| ce20c9c | Thomas Mooney | 22 January 2015, 16:02:48 UTC | Test that the parallelization works. Tests of running Htseq::Count remain in GMT/Htseq/Count.t | 22 January 2015, 16:02:48 UTC |
| 060f783 | Thomas Mooney | 22 January 2015, 15:34:01 UTC | Build the correct hash and call get_or_create() by class. | 22 January 2015, 15:34:01 UTC |
| fcb7058 | Thomas B. Mooney | 21 January 2015, 17:28:40 UTC | Merge pull request #422 from tmooney/memtmp create /tmp path if NE for bwa mem and pass along the AR's scratch directory | 21 January 2015, 17:28:40 UTC |
| 006494c | Thomas Mooney | 21 January 2015, 16:39:31 UTC | Pass along our scratch directory. | 21 January 2015, 16:39:31 UTC |
| 366a04b | Thomas Mooney | 21 January 2015, 16:39:01 UTC | Use create_temp_directory() to create the temp directory. | 21 January 2015, 16:39:01 UTC |
| d571a23 | Thomas B. Mooney | 21 January 2015, 16:06:50 UTC | Merge pull request #419 from tmooney/parallelize_spelling s/paralellize/parallelize/ | 21 January 2015, 16:06:50 UTC |
| 4eb0fdc | Susanna Siebert | 21 January 2015, 15:46:05 UTC | Merge pull request #418 from susannasiebert/variant_reporting_improvements Various ACMG report improvements | 21 January 2015, 15:46:05 UTC |
| aca038f | Travis Abbott | 21 January 2015, 07:00:19 UTC | code cleanup | 21 January 2015, 07:00:19 UTC |
| 0439063 | Travis Abbott | 21 January 2015, 06:50:21 UTC | create /tmp path if NE for bwa mem because some tools just really insist on a prefix existing :p | 21 January 2015, 06:51:30 UTC |
| 0642827 | Thomas Mooney | 20 January 2015, 23:58:25 UTC | s/paralellize/parallelize/ | 20 January 2015, 23:58:25 UTC |
| 56113b3 | APipe Tester | 20 January 2015, 20:25:01 UTC | updated ur submodule to c44bc57 | 20 January 2015, 20:25:01 UTC |
| 3997bac | Susanna Siebert | 20 January 2015, 17:02:07 UTC | Update MafInterpreter to prepend fields with source | 20 January 2015, 17:02:07 UTC |
| eb7ef93 | Susanna Siebert | 20 January 2015, 16:25:34 UTC | Update GmafInterpreter to prepend fields with source | 20 January 2015, 16:25:34 UTC |
| ee5f5f5 | Susanna Siebert | 20 January 2015, 16:24:07 UTC | Update CafInterpreter to prepend fields with source | 20 January 2015, 16:24:07 UTC |
| 4f32992 | APipe Tester | 20 January 2015, 15:49:17 UTC | updated jenkins submodule to ad020c5 | 20 January 2015, 15:49:17 UTC |
| 8b224fb | APipe Tester | 20 January 2015, 15:49:06 UTC | updated ur submodule to c7dae7c | 20 January 2015, 15:49:06 UTC |
| 57722b0 | APipe Tester | 17 January 2015, 13:15:58 UTC | Updated `genome` tab completion. | 17 January 2015, 13:15:58 UTC |
| 4760dbc | APipe Tester | 17 January 2015, 13:14:25 UTC | Updated class browser cache. | 17 January 2015, 13:14:25 UTC |
| 1179cc4 | Susanna Siebert | 16 January 2015, 21:43:47 UTC | remove tumor specific columns from the ACMG report | 16 January 2015, 21:43:47 UTC |
| 564aa7c | Susanna Siebert | 16 January 2015, 21:43:22 UTC | fix valid_callers for germline reports | 16 January 2015, 21:43:22 UTC |
| 82f3e4d | Ricky Ng | 16 January 2015, 20:57:23 UTC | Merge pull request #397 from dummey/master Updating SraToBam.pm to use new input params. | 16 January 2015, 20:57:23 UTC |
| d52fd14 | Nathaniel Nutter | 16 January 2015, 20:42:18 UTC | Merge pull request #404 from nnutter/RT/103374 Minor Improvements to BamWindow Wrapper | 16 January 2015, 20:42:18 UTC |
