| 41ca7bd | Scott Smith | 06 March 2013, 04:51:50 UTC | updated "gmt htseq" and related infrastructure | 06 March 2013, 04:51:50 UTC |
| a7efb91 | Scott Smith | 06 March 2013, 04:50:43 UTC | fix to work with non-deprecated models | 06 March 2013, 04:50:43 UTC |
| b98bbee | Scott Smith | 06 March 2013, 04:47:50 UTC | updated converge{Svs,Indels,Cnvs,Stats}.t | 06 March 2013, 04:47:50 UTC |
| 6981130 | Scott Smith | 06 March 2013, 04:42:21 UTC | updated convergeSnvs.t for changed data | 06 March 2013, 04:42:21 UTC |
| e7841aa | Malachi Griffith | 06 March 2013, 00:06:59 UTC | ClinSeq fix workflow | 06 March 2013, 00:06:59 UTC |
| 838979b | Malachi Griffith | 06 March 2013, 00:06:09 UTC | Htseq - Add to rna extraction types recognized by regex | 06 March 2013, 00:06:09 UTC |
| 5035637 | Malachi Griffith | 06 March 2013, 00:05:07 UTC | Blessing new clinseq build | 06 March 2013, 00:05:07 UTC |
| fd8f52a | Eddie Belter | 05 March 2013, 23:05:44 UTC | Sync: uncommented out a needed method. This was accidentally committed | 05 March 2013, 23:06:11 UTC |
| 82756ad | apregier | 05 March 2013, 22:32:02 UTC | Merge branch 'fireteam2' into gb_master | 05 March 2013, 22:32:02 UTC |
| d76c7f4 | apregier | 05 March 2013, 22:26:21 UTC | In the case where the variant falls in a degenerate codon, the mutation should be labeled silent | 05 March 2013, 22:26:21 UTC |
| 5ce5114 | apregier | 05 March 2013, 21:06:00 UTC | Merge branch 'fireteam2' into gb_master | 05 March 2013, 21:06:00 UTC |
| 796d443 | apregier | 05 March 2013, 20:58:47 UTC | Create derivatives of gtf file for rna-seq-only imported annotation build | 05 March 2013, 20:58:47 UTC |
| d99b702 | Dan Koboldt | 05 March 2013, 20:51:23 UTC | Correction to apparent default setting | 05 March 2013, 20:51:23 UTC |
| 63fe2de | Dan Koboldt | 05 March 2013, 20:50:00 UTC | Corrected a bug. Merge branch 'master' of git+ssh://git/srv/git/genome | 05 March 2013, 20:50:00 UTC |
| 0e67c4a | Dan Koboldt | 05 March 2013, 20:49:49 UTC | Correction to small bug that was causing all gene exons to be printed | 05 March 2013, 20:49:49 UTC |
| b041a07 | Eddie Belter | 05 March 2013, 19:19:03 UTC | MC16s: use default pp id method to get pp in run status command | 05 March 2013, 19:19:03 UTC |
| cfb68e1 | Eddie Belter | 05 March 2013, 18:58:22 UTC | Sync: fail if getting current value encounters error; add msg checks to tests | 05 March 2013, 18:58:30 UTC |
| 74b872c | apregier | 05 March 2013, 18:44:45 UTC | Merge branch 'fireteam2' into gb_master | 05 March 2013, 18:44:45 UTC |
| 2e23edf | apregier | 05 March 2013, 18:43:35 UTC | Remove non-temp file path | 05 March 2013, 18:43:44 UTC |
| 91b4bee | Scott Smith | 05 March 2013, 18:42:18 UTC | Merge branch 'master' of ssh://git/srv/git/genome Conflicts: .gitmodules | 05 March 2013, 18:42:18 UTC |
| fa59da3 | Scott Smith | 05 March 2013, 18:40:19 UTC | add vendor/rna-star -currently empty, testing in-progress | 05 March 2013, 18:40:19 UTC |
| e0606f7 | Eddie Belter | 05 March 2013, 16:50:31 UTC | Sync: get current value before checking if property is updated | 05 March 2013, 16:50:31 UTC |
| 12b8489 | Eddie Belter | 05 March 2013, 16:45:57 UTC | Sync: attempt to update genome entity directly first, then via attrs in base for attrs | 05 March 2013, 16:46:03 UTC |
| 571be86 | apregier | 05 March 2013, 16:45:06 UTC | Merge branch 'fireteam2' into gb_master | 05 March 2013, 16:45:06 UTC |
| fb548b9 | apregier | 05 March 2013, 16:44:25 UTC | Skipped updates do not have errors | 05 March 2013, 16:44:36 UTC |
