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1 commit db2ad3e19068cbafde72ecde75d0638bbb3598ba
2 Author: Heng Li <lh3@live.co.uk>
3 Date: Thu Feb 16 14:45:17 2012 -0500
4
5 removed downsample.c
6
7 commit 6c55c576903992c6fef148fe3b606fbc8bd10655
8 Author: Heng Li <lh3@live.co.uk>
9 Date: Thu Feb 16 14:45:06 2012 -0500
10
11 print to output
12
13 commit db1044a34e6049c87eaa63c39ed6e56f03e7d4c1
14 Author: Heng Li <lh3@live.co.uk>
15 Date: Thu Feb 16 14:39:34 2012 -0500
16
17 removed sample
18
19 Downsampling already exists in "view". View also keeps pairing while "sample" does not.
20
21 commit ffdeed3e5d4a530bfdf6f9ba97fff0ba7add6cba
22 Merge: 2daad7b accf026
23 Author: Heng Li <lh3@live.co.uk>
24 Date: Thu Feb 16 14:22:15 2012 -0500
25
26 Merge branch 'master' of github.com:lh3/samtools
27
28 commit accf0260fd1117e10047344345d40b31a9ec31bb
29 Merge: 9134e0d c554160
30 Author: Heng Li <lh3@me.com>
31 Date: Thu Feb 16 11:21:14 2012 -0800
32
33 Merge pull request #8 from nh13/master
34
35 Patches
36
37 commit c554160df16ec7748cfdda4c7b54c641be7b809f
38 Author: Nils Homer <nils.homer@lifetech.com>
39 Date: Thu Feb 16 14:06:52 2012 -0500
40
41 * more README.md work
42
43 commit 2a81ffe349208d917666808fbc9f3041e0cb57de
44 Author: Nils Homer <nils.homer@lifetech.com>
45 Date: Thu Feb 16 14:06:10 2012 -0500
46
47 * more README work
48
49 commit fb3125f732715f62cded8685a23a002a96ce009b
50 Author: Nils Homer <nils.homer@lifetech.com>
51 Date: Thu Feb 16 14:05:19 2012 -0500
52
53 * more README work
54
55 commit 444d41002c37e1c3d0f9208b4a88126c47276386
56 Author: Nils Homer <nils.homer@lifetech.com>
57 Date: Thu Feb 16 14:02:13 2012 -0500
58
59 * updating README
60
61 commit dec53cb1043fe7efadfde75fa2fd39b76de22e54
62 Author: Nils Homer <nils.homer@lifetech.com>
63 Date: Thu Feb 16 13:55:01 2012 -0500
64
65 updating the README for markdown syntax
66
67 commit 798da18c346dca8ec6005582a0ddb1d5420b04ca
68 Author: Nils Homer <nils.homer@lifetech.com>
69 Date: Thu Feb 16 13:48:35 2012 -0500
70
71 adding a README with the current differences between this repository and
72 the official one
73
74 commit 4d22d86c0f28636662f2144a88cd168e104c4275
75 Author: Nils Homer <nils.homer@lifetech.com>
76 Date: Thu Feb 16 13:35:03 2012 -0500
77
78 adding "samtools sample" to the main
79
80 commit 893c25a37c21005dc42f45d45e9ad78ddc5f29bb
81 Author: Nils Homer <nils.homer@lifetech.com>
82 Date: Thu Feb 16 13:33:51 2012 -0500
83
84 * removing some compile flags to work with OS X
85
86 commit 7ac22f72fdc32edd5c24af6baebfa7db5faf8e7b
87 Author: Jonathan Manning <jonathan.manning@lifetech.com>
88 Date: Thu Feb 16 10:47:14 2012 -0500
89
90 Check write filehandle after opening for write. tamw/tamr is a union type, so change is only semantic.
91
92 Signed-off-by: Nils Homer <nils.homer@lifetech.com>
93
94 commit fef53330416631690f60fdff42b6e43d764170dc
95 Author: Jonathan Manning <jonathan.manning@lifetech.com>
96 Date: Thu Feb 16 10:44:59 2012 -0500
97
98 Catch and report invalid BAM header, instead of segfaulting later on.
99
100 Signed-off-by: Nils Homer <nils.homer@lifetech.com>
101
102 commit 5cc013fe4930bf9b6e7963aab1cd4a3c94f695bc
103 Author: Jonathan Manning <jonathan.manning@lifetech.com>
104 Date: Thu Feb 16 10:44:16 2012 -0500
105
106 Add downsample to examples.
107
108 Signed-off-by: Nils Homer <nils.homer@lifetech.com>
109
110 commit b3fa9e7071532905a81dc7aa48eadc24b8c8846b
111 Author: Jonathan Manning <jonathan.manning@lifetech.com>
112 Date: Thu Feb 16 10:43:48 2012 -0500
113
114 Adjust for leading hard clip on colorspace reads.
115
116 Signed-off-by: Nils Homer <nils.homer@lifetech.com>
117
118 commit 1a9296c1389469d1c1db5b8069f0e11ffcc8abb2
119 Author: Jonathan Manning <jonathan.manning@lifetech.com>
120 Date: Thu Feb 16 10:42:52 2012 -0500
121
122 Add samtools sample command, contributed by Davide Cittaro <davide.cittaro@ifom-ieo-campus.it>.
123
124 Signed-off-by: Nils Homer <nils.homer@lifetech.com>
125
126 commit 2a804f3379748aeba944f1dec306dd726ff3235e
127 Author: Jonathan Manning <jonathan.manning@lifetech.com>
128 Date: Thu Feb 16 10:42:07 2012 -0500
129
130 Add samtools qa command, contributed by Roman Valls Guimera <roman.valls.guimera@scilifelab.se>.
131
132 Signed-off-by: Nils Homer <nils.homer@lifetech.com>
133
134 commit 0f3207fe8fd93e44d40fcf57204079c8c06d24a6
135 Author: Jonathan Manning <jonathan.manning@lifetech.com>
136 Date: Thu Feb 16 10:39:08 2012 -0500
137
138 Makefile cleanup - allow CC, CFLAGS, LDFLAGS to be passed on make command line. Use LDFLAGS in samtools compile.
139
140 Signed-off-by: Nils Homer <nils.homer@lifetech.com>
141
142 commit 6e7df604025f6a86881bf7f4a16f30e15d31538a
143 Author: Jonathan Manning <jonathan.manning@lifetech.com>
144 Date: Thu Feb 16 10:31:15 2012 -0500
145
146 Allow max_mem for sort to be specified with units.
147
148 Signed-off-by: Nils Homer <nils.homer@lifetech.com>
149
150 commit f12ebcaf6e60d34180a27d70e09b743cef140b98
151 Author: Jonathan Manning <jonathan.manning@lifetech.com>
152 Date: Thu Feb 16 10:29:11 2012 -0500
153
154 Allow user defined [lowercase] tags in header elements.
155
156 Signed-off-by: Nils Homer <nils.homer@lifetech.com>
157
158 commit 50b931fa3312dc109537a4260698ddecd0f06a05
159 Author: Jonathan Manning <jonathan.manning@lifetech.com>
160 Date: Thu Feb 16 10:27:11 2012 -0500
161
162 Check lowerbound in text entry box to avoid segfault in tview. Remove redundant call to bam_aux_get.
163
164 Signed-off-by: Nils Homer <nils.homer@lifetech.com>
165
166 commit 5e729da5190949a813d20d329eab7ddb661816bd
167 Author: Nils Homer <nils.homer@lifetech.com>
168 Date: Thu Feb 16 10:31:48 2012 -0500
169
170 * fixing overflow/underflow in integer parsing
171
172 commit fa50a4330b9abedaf07c26e13d31f05e57f1d319
173 Author: Nils Homer <nils.homer@lifetech.com>
174 Date: Thu Feb 16 10:30:40 2012 -0500
175
176 * updating help message for samtools depth
177
178 commit 79e52c9624b6dd3bdfdf439f4b4bc6f774c230a4
179 Author: Nils Homer <nils.homer@lifetech.com>
180 Date: Thu Feb 16 10:29:32 2012 -0500
181
182 * adding support for outputting a circos histogram file in "samtools depth". Use
183 the "-c/-B" options.
184
185 commit 2daad7b52daa86561c0fb65fe366691fad9f5ed3
186 Author: Heng Li <lh3@live.co.uk>
187 Date: Thu Feb 16 09:31:57 2012 -0500
188
189 bugfix: wrong SP; missing DV in the VCF hdr
190
191 commit 9134e0d5047c281ef3bd53da91771d4814a5131c
192 Author: Heng Li <lh3@live.co.uk>
193 Date: Wed Feb 8 11:19:12 2012 -0500
194
195 missing support of DV
196
197 commit 34ebf12078c1d1015a0b8b9a9221243a60b22893
198 Author: Heng Li <lh3@live.co.uk>
199 Date: Wed Feb 8 11:08:56 2012 -0500
200
201 new BCF DV format: number of variant reads
202
203 commit 9589d3312fa2d076f48bdd68e2a5edd419c8070c
204 Author: Heng Li <lh3@live.co.uk>
205 Date: Tue Jan 10 10:30:27 2012 -0500
206
207 scale depth to quality (hidden option)
208
209 commit 704473e14668333ecaca5fb7b238af405c43e3b1
210 Author: Heng Li <lh3@live.co.uk>
211 Date: Tue Jan 10 10:18:17 2012 -0500
212
213 really nothing
214
215 commit 01b307fd287962372bbf07461c88b54f41636817
216 Author: Heng Li <lh3@live.co.uk>
217 Date: Wed Dec 7 13:07:42 2011 -0500
218
219 added an example containing 'B'
220
221 commit c678791f0451ceb9205c1ab5c52c84641863c99a
222 Author: Heng Li <lh3@live.co.uk>
223 Date: Sat Dec 3 12:10:30 2011 -0500
224
225 'B' now moves backward w.r.t. the query
226
227 commit 152119bc06a073933ca830e8e1407538e44626cc
228 Author: Heng Li <lh3@live.co.uk>
229 Date: Fri Dec 2 10:50:12 2011 -0500
230
231 better consensus; a little more robust
232
233 commit 454da4754ac503edda5b1329b67757d797e46e07
234 Author: Heng Li <lh3@live.co.uk>
235 Date: Fri Dec 2 00:20:22 2011 -0500
236
237 in pileup call remove_B()
238
239 commit ff2bcac1cc078ba1879f18c89cfae314439d7086
240 Author: Heng Li <lh3@live.co.uk>
241 Date: Fri Dec 2 00:17:32 2011 -0500
242
243 working on a few toy examples
244
245 commit 745ca7260158d6df7897b52598033ffb055a9e4f
246 Author: Heng Li <lh3@live.co.uk>
247 Date: Thu Dec 1 22:55:39 2011 -0500
248
249 bam_remove_B(); not tested
250
251 commit 07e4cdc7300abfcc82e03105b4689f95cab551cd
252 Author: Heng Li <lh3@live.co.uk>
253 Date: Thu Nov 10 12:58:55 2011 -0500
254
255 baseQ threshold on plain pipleup; removed -E
256
257 commit 322ebf2082dfa91df44b3a996d26c85357e5d5a2
258 Author: Heng Li <lh3@live.co.uk>
259 Date: Wed Oct 19 09:28:04 2011 -0400
260
261 fixed two gcc warnings
262
263 commit a632457b4c4adc50d833b56b5a5231feafaf8193
264 Author: Heng Li <lh3@live.co.uk>
265 Date: Tue Oct 4 10:13:23 2011 -0400
266
267 change size_t to uint32_t in bam_header_t
268
269 This may cause issues on 64-bit big-endian machines. Reported and fixed by Paolo Emilio Mazzon.
270
271 commit af31bf5a78aea03baf6eb90fe50076549d499f6e
272 Author: Heng Li <lh3@live.co.uk>
273 Date: Mon Sep 26 20:17:57 2011 -0400
274
275 rename pad2unpad to depad
276
277 commit 77b198b73dfad1048e5d1c5a64aa75ee7b90f596
278 Author: Heng Li <lh3@live.co.uk>
279 Date: Fri Sep 23 01:22:40 2011 -0400
280
281 convert padded BAM to unpadded BAM
282
283 commit adb9e2342b7b7501d9527d3c23afab10469ae2c6
284 Author: Heng Li <lh3@live.co.uk>
285 Date: Wed Sep 7 11:40:50 2011 -0400
286
287 generate template cigar with "fixmate"
288
289 commit 46e5ab445a0fe880216cbc0daf1225725b569d7a
290 Author: Heng Li <lh3@live.co.uk>
291 Date: Fri Sep 2 12:50:18 2011 -0400
292
293 update kseq.h to the latest version
294
295 commit 68e9e4a73eb91405bb3e56bf0cdaf12d1b487abb
296 Author: Heng Li <lh3@live.co.uk>
297 Date: Fri Sep 2 12:44:45 2011 -0400
298
299 Release samtools-0.1.18
300
301 commit aa06bdadb2d109a79f927f478102f96a1f5fd258
302 Author: Heng Li <lh3@live.co.uk>
303 Date: Fri Sep 2 12:14:17 2011 -0400
304
305 updated the revision number
306
307 commit 267e1e1b6e54c0ab24f94cd9aee9cbd2d1923f9f
308 Merge: 19ff1d3 aebab30
309 Author: Heng Li <lh3@live.co.uk>
310 Date: Fri Sep 2 12:13:08 2011 -0400
311
312 Merge https://github.com/lh3/samtools into reduce
313
314 Conflicts:
315 bam_md.c
316
317 Fixed a few typos in the merge
318
319 commit aebab302399c24eaa6c5ab79d13d6bd5e2e9ea9a
320 Merge: c2c63d0 da62663
321 Author: Heng Li <lh3@live.co.uk>
322 Date: Fri Sep 2 09:03:49 2011 -0700
323
324 Merge pull request #4 from peterjc/x_equals2
325
326 Implement basic support for =/X CIGAR operations
327
328 commit 19ff1d3d7f47d7e61b121292aefe5a74bb8a18d2
329 Author: Heng Li <lh3@live.co.uk>
330 Date: Thu Aug 25 16:38:12 2011 -0400
331
332 reduce BAM size (experimental)
333
334 commit da626630fd98fd4e07ceb4d58c5c9a42d312a85d
335 Author: peterjc <p.j.a.cock@googlemail.com>
336 Date: Mon Aug 22 06:58:08 2011 +0100
337
338 Support =/X CIGAR operations (treated like M)
339
340 commit 461d8003529db77a4d5ecbd108312e868b051a3d
341 Author: peterjc <p.j.a.cock@googlemail.com>
342 Date: Mon Aug 22 05:52:56 2011 +0100
343
344 Define CIGAR equals and X operationss (7 and 8)
345
346 commit c2c63d067113baab41f3bc35fb28f4f00578accb
347 Merge: 7ab3ef3 9a0ed9a
348 Author: Heng Li <lh3@live.co.uk>
349 Date: Thu Aug 18 17:21:54 2011 -0700
350
351 Merge pull request #3 from peterjc/x_equals
352
353 Accept SAM files using = in CIGAR (treats X and = as M)
354
355 commit 9a0ed9a6b85c7981465f459300208dbd93e3c6f5
356 Author: peterjc <p.j.a.cock@googlemail.com>
357 Date: Thu Aug 18 19:28:52 2011 +0100
358
359 Accept SAM files using = in CIGAR (treats X and = as M)
360
361 commit 7ab3ef388c1eb34d7912fd70cc5656c955240263
362 Author: Heng Li <lh3@live.co.uk>
363 Date: Mon Aug 8 10:22:22 2011 -0400
364
365 bugfix: indexing takes huge memory
366
367 This happens when an unmapped mate has coordinate 1. Thank Joel Martin for the fix.
368
369 commit a3f6738593e944354a8f75306687d8b3acf08bf1
370 Merge: a8bdca9 bc67ea2
371 Author: Heng Li <lh3@live.co.uk>
372 Date: Mon Aug 8 09:52:26 2011 -0400
373
374 Merge branch 'master' of github.com:lh3/samtools
375
376 commit bc67ea225da653f36a70b38382d6111dd494f659
377 Author: Petr Danecek <pd3@sanger.ac.uk>
378 Date: Thu Jul 28 20:03:16 2011 +0100
379
380 Variant Distance Bias
381
382 commit deb578f0c49d0b7d8c3bc6be220b4d67e2e7dfdf
383 Author: Petr Danecek <pd3@sanger.ac.uk>
384 Date: Tue Jul 26 09:57:37 2011 +0100
385
386 If there is only one RG tag present in the header and reads are not annotated, don't refuse to work but use the tag instead.
387
388 commit a8bdca9cf482a637b89ee4f98469a93e0ab5e69b
389 Author: Heng Li <lh3@live.co.uk>
390 Date: Mon Jul 25 10:10:55 2011 -0400
391
392 bugfix: LRT2=nan
393
394 commit 0afe33137d046a3e849eeb4a54590f27cbad4228
395 Author: Heng Li <lh3@live.co.uk>
396 Date: Fri Jul 22 21:55:38 2011 -0400
397
398 fixed a bug/typo
399
400 commit 62d5849658c10222d40308c6b53ab4f99a448494
401 Author: Heng Li <lh3@live.co.uk>
402 Date: Fri Jul 15 16:04:19 2011 -0400
403
404 allow to set see in subsampling
405
406 commit 5f46243824cc9435b167973e1d51e13128794ea1
407 Author: Heng Li <lh3@live.co.uk>
408 Date: Fri Jul 15 15:54:47 2011 -0400
409
410 support subsampling
411
412 commit 5e55b6f34fc86cba7cf98d52ccaed405c3ffabbc
413 Author: Heng Li <lh3@live.co.uk>
414 Date: Fri Jul 15 15:53:38 2011 -0400
415
416 support indels
417
418 commit f31c162926d6f43e8b60171789a258d02e1f9be5
419 Author: Heng Li <lh3@live.co.uk>
420 Date: Thu Jul 7 17:02:33 2011 -0400
421
422 do not count indel with "view -Y"
