This repository was archived by the owner on Jun 22, 2026. It is now read-only.
forked from lh3/samtools
-
Notifications
You must be signed in to change notification settings - Fork 0
Expand file tree
/
Copy pathChangeLog.old
More file actions
1737 lines (1387 loc) · 57.4 KB
/
Copy pathChangeLog.old
File metadata and controls
1737 lines (1387 loc) · 57.4 KB
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
------------------------------------------------------------------------
r108 | lh3lh3 | 2009-01-20 11:56:45 +0000 (Tue, 20 Jan 2009) | 2 lines
Changed paths:
M /branches/dev/samtools/examples/Makefile
made it a little more convenient
------------------------------------------------------------------------
r107 | lh3lh3 | 2009-01-20 11:53:30 +0000 (Tue, 20 Jan 2009) | 2 lines
Changed paths:
A /branches/dev/samtools/examples/Makefile
added a Makefile
------------------------------------------------------------------------
r106 | lh3lh3 | 2009-01-20 11:25:05 +0000 (Tue, 20 Jan 2009) | 2 lines
Changed paths:
M /branches/dev/samtools/misc/maq2sam.c
support RG tag
------------------------------------------------------------------------
r105 | lh3lh3 | 2009-01-18 17:37:20 +0000 (Sun, 18 Jan 2009) | 2 lines
Changed paths:
M /branches/dev/samtools/ChangeLog
update changelog
------------------------------------------------------------------------
r104 | lh3lh3 | 2009-01-18 17:31:21 +0000 (Sun, 18 Jan 2009) | 3 lines
Changed paths:
M /branches/dev/samtools/bam.h
M /branches/dev/samtools/bam_lpileup.c
M /branches/dev/samtools/bamtk.c
* samtools-0.1.1-18
* fixed a bug in bam_lpileup.c: segment start and end are not correctly recognized
------------------------------------------------------------------------
r103 | lh3lh3 | 2009-01-18 16:34:03 +0000 (Sun, 18 Jan 2009) | 5 lines
Changed paths:
M /branches/dev/samtools/bam_import.c
M /branches/dev/samtools/bam_index.c
M /branches/dev/samtools/bamtk.c
* samtools-0.1.1-17
* fixed a bug when there are reads without coordinates
* also recognize type 'c' as 'A'
* found a bug in bam_lpileup.c; NOT fixed yet
------------------------------------------------------------------------
r102 | lh3lh3 | 2009-01-17 19:46:49 +0000 (Sat, 17 Jan 2009) | 2 lines
Changed paths:
A /branches/dev/samtools/INSTALL
Instruction for compilation
------------------------------------------------------------------------
r101 | lh3lh3 | 2009-01-17 19:31:36 +0000 (Sat, 17 Jan 2009) | 3 lines
Changed paths:
M /branches/dev/samtools/Makefile
A /branches/dev/samtools/Makefile.lite
M /branches/dev/samtools/bam.h
M /branches/dev/samtools/faidx.c
M /branches/dev/samtools/misc/Makefile
M /branches/dev/samtools/razf.c
* replaced HAVE_RAZF with _NO_RAZF
* added Makefile.lite for people who have trouble with razf.c
------------------------------------------------------------------------
r100 | lh3lh3 | 2009-01-16 10:03:37 +0000 (Fri, 16 Jan 2009) | 3 lines
Changed paths:
M /branches/dev/samtools/bam_mate.c
M /branches/dev/samtools/bamtk.c
M /branches/dev/samtools/misc/wgsim.c
* samtools-0.1.1-15
* fixed another bug in fixmate: unmapped pair has non-zero isize
------------------------------------------------------------------------
r99 | lh3lh3 | 2009-01-16 09:13:36 +0000 (Fri, 16 Jan 2009) | 4 lines
Changed paths:
M /branches/dev/samtools/ChangeLog
M /branches/dev/samtools/bam_mate.c
M /branches/dev/samtools/bamtk.c
* samtools-0.1.1-14
* fixed a bug in fixmate: isize not equal to zero if two ends mapped to
different chr
------------------------------------------------------------------------
r98 | lh3lh3 | 2009-01-15 16:47:41 +0000 (Thu, 15 Jan 2009) | 3 lines
Changed paths:
M /branches/dev/samtools/bam_maqcns.c
M /branches/dev/samtools/bamtk.c
* samtools-0.1.1-13
* fixed the prior for hom indels (Richard pointed this out)
------------------------------------------------------------------------
r97 | lh3lh3 | 2009-01-15 16:38:47 +0000 (Thu, 15 Jan 2009) | 4 lines
Changed paths:
M /branches/dev/samtools/COPYING
M /branches/dev/samtools/bam_sort.c
M /branches/dev/samtools/bamtk.c
M /branches/dev/samtools/source.dot
* samtools-0.1.1-12
* fixed a bug in sort
* update source file graph and copyright information
------------------------------------------------------------------------
r96 | lh3lh3 | 2009-01-14 21:46:14 +0000 (Wed, 14 Jan 2009) | 2 lines
Changed paths:
M /branches/dev/samtools/glf.c
fixed a typo
------------------------------------------------------------------------
r95 | lh3lh3 | 2009-01-14 21:44:53 +0000 (Wed, 14 Jan 2009) | 2 lines
Changed paths:
M /branches/dev/samtools/glf.c
added a main function for glf.c
