3 | 2009-02-26 11:39:08 +0000 (Thu, 26 Feb 2009) | 7 lines
1568 M /trunk/samtools/misc/wgsim.c
1569 M /trunk/samtools/misc/wgsim_eval.pl
1572 * considerable code clean up
1573 * print number of substitutions/indels/errors on each read
1574 * potentially support SOLiD simulation, though not tested at the moment
1575 * wgsim_eval.pl-0.1.2
1576 * change in accordant with wgsim
1578 ------------------------------------------------------------------------
1579 r129 | lh3lh3 | 2009-02-18 22:23:27 +0000 (Wed, 18 Feb 2009) | 3 lines
1581 M /trunk/samtools/bam_index.c
1582 M /trunk/samtools/bamtk.c
1585 * fixed a bug in bam_fetch, caused by completely contained adjacent chunks
1587 ------------------------------------------------------------------------
1588 r128 | bhandsaker | 2009-02-18 19:06:57 +0000 (Wed, 18 Feb 2009) | 2 lines
1590 M /trunk/samtools/bamtk.c
1592 Fix annoying segv when invalid region specified.
1594 ------------------------------------------------------------------------
1595 r127 | lh3lh3 | 2009-02-17 10:49:55 +0000 (Tue, 17 Feb 2009) | 2 lines
1597 D /trunk/samtools/misc/indel_filter.pl
1598 A /trunk/samtools/misc/samtools.pl
1600 * move indel_filter.pl to samtools.pl
1602 ------------------------------------------------------------------------
1603 r126 | lh3lh3 | 2009-02-14 21:22:30 +0000 (Sat, 14 Feb 2009) | 3 lines
1605 M /trunk/samtools/bam_mate.c
1606 M /trunk/samtools/bamtk.c
1609 * fixed a bug in fixmate: SE reads are flagged as BAM_FMUNMAP
1611 ------------------------------------------------------------------------
1612 r125 | lh3lh3 | 2009-02-13 09:54:45 +0000 (Fri, 13 Feb 2009) | 3 lines
1614 M /trunk/samtools/bam_stat.c
1615 M /trunk/samtools/bamtk.c
1618 * fixed a minor bug in flagstat
1620 ------------------------------------------------------------------------
1621 r124 | lh3lh3 | 2009-02-12 11:15:32 +0000 (Thu, 12 Feb 2009) | 3 lines
1623 M /trunk/samtools/bam_maqcns.c
1624 M /trunk/samtools/bamtk.c
1625 M /trunk/samtools/misc/indel_filter.pl
1628 * improve indel caller by setting maximum window size
1630 ------------------------------------------------------------------------
1631 r123 | lh3lh3 | 2009-02-12 10:30:29 +0000 (Thu, 12 Feb 2009) | 2 lines
1633 M /trunk/samtools/bam_plcmd.c
1634 M /trunk/samtools/bamtk.c
1636 * output max mapping quality in indel line
1638 ------------------------------------------------------------------------
1639 r122 | lh3lh3 | 2009-02-11 10:59:10 +0000 (Wed, 11 Feb 2009) | 2 lines
1641 M /trunk/samtools/misc/maq2sam.c
1643 fixed a bug in generating tag AM
1645 ------------------------------------------------------------------------
1646 r121 | lh3lh3 | 2009-02-03 10:43:11 +0000 (Tue, 03 Feb 2009) | 2 lines
1648 M /trunk/samtools/bam_index.c
1649 M /trunk/samtools/bamtk.c
1651 fixed a potential memory problem in indexing
1653 ------------------------------------------------------------------------
1654 r120 | bhandsaker | 2009-02-02 15:52:52 +0000 (Mon, 02 Feb 2009) | 2 lines
1656 M /trunk/samtools/Makefile
1658 Pass LIBS to recursive targets to facilitate building at Broad.
1660 ------------------------------------------------------------------------
1661 r119 | lh3lh3 | 2009-02-02 10:12:15 +0000 (Mon, 02 Feb 2009) | 4 lines
1663 M /trunk/samtools/ChangeLog
1664 M /trunk/samtools/bam_plcmd.c
1665 M /trunk/samtools/bam_stat.c
1666 M /trunk/samtools/bamtk.c
