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23 March 2024, 19:04:16 UTC
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Revision Author Date Message Commit Date
5caf816 dmorton 08 November 2013, 17:55:35 UTC Rnaseq test model should diff clean now 08 November 2013, 17:55:35 UTC
939e137 dmorton 08 November 2013, 16:49:20 UTC Fix silly mistake 08 November 2013, 17:01:38 UTC
affc0dc dmorton 08 November 2013, 15:27:51 UTC DetectFusions command correctly handels linking software-results 08 November 2013, 15:30:01 UTC
400ee8e Travis Abbott 08 November 2013, 14:43:36 UTC improve filter-structures test: look at actual rows of counts that survive the filter, not just the gene names. 08 November 2013, 14:43:36 UTC
707a2ae Travis Abbott 08 November 2013, 14:43:19 UTC 1 at end of module 08 November 2013, 14:43:19 UTC
be869aa Travis Abbott 08 November 2013, 14:32:13 UTC change edge-r filter-structures params: specify percentile/min_count in terms of what it takes to fail the filter (as opposed to survive) & update docs accordingly. 08 November 2013, 14:32:13 UTC
ae1b873 Travis Abbott 08 November 2013, 14:22:58 UTC add help messages to edge-r filter-structures 08 November 2013, 14:22:58 UTC
fb5cd9e Travis Abbott 08 November 2013, 14:18:37 UTC add FilterStructures command for edgeR 08 November 2013, 14:18:37 UTC
c41a804 APipe Tester 08 November 2013, 13:15:35 UTC Updated `genome` tab completion. 08 November 2013, 13:16:21 UTC
9af5eb7 APipe Tester 08 November 2013, 13:14:11 UTC Updated class browser cache. 08 November 2013, 13:16:20 UTC
82d7414 dmorton 08 November 2013, 13:15:08 UTC Fix lookup for picard_version While it is a model parameter, and hence a build parameter, it is only on the model so it can be specified in the processing-profile. This is misleading imo. 08 November 2013, 13:15:08 UTC
680bd32 dmorton 08 November 2013, 07:17:26 UTC Complete transition of chimerascan to a workflow 08 November 2013, 07:17:26 UTC
ce4358d dmorton 08 November 2013, 04:43:02 UTC Fix package name and class name mistakes 08 November 2013, 04:43:02 UTC
c6fd82a Eddie Belter 07 November 2013, 18:22:40 UTC RNA Seq: need to pass build into map_workflow_inputs 07 November 2013, 18:22:40 UTC
825727f Gabriel Sanderson 07 November 2013, 17:02:41 UTC Merge branch 'master' into gb_master 07 November 2013, 17:02:41 UTC
668f89d Gabriel Sanderson 07 November 2013, 17:01:24 UTC Ignore tabix files in control_variants_for_loh also. 07 November 2013, 17:01:24 UTC
af7c061 Thomas Mooney 07 November 2013, 14:59:04 UTC Add a default of 0 for kb requested. If a desired value is not passed and `du` returns 0, List::Util::max returns undef instead of 0. 07 November 2013, 14:59:04 UTC
bd40e47 APipe Tester 07 November 2013, 13:17:02 UTC Updated `gmt` tab completion. 07 November 2013, 13:17:02 UTC
a45fb38 APipe Tester 07 November 2013, 13:16:21 UTC Updated `genome` tab completion. 07 November 2013, 13:16:21 UTC
db8996f APipe Tester 07 November 2013, 13:14:58 UTC Updated class browser cache. 07 November 2013, 13:14:58 UTC
b9d2bda Travis Abbott 07 November 2013, 01:00:38 UTC doc/formatting updates for edge-r 07 November 2013, 01:01:28 UTC
a47dc5b Thomas Mooney 06 November 2013, 23:35:11 UTC Remove exit()s from error conditions. 06 November 2013, 23:35:11 UTC
3976a96 Thomas Mooney 06 November 2013, 23:28:07 UTC Ignore files with BAM paths in them. 06 November 2013, 23:28:07 UTC
39d55e5 Travis Abbott 06 November 2013, 22:49:34 UTC more doc formatting for edge-r classic 06 November 2013, 22:49:34 UTC
bbd19ce Travis Abbott 06 November 2013, 22:45:12 UTC add example output to edge-r help 06 November 2013, 22:45:12 UTC
