1 ------------------------------------------------------------------------
2 r942 | lh3lh3 | 2011-03-31 16:39:50 -0400 (Thu, 31 Mar 2011) | 2 lines
8 ------------------------------------------------------------------------
9 r940 | lh3lh3 | 2011-03-31 16:38:03 -0400 (Thu, 31 Mar 2011) | 2 lines
11 M /trunk/tabix/bedidx.c
14 fixed two bugs due to recent changes
16 ------------------------------------------------------------------------
17 r939 | lh3lh3 | 2011-03-31 16:12:21 -0400 (Thu, 31 Mar 2011) | 2 lines
23 update to the latest bgzf.*
25 ------------------------------------------------------------------------
26 r938 | lh3lh3 | 2011-03-31 16:02:21 -0400 (Thu, 31 Mar 2011) | 2 lines
28 M /trunk/tabix/index.c
30 M /trunk/tabix/tabix.h
34 ------------------------------------------------------------------------
35 r937 | lh3lh3 | 2011-03-31 15:03:49 -0400 (Thu, 31 Mar 2011) | 2 lines
37 M /trunk/tabix/Makefile
38 A /trunk/tabix/bedidx.c
39 M /trunk/tabix/example.gtf.gz.tbi
40 M /trunk/tabix/index.c
42 M /trunk/tabix/tabix.h
44 restructure get_intv() for BED support
46 ------------------------------------------------------------------------
47 r919 | petulda | 2011-02-24 10:14:14 -0500 (Thu, 24 Feb 2011) | 1 line
51 M /trunk/tabix/index.c
54 New -r (reheader) option for efficient header replacement.
55 ------------------------------------------------------------------------
56 r915 | lh3lh3 | 2011-02-22 09:50:57 -0500 (Tue, 22 Feb 2011) | 2 lines
59 A /trunk/tabix/python/setup.py (from /trunk/tabix/setup.py:914)
60 A /trunk/tabix/python/tabixmodule.c (from /trunk/tabix/tabixmodule.c:914)
61 A /trunk/tabix/python/test.py (from /trunk/tabix/test.py:914)
62 D /trunk/tabix/setup.py
63 D /trunk/tabix/tabixmodule.c
64 D /trunk/tabix/test.py
66 move to a new python/ directory
68 ------------------------------------------------------------------------
69 r914 | lh3lh3 | 2011-02-22 09:49:35 -0500 (Tue, 22 Feb 2011) | 2 lines
71 A /trunk/tabix/setup.py
72 A /trunk/tabix/tabixmodule.c
73 A /trunk/tabix/test.py
75 CPython C-API by Hyeshik Chang
77 ------------------------------------------------------------------------
78 r904 | petulda | 2011-01-28 08:06:27 -0500 (Fri, 28 Jan 2011) | 1 line
80 M /trunk/tabix/index.c
82 Check the number of fields on each line and exit nicely without segfault
83 ------------------------------------------------------------------------
84 r901 | petulda | 2011-01-21 06:45:37 -0500 (Fri, 21 Jan 2011) | 1 line
88 Fix: Complain only when VCF is newer, not newer or same mtime
89 ------------------------------------------------------------------------
90 r900 | petulda | 2011-01-21 04:23:04 -0500 (Fri, 21 Jan 2011) | 1 line
94 Prevent the common user mistake and check the timestamps of the vcf and index file
95 ------------------------------------------------------------------------
96 r876 | lh3lh3 | 2010-12-08 12:38:45 -0500 (Wed, 08 Dec 2010) | 2 lines
98 M /trunk/tabix/ChangeLog
100 M /trunk/tabix/main.c
104 ------------------------------------------------------------------------
105 r875 | lh3lh3 | 2010-12-08 12:28:35 -0500 (Wed, 08 Dec 2010) | 2 lines
107 M /trunk/tabix/ChangeLog
108 M /trunk/tabix/index.c
110 Fixed a minor bug in generating index
112 ------------------------------------------------------------------------
113 r855 | petulda | 2010-11-25 11:50:13 -0500 (Thu, 25 Nov 2010) | 1 line
115 M /trunk/tabix/main.c
117 Disable "unknown target name or minus interval" warning.
118 ------------------------------------------------------------------------
119 r775 | petulda | 2010-10-26 15:02:30 -0400 (Tue, 26 Oct 2010) | 1 line