1669 * fixed a bug in generating GLFv2 for indels
1670 * improve flagstat report a little bit
1672 ------------------------------------------------------------------------
1673 r118 | lh3lh3 | 2009-01-29 12:33:23 +0000 (Thu, 29 Jan 2009) | 3 lines
1675 M /trunk/samtools/Makefile
1676 A /trunk/samtools/bam_stat.c
1677 M /trunk/samtools/bamtk.c
1680 * added flagstat command
1682 ------------------------------------------------------------------------
1683 r116 | lh3lh3 | 2009-01-28 13:31:12 +0000 (Wed, 28 Jan 2009) | 2 lines
1685 M /trunk/samtools/ChangeLog
1686 M /trunk/samtools/NEWS
1687 M /trunk/samtools/bamtk.c
1688 M /trunk/samtools/samtools.1
1690 Release SAMtools-0.1.2
1692 ------------------------------------------------------------------------
1693 r115 | lh3lh3 | 2009-01-28 12:54:08 +0000 (Wed, 28 Jan 2009) | 2 lines
1695 A /trunk/samtools/misc/indel_filter.pl
1697 Script for filtering indel results
1699 ------------------------------------------------------------------------
1700 r114 | lh3lh3 | 2009-01-25 11:45:37 +0000 (Sun, 25 Jan 2009) | 2 lines
1702 A /trunk/samtools/misc/zoom2sam.pl
1706 ------------------------------------------------------------------------
1707 r113 | lh3lh3 | 2009-01-24 14:25:07 +0000 (Sat, 24 Jan 2009) | 2 lines
1709 A /trunk/samtools/misc/novo2sam.pl
1711 add a script to convert novo alignment to SAM
1713 ------------------------------------------------------------------------
1714 r112 | lh3lh3 | 2009-01-23 20:57:39 +0000 (Fri, 23 Jan 2009) | 2 lines
1716 M /trunk/samtools/ChangeLog
1717 M /trunk/samtools/ChangeLog.old
1718 M /trunk/samtools/samtools.1
1720 update documentation and ChangeLog
1722 ------------------------------------------------------------------------
1723 r111 | lh3lh3 | 2009-01-23 19:22:59 +0000 (Fri, 23 Jan 2009) | 3 lines
1725 M /trunk/samtools/bam_sort.c
1726 M /trunk/samtools/bamtk.c
1729 * fixed a bug in "merge" command line
1731 ------------------------------------------------------------------------
1732 r110 | lh3lh3 | 2009-01-22 15:36:48 +0000 (Thu, 22 Jan 2009) | 3 lines
1734 M /trunk/samtools/misc/Makefile
1735 A /trunk/samtools/misc/bowtie2sam.pl (from /branches/dev/samtools/misc/bowtie2sam.pl:108)
1736 M /trunk/samtools/misc/export2sam.pl
1737 A /trunk/samtools/misc/soap2sam.pl (from /branches/dev/samtools/misc/soap2sam.pl:108)
1738 A /trunk/samtools/misc/wgsim.c (from /branches/dev/samtools/misc/wgsim.c:108)
1739 A /trunk/samtools/misc/wgsim_eval.pl (from /branches/dev/samtools/misc/wgsim_eval.pl:108)
1741 * merge from branches/dev/
1742 * all future development will happen here
1744 ------------------------------------------------------------------------
1745 r109 | lh3lh3 | 2009-01-22 15:14:27 +0000 (Thu, 22 Jan 2009) | 3 lines
1747 M /trunk/samtools/COPYING
1748 M /trunk/samtools/ChangeLog
1749 A /trunk/samtools/INSTALL (from /branches/dev/samtools/INSTALL:108)
1750 M /trunk/samtools/Makefile
1751 A /trunk/samtools/Makefile.lite (from /branches/dev/samtools/Makefile.lite:108)
1752 M /trunk/samtools/bam.c
1753 M /trunk/samtools/bam.h
1754 M /trunk/samtools/bam_import.c
1755 M /trunk/samtools/bam_index.c
1756 M /trunk/samtools/bam_lpileup.c
1757 M /trunk/samtools/bam_maqcns.c
1758 M /trunk/samtools/bam_maqcns.h
1759 A /trunk/samtools/bam_mate.c (from /branches/dev/samtools/bam_mate.c:108)
1760 M /trunk/samtools/bam_pileup.c
1761 M /trunk/samtools/bam_plcmd.c
