1 ------------------------------------------------------------------------
2 r216 | lh3lh3 | 2009-04-14 22:10:46 +0100 (Tue, 14 Apr 2009) | 4 lines
4 M /trunk/samtools/misc/samtools.pl
7 * improve indelFilter to avoid filtering true indels. The new filter relies
8 on the new pileup indel line implemented in samtools-0.1.2-25
10 ------------------------------------------------------------------------
11 r215 | lh3lh3 | 2009-04-14 22:04:19 +0100 (Tue, 14 Apr 2009) | 4 lines
13 M /trunk/samtools/bam_maqcns.c
14 M /trunk/samtools/bam_plcmd.c
15 M /trunk/samtools/bamtk.c
16 M /trunk/samtools/samtools.1
19 * change the pileup indel line to shows the number of alignments actually
22 ------------------------------------------------------------------------
23 r211 | lh3lh3 | 2009-04-13 12:07:13 +0100 (Mon, 13 Apr 2009) | 2 lines
25 M /trunk/samtools/ChangeLog
27 update ChangeLog from "svn log"
29 ------------------------------------------------------------------------
30 r210 | lh3lh3 | 2009-04-12 20:57:05 +0100 (Sun, 12 Apr 2009) | 4 lines
32 M /trunk/samtools/bam.c
33 M /trunk/samtools/bam_import.c
34 M /trunk/samtools/bam_sort.c
35 M /trunk/samtools/bamtk.c
36 M /trunk/samtools/kseq.h
39 * in merge, gives a warning rather than error if the target sequence length is different
42 ------------------------------------------------------------------------
43 r209 | lh3lh3 | 2009-04-12 20:32:44 +0100 (Sun, 12 Apr 2009) | 3 lines
45 M /trunk/samtools/bam.c
46 M /trunk/samtools/bam_import.c
47 M /trunk/samtools/bamtk.c
50 * recognize '*' at the QUAL field
52 ------------------------------------------------------------------------
53 r208 | lh3lh3 | 2009-04-12 20:08:02 +0100 (Sun, 12 Apr 2009) | 3 lines
55 M /trunk/samtools/bam_import.c
56 M /trunk/samtools/bamtk.c
57 M /trunk/samtools/kseq.h
60 * the field separater is TAB only, now
62 ------------------------------------------------------------------------
63 r207 | lh3lh3 | 2009-04-08 15:18:03 +0100 (Wed, 08 Apr 2009) | 2 lines
65 M /trunk/samtools/examples/ex1.sam.gz
67 * fixed the problem in the example alignment due to the bug in fixmate
69 ------------------------------------------------------------------------
70 r206 | lh3lh3 | 2009-04-08 15:15:05 +0100 (Wed, 08 Apr 2009) | 3 lines
72 M /trunk/samtools/bam_mate.c
73 M /trunk/samtools/bamtk.c
74 M /trunk/samtools/misc/soap2sam.pl
77 * fixed a nasty bug in `fixmate'
79 ------------------------------------------------------------------------
80 r205 | lh3lh3 | 2009-04-08 10:57:08 +0100 (Wed, 08 Apr 2009) | 2 lines
82 M /trunk/samtools/misc/bowtie2sam.pl
83 M /trunk/samtools/misc/soap2sam.pl
84 M /trunk/samtools/misc/wgsim_eval.pl
86 make the script robust to the bugs in SOAP-2.1.7
88 ------------------------------------------------------------------------
89 r200 | lh3lh3 | 2009-04-02 15:14:56 +0100 (Thu, 02 Apr 2009) | 3 lines
91 M /trunk/samtools/bam_stat.c
92 M /trunk/samtools/bamtk.c
95 * check if file is truncated in flagstat
97 ------------------------------------------------------------------------
98 r199 | lh3lh3 | 2009-04-02 15:09:10 +0100 (Thu, 02 Apr 2009) | 3 lines
100 M /trunk/samtools/bamtk.c
103 * print the header if requested
105 ------------------------------------------------------------------------
106 r193 | lh3lh3 | 2009-03-27 15:09:50 +0000 (Fri, 27 Mar 2009) | 3 lines
108 M /trunk/samtools/bam_plcmd.c
109 M /trunk/samtools/bamtk.c
112 * fixed a minor bug reported by Nils Homer
114 ------------------------------------------------------------------------
115 r185 | lh3lh3 | 2009-03-24 11:50:32 +0000 (Tue, 24 Mar 2009) | 2 lines
117 A /trunk/samtools/Makefile (from /trunk/samtools/Makefile.std:184)
118 D /trunk/samtools/Makefile.std
119 A /trunk/samtools/misc/Makefile (from /trunk/samtools/misc/Makefile.std:184)
120 D /trunk/samtools/misc/Makefile.std
122 rename Makefile.std as Makefile. GNU building systerm is not ready and may take some time...
124 ------------------------------------------------------------------------
125 r184 | lh3lh3 | 2009-03-24 10:36:38 +0000 (Tue, 24 Mar 2009) | 4 lines
127 D /trunk/samtools/Makefile
128 A /trunk/samtools/Makefile.std (from /trunk/samtools/Makefile:183)
129 M /trunk/samtools/bam_sort.c
130 M /trunk/samtools/bam_tview.c
131 M /trunk/samtools/bamtk.c
132 D /trunk/samtools/misc/Makefile
133 A /trunk/samtools/misc/Makefile.std (from /trunk/samtools/misc/Makefile:182)
134 M /trunk/samtools/samtools.1
137 * incorporating Nils' changes
138 * rename Makefile to Makefile.std and prepare to add the GNU building systerms (also by Nils)
140 ------------------------------------------------------------------------
141 r183 | lh3lh3 | 2009-03-24 10:30:23 +0000 (Tue, 24 Mar 2009) | 4 lines
143 M /trunk/samtools/Makefile
144 M /trunk/samtools/bam_import.c
145 M /trunk/samtools/bam_maqcns.c
146 M /trunk/samtools/bam_maqcns.h
147 M /trunk/samtools/bam_plcmd.c
148 M /trunk/samtools/bamtk.c
149 M /trunk/samtools/kseq.h
150 A /trunk/samtools/kstring.c
151 A /trunk/samtools/kstring.h
154 * made pileup take a list of proposed indels. An insertion is N at the moment.
