| 2e5a547 | Thomas Mooney | 14 August 2014, 20:31:53 UTC | Update blessed build to account for 18c27496e6ccf11eea6b0f30339b0ca0ffd1f940 | 14 August 2014, 20:31:53 UTC |
| 937ed64 | apregier | 14 August 2014, 20:14:46 UTC | Merge branch 'copy' into gb_master | 14 August 2014, 20:14:46 UTC |
| 73161ea | apregier | 14 August 2014, 20:13:19 UTC | Bam readcount entry of "." is the same as no bam-readcount entry | 14 August 2014, 20:13:51 UTC |
| 41b1145 | Thomas Mooney | 14 August 2014, 19:41:49 UTC | Add index for query commonly used in CQID for subject mappings. | 14 August 2014, 19:41:49 UTC |
| 9d8ee3f | apregier | 14 August 2014, 16:50:45 UTC | Merge branch 'copy' into gb_master | 14 August 2014, 16:50:45 UTC |
| a7cfb38 | apregier | 14 August 2014, 16:43:34 UTC | Revert lumpy commits until we figure it out Revert "changed the paths so that it will run on any machine" This reverts commit eea9994d91c3fa4d39c56063130c5406df5e0f0d. Revert "adds extra output for when the test fails" This reverts commit 02eba26aeffdd0b102f14263b9da9ed5d9121069. Revert "Removed the params hash and renamed variables" This reverts commit f8705fb24e72926dc46a8c95b0e79764adb3e4cf. Revert "removed temporary variables" This reverts commit 472716e3fcdf4f314d8ac97edc83d18edb4548c3. Revert "more changes ugh!" This reverts commit 7122c39cfe9f8b48b819cbd884c8fe86c45af171. Revert "Rempved a bit of excess code" This reverts commit ab5cdc1bc86e7e80837a2bdad49f1bffbcc4a44c. Revert "Removed the extra debug and print statments" This reverts commit 09b89260e199ddc3cda3c4450985505f17be42d0. Revert "removed the extra print statments" This reverts commit cdc666c9cf573ac2a0376f417ba1fbe0867b9c2c. Revert "Fixed the version test error" This reverts commit 6bc926253bfbde18ffee2776658e5c131538faeb. Revert "Added a test to make sure the version exists" This reverts commit 8cf7eb5dc739014f69b91aa3db339658f2a7e0cc. Revert "added a test to make sure the version exists" This reverts commit 8f28018a75202a689cd5027787478ccc47a46eec. Revert "Incororated versioning into the program" This reverts commit f495327276d8e1e7efa7f8755e72bfd85c05d654. Revert "incorporated versioning into the program" This reverts commit f8dd7869ba1ded3d652eda35440fc9f6c4777545. Revert "DB2 lumpy wrote tests to check lumpy script methods" This reverts commit e79cfc78522b2e1f146af63a81cec804a058342f. Revert "DB2 lumpy made methods to find lumpy scripts" This reverts commit 21df0bd263e2ed8a63aaf62b0f654e2739b6e59c. Revert "DV2 lumpy: mean and stdev temp file storage" This reverts commit d1861ab07e5681b49320ccf86b7e221941088487. Revert "Changed some of the print statements to debug" This reverts commit f9d163bcf9e9c0409d18802dc827d2d6cb6fd6f3. Revert "added a Matched samples test" This reverts commit af53ea4f3e576d4cce42d80b81babf2d6ab05d76. Revert "Parameters and the histo files were put in a hash" This reverts commit 959f5d1d46c4679d6363f5b523c7526a06badc40. Revert "rearranged the sr parameters to see if they would work" This reverts commit 32a7df2d67c2799ec0ed3df6e79d9534719c43a8. Revert "updated and improved pe_cmd_arrangement & its test" This reverts commit cc03d83f5fee7781f66af028722cb869a239ae92. Revert "changed mean and stdv to a hash" This reverts commit c25caa31694ae716da057a317c4b41dc92bc2f32. Revert "added a subtest to test the absence of split reads in the bam_file" This reverts commit