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comparison SNV/SNVMix2_source/SNVMix2-v0.12.1-rc1/samtools-0.1.6/ChangeLog @ 0:74f5ea818cea

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author ryanmorin
date Wed, 12 Oct 2011 19:50:38 -0400
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1 ------------------------------------------------------------------------
2 r451 | lh3lh3 | 2009-09-02 10:44:48 +0100 (Wed, 02 Sep 2009) | 4 lines
3 Changed paths:
4 M /trunk/samtools/bam_md.c
5 M /trunk/samtools/bam_rmdup.c
6 M /trunk/samtools/bam_rmdupse.c
7 M /trunk/samtools/bam_sort.c
8 M /trunk/samtools/bamtk.c
9 M /trunk/samtools/samtools.1
10
11 * samtools-0.1.5-34 (r451)
12 * applied the patch by John
13 * improved the help message a little bit
14
15 ------------------------------------------------------------------------
16 r450 | lh3lh3 | 2009-09-02 09:55:55 +0100 (Wed, 02 Sep 2009) | 3 lines
17 Changed paths:
18 M /trunk/samtools/bam_color.c
19 M /trunk/samtools/bamtk.c
20
21 * samtools-0.1.5-33 (r450)
22 * fixed a bug in bam_color.c (on behalf of Nils Homer)
23
24 ------------------------------------------------------------------------
25 r449 | lh3lh3 | 2009-08-29 20:36:41 +0100 (Sat, 29 Aug 2009) | 4 lines
26 Changed paths:
27 M /trunk/samtools/bam_import.c
28 M /trunk/samtools/bam_md.c
29 M /trunk/samtools/bamtk.c
30 M /trunk/samtools/misc/samtools.pl
31
32 * samtools-0.1.5-32 (r449)
33 * fillmd: fixed a bug in modifying MD/NM tags
34 * in import, give a warning if the read is aligned but there is no CIGAR.
35
36 ------------------------------------------------------------------------
37 r448 | lh3lh3 | 2009-08-19 09:44:28 +0100 (Wed, 19 Aug 2009) | 3 lines
38 Changed paths:
39 M /trunk/samtools/ChangeLog
40 M /trunk/samtools/bam_pileup.c
41 M /trunk/samtools/bamtk.c
42 M /trunk/samtools/misc/wgsim_eval.pl
43
44 * samtools-0.1.5-31 (r448)
45 * fixed an issue when the last CIGAR is I or D
46
47 ------------------------------------------------------------------------
48 r447 | lh3lh3 | 2009-08-17 09:34:57 +0100 (Mon, 17 Aug 2009) | 3 lines
49 Changed paths:
50 M /trunk/samtools/bam_aux.c
51 M /trunk/samtools/bamtk.c
52
53 * samtools-0.1.5-30 (r447)
54 * fixed a bug in bam_aux_get(): 'A' is not checked
55
56 ------------------------------------------------------------------------
57 r446 | lh3lh3 | 2009-08-17 09:33:17 +0100 (Mon, 17 Aug 2009) | 2 lines
58 Changed paths:
59 M /trunk/samtools/bam_aux.c
60 M /trunk/samtools/bamtk.c
61
62 *
63
64 ------------------------------------------------------------------------
65 r444 | lh3lh3 | 2009-08-11 10:02:36 +0100 (Tue, 11 Aug 2009) | 3 lines
66 Changed paths:
67 M /trunk/samtools/bam_sort.c
68 M /trunk/samtools/bamtk.c
69
70 * samtools-0.1.5-28 (r444)
71 * bug in "merge -n"
72
73 ------------------------------------------------------------------------
74 r443 | lh3lh3 | 2009-08-11 09:29:11 +0100 (Tue, 11 Aug 2009) | 4 lines
75 Changed paths:
76 M /trunk/samtools/bam.c
77 M /trunk/samtools/bam_import.c
78 M /trunk/samtools/bamtk.c
79
80 * samtools-0.1.5-27 (r443)
81 * SEQ and QUAL can be "*"
82 * parse CIGAR "=" and "X" as "M"
83
84 ------------------------------------------------------------------------
85 r442 | lh3lh3 | 2009-08-07 21:56:38 +0100 (Fri, 07 Aug 2009) | 4 lines
86 Changed paths:
87 M /trunk/samtools/bam_pileup.c
88 M /trunk/samtools/bamtk.c
89 M /trunk/samtools/misc/md5.c
90 M /trunk/samtools/misc/md5.h
91 M /trunk/samtools/misc/md5fa.c
92
93 * samtools-0.1.5-26 (r442)
94 * replace RSA Inc md5.* with ones under permissive lincense
95 * fixed a bug in detecting unsorted bam in pileup
96
97 ------------------------------------------------------------------------
98 r441 | bhandsaker | 2009-08-05 14:41:28 +0100 (Wed, 05 Aug 2009) | 2 lines
99 Changed paths:
100 M /trunk/samtools/bgzf.c
101 M /trunk/samtools/bgzf.h
102 M /trunk/samtools/bgzip.c
103
104 Change copyright notices now that MIT has approved open source distribution.
105
106 ------------------------------------------------------------------------
107 r440 | lh3lh3 | 2009-08-05 10:44:24 +0100 (Wed, 05 Aug 2009) | 3 lines
108 Changed paths:
109 M /trunk/samtools/bam_stat.c
110 M /trunk/samtools/bamtk.c
111
112 * samtools-0.1.5-25 (r436)
113 * in flagstats, do not report singletons if both ends are unmapped
114
115 ------------------------------------------------------------------------
116 r439 | lh3lh3 | 2009-08-04 22:16:51 +0100 (Tue, 04 Aug 2009) | 2 lines
117 Changed paths:
118 M /trunk/samtools/misc/maq2sam.c
119
120 fixed a SERIOUS bug in setting 0x20 flag
121
122 ------------------------------------------------------------------------
123 r438 | lh3lh3 | 2009-08-04 21:50:43 +0100 (Tue, 04 Aug 2009) | 2 lines
124 Changed paths:
125 M /trunk/samtools/misc/samtools.pl
126
127 fixed two minor bugs (suggested by Tim M Storm)
128
129 ------------------------------------------------------------------------
130 r437 | lh3lh3 | 2009-08-04 09:13:24 +0100 (Tue, 04 Aug 2009) | 3 lines
131 Changed paths:
132 M /trunk/samtools/bamtk.c
133 M /trunk/samtools/misc/samtools.pl
134 M /trunk/samtools/sam_view.c
135
136 * samtools-0.1.5-24 (r435)
137 * fixed a typo
138
139 ------------------------------------------------------------------------
140 r434 | lh3lh3 | 2009-08-03 10:40:42 +0100 (Mon, 03 Aug 2009) | 3 lines
141 Changed paths:
142 M /trunk/samtools/bam_tview.c
143 M /trunk/samtools/bamtk.c
144
145 * samtools-0.1.5-23 (r434)
146 * in tview, press 'r' to show read names rather than sequences
147
148 ------------------------------------------------------------------------
149 r433 | lh3lh3 | 2009-08-02 19:13:35 +0100 (Sun, 02 Aug 2009) | 3 lines
150 Changed paths:
151 M /trunk/samtools/knetfile.c
152
153 * tried to fixed the buggy FTP random access in Windows. FAILED.
154 * anyway, MinGW seems to have problem with "%lld".
155
156 ------------------------------------------------------------------------
157 r432 | lh3lh3 | 2009-08-02 00:32:07 +0100 (Sun, 02 Aug 2009) | 5 lines
158 Changed paths:
159 M /trunk/samtools/Makefile.mingw
160 M /trunk/samtools/bamtk.c
161 M /trunk/samtools/faidx.c
162 M /trunk/samtools/razf.c
163 A /trunk/samtools/win32/libcurses.a
164 A /trunk/samtools/win32/xcurses.h
165
166 * samtools-0.1.5-22 (r432)
167 * faidx: fixed compitability issue with _WIN32
168 * razf: fixed potential compitability issue with _WIN32
169 * PDCurses support in Windows
170
171 ------------------------------------------------------------------------
172 r431 | lh3lh3 | 2009-08-01 23:34:54 +0100 (Sat, 01 Aug 2009) | 2 lines
173 Changed paths:
174 M /trunk/samtools/win32/libz.a
175
176 replace the GnuWin32 version of libz.a with my own build with MinGW.
177
178 ------------------------------------------------------------------------
179 r430 | lh3lh3 | 2009-08-01 23:21:07 +0100 (Sat, 01 Aug 2009) | 2 lines
180 Changed paths:
181 M /trunk/samtools/knetfile.c
182
183 add comments
184
185 ------------------------------------------------------------------------
186 r429 | lh3lh3 | 2009-08-01 22:41:19 +0100 (Sat, 01 Aug 2009) | 3 lines
187 Changed paths:
188 M /trunk/samtools/Makefile.mingw
189 M /trunk/samtools/bamtk.c
190 M /trunk/samtools/knetfile.c
191 M /trunk/samtools/knetfile.h
192
193 * samtools-0.1.5-21 (r428)
194 * knetfile.c is now compatible with mingw-winsock
195
196 ------------------------------------------------------------------------
197 r428 | lh3lh3 | 2009-08-01 00:39:07 +0100 (Sat, 01 Aug 2009) | 2 lines
198 Changed paths:
199 M /trunk/samtools/Makefile.mingw
200
201 simplify MinGW Makefile
202
203 ------------------------------------------------------------------------
204 r427 | lh3lh3 | 2009-08-01 00:30:54 +0100 (Sat, 01 Aug 2009) | 5 lines
205 Changed paths:
206 A /trunk/samtools/Makefile.mingw
207 M /trunk/samtools/bam_import.c
208 M /trunk/samtools/bamtk.c
209 A /trunk/samtools/win32
210 A /trunk/samtools/win32/libz.a
211 A /trunk/samtools/win32/zconf.h
212 A /trunk/samtools/win32/zlib.h
213
214 * samtools-0.1.5-20 (r427)
215 * MinGW support. At least SAM<->BAM conversion is working. Other
216 functionality are not tested at the moment.
217 * zlib headers and Windows version of libz.a are included in win32/
218
219 ------------------------------------------------------------------------
220 r426 | lh3lh3 | 2009-07-31 23:32:09 +0100 (Fri, 31 Jul 2009) | 3 lines
221 Changed paths:
222 M /trunk/samtools/bamtk.c
223 M /trunk/samtools/sam_view.c
224
225 * samtools-0.1.5-19 (r426)
226 * fixed a bug caused by recent modifications. Sorry.
227
228 ------------------------------------------------------------------------
229 r425 | lh3lh3 | 2009-07-31 23:23:51 +0100 (Fri, 31 Jul 2009) | 2 lines
230 Changed paths:
231 M /trunk/samtools/bgzf.c
232
233 compatible with Windows binary files
234
235 ------------------------------------------------------------------------
236 r424 | lh3lh3 | 2009-07-31 10:19:59 +0100 (Fri, 31 Jul 2009) | 5 lines
237 Changed paths:
238 M /trunk/samtools/bam_maqcns.c
239 M /trunk/samtools/bam_maqcns.h
240 M /trunk/samtools/bam_plcmd.c
241 M /trunk/samtools/bam_tview.c
242 M /trunk/samtools/bamtk.c
243 M /trunk/samtools/misc/samtools.pl
244
245 * samtools-0.1.5-18 (r423)
246 * output additional information in pileup indel lines, for the purepose
247 of debugging at the moment
248 * in tview, optionally allow to treat reference skip as deletion
249
250 ------------------------------------------------------------------------
251 r423 | lh3lh3 | 2009-07-30 22:00:36 +0100 (Thu, 30 Jul 2009) | 2 lines
252 Changed paths:
253 A /trunk/samtools/misc/psl2sam.pl
254
255 convert BLAT psl to SAM.
256
257 ------------------------------------------------------------------------
258 r422 | lh3lh3 | 2009-07-30 11:24:39 +0100 (Thu, 30 Jul 2009) | 6 lines
259 Changed paths:
260 M /trunk/samtools/ChangeLog
261 M /trunk/samtools/bam.c
262 M /trunk/samtools/bamtk.c
263 M /trunk/samtools/bgzf.c
264 M /trunk/samtools/bgzf.h
265 M /trunk/samtools/knetfile.c
266 M /trunk/samtools/sam.c
267 M /trunk/samtools/sam_view.c
268
269 * samtools-0.1.5-17 (r422)
270 * fixed a but in knetfile.c when seek type is not SEEK_SET
271 * write an empty BGZF block to every BGZF file
272 * check BGZF EOF marker in bam_header_read()
273 * update ChangeLog
274
275 ------------------------------------------------------------------------
276 r421 | lh3lh3 | 2009-07-30 10:03:39 +0100 (Thu, 30 Jul 2009) | 3 lines
277 Changed paths:
278 M /trunk/samtools/bam_import.c
279 M /trunk/samtools/bam_plcmd.c
280 M /trunk/samtools/bamtk.c
281 M /trunk/samtools/misc/samtools.pl
282 M /trunk/samtools/sam.c
283 M /trunk/samtools/sam.h
284 M /trunk/samtools/sam_view.c
285
286 * samtools-0.1.5-16 (r421)
287 * in view and pileup, load header from FASTA index if the input is SAM.
288
289 ------------------------------------------------------------------------
290 r420 | lh3lh3 | 2009-07-29 09:18:55 +0100 (Wed, 29 Jul 2009) | 2 lines
291 Changed paths:
292 M /trunk/samtools/misc/maq2sam.c
293
294 do not set "read 1" if reads are not mapped in the PE mode of maq
295
296 ------------------------------------------------------------------------
297 r419 | lh3lh3 | 2009-07-28 09:52:33 +0100 (Tue, 28 Jul 2009) | 5 lines
298 Changed paths:
299 M /trunk/samtools/bam_import.c
300 M /trunk/samtools/bamtk.c
301 M /trunk/samtools/misc/samtools.pl
302 M /trunk/samtools/misc/wgsim_eval.pl
303
304 * samtools-0.1.5-15 (r419)
305 * in sam_open(), return NULL when the file cannot be opened.
306 * make wgsim_eval.pl more robust to imperfect SAM
307 * add "unique" command to samtools.pl
308
309 ------------------------------------------------------------------------
310 r418 | lh3lh3 | 2009-07-24 14:04:19 +0100 (Fri, 24 Jul 2009) | 2 lines
311 Changed paths:
312 M /trunk/samtools/misc/wgsim_eval.pl
313
314 skip @header lines in SAM
315
316 ------------------------------------------------------------------------
317 r417 | lh3lh3 | 2009-07-24 12:42:38 +0100 (Fri, 24 Jul 2009) | 3 lines
318 Changed paths:
319 M /trunk/samtools/bamtk.c
320 M /trunk/samtools/sam_view.c
321
322 * samtools-0.1.5-14 (r417)
323 * more help in "samtools view" due to the recent changes.