155 * added my kstring library for a bit complex parsing of the position list.
157 ------------------------------------------------------------------------
158 r169 | lh3lh3 | 2009-03-12 13:40:14 +0000 (Thu, 12 Mar 2009) | 3 lines
160 M /trunk/samtools/misc/soap2sam.pl
163 * more robust to truncated soap output
165 ------------------------------------------------------------------------
166 r168 | lh3lh3 | 2009-03-11 10:49:00 +0000 (Wed, 11 Mar 2009) | 2 lines
168 M /trunk/samtools/Makefile.lite
170 added bam_stat.o to Makefile.lite
172 ------------------------------------------------------------------------
173 r167 | lh3lh3 | 2009-03-10 22:11:31 +0000 (Tue, 10 Mar 2009) | 3 lines
175 M /trunk/samtools/bam_maqcns.c
176 M /trunk/samtools/bamtk.c
179 * generate RMS of mapQ instead of max mapQ
181 ------------------------------------------------------------------------
182 r166 | lh3lh3 | 2009-03-10 22:06:45 +0000 (Tue, 10 Mar 2009) | 3 lines
184 M /trunk/samtools/bam_plcmd.c
185 M /trunk/samtools/bamtk.c
186 M /trunk/samtools/glf.c
187 M /trunk/samtools/glf.h
188 M /trunk/samtools/misc/Makefile
193 ------------------------------------------------------------------------
194 r159 | lh3lh3 | 2009-03-03 11:26:08 +0000 (Tue, 03 Mar 2009) | 3 lines
196 M /trunk/samtools/bam_plcmd.c
197 M /trunk/samtools/bamtk.c
200 * fixed a minor bug in displaying pileup
202 ------------------------------------------------------------------------
203 r158 | lh3lh3 | 2009-03-03 11:24:16 +0000 (Tue, 03 Mar 2009) | 3 lines
205 M /trunk/samtools/ChangeLog
206 M /trunk/samtools/bamtk.c
209 * optionally print SAM header
211 ------------------------------------------------------------------------
212 r153 | lh3lh3 | 2009-03-02 10:45:28 +0000 (Mon, 02 Mar 2009) | 3 lines
214 M /trunk/samtools/bamtk.c
215 M /trunk/samtools/glf.c
218 * use "GLF\3" as the magic for GLFv3 files
220 ------------------------------------------------------------------------
221 r152 | lh3lh3 | 2009-03-02 10:39:09 +0000 (Mon, 02 Mar 2009) | 5 lines
223 M /trunk/samtools/Makefile
224 M /trunk/samtools/bam_import.c
225 M /trunk/samtools/bam_index.c
226 M /trunk/samtools/bam_plcmd.c
227 M /trunk/samtools/bamtk.c
228 M /trunk/samtools/glf.c
229 M /trunk/samtools/glf.h
232 * fixed a bug in import: core.bin is undefined for unmapped reads
233 * this bug can be alleviated (not completely solved) in bam_index.c
234 * update to GLFv3: pos is changed to offset for better compression
236 ------------------------------------------------------------------------
237 r151 | lh3lh3 | 2009-03-01 15:18:43 +0000 (Sun, 01 Mar 2009) | 3 lines
239 M /trunk/samtools/misc/wgsim.c
242 * fixed a bug in simulating indels
244 ------------------------------------------------------------------------
245 r145 | lh3lh3 | 2009-02-26 19:43:57 +0000 (Thu, 26 Feb 2009) | 4 lines
247 M /trunk/samtools/misc/wgsim.c
250 * allow to print mismatch information as fastq comment. MAQ does
251 not like long read names.
