1 ------------------------------------------------------------------------
2 r244 | lh3lh3 | 2009-04-25 11:49:40 +0100 (Sat, 25 Apr 2009) | 3 lines
4 M /trunk/samtools/bam_md.c
5 M /trunk/samtools/bamtk.c
7 * samtools-0.1.3-6 (r244)
8 * fixed segfault for unmapped reads
10 ------------------------------------------------------------------------
11 r243 | lh3lh3 | 2009-04-24 21:27:26 +0100 (Fri, 24 Apr 2009) | 5 lines
13 M /trunk/samtools/bam.h
14 M /trunk/samtools/bam_maqcns.c
15 M /trunk/samtools/bam_md.c
16 M /trunk/samtools/bamtk.c
18 * samtools-0.1.3-5 (r243)
19 * fixed a long existing bug which may cause memory leak
21 * consensus calling now works with "=", but indel calling not
23 ------------------------------------------------------------------------
24 r242 | lh3lh3 | 2009-04-24 20:44:46 +0100 (Fri, 24 Apr 2009) | 3 lines
26 M /trunk/samtools/bam_md.c
27 M /trunk/samtools/bamtk.c
29 * samtools-0.1.3-4 (r242)
32 ------------------------------------------------------------------------
33 r240 | lh3lh3 | 2009-04-24 16:40:18 +0100 (Fri, 24 Apr 2009) | 5 lines
35 M /trunk/samtools/Makefile
36 M /trunk/samtools/Makefile.lite
37 M /trunk/samtools/bam.h
38 M /trunk/samtools/bam_aux.c
39 A /trunk/samtools/bam_md.c
40 M /trunk/samtools/bam_plcmd.c
41 M /trunk/samtools/bamtk.c
43 * samtools-0.1.3-3 (r240)
46 * the plain pileup now support "=" bases, but consensus calling and glfgen may fail
48 ------------------------------------------------------------------------
49 r239 | lh3lh3 | 2009-04-24 12:08:20 +0100 (Fri, 24 Apr 2009) | 5 lines
51 M /trunk/samtools/bam.h
52 M /trunk/samtools/bam_aux.c
53 M /trunk/samtools/bamtk.c
55 * samtools-0.1.3-2 (r239)
56 * fixed bugs in bam_aux.c (these functions nevered used by samtools)
57 * removed bam_aux_init()/bam_aux_destroy()
58 * added tagview for testing bam_aux
60 ------------------------------------------------------------------------
61 r235 | lh3lh3 | 2009-04-21 23:17:39 +0100 (Tue, 21 Apr 2009) | 3 lines
63 M /trunk/samtools/bam_pileup.c
64 M /trunk/samtools/bamtk.c
67 * fixed a bug in pileup: the first read in a chromosome may not be printed
69 ------------------------------------------------------------------------
70 r232 | lh3lh3 | 2009-04-16 15:25:43 +0100 (Thu, 16 Apr 2009) | 2 lines
72 M /trunk/samtools/Makefile.lite
74 a missing file in Makefile.lite
76 ------------------------------------------------------------------------
77 r227 | lh3lh3 | 2009-04-15 22:02:53 +0100 (Wed, 15 Apr 2009) | 2 lines
79 M /trunk/samtools/NEWS
80 M /trunk/samtools/bamtk.c
82 Release samtools-0.1.3
84 ------------------------------------------------------------------------
85 r223 | lh3lh3 | 2009-04-15 14:31:32 +0100 (Wed, 15 Apr 2009) | 3 lines
87 M /trunk/samtools/bam_plcmd.c
88 M /trunk/samtools/bamtk.c
91 * make samtools more robust to weird input such as empty file
93 ------------------------------------------------------------------------
94 r222 | lh3lh3 | 2009-04-15 14:05:33 +0100 (Wed, 15 Apr 2009) | 2 lines
96 M /trunk/samtools/ChangeLog
97 M /trunk/samtools/NEWS
98 M /trunk/samtools/samtools.1
100 prepare for release 0.1.3
102 ------------------------------------------------------------------------
103 r221 | lh3lh3 | 2009-04-15 13:32:14 +0100 (Wed, 15 Apr 2009) | 2 lines
105 A /trunk/samtools/misc/blast2sam.pl
107 convert NCBI-BLASTN to SAM
109 ------------------------------------------------------------------------
110 r220 | lh3lh3 | 2009-04-15 13:18:19 +0100 (Wed, 15 Apr 2009) | 3 lines
112 M /trunk/samtools/bam_lpileup.c
113 M /trunk/samtools/bamtk.c
116 * fixed a small memory leak in tview
118 ------------------------------------------------------------------------
119 r219 | lh3lh3 | 2009-04-15 13:00:08 +0100 (Wed, 15 Apr 2009) | 3 lines
121 M /trunk/samtools/bam_rmdup.c
122 M /trunk/samtools/bamtk.c
125 * fixed a bug in rmdup when there are unmapped reads
127 ------------------------------------------------------------------------
128 r218 | lh3lh3 | 2009-04-14 22:28:58 +0100 (Tue, 14 Apr 2009) | 2 lines
130 M /trunk/samtools/ChangeLog
131 M /trunk/samtools/NEWS
133 proposed NEWS for the new release (have not yet)
135 ------------------------------------------------------------------------
136 r216 | lh3lh3 | 2009-04-14 22:10:46 +0100 (Tue, 14 Apr 2009) | 4 lines
138 M /trunk/samtools/misc/samtools.pl
141 * improve indelFilter to avoid filtering true indels. The new filter relies
142 on the new pileup indel line implemented in samtools-0.1.2-25
144 ------------------------------------------------------------------------
145 r215 | lh3lh3 | 2009-04-14 22:04:19 +0100 (Tue, 14 Apr 2009) | 4 lines
147 M /trunk/samtools/bam_maqcns.c
148 M /trunk/samtools/bam_plcmd.c