1762 A /trunk/samtools/bam_rmdup.c (from /branches/dev/samtools/bam_rmdup.c:108)
1763 M /trunk/samtools/bam_sort.c
1764 M /trunk/samtools/bamtk.c
1765 M /trunk/samtools/bgzf.h
1766 M /trunk/samtools/examples/00README.txt
1767 A /trunk/samtools/examples/Makefile (from /branches/dev/samtools/examples/Makefile:108)
1768 D /trunk/samtools/examples/ex1.fa.fai
1769 M /trunk/samtools/examples/ex1.sam.gz
1770 M /trunk/samtools/faidx.c
1771 A /trunk/samtools/glf.c (from /branches/dev/samtools/glf.c:108)
1772 M /trunk/samtools/glf.h
1773 M /trunk/samtools/misc/Makefile
1774 M /trunk/samtools/misc/maq2sam.c
1775 M /trunk/samtools/razf.c
1776 M /trunk/samtools/source.dot
1778 * Merge from branches/dev/
1779 * all future development will happen here at trunk/
1781 ------------------------------------------------------------------------
1782 r79 | bhandsaker | 2009-01-07 21:42:15 +0000 (Wed, 07 Jan 2009) | 2 lines
1784 M /trunk/samtools/bam_maqcns.c
1785 M /trunk/samtools/bam_tview.c
1787 Fix problem with compiling without curses.
1789 ------------------------------------------------------------------------
1790 r63 | lh3lh3 | 2008-12-22 15:58:02 +0000 (Mon, 22 Dec 2008) | 2 lines
1792 A /trunk/samtools (from /branches/dev/samtools:62)
1796 ------------------------------------------------------------------------
1797 r62 | lh3lh3 | 2008-12-22 15:55:13 +0000 (Mon, 22 Dec 2008) | 2 lines
1799 A /branches/dev/samtools/NEWS
1800 M /branches/dev/samtools/bamtk.c
1801 M /branches/dev/samtools/samtools.1
1803 Release samtools-0.1.1
1805 ------------------------------------------------------------------------
1806 r61 | lh3lh3 | 2008-12-22 15:46:08 +0000 (Mon, 22 Dec 2008) | 10 lines
1808 M /branches/dev/samtools/bam_aux.c
1809 M /branches/dev/samtools/bam_index.c
1810 M /branches/dev/samtools/bam_plcmd.c
1811 M /branches/dev/samtools/bam_tview.c
1812 M /branches/dev/samtools/bamtk.c
1813 M /branches/dev/samtools/razf.c
1814 M /branches/dev/samtools/samtools.1
1817 * fixed a bug in razf.c: reset z_eof when razf_seek() is called
1818 * fixed a memory leak in parsing a region
1819 * changed pileup a little bit when -s is in use: output ^ and $
1820 * when a bam is not indexed, output more meaningful error message
1821 * fixed a bug in indexing for small alignment
1822 * fixed a bug in the viewer when we come to the end of a reference file
1823 * updated documentation
1824 * prepare to release 0.1.1
1826 ------------------------------------------------------------------------
1827 r60 | lh3lh3 | 2008-12-22 15:10:16 +0000 (Mon, 22 Dec 2008) | 2 lines
1829 A /branches/dev/samtools/examples
1830 A /branches/dev/samtools/examples/00README.txt
1831 A /branches/dev/samtools/examples/ex1.fa
1832 A /branches/dev/samtools/examples/ex1.fa.fai
1833 A /branches/dev/samtools/examples/ex1.sam.gz
1837 ------------------------------------------------------------------------
1838 r59 | lh3lh3 | 2008-12-22 09:38:15 +0000 (Mon, 22 Dec 2008) | 2 lines
1840 M /branches/dev/samtools/ChangeLog
1844 ------------------------------------------------------------------------
1845 r58 | lh3lh3 | 2008-12-20 23:06:00 +0000 (Sat, 20 Dec 2008) | 3 lines
1847 M /branches/dev/samtools/misc/export2sam.pl
1850 * fixed several bugs
1852 ------------------------------------------------------------------------
1853 r57 | lh3lh3 | 2008-12-20 15:44:20 +0000 (Sat, 20 Dec 2008) | 2 lines
1855 A /branches/dev/samtools/misc/export2sam.pl
