1 ------------------------------------------------------------------------
2 r372 | lh3lh3 | 2009-07-07 09:49:27 +0100 (Tue, 07 Jul 2009) | 3 lines
4 M /trunk/samtools/bamtk.c
5 M /trunk/samtools/sam.c
7 * samtools-0.1.4-23 (r372)
8 * keep header text if "view -t" is used (by Gerton)
10 ------------------------------------------------------------------------
11 r371 | lh3lh3 | 2009-07-07 01:13:32 +0100 (Tue, 07 Jul 2009) | 2 lines
13 M /trunk/samtools/samtools.1
17 ------------------------------------------------------------------------
18 r370 | bhandsaker | 2009-07-02 22:24:34 +0100 (Thu, 02 Jul 2009) | 2 lines
20 M /trunk/samtools/Makefile
22 Introduced LIBPATH variable so this could be overridden to allow samtools to build correct at the Broad.
24 ------------------------------------------------------------------------
25 r369 | lh3lh3 | 2009-07-02 13:36:53 +0100 (Thu, 02 Jul 2009) | 4 lines
27 M /trunk/samtools/ChangeLog
28 M /trunk/samtools/bam_aux.c
29 M /trunk/samtools/bam_plcmd.c
30 M /trunk/samtools/bamtk.c
32 * samtools-0.1.4-22 (r369)
33 * in pileup, optionally print E2 and U2
34 * remove the debugging code in bam_aux_get() (Drat!)
36 ------------------------------------------------------------------------
37 r368 | lh3lh3 | 2009-07-02 11:32:26 +0100 (Thu, 02 Jul 2009) | 6 lines
39 M /trunk/samtools/bam.c
40 M /trunk/samtools/bam.h
41 M /trunk/samtools/bam_aux.c
42 M /trunk/samtools/bam_index.c
43 M /trunk/samtools/bam_lpileup.c
44 M /trunk/samtools/bam_md.c
45 M /trunk/samtools/bam_pileup.c
46 M /trunk/samtools/bam_rmdup.c
47 M /trunk/samtools/bam_stat.c
48 M /trunk/samtools/bam_tview.c
49 M /trunk/samtools/bamtk.c
50 M /trunk/samtools/faidx.c
51 M /trunk/samtools/faidx.h
52 M /trunk/samtools/glf.c
54 * samtools-0.1.4-21 (r368)
55 * propagate errors rather than exit or complain assertion failure. Assertion
56 should be only used for checking internal bugs, but not for external input
57 inconsistency. I was just a bit lazy.
58 * small memory leak may be present on failure, though
60 ------------------------------------------------------------------------
61 r367 | lh3lh3 | 2009-06-30 16:18:42 +0100 (Tue, 30 Jun 2009) | 2 lines
63 M /trunk/samtools/knetfile.c
65 reduce the chance of blocking in FTP connection
67 ------------------------------------------------------------------------
68 r366 | lh3lh3 | 2009-06-30 15:35:21 +0100 (Tue, 30 Jun 2009) | 2 lines
70 M /trunk/samtools/knetfile.c
72 minor changes to knetfile: invalid fd equals -1 rather than 0
74 ------------------------------------------------------------------------
75 r365 | lh3lh3 | 2009-06-30 14:04:30 +0100 (Tue, 30 Jun 2009) | 3 lines
77 M /trunk/samtools/bam_index.c
78 M /trunk/samtools/bamtk.c
79 M /trunk/samtools/knetfile.c
80 M /trunk/samtools/knetfile.h
82 * samtools-0.1.4-20 (r365)
83 * download the BAM index file if it is not found in the current working directory.
85 ------------------------------------------------------------------------
86 r364 | lh3lh3 | 2009-06-30 12:39:07 +0100 (Tue, 30 Jun 2009) | 3 lines
88 M /trunk/samtools/bamtk.c
89 M /trunk/samtools/knetfile.c
91 * samtools-0.1.4-19 (r364)
92 * knetfile: report error when the file is not present on FTP
94 ------------------------------------------------------------------------
95 r363 | lh3lh3 | 2009-06-29 23:23:32 +0100 (Mon, 29 Jun 2009) | 4 lines
97 M /trunk/samtools/bam_tview.c
98 M /trunk/samtools/bamtk.c
99 M /trunk/samtools/bgzf.c
100 M /trunk/samtools/bgzf.h
101 M /trunk/samtools/knetfile.c
102 M /trunk/samtools/knetfile.h
104 * samtools-0.1.4-18 (r363)
105 * knetfile: do not trigger network communication in FTP seek (lazy seek)
106 * bgzf: cache recent blocks (disabled by default)
108 ------------------------------------------------------------------------
109 r362 | lh3lh3 | 2009-06-25 21:04:34 +0100 (Thu, 25 Jun 2009) | 2 lines
111 M /trunk/samtools/bgzf.c
115 ------------------------------------------------------------------------
116 r361 | lh3lh3 | 2009-06-25 21:03:10 +0100 (Thu, 25 Jun 2009) | 3 lines
118 M /trunk/samtools/bam_index.c
119 M /trunk/samtools/bamtk.c
121 * samtools-0.1.4-17 (r361)
122 * if a file is given on FTP, search locally for the BAM index
124 ------------------------------------------------------------------------
125 r360 | lh3lh3 | 2009-06-25 20:44:52 +0100 (Thu, 25 Jun 2009) | 5 lines
127 M /trunk/samtools/Makefile
128 M /trunk/samtools/bam_import.c
129 M /trunk/samtools/bam_index.c
130 M /trunk/samtools/bamtk.c
131 M /trunk/samtools/bgzf.c
132 M /trunk/samtools/bgzf.h
133 M /trunk/samtools/knetfile.c
134 M /trunk/samtools/knetfile.h
136 * samtools-0.1.4-16 (r360)
137 * report more information in index when the input is not sorted
138 * change the behaviour of knet_seek() such that it returns 0 on success
139 * support knetfile library in BGZF
141 ------------------------------------------------------------------------
142 r359 | lh3lh3 | 2009-06-25 17:10:55 +0100 (Thu, 25 Jun 2009) | 2 lines
144 M /trunk/samtools/knetfile.c
145 M /trunk/samtools/knetfile.h
147 fixed bugs in knetfile.*
149 ------------------------------------------------------------------------
150 r358 | lh3lh3 | 2009-06-25 13:53:19 +0100 (Thu, 25 Jun 2009) | 2 lines
152 A /trunk/samtools/knetfile.h
154 this is the header file
156 ------------------------------------------------------------------------
157 r357 | lh3lh3 | 2009-06-25 13:52:03 +0100 (Thu, 25 Jun 2009) | 3 lines
159 A /trunk/samtools/knetfile.c
162 * preliminary version
164 ------------------------------------------------------------------------
165 r354 | lh3lh3 | 2009-06-24 14:02:25 +0100 (Wed, 24 Jun 2009) | 3 lines
167 M /trunk/samtools/bam.c
168 M /trunk/samtools/bamtk.c
170 * samtools-0.1.4-15 (r354)
171 * fixed a memory leak in bam_view1(), although samtools is not using this routine.
173 ------------------------------------------------------------------------
174 r351 | lh3lh3 | 2009-06-18 00:16:26 +0100 (Thu, 18 Jun 2009) | 4 lines
176 M /trunk/samtools/bamtk.c
177 M /trunk/samtools/faidx.c
179 * samtools-0.1.4-13 (r351)
180 * make faidx more tolerant to empty lines right before or after > lines
181 * hope this does not introduce new bugs...
183 ------------------------------------------------------------------------
184 r350 | lh3lh3 | 2009-06-16 14:37:01 +0100 (Tue, 16 Jun 2009) | 3 lines
186 M /trunk/samtools/bam_plcmd.c
187 M /trunk/samtools/bamtk.c
189 * samtools-0.1.4-13 (r350)
190 * fixed a small memory leak in pileup, caused by recent modifications
192 ------------------------------------------------------------------------
193 r347 | lh3lh3 | 2009-06-13 21:20:49 +0100 (Sat, 13 Jun 2009) | 3 lines
195 M /trunk/samtools/bam_plcmd.c
196 M /trunk/samtools/bamtk.c
197 M /trunk/samtools/sam_view.c
199 * samtools-0.1.4-12 (r347)
200 * added `-S' to pileup, similar to `view -S'
202 ------------------------------------------------------------------------
203 r346 | lh3lh3 | 2009-06-13 17:52:31 +0100 (Sat, 13 Jun 2009) | 3 lines
205 M /trunk/samtools/Makefile
206 M /trunk/samtools/bamtk.c
207 M /trunk/samtools/sam_view.c
208 M /trunk/samtools/samtools.1
210 * samtools-0.1.4-11 (r346)
211 * allow to select a read group at view command-line
213 ------------------------------------------------------------------------
214 r344 | lh3lh3 | 2009-06-13 14:06:24 +0100 (Sat, 13 Jun 2009) | 2 lines
216 M /trunk/samtools/examples/calDepth.c
220 ------------------------------------------------------------------------
221 r343 | lh3lh3 | 2009-06-13 14:01:22 +0100 (Sat, 13 Jun 2009) | 2 lines
223 M /trunk/samtools/examples/calDepth.c
227 ------------------------------------------------------------------------
228 r342 | lh3lh3 | 2009-06-13 13:58:48 +0100 (Sat, 13 Jun 2009) | 2 lines
230 M /trunk/samtools/examples/Makefile
231 A /trunk/samtools/examples/calDepth.c
233 added an example of calculating read depth
235 ------------------------------------------------------------------------
236 r341 | lh3lh3 | 2009-06-13 13:00:08 +0100 (Sat, 13 Jun 2009) | 6 lines
238 M /trunk/samtools/Makefile
239 M /trunk/samtools/bam.h
240 M /trunk/samtools/bam_aux.c
241 A /trunk/samtools/bam_color.c
242 M /trunk/samtools/bam_plcmd.c
243 M /trunk/samtools/bam_sort.c
244 M /trunk/samtools/bam_tview.c
245 M /trunk/samtools/bamtk.c
246 M /trunk/samtools/sam.c
247 M /trunk/samtools/sam.h
249 * samtools-0.1.4-10 (r341)
250 * only include key APIs in libbam.a
251 * move color-specific routines to bam_color.c
252 * update documentations
253 * remove the support of -q in pileup
255 ------------------------------------------------------------------------
256 r340 | lh3lh3 | 2009-06-13 11:17:14 +0100 (Sat, 13 Jun 2009) | 6 lines
258 M /trunk/samtools/INSTALL
259 M /trunk/samtools/Makefile
260 M /trunk/samtools/bam_aux.c
261 M /trunk/samtools/bam_import.c
262 M /trunk/samtools/bam_tview.c
263 M /trunk/samtools/bamtk.c
264 M /trunk/samtools/razf.c
265 M /trunk/samtools/sam_view.c
267 * samtools-0.1.4-9 (r340)
268 * added a warning to razf.c if zlib<1.2.2.1
269 * fixed a compilation warning
270 * fixed a segfault caused by @RG parsing
271 * detect NCURSES in bam_tview.c
273 ------------------------------------------------------------------------
274 r339 | lh3lh3 | 2009-06-13 10:35:19 +0100 (Sat, 13 Jun 2009) | 2 lines
276 M /trunk/samtools/INSTALL
280 ------------------------------------------------------------------------
281 r338 | lh3lh3 | 2009-06-13 00:15:24 +0100 (Sat, 13 Jun 2009) | 4 lines
283 M /trunk/samtools/bam.c
284 M /trunk/samtools/bam.h
285 M /trunk/samtools/bam_aux.c
286 M /trunk/samtools/bam_import.c
287 M /trunk/samtools/bamtk.c
288 M /trunk/samtools/kstring.h
289 M /trunk/samtools/sam.c
290 M /trunk/samtools/sam_view.c
292 * samtools-0.1.4-8 (r338)
293 * parse the @RG header lines and allow to choose library at the "samtools view"
296 ------------------------------------------------------------------------
297 r337 | lh3lh3 | 2009-06-12 21:25:50 +0100 (Fri, 12 Jun 2009) | 4 lines
299 M /trunk/samtools/bamtk.c
300 M /trunk/samtools/bgzf.c
301 M /trunk/samtools/bgzf.h
302 M /trunk/samtools/sam.c
303 M /trunk/samtools/sam_view.c
305 * samtools-0.1.4-7 (r337)
306 * bgzf.c: support mode string "wu": uncompressed output
307 * "samtools view" support "-u" command-line option
309 ------------------------------------------------------------------------
310 r336 | lh3lh3 | 2009-06-12 17:20:12 +0100 (Fri, 12 Jun 2009) | 5 lines
312 M /trunk/samtools/Makefile
313 M /trunk/samtools/misc/Makefile
314 M /trunk/samtools/razf.c
315 M /trunk/samtools/razf.h
316 M /trunk/samtools/razip.c
318 * no changes to samtools itself
319 * remove zlib source codes
320 * make RAZF reading compatible with old version of zlib
321 * on old version of zlib, writing is not available
323 ------------------------------------------------------------------------
324 r335 | lh3lh3 | 2009-06-12 16:47:33 +0100 (Fri, 12 Jun 2009) | 2 lines
326 D /trunk/samtools/zlib
328 remove zlib for simplification...