253 ------------------------------------------------------------------------
254 r141 | lh3lh3 | 2009-02-26 14:53:03 +0000 (Thu, 26 Feb 2009) | 6 lines
256 M /trunk/samtools/ChangeLog
257 M /trunk/samtools/misc/wgsim.c
258 M /trunk/samtools/misc/wgsim_eval.pl
261 * fixed a bug about color read coordinates
262 * fixed a bug in read names
263 * wgsim_eval.pl-0.1.3
264 * make the script work with color reads
266 ------------------------------------------------------------------------
267 r140 | lh3lh3 | 2009-02-26 14:02:57 +0000 (Thu, 26 Feb 2009) | 2 lines
269 M /trunk/samtools/misc/Makefile
270 M /trunk/samtools/misc/wgsim.c
272 * wgsim: added a note
274 ------------------------------------------------------------------------
275 r139 | lh3lh3 | 2009-02-26 11:39:08 +0000 (Thu, 26 Feb 2009) | 7 lines
277 M /trunk/samtools/misc/wgsim.c
278 M /trunk/samtools/misc/wgsim_eval.pl
281 * considerable code clean up
282 * print number of substitutions/indels/errors on each read
283 * potentially support SOLiD simulation, though not tested at the moment
284 * wgsim_eval.pl-0.1.2
285 * change in accordant with wgsim
287 ------------------------------------------------------------------------
288 r129 | lh3lh3 | 2009-02-18 22:23:27 +0000 (Wed, 18 Feb 2009) | 3 lines
290 M /trunk/samtools/bam_index.c
291 M /trunk/samtools/bamtk.c
294 * fixed a bug in bam_fetch, caused by completely contained adjacent chunks
296 ------------------------------------------------------------------------
297 r128 | bhandsaker | 2009-02-18 19:06:57 +0000 (Wed, 18 Feb 2009) | 2 lines
299 M /trunk/samtools/bamtk.c
301 Fix annoying segv when invalid region specified.
303 ------------------------------------------------------------------------
304 r127 | lh3lh3 | 2009-02-17 10:49:55 +0000 (Tue, 17 Feb 2009) | 2 lines
306 D /trunk/samtools/misc/indel_filter.pl
307 A /trunk/samtools/misc/samtools.pl
309 * move indel_filter.pl to samtools.pl
311 ------------------------------------------------------------------------
312 r126 | lh3lh3 | 2009-02-14 21:22:30 +0000 (Sat, 14 Feb 2009) | 3 lines
314 M /trunk/samtools/bam_mate.c
315 M /trunk/samtools/bamtk.c
318 * fixed a bug in fixmate: SE reads are flagged as BAM_FMUNMAP
320 ------------------------------------------------------------------------
321 r125 | lh3lh3 | 2009-02-13 09:54:45 +0000 (Fri, 13 Feb 2009) | 3 lines
323 M /trunk/samtools/bam_stat.c
324 M /trunk/samtools/bamtk.c
327 * fixed a minor bug in flagstat
329 ------------------------------------------------------------------------
330 r124 | lh3lh3 | 2009-02-12 11:15:32 +0000 (Thu, 12 Feb 2009) | 3 lines
332 M /trunk/samtools/bam_maqcns.c
333 M /trunk/samtools/bamtk.c
334 M /trunk/samtools/misc/indel_filter.pl
337 * improve indel caller by setting maximum window size
339 ------------------------------------------------------------------------
340 r123 | lh3lh3 | 2009-02-12 10:30:29 +0000 (Thu, 12 Feb 2009) | 2 lines
342 M /trunk/samtools/bam_plcmd.c
343 M /trunk/samtools/bamtk.c
345 * output max mapping quality in indel line
347 ------------------------------------------------------------------------
348 r122 | lh3lh3 | 2009-02-11 10:59:10 +0000 (Wed, 11 Feb 2009) | 2 lines
350 M /trunk/samtools/misc/maq2sam.c
352 fixed a bug in generating tag AM
354 ------------------------------------------------------------------------
355 r121 | lh3lh3 | 2009-02-03 10:43:11 +0000 (Tue, 03 Feb 2009) | 2 lines
357 M /trunk/samtools/bam_index.c
358 M /trunk/samtools/bamtk.c
360 fixed a potential memory problem in indexing
362 ------------------------------------------------------------------------
363 r120 | bhandsaker | 2009-02-02 15:52:52 +0000 (Mon, 02 Feb 2009) | 2 lines
365 M /trunk/samtools/Makefile
367 Pass LIBS to recursive targets to facilitate building at Broad.
369 ------------------------------------------------------------------------
370 r119 | lh3lh3 | 2009-02-02 10:12:15 +0000 (Mon, 02 Feb 2009) | 4 lines
372 M /trunk/samtools/ChangeLog
373 M /trunk/samtools/bam_plcmd.c
374 M /trunk/samtools/bam_stat.c
375 M /trunk/samtools/bamtk.c
378 * fixed a bug in generating GLFv2 for indels
379 * improve flagstat report a little bit
381 ------------------------------------------------------------------------
382 r118 | lh3lh3 | 2009-01-29 12:33:23 +0000 (Thu, 29 Jan 2009) | 3 lines
384 M /trunk/samtools/Makefile
385 A /trunk/samtools/bam_stat.c
386 M /trunk/samtools/bamtk.c
389 * added flagstat command
391 ------------------------------------------------------------------------
392 r116 | lh3lh3 | 2009-01-28 13:31:12 +0000 (Wed, 28 Jan 2009) | 2 lines
394 M /trunk/samtools/ChangeLog
395 M /trunk/samtools/NEWS
396 M /trunk/samtools/bamtk.c
