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date Thu, 20 Feb 2014 00:44:58 -0500
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1 ------------------------------------------------------------------------
2 r925 | lh3lh3 | 2011-02-28 15:45:17 -0500 (Mon, 28 Feb 2011) | 2 lines
3 Changed paths:
4 M /trunk/samtools/phase.c
5
6 minor changes to a heuristic rule
7
8 ------------------------------------------------------------------------
9 r924 | lh3lh3 | 2011-02-28 15:24:04 -0500 (Mon, 28 Feb 2011) | 4 lines
10 Changed paths:
11 M /trunk/samtools/bam.h
12 M /trunk/samtools/bcftools/vcfutils.pl
13 M /trunk/samtools/phase.c
14
15 * 0.1.12-r924:126
16 * fixed a bug in phase (due to recent changes)
17 * fixed a bug in vcf2fq
18
19 ------------------------------------------------------------------------
20 r923 | lh3lh3 | 2011-02-28 12:57:39 -0500 (Mon, 28 Feb 2011) | 5 lines
21 Changed paths:
22 M /trunk/samtools/Makefile
23 M /trunk/samtools/bam.h
24 M /trunk/samtools/bam_plcmd.c
25 M /trunk/samtools/bamtk.c
26 M /trunk/samtools/phase.c
27
28 * put version number in bam.h
29 * write version to BCF
30 * in phase, change the default -q to 37
31 * output a little more information during phasing
32
33 ------------------------------------------------------------------------
34 r922 | lh3lh3 | 2011-02-25 16:40:09 -0500 (Fri, 25 Feb 2011) | 3 lines
35 Changed paths:
36 M /trunk/samtools/bam2bcf.c
37 M /trunk/samtools/bamtk.c
38 M /trunk/samtools/bcftools/bcf.c
39 M /trunk/samtools/bcftools/bcf.tex
40 M /trunk/samtools/bcftools/bcf2qcall.c
41 M /trunk/samtools/bcftools/bcfutils.c
42 M /trunk/samtools/bcftools/ld.c
43 M /trunk/samtools/bcftools/prob1.c
44 M /trunk/samtools/bcftools/vcf.c
45 M /trunk/samtools/cut_target.c
46
47 * change the order of PL/GL according to the latest VCF spec
48 * change the type of SP to int32_t
49
50 ------------------------------------------------------------------------
51 r921 | lh3lh3 | 2011-02-25 14:40:56 -0500 (Fri, 25 Feb 2011) | 2 lines
52 Changed paths:
53 M /trunk/samtools/bcftools/bcf.tex
54
55 update the BCF spec
56
57 ------------------------------------------------------------------------
58 r920 | lh3lh3 | 2011-02-25 00:59:27 -0500 (Fri, 25 Feb 2011) | 2 lines
59 Changed paths:
60 M /trunk/samtools/Makefile
61 M /trunk/samtools/bam_md.c
62 M /trunk/samtools/bam_plcmd.c
63 M /trunk/samtools/bam_sort.c
64 M /trunk/samtools/bamtk.c
65 A /trunk/samtools/cut_target.c
66 M /trunk/samtools/errmod.h
67 M /trunk/samtools/faidx.c
68 M /trunk/samtools/khash.h
69 M /trunk/samtools/kstring.c
70 M /trunk/samtools/kstring.h
71 A /trunk/samtools/phase.c
72 M /trunk/samtools/samtools.1
73
74 added the phase command
75
76 ------------------------------------------------------------------------
77 r918 | lh3lh3 | 2011-02-24 10:05:54 -0500 (Thu, 24 Feb 2011) | 2 lines
78 Changed paths:
79 M /trunk/samtools/bcftools/prob1.c
80 M /trunk/samtools/bcftools/prob1.h
81
82 added "const" to bcf_p1_cal()
83
84 ------------------------------------------------------------------------
85 r917 | lh3lh3 | 2011-02-24 09:36:30 -0500 (Thu, 24 Feb 2011) | 2 lines
86 Changed paths:
87 M /trunk/samtools/bam.c
88
89 more meaningful BAM truncation message
90
91 ------------------------------------------------------------------------
92 r916 | lh3lh3 | 2011-02-24 09:35:06 -0500 (Thu, 24 Feb 2011) | 3 lines
93 Changed paths:
94 M /trunk/samtools/bcftools/bcf.c
95 M /trunk/samtools/bcftools/vcf.c
96
97 * automatically fix errors in GL
98 * output unrecognized FORMAT as "."
99
100 ------------------------------------------------------------------------
101 r913 | lh3lh3 | 2011-02-10 22:59:47 -0500 (Thu, 10 Feb 2011) | 2 lines
102 Changed paths:
103 M /trunk/samtools/bcftools/bcf.h
104 M /trunk/samtools/bcftools/call1.c
105 M /trunk/samtools/bcftools/vcf.c
106
107 finished VCF->BCF conversion
108
109 ------------------------------------------------------------------------
110 r910 | petulda | 2011-02-03 03:13:48 -0500 (Thu, 03 Feb 2011) | 1 line
111 Changed paths:
112 M /trunk/samtools/bcftools/vcfutils.pl
113
114 Prevent division by zero
115 ------------------------------------------------------------------------
116 r909 | lh3lh3 | 2011-02-02 11:29:20 -0500 (Wed, 02 Feb 2011) | 2 lines
117 Changed paths:
118 M /trunk/samtools/bcftools/call1.c
119
120 fixed a typo in the VCF header
121
122 ------------------------------------------------------------------------
123 r908 | lh3lh3 | 2011-02-02 11:28:24 -0500 (Wed, 02 Feb 2011) | 3 lines
124 Changed paths:
125 M /trunk/samtools/bam2bcf.c
126 M /trunk/samtools/bam_index.c
127
128 * fixed an out-of-boundary bug
129 * improved sorting order checking in index
130
131 ------------------------------------------------------------------------
132 r907 | lh3lh3 | 2011-01-29 22:59:20 -0500 (Sat, 29 Jan 2011) | 4 lines
133 Changed paths:
134 M /trunk/samtools/INSTALL
135 M /trunk/samtools/bam_tview.c
136 M /trunk/samtools/knetfile.c
137
138 * avoid a segfault when network connect fails
139 * update INSTALL
140 * fixed a bug in tview on big-endian by Nathan Weeks
141
142 ------------------------------------------------------------------------
143 r903 | lh3lh3 | 2011-01-27 14:50:02 -0500 (Thu, 27 Jan 2011) | 3 lines
144 Changed paths:
145 M /trunk/samtools/bam2bcf_indel.c
146 M /trunk/samtools/bam_md.c
147
148 * fixed a rare memory issue in bam_md.c
149 * fixed a bug in indel calling related to unmapped and refskip reads
150
151 ------------------------------------------------------------------------
152 r902 | lh3lh3 | 2011-01-23 21:46:18 -0500 (Sun, 23 Jan 2011) | 2 lines
153 Changed paths:
154 M /trunk/samtools/bcftools/fet.c
155
156 fixed two minor bugs in Fisher's exact test
157
158 ------------------------------------------------------------------------
159 r899 | petulda | 2011-01-19 09:28:02 -0500 (Wed, 19 Jan 2011) | 1 line
160 Changed paths:
161 M /trunk/samtools/bcftools/vcfutils.pl
162
163 Skip sites with unknown ref
164 ------------------------------------------------------------------------
165 r898 | lh3lh3 | 2011-01-15 12:56:05 -0500 (Sat, 15 Jan 2011) | 2 lines
166 Changed paths:
167 M /trunk/samtools/ChangeLog
168 M /trunk/samtools/bam_maqcns.c
169 M /trunk/samtools/bam_md.c
170
171 move bam_nt16_nt4_table[] from bam_maqcns.c to bam_md.c
172
173 ------------------------------------------------------------------------
174 r896 | lh3lh3 | 2011-01-06 10:52:15 -0500 (Thu, 06 Jan 2011) | 3 lines
175 Changed paths:
176 M /trunk/samtools/bam_plcmd.c
177 M /trunk/samtools/bamtk.c
178 M /trunk/samtools/bcftools/bcf.h
179 M /trunk/samtools/bcftools/bcfutils.c
180 M /trunk/samtools/bcftools/call1.c
181
182 * samtools-0.1.12-10 (r896)
183 * allow to exclude read groups in mpileup
184
185 ------------------------------------------------------------------------
186 r895 | lh3lh3 | 2011-01-04 11:31:29 -0500 (Tue, 04 Jan 2011) | 2 lines
187 Changed paths:
188 M /trunk/samtools/bcftools/bcf.tex
189
190 sorry. It is SP not ST
191
192 ------------------------------------------------------------------------
193 r894 | lh3lh3 | 2011-01-04 11:29:06 -0500 (Tue, 04 Jan 2011) | 2 lines
194 Changed paths:
195 M /trunk/samtools/bcftools/bcf.tex
196
197 added ST
198
199 ------------------------------------------------------------------------
200 r893 | petulda | 2011-01-04 06:55:56 -0500 (Tue, 04 Jan 2011) | 1 line
201 Changed paths:
202 M /trunk/samtools/bcftools/call1.c
203
204 Fixed a typo in read_samples
205 ------------------------------------------------------------------------
206 r892 | jmarshall | 2010-12-28 08:06:49 -0500 (Tue, 28 Dec 2010) | 9 lines
207 Changed paths:
208 M /trunk/samtools/Makefile
209 M /trunk/samtools/bcftools/Makefile
210 M /trunk/samtools/examples/Makefile
211
212 System libraries go *after* user libraries in link commands, because
213 the user libraries may themselves have dependencies that are satisfied
214 by the system libraries. It's not rocket science!
215
216 This makes a difference with some linkers; or with -static or --as-needed.
217
218 The examples/Makefile fix is from Charles Plessy.
219 See also http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=606004
220
221 ------------------------------------------------------------------------
222 r891 | lh3lh3 | 2010-12-21 12:16:33 -0500 (Tue, 21 Dec 2010) | 3 lines
223 Changed paths:
224 M /trunk/samtools/bamtk.c
225 M /trunk/samtools/bcftools/bcf.h
226 M /trunk/samtools/bcftools/bcfutils.c
227 M /trunk/samtools/bcftools/call1.c
228
229 * samtools-0.1.12-9 (r891)
230 * allow to call SNPs from a subset of samples
231
232 ------------------------------------------------------------------------
233 r889 | lh3lh3 | 2010-12-15 11:28:16 -0500 (Wed, 15 Dec 2010) | 3 lines
234 Changed paths:
235 M /trunk/samtools/bam2bcf.c
236 M /trunk/samtools/bamtk.c
237
238 * samtools-0.1.12-12 (r889)
239 * set mapQ as 20 if it equals 255
240
241 ------------------------------------------------------------------------
242 r888 | lh3lh3 | 2010-12-14 22:41:09 -0500 (Tue, 14 Dec 2010) | 2 lines
243 Changed paths:
244 M /trunk/samtools/bam_plcmd.c
245 M /trunk/samtools/bamtk.c
246
247 When -B is applied to mpileup, still use paired reads only unless -A is flagged.
248
249 ------------------------------------------------------------------------
250 r887 | lh3lh3 | 2010-12-14 22:37:05 -0500 (Tue, 14 Dec 2010) | 3 lines
251 Changed paths:
252 M /trunk/samtools/bam_md.c
253 M /trunk/samtools/bam_plcmd.c
254 M /trunk/samtools/bamtk.c
255
256 * samtools-0.1.12-6 (r887)
257 * added a hidden option -E to mpileup/calmd. -E triggers an alternative way to apply BAQ.
258
259 ------------------------------------------------------------------------
260 r886 | lh3lh3 | 2010-12-14 12:51:03 -0500 (Tue, 14 Dec 2010) | 2 lines
261 Changed paths:
262 M /trunk/samtools/bam2bcf_indel.c
263 M /trunk/samtools/bamtk.c
264
265 (Arguably) improved the indel caller a tiny bit for lowCov data.
266
267 ------------------------------------------------------------------------
268 r885 | petulda | 2010-12-14 04:55:46 -0500 (Tue, 14 Dec 2010) | 1 line
269 Changed paths:
270 M /trunk/samtools/bcftools/call1.c
271
272 Fixed the VCF header to pass validation
273 ------------------------------------------------------------------------
274 r884 | lh3lh3 | 2010-12-12 23:02:19 -0500 (Sun, 12 Dec 2010) | 3 lines
275 Changed paths:
276 M /trunk/samtools/bam2bcf_indel.c
277 M /trunk/samtools/bamtk.c
278 M /trunk/samtools/bcftools/vcfutils.pl
279
280 * samtools-0.1.12-4 (r884)
281 * fixed a long-existing flaw in the INDEL calling model
282
283 ------------------------------------------------------------------------
284 r883 | lh3lh3 | 2010-12-11 20:05:42 -0500 (Sat, 11 Dec 2010) | 2 lines
285 Changed paths:
286 M /trunk/samtools/bcftools/bcfutils.c
287 M /trunk/samtools/bcftools/call1.c
288 M /trunk/samtools/bcftools/vcfutils.pl
289
290 compute max SP and max GQ from sample genotypes
291
292 ------------------------------------------------------------------------
293 r880 | lh3lh3 | 2010-12-10 10:50:54 -0500 (Fri, 10 Dec 2010) | 2 lines
294 Changed paths:
295 D /trunk/samtools/bcftools/bcf-fix.pl
296
297 drop bcf-fix.pl as it is redundant by the latest changes
298
299 ------------------------------------------------------------------------
300 r879 | lh3lh3 | 2010-12-10 10:50:29 -0500 (Fri, 10 Dec 2010) | 3 lines
301 Changed paths:
302 M /trunk/samtools/bcftools/call1.c
303 M /trunk/samtools/bcftools/vcf.c
304
305 * fixed a minor issue in printing VCFs
306 * write bcftools specific INFO and FORMAT in the header
307
308 ------------------------------------------------------------------------
309 r878 | lh3lh3 | 2010-12-10 10:09:14 -0500 (Fri, 10 Dec 2010) | 2 lines
310 Changed paths:
311 M /trunk/samtools/bamtk.c
312 M /trunk/samtools/bcftools/bcfutils.c
313 M /trunk/samtools/bcftools/call1.c
314
315 Make sure that the GT genotype field is the first
316
317 ------------------------------------------------------------------------
318 r877 | lh3lh3 | 2010-12-08 17:27:05 -0500 (Wed, 08 Dec 2010) | 7 lines
319 Changed paths:
320 M /trunk/samtools/bam2bcf.c
321 M /trunk/samtools/bam2bcf.h
322 M /trunk/samtools/bam2bcf_indel.c
323 M /trunk/samtools/bam_plcmd.c
324 M /trunk/samtools/bamtk.c
325
326 * samtools-0.1.12-2 (r877)
327
328 * allow to fine control the selection of indel candidates. The current
329 setting is okay for lowCov and highCov with ~100 samples, but it
330 skips too many indels for highCov with >250 samples.
331
332
333 ------------------------------------------------------------------------
334 r874 | lh3lh3 | 2010-12-07 22:40:35 -0500 (Tue, 07 Dec 2010) | 2 lines
335 Changed paths:
336 M /trunk/samtools/bam_plcmd.c
337
338 a spelling error..
339
340 ------------------------------------------------------------------------
341 r873 | lh3lh3 | 2010-12-07 22:39:57 -0500 (Tue, 07 Dec 2010) | 3 lines
342 Changed paths:
343 M /trunk/samtools/bam_plcmd.c
344 M /trunk/samtools/bamtk.c
345
346 * samtools-0.1.12-1 (r873)
347 * added a switch to allow anomalous read pairs in calling
348
349 ------------------------------------------------------------------------
350 r872 | lh3lh3 | 2010-12-07 14:43:54 -0500 (Tue, 07 Dec 2010) | 2 lines
351 Changed paths:
352 M /trunk/samtools/bcftools/vcfutils.pl
353
354 fixed a bug in vcf2fq
355
356 ------------------------------------------------------------------------
357 r869 | lh3lh3 | 2010-12-05 01:18:06 -0500 (Sun, 05 Dec 2010) | 2 lines
358 Changed paths:
359 M /trunk/samtools/bamtk.c
360
361 added a warning for the Windows version
362
363 ------------------------------------------------------------------------
364 r868 | lh3lh3 | 2010-12-05 01:05:51 -0500 (Sun, 05 Dec 2010) | 4 lines
365 Changed paths:
366 M /trunk/samtools/bcftools/call1.c
367
368 In ksprintf(), change "%lf" and "%lg" to "%f" and "%g", respectively.
369 According to the manual page, this change is valid. However, MinGW seems
370 to interpret "%lf" as "%Lf".
371
372 ------------------------------------------------------------------------
373 r867 | lh3lh3 | 2010-12-05 00:35:43 -0500 (Sun, 05 Dec 2010) | 2 lines
374 Changed paths:
375 M /trunk/samtools/Makefile.mingw
376 M /trunk/samtools/bam_aux.c
377
378 bring back the windows support
379
380 ------------------------------------------------------------------------
381 r866 | lh3lh3 | 2010-12-04 23:33:51 -0500 (Sat, 04 Dec 2010) | 2 lines
382 Changed paths:
383 M /trunk/samtools/bam_reheader.c
384 M /trunk/samtools/bcftools/vcfutils.pl
385
386 Fixed a compiling error when knetfile is not used.
387
388 ------------------------------------------------------------------------
389 r865 | lh3lh3 | 2010-12-04 00:13:22 -0500 (Sat, 04 Dec 2010) | 2 lines
390 Changed paths:
391 M /trunk/samtools/bcftools/vcfutils.pl
392
393 vcf->fastq
394
395 ------------------------------------------------------------------------
396 r864 | lh3lh3 | 2010-12-03 17:12:30 -0500 (Fri, 03 Dec 2010) | 3 lines
397 Changed paths:
398 M /trunk/samtools/bcftools/call1.c
399 M /trunk/samtools/bcftools/prob1.c
400 M /trunk/samtools/bcftools/prob1.h
401
402 * remove "-f". Instead always compute consensus quality
403 * increase the upper limit of quality
404
405 ------------------------------------------------------------------------
406 r863 | lh3lh3 | 2010-12-03 15:28:15 -0500 (Fri, 03 Dec 2010) | 2 lines
407 Changed paths:
408 M /trunk/samtools/bcftools/bcf.c
409
410 more informative error message
411
412 ------------------------------------------------------------------------
413 r862 | lh3lh3 | 2010-12-02 16:16:08 -0500 (Thu, 02 Dec 2010) | 2 lines
414 Changed paths:
415 M /trunk/samtools/NEWS
416 M /trunk/samtools/bamtk.c
417
418 Release samtools-0.1.12a
419
420 ------------------------------------------------------------------------
421 r861 | lh3lh3 | 2010-12-02 15:55:06 -0500 (Thu, 02 Dec 2010) | 2 lines
422 Changed paths:
423 M /trunk/samtools/bcftools/call1.c
424
425 a possible fix to DP4=0,0,0,0; have not tested, but should have no side-effect
426
427 ------------------------------------------------------------------------
428 r859 | lh3lh3 | 2010-12-02 11:39:57 -0500 (Thu, 02 Dec 2010) | 2 lines
429 Changed paths:
430 M /trunk/samtools/NEWS
431 M /trunk/samtools/bam_index.c
432 M /trunk/samtools/bamtk.c
433 M /trunk/samtools/samtools.1
434
435 Release samtools-0.1.12
436
437 ------------------------------------------------------------------------
438 r858 | lh3lh3 | 2010-12-02 11:24:41 -0500 (Thu, 02 Dec 2010) | 4 lines
439 Changed paths:
440 M /trunk/samtools/bam_plcmd.c
441 M /trunk/samtools/bamtk.c
442 M /trunk/samtools/bcftools/bcf.c
443
444 * samtools-0.1.11-1 (r858)
445 * fixed a bug in mpileup which causes segfaults
446 * bcftools: do not segfault when BCF contains errors
447
448 ------------------------------------------------------------------------
449 r857 | lh3lh3 | 2010-11-30 23:52:50 -0500 (Tue, 30 Nov 2010) | 2 lines
450 Changed paths:
451 M /trunk/samtools/bam_index.c
452
453 fixed a memory leak in bam_fetch()
454
455 ------------------------------------------------------------------------
456 r856 | lh3lh3 | 2010-11-26 00:07:31 -0500 (Fri, 26 Nov 2010) | 3 lines
457 Changed paths:
458 M /trunk/samtools/bam2bcf_indel.c
459 M /trunk/samtools/bcftools/vcfutils.pl
460
461 * fixed a memory violation
462 * added splitchr to vcfutils.pl
463
464 ------------------------------------------------------------------------
465 r854 | lh3lh3 | 2010-11-23 09:05:08 -0500 (Tue, 23 Nov 2010) | 2 lines
466 Changed paths:
467 M /trunk/samtools/bcftools/ld.c
468
469 fixed a typo/bug in r^2 computation
470
471 ------------------------------------------------------------------------
472 r852 | lh3lh3 | 2010-11-21 22:20:20 -0500 (Sun, 21 Nov 2010) | 2 lines
473 Changed paths:
474 M /trunk/samtools/bamtk.c
475
476 forget to change the version information
477
478 ------------------------------------------------------------------------
479 r851 | lh3lh3 | 2010-11-21 22:16:52 -0500 (Sun, 21 Nov 2010) | 2 lines
480 Changed paths:
481 M /trunk/samtools/ChangeLog
482 M /trunk/samtools/NEWS
483 M /trunk/samtools/bcftools/bcftools.1
484 M /trunk/samtools/samtools.1
485
486 Release samtools-0.1.11
487
488 ------------------------------------------------------------------------
489 r844 | lh3lh3 | 2010-11-19 23:16:08 -0500 (Fri, 19 Nov 2010) | 3 lines
490 Changed paths:
491 M /trunk/samtools/bamtk.c
492 M /trunk/samtools/bcftools/call1.c
493 M /trunk/samtools/bcftools/prob1.c
494 M /trunk/samtools/bcftools/prob1.h
495
496 * samtools-0.1.10-9 (r844)
497 * added the "folded" or reference-free mode for variant calling
498
499 ------------------------------------------------------------------------
500 r843 | lh3lh3 | 2010-11-19 22:26:36 -0500 (Fri, 19 Nov 2010) | 2 lines
501 Changed paths:
502 M /trunk/samtools/NEWS
503 M /trunk/samtools/bam_sort.c
504
505 In merging, if -R is specified, do not abort if the sequence dictionary is different.
506
507 ------------------------------------------------------------------------
508 r842 | jmarshall | 2010-11-19 21:24:28 -0500 (Fri, 19 Nov 2010) | 5 lines
509 Changed paths:
510 M /trunk/samtools/bam_sort.c
511
512 When merging BAM headers, compare the list of target reference sequences
513 strictly (and fail/abort if there is a mismatch), but allow one list to be a
514 prefix of the other. (i.e., check that the lists are identical up until the
515 shorter runs out, and add the excess targets from the longer to the output.)
516
517 ------------------------------------------------------------------------
518 r841 | lh3lh3 | 2010-11-19 14:49:27 -0500 (Fri, 19 Nov 2010) | 4 lines
519 Changed paths:
520 M /trunk/samtools/bam_index.c
521 M /trunk/samtools/bam_pileup.c
522 M /trunk/samtools/bamtk.c
523
524 * samtools-0.1.10 (r841)
525 * fixed a bug in pileup when the first CIGAR operation is D
526 * fixed a bug in view with range query
527
528 ------------------------------------------------------------------------
529 r840 | lh3lh3 | 2010-11-19 13:45:51 -0500 (Fri, 19 Nov 2010) | 10 lines
530 Changed paths:
531 M /trunk/samtools/ChangeLog
532 M /trunk/samtools/bam2bcf.c
533 M /trunk/samtools/bam2bcf.h
534 M /trunk/samtools/bam2bcf_indel.c
535 M /trunk/samtools/bam_plcmd.c
536 M /trunk/samtools/bamtk.c
537
538 * samtools-0.1.10-4 (r840)
539
540 * drop the MNP caller. It is slow while does not diliver too much
541 benefit. Possibly I will work on it in future given more time.
542
543 * there is a segfault in pileup
544
545 * someone has reported segfault from view/index/sort
546
547
548 ------------------------------------------------------------------------
549 r839 | lh3lh3 | 2010-11-18 17:30:11 -0500 (Thu, 18 Nov 2010) | 9 lines
550 Changed paths:
551 M /trunk/samtools/bam2bcf.h
552 M /trunk/samtools/bam2bcf_indel.c
553 M /trunk/samtools/bamtk.c
554
555 * samtools-0.1.10-6 (r839)
556
557 * call MNPs without realignment because it seems to me that it is not
558 worthwhile to significantly slow down SNP calling.
559
560 * the result looks quite different from the previous version. I have
561 work to do...
562
563
564 ------------------------------------------------------------------------
565 r838 | lh3lh3 | 2010-11-18 11:26:09 -0500 (Thu, 18 Nov 2010) | 2 lines
566 Changed paths:
567 M /trunk/samtools/knetfile.c
568
569 Apply a patch by Rob Davis, which improves fault detection.
570
571 ------------------------------------------------------------------------
572 r836 | lh3lh3 | 2010-11-18 11:09:23 -0500 (Thu, 18 Nov 2010) | 3 lines
573 Changed paths:
574 M /trunk/samtools/bam2bcf_indel.c
575 M /trunk/samtools/bamtk.c
576
577 * samtools-r836
578 * initiate MNP realignment when the MNP has at least 0.2% frequency (otherwise too slow)
579
580 ------------------------------------------------------------------------
581 r835 | lh3lh3 | 2010-11-18 00:25:13 -0500 (Thu, 18 Nov 2010) | 3 lines
582 Changed paths:
583 M /trunk/samtools/bcftools/vcfutils.pl
584
585 * modify the filtering rule: also filter SNPs around filtered indels
586 * added MNP filter
587
588 ------------------------------------------------------------------------
589 r834 | lh3lh3 | 2010-11-17 23:13:52 -0500 (Wed, 17 Nov 2010) | 4 lines
590 Changed paths:
591 M /trunk/samtools/bam2bcf.c
592 M /trunk/samtools/bam2bcf_indel.c
593 M /trunk/samtools/bamtk.c
594
595 * samtools-0.1.10-4 (r834)
596 * fixed a silly bug in printing MNP
597 * restrict to at most 1 alternative allele
598
599 ------------------------------------------------------------------------
600 r833 | lh3lh3 | 2010-11-17 21:58:58 -0500 (Wed, 17 Nov 2010) | 2 lines
601 Changed paths:
602 M /trunk/samtools/bam2bcf.c
603 M /trunk/samtools/bamtk.c
604
605 fixed a bug in printing MNPs
606
607 ------------------------------------------------------------------------
608 r832 | lh3lh3 | 2010-11-17 21:47:20 -0500 (Wed, 17 Nov 2010) | 2 lines
609 Changed paths:
610 M /trunk/samtools/bam2bcf_indel.c
611 M /trunk/samtools/bamtk.c
612
613 minor change to how seqQ is applied
614
615 ------------------------------------------------------------------------
616 r831 | lh3lh3 | 2010-11-17 21:41:12 -0500 (Wed, 17 Nov 2010) | 3 lines
617 Changed paths:
618 M /trunk/samtools/bam2bcf.c
619 M /trunk/samtools/bam2bcf.h
620 M /trunk/samtools/bam2bcf_indel.c
621 M /trunk/samtools/bam_plcmd.c
622 M /trunk/samtools/bamtk.c
623
624 * samtools-0.1.10 (r831)
625 * initial MNP caller
626
627 ------------------------------------------------------------------------
628 r829 | lh3lh3 | 2010-11-16 23:14:15 -0500 (Tue, 16 Nov 2010) | 2 lines
629 Changed paths:
630 M /trunk/samtools/ChangeLog
631 M /trunk/samtools/NEWS
632 M /trunk/samtools/bamtk.c
633
634 Release samtools-0.1.10 (r829)
635
636 ------------------------------------------------------------------------
637 r828 | lh3lh3 | 2010-11-16 20:48:49 -0500 (Tue, 16 Nov 2010) | 2 lines
638 Changed paths:
639 M /trunk/samtools/bamtk.c
640
641 update version information: samtools-0.1.9-20 (r828)
642
643 ------------------------------------------------------------------------
644 r827 | lh3lh3 | 2010-11-16 15:32:50 -0500 (Tue, 16 Nov 2010) | 2 lines
645 Changed paths:
646 M /trunk/samtools/bcftools/call1.c
647
648 bcftools: allow to skip indels
649
650 ------------------------------------------------------------------------
651 r826 | lh3lh3 | 2010-11-16 14:11:58 -0500 (Tue, 16 Nov 2010) | 2 lines
652 Changed paths:
653 M /trunk/samtools/bam_md.c
654
655 remove ZQ if both BQ and ZQ are present
656
657 ------------------------------------------------------------------------
658 r825 | lh3lh3 | 2010-11-16 13:51:33 -0500 (Tue, 16 Nov 2010) | 3 lines
659 Changed paths:
660 M /trunk/samtools/bam2bcf_indel.c
661 M /trunk/samtools/bam_md.c
662 M /trunk/samtools/bamtk.c
663 M /trunk/samtools/samtools.1
664
665 * samtools-0.1.9-18 (r825)
666 * change the behaviour of calmd such that by default it does not change the base quality
667
668 ------------------------------------------------------------------------
669 r824 | lh3lh3 | 2010-11-15 23:31:53 -0500 (Mon, 15 Nov 2010) | 4 lines
670 Changed paths:
671 M /trunk/samtools/bam_plcmd.c
672 M /trunk/samtools/bamtk.c
673 M /trunk/samtools/bcftools/call1.c
674 M /trunk/samtools/samtools.1
675
676 * samtools-0.1.9-17 (r824)
677 * added command line options to change the default parameters in indel calling
678 * update the manual
679
680 ------------------------------------------------------------------------
681 r823 | lh3lh3 | 2010-11-15 12:20:13 -0500 (Mon, 15 Nov 2010) | 3 lines
682 Changed paths:
683 M /trunk/samtools/bam2bcf_indel.c
684 M /trunk/samtools/bam_md.c
685 M /trunk/samtools/bamtk.c
686
687 * samtools-0.1.9-r823
688 * the BQ tag is now 64 shifted, not 33 shifted
689
690 ------------------------------------------------------------------------
691 r822 | lh3lh3 | 2010-11-15 00:30:18 -0500 (Mon, 15 Nov 2010) | 3 lines
692 Changed paths:
693 M /trunk/samtools/bam2bcf.c
694 M /trunk/samtools/bam2bcf.h
695 M /trunk/samtools/bamtk.c
696 M /trunk/samtools/bcftools/vcfutils.pl
697 M /trunk/samtools/misc/samtools.pl
698
699 * samtools-0.1.9-16 (r822)
700 * keep the raw depth because in indel calling, DP4 may be way off the true depth
701
702 ------------------------------------------------------------------------
703 r821 | lh3lh3 | 2010-11-13 01:18:31 -0500 (Sat, 13 Nov 2010) | 4 lines
704 Changed paths:
705 M /trunk/samtools/bam_md.c
706 M /trunk/samtools/bamtk.c
707
708 * samtools-0.1.9-15 (r821)
709 * calmd: write BQ
710 * skip realignment if BQ is present
711
712 ------------------------------------------------------------------------
713 r820 | lh3lh3 | 2010-11-13 01:08:26 -0500 (Sat, 13 Nov 2010) | 3 lines
714 Changed paths:
715 M /trunk/samtools/bam2bcf_indel.c
716 M /trunk/samtools/bamtk.c
717
718 * samtools-0.1.9-14 (r820)
719 * penalize reads with excessive differences in indel calling
720
721 ------------------------------------------------------------------------
722 r819 | lh3lh3 | 2010-11-12 21:36:27 -0500 (Fri, 12 Nov 2010) | 3 lines
723 Changed paths:
724 M /trunk/samtools/bam_maqcns.c
725 M /trunk/samtools/bamtk.c
726
727 * samtools-0.1.9-13 (r819)
728 * fixed a bug in pileup given refskip
729
730 ------------------------------------------------------------------------
731 r818 | lh3lh3 | 2010-11-12 13:04:53 -0500 (Fri, 12 Nov 2010) | 3 lines
732 Changed paths:
733 M /trunk/samtools/bam2bcf_indel.c
734 M /trunk/samtools/bamtk.c
735
736 * samtools-r818
737 * for indel calling, do two rounds of probabilistic realignments
738
739 ------------------------------------------------------------------------
740 r817 | lh3lh3 | 2010-11-11 20:04:07 -0500 (Thu, 11 Nov 2010) | 3 lines
741 Changed paths:
742 M /trunk/samtools/bam2bcf_indel.c
743 M /trunk/samtools/bamtk.c
744 M /trunk/samtools/bcftools/vcfutils.pl
745
746 * samtools-0.1.19-11 (r817)
747 * only initiate indel calling when 0.2% of reads contain a gap
748
749 ------------------------------------------------------------------------
750 r816 | lh3lh3 | 2010-11-11 01:22:59 -0500 (Thu, 11 Nov 2010) | 7 lines
751 Changed paths:
752 M /trunk/samtools/bam2bcf_indel.c
753 M /trunk/samtools/bamtk.c
754
755 * samtools-0.1.9-10 (r816)
756
757 * I know why the forward method fails. it is because of zero base
758 qualities. when that is fixed, the forward method seems to give
759 better results than Viterbi, as it should be. I am tired...
760
761
762 ------------------------------------------------------------------------
763 r815 | lh3lh3 | 2010-11-11 00:57:15 -0500 (Thu, 11 Nov 2010) | 2 lines
764 Changed paths:
765 M /trunk/samtools/ChangeLog
766 M /trunk/samtools/bam2bcf_indel.c
767
768 effectively revert to the viterbi version. The forward realignment gives too many false positives.
