Mercurial > repos > dawe > srf2fastq
comparison srf2fastq/io_lib-1.12.2/CHANGES @ 0:d901c9f41a6a default tip
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
author | dawe |
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date | Tue, 07 Jun 2011 17:48:05 -0400 |
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1 Version 1.12.2 (15th Jan 2010) | |
2 -------------- | |
3 | |
4 * Extra options in srf2fastq: -S to output split regions sequentially | |
5 to stdout. -r to request a region to be reverse complemented before | |
6 output. | |
7 | |
8 * API addition | |
9 - Added pooled_alloc.h. This is a general purpose mechanism of | |
10 pooling multiple fixed size memory allocations into fewer malloc() | |
11 library calls. | |
12 - HashTables now have a HASH_POOL_ITEMS option to use the above | |
13 pooling system. This reduces memory wasted and speeds them up. | |
14 | |
15 * Bug fix: Fixed ztr_add_text() so that is leaves two nul bytes on the | |
16 end of TEXT chunks instead of one, as documented in the ZTR | |
17 specification. | |
18 | |
19 * Bug fix: Fixed buffer overrun in parse region chunks; srf2fastq and | |
20 srf2fasta. | |
21 | |
22 * Bug fix: API read_sff_read_data() did not skip ahead to the next | |
23 8-byte boundary. | |
24 | |
25 | |
26 Version 1.12.1 (7th August 2009) | |
27 -------------- | |
28 | |
29 * Fixed the endianness detection in io_lib/os.h when used in | |
30 conjuction with auto-conf. This fix allows for "fat" binaries to be | |
31 built on MacOS X. | |
32 | |
33 * Fixed io_lib-config program to use -lstaden-read instead of -lread. | |
34 | |
35 | |
36 Version 1.12.0 (29th July 2009) | |
37 -------------- | |
38 | |
39 * Renamed the library from libread.so to libstaden-read.so. This was | |
40 already the case for the Fedora bundled RPM. | |
41 | |
42 * Switched to using libtool to allow building of dynamic libraries. | |
43 Note that this is tweaked to not use -rpath though. Proper library | |
44 versioning has been added too. | |
45 | |
46 * Removed deprecated platform specific tools: illumina2srf, | |
47 srf2illumina. | |
48 | |
49 * Srf_info now reports the compressed size of chunks, sorted by type, | |
50 in addition to their counts. It also correctly sums to over 2Gb now | |
51 for base-call counting. | |
52 | |
53 * Various SRF tools have had the maximum sequence length changed from | |
54 1024 to 10000. This allows for even the most gifting capillary traces. | |
55 | |
56 * API | |
57 - The Array functions now take size_t instead of int for the | |
58 array dimensions. (API CHANGE) | |
59 | |
60 - Removed the (unused?) pipe2 function from compress.h. This was | |
61 intended to be internal only, and it now clashes with a new linux | |
62 kernel function. (API CHANGE) | |
63 | |
64 - Added iterators to the HashTable* api. | |
65 | |
66 * Bug fixes | |
67 | |
68 - Fixed a memory allocation bug in the codes2codeset() function. | |
69 | |
70 - ztr2read() should now work better on ZTR structs with no BPOS | |
71 chunk. | |
72 | |
73 - Fixed various srf tools when facing an SRF file containing zero | |
74 chunks in the data block header. | |
75 | |
76 - index_tar handles some GNU tar extensions better (LongLink). | |
77 | |
78 | |
79 Version 1.11.6.1 (9th December 2008) | |
80 ---------------- | |
81 | |
82 * Identical except removal of a debugging printf statement in solexa2srf. | |
83 | |
84 | |
85 Version 1.11.6 (9th December 2008) | |
86 -------------- | |
87 | |
88 * illumina2srf, srf2illumina, srf2fastq | |
89 - We no longer change from log-odds to phred when storing data in | |
90 SRF, instead preferring to just mark it in correct input | |
91 scale. srf2fastq now honours this scale information and so the | |
92 conversion from log-odd to phred is done at the export stage | |
93 instead. (Chris Saunders) | |
94 | |
95 - Bug fix to srf2illumina qcal conversion. Combined with above | |
96 changes the qcal output should now be 100% identical to the | |
97 original data input via illumina2srf. | |
98 | |
99 * API | |
100 - New function srf_next_ztr_flags. This is like srf_next_ztr but | |
101 also returns the SRF flags value (good/bad read, etc). | |
102 | |
103 * srf_filter, srf2fastq, srf_info (Steven Leonard) | |
104 - Improved support for multiple index blocks in SRF files, eg from | |
105 manually concatenated files. | |
106 | |
107 - srf2fastq now sports options for splitting the output into | |
108 multiple fastq files when the input data is a paired-end run. | |
109 | |
110 | |
111 Version 1.11.5 (3rd December 2008) | |
112 -------------- | |
113 | |
114 * Illumina2srf | |
115 - Fixed major bug with using *both* -qf and -qr together. The | |
116 quality values for the reverse strand were shifted by one | |
117 character. | |
118 | |
119 - Fixed qcal quality values so they're not shifted down by 64 | |
120 (illumina format fastq). | |
121 | |
122 - Fixed bugs in parsing directory names if not matching the expected | |
123 format. | |
124 | |
125 * Removed major memory leaks from srf_filter. | |
126 | |
127 * hash_sff now has support for outputting the table of contents to a | |
128 new file rather than appending to an existing sff file or copying | |
129 the entire contents to a new file. | |
130 | |
131 * Various man pages have been added. The list is still incomplete | |
132 though. Additions are most welcome. | |
133 | |
134 * New program: srf_list. This lists and/or counts the number of | |
135 sequences within an SRF file. | |
136 | |
137 | |
138 Version 1.11.4 (11th September 2008) | |
139 -------------- | |
140 | |
141 * New "make check" build target to perform some automated tested. | |
142 Currently limited to testing the SRF tools. | |
143 | |
144 * Fixed machine endianness issues. Specifically this resolves known Intel | |
145 MacOS-X problems. | |
146 | |
147 * New SRF tools | |
148 | |
149 - srf_info: reports simple metrics on the contents of an SRF file. | |
150 | |
151 - srf_filter: slices and dices the SRF file to produce a new one | |
152 with various types of data removed. | |
153 | |
154 * illumina2srf | |
155 | |
156 - Minor float/int rounding change when storing int/nse/sig2 data. | |
157 | |
158 - Improved error detection such that it returns a failure code more | |
159 often given a parsing issue. | |
160 | |
161 - Added -pf/pr parameters for storing Phasing files. | |
162 | |
163 - Reduced memory usage, especially on large numbers of clusters per | |
164 tile. We may now produce multiple DBH blocks per tile. Also major | |
165 reduction to memory when handling the .params files. | |
166 | |
167 - Added storage of 2nd .params file (firecrest). | |
168 | |
169 - Fixed bug in the automatic base-call version identification. | |
170 | |
171 - Fixed a bug with using -qf/qr when not providing all tiles (ie not | |
172 starting from tile number 1). | |
173 | |
174 - Bug fix with storing the reverse matrix file in paired-end runs; a | |
175 duplicate of the forward one was being used instead. | |
176 | |
177 * General SRF | |