397 M /trunk/samtools/samtools.1
399 Release SAMtools-0.1.2
401 ------------------------------------------------------------------------
402 r115 | lh3lh3 | 2009-01-28 12:54:08 +0000 (Wed, 28 Jan 2009) | 2 lines
404 A /trunk/samtools/misc/indel_filter.pl
406 Script for filtering indel results
408 ------------------------------------------------------------------------
409 r114 | lh3lh3 | 2009-01-25 11:45:37 +0000 (Sun, 25 Jan 2009) | 2 lines
411 A /trunk/samtools/misc/zoom2sam.pl
415 ------------------------------------------------------------------------
416 r113 | lh3lh3 | 2009-01-24 14:25:07 +0000 (Sat, 24 Jan 2009) | 2 lines
418 A /trunk/samtools/misc/novo2sam.pl
420 add a script to convert novo alignment to SAM
422 ------------------------------------------------------------------------
423 r112 | lh3lh3 | 2009-01-23 20:57:39 +0000 (Fri, 23 Jan 2009) | 2 lines
425 M /trunk/samtools/ChangeLog
426 M /trunk/samtools/ChangeLog.old
427 M /trunk/samtools/samtools.1
429 update documentation and ChangeLog
431 ------------------------------------------------------------------------
432 r111 | lh3lh3 | 2009-01-23 19:22:59 +0000 (Fri, 23 Jan 2009) | 3 lines
434 M /trunk/samtools/bam_sort.c
435 M /trunk/samtools/bamtk.c
438 * fixed a bug in "merge" command line
440 ------------------------------------------------------------------------
441 r110 | lh3lh3 | 2009-01-22 15:36:48 +0000 (Thu, 22 Jan 2009) | 3 lines
443 M /trunk/samtools/misc/Makefile
444 A /trunk/samtools/misc/bowtie2sam.pl (from /branches/dev/samtools/misc/bowtie2sam.pl:108)
445 M /trunk/samtools/misc/export2sam.pl
446 A /trunk/samtools/misc/soap2sam.pl (from /branches/dev/samtools/misc/soap2sam.pl:108)
447 A /trunk/samtools/misc/wgsim.c (from /branches/dev/samtools/misc/wgsim.c:108)
448 A /trunk/samtools/misc/wgsim_eval.pl (from /branches/dev/samtools/misc/wgsim_eval.pl:108)
450 * merge from branches/dev/
451 * all future development will happen here
453 ------------------------------------------------------------------------
454 r109 | lh3lh3 | 2009-01-22 15:14:27 +0000 (Thu, 22 Jan 2009) | 3 lines
456 M /trunk/samtools/COPYING
457 M /trunk/samtools/ChangeLog
458 A /trunk/samtools/INSTALL (from /branches/dev/samtools/INSTALL:108)
459 M /trunk/samtools/Makefile
460 A /trunk/samtools/Makefile.lite (from /branches/dev/samtools/Makefile.lite:108)
461 M /trunk/samtools/bam.c
462 M /trunk/samtools/bam.h
463 M /trunk/samtools/bam_import.c
464 M /trunk/samtools/bam_index.c
465 M /trunk/samtools/bam_lpileup.c
466 M /trunk/samtools/bam_maqcns.c
467 M /trunk/samtools/bam_maqcns.h
468 A /trunk/samtools/bam_mate.c (from /branches/dev/samtools/bam_mate.c:108)
469 M /trunk/samtools/bam_pileup.c
470 M /trunk/samtools/bam_plcmd.c
471 A /trunk/samtools/bam_rmdup.c (from /branches/dev/samtools/bam_rmdup.c:108)
472 M /trunk/samtools/bam_sort.c
473 M /trunk/samtools/bamtk.c
474 M /trunk/samtools/bgzf.h
475 M /trunk/samtools/examples/00README.txt
476 A /trunk/samtools/examples/Makefile (from /branches/dev/samtools/examples/Makefile:108)
477 D /trunk/samtools/examples/ex1.fa.fai
478 M /trunk/samtools/examples/ex1.sam.gz
479 M /trunk/samtools/faidx.c
480 A /trunk/samtools/glf.c (from /branches/dev/samtools/glf.c:108)
481 M /trunk/samtools/glf.h
482 M /trunk/samtools/misc/Makefile
483 M /trunk/samtools/misc/maq2sam.c
484 M /trunk/samtools/razf.c
485 M /trunk/samtools/source.dot
487 * Merge from branches/dev/
488 * all future development will happen here at trunk/
490 ------------------------------------------------------------------------
491 r79 | bhandsaker | 2009-01-07 21:42:15 +0000 (Wed, 07 Jan 2009) | 2 lines
493 M /trunk/samtools/bam_maqcns.c
494 M /trunk/samtools/bam_tview.c
496 Fix problem with compiling without curses.
498 ------------------------------------------------------------------------
499 r63 | lh3lh3 | 2008-12-22 15:58:02 +0000 (Mon, 22 Dec 2008) | 2 lines
501 A /trunk/samtools (from /branches/dev/samtools:62)
505 ------------------------------------------------------------------------
506 r62 | lh3lh3 | 2008-12-22 15:55:13 +0000 (Mon, 22 Dec 2008) | 2 lines
508 A /branches/dev/samtools/NEWS
509 M /branches/dev/samtools/bamtk.c
510 M /branches/dev/samtools/samtools.1
512 Release samtools-0.1.1
514 ------------------------------------------------------------------------
515 r61 | lh3lh3 | 2008-12-22 15:46:08 +0000 (Mon, 22 Dec 2008) | 10 lines
517 M /branches/dev/samtools/bam_aux.c
518 M /branches/dev/samtools/bam_index.c
519 M /branches/dev/samtools/bam_plcmd.c
520 M /branches/dev/samtools/bam_tview.c
521 M /branches/dev/samtools/bamtk.c
522 M /branches/dev/samtools/razf.c
523 M /branches/dev/samtools/samtools.1