f110094edefd2641913d15a760b2d9599f39117f. Revert "Lumpy fixed mean and stdev subroutine" This reverts commit acec6fdf7283ed59858e174af8e212c0da7f9e76. Revert "Changed the sam-bam converter to picard tools" This reverts commit 9afe92a57e79a651b8a67244cbb0fabcc6e5dd2c. Revert "PE & SR command subroutines and tests added" This reverts commit 84304734796acb317bc0688459236799b444b76d. Revert "Lumpy wrapper - removed read_params command" This reverts commit 6ec2145b9288d4862a09a450be69e8f7e4ff749a. Revert "lumpy stage2 - runs with multiple libraries" This reverts commit b8b757456ba022a563f81e05eb2406bda60be2db. Revert "Lumpy test1" This reverts commit f7d6eb2cf5ca270672ce92bd0e78d40d160f019a. Revert "initial commit" This reverts commit 889b0615a5526b9e0f6f897e0ea9e386db2a71e2. | 14 August 2014, 16:49:48 UTC |
| 05bb7a9 | apregier | 14 August 2014, 16:34:34 UTC | Fix warning about software_result->get | 14 August 2014, 16:49:47 UTC |
| 4eab0c1 | apregier | 14 August 2014, 16:33:59 UTC | Always make file_path and file_content_hash match | 14 August 2014, 16:49:46 UTC |
| a453a62 | apregier | 14 August 2014, 16:13:30 UTC | Update blessed build - changes due to bam-readcount version bump | 14 August 2014, 16:49:46 UTC |
| 5d79a67 | Callie Federer | 14 August 2014, 15:47:19 UTC | updating | 14 August 2014, 15:47:19 UTC |
| 18c2749 | Thomas Mooney | 14 August 2014, 14:19:56 UTC | Don't keep detailed files when use_short_roi_names in effect. (AUE-319) | 14 August 2014, 14:19:56 UTC |
| b91adae | APipe Tester | 14 August 2014, 12:17:27 UTC | Updated `gmt` tab completion. | 14 August 2014, 12:17:27 UTC |
| a2bd29a | APipe Tester | 14 August 2014, 12:16:45 UTC | Updated `genome` tab completion. | 14 August 2014, 12:16:45 UTC |
| 99fd77a | APipe Tester | 14 August 2014, 12:15:07 UTC | Updated class browser cache. | 14 August 2014, 12:15:07 UTC |
| 530ca9d | Jason Walker | 13 August 2014, 17:07:15 UTC | Add AML_RMG to full cle report. | 13 August 2014, 17:07:15 UTC |
| c2f7411 | Jason Walker | 13 August 2014, 17:05:42 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 13 August 2014, 17:05:42 UTC |
| eea9994 | Miranda Fulton | 13 August 2014, 16:42:53 UTC | changed the paths so that it will run on any machine | 13 August 2014, 16:44:22 UTC |
| 02eba26 | Miranda Fulton | 13 August 2014, 16:41:49 UTC | adds extra output for when the test fails | 13 August 2014, 16:44:22 UTC |
| f8705fb | Miranda Fulton | 12 August 2014, 20:57:22 UTC | Removed the params hash and renamed variables | 13 August 2014, 16:44:21 UTC |
| 472716e | Miranda Fulton | 12 August 2014, 19:34:34 UTC | removed temporary variables | 13 August 2014, 16:44:21 UTC |
| 7122c39 | Miranda Fulton | 12 August 2014, 19:23:08 UTC | more changes ugh! | 13 August 2014, 16:44:20 UTC |
| ab5cdc1 | Miranda Fulton | 12 August 2014, 19:11:06 UTC | Rempved a bit of excess code | 13 August 2014, 16:44:20 UTC |
| 09b8926 | Miranda Fulton | 12 August 2014, 18:44:37 UTC | Removed the extra debug and print statments | 13 August 2014, 16:44:19 UTC |
| cdc666c | Miranda Fulton | 12 August 2014, 18:43:47 UTC | removed the extra print statments | 13 August 2014, 16:44:19 UTC |
| 6bc9262 | Miranda Fulton | 11 August 2014, 18:37:57 UTC | Fixed the version test error | 13 August 2014, 16:44:18 UTC |
| 8cf7eb5 | Miranda Fulton | 11 August 2014, 18:22:49 UTC | Added a test to make sure the version exists | 13 August 2014, 16:44:18 UTC |