178 | |
179 - Improved error checking in srf_index_hash. It now spots duplicate | |
180 reads and also has a -c option to check an existing SRF file | |
181 without writing the index. | |
182 | |
183 - Fixed a memory leak in srf_next_ztr(), triggered in srf2fastq -C. | |
184 | |
185 Version 1.11.3 (9th July 2008) | |
186 -------------- | |
187 | |
188 * illumina2srf change: | |
189 | |
190 - IMPORTANT bug fix to illumina2srf when using the "-r" flag to | |
191 store raw (.int and .nse) data. This could often result in | |
192 corrupting the data ZTR meta-data for the SMP4 chunks resulting in | |
193 confusion over which trace channels are raw and which are | |
194 processed. | |
195 | |
196 Fortunately the corruption is reversable. For more details and a | |
197 fix see the ssrformat announcement of the issue: | |
198 | |
199 http://www.bcgsc.ca/pipermail/ssrformat/2008-July/000531.html | |
200 | |
201 * General SRF changes: | |
202 | |
203 - Removed a memory leak in ztr_find_chunks(). | |
204 | |
205 - Added SRFB_NULL_INDEX as an SRF block type. This provides a more | |
206 transparent way to skip over the 8 zero value bytes that may exist | |
207 at the end of an SRF file missing an index block. | |
208 | |
209 * Other changes | |
210 | |
211 - Fixed a bug in extract_seq when operating on multiple files and | |
212 outputting to a file rather than a pipe. An erroneous seek in the | |
213 mFILE code lead to it repeatedly truncating the output, resulting | |
214 in one sequence file at the end instead of multiple files. | |
215 | |
216 | |
217 Version 1.11.2 (4th June 2008) | |
218 -------------- | |
219 | |
220 * solexa2srf/srf2solexa changes: | |
221 | |
222 - Renamed to illumina2srf/srf2illumina. | |
223 | |
224 - Incorporated support the IPAR format (Come Raczy, Illumina). | |
225 | |
226 - Added support for qcal format data (Come Raczy). | |
227 | |
228 - Added -C option to tag data as failing the chastity filter, but it | |
229 is still included in the SRF output (Camil Toma). | |
230 | |
231 - Many more additional features added to srf_dump_all provided by | |
232 Camil Toma. It somewhat overlaps srf2solexa now, but may still | |
233 have it's own use. | |
234 | |
235 - Ztr TEXT chunks now output in srf2solexa. | |
236 | |
237 - Improved ways to specify matrices (-mf/-mr) in solexa2srf. | |
238 | |
239 - solexa2srf is substantially faster when reading gzipped files. | |
240 | |
241 - The -N/-n naming scheme options for solexa2srf now default to the | |
242 same conventions used by GERALD. Added additional %d, %m and %r | |
243 format rules too. | |
244 | |
245 - Calibrated confidence values are now output if -qf or -qr | |
246 paramaters are used, in addition to uncalibrated ones. These are | |
247 stored in phred scale in a CNF1 ZTR chunk. | |
248 | |
249 * srf2fastq now has a -c option to output calibrated confidence values | |
250 (if present). It also supports multiple archives on the command line. | |
251 | |
252 * SRF fixes: | |
253 | |
254 - Better handling of full pathnames in solexa2srf. | |
255 | |
256 - Use binary IO mode; fixes bugs on Windows. | |
257 | |
258 - Fixed an error where some chunks were not compressed properly | |
259 (valid still, just not compressed). | |
260 | |
261 - Removed memory corruption in solexa2srf (in rare cases). | |
262 | |
263 - Fixed bug with binary formatted read_id suffixes (fixed by | |
264 Cristian Goina). | |
265 | |
266 - Initialised memory in hash table code (used in indexing amongst | |
267 other things). | |
268 | |
269 - Indexes very occasionally failed to find a trace that did infact | |
270 exist. | |
271 | |
272 - Removed memory leak in construct_trace_name (patch from John | |
273 Emhoff, Helicos). | |
274 | |
275 - Fixed reading of XML block in srf_read_xml(). From John Emhoff. | |
276 | |
277 | |
278 * Added SRF= format string to TRACE_PATH to facilitate on-the-fly | |
279 extraction from indexed SRF files. This means io_lib can now | |
280 transparently pull traces from an archive or treat it as if it was a | |
281 directory - eg "foo.srf/IL15_..._123:456". | |
282 | |
283 * Bug fix (SF-1898427) - now builds on Fedora. | |
284 | |
285 * Better handling of 64-bit file size sensing in autoconf. | |
286 | |
287 | |
288 Version 1.11.1 (not officially released - internal testing only) | |
289 -------------- | |
290 | |
291 Version 1.11.0 (20th February 2008) | |
292 -------------- | |
293 | |
294 First official release of v1.11.0 and SRF support. | |
295 | |
296 * Further speed improvements to solexa2srf. | |
297 | |
298 * Added extract_qual program (analogous to extract_seq). | |
299 | |
300 * Added new srf2fasta program and also sped up srf2fastq by 25%. | |
301 | |
302 * Solexa2srf now supports storing the raw .int/.nse trace data instead | |
303 of or in addition to the processed .sig2 data. | |
304 | |
305 * Solexa2srf now stores enough to reproduce sufficient firecrest | |
306 output to rerun the solexa basecaller. Specifically that's a couple | |
307 matrix files and 'region' data for paired end runs. | |
308 | |
309 * Minor changes / bug fixes: | |
310 | |
311 - extract_seq no longer attempts to gzip the output by default if | |
312 the input was gzipped | |
313 | |
314 - ztr2read conversion (eg visible in trace_dump) now correctly | |
315 handles ZTR files with multiple SMP4 chunks. | |
316 | |
317 - Fixed memory leaks in various bits of SRF code (srf_extract_linear | |
318 mainly and srf_index_hash). | |
319 | |
320 | |
321 Version 1.11.0b8 (25th January 2008) | |
322 ---------------- | |
323 | |
324 (Hopefully final beta test of SRF code before official 1.11.0 release.) | |
325 | |
326 * Bug fixed the index format. We incorrectly handled null dbhFile and | |
327 containerFile elements plus incorrectly computing the index size. | |
328 | |
329 * Improvements for solexa2srf code. | |
330 - Can store raw vs processed data | |
331 - Stores matrix and .params contents. | |
332 - Optional chastity filtering. | |
333 - Input data may now be gzipped. | |
334 | |
335 * Minor fixes to output of trace_dump and ztr_dump. | |
336 | |
337 * Minor srf_index_hash bug fixes (when dealing with concatenated | |
338 indexed files). | |
339 | |
340 | |
341 Version 1.11.0b7 (11th January 2008) | |
342 ---------------- | |
343 | |
344 * IMPORTANT bug fix to the SRF format. The Data Block Header had the | |
345 blocksize field 4 bytes too large. Now fixed. Old SRF files will not | |
346 be readable by this new code (as they were in error). | |
347 | |
348 | |
349 Version 1.11.0b6 (2nd January 2008) | |
350 ---------------- | |
351 | |
352 * Changes to adhere to SRF v1.3: | |
353 | |
354 * Removal of the readID counter. | |
355 | |
356 * Added support for printf style name formatting. | |
357 | |
358 * Minor index format tweaks (64-bit data, dch/container filenames). | |
359 Index format is therefore now 1.01. | |
360 | |
361 | |
362 Version 1.11.0b5 (8th November 2007) | |
363 ---------------- | |
364 | |
