| 421a043 | Scott Smith | 22 November 2012, 17:59:42 UTC | added breakdancer 1.3.7 | 22 November 2012, 17:59:42 UTC |
| c1fa6cb | Scott Smith | 22 November 2012, 17:01:54 UTC | advance breakdancer | 22 November 2012, 17:01:54 UTC |
| 067b4dc | APipe Tester | 21 November 2012, 21:53:50 UTC | updated ur submodule to c890bcb | 21 November 2012, 21:53:50 UTC |
| 2bcbab6 | Scott Smith | 21 November 2012, 17:04:40 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 21 November 2012, 17:04:40 UTC |
| 0214761 | Scott Smith | 21 November 2012, 17:04:32 UTC | fix typo in clinseq --common-name param | 21 November 2012, 17:04:32 UTC |
| dc2d80b | dmorton | 21 November 2012, 16:35:41 UTC | Add --reuse-bam as option for chimerascan detect_fusion_strategy: "chimerascan 1.2.3 [--reuse-bam=1] will put into the chimerascan staging directory a set of files that pretend to be the files that chimerascan would have created. This makes chimerascan skip the processing that would have produced them. | 21 November 2012, 16:39:30 UTC |
| 71245ca | dmorton | 21 November 2012, 16:22:11 UTC | Fix how we resolve Chimerascan Index | 21 November 2012, 16:35:16 UTC |
| 9ebffa8 | Scott Smith | 21 November 2012, 16:31:21 UTC | switch from snv/generateClonalityPlot.pl to genome model clin-seq generate-clonality-plots | 21 November 2012, 16:31:21 UTC |
| b71ffe9 | Scott Smith | 21 November 2012, 16:05:50 UTC | Activate test for GenerateClonalityPlots.t Also added an optional parameter to shortcut on generating read counts, though testing is not complete on using this. Run time is 17 minutes. | 21 November 2012, 16:05:50 UTC |
| 77be9f7 | Scott Smith | 21 November 2012, 16:05:04 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 21 November 2012, 16:05:04 UTC |
| 605150a | dmorton | 21 November 2012, 15:12:02 UTC | Fix mistake with $self->bowtie_version Also ensure that we only register this build as a user of the index result inside of this UR::Context since this build doesn't exist on the DB yet. | 21 November 2012, 15:13:27 UTC |
| 04506eb | Scott Smith | 21 November 2012, 14:36:05 UTC | activate test case for GenerateClonalityPlots | 21 November 2012, 14:36:05 UTC |
| 67847ff | Thomas Mooney | 21 November 2012, 14:33:12 UTC | Make previously_discovered_variations_build an alias instead of indirect. | 21 November 2012, 14:33:12 UTC |
| 9f76087 | Thomas Mooney | 21 November 2012, 14:22:28 UTC | Get warnings out of the way before output we care about. | 21 November 2012, 14:22:28 UTC |
| 806ee5d | Scott Smith | 21 November 2012, 13:52:51 UTC | test case for GenerateClonalityPlots.t | 21 November 2012, 13:52:51 UTC |
| 9e02552 | Scott Smith | 21 November 2012, 06:10:48 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 21 November 2012, 06:10:48 UTC |
| 75d7322 | Scott Smith | 21 November 2012, 06:10:40 UTC | initial version of clinseq generate-clonality-plots | 21 November 2012, 06:10:40 UTC |
| 64b00f6 | Cyriac Kandoth | 21 November 2012, 04:17:43 UTC | General edits to formatting | 21 November 2012, 04:17:43 UTC |
| 0dbba7c | Obi Griffith | 21 November 2012, 01:49:46 UTC | Created new tool (from clinseq tool) to create igv session xml from a somatic variation build | 21 November 2012, 01:49:46 UTC |
| c0fff9f | Adam Coffman | 20 November 2012, 23:26:15 UTC | Create Chimerscan Index in a different process This allows other builds to utilize the index result as soon as it is created. Additionally the index is committed regardless of the ultimate succeess of the chimerascan run. | 20 November 2012, 23:26:15 UTC |
