1 ------------------------------------------------------------------------
2 r108 | lh3lh3 | 2009-01-20 11:56:45 +0000 (Tue, 20 Jan 2009) | 2 lines
4 M /branches/dev/samtools/examples/Makefile
6 made it a little more convenient
8 ------------------------------------------------------------------------
9 r107 | lh3lh3 | 2009-01-20 11:53:30 +0000 (Tue, 20 Jan 2009) | 2 lines
11 A /branches/dev/samtools/examples/Makefile
15 ------------------------------------------------------------------------
16 r106 | lh3lh3 | 2009-01-20 11:25:05 +0000 (Tue, 20 Jan 2009) | 2 lines
18 M /branches/dev/samtools/misc/maq2sam.c
22 ------------------------------------------------------------------------
23 r105 | lh3lh3 | 2009-01-18 17:37:20 +0000 (Sun, 18 Jan 2009) | 2 lines
25 M /branches/dev/samtools/ChangeLog
29 ------------------------------------------------------------------------
30 r104 | lh3lh3 | 2009-01-18 17:31:21 +0000 (Sun, 18 Jan 2009) | 3 lines
32 M /branches/dev/samtools/bam.h
33 M /branches/dev/samtools/bam_lpileup.c
34 M /branches/dev/samtools/bamtk.c
37 * fixed a bug in bam_lpileup.c: segment start and end are not correctly recognized
39 ------------------------------------------------------------------------
40 r103 | lh3lh3 | 2009-01-18 16:34:03 +0000 (Sun, 18 Jan 2009) | 5 lines
42 M /branches/dev/samtools/bam_import.c
43 M /branches/dev/samtools/bam_index.c
44 M /branches/dev/samtools/bamtk.c
47 * fixed a bug when there are reads without coordinates
48 * also recognize type 'c' as 'A'
49 * found a bug in bam_lpileup.c; NOT fixed yet
51 ------------------------------------------------------------------------
52 r102 | lh3lh3 | 2009-01-17 19:46:49 +0000 (Sat, 17 Jan 2009) | 2 lines
54 A /branches/dev/samtools/INSTALL
56 Instruction for compilation
58 ------------------------------------------------------------------------
59 r101 | lh3lh3 | 2009-01-17 19:31:36 +0000 (Sat, 17 Jan 2009) | 3 lines
61 M /branches/dev/samtools/Makefile
62 A /branches/dev/samtools/Makefile.lite
63 M /branches/dev/samtools/bam.h
64 M /branches/dev/samtools/faidx.c
65 M /branches/dev/samtools/misc/Makefile
66 M /branches/dev/samtools/razf.c
68 * replaced HAVE_RAZF with _NO_RAZF
69 * added Makefile.lite for people who have trouble with razf.c
71 ------------------------------------------------------------------------
72 r100 | lh3lh3 | 2009-01-16 10:03:37 +0000 (Fri, 16 Jan 2009) | 3 lines
74 M /branches/dev/samtools/bam_mate.c
75 M /branches/dev/samtools/bamtk.c
76 M /branches/dev/samtools/misc/wgsim.c
79 * fixed another bug in fixmate: unmapped pair has non-zero isize
81 ------------------------------------------------------------------------
82 r99 | lh3lh3 | 2009-01-16 09:13:36 +0000 (Fri, 16 Jan 2009) | 4 lines
84 M /branches/dev/samtools/ChangeLog
85 M /branches/dev/samtools/bam_mate.c
86 M /branches/dev/samtools/bamtk.c
89 * fixed a bug in fixmate: isize not equal to zero if two ends mapped to
92 ------------------------------------------------------------------------
93 r98 | lh3lh3 | 2009-01-15 16:47:41 +0000 (Thu, 15 Jan 2009) | 3 lines
95 M /branches/dev/samtools/bam_maqcns.c
96 M /branches/dev/samtools/bamtk.c
99 * fixed the prior for hom indels (Richard pointed this out)
101 ------------------------------------------------------------------------
102 r97 | lh3lh3 | 2009-01-15 16:38:47 +0000 (Thu, 15 Jan 2009) | 4 lines
104 M /branches/dev/samtools/COPYING
105 M /branches/dev/samtools/bam_sort.c
106 M /branches/dev/samtools/bamtk.c
107 M /branches/dev/samtools/source.dot
110 * fixed a bug in sort
111 * update source file graph and copyright information
113 ------------------------------------------------------------------------
114 r96 | lh3lh3 | 2009-01-14 21:46:14 +0000 (Wed, 14 Jan 2009) | 2 lines
116 M /branches/dev/samtools/glf.c
120 ------------------------------------------------------------------------
121 r95 | lh3lh3 | 2009-01-14 21:44:53 +0000 (Wed, 14 Jan 2009) | 2 lines
123 M /branches/dev/samtools/glf.c
125 added a main function for glf.c
127 ------------------------------------------------------------------------
128 r94 | lh3lh3 | 2009-01-14 17:14:59 +0000 (Wed, 14 Jan 2009) | 4 lines
130 M /branches/dev/samtools/Makefile
131 M /branches/dev/samtools/bam_plcmd.c
132 M /branches/dev/samtools/bamtk.c
133 M /branches/dev/samtools/bgzf.h
134 A /branches/dev/samtools/glf.c
135 M /branches/dev/samtools/glf.h
138 * generate binary GLFv2
139 * added glfview command to dump GLFv2 binary file
141 ------------------------------------------------------------------------
142 r93 | lh3lh3 | 2009-01-14 15:07:44 +0000 (Wed, 14 Jan 2009) | 4 lines
144 M /branches/dev/samtools/bam_rmdup.c
145 M /branches/dev/samtools/bamtk.c
146 M /branches/dev/samtools/glf.h
149 * fixed several bugs in rmdup
150 * prepare to generate GLF2
152 ------------------------------------------------------------------------
153 r92 | lh3lh3 | 2009-01-14 13:27:44 +0000 (Wed, 14 Jan 2009) | 3 lines
155 M /branches/dev/samtools/Makefile
156 M /branches/dev/samtools/bam.h
157 M /branches/dev/samtools/bam_import.c
158 A /branches/dev/samtools/bam_rmdup.c
159 M /branches/dev/samtools/bamtk.c
162 * implemented rmdup; NOT tested yet
164 ------------------------------------------------------------------------
165 r91 | lh3lh3 | 2009-01-13 20:15:43 +0000 (Tue, 13 Jan 2009) | 2 lines
167 M /branches/dev/samtools/examples/00README.txt
169 update README for typos
171 ------------------------------------------------------------------------
172 r90 | lh3lh3 | 2009-01-13 19:57:50 +0000 (Tue, 13 Jan 2009) | 2 lines
174 M /branches/dev/samtools/examples/ex1.sam.gz
178 ------------------------------------------------------------------------
179 r89 | lh3lh3 | 2009-01-13 17:21:38 +0000 (Tue, 13 Jan 2009) | 3 lines
181 M /branches/dev/samtools/Makefile
182 M /branches/dev/samtools/bam.c
183 A /branches/dev/samtools/bam_mate.c
184 M /branches/dev/samtools/bamtk.c
187 * added fixmate command
189 ------------------------------------------------------------------------
190 r88 | lh3lh3 | 2009-01-13 10:48:23 +0000 (Tue, 13 Jan 2009) | 3 lines
192 M /branches/dev/samtools/bam_plcmd.c
193 M /branches/dev/samtools/bamtk.c
196 * change the reported indel position to the previous way
198 ------------------------------------------------------------------------
199 r87 | lh3lh3 | 2009-01-12 22:12:12 +0000 (Mon, 12 Jan 2009) | 4 lines
201 M /branches/dev/samtools/bam_plcmd.c
202 M /branches/dev/samtools/bamtk.c
206 * allow to change indel calling parameters at the command line
208 ------------------------------------------------------------------------
209 r86 | lh3lh3 | 2009-01-12 21:16:48 +0000 (Mon, 12 Jan 2009) | 4 lines
211 M /branches/dev/samtools/bam.h
212 M /branches/dev/samtools/bam_pileup.c
213 M /branches/dev/samtools/bam_plcmd.c
214 M /branches/dev/samtools/bamtk.c
217 * added two more flags
218 * allowed to select reads shown in pileup with a mask
220 ------------------------------------------------------------------------
221 r85 | lh3lh3 | 2009-01-12 20:47:51 +0000 (Mon, 12 Jan 2009) | 4 lines
223 M /branches/dev/samtools/bam_index.c
224 M /branches/dev/samtools/bam_plcmd.c
225 M /branches/dev/samtools/bamtk.c
228 * fixed a bug in indexing (linear index)
