1 ------------------------------------------------------------------------
2 r332 | lh3lh3 | 2009-06-12 15:21:21 +0100 (Fri, 12 Jun 2009) | 2 lines
4 M /trunk/samtools/AUTHORS
5 M /trunk/samtools/Makefile
6 M /trunk/samtools/misc/Makefile
8 fixed minor things in Makefile
10 ------------------------------------------------------------------------
11 r331 | lh3lh3 | 2009-06-12 15:07:05 +0100 (Fri, 12 Jun 2009) | 4 lines
13 M /trunk/samtools/bamtk.c
15 * samtools-0.1.4-5 (r3310
16 * no change to samtools itself. Version number is increased to reflect the
17 changes in the Makefile building system.
19 ------------------------------------------------------------------------
20 r330 | lh3lh3 | 2009-06-12 15:03:38 +0100 (Fri, 12 Jun 2009) | 2 lines
22 M /trunk/samtools/AUTHORS
23 D /trunk/samtools/README
27 ------------------------------------------------------------------------
28 r329 | lh3lh3 | 2009-06-12 14:52:21 +0100 (Fri, 12 Jun 2009) | 3 lines
30 M /trunk/samtools/misc/novo2sam.pl
32 * updated novoalign converter by Colin Hercus et al.
33 * this version works with indels
35 ------------------------------------------------------------------------
36 r328 | lh3lh3 | 2009-06-12 14:50:53 +0100 (Fri, 12 Jun 2009) | 3 lines
38 M /trunk/samtools/INSTALL
39 M /trunk/samtools/Makefile
40 M /trunk/samtools/misc/Makefile
41 M /trunk/samtools/zlib/Makefile
44 * update INSTALL instruction
46 ------------------------------------------------------------------------
47 r327 | lh3lh3 | 2009-06-12 14:18:29 +0100 (Fri, 12 Jun 2009) | 4 lines
49 A /trunk/samtools/Makefile (from /trunk/samtools/Makefile.generic:325)
50 D /trunk/samtools/Makefile.am
51 D /trunk/samtools/Makefile.generic
52 D /trunk/samtools/Makefile.lite
53 D /trunk/samtools/autogen.sh
54 D /trunk/samtools/cleanup.sh
55 D /trunk/samtools/configure.ac
56 A /trunk/samtools/misc/Makefile (from /trunk/samtools/misc/Makefile.generic:305)
57 D /trunk/samtools/misc/Makefile.am
58 D /trunk/samtools/misc/Makefile.generic
59 M /trunk/samtools/razf.c
60 A /trunk/samtools/zlib
61 A /trunk/samtools/zlib/Makefile
62 A /trunk/samtools/zlib/adler32.c
63 A /trunk/samtools/zlib/compress.c
64 A /trunk/samtools/zlib/crc32.c
65 A /trunk/samtools/zlib/crc32.h
66 A /trunk/samtools/zlib/deflate.c
67 A /trunk/samtools/zlib/deflate.h
68 A /trunk/samtools/zlib/gzio.c
69 A /trunk/samtools/zlib/infback.c
70 A /trunk/samtools/zlib/inffast.c
71 A /trunk/samtools/zlib/inffast.h
72 A /trunk/samtools/zlib/inffixed.h
73 A /trunk/samtools/zlib/inflate.c
74 A /trunk/samtools/zlib/inflate.h
75 A /trunk/samtools/zlib/inftrees.c
76 A /trunk/samtools/zlib/inftrees.h
77 A /trunk/samtools/zlib/trees.c
78 A /trunk/samtools/zlib/trees.h
79 A /trunk/samtools/zlib/uncompr.c
80 A /trunk/samtools/zlib/zconf.h
81 A /trunk/samtools/zlib/zlib.h
82 A /trunk/samtools/zlib/zutil.c
83 A /trunk/samtools/zlib/zutil.h
84 D /trunk/samtools/zutil.h
86 * added zlib-1.2.3 as razip requires that
87 * prepare to changed back to the Makefile building system
88 * unfinished! (will be soon)
90 ------------------------------------------------------------------------
91 r326 | lh3lh3 | 2009-06-12 14:12:03 +0100 (Fri, 12 Jun 2009) | 2 lines
93 M /trunk/samtools/misc/samtools.pl
97 ------------------------------------------------------------------------
98 r325 | lh3lh3 | 2009-06-10 16:27:59 +0100 (Wed, 10 Jun 2009) | 3 lines
100 M /trunk/samtools/bam_maqcns.c
101 M /trunk/samtools/bamtk.c
103 * samtools-0.1.4-4 (r325)
104 * further avoid wrong consensus calls in repetitive regions.
106 ------------------------------------------------------------------------
107 r324 | lh3lh3 | 2009-06-10 15:56:17 +0100 (Wed, 10 Jun 2009) | 4 lines
109 M /trunk/samtools/bam_maqcns.c
110 M /trunk/samtools/bam_plcmd.c
111 M /trunk/samtools/bamtk.c
112 M /trunk/samtools/sam.c
113 M /trunk/samtools/sam.h
115 * samtools-0.1.4-3 (r324)
116 * make maqcns generate the correct call in repetitive regions.
117 * allow filtering on mapQ at the pileup command line
119 ------------------------------------------------------------------------
120 r323 | lh3lh3 | 2009-06-10 10:04:21 +0100 (Wed, 10 Jun 2009) | 3 lines
122 M /trunk/samtools/misc/samtools.pl
124 * samtools.pl-0.3.2 (r322)
125 * indels and SNPs use different mapping quality threshold
127 ------------------------------------------------------------------------
128 r322 | lh3lh3 | 2009-06-10 10:03:22 +0100 (Wed, 10 Jun 2009) | 2 lines
130 M /trunk/samtools/misc/export2sam.pl
134 ------------------------------------------------------------------------
135 r321 | lh3lh3 | 2009-06-09 09:21:48 +0100 (Tue, 09 Jun 2009) | 2 lines
137 M /trunk/samtools/misc/samtools.pl
139 just typo. no real change
141 ------------------------------------------------------------------------
142 r320 | lh3lh3 | 2009-06-08 14:32:51 +0100 (Mon, 08 Jun 2009) | 2 lines
144 M /trunk/samtools/misc/samtools.pl
146 a little bit code cleanup
148 ------------------------------------------------------------------------
149 r319 | lh3lh3 | 2009-06-08 14:22:33 +0100 (Mon, 08 Jun 2009) | 4 lines
151 M /trunk/samtools/misc/samtools.pl
154 * change default parameters
155 * optionally print filtered variants
157 ------------------------------------------------------------------------
158 r318 | lh3lh3 | 2009-06-08 14:14:26 +0100 (Mon, 08 Jun 2009) | 3 lines
160 M /trunk/samtools/misc/samtools.pl
163 * combine snpFilter and indelFilter
165 ------------------------------------------------------------------------
166 r317 | lh3lh3 | 2009-06-08 11:31:42 +0100 (Mon, 08 Jun 2009) | 3 lines
168 M /trunk/samtools/misc/samtools.pl
171 * change a default parameter
173 ------------------------------------------------------------------------
174 r316 | lh3lh3 | 2009-06-08 11:11:06 +0100 (Mon, 08 Jun 2009) | 5 lines
176 M /trunk/samtools/bam_maqcns.c
177 M /trunk/samtools/bam_maqcns.h
178 M /trunk/samtools/bam_plcmd.c
179 M /trunk/samtools/bamtk.c
180 M /trunk/samtools/sam.c
182 * samtools-0.1.4-2 (r316)
183 * pileup: cap mapping quality at 60 (by default)
