| b4fa242 | Nathaniel Nutter | 16 June 2014, 20:42:09 UTC | restore space between options and values Options and values were squished together because it made it easier to secure now-deprecated 'run_as' behavior and because it appeared to work. However, if a user's email started with a lowercase 'L' then the '-u' option would get interpreted as an '-ul' option and fail. | 16 June 2014, 20:42:09 UTC |
| f0256c4 | Thomas Mooney | 16 June 2014, 19:25:47 UTC | Don't assume the genotype file is in the top-level of the allocation. | 16 June 2014, 19:25:47 UTC |
| d1915cb | APipe Tester | 16 June 2014, 18:41:47 UTC | updated ur submodule to 1bbd8d9 | 16 June 2014, 19:14:19 UTC |
| 776da49 | Malachi Griffith | 16 June 2014, 19:01:54 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 16 June 2014, 19:01:54 UTC |
| cc889f7 | Malachi Griffith | 16 June 2014, 19:01:45 UTC | add timeline plots to snv-indel-reports | 16 June 2014, 19:01:45 UTC |
| 9076fd2 | Mark Burnett | 16 June 2014, 15:33:24 UTC | build view: display associated analysis projects | 16 June 2014, 15:35:50 UTC |
| d3a1649 | Mark Burnett | 16 June 2014, 15:32:58 UTC | don't right-pad "Build" heading | 16 June 2014, 15:35:49 UTC |
| d603f1c | Thomas Mooney | 16 June 2014, 15:19:30 UTC | Delete needs to cascade to mappings containing that subject. | 16 June 2014, 15:26:11 UTC |
| aac6387 | apregier | 13 June 2014, 21:11:21 UTC | Merge branch 'updated' into gb_master | 13 June 2014, 21:11:21 UTC |
| be950f7 | apregier | 13 June 2014, 21:07:48 UTC | Make sure contains-tag filter dies if info tag is not in the vcf | 13 June 2014, 21:08:18 UTC |
| 1373ad5 | Gabriel Sanderson | 13 June 2014, 19:26:33 UTC | __errors__ checks that no unavailable_headers are actually provided. Clean up if blocks. | 13 June 2014, 19:26:33 UTC |
| 5246037 | Gabriel Sanderson | 13 June 2014, 19:01:57 UTC | Added a report for annotation-format. The report has many missing columns for now that we can hopefully flesh out a bit. | 13 June 2014, 19:05:22 UTC |
| 5b454f3 | Gabriel Sanderson | 13 June 2014, 18:55:54 UTC | Allow for known unavailable_headers - print null chracters | 13 June 2014, 18:55:54 UTC |
| e11c8ee | Eddie Belter | 12 June 2014, 21:18:35 UTC | Build: remove ignored metrics from both metrics hashes | 13 June 2014, 16:39:56 UTC |
| d4e711b | apregier | 13 June 2014, 16:03:52 UTC | Merge branch 'updated' into gb_master | 13 June 2014, 16:03:52 UTC |
| 7e63e0d | apregier | 13 June 2014, 16:00:16 UTC | Switch to debug message | 13 June 2014, 16:00:16 UTC |
| c1bd741 | apregier | 13 June 2014, 15:45:14 UTC | Merge branch 'updated' into gb_master | 13 June 2014, 15:45:14 UTC |
| 767a9ce | apregier | 13 June 2014, 15:42:48 UTC | Remove breakpoint | 13 June 2014, 15:43:13 UTC |
| bd9db8d | Chris Miller | 13 June 2014, 14:49:05 UTC | got the logic backwards - low pvalues should be removed | 13 June 2014, 14:49:13 UTC |
| c5b9db0 | APipe Tester | 13 June 2014, 12:18:09 UTC | Updated `gmt` tab completion. | 13 June 2014, 12:18:09 UTC |
| a9891ba | APipe Tester | 13 June 2014, 12:17:26 UTC | Updated `genome` tab completion. | 13 June 2014, 12:17:26 UTC |
| e9218f0 | APipe Tester | 13 June 2014, 12:15:55 UTC | Updated class browser cache. | 13 June 2014, 12:15:55 UTC |
| f002008 | Chris Miller | 12 June 2014, 22:19:24 UTC | Pushing tool to remove contaminating reads from variant files | 12 June 2014, 22:19:24 UTC |
| a95cd89 | Chris Miller | 12 June 2014, 18:20:09 UTC | handle headers on cn files | 12 June 2014, 22:18:18 UTC |
| d8b5dca | apregier | 12 June 2014, 21:31:45 UTC | Merge branch 'updated' into gb_master | 12 June 2014, 21:31:45 UTC |