769
770 ------------------------------------------------------------------------
771 r814 | lh3lh3 | 2010-11-11 00:18:02 -0500 (Thu, 11 Nov 2010) | 4 lines
772 Changed paths:
773 M /trunk/samtools/bam2bcf_indel.c
774 M /trunk/samtools/bam_md.c
775 M /trunk/samtools/bam_plcmd.c
776 M /trunk/samtools/bamtk.c
777
778 * samtools-0.1.9-9 (r810)
779 * use forward, instead of viterbi, for realignment
780 * realignment is now quality aware
781
782 ------------------------------------------------------------------------
783 r813 | lh3lh3 | 2010-11-10 22:45:24 -0500 (Wed, 10 Nov 2010) | 2 lines
784 Changed paths:
785 M /trunk/samtools/bam2bcf_indel.c
786 M /trunk/samtools/kprobaln.c
787 M /trunk/samtools/kprobaln.h
788
789 * prepare to replace kaln with kprobaln in realignment
790
791 ------------------------------------------------------------------------
792 r812 | lh3lh3 | 2010-11-10 17:28:50 -0500 (Wed, 10 Nov 2010) | 2 lines
793 Changed paths:
794 M /trunk/samtools/bcftools/bcf.c
795
796 fixed a typo
797
798 ------------------------------------------------------------------------
799 r811 | lh3lh3 | 2010-11-10 16:54:46 -0500 (Wed, 10 Nov 2010) | 2 lines
800 Changed paths:
801 M /trunk/samtools/bcftools/bcf.c
802 M /trunk/samtools/bcftools/bcf.h
803
804 use zlib for direct reading when BCF_LITE is in use
805
806 ------------------------------------------------------------------------
807 r810 | lh3lh3 | 2010-11-10 16:32:13 -0500 (Wed, 10 Nov 2010) | 3 lines
808 Changed paths:
809 M /trunk/samtools/bam2bcf_indel.c
810
811 * do not use reads containing too many mismatches for indel calling
812 * fixed a trivial bug in case of multi-allelic indels
813
814 ------------------------------------------------------------------------
815 r809 | lh3lh3 | 2010-11-10 13:23:02 -0500 (Wed, 10 Nov 2010) | 3 lines
816 Changed paths:
817 M /trunk/samtools/bam2bcf.c
818 M /trunk/samtools/bam2bcf_indel.c
819 M /trunk/samtools/bam_plcmd.c
820 M /trunk/samtools/bamtk.c
821
822 * samtools-0.1.9-8 (r809)
823 * fixed a bug in the indel caller
824
825 ------------------------------------------------------------------------
826 r808 | lh3lh3 | 2010-11-10 12:24:10 -0500 (Wed, 10 Nov 2010) | 2 lines
827 Changed paths:
828 M /trunk/samtools/Makefile
829
830 minor change to makefile
831
832 ------------------------------------------------------------------------
833 r807 | lh3lh3 | 2010-11-10 12:10:21 -0500 (Wed, 10 Nov 2010) | 4 lines
834 Changed paths:
835 M /trunk/samtools/Makefile
836 M /trunk/samtools/bam2bcf.h
837 M /trunk/samtools/bam2bcf_indel.c
838 M /trunk/samtools/bam_plcmd.c
839 M /trunk/samtools/bamtk.c
840 M /trunk/samtools/bcftools/vcfutils.pl
841
842 * samtools-0.1.9-8 (r807)
843 * collect indel candidates only from specified platforms (@RG-PL)
844 * merge varFilter and filter4vcf in vcfutils.pl
845
846 ------------------------------------------------------------------------
847 r806 | lh3lh3 | 2010-11-09 22:05:46 -0500 (Tue, 09 Nov 2010) | 2 lines
848 Changed paths:
849 M /trunk/samtools/bcftools/call1.c
850 M /trunk/samtools/bcftools/prob1.c
851 M /trunk/samtools/bcftools/prob1.h
852
853 bcftools: compute equal-tail (Bayesian) credible interval
854
855 ------------------------------------------------------------------------
856 r805 | lh3lh3 | 2010-11-09 16:28:39 -0500 (Tue, 09 Nov 2010) | 2 lines
857 Changed paths:
858 M /trunk/samtools/bcftools/vcfutils.pl
859
860 added a double-hit filter to avoid overestimated indel likelihood
861
862 ------------------------------------------------------------------------
863 r804 | lh3lh3 | 2010-11-09 14:12:06 -0500 (Tue, 09 Nov 2010) | 3 lines
864 Changed paths:
865 M /trunk/samtools/bam2bcf_indel.c
866 M /trunk/samtools/bamtk.c
867
868 * samtools-0.1.9-7 (r804)
869 * fixed a bug in the gap caller
870
871 ------------------------------------------------------------------------
872 r803 | lh3lh3 | 2010-11-09 10:45:33 -0500 (Tue, 09 Nov 2010) | 4 lines
873 Changed paths:
874 M /trunk/samtools/bam2bcf.c
875 M /trunk/samtools/bam2bcf_indel.c
876 M /trunk/samtools/bamtk.c
877 M /trunk/samtools/bcftools/bcf.c
878 M /trunk/samtools/bcftools/bcf.h
879 M /trunk/samtools/bcftools/prob1.c
880
881 * samtools-0.1.9-6 (r803)
882 * mpileup: apply homopolymer correction when calculating GL, instead of before
883 * bcftools: apply a different prior to indels
884
885 ------------------------------------------------------------------------
886 r802 | lh3lh3 | 2010-11-08 23:53:15 -0500 (Mon, 08 Nov 2010) | 3 lines
887 Changed paths:
888 M /trunk/samtools/bam2bcf.c
889 M /trunk/samtools/bamtk.c
890
891 * samtools-0.1.9-5 (r802)
892 * relax tandem penalty. this will be made a command-line option in future.
893
894 ------------------------------------------------------------------------
895 r801 | lh3lh3 | 2010-11-08 23:35:52 -0500 (Mon, 08 Nov 2010) | 3 lines
896 Changed paths:
897 M /trunk/samtools/bam2bcf.c
898 M /trunk/samtools/bamtk.c
899
900 * samtools-0.1.9-4 (r801)
901 * fixed a minor issue in printing indel VCF
902
903 ------------------------------------------------------------------------
904 r800 | lh3lh3 | 2010-11-08 15:28:14 -0500 (Mon, 08 Nov 2010) | 2 lines
905 Changed paths:
906 M /trunk/samtools/bam2bcf_indel.c
907 M /trunk/samtools/bcftools/vcfutils.pl
908
909 fixed another silly bug in mpileup's indel caller
910
911 ------------------------------------------------------------------------
912 r799 | lh3lh3 | 2010-11-08 14:28:27 -0500 (Mon, 08 Nov 2010) | 2 lines
913 Changed paths:
914 M /trunk/samtools/bam2bcf.c
915
916 fixed a silly bug in the indel caller
917
918 ------------------------------------------------------------------------
919 r798 | lh3lh3 | 2010-11-08 14:07:33 -0500 (Mon, 08 Nov 2010) | 2 lines
920 Changed paths:
921 M /trunk/samtools/ChangeLog
922 M /trunk/samtools/sam_view.c
923 M /trunk/samtools/samtools.1
924
925 Incorporate patches by Marcel Martin for read counting.
926
927 ------------------------------------------------------------------------
928 r797 | lh3lh3 | 2010-11-08 13:39:52 -0500 (Mon, 08 Nov 2010) | 3 lines
929 Changed paths:
930 M /trunk/samtools/bam2bcf.c
931 M /trunk/samtools/bam2bcf.h
932 M /trunk/samtools/bam2bcf_indel.c
933 M /trunk/samtools/bam_plcmd.c
934 M /trunk/samtools/bamtk.c
935
936 * samtools-0.1.9-2 (r797)
937 * mpileup: indel calling seems to be working
938
939 ------------------------------------------------------------------------
940 r796 | lh3lh3 | 2010-11-08 10:54:46 -0500 (Mon, 08 Nov 2010) | 2 lines
941 Changed paths:
942 M /trunk/samtools/bam2bcf.c
943 M /trunk/samtools/bam2bcf.h
944 M /trunk/samtools/bam2bcf_indel.c
945 M /trunk/samtools/bam_plcmd.c
946 M /trunk/samtools/kaln.c
947
948 indel calling is apparently working, but more information needs to be collected
949
950 ------------------------------------------------------------------------
951 r795 | lh3lh3 | 2010-11-08 00:39:18 -0500 (Mon, 08 Nov 2010) | 2 lines
952 Changed paths:
953 M /trunk/samtools/bam2bcf.c
954 M /trunk/samtools/bam2bcf_indel.c
955
956 fixed a few bugs in the indel caller. Probably there are more.
957
958 ------------------------------------------------------------------------
959 r794 | lh3lh3 | 2010-11-07 22:23:16 -0500 (Sun, 07 Nov 2010) | 2 lines
960 Changed paths:
961 M /trunk/samtools/Makefile
962 M /trunk/samtools/bam.h
963 M /trunk/samtools/bam2bcf.c
964 M /trunk/samtools/bam2bcf.h
965 A /trunk/samtools/bam2bcf_indel.c
966 M /trunk/samtools/bam_plcmd.c
967 M /trunk/samtools/kaln.c
968 M /trunk/samtools/kaln.h
969
970 prepare for the indel caller. It is not ready yet.
971
972 ------------------------------------------------------------------------
973 r793 | lh3lh3 | 2010-11-05 11:28:23 -0400 (Fri, 05 Nov 2010) | 2 lines
974 Changed paths:
975 M /trunk/samtools/bam2bcf.c
976 M /trunk/samtools/bam2bcf.h
977 M /trunk/samtools/bam_plcmd.c
978
979 Revert to r790. The recent changes are not good...
980
981 ------------------------------------------------------------------------
982 r792 | lh3lh3 | 2010-11-05 00:19:14 -0400 (Fri, 05 Nov 2010) | 6 lines
983 Changed paths:
984 M /trunk/samtools/bam2bcf.c
985 M /trunk/samtools/bam2bcf.h
986 M /trunk/samtools/bam_plcmd.c
987
988 * this revision is UNSTABLE
989
990 * indel caller seems working, but it is very insensitive and has
991 several things I do not quite understand.
992
993
994 ------------------------------------------------------------------------
995 r791 | lh3lh3 | 2010-11-04 22:58:43 -0400 (Thu, 04 Nov 2010) | 2 lines
996 Changed paths:
997 M /trunk/samtools/bam2bcf.c
998 M /trunk/samtools/bam2bcf.h
999 M /trunk/samtools/bam_plcmd.c
1000
1001 for backup. no effective changes
1002
1003 ------------------------------------------------------------------------
1004 r790 | lh3lh3 | 2010-11-03 15:51:24 -0400 (Wed, 03 Nov 2010) | 2 lines
1005 Changed paths:
1006 M /trunk/samtools/bcftools/vcfutils.pl
1007 M /trunk/samtools/kprobaln.c
1008
1009 fixed a minor problem in the example coming with kprobaln.c
1010
1011 ------------------------------------------------------------------------
1012 r789 | lh3lh3 | 2010-11-02 15:41:27 -0400 (Tue, 02 Nov 2010) | 4 lines
1013 Changed paths:
1014 M /trunk/samtools/Makefile
1015 M /trunk/samtools/bam_md.c
1016 M /trunk/samtools/kaln.c
1017 M /trunk/samtools/kaln.h
1018 A /trunk/samtools/kprobaln.c
1019 A /trunk/samtools/kprobaln.h
1020
1021 Separate kaln and kprobaln as I am preparing further changes. At
1022 present, the results should be identical to the previous.
1023
1024
1025 ------------------------------------------------------------------------
1026 r788 | petulda | 2010-11-02 12:19:04 -0400 (Tue, 02 Nov 2010) | 1 line
1027 Changed paths:
1028 M /trunk/samtools/bam_plcmd.c
1029
1030 Added -b option: read file names from a file
1031 ------------------------------------------------------------------------
1032 r787 | lh3lh3 | 2010-10-29 23:17:22 -0400 (Fri, 29 Oct 2010) | 7 lines
1033 Changed paths:
1034 M /trunk/samtools/bam.h
1035 M /trunk/samtools/bam_pileup.c
1036 M /trunk/samtools/bam_plcmd.c
1037 M /trunk/samtools/bamtk.c
1038
1039 * samtools-0.1.9-2 (r787)
1040
1041 * Allow to set a maximum per-sample depth to reduce memory. However,
1042 BAQ computation is still applied to every read. The speed is not
1043 improved.
1044
1045
1046 ------------------------------------------------------------------------
1047 r786 | lh3lh3 | 2010-10-29 12:10:40 -0400 (Fri, 29 Oct 2010) | 3 lines
1048 Changed paths:
1049 M /trunk/samtools/bam2bcf.c
1050 M /trunk/samtools/bam2bcf.h
1051 M /trunk/samtools/bam_plcmd.c
1052 M /trunk/samtools/bamtk.c
1053 M /trunk/samtools/bcftools/bcf.c
1054 M /trunk/samtools/bcftools/vcf.c
1055
1056 * samtools-0.1.9-1 (r786)
1057 * samtools: optionally perform exact test for each sample
1058
1059 ------------------------------------------------------------------------
1060 r785 | lh3lh3 | 2010-10-29 09:42:25 -0400 (Fri, 29 Oct 2010) | 2 lines
1061 Changed paths:
1062 M /trunk/samtools/bam2bcf.c
1063 M /trunk/samtools/bam2bcf.h
1064 M /trunk/samtools/bam_plcmd.c
1065 M /trunk/samtools/bcftools/bcf.c
1066
1067 Optionally output "DP", the individual read depth
1068
1069 ------------------------------------------------------------------------
1070 r784 | lh3lh3 | 2010-10-27 23:10:27 -0400 (Wed, 27 Oct 2010) | 2 lines
1071 Changed paths:
1072 M /trunk/samtools/samtools.1
1073
1074 acknowledge Petr and John who have greatly contributed to the project.
1075
1076 ------------------------------------------------------------------------
1077 r783 | lh3lh3 | 2010-10-27 22:47:47 -0400 (Wed, 27 Oct 2010) | 2 lines
1078 Changed paths:
1079 M /trunk/samtools/ChangeLog
1080 M /trunk/samtools/NEWS
1081 M /trunk/samtools/bamtk.c
1082 M /trunk/samtools/samtools.1
1083
1084 Release samtools-0.1.9 (r783)
1085
1086 ------------------------------------------------------------------------
1087 r782 | lh3lh3 | 2010-10-27 19:58:54 -0400 (Wed, 27 Oct 2010) | 2 lines
1088 Changed paths:
1089 M /trunk/samtools/bam_plcmd.c
1090
1091 fixed a silly bug in pileup
1092
1093 ------------------------------------------------------------------------
1094 r781 | lh3lh3 | 2010-10-27 14:39:48 -0400 (Wed, 27 Oct 2010) | 5 lines
1095 Changed paths:
1096 M /trunk/samtools/ChangeLog
1097 M /trunk/samtools/bam_plcmd.c
1098 M /trunk/samtools/bam_sort.c
1099 M /trunk/samtools/bamtk.c
1100 M /trunk/samtools/samtools.1
1101
1102 * samtools-0.1.8-22 (r781)
1103 * made BAQ the default behavior of mpileup
1104 * updated manual
1105 * in merge, force to exit given inconsistent header when "-R" is not in use.
1106
1107 ------------------------------------------------------------------------
1108 r780 | lh3lh3 | 2010-10-27 11:01:11 -0400 (Wed, 27 Oct 2010) | 3 lines
1109 Changed paths:
1110 M /trunk/samtools/bam.h
1111 M /trunk/samtools/bam_plcmd.c
1112 M /trunk/samtools/bamtk.c
1113
1114 * samtools-0.1.8-21 (r780)
1115 * minor speedup to pileup
1116
1117 ------------------------------------------------------------------------
1118 r779 | lh3lh3 | 2010-10-27 09:58:56 -0400 (Wed, 27 Oct 2010) | 2 lines
1119 Changed paths:
1120 M /trunk/samtools/bam_pileup.c
1121 M /trunk/samtools/bam_plcmd.c
1122 M /trunk/samtools/examples/toy.sam
1123
1124 improve pileup a little bit
1125
1126 ------------------------------------------------------------------------
1127 r778 | lh3lh3 | 2010-10-27 00:14:43 -0400 (Wed, 27 Oct 2010) | 3 lines
1128 Changed paths:
1129 M /trunk/samtools/bam.h
1130 M /trunk/samtools/bam_pileup.c
1131 M /trunk/samtools/bam_plcmd.c
1132 M /trunk/samtools/bam_tview.c
1133 M /trunk/samtools/bamtk.c
1134
1135 * samtools-0.1.8-20 (r778)
1136 * speed up pileup, although I do not know how much is the improvement
1137
1138 ------------------------------------------------------------------------
1139 r777 | lh3lh3 | 2010-10-26 17:26:04 -0400 (Tue, 26 Oct 2010) | 3 lines
1140 Changed paths:
1141 M /trunk/samtools/bam_maqcns.c
1142 M /trunk/samtools/bam_maqcns.h
1143 M /trunk/samtools/bam_plcmd.c
1144 M /trunk/samtools/bamtk.c
1145 M /trunk/samtools/examples/Makefile
1146
1147 * samtools-0.1.8-19 (r777)
1148 * integrate mpileup features to pileup: min_baseQ, capQ, prob_realn, paired-only and biased prior
1149
1150 ------------------------------------------------------------------------
1151 r776 | lh3lh3 | 2010-10-26 15:27:46 -0400 (Tue, 26 Oct 2010) | 2 lines
1152 Changed paths:
1153 M /trunk/samtools/bam_md.c
1154
1155 remove local realignment (probabilistic realignment is still there)
1156
1157 ------------------------------------------------------------------------
1158 r774 | jmarshall | 2010-10-21 06:52:38 -0400 (Thu, 21 Oct 2010) | 3 lines
1159 Changed paths:
1160 M /trunk/samtools/sam_view.c
1161
1162 Add the relevant filename or region to error messages, and cause a failure
1163 exit status where appropriate. Based on a patch provided by Marcel Martin.
1164
1165 ------------------------------------------------------------------------
1166 r773 | lh3lh3 | 2010-10-19 19:44:31 -0400 (Tue, 19 Oct 2010) | 3 lines
1167 Changed paths:
1168 M /trunk/samtools/examples/toy.sam
1169 M /trunk/samtools/kaln.c
1170
1171 * Minor code changes. No real effect.
1172 * change quality to 30 in toy.sam
1173
1174 ------------------------------------------------------------------------
1175 r772 | lh3lh3 | 2010-10-18 23:40:13 -0400 (Mon, 18 Oct 2010) | 2 lines
1176 Changed paths:
1177 M /trunk/samtools/examples/toy.fa
1178 M /trunk/samtools/examples/toy.sam
1179
1180 added another toy example
1181
1182 ------------------------------------------------------------------------
1183 r771 | lh3lh3 | 2010-10-13 23:32:12 -0400 (Wed, 13 Oct 2010) | 2 lines
1184 Changed paths:
1185 M /trunk/samtools/bcftools/call1.c
1186 M /trunk/samtools/bcftools/ld.c
1187 M /trunk/samtools/bcftools/vcfutils.pl
1188
1189 improve the LD statistics
1190
1191 ------------------------------------------------------------------------
1192 r770 | lh3lh3 | 2010-10-12 23:49:26 -0400 (Tue, 12 Oct 2010) | 3 lines
1193 Changed paths:
1194 M /trunk/samtools/bcftools/call1.c
1195 M /trunk/samtools/bcftools/vcfutils.pl
1196
1197 * a minor fix to the -L option
1198 * add ldstats to vcfutils.pl
1199
1200 ------------------------------------------------------------------------
1201 r769 | lh3lh3 | 2010-10-12 15:51:57 -0400 (Tue, 12 Oct 2010) | 2 lines
1202 Changed paths:
1203 M /trunk/samtools/bcftools/bcf.c
1204
1205 a minor change
1206
1207 ------------------------------------------------------------------------
1208 r768 | lh3lh3 | 2010-10-12 15:49:06 -0400 (Tue, 12 Oct 2010) | 2 lines
1209 Changed paths:
1210 M /trunk/samtools/bcftools/Makefile
1211 A /trunk/samtools/bcftools/ld.c
1212
1213 forget to add the key file
1214
1215 ------------------------------------------------------------------------
1216 r767 | lh3lh3 | 2010-10-12 15:48:46 -0400 (Tue, 12 Oct 2010) | 4 lines
1217 Changed paths:
1218 M /trunk/samtools/bcftools/Makefile
1219 M /trunk/samtools/bcftools/bcf.c
1220 M /trunk/samtools/bcftools/bcf.h
1221 M /trunk/samtools/bcftools/call1.c
1222 M /trunk/samtools/bcftools/prob1.c
1223 M /trunk/samtools/bcftools/vcfutils.pl
1224
1225 * vcfutils.pl: fixed a typo in help message
1226 * added APIs: bcf_append_info() and bcf_cpy()
1227 * calculate adjacent LD
1228
1229 ------------------------------------------------------------------------
1230 r766 | lh3lh3 | 2010-10-11 11:06:40 -0400 (Mon, 11 Oct 2010) | 2 lines
1231 Changed paths:
1232 M /trunk/samtools/bcftools/vcfutils.pl
1233
1234 added filter for samtools/bcftools genetated VCFs
1235
1236 ------------------------------------------------------------------------
1237 r765 | lh3lh3 | 2010-10-05 14:05:18 -0400 (Tue, 05 Oct 2010) | 3 lines
1238 Changed paths:
1239 M /trunk/samtools/bcftools/vcfutils.pl
1240 M /trunk/samtools/kaln.c
1241
1242 * removed a comment line in kaln.c
1243 * vcfutils.pl fillac works when GT is not the first field
1244
1245 ------------------------------------------------------------------------
1246 r764 | petulda | 2010-10-05 08:59:36 -0400 (Tue, 05 Oct 2010) | 1 line
1247 Changed paths:
1248 A /trunk/samtools/bcftools/bcf-fix.pl
1249
1250 Convert VCF output of "bcftools view -bgcv" to a valid VCF file
1251 ------------------------------------------------------------------------
1252 r763 | lh3lh3 | 2010-10-02 22:51:03 -0400 (Sat, 02 Oct 2010) | 4 lines
1253 Changed paths:
1254 M /trunk/samtools/bam_plcmd.c
1255 M /trunk/samtools/bamtk.c
1256 A /trunk/samtools/bcftools/bcftools.1
1257 M /trunk/samtools/bcftools/call1.c
1258 M /trunk/samtools/samtools.1
1259
1260 * samtools-0.1.8-18 (r763)
1261 * added bcftools manual page
1262 * minor fix to mpileup and view command lines
1263
1264 ------------------------------------------------------------------------
1265 r762 | lh3lh3 | 2010-10-02 21:46:25 -0400 (Sat, 02 Oct 2010) | 3 lines
1266 Changed paths:
1267 M /trunk/samtools/bcftools/bcf.c
1268 M /trunk/samtools/bcftools/call1.c
1269 M /trunk/samtools/bcftools/vcfutils.pl
1270
1271 * vcfutils.pl qstats: calculate marginal ts/tv
1272 * allow to call genotypes at variant sites
1273
1274 ------------------------------------------------------------------------
1275 r761 | lh3lh3 | 2010-10-01 00:29:55 -0400 (Fri, 01 Oct 2010) | 3 lines
1276 Changed paths:
1277 M /trunk/samtools/kaln.c
1278 M /trunk/samtools/misc/HmmGlocal.java
1279
1280 I am changing the gap open probability back to 0.001. It seems that
1281 being conservative here is a good thing...
1282
1283 ------------------------------------------------------------------------
1284 r760 | lh3lh3 | 2010-10-01 00:11:27 -0400 (Fri, 01 Oct 2010) | 5 lines
1285 Changed paths:
1286 M /trunk/samtools/bamtk.c
1287 M /trunk/samtools/kaln.c
1288 A /trunk/samtools/misc/HmmGlocal.java
1289
1290 * samtools-0.1.8-17 (r760)
1291 * the default gap open penalty is too small (a typo)
1292 * added comments on hmm_realn
1293 * Java implementation
1294
1295 ------------------------------------------------------------------------
1296 r759 | lh3lh3 | 2010-09-30 10:12:54 -0400 (Thu, 30 Sep 2010) | 2 lines
1297 Changed paths:
1298 M /trunk/samtools/bamtk.c
1299
1300 mark samtools-0.1.8-16 (r759)
1301
1302 ------------------------------------------------------------------------
1303 r758 | lh3lh3 | 2010-09-30 10:12:02 -0400 (Thu, 30 Sep 2010) | 2 lines
1304 Changed paths:
1305 M /trunk/samtools/kaln.c
1306
1307 round to the nearest integer
1308
1309 ------------------------------------------------------------------------
1310 r757 | lh3lh3 | 2010-09-28 17:16:43 -0400 (Tue, 28 Sep 2010) | 4 lines
1311 Changed paths:
1312 M /trunk/samtools/kaln.c
1313
1314 I was trying to accelerate ka_prob_glocal() as this will be the
1315 bottleneck. After an hour, the only gain is to change division to
1316 multiplication. OK. I will stop.
1317
1318 ------------------------------------------------------------------------
1319 r756 | lh3lh3 | 2010-09-28 16:57:49 -0400 (Tue, 28 Sep 2010) | 2 lines
1320 Changed paths:
1321 M /trunk/samtools/kaln.c
1322
1323 this is interesting. multiplication is much faster than division, at least on my Mac
1324
1325 ------------------------------------------------------------------------
1326 r755 | lh3lh3 | 2010-09-28 16:19:13 -0400 (Tue, 28 Sep 2010) | 2 lines
1327 Changed paths:
1328 M /trunk/samtools/kaln.c
1329
1330 minor changes
1331
1332 ------------------------------------------------------------------------
1333 r754 | lh3lh3 | 2010-09-28 15:44:16 -0400 (Tue, 28 Sep 2010) | 2 lines
1334 Changed paths:
1335 M /trunk/samtools/bam_md.c
1336 M /trunk/samtools/bam_plcmd.c
1337 M /trunk/samtools/kaln.c
1338
1339 prob_realn() seems working!
1340
1341 ------------------------------------------------------------------------
1342 r753 | lh3lh3 | 2010-09-28 12:48:23 -0400 (Tue, 28 Sep 2010) | 2 lines
1343 Changed paths:
1344 M /trunk/samtools/kaln.c
1345
1346 minor
1347
1348 ------------------------------------------------------------------------
1349 r752 | lh3lh3 | 2010-09-28 12:47:41 -0400 (Tue, 28 Sep 2010) | 2 lines
1350 Changed paths:
1351 M /trunk/samtools/kaln.c
1352 M /trunk/samtools/kaln.h
1353
1354 Convert phredQ to probabilities
1355
1356 ------------------------------------------------------------------------
1357 r751 | lh3lh3 | 2010-09-28 12:32:08 -0400 (Tue, 28 Sep 2010) | 2 lines
1358 Changed paths:
1359 M /trunk/samtools/kaln.c
1360 M /trunk/samtools/kaln.h
1361
1362 Implement the glocal HMM; discard the extention HMM
1363
1364 ------------------------------------------------------------------------
1365 r750 | lh3lh3 | 2010-09-28 00:06:11 -0400 (Tue, 28 Sep 2010) | 2 lines
1366 Changed paths:
1367 M /trunk/samtools/kaln.c
1368
1369 improve numerical stability
1370
1371 ------------------------------------------------------------------------
1372 r749 | lh3lh3 | 2010-09-27 23:27:54 -0400 (Mon, 27 Sep 2010) | 2 lines
1373 Changed paths:
1374 M /trunk/samtools/kaln.c
1375
1376 more comments
1377
1378 ------------------------------------------------------------------------
1379 r748 | lh3lh3 | 2010-09-27 23:17:16 -0400 (Mon, 27 Sep 2010) | 2 lines
1380 Changed paths:
1381 M /trunk/samtools/kaln.c
1382
1383 fixed a bug in banded DP
1384
1385 ------------------------------------------------------------------------
1386 r747 | lh3lh3 | 2010-09-27 23:05:12 -0400 (Mon, 27 Sep 2010) | 3 lines
1387 Changed paths:
1388 M /trunk/samtools/kaln.c
1389
1390 * fixed that weird issue.
1391 * the banded version is NOT working
1392
1393 ------------------------------------------------------------------------
1394 r746 | lh3lh3 | 2010-09-27 22:57:05 -0400 (Mon, 27 Sep 2010) | 2 lines
1395 Changed paths:
1396 M /trunk/samtools/kaln.c
1397
1398 More comments. This version seems working, but something is a little weird...
1399
1400 ------------------------------------------------------------------------
1401 r745 | lh3lh3 | 2010-09-27 17:21:40 -0400 (Mon, 27 Sep 2010) | 6 lines
1402 Changed paths:
1403 M /trunk/samtools/kaln.c
1404
1405 A little code cleanup. Now the forward and backback algorithms give
1406 nearly identical P(x), which means both are close to the correct
1407 forms. However, I have only tested on toy examples. Minor errors in
1408 the implementation may not be obvious.
1409
1410
1411 ------------------------------------------------------------------------
1412 r744 | lh3lh3 | 2010-09-27 16:55:15 -0400 (Mon, 27 Sep 2010) | 2 lines
1413 Changed paths:
1414 M /trunk/samtools/bam_plcmd.c
1415 M /trunk/samtools/bam_sort.c
1416 M /trunk/samtools/kaln.c
1417 M /trunk/samtools/kaln.h
1418
1419 ...
1420
1421 ------------------------------------------------------------------------
1422 r743 | jmarshall | 2010-09-27 08:19:06 -0400 (Mon, 27 Sep 2010) | 6 lines
1423 Changed paths:
1424 M /trunk/samtools/bam_sort.c
1425
1426 Abort if merge -h's INH.SAM cannot be opened, just as we abort
1427 if any of the IN#.BAM input files cannot be opened.
1428
1429 Also propagate any error indication returned by bam_merge_core()
1430 to samtools merge's exit status.
1431
1432 ------------------------------------------------------------------------
1433 r741 | jmarshall | 2010-09-24 11:08:24 -0400 (Fri, 24 Sep 2010) | 5 lines
1434 Changed paths:
1435 M /trunk/samtools/bam_index.c
1436
1437 Use bam_validate1() to detect garbage records in the event of a corrupt
1438 BAI index file that causes a bam_seek() to an invalid position. At most
1439 one record (namely, the bam_iter_read terminator) is tested per bam_fetch()
1440 call, so the cost is insignificant in the normal case.
1441
1442 ------------------------------------------------------------------------
1443 r740 | jmarshall | 2010-09-24 11:00:19 -0400 (Fri, 24 Sep 2010) | 2 lines
1444 Changed paths:
1445 M /trunk/samtools/bam.c
1446 M /trunk/samtools/bam.h
1447
1448 Add bam_validate1().
1449
1450 ------------------------------------------------------------------------
1451 r739 | lh3lh3 | 2010-09-22 12:07:50 -0400 (Wed, 22 Sep 2010) | 3 lines
1452 Changed paths:
1453 M /trunk/samtools/bam_md.c
1454 M /trunk/samtools/bamtk.c
1455
1456 * samtools-0.1.8-15 (r379)
1457 * allow to change capQ parameter in calmd
1458
1459 ------------------------------------------------------------------------
1460 r738 | jmarshall | 2010-09-22 11:15:33 -0400 (Wed, 22 Sep 2010) | 13 lines
1461 Changed paths:
1462 M /trunk/samtools/bam_index.c
1463 M /trunk/samtools/sam_view.c
1464
1465 When bam_read1() returns an error (return value <= -2), propagate that error
1466 to bam_iter_read()'s own return value. Similarly, also propagate it up to
1467 bam_fetch()'s return value. Previously bam_fetch() always returned 0, and
1468 callers ignored its return value anyway. With this change, 0 continues to
1469 indicate success, while <= -2 (which can be written as < 0, as -1 is never
1470 returned) indicates corrupted input.
1471
1472 bam_iter_read() ought also to propagate errors returned by bam_seek().
1473
1474 main_samview() can now print an error message and fail when bam_fetch()
1475 detects that a .bai index file is corrupted or otherwise does not correspond
1476 to the .bam file it is being used with.
1477
1478 ------------------------------------------------------------------------
1479 r737 | jmarshall | 2010-09-22 10:47:42 -0400 (Wed, 22 Sep 2010) | 3 lines
1480 Changed paths:
1481 M /trunk/samtools/bam_index.c
1482
1483 0 is a successful return value from bam_read1(). (In practice, it never
1484 returns 0 anyway; but all the other callers treat 0 as successful.)
1485
1486 ------------------------------------------------------------------------
1487 r736 | lh3lh3 | 2010-09-20 17:43:08 -0400 (Mon, 20 Sep 2010) | 2 lines
1488 Changed paths:
1489 M /trunk/samtools/bam.h
1490 M /trunk/samtools/bam_index.c
1491 M /trunk/samtools/bam_sort.c
1492
1493 * merge files region-by-region. work on small examples but more tests are needed.
1494
1495 ------------------------------------------------------------------------
1496 r735 | lh3lh3 | 2010-09-20 16:56:24 -0400 (Mon, 20 Sep 2010) | 2 lines
1497 Changed paths:
1498 M /trunk/samtools/bcftools/vcfutils.pl
1499
1500 improve qstats by checking the alleles as well
1501
1502 ------------------------------------------------------------------------
1503 r734 | lh3lh3 | 2010-09-17 18:12:13 -0400 (Fri, 17 Sep 2010) | 2 lines
1504 Changed paths:
1505 M /trunk/samtools/bcftools/vcfutils.pl
1506
1507 convert UCSC SNP SQL dump to VCF
1508
1509 ------------------------------------------------------------------------
1510 r733 | lh3lh3 | 2010-09-17 13:02:11 -0400 (Fri, 17 Sep 2010) | 2 lines
1511 Changed paths:
1512 M /trunk/samtools/bcftools/vcfutils.pl
1513
1514 hapmap2vcf convertor
1515
1516 ------------------------------------------------------------------------
1517 r732 | lh3lh3 | 2010-09-17 10:11:37 -0400 (Fri, 17 Sep 2010) | 3 lines
1518 Changed paths:
1519 M /trunk/samtools/bcftools/Makefile
1520 M /trunk/samtools/bcftools/bcf.c
1521 M /trunk/samtools/bcftools/bcf.h
1522 M /trunk/samtools/bcftools/vcf.c
1523
1524 * added comments
1525 * VCF->BCF is not possible without knowing the sequence dictionary before hand...
