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 |