| 272393c | Isaac Overcast | 25 May 2017, 00:23:43 UTC | "Updating ipyrad/__init__.py to version - 0.6.23 | 25 May 2017, 00:23:43 UTC |
| 32e3d10 | Deren Eaton | 24 May 2017, 13:45:58 UTC | bug fix for numq error in s5 fix for error "ERROR NameError(global name 'numpq' is not defined)" I believe. Needs testing. | 24 May 2017, 13:45:58 UTC |
| 46296d5 | Isaac Overcast | 22 May 2017, 19:45:09 UTC | "Updating ipyrad/__init__.py to version - 0.6.22 | 22 May 2017, 19:45:09 UTC |
| 495eee0 | isaacovercast | 22 May 2017, 19:43:47 UTC | Fixed bug in vcf output for reference mapped. | 22 May 2017, 19:43:47 UTC |
| 3fd6e4e | Isaac Overcast | 19 May 2017, 21:00:55 UTC | "Updating ipyrad/__init__.py to version - 0.6.21 | 19 May 2017, 21:00:55 UTC |
| ebdc15d | Isaac Overcast | 19 May 2017, 20:06:55 UTC | Fix new chrom/pos mechanism to work for all assembly methods. | 19 May 2017, 20:06:55 UTC |
| b051506 | Isaac Overcast | 19 May 2017, 20:01:45 UTC | Change chroms dtype to int64. Reference sequence CHROM is now 1-indexed. Anonymous loci are -1 indexed. | 19 May 2017, 20:01:45 UTC |
| 1962019 | Isaac Overcast | 19 May 2017, 20:00:39 UTC | Switch chroms dataset dtype to int64. | 19 May 2017, 20:00:39 UTC |
| f70b513 | Isaac Overcast | 16 May 2017, 20:00:34 UTC | Fix for alleles output. | 16 May 2017, 20:00:34 UTC |
| 7fc8df1 | Isaac Overcast | 16 May 2017, 17:44:09 UTC | Fix nasty PE refmap merging issue. | 16 May 2017, 17:44:09 UTC |
| fc5cad0 | Isaac Overcast | 16 May 2017, 17:35:39 UTC | Fix massive bug in how unmapped reads are handled in refmap. | 16 May 2017, 17:35:39 UTC |
| 8028781 | deren | 15 May 2017, 15:53:54 UTC | added md5 names to derep and simplified code readability within pairmerging | 15 May 2017, 15:53:54 UTC |
| e16194e | deren | 15 May 2017, 15:50:48 UTC | fix for binary finder | 15 May 2017, 15:50:48 UTC |
| 076ab71 | dereneaton | 10 May 2017, 19:39:10 UTC | added dask to conda recipe | 10 May 2017, 19:39:10 UTC |
| 9952ac9 | dereneaton | 10 May 2017, 19:37:40 UTC | "Updating ipyrad/__init__.py to version - 0.6.20 | 10 May 2017, 19:37:40 UTC |
| cc05e29 | dereneaton | 10 May 2017, 19:36:50 UTC | "Updating ipyrad/__init__.py to version - 0.6.20 | 10 May 2017, 19:36:50 UTC |
| b8b4447 | dereneaton | 10 May 2017, 19:35:48 UTC | "Updating ipyrad/__init__.py to version - 0.6.20 | 10 May 2017, 19:35:48 UTC |
| 33f66db | dereneaton | 10 May 2017, 19:35:30 UTC | added dask dependency | 10 May 2017, 19:35:30 UTC |
| 3e88038 | dereneaton | 10 May 2017, 19:33:48 UTC | "Updating ipyrad/__init__.py to version - 0.6.20 | 10 May 2017, 19:33:48 UTC |
| d9a34b2 | dereneaton | 10 May 2017, 19:29:23 UTC | vcf building with full ref info | 10 May 2017, 19:29:23 UTC |
| 1efe23c | dereneaton | 10 May 2017, 18:26:18 UTC | merge conflict - cosmetic | 10 May 2017, 18:26:18 UTC |
| 3d0a991 | dereneaton | 10 May 2017, 18:24:31 UTC | bug fix to alleles output and support vcf chrompos storage in uint64 | 10 May 2017, 18:24:31 UTC |
| 50c7546 | dereneaton | 10 May 2017, 18:23:41 UTC | cosmetic | 10 May 2017, 18:23:41 UTC |