184 * pileup: always calculate RMS mapq
185 * pileup: allow to output variant sites only
187 ------------------------------------------------------------------------
188 r312 | lh3lh3 | 2009-06-04 13:01:10 +0100 (Thu, 04 Jun 2009) | 3 lines
190 M /trunk/samtools/misc/samtools.pl
195 ------------------------------------------------------------------------
196 r311 | lh3lh3 | 2009-06-03 09:40:40 +0100 (Wed, 03 Jun 2009) | 2 lines
198 M /trunk/samtools/misc/samtools.pl
200 * in snpFilter, suppress non-SNP sites
202 ------------------------------------------------------------------------
203 r310 | lh3lh3 | 2009-06-01 14:35:13 +0100 (Mon, 01 Jun 2009) | 3 lines
205 M /trunk/samtools/misc/samtools.pl
210 ------------------------------------------------------------------------
211 r309 | lh3lh3 | 2009-06-01 14:04:39 +0100 (Mon, 01 Jun 2009) | 3 lines
213 M /trunk/samtools/misc/samtools.pl
218 ------------------------------------------------------------------------
219 r306 | lh3lh3 | 2009-05-28 11:49:35 +0100 (Thu, 28 May 2009) | 3 lines
221 M /trunk/samtools/bgzf.c
223 * minor changes to bgzf: return NULL if fd == -1
224 * suggested by {kdj,jm18}@sanger.ac.uk
226 ------------------------------------------------------------------------
227 r305 | lh3lh3 | 2009-05-28 11:16:08 +0100 (Thu, 28 May 2009) | 2 lines
229 A /trunk/samtools/misc/interpolate_sam.pl
231 Script for paired-end pileup, contributed by Stephen Montgomery.
233 ------------------------------------------------------------------------
234 r304 | lh3lh3 | 2009-05-28 11:08:49 +0100 (Thu, 28 May 2009) | 3 lines
236 M /trunk/samtools/bamtk.c
237 M /trunk/samtools/sam.c
239 * samtools-0.1.4-1 (r304)
240 * fixed a minor bug in printing headers
242 ------------------------------------------------------------------------
243 r297 | lh3lh3 | 2009-05-21 16:06:16 +0100 (Thu, 21 May 2009) | 2 lines
245 M /trunk/samtools/ChangeLog
246 M /trunk/samtools/NEWS
247 M /trunk/samtools/bam_plcmd.c
248 M /trunk/samtools/bamtk.c
249 M /trunk/samtools/misc/maq2sam.c
250 M /trunk/samtools/samtools.1
252 Release samtools-0.1.4
254 ------------------------------------------------------------------------
255 r296 | lh3lh3 | 2009-05-21 12:53:14 +0100 (Thu, 21 May 2009) | 3 lines
257 M /trunk/samtools/bam_maqcns.c
258 M /trunk/samtools/bamtk.c
260 * samtools-0.1.3-24 (r296)
261 * another similar bug in the indel caller
263 ------------------------------------------------------------------------
264 r295 | lh3lh3 | 2009-05-21 12:50:28 +0100 (Thu, 21 May 2009) | 3 lines
266 M /trunk/samtools/bam_maqcns.c
267 M /trunk/samtools/bamtk.c
269 * samtools-0.1.3-23 (r295)
270 * fixed a critical bug in the indel caller
272 ------------------------------------------------------------------------
273 r294 | lh3lh3 | 2009-05-20 13:00:20 +0100 (Wed, 20 May 2009) | 2 lines
275 M /trunk/samtools/bam_stat.c
277 added a missing header file
279 ------------------------------------------------------------------------
280 r293 | lh3lh3 | 2009-05-19 23:44:25 +0100 (Tue, 19 May 2009) | 3 lines
282 M /trunk/samtools/bam_tview.c
283 M /trunk/samtools/bamtk.c
285 * samtools-0.1.3-22 (r293)
286 * open tview in the dot-view mode by default
288 ------------------------------------------------------------------------
289 r292 | lh3lh3 | 2009-05-18 21:01:23 +0100 (Mon, 18 May 2009) | 6 lines
291 M /trunk/samtools/samtools.1
293 Added a note to the manual. Currently SAMtools used unaligned words in
294 several places. Although this does not cause bus errors to me, it may
295 affect portability. Please see the "Bus error" wiki page for more
296 information. Also thank James Bonfields for pointing this out.
299 ------------------------------------------------------------------------
300 r286 | lh3lh3 | 2009-05-14 15:23:13 +0100 (Thu, 14 May 2009) | 3 lines
302 M /trunk/samtools/bam.h
303 M /trunk/samtools/bam_aux.c
304 M /trunk/samtools/bamtk.c
306 * samtools-0.1.3-21 (286)
307 * declare bam_aux_get_core() in bam.h
309 ------------------------------------------------------------------------
310 r276 | lh3lh3 | 2009-05-13 10:07:55 +0100 (Wed, 13 May 2009) | 5 lines
312 M /trunk/samtools/bam.h
313 M /trunk/samtools/bam_index.c
314 M /trunk/samtools/bamtk.c
316 * samtools-0.1.3-20 (r276)
317 * remove bam1_t::hash again. We need to modify the Perl API anyway to
318 make it work with the latest SVN.
319 * As is suggested by Tim, scan "{base}.bai" and "{base}.bam.bai" for index
321 ------------------------------------------------------------------------
322 r275 | lh3lh3 | 2009-05-12 21:14:10 +0100 (Tue, 12 May 2009) | 4 lines
324 M /trunk/samtools/ChangeLog
325 M /trunk/samtools/bam.h
326 M /trunk/samtools/bamtk.c
328 * samtools-0.1.3-19 (r275)
329 * a minor change to the bam1_t struct: added back "void *hash" for the
330 backward compatibility with Bio::DB::Sam
332 ------------------------------------------------------------------------
333 r273 | lh3lh3 | 2009-05-12 14:28:39 +0100 (Tue, 12 May 2009) | 3 lines
335 M /trunk/samtools/bam_rmdupse.c
336 M /trunk/samtools/bamtk.c
338 * samtools-0.1.3-18 (r273)
339 * rmdupse: do not remove unmapped reads
341 ------------------------------------------------------------------------
342 r272 | lh3lh3 | 2009-05-12 14:20:00 +0100 (Tue, 12 May 2009) | 2 lines
344 M /trunk/samtools/bam_rmdupse.c
346 change a parameter. It does nothing
348 ------------------------------------------------------------------------
349 r271 | lh3lh3 | 2009-05-12 14:17:58 +0100 (Tue, 12 May 2009) | 3 lines
351 M /trunk/samtools/Makefile.am
352 M /trunk/samtools/Makefile.generic
353 M /trunk/samtools/Makefile.lite
354 A /trunk/samtools/bam_rmdupse.c
355 M /trunk/samtools/bamtk.c
356 M /trunk/samtools/configure.ac
358 * samtools-0.1.3-17 (r271)
359 * added 'rmdupse' command
361 ------------------------------------------------------------------------
362 r267 | lh3lh3 | 2009-05-05 22:31:41 +0100 (Tue, 05 May 2009) | 3 lines
364 M /trunk/samtools/bamtk.c
365 M /trunk/samtools/sam_view.c
367 * samtools-0.1.3-16 (r267)
368 * in sam_view.c, changed g_flag_on based on the suggestion by Angie Hinrichs
370 ------------------------------------------------------------------------
371 r266 | lh3lh3 | 2009-05-05 22:23:27 +0100 (Tue, 05 May 2009) | 3 lines
373 M /trunk/samtools/bam_import.c
374 M /trunk/samtools/bamtk.c
376 * samtools-0.1.3-15 (r266)
377 * report an error if a non-* reference is present while @SQ is absent
379 ------------------------------------------------------------------------
380 r265 | lh3lh3 | 2009-05-05 22:09:00 +0100 (Tue, 05 May 2009) | 3 lines
382 M /trunk/samtools/bam.h
383 M /trunk/samtools/bam_import.c
384 M /trunk/samtools/bamtk.c
385 M /trunk/samtools/sam.c
386 M /trunk/samtools/sam_view.c
388 * samtools-0.1.3-14 (r262)
389 * make samopen() recognize @SQ header lines
391 ------------------------------------------------------------------------
392 r261 | lh3lh3 | 2009-05-05 15:10:30 +0100 (Tue, 05 May 2009) | 3 lines
394 M /trunk/samtools/bam_plcmd.c
395 M /trunk/samtools/bamtk.c
396 M /trunk/samtools/bgzf.c
397 M /trunk/samtools/sam.c
398 M /trunk/samtools/sam_view.c
400 * samtools-0.1.3-13 (r260)
401 * report error for file I/O error
403 ------------------------------------------------------------------------
404 r260 | lh3lh3 | 2009-05-05 15:01:16 +0100 (Tue, 05 May 2009) | 2 lines
406 M /trunk/samtools/Makefile.am
410 ------------------------------------------------------------------------
411 r259 | lh3lh3 | 2009-05-05 14:52:25 +0100 (Tue, 05 May 2009) | 3 lines
413 M /trunk/samtools/bam.h
414 M /trunk/samtools/bam_pileup.c
415 M /trunk/samtools/bam_plcmd.c
416 M /trunk/samtools/bamtk.c
417 M /trunk/samtools/sam.c
418 M /trunk/samtools/sam.h
420 * samtools-0.1.3-12 (r259)
421 * use the new I/O interface in pileup
423 ------------------------------------------------------------------------