229 * prepare to add glt output from pileup
231 ------------------------------------------------------------------------
232 r84 | lh3lh3 | 2009-01-12 09:22:35 +0000 (Mon, 12 Jan 2009) | 3 lines
234 M /branches/dev/samtools/bam_plcmd.c
235 M /branches/dev/samtools/bamtk.c
238 * fixed a bug in outputing the coordinate of an indel
240 ------------------------------------------------------------------------
241 r83 | lh3lh3 | 2009-01-11 15:18:01 +0000 (Sun, 11 Jan 2009) | 3 lines
243 M /branches/dev/samtools/bam_plcmd.c
244 M /branches/dev/samtools/bamtk.c
247 * pileup: allows to output indel sites only
249 ------------------------------------------------------------------------
250 r82 | lh3lh3 | 2009-01-10 23:34:31 +0000 (Sat, 10 Jan 2009) | 3 lines
252 M /branches/dev/samtools/bam_maqcns.c
253 M /branches/dev/samtools/bam_maqcns.h
254 M /branches/dev/samtools/bam_plcmd.c
255 M /branches/dev/samtools/bamtk.c
258 * implemented a Bayesian indel caller
260 ------------------------------------------------------------------------
261 r81 | lh3lh3 | 2009-01-09 09:54:28 +0000 (Fri, 09 Jan 2009) | 2 lines
263 M /branches/dev/samtools/examples/00README.txt
264 D /branches/dev/samtools/examples/ex1.fa.fai
266 Let users generate ex1.fa.fai.
268 ------------------------------------------------------------------------
269 r80 | lh3lh3 | 2009-01-08 16:10:08 +0000 (Thu, 08 Jan 2009) | 2 lines
271 M /branches/dev/samtools/misc/bowtie2sam.pl
273 make the bowtie converter works for "-k 2"
275 ------------------------------------------------------------------------
276 r78 | lh3lh3 | 2009-01-03 17:25:24 +0000 (Sat, 03 Jan 2009) | 2 lines
278 M /branches/dev/samtools/misc/export2sam.pl
280 fixed a bug for "QC" reads
282 ------------------------------------------------------------------------
283 r77 | lh3lh3 | 2009-01-01 18:32:06 +0000 (Thu, 01 Jan 2009) | 3 lines
285 A /branches/dev/samtools/misc/bowtie2sam.pl
286 M /branches/dev/samtools/misc/soap2sam.pl
288 * soap2sam.pl: added NM tag
289 * bowtie2sam.pl: converter for bowtie
291 ------------------------------------------------------------------------
292 r76 | lh3lh3 | 2008-12-31 23:24:24 +0000 (Wed, 31 Dec 2008) | 2 lines
294 A /branches/dev/samtools/misc/soap2sam.pl
296 soap2sam.pl: convert soap output to SAM
298 ------------------------------------------------------------------------
299 r75 | lh3lh3 | 2008-12-31 17:54:32 +0000 (Wed, 31 Dec 2008) | 3 lines
301 M /branches/dev/samtools/misc/wgsim_eval.pl
303 * wgsim_eval.pl-0.1.1
304 * fixed a bug for a contig name like "NT_012345"
306 ------------------------------------------------------------------------
307 r74 | lh3lh3 | 2008-12-31 16:38:21 +0000 (Wed, 31 Dec 2008) | 2 lines
309 A /branches/dev/samtools/misc/wgsim_eval.pl
311 * evaluate alignment for reads generated by wgsim
313 ------------------------------------------------------------------------
314 r73 | lh3lh3 | 2008-12-31 15:11:22 +0000 (Wed, 31 Dec 2008) | 2 lines
316 M /branches/dev/samtools/misc/Makefile
317 M /branches/dev/samtools/misc/wgsim.c
319 fixed compiling warnings for wgsim
321 ------------------------------------------------------------------------
322 r72 | lh3lh3 | 2008-12-31 13:40:51 +0000 (Wed, 31 Dec 2008) | 2 lines
324 M /branches/dev/samtools/bam_tview.c
326 remove an unused variable (a compiler warning only)
