Mercurial > repos > dawe > srf2fastq
comparison srf2fastq/io_lib-1.12.2/ChangeLog @ 0:d901c9f41a6a default tip
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
author | dawe |
---|---|
date | Tue, 07 Jun 2011 17:48:05 -0400 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:d901c9f41a6a |
---|---|
1 =============================================================================== | |
2 2009-07-29: RELEASE 1.12.2 | |
3 | |
4 ------------------------------------------------------------------------ | |
5 r1952 | jkbonfield | 2010-01-14 17:28:02 +0000 (Thu, 14 Jan 2010) | 2 lines | |
6 Changed paths: | |
7 M /io_lib/trunk/CHANGES | |
8 M /io_lib/trunk/README | |
9 M /io_lib/trunk/configure.in | |
10 | |
11 Updates to produce 1.12.2 | |
12 | |
13 ------------------------------------------------------------------------ | |
14 r1951 | jkbonfield | 2010-01-14 17:21:14 +0000 (Thu, 14 Jan 2010) | 3 lines | |
15 Changed paths: | |
16 M /io_lib/trunk/io_lib/os.h | |
17 | |
18 Guarded HAVE_* definitions behind #ifndef checks to avoid warnings in | |
19 certain cases. | |
20 | |
21 ------------------------------------------------------------------------ | |
22 r1950 | jkbonfield | 2010-01-14 16:44:42 +0000 (Thu, 14 Jan 2010) | 5 lines | |
23 Changed paths: | |
24 M /io_lib/trunk/man/man1/srf2fastq.1 | |
25 M /io_lib/trunk/progs/srf2fastq.c | |
26 | |
27 Added -r option as requested in source forge Patch ID: 2926627, as | |
28 suggested by jmendler. | |
29 | |
30 The exact implementation differs in minor ways. | |
31 ------------------------------------------------------------------------ | |
32 r1939 | jkbonfield | 2010-01-07 09:36:18 +0000 (Thu, 07 Jan 2010) | 3 lines | |
33 Changed paths: | |
34 M /io_lib/trunk/progs/srf2fasta.c | |
35 M /io_lib/trunk/progs/srf2fastq.c | |
36 M /io_lib/trunk/progs/srf_extract_hash.c | |
37 | |
38 Fixed the usage() function to exit 1 instead of 0. | |
39 (Patch from Jordan Mendler) | |
40 | |
41 ------------------------------------------------------------------------ | |
42 r1930 | jkbonfield | 2009-12-03 14:04:01 +0000 (Thu, 03 Dec 2009) | 7 lines | |
43 Changed paths: | |
44 M /io_lib/trunk/io_lib/sff.c | |
45 | |
46 Fixed a bug in read_sff_read_data (with thanks to Tim Massingham). | |
47 After reading the data the function did not pad out to the next 8-byte | |
48 boundary. | |
49 | |
50 This only surfaces when using the library from your own tools as the | |
51 programs supplied with io_lib never read more than a single sff read. | |
52 | |
53 ------------------------------------------------------------------------ | |
54 r1924 | jkbonfield | 2009-11-23 12:20:18 +0000 (Mon, 23 Nov 2009) | 6 lines | |
55 Changed paths: | |
56 M /io_lib/trunk/progs/srf2fastq.c | |
57 | |
58 Applied patch from Jordan Mendler: | |
59 https://sourceforge.net/tracker/index.php?func=detail&aid=2900087&group_id=100316&atid=627060 | |
60 | |
61 This adds a -S (sequential) option to srf2fastq to interleave forward | |
62 and reverse fragments in the same output file as desired by BFast. | |
63 | |
64 ------------------------------------------------------------------------ | |
65 r1851 | daviesrob | 2009-10-02 10:29:05 +0100 (Fri, 02 Oct 2009) | 1 line | |
66 Changed paths: | |
67 M /io_lib/trunk/progs/srf2fastq.c | |
68 | |
69 Fixed buffer overrun in parse_regn | |
70 ------------------------------------------------------------------------ | |
71 r1850 | daviesrob | 2009-10-02 10:02:30 +0100 (Fri, 02 Oct 2009) | 1 line | |
72 Changed paths: | |
73 M /io_lib/trunk/progs/srf_info.c | |
74 | |
75 Fixed buffer overrun in parse_regn | |
76 ------------------------------------------------------------------------ | |
77 r1834 | daviesrob | 2009-09-11 17:48:32 +0100 (Fri, 11 Sep 2009) | 1 line | |
78 Changed paths: | |
79 M /io_lib/trunk/Makefile.am | |
80 M /io_lib/trunk/io_lib/ztr.c | |
81 | |
82 Added pooled_alloc.h to list of include files to install. Fixed | |
83 ztr_add_text so | |
84 that it leaves two NUL bytes on the end of the TEXT chunk, as | |
85 documented in the | |
86 ZTR specification. | |
87 ------------------------------------------------------------------------ | |
88 r1813 | daviesrob | 2009-09-01 12:37:37 +0100 (Tue, 01 Sep 2009) | 1 line | |
89 Changed paths: | |
90 M /io_lib/trunk/io_lib/Makefile.am | |
91 M /io_lib/trunk/io_lib/hash_table.c | |
92 M /io_lib/trunk/io_lib/hash_table.h | |
93 A /io_lib/trunk/io_lib/pooled_alloc.c | |
94 A /io_lib/trunk/io_lib/pooled_alloc.h | |
95 M /io_lib/trunk/io_lib/srf.c | |
96 M /io_lib/trunk/io_lib/srf.h | |
97 | |
98 Added HASH_POOL_ITEMS option to hash table code to allocate HashItems | |
99 in pools, | |
100 which reduces malloc overhead in big hash tables. Also made | |
101 srf_index_add_trace | |
102 _body use pooled storage for trace names. | |
103 | |
104 | |
105 =============================================================================== | |
106 2009-07-29: RELEASE 1.12.1 | |
107 | |
108 ------------------------------------------------------------------------ | |
109 r1806 | jkbonfield | 2009-08-07 16:46:20 +0100 (Fri, 07 Aug 2009) | 1 line | |
110 Changed paths: | |
111 M /io_lib/trunk/README | |
112 M /io_lib/trunk/configure.in | |
113 | |
114 Updated version to 1.12.1 | |
115 ------------------------------------------------------------------------ | |
116 r1805 | jkbonfield | 2009-08-07 16:18:28 +0100 (Fri, 07 Aug 2009) | 1 line | |
117 Changed paths: | |
118 M /io_lib/trunk/Makefile.am | |
119 M /io_lib/trunk/README | |
120 | |
121 Minor edit | |
122 ------------------------------------------------------------------------ | |
123 r1792 | jkbonfield | 2009-08-03 11:58:49 +0100 (Mon, 03 Aug 2009) | 4 lines | |
124 Changed paths: | |
125 M /io_lib/trunk/io_lib/os.h | |
126 | |
127 Moved the autoconf detection of endianness to the start of os.h. This | |
128 means that machine/compiler testing #ifdefs take precedence, allowing | |
129 for cross-compilation and "fat" binaries on MacOS X. | |
130 | |
131 ------------------------------------------------------------------------ | |
132 r1791 | jkbonfield | 2009-08-03 11:56:50 +0100 (Mon, 03 Aug 2009) | 2 lines | |
133 Changed paths: | |
134 M /io_lib/trunk/tests/Makefile.am | |
135 M /io_lib/trunk/tests/srf_index.test | |
136 | |
137 Minor tweaks to checks/dist. | |
138 | |
139 ------------------------------------------------------------------------ | |
140 r1789 | jkbonfield | 2009-07-31 12:17:27 +0100 (Fri, 31 Jul 2009) | 2 lines | |
141 Changed paths: | |
142 M /io_lib/trunk/io_lib-config.in | |
143 | |
144 Fixed -lread to be -lstaden-read | |
145 | |
146 ------------------------------------------------------------------------ | |
147 r1780 | jkbonfield | 2009-07-29 10:07:56 +0100 (Wed, 29 Jul 2009) | 2 lines | |
148 Changed paths: | |
149 M /io_lib/trunk/CHANGES | |
150 M /io_lib/trunk/ChangeLog | |
151 M /io_lib/trunk/README | |
152 | |
153 Minor updates to state version 1.12.0 | |
154 | |
155 | |
156 =============================================================================== | |
157 2009-07-29: RELEASE 1.12.0 | |
158 | |
159 ------------------------------------------------------------------------ | |
160 r1779 | jkbonfield | 2009-07-29 09:53:33 +0100 (Wed, 29 Jul 2009) | 2 lines | |
161 Changed paths: | |
162 M /io_lib/trunk/Makefile.am | |
163 | |
164 The man1 pages are now installed too. | |
165 | |
166 ------------------------------------------------------------------------ | |
167 r1778 | jkbonfield | 2009-07-28 17:42:26 +0100 (Tue, 28 Jul 2009) | 2 lines | |
168 Changed paths: | |
169 M /io_lib/trunk/tests/Makefile.am | |
170 D /io_lib/trunk/tests/data/.params | |
171 A /io_lib/trunk/tests/data/both.info (from /io_lib/trunk/tests/data/slx_out/both.info:1776) | |
172 A /io_lib/trunk/tests/data/both.run (from /io_lib/trunk/tests/data/slx_out/both.run:1776) | |
173 A /io_lib/trunk/tests/data/both.srf (from /io_lib/trunk/tests/data/slx_out/both.srf:1776) | |
174 A /io_lib/trunk/tests/data/proc.info (from /io_lib/trunk/tests/data/slx_out/proc.info:1776) | |
175 A /io_lib/trunk/tests/data/proc.srf (from /io_lib/trunk/tests/data/slx_out/proc.srf:1776) | |
176 A /io_lib/trunk/tests/data/proc.srf.indexed (from /io_lib/trunk/tests/data/slx_out/proc.srf.indexed:1776) | |
177 A /io_lib/trunk/tests/data/raw.info (from /io_lib/trunk/tests/data/slx_out/raw.info:1776) | |
178 A /io_lib/trunk/tests/data/raw.srf (from /io_lib/trunk/tests/data/slx_out/raw.srf:1776) | |
179 A /io_lib/trunk/tests/data/slx-C.fasta (from /io_lib/trunk/tests/data/slx_out/slx-C.fasta:1776) | |
180 A /io_lib/trunk/tests/data/slx-C.fastq (from /io_lib/trunk/tests/data/slx_out/slx-C.fastq:1776) | |
181 A /io_lib/trunk/tests/data/slx.fasta (from /io_lib/trunk/tests/data/slx_out/slx.fasta:1776) | |
182 A /io_lib/trunk/tests/data/slx.fastq (from /io_lib/trunk/tests/data/slx_out/slx.fastq:1776) | |
183 D /io_lib/trunk/tests/data/slx_in | |
184 D /io_lib/trunk/tests/data/slx_out | |
185 A /io_lib/trunk/tests/data/test_run_4_134_369_182.srf (from /io_lib/trunk/tests/data/slx_out/test_run_4_134_369_182.srf:1776) | |
186 A /io_lib/trunk/tests/data/traces.srf (from /io_lib/trunk/tests/data/slx_out/traces.srf:1776) | |
187 D /io_lib/trunk/tests/illumina2srf.test | |
188 M /io_lib/trunk/tests/srf2fasta.test | |
189 M /io_lib/trunk/tests/srf2fastq.test | |
190 D /io_lib/trunk/tests/srf2illumina.test | |
191 M /io_lib/trunk/tests/srf_filter.test | |
192 M /io_lib/trunk/tests/srf_index.test | |
193 M /io_lib/trunk/tests/srf_info.test | |
194 | |
195 Updated tests now that srf2illumina and illumina2srf have been removed. | |
196 | |
197 ------------------------------------------------------------------------ | |
198 r1777 | jkbonfield | 2009-07-28 16:44:43 +0100 (Tue, 28 Jul 2009) | 3 lines | |
199 Changed paths: | |
200 D /io_lib/trunk/Makefile | |
201 M /io_lib/trunk/bootstrap | |
202 D /io_lib/trunk/io_lib/Makefile | |
203 D /io_lib/trunk/progs/Makefile | |
204 | |
205 Removed remnant Makefiles from the old staden package build | |
206 system. All we have left now is the autoconf build files. | |
207 | |
208 ------------------------------------------------------------------------ | |
209 r1775 | jkbonfield | 2009-07-28 16:37:18 +0100 (Tue, 28 Jul 2009) | 8 lines | |
210 Changed paths: | |
211 A /io_lib/branches | |
212 A /io_lib/tags | |
213 A /io_lib/trunk | |
214 A /io_lib/trunk/CHANGES (from /staden/trunk/src/io_lib/CHANGES:1774) | |
215 A /io_lib/trunk/COPYRIGHT (from /staden/trunk/src/io_lib/COPYRIGHT:1774) | |
216 A /io_lib/trunk/ChangeLog (from /staden/trunk/src/io_lib/ChangeLog:1774) | |
217 A /io_lib/trunk/Makefile (from /staden/trunk/src/io_lib/Makefile:1774) | |
218 A /io_lib/trunk/Makefile.am (from /staden/trunk/src/io_lib/Makefile.am:1774) | |
219 A /io_lib/trunk/README (from /staden/trunk/src/io_lib/README:1774) | |
220 A /io_lib/trunk/acinclude.m4 (from /staden/trunk/src/io_lib/acinclude.m4:1774) | |
221 A /io_lib/trunk/bootstrap (from /staden/trunk/src/io_lib/bootstrap:1774) | |
222 A /io_lib/trunk/configure.in (from /staden/trunk/src/io_lib/configure.in:1774) | |
223 A /io_lib/trunk/dependencies (from /staden/trunk/src/io_lib/dependencies:1774) | |
224 A /io_lib/trunk/docs (from /staden/trunk/src/io_lib/docs:1774) | |
225 A /io_lib/trunk/include (from /staden/trunk/src/io_lib/include:1774) | |
226 A /io_lib/trunk/io_lib (from /staden/trunk/src/io_lib/io_lib:1774) | |
227 A /io_lib/trunk/io_lib-config.in (from /staden/trunk/src/io_lib/io_lib-config.in:1774) | |
228 A /io_lib/trunk/io_lib.m4 (from /staden/trunk/src/io_lib/io_lib.m4:1774) | |
229 A /io_lib/trunk/man (from /staden/trunk/src/io_lib/man:1774) | |
230 A /io_lib/trunk/options.mk (from /staden/trunk/src/io_lib/options.mk:1774) | |
231 A /io_lib/trunk/progs (from /staden/trunk/src/io_lib/progs:1774) | |
232 A /io_lib/trunk/tests (from /staden/trunk/src/io_lib/tests:1774) | |
233 D /staden/trunk/src/io_lib/CHANGES | |
234 D /staden/trunk/src/io_lib/COPYRIGHT | |
235 D /staden/trunk/src/io_lib/ChangeLog | |
236 D /staden/trunk/src/io_lib/Makefile | |
237 D /staden/trunk/src/io_lib/Makefile.am | |
238 D /staden/trunk/src/io_lib/README | |
239 D /staden/trunk/src/io_lib/acinclude.m4 | |
240 D /staden/trunk/src/io_lib/bootstrap | |
241 D /staden/trunk/src/io_lib/configure.in | |
242 D /staden/trunk/src/io_lib/dependencies | |
243 D /staden/trunk/src/io_lib/docs | |
244 D /staden/trunk/src/io_lib/include | |
245 D /staden/trunk/src/io_lib/io_lib | |
246 D /staden/trunk/src/io_lib/io_lib-config.in | |
247 D /staden/trunk/src/io_lib/io_lib.m4 | |
248 D /staden/trunk/src/io_lib/man | |
249 D /staden/trunk/src/io_lib/options.mk | |
250 D /staden/trunk/src/io_lib/progs | |
251 D /staden/trunk/src/io_lib/tests | |
252 | |
253 Moved io_lib from staden source tree into it's own top-level | |
254 subversion directory, complete with tags, branches, and trunk. | |
255 | |
256 For now the old tagged copies of io_lib are still in the staden/tags/ | |
257 directory with tag names io_lib-<version>, but that is perhaps right | |
258 and proper (as it's where the code actually resided at that release | |
259 number). | |
260 | |
261 ------------------------------------------------------------------------ | |
262 r1772 | jkbonfield | 2009-07-28 15:32:58 +0100 (Tue, 28 Jul 2009) | 4 lines | |
263 Changed paths: | |
264 M /staden/trunk/src/io_lib/progs/Makefile.am | |
265 D /staden/trunk/src/io_lib/progs/solexa2srf.c | |
266 D /staden/trunk/src/io_lib/progs/srf2solexa.c | |
267 | |
268 Removed Illumina/Solexa specific programs. These are now out of date | |
269 with respect to Illumina's own fork, plus I don't think they belong in | |
270 the largely platform agnostic library. | |
271 | |
272 ------------------------------------------------------------------------ | |
273 r1771 | jkbonfield | 2009-07-28 12:44:07 +0100 (Tue, 28 Jul 2009) | 7 | |
274 lines | |
275 Changed paths: | |
276 M /staden/trunk/src/io_lib/CHANGES | |
277 M /staden/trunk/src/io_lib/ChangeLog | |
278 M /staden/trunk/src/io_lib/README | |
279 M /staden/trunk/src/io_lib/configure.in | |
280 M /staden/trunk/src/io_lib/io_lib/Makefile.am | |
281 | |
282 Preparations for 1.12.0 release. | |
283 | |
284 There is now proper versioning support for the library too. The soname | |
285 used here is libstaden-read.so.1, to distinguish from any earlier | |
286 dynamic libraries. (The ABI definitely has changed over the years in | |
287 incompatible manners.) | |
288 | |
289 ------------------------------------------------------------------------ | |
290 r1770 | jkbonfield | 2009-07-28 09:17:29 +0100 (Tue, 28 Jul 2009) | 1 line | |
291 Changed paths: | |
292 M /staden/trunk/src/io_lib/tests/data/slx_out/both.info | |
293 M /staden/trunk/src/io_lib/tests/data/slx_out/raw.info | |
294 | |
295 Updated for new format srf_info output | |
296 ------------------------------------------------------------------------ | |
297 r1769 | jkbonfield | 2009-07-28 09:16:11 +0100 (Tue, 28 Jul 2009) | 2 lines | |
298 Changed paths: | |
299 M /staden/trunk/src/io_lib/tests/data/slx_out/proc.info | |
300 | |
301 Updated with new format output. | |
302 | |
303 ------------------------------------------------------------------------ | |
304 r1768 | jkbonfield | 2009-07-27 17:49:44 +0100 (Mon, 27 Jul 2009) | 2 lines | |
305 Changed paths: | |
306 M /staden/trunk/src/io_lib/io_lib/vlen.c | |
307 | |
308 Include os.h so we can pick up NEED_VA_COPY definition. | |
309 | |
310 ------------------------------------------------------------------------ | |
311 r1767 | jkbonfield | 2009-07-27 17:48:37 +0100 (Mon, 27 Jul 2009) | 5 lines | |
312 Changed paths: | |
313 M /staden/trunk/src/io_lib/progs/srf_filter.c | |
314 | |
315 Reorganisation to allow chunks to be added as well as removed. At | |
316 present this only supports adding REGN chunks. | |
317 | |
318 (Patch supplied by Steven Leonard.) | |
319 | |
320 ------------------------------------------------------------------------ | |
321 r1766 | jkbonfield | 2009-07-27 17:46:07 +0100 (Mon, 27 Jul 2009) | 3 lines | |
322 Changed paths: | |
323 M /staden/trunk/src/io_lib/progs/index_tar.c | |
324 | |
325 Handle GNU tar extensions: LongLink notation. | |
326 (Patch supplied by Steven Leonard). | |
327 | |
328 ------------------------------------------------------------------------ | |
329 r1765 | jkbonfield | 2009-07-27 17:45:16 +0100 (Mon, 27 Jul 2009) | 4 lines | |
330 Changed paths: | |
331 M /staden/trunk/src/io_lib/progs/srf2fasta.c | |
332 M /staden/trunk/src/io_lib/progs/srf2fastq.c | |
333 M /staden/trunk/src/io_lib/progs/srf_extract_hash.c | |
334 | |
335 Changed the maximum read length from 1024 to 10000. This allows for | |
336 capillary traces to be stored in SRF. | |
337 (Patch supplied by Steven Leonard) | |
338 | |
339 ------------------------------------------------------------------------ | |
340 r1764 | jkbonfield | 2009-07-27 17:43:36 +0100 (Mon, 27 Jul 2009) | 3 lines | |
341 Changed paths: | |
342 M /staden/trunk/src/io_lib/progs/srf_info.c | |
343 | |
344 Use int64_t instead of long for base counts and chunk sizes. | |
345 (Supplied by Steven Leonard.) | |
346 | |
347 ------------------------------------------------------------------------ | |
348 r1763 | jkbonfield | 2009-07-27 16:49:10 +0100 (Mon, 27 Jul 2009) | 3 lines | |
349 Changed paths: | |
350 M /staden/trunk/src/io_lib/man/man1/srf_info.1 | |
351 M /staden/trunk/src/io_lib/progs/srf_info.c | |
352 | |
353 Added compressed chunk size to the per-chunk type output. This allows | |
354 us to see what takes up the most storage in an SRF. | |
355 | |
356 ------------------------------------------------------------------------ | |
357 r1762 | jkbonfield | 2009-07-27 16:47:20 +0100 (Mon, 27 Jul 2009) | 1 line | |
358 Changed paths: | |
359 M /staden/trunk/src/io_lib/io_lib/ztr.c | |
360 | |
361 removed C9Xism | |
362 | |
363 ------------------------------------------------------------------------ | |
364 r1761 | jkbonfield | 2009-07-27 15:01:16 +0100 (Mon, 27 Jul 2009) | 5 lines | |
365 Changed paths: | |
366 M /staden/trunk/src/io_lib/configure.in | |
367 M /staden/trunk/src/io_lib/io_lib/Makefile.am | |
368 M /staden/trunk/src/io_lib/progs/Makefile.am | |
369 | |
370 Re-enabled libtool, with a workaround to remove the infuriating rpath | |
371 nonsense. (It's now 2x slower to configure, 3x slower to compile and | |
