| 3d7b729 | Thomas Mooney | 18 March 2014, 13:11:37 UTC | Don't include "input_values" as a possible input. | 18 March 2014, 13:11:37 UTC |
| 963451a | APipe Tester | 18 March 2014, 12:18:32 UTC | Updated `gmt` tab completion. | 18 March 2014, 12:18:32 UTC |
| 04a27fd | APipe Tester | 18 March 2014, 12:17:46 UTC | Updated `genome` tab completion. | 18 March 2014, 12:17:46 UTC |
| 4efdc3e | APipe Tester | 18 March 2014, 12:16:00 UTC | Updated class browser cache. | 18 March 2014, 12:16:00 UTC |
| 8fa6a0c | Adam Coffman | 17 March 2014, 21:33:53 UTC | add output property to track newly added inst data | 17 March 2014, 21:33:53 UTC |
| 87ba0cb | Thomas Mooney | 17 March 2014, 21:25:51 UTC | Undo half-baked attempt to rename "inputs" accessor. If at some point we'd like to rename these we should just do it instead of cluttering up the module with conflicting definitions and TODOs and deprecations. This attempt didn't even reconcile all the places within Model.pm itself that were affected, so you'd get weirdly different behavior depending which accessor you used. | 17 March 2014, 21:25:51 UTC |
| d8c9d42 | Adam Coffman | 17 March 2014, 21:23:17 UTC | dont increment count when you skip inst data | 17 March 2014, 21:23:17 UTC |
| 9b20d67 | Eddie Belter | 17 March 2014, 20:30:17 UTC | GM: requires dbsnp build and gets reference from it | 17 March 2014, 20:30:28 UTC |
| 3723996 | Thomas Mooney | 17 March 2014, 20:09:38 UTC | Test execute() not create() for failure. | 17 March 2014, 20:09:38 UTC |
| abd585b | Thomas Mooney | 17 March 2014, 20:07:19 UTC | Tell Test::More there's only one test. | 17 March 2014, 20:07:19 UTC |
| 564900c | Michael J. Kiwala | 17 March 2014, 03:23:55 UTC | allow library to be optionally specified | 17 March 2014, 18:41:48 UTC |
| 666866d | Eddie Belter | 14 March 2014, 01:17:19 UTC | GM: if variant is seen, delete the order value and only use genotypes with defined order values | 17 March 2014, 17:35:53 UTC |
| f44b0c9 | Thomas Mooney | 17 March 2014, 17:21:50 UTC | Remove breakpoint. | 17 March 2014, 17:21:50 UTC |
| 13d418e | Thomas Mooney | 17 March 2014, 17:12:32 UTC | Merge branch 'assign-subcommands' | 17 March 2014, 17:12:32 UTC |
| ce309c7 | dmorton | 17 March 2014, 15:05:37 UTC | Make command fail earlier if model_group_name is taken | 17 March 2014, 15:07:17 UTC |
| abaea14 | Thomas Mooney | 17 March 2014, 00:53:22 UTC | Remove remnants of early auto-cron. | 17 March 2014, 00:53:22 UTC |
| bcf7feb | Thomas Mooney | 17 March 2014, 00:48:57 UTC | Remove root of emptied out DV1 tree. Tab completers, rejoice! | 17 March 2014, 00:48:57 UTC |
| 127a211 | Thomas Mooney | 17 March 2014, 00:46:26 UTC | Remove obsolete `gmt copy-eland-alignments`. We don't typically run ELAND anymore, and this command never worked correctly with indexed data. | 17 March 2014, 00:46:26 UTC |
| 6b8d9e7 | Thomas Mooney | 17 March 2014, 00:39:17 UTC | Remove functionality-less `gmt multi-aligner`. | 17 March 2014, 00:39:17 UTC |
| cbe78b1 | Thomas Mooney | 17 March 2014, 00:35:33 UTC | Remove empty `gmt novoalign`. See `gmt novocraft novoalign` instead. | 17 March 2014, 00:35:33 UTC |
