1 ------------------------------------------------------------------------
2 r58 | lh3lh3 | 2008-12-20 23:06:00 +0000 (Sat, 20 Dec 2008) | 3 lines
4 M /branches/dev/samtools/misc/export2sam.pl
9 ------------------------------------------------------------------------
10 r57 | lh3lh3 | 2008-12-20 15:44:20 +0000 (Sat, 20 Dec 2008) | 2 lines
12 A /branches/dev/samtools/misc/export2sam.pl
14 convert Export format to SAM; not thoroughly tested
16 ------------------------------------------------------------------------
17 r56 | lh3lh3 | 2008-12-19 22:13:28 +0000 (Fri, 19 Dec 2008) | 6 lines
19 M /branches/dev/samtools/bam_import.c
20 M /branches/dev/samtools/bam_plcmd.c
21 M /branches/dev/samtools/bam_tview.c
22 M /branches/dev/samtools/bamtk.c
23 A /branches/dev/samtools/source.dot
26 * pileup: generate maq-like simple output
27 * pileup: allow to output pileup at required sites
28 * source.dot: source file relationship graph
29 * tview: fixed a minor bug
31 ------------------------------------------------------------------------
32 r55 | lh3lh3 | 2008-12-19 20:10:26 +0000 (Fri, 19 Dec 2008) | 2 lines
34 D /branches/dev/samtools/misc/all2sam.pl
38 ------------------------------------------------------------------------
39 r54 | lh3lh3 | 2008-12-16 22:34:25 +0000 (Tue, 16 Dec 2008) | 2 lines
41 A /branches/dev/samtools/COPYING
42 M /branches/dev/samtools/bam.h
43 M /branches/dev/samtools/faidx.h
44 M /branches/dev/samtools/khash.h
45 M /branches/dev/samtools/kseq.h
46 M /branches/dev/samtools/ksort.h
47 M /branches/dev/samtools/samtools.1
49 Added copyright information and a bit more documentation. No code change.
51 ------------------------------------------------------------------------
52 r53 | lh3lh3 | 2008-12-16 13:40:18 +0000 (Tue, 16 Dec 2008) | 3 lines
54 M /branches/dev/samtools/bam.c
55 M /branches/dev/samtools/bam.h
56 M /branches/dev/samtools/bam_index.c
57 M /branches/dev/samtools/bam_maqcns.c
58 M /branches/dev/samtools/bamtk.c
61 * improved efficiency of the indel caller for spliced alignments
63 ------------------------------------------------------------------------
64 r52 | lh3lh3 | 2008-12-16 10:28:20 +0000 (Tue, 16 Dec 2008) | 3 lines
66 M /branches/dev/samtools/bam.c
67 M /branches/dev/samtools/bam.h
68 M /branches/dev/samtools/bam_aux.c
69 M /branches/dev/samtools/bam_index.c
70 M /branches/dev/samtools/bamtk.c
73 * a bit code cleanup: reduce the dependency between source files
75 ------------------------------------------------------------------------
76 r51 | lh3lh3 | 2008-12-15 14:29:32 +0000 (Mon, 15 Dec 2008) | 3 lines
78 M /branches/dev/samtools/bam_maqcns.c
79 M /branches/dev/samtools/bam_plcmd.c
80 M /branches/dev/samtools/bamtk.c
85 ------------------------------------------------------------------------
86 r50 | lh3lh3 | 2008-12-15 14:00:13 +0000 (Mon, 15 Dec 2008) | 2 lines
88 M /branches/dev/samtools/ChangeLog
89 M /branches/dev/samtools/bam.h
90 M /branches/dev/samtools/samtools.1
92 update documentation, ChangeLog and a comment
94 ------------------------------------------------------------------------
95 r49 | lh3lh3 | 2008-12-15 13:36:43 +0000 (Mon, 15 Dec 2008) | 6 lines
97 M /branches/dev/samtools/Makefile
98 M /branches/dev/samtools/bam.h
99 M /branches/dev/samtools/bam_maqcns.c
100 M /branches/dev/samtools/bam_maqcns.h
101 M /branches/dev/samtools/bam_pileup.c
102 A /branches/dev/samtools/bam_plcmd.c
103 M /branches/dev/samtools/bamtk.c
104 M /branches/dev/samtools/samtools.1
107 * moved pileup command to a separate source file
109 * added bam_cal_segend(). (NOT WORKING for spliced alignment!!!)
