| 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 |
| 316984c | Susanna Siebert | 24 February 2014, 15:46:44 UTC | Refactor fill_in_site_hash to make get_vcf_file obsolete get_vcf_file was extremly britle due to how it retrieves the variant caller specific vcf files. The refactored fill_in_site_hash subroutine now gets this information from the snvs.detailed.vcf.gz file | 04 March 2014, 16:07:53 UTC |
| c630e60 | Susanna Siebert | 21 February 2014, 20:26:38 UTC | pull out the code that determines the number of callers for each site into seperate subroutine | 04 March 2014, 16:07:52 UTC |
| 822cc38 | Susanna Siebert | 19 February 2014, 18:25:28 UTC | revert Genome::Model::Tools::Somatic::ProcessSomaticVariation restore to original state so that users can execute this command with its original functionality for builds that don't have the new CreateReport executed automatically | 04 March 2014, 16:07:52 UTC |
| 8a018fd | Susanna Siebert | 19 February 2014, 18:20:20 UTC | remove unneeded comments | 04 March 2014, 16:07:51 UTC |
| 647c132 | Susanna Siebert | 06 February 2014, 16:16:52 UTC | test for ResolveIgvReferenceName | 04 March 2014, 16:07:51 UTC |
| af0cc62 | Susanna Siebert | 06 February 2014, 15:54:40 UTC | change default IGV reference name to "unknown" | 04 March 2014, 16:07:50 UTC |
| 12831ad | Susanna Siebert | 03 February 2014, 19:13:37 UTC | new module for determining the IVG reference name | 04 March 2014, 16:07:50 UTC |
| a5e73d6 | Susanna Siebert | 30 January 2014, 21:35:54 UTC | make required_snv_callers and tiers_to_review somatic variation processing profile inputs | 04 March 2014, 16:07:49 UTC |
| 7a796bc | Susanna Siebert | 28 January 2014, 14:53:32 UTC | Integrate ProcessSomaticVariation into somatic variation pipeline rename to CreateReport move to G::M::SomaticVariation::Command::CreateReport integrate into Somatic Variation pipeline by modifying xml file move tests and make small fixes to make them work in new environment | 04 March 2014, 16:07:49 UTC |
| 6661670 | Susanna Siebert | 27 January 2014, 15:26:32 UTC | Handle temporary files more gracefully Replace creation of .tmp files with Genome::Sys->create_temp_file() Replace > with -o option in joinx Remove system calls to rm since Genome::Sys temp files get cleaned up automatically | 04 March 2014, 16:07:46 UTC |
| 2c24710 | Susanna Siebert | 23 January 2014, 21:34:03 UTC | fixed subroutine and variable names to conform to standards | 04 March 2014, 16:07:46 UTC |
| 1391c3e | Susanna Siebert | 23 January 2014, 21:26:58 UTC | refactor functionality of bedToAnno and annoToBed pass in whole line and do processing inside of function instead of splitting and joining parts of the line rename to _zero_to_one_based and _one_to_zero_based, respectively | 04 March 2014, 16:07:45 UTC |
| 7bcb112 | David Morton | 23 January 2014, 19:23:14 UTC | Symlink outputs into the som var build dir | 04 March 2014, 16:07:44 UTC |
| af70bfb | David Morton | 23 January 2014, 16:34:11 UTC | clarify status message | 04 March 2014, 16:07:44 UTC |
| 4075316 | David Morton | 23 January 2014, 15:59:22 UTC | Create and use an allocation instead of needing 'output_dir' as an input | 04 March 2014, 16:07:43 UTC |
| 41ae535 | David Morton | 22 January 2014, 19:24:45 UTC | Update authors | 04 March 2014, 16:07:41 UTC |
| 42641c7 | Susanna Siebert | 22 January 2014, 15:18:40 UTC | split up tests into separate files and made helper module | 04 March 2014, 16:07:40 UTC |