| 42f7e41 | apregier | 05 March 2013, 16:29:46 UTC | Check for properties that are not via attributes and send them to the parent method. | 05 March 2013, 16:44:36 UTC |
| fe29fbc | apregier | 05 March 2013, 03:36:55 UTC | Reenable annotator version 3 tests | 05 March 2013, 16:44:35 UTC |
| 88eb4a1 | apregier | 05 March 2013, 03:36:19 UTC | Fix bugs in annotator | 05 March 2013, 16:44:35 UTC |
| 66ae53c | apregier | 05 March 2013, 03:33:37 UTC | Fix bug in codons_in_range when the exon is very short | 05 March 2013, 16:44:35 UTC |
| 9e0338e | apregier | 05 March 2013, 03:32:49 UTC | Fix warning due to some abandoned builds not having versions | 05 March 2013, 16:44:34 UTC |
| 8846058 | Ling Lin | 05 March 2013, 16:40:10 UTC | Merge branch 'master' of ssh://git/srv/git/genome just wish to merge as prompted. | 05 March 2013, 16:40:10 UTC |
| 2fddde5 | APipe Tester | 04 March 2013, 23:03:34 UTC | updated jenkins submodule to 5f3f651 | 04 March 2013, 23:03:34 UTC |
| 569fdcf | APipe Tester | 04 March 2013, 23:01:12 UTC | updated gms-config submodule to 6ccaa62 | 04 March 2013, 23:01:12 UTC |
| 49259e6 | APipe Tester | 04 March 2013, 22:57:14 UTC | updated gms-config submodule to f4f7915 | 04 March 2013, 22:57:14 UTC |
| c185b2c | APipe Tester | 04 March 2013, 22:50:44 UTC | updated gms-config submodule to 96f904a | 04 March 2013, 22:50:44 UTC |
| 8839798 | Ben Oberkfell | 04 March 2013, 22:47:57 UTC | commit is controlled by the parent process. override commit locally to be a no-op so we do not double commit. | 04 March 2013, 22:47:57 UTC |
| 46cfa59 | Nathan Nutter | 04 March 2013, 21:32:07 UTC | trying to fix compile error and test failures | 04 March 2013, 21:32:27 UTC |
| 74433ec | Malachi Griffith | 04 March 2013, 21:26:34 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 04 March 2013, 21:26:34 UTC |
| 5981d17 | Malachi Griffith | 04 March 2013, 21:26:20 UTC | ClinSeq - Fix missing dirs error for variant sources step | 04 March 2013, 21:26:20 UTC |
| dd34e88 | APipe Tester | 04 March 2013, 21:17:10 UTC | updated configuration-manager submodule to f719544 | 04 March 2013, 21:17:10 UTC |
| 0c03be0 | APipe Tester | 04 March 2013, 21:05:23 UTC | updated configuration-manager submodule to 93070ad | 04 March 2013, 21:05:23 UTC |
| 054eeac | Adam Coffman | 04 March 2013, 20:54:24 UTC | add configuration related submodules | 04 March 2013, 20:58:26 UTC |
| 3e75614 | Adam Coffman | 04 March 2013, 20:44:42 UTC | add config manager and config directory submodules | 04 March 2013, 20:58:25 UTC |
| 3db2f92 | APipe Tester | 04 March 2013, 20:51:09 UTC | updated workflow submodule to 9f9f689 | 04 March 2013, 20:51:09 UTC |
| 00a452d | Eddie Belter | 04 March 2013, 17:55:05 UTC | Sync: syntax err in index illumina sql | 04 March 2013, 17:55:05 UTC |
| ebe22be | Eddie Belter | 04 March 2013, 17:53:44 UTC | Sync: update ri454 test output | 04 March 2013, 17:53:51 UTC |
| 41b15f3 | Scott Smith | 04 March 2013, 17:34:31 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 04 March 2013, 17:34:31 UTC |
| 0d4498b | Scott Smith | 04 March 2013, 17:34:22 UTC | add vendor/htseq | 04 March 2013, 17:34:22 UTC |
| 371679e | Eddie Belter | 28 February 2013, 21:25:03 UTC | Sync: consolidate and add tests for ii | 04 March 2013, 17:32:00 UTC |
| 970ef39 | Eddie Belter | 28 February 2013, 21:24:28 UTC | Sync: try to get current value as direct property from genome entity | 04 March 2013, 17:32:00 UTC |
| 7228ea1 | Eddie Belter | 28 February 2013, 20:46:48 UTC | Sync: add tests for all synced properties for ri454 | 04 March 2013, 17:31:59 UTC |
| af46e82 | Eddie Belter | 28 February 2013, 00:07:59 UTC | Sync: add misc update sub class for rr454 | 04 March 2013, 17:31:59 UTC |
