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https://github.com/genome/genome
23 March 2024, 19:04:16 UTC
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Revision Author Date Message Commit Date
01e8b6b Nathaniel Nutter 29 January 2015, 15:52:22 UTC Merge pull request #438 from nnutter/model-summary add per-model transactions in "Model Summary" 29 January 2015, 15:52:22 UTC
b16f20a APipe Tester 29 January 2015, 13:16:44 UTC Updated `gmt` tab completion. 29 January 2015, 13:16:44 UTC
cc604ed APipe Tester 29 January 2015, 13:15:58 UTC Updated `genome` tab completion. 29 January 2015, 13:15:58 UTC
098c416 APipe Tester 29 January 2015, 13:14:21 UTC Updated class browser cache. 29 January 2015, 13:14:21 UTC
220c354 Susanna Siebert 28 January 2015, 22:51:04 UTC Merge pull request #436 from susannasiebert/variant_reporting_igv Various Variant reporting IGV improvements 28 January 2015, 22:51:04 UTC
237123a Susanna Siebert 28 January 2015, 22:22:08 UTC Make this command _is_hidden_in_docs Since this command uses a hash input it won't be usable from the command line. This will prevent it from being discovered in the docs. 28 January 2015, 22:22:08 UTC
a8deace Susanna Siebert 28 January 2015, 22:21:53 UTC make into Command::V2 28 January 2015, 22:21:53 UTC
f7fdc62 Susanna Siebert 28 January 2015, 18:59:30 UTC some cleanup of igv reference names 28 January 2015, 19:20:24 UTC
dd83d3a Nathaniel Nutter 26 January 2015, 21:34:47 UTC rename variable to avoid confussion 28 January 2015, 19:14:16 UTC
de512a5 Nathaniel Nutter 26 January 2015, 21:35:35 UTC create per-model txns to avoid bad state in auto_batch_size txn 28 January 2015, 19:14:16 UTC
1a23e36 Nathaniel Nutter 28 January 2015, 18:22:17 UTC Merge pull request #435 from nnutter/genome-test fix permissions on genome-test 28 January 2015, 18:22:17 UTC
524ae74 Susanna Siebert 28 January 2015, 16:25:29 UTC clean up documentation 28 January 2015, 16:25:29 UTC
82dc881 Thomas B. Mooney 28 January 2015, 15:09:04 UTC Merge pull request #434 from tmooney/smallrna_statsgenerator_command_twice Don't call execute() twice on the Command. 28 January 2015, 15:09:04 UTC
3c11959 APipe Tester 28 January 2015, 13:16:16 UTC Updated `gmt` tab completion. 28 January 2015, 13:16:16 UTC
c4715ca APipe Tester 28 January 2015, 13:15:35 UTC Updated `genome` tab completion. 28 January 2015, 13:15:35 UTC
8077f0c APipe Tester 28 January 2015, 13:14:00 UTC Updated class browser cache. 28 January 2015, 13:14:00 UTC
f9e50d5 Nathaniel Nutter 28 January 2015, 02:11:17 UTC Merge pull request #417 from litd/master bsmap alignment status and convertion rate from chrM and lambda 28 January 2015, 02:11:17 UTC
5e38d2b Tiandao Li 27 January 2015, 21:03:01 UTC use open_file_for_writing 27 January 2015, 21:03:01 UTC
0548ea0 Tiandao Li 27 January 2015, 20:55:50 UTC change model to build 27 January 2015, 20:55:50 UTC
b9d4195 Tiandao Li 27 January 2015, 20:47:46 UTC change tab to space 27 January 2015, 20:52:10 UTC
ceeee52 Susanna Siebert 27 January 2015, 19:43:34 UTC Merge pull request #431 from davidlmorton/model_report Model report fixes 27 January 2015, 19:43:34 UTC
9516f31 Thomas B. Mooney 27 January 2015, 19:34:31 UTC Merge pull request #433 from tmooney/verify_bam_ram Set LSF memory request for SomVal's VerifyBam step. 27 January 2015, 19:34:31 UTC
21bb554 Susanna Siebert 27 January 2015, 19:25:04 UTC refactor the get_common_translations subroutine into separate subroutines for germline and somatic 27 January 2015, 19:25:04 UTC
4b887a7 Susanna Siebert 27 January 2015, 18:54:13 UTC move determination of report category into its own subroutine in MergedReport 27 January 2015, 18:54:13 UTC