121 M /trunk/tabix/main.c
123 Added -h option to print header lines
124 ------------------------------------------------------------------------
125 r742 | jmarshall | 2010-09-27 06:47:23 -0400 (Mon, 27 Sep 2010) | 2 lines
129 Add svn:ignore properties for intermediate and generated files.
131 ------------------------------------------------------------------------
132 r725 | lh3lh3 | 2010-09-15 13:01:53 -0400 (Wed, 15 Sep 2010) | 2 lines
134 M /trunk/tabix/bgzip.c
136 patches by Peter Chines
138 ------------------------------------------------------------------------
139 r714 | lh3lh3 | 2010-09-07 10:13:25 -0400 (Tue, 07 Sep 2010) | 2 lines
141 M /trunk/tabix/TabixReader.java
142 M /trunk/tabix/index.c
143 M /trunk/tabix/main.c
145 fixed a bug in C/Java when n_off == 0
147 ------------------------------------------------------------------------
148 r712 | lh3lh3 | 2010-09-03 09:21:23 -0400 (Fri, 03 Sep 2010) | 2 lines
150 M /trunk/tabix/TabixReader.java
152 fixed a bug in parsing region strings
154 ------------------------------------------------------------------------
155 r700 | petulda | 2010-08-25 10:42:37 -0400 (Wed, 25 Aug 2010) | 1 line
157 M /trunk/tabix/main.c
159 Fix: Exit with an error rather than segfault when index is not present and region is queried
160 ------------------------------------------------------------------------
161 r696 | petulda | 2010-08-24 10:24:12 -0400 (Tue, 24 Aug 2010) | 1 line
163 M /trunk/tabix/bgzf.c
164 M /trunk/tabix/bgzf.h
165 M /trunk/tabix/index.c
166 M /trunk/tabix/main.c
168 Complain about not-bgzipped files and check for noncontinuous chromosome blocks
169 ------------------------------------------------------------------------
170 r603 | lh3lh3 | 2010-06-28 10:49:39 -0400 (Mon, 28 Jun 2010) | 2 lines
173 M /trunk/tabix/TabixReader.java
174 M /trunk/tabix/index.c
175 M /trunk/tabix/main.c
179 ------------------------------------------------------------------------
180 r597 | lh3lh3 | 2010-06-13 21:08:29 -0400 (Sun, 13 Jun 2010) | 3 lines
182 M /trunk/tabix/index.c
184 Change the namespace of sorting, to avoid function name collision with samtools.
187 ------------------------------------------------------------------------
188 r582 | lh3lh3 | 2010-06-03 10:40:25 -0400 (Thu, 03 Jun 2010) | 2 lines
191 M /trunk/tabix/main.c
192 M /trunk/tabix/tabix.py
196 ------------------------------------------------------------------------
197 r581 | lh3lh3 | 2010-05-24 14:24:24 -0400 (Mon, 24 May 2010) | 2 lines
199 M /trunk/tabix/tabix.py
201 OOP interface with the help from Aaron Quinlan
203 ------------------------------------------------------------------------
204 r580 | lh3lh3 | 2010-05-23 23:36:05 -0400 (Sun, 23 May 2010) | 2 lines
206 M /trunk/tabix/tabix.py
210 ------------------------------------------------------------------------
211 r579 | lh3lh3 | 2010-05-23 23:25:24 -0400 (Sun, 23 May 2010) | 2 lines
213 M /trunk/tabix/tabix.py
215 For Snow Leopard compatibility
217 ------------------------------------------------------------------------
218 r575 | lh3lh3 | 2010-05-12 19:31:27 -0400 (Wed, 12 May 2010) | 4 lines
220 M /trunk/tabix/Makefile
221 M /trunk/tabix/index.c
222 M /trunk/tabix/tabix.h
223 A /trunk/tabix/tabix.py
225 * optionally generate shared library for Mac and Linux
226 * added a python script that directly calls the shared library
227 * added a new API for easy python access
229 ------------------------------------------------------------------------
230 r574 | lh3lh3 | 2010-05-11 12:14:27 -0400 (Tue, 11 May 2010) | 2 lines
232 M /trunk/tabix/ChangeLog
234 M /trunk/tabix/perl/Tabix.pm
