| 04635ee | Clayton Wheeler | 21 August 2012, 18:14:08 UTC | Documented new features. | 21 August 2012, 18:14:08 UTC |
| 1f84378 | Clayton Wheeler | 21 August 2012, 17:17:35 UTC | Fixed interval syntax in maf_tile specs. | 21 August 2012, 17:17:35 UTC |
| 9f880b5 | Clayton Wheeler | 18 August 2012, 01:00:51 UTC | Enable debugging with BIO_MAF_DEBUG environment variable. | 18 August 2012, 01:00:51 UTC |
| b9e5e75 | Clayton Wheeler | 18 August 2012, 00:59:53 UTC | Added debugging code. | 18 August 2012, 01:00:30 UTC |
| 574e211 | Clayton Wheeler | 18 August 2012, 00:59:29 UTC | Remove gaps when tiling. | 18 August 2012, 00:59:29 UTC |
| 77b44ab | Clayton Wheeler | 18 August 2012, 00:58:51 UTC | Apparent no-op change for non_fill. | 18 August 2012, 00:58:51 UTC |
| 2c9d637 | Clayton Wheeler | 18 August 2012, 00:57:20 UTC | Fix interval syntax handling: chr:start-end vs. chr:start:end. | 18 August 2012, 00:57:20 UTC |
| c09a17f | Clayton Wheeler | 18 August 2012, 00:56:29 UTC | Avoid tiling output that is completely non-matching. | 18 August 2012, 00:56:29 UTC |
| 8a4057b | Clayton Wheeler | 15 August 2012, 19:37:06 UTC | Only case-fold sequence data with --upcase. | 15 August 2012, 19:37:06 UTC |
| 8c1deca | Clayton Wheeler | 15 August 2012, 02:01:00 UTC | Added support for a comma-separated list with --species. For Galaxy support. | 15 August 2012, 04:34:42 UTC |
| 5529273 | Clayton Wheeler | 13 August 2012, 20:03:52 UTC | Added --fill-char and --species-file. | 13 August 2012, 20:03:52 UTC |
| 796593a | Clayton Wheeler | 13 August 2012, 19:54:27 UTC | Refactored maf_tile to add exon concatenation feature. | 13 August 2012, 19:54:27 UTC |
| f488a4d | Clayton Wheeler | 09 August 2012, 21:12:55 UTC | Added :upcase parser option. | 09 August 2012, 21:12:55 UTC |
| 56774ed | Clayton Wheeler | 09 August 2012, 19:21:08 UTC | Correctly indicate default log destination as stderr. Was stdout. | 09 August 2012, 19:21:08 UTC |
| 6fd31ba | Clayton Wheeler | 09 August 2012, 02:04:46 UTC | Open BGZF files in binary mode. Works around a possible bug in JRuby 1.7.0.preview2, and seems to improve performance a bit anyway. | 09 August 2012, 19:18:25 UTC |
| fe52753 | Clayton Wheeler | 08 August 2012, 22:08:28 UTC | Updated build date. | 08 August 2012, 22:08:28 UTC |
| ccec33a | Clayton Wheeler | 08 August 2012, 21:01:49 UTC | Documented new options. | 08 August 2012, 21:01:49 UTC |
| c967186 | Clayton Wheeler | 08 August 2012, 20:51:10 UTC | Allow setting arbitrary parser options. | 08 August 2012, 20:51:10 UTC |
| dca38d5 | Clayton Wheeler | 08 August 2012, 05:16:19 UTC | Handle MAF files with no alignment blocks. Closes #112. | 08 August 2012, 05:16:19 UTC |
| 0555e55 | Clayton Wheeler | 08 August 2012, 04:44:12 UTC | Improved informational logging. | 08 August 2012, 04:44:12 UTC |
| d940f5d | Clayton Wheeler | 08 August 2012, 04:42:29 UTC | Allow setting compression level. | 08 August 2012, 04:42:29 UTC |