324
325 ------------------------------------------------------------------------
326 r416 | lh3lh3 | 2009-07-24 12:34:30 +0100 (Fri, 24 Jul 2009) | 3 lines
327 Changed paths:
328 M /trunk/samtools/bam.c
329 M /trunk/samtools/bam.h
330 M /trunk/samtools/bam_import.c
331 M /trunk/samtools/bamtk.c
332 M /trunk/samtools/sam.c
333 M /trunk/samtools/sam.h
334 M /trunk/samtools/sam_view.c
335
336 * samtools-0.1.5-17 (r416)
337 * support import/export SAM with string tags
338
339 ------------------------------------------------------------------------
340 r415 | lh3lh3 | 2009-07-24 11:39:26 +0100 (Fri, 24 Jul 2009) | 3 lines
341 Changed paths:
342 M /trunk/samtools/bam.c
343 M /trunk/samtools/bam.h
344 M /trunk/samtools/bam_import.c
345 M /trunk/samtools/bamtk.c
346 M /trunk/samtools/sam.c
347 M /trunk/samtools/sam.h
348 M /trunk/samtools/sam_view.c
349
350 * samtools-0.1.5-12 (r415)
351 * FLAG now can be in HEX
352
353 ------------------------------------------------------------------------
354 r414 | lh3lh3 | 2009-07-22 22:03:49 +0100 (Wed, 22 Jul 2009) | 2 lines
355 Changed paths:
356 M /trunk/samtools/kstring.h
357
358 fixed a compiling error (thank Ken for fixing it)
359
360 ------------------------------------------------------------------------
361 r412 | lh3lh3 | 2009-07-21 22:19:40 +0100 (Tue, 21 Jul 2009) | 2 lines
362 Changed paths:
363 M /trunk/samtools/kstring.c
364 M /trunk/samtools/kstring.h
365
366 Implemented Boyer-Moore search in the kstring library.
367
368 ------------------------------------------------------------------------
369 r409 | lh3lh3 | 2009-07-17 17:10:20 +0100 (Fri, 17 Jul 2009) | 2 lines
370 Changed paths:
371 M /trunk/samtools/bam_index.c
372
373 do not include knetfile.h when _USE_KNETFILE is not defined
374
375 ------------------------------------------------------------------------
376 r408 | lh3lh3 | 2009-07-17 15:29:21 +0100 (Fri, 17 Jul 2009) | 5 lines
377 Changed paths:
378 M /trunk/samtools/bam_md.c
379 M /trunk/samtools/bam_tview.c
380 M /trunk/samtools/bamtk.c
381 M /trunk/samtools/bgzf.c
382
383 * samtools-0.1.5-11 (r408)
384 * force to overwirte existing MD if it is different from the one calculated
385 from fillmd.
386 * bgzf.c: improved the compatibility with Windows headers
387
388 ------------------------------------------------------------------------
389 r407 | lh3lh3 | 2009-07-17 14:46:56 +0100 (Fri, 17 Jul 2009) | 5 lines
390 Changed paths:
391 M /trunk/samtools/bam.h
392 M /trunk/samtools/bam_aux.c
393 M /trunk/samtools/bam_md.c
394 M /trunk/samtools/bamtk.c
395 M /trunk/samtools/sam.h
396
397 * samtools-0.1.5-10 (r407)
398 * implemented bam_aux_del() to remove a tag
399 * fillmd: generate the NM tag
400 * fillmd: cmd interface improvement
401
402 ------------------------------------------------------------------------
403 r406 | lh3lh3 | 2009-07-16 23:30:40 +0100 (Thu, 16 Jul 2009) | 2 lines
404 Changed paths:
405 M /trunk/samtools/Makefile
406
407 Sorry. The old Makefile is for PDCurses...
408
409 ------------------------------------------------------------------------
410 r405 | lh3lh3 | 2009-07-16 23:30:11 +0100 (Thu, 16 Jul 2009) | 3 lines
411 Changed paths:
412 M /trunk/samtools/Makefile
413 M /trunk/samtools/bam_tview.c
414 M /trunk/samtools/bamtk.c
415
416 * samtools-0.1.5-9 (r405)
417 * improved the compatibility with PDCurses a little bit
418
419 ------------------------------------------------------------------------
420 r404 | lh3lh3 | 2009-07-16 23:23:52 +0100 (Thu, 16 Jul 2009) | 3 lines
421 Changed paths:
422 M /trunk/samtools/Makefile
423 M /trunk/samtools/bam_tview.c
424 M /trunk/samtools/bamtk.c
425
426 * samtools-0.1.5-8 (r404)
427 * compatible with PDCurses
428
429 ------------------------------------------------------------------------
430 r403 | lh3lh3 | 2009-07-16 22:39:39 +0100 (Thu, 16 Jul 2009) | 3 lines
431 Changed paths:
432 M /trunk/samtools/bamtk.c
433 M /trunk/samtools/kseq.h
434
435 * samtools-0.1.5-7 (r403)
436 * fixed a bug in kseq.h for binary files (text files are fine)
437
438 ------------------------------------------------------------------------
439 r402 | lh3lh3 | 2009-07-16 11:49:53 +0100 (Thu, 16 Jul 2009) | 4 lines
440 Changed paths:
441 M /trunk/samtools/bam_import.c
442 M /trunk/samtools/bam_index.c
443 M /trunk/samtools/bamtk.c
444 M /trunk/samtools/bgzf.c
445
446 * samtools-0.1.5-6 (r402)
447 * fixed compiling error when "-D_USE_NETFILE" is not applied
448 * improve portability to MinGW
449
450 ------------------------------------------------------------------------
451 r398 | lh3lh3 | 2009-07-13 10:21:36 +0100 (Mon, 13 Jul 2009) | 3 lines
452 Changed paths:
453 A /trunk/bam-lite/bam.h (from /trunk/samtools/bam.h:395)
454 A /trunk/bam-lite/bam_lite.c (from /trunk/samtools/bam_lite.c:395)
455 D /trunk/samtools/bam_lite.c
456
457 * move bam_lite.c to bam-lite
458 * copy bam.h to bam-lite
459
460 ------------------------------------------------------------------------
461 r395 | lh3lh3 | 2009-07-13 10:12:57 +0100 (Mon, 13 Jul 2009) | 3 lines
462 Changed paths:
463 M /trunk/samtools/bam.h
464 M /trunk/samtools/bam_lite.c
465 M /trunk/samtools/bam_lpileup.c
466 M /trunk/samtools/bam_pileup.c
467 M /trunk/samtools/bamtk.c
468
469 * samtools-0.1.5-5 (r395)
470 * added bam_pileup_file() and removed bam_lpileup_file()
471
472 ------------------------------------------------------------------------
473 r394 | lh3lh3 | 2009-07-13 00:35:10 +0100 (Mon, 13 Jul 2009) | 3 lines
474 Changed paths:
475 M /trunk/samtools/bamtk.c
476 M /trunk/samtools/knetfile.c
477 M /trunk/samtools/knetfile.h
478
479 * samtools-0.1.5-4 (r394)
480 * http_proxy support in knetfile library (check http_proxy ENV)
481
482 ------------------------------------------------------------------------
483 r393 | lh3lh3 | 2009-07-12 23:57:07 +0100 (Sun, 12 Jul 2009) | 5 lines
484 Changed paths:
485 M /trunk/samtools/bam_index.c
486 M /trunk/samtools/bam_tview.c
487 M /trunk/samtools/bamtk.c
488 M /trunk/samtools/knetfile.c
489 M /trunk/samtools/knetfile.h
490
491 * samtools-0.1.5-3 (r393)
492 * knetfile now supports HTTP (no proxy at the moment)
493 * fixed a potential issue in knetfile on opening ordinary file, although I have
494 not seen the sideeffect so far.
495
496 ------------------------------------------------------------------------
497 r392 | lh3lh3 | 2009-07-12 18:50:55 +0100 (Sun, 12 Jul 2009) | 2 lines
498 Changed paths:
499 M /trunk/samtools/samtools.1
500
501 Remove the warning in tview
502
503 ------------------------------------------------------------------------
504 r391 | lh3lh3 | 2009-07-12 18:42:43 +0100 (Sun, 12 Jul 2009) | 3 lines
505 Changed paths:
506 M /trunk/samtools/bam_tview.c
507 M /trunk/samtools/bamtk.c
508
509 * samtools-0.1.5-2 (r391)
510 * do not show a blank screen when no reads mapped
511
512 ------------------------------------------------------------------------
513 r390 | lh3lh3 | 2009-07-09 14:01:42 +0100 (Thu, 09 Jul 2009) | 4 lines
514 Changed paths:
515 M /trunk/samtools/bam.h
516 A /trunk/samtools/bam_lite.c
517 M /trunk/samtools/bamtk.c
518
519 * samtools-0.1.5-1 (r390)
520 * removed useless _IOLIB in bam.h. This should cause no change at all.
521 * added bam_lite.c for light-weight BAM reading
522
523 ------------------------------------------------------------------------
524 r385 | lh3lh3 | 2009-07-07 16:53:29 +0100 (Tue, 07 Jul 2009) | 2 lines
525 Changed paths:
526 M /trunk/samtools/bamtk.c
527 M /trunk/samtools/knetfile.c
528
529 Release samtools-0.1.5c (fixed a bug in piping)
530
531 ------------------------------------------------------------------------
532 r383 | lh3lh3 | 2009-07-07 11:39:55 +0100 (Tue, 07 Jul 2009) | 2 lines
533 Changed paths:
534 M /trunk/samtools/bamtk.c
535 M /trunk/samtools/sam.c
536
537 Release samtools-0.1.5b (BUG! so embarrassing!)
538
539 ------------------------------------------------------------------------
540 r381 | lh3lh3 | 2009-07-07 11:20:06 +0100 (Tue, 07 Jul 2009) | 2 lines
541 Changed paths:
542 M /trunk/samtools/Makefile
543 M /trunk/samtools/bam.h
544 M /trunk/samtools/bam_aux.c
545 M /trunk/samtools/bamtk.c
546
547 Release samtools-0.1.5a (for compatibility with Bio::DB::Sam)
548
549 ------------------------------------------------------------------------
550 r373 | lh3lh3 | 2009-07-07 10:26:57 +0100 (Tue, 07 Jul 2009) | 2 lines
551 Changed paths:
552 M /trunk/samtools/ChangeLog
553 M /trunk/samtools/NEWS
554 M /trunk/samtools/bamtk.c
555 M /trunk/samtools/samtools.1
556
557 Release samtools-0.1.5
558
559 ------------------------------------------------------------------------
560 r372 | lh3lh3 | 2009-07-07 09:49:27 +0100 (Tue, 07 Jul 2009) | 3 lines
561 Changed paths:
562 M /trunk/samtools/bamtk.c
563 M /trunk/samtools/sam.c
564
565 * samtools-0.1.4-23 (r372)
566 * keep header text if "view -t" is used (by Gerton)
567
568 ------------------------------------------------------------------------
569 r371 | lh3lh3 | 2009-07-07 01:13:32 +0100 (Tue, 07 Jul 2009) | 2 lines
570 Changed paths:
571 M /trunk/samtools/samtools.1
572
573 update documentation
574
575 ------------------------------------------------------------------------
576 r370 | bhandsaker | 2009-07-02 22:24:34 +0100 (Thu, 02 Jul 2009) | 2 lines
577 Changed paths:
578 M /trunk/samtools/Makefile
579
580 Introduced LIBPATH variable so this could be overridden to allow samtools to build correct at the Broad.
581
582 ------------------------------------------------------------------------
583 r369 | lh3lh3 | 2009-07-02 13:36:53 +0100 (Thu, 02 Jul 2009) | 4 lines
584 Changed paths:
585 M /trunk/samtools/ChangeLog
586 M /trunk/samtools/bam_aux.c
587 M /trunk/samtools/bam_plcmd.c
588 M /trunk/samtools/bamtk.c
589
590 * samtools-0.1.4-22 (r369)
591 * in pileup, optionally print E2 and U2
592 * remove the debugging code in bam_aux_get() (Drat!)
593
594 ------------------------------------------------------------------------
595 r368 | lh3lh3 | 2009-07-02 11:32:26 +0100 (Thu, 02 Jul 2009) | 6 lines
596 Changed paths:
597 M /trunk/samtools/bam.c
598 M /trunk/samtools/bam.h
599 M /trunk/samtools/bam_aux.c
600 M /trunk/samtools/bam_index.c
601 M /trunk/samtools/bam_lpileup.c
602 M /trunk/samtools/bam_md.c
603 M /trunk/samtools/bam_pileup.c
604 M /trunk/samtools/bam_rmdup.c
605 M /trunk/samtools/bam_stat.c
606 M /trunk/samtools/bam_tview.c
607 M /trunk/samtools/bamtk.c
608 M /trunk/samtools/faidx.c
609 M /trunk/samtools/faidx.h
610 M /trunk/samtools/glf.c
611
612 * samtools-0.1.4-21 (r368)
613 * propagate errors rather than exit or complain assertion failure. Assertion
614 should be only used for checking internal bugs, but not for external input
615 inconsistency. I was just a bit lazy.
616 * small memory leak may be present on failure, though
617
618 ------------------------------------------------------------------------
619 r367 | lh3lh3 | 2009-06-30 16:18:42 +0100 (Tue, 30 Jun 2009) | 2 lines
620 Changed paths:
621 M /trunk/samtools/knetfile.c
622
623 reduce the chance of blocking in FTP connection
624
625 ------------------------------------------------------------------------
626 r366 | lh3lh3 | 2009-06-30 15:35:21 +0100 (Tue, 30 Jun 2009) | 2 lines
627 Changed paths:
628 M /trunk/samtools/knetfile.c
629
630 minor changes to knetfile: invalid fd equals -1 rather than 0
631
632 ------------------------------------------------------------------------
633 r365 | lh3lh3 | 2009-06-30 14:04:30 +0100 (Tue, 30 Jun 2009) | 3 lines
634 Changed paths:
635 M /trunk/samtools/bam_index.c
636 M /trunk/samtools/bamtk.c
637 M /trunk/samtools/knetfile.c
638 M /trunk/samtools/knetfile.h
639
640 * samtools-0.1.4-20 (r365)
641 * download the BAM index file if it is not found in the current working directory.