330 ------------------------------------------------------------------------
331 r334 | lh3lh3 | 2009-06-12 15:43:36 +0100 (Fri, 12 Jun 2009) | 5 lines
333 M /trunk/samtools/bam.h
334 M /trunk/samtools/bam_aux.c
335 M /trunk/samtools/bamtk.c
337 * samtools-0.1.4-6 (r334)
338 * do not export bam_aux_get_core() for Bio::DB::Sam because it has already
339 been implemented in that.
340 * this version works with the latest Bio::DB::Sam (20090612)
342 ------------------------------------------------------------------------
343 r333 | lh3lh3 | 2009-06-12 15:33:42 +0100 (Fri, 12 Jun 2009) | 2 lines
345 M /trunk/samtools/ChangeLog
349 ------------------------------------------------------------------------
350 r332 | lh3lh3 | 2009-06-12 15:21:21 +0100 (Fri, 12 Jun 2009) | 2 lines
352 M /trunk/samtools/AUTHORS
353 M /trunk/samtools/Makefile
354 M /trunk/samtools/misc/Makefile
356 fixed minor things in Makefile
358 ------------------------------------------------------------------------
359 r331 | lh3lh3 | 2009-06-12 15:07:05 +0100 (Fri, 12 Jun 2009) | 4 lines
361 M /trunk/samtools/bamtk.c
363 * samtools-0.1.4-5 (r3310
364 * no change to samtools itself. Version number is increased to reflect the
365 changes in the Makefile building system.
367 ------------------------------------------------------------------------
368 r330 | lh3lh3 | 2009-06-12 15:03:38 +0100 (Fri, 12 Jun 2009) | 2 lines
370 M /trunk/samtools/AUTHORS
371 D /trunk/samtools/README
373 update information...
375 ------------------------------------------------------------------------
376 r329 | lh3lh3 | 2009-06-12 14:52:21 +0100 (Fri, 12 Jun 2009) | 3 lines
378 M /trunk/samtools/misc/novo2sam.pl
380 * updated novoalign converter by Colin Hercus et al.
381 * this version works with indels
383 ------------------------------------------------------------------------
384 r328 | lh3lh3 | 2009-06-12 14:50:53 +0100 (Fri, 12 Jun 2009) | 3 lines
386 M /trunk/samtools/INSTALL
387 M /trunk/samtools/Makefile
388 M /trunk/samtools/misc/Makefile
389 M /trunk/samtools/zlib/Makefile
392 * update INSTALL instruction
394 ------------------------------------------------------------------------
395 r327 | lh3lh3 | 2009-06-12 14:18:29 +0100 (Fri, 12 Jun 2009) | 4 lines
397 A /trunk/samtools/Makefile (from /trunk/samtools/Makefile.generic:325)
398 D /trunk/samtools/Makefile.am
399 D /trunk/samtools/Makefile.generic
400 D /trunk/samtools/Makefile.lite
401 D /trunk/samtools/autogen.sh
402 D /trunk/samtools/cleanup.sh
403 D /trunk/samtools/configure.ac
404 A /trunk/samtools/misc/Makefile (from /trunk/samtools/misc/Makefile.generic:305)
405 D /trunk/samtools/misc/Makefile.am
406 D /trunk/samtools/misc/Makefile.generic
407 M /trunk/samtools/razf.c
408 A /trunk/samtools/zlib
409 A /trunk/samtools/zlib/Makefile
410 A /trunk/samtools/zlib/adler32.c
411 A /trunk/samtools/zlib/compress.c
412 A /trunk/samtools/zlib/crc32.c
413 A /trunk/samtools/zlib/crc32.h
414 A /trunk/samtools/zlib/deflate.c
415 A /trunk/samtools/zlib/deflate.h
416 A /trunk/samtools/zlib/gzio.c
417 A /trunk/samtools/zlib/infback.c
418 A /trunk/samtools/zlib/inffast.c
419 A /trunk/samtools/zlib/inffast.h
420 A /trunk/samtools/zlib/inffixed.h
421 A /trunk/samtools/zlib/inflate.c
422 A /trunk/samtools/zlib/inflate.h
423 A /trunk/samtools/zlib/inftrees.c
424 A /trunk/samtools/zlib/inftrees.h
425 A /trunk/samtools/zlib/trees.c
426 A /trunk/samtools/zlib/trees.h
427 A /trunk/samtools/zlib/uncompr.c
428 A /trunk/samtools/zlib/zconf.h
429 A /trunk/samtools/zlib/zlib.h
430 A /trunk/samtools/zlib/zutil.c
431 A /trunk/samtools/zlib/zutil.h
432 D /trunk/samtools/zutil.h
434 * added zlib-1.2.3 as razip requires that
435 * prepare to changed back to the Makefile building system
436 * unfinished! (will be soon)
438 ------------------------------------------------------------------------
439 r326 | lh3lh3 | 2009-06-12 14:12:03 +0100 (Fri, 12 Jun 2009) | 2 lines
441 M /trunk/samtools/misc/samtools.pl
445 ------------------------------------------------------------------------
446 r325 | lh3lh3 | 2009-06-10 16:27:59 +0100 (Wed, 10 Jun 2009) | 3 lines
448 M /trunk/samtools/bam_maqcns.c
449 M /trunk/samtools/bamtk.c
451 * samtools-0.1.4-4 (r325)
452 * further avoid wrong consensus calls in repetitive regions.
454 ------------------------------------------------------------------------
455 r324 | lh3lh3 | 2009-06-10 15:56:17 +0100 (Wed, 10 Jun 2009) | 4 lines
457 M /trunk/samtools/bam_maqcns.c
458 M /trunk/samtools/bam_plcmd.c
459 M /trunk/samtools/bamtk.c
460 M /trunk/samtools/sam.c
461 M /trunk/samtools/sam.h
463 * samtools-0.1.4-3 (r324)
464 * make maqcns generate the correct call in repetitive regions.
465 * allow filtering on mapQ at the pileup command line
467 ------------------------------------------------------------------------
468 r323 | lh3lh3 | 2009-06-10 10:04:21 +0100 (Wed, 10 Jun 2009) | 3 lines
470 M /trunk/samtools/misc/samtools.pl
472 * samtools.pl-0.3.2 (r322)
473 * indels and SNPs use different mapping quality threshold
475 ------------------------------------------------------------------------
476 r322 | lh3lh3 | 2009-06-10 10:03:22 +0100 (Wed, 10 Jun 2009) | 2 lines
478 M /trunk/samtools/misc/export2sam.pl
482 ------------------------------------------------------------------------
483 r321 | lh3lh3 | 2009-06-09 09:21:48 +0100 (Tue, 09 Jun 2009) | 2 lines
485 M /trunk/samtools/misc/samtools.pl
487 just typo. no real change
489 ------------------------------------------------------------------------
490 r320 | lh3lh3 | 2009-06-08 14:32:51 +0100 (Mon, 08 Jun 2009) | 2 lines
492 M /trunk/samtools/misc/samtools.pl
494 a little bit code cleanup
496 ------------------------------------------------------------------------
497 r319 | lh3lh3 | 2009-06-08 14:22:33 +0100 (Mon, 08 Jun 2009) | 4 lines
499 M /trunk/samtools/misc/samtools.pl
502 * change default parameters
503 * optionally print filtered variants
505 ------------------------------------------------------------------------
506 r318 | lh3lh3 | 2009-06-08 14:14:26 +0100 (Mon, 08 Jun 2009) | 3 lines
508 M /trunk/samtools/misc/samtools.pl
511 * combine snpFilter and indelFilter
513 ------------------------------------------------------------------------
514 r317 | lh3lh3 | 2009-06-08 11:31:42 +0100 (Mon, 08 Jun 2009) | 3 lines
516 M /trunk/samtools/misc/samtools.pl
519 * change a default parameter
521 ------------------------------------------------------------------------
522 r316 | lh3lh3 | 2009-06-08 11:11:06 +0100 (Mon, 08 Jun 2009) | 5 lines
524 M /trunk/samtools/bam_maqcns.c
525 M /trunk/samtools/bam_maqcns.h
526 M /trunk/samtools/bam_plcmd.c
527 M /trunk/samtools/bamtk.c
528 M /trunk/samtools/sam.c
530 * samtools-0.1.4-2 (r316)
531 * pileup: cap mapping quality at 60 (by default)