365 * Major reorganisation of directories. All library code is in subdir | |
366 "io_lib". The code now uses "io_lib/xxx.h" in all include statements | |
367 too. | |
368 | |
369 * Fixed memory leaks in ZTR code | |
370 | |
371 * Various SRF bug fixes and better support for sample OFFS metadata in | |
372 both ZTR/ZTR. | |
373 | |
374 * Added srf_extract_hash program to perform random-access on a hash | |
375 indexed SRF archive. | |
376 | |
377 | |
378 Version 1.11.0b4 (26th October 2007) | |
379 ---------------- | |
380 | |
381 * The SRF format now supported adheres to version 1.2. | |
382 | |
383 * More speedups, in particular focusing on uncompression this time, so | |
384 srf2solexa is an order of magnitude faster. | |
385 | |
386 * ztr2read() now honours the read_sections() options and so is much | |
387 faster when only decoding (say) base and quality values. | |
388 | |
389 * New program srf2fastq. | |
390 | |
391 * Internal changes to various ztr data structures. If you use these | |
392 yourself take note of the new ztr_owns fields to avoid memory leaks. | |
393 | |
394 | |
395 Version 1.11.0b3 (16th October 2007) | |
396 ---------------- | |
397 | |
398 * Major speed improvements for compression. solexa2srf is now 30-35x faster. | |
399 | |
400 * Fixed various buffer overruns and memory leaks reported by valgrind | |
401 in the new deflate interlaced and SRF code. | |
402 | |
403 | |
404 Version 1.11.0b2 (2nd October 2007) | |
405 ---------------- | |
406 | |
407 * Minor version change to fix typoes in Makefile system. | |
408 | |
409 | |
410 Version 1.11.0b1 (28th September 2007) | |
411 ---------------- | |
412 | |
413 Beta release 1. | |
414 | |
415 * Added preliminary SRF support. This consists of a new subdirectory | |
416 'srf' (yes these all really need merging into a single directory, | |
417 but that's a later task), a substantial update to ZTR and a variety | |
418 of SRF tools in progs. | |
419 | |
420 The old huffman_static.[ch] files were renamed and substantially | |
421 worked upon to create deflate_interlaced.[ch]. | |
422 | |
423 Added new compression types. xrle2, tshift and qshift. The latter two | |
424 of these are very specific to trace and quality packings. May need to | |
425 rename to be more generic. | |
426 | |
427 | |
428 Version 1.10.3 (???) | |
429 -------------- | |
430 | |
431 * The HashTable interface now also allows for Bob Jenkins' lookup3 | |
432 64-bit hash function. This allows for substantially larger hash | |
433 tables. | |
434 | |
435 * Replaced tempnam() with tmpfile(). On systems without tmpfile | |
436 (Windows) this is simply a wrapper to use the old tempnam calls. | |
437 | |
438 * hash_extract bug fix for windows: now operates in binary mode. | |
439 | |
440 * INCOMPATIBLE CHANGE: On windows we now use semi-colon as the path | |
441 separator. The reason is that with the MinGW getenv() seems to do | |
442 "clever things" with PATH variables and consequently ends up | |
443 corrupting our clumsy attempt of escaping colons in paths. | |
444 | |
445 * Fasta format is semi-supported in "plain" format. It returns the | |
446 first entry when reading. | |
447 | |
448 * Experimental support for static huffman (STHUFF) compression type. | |
449 | |
450 | |
451 Version 1.10.2 (30th May 2007) | |
452 -------------- | |
453 | |
454 Primarily this is a bug fix release. | |
455 | |
456 * Convert_trace now has -signed and -noneg options to control signed | |
457 vs unsigned issues when shifting trace data about. | |
458 | |
459 * Include files now have C++ extern "C" style guards around them. | |
460 | |
461 * Various programs now accept -ztr command line arguments to force ZTR | |
462 format reading. This is for consistencies sake only and it is | |
463 recommended that users simply let the programs automatically detect | |
464 the file formats. | |
465 | |
466 * Hash_exp now outputs to the same file containing the experiment | |
467 files (in appended hash-table mode). It also has better Windows | |
468 handling (stripping ^M and using binary mode). | |
469 | |
470 * hash_extract bug fix: now only needs at least 1 filename specified | |
471 when fofn mode is not in use. | |
472 | |
473 * mFILE emulation: bug fixes when dealing with ftruncate, append mode, | |
474 checking for read/write flags, new mfcreate_from() function. | |
475 | |
476 * ZTR: added an experimental ZTR_FORM_STHUFF compression scheme. This | |
477 uses static huffman encoding on a predefined hard-coded set of | |
478 huffman tables. The purpose (as yet not put into action) is to allow | |
479 efficient compression of very small data sets for Illumina, AB | |
480 SOLiD, etc style traces. | |
481 | |
482 | |
483 Version 1.10.1 (20th June 2006) | |
484 -------------- | |
485 | |
486 * Trace files are now opened in read-only mode by default | |
487 (open_trace_file func). | |
488 | |
489 | |
490 Version 1.10.0 (15th June 2006) | |
491 -------------- | |
492 | |
493 * Two new environment variables are used, EXP_PATH and TRACE_PATH, to | |
494 replace RAWDATA. EXP_PATH is used when the new open_exp_mfile() | |
495 function is called and TRACE_PATH is used when open_trace_mfile() is | |
496 called. Both default to using RAWDATA when EXP or TRACE env is now | |
497 found. Also defined a trace type TT_ANYTR which is analogous to the | |
498 existing TT_ANY except it will not look for experiment or plain | |
499 format files. | |
500 | |
501 Modified the various example programs to use the appropriate open | |
502 call. This allows for traces and experiment files to have identical | |
503 names, such as is usually the case when querying named trace objects | |
504 from a trace server. | |
505 | |
506 * New program: extract_fastq to generate FASTQ output format. | |
507 | |
508 * New program: hash_exp. This allows multiple experiment files to be | |
509 contatenated together and then indexed so io_lib can still treat | |
510 them as single files. | |
511 | |
512 * The URL based search path mechanism now by default uses libcurl | |
513 instead of wget. This makes it considerably faster. | |
514 | |
515 * If an element in RAWDATA, EXP_PATH or TRACE_PATH now starts with the | |
516 pipe symbol ("|") then the compressed file extension code is negated | |
517 for that search element. (This prevents looking for foo.gz, foo.Z, | |
518 foo.bz2, etc if it fails to find foo.) | |
519 | |
520 * Added HashTableDel() and HashTableRemove() functions to take items | |
521 out of a hash table. | |
522 | |
523 * ZTR's compress_chunk() and uncompress_chunk() functions are now | |
524 externally callable. | |
525 | |
526 * New program io_lib-config. This has --version, --cflags and --libs | |
527 options to query the appropriate configuration when compiling and | |
528 linking against io_lib. There's also a new io_lib.m4 file which | |
529 provides an AC_CHECK_IO_LIB autoconf macro to use io_lib-config and | |
530 generate appropriate Makefile substitutions. | |
531 | |
532 * Updated the autoconf code to support libcurl searching. | |
