1 ------------------------------------------------------------------------
2 r129 | lh3lh3 | 2009-02-18 22:23:27 +0000 (Wed, 18 Feb 2009) | 3 lines
4 M /trunk/samtools/bam_index.c
5 M /trunk/samtools/bamtk.c
8 * fixed a bug in bam_fetch, caused by completely contained adjacent chunks
10 ------------------------------------------------------------------------
11 r128 | bhandsaker | 2009-02-18 19:06:57 +0000 (Wed, 18 Feb 2009) | 2 lines
13 M /trunk/samtools/bamtk.c
15 Fix annoying segv when invalid region specified.
17 ------------------------------------------------------------------------
18 r127 | lh3lh3 | 2009-02-17 10:49:55 +0000 (Tue, 17 Feb 2009) | 2 lines
20 D /trunk/samtools/misc/indel_filter.pl
21 A /trunk/samtools/misc/samtools.pl
23 * move indel_filter.pl to samtools.pl
25 ------------------------------------------------------------------------
26 r126 | lh3lh3 | 2009-02-14 21:22:30 +0000 (Sat, 14 Feb 2009) | 3 lines
28 M /trunk/samtools/bam_mate.c
29 M /trunk/samtools/bamtk.c
32 * fixed a bug in fixmate: SE reads are flagged as BAM_FMUNMAP
34 ------------------------------------------------------------------------
35 r125 | lh3lh3 | 2009-02-13 09:54:45 +0000 (Fri, 13 Feb 2009) | 3 lines
37 M /trunk/samtools/bam_stat.c
38 M /trunk/samtools/bamtk.c
41 * fixed a minor bug in flagstat
43 ------------------------------------------------------------------------
44 r124 | lh3lh3 | 2009-02-12 11:15:32 +0000 (Thu, 12 Feb 2009) | 3 lines
46 M /trunk/samtools/bam_maqcns.c
47 M /trunk/samtools/bamtk.c
48 M /trunk/samtools/misc/indel_filter.pl
51 * improve indel caller by setting maximum window size
53 ------------------------------------------------------------------------
54 r123 | lh3lh3 | 2009-02-12 10:30:29 +0000 (Thu, 12 Feb 2009) | 2 lines
56 M /trunk/samtools/bam_plcmd.c
57 M /trunk/samtools/bamtk.c
59 * output max mapping quality in indel line
61 ------------------------------------------------------------------------
62 r122 | lh3lh3 | 2009-02-11 10:59:10 +0000 (Wed, 11 Feb 2009) | 2 lines
64 M /trunk/samtools/misc/maq2sam.c
66 fixed a bug in generating tag AM
68 ------------------------------------------------------------------------
69 r121 | lh3lh3 | 2009-02-03 10:43:11 +0000 (Tue, 03 Feb 2009) | 2 lines
71 M /trunk/samtools/bam_index.c
72 M /trunk/samtools/bamtk.c
74 fixed a potential memory problem in indexing
76 ------------------------------------------------------------------------
77 r120 | bhandsaker | 2009-02-02 15:52:52 +0000 (Mon, 02 Feb 2009) | 2 lines
79 M /trunk/samtools/Makefile
81 Pass LIBS to recursive targets to facilitate building at Broad.
83 ------------------------------------------------------------------------
84 r119 | lh3lh3 | 2009-02-02 10:12:15 +0000 (Mon, 02 Feb 2009) | 4 lines
86 M /trunk/samtools/ChangeLog
87 M /trunk/samtools/bam_plcmd.c
88 M /trunk/samtools/bam_stat.c
89 M /trunk/samtools/bamtk.c
92 * fixed a bug in generating GLFv2 for indels
93 * improve flagstat report a little bit
95 ------------------------------------------------------------------------
96 r118 | lh3lh3 | 2009-01-29 12:33:23 +0000 (Thu, 29 Jan 2009) | 3 lines
98 M /trunk/samtools/Makefile
99 A /trunk/samtools/bam_stat.c
100 M /trunk/samtools/bamtk.c
