| 2335512 | Travis Abbott | 12 November 2012, 23:33:22 UTC | add optional --file-suffix option to gmt graph mutation-diagram | 12 November 2012, 23:33:22 UTC |
| 52097fe | apregier | 12 November 2012, 22:51:42 UTC | Merge branch 'fix' into gb_master | 12 November 2012, 22:51:42 UTC |
| 300839c | apregier | 12 November 2012, 22:51:09 UTC | Ignore some files for build diffs in somatic variation. This is necessary because of the strelka output files. We also now grep out some lines from all .hq files such as fileDate,cmdline, and startTime | 12 November 2012, 22:51:25 UTC |
| 55164f7 | APipe Tester | 12 November 2012, 20:48:36 UTC | Merge remote-tracking branch 'origin/master' | 12 November 2012, 20:48:36 UTC |
| 1db4ebf | apregier | 12 November 2012, 19:59:12 UTC | Merge branch 'fix' into gb_master | 12 November 2012, 19:59:12 UTC |
| c1a3c59 | apregier | 12 November 2012, 19:55:29 UTC | Update test with new expected outputs | 12 November 2012, 19:55:29 UTC |
| 59d056b | Eddie Belter | 12 November 2012, 19:25:05 UTC | Solexa: rm original fastqs after SX trimming | 12 November 2012, 19:25:12 UTC |
| 581e653 | Thomas Mooney | 12 November 2012, 19:22:18 UTC | Correct locking when software result has an object as input or param. Previously the inputs and params were simply concatenated together; however in the case of objects this would use their memory address, which is unsuitable for a lock across processes. The locks generated should be the same for results without objects--only locks that currently don't work are changing! | 12 November 2012, 19:22:18 UTC |
| d01f505 | Dave Larson | 12 November 2012, 18:47:44 UTC | add change to allow overflow passthrough to work | 12 November 2012, 18:47:44 UTC |
| 929d7aa | Dave Larson | 12 November 2012, 18:27:13 UTC | test making backbone overflow:visible part of style | 12 November 2012, 18:27:13 UTC |
| 8dd99f6 | Dave Larson | 31 October 2012, 14:42:42 UTC | switched to counting non-reference alleles. Made exclusion of non-biallelic loci optional | 12 November 2012, 18:23:08 UTC |
| 41c979b | Malachi Griffith | 12 November 2012, 18:05:32 UTC | Added clinseq module to automatically generate mutation-diagram plots for case and cosmic variants | 12 November 2012, 18:05:32 UTC |
| 23ae45a | Malachi Griffith | 12 November 2012, 18:04:17 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 12 November 2012, 18:04:17 UTC |
| fa1c4a4 | Mark Burnett | 12 November 2012, 17:17:31 UTC | Merge changes I4e776ad9,Ie0a9d9eb,Id002688b,I0c16bbcf,I4f22ddbb * changes: use set operation use UR::Object::Set's server-side aggregate logic add timer instrumentation refactor allocated_kb body into sub improve reliability of the allocate with move test | 12 November 2012, 17:17:31 UTC |
| 6ac0b89 | Mark Burnett | 12 November 2012, 17:11:58 UTC | Merge "fix typo" | 12 November 2012, 17:11:58 UTC |
| b57e427 | Nathan Nutter | 09 November 2012, 21:36:27 UTC | Merge "change paired end inferrence to be less aggressive" | 09 November 2012, 21:36:27 UTC |
| d8cca35 | Malachi Griffith | 09 November 2012, 18:14:03 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 09 November 2012, 18:14:03 UTC |
| d754ca1 | Feiyu Du | 09 November 2012, 17:27:59 UTC | change the description of format FT to be TCGA-compliant | 09 November 2012, 17:27:59 UTC |
| c114b71 | Nathan Nutter | 08 November 2012, 22:50:04 UTC | change paired end inferrence to be less aggressive - If >= 90% paired end then run as paired end. - Else If <= 10% paired end then run as single end. - Else die. Change-Id: I755ce8659ee3d4ac1c2b339881e551289241f013 | 08 November 2012, 22:57:07 UTC |
| ac8bfbf | Thomas Mooney | 08 November 2012, 22:17:31 UTC | Add a few files containing paths to the list ignored by the build diff. | 08 November 2012, 22:17:31 UTC |