533 | |
534 * Renamed SCF's delta_samples[12] functions to be | |
535 scf_delta_samples[12]. (From Saul Kravitz) | |
536 | |
537 * Added a '-error filename' option to convert_trace. (From Saul Kravitz) | |
538 | |
539 * Bug fix: HashTableAdd() now works properly with non-string keys. | |
540 | |
541 * Bug fix to read_dup(). | |
542 | |
543 * Bug fix to xrle which could read past the array bounds. It also now | |
544 handles run-lengths of 256 or more. | |
545 | |
546 * Bug fix: the fwrite_* functions no longer close the FILE pointer | |
547 given to them. | |
548 | |
549 * Bug fix to fdetermine_trace_type(); it now rewinds the file back. | |
550 | |
551 * Bug fix to mfseek and mrewind; they both now clear the EOF flag. | |
552 | |
553 * Bug fix to find_file_dir(). | |
554 | |
555 | |
556 Version 1.9.2 (14th December 2005) | |
557 ------------- | |
558 | |
559 * Added AC_CHECK_LIB calls for the nsl and socket libraries | |
560 (gethostbyname / socket functions). Needed for Solaris compilations. | |
561 | |
562 * In extract_seq, used open_trace_mfile instead of | |
563 open_trace_file. Functionally this is the same, but it is faster. | |
564 | |
565 * fwrite_reading() now frees the temporary mFILE it created. | |
566 | |
567 * mfreopen_compressed() no longer closes the original FILE | |
568 pointer. This brings it back into line with the original | |
569 functionality provided in 1.8.x. It also cures a bug where the old | |
570 file pointer was often left opening meaning operates on many files | |
571 could could cause a resource leak ending in the inability to open | |
572 more trace files. | |
573 | |
574 * Added private_data and private_size to the Read struct. Populate | |
575 these when reading SCF files. | |
576 | |
577 * Hash_extract now returns an error code to the calling process upon | |
578 failure. | |
579 | |
580 * Major overhaul of hash_sff. It no longer loads the entire file into | |
581 memory. It can now cope with adding a hash index to an archive that | |
582 already contains an index. | |
583 | |
584 * Added support for 454's "sorted index" code. NB this is based on the | |
585 extraction code from their getsff.c code and has not been tested | |
586 with a genuine indexed SFF file yet. | |
587 | |
588 * Fixed an uninitialised memory access in mfload(). | |
589 | |
590 * Fixed a bug where hash query searches for items that do not exist | |
591 and map to an empty bucket could cause hangs or crashes. | |
592 | |
593 * Fixed a hang in mfload() when reading a zero length file. | |
594 | |
595 | |
596 Version 1.9.1 | |
597 ------------- | |
598 | |
599 * Implemented the SFF (454) file structure, currently as read-only. | |
600 This is supported both as an archive containing multiple files and | |
601 also as a single SFF entry. | |
602 | |
603 * Allow for SFF=? components in RAWDATA search path. | |
604 | |
605 * Tar files, SFF archives and hashed archives (eg hashed tar, sff, or | |
606 "solid" archives) may now be used as part of a pathname. Eg if a | |
607 tar file foo.tar contains entry xyzzy.ztr then we can ask to fetch | |
608 trace foo.tar/xyzzy.ztr instead of requiring setting of the | |
609 RAWDATA environment variable. | |
610 | |
611 * Changed the HashFile format slightly. It's now format 1.00. | |
612 | |
613 The key difference is that it has a file footer pointing back to the | |
614 hashfile header (so the hashfile can be appended to an archive) and | |
615 it also has an offset in the header to apply to all seeks within the | |
616 archive itself, so it can be prepending to an archive that's already | |
617 been indexed without breaking the offsets. | |
618 | |
619 Extended the hash_tar program to allow control over these header options. | |
620 | |
621 * Fixed divide-by-zero buf when calling mfread for zero | |
622 | |
623 * Removed the warning for unknown ZTR chunk types. It now just | |
624 silently stores them in memory. | |
625 | |
626 * mfopen now honours binary verses ascii differences (and so updated | |
627 Read.c calls accordingly) so that Windows works better. | |
628 | |
629 * Removed file descriptor 'leak' in write_reading(). | |
630 | |
631 * Unset compression_used when opening uncompressed files instead of | |
632 leaving as the last value. | |
633 | |
634 * Fixed a file descriptor (and some memory) leak in | |
635 freopen_compressed. (Bug ID #1289095) | |
636 | |
637 * Fixed the hash file saving and loading so that it works on all | |
638 platforms instead of just x86 linux. There were bugs in assuming the | |
639 size of structures. The assumptions are still there in that I assume | |
640 they pad the same internally (for ease of coding - we can change it | |
641 when we finally see a system which operates differently), but the | |
642 final "boundary" padding has been resolved. | |
643 | |
644 | |
645 Version 1.9.0 | |
646 ------------- | |
647 | |
648 * ***INCOMPATIBILITIES*** to 1.8.12 | |
649 | |
650 - The Exp_info structure now internally contains an "mFILE *" member | |
651 instead of "FILE *" member. If you use the experiment file functions | |
652 for I/O then hopefully it'll still work. However if you directly | |
653 manipulated the Exp_info yourself using fprintf etc then you will | |
654 need to modify your code. | |
655 | |
656 - Some functions no longer have external scope. Most of these did not | |
657 previously have external function prototypes. If you have a burning | |
658 need to use one of these, please contact me directly via sourceforge. | |
659 The full list is: | |
660 | |
661 ctfType (global variable) ztr_encode_samples_C | |
662 replace_nl ztr_encode_samples_G | |
663 ctfDecorrelate ztr_encode_samples_T | |
664 exp_print_line_ ztr_decode_samples | |
665 find_file_tar ztr_encode_bases | |
666 find_file_archive ztr_decode_bases | |
667 find_file_url ztr_encode_positions | |
668 ztr_write_header ztr_decode_positions | |
669 ztr_write_chunk ztr_encode_confidence_1 | |
670 ztr_read_header ztr_decode_confidence_1 | |
671 ztr_read_chunk_hdr ztr_encode_confidence_4 | |
672 compress_chunk ztr_decode_confidence_4 | |
673 uncompress_chunk ztr_encode_text | |
674 ztr_encode_samples_4 ztr_decode_text | |
675 ztr_decode_samples_4 ztr_encode_clips | |
676 ztr_encode_samples_common ztr_decode_clips | |
677 ztr_encode_samples_A | |
678 | |
679 - Some external functions have changed prototypes to use mFILE instead | |
680 of FILE. Most cases of these I've put in place a wrapper function | |
681 with the old name, but not yet all. Functions changed are: | |
682 | |
683 ctfFRead write_scf_samples32 | |
684 ctfFWrite write_scf_base | |
685 exp_print_line write_scf_bases | |
686 exp_print_mline write_scf_bases3 | |
687 exp_print_seq write_scf_comment | |
688 read_scf_header fcompress_file | |
689 read_scf_sample1 fopen_compressed | |
690 read_scf_samples1 freopen_compressed | |
691 read_scf_samples31 be_write_int_1 | |
692 read_scf_sample2 be_write_int_2 | |
693 read_scf_samples2 be_write_int_4 | |
694 read_scf_samples32 be_read_int_1 | |