149 M /trunk/samtools/bamtk.c
150 M /trunk/samtools/samtools.1
153 * change the pileup indel line to shows the number of alignments actually
156 ------------------------------------------------------------------------
157 r211 | lh3lh3 | 2009-04-13 12:07:13 +0100 (Mon, 13 Apr 2009) | 2 lines
159 M /trunk/samtools/ChangeLog
161 update ChangeLog from "svn log"
163 ------------------------------------------------------------------------
164 r210 | lh3lh3 | 2009-04-12 20:57:05 +0100 (Sun, 12 Apr 2009) | 4 lines
166 M /trunk/samtools/bam.c
167 M /trunk/samtools/bam_import.c
168 M /trunk/samtools/bam_sort.c
169 M /trunk/samtools/bamtk.c
170 M /trunk/samtools/kseq.h
173 * in merge, gives a warning rather than error if the target sequence length is different
176 ------------------------------------------------------------------------
177 r209 | lh3lh3 | 2009-04-12 20:32:44 +0100 (Sun, 12 Apr 2009) | 3 lines
179 M /trunk/samtools/bam.c
180 M /trunk/samtools/bam_import.c
181 M /trunk/samtools/bamtk.c
184 * recognize '*' at the QUAL field
186 ------------------------------------------------------------------------
187 r208 | lh3lh3 | 2009-04-12 20:08:02 +0100 (Sun, 12 Apr 2009) | 3 lines
189 M /trunk/samtools/bam_import.c
190 M /trunk/samtools/bamtk.c
191 M /trunk/samtools/kseq.h
194 * the field separater is TAB only, now
196 ------------------------------------------------------------------------
197 r207 | lh3lh3 | 2009-04-08 15:18:03 +0100 (Wed, 08 Apr 2009) | 2 lines
199 M /trunk/samtools/examples/ex1.sam.gz
201 * fixed the problem in the example alignment due to the bug in fixmate
203 ------------------------------------------------------------------------
204 r206 | lh3lh3 | 2009-04-08 15:15:05 +0100 (Wed, 08 Apr 2009) | 3 lines
206 M /trunk/samtools/bam_mate.c
207 M /trunk/samtools/bamtk.c
208 M /trunk/samtools/misc/soap2sam.pl
211 * fixed a nasty bug in `fixmate'
213 ------------------------------------------------------------------------
214 r205 | lh3lh3 | 2009-04-08 10:57:08 +0100 (Wed, 08 Apr 2009) | 2 lines
216 M /trunk/samtools/misc/bowtie2sam.pl
217 M /trunk/samtools/misc/soap2sam.pl
218 M /trunk/samtools/misc/wgsim_eval.pl
220 make the script robust to the bugs in SOAP-2.1.7
222 ------------------------------------------------------------------------
223 r200 | lh3lh3 | 2009-04-02 15:14:56 +0100 (Thu, 02 Apr 2009) | 3 lines
225 M /trunk/samtools/bam_stat.c
226 M /trunk/samtools/bamtk.c
229 * check if file is truncated in flagstat
231 ------------------------------------------------------------------------
232 r199 | lh3lh3 | 2009-04-02 15:09:10 +0100 (Thu, 02 Apr 2009) | 3 lines
234 M /trunk/samtools/bamtk.c
237 * print the header if requested
239 ------------------------------------------------------------------------
240 r193 | lh3lh3 | 2009-03-27 15:09:50 +0000 (Fri, 27 Mar 2009) | 3 lines
242 M /trunk/samtools/bam_plcmd.c
243 M /trunk/samtools/bamtk.c
246 * fixed a minor bug reported by Nils Homer
248 ------------------------------------------------------------------------
249 r185 | lh3lh3 | 2009-03-24 11:50:32 +0000 (Tue, 24 Mar 2009) | 2 lines
251 A /trunk/samtools/Makefile (from /trunk/samtools/Makefile.std:184)
252 D /trunk/samtools/Makefile.std
253 A /trunk/samtools/misc/Makefile (from /trunk/samtools/misc/Makefile.std:184)
254 D /trunk/samtools/misc/Makefile.std
256 rename Makefile.std as Makefile. GNU building systerm is not ready and may take some time...
258 ------------------------------------------------------------------------
259 r184 | lh3lh3 | 2009-03-24 10:36:38 +0000 (Tue, 24 Mar 2009) | 4 lines
261 D /trunk/samtools/Makefile
262 A /trunk/samtools/Makefile.std (from /trunk/samtools/Makefile:183)
263 M /trunk/samtools/bam_sort.c
264 M /trunk/samtools/bam_tview.c
265 M /trunk/samtools/bamtk.c
266 D /trunk/samtools/misc/Makefile
267 A /trunk/samtools/misc/Makefile.std (from /trunk/samtools/misc/Makefile:182)
268 M /trunk/samtools/samtools.1
271 * incorporating Nils' changes
272 * rename Makefile to Makefile.std and prepare to add the GNU building systerms (also by Nils)
274 ------------------------------------------------------------------------
275 r183 | lh3lh3 | 2009-03-24 10:30:23 +0000 (Tue, 24 Mar 2009) | 4 lines
277 M /trunk/samtools/Makefile
278 M /trunk/samtools/bam_import.c
279 M /trunk/samtools/bam_maqcns.c
280 M /trunk/samtools/bam_maqcns.h
281 M /trunk/samtools/bam_plcmd.c
282 M /trunk/samtools/bamtk.c
283 M /trunk/samtools/kseq.h
284 A /trunk/samtools/kstring.c
285 A /trunk/samtools/kstring.h
288 * made pileup take a list of proposed indels. An insertion is N at the moment.
289 * added my kstring library for a bit complex parsing of the position list.