532 * pileup: always calculate RMS mapq
533 * pileup: allow to output variant sites only
535 ------------------------------------------------------------------------
536 r312 | lh3lh3 | 2009-06-04 13:01:10 +0100 (Thu, 04 Jun 2009) | 3 lines
538 M /trunk/samtools/misc/samtools.pl
543 ------------------------------------------------------------------------
544 r311 | lh3lh3 | 2009-06-03 09:40:40 +0100 (Wed, 03 Jun 2009) | 2 lines
546 M /trunk/samtools/misc/samtools.pl
548 * in snpFilter, suppress non-SNP sites
550 ------------------------------------------------------------------------
551 r310 | lh3lh3 | 2009-06-01 14:35:13 +0100 (Mon, 01 Jun 2009) | 3 lines
553 M /trunk/samtools/misc/samtools.pl
558 ------------------------------------------------------------------------
559 r309 | lh3lh3 | 2009-06-01 14:04:39 +0100 (Mon, 01 Jun 2009) | 3 lines
561 M /trunk/samtools/misc/samtools.pl
566 ------------------------------------------------------------------------
567 r306 | lh3lh3 | 2009-05-28 11:49:35 +0100 (Thu, 28 May 2009) | 3 lines
569 M /trunk/samtools/bgzf.c
571 * minor changes to bgzf: return NULL if fd == -1
572 * suggested by {kdj,jm18}@sanger.ac.uk
574 ------------------------------------------------------------------------
575 r305 | lh3lh3 | 2009-05-28 11:16:08 +0100 (Thu, 28 May 2009) | 2 lines
577 A /trunk/samtools/misc/interpolate_sam.pl
579 Script for paired-end pileup, contributed by Stephen Montgomery.
581 ------------------------------------------------------------------------
582 r304 | lh3lh3 | 2009-05-28 11:08:49 +0100 (Thu, 28 May 2009) | 3 lines
584 M /trunk/samtools/bamtk.c
585 M /trunk/samtools/sam.c
587 * samtools-0.1.4-1 (r304)
588 * fixed a minor bug in printing headers
590 ------------------------------------------------------------------------
591 r297 | lh3lh3 | 2009-05-21 16:06:16 +0100 (Thu, 21 May 2009) | 2 lines
593 M /trunk/samtools/ChangeLog
594 M /trunk/samtools/NEWS
595 M /trunk/samtools/bam_plcmd.c
596 M /trunk/samtools/bamtk.c
597 M /trunk/samtools/misc/maq2sam.c
598 M /trunk/samtools/samtools.1
600 Release samtools-0.1.4
602 ------------------------------------------------------------------------
603 r296 | lh3lh3 | 2009-05-21 12:53:14 +0100 (Thu, 21 May 2009) | 3 lines
605 M /trunk/samtools/bam_maqcns.c
606 M /trunk/samtools/bamtk.c
608 * samtools-0.1.3-24 (r296)
609 * another similar bug in the indel caller
611 ------------------------------------------------------------------------
612 r295 | lh3lh3 | 2009-05-21 12:50:28 +0100 (Thu, 21 May 2009) | 3 lines
614 M /trunk/samtools/bam_maqcns.c
615 M /trunk/samtools/bamtk.c
617 * samtools-0.1.3-23 (r295)
618 * fixed a critical bug in the indel caller
620 ------------------------------------------------------------------------
621 r294 | lh3lh3 | 2009-05-20 13:00:20 +0100 (Wed, 20 May 2009) | 2 lines
623 M /trunk/samtools/bam_stat.c
625 added a missing header file
627 ------------------------------------------------------------------------
628 r293 | lh3lh3 | 2009-05-19 23:44:25 +0100 (Tue, 19 May 2009) | 3 lines
630 M /trunk/samtools/bam_tview.c
631 M /trunk/samtools/bamtk.c
633 * samtools-0.1.3-22 (r293)
634 * open tview in the dot-view mode by default
636 ------------------------------------------------------------------------
637 r292 | lh3lh3 | 2009-05-18 21:01:23 +0100 (Mon, 18 May 2009) | 6 lines
639 M /trunk/samtools/samtools.1
641 Added a note to the manual. Currently SAMtools used unaligned words in
642 several places. Although this does not cause bus errors to me, it may
643 affect portability. Please see the "Bus error" wiki page for more
644 information. Also thank James Bonfields for pointing this out.
647 ------------------------------------------------------------------------
648 r286 | lh3lh3 | 2009-05-14 15:23:13 +0100 (Thu, 14 May 2009) | 3 lines
650 M /trunk/samtools/bam.h
651 M /trunk/samtools/bam_aux.c
652 M /trunk/samtools/bamtk.c
654 * samtools-0.1.3-21 (286)
655 * declare bam_aux_get_core() in bam.h
657 ------------------------------------------------------------------------
658 r276 | lh3lh3 | 2009-05-13 10:07:55 +0100 (Wed, 13 May 2009) | 5 lines
660 M /trunk/samtools/bam.h
661 M /trunk/samtools/bam_index.c
662 M /trunk/samtools/bamtk.c
664 * samtools-0.1.3-20 (r276)
665 * remove bam1_t::hash again. We need to modify the Perl API anyway to
666 make it work with the latest SVN.
667 * As is suggested by Tim, scan "{base}.bai" and "{base}.bam.bai" for index
669 ------------------------------------------------------------------------
670 r275 | lh3lh3 | 2009-05-12 21:14:10 +0100 (Tue, 12 May 2009) | 4 lines
672 M /trunk/samtools/ChangeLog
673 M /trunk/samtools/bam.h
674 M /trunk/samtools/bamtk.c
676 * samtools-0.1.3-19 (r275)
677 * a minor change to the bam1_t struct: added back "void *hash" for the
678 backward compatibility with Bio::DB::Sam
680 ------------------------------------------------------------------------
681 r273 | lh3lh3 | 2009-05-12 14:28:39 +0100 (Tue, 12 May 2009) | 3 lines
683 M /trunk/samtools/bam_rmdupse.c
684 M /trunk/samtools/bamtk.c
686 * samtools-0.1.3-18 (r273)
687 * rmdupse: do not remove unmapped reads
689 ------------------------------------------------------------------------
690 r272 | lh3lh3 | 2009-05-12 14:20:00 +0100 (Tue, 12 May 2009) | 2 lines
692 M /trunk/samtools/bam_rmdupse.c
694 change a parameter. It does nothing
696 ------------------------------------------------------------------------
697 r271 | lh3lh3 | 2009-05-12 14:17:58 +0100 (Tue, 12 May 2009) | 3 lines
699 M /trunk/samtools/Makefile.am
700 M /trunk/samtools/Makefile.generic
701 M /trunk/samtools/Makefile.lite
702 A /trunk/samtools/bam_rmdupse.c
703 M /trunk/samtools/bamtk.c
704 M /trunk/samtools/configure.ac
706 * samtools-0.1.3-17 (r271)
707 * added 'rmdupse' command
709 ------------------------------------------------------------------------
710 r267 | lh3lh3 | 2009-05-05 22:31:41 +0100 (Tue, 05 May 2009) | 3 lines
712 M /trunk/samtools/bamtk.c
713 M /trunk/samtools/sam_view.c
715 * samtools-0.1.3-16 (r267)
716 * in sam_view.c, changed g_flag_on based on the suggestion by Angie Hinrichs
718 ------------------------------------------------------------------------
719 r266 | lh3lh3 | 2009-05-05 22:23:27 +0100 (Tue, 05 May 2009) | 3 lines
721 M /trunk/samtools/bam_import.c
722 M /trunk/samtools/bamtk.c
724 * samtools-0.1.3-15 (r266)
725 * report an error if a non-* reference is present while @SQ is absent
727 ------------------------------------------------------------------------
728 r265 | lh3lh3 | 2009-05-05 22:09:00 +0100 (Tue, 05 May 2009) | 3 lines
730 M /trunk/samtools/bam.h
731 M /trunk/samtools/bam_import.c
732 M /trunk/samtools/bamtk.c
733 M /trunk/samtools/sam.c
734 M /trunk/samtools/sam_view.c
736 * samtools-0.1.3-14 (r262)
737 * make samopen() recognize @SQ header lines
739 ------------------------------------------------------------------------
740 r261 | lh3lh3 | 2009-05-05 15:10:30 +0100 (Tue, 05 May 2009) | 3 lines
742 M /trunk/samtools/bam_plcmd.c
743 M /trunk/samtools/bamtk.c
744 M /trunk/samtools/bgzf.c
745 M /trunk/samtools/sam.c
746 M /trunk/samtools/sam_view.c
748 * samtools-0.1.3-13 (r260)
749 * report error for file I/O error
751 ------------------------------------------------------------------------
752 r260 | lh3lh3 | 2009-05-05 15:01:16 +0100 (Tue, 05 May 2009) | 2 lines
754 M /trunk/samtools/Makefile.am
758 ------------------------------------------------------------------------
759 r259 | lh3lh3 | 2009-05-05 14:52:25 +0100 (Tue, 05 May 2009) | 3 lines
761 M /trunk/samtools/bam.h
762 M /trunk/samtools/bam_pileup.c
763 M /trunk/samtools/bam_plcmd.c
764 M /trunk/samtools/bamtk.c
765 M /trunk/samtools/sam.c
766 M /trunk/samtools/sam.h
768 * samtools-0.1.3-12 (r259)
769 * use the new I/O interface in pileup
771 ------------------------------------------------------------------------
772 r258 | lh3lh3 | 2009-05-05 14:33:22 +0100 (Tue, 05 May 2009) | 3 lines
774 M /trunk/samtools/Makefile.generic
775 M /trunk/samtools/Makefile.lite
776 M /trunk/samtools/bam.c
777 M /trunk/samtools/bam.h
778 M /trunk/samtools/bam_import.c
779 M /trunk/samtools/bamtk.c
780 A /trunk/samtools/sam.c
781 A /trunk/samtools/sam.h
782 A /trunk/samtools/sam_view.c
784 * samtools-0.1.3-11 (r258)
785 * unify the interface to BAM and SAM I/O
787 ------------------------------------------------------------------------
788 r257 | lh3lh3 | 2009-05-05 09:53:35 +0100 (Tue, 05 May 2009) | 3 lines
790 M /trunk/samtools/Makefile.lite
791 M /trunk/samtools/bam_plcmd.c
792 M /trunk/samtools/bamtk.c
794 * samtools-0.1.3-10 (r257)
795 * allow hex with "pileup -m"
797 ------------------------------------------------------------------------
798 r256 | lh3lh3 | 2009-05-04 19:16:50 +0100 (Mon, 04 May 2009) | 4 lines
800 M /trunk/samtools/bam_lpileup.c
801 M /trunk/samtools/bamtk.c
803 * samtools-0.1.3-9 (r256)
804 * fixed a bug in bam_lpileup.c
805 * I do not know if this also fixes the bug causing assertion failure in the tview
807 ------------------------------------------------------------------------
808 r251 | lh3lh3 | 2009-04-28 13:53:23 +0100 (Tue, 28 Apr 2009) | 3 lines
810 M /trunk/samtools/bam_pileup.c
811 M /trunk/samtools/bamtk.c
813 * samtools-0.1.3-8 (r251)
814 * fixed a bug when there are reads without coordinates
816 ------------------------------------------------------------------------
817 r250 | lh3lh3 | 2009-04-28 13:43:33 +0100 (Tue, 28 Apr 2009) | 2 lines
819 A /trunk/samtools/AUTHORS
820 A /trunk/samtools/README
821 M /trunk/samtools/cleanup.sh
825 ------------------------------------------------------------------------
826 r249 | lh3lh3 | 2009-04-28 13:37:16 +0100 (Tue, 28 Apr 2009) | 2 lines
828 M /trunk/samtools/Makefile.generic
829 M /trunk/samtools/Makefile.lite
