1 ------------------------------------------------------------------------
2 r153 | lh3lh3 | 2009-03-02 10:45:28 +0000 (Mon, 02 Mar 2009) | 3 lines
4 M /trunk/samtools/bamtk.c
5 M /trunk/samtools/glf.c
8 * use "GLF\3" as the magic for GLFv3 files
10 ------------------------------------------------------------------------
11 r152 | lh3lh3 | 2009-03-02 10:39:09 +0000 (Mon, 02 Mar 2009) | 5 lines
13 M /trunk/samtools/Makefile
14 M /trunk/samtools/bam_import.c
15 M /trunk/samtools/bam_index.c
16 M /trunk/samtools/bam_plcmd.c
17 M /trunk/samtools/bamtk.c
18 M /trunk/samtools/glf.c
19 M /trunk/samtools/glf.h
22 * fixed a bug in import: core.bin is undefined for unmapped reads
23 * this bug can be alleviated (not completely solved) in bam_index.c
24 * update to GLFv3: pos is changed to offset for better compression
26 ------------------------------------------------------------------------
27 r151 | lh3lh3 | 2009-03-01 15:18:43 +0000 (Sun, 01 Mar 2009) | 3 lines
29 M /trunk/samtools/misc/wgsim.c
32 * fixed a bug in simulating indels
34 ------------------------------------------------------------------------
35 r145 | lh3lh3 | 2009-02-26 19:43:57 +0000 (Thu, 26 Feb 2009) | 4 lines
37 M /trunk/samtools/misc/wgsim.c
40 * allow to print mismatch information as fastq comment. MAQ does
41 not like long read names.