| 17d1fa8 | Clayton Wheeler | 08 August 2012, 04:40:57 UTC | Shut down execution on error. | 08 August 2012, 04:40:57 UTC |
| 8b006ff | Clayton Wheeler | 08 August 2012, 03:18:40 UTC | Added Executor for parallel tasks in maf_bgzip. Specifically, this lets a separate thread handle indexing under JRuby. | 08 August 2012, 03:18:40 UTC |
| b13c9ce | Clayton Wheeler | 08 August 2012, 03:16:48 UTC | Log more verbosely on job completion. | 08 August 2012, 03:16:48 UTC |
| b5e877d | Clayton Wheeler | 08 August 2012, 01:28:23 UTC | Run tasks in parallel. Error if output files exist w/o --force. Closes #111. | 08 August 2012, 01:28:23 UTC |
| 4344b9e | Clayton Wheeler | 08 August 2012, 01:27:15 UTC | Added JobRunner tool for running parallel tasks. Uses threads on JRuby and fork() on MRI. | 08 August 2012, 01:27:15 UTC |
| 45a86da | Clayton Wheeler | 08 August 2012, 00:26:28 UTC | Only open indexes as needed in Access. Closes #109. Previously Access would hold all the KyotoIndex objects (and corresponding Kyoto Cabinet DB instances) open. This could lead to problematic memory consumption with a large set of indexes. | 08 August 2012, 00:26:28 UTC |
| 917cf83 | Clayton Wheeler | 08 August 2012, 00:18:33 UTC | Refactored Access to use #with_index. This is preparatory for not holding all indexes open. It required returning Arrays instead of Enumerables when no block is given. | 08 August 2012, 00:18:33 UTC |
| cccb0e0 | Clayton Wheeler | 07 August 2012, 23:08:57 UTC | Track total struct size. | 07 August 2012, 23:08:57 UTC |
| 6c37736 | Clayton Wheeler | 07 August 2012, 23:06:53 UTC | Set Kyoto Cabinet options on index file. Enable linear mode, small mode, and periodic defragmentation. | 07 August 2012, 23:08:08 UTC |
| 3b07347 | Clayton Wheeler | 07 August 2012, 23:02:46 UTC | Initialize KyotoIndex properly in tests. | 07 August 2012, 23:02:46 UTC |
| 97a6337 | Clayton Wheeler | 07 August 2012, 22:59:35 UTC | Validate index version. Closes #105. | 07 August 2012, 22:59:35 UTC |
| ddfa42c | Clayton Wheeler | 07 August 2012, 22:58:39 UTC | Write KC changes after 1000 blocks or 50 MB. | 07 August 2012, 22:58:39 UTC |
| d38ee29 | Clayton Wheeler | 07 August 2012, 02:06:55 UTC | Improved logging for maf_bgzip. | 07 August 2012, 02:06:55 UTC |
| acd405f | Clayton Wheeler | 06 August 2012, 21:31:35 UTC | Added --one-based option. Treats all intervals as 1-based. Needed because some tools like Ensembl output BED files using 1-based intervals, even though this is against the standard. Closes #107. | 06 August 2012, 21:31:35 UTC |
| 4400ad0 | Clayton Wheeler | 06 August 2012, 20:27:26 UTC | Added UCSC extended bin support. Closes #106. | 06 August 2012, 20:27:26 UTC |
| 56c4dd1 | Clayton Wheeler | 06 August 2012, 19:08:00 UTC | Use bio-bgzf 0.2.1. This is the released version allowing setting compression level and reporting write positions. | 06 August 2012, 19:08:00 UTC |