| e82b214 | Susanna Siebert | 16 January 2015, 20:30:34 UTC | Delete DbsnpInterpreter It has been superseded by the CafInterpreter | 16 January 2015, 20:30:34 UTC |
| b999391 | Susanna Siebert | 16 January 2015, 19:50:37 UTC | modify the order of the ACMG report header | 16 January 2015, 19:50:37 UTC |
| 0dd686b | Eddie Belter | 16 January 2015, 19:08:51 UTC | Merge pull request #377 from ebelter/instdata-import Merged the TCGA importer into the basic importer. More PRs to come to smooth out the interface. | 16 January 2015, 19:08:51 UTC |
| 0a8a48b | Susanna Siebert | 16 January 2015, 18:40:29 UTC | Merge pull request #409 from davidlmorton/json_labels Make sample/library name_labels transient | 16 January 2015, 18:40:29 UTC |
| 7f8b788 | Susanna Siebert | 16 January 2015, 14:25:09 UTC | Merge pull request #414 from susannasiebert/variant_reporting_igv Allow bed files to be URIs for IGV sessions | 16 January 2015, 14:25:09 UTC |
| e14605e | Susanna Siebert | 16 January 2015, 14:25:04 UTC | Merge pull request #412 from susannasiebert/variant_reporting_vaf_library_names Make library_names optional for VafInterpreter | 16 January 2015, 14:25:04 UTC |
| c8f5955 | Susanna Siebert | 15 January 2015, 21:24:01 UTC | Merge pull request #406 from susannasiebert/variant_reporting_readcount Fix allele translations for bam readcount | 15 January 2015, 21:24:01 UTC |
| 752b17b | Susanna Siebert | 15 January 2015, 21:19:51 UTC | Add comments to the translate_pure_indels subroutine | 15 January 2015, 21:19:51 UTC |
| 3792c59 | Thomas B. Mooney | 15 January 2015, 20:07:16 UTC | Merge pull request #403 from tmooney/fix_diskallocationstaged_inconsistency Correct abstract method name in G:SR:DiskAllocationStaged | 15 January 2015, 20:07:16 UTC |
| c3e0d12 | David Morton | 15 January 2015, 19:20:15 UTC | Merge pull request #415 from davidlmorton/custom_report Update ShowDoc test data for custom report | 15 January 2015, 19:20:15 UTC |
| 824650b | dmorton | 15 January 2015, 19:17:06 UTC | Update ShowDoc test data for custom report | 15 January 2015, 19:17:06 UTC |
| 521af17 | David Morton | 15 January 2015, 18:22:04 UTC | Merge pull request #400 from davidlmorton/custom_report Added CustomReport | 15 January 2015, 18:22:04 UTC |
| 8b92b8b | dmorton | 15 January 2015, 17:39:44 UTC | Remove old, non-transient, properties | 15 January 2015, 17:39:44 UTC |
| f5d3222 | Thomas B. Mooney | 15 January 2015, 17:08:43 UTC | Merge pull request #411 from tmooney/add_missing_lock_scope Add lock scoping to PAP's upload-result command. | 15 January 2015, 17:08:43 UTC |
| cd38e14 | Mark Burnett | 15 January 2015, 17:07:35 UTC | Merge pull request #413 from mark-burnett/fix-lock-release-all Bugfix: make sure FileBackend release_all deletes symlinks | 15 January 2015, 17:07:35 UTC |
| e4471cd | Susanna Siebert | 15 January 2015, 16:42:23 UTC | allow bed files to be URIs for IGV sessions | 15 January 2015, 16:42:23 UTC |
| 9f9ac6d | Susanna Siebert | 15 January 2015, 16:27:20 UTC | Merge pull request #408 from susannasiebert/variant_reporting_mincovfilter Make min coverage vcf id truly unique by including sample name | 15 January 2015, 16:27:20 UTC |
| f012a09 | Mark Burnett | 15 January 2015, 16:11:06 UTC | S:L:FileBackend remove unused temporary | 15 January 2015, 16:13:31 UTC |
| 622319e | Mark Burnett | 15 January 2015, 16:10:46 UTC | S:L:FileBackend extract write_lock_info | 15 January 2015, 16:13:30 UTC |
