1 ------------------------------------------------------------------------
2 r875 | lh3lh3 | 2010-12-08 12:28:35 -0500 (Wed, 08 Dec 2010) | 2 lines
4 M /trunk/tabix/ChangeLog
7 Fixed a minor bug in generating index
9 ------------------------------------------------------------------------
10 r855 | petulda | 2010-11-25 11:50:13 -0500 (Thu, 25 Nov 2010) | 1 line
14 Disable "unknown target name or minus interval" warning.
15 ------------------------------------------------------------------------
16 r775 | petulda | 2010-10-26 15:02:30 -0400 (Tue, 26 Oct 2010) | 1 line
20 Added -h option to print header lines
21 ------------------------------------------------------------------------
22 r742 | jmarshall | 2010-09-27 06:47:23 -0400 (Mon, 27 Sep 2010) | 2 lines
26 Add svn:ignore properties for intermediate and generated files.
28 ------------------------------------------------------------------------
29 r725 | lh3lh3 | 2010-09-15 13:01:53 -0400 (Wed, 15 Sep 2010) | 2 lines
31 M /trunk/tabix/bgzip.c
33 patches by Peter Chines
35 ------------------------------------------------------------------------
36 r714 | lh3lh3 | 2010-09-07 10:13:25 -0400 (Tue, 07 Sep 2010) | 2 lines
38 M /trunk/tabix/TabixReader.java
39 M /trunk/tabix/index.c
42 fixed a bug in C/Java when n_off == 0
44 ------------------------------------------------------------------------
45 r712 | lh3lh3 | 2010-09-03 09:21:23 -0400 (Fri, 03 Sep 2010) | 2 lines
47 M /trunk/tabix/TabixReader.java
49 fixed a bug in parsing region strings
51 ------------------------------------------------------------------------
52 r700 | petulda | 2010-08-25 10:42:37 -0400 (Wed, 25 Aug 2010) | 1 line
56 Fix: Exit with an error rather than segfault when index is not present and region is queried
57 ------------------------------------------------------------------------
58 r696 | petulda | 2010-08-24 10:24:12 -0400 (Tue, 24 Aug 2010) | 1 line
62 M /trunk/tabix/index.c
65 Complain about not-bgzipped files and check for noncontinuous chromosome blocks
66 ------------------------------------------------------------------------
67 r603 | lh3lh3 | 2010-06-28 10:49:39 -0400 (Mon, 28 Jun 2010) | 2 lines
70 M /trunk/tabix/TabixReader.java
71 M /trunk/tabix/index.c
76 ------------------------------------------------------------------------
77 r597 | lh3lh3 | 2010-06-13 21:08:29 -0400 (Sun, 13 Jun 2010) | 3 lines
79 M /trunk/tabix/index.c
81 Change the namespace of sorting, to avoid function name collision with samtools.
84 ------------------------------------------------------------------------
85 r582 | lh3lh3 | 2010-06-03 10:40:25 -0400 (Thu, 03 Jun 2010) | 2 lines
89 M /trunk/tabix/tabix.py
93 ------------------------------------------------------------------------
94 r581 | lh3lh3 | 2010-05-24 14:24:24 -0400 (Mon, 24 May 2010) | 2 lines
96 M /trunk/tabix/tabix.py
98 OOP interface with the help from Aaron Quinlan
100 ------------------------------------------------------------------------
101 r580 | lh3lh3 | 2010-05-23 23:36:05 -0400 (Sun, 23 May 2010) | 2 lines
103 M /trunk/tabix/tabix.py
107 ------------------------------------------------------------------------
108 r579 | lh3lh3 | 2010-05-23 23:25:24 -0400 (Sun, 23 May 2010) | 2 lines
110 M /trunk/tabix/tabix.py
112 For Snow Leopard compatibility
114 ------------------------------------------------------------------------
115 r575 | lh3lh3 | 2010-05-12 19:31:27 -0400 (Wed, 12 May 2010) | 4 lines
117 M /trunk/tabix/Makefile
118 M /trunk/tabix/index.c
119 M /trunk/tabix/tabix.h
120 A /trunk/tabix/tabix.py
122 * optionally generate shared library for Mac and Linux
123 * added a python script that directly calls the shared library
124 * added a new API for easy python access
126 ------------------------------------------------------------------------