| 28a55a5 | Clayton Wheeler | 05 August 2012, 01:41:07 UTC | Added :retain_text option for fast rewriting of MAF files. For now, only used for maf_bgzip. | 05 August 2012, 01:41:07 UTC |
| 011415b | Clayton Wheeler | 05 August 2012, 01:30:04 UTC | Reworked parser options, defaults, and platform detection. | 05 August 2012, 01:30:04 UTC |
| d962884 | Clayton Wheeler | 05 August 2012, 01:27:26 UTC | Build the new index during the same parser run as BGZF writing. | 05 August 2012, 01:28:27 UTC |
| 3f2ed62 | Clayton Wheeler | 05 August 2012, 00:30:45 UTC | Set the reference sequence from within #index_blocks. | 05 August 2012, 00:30:45 UTC |
| 6542333 | Clayton Wheeler | 05 August 2012, 00:24:10 UTC | Started refactoring index creation. | 05 August 2012, 00:24:10 UTC |
| 891dbfa | Clayton Wheeler | 04 August 2012, 23:07:59 UTC | Avoid memory leak in JRuby. JRuby shares backing store very aggressively for Strings, which is great. Except when you are trying to put Strings in a Hash while parsing them from a multi-GB file. Then it is not great. | 04 August 2012, 23:07:59 UTC |
| 7d5e583 | Clayton Wheeler | 04 August 2012, 22:34:48 UTC | Log thread shenanigans a little better. | 04 August 2012, 22:34:48 UTC |
| f443fdc | Clayton Wheeler | 04 August 2012, 22:34:14 UTC | Use GZipReader instead of a gzip pipe. Performs better. See #104. | 04 August 2012, 22:34:14 UTC |
| 4fc31e2 | Clayton Wheeler | 04 August 2012, 18:50:04 UTC | Index sequence IDs not in species.chrN format as species IDs. | 04 August 2012, 18:50:04 UTC |
| 29aff2c | Clayton Wheeler | 04 August 2012, 18:48:43 UTC | Added standard logging options to maf_bgzip. | 04 August 2012, 18:48:43 UTC |
| aeb30be | Clayton Wheeler | 04 August 2012, 18:47:10 UTC | Print block and offset with indexing errors. Skip 0-length sequences. | 04 August 2012, 18:47:10 UTC |
| d8823c8 | Clayton Wheeler | 04 August 2012, 18:45:21 UTC | Fixed up worker thread exception handling. See #101. (It actually catches exceptions now...) | 04 August 2012, 18:45:21 UTC |
| 20b1461 | Clayton Wheeler | 04 August 2012, 18:43:34 UTC | Added :strict parser option. Default to non-strict. Warn on survivable parse errors (like 'r' lines in UCSC MAF files...), for #47. | 04 August 2012, 18:43:34 UTC |
| 32014e6 | Clayton Wheeler | 04 August 2012, 18:41:41 UTC | Added Block#to_s for debugging. | 04 August 2012, 18:41:41 UTC |
| 3201d60 | Clayton Wheeler | 04 August 2012, 18:40:45 UTC | Be more conservative with memory, for #103. | 04 August 2012, 18:40:45 UTC |
| 5aa41da | Clayton Wheeler | 03 August 2012, 20:28:21 UTC | Version 1.0.1. | 03 August 2012, 20:28:21 UTC |
| 9df02fb | Clayton Wheeler | 03 August 2012, 20:28:14 UTC | Added missing "require 'optparse'". | 03 August 2012, 20:28:14 UTC |
| bd2abbe | Clayton Wheeler | 03 August 2012, 01:02:57 UTC | Version 1.0.0. [ci skip] | 03 August 2012, 01:03:20 UTC |
| c8c4291 | Clayton Wheeler | 03 August 2012, 00:43:16 UTC | Added maf_bgzip(1) to README. | 03 August 2012, 00:43:16 UTC |