424 r258 | lh3lh3 | 2009-05-05 14:33:22 +0100 (Tue, 05 May 2009) | 3 lines
426 M /trunk/samtools/Makefile.generic
427 M /trunk/samtools/Makefile.lite
428 M /trunk/samtools/bam.c
429 M /trunk/samtools/bam.h
430 M /trunk/samtools/bam_import.c
431 M /trunk/samtools/bamtk.c
432 A /trunk/samtools/sam.c
433 A /trunk/samtools/sam.h
434 A /trunk/samtools/sam_view.c
436 * samtools-0.1.3-11 (r258)
437 * unify the interface to BAM and SAM I/O
439 ------------------------------------------------------------------------
440 r257 | lh3lh3 | 2009-05-05 09:53:35 +0100 (Tue, 05 May 2009) | 3 lines
442 M /trunk/samtools/Makefile.lite
443 M /trunk/samtools/bam_plcmd.c
444 M /trunk/samtools/bamtk.c
446 * samtools-0.1.3-10 (r257)
447 * allow hex with "pileup -m"
449 ------------------------------------------------------------------------
450 r256 | lh3lh3 | 2009-05-04 19:16:50 +0100 (Mon, 04 May 2009) | 4 lines
452 M /trunk/samtools/bam_lpileup.c
453 M /trunk/samtools/bamtk.c
455 * samtools-0.1.3-9 (r256)
456 * fixed a bug in bam_lpileup.c
457 * I do not know if this also fixes the bug causing assertion failure in the tview
459 ------------------------------------------------------------------------
460 r251 | lh3lh3 | 2009-04-28 13:53:23 +0100 (Tue, 28 Apr 2009) | 3 lines
462 M /trunk/samtools/bam_pileup.c
463 M /trunk/samtools/bamtk.c
465 * samtools-0.1.3-8 (r251)
466 * fixed a bug when there are reads without coordinates
468 ------------------------------------------------------------------------
469 r250 | lh3lh3 | 2009-04-28 13:43:33 +0100 (Tue, 28 Apr 2009) | 2 lines
471 A /trunk/samtools/AUTHORS
472 A /trunk/samtools/README
473 M /trunk/samtools/cleanup.sh
477 ------------------------------------------------------------------------
478 r249 | lh3lh3 | 2009-04-28 13:37:16 +0100 (Tue, 28 Apr 2009) | 2 lines
480 M /trunk/samtools/Makefile.generic
481 M /trunk/samtools/Makefile.lite
482 M /trunk/samtools/configure.ac
483 M /trunk/samtools/misc/Makefile.generic
485 improve large file support in compilation
487 ------------------------------------------------------------------------
488 r248 | lh3lh3 | 2009-04-28 13:33:24 +0100 (Tue, 28 Apr 2009) | 2 lines
490 M /trunk/samtools/INSTALL
494 ------------------------------------------------------------------------
495 r247 | lh3lh3 | 2009-04-28 13:28:50 +0100 (Tue, 28 Apr 2009) | 2 lines
497 M /trunk/samtools/Makefile.am
498 M /trunk/samtools/autogen.sh
499 M /trunk/samtools/cleanup.sh
500 M /trunk/samtools/configure.ac
501 A /trunk/samtools/misc/Makefile.am
503 fixed various issues about the GNU building scripts
505 ------------------------------------------------------------------------
506 r246 | lh3lh3 | 2009-04-28 13:10:23 +0100 (Tue, 28 Apr 2009) | 4 lines
508 M /trunk/samtools/ChangeLog
509 D /trunk/samtools/Makefile
510 A /trunk/samtools/Makefile.am
511 A /trunk/samtools/Makefile.generic
512 A /trunk/samtools/autogen.sh
513 M /trunk/samtools/bam.h
514 M /trunk/samtools/bam_aux.c
515 M /trunk/samtools/bam_tview.c
516 M /trunk/samtools/bamtk.c
517 A /trunk/samtools/cleanup.sh
518 A /trunk/samtools/configure.ac
519 D /trunk/samtools/misc/Makefile
520 A /trunk/samtools/misc/Makefile.generic (from /trunk/samtools/misc/Makefile:245)
522 * samtools-0.1.3-7 (r246)
523 * incorporated revisions from Nils Homer
524 * enhanced support of displaying color-space reads
526 ------------------------------------------------------------------------
527 r244 | lh3lh3 | 2009-04-25 11:49:40 +0100 (Sat, 25 Apr 2009) | 3 lines
529 M /trunk/samtools/bam_md.c
530 M /trunk/samtools/bamtk.c
532 * samtools-0.1.3-6 (r244)
533 * fixed segfault for unmapped reads
535 ------------------------------------------------------------------------
536 r243 | lh3lh3 | 2009-04-24 21:27:26 +0100 (Fri, 24 Apr 2009) | 5 lines
538 M /trunk/samtools/bam.h
539 M /trunk/samtools/bam_maqcns.c
540 M /trunk/samtools/bam_md.c
541 M /trunk/samtools/bamtk.c
543 * samtools-0.1.3-5 (r243)
544 * fixed a long existing bug which may cause memory leak
546 * consensus calling now works with "=", but indel calling not
548 ------------------------------------------------------------------------
549 r242 | lh3lh3 | 2009-04-24 20:44:46 +0100 (Fri, 24 Apr 2009) | 3 lines
551 M /trunk/samtools/bam_md.c
552 M /trunk/samtools/bamtk.c
554 * samtools-0.1.3-4 (r242)
555 * fixed a memory leak
557 ------------------------------------------------------------------------
558 r240 | lh3lh3 | 2009-04-24 16:40:18 +0100 (Fri, 24 Apr 2009) | 5 lines
560 M /trunk/samtools/Makefile
561 M /trunk/samtools/Makefile.lite
562 M /trunk/samtools/bam.h
563 M /trunk/samtools/bam_aux.c
564 A /trunk/samtools/bam_md.c
565 M /trunk/samtools/bam_plcmd.c
566 M /trunk/samtools/bamtk.c
568 * samtools-0.1.3-3 (r240)
571 * the plain pileup now support "=" bases, but consensus calling and glfgen may fail
573 ------------------------------------------------------------------------
574 r239 | lh3lh3 | 2009-04-24 12:08:20 +0100 (Fri, 24 Apr 2009) | 5 lines
576 M /trunk/samtools/bam.h
577 M /trunk/samtools/bam_aux.c
578 M /trunk/samtools/bamtk.c
580 * samtools-0.1.3-2 (r239)
581 * fixed bugs in bam_aux.c (these functions nevered used by samtools)
582 * removed bam_aux_init()/bam_aux_destroy()
583 * added tagview for testing bam_aux
585 ------------------------------------------------------------------------
586 r235 | lh3lh3 | 2009-04-21 23:17:39 +0100 (Tue, 21 Apr 2009) | 3 lines
588 M /trunk/samtools/bam_pileup.c
589 M /trunk/samtools/bamtk.c
592 * fixed a bug in pileup: the first read in a chromosome may not be printed
594 ------------------------------------------------------------------------
595 r232 | lh3lh3 | 2009-04-16 15:25:43 +0100 (Thu, 16 Apr 2009) | 2 lines
597 M /trunk/samtools/Makefile.lite
599 a missing file in Makefile.lite
601 ------------------------------------------------------------------------
602 r227 | lh3lh3 | 2009-04-15 22:02:53 +0100 (Wed, 15 Apr 2009) | 2 lines
604 M /trunk/samtools/NEWS
605 M /trunk/samtools/bamtk.c
607 Release samtools-0.1.3
609 ------------------------------------------------------------------------
610 r223 | lh3lh3 | 2009-04-15 14:31:32 +0100 (Wed, 15 Apr 2009) | 3 lines
612 M /trunk/samtools/bam_plcmd.c
613 M /trunk/samtools/bamtk.c
616 * make samtools more robust to weird input such as empty file
618 ------------------------------------------------------------------------
619 r222 | lh3lh3 | 2009-04-15 14:05:33 +0100 (Wed, 15 Apr 2009) | 2 lines
621 M /trunk/samtools/ChangeLog
622 M /trunk/samtools/NEWS
623 M /trunk/samtools/samtools.1
625 prepare for release 0.1.3
627 ------------------------------------------------------------------------
628 r221 | lh3lh3 | 2009-04-15 13:32:14 +0100 (Wed, 15 Apr 2009) | 2 lines
630 A /trunk/samtools/misc/blast2sam.pl
632 convert NCBI-BLASTN to SAM
634 ------------------------------------------------------------------------
635 r220 | lh3lh3 | 2009-04-15 13:18:19 +0100 (Wed, 15 Apr 2009) | 3 lines
637 M /trunk/samtools/bam_lpileup.c
638 M /trunk/samtools/bamtk.c
641 * fixed a small memory leak in tview
643 ------------------------------------------------------------------------
644 r219 | lh3lh3 | 2009-04-15 13:00:08 +0100 (Wed, 15 Apr 2009) | 3 lines
646 M /trunk/samtools/bam_rmdup.c
647 M /trunk/samtools/bamtk.c
650 * fixed a bug in rmdup when there are unmapped reads
652 ------------------------------------------------------------------------
653 r218 | lh3lh3 | 2009-04-14 22:28:58 +0100 (Tue, 14 Apr 2009) | 2 lines
655 M /trunk/samtools/ChangeLog
656 M /trunk/samtools/NEWS
658 proposed NEWS for the new release (have not yet)
660 ------------------------------------------------------------------------
661 r216 | lh3lh3 | 2009-04-14 22:10:46 +0100 (Tue, 14 Apr 2009) | 4 lines
663 M /trunk/samtools/misc/samtools.pl
666 * improve indelFilter to avoid filtering true indels. The new filter relies