372 10x more anguish to debug, but at least I can sleep at night knowing | |
373 rpath hasn't had it's wicked way with the code.) | |
374 | |
375 ------------------------------------------------------------------------ | |
376 r1756 | jkbonfield | 2009-07-24 10:27:29 +0100 (Fri, 24 Jul 2009) | 5 lines | |
377 Changed paths: | |
378 M /staden/trunk/src/Makefile.in | |
379 A /staden/trunk/src/io_lib/io_lib/Makefile | |
380 | |
381 Added a Makefile for io_lib/io_lib; so the library itself. This isn't | |
382 expected to be used normally, but it allows me to test local copies of | |
383 io_lib (under a different library name) in conjunction with the staden | |
384 source tree before releasing either. | |
385 | |
386 ------------------------------------------------------------------------ | |
387 r1723 | jkbonfield | 2009-06-22 12:38:26 +0100 (Mon, 22 Jun 2009) | 2 lines | |
388 Changed paths: | |
389 M /staden/trunk/src/io_lib/io_lib/ztr_translate.c | |
390 | |
391 Gracefully handle the case of a trace with no BPOS chunk in ztr2read(). | |
392 | |
393 ------------------------------------------------------------------------ | |
394 r1722 | jkbonfield | 2009-06-22 12:37:32 +0100 (Mon, 22 Jun 2009) | 2 lines | |
395 Changed paths: | |
396 M /staden/trunk/src/io_lib/io_lib/hash_table.c | |
397 M /staden/trunk/src/io_lib/io_lib/hash_table.h | |
398 | |
399 Added the hash table iterator functions (copied from Gap5's hache tables). | |
400 | |
401 ------------------------------------------------------------------------ | |
402 r1721 | jkbonfield | 2009-06-22 12:36:52 +0100 (Mon, 22 Jun 2009) | 2 lines | |
403 Changed paths: | |
404 M /staden/trunk/src/io_lib/io_lib/deflate_interlaced.c | |
405 | |
406 Fixed a memory allocation issue of codes2codeset(). | |
407 | |
408 ------------------------------------------------------------------------ | |
409 r1720 | jkbonfield | 2009-06-22 12:35:21 +0100 (Mon, 22 Jun 2009) | 4 lines | |
410 Changed paths: | |
411 M /staden/trunk/src/io_lib/Makefile | |
412 | |
413 Remove use of curl-config --libs. While useful for linking against | |
414 static libraries, it just adds unwanted dependencies in a dynamic | |
415 build environment. | |
416 | |
417 ------------------------------------------------------------------------ | |
418 r1596 | jkbonfield | 2009-04-20 12:34:23 +0100 (Mon, 20 Apr 2009) | 6 lines | |
419 Changed paths: | |
420 M /staden/trunk/src/io_lib/io_lib/compress.c | |
421 M /staden/trunk/src/io_lib/io_lib/compress.h | |
422 | |
423 Made pipe2() internal as it's not used anywhere else yet. | |
424 | |
425 Also renamed from pipe2 to pipe_into. This resolves SF bug #2629155; | |
426 pipe2 has been added as a system function to glibc 2.9 as an interface | |
427 to the new (2.6.27+) kernel system call of the same name. | |
428 | |
429 ------------------------------------------------------------------------ | |
430 r1526 | jkbonfield | 2009-03-04 14:38:16 +0000 (Wed, 04 Mar 2009) | 5 lines | |
431 Changed paths: | |
432 M /staden/trunk/src/io_lib/progs/srf_info.c | |
433 | |
434 Fixed the same bug with mf_end and ztr_partial_decode from srf.c. | |
435 | |
436 Specifically a ZTR file with no chunks in the srf data block header | |
437 failed. | |
438 | |
439 ------------------------------------------------------------------------ | |
440 r1525 | jkbonfield | 2009-03-04 14:23:58 +0000 (Wed, 04 Mar 2009) | 4 lines | |
441 Changed paths: | |
442 M /staden/trunk/src/io_lib/io_lib/srf.c | |
443 | |
444 Bug fix to srf_next_ztr_flags. When faced with a ZTR header with no | |
445 ZTR chunks in the srf data block header it erroneously set mf_end to | |
446 zero instead of the actual length. | |
447 | |
448 ------------------------------------------------------------------------ | |
449 r1455 | jkbonfield | 2009-01-22 17:19:25 +0000 (Thu, 22 Jan 2009) | 3 lines | |
450 Changed paths: | |
451 M /staden/trunk/src/io_lib/io_lib/array.c | |
452 M /staden/trunk/src/io_lib/io_lib/array.h | |
453 | |
454 Updated the Array struct to use size_t, matching the copy in Misc (yes | |
455 I know, multiple variants is asking for trouble). | |
456 | |
457 ------------------------------------------------------------------------ | |
458 r1428 | jkbonfield | 2008-12-11 10:22:25 +0000 (Thu, 11 Dec 2008) | 3 lines | |
459 Changed paths: | |
460 M /staden/trunk/src/io_lib/progs/srf2solexa.c | |
461 | |
462 Changed dump_qcal so it handles negative log-odds scores. In practice | |
463 I've never seen these occur with the 1.0 solexa pipeline release though. | |
464 | |
465 | |
466 =============================================================================== | |
467 2008-12-10 James Bonfield <jkb@sanger.ac.uk> | |
468 | |
469 * 1.11.6.1 released. | |
470 | |
471 * progs/solexa2srf.c: | |
472 Removal of debugging output. | |
473 | |
474 2008-12-10 James Bonfield <jkb@sanger.ac.uk> | |
475 | |
476 * 1.11.6 released. | |
477 | |
478 2008-12-10 jkbonfield <jkb@sanger.ac.uk> | |
479 | |
480 * progs/solexa2srf.c: | |
481 Fixed the add_qcal_chunk code so it doesn't assume that it can strlen | |
482 the binary quality string. | |
483 | |
484 * man/man1/srf2fastq.1, | |
485 * man/man1/srf_info.1: | |
486 (10:17:27) Updated to reflect newly added options. | |
487 | |
488 * progs/srf2fastq.c: | |
489 (10:19:25) Merged in changes from Steven Leonard. - Extra options | |
490 were added to provide explicit control over the read names | |
491 (whether to add /1, /2, ...) and filenames. - Renamed -p (primer) | |
492 as -e (explicit). | |
493 | |
494 * progs/srf_info.c: | |
495 (10:20:18) Merged in changes from Steven Leonard - Call srf_destroy | |
496 before exiting in various failure cases. This has no real impact | |
497 except to make it easier to look for real memory leaks. | |
498 | |
499 2008-12-09 jkbonfield <jkb@sanger.ac.uk> | |
500 | |
501 * progs/srf2fastq.c: | |
502 (10:20:00) Fixed an error with split file mode - it read past the | |
503 end of an array. | |
504 | |
505 We now check the SCALE option on CNF4 and CNF1 chunks and convert | |
506 the data accordingly to phred. | |
507 | |
508 * progs/solexa2srf.c: | |
509 (10:23:31) Merged in some of the changes made by Chris Saunders | |
510 from Illumina. | |
511 | |
512 Most significantly this now stores CNF1 data in log-odds format and | |
513 sets SCALE meta-data accordingly. This makes srf2illumina work | |
514 better as it doesn't go from log-odds to phred back to log-odds, | |
515 destroying data in rounding. | |
516 | |
517 * tests/data/slx_out/both.info, | |
518 * tests/data/slx_out/both.srf, | |
519 * tests/data/slx_out/proc.info, | |
520 * tests/data/slx_out/proc.srf, | |
521 * tests/data/slx_out/proc.srf.indexed, | |
522 * tests/data/slx_out/raw.info, | |
523 * tests/data/slx_out/raw.srf, | |
524 * tests/data/slx_out/test_run_4_134_369_182.srf, | |
525 * tests/data/slx_out/both.run/4_PROGRAM_ID.txt: | |
526 (12:26:13) Updated to accommodate illumina2srf version string | |
527 change. | |
528 | |
529 * progs/srf_filter.c: | |
530 (12:28:30) Bad case of missing braces! | |
531 | |
532 2008-12-08 jkbonfield <jkb@sanger.ac.uk> | |
533 | |
534 * io_lib/compression.c: | |
535 (12:32:38) Better error handling in tshift method | |
536 | |
537 * io_lib/compress.c, | |
538 * io_lib/compress.h: | |
539 (12:33:40) Added remove_extension() function. (Not yet used by | |
540 io_lib, but potentially handy and used by some external tools.) | |
541 (Steven Leonard) | |
542 | |
543 * progs/srf2solexa.c: | |
544 (12:34:38) Bug fixed the qcal conversion - now use the correct | |
545 lookup table and added .499 to match the rounding used in | |
546 solexa2srf.c. | |
547 | |
548 * progs/srf2fastq.c, | |
549 * progs/srf_filter.c, | |
550 * progs/srf_info.c: | |
551 (12:35:40) Merged in Steven Leonard's changes. | |
552 | |
553 These mainly involve better support for multiple index blocks in | |
554 SRF files (eg concatenated files), support for splitting output | |
555 files in srf2fastq, and extra reporting options in srf_info. | |
556 | |
557 * io_lib/ztr.c, | |
558 * io_lib/ztr.h: | |
559 (17:15:58) Added const to string params in ztr_add_text. | |
560 | |
561 * io_lib/srf.c, | |
562 * io_lib/srf.h: | |
563 (17:23:53) New function srf_next_ztr_flags. This is the same as the | |
564 old srf_next_ztr function except with the addition of an extra | |
565 argument into which the SRF Data Block 'flags' value is copied when | |
566 returning the next trace. | |
567 | |
568 =============================================================================== | |
569 2008-12-04 James Bonfield <jkb@sanger.ac.uk> | |
570 | |
571 * 1.11.5 released. | |
572 | |
573 2008-12-03 jkbonfield <jkb@sanger.ac.uk> | |
574 | |
575 * progs/solexa2srf.c: | |
576 (17:29:10) Fixed qcal format so it now correctly drops quality by | |
577 the 64 offset added in the fastq-a-like strings. | |
578 | |
579 Fixed a bug with the 2-file calibration mode (-qf and -qr). A | |
580 single combined -qf alone works fine, but when pasting the split | |
581 file mode (fwd + rev) a newline crept halfway into the quality | |
582 string causing the reverse qualities to be shifted by one. | |
583 | |
584 * progs/solexa2srf.c: | |
585 (17:29:56) Bumped version to 1.11 | |
586 | |
587 2008-12-02 jkbonfield <jkb@sanger.ac.uk> | |
588 | |
589 * progs/srf_filter.c: | |
590 (14:38:58) Removed some major memory leaks. | |
591 | |
592 * io_lib/srf.c, | |
593 * progs/srf_filter.c: | |
594 (15:01:04) More memory leak fixed (although tiny). | |
595 | |
596 2008-10-23 jkbonfield <jkb@sanger.ac.uk> | |
597 | |
598 * progs/hash_sff.c: | |
599 (14:08:19) Added support for outputting only the table of contents | |
600 to a new file without copying the existing sff files. This is | |
601 useful if we have the original sff files in an archive that we | |
602 cannot modify. | |
603 | |
604 2008-10-07 jkbonfield <jkb@sanger.ac.uk> | |
605 | |
606 * progs/Makefile.am: | |
607 (16:02:51) Added extract_fastq to the list of programs to build. | |
608 | |
609 2008-09-29 jkbonfield <jkb@sanger.ac.uk> | |
610 | |
611 * man/man1/illumina2srf.1, | |
612 * man/man1/srf2fasta.1, | |
613 * man/man1/srf2fastq.1, | |
614 * man/man1/srf_info.1, | |
615 * man/man1/srf_list.1: | |
616 (13:40:01) Added the first draft of several manual pages. | |
617 | |
618 * man/man1/illumina2srf.1: | |
619 (13:44:09) *** empty log message *** | |
620 | |
621 * progs/Makefile.am, | |
622 * progs/srf_list.c: | |
623 (14:00:22) Added new program: srf_list. This lists or counts the | |
624 sequence names within an SRF file. | |
625 | |
626 * io_lib/srf.c: | |
627 (14:01:38) The srf_next_block_details now uses the trace_body | |
628 struct held within the srf struct. This means it can be queried | |
629 after a successful call and is utilised by srf_list to obtain the | |
630 trace body size. | |
631 | |
632 * man/man1/srf_index_hash.1: | |
633 (14:08:36) First draft of man page. | |
634 | |
635 2008-09-18 jkbonfield <jkb@sanger.ac.uk> | |
636 | |
637 * progs/solexa2srf.c: | |
638 (12:59:37) Fixed a bug with parsing the directory name. If it fails | |
639 it left the run number in an inconsistent state. | |
640 | |
641 This shouldn't cause issues in production pipelines, but does if | |
642 you copy the files out of the run folders. | |
643 | |
644 * io_lib/srf.c, | |
645 * io_lib/srf.h, | |
646 * progs/solexa2srf.c: | |
647 (16:33:45) Overhauled the SRF indexing code. | |
648 | |
649 Much of the indexing code in srf_index_hash.c has been moved over | |
650 to srf.c so it can be used by other programs. An API has been | |
651 created too so it is now far easier to create, add to and save an | |
652 index. | |
653 | |
654 Added support for writing indexes in illumina2srf. Note that now if | |
655 no index is written we also write out 8 bytes of zero, indicating | |
656 the length of the index is zero. (This is required by more recent | |
657 versions of the SRF specification.) | |
658 | |
659 Still to do: tools such as srf_filter should be updating the index | |
660 (or at least removing the old ones). This will now be easier to do | |
661 with these code updates. | |
662 | |
663 Updated the tests to check the new illumina2srf -i option too. | |
664 | |
665 * progs/srf_index_hash.c, | |
666 * tests/illumina2srf.test, | |
667 * tests/srf_index.test, | |
668 * tests/data/slx_out/both.srf, | |
669 * tests/data/slx_out/proc.srf, | |
670 * tests/data/slx_out/raw.srf: | |
671 (16:33:46) Overhauled the SRF indexing code. | |
672 | |
673 Much of the indexing code in srf_index_hash.c has been moved over | |
674 to srf.c so it can be used by other programs. An API has been | |
675 created too so it is now far easier to create, add to and save an | |
676 index. | |
677 | |
678 Added support for writing indexes in illumina2srf. Note that now if | |
679 no index is written we also write out 8 bytes of zero, indicating | |
680 the length of the index is zero. (This is required by more recent | |
681 versions of the SRF specification.) | |
682 | |
683 Still to do: tools such as srf_filter should be updating the index | |
684 (or at least removing the old ones). This will now be easier to do | |
685 with these code updates. | |
686 | |
687 Updated the tests to check the new illumina2srf -i option too. | |
688 | |
689 =============================================================================== | |
690 2008-09-11 James Bonfield <jkb@sanger.ac.uk> | |
691 | |
692 * 1.11.4 released. | |
693 | |
694 2008-09-11 James Bonfield <jkb@sanger.ac.uk> | |
695 | |
696 * Makefile.am, | |
697 * bootstrap, | |
698 * configure.in: | |
699 (08:43:42) Updated for version number and inclusion of tests dir. | |
700 | |
701 * io_lib/Attic/Makefile.in: | |
702 (08:43:55) Removed due to being auto-generated from Makefile.am | |
703 | |
704 * io_lib/os.h: | |
705 (08:44:56) Tidy up of endianness detection. I split apart the | |
706 endian step from the os-components (no strdup, etc). Also changed | |
707 the order so that when using autoconf the automatically detected | |
708 settings override any existing assumptions from os.h. | |
709 | |
710 * io_lib/hash_table.h: | |
711 (08:46:10) Included sys/types.h for off_t type. | |
712 | |
713 * CHANGES, | |
714 * ChangeLog, | |
715 * README: | |
716 (10:25:27) Final tweaks for preparing 1.11.4 | |
717 | |
718 * io_lib/srf.h: | |
719 (10:52:37) Changed block_type from char to int. This cures a | |
720 problem on PowerMac (PPC) running Debian where char is by default | |
721 an unsigned type, meaning it cannot be compared to EOF (-1). | |
722 | |
723 * tests/srf_index.test, | |
724 * tests/data/slx_out/Attic/test_run:4:134:369:182.srf, | |
725 * tests/data/slx_out/test_run_4_134_369_182.srf: | |
726 (11:09:11) Renamed test_run:4:134:369:182.srf to | |
727 test_run_4_134_369_182.srf as Windows cannot cope with colons in | |
728 filenames, causing the tar file to fail to unpack. Grrr. | |
729 | |
730 * Makefile.am, | |
731 * io_lib/srf.c, | |
732 * progs/solexa2srf.c, | |
733 * progs/srf2fasta.c, | |
734 * progs/srf2fastq.c, | |
735 * progs/srf2solexa.c, | |
736 * progs/srf_dump_all.c, | |
737 * progs/srf_extract_linear.c, | |
738 * tests/Makefile.am, | |
739 * tests/srf_index.test, | |
740 * tests/srf_info.test: | |
741 (15:25:29) A variety of changes to make the code work correctly | |
742 using msys/mingw on Windows. These mainly revolve around binary | |
743 mode and nl/cr issues. | |
744 | |
745 2008-09-10 James Bonfield <jkb@sanger.ac.uk> | |
746 | |
747 * tests/Makefile.am, | |
748 * tests/illumina2srf.test, | |
749 * tests/srf2fasta.test, | |
750 * tests/srf2fastq.test, | |
751 * tests/srf2illumina.test, | |
752 * tests/srf_filter.test, | |
753 * tests/srf_index.test, | |
754 * tests/srf_info.test, | |
755 * tests/data/.params, | |
756 * tests/data/slx_in/.params, | |
757 * tests/data/slx_in/s_4_0133_int.txt.gz, | |
758 * tests/data/slx_in/s_4_0133_nse.txt.gz, | |
759 * tests/data/slx_in/s_4_0134_int.txt.gz, | |
760 * tests/data/slx_in/s_4_0134_nse.txt.gz, | |
761 * tests/data/slx_in/Bustard1.9.5_28-08-2008_auto/s_4_0133_prb.txt, | |
762 * tests/data/slx_in/Bustard1.9.5_28-08-2008_auto/s_4_0133_qhg.txt, | |
763 * tests/data/slx_in/Bustard1.9.5_28-08-2008_auto/s_4_0133_seq.txt, | |
764 * tests/data/slx_in/Bustard1.9.5_28-08-2008_auto/s_4_0133_sig2.txt, | |
765 * tests/data/slx_in/Bustard1.9.5_28-08-2008_auto/s_4_0134_prb.txt, | |
766 * tests/data/slx_in/Bustard1.9.5_28-08-2008_auto/s_4_0134_qhg.txt, | |
767 * tests/data/slx_in/Bustard1.9.5_28-08-2008_auto/s_4_0134_seq.txt, | |
768 * tests/data/slx_in/Bustard1.9.5_28-08-2008_auto/s_4_0134_sig2.txt, | |
769 * tests/data/slx_in/Bustard1.9.5_28-08-2008_auto/Phasing/s_4_01_phasing.xml, | |
770 * tests/data/slx_in/Matrix/s_4_02_matrix.txt, | |
771 * tests/data/slx_out/both.info, | |
772 * tests/data/slx_out/both.srf, | |
773 * tests/data/slx_out/proc.info, | |
774 * tests/data/slx_out/proc.srf, | |
775 * tests/data/slx_out/proc.srf.indexed, | |
776 * tests/data/slx_out/raw.info, | |
777 * tests/data/slx_out/raw.srf, | |
778 * tests/data/slx_out/slx-C.fasta, | |
779 * tests/data/slx_out/slx-C.fastq, | |
780 * tests/data/slx_out/slx.fasta, | |
781 * tests/data/slx_out/slx.fastq, | |
782 * tests/data/slx_out/test_run:4:134:369:182.srf, | |
783 * tests/data/slx_out/traces.srf, | |
784 * tests/data/slx_out/both.run/4_ILLUMINA_GA_BUSTARD_PARAMS.txt, | |
785 * tests/data/slx_out/both.run/4_ILLUMINA_GA_CHASTITY.txt: | |
786 (15:53:41) First pass at a "make check" target. Currently this is | |
787 centred around the newer code, specifically SRF support. | |
788 | |
789 * tests/data/slx_out/both.run/4_ILLUMINA_GA_FIRECREST_PARAMS.txt, | |
790 * tests/data/slx_out/both.run/4_ILLUMINA_GA_MATRIX_FWD.txt, | |
791 * tests/data/slx_out/both.run/4_ILLUMINA_GA_PHASING_FWD.txt, | |
792 * tests/data/slx_out/both.run/4_PROGRAM_ID.txt, | |
793 * tests/data/slx_out/both.run/s_4_0133_int.txt, | |
794 * tests/data/slx_out/both.run/s_4_0133_nse.txt, | |
795 * tests/data/slx_out/both.run/s_4_0133_prb.txt, | |
796 * tests/data/slx_out/both.run/s_4_0133_seq.txt, | |
797 * tests/data/slx_out/both.run/s_4_0133_sig2.txt, | |
798 * tests/data/slx_out/both.run/s_4_0134_int.txt, | |
799 * tests/data/slx_out/both.run/s_4_0134_nse.txt, | |
800 * tests/data/slx_out/both.run/s_4_0134_prb.txt, | |
801 * tests/data/slx_out/both.run/s_4_0134_seq.txt, | |