642
643 ------------------------------------------------------------------------
644 r364 | lh3lh3 | 2009-06-30 12:39:07 +0100 (Tue, 30 Jun 2009) | 3 lines
645 Changed paths:
646 M /trunk/samtools/bamtk.c
647 M /trunk/samtools/knetfile.c
648
649 * samtools-0.1.4-19 (r364)
650 * knetfile: report error when the file is not present on FTP
651
652 ------------------------------------------------------------------------
653 r363 | lh3lh3 | 2009-06-29 23:23:32 +0100 (Mon, 29 Jun 2009) | 4 lines
654 Changed paths:
655 M /trunk/samtools/bam_tview.c
656 M /trunk/samtools/bamtk.c
657 M /trunk/samtools/bgzf.c
658 M /trunk/samtools/bgzf.h
659 M /trunk/samtools/knetfile.c
660 M /trunk/samtools/knetfile.h
661
662 * samtools-0.1.4-18 (r363)
663 * knetfile: do not trigger network communication in FTP seek (lazy seek)
664 * bgzf: cache recent blocks (disabled by default)
665
666 ------------------------------------------------------------------------
667 r362 | lh3lh3 | 2009-06-25 21:04:34 +0100 (Thu, 25 Jun 2009) | 2 lines
668 Changed paths:
669 M /trunk/samtools/bgzf.c
670
671 write changelog
672
673 ------------------------------------------------------------------------
674 r361 | lh3lh3 | 2009-06-25 21:03:10 +0100 (Thu, 25 Jun 2009) | 3 lines
675 Changed paths:
676 M /trunk/samtools/bam_index.c
677 M /trunk/samtools/bamtk.c
678
679 * samtools-0.1.4-17 (r361)
680 * if a file is given on FTP, search locally for the BAM index
681
682 ------------------------------------------------------------------------
683 r360 | lh3lh3 | 2009-06-25 20:44:52 +0100 (Thu, 25 Jun 2009) | 5 lines
684 Changed paths:
685 M /trunk/samtools/Makefile
686 M /trunk/samtools/bam_import.c
687 M /trunk/samtools/bam_index.c
688 M /trunk/samtools/bamtk.c
689 M /trunk/samtools/bgzf.c
690 M /trunk/samtools/bgzf.h
691 M /trunk/samtools/knetfile.c
692 M /trunk/samtools/knetfile.h
693
694 * samtools-0.1.4-16 (r360)
695 * report more information in index when the input is not sorted
696 * change the behaviour of knet_seek() such that it returns 0 on success
697 * support knetfile library in BGZF
698
699 ------------------------------------------------------------------------
700 r359 | lh3lh3 | 2009-06-25 17:10:55 +0100 (Thu, 25 Jun 2009) | 2 lines
701 Changed paths:
702 M /trunk/samtools/knetfile.c
703 M /trunk/samtools/knetfile.h
704
705 fixed bugs in knetfile.*
706
707 ------------------------------------------------------------------------
708 r358 | lh3lh3 | 2009-06-25 13:53:19 +0100 (Thu, 25 Jun 2009) | 2 lines
709 Changed paths:
710 A /trunk/samtools/knetfile.h
711
712 this is the header file
713
714 ------------------------------------------------------------------------
715 r357 | lh3lh3 | 2009-06-25 13:52:03 +0100 (Thu, 25 Jun 2009) | 3 lines
716 Changed paths:
717 A /trunk/samtools/knetfile.c
718
719 * open a file at FTP
720 * preliminary version
721
722 ------------------------------------------------------------------------
723 r354 | lh3lh3 | 2009-06-24 14:02:25 +0100 (Wed, 24 Jun 2009) | 3 lines
724 Changed paths:
725 M /trunk/samtools/bam.c
726 M /trunk/samtools/bamtk.c
727
728 * samtools-0.1.4-15 (r354)
729 * fixed a memory leak in bam_view1(), although samtools is not using this routine.
730
731 ------------------------------------------------------------------------
732 r351 | lh3lh3 | 2009-06-18 00:16:26 +0100 (Thu, 18 Jun 2009) | 4 lines
733 Changed paths:
734 M /trunk/samtools/bamtk.c
735 M /trunk/samtools/faidx.c
736
737 * samtools-0.1.4-13 (r351)
738 * make faidx more tolerant to empty lines right before or after > lines
739 * hope this does not introduce new bugs...
740
741 ------------------------------------------------------------------------
742 r350 | lh3lh3 | 2009-06-16 14:37:01 +0100 (Tue, 16 Jun 2009) | 3 lines
743 Changed paths:
744 M /trunk/samtools/bam_plcmd.c
745 M /trunk/samtools/bamtk.c
746
747 * samtools-0.1.4-13 (r350)
748 * fixed a small memory leak in pileup, caused by recent modifications
749
750 ------------------------------------------------------------------------
751 r347 | lh3lh3 | 2009-06-13 21:20:49 +0100 (Sat, 13 Jun 2009) | 3 lines
752 Changed paths:
753 M /trunk/samtools/bam_plcmd.c
754 M /trunk/samtools/bamtk.c
755 M /trunk/samtools/sam_view.c
756
757 * samtools-0.1.4-12 (r347)
758 * added `-S' to pileup, similar to `view -S'
759
760 ------------------------------------------------------------------------
761 r346 | lh3lh3 | 2009-06-13 17:52:31 +0100 (Sat, 13 Jun 2009) | 3 lines
762 Changed paths:
763 M /trunk/samtools/Makefile
764 M /trunk/samtools/bamtk.c
765 M /trunk/samtools/sam_view.c
766 M /trunk/samtools/samtools.1
767
768 * samtools-0.1.4-11 (r346)
769 * allow to select a read group at view command-line
770
771 ------------------------------------------------------------------------
772 r344 | lh3lh3 | 2009-06-13 14:06:24 +0100 (Sat, 13 Jun 2009) | 2 lines
773 Changed paths:
774 M /trunk/samtools/examples/calDepth.c
775
776 added more comments
777
778 ------------------------------------------------------------------------
779 r343 | lh3lh3 | 2009-06-13 14:01:22 +0100 (Sat, 13 Jun 2009) | 2 lines
780 Changed paths:
781 M /trunk/samtools/examples/calDepth.c
782
783 nothing really
784
785 ------------------------------------------------------------------------
786 r342 | lh3lh3 | 2009-06-13 13:58:48 +0100 (Sat, 13 Jun 2009) | 2 lines
787 Changed paths:
788 M /trunk/samtools/examples/Makefile
789 A /trunk/samtools/examples/calDepth.c
790
791 added an example of calculating read depth
792
793 ------------------------------------------------------------------------
794 r341 | lh3lh3 | 2009-06-13 13:00:08 +0100 (Sat, 13 Jun 2009) | 6 lines
795 Changed paths:
796 M /trunk/samtools/Makefile
797 M /trunk/samtools/bam.h
798 M /trunk/samtools/bam_aux.c
799 A /trunk/samtools/bam_color.c
800 M /trunk/samtools/bam_plcmd.c
801 M /trunk/samtools/bam_sort.c
802 M /trunk/samtools/bam_tview.c
803 M /trunk/samtools/bamtk.c
804 M /trunk/samtools/sam.c
805 M /trunk/samtools/sam.h
806
807 * samtools-0.1.4-10 (r341)
808 * only include key APIs in libbam.a
809 * move color-specific routines to bam_color.c
810 * update documentations
811 * remove the support of -q in pileup
812
813 ------------------------------------------------------------------------
814 r340 | lh3lh3 | 2009-06-13 11:17:14 +0100 (Sat, 13 Jun 2009) | 6 lines
815 Changed paths:
816 M /trunk/samtools/INSTALL
817 M /trunk/samtools/Makefile
818 M /trunk/samtools/bam_aux.c
819 M /trunk/samtools/bam_import.c
820 M /trunk/samtools/bam_tview.c
821 M /trunk/samtools/bamtk.c
822 M /trunk/samtools/razf.c
823 M /trunk/samtools/sam_view.c
824
825 * samtools-0.1.4-9 (r340)
826 * added a warning to razf.c if zlib<1.2.2.1
827 * fixed a compilation warning
828 * fixed a segfault caused by @RG parsing
829 * detect NCURSES in bam_tview.c
830
831 ------------------------------------------------------------------------
832 r339 | lh3lh3 | 2009-06-13 10:35:19 +0100 (Sat, 13 Jun 2009) | 2 lines
833 Changed paths:
834 M /trunk/samtools/INSTALL
835
836 update INSTALL
837
838 ------------------------------------------------------------------------
839 r338 | lh3lh3 | 2009-06-13 00:15:24 +0100 (Sat, 13 Jun 2009) | 4 lines
840 Changed paths:
841 M /trunk/samtools/bam.c
842 M /trunk/samtools/bam.h
843 M /trunk/samtools/bam_aux.c
844 M /trunk/samtools/bam_import.c
845 M /trunk/samtools/bamtk.c
846 M /trunk/samtools/kstring.h
847 M /trunk/samtools/sam.c
848 M /trunk/samtools/sam_view.c
849
850 * samtools-0.1.4-8 (r338)
851 * parse the @RG header lines and allow to choose library at the "samtools view"
852 command line
853
854 ------------------------------------------------------------------------
855 r337 | lh3lh3 | 2009-06-12 21:25:50 +0100 (Fri, 12 Jun 2009) | 4 lines
856 Changed paths:
857 M /trunk/samtools/bamtk.c
858 M /trunk/samtools/bgzf.c
859 M /trunk/samtools/bgzf.h
860 M /trunk/samtools/sam.c
861 M /trunk/samtools/sam_view.c
862
863 * samtools-0.1.4-7 (r337)
864 * bgzf.c: support mode string "wu": uncompressed output
865 * "samtools view" support "-u" command-line option
866
867 ------------------------------------------------------------------------
868 r336 | lh3lh3 | 2009-06-12 17:20:12 +0100 (Fri, 12 Jun 2009) | 5 lines
869 Changed paths:
870 M /trunk/samtools/Makefile
871 M /trunk/samtools/misc/Makefile
872 M /trunk/samtools/razf.c
873 M /trunk/samtools/razf.h
874 M /trunk/samtools/razip.c
875
876 * no changes to samtools itself
877 * remove zlib source codes
878 * make RAZF reading compatible with old version of zlib
879 * on old version of zlib, writing is not available
880
881 ------------------------------------------------------------------------
882 r335 | lh3lh3 | 2009-06-12 16:47:33 +0100 (Fri, 12 Jun 2009) | 2 lines
883 Changed paths:
884 D /trunk/samtools/zlib
885
886 remove zlib for simplification...
887
888 ------------------------------------------------------------------------
889 r334 | lh3lh3 | 2009-06-12 15:43:36 +0100 (Fri, 12 Jun 2009) | 5 lines
890 Changed paths:
891 M /trunk/samtools/bam.h
892 M /trunk/samtools/bam_aux.c
893 M /trunk/samtools/bamtk.c
894
895 * samtools-0.1.4-6 (r334)
896 * do not export bam_aux_get_core() for Bio::DB::Sam because it has already
897 been implemented in that.
898 * this version works with the latest Bio::DB::Sam (20090612)
899
900 ------------------------------------------------------------------------
901 r333 | lh3lh3 | 2009-06-12 15:33:42 +0100 (Fri, 12 Jun 2009) | 2 lines
902 Changed paths:
903 M /trunk/samtools/ChangeLog
904
905 update ChangeLog
906
907 ------------------------------------------------------------------------
908 r332 | lh3lh3 | 2009-06-12 15:21:21 +0100 (Fri, 12 Jun 2009) | 2 lines
909 Changed paths:
910 M /trunk/samtools/AUTHORS
911 M /trunk/samtools/Makefile
912 M /trunk/samtools/misc/Makefile
913
914 fixed minor things in Makefile
915
916 ------------------------------------------------------------------------
917 r331 | lh3lh3 | 2009-06-12 15:07:05 +0100 (Fri, 12 Jun 2009) | 4 lines
918 Changed paths:
919 M /trunk/samtools/bamtk.c
920
921 * samtools-0.1.4-5 (r3310
922 * no change to samtools itself. Version number is increased to reflect the
923 changes in the Makefile building system.
924
925 ------------------------------------------------------------------------
926 r330 | lh3lh3 | 2009-06-12 15:03:38 +0100 (Fri, 12 Jun 2009) | 2 lines
927 Changed paths:
928 M /trunk/samtools/AUTHORS
929 D /trunk/samtools/README
930
931 update information...
932
933 ------------------------------------------------------------------------
934 r329 | lh3lh3 | 2009-06-12 14:52:21 +0100 (Fri, 12 Jun 2009) | 3 lines
935 Changed paths:
936 M /trunk/samtools/misc/novo2sam.pl
937
938 * updated novoalign converter by Colin Hercus et al.
939 * this version works with indels
940
941 ------------------------------------------------------------------------
942 r328 | lh3lh3 | 2009-06-12 14:50:53 +0100 (Fri, 12 Jun 2009) | 3 lines
943 Changed paths:
944 M /trunk/samtools/INSTALL
945 M /trunk/samtools/Makefile
946 M /trunk/samtools/misc/Makefile
947 M /trunk/samtools/zlib/Makefile
948
949 * update Makefile
950 * update INSTALL instruction
951
952 ------------------------------------------------------------------------
953 r327 | lh3lh3 | 2009-06-12 14:18:29 +0100 (Fri, 12 Jun 2009) | 4 lines
954 Changed paths:
955 A /trunk/samtools/Makefile (from /trunk/samtools/Makefile.generic:325)
956 D /trunk/samtools/Makefile.am
957 D /trunk/samtools/Makefile.generic
958 D /trunk/samtools/Makefile.lite
959 D /trunk/samtools/autogen.sh
960 D /trunk/samtools/cleanup.sh
961 D /trunk/samtools/configure.ac
962 A /trunk/samtools/misc/Makefile (from /trunk/samtools/misc/Makefile.generic:305)
963 D /trunk/samtools/misc/Makefile.am
964 D /trunk/samtools/misc/Makefile.generic
965 M /trunk/samtools/razf.c
966 A /trunk/samtools/zlib
967 A /trunk/samtools/zlib/Makefile
968 A /trunk/samtools/zlib/adler32.c
969 A /trunk/samtools/zlib/compress.c
970 A /trunk/samtools/zlib/crc32.c
971 A /trunk/samtools/zlib/crc32.h
972 A /trunk/samtools/zlib/deflate.c
973 A /trunk/samtools/zlib/deflate.h
974 A /trunk/samtools/zlib/gzio.c
975 A /trunk/samtools/zlib/infback.c
976 A /trunk/samtools/zlib/inffast.c
977 A /trunk/samtools/zlib/inffast.h
978 A /trunk/samtools/zlib/inffixed.h
979 A /trunk/samtools/zlib/inflate.c
980 A /trunk/samtools/zlib/inflate.h
981 A /trunk/samtools/zlib/inftrees.c
982 A /trunk/samtools/zlib/inftrees.h
983 A /trunk/samtools/zlib/trees.c
984 A /trunk/samtools/zlib/trees.h
985 A /trunk/samtools/zlib/uncompr.c
986 A /trunk/samtools/zlib/zconf.h
987 A /trunk/samtools/zlib/zlib.h
988 A /trunk/samtools/zlib/zutil.c
989 A /trunk/samtools/zlib/zutil.h
990 D /trunk/samtools/zutil.h
991
992 * added zlib-1.2.3 as razip requires that
993 * prepare to changed back to the Makefile building system
994 * unfinished! (will be soon)
995
996 ------------------------------------------------------------------------
997 r326 | lh3lh3 | 2009-06-12 14:12:03 +0100 (Fri, 12 Jun 2009) | 2 lines
998 Changed paths:
999 M /trunk/samtools/misc/samtools.pl
1000
1001 Unfinished
1002
1003 ------------------------------------------------------------------------
1004 r325 | lh3lh3 | 2009-06-10 16:27:59 +0100 (Wed, 10 Jun 2009) | 3 lines
1005 Changed paths:
1006 M /trunk/samtools/bam_maqcns.c
1007 M /trunk/samtools/bamtk.c
1008
1009 * samtools-0.1.4-4 (r325)
1010 * further avoid wrong consensus calls in repetitive regions.
1011
1012 ------------------------------------------------------------------------
1013 r324 | lh3lh3 | 2009-06-10 15:56:17 +0100 (Wed, 10 Jun 2009) | 4 lines
1014 Changed paths:
1015 M /trunk/samtools/bam_maqcns.c
1016 M /trunk/samtools/bam_plcmd.c
1017 M /trunk/samtools/bamtk.c
1018 M /trunk/samtools/sam.c
1019 M /trunk/samtools/sam.h
1020
1021 * samtools-0.1.4-3 (r324)
1022 * make maqcns generate the correct call in repetitive regions.