1526
1527 ------------------------------------------------------------------------
1528 r731 | lh3lh3 | 2010-09-17 09:15:53 -0400 (Fri, 17 Sep 2010) | 2 lines
1529 Changed paths:
1530 M /trunk/samtools/bam2bcf.c
1531 M /trunk/samtools/bcftools/bcf.c
1532 M /trunk/samtools/bcftools/bcf.h
1533 M /trunk/samtools/bcftools/bcfutils.c
1534 M /trunk/samtools/bcftools/call1.c
1535 M /trunk/samtools/bcftools/vcf.c
1536
1537 * put n_smpl to "bcf1_t" to simplify API a little
1538
1539 ------------------------------------------------------------------------
1540 r730 | lh3lh3 | 2010-09-16 21:36:01 -0400 (Thu, 16 Sep 2010) | 2 lines
1541 Changed paths:
1542 M /trunk/samtools/bcftools/bcf.h
1543 M /trunk/samtools/bcftools/call1.c
1544 M /trunk/samtools/bcftools/index.c
1545
1546 fixed a bug in indexing
1547
1548 ------------------------------------------------------------------------
1549 r729 | lh3lh3 | 2010-09-16 16:54:48 -0400 (Thu, 16 Sep 2010) | 3 lines
1550 Changed paths:
1551 M /trunk/samtools/bam.c
1552 M /trunk/samtools/bam_md.c
1553 M /trunk/samtools/bam_pileup.c
1554
1555 * fixed a bug in capQ
1556 * valgrind identifies a use of uninitialised value, but I have not fixed it.
1557
1558 ------------------------------------------------------------------------
1559 r728 | lh3lh3 | 2010-09-16 15:03:59 -0400 (Thu, 16 Sep 2010) | 3 lines
1560 Changed paths:
1561 M /trunk/samtools/bgzip.c
1562 M /trunk/samtools/razip.c
1563
1564 * fixed a bug in razip: -c will delete the input file
1565 * copy tabix/bgzip to here
1566
1567 ------------------------------------------------------------------------
1568 r727 | lh3lh3 | 2010-09-16 13:45:49 -0400 (Thu, 16 Sep 2010) | 3 lines
1569 Changed paths:
1570 M /trunk/samtools/bam_md.c
1571 M /trunk/samtools/bam_plcmd.c
1572 M /trunk/samtools/bamtk.c
1573
1574 * samtools-0.1.8-14 (r727)
1575 * allow to change the capQ parameter at the command line
1576
1577 ------------------------------------------------------------------------
1578 r726 | lh3lh3 | 2010-09-16 13:38:43 -0400 (Thu, 16 Sep 2010) | 4 lines
1579 Changed paths:
1580 M /trunk/samtools/bam_md.c
1581 M /trunk/samtools/bam_plcmd.c
1582 M /trunk/samtools/bcftools/vcfutils.pl
1583 M /trunk/samtools/misc/samtools.pl
1584
1585 * added varFilter to vcfutils.pl
1586 * reimplement realn(). now it performs a local alignment
1587 * added cap_mapQ() to cap mapping quality when there are many substitutions
1588
1589 ------------------------------------------------------------------------
1590 r724 | lh3lh3 | 2010-09-15 00:18:31 -0400 (Wed, 15 Sep 2010) | 2 lines
1591 Changed paths:
1592 M /trunk/samtools/bcftools/Makefile
1593 A /trunk/samtools/bcftools/bcf2qcall.c
1594 M /trunk/samtools/bcftools/call1.c
1595
1596 * convert BCF to QCALL input
1597
1598 ------------------------------------------------------------------------
1599 r723 | lh3lh3 | 2010-09-14 22:41:50 -0400 (Tue, 14 Sep 2010) | 2 lines
1600 Changed paths:
1601 M /trunk/samtools/bam_md.c
1602
1603 dynamic band width in realignment
1604
1605 ------------------------------------------------------------------------
1606 r722 | lh3lh3 | 2010-09-14 22:05:32 -0400 (Tue, 14 Sep 2010) | 2 lines
1607 Changed paths:
1608 M /trunk/samtools/bam_md.c
1609 M /trunk/samtools/bam_plcmd.c
1610
1611 fixed a bug in realignment
1612
1613 ------------------------------------------------------------------------
1614 r721 | lh3lh3 | 2010-09-14 20:54:09 -0400 (Tue, 14 Sep 2010) | 2 lines
1615 Changed paths:
1616 M /trunk/samtools/bcftools/prob1.c
1617
1618 fixed a minor issue
1619
1620 ------------------------------------------------------------------------
1621 r720 | lh3lh3 | 2010-09-14 19:25:10 -0400 (Tue, 14 Sep 2010) | 2 lines
1622 Changed paths:
1623 M /trunk/samtools/Makefile
1624 M /trunk/samtools/bam_maqcns.c
1625 M /trunk/samtools/bam_md.c
1626
1627 fixed a bug in realignment
1628
1629 ------------------------------------------------------------------------
1630 r719 | lh3lh3 | 2010-09-14 19:18:24 -0400 (Tue, 14 Sep 2010) | 2 lines
1631 Changed paths:
1632 M /trunk/samtools/bam_plcmd.c
1633
1634 minor changes. It is BUGGY now!
1635
1636 ------------------------------------------------------------------------
1637 r718 | lh3lh3 | 2010-09-14 16:32:33 -0400 (Tue, 14 Sep 2010) | 4 lines
1638 Changed paths:
1639 M /trunk/samtools/bam_md.c
1640 M /trunk/samtools/bam_pileup.c
1641 M /trunk/samtools/kaln.c
1642 M /trunk/samtools/kaln.h
1643
1644 * aggressive gapped aligner is implemented in calmd.
1645 * distinguish gap_open and gap_end_open in banded alignment
1646 * make tview accepts alignment with heading and tailing D
1647
1648 ------------------------------------------------------------------------
1649 r717 | jmarshall | 2010-09-14 09:04:28 -0400 (Tue, 14 Sep 2010) | 2 lines
1650 Changed paths:
1651 M /trunk/samtools
1652
1653 Add svn:ignore properties for generated files that don't appear in "make all".
1654
1655 ------------------------------------------------------------------------
1656 r716 | jmarshall | 2010-09-13 08:37:53 -0400 (Mon, 13 Sep 2010) | 3 lines
1657 Changed paths:
1658 M /trunk/samtools
1659 M /trunk/samtools/bcftools
1660 M /trunk/samtools/misc
1661
1662 Add svn:ignore properties listing the generated files.
1663 (Except for *.o, which we'll assume is in global-ignores.)
1664
1665 ------------------------------------------------------------------------
1666 r715 | lh3lh3 | 2010-09-08 12:53:55 -0400 (Wed, 08 Sep 2010) | 5 lines
1667 Changed paths:
1668 M /trunk/samtools/bamtk.c
1669 M /trunk/samtools/bcftools/call1.c
1670 M /trunk/samtools/bcftools/prob1.c
1671 M /trunk/samtools/sample.c
1672 M /trunk/samtools/sample.h
1673
1674 * samtools-0.1.8-13 (r715)
1675 * fixed a bug in identifying SM across files
1676 * bcftools: estimate heterozygosity
1677 * bcftools: allow to skip sites without reference bases
1678
1679 ------------------------------------------------------------------------
1680 r713 | lh3lh3 | 2010-09-03 17:19:12 -0400 (Fri, 03 Sep 2010) | 2 lines
1681 Changed paths:
1682 M /trunk/samtools/bcftools/Makefile
1683 M /trunk/samtools/bcftools/call1.c
1684 M /trunk/samtools/bcftools/prob1.c
1685 M /trunk/samtools/bcftools/prob1.h
1686
1687 quite a lot changes to the contrast caller, but I still feel something is missing...
1688
1689 ------------------------------------------------------------------------
1690 r711 | lh3lh3 | 2010-09-03 00:30:48 -0400 (Fri, 03 Sep 2010) | 4 lines
1691 Changed paths:
1692 M /trunk/samtools/bcftools/Makefile
1693 M /trunk/samtools/bcftools/call1.c
1694 M /trunk/samtools/bcftools/prob1.c
1695 M /trunk/samtools/bcftools/vcfutils.pl
1696
1697 * changed 3.434 to 4.343 (typo!)
1698 * fixed a bug in the contrast caller
1699 * calculate heterozygosity
1700
1701 ------------------------------------------------------------------------
1702 r710 | lh3lh3 | 2010-09-01 23:24:47 -0400 (Wed, 01 Sep 2010) | 2 lines
1703 Changed paths:
1704 M /trunk/samtools/bcftools/bcf.h
1705 M /trunk/samtools/bcftools/bcfutils.c
1706 M /trunk/samtools/bcftools/call1.c
1707
1708 SNP calling from the GL field
1709
1710 ------------------------------------------------------------------------
1711 r709 | lh3lh3 | 2010-09-01 18:52:30 -0400 (Wed, 01 Sep 2010) | 2 lines
1712 Changed paths:
1713 M /trunk/samtools/bcftools/vcf.c
1714
1715 fixed another problem
1716
1717 ------------------------------------------------------------------------
1718 r708 | lh3lh3 | 2010-09-01 18:31:17 -0400 (Wed, 01 Sep 2010) | 3 lines
1719 Changed paths:
1720 M /trunk/samtools/bcftools/bcf.c
1721 M /trunk/samtools/bcftools/vcf.c
1722
1723 * fixed bugs in parsing VCF
1724 * parser now works with GT/GQ/DP/PL/GL
1725
1726 ------------------------------------------------------------------------
1727 r707 | lh3lh3 | 2010-09-01 15:28:29 -0400 (Wed, 01 Sep 2010) | 2 lines
1728 Changed paths:
1729 M /trunk/samtools/bcftools/Makefile
1730 M /trunk/samtools/bcftools/prob1.c
1731
1732 Do not compile _BCF_QUAD by default
1733
1734 ------------------------------------------------------------------------
1735 r706 | lh3lh3 | 2010-09-01 15:21:41 -0400 (Wed, 01 Sep 2010) | 2 lines
1736 Changed paths:
1737 M /trunk/samtools/bcftools/bcf.c
1738 M /trunk/samtools/bcftools/bcf.h
1739 M /trunk/samtools/bcftools/bcfutils.c
1740 M /trunk/samtools/bcftools/call1.c
1741
1742 Write the correct ALT and PL in the SNP calling mode.
1743
1744 ------------------------------------------------------------------------
1745 r705 | lh3lh3 | 2010-09-01 12:50:33 -0400 (Wed, 01 Sep 2010) | 2 lines
1746 Changed paths:
1747 M /trunk/samtools/bcftools/vcfutils.pl
1748
1749 more commands for my own uses
1750
1751 ------------------------------------------------------------------------
1752 r704 | lh3lh3 | 2010-09-01 09:26:10 -0400 (Wed, 01 Sep 2010) | 2 lines
1753 Changed paths:
1754 A /trunk/samtools/bcftools/vcfutils.pl
1755
1756 Utilities for processing VCF
1757
1758 ------------------------------------------------------------------------
1759 r703 | lh3lh3 | 2010-08-31 16:44:57 -0400 (Tue, 31 Aug 2010) | 2 lines
1760 Changed paths:
1761 M /trunk/samtools/bcftools/Makefile
1762 M /trunk/samtools/bcftools/call1.c
1763 M /trunk/samtools/bcftools/prob1.c
1764 M /trunk/samtools/bcftools/prob1.h
1765
1766 preliminary contrast variant caller
1767
1768 ------------------------------------------------------------------------
1769 r702 | lh3lh3 | 2010-08-31 12:28:39 -0400 (Tue, 31 Aug 2010) | 2 lines
1770 Changed paths:
1771 M /trunk/samtools/bcftools/call1.c
1772 M /trunk/samtools/bcftools/prob1.c
1773 M /trunk/samtools/bcftools/prob1.h
1774
1775 z' and z'' can be calculated
1776
1777 ------------------------------------------------------------------------
1778 r701 | lh3lh3 | 2010-08-31 10:20:57 -0400 (Tue, 31 Aug 2010) | 3 lines
1779 Changed paths:
1780 M /trunk/samtools/bcftools/Makefile
1781 A /trunk/samtools/bcftools/call1.c (from /trunk/samtools/bcftools/vcfout.c:699)
1782 M /trunk/samtools/bcftools/prob1.c
1783 D /trunk/samtools/bcftools/vcfout.c
1784
1785 * rename vcfout.c as call1.c
1786 * prepare to add two-sample comparison
1787
1788 ------------------------------------------------------------------------
1789 r699 | lh3lh3 | 2010-08-24 15:28:16 -0400 (Tue, 24 Aug 2010) | 2 lines
1790 Changed paths:
1791 M /trunk/samtools/bcftools/vcfout.c
1792
1793 fixed a bug in calculating the t statistics
1794
1795 ------------------------------------------------------------------------
1796 r698 | lh3lh3 | 2010-08-24 14:05:50 -0400 (Tue, 24 Aug 2010) | 3 lines
1797 Changed paths:
1798 M /trunk/samtools/bam2bcf.c
1799 M /trunk/samtools/bam2bcf.h
1800 M /trunk/samtools/bamtk.c
1801 M /trunk/samtools/bcftools/kfunc.c
1802 M /trunk/samtools/bcftools/vcfout.c
1803
1804 * samtools-0.1.8-13 (r698)
1805 * perform one-tailed t-test for baseQ, mapQ and endDist
1806
1807 ------------------------------------------------------------------------
1808 r697 | lh3lh3 | 2010-08-24 12:30:13 -0400 (Tue, 24 Aug 2010) | 2 lines
1809 Changed paths:
1810 M /trunk/samtools/bcftools/kfunc.c
1811
1812 added regularized incomplete beta function
1813
1814 ------------------------------------------------------------------------
1815 r695 | lh3lh3 | 2010-08-23 17:36:17 -0400 (Mon, 23 Aug 2010) | 2 lines
1816 Changed paths:
1817 M /trunk/samtools/bam_maqcns.c
1818 M /trunk/samtools/bam_plcmd.c
1819
1820 change the default correlation coefficient
1821
1822 ------------------------------------------------------------------------
1823 r694 | lh3lh3 | 2010-08-23 14:46:52 -0400 (Mon, 23 Aug 2010) | 2 lines
1824 Changed paths:
1825 M /trunk/samtools/bcftools/bcf.c
1826 M /trunk/samtools/bcftools/vcfout.c
1827
1828 print QUAL as floating numbers
1829
1830 ------------------------------------------------------------------------
1831 r693 | lh3lh3 | 2010-08-23 14:06:07 -0400 (Mon, 23 Aug 2010) | 3 lines
1832 Changed paths:
1833 M /trunk/samtools/Makefile
1834 M /trunk/samtools/bam_plcmd.c
1835 M /trunk/samtools/bamtk.c
1836 M /trunk/samtools/examples/Makefile
1837 A /trunk/samtools/sample.c
1838 A /trunk/samtools/sample.h
1839
1840 * samtools-0.1.8-12 (r692)
1841 * group data by samples in "mpileup -g"
1842
1843 ------------------------------------------------------------------------
1844 r692 | lh3lh3 | 2010-08-23 10:58:53 -0400 (Mon, 23 Aug 2010) | 2 lines
1845 Changed paths:
1846 M /trunk/samtools/Makefile
1847 D /trunk/samtools/bam_mcns.c
1848 D /trunk/samtools/bam_mcns.h
1849 M /trunk/samtools/bam_plcmd.c
1850
1851 remove VCF output in mpileup
1852
1853 ------------------------------------------------------------------------
1854 r691 | lh3lh3 | 2010-08-23 10:48:20 -0400 (Mon, 23 Aug 2010) | 3 lines
1855 Changed paths:
1856 M /trunk/samtools/bam2bcf.c
1857 M /trunk/samtools/bam2bcf.h
1858
1859 * use the revised MAQ error model for mpileup
1860 * prepare to remove the independent model from mpileup
1861
1862 ------------------------------------------------------------------------
1863 r690 | lh3lh3 | 2010-08-20 15:46:40 -0400 (Fri, 20 Aug 2010) | 2 lines
1864 Changed paths:
1865 M /trunk/samtools/Makefile
1866 M /trunk/samtools/bam_maqcns.c
1867 M /trunk/samtools/bam_maqcns.h
1868 M /trunk/samtools/bam_plcmd.c
1869 A /trunk/samtools/errmod.c
1870 A /trunk/samtools/errmod.h
1871 M /trunk/samtools/ksort.h
1872
1873 added revised MAQ error model
1874
1875 ------------------------------------------------------------------------
1876 r689 | lh3lh3 | 2010-08-18 09:55:20 -0400 (Wed, 18 Aug 2010) | 2 lines
1877 Changed paths:
1878 M /trunk/samtools/bcftools/prob1.c
1879 M /trunk/samtools/bcftools/prob1.h
1880 M /trunk/samtools/bcftools/vcfout.c
1881
1882 allow to read the prior from the error output. EM iteration is working.
1883
1884 ------------------------------------------------------------------------
1885 r688 | lh3lh3 | 2010-08-17 12:12:20 -0400 (Tue, 17 Aug 2010) | 3 lines
1886 Changed paths:
1887 M /trunk/samtools/bcftools/main.c
1888 M /trunk/samtools/bcftools/vcf.c
1889
1890 * write a little more VCF header
1891 * concatenate BCFs
1892
1893 ------------------------------------------------------------------------
1894 r687 | lh3lh3 | 2010-08-16 20:53:16 -0400 (Mon, 16 Aug 2010) | 2 lines
1895 Changed paths:
1896 M /trunk/samtools/bcftools/bcf.c
1897 M /trunk/samtools/bcftools/bcf.h
1898 M /trunk/samtools/bcftools/bcf.tex
1899
1900 use float for QUAL
1901
1902 ------------------------------------------------------------------------
1903 r686 | lh3lh3 | 2010-08-14 00:11:13 -0400 (Sat, 14 Aug 2010) | 2 lines
1904 Changed paths:
1905 M /trunk/samtools/bcftools/bcf.c
1906 M /trunk/samtools/bcftools/prob1.c
1907
1908 faster for large sample size (in principle)
1909
1910 ------------------------------------------------------------------------
1911 r685 | lh3lh3 | 2010-08-13 23:28:31 -0400 (Fri, 13 Aug 2010) | 4 lines
1912 Changed paths:
1913 M /trunk/samtools/bcftools/prob1.c
1914
1915 * a numerically stable method to calculate z_{jk}
1916 * currently slower than the old method but will be important for large sample size
1917 * in principle, we can speed up for large n, but have not tried
1918
1919 ------------------------------------------------------------------------
1920 r684 | lh3lh3 | 2010-08-11 21:58:31 -0400 (Wed, 11 Aug 2010) | 2 lines
1921 Changed paths:
1922 M /trunk/samtools/bcftools/vcfout.c
1923
1924 fixed an issue in parsing integer
1925
1926 ------------------------------------------------------------------------
1927 r683 | lh3lh3 | 2010-08-09 13:05:07 -0400 (Mon, 09 Aug 2010) | 2 lines
1928 Changed paths:
1929 M /trunk/samtools/bcftools/bcf.c
1930
1931 do not print refname if file is converted from VCF
1932
1933 ------------------------------------------------------------------------
1934 r682 | lh3lh3 | 2010-08-09 12:59:47 -0400 (Mon, 09 Aug 2010) | 3 lines
1935 Changed paths:
1936 M /trunk/samtools/bcftools/vcf.c
1937
1938 * parse PL
1939 * fixed a bug in parsing VCF
1940
1941 ------------------------------------------------------------------------
1942 r681 | lh3lh3 | 2010-08-09 12:49:23 -0400 (Mon, 09 Aug 2010) | 4 lines
1943 Changed paths:
1944 M /trunk/samtools/bcftools/bcf.c
1945 M /trunk/samtools/bcftools/bcf.h
1946 M /trunk/samtools/bcftools/bcfutils.c
1947 M /trunk/samtools/bcftools/main.c
1948 M /trunk/samtools/bcftools/vcf.c
1949 M /trunk/samtools/bcftools/vcfout.c
1950 M /trunk/samtools/bgzf.c
1951 M /trunk/samtools/kstring.c
1952
1953 * fixed a bug in kstrtok@kstring.c
1954 * preliminary VCF parser (not parse everything for now)
1955 * improved view interface
1956
1957 ------------------------------------------------------------------------
1958 r680 | lh3lh3 | 2010-08-09 10:43:13 -0400 (Mon, 09 Aug 2010) | 4 lines
1959 Changed paths:
1960 M /trunk/samtools/bcftools/bcf.c
1961 M /trunk/samtools/bcftools/bcf.h
1962 M /trunk/samtools/bcftools/vcfout.c
1963 M /trunk/samtools/kstring.c
1964 M /trunk/samtools/kstring.h
1965
1966 * improved kstring (added kstrtok)
1967 * removed the limit on the format string length in bcftools
1968 * use kstrtok to parse format which fixed a bug in the old code
1969
1970 ------------------------------------------------------------------------
1971 r679 | lh3lh3 | 2010-08-09 01:12:05 -0400 (Mon, 09 Aug 2010) | 2 lines
1972 Changed paths:
1973 A /trunk/samtools/bcftools/README
1974 M /trunk/samtools/bcftools/vcfout.c
1975
1976 help messages
1977
1978 ------------------------------------------------------------------------
1979 r678 | lh3lh3 | 2010-08-09 00:01:52 -0400 (Mon, 09 Aug 2010) | 2 lines
1980 Changed paths:
1981 M /trunk/samtools/bcftools/vcfout.c
1982
1983 perform single-tail test for ED4
1984
1985 ------------------------------------------------------------------------
1986 r677 | lh3lh3 | 2010-08-08 23:48:35 -0400 (Sun, 08 Aug 2010) | 2 lines
1987 Changed paths:
1988 M /trunk/samtools/bcftools/Makefile
1989 M /trunk/samtools/bcftools/kfunc.c
1990 M /trunk/samtools/bcftools/vcfout.c
1991
1992 * test depth, end distance and HWE
1993
1994 ------------------------------------------------------------------------
1995 r676 | lh3lh3 | 2010-08-08 02:04:15 -0400 (Sun, 08 Aug 2010) | 2 lines
1996 Changed paths:
1997 M /trunk/samtools/bcftools/kfunc.c
1998
1999 reimplement incomplete gamma functions. no copy-paste
2000
2001 ------------------------------------------------------------------------
2002 r675 | lh3lh3 | 2010-08-06 22:42:54 -0400 (Fri, 06 Aug 2010) | 3 lines
2003 Changed paths:
2004 M /trunk/samtools/bam2bcf.c
2005 M /trunk/samtools/bam2bcf.h
2006 M /trunk/samtools/bcftools/fet.c
2007 M /trunk/samtools/bcftools/prob1.c
2008 M /trunk/samtools/bcftools/prob1.h
2009 M /trunk/samtools/bcftools/vcfout.c
2010
2011 * bcftools: add HWE (no testing for now)
2012 * record end dist in a 2x2 table, not avg, std any more
2013
2014 ------------------------------------------------------------------------
2015 r674 | lh3lh3 | 2010-08-06 17:30:16 -0400 (Fri, 06 Aug 2010) | 3 lines
2016 Changed paths:
2017 A /trunk/samtools/bcftools/kfunc.c
2018
2019 * Special functions: log(gamma()), erfc(), P(a,x) (incomplete gamma)
2020 * Not using Numerical Recipe due to licensing issues
2021
2022 ------------------------------------------------------------------------
2023 r673 | lh3lh3 | 2010-08-05 23:46:53 -0400 (Thu, 05 Aug 2010) | 2 lines
2024 Changed paths:
2025 A /trunk/samtools/bcftools/fet.c
2026
2027 Fisher's exact test
2028
2029 ------------------------------------------------------------------------
2030 r672 | lh3lh3 | 2010-08-05 21:48:33 -0400 (Thu, 05 Aug 2010) | 3 lines
2031 Changed paths:
2032 M /trunk/samtools/bam2bcf.c
2033 M /trunk/samtools/bam2bcf.h
2034 M /trunk/samtools/bamtk.c
2035 M /trunk/samtools/examples/Makefile
2036
2037 * samtools-0.1.8-11 (r672)
2038 * collect more stats for allele balance test in bcftools (not yet)
2039
2040 ------------------------------------------------------------------------
2041 r671 | lh3lh3 | 2010-08-05 16:17:58 -0400 (Thu, 05 Aug 2010) | 3 lines
2042 Changed paths:
2043 M /trunk/samtools/bam_plcmd.c
2044 M /trunk/samtools/bcftools/bcf.c
2045 M /trunk/samtools/bcftools/main.c
2046
2047 * the code base is stablized again.
2048 * I will delay the vcf parser, which is quite complicated but with little value for now
2049
2050 ------------------------------------------------------------------------
2051 r670 | lh3lh3 | 2010-08-05 16:03:23 -0400 (Thu, 05 Aug 2010) | 2 lines
2052 Changed paths:
2053 M /trunk/samtools/examples/Makefile
2054
2055 minor
2056
2057 ------------------------------------------------------------------------
2058 r669 | lh3lh3 | 2010-08-05 16:03:08 -0400 (Thu, 05 Aug 2010) | 2 lines
2059 Changed paths:
2060 M /trunk/samtools/bcftools/vcf.c
2061
2062 unfinished vcf parser
2063
2064 ------------------------------------------------------------------------
2065 r668 | lh3lh3 | 2010-08-05 15:46:40 -0400 (Thu, 05 Aug 2010) | 3 lines
2066 Changed paths:
2067 M /trunk/samtools/bcftools/Makefile
2068 M /trunk/samtools/bcftools/bcf.c
2069 M /trunk/samtools/bcftools/bcf.h
2070 M /trunk/samtools/bcftools/bcfutils.c
2071 M /trunk/samtools/bcftools/index.c
2072 M /trunk/samtools/bcftools/main.c
2073 A /trunk/samtools/bcftools/vcf.c
2074 M /trunk/samtools/bcftools/vcfout.c
2075
2076 * added prelimiary VCF parser (not finished)
2077 * change struct a bit
2078
2079 ------------------------------------------------------------------------
2080 r667 | lh3lh3 | 2010-08-03 22:35:27 -0400 (Tue, 03 Aug 2010) | 3 lines
2081 Changed paths:
2082 M /trunk/samtools/bam2bcf.c
2083 M /trunk/samtools/bam2bcf.h
2084 M /trunk/samtools/bam_plcmd.c
2085 M /trunk/samtools/bcftools/bcf.c
2086
2087 * allow to set min base q
2088 * fixed a bug in mpileup -u
2089
2090 ------------------------------------------------------------------------
2091 r666 | lh3lh3 | 2010-08-03 22:08:44 -0400 (Tue, 03 Aug 2010) | 2 lines
2092 Changed paths:
2093 A /trunk/samtools/bcftools/bcf.tex
2094
2095 spec
2096
2097 ------------------------------------------------------------------------
2098 r665 | lh3lh3 | 2010-08-03 21:18:57 -0400 (Tue, 03 Aug 2010) | 2 lines
2099 Changed paths:
2100 M /trunk/samtools/examples/Makefile
2101
2102 added more examples
2103
2104 ------------------------------------------------------------------------
2105 r664 | lh3lh3 | 2010-08-03 21:13:00 -0400 (Tue, 03 Aug 2010) | 2 lines
2106 Changed paths:
2107 M /trunk/samtools/Makefile
2108 M /trunk/samtools/bam2bcf.c
2109 M /trunk/samtools/bam2bcf.h
2110 M /trunk/samtools/bcftools/Makefile
2111
2112 fixed compilation error
2113
2114 ------------------------------------------------------------------------
2115 r662 | lh3lh3 | 2010-08-03 21:04:00 -0400 (Tue, 03 Aug 2010) | 2 lines
2116 Changed paths:
2117 M /trunk/samtools/Makefile
2118 D /trunk/samtools/bcf.c
2119 D /trunk/samtools/bcf.h
2120 A /trunk/samtools/bcftools
2121 A /trunk/samtools/bcftools/Makefile
2122 A /trunk/samtools/bcftools/bcf.c
2123 A /trunk/samtools/bcftools/bcf.h
2124 A /trunk/samtools/bcftools/bcfutils.c
2125 A /trunk/samtools/bcftools/index.c
2126 A /trunk/samtools/bcftools/main.c
2127 A /trunk/samtools/bcftools/prob1.c
2128 A /trunk/samtools/bcftools/prob1.h
2129 A /trunk/samtools/bcftools/vcfout.c
2130
2131 move bcftools to samtools
2132
2133 ------------------------------------------------------------------------
2134 r660 | lh3lh3 | 2010-08-03 15:58:32 -0400 (Tue, 03 Aug 2010) | 2 lines
2135 Changed paths:
2136 M /trunk/samtools/bam2bcf.c
2137
2138 fixed another minor bug
2139
2140 ------------------------------------------------------------------------
2141 r658 | lh3lh3 | 2010-08-03 15:06:45 -0400 (Tue, 03 Aug 2010) | 3 lines
2142 Changed paths:
2143 M /trunk/samtools/bamtk.c
2144 M /trunk/samtools/bcf.c
2145
2146 * samtools-0.1.8-10 (r658)
2147 * fixed a bug in bam2bcf when the reference is N
2148
2149 ------------------------------------------------------------------------
2150 r657 | lh3lh3 | 2010-08-03 14:50:23 -0400 (Tue, 03 Aug 2010) | 3 lines
2151 Changed paths:
2152 M /trunk/samtools/bam2bcf.c
2153 M /trunk/samtools/bam2bcf.h
2154
2155 * fixed a bug
2156 * treat ambiguous ref base as the fifth base
2157
2158 ------------------------------------------------------------------------
2159 r654 | lh3lh3 | 2010-08-02 17:38:27 -0400 (Mon, 02 Aug 2010) | 2 lines
2160 Changed paths:
2161 M /trunk/bcftools/bcf.c
2162 M /trunk/samtools/bcf.c
2163
2164 missing a column in VCF output...
2165
2166 ------------------------------------------------------------------------
2167 r653 | lh3lh3 | 2010-08-02 17:31:33 -0400 (Mon, 02 Aug 2010) | 2 lines
2168 Changed paths:
2169 M /trunk/samtools/bcf.c
2170
2171 fixed a memory leak
2172
2173 ------------------------------------------------------------------------
2174 r651 | lh3lh3 | 2010-08-02 17:27:31 -0400 (Mon, 02 Aug 2010) | 2 lines
2175 Changed paths:
2176 M /trunk/samtools/bcf.c
2177
2178 fixed a bug in bcf reader
2179
2180 ------------------------------------------------------------------------
2181 r650 | lh3lh3 | 2010-08-02 17:00:41 -0400 (Mon, 02 Aug 2010) | 2 lines
2182 Changed paths:
2183 M /trunk/samtools/bam2bcf.c
2184
2185 fixed a bug
2186
2187 ------------------------------------------------------------------------
2188 r649 | lh3lh3 | 2010-08-02 16:49:35 -0400 (Mon, 02 Aug 2010) | 3 lines
2189 Changed paths:
2190 M /trunk/samtools/Makefile
2191 M /trunk/samtools/bam2bcf.c
2192 M /trunk/samtools/bam2bcf.h
2193 M /trunk/samtools/bamtk.c
2194
2195 * samtools-0.1.8-9 (r649)
2196 * lossless representation of PL in BCF output
2197
2198 ------------------------------------------------------------------------
2199 r648 | lh3lh3 | 2010-08-02 16:07:25 -0400 (Mon, 02 Aug 2010) | 2 lines
2200 Changed paths:
2201 M /trunk/samtools/Makefile
2202 A /trunk/samtools/bam2bcf.c
2203 A /trunk/samtools/bam2bcf.h
2204 M /trunk/samtools/bam_plcmd.c
2205 A /trunk/samtools/bcf.c
2206 A /trunk/samtools/bcf.h
2207
2208 Generate binary VCF
2209
2210 ------------------------------------------------------------------------
2211 r644 | lh3lh3 | 2010-07-28 11:59:19 -0400 (Wed, 28 Jul 2010) | 5 lines
2212 Changed paths:
2213 M /trunk/samtools/bam_mcns.c
2214 M /trunk/samtools/bamtk.c
2215
2216 * samtools-0.1.8-8 (r644)
2217 * mpileup becomes a little stable again
2218 * the method is slightly different, but is more theoretically correct
2219 * snp calling is O(n^2) instead of O(n^3)
2220
2221 ------------------------------------------------------------------------
2222 r643 | lh3lh3 | 2010-07-28 11:54:15 -0400 (Wed, 28 Jul 2010) | 3 lines
2223 Changed paths:
2224 M /trunk/samtools/bam_mcns.c
2225
2226 * fixed a STUPID bug, which cost me a lot of time.
2227 * I am going to clean up mcns a little bit
2228
2229 ------------------------------------------------------------------------
2230 r642 | lh3lh3 | 2010-07-27 23:23:07 -0400 (Tue, 27 Jul 2010) | 2 lines
2231 Changed paths:
2232 M /trunk/samtools/bam_mcns.c
2233 M /trunk/samtools/bam_mcns.h
2234 M /trunk/samtools/bam_plcmd.c
2235
2236 supposedly this is THE correct implementation, but more testing is needed
2237
2238 ------------------------------------------------------------------------
2239 r641 | lh3lh3 | 2010-07-27 22:43:39 -0400 (Tue, 27 Jul 2010) | 2 lines
2240 Changed paths:
2241 M /trunk/samtools/bam_mcns.c
2242
2243 NOT ready yet. Going to make further changes...
2244
2245 ------------------------------------------------------------------------
2246 r639 | lh3lh3 | 2010-07-25 22:18:38 -0400 (Sun, 25 Jul 2010) | 3 lines
2247 Changed paths:
2248 M /trunk/samtools/bam_mcns.c
2249 M /trunk/samtools/bam_plcmd.c
2250 M /trunk/samtools/bamtk.c
2251
2252 * samtools-0.1.8-7 (r639)
2253 * fixed the reference allele assignment
2254
2255 ------------------------------------------------------------------------
2256 r638 | lh3lh3 | 2010-07-25 12:01:26 -0400 (Sun, 25 Jul 2010) | 5 lines
2257 Changed paths:
2258 M /trunk/samtools/bam_mcns.c
2259 M /trunk/samtools/bam_mcns.h
2260 M /trunk/samtools/bam_plcmd.c
2261 M /trunk/samtools/bamtk.c
2262
2263 * samtools-0.1.8-6 (r638)
2264 * skip isnan/isinf in case of float underflow
2265 * added the flat prior
2266 * fixed an issue where there are no reads supporting the reference
2267
2268 ------------------------------------------------------------------------
2269 r637 | lh3lh3 | 2010-07-24 14:16:27 -0400 (Sat, 24 Jul 2010) | 2 lines
2270 Changed paths:
2271 M /trunk/samtools/bam_plcmd.c
2272
2273 minor changes
2274
2275 ------------------------------------------------------------------------
2276 r636 | lh3lh3 | 2010-07-24 14:07:27 -0400 (Sat, 24 Jul 2010) | 2 lines
2277 Changed paths:
2278 M /trunk/samtools/bam_mcns.c
2279 M /trunk/samtools/bam_mcns.h
2280 M /trunk/samtools/bam_plcmd.c
2281 M /trunk/samtools/bamtk.c
2282
2283 minor tweaks
2284
2285 ------------------------------------------------------------------------
2286 r635 | lh3lh3 | 2010-07-24 01:49:49 -0400 (Sat, 24 Jul 2010) | 2 lines
2287 Changed paths:
2288 M /trunk/samtools/bam_mcns.c
2289 M /trunk/samtools/bam_mcns.h
2290 M /trunk/samtools/bam_plcmd.c
2291
2292 posterior expectation FINALLY working. I am so tired...
