| 0757dfc | dmorton | 21 April 2014, 23:02:04 UTC | Add variant_type to Annotation::Adaptor and remove variant-type specific accessors for vcf results | 21 April 2014, 23:02:04 UTC |
| bd75500 | dmorton | 21 April 2014, 22:54:21 UTC | Remove annotation_build from Annotation::Adaptor | 21 April 2014, 22:54:21 UTC |
| 6768cd5 | dmorton | 21 April 2014, 22:48:51 UTC | Remove subclasses of Annotation::Adaptor The tests that call the adaptor with the two build classes are still in place. This should make it a little easier for Experts to build workflows (they won't have to define different adaptors for different build classes). | 21 April 2014, 22:48:51 UTC |
| 24db241 | dmorton | 21 April 2014, 18:42:14 UTC | Add accessor 'input_result_file_path' This lets us accept either a DV2 vcf result or our own ResultBase type results as our input_result inputs. | 21 April 2014, 22:21:01 UTC |
| d300410 | dmorton | 21 April 2014, 18:08:51 UTC | remove Detail directory | 21 April 2014, 22:21:01 UTC |
| dab75af | Thomas Mooney | 21 April 2014, 22:18:33 UTC | Remove old `gmt build gc-bias`. See instead `gmt picard collect-gc-bias-metrics`. | 21 April 2014, 22:18:33 UTC |
| db9c0f1 | Eddie Belter | 21 April 2014, 22:10:50 UTC | MC16s: in process sanger: close phred readers; return instead of next | 21 April 2014, 22:15:44 UTC |
| 814c90d | Eddie Belter | 21 April 2014, 22:10:10 UTC | SX: add close method to phred readers | 21 April 2014, 22:15:43 UTC |
| 3a708ce | Thomas Mooney | 21 April 2014, 22:12:15 UTC | Remove tools for working with nonexistent Genome::SequenceDiff | 21 April 2014, 22:12:15 UTC |
| cefc163 | Thomas Mooney | 21 April 2014, 22:02:40 UTC | Remove old `gmt synch`. See `gmt fasta synch` instead. | 21 April 2014, 22:02:40 UTC |
| 42e2419 | Susanna Siebert | 21 April 2014, 19:55:59 UTC | bugfix | 21 April 2014, 19:55:59 UTC |
| 9b9c610 | Susanna Siebert | 21 April 2014, 19:42:00 UTC | filter to keep entries with a specific FT value | 21 April 2014, 19:45:30 UTC |
| 6c4551d | Susanna Siebert | 17 April 2014, 21:26:32 UTC | new module for creating a simple report on an annoted vcf | 21 April 2014, 19:45:29 UTC |
| e3149fd | Susanna Siebert | 17 April 2014, 14:13:23 UTC | added subroutines to return all the (canonical) transcripts in an entry for a given allele | 21 April 2014, 19:45:29 UTC |
| afe5a75 | Thomas Mooney | 21 April 2014, 18:42:43 UTC | Add a v4 to the alignment API. | 21 April 2014, 18:42:43 UTC |
| 54f8aa7 | Adam Coffman | 21 April 2014, 18:35:38 UTC | add AnP accessor to work orders | 21 April 2014, 18:35:38 UTC |
| 0bc0e44 | dmorton | 21 April 2014, 17:31:55 UTC | Start adding validation tests for Annotation::Plan | 21 April 2014, 17:31:55 UTC |
| 84b543c | dmorton | 21 April 2014, 17:28:29 UTC | Pass params to constructor of Annotation::Plan | 21 April 2014, 17:28:29 UTC |
| 18cde27 | dmorton | 21 April 2014, 17:27:29 UTC | Fix allowing Factory to find modules in Genome::Annotation without being in a subdirectory/submodule | 21 April 2014, 17:27:29 UTC |
| 35df146 | dmorton | 21 April 2014, 17:26:39 UTC | Use Params::Validate for get_object And actually instantiate an object | 21 April 2014, 17:26:39 UTC |
| cd9d818 | dmorton | 21 April 2014, 17:25:02 UTC | Make ComponentBase for classes that need to validate params | 21 April 2014, 17:25:02 UTC |
| 5624559 | dmorton | 21 April 2014, 01:56:41 UTC | Added Plan object to represent an Annotation Plan validation stuff is incomplete and untested. | 21 April 2014, 01:56:41 UTC |