| 48bc9fd | Thomas Mooney | 17 March 2014, 00:32:21 UTC | Remove charris insult at root of empty tree `gmt recurrence`. | 17 March 2014, 00:32:21 UTC |
| f2f8647 | Thomas Mooney | 17 March 2014, 00:28:46 UTC | Remove root of empty command tree `gmt import`. | 17 March 2014, 00:28:46 UTC |
| c66e405 | Thomas Mooney | 17 March 2014, 00:23:04 UTC | Remove `gmt sequence` that makes bad assumptions about references. | 17 March 2014, 00:23:04 UTC |
| f71b374 | Thomas Mooney | 16 March 2014, 23:39:57 UTC | Remove vestige of "Composite" model type. | 16 March 2014, 23:39:57 UTC |
| 79393a1 | Thomas Mooney | 16 March 2014, 23:35:51 UTC | Remove last vestige of "ManualReview" model type. One processing-profile deleted: genome=> SELECT * FROM model.processing_profile WHERE subclass_name = 'Genome::ProcessingProfile::ManualReview'; id | type_name | name | subclass_name ---------+---------------+---------------+----------------------------------------- 1984223 | manual review | Manual Review | Genome::ProcessingProfile::ManualReview (1 row) genome=> SELECT * FROM model.processing_profile_param WHERE processing_profile_id = '1984223'; processing_profile_id | param_name | param_value | name | value_class_name | value_id -----------------------+------------+-------------+------+------------------+---------- (0 rows) | 16 March 2014, 23:35:51 UTC |
| 2e399d7 | Thomas Mooney | 16 March 2014, 23:18:57 UTC | Remove unused module G:M:AlignedBase | 16 March 2014, 23:18:57 UTC |
| 1f84e81 | Thomas Mooney | 16 March 2014, 23:03:12 UTC | Remove obsolete `gmt analysis 454 search-runs` command. Try `genome instrument-data list 454` instead. | 16 March 2014, 23:03:12 UTC |
| f1927f6 | Malachi Griffith | 16 March 2014, 16:17:19 UTC | clin-seq - update README.txt | 16 March 2014, 16:17:19 UTC |
| 0aab0ca | APipe Tester | 16 March 2014, 12:18:31 UTC | Updated `gmt` tab completion. | 16 March 2014, 12:18:31 UTC |
| 1cb770d | APipe Tester | 16 March 2014, 12:17:41 UTC | Updated `genome` tab completion. | 16 March 2014, 12:17:41 UTC |
| f5f9188 | APipe Tester | 16 March 2014, 12:16:04 UTC | Updated class browser cache. | 16 March 2014, 12:16:04 UTC |
| fc00624 | Thomas Mooney | 15 March 2014, 21:38:32 UTC | Remove obsolete processing profile report that queries Oracle. | 15 March 2014, 21:38:32 UTC |
| 634c8f3 | Thomas Mooney | 15 March 2014, 21:31:56 UTC | Remove obsolete comments. | 15 March 2014, 21:31:56 UTC |
| 1478cc5 | Thomas Mooney | 15 March 2014, 21:19:37 UTC | Remove obsolete database query tools. These rely on the old Oracle tables and we don't store dbSNP data like this anymore. | 15 March 2014, 21:19:37 UTC |
| a4154e2 | APipe Tester | 15 March 2014, 12:17:30 UTC | Updated `gmt` tab completion. | 15 March 2014, 12:17:30 UTC |
| 4492a5d | APipe Tester | 15 March 2014, 12:16:50 UTC | Updated `genome` tab completion. | 15 March 2014, 12:16:50 UTC |
| 2d595ae | APipe Tester | 15 March 2014, 12:15:23 UTC | Updated class browser cache. | 15 March 2014, 12:15:23 UTC |
| fe08634 | Thomas Mooney | 15 March 2014, 04:49:15 UTC | Remove old "parallel command runner". | 15 March 2014, 04:49:15 UTC |