423
424 commit e412dae587883b4c17e5fbf4b7c33f38bfa8458a
425 Author: Heng Li <lh3@live.co.uk>
426 Date: Thu Jul 7 00:35:25 2011 -0400
427
428 for WIN32 compatibility
429
430 commit 70a52501bcfa63824749893a5ab8ed3c38e34958
431 Author: Heng Li <lh3@live.co.uk>
432 Date: Thu Jul 7 00:32:46 2011 -0400
433
434 for WIN32 compatibility
435
436 commit 00438f14ed5984f08e8f7645a9b95644a812f969
437 Author: Heng Li <lh3@live.co.uk>
438 Date: Wed Jul 6 23:41:45 2011 -0400
439
440 fixed an uninitialized variable
441
442 commit 7609c4a01059c326544b3d0142dfe9c4229d68c6
443 Author: Heng Li <lh3@live.co.uk>
444 Date: Wed Jul 6 23:39:31 2011 -0400
445
446 fixed an uninitialized variable
447
448 commit cec7189a412f80ccb068a73bd28528915c16b0bf
449 Author: Heng Li <lh3@live.co.uk>
450 Date: Wed Jul 6 22:53:19 2011 -0400
451
452 Release samtools-0.1.17
453
454 commit 93c06a249de3bb666029bf07b66de5e8e5e314fa
455 Author: Heng Li <lh3@live.co.uk>
456 Date: Wed Jul 6 09:46:09 2011 -0400
457
458 bugfix: incorrect idxstats for the last seq
459
460 Again, this bug is caused by 3rd-party code for the sorting order checking.
461
462 commit 84f6ca62db6e27b8c4c711e7b5f3ca704bf27b4f
463 Author: Heng Li <lh3@live.co.uk>
464 Date: Tue Jul 5 23:30:23 2011 -0400
465
466 output mapping quality in the old pileup format
467
468 commit 362e05fd670886acaede69b864903d730b9db3ca
469 Author: Heng Li <lh3@live.co.uk>
470 Date: Tue Jul 5 21:59:22 2011 -0400
471
472 added a brief description of the VCF format
473
474 commit e690a696468205e0cc4560016361c997660dd496
475 Author: Heng Li <lh3@live.co.uk>
476 Date: Tue Jul 5 16:23:10 2011 -0400
477
478 improved samtools manual page
479
480 commit 362b4a1408ef3c32311d638aa8d85ce39c1c7b2d
481 Author: Heng Li <lh3@live.co.uk>
482 Date: Tue Jul 5 15:58:29 2011 -0400
483
484 merge bcftools.1 to samtools.1
485
486 commit 643e0e61ba7266efbc9e5bfcb8e41f369ba2ce0a
487 Author: Heng Li <lh3@live.co.uk>
488 Date: Tue Jul 5 13:39:02 2011 -0400
489
490 mpileup: when region set, set reference properly
491
492 commit 613e4d67624a94f62563935fbd5cc294df69605a
493 Author: Heng Li <lh3@live.co.uk>
494 Date: Mon Jul 4 23:29:02 2011 -0400
495
496 compute the min PL diff
497
498 commit 5b7d5d3f52b97ca42c8500eede808dab88a46a53
499 Author: Heng Li <lh3@live.co.uk>
500 Date: Mon Jul 4 22:57:48 2011 -0400
501
502 rename trio.c to mut.c
503
504 commit 84fe96ad64b0365ead93a4115d1684b9bebb98fc
505 Author: Heng Li <lh3@live.co.uk>
506 Date: Sun Jul 3 15:38:51 2011 -0400
507
508 added pair caller interface; not tested
509
510 commit 2f2867b87b84c35319cc416d6173819d5c8a4e8c
511 Author: Heng Li <lh3@live.co.uk>
512 Date: Sun Jul 3 15:24:23 2011 -0400
513
514 inital implementation of a pair caller
515
516 commit e97653cf2ad653c95886933c42a2b5492ccab5ff
517 Author: Heng Li <lh3@live.co.uk>
518 Date: Sun Jul 3 00:06:28 2011 -0400
519
520 convert bam to single-end fastq
521
522 commit e8013e11f7a8db0a8d18c60d130169cca39bf2bd
523 Author: Heng Li <lh3@live.co.uk>
524 Date: Sat Jul 2 14:39:18 2011 -0400
525
526 improve BED parsing
527
528 commit 1025714325fdc636aeee47a76db8dafbbbfde64b
529 Author: Heng Li <lh3@live.co.uk>
530 Date: Fri Jul 1 14:19:54 2011 -0400
531
532 update the manual page
533
534 commit 8022d0039dff47b1c11b2421357d510c1f28ae15
535 Author: Heng Li <lh3@live.co.uk>
536 Date: Fri Jul 1 14:17:03 2011 -0400
537
538 output the best constrained genotypes in trio
539
540 commit 18c87295e12f5bebafdcae00d52000fb94c8a566
541 Author: Heng Li <lh3@live.co.uk>
542 Date: Fri Jul 1 11:18:14 2011 -0400
543
544 added documentations for view -T
545
546 commit daf7a8d96bd495296bf7c7d99cddb808a3ced7d5
547 Author: Heng Li <lh3@live.co.uk>
548 Date: Thu Jun 30 22:45:20 2011 -0400
549
550 fixed a bug in writing SP
551
552 commit e5c32bf9b28c6e3e861db88de56b5dbe11058b61
553 Author: Heng Li <lh3@live.co.uk>
554 Date: Thu Jun 30 22:35:25 2011 -0400
555
556 optionally output read positions in mpileup
557
558 commit 1008051155ec994c1901e18f3eb03ea32a62e5d7
559 Author: Heng Li <lh3@live.co.uk>
560 Date: Thu Jun 30 22:17:25 2011 -0400
561
562 make faidx works with <2GB lines
563
564 commit 2daebb63762425dd3074ddf71582ad189001e394
565 Author: Heng Li <lh3@live.co.uk>
566 Date: Thu Jun 30 17:28:58 2011 -0400
567
568 fixed an issue in the trio caller and the indel caller
569
570 commit 9fdd52cf0716fb342a94946433d564b28b230835
571 Author: Heng Li <lh3@live.co.uk>
572 Date: Thu Jun 30 13:34:01 2011 -0400
573
574 Added trio caller; NOT tested yet
575
576 commit ea22a8ed83625e9c82382b56acc42a2d9cfd17e5
577 Author: Heng Li <lh3@live.co.uk>
578 Date: Thu Jun 30 11:42:29 2011 -0400
579
580 convert PL to 10-likelihood GL
581
582 commit 10d7065267b0d12c2bfcb6c70204fb6944cd395d
583 Author: Heng Li <lh3@live.co.uk>
584 Date: Thu Jun 30 10:49:05 2011 -0400
585
586 fix a compatibility issue with the new bcftools
587
588 commit d340f01f609c61b719d38a6a55629a3fc899e1cd
589 Author: Heng Li <lh3@live.co.uk>
590 Date: Sun Jun 26 23:41:20 2011 -0400
591
592 allow to ignore RG
593
594 commit d6321faf98ebfe899b9409fb23c90a4aa8c6b542
595 Author: Heng Li <lh3@live.co.uk>
596 Date: Sun Jun 5 23:05:21 2011 -0400
597
598 fixed a bug in SO checking due to a recent change
599
600 commit bc995abf666d0c9ab4258f6c1b3518a45a89209f
601 Author: Heng Li <lh3@live.co.uk>
602 Date: Fri Jun 3 14:45:36 2011 -0400
603
604 update the version number
605
606 commit 9e7cd83a08383858d008e0ccb2238a2b93831d6c
607 Author: Heng Li <lh3@live.co.uk>
608 Date: Fri Jun 3 14:43:12 2011 -0400
609
610 smarter way to parse a region string
611
612 commit e58a90a0fde54053dac65352b34c13c3fea815fc
613 Author: Heng Li <lh3@live.co.uk>
614 Date: Wed Jun 1 14:36:22 2011 -0400
615
616 output LRT2 instead of LRT1
617
618 commit 08f78c9af3e5661f04f80bef424232de721dba03
619 Author: Heng Li <lh3@live.co.uk>
620 Date: Wed Jun 1 14:02:28 2011 -0400
621
622 genotype test, but assuming 1-degree
623
624 commit 587b852340d7e60f6f7cf474a92ef77aeab46018
625 Author: Heng Li <lh3@live.co.uk>
626 Date: Wed Jun 1 12:55:19 2011 -0400
627
628 perform 2-degree test by default
629
630 commit 3d38e403c5c830478b7eb157a484776997440501
631 Author: Heng Li <lh3@live.co.uk>
632 Date: Wed Jun 1 12:44:34 2011 -0400
633
634 fixed a typo; but the result is still not good
635
636 commit 06291624f7dcc57445676f3be25d0bc355dd7110
637 Author: Heng Li <lh3@live.co.uk>
638 Date: Wed Jun 1 12:24:18 2011 -0400
639
640 fixed a typo
641
642 commit 63b98aa33636b0d82a435bf49153c8c1502e7d42
643 Author: Heng Li <lh3@live.co.uk>
644 Date: Wed Jun 1 12:23:37 2011 -0400
645
646 added HWE+F<0 filter
647
648 commit 37d926e8999999b593d0637ab7dc379dbd3d6006
649 Author: Heng Li <lh3@live.co.uk>
650 Date: Wed May 4 10:11:59 2011 -0400
651
652 improved sorting order checking in index
653
654 Patches from Jonathan Manning
655
656 commit 1c2dc6762c5f7cd946046b53346513f2f9761dbf
657 Author: Heng Li <lh3@live.co.uk>
658 Date: Tue May 3 23:09:05 2011 -0400
659
660 added r^2 estimate; added Brent's method
661
662 commit c2d3bcd8f98e31668b5f1321222fbc6fd6336e75
663 Author: Heng Li <lh3@live.co.uk>
664 Date: Sun May 1 23:45:23 2011 -0400
665
666 combine several utilites into vcfutils.lua
667
668 commit be2e7362d7593ea4d03fb33cdb6af2aa096ca6c4
669 Author: Heng Li <lh3@live.co.uk>
670 Date: Wed Apr 27 21:09:22 2011 -0400
671
672 minor warning
673
674 commit 683ef0443860813d743cf84fa86dda9bfaf5445a
675 Author: Heng Li <lh3@live.co.uk>
676 Date: Wed Apr 27 10:10:38 2011 -0400
677
678 added versioning
679
680 commit ed72f25ec85671f7646dbc92fa7b5b1dda427f7d
681 Author: Heng Li <lh3@live.co.uk>
682 Date: Wed Apr 27 10:04:02 2011 -0400
683
684 Output ML allele count
685
686 commit 2a9e36d2d6c405b2411ca47458f028ada8fe1000
687 Author: Heng Li <lh3@live.co.uk>
688 Date: Tue Apr 26 16:14:20 2011 -0400
689
690 use ar -s
691
692 commit 7a4f54e6dbcd7c94acbb3f1050a93f94b8a07949
693 Author: Heng Li <lh3@live.co.uk>
694 Date: Sat Apr 23 01:22:31 2011 -0400
695
696 added another type of LRT
697
698 commit b9c5e84762a4aacce3a3771b51ea80967c79a2e5
699 Author: Heng Li <lh3@live.co.uk>
700 Date: Fri Apr 22 16:00:31 2011 -0400
701
702 added version
703
704 commit 8fad6677c5952efd67391581d64e67e02e7f6e68
705 Author: Heng Li <lh3@live.co.uk>
706 Date: Fri Apr 22 00:30:19 2011 -0400
707
708 remove the pileup command
709
710 commit 3a962fb6ebf779de70f9e6effb2d8701a9aa3dd9
711 Author: Heng Li <lh3@live.co.uk>
712 Date: Thu Apr 21 23:10:45 2011 -0400
713
714 Release 0.1.16 (r963:234)
715
716 commit b4d683cffbd98c43f05aff8610b37d63dd7e54aa
717 Author: Heng Li <lh3@live.co.uk>
718 Date: Thu Apr 21 12:44:44 2011 -0400
719
720 fixed a bug when coordinate-less reads are on the reverse strand
721
722 commit c5ec45a128f409debc6a56a798024f53004037dc
723 Author: Heng Li <lh3@live.co.uk>
724 Date: Wed Apr 20 11:36:52 2011 -0400
725
726 added option '-f' to merge to avoid overwritting
727
728 commit 68d431531370d24907c01a27f166f2341d7c4d35
729 Author: Heng Li <lh3@live.co.uk>
730 Date: Wed Apr 20 10:26:58 2011 -0400
731
732 do not print a warning
733
734 commit 32922607e51ad2260c337eb022b9e4aedacb049f
735 Author: Heng Li <lh3@live.co.uk>
736 Date: Wed Apr 20 10:21:06 2011 -0400
737
738 Added ldpair to compute LD between requested pairs
739
740 commit b8d6fa71b91678fa02338257e0707d1e5ca098dd
741 Author: Heng Li <lh3@live.co.uk>
742 Date: Sun Apr 17 21:51:43 2011 -0400
743
744 On a toy sample, type "B" seems to be accepted
745
746 commit 0e7ee9a6bb4029184202aa6e6738105ba0c0510b
747 Author: Heng Li <lh3@live.co.uk>
748 Date: Sun Apr 17 21:21:20 2011 -0400
749
750 added type "B"; not tested yet
751
752 commit a513dfad0ac0062b03871eb6ecf26cb8d18dc895
753 Author: Heng Li <lh3@live.co.uk>
754 Date: Sun Apr 17 19:25:54 2011 -0400
755
756 fixed a bug in bedidx.c: input BED not sorted
757
758 commit de1e192bb0a8a762a54a6eee81d882fab01c3d32
759 Author: Heng Li <lh3@live.co.uk>
760 Date: Sun Apr 17 18:51:08 2011 -0400
761
762 by default, always perform posterior chi^2
763
764 commit df6e0d1099895fc6cd7a19dc89fba95ed6654d35
765 Author: Heng Li <lh3@live.co.uk>
766 Date: Sat Apr 16 12:33:28 2011 -0400
767
768 added debugging
769
770 commit 8ce52e024dc2ef361dbd5399c232163055057e70
771 Author: Heng Li <lh3@live.co.uk>
772 Date: Sat Apr 16 00:59:05 2011 -0400
773
774 avoid a segfault given wrong input
775
776 commit e66b6684fc9a397f91ec29fdeecae9f8eb986a55
777 Author: Heng Li <lh3@live.co.uk>
778 Date: Fri Apr 15 19:55:39 2011 -0400
779
780 do not segfault when there is no PL
781
782 commit 9ce3c584ec0cebfa45576f2ef538df4dad2b7e55
783 Author: Heng Li <lh3@live.co.uk>
784 Date: Fri Apr 15 11:59:55 2011 -0400
785
786 remove another unused part
787
788 commit f53a051d68bf312ac8d5865210fae7a9808c0fb9
789 Author: Heng Li <lh3@live.co.uk>
790 Date: Fri Apr 15 10:41:25 2011 -0400
791
792 print G3 if HWE is small
793
794 commit 4b2c08bb86ca4ed4959e4cb77a28f7d6fc19f5c9
795 Author: Heng Li <lh3@live.co.uk>
796 Date: Fri Apr 15 10:04:34 2011 -0400
797
798 fixed a bug
799
800 actually not fix, but hide it
801
802 commit 088e13c32453fb533b7bb1c65a573f9b90a23625
803 Author: Heng Li <lh3@live.co.uk>
804 Date: Fri Apr 15 09:48:47 2011 -0400
805
806 added LRT based permutation; not used though
807
808 commit 1e3c2001afcb80b5eaa4c3f88df9da7b01b62524
809 Author: Heng Li <lh3@live.co.uk>
810 Date: Fri Apr 15 09:28:55 2011 -0400
811
812 Perform posterior contrast for small LRT
813
814 Posterior contrast is much slower than LRT. Nonetheless, posterior P-value is
815 more robust to sequencing artifacts. Thus we may combine the two to achieve a
816 balance between speed and low FPR.
817
818 commit 6f1b066270902198a7175ff6c1b05ebc8d1919be
819 Author: Heng Li <lh3@live.co.uk>
820 Date: Fri Apr 15 01:36:06 2011 -0400
821
822 Added Brent's method
823
824 commit 3d061e5db25b67b25f6ff87afe4162e121354232
825 Author: Heng Li <lh3@live.co.uk>
826 Date: Thu Apr 14 23:30:10 2011 -0400
827
828 fixed a typo in printing
829
830 commit 7fd14ceb5990bb350b8e97346ef3537d80058def
831 Author: Heng Li <lh3@live.co.uk>
832 Date: Thu Apr 14 23:14:23 2011 -0400
833
834 fixed a stupid bug
835
836 commit f5b2c3459ec098b3cafd9619b9077132516baf58
837 Author: Heng Li <lh3@live.co.uk>
838 Date: Thu Apr 14 22:42:35 2011 -0400
839
840 separate EM and posterior
841
842 Now, constrast is not performed unless -C is in use. EM can be invoked
843 independently with -e without computing the posterior.
844
845 commit 9eefcac963697fae554789b11ae3cb2c23f224d0
846 Author: Heng Li <lh3@live.co.uk>
847 Date: Thu Apr 14 22:00:19 2011 -0400
848
849 further code cleanup; prepare to add EM interface
850
851 commit c2cce52355262743711e4742b0c8542bfcab1cdd
852 Author: Heng Li <lh3@live.co.uk>
853 Date: Thu Apr 14 21:44:03 2011 -0400
854
855 drop EM from prob1
856
857 commit 24016f04bd3bdffb7eeb50cb25854f5007feb70f
858 Author: Heng Li <lh3@live.co.uk>
859 Date: Thu Apr 14 21:08:33 2011 -0400
860
861 drop posterior LRT; prepare for clean up
862
863 commit 3670d8bd88c3eb22873f0a80e2a5913f64ca8c9a
864 Author: Heng Li <lh3@live.co.uk>
865 Date: Thu Apr 14 20:57:43 2011 -0400
866
867 better initial values for LD
868
869 commit d48a8873c060b18b57799cfe3a0e5496ba069457
870 Author: Heng Li <lh3@live.co.uk>
871 Date: Thu Apr 14 20:36:25 2011 -0400
872
873 finished EM
874
875 commit b101f2db476188a950c23f5c1b6185fdb7f8f40b
876 Author: Heng Li <lh3@live.co.uk>
877 Date: Wed Apr 13 01:19:04 2011 -0400
878
879 genotype frequency estimate
880
881 commit d79bdcbf6242ecfb8accba9ac9a22fbcbd543cf2
882 Author: Heng Li <lh3@live.co.uk>
883 Date: Wed Apr 13 00:37:22 2011 -0400
884
885 prepare for code clean up
886
887 commit e0ce416abfc094f0c090957080b1404fd0edf752
888 Author: Heng Li <lh3@live.co.uk>
889 Date: Wed Apr 13 00:34:15 2011 -0400
890
891 rename ld.c to em.c
892
893 commit 45ede3ad181f35c1be24bed5d75841e472357ab7
894 Author: Heng Li <lh3@live.co.uk>
895 Date: Wed Apr 13 00:22:10 2011 -0400
896
897 implemeted EM likelihood ratio test
898
899 The idea is learned from a brief chat with Rasmus Nielsen.
900
901 commit 0454a346b60e42b75a2f742272089810279c7131
902 Author: Heng Li <lh3@live.co.uk>
903 Date: Tue Apr 12 15:45:52 2011 -0400
904
905 added likelihood-ratio test (idea from Nick)
906
907 commit f6287c8646c690440a1554c8958e7268f4134dc2
908 Author: Heng Li <lh3@live.co.uk>
909 Date: Sun Apr 10 18:24:37 2011 -0400
910
911 Release samtools-0.1.15 (r949:203)
912
913 commit de6023f38f4d652438557cf7a0ac6eec324e7416
914 Author: Heng Li <lh3@live.co.uk>
915 Date: Sun Apr 10 15:54:58 2011 -0400
916
917 improved help information
918
919 commit d3b337f2b7eda1e6f8f5575a19d1b5ed55cae279
920 Author: Heng Li <lh3@live.co.uk>
921 Date: Sat Apr 9 16:28:01 2011 -0400
922
923 fixed a minor issue
924
925 commit 82f6e4f49247e75fbd8ec08c285b8d3047b3d235
926 Author: Heng Li <lh3@live.co.uk>
927 Date: Sat Apr 9 15:49:04 2011 -0400
928
929 separate QC-pass and QC-fail reads
930
931 commit 8362b4a255081ee7ca0a4ca2eabc8c76758b6863
932 Author: Heng Li <lh3@live.co.uk>
933 Date: Fri Apr 8 17:45:19 2011 -0400
934
935 added verbose level
936
937 commit f7bf419c290462be7d289249a4a6d28f825b4c93
938 Author: Heng Li <lh3@live.co.uk>
939 Date: Fri Apr 8 16:08:14 2011 -0400
940
941 fixed a bug
942
943 commit 890cbb1ac93b3004fb6cf42ff47195077dcfc8ad
944 Author: Heng Li <lh3@live.co.uk>
945 Date: Fri Apr 8 16:00:37 2011 -0400
946
947 drop unrelated @RG when "-R" is in use
948
949 commit a62dc929c950fb51311b705f5b5bfba8e3f704d7
950 Author: Heng Li <lh3@live.co.uk>
951 Date: Fri Apr 8 16:00:14 2011 -0400
952
953 skip header validation
954
955 commit 39da810e2c56c8f0eff1ab726600b41f26d3d8e9
956 Author: Heng Li <lh3@live.co.uk>
957 Date: Tue Apr 5 23:52:22 2011 -0400
958
959 change error message
960
961 commit c0c50a34df250ef8a7a29b172058cd229be582b5
962 Author: Heng Li <lh3@live.co.uk>
963 Date: Tue Apr 5 23:50:46 2011 -0400
964
965 fixed a bug caused by recent modifications
966
967 commit 25226e8c468404cb5e1b5272efcea57e4193c762
968 Author: Heng Li <lh3@live.co.uk>
969 Date: Tue Apr 5 13:31:19 2011 -0400
970
971 reduce the indel filtering window
972
973 commit 5e18d7014437734f9dac9ab45a95e43ec2526101
974 Author: Heng Li <lh3@live.co.uk>
975 Date: Mon Apr 4 13:56:20 2011 -0400
976
977 only output hwe if it is small enough
978
979 commit 614941fb7dd276de662e7820eb8c7bae871a18cc
980 Author: Heng Li <lh3@live.co.uk>
981 Date: Mon Apr 4 13:34:02 2011 -0400
982
983 added HWE back
984
985 commit 7abe8825aa0bacccdeb38125934ae94d18f0ad4d
986 Author: Heng Li <lh3@live.co.uk>
987 Date: Mon Apr 4 12:46:24 2011 -0400
988
989 EM estimate of genotype frequency
990
991 commit 2bfeff9c645d177416664f1cb811e85cac3ff9e3
992 Author: Heng Li <lh3@live.co.uk>
993 Date: Mon Apr 4 11:29:12 2011 -0400
994
995 minor
996
997 commit 401e40647e7e3abbac6e4ec3d8bb68eb6f2d401b
998 Author: Heng Li <lh3@live.co.uk>
999 Date: Mon Apr 4 11:24:04 2011 -0400
1000
1001 Added genotype freq estimate and association test
1002
1003 commit 6cc226df6e3b480f1bd6e763ce8ef47f785bbb74
1004 Author: Heng Li <lh3@live.co.uk>
1005 Date: Sun Apr 3 20:57:23 2011 -0400
1006
1007 minor changes
1008
1009 commit 7e47a39630e812f09b80369f14606245976f687e
1010 Author: Heng Li <lh3@live.co.uk>
1011 Date: Fri Apr 1 15:21:59 2011 -0400
1012
1013 print the grayscale
1014
1015 commit 2f675d9c0dde3c166c99e335fa17c7873a5ae8d5
1016 Author: Heng Li <lh3@live.co.uk>
1017 Date: Fri Apr 1 08:55:16 2011 -0400
1018
1019 change to comment
1020
1021 commit 0592bb514994544ed84f51e509b233cf8821e0cf
1022 Author: Heng Li <lh3@live.co.uk>
1023 Date: Fri Apr 1 08:54:35 2011 -0400
1024
1025 added base quality filtering
1026
1027 commit fc1b47e04a7b94f6362c45856cbeb89d9d0b5ca5
1028 Author: Heng Li <lh3@live.co.uk>
1029 Date: Thu Mar 31 23:31:14 2011 -0400
1030
1031 fixed a few typos in comments
1032
1033 commit 60be79bc8f0d24656e5e8a329af7e9b5b91d4c8b
1034 Author: Heng Li <lh3@live.co.uk>
1035 Date: Thu Mar 31 23:13:23 2011 -0400
1036
1037 comments
1038
1039 commit 2432864acc25ebe5cee4217dbb0120439077a7f8
1040 Author: Heng Li <lh3@live.co.uk>
1041 Date: Thu Mar 31 22:42:46 2011 -0400
1042
1043 added bam2depth.c, a demo program
1044
1045 commit 39625f7c6bea9ccbfd9af0feb22348d52079f012
1046 Author: Heng Li <lh3@live.co.uk>
1047 Date: Thu Mar 31 16:37:22 2011 -0400
1048
1049 added bgzf_check_bgzf() (used by tabix)