| 3ec90ad | dmorton | 21 April 2014, 01:54:16 UTC | Updated Factory views renamed to reporters gatherers renamed to interpreters removed individualized accessors for *_names and get_* | 21 April 2014, 01:54:16 UTC |
| 41a8d00 | dmorton | 19 April 2014, 03:09:15 UTC | Remove old use statement from test. | 19 April 2014, 03:09:15 UTC |
| ee59a7c | dmorton | 18 April 2014, 21:13:26 UTC | Add Factory/ExpertBase and test | 18 April 2014, 21:21:21 UTC |
| 3e66798 | dmorton | 18 April 2014, 20:25:11 UTC | Change name annotation_build to known_variants | 18 April 2014, 21:21:21 UTC |
| 8f461e6 | dmorton | 18 April 2014, 20:17:51 UTC | Make all inputs to BamReadcount required | 18 April 2014, 21:20:31 UTC |
| 5bd6f1a | dmorton | 18 April 2014, 20:15:08 UTC | Reorganize directories added output_result and variant_type to base classes | 18 April 2014, 21:20:31 UTC |
| 41cbb78 | Dave Larson | 18 April 2014, 17:39:43 UTC | * Skip the header line if it exists * Explicitly use Genome::Model::Tools::Annotate::AminoAcidChange | 18 April 2014, 17:40:30 UTC |
| 31b0a46 | Avinash Ramu | 18 April 2014, 15:44:47 UTC | update clinseq blessed build | 18 April 2014, 15:44:47 UTC |
| 3145ec0 | APipe Tester | 18 April 2014, 12:18:37 UTC | Updated `gmt` tab completion. | 18 April 2014, 12:18:37 UTC |
| 88d7376 | APipe Tester | 18 April 2014, 12:17:54 UTC | Updated `genome` tab completion. | 18 April 2014, 12:17:54 UTC |
| dc85e03 | APipe Tester | 18 April 2014, 12:16:18 UTC | Updated class browser cache. | 18 April 2014, 12:16:18 UTC |
| 5741fff | apregier | 18 April 2014, 00:11:33 UTC | Merge branch 'updated' into gb_master | 18 April 2014, 00:11:33 UTC |
| 8c04275 | apregier | 17 April 2014, 22:58:39 UTC | New option for vep script in v75 | 18 April 2014, 00:10:32 UTC |
| e8e6f2a | apregier | 17 April 2014, 22:57:49 UTC | Ensembl apis and scripts now on github | 18 April 2014, 00:10:32 UTC |
| cfd7c81 | Malachi Griffith | 17 April 2014, 21:56:01 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 17 April 2014, 21:56:01 UTC |
| 3844189 | Malachi Griffith | 17 April 2014, 21:55:49 UTC | clin-seq add first version of docm summary report, hotspot calling of canonical mutation sites | 17 April 2014, 21:55:49 UTC |
| 22524e1 | Gabriel Sanderson | 17 April 2014, 21:51:55 UTC | Renamed attributes | 17 April 2014, 21:51:55 UTC |
| fd06f1b | Thomas Mooney | 17 April 2014, 21:04:35 UTC | Don't subclass InstrumentData when looking for compatible data. This used to be for performance reasons, but does the wrong thing for genotype data. | 17 April 2014, 21:05:21 UTC |
| 07a8034 | apregier | 17 April 2014, 20:58:28 UTC | Merge branch 'updated' into gb_master | 17 April 2014, 20:58:28 UTC |
| 5b48dd3 | apregier | 17 April 2014, 20:24:22 UTC | gzip vep output vcf | 17 April 2014, 20:57:29 UTC |
| 4cbdfc0 | apregier | 17 April 2014, 20:19:30 UTC | Add hgvs option to vep result | 17 April 2014, 20:57:29 UTC |
| d9d7b9f | apregier | 17 April 2014, 20:04:56 UTC | Add hgvs as a vep option fasta must also be specified | 17 April 2014, 20:57:28 UTC |
| dcaaf31 | Anthony Brummett | 17 April 2014, 19:54:10 UTC | extract method to write histogram of insert sizes | 17 April 2014, 20:46:32 UTC |
| a213539 | Anthony Brummett | 17 April 2014, 19:51:28 UTC | extract method to write histogram base quality per cycle file | 17 April 2014, 20:46:32 UTC |
| 702a279 | Anthony Brummett | 17 April 2014, 19:49:04 UTC | extract method to write histogram base quality file | 17 April 2014, 20:46:31 UTC |
| e86f765 | Anthony Brummett | 17 April 2014, 19:46:20 UTC | extract method to write histogram coverage file | 17 April 2014, 20:46:30 UTC |