| 83a8187 | apregier | 12 June 2014, 21:28:29 UTC | Add integration test for custom feature list annotations in vep | 12 June 2014, 21:28:29 UTC |
| 1a3fd52 | apregier | 12 June 2014, 21:25:51 UTC | Require ReferenceSequence rather than ImportedReferenceSequence | 12 June 2014, 21:25:51 UTC |
| fa7d940 | apregier | 12 June 2014, 21:22:16 UTC | Replace file path in vep custom annotation descriptions with the feature list name | 12 June 2014, 21:22:16 UTC |
| 8c77486 | Gabriel Sanderson | 12 June 2014, 19:52:49 UTC | Added a command to create and add a feature list to a refbuild. | 12 June 2014, 19:53:29 UTC |
| 2dbc39e | Gabriel Sanderson | 12 June 2014, 19:33:28 UTC | Cleaned up is_superset_of | 12 June 2014, 19:53:29 UTC |
| 2ffa0d7 | Gabriel Sanderson | 12 June 2014, 18:53:57 UTC | Added methods for getting segdups and self_chain to builds. | 12 June 2014, 19:53:28 UTC |
| dffe991 | Gabriel Sanderson | 11 June 2014, 23:00:35 UTC | RefSeq builds can now get feature lists from ancestors. Add segmental_duplications and self_chain inputs. | 12 June 2014, 19:53:27 UTC |
| 1652d84 | Gabriel Sanderson | 11 June 2014, 21:45:00 UTC | added is_superset_of to determine if reference builds are chromosome-wise supersets | 12 June 2014, 19:53:27 UTC |
| 7a7ce6c | Gabriel Sanderson | 11 June 2014, 21:19:48 UTC | Add chromosome_list method | 12 June 2014, 19:53:26 UTC |
| a126729 | Nathaniel Nutter | 10 June 2014, 22:20:29 UTC | remove debugger option | 12 June 2014, 19:43:11 UTC |
| af24c71 | Nathaniel Nutter | 11 June 2014, 22:43:31 UTC | order allocation timeline_events by created_at | 12 June 2014, 19:31:40 UTC |
| baab519 | Eddie Belter | 12 June 2014, 16:48:49 UTC | Rename custom regex differ in MC16s and DeNovo Assembly | 12 June 2014, 16:48:59 UTC |
| 999700a | Thomas Mooney | 12 June 2014, 15:26:26 UTC | Add primary key on child timline tables. | 12 June 2014, 15:26:26 UTC |
| 18e7746 | APipe Tester | 11 June 2014, 22:19:31 UTC | updated jenkins submodule to 829aa91 | 11 June 2014, 23:17:34 UTC |
| 51b07b6 | Nathaniel Nutter | 10 June 2014, 21:11:14 UTC | add test for touch and fix atime/mtime not being updated | 11 June 2014, 22:35:04 UTC |
| f30d8b6 | Nathaniel Nutter | 10 June 2014, 20:55:00 UTC | convert touch and rename to class/package methods instead of functions | 11 June 2014, 22:35:02 UTC |
| e71d0e1 | Nathaniel Nutter | 10 June 2014, 20:23:17 UTC | add Genome::Sys::rename CORE::rename preserves permissions, uid, and gid even though we might not want to. GNU 'cp' does not, by default, preserve these attributes but also causes more IO. Genome::Sys::rename is meant to be an alternative to CORE::rename that does not preserve these attributes. | 11 June 2014, 22:35:01 UTC |
| a3eecab | Nathaniel Nutter | 10 June 2014, 20:22:41 UTC | add Genome::Sys::touch | 11 June 2014, 22:35:00 UTC |
| ac241ac | Feiyu Du | 11 June 2014, 18:21:13 UTC | bug fix to copy tabix index over to build dir | 11 June 2014, 18:21:13 UTC |
| dc981b4 | Adam Coffman | 11 June 2014, 15:11:23 UTC | bless clinseq build with dgidb source update | 11 June 2014, 15:11:23 UTC |
| 62652c2 | apregier | 10 June 2014, 21:59:27 UTC | Merge branch 'updated' into gb_master | 10 June 2014, 21:59:27 UTC |
| f27feb3 | apregier | 10 June 2014, 21:51:20 UTC | Add Damaging sift/polyphen filter | 10 June 2014, 21:51:20 UTC |
| 9f64707 | apregier | 10 June 2014, 17:51:55 UTC | Merge branch 'updated' into gb_master | 10 June 2014, 17:51:55 UTC |
| 245f7c6 | apregier | 10 June 2014, 17:30:22 UTC | Interpreter also provides sift,polyphen, and condel | 10 June 2014, 17:39:01 UTC |
| 25f5323 | apregier | 10 June 2014, 17:29:45 UTC | Change function name to reflect return value | 10 June 2014, 17:39:00 UTC |