1857 convert Export format to SAM; not thoroughly tested
1859 ------------------------------------------------------------------------
1860 r56 | lh3lh3 | 2008-12-19 22:13:28 +0000 (Fri, 19 Dec 2008) | 6 lines
1862 M /branches/dev/samtools/bam_import.c
1863 M /branches/dev/samtools/bam_plcmd.c
1864 M /branches/dev/samtools/bam_tview.c
1865 M /branches/dev/samtools/bamtk.c
1866 A /branches/dev/samtools/source.dot
1869 * pileup: generate maq-like simple output
1870 * pileup: allow to output pileup at required sites
1871 * source.dot: source file relationship graph
1872 * tview: fixed a minor bug
1874 ------------------------------------------------------------------------
1875 r55 | lh3lh3 | 2008-12-19 20:10:26 +0000 (Fri, 19 Dec 2008) | 2 lines
1877 D /branches/dev/samtools/misc/all2sam.pl
1881 ------------------------------------------------------------------------
1882 r54 | lh3lh3 | 2008-12-16 22:34:25 +0000 (Tue, 16 Dec 2008) | 2 lines
1884 A /branches/dev/samtools/COPYING
1885 M /branches/dev/samtools/bam.h
1886 M /branches/dev/samtools/faidx.h
1887 M /branches/dev/samtools/khash.h
1888 M /branches/dev/samtools/kseq.h
1889 M /branches/dev/samtools/ksort.h
1890 M /branches/dev/samtools/samtools.1
1892 Added copyright information and a bit more documentation. No code change.
1894 ------------------------------------------------------------------------
1895 r53 | lh3lh3 | 2008-12-16 13:40:18 +0000 (Tue, 16 Dec 2008) | 3 lines
1897 M /branches/dev/samtools/bam.c
1898 M /branches/dev/samtools/bam.h
1899 M /branches/dev/samtools/bam_index.c
1900 M /branches/dev/samtools/bam_maqcns.c
1901 M /branches/dev/samtools/bamtk.c
1904 * improved efficiency of the indel caller for spliced alignments
1906 ------------------------------------------------------------------------
1907 r52 | lh3lh3 | 2008-12-16 10:28:20 +0000 (Tue, 16 Dec 2008) | 3 lines
1909 M /branches/dev/samtools/bam.c
1910 M /branches/dev/samtools/bam.h
1911 M /branches/dev/samtools/bam_aux.c
1912 M /branches/dev/samtools/bam_index.c
1913 M /branches/dev/samtools/bamtk.c
1916 * a bit code cleanup: reduce the dependency between source files
1918 ------------------------------------------------------------------------
1919 r51 | lh3lh3 | 2008-12-15 14:29:32 +0000 (Mon, 15 Dec 2008) | 3 lines
1921 M /branches/dev/samtools/bam_maqcns.c
1922 M /branches/dev/samtools/bam_plcmd.c
1923 M /branches/dev/samtools/bamtk.c
1926 * fixed a memory leak
1928 ------------------------------------------------------------------------
1929 r50 | lh3lh3 | 2008-12-15 14:00:13 +0000 (Mon, 15 Dec 2008) | 2 lines
1931 M /branches/dev/samtools/ChangeLog
1932 M /branches/dev/samtools/bam.h
1933 M /branches/dev/samtools/samtools.1
1935 update documentation, ChangeLog and a comment
1937 ------------------------------------------------------------------------
1938 r49 | lh3lh3 | 2008-12-15 13:36:43 +0000 (Mon, 15 Dec 2008) | 6 lines
1940 M /branches/dev/samtools/Makefile
1941 M /branches/dev/samtools/bam.h
1942 M /branches/dev/samtools/bam_maqcns.c
1943 M /branches/dev/samtools/bam_maqcns.h
1944 M /branches/dev/samtools/bam_pileup.c
1945 A /branches/dev/samtools/bam_plcmd.c
1946 M /branches/dev/samtools/bamtk.c
1947 M /branches/dev/samtools/samtools.1
1950 * moved pileup command to a separate source file
1951 * added indel caller
1952 * added bam_cal_segend(). (NOT WORKING for spliced alignment!!!)
