| 406f61d | Nathaniel Nutter | 11 April 2014, 20:59:53 UTC | add periodic announcement while waiting on lock | 14 April 2014, 21:24:03 UTC |
| b5f5617 | Nathaniel Nutter | 14 April 2014, 14:03:01 UTC | set a minimum timeout | 14 April 2014, 21:24:02 UTC |
| f8561f3 | Nathaniel Nutter | 11 April 2014, 20:56:49 UTC | move wait_announce_interval default up to lock_resource | 14 April 2014, 21:24:01 UTC |
| 7a8d5d0 | Gabriel Sanderson | 14 April 2014, 21:18:05 UTC | Rely on output_file_path instead of get_vcf | 14 April 2014, 21:18:15 UTC |
| c522ddb | Adam Coffman | 14 April 2014, 21:08:22 UTC | is_concrete is now a public method | 14 April 2014, 21:08:22 UTC |
| 0245fc2 | Gabriel Sanderson | 14 April 2014, 20:49:28 UTC | Fixed typo in software_result class | 14 April 2014, 20:49:28 UTC |
| 8a68633 | dmorton | 14 April 2014, 18:57:28 UTC | Don't crash build when vcf sample name is different from aligned-reads This happens for example in samples from TCGA because of some logic here: Genome/Model/Tools/Vcf/Convert/Base.pm | 14 April 2014, 18:57:28 UTC |
| a9c1137 | dmorton | 14 April 2014, 16:14:45 UTC | Annotation::Vep classes inherit from Annotation::Detail base classes | 14 April 2014, 16:14:45 UTC |
| c92a10e | dmorton | 14 April 2014, 16:13:00 UTC | Name class correctly and remove unused params before passing on | 14 April 2014, 16:13:00 UTC |
| ed814f9 | dmorton | 14 April 2014, 16:09:15 UTC | Factor out test_cmd_and_result_are_in_sync to TestHelpers | 14 April 2014, 16:09:15 UTC |
| 16498e5 | dmorton | 14 April 2014, 03:09:19 UTC | Add Command and Result to add readcount info to a vcf_result | 14 April 2014, 15:27:33 UTC |
| 64e7621 | dmorton | 14 April 2014, 03:05:54 UTC | Change inputs to AnnotateWithReadcounts We cannot rely on UR to keep is_many properties in any particular order, so we have to combine these two fields. While we're at it, since sample_names aren't in fact useful except to get at the column index in the vcf-header, lets go ahead and just require the index. | 14 April 2014, 15:27:33 UTC |
| 7ce1aa5 | dmorton | 14 April 2014, 03:02:07 UTC | Fix up how to get param_names and input_names In particular, we have to be careful with params on software results. | 14 April 2014, 15:27:32 UTC |
| 77092ef | dmorton | 14 April 2014, 02:54:38 UTC | File::Vcf::Writer can write bgzipped files | 14 April 2014, 15:27:32 UTC |
| f933d61 | dmorton | 11 April 2014, 21:06:07 UTC | Add sample_name accessor for Readcount::Result | 14 April 2014, 15:27:32 UTC |
| e43910c | dmorton | 11 April 2014, 21:04:50 UTC | Make base classes for Annotation commands and results | 14 April 2014, 15:27:32 UTC |
| abc22f5 | dmorton | 11 April 2014, 20:09:36 UTC | Moved command into gmt | 14 April 2014, 15:27:32 UTC |
| bdb8d0b | Eddie Belter | 11 April 2014, 21:33:47 UTC | ClinSeq: rm redirect to dev/null for illumina_info command to investigate failure | 11 April 2014, 21:35:50 UTC |
| f59afd4 | APipe Tester | 11 April 2014, 21:33:00 UTC | updated jenkins submodule to 20afc03 | 11 April 2014, 21:33:00 UTC |
| b9f5fdd | Gabriel Sanderson | 11 April 2014, 20:31:08 UTC | Added Genome::Annotation::Vep and accompanying result and tests. | 11 April 2014, 20:38:38 UTC |
| b228d96 | Gabriel Sanderson | 11 April 2014, 19:17:26 UTC | Add get_tabix_and_gzipped_bed_file to Genome::Featurelist. This will be used for VEP annotation. | 11 April 2014, 20:38:37 UTC |