1050
1051 commit 6de6bd3fb67fd22753a5f07d4cc25bf94e1b5a8c
1052 Author: Heng Li <lh3@live.co.uk>
1053 Date: Thu Mar 31 16:37:08 2011 -0400
1054
1055 fixed a bug in bedidx.c
1056
1057 commit 3b9e257d25b2e81eed1625bc5d2882ed486ef20e
1058 Author: Heng Li <lh3@live.co.uk>
1059 Date: Wed Mar 30 13:27:15 2011 -0400
1060
1061 added bed support to bcftools
1062
1063 commit 47bcce3d14ec4d205283b61e5e653803996c42e0
1064 Author: Heng Li <lh3@live.co.uk>
1065 Date: Wed Mar 30 12:56:40 2011 -0400
1066
1067 Added BED support to "samtools view"
1068
1069 commit a812386017faedfc86c0e6562adbb2138329cfeb
1070 Author: Heng Li <lh3@live.co.uk>
1071 Date: Wed Mar 30 12:47:04 2011 -0400
1072
1073 support BED file
1074
1075 commit 3052dddc929f1825e6e7f7f6f6724d9465d6cf9a
1076 Author: Heng Li <lh3@live.co.uk>
1077 Date: Mon Mar 28 15:51:55 2011 -0400
1078
1079 relax RG matching; proper mismatching message
1080
1081 commit f86d60c8fe25785523f01fae1486d2a6df4ee6ef
1082 Author: Heng Li <lh3@live.co.uk>
1083 Date: Sat Mar 26 10:38:23 2011 -0400
1084
1085 Avoid reporting association when something unexpected, which I do not understand, happens.
1086
1087 commit dd41e6b26fd9fe30218748b9a0a1f49bdb1862b9
1088 Author: Heng Li <lh3@live.co.uk>
1089 Date: Sat Mar 26 10:38:01 2011 -0400
1090
1091 Added -1 to merge
1092
1093 commit 4a0364b0d7f87f1c88d71ec5857a1f1d40710681
1094 Author: Heng Li <lh3@live.co.uk>
1095 Date: Wed Mar 23 16:56:55 2011 -0400
1096
1097 plot pairwise r^2
1098
1099 commit 452629a711582e612bec22b3b082e234bd37039b
1100 Author: Heng Li <lh3@live.co.uk>
1101 Date: Wed Mar 23 14:31:01 2011 -0400
1102
1103 pairwise LD; case-control AF2
1104
1105 commit 52862951adcaecde26ba8f0d9c1897944640a674
1106 Author: Heng Li <lh3@live.co.uk>
1107 Date: Mon Mar 21 23:03:14 2011 -0400
1108
1109 Release samtools-0.1.14 (r933:170)
1110
1111 commit 59a5a8ba8e2940f0e38238f9339f02c91a8a0ce4
1112 Author: Heng Li <lh3@live.co.uk>
1113 Date: Mon Mar 21 13:52:55 2011 -0400
1114
1115 optionally skip loci with too low sample coverage
1116
1117 commit 6434264b5c69514d4fafe62cbd30b3bbaddc1d41
1118 Author: Heng Li <lh3@live.co.uk>
1119 Date: Sat Mar 19 14:38:25 2011 -0400
1120
1121 mpileup support Illumina1.3+ quality; skip non-variant sites when "view -v" is in use
1122
1123 commit 5f59e01987e1d5eca7d6359cae64a9734b18beea
1124 Author: Heng Li <lh3@live.co.uk>
1125 Date: Fri Mar 18 17:19:18 2011 -0400
1126
1127 update version to r933:167
1128
1129 commit 4d2c3c950910aa3d2c87760c3532e458fe01c0fa
1130 Author: Heng Li <lh3@live.co.uk>
1131 Date: Fri Mar 18 16:25:01 2011 -0400
1132
1133 added "-1" to the command-line help
1134
1135 commit 55313a015a7bd6369cf5a66fed7fab2333201dc9
1136 Author: Heng Li <lh3@live.co.uk>
1137 Date: Fri Mar 18 16:22:12 2011 -0400
1138
1139 added the "cat" command (by Chris Saunders)
1140
1141 commit b670272cadf3efa4dc456ac4c76104f73477d60d
1142 Author: Heng Li <lh3@live.co.uk>
1143 Date: Fri Mar 18 15:59:46 2011 -0400
1144
1145 support varying the compression level
1146
1147 commit c5dd3c9ca5f75f880e52c8cd2beae983bcb8d3b1
1148 Author: Heng Li <lh3@live.co.uk>
1149 Date: Wed Mar 16 14:33:45 2011 -0400
1150
1151 update the manual pages
1152
1153 commit 12fb4b596dc51bccd154fc4bd0593442f7937a46
1154 Author: Heng Li <lh3@live.co.uk>
1155 Date: Wed Mar 16 12:49:26 2011 -0400
1156
1157 update changelog
1158
1159 commit e7fe4fd66e02d60a1ca7952ad1938809e77729a9
1160 Author: Heng Li <lh3@live.co.uk>
1161 Date: Wed Mar 16 12:10:05 2011 -0400
1162
1163 do not call indels when the depth is very high
1164
1165 commit 7455eeaa32b949bb3856f75810890aabf7cacb18
1166 Author: Heng Li <lh3@live.co.uk>
1167 Date: Wed Mar 16 11:56:56 2011 -0400
1168
1169 code clean up
1170
1171 commit 5f16679e54ced8e67a75d949f9175c50480b914e
1172 Author: Heng Li <lh3@live.co.uk>
1173 Date: Tue Mar 15 14:45:24 2011 -0400
1174
1175 when -s is specified, change the sample order
1176
1177 commit 7ba95adee09d3b06a7eaf797d25efef837e592f5
1178 Author: Heng Li <lh3@live.co.uk>
1179 Date: Tue Mar 15 14:11:42 2011 -0400
1180
1181 compute the rank in permutation
1182
1183 commit d219783cea7643fc7e10e1bd3a98e9b3165b4506
1184 Author: Heng Li <lh3@live.co.uk>
1185 Date: Sun Mar 13 21:35:13 2011 -0400
1186
1187 I have found a SERIOUS BUG!!!
1188
1189 commit 8e20d04ecdac1a7788eef71c4bb91b8479cf7150
1190 Author: Heng Li <lh3@live.co.uk>
1191 Date: Sun Mar 13 17:04:04 2011 -0400
1192
1193 optionally shuffle samples in a BCF (debugging)
1194
1195 commit fc7b261f181f2a411427bc9ee5d586c883ca9cdc
1196 Author: Heng Li <lh3@live.co.uk>
1197 Date: Fri Mar 11 09:34:20 2011 -0500
1198
1199 fixed a bug
1200
1201 commit b3bbcc3d40994ae85705ab6fef9866ec8c142201
1202 Author: Heng Li <lh3@live.co.uk>
1203 Date: Thu Mar 10 20:25:59 2011 -0500
1204
1205 use mode instead of mean
1206
1207 commit f1161262d137098a19143b5cb0de810e5db3243e
1208 Author: Heng Li <lh3@live.co.uk>
1209 Date: Thu Mar 10 20:09:16 2011 -0500
1210
1211 start from the mean instead of the mode
1212
1213 commit 2ba56f5e99e90674855c4ffc8bf583340b932e1e
1214 Author: Heng Li <lh3@live.co.uk>
1215 Date: Thu Mar 10 17:13:34 2011 -0500
1216
1217 fixed an error in Chi^2 test
1218
1219 commit b4ce7ae400290bc43dd287240479667f99b3b11e
1220 Author: Heng Li <lh3@live.co.uk>
1221 Date: Thu Mar 10 00:23:39 2011 -0500
1222
1223 minor
1224
1225 commit 8487fa5d3a73a43443964e731ea2a4c873c9d4e5
1226 Author: Heng Li <lh3@live.co.uk>
1227 Date: Wed Mar 9 21:33:19 2011 -0500
1228
1229 added -F to accept BCFs generated by old samtools
1230
1231 commit fd51d2093f7fd775a7eaaeea57fa34716ab59ac2
1232 Author: Heng Li <lh3@live.co.uk>
1233 Date: Wed Mar 9 17:39:09 2011 -0500
1234
1235 update version
1236
1237 commit b6da54335df943015a998a934075331b467abb5b
1238 Author: Heng Li <lh3@live.co.uk>
1239 Date: Wed Mar 9 17:37:14 2011 -0500
1240
1241 compute pseudo-chi2 probability
1242
1243 commit 9f73cefdb8935421d872b989dd98fbc8e1295029
1244 Author: Heng Li <lh3@live.co.uk>
1245 Date: Wed Mar 9 15:54:04 2011 -0500
1246
1247 remove a comment which is wrong
1248
1249 commit b10b1e47ece522e97ab8ef23417bcb6454f8b9db
1250 Author: Heng Li <lh3@live.co.uk>
1251 Date: Wed Mar 9 15:51:12 2011 -0500
1252
1253 clean up
1254
1255 commit 353bfae2c6ff59205bd9223db04084cf7f507f01
1256 Author: Heng Li <lh3@live.co.uk>
1257 Date: Wed Mar 9 15:45:29 2011 -0500
1258
1259 for backup
1260
1261 commit 53915d1c6410c2537d18bfa8eb8c657a2233c35e
1262 Author: Heng Li <lh3@live.co.uk>
1263 Date: Wed Mar 9 15:27:56 2011 -0500
1264
1265 having debugging code
1266
1267 commit 0d0dbf66995b1511390d593981eae7b5d36fe17b
1268 Author: Heng Li <lh3@live.co.uk>
1269 Date: Wed Mar 9 14:58:23 2011 -0500
1270
1271 temporary backup
1272
1273 commit 5b74a174a8b637dee43b7f30250df6fb96580e12
1274 Author: Heng Li <lh3@live.co.uk>
1275 Date: Tue Mar 8 15:46:11 2011 -0500
1276
1277 the output makes sense, but there may be a typo...
1278
1279 commit d81ec654b6c0c1eef6b0625d96f14b3155cee7c6
1280 Author: Heng Li <lh3@live.co.uk>
1281 Date: Tue Mar 8 15:19:09 2011 -0500
1282
1283 added contrast2(); fixed a bug in haploid mode
1284
1285 commit 0cfd896fad5f7737cca49efa94a11892dafcd812
1286 Author: Heng Li <lh3@live.co.uk>
1287 Date: Mon Mar 7 21:40:17 2011 -0500
1288
1289 fixed a bug in haploid genotyping
1290
1291 commit ccd52155ef61273f2b42ad9c7b31ff1915f81b24
1292 Author: Heng Li <lh3@live.co.uk>
1293 Date: Sat Mar 5 18:10:35 2011 -0500
1294
1295 fixed a few bugs; still not fully working
1296
1297 commit edc3af753f96f831968ae32f2e0f915b74f31e6e
1298 Author: Heng Li <lh3@live.co.uk>
1299 Date: Fri Mar 4 17:31:33 2011 -0500
1300
1301 drop HWE calculation
1302
1303 commit 92dac194debb66ca0718c21c871822dda2dd5bc1
1304 Author: Heng Li <lh3@live.co.uk>
1305 Date: Fri Mar 4 17:28:35 2011 -0500
1306
1307 implemented hap/dipoind mode; probably BUGGY!
1308
1309 commit 7f26804bc27937e36fdc967e5c76514653ea40f5
1310 Author: Heng Li <lh3@live.co.uk>
1311 Date: Fri Mar 4 16:01:27 2011 -0500
1312
1313 read ploidy
1314
1315 commit e7b7213475b5e61a69aab77ffb02b4983c8e7678
1316 Author: Heng Li <lh3@live.co.uk>
1317 Date: Fri Mar 4 14:12:14 2011 -0500
1318
1319 added math notes
1320
1321 commit 46023e2f21321da83fc8e83e9229757a4e821acb
1322 Author: Heng Li <lh3@live.co.uk>
1323 Date: Fri Mar 4 13:34:10 2011 -0500
1324
1325 update BCF spec
1326
1327 commit 13190c49eeb006ad7013b7f1e9fc1b3beca3ae78
1328 Author: Heng Li <lh3@live.co.uk>
1329 Date: Tue Mar 1 14:45:19 2011 -0500
1330
1331 Release samtools-0.1.13 (r926:134)
1332
1333 commit be8fabbb6001d9fd5263a70a3e21ed6dfe5a9837
1334 Author: Heng Li <lh3@live.co.uk>
1335 Date: Tue Mar 1 14:07:15 2011 -0500
1336
1337 prepare to finalize 0.1.13
1338
1339 commit 1e8c753660978bed7e9289fe50becd596d9314bb
1340 Author: Heng Li <lh3@live.co.uk>
1341 Date: Tue Mar 1 09:40:17 2011 -0500
1342
1343 allow to change whether to drop ambiguous reads
1344
1345 commit 412210bfdb46606023f2e4b9086f2787f0cf1c62
1346 Author: Heng Li <lh3@live.co.uk>
1347 Date: Mon Feb 28 22:01:29 2011 -0500
1348
1349 revert to the old behavior of phase
1350
1351 commit 46035589518cf84738de8666b866e2619457c1fb
1352 Author: Heng Li <lh3@live.co.uk>
1353 Date: Mon Feb 28 16:46:23 2011 -0500
1354
1355 change version number
1356
1357 commit 7f40c33e37fc16fcb0a375ce46ae1d09cafb6d50
1358 Author: Heng Li <lh3@live.co.uk>
1359 Date: Mon Feb 28 16:37:42 2011 -0500
1360
1361 bugfix in indel calling: interger overflow
1362
1363 commit 75849470efbe30042e5ddd516f9bcbe3b9bf6062
1364 Author: Heng Li <lh3@live.co.uk>
1365 Date: Mon Feb 28 15:35:47 2011 -0500
1366
1367 fixed a typo
1368
1369 commit 9e6fb569885f906fabaab7fc2f02eae82f4bd602
1370 Author: Heng Li <lh3@live.co.uk>
1371 Date: Mon Feb 28 15:34:09 2011 -0500
1372
1373 minor changes to heuristic rules
1374
1375 commit 30a799a91f5e2c10b761aa5437f902c6649fceb3
1376 Author: Heng Li <lh3@live.co.uk>
1377 Date: Mon Feb 28 15:20:26 2011 -0500
1378
1379 fixed a bug in the latest change
1380
1381 commit e21ba9df950ea37f5c1b35c2af9ba9a4e0bba02a
1382 Author: Heng Li <lh3@live.co.uk>
1383 Date: Mon Feb 28 12:47:06 2011 -0500
1384
1385 put version in bam.h
1386
1387 commit 918b14780c1dceb39c7010638ecd61c626e17166
1388 Author: Heng Li <lh3@live.co.uk>
1389 Date: Mon Feb 28 12:00:38 2011 -0500
1390
1391 frag_t::phased==0 reads are dumped to chimera.bam
1392
1393 commit 657293c7bdba3ac69f53cd1ffa2874ed8756475e
1394 Author: Heng Li <lh3@live.co.uk>
1395 Date: Mon Feb 28 11:05:29 2011 -0500
1396
1397 change default -q to 37 (previously 40)
1398
1399 commit 33d8d3bea76e466798ea322d68d34deb8d2dff06
1400 Author: Heng Li <lh3@live.co.uk>
1401 Date: Mon Feb 28 10:39:57 2011 -0500
1402
1403 fixed a minor bug in BAM reading
1404
1405 commit daa25d426d42465d76c7317c95772bbb36bb3f47
1406 Author: Heng Li <lh3@live.co.uk>
1407 Date: Sat Feb 26 21:07:24 2011 -0500
1408
1409 suppress gzopen64() warning
1410
1411 commit 9cec4256eb9e7848d4711adb67b540659c141e32
1412 Author: Heng Li <lh3@live.co.uk>
1413 Date: Fri Feb 25 22:14:52 2011 -0500
1414
1415 fixed a long existing bug in vcf2fq
1416
1417 commit 304487c83067a733add71cbc3886fa8c49f7ef2a
1418 Author: Heng Li <lh3@live.co.uk>
1419 Date: Fri Feb 25 16:37:40 2011 -0500
1420
1421 change version number
1422
1423 commit 10ba6bf4f16692760f696f7b17f3719065786f77
1424 Author: Heng Li <lh3@live.co.uk>
1425 Date: Fri Feb 25 16:34:08 2011 -0500
1426
1427 Change the order of PL; change SP to int32_t
1428
1429 commit c5cc2a8036a9c3579fbfde651efec4f6763b0228
1430 Author: Heng Li <lh3@live.co.uk>
1431 Date: Fri Feb 25 14:52:03 2011 -0500
1432
1433 claim X defined in the header
1434
1435 commit 4ee8cb29f6092fd14a89f0cc5d3575112a204f39
1436 Author: Heng Li <lh3@live.co.uk>
1437 Date: Fri Feb 25 14:40:24 2011 -0500
1438
1439 minor changes
1440
1441 commit 00065e9336a2831dc53bee7da2f4719845be1a2a
1442 Author: Heng Li <lh3@live.co.uk>
1443 Date: Fri Feb 25 11:39:06 2011 -0500
1444
1445 fixed an error in the BCF spec
1446
1447 commit 1e2a73afcb72a02aa448718cb017c0438de89f90
1448 Author: Heng Li <lh3@live.co.uk>
1449 Date: Fri Feb 25 11:36:40 2011 -0500
1450
1451 update BCF spec
1452
1453 commit dbf8eedaa38a405cb2fba5b3952b85776f51d035
1454 Author: Heng Li <lh3@live.co.uk>
1455 Date: Fri Feb 25 11:28:43 2011 -0500
1456
1457 update BCF spec
1458
1459 commit eed1d91af9fad3c9d965333a55e623757f9c4e9d
1460 Author: Heng Li <lh3@live.co.uk>
1461 Date: Fri Feb 25 09:51:39 2011 -0500
1462
1463 fixed a flaw in targetcut
1464
1465 commit 59bc980bb832b92a8b0cc244cf106e6150e4db6f
1466 Author: Heng Li <lh3@live.co.uk>
1467 Date: Fri Feb 25 00:54:35 2011 -0500
1468
1469 update manual page
1470
1471 commit fcc4738c4abdca79e3de159e21208df1b98ac76c
1472 Author: Heng Li <lh3@live.co.uk>
1473 Date: Fri Feb 25 00:45:39 2011 -0500
1474
1475 update version format
1476
1477 commit 5748639ae542b7f6b853562edc2bb3faf43030e4
1478 Author: Heng Li <lh3@live.co.uk>
1479 Date: Fri Feb 25 00:45:12 2011 -0500
1480
1481 update version number
1482
1483 commit 06b44cc366cf27ce8976ee6a05810a0b3c48b56d
1484 Author: Heng Li <lh3@live.co.uk>
1485 Date: Fri Feb 25 00:44:21 2011 -0500
1486
1487 update version number
1488
1489 commit ab7f4529d12739ff66fd4c09af9d992ab59c53ef
1490 Author: Heng Li <lh3@live.co.uk>
1491 Date: Fri Feb 25 00:42:55 2011 -0500
1492
1493 various help message
1494
1495 commit a092e1f6f963272f8bb23616986ddaf604fd0f82
1496 Author: Heng Li <lh3@live.co.uk>