110 * updated documentation
112 ------------------------------------------------------------------------
113 r48 | lh3lh3 | 2008-12-12 13:55:36 +0000 (Fri, 12 Dec 2008) | 3 lines
115 M /branches/dev/samtools/bam_maqcns.c
116 M /branches/dev/samtools/bamtk.c
119 * fixed another bug in maqcns when there is a nearby deletion
121 ------------------------------------------------------------------------
122 r47 | lh3lh3 | 2008-12-12 13:42:16 +0000 (Fri, 12 Dec 2008) | 5 lines
124 M /branches/dev/samtools/bam_maqcns.c
125 M /branches/dev/samtools/bam_pileup.c
126 M /branches/dev/samtools/bamtk.c
129 * pileup: outputing consensus is now optional
130 * fixed a bug in glfgen. This bug also exists in maq's glfgen. However,
131 I am not quite sure why the previous version may have problem.
133 ------------------------------------------------------------------------
134 r46 | lh3lh3 | 2008-12-12 11:44:56 +0000 (Fri, 12 Dec 2008) | 6 lines
136 M /branches/dev/samtools/bam_pileup.c
137 M /branches/dev/samtools/bamtk.c
140 * add maq consensus to pileup. However, I will move this part to a new
141 command as strictly speaking, consensus callin is not part of pileup,
142 and imposing it would make it harder to generate for other language
145 ------------------------------------------------------------------------
146 r45 | bhandsaker | 2008-12-11 20:43:56 +0000 (Thu, 11 Dec 2008) | 2 lines
148 M /branches/dev/samtools/bgzf.c
150 Fix bug in tell() after reads that consume to the exact end of a block.
152 ------------------------------------------------------------------------
153 r44 | lh3lh3 | 2008-12-11 09:36:53 +0000 (Thu, 11 Dec 2008) | 2 lines
155 M /branches/dev/samtools/samtools.1
159 ------------------------------------------------------------------------
160 r43 | lh3lh3 | 2008-12-11 09:25:36 +0000 (Thu, 11 Dec 2008) | 4 lines
162 M /branches/dev/samtools/bam_import.c
163 M /branches/dev/samtools/bamtk.c
166 * fixed a bug in parser when there is auxiliary fields
167 * made the parser a bit more robust
169 ------------------------------------------------------------------------
170 r42 | lh3lh3 | 2008-12-10 14:57:29 +0000 (Wed, 10 Dec 2008) | 5 lines
172 M /branches/dev/samtools/bam_index.c
173 M /branches/dev/samtools/bamtk.c
174 M /branches/dev/samtools/bgzf.c
177 * fixed a bug in bgzf (only reading is affected)
178 * fixed a typo in bam_index.c
179 * in bam_index.c, check potential bugs in the underlying I/O library
181 ------------------------------------------------------------------------
182 r41 | lh3lh3 | 2008-12-10 12:53:08 +0000 (Wed, 10 Dec 2008) | 2 lines
184 M /branches/dev/samtools/samtools.1
188 ------------------------------------------------------------------------
189 r40 | lh3lh3 | 2008-12-10 11:52:10 +0000 (Wed, 10 Dec 2008) | 5 lines
191 M /branches/dev/samtools/bam.h
192 M /branches/dev/samtools/bam_pileup.c
193 M /branches/dev/samtools/bamtk.c
196 * tried to make pileup work with clipping (previously not), though NOT tested
197 * removed -v from pileup
198 * made pileup take the reference sequence
200 ------------------------------------------------------------------------
201 r39 | lh3lh3 | 2008-12-09 11:59:28 +0000 (Tue, 09 Dec 2008) | 4 lines
203 M /branches/dev/samtools/bam_import.c
204 M /branches/dev/samtools/bamtk.c
205 M /branches/dev/samtools/samtools.1
208 * in parser, recognize "=", rather than ",", as a match
209 * in parser, correctl parse "=" at the MRNM field.