2293
2294 ------------------------------------------------------------------------
2295 r633 | lh3lh3 | 2010-07-23 13:50:48 -0400 (Fri, 23 Jul 2010) | 2 lines
2296 Changed paths:
2297 M /trunk/samtools/bam_plcmd.c
2298
2299 another minor fix to mpileup
2300
2301 ------------------------------------------------------------------------
2302 r632 | lh3lh3 | 2010-07-23 13:43:31 -0400 (Fri, 23 Jul 2010) | 2 lines
2303 Changed paths:
2304 M /trunk/samtools/bam_plcmd.c
2305
2306 added the format column
2307
2308 ------------------------------------------------------------------------
2309 r631 | lh3lh3 | 2010-07-23 13:25:44 -0400 (Fri, 23 Jul 2010) | 2 lines
2310 Changed paths:
2311 M /trunk/samtools/bam_mcns.c
2312 M /trunk/samtools/bam_mcns.h
2313 M /trunk/samtools/bam_plcmd.c
2314 M /trunk/samtools/bamtk.c
2315
2316 added an alternative prior
2317
2318 ------------------------------------------------------------------------
2319 r628 | lh3lh3 | 2010-07-23 11:48:51 -0400 (Fri, 23 Jul 2010) | 2 lines
2320 Changed paths:
2321 M /trunk/samtools/bam_mcns.c
2322 M /trunk/samtools/bam_mcns.h
2323 M /trunk/samtools/bam_plcmd.c
2324
2325 calculate posterior allele frequency
2326
2327 ------------------------------------------------------------------------
2328 r627 | lh3lh3 | 2010-07-22 21:39:13 -0400 (Thu, 22 Jul 2010) | 3 lines
2329 Changed paths:
2330 M /trunk/samtools/bam_mcns.c
2331 M /trunk/samtools/bam_plcmd.c
2332 M /trunk/samtools/bamtk.c
2333
2334 * samtools-0.1.8-3 (r627)
2335 * multi-sample snp calling appears to work. More tests needed.
2336
2337 ------------------------------------------------------------------------
2338 r626 | lh3lh3 | 2010-07-22 16:37:56 -0400 (Thu, 22 Jul 2010) | 3 lines
2339 Changed paths:
2340 M /trunk/samtools/bam_mcns.c
2341 M /trunk/samtools/bam_mcns.h
2342 M /trunk/samtools/bam_plcmd.c
2343 M /trunk/samtools/bam_tview.c
2344
2345 * preliminary multisample SNP caller.
2346 * something looks not so right, but it largely works
2347
2348 ------------------------------------------------------------------------
2349 r617 | lh3lh3 | 2010-07-14 16:26:27 -0400 (Wed, 14 Jul 2010) | 3 lines
2350 Changed paths:
2351 M /trunk/samtools/bam_mcns.c
2352 M /trunk/samtools/bam_plcmd.c
2353 M /trunk/samtools/bamtk.c
2354
2355 * samtools-0.1.8-2 (r617)
2356 * allele frequency calculation apparently works...
2357
2358 ------------------------------------------------------------------------
2359 r616 | lh3lh3 | 2010-07-14 13:33:51 -0400 (Wed, 14 Jul 2010) | 3 lines
2360 Changed paths:
2361 M /trunk/samtools/Makefile
2362 A /trunk/samtools/bam_mcns.c
2363 A /trunk/samtools/bam_mcns.h
2364 M /trunk/samtools/bam_plcmd.c
2365
2366 * added mutli-sample framework. It is not working, yet.
2367 * improved the mpileup interface
2368
2369 ------------------------------------------------------------------------
2370 r615 | lh3lh3 | 2010-07-13 14:50:12 -0400 (Tue, 13 Jul 2010) | 3 lines
2371 Changed paths:
2372 M /trunk/samtools/bam_plcmd.c
2373 M /trunk/samtools/bamtk.c
2374 M /trunk/samtools/misc/Makefile
2375
2376 * samtools-0.1.8-1 (r615)
2377 * allow to get mpileup at required sites
2378
2379 ------------------------------------------------------------------------
2380 r613 | lh3lh3 | 2010-07-11 22:40:56 -0400 (Sun, 11 Jul 2010) | 2 lines
2381 Changed paths:
2382 M /trunk/samtools/ChangeLog
2383 M /trunk/samtools/NEWS
2384 M /trunk/samtools/bam_plcmd.c
2385 M /trunk/samtools/bamtk.c
2386 M /trunk/samtools/samtools.1
2387
2388 Release samtools-0.1.8
2389
2390 ------------------------------------------------------------------------
2391 r612 | lh3lh3 | 2010-07-11 21:08:56 -0400 (Sun, 11 Jul 2010) | 2 lines
2392 Changed paths:
2393 M /trunk/samtools/knetfile.c
2394
2395 fixed a compiling issue for Windows
2396
2397 ------------------------------------------------------------------------
2398 r611 | lh3lh3 | 2010-07-11 20:59:15 -0400 (Sun, 11 Jul 2010) | 2 lines
2399 Changed paths:
2400 M /trunk/samtools/bam_sort.c
2401
2402 fixed a bug in sorting when output to stdout (by Peter Chines)
2403
2404 ------------------------------------------------------------------------
2405 r610 | lh3lh3 | 2010-07-09 17:05:10 -0400 (Fri, 09 Jul 2010) | 2 lines
2406 Changed paths:
2407 M /trunk/samtools/NEWS
2408 M /trunk/samtools/bam_plcmd.c
2409
2410 change the command line option of pileup
2411
2412 ------------------------------------------------------------------------
2413 r609 | lh3lh3 | 2010-07-09 00:39:34 -0400 (Fri, 09 Jul 2010) | 2 lines
2414 Changed paths:
2415 M /trunk/samtools/bam_pileup.c
2416 A /trunk/samtools/examples/toy.fa
2417 A /trunk/samtools/examples/toy.sam
2418
2419 make pileup work with CIGAR with I/D at the beginning or in the end
2420
2421 ------------------------------------------------------------------------
2422 r608 | lh3lh3 | 2010-07-08 22:36:12 -0400 (Thu, 08 Jul 2010) | 3 lines
2423 Changed paths:
2424 M /trunk/samtools/bam_maqcns.c
2425 M /trunk/samtools/bam_maqcns.h
2426 M /trunk/samtools/bam_plcmd.c
2427 M /trunk/samtools/bam_tview.c
2428
2429 * make tview more friendly
2430 * a temporary remedy for an issue in indel calling
2431
2432 ------------------------------------------------------------------------
2433 r607 | lh3lh3 | 2010-07-08 14:43:52 -0400 (Thu, 08 Jul 2010) | 4 lines
2434 Changed paths:
2435 M /trunk/samtools/bam_maqcns.c
2436 M /trunk/samtools/bam_plcmd.c
2437 M /trunk/samtools/bamtk.c
2438
2439 * samtools-0.1.7-r607
2440 * improved the genotype accuracy for indels
2441 * use the SOAPsnp model for SNP calling by default.
2442
2443 ------------------------------------------------------------------------
2444 r606 | lh3lh3 | 2010-07-08 01:05:19 -0400 (Thu, 08 Jul 2010) | 2 lines
2445 Changed paths:
2446 M /trunk/samtools/misc/Makefile
2447
2448 removed a debugging example
2449
2450 ------------------------------------------------------------------------
2451 r605 | lh3lh3 | 2010-07-08 01:04:09 -0400 (Thu, 08 Jul 2010) | 4 lines
2452 Changed paths:
2453 M /trunk/samtools/bam_maqcns.c
2454 M /trunk/samtools/bamtk.c
2455
2456 * samtools-.1.7-18 (r605)
2457 * fixed an issue when a deletion and mismatch occur at the same time
2458 and the base quality is higher than 40 (if -I40).
2459
2460 ------------------------------------------------------------------------
2461 r604 | lh3lh3 | 2010-07-02 19:32:24 -0400 (Fri, 02 Jul 2010) | 2 lines
2462 Changed paths:
2463 M /trunk/samtools/bam.h
2464 M /trunk/samtools/bam_index.c
2465 M /trunk/samtools/misc/Makefile
2466
2467 fixed a minor bug in idxstats
2468
2469 ------------------------------------------------------------------------
2470 r601 | lh3lh3 | 2010-06-16 09:03:59 -0400 (Wed, 16 Jun 2010) | 2 lines
2471 Changed paths:
2472 M /trunk/samtools/bam_index.c
2473
2474 fixed a minor bug in indexing
2475
2476 ------------------------------------------------------------------------
2477 r600 | lh3lh3 | 2010-06-15 10:17:53 -0400 (Tue, 15 Jun 2010) | 2 lines
2478 Changed paths:
2479 M /trunk/samtools/ChangeLog
2480 M /trunk/samtools/bam.c
2481
2482 change printf() to puts in exporting
2483
2484 ------------------------------------------------------------------------
2485 r599 | lh3lh3 | 2010-06-13 21:41:11 -0400 (Sun, 13 Jun 2010) | 2 lines
2486 Changed paths:
2487 M /trunk/samtools/bamtk.c
2488
2489 minor fix. No actual effect.
2490
2491 ------------------------------------------------------------------------
2492 r598 | lh3lh3 | 2010-06-13 21:32:45 -0400 (Sun, 13 Jun 2010) | 2 lines
2493 Changed paths:
2494 M /trunk/samtools/Makefile
2495
2496 added Makefile targets to compile shared/dynamic library
2497
2498 ------------------------------------------------------------------------
2499 r596 | lh3lh3 | 2010-06-13 19:48:07 -0400 (Sun, 13 Jun 2010) | 3 lines
2500 Changed paths:
2501 M /trunk/samtools/ChangeLog
2502 M /trunk/samtools/bam_index.c
2503 M /trunk/samtools/bamtk.c
2504
2505 * samtools-0.1.7-17 (r596)
2506 * also keep the number of coor-less reads in the index file
2507
2508 ------------------------------------------------------------------------
2509 r595 | lh3lh3 | 2010-06-13 18:54:26 -0400 (Sun, 13 Jun 2010) | 3 lines
2510 Changed paths:
2511 M /trunk/samtools/bam_index.c
2512 M /trunk/samtools/bamtk.c
2513
2514 * samtools-0.1.7-16 (r595)
2515 * write additional information to bam index
2516
2517 ------------------------------------------------------------------------
2518 r594 | lh3lh3 | 2010-06-13 17:29:52 -0400 (Sun, 13 Jun 2010) | 2 lines
2519 Changed paths:
2520 M /trunk/samtools/bam_index.c
2521
2522 fixed a bug for unmapped sequences in indexing
2523
2524 ------------------------------------------------------------------------
2525 r593 | lh3lh3 | 2010-06-12 18:11:32 -0400 (Sat, 12 Jun 2010) | 2 lines
2526 Changed paths:
2527 M /trunk/samtools/bam.h
2528 M /trunk/samtools/bam_index.c
2529 M /trunk/samtools/bam_plcmd.c
2530 M /trunk/samtools/samtools.1
2531
2532 rename iterf as iter
2533
2534 ------------------------------------------------------------------------
2535 r592 | lh3lh3 | 2010-06-12 18:02:38 -0400 (Sat, 12 Jun 2010) | 4 lines
2536 Changed paths:
2537 M /trunk/samtools/ChangeLog
2538 M /trunk/samtools/bam_aux.c
2539 M /trunk/samtools/bam_index.c
2540 M /trunk/samtools/bam_pileup.c
2541 M /trunk/samtools/bam_plcmd.c
2542 M /trunk/samtools/bamtk.c
2543
2544 * samtools-0.1.7-15 (r592)
2545 * fixed a few minor memory leaks in the new pileup code
2546 * improved the functionality of mpileup
2547
2548 ------------------------------------------------------------------------
2549 r591 | lh3lh3 | 2010-06-12 14:09:22 -0400 (Sat, 12 Jun 2010) | 3 lines
2550 Changed paths:
2551 M /trunk/samtools/bam.h
2552 M /trunk/samtools/bam_pileup.c
2553 M /trunk/samtools/bam_plcmd.c
2554 M /trunk/samtools/bamtk.c
2555
2556 * samtools-0.1.7-14 (r591)
2557 * elementary multi-way pileup. More testing and more functionality to be done.
2558
2559 ------------------------------------------------------------------------
2560 r590 | lh3lh3 | 2010-06-12 01:00:24 -0400 (Sat, 12 Jun 2010) | 3 lines
2561 Changed paths:
2562 M /trunk/samtools/bam.h
2563 M /trunk/samtools/bam_pileup.c
2564 M /trunk/samtools/bamtk.c
2565
2566 * samtools-0.1.7-13 (r590)
2567 * added mpileup APIs. No compiling errors, but not tested at all. It is late.
2568
2569 ------------------------------------------------------------------------
2570 r589 | lh3lh3 | 2010-06-11 22:37:09 -0400 (Fri, 11 Jun 2010) | 3 lines
2571 Changed paths:
2572 M /trunk/samtools/bam.h
2573 M /trunk/samtools/bam_pileup.c
2574 M /trunk/samtools/bamtk.c
2575
2576 * samtools-0.1.7-12 (r589)
2577 * added iterator-like APIs for pileup
2578
2579 ------------------------------------------------------------------------
2580 r588 | lh3lh3 | 2010-06-11 17:41:13 -0400 (Fri, 11 Jun 2010) | 3 lines
2581 Changed paths:
2582 M /trunk/samtools/bam_index.c
2583 M /trunk/samtools/bamtk.c
2584
2585 * samtools-0.1.7-11 (r588)
2586 * ported a few improvements from tabix back to samtools
2587
2588 ------------------------------------------------------------------------
2589 r587 | lh3lh3 | 2010-06-11 17:33:16 -0400 (Fri, 11 Jun 2010) | 3 lines
2590 Changed paths:
2591 M /trunk/samtools/bam.h
2592 M /trunk/samtools/bam_index.c
2593 M /trunk/samtools/bamtk.c
2594
2595 * samtools-0.1.7-10 (r587)
2596 * added iterator interface for bam_fetch (ported back from tabix)
2597
2598 ------------------------------------------------------------------------
2599 r586 | lh3lh3 | 2010-06-11 13:23:53 -0400 (Fri, 11 Jun 2010) | 3 lines
2600 Changed paths:
2601 M /trunk/samtools/Makefile
2602 A /trunk/samtools/bam_reheader.c
2603 M /trunk/samtools/bamtk.c
2604 M /trunk/samtools/bgzf.c
2605
2606 * samtools-0.1.7-9 (r586)
2607 * added "reheader" to replace the BAM header
2608
2609 ------------------------------------------------------------------------
2610 r585 | lh3lh3 | 2010-06-11 12:22:06 -0400 (Fri, 11 Jun 2010) | 3 lines
2611 Changed paths:
2612 M /trunk/samtools/bam.c
2613 M /trunk/samtools/bamtk.c
2614 M /trunk/samtools/kstring.h
2615
2616 * samtools-0.1.7-8 (r585)
2617 * speed up "view"
2618
2619 ------------------------------------------------------------------------
2620 r584 | lh3lh3 | 2010-06-11 12:00:41 -0400 (Fri, 11 Jun 2010) | 4 lines
2621 Changed paths:
2622 M /trunk/samtools/bam.c
2623 M /trunk/samtools/bamtk.c
2624 M /trunk/samtools/bgzf.c
2625 M /trunk/samtools/bgzf.h
2626 M /trunk/samtools/kstring.h
2627 M /trunk/samtools/misc/wgsim_eval.pl
2628
2629 * samtools-0.1.7-7 (r584)
2630 * ported tabix BGZF to samtools
2631 * flush BGZF after writing the BAM header and between alignment boundaries
2632
2633 ------------------------------------------------------------------------
2634 r583 | petulda | 2010-06-11 11:58:20 -0400 (Fri, 11 Jun 2010) | 1 line
2635 Changed paths:
2636 A /trunk/samtools/misc/varfilter.py
2637
2638 Initial release on behalf of Aylwyn Scally
2639 ------------------------------------------------------------------------
2640 r561 | petulda | 2010-05-07 08:41:56 -0400 (Fri, 07 May 2010) | 1 line
2641 Changed paths:
2642 M /trunk/samtools/samtools.1
2643
2644 Added a note about the indels coordinates
2645 ------------------------------------------------------------------------
2646 r551 | petulda | 2010-04-23 09:42:13 -0400 (Fri, 23 Apr 2010) | 1 line
2647 Changed paths:
2648 M /trunk/samtools/misc/sam2vcf.pl
2649
2650 Added the possibility to print or not to print the reference allele
2651 ------------------------------------------------------------------------
2652 r546 | petulda | 2010-04-15 04:33:55 -0400 (Thu, 15 Apr 2010) | 1 line
2653 Changed paths:
2654 M /trunk/samtools/sam_header.c
2655
2656 More descriptive message for space separated tags
2657 ------------------------------------------------------------------------
2658 r545 | petulda | 2010-04-14 11:44:50 -0400 (Wed, 14 Apr 2010) | 1 line
2659 Changed paths:
2660 M /trunk/samtools/misc/sam2vcf.pl
2661
2662 Speedup with -i, no need to query the reference all the time
2663 ------------------------------------------------------------------------
2664 r541 | petulda | 2010-03-15 10:03:51 -0400 (Mon, 15 Mar 2010) | 1 line
2665 Changed paths:
2666 M /trunk/samtools/sam_header.c
2667
2668 Fixed the order of sequences in the header
2669 ------------------------------------------------------------------------
2670 r540 | petulda | 2010-03-04 06:28:35 -0500 (Thu, 04 Mar 2010) | 1 line
2671 Changed paths:
2672 M /trunk/samtools/misc/sam2vcf.pl
2673
2674 Added possibility to select indels only and fixed a bug in reporting homozygous indels.
2675 ------------------------------------------------------------------------
2676 r539 | jmarshall | 2010-02-27 06:48:17 -0500 (Sat, 27 Feb 2010) | 4 lines
2677 Changed paths:
2678 M /trunk/samtools/bam.c
2679
2680 Improve the invalid 'BAM\1' magic number error message, and also print it
2681 when no bytes can be read from the alleged BAM file, e.g., in the common
2682 user error case when a SAM file has accidentally been supplied.
2683
2684 ------------------------------------------------------------------------
2685 r538 | petulda | 2010-02-26 10:51:40 -0500 (Fri, 26 Feb 2010) | 1 line
2686 Changed paths:
2687 M /trunk/samtools/AUTHORS
2688 M /trunk/samtools/bam.h
2689 M /trunk/samtools/bam_import.c
2690 M /trunk/samtools/sam_header.c
2691
2692 Improved efficiency of header parsing
2693 ------------------------------------------------------------------------
2694 r537 | lh3lh3 | 2010-02-23 21:08:48 -0500 (Tue, 23 Feb 2010) | 3 lines
2695 Changed paths:
2696 M /trunk/samtools/misc/export2sam.pl
2697
2698 Updated export2sam.pl by Chris Saunders from Illumina.
2699
2700
2701 ------------------------------------------------------------------------
2702 r536 | petulda | 2010-02-17 08:32:53 -0500 (Wed, 17 Feb 2010) | 1 line
2703 Changed paths:
2704 M /trunk/samtools/misc/samtools.pl
2705
2706 Fixed filtering of SNPs near indels. Added min indel and SNP quality filter.
2707 ------------------------------------------------------------------------
2708 r535 | petulda | 2010-02-12 04:52:37 -0500 (Fri, 12 Feb 2010) | 1 line
2709 Changed paths:
2710 M /trunk/samtools/misc/sam2vcf.pl
2711
2712 Print an error for pileups in simple format
2713 ------------------------------------------------------------------------
2714 r534 | lh3lh3 | 2010-02-11 14:01:41 -0500 (Thu, 11 Feb 2010) | 2 lines
2715 Changed paths:
2716 M /trunk/samtools/bam_plcmd.c
2717
2718 added a hidden option in pileup to output the base position (for Erin)
2719
2720 ------------------------------------------------------------------------
2721 r533 | petulda | 2010-02-09 10:12:14 -0500 (Tue, 09 Feb 2010) | 1 line
2722 Changed paths:
2723 M /trunk/samtools/misc/sam2vcf.pl
2724
2725 Added possibility to specify a custom column title for the data column
2726 ------------------------------------------------------------------------
2727 r532 | petulda | 2010-02-09 09:46:09 -0500 (Tue, 09 Feb 2010) | 1 line
2728 Changed paths:
2729 M /trunk/samtools/bam_plcmd.c
2730
2731 Added the -d option to limit maximum depth for indels.
2732 ------------------------------------------------------------------------
2733 r531 | petulda | 2010-02-03 07:57:27 -0500 (Wed, 03 Feb 2010) | 1 line
2734 Changed paths:
2735 M /trunk/samtools/misc/sam2vcf.pl
2736
2737 Added VCF header
2738 ------------------------------------------------------------------------
2739 r530 | lh3lh3 | 2010-02-01 09:13:19 -0500 (Mon, 01 Feb 2010) | 3 lines
2740 Changed paths:
2741 M /trunk/samtools/ChangeLog
2742 M /trunk/samtools/bam_plcmd.c
2743 M /trunk/samtools/bamtk.c
2744 M /trunk/samtools/misc/samtools.pl
2745 M /trunk/samtools/misc/wgsim.c
2746
2747 * samtools-0.1.7-6
2748 * fixed a bug in faidx
2749
2750 ------------------------------------------------------------------------
2751 r529 | jmarshall | 2010-01-11 18:51:49 -0500 (Mon, 11 Jan 2010) | 2 lines
2752 Changed paths:
2753 M /trunk/samtools/faidx.c
2754
2755 Put the right filename in the error message.
2756
2757 ------------------------------------------------------------------------
2758 r528 | lh3lh3 | 2009-12-14 11:26:47 -0500 (Mon, 14 Dec 2009) | 3 lines
2759 Changed paths:
2760 M /trunk/samtools/bam_plcmd.c
2761 M /trunk/samtools/bamtk.c
2762
2763 * samtools-0.1.7-5 (r528)
2764 * further add new consensus generation strategy
2765
2766 ------------------------------------------------------------------------
2767 r527 | petulda | 2009-12-11 12:31:05 -0500 (Fri, 11 Dec 2009) | 1 line
2768 Changed paths:
2769 M /trunk/samtools/knetfile.c
2770
2771 Fixed a bug in knet_seek
2772 ------------------------------------------------------------------------
2773 r526 | petulda | 2009-12-11 07:51:18 -0500 (Fri, 11 Dec 2009) | 1 line
2774 Changed paths:
2775 M /trunk/samtools/misc/sam2vcf.pl
2776
2777 Small fix in VCF format: dot for the empty INFO field
2778 ------------------------------------------------------------------------
2779 r525 | petulda | 2009-12-11 04:36:18 -0500 (Fri, 11 Dec 2009) | 1 line
2780 Changed paths:
2781 M /trunk/samtools/sam_header.c
2782
2783 Allow tabs in the CO header field
2784 ------------------------------------------------------------------------
2785 r524 | jmarshall | 2009-12-10 10:03:58 -0500 (Thu, 10 Dec 2009) | 3 lines
2786 Changed paths:
2787 M /trunk/samtools/Makefile
2788 M /trunk/samtools/Makefile.mingw
2789
2790 Depend on libbam.a rather than the phony target, so that samtools is not
2791 unnecessarily rebuilt every time. Also clean bgzip.
2792
2793 ------------------------------------------------------------------------
2794 r523 | jmarshall | 2009-12-10 09:45:32 -0500 (Thu, 10 Dec 2009) | 4 lines
2795 Changed paths:
2796 M /trunk/samtools/Makefile
2797 M /trunk/samtools/Makefile.mingw
2798
2799 Fix a bug in compiling bgzip: this also needs knetfile.o when _USE_KNETFILE
2800 is defined. Also introduce $(KNETFILE_O) which can be set to empty to
2801 facilitate non-knet builds.
2802
2803 ------------------------------------------------------------------------
2804 r522 | lh3lh3 | 2009-12-01 13:02:36 -0500 (Tue, 01 Dec 2009) | 4 lines
2805 Changed paths:
2806 M /trunk/samtools/bamtk.c
2807 M /trunk/samtools/sam_view.c
2808
2809 * samtools-0.1.7-4 (r522)
2810 * fixed a bug in "view -r"
2811 * added a new option "view -R" to read required read groups from a file
2812
2813 ------------------------------------------------------------------------
2814 r521 | lh3lh3 | 2009-12-01 10:00:12 -0500 (Tue, 01 Dec 2009) | 3 lines
2815 Changed paths:
2816 M /trunk/samtools/bam_md.c
2817 M /trunk/samtools/bamtk.c
2818
2819 * samtools-0.1.7-3 (r521)
2820 * calmd: optionally mask matching bases as N
2821
2822 ------------------------------------------------------------------------
2823 r520 | lh3lh3 | 2009-12-01 09:37:17 -0500 (Tue, 01 Dec 2009) | 4 lines
2824 Changed paths:
2825 M /trunk/samtools/bam_plcmd.c
2826 M /trunk/samtools/bamtk.c
2827 M /trunk/samtools/misc/samtools.pl
2828
2829 * samtools-0.1.7-2 (r520)
2830 * fixed a few issues with compilation in Windows (on behalf of John)
2831 * choose a random base as the consensus (for population genetics studies)
2832
2833 ------------------------------------------------------------------------
2834 r519 | jmarshall | 2009-11-30 10:53:02 -0500 (Mon, 30 Nov 2009) | 6 lines
2835 Changed paths:
2836 M /trunk/samtools/Makefile
2837
2838 Put libraries at the end, so they can resolve references from libbam.a
2839 as well, even with old-fashioned linkers.
2840
2841 Also use libbam.a explicitly rather than "-L. -lbam" to ensure that we get
2842 the freshly built library, not some other libbam.a lying around the system.
2843
2844 ------------------------------------------------------------------------
2845 r518 | jmarshall | 2009-11-30 08:44:56 -0500 (Mon, 30 Nov 2009) | 2 lines
2846 Changed paths:
2847 M /trunk/samtools/Makefile
2848 M /trunk/samtools/misc/Makefile
2849
2850 Also clean *.exe (for Cygwin users using this makefile).
2851
2852 ------------------------------------------------------------------------
2853 r517 | jmarshall | 2009-11-30 07:09:04 -0500 (Mon, 30 Nov 2009) | 2 lines
2854 Changed paths:
2855 M /trunk/samtools/bam_index.c
2856
2857 Index files should be opened in binary mode, not text mode.
2858
2859 ------------------------------------------------------------------------
2860 r516 | lh3lh3 | 2009-11-27 15:18:59 -0500 (Fri, 27 Nov 2009) | 2 lines
2861 Changed paths:
2862 A /trunk/samtools/examples/bam2bed.c
2863
2864 another example program
2865
2866 ------------------------------------------------------------------------
2867 r515 | lh3lh3 | 2009-11-27 10:44:56 -0500 (Fri, 27 Nov 2009) | 3 lines
2868 Changed paths:
2869 M /trunk/samtools/bam_import.c
2870 M /trunk/samtools/bamtk.c
2871 M /trunk/samtools/misc/wgsim_eval.pl
2872 M /trunk/samtools/sam.c
2873
2874 * samtools-0.1.7-1 (r515)
2875 * report an error when .fai contains duplicated names, instead of segfault
2876
2877 ------------------------------------------------------------------------
2878 r514 | jmarshall | 2009-11-24 09:45:35 -0500 (Tue, 24 Nov 2009) | 2 lines
2879 Changed paths:
2880 M /trunk/samtools/bam.c
2881
2882 Format 'c'-encoded auxiliary fields correctly, as *signed* integers.
2883
2884 ------------------------------------------------------------------------
2885 r513 | lh3lh3 | 2009-11-16 10:13:07 -0500 (Mon, 16 Nov 2009) | 2 lines
2886 Changed paths:
2887 M /trunk/samtools/Makefile.mingw
2888
2889 Update Makefile.mingw for the same reason
2890
2891 ------------------------------------------------------------------------
2892 r512 | lh3lh3 | 2009-11-16 10:00:08 -0500 (Mon, 16 Nov 2009) | 2 lines
2893 Changed paths:
2894 M /trunk/samtools/Makefile
2895
2896 Fixed a bug in compiling razip
2897
2898 ------------------------------------------------------------------------
2899 r510 | lh3lh3 | 2009-11-10 10:55:41 -0500 (Tue, 10 Nov 2009) | 2 lines
2900 Changed paths:
2901 M /trunk/samtools/ChangeLog
2902 M /trunk/samtools/NEWS
2903 M /trunk/samtools/bamtk.c
2904 M /trunk/samtools/samtools.1
2905
2906 Release samtools-0.1.7 (r510)
2907
2908 ------------------------------------------------------------------------
2909 r509 | lh3lh3 | 2009-11-06 09:17:09 -0500 (Fri, 06 Nov 2009) | 3 lines
2910 Changed paths:
2911 M /trunk/samtools/bam_plcmd.c
2912 M /trunk/samtools/bamtk.c
2913
2914 * samtools-0.1.6-22 (r509)
2915 * forget to fix a similar problem in glfgen
2916
2917 ------------------------------------------------------------------------
2918 r508 | lh3lh3 | 2009-11-06 09:06:40 -0500 (Fri, 06 Nov 2009) | 3 lines
2919 Changed paths:
2920 M /trunk/samtools/bam_maqcns.c
2921 M /trunk/samtools/bam_plcmd.c
2922 M /trunk/samtools/bamtk.c
2923 M /trunk/samtools/sam_view.c
2924
2925 * samtools-0.1.6-21 (r508)
2926 * fixed a potential bug in the indel caller towards the end of a chromosome
2927
2928 ------------------------------------------------------------------------
2929 r494 | lh3lh3 | 2009-10-26 11:38:00 -0400 (Mon, 26 Oct 2009) | 3 lines
2930 Changed paths:
2931 M /trunk/samtools/bamtk.c
2932 M /trunk/samtools/sam_view.c
2933
2934 * samtools-0.1.6-19 (r494)
2935 * allow to convert Illumina quality (64 based) to the BAM quality
2936
2937 ------------------------------------------------------------------------
2938 r493 | lh3lh3 | 2009-10-26 10:24:39 -0400 (Mon, 26 Oct 2009) | 4 lines
2939 Changed paths:
2940 M /trunk/samtools/Makefile
2941 M /trunk/samtools/bam.c
2942 M /trunk/samtools/bam_import.c
2943 M /trunk/samtools/bamtk.c
2944 M /trunk/samtools/sam.c
2945 M /trunk/samtools/sam_header.c
2946
2947 * samtools-0.1.6-18 (r493)
2948 * fixed the bugs due to improperly incorporating Petr's header parser
2949 * a little code clean up in sam_header.c
2950
2951 ------------------------------------------------------------------------
2952 r492 | petulda | 2009-10-24 09:43:25 -0400 (Sat, 24 Oct 2009) | 1 line
2953 Changed paths:
2954 M /trunk/samtools/sam_header.c
2955
2956 Added sam_header_line_free call for sam_header_parse2
2957 ------------------------------------------------------------------------
2958 r491 | lh3lh3 | 2009-10-24 00:50:16 -0400 (Sat, 24 Oct 2009) | 3 lines
2959 Changed paths:
2960 M /trunk/samtools/sam_view.c
2961
2962 * BUGGY VERSION
2963 * fixed a minor bug
2964
2965 ------------------------------------------------------------------------
2966 r490 | lh3lh3 | 2009-10-24 00:45:12 -0400 (Sat, 24 Oct 2009) | 4 lines
2967 Changed paths:
2968 M /trunk/samtools/bam.c
2969 M /trunk/samtools/bam.h
2970 M /trunk/samtools/bam_import.c
2971 M /trunk/samtools/sam.c
2972
2973 * BUGGY VERSION
2974 * improved the interface a bit
2975 * bug unfixed
2976
2977 ------------------------------------------------------------------------
2978 r489 | lh3lh3 | 2009-10-24 00:41:50 -0400 (Sat, 24 Oct 2009) | 3 lines
2979 Changed paths:
2980 M /trunk/samtools/bam_import.c
2981 M /trunk/samtools/sam_header.c
2982 M /trunk/samtools/sam_header.h
2983
2984 * BUGGY VERSION. Please NOT use it.
2985 * Fixed a minor bug, but the major bug is still there.
2986
2987 ------------------------------------------------------------------------
2988 r488 | lh3lh3 | 2009-10-24 00:17:10 -0400 (Sat, 24 Oct 2009) | 3 lines
2989 Changed paths:
2990 M /trunk/samtools/Makefile
2991 M /trunk/samtools/bam.c
2992 M /trunk/samtools/bam.h
2993 M /trunk/samtools/bam_aux.c
2994 M /trunk/samtools/bam_import.c
2995 M /trunk/samtools/bam_rmdup.c
2996 M /trunk/samtools/bam_rmdupse.c
2997 M /trunk/samtools/kaln.c
2998 M /trunk/samtools/sam.c
2999 M /trunk/samtools/sam_header.c
3000 M /trunk/samtools/sam_header.h
3001 M /trunk/samtools/sam_view.c
3002
3003 * This revision is SERIOUSLY BUGGY. Please NOT use it.