328 ------------------------------------------------------------------------
329 r71 | lh3lh3 | 2008-12-31 13:37:16 +0000 (Wed, 31 Dec 2008) | 2 lines
331 M /branches/dev/samtools/misc/Makefile
332 A /branches/dev/samtools/misc/wgsim.c
334 wgsim: Paired-end reads simulator
336 ------------------------------------------------------------------------
337 r70 | bhandsaker | 2008-12-29 20:27:16 +0000 (Mon, 29 Dec 2008) | 2 lines
339 M /branches/dev/samtools/bam_maqcns.c
340 M /branches/dev/samtools/bam_tview.c
342 Move definition of bam_nt16_nt4_table so we can build without curses.
344 ------------------------------------------------------------------------
345 r62 | lh3lh3 | 2008-12-22 15:55:13 +0000 (Mon, 22 Dec 2008) | 2 lines
347 A /branches/dev/samtools/NEWS
348 M /branches/dev/samtools/bamtk.c
349 M /branches/dev/samtools/samtools.1
351 Release samtools-0.1.1
353 ------------------------------------------------------------------------
354 r61 | lh3lh3 | 2008-12-22 15:46:08 +0000 (Mon, 22 Dec 2008) | 10 lines
356 M /branches/dev/samtools/bam_aux.c
357 M /branches/dev/samtools/bam_index.c
358 M /branches/dev/samtools/bam_plcmd.c
359 M /branches/dev/samtools/bam_tview.c
360 M /branches/dev/samtools/bamtk.c
361 M /branches/dev/samtools/razf.c
362 M /branches/dev/samtools/samtools.1
365 * fixed a bug in razf.c: reset z_eof when razf_seek() is called
366 * fixed a memory leak in parsing a region
367 * changed pileup a little bit when -s is in use: output ^ and $
368 * when a bam is not indexed, output more meaningful error message
369 * fixed a bug in indexing for small alignment
370 * fixed a bug in the viewer when we come to the end of a reference file
371 * updated documentation
372 * prepare to release 0.1.1
374 ------------------------------------------------------------------------
375 r60 | lh3lh3 | 2008-12-22 15:10:16 +0000 (Mon, 22 Dec 2008) | 2 lines
377 A /branches/dev/samtools/examples
378 A /branches/dev/samtools/examples/00README.txt
379 A /branches/dev/samtools/examples/ex1.fa
380 A /branches/dev/samtools/examples/ex1.fa.fai
381 A /branches/dev/samtools/examples/ex1.sam.gz
385 ------------------------------------------------------------------------
386 r59 | lh3lh3 | 2008-12-22 09:38:15 +0000 (Mon, 22 Dec 2008) | 2 lines
388 M /branches/dev/samtools/ChangeLog
392 ------------------------------------------------------------------------
393 r58 | lh3lh3 | 2008-12-20 23:06:00 +0000 (Sat, 20 Dec 2008) | 3 lines
395 M /branches/dev/samtools/misc/export2sam.pl
400 ------------------------------------------------------------------------
401 r57 | lh3lh3 | 2008-12-20 15:44:20 +0000 (Sat, 20 Dec 2008) | 2 lines
403 A /branches/dev/samtools/misc/export2sam.pl
405 convert Export format to SAM; not thoroughly tested
407 ------------------------------------------------------------------------
408 r56 | lh3lh3 | 2008-12-19 22:13:28 +0000 (Fri, 19 Dec 2008) | 6 lines
410 M /branches/dev/samtools/bam_import.c
411 M /branches/dev/samtools/bam_plcmd.c
412 M /branches/dev/samtools/bam_tview.c
413 M /branches/dev/samtools/bamtk.c
414 A /branches/dev/samtools/source.dot
417 * pileup: generate maq-like simple output
418 * pileup: allow to output pileup at required sites
419 * source.dot: source file relationship graph
420 * tview: fixed a minor bug
422 ------------------------------------------------------------------------
423 r55 | lh3lh3 | 2008-12-19 20:10:26 +0000 (Fri, 19 Dec 2008) | 2 lines
425 D /branches/dev/samtools/misc/all2sam.pl
429 ------------------------------------------------------------------------
430 r54 | lh3lh3 | 2008-12-16 22:34:25 +0000 (Tue, 16 Dec 2008) | 2 lines
432 A /branches/dev/samtools/COPYING
433 M /branches/dev/samtools/bam.h
434 M /branches/dev/samtools/faidx.h
435 M /branches/dev/samtools/khash.h
436 M /branches/dev/samtools/kseq.h
437 M /branches/dev/samtools/ksort.h
438 M /branches/dev/samtools/samtools.1
440 Added copyright information and a bit more documentation. No code change.
442 ------------------------------------------------------------------------
443 r53 | lh3lh3 | 2008-12-16 13:40:18 +0000 (Tue, 16 Dec 2008) | 3 lines
445 M /branches/dev/samtools/bam.c
446 M /branches/dev/samtools/bam.h
447 M /branches/dev/samtools/bam_index.c
448 M /branches/dev/samtools/bam_maqcns.c
449 M /branches/dev/samtools/bamtk.c
452 * improved efficiency of the indel caller for spliced alignments
454 ------------------------------------------------------------------------
455 r52 | lh3lh3 | 2008-12-16 10:28:20 +0000 (Tue, 16 Dec 2008) | 3 lines
457 M /branches/dev/samtools/bam.c
458 M /branches/dev/samtools/bam.h
459 M /branches/dev/samtools/bam_aux.c
460 M /branches/dev/samtools/bam_index.c
461 M /branches/dev/samtools/bamtk.c
464 * a bit code cleanup: reduce the dependency between source files
466 ------------------------------------------------------------------------
467 r51 | lh3lh3 | 2008-12-15 14:29:32 +0000 (Mon, 15 Dec 2008) | 3 lines
469 M /branches/dev/samtools/bam_maqcns.c
470 M /branches/dev/samtools/bam_plcmd.c
471 M /branches/dev/samtools/bamtk.c
474 * fixed a memory leak
476 ------------------------------------------------------------------------
477 r50 | lh3lh3 | 2008-12-15 14:00:13 +0000 (Mon, 15 Dec 2008) | 2 lines
479 M /branches/dev/samtools/ChangeLog
480 M /branches/dev/samtools/bam.h
481 M /branches/dev/samtools/samtools.1
483 update documentation, ChangeLog and a comment
485 ------------------------------------------------------------------------
486 r49 | lh3lh3 | 2008-12-15 13:36:43 +0000 (Mon, 15 Dec 2008) | 6 lines
488 M /branches/dev/samtools/Makefile
489 M /branches/dev/samtools/bam.h
490 M /branches/dev/samtools/bam_maqcns.c
491 M /branches/dev/samtools/bam_maqcns.h
492 M /branches/dev/samtools/bam_pileup.c
493 A /branches/dev/samtools/bam_plcmd.c
494 M /branches/dev/samtools/bamtk.c
495 M /branches/dev/samtools/samtools.1
498 * moved pileup command to a separate source file
500 * added bam_cal_segend(). (NOT WORKING for spliced alignment!!!)
501 * updated documentation
503 ------------------------------------------------------------------------
504 r48 | lh3lh3 | 2008-12-12 13:55:36 +0000 (Fri, 12 Dec 2008) | 3 lines
506 M /branches/dev/samtools/bam_maqcns.c
507 M /branches/dev/samtools/bamtk.c
510 * fixed another bug in maqcns when there is a nearby deletion
512 ------------------------------------------------------------------------
513 r47 | lh3lh3 | 2008-12-12 13:42:16 +0000 (Fri, 12 Dec 2008) | 5 lines
515 M /branches/dev/samtools/bam_maqcns.c
516 M /branches/dev/samtools/bam_pileup.c
517 M /branches/dev/samtools/bamtk.c
520 * pileup: outputing consensus is now optional
521 * fixed a bug in glfgen. This bug also exists in maq's glfgen. However,
522 I am not quite sure why the previous version may have problem.
524 ------------------------------------------------------------------------
525 r46 | lh3lh3 | 2008-12-12 11:44:56 +0000 (Fri, 12 Dec 2008) | 6 lines
527 M /branches/dev/samtools/bam_pileup.c
528 M /branches/dev/samtools/bamtk.c
531 * add maq consensus to pileup. However, I will move this part to a new
532 command as strictly speaking, consensus callin is not part of pileup,
533 and imposing it would make it harder to generate for other language
536 ------------------------------------------------------------------------
537 r45 | bhandsaker | 2008-12-11 20:43:56 +0000 (Thu, 11 Dec 2008) | 2 lines
539 M /branches/dev/samtools/bgzf.c
541 Fix bug in tell() after reads that consume to the exact end of a block.
543 ------------------------------------------------------------------------
544 r44 | lh3lh3 | 2008-12-11 09:36:53 +0000 (Thu, 11 Dec 2008) | 2 lines
546 M /branches/dev/samtools/samtools.1
550 ------------------------------------------------------------------------
551 r43 | lh3lh3 | 2008-12-11 09:25:36 +0000 (Thu, 11 Dec 2008) | 4 lines
553 M /branches/dev/samtools/bam_import.c
554 M /branches/dev/samtools/bamtk.c
557 * fixed a bug in parser when there is auxiliary fields
558 * made the parser a bit more robust
560 ------------------------------------------------------------------------
561 r42 | lh3lh3 | 2008-12-10 14:57:29 +0000 (Wed, 10 Dec 2008) | 5 lines
563 M /branches/dev/samtools/bam_index.c
564 M /branches/dev/samtools/bamtk.c
565 M /branches/dev/samtools/bgzf.c
568 * fixed a bug in bgzf (only reading is affected)
569 * fixed a typo in bam_index.c
570 * in bam_index.c, check potential bugs in the underlying I/O library
572 ------------------------------------------------------------------------
573 r41 | lh3lh3 | 2008-12-10 12:53:08 +0000 (Wed, 10 Dec 2008) | 2 lines
575 M /branches/dev/samtools/samtools.1
579 ------------------------------------------------------------------------
580 r40 | lh3lh3 | 2008-12-10 11:52:10 +0000 (Wed, 10 Dec 2008) | 5 lines
582 M /branches/dev/samtools/bam.h
583 M /branches/dev/samtools/bam_pileup.c
584 M /branches/dev/samtools/bamtk.c
587 * tried to make pileup work with clipping (previously not), though NOT tested
588 * removed -v from pileup
589 * made pileup take the reference sequence
591 ------------------------------------------------------------------------
592 r39 | lh3lh3 | 2008-12-09 11:59:28 +0000 (Tue, 09 Dec 2008) | 4 lines
594 M /branches/dev/samtools/bam_import.c
595 M /branches/dev/samtools/bamtk.c
596 M /branches/dev/samtools/samtools.1
599 * in parser, recognize "=", rather than ",", as a match
600 * in parser, correctl parse "=" at the MRNM field.
602 ------------------------------------------------------------------------
603 r38 | lh3lh3 | 2008-12-09 11:39:07 +0000 (Tue, 09 Dec 2008) | 2 lines
605 M /branches/dev/samtools/misc/maq2sam.c
607 fixed a bug in handling maq flag 64 and 192
609 ------------------------------------------------------------------------
610 r37 | lh3lh3 | 2008-12-09 09:53:46 +0000 (Tue, 09 Dec 2008) | 2 lines
612 M /branches/dev/samtools/misc/md5fa.c
614 also calculate unordered md5sum check
616 ------------------------------------------------------------------------
617 r36 | lh3lh3 | 2008-12-09 09:46:21 +0000 (Tue, 09 Dec 2008) | 2 lines
619 M /branches/dev/samtools/misc/md5fa.c
621 fixed a minor bug when there are space in the sequence
623 ------------------------------------------------------------------------
624 r35 | lh3lh3 | 2008-12-09 09:40:45 +0000 (Tue, 09 Dec 2008) | 2 lines
626 M /branches/dev/samtools/misc/md5fa.c
628 fixed a potential memory leak
630 ------------------------------------------------------------------------
631 r34 | lh3lh3 | 2008-12-08 14:52:17 +0000 (Mon, 08 Dec 2008) | 2 lines
633 M /branches/dev/samtools/bam_import.c
634 M /branches/dev/samtools/bam_index.c
635 M /branches/dev/samtools/bamtk.c
637 * fixed a bug in import: bin is wrongly calculated
639 ------------------------------------------------------------------------
640 r33 | lh3lh3 | 2008-12-08 14:08:01 +0000 (Mon, 08 Dec 2008) | 2 lines
642 M /branches/dev/samtools/misc/all2sam.pl
646 ------------------------------------------------------------------------
647 r32 | lh3lh3 | 2008-12-08 12:56:02 +0000 (Mon, 08 Dec 2008) | 3 lines
649 M /branches/dev/samtools/Makefile
650 M /branches/dev/samtools/kseq.h
651 M /branches/dev/samtools/misc/Makefile
652 A /branches/dev/samtools/misc/md5.c
653 A /branches/dev/samtools/misc/md5.h
654 A /branches/dev/samtools/misc/md5fa.c
656 * fixed two warnings in kseq.h
657 * added md5sum utilities
659 ------------------------------------------------------------------------
660 r31 | lh3lh3 | 2008-12-08 11:35:29 +0000 (Mon, 08 Dec 2008) | 5 lines
662 M /branches/dev/samtools/Makefile
663 M /branches/dev/samtools/bam_import.c
664 M /branches/dev/samtools/bamtk.c
665 A /branches/dev/samtools/kseq.h
666 D /branches/dev/samtools/kstream.h
669 * replace kstream with kseq. kseq is a superset of kstream. I need the
670 extra functions in kseq.h.
