| 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 |
| bcb342e | Clayton Wheeler | 26 July 2012, 23:47:21 UTC | Updated gemspec for 0.3.1 release. | 26 July 2012, 23:47:21 UTC |
| 67a5514 | Clayton Wheeler | 26 July 2012, 23:46:33 UTC | Synopsis formatting tweak. | 26 July 2012, 23:46:33 UTC |
| 15c6c76 | Clayton Wheeler | 26 July 2012, 22:27:37 UTC | Started on maf_extract(1). | 26 July 2012, 22:27:37 UTC |
| 076e8ec | Clayton Wheeler | 26 July 2012, 22:27:27 UTC | Don't write empty sequences as FASTA. | 26 July 2012, 22:27:27 UTC |
| 4b32214 | Clayton Wheeler | 26 July 2012, 22:27:14 UTC | Standardized naming for --min-sequences. | 26 July 2012, 22:27:14 UTC |
| 4aa5574 | Clayton Wheeler | 26 July 2012, 22:27:02 UTC | Use --parse-extended and --parse-empty instead of --parse-option. | 26 July 2012, 22:27:02 UTC |
| 4fc83ca | Clayton Wheeler | 26 July 2012, 17:42:19 UTC | Wrap command-line options appropriately. | 26 July 2012, 17:42:19 UTC |
| d47ac9e | Clayton Wheeler | 26 July 2012, 16:02:12 UTC | Regenerated man page. | 26 July 2012, 16:02:12 UTC |
| b3d2b35 | Clayton Wheeler | 26 July 2012, 16:02:04 UTC | Added logging options. | 26 July 2012, 16:02:04 UTC |
| 315e7c1 | Clayton Wheeler | 26 July 2012, 16:00:02 UTC | Use own FASTA output code instead of bigbio. | 26 July 2012, 16:00:02 UTC |
| b1255d7 | Clayton Wheeler | 26 July 2012, 04:15:49 UTC | Write a basic MAF header. | 26 July 2012, 04:15:49 UTC |
| 9b6915b | Clayton Wheeler | 25 July 2012, 23:41:29 UTC | Started writing maf_extract. | 25 July 2012, 23:41:29 UTC |
| 76dd9b9 | Clayton Wheeler | 25 July 2012, 19:33:39 UTC | Made more arg lists explicit. Closes #46. | 25 July 2012, 19:35:50 UTC |
| cdfbcb1 | Clayton Wheeler | 25 July 2012, 19:09:10 UTC | Added standard logging CLI options. | 25 July 2012, 19:09:10 UTC |
| 16ef81e | Clayton Wheeler | 25 July 2012, 19:08:34 UTC | Added debug logging for index creation. | 25 July 2012, 19:08:34 UTC |
| dc8e95d | Clayton Wheeler | 25 July 2012, 19:07:58 UTC | Calculate start time for logging. | 25 July 2012, 19:07:58 UTC |
| 196fa8a | Clayton Wheeler | 25 July 2012, 19:06:58 UTC | Added missing option descriptions. | 25 July 2012, 19:06:58 UTC |
| 4ecd4f0 | Clayton Wheeler | 25 July 2012, 19:05:55 UTC | Remove --threaded option, and just use it by default on JRuby. | 25 July 2012, 19:05:55 UTC |
| de69b7e | Clayton Wheeler | 25 July 2012, 18:26:08 UTC | Converted logging code to bio-logger. | 25 July 2012, 18:26:08 UTC |
| 0067ffd | Clayton Wheeler | 05 July 2012, 14:22:18 UTC | Started switching over to bio-logger for logging. | 25 July 2012, 17:44:32 UTC |
| 759126a | Clayton Wheeler | 24 July 2012, 23:22:44 UTC | Added CLI support and docs for indexing all sequences. Closes #97. | 24 July 2012, 23:22:44 UTC |
| 6952abd | Clayton Wheeler | 24 July 2012, 22:57:15 UTC | Enable indexing all sequences for #97. | 24 July 2012, 22:57:15 UTC |
| 49555e3 | Clayton Wheeler | 24 July 2012, 22:51:36 UTC | Refactored sequence ID assignment. | 24 July 2012, 22:51:36 UTC |