| 67fb1b3 | Gabriel Sanderson | 11 April 2014, 19:16:33 UTC | Added gzip_file to Genome::Sys, which compresses a file to a target path. | 11 April 2014, 20:38:37 UTC |
| a0e4f64 | Gabriel Sanderson | 09 April 2014, 20:10:27 UTC | added vcf.gz test | 11 April 2014, 20:37:03 UTC |
| fe24c91 | Gabriel Sanderson | 09 April 2014, 19:52:30 UTC | Added VCF test. Updated test directories. | 11 April 2014, 20:36:48 UTC |
| 4f26a83 | apregier | 11 April 2014, 19:01:08 UTC | Merge branch 'updated' into gb_master | 11 April 2014, 19:01:08 UTC |
| ccbb5b4 | David Morton | 11 April 2014, 17:45:30 UTC | Improve tests for Adaptor::SomaticVariation | 11 April 2014, 18:36:52 UTC |
| 6090d88 | David Morton | 11 April 2014, 17:43:16 UTC | Add abstract methods to abstract class Adaptor | 11 April 2014, 18:36:51 UTC |
| 6c7aaf4 | David Morton | 11 April 2014, 17:42:36 UTC | Remove unneeded temp variable $results | 11 April 2014, 18:36:50 UTC |
| 75f7c47 | apregier | 10 April 2014, 21:28:41 UTC | Command to add readcount to vcf sample fields We assume that all readcount files are sorted in the same order as the vcf file, and that they contain only variants in the vcf file. | 11 April 2014, 18:36:50 UTC |
| 0c82324 | apregier | 10 April 2014, 20:19:22 UTC | Get original string from bam-readcount entry | 11 April 2014, 18:36:49 UTC |
| 7b2e71b | apregier | 10 April 2014, 20:15:40 UTC | Catch exceptions if vcf results don't exist There may be builds without vcf results, so we can catch those exceptions and simply return undef. | 11 April 2014, 18:36:49 UTC |
| c761754 | apregier | 10 April 2014, 20:14:08 UTC | Throw exception if files don't exist | 11 April 2014, 18:36:48 UTC |
| d405b9b | apregier | 09 April 2014, 21:45:09 UTC | Catch exceptions if vcf result is not available | 11 April 2014, 18:36:47 UTC |
| bd7a3be | Adam Coffman | 11 April 2014, 17:19:02 UTC | adjust UR constraint to match DB constraint | 11 April 2014, 17:19:02 UTC |
| 5d511c0 | Adam Coffman | 11 April 2014, 17:15:06 UTC | migration to widen name column | 11 April 2014, 17:15:06 UTC |
| 016d2e7 | Adam Coffman | 11 April 2014, 15:21:29 UTC | change subject->sample for somval importer | 11 April 2014, 15:21:29 UTC |
| 702ed35 | APipe Tester | 11 April 2014, 12:18:38 UTC | Updated `gmt` tab completion. | 11 April 2014, 12:18:38 UTC |
| da0e271 | APipe Tester | 11 April 2014, 12:17:54 UTC | Updated `genome` tab completion. | 11 April 2014, 12:17:54 UTC |
| c045cf0 | APipe Tester | 11 April 2014, 12:16:21 UTC | Updated class browser cache. | 11 April 2014, 12:16:21 UTC |
| 10d3651 | Nathaniel Nutter | 11 April 2014, 02:15:38 UTC | Revert "switch _new_style_lock to retry" This reverts commit eccbdeaf713350c4f7c80b70626a62e34ad794c2. | 11 April 2014, 02:15:50 UTC |
| fb00a65 | Chris Miller | 10 April 2014, 23:20:38 UTC | adding option to dump mean and median coverage to a file | 10 April 2014, 23:20:45 UTC |
| 28b1ab0 | Eddie Belter | 10 April 2014, 22:41:30 UTC | Sync/GM: do not die if reallocate fails | 10 April 2014, 22:41:51 UTC |
| 00bf30d | Chris Miller | 10 April 2014, 20:18:00 UTC | correctly match up coordinates from assembly validation | 10 April 2014, 20:18:00 UTC |
| 1104d8d | Chris Miller | 10 April 2014, 19:50:25 UTC | report VAF percentages (50) instead of fractions (0.50) for large indels pulled from assembly validation | 10 April 2014, 19:51:06 UTC |