| d942256 | Mark Burnett | 15 January 2015, 16:08:37 UTC | S:L:FileBackend extract tempdir_for_resource | 15 January 2015, 16:13:30 UTC |
| c663571 | Mark Burnett | 15 January 2015, 16:04:11 UTC | S:L:FileBackend fix release_all deleteing symlinks | 15 January 2015, 16:13:29 UTC |
| b54d5e2 | Susanna Siebert | 15 January 2015, 15:24:46 UTC | Make library_names optional for VafInterpreter We use the VafInterpreter without library_names in the MinCoverageObservedInterpreter and the MaxVafObservedInterpreter | 15 January 2015, 15:42:07 UTC |
| 22d4ab2 | Jim Weible | 15 January 2015, 15:03:47 UTC | Merge pull request #410 from jweible/AUE-384 Show tags in Analysis Project View | 15 January 2015, 15:03:47 UTC |
| 2489c05 | Thomas Mooney | 14 January 2015, 22:19:47 UTC | Add lock scoping to PAP's upload-result command. | 14 January 2015, 22:19:47 UTC |
| 8d46a51 | Jim Weible | 14 January 2015, 15:13:30 UTC | show tags in the viewer | 14 January 2015, 15:13:30 UTC |
| f60d087 | Mark Burnett | 14 January 2015, 14:13:50 UTC | Merge pull request #386 from mark-burnett/scoped-locking Add "scope" parameter to Genome:Sys->lock_resource | 14 January 2015, 14:13:50 UTC |
| 46e6fbc | dmorton | 14 January 2015, 01:38:05 UTC | Make sample/library name_labels transient HASH type properties cannot be stored in the DB. | 14 January 2015, 01:38:05 UTC |
| 463c08a | Susanna Siebert | 13 January 2015, 22:14:47 UTC | make min coverage vcf id truly unique by including sample name | 13 January 2015, 22:14:47 UTC |
| 38d6d3c | Travis Abbott | 13 January 2015, 22:04:50 UTC | remove debug message | 13 January 2015, 22:04:50 UTC |
| b85162a | Susanna Siebert | 13 January 2015, 21:16:30 UTC | Merge pull request #401 from susannasiebert/column_sorting Implement a custom sorting algorithm for vaf headers | 13 January 2015, 21:16:30 UTC |
| fd719f0 | Travis Abbott | 13 January 2015, 20:58:01 UTC | Merge pull request #405 from tabbott/shellpipes Shellpipes | 13 January 2015, 20:58:01 UTC |
| 56e0dfc | Susanna Siebert | 13 January 2015, 20:57:06 UTC | implement better way to ensure that the headers are truly unsorted | 13 January 2015, 20:57:06 UTC |
| 0b94b85 | Susanna Siebert | 13 January 2015, 20:39:33 UTC | use defaults for sample and vaf_priority | 13 January 2015, 20:39:33 UTC |
| 2426dbd | Susanna Siebert | 13 January 2015, 20:36:26 UTC | Merge pull request #402 from susannasiebert/variant_reporting_callers Some minor changes to the variant caller interpreter | 13 January 2015, 20:36:26 UTC |
| ead876c | Susanna Siebert | 13 January 2015, 20:26:58 UTC | test vaf interpretation for a long deletion | 13 January 2015, 20:27:08 UTC |
| 1232115 | Susanna Siebert | 13 January 2015, 20:23:45 UTC | Be smarter about how to translate indels - This will now work correctly for all long indels, even if it is at an arbitrary position in the reference - This still doesn't handle mixed cases correctly | 13 January 2015, 20:23:45 UTC |
| 8f81c2a | Susanna Siebert | 13 January 2015, 20:18:08 UTC | ensure that the shuffled header is not the same as the original | 13 January 2015, 20:19:26 UTC |
| 4ded091 | Susanna Siebert | 13 January 2015, 20:08:01 UTC | Use <=> for numerical comparison | 13 January 2015, 20:08:01 UTC |
| 0e6bb80 | Susanna Siebert | 13 January 2015, 20:01:22 UTC | Added some valid callers that were missed | 13 January 2015, 20:01:22 UTC |