| 8d381d6 | Adam Coffman | 20 November 2012, 23:15:44 UTC | Command wrapper for chimerscan index creation | 20 November 2012, 23:15:44 UTC |
| 874b751 | APipe Tester | 20 November 2012, 21:02:06 UTC | updated ur submodule to 7180c47 | 20 November 2012, 21:02:06 UTC |
| 8fb1465 | Scott Smith | 20 November 2012, 20:54:21 UTC | updated Genome::Model::Command::Define::Helper to correctly classify properties as input/param to clean up docs | 20 November 2012, 20:54:21 UTC |
| e94ea49 | Scott Smith | 20 November 2012, 20:40:48 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 20 November 2012, 20:40:48 UTC |
| 31af76e | Scott Smith | 20 November 2012, 20:40:40 UTC | Updated again to work with lastes UR. Docs are still sub-optimal, but in sync with generic Command::V2 logic. | 20 November 2012, 20:40:40 UTC |
| 5e34fbe | APipe Tester | 20 November 2012, 20:35:40 UTC | updated ur submodule to 04305bf | 20 November 2012, 20:35:40 UTC |
| f3b56fc | Scott Smith | 20 November 2012, 20:12:04 UTC | updated Define-docs.t to expect a help message which includes the help_detail ("DESCRIPTION" section) | 20 November 2012, 20:12:04 UTC |
| 790d2e8 | Thomas Mooney | 20 November 2012, 19:45:25 UTC | Fork and run the local version of Genome::Command instead of using shellcmd The test then no longer depends on a deployed version of `genome` being available and compatible with the repository under test. (On the other hand there is no longer a test of whether or not the user could run `genome`... but that seems a different concern than whether or not the documentation can be generated correctly.) | 20 November 2012, 19:45:25 UTC |
| e7df998 | apregier | 20 November 2012, 19:32:47 UTC | Merge branch 'my_annotation' into gb_master | 20 November 2012, 19:32:47 UTC |
| cfc466f | apregier | 20 November 2012, 18:43:08 UTC | Add reference_coordinates option to dbsnp import | 20 November 2012, 19:32:05 UTC |
| 0e5eb7e | apregier | 12 November 2012, 19:06:17 UTC | Update dbsnp import to allow vcf or bed only, and to allow user to specify which chromosomes to import | 20 November 2012, 19:32:04 UTC |
| ffad1b8 | Malachi Griffith | 20 November 2012, 19:30:28 UTC | Added test case for clin-seq update-analysis | 20 November 2012, 19:30:28 UTC |
| eb83548 | APipe Tester | 20 November 2012, 19:28:26 UTC | updated ur submodule to 71d09bd | 20 November 2012, 19:28:26 UTC |
| e670c29 | APipe Tester | 20 November 2012, 18:13:27 UTC | updated ur submodule to 14eae9f | 20 November 2012, 18:13:27 UTC |
| f756b8c | Malachi Griffith | 20 November 2012, 18:12:43 UTC | Updated documentation for clin-seq update analysis | 20 November 2012, 18:12:43 UTC |
| 8086281 | Malachi Griffith | 20 November 2012, 17:23:52 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 20 November 2012, 17:23:52 UTC |
| 81855b2 | Malachi Griffith | 20 November 2012, 17:23:37 UTC | Added extra sample input checks and made tumor/normal sample defs an option to clinseq update-analysis | 20 November 2012, 17:23:37 UTC |
| 865b3e4 | Scott Smith | 20 November 2012, 17:19:32 UTC | fixed warning in Define-docs.t | 20 November 2012, 17:19:32 UTC |
| ee29b52 | Scott Smith | 20 November 2012, 17:00:18 UTC | handle/skip old microarray models which do not have a reference_sequence_build | 20 November 2012, 17:00:18 UTC |
