1 ------------------------------------------------------------------------
2 r296 | lh3lh3 | 2009-05-21 12:53:14 +0100 (Thu, 21 May 2009) | 3 lines
4 M /trunk/samtools/bam_maqcns.c
5 M /trunk/samtools/bamtk.c
7 * samtools-0.1.3-24 (r296)
8 * another similar bug in the indel caller
10 ------------------------------------------------------------------------
11 r295 | lh3lh3 | 2009-05-21 12:50:28 +0100 (Thu, 21 May 2009) | 3 lines
13 M /trunk/samtools/bam_maqcns.c
14 M /trunk/samtools/bamtk.c
16 * samtools-0.1.3-23 (r295)
17 * fixed a critical bug in the indel caller
19 ------------------------------------------------------------------------
20 r294 | lh3lh3 | 2009-05-20 13:00:20 +0100 (Wed, 20 May 2009) | 2 lines
22 M /trunk/samtools/bam_stat.c
24 added a missing header file
26 ------------------------------------------------------------------------
27 r293 | lh3lh3 | 2009-05-19 23:44:25 +0100 (Tue, 19 May 2009) | 3 lines
29 M /trunk/samtools/bam_tview.c
30 M /trunk/samtools/bamtk.c
32 * samtools-0.1.3-22 (r293)
33 * open tview in the dot-view mode by default
35 ------------------------------------------------------------------------
36 r292 | lh3lh3 | 2009-05-18 21:01:23 +0100 (Mon, 18 May 2009) | 6 lines
38 M /trunk/samtools/samtools.1
40 Added a note to the manual. Currently SAMtools used unaligned words in
41 several places. Although this does not cause bus errors to me, it may
42 affect portability. Please see the "Bus error" wiki page for more
43 information. Also thank James Bonfields for pointing this out.
46 ------------------------------------------------------------------------
47 r286 | lh3lh3 | 2009-05-14 15:23:13 +0100 (Thu, 14 May 2009) | 3 lines
49 M /trunk/samtools/bam.h
50 M /trunk/samtools/bam_aux.c
51 M /trunk/samtools/bamtk.c
53 * samtools-0.1.3-21 (286)
54 * declare bam_aux_get_core() in bam.h
56 ------------------------------------------------------------------------
57 r276 | lh3lh3 | 2009-05-13 10:07:55 +0100 (Wed, 13 May 2009) | 5 lines
59 M /trunk/samtools/bam.h
60 M /trunk/samtools/bam_index.c
61 M /trunk/samtools/bamtk.c
63 * samtools-0.1.3-20 (r276)
64 * remove bam1_t::hash again. We need to modify the Perl API anyway to
65 make it work with the latest SVN.
66 * As is suggested by Tim, scan "{base}.bai" and "{base}.bam.bai" for index
68 ------------------------------------------------------------------------
69 r275 | lh3lh3 | 2009-05-12 21:14:10 +0100 (Tue, 12 May 2009) | 4 lines
71 M /trunk/samtools/ChangeLog
72 M /trunk/samtools/bam.h
73 M /trunk/samtools/bamtk.c
75 * samtools-0.1.3-19 (r275)
76 * a minor change to the bam1_t struct: added back "void *hash" for the
77 backward compatibility with Bio::DB::Sam
79 ------------------------------------------------------------------------
80 r273 | lh3lh3 | 2009-05-12 14:28:39 +0100 (Tue, 12 May 2009) | 3 lines
82 M /trunk/samtools/bam_rmdupse.c
83 M /trunk/samtools/bamtk.c
85 * samtools-0.1.3-18 (r273)
86 * rmdupse: do not remove unmapped reads
88 ------------------------------------------------------------------------
89 r272 | lh3lh3 | 2009-05-12 14:20:00 +0100 (Tue, 12 May 2009) | 2 lines
91 M /trunk/samtools/bam_rmdupse.c
93 change a parameter. It does nothing
95 ------------------------------------------------------------------------
96 r271 | lh3lh3 | 2009-05-12 14:17:58 +0100 (Tue, 12 May 2009) | 3 lines
98 M /trunk/samtools/Makefile.am
99 M /trunk/samtools/Makefile.generic
100 M /trunk/samtools/Makefile.lite
101 A /trunk/samtools/bam_rmdupse.c
102 M /trunk/samtools/bamtk.c
103 M /trunk/samtools/configure.ac
105 * samtools-0.1.3-17 (r271)
106 * added 'rmdupse' command
108 ------------------------------------------------------------------------
109 r267 | lh3lh3 | 2009-05-05 22:31:41 +0100 (Tue, 05 May 2009) | 3 lines
111 M /trunk/samtools/bamtk.c
112 M /trunk/samtools/sam_view.c
114 * samtools-0.1.3-16 (r267)
115 * in sam_view.c, changed g_flag_on based on the suggestion by Angie Hinrichs
117 ------------------------------------------------------------------------
118 r266 | lh3lh3 | 2009-05-05 22:23:27 +0100 (Tue, 05 May 2009) | 3 lines
120 M /trunk/samtools/bam_import.c
121 M /trunk/samtools/bamtk.c
123 * samtools-0.1.3-15 (r266)
124 * report an error if a non-* reference is present while @SQ is absent
126 ------------------------------------------------------------------------
127 r265 | lh3lh3 | 2009-05-05 22:09:00 +0100 (Tue, 05 May 2009) | 3 lines
129 M /trunk/samtools/bam.h
130 M /trunk/samtools/bam_import.c
131 M /trunk/samtools/bamtk.c
132 M /trunk/samtools/sam.c
133 M /trunk/samtools/sam_view.c
135 * samtools-0.1.3-14 (r262)
136 * make samopen() recognize @SQ header lines
138 ------------------------------------------------------------------------
139 r261 | lh3lh3 | 2009-05-05 15:10:30 +0100 (Tue, 05 May 2009) | 3 lines
141 M /trunk/samtools/bam_plcmd.c
142 M /trunk/samtools/bamtk.c
143 M /trunk/samtools/bgzf.c
144 M /trunk/samtools/sam.c
145 M /trunk/samtools/sam_view.c
147 * samtools-0.1.3-13 (r260)
148 * report error for file I/O error
150 ------------------------------------------------------------------------
151 r260 | lh3lh3 | 2009-05-05 15:01:16 +0100 (Tue, 05 May 2009) | 2 lines
153 M /trunk/samtools/Makefile.am
157 ------------------------------------------------------------------------
158 r259 | lh3lh3 | 2009-05-05 14:52:25 +0100 (Tue, 05 May 2009) | 3 lines
160 M /trunk/samtools/bam.h
161 M /trunk/samtools/bam_pileup.c
162 M /trunk/samtools/bam_plcmd.c
163 M /trunk/samtools/bamtk.c
164 M /trunk/samtools/sam.c
165 M /trunk/samtools/sam.h
167 * samtools-0.1.3-12 (r259)
168 * use the new I/O interface in pileup
170 ------------------------------------------------------------------------
171 r258 | lh3lh3 | 2009-05-05 14:33:22 +0100 (Tue, 05 May 2009) | 3 lines
173 M /trunk/samtools/Makefile.generic
174 M /trunk/samtools/Makefile.lite
175 M /trunk/samtools/bam.c
176 M /trunk/samtools/bam.h
177 M /trunk/samtools/bam_import.c
178 M /trunk/samtools/bamtk.c
179 A /trunk/samtools/sam.c
180 A /trunk/samtools/sam.h
181 A /trunk/samtools/sam_view.c
183 * samtools-0.1.3-11 (r258)
184 * unify the interface to BAM and SAM I/O
186 ------------------------------------------------------------------------