9e932b4 Travis Abbott 06 November 2013, 22:41:58 UTC forgot to add test case for edgeR ... 06 November 2013, 22:41:58 UTC
f733b1d Travis Abbott 06 November 2013, 22:40:54 UTC row names now get a (blank) column header in edgeR output 06 November 2013, 22:40:54 UTC
760ac8e Travis Abbott 06 November 2013, 22:36:18 UTC add a few comments to edge-r test 06 November 2013, 22:36:18 UTC
0c30ad6 Travis Abbott 06 November 2013, 22:29:20 UTC don't use is_many for groups property not sure if is_many always guarantees that order is preserved 06 November 2013, 22:29:20 UTC
a2e9587 Travis Abbott 06 November 2013, 22:02:33 UTC update edge-r classic docs include description of output format 06 November 2013, 22:02:33 UTC
fd593a6 Travis Abbott 06 November 2013, 21:52:09 UTC update edge-r classic to include class predictions 06 November 2013, 21:53:07 UTC
adb4f43 Gabriel Sanderson 06 November 2013, 21:29:50 UTC Merge branch 'tbi' into gb_master 06 November 2013, 21:29:50 UTC
1df4e32 Gabriel Sanderson 06 November 2013, 21:29:13 UTC Ignore tabix files since they diff every time. 06 November 2013, 21:29:38 UTC
304cb00 Mark Burnett 06 November 2013, 21:04:10 UTC bugfix: move is_x queries to subclasses 06 November 2013, 21:26:39 UTC
35dcdb1 Avinash Ramu 06 November 2013, 21:24:37 UTC added chimerascan filter-output and intersect-sv to clinseq 06 November 2013, 21:24:52 UTC
e9e2723 Travis Abbott 06 November 2013, 21:18:03 UTC add gmt edge-r classic command for diff. exp. analysis 06 November 2013, 21:18:03 UTC
732f15f Eddie Belter 06 November 2013, 20:01:14 UTC RNA Seq: correctly get workflow inputs for chimerascan command 06 November 2013, 20:01:14 UTC
6efcfbe Jim Weible 06 November 2013, 19:50:03 UTC prevent the step from crashing on empty input file 06 November 2013, 19:50:10 UTC
325119e Mark Burnett 06 November 2013, 19:08:03 UTC WorkflowBuilder::Command verifies specified command class 06 November 2013, 19:09:58 UTC
93d974a Thomas Mooney 06 November 2013, 18:35:20 UTC Make this a more sensical UR class definition. 06 November 2013, 18:35:20 UTC
4c785ec Thomas Mooney 06 November 2013, 18:21:38 UTC Match name in link to that of the input property. 06 November 2013, 18:21:38 UTC
98e5459 Thomas Mooney 06 November 2013, 14:45:43 UTC Update somval blessed build. Includes: indel VCF, tabix, and SV validation files 06 November 2013, 14:45:43 UTC
b6daa70 Gabriel Sanderson 06 November 2013, 03:46:18 UTC Merge branch 'blessed' into gb_master 06 November 2013, 03:46:18 UTC
b01b03a Gabriel Sanderson 06 November 2013, 03:45:27 UTC Updated build diffs for tabix files. 06 November 2013, 03:45:27 UTC
8bb943b Thomas Mooney 05 November 2013, 23:05:04 UTC whitespace only 05 November 2013, 23:05:04 UTC
ccc4e35 Thomas Mooney 05 November 2013, 22:18:02 UTC Someone changed this in the database. 05 November 2013, 22:18:02 UTC
cf0e4e3 Gabriel Sanderson 05 November 2013, 21:23:39 UTC Merge branch 'blessed' into gb_master 05 November 2013, 21:23:39 UTC
5c107a9 Gabriel Sanderson 05 November 2013, 21:23:15 UTC updated expected somatic-validation-sv output for varscan-somatic-validation now providing indel vcfs 05 November 2013, 21:23:15 UTC
1b290c7 Eddie Belter 05 November 2013, 21:04:40 UTC Varscan Somatic: add reference and indel filter somatic statuses to indel to match snv 05 November 2013, 21:04:40 UTC
e8948d8 Travis Abbott 05 November 2013, 18:45:54 UTC add format_transcripts method to VepConsequenceParser this re-formats a parsed transcript hash as a CSQ info string. 05 November 2013, 18:45:54 UTC
9f25dfe Travis Abbott 05 November 2013, 17:44:37 UTC Update docs for GF::Vcf::Entry 05 November 2013, 17:52:02 UTC