1497 Date: Thu Feb 24 23:43:13 2011 -0500
1498
1499 disable unfinished functionality
1500
1501 commit f00a78db72b14ee4c6689fc13f20ed31aeaecd40
1502 Author: Heng Li <lh3@live.co.uk>
1503 Date: Thu Feb 24 10:04:56 2011 -0500
1504
1505 added "const" to bcf_p1_cal()
1506
1507 commit 91049c4a8db3bf50dcc9d07506f22fa4ca5b5a96
1508 Author: Heng Li <lh3@live.co.uk>
1509 Date: Wed Feb 23 11:53:47 2011 -0500
1510
1511 randomly allocate unphased reads
1512
1513 commit f4405354a8d4cb3441141fa734573031059d7f57
1514 Author: Heng Li <lh3@live.co.uk>
1515 Date: Tue Feb 22 15:36:07 2011 -0500
1516
1517 fixed a typo
1518
1519 commit 3075e4dc5c7c9d954426aabda6a73fa788357100
1520 Author: Heng Li <lh3@live.co.uk>
1521 Date: Tue Feb 22 15:33:40 2011 -0500
1522
1523 make output more informative
1524
1525 commit 628cf3235e2815a40acf089fb1d3357be6437787
1526 Author: Heng Li <lh3@live.co.uk>
1527 Date: Tue Feb 22 14:50:06 2011 -0500
1528
1529 change the scoring rule; change default k to 13
1530
1531 commit f22fd99831e4b5c74f898719216f359dbe987bbf
1532 Author: Heng Li <lh3@live.co.uk>
1533 Date: Tue Feb 22 14:45:15 2011 -0500
1534
1535 update scoring in masking
1536
1537 commit 2f23547b81984555032aa0eefd064b8e07986fdc
1538 Author: Heng Li <lh3@live.co.uk>
1539 Date: Tue Feb 22 14:37:17 2011 -0500
1540
1541 remove dropreg()
1542
1543 commit 4d8b6b1f1f331ca9041983c66e34a857c3b8f1bb
1544 Author: Heng Li <lh3@live.co.uk>
1545 Date: Tue Feb 22 13:10:16 2011 -0500
1546
1547 accept files from stdin
1548
1549 commit 9b50c5038e6fc0185e29ca5b50fe0806a9a939b9
1550 Author: Heng Li <lh3@live.co.uk>
1551 Date: Tue Feb 22 11:16:57 2011 -0500
1552
1553 fixed a bug in consensus generation
1554
1555 commit 1332ab32fb788fdc81b2ba8653b905d106238fad
1556 Author: Heng Li <lh3@live.co.uk>
1557 Date: Mon Feb 21 22:53:23 2011 -0500
1558
1559 print dropped fragments
1560
1561 commit a288761b4ca1584e51076a71cbc4d72fe923dda1
1562 Author: Heng Li <lh3@live.co.uk>
1563 Date: Mon Feb 21 22:37:04 2011 -0500
1564
1565 bugfix: singletons are not phased
1566
1567 commit 683365f534c0223dea7d72532015ac16a45ba22b
1568 Author: Heng Li <lh3@live.co.uk>
1569 Date: Mon Feb 21 17:27:10 2011 -0500
1570
1571 output singleton blocks
1572
1573 commit 841a4609084d81f1bc81e0b00dd806002461e7d9
1574 Author: Heng Li <lh3@live.co.uk>
1575 Date: Mon Feb 21 15:58:55 2011 -0500
1576
1577 fixed a bug; not working with -l right now
1578
1579 commit fdd57ea31732b5516dc212d72174b60206952636
1580 Author: Heng Li <lh3@live.co.uk>
1581 Date: Mon Feb 21 15:17:00 2011 -0500
1582
1583 skip mapQ==0 reads
1584
1585 commit 4eb6ba75c23c1c9be5f76814fa1b93a2e304b2af
1586 Author: Heng Li <lh3@live.co.uk>
1587 Date: Mon Feb 21 14:03:03 2011 -0500
1588
1589 print the "targetcut" command
1590
1591 commit 0123d9559ba58b026c0dfd15bc26019a193cd21a
1592 Author: Heng Li <lh3@live.co.uk>
1593 Date: Mon Feb 21 11:22:13 2011 -0500
1594
1595 allow to set the maximum depth
1596
1597 commit 0f92eb248a4d06645b2c3d736a0faea8a7a9f731
1598 Author: Heng Li <lh3@live.co.uk>
1599 Date: Mon Feb 21 09:56:41 2011 -0500
1600
1601 use a proper error model to call hets
1602
1603 commit 587a01504af5aea6288740d121dccf48fb8a75f4
1604 Author: Heng Li <lh3@live.co.uk>
1605 Date: Mon Feb 21 09:16:38 2011 -0500
1606
1607 phase is UNFINISHED; strip RG when merging
1608
1609 commit 723bf3cd79e4f4a558373d4c707fa6b3db0fb357
1610 Author: Heng Li <lh3@live.co.uk>
1611 Date: Sat Feb 19 23:38:11 2011 -0500
1612
1613 use a proper model to compute consensus
1614
1615 commit 891a6b02d4a9af2ed98fbaac4915bf1f0da4f6c8
1616 Author: Heng Li <lh3@live.co.uk>
1617 Date: Sat Feb 19 22:14:19 2011 -0500
1618
1619 added comment
1620
1621 commit 8b55e0a581ecc9e4ba754d1f3c8784f3038b6e48
1622 Author: Heng Li <lh3@live.co.uk>
1623 Date: Fri Feb 18 17:23:39 2011 -0500
1624
1625 change the output format
1626
1627 commit 75c36e8c563eddd0a362ba3b38cf0aea21aafb1f
1628 Author: Heng Li <lh3@live.co.uk>
1629 Date: Tue Feb 15 20:31:00 2011 -0500
1630
1631 fixed a bug in writing BAM
1632
1633 commit bb0ce52f066cfebaa35a125d57b353bb717a5165
1634 Author: Heng Li <lh3@live.co.uk>
1635 Date: Mon Feb 14 23:39:09 2011 -0500
1636
1637 skip uncovered; unknown alleles taken as X
1638
1639 commit ba67f4d119c7d06907db3015d337d9a01a3fc9fe
1640 Author: Heng Li <lh3@live.co.uk>
1641 Date: Mon Feb 14 23:21:19 2011 -0500
1642
1643 fixed a bug
1644
1645 commit e4448d49e6129a5e1ee9c7f04f43612f12d6aad6
1646 Author: Heng Li <lh3@live.co.uk>
1647 Date: Mon Feb 14 22:43:09 2011 -0500
1648
1649 prepare to read hets from a list; unfinished
1650
1651 commit 129ea29c1f12177c0a7c3e21676f6210370fc59b
1652 Author: Heng Li <lh3@live.co.uk>
1653 Date: Mon Feb 14 16:32:22 2011 -0500
1654
1655 updated khash.h to 0.2.5
1656
1657 commit 15b44ed93bd949dffcf79ac8dbea6d9b7dfcb58c
1658 Author: Heng Li <lh3@live.co.uk>
1659 Date: Mon Feb 14 16:15:04 2011 -0500
1660
1661 use the latest version of khash
1662
1663 commit 486c05f06f44d981dfb2069bcb43e4b35fd8389c
1664 Author: Heng Li <lh3@live.co.uk>
1665 Date: Mon Feb 14 15:04:40 2011 -0500
1666
1667 change the default -k to 11
1668
1669 commit 07cf9d1e443d73cf053de38dd01671e3781f6e29
1670 Author: Heng Li <lh3@live.co.uk>
1671 Date: Mon Feb 14 14:50:51 2011 -0500
1672
1673 sort fragments by vpos instead of by beg
1674
1675 commit d0d3e7faabf5cbb7e5ff7b294f7e220da807c4c0
1676 Author: Heng Li <lh3@live.co.uk>
1677 Date: Mon Feb 14 14:45:41 2011 -0500
1678
1679 shuffling the two haplotypes for better randomness
1680
1681 commit 3be28eaf5f6033229aedf12ddb11a0084ba01cd8
1682 Author: Heng Li <lh3@live.co.uk>
1683 Date: Mon Feb 14 14:09:17 2011 -0500
1684
1685 write chimeras to a separate BAM
1686
1687 commit 80ccbc26f43918fe42be123cc1da9d3d7ce30816
1688 Author: Heng Li <lh3@live.co.uk>
1689 Date: Mon Feb 14 13:54:13 2011 -0500
1690
1691 no mem leak/violation on small files; correctness is not checked
1692
1693 commit 5c923867432fa14c26a19e3782e7f48d4080f6ac
1694 Author: Heng Li <lh3@live.co.uk>
1695 Date: Mon Feb 14 13:50:25 2011 -0500
1696
1697 bam separation; at least not immediate segfault
1698
1699 commit cea2643ec30a59735bf89b2f562b563bf7263e79
1700 Author: Heng Li <lh3@live.co.uk>
1701 Date: Sun Feb 13 23:24:11 2011 -0500
1702
1703 on the way to implement BAM separation; unfinished
1704
1705 commit 964269cd15036a470ca89e43d0952201a0825671
1706 Author: Heng Li <lh3@live.co.uk>
1707 Date: Sun Feb 13 18:07:56 2011 -0500
1708
1709 keep singletons in the hash table
1710
1711 commit 2d4aa649bd670d5e038a1acaefd33c5fe24ae0e8
1712 Author: Heng Li <lh3@live.co.uk>
1713 Date: Sun Feb 13 17:42:24 2011 -0500
1714
1715 Revert "prepare to add bam separation"
1716
1717 This reverts commit ed6957e5211c2c4cf684dcb8bbb661052c74df6f.
1718
1719 commit ed6957e5211c2c4cf684dcb8bbb661052c74df6f
1720 Author: Heng Li <lh3@live.co.uk>
1721 Date: Sun Feb 13 00:24:28 2011 -0500
1722
1723 prepare to add bam separation
1724
1725 commit d211e652d93791d2e112d334added243ffe5fc3e
1726 Author: Heng Li <lh3@live.co.uk>
1727 Date: Sat Feb 12 18:50:20 2011 -0500
1728
1729 accelerate kstrtok
1730
1731 commit 2d6af49d331ff5afe7b9e9b102e79d7d4512fdbe
1732 Author: Heng Li <lh3@live.co.uk>
1733 Date: Fri Feb 11 21:08:21 2011 -0500
1734
1735 split unlinked blocks
1736
1737 commit 68e4cd1b560b0a6fd4c77e5e51eadde9fda26ea4
1738 Author: Heng Li <lh3@live.co.uk>
1739 Date: Fri Feb 11 10:47:58 2011 -0500
1740
1741 remove heading and tailing ambiguous positions
1742
1743 commit d2b685141426a902ae76660c1fbe8020da150cf8
1744 Author: Heng Li <lh3@live.co.uk>
1745 Date: Fri Feb 11 10:02:21 2011 -0500
1746
1747 code clean up for further features
1748
1749 commit c6980e062d55928b59f287c03e599dd5a37ed509
1750 Author: Heng Li <lh3@live.co.uk>
1751 Date: Fri Feb 11 08:00:08 2011 -0500
1752
1753 change /64 to >>6; the latter is faster
1754
1755 commit 91635b9c2687f24d72ee6a8aad2050a79bb8400f
1756 Merge: 41d4df2 9a7e155
1757 Author: Heng Li <lh3@live.co.uk>
1758 Date: Fri Feb 11 01:22:55 2011 -0500
1759
1760 Merge branch 'master' into devel
1761
1762 commit 9a7e155cc591c1b6c9f7f9cb939364a6becb65b2
1763 Author: Heng Li <lh3@live.co.uk>
1764 Date: Fri Feb 11 01:21:07 2011 -0500
1765
1766 output an unrecognized field as '.'; autofix GL/PL
1767
1768 commit 41d4df2e9545e9abe97151cfe5d6c763f3d00db1
1769 Merge: c00c41c aacce0c
1770 Author: Heng Li <lh3@live.co.uk>
1771 Date: Thu Feb 10 23:00:14 2011 -0500
1772
1773 Merge branch 'master' into devel
1774
1775 commit aacce0ce7276f451e4fddf81832f9e5f7f65198b
1776 Author: Heng Li <lh3@live.co.uk>
1777 Date: Thu Feb 10 22:57:53 2011 -0500
1778
1779 finished VCF->BCF conversion
1780
1781 commit 0e875df643e41d848b709e2fa877de8ae53cdd4c
1782 Author: Heng Li <lh3@live.co.uk>
1783 Date: Thu Feb 10 21:57:28 2011 -0500
1784
1785 fixed a bug in reading VCF files
1786
1787 commit c00c41c2a5da69cccea64adb542a0b365e56b4fc
1788 Author: Heng Li <lh3@live.co.uk>
1789 Date: Thu Feb 10 16:28:37 2011 -0500
1790
1791 suppres one-allele blocks
1792
1793 commit 2e2354b673722e2f00d72970a043f80a66270da1
1794 Author: Heng Li <lh3@live.co.uk>
1795 Date: Thu Feb 10 16:06:56 2011 -0500
1796
1797 fixed the bug in filtering
1798
1799 commit d971e1fe24de4ecaf94055efffc5f641e2bdb563
1800 Author: Heng Li <lh3@live.co.uk>
1801 Date: Thu Feb 10 12:24:23 2011 -0500
1802
1803 prepare to add filtering; buggy right now
1804
1805 commit a0a5a3fbf504c3b02f7b9212e72315c1047cc249
1806 Author: Heng Li <lh3@live.co.uk>
1807 Date: Thu Feb 10 11:55:02 2011 -0500
1808
1809 make masking optional
1810
1811 commit 28db71ccd95054a5f8a47c2332794f8968f6a822
1812 Author: Heng Li <lh3@live.co.uk>
1813 Date: Thu Feb 10 11:40:47 2011 -0500
1814
1815 routine to mask poorly called regions
1816
1817 commit a3f6c439262bc10a4067860440f4d4dde9e0c515
1818 Author: Heng Li <lh3@live.co.uk>
1819 Date: Wed Feb 9 17:18:33 2011 -0500
1820
1821 code clean up: remove globals
1822
1823 commit 0b711978492f6ad39d459d78723c299468906818
1824 Author: Heng Li <lh3@live.co.uk>
1825 Date: Wed Feb 9 16:52:54 2011 -0500
1826
1827 output more information
1828
1829 commit f69d217ae5b691bf42ad07a97f29a7cc6456046f
1830 Author: Heng Li <lh3@live.co.uk>
1831 Date: Wed Feb 9 16:11:54 2011 -0500
1832
1833 fixed another bug in flipping
1834
1835 commit d47882d549337fbcc251597508a2c7faf1bb92e2
1836 Author: Heng Li <lh3@live.co.uk>
1837 Date: Wed Feb 9 16:01:35 2011 -0500
1838
1839 fixed a stupid bug in flipping
1840
1841 commit e33f89de499496537f5fbde396a66557f0353f1b
1842 Author: Heng Li <lh3@live.co.uk>
1843 Date: Wed Feb 9 15:54:42 2011 -0500
1844
1845 fix chimeras; a little weird...
1846
1847 commit 03d3c1d0b945245108ce0942d4772536a32212c7
1848 Author: Heng Li <lh3@live.co.uk>
1849 Date: Wed Feb 9 13:27:35 2011 -0500
1850
1851 no effective change; prepare to fix chimera
1852
1853 commit 6bc0a4676dd2252085a6e67bb06daa5ae05a554f
1854 Author: Heng Li <lh3@live.co.uk>
1855 Date: Wed Feb 9 11:52:58 2011 -0500
1856
1857 better count output
1858
1859 commit dcac515439d25f71125d6de8111da417776ab9ce
1860 Author: Heng Li <lh3@live.co.uk>
1861 Date: Wed Feb 9 10:31:07 2011 -0500
1862
1863 prepare for another way of filtering
1864
1865 commit ca7e4f1899b86d2e077994c789e8f69d699b3cd9
1866 Author: Heng Li <lh3@live.co.uk>
1867 Date: Tue Feb 8 16:10:08 2011 -0500
1868
1869 fixed the bug; I can do better.
1870
1871 commit 0733f77b98af121bdcb198cea6151d159831bb9c
1872 Author: Heng Li <lh3@live.co.uk>
1873 Date: Tue Feb 8 15:55:38 2011 -0500
1874
1875 fixed two bugs; still not working...
1876
1877 commit 80f18cba9ba73c9592380fc1ecd53c351d294782
1878 Author: Heng Li <lh3@live.co.uk>
1879 Date: Tue Feb 8 15:42:58 2011 -0500
1880
1881 filter false SNPs; NOT working right now
1882
1883 commit 69a66e2f96d5b102cd712ff1527a3802fa84c590
1884 Author: Heng Li <lh3@live.co.uk>
1885 Date: Tue Feb 8 14:39:09 2011 -0500
1886
1887 write sequence in the SAM format for debugging
1888
1889 commit b6f1c9d160822af2b713be206f37bd6dde00546a
1890 Author: Heng Li <lh3@live.co.uk>
1891 Date: Mon Feb 7 11:51:21 2011 -0500
1892
1893 fixed two bugs
1894
1895 commit 400aa5c06100af9c47cd5e4ce8b95b7deb84f54b
1896 Author: Heng Li <lh3@live.co.uk>
1897 Date: Mon Feb 7 11:22:38 2011 -0500
1898
1899 Optionally apply BAQ
1900
1901 commit 4c82e0e19682e424f5cdb8381364114c307b329e
1902 Author: Heng Li <lh3@live.co.uk>
1903 Date: Mon Feb 7 01:23:31 2011 -0500
1904
1905 improved output; the result makes sense at a glance
1906
1907 commit dc7853a581ab24bcc496e96b123ccf637e32ed1d
1908 Author: Heng Li <lh3@live.co.uk>
1909 Date: Sun Feb 6 14:12:43 2011 -0500
1910
1911 process per linked block instead of per chr
1912
1913 commit e867d9c6c2e61d9e748e78163e5481dca5697a36
1914 Author: Heng Li <lh3@live.co.uk>
1915 Date: Sun Feb 6 00:45:46 2011 -0500
1916
1917 DP seems to work on toy examples
1918
1919 commit 445ad72fc43d4354d56f5f759790e8ae0be73d02
1920 Author: Heng Li <lh3@live.co.uk>
1921 Date: Sat Feb 5 01:24:42 2011 -0500
1922
1923 implemented backtrack; not tested
1924
1925 commit ba38e180b9cd545956583b22e97e09b4bb12073e
1926 Author: Heng Li <lh3@live.co.uk>
1927 Date: Fri Feb 4 23:55:23 2011 -0500
1928
1929 More "correct" DP; backtrack not implemented
1930
1931 commit d69761fd9351273ccd37ea431b10509add91e7cf
1932 Author: Heng Li <lh3@live.co.uk>
1933 Date: Fri Feb 4 17:22:31 2011 -0500
1934
1935 scratch of dynamic programming; unfinished...