1023 * allow filtering on mapQ at the pileup command line
1024
1025 ------------------------------------------------------------------------
1026 r323 | lh3lh3 | 2009-06-10 10:04:21 +0100 (Wed, 10 Jun 2009) | 3 lines
1027 Changed paths:
1028 M /trunk/samtools/misc/samtools.pl
1029
1030 * samtools.pl-0.3.2 (r322)
1031 * indels and SNPs use different mapping quality threshold
1032
1033 ------------------------------------------------------------------------
1034 r322 | lh3lh3 | 2009-06-10 10:03:22 +0100 (Wed, 10 Jun 2009) | 2 lines
1035 Changed paths:
1036 M /trunk/samtools/misc/export2sam.pl
1037
1038 fixed a typo
1039
1040 ------------------------------------------------------------------------
1041 r321 | lh3lh3 | 2009-06-09 09:21:48 +0100 (Tue, 09 Jun 2009) | 2 lines
1042 Changed paths:
1043 M /trunk/samtools/misc/samtools.pl
1044
1045 just typo. no real change
1046
1047 ------------------------------------------------------------------------
1048 r320 | lh3lh3 | 2009-06-08 14:32:51 +0100 (Mon, 08 Jun 2009) | 2 lines
1049 Changed paths:
1050 M /trunk/samtools/misc/samtools.pl
1051
1052 a little bit code cleanup
1053
1054 ------------------------------------------------------------------------
1055 r319 | lh3lh3 | 2009-06-08 14:22:33 +0100 (Mon, 08 Jun 2009) | 4 lines
1056 Changed paths:
1057 M /trunk/samtools/misc/samtools.pl
1058
1059 * samtools.pl-0.3.1
1060 * change default parameters
1061 * optionally print filtered variants
1062
1063 ------------------------------------------------------------------------
1064 r318 | lh3lh3 | 2009-06-08 14:14:26 +0100 (Mon, 08 Jun 2009) | 3 lines
1065 Changed paths:
1066 M /trunk/samtools/misc/samtools.pl
1067
1068 * samtools.pl-0.3.0
1069 * combine snpFilter and indelFilter
1070
1071 ------------------------------------------------------------------------
1072 r317 | lh3lh3 | 2009-06-08 11:31:42 +0100 (Mon, 08 Jun 2009) | 3 lines
1073 Changed paths:
1074 M /trunk/samtools/misc/samtools.pl
1075
1076 * samtools.pl-0.2.3
1077 * change a default parameter
1078
1079 ------------------------------------------------------------------------
1080 r316 | lh3lh3 | 2009-06-08 11:11:06 +0100 (Mon, 08 Jun 2009) | 5 lines
1081 Changed paths:
1082 M /trunk/samtools/bam_maqcns.c
1083 M /trunk/samtools/bam_maqcns.h
1084 M /trunk/samtools/bam_plcmd.c
1085 M /trunk/samtools/bamtk.c
1086 M /trunk/samtools/sam.c
1087
1088 * samtools-0.1.4-2 (r316)
1089 * pileup: cap mapping quality at 60 (by default)
1090 * pileup: always calculate RMS mapq
1091 * pileup: allow to output variant sites only
1092
1093 ------------------------------------------------------------------------
1094 r312 | lh3lh3 | 2009-06-04 13:01:10 +0100 (Thu, 04 Jun 2009) | 3 lines
1095 Changed paths:
1096 M /trunk/samtools/misc/samtools.pl
1097
1098 * samtools.pl-0.2.2
1099 * added pileup2fq
1100
1101 ------------------------------------------------------------------------
1102 r311 | lh3lh3 | 2009-06-03 09:40:40 +0100 (Wed, 03 Jun 2009) | 2 lines
1103 Changed paths:
1104 M /trunk/samtools/misc/samtools.pl
1105
1106 * in snpFilter, suppress non-SNP sites
1107
1108 ------------------------------------------------------------------------
1109 r310 | lh3lh3 | 2009-06-01 14:35:13 +0100 (Mon, 01 Jun 2009) | 3 lines
1110 Changed paths:
1111 M /trunk/samtools/misc/samtools.pl
1112
1113 * samtools.pl-0.2.1
1114 * fixed a typo
1115
1116 ------------------------------------------------------------------------
1117 r309 | lh3lh3 | 2009-06-01 14:04:39 +0100 (Mon, 01 Jun 2009) | 3 lines
1118 Changed paths:
1119 M /trunk/samtools/misc/samtools.pl
1120
1121 * samtools.pl-0.2.0
1122 * snpFilter
1123
1124 ------------------------------------------------------------------------
1125 r306 | lh3lh3 | 2009-05-28 11:49:35 +0100 (Thu, 28 May 2009) | 3 lines
1126 Changed paths:
1127 M /trunk/samtools/bgzf.c
1128
1129 * minor changes to bgzf: return NULL if fd == -1
1130 * suggested by {kdj,jm18}@sanger.ac.uk
1131
1132 ------------------------------------------------------------------------
1133 r305 | lh3lh3 | 2009-05-28 11:16:08 +0100 (Thu, 28 May 2009) | 2 lines
1134 Changed paths:
1135 A /trunk/samtools/misc/interpolate_sam.pl
1136
1137 Script for paired-end pileup, contributed by Stephen Montgomery.
1138
1139 ------------------------------------------------------------------------
1140 r304 | lh3lh3 | 2009-05-28 11:08:49 +0100 (Thu, 28 May 2009) | 3 lines
1141 Changed paths:
1142 M /trunk/samtools/bamtk.c
1143 M /trunk/samtools/sam.c
1144
1145 * samtools-0.1.4-1 (r304)
1146 * fixed a minor bug in printing headers
1147
1148 ------------------------------------------------------------------------
1149 r297 | lh3lh3 | 2009-05-21 16:06:16 +0100 (Thu, 21 May 2009) | 2 lines
1150 Changed paths:
1151 M /trunk/samtools/ChangeLog
1152 M /trunk/samtools/NEWS
1153 M /trunk/samtools/bam_plcmd.c
1154 M /trunk/samtools/bamtk.c
1155 M /trunk/samtools/misc/maq2sam.c
1156 M /trunk/samtools/samtools.1
1157
1158 Release samtools-0.1.4
1159
1160 ------------------------------------------------------------------------
1161 r296 | lh3lh3 | 2009-05-21 12:53:14 +0100 (Thu, 21 May 2009) | 3 lines
1162 Changed paths:
1163 M /trunk/samtools/bam_maqcns.c
1164 M /trunk/samtools/bamtk.c
1165
1166 * samtools-0.1.3-24 (r296)
1167 * another similar bug in the indel caller
1168
1169 ------------------------------------------------------------------------
1170 r295 | lh3lh3 | 2009-05-21 12:50:28 +0100 (Thu, 21 May 2009) | 3 lines
1171 Changed paths:
1172 M /trunk/samtools/bam_maqcns.c
1173 M /trunk/samtools/bamtk.c
1174
1175 * samtools-0.1.3-23 (r295)
1176 * fixed a critical bug in the indel caller
1177
1178 ------------------------------------------------------------------------
1179 r294 | lh3lh3 | 2009-05-20 13:00:20 +0100 (Wed, 20 May 2009) | 2 lines
1180 Changed paths:
1181 M /trunk/samtools/bam_stat.c
1182
1183 added a missing header file
1184
1185 ------------------------------------------------------------------------
1186 r293 | lh3lh3 | 2009-05-19 23:44:25 +0100 (Tue, 19 May 2009) | 3 lines
1187 Changed paths:
1188 M /trunk/samtools/bam_tview.c
1189 M /trunk/samtools/bamtk.c
1190
1191 * samtools-0.1.3-22 (r293)
1192 * open tview in the dot-view mode by default
1193
1194 ------------------------------------------------------------------------
1195 r292 | lh3lh3 | 2009-05-18 21:01:23 +0100 (Mon, 18 May 2009) | 6 lines
1196 Changed paths:
1197 M /trunk/samtools/samtools.1
1198
1199 Added a note to the manual. Currently SAMtools used unaligned words in
1200 several places. Although this does not cause bus errors to me, it may
1201 affect portability. Please see the "Bus error" wiki page for more
1202 information. Also thank James Bonfields for pointing this out.
1203
1204
1205 ------------------------------------------------------------------------
1206 r286 | lh3lh3 | 2009-05-14 15:23:13 +0100 (Thu, 14 May 2009) | 3 lines
1207 Changed paths:
1208 M /trunk/samtools/bam.h
1209 M /trunk/samtools/bam_aux.c
1210 M /trunk/samtools/bamtk.c
1211
1212 * samtools-0.1.3-21 (286)
1213 * declare bam_aux_get_core() in bam.h
1214
1215 ------------------------------------------------------------------------
1216 r276 | lh3lh3 | 2009-05-13 10:07:55 +0100 (Wed, 13 May 2009) | 5 lines
1217 Changed paths:
1218 M /trunk/samtools/bam.h
1219 M /trunk/samtools/bam_index.c
1220 M /trunk/samtools/bamtk.c
1221
1222 * samtools-0.1.3-20 (r276)
1223 * remove bam1_t::hash again. We need to modify the Perl API anyway to
1224 make it work with the latest SVN.
1225 * As is suggested by Tim, scan "{base}.bai" and "{base}.bam.bai" for index
1226
1227 ------------------------------------------------------------------------
1228 r275 | lh3lh3 | 2009-05-12 21:14:10 +0100 (Tue, 12 May 2009) | 4 lines
1229 Changed paths:
1230 M /trunk/samtools/ChangeLog
1231 M /trunk/samtools/bam.h
1232 M /trunk/samtools/bamtk.c
1233
1234 * samtools-0.1.3-19 (r275)
1235 * a minor change to the bam1_t struct: added back "void *hash" for the
1236 backward compatibility with Bio::DB::Sam
1237
1238 ------------------------------------------------------------------------
1239 r273 | lh3lh3 | 2009-05-12 14:28:39 +0100 (Tue, 12 May 2009) | 3 lines
1240 Changed paths:
1241 M /trunk/samtools/bam_rmdupse.c
1242 M /trunk/samtools/bamtk.c
1243
1244 * samtools-0.1.3-18 (r273)
1245 * rmdupse: do not remove unmapped reads
1246
1247 ------------------------------------------------------------------------
1248 r272 | lh3lh3 | 2009-05-12 14:20:00 +0100 (Tue, 12 May 2009) | 2 lines
1249 Changed paths:
1250 M /trunk/samtools/bam_rmdupse.c
1251
1252 change a parameter. It does nothing
1253
1254 ------------------------------------------------------------------------
1255 r271 | lh3lh3 | 2009-05-12 14:17:58 +0100 (Tue, 12 May 2009) | 3 lines
1256 Changed paths:
1257 M /trunk/samtools/Makefile.am
1258 M /trunk/samtools/Makefile.generic
1259 M /trunk/samtools/Makefile.lite
1260 A /trunk/samtools/bam_rmdupse.c
1261 M /trunk/samtools/bamtk.c
1262 M /trunk/samtools/configure.ac
1263
1264 * samtools-0.1.3-17 (r271)
1265 * added 'rmdupse' command
1266
1267 ------------------------------------------------------------------------
1268 r267 | lh3lh3 | 2009-05-05 22:31:41 +0100 (Tue, 05 May 2009) | 3 lines
1269 Changed paths:
1270 M /trunk/samtools/bamtk.c
1271 M /trunk/samtools/sam_view.c
1272
1273 * samtools-0.1.3-16 (r267)
1274 * in sam_view.c, changed g_flag_on based on the suggestion by Angie Hinrichs
1275
1276 ------------------------------------------------------------------------
1277 r266 | lh3lh3 | 2009-05-05 22:23:27 +0100 (Tue, 05 May 2009) | 3 lines
1278 Changed paths:
1279 M /trunk/samtools/bam_import.c
1280 M /trunk/samtools/bamtk.c
1281
1282 * samtools-0.1.3-15 (r266)
1283 * report an error if a non-* reference is present while @SQ is absent
1284
1285 ------------------------------------------------------------------------
1286 r265 | lh3lh3 | 2009-05-05 22:09:00 +0100 (Tue, 05 May 2009) | 3 lines
1287 Changed paths:
1288 M /trunk/samtools/bam.h
1289 M /trunk/samtools/bam_import.c
1290 M /trunk/samtools/bamtk.c
1291 M /trunk/samtools/sam.c
1292 M /trunk/samtools/sam_view.c
1293
1294 * samtools-0.1.3-14 (r262)
1295 * make samopen() recognize @SQ header lines
1296
1297 ------------------------------------------------------------------------
1298 r261 | lh3lh3 | 2009-05-05 15:10:30 +0100 (Tue, 05 May 2009) | 3 lines
1299 Changed paths:
1300 M /trunk/samtools/bam_plcmd.c
1301 M /trunk/samtools/bamtk.c
1302 M /trunk/samtools/bgzf.c
1303 M /trunk/samtools/sam.c
1304 M /trunk/samtools/sam_view.c
1305
1306 * samtools-0.1.3-13 (r260)
1307 * report error for file I/O error
1308
1309 ------------------------------------------------------------------------
1310 r260 | lh3lh3 | 2009-05-05 15:01:16 +0100 (Tue, 05 May 2009) | 2 lines
1311 Changed paths:
1312 M /trunk/samtools/Makefile.am
1313
1314 update Makefile.am
1315
1316 ------------------------------------------------------------------------
1317 r259 | lh3lh3 | 2009-05-05 14:52:25 +0100 (Tue, 05 May 2009) | 3 lines
1318 Changed paths:
1319 M /trunk/samtools/bam.h
1320 M /trunk/samtools/bam_pileup.c
1321 M /trunk/samtools/bam_plcmd.c
1322 M /trunk/samtools/bamtk.c
1323 M /trunk/samtools/sam.c
1324 M /trunk/samtools/sam.h
1325
1326 * samtools-0.1.3-12 (r259)
1327 * use the new I/O interface in pileup
1328
1329 ------------------------------------------------------------------------
1330 r258 | lh3lh3 | 2009-05-05 14:33:22 +0100 (Tue, 05 May 2009) | 3 lines
1331 Changed paths:
1332 M /trunk/samtools/Makefile.generic
1333 M /trunk/samtools/Makefile.lite
1334 M /trunk/samtools/bam.c
1335 M /trunk/samtools/bam.h
1336 M /trunk/samtools/bam_import.c
1337 M /trunk/samtools/bamtk.c
1338 A /trunk/samtools/sam.c
1339 A /trunk/samtools/sam.h
1340 A /trunk/samtools/sam_view.c
1341
1342 * samtools-0.1.3-11 (r258)
1343 * unify the interface to BAM and SAM I/O
1344
1345 ------------------------------------------------------------------------
1346 r257 | lh3lh3 | 2009-05-05 09:53:35 +0100 (Tue, 05 May 2009) | 3 lines
1347 Changed paths:
1348 M /trunk/samtools/Makefile.lite
1349 M /trunk/samtools/bam_plcmd.c
1350 M /trunk/samtools/bamtk.c
1351
1352 * samtools-0.1.3-10 (r257)
1353 * allow hex with "pileup -m"
1354
1355 ------------------------------------------------------------------------
1356 r256 | lh3lh3 | 2009-05-04 19:16:50 +0100 (Mon, 04 May 2009) | 4 lines
