| 340ac44 | APipe Tester | 05 June 2013, 19:19:49 UTC | updated jenkins submodule to ca57c61 | 05 June 2013, 19:19:49 UTC |
| 5aae7e4 | Ian Ferguson | 05 June 2013, 18:53:53 UTC | Added GMT/Gatk/BaseRecalibrator | 05 June 2013, 18:53:53 UTC |
| d1d59a8 | Ian Ferguson | 05 June 2013, 18:16:57 UTC | Bwasw, use File::Copy move instead of mv | 05 June 2013, 18:17:04 UTC |
| 05e6cd7 | Yang Li | 05 June 2013, 18:10:41 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 05 June 2013, 18:10:41 UTC |
| 25e7c54 | Yang Li | 05 June 2013, 18:08:31 UTC | Add the mutation count barplot tool | 05 June 2013, 18:08:31 UTC |
| ad91d35 | Feiyu Du | 05 June 2013, 13:26:26 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 05 June 2013, 13:26:26 UTC |
| 4b8ce08 | Feiyu Du | 05 June 2013, 13:26:15 UTC | picard version bug fixed | 05 June 2013, 13:26:15 UTC |
| fab6324 | Thomas Mooney | 04 June 2013, 21:50:51 UTC | Old data got deleted again, so blindly update the blessed build for gp:b | 04 June 2013, 21:51:30 UTC |
| 18dd49a | dmorton | 31 May 2013, 21:57:57 UTC | Give up on making cuffdiff a software result The pipeline has to be reworked from the ground up. There are just too many references to the build_dir in all the arguments. | 04 June 2013, 21:49:39 UTC |
| b54e5da | dmorton | 31 May 2013, 21:41:07 UTC | _lock_name no longer is a param | 04 June 2013, 21:49:39 UTC |
| e1c4c59 | Adam Coffman | 04 June 2013, 21:43:39 UTC | call get() in an array context to suppress warning | 04 June 2013, 21:43:39 UTC |
| 1e4f2e3 | Feiyu Du | 04 June 2013, 18:55:29 UTC | print bamqc output | 04 June 2013, 19:52:39 UTC |
| a72253d | Feiyu Du | 22 May 2013, 16:00:23 UTC | add read_length as param | 04 June 2013, 19:52:38 UTC |
| 447e8bd | Feiyu Du | 20 May 2013, 20:04:24 UTC | 1.make read_length parameter to bamqc software result;2.better handle link_result | 04 June 2013, 19:52:37 UTC |
| 8f19709 | Feiyu Du | 13 May 2013, 16:54:29 UTC | Not adding metrics if they already exist | 04 June 2013, 19:52:37 UTC |
| c54bc27 | Feiyu Du | 08 May 2013, 22:08:58 UTC | Add BamQc tool to ref-align pipeline | 04 June 2013, 19:52:36 UTC |
| d0b585a | Ian Ferguson | 04 June 2013, 18:28:46 UTC | Bwasw rewrite Adds missing RG headers and tags, more robust SAM fixer, better error reporting. Squashed commit of the following: commit b9f7b8e3f9e3bb03bcda9be4eac9b38da160fefd Author: Ian Ferguson <iferguso@genome.wustl.edu> Date: Tue Jun 4 13:27:45 2013 -0500 Fix issue with headers in bwasw commit bef593058693bcb3407a33dd6a9cf2e14d34cedc Author: Ian Ferguson <iferguso@genome.wustl.edu> Date: Wed May 29 15:39:17 2013 -0500 Clean up Bwasw _run_aligner, better header handling commit bfc6d676f1c1a08746cde9c6a8dc63dec1187048 Author: Ian Ferguson <iferguso@genome.wustl.edu> Date: Thu May 23 15:34:40 2013 -0500 More Bwasw fixes, testing in pipeline commit 31d3fe0293cc19358788d011eab18480beeaeeb5 Author: Ian Ferguson <iferguso@genome.wustl.edu> Date: Wed May 22 14:13:39 2013 -0500 Manually merge in rusage changes commit a3f769482940e4a3eca0e880ca989128b62a4135 Author: Ian Ferguson <iferguso@genome.wustl.edu> Date: Wed May 22 12:27:31 2013 -0500 Bwasw aligner module development Work in progress: adding RG, refactoring sam fixer | 04 June 2013, 18:28:46 UTC |
| 2cfe10e | Nathan Nutter | 04 June 2013, 15:29:07 UTC | remove `genome model update build-requested` Use `genome model build queue` instead of `genome model update build-requested`. | 04 June 2013, 15:29:07 UTC |