| 876959b | Travis Abbott | 13 January 2015, 19:09:09 UTC | don't throw from Try::Tiny::finally It's implemented in terms of a DESTROY block so throwing from there is a bad idea. | 13 January 2015, 19:09:09 UTC |
| 6806f8e | Travis Abbott | 13 January 2015, 17:34:47 UTC | move ShellPipeline from gmt to Genome::Sys | 13 January 2015, 17:34:47 UTC |
| d60b787 | Travis Abbott | 13 January 2015, 17:31:24 UTC | refactor to use Try::Tiny and Carp::croak | 13 January 2015, 17:31:24 UTC |
| 77520cd | Susanna Siebert | 13 January 2015, 17:01:45 UTC | Merge pull request #380 from susannasiebert/variant_reporting_masterplan Add test for missing parameter in plan file | 13 January 2015, 17:01:45 UTC |
| 9d087f5 | APipe Tester | 13 January 2015, 13:17:04 UTC | Updated `gmt` tab completion. | 13 January 2015, 13:17:04 UTC |
| 51d2ce8 | APipe Tester | 13 January 2015, 13:16:20 UTC | Updated `genome` tab completion. | 13 January 2015, 13:16:20 UTC |
| 4413cb7 | APipe Tester | 13 January 2015, 13:14:42 UTC | Updated class browser cache. | 13 January 2015, 13:14:42 UTC |
| 625abad | Travis Abbott | 13 January 2015, 03:15:20 UTC | gmt/ShellPipeline shouldn't be a Command This class has no business interacting with the command line. It has been demoted to UR::Object. | 13 January 2015, 03:15:20 UTC |
| cdd1f98 | Travis Abbott | 13 January 2015, 03:11:03 UTC | update gmt bwa run-mem to lean on gmt/ShellPipeline the code to deal with error detection in pipes has been pulled out. | 13 January 2015, 03:11:03 UTC |
| e9baddd | Travis Abbott | 13 January 2015, 03:07:45 UTC | generalize shell| execution code from gmt bwa run-mem This is needed in other places as well. It's nice to be able to express a shell pipeline as a list of commands and get thorough error checking... | 13 January 2015, 03:07:45 UTC |
| 339e0e9 | Thomas Mooney | 12 January 2015, 21:57:01 UTC | Use name of the method we really try to call. | 12 January 2015, 21:57:01 UTC |
| 63a6191 | Nathaniel Nutter | 12 January 2015, 21:51:51 UTC | use shellcmd to ensure command does not fail silently `system()` does not set `$@` so the old code was doing no error checking of the command. One could check the return value from `system()`, etc. but that is why `shellcmd()` exists (among other solutions). | 12 January 2015, 21:54:42 UTC |
| dafe6bf | Feiyu Du | 12 January 2015, 21:13:13 UTC | Merge pull request #398 from dufeiyu/fix Fix a bug on comparing flagstat | 12 January 2015, 21:13:13 UTC |
| 418f92d | Susanna Siebert | 12 January 2015, 20:36:55 UTC | add Pindel and GatkSomaticIndel to the list of valid_callers for indels | 12 January 2015, 20:36:55 UTC |
| 836fdce | Susanna Siebert | 12 January 2015, 20:34:46 UTC | Remove default values of valid_callers in the VariantCallersInterpreter - move them to the plan file instead | 12 January 2015, 20:34:46 UTC |
| facf81f | Feiyu Du | 12 January 2015, 19:51:56 UTC | rework compare_flagstat with one line diff expected based on code review | 12 January 2015, 19:51:56 UTC |
| 051bdff | Mark Burnett | 12 January 2015, 19:17:39 UTC | S:Lock make scope parameter mandatory | 12 January 2015, 19:46:53 UTC |
| 3dd0308 | Mark Burnett | 12 January 2015, 19:14:58 UTC | S:Lock limit valid scope names | 12 January 2015, 19:46:51 UTC |