3004 * Start to incorporate header parsing from Petr Danecek
3005
3006 ------------------------------------------------------------------------
3007 r487 | petulda | 2009-10-23 11:44:32 -0400 (Fri, 23 Oct 2009) | 1 line
3008 Changed paths:
3009 M /trunk/samtools/sam_header.c
3010 M /trunk/samtools/sam_header.h
3011
3012 Now possible to merge multiple HeaderDict dictionaries
3013 ------------------------------------------------------------------------
3014 r486 | petulda | 2009-10-22 11:46:58 -0400 (Thu, 22 Oct 2009) | 1 line
3015 Changed paths:
3016 M /trunk/samtools/sam_header.c
3017
3018
3019 ------------------------------------------------------------------------
3020 r485 | petulda | 2009-10-22 11:41:56 -0400 (Thu, 22 Oct 2009) | 1 line
3021 Changed paths:
3022 A /trunk/samtools/sam_header.c
3023 A /trunk/samtools/sam_header.h
3024
3025
3026 ------------------------------------------------------------------------
3027 r484 | lh3lh3 | 2009-10-19 14:31:32 -0400 (Mon, 19 Oct 2009) | 5 lines
3028 Changed paths:
3029 M /trunk/samtools/bam_import.c
3030 M /trunk/samtools/bam_rmdupse.c
3031 M /trunk/samtools/bamtk.c
3032 M /trunk/samtools/examples/Makefile
3033
3034 * samtools-0.1.6-17 (r484)
3035 * fixed a memory leak in rmdupse
3036 * fixed a bug in parsing @RG header lines
3037 * test rmdup in examples/
3038
3039 ------------------------------------------------------------------------
3040 r483 | lh3lh3 | 2009-10-19 13:22:48 -0400 (Mon, 19 Oct 2009) | 4 lines
3041 Changed paths:
3042 M /trunk/samtools/bam_rmdup.c
3043 M /trunk/samtools/bam_rmdupse.c
3044 M /trunk/samtools/bamtk.c
3045
3046 * samtools-0.1.6-16 (r483)
3047 * unify the interface of rmdup and rmdupse
3048 * a new bug found in rg2lib(). Have not been fixed yet.
3049
3050 ------------------------------------------------------------------------
3051 r482 | lh3lh3 | 2009-10-19 13:03:34 -0400 (Mon, 19 Oct 2009) | 4 lines
3052 Changed paths:
3053 M /trunk/samtools/bam.h
3054 M /trunk/samtools/bam_rmdup.c
3055 M /trunk/samtools/bam_rmdupse.c
3056 M /trunk/samtools/bamtk.c
3057 A /trunk/samtools/klist.h
3058
3059 * samtools-0.1.6-15 (r482)
3060 * rewrite rmdupse
3061 * rmdupse is now library aware
3062
3063 ------------------------------------------------------------------------
3064 r481 | lh3lh3 | 2009-10-18 00:07:21 -0400 (Sun, 18 Oct 2009) | 3 lines
3065 Changed paths:
3066 M /trunk/samtools/bam_rmdup.c
3067 M /trunk/samtools/bamtk.c
3068
3069 * samtools-0.1.6-14 (r480)
3070 * rmdup is now RG aware
3071
3072 ------------------------------------------------------------------------
3073 r480 | lh3lh3 | 2009-10-17 22:05:20 -0400 (Sat, 17 Oct 2009) | 2 lines
3074 Changed paths:
3075 M /trunk/samtools/misc/samtools.pl
3076
3077 added a small unitity to parse SRA XML files
3078
3079 ------------------------------------------------------------------------
3080 r479 | lh3lh3 | 2009-10-17 20:57:26 -0400 (Sat, 17 Oct 2009) | 3 lines
3081 Changed paths:
3082 M /trunk/samtools/bam_maqcns.c
3083 M /trunk/samtools/bam_maqcns.h
3084 M /trunk/samtools/bam_plcmd.c
3085 M /trunk/samtools/bam_sort.c
3086 M /trunk/samtools/bamtk.c
3087
3088 * samtools-0.1.6-13 (r479)
3089 * merge: optionally use file names as RG tags
3090
3091 ------------------------------------------------------------------------
3092 r478 | lh3lh3 | 2009-10-14 14:18:12 -0400 (Wed, 14 Oct 2009) | 3 lines
3093 Changed paths:
3094 M /trunk/samtools/bam.c
3095 M /trunk/samtools/bam.h
3096 M /trunk/samtools/bam_maqcns.c
3097 M /trunk/samtools/bamtk.c
3098 M /trunk/samtools/kaln.c
3099
3100 * samtools-0.1.6-12 (r478)
3101 * fixed a bug in the indel caller
3102
3103 ------------------------------------------------------------------------
3104 r477 | lh3lh3 | 2009-10-10 06:12:26 -0400 (Sat, 10 Oct 2009) | 3 lines
3105 Changed paths:
3106 M /trunk/samtools/bam_index.c
3107 M /trunk/samtools/bamtk.c
3108
3109 * samtools-0.1.6-11 (r477)
3110 * fixed a bug due to recent change in bam_index.c (thank Nicole Washington for the patch)
3111
3112 ------------------------------------------------------------------------
3113 r476 | petulda | 2009-10-09 11:45:36 -0400 (Fri, 09 Oct 2009) | 1 line
3114 Changed paths:
3115 A /trunk/samtools/misc/sam2vcf.pl
3116
3117 Added the sam2vcf.pl script.
3118 ------------------------------------------------------------------------
3119 r475 | lh3lh3 | 2009-10-08 10:19:16 -0400 (Thu, 08 Oct 2009) | 2 lines
3120 Changed paths:
3121 M /trunk/samtools/Makefile
3122 M /trunk/samtools/bam.c
3123 M /trunk/samtools/bam.h
3124 M /trunk/samtools/bam_maqcns.c
3125 M /trunk/samtools/bamtk.c
3126 A /trunk/samtools/kaln.c
3127 A /trunk/samtools/kaln.h
3128
3129 Unfinished modification. Please do not use this revision...
3130
3131 ------------------------------------------------------------------------
3132 r474 | petulda | 2009-10-08 06:39:54 -0400 (Thu, 08 Oct 2009) | 1 line
3133 Changed paths:
3134 M /trunk/samtools/knetfile.c
3135
3136 Removed the offending knet_seek message.
3137 ------------------------------------------------------------------------
3138 r473 | petulda | 2009-10-06 09:26:35 -0400 (Tue, 06 Oct 2009) | 1 line
3139 Changed paths:
3140 M /trunk/samtools/knetfile.c
3141 M /trunk/samtools/razf.c
3142
3143 Bug fix - faidx on RAZF compressed files now working.
3144 ------------------------------------------------------------------------
3145 r472 | lh3lh3 | 2009-10-02 08:42:57 -0400 (Fri, 02 Oct 2009) | 2 lines
3146 Changed paths:
3147 M /trunk/samtools/samtools.1
3148
3149 Clarify the meaning of a region like "chr2:1,000,000".
3150
3151 ------------------------------------------------------------------------
3152 r471 | lh3lh3 | 2009-10-02 05:42:19 -0400 (Fri, 02 Oct 2009) | 2 lines
3153 Changed paths:
3154 M /trunk/samtools/misc/novo2sam.pl
3155
3156 Fixed minor bugs in novo2sam.pl (on behalf of Ken Chen and Colin Hercus)
3157
3158 ------------------------------------------------------------------------
3159 r470 | lh3lh3 | 2009-09-29 15:01:27 -0400 (Tue, 29 Sep 2009) | 3 lines
3160 Changed paths:
3161 M /trunk/samtools/Makefile.mingw
3162 M /trunk/samtools/bamtk.c
3163 M /trunk/samtools/knetfile.c
3164 M /trunk/samtools/knetfile.h
3165
3166 * samtools-0.1.6-9 (r470)
3167 * make knetfile.c compatible with MinGW (thank Martin Morgan for the patch)
3168
3169 ------------------------------------------------------------------------
3170 r469 | lh3lh3 | 2009-09-29 08:07:44 -0400 (Tue, 29 Sep 2009) | 3 lines
3171 Changed paths:
3172 M /trunk/samtools/bam_index.c
3173 M /trunk/samtools/bamtk.c
3174
3175 * samtools-0.1.6-9 (r469)
3176 * refactor bam_fetch() for Python binding. On behalf of Leo Goodstadt.
3177
3178 ------------------------------------------------------------------------
3179 r468 | lh3lh3 | 2009-09-28 05:18:29 -0400 (Mon, 28 Sep 2009) | 3 lines
3180 Changed paths:
3181 M /trunk/samtools/bam_sort.c
3182 M /trunk/samtools/bamtk.c
3183 M /trunk/samtools/misc/samtools.pl
3184
3185 * samtools-0.1.6-7 (r468)
3186 * make merge stable
3187
3188 ------------------------------------------------------------------------
3189 r467 | petulda | 2009-09-28 04:51:29 -0400 (Mon, 28 Sep 2009) | 1 line
3190 Changed paths:
3191 M /trunk/samtools/bgzf.c
3192 M /trunk/samtools/bgzip.c
3193 M /trunk/samtools/razf.c
3194 M /trunk/samtools/razip.c
3195
3196 Changed the mode for newly created files to 0666. This allows less strict permissions with umask properly set (e.g. 0002 vs. 0022).
3197 ------------------------------------------------------------------------
3198 r466 | lh3lh3 | 2009-09-24 06:29:19 -0400 (Thu, 24 Sep 2009) | 3 lines
3199 Changed paths:
3200 M /trunk/samtools/ChangeLog
3201 M /trunk/samtools/bam_md.c
3202 M /trunk/samtools/bamtk.c
3203
3204 * samtools-0.1.6-6 (r466)
3205 * do not crash calmd when some sequences are absent from the reference.
3206
3207 ------------------------------------------------------------------------
3208 r464 | jmarshall | 2009-09-23 06:14:32 -0400 (Wed, 23 Sep 2009) | 3 lines
3209 Changed paths:
3210 M /trunk/samtools/bam.c
3211 M /trunk/samtools/knetfile.c
3212
3213 Suppress bgzf_check_EOF() messages when reading from a pipe, as there is
3214 no way to seek on a pipe and the messages always appear.
3215
3216 ------------------------------------------------------------------------
3217 r463 | petulda | 2009-09-16 07:05:41 -0400 (Wed, 16 Sep 2009) | 1 line
3218 Changed paths:
3219 M /trunk/samtools/knetfile.c
3220 M /trunk/samtools/razf.c
3221
3222 A bug fix, "samtools view" is now working again.
3223 ------------------------------------------------------------------------
3224 r462 | lh3lh3 | 2009-09-16 04:51:07 -0400 (Wed, 16 Sep 2009) | 3 lines
3225 Changed paths:
3226 M /trunk/samtools/bamtk.c
3227 M /trunk/samtools/faidx.c
3228 M /trunk/samtools/knetfile.c
3229 M /trunk/samtools/knetfile.h
3230 M /trunk/samtools/razf.c
3231 M /trunk/samtools/razf.h
3232
3233 * samtools-0.1.6-5 (r462)
3234 * Added knetfile support in razf and faidx (on behalf of Petr Danecek)
3235
3236 ------------------------------------------------------------------------
3237 r460 | lh3lh3 | 2009-09-09 07:06:22 -0400 (Wed, 09 Sep 2009) | 2 lines
3238 Changed paths:
3239 M /trunk/samtools/samtools.1
3240
3241 fixed a formatting issue
3242
3243 ------------------------------------------------------------------------
3244 r459 | lh3lh3 | 2009-09-08 18:14:08 -0400 (Tue, 08 Sep 2009) | 3 lines
3245 Changed paths:
3246 M /trunk/samtools/bam_sort.c
3247 M /trunk/samtools/bamtk.c
3248
3249 * samtools-0.1.6-4 (r459)
3250 * make sort output the result to stdout when -o is in use
3251
3252 ------------------------------------------------------------------------
3253 r458 | lh3lh3 | 2009-09-07 05:10:28 -0400 (Mon, 07 Sep 2009) | 4 lines
3254 Changed paths:
3255 M /trunk/samtools/bamtk.c
3256 M /trunk/samtools/faidx.c
3257 M /trunk/samtools/faidx.h
3258 M /trunk/samtools/samtools.1
3259
3260 * samtools-0.1.6-2 (r458)
3261 * added more interface to faidx (by Nils)
3262 * updated documentation
3263
3264 ------------------------------------------------------------------------
3265 r457 | lh3lh3 | 2009-09-05 16:12:04 -0400 (Sat, 05 Sep 2009) | 3 lines
3266 Changed paths:
3267 M /trunk/samtools/bam_sort.c
3268 M /trunk/samtools/bamtk.c
3269
3270 * samtools-0.1.6-2 (r457)
3271 * get rid of three assert() in bam_sort.c
3272
3273 ------------------------------------------------------------------------
3274 r456 | jmarshall | 2009-09-04 12:46:25 -0400 (Fri, 04 Sep 2009) | 3 lines
3275 Changed paths:
3276 M /trunk/samtools/razf.c
3277
3278 Return NULL from _razf_open() (and hence razf_open()/razf_open2())
3279 when opening the file fails.
3280
3281 ------------------------------------------------------------------------
3282 r453 | lh3lh3 | 2009-09-02 08:56:33 -0400 (Wed, 02 Sep 2009) | 2 lines
3283 Changed paths:
3284 M /trunk/samtools/ChangeLog
3285 M /trunk/samtools/NEWS
3286 M /trunk/samtools/bamtk.c
3287 M /trunk/samtools/samtools.1
3288 D /trunk/samtools/source.dot
3289
3290 Release samtools-0.1.6
3291
3292 ------------------------------------------------------------------------
3293 r451 | lh3lh3 | 2009-09-02 05:44:48 -0400 (Wed, 02 Sep 2009) | 4 lines
3294 Changed paths:
3295 M /trunk/samtools/bam_md.c
3296 M /trunk/samtools/bam_rmdup.c
3297 M /trunk/samtools/bam_rmdupse.c
3298 M /trunk/samtools/bam_sort.c
3299 M /trunk/samtools/bamtk.c
3300 M /trunk/samtools/samtools.1
3301
3302 * samtools-0.1.5-34 (r451)
3303 * applied the patch by John
3304 * improved the help message a little bit
3305
3306 ------------------------------------------------------------------------
3307 r450 | lh3lh3 | 2009-09-02 04:55:55 -0400 (Wed, 02 Sep 2009) | 3 lines
3308 Changed paths:
3309 M /trunk/samtools/bam_color.c
3310 M /trunk/samtools/bamtk.c
3311
3312 * samtools-0.1.5-33 (r450)
3313 * fixed a bug in bam_color.c (on behalf of Nils Homer)
3314
3315 ------------------------------------------------------------------------
3316 r449 | lh3lh3 | 2009-08-29 15:36:41 -0400 (Sat, 29 Aug 2009) | 4 lines
3317 Changed paths:
3318 M /trunk/samtools/bam_import.c
3319 M /trunk/samtools/bam_md.c
3320 M /trunk/samtools/bamtk.c
3321 M /trunk/samtools/misc/samtools.pl
3322
3323 * samtools-0.1.5-32 (r449)
3324 * fillmd: fixed a bug in modifying MD/NM tags
3325 * in import, give a warning if the read is aligned but there is no CIGAR.
3326
3327 ------------------------------------------------------------------------
3328 r448 | lh3lh3 | 2009-08-19 04:44:28 -0400 (Wed, 19 Aug 2009) | 3 lines
3329 Changed paths:
3330 M /trunk/samtools/ChangeLog
3331 M /trunk/samtools/bam_pileup.c
3332 M /trunk/samtools/bamtk.c
3333 M /trunk/samtools/misc/wgsim_eval.pl
3334
3335 * samtools-0.1.5-31 (r448)
3336 * fixed an issue when the last CIGAR is I or D
3337
3338 ------------------------------------------------------------------------
3339 r447 | lh3lh3 | 2009-08-17 04:34:57 -0400 (Mon, 17 Aug 2009) | 3 lines
3340 Changed paths:
3341 M /trunk/samtools/bam_aux.c
3342 M /trunk/samtools/bamtk.c
3343
3344 * samtools-0.1.5-30 (r447)
3345 * fixed a bug in bam_aux_get(): 'A' is not checked
3346
3347 ------------------------------------------------------------------------
3348 r446 | lh3lh3 | 2009-08-17 04:33:17 -0400 (Mon, 17 Aug 2009) | 2 lines
3349 Changed paths:
3350 M /trunk/samtools/bam_aux.c
3351 M /trunk/samtools/bamtk.c
3352
3353 *
3354
3355 ------------------------------------------------------------------------
3356 r444 | lh3lh3 | 2009-08-11 05:02:36 -0400 (Tue, 11 Aug 2009) | 3 lines
3357 Changed paths:
3358 M /trunk/samtools/bam_sort.c
3359 M /trunk/samtools/bamtk.c
3360
3361 * samtools-0.1.5-28 (r444)
3362 * bug in "merge -n"
3363
3364 ------------------------------------------------------------------------
3365 r443 | lh3lh3 | 2009-08-11 04:29:11 -0400 (Tue, 11 Aug 2009) | 4 lines
3366 Changed paths:
3367 M /trunk/samtools/bam.c
3368 M /trunk/samtools/bam_import.c
3369 M /trunk/samtools/bamtk.c
3370
3371 * samtools-0.1.5-27 (r443)
3372 * SEQ and QUAL can be "*"
3373 * parse CIGAR "=" and "X" as "M"
3374
3375 ------------------------------------------------------------------------
3376 r442 | lh3lh3 | 2009-08-07 16:56:38 -0400 (Fri, 07 Aug 2009) | 4 lines
3377 Changed paths:
3378 M /trunk/samtools/bam_pileup.c
3379 M /trunk/samtools/bamtk.c
3380 M /trunk/samtools/misc/md5.c
3381 M /trunk/samtools/misc/md5.h
3382 M /trunk/samtools/misc/md5fa.c
3383
3384 * samtools-0.1.5-26 (r442)
3385 * replace RSA Inc md5.* with ones under permissive lincense
3386 * fixed a bug in detecting unsorted bam in pileup
3387
3388 ------------------------------------------------------------------------
3389 r441 | bhandsaker | 2009-08-05 09:41:28 -0400 (Wed, 05 Aug 2009) | 2 lines
3390 Changed paths:
3391 M /trunk/samtools/bgzf.c
3392 M /trunk/samtools/bgzf.h
3393 M /trunk/samtools/bgzip.c
3394
3395 Change copyright notices now that MIT has approved open source distribution.
3396
3397 ------------------------------------------------------------------------
3398 r440 | lh3lh3 | 2009-08-05 05:44:24 -0400 (Wed, 05 Aug 2009) | 3 lines
3399 Changed paths:
3400 M /trunk/samtools/bam_stat.c
3401 M /trunk/samtools/bamtk.c
3402
3403 * samtools-0.1.5-25 (r436)
3404 * in flagstats, do not report singletons if both ends are unmapped
3405
3406 ------------------------------------------------------------------------
3407 r439 | lh3lh3 | 2009-08-04 17:16:51 -0400 (Tue, 04 Aug 2009) | 2 lines
3408 Changed paths:
3409 M /trunk/samtools/misc/maq2sam.c
3410
3411 fixed a SERIOUS bug in setting 0x20 flag
3412
3413 ------------------------------------------------------------------------
3414 r438 | lh3lh3 | 2009-08-04 16:50:43 -0400 (Tue, 04 Aug 2009) | 2 lines
3415 Changed paths:
3416 M /trunk/samtools/misc/samtools.pl
3417
3418 fixed two minor bugs (suggested by Tim M Storm)
3419
3420 ------------------------------------------------------------------------
3421 r437 | lh3lh3 | 2009-08-04 04:13:24 -0400 (Tue, 04 Aug 2009) | 3 lines
3422 Changed paths:
3423 M /trunk/samtools/bamtk.c
3424 M /trunk/samtools/misc/samtools.pl
3425 M /trunk/samtools/sam_view.c
3426
3427 * samtools-0.1.5-24 (r435)
3428 * fixed a typo
3429
3430 ------------------------------------------------------------------------
3431 r434 | lh3lh3 | 2009-08-03 05:40:42 -0400 (Mon, 03 Aug 2009) | 3 lines
3432 Changed paths:
3433 M /trunk/samtools/bam_tview.c
3434 M /trunk/samtools/bamtk.c
3435
3436 * samtools-0.1.5-23 (r434)
3437 * in tview, press 'r' to show read names rather than sequences
3438
3439 ------------------------------------------------------------------------
3440 r433 | lh3lh3 | 2009-08-02 14:13:35 -0400 (Sun, 02 Aug 2009) | 3 lines
3441 Changed paths:
3442 M /trunk/samtools/knetfile.c
3443
3444 * tried to fixed the buggy FTP random access in Windows. FAILED.
3445 * anyway, MinGW seems to have problem with "%lld".
3446
3447 ------------------------------------------------------------------------
3448 r432 | lh3lh3 | 2009-08-01 19:32:07 -0400 (Sat, 01 Aug 2009) | 5 lines
3449 Changed paths:
3450 M /trunk/samtools/Makefile.mingw
3451 M /trunk/samtools/bamtk.c
3452 M /trunk/samtools/faidx.c
3453 M /trunk/samtools/razf.c
3454 A /trunk/samtools/win32/libcurses.a
3455 A /trunk/samtools/win32/xcurses.h
3456
3457 * samtools-0.1.5-22 (r432)
3458 * faidx: fixed compitability issue with _WIN32
3459 * razf: fixed potential compitability issue with _WIN32
3460 * PDCurses support in Windows
3461
3462 ------------------------------------------------------------------------
3463 r431 | lh3lh3 | 2009-08-01 18:34:54 -0400 (Sat, 01 Aug 2009) | 2 lines
3464 Changed paths:
3465 M /trunk/samtools/win32/libz.a
3466
3467 replace the GnuWin32 version of libz.a with my own build with MinGW.
3468
3469 ------------------------------------------------------------------------
3470 r430 | lh3lh3 | 2009-08-01 18:21:07 -0400 (Sat, 01 Aug 2009) | 2 lines
3471 Changed paths:
3472 M /trunk/samtools/knetfile.c
3473
3474 add comments
3475
3476 ------------------------------------------------------------------------
3477 r429 | lh3lh3 | 2009-08-01 17:41:19 -0400 (Sat, 01 Aug 2009) | 3 lines
3478 Changed paths:
3479 M /trunk/samtools/Makefile.mingw
3480 M /trunk/samtools/bamtk.c
3481 M /trunk/samtools/knetfile.c
3482 M /trunk/samtools/knetfile.h
3483
3484 * samtools-0.1.5-21 (r428)
3485 * knetfile.c is now compatible with mingw-winsock
3486
3487 ------------------------------------------------------------------------
3488 r428 | lh3lh3 | 2009-07-31 19:39:07 -0400 (Fri, 31 Jul 2009) | 2 lines
3489 Changed paths:
3490 M /trunk/samtools/Makefile.mingw
3491
3492 simplify MinGW Makefile
3493
3494 ------------------------------------------------------------------------
3495 r427 | lh3lh3 | 2009-07-31 19:30:54 -0400 (Fri, 31 Jul 2009) | 5 lines
3496 Changed paths:
3497 A /trunk/samtools/Makefile.mingw
3498 M /trunk/samtools/bam_import.c
3499 M /trunk/samtools/bamtk.c
3500 A /trunk/samtools/win32
3501 A /trunk/samtools/win32/libz.a
3502 A /trunk/samtools/win32/zconf.h
3503 A /trunk/samtools/win32/zlib.h
3504
3505 * samtools-0.1.5-20 (r427)
3506 * MinGW support. At least SAM<->BAM conversion is working. Other
3507 functionality are not tested at the moment.
3508 * zlib headers and Windows version of libz.a are included in win32/
3509
3510 ------------------------------------------------------------------------
3511 r426 | lh3lh3 | 2009-07-31 18:32:09 -0400 (Fri, 31 Jul 2009) | 3 lines
3512 Changed paths:
3513 M /trunk/samtools/bamtk.c
3514 M /trunk/samtools/sam_view.c
3515
3516 * samtools-0.1.5-19 (r426)
3517 * fixed a bug caused by recent modifications. Sorry.
3518
3519 ------------------------------------------------------------------------
3520 r425 | lh3lh3 | 2009-07-31 18:23:51 -0400 (Fri, 31 Jul 2009) | 2 lines
3521 Changed paths:
3522 M /trunk/samtools/bgzf.c
3523
3524 compatible with Windows binary files
3525
3526 ------------------------------------------------------------------------
3527 r424 | lh3lh3 | 2009-07-31 05:19:59 -0400 (Fri, 31 Jul 2009) | 5 lines
3528 Changed paths:
3529 M /trunk/samtools/bam_maqcns.c
3530 M /trunk/samtools/bam_maqcns.h
3531 M /trunk/samtools/bam_plcmd.c
3532 M /trunk/samtools/bam_tview.c
3533 M /trunk/samtools/bamtk.c
3534 M /trunk/samtools/misc/samtools.pl
3535
3536 * samtools-0.1.5-18 (r423)
3537 * output additional information in pileup indel lines, for the purepose
3538 of debugging at the moment
3539 * in tview, optionally allow to treat reference skip as deletion
3540
3541 ------------------------------------------------------------------------
3542 r423 | lh3lh3 | 2009-07-30 17:00:36 -0400 (Thu, 30 Jul 2009) | 2 lines
3543 Changed paths:
3544 A /trunk/samtools/misc/psl2sam.pl
3545
3546 convert BLAT psl to SAM.
3547
3548 ------------------------------------------------------------------------
3549 r422 | lh3lh3 | 2009-07-30 06:24:39 -0400 (Thu, 30 Jul 2009) | 6 lines
3550 Changed paths:
3551 M /trunk/samtools/ChangeLog
3552 M /trunk/samtools/bam.c
3553 M /trunk/samtools/bamtk.c
3554 M /trunk/samtools/bgzf.c
3555 M /trunk/samtools/bgzf.h
3556 M /trunk/samtools/knetfile.c
3557 M /trunk/samtools/sam.c
3558 M /trunk/samtools/sam_view.c
3559
3560 * samtools-0.1.5-17 (r422)
3561 * fixed a but in knetfile.c when seek type is not SEEK_SET
3562 * write an empty BGZF block to every BGZF file
3563 * check BGZF EOF marker in bam_header_read()
3564 * update ChangeLog
3565
3566 ------------------------------------------------------------------------
3567 r421 | lh3lh3 | 2009-07-30 05:03:39 -0400 (Thu, 30 Jul 2009) | 3 lines
3568 Changed paths:
3569 M /trunk/samtools/bam_import.c
3570 M /trunk/samtools/bam_plcmd.c
3571 M /trunk/samtools/bamtk.c
3572 M /trunk/samtools/misc/samtools.pl
3573 M /trunk/samtools/sam.c
3574 M /trunk/samtools/sam.h
3575 M /trunk/samtools/sam_view.c
3576
3577 * samtools-0.1.5-16 (r421)
3578 * in view and pileup, load header from FASTA index if the input is SAM.
3579
3580 ------------------------------------------------------------------------
3581 r420 | lh3lh3 | 2009-07-29 04:18:55 -0400 (Wed, 29 Jul 2009) | 2 lines
3582 Changed paths:
3583 M /trunk/samtools/misc/maq2sam.c
3584
3585 do not set "read 1" if reads are not mapped in the PE mode of maq
3586
3587 ------------------------------------------------------------------------
3588 r419 | lh3lh3 | 2009-07-28 04:52:33 -0400 (Tue, 28 Jul 2009) | 5 lines
3589 Changed paths:
3590 M /trunk/samtools/bam_import.c
3591 M /trunk/samtools/bamtk.c
3592 M /trunk/samtools/misc/samtools.pl
3593 M /trunk/samtools/misc/wgsim_eval.pl
3594
3595 * samtools-0.1.5-15 (r419)
3596 * in sam_open(), return NULL when the file cannot be opened.
3597 * make wgsim_eval.pl more robust to imperfect SAM
3598 * add "unique" command to samtools.pl
3599
3600 ------------------------------------------------------------------------
3601 r418 | lh3lh3 | 2009-07-24 09:04:19 -0400 (Fri, 24 Jul 2009) | 2 lines
3602 Changed paths:
3603 M /trunk/samtools/misc/wgsim_eval.pl
3604
3605 skip @header lines in SAM
3606
3607 ------------------------------------------------------------------------
3608 r417 | lh3lh3 | 2009-07-24 07:42:38 -0400 (Fri, 24 Jul 2009) | 3 lines
3609 Changed paths:
3610 M /trunk/samtools/bamtk.c
3611 M /trunk/samtools/sam_view.c
3612
3613 * samtools-0.1.5-14 (r417)
3614 * more help in "samtools view" due to the recent changes.
3615
3616 ------------------------------------------------------------------------
3617 r416 | lh3lh3 | 2009-07-24 07:34:30 -0400 (Fri, 24 Jul 2009) | 3 lines
3618 Changed paths:
3619 M /trunk/samtools/bam.c
3620 M /trunk/samtools/bam.h
3621 M /trunk/samtools/bam_import.c
3622 M /trunk/samtools/bamtk.c
3623 M /trunk/samtools/sam.c
3624 M /trunk/samtools/sam.h
3625 M /trunk/samtools/sam_view.c
3626
3627 * samtools-0.1.5-17 (r416)
3628 * support import/export SAM with string tags
3629
3630 ------------------------------------------------------------------------
3631 r415 | lh3lh3 | 2009-07-24 06:39:26 -0400 (Fri, 24 Jul 2009) | 3 lines
3632 Changed paths:
3633 M /trunk/samtools/bam.c
3634 M /trunk/samtools/bam.h
3635 M /trunk/samtools/bam_import.c
3636 M /trunk/samtools/bamtk.c
3637 M /trunk/samtools/sam.c
3638 M /trunk/samtools/sam.h
3639 M /trunk/samtools/sam_view.c
3640
3641 * samtools-0.1.5-12 (r415)
3642 * FLAG now can be in HEX
3643
3644 ------------------------------------------------------------------------
3645 r414 | lh3lh3 | 2009-07-22 17:03:49 -0400 (Wed, 22 Jul 2009) | 2 lines
3646 Changed paths:
3647 M /trunk/samtools/kstring.h
3648
3649 fixed a compiling error (thank Ken for fixing it)
3650
3651 ------------------------------------------------------------------------
3652 r412 | lh3lh3 | 2009-07-21 17:19:40 -0400 (Tue, 21 Jul 2009) | 2 lines
3653 Changed paths:
3654 M /trunk/samtools/kstring.c
3655 M /trunk/samtools/kstring.h
3656
3657 Implemented Boyer-Moore search in the kstring library.
3658
3659 ------------------------------------------------------------------------
3660 r409 | lh3lh3 | 2009-07-17 12:10:20 -0400 (Fri, 17 Jul 2009) | 2 lines
3661 Changed paths:
3662 M /trunk/samtools/bam_index.c
3663
3664 do not include knetfile.h when _USE_KNETFILE is not defined
3665
3666 ------------------------------------------------------------------------
3667 r408 | lh3lh3 | 2009-07-17 10:29:21 -0400 (Fri, 17 Jul 2009) | 5 lines
3668 Changed paths:
3669 M /trunk/samtools/bam_md.c
3670 M /trunk/samtools/bam_tview.c
3671 M /trunk/samtools/bamtk.c
3672 M /trunk/samtools/bgzf.c
3673
3674 * samtools-0.1.5-11 (r408)
3675 * force to overwirte existing MD if it is different from the one calculated
3676 from fillmd.
3677 * bgzf.c: improved the compatibility with Windows headers
3678
3679 ------------------------------------------------------------------------
3680 r407 | lh3lh3 | 2009-07-17 09:46:56 -0400 (Fri, 17 Jul 2009) | 5 lines
3681 Changed paths:
3682 M /trunk/samtools/bam.h
3683 M /trunk/samtools/bam_aux.c
3684 M /trunk/samtools/bam_md.c
3685 M /trunk/samtools/bamtk.c
3686 M /trunk/samtools/sam.h
3687
3688 * samtools-0.1.5-10 (r407)
3689 * implemented bam_aux_del() to remove a tag
3690 * fillmd: generate the NM tag
3691 * fillmd: cmd interface improvement
3692
3693 ------------------------------------------------------------------------
3694 r406 | lh3lh3 | 2009-07-16 18:30:40 -0400 (Thu, 16 Jul 2009) | 2 lines
3695 Changed paths:
3696 M /trunk/samtools/Makefile
3697
3698 Sorry. The old Makefile is for PDCurses...
3699
3700 ------------------------------------------------------------------------
3701 r405 | lh3lh3 | 2009-07-16 18:30:11 -0400 (Thu, 16 Jul 2009) | 3 lines
3702 Changed paths:
3703 M /trunk/samtools/Makefile
3704 M /trunk/samtools/bam_tview.c
3705 M /trunk/samtools/bamtk.c
3706
3707 * samtools-0.1.5-9 (r405)
3708 * improved the compatibility with PDCurses a little bit
3709
3710 ------------------------------------------------------------------------
3711 r404 | lh3lh3 | 2009-07-16 18:23:52 -0400 (Thu, 16 Jul 2009) | 3 lines
3712 Changed paths:
3713 M /trunk/samtools/Makefile
3714 M /trunk/samtools/bam_tview.c
3715 M /trunk/samtools/bamtk.c
3716
3717 * samtools-0.1.5-8 (r404)
3718 * compatible with PDCurses
3719
3720 ------------------------------------------------------------------------
3721 r403 | lh3lh3 | 2009-07-16 17:39:39 -0400 (Thu, 16 Jul 2009) | 3 lines
3722 Changed paths:
3723 M /trunk/samtools/bamtk.c
3724 M /trunk/samtools/kseq.h
3725
3726 * samtools-0.1.5-7 (r403)
3727 * fixed a bug in kseq.h for binary files (text files are fine)
3728
3729 ------------------------------------------------------------------------
3730 r402 | lh3lh3 | 2009-07-16 06:49:53 -0400 (Thu, 16 Jul 2009) | 4 lines
3731 Changed paths:
3732 M /trunk/samtools/bam_import.c
3733 M /trunk/samtools/bam_index.c
3734 M /trunk/samtools/bamtk.c
3735 M /trunk/samtools/bgzf.c
3736
3737 * samtools-0.1.5-6 (r402)
3738 * fixed compiling error when "-D_USE_NETFILE" is not applied
3739 * improve portability to MinGW
3740
3741 ------------------------------------------------------------------------
3742 r398 | lh3lh3 | 2009-07-13 05:21:36 -0400 (Mon, 13 Jul 2009) | 3 lines
3743 Changed paths:
3744 A /trunk/bam-lite/bam.h (from /trunk/samtools/bam.h:395)
3745 A /trunk/bam-lite/bam_lite.c (from /trunk/samtools/bam_lite.c:395)
3746 D /trunk/samtools/bam_lite.c
3747
3748 * move bam_lite.c to bam-lite
3749 * copy bam.h to bam-lite
3750
3751 ------------------------------------------------------------------------
3752 r395 | lh3lh3 | 2009-07-13 05:12:57 -0400 (Mon, 13 Jul 2009) | 3 lines
3753 Changed paths:
3754 M /trunk/samtools/bam.h
3755 M /trunk/samtools/bam_lite.c
3756 M /trunk/samtools/bam_lpileup.c
3757 M /trunk/samtools/bam_pileup.c
3758 M /trunk/samtools/bamtk.c
3759
3760 * samtools-0.1.5-5 (r395)
3761 * added bam_pileup_file() and removed bam_lpileup_file()
3762
3763 ------------------------------------------------------------------------
3764 r394 | lh3lh3 | 2009-07-12 19:35:10 -0400 (Sun, 12 Jul 2009) | 3 lines
3765 Changed paths:
3766 M /trunk/samtools/bamtk.c
3767 M /trunk/samtools/knetfile.c
3768 M /trunk/samtools/knetfile.h
3769
3770 * samtools-0.1.5-4 (r394)
3771 * http_proxy support in knetfile library (check http_proxy ENV)
3772
3773 ------------------------------------------------------------------------
3774 r393 | lh3lh3 | 2009-07-12 18:57:07 -0400 (Sun, 12 Jul 2009) | 5 lines
3775 Changed paths:
3776 M /trunk/samtools/bam_index.c
3777 M /trunk/samtools/bam_tview.c
3778 M /trunk/samtools/bamtk.c
3779 M /trunk/samtools/knetfile.c
3780 M /trunk/samtools/knetfile.h
3781
3782 * samtools-0.1.5-3 (r393)
3783 * knetfile now supports HTTP (no proxy at the moment)
3784 * fixed a potential issue in knetfile on opening ordinary file, although I have
3785 not seen the sideeffect so far.