671 * also compile stand-alone faidx
673 ------------------------------------------------------------------------
674 r30 | lh3lh3 | 2008-12-08 11:17:04 +0000 (Mon, 08 Dec 2008) | 3 lines
676 M /branches/dev/samtools/bam.h
677 M /branches/dev/samtools/bam_sort.c
678 M /branches/dev/samtools/bamtk.c
681 * sorting by read names is available
683 ------------------------------------------------------------------------
684 r29 | lh3lh3 | 2008-12-08 10:29:02 +0000 (Mon, 08 Dec 2008) | 3 lines
686 M /branches/dev/samtools/bam.c
687 M /branches/dev/samtools/bam.h
688 M /branches/dev/samtools/bam_import.c
689 M /branches/dev/samtools/bam_maqcns.c
690 M /branches/dev/samtools/bam_pileup.c
691 M /branches/dev/samtools/bam_sort.c
692 M /branches/dev/samtools/bam_tview.c
693 M /branches/dev/samtools/bamtk.c
694 M /branches/dev/samtools/misc/maq2sam.c
697 * format change to meet the latest specification
699 ------------------------------------------------------------------------
700 r28 | lh3lh3 | 2008-12-04 16:09:21 +0000 (Thu, 04 Dec 2008) | 3 lines
702 M /branches/dev/samtools/bam_maqcns.c
703 M /branches/dev/samtools/misc/maq2sam.c
705 * minor change in maqcns: special care when n==0
706 * change maq2sam to meet the latest specification
708 ------------------------------------------------------------------------
709 r27 | lh3lh3 | 2008-12-04 15:55:44 +0000 (Thu, 04 Dec 2008) | 2 lines
711 M /branches/dev/samtools/razf.c
712 M /branches/dev/samtools/razf.h
714 considerable code clean up in razf
716 ------------------------------------------------------------------------
717 r26 | lh3lh3 | 2008-12-04 15:08:18 +0000 (Thu, 04 Dec 2008) | 2 lines
719 M /branches/dev/samtools/ChangeLog
720 M /branches/dev/samtools/Makefile
721 M /branches/dev/samtools/faidx.c
723 make RAZF optional in faidx.c
725 ------------------------------------------------------------------------
726 r25 | lh3lh3 | 2008-12-01 15:27:22 +0000 (Mon, 01 Dec 2008) | 3 lines
728 M /branches/dev/samtools/Makefile
729 M /branches/dev/samtools/bam.h
730 M /branches/dev/samtools/bam_aux.c
731 M /branches/dev/samtools/bamtk.c
732 M /branches/dev/samtools/samtools.1
735 * added routines for retrieving aux data, NOT TESTED YET!
737 ------------------------------------------------------------------------
738 r24 | lh3lh3 | 2008-12-01 14:29:43 +0000 (Mon, 01 Dec 2008) | 5 lines
740 M /branches/dev/samtools/bam.c
741 M /branches/dev/samtools/bam_import.c
742 M /branches/dev/samtools/bam_maqcns.c
743 M /branches/dev/samtools/bamtk.c
744 M /branches/dev/samtools/bgzf.c
745 M /branches/dev/samtools/samtools.1
748 * bgzf: fixed a potential integer overflow on 32-it machines
749 * maqcns: set the minimum combined quality as 0
750 * supporting hex strings
752 ------------------------------------------------------------------------
753 r23 | lh3lh3 | 2008-11-27 17:14:37 +0000 (Thu, 27 Nov 2008) | 3 lines
755 M /branches/dev/samtools/bam_maqcns.c
756 M /branches/dev/samtools/bamtk.c
759 * fixed the bug in maqcns
761 ------------------------------------------------------------------------
762 r22 | lh3lh3 | 2008-11-27 17:08:11 +0000 (Thu, 27 Nov 2008) | 3 lines
764 M /branches/dev/samtools/Makefile
765 M /branches/dev/samtools/bam.h
766 A /branches/dev/samtools/bam_maqcns.c
767 A /branches/dev/samtools/bam_maqcns.h
768 M /branches/dev/samtools/bam_tview.c
769 M /branches/dev/samtools/bamtk.c
770 A /branches/dev/samtools/glf.h
773 * add MAQ consensus caller, currently BUGGY!
775 ------------------------------------------------------------------------
776 r21 | lh3lh3 | 2008-11-27 13:51:28 +0000 (Thu, 27 Nov 2008) | 4 lines
778 M /branches/dev/samtools/bam_pileup.c
779 M /branches/dev/samtools/bam_tview.c
780 M /branches/dev/samtools/bamtk.c
783 * tview: display padded alignment (but not P operation)
784 * better coordinates and reference sequence
786 ------------------------------------------------------------------------
787 r19 | lh3lh3 | 2008-11-27 09:26:05 +0000 (Thu, 27 Nov 2008) | 2 lines
789 A /branches/dev/samtools/ChangeLog
793 ------------------------------------------------------------------------
794 r18 | lh3lh3 | 2008-11-27 09:24:45 +0000 (Thu, 27 Nov 2008) | 3 lines
796 D /branches/dev/samtools/ChangeLog
797 A /branches/dev/samtools/ChangeLog.old (from /branches/dev/samtools/ChangeLog:6)
799 Rename ChangeLog to ChangeLog.old. This old ChangeLog is generated from
800 the log of my personal SVN repository.
802 ------------------------------------------------------------------------
803 r17 | lh3lh3 | 2008-11-27 09:22:55 +0000 (Thu, 27 Nov 2008) | 6 lines
805 M /branches/dev/samtools/Makefile
806 M /branches/dev/samtools/bamtk.c
807 M /branches/dev/samtools/bgzf.c
810 * declare fseeko and ftello as some Linux may not do this by default and
811 missing these declarations will make bgzf buggy
812 * get rid of some harmless warings
813 * use BGZF by default, now
815 ------------------------------------------------------------------------
816 r16 | lh3lh3 | 2008-11-26 21:19:11 +0000 (Wed, 26 Nov 2008) | 4 lines
818 M /branches/dev/samtools/bam_index.c
819 M /branches/dev/samtools/bamtk.c
820 M /branches/dev/samtools/razf.c
823 * fixed a bug in razf_read()
824 * give more warnings when the file is truncated (or due to bugs in I/O library)
826 ------------------------------------------------------------------------
827 r15 | lh3lh3 | 2008-11-26 20:41:39 +0000 (Wed, 26 Nov 2008) | 2 lines
829 M /branches/dev/samtools/bgzf.c
831 fixed a bug in bgzf.c at the end of the file
833 ------------------------------------------------------------------------
834 r14 | lh3lh3 | 2008-11-26 17:05:18 +0000 (Wed, 26 Nov 2008) | 4 lines
836 M /branches/dev/samtools/bamtk.c
839 * a lot happened to RAZF, although samtools itself is untouched. Better
840 also update the version number anyway to avoid confusion
842 ------------------------------------------------------------------------
843 r13 | lh3lh3 | 2008-11-26 17:03:48 +0000 (Wed, 26 Nov 2008) | 2 lines
845 M /branches/dev/samtools/razf.c
847 a change from Jue, but I think it should not matter
849 ------------------------------------------------------------------------
850 r12 | lh3lh3 | 2008-11-26 16:48:14 +0000 (Wed, 26 Nov 2008) | 3 lines
852 M /branches/dev/samtools/razf.c
854 fixed a potential bug in razf. However, it seems still buggy, just
855 rarely happens, very rarely.