830 M /trunk/samtools/configure.ac
831 M /trunk/samtools/misc/Makefile.generic
833 improve large file support in compilation
835 ------------------------------------------------------------------------
836 r248 | lh3lh3 | 2009-04-28 13:33:24 +0100 (Tue, 28 Apr 2009) | 2 lines
838 M /trunk/samtools/INSTALL
842 ------------------------------------------------------------------------
843 r247 | lh3lh3 | 2009-04-28 13:28:50 +0100 (Tue, 28 Apr 2009) | 2 lines
845 M /trunk/samtools/Makefile.am
846 M /trunk/samtools/autogen.sh
847 M /trunk/samtools/cleanup.sh
848 M /trunk/samtools/configure.ac
849 A /trunk/samtools/misc/Makefile.am
851 fixed various issues about the GNU building scripts
853 ------------------------------------------------------------------------
854 r246 | lh3lh3 | 2009-04-28 13:10:23 +0100 (Tue, 28 Apr 2009) | 4 lines
856 M /trunk/samtools/ChangeLog
857 D /trunk/samtools/Makefile
858 A /trunk/samtools/Makefile.am
859 A /trunk/samtools/Makefile.generic
860 A /trunk/samtools/autogen.sh
861 M /trunk/samtools/bam.h
862 M /trunk/samtools/bam_aux.c
863 M /trunk/samtools/bam_tview.c
864 M /trunk/samtools/bamtk.c
865 A /trunk/samtools/cleanup.sh
866 A /trunk/samtools/configure.ac
867 D /trunk/samtools/misc/Makefile
868 A /trunk/samtools/misc/Makefile.generic (from /trunk/samtools/misc/Makefile:245)
870 * samtools-0.1.3-7 (r246)
871 * incorporated revisions from Nils Homer
872 * enhanced support of displaying color-space reads
874 ------------------------------------------------------------------------
875 r244 | lh3lh3 | 2009-04-25 11:49:40 +0100 (Sat, 25 Apr 2009) | 3 lines
877 M /trunk/samtools/bam_md.c
878 M /trunk/samtools/bamtk.c
880 * samtools-0.1.3-6 (r244)
881 * fixed segfault for unmapped reads
883 ------------------------------------------------------------------------
884 r243 | lh3lh3 | 2009-04-24 21:27:26 +0100 (Fri, 24 Apr 2009) | 5 lines
886 M /trunk/samtools/bam.h
887 M /trunk/samtools/bam_maqcns.c
888 M /trunk/samtools/bam_md.c
889 M /trunk/samtools/bamtk.c
891 * samtools-0.1.3-5 (r243)
892 * fixed a long existing bug which may cause memory leak
894 * consensus calling now works with "=", but indel calling not
896 ------------------------------------------------------------------------
897 r242 | lh3lh3 | 2009-04-24 20:44:46 +0100 (Fri, 24 Apr 2009) | 3 lines
899 M /trunk/samtools/bam_md.c
900 M /trunk/samtools/bamtk.c
902 * samtools-0.1.3-4 (r242)
903 * fixed a memory leak
905 ------------------------------------------------------------------------
906 r240 | lh3lh3 | 2009-04-24 16:40:18 +0100 (Fri, 24 Apr 2009) | 5 lines
908 M /trunk/samtools/Makefile
909 M /trunk/samtools/Makefile.lite
910 M /trunk/samtools/bam.h
911 M /trunk/samtools/bam_aux.c
912 A /trunk/samtools/bam_md.c
913 M /trunk/samtools/bam_plcmd.c
914 M /trunk/samtools/bamtk.c
916 * samtools-0.1.3-3 (r240)
919 * the plain pileup now support "=" bases, but consensus calling and glfgen may fail
921 ------------------------------------------------------------------------
922 r239 | lh3lh3 | 2009-04-24 12:08:20 +0100 (Fri, 24 Apr 2009) | 5 lines
924 M /trunk/samtools/bam.h
925 M /trunk/samtools/bam_aux.c
926 M /trunk/samtools/bamtk.c
928 * samtools-0.1.3-2 (r239)
929 * fixed bugs in bam_aux.c (these functions nevered used by samtools)
930 * removed bam_aux_init()/bam_aux_destroy()
931 * added tagview for testing bam_aux
933 ------------------------------------------------------------------------
934 r235 | lh3lh3 | 2009-04-21 23:17:39 +0100 (Tue, 21 Apr 2009) | 3 lines
936 M /trunk/samtools/bam_pileup.c
937 M /trunk/samtools/bamtk.c
940 * fixed a bug in pileup: the first read in a chromosome may not be printed
942 ------------------------------------------------------------------------
943 r232 | lh3lh3 | 2009-04-16 15:25:43 +0100 (Thu, 16 Apr 2009) | 2 lines
945 M /trunk/samtools/Makefile.lite
947 a missing file in Makefile.lite
949 ------------------------------------------------------------------------
950 r227 | lh3lh3 | 2009-04-15 22:02:53 +0100 (Wed, 15 Apr 2009) | 2 lines
952 M /trunk/samtools/NEWS
953 M /trunk/samtools/bamtk.c
955 Release samtools-0.1.3
957 ------------------------------------------------------------------------
958 r223 | lh3lh3 | 2009-04-15 14:31:32 +0100 (Wed, 15 Apr 2009) | 3 lines
960 M /trunk/samtools/bam_plcmd.c
961 M /trunk/samtools/bamtk.c
964 * make samtools more robust to weird input such as empty file
966 ------------------------------------------------------------------------
967 r222 | lh3lh3 | 2009-04-15 14:05:33 +0100 (Wed, 15 Apr 2009) | 2 lines
969 M /trunk/samtools/ChangeLog
970 M /trunk/samtools/NEWS
971 M /trunk/samtools/samtools.1
973 prepare for release 0.1.3
975 ------------------------------------------------------------------------
976 r221 | lh3lh3 | 2009-04-15 13:32:14 +0100 (Wed, 15 Apr 2009) | 2 lines
978 A /trunk/samtools/misc/blast2sam.pl
980 convert NCBI-BLASTN to SAM
982 ------------------------------------------------------------------------
983 r220 | lh3lh3 | 2009-04-15 13:18:19 +0100 (Wed, 15 Apr 2009) | 3 lines
985 M /trunk/samtools/bam_lpileup.c
986 M /trunk/samtools/bamtk.c
989 * fixed a small memory leak in tview
991 ------------------------------------------------------------------------
992 r219 | lh3lh3 | 2009-04-15 13:00:08 +0100 (Wed, 15 Apr 2009) | 3 lines
994 M /trunk/samtools/bam_rmdup.c
995 M /trunk/samtools/bamtk.c
998 * fixed a bug in rmdup when there are unmapped reads
1000 ------------------------------------------------------------------------
1001 r218 | lh3lh3 | 2009-04-14 22:28:58 +0100 (Tue, 14 Apr 2009) | 2 lines
1003 M /trunk/samtools/ChangeLog
1004 M /trunk/samtools/NEWS
1006 proposed NEWS for the new release (have not yet)
1008 ------------------------------------------------------------------------
1009 r216 | lh3lh3 | 2009-04-14 22:10:46 +0100 (Tue, 14 Apr 2009) | 4 lines
1011 M /trunk/samtools/misc/samtools.pl
1014 * improve indelFilter to avoid filtering true indels. The new filter relies
1015 on the new pileup indel line implemented in samtools-0.1.2-25
1017 ------------------------------------------------------------------------
1018 r215 | lh3lh3 | 2009-04-14 22:04:19 +0100 (Tue, 14 Apr 2009) | 4 lines
1020 M /trunk/samtools/bam_maqcns.c
1021 M /trunk/samtools/bam_plcmd.c
1022 M /trunk/samtools/bamtk.c
1023 M /trunk/samtools/samtools.1
1026 * change the pileup indel line to shows the number of alignments actually
1029 ------------------------------------------------------------------------
1030 r211 | lh3lh3 | 2009-04-13 12:07:13 +0100 (Mon, 13 Apr 2009) | 2 lines
1032 M /trunk/samtools/ChangeLog
1034 update ChangeLog from "svn log"
1036 ------------------------------------------------------------------------
1037 r210 | lh3lh3 | 2009-04-12 20:57:05 +0100 (Sun, 12 Apr 2009) | 4 lines
1039 M /trunk/samtools/bam.c
1040 M /trunk/samtools/bam_import.c
1041 M /trunk/samtools/bam_sort.c
1042 M /trunk/samtools/bamtk.c
1043 M /trunk/samtools/kseq.h
1046 * in merge, gives a warning rather than error if the target sequence length is different
1047 * allow empty header
1049 ------------------------------------------------------------------------
1050 r209 | lh3lh3 | 2009-04-12 20:32:44 +0100 (Sun, 12 Apr 2009) | 3 lines
1052 M /trunk/samtools/bam.c
1053 M /trunk/samtools/bam_import.c
1054 M /trunk/samtools/bamtk.c
1057 * recognize '*' at the QUAL field
1059 ------------------------------------------------------------------------
1060 r208 | lh3lh3 | 2009-04-12 20:08:02 +0100 (Sun, 12 Apr 2009) | 3 lines
1062 M /trunk/samtools/bam_import.c
1063 M /trunk/samtools/bamtk.c
1064 M /trunk/samtools/kseq.h
1067 * the field separater is TAB only, now
1069 ------------------------------------------------------------------------
1070 r207 | lh3lh3 | 2009-04-08 15:18:03 +0100 (Wed, 08 Apr 2009) | 2 lines
1072 M /trunk/samtools/examples/ex1.sam.gz
1074 * fixed the problem in the example alignment due to the bug in fixmate
1076 ------------------------------------------------------------------------
1077 r206 | lh3lh3 | 2009-04-08 15:15:05 +0100 (Wed, 08 Apr 2009) | 3 lines
1079 M /trunk/samtools/bam_mate.c
1080 M /trunk/samtools/bamtk.c
1081 M /trunk/samtools/misc/soap2sam.pl
1084 * fixed a nasty bug in `fixmate'
1086 ------------------------------------------------------------------------
1087 r205 | lh3lh3 | 2009-04-08 10:57:08 +0100 (Wed, 08 Apr 2009) | 2 lines
1089 M /trunk/samtools/misc/bowtie2sam.pl
1090 M /trunk/samtools/misc/soap2sam.pl
1091 M /trunk/samtools/misc/wgsim_eval.pl
1093 make the script robust to the bugs in SOAP-2.1.7
1095 ------------------------------------------------------------------------
1096 r200 | lh3lh3 | 2009-04-02 15:14:56 +0100 (Thu, 02 Apr 2009) | 3 lines
1098 M /trunk/samtools/bam_stat.c
1099 M /trunk/samtools/bamtk.c
1102 * check if file is truncated in flagstat
1104 ------------------------------------------------------------------------
1105 r199 | lh3lh3 | 2009-04-02 15:09:10 +0100 (Thu, 02 Apr 2009) | 3 lines
1107 M /trunk/samtools/bamtk.c
1110 * print the header if requested
1112 ------------------------------------------------------------------------
1113 r193 | lh3lh3 | 2009-03-27 15:09:50 +0000 (Fri, 27 Mar 2009) | 3 lines
1115 M /trunk/samtools/bam_plcmd.c
1116 M /trunk/samtools/bamtk.c
1119 * fixed a minor bug reported by Nils Homer
1121 ------------------------------------------------------------------------
1122 r185 | lh3lh3 | 2009-03-24 11:50:32 +0000 (Tue, 24 Mar 2009) | 2 lines
1124 A /trunk/samtools/Makefile (from /trunk/samtools/Makefile.std:184)
1125 D /trunk/samtools/Makefile.std
1126 A /trunk/samtools/misc/Makefile (from /trunk/samtools/misc/Makefile.std:184)
1127 D /trunk/samtools/misc/Makefile.std
1129 rename Makefile.std as Makefile. GNU building systerm is not ready and may take some time...
