| 8e7ff72 | Avinash Ramu | 07 May 2014, 16:03:25 UTC | update clinseq blessed-cnmops updated | 07 May 2014, 16:03:25 UTC |
| 56e9159 | Avinash Ramu | 07 May 2014, 03:57:26 UTC | update test-dir and fix small bug | 07 May 2014, 03:58:15 UTC |
| b40acc1 | Avinash Ramu | 07 May 2014, 03:56:59 UTC | update exome cnv calling | 07 May 2014, 03:58:15 UTC |
| a618667 | Avinash Ramu | 06 May 2014, 20:12:35 UTC | revert changes to prior value. | 07 May 2014, 03:58:15 UTC |
| 689f1de | Avinash Ramu | 06 May 2014, 19:41:45 UTC | update cnv calling parameters | 07 May 2014, 03:58:14 UTC |
| 41dd20c | Avinash Ramu | 06 May 2014, 19:41:05 UTC | add GMB ClinSeq | 07 May 2014, 03:58:14 UTC |
| 675725b | Avinash Ramu | 06 May 2014, 19:38:37 UTC | add Clinseq class to gmt analysis | 07 May 2014, 03:58:14 UTC |
| b6066ba | Avinash Ramu | 05 May 2014, 04:10:15 UTC | fix fn | 07 May 2014, 03:58:13 UTC |
| 3673bc4 | Avinash Ramu | 05 May 2014, 04:09:46 UTC | minor update to cnv calling | 07 May 2014, 03:58:13 UTC |
| d835c99 | Avinash Ramu | 05 May 2014, 04:08:45 UTC | update test dir | 07 May 2014, 03:58:12 UTC |
| 650ebc1 | Malachi Griffith | 06 May 2014, 22:30:11 UTC | clin-seq - bless new test build | 06 May 2014, 22:30:11 UTC |
| 22b6714 | dmorton | 06 May 2014, 22:12:36 UTC | Commit after resolve_bed_for_reference since it can create SRs | 06 May 2014, 22:13:25 UTC |
| 0260452 | Dave Larson | 06 May 2014, 21:37:04 UTC | cut down on error messages from bam-readcount | 06 May 2014, 21:37:04 UTC |
| 947ca14 | APipe Tester | 06 May 2014, 21:13:14 UTC | updated jenkins submodule to 3c0805d | 06 May 2014, 21:13:14 UTC |
| 7fe795a | Jim Weible | 06 May 2014, 20:02:17 UTC | add profile item status to ShowConfig | 06 May 2014, 20:02:17 UTC |
| 1fee2f8 | Ben Ainscough | 06 May 2014, 19:45:14 UTC | Merge branch 'master' of ssh://git/srv/git/genome forgot to push | 06 May 2014, 19:45:14 UTC |
| cd3317d | Thomas Mooney | 06 May 2014, 18:30:03 UTC | Add sequencing_platform filter afterwards so it doesn't get overwritten. | 06 May 2014, 18:30:03 UTC |
| 3e0f211 | APipe Tester | 06 May 2014, 17:43:14 UTC | updated jenkins submodule to 7d9b110 | 06 May 2014, 17:43:14 UTC |
| dcf738c | APipe Tester | 06 May 2014, 17:40:15 UTC | updated jenkins submodule to 5d959e3 | 06 May 2014, 17:40:15 UTC |
| 66c4741 | APipe Tester | 06 May 2014, 17:34:58 UTC | updated jenkins submodule to 1e815df | 06 May 2014, 17:34:58 UTC |
| f3299dc | dmorton | 06 May 2014, 15:44:27 UTC | Do not keep around the uncompressed vcf file | 06 May 2014, 16:55:24 UTC |
| 03f0ab8 | dmorton | 06 May 2014, 15:43:52 UTC | Various optimizations to improve Reporter performance | 06 May 2014, 16:55:23 UTC |
| 24052c6 | dmorton | 02 May 2014, 17:08:35 UTC | Stop tabix indexing Vep vcf file Apparently the vcf output that vep produces isn't always sorted, so if we want to keep this we'll have to sort the vcf first. None of the other experts tabix index their vcfs, so if this expert isn't run last the final vcf won't be tabix indexed anyways. | 06 May 2014, 16:55:23 UTC |
| 2a96540 | Chris Miller | 06 May 2014, 16:39:19 UTC | typo | 06 May 2014, 16:39:34 UTC |
| 52bdfce | Chris Miller | 06 May 2014, 16:17:30 UTC | handling the case where bam-readcount returns lowercase alleles from a soft-masked genome | 06 May 2014, 16:39:30 UTC |
