1 ------------------------------------------------------------------------
2 r573 | lh3lh3 | 2010-05-11 12:08:30 -0400 (Tue, 11 May 2010) | 2 lines
4 M /trunk/tabix/Makefile
8 ------------------------------------------------------------------------
9 r572 | lh3lh3 | 2010-05-11 11:59:07 -0400 (Tue, 11 May 2010) | 2 lines
11 M /trunk/tabix/perl/MANIFEST
15 ------------------------------------------------------------------------
16 r571 | lh3lh3 | 2010-05-11 11:56:54 -0400 (Tue, 11 May 2010) | 4 lines
18 A /trunk/tabix/example.gtf.gz
19 A /trunk/tabix/example.gtf.gz.tbi
20 M /trunk/tabix/index.c
22 M /trunk/tabix/perl/MANIFEST
23 M /trunk/tabix/perl/Tabix.pm
24 M /trunk/tabix/perl/Tabix.xs
25 A /trunk/tabix/perl/TabixIterator.pm
27 A /trunk/tabix/perl/t/01local.t
28 A /trunk/tabix/perl/t/02remote.t
29 M /trunk/tabix/tabix.1
30 M /trunk/tabix/tabix.h
32 * improved C/Perl APIs
34 * added an tiny example
36 ------------------------------------------------------------------------
37 r570 | lh3lh3 | 2010-05-11 01:04:21 -0400 (Tue, 11 May 2010) | 2 lines
39 M /trunk/tabix/TabixReader.java
41 fixed the same issue in java
43 ------------------------------------------------------------------------
44 r569 | lh3lh3 | 2010-05-11 01:03:24 -0400 (Tue, 11 May 2010) | 3 lines
46 M /trunk/tabix/index.c
47 M /trunk/tabix/perl/Tabix.pm
48 M /trunk/tabix/perl/Tabix.xs
50 * fixed a potential issue in index.c
53 ------------------------------------------------------------------------
54 r568 | lh3lh3 | 2010-05-10 23:46:21 -0400 (Mon, 10 May 2010) | 2 lines
56 M /trunk/tabix/perl/Tabix.xs
58 return an array from get_names()
60 ------------------------------------------------------------------------
61 r567 | lh3lh3 | 2010-05-10 23:38:46 -0400 (Mon, 10 May 2010) | 4 lines
63 M /trunk/tabix/TabixReader.java
64 M /trunk/tabix/index.c
66 A /trunk/tabix/perl/MANIFEST
67 A /trunk/tabix/perl/Makefile.PL
68 A /trunk/tabix/perl/Tabix.pm
69 A /trunk/tabix/perl/Tabix.xs
70 A /trunk/tabix/perl/typemap
71 M /trunk/tabix/tabix.h
73 * added the initial perl binding. The interface needs to be improved.
74 * added a new API for perl binding
75 * fixed a potential bug in java.
77 ------------------------------------------------------------------------
78 r565 | lh3lh3 | 2010-05-09 23:24:35 -0400 (Sun, 09 May 2010) | 2 lines
84 ------------------------------------------------------------------------
85 r564 | lh3lh3 | 2010-05-09 23:01:49 -0400 (Sun, 09 May 2010) | 2 lines
87 M /trunk/tabix/index.c
91 ------------------------------------------------------------------------
92 r563 | lh3lh3 | 2010-05-09 22:58:26 -0400 (Sun, 09 May 2010) | 2 lines
94 A /trunk/tabix/ChangeLog
96 M /trunk/tabix/index.c
98 M /trunk/tabix/tabix.h
100 If nothing bad happens, this will become 0.1.6
102 ------------------------------------------------------------------------
103 r562 | lh3lh3 | 2010-05-09 19:43:56 -0400 (Sun, 09 May 2010) | 2 lines
105 M /trunk/tabix/index.c
109 ------------------------------------------------------------------------
110 r560 | lh3lh3 | 2010-05-05 10:59:09 -0400 (Wed, 05 May 2010) | 3 lines
113 M /trunk/tabix/TabixReader.java
114 M /trunk/tabix/index.c
115 M /trunk/tabix/main.c
116 M /trunk/tabix/tabix.1
117 M /trunk/tabix/tabix.h
119 * Release tabix-0.1.5 (r560)
120 * Improve seeking efficiency. Index file needs to be rebuilt.
