1 ------------------------------------------------------------------------
2 r221 | lh3lh3 | 2009-04-15 13:32:14 +0100 (Wed, 15 Apr 2009) | 2 lines
4 A /trunk/samtools/misc/blast2sam.pl
6 convert NCBI-BLASTN to SAM
8 ------------------------------------------------------------------------
9 r220 | lh3lh3 | 2009-04-15 13:18:19 +0100 (Wed, 15 Apr 2009) | 3 lines
11 M /trunk/samtools/bam_lpileup.c
12 M /trunk/samtools/bamtk.c
15 * fixed a small memory leak in tview
17 ------------------------------------------------------------------------
18 r219 | lh3lh3 | 2009-04-15 13:00:08 +0100 (Wed, 15 Apr 2009) | 3 lines
20 M /trunk/samtools/bam_rmdup.c
21 M /trunk/samtools/bamtk.c
24 * fixed a bug in rmdup when there are unmapped reads
26 ------------------------------------------------------------------------
27 r218 | lh3lh3 | 2009-04-14 22:28:58 +0100 (Tue, 14 Apr 2009) | 2 lines
29 M /trunk/samtools/ChangeLog
30 M /trunk/samtools/NEWS
32 proposed NEWS for the new release (have not yet)
34 ------------------------------------------------------------------------
35 r216 | lh3lh3 | 2009-04-14 22:10:46 +0100 (Tue, 14 Apr 2009) | 4 lines
37 M /trunk/samtools/misc/samtools.pl
40 * improve indelFilter to avoid filtering true indels. The new filter relies
41 on the new pileup indel line implemented in samtools-0.1.2-25
43 ------------------------------------------------------------------------
44 r215 | lh3lh3 | 2009-04-14 22:04:19 +0100 (Tue, 14 Apr 2009) | 4 lines
46 M /trunk/samtools/bam_maqcns.c
47 M /trunk/samtools/bam_plcmd.c
48 M /trunk/samtools/bamtk.c
49 M /trunk/samtools/samtools.1
52 * change the pileup indel line to shows the number of alignments actually
55 ------------------------------------------------------------------------
56 r211 | lh3lh3 | 2009-04-13 12:07:13 +0100 (Mon, 13 Apr 2009) | 2 lines
58 M /trunk/samtools/ChangeLog
60 update ChangeLog from "svn log"
62 ------------------------------------------------------------------------
63 r210 | lh3lh3 | 2009-04-12 20:57:05 +0100 (Sun, 12 Apr 2009) | 4 lines
65 M /trunk/samtools/bam.c
66 M /trunk/samtools/bam_import.c
67 M /trunk/samtools/bam_sort.c
68 M /trunk/samtools/bamtk.c
69 M /trunk/samtools/kseq.h
72 * in merge, gives a warning rather than error if the target sequence length is different
75 ------------------------------------------------------------------------
76 r209 | lh3lh3 | 2009-04-12 20:32:44 +0100 (Sun, 12 Apr 2009) | 3 lines
78 M /trunk/samtools/bam.c
79 M /trunk/samtools/bam_import.c
80 M /trunk/samtools/bamtk.c
83 * recognize '*' at the QUAL field
85 ------------------------------------------------------------------------
86 r208 | lh3lh3 | 2009-04-12 20:08:02 +0100 (Sun, 12 Apr 2009) | 3 lines
88 M /trunk/samtools/bam_import.c
89 M /trunk/samtools/bamtk.c
90 M /trunk/samtools/kseq.h
93 * the field separater is TAB only, now
95 ------------------------------------------------------------------------
96 r207 | lh3lh3 | 2009-04-08 15:18:03 +0100 (Wed, 08 Apr 2009) | 2 lines
98 M /trunk/samtools/examples/ex1.sam.gz
100 * fixed the problem in the example alignment due to the bug in fixmate
102 ------------------------------------------------------------------------
103 r206 | lh3lh3 | 2009-04-08 15:15:05 +0100 (Wed, 08 Apr 2009) | 3 lines
105 M /trunk/samtools/bam_mate.c
106 M /trunk/samtools/bamtk.c
107 M /trunk/samtools/misc/soap2sam.pl
110 * fixed a nasty bug in `fixmate'
112 ------------------------------------------------------------------------
113 r205 | lh3lh3 | 2009-04-08 10:57:08 +0100 (Wed, 08 Apr 2009) | 2 lines
115 M /trunk/samtools/misc/bowtie2sam.pl
116 M /trunk/samtools/misc/soap2sam.pl
117 M /trunk/samtools/misc/wgsim_eval.pl
119 make the script robust to the bugs in SOAP-2.1.7
121 ------------------------------------------------------------------------
122 r200 | lh3lh3 | 2009-04-02 15:14:56 +0100 (Thu, 02 Apr 2009) | 3 lines
124 M /trunk/samtools/bam_stat.c
125 M /trunk/samtools/bamtk.c
128 * check if file is truncated in flagstat
130 ------------------------------------------------------------------------
131 r199 | lh3lh3 | 2009-04-02 15:09:10 +0100 (Thu, 02 Apr 2009) | 3 lines
133 M /trunk/samtools/bamtk.c
136 * print the header if requested
138 ------------------------------------------------------------------------
139 r193 | lh3lh3 | 2009-03-27 15:09:50 +0000 (Fri, 27 Mar 2009) | 3 lines
141 M /trunk/samtools/bam_plcmd.c
142 M /trunk/samtools/bamtk.c
145 * fixed a minor bug reported by Nils Homer
147 ------------------------------------------------------------------------
148 r185 | lh3lh3 | 2009-03-24 11:50:32 +0000 (Tue, 24 Mar 2009) | 2 lines
150 A /trunk/samtools/Makefile (from /trunk/samtools/Makefile.std:184)
151 D /trunk/samtools/Makefile.std
152 A /trunk/samtools/misc/Makefile (from /trunk/samtools/misc/Makefile.std:184)
153 D /trunk/samtools/misc/Makefile.std
155 rename Makefile.std as Makefile. GNU building systerm is not ready and may take some time...