| 2489365 | Thomas Mooney | 06 May 2014, 16:32:43 UTC | Add caller info to auto-unarchive reason. | 06 May 2014, 16:32:43 UTC |
| 28533db | Malachi Griffith | 06 May 2014, 15:49:16 UTC | clin-seq - clean up GMAF values in snv-indel-report | 06 May 2014, 15:49:16 UTC |
| 3fb73f1 | Nathaniel Nutter | 06 May 2014, 15:04:39 UTC | add the requested_at time to user_data in Nessy lock | 06 May 2014, 15:04:39 UTC |
| e11d5fc | Nathaniel Nutter | 06 May 2014, 14:46:20 UTC | reorder statements | 06 May 2014, 14:46:20 UTC |
| e767990 | APipe Tester | 06 May 2014, 12:17:06 UTC | Updated `genome` tab completion. | 06 May 2014, 12:17:06 UTC |
| ac2ee06 | APipe Tester | 06 May 2014, 12:15:38 UTC | Updated class browser cache. | 06 May 2014, 12:15:38 UTC |
| 9dfeab4 | APipe Tester | 05 May 2014, 23:58:38 UTC | updated jenkins submodule to 00a6639 | 05 May 2014, 23:58:38 UTC |
| 6e498d8 | Eddie Belter | 05 May 2014, 22:37:25 UTC | Site TGI: Fix sanger run creation in genome | 05 May 2014, 22:43:01 UTC |
| 1259164 | Eddie Belter | 05 May 2014, 22:36:31 UTC | MC16s: print error msg from eval | 05 May 2014, 22:42:58 UTC |
| c12b56d | Eddie Belter | 05 May 2014, 22:31:01 UTC | InstData Import: remove some of the old importers | 05 May 2014, 22:31:01 UTC |
| e53abf1 | Eddie Belter | 05 May 2014, 21:58:39 UTC | InstData Import: quote nomenclature in import command | 05 May 2014, 21:59:20 UTC |
| ad4fa33 | Nathaniel Nutter | 02 May 2014, 16:51:37 UTC | config TestTracker to use genome-prove | 05 May 2014, 21:55:51 UTC |
| cd6435c | Nathaniel Nutter | 05 May 2014, 20:18:27 UTC | use genome-perl instead of just perl | 05 May 2014, 21:46:35 UTC |
| 1bc64d0 | Nathaniel Nutter | 05 May 2014, 19:41:43 UTC | remove script that uses a non-existant package This script used a non-existant package, Workflow::Server::HTTPD, so does not compile. As such, the script is being removed. | 05 May 2014, 19:44:18 UTC |
| 7e7277d | Eddie Belter | 05 May 2014, 19:30:44 UTC | InstData: add library as input to sra to bam, use the sample name in the samtools cmd | 05 May 2014, 19:31:21 UTC |
| a8d247a | Eddie Belter | 05 May 2014, 19:30:02 UTC | InstData Import: add tmp placeholders for gtmp, mtmp and kbtmp | 05 May 2014, 19:31:21 UTC |
| 04ac950 | Eddie Belter | 22 April 2014, 00:42:55 UTC | InstData Import: tests use library instead of sample | 05 May 2014, 19:31:20 UTC |
| 54ba164 | Eddie Belter | 22 April 2014, 00:11:36 UTC | InstData Import: manager uses library instead of sample | 05 May 2014, 19:31:20 UTC |
| 1ff269f | Eddie Belter | 21 April 2014, 23:11:49 UTC | InstData Import: update manager doc | 05 May 2014, 19:31:19 UTC |
| 4b6622a | Eddie Belter | 21 April 2014, 23:06:28 UTC | Sample Import: updated to commnad v2 | 05 May 2014, 19:31:18 UTC |
| 7e394f6 | Eddie Belter | 14 April 2014, 22:59:47 UTC | InstData Import: cahnge tmp space spec to just by tmp, no kb or mb | 05 May 2014, 19:31:18 UTC |
| a6c1dc9 | Eddie Belter | 14 April 2014, 22:51:38 UTC | InstData Import: substitute tmp kb and mb in launch command using required amount of space needed | 05 May 2014, 19:31:17 UTC |
| 932a338 | Eddie Belter | 14 April 2014, 22:50:31 UTC | InstData Import: fix error message in helpers | 05 May 2014, 19:31:17 UTC |