------------------------------------------------------------------------
r94 | lh3lh3 | 2009-01-14 17:14:59 +0000 (Wed, 14 Jan 2009) | 4 lines
Changed paths:
M /branches/dev/samtools/Makefile
M /branches/dev/samtools/bam_plcmd.c
M /branches/dev/samtools/bamtk.c
M /branches/dev/samtools/bgzf.h
A /branches/dev/samtools/glf.c
M /branches/dev/samtools/glf.h
* samtools-0.1.1-11
* generate binary GLFv2
* added glfview command to dump GLFv2 binary file
------------------------------------------------------------------------
r93 | lh3lh3 | 2009-01-14 15:07:44 +0000 (Wed, 14 Jan 2009) | 4 lines
Changed paths:
M /branches/dev/samtools/bam_rmdup.c
M /branches/dev/samtools/bamtk.c
M /branches/dev/samtools/glf.h
* samtools-0.1.1-10
* fixed several bugs in rmdup
* prepare to generate GLF2
------------------------------------------------------------------------
r92 | lh3lh3 | 2009-01-14 13:27:44 +0000 (Wed, 14 Jan 2009) | 3 lines
Changed paths:
M /branches/dev/samtools/Makefile
M /branches/dev/samtools/bam.h
M /branches/dev/samtools/bam_import.c
A /branches/dev/samtools/bam_rmdup.c
M /branches/dev/samtools/bamtk.c
* samtools-0.1.1-9
* implemented rmdup; NOT tested yet
------------------------------------------------------------------------
r91 | lh3lh3 | 2009-01-13 20:15:43 +0000 (Tue, 13 Jan 2009) | 2 lines
Changed paths:
M /branches/dev/samtools/examples/00README.txt
update README for typos
------------------------------------------------------------------------
r90 | lh3lh3 | 2009-01-13 19:57:50 +0000 (Tue, 13 Jan 2009) | 2 lines
Changed paths:
M /branches/dev/samtools/examples/ex1.sam.gz
update example
------------------------------------------------------------------------
r89 | lh3lh3 | 2009-01-13 17:21:38 +0000 (Tue, 13 Jan 2009) | 3 lines
Changed paths:
M /branches/dev/samtools/Makefile
M /branches/dev/samtools/bam.c
A /branches/dev/samtools/bam_mate.c
M /branches/dev/samtools/bamtk.c
* samtools-0.1.1-8
* added fixmate command
------------------------------------------------------------------------
r88 | lh3lh3 | 2009-01-13 10:48:23 +0000 (Tue, 13 Jan 2009) | 3 lines
Changed paths:
M /branches/dev/samtools/bam_plcmd.c
M /branches/dev/samtools/bamtk.c
* samtools-0.1.1-7
* change the reported indel position to the previous way
------------------------------------------------------------------------
r87 | lh3lh3 | 2009-01-12 22:12:12 +0000 (Mon, 12 Jan 2009) | 4 lines
Changed paths:
M /branches/dev/samtools/bam_plcmd.c
M /branches/dev/samtools/bamtk.c
* samtools-0.1.1-6
* addd glt output
* allow to change indel calling parameters at the command line
------------------------------------------------------------------------
r86 | lh3lh3 | 2009-01-12 21:16:48 +0000 (Mon, 12 Jan 2009) | 4 lines
Changed paths:
M /branches/dev/samtools/bam.h
M /branches/dev/samtools/bam_pileup.c
M /branches/dev/samtools/bam_plcmd.c
M /branches/dev/samtools/bamtk.c
* samtools-0.1.1-5
* added two more flags
* allowed to select reads shown in pileup with a mask
------------------------------------------------------------------------
r85 | lh3lh3 | 2009-01-12 20:47:51 +0000 (Mon, 12 Jan 2009) | 4 lines
Changed paths:
M /branches/dev/samtools/bam_index.c
M /branches/dev/samtools/bam_plcmd.c
M /branches/dev/samtools/bamtk.c
* samtools-0.1.1-4
* fixed a bug in indexing (linear index)
* prepare to add glt output from pileup
------------------------------------------------------------------------
r84 | lh3lh3 | 2009-01-12 09:22:35 +0000 (Mon, 12 Jan 2009) | 3 lines
Changed paths:
M /branches/dev/samtools/bam_plcmd.c
M /branches/dev/samtools/bamtk.c
* samtools-0.1.1-3
* fixed a bug in outputing the coordinate of an indel
------------------------------------------------------------------------
r83 | lh3lh3 | 2009-01-11 15:18:01 +0000 (Sun, 11 Jan 2009) | 3 lines
Changed paths:
M /branches/dev/samtools/bam_plcmd.c
M /branches/dev/samtools/bamtk.c
* samtools-0.1.1-2
* pileup: allows to output indel sites only
------------------------------------------------------------------------
r82 | lh3lh3 | 2009-01-10 23:34:31 +0000 (Sat, 10 Jan 2009) | 3 lines
Changed paths:
M /branches/dev/samtools/bam_maqcns.c
M /branches/dev/samtools/bam_maqcns.h
M /branches/dev/samtools/bam_plcmd.c
M /branches/dev/samtools/bamtk.c
* samtools-0.1.1-1
* implemented a Bayesian indel caller
------------------------------------------------------------------------
r81 | lh3lh3 | 2009-01-09 09:54:28 +0000 (Fri, 09 Jan 2009) | 2 lines
Changed paths:
M /branches/dev/samtools/examples/00README.txt
D /branches/dev/samtools/examples/ex1.fa.fai
Let users generate ex1.fa.fai.