| 3ad7766 | Scott Smith | 20 November 2012, 16:29:17 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 20 November 2012, 16:29:17 UTC |
| 66aef92 | Scott Smith | 20 November 2012, 16:29:09 UTC | added a test case for "genome model define" | 20 November 2012, 16:29:09 UTC |
| 91469cf | Thomas Mooney | 20 November 2012, 16:13:21 UTC | Remove stray whitespace. | 20 November 2012, 16:13:21 UTC |
| d88201f | Travis Abbott | 19 November 2012, 20:42:25 UTC | fix more invalid vcf header entries from polymutt | 19 November 2012, 20:42:25 UTC |
| 0b328dd | apregier | 19 November 2012, 20:32:06 UTC | Merge branch 'fix' into gb_master | 19 November 2012, 20:32:06 UTC |
| ff448ec | apregier | 19 November 2012, 20:31:37 UTC | Fix build query | 19 November 2012, 20:31:49 UTC |
| a03c181 | apregier | 19 November 2012, 18:44:07 UTC | Revert "Revert "Add software versioning for import annotation"" This reverts commit d2042cc769a0c91c5136177d54bec7b78d7982cf. | 19 November 2012, 20:31:49 UTC |
| 9c1c3d9 | dmorton | 19 November 2012, 18:10:01 UTC | Added some color to 'model build start' command | 19 November 2012, 19:53:46 UTC |
| 9019da4 | dmorton | 16 November 2012, 15:29:13 UTC | Fix some SoftwareResults not saving all properties Also cache the results of getting fastqs from bams | 19 November 2012, 19:53:03 UTC |
| 46b1ef7 | Mark Burnett | 12 November 2012, 18:37:12 UTC | add annotation step to Somatic Validation | 19 November 2012, 18:11:05 UTC |
| 6e44ffc | Mark Burnett | 13 November 2012, 22:03:37 UTC | Add globbing path method to DV2:Classify:Tier | 19 November 2012, 18:11:05 UTC |
| 9478c36 | Mark Burnett | 15 November 2012, 14:41:18 UTC | change symlink filename filter exclude 'lq' files when doing 'hq', and vice versa | 19 November 2012, 18:11:05 UTC |
| 12e1ce0 | Mark Burnett | 13 November 2012, 22:02:12 UTC | fix Validation TierVariants to also tier lq variants | 19 November 2012, 18:10:41 UTC |
| 600c530 | apregier | 19 November 2012, 18:01:02 UTC | Merge branch 'fix' into gb_master | 19 November 2012, 18:01:02 UTC |
| d2042cc | apregier | 19 November 2012, 18:00:36 UTC | Revert "Add software versioning for import annotation" This reverts commit 3e17dab4537603c768704639d02b8692779df33a. | 19 November 2012, 18:00:36 UTC |
| b9adb03 | Scott Smith | 19 November 2012, 17:53:18 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 19 November 2012, 17:53:18 UTC |
| d575fc6 | Scott Smith | 19 November 2012, 17:51:58 UTC | made the "genome model differential-expression" Command.pm not abstract, so it will appper correctly in docs. | 19 November 2012, 17:51:58 UTC |
| a872374 | apregier | 19 November 2012, 16:28:40 UTC | Merge branch 'fix' into gb_master | 19 November 2012, 16:28:40 UTC |
| 3e17dab | apregier | 19 November 2012, 16:28:00 UTC | Add software versioning for import annotation | 19 November 2012, 16:28:08 UTC |
| eaac45c | Malachi Griffith | 19 November 2012, 00:57:57 UTC | Added basic clin-seq indel converge script | 19 November 2012, 00:57:57 UTC |
| e12c360 | Malachi Griffith | 18 November 2012, 17:35:02 UTC | Added standard lister for genome model differentia-expression | 18 November 2012, 17:35:02 UTC |
| 1cb64cb | Malachi Griffith | 18 November 2012, 17:32:55 UTC | Minor update to cufflinks converge tool | 18 November 2012, 17:32:55 UTC |
| d0859fc | Obi Griffith | 17 November 2012, 17:47:47 UTC | Fixed CnView to handle case of segments file with no data rows - possible in completely copy neutral genome | 17 November 2012, 17:47:47 UTC |