857 ------------------------------------------------------------------------
858 r11 | lh3lh3 | 2008-11-26 14:02:56 +0000 (Wed, 26 Nov 2008) | 2 lines
860 M /branches/dev/samtools/razf.c
862 fixed a bug in razf, with the help of Jue
864 ------------------------------------------------------------------------
865 r10 | lh3lh3 | 2008-11-26 11:55:32 +0000 (Wed, 26 Nov 2008) | 2 lines
867 M /branches/dev/samtools/bam_index.c
871 ------------------------------------------------------------------------
872 r9 | lh3lh3 | 2008-11-26 11:37:05 +0000 (Wed, 26 Nov 2008) | 2 lines
874 M /branches/dev/samtools/Makefile
875 M /branches/dev/samtools/bam.h
876 M /branches/dev/samtools/razf.c
877 M /branches/dev/samtools/razf.h
879 * Jue has updated razf to realize Bob's scheme
881 ------------------------------------------------------------------------
882 r7 | lh3lh3 | 2008-11-25 20:37:37 +0000 (Tue, 25 Nov 2008) | 2 lines
884 A /branches/dev/samtools/samtools.1
888 ------------------------------------------------------------------------
889 r6 | lh3lh3 | 2008-11-25 20:37:16 +0000 (Tue, 25 Nov 2008) | 3 lines
891 A /branches/dev/samtools/ChangeLog
892 A /branches/dev/samtools/Makefile
893 A /branches/dev/samtools/bam.c
894 A /branches/dev/samtools/bam.h
895 A /branches/dev/samtools/bam_aux.c
896 A /branches/dev/samtools/bam_endian.h
897 A /branches/dev/samtools/bam_import.c
898 A /branches/dev/samtools/bam_index.c
899 A /branches/dev/samtools/bam_lpileup.c
900 A /branches/dev/samtools/bam_pileup.c
901 A /branches/dev/samtools/bam_sort.c
902 A /branches/dev/samtools/bam_tview.c
903 A /branches/dev/samtools/bamtk.c
904 A /branches/dev/samtools/bgzf.c
905 A /branches/dev/samtools/bgzf.h
906 A /branches/dev/samtools/bgzip.c
907 A /branches/dev/samtools/faidx.c
908 A /branches/dev/samtools/faidx.h
909 A /branches/dev/samtools/khash.h
910 A /branches/dev/samtools/ksort.h
911 A /branches/dev/samtools/kstream.h
912 A /branches/dev/samtools/misc
913 A /branches/dev/samtools/misc/Makefile
914 A /branches/dev/samtools/misc/all2sam.pl
915 A /branches/dev/samtools/misc/maq2sam.c
916 A /branches/dev/samtools/razf.c
917 A /branches/dev/samtools/razf.h
918 A /branches/dev/samtools/razip.c
919 A /branches/dev/samtools/zutil.h
921 The initial version of samtools, replicated from my local SVN repository.
922 The current version is: 0.1.0-42. All future development will happen here.
924 ------------------------------------------------------------------------
925 r5 | lh3lh3 | 2008-11-25 20:30:49 +0000 (Tue, 25 Nov 2008) | 2 lines
927 A /branches/dev/samtools
931 ------------------------------------------------------------------------
932 ------------------------------------------------------------------------
933 r703 | lh3 | 2008-11-25 20:20:02 +0000 (Tue, 25 Nov 2008) | 2 lines
935 M /branches/prog/bam/samtools.1
937 rename bamtk to samtools
939 ------------------------------------------------------------------------
940 r702 | lh3 | 2008-11-25 20:15:09 +0000 (Tue, 25 Nov 2008) | 2 lines
942 D /branches/prog/bam/bamtk.1
943 A /branches/prog/bam/samtools.1 (from /branches/prog/bam/bamtk.1:679)
945 rename bamtk.1 to samtools.1
947 ------------------------------------------------------------------------
948 r701 | lh3 | 2008-11-25 13:29:10 +0000 (Tue, 25 Nov 2008) | 3 lines
950 M /branches/prog/bam/Makefile
951 M /branches/prog/bam/bam.c
952 M /branches/prog/bam/bam.h
953 M /branches/prog/bam/bam_import.c
954 M /branches/prog/bam/bam_index.c
955 M /branches/prog/bam/bam_pileup.c
956 M /branches/prog/bam/bamtk.c
957 M /branches/prog/bam/misc/Makefile
960 * small (but a bit dangerous) changes to meet the latest specification
962 ------------------------------------------------------------------------
963 r700 | lh3 | 2008-11-25 13:15:11 +0000 (Tue, 25 Nov 2008) | 2 lines
965 A /branches/prog/bam/misc/all2sam.pl (from /branches/prog/bam/misc/all2tam.pl:649)
966 D /branches/prog/bam/misc/all2tam.pl
967 A /branches/prog/bam/misc/maq2sam.c (from /branches/prog/bam/misc/maq2tam.c:699)
968 D /branches/prog/bam/misc/maq2tam.c
972 ------------------------------------------------------------------------
973 r699 | lh3 | 2008-11-25 13:14:49 +0000 (Tue, 25 Nov 2008) | 2 lines
975 M /branches/prog/bam/misc/maq2tam.c
977 change for the new specification
979 ------------------------------------------------------------------------
980 r698 | lh3 | 2008-11-24 13:15:20 +0000 (Mon, 24 Nov 2008) | 3 lines
982 M /branches/prog/bam/bam.h
983 M /branches/prog/bam/razf.c
984 M /branches/prog/bam/razf.h
986 * add a fake BGZF mode to razf. It is fake in that it loads razf index into
987 memory but gives BGZF like virtual offset
989 ------------------------------------------------------------------------
990 r697 | lh3 | 2008-11-24 09:53:44 +0000 (Mon, 24 Nov 2008) | 2 lines
992 A /branches/prog/bam/ChangeLog
996 ------------------------------------------------------------------------
997 r696 | lh3 | 2008-11-24 09:53:23 +0000 (Mon, 24 Nov 2008) | 2 lines
999 M /branches/prog/bam/bgzf.c
1001 updated bgzf, on behalf of Bob
1003 ------------------------------------------------------------------------
1004 r695 | lh3 | 2008-11-23 11:40:31 +0000 (Sun, 23 Nov 2008) | 2 lines
1006 M /branches/prog/bam/bam_index.c
1007 M /branches/prog/bam/razf.c
1011 ------------------------------------------------------------------------
1012 r694 | lh3 | 2008-11-22 16:23:52 +0000 (Sat, 22 Nov 2008) | 4 lines
1014 M /branches/prog/bam/bam_index.c
1015 M /branches/prog/bam/bam_lpileup.c
1016 M /branches/prog/bam/bam_tview.c
1017 M /branches/prog/bam/bamtk.c
1020 * fixed two small memory leaks
1021 * fixed a memory problem when seek outside the length of the sequence
1023 ------------------------------------------------------------------------
1024 r693 | lh3 | 2008-11-22 16:10:04 +0000 (Sat, 22 Nov 2008) | 3 lines
1026 M /branches/prog/bam/bam_index.c
1027 M /branches/prog/bam/bamtk.c
1030 * fixed an uninitialized warning. This does not matter in fact
1032 ------------------------------------------------------------------------
1033 r692 | lh3 | 2008-11-22 15:44:05 +0000 (Sat, 22 Nov 2008) | 2 lines
1035 M /branches/prog/bam/razf.c
1036 M /branches/prog/bam/razf.h
1040 ------------------------------------------------------------------------
1041 r691 | lh3 | 2008-11-21 21:30:39 +0000 (Fri, 21 Nov 2008) | 4 lines
1043 M /branches/prog/bam/Makefile
1044 M /branches/prog/bam/bam.h
1045 M /branches/prog/bam/bam_index.c
1046 M /branches/prog/bam/bamtk.c
1047 M /branches/prog/bam/bgzip.c
1050 * get rid of some warings in bgzip.c
1051 * potentially improve performance in indexing for BGZF
1053 ------------------------------------------------------------------------
1054 r690 | lh3 | 2008-11-21 21:15:51 +0000 (Fri, 21 Nov 2008) | 2 lines
1056 M /branches/prog/bam/bgzf.c
1058 I think I have fixed the bug in bgzf
1060 ------------------------------------------------------------------------
1061 r689 | lh3 | 2008-11-21 20:48:56 +0000 (Fri, 21 Nov 2008) | 2 lines
1063 M /branches/prog/bam/bgzf.c
1067 ------------------------------------------------------------------------
1068 r688 | lh3 | 2008-11-21 20:37:27 +0000 (Fri, 21 Nov 2008) | 2 lines
1070 M /branches/prog/bam/bam.h
1071 M /branches/prog/bam/bam_index.c
1073 fixed a bug due to the name change in _IOLIB
1075 ------------------------------------------------------------------------
1076 r687 | lh3 | 2008-11-21 14:42:56 +0000 (Fri, 21 Nov 2008) | 2 lines
1078 M /branches/prog/bam/bgzf.c
1082 ------------------------------------------------------------------------