103 * added flagstat command
105 ------------------------------------------------------------------------
106 r116 | lh3lh3 | 2009-01-28 13:31:12 +0000 (Wed, 28 Jan 2009) | 2 lines
108 M /trunk/samtools/ChangeLog
109 M /trunk/samtools/NEWS
110 M /trunk/samtools/bamtk.c
111 M /trunk/samtools/samtools.1
113 Release SAMtools-0.1.2
115 ------------------------------------------------------------------------
116 r115 | lh3lh3 | 2009-01-28 12:54:08 +0000 (Wed, 28 Jan 2009) | 2 lines
118 A /trunk/samtools/misc/indel_filter.pl
120 Script for filtering indel results
122 ------------------------------------------------------------------------
123 r114 | lh3lh3 | 2009-01-25 11:45:37 +0000 (Sun, 25 Jan 2009) | 2 lines
125 A /trunk/samtools/misc/zoom2sam.pl
129 ------------------------------------------------------------------------
130 r113 | lh3lh3 | 2009-01-24 14:25:07 +0000 (Sat, 24 Jan 2009) | 2 lines
132 A /trunk/samtools/misc/novo2sam.pl
134 add a script to convert novo alignment to SAM
136 ------------------------------------------------------------------------
137 r112 | lh3lh3 | 2009-01-23 20:57:39 +0000 (Fri, 23 Jan 2009) | 2 lines
139 M /trunk/samtools/ChangeLog
140 M /trunk/samtools/ChangeLog.old
141 M /trunk/samtools/samtools.1
143 update documentation and ChangeLog
145 ------------------------------------------------------------------------
146 r111 | lh3lh3 | 2009-01-23 19:22:59 +0000 (Fri, 23 Jan 2009) | 3 lines
148 M /trunk/samtools/bam_sort.c
149 M /trunk/samtools/bamtk.c
152 * fixed a bug in "merge" command line
154 ------------------------------------------------------------------------
155 r110 | lh3lh3 | 2009-01-22 15:36:48 +0000 (Thu, 22 Jan 2009) | 3 lines
157 M /trunk/samtools/misc/Makefile
158 A /trunk/samtools/misc/bowtie2sam.pl (from /branches/dev/samtools/misc/bowtie2sam.pl:108)
159 M /trunk/samtools/misc/export2sam.pl
160 A /trunk/samtools/misc/soap2sam.pl (from /branches/dev/samtools/misc/soap2sam.pl:108)
161 A /trunk/samtools/misc/wgsim.c (from /branches/dev/samtools/misc/wgsim.c:108)
162 A /trunk/samtools/misc/wgsim_eval.pl (from /branches/dev/samtools/misc/wgsim_eval.pl:108)
164 * merge from branches/dev/
165 * all future development will happen here
167 ------------------------------------------------------------------------
168 r109 | lh3lh3 | 2009-01-22 15:14:27 +0000 (Thu, 22 Jan 2009) | 3 lines
170 M /trunk/samtools/COPYING
171 M /trunk/samtools/ChangeLog
172 A /trunk/samtools/INSTALL (from /branches/dev/samtools/INSTALL:108)
173 M /trunk/samtools/Makefile
174 A /trunk/samtools/Makefile.lite (from /branches/dev/samtools/Makefile.lite:108)
175 M /trunk/samtools/bam.c
176 M /trunk/samtools/bam.h
177 M /trunk/samtools/bam_import.c
178 M /trunk/samtools/bam_index.c
179 M /trunk/samtools/bam_lpileup.c
180 M /trunk/samtools/bam_maqcns.c
181 M /trunk/samtools/bam_maqcns.h
182 A /trunk/samtools/bam_mate.c (from /branches/dev/samtools/bam_mate.c:108)
183 M /trunk/samtools/bam_pileup.c
184 M /trunk/samtools/bam_plcmd.c
185 A /trunk/samtools/bam_rmdup.c (from /branches/dev/samtools/bam_rmdup.c:108)
186 M /trunk/samtools/bam_sort.c
187 M /trunk/samtools/bamtk.c
188 M /trunk/samtools/bgzf.h
189 M /trunk/samtools/examples/00README.txt
