| eab41ea | APipe Tester | 14 May 2013, 16:11:28 UTC | Updated `genome` tab completion. | 14 May 2013, 16:11:28 UTC |
| e2a58ec | kmeltzst | 14 May 2013, 15:39:09 UTC | added option for gzipped vcf file | 14 May 2013, 15:39:57 UTC |
| d5dfb4b | Malachi Griffith | 14 May 2013, 15:11:25 UTC | ClinSeq - SummarizeModels, diffs check out, updating test result | 14 May 2013, 15:11:25 UTC |
| d4ee502 | APipe Tester | 14 May 2013, 15:04:37 UTC | updated ur submodule to bbd15c4 | 14 May 2013, 15:04:37 UTC |
| 696be32 | Jason Walker | 14 May 2013, 14:15:34 UTC | Compile error. Add comma. | 14 May 2013, 14:15:34 UTC |
| 8f9c14e | Jason Walker | 14 May 2013, 13:28:40 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 14 May 2013, 13:28:40 UTC |
| c638adc | Jason Walker | 14 May 2013, 13:28:28 UTC | Changes to the metric keys caused missing values from the output metrics. | 14 May 2013, 13:28:28 UTC |
| 311982e | Malachi Griffith | 13 May 2013, 21:07:59 UTC | DumpIgvXml - Fix test result location so that old and new commits will pass test | 13 May 2013, 21:07:59 UTC |
| 082d315 | Malachi Griffith | 13 May 2013, 21:01:51 UTC | Update test result for clin-seq DumpIgvSessionXml | 13 May 2013, 21:01:51 UTC |
| 423cb59 | Ian Ferguson | 13 May 2013, 20:01:01 UTC | Bwa, Bwasw, Bwamem now respect thread count in PP. The Bwa, Bwasw, and Bwamem aligner modules now base their LSF CPU requirement off of the thread count argument (if specified) in read_aligner_params in the processing-profile. | 13 May 2013, 20:03:57 UTC |
| 649e2dc | Eddie Belter | 13 May 2013, 18:58:28 UTC | AQID mc16s.t: rm GSC from comments | 13 May 2013, 18:58:38 UTC |
| 99e4d9b | Veena Bhonagiri | 13 May 2013, 15:48:48 UTC | Added code so any version of acedb can be used | 13 May 2013, 15:48:48 UTC |
| a388067 | Kyung Kim | 10 May 2013, 22:05:03 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 10 May 2013, 22:05:03 UTC |
| 0bb37f1 | Kyung Kim | 10 May 2013, 21:13:42 UTC | DeNovo: update soap blessed build | 10 May 2013, 21:42:14 UTC |
| ae64b02 | Kyung Kim | 10 May 2013, 19:27:36 UTC | DeNovo: rm merge sx results and link result, they are in one step now | 10 May 2013, 21:42:14 UTC |
| de59666 | Kyung Kim | 10 May 2013, 19:19:45 UTC | SX: rm old processor test | 10 May 2013, 21:42:13 UTC |
| ee2cd26 | Kyung Kim | 10 May 2013, 19:02:13 UTC | Added new param to test | 10 May 2013, 21:42:13 UTC |
| 3321475 | apregier | 10 May 2013, 16:10:12 UTC | DeNovo: soap parallelizes process instrument data | 10 May 2013, 21:42:12 UTC |
| bb8673d | apregier | 10 May 2013, 16:09:07 UTC | Assemble step fails if assembler fails | 10 May 2013, 21:42:11 UTC |
| e21f328 | apregier | 10 May 2013, 16:08:10 UTC | Remove db::singles | 10 May 2013, 21:42:11 UTC |
| fc99bf1 | apregier | 10 May 2013, 16:02:47 UTC | Take average of insert size | 10 May 2013, 21:42:10 UTC |
| 9b588c0 | Eddie Belter | 10 May 2013, 14:47:04 UTC | DeNovo: get allpaths test to pass using merged SX results | 10 May 2013, 21:42:09 UTC |
| 3828ce4 | Eddie Belter | 10 May 2013, 14:46:38 UTC | DeNovo: add status msgs to assemble step | 10 May 2013, 21:42:09 UTC |
| 13bc2aa | Eddie Belter | 09 May 2013, 22:31:45 UTC | DeNovo: calculate reads attempted and processed in merge and link sx results step | 10 May 2013, 21:42:08 UTC |
