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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
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
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
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
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
b999391 Susanna Siebert 16 January 2015, 19:50:37 UTC modify the order of the ACMG report header 16 January 2015, 19:50:37 UTC
0dd686b Eddie Belter 16 January 2015, 19:08:51 UTC Merge pull request #377 from ebelter/instdata-import Merged the TCGA importer into the basic importer. More PRs to come to smooth out the interface. 16 January 2015, 19:08:51 UTC
0a8a48b Susanna Siebert 16 January 2015, 18:40:29 UTC Merge pull request #409 from davidlmorton/json_labels Make sample/library name_labels transient 16 January 2015, 18:40:29 UTC
e892c90 Tiandao Li 16 January 2015, 15:58:34 UTC Merge branch 'master' of https://github.com/genome/genome 16 January 2015, 15:58:34 UTC
7f8b788 Susanna Siebert 16 January 2015, 14:25:09 UTC Merge pull request #414 from susannasiebert/variant_reporting_igv Allow bed files to be URIs for IGV sessions 16 January 2015, 14:25:09 UTC
e14605e Susanna Siebert 16 January 2015, 14:25:04 UTC Merge pull request #412 from susannasiebert/variant_reporting_vaf_library_names Make library_names optional for VafInterpreter 16 January 2015, 14:25:04 UTC
aebb819 Tiandao Li 15 January 2015, 21:48:35 UTC Merge branch 'master' of https://github.com/genome/genome 15 January 2015, 21:48:35 UTC
c8f5955 Susanna Siebert 15 January 2015, 21:24:01 UTC Merge pull request #406 from susannasiebert/variant_reporting_readcount Fix allele translations for bam readcount 15 January 2015, 21:24:01 UTC
752b17b Susanna Siebert 15 January 2015, 21:19:51 UTC Add comments to the translate_pure_indels subroutine 15 January 2015, 21:19:51 UTC
3792c59 Thomas B. Mooney 15 January 2015, 20:07:16 UTC Merge pull request #403 from tmooney/fix_diskallocationstaged_inconsistency Correct abstract method name in G:SR:DiskAllocationStaged 15 January 2015, 20:07:16 UTC
274c3c2 Tiandao Li 15 January 2015, 19:30:41 UTC bsmap alignment status and convertion rate from chrM and lambda 15 January 2015, 19:30:41 UTC
c3e0d12 David Morton 15 January 2015, 19:20:15 UTC Merge pull request #415 from davidlmorton/custom_report Update ShowDoc test data for custom report 15 January 2015, 19:20:15 UTC
824650b dmorton 15 January 2015, 19:17:06 UTC Update ShowDoc test data for custom report 15 January 2015, 19:17:06 UTC
521af17 David Morton 15 January 2015, 18:22:04 UTC Merge pull request #400 from davidlmorton/custom_report Added CustomReport 15 January 2015, 18:22:04 UTC
8b92b8b dmorton 15 January 2015, 17:39:44 UTC Remove old, non-transient, properties 15 January 2015, 17:39:44 UTC
f5d3222 Thomas B. Mooney 15 January 2015, 17:08:43 UTC Merge pull request #411 from tmooney/add_missing_lock_scope Add lock scoping to PAP's upload-result command. 15 January 2015, 17:08:43 UTC
cd38e14 Mark Burnett 15 January 2015, 17:07:35 UTC Merge pull request #413 from mark-burnett/fix-lock-release-all Bugfix: make sure FileBackend release_all deletes symlinks 15 January 2015, 17:07:35 UTC
e4471cd Susanna Siebert 15 January 2015, 16:42:23 UTC allow bed files to be URIs for IGV sessions 15 January 2015, 16:42:23 UTC
9f9ac6d Susanna Siebert 15 January 2015, 16:27:20 UTC Merge pull request #408 from susannasiebert/variant_reporting_mincovfilter Make min coverage vcf id truly unique by including sample name 15 January 2015, 16:27:20 UTC
f012a09 Mark Burnett 15 January 2015, 16:11:06 UTC S:L:FileBackend remove unused temporary 15 January 2015, 16:13:31 UTC
622319e Mark Burnett 15 January 2015, 16:10:46 UTC S:L:FileBackend extract write_lock_info 15 January 2015, 16:13:30 UTC
d942256 Mark Burnett 15 January 2015, 16:08:37 UTC S:L:FileBackend extract tempdir_for_resource 15 January 2015, 16:13:30 UTC
c663571 Mark Burnett 15 January 2015, 16:04:11 UTC S:L:FileBackend fix release_all deleteing symlinks 15 January 2015, 16:13:29 UTC
b54d5e2 Susanna Siebert 15 January 2015, 15:24:46 UTC Make library_names optional for VafInterpreter We use the VafInterpreter without library_names in the MinCoverageObservedInterpreter and the MaxVafObservedInterpreter 15 January 2015, 15:42:07 UTC
22d4ab2 Jim Weible 15 January 2015, 15:03:47 UTC Merge pull request #410 from jweible/AUE-384 Show tags in Analysis Project View 15 January 2015, 15:03:47 UTC
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