------------------------------------------------------------------------
r80 | lh3lh3 | 2009-01-08 16:10:08 +0000 (Thu, 08 Jan 2009) | 2 lines
Changed paths:
M /branches/dev/samtools/misc/bowtie2sam.pl
make the bowtie converter works for "-k 2"
------------------------------------------------------------------------
r78 | lh3lh3 | 2009-01-03 17:25:24 +0000 (Sat, 03 Jan 2009) | 2 lines
Changed paths:
M /branches/dev/samtools/misc/export2sam.pl
fixed a bug for "QC" reads
------------------------------------------------------------------------
r77 | lh3lh3 | 2009-01-01 18:32:06 +0000 (Thu, 01 Jan 2009) | 3 lines
Changed paths:
A /branches/dev/samtools/misc/bowtie2sam.pl
M /branches/dev/samtools/misc/soap2sam.pl
* soap2sam.pl: added NM tag
* bowtie2sam.pl: converter for bowtie
------------------------------------------------------------------------
r76 | lh3lh3 | 2008-12-31 23:24:24 +0000 (Wed, 31 Dec 2008) | 2 lines
Changed paths:
A /branches/dev/samtools/misc/soap2sam.pl
soap2sam.pl: convert soap output to SAM
------------------------------------------------------------------------
r75 | lh3lh3 | 2008-12-31 17:54:32 +0000 (Wed, 31 Dec 2008) | 3 lines
Changed paths:
M /branches/dev/samtools/misc/wgsim_eval.pl
* wgsim_eval.pl-0.1.1
* fixed a bug for a contig name like "NT_012345"
------------------------------------------------------------------------
r74 | lh3lh3 | 2008-12-31 16:38:21 +0000 (Wed, 31 Dec 2008) | 2 lines
Changed paths:
A /branches/dev/samtools/misc/wgsim_eval.pl
* evaluate alignment for reads generated by wgsim
------------------------------------------------------------------------
r73 | lh3lh3 | 2008-12-31 15:11:22 +0000 (Wed, 31 Dec 2008) | 2 lines
Changed paths:
M /branches/dev/samtools/misc/Makefile
M /branches/dev/samtools/misc/wgsim.c
fixed compiling warnings for wgsim
------------------------------------------------------------------------
r72 | lh3lh3 | 2008-12-31 13:40:51 +0000 (Wed, 31 Dec 2008) | 2 lines
Changed paths:
M /branches/dev/samtools/bam_tview.c
remove an unused variable (a compiler warning only)
------------------------------------------------------------------------
r71 | lh3lh3 | 2008-12-31 13:37:16 +0000 (Wed, 31 Dec 2008) | 2 lines
Changed paths:
M /branches/dev/samtools/misc/Makefile
A /branches/dev/samtools/misc/wgsim.c
wgsim: Paired-end reads simulator
------------------------------------------------------------------------
r70 | bhandsaker | 2008-12-29 20:27:16 +0000 (Mon, 29 Dec 2008) | 2 lines
Changed paths:
M /branches/dev/samtools/bam_maqcns.c
M /branches/dev/samtools/bam_tview.c
Move definition of bam_nt16_nt4_table so we can build without curses.