695 read_scf_base be_read_int_2 | |
696 read_scf_bases be_read_int_4 | |
697 read_scf_bases3 le_write_int_1 | |
698 read_scf_comment le_write_int_2 | |
699 write_scf_header le_write_int_4 | |
700 write_scf_sample1 le_read_int_1 | |
701 write_scf_samples1 le_read_int_2 | |
702 write_scf_samples31 le_read_int_4 | |
703 write_scf_samples2 fdetermine_trace_type | |
704 | |
705 - Removed support for the OLD unix "pack" program as a valid trace | |
706 compression algorithm. | |
707 | |
708 - Removed CORBA support. (It wasn't enabled and I've no idea if it | |
709 even worked as I cannot test it.) | |
710 | |
711 - The default search order for RAWDATA now has the current working | |
712 directory at the end of RAWDATA instead of the start. | |
713 | |
714 * Significant speed ups, particularly when dealing with reading | |
715 gzipped files or when extracting data from tar files. | |
716 | |
717 * New external functions for faster access via mFILE (memory-file) | |
718 structs. These mimic the fread/fwrite calls, but with mfread/mfwrite | |
719 etc. | |
720 | |
721 * Numerous minor tweaks and updates to fix compiler warnings on more | |
722 stricter modes of the Intel C Compiler. | |
723 | |
724 * Preliminary support for storing pyrosequencing style traces. This | |
725 has been modeled on the flowgram data from 454, but should be | |
726 applicable to other platforms. ZTR has been updated to incorporate | |
727 this too. | |
728 | |
729 The Read structure also has flow, flow_order, nflows and flow_raw | |
730 elements too. Code to convert these into the more usual traceA/C/G/T | |
731 arrays exists currently as part of Trev (in tk_utils in the Staden | |
732 Package), but this may move into io_lib for the next official release. | |
733 | |
734 * New hash_tar and hash_extract programs. These replace the index_tar | |
735 program for rast random access. For RAWDATA include "HASH=hashfile" | |
736 as an element to get io_lib to use the archive hash. It's possible | |
737 to create hash files of most archive formats as the hash itself | |
738 contains the offset and size of each item in the archive. This means | |
739 that extracting an item does not need to know the format of the | |
740 original archive. | |
741 | |
742 Some benchmarks show that on ext3 it's actually faster to extract | |
743 files from the hash than directly via the directory. This was | |
744 testing with ~200,000 files, whereupon directory lookups become | |
745 slow. I'd imagine ResierFS or similar to be faster. | |
746 | |
747 * Added an XRLE encoding for ZTR. This is similar to the existing RLE | |
748 mechanism but it copes with run length encoding of items larger than | |
749 a single byte. It's current use is for storing the 4-base repeating | |
750 flow order in 454 data. | |
751 | |
752 | |
753 Version 1.8.12 | |
754 -------------- | |
755 | |
756 * The ABI format code now reads the confidence values from KB (via | |
757 PCON field). | |
758 | |
759 * New program: trace_dump. Like scf_dump, but deals with generic input | |
760 formats. | |
761 | |
762 * Slightly more sensible average spacing calculation in the ABI | |
763 reading code. It's still not perfect, but is only used when the real | |
764 spacing value is negative or zero. | |
765 | |
766 * Disabled the base-reordering fix for ABI files. We believe the bug | |
767 causing this no longer exists. | |
768 | |
769 * Expriment file format: added FT (EMBL feature table) and LF | |
770 (LiGation; a combination of LI and LE) records. | |
771 | |
772 * Experiment files: strip out digits from the sequence we read | |
773 (for better support of EMBL files). | |
774 | |
775 * Experiment files: fixed a potential buffer overrun in the conversion | |
776 of binary confidence values to ascii values. | |
777 | |
778 * Minor improvements to portability (INT_MAX vs MAXINT2) and removal | |
779 of some compilation warnings. | |
780 | |
781 * Extract_seq now accepts a -fofn argument. | |
782 | |
783 * New functions: read_update_base_positions() and | |
784 read_udpate_confidence_values() to replace read_update_opos(). | |
785 These apply an edit buffer to the sequence details and are used (for | |
786 example) within Trev for saving edits back to a trace file. | |
787 | |
788 * Better error handling in fcompress_file(). | |
789 | |
790 * New specifiers in RAWDATA. Added a generic URL format (eg | |
791 "URL=http://some/where/trace=%s") implemented via use of wget. There | |
792 is also an ARC= format to make use of the Sanger Trace Archive, | |
793 although currently this will not work externally. | |
794 | |
795 * Zero memory used in read_alloc(). Fixes to read_dup(). | |
796 | |
797 | |
798 Version 1.8.11 | |
799 -------------- | |
800 | |
801 * Rewrote the background subtraction in convert_trace to deal with each | |
802 channel independently. | |
803 | |
804 * Make install now install the include files (all of them, although not all | |
805 are strictly required) in $prefix/include/io_lib/. | |
806 | |
807 * Moved the ABI filter wheel order (FWO) reading from outside the sample | |
808 reading code into the general reading bit as this is needed for reading the | |
809 comments too (it also applies to the order of the signal strengths). Hence | |
810 when the READ_COMMENTS section only is defined it now works correctly. | |
811 | |
812 * Moved the DataCount #defines into static values and added a | |
813 abi_set_data_counts function to change these. This allows reading of the raw | |
814 data from ABI files. This is used within the new convert_trace -abi_data | |
815 option. | |
816 | |
817 * Removed a one-byte write buffer overflow in the CTF writing code. | |
818 | |
819 * New Experiment file records WL and WR for indicating clip points within a WT | |
820 trace. | |
821 | |
822 * Removed the saved copy of fp for exp_fread_info in 'e' structure as it | |
823 doesn't belong to us. (If we do store it there then the exp_destroy_info | |
824 function will free it and this causes bugs.). POTENTIAL INCOMPATIBILITY: | |
825 if you assumed that exp_destroy_info closed the files that you opened and | |
826 passed into exp_fread_info, then this is no longer true. | |
827 | |
828 * New function read_dup() to copy a Read structure. | |
829 | |
830 * get_read_conf() now deals with loading confidence values from any suitable | |
831 format and not just SCF. | |
832 | |
833 * Fixed memory leak in ztr (ztr->text_segments). | |
834 | |
835 | |
836 Version 1.8.10 | |
837 -------------- | |
838 | |
839 * Added Steven Leonard's changes to index_tar. It no longer adds index entries | |
840 for directories, unless -d is specified. It also now supports longer names | |
841 using the @LongLink tar extension. | |
842 | |
843 * Fixed a bug in exp2read where the base positions were random if experiment | |
844 files are loaded without referencing a trace and without having ON lines. | |
845 | |
846 * New program get_comment. This queries and extracts text fields held within | |
847 the Read 'info' section | |