| c9f0f1e | Thomas Mooney | 10 June 2014, 15:27:38 UTC | New command to monitor library and sample renames. | 10 June 2014, 15:27:38 UTC |
| a19b475 | Thomas Mooney | 10 June 2014, 13:30:27 UTC | Remove extra ":" in doc text. | 10 June 2014, 13:30:27 UTC |
| 2fa85dd | APipe Tester | 10 June 2014, 12:19:00 UTC | Updated `gmt` tab completion. | 10 June 2014, 12:19:00 UTC |
| b5c8642 | APipe Tester | 10 June 2014, 12:18:14 UTC | Updated `genome` tab completion. | 10 June 2014, 12:18:14 UTC |
| e47e0be | Avinash Ramu | 10 June 2014, 02:20:31 UTC | update clinseq-blessed This build has changes to DGIdb. An additional source is being added. | 10 June 2014, 02:20:31 UTC |
| e3b4a0d | Avinash Ramu | 09 June 2014, 20:36:42 UTC | update CNV plotting and ROC metrics | 10 June 2014, 02:18:14 UTC |
| 35c24eb | Avinash Ramu | 08 June 2014, 05:58:39 UTC | update stats plot | 10 June 2014, 02:18:13 UTC |
| c037747 | Avinash Ramu | 05 June 2014, 19:53:56 UTC | add tool for plotting clinseq stats | 10 June 2014, 02:18:13 UTC |
| e3a6f05 | Eddie Belter | 09 June 2014, 22:49:27 UTC | Sample import: sort sample/ind attr names | 09 June 2014, 22:49:49 UTC |
| c77a9d3 | Eddie Belter | 09 June 2014, 22:40:01 UTC | Sample Import: allow more EMBL-EBI names | 09 June 2014, 22:49:48 UTC |
| e691c30 | Eddie Belter | 09 June 2014, 22:39:11 UTC | Sample Import: add is_optioonal to calculated importer properties to avoid command errors | 09 June 2014, 22:49:48 UTC |
| eb1d723 | Eddie Belter | 09 June 2014, 21:24:23 UTC | Sample Import: cleanup getting property meta from entity | 09 June 2014, 22:49:47 UTC |
| af5512d | Eddie Belter | 09 June 2014, 18:54:21 UTC | Sample import: rm unused storing of properties | 09 June 2014, 22:49:46 UTC |
| c833dc4 | Eddie Belter | 06 June 2014, 22:08:45 UTC | Sample import test update | 09 June 2014, 22:49:45 UTC |
| 9305f1c | Dave Larson | 09 June 2014, 21:44:16 UTC | remove readlength error message as it is no longer needed. Also add error message if an alignment result is missing. | 09 June 2014, 21:44:35 UTC |
| aa23dea | Avinash Ramu | 09 June 2014, 21:01:09 UTC | update clinseq blessed | 09 June 2014, 21:06:40 UTC |
| 3001cce | Avinash Ramu | 09 June 2014, 21:00:05 UTC | update tests | 09 June 2014, 21:06:40 UTC |
| 3fabb48 | Avinash Ramu | 08 June 2014, 06:00:15 UTC | skip LIMS reports for now | 09 June 2014, 21:06:39 UTC |
| 10b0ee6 | APipe Tester | 09 June 2014, 15:32:06 UTC | updated jenkins submodule to da389bf | 09 June 2014, 15:32:06 UTC |
| 8091f3a | Nathaniel Nutter | 05 June 2014, 21:55:28 UTC | remove 'other' permission bits This is only a half-measure to reflect the new policy that 'other' shouldn't have access to Genome or its output. | 06 June 2014, 19:58:43 UTC |
| 7f922fa | Nathaniel Nutter | 05 June 2014, 21:37:04 UTC | remove set_file_permissions and set_directory_permissions Remove set_file_permissions and set_directory_permissions to be replaced with 'mode' and File::Find::Rule. | 06 June 2014, 19:58:39 UTC |
| 39ea406 | Nathaniel Nutter | 05 June 2014, 21:33:15 UTC | remove unused function | 06 June 2014, 19:58:38 UTC |
| d8387a2 | Gabriel Sanderson | 06 June 2014, 18:49:47 UTC | Updated tier 1 consequence types per cmiller. | 06 June 2014, 18:50:52 UTC |
| d18c6c7 | Yevgeniy Gindin | 06 June 2014, 15:43:51 UTC | Added more tests | 06 June 2014, 15:43:51 UTC |
| e7eda0a | APipe Tester | 06 June 2014, 12:17:55 UTC | Updated `gmt` tab completion. | 06 June 2014, 12:17:55 UTC |
| 9b5f6f7 | APipe Tester | 06 June 2014, 12:17:13 UTC | Updated `genome` tab completion. | 06 June 2014, 12:17:13 UTC |