| 585cbb7 | apregier | 09 May 2013, 20:35:11 UTC | Allpaths uses SxResults | 10 May 2013, 21:42:08 UTC |
| a034a3f | Eddie Belter | 09 May 2013, 21:10:15 UTC | DeNovo: update status msg on merge step | 10 May 2013, 21:42:07 UTC |
| a67f7a5 | Eddie Belter | 09 May 2013, 21:08:18 UTC | Sx Processor: make processor optional | 10 May 2013, 21:42:06 UTC |
| ff6ba58 | Eddie Belter | 09 May 2013, 21:00:41 UTC | DeNovo: new assemble build step | 10 May 2013, 21:42:06 UTC |
| 6eca376 | Eddie Belter | 09 May 2013, 21:00:12 UTC | SX Result: rm dumper statement | 10 May 2013, 21:42:04 UTC |
| 56086d5 | Eddie Belter | 09 May 2013, 20:59:24 UTC | DeNovo: merge and link sx results build step | 10 May 2013, 21:42:03 UTC |
| d030cb9 | Eddie Belter | 09 May 2013, 20:46:33 UTC | SX Result: update merged result to use new methods in base result | 10 May 2013, 21:42:02 UTC |
| 8cb0e9e | Eddie Belter | 09 May 2013, 19:24:26 UTC | SX Processor: complete final sx params method | 10 May 2013, 21:42:02 UTC |
| 05b1ac9 | Eddie Belter | 09 May 2013, 18:40:43 UTC | DeNovo: input_build is now just build. | 10 May 2013, 21:42:01 UTC |
| 03ffcd6 | Eddie Belter | 09 May 2013, 17:24:26 UTC | DeNovo: update workflow to use new build steps | 10 May 2013, 21:42:00 UTC |
| 6f601ff | Eddie Belter | 09 May 2013, 00:18:33 UTC | DeNovo: pass in command class name to add operation in pp | 10 May 2013, 21:42:00 UTC |
| 4cd2b62 | Eddie Belter | 09 May 2013, 00:10:54 UTC | DeNovo: update process inst data to use sx processor api | 10 May 2013, 21:41:59 UTC |
| 22e7f05 | Eddie Belter | 09 May 2013, 00:03:37 UTC | SX Processor: change API to be able to return merged sx result params and all final sx result params | 10 May 2013, 21:41:58 UTC |
| 9894dea | Eddie Belter | 08 May 2013, 17:25:35 UTC | SX Result: move resolve_merged_input_type from SX result to merged result | 10 May 2013, 21:41:58 UTC |
| b3dbc7e | Eddie Belter | 08 May 2013, 17:23:01 UTC | SX Result: reorged methods, updated status msgs | 10 May 2013, 21:41:57 UTC |
| 89d6c18 | Kyung Kim | 10 May 2013, 21:31:31 UTC | SX: sam and bam reader test reads 2 from sam/bam | 10 May 2013, 21:37:29 UTC |
| dc61a03 | Adam Coffman | 10 May 2013, 21:24:00 UTC | fix typo in error msg | 10 May 2013, 21:24:00 UTC |
| 0e46f18 | Kyung Kim | 10 May 2013, 21:17:08 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 10 May 2013, 21:17:08 UTC |
| f4d7162 | Kyung Kim | 10 May 2013, 21:16:41 UTC | SX: sam/bam reader complements seqs w/ reverse complemented flag | 10 May 2013, 21:16:41 UTC |
| 56e2726 | Kyung Kim | 10 May 2013, 21:13:17 UTC | SX: reader sorts seqs by name | 10 May 2013, 21:13:17 UTC |
| 6bea0c1 | Chris Miller | 10 May 2013, 20:25:51 UTC | added sanity checks to handle the case where no segs will be plot | 10 May 2013, 20:26:04 UTC |
| 30391a2 | Kyung Kim | 10 May 2013, 20:09:44 UTC | SX: add complement function | 10 May 2013, 20:09:44 UTC |
| f21a7f7 | Gabriel Sanderson | 09 May 2013, 22:45:22 UTC | Merge branch 'master' into gb_master | 09 May 2013, 22:45:22 UTC |
| d043a8d | Gabriel Sanderson | 09 May 2013, 22:43:54 UTC | added test case for convert_file_with_alpha_gt_values_to_numeric | 09 May 2013, 22:44:31 UTC |
| 8af948d | APipe Tester | 09 May 2013, 18:37:11 UTC | Updated `gmt` tab completion. | 09 May 2013, 18:37:11 UTC |
| 1eea829 | APipe Tester | 09 May 2013, 18:35:20 UTC | Updated `genome` tab completion. | 09 May 2013, 18:35:20 UTC |