526 * fixed a bug in razf.c: reset z_eof when razf_seek() is called
527 * fixed a memory leak in parsing a region
528 * changed pileup a little bit when -s is in use: output ^ and $
529 * when a bam is not indexed, output more meaningful error message
530 * fixed a bug in indexing for small alignment
531 * fixed a bug in the viewer when we come to the end of a reference file
532 * updated documentation
533 * prepare to release 0.1.1
535 ------------------------------------------------------------------------
536 r60 | lh3lh3 | 2008-12-22 15:10:16 +0000 (Mon, 22 Dec 2008) | 2 lines
538 A /branches/dev/samtools/examples
539 A /branches/dev/samtools/examples/00README.txt
540 A /branches/dev/samtools/examples/ex1.fa
541 A /branches/dev/samtools/examples/ex1.fa.fai
542 A /branches/dev/samtools/examples/ex1.sam.gz
546 ------------------------------------------------------------------------
547 r59 | lh3lh3 | 2008-12-22 09:38:15 +0000 (Mon, 22 Dec 2008) | 2 lines
549 M /branches/dev/samtools/ChangeLog
553 ------------------------------------------------------------------------
554 r58 | lh3lh3 | 2008-12-20 23:06:00 +0000 (Sat, 20 Dec 2008) | 3 lines
556 M /branches/dev/samtools/misc/export2sam.pl
561 ------------------------------------------------------------------------
562 r57 | lh3lh3 | 2008-12-20 15:44:20 +0000 (Sat, 20 Dec 2008) | 2 lines
564 A /branches/dev/samtools/misc/export2sam.pl
566 convert Export format to SAM; not thoroughly tested
568 ------------------------------------------------------------------------
569 r56 | lh3lh3 | 2008-12-19 22:13:28 +0000 (Fri, 19 Dec 2008) | 6 lines
571 M /branches/dev/samtools/bam_import.c
572 M /branches/dev/samtools/bam_plcmd.c
573 M /branches/dev/samtools/bam_tview.c
574 M /branches/dev/samtools/bamtk.c
575 A /branches/dev/samtools/source.dot
578 * pileup: generate maq-like simple output
579 * pileup: allow to output pileup at required sites
580 * source.dot: source file relationship graph
581 * tview: fixed a minor bug
583 ------------------------------------------------------------------------
584 r55 | lh3lh3 | 2008-12-19 20:10:26 +0000 (Fri, 19 Dec 2008) | 2 lines
586 D /branches/dev/samtools/misc/all2sam.pl
590 ------------------------------------------------------------------------
591 r54 | lh3lh3 | 2008-12-16 22:34:25 +0000 (Tue, 16 Dec 2008) | 2 lines
593 A /branches/dev/samtools/COPYING
594 M /branches/dev/samtools/bam.h
595 M /branches/dev/samtools/faidx.h
596 M /branches/dev/samtools/khash.h
597 M /branches/dev/samtools/kseq.h
598 M /branches/dev/samtools/ksort.h
599 M /branches/dev/samtools/samtools.1
601 Added copyright information and a bit more documentation. No code change.
603 ------------------------------------------------------------------------
604 r53 | lh3lh3 | 2008-12-16 13:40:18 +0000 (Tue, 16 Dec 2008) | 3 lines
606 M /branches/dev/samtools/bam.c
607 M /branches/dev/samtools/bam.h
608 M /branches/dev/samtools/bam_index.c
609 M /branches/dev/samtools/bam_maqcns.c
610 M /branches/dev/samtools/bamtk.c
613 * improved efficiency of the indel caller for spliced alignments
615 ------------------------------------------------------------------------
616 r52 | lh3lh3 | 2008-12-16 10:28:20 +0000 (Tue, 16 Dec 2008) | 3 lines
618 M /branches/dev/samtools/bam.c
619 M /branches/dev/samtools/bam.h
620 M /branches/dev/samtools/bam_aux.c
621 M /branches/dev/samtools/bam_index.c
622 M /branches/dev/samtools/bamtk.c
625 * a bit code cleanup: reduce the dependency between source files
627 ------------------------------------------------------------------------
628 r51 | lh3lh3 | 2008-12-15 14:29:32 +0000 (Mon, 15 Dec 2008) | 3 lines
630 M /branches/dev/samtools/bam_maqcns.c
631 M /branches/dev/samtools/bam_plcmd.c
632 M /branches/dev/samtools/bamtk.c
635 * fixed a memory leak
637 ------------------------------------------------------------------------
638 r50 | lh3lh3 | 2008-12-15 14:00:13 +0000 (Mon, 15 Dec 2008) | 2 lines
640 M /branches/dev/samtools/ChangeLog
641 M /branches/dev/samtools/bam.h
642 M /branches/dev/samtools/samtools.1
644 update documentation, ChangeLog and a comment
646 ------------------------------------------------------------------------
647 r49 | lh3lh3 | 2008-12-15 13:36:43 +0000 (Mon, 15 Dec 2008) | 6 lines
649 M /branches/dev/samtools/Makefile
650 M /branches/dev/samtools/bam.h
651 M /branches/dev/samtools/bam_maqcns.c
652 M /branches/dev/samtools/bam_maqcns.h
653 M /branches/dev/samtools/bam_pileup.c
654 A /branches/dev/samtools/bam_plcmd.c
655 M /branches/dev/samtools/bamtk.c
656 M /branches/dev/samtools/samtools.1
659 * moved pileup command to a separate source file
661 * added bam_cal_segend(). (NOT WORKING for spliced alignment!!!)