| df967e5 | Nathan Nutter | 08 November 2012, 22:05:29 UTC | use set operation This is still pretty hairy since we have to prevent UR from caching aggregate value. Change-Id: I4e776ad91612a34b379c168143d1765cf507eca5 | 08 November 2012, 22:14:25 UTC |
| 6b21c7b | Nathan Nutter | 08 November 2012, 21:52:07 UTC | use UR::Object::Set's server-side aggregate logic Change-Id: Ie0a9d9eb63b4508b443c7a405f2c4a462b159c1d | 08 November 2012, 22:14:24 UTC |
| ad0ee65 | Nathan Nutter | 08 November 2012, 21:23:08 UTC | add timer instrumentation Change-Id: Id002688b67d5e6e5f84988bb6572b5babb6856d8 | 08 November 2012, 22:14:23 UTC |
| c4b35dc | Nathan Nutter | 08 November 2012, 21:09:27 UTC | refactor allocated_kb body into sub Change-Id: I0c16bbcf5720a9b4f712b4f5e1a4f4892d89e3f3 | 08 November 2012, 22:14:22 UTC |
| 1a6603e | Nathan Nutter | 08 November 2012, 22:14:05 UTC | improve reliability of the allocate with move test Change-Id: I4f22ddbbd84d8c9973c6ef46783ac681a17469aa | 08 November 2012, 22:14:22 UTC |
| f315b72 | Anthony Brummett | 08 November 2012, 21:22:56 UTC | value_class_name was listed as an ID property, but not as a primary key column, so deletions were not working | 08 November 2012, 21:53:58 UTC |
| 2e763a4 | Nathan Nutter | 08 November 2012, 21:05:38 UTC | fix typo Change-Id: I5e4c644b5f05cc3bd8b74dc8e83e6b6b8fdf913c | 08 November 2012, 21:05:38 UTC |
| 7fc1648 | Adam Coffman | 08 November 2012, 20:52:08 UTC | Merge "Refactored logic into helper function Change-Id: I6bc17bc75d298c7aefa9e0ad94808c244480eefa" | 08 November 2012, 20:52:08 UTC |
| 9b9dfbc | APipe Tester | 08 November 2012, 20:38:03 UTC | Merge remote-tracking branch 'origin/master' | 08 November 2012, 20:38:03 UTC |
| d563ebd | Mark Burnett | 08 November 2012, 20:02:17 UTC | Merge "remove "random" call to volume" | 08 November 2012, 20:02:17 UTC |
| 67d172f | Mark Burnett | 08 November 2012, 20:00:02 UTC | Merge "only reload when committing" | 08 November 2012, 20:00:02 UTC |
| 8b7b512 | dmorton | 08 November 2012, 19:52:32 UTC | Refactored logic into helper function Change-Id: I6bc17bc75d298c7aefa9e0ad94808c244480eefa removed unused lib and whitespace Change-Id: Iec797bf4e4487dc03a95ec70c5e8442a5279aa2b Add --bowtie-version specification to chimerascan params You can now do something like: fusion_detection_strategy: 'chimerascan -v 0.4.5 [-p 2 --bowtie-version=0.12.7]' and only '-p 2' will be passed on to chimerascan and we take care of telling chimerascan what version of bowtie to use. You must supply a bowtie-version, and it currently must be of major version 0. Change-Id: I179271018de084d8a8f9caa713094a3347a39678 | 08 November 2012, 19:52:32 UTC |
| 940c28c | Cyriac Kandoth | 08 November 2012, 19:45:46 UTC | Added a hash to properly classify biotypes into ncRNA and pseudogenes. | 08 November 2012, 19:45:46 UTC |
| 7abd168 | Adam Coffman | 08 November 2012, 19:16:34 UTC | Merge "Fix how fusion_detection_strategy is parsed" | 08 November 2012, 19:16:34 UTC |
| 42f6365 | Malachi Griffith | 08 November 2012, 17:38:21 UTC | Minor update to clinseq update-analysis | 08 November 2012, 17:38:21 UTC |
| 8acb73b | Travis Abbott | 08 November 2012, 16:47:23 UTC | Fix dbsnp info field calculation | 08 November 2012, 16:48:13 UTC |
| b925f6d | dmorton | 08 November 2012, 16:15:35 UTC | Fix how fusion_detection_strategy is parsed Didn't take into account spaces in detector_params. Build shouldn't reference model explicitly. Change-Id: I6d685df2a3a38ce9efe1fa4b6da55d20af6a8ec7 | 08 November 2012, 16:33:57 UTC |
| 4148944 | Thomas Mooney | 08 November 2012, 16:12:57 UTC | Change somatic-variation PP to the Oct 2012 defaults (RT#87515) | 08 November 2012, 16:12:57 UTC |