7378765 Susanna Siebert 27 January 2015, 15:37:15 UTC add bed file labels 27 January 2015, 18:10:26 UTC
257a458 Nathaniel Nutter 27 January 2015, 17:25:28 UTC fix permissions on genome-test 27 January 2015, 17:25:28 UTC
acfbfac Thomas Mooney 27 January 2015, 15:03:03 UTC Normalize whitespace: tabs to spaces. 27 January 2015, 15:03:03 UTC
0e576e4 Thomas Mooney 27 January 2015, 14:58:13 UTC Remove trailing whitespace. 27 January 2015, 14:58:13 UTC
ee89178 Thomas Mooney 27 January 2015, 14:55:24 UTC Avoid re-execution of the command. 27 January 2015, 14:55:24 UTC
7a39ad8 APipe Tester 27 January 2015, 13:17:15 UTC Updated `gmt` tab completion. 27 January 2015, 13:17:15 UTC
705be1b APipe Tester 27 January 2015, 13:16:32 UTC Updated `genome` tab completion. 27 January 2015, 13:16:32 UTC
a8acddf APipe Tester 27 January 2015, 13:14:59 UTC Updated class browser cache. 27 January 2015, 13:14:59 UTC
c49d820 Susanna Siebert 26 January 2015, 21:32:02 UTC use sample name labels for bams 26 January 2015, 21:32:02 UTC
51753a2 Susanna Siebert 26 January 2015, 19:08:25 UTC germline only has tumor sample 26 January 2015, 19:08:25 UTC
8f6014a Nathaniel Nutter 26 January 2015, 18:53:49 UTC Merge pull request #428 from nnutter/compile fix compile.t to not error on detached heads 26 January 2015, 18:53:49 UTC
5fbe03c Nathaniel Nutter 26 January 2015, 18:53:42 UTC Merge pull request #427 from nnutter/genome-test add genome-test 26 January 2015, 18:53:42 UTC
0264269 Ian Ferguson 26 January 2015, 18:24:00 UTC Merge pull request #432 from iferguson90/update-gmt-bwa Add new version of Bwa to GMT::Bwa 26 January 2015, 18:24:00 UTC
f49521f dmorton 26 January 2015, 18:07:03 UTC Provide translations for somatic models as well 26 January 2015, 18:07:03 UTC
2e4f90f Thomas Mooney 26 January 2015, 18:06:04 UTC Set LSF memory request for SomVal's VerifyBam step. 26 January 2015, 18:06:04 UTC
193560d Ian Ferguson 26 January 2015, 17:40:24 UTC Add new version of Bwa to GMT::Bwa 26 January 2015, 17:40:24 UTC
e719cb9 Susanna Siebert 24 January 2015, 00:39:41 UTC use DumpIgvXmlBasic tool to create IGV XML 26 January 2015, 16:37:11 UTC
e7cb9bb Susanna Siebert 24 January 2015, 00:39:09 UTC Basic IGV XML creator that uses only resource tags 26 January 2015, 16:32:19 UTC
d8df038 Thomas B. Mooney 26 January 2015, 14:33:12 UTC Merge pull request #426 from tmooney/htseq_count_parallelize A few more fixes and a test for GMT::Htseq::Count::Result 26 January 2015, 14:33:12 UTC
992bf9c Thomas B. Mooney 26 January 2015, 14:29:32 UTC Merge pull request #421 from tmooney/flexbar_parameter_change Flexbar --(no-)length-dist parameter 26 January 2015, 14:29:32 UTC
c7e5db9 Thomas B. Mooney 26 January 2015, 14:29:11 UTC Merge pull request #423 from tmooney/better_analysis_project_delete Change cascading behavior of Analysis Project delete(). 26 January 2015, 14:29:11 UTC
315c56b dmorton 24 January 2015, 17:33:14 UTC Fix translation genration for model-reports This also adds a note to the generated process that will allow you to determine how the process was generated (in this case, what model it corresponds to). 24 January 2015, 17:33:14 UTC
33f43cd dmorton 24 January 2015, 17:32:38 UTC Allow one to attach notes to a Genome::Process 24 January 2015, 17:32:38 UTC
9196b8a Eddie Belter 23 January 2015, 17:29:29 UTC Merge pull request #430 from ebelter/fastq-to-bam2 InstData Import: fix try/catch in fastq to bam 23 January 2015, 17:29:29 UTC
0eb3b65 Eddie Belter 23 January 2015, 02:09:34 UTC InstData Import: fix try/catch in fastq to bam 23 January 2015, 02:09:34 UTC
0be7bbf Eddie Belter 23 January 2015, 01:23:28 UTC Merge pull request #425 from ebelter/fastq-to-bam InstData Import: unzip fastqs before running picard sam to fastq; up picard 23 January 2015, 01:23:28 UTC