667 on the new pileup indel line implemented in samtools-0.1.2-25
669 ------------------------------------------------------------------------
670 r215 | lh3lh3 | 2009-04-14 22:04:19 +0100 (Tue, 14 Apr 2009) | 4 lines
672 M /trunk/samtools/bam_maqcns.c
673 M /trunk/samtools/bam_plcmd.c
674 M /trunk/samtools/bamtk.c
675 M /trunk/samtools/samtools.1
678 * change the pileup indel line to shows the number of alignments actually
681 ------------------------------------------------------------------------
682 r211 | lh3lh3 | 2009-04-13 12:07:13 +0100 (Mon, 13 Apr 2009) | 2 lines
684 M /trunk/samtools/ChangeLog
686 update ChangeLog from "svn log"
688 ------------------------------------------------------------------------
689 r210 | lh3lh3 | 2009-04-12 20:57:05 +0100 (Sun, 12 Apr 2009) | 4 lines
691 M /trunk/samtools/bam.c
692 M /trunk/samtools/bam_import.c
693 M /trunk/samtools/bam_sort.c
694 M /trunk/samtools/bamtk.c
695 M /trunk/samtools/kseq.h
698 * in merge, gives a warning rather than error if the target sequence length is different
701 ------------------------------------------------------------------------
702 r209 | lh3lh3 | 2009-04-12 20:32:44 +0100 (Sun, 12 Apr 2009) | 3 lines
704 M /trunk/samtools/bam.c
705 M /trunk/samtools/bam_import.c
706 M /trunk/samtools/bamtk.c
709 * recognize '*' at the QUAL field
711 ------------------------------------------------------------------------
712 r208 | lh3lh3 | 2009-04-12 20:08:02 +0100 (Sun, 12 Apr 2009) | 3 lines
714 M /trunk/samtools/bam_import.c
715 M /trunk/samtools/bamtk.c
716 M /trunk/samtools/kseq.h
719 * the field separater is TAB only, now
721 ------------------------------------------------------------------------
722 r207 | lh3lh3 | 2009-04-08 15:18:03 +0100 (Wed, 08 Apr 2009) | 2 lines
724 M /trunk/samtools/examples/ex1.sam.gz
726 * fixed the problem in the example alignment due to the bug in fixmate
728 ------------------------------------------------------------------------
729 r206 | lh3lh3 | 2009-04-08 15:15:05 +0100 (Wed, 08 Apr 2009) | 3 lines
731 M /trunk/samtools/bam_mate.c
732 M /trunk/samtools/bamtk.c
733 M /trunk/samtools/misc/soap2sam.pl
736 * fixed a nasty bug in `fixmate'
738 ------------------------------------------------------------------------
739 r205 | lh3lh3 | 2009-04-08 10:57:08 +0100 (Wed, 08 Apr 2009) | 2 lines
741 M /trunk/samtools/misc/bowtie2sam.pl
742 M /trunk/samtools/misc/soap2sam.pl
743 M /trunk/samtools/misc/wgsim_eval.pl
745 make the script robust to the bugs in SOAP-2.1.7
747 ------------------------------------------------------------------------
748 r200 | lh3lh3 | 2009-04-02 15:14:56 +0100 (Thu, 02 Apr 2009) | 3 lines
750 M /trunk/samtools/bam_stat.c
751 M /trunk/samtools/bamtk.c
754 * check if file is truncated in flagstat
756 ------------------------------------------------------------------------
757 r199 | lh3lh3 | 2009-04-02 15:09:10 +0100 (Thu, 02 Apr 2009) | 3 lines
759 M /trunk/samtools/bamtk.c
762 * print the header if requested
764 ------------------------------------------------------------------------
765 r193 | lh3lh3 | 2009-03-27 15:09:50 +0000 (Fri, 27 Mar 2009) | 3 lines
767 M /trunk/samtools/bam_plcmd.c
768 M /trunk/samtools/bamtk.c
771 * fixed a minor bug reported by Nils Homer
773 ------------------------------------------------------------------------
774 r185 | lh3lh3 | 2009-03-24 11:50:32 +0000 (Tue, 24 Mar 2009) | 2 lines
776 A /trunk/samtools/Makefile (from /trunk/samtools/Makefile.std:184)
777 D /trunk/samtools/Makefile.std
778 A /trunk/samtools/misc/Makefile (from /trunk/samtools/misc/Makefile.std:184)
779 D /trunk/samtools/misc/Makefile.std
781 rename Makefile.std as Makefile. GNU building systerm is not ready and may take some time...
783 ------------------------------------------------------------------------
784 r184 | lh3lh3 | 2009-03-24 10:36:38 +0000 (Tue, 24 Mar 2009) | 4 lines
786 D /trunk/samtools/Makefile
787 A /trunk/samtools/Makefile.std (from /trunk/samtools/Makefile:183)
788 M /trunk/samtools/bam_sort.c
789 M /trunk/samtools/bam_tview.c
790 M /trunk/samtools/bamtk.c
791 D /trunk/samtools/misc/Makefile
792 A /trunk/samtools/misc/Makefile.std (from /trunk/samtools/misc/Makefile:182)
793 M /trunk/samtools/samtools.1
796 * incorporating Nils' changes
797 * rename Makefile to Makefile.std and prepare to add the GNU building systerms (also by Nils)
799 ------------------------------------------------------------------------
800 r183 | lh3lh3 | 2009-03-24 10:30:23 +0000 (Tue, 24 Mar 2009) | 4 lines
802 M /trunk/samtools/Makefile
803 M /trunk/samtools/bam_import.c
804 M /trunk/samtools/bam_maqcns.c
805 M /trunk/samtools/bam_maqcns.h
806 M /trunk/samtools/bam_plcmd.c
807 M /trunk/samtools/bamtk.c
808 M /trunk/samtools/kseq.h
809 A /trunk/samtools/kstring.c
810 A /trunk/samtools/kstring.h
813 * made pileup take a list of proposed indels. An insertion is N at the moment.
814 * added my kstring library for a bit complex parsing of the position list.
816 ------------------------------------------------------------------------
817 r169 | lh3lh3 | 2009-03-12 13:40:14 +0000 (Thu, 12 Mar 2009) | 3 lines
819 M /trunk/samtools/misc/soap2sam.pl
822 * more robust to truncated soap output
824 ------------------------------------------------------------------------
825 r168 | lh3lh3 | 2009-03-11 10:49:00 +0000 (Wed, 11 Mar 2009) | 2 lines
827 M /trunk/samtools/Makefile.lite
829 added bam_stat.o to Makefile.lite
831 ------------------------------------------------------------------------
832 r167 | lh3lh3 | 2009-03-10 22:11:31 +0000 (Tue, 10 Mar 2009) | 3 lines
834 M /trunk/samtools/bam_maqcns.c
835 M /trunk/samtools/bamtk.c
838 * generate RMS of mapQ instead of max mapQ
840 ------------------------------------------------------------------------
841 r166 | lh3lh3 | 2009-03-10 22:06:45 +0000 (Tue, 10 Mar 2009) | 3 lines
843 M /trunk/samtools/bam_plcmd.c
844 M /trunk/samtools/bamtk.c
845 M /trunk/samtools/glf.c
846 M /trunk/samtools/glf.h
847 M /trunk/samtools/misc/Makefile
852 ------------------------------------------------------------------------
853 r159 | lh3lh3 | 2009-03-03 11:26:08 +0000 (Tue, 03 Mar 2009) | 3 lines
855 M /trunk/samtools/bam_plcmd.c
856 M /trunk/samtools/bamtk.c
859 * fixed a minor bug in displaying pileup
861 ------------------------------------------------------------------------
862 r158 | lh3lh3 | 2009-03-03 11:24:16 +0000 (Tue, 03 Mar 2009) | 3 lines
864 M /trunk/samtools/ChangeLog
865 M /trunk/samtools/bamtk.c
868 * optionally print SAM header
870 ------------------------------------------------------------------------
871 r153 | lh3lh3 | 2009-03-02 10:45:28 +0000 (Mon, 02 Mar 2009) | 3 lines
873 M /trunk/samtools/bamtk.c
874 M /trunk/samtools/glf.c
877 * use "GLF\3" as the magic for GLFv3 files
879 ------------------------------------------------------------------------
880 r152 | lh3lh3 | 2009-03-02 10:39:09 +0000 (Mon, 02 Mar 2009) | 5 lines
882 M /trunk/samtools/Makefile
883 M /trunk/samtools/bam_import.c
884 M /trunk/samtools/bam_index.c
885 M /trunk/samtools/bam_plcmd.c
886 M /trunk/samtools/bamtk.c
887 M /trunk/samtools/glf.c
888 M /trunk/samtools/glf.h
891 * fixed a bug in import: core.bin is undefined for unmapped reads
892 * this bug can be alleviated (not completely solved) in bam_index.c
893 * update to GLFv3: pos is changed to offset for better compression
895 ------------------------------------------------------------------------
896 r151 | lh3lh3 | 2009-03-01 15:18:43 +0000 (Sun, 01 Mar 2009) | 3 lines
898 M /trunk/samtools/misc/wgsim.c
901 * fixed a bug in simulating indels
903 ------------------------------------------------------------------------
904 r145 | lh3lh3 | 2009-02-26 19:43:57 +0000 (Thu, 26 Feb 2009) | 4 lines
906 M /trunk/samtools/misc/wgsim.c
909 * allow to print mismatch information as fastq comment. MAQ does
910 not like long read names.