| a4d4436 | Thomas Mooney | 15 March 2014, 04:43:32 UTC | Remove broken/obsolete `gmt hmp-shotgun align-metagenomes`. | 15 March 2014, 04:43:32 UTC |
| 1c3315a | Thomas Mooney | 15 March 2014, 04:31:19 UTC | Remove outdated reference from error message. | 15 March 2014, 04:31:19 UTC |
| fdb5c73 | Thomas Mooney | 15 March 2014, 04:26:38 UTC | Remove obsolete and long-broken "SimpleAlignment" pipeline. Leave a hollow model class so existing instances can be instantiated. | 15 March 2014, 04:26:38 UTC |
| 7b89b47 | Nathaniel Nutter | 14 March 2014, 20:28:34 UTC | external updates hcc1395-somatic-wgs => hcc1395-somatic-wgs-old hcc1395-somatic-exome => hcc1395-somatic-exome-old added cancer_annotation_db | 14 March 2014, 20:30:23 UTC |
| ac11911 | APipe Tester | 14 March 2014, 20:25:03 UTC | updated jenkins submodule to 5422d4c | 14 March 2014, 20:25:03 UTC |
| 13b39d1 | Feiyu Du | 14 March 2014, 19:54:09 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 14 March 2014, 19:54:09 UTC |
| d02cc8f | Feiyu Du | 14 March 2014, 19:43:00 UTC | skip bamerror-rate run for bwa0.7.7 | 14 March 2014, 19:43:00 UTC |
| 770d5c7 | Eddie Belter | 14 March 2014, 19:30:13 UTC | GM: set dbsnp build during verify for start | 14 March 2014, 19:30:13 UTC |
| ff9186d | Eddie Belter | 14 March 2014, 19:29:39 UTC | GM: do not add instdata to builds, it should get copied | 14 March 2014, 19:29:39 UTC |
| 815baa4 | Eddie Belter | 14 March 2014, 17:37:38 UTC | GM: use build when running extract command | 14 March 2014, 17:54:39 UTC |
| 3956883 | Nathaniel Nutter | 14 March 2014, 17:01:32 UTC | remove debug messages that were producing very large log files These debug messages do not seem to provide much information and are called millions of times resulting in very large log files. | 14 March 2014, 17:01:32 UTC |
| 66b9bb3 | Malachi Griffith | 14 March 2014, 15:21:52 UTC | blessing new clin-seq build to account for recent improvements to mutation-diagram | 14 March 2014, 15:21:52 UTC |
| 96731be | APipe Tester | 14 March 2014, 12:17:59 UTC | Updated `gmt` tab completion. | 14 March 2014, 12:17:59 UTC |
| db40318 | APipe Tester | 14 March 2014, 12:17:18 UTC | Updated `genome` tab completion. | 14 March 2014, 12:17:18 UTC |
| 621ec55 | APipe Tester | 14 March 2014, 12:15:49 UTC | Updated class browser cache. | 14 March 2014, 12:15:49 UTC |
| 12405f0 | Thomas Mooney | 14 March 2014, 04:27:34 UTC | Remove obsolete `gmt snp filters dtr-see-five` which depended on `gmt maq`. | 14 March 2014, 04:27:34 UTC |
| fdf18c9 | Thomas Mooney | 14 March 2014, 04:26:01 UTC | Remove apologetic placeholder noting MAQ's removal. | 14 March 2014, 04:26:01 UTC |
| 1205d06 | Thomas Mooney | 14 March 2014, 04:23:42 UTC | Remove obsolete MAQ processing workflow. | 14 March 2014, 04:23:42 UTC |
| 3d7a022 | Thomas Mooney | 14 March 2014, 04:17:26 UTC | Remove obsolete maq-running functionality. | 14 March 2014, 04:17:26 UTC |
| 13be61b | Thomas Mooney | 14 March 2014, 04:07:55 UTC | Remove disused MAQ method. | 14 March 2014, 04:07:55 UTC |
| 425b0e8 | Thomas Mooney | 14 March 2014, 04:03:35 UTC | Remove obsolete `gmt ref-seq prepare` that refers to nonexistent MAQ command. | 14 March 2014, 04:03:35 UTC |