187 r257 | lh3lh3 | 2009-05-05 09:53:35 +0100 (Tue, 05 May 2009) | 3 lines
189 M /trunk/samtools/Makefile.lite
190 M /trunk/samtools/bam_plcmd.c
191 M /trunk/samtools/bamtk.c
193 * samtools-0.1.3-10 (r257)
194 * allow hex with "pileup -m"
196 ------------------------------------------------------------------------
197 r256 | lh3lh3 | 2009-05-04 19:16:50 +0100 (Mon, 04 May 2009) | 4 lines
199 M /trunk/samtools/bam_lpileup.c
200 M /trunk/samtools/bamtk.c
202 * samtools-0.1.3-9 (r256)
203 * fixed a bug in bam_lpileup.c
204 * I do not know if this also fixes the bug causing assertion failure in the tview
206 ------------------------------------------------------------------------
207 r251 | lh3lh3 | 2009-04-28 13:53:23 +0100 (Tue, 28 Apr 2009) | 3 lines
209 M /trunk/samtools/bam_pileup.c
210 M /trunk/samtools/bamtk.c
212 * samtools-0.1.3-8 (r251)
213 * fixed a bug when there are reads without coordinates
215 ------------------------------------------------------------------------
216 r250 | lh3lh3 | 2009-04-28 13:43:33 +0100 (Tue, 28 Apr 2009) | 2 lines
218 A /trunk/samtools/AUTHORS
219 A /trunk/samtools/README
220 M /trunk/samtools/cleanup.sh
224 ------------------------------------------------------------------------
225 r249 | lh3lh3 | 2009-04-28 13:37:16 +0100 (Tue, 28 Apr 2009) | 2 lines
227 M /trunk/samtools/Makefile.generic
228 M /trunk/samtools/Makefile.lite
229 M /trunk/samtools/configure.ac
230 M /trunk/samtools/misc/Makefile.generic
232 improve large file support in compilation
234 ------------------------------------------------------------------------
235 r248 | lh3lh3 | 2009-04-28 13:33:24 +0100 (Tue, 28 Apr 2009) | 2 lines
237 M /trunk/samtools/INSTALL
241 ------------------------------------------------------------------------
242 r247 | lh3lh3 | 2009-04-28 13:28:50 +0100 (Tue, 28 Apr 2009) | 2 lines
244 M /trunk/samtools/Makefile.am
245 M /trunk/samtools/autogen.sh
246 M /trunk/samtools/cleanup.sh
247 M /trunk/samtools/configure.ac
248 A /trunk/samtools/misc/Makefile.am
250 fixed various issues about the GNU building scripts
252 ------------------------------------------------------------------------
253 r246 | lh3lh3 | 2009-04-28 13:10:23 +0100 (Tue, 28 Apr 2009) | 4 lines
255 M /trunk/samtools/ChangeLog
256 D /trunk/samtools/Makefile
257 A /trunk/samtools/Makefile.am
258 A /trunk/samtools/Makefile.generic
259 A /trunk/samtools/autogen.sh
260 M /trunk/samtools/bam.h
261 M /trunk/samtools/bam_aux.c
262 M /trunk/samtools/bam_tview.c
263 M /trunk/samtools/bamtk.c
264 A /trunk/samtools/cleanup.sh
265 A /trunk/samtools/configure.ac
266 D /trunk/samtools/misc/Makefile
267 A /trunk/samtools/misc/Makefile.generic (from /trunk/samtools/misc/Makefile:245)
269 * samtools-0.1.3-7 (r246)
270 * incorporated revisions from Nils Homer
271 * enhanced support of displaying color-space reads
273 ------------------------------------------------------------------------
274 r244 | lh3lh3 | 2009-04-25 11:49:40 +0100 (Sat, 25 Apr 2009) | 3 lines
276 M /trunk/samtools/bam_md.c
277 M /trunk/samtools/bamtk.c
279 * samtools-0.1.3-6 (r244)
280 * fixed segfault for unmapped reads
282 ------------------------------------------------------------------------
283 r243 | lh3lh3 | 2009-04-24 21:27:26 +0100 (Fri, 24 Apr 2009) | 5 lines
285 M /trunk/samtools/bam.h
286 M /trunk/samtools/bam_maqcns.c
287 M /trunk/samtools/bam_md.c
288 M /trunk/samtools/bamtk.c
290 * samtools-0.1.3-5 (r243)
291 * fixed a long existing bug which may cause memory leak
293 * consensus calling now works with "=", but indel calling not
295 ------------------------------------------------------------------------
296 r242 | lh3lh3 | 2009-04-24 20:44:46 +0100 (Fri, 24 Apr 2009) | 3 lines
298 M /trunk/samtools/bam_md.c
299 M /trunk/samtools/bamtk.c
301 * samtools-0.1.3-4 (r242)
302 * fixed a memory leak
304 ------------------------------------------------------------------------
305 r240 | lh3lh3 | 2009-04-24 16:40:18 +0100 (Fri, 24 Apr 2009) | 5 lines
307 M /trunk/samtools/Makefile
308 M /trunk/samtools/Makefile.lite
309 M /trunk/samtools/bam.h
310 M /trunk/samtools/bam_aux.c
311 A /trunk/samtools/bam_md.c
312 M /trunk/samtools/bam_plcmd.c
313 M /trunk/samtools/bamtk.c
315 * samtools-0.1.3-3 (r240)
318 * the plain pileup now support "=" bases, but consensus calling and glfgen may fail
320 ------------------------------------------------------------------------
321 r239 | lh3lh3 | 2009-04-24 12:08:20 +0100 (Fri, 24 Apr 2009) | 5 lines
323 M /trunk/samtools/bam.h
324 M /trunk/samtools/bam_aux.c
325 M /trunk/samtools/bamtk.c
327 * samtools-0.1.3-2 (r239)
328 * fixed bugs in bam_aux.c (these functions nevered used by samtools)
329 * removed bam_aux_init()/bam_aux_destroy()
330 * added tagview for testing bam_aux
332 ------------------------------------------------------------------------
333 r235 | lh3lh3 | 2009-04-21 23:17:39 +0100 (Tue, 21 Apr 2009) | 3 lines
335 M /trunk/samtools/bam_pileup.c
336 M /trunk/samtools/bamtk.c
339 * fixed a bug in pileup: the first read in a chromosome may not be printed
341 ------------------------------------------------------------------------
342 r232 | lh3lh3 | 2009-04-16 15:25:43 +0100 (Thu, 16 Apr 2009) | 2 lines
344 M /trunk/samtools/Makefile.lite
346 a missing file in Makefile.lite
348 ------------------------------------------------------------------------
349 r227 | lh3lh3 | 2009-04-15 22:02:53 +0100 (Wed, 15 Apr 2009) | 2 lines
351 M /trunk/samtools/NEWS
352 M /trunk/samtools/bamtk.c
354 Release samtools-0.1.3
356 ------------------------------------------------------------------------
357 r223 | lh3lh3 | 2009-04-15 14:31:32 +0100 (Wed, 15 Apr 2009) | 3 lines
359 M /trunk/samtools/bam_plcmd.c
360 M /trunk/samtools/bamtk.c
363 * make samtools more robust to weird input such as empty file
365 ------------------------------------------------------------------------
366 r222 | lh3lh3 | 2009-04-15 14:05:33 +0100 (Wed, 15 Apr 2009) | 2 lines
368 M /trunk/samtools/ChangeLog
369 M /trunk/samtools/NEWS
370 M /trunk/samtools/samtools.1
372 prepare for release 0.1.3
374 ------------------------------------------------------------------------