1083 r686 | lh3 | 2008-11-21 14:37:59 +0000 (Fri, 21 Nov 2008) | 2 lines
1085 A /branches/prog/bam/bgzf.c
1086 A /branches/prog/bam/bgzf.h
1087 A /branches/prog/bam/bgzip.c
1089 Bob's BGZF format, although currently buggy
1091 ------------------------------------------------------------------------
1092 r685 | lh3 | 2008-11-21 09:48:20 +0000 (Fri, 21 Nov 2008) | 3 lines
1094 M /branches/prog/bam/bam_index.c
1095 M /branches/prog/bam/bam_tview.c
1096 M /branches/prog/bam/bamtk.c
1099 * improve interface a little bit
1101 ------------------------------------------------------------------------
1102 r684 | lh3 | 2008-11-21 09:30:18 +0000 (Fri, 21 Nov 2008) | 3 lines
1104 M /branches/prog/bam/bam_tview.c
1105 M /branches/prog/bam/bamtk.c
1108 * improve the interface of tview, a little bit
1110 ------------------------------------------------------------------------
1111 r683 | lh3 | 2008-11-20 22:33:54 +0000 (Thu, 20 Nov 2008) | 2 lines
1113 M /branches/prog/bam/bam_tview.c
1115 a little better viewer
1117 ------------------------------------------------------------------------
1118 r682 | lh3 | 2008-11-20 22:27:01 +0000 (Thu, 20 Nov 2008) | 3 lines
1120 M /branches/prog/bam/bam.h
1121 M /branches/prog/bam/bam_tview.c
1122 M /branches/prog/bam/bamtk.c
1127 ------------------------------------------------------------------------
1128 r681 | lh3 | 2008-11-20 20:51:16 +0000 (Thu, 20 Nov 2008) | 3 lines
1130 M /branches/prog/bam/Makefile
1131 M /branches/prog/bam/bam_tview.c
1132 M /branches/prog/bam/bamtk.c
1135 * tview is now a component of bamtk
1137 ------------------------------------------------------------------------
1138 r680 | lh3 | 2008-11-20 19:17:30 +0000 (Thu, 20 Nov 2008) | 2 lines
1140 A /branches/prog/bam/bam_tview.c
1142 text alignment viewer
1144 ------------------------------------------------------------------------
1145 r679 | lh3 | 2008-11-20 19:17:15 +0000 (Thu, 20 Nov 2008) | 5 lines
1147 M /branches/prog/bam/Makefile
1148 M /branches/prog/bam/bam.h
1149 M /branches/prog/bam/bam_index.c
1150 M /branches/prog/bam/bam_lpileup.c
1151 M /branches/prog/bam/bam_pileup.c
1152 M /branches/prog/bam/bamtk.1
1153 M /branches/prog/bam/bamtk.c
1154 M /branches/prog/bam/faidx.c
1157 * added routines to reset pileup bufferes
1158 * fixed a bug in faidx
1159 * add text alignment viewer
1161 ------------------------------------------------------------------------
1162 r678 | lh3 | 2008-11-20 11:05:02 +0000 (Thu, 20 Nov 2008) | 2 lines
1164 M /branches/prog/bam/Makefile
1165 A /branches/prog/bam/bam_lpileup.c (from /branches/prog/bam/bam_tview.c:668)
1166 D /branches/prog/bam/bam_tview.c
1168 rename tview as lpileup
1170 ------------------------------------------------------------------------
1171 r677 | lh3 | 2008-11-20 10:08:52 +0000 (Thu, 20 Nov 2008) | 2 lines
1173 M /branches/prog/bam/razf.c
1177 ------------------------------------------------------------------------
1178 r676 | lh3 | 2008-11-19 22:52:20 +0000 (Wed, 19 Nov 2008) | 2 lines
1180 M /branches/prog/bam/bam.h
1181 M /branches/prog/bam/bam_index.c
1182 M /branches/prog/bam/faidx.h
1186 ------------------------------------------------------------------------
1187 r674 | lh3 | 2008-11-19 21:39:17 +0000 (Wed, 19 Nov 2008) | 2 lines
1189 M /branches/prog/bam/bam.h
1190 M /branches/prog/bam/bamtk.1
1191 M /branches/prog/bam/faidx.h
1193 update documentation
1195 ------------------------------------------------------------------------
1196 r673 | lh3 | 2008-11-19 21:19:03 +0000 (Wed, 19 Nov 2008) | 2 lines
1198 A /branches/prog/bam/bamtk.1
1202 ------------------------------------------------------------------------
1203 r672 | lh3 | 2008-11-19 16:40:49 +0000 (Wed, 19 Nov 2008) | 3 lines
1205 M /branches/prog/bam/bamtk.c
1206 M /branches/prog/bam/faidx.c
1209 * make faidx more error resistant
1211 ------------------------------------------------------------------------
1212 r671 | lh3 | 2008-11-19 16:09:55 +0000 (Wed, 19 Nov 2008) | 2 lines
1214 M /branches/prog/bam/faidx.h
1218 ------------------------------------------------------------------------
1219 r670 | lh3 | 2008-11-19 16:02:39 +0000 (Wed, 19 Nov 2008) | 3 lines
1221 M /branches/prog/bam/bam_pileup.c
1222 M /branches/prog/bam/bamtk.c
1223 M /branches/prog/bam/faidx.c
1226 * show reference sequence in pileup -v (not in the default pileup)
1228 ------------------------------------------------------------------------
1229 r669 | lh3 | 2008-11-19 14:51:17 +0000 (Wed, 19 Nov 2008) | 3 lines
1231 M /branches/prog/bam/Makefile
1232 M /branches/prog/bam/bamtk.c
1233 M /branches/prog/bam/faidx.c
1236 * put faidx in bamtk and remove faidx_main.c
1238 ------------------------------------------------------------------------
1239 r668 | lh3 | 2008-11-19 14:15:05 +0000 (Wed, 19 Nov 2008) | 4 lines
1241 M /branches/prog/bam/Makefile
1242 M /branches/prog/bam/bam_index.c
1243 M /branches/prog/bam/bam_tview.c
1244 M /branches/prog/bam/bamtk.c
1245 A /branches/prog/bam/faidx.c
1246 A /branches/prog/bam/faidx.h
1247 M /branches/prog/bam/razf.c
1250 * fixed a bug in tview.c
1251 * prepare to add faidx
1253 ------------------------------------------------------------------------
1254 r667 | lh3 | 2008-11-19 10:20:45 +0000 (Wed, 19 Nov 2008) | 2 lines
1256 M /branches/prog/bam/bam.h
1257 M /branches/prog/bam/razf.c
1258 M /branches/prog/bam/razf.h
1260 gzip-compatible razf
1262 ------------------------------------------------------------------------
1263 r664 | lh3 | 2008-11-18 12:50:23 +0000 (Tue, 18 Nov 2008) | 5 lines
1265 M /branches/prog/bam/bam.h
1266 M /branches/prog/bam/bam_index.c
1267 M /branches/prog/bam/bamtk.c
1270 * fetch: fixed a bug at an array boundary
1271 * fetch: fixed a bug when the whole chromosome is retrieved
1274 ------------------------------------------------------------------------
1275 r663 | lh3 | 2008-11-17 21:29:22 +0000 (Mon, 17 Nov 2008) | 3 lines
1277 M /branches/prog/bam/Makefile
1278 M /branches/prog/bam/bam.c
1279 M /branches/prog/bam/bam.h
1280 M /branches/prog/bam/bam_import.c
1281 M /branches/prog/bam/bam_pileup.c
1282 M /branches/prog/bam/bam_tview.c
1283 M /branches/prog/bam/bamtk.c
1286 * put l_qseq into core and move l_aux to bam1_t
1288 ------------------------------------------------------------------------
1289 r662 | lh3 | 2008-11-17 20:55:16 +0000 (Mon, 17 Nov 2008) | 3 lines
1291 M /branches/prog/bam/bam.c
1292 M /branches/prog/bam/bam.h
1293 M /branches/prog/bam/bam_import.c
1294 M /branches/prog/bam/bam_index.c
1295 M /branches/prog/bam/bam_pileup.c
1296 M /branches/prog/bam/bamtk.c
1299 * save seq and qual separately
1301 ------------------------------------------------------------------------
1302 r661 | lh3 | 2008-11-17 13:09:37 +0000 (Mon, 17 Nov 2008) | 2 lines
1304 M /branches/prog/bam/bam.h
1308 ------------------------------------------------------------------------
1309 r660 | lh3 | 2008-11-17 13:06:14 +0000 (Mon, 17 Nov 2008) | 2 lines
1311 M /branches/prog/bam/bam.h
1315 ------------------------------------------------------------------------
1316 r659 | lh3 | 2008-11-17 12:55:08 +0000 (Mon, 17 Nov 2008) | 3 lines
1318 M /branches/prog/bam/bam_pileup.c
1319 M /branches/prog/bam/bamtk.c
1322 * make tview work for TAM
1324 ------------------------------------------------------------------------
1325 r658 | lh3 | 2008-11-17 12:50:21 +0000 (Mon, 17 Nov 2008) | 3 lines
1327 M /branches/prog/bam/Makefile
1328 M /branches/prog/bam/bam.h
1329 M /branches/prog/bam/bam_pileup.c
1330 M /branches/prog/bam/bam_tview.c
1331 M /branches/prog/bam/bamtk.c
1334 * make tview as an independent module