190 A /trunk/samtools/examples/Makefile (from /branches/dev/samtools/examples/Makefile:108)
191 D /trunk/samtools/examples/ex1.fa.fai
192 M /trunk/samtools/examples/ex1.sam.gz
193 M /trunk/samtools/faidx.c
194 A /trunk/samtools/glf.c (from /branches/dev/samtools/glf.c:108)
195 M /trunk/samtools/glf.h
196 M /trunk/samtools/misc/Makefile
197 M /trunk/samtools/misc/maq2sam.c
198 M /trunk/samtools/razf.c
199 M /trunk/samtools/source.dot
201 * Merge from branches/dev/
202 * all future development will happen here at trunk/
204 ------------------------------------------------------------------------
205 r79 | bhandsaker | 2009-01-07 21:42:15 +0000 (Wed, 07 Jan 2009) | 2 lines
207 M /trunk/samtools/bam_maqcns.c
208 M /trunk/samtools/bam_tview.c
210 Fix problem with compiling without curses.
212 ------------------------------------------------------------------------
213 r63 | lh3lh3 | 2008-12-22 15:58:02 +0000 (Mon, 22 Dec 2008) | 2 lines
215 A /trunk/samtools (from /branches/dev/samtools:62)
219 ------------------------------------------------------------------------
220 r62 | lh3lh3 | 2008-12-22 15:55:13 +0000 (Mon, 22 Dec 2008) | 2 lines
222 A /branches/dev/samtools/NEWS
223 M /branches/dev/samtools/bamtk.c
224 M /branches/dev/samtools/samtools.1
226 Release samtools-0.1.1
228 ------------------------------------------------------------------------
229 r61 | lh3lh3 | 2008-12-22 15:46:08 +0000 (Mon, 22 Dec 2008) | 10 lines
231 M /branches/dev/samtools/bam_aux.c
232 M /branches/dev/samtools/bam_index.c
233 M /branches/dev/samtools/bam_plcmd.c
234 M /branches/dev/samtools/bam_tview.c
235 M /branches/dev/samtools/bamtk.c
236 M /branches/dev/samtools/razf.c
237 M /branches/dev/samtools/samtools.1
240 * fixed a bug in razf.c: reset z_eof when razf_seek() is called
241 * fixed a memory leak in parsing a region
242 * changed pileup a little bit when -s is in use: output ^ and $
243 * when a bam is not indexed, output more meaningful error message
244 * fixed a bug in indexing for small alignment
245 * fixed a bug in the viewer when we come to the end of a reference file
246 * updated documentation
247 * prepare to release 0.1.1
249 ------------------------------------------------------------------------
250 r60 | lh3lh3 | 2008-12-22 15:10:16 +0000 (Mon, 22 Dec 2008) | 2 lines
252 A /branches/dev/samtools/examples
253 A /branches/dev/samtools/examples/00README.txt
254 A /branches/dev/samtools/examples/ex1.fa
255 A /branches/dev/samtools/examples/ex1.fa.fai
256 A /branches/dev/samtools/examples/ex1.sam.gz
260 ------------------------------------------------------------------------
261 r59 | lh3lh3 | 2008-12-22 09:38:15 +0000 (Mon, 22 Dec 2008) | 2 lines
263 M /branches/dev/samtools/ChangeLog
267 ------------------------------------------------------------------------
268 r58 | lh3lh3 | 2008-12-20 23:06:00 +0000 (Sat, 20 Dec 2008) | 3 lines
270 M /branches/dev/samtools/misc/export2sam.pl
275 ------------------------------------------------------------------------
276 r57 | lh3lh3 | 2008-12-20 15:44:20 +0000 (Sat, 20 Dec 2008) | 2 lines
278 A /branches/dev/samtools/misc/export2sam.pl
280 convert Export format to SAM; not thoroughly tested