1131 ------------------------------------------------------------------------
1132 r184 | lh3lh3 | 2009-03-24 10:36:38 +0000 (Tue, 24 Mar 2009) | 4 lines
1134 D /trunk/samtools/Makefile
1135 A /trunk/samtools/Makefile.std (from /trunk/samtools/Makefile:183)
1136 M /trunk/samtools/bam_sort.c
1137 M /trunk/samtools/bam_tview.c
1138 M /trunk/samtools/bamtk.c
1139 D /trunk/samtools/misc/Makefile
1140 A /trunk/samtools/misc/Makefile.std (from /trunk/samtools/misc/Makefile:182)
1141 M /trunk/samtools/samtools.1
1144 * incorporating Nils' changes
1145 * rename Makefile to Makefile.std and prepare to add the GNU building systerms (also by Nils)
1147 ------------------------------------------------------------------------
1148 r183 | lh3lh3 | 2009-03-24 10:30:23 +0000 (Tue, 24 Mar 2009) | 4 lines
1150 M /trunk/samtools/Makefile
1151 M /trunk/samtools/bam_import.c
1152 M /trunk/samtools/bam_maqcns.c
1153 M /trunk/samtools/bam_maqcns.h
1154 M /trunk/samtools/bam_plcmd.c
1155 M /trunk/samtools/bamtk.c
1156 M /trunk/samtools/kseq.h
1157 A /trunk/samtools/kstring.c
1158 A /trunk/samtools/kstring.h
1161 * made pileup take a list of proposed indels. An insertion is N at the moment.
1162 * added my kstring library for a bit complex parsing of the position list.
1164 ------------------------------------------------------------------------
1165 r169 | lh3lh3 | 2009-03-12 13:40:14 +0000 (Thu, 12 Mar 2009) | 3 lines
1167 M /trunk/samtools/misc/soap2sam.pl
1170 * more robust to truncated soap output
1172 ------------------------------------------------------------------------
1173 r168 | lh3lh3 | 2009-03-11 10:49:00 +0000 (Wed, 11 Mar 2009) | 2 lines
1175 M /trunk/samtools/Makefile.lite
1177 added bam_stat.o to Makefile.lite
1179 ------------------------------------------------------------------------
1180 r167 | lh3lh3 | 2009-03-10 22:11:31 +0000 (Tue, 10 Mar 2009) | 3 lines
1182 M /trunk/samtools/bam_maqcns.c
1183 M /trunk/samtools/bamtk.c
1186 * generate RMS of mapQ instead of max mapQ
1188 ------------------------------------------------------------------------
1189 r166 | lh3lh3 | 2009-03-10 22:06:45 +0000 (Tue, 10 Mar 2009) | 3 lines
1191 M /trunk/samtools/bam_plcmd.c
1192 M /trunk/samtools/bamtk.c
1193 M /trunk/samtools/glf.c
1194 M /trunk/samtools/glf.h
1195 M /trunk/samtools/misc/Makefile
1200 ------------------------------------------------------------------------
1201 r159 | lh3lh3 | 2009-03-03 11:26:08 +0000 (Tue, 03 Mar 2009) | 3 lines
1203 M /trunk/samtools/bam_plcmd.c
1204 M /trunk/samtools/bamtk.c
1207 * fixed a minor bug in displaying pileup
1209 ------------------------------------------------------------------------
1210 r158 | lh3lh3 | 2009-03-03 11:24:16 +0000 (Tue, 03 Mar 2009) | 3 lines
1212 M /trunk/samtools/ChangeLog
1213 M /trunk/samtools/bamtk.c
1216 * optionally print SAM header
1218 ------------------------------------------------------------------------
1219 r153 | lh3lh3 | 2009-03-02 10:45:28 +0000 (Mon, 02 Mar 2009) | 3 lines
1221 M /trunk/samtools/bamtk.c
1222 M /trunk/samtools/glf.c
1225 * use "GLF\3" as the magic for GLFv3 files
1227 ------------------------------------------------------------------------
1228 r152 | lh3lh3 | 2009-03-02 10:39:09 +0000 (Mon, 02 Mar 2009) | 5 lines
1230 M /trunk/samtools/Makefile
1231 M /trunk/samtools/bam_import.c
1232 M /trunk/samtools/bam_index.c
1233 M /trunk/samtools/bam_plcmd.c
1234 M /trunk/samtools/bamtk.c
1235 M /trunk/samtools/glf.c
1236 M /trunk/samtools/glf.h
1239 * fixed a bug in import: core.bin is undefined for unmapped reads
1240 * this bug can be alleviated (not completely solved) in bam_index.c
1241 * update to GLFv3: pos is changed to offset for better compression
1243 ------------------------------------------------------------------------
1244 r151 | lh3lh3 | 2009-03-01 15:18:43 +0000 (Sun, 01 Mar 2009) | 3 lines
1246 M /trunk/samtools/misc/wgsim.c
1249 * fixed a bug in simulating indels
1251 ------------------------------------------------------------------------
1252 r145 | lh3lh3 | 2009-02-26 19:43:57 +0000 (Thu, 26 Feb 2009) | 4 lines
1254 M /trunk/samtools/misc/wgsim.c
1257 * allow to print mismatch information as fastq comment. MAQ does
1258 not like long read names.