| 584bb75 | Susanna Siebert | 21 January 2014, 18:48:27 UTC | removed breakpoint | 04 March 2014, 16:07:40 UTC |
| 04e27a0 | Susanna Siebert | 21 January 2014, 18:37:09 UTC | replace tumor_model with tumor_build test execution without target_regions set | 04 March 2014, 16:07:39 UTC |
| 31039f1 | Susanna Siebert | 21 January 2014, 18:36:04 UTC | bugfix | 04 March 2014, 16:07:38 UTC |
| 004ea78 | Susanna Siebert | 21 January 2014, 16:34:09 UTC | move main testing functionality to separate subroutine | 04 March 2014, 16:07:38 UTC |
| 2c400cd | Susanna Siebert | 17 January 2014, 17:38:26 UTC | removed unneeded lines of code | 04 March 2014, 16:07:37 UTC |
| 7219ace | Susanna Siebert | 17 January 2014, 17:30:16 UTC | replace somatic_variation_model with somatic_variation_build using the somatic_variation_build is generally safer and more reliable than using the model | 04 March 2014, 16:07:37 UTC |
| a8dc61d | Susanna Siebert | 17 January 2014, 15:55:55 UTC | Remove create_review_files input param create_review_files was nearly always turned on by the users of this module. Removing this option now always executes _create_review_files. igv_reference_name was made a mandatory input as it's required for create_review_files added tests for review files created convenience output params for review directory and files | 04 March 2014, 16:07:36 UTC |
| 9fe0186 | Susanna Siebert | 16 January 2014, 20:17:24 UTC | Remove the get_read_counts input param get_read_counts was nearly always turned on by the users of this module. Removing this option now always executes read_counts. turned get_read_counts on in the test and updated test data to make tests pass | 04 March 2014, 16:07:35 UTC |
| 89dc471 | Susanna Siebert | 16 January 2014, 16:14:03 UTC | Code cleanup | 04 March 2014, 16:07:35 UTC |
| aaa75eb | Susanna Siebert | 16 January 2014, 16:13:32 UTC | Bugfix: replaced my with return | 04 March 2014, 16:07:34 UTC |
| d162aab | Susanna Siebert | 16 January 2014, 16:10:26 UTC | Remove the create_archive and include_vcfs_in_archive input params The archiving functionality was only used for production managers. Cmiller says that it can be removed for the pipeline. | 04 March 2014, 16:07:33 UTC |
| 174414c | Susanna Siebert | 16 January 2014, 16:01:15 UTC | Remove the add_tiers input param add_tiers was set to default 0 but nearly always turned on by the users of this module. Removing this option now always executes addTiering. | 04 March 2014, 16:07:33 UTC |
| 3384c89 | Susanna Siebert | 16 January 2014, 15:06:16 UTC | Remove the process_svs input param process_svs was set to default 0 and rarely ever turned on by the users of this module. Removing this option now doesn't process the sv file which basically only used to copy the sv file from the build to the output_dir and include it in the archive. | 04 March 2014, 16:07:32 UTC |
| 9f05f20 | Susanna Siebert | 16 January 2014, 14:58:04 UTC | Remove the add_dbsnp_and_gmaf input param add_dbsnp_and_gmaf was set to default 1 and rarely ever turned off by the users of this module. Removing this option now always executes _add_dbsnp_and_gmaf. | 04 March 2014, 16:07:32 UTC |
| 7ecd137 | David Morton | 15 January 2014, 21:32:40 UTC | Execute function works Only testing the execute function now instead of the implementation. The report generated is identical to that created by the command in snapshot 'genome-3415' run on model 2892845764, with the same inputs we provide in the test. | 04 March 2014, 16:07:31 UTC |