1936
1937 commit 769ffcb44e26e59300791658801d321559b33858
1938 Author: Heng Li <lh3@live.co.uk>
1939 Date: Fri Feb 4 16:29:55 2011 -0500
1940
1941 UNFINISHED commit.
1942
1943 commit 9adab9591317c3467f3d8cdf2d19ec1f65d1b5b7
1944 Author: Heng Li <lh3@live.co.uk>
1945 Date: Thu Feb 3 16:20:59 2011 -0500
1946
1947 another way of counting; can be even faster
1948
1949 commit bbafbdc01ed1ceaab44927def1ad47c4c78aeb9c
1950 Author: Heng Li <lh3@live.co.uk>
1951 Date: Thu Feb 3 14:48:20 2011 -0500
1952
1953 for backup
1954
1955 commit eba7446389cad62a19133bced1386a4334dcab79
1956 Merge: a44a98e f01a593
1957 Author: Heng Li <lh3@live.co.uk>
1958 Date: Wed Feb 2 14:06:07 2011 -0500
1959
1960 Merge branch 'master' into devel
1961
1962 commit f01a5930445b5fda7e6b5b813ed63c652160ada2
1963 Author: Heng Li <lh3@live.co.uk>
1964 Date: Wed Feb 2 11:31:54 2011 -0500
1965
1966 Better truncation warning when EOF is absent
1967
1968 commit dd3ee5ed26c8bbef4a62fa5b2bfb0a75833f2c31
1969 Author: Heng Li <lh3@live.co.uk>
1970 Date: Wed Feb 2 10:38:28 2011 -0500
1971
1972 fixed a typo in BCF/VCF headers
1973
1974 commit b9d1137c55f401387113d1ad8a387489afe741db
1975 Author: Heng Li <lh3@live.co.uk>
1976 Date: Wed Feb 2 09:13:44 2011 -0500
1977
1978 fixed an out-of-boundary bug (fixed by Roel Kluin)
1979
1980 commit a44a98e16559b9672e8a3492c8f8c640074b7ee2
1981 Merge: ef68a14 d0443d5
1982 Author: Heng Li <lh3@live.co.uk>
1983 Date: Tue Feb 1 21:54:48 2011 -0500
1984
1985 Merge branch 'master' into devel
1986
1987 commit d0443d5c2f648e0f69bd4c56eaac7868e501c18b
1988 Author: Heng Li <lh3@live.co.uk>
1989 Date: Tue Feb 1 17:31:52 2011 -0500
1990
1991 improved sorting order checking
1992
1993 commit ef68a14fab91399b2ecd38345936c3d6e7391cf3
1994 Merge: 1e597b3 1a39a2e
1995 Author: Heng Li <lh3@live.co.uk>
1996 Date: Tue Feb 1 15:12:37 2011 -0500
1997
1998 Merge branch 'master' into devel
1999
2000 commit 1a39a2eb08a270e20a34a0983e8bed6ffb3e2008
2001 Author: Heng Li <lh3@live.co.uk>
2002 Date: Tue Feb 1 15:12:14 2011 -0500
2003
2004 more precise error message
2005
2006 commit e028e7a47c02232e06a9dd3009262c00dede1060
2007 Author: Heng Li <lh3@live.co.uk>
2008 Date: Tue Feb 1 14:48:01 2011 -0500
2009
2010 improved sorting order validation in index
2011
2012 commit 1e597b3356744e2b791b12c9187f91c8054511d5
2013 Author: Heng Li <lh3@live.co.uk>
2014 Date: Tue Feb 1 14:44:27 2011 -0500
2015
2016 testing only; not working
2017
2018 commit 5753ace1e54228822d8ee95f69943f586e42f6e8
2019 Author: Heng Li <lh3@live.co.uk>
2020 Date: Mon Jan 31 17:37:08 2011 -0500
2021
2022 reduce the effect of seq errors at the cost of SN
2023
2024 commit 6f239ce5e0abd47babee33174476d48b723260d8
2025 Author: Heng Li <lh3@live.co.uk>
2026 Date: Mon Jan 31 17:29:34 2011 -0500
2027
2028 added testing code
2029
2030 commit 3db42fe22d27d61ab5735cd2308f73d93def8ebe
2031 Author: Heng Li <lh3@live.co.uk>
2032 Date: Mon Jan 31 14:33:21 2011 -0500
2033
2034 routine for phasing fosmid resequencing (incomplete)
2035
2036 commit ed88f2797323229ae8f38fbcd107b231007956a8
2037 Author: Heng Li <lh3@live.co.uk>
2038 Date: Mon Jan 31 10:12:53 2011 -0500
2039
2040 SAM output
2041
2042 commit abc6acae28dc4794f6422255f077cf370d34e414
2043 Merge: f1985a9 b133dbf
2044 Author: Heng Li <lh3@live.co.uk>
2045 Date: Sat Jan 29 22:56:10 2011 -0500
2046
2047 Merge branch 'master' into devel
2048
2049 commit b133dbf82de4e8cea5eb56e5bbf0c4b3e9368fd5
2050 Author: Heng Li <lh3@live.co.uk>
2051 Date: Sat Jan 29 22:37:11 2011 -0500
2052
2053 fixed a bug in tview on big-endian by Nathan Weeks
2054
2055 commit 9d3fdaef29f91e21dbfcb9ff0165b9573e7c1042
2056 Author: Heng Li <lh3@live.co.uk>
2057 Date: Sat Jan 29 22:24:00 2011 -0500
2058
2059 update INSTALL
2060
2061 commit 9d074a38bde53961f96157b6fb3683b6dded38d7
2062 Author: Heng Li <lh3@live.co.uk>
2063 Date: Sat Jan 29 21:56:25 2011 -0500
2064
2065 avoid a segfault when network connect fails
2066
2067 commit f1985a93f7455b3ea1b0ef9b959d50b896ccd620
2068 Author: Heng Li <lh3@live.co.uk>
2069 Date: Sat Jan 29 21:53:18 2011 -0500
2070
2071 fixed a bug about bit ordering
2072
2073 commit d09797db6fef648a6823cbe718d67664660c6ebe
2074 Author: Heng Li <lh3@live.co.uk>
2075 Date: Thu Jan 27 16:53:19 2011 -0500
2076
2077 point out there are 4 or fewer free parameters
2078
2079 commit 5fd1717650ed68ab6c55d094d1648c16a054891a
2080 Author: Heng Li <lh3@live.co.uk>
2081 Date: Thu Jan 27 16:09:18 2011 -0500
2082
2083 updated .gitignore
2084
2085 commit fccb19fbe8f9de91f59d85bb49a248683dc6266c
2086 Author: Heng Li <lh3@live.co.uk>
2087 Date: Thu Jan 27 16:08:14 2011 -0500
2088
2089 fixed a bug; better scoring
2090
2091 commit b4dcb844bde3d09eedcd9f6832186ece60ae5afd
2092 Merge: ffc3e89 6f502de
2093 Author: Heng Li <lh3@live.co.uk>
2094 Date: Thu Jan 27 14:50:30 2011 -0500
2095
2096 Merge branch 'master' into devel
2097
2098 commit 6f502dec46b18dae4bb5b2319715d028b5e193d0
2099 Author: Heng Li <lh3@live.co.uk>
2100 Date: Thu Jan 27 14:47:31 2011 -0500
2101
2102 skip unmapped and ref-skip reads in indel calling
2103
2104 commit 3639f37dd8257b24560c35effcc3b6c16c3c1bcb
2105 Author: Heng Li <lh3@live.co.uk>
2106 Date: Thu Jan 27 14:19:15 2011 -0500
2107
2108 fixed an out-of-boundary bug in rare cases
2109
2110 commit ffc3e89678ab9052b84f403da1e43044b045e73f
2111 Author: Heng Li <lh3@live.co.uk>
2112 Date: Thu Jan 27 14:00:17 2011 -0500
2113
2114 targetcut can be compiled, though probably buggy
2115
2116 commit f452b3ac51306865ddde31a8d715b155d4d3e6e6
2117 Author: Heng Li <lh3@live.co.uk>
2118 Date: Wed Jan 26 18:58:43 2011 -0500
2119
2120 this is for a very special application...
2121
2122 commit ca1451c6406c7ee757cb31349ea0b8de70db0656
2123 Author: Heng Li <lh3@live.co.uk>
2124 Date: Wed Jan 26 18:48:09 2011 -0500
2125
2126 fixed compiling errors
2127
2128 commit 085b87a7642865f17239fb6a436e626e25417838
2129 Author: Heng Li <lh3@live.co.uk>
2130 Date: Wed Jan 26 18:45:09 2011 -0500
2131
2132 This script was put in a wrong place...
2133
2134 commit 090d360828622520de60385af4928ce1aebe0e48
2135 Author: Heng Li <lh3@live.co.uk>
2136 Date: Wed Jan 26 18:33:58 2011 -0500
2137
2138 Imported from samtools-r902
2139 ------------------------------------------------------------------------
2140 r108 | lh3lh3 | 2009-01-20 11:56:45 +0000 (Tue, 20 Jan 2009) | 2 lines
2141 Changed paths:
2142 M /branches/dev/samtools/examples/Makefile
2143
2144 made it a little more convenient
2145
2146 ------------------------------------------------------------------------
2147 r107 | lh3lh3 | 2009-01-20 11:53:30 +0000 (Tue, 20 Jan 2009) | 2 lines
2148 Changed paths:
2149 A /branches/dev/samtools/examples/Makefile
2150
2151 added a Makefile
2152
2153 ------------------------------------------------------------------------
2154 r106 | lh3lh3 | 2009-01-20 11:25:05 +0000 (Tue, 20 Jan 2009) | 2 lines
2155 Changed paths:
2156 M /branches/dev/samtools/misc/maq2sam.c
2157
2158 support RG tag
2159
2160 ------------------------------------------------------------------------
2161 r105 | lh3lh3 | 2009-01-18 17:37:20 +0000 (Sun, 18 Jan 2009) | 2 lines
2162 Changed paths:
2163 M /branches/dev/samtools/ChangeLog
2164
2165 update changelog
2166
2167 ------------------------------------------------------------------------
2168 r104 | lh3lh3 | 2009-01-18 17:31:21 +0000 (Sun, 18 Jan 2009) | 3 lines
2169 Changed paths:
2170 M /branches/dev/samtools/bam.h
2171 M /branches/dev/samtools/bam_lpileup.c
2172 M /branches/dev/samtools/bamtk.c
2173
2174 * samtools-0.1.1-18
2175 * fixed a bug in bam_lpileup.c: segment start and end are not correctly recognized
2176
2177 ------------------------------------------------------------------------
2178 r103 | lh3lh3 | 2009-01-18 16:34:03 +0000 (Sun, 18 Jan 2009) | 5 lines
2179 Changed paths:
2180 M /branches/dev/samtools/bam_import.c
2181 M /branches/dev/samtools/bam_index.c
2182 M /branches/dev/samtools/bamtk.c
2183
2184 * samtools-0.1.1-17
2185 * fixed a bug when there are reads without coordinates
2186 * also recognize type 'c' as 'A'
2187 * found a bug in bam_lpileup.c; NOT fixed yet
2188
2189 ------------------------------------------------------------------------
2190 r102 | lh3lh3 | 2009-01-17 19:46:49 +0000 (Sat, 17 Jan 2009) | 2 lines
2191 Changed paths:
2192 A /branches/dev/samtools/INSTALL
2193
2194 Instruction for compilation
2195
2196 ------------------------------------------------------------------------
2197 r101 | lh3lh3 | 2009-01-17 19:31:36 +0000 (Sat, 17 Jan 2009) | 3 lines
2198 Changed paths:
2199 M /branches/dev/samtools/Makefile
2200 A /branches/dev/samtools/Makefile.lite
2201 M /branches/dev/samtools/bam.h
2202 M /branches/dev/samtools/faidx.c
2203 M /branches/dev/samtools/misc/Makefile
2204 M /branches/dev/samtools/razf.c
2205
2206 * replaced HAVE_RAZF with _NO_RAZF
2207 * added Makefile.lite for people who have trouble with razf.c
2208
2209 ------------------------------------------------------------------------
2210 r100 | lh3lh3 | 2009-01-16 10:03:37 +0000 (Fri, 16 Jan 2009) | 3 lines
2211 Changed paths:
2212 M /branches/dev/samtools/bam_mate.c
2213 M /branches/dev/samtools/bamtk.c
2214 M /branches/dev/samtools/misc/wgsim.c
2215
2216 * samtools-0.1.1-15
2217 * fixed another bug in fixmate: unmapped pair has non-zero isize
2218
2219 ------------------------------------------------------------------------
2220 r99 | lh3lh3 | 2009-01-16 09:13:36 +0000 (Fri, 16 Jan 2009) | 4 lines
2221 Changed paths:
2222 M /branches/dev/samtools/ChangeLog
2223 M /branches/dev/samtools/bam_mate.c
2224 M /branches/dev/samtools/bamtk.c
2225
2226 * samtools-0.1.1-14
2227 * fixed a bug in fixmate: isize not equal to zero if two ends mapped to
2228 different chr
2229
2230 ------------------------------------------------------------------------
2231 r98 | lh3lh3 | 2009-01-15 16:47:41 +0000 (Thu, 15 Jan 2009) | 3 lines
2232 Changed paths:
2233 M /branches/dev/samtools/bam_maqcns.c
2234 M /branches/dev/samtools/bamtk.c
2235
2236 * samtools-0.1.1-13
2237 * fixed the prior for hom indels (Richard pointed this out)
2238
2239 ------------------------------------------------------------------------
2240 r97 | lh3lh3 | 2009-01-15 16:38:47 +0000 (Thu, 15 Jan 2009) | 4 lines
2241 Changed paths:
2242 M /branches/dev/samtools/COPYING
2243 M /branches/dev/samtools/bam_sort.c
2244 M /branches/dev/samtools/bamtk.c
2245 M /branches/dev/samtools/source.dot
2246
2247 * samtools-0.1.1-12
2248 * fixed a bug in sort
2249 * update source file graph and copyright information
2250
2251 ------------------------------------------------------------------------
2252 r96 | lh3lh3 | 2009-01-14 21:46:14 +0000 (Wed, 14 Jan 2009) | 2 lines
2253 Changed paths:
2254 M /branches/dev/samtools/glf.c
2255
2256 fixed a typo
2257
2258 ------------------------------------------------------------------------
2259 r95 | lh3lh3 | 2009-01-14 21:44:53 +0000 (Wed, 14 Jan 2009) | 2 lines
2260 Changed paths:
2261 M /branches/dev/samtools/glf.c
2262
2263 added a main function for glf.c
2264
2265 ------------------------------------------------------------------------
2266 r94 | lh3lh3 | 2009-01-14 17:14:59 +0000 (Wed, 14 Jan 2009) | 4 lines
2267 Changed paths:
2268 M /branches/dev/samtools/Makefile
2269 M /branches/dev/samtools/bam_plcmd.c
2270 M /branches/dev/samtools/bamtk.c
2271 M /branches/dev/samtools/bgzf.h
2272 A /branches/dev/samtools/glf.c
2273 M /branches/dev/samtools/glf.h
2274
2275 * samtools-0.1.1-11
2276 * generate binary GLFv2
2277 * added glfview command to dump GLFv2 binary file
2278
2279 ------------------------------------------------------------------------
2280 r93 | lh3lh3 | 2009-01-14 15:07:44 +0000 (Wed, 14 Jan 2009) | 4 lines
2281 Changed paths:
2282 M /branches/dev/samtools/bam_rmdup.c
2283 M /branches/dev/samtools/bamtk.c
2284 M /branches/dev/samtools/glf.h
2285
2286 * samtools-0.1.1-10
2287 * fixed several bugs in rmdup
2288 * prepare to generate GLF2
2289
2290 ------------------------------------------------------------------------
2291 r92 | lh3lh3 | 2009-01-14 13:27:44 +0000 (Wed, 14 Jan 2009) | 3 lines
2292 Changed paths:
2293 M /branches/dev/samtools/Makefile
2294 M /branches/dev/samtools/bam.h
2295 M /branches/dev/samtools/bam_import.c
2296 A /branches/dev/samtools/bam_rmdup.c
2297 M /branches/dev/samtools/bamtk.c
2298
2299 * samtools-0.1.1-9
2300 * implemented rmdup; NOT tested yet
2301
2302 ------------------------------------------------------------------------
2303 r91 | lh3lh3 | 2009-01-13 20:15:43 +0000 (Tue, 13 Jan 2009) | 2 lines
2304 Changed paths:
2305 M /branches/dev/samtools/examples/00README.txt
2306
2307 update README for typos
2308
2309 ------------------------------------------------------------------------
2310 r90 | lh3lh3 | 2009-01-13 19:57:50 +0000 (Tue, 13 Jan 2009) | 2 lines
2311 Changed paths:
2312 M /branches/dev/samtools/examples/ex1.sam.gz
2313
2314 update example
2315
2316 ------------------------------------------------------------------------
2317 r89 | lh3lh3 | 2009-01-13 17:21:38 +0000 (Tue, 13 Jan 2009) | 3 lines
2318 Changed paths:
2319 M /branches/dev/samtools/Makefile
2320 M /branches/dev/samtools/bam.c
2321 A /branches/dev/samtools/bam_mate.c
2322 M /branches/dev/samtools/bamtk.c
2323
2324 * samtools-0.1.1-8
2325 * added fixmate command
2326
2327 ------------------------------------------------------------------------
2328 r88 | lh3lh3 | 2009-01-13 10:48:23 +0000 (Tue, 13 Jan 2009) | 3 lines
2329 Changed paths:
2330 M /branches/dev/samtools/bam_plcmd.c
2331 M /branches/dev/samtools/bamtk.c
2332
2333 * samtools-0.1.1-7
2334 * change the reported indel position to the previous way
2335
2336 ------------------------------------------------------------------------
2337 r87 | lh3lh3 | 2009-01-12 22:12:12 +0000 (Mon, 12 Jan 2009) | 4 lines
2338 Changed paths:
2339 M /branches/dev/samtools/bam_plcmd.c
2340 M /branches/dev/samtools/bamtk.c
2341
2342 * samtools-0.1.1-6
2343 * addd glt output
2344 * allow to change indel calling parameters at the command line
2345
2346 ------------------------------------------------------------------------
2347 r86 | lh3lh3 | 2009-01-12 21:16:48 +0000 (Mon, 12 Jan 2009) | 4 lines
2348 Changed paths:
2349 M /branches/dev/samtools/bam.h
2350 M /branches/dev/samtools/bam_pileup.c
2351 M /branches/dev/samtools/bam_plcmd.c
2352 M /branches/dev/samtools/bamtk.c
2353
2354 * samtools-0.1.1-5
2355 * added two more flags
2356 * allowed to select reads shown in pileup with a mask
2357
2358 ------------------------------------------------------------------------
2359 r85 | lh3lh3 | 2009-01-12 20:47:51 +0000 (Mon, 12 Jan 2009) | 4 lines
2360 Changed paths:
2361 M /branches/dev/samtools/bam_index.c
2362 M /branches/dev/samtools/bam_plcmd.c
2363 M /branches/dev/samtools/bamtk.c
2364
2365 * samtools-0.1.1-4
2366 * fixed a bug in indexing (linear index)
2367 * prepare to add glt output from pileup
2368
2369 ------------------------------------------------------------------------
2370 r84 | lh3lh3 | 2009-01-12 09:22:35 +0000 (Mon, 12 Jan 2009) | 3 lines
2371 Changed paths:
2372 M /branches/dev/samtools/bam_plcmd.c
2373 M /branches/dev/samtools/bamtk.c
2374
2375 * samtools-0.1.1-3
2376 * fixed a bug in outputing the coordinate of an indel
2377
2378 ------------------------------------------------------------------------
2379 r83 | lh3lh3 | 2009-01-11 15:18:01 +0000 (Sun, 11 Jan 2009) | 3 lines
2380 Changed paths:
2381 M /branches/dev/samtools/bam_plcmd.c
2382 M /branches/dev/samtools/bamtk.c
2383
2384 * samtools-0.1.1-2
2385 * pileup: allows to output indel sites only
2386
2387 ------------------------------------------------------------------------
2388 r82 | lh3lh3 | 2009-01-10 23:34:31 +0000 (Sat, 10 Jan 2009) | 3 lines
2389 Changed paths:
2390 M /branches/dev/samtools/bam_maqcns.c
2391 M /branches/dev/samtools/bam_maqcns.h
2392 M /branches/dev/samtools/bam_plcmd.c
2393 M /branches/dev/samtools/bamtk.c
2394
2395 * samtools-0.1.1-1
2396 * implemented a Bayesian indel caller
2397
2398 ------------------------------------------------------------------------
2399 r81 | lh3lh3 | 2009-01-09 09:54:28 +0000 (Fri, 09 Jan 2009) | 2 lines
2400 Changed paths:
2401 M /branches/dev/samtools/examples/00README.txt
2402 D /branches/dev/samtools/examples/ex1.fa.fai
2403
2404 Let users generate ex1.fa.fai.
2405
2406 ------------------------------------------------------------------------
2407 r80 | lh3lh3 | 2009-01-08 16:10:08 +0000 (Thu, 08 Jan 2009) | 2 lines
2408 Changed paths:
2409 M /branches/dev/samtools/misc/bowtie2sam.pl
2410
2411 make the bowtie converter works for "-k 2"
2412
2413 ------------------------------------------------------------------------
2414 r78 | lh3lh3 | 2009-01-03 17:25:24 +0000 (Sat, 03 Jan 2009) | 2 lines
2415 Changed paths:
2416 M /branches/dev/samtools/misc/export2sam.pl
2417
2418 fixed a bug for "QC" reads
2419
2420 ------------------------------------------------------------------------
2421 r77 | lh3lh3 | 2009-01-01 18:32:06 +0000 (Thu, 01 Jan 2009) | 3 lines
2422 Changed paths:
2423 A /branches/dev/samtools/misc/bowtie2sam.pl
2424 M /branches/dev/samtools/misc/soap2sam.pl
2425
2426 * soap2sam.pl: added NM tag
2427 * bowtie2sam.pl: converter for bowtie
2428
2429 ------------------------------------------------------------------------
2430 r76 | lh3lh3 | 2008-12-31 23:24:24 +0000 (Wed, 31 Dec 2008) | 2 lines
2431 Changed paths:
2432 A /branches/dev/samtools/misc/soap2sam.pl
2433
2434 soap2sam.pl: convert soap output to SAM
2435
2436 ------------------------------------------------------------------------
2437 r75 | lh3lh3 | 2008-12-31 17:54:32 +0000 (Wed, 31 Dec 2008) | 3 lines
2438 Changed paths:
2439 M /branches/dev/samtools/misc/wgsim_eval.pl
2440
2441 * wgsim_eval.pl-0.1.1
2442 * fixed a bug for a contig name like "NT_012345"
2443
2444 ------------------------------------------------------------------------
2445 r74 | lh3lh3 | 2008-12-31 16:38:21 +0000 (Wed, 31 Dec 2008) | 2 lines
2446 Changed paths:
2447 A /branches/dev/samtools/misc/wgsim_eval.pl
2448
2449 * evaluate alignment for reads generated by wgsim
2450
2451 ------------------------------------------------------------------------
2452 r73 | lh3lh3 | 2008-12-31 15:11:22 +0000 (Wed, 31 Dec 2008) | 2 lines
2453 Changed paths:
2454 M /branches/dev/samtools/misc/Makefile
2455 M /branches/dev/samtools/misc/wgsim.c
2456
2457 fixed compiling warnings for wgsim
2458
2459 ------------------------------------------------------------------------
2460 r72 | lh3lh3 | 2008-12-31 13:40:51 +0000 (Wed, 31 Dec 2008) | 2 lines
2461 Changed paths:
2462 M /branches/dev/samtools/bam_tview.c
2463
2464 remove an unused variable (a compiler warning only)