| 8530a41 | dereneaton | 10 May 2017, 18:23:22 UTC | simpler and slightly faster consens calls and lower memory and stores chrompos as uint64s | 10 May 2017, 18:23:22 UTC |
| 3362818 | dereneaton | 10 May 2017, 18:22:21 UTC | chrompos now stored as uint64 | 10 May 2017, 18:22:21 UTC |
| 77095e4 | deren | 10 May 2017, 15:13:29 UTC | cosmetic | 10 May 2017, 15:13:29 UTC |
| 9891869 | deren | 10 May 2017, 15:13:11 UTC | reducing memory load in race conditions for parallel cutadapt jobs | 10 May 2017, 15:13:11 UTC |
| d3fb02a | deren | 10 May 2017, 15:12:28 UTC | cosmetic | 10 May 2017, 15:12:28 UTC |
| 996138d | deren | 08 May 2017, 17:39:57 UTC | tunnel video up; cosmetic | 08 May 2017, 17:39:57 UTC |
| f6801cc | Isaac Overcast | 06 May 2017, 01:07:37 UTC | Squash Cosmetic commit logs in releasenotes. Add more informative header in step 7 stats file. | 06 May 2017, 01:07:37 UTC |
| 63a1f43 | Isaac Overcast | 05 May 2017, 17:37:46 UTC | Trying to catch bad alignment for PE in step 6. | 05 May 2017, 17:37:46 UTC |
| 98778ff | Isaac Overcast | 04 May 2017, 18:23:43 UTC | "Updating ipyrad/__init__.py to version - 0.6.19 | 04 May 2017, 18:23:43 UTC |
| 44559fb | Isaac Overcast | 04 May 2017, 18:23:20 UTC | Handle empty locus when building alleles file. | 04 May 2017, 18:23:20 UTC |
| 38c8268 | dereneaton | 04 May 2017, 07:13:15 UTC | workshop notebook uploaded | 04 May 2017, 07:13:15 UTC |
| 4bf41fe | dereneaton | 03 May 2017, 11:45:57 UTC | "Updating ipyrad/__init__.py to version - 0.6.18 | 03 May 2017, 11:45:57 UTC |
| 6c68ccf | dereneaton | 03 May 2017, 11:34:53 UTC | "Updating ipyrad/__init__.py to version - 0.6.18 | 03 May 2017, 11:34:53 UTC |
| e8984d2 | dereneaton | 03 May 2017, 11:34:16 UTC | update to analysis tools | 03 May 2017, 11:34:16 UTC |
| 1c895cf | dereneaton | 01 May 2017, 00:32:28 UTC | accepted the local bpp notebook | 01 May 2017, 00:32:28 UTC |
| 37d93ae | dereneaton | 01 May 2017, 00:20:52 UTC | complete bpp notebook up | 01 May 2017, 00:20:52 UTC |
| 469f6cd | deren | 29 April 2017, 22:53:51 UTC | notebook updates | 29 April 2017, 22:53:51 UTC |
| 0f6ec2e | deren | 29 April 2017, 22:50:41 UTC | cosmetic | 29 April 2017, 22:50:41 UTC |
| b427f01 | deren | 29 April 2017, 22:50:25 UTC | cosmetic changes | 29 April 2017, 22:50:25 UTC |
| bc1babe | deren | 29 April 2017, 22:48:53 UTC | raxml docs | 29 April 2017, 22:48:53 UTC |
| 5b1db2d | deren | 29 April 2017, 22:44:45 UTC | raxml cookbook up | 29 April 2017, 22:44:45 UTC |
| 15de624 | deren | 29 April 2017, 21:10:48 UTC | docs update | 29 April 2017, 21:10:48 UTC |
| d52f229 | deren | 29 April 2017, 17:39:07 UTC | raxml docs updated | 29 April 2017, 17:39:07 UTC |
| d931b19 | deren | 29 April 2017, 16:52:59 UTC | links to miniconda updated | 29 April 2017, 16:52:59 UTC |
| 5ba0508 | deren | 29 April 2017, 16:20:59 UTC | fix for tetrad restarting bootstraps | 29 April 2017, 16:20:59 UTC |
| e87aa22 | deren | 29 April 2017, 15:54:08 UTC | removed bitarray dependency | 29 April 2017, 15:54:08 UTC |