------------------------------------------------------------------------
r62 | lh3lh3 | 2008-12-22 15:55:13 +0000 (Mon, 22 Dec 2008) | 2 lines
Changed paths:
A /branches/dev/samtools/NEWS
M /branches/dev/samtools/bamtk.c
M /branches/dev/samtools/samtools.1
Release samtools-0.1.1
------------------------------------------------------------------------
r61 | lh3lh3 | 2008-12-22 15:46:08 +0000 (Mon, 22 Dec 2008) | 10 lines
Changed paths:
M /branches/dev/samtools/bam_aux.c
M /branches/dev/samtools/bam_index.c
M /branches/dev/samtools/bam_plcmd.c
M /branches/dev/samtools/bam_tview.c
M /branches/dev/samtools/bamtk.c
M /branches/dev/samtools/razf.c
M /branches/dev/samtools/samtools.1
* samtools-0.1.0-66
* fixed a bug in razf.c: reset z_eof when razf_seek() is called
* fixed a memory leak in parsing a region
* changed pileup a little bit when -s is in use: output ^ and $
* when a bam is not indexed, output more meaningful error message
* fixed a bug in indexing for small alignment
* fixed a bug in the viewer when we come to the end of a reference file
* updated documentation
* prepare to release 0.1.1
------------------------------------------------------------------------
r60 | lh3lh3 | 2008-12-22 15:10:16 +0000 (Mon, 22 Dec 2008) | 2 lines
Changed paths:
A /branches/dev/samtools/examples
A /branches/dev/samtools/examples/00README.txt
A /branches/dev/samtools/examples/ex1.fa
A /branches/dev/samtools/examples/ex1.fa.fai
A /branches/dev/samtools/examples/ex1.sam.gz
example
------------------------------------------------------------------------
r59 | lh3lh3 | 2008-12-22 09:38:15 +0000 (Mon, 22 Dec 2008) | 2 lines
Changed paths:
M /branches/dev/samtools/ChangeLog
update ChangeLog
------------------------------------------------------------------------
r58 | lh3lh3 | 2008-12-20 23:06:00 +0000 (Sat, 20 Dec 2008) | 3 lines
Changed paths:
M /branches/dev/samtools/misc/export2sam.pl
* added comments
* fixed several bugs
------------------------------------------------------------------------
r57 | lh3lh3 | 2008-12-20 15:44:20 +0000 (Sat, 20 Dec 2008) | 2 lines
Changed paths:
A /branches/dev/samtools/misc/export2sam.pl
convert Export format to SAM; not thoroughly tested
------------------------------------------------------------------------
r56 | lh3lh3 | 2008-12-19 22:13:28 +0000 (Fri, 19 Dec 2008) | 6 lines
Changed paths:
M /branches/dev/samtools/bam_import.c
M /branches/dev/samtools/bam_plcmd.c
M /branches/dev/samtools/bam_tview.c
M /branches/dev/samtools/bamtk.c
A /branches/dev/samtools/source.dot
* samtools-0.1.0-65
* pileup: generate maq-like simple output
* pileup: allow to output pileup at required sites
* source.dot: source file relationship graph
* tview: fixed a minor bug
------------------------------------------------------------------------
r55 | lh3lh3 | 2008-12-19 20:10:26 +0000 (Fri, 19 Dec 2008) | 2 lines
Changed paths:
D /branches/dev/samtools/misc/all2sam.pl
remove all2sam.pl
------------------------------------------------------------------------
r54 | lh3lh3 | 2008-12-16 22:34:25 +0000 (Tue, 16 Dec 2008) | 2 lines
Changed paths:
A /branches/dev/samtools/COPYING
M /branches/dev/samtools/bam.h
M /branches/dev/samtools/faidx.h
M /branches/dev/samtools/khash.h
M /branches/dev/samtools/kseq.h
M /branches/dev/samtools/ksort.h
M /branches/dev/samtools/samtools.1
Added copyright information and a bit more documentation. No code change.
------------------------------------------------------------------------
r53 | lh3lh3 | 2008-12-16 13:40:18 +0000 (Tue, 16 Dec 2008) | 3 lines
Changed paths:
M /branches/dev/samtools/bam.c
M /branches/dev/samtools/bam.h
M /branches/dev/samtools/bam_index.c
M /branches/dev/samtools/bam_maqcns.c
M /branches/dev/samtools/bamtk.c
* samtools-0.1.0-64
* improved efficiency of the indel caller for spliced alignments
------------------------------------------------------------------------
r52 | lh3lh3 | 2008-12-16 10:28:20 +0000 (Tue, 16 Dec 2008) | 3 lines
Changed paths:
M /branches/dev/samtools/bam.c
M /branches/dev/samtools/bam.h
M /branches/dev/samtools/bam_aux.c
M /branches/dev/samtools/bam_index.c
M /branches/dev/samtools/bamtk.c
* samtools-0.1.0-63
* a bit code cleanup: reduce the dependency between source files
------------------------------------------------------------------------
r51 | lh3lh3 | 2008-12-15 14:29:32 +0000 (Mon, 15 Dec 2008) | 3 lines
Changed paths:
M /branches/dev/samtools/bam_maqcns.c
M /branches/dev/samtools/bam_plcmd.c
M /branches/dev/samtools/bamtk.c
* samtools-0.1.0-62
* fixed a memory leak
------------------------------------------------------------------------
r50 | lh3lh3 | 2008-12-15 14:00:13 +0000 (Mon, 15 Dec 2008) | 2 lines
Changed paths:
M /branches/dev/samtools/ChangeLog
M /branches/dev/samtools/bam.h
M /branches/dev/samtools/samtools.1
update documentation, ChangeLog and a comment
------------------------------------------------------------------------
r49 | lh3lh3 | 2008-12-15 13:36:43 +0000 (Mon, 15 Dec 2008) | 6 lines
Changed paths:
M /branches/dev/samtools/Makefile
M /branches/dev/samtools/bam.h
M /branches/dev/samtools/bam_maqcns.c
M /branches/dev/samtools/bam_maqcns.h
M /branches/dev/samtools/bam_pileup.c
A /branches/dev/samtools/bam_plcmd.c
M /branches/dev/samtools/bamtk.c
M /branches/dev/samtools/samtools.1
* samtools-0.1.0-61
* moved pileup command to a separate source file
* added indel caller
* added bam_cal_segend(). (NOT WORKING for spliced alignment!!!)