43 ------------------------------------------------------------------------
44 r141 | lh3lh3 | 2009-02-26 14:53:03 +0000 (Thu, 26 Feb 2009) | 6 lines
46 M /trunk/samtools/ChangeLog
47 M /trunk/samtools/misc/wgsim.c
48 M /trunk/samtools/misc/wgsim_eval.pl
51 * fixed a bug about color read coordinates
52 * fixed a bug in read names
54 * make the script work with color reads
56 ------------------------------------------------------------------------
57 r140 | lh3lh3 | 2009-02-26 14:02:57 +0000 (Thu, 26 Feb 2009) | 2 lines
59 M /trunk/samtools/misc/Makefile
60 M /trunk/samtools/misc/wgsim.c
64 ------------------------------------------------------------------------
65 r139 | lh3lh3 | 2009-02-26 11:39:08 +0000 (Thu, 26 Feb 2009) | 7 lines
67 M /trunk/samtools/misc/wgsim.c
68 M /trunk/samtools/misc/wgsim_eval.pl
71 * considerable code clean up
72 * print number of substitutions/indels/errors on each read
73 * potentially support SOLiD simulation, though not tested at the moment
75 * change in accordant with wgsim
77 ------------------------------------------------------------------------
78 r129 | lh3lh3 | 2009-02-18 22:23:27 +0000 (Wed, 18 Feb 2009) | 3 lines
80 M /trunk/samtools/bam_index.c
81 M /trunk/samtools/bamtk.c
84 * fixed a bug in bam_fetch, caused by completely contained adjacent chunks
86 ------------------------------------------------------------------------
87 r128 | bhandsaker | 2009-02-18 19:06:57 +0000 (Wed, 18 Feb 2009) | 2 lines
89 M /trunk/samtools/bamtk.c
91 Fix annoying segv when invalid region specified.
93 ------------------------------------------------------------------------
94 r127 | lh3lh3 | 2009-02-17 10:49:55 +0000 (Tue, 17 Feb 2009) | 2 lines
96 D /trunk/samtools/misc/indel_filter.pl
97 A /trunk/samtools/misc/samtools.pl
99 * move indel_filter.pl to samtools.pl
101 ------------------------------------------------------------------------
102 r126 | lh3lh3 | 2009-02-14 21:22:30 +0000 (Sat, 14 Feb 2009) | 3 lines
104 M /trunk/samtools/bam_mate.c
105 M /trunk/samtools/bamtk.c
108 * fixed a bug in fixmate: SE reads are flagged as BAM_FMUNMAP
110 ------------------------------------------------------------------------
111 r125 | lh3lh3 | 2009-02-13 09:54:45 +0000 (Fri, 13 Feb 2009) | 3 lines
113 M /trunk/samtools/bam_stat.c
114 M /trunk/samtools/bamtk.c
117 * fixed a minor bug in flagstat
119 ------------------------------------------------------------------------
120 r124 | lh3lh3 | 2009-02-12 11:15:32 +0000 (Thu, 12 Feb 2009) | 3 lines
122 M /trunk/samtools/bam_maqcns.c
123 M /trunk/samtools/bamtk.c
124 M /trunk/samtools/misc/indel_filter.pl
127 * improve indel caller by setting maximum window size
129 ------------------------------------------------------------------------
130 r123 | lh3lh3 | 2009-02-12 10:30:29 +0000 (Thu, 12 Feb 2009) | 2 lines
132 M /trunk/samtools/bam_plcmd.c
133 M /trunk/samtools/bamtk.c
135 * output max mapping quality in indel line
137 ------------------------------------------------------------------------
138 r122 | lh3lh3 | 2009-02-11 10:59:10 +0000 (Wed, 11 Feb 2009) | 2 lines
140 M /trunk/samtools/misc/maq2sam.c
142 fixed a bug in generating tag AM
144 ------------------------------------------------------------------------
145 r121 | lh3lh3 | 2009-02-03 10:43:11 +0000 (Tue, 03 Feb 2009) | 2 lines
147 M /trunk/samtools/bam_index.c
148 M /trunk/samtools/bamtk.c
150 fixed a potential memory problem in indexing
152 ------------------------------------------------------------------------
153 r120 | bhandsaker | 2009-02-02 15:52:52 +0000 (Mon, 02 Feb 2009) | 2 lines
155 M /trunk/samtools/Makefile
157 Pass LIBS to recursive targets to facilitate building at Broad.
159 ------------------------------------------------------------------------
160 r119 | lh3lh3 | 2009-02-02 10:12:15 +0000 (Mon, 02 Feb 2009) | 4 lines
162 M /trunk/samtools/ChangeLog
163 M /trunk/samtools/bam_plcmd.c
164 M /trunk/samtools/bam_stat.c
165 M /trunk/samtools/bamtk.c
168 * fixed a bug in generating GLFv2 for indels
169 * improve flagstat report a little bit
171 ------------------------------------------------------------------------
172 r118 | lh3lh3 | 2009-01-29 12:33:23 +0000 (Thu, 29 Jan 2009) | 3 lines
174 M /trunk/samtools/Makefile
175 A /trunk/samtools/bam_stat.c
176 M /trunk/samtools/bamtk.c
179 * added flagstat command
181 ------------------------------------------------------------------------
182 r116 | lh3lh3 | 2009-01-28 13:31:12 +0000 (Wed, 28 Jan 2009) | 2 lines
184 M /trunk/samtools/ChangeLog
185 M /trunk/samtools/NEWS
186 M /trunk/samtools/bamtk.c
187 M /trunk/samtools/samtools.1
189 Release SAMtools-0.1.2
