| b65a56c | dmorton | 06 March 2014, 21:24:26 UTC | Lean on new FeatureList functionality in CCSVCF | 06 March 2014, 22:46:30 UTC |
| 58f1400 | APipe Tester | 06 March 2014, 22:33:56 UTC | updated jenkins submodule to 5e98e09 | 06 March 2014, 22:33:56 UTC |
| 335e5c6 | Gabriel Sanderson | 06 March 2014, 21:51:46 UTC | Added resolve_roi_for_reference, which checks references before converting the bed file. Also do a basic check for "chr" chromosomes if they do not belong. | 06 March 2014, 21:58:14 UTC |
| c57c419 | Gabriel Sanderson | 06 March 2014, 20:36:18 UTC | target_bed checks to make sure it exists when accessed | 06 March 2014, 21:58:13 UTC |
| 1702189 | Gabriel Sanderson | 06 March 2014, 20:15:49 UTC | Removed caching -- using software results now. | 06 March 2014, 21:58:12 UTC |
| 7b18010 | Gabriel Sanderson | 06 March 2014, 20:13:20 UTC | Remove old TODO | 06 March 2014, 21:58:10 UTC |
| efbbf50 | Gabriel Sanderson | 06 March 2014, 20:12:28 UTC | Start using ConvertedBedResult instead of directly calling convert_bed | 06 March 2014, 21:58:08 UTC |
| 84d56e0 | Gabriel Sanderson | 06 March 2014, 02:11:32 UTC | Added ConvertedBedResult to act as a software result for feature list bed files, once they are converted to another reference sequence. | 06 March 2014, 21:58:06 UTC |
| 2c7ca6a | Thomas Mooney | 06 March 2014, 20:28:30 UTC | Fix typo: symlinke => symlink. | 06 March 2014, 20:28:30 UTC |
| c844d7e | dmorton | 06 March 2014, 19:25:42 UTC | remove die condition in vcf Backfill When we create vcf files from mpileup (in dv2) the converter does not put in a AD field and always leaves the BQ field set to '.' so we cannot possibly satisfy this condition. The code will just accept the newly discovered evidence for alts at this site. | 06 March 2014, 19:30:51 UTC |
| b5f5a9d | apregier | 06 March 2014, 18:17:26 UTC | Merge branch 'my_annotation' into gb_master | 06 March 2014, 18:17:26 UTC |
| 646b6f2 | apregier | 06 March 2014, 18:15:13 UTC | Restore Job::Iterator package | 06 March 2014, 18:16:30 UTC |
| 0d251f0 | Jim Weible | 06 March 2014, 16:20:47 UTC | note the annoation-version param is deprecated | 06 March 2014, 16:20:47 UTC |
| 19db5d7 | Jim Weible | 06 March 2014, 16:20:25 UTC | handle annotation data set correctly in the test | 06 March 2014, 16:20:25 UTC |
| edce14c | Jim Weible | 28 February 2014, 15:57:28 UTC | Revert "Revert "do the right thing with the copycat annotation"" This reverts commit e06fc4e36dd8092fee0b1f22eb730ce3a5a6ac8d. | 06 March 2014, 14:03:59 UTC |
| 5fe2924 | Jim Weible | 28 February 2014, 15:57:26 UTC | Revert "Revert "write our temp files to a reasonable place"" This reverts commit 3cd0df3a9b7e6715ec16ea6cf02ef7706778bbbb. | 06 March 2014, 14:03:58 UTC |
| a122cae | Jim Weible | 28 February 2014, 15:57:24 UTC | Revert "Revert "fix up some copy pasta error messages"" This reverts commit 6055056b0dba9c93204e845b582a5f213384acdd. | 06 March 2014, 14:03:58 UTC |
| 8767185 | Jim Weible | 28 February 2014, 15:57:13 UTC | Revert "Revert "create a dummy expected output file as standard for cnv detectors"" This reverts commit 5abef98c7ca3d5782240449500339ead9fc2b03e. | 06 March 2014, 14:03:57 UTC |
