| c52bc65 | Clayton Wheeler | 05 July 2012, 22:44:01 UTC | Enable declarative gap removal with parser option. | 05 July 2012, 22:44:01 UTC |
| abe5bb7 | Clayton Wheeler | 05 July 2012, 22:43:06 UTC | Allow setting options after creating the Parser. | 05 July 2012, 22:43:06 UTC |
| e7951ca | Clayton Wheeler | 05 July 2012, 22:25:49 UTC | Moved Header, Block, Sequence, EmptySequence into maf.rb. | 05 July 2012, 22:25:49 UTC |
| 5ffea76 | Clayton Wheeler | 01 July 2012, 19:29:48 UTC | Added Cucumber feature for gap removal. | 01 July 2012, 19:29:48 UTC |
| 3eff1f6 | Clayton Wheeler | 29 June 2012, 19:00:59 UTC | Added code to find and remove gaps. | 29 June 2012, 19:00:59 UTC |
| 8e9d226 | Clayton Wheeler | 29 June 2012, 17:29:50 UTC | Mark filtered blocks. | 29 June 2012, 17:29:50 UTC |
| eda7485 | Clayton Wheeler | 29 June 2012, 05:48:26 UTC | Add link to published gem. | 29 June 2012, 05:48:26 UTC |
| 718c414 | Clayton Wheeler | 29 June 2012, 05:26:03 UTC | Ditched jeweler, set up (hopefully) proper gemspec. | 29 June 2012, 05:26:58 UTC |
| c55d3d8 | Clayton Wheeler | 29 June 2012, 04:13:58 UTC | Version bump to 0.1.0 | 29 June 2012, 04:13:58 UTC |
| 23338d7 | Clayton Wheeler | 29 June 2012, 04:03:22 UTC | Specify TimeUnit::SECONDS properly. | 29 June 2012, 04:03:22 UTC |
| 6667b38 | Clayton Wheeler | 29 June 2012, 03:57:55 UTC | Wait for worker threads properly. | 29 June 2012, 03:57:55 UTC |
| 3b78293 | Clayton Wheeler | 29 June 2012, 03:55:19 UTC | Argh. exit 0 | 29 June 2012, 03:55:19 UTC |
| f991aee | Clayton Wheeler | 29 June 2012, 03:44:53 UTC | Try to log JVM crashes a bit better... | 29 June 2012, 03:44:53 UTC |
| 1970976 | Clayton Wheeler | 29 June 2012, 03:13:14 UTC | Try to avoid race condition with worker thread completion. | 29 June 2012, 03:13:14 UTC |
| 6b1658f | Clayton Wheeler | 29 June 2012, 03:12:55 UTC | Skip ronn under JRuby. | 29 June 2012, 03:12:55 UTC |
| 79499fd | Clayton Wheeler | 29 June 2012, 02:16:03 UTC | Lots of documentation work. | 29 June 2012, 02:16:03 UTC |
| ad77879 | Clayton Wheeler | 29 June 2012, 02:15:09 UTC | Use redcarpet with YARD for Github-flavored Markdown. | 29 June 2012, 02:15:09 UTC |
| b6d9180 | Clayton Wheeler | 28 June 2012, 17:40:39 UTC | Use 4 threads for index scans by default, unless running profiler. | 28 June 2012, 17:40:39 UTC |
| b544bba | Clayton Wheeler | 28 June 2012, 17:40:21 UTC | Skip irrelevant intervals. Use Ranges instead of GenomicIntervals. | 28 June 2012, 17:40:21 UTC |
| 8ec106e | Clayton Wheeler | 28 June 2012, 16:23:11 UTC | Worker threads and profiling for index scans. | 28 June 2012, 16:23:11 UTC |
| 09fb758 | Clayton Wheeler | 28 June 2012, 16:16:29 UTC | Improve error reporting. Was reporting current number of jobs in queue, not total number. | 28 June 2012, 16:16:29 UTC |
| a760140 | Clayton Wheeler | 28 June 2012, 16:15:59 UTC | Added convenience methods for parser options. | 28 June 2012, 16:15:59 UTC |
| 844984b | Clayton Wheeler | 28 June 2012, 16:15:33 UTC | Use #take_while to avoid unnecessary matching. | 28 June 2012, 16:15:33 UTC |
| 246cf2f | Clayton Wheeler | 28 June 2012, 06:15:56 UTC | Added YARD docs. | 28 June 2012, 06:15:56 UTC |
| 018cfa8 | Clayton Wheeler | 28 June 2012, 06:15:40 UTC | Added YARD options for documentation generation. | 28 June 2012, 06:15:40 UTC |