| 56ee141 | Anthony Brummett | 17 April 2014, 19:42:30 UTC | extract method to save the error rate by position info | 17 April 2014, 20:46:30 UTC |
| 314a1a1 | Anthony Brummett | 17 April 2014, 19:37:44 UTC | extract method to load quality by cycle info | 17 April 2014, 20:46:29 UTC |
| 6d37fd0 | Anthony Brummett | 17 April 2014, 19:35:42 UTC | extract method to load quality distribution | 17 April 2014, 20:46:28 UTC |
| 82239e1 | Anthony Brummett | 17 April 2014, 19:31:47 UTC | extract method to load gc bias metrics | 17 April 2014, 20:46:28 UTC |
| 518a504 | Anthony Brummett | 17 April 2014, 19:20:10 UTC | extract method to get the insert size metrics | 17 April 2014, 20:46:27 UTC |
| 748fb81 | Anthony Brummett | 17 April 2014, 16:36:04 UTC | extract method to get the error rate metrics | 17 April 2014, 20:46:27 UTC |
| 096de4d | Anthony Brummett | 17 April 2014, 16:32:23 UTC | make a class to represent a label+directory pair | 17 April 2014, 20:46:26 UTC |
| 61a9eeb | Anthony Brummett | 17 April 2014, 16:00:27 UTC | extract method to get the mark duplicates metrics | 17 April 2014, 20:46:25 UTC |
| cc0fb12 | Anthony Brummett | 17 April 2014, 15:51:50 UTC | extract method to get the alignment summary metric data from an output dir | 17 April 2014, 20:46:25 UTC |
| f48f393 | Anthony Brummett | 17 April 2014, 15:37:03 UTC | extract methods to turn the text list of things into Perl lists | 17 April 2014, 20:46:24 UTC |
| 36d7a31 | Anthony Brummett | 17 April 2014, 15:33:24 UTC | extract method to create writer | 17 April 2014, 20:46:24 UTC |
| e505fc5 | Anthony Brummett | 17 April 2014, 15:32:19 UTC | extract method to validate labels and directories have the same number of members | 17 April 2014, 20:46:23 UTC |
| 4d9b7a2 | Anthony Brummett | 17 April 2014, 15:14:58 UTC | remove breakpoint | 17 April 2014, 20:46:23 UTC |
| 385985a | Anthony Brummett | 17 April 2014, 15:13:08 UTC | remove unnecessary variable | 17 April 2014, 20:46:22 UTC |
| 7174f63 | Anthony Brummett | 16 April 2014, 19:15:39 UTC | Get in_place_of_null_value set to enpty-string unless otherwise specified The UR mutator wasn't seeing that undef was different than empty string, which matches UR behavior in other places | 17 April 2014, 20:46:21 UTC |
| b7c9653 | Anthony Brummett | 16 April 2014, 19:13:20 UTC | avoid an uninitialized value warning by checking for undef the right way | 17 April 2014, 20:46:21 UTC |
| 300f9a4 | Anthony Brummett | 16 April 2014, 19:12:46 UTC | The ErrorRate files can have comments at the top of them | 17 April 2014, 20:46:20 UTC |
| 2168773 | APipe Tester | 17 April 2014, 20:44:20 UTC | updated workflow submodule to e975bcf | 17 April 2014, 20:44:20 UTC |
| 78e02e5 | Feiyu Du | 17 April 2014, 20:24:33 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 17 April 2014, 20:24:33 UTC |
| f300b31 | Feiyu Du | 17 April 2014, 20:24:27 UTC | add lsf_resource to copycat somatic | 17 April 2014, 20:24:27 UTC |
| caac238 | Nathaniel Nutter | 17 April 2014, 20:19:28 UTC | update UR submodule URL | 17 April 2014, 20:19:28 UTC |
| 5a27199 | Adam Coffman | 17 April 2014, 15:50:59 UTC | update brc46 regex on sample importer to support CSB | 17 April 2014, 15:50:59 UTC |
| 3a23021 | dmorton | 17 April 2014, 15:18:31 UTC | Pull output_file_path into base class | 17 April 2014, 15:28:25 UTC |
| 9ee42e6 | dmorton | 17 April 2014, 15:16:00 UTC | whitespace | 17 April 2014, 15:28:25 UTC |