| 6cf65de | APipe Tester | 06 March 2014, 13:17:37 UTC | Updated `gmt` tab completion. | 06 March 2014, 13:17:37 UTC |
| 1875d90 | APipe Tester | 06 March 2014, 13:16:49 UTC | Updated `genome` tab completion. | 06 March 2014, 13:16:49 UTC |
| 76987f0 | APipe Tester | 06 March 2014, 13:15:12 UTC | Updated class browser cache. | 06 March 2014, 13:15:12 UTC |
| f99c881 | apregier | 06 March 2014, 02:32:45 UTC | Merge branch 'my_annotation' into gb_master | 06 March 2014, 02:32:45 UTC |
| 1a02f30 | apregier | 06 March 2014, 02:31:01 UTC | Don't break /gsc/bin/perl | 06 March 2014, 02:31:01 UTC |
| 430fa0e | apregier | 06 March 2014, 02:03:12 UTC | Merge branch 'my_annotation' into gb_master | 06 March 2014, 02:03:12 UTC |
| a738e51 | apregier | 05 March 2014, 22:58:54 UTC | Check that builds weren't succeeded in between. | 05 March 2014, 22:58:54 UTC |
| 9a5d121 | apregier | 05 March 2014, 22:25:19 UTC | Update cron | 05 March 2014, 22:25:41 UTC |
| 3816181 | apregier | 05 March 2014, 22:23:36 UTC | Use exceptions | 05 March 2014, 22:25:41 UTC |
| b096bb7 | apregier | 04 March 2014, 21:59:22 UTC | Rewrite scan cron | 05 March 2014, 22:25:40 UTC |
| b2b82c6 | APipe Tester | 05 March 2014, 22:22:16 UTC | updated jenkins submodule to 8a9a322 | 05 March 2014, 22:22:16 UTC |
| 609cb07 | dmorton | 05 March 2014, 20:51:17 UTC | Stop trying to parse snv_detection_strategy for samtools info This was problematic for builds that had processing profiles that specified 'mpileup -BuDS' for instance since 'mpileup' is not a samtools pileup param. | 05 March 2014, 20:53:09 UTC |
| ec22ef5 | Chris Miller | 05 March 2014, 20:24:32 UTC | updated stderr message to make sense | 05 March 2014, 20:24:32 UTC |
| 0f66486 | Chris Miller | 05 March 2014, 20:02:47 UTC | fixing hash reference bug | 05 March 2014, 20:08:59 UTC |
| 3d6b4fd | Chris Miller | 05 March 2014, 19:36:38 UTC | adding reference-transcripts option to specify one that differs from the model | 05 March 2014, 20:08:58 UTC |
| 61bd7e1 | Susanna Siebert | 05 March 2014, 19:34:19 UTC | need to use Test::More instead of Genome::Model::SomaticVariation::Command::TestHelpers | 05 March 2014, 19:34:19 UTC |
| d90d1d7 | Susanna Siebert | 05 March 2014, 19:09:12 UTC | fixed package name | 05 March 2014, 19:22:40 UTC |
| f1ac2c9 | Thomas Mooney | 05 March 2014, 16:42:54 UTC | Only examine the first 1000 lines of the BAM when discerning read length. Otherwise for large BAMs this process takes a *long* time without much gain in accuracy. | 05 March 2014, 16:42:54 UTC |
| 1ddec2d | Susanna Siebert | 05 March 2014, 15:12:02 UTC | don't compare the output from reports/review.xml as that file will always be different | 05 March 2014, 15:12:29 UTC |
| 8ab9897 | APipe Tester | 05 March 2014, 14:00:26 UTC | updated workflow submodule to 4332dce | 05 March 2014, 14:00:26 UTC |
| 2523308 | Nathaniel Nutter | 05 March 2014, 05:16:37 UTC | pull up fetch utility | 05 March 2014, 05:16:37 UTC |