| 50597c1 | apregier | 03 June 2013, 19:30:32 UTC | Resolve-attribute returns unique values, so count may not be the same | 03 June 2013, 19:47:26 UTC |
| 1f2f6cc | Chris Miller | 03 June 2013, 19:21:05 UTC | fixed splitting bug and made it retain anno file headers | 03 June 2013, 19:21:12 UTC |
| 89719e8 | nnutter | 02 May 2013, 18:25:29 UTC | validate result's lookup_hash I caught bit by setting test_name manually instead of by using set_test_name so I added this validation to fail clearly. | 03 June 2013, 18:19:43 UTC |
| 1898459 | nnutter | 30 April 2013, 20:37:55 UTC | whitespace | 03 June 2013, 18:19:42 UTC |
| e5b6aef | Jim Weible | 03 June 2013, 17:58:38 UTC | fix broken VcfMergeAnnotation test | 03 June 2013, 17:58:38 UTC |
| 72d19b4 | Chris Miller | 03 June 2013, 17:26:03 UTC | adding lister for mut-sig models | 03 June 2013, 17:26:16 UTC |
| 68c86f9 | Yang Li | 03 June 2013, 17:17:24 UTC | Removed duplicate files | 03 June 2013, 17:17:24 UTC |
| af03306 | Yang Li | 03 June 2013, 17:07:34 UTC | Updated comments: removed debugging comments. | 03 June 2013, 17:07:34 UTC |
| 78ebc1d | Yang Li | 03 June 2013, 17:00:44 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 03 June 2013, 17:00:44 UTC |
| 4c5495b | Yang Li | 03 June 2013, 17:00:05 UTC | Updates | 03 June 2013, 17:00:05 UTC |
| b6a7ca5 | Yang Li | 03 June 2013, 16:56:17 UTC | Adding a Vcf merging tool for Vep annotation | 03 June 2013, 16:56:17 UTC |
| 6fe1386 | Jim Weible | 03 June 2013, 15:26:12 UTC | update clinseq TestGenomeCommands.t to reflect new builds | 03 June 2013, 15:26:12 UTC |
| 948ee41 | dmorton | 30 May 2013, 22:07:40 UTC | Add Command/WithSoftwareResult and friends Also update GMTCuffdiffWrapper to use it instead of WithSavedResult | 30 May 2013, 22:27:32 UTC |
| 403e950 | dmorton | 30 May 2013, 22:10:01 UTC | _prepare_staging_directory returns $tempdir instead of 1 | 30 May 2013, 22:27:32 UTC |
| 2960f1b | dmorton | 29 May 2013, 16:45:50 UTC | whitespace | 30 May 2013, 22:27:31 UTC |
| 7db3708 | dmorton | 24 May 2013, 20:22:32 UTC | Added genome model admin find-in-latest-build | 30 May 2013, 22:27:31 UTC |
| ae220a5 | Travis Abbott | 30 May 2013, 16:04:17 UTC | remove properties from AlignedBamResult, it isn't even a real thing! | 30 May 2013, 16:04:17 UTC |
| 91ce1ba | APipe Tester | 30 May 2013, 15:07:21 UTC | updated ur submodule to 2f1d921 | 30 May 2013, 15:07:21 UTC |
| 8d86247 | Chris Miller | 30 May 2013, 14:54:47 UTC | plotcn2 fix | 30 May 2013, 14:54:47 UTC |
| fe3b0d0 | Travis Abbott | 29 May 2013, 22:12:19 UTC | add AlignedBamResult class it is a software result it has a bam file | 29 May 2013, 22:12:19 UTC |
| 946bbbd | apregier | 29 May 2013, 21:35:46 UTC | Properly use multiple known arguments | 29 May 2013, 22:00:07 UTC |
| 7befe26 | apregier | 29 May 2013, 21:10:44 UTC | Merge branch 'updated' into gb_master | 29 May 2013, 21:10:44 UTC |
| 2188e3e | apregier | 29 May 2013, 21:09:35 UTC | Known allele input to gatk can be a list | 29 May 2013, 21:09:53 UTC |
| 281064f | apregier | 29 May 2013, 21:09:10 UTC | Gatk inputs that are lists need to be compiled in an input file | 29 May 2013, 21:09:53 UTC |
| d4456cb | Thomas Mooney | 29 May 2013, 19:46:58 UTC | Add support for specifying a "refiner" in the alignment strategy. (An implementation for using it is forthcoming.) | 29 May 2013, 19:46:58 UTC |