| 0afaec7 | Eddie Belter | 14 April 2014, 22:16:44 UTC | InstData Import Manager: check if source file exists | 05 May 2014, 19:31:16 UTC |
| fb60216 | Eddie Belter | 14 April 2014, 21:51:48 UTC | InstData Import Manager: check for errors from separated value reader | 05 May 2014, 19:31:16 UTC |
| 5418869 | Ben Ainscough | 05 May 2014, 19:13:38 UTC | added check to rna-seq step | 05 May 2014, 19:13:38 UTC |
| c394e9d | Thomas Mooney | 05 May 2014, 19:01:54 UTC | Fix typo s/falgged/flagged/ | 05 May 2014, 19:01:54 UTC |
| b56dca6 | Chris Miller | 05 May 2014, 16:46:51 UTC | adding missing tab to header | 05 May 2014, 16:46:51 UTC |
| 0033736 | Thomas Mooney | 05 May 2014, 14:29:01 UTC | Remove trailing tab. | 05 May 2014, 14:29:01 UTC |
| 2fbc429 | Avinash Ramu | 02 May 2014, 21:03:45 UTC | handle case where tumor, normal arrays differ | 02 May 2014, 21:03:45 UTC |
| f7db0cd | Avinash Ramu | 02 May 2014, 20:44:01 UTC | remove BAMs from diff | 02 May 2014, 20:45:06 UTC |
| a4323b2 | APipe Tester | 02 May 2014, 19:17:13 UTC | updated jenkins submodule to fd08b91 | 02 May 2014, 19:17:13 UTC |
| c28fa6e | dmorton | 02 May 2014, 15:49:58 UTC | Fix missing use statement | 02 May 2014, 15:55:30 UTC |
| b7749cc | dmorton | 02 May 2014, 15:49:34 UTC | All Filters are now Interpreters too | 02 May 2014, 15:55:30 UTC |
| bc954d2 | dmorton | 02 May 2014, 02:39:42 UTC | Add user relationships between software-results | 02 May 2014, 15:55:30 UTC |
| 2c3082f | Avinash Ramu | 02 May 2014, 13:15:59 UTC | update clinseq blessed LIMS updated to the latest genome-snapshot which caused some of the alignment metrics to change. | 02 May 2014, 13:16:56 UTC |
| 9cf5a24 | APipe Tester | 02 May 2014, 12:18:18 UTC | Updated `gmt` tab completion. | 02 May 2014, 12:18:18 UTC |
| 3507bf0 | APipe Tester | 02 May 2014, 12:17:37 UTC | Updated `genome` tab completion. | 02 May 2014, 12:17:37 UTC |
| 3403e8e | APipe Tester | 02 May 2014, 12:16:06 UTC | Updated class browser cache. | 02 May 2014, 12:16:06 UTC |
| 676f052 | dmorton | 02 May 2014, 01:38:19 UTC | Add AnnotateBuild command | 02 May 2014, 02:31:45 UTC |
| aaa3226 | dmorton | 02 May 2014, 01:36:43 UTC | make feature_list_ids_and_tags an optional output | 02 May 2014, 02:31:45 UTC |
| 5a27e72 | dmorton | 02 May 2014, 01:35:50 UTC | Add logging info | 02 May 2014, 02:31:45 UTC |
| 69cb1b2 | dmorton | 02 May 2014, 01:34:31 UTC | Adaptors do their work in shortcut | 02 May 2014, 02:31:45 UTC |
| 04a66ac | dmorton | 02 May 2014, 01:20:58 UTC | Expert::CommandBase handles shortcut and execute | 02 May 2014, 02:31:45 UTC |
| e1e22fd | dmorton | 01 May 2014, 21:17:19 UTC | Add ability to write plan to file | 02 May 2014, 02:31:45 UTC |
| 8166bd6 | Eddie Belter | 01 May 2014, 22:39:14 UTC | GM: add checking vcf in extract to vcf tests | 01 May 2014, 22:39:14 UTC |
| 2bf9a69 | Eddie Belter | 01 May 2014, 22:36:10 UTC | GM: add tests for sample priority to extract to vcf fails | 01 May 2014, 22:36:10 UTC |
| 5b7edc2 | Eddie Belter | 01 May 2014, 22:30:26 UTC | GM: add extract to vcf from sample test | 01 May 2014, 22:30:26 UTC |
| c7d0364 | Eddie Belter | 01 May 2014, 22:30:06 UTC | GM: fixed external filter in extract to vcf | 01 May 2014, 22:30:06 UTC |
| 9d79302 | Eddie Belter | 01 May 2014, 21:57:26 UTC | GM: get all inst data for a sample via the microarry libs plus default genotype data in extract to vcf | 01 May 2014, 21:57:26 UTC |