| 7ffcbd1 | dmorton | 17 April 2014, 15:15:12 UTC | All Annotation::Detail::Commands and Results have input_result input | 17 April 2014, 15:28:25 UTC |
| acf833a | dmorton | 17 April 2014, 14:57:13 UTC | Add output_file_path as interface in base Result class | 17 April 2014, 14:57:13 UTC |
| 3bc3237 | dmorton | 17 April 2014, 13:51:04 UTC | whitespace | 17 April 2014, 13:51:04 UTC |
| 055092b | dmorton | 16 April 2014, 21:54:58 UTC | Rename AddReadcounts to Readcount | 17 April 2014, 13:49:52 UTC |
| 9982f12 | dmorton | 16 April 2014, 21:42:49 UTC | Renamed Readcount to RunBamReadcount | 17 April 2014, 13:49:52 UTC |
| a9eefb1 | dmorton | 16 April 2014, 21:35:34 UTC | Renamed JoinxVcfAnnotate to just Joinx It is already in the Annotation directory. | 17 April 2014, 13:49:51 UTC |
| 6433e7c | APipe Tester | 17 April 2014, 12:17:54 UTC | Updated `genome` tab completion. | 17 April 2014, 12:17:54 UTC |
| a44d496 | APipe Tester | 17 April 2014, 12:16:25 UTC | Updated class browser cache. | 17 April 2014, 12:16:25 UTC |
| 23ca9a2 | Avinash Ramu | 17 April 2014, 03:56:14 UTC | remove whitespace at end of line | 17 April 2014, 03:56:14 UTC |
| 098809a | Avinash Ramu | 17 April 2014, 00:28:18 UTC | update clinseq blessed build | 17 April 2014, 00:29:02 UTC |
| 583ce8e | Avinash Ramu | 16 April 2014, 23:04:00 UTC | update test build for makecircosplot | 17 April 2014, 00:29:01 UTC |
| 07a3f89 | Avinash Ramu | 16 April 2014, 23:03:12 UTC | look in samtools results for snv sources | 17 April 2014, 00:28:59 UTC |
| 9acf9eb | Avinash Ramu | 16 April 2014, 21:07:18 UTC | update test-data directory | 17 April 2014, 00:28:59 UTC |
| 9bf5506 | Avinash Ramu | 16 April 2014, 20:59:25 UTC | change expected number of diffs | 17 April 2014, 00:28:58 UTC |
| 259b49d | Avinash Ramu | 16 April 2014, 19:01:15 UTC | update test directory | 17 April 2014, 00:28:57 UTC |
| 2a5b88b | Avinash Ramu | 16 April 2014, 19:00:50 UTC | remove output of build_dir | 17 April 2014, 00:28:56 UTC |
| e345665 | Avinash Ramu | 16 April 2014, 15:29:00 UTC | update location of fusion file within clinseq build | 17 April 2014, 00:28:55 UTC |
| 34f32f0 | Avinash Ramu | 16 April 2014, 15:28:31 UTC | don't die if BAMQC results already. | 17 April 2014, 00:28:55 UTC |
| f7002ee | Avinash Ramu | 16 April 2014, 15:27:23 UTC | use a hash reference directly | 17 April 2014, 00:28:54 UTC |
| ed246b5 | Avinash Ramu | 16 April 2014, 15:24:53 UTC | refactor get_common_name | 17 April 2014, 00:28:53 UTC |
| 94e6dfa | Avinash Ramu | 16 April 2014, 15:24:22 UTC | get perlane bamqc and per build bamqc reports | 17 April 2014, 00:28:53 UTC |
| ebf487b | Avinash Ramu | 15 April 2014, 15:22:22 UTC | add test for InstrumentDataAlignmentBams | 17 April 2014, 00:28:52 UTC |
| bc55023 | Avinash Ramu | 15 April 2014, 15:18:36 UTC | add method to access lane/bamqcpath easily | 17 April 2014, 00:28:51 UTC |
| 5fe7d35 | Avinash Ramu | 14 April 2014, 20:06:47 UTC | reorganize fusion files' location | 17 April 2014, 00:28:51 UTC |
| 78bed09 | Avinash Ramu | 14 April 2014, 19:55:30 UTC | refactor summarize_builds 1 | 17 April 2014, 00:28:50 UTC |
| c5d9156 | Avinash Ramu | 14 April 2014, 19:54:20 UTC | use tsv reader instead of awk to parse files | 17 April 2014, 00:28:50 UTC |
| 3aa58f7 | apregier | 16 April 2014, 22:09:20 UTC | Merge branch 'updated' into gb_master | 16 April 2014, 22:09:20 UTC |
| f43268f | apregier | 16 April 2014, 22:02:09 UTC | annotation_builds input is many Multiple builds aren't currently supported but this way we can implement it without changing the software result input | 16 April 2014, 22:02:09 UTC |