662 * updated documentation
664 ------------------------------------------------------------------------
665 r48 | lh3lh3 | 2008-12-12 13:55:36 +0000 (Fri, 12 Dec 2008) | 3 lines
667 M /branches/dev/samtools/bam_maqcns.c
668 M /branches/dev/samtools/bamtk.c
671 * fixed another bug in maqcns when there is a nearby deletion
673 ------------------------------------------------------------------------
674 r47 | lh3lh3 | 2008-12-12 13:42:16 +0000 (Fri, 12 Dec 2008) | 5 lines
676 M /branches/dev/samtools/bam_maqcns.c
677 M /branches/dev/samtools/bam_pileup.c
678 M /branches/dev/samtools/bamtk.c
681 * pileup: outputing consensus is now optional
682 * fixed a bug in glfgen. This bug also exists in maq's glfgen. However,
683 I am not quite sure why the previous version may have problem.
685 ------------------------------------------------------------------------
686 r46 | lh3lh3 | 2008-12-12 11:44:56 +0000 (Fri, 12 Dec 2008) | 6 lines
688 M /branches/dev/samtools/bam_pileup.c
689 M /branches/dev/samtools/bamtk.c
692 * add maq consensus to pileup. However, I will move this part to a new
693 command as strictly speaking, consensus callin is not part of pileup,
694 and imposing it would make it harder to generate for other language
697 ------------------------------------------------------------------------
698 r45 | bhandsaker | 2008-12-11 20:43:56 +0000 (Thu, 11 Dec 2008) | 2 lines
700 M /branches/dev/samtools/bgzf.c
702 Fix bug in tell() after reads that consume to the exact end of a block.
704 ------------------------------------------------------------------------
705 r44 | lh3lh3 | 2008-12-11 09:36:53 +0000 (Thu, 11 Dec 2008) | 2 lines
707 M /branches/dev/samtools/samtools.1
711 ------------------------------------------------------------------------
712 r43 | lh3lh3 | 2008-12-11 09:25:36 +0000 (Thu, 11 Dec 2008) | 4 lines
714 M /branches/dev/samtools/bam_import.c
715 M /branches/dev/samtools/bamtk.c
718 * fixed a bug in parser when there is auxiliary fields
719 * made the parser a bit more robust
721 ------------------------------------------------------------------------
722 r42 | lh3lh3 | 2008-12-10 14:57:29 +0000 (Wed, 10 Dec 2008) | 5 lines
724 M /branches/dev/samtools/bam_index.c
725 M /branches/dev/samtools/bamtk.c
726 M /branches/dev/samtools/bgzf.c
729 * fixed a bug in bgzf (only reading is affected)
730 * fixed a typo in bam_index.c
731 * in bam_index.c, check potential bugs in the underlying I/O library
733 ------------------------------------------------------------------------
734 r41 | lh3lh3 | 2008-12-10 12:53:08 +0000 (Wed, 10 Dec 2008) | 2 lines
736 M /branches/dev/samtools/samtools.1
740 ------------------------------------------------------------------------
741 r40 | lh3lh3 | 2008-12-10 11:52:10 +0000 (Wed, 10 Dec 2008) | 5 lines
743 M /branches/dev/samtools/bam.h
744 M /branches/dev/samtools/bam_pileup.c
745 M /branches/dev/samtools/bamtk.c
748 * tried to make pileup work with clipping (previously not), though NOT tested
749 * removed -v from pileup
750 * made pileup take the reference sequence
752 ------------------------------------------------------------------------
753 r39 | lh3lh3 | 2008-12-09 11:59:28 +0000 (Tue, 09 Dec 2008) | 4 lines
755 M /branches/dev/samtools/bam_import.c
756 M /branches/dev/samtools/bamtk.c
757 M /branches/dev/samtools/samtools.1
760 * in parser, recognize "=", rather than ",", as a match
761 * in parser, correctl parse "=" at the MRNM field.
763 ------------------------------------------------------------------------
764 r38 | lh3lh3 | 2008-12-09 11:39:07 +0000 (Tue, 09 Dec 2008) | 2 lines
766 M /branches/dev/samtools/misc/maq2sam.c
768 fixed a bug in handling maq flag 64 and 192
770 ------------------------------------------------------------------------
771 r37 | lh3lh3 | 2008-12-09 09:53:46 +0000 (Tue, 09 Dec 2008) | 2 lines
773 M /branches/dev/samtools/misc/md5fa.c
775 also calculate unordered md5sum check
777 ------------------------------------------------------------------------
778 r36 | lh3lh3 | 2008-12-09 09:46:21 +0000 (Tue, 09 Dec 2008) | 2 lines
780 M /branches/dev/samtools/misc/md5fa.c
782 fixed a minor bug when there are space in the sequence
784 ------------------------------------------------------------------------
785 r35 | lh3lh3 | 2008-12-09 09:40:45 +0000 (Tue, 09 Dec 2008) | 2 lines
787 M /branches/dev/samtools/misc/md5fa.c
789 fixed a potential memory leak
791 ------------------------------------------------------------------------
792 r34 | lh3lh3 | 2008-12-08 14:52:17 +0000 (Mon, 08 Dec 2008) | 2 lines
794 M /branches/dev/samtools/bam_import.c
795 M /branches/dev/samtools/bam_index.c
796 M /branches/dev/samtools/bamtk.c
798 * fixed a bug in import: bin is wrongly calculated
800 ------------------------------------------------------------------------
801 r33 | lh3lh3 | 2008-12-08 14:08:01 +0000 (Mon, 08 Dec 2008) | 2 lines
803 M /branches/dev/samtools/misc/all2sam.pl
807 ------------------------------------------------------------------------
808 r32 | lh3lh3 | 2008-12-08 12:56:02 +0000 (Mon, 08 Dec 2008) | 3 lines
810 M /branches/dev/samtools/Makefile
811 M /branches/dev/samtools/kseq.h
812 M /branches/dev/samtools/misc/Makefile
813 A /branches/dev/samtools/misc/md5.c
814 A /branches/dev/samtools/misc/md5.h
815 A /branches/dev/samtools/misc/md5fa.c
817 * fixed two warnings in kseq.h
818 * added md5sum utilities
820 ------------------------------------------------------------------------
821 r31 | lh3lh3 | 2008-12-08 11:35:29 +0000 (Mon, 08 Dec 2008) | 5 lines
823 M /branches/dev/samtools/Makefile
824 M /branches/dev/samtools/bam_import.c
825 M /branches/dev/samtools/bamtk.c
826 A /branches/dev/samtools/kseq.h
827 D /branches/dev/samtools/kstream.h
830 * replace kstream with kseq. kseq is a superset of kstream. I need the
831 extra functions in kseq.h.