912 ------------------------------------------------------------------------
913 r141 | lh3lh3 | 2009-02-26 14:53:03 +0000 (Thu, 26 Feb 2009) | 6 lines
915 M /trunk/samtools/ChangeLog
916 M /trunk/samtools/misc/wgsim.c
917 M /trunk/samtools/misc/wgsim_eval.pl
920 * fixed a bug about color read coordinates
921 * fixed a bug in read names
922 * wgsim_eval.pl-0.1.3
923 * make the script work with color reads
925 ------------------------------------------------------------------------
926 r140 | lh3lh3 | 2009-02-26 14:02:57 +0000 (Thu, 26 Feb 2009) | 2 lines
928 M /trunk/samtools/misc/Makefile
929 M /trunk/samtools/misc/wgsim.c
931 * wgsim: added a note
933 ------------------------------------------------------------------------
934 r139 | lh3lh3 | 2009-02-26 11:39:08 +0000 (Thu, 26 Feb 2009) | 7 lines
936 M /trunk/samtools/misc/wgsim.c
937 M /trunk/samtools/misc/wgsim_eval.pl
940 * considerable code clean up
941 * print number of substitutions/indels/errors on each read
942 * potentially support SOLiD simulation, though not tested at the moment
943 * wgsim_eval.pl-0.1.2
944 * change in accordant with wgsim
946 ------------------------------------------------------------------------
947 r129 | lh3lh3 | 2009-02-18 22:23:27 +0000 (Wed, 18 Feb 2009) | 3 lines
949 M /trunk/samtools/bam_index.c
950 M /trunk/samtools/bamtk.c
953 * fixed a bug in bam_fetch, caused by completely contained adjacent chunks
955 ------------------------------------------------------------------------
956 r128 | bhandsaker | 2009-02-18 19:06:57 +0000 (Wed, 18 Feb 2009) | 2 lines
958 M /trunk/samtools/bamtk.c
960 Fix annoying segv when invalid region specified.
962 ------------------------------------------------------------------------
963 r127 | lh3lh3 | 2009-02-17 10:49:55 +0000 (Tue, 17 Feb 2009) | 2 lines
965 D /trunk/samtools/misc/indel_filter.pl
966 A /trunk/samtools/misc/samtools.pl
968 * move indel_filter.pl to samtools.pl
970 ------------------------------------------------------------------------
971 r126 | lh3lh3 | 2009-02-14 21:22:30 +0000 (Sat, 14 Feb 2009) | 3 lines
973 M /trunk/samtools/bam_mate.c
974 M /trunk/samtools/bamtk.c
977 * fixed a bug in fixmate: SE reads are flagged as BAM_FMUNMAP
979 ------------------------------------------------------------------------
980 r125 | lh3lh3 | 2009-02-13 09:54:45 +0000 (Fri, 13 Feb 2009) | 3 lines
982 M /trunk/samtools/bam_stat.c
983 M /trunk/samtools/bamtk.c
986 * fixed a minor bug in flagstat
988 ------------------------------------------------------------------------
989 r124 | lh3lh3 | 2009-02-12 11:15:32 +0000 (Thu, 12 Feb 2009) | 3 lines
991 M /trunk/samtools/bam_maqcns.c
992 M /trunk/samtools/bamtk.c
993 M /trunk/samtools/misc/indel_filter.pl
996 * improve indel caller by setting maximum window size
998 ------------------------------------------------------------------------
999 r123 | lh3lh3 | 2009-02-12 10:30:29 +0000 (Thu, 12 Feb 2009) | 2 lines
1001 M /trunk/samtools/bam_plcmd.c
1002 M /trunk/samtools/bamtk.c
1004 * output max mapping quality in indel line
1006 ------------------------------------------------------------------------
1007 r122 | lh3lh3 | 2009-02-11 10:59:10 +0000 (Wed, 11 Feb 2009) | 2 lines
1009 M /trunk/samtools/misc/maq2sam.c
1011 fixed a bug in generating tag AM
1013 ------------------------------------------------------------------------
1014 r121 | lh3lh3 | 2009-02-03 10:43:11 +0000 (Tue, 03 Feb 2009) | 2 lines
1016 M /trunk/samtools/bam_index.c
1017 M /trunk/samtools/bamtk.c
1019 fixed a potential memory problem in indexing
1021 ------------------------------------------------------------------------
1022 r120 | bhandsaker | 2009-02-02 15:52:52 +0000 (Mon, 02 Feb 2009) | 2 lines
1024 M /trunk/samtools/Makefile
1026 Pass LIBS to recursive targets to facilitate building at Broad.
1028 ------------------------------------------------------------------------
1029 r119 | lh3lh3 | 2009-02-02 10:12:15 +0000 (Mon, 02 Feb 2009) | 4 lines
1031 M /trunk/samtools/ChangeLog
1032 M /trunk/samtools/bam_plcmd.c
1033 M /trunk/samtools/bam_stat.c
1034 M /trunk/samtools/bamtk.c
1037 * fixed a bug in generating GLFv2 for indels
1038 * improve flagstat report a little bit
1040 ------------------------------------------------------------------------
1041 r118 | lh3lh3 | 2009-01-29 12:33:23 +0000 (Thu, 29 Jan 2009) | 3 lines
1043 M /trunk/samtools/Makefile
1044 A /trunk/samtools/bam_stat.c
1045 M /trunk/samtools/bamtk.c
1048 * added flagstat command
1050 ------------------------------------------------------------------------
1051 r116 | lh3lh3 | 2009-01-28 13:31:12 +0000 (Wed, 28 Jan 2009) | 2 lines
1053 M /trunk/samtools/ChangeLog
1054 M /trunk/samtools/NEWS
1055 M /trunk/samtools/bamtk.c
1056 M /trunk/samtools/samtools.1
1058 Release SAMtools-0.1.2
1060 ------------------------------------------------------------------------
1061 r115 | lh3lh3 | 2009-01-28 12:54:08 +0000 (Wed, 28 Jan 2009) | 2 lines
1063 A /trunk/samtools/misc/indel_filter.pl
1065 Script for filtering indel results
1067 ------------------------------------------------------------------------
1068 r114 | lh3lh3 | 2009-01-25 11:45:37 +0000 (Sun, 25 Jan 2009) | 2 lines
1070 A /trunk/samtools/misc/zoom2sam.pl
1074 ------------------------------------------------------------------------
1075 r113 | lh3lh3 | 2009-01-24 14:25:07 +0000 (Sat, 24 Jan 2009) | 2 lines
1077 A /trunk/samtools/misc/novo2sam.pl
1079 add a script to convert novo alignment to SAM
1081 ------------------------------------------------------------------------
1082 r112 | lh3lh3 | 2009-01-23 20:57:39 +0000 (Fri, 23 Jan 2009) | 2 lines
1084 M /trunk/samtools/ChangeLog
1085 M /trunk/samtools/ChangeLog.old
1086 M /trunk/samtools/samtools.1
1088 update documentation and ChangeLog
1090 ------------------------------------------------------------------------
1091 r111 | lh3lh3 | 2009-01-23 19:22:59 +0000 (Fri, 23 Jan 2009) | 3 lines
1093 M /trunk/samtools/bam_sort.c
1094 M /trunk/samtools/bamtk.c
1097 * fixed a bug in "merge" command line
1099 ------------------------------------------------------------------------
1100 r110 | lh3lh3 | 2009-01-22 15:36:48 +0000 (Thu, 22 Jan 2009) | 3 lines
1102 M /trunk/samtools/misc/Makefile
1103 A /trunk/samtools/misc/bowtie2sam.pl (from /branches/dev/samtools/misc/bowtie2sam.pl:108)
1104 M /trunk/samtools/misc/export2sam.pl
1105 A /trunk/samtools/misc/soap2sam.pl (from /branches/dev/samtools/misc/soap2sam.pl:108)
1106 A /trunk/samtools/misc/wgsim.c (from /branches/dev/samtools/misc/wgsim.c:108)
1107 A /trunk/samtools/misc/wgsim_eval.pl (from /branches/dev/samtools/misc/wgsim_eval.pl:108)
1109 * merge from branches/dev/
1110 * all future development will happen here
1112 ------------------------------------------------------------------------
1113 r109 | lh3lh3 | 2009-01-22 15:14:27 +0000 (Thu, 22 Jan 2009) | 3 lines
1115 M /trunk/samtools/COPYING
1116 M /trunk/samtools/ChangeLog
1117 A /trunk/samtools/INSTALL (from /branches/dev/samtools/INSTALL:108)
1118 M /trunk/samtools/Makefile
1119 A /trunk/samtools/Makefile.lite (from /branches/dev/samtools/Makefile.lite:108)
1120 M /trunk/samtools/bam.c
1121 M /trunk/samtools/bam.h