1953 * updated documentation
1955 ------------------------------------------------------------------------
1956 r48 | lh3lh3 | 2008-12-12 13:55:36 +0000 (Fri, 12 Dec 2008) | 3 lines
1958 M /branches/dev/samtools/bam_maqcns.c
1959 M /branches/dev/samtools/bamtk.c
1962 * fixed another bug in maqcns when there is a nearby deletion
1964 ------------------------------------------------------------------------
1965 r47 | lh3lh3 | 2008-12-12 13:42:16 +0000 (Fri, 12 Dec 2008) | 5 lines
1967 M /branches/dev/samtools/bam_maqcns.c
1968 M /branches/dev/samtools/bam_pileup.c
1969 M /branches/dev/samtools/bamtk.c
1972 * pileup: outputing consensus is now optional
1973 * fixed a bug in glfgen. This bug also exists in maq's glfgen. However,
1974 I am not quite sure why the previous version may have problem.
1976 ------------------------------------------------------------------------
1977 r46 | lh3lh3 | 2008-12-12 11:44:56 +0000 (Fri, 12 Dec 2008) | 6 lines
1979 M /branches/dev/samtools/bam_pileup.c
1980 M /branches/dev/samtools/bamtk.c
1983 * add maq consensus to pileup. However, I will move this part to a new
1984 command as strictly speaking, consensus callin is not part of pileup,
1985 and imposing it would make it harder to generate for other language
1988 ------------------------------------------------------------------------
1989 r45 | bhandsaker | 2008-12-11 20:43:56 +0000 (Thu, 11 Dec 2008) | 2 lines
1991 M /branches/dev/samtools/bgzf.c
1993 Fix bug in tell() after reads that consume to the exact end of a block.
1995 ------------------------------------------------------------------------
1996 r44 | lh3lh3 | 2008-12-11 09:36:53 +0000 (Thu, 11 Dec 2008) | 2 lines
1998 M /branches/dev/samtools/samtools.1
2002 ------------------------------------------------------------------------
2003 r43 | lh3lh3 | 2008-12-11 09:25:36 +0000 (Thu, 11 Dec 2008) | 4 lines
2005 M /branches/dev/samtools/bam_import.c
2006 M /branches/dev/samtools/bamtk.c
2009 * fixed a bug in parser when there is auxiliary fields
2010 * made the parser a bit more robust
2012 ------------------------------------------------------------------------
2013 r42 | lh3lh3 | 2008-12-10 14:57:29 +0000 (Wed, 10 Dec 2008) | 5 lines
2015 M /branches/dev/samtools/bam_index.c
2016 M /branches/dev/samtools/bamtk.c
2017 M /branches/dev/samtools/bgzf.c
2020 * fixed a bug in bgzf (only reading is affected)
2021 * fixed a typo in bam_index.c
2022 * in bam_index.c, check potential bugs in the underlying I/O library
2024 ------------------------------------------------------------------------
2025 r41 | lh3lh3 | 2008-12-10 12:53:08 +0000 (Wed, 10 Dec 2008) | 2 lines
2027 M /branches/dev/samtools/samtools.1
2031 ------------------------------------------------------------------------
2032 r40 | lh3lh3 | 2008-12-10 11:52:10 +0000 (Wed, 10 Dec 2008) | 5 lines
2034 M /branches/dev/samtools/bam.h
2035 M /branches/dev/samtools/bam_pileup.c
2036 M /branches/dev/samtools/bamtk.c
2039 * tried to make pileup work with clipping (previously not), though NOT tested
2040 * removed -v from pileup
2041 * made pileup take the reference sequence
2043 ------------------------------------------------------------------------
2044 r39 | lh3lh3 | 2008-12-09 11:59:28 +0000 (Tue, 09 Dec 2008) | 4 lines
2046 M /branches/dev/samtools/bam_import.c
2047 M /branches/dev/samtools/bamtk.c
2048 M /branches/dev/samtools/samtools.1
2051 * in parser, recognize "=", rather than ",", as a match
2052 * in parser, correctl parse "=" at the MRNM field.