| abaefc9 | Thomas Mooney | 14 March 2014, 03:53:37 UTC | Remove old `gmt analysis limi-snps`. | 14 March 2014, 03:53:37 UTC |
| 1344261 | Thomas Mooney | 14 March 2014, 03:46:22 UTC | Remove old `gmt analysis illumina model-readcount-errors` command. | 14 March 2014, 03:46:58 UTC |
| 6438137 | Thomas Mooney | 14 March 2014, 03:40:40 UTC | Remove old `gmt analysis identity-by-descent find-regions` command. | 14 March 2014, 03:46:57 UTC |
| d657a7e | Dave Larson | 14 March 2014, 03:45:23 UTC | fix for positioning some subset of splice alterations | 14 March 2014, 03:45:23 UTC |
| adbafae | Thomas Mooney | 14 March 2014, 03:29:23 UTC | Remove root of empty `gmt analysis case-control` tree. Its child was removed in 50cd1701b469be57fe94e5d13d187e705583cfe9. | 14 March 2014, 03:29:23 UTC |
| 281c662 | Thomas Mooney | 14 March 2014, 03:13:48 UTC | Remove `genome model set-default` for deprecated is_default property. | 14 March 2014, 03:13:48 UTC |
| 972a9b9 | Thomas Mooney | 14 March 2014, 03:12:44 UTC | Remove obsolete `gmt analysis add-and-build` command. | 14 March 2014, 03:12:44 UTC |
| fe5f896 | Thomas Mooney | 14 March 2014, 02:47:56 UTC | Remove obsolete maq wrapper `gmt analysis xenograft get-mouse-aligned`. | 14 March 2014, 02:47:56 UTC |
| d399e39 | Thomas Mooney | 14 March 2014, 02:44:50 UTC | Remove old `gmt analysis hapmap extract-genotypes` command. Last used September 2010. | 14 March 2014, 02:44:50 UTC |
| 8ce13e6 | Eddie Belter | 14 March 2014, 00:29:01 UTC | GM: read unannotated csv creates vcf entry on the fly | 14 March 2014, 00:29:13 UTC |
| b7b2133 | Eddie Belter | 14 March 2014, 00:18:59 UTC | GM: remove unused use in write csv | 14 March 2014, 00:29:12 UTC |
| 1bfcb3d | Thomas Mooney | 13 March 2014, 23:18:38 UTC | Split singleton reads into separate BAMs before import. | 13 March 2014, 23:18:38 UTC |
| b149c4c | Adam Coffman | 13 March 2014, 22:51:44 UTC | hook up observers for apconfig event logging | 13 March 2014, 22:51:44 UTC |
| 989af61 | Adam Coffman | 13 March 2014, 22:06:59 UTC | add timeline event classes for apconfig | 13 March 2014, 22:06:59 UTC |
| d4df713 | Adam Coffman | 13 March 2014, 22:03:46 UTC | add migrations for ap config event logging | 13 March 2014, 22:03:46 UTC |
| fd25bb1 | Feiyu Du | 13 March 2014, 18:03:39 UTC | Add Bwa0.7.7 | 13 March 2014, 18:03:39 UTC |
| 4822868 | Thomas Mooney | 13 March 2014, 17:58:13 UTC | Remove old `gmt analysis solid unmapped-from-bam` command. | 13 March 2014, 17:58:13 UTC |
| dc6369d | Eddie Belter | 13 March 2014, 17:10:24 UTC | GM: rm skip indel warning msg | 13 March 2014, 17:10:39 UTC |
| 5778e1d | dmorton | 13 March 2014, 16:59:49 UTC | Add command to assist with creating batches of somatic-variation models | 13 March 2014, 17:01:05 UTC |
| 4875247 | Thomas Mooney | 13 March 2014, 15:59:29 UTC | Remove tests for removed VM site modules. | 13 March 2014, 15:59:29 UTC |
| 4281ee7 | Thomas Mooney | 13 March 2014, 15:56:41 UTC | Remove obsolete VM site modules. | 13 March 2014, 15:56:41 UTC |