3786
3787 ------------------------------------------------------------------------
3788 r392 | lh3lh3 | 2009-07-12 13:50:55 -0400 (Sun, 12 Jul 2009) | 2 lines
3789 Changed paths:
3790 M /trunk/samtools/samtools.1
3791
3792 Remove the warning in tview
3793
3794 ------------------------------------------------------------------------
3795 r391 | lh3lh3 | 2009-07-12 13:42:43 -0400 (Sun, 12 Jul 2009) | 3 lines
3796 Changed paths:
3797 M /trunk/samtools/bam_tview.c
3798 M /trunk/samtools/bamtk.c
3799
3800 * samtools-0.1.5-2 (r391)
3801 * do not show a blank screen when no reads mapped
3802
3803 ------------------------------------------------------------------------
3804 r390 | lh3lh3 | 2009-07-09 09:01:42 -0400 (Thu, 09 Jul 2009) | 4 lines
3805 Changed paths:
3806 M /trunk/samtools/bam.h
3807 A /trunk/samtools/bam_lite.c
3808 M /trunk/samtools/bamtk.c
3809
3810 * samtools-0.1.5-1 (r390)
3811 * removed useless _IOLIB in bam.h. This should cause no change at all.
3812 * added bam_lite.c for light-weight BAM reading
3813
3814 ------------------------------------------------------------------------
3815 r385 | lh3lh3 | 2009-07-07 11:53:29 -0400 (Tue, 07 Jul 2009) | 2 lines
3816 Changed paths:
3817 M /trunk/samtools/bamtk.c
3818 M /trunk/samtools/knetfile.c
3819
3820 Release samtools-0.1.5c (fixed a bug in piping)
3821
3822 ------------------------------------------------------------------------
3823 r383 | lh3lh3 | 2009-07-07 06:39:55 -0400 (Tue, 07 Jul 2009) | 2 lines
3824 Changed paths:
3825 M /trunk/samtools/bamtk.c
3826 M /trunk/samtools/sam.c
3827
3828 Release samtools-0.1.5b (BUG! so embarrassing!)
3829
3830 ------------------------------------------------------------------------
3831 r381 | lh3lh3 | 2009-07-07 06:20:06 -0400 (Tue, 07 Jul 2009) | 2 lines
3832 Changed paths:
3833 M /trunk/samtools/Makefile
3834 M /trunk/samtools/bam.h
3835 M /trunk/samtools/bam_aux.c
3836 M /trunk/samtools/bamtk.c
3837
3838 Release samtools-0.1.5a (for compatibility with Bio::DB::Sam)
3839
3840 ------------------------------------------------------------------------
3841 r373 | lh3lh3 | 2009-07-07 05:26:57 -0400 (Tue, 07 Jul 2009) | 2 lines
3842 Changed paths:
3843 M /trunk/samtools/ChangeLog
3844 M /trunk/samtools/NEWS
3845 M /trunk/samtools/bamtk.c
3846 M /trunk/samtools/samtools.1
3847
3848 Release samtools-0.1.5
3849
3850 ------------------------------------------------------------------------
3851 r372 | lh3lh3 | 2009-07-07 04:49:27 -0400 (Tue, 07 Jul 2009) | 3 lines
3852 Changed paths:
3853 M /trunk/samtools/bamtk.c
3854 M /trunk/samtools/sam.c
3855
3856 * samtools-0.1.4-23 (r372)
3857 * keep header text if "view -t" is used (by Gerton)
3858
3859 ------------------------------------------------------------------------
3860 r371 | lh3lh3 | 2009-07-06 20:13:32 -0400 (Mon, 06 Jul 2009) | 2 lines
3861 Changed paths:
3862 M /trunk/samtools/samtools.1
3863
3864 update documentation
3865
3866 ------------------------------------------------------------------------
3867 r370 | bhandsaker | 2009-07-02 17:24:34 -0400 (Thu, 02 Jul 2009) | 2 lines
3868 Changed paths:
3869 M /trunk/samtools/Makefile
3870
3871 Introduced LIBPATH variable so this could be overridden to allow samtools to build correct at the Broad.
3872
3873 ------------------------------------------------------------------------
3874 r369 | lh3lh3 | 2009-07-02 08:36:53 -0400 (Thu, 02 Jul 2009) | 4 lines
3875 Changed paths:
3876 M /trunk/samtools/ChangeLog
3877 M /trunk/samtools/bam_aux.c
3878 M /trunk/samtools/bam_plcmd.c
3879 M /trunk/samtools/bamtk.c
3880
3881 * samtools-0.1.4-22 (r369)
3882 * in pileup, optionally print E2 and U2
3883 * remove the debugging code in bam_aux_get() (Drat!)
3884
3885 ------------------------------------------------------------------------
3886 r368 | lh3lh3 | 2009-07-02 06:32:26 -0400 (Thu, 02 Jul 2009) | 6 lines
3887 Changed paths:
3888 M /trunk/samtools/bam.c
3889 M /trunk/samtools/bam.h
3890 M /trunk/samtools/bam_aux.c
3891 M /trunk/samtools/bam_index.c
3892 M /trunk/samtools/bam_lpileup.c
3893 M /trunk/samtools/bam_md.c
3894 M /trunk/samtools/bam_pileup.c
3895 M /trunk/samtools/bam_rmdup.c
3896 M /trunk/samtools/bam_stat.c
3897 M /trunk/samtools/bam_tview.c
3898 M /trunk/samtools/bamtk.c
3899 M /trunk/samtools/faidx.c
3900 M /trunk/samtools/faidx.h
3901 M /trunk/samtools/glf.c
3902
3903 * samtools-0.1.4-21 (r368)
3904 * propagate errors rather than exit or complain assertion failure. Assertion
3905 should be only used for checking internal bugs, but not for external input
3906 inconsistency. I was just a bit lazy.
3907 * small memory leak may be present on failure, though
3908
3909 ------------------------------------------------------------------------
3910 r367 | lh3lh3 | 2009-06-30 11:18:42 -0400 (Tue, 30 Jun 2009) | 2 lines
3911 Changed paths:
3912 M /trunk/samtools/knetfile.c
3913
3914 reduce the chance of blocking in FTP connection
3915
3916 ------------------------------------------------------------------------
3917 r366 | lh3lh3 | 2009-06-30 10:35:21 -0400 (Tue, 30 Jun 2009) | 2 lines
3918 Changed paths:
3919 M /trunk/samtools/knetfile.c
3920
3921 minor changes to knetfile: invalid fd equals -1 rather than 0
3922
3923 ------------------------------------------------------------------------
3924 r365 | lh3lh3 | 2009-06-30 09:04:30 -0400 (Tue, 30 Jun 2009) | 3 lines
3925 Changed paths:
3926 M /trunk/samtools/bam_index.c
3927 M /trunk/samtools/bamtk.c
3928 M /trunk/samtools/knetfile.c
3929 M /trunk/samtools/knetfile.h
3930
3931 * samtools-0.1.4-20 (r365)
3932 * download the BAM index file if it is not found in the current working directory.
3933
3934 ------------------------------------------------------------------------
3935 r364 | lh3lh3 | 2009-06-30 07:39:07 -0400 (Tue, 30 Jun 2009) | 3 lines
3936 Changed paths:
3937 M /trunk/samtools/bamtk.c
3938 M /trunk/samtools/knetfile.c
3939
3940 * samtools-0.1.4-19 (r364)
3941 * knetfile: report error when the file is not present on FTP
3942
3943 ------------------------------------------------------------------------
3944 r363 | lh3lh3 | 2009-06-29 18:23:32 -0400 (Mon, 29 Jun 2009) | 4 lines
3945 Changed paths:
3946 M /trunk/samtools/bam_tview.c
3947 M /trunk/samtools/bamtk.c
3948 M /trunk/samtools/bgzf.c
3949 M /trunk/samtools/bgzf.h
3950 M /trunk/samtools/knetfile.c
3951 M /trunk/samtools/knetfile.h
3952
3953 * samtools-0.1.4-18 (r363)
3954 * knetfile: do not trigger network communication in FTP seek (lazy seek)
3955 * bgzf: cache recent blocks (disabled by default)
3956
3957 ------------------------------------------------------------------------
3958 r362 | lh3lh3 | 2009-06-25 16:04:34 -0400 (Thu, 25 Jun 2009) | 2 lines
3959 Changed paths:
3960 M /trunk/samtools/bgzf.c
3961
3962 write changelog
3963
3964 ------------------------------------------------------------------------
3965 r361 | lh3lh3 | 2009-06-25 16:03:10 -0400 (Thu, 25 Jun 2009) | 3 lines
3966 Changed paths:
3967 M /trunk/samtools/bam_index.c
3968 M /trunk/samtools/bamtk.c
3969
3970 * samtools-0.1.4-17 (r361)
3971 * if a file is given on FTP, search locally for the BAM index
3972
3973 ------------------------------------------------------------------------
3974 r360 | lh3lh3 | 2009-06-25 15:44:52 -0400 (Thu, 25 Jun 2009) | 5 lines
3975 Changed paths:
3976 M /trunk/samtools/Makefile
3977 M /trunk/samtools/bam_import.c
3978 M /trunk/samtools/bam_index.c
3979 M /trunk/samtools/bamtk.c
3980 M /trunk/samtools/bgzf.c
3981 M /trunk/samtools/bgzf.h
3982 M /trunk/samtools/knetfile.c
3983 M /trunk/samtools/knetfile.h
3984
3985 * samtools-0.1.4-16 (r360)
3986 * report more information in index when the input is not sorted
3987 * change the behaviour of knet_seek() such that it returns 0 on success
3988 * support knetfile library in BGZF
3989
3990 ------------------------------------------------------------------------
3991 r359 | lh3lh3 | 2009-06-25 12:10:55 -0400 (Thu, 25 Jun 2009) | 2 lines
3992 Changed paths:
3993 M /trunk/samtools/knetfile.c
3994 M /trunk/samtools/knetfile.h
3995
3996 fixed bugs in knetfile.*
3997
3998 ------------------------------------------------------------------------
3999 r358 | lh3lh3 | 2009-06-25 08:53:19 -0400 (Thu, 25 Jun 2009) | 2 lines
4000 Changed paths:
4001 A /trunk/samtools/knetfile.h
4002
4003 this is the header file
4004
4005 ------------------------------------------------------------------------
4006 r357 | lh3lh3 | 2009-06-25 08:52:03 -0400 (Thu, 25 Jun 2009) | 3 lines
4007 Changed paths:
4008 A /trunk/samtools/knetfile.c
4009
4010 * open a file at FTP
4011 * preliminary version
4012
4013 ------------------------------------------------------------------------
4014 r354 | lh3lh3 | 2009-06-24 09:02:25 -0400 (Wed, 24 Jun 2009) | 3 lines
4015 Changed paths:
4016 M /trunk/samtools/bam.c
4017 M /trunk/samtools/bamtk.c
4018
4019 * samtools-0.1.4-15 (r354)
4020 * fixed a memory leak in bam_view1(), although samtools is not using this routine.
4021
4022 ------------------------------------------------------------------------
4023 r351 | lh3lh3 | 2009-06-17 19:16:26 -0400 (Wed, 17 Jun 2009) | 4 lines
4024 Changed paths:
4025 M /trunk/samtools/bamtk.c
4026 M /trunk/samtools/faidx.c
4027
4028 * samtools-0.1.4-13 (r351)
4029 * make faidx more tolerant to empty lines right before or after > lines
4030 * hope this does not introduce new bugs...
4031
4032 ------------------------------------------------------------------------
4033 r350 | lh3lh3 | 2009-06-16 09:37:01 -0400 (Tue, 16 Jun 2009) | 3 lines
4034 Changed paths:
4035 M /trunk/samtools/bam_plcmd.c
4036 M /trunk/samtools/bamtk.c
4037
4038 * samtools-0.1.4-13 (r350)
4039 * fixed a small memory leak in pileup, caused by recent modifications
4040
4041 ------------------------------------------------------------------------
4042 r347 | lh3lh3 | 2009-06-13 16:20:49 -0400 (Sat, 13 Jun 2009) | 3 lines
4043 Changed paths:
4044 M /trunk/samtools/bam_plcmd.c
4045 M /trunk/samtools/bamtk.c
4046 M /trunk/samtools/sam_view.c
4047
4048 * samtools-0.1.4-12 (r347)
4049 * added `-S' to pileup, similar to `view -S'
4050
4051 ------------------------------------------------------------------------
4052 r346 | lh3lh3 | 2009-06-13 12:52:31 -0400 (Sat, 13 Jun 2009) | 3 lines
4053 Changed paths:
4054 M /trunk/samtools/Makefile
4055 M /trunk/samtools/bamtk.c
4056 M /trunk/samtools/sam_view.c
4057 M /trunk/samtools/samtools.1
4058
4059 * samtools-0.1.4-11 (r346)
4060 * allow to select a read group at view command-line
4061
4062 ------------------------------------------------------------------------
4063 r344 | lh3lh3 | 2009-06-13 09:06:24 -0400 (Sat, 13 Jun 2009) | 2 lines
4064 Changed paths:
4065 M /trunk/samtools/examples/calDepth.c
4066
4067 added more comments
4068
4069 ------------------------------------------------------------------------
4070 r343 | lh3lh3 | 2009-06-13 09:01:22 -0400 (Sat, 13 Jun 2009) | 2 lines
4071 Changed paths:
4072 M /trunk/samtools/examples/calDepth.c
4073
4074 nothing really
4075
4076 ------------------------------------------------------------------------
4077 r342 | lh3lh3 | 2009-06-13 08:58:48 -0400 (Sat, 13 Jun 2009) | 2 lines
4078 Changed paths:
4079 M /trunk/samtools/examples/Makefile
4080 A /trunk/samtools/examples/calDepth.c
4081
4082 added an example of calculating read depth
4083
4084 ------------------------------------------------------------------------
4085 r341 | lh3lh3 | 2009-06-13 08:00:08 -0400 (Sat, 13 Jun 2009) | 6 lines
4086 Changed paths:
4087 M /trunk/samtools/Makefile
4088 M /trunk/samtools/bam.h
4089 M /trunk/samtools/bam_aux.c
4090 A /trunk/samtools/bam_color.c
4091 M /trunk/samtools/bam_plcmd.c
4092 M /trunk/samtools/bam_sort.c
4093 M /trunk/samtools/bam_tview.c
4094 M /trunk/samtools/bamtk.c
4095 M /trunk/samtools/sam.c
4096 M /trunk/samtools/sam.h
4097
4098 * samtools-0.1.4-10 (r341)
4099 * only include key APIs in libbam.a
4100 * move color-specific routines to bam_color.c
4101 * update documentations
4102 * remove the support of -q in pileup
4103
4104 ------------------------------------------------------------------------
4105 r340 | lh3lh3 | 2009-06-13 06:17:14 -0400 (Sat, 13 Jun 2009) | 6 lines
4106 Changed paths:
4107 M /trunk/samtools/INSTALL
4108 M /trunk/samtools/Makefile
4109 M /trunk/samtools/bam_aux.c
4110 M /trunk/samtools/bam_import.c
4111 M /trunk/samtools/bam_tview.c
4112 M /trunk/samtools/bamtk.c
4113 M /trunk/samtools/razf.c
4114 M /trunk/samtools/sam_view.c
4115
4116 * samtools-0.1.4-9 (r340)
4117 * added a warning to razf.c if zlib<1.2.2.1
4118 * fixed a compilation warning
4119 * fixed a segfault caused by @RG parsing
4120 * detect NCURSES in bam_tview.c
4121
4122 ------------------------------------------------------------------------
4123 r339 | lh3lh3 | 2009-06-13 05:35:19 -0400 (Sat, 13 Jun 2009) | 2 lines
4124 Changed paths:
4125 M /trunk/samtools/INSTALL
4126
4127 update INSTALL
4128
4129 ------------------------------------------------------------------------
4130 r338 | lh3lh3 | 2009-06-12 19:15:24 -0400 (Fri, 12 Jun 2009) | 4 lines
4131 Changed paths:
4132 M /trunk/samtools/bam.c
4133 M /trunk/samtools/bam.h
4134 M /trunk/samtools/bam_aux.c
4135 M /trunk/samtools/bam_import.c
4136 M /trunk/samtools/bamtk.c
4137 M /trunk/samtools/kstring.h
4138 M /trunk/samtools/sam.c
4139 M /trunk/samtools/sam_view.c
4140
4141 * samtools-0.1.4-8 (r338)
4142 * parse the @RG header lines and allow to choose library at the "samtools view"
4143 command line
4144
4145 ------------------------------------------------------------------------
4146 r337 | lh3lh3 | 2009-06-12 16:25:50 -0400 (Fri, 12 Jun 2009) | 4 lines
4147 Changed paths:
4148 M /trunk/samtools/bamtk.c
4149 M /trunk/samtools/bgzf.c
4150 M /trunk/samtools/bgzf.h
4151 M /trunk/samtools/sam.c
4152 M /trunk/samtools/sam_view.c
4153
4154 * samtools-0.1.4-7 (r337)
4155 * bgzf.c: support mode string "wu": uncompressed output
4156 * "samtools view" support "-u" command-line option
4157
4158 ------------------------------------------------------------------------
4159 r336 | lh3lh3 | 2009-06-12 12:20:12 -0400 (Fri, 12 Jun 2009) | 5 lines
4160 Changed paths:
4161 M /trunk/samtools/Makefile
4162 M /trunk/samtools/misc/Makefile
4163 M /trunk/samtools/razf.c
4164 M /trunk/samtools/razf.h
4165 M /trunk/samtools/razip.c
4166
4167 * no changes to samtools itself
4168 * remove zlib source codes
4169 * make RAZF reading compatible with old version of zlib
4170 * on old version of zlib, writing is not available
4171
4172 ------------------------------------------------------------------------
4173 r335 | lh3lh3 | 2009-06-12 11:47:33 -0400 (Fri, 12 Jun 2009) | 2 lines
4174 Changed paths:
4175 D /trunk/samtools/zlib
4176
4177 remove zlib for simplification...
4178
4179 ------------------------------------------------------------------------
4180 r334 | lh3lh3 | 2009-06-12 10:43:36 -0400 (Fri, 12 Jun 2009) | 5 lines
4181 Changed paths:
4182 M /trunk/samtools/bam.h
4183 M /trunk/samtools/bam_aux.c
4184 M /trunk/samtools/bamtk.c
4185
4186 * samtools-0.1.4-6 (r334)
4187 * do not export bam_aux_get_core() for Bio::DB::Sam because it has already
4188 been implemented in that.
4189 * this version works with the latest Bio::DB::Sam (20090612)
4190
4191 ------------------------------------------------------------------------
4192 r333 | lh3lh3 | 2009-06-12 10:33:42 -0400 (Fri, 12 Jun 2009) | 2 lines
4193 Changed paths:
4194 M /trunk/samtools/ChangeLog
4195
4196 update ChangeLog
4197
4198 ------------------------------------------------------------------------
4199 r332 | lh3lh3 | 2009-06-12 10:21:21 -0400 (Fri, 12 Jun 2009) | 2 lines
4200 Changed paths:
4201 M /trunk/samtools/AUTHORS
4202 M /trunk/samtools/Makefile
4203 M /trunk/samtools/misc/Makefile
4204
4205 fixed minor things in Makefile
4206
4207 ------------------------------------------------------------------------
4208 r331 | lh3lh3 | 2009-06-12 10:07:05 -0400 (Fri, 12 Jun 2009) | 4 lines
4209 Changed paths:
4210 M /trunk/samtools/bamtk.c
4211
4212 * samtools-0.1.4-5 (r3310
4213 * no change to samtools itself. Version number is increased to reflect the
4214 changes in the Makefile building system.
4215
4216 ------------------------------------------------------------------------
4217 r330 | lh3lh3 | 2009-06-12 10:03:38 -0400 (Fri, 12 Jun 2009) | 2 lines
4218 Changed paths:
4219 M /trunk/samtools/AUTHORS
4220 D /trunk/samtools/README
4221
4222 update information...
4223
4224 ------------------------------------------------------------------------
4225 r329 | lh3lh3 | 2009-06-12 09:52:21 -0400 (Fri, 12 Jun 2009) | 3 lines
4226 Changed paths:
4227 M /trunk/samtools/misc/novo2sam.pl
4228
4229 * updated novoalign converter by Colin Hercus et al.
4230 * this version works with indels
4231
4232 ------------------------------------------------------------------------
4233 r328 | lh3lh3 | 2009-06-12 09:50:53 -0400 (Fri, 12 Jun 2009) | 3 lines
4234 Changed paths:
4235 M /trunk/samtools/INSTALL
4236 M /trunk/samtools/Makefile
4237 M /trunk/samtools/misc/Makefile
4238 M /trunk/samtools/zlib/Makefile
4239
4240 * update Makefile
4241 * update INSTALL instruction
4242
4243 ------------------------------------------------------------------------
4244 r327 | lh3lh3 | 2009-06-12 09:18:29 -0400 (Fri, 12 Jun 2009) | 4 lines
4245 Changed paths:
4246 A /trunk/samtools/Makefile (from /trunk/samtools/Makefile.generic:325)
4247 D /trunk/samtools/Makefile.am
4248 D /trunk/samtools/Makefile.generic
4249 D /trunk/samtools/Makefile.lite
4250 D /trunk/samtools/autogen.sh
4251 D /trunk/samtools/cleanup.sh
4252 D /trunk/samtools/configure.ac
4253 A /trunk/samtools/misc/Makefile (from /trunk/samtools/misc/Makefile.generic:305)
4254 D /trunk/samtools/misc/Makefile.am
4255 D /trunk/samtools/misc/Makefile.generic
4256 M /trunk/samtools/razf.c
4257 A /trunk/samtools/zlib
4258 A /trunk/samtools/zlib/Makefile
4259 A /trunk/samtools/zlib/adler32.c
4260 A /trunk/samtools/zlib/compress.c
4261 A /trunk/samtools/zlib/crc32.c
4262 A /trunk/samtools/zlib/crc32.h
4263 A /trunk/samtools/zlib/deflate.c
4264 A /trunk/samtools/zlib/deflate.h
4265 A /trunk/samtools/zlib/gzio.c
4266 A /trunk/samtools/zlib/infback.c
4267 A /trunk/samtools/zlib/inffast.c
4268 A /trunk/samtools/zlib/inffast.h
4269 A /trunk/samtools/zlib/inffixed.h
4270 A /trunk/samtools/zlib/inflate.c
4271 A /trunk/samtools/zlib/inflate.h
4272 A /trunk/samtools/zlib/inftrees.c
4273 A /trunk/samtools/zlib/inftrees.h
4274 A /trunk/samtools/zlib/trees.c
4275 A /trunk/samtools/zlib/trees.h
4276 A /trunk/samtools/zlib/uncompr.c
4277 A /trunk/samtools/zlib/zconf.h
4278 A /trunk/samtools/zlib/zlib.h
4279 A /trunk/samtools/zlib/zutil.c
4280 A /trunk/samtools/zlib/zutil.h
4281 D /trunk/samtools/zutil.h
4282
4283 * added zlib-1.2.3 as razip requires that
4284 * prepare to changed back to the Makefile building system
4285 * unfinished! (will be soon)
4286
4287 ------------------------------------------------------------------------
4288 r326 | lh3lh3 | 2009-06-12 09:12:03 -0400 (Fri, 12 Jun 2009) | 2 lines
4289 Changed paths:
4290 M /trunk/samtools/misc/samtools.pl
4291
4292 Unfinished
4293
4294 ------------------------------------------------------------------------
4295 r325 | lh3lh3 | 2009-06-10 11:27:59 -0400 (Wed, 10 Jun 2009) | 3 lines
4296 Changed paths:
4297 M /trunk/samtools/bam_maqcns.c
4298 M /trunk/samtools/bamtk.c
4299
4300 * samtools-0.1.4-4 (r325)
4301 * further avoid wrong consensus calls in repetitive regions.
4302
4303 ------------------------------------------------------------------------
4304 r324 | lh3lh3 | 2009-06-10 10:56:17 -0400 (Wed, 10 Jun 2009) | 4 lines
4305 Changed paths:
4306 M /trunk/samtools/bam_maqcns.c
4307 M /trunk/samtools/bam_plcmd.c
4308 M /trunk/samtools/bamtk.c
4309 M /trunk/samtools/sam.c
4310 M /trunk/samtools/sam.h
4311
4312 * samtools-0.1.4-3 (r324)
4313 * make maqcns generate the correct call in repetitive regions.
4314 * allow filtering on mapQ at the pileup command line
4315
4316 ------------------------------------------------------------------------
4317 r323 | lh3lh3 | 2009-06-10 05:04:21 -0400 (Wed, 10 Jun 2009) | 3 lines
4318 Changed paths:
4319 M /trunk/samtools/misc/samtools.pl
4320
4321 * samtools.pl-0.3.2 (r322)
4322 * indels and SNPs use different mapping quality threshold
4323
4324 ------------------------------------------------------------------------
4325 r322 | lh3lh3 | 2009-06-10 05:03:22 -0400 (Wed, 10 Jun 2009) | 2 lines
4326 Changed paths:
4327 M /trunk/samtools/misc/export2sam.pl
4328
4329 fixed a typo
4330
4331 ------------------------------------------------------------------------
4332 r321 | lh3lh3 | 2009-06-09 04:21:48 -0400 (Tue, 09 Jun 2009) | 2 lines
4333 Changed paths:
4334 M /trunk/samtools/misc/samtools.pl
4335
4336 just typo. no real change
4337
4338 ------------------------------------------------------------------------
4339 r320 | lh3lh3 | 2009-06-08 09:32:51 -0400 (Mon, 08 Jun 2009) | 2 lines
4340 Changed paths:
4341 M /trunk/samtools/misc/samtools.pl
4342
4343 a little bit code cleanup
4344
4345 ------------------------------------------------------------------------
4346 r319 | lh3lh3 | 2009-06-08 09:22:33 -0400 (Mon, 08 Jun 2009) | 4 lines
4347 Changed paths:
4348 M /trunk/samtools/misc/samtools.pl
4349
4350 * samtools.pl-0.3.1
4351 * change default parameters
4352 * optionally print filtered variants
4353
4354 ------------------------------------------------------------------------
4355 r318 | lh3lh3 | 2009-06-08 09:14:26 -0400 (Mon, 08 Jun 2009) | 3 lines
4356 Changed paths:
4357 M /trunk/samtools/misc/samtools.pl
4358
4359 * samtools.pl-0.3.0
4360 * combine snpFilter and indelFilter
4361
4362 ------------------------------------------------------------------------
4363 r317 | lh3lh3 | 2009-06-08 06:31:42 -0400 (Mon, 08 Jun 2009) | 3 lines
4364 Changed paths:
4365 M /trunk/samtools/misc/samtools.pl
4366
4367 * samtools.pl-0.2.3
4368 * change a default parameter
4369
4370 ------------------------------------------------------------------------
4371 r316 | lh3lh3 | 2009-06-08 06:11:06 -0400 (Mon, 08 Jun 2009) | 5 lines
4372 Changed paths:
4373 M /trunk/samtools/bam_maqcns.c
4374 M /trunk/samtools/bam_maqcns.h
4375 M /trunk/samtools/bam_plcmd.c
4376 M /trunk/samtools/bamtk.c
4377 M /trunk/samtools/sam.c
4378
4379 * samtools-0.1.4-2 (r316)
4380 * pileup: cap mapping quality at 60 (by default)
4381 * pileup: always calculate RMS mapq
4382 * pileup: allow to output variant sites only
4383
4384 ------------------------------------------------------------------------
4385 r312 | lh3lh3 | 2009-06-04 08:01:10 -0400 (Thu, 04 Jun 2009) | 3 lines
4386 Changed paths:
4387 M /trunk/samtools/misc/samtools.pl
4388
4389 * samtools.pl-0.2.2
4390 * added pileup2fq
4391
4392 ------------------------------------------------------------------------
4393 r311 | lh3lh3 | 2009-06-03 04:40:40 -0400 (Wed, 03 Jun 2009) | 2 lines
4394 Changed paths:
4395 M /trunk/samtools/misc/samtools.pl
4396
4397 * in snpFilter, suppress non-SNP sites
4398
4399 ------------------------------------------------------------------------
4400 r310 | lh3lh3 | 2009-06-01 09:35:13 -0400 (Mon, 01 Jun 2009) | 3 lines
4401 Changed paths:
4402 M /trunk/samtools/misc/samtools.pl
4403
4404 * samtools.pl-0.2.1
4405 * fixed a typo
4406
4407 ------------------------------------------------------------------------
4408 r309 | lh3lh3 | 2009-06-01 09:04:39 -0400 (Mon, 01 Jun 2009) | 3 lines
4409 Changed paths:
4410 M /trunk/samtools/misc/samtools.pl
4411
4412 * samtools.pl-0.2.0
4413 * snpFilter
4414
4415 ------------------------------------------------------------------------
4416 r306 | lh3lh3 | 2009-05-28 06:49:35 -0400 (Thu, 28 May 2009) | 3 lines
4417 Changed paths:
4418 M /trunk/samtools/bgzf.c
4419
4420 * minor changes to bgzf: return NULL if fd == -1
4421 * suggested by {kdj,jm18}@sanger.ac.uk
4422
4423 ------------------------------------------------------------------------
4424 r305 | lh3lh3 | 2009-05-28 06:16:08 -0400 (Thu, 28 May 2009) | 2 lines
4425 Changed paths:
4426 A /trunk/samtools/misc/interpolate_sam.pl
4427
4428 Script for paired-end pileup, contributed by Stephen Montgomery.
4429
4430 ------------------------------------------------------------------------
4431 r304 | lh3lh3 | 2009-05-28 06:08:49 -0400 (Thu, 28 May 2009) | 3 lines
4432 Changed paths:
4433 M /trunk/samtools/bamtk.c
4434 M /trunk/samtools/sam.c
4435
4436 * samtools-0.1.4-1 (r304)
4437 * fixed a minor bug in printing headers
4438
4439 ------------------------------------------------------------------------
4440 r297 | lh3lh3 | 2009-05-21 11:06:16 -0400 (Thu, 21 May 2009) | 2 lines
4441 Changed paths:
4442 M /trunk/samtools/ChangeLog
4443 M /trunk/samtools/NEWS
4444 M /trunk/samtools/bam_plcmd.c
4445 M /trunk/samtools/bamtk.c
4446 M /trunk/samtools/misc/maq2sam.c
4447 M /trunk/samtools/samtools.1
4448
4449 Release samtools-0.1.4
4450
4451 ------------------------------------------------------------------------
4452 r296 | lh3lh3 | 2009-05-21 07:53:14 -0400 (Thu, 21 May 2009) | 3 lines
4453 Changed paths:
4454 M /trunk/samtools/bam_maqcns.c
4455 M /trunk/samtools/bamtk.c
4456
4457 * samtools-0.1.3-24 (r296)
4458 * another similar bug in the indel caller
4459
4460 ------------------------------------------------------------------------
4461 r295 | lh3lh3 | 2009-05-21 07:50:28 -0400 (Thu, 21 May 2009) | 3 lines
4462 Changed paths:
4463 M /trunk/samtools/bam_maqcns.c
4464 M /trunk/samtools/bamtk.c
4465
4466 * samtools-0.1.3-23 (r295)
4467 * fixed a critical bug in the indel caller
4468
4469 ------------------------------------------------------------------------
4470 r294 | lh3lh3 | 2009-05-20 08:00:20 -0400 (Wed, 20 May 2009) | 2 lines
4471 Changed paths:
4472 M /trunk/samtools/bam_stat.c
4473
4474 added a missing header file
4475
4476 ------------------------------------------------------------------------
4477 r293 | lh3lh3 | 2009-05-19 18:44:25 -0400 (Tue, 19 May 2009) | 3 lines
4478 Changed paths:
4479 M /trunk/samtools/bam_tview.c
4480 M /trunk/samtools/bamtk.c
4481
4482 * samtools-0.1.3-22 (r293)
4483 * open tview in the dot-view mode by default
4484
4485 ------------------------------------------------------------------------
4486 r292 | lh3lh3 | 2009-05-18 16:01:23 -0400 (Mon, 18 May 2009) | 6 lines
4487 Changed paths:
4488 M /trunk/samtools/samtools.1
4489
4490 Added a note to the manual. Currently SAMtools used unaligned words in
4491 several places. Although this does not cause bus errors to me, it may
4492 affect portability. Please see the "Bus error" wiki page for more
4493 information. Also thank James Bonfields for pointing this out.