| 8f28018 | Miranda Fulton | 11 August 2014, 18:21:43 UTC | added a test to make sure the version exists | 13 August 2014, 16:44:17 UTC |
| f495327 | Miranda Fulton | 11 August 2014, 16:16:23 UTC | Incororated versioning into the program | 13 August 2014, 16:44:17 UTC |
| f8dd786 | Miranda Fulton | 11 August 2014, 16:15:09 UTC | incorporated versioning into the program | 13 August 2014, 16:44:16 UTC |
| e79cfc7 | Miranda Fulton | 06 August 2014, 21:53:09 UTC | DB2 lumpy wrote tests to check lumpy script methods | 13 August 2014, 16:44:16 UTC |
| 21df0bd | Miranda Fulton | 06 August 2014, 21:51:59 UTC | DB2 lumpy made methods to find lumpy scripts | 13 August 2014, 16:44:15 UTC |
| d1861ab | Miranda Fulton | 06 August 2014, 20:29:19 UTC | DV2 lumpy: mean and stdev temp file storage | 13 August 2014, 16:44:14 UTC |
| f9d163b | Miranda Fulton | 04 August 2014, 16:52:09 UTC | Changed some of the print statements to debug | 13 August 2014, 16:44:14 UTC |
| af53ea4 | Miranda Fulton | 04 August 2014, 16:47:21 UTC | added a Matched samples test | 13 August 2014, 16:44:13 UTC |
| 959f5d1 | Miranda Fulton | 28 July 2014, 15:28:49 UTC | Parameters and the histo files were put in a hash | 13 August 2014, 16:44:13 UTC |
| 32a7df2 | Miranda Fulton | 25 July 2014, 17:09:56 UTC | rearranged the sr parameters to see if they would work | 13 August 2014, 16:44:12 UTC |
| cc03d83 | Miranda Fulton | 25 July 2014, 17:07:03 UTC | updated and improved pe_cmd_arrangement & its test | 13 August 2014, 16:44:12 UTC |
| c25caa3 | Miranda Fulton | 25 July 2014, 15:51:16 UTC | changed mean and stdv to a hash | 13 August 2014, 16:44:11 UTC |
| f110094 | Miranda Fulton | 25 July 2014, 14:46:27 UTC | added a subtest to test the absence of split reads in the bam_file | 13 August 2014, 16:44:10 UTC |
| acec6fd | Miranda Fulton | 25 July 2014, 14:12:08 UTC | Lumpy fixed mean and stdev subroutine | 13 August 2014, 16:44:10 UTC |
| 9afe92a | Miranda Fulton | 24 July 2014, 15:38:14 UTC | Changed the sam-bam converter to picard tools | 13 August 2014, 16:44:09 UTC |
| 8430473 | Miranda Fulton | 23 July 2014, 18:43:32 UTC | PE & SR command subroutines and tests added | 13 August 2014, 16:44:09 UTC |
| 6ec2145 | Miranda Fulton | 23 July 2014, 17:06:57 UTC | Lumpy wrapper - removed read_params command | 13 August 2014, 16:44:08 UTC |
| b8b7574 | Miranda Fulton | 22 July 2014, 20:45:37 UTC | lumpy stage2 - runs with multiple libraries | 13 August 2014, 16:44:08 UTC |
| f7d6eb2 | Miranda Fulton | 17 July 2014, 18:21:22 UTC | Lumpy test1 | 13 August 2014, 16:44:07 UTC |
| 889b061 | Miranda Fulton | 17 July 2014, 15:48:27 UTC | initial commit | 13 August 2014, 16:44:06 UTC |
| 7739781 | Callie Federer | 13 August 2014, 15:15:24 UTC | adding .. | 13 August 2014, 15:15:24 UTC |
| aaa6c02 | Jason Walker | 13 August 2014, 15:14:07 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 13 August 2014, 15:14:07 UTC |
| 9709ef2 | Thomas Mooney | 13 August 2014, 14:49:51 UTC | New FeatureList importer designed for LIMS capture set use. Provides additional validation and sanitization around creation so that the FL is suitable for use as an ROI in pipelines. | 13 August 2014, 14:49:51 UTC |
| 070480c | Thomas Mooney | 13 August 2014, 14:41:47 UTC | Extract track parsing and format calculation up into FeatureList itself Use the former for our other track parsing. | 13 August 2014, 14:41:47 UTC |