291 ------------------------------------------------------------------------
292 r169 | lh3lh3 | 2009-03-12 13:40:14 +0000 (Thu, 12 Mar 2009) | 3 lines
294 M /trunk/samtools/misc/soap2sam.pl
297 * more robust to truncated soap output
299 ------------------------------------------------------------------------
300 r168 | lh3lh3 | 2009-03-11 10:49:00 +0000 (Wed, 11 Mar 2009) | 2 lines
302 M /trunk/samtools/Makefile.lite
304 added bam_stat.o to Makefile.lite
306 ------------------------------------------------------------------------
307 r167 | lh3lh3 | 2009-03-10 22:11:31 +0000 (Tue, 10 Mar 2009) | 3 lines
309 M /trunk/samtools/bam_maqcns.c
310 M /trunk/samtools/bamtk.c
313 * generate RMS of mapQ instead of max mapQ
315 ------------------------------------------------------------------------
316 r166 | lh3lh3 | 2009-03-10 22:06:45 +0000 (Tue, 10 Mar 2009) | 3 lines
318 M /trunk/samtools/bam_plcmd.c
319 M /trunk/samtools/bamtk.c
320 M /trunk/samtools/glf.c
321 M /trunk/samtools/glf.h
322 M /trunk/samtools/misc/Makefile
327 ------------------------------------------------------------------------
328 r159 | lh3lh3 | 2009-03-03 11:26:08 +0000 (Tue, 03 Mar 2009) | 3 lines
330 M /trunk/samtools/bam_plcmd.c
331 M /trunk/samtools/bamtk.c
334 * fixed a minor bug in displaying pileup
336 ------------------------------------------------------------------------
337 r158 | lh3lh3 | 2009-03-03 11:24:16 +0000 (Tue, 03 Mar 2009) | 3 lines
339 M /trunk/samtools/ChangeLog
340 M /trunk/samtools/bamtk.c
343 * optionally print SAM header
345 ------------------------------------------------------------------------
346 r153 | lh3lh3 | 2009-03-02 10:45:28 +0000 (Mon, 02 Mar 2009) | 3 lines
348 M /trunk/samtools/bamtk.c
349 M /trunk/samtools/glf.c
352 * use "GLF\3" as the magic for GLFv3 files
354 ------------------------------------------------------------------------
355 r152 | lh3lh3 | 2009-03-02 10:39:09 +0000 (Mon, 02 Mar 2009) | 5 lines
357 M /trunk/samtools/Makefile
358 M /trunk/samtools/bam_import.c
359 M /trunk/samtools/bam_index.c
360 M /trunk/samtools/bam_plcmd.c
361 M /trunk/samtools/bamtk.c
362 M /trunk/samtools/glf.c
363 M /trunk/samtools/glf.h
366 * fixed a bug in import: core.bin is undefined for unmapped reads
367 * this bug can be alleviated (not completely solved) in bam_index.c
368 * update to GLFv3: pos is changed to offset for better compression
370 ------------------------------------------------------------------------
371 r151 | lh3lh3 | 2009-03-01 15:18:43 +0000 (Sun, 01 Mar 2009) | 3 lines
373 M /trunk/samtools/misc/wgsim.c
376 * fixed a bug in simulating indels
378 ------------------------------------------------------------------------
379 r145 | lh3lh3 | 2009-02-26 19:43:57 +0000 (Thu, 26 Feb 2009) | 4 lines
381 M /trunk/samtools/misc/wgsim.c
384 * allow to print mismatch information as fastq comment. MAQ does
385 not like long read names.