122 ------------------------------------------------------------------------
123 r559 | lh3lh3 | 2010-05-04 23:11:42 -0400 (Tue, 04 May 2010) | 2 lines
125 M /trunk/tabix/main.c
127 Release tabix-0.1.4 (r559)
129 ------------------------------------------------------------------------
130 r558 | lh3lh3 | 2010-05-01 12:48:01 -0400 (Sat, 01 May 2010) | 2 lines
132 M /trunk/tabix/TabixReader.java
134 implement SAM/VCF support; NOT tested yet
136 ------------------------------------------------------------------------
137 r557 | lh3lh3 | 2010-05-01 00:42:34 -0400 (Sat, 01 May 2010) | 2 lines
139 A /trunk/tabix/TabixReader.java
141 The Java implementation of tabix.
143 ------------------------------------------------------------------------
144 r556 | lh3lh3 | 2010-04-30 22:34:07 -0400 (Fri, 30 Apr 2010) | 4 lines
146 M /trunk/tabix/index.c
147 M /trunk/tabix/knetfile.c
148 M /trunk/tabix/main.c
150 * tabix-0.1.3-3 (r556)
151 * fixed a small memory leak in knetfile
152 * fixed a minor bug for remote downloading
154 ------------------------------------------------------------------------
155 r555 | lh3lh3 | 2010-04-30 22:15:12 -0400 (Fri, 30 Apr 2010) | 4 lines
157 M /trunk/tabix/Makefile
158 M /trunk/tabix/index.c
159 M /trunk/tabix/main.c
161 * tabix-0.1.3-2 (r555)
162 * do not overwrite index file by default
163 * a little code cleanup
165 ------------------------------------------------------------------------
166 r554 | lh3lh3 | 2010-04-30 21:44:31 -0400 (Fri, 30 Apr 2010) | 2 lines
168 M /trunk/tabix/index.c
170 fixed a potential bug for UCSC-like coordinate
172 ------------------------------------------------------------------------
173 r553 | lh3lh3 | 2010-04-28 17:43:41 -0400 (Wed, 28 Apr 2010) | 2 lines
175 M /trunk/tabix/tabix.tex
177 minor clarification to the format spec
179 ------------------------------------------------------------------------
180 r552 | lh3lh3 | 2010-04-28 16:33:07 -0400 (Wed, 28 Apr 2010) | 3 lines
182 M /trunk/tabix/Makefile
183 M /trunk/tabix/bgzip.c
184 A /trunk/tabix/tabix.tex
186 * added the format specification
187 * fixed a typo in bgzip
189 ------------------------------------------------------------------------
190 r550 | petulda | 2010-04-22 11:03:24 -0400 (Thu, 22 Apr 2010) | 1 line
192 M /trunk/tabix/bgzip.c
194 The behaviour changed slightly to mimic gzip. Detect if std descriptors are connected to the terminal.
195 ------------------------------------------------------------------------
196 r549 | petulda | 2010-04-22 09:46:10 -0400 (Thu, 22 Apr 2010) | 1 line
198 M /trunk/tabix/bgzip.c
200 Fix in src/dst file detection and slight change of behaviour
201 ------------------------------------------------------------------------
202 r548 | petulda | 2010-04-19 04:39:46 -0400 (Mon, 19 Apr 2010) | 1 line
204 M /trunk/tabix/index.c
206 Close file descriptor in ti_list_chromosomes
207 ------------------------------------------------------------------------
208 r547 | petulda | 2010-04-16 09:27:11 -0400 (Fri, 16 Apr 2010) | 1 line
210 M /trunk/tabix/index.c
211 M /trunk/tabix/main.c
212 M /trunk/tabix/tabix.h
214 Added the -l option for listing chromosomes
215 ------------------------------------------------------------------------
216 r544 | lh3lh3 | 2010-03-29 10:58:48 -0400 (Mon, 29 Mar 2010) | 2 lines
218 M /trunk/tabix/main.c
220 removed a line of debugging code
222 ------------------------------------------------------------------------
223 r543 | lh3lh3 | 2010-03-19 12:29:16 -0400 (Fri, 19 Mar 2010) | 3 lines
225 M /trunk/tabix/index.c
226 M /trunk/tabix/main.c
227 M /trunk/tabix/tabix.1
230 * fixed another off-by-one bug