191 ------------------------------------------------------------------------
192 r115 | lh3lh3 | 2009-01-28 12:54:08 +0000 (Wed, 28 Jan 2009) | 2 lines
194 A /trunk/samtools/misc/indel_filter.pl
196 Script for filtering indel results
198 ------------------------------------------------------------------------
199 r114 | lh3lh3 | 2009-01-25 11:45:37 +0000 (Sun, 25 Jan 2009) | 2 lines
201 A /trunk/samtools/misc/zoom2sam.pl
205 ------------------------------------------------------------------------
206 r113 | lh3lh3 | 2009-01-24 14:25:07 +0000 (Sat, 24 Jan 2009) | 2 lines
208 A /trunk/samtools/misc/novo2sam.pl
210 add a script to convert novo alignment to SAM
212 ------------------------------------------------------------------------
213 r112 | lh3lh3 | 2009-01-23 20:57:39 +0000 (Fri, 23 Jan 2009) | 2 lines
215 M /trunk/samtools/ChangeLog
216 M /trunk/samtools/ChangeLog.old
217 M /trunk/samtools/samtools.1
219 update documentation and ChangeLog
221 ------------------------------------------------------------------------
222 r111 | lh3lh3 | 2009-01-23 19:22:59 +0000 (Fri, 23 Jan 2009) | 3 lines
224 M /trunk/samtools/bam_sort.c
225 M /trunk/samtools/bamtk.c
228 * fixed a bug in "merge" command line
230 ------------------------------------------------------------------------
231 r110 | lh3lh3 | 2009-01-22 15:36:48 +0000 (Thu, 22 Jan 2009) | 3 lines
233 M /trunk/samtools/misc/Makefile
234 A /trunk/samtools/misc/bowtie2sam.pl (from /branches/dev/samtools/misc/bowtie2sam.pl:108)
235 M /trunk/samtools/misc/export2sam.pl
236 A /trunk/samtools/misc/soap2sam.pl (from /branches/dev/samtools/misc/soap2sam.pl:108)
237 A /trunk/samtools/misc/wgsim.c (from /branches/dev/samtools/misc/wgsim.c:108)
238 A /trunk/samtools/misc/wgsim_eval.pl (from /branches/dev/samtools/misc/wgsim_eval.pl:108)
240 * merge from branches/dev/
241 * all future development will happen here
243 ------------------------------------------------------------------------
244 r109 | lh3lh3 | 2009-01-22 15:14:27 +0000 (Thu, 22 Jan 2009) | 3 lines
246 M /trunk/samtools/COPYING
247 M /trunk/samtools/ChangeLog
248 A /trunk/samtools/INSTALL (from /branches/dev/samtools/INSTALL:108)
249 M /trunk/samtools/Makefile
250 A /trunk/samtools/Makefile.lite (from /branches/dev/samtools/Makefile.lite:108)
251 M /trunk/samtools/bam.c
252 M /trunk/samtools/bam.h
253 M /trunk/samtools/bam_import.c
254 M /trunk/samtools/bam_index.c
255 M /trunk/samtools/bam_lpileup.c
256 M /trunk/samtools/bam_maqcns.c
257 M /trunk/samtools/bam_maqcns.h
258 A /trunk/samtools/bam_mate.c (from /branches/dev/samtools/bam_mate.c:108)
259 M /trunk/samtools/bam_pileup.c
260 M /trunk/samtools/bam_plcmd.c
261 A /trunk/samtools/bam_rmdup.c (from /branches/dev/samtools/bam_rmdup.c:108)
262 M /trunk/samtools/bam_sort.c
263 M /trunk/samtools/bamtk.c
264 M /trunk/samtools/bgzf.h
265 M /trunk/samtools/examples/00README.txt
266 A /trunk/samtools/examples/Makefile (from /branches/dev/samtools/examples/Makefile:108)
267 D /trunk/samtools/examples/ex1.fa.fai
268 M /trunk/samtools/examples/ex1.sam.gz
269 M /trunk/samtools/faidx.c
270 A /trunk/samtools/glf.c (from /branches/dev/samtools/glf.c:108)
271 M /trunk/samtools/glf.h
272 M /trunk/samtools/misc/Makefile
273 M /trunk/samtools/misc/maq2sam.c
274 M /trunk/samtools/razf.c
275 M /trunk/samtools/source.dot
277 * Merge from branches/dev/
278 * all future development will happen here at trunk/
280 ------------------------------------------------------------------------
281 r79 | bhandsaker | 2009-01-07 21:42:15 +0000 (Wed, 07 Jan 2009) | 2 lines
283 M /trunk/samtools/bam_maqcns.c
284 M /trunk/samtools/bam_tview.c
286 Fix problem with compiling without curses.
288 ------------------------------------------------------------------------
289 r63 | lh3lh3 | 2008-12-22 15:58:02 +0000 (Mon, 22 Dec 2008) | 2 lines
291 A /trunk/samtools (from /branches/dev/samtools:62)
295 ------------------------------------------------------------------------
296 r62 | lh3lh3 | 2008-12-22 15:55:13 +0000 (Mon, 22 Dec 2008) | 2 lines
298 A /branches/dev/samtools/NEWS
299 M /branches/dev/samtools/bamtk.c
300 M /branches/dev/samtools/samtools.1
302 Release samtools-0.1.1
304 ------------------------------------------------------------------------
305 r61 | lh3lh3 | 2008-12-22 15:46:08 +0000 (Mon, 22 Dec 2008) | 10 lines
307 M /branches/dev/samtools/bam_aux.c
308 M /branches/dev/samtools/bam_index.c
309 M /branches/dev/samtools/bam_plcmd.c
310 M /branches/dev/samtools/bam_tview.c
311 M /branches/dev/samtools/bamtk.c
312 M /branches/dev/samtools/razf.c
313 M /branches/dev/samtools/samtools.1
316 * fixed a bug in razf.c: reset z_eof when razf_seek() is called