b0384fc Eddie Belter 23 January 2015, 00:14:32 UTC InstData Import: use try::tiny instead of eval 23 January 2015, 00:14:32 UTC
88b22ff Eddie Belter 22 January 2015, 23:16:09 UTC InstData Import: remove Archive::Extract artifacts 22 January 2015, 23:16:09 UTC
b6e5632 Eddie Belter 22 January 2015, 23:14:42 UTC InstData Import: bumped test dir version because of bumping the picard fastq to sam version 22 January 2015, 23:14:42 UTC
82a5e7c Nathaniel Nutter 14 January 2015, 22:07:01 UTC add genome-test CHANGELOG: Run tests now by running `genome-test`. `genome-test` is basically an alias to `genome-test-env test-tracker prove` that will default to using the `--lsf` and `--git` options if no options are specified. 22 January 2015, 17:35:05 UTC
174e921 Nathaniel Nutter 17 January 2015, 04:04:45 UTC fix compile.t to not error on detached heads Using '@{u}' assumes 1) that you're on a branch and 2) that that branch has an upstream branch. So if one was on a detached head (checking out a PR, etc.) then this test would error and fail. This changes compile.t to fallback on compile checking everything if it can't guess a way to only check what has changed. 22 January 2015, 17:23:23 UTC
82715f8 Thomas Mooney 22 January 2015, 16:39:09 UTC Remove eval that dies on caught errors. 22 January 2015, 16:39:09 UTC
ce20c9c Thomas Mooney 22 January 2015, 16:02:48 UTC Test that the parallelization works. Tests of running Htseq::Count remain in GMT/Htseq/Count.t 22 January 2015, 16:02:48 UTC
060f783 Thomas Mooney 22 January 2015, 15:34:01 UTC Build the correct hash and call get_or_create() by class. 22 January 2015, 15:34:01 UTC
1d9a81a Eddie Belter 22 January 2015, 02:46:58 UTC InstData Import: unzip fastqs before running picard sam to fastq; up picard version to 1.113 22 January 2015, 02:46:58 UTC
e403e1a Thomas Mooney 22 January 2015, 00:10:58 UTC Change cascading behavior of AnP delete(). * Refuse to delete if models or instrument data are assigned. * Cascade to delete any existing timeline events. 22 January 2015, 00:10:58 UTC
bcd1879 Thomas Mooney 21 January 2015, 22:33:56 UTC Add optional length-dist parameter. 21 January 2015, 22:33:56 UTC
8cae0a1 Thomas Mooney 21 January 2015, 20:13:00 UTC Change other version checks to inequalities. 21 January 2015, 20:13:00 UTC
0400f66 Thomas Mooney 21 January 2015, 19:55:29 UTC Reorganize--locate with other version-dependent subroutines. 21 January 2015, 19:55:29 UTC
fcb7058 Thomas B. Mooney 21 January 2015, 17:28:40 UTC Merge pull request #422 from tmooney/memtmp create /tmp path if NE for bwa mem and pass along the AR's scratch directory 21 January 2015, 17:28:40 UTC
006494c Thomas Mooney 21 January 2015, 16:39:31 UTC Pass along our scratch directory. 21 January 2015, 16:39:31 UTC
366a04b Thomas Mooney 21 January 2015, 16:39:01 UTC Use create_temp_directory() to create the temp directory. 21 January 2015, 16:39:01 UTC
d571a23 Thomas B. Mooney 21 January 2015, 16:06:50 UTC Merge pull request #419 from tmooney/parallelize_spelling s/paralellize/parallelize/ 21 January 2015, 16:06:50 UTC
4eb0fdc Susanna Siebert 21 January 2015, 15:46:05 UTC Merge pull request #418 from susannasiebert/variant_reporting_improvements Various ACMG report improvements 21 January 2015, 15:46:05 UTC
8ca6606 Thomas Mooney 21 January 2015, 15:19:21 UTC Documentation tweaks. 21 January 2015, 15:25:54 UTC
43c21fa Thomas Mooney 21 January 2015, 15:13:49 UTC Whitespace. 21 January 2015, 15:25:53 UTC
a9fc088 Thomas Mooney 21 January 2015, 15:08:44 UTC Pass appropriate length-dist option depending on flexbar version. 21 January 2015, 15:08:44 UTC