| 7a17ef5 | Clayton Wheeler | 28 June 2012, 05:55:36 UTC | Removed unused filters argument. | 28 June 2012, 05:55:36 UTC |
| 2725007 | Clayton Wheeler | 28 June 2012, 05:53:19 UTC | Eliminate Parser#read_chunk. | 28 June 2012, 05:53:19 UTC |
| 76e9c80 | Clayton Wheeler | 28 June 2012, 05:48:57 UTC | Comment out chunk_shift logic for now. | 28 June 2012, 05:48:57 UTC |
| d7e3dda | Clayton Wheeler | 28 June 2012, 02:37:33 UTC | Deal with sorting and spanning ranges a bit better. Thanks Artem! | 28 June 2012, 02:37:33 UTC |
| 774ab2f | Clayton Wheeler | 28 June 2012, 02:36:49 UTC | Added a couple of microbenchmarks. | 28 June 2012, 02:36:49 UTC |
| 7173b33 | Clayton Wheeler | 28 June 2012, 02:06:44 UTC | Linked maf_to_fasta man page. | 28 June 2012, 02:06:44 UTC |
| ebff3f0 | Clayton Wheeler | 28 June 2012, 02:06:33 UTC | Fixed man:publish target. | 28 June 2012, 02:06:33 UTC |
| cd386a2 | Clayton Wheeler | 28 June 2012, 01:48:52 UTC | Fixed formatting in synopsis. | 28 June 2012, 01:48:52 UTC |
| 655c547 | Clayton Wheeler | 28 June 2012, 01:48:29 UTC | Added development notes. | 28 June 2012, 01:48:29 UTC |
| 2070bcc | Clayton Wheeler | 27 June 2012, 23:50:54 UTC | Made number of passes configurable. | 27 June 2012, 23:50:54 UTC |
| baa63e3 | Clayton Wheeler | 27 June 2012, 23:50:35 UTC | Overhauled man page generation. | 27 June 2012, 23:50:35 UTC |
| 254d160 | Clayton Wheeler | 27 June 2012, 23:50:23 UTC | Updated header/footer data. | 27 June 2012, 23:50:23 UTC |
| 5545bad | Clayton Wheeler | 27 June 2012, 23:49:45 UTC | Ignore generated HTML. | 27 June 2012, 23:49:45 UTC |
| 4c9c1cf | Clayton Wheeler | 27 June 2012, 23:49:33 UTC | Added maf_to_fasta man page. | 27 June 2012, 23:49:33 UTC |
| cb47e67 | Clayton Wheeler | 27 June 2012, 20:34:37 UTC | Commit maf_index.1 for the benefit of gem-man. | 27 June 2012, 20:34:37 UTC |
| 39ce766 | Clayton Wheeler | 27 June 2012, 20:28:40 UTC | Try another tack with Markdown rendering. [ci skip] | 27 June 2012, 20:28:40 UTC |
| 4d49539 | Clayton Wheeler | 27 June 2012, 20:22:10 UTC | Added link to maf_index(1). [ci skip] | 27 June 2012, 20:22:10 UTC |
| 0d37150 | Clayton Wheeler | 27 June 2012, 20:18:30 UTC | Conditionalized ronn tasks. | 27 June 2012, 20:18:30 UTC |
| 62b9a98 | Clayton Wheeler | 27 June 2012, 20:14:17 UTC | Set up man page publishing. | 27 June 2012, 20:14:17 UTC |
| e726301 | Clayton Wheeler | 27 June 2012, 19:46:32 UTC | Test Github Markdown rendering. [ci skip] | 27 June 2012, 19:46:32 UTC |
| aeeb39c | Clayton Wheeler | 27 June 2012, 18:54:51 UTC | Man page improvements. | 27 June 2012, 18:54:51 UTC |
| dc0de0b | Clayton Wheeler | 27 June 2012, 18:54:38 UTC | Added ronn:server task. | 27 June 2012, 18:54:38 UTC |
| 4031538 | Clayton Wheeler | 27 June 2012, 18:22:18 UTC | Generate man pages with ronn. | 27 June 2012, 18:22:18 UTC |
| 27aa1c5 | Clayton Wheeler | 27 June 2012, 15:37:40 UTC | Uncomment Travis CI build status image. | 27 June 2012, 15:37:40 UTC |
| ef81a7e | Clayton Wheeler | 26 June 2012, 22:12:45 UTC | Updated Kyoto Cabinet discussion in docs. | 26 June 2012, 22:12:45 UTC |
| c6d65b6 | Clayton Wheeler | 26 June 2012, 22:05:36 UTC | Merge remote-tracking branch 'pjotrp/master' | 26 June 2012, 22:05:36 UTC |