235 M /trunk/tabix/perl/TabixIterator.pm
236 M /trunk/tabix/tabix.1
240 ------------------------------------------------------------------------
241 r573 | lh3lh3 | 2010-05-11 12:08:30 -0400 (Tue, 11 May 2010) | 2 lines
243 M /trunk/tabix/Makefile
247 ------------------------------------------------------------------------
248 r572 | lh3lh3 | 2010-05-11 11:59:07 -0400 (Tue, 11 May 2010) | 2 lines
250 M /trunk/tabix/perl/MANIFEST
254 ------------------------------------------------------------------------
255 r571 | lh3lh3 | 2010-05-11 11:56:54 -0400 (Tue, 11 May 2010) | 4 lines
257 A /trunk/tabix/example.gtf.gz
258 A /trunk/tabix/example.gtf.gz.tbi
259 M /trunk/tabix/index.c
260 M /trunk/tabix/main.c
261 M /trunk/tabix/perl/MANIFEST
262 M /trunk/tabix/perl/Tabix.pm
263 M /trunk/tabix/perl/Tabix.xs
264 A /trunk/tabix/perl/TabixIterator.pm
265 A /trunk/tabix/perl/t
266 A /trunk/tabix/perl/t/01local.t
267 A /trunk/tabix/perl/t/02remote.t
268 M /trunk/tabix/tabix.1
269 M /trunk/tabix/tabix.h
271 * improved C/Perl APIs
272 * added test for Perl
273 * added an tiny example
275 ------------------------------------------------------------------------
276 r570 | lh3lh3 | 2010-05-11 01:04:21 -0400 (Tue, 11 May 2010) | 2 lines
278 M /trunk/tabix/TabixReader.java
280 fixed the same issue in java
282 ------------------------------------------------------------------------
283 r569 | lh3lh3 | 2010-05-11 01:03:24 -0400 (Tue, 11 May 2010) | 3 lines
285 M /trunk/tabix/index.c
286 M /trunk/tabix/perl/Tabix.pm
287 M /trunk/tabix/perl/Tabix.xs
289 * fixed a potential issue in index.c
292 ------------------------------------------------------------------------
293 r568 | lh3lh3 | 2010-05-10 23:46:21 -0400 (Mon, 10 May 2010) | 2 lines
295 M /trunk/tabix/perl/Tabix.xs
297 return an array from get_names()
299 ------------------------------------------------------------------------
300 r567 | lh3lh3 | 2010-05-10 23:38:46 -0400 (Mon, 10 May 2010) | 4 lines
302 M /trunk/tabix/TabixReader.java
303 M /trunk/tabix/index.c
305 A /trunk/tabix/perl/MANIFEST
306 A /trunk/tabix/perl/Makefile.PL
307 A /trunk/tabix/perl/Tabix.pm
308 A /trunk/tabix/perl/Tabix.xs
309 A /trunk/tabix/perl/typemap
310 M /trunk/tabix/tabix.h
312 * added the initial perl binding. The interface needs to be improved.
313 * added a new API for perl binding
314 * fixed a potential bug in java.
316 ------------------------------------------------------------------------
317 r565 | lh3lh3 | 2010-05-09 23:24:35 -0400 (Sun, 09 May 2010) | 2 lines
319 M /trunk/tabix/main.c
323 ------------------------------------------------------------------------
324 r564 | lh3lh3 | 2010-05-09 23:01:49 -0400 (Sun, 09 May 2010) | 2 lines
326 M /trunk/tabix/index.c
330 ------------------------------------------------------------------------
331 r563 | lh3lh3 | 2010-05-09 22:58:26 -0400 (Sun, 09 May 2010) | 2 lines
333 A /trunk/tabix/ChangeLog
335 M /trunk/tabix/index.c
336 M /trunk/tabix/main.c
337 M /trunk/tabix/tabix.h
339 If nothing bad happens, this will become 0.1.6
341 ------------------------------------------------------------------------
342 r562 | lh3lh3 | 2010-05-09 19:43:56 -0400 (Sun, 09 May 2010) | 2 lines
344 M /trunk/tabix/index.c
348 ------------------------------------------------------------------------
349 r560 | lh3lh3 | 2010-05-05 10:59:09 -0400 (Wed, 05 May 2010) | 3 lines
352 M /trunk/tabix/TabixReader.java
353 M /trunk/tabix/index.c
354 M /trunk/tabix/main.c
355 M /trunk/tabix/tabix.1
356 M /trunk/tabix/tabix.h
358 * Release tabix-0.1.5 (r560)
359 * Improve seeking efficiency. Index file needs to be rebuilt.