375 r221 | lh3lh3 | 2009-04-15 13:32:14 +0100 (Wed, 15 Apr 2009) | 2 lines
377 A /trunk/samtools/misc/blast2sam.pl
379 convert NCBI-BLASTN to SAM
381 ------------------------------------------------------------------------
382 r220 | lh3lh3 | 2009-04-15 13:18:19 +0100 (Wed, 15 Apr 2009) | 3 lines
384 M /trunk/samtools/bam_lpileup.c
385 M /trunk/samtools/bamtk.c
388 * fixed a small memory leak in tview
390 ------------------------------------------------------------------------
391 r219 | lh3lh3 | 2009-04-15 13:00:08 +0100 (Wed, 15 Apr 2009) | 3 lines
393 M /trunk/samtools/bam_rmdup.c
394 M /trunk/samtools/bamtk.c
397 * fixed a bug in rmdup when there are unmapped reads
399 ------------------------------------------------------------------------
400 r218 | lh3lh3 | 2009-04-14 22:28:58 +0100 (Tue, 14 Apr 2009) | 2 lines
402 M /trunk/samtools/ChangeLog
403 M /trunk/samtools/NEWS
405 proposed NEWS for the new release (have not yet)
407 ------------------------------------------------------------------------
408 r216 | lh3lh3 | 2009-04-14 22:10:46 +0100 (Tue, 14 Apr 2009) | 4 lines
410 M /trunk/samtools/misc/samtools.pl
413 * improve indelFilter to avoid filtering true indels. The new filter relies
414 on the new pileup indel line implemented in samtools-0.1.2-25
416 ------------------------------------------------------------------------
417 r215 | lh3lh3 | 2009-04-14 22:04:19 +0100 (Tue, 14 Apr 2009) | 4 lines
419 M /trunk/samtools/bam_maqcns.c
420 M /trunk/samtools/bam_plcmd.c
421 M /trunk/samtools/bamtk.c
422 M /trunk/samtools/samtools.1
425 * change the pileup indel line to shows the number of alignments actually
428 ------------------------------------------------------------------------
429 r211 | lh3lh3 | 2009-04-13 12:07:13 +0100 (Mon, 13 Apr 2009) | 2 lines
431 M /trunk/samtools/ChangeLog
433 update ChangeLog from "svn log"
435 ------------------------------------------------------------------------
436 r210 | lh3lh3 | 2009-04-12 20:57:05 +0100 (Sun, 12 Apr 2009) | 4 lines
438 M /trunk/samtools/bam.c
439 M /trunk/samtools/bam_import.c
440 M /trunk/samtools/bam_sort.c
441 M /trunk/samtools/bamtk.c
442 M /trunk/samtools/kseq.h
445 * in merge, gives a warning rather than error if the target sequence length is different
448 ------------------------------------------------------------------------
449 r209 | lh3lh3 | 2009-04-12 20:32:44 +0100 (Sun, 12 Apr 2009) | 3 lines
451 M /trunk/samtools/bam.c
452 M /trunk/samtools/bam_import.c
453 M /trunk/samtools/bamtk.c
456 * recognize '*' at the QUAL field
458 ------------------------------------------------------------------------
459 r208 | lh3lh3 | 2009-04-12 20:08:02 +0100 (Sun, 12 Apr 2009) | 3 lines
461 M /trunk/samtools/bam_import.c
462 M /trunk/samtools/bamtk.c
463 M /trunk/samtools/kseq.h
466 * the field separater is TAB only, now
468 ------------------------------------------------------------------------
469 r207 | lh3lh3 | 2009-04-08 15:18:03 +0100 (Wed, 08 Apr 2009) | 2 lines
471 M /trunk/samtools/examples/ex1.sam.gz
473 * fixed the problem in the example alignment due to the bug in fixmate
475 ------------------------------------------------------------------------
476 r206 | lh3lh3 | 2009-04-08 15:15:05 +0100 (Wed, 08 Apr 2009) | 3 lines
478 M /trunk/samtools/bam_mate.c
479 M /trunk/samtools/bamtk.c
480 M /trunk/samtools/misc/soap2sam.pl
483 * fixed a nasty bug in `fixmate'
485 ------------------------------------------------------------------------
486 r205 | lh3lh3 | 2009-04-08 10:57:08 +0100 (Wed, 08 Apr 2009) | 2 lines
488 M /trunk/samtools/misc/bowtie2sam.pl
489 M /trunk/samtools/misc/soap2sam.pl
490 M /trunk/samtools/misc/wgsim_eval.pl
492 make the script robust to the bugs in SOAP-2.1.7
494 ------------------------------------------------------------------------
495 r200 | lh3lh3 | 2009-04-02 15:14:56 +0100 (Thu, 02 Apr 2009) | 3 lines
497 M /trunk/samtools/bam_stat.c
498 M /trunk/samtools/bamtk.c
501 * check if file is truncated in flagstat
503 ------------------------------------------------------------------------
504 r199 | lh3lh3 | 2009-04-02 15:09:10 +0100 (Thu, 02 Apr 2009) | 3 lines
506 M /trunk/samtools/bamtk.c
509 * print the header if requested
511 ------------------------------------------------------------------------
512 r193 | lh3lh3 | 2009-03-27 15:09:50 +0000 (Fri, 27 Mar 2009) | 3 lines
514 M /trunk/samtools/bam_plcmd.c
515 M /trunk/samtools/bamtk.c
518 * fixed a minor bug reported by Nils Homer
520 ------------------------------------------------------------------------
521 r185 | lh3lh3 | 2009-03-24 11:50:32 +0000 (Tue, 24 Mar 2009) | 2 lines
523 A /trunk/samtools/Makefile (from /trunk/samtools/Makefile.std:184)
524 D /trunk/samtools/Makefile.std
525 A /trunk/samtools/misc/Makefile (from /trunk/samtools/misc/Makefile.std:184)
526 D /trunk/samtools/misc/Makefile.std
528 rename Makefile.std as Makefile. GNU building systerm is not ready and may take some time...
530 ------------------------------------------------------------------------
531 r184 | lh3lh3 | 2009-03-24 10:36:38 +0000 (Tue, 24 Mar 2009) | 4 lines
533 D /trunk/samtools/Makefile
534 A /trunk/samtools/Makefile.std (from /trunk/samtools/Makefile:183)
535 M /trunk/samtools/bam_sort.c
536 M /trunk/samtools/bam_tview.c
537 M /trunk/samtools/bamtk.c
538 D /trunk/samtools/misc/Makefile
539 A /trunk/samtools/misc/Makefile.std (from /trunk/samtools/misc/Makefile:182)
540 M /trunk/samtools/samtools.1
543 * incorporating Nils' changes
544 * rename Makefile to Makefile.std and prepare to add the GNU building systerms (also by Nils)
546 ------------------------------------------------------------------------
547 r183 | lh3lh3 | 2009-03-24 10:30:23 +0000 (Tue, 24 Mar 2009) | 4 lines
549 M /trunk/samtools/Makefile
550 M /trunk/samtools/bam_import.c
551 M /trunk/samtools/bam_maqcns.c
552 M /trunk/samtools/bam_maqcns.h
553 M /trunk/samtools/bam_plcmd.c
554 M /trunk/samtools/bamtk.c
555 M /trunk/samtools/kseq.h
556 A /trunk/samtools/kstring.c
557 A /trunk/samtools/kstring.h
560 * made pileup take a list of proposed indels. An insertion is N at the moment.
561 * added my kstring library for a bit complex parsing of the position list.