1260 ------------------------------------------------------------------------
1261 r141 | lh3lh3 | 2009-02-26 14:53:03 +0000 (Thu, 26 Feb 2009) | 6 lines
1263 M /trunk/samtools/ChangeLog
1264 M /trunk/samtools/misc/wgsim.c
1265 M /trunk/samtools/misc/wgsim_eval.pl
1268 * fixed a bug about color read coordinates
1269 * fixed a bug in read names
1270 * wgsim_eval.pl-0.1.3
1271 * make the script work with color reads
1273 ------------------------------------------------------------------------
1274 r140 | lh3lh3 | 2009-02-26 14:02:57 +0000 (Thu, 26 Feb 2009) | 2 lines
1276 M /trunk/samtools/misc/Makefile
1277 M /trunk/samtools/misc/wgsim.c
1279 * wgsim: added a note
1281 ------------------------------------------------------------------------
1282 r139 | lh3lh3 | 2009-02-26 11:39:08 +0000 (Thu, 26 Feb 2009) | 7 lines
1284 M /trunk/samtools/misc/wgsim.c
1285 M /trunk/samtools/misc/wgsim_eval.pl
1288 * considerable code clean up
1289 * print number of substitutions/indels/errors on each read
1290 * potentially support SOLiD simulation, though not tested at the moment
1291 * wgsim_eval.pl-0.1.2
1292 * change in accordant with wgsim
1294 ------------------------------------------------------------------------
1295 r129 | lh3lh3 | 2009-02-18 22:23:27 +0000 (Wed, 18 Feb 2009) | 3 lines
1297 M /trunk/samtools/bam_index.c
1298 M /trunk/samtools/bamtk.c
1301 * fixed a bug in bam_fetch, caused by completely contained adjacent chunks
1303 ------------------------------------------------------------------------
1304 r128 | bhandsaker | 2009-02-18 19:06:57 +0000 (Wed, 18 Feb 2009) | 2 lines
1306 M /trunk/samtools/bamtk.c
1308 Fix annoying segv when invalid region specified.
1310 ------------------------------------------------------------------------
1311 r127 | lh3lh3 | 2009-02-17 10:49:55 +0000 (Tue, 17 Feb 2009) | 2 lines
1313 D /trunk/samtools/misc/indel_filter.pl
1314 A /trunk/samtools/misc/samtools.pl
1316 * move indel_filter.pl to samtools.pl
1318 ------------------------------------------------------------------------
1319 r126 | lh3lh3 | 2009-02-14 21:22:30 +0000 (Sat, 14 Feb 2009) | 3 lines
1321 M /trunk/samtools/bam_mate.c
1322 M /trunk/samtools/bamtk.c
1325 * fixed a bug in fixmate: SE reads are flagged as BAM_FMUNMAP
1327 ------------------------------------------------------------------------
1328 r125 | lh3lh3 | 2009-02-13 09:54:45 +0000 (Fri, 13 Feb 2009) | 3 lines
1330 M /trunk/samtools/bam_stat.c
1331 M /trunk/samtools/bamtk.c
1334 * fixed a minor bug in flagstat
1336 ------------------------------------------------------------------------
1337 r124 | lh3lh3 | 2009-02-12 11:15:32 +0000 (Thu, 12 Feb 2009) | 3 lines
1339 M /trunk/samtools/bam_maqcns.c
1340 M /trunk/samtools/bamtk.c
1341 M /trunk/samtools/misc/indel_filter.pl
1344 * improve indel caller by setting maximum window size
1346 ------------------------------------------------------------------------
1347 r123 | lh3lh3 | 2009-02-12 10:30:29 +0000 (Thu, 12 Feb 2009) | 2 lines
1349 M /trunk/samtools/bam_plcmd.c
1350 M /trunk/samtools/bamtk.c
1352 * output max mapping quality in indel line
1354 ------------------------------------------------------------------------
1355 r122 | lh3lh3 | 2009-02-11 10:59:10 +0000 (Wed, 11 Feb 2009) | 2 lines
1357 M /trunk/samtools/misc/maq2sam.c
1359 fixed a bug in generating tag AM
1361 ------------------------------------------------------------------------
1362 r121 | lh3lh3 | 2009-02-03 10:43:11 +0000 (Tue, 03 Feb 2009) | 2 lines
1364 M /trunk/samtools/bam_index.c
1365 M /trunk/samtools/bamtk.c
1367 fixed a potential memory problem in indexing
1369 ------------------------------------------------------------------------
1370 r120 | bhandsaker | 2009-02-02 15:52:52 +0000 (Mon, 02 Feb 2009) | 2 lines
1372 M /trunk/samtools/Makefile
1374 Pass LIBS to recursive targets to facilitate building at Broad.
1376 ------------------------------------------------------------------------
1377 r119 | lh3lh3 | 2009-02-02 10:12:15 +0000 (Mon, 02 Feb 2009) | 4 lines
1379 M /trunk/samtools/ChangeLog
1380 M /trunk/samtools/bam_plcmd.c
1381 M /trunk/samtools/bam_stat.c
1382 M /trunk/samtools/bamtk.c
1385 * fixed a bug in generating GLFv2 for indels
1386 * improve flagstat report a little bit
1388 ------------------------------------------------------------------------
1389 r118 | lh3lh3 | 2009-01-29 12:33:23 +0000 (Thu, 29 Jan 2009) | 3 lines
1391 M /trunk/samtools/Makefile
1392 A /trunk/samtools/bam_stat.c
1393 M /trunk/samtools/bamtk.c
1396 * added flagstat command
1398 ------------------------------------------------------------------------
1399 r116 | lh3lh3 | 2009-01-28 13:31:12 +0000 (Wed, 28 Jan 2009) | 2 lines
1401 M /trunk/samtools/ChangeLog
1402 M /trunk/samtools/NEWS
1403 M /trunk/samtools/bamtk.c
1404 M /trunk/samtools/samtools.1
1406 Release SAMtools-0.1.2
1408 ------------------------------------------------------------------------
1409 r115 | lh3lh3 | 2009-01-28 12:54:08 +0000 (Wed, 28 Jan 2009) | 2 lines
1411 A /trunk/samtools/misc/indel_filter.pl
1413 Script for filtering indel results
1415 ------------------------------------------------------------------------
1416 r114 | lh3lh3 | 2009-01-25 11:45:37 +0000 (Sun, 25 Jan 2009) | 2 lines
1418 A /trunk/samtools/misc/zoom2sam.pl
1422 ------------------------------------------------------------------------
1423 r113 | lh3lh3 | 2009-01-24 14:25:07 +0000 (Sat, 24 Jan 2009) | 2 lines
1425 A /trunk/samtools/misc/novo2sam.pl
1427 add a script to convert novo alignment to SAM
1429 ------------------------------------------------------------------------
1430 r112 | lh3lh3 | 2009-01-23 20:57:39 +0000 (Fri, 23 Jan 2009) | 2 lines
1432 M /trunk/samtools/ChangeLog
1433 M /trunk/samtools/ChangeLog.old
1434 M /trunk/samtools/samtools.1
1436 update documentation and ChangeLog
1438 ------------------------------------------------------------------------
1439 r111 | lh3lh3 | 2009-01-23 19:22:59 +0000 (Fri, 23 Jan 2009) | 3 lines
1441 M /trunk/samtools/bam_sort.c
1442 M /trunk/samtools/bamtk.c
1445 * fixed a bug in "merge" command line
1447 ------------------------------------------------------------------------
1448 r110 | lh3lh3 | 2009-01-22 15:36:48 +0000 (Thu, 22 Jan 2009) | 3 lines
1450 M /trunk/samtools/misc/Makefile
1451 A /trunk/samtools/misc/bowtie2sam.pl (from /branches/dev/samtools/misc/bowtie2sam.pl:108)
1452 M /trunk/samtools/misc/export2sam.pl
1453 A /trunk/samtools/misc/soap2sam.pl (from /branches/dev/samtools/misc/soap2sam.pl:108)
1454 A /trunk/samtools/misc/wgsim.c (from /branches/dev/samtools/misc/wgsim.c:108)
1455 A /trunk/samtools/misc/wgsim_eval.pl (from /branches/dev/samtools/misc/wgsim_eval.pl:108)
1457 * merge from branches/dev/
1458 * all future development will happen here
1460 ------------------------------------------------------------------------
1461 r109 | lh3lh3 | 2009-01-22 15:14:27 +0000 (Thu, 22 Jan 2009) | 3 lines
1463 M /trunk/samtools/COPYING
1464 M /trunk/samtools/ChangeLog
1465 A /trunk/samtools/INSTALL (from /branches/dev/samtools/INSTALL:108)
1466 M /trunk/samtools/Makefile
1467 A /trunk/samtools/Makefile.lite (from /branches/dev/samtools/Makefile.lite:108)
1468 M /trunk/samtools/bam.c
1469 M /trunk/samtools/bam.h
1470 M /trunk/samtools/bam_import.c
1471 M /trunk/samtools/bam_index.c
1472 M /trunk/samtools/bam_lpileup.c
1473 M /trunk/samtools/bam_maqcns.c
1474 M /trunk/samtools/bam_maqcns.h
1475 A /trunk/samtools/bam_mate.c (from /branches/dev/samtools/bam_mate.c:108)
1476 M /trunk/samtools/bam_pileup.c
1477 M /trunk/samtools/bam_plcmd.c
1478 A /trunk/samtools/bam_rmdup.c (from /branches/dev/samtools/bam_rmdup.c:108)
1479 M /trunk/samtools/bam_sort.c
1480 M /trunk/samtools/bamtk.c
1481 M /trunk/samtools/bgzf.h
1482 M /trunk/samtools/examples/00README.txt
1483 A /trunk/samtools/examples/Makefile (from /branches/dev/samtools/examples/Makefile:108)
1484 D /trunk/samtools/examples/ex1.fa.fai
1485 M /trunk/samtools/examples/ex1.sam.gz
1486 M /trunk/samtools/faidx.c
1487 A /trunk/samtools/glf.c (from /branches/dev/samtools/glf.c:108)
1488 M /trunk/samtools/glf.h
1489 M /trunk/samtools/misc/Makefile
1490 M /trunk/samtools/misc/maq2sam.c
1491 M /trunk/samtools/razf.c
1492 M /trunk/samtools/source.dot
1494 * Merge from branches/dev/
1495 * all future development will happen here at trunk/
1497 ------------------------------------------------------------------------
1498 r79 | bhandsaker | 2009-01-07 21:42:15 +0000 (Wed, 07 Jan 2009) | 2 lines
1500 M /trunk/samtools/bam_maqcns.c
1501 M /trunk/samtools/bam_tview.c
1503 Fix problem with compiling without curses.
1505 ------------------------------------------------------------------------
1506 r63 | lh3lh3 | 2008-12-22 15:58:02 +0000 (Mon, 22 Dec 2008) | 2 lines
1508 A /trunk/samtools (from /branches/dev/samtools:62)
1512 ------------------------------------------------------------------------
1513 r62 | lh3lh3 | 2008-12-22 15:55:13 +0000 (Mon, 22 Dec 2008) | 2 lines
1515 A /branches/dev/samtools/NEWS
1516 M /branches/dev/samtools/bamtk.c
1517 M /branches/dev/samtools/samtools.1
1519 Release samtools-0.1.1
1521 ------------------------------------------------------------------------
1522 r61 | lh3lh3 | 2008-12-22 15:46:08 +0000 (Mon, 22 Dec 2008) | 10 lines
1524 M /branches/dev/samtools/bam_aux.c
1525 M /branches/dev/samtools/bam_index.c
1526 M /branches/dev/samtools/bam_plcmd.c
1527 M /branches/dev/samtools/bam_tview.c
1528 M /branches/dev/samtools/bamtk.c
1529 M /branches/dev/samtools/razf.c
1530 M /branches/dev/samtools/samtools.1
1533 * fixed a bug in razf.c: reset z_eof when razf_seek() is called
1534 * fixed a memory leak in parsing a region
1535 * changed pileup a little bit when -s is in use: output ^ and $
1536 * when a bam is not indexed, output more meaningful error message
1537 * fixed a bug in indexing for small alignment
1538 * fixed a bug in the viewer when we come to the end of a reference file
1539 * updated documentation
1540 * prepare to release 0.1.1
1542 ------------------------------------------------------------------------
1543 r60 | lh3lh3 | 2008-12-22 15:10:16 +0000 (Mon, 22 Dec 2008) | 2 lines
1545 A /branches/dev/samtools/examples