387 ------------------------------------------------------------------------
388 r141 | lh3lh3 | 2009-02-26 14:53:03 +0000 (Thu, 26 Feb 2009) | 6 lines
390 M /trunk/samtools/ChangeLog
391 M /trunk/samtools/misc/wgsim.c
392 M /trunk/samtools/misc/wgsim_eval.pl
395 * fixed a bug about color read coordinates
396 * fixed a bug in read names
397 * wgsim_eval.pl-0.1.3
398 * make the script work with color reads
400 ------------------------------------------------------------------------
401 r140 | lh3lh3 | 2009-02-26 14:02:57 +0000 (Thu, 26 Feb 2009) | 2 lines
403 M /trunk/samtools/misc/Makefile
404 M /trunk/samtools/misc/wgsim.c
406 * wgsim: added a note
408 ------------------------------------------------------------------------
409 r139 | lh3lh3 | 2009-02-26 11:39:08 +0000 (Thu, 26 Feb 2009) | 7 lines
411 M /trunk/samtools/misc/wgsim.c
412 M /trunk/samtools/misc/wgsim_eval.pl
415 * considerable code clean up
416 * print number of substitutions/indels/errors on each read
417 * potentially support SOLiD simulation, though not tested at the moment
418 * wgsim_eval.pl-0.1.2
419 * change in accordant with wgsim
421 ------------------------------------------------------------------------
422 r129 | lh3lh3 | 2009-02-18 22:23:27 +0000 (Wed, 18 Feb 2009) | 3 lines
424 M /trunk/samtools/bam_index.c
425 M /trunk/samtools/bamtk.c
428 * fixed a bug in bam_fetch, caused by completely contained adjacent chunks
430 ------------------------------------------------------------------------
431 r128 | bhandsaker | 2009-02-18 19:06:57 +0000 (Wed, 18 Feb 2009) | 2 lines
433 M /trunk/samtools/bamtk.c
435 Fix annoying segv when invalid region specified.
437 ------------------------------------------------------------------------
438 r127 | lh3lh3 | 2009-02-17 10:49:55 +0000 (Tue, 17 Feb 2009) | 2 lines
440 D /trunk/samtools/misc/indel_filter.pl
441 A /trunk/samtools/misc/samtools.pl
443 * move indel_filter.pl to samtools.pl
445 ------------------------------------------------------------------------
446 r126 | lh3lh3 | 2009-02-14 21:22:30 +0000 (Sat, 14 Feb 2009) | 3 lines
448 M /trunk/samtools/bam_mate.c
449 M /trunk/samtools/bamtk.c
452 * fixed a bug in fixmate: SE reads are flagged as BAM_FMUNMAP
454 ------------------------------------------------------------------------
455 r125 | lh3lh3 | 2009-02-13 09:54:45 +0000 (Fri, 13 Feb 2009) | 3 lines
457 M /trunk/samtools/bam_stat.c
458 M /trunk/samtools/bamtk.c
461 * fixed a minor bug in flagstat
463 ------------------------------------------------------------------------
464 r124 | lh3lh3 | 2009-02-12 11:15:32 +0000 (Thu, 12 Feb 2009) | 3 lines
466 M /trunk/samtools/bam_maqcns.c
467 M /trunk/samtools/bamtk.c
468 M /trunk/samtools/misc/indel_filter.pl
471 * improve indel caller by setting maximum window size
473 ------------------------------------------------------------------------
474 r123 | lh3lh3 | 2009-02-12 10:30:29 +0000 (Thu, 12 Feb 2009) | 2 lines
476 M /trunk/samtools/bam_plcmd.c
477 M /trunk/samtools/bamtk.c
479 * output max mapping quality in indel line
481 ------------------------------------------------------------------------
482 r122 | lh3lh3 | 2009-02-11 10:59:10 +0000 (Wed, 11 Feb 2009) | 2 lines
484 M /trunk/samtools/misc/maq2sam.c
486 fixed a bug in generating tag AM
488 ------------------------------------------------------------------------
489 r121 | lh3lh3 | 2009-02-03 10:43:11 +0000 (Tue, 03 Feb 2009) | 2 lines
491 M /trunk/samtools/bam_index.c
492 M /trunk/samtools/bamtk.c
494 fixed a potential memory problem in indexing
496 ------------------------------------------------------------------------
497 r120 | bhandsaker | 2009-02-02 15:52:52 +0000 (Mon, 02 Feb 2009) | 2 lines
499 M /trunk/samtools/Makefile
501 Pass LIBS to recursive targets to facilitate building at Broad.
503 ------------------------------------------------------------------------
504 r119 | lh3lh3 | 2009-02-02 10:12:15 +0000 (Mon, 02 Feb 2009) | 4 lines
506 M /trunk/samtools/ChangeLog
507 M /trunk/samtools/bam_plcmd.c
508 M /trunk/samtools/bam_stat.c
509 M /trunk/samtools/bamtk.c
512 * fixed a bug in generating GLFv2 for indels
513 * improve flagstat report a little bit
515 ------------------------------------------------------------------------
516 r118 | lh3lh3 | 2009-01-29 12:33:23 +0000 (Thu, 29 Jan 2009) | 3 lines
518 M /trunk/samtools/Makefile
519 A /trunk/samtools/bam_stat.c
520 M /trunk/samtools/bamtk.c
523 * added flagstat command
525 ------------------------------------------------------------------------
526 r116 | lh3lh3 | 2009-01-28 13:31:12 +0000 (Wed, 28 Jan 2009) | 2 lines
528 M /trunk/samtools/ChangeLog
529 M /trunk/samtools/NEWS
530 M /trunk/samtools/bamtk.c
531 M /trunk/samtools/samtools.1
533 Release SAMtools-0.1.2
535 ------------------------------------------------------------------------
536 r115 | lh3lh3 | 2009-01-28 12:54:08 +0000 (Wed, 28 Jan 2009) | 2 lines
538 A /trunk/samtools/misc/indel_filter.pl
540 Script for filtering indel results
542 ------------------------------------------------------------------------
543 r114 | lh3lh3 | 2009-01-25 11:45:37 +0000 (Sun, 25 Jan 2009) | 2 lines
545 A /trunk/samtools/misc/zoom2sam.pl
549 ------------------------------------------------------------------------
550 r113 | lh3lh3 | 2009-01-24 14:25:07 +0000 (Sat, 24 Jan 2009) | 2 lines
552 A /trunk/samtools/misc/novo2sam.pl
554 add a script to convert novo alignment to SAM
556 ------------------------------------------------------------------------
557 r112 | lh3lh3 | 2009-01-23 20:57:39 +0000 (Fri, 23 Jan 2009) | 2 lines
559 M /trunk/samtools/ChangeLog
560 M /trunk/samtools/ChangeLog.old
561 M /trunk/samtools/samtools.1
563 update documentation and ChangeLog
565 ------------------------------------------------------------------------
566 r111 | lh3lh3 | 2009-01-23 19:22:59 +0000 (Fri, 23 Jan 2009) | 3 lines
568 M /trunk/samtools/bam_sort.c
569 M /trunk/samtools/bamtk.c
572 * fixed a bug in "merge" command line
574 ------------------------------------------------------------------------
575 r110 | lh3lh3 | 2009-01-22 15:36:48 +0000 (Thu, 22 Jan 2009) | 3 lines
577 M /trunk/samtools/misc/Makefile
578 A /trunk/samtools/misc/bowtie2sam.pl (from /branches/dev/samtools/misc/bowtie2sam.pl:108)
579 M /trunk/samtools/misc/export2sam.pl
580 A /trunk/samtools/misc/soap2sam.pl (from /branches/dev/samtools/misc/soap2sam.pl:108)
581 A /trunk/samtools/misc/wgsim.c (from /branches/dev/samtools/misc/wgsim.c:108)
582 A /trunk/samtools/misc/wgsim_eval.pl (from /branches/dev/samtools/misc/wgsim_eval.pl:108)
584 * merge from branches/dev/
585 * all future development will happen here
587 ------------------------------------------------------------------------
588 r109 | lh3lh3 | 2009-01-22 15:14:27 +0000 (Thu, 22 Jan 2009) | 3 lines
590 M /trunk/samtools/COPYING
591 M /trunk/samtools/ChangeLog
592 A /trunk/samtools/INSTALL (from /branches/dev/samtools/INSTALL:108)
593 M /trunk/samtools/Makefile
594 A /trunk/samtools/Makefile.lite (from /branches/dev/samtools/Makefile.lite:108)
