| 4c01660 | Eddie Belter | 07 August 2015, 21:10:04 UTC | Merge pull request #920 from ebelter/recreate-per-lane-bam Recreate Per Lane Bam: function name typo | 07 August 2015, 21:10:04 UTC |
| 7bcc878 | Eddie Belter | 07 August 2015, 19:15:53 UTC | Recreate Per Lane Bam: function name typo | 07 August 2015, 19:15:53 UTC |
| 5f1c4ce | Adam Coffman | 07 August 2015, 14:36:55 UTC | Merge pull request #913 from acoffman/remove_file_summary_creation Remove FileSummary creation when allocations are purged | 07 August 2015, 14:36:55 UTC |
| 635cf1c | APipe Tester | 07 August 2015, 12:19:44 UTC | Updated `gmt` tab completion. | 07 August 2015, 12:19:44 UTC |
| f32bd05 | APipe Tester | 07 August 2015, 12:18:53 UTC | Updated `genome` tab completion. | 07 August 2015, 12:18:53 UTC |
| 6313d4f | Avinash Ramu | 06 August 2015, 21:43:27 UTC | Merge pull request #916 from gatoravi/add_CRC_to_clinseq_update_analysis Add CRC as a valid tumor common-name | 06 August 2015, 21:43:27 UTC |
| bde6164 | Avinash Ramu | 06 August 2015, 20:00:44 UTC | Add CRC as a valid tumor common-name | 06 August 2015, 20:00:44 UTC |
| b69232e | Chris Miller | 06 August 2015, 18:54:01 UTC | Merge pull request #911 from chrisamiller/concordance adding example file, changing 'reference-genome' param to 'reference-fasta', | 06 August 2015, 18:54:01 UTC |
| b329f94 | Adam Coffman | 06 August 2015, 16:42:45 UTC | Remove FileSummary creation when allocations are purged | 06 August 2015, 17:26:42 UTC |
| cfaf2ed | Thomas B. Mooney | 06 August 2015, 13:32:15 UTC | Merge pull request #907 from tmooney/sr_users_save_hash Save a copy of the users hash. | 06 August 2015, 13:32:15 UTC |
| b21d2f3 | APipe Tester | 06 August 2015, 12:18:18 UTC | Updated `genome` tab completion. | 06 August 2015, 12:18:18 UTC |
| 8c52658 | Chris Miller | 06 August 2015, 01:47:39 UTC | changing reference param suitable | 06 August 2015, 01:47:39 UTC |
| b1c3376 | Chris Miller | 06 August 2015, 01:12:01 UTC | adding example file, changing 'reference-genome' param to 'reference-fasta', and cleaning up extraneous comments | 06 August 2015, 01:12:01 UTC |
| 7ce64c4 | Thomas B. Mooney | 05 August 2015, 22:43:04 UTC | Merge pull request #894 from tmooney/allow_perl_access_to_model_summary Allow Programmatic Access to ModelSummary information | 05 August 2015, 22:43:04 UTC |
| 9039bf6 | Allison Penner Regier | 05 August 2015, 20:03:13 UTC | Merge pull request #908 from apregier/add_cle_test2 Add cle test2 | 05 August 2015, 20:03:13 UTC |
| 4307858 | apregier | 05 August 2015, 18:58:17 UTC | Simplify | 05 August 2015, 18:58:17 UTC |
| 31d7636 | apregier | 05 August 2015, 18:54:38 UTC | Use yaml block literal Makes it easier to read, and found a missing \n | 05 August 2015, 18:54:38 UTC |
| a4f871b | Eddie Belter | 05 August 2015, 18:31:36 UTC | Merge pull request #903 from ebelter/gm-rm-instrument-type Genotype Microarray: Remove instrument type param | 05 August 2015, 18:31:36 UTC |
| a200f39 | apregier | 05 August 2015, 18:24:21 UTC | Add cle test config | 05 August 2015, 18:24:21 UTC |
| 024f387 | apregier | 03 August 2015, 18:22:36 UTC | Add has_diffs convenience method | 05 August 2015, 17:56:25 UTC |
| ba6ef84 | Thomas B. Mooney | 05 August 2015, 14:59:47 UTC | Merge pull request #905 from tmooney/existance A Great Vowel Shift | 05 August 2015, 14:59:47 UTC |
