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 |
1a8c3b9 | Gue Su Chang | 04 March 2014, 22:26:45 UTC | New gmt analsysi module of Genome::Model::Tools::Analysis::Coverage::MergeReadcounts added | 04 March 2014, 22:26:45 UTC |
2409c33 | Thomas Mooney | 04 March 2014, 22:08:12 UTC | Disable test that uses a mediawiki install. | 04 March 2014, 22:08:12 UTC |
81139e8 | Mark Burnett | 04 March 2014, 21:41:22 UTC | modify genome-teset-env to avoid pointing at gscweb | 04 March 2014, 21:45:11 UTC |
9c93ace | Jason Walker | 04 March 2014, 18:59:57 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 04 March 2014, 18:59:57 UTC |
19c5813 | Jason Walker | 04 March 2014, 18:59:46 UTC | Remove the hardcoded memory param to samtools sort since it was less than the default in samtools 0.1.18 | 04 March 2014, 18:59:46 UTC |
3f92827 | Nathaniel Nutter | 04 March 2014, 18:19:03 UTC | precious newline | 04 March 2014, 18:19:03 UTC |
716bac1 | Jason Walker | 04 March 2014, 17:49:42 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 04 March 2014, 17:49:42 UTC |
90c6901 | Jason Walker | 04 March 2014, 17:49:35 UTC | Update the Define-docs.t expected output for rna-seq since annotation_build is now optional. | 04 March 2014, 17:49:35 UTC |
dddde07 | Nathaniel Nutter | 04 March 2014, 17:44:11 UTC | remove unauthenticated query to web view URL Access to web view URLs will soon require authentication which would cause this to fail. Since it is a caching optimization I am just removing it. | 04 March 2014, 17:45:44 UTC |
0db4b69 | Jason Walker | 04 March 2014, 17:21:42 UTC | Updated test to account for TopHat aligner params diff when making an annotation/transcriptome index | 04 March 2014, 17:21:42 UTC |
945f9f7 | Jason Walker | 04 March 2014, 17:05:35 UTC | Add support for de novo TopHat alignment. Make inputs annotation_build and mask_reference_transcripts optional. | 04 March 2014, 17:05:35 UTC |
e81ef6e | Jason Walker | 04 March 2014, 17:03:28 UTC | Look for LSF job ID as job_id rather than bjob_id | 04 March 2014, 17:03:28 UTC |
2d9a00f | Jason Walker | 04 March 2014, 16:58:55 UTC | Add a space in the tophat params to correctly create a transcriptome only alignment while generating the annotation index. | 04 March 2014, 16:58:55 UTC |
e038743 | Jason Walker | 04 March 2014, 16:56:41 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 04 March 2014, 16:56:41 UTC |
4f2af84 | Susanna Siebert | 04 March 2014, 16:05:21 UTC | new blessed build for somatic variation pipeline changes | 04 March 2014, 16:07:57 UTC |
cffcb88 | Susanna Siebert | 04 March 2014, 14:19:05 UTC | set output parameter values in the execute not calculated properties anymore values need to be different in the corner case that input files don't exist and we need to 'skip' this step | 04 March 2014, 16:07:57 UTC |
9d4abe2 | Susanna Siebert | 03 March 2014, 18:47:42 UTC | test for when input files don't exist test should run and command should execute sucessfully no ouput should be written | 04 March 2014, 16:07:56 UTC |
7634297 | Susanna Siebert | 03 March 2014, 18:46:22 UTC | add functionality to check whether or not the output should exist depending on the test | 04 March 2014, 16:07:56 UTC |
e5907e4 | Susanna Siebert | 03 March 2014, 18:44:27 UTC | Don't fail if the input files don't exist but exit successfully with appropriate log messages | 04 March 2014, 16:07:55 UTC |
4222944 | Susanna Siebert | 03 March 2014, 15:00:48 UTC | updated fill_in_site_hash to use correct sample name the code tries to match the header line of the snvs.detailed.vcf.gz file which is based on $self->somatic_variation_build->tumor_build->subject->name not on x $self->somatic_variation_build->get_subject_name. Most of the times these match but sometimes they are different, e.g. in the somatic variation tests | 04 March 2014, 16:07:54 UTC |
3c881c9 | Susanna Siebert | 24 February 2014, 18:32:06 UTC | make add_tiers more robust - remove the outfile parameter - use the result_file_path subroutine to determine the output file instead of just calling add_suffix | 04 March 2014, 16:07:54 UTC |
e829d82 | Susanna Siebert | 24 February 2014, 16:48:11 UTC | Remove unneccesary conversions between bed and anno format | 04 March 2014, 16:07:53 UTC |