157 ------------------------------------------------------------------------
158 r184 | lh3lh3 | 2009-03-24 10:36:38 +0000 (Tue, 24 Mar 2009) | 4 lines
160 D /trunk/samtools/Makefile
161 A /trunk/samtools/Makefile.std (from /trunk/samtools/Makefile:183)
162 M /trunk/samtools/bam_sort.c
163 M /trunk/samtools/bam_tview.c
164 M /trunk/samtools/bamtk.c
165 D /trunk/samtools/misc/Makefile
166 A /trunk/samtools/misc/Makefile.std (from /trunk/samtools/misc/Makefile:182)
167 M /trunk/samtools/samtools.1
170 * incorporating Nils' changes
171 * rename Makefile to Makefile.std and prepare to add the GNU building systerms (also by Nils)
173 ------------------------------------------------------------------------
174 r183 | lh3lh3 | 2009-03-24 10:30:23 +0000 (Tue, 24 Mar 2009) | 4 lines
176 M /trunk/samtools/Makefile
177 M /trunk/samtools/bam_import.c
178 M /trunk/samtools/bam_maqcns.c
179 M /trunk/samtools/bam_maqcns.h
180 M /trunk/samtools/bam_plcmd.c
181 M /trunk/samtools/bamtk.c
182 M /trunk/samtools/kseq.h
183 A /trunk/samtools/kstring.c
184 A /trunk/samtools/kstring.h
187 * made pileup take a list of proposed indels. An insertion is N at the moment.
188 * added my kstring library for a bit complex parsing of the position list.
190 ------------------------------------------------------------------------
191 r169 | lh3lh3 | 2009-03-12 13:40:14 +0000 (Thu, 12 Mar 2009) | 3 lines
193 M /trunk/samtools/misc/soap2sam.pl
196 * more robust to truncated soap output
198 ------------------------------------------------------------------------
199 r168 | lh3lh3 | 2009-03-11 10:49:00 +0000 (Wed, 11 Mar 2009) | 2 lines
201 M /trunk/samtools/Makefile.lite
203 added bam_stat.o to Makefile.lite
205 ------------------------------------------------------------------------
206 r167 | lh3lh3 | 2009-03-10 22:11:31 +0000 (Tue, 10 Mar 2009) | 3 lines
208 M /trunk/samtools/bam_maqcns.c
209 M /trunk/samtools/bamtk.c
212 * generate RMS of mapQ instead of max mapQ
214 ------------------------------------------------------------------------
215 r166 | lh3lh3 | 2009-03-10 22:06:45 +0000 (Tue, 10 Mar 2009) | 3 lines
217 M /trunk/samtools/bam_plcmd.c
218 M /trunk/samtools/bamtk.c
219 M /trunk/samtools/glf.c
220 M /trunk/samtools/glf.h
221 M /trunk/samtools/misc/Makefile
226 ------------------------------------------------------------------------
227 r159 | lh3lh3 | 2009-03-03 11:26:08 +0000 (Tue, 03 Mar 2009) | 3 lines
229 M /trunk/samtools/bam_plcmd.c
230 M /trunk/samtools/bamtk.c
233 * fixed a minor bug in displaying pileup
235 ------------------------------------------------------------------------
236 r158 | lh3lh3 | 2009-03-03 11:24:16 +0000 (Tue, 03 Mar 2009) | 3 lines
238 M /trunk/samtools/ChangeLog
239 M /trunk/samtools/bamtk.c
242 * optionally print SAM header
244 ------------------------------------------------------------------------
245 r153 | lh3lh3 | 2009-03-02 10:45:28 +0000 (Mon, 02 Mar 2009) | 3 lines
247 M /trunk/samtools/bamtk.c
248 M /trunk/samtools/glf.c
251 * use "GLF\3" as the magic for GLFv3 files
253 ------------------------------------------------------------------------
254 r152 | lh3lh3 | 2009-03-02 10:39:09 +0000 (Mon, 02 Mar 2009) | 5 lines
256 M /trunk/samtools/Makefile
257 M /trunk/samtools/bam_import.c
258 M /trunk/samtools/bam_index.c
259 M /trunk/samtools/bam_plcmd.c
260 M /trunk/samtools/bamtk.c
261 M /trunk/samtools/glf.c
262 M /trunk/samtools/glf.h
265 * fixed a bug in import: core.bin is undefined for unmapped reads
266 * this bug can be alleviated (not completely solved) in bam_index.c
267 * update to GLFv3: pos is changed to offset for better compression
269 ------------------------------------------------------------------------
270 r151 | lh3lh3 | 2009-03-01 15:18:43 +0000 (Sun, 01 Mar 2009) | 3 lines
272 M /trunk/samtools/misc/wgsim.c
275 * fixed a bug in simulating indels
277 ------------------------------------------------------------------------
278 r145 | lh3lh3 | 2009-02-26 19:43:57 +0000 (Thu, 26 Feb 2009) | 4 lines
280 M /trunk/samtools/misc/wgsim.c
283 * allow to print mismatch information as fastq comment. MAQ does
284 not like long read names.