* updated documentation
------------------------------------------------------------------------
r48 | lh3lh3 | 2008-12-12 13:55:36 +0000 (Fri, 12 Dec 2008) | 3 lines
Changed paths:
M /branches/dev/samtools/bam_maqcns.c
M /branches/dev/samtools/bamtk.c
* samtools-0.1.0-60
* fixed another bug in maqcns when there is a nearby deletion
------------------------------------------------------------------------
r47 | lh3lh3 | 2008-12-12 13:42:16 +0000 (Fri, 12 Dec 2008) | 5 lines
Changed paths:
M /branches/dev/samtools/bam_maqcns.c
M /branches/dev/samtools/bam_pileup.c
M /branches/dev/samtools/bamtk.c
* samtools-0.1.0-59
* pileup: outputing consensus is now optional
* fixed a bug in glfgen. This bug also exists in maq's glfgen. However,
I am not quite sure why the previous version may have problem.
------------------------------------------------------------------------
r46 | lh3lh3 | 2008-12-12 11:44:56 +0000 (Fri, 12 Dec 2008) | 6 lines
Changed paths:
M /branches/dev/samtools/bam_pileup.c
M /branches/dev/samtools/bamtk.c
* samtools-0.1.0-58
* add maq consensus to pileup. However, I will move this part to a new
command as strictly speaking, consensus callin is not part of pileup,
and imposing it would make it harder to generate for other language
bindings.
------------------------------------------------------------------------
r45 | bhandsaker | 2008-12-11 20:43:56 +0000 (Thu, 11 Dec 2008) | 2 lines
Changed paths:
M /branches/dev/samtools/bgzf.c
Fix bug in tell() after reads that consume to the exact end of a block.
------------------------------------------------------------------------
r44 | lh3lh3 | 2008-12-11 09:36:53 +0000 (Thu, 11 Dec 2008) | 2 lines
Changed paths:
M /branches/dev/samtools/samtools.1
update manual
------------------------------------------------------------------------
r43 | lh3lh3 | 2008-12-11 09:25:36 +0000 (Thu, 11 Dec 2008) | 4 lines
Changed paths:
M /branches/dev/samtools/bam_import.c
M /branches/dev/samtools/bamtk.c
* samtools-0.1.0-57
* fixed a bug in parser when there is auxiliary fields
* made the parser a bit more robust
------------------------------------------------------------------------
r42 | lh3lh3 | 2008-12-10 14:57:29 +0000 (Wed, 10 Dec 2008) | 5 lines
Changed paths:
M /branches/dev/samtools/bam_index.c
M /branches/dev/samtools/bamtk.c
M /branches/dev/samtools/bgzf.c
* samtools-0.1.0-56
* fixed a bug in bgzf (only reading is affected)
* fixed a typo in bam_index.c
* in bam_index.c, check potential bugs in the underlying I/O library
------------------------------------------------------------------------
r41 | lh3lh3 | 2008-12-10 12:53:08 +0000 (Wed, 10 Dec 2008) | 2 lines
Changed paths:
M /branches/dev/samtools/samtools.1
update manual
------------------------------------------------------------------------
r40 | lh3lh3 | 2008-12-10 11:52:10 +0000 (Wed, 10 Dec 2008) | 5 lines
Changed paths:
M /branches/dev/samtools/bam.h
M /branches/dev/samtools/bam_pileup.c
M /branches/dev/samtools/bamtk.c
* samtools-0.1.0-55
* tried to make pileup work with clipping (previously not), though NOT tested
* removed -v from pileup
* made pileup take the reference sequence
------------------------------------------------------------------------
r39 | lh3lh3 | 2008-12-09 11:59:28 +0000 (Tue, 09 Dec 2008) | 4 lines
Changed paths:
M /branches/dev/samtools/bam_import.c
M /branches/dev/samtools/bamtk.c
M /branches/dev/samtools/samtools.1
* samtools-0.1.0-54
* in parser, recognize "=", rather than ",", as a match
* in parser, correctl parse "=" at the MRNM field.