802 * tests/data/slx_out/both.run/s_4_0134_sig2.txt: | |
803 (15:53:42) First pass at a "make check" target. Currently this is | |
804 centred around the newer code, specifically SRF support. | |
805 | |
806 * tests/Makefile.am, | |
807 * tests/illumina2srf.test, | |
808 * tests/srf2fasta.test, | |
809 * tests/srf2fastq.test, | |
810 * tests/srf2illumina.test, | |
811 * tests/srf_filter.test, | |
812 * tests/srf_index.test, | |
813 * tests/srf_info.test: | |
814 (16:13:19) Fixed tests to use $outdir for output directory so we | |
815 can neatly tidy it up for make distclean. Without this make | |
816 distcheck fails. | |
817 | |
818 * tests/Makefile.am, | |
819 * tests/illumina2srf.test, | |
820 * tests/srf2fasta.test, | |
821 * tests/srf2fastq.test, | |
822 * tests/srf2illumina.test, | |
823 * tests/srf_filter.test, | |
824 * tests/srf_index.test, | |
825 * tests/srf_info.test: | |
826 (16:43:33) Fixed some bashisms and switched to make use of srcdir | |
827 instead of top_srcdir/tests. | |
828 | |
829 2008-09-09 James Bonfield <jkb@sanger.ac.uk> | |
830 | |
831 * acinclude.m4: | |
832 (13:27:35) Fixed the LIBCURL_CHECK_CONFIG code to not believe the | |
833 output from "curl-config --libs". We try -lcurl first off to see if | |
834 that also works. The reason is simply that curl-config --libs | |
835 typically loves to explicitly specify all the implicit | |
836 dependencies, such as -lssl -lcrypto -ldl, etc. This in turn locks | |
837 compiled io_lib libraries and binaries into requiring very specific | |
838 version of system libraries. | |
839 | |
840 * io_lib/Attic/Makefile.in: | |
841 (13:27:57) *** empty log message *** | |
842 | |
843 * io_lib/compression.c: | |
844 (13:30:24) Minor speed tweaks to qshift and unqshift | |
845 | |
846 * io_lib/mFILE.c, | |
847 * progs/solexa2srf.c: | |
848 (13:31:41) Added include of io_lib_config.h for autoconf builds so | |
849 that the ftello and similar functions get the correct prototypes. | |
850 | |
851 * io_lib/srf.c, | |
852 * io_lib/srf.h: | |
853 (13:32:44) Made partial_decode_ztr non-static and added it, along | |
854 with ztr_dup and construct_trace_name to the external header file | |
855 for use in other parts of io_lib. | |
856 | |
857 * progs/Makefile.am, | |
858 * progs/srf_filter.c, | |
859 * progs/srf_info.c: | |
860 (13:36:40) Added two new programs from Steven Leonard. | |
861 | |
862 srf_info: dumps out basic information on the contents of an SRF | |
863 file, including the read name prefixes used, how many | |
864 DBs per DBH and frequencies of ZTR chunk and meta-data | |
865 strings. | |
866 | |
867 srf_filter: a tool to produce new srf files by filtering in or out | |
868 data from an existing srf file. This can be performed | |
869 either at the entire trace level (eg tagged as good or | |
870 bad) or also at individual ZTR chunk levels (eg processed | |
871 data only). | |
872 | |
873 * progs/srf2fasta.c, | |
874 * progs/srf2fastq.c: | |
875 (13:37:37) Include string.h for additional prototypes (for -Wall | |
876 -Wno-paranthesis compilations). | |
877 | |
878 * progs/srf_extract_hash.c: | |
879 (13:38:47) Major overhaul from Steven Leonard. It now supports a | |
880 -fastq option to output fastq instead of ZTR files and optionally | |
881 can use calibrated or non-calibrated confidence values too. | |
882 | |
883 * progs/srf_extract_linear.c: | |
884 (13:39:44) Added support for SRFB_NULL_INDEX so that srf files with | |
885 a blank index do not causes crashes. | |
886 | |
887 * progs/srf_index_hash.c: | |
888 (13:40:44) Added extra error checking from Steven Leonard to spot | |
889 duplicate read names. The new -c option also allows checking of an | |
890 existing srf file without attempting to write a new index. | |
891 | |
892 2008-09-08 James Bonfield <jkb@sanger.ac.uk> | |
893 | |
894 * progs/solexa2srf.c: | |
895 (08:40:20) Fixed bug reported by Robert Sanders. The fwd matrix was | |
896 being written twice on paired-end runs instead of fwd+reverse. | |
897 | |
898 * COPYRIGHT, | |
899 * io_lib/open_trace_file.c, | |
900 * io_lib/sff.c: | |
901 (10:56:46) Updated 454's copyright notice (following correspondence | |
902 from Jim Knight at 454) to explicitly include permission to modify | |
903 and redistribute the code. | |
904 | |
905 Also updated the GRL licence to be explicit rather than just an | |
906 implied BSD style. | |
907 | |
908 2008-08-29 James Bonfield <jkb@sanger.ac.uk> | |
909 | |
910 * io_lib/deflate_interlaced.c: | |
911 (09:00:39) Added external codes2codeset() function to turn | |
912 bit-length arrays into codesets. Useful for tools that wish to use | |
913 this code to use their own precomputed huffman trees. | |
914 | |
915 * io_lib/deflate_interlaced.h: | |
916 (09:00:53) *** empty log message *** | |
917 | |
918 * progs/solexa2srf.c: | |
919 (09:01:21) Renamed ILLUMINA_GA_PARAMS and ILLUMINA_GA_PARAMS2 to | |
920 ILLUMINA_GA_BUSTARD_PARAMS and ILLUMINA_GA_FIRECREST_PARAMS. | |
921 | |
922 2008-08-26 James Bonfield <jkb@sanger.ac.uk> | |
923 | |
924 * progs/solexa2srf.c: | |
925 (11:07:09) Added the second .params file (Data directory). | |
926 | |
927 Major reduction in memory usage when adding the .params files; we | |
928 only hold this in memory for the first ZTR file per DBH as it ends | |
929 up in the header anyway. (This also speeds things up too.) | |
930 | |
931 2008-08-08 James Bonfield <jkb@sanger.ac.uk> | |
932 | |
933 * progs/solexa2srf.c: | |
934 (10:21:28) Fixed a bug in parse_4_float when handling strings with | |
935 leading zeroes after the point, eg "17.04". Fortunately this is | |
936 never triggered in the solexa data as it's always one single value | |
937 after the decimal point. | |
938 | |
939 * configure.in, | |
940 * io_lib/os.h: | |
941 (10:33:29) Applied Chris Saunders' patch to use autoconf for | |
942 checking machine endianness. | |
943 | |
944 * progs/solexa2srf.c: | |
945 (16:52:10) Added a MAX_READS_PER_DBH #define to solexa2srf | |
946 (defaults at 10000) to reduce the maximum number of traces per tile | |
947 we process between SRF data block headers. This helps reduce the | |
948 maximum memory usage which is especially important on dense GA2 | |
949 runs where 200,000 clusters in a tile can be achieved. | |
950 | |
951 Also fixed a bug with using -qf/-qr when not supplying a list of | |
952 tiles consecutively starting with tile 1. | |
953 | |
954 2008-08-05 James Bonfield <jkb@sanger.ac.uk> | |
955 | |
956 * io_lib/srf.c: | |
957 (08:18:14) Fixed memory leak in srf_next_ztr reported by Rob Egan. | |
958 Triggered by srf2fastq -C. | |
959 | |
960 2008-07-24 James Bonfield <jkb@sanger.ac.uk> | |
961 | |
962 * progs/solexa2srf.c: | |
963 (15:47:32) Updated version to v1.10 | |
964 | |
965 Added -pf/-pr parameters to allow the phasing files to be stored. | |
966 By default it attempts to derive these filenames from the fwd/rev | |
967 cycle numbers. | |
968 | |
969 Auto-compute the basecaller name and version string from the | |
970 directory name. | |
971 | |
972 * progs/solexa2srf.c: | |
973 (15:58:15) Bug fix to get_base_caller() so that it can identify the | |
974 directory when given a full pathname to elsewhere other than the | |
975 cwd. | |
976 | |
977 2008-07-18 James Bonfield <jkb@sanger.ac.uk> | |
978 | |
979 * progs/solexa2srf.c: | |
980 (15:54:51) No longer iterate through tiles printing up . or ! | |
981 depending on whether we encounter an error. Now it just aborts at | |
982 the point of failure. | |
983 | |
984 Also made the parsing code more robust as in a couple specific | |
985 cases it only wrote to stderr without actually generating a | |
986 non-zero exit code. | |
987 | |
988 These mean the tool is more amenable to running in a production | |
989 pipeline. If it gets any error at all it'll be more obvious and | |
990 forces attention. | |
991 | |
992 2008-07-11 James Bonfield <jkb@sanger.ac.uk> | |
993 | |
994 * progs/solexa2srf.c: | |
995 (11:35:28) Updated the rounding of int/nse/sig2 to all use the | |
996 rint() function to round to closest integer value. Previously | |
997 int/nse rounded down and sig2 rounded closest. (Although the | |
998 rounding on sig2 was via +/- 0.5 and so the half-way cases | |
999 sometimes give different answers to the new code using rint()). | |
1000 | |
1001 It has a very minor impact overall, but it is now consistent. | |
1002 | |
1003 =============================================================================== | |
1004 2008-07-09 James Bonfield <jkb@sanger.ac.uk> | |
1005 | |
1006 * 1.11.3 released. | |
1007 | |
1008 2008-07-09 jkbonfield <jkb@sanger.ac.uk> | |
1009 | |
1010 * io_lib/mFILE.c: | |
1011 * io_lib/Read.c, | |
1012 * io_lib/mFILE.h: | |
1013 (13:54:59) Fixed a bug visible with "extract_seq -fasta_out -fofn f | |
1014 -output f.fasta" whereby only the last file was visible. This is | |
1015 due to the mFILE mechanism and an explicit fseek upon writing each | |
1016 file. Fixed this by using an extended freopen option ("wbx" instead | |
1017 of "wb") to override this feature. It's not ideal, but gets the job | |
1018 done - I hope. | |
1019 | |
1020 2008-07-08 jkbonfield <jkb@sanger.ac.uk> | |
1021 | |
1022 * io_lib/srf.c, | |
1023 * io_lib/srf.h: | |
1024 (13:22:57) Added SRFB_NULL_INDEX as an SRF block type. It's | |
1025 essentially type 0 and is defined to be 8 long (with 7 more zeros). | |
1026 The purpose is to transparently gloss over the 8-zeros that may be | |
1027 on the end of some files indicating a missing index block. | |
1028 | |
1029 * progs/solexa2srf.c: | |
1030 (13:34:40) MAJOR BUG FIX! | |
1031 | |
1032 Fixed a bug in reorder_ztr() whereby the sorted order of multiple | |
1033 chunks of the same chunk type were not "stable". The result of this | |
1034 is that 3 SMP4 chunks (say A, B, C) may end up sorted A, B, C with | |
1035 nchunks==9 and C, A, B with nchunks==15. Given that an optimisation | |
1036 means that we change the number of chunks depending on whether | |
1037 we've encoded HUFF chunks this causes a "corruption" in as far as | |
1038 the correct data is stored but with potentially an incorrect | |
1039 meta-data block for the first SMP4 chunk. | |
1040 | |
1041 See srf_fix.c to reverse this problem. | |
1042 | |
1043 Also added a warning regarding the -C option and -qf option. These | |
1044 are inherently incompatible (right now) as purity filtered data is | |
1045 not calibrated. | |
1046 | |
1047 Updated version to v1.8 | |
1048 | |
1049 2008-06-12 jkbonfield <jkb@sanger.ac.uk> | |
1050 | |
1051 * progs/srf2fasta.c, | |
1052 * progs/srf2fastq.c: | |
1053 (10:44:23) Removed memory leaks from using ztr_find_chunks and not | |
1054 freeing the result. | |
1055 | |
1056 =============================================================================== | |
1057 2008-06-04 James Bonfield <jkb@sanger.ac.uk> | |
1058 | |
1059 * 1.11.2 released. | |
1060 | |
1061 2008-06-04 jkbonfield <jkb@sanger.ac.uk> | |
1062 | |
1063 * docs/ZTR_format: | |
1064 (13:06:36) Added some text regarding *ideas* for version 2. These | |
1065 are not officially part of any stanard yet. | |
1066 | |
1067 * io_lib/compression.c: | |
1068 (13:06:54) Comment change only. | |
1069 | |
1070 2008-06-03 jkbonfield <jkb@sanger.ac.uk> | |
1071 | |
1072 * io_lib/srf.c: | |
1073 (16:23:50) Applied bug fix from John Emhoff: srf_read_xml was | |
1074 incorrectly interpreting the XML length as the length of the XML | |
1075 string rather than the entire SRF block itself including header. It | |
1076 now agrees with srf_write_xml, which interpreted this correctly. | |
1077 | |
1078 2008-05-23 jkbonfield <jkb@sanger.ac.uk> | |
1079 | |
1080 * docs/ZTR_format: | |
1081 (08:38:05) Documented TYPE meta-data for SMP4 and removed the | |
1082 comment about being mutually exclusive with SAMP. | |
1083 | |
1084 Added explanation of log-odds vs phred scales. | |
1085 | |
1086 Added CNF1 chunk type (how did I miss this before?). | |
1087 | |
1088 2008-05-21 jkbonfield <jkb@sanger.ac.uk> | |
1089 | |
1090 * io_lib/srf.c: | |
1091 (09:12:23) Fixed memory leak in construct_trace_name. (Patch from | |
1092 John Emhoff at Heliocos.) | |
1093 | |
1094 2008-05-14 jkbonfield <jkb@sanger.ac.uk> | |
1095 | |
1096 * progs/solexa2srf.c: | |
1097 (13:08:34) Fixed floating point to integer rounding of trace data | |
1098 to round to closest instead of floor(value). | |
1099 | |
1100 * io_lib/srf.c, | |
1101 * io_lib/srf.h, | |
1102 * progs/solexa2srf.c, | |
1103 * progs/srf2fasta.c, | |
1104 * progs/srf2fastq.c, | |
1105 * progs/srf2solexa.c, | |
1106 * progs/srf_dump_all.c: | |
1107 (14:13:15) Added changes from Camil Toma (albeit modified here and | |
1108 there) to incorporate the -C option to various tools. This allows | |
1109 for chastity filtered data to be stored in SRF, but tagged as being | |
1110 bad data. We then get the option to filter it on extraction | |
1111 instead. | |
1112 | |
1113 2008-05-13 jkbonfield <jkb@sanger.ac.uk> | |
1114 | |
1115 * progs/solexa2srf.c: | |
1116 (14:25:53) Reverted the footer position change in encode_ztr() back | |
1117 (to the 20th February 2008) to taking out the meta-data into the | |
1118 header block too. Although this contains variable data (OFFS=value) | |
1119 it's the same for all members of a tile. | |
1120 | |
1121 2008-05-08 jkbonfield <jkb@sanger.ac.uk> | |
1122 | |
1123 * io_lib/open_trace_file.c: | |
1124 (11:06:53) Sped up searching in SRF files by stripping off the | |
1125 directory name when calling srf_find_trace(). (It got to this | |
1126 before eventually, but only after searching various false | |
1127 combinations.) | |
1128 | |
1129 * io_lib/os.h: | |
1130 (11:07:31) Minor change to prevent errors when compiling within the | |
1131 Staden Package. No impact for autoconf version. | |
1132 | |
1133 * io_lib/srf.c: | |
1134 (11:08:18) Fixed bug in srf_find_trace that caused it to rarely | |
1135 fail to find a trace when querying the hash table. | |
1136 | |
1137 2008-05-06 jkbonfield <jkb@sanger.ac.uk> | |
1138 | |
1139 * docs/ZTR_format: | |
1140 (11:44:51) Fixed error in the pictoral diagram describing the magic | |
1141 number. (It is correct everywhere else.) | |
1142 | |
1143 * io_lib/open_trace_file.c: | |
1144 (14:27:24) Added SRF interfaces to open_trace_file meaning we can | |
1145 now try specifying traces file fubar.srf/tname or | |
1146 TRACE_PATH=SRF=fubar.srf and tname. | |
1147 | |
1148 * configure.in, | |
1149 * io_lib/ztr.c, | |
1150 * progs/Makefile.am, | |
1151 * progs/solexa2srf.c, | |
1152 * progs/srf2solexa.c: | |
1153 (15:35:36) Implemented Come Raczy's (Illumina) changes. These | |
1154 involved renaming the solexa2srf and srf2solexa tools to be | |
1155 illumina2srf and srf2illumina and the addition of qcal support in | |
1156 preparation for the GA v1.0 release. | |
1157 | |
1158 Note that currently the filenames are the same as before, in order | |
1159 to preserve change history. | |
1160 | |
1161 * Makefile: | |
1162 (15:43:33) Added srf.o to the Staden Package Makefile (NB: not part | |
1163 of the autoconf system.) | |
1164 | |
1165 2008-04-15 jkbonfield <jkb@sanger.ac.uk> | |
1166 | |
1167 * io_lib/hash_table.c: | |
1168 (15:09:41) Initialises pb and pc in hash() function when using | |
1169 HASH_FUNC_JENKINS3. Bug reported by Cristian Goina. | |
1170 | |
1171 2008-04-08 jkbonfield <jkb@sanger.ac.uk> | |
1172 | |
1173 * progs/solexa2srf.c: | |
1174 (11:22:33) Fixed a code inefficiency when using -qf and -qr. | |
1175 | |
1176 * io_lib/srf.c, | |
1177 * io_lib/srf.h: | |
1178 (16:16:55) Fixed bugs regarding binary format read_id suffixes, | |
1179 reported and mostly patched by Cristian Goina. | |
1180 | |
1181 The srf_trace_body_t struct now has a read_id_length field. | |
1182 | |
1183 The srf_construct_trace_body() function has an extra argument to | |
1184 pass in the length, or -1 if unknown (it'll use strlen then). | |
1185 | |
1186 New function srf_write_pstringb to write binary pstrings, avoiding | |
1187 the requirement for strlen(). | |
1188 | |
1189 * progs/solexa2srf.c: | |
1190 (16:21:57) Added extra arg to srf_construct_trace_body call (see | |
1191 srf.c change log). | |
1192 | |
1193 Fixed a bug introduced in the recent efficiency improvements for | |
1194 -qf/-qr. These meant that many sequences were incorrectly skipped. | |
1195 | |
1196 2008-04-07 jkbonfield <jkb@sanger.ac.uk> | |
1197 | |
1198 * progs/solexa2srf.c: | |
1199 (08:54:06) Increased the estimation of number of bytes per cycle in | |
1200 the allocation in get_sig(). | |
1201 | |
1202 * progs/solexa2srf.c: | |
1203 (15:11:06) Fixed error that crept in when error checking was added | |
1204 to compress_chunk calls. Missing curly braces meant that some | |
1205 chunks were not compressed while other chunks got needless | |
1206 additional layers of compression. | |
1207 | |
1208 2008-04-03 jkbonfield <jkb@sanger.ac.uk> | |
1209 | |
1210 * progs/solexa2srf.c: | |
1211 (15:57:06) The defaults for -N and -n are now using the same naming | |
1212 conventions used in Gerald during the fastq generation steps. To do | |
1213 this is looks at the run folder root directory name to get the run | |
1214 date, machine name and run number. (These are available for use as | |
1215 %d, %m and %r in the format strings.) | |
1216 | |
1217 Calibrated confidence values are now automatically included if the | |
1218 -qf or -qr parameters are used (specifying the fastq filename). | |
1219 Note this only works currently if the number of bases after | |
1220 calibration is the same as the number before. The calibrated | |
1221 confidence values are written in a CNF1 ztr chunk (in addition to | |
1222 the existing CNF4 chunk for uncalibrated values) and are rescaled | |
1223 to adhere to the phred scale (-10 * log10(1-P)). | |
1224 | |
1225 Added meta-data to the confidence chunks (CNF1 and CNF4) with a | |
1226 SCALE key. The value is either LO (log-odds) or PH (phred). This | |
1227 increases file size somewhat as it's written once per trace, but | |
1228 the long-term goal is to upgrade ZTR to support the ability to | |
1229 specific default meta-data keys/values. | |
1230 | |
1231 * progs/srf2fastq.c: | |
1232 (15:57:58) Added a -c option to output calibrated confidence values | |
1233 instead of uncalibrated ones. | |
1234 | |