286 ------------------------------------------------------------------------
287 r141 | lh3lh3 | 2009-02-26 14:53:03 +0000 (Thu, 26 Feb 2009) | 6 lines
289 M /trunk/samtools/ChangeLog
290 M /trunk/samtools/misc/wgsim.c
291 M /trunk/samtools/misc/wgsim_eval.pl
294 * fixed a bug about color read coordinates
295 * fixed a bug in read names
296 * wgsim_eval.pl-0.1.3
297 * make the script work with color reads
299 ------------------------------------------------------------------------
300 r140 | lh3lh3 | 2009-02-26 14:02:57 +0000 (Thu, 26 Feb 2009) | 2 lines
302 M /trunk/samtools/misc/Makefile
303 M /trunk/samtools/misc/wgsim.c
305 * wgsim: added a note
307 ------------------------------------------------------------------------
308 r139 | lh3lh3 | 2009-02-26 11:39:08 +0000 (Thu, 26 Feb 2009) | 7 lines
310 M /trunk/samtools/misc/wgsim.c
311 M /trunk/samtools/misc/wgsim_eval.pl
314 * considerable code clean up
315 * print number of substitutions/indels/errors on each read
316 * potentially support SOLiD simulation, though not tested at the moment
317 * wgsim_eval.pl-0.1.2
318 * change in accordant with wgsim
320 ------------------------------------------------------------------------
321 r129 | lh3lh3 | 2009-02-18 22:23:27 +0000 (Wed, 18 Feb 2009) | 3 lines
323 M /trunk/samtools/bam_index.c
324 M /trunk/samtools/bamtk.c
327 * fixed a bug in bam_fetch, caused by completely contained adjacent chunks
329 ------------------------------------------------------------------------
330 r128 | bhandsaker | 2009-02-18 19:06:57 +0000 (Wed, 18 Feb 2009) | 2 lines
332 M /trunk/samtools/bamtk.c
334 Fix annoying segv when invalid region specified.
336 ------------------------------------------------------------------------
337 r127 | lh3lh3 | 2009-02-17 10:49:55 +0000 (Tue, 17 Feb 2009) | 2 lines
339 D /trunk/samtools/misc/indel_filter.pl
340 A /trunk/samtools/misc/samtools.pl
342 * move indel_filter.pl to samtools.pl
344 ------------------------------------------------------------------------
345 r126 | lh3lh3 | 2009-02-14 21:22:30 +0000 (Sat, 14 Feb 2009) | 3 lines
347 M /trunk/samtools/bam_mate.c
348 M /trunk/samtools/bamtk.c
351 * fixed a bug in fixmate: SE reads are flagged as BAM_FMUNMAP
353 ------------------------------------------------------------------------
354 r125 | lh3lh3 | 2009-02-13 09:54:45 +0000 (Fri, 13 Feb 2009) | 3 lines
356 M /trunk/samtools/bam_stat.c
357 M /trunk/samtools/bamtk.c
360 * fixed a minor bug in flagstat
362 ------------------------------------------------------------------------
363 r124 | lh3lh3 | 2009-02-12 11:15:32 +0000 (Thu, 12 Feb 2009) | 3 lines
365 M /trunk/samtools/bam_maqcns.c
366 M /trunk/samtools/bamtk.c
367 M /trunk/samtools/misc/indel_filter.pl
370 * improve indel caller by setting maximum window size
372 ------------------------------------------------------------------------
373 r123 | lh3lh3 | 2009-02-12 10:30:29 +0000 (Thu, 12 Feb 2009) | 2 lines
375 M /trunk/samtools/bam_plcmd.c
376 M /trunk/samtools/bamtk.c
378 * output max mapping quality in indel line
380 ------------------------------------------------------------------------
381 r122 | lh3lh3 | 2009-02-11 10:59:10 +0000 (Wed, 11 Feb 2009) | 2 lines
383 M /trunk/samtools/misc/maq2sam.c
385 fixed a bug in generating tag AM
387 ------------------------------------------------------------------------
388 r121 | lh3lh3 | 2009-02-03 10:43:11 +0000 (Tue, 03 Feb 2009) | 2 lines
390 M /trunk/samtools/bam_index.c
391 M /trunk/samtools/bamtk.c
393 fixed a potential memory problem in indexing
395 ------------------------------------------------------------------------
396 r120 | bhandsaker | 2009-02-02 15:52:52 +0000 (Mon, 02 Feb 2009) | 2 lines
398 M /trunk/samtools/Makefile
400 Pass LIBS to recursive targets to facilitate building at Broad.
402 ------------------------------------------------------------------------
403 r119 | lh3lh3 | 2009-02-02 10:12:15 +0000 (Mon, 02 Feb 2009) | 4 lines
405 M /trunk/samtools/ChangeLog
406 M /trunk/samtools/bam_plcmd.c
407 M /trunk/samtools/bam_stat.c
408 M /trunk/samtools/bamtk.c
411 * fixed a bug in generating GLFv2 for indels
412 * improve flagstat report a little bit
414 ------------------------------------------------------------------------
415 r118 | lh3lh3 | 2009-01-29 12:33:23 +0000 (Thu, 29 Jan 2009) | 3 lines
417 M /trunk/samtools/Makefile
418 A /trunk/samtools/bam_stat.c
419 M /trunk/samtools/bamtk.c
422 * added flagstat command
424 ------------------------------------------------------------------------
425 r116 | lh3lh3 | 2009-01-28 13:31:12 +0000 (Wed, 28 Jan 2009) | 2 lines
427 M /trunk/samtools/ChangeLog
428 M /trunk/samtools/NEWS
429 M /trunk/samtools/bamtk.c