| c8f61f1 | Thomas Mooney | 12 August 2014, 21:46:46 UTC | Clear out the temp dir to avoid double-counting in reallocate. | 12 August 2014, 21:46:46 UTC |
| 0234e62 | Dave Larson | 12 August 2014, 20:37:23 UTC | update readcount version to 0.6 | 12 August 2014, 20:37:23 UTC |
| ba79fc7 | Callie Federer | 12 August 2014, 20:33:06 UTC | adding | 12 August 2014, 20:33:06 UTC |
| f2677b0 | Jason Walker | 12 August 2014, 20:25:31 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 12 August 2014, 20:25:31 UTC |
| 54ee538 | apregier | 12 August 2014, 20:15:47 UTC | Merge branch 'copy' into gb_master | 12 August 2014, 20:15:47 UTC |
| 7bd9fc4 | apregier | 12 August 2014, 20:12:09 UTC | Header not required for this subroutine | 12 August 2014, 20:12:41 UTC |
| f87d06a | apregier | 12 August 2014, 20:11:10 UTC | Don't insert bamreadcount info for positions where there is both an insertion and deletion, but also don't get hung up on these positions. | 12 August 2014, 20:12:39 UTC |
| 2a64b2b | Jason Walker | 12 August 2014, 19:45:54 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 12 August 2014, 19:45:54 UTC |
| 9b40be1 | Jason Walker | 12 August 2014, 19:44:56 UTC | Add additional status message and capture dirmove errors on purge. | 12 August 2014, 19:44:56 UTC |
| fe67e35 | Callie Federer | 12 August 2014, 19:25:41 UTC | adding | 12 August 2014, 19:25:41 UTC |
| b1b2a50 | apregier | 12 August 2014, 17:47:35 UTC | Merge branch 'copy' into gb_master | 12 August 2014, 17:47:35 UTC |
| 74d8914 | apregier | 12 August 2014, 17:46:04 UTC | Update blessed builds | 12 August 2014, 17:46:35 UTC |
| 9b43dd9 | Michael J. Kiwala | 12 August 2014, 17:40:22 UTC | Add explicit 'use Bio::SeqIO' | 12 August 2014, 17:45:58 UTC |
| 4ef2475 | apregier | 12 August 2014, 15:54:18 UTC | Merge branch 'copy' into gb_master | 12 August 2014, 15:54:18 UTC |
| 29c30ae | apregier | 12 August 2014, 15:52:58 UTC | Use tumor bam from d30 build rather than normal bam | 12 August 2014, 15:53:18 UTC |
| 953c136 | Adam Coffman | 12 August 2014, 15:14:09 UTC | make config_item field optional in UR as well as database | 12 August 2014, 15:14:09 UTC |
| 1a5f6bc | Avinash Ramu | 12 August 2014, 14:44:30 UTC | update clinseq blessed | 12 August 2014, 14:44:49 UTC |
| 1f44741 | Thomas Mooney | 12 August 2014, 14:39:09 UTC | Adhere to standard practice of a bare return when create() fails. This will allow SR's get_or_create() to find the newly minted object when we entered create() because we had been waiting on a lock. | 12 August 2014, 14:39:09 UTC |
| c89e020 | APipe Tester | 12 August 2014, 12:16:31 UTC | Updated `genome` tab completion. | 12 August 2014, 12:16:31 UTC |
| 3b1dd65 | APipe Tester | 12 August 2014, 12:15:00 UTC | Updated class browser cache. | 12 August 2014, 12:15:00 UTC |
| d02ece9 | Avinash Ramu | 12 August 2014, 03:21:32 UTC | check for NaN | 12 August 2014, 03:29:39 UTC |
| b44b9e8 | Avinash Ramu | 12 August 2014, 03:20:30 UTC | annotate filtered file | 12 August 2014, 03:29:38 UTC |
| 9832d12 | Avinash Ramu | 11 August 2014, 04:38:18 UTC | update Cnmops test | 12 August 2014, 03:29:37 UTC |
| 7a5c99a | Avinash Ramu | 10 August 2014, 02:31:41 UTC | get posterior probs from Cnmops | 12 August 2014, 03:29:37 UTC |
| 71bd926 | Avinash Ramu | 10 August 2014, 02:31:03 UTC | update test | 12 August 2014, 03:29:37 UTC |