| 393784e | Nathaniel Nutter | 05 March 2014, 04:56:13 UTC | refactor URL fetching Extracted similar code into a utility function and updated to use File::Fetch instead of shelling out to curl. | 05 March 2014, 04:56:13 UTC |
| ca74757 | Nathaniel Nutter | 05 March 2014, 01:14:35 UTC | delegate to local version if it is found If we update either of these normally people would't get them until they get deployed. With this delegation code in there it will try use the fact that someone is in a Git repo with the same executable to delegate to it. | 05 March 2014, 01:15:47 UTC |
| 5d93215 | Nathaniel Nutter | 04 March 2014, 21:41:57 UTC | fixes RT #98012, shellcmd STDERR/STDOUT FCGI bug | 05 March 2014, 00:49:37 UTC |
| 0d56bbc | Nathaniel Nutter | 04 March 2014, 20:10:58 UTC | can't use non-string variables in 3-argument open due to FCGI (I think) FCGI ties STDERR, STDOUT, and STDIN which overrides open calls. In the case of a 3-argument open it does: eval("$rc = open($_[0], $_[1], $_[2])"); Which means that the variables can't be "the normal 'reference to a glob'" as is supposed to be the case. | 05 March 2014, 00:49:36 UTC |
| bbd8827 | Nathaniel Nutter | 04 March 2014, 20:08:01 UTC | use parens | 05 March 2014, 00:49:35 UTC |
| 25785ae | Nathaniel Nutter | 04 March 2014, 20:06:28 UTC | only backup STDOUT/STDERR if redirected | 05 March 2014, 00:49:33 UTC |
| b26285a | Nathaniel Nutter | 04 March 2014, 23:58:57 UTC | reload allocations so they are no longer archived in memory | 05 March 2014, 00:34:39 UTC |
| 3ab93cd | Nathaniel Nutter | 05 March 2014, 00:33:36 UTC | test's models were updated with new processing profile (DV2 bug fix) | 05 March 2014, 00:34:38 UTC |
| d6bc402 | Nathaniel Nutter | 04 March 2014, 23:40:24 UTC | updated expected output for new GENOME_TEST_INPUTS Changed from/to: https://gscweb.gsc.wustl.edu file:// | 04 March 2014, 23:45:55 UTC |
| 36fde30 | Nathaniel Nutter | 04 March 2014, 23:28:55 UTC | disable test for one week b/c of disk maintenance | 04 March 2014, 23:45:54 UTC |
| 64a4ad5 | Nathaniel Nutter | 04 March 2014, 23:07:23 UTC | updated expected output due to new processing profiles and env Here are the pairs of changes that were made: Oct 2012 Default Somatic Variation WGS Oct 2012 Default Somatic Variation WGS -- DV2 filter params bug fix Oct 2012 Default Somatic Variation Exome Oct 2012 Default Somatic Variation Exome -- DV2 filter params bug fix Oct 2012 Default Somatic Variation WGS (2762562) Oct 2012 Default Somatic Variation WGS -- DV2 filter params bug fix (b359413673b040d2b29b7810e71c4882) Oct 2012 Default Somatic Variation Exome (2762563) Oct 2012 Default Somatic Variation Exome -- DV2 filter params bug fix (ccdea755cabe46fb826394f6ba388ccc) https://gscweb.gsc.wustl.edu file:// | 04 March 2014, 23:15:07 UTC |
| 9425de5 | Nathaniel Nutter | 04 March 2014, 22:45:50 UTC | use curl since it support file:// URLs | 04 March 2014, 23:15:06 UTC |
| 6bc6a8b | Nathaniel Nutter | 04 March 2014, 22:39:25 UTC | use curl since it support file:// URLs | 04 March 2014, 23:15:05 UTC |
| 4bf08e3 | Nathaniel Nutter | 04 March 2014, 22:30:26 UTC | use curl since it support file:// URLs | 04 March 2014, 23:15:05 UTC |