1235 Plus additionally it should be able to handle multiple archives on | |
1236 the command line instead of a single one. | |
1237 | |
1238 * progs/solexa2srf.c: | |
1239 (17:00:28) Added support for using popen() to gzip -cd instead of | |
1240 using gzopen. The reason is that it's between 3 and 5 times faster | |
1241 doing that. I'm unsure why, but overall it sped up solexa2srf -r 3 | |
1242 fold when the Firecrest data is gzipped. | |
1243 | |
1244 2008-04-02 jkbonfield <jkb@sanger.ac.uk> | |
1245 | |
1246 * progs/solexa2srf.c: | |
1247 (09:14:45) Fixed the footer(aka body) position calculation so it | |
1248 works still on trace files containing no trace data at all. Ie | |
1249 solexa2srf -P. | |
1250 | |
1251 * progs/solexa2srf.c: | |
1252 (09:28:02) Added Camil Toma's (Broad) changes to support -mf and | |
1253 -mr paremeters. These provide finer grained control over the | |
1254 filenames of the forward and reverse matrices. | |
1255 | |
1256 * progs/srf2solexa.c: | |
1257 (09:29:04) Added Camil Toma's (Broad) changes to extract text files | |
1258 embedded in ZTR TEXT chunks. | |
1259 | |
1260 * progs/srf_dump_all.c: | |
1261 (10:54:29) Added Camil Toma's (Broad) changes to srf_dump_all. | |
1262 These add multiple new features, increasing the source length 7 | |
1263 fold. | |
1264 | |
1265 * progs/srf2solexa.c, | |
1266 * progs/srf_dump_all.c: | |
1267 (10:56:06) Fixed bug reported by Cristian Goina (JCVI): we now use | |
1268 srf_open with mode "rb" instead of "r". This resolves an issue on | |
1269 Windows/DOS when dealing with binary data including ^Z characters | |
1270 being interpreted as EOF. | |
1271 | |
1272 * progs/srf_dump_all.c: | |
1273 (11:05:25) Fixed missing newlines in the standard "dump" format. | |
1274 | |
1275 2008-03-20 jkbonfield <jkb@sanger.ac.uk> | |
1276 | |
1277 * io_lib/hash_table.c, | |
1278 * progs/hash_list.c: | |
1279 (09:45:07) Added more includes of io_lib_config.h to ensure 64-bit | |
1280 file support works correctly. | |
1281 | |
1282 2008-03-13 jkbonfield <jkb@sanger.ac.uk> | |
1283 | |
1284 * progs/solexa2srf.c: | |
1285 (09:32:15) Fixed an error when passing in fully qualified | |
1286 pathnames. We now chdir() to the directory containing the seq.txt | |
1287 file and work from there. | |
1288 | |
1289 Also some functions involved in supporting fastq files with | |
1290 callibrated confidence values. This is unfinished and needs more | |
1291 work, specifically it doesn't do anything with the sequence/qual | |
1292 yet (just parses it) and the entire operation should probably work | |
1293 from the GERALD directory instead of the Bustard directory. Hence | |
1294 for now the -qf and -qr options are undocumented. | |
1295 | |
1296 * progs/solexa2srf.c: | |
1297 (11:53:32) Incorporated Come Razy's changes to solexa2srf, with a | |
1298 few modifications to adhere to C89 instead of C9X C standards. | |
1299 | |
1300 These add support for the new Illumina IPAR file format via the -I | |
1301 command line option. | |
1302 | |
1303 2008-02-29 jkbonfield <jkb@sanger.ac.uk> | |
1304 | |
1305 * acinclude.m4, | |
1306 * configure.in: | |
1307 (14:10:53) Fixed autoconf build environment for Fedora. We no | |
1308 longer assume /usr/lib is a valid default for zlib, instead relying | |
1309 on either the compiler to find it or an explicit --with-zlib | |
1310 option. | |
1311 | |
1312 See SF bug 1898427 | |
1313 https://sourceforge.net/tracker/index.php?func=detail&aid=1898427&g | |
1314 roup_id=100316&atid=627058 | |
1315 | |
1316 =============================================================================== | |
1317 2008-02-20 James Bonfield <jkb@sanger.ac.uk> | |
1318 | |
1319 * 1.11.0 released. | |
1320 | |
1321 2008-02-20 James Bonfield <jkb@sanger.ac.uk> | |
1322 | |
1323 * progs/srf2fastq.c: | |
1324 (12:49:09) Removed the ztr2read conversion and operate | |
1325 directly on | |
1326 the ztr struct. This is now 25% faster. | |
1327 | |
1328 * progs/srf2fasta.c: | |
1329 (12:49:30) New program - trivially modelled on srf2fastq.c | |
1330 | |
1331 * progs/solexa2srf.c: | |
1332 (10:33:36) Altered the header/footer split for ZTR to stop just | |
1333 before the metadata part of a SMP4 chunk. Previously it was after | |
1334 this and just before the data, but now we can have multiple SMP4 | |
1335 chunks in a single ZTR file this was breaking things. | |
1336 | |
1337 2008-02-18 James Bonfield <jkb@sanger.ac.uk> | |
1338 | |
1339 * io_lib/ztr.h: | |
1340 (16:53:52) Added ZTR_TYPE_REGN definition. We have no explicit code | |
1341 to implement this yet in ztr.c, but for now it's in solexa2srf. | |
1342 | |
1343 * progs/solexa2srf.c: | |
1344 (16:55:38) Added support for specifying the start coord for the 2nd | |
1345 read in a paired-read run (solexa2srf -2 <cycle.no.>). This also | |
1346 adds a REGN chunk to the ZTR file and stores the second matrix file | |
1347 too. | |
1348 | |
1349 * progs/srf2solexa.c: | |
1350 (16:56:39) Major overhaul to support raw data as well as processed | |
1351 data. Still to-do: write out .params and the two matrix files. | |
1352 | |
1353 2008-02-15 James Bonfield <jkb@sanger.ac.uk> | |
1354 | |
1355 * io_lib/srf.c: | |
1356 (10:05:54) Fixed memory leak in srf_read_trace_body usage. This was | |
1357 primarily visible from within srf_index_hash. | |
1358 | |
1359 * progs/srf2solexa.c, | |
1360 * io_lib/srf.c, | |
1361 * progs/srf_index_hash.c, | |
1362 * progs/srf_extract_hash.c: | |
1363 (12:35:19) Added include of io_lib-config.h to ensure picking up | |
1364 the correct compiler definitions for 64-bit file size support. | |
1365 | |
1366 * progs/srf_extract_linear.c: | |
1367 (12:40:55) Fixed memory leaks. | |
1368 | |
1369 2008-02-14 James Bonfield <jkb@sanger.ac.uk> | |
1370 | |
1371 * progs/solexa2srf.c: | |
1372 (17:02:42) Don't bother performing ZTR_FORM_TSHIFT transformation | |
1373 on the solexa noise data as it doesn't help it at all. Also hard | |
1374 coded the interlaced huffman to operate in batches of 2 instead of | |
1375 8 for noise data for the same reason. | |
1376 | |
1377 * io_lib/ztr_translate.c: | |
1378 (17:07:15) ztr2read() now correctly handles translation of ZTR | |
1379 files with multiple samples in. Specifically it only sets the Read | |
1380 struct baseline and trace[ACGT] arrays when the TYPE meta-data | |
1381 field is blank, PROC or A,C,G T. | |
1382 | |
1383 This fixes trace_dump etc on solexa srf files, (note that the srf | |
1384 files themselves were perfect valid anyway). | |
1385 | |
1386 2008-02-06 James Bonfield <jkb@sanger.ac.uk> | |
1387 | |
1388 * progs/extract_seq.c: | |
1389 (11:04:38) Use set_compression_method to explicitly disable gzipped | |
1390 output from extract_seq (which is by default on if the input is | |
1391 gzipped). | |
1392 | |
1393 * io_lib/Makefile.in, | |
1394 * progs/Makefile.am, | |
1395 * progs/extract_qual.c: | |
1396 (11:04:59) Added Steven Leonard's extract_qual program (derived | |
1397 from extract_seq). | |
1398 | |
1399 2008-01-28 James Bonfield <jkb@sanger.ac.uk> | |
1400 | |
1401 * progs/solexa2srf.c: | |
1402 (09:47:42) Sped up parse_4_int and parse_4_float substantially. | |
1403 | |
1404 2008-01-25 James Bonfield <jkb@sanger.ac.uk> | |
1405 | |
1406 * Tagged iolib-1-11-0b8 | |
1407 | |
1408 * progs/solexa2srf.c: | |
1409 (11:38:34) Fixed small memory leak in zfopen/zfclose. | |
1410 | |
1411 Fixed a bug where reorder_ztr could put CNF4 before BASE, | |
1412 breaking | |
1413 the decoding. | |
1414 | |
1415 Added support for loading solexa matrix and params files into | |
1416 appropriately named TEXT key/value pairs. It also adds the | |
1417 PROGRAM_ID there now too. | |
1418 | |
1419 Sped up chastity filtering. We now only read the line of text | |
1420 rather than decode it for data that is filtered. | |
1421 | |
1422 Minor tweaks to program usage output. | |
1423 | |
1424 * progs/trace_dump.c: | |
1425 (11:39:09) Updated output to be more inline with | |
1426 srf_dump_all. Also | |
1427 now supports baseline properly. | |
1428 | |
1429 * progs/ztr_dump.c: | |
1430 (11:39:34) Added ZTR_FORM_XRLE2, ZTR_FORM_QSHIFT and | |
1431 ZTR_FORM_TSHIFT. | |
1432 | |
1433 2008-01-24 James Bonfield <jkb@sanger.ac.uk> | |
1434 | |
1435 * io_lib/ztr.c, | |
1436 * io_lib/ztr.h: | |
1437 (17:17:52) Two new utility functions that are *long* overdue. | |
1438 | |
1439 ztr_new_chunk() - creates and initialises a new chunk in a ztr | |
1440 struct. | |
1441 | |
1442 ztr_add_text() - adds arbitrary key/value pairs to the TEXT | |
1443 chunk, | |
1444 creating it if required. | |
1445 | |
1446 2008-01-22 James Bonfield <jkb@sanger.ac.uk> | |
1447 | |
1448 * io_lib/srf.c, | |
1449 * io_lib/srf.h: | |
1450 (11:07:40) Allow for srf_read_index_hdr() to be used to read | |
1451 an index internal to the file rather than at the end of the | |
1452 file. To accommodate this an extra "no_seek" argument has been | |
1453 added. | |
1454 | |
1455 * progs/solexa2srf.c: | |
1456 (11:10:56) Support multiple trace channels (raw "int" & noise, | |
1457 in addition to or instead of the processed data). | |
1458 | |
1459 Input data may now optionally be compressed. | |
1460 | |
1461 Added a -c option to do chastity filtering via the .qhg files. | |
1462 | |
1463 Improved the dynamic range filtering. We no longer trim all | |
1464 negative values in preference for high positive values. Instead we | |
1465 set the clip points to trim the least number of total values. | |
1466 | |
1467 * progs/srf2solexa.c: | |
1468 (11:11:35) Fixed the baseline subtraction. It now uses the | |
1469 correct value instead of a hardcoded 32768. | |
1470 | |
1471 * progs/srf_extract_linear.c: | |
1472 (11:12:15) Changed to use the new srf_read_index_hdr arguments. | |
1473 | |
1474 * progs/srf_index_hash.c: | |
1475 (11:13:12) Improved index support when the input is | |
1476 concatenated SRF files already containing indices. It now | |
1477 overwrites the last index. | |
1478 | |
1479 * progs/ztr_dump.c: | |
1480 (11:13:47) Added display of meta-data TYPE field for trace | |
1481 sample chunks. | |
1482 | |
1483 2008-01-14 James Bonfield <jkb@sanger.ac.uk> | |
1484 | |
1485 * io_lib/srf.c, | |
1486 * io_lib/srf.h, | |
1487 * progs/srf_index_hash.c: | |
1488 (16:57:36) Bug fixes to do with reading and writing the index | |
1489 format. We incorrectly handled having null dbhFile and | |
1490 containerFile elements, plus also computed the index size wrong | |
1491 for these fields too. | |
1492 | |
1493 =============================================================================== | |
1494 2008-01-11 James Bonfield <jkb@sanger.ac.uk> | |
1495 | |
1496 * 1.11.0b7 released. | |
1497 | |
1498 * io_lib/srf.c: | |
1499 (11:35:09) IMPORTANT BUG FIX: The SRF Data Block Header | |
1500 had the blockSize field 4 bytes too large, so SRF files produced | |
1501 did not conform to the standard. | |
1502 Also fixed SRF reading support for when headerBlob is zero length. | |
1503 We then delay ztr decoding until we've read the actual data blob. | |
1504 | |
1505 * io_lib/compression.c, | |
1506 * io_lib/deflate_interlaced.c, | |
1507 * io_lib/deflate_interlaced.h, | |
1508 * io_lib/srf.c, | |
1509 * io_lib/ztr.c, | |
1510 * io_lib/ztr_translate.c, | |
1511 * progs/solexa2srf.c: | |
1512 (12:26:11) Added missing prototypes and fixed various signed vs | |
1513 unsigned assignments, as spotted by the Intel C Compiler. | |
1514 | |
1515 2008-01-02 James Bonfield <jkb@sanger.ac.uk> | |
1516 | |
1517 * Tagged iolib-1-11-0b6 | |
1518 | |
1519 2008-01-02 James Bonfield <jkb@sanger.ac.uk> | |
1520 | |
1521 * io_lib/srf.c: | |
1522 (11:41:00) Removed some debugging output | |
1523 | |
1524 2007-12-12 James Bonfield <jkb@sanger.ac.uk> | |
1525 | |
1526 * io_lib/srf.c, | |
1527 * io_lib/srf.h, | |
1528 * progs/srf_index_hash.c: | |
1529 (18:50:46) Updates to SRF 1.3. This includes removal of the readID | |
1530 counter and added support for printf style formatting. It also has | |
1531 some tweaks to the format for the index (32-bit vs 64-bit and | |
1532 dbh/container file strings). | |
1533 | |
1534 Both versions have therefore been bumped (SRF 1.3 and index 1.01). | |
1535 | |
1536 TODO: support for extracting data from an SRF file that's split | |
1537 with container headers, trace headers and trace bodies all in | |
1538 separate files. | |
1539 | |
1540 2007-11-12 James Bonfield <jkb@sanger.ac.uk> | |
1541 | |
1542 * Tagged iolib-1-11-0b5 | |
1543 | |
1544 2007-11-08 James Bonfield <jkb@sanger.ac.uk> | |
1545 | |
1546 * io_lib/Read.c, | |
1547 * io_lib/Read.h, | |
1548 * io_lib/abi.h, | |
1549 * io_lib/alf.h, | |
1550 * io_lib/array.c, | |
1551 * io_lib/array.h, | |
1552 * io_lib/compress.c, | |
1553 * io_lib/compress.h, | |
1554 * io_lib/compression.c, | |
1555 * io_lib/compression.h, | |
1556 * io_lib/ctfCompress.c, | |
1557 * io_lib/deflate_interlaced.c, | |
1558 * io_lib/deflate_interlaced.h, | |
1559 * io_lib/error.c, | |
1560 * io_lib/error.h, | |
1561 * io_lib/expFileIO.c: | |
1562 * io_lib/expFileIO.h, | |
1563 * io_lib/files.c, | |
1564 * io_lib/find.c, | |
1565 * io_lib/fpoint.c, | |
1566 * io_lib/fpoint.h, | |
1567 * io_lib/hash_table.c, | |
1568 * io_lib/hash_table.h, | |
1569 * io_lib/jenkins_lookup3.c, | |
1570 * io_lib/jenkins_lookup3.h, | |
1571 * io_lib/mFILE.c, | |
1572 * io_lib/mFILE.h, | |
1573 * io_lib/mach-io.c, | |
1574 * io_lib/mach-io.h, | |
1575 * io_lib/misc.h, | |
1576 * io_lib/misc_scf.c, | |
1577 * io_lib/open_trace_file.c, | |
1578 * io_lib/open_trace_file.h, | |
1579 * io_lib/os.h, | |
1580 * io_lib/plain.h, | |
1581 * io_lib/read_alloc.c, | |
1582 * io_lib/read_scf.c, | |
1583 * io_lib/scf.h, | |
1584 * io_lib/scf_extras.c, | |
1585 * io_lib/scf_extras.h, | |
1586 * io_lib/seqIOABI.c, | |
1587 * io_lib/seqIOABI.h, | |
1588 * io_lib/seqIOALF.c, | |
1589 * io_lib/seqIOCTF.c, | |
1590 * io_lib/seqIOCTF.h, | |
1591 * io_lib/seqIOPlain.c, | |
1592 * io_lib/sff.c, | |
1593 * io_lib/sff.h, | |
1594 * io_lib/srf.c, | |
1595 * io_lib/srf.h, | |
1596 * io_lib/stdio_hack.h, | |
1597 * io_lib/strings.c, | |
1598 * io_lib/tar_format.h, | |
1599 * io_lib/traceType.c, | |
1600 * io_lib/traceType.h, | |
1601 * io_lib/translate.c, | |
1602 * io_lib/translate.h: | |
1603 * io_lib/Makefile.am, | |
1604 * io_lib/Makefile.in, | |
1605 * io_lib/vlen.c, | |
1606 * io_lib/vlen.h, | |
1607 * io_lib/write_scf.c, | |
1608 * io_lib/xalloc.c, | |
1609 * io_lib/xalloc.h, | |
1610 * io_lib/ztr.c, | |
1611 * io_lib/ztr.h, | |
1612 * io_lib/ztr_translate.c: | |
1613 (14:58:14) Renamed files from | |
1614 {abi,alf,ctf,exp_file,plain,read,scf,sff,srf,utils,ztr} subdirs to | |
1615 a single io_lib subdir. | |
1616 | |
1617 The purpose of this is so that code can #include <io_lib/foo.h> | |
1618 from both within this source tree and externally when compiling | |
1619 against io_lib, resolving problems when including files that then | |
1620 include other io_lib files. Plus it's simply tidier this way. | |
1621 | |
1622 * io_lib/Read.c: | |
1623 * io_lib/Read.h, | |
1624 * io_lib/abi.h, | |
1625 * io_lib/alf.h, | |
1626 * io_lib/array.c, | |
1627 * io_lib/compress.c, | |
1628 * io_lib/compress.h, | |
1629 * io_lib/compression.c, | |
1630 * io_lib/compression.h, | |
1631 * io_lib/ctfCompress.c, | |
1632 * io_lib/deflate_interlaced.c, | |
1633 * io_lib/expFileIO.c, | |
1634 * io_lib/expFileIO.h, | |
1635 * io_lib/files.c, | |
1636 * io_lib/find.c, | |
1637 * io_lib/fpoint.c, | |
1638 * io_lib/hash_table.c, | |
1639 * io_lib/jenkins_lookup3.c, | |
1640 * io_lib/mFILE.c, | |
1641 * io_lib/mach-io.c, | |
1642 * io_lib/mach-io.h, | |
1643 * io_lib/misc.h, | |
1644 * io_lib/misc_scf.c, | |
1645 * io_lib/open_trace_file.c, | |
1646 * io_lib/open_trace_file.h, | |
1647 * io_lib/plain.h, | |
1648 * io_lib/read_alloc.c, | |
1649 * io_lib/read_scf.c, | |
1650 * io_lib/scf.h, | |
1651 * io_lib/scf_extras.c, | |
1652 * io_lib/scf_extras.h, | |
1653 * io_lib/seqIOABI.c, | |
1654 * io_lib/seqIOABI.h, | |
1655 * io_lib/seqIOALF.c, | |
1656 * io_lib/seqIOCTF.c, | |
1657 * io_lib/seqIOCTF.h, | |
1658 * io_lib/seqIOPlain.c, | |
1659 * io_lib/sff.c, | |
1660 * io_lib/sff.h, | |
1661 * io_lib/srf.c, | |
1662 * io_lib/srf.h, | |
1663 * io_lib/stdio_hack.h, | |
1664 * io_lib/strings.c, | |
1665 * io_lib/traceType.c, | |
1666 * io_lib/traceType.h, | |
1667 * io_lib/translate.c, | |
1668 * io_lib/translate.h, | |
1669 * io_lib/vlen.c, | |
1670 * io_lib/write_scf.c, | |
1671 * io_lib/xalloc.c, | |
1672 * io_lib/ztr.c, | |
1673 * io_lib/ztr.h, | |
1674 * io_lib/ztr_translate.c, | |
1675 * progs/Makefile.am, | |
1676 * progs/append_sff.c, | |
1677 * progs/convert_trace.c, | |
1678 * progs/extract_fastq.c, | |
1679 * progs/extract_seq.c, | |
1680 * progs/get_comment.c, | |
1681 * progs/hash_exp.c, | |
1682 * progs/hash_extract.c: | |
1683 * progs/hash_list.c, | |
1684 * progs/hash_sff.c, | |
1685 * progs/hash_tar.c, | |
1686 * progs/index_tar.c, | |
1687 * progs/makeSCF.c, | |
1688 * progs/scf_dump.c, | |
1689 * progs/scf_info.c, | |
1690 * progs/scf_update.c, | |
1691 * progs/solexa2srf.c, | |
1692 * progs/srf2fastq.c, | |
1693 * progs/srf2solexa.c, | |
1694 * progs/srf_dump_all.c, | |
1695 * progs/srf_extract_hash.c, | |
1696 * progs/srf_extract_linear.c, | |
1697 * progs/srf_index_hash.c, | |
1698 * progs/trace_dump.c, | |
1699 * progs/ztr_dump.c: | |
1700 (17:24:16) Modify the include paths to use "io_lib/foo.h" instead | |
1701 of "foo.h" or <foo.h>. | |
1702 | |
1703 The advantage of this is that the source for external programs | |
1704 compiled and linked against io_lib can use exactly the same | |
1705 #include statements as the progs/* files. | |
1706 | |
1707 * Makefile.am, | |
1708 * configure.in: | |
1709 (17:37:00) Updated to handle the filename movements. | |
1710 | |
1711 * docs/Hash_File_Format, | |
1712 * docs/ZTR_format: | |
1713 (17:42:14) Moved from elsewhere | |
1714 | |
1715 2007-11-06 James Bonfield <jkb@sanger.ac.uk> | |
1716 | |
1717 * README, | |
1718 * CHANGES | |
1719 Updated | |
1720 | |
1721 * progs/Makefile.am: | |
1722 (10:09:33) Added srf_extract_hash; demonstration of using | |
1723 srf_find_trace to query a hash table index. | |
1724 | |
1725 * progs/srf_extract_hash.c: | |
1726 (10:09:34) Added srf_extract_hash; demonstration of using | |
1727 srf_find_trace to query a hash table index. | |
1728 | |
1729 * srf/srf.h: | |