848 | |
849 * Overhaul of convert_trace to support the makeSCF options (normalise etc). | |
850 | |
851 | |
852 Version 1.8.9 | |
853 ------------- | |
854 | |
855 Sorry this isn't a proper changes-by-source listing. Any suggestions for how I | |
856 collate the 'cvs log' output into something more concise? The below text is | |
857 simply a list of changes, but more complete than in the NEWS file. | |
858 | |
859 * ZTR spec updated to v1.2. The chebyshev predictor has been rewritten in | |
860 integer format. The old chebyshev still has a format type allocated to it | |
861 (73), but the new ICHEB format (74) is now the default. The old floating | |
862 point method was potentially unstable (eg when running on non IEEE fp | |
863 systems). The new method also seems to save a bit more space. | |
864 | |
865 * The docs and code disagreed for CNF4 storage. Changed the docs to reflect | |
866 the code (which does as intended). | |
867 | |
868 * ZTR speed increase. Follow1 is substantially faster, increasing write | |
869 times by about 10%. | |
870 | |
871 * New named formats types. ZTR1, ZTR2 and ZTR3. ZTR defaults to ZTR2, but we | |
872 can explicitly ask for another compression level if desired. Also explicit | |
873 statement of format (TT_ZTR instead of TT_ANY) removes the need for | |
874 a rewind() call and so ZTR can now work through a pipe. | |
875 | |
876 * General tidy up to remove a few compilation warnings (missing include files, | |
877 signed vs unsigned issues, etc). | |
878 | |
879 * Initial support is included for BioLIMS integration, but this is not | |
880 complete. (Unfortunately it requires access to a non-public library.) | |
881 | |
882 * New function compress_str2int - opposite of existing compress_int2str. | |
883 | |
884 * (Steven Leonard). Uses zlib for gzip compression and decompression. | |
885 | |
886 | |
887 | |
888 | |
889 | |
890 These are extracts from the full Staden Package change log. They may not be | |
891 immediately obvious when taken out of context, but we feel this information | |
892 may still be useful to the users of io_lib. | |
893 | |
894 23rd August 2000, James | |
895 ----------------------- | |
896 1. Removed find_trace_file and added an open_trace_file function. | |
897 The idea is that searching for a files existance is better done by attempting | |
898 to open it. This in turn allows for more possibilities of file searching. | |
899 Makefile | |
900 utils/open_trace_file.c | |
901 read/Read.c | |
902 read/scf_extras.c | |
903 read/translate.[ch] | |
904 progs/extract_seq.c | |
905 | |
906 2. Added a TAR option to RAWDATA. We can now read trace files directly from | |
907 tar files (although they cannot be written to directly). | |
908 utils/open_trace_file.c | |
909 utils/tar_format.h | |
910 | |
911 3. Created an index_tar program to optimise tar reading, although it is not | |
912 mandatory. | |
913 progs/index_tar.c | |
914 progs/Makefile | |
915 | |
916 4. Fixed a bug when dealing with plain text files containing spaces. | |
917 plain/seqIOPlain.c | |
918 | |
919 | |
920 31st July 2000, James | |
921 --------------------- | |
922 1. Renamed TTFF to be ZTR. | |
923 read/Read.[ch] | |
924 utils/traceType.c | |
925 utils/compress.c | |
926 ttff/* -> ztr/* | |
927 README | |
928 | |
929 2. ZTR reading will now stop when it spots a ZTR magic number. This allows | |
930 concatenation of ZTR files. | |
931 ztr/ztr.[ch] | |
932 | |
933 | |
934 15th June 2000, James | |
935 --------------------- | |
936 1. Added a TTFF_FOLLOW filter type to TTFF. This is enabled with compression | |
937 level 2 for the chromatogram data. | |
938 io_lib/ttff/ttff.[ch] | |
939 io_lib/ttff/compression.[ch] | |
940 | |
941 9th June 2000, James | |
942 -------------------- | |
943 * RELEASED 1.8.4 */ | |
944 | |
945 1. Added zlib bits to windows compilation. | |
946 io_lib/mk/windows.mk | |
947 | |
948 2. Updated convert_trace. It can now reduce sample-size to 8-bit (with the | |
949 "-8" option) and the formats may now be specified as either integer or text | |
950 format. The text format is case insensitive. | |
951 io_lib/progs/convert_trace.c | |
952 io_lib/utils/traceType.c | |
953 | |
954 3. More windows binary vs ascii fixes. When reading we switch to binary mode | |
955 before attempting fdetermine_trace_type, otherwise it fails to auto-detect | |
956 TTFF (which includes a newline as part of the magic number). Also added a | |
957 _setmode() call to the fwrite_reading code too. | |
958 io_lib/read/Read.c | |
959 | |
960 4. Changed the default compression technique of TTFF to that used in 1.8.2. I | |
961 accidently left it set to the experimental dynamic-delta method in 1.8.3, | |
962 which currently doesn't have the uncompression function! Also removed lots of | |
963 debugging output. | |
964 io_lib/ttff/ttff.c | |
965 io_lib/ttff/ttff_translate.c | |
966 | |
967 5. Bug fix to exp2read - when no right hand quality cutoff is specified we | |
968 were defaulting to the left end of the trace, instead of the right end. (This | |
969 only happens when opening experiment files which do not have clip points.) | |
970 io_lib/read/translate.c | |
971 | |
972 6. Changed the strftime() format in ABI reading code to use %H:%M:%S instead | |
973 of %T, as %T doesn't appear to be part of ANSI (I think it's probably | |
974 XPG4-UNIX). It worked on Unix machines, but not on MS Windows. | |
975 io_lib/abi/seqIOABI.c | |
976 | |
977 | |
978 8th June 2000, James | |
979 -------------------- | |
980 * RELEASED 1.8.3 */ | |
981 | |
982 1. Updated the CTF support so that it includes a couple of new block | |
983 types. This allows for base positions being non-sequentially ordered, as is | |
984 possible in severe compressions. | |
985 io_lib/ctf/ctfCompress.c | |
986 | |
987 2. Overhaul of TTFF format - now more PNG based in style. Still highly | |
988 experimental. | |
989 io_lib/ttff/* | |
990 | |
991 | |
992 16th May 2000, James | |
993 -------------------- | |
994 * RELEASED 1.8.0 */ | |
995 | |
996 1. Added szip support. Szip generally gives better compression ratios than | |
997 gzip and often marginally better than bzip2, but is generally considerably | |
998 slower at decompression. | |
999 io_lib/utils/compress.[ch] | |
1000 | |
1001 2. Merged in Jean Thierre-Mieg's CTF code. This is a compressed trace format | |
1002 which holds the same data as SCF, but in reduce space. | |
1003 io_lib/read/Read.[ch] | |
1004 io_lib/utils/traceType.c | |
1005 io_lib/ctf/* | |
1006 | |
1007 3. Added my own highly experimental TTFF format. (Thanks to Jean Thierre-Mieg | |
1008 for re-awakining my interest in this.) TTFF files are typically equivalent in | |
1009 size to bzip2'ed SCF files, but are much quicker to write than any of the | |
1010 currently supported compressed formats. Depends on zlib. | |
1011 io_lib/read/Read.[ch] | |
1012 io_lib/utils/traceType.c | |
1013 io_lib/ttff/* | |
1014 | |
1015 4. Reorganised the Makefiles for easier building. | |
1016 */Makefile | |