| b179811 | Mark Burnett | 12 January 2015, 16:37:54 UTC | Update calls to Sys->lock_resource - Remove their root directories, usually $ENV{GENOME_LOCK_DIR} - Add "site" parameter to call | 12 January 2015, 19:46:50 UTC |
| a52359c | Mark Burnett | 12 January 2015, 16:34:19 UTC | Site:TGI:E:S:Lock add "unknown" scope | 12 January 2015, 19:46:48 UTC |
| 57bd053 | Mark Burnett | 12 January 2015, 16:31:03 UTC | Site:TGI:E:Sys remove unused test code | 12 January 2015, 19:46:47 UTC |
| d7b5186 | Mark Burnett | 12 January 2015, 16:30:20 UTC | S:L:FileBackend bugfix -- has_lock checks for existance | 12 January 2015, 19:46:46 UTC |
| 75fd39f | Mark Burnett | 07 January 2015, 19:39:27 UTC | S:L:FileBackend convert to non-singleton | 12 January 2015, 19:46:45 UTC |
| 5cb8b8c | Mark Burnett | 07 January 2015, 19:15:37 UTC | S:L:FileBackend switch *_message to Genome::Logger | 12 January 2015, 19:46:43 UTC |
| 23896d2 | Mark Burnett | 07 January 2015, 14:26:48 UTC | S:Lock forbid locking a resource in two scopes | 12 January 2015, 19:46:42 UTC |
| 936fc0e | Mark Burnett | 07 January 2015, 14:19:50 UTC | Revert "S:L:NessyBackend strip leading path from resource" This reverts commit 246351f727df76bc6a973a604b5b5e361567c642. | 12 January 2015, 19:46:41 UTC |
| cb46335 | Mark Burnett | 07 January 2015, 14:19:16 UTC | S:Lock remove experimental "any" scope | 12 January 2015, 19:46:39 UTC |
| ac4a84d | Susanna Siebert | 12 January 2015, 19:16:10 UTC | Remove code duplication | 12 January 2015, 19:16:10 UTC |
| f59e69e | Susanna Siebert | 12 January 2015, 17:00:39 UTC | remove duplicate test | 12 January 2015, 17:00:39 UTC |
| 29b45c9 | Susanna Siebert | 12 January 2015, 16:39:10 UTC | no need to sort the vaf headers anymore since they are returned in sorted order | 12 January 2015, 16:39:10 UTC |
| 8eba9dd | Susanna Siebert | 12 January 2015, 16:35:48 UTC | Implement a sorting algorithm for vaf headers - Sort vaf fields as ref_count, var_count, vaf - Sort CLE sample labels as Normal, Discovery, Followup - Also ensure that the library names are taken into account and that samples without labels get sorted correctly | 12 January 2015, 16:35:48 UTC |
| 341aada | Susanna Siebert | 12 January 2015, 15:23:34 UTC | Merge pull request #391 from susannasiebert/process Add functionality to compare Genome::Process output files | 12 January 2015, 15:23:34 UTC |
| cefae91 | Thomas B. Mooney | 12 January 2015, 15:03:28 UTC | Merge pull request #396 from tmooney/speedup_copycat_annotation_lister Speedup CopyCat Annotation Lister | 12 January 2015, 15:03:28 UTC |
| c12aa72 | dmorton | 10 January 2015, 18:12:01 UTC | Added CustomReport This report lets you specify the header columns in the plan file. | 10 January 2015, 18:12:01 UTC |
| fb85a7b | Feiyu Du | 09 January 2015, 20:17:08 UTC | fix a bug on comparing flagstat | 09 January 2015, 20:17:08 UTC |
| 07823e8 | Susanna Siebert | 09 January 2015, 19:46:57 UTC | use original file paths for diff message | 09 January 2015, 19:46:57 UTC |
| 775353d | Susanna Siebert | 09 January 2015, 19:35:38 UTC | always use relative paths for diff hash keys | 09 January 2015, 19:35:38 UTC |
| 79f06fb | Susanna Siebert | 09 January 2015, 19:34:42 UTC | remove unneeded subroutine | 09 January 2015, 19:34:42 UTC |
| 279b343 | Ricky Ng | 09 January 2015, 18:04:28 UTC | Refactored obsolete function param. convert_fastq_to_bam | 09 January 2015, 18:04:28 UTC |