2054 ------------------------------------------------------------------------
2055 r38 | lh3lh3 | 2008-12-09 11:39:07 +0000 (Tue, 09 Dec 2008) | 2 lines
2057 M /branches/dev/samtools/misc/maq2sam.c
2059 fixed a bug in handling maq flag 64 and 192
2061 ------------------------------------------------------------------------
2062 r37 | lh3lh3 | 2008-12-09 09:53:46 +0000 (Tue, 09 Dec 2008) | 2 lines
2064 M /branches/dev/samtools/misc/md5fa.c
2066 also calculate unordered md5sum check
2068 ------------------------------------------------------------------------
2069 r36 | lh3lh3 | 2008-12-09 09:46:21 +0000 (Tue, 09 Dec 2008) | 2 lines
2071 M /branches/dev/samtools/misc/md5fa.c
2073 fixed a minor bug when there are space in the sequence
2075 ------------------------------------------------------------------------
2076 r35 | lh3lh3 | 2008-12-09 09:40:45 +0000 (Tue, 09 Dec 2008) | 2 lines
2078 M /branches/dev/samtools/misc/md5fa.c
2080 fixed a potential memory leak
2082 ------------------------------------------------------------------------
2083 r34 | lh3lh3 | 2008-12-08 14:52:17 +0000 (Mon, 08 Dec 2008) | 2 lines
2085 M /branches/dev/samtools/bam_import.c
2086 M /branches/dev/samtools/bam_index.c
2087 M /branches/dev/samtools/bamtk.c
2089 * fixed a bug in import: bin is wrongly calculated
2091 ------------------------------------------------------------------------
2092 r33 | lh3lh3 | 2008-12-08 14:08:01 +0000 (Mon, 08 Dec 2008) | 2 lines
2094 M /branches/dev/samtools/misc/all2sam.pl
2098 ------------------------------------------------------------------------
2099 r32 | lh3lh3 | 2008-12-08 12:56:02 +0000 (Mon, 08 Dec 2008) | 3 lines
2101 M /branches/dev/samtools/Makefile
2102 M /branches/dev/samtools/kseq.h
2103 M /branches/dev/samtools/misc/Makefile
2104 A /branches/dev/samtools/misc/md5.c
2105 A /branches/dev/samtools/misc/md5.h
2106 A /branches/dev/samtools/misc/md5fa.c
2108 * fixed two warnings in kseq.h
2109 * added md5sum utilities
2111 ------------------------------------------------------------------------
2112 r31 | lh3lh3 | 2008-12-08 11:35:29 +0000 (Mon, 08 Dec 2008) | 5 lines
2114 M /branches/dev/samtools/Makefile
2115 M /branches/dev/samtools/bam_import.c
2116 M /branches/dev/samtools/bamtk.c
2117 A /branches/dev/samtools/kseq.h
2118 D /branches/dev/samtools/kstream.h
2121 * replace kstream with kseq. kseq is a superset of kstream. I need the
2122 extra functions in kseq.h.
2123 * also compile stand-alone faidx
2125 ------------------------------------------------------------------------
2126 r30 | lh3lh3 | 2008-12-08 11:17:04 +0000 (Mon, 08 Dec 2008) | 3 lines
2128 M /branches/dev/samtools/bam.h
2129 M /branches/dev/samtools/bam_sort.c
2130 M /branches/dev/samtools/bamtk.c
2133 * sorting by read names is available
2135 ------------------------------------------------------------------------
2136 r29 | lh3lh3 | 2008-12-08 10:29:02 +0000 (Mon, 08 Dec 2008) | 3 lines
2138 M /branches/dev/samtools/bam.c
2139 M /branches/dev/samtools/bam.h
2140 M /branches/dev/samtools/bam_import.c
2141 M /branches/dev/samtools/bam_maqcns.c
2142 M /branches/dev/samtools/bam_pileup.c
2143 M /branches/dev/samtools/bam_sort.c
2144 M /branches/dev/samtools/bam_tview.c
2145 M /branches/dev/samtools/bamtk.c
2146 M /branches/dev/samtools/misc/maq2sam.c
2149 * format change to meet the latest specification
2151 ------------------------------------------------------------------------
2152 r28 | lh3lh3 | 2008-12-04 16:09:21 +0000 (Thu, 04 Dec 2008) | 3 lines
2154 M /branches/dev/samtools/bam_maqcns.c
2155 M /branches/dev/samtools/misc/maq2sam.c
2157 * minor change in maqcns: special care when n==0
2158 * change maq2sam to meet the latest specification
2160 ------------------------------------------------------------------------
2161 r27 | lh3lh3 | 2008-12-04 15:55:44 +0000 (Thu, 04 Dec 2008) | 2 lines
2163 M /branches/dev/samtools/razf.c
2164 M /branches/dev/samtools/razf.h
2166 considerable code clean up in razf
2168 ------------------------------------------------------------------------
2169 r26 | lh3lh3 | 2008-12-04 15:08:18 +0000 (Thu, 04 Dec 2008) | 2 lines
2171 M /branches/dev/samtools/ChangeLog
2172 M /branches/dev/samtools/Makefile
2173 M /branches/dev/samtools/faidx.c
2175 make RAZF optional in faidx.c
2177 ------------------------------------------------------------------------
2178 r25 | lh3lh3 | 2008-12-01 15:27:22 +0000 (Mon, 01 Dec 2008) | 3 lines
2180 M /branches/dev/samtools/Makefile
2181 M /branches/dev/samtools/bam.h
2182 M /branches/dev/samtools/bam_aux.c
2183 M /branches/dev/samtools/bamtk.c
2184 M /branches/dev/samtools/samtools.1
2187 * added routines for retrieving aux data, NOT TESTED YET!