| 9758dc2 | David Morton | 15 January 2014, 19:16:46 UTC | fix remaining use case for _build_dir | 04 March 2014, 16:07:30 UTC |
| 90855d8 | David Morton | 15 January 2014, 19:14:23 UTC | Remove totally unneccessary code | 04 March 2014, 16:07:30 UTC |
| eb825e0 | David Morton | 15 January 2014, 19:10:09 UTC | Removed filter regions/sites functionality Made functions explicitly output into the _full_output_dir instead of inferring their outputs from their inputs. | 04 March 2014, 16:07:29 UTC |
| fdf5bf8 | Susanna Siebert | 15 January 2014, 15:52:04 UTC | remove filter_sites processing | 04 March 2014, 16:07:29 UTC |
| 8e408d0 | Susanna Siebert | 15 January 2014, 15:40:58 UTC | Remove explicit is_optional for inputs in the has_optional_input list | 04 March 2014, 16:07:28 UTC |
| 3ebbdfa | Susanna Siebert | 15 January 2014, 15:29:05 UTC | remove unused inputs variant_list_is_one_based sites_to_pass | 04 March 2014, 16:07:27 UTC |
| cad5623 | Susanna Siebert | 15 January 2014, 15:26:33 UTC | explicitly import basename subroutine | 04 March 2014, 16:07:27 UTC |
| 7743245 | Susanna Siebert | 15 January 2014, 15:24:13 UTC | transient variable for _build_dir remove build_dir from various subroutine parameters prefix transient variables with _ | 04 March 2014, 16:07:26 UTC |
| c0453ed | Susanna Siebert | 15 January 2014, 15:20:30 UTC | bug fix for ++ and -- | 04 March 2014, 16:07:25 UTC |
| eaa1149 | Susanna Siebert | 15 January 2014, 15:07:54 UTC | update test data to V3 and remove tiering_bed_files_v3 data directory | 04 March 2014, 16:07:25 UTC |
| d6916a4 | David Morton | 13 January 2014, 20:57:11 UTC | Update test_data to version 2: removed symlinks to real build data region-limited to chromosome 3 | 04 March 2014, 16:07:24 UTC |
| 432e041 | David Morton | 13 January 2014, 20:18:25 UTC | Add annotation to test | 04 March 2014, 16:07:24 UTC |
| 8a32abe | David Morton | 13 January 2014, 20:15:12 UTC | Allow for test data versioning | 04 March 2014, 16:07:23 UTC |
| c37ab1a | Susanna Siebert | 10 January 2014, 15:46:58 UTC | test case for removeUnsupportedSites subroutine | 04 March 2014, 16:07:22 UTC |
| 18567cc | Susanna Siebert | 10 January 2014, 15:46:16 UTC | store full_output_dir in a variable | 04 March 2014, 16:07:22 UTC |
| 0fbc359 | Susanna Siebert | 10 January 2014, 15:44:21 UTC | retrieve variables inside of removeUnsupportedSites subroutine instead of passing them along | 04 March 2014, 16:07:21 UTC |
| f8c565f | Susanna Siebert | 10 January 2014, 15:26:46 UTC | subtest for _filter_regions subroutine | 04 March 2014, 16:07:20 UTC |
| a0b6719 | Susanna Siebert | 09 January 2014, 21:44:48 UTC | subtest for removeFilterSites subroutine | 04 March 2014, 16:07:19 UTC |
| 7614a13 | Susanna Siebert | 09 January 2014, 21:30:31 UTC | test case for getFilterSites subroutine | 04 March 2014, 16:07:18 UTC |
| f41a243 | Susanna Siebert | 09 January 2014, 21:21:30 UTC | add compare_ok tests to stage_snv_file and stage_indel_file subtests | 04 March 2014, 16:07:17 UTC |
| 58c892f | Susanna Siebert | 09 January 2014, 21:18:48 UTC | bug fix in removeFilterSites | 04 March 2014, 16:07:17 UTC |
| 54b94a5 | Susanna Siebert | 09 January 2014, 21:17:04 UTC | use somatic variation model as input instead of its id | 04 March 2014, 16:07:16 UTC |
| c53f04f | Susanna Siebert | 07 January 2014, 20:34:16 UTC | added test for _filter_off_target_regions subroutine | 04 March 2014, 16:07:15 UTC |