1357 Changed paths:
1358 M /trunk/samtools/bam_lpileup.c
1359 M /trunk/samtools/bamtk.c
1360
1361 * samtools-0.1.3-9 (r256)
1362 * fixed a bug in bam_lpileup.c
1363 * I do not know if this also fixes the bug causing assertion failure in the tview
1364
1365 ------------------------------------------------------------------------
1366 r251 | lh3lh3 | 2009-04-28 13:53:23 +0100 (Tue, 28 Apr 2009) | 3 lines
1367 Changed paths:
1368 M /trunk/samtools/bam_pileup.c
1369 M /trunk/samtools/bamtk.c
1370
1371 * samtools-0.1.3-8 (r251)
1372 * fixed a bug when there are reads without coordinates
1373
1374 ------------------------------------------------------------------------
1375 r250 | lh3lh3 | 2009-04-28 13:43:33 +0100 (Tue, 28 Apr 2009) | 2 lines
1376 Changed paths:
1377 A /trunk/samtools/AUTHORS
1378 A /trunk/samtools/README
1379 M /trunk/samtools/cleanup.sh
1380
1381 added missing files
1382
1383 ------------------------------------------------------------------------
1384 r249 | lh3lh3 | 2009-04-28 13:37:16 +0100 (Tue, 28 Apr 2009) | 2 lines
1385 Changed paths:
1386 M /trunk/samtools/Makefile.generic
1387 M /trunk/samtools/Makefile.lite
1388 M /trunk/samtools/configure.ac
1389 M /trunk/samtools/misc/Makefile.generic
1390
1391 improve large file support in compilation
1392
1393 ------------------------------------------------------------------------
1394 r248 | lh3lh3 | 2009-04-28 13:33:24 +0100 (Tue, 28 Apr 2009) | 2 lines
1395 Changed paths:
1396 M /trunk/samtools/INSTALL
1397
1398 update INSTALL
1399
1400 ------------------------------------------------------------------------
1401 r247 | lh3lh3 | 2009-04-28 13:28:50 +0100 (Tue, 28 Apr 2009) | 2 lines
1402 Changed paths:
1403 M /trunk/samtools/Makefile.am
1404 M /trunk/samtools/autogen.sh
1405 M /trunk/samtools/cleanup.sh
1406 M /trunk/samtools/configure.ac
1407 A /trunk/samtools/misc/Makefile.am
1408
1409 fixed various issues about the GNU building scripts
1410
1411 ------------------------------------------------------------------------
1412 r246 | lh3lh3 | 2009-04-28 13:10:23 +0100 (Tue, 28 Apr 2009) | 4 lines
1413 Changed paths:
1414 M /trunk/samtools/ChangeLog
1415 D /trunk/samtools/Makefile
1416 A /trunk/samtools/Makefile.am
1417 A /trunk/samtools/Makefile.generic
1418 A /trunk/samtools/autogen.sh
1419 M /trunk/samtools/bam.h
1420 M /trunk/samtools/bam_aux.c
1421 M /trunk/samtools/bam_tview.c
1422 M /trunk/samtools/bamtk.c
1423 A /trunk/samtools/cleanup.sh
1424 A /trunk/samtools/configure.ac
1425 D /trunk/samtools/misc/Makefile
1426 A /trunk/samtools/misc/Makefile.generic (from /trunk/samtools/misc/Makefile:245)
1427
1428 * samtools-0.1.3-7 (r246)
1429 * incorporated revisions from Nils Homer
1430 * enhanced support of displaying color-space reads
1431
1432 ------------------------------------------------------------------------
1433 r244 | lh3lh3 | 2009-04-25 11:49:40 +0100 (Sat, 25 Apr 2009) | 3 lines
1434 Changed paths:
1435 M /trunk/samtools/bam_md.c
1436 M /trunk/samtools/bamtk.c
1437
1438 * samtools-0.1.3-6 (r244)
1439 * fixed segfault for unmapped reads
1440
1441 ------------------------------------------------------------------------
1442 r243 | lh3lh3 | 2009-04-24 21:27:26 +0100 (Fri, 24 Apr 2009) | 5 lines
1443 Changed paths:
1444 M /trunk/samtools/bam.h
1445 M /trunk/samtools/bam_maqcns.c
1446 M /trunk/samtools/bam_md.c
1447 M /trunk/samtools/bamtk.c
1448
1449 * samtools-0.1.3-5 (r243)
1450 * fixed a long existing bug which may cause memory leak
1451 * check MD
1452 * consensus calling now works with "=", but indel calling not
1453
1454 ------------------------------------------------------------------------
1455 r242 | lh3lh3 | 2009-04-24 20:44:46 +0100 (Fri, 24 Apr 2009) | 3 lines
1456 Changed paths:
1457 M /trunk/samtools/bam_md.c
1458 M /trunk/samtools/bamtk.c
1459
1460 * samtools-0.1.3-4 (r242)
1461 * fixed a memory leak
1462
1463 ------------------------------------------------------------------------
1464 r240 | lh3lh3 | 2009-04-24 16:40:18 +0100 (Fri, 24 Apr 2009) | 5 lines
1465 Changed paths:
1466 M /trunk/samtools/Makefile
1467 M /trunk/samtools/Makefile.lite
1468 M /trunk/samtools/bam.h
1469 M /trunk/samtools/bam_aux.c
1470 A /trunk/samtools/bam_md.c
1471 M /trunk/samtools/bam_plcmd.c
1472 M /trunk/samtools/bamtk.c
1473
1474 * samtools-0.1.3-3 (r240)
1475 * generate MD tag
1476 * generate "=" bases
1477 * the plain pileup now support "=" bases, but consensus calling and glfgen may fail
1478
1479 ------------------------------------------------------------------------
1480 r239 | lh3lh3 | 2009-04-24 12:08:20 +0100 (Fri, 24 Apr 2009) | 5 lines
1481 Changed paths:
1482 M /trunk/samtools/bam.h
1483 M /trunk/samtools/bam_aux.c
1484 M /trunk/samtools/bamtk.c
1485
1486 * samtools-0.1.3-2 (r239)
1487 * fixed bugs in bam_aux.c (these functions nevered used by samtools)
1488 * removed bam_aux_init()/bam_aux_destroy()
1489 * added tagview for testing bam_aux
1490
1491 ------------------------------------------------------------------------
1492 r235 | lh3lh3 | 2009-04-21 23:17:39 +0100 (Tue, 21 Apr 2009) | 3 lines
1493 Changed paths:
1494 M /trunk/samtools/bam_pileup.c
1495 M /trunk/samtools/bamtk.c
1496
1497 * samtools-0.1.3-1
1498 * fixed a bug in pileup: the first read in a chromosome may not be printed
1499
1500 ------------------------------------------------------------------------
1501 r232 | lh3lh3 | 2009-04-16 15:25:43 +0100 (Thu, 16 Apr 2009) | 2 lines
1502 Changed paths:
1503 M /trunk/samtools/Makefile.lite
1504
1505 a missing file in Makefile.lite
1506
1507 ------------------------------------------------------------------------
1508 r227 | lh3lh3 | 2009-04-15 22:02:53 +0100 (Wed, 15 Apr 2009) | 2 lines
1509 Changed paths:
1510 M /trunk/samtools/NEWS
1511 M /trunk/samtools/bamtk.c
1512
1513 Release samtools-0.1.3
1514
1515 ------------------------------------------------------------------------
1516 r223 | lh3lh3 | 2009-04-15 14:31:32 +0100 (Wed, 15 Apr 2009) | 3 lines
1517 Changed paths:
1518 M /trunk/samtools/bam_plcmd.c
1519 M /trunk/samtools/bamtk.c
1520
1521 * samtools-0.1.2-28
1522 * make samtools more robust to weird input such as empty file
1523
1524 ------------------------------------------------------------------------
1525 r222 | lh3lh3 | 2009-04-15 14:05:33 +0100 (Wed, 15 Apr 2009) | 2 lines
1526 Changed paths:
1527 M /trunk/samtools/ChangeLog
1528 M /trunk/samtools/NEWS
1529 M /trunk/samtools/samtools.1
1530
1531 prepare for release 0.1.3
1532
1533 ------------------------------------------------------------------------
1534 r221 | lh3lh3 | 2009-04-15 13:32:14 +0100 (Wed, 15 Apr 2009) | 2 lines
1535 Changed paths:
1536 A /trunk/samtools/misc/blast2sam.pl
1537
1538 convert NCBI-BLASTN to SAM
1539
1540 ------------------------------------------------------------------------
1541 r220 | lh3lh3 | 2009-04-15 13:18:19 +0100 (Wed, 15 Apr 2009) | 3 lines
1542 Changed paths:
1543 M /trunk/samtools/bam_lpileup.c
1544 M /trunk/samtools/bamtk.c
1545
1546 * samtools-0.1.2-27
1547 * fixed a small memory leak in tview
1548
1549 ------------------------------------------------------------------------
1550 r219 | lh3lh3 | 2009-04-15 13:00:08 +0100 (Wed, 15 Apr 2009) | 3 lines
1551 Changed paths:
1552 M /trunk/samtools/bam_rmdup.c
1553 M /trunk/samtools/bamtk.c
1554
1555 * samtools-0.1.2-26
1556 * fixed a bug in rmdup when there are unmapped reads
1557
1558 ------------------------------------------------------------------------
1559 r218 | lh3lh3 | 2009-04-14 22:28:58 +0100 (Tue, 14 Apr 2009) | 2 lines
1560 Changed paths:
1561 M /trunk/samtools/ChangeLog
1562 M /trunk/samtools/NEWS
1563
1564 proposed NEWS for the new release (have not yet)
1565
1566 ------------------------------------------------------------------------
1567 r216 | lh3lh3 | 2009-04-14 22:10:46 +0100 (Tue, 14 Apr 2009) | 4 lines
1568 Changed paths:
1569 M /trunk/samtools/misc/samtools.pl
1570
1571 * samtools.pl-0.1.1
1572 * improve indelFilter to avoid filtering true indels. The new filter relies
1573 on the new pileup indel line implemented in samtools-0.1.2-25
1574
1575 ------------------------------------------------------------------------
1576 r215 | lh3lh3 | 2009-04-14 22:04:19 +0100 (Tue, 14 Apr 2009) | 4 lines
1577 Changed paths:
1578 M /trunk/samtools/bam_maqcns.c
1579 M /trunk/samtools/bam_plcmd.c
1580 M /trunk/samtools/bamtk.c
1581 M /trunk/samtools/samtools.1
1582
1583 * samtools-0.1.2-25
1584 * change the pileup indel line to shows the number of alignments actually
1585 containing indels
1586
1587 ------------------------------------------------------------------------
1588 r211 | lh3lh3 | 2009-04-13 12:07:13 +0100 (Mon, 13 Apr 2009) | 2 lines
1589 Changed paths:
1590 M /trunk/samtools/ChangeLog
1591
1592 update ChangeLog from "svn log"
1593
1594 ------------------------------------------------------------------------
1595 r210 | lh3lh3 | 2009-04-12 20:57:05 +0100 (Sun, 12 Apr 2009) | 4 lines
1596 Changed paths:
1597 M /trunk/samtools/bam.c
1598 M /trunk/samtools/bam_import.c
1599 M /trunk/samtools/bam_sort.c
1600 M /trunk/samtools/bamtk.c
1601 M /trunk/samtools/kseq.h
1602
1603 * samtools-0.1.2-24
1604 * in merge, gives a warning rather than error if the target sequence length is different
1605 * allow empty header
1606
1607 ------------------------------------------------------------------------
1608 r209 | lh3lh3 | 2009-04-12 20:32:44 +0100 (Sun, 12 Apr 2009) | 3 lines
1609 Changed paths:
1610 M /trunk/samtools/bam.c
1611 M /trunk/samtools/bam_import.c
1612 M /trunk/samtools/bamtk.c
1613
1614 * samtools-0.1.2-23
1615 * recognize '*' at the QUAL field
1616
1617 ------------------------------------------------------------------------
1618 r208 | lh3lh3 | 2009-04-12 20:08:02 +0100 (Sun, 12 Apr 2009) | 3 lines
1619 Changed paths:
1620 M /trunk/samtools/bam_import.c
1621 M /trunk/samtools/bamtk.c
1622 M /trunk/samtools/kseq.h
1623
1624 * samtools-0.1.2-22
1625 * the field separater is TAB only, now
1626
1627 ------------------------------------------------------------------------
1628 r207 | lh3lh3 | 2009-04-08 15:18:03 +0100 (Wed, 08 Apr 2009) | 2 lines
1629 Changed paths:
1630 M /trunk/samtools/examples/ex1.sam.gz
1631
1632 * fixed the problem in the example alignment due to the bug in fixmate
1633
1634 ------------------------------------------------------------------------
1635 r206 | lh3lh3 | 2009-04-08 15:15:05 +0100 (Wed, 08 Apr 2009) | 3 lines
1636 Changed paths:
1637 M /trunk/samtools/bam_mate.c
1638 M /trunk/samtools/bamtk.c
1639 M /trunk/samtools/misc/soap2sam.pl
1640
1641 * samtools-0.1.2-21
1642 * fixed a nasty bug in `fixmate'
1643
1644 ------------------------------------------------------------------------
1645 r205 | lh3lh3 | 2009-04-08 10:57:08 +0100 (Wed, 08 Apr 2009) | 2 lines
1646 Changed paths:
1647 M /trunk/samtools/misc/bowtie2sam.pl
1648 M /trunk/samtools/misc/soap2sam.pl
1649 M /trunk/samtools/misc/wgsim_eval.pl
1650
1651 make the script robust to the bugs in SOAP-2.1.7
1652
1653 ------------------------------------------------------------------------
1654 r200 | lh3lh3 | 2009-04-02 15:14:56 +0100 (Thu, 02 Apr 2009) | 3 lines
1655 Changed paths:
1656 M /trunk/samtools/bam_stat.c
1657 M /trunk/samtools/bamtk.c
1658
1659 * samtools-0.1.2-20
1660 * check if file is truncated in flagstat
1661
1662 ------------------------------------------------------------------------
1663 r199 | lh3lh3 | 2009-04-02 15:09:10 +0100 (Thu, 02 Apr 2009) | 3 lines
1664 Changed paths:
1665 M /trunk/samtools/bamtk.c
1666
1667 * samtools-0.1.2-19
1668 * print the header if requested
1669
1670 ------------------------------------------------------------------------
1671 r193 | lh3lh3 | 2009-03-27 15:09:50 +0000 (Fri, 27 Mar 2009) | 3 lines
1672 Changed paths:
1673 M /trunk/samtools/bam_plcmd.c
1674 M /trunk/samtools/bamtk.c
1675
1676 * samtools-0.1.2-18
1677 * fixed a minor bug reported by Nils Homer
1678
1679 ------------------------------------------------------------------------
1680 r185 | lh3lh3 | 2009-03-24 11:50:32 +0000 (Tue, 24 Mar 2009) | 2 lines
1681 Changed paths:
1682 A /trunk/samtools/Makefile (from /trunk/samtools/Makefile.std:184)
1683 D /trunk/samtools/Makefile.std
1684 A /trunk/samtools/misc/Makefile (from /trunk/samtools/misc/Makefile.std:184)
1685 D /trunk/samtools/misc/Makefile.std
1686
1687 rename Makefile.std as Makefile. GNU building systerm is not ready and may take some time...