1122 M /trunk/samtools/bam_import.c
1123 M /trunk/samtools/bam_index.c
1124 M /trunk/samtools/bam_lpileup.c
1125 M /trunk/samtools/bam_maqcns.c
1126 M /trunk/samtools/bam_maqcns.h
1127 A /trunk/samtools/bam_mate.c (from /branches/dev/samtools/bam_mate.c:108)
1128 M /trunk/samtools/bam_pileup.c
1129 M /trunk/samtools/bam_plcmd.c
1130 A /trunk/samtools/bam_rmdup.c (from /branches/dev/samtools/bam_rmdup.c:108)
1131 M /trunk/samtools/bam_sort.c
1132 M /trunk/samtools/bamtk.c
1133 M /trunk/samtools/bgzf.h
1134 M /trunk/samtools/examples/00README.txt
1135 A /trunk/samtools/examples/Makefile (from /branches/dev/samtools/examples/Makefile:108)
1136 D /trunk/samtools/examples/ex1.fa.fai
1137 M /trunk/samtools/examples/ex1.sam.gz
1138 M /trunk/samtools/faidx.c
1139 A /trunk/samtools/glf.c (from /branches/dev/samtools/glf.c:108)
1140 M /trunk/samtools/glf.h
1141 M /trunk/samtools/misc/Makefile
1142 M /trunk/samtools/misc/maq2sam.c
1143 M /trunk/samtools/razf.c
1144 M /trunk/samtools/source.dot
1146 * Merge from branches/dev/
1147 * all future development will happen here at trunk/
1149 ------------------------------------------------------------------------
1150 r79 | bhandsaker | 2009-01-07 21:42:15 +0000 (Wed, 07 Jan 2009) | 2 lines
1152 M /trunk/samtools/bam_maqcns.c
1153 M /trunk/samtools/bam_tview.c
1155 Fix problem with compiling without curses.
1157 ------------------------------------------------------------------------
1158 r63 | lh3lh3 | 2008-12-22 15:58:02 +0000 (Mon, 22 Dec 2008) | 2 lines
1160 A /trunk/samtools (from /branches/dev/samtools:62)
1164 ------------------------------------------------------------------------
1165 r62 | lh3lh3 | 2008-12-22 15:55:13 +0000 (Mon, 22 Dec 2008) | 2 lines
1167 A /branches/dev/samtools/NEWS
1168 M /branches/dev/samtools/bamtk.c
1169 M /branches/dev/samtools/samtools.1
1171 Release samtools-0.1.1
1173 ------------------------------------------------------------------------
1174 r61 | lh3lh3 | 2008-12-22 15:46:08 +0000 (Mon, 22 Dec 2008) | 10 lines
1176 M /branches/dev/samtools/bam_aux.c
1177 M /branches/dev/samtools/bam_index.c
1178 M /branches/dev/samtools/bam_plcmd.c
1179 M /branches/dev/samtools/bam_tview.c
1180 M /branches/dev/samtools/bamtk.c
1181 M /branches/dev/samtools/razf.c
1182 M /branches/dev/samtools/samtools.1
1185 * fixed a bug in razf.c: reset z_eof when razf_seek() is called
1186 * fixed a memory leak in parsing a region
1187 * changed pileup a little bit when -s is in use: output ^ and $
1188 * when a bam is not indexed, output more meaningful error message
1189 * fixed a bug in indexing for small alignment
1190 * fixed a bug in the viewer when we come to the end of a reference file
1191 * updated documentation
1192 * prepare to release 0.1.1
1194 ------------------------------------------------------------------------
1195 r60 | lh3lh3 | 2008-12-22 15:10:16 +0000 (Mon, 22 Dec 2008) | 2 lines
1197 A /branches/dev/samtools/examples
1198 A /branches/dev/samtools/examples/00README.txt
1199 A /branches/dev/samtools/examples/ex1.fa
1200 A /branches/dev/samtools/examples/ex1.fa.fai
1201 A /branches/dev/samtools/examples/ex1.sam.gz
1205 ------------------------------------------------------------------------
1206 r59 | lh3lh3 | 2008-12-22 09:38:15 +0000 (Mon, 22 Dec 2008) | 2 lines
1208 M /branches/dev/samtools/ChangeLog
1212 ------------------------------------------------------------------------
1213 r58 | lh3lh3 | 2008-12-20 23:06:00 +0000 (Sat, 20 Dec 2008) | 3 lines
1215 M /branches/dev/samtools/misc/export2sam.pl
1218 * fixed several bugs
1220 ------------------------------------------------------------------------
1221 r57 | lh3lh3 | 2008-12-20 15:44:20 +0000 (Sat, 20 Dec 2008) | 2 lines
1223 A /branches/dev/samtools/misc/export2sam.pl
1225 convert Export format to SAM; not thoroughly tested
1227 ------------------------------------------------------------------------
1228 r56 | lh3lh3 | 2008-12-19 22:13:28 +0000 (Fri, 19 Dec 2008) | 6 lines
1230 M /branches/dev/samtools/bam_import.c
1231 M /branches/dev/samtools/bam_plcmd.c
1232 M /branches/dev/samtools/bam_tview.c
1233 M /branches/dev/samtools/bamtk.c
1234 A /branches/dev/samtools/source.dot
1237 * pileup: generate maq-like simple output
1238 * pileup: allow to output pileup at required sites
1239 * source.dot: source file relationship graph
1240 * tview: fixed a minor bug
1242 ------------------------------------------------------------------------
1243 r55 | lh3lh3 | 2008-12-19 20:10:26 +0000 (Fri, 19 Dec 2008) | 2 lines
1245 D /branches/dev/samtools/misc/all2sam.pl
1249 ------------------------------------------------------------------------
1250 r54 | lh3lh3 | 2008-12-16 22:34:25 +0000 (Tue, 16 Dec 2008) | 2 lines
1252 A /branches/dev/samtools/COPYING
1253 M /branches/dev/samtools/bam.h
1254 M /branches/dev/samtools/faidx.h
1255 M /branches/dev/samtools/khash.h
1256 M /branches/dev/samtools/kseq.h
1257 M /branches/dev/samtools/ksort.h
1258 M /branches/dev/samtools/samtools.1
1260 Added copyright information and a bit more documentation. No code change.
1262 ------------------------------------------------------------------------
1263 r53 | lh3lh3 | 2008-12-16 13:40:18 +0000 (Tue, 16 Dec 2008) | 3 lines
1265 M /branches/dev/samtools/bam.c
1266 M /branches/dev/samtools/bam.h
1267 M /branches/dev/samtools/bam_index.c
1268 M /branches/dev/samtools/bam_maqcns.c
1269 M /branches/dev/samtools/bamtk.c
1272 * improved efficiency of the indel caller for spliced alignments
1274 ------------------------------------------------------------------------
1275 r52 | lh3lh3 | 2008-12-16 10:28:20 +0000 (Tue, 16 Dec 2008) | 3 lines
1277 M /branches/dev/samtools/bam.c
1278 M /branches/dev/samtools/bam.h
1279 M /branches/dev/samtools/bam_aux.c
1280 M /branches/dev/samtools/bam_index.c
1281 M /branches/dev/samtools/bamtk.c
1284 * a bit code cleanup: reduce the dependency between source files
1286 ------------------------------------------------------------------------
1287 r51 | lh3lh3 | 2008-12-15 14:29:32 +0000 (Mon, 15 Dec 2008) | 3 lines
1289 M /branches/dev/samtools/bam_maqcns.c
1290 M /branches/dev/samtools/bam_plcmd.c
1291 M /branches/dev/samtools/bamtk.c
1294 * fixed a memory leak
1296 ------------------------------------------------------------------------
1297 r50 | lh3lh3 | 2008-12-15 14:00:13 +0000 (Mon, 15 Dec 2008) | 2 lines
1299 M /branches/dev/samtools/ChangeLog
1300 M /branches/dev/samtools/bam.h
1301 M /branches/dev/samtools/samtools.1
1303 update documentation, ChangeLog and a comment
1305 ------------------------------------------------------------------------
1306 r49 | lh3lh3 | 2008-12-15 13:36:43 +0000 (Mon, 15 Dec 2008) | 6 lines
1308 M /branches/dev/samtools/Makefile
1309 M /branches/dev/samtools/bam.h
1310 M /branches/dev/samtools/bam_maqcns.c
1311 M /branches/dev/samtools/bam_maqcns.h
1312 M /branches/dev/samtools/bam_pileup.c
1313 A /branches/dev/samtools/bam_plcmd.c
1314 M /branches/dev/samtools/bamtk.c
1315 M /branches/dev/samtools/samtools.1
1318 * moved pileup command to a separate source file
1319 * added indel caller
1320 * added bam_cal_segend(). (NOT WORKING for spliced alignment!!!)
