| 4e60002 | Allison Penner Regier | 08 February 2018, 19:09:37 UTC | Merge pull request #125 from hall-lab/new_exclude Add new exclude files | 08 February 2018, 19:09:37 UTC |
| bb19df6 | apregier | 08 February 2018, 19:06:20 UTC | Add new exclude files | 08 February 2018, 19:06:20 UTC |
| 30f8dc6 | Colby Chiang | 26 April 2017, 21:01:34 UTC | revert LUMPY to avoid htslib conflicts with speedseq make (#106) | 26 April 2017, 21:01:34 UTC |
| 8814723 | Colby Chiang | 19 April 2017, 14:00:33 UTC | bump svtyper to 1.4 | 19 April 2017, 14:00:33 UTC |
| c411756 | Colby Chiang | 17 April 2017, 23:16:48 UTC | Merge branch 'v0.1.2_cram_support' of github.com:hall-lab/speedseq into v0.1.2_cram_support | 17 April 2017, 23:16:48 UTC |
| 0c3044c | Colby Chiang | 17 April 2017, 23:16:27 UTC | update lumpy | 17 April 2017, 23:16:27 UTC |
| 6010b7c | Colby Chiang | 17 April 2017, 22:54:09 UTC | cnvnator instructions | 17 April 2017, 22:54:09 UTC |
| 3c34485 | Colby Chiang | 17 April 2017, 22:51:52 UTC | update cnvnator installation instructions | 17 April 2017, 22:51:52 UTC |
| e002f78 | Colby Chiang | 17 April 2017, 22:50:10 UTC | remove samtools submodule | 17 April 2017, 22:50:10 UTC |
| 798e92f | Colby Chiang | 17 April 2017, 22:29:17 UTC | compilation for official cnvnator | 17 April 2017, 22:29:17 UTC |
| 8198ad9 | Colby Chiang | 17 April 2017, 20:13:34 UTC | add samtools for cnvnator | 17 April 2017, 20:13:34 UTC |
| 176e463 | Colby Chiang | 17 April 2017, 18:38:52 UTC | use official cnvnator | 17 April 2017, 18:38:52 UTC |
| 8190a77 | Colby Chiang | 17 April 2017, 18:21:08 UTC | bump to svtyper v0.1.3 | 17 April 2017, 18:21:08 UTC |
| e4fcb26 | Colby Chiang | 28 March 2017, 16:19:02 UTC | Revert "command line arg for ref FASTA (for CRAM reading)" Providing FASTA to wrapper does not help, since cnvnator internally calls samtools This reverts commit afa9d61e1e817bef26f3e5fbd32e4bcbd7fa83cb. | 28 March 2017, 16:19:02 UTC |
| afa9d61 | Colby Chiang | 28 March 2017, 15:33:40 UTC | command line arg for ref FASTA (for CRAM reading) | 28 March 2017, 15:33:40 UTC |
| 6041302 | Colby Chiang | 28 March 2017, 15:21:15 UTC | Merge pull request #103 from ernfrid/v0.1.2_cram_support V0.1.2 cram support | 28 March 2017, 15:21:15 UTC |
| 032bb7a | Dave Larson | 11 March 2017, 03:10:17 UTC | use latest svtyper | 11 March 2017, 03:10:17 UTC |
| 03267b8 | Dave Larson | 11 March 2017, 03:09:27 UTC | use samtools in config and for cnvnator_wrapper | 11 March 2017, 03:09:27 UTC |
| 9c153eb | Dave Larson | 07 March 2017, 05:33:31 UTC | add cram compatible lumpy update | 07 March 2017, 05:33:31 UTC |
| cb1eb1c | Dave Larson | 07 March 2017, 05:18:52 UTC | remove lumpy submodule | 07 March 2017, 05:18:52 UTC |
| 905ccf9 | Dave Larson | 07 March 2017, 04:55:30 UTC | add hexdump to autogenerated config | 07 March 2017, 04:55:30 UTC |
| c6f7fe6 | Dave Larson | 07 March 2017, 04:54:35 UTC | abstract hexdump into an environment variable | 07 March 2017, 04:54:35 UTC |
| 1854e02 | Dave Larson | 07 March 2017, 04:53:04 UTC | separate wrappers from cnvnator in makefile | 07 March 2017, 04:53:04 UTC |
| ecb338a | Dave Larson | 21 December 2016, 22:37:53 UTC | make regex exclusion somewhat configurable. Should work alright for human. | 07 March 2017, 04:48:46 UTC |
| fcbaac1 | Dave Larson | 21 December 2016, 21:06:41 UTC | allow specification of samtools binary | 07 March 2017, 04:48:46 UTC |