430 M /trunk/samtools/samtools.1
432 Release SAMtools-0.1.2
434 ------------------------------------------------------------------------
435 r115 | lh3lh3 | 2009-01-28 12:54:08 +0000 (Wed, 28 Jan 2009) | 2 lines
437 A /trunk/samtools/misc/indel_filter.pl
439 Script for filtering indel results
441 ------------------------------------------------------------------------
442 r114 | lh3lh3 | 2009-01-25 11:45:37 +0000 (Sun, 25 Jan 2009) | 2 lines
444 A /trunk/samtools/misc/zoom2sam.pl
448 ------------------------------------------------------------------------
449 r113 | lh3lh3 | 2009-01-24 14:25:07 +0000 (Sat, 24 Jan 2009) | 2 lines
451 A /trunk/samtools/misc/novo2sam.pl
453 add a script to convert novo alignment to SAM
455 ------------------------------------------------------------------------
456 r112 | lh3lh3 | 2009-01-23 20:57:39 +0000 (Fri, 23 Jan 2009) | 2 lines
458 M /trunk/samtools/ChangeLog
459 M /trunk/samtools/ChangeLog.old
460 M /trunk/samtools/samtools.1
462 update documentation and ChangeLog
464 ------------------------------------------------------------------------
465 r111 | lh3lh3 | 2009-01-23 19:22:59 +0000 (Fri, 23 Jan 2009) | 3 lines
467 M /trunk/samtools/bam_sort.c
468 M /trunk/samtools/bamtk.c
471 * fixed a bug in "merge" command line
473 ------------------------------------------------------------------------
474 r110 | lh3lh3 | 2009-01-22 15:36:48 +0000 (Thu, 22 Jan 2009) | 3 lines
476 M /trunk/samtools/misc/Makefile
477 A /trunk/samtools/misc/bowtie2sam.pl (from /branches/dev/samtools/misc/bowtie2sam.pl:108)
478 M /trunk/samtools/misc/export2sam.pl
479 A /trunk/samtools/misc/soap2sam.pl (from /branches/dev/samtools/misc/soap2sam.pl:108)
480 A /trunk/samtools/misc/wgsim.c (from /branches/dev/samtools/misc/wgsim.c:108)
481 A /trunk/samtools/misc/wgsim_eval.pl (from /branches/dev/samtools/misc/wgsim_eval.pl:108)
483 * merge from branches/dev/
484 * all future development will happen here
486 ------------------------------------------------------------------------
487 r109 | lh3lh3 | 2009-01-22 15:14:27 +0000 (Thu, 22 Jan 2009) | 3 lines
489 M /trunk/samtools/COPYING
490 M /trunk/samtools/ChangeLog
491 A /trunk/samtools/INSTALL (from /branches/dev/samtools/INSTALL:108)
492 M /trunk/samtools/Makefile
493 A /trunk/samtools/Makefile.lite (from /branches/dev/samtools/Makefile.lite:108)
494 M /trunk/samtools/bam.c
495 M /trunk/samtools/bam.h
496 M /trunk/samtools/bam_import.c
497 M /trunk/samtools/bam_index.c
498 M /trunk/samtools/bam_lpileup.c
499 M /trunk/samtools/bam_maqcns.c
500 M /trunk/samtools/bam_maqcns.h
501 A /trunk/samtools/bam_mate.c (from /branches/dev/samtools/bam_mate.c:108)
502 M /trunk/samtools/bam_pileup.c
503 M /trunk/samtools/bam_plcmd.c
504 A /trunk/samtools/bam_rmdup.c (from /branches/dev/samtools/bam_rmdup.c:108)
505 M /trunk/samtools/bam_sort.c
506 M /trunk/samtools/bamtk.c
507 M /trunk/samtools/bgzf.h
508 M /trunk/samtools/examples/00README.txt
509 A /trunk/samtools/examples/Makefile (from /branches/dev/samtools/examples/Makefile:108)
510 D /trunk/samtools/examples/ex1.fa.fai
511 M /trunk/samtools/examples/ex1.sam.gz
512 M /trunk/samtools/faidx.c
513 A /trunk/samtools/glf.c (from /branches/dev/samtools/glf.c:108)
514 M /trunk/samtools/glf.h
515 M /trunk/samtools/misc/Makefile
516 M /trunk/samtools/misc/maq2sam.c
517 M /trunk/samtools/razf.c
518 M /trunk/samtools/source.dot
520 * Merge from branches/dev/
521 * all future development will happen here at trunk/
523 ------------------------------------------------------------------------
524 r79 | bhandsaker | 2009-01-07 21:42:15 +0000 (Wed, 07 Jan 2009) | 2 lines
526 M /trunk/samtools/bam_maqcns.c
527 M /trunk/samtools/bam_tview.c
529 Fix problem with compiling without curses.
531 ------------------------------------------------------------------------
532 r63 | lh3lh3 | 2008-12-22 15:58:02 +0000 (Mon, 22 Dec 2008) | 2 lines
534 A /trunk/samtools (from /branches/dev/samtools:62)
538 ------------------------------------------------------------------------
539 r62 | lh3lh3 | 2008-12-22 15:55:13 +0000 (Mon, 22 Dec 2008) | 2 lines
541 A /branches/dev/samtools/NEWS
542 M /branches/dev/samtools/bamtk.c
543 M /branches/dev/samtools/samtools.1
545 Release samtools-0.1.1
547 ------------------------------------------------------------------------
548 r61 | lh3lh3 | 2008-12-22 15:46:08 +0000 (Mon, 22 Dec 2008) | 10 lines
550 M /branches/dev/samtools/bam_aux.c
551 M /branches/dev/samtools/bam_index.c
552 M /branches/dev/samtools/bam_plcmd.c
553 M /branches/dev/samtools/bam_tview.c
554 M /branches/dev/samtools/bamtk.c
555 M /branches/dev/samtools/razf.c
556 M /branches/dev/samtools/samtools.1