| de572c5 | Jasreet Hundal | 09 May 2013, 18:22:26 UTC | New tool for parsing NetMHC3.2 stdout from web | 09 May 2013, 18:22:26 UTC |
| 718668d | APipe Tester | 09 May 2013, 17:39:10 UTC | Updated `genome` tab completion. | 09 May 2013, 17:39:10 UTC |
| 20786d8 | apregier | 09 May 2013, 17:17:02 UTC | Correctly get 1-based roi | 09 May 2013, 17:17:21 UTC |
| 901263a | Scott Smith | 09 May 2013, 14:28:47 UTC | make processing-profile diff flag differing properties | 09 May 2013, 14:28:47 UTC |
| 7d56809 | Scott Smith | 09 May 2013, 14:26:46 UTC | ensure changes to inputs or other model properties are applied to new models, not just processing profile changes | 09 May 2013, 14:26:46 UTC |
| 76ec43d | Thomas Mooney | 09 May 2013, 13:57:23 UTC | Bring back defaults required for MGAP pipeline... | 09 May 2013, 13:57:23 UTC |
| a4dc19a | Thomas Mooney | 08 May 2013, 14:48:45 UTC | Old data is gone again, so update blessed build blindly. | 09 May 2013, 13:55:54 UTC |
| 3fb56c7 | Dave Larson | 08 May 2013, 21:52:04 UTC | If we subtract one from the VCF coord then we need to add it back when we output it. Also, we should check that our filehandles opened. CHANGELOG: Fix VCF output for liftover tool (had an off by one error). | 08 May 2013, 21:52:04 UTC |
| 265973f | Ian Ferguson | 08 May 2013, 20:52:14 UTC | Better error checking for Bwasw | 08 May 2013, 20:52:29 UTC |
| 061b276 | Eddie Belter | 08 May 2013, 20:36:01 UTC | MC16s: add clusters to solexa inst data for est kb usage | 08 May 2013, 20:36:01 UTC |
| 1b44969 | APipe Tester | 08 May 2013, 20:05:42 UTC | Updated `gmt` tab completion. | 08 May 2013, 20:05:42 UTC |
| 2c07baa | APipe Tester | 08 May 2013, 20:04:34 UTC | Updated `genome` tab completion. | 08 May 2013, 20:04:34 UTC |
| 17c5c81 | Chris Miller | 08 May 2013, 19:56:40 UTC | fixed test | 08 May 2013, 19:56:40 UTC |
| 4c31c93 | Chris Miller | 08 May 2013, 19:54:43 UTC | Merge branch 'capturePlot' | 08 May 2013, 19:54:43 UTC |
| e6f89c7 | Chris Miller | 08 May 2013, 19:54:03 UTC | tool to plot coverage over target regions. And hey, I even wrote a crappy test | 08 May 2013, 19:54:03 UTC |
| 8ae229d | Jim Weible | 08 May 2013, 19:41:12 UTC | bless somatic variation test | 08 May 2013, 19:41:12 UTC |
| 06ba9d4 | Chris Miller | 08 May 2013, 18:48:55 UTC | cleaned up whitespace and removed testing code | 08 May 2013, 18:48:55 UTC |
| 66f4e0e | APipe Tester | 08 May 2013, 18:28:13 UTC | Updated `gmt` tab completion. | 08 May 2013, 18:28:13 UTC |
| 3d4e736 | APipe Tester | 08 May 2013, 18:27:09 UTC | Updated `genome` tab completion. | 08 May 2013, 18:27:09 UTC |
| fde438b | Chris Miller | 08 May 2013, 18:18:03 UTC | Merge branch 'plotSegsNew' | 08 May 2013, 18:18:03 UTC |
| 087782d | Chris Miller | 08 May 2013, 18:17:08 UTC | barebones test for this tool | 08 May 2013, 18:17:08 UTC |
| 226635d | Chris Miller | 08 May 2013, 18:15:05 UTC | added min mapability option | 08 May 2013, 18:15:05 UTC |
| 0f73d05 | Chris Miller | 08 May 2013, 18:14:41 UTC | new tool to plot cn and coverage | 08 May 2013, 18:14:41 UTC |
| 354b1cc | APipe Tester | 08 May 2013, 17:08:02 UTC | Updated `gmt` tab completion. | 08 May 2013, 17:08:02 UTC |
| 3e013a2 | APipe Tester | 08 May 2013, 17:07:13 UTC | Updated `genome` tab completion. | 08 May 2013, 17:07:13 UTC |