1546 A /branches/dev/samtools/examples/00README.txt
1547 A /branches/dev/samtools/examples/ex1.fa
1548 A /branches/dev/samtools/examples/ex1.fa.fai
1549 A /branches/dev/samtools/examples/ex1.sam.gz
1553 ------------------------------------------------------------------------
1554 r59 | lh3lh3 | 2008-12-22 09:38:15 +0000 (Mon, 22 Dec 2008) | 2 lines
1556 M /branches/dev/samtools/ChangeLog
1560 ------------------------------------------------------------------------
1561 r58 | lh3lh3 | 2008-12-20 23:06:00 +0000 (Sat, 20 Dec 2008) | 3 lines
1563 M /branches/dev/samtools/misc/export2sam.pl
1566 * fixed several bugs
1568 ------------------------------------------------------------------------
1569 r57 | lh3lh3 | 2008-12-20 15:44:20 +0000 (Sat, 20 Dec 2008) | 2 lines
1571 A /branches/dev/samtools/misc/export2sam.pl
1573 convert Export format to SAM; not thoroughly tested
1575 ------------------------------------------------------------------------
1576 r56 | lh3lh3 | 2008-12-19 22:13:28 +0000 (Fri, 19 Dec 2008) | 6 lines
1578 M /branches/dev/samtools/bam_import.c
1579 M /branches/dev/samtools/bam_plcmd.c
1580 M /branches/dev/samtools/bam_tview.c
1581 M /branches/dev/samtools/bamtk.c
1582 A /branches/dev/samtools/source.dot
1585 * pileup: generate maq-like simple output
1586 * pileup: allow to output pileup at required sites
1587 * source.dot: source file relationship graph
1588 * tview: fixed a minor bug
1590 ------------------------------------------------------------------------
1591 r55 | lh3lh3 | 2008-12-19 20:10:26 +0000 (Fri, 19 Dec 2008) | 2 lines
1593 D /branches/dev/samtools/misc/all2sam.pl
1597 ------------------------------------------------------------------------
1598 r54 | lh3lh3 | 2008-12-16 22:34:25 +0000 (Tue, 16 Dec 2008) | 2 lines
1600 A /branches/dev/samtools/COPYING
1601 M /branches/dev/samtools/bam.h
1602 M /branches/dev/samtools/faidx.h
1603 M /branches/dev/samtools/khash.h
1604 M /branches/dev/samtools/kseq.h
1605 M /branches/dev/samtools/ksort.h
1606 M /branches/dev/samtools/samtools.1
1608 Added copyright information and a bit more documentation. No code change.
1610 ------------------------------------------------------------------------
1611 r53 | lh3lh3 | 2008-12-16 13:40:18 +0000 (Tue, 16 Dec 2008) | 3 lines
1613 M /branches/dev/samtools/bam.c
1614 M /branches/dev/samtools/bam.h
1615 M /branches/dev/samtools/bam_index.c
1616 M /branches/dev/samtools/bam_maqcns.c
1617 M /branches/dev/samtools/bamtk.c
1620 * improved efficiency of the indel caller for spliced alignments
1622 ------------------------------------------------------------------------
1623 r52 | lh3lh3 | 2008-12-16 10:28:20 +0000 (Tue, 16 Dec 2008) | 3 lines
1625 M /branches/dev/samtools/bam.c
1626 M /branches/dev/samtools/bam.h
1627 M /branches/dev/samtools/bam_aux.c
1628 M /branches/dev/samtools/bam_index.c
1629 M /branches/dev/samtools/bamtk.c
1632 * a bit code cleanup: reduce the dependency between source files
1634 ------------------------------------------------------------------------
1635 r51 | lh3lh3 | 2008-12-15 14:29:32 +0000 (Mon, 15 Dec 2008) | 3 lines
1637 M /branches/dev/samtools/bam_maqcns.c
1638 M /branches/dev/samtools/bam_plcmd.c
1639 M /branches/dev/samtools/bamtk.c
1642 * fixed a memory leak
1644 ------------------------------------------------------------------------
1645 r50 | lh3lh3 | 2008-12-15 14:00:13 +0000 (Mon, 15 Dec 2008) | 2 lines
1647 M /branches/dev/samtools/ChangeLog
1648 M /branches/dev/samtools/bam.h
1649 M /branches/dev/samtools/samtools.1
1651 update documentation, ChangeLog and a comment
1653 ------------------------------------------------------------------------
1654 r49 | lh3lh3 | 2008-12-15 13:36:43 +0000 (Mon, 15 Dec 2008) | 6 lines
1656 M /branches/dev/samtools/Makefile
1657 M /branches/dev/samtools/bam.h
1658 M /branches/dev/samtools/bam_maqcns.c
1659 M /branches/dev/samtools/bam_maqcns.h
1660 M /branches/dev/samtools/bam_pileup.c
1661 A /branches/dev/samtools/bam_plcmd.c
1662 M /branches/dev/samtools/bamtk.c
1663 M /branches/dev/samtools/samtools.1
1666 * moved pileup command to a separate source file
1667 * added indel caller
1668 * added bam_cal_segend(). (NOT WORKING for spliced alignment!!!)
1669 * updated documentation
1671 ------------------------------------------------------------------------
1672 r48 | lh3lh3 | 2008-12-12 13:55:36 +0000 (Fri, 12 Dec 2008) | 3 lines
1674 M /branches/dev/samtools/bam_maqcns.c
1675 M /branches/dev/samtools/bamtk.c
1678 * fixed another bug in maqcns when there is a nearby deletion
1680 ------------------------------------------------------------------------
1681 r47 | lh3lh3 | 2008-12-12 13:42:16 +0000 (Fri, 12 Dec 2008) | 5 lines
1683 M /branches/dev/samtools/bam_maqcns.c
1684 M /branches/dev/samtools/bam_pileup.c
1685 M /branches/dev/samtools/bamtk.c
1688 * pileup: outputing consensus is now optional
1689 * fixed a bug in glfgen. This bug also exists in maq's glfgen. However,
1690 I am not quite sure why the previous version may have problem.
1692 ------------------------------------------------------------------------
1693 r46 | lh3lh3 | 2008-12-12 11:44:56 +0000 (Fri, 12 Dec 2008) | 6 lines
1695 M /branches/dev/samtools/bam_pileup.c
1696 M /branches/dev/samtools/bamtk.c
1699 * add maq consensus to pileup. However, I will move this part to a new
1700 command as strictly speaking, consensus callin is not part of pileup,
1701 and imposing it would make it harder to generate for other language
1704 ------------------------------------------------------------------------
1705 r45 | bhandsaker | 2008-12-11 20:43:56 +0000 (Thu, 11 Dec 2008) | 2 lines
1707 M /branches/dev/samtools/bgzf.c
1709 Fix bug in tell() after reads that consume to the exact end of a block.
1711 ------------------------------------------------------------------------
1712 r44 | lh3lh3 | 2008-12-11 09:36:53 +0000 (Thu, 11 Dec 2008) | 2 lines
1714 M /branches/dev/samtools/samtools.1
1718 ------------------------------------------------------------------------
1719 r43 | lh3lh3 | 2008-12-11 09:25:36 +0000 (Thu, 11 Dec 2008) | 4 lines
1721 M /branches/dev/samtools/bam_import.c
1722 M /branches/dev/samtools/bamtk.c
1725 * fixed a bug in parser when there is auxiliary fields
1726 * made the parser a bit more robust
1728 ------------------------------------------------------------------------
1729 r42 | lh3lh3 | 2008-12-10 14:57:29 +0000 (Wed, 10 Dec 2008) | 5 lines
1731 M /branches/dev/samtools/bam_index.c
1732 M /branches/dev/samtools/bamtk.c
1733 M /branches/dev/samtools/bgzf.c
1736 * fixed a bug in bgzf (only reading is affected)
1737 * fixed a typo in bam_index.c
1738 * in bam_index.c, check potential bugs in the underlying I/O library
1740 ------------------------------------------------------------------------
1741 r41 | lh3lh3 | 2008-12-10 12:53:08 +0000 (Wed, 10 Dec 2008) | 2 lines
1743 M /branches/dev/samtools/samtools.1
1747 ------------------------------------------------------------------------
1748 r40 | lh3lh3 | 2008-12-10 11:52:10 +0000 (Wed, 10 Dec 2008) | 5 lines
1750 M /branches/dev/samtools/bam.h
1751 M /branches/dev/samtools/bam_pileup.c
1752 M /branches/dev/samtools/bamtk.c
1755 * tried to make pileup work with clipping (previously not), though NOT tested
1756 * removed -v from pileup
1757 * made pileup take the reference sequence
1759 ------------------------------------------------------------------------
1760 r39 | lh3lh3 | 2008-12-09 11:59:28 +0000 (Tue, 09 Dec 2008) | 4 lines
1762 M /branches/dev/samtools/bam_import.c
1763 M /branches/dev/samtools/bamtk.c
1764 M /branches/dev/samtools/samtools.1
1767 * in parser, recognize "=", rather than ",", as a match
1768 * in parser, correctl parse "=" at the MRNM field.
1770 ------------------------------------------------------------------------
1771 r38 | lh3lh3 | 2008-12-09 11:39:07 +0000 (Tue, 09 Dec 2008) | 2 lines
1773 M /branches/dev/samtools/misc/maq2sam.c
1775 fixed a bug in handling maq flag 64 and 192
1777 ------------------------------------------------------------------------
1778 r37 | lh3lh3 | 2008-12-09 09:53:46 +0000 (Tue, 09 Dec 2008) | 2 lines
1780 M /branches/dev/samtools/misc/md5fa.c
1782 also calculate unordered md5sum check
1784 ------------------------------------------------------------------------
1785 r36 | lh3lh3 | 2008-12-09 09:46:21 +0000 (Tue, 09 Dec 2008) | 2 lines
1787 M /branches/dev/samtools/misc/md5fa.c
1789 fixed a minor bug when there are space in the sequence
1791 ------------------------------------------------------------------------
1792 r35 | lh3lh3 | 2008-12-09 09:40:45 +0000 (Tue, 09 Dec 2008) | 2 lines
1794 M /branches/dev/samtools/misc/md5fa.c
1796 fixed a potential memory leak
1798 ------------------------------------------------------------------------
1799 r34 | lh3lh3 | 2008-12-08 14:52:17 +0000 (Mon, 08 Dec 2008) | 2 lines
1801 M /branches/dev/samtools/bam_import.c
1802 M /branches/dev/samtools/bam_index.c
1803 M /branches/dev/samtools/bamtk.c
1805 * fixed a bug in import: bin is wrongly calculated
1807 ------------------------------------------------------------------------
1808 r33 | lh3lh3 | 2008-12-08 14:08:01 +0000 (Mon, 08 Dec 2008) | 2 lines
1810 M /branches/dev/samtools/misc/all2sam.pl
1814 ------------------------------------------------------------------------
1815 r32 | lh3lh3 | 2008-12-08 12:56:02 +0000 (Mon, 08 Dec 2008) | 3 lines
1817 M /branches/dev/samtools/Makefile
1818 M /branches/dev/samtools/kseq.h
1819 M /branches/dev/samtools/misc/Makefile
1820 A /branches/dev/samtools/misc/md5.c
1821 A /branches/dev/samtools/misc/md5.h
1822 A /branches/dev/samtools/misc/md5fa.c
1824 * fixed two warnings in kseq.h
1825 * added md5sum utilities
1827 ------------------------------------------------------------------------
1828 r31 | lh3lh3 | 2008-12-08 11:35:29 +0000 (Mon, 08 Dec 2008) | 5 lines
1830 M /branches/dev/samtools/Makefile
1831 M /branches/dev/samtools/bam_import.c
1832 M /branches/dev/samtools/bamtk.c
1833 A /branches/dev/samtools/kseq.h
1834 D /branches/dev/samtools/kstream.h
1837 * replace kstream with kseq. kseq is a superset of kstream. I need the
1838 extra functions in kseq.h.