| 9faf487 | Eddie Belter | 01 May 2014, 21:56:19 UTC | GM: add import_date to test inst data | 01 May 2014, 21:56:19 UTC |
| efd4554 | Gabriel Sanderson | 01 May 2014, 19:41:28 UTC | Attempt to get instrument data via default_genotype_data first before falling back to a library->get by name | 01 May 2014, 20:19:42 UTC |
| 8f624ab | dmorton | 01 May 2014, 19:46:37 UTC | Annotation Plan is passed in to Adaptors and Wrapper | 01 May 2014, 20:12:16 UTC |
| 73dbe1c | dmorton | 01 May 2014, 18:48:34 UTC | Allow plans to be serialized and deserialized using JSON | 01 May 2014, 20:12:15 UTC |
| 49375fd | Travis Abbott | 01 May 2014, 18:24:45 UTC | bless new som-val-sv build (due to new bam-readcount) | 01 May 2014, 18:24:45 UTC |
| fda1912 | Avinash Ramu | 01 May 2014, 18:12:25 UTC | update clinseq blessed build bam-readcounts was updated which changes some of the read-counting output. | 01 May 2014, 18:12:25 UTC |
| 886f002 | Avinash Ramu | 01 May 2014, 16:34:54 UTC | small mod to sciclone doc | 01 May 2014, 16:35:52 UTC |
| 1d61efa | APipe Tester | 01 May 2014, 16:17:34 UTC | updated jenkins submodule to f35ef3e | 01 May 2014, 16:17:34 UTC |
| 53b8847 | Nathaniel Nutter | 01 May 2014, 14:09:08 UTC | add lib/perl prefix to Genome blacklists and escape periods | 01 May 2014, 15:59:12 UTC |
| a6171a1 | dmorton | 01 May 2014, 15:20:46 UTC | Add execution test for MasterCommand | 01 May 2014, 15:49:50 UTC |
| 245b28d | dmorton | 01 May 2014, 15:20:10 UTC | Mocked build's tumor_build has a subject name | 01 May 2014, 15:49:49 UTC |
| 298ae86 | dmorton | 01 May 2014, 15:19:44 UTC | wrapper passes in tranlations | 01 May 2014, 15:49:49 UTC |
| 3c0bf84 | dmorton | 01 May 2014, 15:18:58 UTC | Make sure all inputs to workflow are provided | 01 May 2014, 15:49:49 UTC |
| 817537b | dmorton | 01 May 2014, 15:18:15 UTC | change name from single-vep to just vep | 01 May 2014, 15:49:49 UTC |
| c3ab42f | dmorton | 01 May 2014, 15:17:37 UTC | fix typo on valid_values | 01 May 2014, 15:49:49 UTC |
| ccfd768 | dmorton | 01 May 2014, 15:17:05 UTC | use required library | 01 May 2014, 15:49:49 UTC |
| 4328086 | dmorton | 01 May 2014, 15:16:39 UTC | Add checks around translation | 01 May 2014, 15:49:49 UTC |
| 8340f16 | dmorton | 01 May 2014, 15:15:27 UTC | builds have snv and indel annotation plans | 01 May 2014, 15:49:49 UTC |
| 3e1f083 | dmorton | 01 May 2014, 15:13:03 UTC | Add get_detailed_vcf_result accessor | 01 May 2014, 15:49:48 UTC |
| 16b73b1 | APipe Tester | 01 May 2014, 15:01:28 UTC | updated jenkins submodule to 26b3875 | 01 May 2014, 15:01:28 UTC |
| eebece3 | APipe Tester | 01 May 2014, 14:50:44 UTC | updated jenkins submodule to a188921 | 01 May 2014, 14:50:44 UTC |
| 66698e5 | apregier | 01 May 2014, 14:48:57 UTC | Rename class | 01 May 2014, 14:48:57 UTC |
| 0701aa4 | Gabriel Sanderson | 01 May 2014, 01:07:51 UTC | Print sample id instead of the object during error | 01 May 2014, 01:07:51 UTC |
| acd8ee9 | Gabriel Sanderson | 01 May 2014, 00:22:41 UTC | Die cleanly when we fail to get a library in _resolve_source_for_sample. | 01 May 2014, 00:22:41 UTC |
| d57343b | Thomas Mooney | 30 April 2014, 22:51:19 UTC | Be more lenient about which models to assign to the group. | 30 April 2014, 22:51:19 UTC |