| a2274bf | APipe Tester | 08 November 2012, 16:07:08 UTC | updated ur submodule to 1ab73d5 | 08 November 2012, 16:07:08 UTC |
| f3e0a82 | Thomas Mooney | 08 November 2012, 14:08:38 UTC | Testing with live data continues to make us cry. Update expected results. | 08 November 2012, 14:08:38 UTC |
| fe86aeb | Thomas Mooney | 08 November 2012, 03:31:10 UTC | Only annotate if we have something to annotate. | 08 November 2012, 03:31:10 UTC |
| 23359bc | Eddie Belter | 08 November 2012, 00:57:05 UTC | DV2 Breakdancer: add fastq validation when running -d | 08 November 2012, 00:57:41 UTC |
| 06da733 | Eddie Belter | 08 November 2012, 00:56:36 UTC | SX: add validate method to seq reader | 08 November 2012, 00:57:41 UTC |
| 45609aa | Scott Smith | 06 November 2012, 21:35:42 UTC | md5 fastqs | 08 November 2012, 00:57:40 UTC |
| 85c8dcf | Scott Smith | 06 November 2012, 16:55:59 UTC | remove hard-coded nomenclature in instrument data attribute constructor | 08 November 2012, 00:57:40 UTC |
| 43d10c9 | Scott Smith | 06 November 2012, 16:50:10 UTC | made the default nomenclature for instrument data come from an environment config not a hard-coded value | 08 November 2012, 00:57:40 UTC |
| 56ff4df | Eddie Belter | 08 November 2012, 00:39:54 UTC | MC16s 454 test: lower the number of levels when checking classifications b/c it is not deterministic | 08 November 2012, 00:39:54 UTC |
| 5cc44d4 | Chris Miller | 07 November 2012, 22:53:13 UTC | checking for the presence of the variable before trying to split it - a novel idea | 07 November 2012, 22:53:47 UTC |
| 7501659 | Thomas Mooney | 07 November 2012, 22:35:54 UTC | Examine one level deeper (i.e. via the merged results) for the build | 07 November 2012, 22:35:54 UTC |
| 6da4897 | Travis Abbott | 07 November 2012, 22:30:27 UTC | add missing : in phenotype correlation dbsnp info fields | 07 November 2012, 22:30:27 UTC |
| 290654f | Travis Abbott | 07 November 2012, 21:03:06 UTC | update dbsnp info fields in phenotypecorrelation in dbsnp137+, the CLN field has become PM. As an intermediate step on the path to having an annotation_strategy as part of the processing profile, there is now a method that returns the proper info fields for a given dbsnp version. | 07 November 2012, 21:04:31 UTC |
| c2309aa | Nathan Nutter | 06 November 2012, 22:02:19 UTC | remove "random" call to volume Change-Id: Ib02ec6b91ccd50b6d4bd4862d0345b47aca8d085 | 07 November 2012, 20:21:11 UTC |
| 89bb1d3 | Nathan Nutter | 07 November 2012, 20:08:03 UTC | only reload when committing Change-Id: I4ae0489f51ec6e8ba086c44d3705ad4d3e6a0868 | 07 November 2012, 20:21:02 UTC |
| 608ecf3 | APipe Tester | 07 November 2012, 19:10:10 UTC | Merge remote-tracking branch 'origin/master' | 07 November 2012, 19:10:10 UTC |
| a2590ee | Thomas Mooney | 07 November 2012, 18:20:32 UTC | Skip tiering if there were no qualifying variants. | 07 November 2012, 18:20:32 UTC |
| 19e13b6 | Nathan Nutter | 07 November 2012, 17:00:48 UTC | Merge "Fix how we find Chimerascan for a given version." | 07 November 2012, 17:00:48 UTC |
| f362bfe | Thomas Mooney | 07 November 2012, 15:33:16 UTC | Make annotation build required on validation builds. | 07 November 2012, 15:33:16 UTC |
| c16f0cb | Gabriel Sanderson | 06 November 2012, 23:27:22 UTC | Merge branch 'master' into gb_master | 06 November 2012, 23:27:22 UTC |
| 4de72d5 | Gabriel Sanderson | 06 November 2012, 23:27:06 UTC | If all vcf files are not present, inform the user which builds did and did not have them. | 06 November 2012, 23:27:06 UTC |
| 430aa53 | dmorton | 05 November 2012, 22:44:43 UTC | Fix how we find Chimerascan for a given version. It didn't used to try to find the installation in the typical debian install location. Change-Id: I8ef0f9f0ddc02ef4cb3c01fbacea3ae795b1e8d4 | 06 November 2012, 22:47:59 UTC |