559 * fixed a bug in razf.c: reset z_eof when razf_seek() is called
560 * fixed a memory leak in parsing a region
561 * changed pileup a little bit when -s is in use: output ^ and $
562 * when a bam is not indexed, output more meaningful error message
563 * fixed a bug in indexing for small alignment
564 * fixed a bug in the viewer when we come to the end of a reference file
565 * updated documentation
566 * prepare to release 0.1.1
568 ------------------------------------------------------------------------
569 r60 | lh3lh3 | 2008-12-22 15:10:16 +0000 (Mon, 22 Dec 2008) | 2 lines
571 A /branches/dev/samtools/examples
572 A /branches/dev/samtools/examples/00README.txt
573 A /branches/dev/samtools/examples/ex1.fa
574 A /branches/dev/samtools/examples/ex1.fa.fai
575 A /branches/dev/samtools/examples/ex1.sam.gz
579 ------------------------------------------------------------------------
580 r59 | lh3lh3 | 2008-12-22 09:38:15 +0000 (Mon, 22 Dec 2008) | 2 lines
582 M /branches/dev/samtools/ChangeLog
586 ------------------------------------------------------------------------
587 r58 | lh3lh3 | 2008-12-20 23:06:00 +0000 (Sat, 20 Dec 2008) | 3 lines
589 M /branches/dev/samtools/misc/export2sam.pl
594 ------------------------------------------------------------------------
595 r57 | lh3lh3 | 2008-12-20 15:44:20 +0000 (Sat, 20 Dec 2008) | 2 lines
597 A /branches/dev/samtools/misc/export2sam.pl
599 convert Export format to SAM; not thoroughly tested
601 ------------------------------------------------------------------------
602 r56 | lh3lh3 | 2008-12-19 22:13:28 +0000 (Fri, 19 Dec 2008) | 6 lines
604 M /branches/dev/samtools/bam_import.c
605 M /branches/dev/samtools/bam_plcmd.c
606 M /branches/dev/samtools/bam_tview.c
607 M /branches/dev/samtools/bamtk.c
608 A /branches/dev/samtools/source.dot
611 * pileup: generate maq-like simple output
612 * pileup: allow to output pileup at required sites
613 * source.dot: source file relationship graph
614 * tview: fixed a minor bug
616 ------------------------------------------------------------------------
617 r55 | lh3lh3 | 2008-12-19 20:10:26 +0000 (Fri, 19 Dec 2008) | 2 lines
619 D /branches/dev/samtools/misc/all2sam.pl
623 ------------------------------------------------------------------------
624 r54 | lh3lh3 | 2008-12-16 22:34:25 +0000 (Tue, 16 Dec 2008) | 2 lines
626 A /branches/dev/samtools/COPYING
627 M /branches/dev/samtools/bam.h
628 M /branches/dev/samtools/faidx.h
629 M /branches/dev/samtools/khash.h
630 M /branches/dev/samtools/kseq.h
631 M /branches/dev/samtools/ksort.h
632 M /branches/dev/samtools/samtools.1
634 Added copyright information and a bit more documentation. No code change.
636 ------------------------------------------------------------------------
637 r53 | lh3lh3 | 2008-12-16 13:40:18 +0000 (Tue, 16 Dec 2008) | 3 lines
639 M /branches/dev/samtools/bam.c
640 M /branches/dev/samtools/bam.h
641 M /branches/dev/samtools/bam_index.c
642 M /branches/dev/samtools/bam_maqcns.c
643 M /branches/dev/samtools/bamtk.c
646 * improved efficiency of the indel caller for spliced alignments
648 ------------------------------------------------------------------------
649 r52 | lh3lh3 | 2008-12-16 10:28:20 +0000 (Tue, 16 Dec 2008) | 3 lines
651 M /branches/dev/samtools/bam.c
652 M /branches/dev/samtools/bam.h
653 M /branches/dev/samtools/bam_aux.c
654 M /branches/dev/samtools/bam_index.c
655 M /branches/dev/samtools/bamtk.c
658 * a bit code cleanup: reduce the dependency between source files
660 ------------------------------------------------------------------------
661 r51 | lh3lh3 | 2008-12-15 14:29:32 +0000 (Mon, 15 Dec 2008) | 3 lines
663 M /branches/dev/samtools/bam_maqcns.c
664 M /branches/dev/samtools/bam_plcmd.c
665 M /branches/dev/samtools/bamtk.c
668 * fixed a memory leak
670 ------------------------------------------------------------------------
671 r50 | lh3lh3 | 2008-12-15 14:00:13 +0000 (Mon, 15 Dec 2008) | 2 lines
673 M /branches/dev/samtools/ChangeLog
674 M /branches/dev/samtools/bam.h
675 M /branches/dev/samtools/samtools.1
677 update documentation, ChangeLog and a comment
679 ------------------------------------------------------------------------
680 r49 | lh3lh3 | 2008-12-15 13:36:43 +0000 (Mon, 15 Dec 2008) | 6 lines
682 M /branches/dev/samtools/Makefile
683 M /branches/dev/samtools/bam.h
684 M /branches/dev/samtools/bam_maqcns.c
685 M /branches/dev/samtools/bam_maqcns.h
686 M /branches/dev/samtools/bam_pileup.c
687 A /branches/dev/samtools/bam_plcmd.c
688 M /branches/dev/samtools/bamtk.c
689 M /branches/dev/samtools/samtools.1
692 * moved pileup command to a separate source file
694 * added bam_cal_segend(). (NOT WORKING for spliced alignment!!!)