| eccbdea | Nathaniel Nutter | 10 April 2014, 00:36:34 UTC | switch _new_style_lock to retry In order to provide periodic status updates while waiting on locks like the NFS backend did switch _new_style_lock's timeout to block_sleep and retry max_try times instead of doing one block_sleep * max_try attempt. | 10 April 2014, 19:26:17 UTC |
| 7567de7 | Nathaniel Nutter | 09 April 2014, 22:34:49 UTC | move defaults up so they get passed to both backends | 10 April 2014, 19:26:16 UTC |
| 569f0fa | dmorton | 10 April 2014, 15:45:08 UTC | Don't die when variants-directory isn't found. This behavior is relied on in numerous places in ReferenceAlignment builds. In SomaticVariation and SomaticValidation, I didn't see any eval statements preceeding the calls to ->variants_directory so I think it is safe to relax this check. | 10 April 2014, 15:48:57 UTC |
| c684828 | Susanna Siebert | 10 April 2014, 13:12:12 UTC | Merge branch 'clip_overlap' | 10 April 2014, 13:12:12 UTC |
| f539988 | Susanna Siebert | 10 April 2014, 13:10:14 UTC | implement shortcut method for RefineReads | 10 April 2014, 13:10:14 UTC |
| 2b586fc | APipe Tester | 10 April 2014, 12:19:06 UTC | Updated `gmt` tab completion. | 10 April 2014, 12:19:06 UTC |
| 8d4d335 | APipe Tester | 10 April 2014, 12:18:25 UTC | Updated `genome` tab completion. | 10 April 2014, 12:18:25 UTC |
| 4cfd38e | APipe Tester | 10 April 2014, 12:16:47 UTC | Updated class browser cache. | 10 April 2014, 12:16:47 UTC |
| e315550 | apregier | 09 April 2014, 21:37:12 UTC | Somatic variation adaptor for annotation subsystem | 09 April 2014, 21:37:53 UTC |
| 3749246 | Nathaniel Nutter | 09 April 2014, 21:29:52 UTC | reduce usage metrics rate | 09 April 2014, 21:29:52 UTC |
| e526512 | Nathaniel Nutter | 09 April 2014, 21:27:10 UTC | combine logic | 09 April 2014, 21:27:39 UTC |
| 3853107 | Nathaniel Nutter | 09 April 2014, 21:23:52 UTC | add logic to reduce the amount of logging We have been logging 100 records per second (8.6M per day). To reduce this we will now only log 'gmt' and 'genome' commands on blades. | 09 April 2014, 21:27:38 UTC |
| c05b290 | Nathaniel Nutter | 09 April 2014, 21:23:15 UTC | memoize import instead of running on require | 09 April 2014, 21:27:38 UTC |
| 681ac65 | Nathaniel Nutter | 09 April 2014, 21:20:41 UTC | extract should_record_usage | 09 April 2014, 21:27:37 UTC |
| c481639 | Nathaniel Nutter | 09 April 2014, 21:19:30 UTC | extract method genome_path to avoid uninitialized value warning | 09 April 2014, 21:27:36 UTC |
| 9f68ff8 | dmorton | 09 April 2014, 20:41:13 UTC | Add accessor for DV2 detailed vcf results | 09 April 2014, 21:13:16 UTC |
| d558061 | Nathaniel Nutter | 09 April 2014, 20:45:50 UTC | croak if child fails to acquire lock | 09 April 2014, 20:45:50 UTC |
| 312853d | Michael J. Kiwala | 09 April 2014, 18:45:27 UTC | Allow imported data if it comes from a bam file | 09 April 2014, 18:59:52 UTC |
| f4c429d | dmorton | 09 April 2014, 17:12:15 UTC | Use MixIn class to access DV2 results. | 09 April 2014, 17:54:04 UTC |
| 8afe9a5 | dmorton | 09 April 2014, 16:53:01 UTC | Make accessors for get_detailed_{snvs,indels}_vcf | 09 April 2014, 17:54:04 UTC |