| 27fcec5 | Malachi Griffith | 16 November 2012, 22:24:59 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 16 November 2012, 22:24:59 UTC |
| e01534b | Malachi Griffith | 16 November 2012, 22:24:45 UTC | Added option for debugging purposes | 16 November 2012, 22:24:45 UTC |
| ad00d51 | Dave Larson | 16 November 2012, 22:12:57 UTC | guard against array overrun in cases where the number of domains is extreme | 16 November 2012, 22:12:57 UTC |
| 7363a8e | Dave Larson | 16 November 2012, 21:15:52 UTC | dispense with overflow specification, and child svg elements. Add translation onto Views. May fix clipping and doc issues. | 16 November 2012, 21:15:57 UTC |
| 107e79b | Obi Griffith | 16 November 2012, 21:14:17 UTC | added note about CnView script being replaced by tool | 16 November 2012, 21:14:17 UTC |
| a940035 | Obi Griffith | 16 November 2012, 20:56:40 UTC | Updated CnView command in ClinSeq to use new CnView gmt | 16 November 2012, 20:56:40 UTC |
| d567223 | Ben Oberkfell | 16 November 2012, 20:13:29 UTC | Merge branch 'master' of git:/srv/git/genome | 16 November 2012, 20:13:29 UTC |
| 5c3e589 | Ben Oberkfell | 16 November 2012, 19:58:42 UTC | fix for when querying postgres & generating allocations | 16 November 2012, 19:58:42 UTC |
| 5e89af3 | Obi Griffith | 16 November 2012, 18:16:43 UTC | fixed CnView tests cases to not diff jpegs, instead check for existence and non-zero | 16 November 2012, 18:16:43 UTC |
| 608fc4a | Brian Derickson | 16 November 2012, 17:45:44 UTC | new class for grid_jobs_finished table | 16 November 2012, 17:46:02 UTC |
| 28caf0f | Adam Coffman | 16 November 2012, 16:24:13 UTC | whitespace | 16 November 2012, 16:24:13 UTC |
| 073f77c | Obi Griffith | 16 November 2012, 01:55:10 UTC | test cases for "gmt copy-number cn-view" | 16 November 2012, 01:55:10 UTC |
| c126468 | Malachi Griffith | 16 November 2012, 00:04:26 UTC | Minor updates to clin-seq | 16 November 2012, 00:04:26 UTC |
| 3bfb588 | Obi Griffith | 16 November 2012, 00:02:39 UTC | updated cnview to display HMM segments | 16 November 2012, 00:02:39 UTC |
| 7d614e6 | Adam Coffman | 15 November 2012, 23:50:03 UTC | gmt wrapper for Picard FilterSamReads tool | 15 November 2012, 23:50:03 UTC |
| 46a7352 | Travis Abbott | 15 November 2012, 23:38:27 UTC | relationship therapy - MergeAndFixVcfs in gmt relationship merge-and-fix-vcfs improve performance by keeping an iterator into the current chromosome for the denovo file rather than looping over all denovo positions in said chromosome for each position in the standard file. before switching to a new chromosome, dump all remaining (unprocessed) denovo sites to the output. previously, these were dumped at the very end of the file, so if the denovo file contained sites on chr1 with pos greater than any site in the standard file on chr1, they would appear at the end of the file rather than prior to chr2. this change makes the output much closer to sorted, but... joinx sort the final output file, since the chromosome order of the input files depends on the reference sequence in use. the ticket that spawned this work was using hg18, so X,Y are found between 9,10, which may cause problems down the road. this (hopefully) fixes rt#86339 | 15 November 2012, 23:38:27 UTC |
| 1fd161d | Travis Abbott | 15 November 2012, 23:37:29 UTC | return error in gmt::Joinx::Sort return value of sys::shellcmd in joinx::sort->execute | 15 November 2012, 23:37:29 UTC |