832 * also compile stand-alone faidx
834 ------------------------------------------------------------------------
835 r30 | lh3lh3 | 2008-12-08 11:17:04 +0000 (Mon, 08 Dec 2008) | 3 lines
837 M /branches/dev/samtools/bam.h
838 M /branches/dev/samtools/bam_sort.c
839 M /branches/dev/samtools/bamtk.c
842 * sorting by read names is available
844 ------------------------------------------------------------------------
845 r29 | lh3lh3 | 2008-12-08 10:29:02 +0000 (Mon, 08 Dec 2008) | 3 lines
847 M /branches/dev/samtools/bam.c
848 M /branches/dev/samtools/bam.h
849 M /branches/dev/samtools/bam_import.c
850 M /branches/dev/samtools/bam_maqcns.c
851 M /branches/dev/samtools/bam_pileup.c
852 M /branches/dev/samtools/bam_sort.c
853 M /branches/dev/samtools/bam_tview.c
854 M /branches/dev/samtools/bamtk.c
855 M /branches/dev/samtools/misc/maq2sam.c
858 * format change to meet the latest specification
860 ------------------------------------------------------------------------
861 r28 | lh3lh3 | 2008-12-04 16:09:21 +0000 (Thu, 04 Dec 2008) | 3 lines
863 M /branches/dev/samtools/bam_maqcns.c
864 M /branches/dev/samtools/misc/maq2sam.c
866 * minor change in maqcns: special care when n==0
867 * change maq2sam to meet the latest specification
869 ------------------------------------------------------------------------
870 r27 | lh3lh3 | 2008-12-04 15:55:44 +0000 (Thu, 04 Dec 2008) | 2 lines
872 M /branches/dev/samtools/razf.c
873 M /branches/dev/samtools/razf.h
875 considerable code clean up in razf
877 ------------------------------------------------------------------------
878 r26 | lh3lh3 | 2008-12-04 15:08:18 +0000 (Thu, 04 Dec 2008) | 2 lines
880 M /branches/dev/samtools/ChangeLog
881 M /branches/dev/samtools/Makefile
882 M /branches/dev/samtools/faidx.c
884 make RAZF optional in faidx.c
886 ------------------------------------------------------------------------
887 r25 | lh3lh3 | 2008-12-01 15:27:22 +0000 (Mon, 01 Dec 2008) | 3 lines
889 M /branches/dev/samtools/Makefile
890 M /branches/dev/samtools/bam.h
891 M /branches/dev/samtools/bam_aux.c
892 M /branches/dev/samtools/bamtk.c
893 M /branches/dev/samtools/samtools.1
896 * added routines for retrieving aux data, NOT TESTED YET!
898 ------------------------------------------------------------------------
899 r24 | lh3lh3 | 2008-12-01 14:29:43 +0000 (Mon, 01 Dec 2008) | 5 lines
901 M /branches/dev/samtools/bam.c
902 M /branches/dev/samtools/bam_import.c
903 M /branches/dev/samtools/bam_maqcns.c
904 M /branches/dev/samtools/bamtk.c
905 M /branches/dev/samtools/bgzf.c
906 M /branches/dev/samtools/samtools.1
909 * bgzf: fixed a potential integer overflow on 32-it machines
910 * maqcns: set the minimum combined quality as 0
911 * supporting hex strings
913 ------------------------------------------------------------------------
914 r23 | lh3lh3 | 2008-11-27 17:14:37 +0000 (Thu, 27 Nov 2008) | 3 lines
916 M /branches/dev/samtools/bam_maqcns.c
917 M /branches/dev/samtools/bamtk.c
920 * fixed the bug in maqcns
922 ------------------------------------------------------------------------
923 r22 | lh3lh3 | 2008-11-27 17:08:11 +0000 (Thu, 27 Nov 2008) | 3 lines
925 M /branches/dev/samtools/Makefile
926 M /branches/dev/samtools/bam.h
927 A /branches/dev/samtools/bam_maqcns.c
928 A /branches/dev/samtools/bam_maqcns.h
929 M /branches/dev/samtools/bam_tview.c
930 M /branches/dev/samtools/bamtk.c
931 A /branches/dev/samtools/glf.h
934 * add MAQ consensus caller, currently BUGGY!
936 ------------------------------------------------------------------------
937 r21 | lh3lh3 | 2008-11-27 13:51:28 +0000 (Thu, 27 Nov 2008) | 4 lines
939 M /branches/dev/samtools/bam_pileup.c
940 M /branches/dev/samtools/bam_tview.c
941 M /branches/dev/samtools/bamtk.c
944 * tview: display padded alignment (but not P operation)
945 * better coordinates and reference sequence
947 ------------------------------------------------------------------------
948 r19 | lh3lh3 | 2008-11-27 09:26:05 +0000 (Thu, 27 Nov 2008) | 2 lines
950 A /branches/dev/samtools/ChangeLog
954 ------------------------------------------------------------------------
955 r18 | lh3lh3 | 2008-11-27 09:24:45 +0000 (Thu, 27 Nov 2008) | 3 lines
957 D /branches/dev/samtools/ChangeLog
958 A /branches/dev/samtools/ChangeLog.old (from /branches/dev/samtools/ChangeLog:6)
960 Rename ChangeLog to ChangeLog.old. This old ChangeLog is generated from
961 the log of my personal SVN repository.