2189 ------------------------------------------------------------------------
2190 r24 | lh3lh3 | 2008-12-01 14:29:43 +0000 (Mon, 01 Dec 2008) | 5 lines
2192 M /branches/dev/samtools/bam.c
2193 M /branches/dev/samtools/bam_import.c
2194 M /branches/dev/samtools/bam_maqcns.c
2195 M /branches/dev/samtools/bamtk.c
2196 M /branches/dev/samtools/bgzf.c
2197 M /branches/dev/samtools/samtools.1
2200 * bgzf: fixed a potential integer overflow on 32-it machines
2201 * maqcns: set the minimum combined quality as 0
2202 * supporting hex strings
2204 ------------------------------------------------------------------------
2205 r23 | lh3lh3 | 2008-11-27 17:14:37 +0000 (Thu, 27 Nov 2008) | 3 lines
2207 M /branches/dev/samtools/bam_maqcns.c
2208 M /branches/dev/samtools/bamtk.c
2211 * fixed the bug in maqcns
2213 ------------------------------------------------------------------------
2214 r22 | lh3lh3 | 2008-11-27 17:08:11 +0000 (Thu, 27 Nov 2008) | 3 lines
2216 M /branches/dev/samtools/Makefile
2217 M /branches/dev/samtools/bam.h
2218 A /branches/dev/samtools/bam_maqcns.c
2219 A /branches/dev/samtools/bam_maqcns.h
2220 M /branches/dev/samtools/bam_tview.c
2221 M /branches/dev/samtools/bamtk.c
2222 A /branches/dev/samtools/glf.h
2225 * add MAQ consensus caller, currently BUGGY!
2227 ------------------------------------------------------------------------
2228 r21 | lh3lh3 | 2008-11-27 13:51:28 +0000 (Thu, 27 Nov 2008) | 4 lines
2230 M /branches/dev/samtools/bam_pileup.c
2231 M /branches/dev/samtools/bam_tview.c
2232 M /branches/dev/samtools/bamtk.c
2235 * tview: display padded alignment (but not P operation)
2236 * better coordinates and reference sequence
2238 ------------------------------------------------------------------------
2239 r19 | lh3lh3 | 2008-11-27 09:26:05 +0000 (Thu, 27 Nov 2008) | 2 lines
2241 A /branches/dev/samtools/ChangeLog
2245 ------------------------------------------------------------------------
2246 r18 | lh3lh3 | 2008-11-27 09:24:45 +0000 (Thu, 27 Nov 2008) | 3 lines
2248 D /branches/dev/samtools/ChangeLog
2249 A /branches/dev/samtools/ChangeLog.old (from /branches/dev/samtools/ChangeLog:6)
2251 Rename ChangeLog to ChangeLog.old. This old ChangeLog is generated from
2252 the log of my personal SVN repository.
2254 ------------------------------------------------------------------------
2255 r17 | lh3lh3 | 2008-11-27 09:22:55 +0000 (Thu, 27 Nov 2008) | 6 lines
2257 M /branches/dev/samtools/Makefile
2258 M /branches/dev/samtools/bamtk.c
2259 M /branches/dev/samtools/bgzf.c
2262 * declare fseeko and ftello as some Linux may not do this by default and
2263 missing these declarations will make bgzf buggy
2264 * get rid of some harmless warings
2265 * use BGZF by default, now
2267 ------------------------------------------------------------------------
2268 r16 | lh3lh3 | 2008-11-26 21:19:11 +0000 (Wed, 26 Nov 2008) | 4 lines
2270 M /branches/dev/samtools/bam_index.c
2271 M /branches/dev/samtools/bamtk.c
2272 M /branches/dev/samtools/razf.c
2275 * fixed a bug in razf_read()
2276 * give more warnings when the file is truncated (or due to bugs in I/O library)
2278 ------------------------------------------------------------------------
2279 r15 | lh3lh3 | 2008-11-26 20:41:39 +0000 (Wed, 26 Nov 2008) | 2 lines
2281 M /branches/dev/samtools/bgzf.c
2283 fixed a bug in bgzf.c at the end of the file
2285 ------------------------------------------------------------------------
2286 r14 | lh3lh3 | 2008-11-26 17:05:18 +0000 (Wed, 26 Nov 2008) | 4 lines
2288 M /branches/dev/samtools/bamtk.c
2291 * a lot happened to RAZF, although samtools itself is untouched. Better
2292 also update the version number anyway to avoid confusion
2294 ------------------------------------------------------------------------
2295 r13 | lh3lh3 | 2008-11-26 17:03:48 +0000 (Wed, 26 Nov 2008) | 2 lines
2297 M /branches/dev/samtools/razf.c
2299 a change from Jue, but I think it should not matter
2301 ------------------------------------------------------------------------
2302 r12 | lh3lh3 | 2008-11-26 16:48:14 +0000 (Wed, 26 Nov 2008) | 3 lines
2304 M /branches/dev/samtools/razf.c
2306 fixed a potential bug in razf. However, it seems still buggy, just
2307 rarely happens, very rarely.