------------------------------------------------------------------------
r38 | lh3lh3 | 2008-12-09 11:39:07 +0000 (Tue, 09 Dec 2008) | 2 lines
Changed paths:
M /branches/dev/samtools/misc/maq2sam.c
fixed a bug in handling maq flag 64 and 192
------------------------------------------------------------------------
r37 | lh3lh3 | 2008-12-09 09:53:46 +0000 (Tue, 09 Dec 2008) | 2 lines
Changed paths:
M /branches/dev/samtools/misc/md5fa.c
also calculate unordered md5sum check
------------------------------------------------------------------------
r36 | lh3lh3 | 2008-12-09 09:46:21 +0000 (Tue, 09 Dec 2008) | 2 lines
Changed paths:
M /branches/dev/samtools/misc/md5fa.c
fixed a minor bug when there are space in the sequence
------------------------------------------------------------------------
r35 | lh3lh3 | 2008-12-09 09:40:45 +0000 (Tue, 09 Dec 2008) | 2 lines
Changed paths:
M /branches/dev/samtools/misc/md5fa.c
fixed a potential memory leak
------------------------------------------------------------------------
r34 | lh3lh3 | 2008-12-08 14:52:17 +0000 (Mon, 08 Dec 2008) | 2 lines
Changed paths:
M /branches/dev/samtools/bam_import.c
M /branches/dev/samtools/bam_index.c
M /branches/dev/samtools/bamtk.c
* fixed a bug in import: bin is wrongly calculated
------------------------------------------------------------------------
r33 | lh3lh3 | 2008-12-08 14:08:01 +0000 (Mon, 08 Dec 2008) | 2 lines
Changed paths:
M /branches/dev/samtools/misc/all2sam.pl
nothing, really
------------------------------------------------------------------------
r32 | lh3lh3 | 2008-12-08 12:56:02 +0000 (Mon, 08 Dec 2008) | 3 lines
Changed paths:
M /branches/dev/samtools/Makefile
M /branches/dev/samtools/kseq.h
M /branches/dev/samtools/misc/Makefile
A /branches/dev/samtools/misc/md5.c
A /branches/dev/samtools/misc/md5.h
A /branches/dev/samtools/misc/md5fa.c
* fixed two warnings in kseq.h
* added md5sum utilities
------------------------------------------------------------------------
r31 | lh3lh3 | 2008-12-08 11:35:29 +0000 (Mon, 08 Dec 2008) | 5 lines
Changed paths:
M /branches/dev/samtools/Makefile
M /branches/dev/samtools/bam_import.c
M /branches/dev/samtools/bamtk.c
A /branches/dev/samtools/kseq.h
D /branches/dev/samtools/kstream.h
* samtools-0.1.0-52
* replace kstream with kseq. kseq is a superset of kstream. I need the
extra functions in kseq.h.
* also compile stand-alone faidx
------------------------------------------------------------------------
r30 | lh3lh3 | 2008-12-08 11:17:04 +0000 (Mon, 08 Dec 2008) | 3 lines
Changed paths:
M /branches/dev/samtools/bam.h
M /branches/dev/samtools/bam_sort.c
M /branches/dev/samtools/bamtk.c
* samtools-0.1.0-51
* sorting by read names is available
------------------------------------------------------------------------
r29 | lh3lh3 | 2008-12-08 10:29:02 +0000 (Mon, 08 Dec 2008) | 3 lines
Changed paths:
M /branches/dev/samtools/bam.c
M /branches/dev/samtools/bam.h
M /branches/dev/samtools/bam_import.c
M /branches/dev/samtools/bam_maqcns.c
M /branches/dev/samtools/bam_pileup.c
M /branches/dev/samtools/bam_sort.c
M /branches/dev/samtools/bam_tview.c
M /branches/dev/samtools/bamtk.c
M /branches/dev/samtools/misc/maq2sam.c
* samtools-0.1.0-50
* format change to meet the latest specification
------------------------------------------------------------------------
r28 | lh3lh3 | 2008-12-04 16:09:21 +0000 (Thu, 04 Dec 2008) | 3 lines
Changed paths:
M /branches/dev/samtools/bam_maqcns.c
M /branches/dev/samtools/misc/maq2sam.c
* minor change in maqcns: special care when n==0
* change maq2sam to meet the latest specification
------------------------------------------------------------------------
r27 | lh3lh3 | 2008-12-04 15:55:44 +0000 (Thu, 04 Dec 2008) | 2 lines
Changed paths:
M /branches/dev/samtools/razf.c
M /branches/dev/samtools/razf.h
considerable code clean up in razf
------------------------------------------------------------------------
r26 | lh3lh3 | 2008-12-04 15:08:18 +0000 (Thu, 04 Dec 2008) | 2 lines
Changed paths:
M /branches/dev/samtools/ChangeLog
M /branches/dev/samtools/Makefile
M /branches/dev/samtools/faidx.c
make RAZF optional in faidx.c
------------------------------------------------------------------------
r25 | lh3lh3 | 2008-12-01 15:27:22 +0000 (Mon, 01 Dec 2008) | 3 lines
Changed paths:
M /branches/dev/samtools/Makefile
M /branches/dev/samtools/bam.h
M /branches/dev/samtools/bam_aux.c
M /branches/dev/samtools/bamtk.c
M /branches/dev/samtools/samtools.1
* samtools-0.1.0-49
* added routines for retrieving aux data, NOT TESTED YET!