1336 ------------------------------------------------------------------------
1337 r657 | lh3 | 2008-11-17 11:26:06 +0000 (Mon, 17 Nov 2008) | 2 lines
1339 M /branches/prog/bam/Makefile
1340 M /branches/prog/bam/bam.h
1341 M /branches/prog/bam/bam_pileup.c
1345 ------------------------------------------------------------------------
1346 r656 | lh3 | 2008-11-16 21:33:19 +0000 (Sun, 16 Nov 2008) | 3 lines
1348 M /branches/prog/bam/bam_pileup.c
1349 M /branches/prog/bam/bamtk.c
1352 * also add tview for TAM
1354 ------------------------------------------------------------------------
1355 r655 | lh3 | 2008-11-16 21:29:46 +0000 (Sun, 16 Nov 2008) | 3 lines
1357 M /branches/prog/bam/Makefile
1358 M /branches/prog/bam/bam_tview.c
1359 M /branches/prog/bam/bamtk.c
1362 * make tview more efficient for deep depth
1364 ------------------------------------------------------------------------
1365 r654 | lh3 | 2008-11-16 20:52:19 +0000 (Sun, 16 Nov 2008) | 4 lines
1367 M /branches/prog/bam/Makefile
1368 M /branches/prog/bam/bam_import.c
1369 M /branches/prog/bam/bam_pileup.c
1370 A /branches/prog/bam/bam_tview.c
1371 M /branches/prog/bam/bamtk.c
1374 * fixed bug in the TAM parser: lowercase not recognized
1375 * unfinished function to leveled pileup (tview)
1377 ------------------------------------------------------------------------
1378 r653 | lh3 | 2008-11-15 12:58:36 +0000 (Sat, 15 Nov 2008) | 3 lines
1380 M /branches/prog/bam/bam.h
1381 M /branches/prog/bam/bam_pileup.c
1382 M /branches/prog/bam/bamtk.c
1385 * pileup now display deleted bases as '*'
1387 ------------------------------------------------------------------------
1388 r652 | lh3 | 2008-11-15 09:58:39 +0000 (Sat, 15 Nov 2008) | 4 lines
1390 M /branches/prog/bam/bam_index.c
1391 M /branches/prog/bam/bamtk.c
1394 * fixed a bug in fetch()
1395 * reduce memory in indexing
1397 ------------------------------------------------------------------------
1398 r651 | lh3 | 2008-11-14 21:56:05 +0000 (Fri, 14 Nov 2008) | 5 lines
1400 M /branches/prog/bam/Makefile
1401 M /branches/prog/bam/bam.h
1402 M /branches/prog/bam/bam_index.c
1403 M /branches/prog/bam/bamtk.c
1406 * important changes are made to index: the index size is increased, but
1407 now we have no limit on file sizes and the new method potentially
1408 works with BGZF, Bob's new compression format.
1410 ------------------------------------------------------------------------
1411 r650 | lh3 | 2008-11-14 16:03:22 +0000 (Fri, 14 Nov 2008) | 4 lines
1413 M /branches/prog/bam/bam.h
1414 M /branches/prog/bam/bam_index.c
1415 M /branches/prog/bam/bamtk.c
1418 * more comments in bam.h
1419 * fixed a bug in bam_index.c
1421 ------------------------------------------------------------------------
1422 r649 | lh3 | 2008-11-13 16:04:18 +0000 (Thu, 13 Nov 2008) | 4 lines
1424 M /branches/prog/bam/bam.c
1425 M /branches/prog/bam/bam.h
1426 M /branches/prog/bam/bam_import.c
1427 M /branches/prog/bam/bam_index.c
1428 M /branches/prog/bam/bam_pileup.c
1429 M /branches/prog/bam/bam_sort.c
1430 M /branches/prog/bam/bamtk.c
1433 * use macros to retrieve pointers from bam1_t and thus reduce the size
1436 ------------------------------------------------------------------------
1437 r648 | lh3 | 2008-11-13 13:21:39 +0000 (Thu, 13 Nov 2008) | 3 lines
1439 M /branches/prog/bam/bam_sort.c
1440 M /branches/prog/bam/bamtk.c
1443 * make more things work over pipe
1445 ------------------------------------------------------------------------
1446 r647 | lh3 | 2008-11-13 12:49:28 +0000 (Thu, 13 Nov 2008) | 2 lines
1448 M /branches/prog/bam/misc/maq2tam.c
1450 fixed a bug in maq2tam
1452 ------------------------------------------------------------------------
1453 r646 | lh3 | 2008-11-13 11:46:59 +0000 (Thu, 13 Nov 2008) | 3 lines
1455 M /branches/prog/bam/Makefile
1456 M /branches/prog/bam/misc/Makefile
1457 M /branches/prog/bam/misc/maq2tam.c
1459 * bug fix in maq2tam.c
1462 ------------------------------------------------------------------------
1463 r645 | lh3 | 2008-11-13 11:39:46 +0000 (Thu, 13 Nov 2008) | 3 lines
1465 A /branches/prog/bam/misc/Makefile
1466 M /branches/prog/bam/misc/maq2tam.c
1471 ------------------------------------------------------------------------
1472 r644 | lh3 | 2008-11-13 11:25:45 +0000 (Thu, 13 Nov 2008) | 2 lines
1474 M /branches/prog/bam/razf.c
1476 fixed the bug in buffered write (on behalf of Jue)
1478 ------------------------------------------------------------------------
1479 r643 | lh3 | 2008-11-13 10:53:42 +0000 (Thu, 13 Nov 2008) | 2 lines
1481 D /branches/prog/bam/all2tam.pl
1482 A /branches/prog/bam/misc/all2tam.pl (from /branches/prog/bam/all2tam.pl:642)
1486 ------------------------------------------------------------------------
1487 r642 | lh3 | 2008-11-13 10:53:23 +0000 (Thu, 13 Nov 2008) | 2 lines
1489 M /branches/prog/bam/all2tam.pl
1493 ------------------------------------------------------------------------
1494 r641 | lh3 | 2008-11-13 10:53:12 +0000 (Thu, 13 Nov 2008) | 2 lines
1496 D /branches/prog/bam/utils
1500 ------------------------------------------------------------------------
1501 r640 | lh3 | 2008-11-13 10:52:50 +0000 (Thu, 13 Nov 2008) | 2 lines
1503 A /branches/prog/bam/misc (from /branches/prog/bam/utils:639)
1507 ------------------------------------------------------------------------
1508 r639 | lh3 | 2008-11-13 10:52:35 +0000 (Thu, 13 Nov 2008) | 2 lines
1510 A /branches/prog/bam/utils
1511 A /branches/prog/bam/utils/maq2tam.c
1513 utilities (converters and so on)
1515 ------------------------------------------------------------------------
1516 r638 | lh3 | 2008-11-12 22:24:22 +0000 (Wed, 12 Nov 2008) | 4 lines
1518 M /branches/prog/bam/bam.c
1519 M /branches/prog/bam/bam.h
1520 M /branches/prog/bam/bam_import.c
1521 M /branches/prog/bam/bamtk.c
1524 * copy the text header to BAM
1525 * add BAM1 header flag
1527 ------------------------------------------------------------------------
1528 r637 | lh3 | 2008-11-12 14:56:08 +0000 (Wed, 12 Nov 2008) | 4 lines
1530 M /branches/prog/bam/bam.h
1531 M /branches/prog/bam/bam_index.c
1532 M /branches/prog/bam/bamtk.c
1533 M /branches/prog/bam/razf.c
1536 * fixed a bug in razf
1537 * improved and fixed potential bugs in index
1539 ------------------------------------------------------------------------
1540 r636 | lh3 | 2008-11-12 11:57:13 +0000 (Wed, 12 Nov 2008) | 2 lines
1542 M /branches/prog/bam/bam.h
1543 M /branches/prog/bam/bam_index.c
1544 M /branches/prog/bam/bam_pileup.c
1545 M /branches/prog/bam/bamtk.c
1547 update documentation in the HeaderDOC format
1549 ------------------------------------------------------------------------
1550 r635 | lh3 | 2008-11-12 10:08:38 +0000 (Wed, 12 Nov 2008) | 4 lines
1552 M /branches/prog/bam/bam.c
1553 M /branches/prog/bam/bam.h
1554 M /branches/prog/bam/bam_import.c
1555 M /branches/prog/bam/bam_index.c
1556 M /branches/prog/bam/bam_pileup.c
1557 M /branches/prog/bam/bamtk.c
1560 * more documentations
1561 * rename baf1_core_t as bam1_core_t
1563 ------------------------------------------------------------------------
1564 r634 | lh3 | 2008-11-11 23:00:35 +0000 (Tue, 11 Nov 2008) | 2 lines
1566 M /branches/prog/bam/bam.h
1567 M /branches/prog/bam/bam_pileup.c
1571 ------------------------------------------------------------------------
1572 r633 | lh3 | 2008-11-11 21:23:49 +0000 (Tue, 11 Nov 2008) | 4 lines
1574 M /branches/prog/bam/bam_index.c
1575 M /branches/prog/bam/bam_pileup.c
1576 M /branches/prog/bam/bamtk.c
1579 * give up regional pileup. We can now use pipe to mimic that.