| 3fc5e15 | Thomas Mooney | 05 August 2015, 14:46:11 UTC | Save a copy of the users hash. This fixes a bug where someone else with the reference was manipulating the hash between passing it and us using it, making our users disappear. | 05 August 2015, 14:47:59 UTC |
| 4993382 | APipe Tester | 05 August 2015, 12:18:35 UTC | Updated `genome` tab completion. | 05 August 2015, 12:18:35 UTC |
| a69ae17 | APipe Tester | 05 August 2015, 12:16:47 UTC | Updated class browser cache. | 05 August 2015, 12:16:47 UTC |
| 2440afb | Thomas B. Mooney | 04 August 2015, 20:15:39 UTC | Merge pull request #902 from tmooney/handle_inactive_status_in_purge Account for the existence of other non-disabled statuses. | 04 August 2015, 20:15:39 UTC |
| 481d8ff | Thomas B. Mooney | 04 August 2015, 19:33:50 UTC | Merge pull request #900 from tmooney/only_disconnect_if_waiting_on_lock Don't disconnect if we're not going to wait on the lock. | 04 August 2015, 19:33:50 UTC |
| 30370d1 | Thomas Mooney | 04 August 2015, 19:03:00 UTC | Remove a c. | 04 August 2015, 19:03:00 UTC |
| a8ef952 | Thomas Mooney | 04 August 2015, 19:01:00 UTC | Anglicize "existance" to "existence". | 04 August 2015, 19:01:00 UTC |
| 433e762 | Eddie Belter | 04 August 2015, 17:55:08 UTC | Merge pull request #899 from ebelter/picard-versions Picard | 04 August 2015, 17:55:08 UTC |
| 1099c65 | Eddie Belter | 04 August 2015, 17:54:55 UTC | Merge pull request #898 from ebelter/test-doc Utility Test data_dir: add doc, use validate_pos | 04 August 2015, 17:54:55 UTC |
| 0b671eb | Indraniel | 04 August 2015, 13:38:25 UTC | Merge pull request #876 from indraniel/CLE-BIO-1491-addons CLE "variant-reporting wrappers gold-evaluation" addons - add fixes to the 'GoldEvaluation' variant reporting wrapper - introduce tests for both the 'GoldEvaluation' and 'ModelReport' variant reporting wrappers - introduce an abstract base class 'Utils' for common logic to all variant reports | 04 August 2015, 13:38:25 UTC |
| 7106cf1 | Eddie Belter | 03 August 2015, 22:02:33 UTC | Genotype Microarray: Remove instrument type param | 03 August 2015, 22:02:33 UTC |
| 1621125 | Thomas B. Mooney | 03 August 2015, 21:01:08 UTC | Merge pull request #896 from tmooney/indices_set_archivable_false Primary References and Indices Default to Not Archivable | 03 August 2015, 21:01:08 UTC |
| b96e431 | Thomas Mooney | 03 August 2015, 20:06:15 UTC | Account for the existences of other non-disabled statuses. | 03 August 2015, 20:06:15 UTC |
| bbf3093 | Indraniel Das | 03 August 2015, 19:32:45 UTC | + aregier's 2nd recommendation - refactoring 'get_library_name_labels'. Putting a method common across all three report types into a new abstract base class. - Once the UR Roles (https://github.com/genome/UR/pull/63) are released, the base class (Genome::VariantReporting::Command::Wrappers::Utils) can be converted into a proper role. | 03 August 2015, 19:32:45 UTC |
| e3f9c4c | Indraniel Das | 03 August 2015, 19:05:22 UTC | + add a test for the ModelReport module | 03 August 2015, 19:05:22 UTC |
| acfd7f4 | Indraniel Das | 03 August 2015, 19:04:37 UTC | + apply aregier's first suggestion - remove unneeded 'get_common_translations' method | 03 August 2015, 19:04:37 UTC |
| 9bc8f03 | Eddie Belter | 03 August 2015, 18:47:43 UTC | Utility Test: spell check | 03 August 2015, 18:47:43 UTC |