| efcdee6 | Dave Larson | 16 December 2016, 22:09:51 UTC | add timestamps, threading, and whitespace fixes | 07 March 2017, 04:48:46 UTC |
| ee71707 | Dave Larson | 07 December 2016, 19:56:08 UTC | remove some dead code | 07 March 2017, 04:48:46 UTC |
| da9c200 | Dave Larson | 07 December 2016, 19:52:34 UTC | introduce changes made by idas | 07 March 2017, 04:48:46 UTC |
| 122be14 | apregier | 10 August 2016, 16:52:26 UTC | Merge in Colbys fix from the main repo to allow arbitrary numbers of fields in the SQ header | 07 March 2017, 04:48:46 UTC |
| 0ccb472 | apregier | 10 August 2016, 16:42:40 UTC | Need -t argument for compatibility even though it is not used | 07 March 2017, 04:48:46 UTC |
| 6f8bde7 | apregier | 24 May 2016, 19:13:08 UTC | Exclude alts and decoys | 07 March 2017, 04:48:46 UTC |
| 65cc034 | apregier | 24 May 2016, 19:12:18 UTC | Simplify cnvnator_wrapper and use deployed version of new cnvnator | 07 March 2017, 04:48:46 UTC |
| 63b3c1d | apregier | 04 May 2016, 18:47:10 UTC | cnvnator wrapper with modification so it doesn't hang on large bam header inputs | 07 March 2017, 04:48:46 UTC |
| 25937f1 | Indraniel Das | 04 January 2017, 21:19:05 UTC | + inspect the binary file header to detect CRAM/BAM - use hexdump to determine the CRAM or BAM file type - error out if not given a proper CRAM or BAM as input | 07 March 2017, 04:40:03 UTC |
| 7527c58 | Dave Larson | 16 December 2016, 22:28:04 UTC | detect CRAM file by extension and add flags for sambamba | 07 March 2017, 04:40:03 UTC |
| 75863fa | Colby Chiang | 09 January 2017, 23:19:19 UTC | bump version tags | 09 January 2017, 23:19:19 UTC |
| 3a87538 | Colby Chiang | 14 December 2016, 16:44:57 UTC | FAQ to address #31 and #94 | 14 December 2016, 16:44:57 UTC |
| 92cbc32 | Colby Chiang | 13 December 2016, 20:02:58 UTC | bump svtyper to v0.1.1 | 13 December 2016, 20:02:58 UTC |
| 59a2b58 | Colby Chiang | 06 December 2016, 17:52:10 UTC | temporarily rollback svtyper to v0.0.4, to avoid a bug in dup and inversion genotyping | 06 December 2016, 17:52:10 UTC |
| 5f4fe08 | Colby Chiang | 21 November 2016, 18:59:32 UTC | bump svtyper to v0.1.0 | 21 November 2016, 18:59:32 UTC |
| 6f93db3 | Colby Chiang | 21 November 2016, 18:56:17 UTC | Merge branch 'master' of github.com:cc2qe/speedseq # Please enter a commit message to explain why this merge is necessary, # especially if it merges an updated upstream into a topic branch. # # Lines starting with '#' will be ignored, and an empty message aborts # the commit. | 21 November 2016, 18:56:17 UTC |
| 9835a76 | Colby Chiang | 21 November 2016, 18:50:57 UTC | bump svtyper | 21 November 2016, 18:50:57 UTC |
| 87b19b6 | Colby Chiang | 02 November 2016, 19:11:15 UTC | Update Makefile add pthread | 02 November 2016, 19:11:15 UTC |
| 5afc7b1 | Colby Chiang | 01 November 2016, 21:45:35 UTC | Merge pull request #93 from ahwagner/patch-1 minor README fix | 01 November 2016, 21:45:35 UTC |
| 3ab092d | Alex Handler Wagner, PhD | 01 November 2016, 20:57:00 UTC | Update README second make file is two directories up from src/samtools. | 01 November 2016, 20:57:00 UTC |
| 494f8fc | Colby Chiang | 10 August 2016, 19:26:58 UTC | fix bug in cnvnator header parsing | 10 August 2016, 19:26:58 UTC |
| a2ef587 | Colby Chiang | 13 July 2016, 16:37:53 UTC | don't include overwritten readgroups in header when using the '-R' option for realign | 13 July 2016, 16:37:53 UTC |
| 815abec | Colby Chiang | 13 July 2016, 16:04:48 UTC | fix realign command for BAMs with readgroups (#82) | 13 July 2016, 16:04:48 UTC |