2465
2466 ------------------------------------------------------------------------
2467 r71 | lh3lh3 | 2008-12-31 13:37:16 +0000 (Wed, 31 Dec 2008) | 2 lines
2468 Changed paths:
2469 M /branches/dev/samtools/misc/Makefile
2470 A /branches/dev/samtools/misc/wgsim.c
2471
2472 wgsim: Paired-end reads simulator
2473
2474 ------------------------------------------------------------------------
2475 r70 | bhandsaker | 2008-12-29 20:27:16 +0000 (Mon, 29 Dec 2008) | 2 lines
2476 Changed paths:
2477 M /branches/dev/samtools/bam_maqcns.c
2478 M /branches/dev/samtools/bam_tview.c
2479
2480 Move definition of bam_nt16_nt4_table so we can build without curses.
2481
2482 ------------------------------------------------------------------------
2483 r62 | lh3lh3 | 2008-12-22 15:55:13 +0000 (Mon, 22 Dec 2008) | 2 lines
2484 Changed paths:
2485 A /branches/dev/samtools/NEWS
2486 M /branches/dev/samtools/bamtk.c
2487 M /branches/dev/samtools/samtools.1
2488
2489 Release samtools-0.1.1
2490
2491 ------------------------------------------------------------------------
2492 r61 | lh3lh3 | 2008-12-22 15:46:08 +0000 (Mon, 22 Dec 2008) | 10 lines
2493 Changed paths:
2494 M /branches/dev/samtools/bam_aux.c
2495 M /branches/dev/samtools/bam_index.c
2496 M /branches/dev/samtools/bam_plcmd.c
2497 M /branches/dev/samtools/bam_tview.c
2498 M /branches/dev/samtools/bamtk.c
2499 M /branches/dev/samtools/razf.c
2500 M /branches/dev/samtools/samtools.1
2501
2502 * samtools-0.1.0-66
2503 * fixed a bug in razf.c: reset z_eof when razf_seek() is called
2504 * fixed a memory leak in parsing a region
2505 * changed pileup a little bit when -s is in use: output ^ and $
2506 * when a bam is not indexed, output more meaningful error message
2507 * fixed a bug in indexing for small alignment
2508 * fixed a bug in the viewer when we come to the end of a reference file
2509 * updated documentation
2510 * prepare to release 0.1.1
2511
2512 ------------------------------------------------------------------------
2513 r60 | lh3lh3 | 2008-12-22 15:10:16 +0000 (Mon, 22 Dec 2008) | 2 lines
2514 Changed paths:
2515 A /branches/dev/samtools/examples
2516 A /branches/dev/samtools/examples/00README.txt
2517 A /branches/dev/samtools/examples/ex1.fa
2518 A /branches/dev/samtools/examples/ex1.fa.fai
2519 A /branches/dev/samtools/examples/ex1.sam.gz
2520
2521 example
2522
2523 ------------------------------------------------------------------------
2524 r59 | lh3lh3 | 2008-12-22 09:38:15 +0000 (Mon, 22 Dec 2008) | 2 lines
2525 Changed paths:
2526 M /branches/dev/samtools/ChangeLog
2527
2528 update ChangeLog
2529
2530 ------------------------------------------------------------------------
2531 r58 | lh3lh3 | 2008-12-20 23:06:00 +0000 (Sat, 20 Dec 2008) | 3 lines
2532 Changed paths:
2533 M /branches/dev/samtools/misc/export2sam.pl
2534
2535 * added comments
2536 * fixed several bugs
2537
2538 ------------------------------------------------------------------------
2539 r57 | lh3lh3 | 2008-12-20 15:44:20 +0000 (Sat, 20 Dec 2008) | 2 lines
2540 Changed paths:
2541 A /branches/dev/samtools/misc/export2sam.pl
2542
2543 convert Export format to SAM; not thoroughly tested
2544
2545 ------------------------------------------------------------------------
2546 r56 | lh3lh3 | 2008-12-19 22:13:28 +0000 (Fri, 19 Dec 2008) | 6 lines
2547 Changed paths:
2548 M /branches/dev/samtools/bam_import.c
2549 M /branches/dev/samtools/bam_plcmd.c
2550 M /branches/dev/samtools/bam_tview.c
2551 M /branches/dev/samtools/bamtk.c
2552 A /branches/dev/samtools/source.dot
2553
2554 * samtools-0.1.0-65
2555 * pileup: generate maq-like simple output
2556 * pileup: allow to output pileup at required sites
2557 * source.dot: source file relationship graph
2558 * tview: fixed a minor bug
2559
2560 ------------------------------------------------------------------------
2561 r55 | lh3lh3 | 2008-12-19 20:10:26 +0000 (Fri, 19 Dec 2008) | 2 lines
2562 Changed paths:
2563 D /branches/dev/samtools/misc/all2sam.pl
2564
2565 remove all2sam.pl
2566
2567 ------------------------------------------------------------------------
2568 r54 | lh3lh3 | 2008-12-16 22:34:25 +0000 (Tue, 16 Dec 2008) | 2 lines
2569 Changed paths:
2570 A /branches/dev/samtools/COPYING
2571 M /branches/dev/samtools/bam.h
2572 M /branches/dev/samtools/faidx.h
2573 M /branches/dev/samtools/khash.h
2574 M /branches/dev/samtools/kseq.h
2575 M /branches/dev/samtools/ksort.h
2576 M /branches/dev/samtools/samtools.1
2577
2578 Added copyright information and a bit more documentation. No code change.
2579
2580 ------------------------------------------------------------------------
2581 r53 | lh3lh3 | 2008-12-16 13:40:18 +0000 (Tue, 16 Dec 2008) | 3 lines
2582 Changed paths:
2583 M /branches/dev/samtools/bam.c
2584 M /branches/dev/samtools/bam.h
2585 M /branches/dev/samtools/bam_index.c
2586 M /branches/dev/samtools/bam_maqcns.c
2587 M /branches/dev/samtools/bamtk.c
2588
2589 * samtools-0.1.0-64
2590 * improved efficiency of the indel caller for spliced alignments
2591
2592 ------------------------------------------------------------------------
2593 r52 | lh3lh3 | 2008-12-16 10:28:20 +0000 (Tue, 16 Dec 2008) | 3 lines
2594 Changed paths:
2595 M /branches/dev/samtools/bam.c
2596 M /branches/dev/samtools/bam.h
2597 M /branches/dev/samtools/bam_aux.c
2598 M /branches/dev/samtools/bam_index.c
2599 M /branches/dev/samtools/bamtk.c
2600
2601 * samtools-0.1.0-63
2602 * a bit code cleanup: reduce the dependency between source files
2603
2604 ------------------------------------------------------------------------
2605 r51 | lh3lh3 | 2008-12-15 14:29:32 +0000 (Mon, 15 Dec 2008) | 3 lines
2606 Changed paths:
2607 M /branches/dev/samtools/bam_maqcns.c
2608 M /branches/dev/samtools/bam_plcmd.c
2609 M /branches/dev/samtools/bamtk.c
2610
2611 * samtools-0.1.0-62
2612 * fixed a memory leak
2613
2614 ------------------------------------------------------------------------
2615 r50 | lh3lh3 | 2008-12-15 14:00:13 +0000 (Mon, 15 Dec 2008) | 2 lines
2616 Changed paths:
2617 M /branches/dev/samtools/ChangeLog
2618 M /branches/dev/samtools/bam.h
2619 M /branches/dev/samtools/samtools.1
2620
2621 update documentation, ChangeLog and a comment
2622
2623 ------------------------------------------------------------------------
2624 r49 | lh3lh3 | 2008-12-15 13:36:43 +0000 (Mon, 15 Dec 2008) | 6 lines
2625 Changed paths:
2626 M /branches/dev/samtools/Makefile
2627 M /branches/dev/samtools/bam.h
2628 M /branches/dev/samtools/bam_maqcns.c
2629 M /branches/dev/samtools/bam_maqcns.h
2630 M /branches/dev/samtools/bam_pileup.c
2631 A /branches/dev/samtools/bam_plcmd.c
2632 M /branches/dev/samtools/bamtk.c
2633 M /branches/dev/samtools/samtools.1
2634
2635 * samtools-0.1.0-61
2636 * moved pileup command to a separate source file
2637 * added indel caller
2638 * added bam_cal_segend(). (NOT WORKING for spliced alignment!!!)
2639 * updated documentation
2640
2641 ------------------------------------------------------------------------
2642 r48 | lh3lh3 | 2008-12-12 13:55:36 +0000 (Fri, 12 Dec 2008) | 3 lines
2643 Changed paths:
2644 M /branches/dev/samtools/bam_maqcns.c
2645 M /branches/dev/samtools/bamtk.c
2646
2647 * samtools-0.1.0-60
2648 * fixed another bug in maqcns when there is a nearby deletion
2649
2650 ------------------------------------------------------------------------
2651 r47 | lh3lh3 | 2008-12-12 13:42:16 +0000 (Fri, 12 Dec 2008) | 5 lines
2652 Changed paths:
2653 M /branches/dev/samtools/bam_maqcns.c
2654 M /branches/dev/samtools/bam_pileup.c
2655 M /branches/dev/samtools/bamtk.c
2656
2657 * samtools-0.1.0-59
2658 * pileup: outputing consensus is now optional
2659 * fixed a bug in glfgen. This bug also exists in maq's glfgen. However,
2660 I am not quite sure why the previous version may have problem.
2661
2662 ------------------------------------------------------------------------
2663 r46 | lh3lh3 | 2008-12-12 11:44:56 +0000 (Fri, 12 Dec 2008) | 6 lines
2664 Changed paths:
2665 M /branches/dev/samtools/bam_pileup.c
2666 M /branches/dev/samtools/bamtk.c
2667
2668 * samtools-0.1.0-58
2669 * add maq consensus to pileup. However, I will move this part to a new
2670 command as strictly speaking, consensus callin is not part of pileup,
2671 and imposing it would make it harder to generate for other language
2672 bindings.
2673
2674 ------------------------------------------------------------------------
2675 r45 | bhandsaker | 2008-12-11 20:43:56 +0000 (Thu, 11 Dec 2008) | 2 lines
2676 Changed paths:
2677 M /branches/dev/samtools/bgzf.c
2678
2679 Fix bug in tell() after reads that consume to the exact end of a block.
2680
2681 ------------------------------------------------------------------------
2682 r44 | lh3lh3 | 2008-12-11 09:36:53 +0000 (Thu, 11 Dec 2008) | 2 lines
2683 Changed paths:
2684 M /branches/dev/samtools/samtools.1
2685
2686 update manual
2687
2688 ------------------------------------------------------------------------
2689 r43 | lh3lh3 | 2008-12-11 09:25:36 +0000 (Thu, 11 Dec 2008) | 4 lines
2690 Changed paths:
2691 M /branches/dev/samtools/bam_import.c
2692 M /branches/dev/samtools/bamtk.c
2693
2694 * samtools-0.1.0-57
2695 * fixed a bug in parser when there is auxiliary fields
2696 * made the parser a bit more robust
2697
2698 ------------------------------------------------------------------------
2699 r42 | lh3lh3 | 2008-12-10 14:57:29 +0000 (Wed, 10 Dec 2008) | 5 lines
2700 Changed paths:
2701 M /branches/dev/samtools/bam_index.c
2702 M /branches/dev/samtools/bamtk.c
2703 M /branches/dev/samtools/bgzf.c
2704
2705 * samtools-0.1.0-56
2706 * fixed a bug in bgzf (only reading is affected)
2707 * fixed a typo in bam_index.c
2708 * in bam_index.c, check potential bugs in the underlying I/O library
2709
2710 ------------------------------------------------------------------------
2711 r41 | lh3lh3 | 2008-12-10 12:53:08 +0000 (Wed, 10 Dec 2008) | 2 lines
2712 Changed paths:
2713 M /branches/dev/samtools/samtools.1
2714
2715 update manual
2716
2717 ------------------------------------------------------------------------
2718 r40 | lh3lh3 | 2008-12-10 11:52:10 +0000 (Wed, 10 Dec 2008) | 5 lines
2719 Changed paths:
2720 M /branches/dev/samtools/bam.h
2721 M /branches/dev/samtools/bam_pileup.c
2722 M /branches/dev/samtools/bamtk.c
2723
2724 * samtools-0.1.0-55
2725 * tried to make pileup work with clipping (previously not), though NOT tested
2726 * removed -v from pileup
2727 * made pileup take the reference sequence
2728
2729 ------------------------------------------------------------------------
2730 r39 | lh3lh3 | 2008-12-09 11:59:28 +0000 (Tue, 09 Dec 2008) | 4 lines
2731 Changed paths:
2732 M /branches/dev/samtools/bam_import.c
2733 M /branches/dev/samtools/bamtk.c
2734 M /branches/dev/samtools/samtools.1
2735
2736 * samtools-0.1.0-54
2737 * in parser, recognize "=", rather than ",", as a match
2738 * in parser, correctl parse "=" at the MRNM field.
2739
2740 ------------------------------------------------------------------------
2741 r38 | lh3lh3 | 2008-12-09 11:39:07 +0000 (Tue, 09 Dec 2008) | 2 lines
2742 Changed paths:
2743 M /branches/dev/samtools/misc/maq2sam.c
2744
2745 fixed a bug in handling maq flag 64 and 192
2746
2747 ------------------------------------------------------------------------
2748 r37 | lh3lh3 | 2008-12-09 09:53:46 +0000 (Tue, 09 Dec 2008) | 2 lines
2749 Changed paths:
2750 M /branches/dev/samtools/misc/md5fa.c
2751
2752 also calculate unordered md5sum check
2753
2754 ------------------------------------------------------------------------
2755 r36 | lh3lh3 | 2008-12-09 09:46:21 +0000 (Tue, 09 Dec 2008) | 2 lines
2756 Changed paths:
2757 M /branches/dev/samtools/misc/md5fa.c
2758
2759 fixed a minor bug when there are space in the sequence
2760
2761 ------------------------------------------------------------------------
2762 r35 | lh3lh3 | 2008-12-09 09:40:45 +0000 (Tue, 09 Dec 2008) | 2 lines
2763 Changed paths:
2764 M /branches/dev/samtools/misc/md5fa.c
2765
2766 fixed a potential memory leak
2767
2768 ------------------------------------------------------------------------
2769 r34 | lh3lh3 | 2008-12-08 14:52:17 +0000 (Mon, 08 Dec 2008) | 2 lines
2770 Changed paths:
2771 M /branches/dev/samtools/bam_import.c
2772 M /branches/dev/samtools/bam_index.c
2773 M /branches/dev/samtools/bamtk.c
2774
2775 * fixed a bug in import: bin is wrongly calculated
2776
2777 ------------------------------------------------------------------------
2778 r33 | lh3lh3 | 2008-12-08 14:08:01 +0000 (Mon, 08 Dec 2008) | 2 lines
2779 Changed paths:
2780 M /branches/dev/samtools/misc/all2sam.pl
2781
2782 nothing, really
2783
2784 ------------------------------------------------------------------------
2785 r32 | lh3lh3 | 2008-12-08 12:56:02 +0000 (Mon, 08 Dec 2008) | 3 lines
2786 Changed paths:
2787 M /branches/dev/samtools/Makefile
2788 M /branches/dev/samtools/kseq.h
2789 M /branches/dev/samtools/misc/Makefile
2790 A /branches/dev/samtools/misc/md5.c
2791 A /branches/dev/samtools/misc/md5.h
2792 A /branches/dev/samtools/misc/md5fa.c
2793
2794 * fixed two warnings in kseq.h
2795 * added md5sum utilities
2796
2797 ------------------------------------------------------------------------
2798 r31 | lh3lh3 | 2008-12-08 11:35:29 +0000 (Mon, 08 Dec 2008) | 5 lines
2799 Changed paths:
2800 M /branches/dev/samtools/Makefile
2801 M /branches/dev/samtools/bam_import.c
2802 M /branches/dev/samtools/bamtk.c
2803 A /branches/dev/samtools/kseq.h
2804 D /branches/dev/samtools/kstream.h
2805
2806 * samtools-0.1.0-52
2807 * replace kstream with kseq. kseq is a superset of kstream. I need the
2808 extra functions in kseq.h.
2809 * also compile stand-alone faidx
2810
2811 ------------------------------------------------------------------------
2812 r30 | lh3lh3 | 2008-12-08 11:17:04 +0000 (Mon, 08 Dec 2008) | 3 lines
2813 Changed paths:
2814 M /branches/dev/samtools/bam.h
2815 M /branches/dev/samtools/bam_sort.c
2816 M /branches/dev/samtools/bamtk.c
2817
2818 * samtools-0.1.0-51
2819 * sorting by read names is available
2820
2821 ------------------------------------------------------------------------
2822 r29 | lh3lh3 | 2008-12-08 10:29:02 +0000 (Mon, 08 Dec 2008) | 3 lines
2823 Changed paths:
2824 M /branches/dev/samtools/bam.c
2825 M /branches/dev/samtools/bam.h
2826 M /branches/dev/samtools/bam_import.c
2827 M /branches/dev/samtools/bam_maqcns.c
2828 M /branches/dev/samtools/bam_pileup.c
2829 M /branches/dev/samtools/bam_sort.c
2830 M /branches/dev/samtools/bam_tview.c
2831 M /branches/dev/samtools/bamtk.c
2832 M /branches/dev/samtools/misc/maq2sam.c
2833
2834 * samtools-0.1.0-50
2835 * format change to meet the latest specification
2836
2837 ------------------------------------------------------------------------
2838 r28 | lh3lh3 | 2008-12-04 16:09:21 +0000 (Thu, 04 Dec 2008) | 3 lines
2839 Changed paths:
2840 M /branches/dev/samtools/bam_maqcns.c
2841 M /branches/dev/samtools/misc/maq2sam.c
2842
2843 * minor change in maqcns: special care when n==0
2844 * change maq2sam to meet the latest specification
2845
2846 ------------------------------------------------------------------------
2847 r27 | lh3lh3 | 2008-12-04 15:55:44 +0000 (Thu, 04 Dec 2008) | 2 lines
2848 Changed paths:
2849 M /branches/dev/samtools/razf.c
2850 M /branches/dev/samtools/razf.h
2851
2852 considerable code clean up in razf
2853
2854 ------------------------------------------------------------------------
2855 r26 | lh3lh3 | 2008-12-04 15:08:18 +0000 (Thu, 04 Dec 2008) | 2 lines
2856 Changed paths:
2857 M /branches/dev/samtools/ChangeLog
2858 M /branches/dev/samtools/Makefile
2859 M /branches/dev/samtools/faidx.c
2860
2861 make RAZF optional in faidx.c
2862
2863 ------------------------------------------------------------------------
2864 r25 | lh3lh3 | 2008-12-01 15:27:22 +0000 (Mon, 01 Dec 2008) | 3 lines
2865 Changed paths:
2866 M /branches/dev/samtools/Makefile
2867 M /branches/dev/samtools/bam.h
2868 M /branches/dev/samtools/bam_aux.c
2869 M /branches/dev/samtools/bamtk.c
2870 M /branches/dev/samtools/samtools.1
2871
2872 * samtools-0.1.0-49
2873 * added routines for retrieving aux data, NOT TESTED YET!
2874
2875 ------------------------------------------------------------------------
2876 r24 | lh3lh3 | 2008-12-01 14:29:43 +0000 (Mon, 01 Dec 2008) | 5 lines
2877 Changed paths:
2878 M /branches/dev/samtools/bam.c
2879 M /branches/dev/samtools/bam_import.c
2880 M /branches/dev/samtools/bam_maqcns.c
2881 M /branches/dev/samtools/bamtk.c
2882 M /branches/dev/samtools/bgzf.c
2883 M /branches/dev/samtools/samtools.1
2884
2885 * samtools-0.1.0-48
2886 * bgzf: fixed a potential integer overflow on 32-it machines
2887 * maqcns: set the minimum combined quality as 0
2888 * supporting hex strings
2889
2890 ------------------------------------------------------------------------
2891 r23 | lh3lh3 | 2008-11-27 17:14:37 +0000 (Thu, 27 Nov 2008) | 3 lines
2892 Changed paths:
2893 M /branches/dev/samtools/bam_maqcns.c
2894 M /branches/dev/samtools/bamtk.c
2895
2896 * samtools-0.1.0-47
2897 * fixed the bug in maqcns
2898
2899 ------------------------------------------------------------------------
2900 r22 | lh3lh3 | 2008-11-27 17:08:11 +0000 (Thu, 27 Nov 2008) | 3 lines
2901 Changed paths:
2902 M /branches/dev/samtools/Makefile
2903 M /branches/dev/samtools/bam.h
2904 A /branches/dev/samtools/bam_maqcns.c
2905 A /branches/dev/samtools/bam_maqcns.h
2906 M /branches/dev/samtools/bam_tview.c
2907 M /branches/dev/samtools/bamtk.c
2908 A /branches/dev/samtools/glf.h
2909
2910 * samtools-0.1.0-46
2911 * add MAQ consensus caller, currently BUGGY!
2912
2913 ------------------------------------------------------------------------
2914 r21 | lh3lh3 | 2008-11-27 13:51:28 +0000 (Thu, 27 Nov 2008) | 4 lines
2915 Changed paths:
2916 M /branches/dev/samtools/bam_pileup.c
2917 M /branches/dev/samtools/bam_tview.c
2918 M /branches/dev/samtools/bamtk.c
2919
2920 * samtools-0.1.0-45
2921 * tview: display padded alignment (but not P operation)
2922 * better coordinates and reference sequence
2923
2924 ------------------------------------------------------------------------
2925 r19 | lh3lh3 | 2008-11-27 09:26:05 +0000 (Thu, 27 Nov 2008) | 2 lines
2926 Changed paths:
2927 A /branches/dev/samtools/ChangeLog
2928
2929 new ChangeLog
2930
2931 ------------------------------------------------------------------------
2932 r18 | lh3lh3 | 2008-11-27 09:24:45 +0000 (Thu, 27 Nov 2008) | 3 lines
2933 Changed paths:
2934 D /branches/dev/samtools/ChangeLog
2935 A /branches/dev/samtools/ChangeLog.old (from /branches/dev/samtools/ChangeLog:6)
2936
2937 Rename ChangeLog to ChangeLog.old. This old ChangeLog is generated from
2938 the log of my personal SVN repository.
