| 70bee8a | Eddie Belter | 20 August 2014, 23:43:34 UTC | InstData Import: add insert extension to bam path to Helpers | 20 August 2014, 23:43:53 UTC |
| 11f2deb | Ian Ferguson | 20 August 2014, 22:29:53 UTC | Escape --intervals args in GMT::Mutect shell cmd | 20 August 2014, 22:35:04 UTC |
| f17efe6 | Eddie Belter | 20 August 2014, 17:45:06 UTC | InstData: rm microarray command tree | 20 August 2014, 22:31:28 UTC |
| 31dd6ed | Eddie Belter | 01 August 2014, 19:36:40 UTC | InstData Import: tcga bam test no longer decrements the dummy id | 20 August 2014, 22:31:28 UTC |
| 9838346 | Eddie Belter | 01 August 2014, 19:35:14 UTC | InstData Import: tcga bam no longer test model is created | 20 August 2014, 22:31:27 UTC |
| 23bd608 | dmorton | 20 August 2014, 21:38:55 UTC | Add input_a and input_b properties | 20 August 2014, 22:29:56 UTC |
| c5af00e | dmorton | 20 August 2014, 20:16:55 UTC | Ensure that the previous_result shares the test_name of this result This is when looking up the previous_result from the current_result. | 20 August 2014, 22:29:56 UTC |
| 720d9aa | dmorton | 20 August 2014, 20:15:52 UTC | Use the previous results test_name It is an error if the previous_result could have a different test name from the current result. | 20 August 2014, 22:29:56 UTC |
| 09145b1 | dmorton | 20 August 2014, 18:00:20 UTC | Don't look for vcf results when there aren't any Combine results whose input results did not both make a vcf result don't have an associated vcf result of their own. | 20 August 2014, 22:29:56 UTC |
| 74715d5 | dmorton | 20 August 2014, 17:59:13 UTC | Use the same test_name as the DV2 result Instead of relying on the environment variable to be the same as it was when the result was generated, we use the same test_name as that result when looking for the associated vcf-result | 20 August 2014, 22:29:56 UTC |
| 50351ed | Thomas Mooney | 20 August 2014, 22:24:03 UTC | s/instrumetn/instrument/ | 20 August 2014, 22:24:03 UTC |
| 13a1b4e | Thomas Mooney | 20 August 2014, 22:05:23 UTC | s/ teh / the /g | 20 August 2014, 22:05:23 UTC |
| f6b48bc | Thomas Mooney | 20 August 2014, 22:03:33 UTC | s/ adn / and /g | 20 August 2014, 22:03:33 UTC |
| 64cb7e5 | Thomas Mooney | 20 August 2014, 21:59:47 UTC | Fix spelling of "allocation" | 20 August 2014, 21:59:47 UTC |
| 43ecb7b | Thomas Mooney | 20 August 2014, 21:57:01 UTC | s/eror/error/ | 20 August 2014, 21:57:01 UTC |
| 5198783 | Thomas Mooney | 20 August 2014, 21:51:36 UTC | s/ ot / to /g | 20 August 2014, 21:51:36 UTC |
| 1a59ebb | Thomas Mooney | 20 August 2014, 21:49:51 UTC | s/buid ot/build to/ | 20 August 2014, 21:49:51 UTC |
| ffebd11 | Thomas Mooney | 20 August 2014, 21:47:26 UTC | s/succeded/succeeded/g | 20 August 2014, 21:47:26 UTC |
| 20df7bc | Thomas Mooney | 20 August 2014, 21:46:20 UTC | Fix typo "suceed" => "succeeded" | 20 August 2014, 21:46:20 UTC |
| 8ddbd6f | Thomas Mooney | 20 August 2014, 21:42:17 UTC | Fill in a brief help_detail since help_brief doesn't appear in --help | 20 August 2014, 21:42:17 UTC |
| 965953d | Thomas Mooney | 20 August 2014, 21:39:41 UTC | Add a doc line for --model. | 20 August 2014, 21:39:41 UTC |
| 9096382 | Thomas Mooney | 20 August 2014, 21:37:55 UTC | s/compatable/compatible/g | 20 August 2014, 21:37:55 UTC |
| 2b82646 | Thomas Mooney | 20 August 2014, 21:30:03 UTC | Update somval model naming to prefer the "tumor_sample" information. | 20 August 2014, 21:30:03 UTC |
| 99047c5 | apregier | 20 August 2014, 20:31:18 UTC | Merge branch 'copy' into gb_master | 20 August 2014, 20:31:18 UTC |