| 66ec893 | Gue Su Chang | 04 March 2014, 23:07:19 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 04 March 2014, 23:07:19 UTC |
| bfdf8df | Eddie Belter | 04 March 2014, 22:19:42 UTC | GM: create original genotpye VCF! | 04 March 2014, 22:33:52 UTC |
| fffee3c | Eddie Belter | 04 March 2014, 22:19:14 UTC | GM: update name of vcf file method | 04 March 2014, 22:33:51 UTC |
| 42fe08c | Eddie Belter | 04 March 2014, 21:58:27 UTC | GM: excute build test uses test module | 04 March 2014, 22:33:51 UTC |
| c489de5 | Eddie Belter | 04 March 2014, 21:57:51 UTC | GM: rm setting ref, dbsnp and instdata to builds in test module | 04 March 2014, 22:33:50 UTC |
| 7f10049 | Eddie Belter | 04 March 2014, 21:24:41 UTC | GM: update r/w test | 04 March 2014, 22:33:50 UTC |
| d276aff | Eddie Belter | 04 March 2014, 21:23:01 UTC | GM: update test for default csv headers | 04 March 2014, 22:33:49 UTC |
| a294c12 | Eddie Belter | 04 March 2014, 21:22:10 UTC | GM: rm expected genotypes from test module | 04 March 2014, 22:33:49 UTC |
| 1520584 | Eddie Belter | 04 March 2014, 21:21:21 UTC | GM: updates to vcf helper and test | 04 March 2014, 22:33:48 UTC |
| bdf46eb | Eddie Belter | 04 March 2014, 21:05:42 UTC | GM: update extract to use factories | 04 March 2014, 22:33:48 UTC |
| 048e8cc | Eddie Belter | 04 March 2014, 21:05:13 UTC | GM: fix getting info when decorating vcf entry; add test | 04 March 2014, 22:33:47 UTC |
| 037b361 | Eddie Belter | 04 March 2014, 19:22:01 UTC | GM: use params fro build_reader; reader factory test uses test module | 04 March 2014, 22:33:47 UTC |
| 39bc084 | Eddie Belter | 04 March 2014, 19:10:19 UTC | GM: use sampel_name instead of sample_id in default csv header | 04 March 2014, 22:33:46 UTC |
| aad0b9d | Eddie Belter | 04 March 2014, 19:09:50 UTC | GM: more read/write tests | 04 March 2014, 22:33:46 UTC |
| 2ffd4f9 | Eddie Belter | 04 March 2014, 19:08:17 UTC | GM: factory to create entries | 04 March 2014, 22:33:45 UTC |
| 25a5abb | Eddie Belter | 04 March 2014, 19:04:12 UTC | GM: read tsv returns a hash | 04 March 2014, 22:33:45 UTC |
| c18654c | Eddie Belter | 27 February 2014, 23:20:18 UTC | GM: set format to csv if separator is set in writer factory | 04 March 2014, 22:33:44 UTC |
| 365a873 | Eddie Belter | 27 February 2014, 23:19:29 UTC | GM: update test objects | 04 March 2014, 22:33:44 UTC |
| 65761dd | Eddie Belter | 27 February 2014, 23:18:53 UTC | GM: add next method as alias for read to read tsv | 04 March 2014, 22:33:43 UTC |
| b810d23 | Eddie Belter | 27 February 2014, 23:18:24 UTC | GM: updates to work w/ updated extract command | 04 March 2014, 22:33:43 UTC |
| f180245 | Eddie Belter | 27 February 2014, 23:17:53 UTC | GM: extract command tests | 04 March 2014, 22:33:42 UTC |
| 696e486 | Eddie Belter | 27 February 2014, 02:08:19 UTC | GM: rm unused code from read write test | 04 March 2014, 22:33:42 UTC |
| 20c9bc7 | Eddie Belter | 27 February 2014, 02:07:25 UTC | GM: rename info to vcf/csv helpers | 04 March 2014, 22:33:41 UTC |
| 44011f4 | Eddie Belter | 27 February 2014, 00:30:48 UTC | GM: add format sample info to expected genotypes | 04 March 2014, 22:33:41 UTC |