282 ------------------------------------------------------------------------
283 r56 | lh3lh3 | 2008-12-19 22:13:28 +0000 (Fri, 19 Dec 2008) | 6 lines
285 M /branches/dev/samtools/bam_import.c
286 M /branches/dev/samtools/bam_plcmd.c
287 M /branches/dev/samtools/bam_tview.c
288 M /branches/dev/samtools/bamtk.c
289 A /branches/dev/samtools/source.dot
292 * pileup: generate maq-like simple output
293 * pileup: allow to output pileup at required sites
294 * source.dot: source file relationship graph
295 * tview: fixed a minor bug
297 ------------------------------------------------------------------------
298 r55 | lh3lh3 | 2008-12-19 20:10:26 +0000 (Fri, 19 Dec 2008) | 2 lines
300 D /branches/dev/samtools/misc/all2sam.pl
304 ------------------------------------------------------------------------
305 r54 | lh3lh3 | 2008-12-16 22:34:25 +0000 (Tue, 16 Dec 2008) | 2 lines
307 A /branches/dev/samtools/COPYING
308 M /branches/dev/samtools/bam.h
309 M /branches/dev/samtools/faidx.h
310 M /branches/dev/samtools/khash.h
311 M /branches/dev/samtools/kseq.h
312 M /branches/dev/samtools/ksort.h
313 M /branches/dev/samtools/samtools.1
315 Added copyright information and a bit more documentation. No code change.
317 ------------------------------------------------------------------------
318 r53 | lh3lh3 | 2008-12-16 13:40:18 +0000 (Tue, 16 Dec 2008) | 3 lines
320 M /branches/dev/samtools/bam.c
321 M /branches/dev/samtools/bam.h
322 M /branches/dev/samtools/bam_index.c
323 M /branches/dev/samtools/bam_maqcns.c
324 M /branches/dev/samtools/bamtk.c
327 * improved efficiency of the indel caller for spliced alignments
329 ------------------------------------------------------------------------
330 r52 | lh3lh3 | 2008-12-16 10:28:20 +0000 (Tue, 16 Dec 2008) | 3 lines
332 M /branches/dev/samtools/bam.c
333 M /branches/dev/samtools/bam.h
334 M /branches/dev/samtools/bam_aux.c
335 M /branches/dev/samtools/bam_index.c
336 M /branches/dev/samtools/bamtk.c
339 * a bit code cleanup: reduce the dependency between source files
341 ------------------------------------------------------------------------
342 r51 | lh3lh3 | 2008-12-15 14:29:32 +0000 (Mon, 15 Dec 2008) | 3 lines
344 M /branches/dev/samtools/bam_maqcns.c
345 M /branches/dev/samtools/bam_plcmd.c
346 M /branches/dev/samtools/bamtk.c
349 * fixed a memory leak
351 ------------------------------------------------------------------------
352 r50 | lh3lh3 | 2008-12-15 14:00:13 +0000 (Mon, 15 Dec 2008) | 2 lines
354 M /branches/dev/samtools/ChangeLog
355 M /branches/dev/samtools/bam.h
356 M /branches/dev/samtools/samtools.1
358 update documentation, ChangeLog and a comment
360 ------------------------------------------------------------------------
361 r49 | lh3lh3 | 2008-12-15 13:36:43 +0000 (Mon, 15 Dec 2008) | 6 lines
363 M /branches/dev/samtools/Makefile
364 M /branches/dev/samtools/bam.h
365 M /branches/dev/samtools/bam_maqcns.c
366 M /branches/dev/samtools/bam_maqcns.h
367 M /branches/dev/samtools/bam_pileup.c
368 A /branches/dev/samtools/bam_plcmd.c
369 M /branches/dev/samtools/bamtk.c
370 M /branches/dev/samtools/samtools.1
373 * moved pileup command to a separate source file
375 * added bam_cal_segend(). (NOT WORKING for spliced alignment!!!)