aca038f Travis Abbott 21 January 2015, 07:00:19 UTC code cleanup 21 January 2015, 07:00:19 UTC
0439063 Travis Abbott 21 January 2015, 06:50:21 UTC create /tmp path if NE for bwa mem because some tools just really insist on a prefix existing :p 21 January 2015, 06:51:30 UTC
0642827 Thomas Mooney 20 January 2015, 23:58:25 UTC s/paralellize/parallelize/ 20 January 2015, 23:58:25 UTC
6d92cc4 Tiandao Li 20 January 2015, 22:37:28 UTC final touches 20 January 2015, 22:37:28 UTC
e937a33 Tiandao Li 20 January 2015, 22:31:58 UTC use whole_rmdup_bam_flagstat_file instead of reaching into build's data_directory 20 January 2015, 22:31:58 UTC
919c54a Tiandao Li 20 January 2015, 22:27:31 UTC allow model to be specific with command UI 20 January 2015, 22:27:31 UTC
ba5028e Tiandao Li 20 January 2015, 22:18:46 UTC separate model-based logic into a model command 20 January 2015, 22:24:11 UTC
d76b2c1 Tiandao Li 20 January 2015, 22:00:36 UTC fix compiler error 20 January 2015, 22:00:36 UTC
60eacd8 Tiandao Li 20 January 2015, 21:49:47 UTC use header instead of indices 20 January 2015, 21:49:47 UTC
41eb41a Tiandao Li 20 January 2015, 21:34:08 UTC modify bs_rate 20 January 2015, 21:34:08 UTC
cd07a8a Tiandao Li 20 January 2015, 21:28:13 UTC use default file handle to deduplicate output 20 January 2015, 21:28:13 UTC
215363b Tiandao Li 20 January 2015, 21:06:01 UTC read flagstat info 20 January 2015, 21:06:01 UTC
27cc2d6 Tiandao Li 20 January 2015, 20:40:31 UTC depulicate chrom bs reads 20 January 2015, 20:40:31 UTC
4e658d8 Tiandao Li 20 January 2015, 20:27:07 UTC add 1 tab for return 1. 20 January 2015, 20:27:07 UTC
56113b3 APipe Tester 20 January 2015, 20:25:01 UTC updated ur submodule to c44bc57 20 January 2015, 20:25:01 UTC
0cdaed8 Tiandao Li 20 January 2015, 20:12:27 UTC remove duplicated comments 20 January 2015, 20:22:49 UTC
f71b466 Tiandao Li 20 January 2015, 18:52:16 UTC Merge branch 'master' of https://github.com/genome/genome 20 January 2015, 18:52:16 UTC
3997bac Susanna Siebert 20 January 2015, 17:02:07 UTC Update MafInterpreter to prepend fields with source 20 January 2015, 17:02:07 UTC
eb7ef93 Susanna Siebert 20 January 2015, 16:25:34 UTC Update GmafInterpreter to prepend fields with source 20 January 2015, 16:25:34 UTC
ee5f5f5 Susanna Siebert 20 January 2015, 16:24:07 UTC Update CafInterpreter to prepend fields with source 20 January 2015, 16:24:07 UTC
4f32992 APipe Tester 20 January 2015, 15:49:17 UTC updated jenkins submodule to ad020c5 20 January 2015, 15:49:17 UTC
8b224fb APipe Tester 20 January 2015, 15:49:06 UTC updated ur submodule to c7dae7c 20 January 2015, 15:49:06 UTC
57722b0 APipe Tester 17 January 2015, 13:15:58 UTC Updated `genome` tab completion. 17 January 2015, 13:15:58 UTC
4760dbc APipe Tester 17 January 2015, 13:14:25 UTC Updated class browser cache. 17 January 2015, 13:14:25 UTC
1179cc4 Susanna Siebert 16 January 2015, 21:43:47 UTC remove tumor specific columns from the ACMG report 16 January 2015, 21:43:47 UTC
564aa7c Susanna Siebert 16 January 2015, 21:43:22 UTC fix valid_callers for germline reports 16 January 2015, 21:43:22 UTC
82f3e4d Ricky Ng 16 January 2015, 20:57:23 UTC Merge pull request #397 from dummey/master Updating SraToBam.pm to use new input params. 16 January 2015, 20:57:23 UTC
d52fd14 Nathaniel Nutter 16 January 2015, 20:42:18 UTC Merge pull request #404 from nnutter/RT/103374 Minor Improvements to BamWindow Wrapper 16 January 2015, 20:42:18 UTC
e82b214 Susanna Siebert 16 January 2015, 20:30:34 UTC Delete DbsnpInterpreter It has been superseded by the CafInterpreter 16 January 2015, 20:30:34 UTC
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