2939
2940 ------------------------------------------------------------------------
2941 r17 | lh3lh3 | 2008-11-27 09:22:55 +0000 (Thu, 27 Nov 2008) | 6 lines
2942 Changed paths:
2943 M /branches/dev/samtools/Makefile
2944 M /branches/dev/samtools/bamtk.c
2945 M /branches/dev/samtools/bgzf.c
2946
2947 * samtools-0.1.0-44
2948 * declare fseeko and ftello as some Linux may not do this by default and
2949 missing these declarations will make bgzf buggy
2950 * get rid of some harmless warings
2951 * use BGZF by default, now
2952
2953 ------------------------------------------------------------------------
2954 r16 | lh3lh3 | 2008-11-26 21:19:11 +0000 (Wed, 26 Nov 2008) | 4 lines
2955 Changed paths:
2956 M /branches/dev/samtools/bam_index.c
2957 M /branches/dev/samtools/bamtk.c
2958 M /branches/dev/samtools/razf.c
2959
2960 * samtools-0.1.0-43
2961 * fixed a bug in razf_read()
2962 * give more warnings when the file is truncated (or due to bugs in I/O library)
2963
2964 ------------------------------------------------------------------------
2965 r15 | lh3lh3 | 2008-11-26 20:41:39 +0000 (Wed, 26 Nov 2008) | 2 lines
2966 Changed paths:
2967 M /branches/dev/samtools/bgzf.c
2968
2969 fixed a bug in bgzf.c at the end of the file
2970
2971 ------------------------------------------------------------------------
2972 r14 | lh3lh3 | 2008-11-26 17:05:18 +0000 (Wed, 26 Nov 2008) | 4 lines
2973 Changed paths:
2974 M /branches/dev/samtools/bamtk.c
2975
2976 * samtools-0.1.0-42
2977 * a lot happened to RAZF, although samtools itself is untouched. Better
2978 also update the version number anyway to avoid confusion
2979
2980 ------------------------------------------------------------------------
2981 r13 | lh3lh3 | 2008-11-26 17:03:48 +0000 (Wed, 26 Nov 2008) | 2 lines
2982 Changed paths:
2983 M /branches/dev/samtools/razf.c
2984
2985 a change from Jue, but I think it should not matter
2986
2987 ------------------------------------------------------------------------
2988 r12 | lh3lh3 | 2008-11-26 16:48:14 +0000 (Wed, 26 Nov 2008) | 3 lines
2989 Changed paths:
2990 M /branches/dev/samtools/razf.c
2991
2992 fixed a potential bug in razf. However, it seems still buggy, just
2993 rarely happens, very rarely.
2994
2995 ------------------------------------------------------------------------
2996 r11 | lh3lh3 | 2008-11-26 14:02:56 +0000 (Wed, 26 Nov 2008) | 2 lines
2997 Changed paths:
2998 M /branches/dev/samtools/razf.c
2999
3000 fixed a bug in razf, with the help of Jue
3001
3002 ------------------------------------------------------------------------
3003 r10 | lh3lh3 | 2008-11-26 11:55:32 +0000 (Wed, 26 Nov 2008) | 2 lines
3004 Changed paths:
3005 M /branches/dev/samtools/bam_index.c
3006
3007 remove a comment
3008
3009 ------------------------------------------------------------------------
3010 r9 | lh3lh3 | 2008-11-26 11:37:05 +0000 (Wed, 26 Nov 2008) | 2 lines
3011 Changed paths:
3012 M /branches/dev/samtools/Makefile
3013 M /branches/dev/samtools/bam.h
3014 M /branches/dev/samtools/razf.c
3015 M /branches/dev/samtools/razf.h
3016
3017 * Jue has updated razf to realize Bob's scheme
3018
3019 ------------------------------------------------------------------------
3020 r7 | lh3lh3 | 2008-11-25 20:37:37 +0000 (Tue, 25 Nov 2008) | 2 lines
3021 Changed paths:
3022 A /branches/dev/samtools/samtools.1
3023
3024 the manual page
3025
3026 ------------------------------------------------------------------------
3027 r6 | lh3lh3 | 2008-11-25 20:37:16 +0000 (Tue, 25 Nov 2008) | 3 lines
3028 Changed paths:
3029 A /branches/dev/samtools/ChangeLog
3030 A /branches/dev/samtools/Makefile
3031 A /branches/dev/samtools/bam.c
3032 A /branches/dev/samtools/bam.h
3033 A /branches/dev/samtools/bam_aux.c
3034 A /branches/dev/samtools/bam_endian.h
3035 A /branches/dev/samtools/bam_import.c
3036 A /branches/dev/samtools/bam_index.c
3037 A /branches/dev/samtools/bam_lpileup.c
3038 A /branches/dev/samtools/bam_pileup.c
3039 A /branches/dev/samtools/bam_sort.c
3040 A /branches/dev/samtools/bam_tview.c
3041 A /branches/dev/samtools/bamtk.c
3042 A /branches/dev/samtools/bgzf.c
3043 A /branches/dev/samtools/bgzf.h
3044 A /branches/dev/samtools/bgzip.c
3045 A /branches/dev/samtools/faidx.c
3046 A /branches/dev/samtools/faidx.h
3047 A /branches/dev/samtools/khash.h
3048 A /branches/dev/samtools/ksort.h
3049 A /branches/dev/samtools/kstream.h
3050 A /branches/dev/samtools/misc
3051 A /branches/dev/samtools/misc/Makefile
3052 A /branches/dev/samtools/misc/all2sam.pl
3053 A /branches/dev/samtools/misc/maq2sam.c
3054 A /branches/dev/samtools/razf.c
3055 A /branches/dev/samtools/razf.h
3056 A /branches/dev/samtools/razip.c
3057 A /branches/dev/samtools/zutil.h
3058
3059 The initial version of samtools, replicated from my local SVN repository.
3060 The current version is: 0.1.0-42. All future development will happen here.
3061
3062 ------------------------------------------------------------------------
3063 r5 | lh3lh3 | 2008-11-25 20:30:49 +0000 (Tue, 25 Nov 2008) | 2 lines
3064 Changed paths:
3065 A /branches/dev/samtools
3066
3067 samtools (C version)
3068
3069 ------------------------------------------------------------------------
3070 ------------------------------------------------------------------------
3071 r703 | lh3 | 2008-11-25 20:20:02 +0000 (Tue, 25 Nov 2008) | 2 lines
3072 Changed paths:
3073 M /branches/prog/bam/samtools.1
3074
3075 rename bamtk to samtools
3076
3077 ------------------------------------------------------------------------
3078 r702 | lh3 | 2008-11-25 20:15:09 +0000 (Tue, 25 Nov 2008) | 2 lines
3079 Changed paths:
3080 D /branches/prog/bam/bamtk.1
3081 A /branches/prog/bam/samtools.1 (from /branches/prog/bam/bamtk.1:679)
3082
3083 rename bamtk.1 to samtools.1
3084
3085 ------------------------------------------------------------------------
3086 r701 | lh3 | 2008-11-25 13:29:10 +0000 (Tue, 25 Nov 2008) | 3 lines
3087 Changed paths:
3088 M /branches/prog/bam/Makefile
3089 M /branches/prog/bam/bam.c
3090 M /branches/prog/bam/bam.h
3091 M /branches/prog/bam/bam_import.c
3092 M /branches/prog/bam/bam_index.c
3093 M /branches/prog/bam/bam_pileup.c
3094 M /branches/prog/bam/bamtk.c
3095 M /branches/prog/bam/misc/Makefile
3096
3097 * samtools-0.1.0-41
3098 * small (but a bit dangerous) changes to meet the latest specification
3099
3100 ------------------------------------------------------------------------
3101 r700 | lh3 | 2008-11-25 13:15:11 +0000 (Tue, 25 Nov 2008) | 2 lines
3102 Changed paths:
3103 A /branches/prog/bam/misc/all2sam.pl (from /branches/prog/bam/misc/all2tam.pl:649)
3104 D /branches/prog/bam/misc/all2tam.pl
3105 A /branches/prog/bam/misc/maq2sam.c (from /branches/prog/bam/misc/maq2tam.c:699)
3106 D /branches/prog/bam/misc/maq2tam.c
3107
3108 rename tam to sam
3109
3110 ------------------------------------------------------------------------
3111 r699 | lh3 | 2008-11-25 13:14:49 +0000 (Tue, 25 Nov 2008) | 2 lines
3112 Changed paths:
3113 M /branches/prog/bam/misc/maq2tam.c
3114
3115 change for the new specification
3116
3117 ------------------------------------------------------------------------
3118 r698 | lh3 | 2008-11-24 13:15:20 +0000 (Mon, 24 Nov 2008) | 3 lines
3119 Changed paths:
3120 M /branches/prog/bam/bam.h
3121 M /branches/prog/bam/razf.c
3122 M /branches/prog/bam/razf.h
3123
3124 * add a fake BGZF mode to razf. It is fake in that it loads razf index into
3125 memory but gives BGZF like virtual offset
3126
3127 ------------------------------------------------------------------------
3128 r697 | lh3 | 2008-11-24 09:53:44 +0000 (Mon, 24 Nov 2008) | 2 lines
3129 Changed paths:
3130 A /branches/prog/bam/ChangeLog
3131
3132 change log
3133
3134 ------------------------------------------------------------------------
3135 r696 | lh3 | 2008-11-24 09:53:23 +0000 (Mon, 24 Nov 2008) | 2 lines
3136 Changed paths:
3137 M /branches/prog/bam/bgzf.c
3138
3139 updated bgzf, on behalf of Bob
3140
3141 ------------------------------------------------------------------------
3142 r695 | lh3 | 2008-11-23 11:40:31 +0000 (Sun, 23 Nov 2008) | 2 lines
3143 Changed paths:
3144 M /branches/prog/bam/bam_index.c
3145 M /branches/prog/bam/razf.c
3146
3147 fixed a bug in razf
3148
3149 ------------------------------------------------------------------------
3150 r694 | lh3 | 2008-11-22 16:23:52 +0000 (Sat, 22 Nov 2008) | 4 lines
3151 Changed paths:
3152 M /branches/prog/bam/bam_index.c
3153 M /branches/prog/bam/bam_lpileup.c
3154 M /branches/prog/bam/bam_tview.c
3155 M /branches/prog/bam/bamtk.c
3156
3157 * bam-0.1.0-40
3158 * fixed two small memory leaks
3159 * fixed a memory problem when seek outside the length of the sequence
3160
3161 ------------------------------------------------------------------------
3162 r693 | lh3 | 2008-11-22 16:10:04 +0000 (Sat, 22 Nov 2008) | 3 lines
3163 Changed paths:
3164 M /branches/prog/bam/bam_index.c
3165 M /branches/prog/bam/bamtk.c
3166
3167 * bam-0.1.0-39
3168 * fixed an uninitialized warning. This does not matter in fact
3169
3170 ------------------------------------------------------------------------
3171 r692 | lh3 | 2008-11-22 15:44:05 +0000 (Sat, 22 Nov 2008) | 2 lines
3172 Changed paths:
3173 M /branches/prog/bam/razf.c
3174 M /branches/prog/bam/razf.h
3175
3176 Jue's new razf
3177
3178 ------------------------------------------------------------------------
3179 r691 | lh3 | 2008-11-21 21:30:39 +0000 (Fri, 21 Nov 2008) | 4 lines
3180 Changed paths:
3181 M /branches/prog/bam/Makefile
3182 M /branches/prog/bam/bam.h
3183 M /branches/prog/bam/bam_index.c
3184 M /branches/prog/bam/bamtk.c
3185 M /branches/prog/bam/bgzip.c
3186
3187 * bam-0.1.0-38
3188 * get rid of some warings in bgzip.c
3189 * potentially improve performance in indexing for BGZF
3190
3191 ------------------------------------------------------------------------
3192 r690 | lh3 | 2008-11-21 21:15:51 +0000 (Fri, 21 Nov 2008) | 2 lines
3193 Changed paths:
3194 M /branches/prog/bam/bgzf.c
3195
3196 I think I have fixed the bug in bgzf
3197
3198 ------------------------------------------------------------------------
3199 r689 | lh3 | 2008-11-21 20:48:56 +0000 (Fri, 21 Nov 2008) | 2 lines
3200 Changed paths:
3201 M /branches/prog/bam/bgzf.c
3202
3203 bug fix by Bob
3204
3205 ------------------------------------------------------------------------
3206 r688 | lh3 | 2008-11-21 20:37:27 +0000 (Fri, 21 Nov 2008) | 2 lines
3207 Changed paths:
3208 M /branches/prog/bam/bam.h
3209 M /branches/prog/bam/bam_index.c
3210
3211 fixed a bug due to the name change in _IOLIB
3212
3213 ------------------------------------------------------------------------
3214 r687 | lh3 | 2008-11-21 14:42:56 +0000 (Fri, 21 Nov 2008) | 2 lines
3215 Changed paths:
3216 M /branches/prog/bam/bgzf.c
3217
3218 fix small things
3219
3220 ------------------------------------------------------------------------
3221 r686 | lh3 | 2008-11-21 14:37:59 +0000 (Fri, 21 Nov 2008) | 2 lines
3222 Changed paths:
3223 A /branches/prog/bam/bgzf.c
3224 A /branches/prog/bam/bgzf.h
3225 A /branches/prog/bam/bgzip.c
3226
3227 Bob's BGZF format, although currently buggy
3228
3229 ------------------------------------------------------------------------
3230 r685 | lh3 | 2008-11-21 09:48:20 +0000 (Fri, 21 Nov 2008) | 3 lines
3231 Changed paths:
3232 M /branches/prog/bam/bam_index.c
3233 M /branches/prog/bam/bam_tview.c
3234 M /branches/prog/bam/bamtk.c
3235
3236 * bam-0.1.0-37
3237 * improve interface a little bit
3238
3239 ------------------------------------------------------------------------
3240 r684 | lh3 | 2008-11-21 09:30:18 +0000 (Fri, 21 Nov 2008) | 3 lines
3241 Changed paths:
3242 M /branches/prog/bam/bam_tview.c
3243 M /branches/prog/bam/bamtk.c
3244
3245 * bam-0.1.0-36
3246 * improve the interface of tview, a little bit
3247
3248 ------------------------------------------------------------------------
3249 r683 | lh3 | 2008-11-20 22:33:54 +0000 (Thu, 20 Nov 2008) | 2 lines
3250 Changed paths:
3251 M /branches/prog/bam/bam_tview.c
3252
3253 a little better viewer
3254
3255 ------------------------------------------------------------------------
3256 r682 | lh3 | 2008-11-20 22:27:01 +0000 (Thu, 20 Nov 2008) | 3 lines
3257 Changed paths:
3258 M /branches/prog/bam/bam.h
3259 M /branches/prog/bam/bam_tview.c
3260 M /branches/prog/bam/bamtk.c
3261
3262 * bamtk-0.1.0-35
3263 * better viewer
3264
3265 ------------------------------------------------------------------------
3266 r681 | lh3 | 2008-11-20 20:51:16 +0000 (Thu, 20 Nov 2008) | 3 lines
3267 Changed paths:
3268 M /branches/prog/bam/Makefile
3269 M /branches/prog/bam/bam_tview.c
3270 M /branches/prog/bam/bamtk.c
3271
3272 * bamtk-0.1.0-34
3273 * tview is now a component of bamtk
3274
3275 ------------------------------------------------------------------------
3276 r680 | lh3 | 2008-11-20 19:17:30 +0000 (Thu, 20 Nov 2008) | 2 lines
3277 Changed paths:
3278 A /branches/prog/bam/bam_tview.c
3279
3280 text alignment viewer
3281
3282 ------------------------------------------------------------------------
3283 r679 | lh3 | 2008-11-20 19:17:15 +0000 (Thu, 20 Nov 2008) | 5 lines
3284 Changed paths:
3285 M /branches/prog/bam/Makefile
3286 M /branches/prog/bam/bam.h
3287 M /branches/prog/bam/bam_index.c
3288 M /branches/prog/bam/bam_lpileup.c
3289 M /branches/prog/bam/bam_pileup.c
3290 M /branches/prog/bam/bamtk.1
3291 M /branches/prog/bam/bamtk.c
3292 M /branches/prog/bam/faidx.c
3293
3294 * bamtk-0.1.0-33
3295 * added routines to reset pileup bufferes
3296 * fixed a bug in faidx
3297 * add text alignment viewer
3298
3299 ------------------------------------------------------------------------
3300 r678 | lh3 | 2008-11-20 11:05:02 +0000 (Thu, 20 Nov 2008) | 2 lines
3301 Changed paths:
3302 M /branches/prog/bam/Makefile
3303 A /branches/prog/bam/bam_lpileup.c (from /branches/prog/bam/bam_tview.c:668)
3304 D /branches/prog/bam/bam_tview.c
3305
3306 rename tview as lpileup
3307
3308 ------------------------------------------------------------------------
3309 r677 | lh3 | 2008-11-20 10:08:52 +0000 (Thu, 20 Nov 2008) | 2 lines
3310 Changed paths:
3311 M /branches/prog/bam/razf.c
3312
3313 fixed a bug in razf
3314
3315 ------------------------------------------------------------------------
3316 r676 | lh3 | 2008-11-19 22:52:20 +0000 (Wed, 19 Nov 2008) | 2 lines
3317 Changed paths:
3318 M /branches/prog/bam/bam.h
3319 M /branches/prog/bam/bam_index.c
3320 M /branches/prog/bam/faidx.h
3321
3322 add documentations
3323
3324 ------------------------------------------------------------------------
3325 r674 | lh3 | 2008-11-19 21:39:17 +0000 (Wed, 19 Nov 2008) | 2 lines
3326 Changed paths:
3327 M /branches/prog/bam/bam.h
3328 M /branches/prog/bam/bamtk.1
3329 M /branches/prog/bam/faidx.h
3330
3331 update documentation
3332
3333 ------------------------------------------------------------------------
3334 r673 | lh3 | 2008-11-19 21:19:03 +0000 (Wed, 19 Nov 2008) | 2 lines
3335 Changed paths:
3336 A /branches/prog/bam/bamtk.1
3337
3338 add manual page
3339
3340 ------------------------------------------------------------------------
3341 r672 | lh3 | 2008-11-19 16:40:49 +0000 (Wed, 19 Nov 2008) | 3 lines
3342 Changed paths:
3343 M /branches/prog/bam/bamtk.c
3344 M /branches/prog/bam/faidx.c
3345
3346 * bamtk-0.1.0-32
3347 * make faidx more error resistant
3348
3349 ------------------------------------------------------------------------
3350 r671 | lh3 | 2008-11-19 16:09:55 +0000 (Wed, 19 Nov 2008) | 2 lines
3351 Changed paths:
3352 M /branches/prog/bam/faidx.h
3353
3354 add index
3355
3356 ------------------------------------------------------------------------
3357 r670 | lh3 | 2008-11-19 16:02:39 +0000 (Wed, 19 Nov 2008) | 3 lines
3358 Changed paths:
3359 M /branches/prog/bam/bam_pileup.c
3360 M /branches/prog/bam/bamtk.c
3361 M /branches/prog/bam/faidx.c
3362
3363 * bamtk-0.1.0-31
3364 * show reference sequence in pileup -v (not in the default pileup)
3365
3366 ------------------------------------------------------------------------
3367 r669 | lh3 | 2008-11-19 14:51:17 +0000 (Wed, 19 Nov 2008) | 3 lines
3368 Changed paths:
3369 M /branches/prog/bam/Makefile
3370 M /branches/prog/bam/bamtk.c
3371 M /branches/prog/bam/faidx.c
3372
3373 * bamtk-0.1.0-30
3374 * put faidx in bamtk and remove faidx_main.c
3375
3376 ------------------------------------------------------------------------
3377 r668 | lh3 | 2008-11-19 14:15:05 +0000 (Wed, 19 Nov 2008) | 4 lines
3378 Changed paths:
3379 M /branches/prog/bam/Makefile
3380 M /branches/prog/bam/bam_index.c
3381 M /branches/prog/bam/bam_tview.c
3382 M /branches/prog/bam/bamtk.c
3383 A /branches/prog/bam/faidx.c
3384 A /branches/prog/bam/faidx.h
3385 M /branches/prog/bam/razf.c
3386
3387 * bamtk-0.1.0-29
3388 * fixed a bug in tview.c
3389 * prepare to add faidx
3390
3391 ------------------------------------------------------------------------
3392 r667 | lh3 | 2008-11-19 10:20:45 +0000 (Wed, 19 Nov 2008) | 2 lines
3393 Changed paths:
3394 M /branches/prog/bam/bam.h
3395 M /branches/prog/bam/razf.c