211 ------------------------------------------------------------------------
212 r38 | lh3lh3 | 2008-12-09 11:39:07 +0000 (Tue, 09 Dec 2008) | 2 lines
214 M /branches/dev/samtools/misc/maq2sam.c
216 fixed a bug in handling maq flag 64 and 192
218 ------------------------------------------------------------------------
219 r37 | lh3lh3 | 2008-12-09 09:53:46 +0000 (Tue, 09 Dec 2008) | 2 lines
221 M /branches/dev/samtools/misc/md5fa.c
223 also calculate unordered md5sum check
225 ------------------------------------------------------------------------
226 r36 | lh3lh3 | 2008-12-09 09:46:21 +0000 (Tue, 09 Dec 2008) | 2 lines
228 M /branches/dev/samtools/misc/md5fa.c
230 fixed a minor bug when there are space in the sequence
232 ------------------------------------------------------------------------
233 r35 | lh3lh3 | 2008-12-09 09:40:45 +0000 (Tue, 09 Dec 2008) | 2 lines
235 M /branches/dev/samtools/misc/md5fa.c
237 fixed a potential memory leak
239 ------------------------------------------------------------------------
240 r34 | lh3lh3 | 2008-12-08 14:52:17 +0000 (Mon, 08 Dec 2008) | 2 lines
242 M /branches/dev/samtools/bam_import.c
243 M /branches/dev/samtools/bam_index.c
244 M /branches/dev/samtools/bamtk.c
246 * fixed a bug in import: bin is wrongly calculated
248 ------------------------------------------------------------------------
249 r33 | lh3lh3 | 2008-12-08 14:08:01 +0000 (Mon, 08 Dec 2008) | 2 lines
251 M /branches/dev/samtools/misc/all2sam.pl
255 ------------------------------------------------------------------------
256 r32 | lh3lh3 | 2008-12-08 12:56:02 +0000 (Mon, 08 Dec 2008) | 3 lines
258 M /branches/dev/samtools/Makefile
259 M /branches/dev/samtools/kseq.h
260 M /branches/dev/samtools/misc/Makefile
261 A /branches/dev/samtools/misc/md5.c
262 A /branches/dev/samtools/misc/md5.h
263 A /branches/dev/samtools/misc/md5fa.c
265 * fixed two warnings in kseq.h
266 * added md5sum utilities
268 ------------------------------------------------------------------------
269 r31 | lh3lh3 | 2008-12-08 11:35:29 +0000 (Mon, 08 Dec 2008) | 5 lines
271 M /branches/dev/samtools/Makefile
272 M /branches/dev/samtools/bam_import.c
273 M /branches/dev/samtools/bamtk.c
274 A /branches/dev/samtools/kseq.h
275 D /branches/dev/samtools/kstream.h
278 * replace kstream with kseq. kseq is a superset of kstream. I need the
279 extra functions in kseq.h.
280 * also compile stand-alone faidx
282 ------------------------------------------------------------------------
283 r30 | lh3lh3 | 2008-12-08 11:17:04 +0000 (Mon, 08 Dec 2008) | 3 lines
285 M /branches/dev/samtools/bam.h
286 M /branches/dev/samtools/bam_sort.c
287 M /branches/dev/samtools/bamtk.c
290 * sorting by read names is available
292 ------------------------------------------------------------------------
293 r29 | lh3lh3 | 2008-12-08 10:29:02 +0000 (Mon, 08 Dec 2008) | 3 lines
295 M /branches/dev/samtools/bam.c
296 M /branches/dev/samtools/bam.h
297 M /branches/dev/samtools/bam_import.c
298 M /branches/dev/samtools/bam_maqcns.c
299 M /branches/dev/samtools/bam_pileup.c
300 M /branches/dev/samtools/bam_sort.c
301 M /branches/dev/samtools/bam_tview.c
302 M /branches/dev/samtools/bamtk.c
303 M /branches/dev/samtools/misc/maq2sam.c
306 * format change to meet the latest specification
308 ------------------------------------------------------------------------
309 r28 | lh3lh3 | 2008-12-04 16:09:21 +0000 (Thu, 04 Dec 2008) | 3 lines
311 M /branches/dev/samtools/bam_maqcns.c
312 M /branches/dev/samtools/misc/maq2sam.c
314 * minor change in maqcns: special care when n==0
315 * change maq2sam to meet the latest specification
317 ------------------------------------------------------------------------
318 r27 | lh3lh3 | 2008-12-04 15:55:44 +0000 (Thu, 04 Dec 2008) | 2 lines
320 M /branches/dev/samtools/razf.c
321 M /branches/dev/samtools/razf.h
323 considerable code clean up in razf
325 ------------------------------------------------------------------------
326 r26 | lh3lh3 | 2008-12-04 15:08:18 +0000 (Thu, 04 Dec 2008) | 2 lines
328 M /branches/dev/samtools/ChangeLog
329 M /branches/dev/samtools/Makefile
330 M /branches/dev/samtools/faidx.c
332 make RAZF optional in faidx.c
334 ------------------------------------------------------------------------
335 r25 | lh3lh3 | 2008-12-01 15:27:22 +0000 (Mon, 01 Dec 2008) | 3 lines
337 M /branches/dev/samtools/Makefile
338 M /branches/dev/samtools/bam.h
339 M /branches/dev/samtools/bam_aux.c
340 M /branches/dev/samtools/bamtk.c
341 M /branches/dev/samtools/samtools.1
344 * added routines for retrieving aux data, NOT TESTED YET!