1730 (10:10:15) Bug fix: updated version string to 1.2. (We were already | |
1731 writing using the 1.2 standard but claiming 1.1) | |
1732 | |
1733 * srf/srf.c: | |
1734 (10:12:04) Bug fix when using glibc: added explicit include of | |
1735 io_lib_config.h prior to stdio.h so the AC_SYS_LARGEFILE autoconf | |
1736 magic does its tricks. This is only required for glibc, which | |
1737 appears broken by default as it doesn't contain a prototype for | |
1738 fseeko despite exporting the system, unless explicit macros are | |
1739 defined. | |
1740 | |
1741 2007-11-02 James Bonfield <jkb@sanger.ac.uk> | |
1742 | |
1743 * progs/solexa2srf.c: | |
1744 (13:57:30) Improved handling of out-of-range data. Specifically | |
1745 what happens when the minimum value in a trace is -40000 and the | |
1746 maximum value is +50000. We now clip -ve values if the range | |
1747 doesn't fit. | |
1748 | |
1749 * ztr/ztr_translate.c: | |
1750 (13:59:41) Added SMP4 'OFFS' metadata and Read->baseline support | |
1751 when converting from read2ztr. | |
1752 | |
1753 2007-11-01 James Bonfield <jkb@sanger.ac.uk> | |
1754 | |
1755 * srf/srf.c: | |
1756 (14:24:30) More error checking paranoia in SRF support; given that | |
1757 fwrite() can sometimes claim success even when it failed we now | |
1758 explicitly call ferror and check fclose() return. | |
1759 | |
1760 * ztr/FORMAT, | |
1761 * ztr/ztr.c, | |
1762 * ztr/ztr.h, | |
1763 * ztr/ztr_translate.c: | |
1764 (14:26:02) Better support for ZTR v1.2. We now correctly handle | |
1765 SAMP/SMP4 metadata fields and make use of OFFS when converting to | |
1766 Read. | |
1767 | |
1768 * progs/solexa2srf.c, | |
1769 * progs/srf_dump_all.c: | |
1770 (14:26:35) Improved support for ztr OFFS metadata and removed the | |
1771 old crufty SHIFT_BY #define. | |
1772 | |
1773 * progs/solexa2srf.c: | |
1774 (17:35:58) Bug fix: we were missing the trailing nul of the trace | |
1775 OFFS metadata value. | |
1776 | |
1777 Also the setting of min_val when the range is too high was invalid. | |
1778 Note further work is needed here as we've already truncated to | |
1779 16-bit making it impossible to tell where the wraparound occurs. | |
1780 | |
1781 * ztr/ztr.c, | |
1782 * ztr/ztr_translate.c: | |
1783 (18:00:55) Fixed memory leaks. | |
1784 | |
1785 2007-10-26 James Bonfield <jkb@sanger.ac.uk> | |
1786 | |
1787 * progs/Makefile.am, | |
1788 * progs/srf2fastq.c: | |
1789 (10:35:56) Added srf2fastq conversion to demonstrate usage of | |
1790 read_sections() and as a benchmark for pure sequence+quality | |
1791 extraction. (It appears to cope at about 100,000 sequences/second.) | |
1792 | |
1793 * ztr/deflate_interlaced.c, | |
1794 * ztr/deflate_interlaced.h: | |
1795 (10:38:04) Changed generate_code_set and huffman_codeset_destroy to | |
1796 keep the same huffman_codeset_t structure for all uses of one of | |
1797 the predetermined CODE_* codesets. | |
1798 | |
1799 * ztr/ztr_translate.c: | |
1800 (10:40:37) ztr2read() now honours the read_sections() setting. To | |
1801 do this it also means it uncompresses data on the fly, but only for | |
1802 chunk types that it needs to. Hence this code no longer needs | |
1803 uncompress_ztr() calling first either. | |
1804 | |
1805 * srf/srf.c, | |
1806 * srf/srf.h: | |
1807 (10:46:07) Moved some static local variables out of srf_next_ztr | |
1808 into the srf_t object. This means the code should be | |
1809 multi-threaded. | |
1810 | |
1811 * ztr/FORMAT: | |
1812 (10:47:07) Current v1.3 draft | |
1813 | |
1814 * ztr/Attic/deflate_simple.c, | |
1815 * ztr/Attic/deflate_simple.h: | |
1816 (10:50:32) Replaced by deflate_interlaced.[ch] some time ago. | |
1817 | |
1818 * progs/srf2solexa.c: | |
1819 (11:35:59) Switched to using srf_next_ztr() in order to avoid | |
1820 repeated huffman codeset decoding. Now much faster. | |
1821 | |
1822 * CHANGES: | |
1823 (14:28:27) *** empty log message *** | |
1824 | |
1825 * README, | |
1826 * configure.in: | |
1827 (14:31:48) *** empty log message *** | |
1828 | |
1829 2007-10-25 James Bonfield <jkb@sanger.ac.uk> | |
1830 | |
1831 * progs/srf_dump_all.c, | |
1832 * progs/srf_extract_linear.c, | |
1833 * srf/srf.c, | |
1834 * srf/srf.h, | |
1835 * ztr/compression.c, | |
1836 * ztr/deflate_interlaced.c, | |
1837 * ztr/deflate_interlaced.h, | |
1838 * ztr/ztr.c, | |
1839 * ztr/ztr.h: | |
1840 (14:21:16) Upgraded SRF to support v1.2 specification. NOTE: No | |
1841 support is kept for v1.1! | |
1842 | |
1843 Dramatically improved the speed of sequential decoding (eg in | |
1844 srf_dump_all) by use of caching huffman_codeset_t structs. | |
1845 | |
1846 * progs/srf_dump_all.c: | |
1847 (16:55:24) Added unused (#if-ed out) printf variant. It's for | |
1848 possible efficiency gains, but ignoring for now. | |
1849 | |
1850 * ztr/compression.c, | |
1851 * ztr/deflate_interlaced.c: | |
1852 (16:56:06) Fixed unsthuff uncompression for the predfined CODE_* | |
1853 huffman trees. | |
1854 | |
1855 2007-10-17 James Bonfield <jkb@sanger.ac.uk> | |
1856 | |
1857 * progs/solexa2srf.c: | |
1858 (16:56:11) Dropped ZLIB compression of BPOS as A) it's tiny anyway | |
1859 and B) we don't want to waste time compressing it over and over | |
1860 again. (TODO: actually we don't need to encode it over and over | |
1861 again either.) | |
1862 | |
1863 =============================================================================== | |
1864 2007-10-16 James Bonfield <jkb@sanger.ac.uk> | |
1865 | |
1866 * progs/solexa2srf.c, | |
1867 * srf/srf.c, | |
1868 * ztr/compression.c, | |
1869 * ztr/deflate_interlaced.c, | |
1870 * ztr/deflate_interlaced.h, | |
1871 * ztr/ztr.c: | |
1872 * ztr/ztr.h: | |
1873 (08:36:06) Improvements to speed following code profiling. | |
1874 | |
1875 * progs/solexa2srf.c: | |
1876 (16:49:38) Major overhaul of parsing code. We now roll our own | |
1877 specialist parser instead of using strtok and sscanf. This has | |
1878 approximately doubled the speed (so maybe 4-5x faster in the | |
1879 parsing component). | |
1880 | |
1881 * configure.in: | |
1882 (16:52:06) Boost version to 1.11.0b3 | |
1883 | |
1884 2007-10-11 James Bonfield <jkb@sanger.ac.uk> | |
1885 | |
1886 * ztr/deflate_interlaced.c: | |
1887 (13:34:48) Fixed a buffer overrun. | |
1888 | |
1889 * ztr/compression.c: | |
1890 (13:35:59) Removed a small memory leak and improved initialisation | |
1891 in tshift to avoid (harmless) valgrind error. | |
1892 | |
1893 * progs/srf2solexa.c, | |
1894 * progs/srf_dump_all.c, | |
1895 * srf/srf.c: | |
1896 (13:37:29) Removed memory leaks. | |
1897 | |
1898 2007-10-02 James Bonfield <jkb@sanger.ac.uk> | |
1899 | |
1900 * README, | |
1901 * ztr/FORMAT: | |
1902 (08:55:47) Minor doc updates | |
1903 | |
1904 * read/Makefile.am: | |
1905 (08:57:02) Fixed src vs srf typo. | |
1906 | |
1907 * README: | |
1908 (08:58:09) Version change | |
1909 | |
1910 * configure.in: | |
1911 (08:59:11) Version change | |
1912 | |
1913 2007-09-28 James Bonfield <jkb@sanger.ac.uk> | |
1914 | |
1915 * Makefile.am, | |
1916 * configure.in, | |
1917 * progs/Makefile.am, | |
1918 * progs/solexa2srf.c, | |
1919 * progs/srf2solexa.c, | |
1920 * progs/srf_dump_all.c: | |
1921 (11:07:15) File Edit Options Buffers Tools Help Version 1.11.0b1 | |
1922 | |
1923 Added preliminary SRF support. This consists of a new subdirectory | |
1924 'srf' (yes these all really need merging into a single directory, | |
1925 but that's a later task), a substantial update to ZTR and a variety | |
1926 of SRF tools in progs. | |
1927 | |
1928 The old huffman_static.[ch] files were renamed and substantially | |
1929 worked upon to create deflate_interlaced.[ch]. | |
1930 | |
1931 Added new compression types. xrle2, tshift and qshift. The latter | |
1932 two of these are very specific to trace and quality packings. May | |
1933 need to rename to be more generic. | |
1934 | |
1935 * progs/srf_extract_linear.c, | |
1936 * progs/srf_index_hash.c, | |
1937 * progs/ztr_dump.c, | |
1938 * read/Makefile.am, | |
1939 * srf/srf.c, | |
1940 * srf/srf.h, | |
1941 * ztr/compression.c, | |
1942 * ztr/compression.h, | |
1943 * ztr/deflate_interlaced.c, | |
1944 * ztr/deflate_interlaced.h, | |
1945 * ztr/Attic/huffman_static.c, | |
1946 * ztr/Attic/huffman_static.h, | |
1947 * ztr/ztr.c, | |
1948 * ztr/ztr.h: | |
1949 (11:07:16) File Edit Options Buffers Tools Help Version 1.11.0b1 | |
1950 | |
1951 Added preliminary SRF support. This consists of a new subdirectory | |
1952 'srf' (yes these all really need merging into a single directory, | |
1953 but that's a later task), a substantial update to ZTR and a variety | |
1954 of SRF tools in progs. | |
1955 | |
1956 The old huffman_static.[ch] files were renamed and substantially | |
1957 worked upon to create deflate_interlaced.[ch]. | |
1958 | |
1959 Added new compression types. xrle2, tshift and qshift. The latter | |
1960 two of these are very specific to trace and quality packings. May | |
1961 need to rename to be more generic. | |
1962 | |
1963 * ztr/compression.c: | |
1964 (15:28:12) Fixed a bug in run length encoding XRLE2 format when | |
1965 dealing with very long repeat runs. | |
1966 | |
1967 * ztr/FORMAT-1.2: | |
1968 (15:34:26) Fixed error in XRLE description. | |
1969 | |
1970 * ztr/FORMAT: | |
1971 (15:34:41) Further updates documenting version 1.3 changes | |
1972 | |
1973 2007-09-03 James Bonfield <jkb@sanger.ac.uk> | |
1974 | |
1975 * ztr/Attic/deflate_simple.c, | |
1976 * ztr/Attic/deflate_simple.h: | |
1977 (11:11:12) Mostly a rename from huffman_static to deflate_simple, | |
1978 but also a large overhaul and redesign. This code implements the | |
1979 huffman component of the Deflate algorithm. | |
1980 | |
1981 * ztr/compression.c, | |
1982 * ztr/compression.h, | |
1983 * ztr/ztr.c, | |
1984 * ztr/ztr.h: | |
1985 (11:12:16) Updates to deal with the change from huffman_static to | |
1986 deflate_simple. | |
1987 | |
1988 * Makefile: | |
1989 * Makefile.am, | |
1990 * read/Makefile.am: | |
1991 * progs/ztr_dump.c: | |
1992 (11:35:50) Update for rename of huffman_static.h to | |
1993 deflate_simple.h | |
1994 | |
1995 2007-08-15 James Bonfield <jkb@sanger.ac.uk> | |
1996 | |
1997 * ztr/compression.c, | |
1998 * ztr/Attic/huffman_static.c, | |
1999 * ztr/Attic/huffman_static.h: | |
2000 (15:30:04) Major overhaul of huffman_static.c. | |
2001 | |
2002 It's been substantially tuned for speed and also has several bug | |
2003 fixes to ensure we have a consistent sort function before applying | |
2004 the canonical_codes function (which previously meant differing | |
2005 qsort implementations would give different codes). | |
2006 | |
2007 * ztr/FORMAT-1.2: | |
2008 (15:31:58) Created a snapshot of FORMAT for ZTR v1.2 only | |
2009 | |
2010 2007-07-16 James Bonfield <jkb@sanger.ac.uk> | |
2011 | |
2012 * acinclude.m4, | |
2013 * configure.in: | |
2014 (08:03:42) Updated configure.in to support --with-lib=DIR. | |
2015 | |
2016 * utils/files.c: | |
2017 (08:05:23) Switched from using tempnam() to tmpfile(). This meant | |
2018 recreating tmpfile() wrapper on MS Windows to avoid bugs with it | |
2019 always attempting to write to the root directory, regardless of | |
2020 user privs. | |
2021 | |
2022 * utils/open_trace_file.c, | |
2023 * utils/os.h: | |
2024 (08:05:24) Switched from using tempnam() to tmpfile(). This meant | |
2025 recreating tmpfile() wrapper on MS Windows to avoid bugs with it | |
2026 always attempting to write to the root directory, regardless of | |
2027 user privs. | |
2028 | |
2029 * progs/hash_extract.c: | |
2030 (09:01:39) Fixed bug on windows: we now set stdout to be binary | |
2031 mode first. | |
2032 | |
2033 * utils/open_trace_file.c: | |
2034 (09:02:51) INCOMPATIBLE CHANGE: On windows we now use semi-colon as | |
2035 the path separator. The reason is that with the MinGW getenv() | |
2036 seems to do "clever things" with PATH variables and consequently | |
2037 ends up corrupting our clumsy attempt of escaping colons in paths. | |
2038 | |
2039 2007-07-11 James Bonfield <jkb@sanger.ac.uk> | |
2040 | |
2041 * Makefile, | |
2042 * Makefile.am, | |
2043 * read/Makefile.am, | |
2044 * utils/hash_table.c, | |
2045 * utils/hash_table.h, | |
2046 * utils/jenkins_lookup3.c, | |
2047 * utils/jenkins_lookup3.h: | |
2048 (13:57:26) Added Bob Jenkins' lookup3.c code to the hash_table | |
2049 support. It also now uses this for 64-bit hashing. | |
2050 | |
2051 2007-07-06 James Bonfield <jkb@sanger.ac.uk> | |
2052 | |
2053 * ztr/Attic/huffman_static.c: | |
2054 (09:06:46) Bug fix to last commit - finish adding the CODE_ENGLISH | |
2055 and removal of other code sets. | |
2056 | |
2057 2007-07-05 James Bonfield <jkb@sanger.ac.uk> | |
2058 | |
2059 * plain/seqIOPlain.c: | |
2060 (08:27:43) For FASTA format files we now, eventually, read the | |
2061 first sequence. | |
2062 | |
2063 * ztr/FORMAT, | |
2064 * ztr/Attic/huffman_static.c, | |
2065 * ztr/Attic/huffman_static.h, | |
2066 * ztr/ztr.c, | |
2067 * ztr/ztr.h: | |
2068 (08:28:30) Work-in-progress update to support HUFF chunks and | |
2069 STHUFF (static huffman) compression methods. | |
2070 | |
2071 * progs/ztr_dump.c: | |
2072 (08:29:15) Updated to support the new static-huffman compression | |
2073 method. | |
2074 | |
2075 * ztr/Attic/huffman_static.c, | |
2076 * ztr/Attic/huffman_static.h: | |
2077 (10:45:48) Removed potentially variable huffman trees (solexa | |
2078 trace, confidence values) and added an english text tree. This was | |
2079 based on War of the Worlds, The Gold Bug, 200000 Leagues Under the | |
2080 Sea and the "man ascii" unix manual page for a bit of variety. It | |
2081 also includes the SYM_ANY escape code for handling out-of-band | |
2082 data. | |
2083 | |
2084 =============================================================================== | |
2085 2007-05-30 James Bonfield <jkb@sanger.ac.uk> | |
2086 | |
2087 * progs/extract_seq.c: | |
2088 (11:10:59) Fixed usage string (added -ztr). | |
2089 | |
2090 * io_lib-config.in: | |
2091 (11:11:26) Added explicit @LIBZ@ to --libs. | |
2092 | |
2093 * progs/hash_sff.c: | |
2094 (11:12:07) Fixed FILE handling bug. | |
2095 | |
2096 * ztr/ztr.c: | |
2097 (11:13:07) Maded entropy() static to avoid clash with ztr_dump.c | |
2098 | |
2099 * CHANGES, | |
2100 * README, | |
2101 * configure.in: | |
2102 (11:34:53) Updated to version 1.10.2 | |
2103 | |
2104 2007-04-19 James Bonfield <jkb@sanger.ac.uk> | |
2105 | |
2106 * utils/hash_table.c: | |
2107 (16:18:19) Fixed a memory leak and also changed to use off_t | |
2108 instead of long for file offsets. | |
2109 | |
2110 * ztr/Attic/huffman_static.c: | |
2111 * ztr/Attic/huffman_static.h: | |
2112 * ztr/ztr.c: | |
2113 * ztr/ztr.h: | |
2114 * Makefile: | |
2115 * Makefile.am: | |
2116 * read/Makefile.am: | |
2117 (16:21:59) Added HUFFMAN_STATIC ZTR compression method. | |
2118 | |
2119 * configure.in: | |
2120 * abi/fpoint.h: | |
2121 * abi/seqIOABI.h: | |
2122 * ctf/seqIOCTF.h, | |
2123 * exp_file/expFileIO.h: | |
2124 * progs/convert_trace.c, | |
2125 * progs/extract_fastq.c: | |
2126 * progs/extract_seq.c: | |
2127 * progs/hash_sff.c, | |
2128 * progs/makeSCF.c: | |
2129 * progs/ztr_dump.c: | |
2130 * read/Read.h: | |
2131 * read/scf_extras.h: | |
2132 * read/translate.h: | |
2133 * scf/scf.h: | |
2134 * sff/sff.h: | |
2135 * utils/array.h: | |
2136 * utils/compress.h: | |
2137 * utils/error.h: | |
2138 * utils/hash_table.h: | |
2139 * utils/mFILE.h: | |
2140 * utils/mach-io.h: | |
2141 * utils/misc.h: | |
2142 * utils/open_trace_file.h: | |
2143 * utils/os.h: | |
2144 * utils/stdio_hack.h: | |
2145 * utils/tar_format.h: | |
2146 * utils/traceType.h: | |
2147 * utils/vlen.h: | |
2148 * utils/xalloc.h: | |
2149 * ztr/compression.h: | |
2150 (16:30:14) Added extern "C" {...} guards around all header files to | |
2151 ease use from within C++ source. | |
2152 | |
2153 2006-08-07 James Bonfield <jkb@sanger.ac.uk> | |
2154 | |
2155 * progs/convert_trace.c: | |
2156 (14:12:39) Added -signed and -noneg options to perform shifting of | |
2157 trace data to avoid the unsigned issues for TRACE. | |
2158 | |
2159 2006-07-18 James Bonfield <jkb@sanger.ac.uk> | |
2160 | |
2161 * utils/traceType.c: | |
2162 (13:44:13) Added support for anytr in str2int and int2str | |
2163 conversions. | |
2164 | |
2165 2006-07-06 James Bonfield <jkb@sanger.ac.uk> | |
2166 | |
2167 * progs/hash_exp.c: | |
2168 (08:45:18) Use binary mode, for windows. | |
2169 | |
2170 * progs/hash_exp.c: | |
2171 (09:20:20) Remove control-M from end of line when indexing ID | |
2172 lines. | |
2173 | |
2174 * progs/hash_exp.c: | |
2175 (09:22:52) Oops; removal of debugging info | |
2176 | |
2177 2006-07-05 James Bonfield <jkb@sanger.ac.uk> | |
2178 | |
2179 * Makefile, | |
2180 * dependencies: | |
2181 (15:45:01) Fixed dependency generation for io_lib | |
2182 | |
2183 2006-07-04 James Bonfield <jkb@sanger.ac.uk> | |
2184 | |
2185 * utils/mFILE.c, | |
2186 * utils/mFILE.h: | |
2187 (13:43:28) Added mfcreate_from(). It has a usage syntax identical | |
2188 to mfreopen(), but unlike mfreopen() it doesn't do anything with | |
2189 the file pointer (neither closing ie or remembering it in the | |
2190 structure). | |
2191 | |
2192 * progs/extract_fastq.c: | |
2193 (16:19:30) Pathname hacking and listed -ztr on command line. | |
2194 | |
2195 * progs/extract_seq.c, | |
2196 * progs/makeSCF.c: | |
2197 (16:20:17) Added -ztr as a command line option. | |
2198 | |
2199 * progs/hash_exp.c: | |
2200 (16:21:14) Hash_exp now outputs to the same file containing the | |
2201 experiment files (in appended hash-table mode). | |
2202 | |
2203 * progs/hash_extract.c: | |
2204 (16:21:53) Bug fix: now only needs at least 1 filename specified | |
2205 when fofn mode is not in use. | |
2206 | |
2207 * progs/hash_list.c: | |
2208 (16:22:40) error detection and protection | |
2209 | |
2210 2006-06-27 James Bonfield <jkb@sanger.ac.uk> | |
2211 | |
2212 * utils/mFILE.c: | |
2213 (11:16:21) Bug fix to the previous change: mstdin(), mstdout() and | |
2214 mstderr() now correctly mark their streams and read and write | |
2215 capable. | |
2216 | |
2217 * utils/mFILE.c, | |
2218 * utils/mFILE.h: | |
2219 (15:48:15) Added mfdetach() to allow the file pointer to be closed | |
2220 without deallocating the mFILE structure. | |
2221 | |
2222 Also removed the mFILE->fname component and replaced uses with | |