| 7c63c49 | Eddie Belter | 28 February 2013, 00:07:30 UTC | Sync: add rr454 to misc update | 04 March 2013, 17:31:58 UTC |
| b02f6ad | Eddie Belter | 28 February 2013, 00:07:10 UTC | Sync: update ri454 table doc | 04 March 2013, 17:31:58 UTC |
| a1ea126 | Eddie Belter | 27 February 2013, 23:20:28 UTC | Sync: add comment to misc update lib test | 04 March 2013, 17:31:58 UTC |
| 1bfcd60 | Eddie Belter | 27 February 2013, 23:19:02 UTC | Sync: some how lost the conversion of misc update ri454 to base for attributes - rewrote | 04 March 2013, 17:31:57 UTC |
| 267635f | Eddie Belter | 27 February 2013, 22:52:27 UTC | Sync: convert misc update ii to base for attrs | 04 March 2013, 17:31:57 UTC |
| baf758e | Eddie Belter | 27 February 2013, 21:36:50 UTC | Sync: base for entities that have attrs | 04 March 2013, 17:31:56 UTC |
| a52b03a | Eddie Belter | 27 February 2013, 21:34:41 UTC | Sync: subjects and inst data misc updates use base for attrs | 04 March 2013, 17:31:56 UTC |
| fdc6a94 | Eddie Belter | 27 February 2013, 21:32:44 UTC | Sync: mv subject to base for attrs; update class name | 04 March 2013, 17:31:56 UTC |
| f33fc72 | Eddie Belter | 27 February 2013, 21:30:05 UTC | Sync: Library summary uses base; temp broke subject and inst data misc updates | 04 March 2013, 17:31:55 UTC |
| 94d5c90 | Eddie Belter | 27 February 2013, 21:12:17 UTC | Sync: misc update subject uses base class | 04 March 2013, 17:31:55 UTC |
| d23e237 | Eddie Belter | 27 February 2013, 20:59:21 UTC | Sync: update comments in ri454 | 04 March 2013, 17:31:54 UTC |
| 9b721b0 | Eddie Belter | 27 February 2013, 20:58:50 UTC | Sync: add run region 454 class mappings to misc update | 04 March 2013, 17:31:54 UTC |
| 9477c8d | Eddie Belter | 27 February 2013, 16:15:49 UTC | Sync: add misc update class for region index 454 plus test | 04 March 2013, 17:31:54 UTC |
| 1cd439a | Eddie Belter | 27 February 2013, 16:15:22 UTC | Sync: add region index 454 to misc update | 04 March 2013, 17:31:53 UTC |
| 82a2353 | Eddie Belter | 27 February 2013, 16:14:57 UTC | Sync: add lims table summary and property syncing helpers to RI454 | 04 March 2013, 17:31:53 UTC |
| ac04bea | Eddie Belter | 27 February 2013, 02:33:56 UTC | Sync: use lower case version of subject property name | 04 March 2013, 17:31:52 UTC |
| b42c9d2 | Eddie Belter | 27 February 2013, 02:09:48 UTC | Sync: add index illumina misc update with base class | 04 March 2013, 17:31:52 UTC |
| 03358d2 | Eddie Belter | 27 February 2013, 02:09:00 UTC | Sync: add index illumina to misc update; store genome entity; add genome property method | 04 March 2013, 17:31:52 UTC |
| b4aaca5 | Eddie Belter | 27 February 2013, 01:52:22 UTC | Sync: add lims table info; add properties to copy, keep updated and lims to genome conversion | 04 March 2013, 17:31:51 UTC |
| 0d1bd23 | Scott Smith | 04 March 2013, 17:27:19 UTC | Updated to support black/white lists for alignments, updated test output | 04 March 2013, 17:27:19 UTC |
| 1e6d05e | Nathan Nutter | 04 March 2013, 17:23:35 UTC | fix typo | 04 March 2013, 17:25:39 UTC |
| c93e356 | APipe Tester | 04 March 2013, 17:14:57 UTC | Updated `gmt` tab completion. | 04 March 2013, 17:14:57 UTC |
| 71c6628 | APipe Tester | 04 March 2013, 17:14:11 UTC | Updated `genome` tab completion. | 04 March 2013, 17:14:11 UTC |
| 5db4ad3 | APipe Tester | 04 March 2013, 15:01:08 UTC | updated getopt-complete submodule to 790cd66 | 04 March 2013, 15:01:08 UTC |
| eddce15 | APipe Tester | 04 March 2013, 15:00:58 UTC | updated ur submodule to 7fd973b | 04 March 2013, 15:00:58 UTC |
