| 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 |
| 5dc660b | Eddie Belter | 21 February 2014, 19:00:35 UTC | GM: move some param handling to writer classes from writer factory | 04 March 2014, 22:33:28 UTC |
| e6b7324 | Eddie Belter | 19 February 2014, 23:36:51 UTC | Utility: writer sets orginal output to - for STDOUT | 04 March 2014, 22:33:26 UTC |
| f752d35 | Eddie Belter | 19 February 2014, 23:35:41 UTC | GM: make default headers a function in write csv | 04 March 2014, 22:33:24 UTC |
| 824a767 | Eddie Belter | 19 February 2014, 22:59:36 UTC | GM: CSV writer | 04 March 2014, 22:33:24 UTC |
| 98fc0c5 | Eddie Belter | 19 February 2014, 22:34:42 UTC | GM: merge reader test into one that will also test writing | 04 March 2014, 22:33:23 UTC |
| 190c848 | Eddie Belter | 19 February 2014, 22:33:50 UTC | GM: extract command doc update | 04 March 2014, 22:33:22 UTC |
| edb8ca5 | Eddie Belter | 19 February 2014, 22:33:26 UTC | GM: make the return value of read tsv and annotate consistent to read tsv | 04 March 2014, 22:33:22 UTC |
| eb28d85 | Eddie Belter | 19 February 2014, 22:32:29 UTC | GM: do not set id from snp name in read tsv | 04 March 2014, 22:33:21 UTC |
| 0479ef2 | Eddie Belter | 18 February 2014, 23:57:15 UTC | GM: remove instdata extract command, use model extract commmand | 04 March 2014, 22:33:20 UTC |
| cd590d2 | Eddie Belter | 18 February 2014, 23:33:53 UTC | GM: fix sample type priority values, make resolve_source public | 04 March 2014, 22:33:19 UTC |
| 770e9a7 | Eddie Belter | 18 February 2014, 22:36:02 UTC | GM: extract counts alleles | 04 March 2014, 22:33:17 UTC |
| a50d373 | Eddie Belter | 18 February 2014, 21:52:52 UTC | GM: rm alleles prop from read tsv | 04 March 2014, 22:33:16 UTC |
| 3458b13 | Eddie Belter | 18 February 2014, 21:51:52 UTC | GM: extract command genotype metrics fixed, get gm builds instead of models | 04 March 2014, 22:33:16 UTC |
| 3601119 | Eddie Belter | 18 February 2014, 18:26:18 UTC | GM: merge extract commands | 04 March 2014, 22:33:15 UTC |
| 41a4e15 | Eddie Belter | 18 February 2014, 18:00:01 UTC | GM: writer factory use \t for TAB; correctly sets defaults | 04 March 2014, 22:33:14 UTC |
| ebb2967 | Eddie Belter | 18 February 2014, 00:48:43 UTC | SRV: add param to fill in null value | 04 March 2014, 22:33:14 UTC |
| 6304d81 | Eddie Belter | 18 February 2014, 00:46:00 UTC | GM: writer factory to write genotype file | 04 March 2014, 22:33:13 UTC |
| 34f90ac | Eddie Belter | 17 February 2014, 22:02:11 UTC | GM: extracted reading of inst data genotype file into separate class | 04 March 2014, 22:33:13 UTC |
| bbc8fa4 | Eddie Belter | 17 February 2014, 20:43:58 UTC | GM: make orignal genotype file reader just a tsv reader | 04 March 2014, 22:33:12 UTC |
| 6d0cca0 | Eddie Belter | 17 February 2014, 20:00:19 UTC | GM: factory to create a genotpye file reader | 04 March 2014, 22:33:12 UTC |
| 1c561bb | Eddie Belter | 14 February 2014, 21:34:14 UTC | GM: move original genotype reader to genotype file dir that will hold other readers/writers | 04 March 2014, 22:33:11 UTC |