------------------------------------------------------------------------
r24 | lh3lh3 | 2008-12-01 14:29:43 +0000 (Mon, 01 Dec 2008) | 5 lines
Changed paths:
M /branches/dev/samtools/bam.c
M /branches/dev/samtools/bam_import.c
M /branches/dev/samtools/bam_maqcns.c
M /branches/dev/samtools/bamtk.c
M /branches/dev/samtools/bgzf.c
M /branches/dev/samtools/samtools.1
* samtools-0.1.0-48
* bgzf: fixed a potential integer overflow on 32-it machines
* maqcns: set the minimum combined quality as 0
* supporting hex strings
------------------------------------------------------------------------
r23 | lh3lh3 | 2008-11-27 17:14:37 +0000 (Thu, 27 Nov 2008) | 3 lines
Changed paths:
M /branches/dev/samtools/bam_maqcns.c
M /branches/dev/samtools/bamtk.c
* samtools-0.1.0-47
* fixed the bug in maqcns
------------------------------------------------------------------------
r22 | lh3lh3 | 2008-11-27 17:08:11 +0000 (Thu, 27 Nov 2008) | 3 lines
Changed paths:
M /branches/dev/samtools/Makefile
M /branches/dev/samtools/bam.h
A /branches/dev/samtools/bam_maqcns.c
A /branches/dev/samtools/bam_maqcns.h
M /branches/dev/samtools/bam_tview.c
M /branches/dev/samtools/bamtk.c
A /branches/dev/samtools/glf.h
* samtools-0.1.0-46
* add MAQ consensus caller, currently BUGGY!
------------------------------------------------------------------------
r21 | lh3lh3 | 2008-11-27 13:51:28 +0000 (Thu, 27 Nov 2008) | 4 lines
Changed paths:
M /branches/dev/samtools/bam_pileup.c
M /branches/dev/samtools/bam_tview.c
M /branches/dev/samtools/bamtk.c
* samtools-0.1.0-45
* tview: display padded alignment (but not P operation)
* better coordinates and reference sequence
------------------------------------------------------------------------
r19 | lh3lh3 | 2008-11-27 09:26:05 +0000 (Thu, 27 Nov 2008) | 2 lines
Changed paths:
A /branches/dev/samtools/ChangeLog
new ChangeLog
------------------------------------------------------------------------
r18 | lh3lh3 | 2008-11-27 09:24:45 +0000 (Thu, 27 Nov 2008) | 3 lines
Changed paths:
D /branches/dev/samtools/ChangeLog
A /branches/dev/samtools/ChangeLog.old (from /branches/dev/samtools/ChangeLog:6)
Rename ChangeLog to ChangeLog.old. This old ChangeLog is generated from
the log of my personal SVN repository.
------------------------------------------------------------------------
r17 | lh3lh3 | 2008-11-27 09:22:55 +0000 (Thu, 27 Nov 2008) | 6 lines
Changed paths:
M /branches/dev/samtools/Makefile
M /branches/dev/samtools/bamtk.c
M /branches/dev/samtools/bgzf.c
* samtools-0.1.0-44
* declare fseeko and ftello as some Linux may not do this by default and
missing these declarations will make bgzf buggy
* get rid of some harmless warings
* use BGZF by default, now
------------------------------------------------------------------------
r16 | lh3lh3 | 2008-11-26 21:19:11 +0000 (Wed, 26 Nov 2008) | 4 lines
Changed paths:
M /branches/dev/samtools/bam_index.c
M /branches/dev/samtools/bamtk.c
M /branches/dev/samtools/razf.c
* samtools-0.1.0-43
* fixed a bug in razf_read()
* give more warnings when the file is truncated (or due to bugs in I/O library)
------------------------------------------------------------------------
r15 | lh3lh3 | 2008-11-26 20:41:39 +0000 (Wed, 26 Nov 2008) | 2 lines
Changed paths:
M /branches/dev/samtools/bgzf.c
fixed a bug in bgzf.c at the end of the file
------------------------------------------------------------------------
r14 | lh3lh3 | 2008-11-26 17:05:18 +0000 (Wed, 26 Nov 2008) | 4 lines
Changed paths:
M /branches/dev/samtools/bamtk.c
* samtools-0.1.0-42
* a lot happened to RAZF, although samtools itself is untouched. Better
also update the version number anyway to avoid confusion
------------------------------------------------------------------------
r13 | lh3lh3 | 2008-11-26 17:03:48 +0000 (Wed, 26 Nov 2008) | 2 lines
Changed paths:
M /branches/dev/samtools/razf.c
a change from Jue, but I think it should not matter
------------------------------------------------------------------------
r12 | lh3lh3 | 2008-11-26 16:48:14 +0000 (Wed, 26 Nov 2008) | 3 lines
Changed paths:
M /branches/dev/samtools/razf.c
fixed a potential bug in razf. However, it seems still buggy, just
rarely happens, very rarely.