1688
1689 ------------------------------------------------------------------------
1690 r184 | lh3lh3 | 2009-03-24 10:36:38 +0000 (Tue, 24 Mar 2009) | 4 lines
1691 Changed paths:
1692 D /trunk/samtools/Makefile
1693 A /trunk/samtools/Makefile.std (from /trunk/samtools/Makefile:183)
1694 M /trunk/samtools/bam_sort.c
1695 M /trunk/samtools/bam_tview.c
1696 M /trunk/samtools/bamtk.c
1697 D /trunk/samtools/misc/Makefile
1698 A /trunk/samtools/misc/Makefile.std (from /trunk/samtools/misc/Makefile:182)
1699 M /trunk/samtools/samtools.1
1700
1701 * samtools-0.1.2-17
1702 * incorporating Nils' changes
1703 * rename Makefile to Makefile.std and prepare to add the GNU building systerms (also by Nils)
1704
1705 ------------------------------------------------------------------------
1706 r183 | lh3lh3 | 2009-03-24 10:30:23 +0000 (Tue, 24 Mar 2009) | 4 lines
1707 Changed paths:
1708 M /trunk/samtools/Makefile
1709 M /trunk/samtools/bam_import.c
1710 M /trunk/samtools/bam_maqcns.c
1711 M /trunk/samtools/bam_maqcns.h
1712 M /trunk/samtools/bam_plcmd.c
1713 M /trunk/samtools/bamtk.c
1714 M /trunk/samtools/kseq.h
1715 A /trunk/samtools/kstring.c
1716 A /trunk/samtools/kstring.h
1717
1718 * samtools-0.1.2-16
1719 * made pileup take a list of proposed indels. An insertion is N at the moment.
1720 * added my kstring library for a bit complex parsing of the position list.
1721
1722 ------------------------------------------------------------------------
1723 r169 | lh3lh3 | 2009-03-12 13:40:14 +0000 (Thu, 12 Mar 2009) | 3 lines
1724 Changed paths:
1725 M /trunk/samtools/misc/soap2sam.pl
1726
1727 * soap2sam.pl-0.1.2
1728 * more robust to truncated soap output
1729
1730 ------------------------------------------------------------------------
1731 r168 | lh3lh3 | 2009-03-11 10:49:00 +0000 (Wed, 11 Mar 2009) | 2 lines
1732 Changed paths:
1733 M /trunk/samtools/Makefile.lite
1734
1735 added bam_stat.o to Makefile.lite
1736
1737 ------------------------------------------------------------------------
1738 r167 | lh3lh3 | 2009-03-10 22:11:31 +0000 (Tue, 10 Mar 2009) | 3 lines
1739 Changed paths:
1740 M /trunk/samtools/bam_maqcns.c
1741 M /trunk/samtools/bamtk.c
1742
1743 * samtools-0.1.2-15
1744 * generate RMS of mapQ instead of max mapQ
1745
1746 ------------------------------------------------------------------------
1747 r166 | lh3lh3 | 2009-03-10 22:06:45 +0000 (Tue, 10 Mar 2009) | 3 lines
1748 Changed paths:
1749 M /trunk/samtools/bam_plcmd.c
1750 M /trunk/samtools/bamtk.c
1751 M /trunk/samtools/glf.c
1752 M /trunk/samtools/glf.h
1753 M /trunk/samtools/misc/Makefile
1754
1755 * samtools-0.1.2-14
1756 * implemented GLFv3
1757
1758 ------------------------------------------------------------------------
1759 r159 | lh3lh3 | 2009-03-03 11:26:08 +0000 (Tue, 03 Mar 2009) | 3 lines
1760 Changed paths:
1761 M /trunk/samtools/bam_plcmd.c
1762 M /trunk/samtools/bamtk.c
1763
1764 * samtools-0.1.2-13
1765 * fixed a minor bug in displaying pileup
1766
1767 ------------------------------------------------------------------------
1768 r158 | lh3lh3 | 2009-03-03 11:24:16 +0000 (Tue, 03 Mar 2009) | 3 lines
1769 Changed paths:
1770 M /trunk/samtools/ChangeLog
1771 M /trunk/samtools/bamtk.c
1772
1773 * samtools-0.1.2-12
1774 * optionally print SAM header
1775
1776 ------------------------------------------------------------------------
1777 r153 | lh3lh3 | 2009-03-02 10:45:28 +0000 (Mon, 02 Mar 2009) | 3 lines
1778 Changed paths:
1779 M /trunk/samtools/bamtk.c
1780 M /trunk/samtools/glf.c
1781
1782 * samtools-0.1.2-11
1783 * use "GLF\3" as the magic for GLFv3 files
1784
1785 ------------------------------------------------------------------------
1786 r152 | lh3lh3 | 2009-03-02 10:39:09 +0000 (Mon, 02 Mar 2009) | 5 lines
1787 Changed paths:
1788 M /trunk/samtools/Makefile
1789 M /trunk/samtools/bam_import.c
1790 M /trunk/samtools/bam_index.c
1791 M /trunk/samtools/bam_plcmd.c
1792 M /trunk/samtools/bamtk.c
1793 M /trunk/samtools/glf.c
1794 M /trunk/samtools/glf.h
1795
1796 * samtools-0.1.2-10
1797 * fixed a bug in import: core.bin is undefined for unmapped reads
1798 * this bug can be alleviated (not completely solved) in bam_index.c
1799 * update to GLFv3: pos is changed to offset for better compression
1800
1801 ------------------------------------------------------------------------
1802 r151 | lh3lh3 | 2009-03-01 15:18:43 +0000 (Sun, 01 Mar 2009) | 3 lines
1803 Changed paths:
1804 M /trunk/samtools/misc/wgsim.c
1805
1806 * wgsim-0.2.3
1807 * fixed a bug in simulating indels
1808
1809 ------------------------------------------------------------------------
1810 r145 | lh3lh3 | 2009-02-26 19:43:57 +0000 (Thu, 26 Feb 2009) | 4 lines
1811 Changed paths:
1812 M /trunk/samtools/misc/wgsim.c
1813
1814 * wgsim-0.2.2
1815 * allow to print mismatch information as fastq comment. MAQ does
1816 not like long read names.