2309 ------------------------------------------------------------------------
2310 r11 | lh3lh3 | 2008-11-26 14:02:56 +0000 (Wed, 26 Nov 2008) | 2 lines
2312 M /branches/dev/samtools/razf.c
2314 fixed a bug in razf, with the help of Jue
2316 ------------------------------------------------------------------------
2317 r10 | lh3lh3 | 2008-11-26 11:55:32 +0000 (Wed, 26 Nov 2008) | 2 lines
2319 M /branches/dev/samtools/bam_index.c
2323 ------------------------------------------------------------------------
2324 r9 | lh3lh3 | 2008-11-26 11:37:05 +0000 (Wed, 26 Nov 2008) | 2 lines
2326 M /branches/dev/samtools/Makefile
2327 M /branches/dev/samtools/bam.h
2328 M /branches/dev/samtools/razf.c
2329 M /branches/dev/samtools/razf.h
2331 * Jue has updated razf to realize Bob's scheme
2333 ------------------------------------------------------------------------
2334 r7 | lh3lh3 | 2008-11-25 20:37:37 +0000 (Tue, 25 Nov 2008) | 2 lines
2336 A /branches/dev/samtools/samtools.1
2340 ------------------------------------------------------------------------
2341 r6 | lh3lh3 | 2008-11-25 20:37:16 +0000 (Tue, 25 Nov 2008) | 3 lines
2343 A /branches/dev/samtools/ChangeLog
2344 A /branches/dev/samtools/Makefile
2345 A /branches/dev/samtools/bam.c
2346 A /branches/dev/samtools/bam.h
2347 A /branches/dev/samtools/bam_aux.c
2348 A /branches/dev/samtools/bam_endian.h
2349 A /branches/dev/samtools/bam_import.c
2350 A /branches/dev/samtools/bam_index.c
2351 A /branches/dev/samtools/bam_lpileup.c
2352 A /branches/dev/samtools/bam_pileup.c
2353 A /branches/dev/samtools/bam_sort.c
2354 A /branches/dev/samtools/bam_tview.c
2355 A /branches/dev/samtools/bamtk.c
2356 A /branches/dev/samtools/bgzf.c
2357 A /branches/dev/samtools/bgzf.h
2358 A /branches/dev/samtools/bgzip.c
2359 A /branches/dev/samtools/faidx.c
2360 A /branches/dev/samtools/faidx.h
2361 A /branches/dev/samtools/khash.h
2362 A /branches/dev/samtools/ksort.h
2363 A /branches/dev/samtools/kstream.h
2364 A /branches/dev/samtools/misc
2365 A /branches/dev/samtools/misc/Makefile
2366 A /branches/dev/samtools/misc/all2sam.pl
2367 A /branches/dev/samtools/misc/maq2sam.c
2368 A /branches/dev/samtools/razf.c
2369 A /branches/dev/samtools/razf.h
2370 A /branches/dev/samtools/razip.c
2371 A /branches/dev/samtools/zutil.h
2373 The initial version of samtools, replicated from my local SVN repository.
2374 The current version is: 0.1.0-42. All future development will happen here.
2376 ------------------------------------------------------------------------
2377 r5 | lh3lh3 | 2008-11-25 20:30:49 +0000 (Tue, 25 Nov 2008) | 2 lines
2379 A /branches/dev/samtools
2381 samtools (C version)
2383 ------------------------------------------------------------------------