563 ------------------------------------------------------------------------
564 r169 | lh3lh3 | 2009-03-12 13:40:14 +0000 (Thu, 12 Mar 2009) | 3 lines
566 M /trunk/samtools/misc/soap2sam.pl
569 * more robust to truncated soap output
571 ------------------------------------------------------------------------
572 r168 | lh3lh3 | 2009-03-11 10:49:00 +0000 (Wed, 11 Mar 2009) | 2 lines
574 M /trunk/samtools/Makefile.lite
576 added bam_stat.o to Makefile.lite
578 ------------------------------------------------------------------------
579 r167 | lh3lh3 | 2009-03-10 22:11:31 +0000 (Tue, 10 Mar 2009) | 3 lines
581 M /trunk/samtools/bam_maqcns.c
582 M /trunk/samtools/bamtk.c
585 * generate RMS of mapQ instead of max mapQ
587 ------------------------------------------------------------------------
588 r166 | lh3lh3 | 2009-03-10 22:06:45 +0000 (Tue, 10 Mar 2009) | 3 lines
590 M /trunk/samtools/bam_plcmd.c
591 M /trunk/samtools/bamtk.c
592 M /trunk/samtools/glf.c
593 M /trunk/samtools/glf.h
594 M /trunk/samtools/misc/Makefile
599 ------------------------------------------------------------------------
600 r159 | lh3lh3 | 2009-03-03 11:26:08 +0000 (Tue, 03 Mar 2009) | 3 lines
602 M /trunk/samtools/bam_plcmd.c
603 M /trunk/samtools/bamtk.c
606 * fixed a minor bug in displaying pileup
608 ------------------------------------------------------------------------
609 r158 | lh3lh3 | 2009-03-03 11:24:16 +0000 (Tue, 03 Mar 2009) | 3 lines
611 M /trunk/samtools/ChangeLog
612 M /trunk/samtools/bamtk.c
615 * optionally print SAM header
617 ------------------------------------------------------------------------
618 r153 | lh3lh3 | 2009-03-02 10:45:28 +0000 (Mon, 02 Mar 2009) | 3 lines
620 M /trunk/samtools/bamtk.c
621 M /trunk/samtools/glf.c
624 * use "GLF\3" as the magic for GLFv3 files
626 ------------------------------------------------------------------------
627 r152 | lh3lh3 | 2009-03-02 10:39:09 +0000 (Mon, 02 Mar 2009) | 5 lines
629 M /trunk/samtools/Makefile
630 M /trunk/samtools/bam_import.c
631 M /trunk/samtools/bam_index.c
632 M /trunk/samtools/bam_plcmd.c
633 M /trunk/samtools/bamtk.c
634 M /trunk/samtools/glf.c
635 M /trunk/samtools/glf.h
638 * fixed a bug in import: core.bin is undefined for unmapped reads
639 * this bug can be alleviated (not completely solved) in bam_index.c
640 * update to GLFv3: pos is changed to offset for better compression
642 ------------------------------------------------------------------------
643 r151 | lh3lh3 | 2009-03-01 15:18:43 +0000 (Sun, 01 Mar 2009) | 3 lines
645 M /trunk/samtools/misc/wgsim.c
648 * fixed a bug in simulating indels
650 ------------------------------------------------------------------------
651 r145 | lh3lh3 | 2009-02-26 19:43:57 +0000 (Thu, 26 Feb 2009) | 4 lines
653 M /trunk/samtools/misc/wgsim.c
656 * allow to print mismatch information as fastq comment. MAQ does
657 not like long read names.