| 6118e27 | apregier | 20 August 2014, 20:29:25 UTC | Use new enforce-equal-unordered for seg-dup field | 20 August 2014, 20:30:14 UTC |
| e60c88f | Thomas Mooney | 20 August 2014, 20:28:38 UTC | Remove unused option "auto_increment". | 20 August 2014, 20:28:38 UTC |
| 40f3489 | Jim Weible | 20 August 2014, 19:30:22 UTC | require an instrument data and a merged alignment result so this does something that makes slightly more sense | 20 August 2014, 19:30:22 UTC |
| 79033da | Jim Weible | 20 August 2014, 18:57:38 UTC | basic index illumina replacement | 20 August 2014, 18:57:48 UTC |
| dfdc6ab | Susanna Siebert | 20 August 2014, 18:36:36 UTC | Merge branch 'variant_reporting_simple_vcf' | 20 August 2014, 18:36:36 UTC |
| 8f3af63 | Susanna Siebert | 20 August 2014, 18:25:12 UTC | test for VcfReporter | 20 August 2014, 18:25:12 UTC |
| 8a705c0 | Susanna Siebert | 20 August 2014, 18:24:39 UTC | minor refactor to make testing easier | 20 August 2014, 18:24:39 UTC |
| 7e6ef3c | Thomas Mooney | 20 August 2014, 17:46:37 UTC | Use generic attribute hint instead of hinting each individual attribute. This reduces the complexity of the underlying SQL to a single JOIN for all attributes instead of one per requested attribute. (In testing this shaved four seconds from a commonly-used query in ClinSeq.) | 20 August 2014, 17:46:37 UTC |
| a5bdf09 | apregier | 20 August 2014, 17:13:29 UTC | Merge branch 'copy' into gb_master | 20 August 2014, 17:13:29 UTC |
| 4db4deb | apregier | 20 August 2014, 16:09:48 UTC | Extract method to calculate new line | 20 August 2014, 17:10:33 UTC |
| dc8dfe0 | apregier | 20 August 2014, 16:05:27 UTC | Extract calculate new header method | 20 August 2014, 17:10:32 UTC |
| 4411386 | apregier | 20 August 2014, 16:02:10 UTC | Extract get_keys_to_append method | 20 August 2014, 17:10:32 UTC |
| 13e034b | apregier | 20 August 2014, 15:56:48 UTC | Use get_header subroutine | 20 August 2014, 17:10:31 UTC |
| 9f213e9 | apregier | 20 August 2014, 15:52:45 UTC | Split up all per-library columns | 20 August 2014, 17:10:31 UTC |
| f91a970 | apregier | 20 August 2014, 15:39:15 UTC | Specify split indicators instead of actual columns to split | 20 August 2014, 17:10:30 UTC |
| 0442cd5 | apregier | 20 August 2014, 15:18:38 UTC | Expand functionality of post-processor to split up files with key::value pairs into separate columns | 20 August 2014, 17:10:29 UTC |
| d8e2cdd | Thomas Mooney | 20 August 2014, 15:52:39 UTC | Don't copy disabled configs | 20 August 2014, 15:52:39 UTC |
| 6e8a534 | Susanna Siebert | 20 August 2014, 15:44:40 UTC | update ContainsTagFilter to not use custom available_fields anymore | 20 August 2014, 15:44:40 UTC |
| d6afbe7 | Susanna Siebert | 20 August 2014, 15:42:37 UTC | Use list of filters given in the CLE specifications - add vcf_id and vcf_description subroutines to each of the filters used - update requires_interpreters list - update plan file | 20 August 2014, 15:42:37 UTC |
| 403c579 | Susanna Siebert | 19 August 2014, 20:17:17 UTC | implement how to add interpretations to the info field | 20 August 2014, 15:38:55 UTC |
| 381b36a | APipe Tester | 20 August 2014, 12:17:13 UTC | Updated `genome` tab completion. | 20 August 2014, 12:17:13 UTC |
| fb534cf | APipe Tester | 20 August 2014, 12:15:29 UTC | Updated class browser cache. | 20 August 2014, 12:15:29 UTC |
| c6ae51a | Nathaniel Nutter | 19 August 2014, 21:21:28 UTC | remove references to /gsc/var/cache/testsuite/data Remove references to /gsc/var/cache/testsuite/data which is the value of GENOME_TEST_INPUTS. | 19 August 2014, 21:37:05 UTC |