1321 * updated documentation
1323 ------------------------------------------------------------------------
1324 r48 | lh3lh3 | 2008-12-12 13:55:36 +0000 (Fri, 12 Dec 2008) | 3 lines
1326 M /branches/dev/samtools/bam_maqcns.c
1327 M /branches/dev/samtools/bamtk.c
1330 * fixed another bug in maqcns when there is a nearby deletion
1332 ------------------------------------------------------------------------
1333 r47 | lh3lh3 | 2008-12-12 13:42:16 +0000 (Fri, 12 Dec 2008) | 5 lines
1335 M /branches/dev/samtools/bam_maqcns.c
1336 M /branches/dev/samtools/bam_pileup.c
1337 M /branches/dev/samtools/bamtk.c
1340 * pileup: outputing consensus is now optional
1341 * fixed a bug in glfgen. This bug also exists in maq's glfgen. However,
1342 I am not quite sure why the previous version may have problem.
1344 ------------------------------------------------------------------------
1345 r46 | lh3lh3 | 2008-12-12 11:44:56 +0000 (Fri, 12 Dec 2008) | 6 lines
1347 M /branches/dev/samtools/bam_pileup.c
1348 M /branches/dev/samtools/bamtk.c
1351 * add maq consensus to pileup. However, I will move this part to a new
1352 command as strictly speaking, consensus callin is not part of pileup,
1353 and imposing it would make it harder to generate for other language
1356 ------------------------------------------------------------------------
1357 r45 | bhandsaker | 2008-12-11 20:43:56 +0000 (Thu, 11 Dec 2008) | 2 lines
1359 M /branches/dev/samtools/bgzf.c
1361 Fix bug in tell() after reads that consume to the exact end of a block.
1363 ------------------------------------------------------------------------
1364 r44 | lh3lh3 | 2008-12-11 09:36:53 +0000 (Thu, 11 Dec 2008) | 2 lines
1366 M /branches/dev/samtools/samtools.1
1370 ------------------------------------------------------------------------
1371 r43 | lh3lh3 | 2008-12-11 09:25:36 +0000 (Thu, 11 Dec 2008) | 4 lines
1373 M /branches/dev/samtools/bam_import.c
1374 M /branches/dev/samtools/bamtk.c
1377 * fixed a bug in parser when there is auxiliary fields
1378 * made the parser a bit more robust
1380 ------------------------------------------------------------------------
1381 r42 | lh3lh3 | 2008-12-10 14:57:29 +0000 (Wed, 10 Dec 2008) | 5 lines
1383 M /branches/dev/samtools/bam_index.c
1384 M /branches/dev/samtools/bamtk.c
1385 M /branches/dev/samtools/bgzf.c
1388 * fixed a bug in bgzf (only reading is affected)
1389 * fixed a typo in bam_index.c
1390 * in bam_index.c, check potential bugs in the underlying I/O library
1392 ------------------------------------------------------------------------
1393 r41 | lh3lh3 | 2008-12-10 12:53:08 +0000 (Wed, 10 Dec 2008) | 2 lines
1395 M /branches/dev/samtools/samtools.1
1399 ------------------------------------------------------------------------
1400 r40 | lh3lh3 | 2008-12-10 11:52:10 +0000 (Wed, 10 Dec 2008) | 5 lines
1402 M /branches/dev/samtools/bam.h
1403 M /branches/dev/samtools/bam_pileup.c
1404 M /branches/dev/samtools/bamtk.c
1407 * tried to make pileup work with clipping (previously not), though NOT tested
1408 * removed -v from pileup
1409 * made pileup take the reference sequence
1411 ------------------------------------------------------------------------
1412 r39 | lh3lh3 | 2008-12-09 11:59:28 +0000 (Tue, 09 Dec 2008) | 4 lines
1414 M /branches/dev/samtools/bam_import.c
1415 M /branches/dev/samtools/bamtk.c
1416 M /branches/dev/samtools/samtools.1
1419 * in parser, recognize "=", rather than ",", as a match
1420 * in parser, correctl parse "=" at the MRNM field.
1422 ------------------------------------------------------------------------
1423 r38 | lh3lh3 | 2008-12-09 11:39:07 +0000 (Tue, 09 Dec 2008) | 2 lines
1425 M /branches/dev/samtools/misc/maq2sam.c
1427 fixed a bug in handling maq flag 64 and 192
1429 ------------------------------------------------------------------------
1430 r37 | lh3lh3 | 2008-12-09 09:53:46 +0000 (Tue, 09 Dec 2008) | 2 lines
1432 M /branches/dev/samtools/misc/md5fa.c
1434 also calculate unordered md5sum check
1436 ------------------------------------------------------------------------
1437 r36 | lh3lh3 | 2008-12-09 09:46:21 +0000 (Tue, 09 Dec 2008) | 2 lines
1439 M /branches/dev/samtools/misc/md5fa.c
1441 fixed a minor bug when there are space in the sequence
1443 ------------------------------------------------------------------------
1444 r35 | lh3lh3 | 2008-12-09 09:40:45 +0000 (Tue, 09 Dec 2008) | 2 lines
1446 M /branches/dev/samtools/misc/md5fa.c
1448 fixed a potential memory leak
1450 ------------------------------------------------------------------------
1451 r34 | lh3lh3 | 2008-12-08 14:52:17 +0000 (Mon, 08 Dec 2008) | 2 lines
1453 M /branches/dev/samtools/bam_import.c
1454 M /branches/dev/samtools/bam_index.c
1455 M /branches/dev/samtools/bamtk.c
1457 * fixed a bug in import: bin is wrongly calculated
1459 ------------------------------------------------------------------------
1460 r33 | lh3lh3 | 2008-12-08 14:08:01 +0000 (Mon, 08 Dec 2008) | 2 lines
1462 M /branches/dev/samtools/misc/all2sam.pl
1466 ------------------------------------------------------------------------
1467 r32 | lh3lh3 | 2008-12-08 12:56:02 +0000 (Mon, 08 Dec 2008) | 3 lines
1469 M /branches/dev/samtools/Makefile
1470 M /branches/dev/samtools/kseq.h
1471 M /branches/dev/samtools/misc/Makefile
1472 A /branches/dev/samtools/misc/md5.c
1473 A /branches/dev/samtools/misc/md5.h
1474 A /branches/dev/samtools/misc/md5fa.c
1476 * fixed two warnings in kseq.h
1477 * added md5sum utilities
1479 ------------------------------------------------------------------------
1480 r31 | lh3lh3 | 2008-12-08 11:35:29 +0000 (Mon, 08 Dec 2008) | 5 lines
1482 M /branches/dev/samtools/Makefile
1483 M /branches/dev/samtools/bam_import.c
1484 M /branches/dev/samtools/bamtk.c
1485 A /branches/dev/samtools/kseq.h
1486 D /branches/dev/samtools/kstream.h
1489 * replace kstream with kseq. kseq is a superset of kstream. I need the
1490 extra functions in kseq.h.
1491 * also compile stand-alone faidx
1493 ------------------------------------------------------------------------
1494 r30 | lh3lh3 | 2008-12-08 11:17:04 +0000 (Mon, 08 Dec 2008) | 3 lines
1496 M /branches/dev/samtools/bam.h
1497 M /branches/dev/samtools/bam_sort.c
1498 M /branches/dev/samtools/bamtk.c
1501 * sorting by read names is available
1503 ------------------------------------------------------------------------
1504 r29 | lh3lh3 | 2008-12-08 10:29:02 +0000 (Mon, 08 Dec 2008) | 3 lines
1506 M /branches/dev/samtools/bam.c
1507 M /branches/dev/samtools/bam.h
1508 M /branches/dev/samtools/bam_import.c
1509 M /branches/dev/samtools/bam_maqcns.c
1510 M /branches/dev/samtools/bam_pileup.c
1511 M /branches/dev/samtools/bam_sort.c
1512 M /branches/dev/samtools/bam_tview.c
1513 M /branches/dev/samtools/bamtk.c
1514 M /branches/dev/samtools/misc/maq2sam.c
1517 * format change to meet the latest specification
1519 ------------------------------------------------------------------------
1520 r28 | lh3lh3 | 2008-12-04 16:09:21 +0000 (Thu, 04 Dec 2008) | 3 lines
1522 M /branches/dev/samtools/bam_maqcns.c
1523 M /branches/dev/samtools/misc/maq2sam.c
1525 * minor change in maqcns: special care when n==0
1526 * change maq2sam to meet the latest specification
1528 ------------------------------------------------------------------------
1529 r27 | lh3lh3 | 2008-12-04 15:55:44 +0000 (Thu, 04 Dec 2008) | 2 lines
1531 M /branches/dev/samtools/razf.c
1532 M /branches/dev/samtools/razf.h
1534 considerable code clean up in razf
1536 ------------------------------------------------------------------------
1537 r26 | lh3lh3 | 2008-12-04 15:08:18 +0000 (Thu, 04 Dec 2008) | 2 lines
1539 M /branches/dev/samtools/ChangeLog
1540 M /branches/dev/samtools/Makefile
1541 M /branches/dev/samtools/faidx.c
1543 make RAZF optional in faidx.c
1545 ------------------------------------------------------------------------
1546 r25 | lh3lh3 | 2008-12-01 15:27:22 +0000 (Mon, 01 Dec 2008) | 3 lines
1548 M /branches/dev/samtools/Makefile
1549 M /branches/dev/samtools/bam.h
1550 M /branches/dev/samtools/bam_aux.c
1551 M /branches/dev/samtools/bamtk.c
1552 M /branches/dev/samtools/samtools.1
1555 * added routines for retrieving aux data, NOT TESTED YET!