| 0a72a5e | Avinash Ramu | 21 July 2014, 18:45:56 UTC | add type of change | 12 August 2014, 03:29:36 UTC |
| 2669a6b | Avinash Ramu | 21 July 2014, 18:31:11 UTC | add clinseq file accessors | 12 August 2014, 03:29:36 UTC |
| 028f0f1 | Avinash Ramu | 21 July 2014, 18:29:48 UTC | add cancerrelevancescore converge tool | 12 August 2014, 03:29:35 UTC |
| 34ae163 | Avinash Ramu | 18 July 2014, 15:40:20 UTC | update exome_cnv cnvhmm file | 12 August 2014, 03:29:34 UTC |
| b9791dc | Avinash Ramu | 15 July 2014, 19:56:50 UTC | Add mutspec clinseq file access | 12 August 2014, 03:29:34 UTC |
| 58e080e | Avinash Ramu | 14 July 2014, 16:35:38 UTC | add mutation-spectrum converge | 12 August 2014, 03:29:34 UTC |
| 0612607 | Avinash Ramu | 09 July 2014, 15:37:28 UTC | change column header | 12 August 2014, 03:29:33 UTC |
| 4b86ded | Avinash Ramu | 09 July 2014, 15:26:05 UTC | add header line | 12 August 2014, 03:29:33 UTC |
| c396866 | Avinash Ramu | 07 July 2014, 20:30:37 UTC | get data-source from path | 12 August 2014, 03:29:32 UTC |
| 1e4907f | Avinash Ramu | 07 July 2014, 20:29:56 UTC | use different temp-sorted file | 12 August 2014, 03:29:32 UTC |
| dacacc7 | Avinash Ramu | 07 July 2014, 17:42:10 UTC | add stats files | 12 August 2014, 03:29:31 UTC |
| 7d1ccf8 | Avinash Ramu | 07 July 2014, 17:08:31 UTC | add file accessors | 12 August 2014, 03:29:31 UTC |
| de0db0d | Thomas Mooney | 11 August 2014, 17:41:32 UTC | Initial version of a FeatureList merge tool. BED-merging code taken from GSCApp::BEDFile. | 11 August 2014, 22:54:41 UTC |
| a148dbf | apregier | 11 August 2014, 22:34:31 UTC | Merge branch 'copy' into gb_master | 11 August 2014, 22:34:31 UTC |
| 25c11cb | apregier | 11 August 2014, 22:33:49 UTC | If there is no information about the af for an allele, always pass the filter | 11 August 2014, 22:33:49 UTC |
| 3bca94b | apregier | 11 August 2014, 22:27:11 UTC | When no CAF is available, it should pass | 11 August 2014, 22:27:11 UTC |
| ae980b3 | apregier | 11 August 2014, 22:16:57 UTC | Merge branch 'copy' into gb_master | 11 August 2014, 22:16:57 UTC |
| fb3b1fe | apregier | 11 August 2014, 22:14:15 UTC | Revert "Revert "Bump vcf_version due to a bump in the default joinx version"" This reverts commit 578c984a0092b71b2bf8c143897cdcdcedc14421. No takesies backsies!!! | 11 August 2014, 22:14:15 UTC |
| c77d7a0 | Thomas Mooney | 11 August 2014, 22:11:49 UTC | Make generic SR expunge process for when deleting an object. Use it for InstrumentData and Sample deletion. | 11 August 2014, 22:11:49 UTC |
| 9675e04 | apregier | 11 August 2014, 21:54:43 UTC | Merge branch 'copy' into gb_master | 11 August 2014, 21:54:43 UTC |
| 99f6fc4 | apregier | 11 August 2014, 21:50:46 UTC | Make verify bam id code respect test name and add user relationship | 11 August 2014, 21:51:38 UTC |
| 62394d6 | Eddie Belter | 11 August 2014, 19:48:48 UTC | File VCF: rm dumper statement | 11 August 2014, 19:49:09 UTC |
| 9f0c7d3 | apregier | 11 August 2014, 19:35:53 UTC | Merge branch 'copy' into gb_master | 11 August 2014, 19:35:53 UTC |
| 7447f1d | apregier | 11 August 2014, 19:31:06 UTC | snv detection strategy is optional | 11 August 2014, 19:33:25 UTC |
| 578c984 | dmorton | 11 August 2014, 19:20:48 UTC | Revert "Bump vcf_version due to a bump in the default joinx version" This reverts commit 5993ebd598c94bba2847bcd8cdcc17a049ca7311. | 11 August 2014, 19:20:48 UTC |