| 9ac0fd8 | Nathaniel Nutter | 06 November 2012, 21:16:55 UTC | work around weird openmpi behavior | 06 November 2012, 21:17:21 UTC |
| 5f80fc0 | apregier | 06 November 2012, 20:54:16 UTC | Merge branch 'fireteam2' into gb_master | 06 November 2012, 20:54:16 UTC |
| 6fb8260 | apregier | 06 November 2012, 20:53:52 UTC | Use Ensembl BiotypeMapper API | 06 November 2012, 20:53:52 UTC |
| a98c349 | dmorton | 06 November 2012, 20:08:41 UTC | Fix how get_vcf_header was being used. | 06 November 2012, 20:08:41 UTC |
| 8030ff5 | dmorton | 06 November 2012, 20:06:57 UTC | Fix mistake in Utility/Vcf get_vcf_header had stupid parameter handling mistake. Added test for get_vcf_header. | 06 November 2012, 20:06:57 UTC |
| 8fbf3d5 | Nathaniel Nutter | 06 November 2012, 16:13:45 UTC | fix invalid call to mkpath mkpath was probably meant to be File::Path's make_path but even more so it should be Genome::Sys->create_directory | 06 November 2012, 16:43:16 UTC |
| d88587d | Scott Smith | 06 November 2012, 16:31:35 UTC | add parens to remove warning | 06 November 2012, 16:31:35 UTC |
| 04f8fda | Scott Smith | 06 November 2012, 16:26:58 UTC | Genome::Sys - pulled snapshot_revision from Genome/Sys/TGI/Extension/Sys.pm, and broke out one method for the TGI-specific part, which shortens directory names. That method is still in the old module but is only called when present. | 06 November 2012, 16:26:58 UTC |
| a9626c0 | Scott Smith | 06 November 2012, 16:25:11 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 06 November 2012, 16:25:11 UTC |
| dcc026e | Scott Smith | 06 November 2012, 15:51:09 UTC | Genome::Sys - pulled snapshot_revision from Genome/Sys/TGI/Extension/Sys.pm, and broke out one method for the TGI-specific part, which shortens directory names. That method is still in the old module but is only called when present. | 06 November 2012, 15:51:09 UTC |
| 1d8e5cc | Chris Miller | 06 November 2012, 15:23:32 UTC | added option to keep ambiguous calls, added checks to prevent crashing on maf creation when tiering isn't specified | 06 November 2012, 15:23:47 UTC |
| 50fd43c | Chris Miller | 06 November 2012, 15:22:20 UTC | pindel vaf filter obsoleted some code | 06 November 2012, 15:23:47 UTC |
| 9d2291e | Scott Smith | 06 November 2012, 07:18:46 UTC | replaced calls to UR::Time->now with UR::Context->current->now | 06 November 2012, 07:18:46 UTC |
| 9f2aa6b | Scott Smith | 06 November 2012, 06:19:41 UTC | findreplace for all UR::BoolExpr ->specified_value_for_property_name to ->value_for | 06 November 2012, 06:19:41 UTC |
| 3d5c75b | Eddie Belter | 05 November 2012, 23:58:47 UTC | CHANGELOG: Add trimmer info to BWA intermediate alignment results | 06 November 2012, 00:01:05 UTC |
| 26ad9a9 | Feiyu Du | 05 November 2012, 21:01:19 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 05 November 2012, 21:01:19 UTC |
| 344594e | Feiyu Du | 05 November 2012, 21:01:10 UTC | Increase the mem limit to prevent unnecessary build failures due to mem limit | 05 November 2012, 21:01:10 UTC |
| 56222e1 | Gabriel Sanderson | 05 November 2012, 20:58:59 UTC | Merge branch 'master' into gb_master | 05 November 2012, 20:58:59 UTC |
| 194e007 | Gabriel Sanderson | 05 November 2012, 20:58:33 UTC | Print better error messages when there are duplicate subjects in the input. | 05 November 2012, 20:58:42 UTC |
| 2bed630 | Jim Weible | 05 November 2012, 20:27:46 UTC | compensate for Joinx intersect not sorting (Joinx Union does) | 05 November 2012, 20:27:46 UTC |