317 * fixed a memory leak in parsing a region
318 * changed pileup a little bit when -s is in use: output ^ and $
319 * when a bam is not indexed, output more meaningful error message
320 * fixed a bug in indexing for small alignment
321 * fixed a bug in the viewer when we come to the end of a reference file
322 * updated documentation
323 * prepare to release 0.1.1
325 ------------------------------------------------------------------------
326 r60 | lh3lh3 | 2008-12-22 15:10:16 +0000 (Mon, 22 Dec 2008) | 2 lines
328 A /branches/dev/samtools/examples
329 A /branches/dev/samtools/examples/00README.txt
330 A /branches/dev/samtools/examples/ex1.fa
331 A /branches/dev/samtools/examples/ex1.fa.fai
332 A /branches/dev/samtools/examples/ex1.sam.gz
336 ------------------------------------------------------------------------
337 r59 | lh3lh3 | 2008-12-22 09:38:15 +0000 (Mon, 22 Dec 2008) | 2 lines
339 M /branches/dev/samtools/ChangeLog
343 ------------------------------------------------------------------------
344 r58 | lh3lh3 | 2008-12-20 23:06:00 +0000 (Sat, 20 Dec 2008) | 3 lines
346 M /branches/dev/samtools/misc/export2sam.pl
351 ------------------------------------------------------------------------
352 r57 | lh3lh3 | 2008-12-20 15:44:20 +0000 (Sat, 20 Dec 2008) | 2 lines
354 A /branches/dev/samtools/misc/export2sam.pl
356 convert Export format to SAM; not thoroughly tested
358 ------------------------------------------------------------------------
359 r56 | lh3lh3 | 2008-12-19 22:13:28 +0000 (Fri, 19 Dec 2008) | 6 lines
361 M /branches/dev/samtools/bam_import.c
362 M /branches/dev/samtools/bam_plcmd.c
363 M /branches/dev/samtools/bam_tview.c
364 M /branches/dev/samtools/bamtk.c
365 A /branches/dev/samtools/source.dot
368 * pileup: generate maq-like simple output
369 * pileup: allow to output pileup at required sites
370 * source.dot: source file relationship graph
371 * tview: fixed a minor bug
373 ------------------------------------------------------------------------
374 r55 | lh3lh3 | 2008-12-19 20:10:26 +0000 (Fri, 19 Dec 2008) | 2 lines
376 D /branches/dev/samtools/misc/all2sam.pl
380 ------------------------------------------------------------------------
381 r54 | lh3lh3 | 2008-12-16 22:34:25 +0000 (Tue, 16 Dec 2008) | 2 lines
383 A /branches/dev/samtools/COPYING
384 M /branches/dev/samtools/bam.h
385 M /branches/dev/samtools/faidx.h
386 M /branches/dev/samtools/khash.h
387 M /branches/dev/samtools/kseq.h
388 M /branches/dev/samtools/ksort.h
389 M /branches/dev/samtools/samtools.1
391 Added copyright information and a bit more documentation. No code change.
393 ------------------------------------------------------------------------
394 r53 | lh3lh3 | 2008-12-16 13:40:18 +0000 (Tue, 16 Dec 2008) | 3 lines
396 M /branches/dev/samtools/bam.c
397 M /branches/dev/samtools/bam.h
398 M /branches/dev/samtools/bam_index.c
399 M /branches/dev/samtools/bam_maqcns.c
400 M /branches/dev/samtools/bamtk.c
403 * improved efficiency of the indel caller for spliced alignments
405 ------------------------------------------------------------------------
406 r52 | lh3lh3 | 2008-12-16 10:28:20 +0000 (Tue, 16 Dec 2008) | 3 lines
408 M /branches/dev/samtools/bam.c
409 M /branches/dev/samtools/bam.h
410 M /branches/dev/samtools/bam_aux.c
411 M /branches/dev/samtools/bam_index.c
412 M /branches/dev/samtools/bamtk.c
415 * a bit code cleanup: reduce the dependency between source files
417 ------------------------------------------------------------------------
418 r51 | lh3lh3 | 2008-12-15 14:29:32 +0000 (Mon, 15 Dec 2008) | 3 lines
420 M /branches/dev/samtools/bam_maqcns.c
421 M /branches/dev/samtools/bam_plcmd.c
422 M /branches/dev/samtools/bamtk.c
425 * fixed a memory leak
427 ------------------------------------------------------------------------
428 r50 | lh3lh3 | 2008-12-15 14:00:13 +0000 (Mon, 15 Dec 2008) | 2 lines
430 M /branches/dev/samtools/ChangeLog
431 M /branches/dev/samtools/bam.h
432 M /branches/dev/samtools/samtools.1
434 update documentation, ChangeLog and a comment
436 ------------------------------------------------------------------------
437 r49 | lh3lh3 | 2008-12-15 13:36:43 +0000 (Mon, 15 Dec 2008) | 6 lines
439 M /branches/dev/samtools/Makefile
440 M /branches/dev/samtools/bam.h
441 M /branches/dev/samtools/bam_maqcns.c
442 M /branches/dev/samtools/bam_maqcns.h
443 M /branches/dev/samtools/bam_pileup.c
444 A /branches/dev/samtools/bam_plcmd.c
445 M /branches/dev/samtools/bamtk.c
446 M /branches/dev/samtools/samtools.1
449 * moved pileup command to a separate source file
451 * added bam_cal_segend(). (NOT WORKING for spliced alignment!!!)