346 ------------------------------------------------------------------------
347 r24 | lh3lh3 | 2008-12-01 14:29:43 +0000 (Mon, 01 Dec 2008) | 5 lines
349 M /branches/dev/samtools/bam.c
350 M /branches/dev/samtools/bam_import.c
351 M /branches/dev/samtools/bam_maqcns.c
352 M /branches/dev/samtools/bamtk.c
353 M /branches/dev/samtools/bgzf.c
354 M /branches/dev/samtools/samtools.1
357 * bgzf: fixed a potential integer overflow on 32-it machines
358 * maqcns: set the minimum combined quality as 0
359 * supporting hex strings
361 ------------------------------------------------------------------------
362 r23 | lh3lh3 | 2008-11-27 17:14:37 +0000 (Thu, 27 Nov 2008) | 3 lines
364 M /branches/dev/samtools/bam_maqcns.c
365 M /branches/dev/samtools/bamtk.c
368 * fixed the bug in maqcns
370 ------------------------------------------------------------------------
371 r22 | lh3lh3 | 2008-11-27 17:08:11 +0000 (Thu, 27 Nov 2008) | 3 lines
373 M /branches/dev/samtools/Makefile
374 M /branches/dev/samtools/bam.h
375 A /branches/dev/samtools/bam_maqcns.c
376 A /branches/dev/samtools/bam_maqcns.h
377 M /branches/dev/samtools/bam_tview.c
378 M /branches/dev/samtools/bamtk.c
379 A /branches/dev/samtools/glf.h
382 * add MAQ consensus caller, currently BUGGY!
384 ------------------------------------------------------------------------
385 r21 | lh3lh3 | 2008-11-27 13:51:28 +0000 (Thu, 27 Nov 2008) | 4 lines
387 M /branches/dev/samtools/bam_pileup.c
388 M /branches/dev/samtools/bam_tview.c
389 M /branches/dev/samtools/bamtk.c
392 * tview: display padded alignment (but not P operation)
393 * better coordinates and reference sequence
395 ------------------------------------------------------------------------
396 r19 | lh3lh3 | 2008-11-27 09:26:05 +0000 (Thu, 27 Nov 2008) | 2 lines
398 A /branches/dev/samtools/ChangeLog
402 ------------------------------------------------------------------------
403 r18 | lh3lh3 | 2008-11-27 09:24:45 +0000 (Thu, 27 Nov 2008) | 3 lines
405 D /branches/dev/samtools/ChangeLog
406 A /branches/dev/samtools/ChangeLog.old (from /branches/dev/samtools/ChangeLog:6)
408 Rename ChangeLog to ChangeLog.old. This old ChangeLog is generated from
409 the log of my personal SVN repository.