| 5f58d57 | Clayton Wheeler | 24 July 2012, 19:20:47 UTC | Added docs to Tiler. | 24 July 2012, 19:20:47 UTC |
| 6f5499a | Clayton Wheeler | 24 July 2012, 17:11:12 UTC | Allow specifying tiling fill char. Closes #96. | 24 July 2012, 17:11:12 UTC |
| e4ac9bd | Clayton Wheeler | 24 July 2012, 17:03:10 UTC | Added Tiler#build_bio_alignment for #94. | 24 July 2012, 17:03:10 UTC |
| 50583e3 | Clayton Wheeler | 18 July 2012, 20:12:54 UTC | Reformatted code blocks for syntax highlighting. | 18 July 2012, 20:12:54 UTC |
| d2dc70b | Clayton Wheeler | 18 July 2012, 19:57:24 UTC | GFM with fixed indentation. [ci skip] | 18 July 2012, 19:57:24 UTC |
| e589182 | Clayton Wheeler | 18 July 2012, 19:53:13 UTC | Github-flavored Markdown test. [ci skip] | 18 July 2012, 19:53:13 UTC |
| dd14751 | Clayton Wheeler | 18 July 2012, 19:38:32 UTC | Attempt to fix release issue with jruby-openssl on JRuby. | 18 July 2012, 19:38:32 UTC |
| 2908764 | Clayton Wheeler | 18 July 2012, 19:23:01 UTC | Regenerated man pages. | 18 July 2012, 19:23:01 UTC |
| 904d07a | Clayton Wheeler | 18 July 2012, 19:22:53 UTC | Rephrased discussion of MAF files vs. directories. | 18 July 2012, 19:22:53 UTC |
| ed7f49e | Clayton Wheeler | 18 July 2012, 19:18:50 UTC | s/gap-filling/tiling/g | 18 July 2012, 19:18:50 UTC |
| d3bd13e | Clayton Wheeler | 18 July 2012, 19:02:20 UTC | Minor doc fixes for Access. [ci skip] | 18 July 2012, 19:02:31 UTC |
| 53e23f4 | Clayton Wheeler | 18 July 2012, 18:18:02 UTC | Added API docs for Access. | 18 July 2012, 18:18:02 UTC |
| cead995 | Clayton Wheeler | 18 July 2012, 17:58:32 UTC | Documented #slice and :as_bio_alignment. | 18 July 2012, 17:58:32 UTC |
| 22cde08 | Clayton Wheeler | 18 July 2012, 17:58:03 UTC | Removed stray commented code. | 18 July 2012, 17:58:03 UTC |
| 337ea0c | Clayton Wheeler | 18 July 2012, 17:51:07 UTC | Fixed #slice output. Closes #91. | 18 July 2012, 17:51:07 UTC |
| 4cbcccf | Clayton Wheeler | 18 July 2012, 15:36:05 UTC | Updated gemspec for 0.3.0. | 18 July 2012, 15:36:05 UTC |
| 273a87b | Clayton Wheeler | 18 July 2012, 15:26:37 UTC | Added CLI specs. Closes #81. | 18 July 2012, 15:33:09 UTC |
| 7b89b52 | Clayton Wheeler | 18 July 2012, 04:05:02 UTC | Added a @no_jruby tag. | 18 July 2012, 04:05:02 UTC |
| d593aa5 | Clayton Wheeler | 18 July 2012, 03:56:24 UTC | Updated maf_tile(1). | 18 July 2012, 03:56:24 UTC |
| e6e71a2 | Clayton Wheeler | 18 July 2012, 03:55:57 UTC | Temporarily fix man page generation. | 18 July 2012, 03:55:57 UTC |
| 7844a15 | Clayton Wheeler | 17 July 2012, 18:30:28 UTC | Updated maf_tile(1) for directory handling, implicit indexing. | 17 July 2012, 18:30:28 UTC |
| 4450914 | Clayton Wheeler | 17 July 2012, 17:28:59 UTC | Operate on a directory, given an explicit sequence in --interval. Closes #89. For #82. | 17 July 2012, 17:28:59 UTC |
| 2cefbe9 | Clayton Wheeler | 17 July 2012, 17:27:50 UTC | Return [], not nil, from KyotoIndex#find with no results. | 17 July 2012, 17:27:50 UTC |