361 ------------------------------------------------------------------------
362 r559 | lh3lh3 | 2010-05-04 23:11:42 -0400 (Tue, 04 May 2010) | 2 lines
364 M /trunk/tabix/main.c
366 Release tabix-0.1.4 (r559)
368 ------------------------------------------------------------------------
369 r558 | lh3lh3 | 2010-05-01 12:48:01 -0400 (Sat, 01 May 2010) | 2 lines
371 M /trunk/tabix/TabixReader.java
373 implement SAM/VCF support; NOT tested yet
375 ------------------------------------------------------------------------
376 r557 | lh3lh3 | 2010-05-01 00:42:34 -0400 (Sat, 01 May 2010) | 2 lines
378 A /trunk/tabix/TabixReader.java
380 The Java implementation of tabix.
382 ------------------------------------------------------------------------
383 r556 | lh3lh3 | 2010-04-30 22:34:07 -0400 (Fri, 30 Apr 2010) | 4 lines
385 M /trunk/tabix/index.c
386 M /trunk/tabix/knetfile.c
387 M /trunk/tabix/main.c
389 * tabix-0.1.3-3 (r556)
390 * fixed a small memory leak in knetfile
391 * fixed a minor bug for remote downloading
393 ------------------------------------------------------------------------
394 r555 | lh3lh3 | 2010-04-30 22:15:12 -0400 (Fri, 30 Apr 2010) | 4 lines
396 M /trunk/tabix/Makefile
397 M /trunk/tabix/index.c
398 M /trunk/tabix/main.c
400 * tabix-0.1.3-2 (r555)
401 * do not overwrite index file by default
402 * a little code cleanup
404 ------------------------------------------------------------------------
405 r554 | lh3lh3 | 2010-04-30 21:44:31 -0400 (Fri, 30 Apr 2010) | 2 lines
407 M /trunk/tabix/index.c
409 fixed a potential bug for UCSC-like coordinate
411 ------------------------------------------------------------------------
412 r553 | lh3lh3 | 2010-04-28 17:43:41 -0400 (Wed, 28 Apr 2010) | 2 lines
414 M /trunk/tabix/tabix.tex
416 minor clarification to the format spec
418 ------------------------------------------------------------------------
419 r552 | lh3lh3 | 2010-04-28 16:33:07 -0400 (Wed, 28 Apr 2010) | 3 lines
421 M /trunk/tabix/Makefile
422 M /trunk/tabix/bgzip.c
423 A /trunk/tabix/tabix.tex
425 * added the format specification
426 * fixed a typo in bgzip
428 ------------------------------------------------------------------------
429 r550 | petulda | 2010-04-22 11:03:24 -0400 (Thu, 22 Apr 2010) | 1 line
431 M /trunk/tabix/bgzip.c
433 The behaviour changed slightly to mimic gzip. Detect if std descriptors are connected to the terminal.
434 ------------------------------------------------------------------------
435 r549 | petulda | 2010-04-22 09:46:10 -0400 (Thu, 22 Apr 2010) | 1 line
437 M /trunk/tabix/bgzip.c
439 Fix in src/dst file detection and slight change of behaviour
440 ------------------------------------------------------------------------
441 r548 | petulda | 2010-04-19 04:39:46 -0400 (Mon, 19 Apr 2010) | 1 line
443 M /trunk/tabix/index.c
445 Close file descriptor in ti_list_chromosomes
446 ------------------------------------------------------------------------
447 r547 | petulda | 2010-04-16 09:27:11 -0400 (Fri, 16 Apr 2010) | 1 line
449 M /trunk/tabix/index.c
450 M /trunk/tabix/main.c
451 M /trunk/tabix/tabix.h
453 Added the -l option for listing chromosomes
454 ------------------------------------------------------------------------
455 r544 | lh3lh3 | 2010-03-29 10:58:48 -0400 (Mon, 29 Mar 2010) | 2 lines
457 M /trunk/tabix/main.c
459 removed a line of debugging code
461 ------------------------------------------------------------------------
462 r543 | lh3lh3 | 2010-03-19 12:29:16 -0400 (Fri, 19 Mar 2010) | 3 lines
464 M /trunk/tabix/index.c
465 M /trunk/tabix/main.c
466 M /trunk/tabix/tabix.1
469 * fixed another off-by-one bug