| b4f5d52 | Nathaniel Nutter | 09 April 2014, 17:17:36 UTC | use a default creation_time (epoch) To avoid uninitialized value warnings use a default value for creation_time (epoch). Otherwise assumptions about creation_time being defined, e.g. trying to sort allocations by creation_time, may produce uninitialized value warnings. Test that creation_time is set to ensure this didn't break the creation_time accessor. CHANGELOG: Genome::Disk::Allocation's creation_time now returns a default value, the epoch, instead of undef. | 09 April 2014, 17:29:12 UTC |
| a67926e | Nathaniel Nutter | 08 April 2014, 23:10:56 UTC | remove ability to try to lock the same resource twice I searched for "wait_on_self" and only found it set in its own test. With wait_on_self defaulting to false if something tried to lock the same resource twice it would unlock its current lock and then acquire a new lock. This should almost certainly be a fatal error because it probably means something else forgot to unlock its lock or if this is a means of "sharing" a lock it means something else could acquire the lock out from under this process. CHANGELOG: It is no longer possible to lock the same resource twice (in the same process). | 09 April 2014, 17:27:36 UTC |
| 6887b3a | dmorton | 09 April 2014, 15:20:26 UTC | Make Annotation/Readcount command and SR | 09 April 2014, 15:45:00 UTC |
| 8f01f66 | dmorton | 09 April 2014, 15:19:36 UTC | Whitespace | 09 April 2014, 15:44:10 UTC |
| 765c7fd | dmorton | 09 April 2014, 15:18:24 UTC | Add ability to *not* remove filtered calls | 09 April 2014, 15:44:10 UTC |
| 56b4b87 | APipe Tester | 09 April 2014, 12:18:55 UTC | Updated `gmt` tab completion. | 09 April 2014, 12:18:55 UTC |
| bb3fbd1 | APipe Tester | 09 April 2014, 12:18:10 UTC | Updated `genome` tab completion. | 09 April 2014, 12:18:10 UTC |
| d215b5a | Chris Miller | 08 April 2014, 21:25:43 UTC | making sample-names a required input | 08 April 2014, 21:25:43 UTC |
| c635076 | APipe Tester | 08 April 2014, 20:18:48 UTC | updated graphite submodule to fe06c16 | 08 April 2014, 20:18:48 UTC |
| 1667b04 | Adam Coffman | 08 April 2014, 18:18:26 UTC | update doc to indicate that IDs or Names are now accepted | 08 April 2014, 18:18:26 UTC |
| c5bf0d1 | Adam Coffman | 08 April 2014, 18:16:24 UTC | make SomVal AnP pairing importer support sample names as well as ids | 08 April 2014, 18:16:24 UTC |
| 7c822d2 | Susanna Siebert | 08 April 2014, 18:02:27 UTC | handle return value of _validate_results correctly | 08 April 2014, 18:02:27 UTC |
| c695545 | Susanna Siebert | 08 April 2014, 18:02:00 UTC | link merge result to first refinement step only | 08 April 2014, 18:02:00 UTC |
| 72ce0b7 | apregier | 07 April 2014, 18:37:37 UTC | Don't try to shortcut to vcf in build | 08 April 2014, 17:40:03 UTC |
| 9e68bcf | Susanna Siebert | 07 April 2014, 18:52:53 UTC | replace all usages of merged_alignment_bam_path with bam_file | 08 April 2014, 17:40:02 UTC |
| 6ba655e | Susanna Siebert | 07 April 2014, 17:54:17 UTC | use the bam_file property instead of merged_alignment_bam_path so it also works for clip overlap and gatk results | 08 April 2014, 17:40:01 UTC |
| 3d92b62 | Susanna Siebert | 07 April 2014, 15:52:20 UTC | only hook up the last step to the output connector | 08 April 2014, 17:40:00 UTC |
| 79349f5 | Susanna Siebert | 04 April 2014, 21:19:52 UTC | used packaged version | 08 April 2014, 17:39:59 UTC |
| 4a0a434 | Susanna Siebert | 04 April 2014, 21:13:01 UTC | update submodules to include bamUtil | 08 April 2014, 17:39:58 UTC |