| 583e4e8 | Cyriac Kandoth | 03 March 2013, 23:02:41 UTC | Friendlier variable names, corrected docs, and tweaked thresholds | 03 March 2013, 23:02:41 UTC |
| cb63b9c | Nathan Nutter | 02 March 2013, 03:39:16 UTC | update .test-tracker.conf for new format | 02 March 2013, 03:44:50 UTC |
| 42e1656 | Nathan Nutter | 27 February 2013, 20:17:49 UTC | Use Perl's -S intead of `which`. | 02 March 2013, 03:44:49 UTC |
| 311f699 | Nathan Nutter | 26 February 2013, 20:49:04 UTC | Merge branch 'volume_cron' | 02 March 2013, 03:44:47 UTC |
| e56435d | Nathan Nutter | 26 February 2013, 20:15:18 UTC | add very primitive test | 02 March 2013, 03:44:46 UTC |
| dc72742 | Nathan Nutter | 26 February 2013, 19:33:09 UTC | add command to pull volumes out of service if they are over soft limit | 02 March 2013, 03:44:45 UTC |
| 02ab3f5 | Nathan Nutter | 26 February 2013, 19:32:31 UTC | set valid values on disk_status and can_allocate | 02 March 2013, 03:44:44 UTC |
| 4b632ec | Nathan Nutter | 26 February 2013, 19:30:24 UTC | refactor is_over_soft_limit - Move "rolling back" messages into Genome::Disk::Allocation, they don't belong in Genome::Disk::Volume. - Split is_over_soft_limit logic into is_used_over_soft_limit and is_allocated_over_soft_limit so "outsiders" can "query" this. | 02 March 2013, 03:44:42 UTC |
| 5f99b9c | Malachi Griffith | 02 March 2013, 00:46:11 UTC | Added variant sources output to clinseq | 02 March 2013, 00:46:11 UTC |
| 704172a | Ling Lin | 01 March 2013, 23:04:16 UTC | program for retrieving exon infomation for a given gene list | 01 March 2013, 23:04:16 UTC |
| 19d6681 | Nathan Nutter | 01 March 2013, 22:36:30 UTC | refactor test and use compare_ok instead of diff | 01 March 2013, 22:36:30 UTC |
| 9982a37 | Jason Walker | 01 March 2013, 21:54:58 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 01 March 2013, 21:54:58 UTC |
| b86b0f9 | Jason Walker | 01 March 2013, 21:54:53 UTC | Initial attempt to generate an empty variants aspect for comparison. | 01 March 2013, 21:54:53 UTC |
| 92958af | apregier | 01 March 2013, 21:37:25 UTC | Cache substructures and fix some bugs | 01 March 2013, 21:37:46 UTC |
| 5ea2187 | Malachi Griffith | 01 March 2013, 20:04:13 UTC | ClinSeq - Major update to convert scripts to command, wrap them in unit tests, and drop into the ClinSeq workflow | 01 March 2013, 20:04:13 UTC |
| 0a1e8f6 | Scott Smith | 01 March 2013, 04:03:10 UTC | Updated Genome::Command::WithSavedResults to break inputs down and run N subordinate commands. No mereg logic yet, and no workflow around the parts (not parallelized, just divided). | 01 March 2013, 04:03:10 UTC |
| 78c450b | Scott Smith | 01 March 2013, 01:05:54 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 01 March 2013, 01:05:54 UTC |
| 6caa087 | Malachi Griffith | 01 March 2013, 00:59:06 UTC | ClinSeq - fix test plan for some converge tests | 01 March 2013, 00:59:06 UTC |
| 8afdab4 | Scott Smith | 01 March 2013, 00:55:28 UTC | added example_values to "gmt htseq count", and "where" filter, currently unused | 01 March 2013, 00:55:28 UTC |
| ada68c6 | Malachi Griffith | 01 March 2013, 00:45:51 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 01 March 2013, 00:45:51 UTC |
| 6d95712 | Obi Griffith | 01 March 2013, 00:45:10 UTC | fixed test after changing allowed tumor common names | 01 March 2013, 00:45:10 UTC |
| 9f70b95 | Malachi Griffith | 28 February 2013, 23:34:22 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 28 February 2013, 23:34:22 UTC |
| 4a8bc8a | Scott Smith | 28 February 2013, 23:33:00 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 28 February 2013, 23:33:00 UTC |