1817
1818 ------------------------------------------------------------------------
1819 r141 | lh3lh3 | 2009-02-26 14:53:03 +0000 (Thu, 26 Feb 2009) | 6 lines
1820 Changed paths:
1821 M /trunk/samtools/ChangeLog
1822 M /trunk/samtools/misc/wgsim.c
1823 M /trunk/samtools/misc/wgsim_eval.pl
1824
1825 * wgsim-0.2.1
1826 * fixed a bug about color read coordinates
1827 * fixed a bug in read names
1828 * wgsim_eval.pl-0.1.3
1829 * make the script work with color reads
1830
1831 ------------------------------------------------------------------------
1832 r140 | lh3lh3 | 2009-02-26 14:02:57 +0000 (Thu, 26 Feb 2009) | 2 lines
1833 Changed paths:
1834 M /trunk/samtools/misc/Makefile
1835 M /trunk/samtools/misc/wgsim.c
1836
1837 * wgsim: added a note
1838
1839 ------------------------------------------------------------------------
1840 r139 | lh3lh3 | 2009-02-26 11:39:08 +0000 (Thu, 26 Feb 2009) | 7 lines
1841 Changed paths:
1842 M /trunk/samtools/misc/wgsim.c
1843 M /trunk/samtools/misc/wgsim_eval.pl
1844
1845 * wgsim-0.2.0
1846 * considerable code clean up
1847 * print number of substitutions/indels/errors on each read
1848 * potentially support SOLiD simulation, though not tested at the moment
1849 * wgsim_eval.pl-0.1.2
1850 * change in accordant with wgsim
1851
1852 ------------------------------------------------------------------------
1853 r129 | lh3lh3 | 2009-02-18 22:23:27 +0000 (Wed, 18 Feb 2009) | 3 lines
1854 Changed paths:
1855 M /trunk/samtools/bam_index.c
1856 M /trunk/samtools/bamtk.c
1857
1858 * samtools-0.1.2-9
1859 * fixed a bug in bam_fetch, caused by completely contained adjacent chunks
1860
1861 ------------------------------------------------------------------------
1862 r128 | bhandsaker | 2009-02-18 19:06:57 +0000 (Wed, 18 Feb 2009) | 2 lines
1863 Changed paths:
1864 M /trunk/samtools/bamtk.c
1865
1866 Fix annoying segv when invalid region specified.
1867
1868 ------------------------------------------------------------------------
1869 r127 | lh3lh3 | 2009-02-17 10:49:55 +0000 (Tue, 17 Feb 2009) | 2 lines
1870 Changed paths:
1871 D /trunk/samtools/misc/indel_filter.pl
1872 A /trunk/samtools/misc/samtools.pl
1873
1874 * move indel_filter.pl to samtools.pl
1875
1876 ------------------------------------------------------------------------
1877 r126 | lh3lh3 | 2009-02-14 21:22:30 +0000 (Sat, 14 Feb 2009) | 3 lines
1878 Changed paths:
1879 M /trunk/samtools/bam_mate.c
1880 M /trunk/samtools/bamtk.c
1881
1882 * samtools-0.1.2-7
1883 * fixed a bug in fixmate: SE reads are flagged as BAM_FMUNMAP
1884
1885 ------------------------------------------------------------------------
1886 r125 | lh3lh3 | 2009-02-13 09:54:45 +0000 (Fri, 13 Feb 2009) | 3 lines
1887 Changed paths:
1888 M /trunk/samtools/bam_stat.c
1889 M /trunk/samtools/bamtk.c
1890
1891 * samtools-0.1.2-7
1892 * fixed a minor bug in flagstat
1893
1894 ------------------------------------------------------------------------
1895 r124 | lh3lh3 | 2009-02-12 11:15:32 +0000 (Thu, 12 Feb 2009) | 3 lines
1896 Changed paths:
1897 M /trunk/samtools/bam_maqcns.c
1898 M /trunk/samtools/bamtk.c
1899 M /trunk/samtools/misc/indel_filter.pl
1900
1901 * samtools-0.1.2-6
1902 * improve indel caller by setting maximum window size
1903
1904 ------------------------------------------------------------------------
1905 r123 | lh3lh3 | 2009-02-12 10:30:29 +0000 (Thu, 12 Feb 2009) | 2 lines
1906 Changed paths:
1907 M /trunk/samtools/bam_plcmd.c
1908 M /trunk/samtools/bamtk.c
1909
1910 * output max mapping quality in indel line
1911
1912 ------------------------------------------------------------------------
1913 r122 | lh3lh3 | 2009-02-11 10:59:10 +0000 (Wed, 11 Feb 2009) | 2 lines
1914 Changed paths:
1915 M /trunk/samtools/misc/maq2sam.c
1916
1917 fixed a bug in generating tag AM
1918
1919 ------------------------------------------------------------------------
1920 r121 | lh3lh3 | 2009-02-03 10:43:11 +0000 (Tue, 03 Feb 2009) | 2 lines
1921 Changed paths:
1922 M /trunk/samtools/bam_index.c
1923 M /trunk/samtools/bamtk.c
1924
1925 fixed a potential memory problem in indexing
1926
1927 ------------------------------------------------------------------------
1928 r120 | bhandsaker | 2009-02-02 15:52:52 +0000 (Mon, 02 Feb 2009) | 2 lines
1929 Changed paths:
1930 M /trunk/samtools/Makefile
1931
1932 Pass LIBS to recursive targets to facilitate building at Broad.
1933
1934 ------------------------------------------------------------------------
1935 r119 | lh3lh3 | 2009-02-02 10:12:15 +0000 (Mon, 02 Feb 2009) | 4 lines
1936 Changed paths:
1937 M /trunk/samtools/ChangeLog
1938 M /trunk/samtools/bam_plcmd.c
1939 M /trunk/samtools/bam_stat.c
1940 M /trunk/samtools/bamtk.c
1941
1942 * samtools-0.1.2-3
1943 * fixed a bug in generating GLFv2 for indels
1944 * improve flagstat report a little bit
1945
1946 ------------------------------------------------------------------------
1947 r118 | lh3lh3 | 2009-01-29 12:33:23 +0000 (Thu, 29 Jan 2009) | 3 lines
1948 Changed paths:
1949 M /trunk/samtools/Makefile
1950 A /trunk/samtools/bam_stat.c
1951 M /trunk/samtools/bamtk.c
1952
1953 * samtools-0.1.2-1
1954 * added flagstat command
1955
1956 ------------------------------------------------------------------------
1957 r116 | lh3lh3 | 2009-01-28 13:31:12 +0000 (Wed, 28 Jan 2009) | 2 lines
1958 Changed paths:
1959 M /trunk/samtools/ChangeLog
1960 M /trunk/samtools/NEWS
1961 M /trunk/samtools/bamtk.c
1962 M /trunk/samtools/samtools.1
1963
1964 Release SAMtools-0.1.2
1965
1966 ------------------------------------------------------------------------
1967 r115 | lh3lh3 | 2009-01-28 12:54:08 +0000 (Wed, 28 Jan 2009) | 2 lines
1968 Changed paths:
1969 A /trunk/samtools/misc/indel_filter.pl
1970
1971 Script for filtering indel results
1972
1973 ------------------------------------------------------------------------
1974 r114 | lh3lh3 | 2009-01-25 11:45:37 +0000 (Sun, 25 Jan 2009) | 2 lines
1975 Changed paths:
1976 A /trunk/samtools/misc/zoom2sam.pl
1977
1978 convert ZOOM to SAM
1979
1980 ------------------------------------------------------------------------
1981 r113 | lh3lh3 | 2009-01-24 14:25:07 +0000 (Sat, 24 Jan 2009) | 2 lines
1982 Changed paths:
1983 A /trunk/samtools/misc/novo2sam.pl
1984
1985 add a script to convert novo alignment to SAM
1986
1987 ------------------------------------------------------------------------
1988 r112 | lh3lh3 | 2009-01-23 20:57:39 +0000 (Fri, 23 Jan 2009) | 2 lines
1989 Changed paths:
1990 M /trunk/samtools/ChangeLog
1991 M /trunk/samtools/ChangeLog.old
1992 M /trunk/samtools/samtools.1
1993
1994 update documentation and ChangeLog
1995
1996 ------------------------------------------------------------------------
1997 r111 | lh3lh3 | 2009-01-23 19:22:59 +0000 (Fri, 23 Jan 2009) | 3 lines
1998 Changed paths:
1999 M /trunk/samtools/bam_sort.c
2000 M /trunk/samtools/bamtk.c
2001
2002 * samtools-0.1.1-19
2003 * fixed a bug in "merge" command line
2004
2005 ------------------------------------------------------------------------
2006 r110 | lh3lh3 | 2009-01-22 15:36:48 +0000 (Thu, 22 Jan 2009) | 3 lines
2007 Changed paths:
2008 M /trunk/samtools/misc/Makefile
2009 A /trunk/samtools/misc/bowtie2sam.pl (from /branches/dev/samtools/misc/bowtie2sam.pl:108)
2010 M /trunk/samtools/misc/export2sam.pl
2011 A /trunk/samtools/misc/soap2sam.pl (from /branches/dev/samtools/misc/soap2sam.pl:108)
2012 A /trunk/samtools/misc/wgsim.c (from /branches/dev/samtools/misc/wgsim.c:108)
2013 A /trunk/samtools/misc/wgsim_eval.pl (from /branches/dev/samtools/misc/wgsim_eval.pl:108)
2014
2015 * merge from branches/dev/
2016 * all future development will happen here
2017
2018 ------------------------------------------------------------------------
2019 r109 | lh3lh3 | 2009-01-22 15:14:27 +0000 (Thu, 22 Jan 2009) | 3 lines
2020 Changed paths:
2021 M /trunk/samtools/COPYING
2022 M /trunk/samtools/ChangeLog
2023 A /trunk/samtools/INSTALL (from /branches/dev/samtools/INSTALL:108)
2024 M /trunk/samtools/Makefile
2025 A /trunk/samtools/Makefile.lite (from /branches/dev/samtools/Makefile.lite:108)
2026 M /trunk/samtools/bam.c
2027 M /trunk/samtools/bam.h
2028 M /trunk/samtools/bam_import.c
2029 M /trunk/samtools/bam_index.c
2030 M /trunk/samtools/bam_lpileup.c
2031 M /trunk/samtools/bam_maqcns.c
2032 M /trunk/samtools/bam_maqcns.h
2033 A /trunk/samtools/bam_mate.c (from /branches/dev/samtools/bam_mate.c:108)
2034 M /trunk/samtools/bam_pileup.c
2035 M /trunk/samtools/bam_plcmd.c
2036 A /trunk/samtools/bam_rmdup.c (from /branches/dev/samtools/bam_rmdup.c:108)
2037 M /trunk/samtools/bam_sort.c
2038 M /trunk/samtools/bamtk.c
2039 M /trunk/samtools/bgzf.h
2040 M /trunk/samtools/examples/00README.txt
2041 A /trunk/samtools/examples/Makefile (from /branches/dev/samtools/examples/Makefile:108)
2042 D /trunk/samtools/examples/ex1.fa.fai
2043 M /trunk/samtools/examples/ex1.sam.gz
2044 M /trunk/samtools/faidx.c
2045 A /trunk/samtools/glf.c (from /branches/dev/samtools/glf.c:108)
2046 M /trunk/samtools/glf.h
2047 M /trunk/samtools/misc/Makefile
2048 M /trunk/samtools/misc/maq2sam.c
2049 M /trunk/samtools/razf.c
2050 M /trunk/samtools/source.dot
2051
2052 * Merge from branches/dev/
2053 * all future development will happen here at trunk/
2054
2055 ------------------------------------------------------------------------
2056 r79 | bhandsaker | 2009-01-07 21:42:15 +0000 (Wed, 07 Jan 2009) | 2 lines
2057 Changed paths:
2058 M /trunk/samtools/bam_maqcns.c
2059 M /trunk/samtools/bam_tview.c
2060
2061 Fix problem with compiling without curses.
2062
2063 ------------------------------------------------------------------------
2064 r63 | lh3lh3 | 2008-12-22 15:58:02 +0000 (Mon, 22 Dec 2008) | 2 lines
2065 Changed paths:
2066 A /trunk/samtools (from /branches/dev/samtools:62)
2067
2068 Create trunk copy
2069
2070 ------------------------------------------------------------------------
2071 r62 | lh3lh3 | 2008-12-22 15:55:13 +0000 (Mon, 22 Dec 2008) | 2 lines
2072 Changed paths:
2073 A /branches/dev/samtools/NEWS
2074 M /branches/dev/samtools/bamtk.c
2075 M /branches/dev/samtools/samtools.1
2076
2077 Release samtools-0.1.1
2078
2079 ------------------------------------------------------------------------
2080 r61 | lh3lh3 | 2008-12-22 15:46:08 +0000 (Mon, 22 Dec 2008) | 10 lines
2081 Changed paths:
2082 M /branches/dev/samtools/bam_aux.c
2083 M /branches/dev/samtools/bam_index.c
2084 M /branches/dev/samtools/bam_plcmd.c
2085 M /branches/dev/samtools/bam_tview.c
2086 M /branches/dev/samtools/bamtk.c
2087 M /branches/dev/samtools/razf.c
2088 M /branches/dev/samtools/samtools.1
2089
2090 * samtools-0.1.0-66
2091 * fixed a bug in razf.c: reset z_eof when razf_seek() is called
2092 * fixed a memory leak in parsing a region
2093 * changed pileup a little bit when -s is in use: output ^ and $
2094 * when a bam is not indexed, output more meaningful error message
2095 * fixed a bug in indexing for small alignment
2096 * fixed a bug in the viewer when we come to the end of a reference file
2097 * updated documentation
2098 * prepare to release 0.1.1
2099
2100 ------------------------------------------------------------------------
2101 r60 | lh3lh3 | 2008-12-22 15:10:16 +0000 (Mon, 22 Dec 2008) | 2 lines
2102 Changed paths:
2103 A /branches/dev/samtools/examples
2104 A /branches/dev/samtools/examples/00README.txt
2105 A /branches/dev/samtools/examples/ex1.fa
2106 A /branches/dev/samtools/examples/ex1.fa.fai
2107 A /branches/dev/samtools/examples/ex1.sam.gz
2108
2109 example
2110
2111 ------------------------------------------------------------------------
2112 r59 | lh3lh3 | 2008-12-22 09:38:15 +0000 (Mon, 22 Dec 2008) | 2 lines
2113 Changed paths:
2114 M /branches/dev/samtools/ChangeLog
2115
2116 update ChangeLog
2117
2118 ------------------------------------------------------------------------
2119 r58 | lh3lh3 | 2008-12-20 23:06:00 +0000 (Sat, 20 Dec 2008) | 3 lines
2120 Changed paths:
2121 M /branches/dev/samtools/misc/export2sam.pl
2122
2123 * added comments
2124 * fixed several bugs
2125
2126 ------------------------------------------------------------------------
2127 r57 | lh3lh3 | 2008-12-20 15:44:20 +0000 (Sat, 20 Dec 2008) | 2 lines
2128 Changed paths:
2129 A /branches/dev/samtools/misc/export2sam.pl
2130
2131 convert Export format to SAM; not thoroughly tested
2132
2133 ------------------------------------------------------------------------
2134 r56 | lh3lh3 | 2008-12-19 22:13:28 +0000 (Fri, 19 Dec 2008) | 6 lines
2135 Changed paths:
2136 M /branches/dev/samtools/bam_import.c
2137 M /branches/dev/samtools/bam_plcmd.c
2138 M /branches/dev/samtools/bam_tview.c
2139 M /branches/dev/samtools/bamtk.c
2140 A /branches/dev/samtools/source.dot
2141
2142 * samtools-0.1.0-65
2143 * pileup: generate maq-like simple output
2144 * pileup: allow to output pileup at required sites
2145 * source.dot: source file relationship graph
2146 * tview: fixed a minor bug
2147
2148 ------------------------------------------------------------------------
2149 r55 | lh3lh3 | 2008-12-19 20:10:26 +0000 (Fri, 19 Dec 2008) | 2 lines
2150 Changed paths:
2151 D /branches/dev/samtools/misc/all2sam.pl
2152
2153 remove all2sam.pl
2154
2155 ------------------------------------------------------------------------
2156 r54 | lh3lh3 | 2008-12-16 22:34:25 +0000 (Tue, 16 Dec 2008) | 2 lines
2157 Changed paths:
2158 A /branches/dev/samtools/COPYING
2159 M /branches/dev/samtools/bam.h
2160 M /branches/dev/samtools/faidx.h
2161 M /branches/dev/samtools/khash.h
2162 M /branches/dev/samtools/kseq.h
2163 M /branches/dev/samtools/ksort.h
2164 M /branches/dev/samtools/samtools.1
2165
2166 Added copyright information and a bit more documentation. No code change.
2167
2168 ------------------------------------------------------------------------
2169 r53 | lh3lh3 | 2008-12-16 13:40:18 +0000 (Tue, 16 Dec 2008) | 3 lines
2170 Changed paths:
2171 M /branches/dev/samtools/bam.c
2172 M /branches/dev/samtools/bam.h
2173 M /branches/dev/samtools/bam_index.c
2174 M /branches/dev/samtools/bam_maqcns.c
2175 M /branches/dev/samtools/bamtk.c
2176
2177 * samtools-0.1.0-64
2178 * improved efficiency of the indel caller for spliced alignments
2179
2180 ------------------------------------------------------------------------
2181 r52 | lh3lh3 | 2008-12-16 10:28:20 +0000 (Tue, 16 Dec 2008) | 3 lines
2182 Changed paths:
2183 M /branches/dev/samtools/bam.c
2184 M /branches/dev/samtools/bam.h
2185 M /branches/dev/samtools/bam_aux.c
2186 M /branches/dev/samtools/bam_index.c
2187 M /branches/dev/samtools/bamtk.c
2188
2189 * samtools-0.1.0-63
2190 * a bit code cleanup: reduce the dependency between source files
2191
2192 ------------------------------------------------------------------------
2193 r51 | lh3lh3 | 2008-12-15 14:29:32 +0000 (Mon, 15 Dec 2008) | 3 lines
2194 Changed paths:
2195 M /branches/dev/samtools/bam_maqcns.c
2196 M /branches/dev/samtools/bam_plcmd.c
2197 M /branches/dev/samtools/bamtk.c
2198
2199 * samtools-0.1.0-62
2200 * fixed a memory leak
2201
2202 ------------------------------------------------------------------------
2203 r50 | lh3lh3 | 2008-12-15 14:00:13 +0000 (Mon, 15 Dec 2008) | 2 lines
2204 Changed paths:
2205 M /branches/dev/samtools/ChangeLog
2206 M /branches/dev/samtools/bam.h
2207 M /branches/dev/samtools/samtools.1
2208
2209 update documentation, ChangeLog and a comment
2210
2211 ------------------------------------------------------------------------
2212 r49 | lh3lh3 | 2008-12-15 13:36:43 +0000 (Mon, 15 Dec 2008) | 6 lines
2213 Changed paths:
2214 M /branches/dev/samtools/Makefile
2215 M /branches/dev/samtools/bam.h
2216 M /branches/dev/samtools/bam_maqcns.c
2217 M /branches/dev/samtools/bam_maqcns.h
2218 M /branches/dev/samtools/bam_pileup.c
2219 A /branches/dev/samtools/bam_plcmd.c
2220 M /branches/dev/samtools/bamtk.c
2221 M /branches/dev/samtools/samtools.1
2222
2223 * samtools-0.1.0-61
2224 * moved pileup command to a separate source file
2225 * added indel caller
2226 * added bam_cal_segend(). (NOT WORKING for spliced alignment!!!)
2227 * updated documentation
2228
2229 ------------------------------------------------------------------------
2230 r48 | lh3lh3 | 2008-12-12 13:55:36 +0000 (Fri, 12 Dec 2008) | 3 lines
2231 Changed paths:
2232 M /branches/dev/samtools/bam_maqcns.c
2233 M /branches/dev/samtools/bamtk.c
2234
2235 * samtools-0.1.0-60
2236 * fixed another bug in maqcns when there is a nearby deletion
2237
2238 ------------------------------------------------------------------------
2239 r47 | lh3lh3 | 2008-12-12 13:42:16 +0000 (Fri, 12 Dec 2008) | 5 lines
2240 Changed paths:
2241 M /branches/dev/samtools/bam_maqcns.c
2242 M /branches/dev/samtools/bam_pileup.c
2243 M /branches/dev/samtools/bamtk.c
2244
2245 * samtools-0.1.0-59
2246 * pileup: outputing consensus is now optional
2247 * fixed a bug in glfgen. This bug also exists in maq's glfgen. However,
2248 I am not quite sure why the previous version may have problem.
2249
2250 ------------------------------------------------------------------------
2251 r46 | lh3lh3 | 2008-12-12 11:44:56 +0000 (Fri, 12 Dec 2008) | 6 lines
2252 Changed paths:
2253 M /branches/dev/samtools/bam_pileup.c
2254 M /branches/dev/samtools/bamtk.c
2255
2256 * samtools-0.1.0-58
2257 * add maq consensus to pileup. However, I will move this part to a new
2258 command as strictly speaking, consensus callin is not part of pileup,
2259 and imposing it would make it harder to generate for other language
2260 bindings.
2261
2262 ------------------------------------------------------------------------
2263 r45 | bhandsaker | 2008-12-11 20:43:56 +0000 (Thu, 11 Dec 2008) | 2 lines
2264 Changed paths:
2265 M /branches/dev/samtools/bgzf.c
2266
2267 Fix bug in tell() after reads that consume to the exact end of a block.
2268
2269 ------------------------------------------------------------------------
2270 r44 | lh3lh3 | 2008-12-11 09:36:53 +0000 (Thu, 11 Dec 2008) | 2 lines
2271 Changed paths:
2272 M /branches/dev/samtools/samtools.1
2273
2274 update manual
2275
2276 ------------------------------------------------------------------------
2277 r43 | lh3lh3 | 2008-12-11 09:25:36 +0000 (Thu, 11 Dec 2008) | 4 lines
2278 Changed paths:
2279 M /branches/dev/samtools/bam_import.c
2280 M /branches/dev/samtools/bamtk.c
2281
2282 * samtools-0.1.0-57
2283 * fixed a bug in parser when there is auxiliary fields
2284 * made the parser a bit more robust
2285
2286 ------------------------------------------------------------------------
2287 r42 | lh3lh3 | 2008-12-10 14:57:29 +0000 (Wed, 10 Dec 2008) | 5 lines
2288 Changed paths:
2289 M /branches/dev/samtools/bam_index.c
2290 M /branches/dev/samtools/bamtk.c
2291 M /branches/dev/samtools/bgzf.c
2292
2293 * samtools-0.1.0-56
2294 * fixed a bug in bgzf (only reading is affected)
2295 * fixed a typo in bam_index.c
2296 * in bam_index.c, check potential bugs in the underlying I/O library
2297
2298 ------------------------------------------------------------------------
2299 r41 | lh3lh3 | 2008-12-10 12:53:08 +0000 (Wed, 10 Dec 2008) | 2 lines
2300 Changed paths:
2301 M /branches/dev/samtools/samtools.1
2302
2303 update manual
2304
2305 ------------------------------------------------------------------------
2306 r40 | lh3lh3 | 2008-12-10 11:52:10 +0000 (Wed, 10 Dec 2008) | 5 lines
2307 Changed paths:
2308 M /branches/dev/samtools/bam.h
2309 M /branches/dev/samtools/bam_pileup.c
2310 M /branches/dev/samtools/bamtk.c
2311
2312 * samtools-0.1.0-55
2313 * tried to make pileup work with clipping (previously not), though NOT tested
2314 * removed -v from pileup
2315 * made pileup take the reference sequence
2316
2317 ------------------------------------------------------------------------
2318 r39 | lh3lh3 | 2008-12-09 11:59:28 +0000 (Tue, 09 Dec 2008) | 4 lines
2319 Changed paths:
2320 M /branches/dev/samtools/bam_import.c
2321 M /branches/dev/samtools/bamtk.c
2322 M /branches/dev/samtools/samtools.1
2323
2324 * samtools-0.1.0-54
2325 * in parser, recognize "=", rather than ",", as a match
2326 * in parser, correctl parse "=" at the MRNM field.