------------------------------------------------------------------------
r11 | lh3lh3 | 2008-11-26 14:02:56 +0000 (Wed, 26 Nov 2008) | 2 lines
Changed paths:
M /branches/dev/samtools/razf.c
fixed a bug in razf, with the help of Jue
------------------------------------------------------------------------
r10 | lh3lh3 | 2008-11-26 11:55:32 +0000 (Wed, 26 Nov 2008) | 2 lines
Changed paths:
M /branches/dev/samtools/bam_index.c
remove a comment
------------------------------------------------------------------------
r9 | lh3lh3 | 2008-11-26 11:37:05 +0000 (Wed, 26 Nov 2008) | 2 lines
Changed paths:
M /branches/dev/samtools/Makefile
M /branches/dev/samtools/bam.h
M /branches/dev/samtools/razf.c
M /branches/dev/samtools/razf.h
* Jue has updated razf to realize Bob's scheme
------------------------------------------------------------------------
r7 | lh3lh3 | 2008-11-25 20:37:37 +0000 (Tue, 25 Nov 2008) | 2 lines
Changed paths:
A /branches/dev/samtools/samtools.1
the manual page
------------------------------------------------------------------------
r6 | lh3lh3 | 2008-11-25 20:37:16 +0000 (Tue, 25 Nov 2008) | 3 lines
Changed paths:
A /branches/dev/samtools/ChangeLog
A /branches/dev/samtools/Makefile
A /branches/dev/samtools/bam.c
A /branches/dev/samtools/bam.h
A /branches/dev/samtools/bam_aux.c
A /branches/dev/samtools/bam_endian.h
A /branches/dev/samtools/bam_import.c
A /branches/dev/samtools/bam_index.c
A /branches/dev/samtools/bam_lpileup.c
A /branches/dev/samtools/bam_pileup.c
A /branches/dev/samtools/bam_sort.c
A /branches/dev/samtools/bam_tview.c
A /branches/dev/samtools/bamtk.c
A /branches/dev/samtools/bgzf.c
A /branches/dev/samtools/bgzf.h
A /branches/dev/samtools/bgzip.c
A /branches/dev/samtools/faidx.c
A /branches/dev/samtools/faidx.h
A /branches/dev/samtools/khash.h
A /branches/dev/samtools/ksort.h
A /branches/dev/samtools/kstream.h
A /branches/dev/samtools/misc
A /branches/dev/samtools/misc/Makefile
A /branches/dev/samtools/misc/all2sam.pl
A /branches/dev/samtools/misc/maq2sam.c
A /branches/dev/samtools/razf.c
A /branches/dev/samtools/razf.h
A /branches/dev/samtools/razip.c
A /branches/dev/samtools/zutil.h
The initial version of samtools, replicated from my local SVN repository.
The current version is: 0.1.0-42. All future development will happen here.
------------------------------------------------------------------------
r5 | lh3lh3 | 2008-11-25 20:30:49 +0000 (Tue, 25 Nov 2008) | 2 lines
Changed paths:
A /branches/dev/samtools
samtools (C version)
------------------------------------------------------------------------
------------------------------------------------------------------------
r703 | lh3 | 2008-11-25 20:20:02 +0000 (Tue, 25 Nov 2008) | 2 lines
Changed paths:
M /branches/prog/bam/samtools.1
rename bamtk to samtools
------------------------------------------------------------------------
r702 | lh3 | 2008-11-25 20:15:09 +0000 (Tue, 25 Nov 2008) | 2 lines
Changed paths:
D /branches/prog/bam/bamtk.1
A /branches/prog/bam/samtools.1 (from /branches/prog/bam/bamtk.1:679)
rename bamtk.1 to samtools.1
------------------------------------------------------------------------
r701 | lh3 | 2008-11-25 13:29:10 +0000 (Tue, 25 Nov 2008) | 3 lines
Changed paths:
M /branches/prog/bam/Makefile
M /branches/prog/bam/bam.c
M /branches/prog/bam/bam.h
M /branches/prog/bam/bam_import.c
M /branches/prog/bam/bam_index.c
M /branches/prog/bam/bam_pileup.c
M /branches/prog/bam/bamtk.c
M /branches/prog/bam/misc/Makefile
* samtools-0.1.0-41
* small (but a bit dangerous) changes to meet the latest specification
------------------------------------------------------------------------
r700 | lh3 | 2008-11-25 13:15:11 +0000 (Tue, 25 Nov 2008) | 2 lines
Changed paths:
A /branches/prog/bam/misc/all2sam.pl (from /branches/prog/bam/misc/all2tam.pl:649)
D /branches/prog/bam/misc/all2tam.pl
A /branches/prog/bam/misc/maq2sam.c (from /branches/prog/bam/misc/maq2tam.c:699)
D /branches/prog/bam/misc/maq2tam.c
rename tam to sam
------------------------------------------------------------------------
r699 | lh3 | 2008-11-25 13:14:49 +0000 (Tue, 25 Nov 2008) | 2 lines
Changed paths:
M /branches/prog/bam/misc/maq2tam.c
change for the new specification
------------------------------------------------------------------------
r698 | lh3 | 2008-11-24 13:15:20 +0000 (Mon, 24 Nov 2008) | 3 lines
Changed paths:
M /branches/prog/bam/bam.h
M /branches/prog/bam/razf.c
M /branches/prog/bam/razf.h
* add a fake BGZF mode to razf. It is fake in that it loads razf index into
memory but gives BGZF like virtual offset
------------------------------------------------------------------------
r697 | lh3 | 2008-11-24 09:53:44 +0000 (Mon, 24 Nov 2008) | 2 lines
Changed paths:
A /branches/prog/bam/ChangeLog
change log
------------------------------------------------------------------------
r696 | lh3 | 2008-11-24 09:53:23 +0000 (Mon, 24 Nov 2008) | 2 lines
Changed paths:
M /branches/prog/bam/bgzf.c