376 * updated documentation
378 ------------------------------------------------------------------------
379 r48 | lh3lh3 | 2008-12-12 13:55:36 +0000 (Fri, 12 Dec 2008) | 3 lines
381 M /branches/dev/samtools/bam_maqcns.c
382 M /branches/dev/samtools/bamtk.c
385 * fixed another bug in maqcns when there is a nearby deletion
387 ------------------------------------------------------------------------
388 r47 | lh3lh3 | 2008-12-12 13:42:16 +0000 (Fri, 12 Dec 2008) | 5 lines
390 M /branches/dev/samtools/bam_maqcns.c
391 M /branches/dev/samtools/bam_pileup.c
392 M /branches/dev/samtools/bamtk.c
395 * pileup: outputing consensus is now optional
396 * fixed a bug in glfgen. This bug also exists in maq's glfgen. However,
397 I am not quite sure why the previous version may have problem.
399 ------------------------------------------------------------------------
400 r46 | lh3lh3 | 2008-12-12 11:44:56 +0000 (Fri, 12 Dec 2008) | 6 lines
402 M /branches/dev/samtools/bam_pileup.c
403 M /branches/dev/samtools/bamtk.c
406 * add maq consensus to pileup. However, I will move this part to a new
407 command as strictly speaking, consensus callin is not part of pileup,
408 and imposing it would make it harder to generate for other language
411 ------------------------------------------------------------------------
412 r45 | bhandsaker | 2008-12-11 20:43:56 +0000 (Thu, 11 Dec 2008) | 2 lines
414 M /branches/dev/samtools/bgzf.c
416 Fix bug in tell() after reads that consume to the exact end of a block.
418 ------------------------------------------------------------------------
419 r44 | lh3lh3 | 2008-12-11 09:36:53 +0000 (Thu, 11 Dec 2008) | 2 lines
421 M /branches/dev/samtools/samtools.1
425 ------------------------------------------------------------------------
426 r43 | lh3lh3 | 2008-12-11 09:25:36 +0000 (Thu, 11 Dec 2008) | 4 lines
428 M /branches/dev/samtools/bam_import.c
429 M /branches/dev/samtools/bamtk.c
432 * fixed a bug in parser when there is auxiliary fields
433 * made the parser a bit more robust
435 ------------------------------------------------------------------------
436 r42 | lh3lh3 | 2008-12-10 14:57:29 +0000 (Wed, 10 Dec 2008) | 5 lines
438 M /branches/dev/samtools/bam_index.c
439 M /branches/dev/samtools/bamtk.c
440 M /branches/dev/samtools/bgzf.c
443 * fixed a bug in bgzf (only reading is affected)
444 * fixed a typo in bam_index.c
445 * in bam_index.c, check potential bugs in the underlying I/O library
447 ------------------------------------------------------------------------
448 r41 | lh3lh3 | 2008-12-10 12:53:08 +0000 (Wed, 10 Dec 2008) | 2 lines
450 M /branches/dev/samtools/samtools.1
454 ------------------------------------------------------------------------
455 r40 | lh3lh3 | 2008-12-10 11:52:10 +0000 (Wed, 10 Dec 2008) | 5 lines
457 M /branches/dev/samtools/bam.h
458 M /branches/dev/samtools/bam_pileup.c
459 M /branches/dev/samtools/bamtk.c
462 * tried to make pileup work with clipping (previously not), though NOT tested
463 * removed -v from pileup
464 * made pileup take the reference sequence
466 ------------------------------------------------------------------------
467 r39 | lh3lh3 | 2008-12-09 11:59:28 +0000 (Tue, 09 Dec 2008) | 4 lines
469 M /branches/dev/samtools/bam_import.c
470 M /branches/dev/samtools/bamtk.c
471 M /branches/dev/samtools/samtools.1
474 * in parser, recognize "=", rather than ",", as a match
475 * in parser, correctl parse "=" at the MRNM field.