127 r574 | lh3lh3 | 2010-05-11 12:14:27 -0400 (Tue, 11 May 2010) | 2 lines
129 M /trunk/tabix/ChangeLog
131 M /trunk/tabix/perl/Tabix.pm
132 M /trunk/tabix/perl/TabixIterator.pm
133 M /trunk/tabix/tabix.1
137 ------------------------------------------------------------------------
138 r573 | lh3lh3 | 2010-05-11 12:08:30 -0400 (Tue, 11 May 2010) | 2 lines
140 M /trunk/tabix/Makefile
144 ------------------------------------------------------------------------
145 r572 | lh3lh3 | 2010-05-11 11:59:07 -0400 (Tue, 11 May 2010) | 2 lines
147 M /trunk/tabix/perl/MANIFEST
151 ------------------------------------------------------------------------
152 r571 | lh3lh3 | 2010-05-11 11:56:54 -0400 (Tue, 11 May 2010) | 4 lines
154 A /trunk/tabix/example.gtf.gz
155 A /trunk/tabix/example.gtf.gz.tbi
156 M /trunk/tabix/index.c
157 M /trunk/tabix/main.c
158 M /trunk/tabix/perl/MANIFEST
159 M /trunk/tabix/perl/Tabix.pm
160 M /trunk/tabix/perl/Tabix.xs
161 A /trunk/tabix/perl/TabixIterator.pm
162 A /trunk/tabix/perl/t
163 A /trunk/tabix/perl/t/01local.t
164 A /trunk/tabix/perl/t/02remote.t
165 M /trunk/tabix/tabix.1
166 M /trunk/tabix/tabix.h
168 * improved C/Perl APIs
169 * added test for Perl
170 * added an tiny example
172 ------------------------------------------------------------------------
173 r570 | lh3lh3 | 2010-05-11 01:04:21 -0400 (Tue, 11 May 2010) | 2 lines
175 M /trunk/tabix/TabixReader.java
177 fixed the same issue in java
179 ------------------------------------------------------------------------
180 r569 | lh3lh3 | 2010-05-11 01:03:24 -0400 (Tue, 11 May 2010) | 3 lines
182 M /trunk/tabix/index.c
183 M /trunk/tabix/perl/Tabix.pm
184 M /trunk/tabix/perl/Tabix.xs
186 * fixed a potential issue in index.c
189 ------------------------------------------------------------------------
190 r568 | lh3lh3 | 2010-05-10 23:46:21 -0400 (Mon, 10 May 2010) | 2 lines
192 M /trunk/tabix/perl/Tabix.xs
194 return an array from get_names()
196 ------------------------------------------------------------------------
197 r567 | lh3lh3 | 2010-05-10 23:38:46 -0400 (Mon, 10 May 2010) | 4 lines
199 M /trunk/tabix/TabixReader.java
200 M /trunk/tabix/index.c
202 A /trunk/tabix/perl/MANIFEST
203 A /trunk/tabix/perl/Makefile.PL
204 A /trunk/tabix/perl/Tabix.pm
205 A /trunk/tabix/perl/Tabix.xs
206 A /trunk/tabix/perl/typemap
207 M /trunk/tabix/tabix.h
209 * added the initial perl binding. The interface needs to be improved.
210 * added a new API for perl binding
211 * fixed a potential bug in java.
213 ------------------------------------------------------------------------
214 r565 | lh3lh3 | 2010-05-09 23:24:35 -0400 (Sun, 09 May 2010) | 2 lines
216 M /trunk/tabix/main.c
220 ------------------------------------------------------------------------
221 r564 | lh3lh3 | 2010-05-09 23:01:49 -0400 (Sun, 09 May 2010) | 2 lines
223 M /trunk/tabix/index.c
227 ------------------------------------------------------------------------
228 r563 | lh3lh3 | 2010-05-09 22:58:26 -0400 (Sun, 09 May 2010) | 2 lines
230 A /trunk/tabix/ChangeLog
232 M /trunk/tabix/index.c
233 M /trunk/tabix/main.c
234 M /trunk/tabix/tabix.h
236 If nothing bad happens, this will become 0.1.6
238 ------------------------------------------------------------------------
239 r562 | lh3lh3 | 2010-05-09 19:43:56 -0400 (Sun, 09 May 2010) | 2 lines
241 M /trunk/tabix/index.c
245 ------------------------------------------------------------------------
246 r560 | lh3lh3 | 2010-05-05 10:59:09 -0400 (Wed, 05 May 2010) | 3 lines
249 M /trunk/tabix/TabixReader.java
250 M /trunk/tabix/index.c
251 M /trunk/tabix/main.c
252 M /trunk/tabix/tabix.1
253 M /trunk/tabix/tabix.h
255 * Release tabix-0.1.5 (r560)
256 * Improve seeking efficiency. Index file needs to be rebuilt.