2327
2328 ------------------------------------------------------------------------
2329 r38 | lh3lh3 | 2008-12-09 11:39:07 +0000 (Tue, 09 Dec 2008) | 2 lines
2330 Changed paths:
2331 M /branches/dev/samtools/misc/maq2sam.c
2332
2333 fixed a bug in handling maq flag 64 and 192
2334
2335 ------------------------------------------------------------------------
2336 r37 | lh3lh3 | 2008-12-09 09:53:46 +0000 (Tue, 09 Dec 2008) | 2 lines
2337 Changed paths:
2338 M /branches/dev/samtools/misc/md5fa.c
2339
2340 also calculate unordered md5sum check
2341
2342 ------------------------------------------------------------------------
2343 r36 | lh3lh3 | 2008-12-09 09:46:21 +0000 (Tue, 09 Dec 2008) | 2 lines
2344 Changed paths:
2345 M /branches/dev/samtools/misc/md5fa.c
2346
2347 fixed a minor bug when there are space in the sequence
2348
2349 ------------------------------------------------------------------------
2350 r35 | lh3lh3 | 2008-12-09 09:40:45 +0000 (Tue, 09 Dec 2008) | 2 lines
2351 Changed paths:
2352 M /branches/dev/samtools/misc/md5fa.c
2353
2354 fixed a potential memory leak
2355
2356 ------------------------------------------------------------------------
2357 r34 | lh3lh3 | 2008-12-08 14:52:17 +0000 (Mon, 08 Dec 2008) | 2 lines
2358 Changed paths:
2359 M /branches/dev/samtools/bam_import.c
2360 M /branches/dev/samtools/bam_index.c
2361 M /branches/dev/samtools/bamtk.c
2362
2363 * fixed a bug in import: bin is wrongly calculated
2364
2365 ------------------------------------------------------------------------
2366 r33 | lh3lh3 | 2008-12-08 14:08:01 +0000 (Mon, 08 Dec 2008) | 2 lines
2367 Changed paths:
2368 M /branches/dev/samtools/misc/all2sam.pl
2369
2370 nothing, really
2371
2372 ------------------------------------------------------------------------
2373 r32 | lh3lh3 | 2008-12-08 12:56:02 +0000 (Mon, 08 Dec 2008) | 3 lines
2374 Changed paths:
2375 M /branches/dev/samtools/Makefile
2376 M /branches/dev/samtools/kseq.h
2377 M /branches/dev/samtools/misc/Makefile
2378 A /branches/dev/samtools/misc/md5.c
2379 A /branches/dev/samtools/misc/md5.h
2380 A /branches/dev/samtools/misc/md5fa.c
2381
2382 * fixed two warnings in kseq.h
2383 * added md5sum utilities
2384
2385 ------------------------------------------------------------------------
2386 r31 | lh3lh3 | 2008-12-08 11:35:29 +0000 (Mon, 08 Dec 2008) | 5 lines
2387 Changed paths:
2388 M /branches/dev/samtools/Makefile
2389 M /branches/dev/samtools/bam_import.c
2390 M /branches/dev/samtools/bamtk.c
2391 A /branches/dev/samtools/kseq.h
2392 D /branches/dev/samtools/kstream.h
2393
2394 * samtools-0.1.0-52
2395 * replace kstream with kseq. kseq is a superset of kstream. I need the
2396 extra functions in kseq.h.
2397 * also compile stand-alone faidx
2398
2399 ------------------------------------------------------------------------
2400 r30 | lh3lh3 | 2008-12-08 11:17:04 +0000 (Mon, 08 Dec 2008) | 3 lines
2401 Changed paths:
2402 M /branches/dev/samtools/bam.h
2403 M /branches/dev/samtools/bam_sort.c
2404 M /branches/dev/samtools/bamtk.c
2405
2406 * samtools-0.1.0-51
2407 * sorting by read names is available
2408
2409 ------------------------------------------------------------------------
2410 r29 | lh3lh3 | 2008-12-08 10:29:02 +0000 (Mon, 08 Dec 2008) | 3 lines
2411 Changed paths:
2412 M /branches/dev/samtools/bam.c
2413 M /branches/dev/samtools/bam.h
2414 M /branches/dev/samtools/bam_import.c
2415 M /branches/dev/samtools/bam_maqcns.c
2416 M /branches/dev/samtools/bam_pileup.c
2417 M /branches/dev/samtools/bam_sort.c
2418 M /branches/dev/samtools/bam_tview.c
2419 M /branches/dev/samtools/bamtk.c
2420 M /branches/dev/samtools/misc/maq2sam.c
2421
2422 * samtools-0.1.0-50
2423 * format change to meet the latest specification
2424
2425 ------------------------------------------------------------------------
2426 r28 | lh3lh3 | 2008-12-04 16:09:21 +0000 (Thu, 04 Dec 2008) | 3 lines
2427 Changed paths:
2428 M /branches/dev/samtools/bam_maqcns.c
2429 M /branches/dev/samtools/misc/maq2sam.c
2430
2431 * minor change in maqcns: special care when n==0
2432 * change maq2sam to meet the latest specification
2433
2434 ------------------------------------------------------------------------
2435 r27 | lh3lh3 | 2008-12-04 15:55:44 +0000 (Thu, 04 Dec 2008) | 2 lines
2436 Changed paths:
2437 M /branches/dev/samtools/razf.c
2438 M /branches/dev/samtools/razf.h
2439
2440 considerable code clean up in razf
2441
2442 ------------------------------------------------------------------------
2443 r26 | lh3lh3 | 2008-12-04 15:08:18 +0000 (Thu, 04 Dec 2008) | 2 lines
2444 Changed paths:
2445 M /branches/dev/samtools/ChangeLog
2446 M /branches/dev/samtools/Makefile
2447 M /branches/dev/samtools/faidx.c
2448
2449 make RAZF optional in faidx.c
2450
2451 ------------------------------------------------------------------------
2452 r25 | lh3lh3 | 2008-12-01 15:27:22 +0000 (Mon, 01 Dec 2008) | 3 lines
2453 Changed paths:
2454 M /branches/dev/samtools/Makefile
2455 M /branches/dev/samtools/bam.h
2456 M /branches/dev/samtools/bam_aux.c
2457 M /branches/dev/samtools/bamtk.c
2458 M /branches/dev/samtools/samtools.1
2459
2460 * samtools-0.1.0-49
2461 * added routines for retrieving aux data, NOT TESTED YET!
2462
2463 ------------------------------------------------------------------------
2464 r24 | lh3lh3 | 2008-12-01 14:29:43 +0000 (Mon, 01 Dec 2008) | 5 lines
2465 Changed paths:
2466 M /branches/dev/samtools/bam.c
2467 M /branches/dev/samtools/bam_import.c
2468 M /branches/dev/samtools/bam_maqcns.c
2469 M /branches/dev/samtools/bamtk.c
2470 M /branches/dev/samtools/bgzf.c
2471 M /branches/dev/samtools/samtools.1
2472
2473 * samtools-0.1.0-48
2474 * bgzf: fixed a potential integer overflow on 32-it machines
2475 * maqcns: set the minimum combined quality as 0
2476 * supporting hex strings
2477
2478 ------------------------------------------------------------------------
2479 r23 | lh3lh3 | 2008-11-27 17:14:37 +0000 (Thu, 27 Nov 2008) | 3 lines
2480 Changed paths:
2481 M /branches/dev/samtools/bam_maqcns.c
2482 M /branches/dev/samtools/bamtk.c
2483
2484 * samtools-0.1.0-47
2485 * fixed the bug in maqcns
2486
2487 ------------------------------------------------------------------------
2488 r22 | lh3lh3 | 2008-11-27 17:08:11 +0000 (Thu, 27 Nov 2008) | 3 lines
2489 Changed paths:
2490 M /branches/dev/samtools/Makefile
2491 M /branches/dev/samtools/bam.h
2492 A /branches/dev/samtools/bam_maqcns.c
2493 A /branches/dev/samtools/bam_maqcns.h
2494 M /branches/dev/samtools/bam_tview.c
2495 M /branches/dev/samtools/bamtk.c
2496 A /branches/dev/samtools/glf.h
2497
2498 * samtools-0.1.0-46
2499 * add MAQ consensus caller, currently BUGGY!
2500
2501 ------------------------------------------------------------------------
2502 r21 | lh3lh3 | 2008-11-27 13:51:28 +0000 (Thu, 27 Nov 2008) | 4 lines
2503 Changed paths:
2504 M /branches/dev/samtools/bam_pileup.c
2505 M /branches/dev/samtools/bam_tview.c
2506 M /branches/dev/samtools/bamtk.c
2507
2508 * samtools-0.1.0-45
2509 * tview: display padded alignment (but not P operation)
2510 * better coordinates and reference sequence
2511
2512 ------------------------------------------------------------------------
2513 r19 | lh3lh3 | 2008-11-27 09:26:05 +0000 (Thu, 27 Nov 2008) | 2 lines
2514 Changed paths:
2515 A /branches/dev/samtools/ChangeLog
2516
2517 new ChangeLog
2518
2519 ------------------------------------------------------------------------
2520 r18 | lh3lh3 | 2008-11-27 09:24:45 +0000 (Thu, 27 Nov 2008) | 3 lines
2521 Changed paths:
2522 D /branches/dev/samtools/ChangeLog
2523 A /branches/dev/samtools/ChangeLog.old (from /branches/dev/samtools/ChangeLog:6)
2524
2525 Rename ChangeLog to ChangeLog.old. This old ChangeLog is generated from
2526 the log of my personal SVN repository.
2527
2528 ------------------------------------------------------------------------
2529 r17 | lh3lh3 | 2008-11-27 09:22:55 +0000 (Thu, 27 Nov 2008) | 6 lines
2530 Changed paths:
2531 M /branches/dev/samtools/Makefile
2532 M /branches/dev/samtools/bamtk.c
2533 M /branches/dev/samtools/bgzf.c
2534
2535 * samtools-0.1.0-44
2536 * declare fseeko and ftello as some Linux may not do this by default and
2537 missing these declarations will make bgzf buggy
2538 * get rid of some harmless warings
2539 * use BGZF by default, now
2540
2541 ------------------------------------------------------------------------
2542 r16 | lh3lh3 | 2008-11-26 21:19:11 +0000 (Wed, 26 Nov 2008) | 4 lines
2543 Changed paths:
2544 M /branches/dev/samtools/bam_index.c
2545 M /branches/dev/samtools/bamtk.c
2546 M /branches/dev/samtools/razf.c
2547
2548 * samtools-0.1.0-43
2549 * fixed a bug in razf_read()
2550 * give more warnings when the file is truncated (or due to bugs in I/O library)
2551
2552 ------------------------------------------------------------------------
2553 r15 | lh3lh3 | 2008-11-26 20:41:39 +0000 (Wed, 26 Nov 2008) | 2 lines
2554 Changed paths:
2555 M /branches/dev/samtools/bgzf.c
2556
2557 fixed a bug in bgzf.c at the end of the file
2558
2559 ------------------------------------------------------------------------
2560 r14 | lh3lh3 | 2008-11-26 17:05:18 +0000 (Wed, 26 Nov 2008) | 4 lines
2561 Changed paths:
2562 M /branches/dev/samtools/bamtk.c
2563
2564 * samtools-0.1.0-42
2565 * a lot happened to RAZF, although samtools itself is untouched. Better
2566 also update the version number anyway to avoid confusion
2567
2568 ------------------------------------------------------------------------
2569 r13 | lh3lh3 | 2008-11-26 17:03:48 +0000 (Wed, 26 Nov 2008) | 2 lines
2570 Changed paths:
2571 M /branches/dev/samtools/razf.c
2572
2573 a change from Jue, but I think it should not matter
2574
2575 ------------------------------------------------------------------------
2576 r12 | lh3lh3 | 2008-11-26 16:48:14 +0000 (Wed, 26 Nov 2008) | 3 lines
2577 Changed paths:
2578 M /branches/dev/samtools/razf.c
2579
2580 fixed a potential bug in razf. However, it seems still buggy, just
2581 rarely happens, very rarely.
2582
2583 ------------------------------------------------------------------------
2584 r11 | lh3lh3 | 2008-11-26 14:02:56 +0000 (Wed, 26 Nov 2008) | 2 lines
2585 Changed paths:
2586 M /branches/dev/samtools/razf.c
2587
2588 fixed a bug in razf, with the help of Jue
2589
2590 ------------------------------------------------------------------------
2591 r10 | lh3lh3 | 2008-11-26 11:55:32 +0000 (Wed, 26 Nov 2008) | 2 lines
2592 Changed paths:
2593 M /branches/dev/samtools/bam_index.c
2594
2595 remove a comment
2596
2597 ------------------------------------------------------------------------
2598 r9 | lh3lh3 | 2008-11-26 11:37:05 +0000 (Wed, 26 Nov 2008) | 2 lines
2599 Changed paths:
2600 M /branches/dev/samtools/Makefile
2601 M /branches/dev/samtools/bam.h
2602 M /branches/dev/samtools/razf.c
2603 M /branches/dev/samtools/razf.h
2604
2605 * Jue has updated razf to realize Bob's scheme
2606
2607 ------------------------------------------------------------------------
2608 r7 | lh3lh3 | 2008-11-25 20:37:37 +0000 (Tue, 25 Nov 2008) | 2 lines
2609 Changed paths:
2610 A /branches/dev/samtools/samtools.1
2611
2612 the manual page
2613
2614 ------------------------------------------------------------------------
2615 r6 | lh3lh3 | 2008-11-25 20:37:16 +0000 (Tue, 25 Nov 2008) | 3 lines
2616 Changed paths:
2617 A /branches/dev/samtools/ChangeLog
2618 A /branches/dev/samtools/Makefile
2619 A /branches/dev/samtools/bam.c
2620 A /branches/dev/samtools/bam.h
2621 A /branches/dev/samtools/bam_aux.c
2622 A /branches/dev/samtools/bam_endian.h
2623 A /branches/dev/samtools/bam_import.c
2624 A /branches/dev/samtools/bam_index.c
2625 A /branches/dev/samtools/bam_lpileup.c
2626 A /branches/dev/samtools/bam_pileup.c
2627 A /branches/dev/samtools/bam_sort.c
2628 A /branches/dev/samtools/bam_tview.c
2629 A /branches/dev/samtools/bamtk.c
2630 A /branches/dev/samtools/bgzf.c
2631 A /branches/dev/samtools/bgzf.h
2632 A /branches/dev/samtools/bgzip.c
2633 A /branches/dev/samtools/faidx.c
2634 A /branches/dev/samtools/faidx.h
2635 A /branches/dev/samtools/khash.h
2636 A /branches/dev/samtools/ksort.h
2637 A /branches/dev/samtools/kstream.h
2638 A /branches/dev/samtools/misc
2639 A /branches/dev/samtools/misc/Makefile
2640 A /branches/dev/samtools/misc/all2sam.pl
2641 A /branches/dev/samtools/misc/maq2sam.c
2642 A /branches/dev/samtools/razf.c
2643 A /branches/dev/samtools/razf.h
2644 A /branches/dev/samtools/razip.c
2645 A /branches/dev/samtools/zutil.h
2646
2647 The initial version of samtools, replicated from my local SVN repository.
2648 The current version is: 0.1.0-42. All future development will happen here.
2649
2650 ------------------------------------------------------------------------
2651 r5 | lh3lh3 | 2008-11-25 20:30:49 +0000 (Tue, 25 Nov 2008) | 2 lines
2652 Changed paths:
2653 A /branches/dev/samtools
2654
2655 samtools (C version)
2656
2657 ------------------------------------------------------------------------