| 16dbb1e | Eddie Belter | 27 February 2014, 00:29:15 UTC | GM: add sample names to vcf header | 04 March 2014, 22:33:40 UTC |
| 4debfd4 | Eddie Belter | 27 February 2014, 00:28:47 UTC | GM: writer factory requires sample name | 04 March 2014, 22:33:40 UTC |
| 74fa93a | Eddie Belter | 26 February 2014, 23:35:45 UTC | VCF: add colum_headers function | 04 March 2014, 22:33:39 UTC |
| a96dc1e | Eddie Belter | 26 February 2014, 23:32:37 UTC | GM: interface for test objects | 04 March 2014, 22:33:39 UTC |
| bb20dee | Eddie Belter | 26 February 2014, 23:32:24 UTC | GM: read/write test use factories | 04 March 2014, 22:33:38 UTC |
| c7f6b93 | Eddie Belter | 26 February 2014, 23:32:12 UTC | GM: rename default header to info | 04 March 2014, 22:33:38 UTC |
| 1fa956a | Eddie Belter | 26 February 2014, 22:55:33 UTC | GM: writer factory tweeks | 04 March 2014, 22:33:37 UTC |
| e99b65b | Eddie Belter | 26 February 2014, 22:26:24 UTC | SVW: replace ref w/ scalar util reftype; use symbol table to point write and print to write_one | 04 March 2014, 22:33:37 UTC |
| 5357e99 | Eddie Belter | 26 February 2014, 22:18:59 UTC | GM: add info hash method to reads tsv and annotate | 04 March 2014, 22:33:36 UTC |
| 2aa369c | Eddie Belter | 26 February 2014, 22:17:50 UTC | GM: rm write classes; handle params/header in factory | 04 March 2014, 22:33:36 UTC |
| 95f95da | Eddie Belter | 25 February 2014, 00:31:36 UTC | GM: read tsv and annotate returns a vcf entry | 04 March 2014, 22:33:35 UTC |
| b42b15d | Eddie Belter | 25 February 2014, 00:20:50 UTC | GM: reader factory returns reader for build vcf or inst data genotype file | 04 March 2014, 22:33:35 UTC |
| 57e3506 | Eddie Belter | 24 February 2014, 23:45:17 UTC | GM: add original genotype vcf method to build | 04 March 2014, 22:33:34 UTC |
| c1b6411 | Eddie Belter | 24 February 2014, 18:56:09 UTC | GM: rm unneeded use from writer factory | 04 March 2014, 22:33:34 UTC |
| 1900e40 | Eddie Belter | 21 February 2014, 23:59:49 UTC | GM: r/w test uses reader wrapper class | 04 March 2014, 22:33:33 UTC |
| cd164ab | Eddie Belter | 21 February 2014, 23:54:59 UTC | GM: write vcf is wrapper for file vcf writer | 04 March 2014, 22:33:33 UTC |
| 781bd9d | Eddie Belter | 21 February 2014, 23:33:09 UTC | GM: complete converting genotype to vcf entry | 04 March 2014, 22:33:32 UTC |
| cd4059a | Eddie Belter | 21 February 2014, 23:31:45 UTC | GM: add GT format header | 04 March 2014, 22:33:32 UTC |
| 452b5c5 | Eddie Belter | 21 February 2014, 23:31:16 UTC | VCF Writer: not redefining name before blessing | 04 March 2014, 22:33:31 UTC |
| 94c1d3a | Eddie Belter | 21 February 2014, 21:44:26 UTC | GM: additions to genotype file default header | 04 March 2014, 22:33:31 UTC |
| 361583e | Eddie Belter | 21 February 2014, 20:34:07 UTC | GM: Default vcf header | 04 March 2014, 22:33:30 UTC |
| 737b3fb | Eddie Belter | 21 February 2014, 19:48:48 UTC | GM: add reader that will read from the underlying reader and then return a vcf entry | 04 March 2014, 22:33:30 UTC |
| bb759f5 | Eddie Belter | 21 February 2014, 19:00:50 UTC | GM: add vcf writer | 04 March 2014, 22:33:29 UTC |