1017 | |
1018 5. New program "convert_trace". Primarily a test tool at present as it needs | |
1019 a friendlier interface. | |
1020 progs/convert_trace.c | |
1021 | |
1022 | |
1023 20th April 2000, James | |
1024 ---------------------- | |
1025 1. Removed a file-descriptor leak in extract_seq. | |
1026 io_lib/progs/extract_seq.c | |
1027 | |
1028 22nd March 2000, James | |
1029 ---------------------- | |
1030 1. Fixed bug in time formatting from ABI files. We used strftime code | |
1031 %a without setting tm.tm_wday (number of days since sunday). It's not | |
1032 easy to work that out, so we convert from struct tm to time_t, which | |
1033 resets any errornous elements of struct tm. Also fixed a silly error | |
1034 where the end time was set to the start time (incorrectly). | |
1035 io_lib/abi/seqIOABI.c | |
1036 | |
1037 25th February 2000, James | |
1038 ------------------------- | |
1039 2. Added checks for QR <= QL in the exp2read conversion function. This caused | |
1040 trev to display incorrectly (blanking incorrect screen portions) when dealing | |
1041 with inconsistent experiment files. Also changed qclip so that it doesn't | |
1042 create this inconsistent case. | |
1043 io_lib/read/translate.c | |
1044 | |
1045 1st February 2000, Kathryn | |
1046 -------------------------- | |
1047 1. Fixed bug which caused init_exp to crash when QL was more than 5 digits. | |
1048 Increased it to handle 15 digits. | |
1049 io_lib/read/translate.c | |
1050 | |
1051 27th January 2000, James | |
1052 ------------------------ | |
1053 1. Moved Gap4's copy of scf_extras into io_lib, and renamed io_liub's | |
1054 scf_bits to be scf_extras (to avoid editing too many #include statements). | |
1055 Without this we were getting errors due to dynamic linking using odd | |
1056 copies. Eg loading libread.so and then libgap.so meant that | |
1057 find_trace_file called from edUtils2.c (libgap.so) would pick up the first | |
1058 copy from libread.so, despite the fact that there's also a copy in the | |
1059 same libgap.so. | |
1060 gap4/scf_extras.[ch] | |
1061 io_lib/scf_bits.[ch] | |
1062 | |
1063 25th January 2000, Kathryn | |
1064 -------------------------- | |
1065 1. Fixed crash in qclip due to insufficent arguments being passed to | |
1066 find_trace_file and also fixed an array bounds error in scan_right of qclip.c | |
1067 io_lib/read/scf_bits.c | |
1068 | |
1069 19th January 2000, James | |
1070 ------------------------ | |
1071 4. Copied bits of the fakii and cap2/3 scf/expFile reading code into | |
1072 io_lib. Not all of this is in there, just the things which seem to be | |
1073 common and sensibly fit there. This also helps qclip to build on Windows. | |
1074 FIXME: We should now remove some of this code from Gap4. | |
1075 Also fixed a small memory leak in fopen_compressed() - it wasn't freeing | |
1076 the result of tempnam(). | |
1077 io_lib/read/translate.c | |
1078 io_lib/read/scf_bits.[ch] | |
1079 io_lib/read/seqInfo.[ch] | |
1080 io_lib/utils/files.c | |
1081 io_lib/utils/compress.c | |
1082 | |
1083 31st August 1999, James | |
1084 ----------------------- | |
1085 1. -fasta_out mode of extract_seq now changes - to N. | |
1086 io_lib/progs/extract_seq.c | |
1087 | |
1088 27th August 1999, James | |
1089 ----------------------- | |
1090 1. The order of information items added by the abi to scf code has | |
1091 changed, to make it more sensible. Also fixed a bug in the textual (rather | |
1092 than numerical) date output, and wrote this to the DATE field. | |
1093 io_lib/abi/seqIOABI.c | |
1094 | |
1095 2. makeSCF no longer adds a MACH field, as this was redudant. | |
1096 io_lib/abi/makeSCF.c | |
1097 | |
1098 3. Extract_seq now has proper use of CL and CR when using -cosmid_only. It | |
1099 was assuming they were the same as QL/QR and SL/SR, which is not the case | |
1100 (rather it's like having a CS line of `CL`..`CR`). Extract_seq also now | |
1101 has a -fasta_out format option and can handle multiple files, which makes | |
1102 it easier to produce a fasta file from multiple experiment files. | |
1103 io_lib/progs/extract_seq.c | |
1104 | |
1105 4th August 1999, James | |
1106 ---------------------- | |
1107 1. The exp2read() function in io_lib now initialises the confidence arrays | |
1108 (eg r->prob_A) to zero, or to the experiment file AV line. | |
1109 io_lib/read/translate.c | |
1110 | |
1111 2nd June 1999, James | |
1112 -------------------- | |
1113 1. The MegaBACE sequencer creates ABI files. However it does so in a odd way. | |
1114 Sometimes the samples arrays are truncated such that bases are positioned | |
1115 above samples which are not stored in the ABI file. We now realloc the samples | |
1116 array in such cases and fill out the remainder with blank data. This removes a | |
1117 crash in trev when viewing such data. | |
1118 io_lib/abi/seqIOABI.c | |
1119 | |
1120 2. Fixed a memory corruption of io-lib compression. The switch to use tempnam | |
1121 (for Windows) implies that the filename returned is no longer allocated by us. | |
1122 Unfortunately we forgot to remove the xfree(fname) calls. | |
1123 src/io_lib/utils/compress.c | |
1124 | |
1125 18th May 1999, James | |
1126 -------------------- | |
1127 1. Fixed the trace rescaling option of makeSCF. We now go through the rescale | |
1128 function twice. Once to work out the maximum value, and again to do the | |
1129 rescaling. This fixes a bug where the maximum value after rescaling was | |
1130 sometimes above 65536 and hence cause "trace wraparound" effects. | |
1131 io_lib/progs/makeSCF.c | |
1132 | |
1133 26th April 1999, JohnT | |
1134 ---------------------- | |
1135 1. Allow : to be entered in RAW_DATA by using :: | |
1136 Misc/find.c | |
1137 io_lib/utils/find.c | |
1138 | |
1139 2. Support for fetching trace files using Corba | |
1140 Modified: | |
1141 Misc/find.c | |
1142 mk/misc.mk | |
1143 io_lib/utils/find.c | |
1144 init_exp/init_exp.c | |
1145 io_lib/read/Makefile | |
1146 io_lib/utils/find.c | |
1147 io_lib/utils/compress.c | |
1148 io_lib/utils/Makefile | |
1149 mk/global.mk | |
1150 Added: | |
1151 io_lib/utils/corba.cpp | |
1152 io_lib/utils/stcorba.h | |
1153 Generated from IDL: | |
1154 io_lib/utils/trace.h | |
1155 io_lib/utils/trace.cpp | |
1156 io_lib/utils/basicServer.h | |
1157 io_lib/utils/basicServer.cpp | |
1158 | |
1159 | |
1160 3. Added ABI utility progs to NT port | |
1161 mk/abi.mk | |
1162 | |
1163 4. Added Windows 95 support | |
1164 io_lib/utils/compress.c | |
1165 mk/WINNT.mk | |
1166 | |
1167 5th March 1999, JohnT | |
1168 --------------------- | |
1169 Various changes for WINNT support as follows: | |
1170 io_lib/utils - Don't redirect to /dev/null on WINNT | |
1171 | |
1172 3rd February 1999, James | |
1173 ------------------------ | |
1174 1. Fixed problems reported by Insure on Windows NT. | |
1175 These are mainly lack of prototypes (malloc/memcpy) and not returning properly | |
1176 from 'int' functions. However one fix to seqed_translate.c (find_line_start3) | |