| c0e5d7e | Clayton Wheeler | 26 June 2012, 21:36:21 UTC | Try using OpenJDK 6 on Travis CI. | 26 June 2012, 21:36:21 UTC |
| b20880e | Clayton Wheeler | 26 June 2012, 21:11:03 UTC | Let the gem install KC Java support. | 26 June 2012, 21:11:03 UTC |
| 2d50d00 | Clayton Wheeler | 26 June 2012, 20:15:03 UTC | Use the published gem version instead of the Github version. | 26 June 2012, 20:15:03 UTC |
| e50ba52 | Clayton Wheeler | 26 June 2012, 20:06:50 UTC | Switch to kyotocabinet-java v0.2.0, allowing "require 'kyotocabinet'" | 26 June 2012, 20:06:50 UTC |
| 6c368d7 | Clayton Wheeler | 26 June 2012, 19:43:12 UTC | Switched to kyotocabinet-java gem. | 26 June 2012, 19:43:12 UTC |
| 4284bd7 | Pjotr Prins | 25 June 2012, 10:25:12 UTC | Added some instructions for building on Debian - lifted from the Debian package | 25 June 2012, 10:25:12 UTC |
| bde38f9 | Pjotr Prins | 25 June 2012, 09:47:13 UTC | Remove README.rdoc | 25 June 2012, 09:47:13 UTC |
| edbeb8e | Clayton Wheeler | 22 June 2012, 21:13:35 UTC | Parallelized sequential parsing with Enumerator. | 22 June 2012, 21:13:35 UTC |
| 5ec24a9 | Clayton Wheeler | 22 June 2012, 21:12:45 UTC | Write a block at a time. | 22 June 2012, 21:12:45 UTC |
| c8fd7a7 | Clayton Wheeler | 22 June 2012, 21:12:20 UTC | Added maf_write script. | 22 June 2012, 21:12:20 UTC |
| 05a952a | Clayton Wheeler | 22 June 2012, 21:11:00 UTC | Expose parser options slightly differently. | 22 June 2012, 21:11:00 UTC |
| aa77d6b | Clayton Wheeler | 22 June 2012, 19:52:25 UTC | Add blank line after alignment blocks. | 22 June 2012, 19:52:25 UTC |
| 8aae6b9 | Clayton Wheeler | 22 June 2012, 19:41:11 UTC | Added output and testing for i, e, q lines. | 22 June 2012, 19:41:11 UTC |
| 80a6dd0 | Clayton Wheeler | 22 June 2012, 18:59:06 UTC | Merge branch 'master' into extended2 | 22 June 2012, 18:59:06 UTC |
| 2cc583f | Clayton Wheeler | 22 June 2012, 18:48:38 UTC | Added basic MAF output. | 22 June 2012, 18:48:38 UTC |
| 011f832 | Clayton Wheeler | 14 June 2012, 05:26:40 UTC | Initial functional implementation of i, e, q line parsing. Conflicts: lib/bio/maf/parser.rb | 21 June 2012, 21:13:57 UTC |
| d9913c6 | Clayton Wheeler | 21 June 2012, 20:42:16 UTC | Fixed a strange JRuby bug with sequence filters. | 21 June 2012, 20:42:16 UTC |
| 48062c6 | Clayton Wheeler | 21 June 2012, 20:41:50 UTC | Removed more dead code. | 21 June 2012, 20:41:50 UTC |
| 47c3bf3 | Clayton Wheeler | 21 June 2012, 18:38:43 UTC | Removed extra parallel I/O implementations. | 21 June 2012, 18:38:43 UTC |
| 0b72107 | Clayton Wheeler | 21 June 2012, 18:28:22 UTC | Use LinkedBlockingQueue, improve output. | 21 June 2012, 18:28:22 UTC |
| 7f61aa8 | Clayton Wheeler | 21 June 2012, 18:26:04 UTC | Repeat to test HotSpot, JRuby JIT warmup. | 21 June 2012, 18:26:04 UTC |
| 7920493 | Clayton Wheeler | 21 June 2012, 18:25:14 UTC | Tweaking, refactoring control logic. | 21 June 2012, 18:25:14 UTC |
| 9d1ac1c | Clayton Wheeler | 20 June 2012, 21:23:13 UTC | Shut down worker threads properly. | 20 June 2012, 21:23:13 UTC |
| 5ef5b71 | Clayton Wheeler | 20 June 2012, 19:37:16 UTC | Fixed unintentional laziness causing single-threaded parsing. | 20 June 2012, 19:37:16 UTC |
| ffdcae2 | Clayton Wheeler | 19 June 2012, 21:25:36 UTC | Added third parallel I/O implementation, separate IO and parsing. | 19 June 2012, 21:25:36 UTC |