695 * updated documentation
697 ------------------------------------------------------------------------
698 r48 | lh3lh3 | 2008-12-12 13:55:36 +0000 (Fri, 12 Dec 2008) | 3 lines
700 M /branches/dev/samtools/bam_maqcns.c
701 M /branches/dev/samtools/bamtk.c
704 * fixed another bug in maqcns when there is a nearby deletion
706 ------------------------------------------------------------------------
707 r47 | lh3lh3 | 2008-12-12 13:42:16 +0000 (Fri, 12 Dec 2008) | 5 lines
709 M /branches/dev/samtools/bam_maqcns.c
710 M /branches/dev/samtools/bam_pileup.c
711 M /branches/dev/samtools/bamtk.c
714 * pileup: outputing consensus is now optional
715 * fixed a bug in glfgen. This bug also exists in maq's glfgen. However,
716 I am not quite sure why the previous version may have problem.
718 ------------------------------------------------------------------------
719 r46 | lh3lh3 | 2008-12-12 11:44:56 +0000 (Fri, 12 Dec 2008) | 6 lines
721 M /branches/dev/samtools/bam_pileup.c
722 M /branches/dev/samtools/bamtk.c
725 * add maq consensus to pileup. However, I will move this part to a new
726 command as strictly speaking, consensus callin is not part of pileup,
727 and imposing it would make it harder to generate for other language
730 ------------------------------------------------------------------------
731 r45 | bhandsaker | 2008-12-11 20:43:56 +0000 (Thu, 11 Dec 2008) | 2 lines
733 M /branches/dev/samtools/bgzf.c
735 Fix bug in tell() after reads that consume to the exact end of a block.
737 ------------------------------------------------------------------------
738 r44 | lh3lh3 | 2008-12-11 09:36:53 +0000 (Thu, 11 Dec 2008) | 2 lines
740 M /branches/dev/samtools/samtools.1
744 ------------------------------------------------------------------------
745 r43 | lh3lh3 | 2008-12-11 09:25:36 +0000 (Thu, 11 Dec 2008) | 4 lines
747 M /branches/dev/samtools/bam_import.c
748 M /branches/dev/samtools/bamtk.c
751 * fixed a bug in parser when there is auxiliary fields
752 * made the parser a bit more robust
754 ------------------------------------------------------------------------
755 r42 | lh3lh3 | 2008-12-10 14:57:29 +0000 (Wed, 10 Dec 2008) | 5 lines
757 M /branches/dev/samtools/bam_index.c
758 M /branches/dev/samtools/bamtk.c
759 M /branches/dev/samtools/bgzf.c
762 * fixed a bug in bgzf (only reading is affected)
763 * fixed a typo in bam_index.c
764 * in bam_index.c, check potential bugs in the underlying I/O library
766 ------------------------------------------------------------------------
767 r41 | lh3lh3 | 2008-12-10 12:53:08 +0000 (Wed, 10 Dec 2008) | 2 lines
769 M /branches/dev/samtools/samtools.1
773 ------------------------------------------------------------------------
774 r40 | lh3lh3 | 2008-12-10 11:52:10 +0000 (Wed, 10 Dec 2008) | 5 lines
776 M /branches/dev/samtools/bam.h
777 M /branches/dev/samtools/bam_pileup.c
778 M /branches/dev/samtools/bamtk.c
781 * tried to make pileup work with clipping (previously not), though NOT tested
782 * removed -v from pileup
783 * made pileup take the reference sequence
785 ------------------------------------------------------------------------
786 r39 | lh3lh3 | 2008-12-09 11:59:28 +0000 (Tue, 09 Dec 2008) | 4 lines
788 M /branches/dev/samtools/bam_import.c
789 M /branches/dev/samtools/bamtk.c
790 M /branches/dev/samtools/samtools.1
793 * in parser, recognize "=", rather than ",", as a match
794 * in parser, correctl parse "=" at the MRNM field.
796 ------------------------------------------------------------------------
797 r38 | lh3lh3 | 2008-12-09 11:39:07 +0000 (Tue, 09 Dec 2008) | 2 lines
799 M /branches/dev/samtools/misc/maq2sam.c
801 fixed a bug in handling maq flag 64 and 192
803 ------------------------------------------------------------------------
804 r37 | lh3lh3 | 2008-12-09 09:53:46 +0000 (Tue, 09 Dec 2008) | 2 lines
806 M /branches/dev/samtools/misc/md5fa.c
808 also calculate unordered md5sum check
810 ------------------------------------------------------------------------
811 r36 | lh3lh3 | 2008-12-09 09:46:21 +0000 (Tue, 09 Dec 2008) | 2 lines
813 M /branches/dev/samtools/misc/md5fa.c
815 fixed a minor bug when there are space in the sequence
817 ------------------------------------------------------------------------
818 r35 | lh3lh3 | 2008-12-09 09:40:45 +0000 (Tue, 09 Dec 2008) | 2 lines
820 M /branches/dev/samtools/misc/md5fa.c
822 fixed a potential memory leak
824 ------------------------------------------------------------------------
825 r34 | lh3lh3 | 2008-12-08 14:52:17 +0000 (Mon, 08 Dec 2008) | 2 lines
827 M /branches/dev/samtools/bam_import.c
828 M /branches/dev/samtools/bam_index.c
829 M /branches/dev/samtools/bamtk.c
831 * fixed a bug in import: bin is wrongly calculated
833 ------------------------------------------------------------------------
834 r33 | lh3lh3 | 2008-12-08 14:08:01 +0000 (Mon, 08 Dec 2008) | 2 lines
836 M /branches/dev/samtools/misc/all2sam.pl
840 ------------------------------------------------------------------------
841 r32 | lh3lh3 | 2008-12-08 12:56:02 +0000 (Mon, 08 Dec 2008) | 3 lines
843 M /branches/dev/samtools/Makefile
844 M /branches/dev/samtools/kseq.h
845 M /branches/dev/samtools/misc/Makefile
846 A /branches/dev/samtools/misc/md5.c
847 A /branches/dev/samtools/misc/md5.h
848 A /branches/dev/samtools/misc/md5fa.c
850 * fixed two warnings in kseq.h
851 * added md5sum utilities
853 ------------------------------------------------------------------------
854 r31 | lh3lh3 | 2008-12-08 11:35:29 +0000 (Mon, 08 Dec 2008) | 5 lines
856 M /branches/dev/samtools/Makefile
857 M /branches/dev/samtools/bam_import.c
858 M /branches/dev/samtools/bamtk.c
859 A /branches/dev/samtools/kseq.h
860 D /branches/dev/samtools/kstream.h
863 * replace kstream with kseq. kseq is a superset of kstream. I need the
864 extra functions in kseq.h.