4494
4495
4496 ------------------------------------------------------------------------
4497 r286 | lh3lh3 | 2009-05-14 10:23:13 -0400 (Thu, 14 May 2009) | 3 lines
4498 Changed paths:
4499 M /trunk/samtools/bam.h
4500 M /trunk/samtools/bam_aux.c
4501 M /trunk/samtools/bamtk.c
4502
4503 * samtools-0.1.3-21 (286)
4504 * declare bam_aux_get_core() in bam.h
4505
4506 ------------------------------------------------------------------------
4507 r276 | lh3lh3 | 2009-05-13 05:07:55 -0400 (Wed, 13 May 2009) | 5 lines
4508 Changed paths:
4509 M /trunk/samtools/bam.h
4510 M /trunk/samtools/bam_index.c
4511 M /trunk/samtools/bamtk.c
4512
4513 * samtools-0.1.3-20 (r276)
4514 * remove bam1_t::hash again. We need to modify the Perl API anyway to
4515 make it work with the latest SVN.
4516 * As is suggested by Tim, scan "{base}.bai" and "{base}.bam.bai" for index
4517
4518 ------------------------------------------------------------------------
4519 r275 | lh3lh3 | 2009-05-12 16:14:10 -0400 (Tue, 12 May 2009) | 4 lines
4520 Changed paths:
4521 M /trunk/samtools/ChangeLog
4522 M /trunk/samtools/bam.h
4523 M /trunk/samtools/bamtk.c
4524
4525 * samtools-0.1.3-19 (r275)
4526 * a minor change to the bam1_t struct: added back "void *hash" for the
4527 backward compatibility with Bio::DB::Sam
4528
4529 ------------------------------------------------------------------------
4530 r273 | lh3lh3 | 2009-05-12 09:28:39 -0400 (Tue, 12 May 2009) | 3 lines
4531 Changed paths:
4532 M /trunk/samtools/bam_rmdupse.c
4533 M /trunk/samtools/bamtk.c
4534
4535 * samtools-0.1.3-18 (r273)
4536 * rmdupse: do not remove unmapped reads
4537
4538 ------------------------------------------------------------------------
4539 r272 | lh3lh3 | 2009-05-12 09:20:00 -0400 (Tue, 12 May 2009) | 2 lines
4540 Changed paths:
4541 M /trunk/samtools/bam_rmdupse.c
4542
4543 change a parameter. It does nothing
4544
4545 ------------------------------------------------------------------------
4546 r271 | lh3lh3 | 2009-05-12 09:17:58 -0400 (Tue, 12 May 2009) | 3 lines
4547 Changed paths:
4548 M /trunk/samtools/Makefile.am
4549 M /trunk/samtools/Makefile.generic
4550 M /trunk/samtools/Makefile.lite
4551 A /trunk/samtools/bam_rmdupse.c
4552 M /trunk/samtools/bamtk.c
4553 M /trunk/samtools/configure.ac
4554
4555 * samtools-0.1.3-17 (r271)
4556 * added 'rmdupse' command
4557
4558 ------------------------------------------------------------------------
4559 r267 | lh3lh3 | 2009-05-05 17:31:41 -0400 (Tue, 05 May 2009) | 3 lines
4560 Changed paths:
4561 M /trunk/samtools/bamtk.c
4562 M /trunk/samtools/sam_view.c
4563
4564 * samtools-0.1.3-16 (r267)
4565 * in sam_view.c, changed g_flag_on based on the suggestion by Angie Hinrichs
4566
4567 ------------------------------------------------------------------------
4568 r266 | lh3lh3 | 2009-05-05 17:23:27 -0400 (Tue, 05 May 2009) | 3 lines
4569 Changed paths:
4570 M /trunk/samtools/bam_import.c
4571 M /trunk/samtools/bamtk.c
4572
4573 * samtools-0.1.3-15 (r266)
4574 * report an error if a non-* reference is present while @SQ is absent
4575
4576 ------------------------------------------------------------------------
4577 r265 | lh3lh3 | 2009-05-05 17:09:00 -0400 (Tue, 05 May 2009) | 3 lines
4578 Changed paths:
4579 M /trunk/samtools/bam.h
4580 M /trunk/samtools/bam_import.c
4581 M /trunk/samtools/bamtk.c
4582 M /trunk/samtools/sam.c
4583 M /trunk/samtools/sam_view.c
4584
4585 * samtools-0.1.3-14 (r262)
4586 * make samopen() recognize @SQ header lines
4587
4588 ------------------------------------------------------------------------
4589 r261 | lh3lh3 | 2009-05-05 10:10:30 -0400 (Tue, 05 May 2009) | 3 lines
4590 Changed paths:
4591 M /trunk/samtools/bam_plcmd.c
4592 M /trunk/samtools/bamtk.c
4593 M /trunk/samtools/bgzf.c
4594 M /trunk/samtools/sam.c
4595 M /trunk/samtools/sam_view.c
4596
4597 * samtools-0.1.3-13 (r260)
4598 * report error for file I/O error
4599
4600 ------------------------------------------------------------------------
4601 r260 | lh3lh3 | 2009-05-05 10:01:16 -0400 (Tue, 05 May 2009) | 2 lines
4602 Changed paths:
4603 M /trunk/samtools/Makefile.am
4604
4605 update Makefile.am
4606
4607 ------------------------------------------------------------------------
4608 r259 | lh3lh3 | 2009-05-05 09:52:25 -0400 (Tue, 05 May 2009) | 3 lines
4609 Changed paths:
4610 M /trunk/samtools/bam.h
4611 M /trunk/samtools/bam_pileup.c
4612 M /trunk/samtools/bam_plcmd.c
4613 M /trunk/samtools/bamtk.c
4614 M /trunk/samtools/sam.c
4615 M /trunk/samtools/sam.h
4616
4617 * samtools-0.1.3-12 (r259)
4618 * use the new I/O interface in pileup
4619
4620 ------------------------------------------------------------------------
4621 r258 | lh3lh3 | 2009-05-05 09:33:22 -0400 (Tue, 05 May 2009) | 3 lines
4622 Changed paths:
4623 M /trunk/samtools/Makefile.generic
4624 M /trunk/samtools/Makefile.lite
4625 M /trunk/samtools/bam.c
4626 M /trunk/samtools/bam.h
4627 M /trunk/samtools/bam_import.c
4628 M /trunk/samtools/bamtk.c
4629 A /trunk/samtools/sam.c
4630 A /trunk/samtools/sam.h
4631 A /trunk/samtools/sam_view.c
4632
4633 * samtools-0.1.3-11 (r258)
4634 * unify the interface to BAM and SAM I/O
4635
4636 ------------------------------------------------------------------------
4637 r257 | lh3lh3 | 2009-05-05 04:53:35 -0400 (Tue, 05 May 2009) | 3 lines
4638 Changed paths:
4639 M /trunk/samtools/Makefile.lite
4640 M /trunk/samtools/bam_plcmd.c
4641 M /trunk/samtools/bamtk.c
4642
4643 * samtools-0.1.3-10 (r257)
4644 * allow hex with "pileup -m"
4645
4646 ------------------------------------------------------------------------
4647 r256 | lh3lh3 | 2009-05-04 14:16:50 -0400 (Mon, 04 May 2009) | 4 lines
4648 Changed paths:
4649 M /trunk/samtools/bam_lpileup.c
4650 M /trunk/samtools/bamtk.c
4651
4652 * samtools-0.1.3-9 (r256)
4653 * fixed a bug in bam_lpileup.c
4654 * I do not know if this also fixes the bug causing assertion failure in the tview
4655
4656 ------------------------------------------------------------------------
4657 r251 | lh3lh3 | 2009-04-28 08:53:23 -0400 (Tue, 28 Apr 2009) | 3 lines
4658 Changed paths:
4659 M /trunk/samtools/bam_pileup.c
4660 M /trunk/samtools/bamtk.c
4661
4662 * samtools-0.1.3-8 (r251)
4663 * fixed a bug when there are reads without coordinates
4664
4665 ------------------------------------------------------------------------
4666 r250 | lh3lh3 | 2009-04-28 08:43:33 -0400 (Tue, 28 Apr 2009) | 2 lines
4667 Changed paths:
4668 A /trunk/samtools/AUTHORS
4669 A /trunk/samtools/README
4670 M /trunk/samtools/cleanup.sh
4671
4672 added missing files
4673
4674 ------------------------------------------------------------------------
4675 r249 | lh3lh3 | 2009-04-28 08:37:16 -0400 (Tue, 28 Apr 2009) | 2 lines
4676 Changed paths:
4677 M /trunk/samtools/Makefile.generic
4678 M /trunk/samtools/Makefile.lite
4679 M /trunk/samtools/configure.ac
4680 M /trunk/samtools/misc/Makefile.generic
4681
4682 improve large file support in compilation
4683
4684 ------------------------------------------------------------------------
4685 r248 | lh3lh3 | 2009-04-28 08:33:24 -0400 (Tue, 28 Apr 2009) | 2 lines
4686 Changed paths:
4687 M /trunk/samtools/INSTALL
4688
4689 update INSTALL
4690
4691 ------------------------------------------------------------------------
4692 r247 | lh3lh3 | 2009-04-28 08:28:50 -0400 (Tue, 28 Apr 2009) | 2 lines
4693 Changed paths:
4694 M /trunk/samtools/Makefile.am
4695 M /trunk/samtools/autogen.sh
4696 M /trunk/samtools/cleanup.sh
4697 M /trunk/samtools/configure.ac
4698 A /trunk/samtools/misc/Makefile.am
4699
4700 fixed various issues about the GNU building scripts
4701
4702 ------------------------------------------------------------------------
4703 r246 | lh3lh3 | 2009-04-28 08:10:23 -0400 (Tue, 28 Apr 2009) | 4 lines
4704 Changed paths:
4705 M /trunk/samtools/ChangeLog
4706 D /trunk/samtools/Makefile
4707 A /trunk/samtools/Makefile.am
4708 A /trunk/samtools/Makefile.generic
4709 A /trunk/samtools/autogen.sh
4710 M /trunk/samtools/bam.h
4711 M /trunk/samtools/bam_aux.c
4712 M /trunk/samtools/bam_tview.c
4713 M /trunk/samtools/bamtk.c
4714 A /trunk/samtools/cleanup.sh
4715 A /trunk/samtools/configure.ac
4716 D /trunk/samtools/misc/Makefile
4717 A /trunk/samtools/misc/Makefile.generic (from /trunk/samtools/misc/Makefile:245)
4718
4719 * samtools-0.1.3-7 (r246)
4720 * incorporated revisions from Nils Homer
4721 * enhanced support of displaying color-space reads
4722
4723 ------------------------------------------------------------------------
4724 r244 | lh3lh3 | 2009-04-25 06:49:40 -0400 (Sat, 25 Apr 2009) | 3 lines
4725 Changed paths:
4726 M /trunk/samtools/bam_md.c
4727 M /trunk/samtools/bamtk.c
4728
4729 * samtools-0.1.3-6 (r244)
4730 * fixed segfault for unmapped reads
4731
4732 ------------------------------------------------------------------------
4733 r243 | lh3lh3 | 2009-04-24 16:27:26 -0400 (Fri, 24 Apr 2009) | 5 lines
4734 Changed paths:
4735 M /trunk/samtools/bam.h
4736 M /trunk/samtools/bam_maqcns.c
4737 M /trunk/samtools/bam_md.c
4738 M /trunk/samtools/bamtk.c
4739
4740 * samtools-0.1.3-5 (r243)
4741 * fixed a long existing bug which may cause memory leak
4742 * check MD
4743 * consensus calling now works with "=", but indel calling not
4744
4745 ------------------------------------------------------------------------
4746 r242 | lh3lh3 | 2009-04-24 15:44:46 -0400 (Fri, 24 Apr 2009) | 3 lines
4747 Changed paths:
4748 M /trunk/samtools/bam_md.c
4749 M /trunk/samtools/bamtk.c
4750
4751 * samtools-0.1.3-4 (r242)
4752 * fixed a memory leak
4753
4754 ------------------------------------------------------------------------
4755 r240 | lh3lh3 | 2009-04-24 11:40:18 -0400 (Fri, 24 Apr 2009) | 5 lines
4756 Changed paths:
4757 M /trunk/samtools/Makefile
4758 M /trunk/samtools/Makefile.lite
4759 M /trunk/samtools/bam.h
4760 M /trunk/samtools/bam_aux.c
4761 A /trunk/samtools/bam_md.c
4762 M /trunk/samtools/bam_plcmd.c
4763 M /trunk/samtools/bamtk.c
4764
4765 * samtools-0.1.3-3 (r240)
4766 * generate MD tag
4767 * generate "=" bases
4768 * the plain pileup now support "=" bases, but consensus calling and glfgen may fail
4769
4770 ------------------------------------------------------------------------
4771 r239 | lh3lh3 | 2009-04-24 07:08:20 -0400 (Fri, 24 Apr 2009) | 5 lines
4772 Changed paths:
4773 M /trunk/samtools/bam.h
4774 M /trunk/samtools/bam_aux.c
4775 M /trunk/samtools/bamtk.c
4776
4777 * samtools-0.1.3-2 (r239)
4778 * fixed bugs in bam_aux.c (these functions nevered used by samtools)
4779 * removed bam_aux_init()/bam_aux_destroy()
4780 * added tagview for testing bam_aux
4781
4782 ------------------------------------------------------------------------
4783 r235 | lh3lh3 | 2009-04-21 18:17:39 -0400 (Tue, 21 Apr 2009) | 3 lines
4784 Changed paths:
4785 M /trunk/samtools/bam_pileup.c
4786 M /trunk/samtools/bamtk.c
4787
4788 * samtools-0.1.3-1
4789 * fixed a bug in pileup: the first read in a chromosome may not be printed
4790
4791 ------------------------------------------------------------------------
4792 r232 | lh3lh3 | 2009-04-16 10:25:43 -0400 (Thu, 16 Apr 2009) | 2 lines
4793 Changed paths:
4794 M /trunk/samtools/Makefile.lite
4795
4796 a missing file in Makefile.lite
4797
4798 ------------------------------------------------------------------------
4799 r227 | lh3lh3 | 2009-04-15 17:02:53 -0400 (Wed, 15 Apr 2009) | 2 lines
4800 Changed paths:
4801 M /trunk/samtools/NEWS
4802 M /trunk/samtools/bamtk.c
4803
4804 Release samtools-0.1.3
4805
4806 ------------------------------------------------------------------------
4807 r223 | lh3lh3 | 2009-04-15 09:31:32 -0400 (Wed, 15 Apr 2009) | 3 lines
4808 Changed paths:
4809 M /trunk/samtools/bam_plcmd.c
4810 M /trunk/samtools/bamtk.c
4811
4812 * samtools-0.1.2-28
4813 * make samtools more robust to weird input such as empty file
4814
4815 ------------------------------------------------------------------------
4816 r222 | lh3lh3 | 2009-04-15 09:05:33 -0400 (Wed, 15 Apr 2009) | 2 lines
4817 Changed paths:
4818 M /trunk/samtools/ChangeLog
4819 M /trunk/samtools/NEWS
4820 M /trunk/samtools/samtools.1
4821
4822 prepare for release 0.1.3
4823
4824 ------------------------------------------------------------------------
4825 r221 | lh3lh3 | 2009-04-15 08:32:14 -0400 (Wed, 15 Apr 2009) | 2 lines
4826 Changed paths:
4827 A /trunk/samtools/misc/blast2sam.pl
4828
4829 convert NCBI-BLASTN to SAM
4830
4831 ------------------------------------------------------------------------
4832 r220 | lh3lh3 | 2009-04-15 08:18:19 -0400 (Wed, 15 Apr 2009) | 3 lines
4833 Changed paths:
4834 M /trunk/samtools/bam_lpileup.c
4835 M /trunk/samtools/bamtk.c
4836
4837 * samtools-0.1.2-27
4838 * fixed a small memory leak in tview
4839
4840 ------------------------------------------------------------------------
4841 r219 | lh3lh3 | 2009-04-15 08:00:08 -0400 (Wed, 15 Apr 2009) | 3 lines
4842 Changed paths:
4843 M /trunk/samtools/bam_rmdup.c
4844 M /trunk/samtools/bamtk.c
4845
4846 * samtools-0.1.2-26
4847 * fixed a bug in rmdup when there are unmapped reads
4848
4849 ------------------------------------------------------------------------
4850 r218 | lh3lh3 | 2009-04-14 17:28:58 -0400 (Tue, 14 Apr 2009) | 2 lines
4851 Changed paths:
4852 M /trunk/samtools/ChangeLog
4853 M /trunk/samtools/NEWS
4854
4855 proposed NEWS for the new release (have not yet)
4856
4857 ------------------------------------------------------------------------
4858 r216 | lh3lh3 | 2009-04-14 17:10:46 -0400 (Tue, 14 Apr 2009) | 4 lines
4859 Changed paths:
4860 M /trunk/samtools/misc/samtools.pl
4861
4862 * samtools.pl-0.1.1
4863 * improve indelFilter to avoid filtering true indels. The new filter relies
4864 on the new pileup indel line implemented in samtools-0.1.2-25
4865
4866 ------------------------------------------------------------------------
4867 r215 | lh3lh3 | 2009-04-14 17:04:19 -0400 (Tue, 14 Apr 2009) | 4 lines
4868 Changed paths:
4869 M /trunk/samtools/bam_maqcns.c
4870 M /trunk/samtools/bam_plcmd.c
4871 M /trunk/samtools/bamtk.c
4872 M /trunk/samtools/samtools.1
4873
4874 * samtools-0.1.2-25
4875 * change the pileup indel line to shows the number of alignments actually
4876 containing indels
4877
4878 ------------------------------------------------------------------------
4879 r211 | lh3lh3 | 2009-04-13 07:07:13 -0400 (Mon, 13 Apr 2009) | 2 lines
4880 Changed paths:
4881 M /trunk/samtools/ChangeLog
4882
4883 update ChangeLog from "svn log"
4884
4885 ------------------------------------------------------------------------
4886 r210 | lh3lh3 | 2009-04-12 15:57:05 -0400 (Sun, 12 Apr 2009) | 4 lines
4887 Changed paths:
4888 M /trunk/samtools/bam.c
4889 M /trunk/samtools/bam_import.c
4890 M /trunk/samtools/bam_sort.c
4891 M /trunk/samtools/bamtk.c
4892 M /trunk/samtools/kseq.h
4893
4894 * samtools-0.1.2-24
4895 * in merge, gives a warning rather than error if the target sequence length is different
4896 * allow empty header
4897
4898 ------------------------------------------------------------------------
4899 r209 | lh3lh3 | 2009-04-12 15:32:44 -0400 (Sun, 12 Apr 2009) | 3 lines
4900 Changed paths:
4901 M /trunk/samtools/bam.c
4902 M /trunk/samtools/bam_import.c
4903 M /trunk/samtools/bamtk.c
4904
4905 * samtools-0.1.2-23
4906 * recognize '*' at the QUAL field
4907
4908 ------------------------------------------------------------------------
4909 r208 | lh3lh3 | 2009-04-12 15:08:02 -0400 (Sun, 12 Apr 2009) | 3 lines
4910 Changed paths:
4911 M /trunk/samtools/bam_import.c
4912 M /trunk/samtools/bamtk.c
4913 M /trunk/samtools/kseq.h
4914
4915 * samtools-0.1.2-22
4916 * the field separater is TAB only, now
4917
4918 ------------------------------------------------------------------------
4919 r207 | lh3lh3 | 2009-04-08 10:18:03 -0400 (Wed, 08 Apr 2009) | 2 lines
4920 Changed paths:
4921 M /trunk/samtools/examples/ex1.sam.gz
4922
4923 * fixed the problem in the example alignment due to the bug in fixmate
4924
4925 ------------------------------------------------------------------------
4926 r206 | lh3lh3 | 2009-04-08 10:15:05 -0400 (Wed, 08 Apr 2009) | 3 lines
4927 Changed paths:
4928 M /trunk/samtools/bam_mate.c
4929 M /trunk/samtools/bamtk.c
4930 M /trunk/samtools/misc/soap2sam.pl
4931
4932 * samtools-0.1.2-21
4933 * fixed a nasty bug in `fixmate'
4934
4935 ------------------------------------------------------------------------
4936 r205 | lh3lh3 | 2009-04-08 05:57:08 -0400 (Wed, 08 Apr 2009) | 2 lines
4937 Changed paths:
4938 M /trunk/samtools/misc/bowtie2sam.pl
4939 M /trunk/samtools/misc/soap2sam.pl
4940 M /trunk/samtools/misc/wgsim_eval.pl
4941
4942 make the script robust to the bugs in SOAP-2.1.7
4943
4944 ------------------------------------------------------------------------
4945 r200 | lh3lh3 | 2009-04-02 10:14:56 -0400 (Thu, 02 Apr 2009) | 3 lines
4946 Changed paths:
4947 M /trunk/samtools/bam_stat.c
4948 M /trunk/samtools/bamtk.c
4949
4950 * samtools-0.1.2-20
4951 * check if file is truncated in flagstat
4952
4953 ------------------------------------------------------------------------
4954 r199 | lh3lh3 | 2009-04-02 10:09:10 -0400 (Thu, 02 Apr 2009) | 3 lines
4955 Changed paths:
4956 M /trunk/samtools/bamtk.c
4957
4958 * samtools-0.1.2-19
4959 * print the header if requested
4960
4961 ------------------------------------------------------------------------
4962 r193 | lh3lh3 | 2009-03-27 11:09:50 -0400 (Fri, 27 Mar 2009) | 3 lines
4963 Changed paths:
4964 M /trunk/samtools/bam_plcmd.c
4965 M /trunk/samtools/bamtk.c
4966
4967 * samtools-0.1.2-18
4968 * fixed a minor bug reported by Nils Homer
4969
4970 ------------------------------------------------------------------------
4971 r185 | lh3lh3 | 2009-03-24 07:50:32 -0400 (Tue, 24 Mar 2009) | 2 lines
4972 Changed paths:
4973 A /trunk/samtools/Makefile (from /trunk/samtools/Makefile.std:184)
4974 D /trunk/samtools/Makefile.std
4975 A /trunk/samtools/misc/Makefile (from /trunk/samtools/misc/Makefile.std:184)
4976 D /trunk/samtools/misc/Makefile.std
4977
4978 rename Makefile.std as Makefile. GNU building systerm is not ready and may take some time...
4979
4980 ------------------------------------------------------------------------
4981 r184 | lh3lh3 | 2009-03-24 06:36:38 -0400 (Tue, 24 Mar 2009) | 4 lines
4982 Changed paths:
4983 D /trunk/samtools/Makefile
4984 A /trunk/samtools/Makefile.std (from /trunk/samtools/Makefile:183)
4985 M /trunk/samtools/bam_sort.c
4986 M /trunk/samtools/bam_tview.c
4987 M /trunk/samtools/bamtk.c
4988 D /trunk/samtools/misc/Makefile
4989 A /trunk/samtools/misc/Makefile.std (from /trunk/samtools/misc/Makefile:182)
4990 M /trunk/samtools/samtools.1
4991
4992 * samtools-0.1.2-17
4993 * incorporating Nils' changes
4994 * rename Makefile to Makefile.std and prepare to add the GNU building systerms (also by Nils)
4995
4996 ------------------------------------------------------------------------
4997 r183 | lh3lh3 | 2009-03-24 06:30:23 -0400 (Tue, 24 Mar 2009) | 4 lines
4998 Changed paths:
4999 M /trunk/samtools/Makefile
5000 M /trunk/samtools/bam_import.c
5001 M /trunk/samtools/bam_maqcns.c
5002 M /trunk/samtools/bam_maqcns.h
5003 M /trunk/samtools/bam_plcmd.c
5004 M /trunk/samtools/bamtk.c
5005 M /trunk/samtools/kseq.h
5006 A /trunk/samtools/kstring.c
5007 A /trunk/samtools/kstring.h
5008
5009 * samtools-0.1.2-16
5010 * made pileup take a list of proposed indels. An insertion is N at the moment.
5011 * added my kstring library for a bit complex parsing of the position list.
5012
5013 ------------------------------------------------------------------------
5014 r169 | lh3lh3 | 2009-03-12 09:40:14 -0400 (Thu, 12 Mar 2009) | 3 lines
5015 Changed paths:
5016 M /trunk/samtools/misc/soap2sam.pl
5017
5018 * soap2sam.pl-0.1.2
5019 * more robust to truncated soap output
5020
5021 ------------------------------------------------------------------------
5022 r168 | lh3lh3 | 2009-03-11 06:49:00 -0400 (Wed, 11 Mar 2009) | 2 lines
5023 Changed paths:
5024 M /trunk/samtools/Makefile.lite
5025
5026 added bam_stat.o to Makefile.lite
5027
5028 ------------------------------------------------------------------------
5029 r167 | lh3lh3 | 2009-03-10 18:11:31 -0400 (Tue, 10 Mar 2009) | 3 lines
5030 Changed paths:
5031 M /trunk/samtools/bam_maqcns.c
5032 M /trunk/samtools/bamtk.c
5033
5034 * samtools-0.1.2-15
5035 * generate RMS of mapQ instead of max mapQ
5036
5037 ------------------------------------------------------------------------
5038 r166 | lh3lh3 | 2009-03-10 18:06:45 -0400 (Tue, 10 Mar 2009) | 3 lines
5039 Changed paths:
5040 M /trunk/samtools/bam_plcmd.c
5041 M /trunk/samtools/bamtk.c
5042 M /trunk/samtools/glf.c
5043 M /trunk/samtools/glf.h
5044 M /trunk/samtools/misc/Makefile
5045
5046 * samtools-0.1.2-14
5047 * implemented GLFv3
5048
5049 ------------------------------------------------------------------------
5050 r159 | lh3lh3 | 2009-03-03 06:26:08 -0500 (Tue, 03 Mar 2009) | 3 lines
5051 Changed paths:
5052 M /trunk/samtools/bam_plcmd.c
5053 M /trunk/samtools/bamtk.c
5054
5055 * samtools-0.1.2-13
5056 * fixed a minor bug in displaying pileup
5057
5058 ------------------------------------------------------------------------
5059 r158 | lh3lh3 | 2009-03-03 06:24:16 -0500 (Tue, 03 Mar 2009) | 3 lines
5060 Changed paths:
5061 M /trunk/samtools/ChangeLog
5062 M /trunk/samtools/bamtk.c
5063
5064 * samtools-0.1.2-12
5065 * optionally print SAM header
5066
5067 ------------------------------------------------------------------------
5068 r153 | lh3lh3 | 2009-03-02 05:45:28 -0500 (Mon, 02 Mar 2009) | 3 lines
5069 Changed paths:
5070 M /trunk/samtools/bamtk.c
5071 M /trunk/samtools/glf.c
5072
5073 * samtools-0.1.2-11
5074 * use "GLF\3" as the magic for GLFv3 files
5075
5076 ------------------------------------------------------------------------
5077 r152 | lh3lh3 | 2009-03-02 05:39:09 -0500 (Mon, 02 Mar 2009) | 5 lines
5078 Changed paths:
5079 M /trunk/samtools/Makefile
5080 M /trunk/samtools/bam_import.c
5081 M /trunk/samtools/bam_index.c
5082 M /trunk/samtools/bam_plcmd.c
5083 M /trunk/samtools/bamtk.c
5084 M /trunk/samtools/glf.c
5085 M /trunk/samtools/glf.h
5086
5087 * samtools-0.1.2-10
5088 * fixed a bug in import: core.bin is undefined for unmapped reads
5089 * this bug can be alleviated (not completely solved) in bam_index.c
5090 * update to GLFv3: pos is changed to offset for better compression
5091
5092 ------------------------------------------------------------------------
5093 r151 | lh3lh3 | 2009-03-01 10:18:43 -0500 (Sun, 01 Mar 2009) | 3 lines
5094 Changed paths:
5095 M /trunk/samtools/misc/wgsim.c
5096
5097 * wgsim-0.2.3
5098 * fixed a bug in simulating indels
5099
5100 ------------------------------------------------------------------------
5101 r145 | lh3lh3 | 2009-02-26 14:43:57 -0500 (Thu, 26 Feb 2009) | 4 lines
5102 Changed paths:
5103 M /trunk/samtools/misc/wgsim.c
5104
5105 * wgsim-0.2.2
5106 * allow to print mismatch information as fastq comment. MAQ does
5107 not like long read names.