595 M /trunk/samtools/bam.c
596 M /trunk/samtools/bam.h
597 M /trunk/samtools/bam_import.c
598 M /trunk/samtools/bam_index.c
599 M /trunk/samtools/bam_lpileup.c
600 M /trunk/samtools/bam_maqcns.c
601 M /trunk/samtools/bam_maqcns.h
602 A /trunk/samtools/bam_mate.c (from /branches/dev/samtools/bam_mate.c:108)
603 M /trunk/samtools/bam_pileup.c
604 M /trunk/samtools/bam_plcmd.c
605 A /trunk/samtools/bam_rmdup.c (from /branches/dev/samtools/bam_rmdup.c:108)
606 M /trunk/samtools/bam_sort.c
607 M /trunk/samtools/bamtk.c
608 M /trunk/samtools/bgzf.h
609 M /trunk/samtools/examples/00README.txt
610 A /trunk/samtools/examples/Makefile (from /branches/dev/samtools/examples/Makefile:108)
611 D /trunk/samtools/examples/ex1.fa.fai
612 M /trunk/samtools/examples/ex1.sam.gz
613 M /trunk/samtools/faidx.c
614 A /trunk/samtools/glf.c (from /branches/dev/samtools/glf.c:108)
615 M /trunk/samtools/glf.h
616 M /trunk/samtools/misc/Makefile
617 M /trunk/samtools/misc/maq2sam.c
618 M /trunk/samtools/razf.c
619 M /trunk/samtools/source.dot
621 * Merge from branches/dev/
622 * all future development will happen here at trunk/
624 ------------------------------------------------------------------------
625 r79 | bhandsaker | 2009-01-07 21:42:15 +0000 (Wed, 07 Jan 2009) | 2 lines
627 M /trunk/samtools/bam_maqcns.c
628 M /trunk/samtools/bam_tview.c
630 Fix problem with compiling without curses.
632 ------------------------------------------------------------------------
633 r63 | lh3lh3 | 2008-12-22 15:58:02 +0000 (Mon, 22 Dec 2008) | 2 lines
635 A /trunk/samtools (from /branches/dev/samtools:62)
639 ------------------------------------------------------------------------
640 r62 | lh3lh3 | 2008-12-22 15:55:13 +0000 (Mon, 22 Dec 2008) | 2 lines
642 A /branches/dev/samtools/NEWS
643 M /branches/dev/samtools/bamtk.c
644 M /branches/dev/samtools/samtools.1
646 Release samtools-0.1.1
648 ------------------------------------------------------------------------
649 r61 | lh3lh3 | 2008-12-22 15:46:08 +0000 (Mon, 22 Dec 2008) | 10 lines
651 M /branches/dev/samtools/bam_aux.c
652 M /branches/dev/samtools/bam_index.c
653 M /branches/dev/samtools/bam_plcmd.c
654 M /branches/dev/samtools/bam_tview.c
655 M /branches/dev/samtools/bamtk.c
656 M /branches/dev/samtools/razf.c
657 M /branches/dev/samtools/samtools.1
660 * fixed a bug in razf.c: reset z_eof when razf_seek() is called
661 * fixed a memory leak in parsing a region
662 * changed pileup a little bit when -s is in use: output ^ and $
663 * when a bam is not indexed, output more meaningful error message
664 * fixed a bug in indexing for small alignment
665 * fixed a bug in the viewer when we come to the end of a reference file
666 * updated documentation
667 * prepare to release 0.1.1
669 ------------------------------------------------------------------------
670 r60 | lh3lh3 | 2008-12-22 15:10:16 +0000 (Mon, 22 Dec 2008) | 2 lines
672 A /branches/dev/samtools/examples
673 A /branches/dev/samtools/examples/00README.txt
674 A /branches/dev/samtools/examples/ex1.fa
675 A /branches/dev/samtools/examples/ex1.fa.fai
676 A /branches/dev/samtools/examples/ex1.sam.gz
680 ------------------------------------------------------------------------
681 r59 | lh3lh3 | 2008-12-22 09:38:15 +0000 (Mon, 22 Dec 2008) | 2 lines
683 M /branches/dev/samtools/ChangeLog
687 ------------------------------------------------------------------------
688 r58 | lh3lh3 | 2008-12-20 23:06:00 +0000 (Sat, 20 Dec 2008) | 3 lines
690 M /branches/dev/samtools/misc/export2sam.pl
695 ------------------------------------------------------------------------
696 r57 | lh3lh3 | 2008-12-20 15:44:20 +0000 (Sat, 20 Dec 2008) | 2 lines
698 A /branches/dev/samtools/misc/export2sam.pl
700 convert Export format to SAM; not thoroughly tested
702 ------------------------------------------------------------------------
703 r56 | lh3lh3 | 2008-12-19 22:13:28 +0000 (Fri, 19 Dec 2008) | 6 lines
705 M /branches/dev/samtools/bam_import.c
706 M /branches/dev/samtools/bam_plcmd.c
707 M /branches/dev/samtools/bam_tview.c
708 M /branches/dev/samtools/bamtk.c
709 A /branches/dev/samtools/source.dot
712 * pileup: generate maq-like simple output
713 * pileup: allow to output pileup at required sites
714 * source.dot: source file relationship graph
715 * tview: fixed a minor bug
717 ------------------------------------------------------------------------
718 r55 | lh3lh3 | 2008-12-19 20:10:26 +0000 (Fri, 19 Dec 2008) | 2 lines
720 D /branches/dev/samtools/misc/all2sam.pl
724 ------------------------------------------------------------------------
725 r54 | lh3lh3 | 2008-12-16 22:34:25 +0000 (Tue, 16 Dec 2008) | 2 lines
727 A /branches/dev/samtools/COPYING
728 M /branches/dev/samtools/bam.h
729 M /branches/dev/samtools/faidx.h
730 M /branches/dev/samtools/khash.h
731 M /branches/dev/samtools/kseq.h
732 M /branches/dev/samtools/ksort.h
733 M /branches/dev/samtools/samtools.1
735 Added copyright information and a bit more documentation. No code change.
737 ------------------------------------------------------------------------
738 r53 | lh3lh3 | 2008-12-16 13:40:18 +0000 (Tue, 16 Dec 2008) | 3 lines
740 M /branches/dev/samtools/bam.c
741 M /branches/dev/samtools/bam.h
742 M /branches/dev/samtools/bam_index.c
743 M /branches/dev/samtools/bam_maqcns.c
744 M /branches/dev/samtools/bamtk.c
747 * improved efficiency of the indel caller for spliced alignments
749 ------------------------------------------------------------------------
750 r52 | lh3lh3 | 2008-12-16 10:28:20 +0000 (Tue, 16 Dec 2008) | 3 lines
752 M /branches/dev/samtools/bam.c
753 M /branches/dev/samtools/bam.h
754 M /branches/dev/samtools/bam_aux.c
755 M /branches/dev/samtools/bam_index.c
756 M /branches/dev/samtools/bamtk.c
759 * a bit code cleanup: reduce the dependency between source files
761 ------------------------------------------------------------------------
762 r51 | lh3lh3 | 2008-12-15 14:29:32 +0000 (Mon, 15 Dec 2008) | 3 lines
764 M /branches/dev/samtools/bam_maqcns.c
765 M /branches/dev/samtools/bam_plcmd.c
766 M /branches/dev/samtools/bamtk.c
769 * fixed a memory leak
771 ------------------------------------------------------------------------
772 r50 | lh3lh3 | 2008-12-15 14:00:13 +0000 (Mon, 15 Dec 2008) | 2 lines
774 M /branches/dev/samtools/ChangeLog
775 M /branches/dev/samtools/bam.h
776 M /branches/dev/samtools/samtools.1
778 update documentation, ChangeLog and a comment
780 ------------------------------------------------------------------------
781 r49 | lh3lh3 | 2008-12-15 13:36:43 +0000 (Mon, 15 Dec 2008) | 6 lines
783 M /branches/dev/samtools/Makefile
784 M /branches/dev/samtools/bam.h
785 M /branches/dev/samtools/bam_maqcns.c
786 M /branches/dev/samtools/bam_maqcns.h
787 M /branches/dev/samtools/bam_pileup.c
788 A /branches/dev/samtools/bam_plcmd.c
789 M /branches/dev/samtools/bamtk.c
790 M /branches/dev/samtools/samtools.1
793 * moved pileup command to a separate source file
795 * added bam_cal_segend(). (NOT WORKING for spliced alignment!!!)