| 6ab854d | Susanna Siebert | 31 March 2014, 19:53:55 UTC | test for clip overlap, then gatk | 08 April 2014, 17:39:57 UTC |
| 631d645 | Susanna Siebert | 31 March 2014, 19:53:07 UTC | index bam after clipping since downstream tools might expect index | 08 April 2014, 17:39:57 UTC |
| cd557bb | Susanna Siebert | 31 March 2014, 19:51:05 UTC | rename input/output_bam to input/output_file the tool supports both bam and sam add a file_format parameter to distinguish the two cases | 08 April 2014, 17:39:56 UTC |
| 96414e9 | Susanna Siebert | 31 March 2014, 19:48:52 UTC | use the bam_path provided by Genome::InstrumentData::AlignedBamResult instead of custom output_bam_path | 08 April 2014, 17:39:55 UTC |
| 1f26f6b | Susanna Siebert | 31 March 2014, 16:22:22 UTC | handle wiring up of two refinement operations to each other | 08 April 2014, 17:39:53 UTC |
| f8bdae4 | Susanna Siebert | 31 March 2014, 16:20:24 UTC | refactor the refiner input handling to work with multiple refiners | 08 April 2014, 17:39:52 UTC |
| 1e711f8 | Susanna Siebert | 31 March 2014, 16:19:10 UTC | return the shortcut result when shortcutting, not 1 | 08 April 2014, 17:39:52 UTC |
| bdb1d1f | Susanna Siebert | 31 March 2014, 16:16:13 UTC | bugfixes in the test The gatk_results need to be uniquified between the different subtests. This is achieved by adding the know_sites build to the retrieval method. For the gatk and clipoverlap combined test the retrieval of the clip overlap result should use the gatk results since that is the previous step (not the merge). | 08 April 2014, 17:39:50 UTC |
| aa7c76b | Susanna Siebert | 31 March 2014, 16:16:01 UTC | subtest renamed for clarity | 08 April 2014, 17:39:49 UTC |
| 8bb3b5a | Gabriel Sanderson | 28 March 2014, 23:30:39 UTC | Added a bunch of code to begin considering multiple refiners. Refiner operation names and refiner properties on the input_connector are now unique by refiner name (multiple instances of the same refiner will not work right now). Some code cleanup is needed. Also we still need to make the "wire" methods work for multiple refine operations. | 08 April 2014, 17:39:48 UTC |
| f0a4cab | Susanna Siebert | 28 March 2014, 18:28:42 UTC | new test for gatk and clip overlap refinement (doesn't pass yet) | 08 April 2014, 17:39:47 UTC |
| 8fbe7fd | Susanna Siebert | 28 March 2014, 18:16:38 UTC | RefineAlignments should really be the RefineReads base class | 08 April 2014, 17:39:46 UTC |
| a4f269f | Susanna Siebert | 28 March 2014, 16:00:34 UTC | refactor for clarity | 08 April 2014, 17:39:45 UTC |
| 84cb130 | Gabriel Sanderson | 27 March 2014, 22:28:32 UTC | Added a test for running clip overlap after merge instead of gatk. Passes. Had to add a hack -- optional known_sites in clip_overlap. This should be pulled into a base class for refine reads and made optional (but required for gatk) | 08 April 2014, 17:39:45 UTC |
| 8b24b29 | Gabriel Sanderson | 27 March 2014, 22:05:10 UTC | removed breakpoint | 08 April 2014, 17:39:44 UTC |
| 7ab8a00 | Gabriel Sanderson | 27 March 2014, 21:51:46 UTC | removed unnecessary id specification when defining objects | 08 April 2014, 17:39:43 UTC |
| 81cefaf | Gabriel Sanderson | 27 March 2014, 21:42:49 UTC | Use instrument data objects instead of hardcoded ids | 08 April 2014, 17:39:42 UTC |