1557 ------------------------------------------------------------------------
1558 r24 | lh3lh3 | 2008-12-01 14:29:43 +0000 (Mon, 01 Dec 2008) | 5 lines
1560 M /branches/dev/samtools/bam.c
1561 M /branches/dev/samtools/bam_import.c
1562 M /branches/dev/samtools/bam_maqcns.c
1563 M /branches/dev/samtools/bamtk.c
1564 M /branches/dev/samtools/bgzf.c
1565 M /branches/dev/samtools/samtools.1
1568 * bgzf: fixed a potential integer overflow on 32-it machines
1569 * maqcns: set the minimum combined quality as 0
1570 * supporting hex strings
1572 ------------------------------------------------------------------------
1573 r23 | lh3lh3 | 2008-11-27 17:14:37 +0000 (Thu, 27 Nov 2008) | 3 lines
1575 M /branches/dev/samtools/bam_maqcns.c
1576 M /branches/dev/samtools/bamtk.c
1579 * fixed the bug in maqcns
1581 ------------------------------------------------------------------------
1582 r22 | lh3lh3 | 2008-11-27 17:08:11 +0000 (Thu, 27 Nov 2008) | 3 lines
1584 M /branches/dev/samtools/Makefile
1585 M /branches/dev/samtools/bam.h
1586 A /branches/dev/samtools/bam_maqcns.c
1587 A /branches/dev/samtools/bam_maqcns.h
1588 M /branches/dev/samtools/bam_tview.c
1589 M /branches/dev/samtools/bamtk.c
1590 A /branches/dev/samtools/glf.h
1593 * add MAQ consensus caller, currently BUGGY!
1595 ------------------------------------------------------------------------
1596 r21 | lh3lh3 | 2008-11-27 13:51:28 +0000 (Thu, 27 Nov 2008) | 4 lines
1598 M /branches/dev/samtools/bam_pileup.c
1599 M /branches/dev/samtools/bam_tview.c
1600 M /branches/dev/samtools/bamtk.c
1603 * tview: display padded alignment (but not P operation)
1604 * better coordinates and reference sequence
1606 ------------------------------------------------------------------------
1607 r19 | lh3lh3 | 2008-11-27 09:26:05 +0000 (Thu, 27 Nov 2008) | 2 lines
1609 A /branches/dev/samtools/ChangeLog
1613 ------------------------------------------------------------------------
1614 r18 | lh3lh3 | 2008-11-27 09:24:45 +0000 (Thu, 27 Nov 2008) | 3 lines
1616 D /branches/dev/samtools/ChangeLog
1617 A /branches/dev/samtools/ChangeLog.old (from /branches/dev/samtools/ChangeLog:6)
1619 Rename ChangeLog to ChangeLog.old. This old ChangeLog is generated from
1620 the log of my personal SVN repository.
1622 ------------------------------------------------------------------------
1623 r17 | lh3lh3 | 2008-11-27 09:22:55 +0000 (Thu, 27 Nov 2008) | 6 lines
1625 M /branches/dev/samtools/Makefile
1626 M /branches/dev/samtools/bamtk.c
1627 M /branches/dev/samtools/bgzf.c
1630 * declare fseeko and ftello as some Linux may not do this by default and
1631 missing these declarations will make bgzf buggy
1632 * get rid of some harmless warings
1633 * use BGZF by default, now
1635 ------------------------------------------------------------------------
1636 r16 | lh3lh3 | 2008-11-26 21:19:11 +0000 (Wed, 26 Nov 2008) | 4 lines
1638 M /branches/dev/samtools/bam_index.c
1639 M /branches/dev/samtools/bamtk.c
1640 M /branches/dev/samtools/razf.c
1643 * fixed a bug in razf_read()
1644 * give more warnings when the file is truncated (or due to bugs in I/O library)
1646 ------------------------------------------------------------------------
1647 r15 | lh3lh3 | 2008-11-26 20:41:39 +0000 (Wed, 26 Nov 2008) | 2 lines
1649 M /branches/dev/samtools/bgzf.c
1651 fixed a bug in bgzf.c at the end of the file
1653 ------------------------------------------------------------------------
1654 r14 | lh3lh3 | 2008-11-26 17:05:18 +0000 (Wed, 26 Nov 2008) | 4 lines
1656 M /branches/dev/samtools/bamtk.c
1659 * a lot happened to RAZF, although samtools itself is untouched. Better
1660 also update the version number anyway to avoid confusion
1662 ------------------------------------------------------------------------
1663 r13 | lh3lh3 | 2008-11-26 17:03:48 +0000 (Wed, 26 Nov 2008) | 2 lines
1665 M /branches/dev/samtools/razf.c
1667 a change from Jue, but I think it should not matter
1669 ------------------------------------------------------------------------
1670 r12 | lh3lh3 | 2008-11-26 16:48:14 +0000 (Wed, 26 Nov 2008) | 3 lines
1672 M /branches/dev/samtools/razf.c
1674 fixed a potential bug in razf. However, it seems still buggy, just
1675 rarely happens, very rarely.
1677 ------------------------------------------------------------------------
1678 r11 | lh3lh3 | 2008-11-26 14:02:56 +0000 (Wed, 26 Nov 2008) | 2 lines
1680 M /branches/dev/samtools/razf.c
1682 fixed a bug in razf, with the help of Jue
1684 ------------------------------------------------------------------------
1685 r10 | lh3lh3 | 2008-11-26 11:55:32 +0000 (Wed, 26 Nov 2008) | 2 lines
1687 M /branches/dev/samtools/bam_index.c
1691 ------------------------------------------------------------------------
1692 r9 | lh3lh3 | 2008-11-26 11:37:05 +0000 (Wed, 26 Nov 2008) | 2 lines
1694 M /branches/dev/samtools/Makefile
1695 M /branches/dev/samtools/bam.h
1696 M /branches/dev/samtools/razf.c
1697 M /branches/dev/samtools/razf.h
1699 * Jue has updated razf to realize Bob's scheme
1701 ------------------------------------------------------------------------
1702 r7 | lh3lh3 | 2008-11-25 20:37:37 +0000 (Tue, 25 Nov 2008) | 2 lines
1704 A /branches/dev/samtools/samtools.1
1708 ------------------------------------------------------------------------
1709 r6 | lh3lh3 | 2008-11-25 20:37:16 +0000 (Tue, 25 Nov 2008) | 3 lines
1711 A /branches/dev/samtools/ChangeLog
1712 A /branches/dev/samtools/Makefile
1713 A /branches/dev/samtools/bam.c
1714 A /branches/dev/samtools/bam.h
1715 A /branches/dev/samtools/bam_aux.c
1716 A /branches/dev/samtools/bam_endian.h
1717 A /branches/dev/samtools/bam_import.c
1718 A /branches/dev/samtools/bam_index.c
1719 A /branches/dev/samtools/bam_lpileup.c
1720 A /branches/dev/samtools/bam_pileup.c
1721 A /branches/dev/samtools/bam_sort.c
1722 A /branches/dev/samtools/bam_tview.c
1723 A /branches/dev/samtools/bamtk.c
1724 A /branches/dev/samtools/bgzf.c
1725 A /branches/dev/samtools/bgzf.h
1726 A /branches/dev/samtools/bgzip.c
1727 A /branches/dev/samtools/faidx.c
1728 A /branches/dev/samtools/faidx.h
1729 A /branches/dev/samtools/khash.h
1730 A /branches/dev/samtools/ksort.h
1731 A /branches/dev/samtools/kstream.h
1732 A /branches/dev/samtools/misc
1733 A /branches/dev/samtools/misc/Makefile
1734 A /branches/dev/samtools/misc/all2sam.pl
1735 A /branches/dev/samtools/misc/maq2sam.c
1736 A /branches/dev/samtools/razf.c
1737 A /branches/dev/samtools/razf.h
1738 A /branches/dev/samtools/razip.c
1739 A /branches/dev/samtools/zutil.h
1741 The initial version of samtools, replicated from my local SVN repository.
1742 The current version is: 0.1.0-42. All future development will happen here.
1744 ------------------------------------------------------------------------
1745 r5 | lh3lh3 | 2008-11-25 20:30:49 +0000 (Tue, 25 Nov 2008) | 2 lines
1747 A /branches/dev/samtools
1749 samtools (C version)
1751 ------------------------------------------------------------------------