659 ------------------------------------------------------------------------
660 r141 | lh3lh3 | 2009-02-26 14:53:03 +0000 (Thu, 26 Feb 2009) | 6 lines
662 M /trunk/samtools/ChangeLog
663 M /trunk/samtools/misc/wgsim.c
664 M /trunk/samtools/misc/wgsim_eval.pl
667 * fixed a bug about color read coordinates
668 * fixed a bug in read names
669 * wgsim_eval.pl-0.1.3
670 * make the script work with color reads
672 ------------------------------------------------------------------------
673 r140 | lh3lh3 | 2009-02-26 14:02:57 +0000 (Thu, 26 Feb 2009) | 2 lines
675 M /trunk/samtools/misc/Makefile
676 M /trunk/samtools/misc/wgsim.c
678 * wgsim: added a note
680 ------------------------------------------------------------------------
681 r139 | lh3lh3 | 2009-02-26 11:39:08 +0000 (Thu, 26 Feb 2009) | 7 lines
683 M /trunk/samtools/misc/wgsim.c
684 M /trunk/samtools/misc/wgsim_eval.pl
687 * considerable code clean up
688 * print number of substitutions/indels/errors on each read
689 * potentially support SOLiD simulation, though not tested at the moment
690 * wgsim_eval.pl-0.1.2
691 * change in accordant with wgsim
693 ------------------------------------------------------------------------
694 r129 | lh3lh3 | 2009-02-18 22:23:27 +0000 (Wed, 18 Feb 2009) | 3 lines
696 M /trunk/samtools/bam_index.c
697 M /trunk/samtools/bamtk.c
700 * fixed a bug in bam_fetch, caused by completely contained adjacent chunks
702 ------------------------------------------------------------------------
703 r128 | bhandsaker | 2009-02-18 19:06:57 +0000 (Wed, 18 Feb 2009) | 2 lines
705 M /trunk/samtools/bamtk.c
707 Fix annoying segv when invalid region specified.
709 ------------------------------------------------------------------------
710 r127 | lh3lh3 | 2009-02-17 10:49:55 +0000 (Tue, 17 Feb 2009) | 2 lines
712 D /trunk/samtools/misc/indel_filter.pl
713 A /trunk/samtools/misc/samtools.pl
715 * move indel_filter.pl to samtools.pl
717 ------------------------------------------------------------------------
718 r126 | lh3lh3 | 2009-02-14 21:22:30 +0000 (Sat, 14 Feb 2009) | 3 lines
720 M /trunk/samtools/bam_mate.c
721 M /trunk/samtools/bamtk.c
724 * fixed a bug in fixmate: SE reads are flagged as BAM_FMUNMAP
726 ------------------------------------------------------------------------
727 r125 | lh3lh3 | 2009-02-13 09:54:45 +0000 (Fri, 13 Feb 2009) | 3 lines
729 M /trunk/samtools/bam_stat.c
730 M /trunk/samtools/bamtk.c
733 * fixed a minor bug in flagstat
735 ------------------------------------------------------------------------
736 r124 | lh3lh3 | 2009-02-12 11:15:32 +0000 (Thu, 12 Feb 2009) | 3 lines
738 M /trunk/samtools/bam_maqcns.c
739 M /trunk/samtools/bamtk.c
740 M /trunk/samtools/misc/indel_filter.pl
743 * improve indel caller by setting maximum window size
745 ------------------------------------------------------------------------
746 r123 | lh3lh3 | 2009-02-12 10:30:29 +0000 (Thu, 12 Feb 2009) | 2 lines
748 M /trunk/samtools/bam_plcmd.c
749 M /trunk/samtools/bamtk.c
751 * output max mapping quality in indel line
753 ------------------------------------------------------------------------
754 r122 | lh3lh3 | 2009-02-11 10:59:10 +0000 (Wed, 11 Feb 2009) | 2 lines
756 M /trunk/samtools/misc/maq2sam.c
758 fixed a bug in generating tag AM
760 ------------------------------------------------------------------------
761 r121 | lh3lh3 | 2009-02-03 10:43:11 +0000 (Tue, 03 Feb 2009) | 2 lines
763 M /trunk/samtools/bam_index.c
764 M /trunk/samtools/bamtk.c
766 fixed a potential memory problem in indexing
768 ------------------------------------------------------------------------
769 r120 | bhandsaker | 2009-02-02 15:52:52 +0000 (Mon, 02 Feb 2009) | 2 lines
771 M /trunk/samtools/Makefile
773 Pass LIBS to recursive targets to facilitate building at Broad.
775 ------------------------------------------------------------------------
776 r119 | lh3lh3 | 2009-02-02 10:12:15 +0000 (Mon, 02 Feb 2009) | 4 lines
778 M /trunk/samtools/ChangeLog
779 M /trunk/samtools/bam_plcmd.c
780 M /trunk/samtools/bam_stat.c
781 M /trunk/samtools/bamtk.c
784 * fixed a bug in generating GLFv2 for indels
785 * improve flagstat report a little bit
787 ------------------------------------------------------------------------
788 r118 | lh3lh3 | 2009-01-29 12:33:23 +0000 (Thu, 29 Jan 2009) | 3 lines
790 M /trunk/samtools/Makefile
791 A /trunk/samtools/bam_stat.c
792 M /trunk/samtools/bamtk.c
795 * added flagstat command
797 ------------------------------------------------------------------------
798 r116 | lh3lh3 | 2009-01-28 13:31:12 +0000 (Wed, 28 Jan 2009) | 2 lines
800 M /trunk/samtools/ChangeLog
801 M /trunk/samtools/NEWS
802 M /trunk/samtools/bamtk.c
803 M /trunk/samtools/samtools.1
805 Release SAMtools-0.1.2
807 ------------------------------------------------------------------------
808 r115 | lh3lh3 | 2009-01-28 12:54:08 +0000 (Wed, 28 Jan 2009) | 2 lines
810 A /trunk/samtools/misc/indel_filter.pl
812 Script for filtering indel results
814 ------------------------------------------------------------------------
815 r114 | lh3lh3 | 2009-01-25 11:45:37 +0000 (Sun, 25 Jan 2009) | 2 lines
817 A /trunk/samtools/misc/zoom2sam.pl
821 ------------------------------------------------------------------------
822 r113 | lh3lh3 | 2009-01-24 14:25:07 +0000 (Sat, 24 Jan 2009) | 2 lines
824 A /trunk/samtools/misc/novo2sam.pl
826 add a script to convert novo alignment to SAM
828 ------------------------------------------------------------------------
829 r112 | lh3lh3 | 2009-01-23 20:57:39 +0000 (Fri, 23 Jan 2009) | 2 lines
831 M /trunk/samtools/ChangeLog
832 M /trunk/samtools/ChangeLog.old
833 M /trunk/samtools/samtools.1
835 update documentation and ChangeLog
837 ------------------------------------------------------------------------
838 r111 | lh3lh3 | 2009-01-23 19:22:59 +0000 (Fri, 23 Jan 2009) | 3 lines
840 M /trunk/samtools/bam_sort.c
841 M /trunk/samtools/bamtk.c
844 * fixed a bug in "merge" command line
846 ------------------------------------------------------------------------
847 r110 | lh3lh3 | 2009-01-22 15:36:48 +0000 (Thu, 22 Jan 2009) | 3 lines
849 M /trunk/samtools/misc/Makefile
850 A /trunk/samtools/misc/bowtie2sam.pl (from /branches/dev/samtools/misc/bowtie2sam.pl:108)
851 M /trunk/samtools/misc/export2sam.pl
852 A /trunk/samtools/misc/soap2sam.pl (from /branches/dev/samtools/misc/soap2sam.pl:108)
853 A /trunk/samtools/misc/wgsim.c (from /branches/dev/samtools/misc/wgsim.c:108)
854 A /trunk/samtools/misc/wgsim_eval.pl (from /branches/dev/samtools/misc/wgsim_eval.pl:108)
856 * merge from branches/dev/
857 * all future development will happen here
859 ------------------------------------------------------------------------
860 r109 | lh3lh3 | 2009-01-22 15:14:27 +0000 (Thu, 22 Jan 2009) | 3 lines
862 M /trunk/samtools/COPYING
863 M /trunk/samtools/ChangeLog
864 A /trunk/samtools/INSTALL (from /branches/dev/samtools/INSTALL:108)
865 M /trunk/samtools/Makefile
866 A /trunk/samtools/Makefile.lite (from /branches/dev/samtools/Makefile.lite:108)
867 M /trunk/samtools/bam.c