258 ------------------------------------------------------------------------
259 r559 | lh3lh3 | 2010-05-04 23:11:42 -0400 (Tue, 04 May 2010) | 2 lines
261 M /trunk/tabix/main.c
263 Release tabix-0.1.4 (r559)
265 ------------------------------------------------------------------------
266 r558 | lh3lh3 | 2010-05-01 12:48:01 -0400 (Sat, 01 May 2010) | 2 lines
268 M /trunk/tabix/TabixReader.java
270 implement SAM/VCF support; NOT tested yet
272 ------------------------------------------------------------------------
273 r557 | lh3lh3 | 2010-05-01 00:42:34 -0400 (Sat, 01 May 2010) | 2 lines
275 A /trunk/tabix/TabixReader.java
277 The Java implementation of tabix.
279 ------------------------------------------------------------------------
280 r556 | lh3lh3 | 2010-04-30 22:34:07 -0400 (Fri, 30 Apr 2010) | 4 lines
282 M /trunk/tabix/index.c
283 M /trunk/tabix/knetfile.c
284 M /trunk/tabix/main.c
286 * tabix-0.1.3-3 (r556)
287 * fixed a small memory leak in knetfile
288 * fixed a minor bug for remote downloading
290 ------------------------------------------------------------------------
291 r555 | lh3lh3 | 2010-04-30 22:15:12 -0400 (Fri, 30 Apr 2010) | 4 lines
293 M /trunk/tabix/Makefile
294 M /trunk/tabix/index.c
295 M /trunk/tabix/main.c
297 * tabix-0.1.3-2 (r555)
298 * do not overwrite index file by default
299 * a little code cleanup
301 ------------------------------------------------------------------------
302 r554 | lh3lh3 | 2010-04-30 21:44:31 -0400 (Fri, 30 Apr 2010) | 2 lines
304 M /trunk/tabix/index.c
306 fixed a potential bug for UCSC-like coordinate
308 ------------------------------------------------------------------------
309 r553 | lh3lh3 | 2010-04-28 17:43:41 -0400 (Wed, 28 Apr 2010) | 2 lines
311 M /trunk/tabix/tabix.tex
313 minor clarification to the format spec
315 ------------------------------------------------------------------------
316 r552 | lh3lh3 | 2010-04-28 16:33:07 -0400 (Wed, 28 Apr 2010) | 3 lines
318 M /trunk/tabix/Makefile
319 M /trunk/tabix/bgzip.c
320 A /trunk/tabix/tabix.tex
322 * added the format specification
323 * fixed a typo in bgzip
325 ------------------------------------------------------------------------
326 r550 | petulda | 2010-04-22 11:03:24 -0400 (Thu, 22 Apr 2010) | 1 line
328 M /trunk/tabix/bgzip.c
330 The behaviour changed slightly to mimic gzip. Detect if std descriptors are connected to the terminal.
331 ------------------------------------------------------------------------
332 r549 | petulda | 2010-04-22 09:46:10 -0400 (Thu, 22 Apr 2010) | 1 line
334 M /trunk/tabix/bgzip.c
336 Fix in src/dst file detection and slight change of behaviour
337 ------------------------------------------------------------------------
338 r548 | petulda | 2010-04-19 04:39:46 -0400 (Mon, 19 Apr 2010) | 1 line
340 M /trunk/tabix/index.c
342 Close file descriptor in ti_list_chromosomes
343 ------------------------------------------------------------------------
344 r547 | petulda | 2010-04-16 09:27:11 -0400 (Fri, 16 Apr 2010) | 1 line
346 M /trunk/tabix/index.c
347 M /trunk/tabix/main.c
348 M /trunk/tabix/tabix.h
350 Added the -l option for listing chromosomes
351 ------------------------------------------------------------------------
352 r544 | lh3lh3 | 2010-03-29 10:58:48 -0400 (Mon, 29 Mar 2010) | 2 lines
354 M /trunk/tabix/main.c
356 removed a line of debugging code
358 ------------------------------------------------------------------------
359 r543 | lh3lh3 | 2010-03-19 12:29:16 -0400 (Fri, 19 Mar 2010) | 3 lines
361 M /trunk/tabix/index.c
362 M /trunk/tabix/main.c
363 M /trunk/tabix/tabix.1
366 * fixed another off-by-one bug