477 ------------------------------------------------------------------------
478 r38 | lh3lh3 | 2008-12-09 11:39:07 +0000 (Tue, 09 Dec 2008) | 2 lines
480 M /branches/dev/samtools/misc/maq2sam.c
482 fixed a bug in handling maq flag 64 and 192
484 ------------------------------------------------------------------------
485 r37 | lh3lh3 | 2008-12-09 09:53:46 +0000 (Tue, 09 Dec 2008) | 2 lines
487 M /branches/dev/samtools/misc/md5fa.c
489 also calculate unordered md5sum check
491 ------------------------------------------------------------------------
492 r36 | lh3lh3 | 2008-12-09 09:46:21 +0000 (Tue, 09 Dec 2008) | 2 lines
494 M /branches/dev/samtools/misc/md5fa.c
496 fixed a minor bug when there are space in the sequence
498 ------------------------------------------------------------------------
499 r35 | lh3lh3 | 2008-12-09 09:40:45 +0000 (Tue, 09 Dec 2008) | 2 lines
501 M /branches/dev/samtools/misc/md5fa.c
503 fixed a potential memory leak
505 ------------------------------------------------------------------------
506 r34 | lh3lh3 | 2008-12-08 14:52:17 +0000 (Mon, 08 Dec 2008) | 2 lines
508 M /branches/dev/samtools/bam_import.c
509 M /branches/dev/samtools/bam_index.c
510 M /branches/dev/samtools/bamtk.c
512 * fixed a bug in import: bin is wrongly calculated
514 ------------------------------------------------------------------------
515 r33 | lh3lh3 | 2008-12-08 14:08:01 +0000 (Mon, 08 Dec 2008) | 2 lines
517 M /branches/dev/samtools/misc/all2sam.pl
521 ------------------------------------------------------------------------
522 r32 | lh3lh3 | 2008-12-08 12:56:02 +0000 (Mon, 08 Dec 2008) | 3 lines
524 M /branches/dev/samtools/Makefile
525 M /branches/dev/samtools/kseq.h
526 M /branches/dev/samtools/misc/Makefile
527 A /branches/dev/samtools/misc/md5.c
528 A /branches/dev/samtools/misc/md5.h
529 A /branches/dev/samtools/misc/md5fa.c
531 * fixed two warnings in kseq.h
532 * added md5sum utilities
534 ------------------------------------------------------------------------
535 r31 | lh3lh3 | 2008-12-08 11:35:29 +0000 (Mon, 08 Dec 2008) | 5 lines
537 M /branches/dev/samtools/Makefile
538 M /branches/dev/samtools/bam_import.c
539 M /branches/dev/samtools/bamtk.c
540 A /branches/dev/samtools/kseq.h
541 D /branches/dev/samtools/kstream.h
544 * replace kstream with kseq. kseq is a superset of kstream. I need the
545 extra functions in kseq.h.
546 * also compile stand-alone faidx
548 ------------------------------------------------------------------------
549 r30 | lh3lh3 | 2008-12-08 11:17:04 +0000 (Mon, 08 Dec 2008) | 3 lines
551 M /branches/dev/samtools/bam.h
552 M /branches/dev/samtools/bam_sort.c
553 M /branches/dev/samtools/bamtk.c
556 * sorting by read names is available
558 ------------------------------------------------------------------------
559 r29 | lh3lh3 | 2008-12-08 10:29:02 +0000 (Mon, 08 Dec 2008) | 3 lines
561 M /branches/dev/samtools/bam.c
562 M /branches/dev/samtools/bam.h
563 M /branches/dev/samtools/bam_import.c
564 M /branches/dev/samtools/bam_maqcns.c
565 M /branches/dev/samtools/bam_pileup.c
566 M /branches/dev/samtools/bam_sort.c
567 M /branches/dev/samtools/bam_tview.c
568 M /branches/dev/samtools/bamtk.c
569 M /branches/dev/samtools/misc/maq2sam.c
572 * format change to meet the latest specification
574 ------------------------------------------------------------------------
575 r28 | lh3lh3 | 2008-12-04 16:09:21 +0000 (Thu, 04 Dec 2008) | 3 lines
577 M /branches/dev/samtools/bam_maqcns.c
578 M /branches/dev/samtools/misc/maq2sam.c
580 * minor change in maqcns: special care when n==0
581 * change maq2sam to meet the latest specification
583 ------------------------------------------------------------------------
584 r27 | lh3lh3 | 2008-12-04 15:55:44 +0000 (Thu, 04 Dec 2008) | 2 lines
586 M /branches/dev/samtools/razf.c
587 M /branches/dev/samtools/razf.h
589 considerable code clean up in razf
591 ------------------------------------------------------------------------
592 r26 | lh3lh3 | 2008-12-04 15:08:18 +0000 (Thu, 04 Dec 2008) | 2 lines
594 M /branches/dev/samtools/ChangeLog
595 M /branches/dev/samtools/Makefile
596 M /branches/dev/samtools/faidx.c
598 make RAZF optional in faidx.c
600 ------------------------------------------------------------------------
601 r25 | lh3lh3 | 2008-12-01 15:27:22 +0000 (Mon, 01 Dec 2008) | 3 lines
603 M /branches/dev/samtools/Makefile
604 M /branches/dev/samtools/bam.h
605 M /branches/dev/samtools/bam_aux.c
606 M /branches/dev/samtools/bamtk.c
607 M /branches/dev/samtools/samtools.1
610 * added routines for retrieving aux data, NOT TESTED YET!