| cc4cea2 | apregier | 19 August 2014, 20:49:07 UTC | Merge branch 'copy' into gb_master | 19 August 2014, 20:49:07 UTC |
| 26dcd50 | apregier | 19 August 2014, 20:39:48 UTC | Add max_alt_af field to full reporter | 19 August 2014, 20:42:29 UTC |
| 4546a92 | apregier | 19 August 2014, 20:28:12 UTC | Ignore null af values | 19 August 2014, 20:42:27 UTC |
| 1c0757b | apregier | 19 August 2014, 20:27:15 UTC | Add highest_alt_af interpretation | 19 August 2014, 20:42:26 UTC |
| 5dbca43 | apregier | 19 August 2014, 20:05:37 UTC | Correctly parse out CAF in interpreter | 19 August 2014, 20:42:25 UTC |
| edbd5ba | apregier | 19 August 2014, 19:57:23 UTC | Refactor to move caf_parser into a base class | 19 August 2014, 20:42:24 UTC |
| 24af32c | Malachi Griffith | 19 August 2014, 20:24:23 UTC | clin-seq: minor tidy of summarize-builds | 19 August 2014, 20:24:23 UTC |
| 45719a7 | Susanna Siebert | 19 August 2014, 17:43:38 UTC | vcf entry interpreter and plan file needed for vcf reporter | 19 August 2014, 20:18:02 UTC |
| ad02839 | Susanna Siebert | 19 August 2014, 17:39:08 UTC | first pass at simple vcf reporter | 19 August 2014, 20:18:01 UTC |
| 81b5c1c | Susanna Siebert | 13 August 2014, 15:06:13 UTC | add references to the reporter object of the filters and interpreters used | 19 August 2014, 20:18:01 UTC |
| f95acb2 | Gabriel Sanderson | 19 August 2014, 20:15:00 UTC | Add set_info_field method for adding new/changing info fields. | 19 August 2014, 20:15:44 UTC |
| d82ca46 | Gabriel Sanderson | 19 August 2014, 19:50:18 UTC | Refactor info_to_string out of to_string. | 19 August 2014, 20:15:43 UTC |
| db66edc | apregier | 19 August 2014, 19:21:05 UTC | Merge branch 'copy' into gb_master | 19 August 2014, 19:21:05 UTC |
| d65340c | apregier | 19 August 2014, 19:09:47 UTC | Don't do acmg report for somatic variants | 19 August 2014, 19:10:17 UTC |
| e13b7d1 | apregier | 19 August 2014, 18:44:59 UTC | Add germline report to wrapper | 19 August 2014, 19:10:17 UTC |
| 1867200 | apregier | 19 August 2014, 18:21:08 UTC | Make normal and tumor samples optional | 19 August 2014, 19:10:16 UTC |
| 819ec9b | dmorton | 14 August 2014, 18:14:52 UTC | Make the lookup of vcf result more specific This should aleviate some situations that previously lead to failures: 1) When the parameters to a detector/filter change, downstream shortcut attempts could find multiple vcf results. 2) When a test-name was set on a detector result or the vcf result, downstream shortcut attempts could find multiple vcf results. Now, the get_vcf_result method will do a get_with_lock for filters and combine results which requires that all params and inputs be specified. | 19 August 2014, 18:50:25 UTC |
| 45fed47 | apregier | 19 August 2014, 15:23:58 UTC | Merge branch 'updated' into gb_master | 19 August 2014, 15:23:58 UTC |
| 50e4fb6 | apregier | 19 August 2014, 15:00:11 UTC | Another tweak to vep csq parser | 19 August 2014, 15:00:33 UTC |
| f9a7c0f | APipe Tester | 19 August 2014, 12:16:31 UTC | Updated `genome` tab completion. | 19 August 2014, 12:16:31 UTC |
| aa4e711 | APipe Tester | 19 August 2014, 12:15:02 UTC | Updated class browser cache. | 19 August 2014, 12:15:02 UTC |
| 7acf07a | Eddie Belter | 18 August 2014, 22:39:32 UTC | Model RefCov: attempt to target and genome bp from result metrics, then bed/seqdict | 18 August 2014, 22:45:56 UTC |
| 743c78e | Avinash Ramu | 18 August 2014, 19:23:13 UTC | update clinseq blessed | 18 August 2014, 19:23:13 UTC |
| 521b699 | Avinash Ramu | 18 August 2014, 18:54:21 UTC | update test data | 18 August 2014, 19:10:37 UTC |