| 41c6ae9 | Thomas Mooney | 05 November 2012, 19:11:43 UTC | Add review step to the end of the SomaticValidation pipeline. CHANGELOG: The SomaticValidation pipeline has a new step at the end that compares the variants it found with those variants previously found in the original SomaticVariation run. | 05 November 2012, 19:11:43 UTC |
| 6482b9e | Thomas Mooney | 05 November 2012, 19:09:37 UTC | Refinements to the new variant review at the end of SomaticValidation *Only review tier 1 UHC variants. *Add tiering/annotation for validated variants. *A bit of cleanup | 05 November 2012, 19:09:37 UTC |
| cd7902e | Nathan Dees | 05 November 2012, 18:30:31 UTC | fixed error in purity calculation for wgs analysis type | 05 November 2012, 18:30:31 UTC |
| e47ff53 | Nathan Dees | 05 November 2012, 17:28:10 UTC | fixed a print message | 05 November 2012, 17:28:10 UTC |
| 0d27123 | Nathan Dees | 05 November 2012, 17:25:08 UTC | first pass at a C->T base checker and P-value generator for counting bases before or after C->T mutation | 05 November 2012, 17:25:08 UTC |
| 5560356 | Nathan Dees | 05 November 2012, 17:20:12 UTC | removed dbsingle | 05 November 2012, 17:20:12 UTC |
| cdf05ef | Nathan Dees | 05 November 2012, 16:55:22 UTC | fixed case when type is defined but does not actually indicate INS DEL or SNP | 05 November 2012, 16:55:22 UTC |
| f81a839 | Nathan Dees | 05 November 2012, 16:48:40 UTC | added function to perform p-value for sequence context and print results | 05 November 2012, 16:48:40 UTC |
| 719053f | Nathan Dees | 05 November 2012, 16:47:34 UTC | changed some headings; changed the scale of the differential plot | 05 November 2012, 16:47:34 UTC |
| 837f5ad | Nathan Dees | 05 November 2012, 16:36:17 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 05 November 2012, 16:36:17 UTC |
| c07d714 | Nathan Dees | 05 November 2012, 16:36:06 UTC | indented | 05 November 2012, 16:36:06 UTC |
| d6be815 | Nathaniel Nutter | 03 November 2012, 02:11:35 UTC | fix uninitialized warning for exclude_mount_path | 03 November 2012, 02:11:35 UTC |
| 6b17d50 | Nathaniel Nutter | 03 November 2012, 02:11:10 UTC | fix for Oracle conversion error due to "not like" | 03 November 2012, 02:11:10 UTC |
| 13ce279 | Mark Burnett | 02 November 2012, 23:39:26 UTC | Add grow_only option to reallocate command | 02 November 2012, 23:40:03 UTC |
| ae7c05c | Cyriac Kandoth | 02 November 2012, 23:27:50 UTC | Change default method to correlate mut status to quantitative data | 02 November 2012, 23:27:50 UTC |
| a7ad428 | Anthony Brummett | 02 November 2012, 21:50:30 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 02 November 2012, 21:50:30 UTC |
| 7883fd7 | Anthony Brummett | 02 November 2012, 21:47:31 UTC | Fix bugs when moving allocations The param exclude_mount_paths was only ever used with one item, and was not getting serialized properly, so we'll only use it as a scalar, Top-level directories in volumes are not writable, so we won't be able to make top-level directories for unarchive_allocation_destination and move_allocation_destination during moves and unarchives. The change just tacks on the additional string to the end of the directory name already being used before moving the name back | 02 November 2012, 21:47:31 UTC |
| a19e1b1 | Adam Coffman | 02 November 2012, 21:31:22 UTC | Add bowtie_version accessor to Merged Alignment Results Also, add a generic method to Merged Alignment results that attempts to discern a scalar property value from its underlying alignment results. | 02 November 2012, 21:31:22 UTC |
| a57dc7d | Cyriac Kandoth | 02 November 2012, 21:03:30 UTC | Fixed: some ncRNA were being classified as UTR | 02 November 2012, 21:03:30 UTC |
| 4997465 | Malachi Griffith | 02 November 2012, 20:47:31 UTC | Cosmetic updates to clinseq comments | 02 November 2012, 20:47:31 UTC |