452 * updated documentation
454 ------------------------------------------------------------------------
455 r48 | lh3lh3 | 2008-12-12 13:55:36 +0000 (Fri, 12 Dec 2008) | 3 lines
457 M /branches/dev/samtools/bam_maqcns.c
458 M /branches/dev/samtools/bamtk.c
461 * fixed another bug in maqcns when there is a nearby deletion
463 ------------------------------------------------------------------------
464 r47 | lh3lh3 | 2008-12-12 13:42:16 +0000 (Fri, 12 Dec 2008) | 5 lines
466 M /branches/dev/samtools/bam_maqcns.c
467 M /branches/dev/samtools/bam_pileup.c
468 M /branches/dev/samtools/bamtk.c
471 * pileup: outputing consensus is now optional
472 * fixed a bug in glfgen. This bug also exists in maq's glfgen. However,
473 I am not quite sure why the previous version may have problem.
475 ------------------------------------------------------------------------
476 r46 | lh3lh3 | 2008-12-12 11:44:56 +0000 (Fri, 12 Dec 2008) | 6 lines
478 M /branches/dev/samtools/bam_pileup.c
479 M /branches/dev/samtools/bamtk.c
482 * add maq consensus to pileup. However, I will move this part to a new
483 command as strictly speaking, consensus callin is not part of pileup,
484 and imposing it would make it harder to generate for other language
487 ------------------------------------------------------------------------
488 r45 | bhandsaker | 2008-12-11 20:43:56 +0000 (Thu, 11 Dec 2008) | 2 lines
490 M /branches/dev/samtools/bgzf.c
492 Fix bug in tell() after reads that consume to the exact end of a block.
494 ------------------------------------------------------------------------
495 r44 | lh3lh3 | 2008-12-11 09:36:53 +0000 (Thu, 11 Dec 2008) | 2 lines
497 M /branches/dev/samtools/samtools.1
501 ------------------------------------------------------------------------
502 r43 | lh3lh3 | 2008-12-11 09:25:36 +0000 (Thu, 11 Dec 2008) | 4 lines
504 M /branches/dev/samtools/bam_import.c
505 M /branches/dev/samtools/bamtk.c
508 * fixed a bug in parser when there is auxiliary fields
509 * made the parser a bit more robust
511 ------------------------------------------------------------------------
512 r42 | lh3lh3 | 2008-12-10 14:57:29 +0000 (Wed, 10 Dec 2008) | 5 lines
514 M /branches/dev/samtools/bam_index.c
515 M /branches/dev/samtools/bamtk.c
516 M /branches/dev/samtools/bgzf.c
519 * fixed a bug in bgzf (only reading is affected)
520 * fixed a typo in bam_index.c
521 * in bam_index.c, check potential bugs in the underlying I/O library
523 ------------------------------------------------------------------------
524 r41 | lh3lh3 | 2008-12-10 12:53:08 +0000 (Wed, 10 Dec 2008) | 2 lines
526 M /branches/dev/samtools/samtools.1
530 ------------------------------------------------------------------------
531 r40 | lh3lh3 | 2008-12-10 11:52:10 +0000 (Wed, 10 Dec 2008) | 5 lines
533 M /branches/dev/samtools/bam.h
534 M /branches/dev/samtools/bam_pileup.c
535 M /branches/dev/samtools/bamtk.c
538 * tried to make pileup work with clipping (previously not), though NOT tested
539 * removed -v from pileup
540 * made pileup take the reference sequence
542 ------------------------------------------------------------------------
543 r39 | lh3lh3 | 2008-12-09 11:59:28 +0000 (Tue, 09 Dec 2008) | 4 lines
545 M /branches/dev/samtools/bam_import.c
546 M /branches/dev/samtools/bamtk.c
547 M /branches/dev/samtools/samtools.1
550 * in parser, recognize "=", rather than ",", as a match
551 * in parser, correctl parse "=" at the MRNM field.