| fbe4599 | Eddie Belter | 03 August 2015, 18:46:07 UTC | Picard: spellcheck | 03 August 2015, 18:46:07 UTC |
| 683652a | Thomas Mooney | 03 August 2015, 18:20:38 UTC | Don't disconnect if we're not going to wait on the lock. | 03 August 2015, 18:20:38 UTC |
| 029abd6 | Thomas B. Mooney | 03 August 2015, 15:36:22 UTC | Merge pull request #891 from tmooney/tolerate_unused_annotation_input Only schedule annotation if we have variants to annotate. | 03 August 2015, 15:36:22 UTC |
| 1c9330c | Thomas Mooney | 30 July 2015, 20:11:10 UTC | Prevent archiving of basic data. Typically these allocations are too small to archive, anyway! | 03 August 2015, 15:30:22 UTC |
| 2bb803e | Thomas Mooney | 30 July 2015, 19:56:00 UTC | Don't allow archiving of main indices. (Indices for "rederivable" references are not widely used and so can generally still be archived.) | 03 August 2015, 15:30:22 UTC |
| ce51605 | Allison Penner Regier | 03 August 2015, 15:20:10 UTC | Merge pull request #897 from apregier/build_diff_change Don't require builds to be from the same model to diff | 03 August 2015, 15:20:10 UTC |
| 7bb901c | Eddie Belter | 31 July 2015, 23:16:40 UTC | RefAlign GC: use Picard GC versions as valid values | 31 July 2015, 23:16:40 UTC |
| 9cd1bd9 | Eddie Belter | 31 July 2015, 23:06:05 UTC | Picard: restrict by min version when returning available versions | 31 July 2015, 23:15:09 UTC |
| 43a7eee | Eddie Belter | 29 July 2015, 01:24:28 UTC | Picard: add test names to GC | 31 July 2015, 23:15:08 UTC |
| 2ed91ac | Eddie Belter | 29 July 2015, 01:21:23 UTC | Picard: remove unused ignore_state function from genotype concordance | 31 July 2015, 23:15:07 UTC |
| da5d610 | Eddie Belter | 29 July 2015, 01:19:56 UTC | Picard: make genotype concordance inherit from base | 31 July 2015, 23:15:06 UTC |
| 52473d4 | Eddie Belter | 29 July 2015, 01:07:12 UTC | Picard: have enforce min version use version set on class and verify during execute | 31 July 2015, 23:15:06 UTC |
| 7550f72 | Eddie Belter | 28 July 2015, 22:23:03 UTC | Picard: add minimum_version_required method | 31 July 2015, 23:15:04 UTC |
| e98239b | Eddie Belter | 31 July 2015, 22:18:14 UTC | Utility Test: use validate_pos for data_dir | 31 July 2015, 22:22:53 UTC |
| d00a4bb | Eddie Belter | 31 July 2015, 22:17:15 UTC | Utility Test: add data_dir perldoc | 31 July 2015, 22:17:47 UTC |
| 8291dee | apregier | 31 July 2015, 17:10:57 UTC | Don't require builds to be from the same model to diff We have a use case for CLE regression testing where we are making new models in a testdb and want to diff the resulting builds with builds from old models. They should be equivalent, but not the same model. I don't see any reason why this check adds to the integrity of the diff | 31 July 2015, 17:13:27 UTC |
| f941263 | Thomas B. Mooney | 30 July 2015, 18:50:54 UTC | Merge pull request #893 from tmooney/somvar_loh_requires_normal_snv_detection Don't try to run LOH without a normal to compare to. | 30 July 2015, 18:50:54 UTC |
| 21ac56c | APipe Tester | 30 July 2015, 12:19:39 UTC | Updated `gmt` tab completion. | 30 July 2015, 12:19:39 UTC |
| f9d4e66 | APipe Tester | 30 July 2015, 12:18:46 UTC | Updated `genome` tab completion. | 30 July 2015, 12:18:46 UTC |