| a2d62ba | Colby Chiang | 13 July 2016, 14:42:55 UTC | more descriptive message on generating fasta index #83 | 13 July 2016, 14:42:55 UTC |
| d8b4e8c | Colby Chiang | 12 July 2016, 21:08:22 UTC | fix 'no chromosomes found' error in cnvnator, for BAMs with extra header metadata | 12 July 2016, 21:08:22 UTC |
| 2cb0fb8 | Colby Chiang | 20 June 2016, 14:39:40 UTC | fix bug in VEP annotation of non-autosomes #81 | 20 June 2016, 14:39:40 UTC |
| 6fe658e | Colby Chiang | 15 June 2016, 19:03:31 UTC | Update README.md document the -P option for speedseq sv | 15 June 2016, 19:03:31 UTC |
| f3ca93d | Colby Chiang | 30 May 2016, 16:34:00 UTC | fixed a couple bugs related to #35 | 30 May 2016, 16:34:00 UTC |
| b122aba | Colby Chiang | 30 May 2016, 15:18:11 UTC | realign: auto-generate readgroup info (when input BAMs lack RGs), or allow the user to specify them on command line https://github.com/hall-lab/speedseq/issues/35 | 30 May 2016, 15:18:11 UTC |
| 24cf60f | Colby Chiang | 05 April 2016, 14:14:16 UTC | Merge branch 'master' of github.com:cc2qe/speedseq | 05 April 2016, 14:14:16 UTC |
| 9f18cd9 | Colby Chiang | 05 April 2016, 14:14:05 UTC | bump svtyper | 05 April 2016, 14:14:05 UTC |
| 03898a0 | Colby Chiang | 30 March 2016, 16:22:38 UTC | Update README.md forgot a word | 30 March 2016, 16:22:38 UTC |
| 4771cc8 | Colby Chiang | 11 March 2016, 20:55:26 UTC | bump again | 11 March 2016, 20:55:26 UTC |
| 655f1a7 | Colby Chiang | 11 March 2016, 20:06:29 UTC | bump again | 11 March 2016, 20:06:29 UTC |
| 9185e8d | Colby Chiang | 11 March 2016, 19:32:43 UTC | bump svtyper | 11 March 2016, 19:32:43 UTC |
| bd9aa63 | Colby Chiang | 28 January 2016, 18:13:43 UTC | pipefail caused 147 exit statuses, like in | 28 January 2016, 18:13:43 UTC |
| f2b23b5 | Colby Chiang | 22 January 2016, 16:59:33 UTC | verbose is now the default | 22 January 2016, 16:59:33 UTC |
| e99d565 | Colby Chiang | 12 January 2016, 17:11:46 UTC | update sambamba, add realign test | 12 January 2016, 17:11:46 UTC |
| 550f598 | Colby Chiang | 30 November 2015, 19:07:39 UTC | add pipefail | 30 November 2015, 19:07:39 UTC |
| 7fc8bca | Colby Chiang | 30 November 2015, 17:14:29 UTC | add dino | 30 November 2015, 17:14:29 UTC |
| 6719825 | Colby Chiang | 30 November 2015, 17:13:00 UTC | Merge branch 'master' of github.com:cc2qe/speedseq | 30 November 2015, 17:13:00 UTC |
| 0eab42e | Colby Chiang | 30 November 2015, 17:12:48 UTC | address #63 with VEP assembly parameter -a for 'var', 'somatic', and 'sv' | 30 November 2015, 17:12:48 UTC |
| a95704a | Colby Chiang | 13 November 2015, 19:19:56 UTC | force bitwise sorting, #53 | 13 November 2015, 19:19:56 UTC |
| faa2e90 | Colby Chiang | 13 November 2015, 17:52:01 UTC | update prereqs for gawk https://github.com/hall-lab/speedseq/issues/51 | 13 November 2015, 17:52:01 UTC |
| c465d82 | Colby Chiang | 27 October 2015, 12:47:36 UTC | Merge branch 'cnvnator_windows' | 27 October 2015, 12:47:36 UTC |
| e221fbb | Colby Chiang | 27 October 2015, 12:46:58 UTC | allow user-specified window size #38 | 27 October 2015, 12:46:58 UTC |
| b3520fa | Colby Chiang | 27 October 2015, 12:22:38 UTC | if reference index absent, speedseq automatically indexes reference with BWA before realign #49 | 27 October 2015, 12:22:38 UTC |
| c1058b7 | Colby Chiang | 26 October 2015, 19:13:31 UTC | bump lumpy | 26 October 2015, 19:13:31 UTC |