868 M /trunk/samtools/bam.h
869 M /trunk/samtools/bam_import.c
870 M /trunk/samtools/bam_index.c
871 M /trunk/samtools/bam_lpileup.c
872 M /trunk/samtools/bam_maqcns.c
873 M /trunk/samtools/bam_maqcns.h
874 A /trunk/samtools/bam_mate.c (from /branches/dev/samtools/bam_mate.c:108)
875 M /trunk/samtools/bam_pileup.c
876 M /trunk/samtools/bam_plcmd.c
877 A /trunk/samtools/bam_rmdup.c (from /branches/dev/samtools/bam_rmdup.c:108)
878 M /trunk/samtools/bam_sort.c
879 M /trunk/samtools/bamtk.c
880 M /trunk/samtools/bgzf.h
881 M /trunk/samtools/examples/00README.txt
882 A /trunk/samtools/examples/Makefile (from /branches/dev/samtools/examples/Makefile:108)
883 D /trunk/samtools/examples/ex1.fa.fai
884 M /trunk/samtools/examples/ex1.sam.gz
885 M /trunk/samtools/faidx.c
886 A /trunk/samtools/glf.c (from /branches/dev/samtools/glf.c:108)
887 M /trunk/samtools/glf.h
888 M /trunk/samtools/misc/Makefile
889 M /trunk/samtools/misc/maq2sam.c
890 M /trunk/samtools/razf.c
891 M /trunk/samtools/source.dot
893 * Merge from branches/dev/
894 * all future development will happen here at trunk/
896 ------------------------------------------------------------------------
897 r79 | bhandsaker | 2009-01-07 21:42:15 +0000 (Wed, 07 Jan 2009) | 2 lines
899 M /trunk/samtools/bam_maqcns.c
900 M /trunk/samtools/bam_tview.c
902 Fix problem with compiling without curses.
904 ------------------------------------------------------------------------
905 r63 | lh3lh3 | 2008-12-22 15:58:02 +0000 (Mon, 22 Dec 2008) | 2 lines
907 A /trunk/samtools (from /branches/dev/samtools:62)
911 ------------------------------------------------------------------------
912 r62 | lh3lh3 | 2008-12-22 15:55:13 +0000 (Mon, 22 Dec 2008) | 2 lines
914 A /branches/dev/samtools/NEWS
915 M /branches/dev/samtools/bamtk.c
916 M /branches/dev/samtools/samtools.1
918 Release samtools-0.1.1
920 ------------------------------------------------------------------------
921 r61 | lh3lh3 | 2008-12-22 15:46:08 +0000 (Mon, 22 Dec 2008) | 10 lines
923 M /branches/dev/samtools/bam_aux.c
924 M /branches/dev/samtools/bam_index.c
925 M /branches/dev/samtools/bam_plcmd.c
926 M /branches/dev/samtools/bam_tview.c
927 M /branches/dev/samtools/bamtk.c
928 M /branches/dev/samtools/razf.c
929 M /branches/dev/samtools/samtools.1
932 * fixed a bug in razf.c: reset z_eof when razf_seek() is called
933 * fixed a memory leak in parsing a region
934 * changed pileup a little bit when -s is in use: output ^ and $
935 * when a bam is not indexed, output more meaningful error message
936 * fixed a bug in indexing for small alignment
937 * fixed a bug in the viewer when we come to the end of a reference file
938 * updated documentation
939 * prepare to release 0.1.1
941 ------------------------------------------------------------------------
942 r60 | lh3lh3 | 2008-12-22 15:10:16 +0000 (Mon, 22 Dec 2008) | 2 lines
944 A /branches/dev/samtools/examples
945 A /branches/dev/samtools/examples/00README.txt
946 A /branches/dev/samtools/examples/ex1.fa
947 A /branches/dev/samtools/examples/ex1.fa.fai
948 A /branches/dev/samtools/examples/ex1.sam.gz
952 ------------------------------------------------------------------------
953 r59 | lh3lh3 | 2008-12-22 09:38:15 +0000 (Mon, 22 Dec 2008) | 2 lines
955 M /branches/dev/samtools/ChangeLog
959 ------------------------------------------------------------------------
960 r58 | lh3lh3 | 2008-12-20 23:06:00 +0000 (Sat, 20 Dec 2008) | 3 lines
962 M /branches/dev/samtools/misc/export2sam.pl
967 ------------------------------------------------------------------------
968 r57 | lh3lh3 | 2008-12-20 15:44:20 +0000 (Sat, 20 Dec 2008) | 2 lines
970 A /branches/dev/samtools/misc/export2sam.pl
972 convert Export format to SAM; not thoroughly tested
974 ------------------------------------------------------------------------
975 r56 | lh3lh3 | 2008-12-19 22:13:28 +0000 (Fri, 19 Dec 2008) | 6 lines
977 M /branches/dev/samtools/bam_import.c
978 M /branches/dev/samtools/bam_plcmd.c
979 M /branches/dev/samtools/bam_tview.c
980 M /branches/dev/samtools/bamtk.c
981 A /branches/dev/samtools/source.dot
984 * pileup: generate maq-like simple output
985 * pileup: allow to output pileup at required sites
986 * source.dot: source file relationship graph
987 * tview: fixed a minor bug
989 ------------------------------------------------------------------------
990 r55 | lh3lh3 | 2008-12-19 20:10:26 +0000 (Fri, 19 Dec 2008) | 2 lines
992 D /branches/dev/samtools/misc/all2sam.pl
996 ------------------------------------------------------------------------
997 r54 | lh3lh3 | 2008-12-16 22:34:25 +0000 (Tue, 16 Dec 2008) | 2 lines
999 A /branches/dev/samtools/COPYING
1000 M /branches/dev/samtools/bam.h
1001 M /branches/dev/samtools/faidx.h
1002 M /branches/dev/samtools/khash.h
1003 M /branches/dev/samtools/kseq.h
1004 M /branches/dev/samtools/ksort.h
1005 M /branches/dev/samtools/samtools.1
1007 Added copyright information and a bit more documentation. No code change.
1009 ------------------------------------------------------------------------
1010 r53 | lh3lh3 | 2008-12-16 13:40:18 +0000 (Tue, 16 Dec 2008) | 3 lines
1012 M /branches/dev/samtools/bam.c
1013 M /branches/dev/samtools/bam.h
1014 M /branches/dev/samtools/bam_index.c
1015 M /branches/dev/samtools/bam_maqcns.c
1016 M /branches/dev/samtools/bamtk.c
1019 * improved efficiency of the indel caller for spliced alignments
1021 ------------------------------------------------------------------------
1022 r52 | lh3lh3 | 2008-12-16 10:28:20 +0000 (Tue, 16 Dec 2008) | 3 lines
1024 M /branches/dev/samtools/bam.c
1025 M /branches/dev/samtools/bam.h
1026 M /branches/dev/samtools/bam_aux.c
1027 M /branches/dev/samtools/bam_index.c
1028 M /branches/dev/samtools/bamtk.c
1031 * a bit code cleanup: reduce the dependency between source files
1033 ------------------------------------------------------------------------
1034 r51 | lh3lh3 | 2008-12-15 14:29:32 +0000 (Mon, 15 Dec 2008) | 3 lines
1036 M /branches/dev/samtools/bam_maqcns.c
1037 M /branches/dev/samtools/bam_plcmd.c
1038 M /branches/dev/samtools/bamtk.c
1041 * fixed a memory leak
1043 ------------------------------------------------------------------------
1044 r50 | lh3lh3 | 2008-12-15 14:00:13 +0000 (Mon, 15 Dec 2008) | 2 lines
1046 M /branches/dev/samtools/ChangeLog
1047 M /branches/dev/samtools/bam.h
1048 M /branches/dev/samtools/samtools.1
1050 update documentation, ChangeLog and a comment
1052 ------------------------------------------------------------------------
1053 r49 | lh3lh3 | 2008-12-15 13:36:43 +0000 (Mon, 15 Dec 2008) | 6 lines
1055 M /branches/dev/samtools/Makefile
1056 M /branches/dev/samtools/bam.h
1057 M /branches/dev/samtools/bam_maqcns.c
1058 M /branches/dev/samtools/bam_maqcns.h
1059 M /branches/dev/samtools/bam_pileup.c
1060 A /branches/dev/samtools/bam_plcmd.c
1061 M /branches/dev/samtools/bamtk.c
1062 M /branches/dev/samtools/samtools.1
1065 * moved pileup command to a separate source file
1066 * added indel caller
1067 * added bam_cal_segend(). (NOT WORKING for spliced alignment!!!)