| 0749a7f | Clayton Wheeler | 03 August 2012, 00:30:06 UTC | Regenerated man pages. | 03 August 2012, 00:30:06 UTC |
| 99aecdf | Clayton Wheeler | 03 August 2012, 00:29:30 UTC | Added maf_bgzip(1). | 03 August 2012, 00:29:30 UTC |
| 68ba547 | Clayton Wheeler | 02 August 2012, 22:47:13 UTC | Let gzip(1) do the work on gzipped files. | 02 August 2012, 22:47:13 UTC |
| 2c011bd | Clayton Wheeler | 02 August 2012, 22:43:53 UTC | Add an --all option as in maf_index(1). | 02 August 2012, 22:43:53 UTC |
| f5dc2f9 | Clayton Wheeler | 02 August 2012, 21:24:59 UTC | Bumped version to 0.4.0. [ci skip] | 02 August 2012, 21:26:07 UTC |
| 9c8cf30 | Clayton Wheeler | 02 August 2012, 20:29:34 UTC | Don't run maf_bgzip tests on JRuby. | 02 August 2012, 20:29:34 UTC |
| 298fcb5 | Clayton Wheeler | 02 August 2012, 20:26:10 UTC | Integrated .maf.gz handling, added Cucumber feature. | 02 August 2012, 20:26:10 UTC |
| 6834d67 | Clayton Wheeler | 02 August 2012, 20:25:04 UTC | Require zlib for handling regular gzipped files. | 02 August 2012, 20:25:04 UTC |
| cebd770 | Clayton Wheeler | 02 August 2012, 20:10:43 UTC | Require bio-bgzf 0.2.0. | 02 August 2012, 20:10:43 UTC |
| 3016500 | Clayton Wheeler | 02 August 2012, 20:10:31 UTC | Minor documentation improvements. | 02 August 2012, 20:10:31 UTC |
| 5ac2503 | Clayton Wheeler | 02 August 2012, 20:09:52 UTC | Enable opening a parser with an open IO stream. | 02 August 2012, 20:09:52 UTC |
| 68cc61e | Clayton Wheeler | 02 August 2012, 20:08:07 UTC | Standardize on .maf.bgz. | 02 August 2012, 20:08:07 UTC |
| 3605ab3 | Clayton Wheeler | 02 August 2012, 20:07:03 UTC | Commented out local bio-bgzf entry. | 02 August 2012, 20:07:03 UTC |
| a35bbc5 | Clayton Wheeler | 01 August 2012, 08:13:52 UTC | Added maf_bgzip. | 01 August 2012, 08:13:52 UTC |
| cc5b408 | Clayton Wheeler | 01 August 2012, 08:13:38 UTC | Use IO#write instead of IO#puts. | 01 August 2012, 08:13:38 UTC |
| a5f2371 | Clayton Wheeler | 01 August 2012, 08:13:14 UTC | Skip unpacking an array. | 01 August 2012, 08:13:14 UTC |
| 638f4b2 | Clayton Wheeler | 01 August 2012, 08:12:25 UTC | Added comments. | 01 August 2012, 08:12:25 UTC |
| 8438418 | Clayton Wheeler | 01 August 2012, 05:31:51 UTC | Fixed _merge_bgzf_fetch_list on JRuby. | 01 August 2012, 05:31:51 UTC |
| 1016376 | Clayton Wheeler | 01 August 2012, 05:31:27 UTC | Improved comments. | 01 August 2012, 05:31:27 UTC |
| 6916ef8 | Clayton Wheeler | 01 August 2012, 04:53:17 UTC | BGZF-aware fetch list merging. Handle sparse fetch lists. | 01 August 2012, 04:53:40 UTC |
| 7f37e50 | Clayton Wheeler | 01 August 2012, 04:52:02 UTC | Removed ThreadedChunkReader stuff. | 01 August 2012, 04:52:02 UTC |
| 8daa2da | Clayton Wheeler | 01 August 2012, 04:51:43 UTC | Dump indexes using repackaged Bio::BGZF::vo_* functions. | 01 August 2012, 04:51:43 UTC |
| d9f5cc1 | Clayton Wheeler | 31 July 2012, 19:31:38 UTC | Use #write instead of #puts to write block. | 31 July 2012, 19:31:38 UTC |