1839 * also compile stand-alone faidx
1841 ------------------------------------------------------------------------
1842 r30 | lh3lh3 | 2008-12-08 11:17:04 +0000 (Mon, 08 Dec 2008) | 3 lines
1844 M /branches/dev/samtools/bam.h
1845 M /branches/dev/samtools/bam_sort.c
1846 M /branches/dev/samtools/bamtk.c
1849 * sorting by read names is available
1851 ------------------------------------------------------------------------
1852 r29 | lh3lh3 | 2008-12-08 10:29:02 +0000 (Mon, 08 Dec 2008) | 3 lines
1854 M /branches/dev/samtools/bam.c
1855 M /branches/dev/samtools/bam.h
1856 M /branches/dev/samtools/bam_import.c
1857 M /branches/dev/samtools/bam_maqcns.c
1858 M /branches/dev/samtools/bam_pileup.c
1859 M /branches/dev/samtools/bam_sort.c
1860 M /branches/dev/samtools/bam_tview.c
1861 M /branches/dev/samtools/bamtk.c
1862 M /branches/dev/samtools/misc/maq2sam.c
1865 * format change to meet the latest specification
1867 ------------------------------------------------------------------------
1868 r28 | lh3lh3 | 2008-12-04 16:09:21 +0000 (Thu, 04 Dec 2008) | 3 lines
1870 M /branches/dev/samtools/bam_maqcns.c
1871 M /branches/dev/samtools/misc/maq2sam.c
1873 * minor change in maqcns: special care when n==0
1874 * change maq2sam to meet the latest specification
1876 ------------------------------------------------------------------------
1877 r27 | lh3lh3 | 2008-12-04 15:55:44 +0000 (Thu, 04 Dec 2008) | 2 lines
1879 M /branches/dev/samtools/razf.c
1880 M /branches/dev/samtools/razf.h
1882 considerable code clean up in razf
1884 ------------------------------------------------------------------------
1885 r26 | lh3lh3 | 2008-12-04 15:08:18 +0000 (Thu, 04 Dec 2008) | 2 lines
1887 M /branches/dev/samtools/ChangeLog
1888 M /branches/dev/samtools/Makefile
1889 M /branches/dev/samtools/faidx.c
1891 make RAZF optional in faidx.c
1893 ------------------------------------------------------------------------
1894 r25 | lh3lh3 | 2008-12-01 15:27:22 +0000 (Mon, 01 Dec 2008) | 3 lines
1896 M /branches/dev/samtools/Makefile
1897 M /branches/dev/samtools/bam.h
1898 M /branches/dev/samtools/bam_aux.c
1899 M /branches/dev/samtools/bamtk.c
1900 M /branches/dev/samtools/samtools.1
1903 * added routines for retrieving aux data, NOT TESTED YET!
1905 ------------------------------------------------------------------------
1906 r24 | lh3lh3 | 2008-12-01 14:29:43 +0000 (Mon, 01 Dec 2008) | 5 lines
1908 M /branches/dev/samtools/bam.c
1909 M /branches/dev/samtools/bam_import.c
1910 M /branches/dev/samtools/bam_maqcns.c
1911 M /branches/dev/samtools/bamtk.c
1912 M /branches/dev/samtools/bgzf.c
1913 M /branches/dev/samtools/samtools.1
1916 * bgzf: fixed a potential integer overflow on 32-it machines
1917 * maqcns: set the minimum combined quality as 0
1918 * supporting hex strings
1920 ------------------------------------------------------------------------
1921 r23 | lh3lh3 | 2008-11-27 17:14:37 +0000 (Thu, 27 Nov 2008) | 3 lines
1923 M /branches/dev/samtools/bam_maqcns.c
1924 M /branches/dev/samtools/bamtk.c
1927 * fixed the bug in maqcns
1929 ------------------------------------------------------------------------
1930 r22 | lh3lh3 | 2008-11-27 17:08:11 +0000 (Thu, 27 Nov 2008) | 3 lines
1932 M /branches/dev/samtools/Makefile
1933 M /branches/dev/samtools/bam.h
1934 A /branches/dev/samtools/bam_maqcns.c
1935 A /branches/dev/samtools/bam_maqcns.h
1936 M /branches/dev/samtools/bam_tview.c
1937 M /branches/dev/samtools/bamtk.c
1938 A /branches/dev/samtools/glf.h
1941 * add MAQ consensus caller, currently BUGGY!
1943 ------------------------------------------------------------------------
1944 r21 | lh3lh3 | 2008-11-27 13:51:28 +0000 (Thu, 27 Nov 2008) | 4 lines
1946 M /branches/dev/samtools/bam_pileup.c
1947 M /branches/dev/samtools/bam_tview.c
1948 M /branches/dev/samtools/bamtk.c
1951 * tview: display padded alignment (but not P operation)
1952 * better coordinates and reference sequence
1954 ------------------------------------------------------------------------
1955 r19 | lh3lh3 | 2008-11-27 09:26:05 +0000 (Thu, 27 Nov 2008) | 2 lines
1957 A /branches/dev/samtools/ChangeLog
1961 ------------------------------------------------------------------------
1962 r18 | lh3lh3 | 2008-11-27 09:24:45 +0000 (Thu, 27 Nov 2008) | 3 lines
1964 D /branches/dev/samtools/ChangeLog
1965 A /branches/dev/samtools/ChangeLog.old (from /branches/dev/samtools/ChangeLog:6)
1967 Rename ChangeLog to ChangeLog.old. This old ChangeLog is generated from
1968 the log of my personal SVN repository.
1970 ------------------------------------------------------------------------
1971 r17 | lh3lh3 | 2008-11-27 09:22:55 +0000 (Thu, 27 Nov 2008) | 6 lines
1973 M /branches/dev/samtools/Makefile
1974 M /branches/dev/samtools/bamtk.c
1975 M /branches/dev/samtools/bgzf.c
1978 * declare fseeko and ftello as some Linux may not do this by default and
1979 missing these declarations will make bgzf buggy
1980 * get rid of some harmless warings
1981 * use BGZF by default, now
1983 ------------------------------------------------------------------------
1984 r16 | lh3lh3 | 2008-11-26 21:19:11 +0000 (Wed, 26 Nov 2008) | 4 lines
1986 M /branches/dev/samtools/bam_index.c
1987 M /branches/dev/samtools/bamtk.c
1988 M /branches/dev/samtools/razf.c
1991 * fixed a bug in razf_read()
1992 * give more warnings when the file is truncated (or due to bugs in I/O library)
1994 ------------------------------------------------------------------------
1995 r15 | lh3lh3 | 2008-11-26 20:41:39 +0000 (Wed, 26 Nov 2008) | 2 lines
1997 M /branches/dev/samtools/bgzf.c
1999 fixed a bug in bgzf.c at the end of the file
2001 ------------------------------------------------------------------------
2002 r14 | lh3lh3 | 2008-11-26 17:05:18 +0000 (Wed, 26 Nov 2008) | 4 lines
2004 M /branches/dev/samtools/bamtk.c
2007 * a lot happened to RAZF, although samtools itself is untouched. Better
2008 also update the version number anyway to avoid confusion
2010 ------------------------------------------------------------------------
2011 r13 | lh3lh3 | 2008-11-26 17:03:48 +0000 (Wed, 26 Nov 2008) | 2 lines
2013 M /branches/dev/samtools/razf.c
2015 a change from Jue, but I think it should not matter
2017 ------------------------------------------------------------------------
2018 r12 | lh3lh3 | 2008-11-26 16:48:14 +0000 (Wed, 26 Nov 2008) | 3 lines
2020 M /branches/dev/samtools/razf.c
2022 fixed a potential bug in razf. However, it seems still buggy, just
2023 rarely happens, very rarely.
2025 ------------------------------------------------------------------------
2026 r11 | lh3lh3 | 2008-11-26 14:02:56 +0000 (Wed, 26 Nov 2008) | 2 lines
2028 M /branches/dev/samtools/razf.c
2030 fixed a bug in razf, with the help of Jue
2032 ------------------------------------------------------------------------
2033 r10 | lh3lh3 | 2008-11-26 11:55:32 +0000 (Wed, 26 Nov 2008) | 2 lines
2035 M /branches/dev/samtools/bam_index.c
2039 ------------------------------------------------------------------------
2040 r9 | lh3lh3 | 2008-11-26 11:37:05 +0000 (Wed, 26 Nov 2008) | 2 lines
2042 M /branches/dev/samtools/Makefile
2043 M /branches/dev/samtools/bam.h
2044 M /branches/dev/samtools/razf.c
2045 M /branches/dev/samtools/razf.h
2047 * Jue has updated razf to realize Bob's scheme
2049 ------------------------------------------------------------------------
2050 r7 | lh3lh3 | 2008-11-25 20:37:37 +0000 (Tue, 25 Nov 2008) | 2 lines
2052 A /branches/dev/samtools/samtools.1
2056 ------------------------------------------------------------------------
2057 r6 | lh3lh3 | 2008-11-25 20:37:16 +0000 (Tue, 25 Nov 2008) | 3 lines
2059 A /branches/dev/samtools/ChangeLog
2060 A /branches/dev/samtools/Makefile
2061 A /branches/dev/samtools/bam.c
2062 A /branches/dev/samtools/bam.h
2063 A /branches/dev/samtools/bam_aux.c
2064 A /branches/dev/samtools/bam_endian.h
2065 A /branches/dev/samtools/bam_import.c
2066 A /branches/dev/samtools/bam_index.c
2067 A /branches/dev/samtools/bam_lpileup.c
2068 A /branches/dev/samtools/bam_pileup.c
2069 A /branches/dev/samtools/bam_sort.c
2070 A /branches/dev/samtools/bam_tview.c
2071 A /branches/dev/samtools/bamtk.c
2072 A /branches/dev/samtools/bgzf.c
2073 A /branches/dev/samtools/bgzf.h
2074 A /branches/dev/samtools/bgzip.c
2075 A /branches/dev/samtools/faidx.c
2076 A /branches/dev/samtools/faidx.h
2077 A /branches/dev/samtools/khash.h
2078 A /branches/dev/samtools/ksort.h
2079 A /branches/dev/samtools/kstream.h
2080 A /branches/dev/samtools/misc
2081 A /branches/dev/samtools/misc/Makefile
2082 A /branches/dev/samtools/misc/all2sam.pl
2083 A /branches/dev/samtools/misc/maq2sam.c
2084 A /branches/dev/samtools/razf.c
2085 A /branches/dev/samtools/razf.h
2086 A /branches/dev/samtools/razip.c
2087 A /branches/dev/samtools/zutil.h
2089 The initial version of samtools, replicated from my local SVN repository.
2090 The current version is: 0.1.0-42. All future development will happen here.
2092 ------------------------------------------------------------------------
2093 r5 | lh3lh3 | 2008-11-25 20:30:49 +0000 (Tue, 25 Nov 2008) | 2 lines
2095 A /branches/dev/samtools
2097 samtools (C version)
2099 ------------------------------------------------------------------------