1580 * for index file, change suffix .idx to .bmi
1582 ------------------------------------------------------------------------
1583 r632 | lh3 | 2008-11-11 21:00:11 +0000 (Tue, 11 Nov 2008) | 3 lines
1585 M /branches/prog/bam/bam.h
1586 M /branches/prog/bam/bam_import.c
1587 M /branches/prog/bam/bam_pileup.c
1588 M /branches/prog/bam/bamtk.c
1589 M /branches/prog/bam/razf.c
1592 * make pileup work on TAM
1594 ------------------------------------------------------------------------
1595 r631 | lh3 | 2008-11-11 09:20:29 +0000 (Tue, 11 Nov 2008) | 4 lines
1597 M /branches/prog/bam/bam_pileup.c
1598 M /branches/prog/bam/bamtk.c
1599 M /branches/prog/bam/razf.c
1600 M /branches/prog/bam/razf.h
1601 M /branches/prog/bam/razip.c
1604 * razf now supports streaming
1605 * prepare to improve pileup (have not yet)
1607 ------------------------------------------------------------------------
1608 r630 | lh3 | 2008-11-10 18:34:40 +0000 (Mon, 10 Nov 2008) | 3 lines
1610 M /branches/prog/bam/bam.h
1611 M /branches/prog/bam/bam_import.c
1612 M /branches/prog/bam/bam_pileup.c
1613 M /branches/prog/bam/bamtk.c
1616 * improve the interface of TAM parser
1618 ------------------------------------------------------------------------
1619 r629 | lh3 | 2008-11-10 13:06:13 +0000 (Mon, 10 Nov 2008) | 3 lines
1621 M /branches/prog/bam/bam_pileup.c
1622 M /branches/prog/bam/bamtk.c
1627 ------------------------------------------------------------------------
1628 r628 | lh3 | 2008-11-10 12:56:36 +0000 (Mon, 10 Nov 2008) | 3 lines
1630 M /branches/prog/bam/bam.c
1631 M /branches/prog/bam/bam.h
1632 M /branches/prog/bam/bam_pileup.c
1633 M /branches/prog/bam/bamtk.c
1636 * fixed a bug in bam_pileup.c
1638 ------------------------------------------------------------------------
1639 r627 | lh3 | 2008-11-10 11:32:46 +0000 (Mon, 10 Nov 2008) | 4 lines
1641 M /branches/prog/bam/bam.h
1642 M /branches/prog/bam/bam_pileup.c
1643 M /branches/prog/bam/bamtk.c
1644 M /branches/prog/bam/razf.c
1647 * fixed a bug in razf.c, caused by my modifications
1648 * improve the interface of pileup. Now it will be slower but more flexible
1650 ------------------------------------------------------------------------
1651 r626 | lh3 | 2008-11-09 20:51:04 +0000 (Sun, 09 Nov 2008) | 3 lines
1653 M /branches/prog/bam/bam.h
1654 M /branches/prog/bam/bamtk.c
1657 * view: dumping binary output
1659 ------------------------------------------------------------------------
1660 r625 | lh3 | 2008-11-09 20:31:54 +0000 (Sun, 09 Nov 2008) | 3 lines
1662 M /branches/prog/bam/bam.c
1663 M /branches/prog/bam/bam.h
1664 M /branches/prog/bam/bam_import.c
1665 M /branches/prog/bam/bam_index.c
1666 M /branches/prog/bam/bam_pileup.c
1667 M /branches/prog/bam/bam_sort.c
1668 M /branches/prog/bam/bamtk.c
1673 ------------------------------------------------------------------------
1674 r624 | lh3 | 2008-11-09 15:07:32 +0000 (Sun, 09 Nov 2008) | 2 lines
1676 M /branches/prog/bam/bam.h
1680 ------------------------------------------------------------------------
1681 r623 | lh3 | 2008-11-08 22:32:49 +0000 (Sat, 08 Nov 2008) | 4 lines
1683 M /branches/prog/bam/bam_index.c
1684 M /branches/prog/bam/bamtk.c
1687 * improve indexing for a mixture of long and short reads, although currently
1688 I do not know whether it really works...
1690 ------------------------------------------------------------------------
1691 r622 | lh3 | 2008-11-08 22:13:58 +0000 (Sat, 08 Nov 2008) | 3 lines
1693 M /branches/prog/bam/bam_index.c
1694 M /branches/prog/bam/bamtk.c
1697 * prepare for improving indexing algorithm
1699 ------------------------------------------------------------------------
1700 r621 | lh3 | 2008-11-08 20:28:09 +0000 (Sat, 08 Nov 2008) | 4 lines
1702 A /branches/prog/bam/all2tam.pl
1703 M /branches/prog/bam/bam.c
1704 M /branches/prog/bam/bam.h
1705 M /branches/prog/bam/bam_import.c
1706 M /branches/prog/bam/bamtk.c
1707 D /branches/prog/bam/tam_utils.pl
1711 * rename tam_utils.pl to all2tam.pl
1713 ------------------------------------------------------------------------
1714 r620 | lh3 | 2008-11-08 17:17:22 +0000 (Sat, 08 Nov 2008) | 2 lines
1716 A /branches/prog/bam
1717 A /branches/prog/bam/Makefile
1718 A /branches/prog/bam/bam.c
1719 A /branches/prog/bam/bam.h
1720 A /branches/prog/bam/bam_endian.h
1721 A /branches/prog/bam/bam_import.c
1722 A /branches/prog/bam/bam_index.c
1723 A /branches/prog/bam/bam_pileup.c
1724 A /branches/prog/bam/bam_sort.c
1725 A /branches/prog/bam/bamtk.c
1726 A /branches/prog/bam/khash.h
1727 A /branches/prog/bam/ksort.h
1728 A /branches/prog/bam/kstream.h
1729 A /branches/prog/bam/razf.c
1730 A /branches/prog/bam/razf.h
1731 A /branches/prog/bam/razip.c
1732 A /branches/prog/bam/tam_utils.pl
1733 A /branches/prog/bam/zutil.h
1735 The Binary Alignment/Mapping format.
1737 ------------------------------------------------------------------------