1177 was a array read overflow. | |
1178 io_lib/progs/makeSCF.c | |
1179 | |
1180 18th January 1999, James | |
1181 ------------------------ | |
1182 1. Changed the read2exp io_lib translation function so that it can accept | |
1183 lowercase a,c,g,t. Oddly enough it was already coded to accept lowercase IUB | |
1184 codes, but we missed out a,c,g and t! | |
1185 io_lib/read/translate.c | |
1186 | |
1187 15th January 1999, JohnT | |
1188 ----------------------- | |
1189 Modified files thoughout for Windows NT Compatibility as follows: | |
1190 | |
1191 8. need to explicitly set text or binary file mode under WINNT | |
1192 io_lib/exp_file/expFileIO.c | |
1193 | |
1194 18. need to include stddef.h for size_t with Visual C++ | |
1195 io_lib/utils/array.h | |
1196 | |
1197 19. need to have target LIBS (not LIB) and correct ordering for correct make | |
1198 on WINNT. Also need additional abstractions to allow for different compile | |
1199 and link calling conventions with Visual C++, and have rules for building | |
1200 Windows .def files. | |
1201 io_lib/abi/Makefile | |
1202 io_lib/alf/Makefile | |
1203 io_lib/exp_file/Makefile | |
1204 io_lib/plain/Makefile | |
1205 io_lib/progs/Makefile | |
1206 io_lib/read/Makefile | |
1207 io_lib/scf/Makefile | |
1208 io_lib/utils/Makefile | |
1209 | |
1210 18th December 1998, James | |
1211 ------------------------- | |
1212 1. Added bzip2 recognition to the (de)compression code of io_lib. This is now | |
1213 the latest bzip, and is recognised by phred (unlike bzip version 1). Bzip2 is | |
1214 approx the same as bzip1, but more or less twice as fast for decompression. | |
1215 io_lib/utils/compress.c | |
1216 | |
1217 27th November 1998, James | |
1218 ------------------------- | |
1219 1. Fixed the trace file searching mechanism in io_lib. When loading an | |
1220 experiment file with LN/LT lines, we now first search for the trace file | |
1221 relative to the location of the experiment file. | |
1222 io_lib/read/Read.c | |
1223 io_lib/read/translate.[ch] | |
1224 | |
1225 16th November 1998, James | |
1226 ------------------------- | |
1227 4. Added NT (NoTe) and GD (Gap4 Database) line types to the experiment file. | |
1228 io_lib/exp_file/expFile.[ch] | |
1229 | |
1230 24th September 1998, James | |
1231 -------------------------- | |
1232 1. The scf reading and writing code now handles traces with zero bases. | |
1233 Previously this failed after a malloc(0). | |
1234 io_lib/scf/read_scf.c | |
1235 io_lib/scf/write_scf.c | |
1236 | |
1237 2. The ABI file reading code has been tidied up. It now also supports | |
1238 conversion of more ABI fields, including RUND, RUNT, SPAC(2), CMNT, LANE and | |
1239 MTXF. | |
1240 io_lib/abi/seqIOABI.c | |
1241 | |
1242 17th July 1998, James | |
1243 --------------------- | |
1244 1. Extract_seq now copes with sequences containing no SQ line (instead of just | |
1245 SEGV). | |
1246 io_lib/progs/extract_seq | |
1247 | |
1248 9th July 1998, James | |
1249 -------------------- | |
1250 1. Enforce IUBC code set in io_lib when converting from trace (any format) to | |
1251 experiment file. We leave the IUBC 'N' intact. | |
1252 io_lib/read/translate.c | |
1253 | |
1254 28th May 1998, James | |
1255 -------------------- | |
1256 1. Added a read_sections() function to io_lib so that programs can state | |
1257 which bits of a trace file they are interested in. The loading code only | |
1258 then parses those bits. This can give big increases to things like init_exp | |
1259 which only wants bases and does not care about the delta-delta format of SCF | |
1260 trace data. | |
1261 io_lib/read/Read.h | |
1262 io_lib/read/translate.c | |
1263 io_lib/scf/scf.h | |
1264 io_lib/scf/read_scf.c | |
1265 io_lib/abi/seqIOABI.c | |
1266 io_lib/alf/seqIOALF.c | |
1267 init_exp/init_exp.c | |
1268 | |
1269 3. Extract GELN (gel name) from ABI file when converting to SCF. | |
1270 io_lib/abi/seqIOABI.[ch] | |
1271 | |
1272 2. Improved the makeSCF -normalise option. Background subtraction is now | |
1273 cleaner (and simpler) and it also now scales the heights. Moved it to io_lib | |
1274 as it's now freely available. | |
1275 io_lib/progs/makeSCF.c | |
1276 | |
1277 23rd March 1998, James | |
1278 ---------------------- | |
1279 1. Removed the change made on 7th May 1997 to seqIOPlain.c. This code is used | |
1280 by extract_seq, and so clipping in seqIOPlain causes double clipping (and | |
1281 hence wrong sections). | |
1282 io_lib/plain/seqIOPlain.c | |
1283 | |
1284 11th March 1998, James | |
1285 ---------------------- | |
1286 2. Removed the requirement of EXP_FILE_LINE_LENGTH in exp_fread_info(). | |
1287 This allows for (eg) tags with very long comments to be read in without | |
1288 being truncated. | |
1289 io_lib/exp_file/expFileIO.c | |
1290 | |
1291 4th March 1998, James | |
1292 --------------------- | |
1293 1. Following advice from Leif Hansson <leif.hansson@mbox4.swipnet.se>, the ALF | |
1294 reading code now reads the "Raw data" subfile when the "Processed data" | |
1295 subfile is not present, as "Processed data" is apparently an optional output | |
1296 of the pharmacia software. Raw data is in the same format, although I do not | |
1297 know what processing takes place to convert it to Processed data. (Looking at | |
1298 some real traces, apparently none!) | |
1299 io_lib/alf/seqIOALF.c | |
1300 | |
1301 24th February 1998, James | |
1302 ------------------------- | |
1303 1. Added an ABI in MacBinary format file type detector so that these are | |
1304 now autodetected. | |
1305 io_lib/utils/traceType.c | |
1306 | |
1307 15th January 1998, James | |
1308 ------------------------ | |
1309 1. Rewrote the delta_samples1/2 functions to be faster. Times vary between 0.55 | |
1310 and 0.7 fractions of the original time. | |
1311 io_lib/scf/misc_scf.c | |
1312 | |
1313 4th December 1997, James | |
1314 ------------------------ | |
1315 1. First post-release bug fix. | |
1316 Io_lib incorrect sets read->trace_name when reading anything except SCF files. | |
1317 This means that when outputting to an experiment file no LN line is present. | |
1318 io_lib/read/Read.c | |
1319 | |
1320 1st October 1997, James | |
1321 ----------------------- | |
1322 1. Allow for SCF files to contain 0 bases. This mainly affects memory | |
1323 allocation, but also the display widget. | |
1324 io_lib/scf/read_scf.c | |
1325 io_lib/utils/read_alloc.c | |
1326 | |
1327 28/29th August 1997, James | |
1328 -------------------------- | |
1329 2. Added a few changes to make the code more portable for the Mac. Not really | |
1330 used at present. | |
1331 Misc/os.h | |
1332 Misc/files.c | |
1333 io_lib/utils/traceType.c | |
1334 io_lib/read/translate.c | |
1335 io_lib/utils/compress.c | |
1336 | |
1337 30th June 1997, James | |
1338 --------------------- | |
1339 1. The exp2read function produced invalid rightCutoff values (INT_MAX) when no | |
1340 QR line is present. It now correctly sets it to 0. | |
1341 io_lib/read/translate.c | |
1342 |