796 * updated documentation
798 ------------------------------------------------------------------------
799 r48 | lh3lh3 | 2008-12-12 13:55:36 +0000 (Fri, 12 Dec 2008) | 3 lines
801 M /branches/dev/samtools/bam_maqcns.c
802 M /branches/dev/samtools/bamtk.c
805 * fixed another bug in maqcns when there is a nearby deletion
807 ------------------------------------------------------------------------
808 r47 | lh3lh3 | 2008-12-12 13:42:16 +0000 (Fri, 12 Dec 2008) | 5 lines
810 M /branches/dev/samtools/bam_maqcns.c
811 M /branches/dev/samtools/bam_pileup.c
812 M /branches/dev/samtools/bamtk.c
815 * pileup: outputing consensus is now optional
816 * fixed a bug in glfgen. This bug also exists in maq's glfgen. However,
817 I am not quite sure why the previous version may have problem.
819 ------------------------------------------------------------------------
820 r46 | lh3lh3 | 2008-12-12 11:44:56 +0000 (Fri, 12 Dec 2008) | 6 lines
822 M /branches/dev/samtools/bam_pileup.c
823 M /branches/dev/samtools/bamtk.c
826 * add maq consensus to pileup. However, I will move this part to a new
827 command as strictly speaking, consensus callin is not part of pileup,
828 and imposing it would make it harder to generate for other language
831 ------------------------------------------------------------------------
832 r45 | bhandsaker | 2008-12-11 20:43:56 +0000 (Thu, 11 Dec 2008) | 2 lines
834 M /branches/dev/samtools/bgzf.c
836 Fix bug in tell() after reads that consume to the exact end of a block.
838 ------------------------------------------------------------------------
839 r44 | lh3lh3 | 2008-12-11 09:36:53 +0000 (Thu, 11 Dec 2008) | 2 lines
841 M /branches/dev/samtools/samtools.1
845 ------------------------------------------------------------------------
846 r43 | lh3lh3 | 2008-12-11 09:25:36 +0000 (Thu, 11 Dec 2008) | 4 lines
848 M /branches/dev/samtools/bam_import.c
849 M /branches/dev/samtools/bamtk.c
852 * fixed a bug in parser when there is auxiliary fields
853 * made the parser a bit more robust
855 ------------------------------------------------------------------------
856 r42 | lh3lh3 | 2008-12-10 14:57:29 +0000 (Wed, 10 Dec 2008) | 5 lines
858 M /branches/dev/samtools/bam_index.c
859 M /branches/dev/samtools/bamtk.c
860 M /branches/dev/samtools/bgzf.c
863 * fixed a bug in bgzf (only reading is affected)
864 * fixed a typo in bam_index.c
865 * in bam_index.c, check potential bugs in the underlying I/O library
867 ------------------------------------------------------------------------
868 r41 | lh3lh3 | 2008-12-10 12:53:08 +0000 (Wed, 10 Dec 2008) | 2 lines
870 M /branches/dev/samtools/samtools.1
874 ------------------------------------------------------------------------
875 r40 | lh3lh3 | 2008-12-10 11:52:10 +0000 (Wed, 10 Dec 2008) | 5 lines
877 M /branches/dev/samtools/bam.h
878 M /branches/dev/samtools/bam_pileup.c
879 M /branches/dev/samtools/bamtk.c
882 * tried to make pileup work with clipping (previously not), though NOT tested
883 * removed -v from pileup
884 * made pileup take the reference sequence
886 ------------------------------------------------------------------------
887 r39 | lh3lh3 | 2008-12-09 11:59:28 +0000 (Tue, 09 Dec 2008) | 4 lines
889 M /branches/dev/samtools/bam_import.c
890 M /branches/dev/samtools/bamtk.c
891 M /branches/dev/samtools/samtools.1
894 * in parser, recognize "=", rather than ",", as a match
895 * in parser, correctl parse "=" at the MRNM field.
897 ------------------------------------------------------------------------
898 r38 | lh3lh3 | 2008-12-09 11:39:07 +0000 (Tue, 09 Dec 2008) | 2 lines
900 M /branches/dev/samtools/misc/maq2sam.c
902 fixed a bug in handling maq flag 64 and 192
904 ------------------------------------------------------------------------
905 r37 | lh3lh3 | 2008-12-09 09:53:46 +0000 (Tue, 09 Dec 2008) | 2 lines
907 M /branches/dev/samtools/misc/md5fa.c
909 also calculate unordered md5sum check
911 ------------------------------------------------------------------------
912 r36 | lh3lh3 | 2008-12-09 09:46:21 +0000 (Tue, 09 Dec 2008) | 2 lines
914 M /branches/dev/samtools/misc/md5fa.c
916 fixed a minor bug when there are space in the sequence
918 ------------------------------------------------------------------------
919 r35 | lh3lh3 | 2008-12-09 09:40:45 +0000 (Tue, 09 Dec 2008) | 2 lines
921 M /branches/dev/samtools/misc/md5fa.c
923 fixed a potential memory leak
925 ------------------------------------------------------------------------
926 r34 | lh3lh3 | 2008-12-08 14:52:17 +0000 (Mon, 08 Dec 2008) | 2 lines
928 M /branches/dev/samtools/bam_import.c
929 M /branches/dev/samtools/bam_index.c
930 M /branches/dev/samtools/bamtk.c
932 * fixed a bug in import: bin is wrongly calculated
934 ------------------------------------------------------------------------
935 r33 | lh3lh3 | 2008-12-08 14:08:01 +0000 (Mon, 08 Dec 2008) | 2 lines
937 M /branches/dev/samtools/misc/all2sam.pl
941 ------------------------------------------------------------------------
942 r32 | lh3lh3 | 2008-12-08 12:56:02 +0000 (Mon, 08 Dec 2008) | 3 lines
944 M /branches/dev/samtools/Makefile
945 M /branches/dev/samtools/kseq.h
946 M /branches/dev/samtools/misc/Makefile
947 A /branches/dev/samtools/misc/md5.c
948 A /branches/dev/samtools/misc/md5.h
949 A /branches/dev/samtools/misc/md5fa.c
951 * fixed two warnings in kseq.h
952 * added md5sum utilities
954 ------------------------------------------------------------------------
955 r31 | lh3lh3 | 2008-12-08 11:35:29 +0000 (Mon, 08 Dec 2008) | 5 lines
957 M /branches/dev/samtools/Makefile
958 M /branches/dev/samtools/bam_import.c
959 M /branches/dev/samtools/bamtk.c
960 A /branches/dev/samtools/kseq.h
961 D /branches/dev/samtools/kstream.h
964 * replace kstream with kseq. kseq is a superset of kstream. I need the
965 extra functions in kseq.h.