| 5f794f6 | APipe Tester | 29 May 2013, 19:08:12 UTC | updated ur submodule to 36a08fd | 29 May 2013, 19:08:12 UTC |
| 704163b | APipe Tester | 29 May 2013, 18:57:05 UTC | updated workflow submodule to aabd90b | 29 May 2013, 18:57:05 UTC |
| 30285e8 | Eddie Belter | 29 May 2013, 17:26:50 UTC | Imported inst data: use lane attr first, then parse from subset name | 29 May 2013, 17:26:50 UTC |
| 3be6086 | APipe Tester | 29 May 2013, 15:40:50 UTC | updated ur submodule to e6d0e41 | 29 May 2013, 15:40:50 UTC |
| 902c3a5 | apregier | 29 May 2013, 15:31:03 UTC | Merge branch 'updated' into gb_master | 29 May 2013, 15:31:03 UTC |
| 7e192fe | apregier | 28 May 2013, 21:32:56 UTC | Test realigner-target-creator tool | 29 May 2013, 15:30:10 UTC |
| a933382 | apregier | 28 May 2013, 21:32:31 UTC | We will add options as needed | 29 May 2013, 15:30:09 UTC |
| f19df5d | apregier | 28 May 2013, 20:36:47 UTC | Check known input | 29 May 2013, 15:30:09 UTC |
| 45e014e | apregier | 28 May 2013, 20:35:36 UTC | Add knownAllele option for indel-realigner | 29 May 2013, 15:30:08 UTC |
| b92e0e1 | apregier | 28 May 2013, 20:35:05 UTC | Fix typo | 29 May 2013, 15:30:08 UTC |
| e154714 | apregier | 28 May 2013, 20:00:33 UTC | Move IndelRealigner functionality into class of same name | 29 May 2013, 15:30:07 UTC |
| 84a52a1 | apregier | 28 May 2013, 19:59:26 UTC | New gatk tool | 29 May 2013, 15:30:07 UTC |
| 3a33b5c | APipe Tester | 29 May 2013, 15:22:31 UTC | updated ur submodule to a50e2d1 | 29 May 2013, 15:22:31 UTC |
| 5af561c | APipe Tester | 29 May 2013, 15:08:09 UTC | updated ur submodule to 56edefb | 29 May 2013, 15:08:09 UTC |
| d12d77c | APipe Tester | 29 May 2013, 14:54:15 UTC | updated ur submodule to 6b4a3ed | 29 May 2013, 14:54:15 UTC |
| b13934a | APipe Tester | 29 May 2013, 14:40:02 UTC | updated ur submodule to 2ef9c9b | 29 May 2013, 14:40:02 UTC |
| 27a4737 | APipe Tester | 29 May 2013, 14:25:58 UTC | updated ur submodule to 2457a58 | 29 May 2013, 14:25:58 UTC |
| 2780711 | APipe Tester | 29 May 2013, 14:13:32 UTC | updated ur submodule to 2397293 | 29 May 2013, 14:13:32 UTC |
| 8121975 | APipe Tester | 29 May 2013, 14:01:47 UTC | updated ur submodule to 4e393cb | 29 May 2013, 14:01:47 UTC |
| f203f06 | APipe Tester | 29 May 2013, 13:49:06 UTC | updated ur submodule to 956c74a | 29 May 2013, 13:49:06 UTC |
| ffeed02 | APipe Tester | 29 May 2013, 13:38:47 UTC | updated ur submodule to a2cd7b1 | 29 May 2013, 13:38:47 UTC |
| 8d2b725 | APipe Tester | 29 May 2013, 13:25:40 UTC | updated ur submodule to 66c3ca7 | 29 May 2013, 13:25:40 UTC |
| c6f3b11 | APipe Tester | 29 May 2013, 13:14:19 UTC | updated ur submodule to 5008e76 | 29 May 2013, 13:14:19 UTC |
| 5dd2b26 | APipe Tester | 29 May 2013, 13:02:27 UTC | updated ur submodule to 9a35dbb | 29 May 2013, 13:02:27 UTC |
| 4136bd9 | APipe Tester | 29 May 2013, 12:49:56 UTC | updated ur submodule to 3846409 | 29 May 2013, 12:49:56 UTC |
| 4bc0eeb | APipe Tester | 29 May 2013, 12:37:05 UTC | updated ur submodule to c40a459 | 29 May 2013, 12:37:05 UTC |
| 148535c | APipe Tester | 29 May 2013, 12:23:19 UTC | updated ur submodule to 713c33a | 29 May 2013, 12:23:19 UTC |
| d132c91 | APipe Tester | 29 May 2013, 12:10:54 UTC | updated ur submodule to 7a5d244 | 29 May 2013, 12:10:54 UTC |