471 ------------------------------------------------------------------------
472 r542 | lh3lh3 | 2010-03-16 22:35:52 -0400 (Tue, 16 Mar 2010) | 2 lines
474 M /trunk/tabix/index.c
475 M /trunk/tabix/main.c
476 M /trunk/tabix/tabix.1
480 ------------------------------------------------------------------------
481 r506 | lh3lh3 | 2009-11-02 23:20:12 -0500 (Mon, 02 Nov 2009) | 2 lines
483 M /trunk/tabix/main.c
487 ------------------------------------------------------------------------
488 r505 | lh3lh3 | 2009-11-02 23:15:49 -0500 (Mon, 02 Nov 2009) | 2 lines
490 A /trunk/tabix/tabix.1
494 ------------------------------------------------------------------------
495 r504 | lh3lh3 | 2009-11-02 11:08:18 -0500 (Mon, 02 Nov 2009) | 5 lines
497 M /trunk/tabix/Makefile
498 M /trunk/tabix/bgzip.c
499 M /trunk/tabix/index.c
500 M /trunk/tabix/main.c
501 M /trunk/tabix/tabix.h
503 * tabix-0.0.0-5 (r504)
504 * fixed a critical bug in fetching data (a typo in fact)
505 * support SAM (tested on ex1.sam) and VCF (not tested)
506 * improve the command-line interface
508 ------------------------------------------------------------------------
509 r503 | lh3lh3 | 2009-11-02 10:04:43 -0500 (Mon, 02 Nov 2009) | 3 lines
511 M /trunk/tabix/Makefile
512 M /trunk/tabix/index.c
513 M /trunk/tabix/main.c
515 * tabix-0.0.0-4 (r503)
516 * index files are bgzf compressed
518 ------------------------------------------------------------------------
519 r502 | lh3lh3 | 2009-11-02 09:47:25 -0500 (Mon, 02 Nov 2009) | 4 lines
521 M /trunk/tabix/index.c
522 M /trunk/tabix/main.c
523 M /trunk/tabix/tabix.h
525 * tabix-0.0.0-3 (r502)
526 * support meta lines (not tested)
527 * I am going to make the index file in the BGZF format
529 ------------------------------------------------------------------------
530 r501 | lh3lh3 | 2009-11-01 22:03:07 -0500 (Sun, 01 Nov 2009) | 3 lines
532 M /trunk/tabix/Makefile
533 M /trunk/tabix/bgzf.h
534 M /trunk/tabix/index.c
535 M /trunk/tabix/main.c
537 * tabix-0.0.0-2 (r501)
538 * accelerate ti_readline()
540 ------------------------------------------------------------------------
541 r500 | lh3lh3 | 2009-11-01 20:49:52 -0500 (Sun, 01 Nov 2009) | 3 lines
543 M /trunk/tabix/Makefile
544 M /trunk/tabix/bgzip.c
545 M /trunk/tabix/index.c
546 M /trunk/tabix/main.c
548 * tabix-0.0.0-1 (r500)
551 ------------------------------------------------------------------------
552 r499 | lh3lh3 | 2009-11-01 14:04:52 -0500 (Sun, 01 Nov 2009) | 2 lines
554 D /trunk/tabix/parser.c
558 ------------------------------------------------------------------------
559 r498 | lh3lh3 | 2009-11-01 14:04:08 -0500 (Sun, 01 Nov 2009) | 2 lines
561 M /trunk/tabix/bgzip.c
563 bgzip is more like gzip in its command-line interface
565 ------------------------------------------------------------------------
566 r497 | lh3lh3 | 2009-11-01 13:43:35 -0500 (Sun, 01 Nov 2009) | 2 lines
568 A /trunk/tabix/Makefile
569 A /trunk/tabix/bam_endian.h
570 A /trunk/tabix/bgzf.c
571 A /trunk/tabix/bgzf.h
572 A /trunk/tabix/bgzip.c
573 A /trunk/tabix/index.c
574 A /trunk/tabix/khash.h
575 A /trunk/tabix/knetfile.c
576 A /trunk/tabix/knetfile.h
577 A /trunk/tabix/ksort.h
578 A /trunk/tabix/kstring.c
579 A /trunk/tabix/kstring.h
580 A /trunk/tabix/main.c
581 A /trunk/tabix/parser.c
582 A /trunk/tabix/tabix.h
584 initial source code. It is BUGGY!
586 ------------------------------------------------------------------------
587 r496 | lh3lh3 | 2009-11-01 13:42:39 -0500 (Sun, 01 Nov 2009) | 2 lines
591 A generic indexer for TAB-delimited genome position files
593 ------------------------------------------------------------------------