| 2cc9399 | Thomas Mooney | 13 March 2014, 15:46:43 UTC | Remove old summary command that references disused database table. | 13 March 2014, 15:46:43 UTC |
| 48b6340 | Thomas Mooney | 13 March 2014, 15:41:23 UTC | Remove parent command now that subcommands no longer exist. | 13 March 2014, 15:41:23 UTC |
| bcde6f1 | Thomas Mooney | 13 March 2014, 15:40:03 UTC | Remove old `gmt analysis solexa variant-contigs` command. | 13 March 2014, 15:40:03 UTC |
| 15918cd | Thomas Mooney | 13 March 2014, 15:38:42 UTC | Remove old command that ran novoalign from a home directory. | 13 March 2014, 15:38:42 UTC |
| faa350f | Thomas Mooney | 13 March 2014, 15:37:34 UTC | Remove disused `gmt analysis solexa unmapped-from-bam` command. | 13 March 2014, 15:37:34 UTC |
| 8bb4495 | Thomas Mooney | 13 March 2014, 15:31:06 UTC | Remove `gmt analysis solexa split-reads` that references disused table. | 13 March 2014, 15:31:06 UTC |
| cf6fdb7 | Thomas Mooney | 13 March 2014, 15:30:03 UTC | Remove `gmt analysis solexa search-runs` that references disused table. | 13 March 2014, 15:30:03 UTC |
| 661f131 | Thomas Mooney | 13 March 2014, 15:27:52 UTC | Remove `gmt analysis solexa process-alignments` that references disused table. | 13 March 2014, 15:27:52 UTC |
| dd4290f | Thomas Mooney | 13 March 2014, 15:24:53 UTC | Remove old command that references disused DB table. | 13 March 2014, 15:24:53 UTC |
| 50c43ae | Thomas Mooney | 13 March 2014, 15:20:15 UTC | Remove old `gmt analysis solexa indel-contigs` command. | 13 March 2014, 15:20:15 UTC |
| 91a9ca2 | Thomas Mooney | 13 March 2014, 15:17:41 UTC | Remove old lister wrapper `gmt analysis solexa find-models` | 13 March 2014, 15:17:41 UTC |
| b9c5ebc | Thomas Mooney | 13 March 2014, 15:14:21 UTC | Remove disused command `gmt analysis solexa contig-results` | 13 March 2014, 15:14:21 UTC |
| e9be1ef | Thomas Mooney | 13 March 2014, 15:09:26 UTC | Remove old `gmt analysis solexa bam-to-fastq`. Other remaining commands to do this include: gmt sam bam-to-fastq gmt picard sam-to-fastq | 13 March 2014, 15:09:26 UTC |
| 29ad63d | Thomas Mooney | 13 March 2014, 15:04:19 UTC | Removed disused command `gmt analysis solexa align-reads`. | 13 March 2014, 15:04:19 UTC |
| 028c5ea | Thomas Mooney | 13 March 2014, 15:00:24 UTC | Remove broken and disused `gmt analysis solexa build-models` command. | 13 March 2014, 15:00:24 UTC |
| f504b12 | Thomas Mooney | 13 March 2014, 14:25:16 UTC | Update textual references to assign commands to use new subcommands. | 13 March 2014, 14:25:16 UTC |
| 19ab23c | Thomas Mooney | 12 March 2014, 21:23:13 UTC | CQID now only assigns data from a matching analysis project. CHANGELOG: Automatically generated models for Analysis Projects will only assign instrument data belonging to those Analysis Projects. | 13 March 2014, 13:32:40 UTC |
| 84bd450 | Thomas Mooney | 13 March 2014, 13:27:30 UTC | New model instrument-data assign command for Analysis Projects. | 13 March 2014, 13:32:39 UTC |
| a6d5b54 | APipe Tester | 13 March 2014, 12:17:38 UTC | Updated `genome` tab completion. | 13 March 2014, 12:17:38 UTC |
| d6dec17 | APipe Tester | 13 March 2014, 12:15:47 UTC | Updated class browser cache. | 13 March 2014, 12:15:47 UTC |