966 * also compile stand-alone faidx
968 ------------------------------------------------------------------------
969 r30 | lh3lh3 | 2008-12-08 11:17:04 +0000 (Mon, 08 Dec 2008) | 3 lines
971 M /branches/dev/samtools/bam.h
972 M /branches/dev/samtools/bam_sort.c
973 M /branches/dev/samtools/bamtk.c
976 * sorting by read names is available
978 ------------------------------------------------------------------------
979 r29 | lh3lh3 | 2008-12-08 10:29:02 +0000 (Mon, 08 Dec 2008) | 3 lines
981 M /branches/dev/samtools/bam.c
982 M /branches/dev/samtools/bam.h
983 M /branches/dev/samtools/bam_import.c
984 M /branches/dev/samtools/bam_maqcns.c
985 M /branches/dev/samtools/bam_pileup.c
986 M /branches/dev/samtools/bam_sort.c
987 M /branches/dev/samtools/bam_tview.c
988 M /branches/dev/samtools/bamtk.c
989 M /branches/dev/samtools/misc/maq2sam.c
992 * format change to meet the latest specification
994 ------------------------------------------------------------------------
995 r28 | lh3lh3 | 2008-12-04 16:09:21 +0000 (Thu, 04 Dec 2008) | 3 lines
997 M /branches/dev/samtools/bam_maqcns.c
998 M /branches/dev/samtools/misc/maq2sam.c
1000 * minor change in maqcns: special care when n==0
1001 * change maq2sam to meet the latest specification
1003 ------------------------------------------------------------------------
1004 r27 | lh3lh3 | 2008-12-04 15:55:44 +0000 (Thu, 04 Dec 2008) | 2 lines
1006 M /branches/dev/samtools/razf.c
1007 M /branches/dev/samtools/razf.h
1009 considerable code clean up in razf
1011 ------------------------------------------------------------------------
1012 r26 | lh3lh3 | 2008-12-04 15:08:18 +0000 (Thu, 04 Dec 2008) | 2 lines
1014 M /branches/dev/samtools/ChangeLog
1015 M /branches/dev/samtools/Makefile
1016 M /branches/dev/samtools/faidx.c
1018 make RAZF optional in faidx.c
1020 ------------------------------------------------------------------------
1021 r25 | lh3lh3 | 2008-12-01 15:27:22 +0000 (Mon, 01 Dec 2008) | 3 lines
1023 M /branches/dev/samtools/Makefile
1024 M /branches/dev/samtools/bam.h
1025 M /branches/dev/samtools/bam_aux.c
1026 M /branches/dev/samtools/bamtk.c
1027 M /branches/dev/samtools/samtools.1
1030 * added routines for retrieving aux data, NOT TESTED YET!
1032 ------------------------------------------------------------------------
1033 r24 | lh3lh3 | 2008-12-01 14:29:43 +0000 (Mon, 01 Dec 2008) | 5 lines
1035 M /branches/dev/samtools/bam.c
1036 M /branches/dev/samtools/bam_import.c
1037 M /branches/dev/samtools/bam_maqcns.c
1038 M /branches/dev/samtools/bamtk.c
1039 M /branches/dev/samtools/bgzf.c
1040 M /branches/dev/samtools/samtools.1
1043 * bgzf: fixed a potential integer overflow on 32-it machines
1044 * maqcns: set the minimum combined quality as 0
1045 * supporting hex strings
1047 ------------------------------------------------------------------------
1048 r23 | lh3lh3 | 2008-11-27 17:14:37 +0000 (Thu, 27 Nov 2008) | 3 lines
1050 M /branches/dev/samtools/bam_maqcns.c
1051 M /branches/dev/samtools/bamtk.c
1054 * fixed the bug in maqcns
1056 ------------------------------------------------------------------------
1057 r22 | lh3lh3 | 2008-11-27 17:08:11 +0000 (Thu, 27 Nov 2008) | 3 lines
1059 M /branches/dev/samtools/Makefile
1060 M /branches/dev/samtools/bam.h
1061 A /branches/dev/samtools/bam_maqcns.c
1062 A /branches/dev/samtools/bam_maqcns.h
1063 M /branches/dev/samtools/bam_tview.c
1064 M /branches/dev/samtools/bamtk.c
1065 A /branches/dev/samtools/glf.h
1068 * add MAQ consensus caller, currently BUGGY!
