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23 March 2024, 19:04:16 UTC
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Revision Author Date Message Commit Date
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
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
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