| cb04235 | APipe Tester | 06 June 2014, 12:15:36 UTC | Updated class browser cache. | 06 June 2014, 12:15:36 UTC |
| 4ba0997 | Avinash Ramu | 06 June 2014, 05:08:33 UTC | Rename file in diff-ignore as well. | 06 June 2014, 05:08:33 UTC |
| 7612b75 | Avinash Ramu | 05 June 2014, 21:47:41 UTC | rename summarize-builds | 05 June 2014, 21:48:48 UTC |
| 557d79c | ygindin | 05 June 2014, 21:38:21 UTC | fixed mis-placed use statement | 05 June 2014, 21:38:21 UTC |
| 8728152 | ygindin | 05 June 2014, 21:21:11 UTC | small change | 05 June 2014, 21:21:11 UTC |
| 7a545b4 | ygindin | 05 June 2014, 21:18:02 UTC | Added ProcessManualReview | 05 June 2014, 21:18:02 UTC |
| 12d6dc2 | Gabriel Sanderson | 05 June 2014, 21:02:23 UTC | Added Tier 1 filter and related test. The tier 1 consequence types list needs to be updated, this is just a handful of valid types so far. | 05 June 2014, 21:03:30 UTC |
| 86ecfbb | Nathaniel Nutter | 05 June 2014, 20:35:37 UTC | remove write instead of setting absolute permissions Setting absolute permissions is often not the correct thing to do because it doesn't account for other bits the file/directory might have, e.g. setgid, or executable. So, for example, instead of setting thing readonly by doing `chmod 444` one could instead do `chmod a-w`. | 05 June 2014, 20:41:00 UTC |
| 775c235 | Nathaniel Nutter | 05 June 2014, 18:54:50 UTC | remove commented out code | 05 June 2014, 20:40:58 UTC |
| 5574852 | Nathaniel Nutter | 04 June 2014, 21:05:25 UTC | fix importing a function into base_class causing result class to break This is super weird. Why would a parent class override a subclass? I hope it's safe to limit this behavior to just properties. Importing 'mode' into Genome::SoftwareResult::Stageable broke Genome::Model::Tools::Htseq::Count because that class has a property named 'mode'. | 05 June 2014, 20:40:57 UTC |
| 8254768 | Nathaniel Nutter | 03 June 2014, 22:27:50 UTC | switch from glob to File::Find::Rule | 05 June 2014, 20:40:56 UTC |
| 7e366ab | Nathaniel Nutter | 03 June 2014, 22:15:51 UTC | include path in error message | 05 June 2014, 20:40:55 UTC |
| 0c587bd | Nathaniel Nutter | 03 June 2014, 21:22:01 UTC | remove write instead of setting absolute permissions | 05 June 2014, 20:40:54 UTC |
| 8eb8b24 | Nathaniel Nutter | 03 June 2014, 21:18:26 UTC | remove write instead of setting absolute permissions | 05 June 2014, 20:40:53 UTC |
| 4dc7b43 | Nathaniel Nutter | 03 June 2014, 21:17:34 UTC | remove write instead of setting absolute permissions | 05 June 2014, 20:40:52 UTC |
| 0785c43 | Nathaniel Nutter | 03 June 2014, 21:14:34 UTC | remove write instead of setting absolute permissions | 05 June 2014, 20:40:51 UTC |
| 4ea3c1a | Nathaniel Nutter | 03 June 2014, 21:13:14 UTC | remove write instead of setting absolute permissions | 05 June 2014, 20:40:50 UTC |
| 2074625 | Nathaniel Nutter | 03 June 2014, 21:12:16 UTC | remove write instead of setting absolute permissions | 05 June 2014, 20:40:49 UTC |
| 91a0613 | ygindin | 05 June 2014, 16:03:07 UTC | Fixed relative paths issue | 05 June 2014, 16:03:07 UTC |
| 648d2f1 | apregier | 05 June 2014, 15:08:09 UTC | Merge branch 'updated' into gb_master | 05 June 2014, 15:08:09 UTC |
| 50cec18 | apregier | 04 June 2014, 22:09:45 UTC | Use class method instead of object method | 05 June 2014, 15:06:56 UTC |
| dab295c | apregier | 04 June 2014, 22:09:21 UTC | Use class method instead of object method | 05 June 2014, 15:06:56 UTC |
| 82c61a1 | apregier | 04 June 2014, 22:08:46 UTC | Add class method to get sample_name_in_vcf | 05 June 2014, 15:06:55 UTC |
| fac9c68 | apregier | 03 June 2014, 19:21:00 UTC | Use sample->name_in_vcf | 05 June 2014, 15:06:54 UTC |