| c6ae1bc | Colby Chiang | 12 October 2015, 19:54:59 UTC | Update README.md | 12 October 2015, 19:54:59 UTC |
| 0238d5c | Colby Chiang | 08 September 2015, 17:31:35 UTC | Merge branch 'master' of github.com:cc2qe/speedseq | 08 September 2015, 17:31:35 UTC |
| be66448 | Colby Chiang | 08 September 2015, 17:31:18 UTC | bumpy lumpy to address zero-length read, remove element issue | 08 September 2015, 17:31:18 UTC |
| 93962db | Colby Chiang | 03 September 2015, 13:45:19 UTC | svg logo | 03 September 2015, 13:45:19 UTC |
| 00d31ab | Colby Chiang | 03 September 2015, 13:35:54 UTC | add logo | 03 September 2015, 13:35:54 UTC |
| 720bc91 | Colby Chiang | 27 August 2015, 15:14:20 UTC | added license, #43 | 27 August 2015, 15:14:20 UTC |
| 83c6974 | Colby Chiang | 27 August 2015, 14:59:30 UTC | Update README.md updated the paths for the new git home. | 27 August 2015, 14:59:30 UTC |
| aa7e66a | Colby Chiang | 24 August 2015, 22:15:54 UTC | hopefully fixed error with empty cigar string related to modifications in pysam 0.8.1 (None instead of [] #30 ) | 24 August 2015, 22:15:54 UTC |
| 5e94c4d | Colby Chiang | 18 August 2015, 14:29:04 UTC | Merge pull request #39 from s-boardman/master Corrected CNVnator command echo for verbose output | 18 August 2015, 14:29:04 UTC |
| 9453bc8 | s-boardman | 18 August 2015, 13:28:13 UTC | Corrected CNVnator command echo for verbose output | 18 August 2015, 13:28:13 UTC |
| 3813e40 | Colby Chiang | 17 August 2015, 19:01:19 UTC | Update README.md | 17 August 2015, 19:01:19 UTC |
| b922cf1 | Colby Chiang | 17 August 2015, 18:59:38 UTC | Update README.md | 17 August 2015, 18:59:38 UTC |
| 2fab141 | Colby Chiang | 17 August 2015, 18:59:07 UTC | Update README.md | 17 August 2015, 18:59:07 UTC |
| 67a278a | Colby Chiang | 17 August 2015, 18:58:19 UTC | Update README.md | 17 August 2015, 18:58:19 UTC |
| 8988cf7 | Colby Chiang | 17 August 2015, 18:56:33 UTC | Update README.md | 17 August 2015, 18:56:33 UTC |
| 790b669 | Colby Chiang | 17 August 2015, 18:16:32 UTC | merge developmental features to master | 17 August 2015, 18:16:32 UTC |
| dd1df95 | Colby Chiang | 17 August 2015, 18:13:58 UTC | remove hall config from master | 17 August 2015, 18:13:58 UTC |
| 54fb5f4 | Colby Chiang | 17 August 2015, 18:13:19 UTC | Merge branch 'gms' | 17 August 2015, 18:13:19 UTC |
| 5fe5fa0 | Colby Chiang | 17 August 2015, 18:06:16 UTC | bump freebayes version | 17 August 2015, 18:06:16 UTC |
| 4d06869 | Colby Chiang | 17 August 2015, 18:03:04 UTC | bump versions for supplementary read support | 17 August 2015, 18:03:04 UTC |
| 27906e6 | Colby Chiang | 03 August 2015, 21:22:12 UTC | bump freebayes to version v0.9.21 | 03 August 2015, 21:22:12 UTC |
| e250f97 | Colby Chiang | 03 July 2015, 21:05:52 UTC | more explicit about pysam versions addresses https://github.com/cc2qe/speedseq/issues/30 and https://github.com/cc2qe/speedseq/issues/29 | 03 July 2015, 21:05:52 UTC |
| b42ba66 | Colby Chiang | 26 June 2015, 01:17:24 UTC | bump svtyper | 26 June 2015, 01:17:24 UTC |
| 82f5230 | Colby Chiang | 26 June 2015, 01:14:40 UTC | bump lumpy to handle supplementary flag and bamkit | 26 June 2015, 01:14:40 UTC |
| 41a2a50 | Colby Chiang | 26 June 2015, 01:06:19 UTC | bump samblaster to 0.1.22 | 26 June 2015, 01:06:19 UTC |
| 94b8f89 | Colby Chiang | 05 June 2015, 18:37:52 UTC | annoate copy number of BND variants | 05 June 2015, 18:37:52 UTC |
| 3244a4a | Colby Chiang | 18 May 2015, 18:59:21 UTC | bump submodules | 18 May 2015, 18:59:21 UTC |