232 ------------------------------------------------------------------------
233 r542 | lh3lh3 | 2010-03-16 22:35:52 -0400 (Tue, 16 Mar 2010) | 2 lines
235 M /trunk/tabix/index.c
236 M /trunk/tabix/main.c
237 M /trunk/tabix/tabix.1
241 ------------------------------------------------------------------------
242 r506 | lh3lh3 | 2009-11-02 23:20:12 -0500 (Mon, 02 Nov 2009) | 2 lines
244 M /trunk/tabix/main.c
248 ------------------------------------------------------------------------
249 r505 | lh3lh3 | 2009-11-02 23:15:49 -0500 (Mon, 02 Nov 2009) | 2 lines
251 A /trunk/tabix/tabix.1
255 ------------------------------------------------------------------------
256 r504 | lh3lh3 | 2009-11-02 11:08:18 -0500 (Mon, 02 Nov 2009) | 5 lines
258 M /trunk/tabix/Makefile
259 M /trunk/tabix/bgzip.c
260 M /trunk/tabix/index.c
261 M /trunk/tabix/main.c
262 M /trunk/tabix/tabix.h
264 * tabix-0.0.0-5 (r504)
265 * fixed a critical bug in fetching data (a typo in fact)
266 * support SAM (tested on ex1.sam) and VCF (not tested)
267 * improve the command-line interface
269 ------------------------------------------------------------------------
270 r503 | lh3lh3 | 2009-11-02 10:04:43 -0500 (Mon, 02 Nov 2009) | 3 lines
272 M /trunk/tabix/Makefile
273 M /trunk/tabix/index.c
274 M /trunk/tabix/main.c
276 * tabix-0.0.0-4 (r503)
277 * index files are bgzf compressed
279 ------------------------------------------------------------------------
280 r502 | lh3lh3 | 2009-11-02 09:47:25 -0500 (Mon, 02 Nov 2009) | 4 lines
282 M /trunk/tabix/index.c
283 M /trunk/tabix/main.c
284 M /trunk/tabix/tabix.h
286 * tabix-0.0.0-3 (r502)
287 * support meta lines (not tested)
288 * I am going to make the index file in the BGZF format
290 ------------------------------------------------------------------------
291 r501 | lh3lh3 | 2009-11-01 22:03:07 -0500 (Sun, 01 Nov 2009) | 3 lines
293 M /trunk/tabix/Makefile
294 M /trunk/tabix/bgzf.h
295 M /trunk/tabix/index.c
296 M /trunk/tabix/main.c
298 * tabix-0.0.0-2 (r501)
299 * accelerate ti_readline()
301 ------------------------------------------------------------------------
302 r500 | lh3lh3 | 2009-11-01 20:49:52 -0500 (Sun, 01 Nov 2009) | 3 lines
304 M /trunk/tabix/Makefile
305 M /trunk/tabix/bgzip.c
306 M /trunk/tabix/index.c
307 M /trunk/tabix/main.c
309 * tabix-0.0.0-1 (r500)
312 ------------------------------------------------------------------------
313 r499 | lh3lh3 | 2009-11-01 14:04:52 -0500 (Sun, 01 Nov 2009) | 2 lines
315 D /trunk/tabix/parser.c
319 ------------------------------------------------------------------------
320 r498 | lh3lh3 | 2009-11-01 14:04:08 -0500 (Sun, 01 Nov 2009) | 2 lines
322 M /trunk/tabix/bgzip.c
324 bgzip is more like gzip in its command-line interface
326 ------------------------------------------------------------------------
327 r497 | lh3lh3 | 2009-11-01 13:43:35 -0500 (Sun, 01 Nov 2009) | 2 lines
329 A /trunk/tabix/Makefile
330 A /trunk/tabix/bam_endian.h
331 A /trunk/tabix/bgzf.c
332 A /trunk/tabix/bgzf.h
333 A /trunk/tabix/bgzip.c
334 A /trunk/tabix/index.c
335 A /trunk/tabix/khash.h
336 A /trunk/tabix/knetfile.c
337 A /trunk/tabix/knetfile.h
338 A /trunk/tabix/ksort.h
339 A /trunk/tabix/kstring.c
340 A /trunk/tabix/kstring.h
341 A /trunk/tabix/main.c
342 A /trunk/tabix/parser.c
343 A /trunk/tabix/tabix.h
345 initial source code. It is BUGGY!
347 ------------------------------------------------------------------------
348 r496 | lh3lh3 | 2009-11-01 13:42:39 -0500 (Sun, 01 Nov 2009) | 2 lines
352 A generic indexer for TAB-delimited genome position files
354 ------------------------------------------------------------------------