2223 checks to mode & MF_WRITE. | |
2224 | |
2225 * utils/mFILE.c, | |
2226 * utils/mFILE.h: | |
2227 (15:58:52) Corrected duff spelling! | |
2228 | |
2229 2006-06-26 James Bonfield <jkb@sanger.ac.uk> | |
2230 | |
2231 * utils/mFILE.c, | |
2232 * utils/mFILE.h: | |
2233 (16:47:30) Fixed a bug in mfflush whereby it could attempt to write | |
2234 HUGE amounts of data (-ve size) when files are truncated before | |
2235 flushing; it now fseeks before doing the write and checks if the | |
2236 size is +ve. | |
2237 | |
2238 Also fixed mfwrite to correctly reset the flush_pos record. | |
2239 | |
2240 Added a mode field to the mFILE structure so we can keep track of | |
2241 append and read-only flags. These are checked for in the mfwrite | |
2242 function so mfwrite now writes to the correct location when append | |
2243 mode is used (ie forced to the end of file) and it now returns 0 | |
2244 when attempting to write to a read-only mFILE. | |
2245 | |
2246 =============================================================================== | |
2247 2006-06-20 awhitwham <awhitwham@sanger.ac.uk> | |
2248 | |
2249 * utils/open_trace_file.c: | |
2250 (11:37:24) Changed to open trace files as read only | |
2251 | |
2252 * configure.in: | |
2253 (13:42:57) Updated to version 1.10.1 | |
2254 | |
2255 2006-06-15 James Bonfield <jkb@sanger.ac.uk> | |
2256 | |
2257 * io_lib.m4: | |
2258 (10:58:46) First working(?) version; testing on the Internal Trace | |
2259 Server. | |
2260 | |
2261 * io_lib.m4: | |
2262 (11:18:39) bug fix IO_LIB_CPPFLAGS & IO_LIB_LDFLAGS initialisation" | |
2263 | |
2264 * Makefile.am: | |
2265 (11:25:57) Added io_lib-config to install scripts | |
2266 | |
2267 * progs/Makefile.am: | |
2268 (11:26:28) Added LIBCURL flags | |
2269 | |
2270 * read/Makefile.am: | |
2271 (11:26:54) Added LIBCURL_CPPFLAGS usage. | |
2272 | |
2273 * CHANGES: | |
2274 (15:40:12) *** empty log message *** | |
2275 | |
2276 * progs/Makefile.am: | |
2277 (15:40:28) Added ztr_dump to the list of progs. | |
2278 | |
2279 * progs/ztr_dump.c: | |
2280 (15:41:05) Support for log2 format. | |
2281 | |
2282 * ztr/compression.c, | |
2283 * ztr/compression.h, | |
2284 * ztr/ztr.c: | |
2285 (15:42:06) Added a ZTR_FORM_LOG2 compression technique. It's an | |
2286 experimental lossy compression and is turned off right now; the | |
2287 space saving was only about 10% and if we go lossy I want big | |
2288 changes not small ones. | |
2289 | |
2290 * ztr/ztr.h: | |
2291 (15:42:07) Added a ZTR_FORM_LOG2 compression technique. It's an | |
2292 experimental lossy compression and is turned off right now; the | |
2293 space saving was only about 10% and if we go lossy I want big | |
2294 changes not small ones. | |
2295 | |
2296 * README: | |
2297 (15:43:46) *** empty log message *** | |
2298 | |
2299 2006-06-14 James Bonfield <jkb@sanger.ac.uk> | |
2300 | |
2301 * progs/convert_trace.c: | |
2302 (08:53:43) Added a -error option to request stderr goes to a file | |
2303 instead of stderr. (from Saul Kravitz) | |
2304 | |
2305 * scf/misc_scf.c, | |
2306 * scf/read_scf.c, | |
2307 * scf/write_scf.c: | |
2308 (08:58:12) Renamed delta_samples[12] to be scf_delta_samples[12]. | |
2309 (patch supplied by Saul Kravitz) | |
2310 | |
2311 * scf/scf.h: | |
2312 (08:58:29) Renamed delta_samples[12] to be scf_delta_samples[12]. | |
2313 (patch supplied by Saul Kravitz) | |
2314 | |
2315 * utils/open_trace_file.c: | |
2316 (08:58:55) Comment update | |
2317 | |
2318 * utils/open_trace_file.c: | |
2319 * Makefile: | |
2320 (16:28:29) Renamed USE_LIBCURL to be HAVE_LIBCURL to make it | |
2321 compatible with autoconf. | |
2322 | |
2323 * bootstrap: | |
2324 (16:28:56) Added removal of io_lib-config | |
2325 | |
2326 * acinclude.m4, | |
2327 * configure.in: | |
2328 (16:29:55) Added libcurl checking code (in acinclude.m4). | |
2329 | |
2330 * io_lib-config.in: | |
2331 (16:31:18) New io_lib-config program to query the compile and link | |
2332 parameters needed when using io_lib. | |
2333 | |
2334 * io_lib.m4: | |
2335 (16:46:32) Initial draft (unchecked) of autoconf macros for use by | |
2336 packages (in configure.in) that want to make use of io_lib. | |
2337 | |
2338 2006-06-13 James Bonfield <jkb@sanger.ac.uk> | |
2339 | |
2340 * progs/Makefile: | |
2341 (11:50:47) Added ZLIB_INC include path. | |
2342 | |
2343 2006-06-09 James Bonfield <jkb@sanger.ac.uk> | |
2344 | |
2345 * utils/open_trace_file.c: | |
2346 (08:53:24) Somewhere along the line I managed to break the most | |
2347 common of all search mechanisms; local filenames on disk! Fixed | |
2348 find_file_dir(). | |
2349 | |
2350 2006-06-08 James Bonfield <jkb@sanger.ac.uk> | |
2351 | |
2352 * Makefile, | |
2353 * utils/open_trace_file.c: | |
2354 (13:21:59) Added libcurl support and made this the default instead | |
2355 of using WGET for URL based accesses. Fixed a bug in the old wget | |
2356 code also though involving handling of zero-sized replies. | |
2357 | |
2358 Removed the compressed file extension iteration code in | |
2359 find_file_dir as it's now included in the master open_trace_file | |
2360 function instead (and so was yielding stats on fubar.scf.gz.bz2 and | |
2361 similar). It's also now possible to turn off the compressed file | |
2362 extension iteration code by prefixing a search path element with a | |
2363 "|" symbol. | |
2364 | |
2365 Replaced RAWDATA environment with EXP_PATH and TRACE_PATH. These | |
2366 default back to RAWDATA when not defined. Created new functions | |
2367 named open_exp_file and open_exp_mfile which use EXP_PATH instead | |
2368 of TRACE_PATH. These allow for experiment files and trace files to | |
2369 share the same names (as is the case in external "trace servers") | |
2370 but use different accessor routes to return the data. | |
2371 | |
2372 * utils/open_trace_file.h: | |
2373 (13:22:40) New prototypes or the open_exp_{file,mfile} code and | |
2374 iolib_[sg]et_{trace,exp}_path calls. | |
2375 | |
2376 * progs/Makefile, | |
2377 * progs/hash_exp.c: | |
2378 (13:25:15) New program hash_exp. This allows for multiple | |
2379 experiment files to be concatenated together instead a single | |
2380 multi-sequence file and then be indexed (using hash_exp) to allow | |
2381 for a HASH=... EXP_PATH element to extract the data back out again. | |
2382 | |
2383 * progs/convert_trace.c, | |
2384 * progs/extract_seq.c, | |
2385 * read/Read.c, | |
2386 * read/Read.h, | |
2387 * read/scf_extras.c, | |
2388 * read/translate.c: | |
2389 (13:28:29) Make use of open_exp_mfile instead of open_trace_mfile | |
2390 when we know we've explicitly requested a file in EXP format. This | |
2391 ensures we'll use the correct search path where appropriate. | |
2392 | |
2393 Also defined an ANYTR trace format which is identical to the old | |
2394 ANY format except that it excludes EXP and PLN (ie "ANY TRace"). | |
2395 Again this is used internally to ensure we pick the correct search | |
2396 path when dealing with fetching traces and/or experiment files. | |
2397 | |
2398 * utils/mFILE.c: | |
2399 (13:29:23) Fixed a bug in mfseek and mrewind. Both now clear the | |
2400 EOF flag. | |
2401 | |
2402 * utils/traceType.c: | |
2403 (13:33:16) Bug fix to fdetermine_trace_type: now rewinds back. | |
2404 | |
2405 * Makefile: | |
2406 (15:21:02) Fixed the include/.links target (added sff) | |
2407 | |
2408 * progs/Makefile, | |
2409 * progs/extract_fastq.c: | |
2410 (15:22:24) Added extract_fastq program. | |
2411 | |
2412 2006-05-30 James Bonfield <jkb@sanger.ac.uk> | |
2413 | |
2414 * ztr/compression.c: | |
2415 (08:46:57) Fixed a bug in xrle(); it now correctly handles runs of | |
2416 256 or more. | |
2417 | |
2418 2006-04-12 James Bonfield <jkb@sanger.ac.uk> | |
2419 | |
2420 * read/Read.c: | |
2421 (10:53:27) Changed various fwrite_* functions to not close the FILE | |
2422 pointer given to them. | |
2423 | |
2424 2006-02-28 James Bonfield <jkb@sanger.ac.uk> | |
2425 | |
2426 * ztr/compression.c: | |
2427 (17:10:36) Fixed bug reading past memory in xrle(). (Thanks to | |
2428 Kathryn Beal for identifying this.) | |
2429 | |
2430 2006-02-27 James Bonfield <jkb@sanger.ac.uk> | |
2431 | |
2432 * ztr/ztr.c, | |
2433 * ztr/ztr.h: | |
2434 (14:40:06) Removed static from compress_chunk and uncompress_chunk. | |
2435 Added prototypes to ztr.h. | |
2436 | |
2437 2006-02-23 James Bonfield <jkb@sanger.ac.uk> | |
2438 | |
2439 * utils/read_alloc.c: | |
2440 (15:08:36) Fixed a bug in read_dup and not initialising read->info. | |
2441 | |
2442 * utils/read_alloc.c: | |
2443 (16:00:44) Fixed typo. | |
2444 | |
2445 2006-02-20 James Bonfield <jkb@sanger.ac.uk> | |
2446 | |
2447 * utils/hash_table.c: | |
2448 (12:16:50) Allow HashTableAdd to take a non-string for the key. | |
2449 | |
2450 2006-01-26 James Bonfield <jkb@sanger.ac.uk> | |
2451 | |
2452 * utils/hash_table.c, | |
2453 * utils/hash_table.h: | |
2454 (09:37:02) Fixed HashTableAdd with non-string keys and without | |
2455 HASH_NONVOLATILE_KEYS defined. It used strdup, but now allocates | |
2456 and memcpys. | |
2457 | |
2458 Added HashTableDel and HashTableRemove functions. HashTableDel | |
2459 removes and destroys a specified HashItem. HashTableRemove removes | |
2460 and destroys all items attached to a given key. | |
2461 | |
2462 =============================================================================== | |
2463 2005-12-14 James Bonfield <jkb@sanger.ac.uk> | |
2464 | |
2465 * CHANGES, | |
2466 * README, | |
2467 * configure.in: | |
2468 (14:35:00) Update for 1.9.2 | |
2469 | |
2470 2005-12-09 James Bonfield <jkb@sanger.ac.uk> | |
2471 | |
2472 * configure.in: | |
2473 (17:32:31) Added AC_CHECK_LIB calls for nsl and socket | |
2474 (gethostbyname and socket). Needed for Solaris compilations. | |
2475 | |
2476 2005-11-16 James Bonfield <jkb@sanger.ac.uk> | |
2477 | |
2478 * progs/extract_seq.c: | |
2479 (14:14:16) Used open_trace_mfile instead of open_trace_file to | |
2480 avoid the need for temporary files and hence speeds this up. | |
2481 | |
2482 * read/Read.c: | |
2483 (14:23:23) fwrite_reading now frees the temporary mFILE it created. | |
2484 | |
2485 * read/Read.h, | |
2486 * read/translate.c: | |
2487 (14:45:41) Added private_data and private_size to the Read | |
2488 structure & populate from SCF. | |
2489 | |
2490 * utils/compress.c: | |
2491 (14:48:51) mfreopen_compressed no longer closes the original FILE*. | |
2492 This makes it backwards compatible once more with the original | |
2493 version and also cures a bug whereby the old file pointer was often | |
2494 left open, leading to running out of file descriptors. | |
2495 | |
2496 * utils/mFILE.c: | |
2497 (15:05:51) Fixed uninitialised check when filename was specified | |
2498 but not found in mfload. | |
2499 | |
2500 * utils/read_alloc.c: | |
2501 (15:17:01) Added private_data to read struct | |
2502 | |
2503 2005-11-10 James Bonfield <jkb@sanger.ac.uk> | |
2504 | |
2505 * progs/hash_extract.c: | |
2506 (11:32:06) Now returns an error code (to the calling process) if it | |
2507 failed to extract a sequence. | |
2508 | |
2509 * utils/hash_table.c: | |
2510 (11:33:07) Fixed problem in hashquery when searching for something | |
2511 that has a hash key not present (ie empty hash bucket). | |
2512 | |
2513 =============================================================================== | |
2514 2005-10-27 James Bonfield <jkb@sanger.ac.uk> | |
2515 | |
2516 * utils/mFILE.c: | |
2517 (15:46:45) Fixed hang in mfload when given zero length files. | |
2518 | |
2519 2005-10-25 James Bonfield <jkb@sanger.ac.uk> | |
2520 | |
2521 * read/translate.c: | |
2522 (08:20:26) NDEBUG checks | |
2523 | |
2524 2005-10-21 James Bonfield <jkb@sanger.ac.uk> | |
2525 | |
2526 * bootstrap: | |
2527 (09:15:23) Removed more auto-generated files. | |
2528 | |
2529 * configure.in, | |
2530 * progs/Makefile.am: | |
2531 (09:16:43) Further removal of libtool specific bits (AC_CHECK_LIB). | |
2532 | |
2533 * Makefile: | |
2534 (16:03:35) Fixed bug with IOLIB_ZTR vs IOLIB_SFF macro. | |
2535 | |
2536 * Makefile.am, | |
2537 * bootstrap, | |
2538 * configure.in, | |
2539 * read/Read.h, | |
2540 * utils/compress.c: | |
2541 (16:04:48) Replaced automake's generated config.h file | |
2542 io_lib_config and allow for it to be installed with "make install". | |
2543 | |
2544 * progs/Makefile.am: | |
2545 (16:05:19) Added append_sff to the targets. | |
2546 | |
2547 * read/translate.c: | |
2548 (16:05:42) Disabled asserts | |
2549 | |
2550 * utils/mFILE.c: | |
2551 (16:06:25) Fixed bug in mfgetc when dealing with 8-bit data. It | |
2552 always now returns unsigned values except when EOF | |
2553 | |
2554 * utils/open_trace_file.c: | |
2555 (16:07:20) Updated TAR magic number to be just the 5 first bytes as | |
2556 the 6th differs between systems (space vs nul). | |
2557 | |
2558 2005-10-20 James Bonfield <jkb@sanger.ac.uk> | |
2559 | |
2560 * sff/sff.c: | |
2561 (13:31:22) Split the read functions into read & decode functions so | |
2562 that we can unpack SFF structs from other sources. | |
2563 | |
2564 * progs/Makefile, | |
2565 * progs/append_sff.c: | |
2566 (13:31:58) Added an append_sff.c program, to combine multiple SFF | |
2567 archives into a single archive. | |
2568 | |
2569 2005-10-18 James Bonfield <jkb@sanger.ac.uk> | |
2570 | |
2571 * progs/convert_trace.c: | |
2572 (16:41:44) Modified to check RAWDATA search path when loading | |
2573 traces. | |
2574 | |
2575 * progs/hash_sff.c: | |
2576 (16:42:58) Major overhaul to not load the entire SFF file into | |
2577 memory. It also handles copying the SFF file to a new file and | |
2578 adding an index to an SFF archive that already has an index. | |
2579 | |
2580 * sff/sff.c, | |
2581 * sff/sff.h: | |
2582 (16:44:31) Restructured read functions to load & decode functions | |
2583 so we can decode SFF data blocks obtained via other means (eg as | |
2584 used in the indexing code). | |
2585 | |
2586 * utils/open_trace_file.c: | |
2587 (16:45:42) Added SFF "sorted index" code, based on 454's getsff.c | |
2588 implementation. Also restructured the SFF querying code a bit so | |
2589 that it caches this data. | |
2590 | |
2591 2005-10-14 James Bonfield <jkb@sanger.ac.uk> | |
2592 | |
2593 * CHANGES: | |
2594 (16:07:36) *** empty log message *** | |
2595 | |
2596 * exp_file/expFileIO.c: | |
2597 (16:08:32) Renamed _MSV_VER to _WIN32 so that the binary/ascii | |
2598 conversions for experiment file IO works once more under Windows. | |
2599 | |
2600 * progs/Makefile, | |
2601 * progs/Makefile.am, | |
2602 * progs/hash_sff.c: | |
2603 (16:09:08) Added hash_sff program. This adds a .hsh format index to | |
2604 the SFF container. | |
2605 | |
2606 * sff/sff.c, | |
2607 * sff/sff.h: | |
2608 (16:10:10) A total rewrite of the SFF code due to the recent | |
2609 changes in file format. This code handles access of a *single* SFF | |
2610 entry. The code to manipulate multi-file SFF (ie the container) is | |
2611 in open_trace_file.c. | |
2612 | |
2613 * utils/hash_table.c, | |
2614 * utils/hash_table.h: | |
2615 (16:11:33) HashFileSave now returns the length of the saved hash. | |
2616 | |
2617 HashFileFopen now sets afp by default to be the same as hfp. Extra | |
2618 checking has been added when closing these file pointers to ensure | |
2619 we don't close twice if they point to the same FILE*. | |
2620 | |
2621 * utils/mFILE.c, | |
2622 * utils/mFILE.h: | |
2623 (16:12:58) Added an mfascii() function. This allows for changing | |
2624 from binary to ascii after a file has been opened. It should be | |
2625 called in place of where the windows-specific _set_mode() function | |
2626 would be used. | |
2627 | |
2628 There is currently no analagous ascii-to-binary conversion, but I | |
2629 have not yet found a need for it either. | |
2630 | |
2631 * utils/mach-io.c, | |
2632 * utils/mach-io.h: | |
2633 (16:13:29) Added [bl]e_{read,write}_int_8 functions for use with | |
2634 8-byte data types found in SFF. | |
2635 | |
2636 * utils/open_trace_file.c: | |
2637 (16:14:55) Added a SFF= format for the RAWDATA search path. This | |
2638 handles the SFF container in much the same way that TAR= and HASH= | |
2639 works. | |
2640 | |
2641 Also for all three of these types you can now do archive/entry | |
2642 instead. Eg "extract_seq traces.tar/xyz.ztr" will work and it'll | |
2643 even look for traces.tar in RAWDATA if required. | |
2644 | |
2645 * utils/os.h: | |
2646 (16:15:19) Added a uint1 typedef for completeness. | |
2647 | |
2648 * Makefile.am, | |
2649 * read/Makefile.am: | |
2650 (16:16:06) Makefile support for new sff.c files. | |
2651 | |
2652 * dependencies: | |
2653 (16:16:23) *** empty log message *** | |
2654 | |
2655 * configure.in: | |
2656 (16:16:43) Updated to version 1.9.1. | |
2657 | |
2658 2005-10-04 James Bonfield <jkb@sanger.ac.uk> | |
2659 | |
2660 * Makefile: | |
2661 (08:54:30) Added sff to make distsrc | |
2662 | |
2663 * utils/hash_table.c: | |
2664 (11:34:03) Cast ptrdiff_t value to int for %.*s argument. | |
2665 | |
2666 2005-09-29 James Bonfield <jkb@sanger.ac.uk> | |
2667 | |
2668 * utils/hash_table.c, | |
2669 * utils/hash_table.h: | |
2670 (16:04:06) Fixed the hash file saving and loading so that it works | |
2671 on all platforms instead of just x86 linux. There were bugs in | |
2672 assuming the size of structures. The assumptions are still there in | |
2673 that I assume they pad the same internally (for ease of coding - we | |
2674 can change it when we finally see a system which operates | |
2675 differently), but the final "boundary" padding has been resolved. | |
2676 | |
2677 2005-09-28 James Bonfield <jkb@sanger.ac.uk> | |
2678 | |
2679 * progs/hash_list.c: | |
2680 (10:16:49) *** empty log message *** | |
2681 | |
2682 2005-09-19 James Bonfield <jkb@sanger.ac.uk> | |
2683 | |
2684 * utils/compress.c: | |
2685 (13:58:02) Fixed a file descriptor (and some memory) leak in | |
2686 freopen_compressed. (Bug ID 1289095) | |
2687 | |
2688 2005-09-08 James Bonfield <jkb@sanger.ac.uk> | |
2689 | |
2690 * ztr/ztr.c, | |
2691 * ztr/ztr_translate.c: | |
2692 (11:29:06) Don't try to compress SAMP chunks with meta-data PYRW as | |
2693 the raw pyrosequencing data from 454 doesn't compress. | |
2694 | |
2695 * progs/Makefile, | |
2696 * progs/hash_tar.c, | |
2697 * utils/Hash_File_Format, | |
2698 * utils/hash_table.c, | |