| 5b7667f | Clayton Wheeler | 17 July 2012, 16:48:15 UTC | Don't run Aruba features under JRuby. (Not JRuby's fault... see cucumber/aruba#117.) | 17 July 2012, 16:48:15 UTC |
| 51ff92d | Clayton Wheeler | 17 July 2012, 16:30:26 UTC | rename: gap-filling -> tiling. | 17 July 2012, 16:30:26 UTC |
| 96794ef | Clayton Wheeler | 17 July 2012, 16:23:59 UTC | Documented Block#slice. | 17 July 2012, 16:23:59 UTC |
| 6f07eb2 | Clayton Wheeler | 17 July 2012, 15:53:43 UTC | Removed obsolete comments. | 17 July 2012, 15:54:42 UTC |
| 8e91e0b | Clayton Wheeler | 17 July 2012, 15:44:01 UTC | Specified maf_tile script behavior further. | 17 July 2012, 15:44:01 UTC |
| fe1074e | Clayton Wheeler | 17 July 2012, 15:43:44 UTC | Removed some debug output. | 17 July 2012, 15:43:44 UTC |
| ce4c577 | Clayton Wheeler | 17 July 2012, 15:43:29 UTC | Don't set a nil reference. | 17 July 2012, 15:43:29 UTC |
| fc2d78d | Clayton Wheeler | 17 July 2012, 04:09:51 UTC | Refactored option application. Also skip setting up FASTARangeReader explicitly. | 17 July 2012, 04:09:51 UTC |
| 14f7c3c | Clayton Wheeler | 17 July 2012, 04:05:40 UTC | Removed unnecessary Tiler initialization. | 17 July 2012, 04:05:40 UTC |
| 2b1ffdb | Clayton Wheeler | 17 July 2012, 04:03:38 UTC | Rewrite maf_tile to use Access API for #82. | 17 July 2012, 04:03:38 UTC |
| fcd32b0 | Clayton Wheeler | 17 July 2012, 04:03:03 UTC | Added test case for #88. | 17 July 2012, 04:03:03 UTC |
| 3ee6988 | Clayton Wheeler | 17 July 2012, 04:02:21 UTC | Overhaul of block filtering and #parse_block. For #86, #87. | 17 July 2012, 04:02:21 UTC |
| d1328ab | Clayton Wheeler | 16 July 2012, 23:38:22 UTC | Added Access.file(maf, index=nil). Allows access to a single MAF file through a uniform API, for #82. Also creates transient indexes for the single-file case, if needed, for #85. | 16 July 2012, 23:38:22 UTC |
| 95e7d54 | Clayton Wheeler | 16 July 2012, 23:36:44 UTC | Option-setting tricks to accommodate dup'ing option hashes. | 16 July 2012, 23:36:44 UTC |
| 00a6be4 | Clayton Wheeler | 16 July 2012, 22:18:39 UTC | Nomenclature fix, s/stitch/join/g, for #83. | 16 July 2012, 22:18:39 UTC |
| c9a2fae | Clayton Wheeler | 16 July 2012, 20:26:20 UTC | Added Aruba Cucumber specs for maf_tile. | 16 July 2012, 20:26:40 UTC |
| fd46ba0 | Clayton Wheeler | 16 July 2012, 15:28:47 UTC | Added convenience methods for synteny data from 'i' lines. For #68. | 16 July 2012, 15:29:05 UTC |
| 7c20449 | Clayton Wheeler | 13 July 2012, 17:32:45 UTC | Reimplemented block stream wrapping, :as_bio_alignment. For #70. | 13 July 2012, 17:32:45 UTC |
| c5578e7 | Clayton Wheeler | 13 July 2012, 17:12:08 UTC | Experimenting with block stream wrapping. | 13 July 2012, 17:12:08 UTC |
| 8b95518 | Clayton Wheeler | 12 July 2012, 23:47:41 UTC | Added basic conversion to bio-alignment, for #70. | 12 July 2012, 23:47:41 UTC |
| 511f3bd | Clayton Wheeler | 12 July 2012, 23:17:43 UTC | Use kyotocabinet-java 0.3.0. | 12 July 2012, 23:17:43 UTC |