| b365155 | Avinash Ramu | 18 August 2014, 18:53:52 UTC | update test builds | 18 August 2014, 19:10:36 UTC |
| 68efdb1 | Avinash Ramu | 18 August 2014, 17:13:10 UTC | update test | 18 August 2014, 19:10:36 UTC |
| f587a38 | Avinash Ramu | 18 August 2014, 14:57:42 UTC | update snv_indel_report filter | 18 August 2014, 19:10:35 UTC |
| a88c961 | Avinash Ramu | 18 August 2014, 12:47:08 UTC | get RNASeq read counts 1 | 18 August 2014, 19:10:35 UTC |
| f50a35e | Avinash Ramu | 16 August 2014, 11:21:41 UTC | increase max indelsize | 18 August 2014, 19:10:34 UTC |
| 5180972 | Avinash Ramu | 16 August 2014, 04:58:41 UTC | update column names | 18 August 2014, 19:10:34 UTC |
| 37fcdf3 | Avinash Ramu | 15 August 2014, 19:34:26 UTC | make extradescription uniform for diff samples | 18 August 2014, 19:10:33 UTC |
| f5fa341 | Avinash Ramu | 15 August 2014, 19:30:54 UTC | Sort bed file | 18 August 2014, 19:10:33 UTC |
| 9283a2e | Avinash Ramu | 15 August 2014, 19:29:26 UTC | check for divide by zero | 18 August 2014, 19:10:32 UTC |
| 7547613 | Avinash Ramu | 15 August 2014, 19:29:01 UTC | update clinseq exome cnv file | 18 August 2014, 19:10:32 UTC |
| 89c0cc5 | Avinash Ramu | 14 August 2014, 21:35:43 UTC | add mutationtype converge | 18 August 2014, 19:10:31 UTC |
| 1cd4fab | Avinash Ramu | 14 August 2014, 21:34:51 UTC | include datatype in label | 18 August 2014, 19:10:31 UTC |
| 68de349 | Avinash Ramu | 14 August 2014, 21:02:42 UTC | update stats plot | 18 August 2014, 19:10:30 UTC |
| 8ef4c97 | Avinash Ramu | 30 July 2014, 21:03:47 UTC | add clinseq fileaccessors | 18 August 2014, 19:10:30 UTC |
| 771ed66 | Avinash Ramu | 30 July 2014, 20:28:49 UTC | add test for MutationSpectrum clinseq converge | 18 August 2014, 19:10:29 UTC |
| 4fb964b | Avinash Ramu | 30 July 2014, 20:18:14 UTC | update CNV summary tool. | 18 August 2014, 19:10:28 UTC |
| ba2f0ec | Avinash Ramu | 22 July 2014, 22:10:43 UTC | format plot | 18 August 2014, 19:10:27 UTC |
| bfcdb21 | Avinash Ramu | 22 July 2014, 21:32:55 UTC | indent | 18 August 2014, 19:10:26 UTC |
| ad05c99 | Avinash Ramu | 22 July 2014, 21:31:04 UTC | update plotting parameters | 18 August 2014, 19:10:26 UTC |
| 59f149e | Avinash Ramu | 22 July 2014, 18:40:00 UTC | rename labels | 18 August 2014, 19:10:25 UTC |
| 9ff11ca | Avinash Ramu | 15 July 2014, 19:56:50 UTC | Add mutspec clinseq file access | 18 August 2014, 19:10:25 UTC |
| f2c8eb9 | Avinash Ramu | 07 July 2014, 17:08:31 UTC | add file accessors | 18 August 2014, 19:10:24 UTC |
| 9e20446 | Eddie Belter | 18 August 2014, 17:37:15 UTC | InstData Import: delete is_paired_end if in incoming instdata properties | 18 August 2014, 17:37:15 UTC |
| 2e1209b | apregier | 15 August 2014, 20:41:26 UTC | Merge branch 'copy' into gb_master | 15 August 2014, 20:41:26 UTC |
| 452b8b8 | apregier | 15 August 2014, 20:35:59 UTC | Adjust vep csq parser to reflect what vep actually does It seems that if the first base of the indel alt matches the reference sequence it gets chopped off, otherwise it doesn't | 15 August 2014, 20:37:06 UTC |
| f0f1e2d | Callie Federer | 15 August 2014, 20:29:58 UTC | adding .. | 15 August 2014, 20:29:58 UTC |
| 5d95275 | Callie Federer | 15 August 2014, 20:11:56 UTC | adding .. | 15 August 2014, 20:11:56 UTC |
| f9a9ac5 | APipe Tester | 15 August 2014, 12:17:29 UTC | Updated `gmt` tab completion. | 15 August 2014, 12:17:29 UTC |
| 8a29f78 | APipe Tester | 15 August 2014, 12:16:48 UTC | Updated `genome` tab completion. | 15 August 2014, 12:16:48 UTC |