612 ------------------------------------------------------------------------
613 r24 | lh3lh3 | 2008-12-01 14:29:43 +0000 (Mon, 01 Dec 2008) | 5 lines
615 M /branches/dev/samtools/bam.c
616 M /branches/dev/samtools/bam_import.c
617 M /branches/dev/samtools/bam_maqcns.c
618 M /branches/dev/samtools/bamtk.c
619 M /branches/dev/samtools/bgzf.c
620 M /branches/dev/samtools/samtools.1
623 * bgzf: fixed a potential integer overflow on 32-it machines
624 * maqcns: set the minimum combined quality as 0
625 * supporting hex strings
627 ------------------------------------------------------------------------
628 r23 | lh3lh3 | 2008-11-27 17:14:37 +0000 (Thu, 27 Nov 2008) | 3 lines
630 M /branches/dev/samtools/bam_maqcns.c
631 M /branches/dev/samtools/bamtk.c
634 * fixed the bug in maqcns
636 ------------------------------------------------------------------------
637 r22 | lh3lh3 | 2008-11-27 17:08:11 +0000 (Thu, 27 Nov 2008) | 3 lines
639 M /branches/dev/samtools/Makefile
640 M /branches/dev/samtools/bam.h
641 A /branches/dev/samtools/bam_maqcns.c
642 A /branches/dev/samtools/bam_maqcns.h
643 M /branches/dev/samtools/bam_tview.c
644 M /branches/dev/samtools/bamtk.c
645 A /branches/dev/samtools/glf.h
648 * add MAQ consensus caller, currently BUGGY!
650 ------------------------------------------------------------------------
651 r21 | lh3lh3 | 2008-11-27 13:51:28 +0000 (Thu, 27 Nov 2008) | 4 lines
653 M /branches/dev/samtools/bam_pileup.c
654 M /branches/dev/samtools/bam_tview.c
655 M /branches/dev/samtools/bamtk.c
658 * tview: display padded alignment (but not P operation)
659 * better coordinates and reference sequence
661 ------------------------------------------------------------------------
662 r19 | lh3lh3 | 2008-11-27 09:26:05 +0000 (Thu, 27 Nov 2008) | 2 lines
664 A /branches/dev/samtools/ChangeLog
668 ------------------------------------------------------------------------
669 r18 | lh3lh3 | 2008-11-27 09:24:45 +0000 (Thu, 27 Nov 2008) | 3 lines
671 D /branches/dev/samtools/ChangeLog
672 A /branches/dev/samtools/ChangeLog.old (from /branches/dev/samtools/ChangeLog:6)
674 Rename ChangeLog to ChangeLog.old. This old ChangeLog is generated from
675 the log of my personal SVN repository.
677 ------------------------------------------------------------------------
678 r17 | lh3lh3 | 2008-11-27 09:22:55 +0000 (Thu, 27 Nov 2008) | 6 lines
680 M /branches/dev/samtools/Makefile
681 M /branches/dev/samtools/bamtk.c
682 M /branches/dev/samtools/bgzf.c
685 * declare fseeko and ftello as some Linux may not do this by default and
686 missing these declarations will make bgzf buggy
687 * get rid of some harmless warings
688 * use BGZF by default, now
690 ------------------------------------------------------------------------
691 r16 | lh3lh3 | 2008-11-26 21:19:11 +0000 (Wed, 26 Nov 2008) | 4 lines
693 M /branches/dev/samtools/bam_index.c
694 M /branches/dev/samtools/bamtk.c
695 M /branches/dev/samtools/razf.c
698 * fixed a bug in razf_read()
699 * give more warnings when the file is truncated (or due to bugs in I/O library)
701 ------------------------------------------------------------------------
702 r15 | lh3lh3 | 2008-11-26 20:41:39 +0000 (Wed, 26 Nov 2008) | 2 lines
704 M /branches/dev/samtools/bgzf.c
706 fixed a bug in bgzf.c at the end of the file
708 ------------------------------------------------------------------------
709 r14 | lh3lh3 | 2008-11-26 17:05:18 +0000 (Wed, 26 Nov 2008) | 4 lines
711 M /branches/dev/samtools/bamtk.c
714 * a lot happened to RAZF, although samtools itself is untouched. Better
715 also update the version number anyway to avoid confusion
717 ------------------------------------------------------------------------
718 r13 | lh3lh3 | 2008-11-26 17:03:48 +0000 (Wed, 26 Nov 2008) | 2 lines
720 M /branches/dev/samtools/razf.c
722 a change from Jue, but I think it should not matter
724 ------------------------------------------------------------------------
725 r12 | lh3lh3 | 2008-11-26 16:48:14 +0000 (Wed, 26 Nov 2008) | 3 lines
727 M /branches/dev/samtools/razf.c
729 fixed a potential bug in razf. However, it seems still buggy, just
730 rarely happens, very rarely.