2699 * utils/hash_table.h: | |
2700 (11:30:56) Changed the HashFile format slightly. It's now format | |
2701 1.00. | |
2702 | |
2703 The key difference is that it has a file footer pointing back to | |
2704 the hashfile header (so the hashfile can be appended to an archive) | |
2705 and it also has an offset in the header to apply to all seeks | |
2706 within the archive itself, so it can be prepending to an archive | |
2707 that's already been indexed without breaking the offsets. | |
2708 | |
2709 Extended the hash_tar program to allow control over these header | |
2710 options. | |
2711 | |
2712 2005-08-26 James Bonfield <jkb@sanger.ac.uk> | |
2713 | |
2714 * dependencies: | |
2715 (08:24:32) Rebuilt | |
2716 | |
2717 2005-08-25 James Bonfield <jkb@sanger.ac.uk> | |
2718 | |
2719 * progs/makeSCF.c, | |
2720 * ztr/ztr.c: | |
2721 (10:22:20) General code tidyup to prevent warnings. | |
2722 | |
2723 2005-08-15 James Bonfield <jkb@sanger.ac.uk> | |
2724 | |
2725 * utils/hash_table.c: | |
2726 (15:25:18) Fixed HashTableLoad so it correctly stores the HashTable | |
2727 in the HashFile structure. It also now checks for the correct size | |
2728 of file to load. | |
2729 | |
2730 * sff/sff.c, | |
2731 * sff/sff.h: | |
2732 (15:25:44) Added SFF (454 flowgram) file reading support. | |
2733 | |
2734 2005-08-10 James Bonfield <jkb@sanger.ac.uk> | |
2735 | |
2736 * Makefile, | |
2737 * README, | |
2738 * options.mk: | |
2739 (15:15:24) Added draft SFF format support. I need to verify if the | |
2740 example data files I tested this with are correct or if the SFF | |
2741 draft spec is correct (as they differ marginally in places). Hence | |
2742 this format may change soon. | |
2743 | |
2744 * read/Read.c, | |
2745 * read/Read.h, | |
2746 * utils/traceType.c: | |
2747 (15:15:25) Added draft SFF format support. I need to verify if the | |
2748 example data files I tested this with are correct or if the SFF | |
2749 draft spec is correct (as they differ marginally in places). Hence | |
2750 this format may change soon. | |
2751 | |
2752 * progs/ztr_dump.c: | |
2753 (15:16:31) Added (commented out) code for extra debugging. | |
2754 | |
2755 * progs/Makefile: | |
2756 (15:16:48) Added hash_extract to the Makefile. | |
2757 | |
2758 2005-07-22 James Bonfield <jkb@sanger.ac.uk> | |
2759 | |
2760 * utils/compress.c: | |
2761 (15:52:07) Unset compression_used when opening uncompressed files | |
2762 instead of leaving as the last value. | |
2763 | |
2764 2005-07-15 James Bonfield <jkb@sanger.ac.uk> | |
2765 | |
2766 * read/Read.c: | |
2767 (15:16:58) Removed file descriptor 'leak' in write_reading(). | |
2768 | |
2769 2005-07-14 James Bonfield <jkb@sanger.ac.uk> | |
2770 | |
2771 * exp_file/expFileIO.c: | |
2772 (13:53:45) Commenting only | |
2773 | |
2774 * read/Read.c, | |
2775 * utils/mFILE.c: | |
2776 (13:54:54) mfopen now honours binary verses ascii differences (and | |
2777 so updated Read.c calls accordingly) so that Windows works better. | |
2778 | |
2779 Also improved append mode of opening. | |
2780 | |
2781 2005-07-13 James Bonfield <jkb@sanger.ac.uk> | |
2782 | |
2783 * ztr/ztr.c: | |
2784 (08:41:16) Removed the warning for unknown chunk types. It now just | |
2785 silently stores them in memory. | |
2786 | |
2787 2005-07-11 James Bonfield <jkb@sanger.ac.uk> | |
2788 | |
2789 * utils/mFILE.c: | |
2790 (14:01:50) Fixed divide-by-zero buf when calling mfread for zero | |
2791 bytes. | |
2792 | |
2793 * read/Read.c: | |
2794 (16:07:38) Fixed IO_LIB_* macros to be IOLIB_* macros. | |
2795 | |
2796 2005-07-07 James Bonfield <jkb@sanger.ac.uk> | |
2797 | |
2798 * Makefile.am: | |
2799 * progs/Makefile.am: | |
2800 (09:01:50) Removed libtool requirements. | |
2801 | |
2802 * configure.in: | |
2803 (09:02:07) Removed use of libtool. | |
2804 | |
2805 * Attic/Makefile.in, | |
2806 * abi/Attic/Makefile.in: | |
2807 * alf/Attic/Makefile.in, | |
2808 * ctf/Attic/Makefile.in: | |
2809 * exp_file/Attic/Makefile.in, | |
2810 * plain/Attic/Makefile.in: | |
2811 * progs/Attic/Makefile.in, | |
2812 * read/Attic/Makefile.in, | |
2813 * scf/Attic/Makefile.in: | |
2814 * utils/Attic/Makefile.in, | |
2815 * ztr/Attic/Makefile.in: | |
2816 * Attic/config.h.in: | |
2817 * Attic/configure: | |
2818 * Attic/depcomp, | |
2819 * Attic/install-sh, | |
2820 * Attic/ltmain.sh, | |
2821 * Attic/missing: | |
2822 * abi/Attic/Makefile.am, | |
2823 * alf/Attic/Makefile.am, | |
2824 * ctf/Attic/Makefile.am: | |
2825 * exp_file/Attic/Makefile.am, | |
2826 * plain/Attic/Makefile.am, | |
2827 * scf/Attic/Makefile.am, | |
2828 * utils/Attic/Makefile.am, | |
2829 * ztr/Attic/Makefile.am: | |
2830 (09:09:50) Removed as these have now been collapsed into the | |
2831 read/Makefile.am. | |
2832 | |
2833 * README: | |
2834 (09:10:19) *** empty log message *** | |
2835 | |
2836 * read/Makefile.am: | |
2837 (09:12:18) Subsumed the other */Makefile.am files. | |
2838 | |
2839 * progs/hash_tar.c: | |
2840 (09:12:48) On Windows, set stdout to be _O_BINARY. | |
2841 | |
2842 * read/Read.c: | |
2843 (09:13:22) Fixed the _O_BINARY setting code on windows to check for | |
2844 fp being valid and to use the mf->fp instead of fp. | |
2845 | |
2846 * utils/compress.c: | |
2847 (09:15:30) Added checks for HAVE_SYS_WAIT_H for Windows handling. | |
2848 | |
2849 * utils/compress.c: | |
2850 (09:20:04) Moved HAVE_ZLIB_H from compress.c and put in os.h (when | |
2851 autoconf is not in use). | |
2852 | |
2853 * utils/hash_table.c: | |
2854 (09:21:45) Changed bucket_pos from int64_t to int32_t (as was | |
2855 intended) so it works on windows correctly. | |
2856 | |
2857 * utils/mFILE.c: | |
2858 (09:22:50) Added more _O_BINARY checks for windows. | |
2859 | |
2860 * utils/open_trace_file.c: | |
2861 (09:23:28) Added error checking in open_trace_file(). | |
2862 | |
2863 * bootstrap: | |
2864 (10:28:38) Added to simplify initialisation of the autoconf system. | |
2865 | |
2866 * utils/os.h: | |
2867 (10:34:54) Moved os.h from include to utils. | |
2868 | |
2869 * Makefile.am: | |
2870 (10:49:17) Fixed missing backslash in pkginclude_HEADERS. | |
2871 | |
2872 * Attic/config.guess, | |
2873 * Attic/config.sub, | |
2874 * Attic/ltconfig, | |
2875 * Attic/mkinstalldirs, | |
2876 * Attic/stamp-h.in: | |
2877 (10:55:09) Removed more auto-generated files from CVS tree. | |
2878 | |
2879 * read/Read.h: | |
2880 (14:28:29) *** empty log message *** | |
2881 | |
2882 2005-07-04 James Bonfield <jkb@sanger.ac.uk> | |
2883 | |
2884 * README: | |
2885 (09:24:49) *** empty log message *** | |
2886 | |
2887 * CHANGES: | |
2888 (09:24:50) *** empty log message *** | |
2889 | |
2890 * Makefile.am, | |
2891 * progs/Makefile.am, | |
2892 * read/Makefile.am, | |
2893 * scf/Attic/Makefile.am, | |
2894 * utils/Attic/Makefile.am: | |
2895 (09:25:34) Adjusted EXTRA_DIST definitions to only include files we | |
2896 still appear to have! | |
2897 | |
2898 * Attic/Makefile.in, | |
2899 * progs/Attic/Makefile.in: | |
2900 * read/Attic/Makefile.in, | |
2901 * scf/Attic/Makefile.in, | |
2902 * utils/Attic/Makefile.in: | |
2903 * Attic/config.h.in, | |
2904 * Attic/configure: | |
2905 * configure.in: | |
2906 (09:27:05) Updated to use newer AC_INIT syntax. | |
2907 | |
2908 * read/Read.c: | |
2909 (10:21:50) Made the default output format ZTR. Do not compress | |
2910 output (via gzip for example) if ZTR2 or ZTR3 is used. | |
2911 | |
2912 * utils/compress.c: | |
2913 (10:25:19) If HAVE_ZLIB isn't defined then the memgzip/memgunzip | |
2914 functions are now also not built (and hence removes compilation | |
2915 errors). | |
2916 | |
2917 The pipe2 function now uses waitpid to avoid zombies. | |
2918 | |
2919 * utils/mFILE.c, | |
2920 * utils/mFILE.h: | |
2921 (10:29:41) Added mfrecreate() function to change an existing | |
2922 mFILE to point to new data. Better handling of append mode in | |
2923 mfreopen. Fixed mf->fname such that it's now always a pointer to | |
2924 malloced data. Added mfdestroy to deallocate memory, but without | |
2925 flushing or closing file descriptors. Changed mfflush to write data | |
2926 regardless of whether it's stdin/stdout. This means that | |
2927 mfflush+mfdestroy can be used to close an mFILE without closing | |
2928 the underlying FILE pointer used. Added mftruncate. Rewrote mfread | |
2929 to do a single memcpy instead of looped memcpys. | |
2930 | |
2931 =============================================================================== | |
2932 2005-06-29 James Bonfield <jkb@sanger.ac.uk> | |
2933 | |
2934 * CHANGES, | |
2935 * Makefile, | |
2936 * README, | |
2937 * dependencies: | |
2938 (13:33:14) Version 1.9.0-test | |
2939 | |
2940 * Significant speed ups, particularly when dealing with reading | |
2941 gzipped files or when extracting data from tar files. | |
2942 | |
2943 * New external functions for faster access via mFILE (memory-file) | |
2944 structs. These mimic the fread/fwrite calls, but with | |
2945 mfread/mfwrite etc. | |
2946 | |
2947 * Some functions previously available in external scope, but not | |
2948 defined in header files, have now been made internal only | |
2949 ("static"). Please contact me if you were using these and have a | |
2950 burning need for them to remain external. | |
2951 | |
2952 * Numerous minor tweaks and updates to fix compiler warnings on | |
2953 more stricter modes of the Intel C Compiler. | |
2954 | |
2955 * Preliminary support for storing pyrosequencing style traces. This | |
2956 has been modeled on the flowgram data from 454, but should be | |
2957 applicable to other platforms. ZTR has been updated to incorporate | |
2958 this too. | |
2959 | |
2960 The Read structure also has flow, flow_order, nflows and flow_raw | |
2961 elements too. Code to convert these into the more usual | |
2962 traceA/C/G/T arrays exists currently as part of Trev (in tk_utils | |
2963 in the Staden Package), but this may move into io_lib for the | |
2964 next official release. | |
2965 | |
2966 * New hash_tar and hash_extract programs. These replace the | |
2967 index_tar program for rast random access. For RAWDATA include | |
2968 "HASH=hashfile" as an element to get io_lib to use the archive | |
2969 hash. It's possible to create hash files of most archive formats | |
2970 as the hash itself contains the offset and size of each item in | |
2971 the archive. This means that extracting an item does not need to | |
2972 know the format of the original archive. | |
2973 | |
2974 Some benchmarks show that on ext3 it's actually faster to extract | |
2975 files from the hash than directly via the directory. This was | |
2976 testing with ~200,000 files, whereupon directory lookups become | |
2977 slow. I'd imagine ResierFS or similar to be faster. | |
2978 | |
2979 * Added an XRLE encoding for ZTR. This is similar to the existing | |
2980 RLE mechanism but it copes with run length encoding of items | |
2981 larger than a single byte. It's current use is for storing the | |
2982 4-base repeating flow order in 454 data. | |
2983 | |
2984 * Potential incompatibilities: | |
2985 | |
2986 - The Exp_info structure now has an "mFILE *fp" member instead of | |
2987 "FILE *fp". | |
2988 | |
2989 - As mentioned above, some functions are no longer external. | |
2990 These include many ctf functions, ztr_(de)compress, | |
2991 ztr_chunk_(read/write), be_read_*, be_write_*, | |
2992 | |
2993 - The default search order for RAWDATA is that the current | |
2994 directory is searched after the rest of rawdata instead of | |
2995 before. | |
2996 | |
2997 - Removed support for the old unix "pack" program as a | |
2998 compression tool. | |
2999 | |
3000 * abi/abi.h, | |
3001 * abi/fpoint.c, | |
3002 * abi/seqIOABI.c, | |
3003 * abi/seqIOABI.h, | |
3004 * alf/alf.h, | |
3005 * alf/seqIOALF.c, | |
3006 * ctf/ctfCompress.c, | |
3007 * ctf/seqIOCTF.c, | |
3008 * ctf/seqIOCTF.h, | |
3009 * exp_file/expFileIO.c, | |
3010 * exp_file/expFileIO.h, | |
3011 * plain/plain.h: | |
3012 (13:33:32) Version 1.9.0-test | |
3013 | |
3014 * Significant speed ups, particularly when dealing with reading | |
3015 gzipped files or when extracting data from tar files. | |
3016 | |
3017 * New external functions for faster access via mFILE (memory-file) | |
3018 structs. These mimic the fread/fwrite calls, but with | |
3019 mfread/mfwrite etc. | |
3020 | |
3021 * Some functions previously available in external scope, but not | |
3022 defined in header files, have now been made internal only | |
3023 ("static"). Please contact me if you were using these and have a | |
3024 burning need for them to remain external. | |
3025 | |
3026 * Numerous minor tweaks and updates to fix compiler warnings on | |
3027 more stricter modes of the Intel C Compiler. | |
3028 | |
3029 * Preliminary support for storing pyrosequencing style traces. This | |
3030 has been modeled on the flowgram data from 454, but should be | |
3031 applicable to other platforms. ZTR has been updated to incorporate | |
3032 this too. | |
3033 | |
3034 The Read structure also has flow, flow_order, nflows and flow_raw | |
3035 elements too. Code to convert these into the more usual | |
3036 traceA/C/G/T arrays exists currently as part of Trev (in tk_utils | |
3037 in the Staden Package), but this may move into io_lib for the | |
3038 next official release. | |
3039 | |
3040 * New hash_tar and hash_extract programs. These replace the | |
3041 index_tar program for rast random access. For RAWDATA include | |
3042 "HASH=hashfile" as an element to get io_lib to use the archive | |
3043 hash. It's possible to create hash files of most archive formats | |
3044 as the hash itself contains the offset and size of each item in | |
3045 the archive. This means that extracting an item does not need to | |
3046 know the format of the original archive. | |
3047 | |
3048 Some benchmarks show that on ext3 it's actually faster to extract | |
3049 files from the hash than directly via the directory. This was | |
3050 testing with ~200,000 files, whereupon directory lookups become | |
3051 slow. I'd imagine ResierFS or similar to be faster. | |
3052 | |
3053 * Added an XRLE encoding for ZTR. This is similar to the existing | |
3054 RLE mechanism but it copes with run length encoding of items | |
3055 larger than a single byte. It's current use is for storing the | |
3056 4-base repeating flow order in 454 data. | |
3057 | |
3058 * Potential incompatibilities: | |
3059 | |
3060 - The Exp_info structure now has an "mFILE *fp" member instead of | |
3061 "FILE *fp". | |
3062 | |
3063 - As mentioned above, some functions are no longer external. | |
3064 These include many ctf functions, ztr_(de)compress, | |
3065 ztr_chunk_(read/write), be_read_*, be_write_*, | |
3066 | |
3067 - The default search order for RAWDATA is that the current | |
3068 directory is searched after the rest of rawdata instead of | |
3069 before. | |
3070 | |
3071 - Removed support for the old unix "pack" program as a | |
3072 compression tool. | |
3073 | |
3074 * plain/seqIOPlain.c, | |
3075 * progs/Makefile, | |
3076 * progs/convert_trace.c, | |
3077 * progs/extract_seq.c, | |
3078 * progs/get_comment.c, | |
3079 * progs/hash_extract.c, | |
3080 * progs/hash_tar.c, | |
3081 * progs/makeSCF.c, | |
3082 * progs/trace_dump.c, | |
3083 * progs/ztr_dump.c, | |
3084 * read/Read.c, | |
3085 * read/Read.h, | |
3086 * read/scf_extras.c, | |
3087 * read/translate.c, | |
3088 * scf/misc_scf.c, | |
3089 * scf/read_scf.c, | |
3090 * scf/scf.h, | |
3091 * scf/write_scf.c, | |
3092 * utils/compress.c, | |
3093 * utils/compress.h, | |
3094 * utils/hash_table.c, | |
3095 * utils/hash_table.h, | |
3096 * utils/mach-io.c, | |
3097 * utils/mach-io.h, | |
3098 * utils/open_trace_file.c, | |
3099 * utils/open_trace_file.h, | |
3100 * utils/read_alloc.c, | |
3101 * utils/traceType.c, | |
3102 * utils/traceType.h, | |
3103 * ztr/FORMAT, | |
3104 * ztr/compression.c, | |
3105 * ztr/compression.h, | |
3106 * ztr/ztr.c, | |
3107 * ztr/ztr.h, | |
3108 * ztr/ztr_translate.c: | |
3109 (13:33:33) Version 1.9.0-test | |
3110 | |
3111 * Significant speed ups, particularly when dealing with reading | |
3112 gzipped files or when extracting data from tar files. | |
3113 | |
3114 * New external functions for faster access via mFILE (memory-file) | |
3115 structs. These mimic the fread/fwrite calls, but with | |
3116 mfread/mfwrite etc. | |
3117 | |
3118 * Some functions previously available in external scope, but not | |
3119 defined in header files, have now been made internal only | |
3120 ("static"). Please contact me if you were using these and have a | |
3121 burning need for them to remain external. | |
3122 | |
3123 * Numerous minor tweaks and updates to fix compiler warnings on | |
3124 more stricter modes of the Intel C Compiler. | |
3125 | |
3126 * Preliminary support for storing pyrosequencing style traces. This | |
3127 has been modeled on the flowgram data from 454, but should be | |
3128 applicable to other platforms. ZTR has been updated to incorporate | |
3129 this too. | |
3130 | |
3131 The Read structure also has flow, flow_order, nflows and flow_raw | |
3132 elements too. Code to convert these into the more usual | |
3133 traceA/C/G/T arrays exists currently as part of Trev (in tk_utils | |
3134 in the Staden Package), but this may move into io_lib for the | |
3135 next official release. | |
3136 | |
3137 * New hash_tar and hash_extract programs. These replace the | |
3138 index_tar program for rast random access. For RAWDATA include | |
3139 "HASH=hashfile" as an element to get io_lib to use the archive | |
3140 hash. It's possible to create hash files of most archive formats | |
3141 as the hash itself contains the offset and size of each item in | |
3142 the archive. This means that extracting an item does not need to | |
3143 know the format of the original archive. | |
3144 | |
3145 Some benchmarks show that on ext3 it's actually faster to extract | |
3146 files from the hash than directly via the directory. This was | |
3147 testing with ~200,000 files, whereupon directory lookups become | |
3148 slow. I'd imagine ResierFS or similar to be faster. | |
3149 | |
3150 * Added an XRLE encoding for ZTR. This is similar to the existing | |
3151 RLE mechanism but it copes with run length encoding of items | |
3152 larger than a single byte. It's current use is for storing the | |