411 ------------------------------------------------------------------------
412 r17 | lh3lh3 | 2008-11-27 09:22:55 +0000 (Thu, 27 Nov 2008) | 6 lines
414 M /branches/dev/samtools/Makefile
415 M /branches/dev/samtools/bamtk.c
416 M /branches/dev/samtools/bgzf.c
419 * declare fseeko and ftello as some Linux may not do this by default and
420 missing these declarations will make bgzf buggy
421 * get rid of some harmless warings
422 * use BGZF by default, now
424 ------------------------------------------------------------------------
425 r16 | lh3lh3 | 2008-11-26 21:19:11 +0000 (Wed, 26 Nov 2008) | 4 lines
427 M /branches/dev/samtools/bam_index.c
428 M /branches/dev/samtools/bamtk.c
429 M /branches/dev/samtools/razf.c
432 * fixed a bug in razf_read()
433 * give more warnings when the file is truncated (or due to bugs in I/O library)
435 ------------------------------------------------------------------------
436 r15 | lh3lh3 | 2008-11-26 20:41:39 +0000 (Wed, 26 Nov 2008) | 2 lines
438 M /branches/dev/samtools/bgzf.c
440 fixed a bug in bgzf.c at the end of the file
442 ------------------------------------------------------------------------
443 r14 | lh3lh3 | 2008-11-26 17:05:18 +0000 (Wed, 26 Nov 2008) | 4 lines
445 M /branches/dev/samtools/bamtk.c
448 * a lot happened to RAZF, although samtools itself is untouched. Better
449 also update the version number anyway to avoid confusion
451 ------------------------------------------------------------------------
452 r13 | lh3lh3 | 2008-11-26 17:03:48 +0000 (Wed, 26 Nov 2008) | 2 lines
454 M /branches/dev/samtools/razf.c
456 a change from Jue, but I think it should not matter
458 ------------------------------------------------------------------------
459 r12 | lh3lh3 | 2008-11-26 16:48:14 +0000 (Wed, 26 Nov 2008) | 3 lines
461 M /branches/dev/samtools/razf.c
463 fixed a potential bug in razf. However, it seems still buggy, just
464 rarely happens, very rarely.
466 ------------------------------------------------------------------------
467 r11 | lh3lh3 | 2008-11-26 14:02:56 +0000 (Wed, 26 Nov 2008) | 2 lines
469 M /branches/dev/samtools/razf.c
471 fixed a bug in razf, with the help of Jue
473 ------------------------------------------------------------------------
474 r10 | lh3lh3 | 2008-11-26 11:55:32 +0000 (Wed, 26 Nov 2008) | 2 lines
476 M /branches/dev/samtools/bam_index.c
480 ------------------------------------------------------------------------
481 r9 | lh3lh3 | 2008-11-26 11:37:05 +0000 (Wed, 26 Nov 2008) | 2 lines
483 M /branches/dev/samtools/Makefile
484 M /branches/dev/samtools/bam.h
485 M /branches/dev/samtools/razf.c
486 M /branches/dev/samtools/razf.h
488 * Jue has updated razf to realize Bob's scheme
490 ------------------------------------------------------------------------
491 r7 | lh3lh3 | 2008-11-25 20:37:37 +0000 (Tue, 25 Nov 2008) | 2 lines
493 A /branches/dev/samtools/samtools.1
497 ------------------------------------------------------------------------
498 r6 | lh3lh3 | 2008-11-25 20:37:16 +0000 (Tue, 25 Nov 2008) | 3 lines
500 A /branches/dev/samtools/ChangeLog
501 A /branches/dev/samtools/Makefile
502 A /branches/dev/samtools/bam.c
503 A /branches/dev/samtools/bam.h
504 A /branches/dev/samtools/bam_aux.c
505 A /branches/dev/samtools/bam_endian.h
506 A /branches/dev/samtools/bam_import.c
507 A /branches/dev/samtools/bam_index.c
508 A /branches/dev/samtools/bam_lpileup.c
509 A /branches/dev/samtools/bam_pileup.c
510 A /branches/dev/samtools/bam_sort.c
511 A /branches/dev/samtools/bam_tview.c
512 A /branches/dev/samtools/bamtk.c
513 A /branches/dev/samtools/bgzf.c
514 A /branches/dev/samtools/bgzf.h
515 A /branches/dev/samtools/bgzip.c
516 A /branches/dev/samtools/faidx.c
517 A /branches/dev/samtools/faidx.h
518 A /branches/dev/samtools/khash.h
519 A /branches/dev/samtools/ksort.h
520 A /branches/dev/samtools/kstream.h
521 A /branches/dev/samtools/misc
522 A /branches/dev/samtools/misc/Makefile
523 A /branches/dev/samtools/misc/all2sam.pl
524 A /branches/dev/samtools/misc/maq2sam.c
525 A /branches/dev/samtools/razf.c
526 A /branches/dev/samtools/razf.h
527 A /branches/dev/samtools/razip.c
528 A /branches/dev/samtools/zutil.h
530 The initial version of samtools, replicated from my local SVN repository.
531 The current version is: 0.1.0-42. All future development will happen here.
533 ------------------------------------------------------------------------
534 r5 | lh3lh3 | 2008-11-25 20:30:49 +0000 (Tue, 25 Nov 2008) | 2 lines
536 A /branches/dev/samtools
540 ------------------------------------------------------------------------