| 27025fe | Eddie Belter | 29 July 2015, 20:46:15 UTC | Merge pull request #886 from ebelter/gm-cc GM Concordance | 29 July 2015, 20:46:15 UTC |
| 0b16aac | Thomas Mooney | 29 July 2015, 18:53:02 UTC | Temporary fix: Load Set type before creating Pool to prevent crash. | 29 July 2015, 18:53:34 UTC |
| 16af5b7 | Thomas Mooney | 29 July 2015, 18:52:46 UTC | Pull in build status determination. | 29 July 2015, 18:52:46 UTC |
| 451b0b5 | Thomas Mooney | 29 July 2015, 18:15:33 UTC | Use an AutoUnloadPool instead of unloading in batches. | 29 July 2015, 18:15:33 UTC |
| c8e9b49 | Thomas Mooney | 29 July 2015, 17:46:47 UTC | Extract a subroutine to generate the model summary. That way we can all generate_model_summary() directly in Perl to get a hash of the data for other use. | 29 July 2015, 17:52:34 UTC |
| cc80ae5 | Thomas Mooney | 29 July 2015, 17:01:19 UTC | Check the model instead of the build. (Some build types don't provide direct access to the PP params.) | 29 July 2015, 17:48:41 UTC |
| d0f386d | Thomas Mooney | 29 July 2015, 17:28:53 UTC | Stop truncating model names. We don't customarily include the PP name in the model name any more, so if it is there it is more useful to know. | 29 July 2015, 17:28:53 UTC |
| 18fdd06 | Thomas Mooney | 29 July 2015, 17:22:47 UTC | Only create closures if we plan to use them. * One is only used one place now, so extract the contents. | 29 July 2015, 17:22:47 UTC |
| 327aaca | Thomas Mooney | 29 July 2015, 17:12:06 UTC | Consolidate actions. | 29 July 2015, 17:12:06 UTC |
| b857579 | Thomas B. Mooney | 29 July 2015, 15:34:21 UTC | Merge pull request #880 from tmooney/dump_flagstats_on_error Dump flagstat data when comparison fails. | 29 July 2015, 15:34:21 UTC |
| b46679b | Thomas B. Mooney | 29 July 2015, 15:33:54 UTC | Merge pull request #892 from tmooney/cleanup_sync_sys_user_with_ldap LDAP Synch: Fix counting bug and cleanup | 29 July 2015, 15:33:54 UTC |
| b6cb0e5 | Allison Penner Regier | 29 July 2015, 15:32:37 UTC | Merge pull request #887 from apregier/bedpe Add the ability to specify a minimum number of hits required | 29 July 2015, 15:32:37 UTC |
| 52ca980 | Thomas Mooney | 29 July 2015, 13:43:38 UTC | Don't try to run LOH without a normal to compare to. | 29 July 2015, 14:14:59 UTC |
| cf0c7b8 | APipe Tester | 29 July 2015, 12:19:21 UTC | Updated `genome` tab completion. | 29 July 2015, 12:19:21 UTC |
| e18cb9a | APipe Tester | 29 July 2015, 12:17:30 UTC | Updated class browser cache. | 29 July 2015, 12:17:30 UTC |
| bc87355 | Eddie Belter | 29 July 2015, 01:43:35 UTC | BedTools: use perl built-in version handling | 29 July 2015, 01:43:35 UTC |
| 1632741 | Eddie Belter | 29 July 2015, 01:42:57 UTC | Genotype Concordance: rm default value for bedtools version, add it to doc as recommended | 29 July 2015, 01:42:57 UTC |
| bd0a93b | Eddie Belter | 28 July 2015, 22:15:43 UTC | Merge pull request #889 from ebelter/rm-iferg RM Refs to iferguso and Related Clean Up | 28 July 2015, 22:15:43 UTC |
| 4b357c2 | Eddie Belter | 28 July 2015, 22:13:44 UTC | Merge pull request #890 from ebelter/rm-downstream-model-props Model: rm downstream models property and useless test | 28 July 2015, 22:13:44 UTC |
| 1a33525 | Thomas B. Mooney | 28 July 2015, 21:54:15 UTC | Merge pull request #884 from iferguson90/errorrate Update BamQC to use packaged bam-errorrate | 28 July 2015, 21:54:15 UTC |