| 53f7360 | APipe Tester | 29 May 2013, 11:59:31 UTC | updated ur submodule to f8d2ec4 | 29 May 2013, 11:59:31 UTC |
| 2ced68a | APipe Tester | 29 May 2013, 11:48:09 UTC | updated ur submodule to a85dc58 | 29 May 2013, 11:48:09 UTC |
| 5631e75 | APipe Tester | 29 May 2013, 11:36:36 UTC | updated ur submodule to a5a40b5 | 29 May 2013, 11:36:36 UTC |
| 28ab633 | APipe Tester | 29 May 2013, 11:22:15 UTC | updated ur submodule to ccb4f6c | 29 May 2013, 11:22:15 UTC |
| 6d19b12 | APipe Tester | 29 May 2013, 11:10:16 UTC | updated ur submodule to d13cf7d | 29 May 2013, 11:10:16 UTC |
| ace3a7c | APipe Tester | 29 May 2013, 10:58:53 UTC | updated ur submodule to 5a0ee9e | 29 May 2013, 10:58:53 UTC |
| bd32a11 | APipe Tester | 29 May 2013, 10:46:58 UTC | updated ur submodule to 4265e09 | 29 May 2013, 10:46:58 UTC |
| 8ab8d93 | APipe Tester | 29 May 2013, 10:34:58 UTC | updated ur submodule to 8d60664 | 29 May 2013, 10:34:58 UTC |
| be3c703 | APipe Tester | 29 May 2013, 10:22:09 UTC | updated ur submodule to e85cdcf | 29 May 2013, 10:22:09 UTC |
| b797d37 | APipe Tester | 29 May 2013, 10:10:40 UTC | updated ur submodule to d701dd4 | 29 May 2013, 10:10:40 UTC |
| 31f8f76 | APipe Tester | 29 May 2013, 09:58:45 UTC | updated ur submodule to 7fc391e | 29 May 2013, 09:58:45 UTC |
| ec7c653 | APipe Tester | 29 May 2013, 09:46:46 UTC | updated ur submodule to 35976f5 | 29 May 2013, 09:46:46 UTC |
| 3c0be16 | APipe Tester | 29 May 2013, 09:35:27 UTC | updated ur submodule to 25e2627 | 29 May 2013, 09:35:27 UTC |
| f98a3f2 | APipe Tester | 29 May 2013, 09:22:02 UTC | updated ur submodule to 431bd58 | 29 May 2013, 09:22:02 UTC |
| 3af427a | APipe Tester | 29 May 2013, 09:10:05 UTC | updated ur submodule to 949f1d9 | 29 May 2013, 09:10:05 UTC |
| 9887eae | APipe Tester | 29 May 2013, 08:59:10 UTC | updated ur submodule to 77bfe77 | 29 May 2013, 08:59:10 UTC |
| 83240d5 | APipe Tester | 29 May 2013, 08:46:58 UTC | updated ur submodule to 22747b7 | 29 May 2013, 08:46:58 UTC |
| a4eb3ee | APipe Tester | 29 May 2013, 08:35:19 UTC | updated ur submodule to 1867828 | 29 May 2013, 08:35:19 UTC |
| f08817f | APipe Tester | 29 May 2013, 08:22:23 UTC | updated ur submodule to 87cc0ce | 29 May 2013, 08:22:23 UTC |
| 1bce9a3 | APipe Tester | 29 May 2013, 08:10:04 UTC | updated ur submodule to 346ce11 | 29 May 2013, 08:10:04 UTC |
| 31ac903 | APipe Tester | 29 May 2013, 07:58:52 UTC | updated ur submodule to 8ffbd6e | 29 May 2013, 07:58:52 UTC |
| ba93621 | APipe Tester | 29 May 2013, 07:46:49 UTC | updated ur submodule to f3b7cce | 29 May 2013, 07:46:49 UTC |
| 0c76a92 | APipe Tester | 29 May 2013, 07:34:57 UTC | updated ur submodule to 0b3baab | 29 May 2013, 07:34:57 UTC |
| 452f63c | APipe Tester | 29 May 2013, 07:22:00 UTC | updated ur submodule to 74dfc65 | 29 May 2013, 07:22:00 UTC |
| 30289a3 | APipe Tester | 29 May 2013, 07:10:01 UTC | updated ur submodule to 33a28aa | 29 May 2013, 07:10:01 UTC |
| 0eda13f | APipe Tester | 29 May 2013, 06:58:47 UTC | updated ur submodule to b7d84d1 | 29 May 2013, 06:58:47 UTC |
| 155a92b | APipe Tester | 29 May 2013, 06:46:51 UTC | updated ur submodule to 6efa574 | 29 May 2013, 06:46:51 UTC |
| d2fa443 | APipe Tester | 29 May 2013, 06:35:33 UTC | updated ur submodule to 0bacbf9 | 29 May 2013, 06:35:33 UTC |
| 4a13aa2 | APipe Tester | 29 May 2013, 06:22:27 UTC | updated ur submodule to 34db17a | 29 May 2013, 06:22:27 UTC |