368 ------------------------------------------------------------------------
369 r542 | lh3lh3 | 2010-03-16 22:35:52 -0400 (Tue, 16 Mar 2010) | 2 lines
371 M /trunk/tabix/index.c
372 M /trunk/tabix/main.c
373 M /trunk/tabix/tabix.1
377 ------------------------------------------------------------------------
378 r506 | lh3lh3 | 2009-11-02 23:20:12 -0500 (Mon, 02 Nov 2009) | 2 lines
380 M /trunk/tabix/main.c
384 ------------------------------------------------------------------------
385 r505 | lh3lh3 | 2009-11-02 23:15:49 -0500 (Mon, 02 Nov 2009) | 2 lines
387 A /trunk/tabix/tabix.1
391 ------------------------------------------------------------------------
392 r504 | lh3lh3 | 2009-11-02 11:08:18 -0500 (Mon, 02 Nov 2009) | 5 lines
394 M /trunk/tabix/Makefile
395 M /trunk/tabix/bgzip.c
396 M /trunk/tabix/index.c
397 M /trunk/tabix/main.c
398 M /trunk/tabix/tabix.h
400 * tabix-0.0.0-5 (r504)
401 * fixed a critical bug in fetching data (a typo in fact)
402 * support SAM (tested on ex1.sam) and VCF (not tested)
403 * improve the command-line interface
405 ------------------------------------------------------------------------
406 r503 | lh3lh3 | 2009-11-02 10:04:43 -0500 (Mon, 02 Nov 2009) | 3 lines
408 M /trunk/tabix/Makefile
409 M /trunk/tabix/index.c
410 M /trunk/tabix/main.c
412 * tabix-0.0.0-4 (r503)
413 * index files are bgzf compressed
415 ------------------------------------------------------------------------
416 r502 | lh3lh3 | 2009-11-02 09:47:25 -0500 (Mon, 02 Nov 2009) | 4 lines
418 M /trunk/tabix/index.c
419 M /trunk/tabix/main.c
420 M /trunk/tabix/tabix.h
422 * tabix-0.0.0-3 (r502)
423 * support meta lines (not tested)
424 * I am going to make the index file in the BGZF format
426 ------------------------------------------------------------------------
427 r501 | lh3lh3 | 2009-11-01 22:03:07 -0500 (Sun, 01 Nov 2009) | 3 lines
429 M /trunk/tabix/Makefile
430 M /trunk/tabix/bgzf.h
431 M /trunk/tabix/index.c
432 M /trunk/tabix/main.c
434 * tabix-0.0.0-2 (r501)
435 * accelerate ti_readline()
437 ------------------------------------------------------------------------
438 r500 | lh3lh3 | 2009-11-01 20:49:52 -0500 (Sun, 01 Nov 2009) | 3 lines
440 M /trunk/tabix/Makefile
441 M /trunk/tabix/bgzip.c
442 M /trunk/tabix/index.c
443 M /trunk/tabix/main.c
445 * tabix-0.0.0-1 (r500)
448 ------------------------------------------------------------------------
449 r499 | lh3lh3 | 2009-11-01 14:04:52 -0500 (Sun, 01 Nov 2009) | 2 lines
451 D /trunk/tabix/parser.c
455 ------------------------------------------------------------------------
456 r498 | lh3lh3 | 2009-11-01 14:04:08 -0500 (Sun, 01 Nov 2009) | 2 lines
458 M /trunk/tabix/bgzip.c
460 bgzip is more like gzip in its command-line interface
462 ------------------------------------------------------------------------
463 r497 | lh3lh3 | 2009-11-01 13:43:35 -0500 (Sun, 01 Nov 2009) | 2 lines
465 A /trunk/tabix/Makefile
466 A /trunk/tabix/bam_endian.h
467 A /trunk/tabix/bgzf.c
468 A /trunk/tabix/bgzf.h
469 A /trunk/tabix/bgzip.c
470 A /trunk/tabix/index.c
471 A /trunk/tabix/khash.h
472 A /trunk/tabix/knetfile.c
473 A /trunk/tabix/knetfile.h
474 A /trunk/tabix/ksort.h
475 A /trunk/tabix/kstring.c
476 A /trunk/tabix/kstring.h
477 A /trunk/tabix/main.c
478 A /trunk/tabix/parser.c
479 A /trunk/tabix/tabix.h
481 initial source code. It is BUGGY!
483 ------------------------------------------------------------------------
484 r496 | lh3lh3 | 2009-11-01 13:42:39 -0500 (Sun, 01 Nov 2009) | 2 lines
488 A generic indexer for TAB-delimited genome position files
490 ------------------------------------------------------------------------