3396 M /branches/prog/bam/razf.h
3397
3398 gzip-compatible razf
3399
3400 ------------------------------------------------------------------------
3401 r664 | lh3 | 2008-11-18 12:50:23 +0000 (Tue, 18 Nov 2008) | 5 lines
3402 Changed paths:
3403 M /branches/prog/bam/bam.h
3404 M /branches/prog/bam/bam_index.c
3405 M /branches/prog/bam/bamtk.c
3406
3407 * bamtk-0.1.0-28
3408 * fetch: fixed a bug at an array boundary
3409 * fetch: fixed a bug when the whole chromosome is retrieved
3410 * add linear index
3411
3412 ------------------------------------------------------------------------
3413 r663 | lh3 | 2008-11-17 21:29:22 +0000 (Mon, 17 Nov 2008) | 3 lines
3414 Changed paths:
3415 M /branches/prog/bam/Makefile
3416 M /branches/prog/bam/bam.c
3417 M /branches/prog/bam/bam.h
3418 M /branches/prog/bam/bam_import.c
3419 M /branches/prog/bam/bam_pileup.c
3420 M /branches/prog/bam/bam_tview.c
3421 M /branches/prog/bam/bamtk.c
3422
3423 * bamtk-0.1.0-27
3424 * put l_qseq into core and move l_aux to bam1_t
3425
3426 ------------------------------------------------------------------------
3427 r662 | lh3 | 2008-11-17 20:55:16 +0000 (Mon, 17 Nov 2008) | 3 lines
3428 Changed paths:
3429 M /branches/prog/bam/bam.c
3430 M /branches/prog/bam/bam.h
3431 M /branches/prog/bam/bam_import.c
3432 M /branches/prog/bam/bam_index.c
3433 M /branches/prog/bam/bam_pileup.c
3434 M /branches/prog/bam/bamtk.c
3435
3436 * bamtk-0.1.0-26
3437 * save seq and qual separately
3438
3439 ------------------------------------------------------------------------
3440 r661 | lh3 | 2008-11-17 13:09:37 +0000 (Mon, 17 Nov 2008) | 2 lines
3441 Changed paths:
3442 M /branches/prog/bam/bam.h
3443
3444 little
3445
3446 ------------------------------------------------------------------------
3447 r660 | lh3 | 2008-11-17 13:06:14 +0000 (Mon, 17 Nov 2008) | 2 lines
3448 Changed paths:
3449 M /branches/prog/bam/bam.h
3450
3451 more documentations
3452
3453 ------------------------------------------------------------------------
3454 r659 | lh3 | 2008-11-17 12:55:08 +0000 (Mon, 17 Nov 2008) | 3 lines
3455 Changed paths:
3456 M /branches/prog/bam/bam_pileup.c
3457 M /branches/prog/bam/bamtk.c
3458
3459 * bamtk-0.1.0-25
3460 * make tview work for TAM
3461
3462 ------------------------------------------------------------------------
3463 r658 | lh3 | 2008-11-17 12:50:21 +0000 (Mon, 17 Nov 2008) | 3 lines
3464 Changed paths:
3465 M /branches/prog/bam/Makefile
3466 M /branches/prog/bam/bam.h
3467 M /branches/prog/bam/bam_pileup.c
3468 M /branches/prog/bam/bam_tview.c
3469 M /branches/prog/bam/bamtk.c
3470
3471 * bamtk-0.1.0-24
3472 * make tview as an independent module
3473
3474 ------------------------------------------------------------------------
3475 r657 | lh3 | 2008-11-17 11:26:06 +0000 (Mon, 17 Nov 2008) | 2 lines
3476 Changed paths:
3477 M /branches/prog/bam/Makefile
3478 M /branches/prog/bam/bam.h
3479 M /branches/prog/bam/bam_pileup.c
3480
3481 change little
3482
3483 ------------------------------------------------------------------------
3484 r656 | lh3 | 2008-11-16 21:33:19 +0000 (Sun, 16 Nov 2008) | 3 lines
3485 Changed paths:
3486 M /branches/prog/bam/bam_pileup.c
3487 M /branches/prog/bam/bamtk.c
3488
3489 * bamtk-0.1.0-23
3490 * also add tview for TAM
3491
3492 ------------------------------------------------------------------------
3493 r655 | lh3 | 2008-11-16 21:29:46 +0000 (Sun, 16 Nov 2008) | 3 lines
3494 Changed paths:
3495 M /branches/prog/bam/Makefile
3496 M /branches/prog/bam/bam_tview.c
3497 M /branches/prog/bam/bamtk.c
3498
3499 * bamtk-0.1.0-22
3500 * make tview more efficient for deep depth
3501
3502 ------------------------------------------------------------------------
3503 r654 | lh3 | 2008-11-16 20:52:19 +0000 (Sun, 16 Nov 2008) | 4 lines
3504 Changed paths:
3505 M /branches/prog/bam/Makefile
3506 M /branches/prog/bam/bam_import.c
3507 M /branches/prog/bam/bam_pileup.c
3508 A /branches/prog/bam/bam_tview.c
3509 M /branches/prog/bam/bamtk.c
3510
3511 * bamtk-0.1.0-21
3512 * fixed bug in the TAM parser: lowercase not recognized
3513 * unfinished function to leveled pileup (tview)
3514
3515 ------------------------------------------------------------------------
3516 r653 | lh3 | 2008-11-15 12:58:36 +0000 (Sat, 15 Nov 2008) | 3 lines
3517 Changed paths:
3518 M /branches/prog/bam/bam.h
3519 M /branches/prog/bam/bam_pileup.c
3520 M /branches/prog/bam/bamtk.c
3521
3522 * bamtk-0.1.0-20
3523 * pileup now display deleted bases as '*'
3524
3525 ------------------------------------------------------------------------
3526 r652 | lh3 | 2008-11-15 09:58:39 +0000 (Sat, 15 Nov 2008) | 4 lines
3527 Changed paths:
3528 M /branches/prog/bam/bam_index.c
3529 M /branches/prog/bam/bamtk.c
3530
3531 * bamtk-0.1.0-19
3532 * fixed a bug in fetch()
3533 * reduce memory in indexing
3534
3535 ------------------------------------------------------------------------
3536 r651 | lh3 | 2008-11-14 21:56:05 +0000 (Fri, 14 Nov 2008) | 5 lines
3537 Changed paths:
3538 M /branches/prog/bam/Makefile
3539 M /branches/prog/bam/bam.h
3540 M /branches/prog/bam/bam_index.c
3541 M /branches/prog/bam/bamtk.c
3542
3543 * bamtk-0.1.0-18
3544 * important changes are made to index: the index size is increased, but
3545 now we have no limit on file sizes and the new method potentially
3546 works with BGZF, Bob's new compression format.
3547
3548 ------------------------------------------------------------------------
3549 r650 | lh3 | 2008-11-14 16:03:22 +0000 (Fri, 14 Nov 2008) | 4 lines
3550 Changed paths:
3551 M /branches/prog/bam/bam.h
3552 M /branches/prog/bam/bam_index.c
3553 M /branches/prog/bam/bamtk.c
3554
3555 * bamtk-0.1.0-17
3556 * more comments in bam.h
3557 * fixed a bug in bam_index.c
3558
3559 ------------------------------------------------------------------------
3560 r649 | lh3 | 2008-11-13 16:04:18 +0000 (Thu, 13 Nov 2008) | 4 lines
3561 Changed paths:
3562 M /branches/prog/bam/bam.c
3563 M /branches/prog/bam/bam.h
3564 M /branches/prog/bam/bam_import.c
3565 M /branches/prog/bam/bam_index.c
3566 M /branches/prog/bam/bam_pileup.c
3567 M /branches/prog/bam/bam_sort.c
3568 M /branches/prog/bam/bamtk.c
3569
3570 * bamtk-0.1.0-16
3571 * use macros to retrieve pointers from bam1_t and thus reduce the size
3572 of bam1_t struct.
3573
3574 ------------------------------------------------------------------------
3575 r648 | lh3 | 2008-11-13 13:21:39 +0000 (Thu, 13 Nov 2008) | 3 lines
3576 Changed paths:
3577 M /branches/prog/bam/bam_sort.c
3578 M /branches/prog/bam/bamtk.c
3579
3580 * bamtk-0.1.0-15
3581 * make more things work over pipe
3582
3583 ------------------------------------------------------------------------
3584 r647 | lh3 | 2008-11-13 12:49:28 +0000 (Thu, 13 Nov 2008) | 2 lines
3585 Changed paths:
3586 M /branches/prog/bam/misc/maq2tam.c
3587
3588 fixed a bug in maq2tam
3589
3590 ------------------------------------------------------------------------
3591 r646 | lh3 | 2008-11-13 11:46:59 +0000 (Thu, 13 Nov 2008) | 3 lines
3592 Changed paths:
3593 M /branches/prog/bam/Makefile
3594 M /branches/prog/bam/misc/Makefile
3595 M /branches/prog/bam/misc/maq2tam.c
3596
3597 * bug fix in maq2tam.c
3598 * improve Makefile
3599
3600 ------------------------------------------------------------------------
3601 r645 | lh3 | 2008-11-13 11:39:46 +0000 (Thu, 13 Nov 2008) | 3 lines
3602 Changed paths:
3603 A /branches/prog/bam/misc/Makefile
3604 M /branches/prog/bam/misc/maq2tam.c
3605
3606 * corrected maq2tam
3607 * add Makefile
3608
3609 ------------------------------------------------------------------------
3610 r644 | lh3 | 2008-11-13 11:25:45 +0000 (Thu, 13 Nov 2008) | 2 lines
3611 Changed paths:
3612 M /branches/prog/bam/razf.c
3613
3614 fixed the bug in buffered write (on behalf of Jue)
3615
3616 ------------------------------------------------------------------------
3617 r643 | lh3 | 2008-11-13 10:53:42 +0000 (Thu, 13 Nov 2008) | 2 lines
3618 Changed paths:
3619 D /branches/prog/bam/all2tam.pl
3620 A /branches/prog/bam/misc/all2tam.pl (from /branches/prog/bam/all2tam.pl:642)
3621
3622 move to misc
3623
3624 ------------------------------------------------------------------------
3625 r642 | lh3 | 2008-11-13 10:53:23 +0000 (Thu, 13 Nov 2008) | 2 lines
3626 Changed paths:
3627 M /branches/prog/bam/all2tam.pl
3628
3629 change tag
3630
3631 ------------------------------------------------------------------------
3632 r641 | lh3 | 2008-11-13 10:53:12 +0000 (Thu, 13 Nov 2008) | 2 lines
3633 Changed paths:
3634 D /branches/prog/bam/utils
3635
3636 has been renamed
3637
3638 ------------------------------------------------------------------------
3639 r640 | lh3 | 2008-11-13 10:52:50 +0000 (Thu, 13 Nov 2008) | 2 lines
3640 Changed paths:
3641 A /branches/prog/bam/misc (from /branches/prog/bam/utils:639)
3642
3643 rename
3644
3645 ------------------------------------------------------------------------
3646 r639 | lh3 | 2008-11-13 10:52:35 +0000 (Thu, 13 Nov 2008) | 2 lines
3647 Changed paths:
3648 A /branches/prog/bam/utils
3649 A /branches/prog/bam/utils/maq2tam.c
3650
3651 utilities (converters and so on)
3652
3653 ------------------------------------------------------------------------
3654 r638 | lh3 | 2008-11-12 22:24:22 +0000 (Wed, 12 Nov 2008) | 4 lines
3655 Changed paths:
3656 M /branches/prog/bam/bam.c
3657 M /branches/prog/bam/bam.h
3658 M /branches/prog/bam/bam_import.c
3659 M /branches/prog/bam/bamtk.c
3660
3661 * bamtk-0.1.0-14
3662 * copy the text header to BAM
3663 * add BAM1 header flag
3664
3665 ------------------------------------------------------------------------
3666 r637 | lh3 | 2008-11-12 14:56:08 +0000 (Wed, 12 Nov 2008) | 4 lines
3667 Changed paths:
3668 M /branches/prog/bam/bam.h
3669 M /branches/prog/bam/bam_index.c
3670 M /branches/prog/bam/bamtk.c
3671 M /branches/prog/bam/razf.c
3672
3673 * bamtk-0.1.0-13
3674 * fixed a bug in razf
3675 * improved and fixed potential bugs in index
3676
3677 ------------------------------------------------------------------------
3678 r636 | lh3 | 2008-11-12 11:57:13 +0000 (Wed, 12 Nov 2008) | 2 lines
3679 Changed paths:
3680 M /branches/prog/bam/bam.h
3681 M /branches/prog/bam/bam_index.c
3682 M /branches/prog/bam/bam_pileup.c
3683 M /branches/prog/bam/bamtk.c
3684
3685 update documentation in the HeaderDOC format
3686
3687 ------------------------------------------------------------------------
3688 r635 | lh3 | 2008-11-12 10:08:38 +0000 (Wed, 12 Nov 2008) | 4 lines
3689 Changed paths:
3690 M /branches/prog/bam/bam.c
3691 M /branches/prog/bam/bam.h
3692 M /branches/prog/bam/bam_import.c
3693 M /branches/prog/bam/bam_index.c
3694 M /branches/prog/bam/bam_pileup.c
3695 M /branches/prog/bam/bamtk.c
3696
3697 * bamtk-0.1.0-12
3698 * more documentations
3699 * rename baf1_core_t as bam1_core_t
3700
3701 ------------------------------------------------------------------------
3702 r634 | lh3 | 2008-11-11 23:00:35 +0000 (Tue, 11 Nov 2008) | 2 lines
3703 Changed paths:
3704 M /branches/prog/bam/bam.h
3705 M /branches/prog/bam/bam_pileup.c
3706
3707 documentation
3708
3709 ------------------------------------------------------------------------
3710 r633 | lh3 | 2008-11-11 21:23:49 +0000 (Tue, 11 Nov 2008) | 4 lines
3711 Changed paths:
3712 M /branches/prog/bam/bam_index.c
3713 M /branches/prog/bam/bam_pileup.c
3714 M /branches/prog/bam/bamtk.c
3715
3716 * bamtk-0.1.0-11
3717 * give up regional pileup. We can now use pipe to mimic that.
3718 * for index file, change suffix .idx to .bmi
3719
3720 ------------------------------------------------------------------------
3721 r632 | lh3 | 2008-11-11 21:00:11 +0000 (Tue, 11 Nov 2008) | 3 lines
3722 Changed paths:
3723 M /branches/prog/bam/bam.h
3724 M /branches/prog/bam/bam_import.c
3725 M /branches/prog/bam/bam_pileup.c
3726 M /branches/prog/bam/bamtk.c
3727 M /branches/prog/bam/razf.c
3728
3729 * bamtk-0.1.0-10
3730 * make pileup work on TAM
3731
3732 ------------------------------------------------------------------------
3733 r631 | lh3 | 2008-11-11 09:20:29 +0000 (Tue, 11 Nov 2008) | 4 lines
3734 Changed paths:
3735 M /branches/prog/bam/bam_pileup.c
3736 M /branches/prog/bam/bamtk.c
3737 M /branches/prog/bam/razf.c
3738 M /branches/prog/bam/razf.h
3739 M /branches/prog/bam/razip.c
3740
3741 * bamtk-0.1.0-9
3742 * razf now supports streaming
3743 * prepare to improve pileup (have not yet)
3744
3745 ------------------------------------------------------------------------
3746 r630 | lh3 | 2008-11-10 18:34:40 +0000 (Mon, 10 Nov 2008) | 3 lines
3747 Changed paths:
3748 M /branches/prog/bam/bam.h
3749 M /branches/prog/bam/bam_import.c
3750 M /branches/prog/bam/bam_pileup.c
3751 M /branches/prog/bam/bamtk.c
3752
3753 * bamtk-0.1.0-8
3754 * improve the interface of TAM parser
3755
3756 ------------------------------------------------------------------------
3757 r629 | lh3 | 2008-11-10 13:06:13 +0000 (Mon, 10 Nov 2008) | 3 lines
3758 Changed paths:
3759 M /branches/prog/bam/bam_pileup.c
3760 M /branches/prog/bam/bamtk.c
3761
3762 * bamtk-0.1.0-7
3763 * almost nothing
3764
3765 ------------------------------------------------------------------------
3766 r628 | lh3 | 2008-11-10 12:56:36 +0000 (Mon, 10 Nov 2008) | 3 lines
3767 Changed paths:
3768 M /branches/prog/bam/bam.c
3769 M /branches/prog/bam/bam.h
3770 M /branches/prog/bam/bam_pileup.c
3771 M /branches/prog/bam/bamtk.c
3772
3773 * bamtk-0.1.0-6
3774 * fixed a bug in bam_pileup.c
3775
3776 ------------------------------------------------------------------------
3777 r627 | lh3 | 2008-11-10 11:32:46 +0000 (Mon, 10 Nov 2008) | 4 lines
3778 Changed paths:
3779 M /branches/prog/bam/bam.h
3780 M /branches/prog/bam/bam_pileup.c
3781 M /branches/prog/bam/bamtk.c
3782 M /branches/prog/bam/razf.c
3783
3784 * bamtk-0.1.0-5
3785 * fixed a bug in razf.c, caused by my modifications
3786 * improve the interface of pileup. Now it will be slower but more flexible
3787
3788 ------------------------------------------------------------------------
3789 r626 | lh3 | 2008-11-09 20:51:04 +0000 (Sun, 09 Nov 2008) | 3 lines
3790 Changed paths:
3791 M /branches/prog/bam/bam.h
3792 M /branches/prog/bam/bamtk.c
3793
3794 * bamtk-0.1.0-4
3795 * view: dumping binary output
3796
3797 ------------------------------------------------------------------------
3798 r625 | lh3 | 2008-11-09 20:31:54 +0000 (Sun, 09 Nov 2008) | 3 lines
3799 Changed paths:
3800 M /branches/prog/bam/bam.c
3801 M /branches/prog/bam/bam.h
3802 M /branches/prog/bam/bam_import.c
3803 M /branches/prog/bam/bam_index.c
3804 M /branches/prog/bam/bam_pileup.c
3805 M /branches/prog/bam/bam_sort.c
3806 M /branches/prog/bam/bamtk.c
3807
3808 * bamtk-0.1.0-3
3809 * rename functions
3810
3811 ------------------------------------------------------------------------
3812 r624 | lh3 | 2008-11-09 15:07:32 +0000 (Sun, 09 Nov 2008) | 2 lines
3813 Changed paths:
3814 M /branches/prog/bam/bam.h
3815
3816 add comments
3817
3818 ------------------------------------------------------------------------
3819 r623 | lh3 | 2008-11-08 22:32:49 +0000 (Sat, 08 Nov 2008) | 4 lines
3820 Changed paths:
3821 M /branches/prog/bam/bam_index.c
3822 M /branches/prog/bam/bamtk.c
3823
3824 * bamtk-0.1.0-2
3825 * improve indexing for a mixture of long and short reads, although currently
3826 I do not know whether it really works...
3827
3828 ------------------------------------------------------------------------
3829 r622 | lh3 | 2008-11-08 22:13:58 +0000 (Sat, 08 Nov 2008) | 3 lines
3830 Changed paths:
3831 M /branches/prog/bam/bam_index.c
3832 M /branches/prog/bam/bamtk.c
3833
3834 * bamtk-0.1.0-1
3835 * prepare for improving indexing algorithm
3836
3837 ------------------------------------------------------------------------
3838 r621 | lh3 | 2008-11-08 20:28:09 +0000 (Sat, 08 Nov 2008) | 4 lines
3839 Changed paths:
3840 A /branches/prog/bam/all2tam.pl
3841 M /branches/prog/bam/bam.c
3842 M /branches/prog/bam/bam.h
3843 M /branches/prog/bam/bam_import.c
3844 M /branches/prog/bam/bamtk.c
3845 D /branches/prog/bam/tam_utils.pl
3846
3847 * bamtk-0.1.0
3848 * smarter integers
3849 * rename tam_utils.pl to all2tam.pl
3850
3851 ------------------------------------------------------------------------
3852 r620 | lh3 | 2008-11-08 17:17:22 +0000 (Sat, 08 Nov 2008) | 2 lines
3853 Changed paths:
3854 A /branches/prog/bam
3855 A /branches/prog/bam/Makefile
3856 A /branches/prog/bam/bam.c
3857 A /branches/prog/bam/bam.h
3858 A /branches/prog/bam/bam_endian.h
3859 A /branches/prog/bam/bam_import.c
3860 A /branches/prog/bam/bam_index.c
3861 A /branches/prog/bam/bam_pileup.c
3862 A /branches/prog/bam/bam_sort.c
3863 A /branches/prog/bam/bamtk.c
3864 A /branches/prog/bam/khash.h
3865 A /branches/prog/bam/ksort.h
3866 A /branches/prog/bam/kstream.h
3867 A /branches/prog/bam/razf.c
3868 A /branches/prog/bam/razf.h
3869 A /branches/prog/bam/razip.c
3870 A /branches/prog/bam/tam_utils.pl
3871 A /branches/prog/bam/zutil.h
3872
3873 The Binary Alignment/Mapping format.
3874
3875 ------------------------------------------------------------------------