732 ------------------------------------------------------------------------
733 r11 | lh3lh3 | 2008-11-26 14:02:56 +0000 (Wed, 26 Nov 2008) | 2 lines
735 M /branches/dev/samtools/razf.c
737 fixed a bug in razf, with the help of Jue
739 ------------------------------------------------------------------------
740 r10 | lh3lh3 | 2008-11-26 11:55:32 +0000 (Wed, 26 Nov 2008) | 2 lines
742 M /branches/dev/samtools/bam_index.c
746 ------------------------------------------------------------------------
747 r9 | lh3lh3 | 2008-11-26 11:37:05 +0000 (Wed, 26 Nov 2008) | 2 lines
749 M /branches/dev/samtools/Makefile
750 M /branches/dev/samtools/bam.h
751 M /branches/dev/samtools/razf.c
752 M /branches/dev/samtools/razf.h
754 * Jue has updated razf to realize Bob's scheme
756 ------------------------------------------------------------------------
757 r7 | lh3lh3 | 2008-11-25 20:37:37 +0000 (Tue, 25 Nov 2008) | 2 lines
759 A /branches/dev/samtools/samtools.1
763 ------------------------------------------------------------------------
764 r6 | lh3lh3 | 2008-11-25 20:37:16 +0000 (Tue, 25 Nov 2008) | 3 lines
766 A /branches/dev/samtools/ChangeLog
767 A /branches/dev/samtools/Makefile
768 A /branches/dev/samtools/bam.c
769 A /branches/dev/samtools/bam.h
770 A /branches/dev/samtools/bam_aux.c
771 A /branches/dev/samtools/bam_endian.h
772 A /branches/dev/samtools/bam_import.c
773 A /branches/dev/samtools/bam_index.c
774 A /branches/dev/samtools/bam_lpileup.c
775 A /branches/dev/samtools/bam_pileup.c
776 A /branches/dev/samtools/bam_sort.c
777 A /branches/dev/samtools/bam_tview.c
778 A /branches/dev/samtools/bamtk.c
779 A /branches/dev/samtools/bgzf.c
780 A /branches/dev/samtools/bgzf.h
781 A /branches/dev/samtools/bgzip.c
782 A /branches/dev/samtools/faidx.c
783 A /branches/dev/samtools/faidx.h
784 A /branches/dev/samtools/khash.h
785 A /branches/dev/samtools/ksort.h
786 A /branches/dev/samtools/kstream.h
787 A /branches/dev/samtools/misc
788 A /branches/dev/samtools/misc/Makefile
789 A /branches/dev/samtools/misc/all2sam.pl
790 A /branches/dev/samtools/misc/maq2sam.c
791 A /branches/dev/samtools/razf.c
792 A /branches/dev/samtools/razf.h
793 A /branches/dev/samtools/razip.c
794 A /branches/dev/samtools/zutil.h
796 The initial version of samtools, replicated from my local SVN repository.
797 The current version is: 0.1.0-42. All future development will happen here.
799 ------------------------------------------------------------------------
800 r5 | lh3lh3 | 2008-11-25 20:30:49 +0000 (Tue, 25 Nov 2008) | 2 lines
802 A /branches/dev/samtools
806 ------------------------------------------------------------------------