3153 4-base repeating flow order in 454 data. | |
3154 | |
3155 * Potential incompatibilities: | |
3156 | |
3157 - The Exp_info structure now has an "mFILE *fp" member instead of | |
3158 "FILE *fp". | |
3159 | |
3160 - As mentioned above, some functions are no longer external. | |
3161 These include many ctf functions, ztr_(de)compress, | |
3162 ztr_chunk_(read/write), be_read_*, be_write_*, | |
3163 | |
3164 - The default search order for RAWDATA is that the current | |
3165 directory is searched after the rest of rawdata instead of | |
3166 before. | |
3167 | |
3168 - Removed support for the old unix "pack" program as a | |
3169 compression tool. | |
3170 | |
3171 * utils/vlen.c, | |
3172 * utils/vlen.h: | |
3173 (13:35:42) vlen/vflen functions to estimate the maximum data size | |
3174 written out by a printf style function. This is used by the new | |
3175 mFILE functions. | |
3176 | |
3177 * utils/mFILE.c, | |
3178 * utils/mFILE.h: | |
3179 (13:39:13) mFILE struct support. This is basically a set of | |
3180 functions to similulate stdio file support on a block of memory | |
3181 instead of a file, for purposes of speed and to avoid the need of | |
3182 writing data out to a file only to be opened and read back in again | |
3183 (which happened a lot before). | |
3184 | |
3185 stdio_hack.h is, like it says, a hacky bunch of #defines to turn | |
3186 stdio functions and io_lib functions into their mFILE equivalents. | |
3187 It is used internally to convert old code (eg ABI file reading) to | |
3188 use mFILE structures, but can also be used by the brave to update | |
3189 their own code. Use with extreme caution. | |
3190 | |
3191 * utils/stdio_hack.h: | |
3192 (13:39:14) mFILE struct support. This is basically a set of | |
3193 functions to similulate stdio file support on a block of memory | |
3194 instead of a file, for purposes of speed and to avoid the need of | |
3195 writing data out to a file only to be opened and read back in again | |
3196 (which happened a lot before). | |
3197 | |
3198 stdio_hack.h is, like it says, a hacky bunch of #defines to turn | |
3199 stdio functions and io_lib functions into their mFILE equivalents. | |
3200 It is used internally to convert old code (eg ABI file reading) to | |
3201 use mFILE structures, but can also be used by the brave to update | |
3202 their own code. Use with extreme caution. | |
3203 | |
3204 2005-06-08 James Bonfield <jkb@sanger.ac.uk> | |
3205 | |
3206 * utils/hash_table.c: | |
3207 * utils/hash_table.h: | |
3208 * progs/hash_extract.c, | |
3209 * progs/hash_tar.c: | |
3210 (08:37:49) Added some simple hash table functions. Layered on top | |
3211 of these are HashFiles, which allow hash table indexing of files to | |
3212 be stored on disk. hash_tar and hash_extract test programs | |
3213 illustrate its use on tar files, much like index_tar does. | |
3214 | |
3215 * utils/open_trace_file.c: | |
3216 (08:38:22) Added support for integrating the new hashfile code via | |
3217 a "HASH=hashfile" RAWDATA setting. | |
3218 | |
3219 2005-04-27 James Bonfield <jkb@sanger.ac.uk> | |
3220 | |
3221 * progs/get_comment.c: | |
3222 (16:15:51) Removed "might be used uninitialised" warning messages | |
3223 from the compiler. | |
3224 | |
3225 2005-02-09 James Bonfield <jkb@sanger.ac.uk> | |
3226 | |
3227 * abi/seqIOABI.c: | |
3228 (10:08:03) Added getABIIndexEntrySW and modified getABIString to | |
3229 correctly determine the string type (pascal vs C-string). This | |
3230 means MODL numbers now come out as 3730 instead of 730 (for | |
3231 example). | |
3232 | |
3233 2004-12-06 James Bonfield <jkb@sanger.ac.uk> | |
3234 | |
3235 * progs/ztr_dump.c: | |
3236 (17:41:58) Corrected minor compiler warnings. | |
3237 | |
3238 2004-11-16 James Bonfield <jkb@sanger.ac.uk> | |
3239 | |
3240 * exp_file/expFileIO.c: | |
3241 (12:10:16) Major speed up of reading large experiment files. Tested | |
3242 on a 1Mb sequence with AV, ON and SQ lines the new code is 1000 | |
3243 times faster on the Alpha. | |
3244 | |
3245 Primarily the difference comes from removing O(N^2) complexities by | |
3246 removing strcat & strlen type of operations. | |
3247 | |
3248 2004-10-29 James Bonfield <jkb@sanger.ac.uk> | |
3249 | |
3250 * Makefile: | |
3251 (10:42:10) Automatically create binary output directories. | |
3252 | |
3253 2004-10-21 James Bonfield <jkb@sanger.ac.uk> | |
3254 | |
3255 * dependencies: | |
3256 (11:39:28) *** empty log message *** | |
3257 | |
3258 2004-10-14 James Bonfield <jkb@sanger.ac.uk> | |
3259 | |
3260 * progs/convert_trace.c: | |
3261 (15:38:18) Added a "-subtract <amount>" option to allow removal of | |
3262 a specific DC offset. | |
3263 | |
3264 2004-10-08 James Bonfield <jkb@sanger.ac.uk> | |
3265 | |
3266 * progs/convert_trace.c: | |
3267 (14:49:06) Fixed a divide-by-zero error in the normalisation code. | |
3268 | |
3269 2004-10-01 James Bonfield <jkb@sanger.ac.uk> | |
3270 | |
3271 * progs/convert_trace.c: | |
3272 (10:56:07) Rewrote rescale_heights (the "-normalise" option) using | |
3273 an amplitude tracker with an attack & delay model. This seems to | |
3274 work well at adjusting for both gradual amplitude variations and | |
3275 for downscaling huge dye-blobs. | |
3276 | |
3277 2004-08-17 James Bonfield <jkb@sanger.ac.uk> | |
3278 | |
3279 * progs/Makefile, | |
3280 * progs/Makefile.am, | |
3281 * progs/ztr_dump.c: | |
3282 (13:37:17) Added a ztr_dump program. | |
3283 | |
3284 2004-08-05 James Bonfield <jkb@sanger.ac.uk> | |
3285 | |
3286 * progs/index_tar.c: | |
3287 (09:32:05) Fix bug submitted by Steve Leonard. If a directory is | |
3288 too large to fit in the name (>100) but short enough to fit in the | |
3289 prefix the name field will be empty, this is not the cas for | |
3290 ordinary files where the name field is always non-empty. | |
3291 | |
3292 2004-07-26 James Bonfield <jkb@sanger.ac.uk> | |
3293 | |
3294 * exp_file/expFileIO.c: | |
3295 (14:24:35) MinGW port | |
3296 | |
3297 * utils/open_trace_file.c: | |
3298 (14:26:13) MinGW port | |
3299 | |
3300 =============================================================================== | |
3301 2004-06-01 James Bonfield <jkb@sanger.ac.uk> | |
3302 | |
3303 * CHANGES, | |
3304 * Makefile.am, | |
3305 * Attic/Makefile.in, | |
3306 * README, | |
3307 * Attic/config.guess, | |
3308 * Attic/config.h.in, | |
3309 * Attic/config.sub, | |
3310 * Attic/configure, | |
3311 * configure.in, | |
3312 * Attic/depcomp, | |
3313 * Attic/install-sh, | |
3314 * Attic/ltmain.sh, | |
3315 * Attic/missing, | |
3316 * Attic/mkinstalldirs: | |
3317 * abi/Attic/Makefile.in, | |
3318 * alf/Attic/Makefile.in: | |
3319 * ctf/Attic/Makefile.in, | |
3320 * exp_file/Attic/Makefile.in, | |
3321 * plain/Attic/Makefile.in, | |
3322 * progs/Makefile.am, | |
3323 * progs/Attic/Makefile.in, | |
3324 * read/Attic/Makefile.in, | |
3325 * scf/Attic/Makefile.in, | |
3326 * utils/Attic/Makefile.in, | |
3327 * ztr/Attic/Makefile.in: | |
3328 (08:54:51) Updated notes to claim this is version 1.8.12 and | |
3329 rebuilt all the automake/autoconf/libtool generated files. | |
3330 | |
3331 2004-05-13 James Bonfield <jkb@sanger.ac.uk> | |
3332 | |
3333 * abi/seqIOABI.c: | |
3334 (16:14:10) Improved spacing fix. | |
3335 | |
3336 2004-05-12 James Bonfield <jkb@sanger.ac.uk> | |
3337 | |
3338 * abi/seqIOABI.c: | |
3339 (08:27:40) Applied change suggested by Saul A. Kravitz. The | |
3340 fallback fspacing is now calculated over the range that basecalls | |
3341 exist rather than the total length of trace. | |
3342 | |
3343 2004-03-03 James Bonfield <jkb@sanger.ac.uk> | |
3344 | |
3345 * ztr/ztr_translate.c: | |
3346 (17:45:52) Treat Read->basePos as 16-bit, which means hard-coding | |
3347 the first two bytes in ztr_encode_positions for each pos as zero. | |
3348 | |
3349 2004-02-19 James Bonfield <jkb@sanger.ac.uk> | |
3350 | |
3351 * exp_file/expFileIO.c: | |
3352 (12:13:52) Fixed typo in LG qualifier (was LF). | |
3353 | |
3354 * exp_file/expFileIO.h: | |
3355 (13:48:59) More type fixes; EFLT_LG was given the same number as | |
3356 _FT. Now diff. | |
3357 | |
3358 2004-02-12 James Bonfield <jkb@sanger.ac.uk> | |
3359 | |
3360 * dependencies: | |
3361 (10:32:01) *** empty log message *** | |
3362 | |
3363 2004-02-09 James Bonfield <jkb@sanger.ac.uk> | |
3364 | |
3365 * exp_file/expFileIO.c, | |
3366 * exp_file/expFileIO.h: | |
3367 (14:39:52) Added LG (LiGation) to experiment file definition. | |
3368 | |
3369 2004-01-13 James Bonfield <jkb@sanger.ac.uk> | |
3370 | |
3371 * read/translate.c: | |
3372 (17:02:00) In read2exp only set the file format to be TT_EXP when | |
3373 'redirection to trace' is not enabled (ie it indicates where the | |
3374 sequence came from, EXP or SCF/ZTR/...). | |
3375 | |
3376 2003-11-17 James Bonfield <jkb@sanger.ac.uk> | |
3377 | |
3378 * utils/open_trace_file.c: | |
3379 (14:52:28) Added ARC= and URL= RAWDATA search methods to fetch | |
3380 traces via the ensembl trace archive and via a URL. | |
3381 | |
3382 2003-10-24 James Bonfield <jkb@sanger.ac.uk> | |
3383 | |
3384 * abi/seqIOABI.c: | |
3385 (08:24:07) Protect against the base spacing being listed as a | |
3386 negative number in the ABI file. | |
3387 | |
3388 * progs/extract_seq.c: | |
3389 (08:24:29) Added a -fofn option | |
3390 | |
3391 * utils/compress.c: | |
3392 (08:24:57) More error checking on writing compressed files. | |
3393 | |
3394 2003-07-10 James Bonfield <jkb@sanger.ac.uk> | |
3395 | |
3396 * Makefile: | |
3397 (11:14:14) Put back the Staden Makefile as I accidently overwrote | |
3398 this with the autoconf generate one. | |
3399 | |
3400 * progs/Makefile: | |
3401 (11:14:18) *** empty log message *** | |
3402 | |
3403 2003-07-07 James Bonfield <jkb@sanger.ac.uk> | |
3404 | |
3405 * abi/seqIOABI.c, | |
3406 * abi/seqIOABI.h: | |
3407 (11:20:37) Confidence values (PCON 1) are now loaded from ABI | |
3408 files. | |
3409 | |
3410 * Makefile.am: | |
3411 * Attic/Makefile.in, | |
3412 * Attic/config.guess, | |
3413 * Attic/config.h.in, | |
3414 * Attic/config.sub, | |
3415 * Attic/configure, | |
3416 * configure.in, | |
3417 * Attic/install-sh, | |
3418 * Attic/ltconfig, | |
3419 * Attic/ltmain.sh, | |
3420 * Attic/missing, | |
3421 * Attic/mkinstalldirs, | |
3422 * Attic/stamp-h.in: | |
3423 (11:24:47) Added automake/autoconf/libtool files to CVS tree. Not | |
3424 all of these are 'source' files as some are generated by others, | |
3425 but for ease of compilation the output from these tools is | |
3426 distribute too, meaning that only './configure' needs to be run. | |
3427 | |
3428 * abi/Attic/Makefile.am, | |
3429 * abi/Attic/Makefile.in: | |
3430 (11:24:52) *** empty log message *** | |
3431 | |
3432 * alf/Attic/Makefile.am, | |
3433 * alf/Attic/Makefile.in, | |
3434 * ctf/Attic/Makefile.am, | |
3435 * ctf/Attic/Makefile.in, | |
3436 * exp_file/Attic/Makefile.am, | |
3437 * exp_file/Attic/Makefile.in, | |
3438 * plain/Attic/Makefile.am, | |
3439 * plain/Attic/Makefile.in, | |
3440 * progs/Makefile.am: | |
3441 (11:25:02) *** empty log message *** | |
3442 | |
3443 * progs/Attic/Makefile.in, | |
3444 * read/Makefile.am, | |
3445 * read/Attic/Makefile.in, | |
3446 * scf/Attic/Makefile.am, | |
3447 * scf/Attic/Makefile.in, | |
3448 * utils/Attic/Makefile.am, | |
3449 * utils/Attic/Makefile.in, | |
3450 * ztr/Attic/Makefile.am, | |
3451 * ztr/Attic/Makefile.in: | |
3452 (11:25:03) *** empty log message *** | |
3453 | |
3454 * Makefile: | |
3455 (11:48:43) Updates to automake/conf system. | |
3456 | |
3457 * Makefile.am, | |
3458 * Attic/Makefile.in, | |
3459 * Attic/config.guess, | |
3460 * Attic/config.h.in, | |
3461 * Attic/config.sub, | |
3462 * Attic/configure, | |
3463 * Attic/depcomp, | |
3464 * Attic/ltmain.sh: | |
3465 (11:48:44) Updates to automake/conf system. | |
3466 | |
3467 * abi/Attic/Makefile.am, | |
3468 * abi/Attic/Makefile.in, | |
3469 * alf/Attic/Makefile.am, | |
3470 * alf/Attic/Makefile.in, | |
3471 * ctf/Attic/Makefile.am, | |
3472 * ctf/Attic/Makefile.in, | |
3473 * exp_file/Attic/Makefile.am, | |
3474 * exp_file/Attic/Makefile.in, | |
3475 * plain/Attic/Makefile.am, | |
3476 * plain/Attic/Makefile.in, | |
3477 * progs/Makefile, | |
3478 * progs/Makefile.am: | |
3479 (11:48:50) *** empty log message *** | |
3480 | |
3481 * progs/Attic/Makefile.in, | |
3482 * read/Makefile.am, | |
3483 * read/Attic/Makefile.in, | |
3484 * read/Read.h, | |
3485 * scf/Attic/Makefile.am, | |
3486 * scf/Attic/Makefile.in, | |
3487 * utils/Attic/Makefile.am, | |
3488 * utils/Attic/Makefile.in, | |
3489 * ztr/Attic/Makefile.am: | |
3490 (11:48:51) *** empty log message *** | |
3491 | |
3492 * ztr/Attic/Makefile.in: | |
3493 (11:48:54) *** empty log message *** | |
3494 | |
3495 * read/Read.h: | |
3496 (11:56:56) *** empty log message *** | |
3497 | |
3498 2003-06-09 James Bonfield <jkb@sanger.ac.uk> | |
3499 | |
3500 * CHANGES, | |
3501 * COPYRIGHT, | |
3502 * Makefile, | |
3503 * README, | |
3504 * options.mk, | |
3505 * abi/abi.h, | |
3506 * abi/fpoint.c, | |
3507 * abi/fpoint.h, | |
3508 * abi/seqIOABI.c: | |
3509 (11:24:36) Import of Staden Package 2003.0b2 | |
3510 | |
3511 * CHANGES, | |
3512 * COPYRIGHT, | |
3513 * Makefile, | |
3514 * README, | |
3515 * options.mk, | |
3516 * abi/abi.h, | |
3517 * abi/fpoint.c, | |
3518 * abi/fpoint.h, | |
3519 * abi/seqIOABI.c: | |
3520 (11:24:36) branches: 1.1.1; Initial revision | |
3521 | |
3522 * abi/seqIOABI.h, | |
3523 * alf/alf.h, | |
3524 * alf/seqIOALF.c, | |
3525 * ctf/ctfCompress.c, | |
3526 * ctf/seqIOCTF.c, | |
3527 * ctf/seqIOCTF.h, | |
3528 * exp_file/expFileIO.c, | |
3529 * exp_file/expFileIO.h, | |
3530 * plain/plain.h, | |
3531 * plain/seqIOPlain.c, | |
3532 * progs/Makefile, | |
3533 * progs/convert_trace.c, | |
3534 * progs/extract_seq.c, | |
3535 * progs/get_comment.c, | |
3536 * progs/index_tar.c, | |
3537 * progs/makeSCF.c, | |
3538 * progs/scf_dump.c, | |
3539 * progs/scf_info.c, | |
3540 * progs/scf_update.c, | |
3541 * progs/trace_dump.c, | |
3542 * read/Read.c, | |
3543 * read/Read.h, | |
3544 * read/scf_extras.c, | |
3545 * read/scf_extras.h, | |
3546 * read/translate.c, | |
3547 * read/translate.h, | |
3548 * scf/misc_scf.c, | |
3549 * scf/read_scf.c, | |
3550 * scf/scf.h, | |
3551 * scf/write_scf.c, | |
3552 * utils/array.c, | |
3553 * utils/array.h, | |
3554 * utils/compress.c, | |
3555 * utils/compress.h, | |
3556 * utils/error.c, | |
3557 * utils/error.h, | |
3558 * utils/files.c, | |
3559 * utils/find.c, | |
3560 * utils/mach-io.c, | |
3561 * utils/mach-io.h, | |
3562 * utils/misc.h, | |
3563 * utils/open_trace_file.c, | |
3564 * utils/open_trace_file.h, | |
3565 * utils/read_alloc.c, | |
3566 * utils/strings.c, | |
3567 * utils/tar_format.h, | |
3568 * utils/traceType.c: | |
3569 (11:24:37) Import of Staden Package 2003.0b2 | |
3570 | |
3571 * abi/seqIOABI.h, | |
3572 * alf/alf.h, | |
3573 * alf/seqIOALF.c, | |
3574 * ctf/ctfCompress.c, | |
3575 * ctf/seqIOCTF.c, | |
3576 * ctf/seqIOCTF.h, | |
3577 * exp_file/expFileIO.c, | |
3578 * exp_file/expFileIO.h, | |
3579 * plain/plain.h, | |
3580 * plain/seqIOPlain.c, | |
3581 * progs/Makefile, | |
3582 * progs/convert_trace.c, | |
3583 * progs/extract_seq.c, | |
3584 * progs/get_comment.c, | |
3585 * progs/index_tar.c, | |
3586 * progs/makeSCF.c, | |
3587 * progs/scf_dump.c, | |
3588 * progs/scf_info.c, | |
3589 * progs/scf_update.c, | |
3590 * progs/trace_dump.c, | |
3591 * read/Read.c, | |
3592 * read/Read.h, | |
3593 * read/scf_extras.c, | |
3594 * read/scf_extras.h, | |
3595 * read/translate.c, | |
3596 * read/translate.h, | |
3597 * scf/misc_scf.c, | |
3598 * scf/read_scf.c, | |
3599 * scf/scf.h, | |
3600 * scf/write_scf.c, | |
3601 * utils/array.c, | |
3602 * utils/array.h, | |
3603 * utils/compress.c, | |
3604 * utils/compress.h, | |
3605 * utils/error.c, | |
3606 * utils/error.h, | |
3607 * utils/files.c, | |
3608 * utils/find.c, | |
3609 * utils/mach-io.c, | |
3610 * utils/mach-io.h, | |
3611 * utils/misc.h, | |
3612 * utils/open_trace_file.c, | |
3613 * utils/open_trace_file.h, | |
3614 * utils/read_alloc.c, | |
3615 * utils/strings.c, | |
3616 * utils/tar_format.h, | |
3617 * utils/traceType.c: | |
3618 (11:24:37) branches: 1.1.1; Initial revision | |
3619 | |
3620 * man/man3/ExperimentFile.3, | |
3621 * man/man3/exp2read.3, | |
3622 * man/man3/fread_reading.3, | |
3623 * man/man3/fread_scf.3, | |
3624 * man/man3/fwrite_reading.3, | |
3625 * man/man3/fwrite_scf.3, | |
3626 * man/man3/read2exp.3, | |
3627 * man/man3/read2scf.3, | |
3628 * man/man3/read_allocate.3, | |
3629 * man/man3/read_deallocate.3, | |
3630 * man/man3/read_reading.3, | |
3631 * man/man3/read_scf.3, | |
3632 * man/man3/read_scf_header.3, | |
3633 * man/man3/scf2read.3, | |
3634 * man/man3/write_reading.3, | |
3635 * man/man3/write_scf.3, | |
3636 * man/man3/write_scf_header.3, | |
3637 * man/man4/Read.4, | |
3638 * utils/traceType.h, | |
3639 * utils/xalloc.c, | |
3640 * utils/xalloc.h, | |
3641 * ztr/FORMAT, | |
3642 * ztr/compression.c, | |
3643 * ztr/compression.h, | |
3644 * ztr/ztr.c, | |
3645 * ztr/ztr.h, | |
3646 * ztr/ztr_translate.c: | |
3647 (11:24:38) Import of Staden Package 2003.0b2 | |
3648 | |
3649 * man/man3/ExperimentFile.3, | |
3650 * man/man3/exp2read.3, | |
3651 * man/man3/fread_reading.3, | |
3652 * man/man3/fread_scf.3, | |
3653 * man/man3/fwrite_reading.3, | |
3654 * man/man3/fwrite_scf.3, | |
3655 * man/man3/read2exp.3, | |
3656 * man/man3/read2scf.3, | |
3657 * man/man3/read_allocate.3, | |
3658 * man/man3/read_deallocate.3, | |
3659 * man/man3/read_reading.3, | |
3660 * man/man3/read_scf.3, | |
3661 * man/man3/read_scf_header.3, | |
3662 * man/man3/scf2read.3, | |
3663 * man/man3/write_reading.3, | |
3664 * man/man3/write_scf.3, | |
3665 * man/man3/write_scf_header.3, | |
3666 * man/man4/Read.4, | |
3667 * utils/traceType.h, | |
3668 * utils/xalloc.c, | |
3669 * utils/xalloc.h, | |
3670 * ztr/FORMAT, | |
3671 * ztr/compression.c, | |
3672 * ztr/compression.h, | |
3673 * ztr/ztr.c, | |
3674 * ztr/ztr.h, | |
3675 * ztr/ztr_translate.c: | |
3676 (11:24:38) branches: 1.1.1; Initial revision | |
3677 | |
3678 * Makefile: | |
3679 (11:59:11) Added include/.links target to main library instead of | |
3680 progs, thus making the build work cleanly from a newly checked out | |
3681 copy. | |
3682 | |
3683 * Makefile: | |
3684 (14:22:43) Fix .links code. | |
3685 |