865 * also compile stand-alone faidx
867 ------------------------------------------------------------------------
868 r30 | lh3lh3 | 2008-12-08 11:17:04 +0000 (Mon, 08 Dec 2008) | 3 lines
870 M /branches/dev/samtools/bam.h
871 M /branches/dev/samtools/bam_sort.c
872 M /branches/dev/samtools/bamtk.c
875 * sorting by read names is available
877 ------------------------------------------------------------------------
878 r29 | lh3lh3 | 2008-12-08 10:29:02 +0000 (Mon, 08 Dec 2008) | 3 lines
880 M /branches/dev/samtools/bam.c
881 M /branches/dev/samtools/bam.h
882 M /branches/dev/samtools/bam_import.c
883 M /branches/dev/samtools/bam_maqcns.c
884 M /branches/dev/samtools/bam_pileup.c
885 M /branches/dev/samtools/bam_sort.c
886 M /branches/dev/samtools/bam_tview.c
887 M /branches/dev/samtools/bamtk.c
888 M /branches/dev/samtools/misc/maq2sam.c
891 * format change to meet the latest specification
893 ------------------------------------------------------------------------
894 r28 | lh3lh3 | 2008-12-04 16:09:21 +0000 (Thu, 04 Dec 2008) | 3 lines
896 M /branches/dev/samtools/bam_maqcns.c
897 M /branches/dev/samtools/misc/maq2sam.c
899 * minor change in maqcns: special care when n==0
900 * change maq2sam to meet the latest specification
902 ------------------------------------------------------------------------
903 r27 | lh3lh3 | 2008-12-04 15:55:44 +0000 (Thu, 04 Dec 2008) | 2 lines
905 M /branches/dev/samtools/razf.c
906 M /branches/dev/samtools/razf.h
908 considerable code clean up in razf
910 ------------------------------------------------------------------------
911 r26 | lh3lh3 | 2008-12-04 15:08:18 +0000 (Thu, 04 Dec 2008) | 2 lines
913 M /branches/dev/samtools/ChangeLog
914 M /branches/dev/samtools/Makefile
915 M /branches/dev/samtools/faidx.c
917 make RAZF optional in faidx.c
919 ------------------------------------------------------------------------
920 r25 | lh3lh3 | 2008-12-01 15:27:22 +0000 (Mon, 01 Dec 2008) | 3 lines
922 M /branches/dev/samtools/Makefile
923 M /branches/dev/samtools/bam.h
924 M /branches/dev/samtools/bam_aux.c
925 M /branches/dev/samtools/bamtk.c
926 M /branches/dev/samtools/samtools.1
929 * added routines for retrieving aux data, NOT TESTED YET!
931 ------------------------------------------------------------------------
932 r24 | lh3lh3 | 2008-12-01 14:29:43 +0000 (Mon, 01 Dec 2008) | 5 lines
934 M /branches/dev/samtools/bam.c
935 M /branches/dev/samtools/bam_import.c
936 M /branches/dev/samtools/bam_maqcns.c
937 M /branches/dev/samtools/bamtk.c
938 M /branches/dev/samtools/bgzf.c
939 M /branches/dev/samtools/samtools.1
942 * bgzf: fixed a potential integer overflow on 32-it machines
943 * maqcns: set the minimum combined quality as 0
944 * supporting hex strings
946 ------------------------------------------------------------------------
947 r23 | lh3lh3 | 2008-11-27 17:14:37 +0000 (Thu, 27 Nov 2008) | 3 lines
949 M /branches/dev/samtools/bam_maqcns.c
950 M /branches/dev/samtools/bamtk.c
953 * fixed the bug in maqcns
955 ------------------------------------------------------------------------
956 r22 | lh3lh3 | 2008-11-27 17:08:11 +0000 (Thu, 27 Nov 2008) | 3 lines
958 M /branches/dev/samtools/Makefile
959 M /branches/dev/samtools/bam.h
960 A /branches/dev/samtools/bam_maqcns.c
961 A /branches/dev/samtools/bam_maqcns.h
962 M /branches/dev/samtools/bam_tview.c
963 M /branches/dev/samtools/bamtk.c
964 A /branches/dev/samtools/glf.h
967 * add MAQ consensus caller, currently BUGGY!
969 ------------------------------------------------------------------------
970 r21 | lh3lh3 | 2008-11-27 13:51:28 +0000 (Thu, 27 Nov 2008) | 4 lines
972 M /branches/dev/samtools/bam_pileup.c
973 M /branches/dev/samtools/bam_tview.c
974 M /branches/dev/samtools/bamtk.c
977 * tview: display padded alignment (but not P operation)
978 * better coordinates and reference sequence
980 ------------------------------------------------------------------------
981 r19 | lh3lh3 | 2008-11-27 09:26:05 +0000 (Thu, 27 Nov 2008) | 2 lines
983 A /branches/dev/samtools/ChangeLog
987 ------------------------------------------------------------------------
988 r18 | lh3lh3 | 2008-11-27 09:24:45 +0000 (Thu, 27 Nov 2008) | 3 lines
990 D /branches/dev/samtools/ChangeLog
991 A /branches/dev/samtools/ChangeLog.old (from /branches/dev/samtools/ChangeLog:6)
993 Rename ChangeLog to ChangeLog.old. This old ChangeLog is generated from
994 the log of my personal SVN repository.