| 0a13d39 | deren | 29 April 2017, 00:22:47 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 29 April 2017, 00:22:47 UTC |
| 99128ae | deren | 29 April 2017, 00:22:34 UTC | adding restart checkpoints in step6 | 29 April 2017, 00:22:34 UTC |
| ce37e35 | dereneaton | 26 April 2017, 22:13:26 UTC | "Updating ipyrad/__init__.py to version - 0.6.17 | 26 April 2017, 22:13:26 UTC |
| 85c8b57 | deren | 26 April 2017, 22:11:01 UTC | support for alleles file in bpp tools | 26 April 2017, 22:11:01 UTC |
| 204cbf5 | deren | 26 April 2017, 22:10:37 UTC | align names in alleles output | 26 April 2017, 22:10:37 UTC |
| 79d9927 | deren | 26 April 2017, 00:40:27 UTC | bugfix to name padding in .alleles output | 26 April 2017, 00:40:27 UTC |
| 5055970 | deren | 26 April 2017, 00:40:01 UTC | slight delay between jobs | 26 April 2017, 00:40:01 UTC |
| c9f3874 | deren | 25 April 2017, 20:16:28 UTC | bpp store asyncs | 25 April 2017, 20:16:28 UTC |
| e12e3bd | deren | 25 April 2017, 20:09:11 UTC | bpp store asyncs | 25 April 2017, 20:09:11 UTC |
| 4299ecb | deren | 25 April 2017, 20:06:24 UTC | update bpp cookbook | 25 April 2017, 20:06:24 UTC |
| 5ed5691 | deren | 25 April 2017, 19:57:58 UTC | testing html | 25 April 2017, 19:57:58 UTC |
| 93aee54 | deren | 25 April 2017, 19:36:32 UTC | testing html | 25 April 2017, 19:36:32 UTC |
| a1c5b40 | deren | 25 April 2017, 18:23:37 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 25 April 2017, 18:23:37 UTC |
| 5e328db | deren | 25 April 2017, 18:23:31 UTC | new filter_adapters=3 option adds filtering of poly-repeats | 25 April 2017, 18:23:31 UTC |
| 734ea4a | deren | 25 April 2017, 17:04:13 UTC | conda recipe update for cutadapt w/o need of add-channel | 25 April 2017, 17:04:13 UTC |
| 3cb8475 | deren | 25 April 2017, 05:33:02 UTC | "Updating ipyrad/__init__.py to version - 0.6.16 | 25 April 2017, 05:33:02 UTC |
| a8489e4 | deren | 25 April 2017, 05:32:38 UTC | alleles output now supported | 25 April 2017, 05:32:38 UTC |
| cec8e4e | deren | 25 April 2017, 03:25:16 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 25 April 2017, 03:25:16 UTC |
| 3001c5e | Isaac Overcast | 24 April 2017, 13:23:29 UTC | Additional documentation for max_alleles_consens parameter. | 24 April 2017, 13:23:29 UTC |
| f559eed | deren | 22 April 2017, 01:37:48 UTC | support alleles output, minor bug fixes for step6, much faster alignment step6 | 22 April 2017, 01:37:48 UTC |
| de6bb1d | deren | 21 April 2017, 22:37:10 UTC | lower default 'cov' value for vsearch within clustering in RAD/ddrad/pairddrad | 21 April 2017, 22:37:10 UTC |
| e43f874 | deren | 21 April 2017, 22:36:33 UTC | tetrad bug, use same ipyclient for consensus tree building | 21 April 2017, 22:36:33 UTC |
| ea0f816 | deren | 21 April 2017, 22:36:06 UTC | store asyncs in the structure object | 21 April 2017, 22:36:06 UTC |
| 3d5c26e | deren | 20 April 2017, 20:11:41 UTC | cosmetic | 20 April 2017, 20:11:41 UTC |
| 9788c2f | deren | 20 April 2017, 18:31:51 UTC | allow passing in ipyclient explicitly in .run() in tetrad | 20 April 2017, 18:31:51 UTC |