919e1ab APipe Tester 05 November 2013, 13:17:40 UTC Updated `gmt` tab completion. 05 November 2013, 13:17:40 UTC
1026e2d APipe Tester 05 November 2013, 13:16:50 UTC Updated `genome` tab completion. 05 November 2013, 13:16:50 UTC
d4c433c APipe Tester 05 November 2013, 13:14:55 UTC Updated class browser cache. 05 November 2013, 13:14:55 UTC
7b6680c Travis Abbott 04 November 2013, 22:58:11 UTC add filtering to Vep Consequence Parser. 04 November 2013, 22:58:31 UTC
620e672 Jason Walker 04 November 2013, 22:19:54 UTC A warning message if the junctions output is not found in a build for a model. 04 November 2013, 22:19:54 UTC
e00ec25 Adam Coffman 04 November 2013, 21:57:52 UTC small changes related to purging 04 November 2013, 21:57:52 UTC
8d3e751 Chris Miller 04 November 2013, 21:38:29 UTC adding VCF convertors for varscan-somatic-validation 04 November 2013, 21:51:06 UTC
6662cad dmorton 04 November 2013, 21:39:30 UTC DetectFusions command has input of build_id instead of build 04 November 2013, 21:41:58 UTC
55b2955 Chris Miller 04 November 2013, 21:35:47 UTC doc updates 04 November 2013, 21:36:00 UTC
96e733b dmorton 04 November 2013, 21:23:20 UTC Fix silly mistakes 04 November 2013, 21:23:50 UTC
0ac5f2b Mark Burnett 04 November 2013, 20:49:59 UTC rename id to allocation_id 04 November 2013, 21:17:54 UTC
d12c8c4 dmorton 04 November 2013, 21:13:36 UTC Chimerascan builds and executes workflow 04 November 2013, 21:14:46 UTC
50031f1 dmorton 04 November 2013, 18:21:56 UTC Make Result directory structure echo Command structure 04 November 2013, 21:14:46 UTC
e314172 dmorton 04 November 2013, 18:12:24 UTC Pull decision logic out of RnaSeq Model DetectFusions command now determines what commands to fire off to do fusion detection based on the parameters it is passed. 04 November 2013, 21:14:45 UTC
25ac471 dmorton 04 November 2013, 17:22:48 UTC Reimagined directory structure yet again 04 November 2013, 21:14:45 UTC
db86a76 dmorton 04 November 2013, 16:45:12 UTC Rearrange directory structure for Chimerascan Commands 04 November 2013, 21:14:44 UTC
1344473 dmorton 01 November 2013, 19:55:15 UTC Cleaned up command directory in rnaseq 04 November 2013, 21:14:44 UTC
73c4fc3 dmorton 31 October 2013, 21:29:07 UTC Fix weird lib managment 04 November 2013, 21:14:43 UTC
302e6fd dmorton 29 October 2013, 18:55:19 UTC Deduplicate logic surrounding Chimerascan commands The old vanilla Chimerascan and ChimerascanVrl differ but the commands are essentially identical, so the command logic was pulled into a base class. 04 November 2013, 21:14:42 UTC
2d90ed6 dmorton 29 October 2013, 18:27:49 UTC Rearranged directory structure for chimerascan The old structure was messy and didn't clearly segregate chimerascan from any of the other detectors. We want to add additional chimerascan related code here like the filtering that is always done after chimerascan is run but in the old structure it wasn't clear where to put it. 04 November 2013, 21:14:42 UTC
f6704c8 Adam Coffman 04 November 2013, 21:14:38 UTC fully qualify name of find method 04 November 2013, 21:14:38 UTC
2707023 dmorton 04 November 2013, 21:00:23 UTC build view finds all software results for a build Instead of using ->results we now use ->all_results which has the advantage of finding results that use other results not just results that the build was using 04 November 2013, 21:00:23 UTC
7649c5e dmorton 04 November 2013, 20:51:55 UTC Updated test data for varscan consensus Hand curated the diffs due to switching to varscan 2.3.6 as the default. 04 November 2013, 20:51:55 UTC