996 ------------------------------------------------------------------------
997 r17 | lh3lh3 | 2008-11-27 09:22:55 +0000 (Thu, 27 Nov 2008) | 6 lines
999 M /branches/dev/samtools/Makefile
1000 M /branches/dev/samtools/bamtk.c
1001 M /branches/dev/samtools/bgzf.c
1004 * declare fseeko and ftello as some Linux may not do this by default and
1005 missing these declarations will make bgzf buggy
1006 * get rid of some harmless warings
1007 * use BGZF by default, now
1009 ------------------------------------------------------------------------
1010 r16 | lh3lh3 | 2008-11-26 21:19:11 +0000 (Wed, 26 Nov 2008) | 4 lines
1012 M /branches/dev/samtools/bam_index.c
1013 M /branches/dev/samtools/bamtk.c
1014 M /branches/dev/samtools/razf.c
1017 * fixed a bug in razf_read()
1018 * give more warnings when the file is truncated (or due to bugs in I/O library)
1020 ------------------------------------------------------------------------
1021 r15 | lh3lh3 | 2008-11-26 20:41:39 +0000 (Wed, 26 Nov 2008) | 2 lines
1023 M /branches/dev/samtools/bgzf.c
1025 fixed a bug in bgzf.c at the end of the file
1027 ------------------------------------------------------------------------
1028 r14 | lh3lh3 | 2008-11-26 17:05:18 +0000 (Wed, 26 Nov 2008) | 4 lines
1030 M /branches/dev/samtools/bamtk.c
1033 * a lot happened to RAZF, although samtools itself is untouched. Better
1034 also update the version number anyway to avoid confusion
1036 ------------------------------------------------------------------------
1037 r13 | lh3lh3 | 2008-11-26 17:03:48 +0000 (Wed, 26 Nov 2008) | 2 lines
1039 M /branches/dev/samtools/razf.c
1041 a change from Jue, but I think it should not matter
1043 ------------------------------------------------------------------------
1044 r12 | lh3lh3 | 2008-11-26 16:48:14 +0000 (Wed, 26 Nov 2008) | 3 lines
1046 M /branches/dev/samtools/razf.c
1048 fixed a potential bug in razf. However, it seems still buggy, just
1049 rarely happens, very rarely.
1051 ------------------------------------------------------------------------
1052 r11 | lh3lh3 | 2008-11-26 14:02:56 +0000 (Wed, 26 Nov 2008) | 2 lines
1054 M /branches/dev/samtools/razf.c
1056 fixed a bug in razf, with the help of Jue
1058 ------------------------------------------------------------------------
1059 r10 | lh3lh3 | 2008-11-26 11:55:32 +0000 (Wed, 26 Nov 2008) | 2 lines
1061 M /branches/dev/samtools/bam_index.c
1065 ------------------------------------------------------------------------
1066 r9 | lh3lh3 | 2008-11-26 11:37:05 +0000 (Wed, 26 Nov 2008) | 2 lines
1068 M /branches/dev/samtools/Makefile
1069 M /branches/dev/samtools/bam.h
1070 M /branches/dev/samtools/razf.c
1071 M /branches/dev/samtools/razf.h
1073 * Jue has updated razf to realize Bob's scheme
1075 ------------------------------------------------------------------------
1076 r7 | lh3lh3 | 2008-11-25 20:37:37 +0000 (Tue, 25 Nov 2008) | 2 lines
1078 A /branches/dev/samtools/samtools.1
1082 ------------------------------------------------------------------------
1083 r6 | lh3lh3 | 2008-11-25 20:37:16 +0000 (Tue, 25 Nov 2008) | 3 lines
1085 A /branches/dev/samtools/ChangeLog
1086 A /branches/dev/samtools/Makefile
1087 A /branches/dev/samtools/bam.c
1088 A /branches/dev/samtools/bam.h
1089 A /branches/dev/samtools/bam_aux.c
1090 A /branches/dev/samtools/bam_endian.h
1091 A /branches/dev/samtools/bam_import.c
1092 A /branches/dev/samtools/bam_index.c
1093 A /branches/dev/samtools/bam_lpileup.c
1094 A /branches/dev/samtools/bam_pileup.c
1095 A /branches/dev/samtools/bam_sort.c
1096 A /branches/dev/samtools/bam_tview.c
1097 A /branches/dev/samtools/bamtk.c
1098 A /branches/dev/samtools/bgzf.c
1099 A /branches/dev/samtools/bgzf.h
1100 A /branches/dev/samtools/bgzip.c
1101 A /branches/dev/samtools/faidx.c
1102 A /branches/dev/samtools/faidx.h
1103 A /branches/dev/samtools/khash.h
1104 A /branches/dev/samtools/ksort.h
1105 A /branches/dev/samtools/kstream.h
1106 A /branches/dev/samtools/misc
1107 A /branches/dev/samtools/misc/Makefile
1108 A /branches/dev/samtools/misc/all2sam.pl
1109 A /branches/dev/samtools/misc/maq2sam.c
1110 A /branches/dev/samtools/razf.c
1111 A /branches/dev/samtools/razf.h
1112 A /branches/dev/samtools/razip.c
1113 A /branches/dev/samtools/zutil.h
1115 The initial version of samtools, replicated from my local SVN repository.
1116 The current version is: 0.1.0-42. All future development will happen here.
1118 ------------------------------------------------------------------------
1119 r5 | lh3lh3 | 2008-11-25 20:30:49 +0000 (Tue, 25 Nov 2008) | 2 lines
1121 A /branches/dev/samtools
1123 samtools (C version)
1125 ------------------------------------------------------------------------