| 5aed65c | Clayton Wheeler | 29 July 2012, 21:13:02 UTC | Documented BGZF support. [ci skip] | 29 July 2012, 21:13:27 UTC |
| e000dd7 | Clayton Wheeler | 29 July 2012, 18:59:01 UTC | Use bio-bgzf 0.1.1 for CRC fix. | 29 July 2012, 18:59:01 UTC |
| 73e0218 | Clayton Wheeler | 29 July 2012, 18:57:46 UTC | Use repackaged name of Bio::BGZF::Reader. | 29 July 2012, 18:57:46 UTC |
| e93b77b | Clayton Wheeler | 29 July 2012, 18:40:24 UTC | Use published bio-bgzf gem, version 0.1.0. | 29 July 2012, 18:40:24 UTC |
| d7da4f0 | Clayton Wheeler | 29 July 2012, 06:54:23 UTC | Removed :chunk_reader from docs. | 29 July 2012, 06:54:23 UTC |
| edf8385 | Clayton Wheeler | 28 July 2012, 21:31:07 UTC | Rewrote all the ThreadedChunkReader stuff. It is used automatically on JRuby now, and it doesn't start the read-ahead until the second #read_chunk call. | 28 July 2012, 21:31:07 UTC |
| 9bc9b84 | Clayton Wheeler | 28 July 2012, 16:50:04 UTC | Rewrote index discovery. Now copes with BGZF files. Also, scans directories for indexes, then locates their corresponding MAF files. | 28 July 2012, 16:50:04 UTC |
| 01841db | Clayton Wheeler | 28 July 2012, 16:48:45 UTC | Store MAF filename in index. | 28 July 2012, 16:48:45 UTC |
| fe46a18 | Clayton Wheeler | 28 July 2012, 16:19:30 UTC | Added tests for BGZF support. | 28 July 2012, 16:19:30 UTC |
| bb2e922 | Clayton Wheeler | 28 July 2012, 16:19:11 UTC | Set up ChunkReader in a smarter way. | 28 July 2012, 16:19:11 UTC |
| d3eeaae | Clayton Wheeler | 28 July 2012, 16:12:27 UTC | Require bundler/setup to pull in bio-bgzf. | 28 July 2012, 16:12:27 UTC |
| 33c7ce7 | Clayton Wheeler | 28 July 2012, 15:08:37 UTC | Track compression format, dump BGZF virtual offsets. | 28 July 2012, 15:08:37 UTC |
| 6e323ed | Clayton Wheeler | 28 July 2012, 14:51:40 UTC | Added BGZFChunkReader. | 28 July 2012, 14:51:40 UTC |
| d3225e6 | Clayton Wheeler | 28 July 2012, 14:51:20 UTC | Added local bio-bgzf gem. | 28 July 2012, 14:51:20 UTC |
| ccd7d13 | Clayton Wheeler | 27 July 2012, 01:20:18 UTC | Bumped version to 0.3.2. Fixes maf_extract --interval arg syntax problem. | 27 July 2012, 01:20:18 UTC |
| ec541e0 | Clayton Wheeler | 27 July 2012, 01:18:31 UTC | Fixed link notation. Hopefully. Wish I had a better Markdown preview facility... | 27 July 2012, 01:18:31 UTC |
| 690c3b6 | Clayton Wheeler | 27 July 2012, 01:15:06 UTC | Added maf_extract examples to docs. | 27 July 2012, 01:15:06 UTC |
| 748fa4e | Clayton Wheeler | 27 July 2012, 01:11:43 UTC | Fixed --interval arg syntax to agree with UCSC. | 27 July 2012, 01:11:43 UTC |
| 60407f9 | Clayton Wheeler | 27 July 2012, 01:10:29 UTC | Added note about the master branch. | 27 July 2012, 01:10:29 UTC |
| 81fc7c5 | Clayton Wheeler | 26 July 2012, 23:54:51 UTC | Added note about Bio::MAF::Access and maf_tile(1). | 26 July 2012, 23:54:51 UTC |
| 7bcede3 | Clayton Wheeler | 26 July 2012, 23:47:56 UTC | Removed explicit setting of executables. | 26 July 2012, 23:48:47 UTC |