| a478372 | Susanna Siebert | 07 January 2014, 20:33:55 UTC | added test for cleanFile subroutine | 04 March 2014, 16:07:15 UTC |
| 0aa2dcf | Susanna Siebert | 07 January 2014, 20:33:14 UTC | fixed spelling error | 04 March 2014, 16:07:14 UTC |
| 6dc804e | Susanna Siebert | 07 January 2014, 20:32:13 UTC | made data directory for somatic variation build | 04 March 2014, 16:07:14 UTC |
| 979d4d4 | Susanna Siebert | 07 January 2014, 20:30:57 UTC | make subroutine that stages sv files for execution | 04 March 2014, 16:07:13 UTC |
| 5de1110 | Susanna Siebert | 07 January 2014, 20:29:23 UTC | make subroutine that stages indel files for execution | 04 March 2014, 16:07:12 UTC |
| 38a4acd | Susanna Siebert | 07 January 2014, 20:25:30 UTC | make subroutine that stages snv files for execution | 04 March 2014, 16:07:12 UTC |
| f676b1c | Susanna Siebert | 07 January 2014, 18:49:26 UTC | added test for get_or_create_filter_file subroutine | 04 March 2014, 16:07:11 UTC |
| daf7be4 | Susanna Siebert | 07 January 2014, 18:48:16 UTC | added test for get_or_create_featurelist_file subroutine | 04 March 2014, 16:07:10 UTC |
| b7ca3a4 | Susanna Siebert | 07 January 2014, 18:42:18 UTC | test for create_directories subroutine | 04 March 2014, 16:07:10 UTC |
| d56a83a | Susanna Siebert | 07 January 2014, 18:38:48 UTC | added tests for creating Genome::Model::Tools::Somatic::ProcessSomaticVariation object | 04 March 2014, 16:07:09 UTC |
| 9cb3196 | Susanna Siebert | 07 January 2014, 18:35:58 UTC | make subroutine that creates directory structure for execution | 04 March 2014, 16:07:09 UTC |
| f69ea6e | Susanna Siebert | 03 January 2014, 14:48:13 UTC | rename create_or_get_featurelist_file to get_or_create_featurelist_file | 04 March 2014, 16:07:08 UTC |
| b785c4a | Susanna Siebert | 03 January 2014, 14:47:05 UTC | make full output dir name its own property for easier access throughout the program | 04 March 2014, 16:07:07 UTC |
| 074d5d3 | Susanna Siebert | 03 January 2014, 14:44:51 UTC | make subdir name its own property for easier access throughout the program | 04 March 2014, 16:07:07 UTC |
| f5bcaf7 | Susanna Siebert | 03 January 2014, 14:34:57 UTC | move sample name logic into the property definition | 04 March 2014, 16:07:06 UTC |
| c41b112 | Susanna Siebert | 02 January 2014, 16:25:40 UTC | work on $self->process_svs instead of copy to make value accessible to subroutines | 04 March 2014, 16:07:06 UTC |
| e337ea3 | Susanna Siebert | 02 January 2014, 16:12:05 UTC | refactor to use $self->warning/status/error_message and confess | 04 March 2014, 16:07:05 UTC |
| 8be6771 | Susanna Siebert | 02 January 2014, 16:07:15 UTC | change _create_archive to not pass in archive_dir but calculate from self | 04 March 2014, 16:07:04 UTC |
| 4a87743 | Susanna Siebert | 30 December 2013, 22:10:11 UTC | fixed formatting | 04 March 2014, 16:07:04 UTC |
| c927e6f | Susanna Siebert | 30 December 2013, 21:45:51 UTC | change order of operations a bit to make code easier to read | 04 March 2014, 16:07:03 UTC |
| 4b4dbc0 | Susanna Siebert | 30 December 2013, 21:43:36 UTC | set ->sample_name with updated sample name so that it can easily be retrieved later | 04 March 2014, 16:07:03 UTC |
| 3a4cc68 | Susanna Siebert | 30 December 2013, 21:41:37 UTC | pull code for creation of filter file into own subroutine get_or_create_filter_file | 04 March 2014, 16:07:02 UTC |
| afcbd17 | Susanna Siebert | 30 December 2013, 21:39:59 UTC | rename create_or_get_featurelist to create_or_get_featurelist_file | 04 March 2014, 16:07:01 UTC |