a574231 dmorton 04 November 2013, 20:43:09 UTC Updated test data for create-cross-sample-vcf Hand curated the diffs due to switching to varscan 2.3.6 as the default. 04 November 2013, 20:44:01 UTC
75314f4 dmorton 04 November 2013, 20:14:32 UTC New test data for indels Hand curated the diffs due to switching to varscan 2.3.6 as the default. 04 November 2013, 20:44:00 UTC
dc4784d dmorton 04 November 2013, 20:13:51 UTC Make test name more descriptive 04 November 2013, 20:44:00 UTC
9a7cc14 Gabriel Sanderson 04 November 2013, 19:39:40 UTC Merge branch 'master' into gb_master 04 November 2013, 19:39:40 UTC
9197743 Gabriel Sanderson 04 November 2013, 19:37:31 UTC Updated blessed builds for tabix indexing vcf changes 04 November 2013, 19:37:31 UTC
799ee7a Dan Koboldt 04 November 2013, 16:25:09 UTC Changed VarScan default version to v2.3.6 04 November 2013, 16:25:09 UTC
84c7fca Jim Weible 04 November 2013, 16:14:50 UTC fix the use_ok to test the correct module 04 November 2013, 16:14:50 UTC
1a2a22c Jim Weible 01 November 2013, 16:34:47 UTC separate CreateCrossSampleVcf into an indel and snv version 04 November 2013, 15:48:35 UTC
b795fa0 Thomas Mooney 04 November 2013, 14:22:06 UTC Restore basic form of Genome::File::Vcf even though read/write ops move out. (This class is still referenced in the build input table!) 04 November 2013, 14:22:06 UTC
facbfc4 APipe Tester 02 November 2013, 12:16:47 UTC Updated `genome` tab completion. 02 November 2013, 12:16:47 UTC
f0719c8 Gabriel Sanderson 01 November 2013, 23:09:06 UTC Merge branch 'tabix' into gb_master 01 November 2013, 23:09:06 UTC
c210e89 Gabriel Sanderson 01 November 2013, 23:06:30 UTC CHANGELOG: Tabix index all vcf files in DV2. 01 November 2013, 23:08:03 UTC
e6b36f8 Malachi Griffith 01 November 2013, 22:43:43 UTC Add verbose option to genome model metadata import 01 November 2013, 22:43:43 UTC
d1d6acd Malachi Griffith 01 November 2013, 19:46:52 UTC Update Genome::Model::Export::Metadata to skip Genome::Model::Metric objects because we are not exporting the builds these metrics are associated with. Otherwise when we try to import these metrics we are blocked by foreign key constraints 01 November 2013, 19:46:52 UTC
4a1408e Avinash Ramu 01 November 2013, 18:17:37 UTC updated status_message() calls 01 November 2013, 18:18:12 UTC
a9fc08c Malachi Griffith 01 November 2013, 18:13:00 UTC Minor fix to comparisons in genome model export metadata 01 November 2013, 18:13:00 UTC
03663b6 Chris Miller 01 November 2013, 14:04:32 UTC updated header regex to be a little less agressive 01 November 2013, 14:04:32 UTC
08a2f47 APipe Tester 01 November 2013, 12:15:57 UTC Updated `genome` tab completion. 01 November 2013, 12:15:57 UTC
f369d3f APipe Tester 01 November 2013, 12:14:39 UTC Updated class browser cache. 01 November 2013, 12:14:39 UTC
fa6dda7 Mark Burnett 31 October 2013, 21:56:46 UTC extract _purge to Purger 31 October 2013, 22:25:44 UTC
c31099a Mark Burnett 31 October 2013, 21:25:18 UTC formatting 31 October 2013, 21:25:18 UTC
b3deb25 Mark Burnett 31 October 2013, 21:08:54 UTC extract _{un,}archive to {Una,A}rchiver 31 October 2013, 21:22:37 UTC
add21ca Mark Burnett 31 October 2013, 20:53:15 UTC formatting 31 October 2013, 21:22:37 UTC
c1329dd Mark Burnett 31 October 2013, 20:44:10 UTC fix idempotent move test This test reaches into the internals of the Mover. 31 October 2013, 21:22:36 UTC
a66d676 Mark Burnett 31 October 2013, 16:20:21 UTC rename move_shadow_path to _get_move_shadow_path 31 October 2013, 21:22:36 UTC
dd0dbdb Mark Burnett 31 October 2013, 16:19:51 UTC rename move_shadow_params to _get_move_shadow_params 31 October 2013, 21:22:35 UTC
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