| d6ad138 | deren | 20 April 2017, 18:28:43 UTC | fix for time stamp issue in tetrad | 20 April 2017, 18:28:43 UTC |
| 3e44dbe | iovercast | 20 April 2017, 11:24:56 UTC | Better testing for existence of all R2 files for merged assemblies. | 20 April 2017, 11:24:56 UTC |
| 0a102da | deren | 18 April 2017, 19:20:13 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 18 April 2017, 19:20:13 UTC |
| 22c136b | deren | 18 April 2017, 19:19:59 UTC | notebook updates | 18 April 2017, 19:19:59 UTC |
| 2787123 | deren | 18 April 2017, 19:06:17 UTC | tunnel docs update | 18 April 2017, 19:06:17 UTC |
| 74e18c8 | deren | 18 April 2017, 18:52:11 UTC | updated HPC docs | 18 April 2017, 18:52:11 UTC |
| 1ed135e | deren | 18 April 2017, 18:44:26 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 18 April 2017, 18:44:26 UTC |
| 423af2d | deren | 18 April 2017, 18:44:17 UTC | tetrad cookbook updated | 18 April 2017, 18:44:17 UTC |
| 15a94d7 | deren | 18 April 2017, 18:36:57 UTC | HPC docs update | 18 April 2017, 18:36:57 UTC |
| e04c5fd | deren | 18 April 2017, 17:40:19 UTC | bpp cookbook good to go | 18 April 2017, 17:40:19 UTC |
| ef6484d | deren | 18 April 2017, 14:20:37 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 18 April 2017, 14:20:37 UTC |
| 686d88e | deren | 18 April 2017, 14:20:25 UTC | update tetrad notebook | 18 April 2017, 14:20:25 UTC |
| 463da93 | deren | 18 April 2017, 14:06:22 UTC | missing import | 18 April 2017, 14:06:22 UTC |
| 65d9af0 | Isaac Overcast | 18 April 2017, 07:32:43 UTC | "Updating ipyrad/__init__.py to version - 0.6.15 | 18 April 2017, 07:32:43 UTC |
| 9d69b0b | Isaac Overcast | 18 April 2017, 07:31:19 UTC | Actually fix gphocs output. | 18 April 2017, 07:31:19 UTC |
| d9ed5c3 | deren | 14 April 2017, 04:29:18 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 14 April 2017, 04:29:18 UTC |
| 4f4589d | deren | 14 April 2017, 04:28:57 UTC | allow passing in ipyclient in API | 14 April 2017, 04:28:57 UTC |
| 011a496 | deren | 13 April 2017, 23:30:38 UTC | baba notebook update | 13 April 2017, 23:30:38 UTC |
| 2172cc9 | deren | 13 April 2017, 23:17:23 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 13 April 2017, 23:17:23 UTC |
| d522515 | deren | 13 April 2017, 23:14:56 UTC | cleaner api for bpp object | 13 April 2017, 23:14:56 UTC |
| 17b66b0 | deren | 13 April 2017, 23:12:21 UTC | new analysis setup | 13 April 2017, 23:12:21 UTC |
| 5f8e135 | deren | 13 April 2017, 19:04:26 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 13 April 2017, 19:04:26 UTC |
| 0411f58 | deren | 13 April 2017, 19:04:19 UTC | updated analysis tools without ete | 13 April 2017, 19:04:19 UTC |
| 2bbb0d6 | Isaac Overcast | 13 April 2017, 12:46:03 UTC | "Updating ipyrad/__init__.py to version - 0.6.14 | 13 April 2017, 12:46:03 UTC |
| 4106d28 | Isaac Overcast | 13 April 2017, 12:45:41 UTC | Fixed CHROM/POS output for reference mapped loci. | 13 April 2017, 12:45:41 UTC |
| 1e390a3 | Isaac Overcast | 13 April 2017, 07:48:52 UTC | "Updating ipyrad/__init__.py to version - 0.6.13 | 13 April 2017, 07:48:52 UTC |
