| 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 |
| aa12ef6 | APipe Tester | 29 May 2013, 06:10:31 UTC | updated ur submodule to a583e96 | 29 May 2013, 06:10:31 UTC |
| cf89fbc | APipe Tester | 29 May 2013, 05:59:06 UTC | updated ur submodule to 69b0724 | 29 May 2013, 05:59:06 UTC |
| 77f1648 | APipe Tester | 29 May 2013, 05:47:03 UTC | updated ur submodule to a8ce70a | 29 May 2013, 05:47:03 UTC |
| 7ad70be | APipe Tester | 29 May 2013, 05:34:55 UTC | updated ur submodule to f21fba3 | 29 May 2013, 05:34:55 UTC |
| 733655d | APipe Tester | 29 May 2013, 05:21:49 UTC | updated ur submodule to fc30e74 | 29 May 2013, 05:21:49 UTC |
| e562bdf | APipe Tester | 29 May 2013, 05:10:03 UTC | updated ur submodule to 6957e30 | 29 May 2013, 05:10:03 UTC |
| a4dddb4 | APipe Tester | 29 May 2013, 04:59:08 UTC | updated ur submodule to 812b708 | 29 May 2013, 04:59:08 UTC |
| 034486d | APipe Tester | 29 May 2013, 04:47:04 UTC | updated ur submodule to 89cbe9b | 29 May 2013, 04:47:04 UTC |
| 469528a | APipe Tester | 29 May 2013, 04:35:48 UTC | updated ur submodule to 7cba353 | 29 May 2013, 04:35:48 UTC |
| 0081af6 | APipe Tester | 29 May 2013, 04:22:32 UTC | updated ur submodule to f587067 | 29 May 2013, 04:22:32 UTC |
| 86979ff | APipe Tester | 29 May 2013, 04:10:20 UTC | updated ur submodule to 6927740 | 29 May 2013, 04:10:20 UTC |
| 0c00269 | APipe Tester | 29 May 2013, 03:58:42 UTC | updated ur submodule to 734a530 | 29 May 2013, 03:58:42 UTC |
| a1155ca | APipe Tester | 29 May 2013, 03:47:15 UTC | updated ur submodule to e97c7d0 | 29 May 2013, 03:47:15 UTC |
| 6bfc485 | APipe Tester | 29 May 2013, 03:35:38 UTC | updated ur submodule to 5a178fe | 29 May 2013, 03:35:38 UTC |
| 0fa0b0d | APipe Tester | 29 May 2013, 03:22:08 UTC | updated ur submodule to b23d1af | 29 May 2013, 03:22:08 UTC |
| f047557 | APipe Tester | 29 May 2013, 03:10:10 UTC | updated ur submodule to 394773c | 29 May 2013, 03:10:10 UTC |
| 3ddfd0b | APipe Tester | 29 May 2013, 02:58:39 UTC | updated ur submodule to a3ec14c | 29 May 2013, 02:58:39 UTC |
| e701fc0 | APipe Tester | 29 May 2013, 02:47:08 UTC | updated ur submodule to 98a765e | 29 May 2013, 02:47:08 UTC |
| 4117366 | APipe Tester | 29 May 2013, 02:34:27 UTC | updated ur submodule to 715ad85 | 29 May 2013, 02:34:27 UTC |
| a8c3072 | APipe Tester | 29 May 2013, 02:22:34 UTC | updated ur submodule to 01966c1 | 29 May 2013, 02:22:34 UTC |
| 42d4cf2 | Scott Smith | 29 May 2013, 02:18:53 UTC | cosmetic | 29 May 2013, 02:18:53 UTC |
| 008f141 | APipe Tester | 29 May 2013, 02:10:31 UTC | updated ur submodule to a1adbe4 | 29 May 2013, 02:10:31 UTC |
| 6416778 | APipe Tester | 29 May 2013, 01:58:39 UTC | updated ur submodule to 4cc3b47 | 29 May 2013, 01:58:39 UTC |
| ec4ecc9 | APipe Tester | 29 May 2013, 01:47:08 UTC | updated ur submodule to a0585d9 | 29 May 2013, 01:47:08 UTC |
| d34706c | APipe Tester | 29 May 2013, 01:34:56 UTC | updated ur submodule to 6b836b9 | 29 May 2013, 01:34:56 UTC |
| 77e4370 | APipe Tester | 29 May 2013, 01:22:11 UTC | updated ur submodule to c5310ea | 29 May 2013, 01:22:11 UTC |
| fc518c7 | APipe Tester | 29 May 2013, 01:10:29 UTC | updated ur submodule to af15263 | 29 May 2013, 01:10:29 UTC |
| fff7515 | APipe Tester | 29 May 2013, 00:58:49 UTC | updated ur submodule to f7d8828 | 29 May 2013, 00:58:49 UTC |
| c58d135 | APipe Tester | 29 May 2013, 00:47:08 UTC | updated ur submodule to 714ad7f | 29 May 2013, 00:47:08 UTC |
| df3d2fe | APipe Tester | 29 May 2013, 00:35:29 UTC | updated ur submodule to a099c62 | 29 May 2013, 00:35:29 UTC |
| 5b30b95 | APipe Tester | 29 May 2013, 00:22:17 UTC | updated ur submodule to 8d194e1 | 29 May 2013, 00:22:17 UTC |
| d76572f | APipe Tester | 29 May 2013, 00:10:31 UTC | updated ur submodule to 679b60f | 29 May 2013, 00:10:31 UTC |
| 328aa66 | APipe Tester | 28 May 2013, 23:59:58 UTC | updated ur submodule to c15e143 | 28 May 2013, 23:59:58 UTC |
| 1bbf026 | APipe Tester | 28 May 2013, 23:55:05 UTC | updated workflow submodule to 85f6ae5 | 28 May 2013, 23:55:05 UTC |
| f3430d3 | APipe Tester | 28 May 2013, 23:48:17 UTC | updated ur submodule to f4157ac | 28 May 2013, 23:48:17 UTC |
| 9ca267d | APipe Tester | 28 May 2013, 23:42:46 UTC | updated workflow submodule to f54f88a | 28 May 2013, 23:42:46 UTC |
| 425e4cf | APipe Tester | 28 May 2013, 23:36:16 UTC | updated ur submodule to 497193e | 28 May 2013, 23:36:16 UTC |