| 48edcdc | dmorton | 15 November 2012, 20:59:13 UTC | Refactored RnaSeq ChimerascanResult In preparation to allow it reuse bams. | 15 November 2012, 21:00:29 UTC |
| 29a7ce3 | APipe Tester | 15 November 2012, 17:46:50 UTC | updated ur submodule to b174fb0 | 15 November 2012, 17:46:50 UTC |
| de1be5e | Feiyu Du | 15 November 2012, 17:21:31 UTC | add files to ignore by diff | 15 November 2012, 17:21:31 UTC |
| 9bfc065 | Kyung Kim | 15 November 2012, 16:46:37 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 15 November 2012, 16:46:37 UTC |
| 8f459e2 | Kyung Kim | 15 November 2012, 16:46:27 UTC | New tool to remove specified positions from fasta file | 15 November 2012, 16:46:27 UTC |
| b45e640 | Obi Griffith | 15 November 2012, 00:58:15 UTC | working on adding segments to CnView analysis | 15 November 2012, 00:58:15 UTC |
| 2df102e | Kyung Kim | 14 November 2012, 22:40:56 UTC | Get reads from repeatmasker input file and proceed on when *masked file is missing after repeatmasker run | 14 November 2012, 22:40:56 UTC |
| 92f4ad3 | Gabriel Sanderson | 14 November 2012, 22:12:39 UTC | Merge branch 'tcga' into gb_master | 14 November 2012, 22:12:39 UTC |
| 7871f7e | Gabriel Sanderson | 14 November 2012, 22:11:28 UTC | CHANGELOG: SomaticVariation now makes a snvs_tcga.tar.gz which is tcga compliant. | 14 November 2012, 22:12:21 UTC |
| 5b194f9 | APipe Tester | 14 November 2012, 21:32:50 UTC | updated jenkins submodule to 6dbe3a7 | 14 November 2012, 21:32:50 UTC |
| c107b96 | Thomas Mooney | 14 November 2012, 20:48:37 UTC | Remove old error mailing--this caused errors since App::Mail isn't imported. The result was that exit() wasn't reached and both sides of the fork continued when the command had been eval{}ed (such as under workflow. | 14 November 2012, 20:48:37 UTC |
| 71c03b2 | Scott Smith | 14 November 2012, 20:18:31 UTC | fix warning message in dbpath in Genome::Sys | 14 November 2012, 20:18:31 UTC |
| 2c5671f | Scott Smith | 14 November 2012, 20:16:11 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 14 November 2012, 20:16:11 UTC |
| c2ceab4 | Nathan Nutter | 14 November 2012, 16:52:08 UTC | updated ur submodule (includes Tony's Oracle 11 fix) Change-Id: I1d7041c8d81a8a42ebde08465586dac2c59685df | 14 November 2012, 16:53:01 UTC |
| f492fb2 | Jason Walker | 14 November 2012, 14:48:03 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 14 November 2012, 14:48:03 UTC |
| 20db422 | Jason Walker | 14 November 2012, 14:47:00 UTC | Revert changes that used the python module from chimerascan to convert GTF to genePred format. The CDS start stop is not working with Picard CollectRnaSeqMetrics | 14 November 2012, 14:47:00 UTC |
| 3252ce8 | Scott Smith | 14 November 2012, 02:31:05 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 14 November 2012, 02:31:05 UTC |
| 8a8501f | Obi Griffith | 14 November 2012, 01:39:49 UTC | merge branch 'master' of ssh://git/srv/git/genome | 14 November 2012, 01:39:49 UTC |
| 6a32657 | Obi Griffith | 14 November 2012, 01:39:28 UTC | refactored CnView tool | 14 November 2012, 01:39:28 UTC |
| f7f2f81 | Gabriel Sanderson | 14 November 2012, 00:17:58 UTC | Merge branch 'tcga' into gb_master | 14 November 2012, 00:17:58 UTC |
| e5f441a | Gabriel Sanderson | 14 November 2012, 00:17:47 UTC | Fixed package_file_for_tcga | 14 November 2012, 00:17:47 UTC |