553 ------------------------------------------------------------------------
554 r38 | lh3lh3 | 2008-12-09 11:39:07 +0000 (Tue, 09 Dec 2008) | 2 lines
556 M /branches/dev/samtools/misc/maq2sam.c
558 fixed a bug in handling maq flag 64 and 192
560 ------------------------------------------------------------------------
561 r37 | lh3lh3 | 2008-12-09 09:53:46 +0000 (Tue, 09 Dec 2008) | 2 lines
563 M /branches/dev/samtools/misc/md5fa.c
565 also calculate unordered md5sum check
567 ------------------------------------------------------------------------
568 r36 | lh3lh3 | 2008-12-09 09:46:21 +0000 (Tue, 09 Dec 2008) | 2 lines
570 M /branches/dev/samtools/misc/md5fa.c
572 fixed a minor bug when there are space in the sequence
574 ------------------------------------------------------------------------
575 r35 | lh3lh3 | 2008-12-09 09:40:45 +0000 (Tue, 09 Dec 2008) | 2 lines
577 M /branches/dev/samtools/misc/md5fa.c
579 fixed a potential memory leak
581 ------------------------------------------------------------------------
582 r34 | lh3lh3 | 2008-12-08 14:52:17 +0000 (Mon, 08 Dec 2008) | 2 lines
584 M /branches/dev/samtools/bam_import.c
585 M /branches/dev/samtools/bam_index.c
586 M /branches/dev/samtools/bamtk.c
588 * fixed a bug in import: bin is wrongly calculated
590 ------------------------------------------------------------------------
591 r33 | lh3lh3 | 2008-12-08 14:08:01 +0000 (Mon, 08 Dec 2008) | 2 lines
593 M /branches/dev/samtools/misc/all2sam.pl
597 ------------------------------------------------------------------------
598 r32 | lh3lh3 | 2008-12-08 12:56:02 +0000 (Mon, 08 Dec 2008) | 3 lines
600 M /branches/dev/samtools/Makefile
601 M /branches/dev/samtools/kseq.h
602 M /branches/dev/samtools/misc/Makefile
603 A /branches/dev/samtools/misc/md5.c
604 A /branches/dev/samtools/misc/md5.h
605 A /branches/dev/samtools/misc/md5fa.c
607 * fixed two warnings in kseq.h
608 * added md5sum utilities
610 ------------------------------------------------------------------------
611 r31 | lh3lh3 | 2008-12-08 11:35:29 +0000 (Mon, 08 Dec 2008) | 5 lines
613 M /branches/dev/samtools/Makefile
614 M /branches/dev/samtools/bam_import.c
615 M /branches/dev/samtools/bamtk.c
616 A /branches/dev/samtools/kseq.h
617 D /branches/dev/samtools/kstream.h
620 * replace kstream with kseq. kseq is a superset of kstream. I need the
621 extra functions in kseq.h.
622 * also compile stand-alone faidx
624 ------------------------------------------------------------------------
625 r30 | lh3lh3 | 2008-12-08 11:17:04 +0000 (Mon, 08 Dec 2008) | 3 lines
627 M /branches/dev/samtools/bam.h
628 M /branches/dev/samtools/bam_sort.c
629 M /branches/dev/samtools/bamtk.c
632 * sorting by read names is available
634 ------------------------------------------------------------------------
635 r29 | lh3lh3 | 2008-12-08 10:29:02 +0000 (Mon, 08 Dec 2008) | 3 lines
637 M /branches/dev/samtools/bam.c
638 M /branches/dev/samtools/bam.h
639 M /branches/dev/samtools/bam_import.c
640 M /branches/dev/samtools/bam_maqcns.c
641 M /branches/dev/samtools/bam_pileup.c
642 M /branches/dev/samtools/bam_sort.c
643 M /branches/dev/samtools/bam_tview.c
644 M /branches/dev/samtools/bamtk.c
645 M /branches/dev/samtools/misc/maq2sam.c
648 * format change to meet the latest specification
650 ------------------------------------------------------------------------
651 r28 | lh3lh3 | 2008-12-04 16:09:21 +0000 (Thu, 04 Dec 2008) | 3 lines
653 M /branches/dev/samtools/bam_maqcns.c
654 M /branches/dev/samtools/misc/maq2sam.c
656 * minor change in maqcns: special care when n==0
657 * change maq2sam to meet the latest specification
659 ------------------------------------------------------------------------
660 r27 | lh3lh3 | 2008-12-04 15:55:44 +0000 (Thu, 04 Dec 2008) | 2 lines
662 M /branches/dev/samtools/razf.c
663 M /branches/dev/samtools/razf.h
665 considerable code clean up in razf
667 ------------------------------------------------------------------------
668 r26 | lh3lh3 | 2008-12-04 15:08:18 +0000 (Thu, 04 Dec 2008) | 2 lines
670 M /branches/dev/samtools/ChangeLog
671 M /branches/dev/samtools/Makefile
672 M /branches/dev/samtools/faidx.c
674 make RAZF optional in faidx.c
676 ------------------------------------------------------------------------
677 r25 | lh3lh3 | 2008-12-01 15:27:22 +0000 (Mon, 01 Dec 2008) | 3 lines
679 M /branches/dev/samtools/Makefile
680 M /branches/dev/samtools/bam.h
681 M /branches/dev/samtools/bam_aux.c
682 M /branches/dev/samtools/bamtk.c
683 M /branches/dev/samtools/samtools.1
686 * added routines for retrieving aux data, NOT TESTED YET!