| 8328647 | Clayton Wheeler | 19 June 2012, 20:35:16 UTC | Further tweaks, still haven't got I/O vs. processing balanced right. | 19 June 2012, 20:35:16 UTC |
| c89f055 | Clayton Wheeler | 19 June 2012, 20:34:41 UTC | Added debugging output. | 19 June 2012, 20:34:41 UTC |
| 239b417 | Clayton Wheeler | 19 June 2012, 17:06:00 UTC | Refactored and improved a bit, still not working quite right. | 19 June 2012, 17:06:00 UTC |
| d7ad4d6 | Clayton Wheeler | 18 June 2012, 19:00:28 UTC | Added more robust parallel I/O code. (Not completely debugged.) | 18 June 2012, 19:00:28 UTC |
| 1f5b6b2 | Clayton Wheeler | 18 June 2012, 18:59:45 UTC | Added parallel index scans. (Not working so well, yet.) | 18 June 2012, 18:59:45 UTC |
| fe0aa52 | Clayton Wheeler | 16 June 2012, 19:01:33 UTC | Sorted out live thread tracking. | 16 June 2012, 19:01:33 UTC |
| 7cfae9b | Clayton Wheeler | 16 June 2012, 16:34:35 UTC | Refactored index access. | 16 June 2012, 16:34:35 UTC |
| 1f9d9d9 | Clayton Wheeler | 16 June 2012, 16:16:39 UTC | Initial implementation of multithreaded parsing, for #41. | 16 June 2012, 16:16:39 UTC |
| 4deee85 | Clayton Wheeler | 14 June 2012, 19:21:39 UTC | Optimize block overlap tests. Closes #37. | 14 June 2012, 19:21:39 UTC |
| 4ea7904 | Clayton Wheeler | 14 June 2012, 18:34:54 UTC | Refactored random access, added JRuby parallel mode. | 14 June 2012, 18:34:54 UTC |
| 671f674 | Clayton Wheeler | 14 June 2012, 17:25:51 UTC | Use #count for an Enumerator. | 14 June 2012, 17:25:51 UTC |
| 418c4a2 | Clayton Wheeler | 14 June 2012, 17:25:27 UTC | Improve error reporting. | 14 June 2012, 17:25:27 UTC |
| 271ddcf | Clayton Wheeler | 14 June 2012, 17:15:49 UTC | Initial refactoring of parser to extract ParseContext. | 14 June 2012, 17:15:49 UTC |
| b039e92 | Clayton Wheeler | 14 June 2012, 17:14:28 UTC | Added a benchmark for string splitting. | 14 June 2012, 17:14:28 UTC |
| e4fcd94 | Clayton Wheeler | 14 June 2012, 03:54:55 UTC | Allow parser selection. | 14 June 2012, 03:54:55 UTC |
| 588eda7 | Clayton Wheeler | 14 June 2012, 02:09:53 UTC | Added maf_dump_blocks script. | 14 June 2012, 02:09:53 UTC |
| 778d567 | Clayton Wheeler | 14 June 2012, 02:09:43 UTC | Added benchmark scripts. | 14 June 2012, 02:09:43 UTC |
| b519468 | Clayton Wheeler | 14 June 2012, 02:04:00 UTC | Removed stray print statement. | 14 June 2012, 02:04:00 UTC |
| 59b88a0 | Clayton Wheeler | 14 June 2012, 02:03:49 UTC | Suppress simplecov warnings on JRuby. | 14 June 2012, 02:03:49 UTC |
| 9da7ba2 | Clayton Wheeler | 14 June 2012, 01:59:14 UTC | Refactored parse_block to at least break it up a bit. | 14 June 2012, 01:59:14 UTC |
| b54f3c5 | Clayton Wheeler | 14 June 2012, 01:35:14 UTC | Handle alignment blocks spanning >2 chunks. Closes #5. | 14 June 2012, 01:35:14 UTC |
| 04d0cf1 | Clayton Wheeler | 14 June 2012, 01:16:20 UTC | Added test for #5, chunks with no block starts. | 14 June 2012, 01:16:20 UTC |
| c73545e | Clayton Wheeler | 13 June 2012, 23:30:37 UTC | Merge branch 'kcjava' Conflicts: lib/bio/maf/parser.rb | 13 June 2012, 23:30:37 UTC |
| f80fea1 | Clayton Wheeler | 13 June 2012, 23:24:09 UTC | Tests pass on JRuby now. Final cleanup and build notes. | 13 June 2012, 23:24:09 UTC |