1068 * updated documentation
1070 ------------------------------------------------------------------------
1071 r48 | lh3lh3 | 2008-12-12 13:55:36 +0000 (Fri, 12 Dec 2008) | 3 lines
1073 M /branches/dev/samtools/bam_maqcns.c
1074 M /branches/dev/samtools/bamtk.c
1077 * fixed another bug in maqcns when there is a nearby deletion
1079 ------------------------------------------------------------------------
1080 r47 | lh3lh3 | 2008-12-12 13:42:16 +0000 (Fri, 12 Dec 2008) | 5 lines
1082 M /branches/dev/samtools/bam_maqcns.c
1083 M /branches/dev/samtools/bam_pileup.c
1084 M /branches/dev/samtools/bamtk.c
1087 * pileup: outputing consensus is now optional
1088 * fixed a bug in glfgen. This bug also exists in maq's glfgen. However,
1089 I am not quite sure why the previous version may have problem.
1091 ------------------------------------------------------------------------
1092 r46 | lh3lh3 | 2008-12-12 11:44:56 +0000 (Fri, 12 Dec 2008) | 6 lines
1094 M /branches/dev/samtools/bam_pileup.c
1095 M /branches/dev/samtools/bamtk.c
1098 * add maq consensus to pileup. However, I will move this part to a new
1099 command as strictly speaking, consensus callin is not part of pileup,
1100 and imposing it would make it harder to generate for other language
1103 ------------------------------------------------------------------------
1104 r45 | bhandsaker | 2008-12-11 20:43:56 +0000 (Thu, 11 Dec 2008) | 2 lines
1106 M /branches/dev/samtools/bgzf.c
1108 Fix bug in tell() after reads that consume to the exact end of a block.
1110 ------------------------------------------------------------------------
1111 r44 | lh3lh3 | 2008-12-11 09:36:53 +0000 (Thu, 11 Dec 2008) | 2 lines
1113 M /branches/dev/samtools/samtools.1
1117 ------------------------------------------------------------------------
1118 r43 | lh3lh3 | 2008-12-11 09:25:36 +0000 (Thu, 11 Dec 2008) | 4 lines
1120 M /branches/dev/samtools/bam_import.c
1121 M /branches/dev/samtools/bamtk.c
1124 * fixed a bug in parser when there is auxiliary fields
1125 * made the parser a bit more robust
1127 ------------------------------------------------------------------------
1128 r42 | lh3lh3 | 2008-12-10 14:57:29 +0000 (Wed, 10 Dec 2008) | 5 lines
1130 M /branches/dev/samtools/bam_index.c
1131 M /branches/dev/samtools/bamtk.c
1132 M /branches/dev/samtools/bgzf.c
1135 * fixed a bug in bgzf (only reading is affected)
1136 * fixed a typo in bam_index.c
1137 * in bam_index.c, check potential bugs in the underlying I/O library
1139 ------------------------------------------------------------------------
1140 r41 | lh3lh3 | 2008-12-10 12:53:08 +0000 (Wed, 10 Dec 2008) | 2 lines
1142 M /branches/dev/samtools/samtools.1
1146 ------------------------------------------------------------------------
1147 r40 | lh3lh3 | 2008-12-10 11:52:10 +0000 (Wed, 10 Dec 2008) | 5 lines
1149 M /branches/dev/samtools/bam.h
1150 M /branches/dev/samtools/bam_pileup.c
1151 M /branches/dev/samtools/bamtk.c
1154 * tried to make pileup work with clipping (previously not), though NOT tested
1155 * removed -v from pileup
1156 * made pileup take the reference sequence
1158 ------------------------------------------------------------------------
1159 r39 | lh3lh3 | 2008-12-09 11:59:28 +0000 (Tue, 09 Dec 2008) | 4 lines
1161 M /branches/dev/samtools/bam_import.c
1162 M /branches/dev/samtools/bamtk.c
1163 M /branches/dev/samtools/samtools.1
1166 * in parser, recognize "=", rather than ",", as a match
1167 * in parser, correctl parse "=" at the MRNM field.
1169 ------------------------------------------------------------------------
1170 r38 | lh3lh3 | 2008-12-09 11:39:07 +0000 (Tue, 09 Dec 2008) | 2 lines
1172 M /branches/dev/samtools/misc/maq2sam.c
1174 fixed a bug in handling maq flag 64 and 192
1176 ------------------------------------------------------------------------
1177 r37 | lh3lh3 | 2008-12-09 09:53:46 +0000 (Tue, 09 Dec 2008) | 2 lines
1179 M /branches/dev/samtools/misc/md5fa.c
1181 also calculate unordered md5sum check
1183 ------------------------------------------------------------------------
1184 r36 | lh3lh3 | 2008-12-09 09:46:21 +0000 (Tue, 09 Dec 2008) | 2 lines
1186 M /branches/dev/samtools/misc/md5fa.c
1188 fixed a minor bug when there are space in the sequence
1190 ------------------------------------------------------------------------
1191 r35 | lh3lh3 | 2008-12-09 09:40:45 +0000 (Tue, 09 Dec 2008) | 2 lines
1193 M /branches/dev/samtools/misc/md5fa.c
1195 fixed a potential memory leak
1197 ------------------------------------------------------------------------
1198 r34 | lh3lh3 | 2008-12-08 14:52:17 +0000 (Mon, 08 Dec 2008) | 2 lines
1200 M /branches/dev/samtools/bam_import.c
1201 M /branches/dev/samtools/bam_index.c
1202 M /branches/dev/samtools/bamtk.c
1204 * fixed a bug in import: bin is wrongly calculated
1206 ------------------------------------------------------------------------
1207 r33 | lh3lh3 | 2008-12-08 14:08:01 +0000 (Mon, 08 Dec 2008) | 2 lines
1209 M /branches/dev/samtools/misc/all2sam.pl
1213 ------------------------------------------------------------------------
1214 r32 | lh3lh3 | 2008-12-08 12:56:02 +0000 (Mon, 08 Dec 2008) | 3 lines
1216 M /branches/dev/samtools/Makefile
1217 M /branches/dev/samtools/kseq.h
1218 M /branches/dev/samtools/misc/Makefile
1219 A /branches/dev/samtools/misc/md5.c
1220 A /branches/dev/samtools/misc/md5.h
1221 A /branches/dev/samtools/misc/md5fa.c
1223 * fixed two warnings in kseq.h
1224 * added md5sum utilities
1226 ------------------------------------------------------------------------
1227 r31 | lh3lh3 | 2008-12-08 11:35:29 +0000 (Mon, 08 Dec 2008) | 5 lines
1229 M /branches/dev/samtools/Makefile
1230 M /branches/dev/samtools/bam_import.c
1231 M /branches/dev/samtools/bamtk.c
1232 A /branches/dev/samtools/kseq.h
1233 D /branches/dev/samtools/kstream.h
1236 * replace kstream with kseq. kseq is a superset of kstream. I need the
1237 extra functions in kseq.h.
1238 * also compile stand-alone faidx
1240 ------------------------------------------------------------------------
1241 r30 | lh3lh3 | 2008-12-08 11:17:04 +0000 (Mon, 08 Dec 2008) | 3 lines
1243 M /branches/dev/samtools/bam.h
1244 M /branches/dev/samtools/bam_sort.c
1245 M /branches/dev/samtools/bamtk.c
1248 * sorting by read names is available
1250 ------------------------------------------------------------------------
1251 r29 | lh3lh3 | 2008-12-08 10:29:02 +0000 (Mon, 08 Dec 2008) | 3 lines
1253 M /branches/dev/samtools/bam.c
1254 M /branches/dev/samtools/bam.h
1255 M /branches/dev/samtools/bam_import.c
1256 M /branches/dev/samtools/bam_maqcns.c
1257 M /branches/dev/samtools/bam_pileup.c
1258 M /branches/dev/samtools/bam_sort.c
1259 M /branches/dev/samtools/bam_tview.c
1260 M /branches/dev/samtools/bamtk.c
1261 M /branches/dev/samtools/misc/maq2sam.c
1264 * format change to meet the latest specification
1266 ------------------------------------------------------------------------
1267 r28 | lh3lh3 | 2008-12-04 16:09:21 +0000 (Thu, 04 Dec 2008) | 3 lines
1269 M /branches/dev/samtools/bam_maqcns.c
1270 M /branches/dev/samtools/misc/maq2sam.c
1272 * minor change in maqcns: special care when n==0
1273 * change maq2sam to meet the latest specification
1275 ------------------------------------------------------------------------
1276 r27 | lh3lh3 | 2008-12-04 15:55:44 +0000 (Thu, 04 Dec 2008) | 2 lines
1278 M /branches/dev/samtools/razf.c
1279 M /branches/dev/samtools/razf.h
1281 considerable code clean up in razf
1283 ------------------------------------------------------------------------
1284 r26 | lh3lh3 | 2008-12-04 15:08:18 +0000 (Thu, 04 Dec 2008) | 2 lines
1286 M /branches/dev/samtools/ChangeLog
1287 M /branches/dev/samtools/Makefile
1288 M /branches/dev/samtools/faidx.c
1290 make RAZF optional in faidx.c
1292 ------------------------------------------------------------------------
1293 r25 | lh3lh3 | 2008-12-01 15:27:22 +0000 (Mon, 01 Dec 2008) | 3 lines
1295 M /branches/dev/samtools/Makefile
1296 M /branches/dev/samtools/bam.h
1297 M /branches/dev/samtools/bam_aux.c
1298 M /branches/dev/samtools/bamtk.c
1299 M /branches/dev/samtools/samtools.1
1302 * added routines for retrieving aux data, NOT TESTED YET!