688 ------------------------------------------------------------------------
689 r24 | lh3lh3 | 2008-12-01 14:29:43 +0000 (Mon, 01 Dec 2008) | 5 lines
691 M /branches/dev/samtools/bam.c
692 M /branches/dev/samtools/bam_import.c
693 M /branches/dev/samtools/bam_maqcns.c
694 M /branches/dev/samtools/bamtk.c
695 M /branches/dev/samtools/bgzf.c
696 M /branches/dev/samtools/samtools.1
699 * bgzf: fixed a potential integer overflow on 32-it machines
700 * maqcns: set the minimum combined quality as 0
701 * supporting hex strings
703 ------------------------------------------------------------------------
704 r23 | lh3lh3 | 2008-11-27 17:14:37 +0000 (Thu, 27 Nov 2008) | 3 lines
706 M /branches/dev/samtools/bam_maqcns.c
707 M /branches/dev/samtools/bamtk.c
710 * fixed the bug in maqcns
712 ------------------------------------------------------------------------
713 r22 | lh3lh3 | 2008-11-27 17:08:11 +0000 (Thu, 27 Nov 2008) | 3 lines
715 M /branches/dev/samtools/Makefile
716 M /branches/dev/samtools/bam.h
717 A /branches/dev/samtools/bam_maqcns.c
718 A /branches/dev/samtools/bam_maqcns.h
719 M /branches/dev/samtools/bam_tview.c
720 M /branches/dev/samtools/bamtk.c
721 A /branches/dev/samtools/glf.h
724 * add MAQ consensus caller, currently BUGGY!
726 ------------------------------------------------------------------------
727 r21 | lh3lh3 | 2008-11-27 13:51:28 +0000 (Thu, 27 Nov 2008) | 4 lines
729 M /branches/dev/samtools/bam_pileup.c
730 M /branches/dev/samtools/bam_tview.c
731 M /branches/dev/samtools/bamtk.c
734 * tview: display padded alignment (but not P operation)
735 * better coordinates and reference sequence
737 ------------------------------------------------------------------------
738 r19 | lh3lh3 | 2008-11-27 09:26:05 +0000 (Thu, 27 Nov 2008) | 2 lines
740 A /branches/dev/samtools/ChangeLog
744 ------------------------------------------------------------------------
745 r18 | lh3lh3 | 2008-11-27 09:24:45 +0000 (Thu, 27 Nov 2008) | 3 lines
747 D /branches/dev/samtools/ChangeLog
748 A /branches/dev/samtools/ChangeLog.old (from /branches/dev/samtools/ChangeLog:6)
750 Rename ChangeLog to ChangeLog.old. This old ChangeLog is generated from
751 the log of my personal SVN repository.