| bd099ec | apregier | 28 July 2015, 21:49:11 UTC | Use error_message | 28 July 2015, 21:49:11 UTC |
| f974a2e | apregier | 28 July 2015, 20:21:30 UTC | Use Genome::Sys->open_file_for_reading instead of IO::File | 28 July 2015, 20:21:30 UTC |
| 90aa684 | apregier | 28 July 2015, 20:18:30 UTC | Refactor: access property from class directly | 28 July 2015, 20:18:30 UTC |
| 7430213 | apregier | 28 July 2015, 20:16:49 UTC | Use perl shortcut for chomping an array | 28 July 2015, 20:16:49 UTC |
| 56d6c1f | apregier | 28 July 2015, 20:15:54 UTC | Check whether output filehandle exists | 28 July 2015, 20:15:54 UTC |
| a653e09 | Thomas B. Mooney | 28 July 2015, 17:39:15 UTC | Merge pull request #879 from tmooney/disconnect_dbh_before_long_waiting_things Disconnect Database Handles before potentially long-running actions | 28 July 2015, 17:39:15 UTC |
| c3125a1 | Thomas B. Mooney | 28 July 2015, 14:46:06 UTC | Merge pull request #865 from tmooney/deduplicate_reference_indices Deduplicate Aligner and Annotation Index Classes | 28 July 2015, 14:46:06 UTC |
| 838ccdb | Jason Walker | 28 July 2015, 14:13:13 UTC | Merge pull request #851 from jasonwalker80/library_duplication_rates Library Duplication Rates from Reference Alignment builds | 28 July 2015, 14:13:13 UTC |
| 76043d8 | Thomas Mooney | 28 July 2015, 14:12:54 UTC | Include a newline in printed message. | 28 July 2015, 14:12:54 UTC |
| 940d4cd | Thomas Mooney | 28 July 2015, 14:12:12 UTC | Refer to correct key when getting counts. | 28 July 2015, 14:12:12 UTC |
| a406746 | Thomas Mooney | 28 July 2015, 14:11:53 UTC | Whitespace. | 28 July 2015, 14:11:53 UTC |
| be673d7 | Thomas Mooney | 28 July 2015, 13:17:46 UTC | Only schedule annotation if we have variants to annotate. | 28 July 2015, 13:17:46 UTC |
| 2079ea5 | Eddie Belter | 27 July 2015, 19:40:52 UTC | Model: rm _model_value from Input | 27 July 2015, 19:40:52 UTC |
| ed245d3 | APipe Tester | 27 July 2015, 18:27:24 UTC | updated jenkins submodule to 6a39f4b | 27 July 2015, 19:22:27 UTC |
| 95bdd7c | Eddie Belter | 27 July 2015, 19:11:06 UTC | BedTools: uncapitalize Version in function name | 27 July 2015, 19:11:12 UTC |
| adb61bc | Eddie Belter | 27 July 2015, 19:01:21 UTC | Model: rm downstream models property and test that did not really test anything | 27 July 2015, 19:01:21 UTC |
| 940b82b | Eddie Belter | 27 July 2015, 18:54:59 UTC | Merge pull request #878 from ebelter/model-rm-trigger-downstream-models Model: remove unused _trigger_downstream_builds | 27 July 2015, 18:54:59 UTC |
| 6993458 | Eddie Belter | 27 July 2015, 18:51:07 UTC | AR Bfast: rm iferguso TODO | 27 July 2015, 18:51:07 UTC |
| ca5205b | Eddie Belter | 27 July 2015, 18:50:02 UTC | AR Mosaik: rm iferguso TODOs | 27 July 2015, 18:50:02 UTC |
| 9b3df87 | Eddie Belter | 27 July 2015, 18:49:16 UTC | AR Crossmatch: remove non-matching command that is never run | 27 July 2015, 18:49:16 UTC |
| 0ac0e26 | Eddie Belter | 27 July 2015, 18:47:11 UTC | AR Crossmatch: remove iferguso comments | 27 July 2015, 18:47:11 UTC |
| 2db6279 | Eddie Belter | 27 July 2015, 18:43:42 UTC | AR Crossmatch: remove fastq file check | 27 July 2015, 18:43:42 UTC |
| afbb7f4 | Eddie Belter | 27 July 2015, 18:40:24 UTC | AR Crossmatch: fix indent | 27 July 2015, 18:40:24 UTC |