5108
5109 ------------------------------------------------------------------------
5110 r141 | lh3lh3 | 2009-02-26 09:53:03 -0500 (Thu, 26 Feb 2009) | 6 lines
5111 Changed paths:
5112 M /trunk/samtools/ChangeLog
5113 M /trunk/samtools/misc/wgsim.c
5114 M /trunk/samtools/misc/wgsim_eval.pl
5115
5116 * wgsim-0.2.1
5117 * fixed a bug about color read coordinates
5118 * fixed a bug in read names
5119 * wgsim_eval.pl-0.1.3
5120 * make the script work with color reads
5121
5122 ------------------------------------------------------------------------
5123 r140 | lh3lh3 | 2009-02-26 09:02:57 -0500 (Thu, 26 Feb 2009) | 2 lines
5124 Changed paths:
5125 M /trunk/samtools/misc/Makefile
5126 M /trunk/samtools/misc/wgsim.c
5127
5128 * wgsim: added a note
5129
5130 ------------------------------------------------------------------------
5131 r139 | lh3lh3 | 2009-02-26 06:39:08 -0500 (Thu, 26 Feb 2009) | 7 lines
5132 Changed paths:
5133 M /trunk/samtools/misc/wgsim.c
5134 M /trunk/samtools/misc/wgsim_eval.pl
5135
5136 * wgsim-0.2.0
5137 * considerable code clean up
5138 * print number of substitutions/indels/errors on each read
5139 * potentially support SOLiD simulation, though not tested at the moment
5140 * wgsim_eval.pl-0.1.2
5141 * change in accordant with wgsim
5142
5143 ------------------------------------------------------------------------
5144 r129 | lh3lh3 | 2009-02-18 17:23:27 -0500 (Wed, 18 Feb 2009) | 3 lines
5145 Changed paths:
5146 M /trunk/samtools/bam_index.c
5147 M /trunk/samtools/bamtk.c
5148
5149 * samtools-0.1.2-9
5150 * fixed a bug in bam_fetch, caused by completely contained adjacent chunks
5151
5152 ------------------------------------------------------------------------
5153 r128 | bhandsaker | 2009-02-18 14:06:57 -0500 (Wed, 18 Feb 2009) | 2 lines
5154 Changed paths:
5155 M /trunk/samtools/bamtk.c
5156
5157 Fix annoying segv when invalid region specified.
5158
5159 ------------------------------------------------------------------------
5160 r127 | lh3lh3 | 2009-02-17 05:49:55 -0500 (Tue, 17 Feb 2009) | 2 lines
5161 Changed paths:
5162 D /trunk/samtools/misc/indel_filter.pl
5163 A /trunk/samtools/misc/samtools.pl
5164
5165 * move indel_filter.pl to samtools.pl
5166
5167 ------------------------------------------------------------------------
5168 r126 | lh3lh3 | 2009-02-14 16:22:30 -0500 (Sat, 14 Feb 2009) | 3 lines
5169 Changed paths:
5170 M /trunk/samtools/bam_mate.c
5171 M /trunk/samtools/bamtk.c
5172
5173 * samtools-0.1.2-7
5174 * fixed a bug in fixmate: SE reads are flagged as BAM_FMUNMAP
5175
5176 ------------------------------------------------------------------------
5177 r125 | lh3lh3 | 2009-02-13 04:54:45 -0500 (Fri, 13 Feb 2009) | 3 lines
5178 Changed paths:
5179 M /trunk/samtools/bam_stat.c
5180 M /trunk/samtools/bamtk.c
5181
5182 * samtools-0.1.2-7
5183 * fixed a minor bug in flagstat
5184
5185 ------------------------------------------------------------------------
5186 r124 | lh3lh3 | 2009-02-12 06:15:32 -0500 (Thu, 12 Feb 2009) | 3 lines
5187 Changed paths:
5188 M /trunk/samtools/bam_maqcns.c
5189 M /trunk/samtools/bamtk.c
5190 M /trunk/samtools/misc/indel_filter.pl
5191
5192 * samtools-0.1.2-6
5193 * improve indel caller by setting maximum window size
5194
5195 ------------------------------------------------------------------------
5196 r123 | lh3lh3 | 2009-02-12 05:30:29 -0500 (Thu, 12 Feb 2009) | 2 lines
5197 Changed paths:
5198 M /trunk/samtools/bam_plcmd.c
5199 M /trunk/samtools/bamtk.c
5200
5201 * output max mapping quality in indel line
5202
5203 ------------------------------------------------------------------------
5204 r122 | lh3lh3 | 2009-02-11 05:59:10 -0500 (Wed, 11 Feb 2009) | 2 lines
5205 Changed paths:
5206 M /trunk/samtools/misc/maq2sam.c
5207
5208 fixed a bug in generating tag AM
5209
5210 ------------------------------------------------------------------------
5211 r121 | lh3lh3 | 2009-02-03 05:43:11 -0500 (Tue, 03 Feb 2009) | 2 lines
5212 Changed paths:
5213 M /trunk/samtools/bam_index.c
5214 M /trunk/samtools/bamtk.c
5215
5216 fixed a potential memory problem in indexing
5217
5218 ------------------------------------------------------------------------
5219 r120 | bhandsaker | 2009-02-02 10:52:52 -0500 (Mon, 02 Feb 2009) | 2 lines
5220 Changed paths:
5221 M /trunk/samtools/Makefile
5222
5223 Pass LIBS to recursive targets to facilitate building at Broad.
5224
5225 ------------------------------------------------------------------------
5226 r119 | lh3lh3 | 2009-02-02 05:12:15 -0500 (Mon, 02 Feb 2009) | 4 lines
5227 Changed paths:
5228 M /trunk/samtools/ChangeLog
5229 M /trunk/samtools/bam_plcmd.c
5230 M /trunk/samtools/bam_stat.c
5231 M /trunk/samtools/bamtk.c
5232
5233 * samtools-0.1.2-3
5234 * fixed a bug in generating GLFv2 for indels
5235 * improve flagstat report a little bit
5236
5237 ------------------------------------------------------------------------
5238 r118 | lh3lh3 | 2009-01-29 07:33:23 -0500 (Thu, 29 Jan 2009) | 3 lines
5239 Changed paths:
5240 M /trunk/samtools/Makefile
5241 A /trunk/samtools/bam_stat.c
5242 M /trunk/samtools/bamtk.c
5243
5244 * samtools-0.1.2-1
5245 * added flagstat command
5246
5247 ------------------------------------------------------------------------
5248 r116 | lh3lh3 | 2009-01-28 08:31:12 -0500 (Wed, 28 Jan 2009) | 2 lines
5249 Changed paths:
5250 M /trunk/samtools/ChangeLog
5251 M /trunk/samtools/NEWS
5252 M /trunk/samtools/bamtk.c
5253 M /trunk/samtools/samtools.1
5254
5255 Release SAMtools-0.1.2
5256
5257 ------------------------------------------------------------------------
5258 r115 | lh3lh3 | 2009-01-28 07:54:08 -0500 (Wed, 28 Jan 2009) | 2 lines
5259 Changed paths:
5260 A /trunk/samtools/misc/indel_filter.pl
5261
5262 Script for filtering indel results
5263
5264 ------------------------------------------------------------------------
5265 r114 | lh3lh3 | 2009-01-25 06:45:37 -0500 (Sun, 25 Jan 2009) | 2 lines
5266 Changed paths:
5267 A /trunk/samtools/misc/zoom2sam.pl
5268
5269 convert ZOOM to SAM
5270
5271 ------------------------------------------------------------------------
5272 r113 | lh3lh3 | 2009-01-24 09:25:07 -0500 (Sat, 24 Jan 2009) | 2 lines
5273 Changed paths:
5274 A /trunk/samtools/misc/novo2sam.pl
5275
5276 add a script to convert novo alignment to SAM
5277
5278 ------------------------------------------------------------------------
5279 r112 | lh3lh3 | 2009-01-23 15:57:39 -0500 (Fri, 23 Jan 2009) | 2 lines
5280 Changed paths:
5281 M /trunk/samtools/ChangeLog
5282 M /trunk/samtools/ChangeLog.old
5283 M /trunk/samtools/samtools.1
5284
5285 update documentation and ChangeLog
5286
5287 ------------------------------------------------------------------------
5288 r111 | lh3lh3 | 2009-01-23 14:22:59 -0500 (Fri, 23 Jan 2009) | 3 lines
5289 Changed paths:
5290 M /trunk/samtools/bam_sort.c
5291 M /trunk/samtools/bamtk.c
5292
5293 * samtools-0.1.1-19
5294 * fixed a bug in "merge" command line
5295
5296 ------------------------------------------------------------------------
5297 r110 | lh3lh3 | 2009-01-22 10:36:48 -0500 (Thu, 22 Jan 2009) | 3 lines
5298 Changed paths:
5299 M /trunk/samtools/misc/Makefile
5300 A /trunk/samtools/misc/bowtie2sam.pl (from /branches/dev/samtools/misc/bowtie2sam.pl:108)
5301 M /trunk/samtools/misc/export2sam.pl
5302 A /trunk/samtools/misc/soap2sam.pl (from /branches/dev/samtools/misc/soap2sam.pl:108)
5303 A /trunk/samtools/misc/wgsim.c (from /branches/dev/samtools/misc/wgsim.c:108)
5304 A /trunk/samtools/misc/wgsim_eval.pl (from /branches/dev/samtools/misc/wgsim_eval.pl:108)
5305
5306 * merge from branches/dev/
5307 * all future development will happen here
5308
5309 ------------------------------------------------------------------------
5310 r109 | lh3lh3 | 2009-01-22 10:14:27 -0500 (Thu, 22 Jan 2009) | 3 lines
5311 Changed paths:
5312 M /trunk/samtools/COPYING
5313 M /trunk/samtools/ChangeLog
5314 A /trunk/samtools/INSTALL (from /branches/dev/samtools/INSTALL:108)
5315 M /trunk/samtools/Makefile
5316 A /trunk/samtools/Makefile.lite (from /branches/dev/samtools/Makefile.lite:108)
5317 M /trunk/samtools/bam.c
5318 M /trunk/samtools/bam.h
5319 M /trunk/samtools/bam_import.c
5320 M /trunk/samtools/bam_index.c
5321 M /trunk/samtools/bam_lpileup.c
5322 M /trunk/samtools/bam_maqcns.c
5323 M /trunk/samtools/bam_maqcns.h
5324 A /trunk/samtools/bam_mate.c (from /branches/dev/samtools/bam_mate.c:108)
5325 M /trunk/samtools/bam_pileup.c
5326 M /trunk/samtools/bam_plcmd.c
5327 A /trunk/samtools/bam_rmdup.c (from /branches/dev/samtools/bam_rmdup.c:108)
5328 M /trunk/samtools/bam_sort.c
5329 M /trunk/samtools/bamtk.c
5330 M /trunk/samtools/bgzf.h
5331 M /trunk/samtools/examples/00README.txt
5332 A /trunk/samtools/examples/Makefile (from /branches/dev/samtools/examples/Makefile:108)
5333 D /trunk/samtools/examples/ex1.fa.fai
5334 M /trunk/samtools/examples/ex1.sam.gz
5335 M /trunk/samtools/faidx.c
5336 A /trunk/samtools/glf.c (from /branches/dev/samtools/glf.c:108)
5337 M /trunk/samtools/glf.h
5338 M /trunk/samtools/misc/Makefile
5339 M /trunk/samtools/misc/maq2sam.c
5340 M /trunk/samtools/razf.c
5341 M /trunk/samtools/source.dot
5342
5343 * Merge from branches/dev/
5344 * all future development will happen here at trunk/
5345
5346 ------------------------------------------------------------------------
5347 r79 | bhandsaker | 2009-01-07 16:42:15 -0500 (Wed, 07 Jan 2009) | 2 lines
5348 Changed paths:
5349 M /trunk/samtools/bam_maqcns.c
5350 M /trunk/samtools/bam_tview.c
5351
5352 Fix problem with compiling without curses.
5353
5354 ------------------------------------------------------------------------
5355 r63 | lh3lh3 | 2008-12-22 10:58:02 -0500 (Mon, 22 Dec 2008) | 2 lines
5356 Changed paths:
5357 A /trunk/samtools (from /branches/dev/samtools:62)
5358
5359 Create trunk copy
5360
5361 ------------------------------------------------------------------------
5362 r62 | lh3lh3 | 2008-12-22 10:55:13 -0500 (Mon, 22 Dec 2008) | 2 lines
5363 Changed paths:
5364 A /branches/dev/samtools/NEWS
5365 M /branches/dev/samtools/bamtk.c
5366 M /branches/dev/samtools/samtools.1
5367
5368 Release samtools-0.1.1
5369
5370 ------------------------------------------------------------------------
5371 r61 | lh3lh3 | 2008-12-22 10:46:08 -0500 (Mon, 22 Dec 2008) | 10 lines
5372 Changed paths:
5373 M /branches/dev/samtools/bam_aux.c
5374 M /branches/dev/samtools/bam_index.c
5375 M /branches/dev/samtools/bam_plcmd.c
5376 M /branches/dev/samtools/bam_tview.c
5377 M /branches/dev/samtools/bamtk.c
5378 M /branches/dev/samtools/razf.c
5379 M /branches/dev/samtools/samtools.1
5380
5381 * samtools-0.1.0-66
5382 * fixed a bug in razf.c: reset z_eof when razf_seek() is called
5383 * fixed a memory leak in parsing a region
5384 * changed pileup a little bit when -s is in use: output ^ and $
5385 * when a bam is not indexed, output more meaningful error message
5386 * fixed a bug in indexing for small alignment
5387 * fixed a bug in the viewer when we come to the end of a reference file
5388 * updated documentation
5389 * prepare to release 0.1.1
5390
5391 ------------------------------------------------------------------------
5392 r60 | lh3lh3 | 2008-12-22 10:10:16 -0500 (Mon, 22 Dec 2008) | 2 lines
5393 Changed paths:
5394 A /branches/dev/samtools/examples
5395 A /branches/dev/samtools/examples/00README.txt
5396 A /branches/dev/samtools/examples/ex1.fa
5397 A /branches/dev/samtools/examples/ex1.fa.fai
5398 A /branches/dev/samtools/examples/ex1.sam.gz
5399
5400 example
5401
5402 ------------------------------------------------------------------------
5403 r59 | lh3lh3 | 2008-12-22 04:38:15 -0500 (Mon, 22 Dec 2008) | 2 lines
5404 Changed paths:
5405 M /branches/dev/samtools/ChangeLog
5406
5407 update ChangeLog
5408
5409 ------------------------------------------------------------------------
5410 r58 | lh3lh3 | 2008-12-20 18:06:00 -0500 (Sat, 20 Dec 2008) | 3 lines
5411 Changed paths:
5412 M /branches/dev/samtools/misc/export2sam.pl
5413
5414 * added comments
5415 * fixed several bugs
5416
5417 ------------------------------------------------------------------------
5418 r57 | lh3lh3 | 2008-12-20 10:44:20 -0500 (Sat, 20 Dec 2008) | 2 lines
5419 Changed paths:
5420 A /branches/dev/samtools/misc/export2sam.pl
5421
5422 convert Export format to SAM; not thoroughly tested
5423
5424 ------------------------------------------------------------------------
5425 r56 | lh3lh3 | 2008-12-19 17:13:28 -0500 (Fri, 19 Dec 2008) | 6 lines
5426 Changed paths:
5427 M /branches/dev/samtools/bam_import.c
5428 M /branches/dev/samtools/bam_plcmd.c
5429 M /branches/dev/samtools/bam_tview.c
5430 M /branches/dev/samtools/bamtk.c
5431 A /branches/dev/samtools/source.dot
5432
5433 * samtools-0.1.0-65
5434 * pileup: generate maq-like simple output
5435 * pileup: allow to output pileup at required sites
5436 * source.dot: source file relationship graph
5437 * tview: fixed a minor bug
5438
5439 ------------------------------------------------------------------------
5440 r55 | lh3lh3 | 2008-12-19 15:10:26 -0500 (Fri, 19 Dec 2008) | 2 lines
5441 Changed paths:
5442 D /branches/dev/samtools/misc/all2sam.pl
5443
5444 remove all2sam.pl
5445
5446 ------------------------------------------------------------------------
5447 r54 | lh3lh3 | 2008-12-16 17:34:25 -0500 (Tue, 16 Dec 2008) | 2 lines
5448 Changed paths:
5449 A /branches/dev/samtools/COPYING
5450 M /branches/dev/samtools/bam.h
5451 M /branches/dev/samtools/faidx.h
5452 M /branches/dev/samtools/khash.h
5453 M /branches/dev/samtools/kseq.h
5454 M /branches/dev/samtools/ksort.h
5455 M /branches/dev/samtools/samtools.1
5456
5457 Added copyright information and a bit more documentation. No code change.
5458
5459 ------------------------------------------------------------------------
5460 r53 | lh3lh3 | 2008-12-16 08:40:18 -0500 (Tue, 16 Dec 2008) | 3 lines
5461 Changed paths:
5462 M /branches/dev/samtools/bam.c
5463 M /branches/dev/samtools/bam.h
5464 M /branches/dev/samtools/bam_index.c
5465 M /branches/dev/samtools/bam_maqcns.c
5466 M /branches/dev/samtools/bamtk.c
5467
5468 * samtools-0.1.0-64
5469 * improved efficiency of the indel caller for spliced alignments
5470
5471 ------------------------------------------------------------------------
5472 r52 | lh3lh3 | 2008-12-16 05:28:20 -0500 (Tue, 16 Dec 2008) | 3 lines
5473 Changed paths:
5474 M /branches/dev/samtools/bam.c
5475 M /branches/dev/samtools/bam.h
5476 M /branches/dev/samtools/bam_aux.c
5477 M /branches/dev/samtools/bam_index.c
5478 M /branches/dev/samtools/bamtk.c
5479
5480 * samtools-0.1.0-63
5481 * a bit code cleanup: reduce the dependency between source files
5482
5483 ------------------------------------------------------------------------
5484 r51 | lh3lh3 | 2008-12-15 09:29:32 -0500 (Mon, 15 Dec 2008) | 3 lines
5485 Changed paths:
5486 M /branches/dev/samtools/bam_maqcns.c
5487 M /branches/dev/samtools/bam_plcmd.c
5488 M /branches/dev/samtools/bamtk.c
5489
5490 * samtools-0.1.0-62
5491 * fixed a memory leak
5492
5493 ------------------------------------------------------------------------
5494 r50 | lh3lh3 | 2008-12-15 09:00:13 -0500 (Mon, 15 Dec 2008) | 2 lines
5495 Changed paths:
5496 M /branches/dev/samtools/ChangeLog
5497 M /branches/dev/samtools/bam.h
5498 M /branches/dev/samtools/samtools.1
5499
5500 update documentation, ChangeLog and a comment
5501
5502 ------------------------------------------------------------------------
5503 r49 | lh3lh3 | 2008-12-15 08:36:43 -0500 (Mon, 15 Dec 2008) | 6 lines
5504 Changed paths:
5505 M /branches/dev/samtools/Makefile
5506 M /branches/dev/samtools/bam.h
5507 M /branches/dev/samtools/bam_maqcns.c
5508 M /branches/dev/samtools/bam_maqcns.h
5509 M /branches/dev/samtools/bam_pileup.c
5510 A /branches/dev/samtools/bam_plcmd.c
5511 M /branches/dev/samtools/bamtk.c
5512 M /branches/dev/samtools/samtools.1
5513
5514 * samtools-0.1.0-61
5515 * moved pileup command to a separate source file
5516 * added indel caller
5517 * added bam_cal_segend(). (NOT WORKING for spliced alignment!!!)
5518 * updated documentation
5519
5520 ------------------------------------------------------------------------
5521 r48 | lh3lh3 | 2008-12-12 08:55:36 -0500 (Fri, 12 Dec 2008) | 3 lines
5522 Changed paths:
5523 M /branches/dev/samtools/bam_maqcns.c
5524 M /branches/dev/samtools/bamtk.c
5525
5526 * samtools-0.1.0-60
5527 * fixed another bug in maqcns when there is a nearby deletion
5528
5529 ------------------------------------------------------------------------
5530 r47 | lh3lh3 | 2008-12-12 08:42:16 -0500 (Fri, 12 Dec 2008) | 5 lines
5531 Changed paths:
5532 M /branches/dev/samtools/bam_maqcns.c
5533 M /branches/dev/samtools/bam_pileup.c
5534 M /branches/dev/samtools/bamtk.c
5535
5536 * samtools-0.1.0-59
5537 * pileup: outputing consensus is now optional
5538 * fixed a bug in glfgen. This bug also exists in maq's glfgen. However,
5539 I am not quite sure why the previous version may have problem.
5540
5541 ------------------------------------------------------------------------
5542 r46 | lh3lh3 | 2008-12-12 06:44:56 -0500 (Fri, 12 Dec 2008) | 6 lines
5543 Changed paths:
5544 M /branches/dev/samtools/bam_pileup.c
5545 M /branches/dev/samtools/bamtk.c
5546
5547 * samtools-0.1.0-58
5548 * add maq consensus to pileup. However, I will move this part to a new
5549 command as strictly speaking, consensus callin is not part of pileup,
5550 and imposing it would make it harder to generate for other language
5551 bindings.
5552
5553 ------------------------------------------------------------------------
5554 r45 | bhandsaker | 2008-12-11 15:43:56 -0500 (Thu, 11 Dec 2008) | 2 lines
5555 Changed paths:
5556 M /branches/dev/samtools/bgzf.c
5557
5558 Fix bug in tell() after reads that consume to the exact end of a block.
5559
5560 ------------------------------------------------------------------------
5561 r44 | lh3lh3 | 2008-12-11 04:36:53 -0500 (Thu, 11 Dec 2008) | 2 lines
5562 Changed paths:
5563 M /branches/dev/samtools/samtools.1
5564
5565 update manual
5566
5567 ------------------------------------------------------------------------
5568 r43 | lh3lh3 | 2008-12-11 04:25:36 -0500 (Thu, 11 Dec 2008) | 4 lines
5569 Changed paths:
5570 M /branches/dev/samtools/bam_import.c
5571 M /branches/dev/samtools/bamtk.c
5572
5573 * samtools-0.1.0-57
5574 * fixed a bug in parser when there is auxiliary fields
5575 * made the parser a bit more robust
5576
5577 ------------------------------------------------------------------------
5578 r42 | lh3lh3 | 2008-12-10 09:57:29 -0500 (Wed, 10 Dec 2008) | 5 lines
5579 Changed paths:
5580 M /branches/dev/samtools/bam_index.c
5581 M /branches/dev/samtools/bamtk.c
5582 M /branches/dev/samtools/bgzf.c
5583
5584 * samtools-0.1.0-56
5585 * fixed a bug in bgzf (only reading is affected)
5586 * fixed a typo in bam_index.c
5587 * in bam_index.c, check potential bugs in the underlying I/O library
5588
5589 ------------------------------------------------------------------------
5590 r41 | lh3lh3 | 2008-12-10 07:53:08 -0500 (Wed, 10 Dec 2008) | 2 lines
5591 Changed paths:
5592 M /branches/dev/samtools/samtools.1
5593
5594 update manual
5595
5596 ------------------------------------------------------------------------
5597 r40 | lh3lh3 | 2008-12-10 06:52:10 -0500 (Wed, 10 Dec 2008) | 5 lines
5598 Changed paths:
5599 M /branches/dev/samtools/bam.h
5600 M /branches/dev/samtools/bam_pileup.c
5601 M /branches/dev/samtools/bamtk.c
5602
5603 * samtools-0.1.0-55
5604 * tried to make pileup work with clipping (previously not), though NOT tested
5605 * removed -v from pileup
5606 * made pileup take the reference sequence
5607
5608 ------------------------------------------------------------------------
5609 r39 | lh3lh3 | 2008-12-09 06:59:28 -0500 (Tue, 09 Dec 2008) | 4 lines
5610 Changed paths:
5611 M /branches/dev/samtools/bam_import.c
5612 M /branches/dev/samtools/bamtk.c
5613 M /branches/dev/samtools/samtools.1
5614
5615 * samtools-0.1.0-54
5616 * in parser, recognize "=", rather than ",", as a match
5617 * in parser, correctl parse "=" at the MRNM field.
5618
5619 ------------------------------------------------------------------------
5620 r38 | lh3lh3 | 2008-12-09 06:39:07 -0500 (Tue, 09 Dec 2008) | 2 lines
5621 Changed paths:
5622 M /branches/dev/samtools/misc/maq2sam.c
5623
5624 fixed a bug in handling maq flag 64 and 192
5625
5626 ------------------------------------------------------------------------
5627 r37 | lh3lh3 | 2008-12-09 04:53:46 -0500 (Tue, 09 Dec 2008) | 2 lines
5628 Changed paths:
5629 M /branches/dev/samtools/misc/md5fa.c
5630
5631 also calculate unordered md5sum check
5632
5633 ------------------------------------------------------------------------
5634 r36 | lh3lh3 | 2008-12-09 04:46:21 -0500 (Tue, 09 Dec 2008) | 2 lines
5635 Changed paths:
5636 M /branches/dev/samtools/misc/md5fa.c
5637
5638 fixed a minor bug when there are space in the sequence
5639
5640 ------------------------------------------------------------------------
5641 r35 | lh3lh3 | 2008-12-09 04:40:45 -0500 (Tue, 09 Dec 2008) | 2 lines
5642 Changed paths:
5643 M /branches/dev/samtools/misc/md5fa.c
5644
5645 fixed a potential memory leak
5646
5647 ------------------------------------------------------------------------
5648 r34 | lh3lh3 | 2008-12-08 09:52:17 -0500 (Mon, 08 Dec 2008) | 2 lines
5649 Changed paths:
5650 M /branches/dev/samtools/bam_import.c
5651 M /branches/dev/samtools/bam_index.c
5652 M /branches/dev/samtools/bamtk.c
5653
5654 * fixed a bug in import: bin is wrongly calculated
5655
5656 ------------------------------------------------------------------------
5657 r33 | lh3lh3 | 2008-12-08 09:08:01 -0500 (Mon, 08 Dec 2008) | 2 lines
5658 Changed paths:
5659 M /branches/dev/samtools/misc/all2sam.pl
5660
5661 nothing, really
5662
5663 ------------------------------------------------------------------------
5664 r32 | lh3lh3 | 2008-12-08 07:56:02 -0500 (Mon, 08 Dec 2008) | 3 lines
5665 Changed paths:
5666 M /branches/dev/samtools/Makefile
5667 M /branches/dev/samtools/kseq.h
5668 M /branches/dev/samtools/misc/Makefile
5669 A /branches/dev/samtools/misc/md5.c
5670 A /branches/dev/samtools/misc/md5.h
5671 A /branches/dev/samtools/misc/md5fa.c
5672
5673 * fixed two warnings in kseq.h
5674 * added md5sum utilities
5675
5676 ------------------------------------------------------------------------
5677 r31 | lh3lh3 | 2008-12-08 06:35:29 -0500 (Mon, 08 Dec 2008) | 5 lines
5678 Changed paths:
5679 M /branches/dev/samtools/Makefile
5680 M /branches/dev/samtools/bam_import.c
5681 M /branches/dev/samtools/bamtk.c
5682 A /branches/dev/samtools/kseq.h
5683 D /branches/dev/samtools/kstream.h
5684
5685 * samtools-0.1.0-52
5686 * replace kstream with kseq. kseq is a superset of kstream. I need the
5687 extra functions in kseq.h.
5688 * also compile stand-alone faidx
5689
5690 ------------------------------------------------------------------------
5691 r30 | lh3lh3 | 2008-12-08 06:17:04 -0500 (Mon, 08 Dec 2008) | 3 lines
5692 Changed paths:
5693 M /branches/dev/samtools/bam.h
5694 M /branches/dev/samtools/bam_sort.c
5695 M /branches/dev/samtools/bamtk.c
5696
5697 * samtools-0.1.0-51
5698 * sorting by read names is available
5699
5700 ------------------------------------------------------------------------
5701 r29 | lh3lh3 | 2008-12-08 05:29:02 -0500 (Mon, 08 Dec 2008) | 3 lines
5702 Changed paths:
5703 M /branches/dev/samtools/bam.c
5704 M /branches/dev/samtools/bam.h
5705 M /branches/dev/samtools/bam_import.c
5706 M /branches/dev/samtools/bam_maqcns.c
5707 M /branches/dev/samtools/bam_pileup.c
5708 M /branches/dev/samtools/bam_sort.c
5709 M /branches/dev/samtools/bam_tview.c
5710 M /branches/dev/samtools/bamtk.c
5711 M /branches/dev/samtools/misc/maq2sam.c
5712
5713 * samtools-0.1.0-50
5714 * format change to meet the latest specification
5715
5716 ------------------------------------------------------------------------
5717 r28 | lh3lh3 | 2008-12-04 11:09:21 -0500 (Thu, 04 Dec 2008) | 3 lines
5718 Changed paths:
5719 M /branches/dev/samtools/bam_maqcns.c
5720 M /branches/dev/samtools/misc/maq2sam.c
5721
5722 * minor change in maqcns: special care when n==0
5723 * change maq2sam to meet the latest specification
5724
5725 ------------------------------------------------------------------------
5726 r27 | lh3lh3 | 2008-12-04 10:55:44 -0500 (Thu, 04 Dec 2008) | 2 lines
5727 Changed paths:
5728 M /branches/dev/samtools/razf.c
5729 M /branches/dev/samtools/razf.h
5730
5731 considerable code clean up in razf
5732
5733 ------------------------------------------------------------------------
5734 r26 | lh3lh3 | 2008-12-04 10:08:18 -0500 (Thu, 04 Dec 2008) | 2 lines
5735 Changed paths:
5736 M /branches/dev/samtools/ChangeLog
5737 M /branches/dev/samtools/Makefile
5738 M /branches/dev/samtools/faidx.c
5739
5740 make RAZF optional in faidx.c
5741
5742 ------------------------------------------------------------------------
5743 r25 | lh3lh3 | 2008-12-01 10:27:22 -0500 (Mon, 01 Dec 2008) | 3 lines
5744 Changed paths:
5745 M /branches/dev/samtools/Makefile
5746 M /branches/dev/samtools/bam.h
5747 M /branches/dev/samtools/bam_aux.c
5748 M /branches/dev/samtools/bamtk.c
5749 M /branches/dev/samtools/samtools.1
5750
5751 * samtools-0.1.0-49
5752 * added routines for retrieving aux data, NOT TESTED YET!
5753
5754 ------------------------------------------------------------------------
5755 r24 | lh3lh3 | 2008-12-01 09:29:43 -0500 (Mon, 01 Dec 2008) | 5 lines
5756 Changed paths:
5757 M /branches/dev/samtools/bam.c
5758 M /branches/dev/samtools/bam_import.c
5759 M /branches/dev/samtools/bam_maqcns.c
5760 M /branches/dev/samtools/bamtk.c
5761 M /branches/dev/samtools/bgzf.c
5762 M /branches/dev/samtools/samtools.1
5763
5764 * samtools-0.1.0-48
5765 * bgzf: fixed a potential integer overflow on 32-it machines
5766 * maqcns: set the minimum combined quality as 0
5767 * supporting hex strings
5768
5769 ------------------------------------------------------------------------
5770 r23 | lh3lh3 | 2008-11-27 12:14:37 -0500 (Thu, 27 Nov 2008) | 3 lines
5771 Changed paths:
5772 M /branches/dev/samtools/bam_maqcns.c
5773 M /branches/dev/samtools/bamtk.c
5774
5775 * samtools-0.1.0-47
5776 * fixed the bug in maqcns
5777
5778 ------------------------------------------------------------------------
5779 r22 | lh3lh3 | 2008-11-27 12:08:11 -0500 (Thu, 27 Nov 2008) | 3 lines
5780 Changed paths:
5781 M /branches/dev/samtools/Makefile
5782 M /branches/dev/samtools/bam.h
5783 A /branches/dev/samtools/bam_maqcns.c
5784 A /branches/dev/samtools/bam_maqcns.h
5785 M /branches/dev/samtools/bam_tview.c
5786 M /branches/dev/samtools/bamtk.c
5787 A /branches/dev/samtools/glf.h
5788
5789 * samtools-0.1.0-46
5790 * add MAQ consensus caller, currently BUGGY!
5791
5792 ------------------------------------------------------------------------
5793 r21 | lh3lh3 | 2008-11-27 08:51:28 -0500 (Thu, 27 Nov 2008) | 4 lines
5794 Changed paths:
5795 M /branches/dev/samtools/bam_pileup.c
5796 M /branches/dev/samtools/bam_tview.c
5797 M /branches/dev/samtools/bamtk.c
5798
5799 * samtools-0.1.0-45
5800 * tview: display padded alignment (but not P operation)
5801 * better coordinates and reference sequence
5802
5803 ------------------------------------------------------------------------
5804 r19 | lh3lh3 | 2008-11-27 04:26:05 -0500 (Thu, 27 Nov 2008) | 2 lines
5805 Changed paths:
5806 A /branches/dev/samtools/ChangeLog
5807
5808 new ChangeLog
5809
5810 ------------------------------------------------------------------------
5811 r18 | lh3lh3 | 2008-11-27 04:24:45 -0500 (Thu, 27 Nov 2008) | 3 lines
5812 Changed paths:
5813 D /branches/dev/samtools/ChangeLog
5814 A /branches/dev/samtools/ChangeLog.old (from /branches/dev/samtools/ChangeLog:6)
5815
5816 Rename ChangeLog to ChangeLog.old. This old ChangeLog is generated from
5817 the log of my personal SVN repository.
5818
5819 ------------------------------------------------------------------------
5820 r17 | lh3lh3 | 2008-11-27 04:22:55 -0500 (Thu, 27 Nov 2008) | 6 lines
5821 Changed paths:
5822 M /branches/dev/samtools/Makefile
5823 M /branches/dev/samtools/bamtk.c
5824 M /branches/dev/samtools/bgzf.c
5825
5826 * samtools-0.1.0-44
5827 * declare fseeko and ftello as some Linux may not do this by default and
5828 missing these declarations will make bgzf buggy
5829 * get rid of some harmless warings
5830 * use BGZF by default, now
5831
5832 ------------------------------------------------------------------------
5833 r16 | lh3lh3 | 2008-11-26 16:19:11 -0500 (Wed, 26 Nov 2008) | 4 lines
5834 Changed paths:
5835 M /branches/dev/samtools/bam_index.c
5836 M /branches/dev/samtools/bamtk.c
5837 M /branches/dev/samtools/razf.c
5838
5839 * samtools-0.1.0-43
5840 * fixed a bug in razf_read()
5841 * give more warnings when the file is truncated (or due to bugs in I/O library)
5842
5843 ------------------------------------------------------------------------
5844 r15 | lh3lh3 | 2008-11-26 15:41:39 -0500 (Wed, 26 Nov 2008) | 2 lines
5845 Changed paths:
5846 M /branches/dev/samtools/bgzf.c
5847
5848 fixed a bug in bgzf.c at the end of the file
5849
5850 ------------------------------------------------------------------------
5851 r14 | lh3lh3 | 2008-11-26 12:05:18 -0500 (Wed, 26 Nov 2008) | 4 lines
5852 Changed paths:
5853 M /branches/dev/samtools/bamtk.c
5854
5855 * samtools-0.1.0-42
5856 * a lot happened to RAZF, although samtools itself is untouched. Better
5857 also update the version number anyway to avoid confusion
5858
5859 ------------------------------------------------------------------------
5860 r13 | lh3lh3 | 2008-11-26 12:03:48 -0500 (Wed, 26 Nov 2008) | 2 lines
5861 Changed paths:
5862 M /branches/dev/samtools/razf.c
5863
5864 a change from Jue, but I think it should not matter
5865
5866 ------------------------------------------------------------------------
5867 r12 | lh3lh3 | 2008-11-26 11:48:14 -0500 (Wed, 26 Nov 2008) | 3 lines
5868 Changed paths:
5869 M /branches/dev/samtools/razf.c
5870
5871 fixed a potential bug in razf. However, it seems still buggy, just
5872 rarely happens, very rarely.
5873
5874 ------------------------------------------------------------------------
5875 r11 | lh3lh3 | 2008-11-26 09:02:56 -0500 (Wed, 26 Nov 2008) | 2 lines
5876 Changed paths:
5877 M /branches/dev/samtools/razf.c
5878
5879 fixed a bug in razf, with the help of Jue
5880
5881 ------------------------------------------------------------------------
5882 r10 | lh3lh3 | 2008-11-26 06:55:32 -0500 (Wed, 26 Nov 2008) | 2 lines
5883 Changed paths:
5884 M /branches/dev/samtools/bam_index.c
5885
5886 remove a comment
5887
5888 ------------------------------------------------------------------------
5889 r9 | lh3lh3 | 2008-11-26 06:37:05 -0500 (Wed, 26 Nov 2008) | 2 lines
5890 Changed paths:
5891 M /branches/dev/samtools/Makefile
5892 M /branches/dev/samtools/bam.h
5893 M /branches/dev/samtools/razf.c
5894 M /branches/dev/samtools/razf.h
5895
5896 * Jue has updated razf to realize Bob's scheme
5897
5898 ------------------------------------------------------------------------
5899 r7 | lh3lh3 | 2008-11-25 15:37:37 -0500 (Tue, 25 Nov 2008) | 2 lines
5900 Changed paths:
5901 A /branches/dev/samtools/samtools.1
5902
5903 the manual page
5904
5905 ------------------------------------------------------------------------
5906 r6 | lh3lh3 | 2008-11-25 15:37:16 -0500 (Tue, 25 Nov 2008) | 3 lines
5907 Changed paths:
5908 A /branches/dev/samtools/ChangeLog
5909 A /branches/dev/samtools/Makefile
5910 A /branches/dev/samtools/bam.c
5911 A /branches/dev/samtools/bam.h
5912 A /branches/dev/samtools/bam_aux.c
5913 A /branches/dev/samtools/bam_endian.h
5914 A /branches/dev/samtools/bam_import.c
5915 A /branches/dev/samtools/bam_index.c
5916 A /branches/dev/samtools/bam_lpileup.c
5917 A /branches/dev/samtools/bam_pileup.c
5918 A /branches/dev/samtools/bam_sort.c
5919 A /branches/dev/samtools/bam_tview.c
5920 A /branches/dev/samtools/bamtk.c
5921 A /branches/dev/samtools/bgzf.c
5922 A /branches/dev/samtools/bgzf.h
5923 A /branches/dev/samtools/bgzip.c
5924 A /branches/dev/samtools/faidx.c
5925 A /branches/dev/samtools/faidx.h
5926 A /branches/dev/samtools/khash.h
5927 A /branches/dev/samtools/ksort.h
5928 A /branches/dev/samtools/kstream.h
5929 A /branches/dev/samtools/misc
5930 A /branches/dev/samtools/misc/Makefile
5931 A /branches/dev/samtools/misc/all2sam.pl
5932 A /branches/dev/samtools/misc/maq2sam.c
5933 A /branches/dev/samtools/razf.c
5934 A /branches/dev/samtools/razf.h
5935 A /branches/dev/samtools/razip.c
5936 A /branches/dev/samtools/zutil.h
5937
5938 The initial version of samtools, replicated from my local SVN repository.
5939 The current version is: 0.1.0-42. All future development will happen here.
5940
5941 ------------------------------------------------------------------------
5942 r5 | lh3lh3 | 2008-11-25 15:30:49 -0500 (Tue, 25 Nov 2008) | 2 lines
5943 Changed paths:
5944 A /branches/dev/samtools
5945
5946 samtools (C version)
5947
5948 ------------------------------------------------------------------------