753 ------------------------------------------------------------------------
754 r17 | lh3lh3 | 2008-11-27 09:22:55 +0000 (Thu, 27 Nov 2008) | 6 lines
756 M /branches/dev/samtools/Makefile
757 M /branches/dev/samtools/bamtk.c
758 M /branches/dev/samtools/bgzf.c
761 * declare fseeko and ftello as some Linux may not do this by default and
762 missing these declarations will make bgzf buggy
763 * get rid of some harmless warings
764 * use BGZF by default, now
766 ------------------------------------------------------------------------
767 r16 | lh3lh3 | 2008-11-26 21:19:11 +0000 (Wed, 26 Nov 2008) | 4 lines
769 M /branches/dev/samtools/bam_index.c
770 M /branches/dev/samtools/bamtk.c
771 M /branches/dev/samtools/razf.c
774 * fixed a bug in razf_read()
775 * give more warnings when the file is truncated (or due to bugs in I/O library)
777 ------------------------------------------------------------------------
778 r15 | lh3lh3 | 2008-11-26 20:41:39 +0000 (Wed, 26 Nov 2008) | 2 lines
780 M /branches/dev/samtools/bgzf.c
782 fixed a bug in bgzf.c at the end of the file
784 ------------------------------------------------------------------------
785 r14 | lh3lh3 | 2008-11-26 17:05:18 +0000 (Wed, 26 Nov 2008) | 4 lines
787 M /branches/dev/samtools/bamtk.c
790 * a lot happened to RAZF, although samtools itself is untouched. Better
791 also update the version number anyway to avoid confusion
793 ------------------------------------------------------------------------
794 r13 | lh3lh3 | 2008-11-26 17:03:48 +0000 (Wed, 26 Nov 2008) | 2 lines
796 M /branches/dev/samtools/razf.c
798 a change from Jue, but I think it should not matter
800 ------------------------------------------------------------------------
801 r12 | lh3lh3 | 2008-11-26 16:48:14 +0000 (Wed, 26 Nov 2008) | 3 lines
803 M /branches/dev/samtools/razf.c
805 fixed a potential bug in razf. However, it seems still buggy, just
806 rarely happens, very rarely.
808 ------------------------------------------------------------------------
809 r11 | lh3lh3 | 2008-11-26 14:02:56 +0000 (Wed, 26 Nov 2008) | 2 lines
811 M /branches/dev/samtools/razf.c
813 fixed a bug in razf, with the help of Jue
815 ------------------------------------------------------------------------
816 r10 | lh3lh3 | 2008-11-26 11:55:32 +0000 (Wed, 26 Nov 2008) | 2 lines
818 M /branches/dev/samtools/bam_index.c
822 ------------------------------------------------------------------------
823 r9 | lh3lh3 | 2008-11-26 11:37:05 +0000 (Wed, 26 Nov 2008) | 2 lines
825 M /branches/dev/samtools/Makefile
826 M /branches/dev/samtools/bam.h
827 M /branches/dev/samtools/razf.c
828 M /branches/dev/samtools/razf.h
830 * Jue has updated razf to realize Bob's scheme
832 ------------------------------------------------------------------------
833 r7 | lh3lh3 | 2008-11-25 20:37:37 +0000 (Tue, 25 Nov 2008) | 2 lines
835 A /branches/dev/samtools/samtools.1
839 ------------------------------------------------------------------------
840 r6 | lh3lh3 | 2008-11-25 20:37:16 +0000 (Tue, 25 Nov 2008) | 3 lines
842 A /branches/dev/samtools/ChangeLog
843 A /branches/dev/samtools/Makefile
844 A /branches/dev/samtools/bam.c
845 A /branches/dev/samtools/bam.h
846 A /branches/dev/samtools/bam_aux.c
847 A /branches/dev/samtools/bam_endian.h
848 A /branches/dev/samtools/bam_import.c
849 A /branches/dev/samtools/bam_index.c
850 A /branches/dev/samtools/bam_lpileup.c
851 A /branches/dev/samtools/bam_pileup.c
852 A /branches/dev/samtools/bam_sort.c
853 A /branches/dev/samtools/bam_tview.c
854 A /branches/dev/samtools/bamtk.c
855 A /branches/dev/samtools/bgzf.c
856 A /branches/dev/samtools/bgzf.h
857 A /branches/dev/samtools/bgzip.c
858 A /branches/dev/samtools/faidx.c
859 A /branches/dev/samtools/faidx.h
860 A /branches/dev/samtools/khash.h
861 A /branches/dev/samtools/ksort.h
862 A /branches/dev/samtools/kstream.h
863 A /branches/dev/samtools/misc
864 A /branches/dev/samtools/misc/Makefile
865 A /branches/dev/samtools/misc/all2sam.pl
866 A /branches/dev/samtools/misc/maq2sam.c
867 A /branches/dev/samtools/razf.c
868 A /branches/dev/samtools/razf.h
869 A /branches/dev/samtools/razip.c
870 A /branches/dev/samtools/zutil.h
872 The initial version of samtools, replicated from my local SVN repository.
873 The current version is: 0.1.0-42. All future development will happen here.
875 ------------------------------------------------------------------------
876 r5 | lh3lh3 | 2008-11-25 20:30:49 +0000 (Tue, 25 Nov 2008) | 2 lines
878 A /branches/dev/samtools
882 ------------------------------------------------------------------------