| 81a65e7 | Eddie Belter | 08 May 2013, 17:01:47 UTC | SX Merged Result: update sx limit command | 08 May 2013, 17:01:47 UTC |
| 7921d74 | Eddie Belter | 08 May 2013, 16:57:55 UTC | SX Limit: fix randomization bug | 08 May 2013, 16:58:04 UTC |
| c57d18d | Eddie Belter | 08 May 2013, 15:29:10 UTC | MC16s: update test inst data | 08 May 2013, 15:29:39 UTC |
| 862a33b | Eddie Belter | 07 May 2013, 20:25:29 UTC | DeNovo: merge sx results build step | 08 May 2013, 15:29:38 UTC |
| 9943d0d | Eddie Belter | 07 May 2013, 20:09:27 UTC | DeNovo: link inst data to taxon in build test | 08 May 2013, 15:29:38 UTC |
| b6f5432 | Eddie Belter | 07 May 2013, 20:09:01 UTC | DeNovo: rm "read" from sx processor | 08 May 2013, 15:29:37 UTC |
| b1f49cc | Eddie Belter | 07 May 2013, 18:50:38 UTC | SX: rm status messages when validating command in validate | 08 May 2013, 15:29:37 UTC |
| c3b9025 | Eddie Belter | 07 May 2013, 18:50:01 UTC | DeNovo: build test uses new style read processor | 08 May 2013, 15:29:36 UTC |
| 109d5dd | Eddie Belter | 07 May 2013, 18:49:05 UTC | DeNovo: move getting sx param into own method for process inst data | 08 May 2013, 15:29:36 UTC |
| a413c5d | Eddie Belter | 07 May 2013, 18:45:33 UTC | DeNovo: use sx processor to validate read processor | 08 May 2013, 15:29:35 UTC |
| c9c551a | Eddie Belter | 07 May 2013, 18:41:56 UTC | SX Processor: add sx command validation | 08 May 2013, 15:29:34 UTC |
| 58a733a | Eddie Belter | 07 May 2013, 18:16:07 UTC | DeNovo: rm commented out lines form pp | 08 May 2013, 15:29:34 UTC |
| 9fc2903 | Eddie Belter | 07 May 2013, 18:15:00 UTC | SX Processor: remove read refs | 08 May 2013, 15:29:33 UTC |
| d6f0b23 | Eddie Belter | 07 May 2013, 16:20:52 UTC | DeNovo: add coverage to sx result params for multiple inst data | 08 May 2013, 15:29:33 UTC |
| a5276f7 | Eddie Belter | 07 May 2013, 16:00:24 UTC | DeNovo: finish converting from getting read processor to getting sx result params | 08 May 2013, 15:29:32 UTC |
| 69ae8e3 | Eddie Belter | 07 May 2013, 15:36:28 UTC | DeNovo: rename determine sx processing to sx result params | 08 May 2013, 15:29:32 UTC |
| 84ba194 | Eddie Belter | 07 May 2013, 15:12:30 UTC | DeNovo: add determine processing for multiple inst data to SX read processor | 08 May 2013, 15:29:31 UTC |
| 75317ae | Eddie Belter | 06 May 2013, 23:14:18 UTC | DeNovo: link sx result build step | 08 May 2013, 15:29:30 UTC |
| 63ed1e8 | Eddie Belter | 06 May 2013, 23:13:54 UTC | DeNovo: test and example builds | 08 May 2013, 15:29:30 UTC |
| 231ef9c | Eddie Belter | 06 May 2013, 22:23:08 UTC | DeNovo: new process inst data uses new sx read processor | 08 May 2013, 15:29:29 UTC |
| c5a8fba | Eddie Belter | 06 May 2013, 22:22:23 UTC | DeNovo SX: return sx result params when only have default processor | 08 May 2013, 15:29:29 UTC |
| 2deb0a5 | Eddie Belter | 06 May 2013, 19:47:08 UTC | DeNovo SX: add params to processing for inst data | 08 May 2013, 15:29:28 UTC |
| 3835438 | Eddie Belter | 03 May 2013, 19:10:11 UTC | SX Result: update quality type for archive path | 08 May 2013, 15:29:27 UTC |
| 57c62cc | APipe Tester | 07 May 2013, 19:59:25 UTC | updated ur submodule to b15f85a | 07 May 2013, 19:59:25 UTC |
| 6d9027b | APipe Tester | 07 May 2013, 19:21:53 UTC | Updated `gmt` tab completion. | 07 May 2013, 19:21:53 UTC |