963 ------------------------------------------------------------------------
964 r17 | lh3lh3 | 2008-11-27 09:22:55 +0000 (Thu, 27 Nov 2008) | 6 lines
966 M /branches/dev/samtools/Makefile
967 M /branches/dev/samtools/bamtk.c
968 M /branches/dev/samtools/bgzf.c
971 * declare fseeko and ftello as some Linux may not do this by default and
972 missing these declarations will make bgzf buggy
973 * get rid of some harmless warings
974 * use BGZF by default, now
976 ------------------------------------------------------------------------
977 r16 | lh3lh3 | 2008-11-26 21:19:11 +0000 (Wed, 26 Nov 2008) | 4 lines
979 M /branches/dev/samtools/bam_index.c
980 M /branches/dev/samtools/bamtk.c
981 M /branches/dev/samtools/razf.c
984 * fixed a bug in razf_read()
985 * give more warnings when the file is truncated (or due to bugs in I/O library)
987 ------------------------------------------------------------------------
988 r15 | lh3lh3 | 2008-11-26 20:41:39 +0000 (Wed, 26 Nov 2008) | 2 lines
990 M /branches/dev/samtools/bgzf.c
992 fixed a bug in bgzf.c at the end of the file
994 ------------------------------------------------------------------------
995 r14 | lh3lh3 | 2008-11-26 17:05:18 +0000 (Wed, 26 Nov 2008) | 4 lines
997 M /branches/dev/samtools/bamtk.c
1000 * a lot happened to RAZF, although samtools itself is untouched. Better
1001 also update the version number anyway to avoid confusion
1003 ------------------------------------------------------------------------
1004 r13 | lh3lh3 | 2008-11-26 17:03:48 +0000 (Wed, 26 Nov 2008) | 2 lines
1006 M /branches/dev/samtools/razf.c
1008 a change from Jue, but I think it should not matter
1010 ------------------------------------------------------------------------
1011 r12 | lh3lh3 | 2008-11-26 16:48:14 +0000 (Wed, 26 Nov 2008) | 3 lines
1013 M /branches/dev/samtools/razf.c
1015 fixed a potential bug in razf. However, it seems still buggy, just
1016 rarely happens, very rarely.
1018 ------------------------------------------------------------------------
1019 r11 | lh3lh3 | 2008-11-26 14:02:56 +0000 (Wed, 26 Nov 2008) | 2 lines
1021 M /branches/dev/samtools/razf.c
1023 fixed a bug in razf, with the help of Jue
1025 ------------------------------------------------------------------------
1026 r10 | lh3lh3 | 2008-11-26 11:55:32 +0000 (Wed, 26 Nov 2008) | 2 lines
1028 M /branches/dev/samtools/bam_index.c
1032 ------------------------------------------------------------------------
1033 r9 | lh3lh3 | 2008-11-26 11:37:05 +0000 (Wed, 26 Nov 2008) | 2 lines
1035 M /branches/dev/samtools/Makefile
1036 M /branches/dev/samtools/bam.h
1037 M /branches/dev/samtools/razf.c
1038 M /branches/dev/samtools/razf.h
1040 * Jue has updated razf to realize Bob's scheme
1042 ------------------------------------------------------------------------
1043 r7 | lh3lh3 | 2008-11-25 20:37:37 +0000 (Tue, 25 Nov 2008) | 2 lines
1045 A /branches/dev/samtools/samtools.1
1049 ------------------------------------------------------------------------
1050 r6 | lh3lh3 | 2008-11-25 20:37:16 +0000 (Tue, 25 Nov 2008) | 3 lines
1052 A /branches/dev/samtools/ChangeLog
1053 A /branches/dev/samtools/Makefile
1054 A /branches/dev/samtools/bam.c
1055 A /branches/dev/samtools/bam.h
1056 A /branches/dev/samtools/bam_aux.c
1057 A /branches/dev/samtools/bam_endian.h
1058 A /branches/dev/samtools/bam_import.c
1059 A /branches/dev/samtools/bam_index.c
1060 A /branches/dev/samtools/bam_lpileup.c
1061 A /branches/dev/samtools/bam_pileup.c
1062 A /branches/dev/samtools/bam_sort.c
1063 A /branches/dev/samtools/bam_tview.c
1064 A /branches/dev/samtools/bamtk.c
1065 A /branches/dev/samtools/bgzf.c
1066 A /branches/dev/samtools/bgzf.h
1067 A /branches/dev/samtools/bgzip.c
1068 A /branches/dev/samtools/faidx.c
1069 A /branches/dev/samtools/faidx.h
1070 A /branches/dev/samtools/khash.h
1071 A /branches/dev/samtools/ksort.h
1072 A /branches/dev/samtools/kstream.h
1073 A /branches/dev/samtools/misc
1074 A /branches/dev/samtools/misc/Makefile
1075 A /branches/dev/samtools/misc/all2sam.pl
1076 A /branches/dev/samtools/misc/maq2sam.c
1077 A /branches/dev/samtools/razf.c
1078 A /branches/dev/samtools/razf.h
1079 A /branches/dev/samtools/razip.c
1080 A /branches/dev/samtools/zutil.h
1082 The initial version of samtools, replicated from my local SVN repository.
1083 The current version is: 0.1.0-42. All future development will happen here.
1085 ------------------------------------------------------------------------
1086 r5 | lh3lh3 | 2008-11-25 20:30:49 +0000 (Tue, 25 Nov 2008) | 2 lines
1088 A /branches/dev/samtools
1090 samtools (C version)
1092 ------------------------------------------------------------------------