1070 ------------------------------------------------------------------------
1071 r21 | lh3lh3 | 2008-11-27 13:51:28 +0000 (Thu, 27 Nov 2008) | 4 lines
1073 M /branches/dev/samtools/bam_pileup.c
1074 M /branches/dev/samtools/bam_tview.c
1075 M /branches/dev/samtools/bamtk.c
1078 * tview: display padded alignment (but not P operation)
1079 * better coordinates and reference sequence
1081 ------------------------------------------------------------------------
1082 r19 | lh3lh3 | 2008-11-27 09:26:05 +0000 (Thu, 27 Nov 2008) | 2 lines
1084 A /branches/dev/samtools/ChangeLog
1088 ------------------------------------------------------------------------
1089 r18 | lh3lh3 | 2008-11-27 09:24:45 +0000 (Thu, 27 Nov 2008) | 3 lines
1091 D /branches/dev/samtools/ChangeLog
1092 A /branches/dev/samtools/ChangeLog.old (from /branches/dev/samtools/ChangeLog:6)
1094 Rename ChangeLog to ChangeLog.old. This old ChangeLog is generated from
1095 the log of my personal SVN repository.
1097 ------------------------------------------------------------------------
1098 r17 | lh3lh3 | 2008-11-27 09:22:55 +0000 (Thu, 27 Nov 2008) | 6 lines
1100 M /branches/dev/samtools/Makefile
1101 M /branches/dev/samtools/bamtk.c
1102 M /branches/dev/samtools/bgzf.c
1105 * declare fseeko and ftello as some Linux may not do this by default and
1106 missing these declarations will make bgzf buggy
1107 * get rid of some harmless warings
1108 * use BGZF by default, now
1110 ------------------------------------------------------------------------
1111 r16 | lh3lh3 | 2008-11-26 21:19:11 +0000 (Wed, 26 Nov 2008) | 4 lines
1113 M /branches/dev/samtools/bam_index.c
1114 M /branches/dev/samtools/bamtk.c
1115 M /branches/dev/samtools/razf.c
1118 * fixed a bug in razf_read()
1119 * give more warnings when the file is truncated (or due to bugs in I/O library)
1121 ------------------------------------------------------------------------
1122 r15 | lh3lh3 | 2008-11-26 20:41:39 +0000 (Wed, 26 Nov 2008) | 2 lines
1124 M /branches/dev/samtools/bgzf.c
1126 fixed a bug in bgzf.c at the end of the file
1128 ------------------------------------------------------------------------
1129 r14 | lh3lh3 | 2008-11-26 17:05:18 +0000 (Wed, 26 Nov 2008) | 4 lines
1131 M /branches/dev/samtools/bamtk.c
1134 * a lot happened to RAZF, although samtools itself is untouched. Better
1135 also update the version number anyway to avoid confusion
1137 ------------------------------------------------------------------------
1138 r13 | lh3lh3 | 2008-11-26 17:03:48 +0000 (Wed, 26 Nov 2008) | 2 lines
1140 M /branches/dev/samtools/razf.c
1142 a change from Jue, but I think it should not matter
1144 ------------------------------------------------------------------------
1145 r12 | lh3lh3 | 2008-11-26 16:48:14 +0000 (Wed, 26 Nov 2008) | 3 lines
1147 M /branches/dev/samtools/razf.c
1149 fixed a potential bug in razf. However, it seems still buggy, just
1150 rarely happens, very rarely.
1152 ------------------------------------------------------------------------
1153 r11 | lh3lh3 | 2008-11-26 14:02:56 +0000 (Wed, 26 Nov 2008) | 2 lines
1155 M /branches/dev/samtools/razf.c
1157 fixed a bug in razf, with the help of Jue
1159 ------------------------------------------------------------------------
1160 r10 | lh3lh3 | 2008-11-26 11:55:32 +0000 (Wed, 26 Nov 2008) | 2 lines
1162 M /branches/dev/samtools/bam_index.c
1166 ------------------------------------------------------------------------
1167 r9 | lh3lh3 | 2008-11-26 11:37:05 +0000 (Wed, 26 Nov 2008) | 2 lines
1169 M /branches/dev/samtools/Makefile
1170 M /branches/dev/samtools/bam.h
1171 M /branches/dev/samtools/razf.c
1172 M /branches/dev/samtools/razf.h
1174 * Jue has updated razf to realize Bob's scheme
1176 ------------------------------------------------------------------------
1177 r7 | lh3lh3 | 2008-11-25 20:37:37 +0000 (Tue, 25 Nov 2008) | 2 lines
1179 A /branches/dev/samtools/samtools.1
1183 ------------------------------------------------------------------------
1184 r6 | lh3lh3 | 2008-11-25 20:37:16 +0000 (Tue, 25 Nov 2008) | 3 lines
1186 A /branches/dev/samtools/ChangeLog
1187 A /branches/dev/samtools/Makefile
1188 A /branches/dev/samtools/bam.c
1189 A /branches/dev/samtools/bam.h
1190 A /branches/dev/samtools/bam_aux.c
1191 A /branches/dev/samtools/bam_endian.h
1192 A /branches/dev/samtools/bam_import.c
1193 A /branches/dev/samtools/bam_index.c
1194 A /branches/dev/samtools/bam_lpileup.c
1195 A /branches/dev/samtools/bam_pileup.c
1196 A /branches/dev/samtools/bam_sort.c
1197 A /branches/dev/samtools/bam_tview.c
1198 A /branches/dev/samtools/bamtk.c
1199 A /branches/dev/samtools/bgzf.c
1200 A /branches/dev/samtools/bgzf.h
1201 A /branches/dev/samtools/bgzip.c
1202 A /branches/dev/samtools/faidx.c
1203 A /branches/dev/samtools/faidx.h
1204 A /branches/dev/samtools/khash.h
1205 A /branches/dev/samtools/ksort.h
1206 A /branches/dev/samtools/kstream.h
1207 A /branches/dev/samtools/misc
1208 A /branches/dev/samtools/misc/Makefile
1209 A /branches/dev/samtools/misc/all2sam.pl
1210 A /branches/dev/samtools/misc/maq2sam.c
1211 A /branches/dev/samtools/razf.c
1212 A /branches/dev/samtools/razf.h
1213 A /branches/dev/samtools/razip.c
1214 A /branches/dev/samtools/zutil.h
1216 The initial version of samtools, replicated from my local SVN repository.
1217 The current version is: 0.1.0-42. All future development will happen here.
1219 ------------------------------------------------------------------------
1220 r5 | lh3lh3 | 2008-11-25 20:30:49 +0000 (Tue, 25 Nov 2008) | 2 lines
1222 A /branches/dev/samtools
1224 samtools (C version)
1226 ------------------------------------------------------------------------