1304 ------------------------------------------------------------------------
1305 r24 | lh3lh3 | 2008-12-01 14:29:43 +0000 (Mon, 01 Dec 2008) | 5 lines
1307 M /branches/dev/samtools/bam.c
1308 M /branches/dev/samtools/bam_import.c
1309 M /branches/dev/samtools/bam_maqcns.c
1310 M /branches/dev/samtools/bamtk.c
1311 M /branches/dev/samtools/bgzf.c
1312 M /branches/dev/samtools/samtools.1
1315 * bgzf: fixed a potential integer overflow on 32-it machines
1316 * maqcns: set the minimum combined quality as 0
1317 * supporting hex strings
1319 ------------------------------------------------------------------------
1320 r23 | lh3lh3 | 2008-11-27 17:14:37 +0000 (Thu, 27 Nov 2008) | 3 lines
1322 M /branches/dev/samtools/bam_maqcns.c
1323 M /branches/dev/samtools/bamtk.c
1326 * fixed the bug in maqcns
1328 ------------------------------------------------------------------------
1329 r22 | lh3lh3 | 2008-11-27 17:08:11 +0000 (Thu, 27 Nov 2008) | 3 lines
1331 M /branches/dev/samtools/Makefile
1332 M /branches/dev/samtools/bam.h
1333 A /branches/dev/samtools/bam_maqcns.c
1334 A /branches/dev/samtools/bam_maqcns.h
1335 M /branches/dev/samtools/bam_tview.c
1336 M /branches/dev/samtools/bamtk.c
1337 A /branches/dev/samtools/glf.h
1340 * add MAQ consensus caller, currently BUGGY!
1342 ------------------------------------------------------------------------
1343 r21 | lh3lh3 | 2008-11-27 13:51:28 +0000 (Thu, 27 Nov 2008) | 4 lines
1345 M /branches/dev/samtools/bam_pileup.c
1346 M /branches/dev/samtools/bam_tview.c
1347 M /branches/dev/samtools/bamtk.c
1350 * tview: display padded alignment (but not P operation)
1351 * better coordinates and reference sequence
1353 ------------------------------------------------------------------------
1354 r19 | lh3lh3 | 2008-11-27 09:26:05 +0000 (Thu, 27 Nov 2008) | 2 lines
1356 A /branches/dev/samtools/ChangeLog
1360 ------------------------------------------------------------------------
1361 r18 | lh3lh3 | 2008-11-27 09:24:45 +0000 (Thu, 27 Nov 2008) | 3 lines
1363 D /branches/dev/samtools/ChangeLog
1364 A /branches/dev/samtools/ChangeLog.old (from /branches/dev/samtools/ChangeLog:6)
1366 Rename ChangeLog to ChangeLog.old. This old ChangeLog is generated from
1367 the log of my personal SVN repository.
1369 ------------------------------------------------------------------------
1370 r17 | lh3lh3 | 2008-11-27 09:22:55 +0000 (Thu, 27 Nov 2008) | 6 lines
1372 M /branches/dev/samtools/Makefile
1373 M /branches/dev/samtools/bamtk.c
1374 M /branches/dev/samtools/bgzf.c
1377 * declare fseeko and ftello as some Linux may not do this by default and
1378 missing these declarations will make bgzf buggy
1379 * get rid of some harmless warings
1380 * use BGZF by default, now
1382 ------------------------------------------------------------------------
1383 r16 | lh3lh3 | 2008-11-26 21:19:11 +0000 (Wed, 26 Nov 2008) | 4 lines
1385 M /branches/dev/samtools/bam_index.c
1386 M /branches/dev/samtools/bamtk.c
1387 M /branches/dev/samtools/razf.c
1390 * fixed a bug in razf_read()
1391 * give more warnings when the file is truncated (or due to bugs in I/O library)
1393 ------------------------------------------------------------------------
1394 r15 | lh3lh3 | 2008-11-26 20:41:39 +0000 (Wed, 26 Nov 2008) | 2 lines
1396 M /branches/dev/samtools/bgzf.c
1398 fixed a bug in bgzf.c at the end of the file
1400 ------------------------------------------------------------------------
1401 r14 | lh3lh3 | 2008-11-26 17:05:18 +0000 (Wed, 26 Nov 2008) | 4 lines
1403 M /branches/dev/samtools/bamtk.c
1406 * a lot happened to RAZF, although samtools itself is untouched. Better
1407 also update the version number anyway to avoid confusion
1409 ------------------------------------------------------------------------
1410 r13 | lh3lh3 | 2008-11-26 17:03:48 +0000 (Wed, 26 Nov 2008) | 2 lines
1412 M /branches/dev/samtools/razf.c
1414 a change from Jue, but I think it should not matter
1416 ------------------------------------------------------------------------
1417 r12 | lh3lh3 | 2008-11-26 16:48:14 +0000 (Wed, 26 Nov 2008) | 3 lines
1419 M /branches/dev/samtools/razf.c
1421 fixed a potential bug in razf. However, it seems still buggy, just
1422 rarely happens, very rarely.
1424 ------------------------------------------------------------------------
1425 r11 | lh3lh3 | 2008-11-26 14:02:56 +0000 (Wed, 26 Nov 2008) | 2 lines
1427 M /branches/dev/samtools/razf.c
1429 fixed a bug in razf, with the help of Jue
1431 ------------------------------------------------------------------------
1432 r10 | lh3lh3 | 2008-11-26 11:55:32 +0000 (Wed, 26 Nov 2008) | 2 lines
1434 M /branches/dev/samtools/bam_index.c
1438 ------------------------------------------------------------------------
1439 r9 | lh3lh3 | 2008-11-26 11:37:05 +0000 (Wed, 26 Nov 2008) | 2 lines
1441 M /branches/dev/samtools/Makefile
1442 M /branches/dev/samtools/bam.h
1443 M /branches/dev/samtools/razf.c
1444 M /branches/dev/samtools/razf.h
1446 * Jue has updated razf to realize Bob's scheme
1448 ------------------------------------------------------------------------
1449 r7 | lh3lh3 | 2008-11-25 20:37:37 +0000 (Tue, 25 Nov 2008) | 2 lines
1451 A /branches/dev/samtools/samtools.1
1455 ------------------------------------------------------------------------
1456 r6 | lh3lh3 | 2008-11-25 20:37:16 +0000 (Tue, 25 Nov 2008) | 3 lines
1458 A /branches/dev/samtools/ChangeLog
1459 A /branches/dev/samtools/Makefile
1460 A /branches/dev/samtools/bam.c
1461 A /branches/dev/samtools/bam.h
1462 A /branches/dev/samtools/bam_aux.c
1463 A /branches/dev/samtools/bam_endian.h
1464 A /branches/dev/samtools/bam_import.c
1465 A /branches/dev/samtools/bam_index.c
1466 A /branches/dev/samtools/bam_lpileup.c
1467 A /branches/dev/samtools/bam_pileup.c
1468 A /branches/dev/samtools/bam_sort.c
1469 A /branches/dev/samtools/bam_tview.c
1470 A /branches/dev/samtools/bamtk.c
1471 A /branches/dev/samtools/bgzf.c
1472 A /branches/dev/samtools/bgzf.h
1473 A /branches/dev/samtools/bgzip.c
1474 A /branches/dev/samtools/faidx.c
1475 A /branches/dev/samtools/faidx.h
1476 A /branches/dev/samtools/khash.h
1477 A /branches/dev/samtools/ksort.h
1478 A /branches/dev/samtools/kstream.h
1479 A /branches/dev/samtools/misc
1480 A /branches/dev/samtools/misc/Makefile
1481 A /branches/dev/samtools/misc/all2sam.pl
1482 A /branches/dev/samtools/misc/maq2sam.c
1483 A /branches/dev/samtools/razf.c
1484 A /branches/dev/samtools/razf.h
1485 A /branches/dev/samtools/razip.c
1486 A /branches/dev/samtools/zutil.h
1488 The initial version of samtools, replicated from my local SVN repository.
1489 The current version is: 0.1.0-42. All future development will happen here.
1491 ------------------------------------------------------------------------
1492 r5 | lh3lh3 | 2008-11-25 20:30:49 +0000 (Tue, 25 Nov 2008) | 2 lines
1494 A /branches/dev/samtools
1496 samtools (C version)
1498 ------------------------------------------------------------------------