| 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 |
| 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 |
