| ae75117 | dereneaton | 15 June 2017, 19:17:38 UTC | "Updating ipyrad/__init__.py to version - 0.7.0 | 15 June 2017, 19:17:38 UTC |
| 72be32c | dereneaton | 15 June 2017, 19:15:11 UTC | put a temporary block on denovo+ref | 15 June 2017, 19:15:11 UTC |
| 91fb930 | dereneaton | 15 June 2017, 19:09:40 UTC | cookbooks | 15 June 2017, 19:09:40 UTC |
| efba2e6 | dereneaton | 15 June 2017, 18:43:36 UTC | cookbook updates | 15 June 2017, 18:43:36 UTC |
| bf103af | dereneaton | 15 June 2017, 18:42:56 UTC | cosmetic | 15 June 2017, 18:42:56 UTC |
| 121a60d | dereneaton | 15 June 2017, 18:42:40 UTC | added treemix ipa funcs | 15 June 2017, 18:42:40 UTC |
| 1883f30 | dereneaton | 15 June 2017, 18:42:14 UTC | conda recipe | 15 June 2017, 18:42:14 UTC |
| ad5d83b | dereneaton | 15 June 2017, 18:41:55 UTC | update conda recipe | 15 June 2017, 18:41:55 UTC |
| 1a21b46 | dereneaton | 15 June 2017, 18:40:50 UTC | notebook updates | 15 June 2017, 18:40:50 UTC |
| 15e01f4 | dereneaton | 14 June 2017, 16:57:39 UTC | mods to bpp ipa object | 14 June 2017, 16:57:39 UTC |
| dc5c422 | deren | 13 June 2017, 20:46:19 UTC | hide treemix for now | 13 June 2017, 20:46:19 UTC |
| 1a9db3b | deren | 13 June 2017, 20:45:42 UTC | added notebook for popdata structure ipa | 13 June 2017, 20:45:42 UTC |
| 4fb9b20 | deren | 13 June 2017, 20:44:59 UTC | merge conflict | 13 June 2017, 20:44:59 UTC |
| 2a98349 | deren | 13 June 2017, 19:42:46 UTC | missing newline in alleles | 13 June 2017, 19:42:46 UTC |
| 4a827c2 | deren | 13 June 2017, 19:42:16 UTC | cosmetic | 13 June 2017, 19:42:16 UTC |
| cba4e5d | deren | 13 June 2017, 19:41:57 UTC | ipa fix raxml | 13 June 2017, 19:41:57 UTC |
| 676c870 | deren | 13 June 2017, 19:41:06 UTC | ipa structure file clobber fix | 13 June 2017, 19:41:06 UTC |
| d901afc | deren | 13 June 2017, 19:38:30 UTC | merge conflict | 13 June 2017, 19:38:30 UTC |
| d1d4eb4 | dereneaton | 13 June 2017, 18:33:53 UTC | update bpp notebook | 13 June 2017, 18:33:53 UTC |
| b1f1852 | dereneaton | 13 June 2017, 17:08:44 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 13 June 2017, 17:08:44 UTC |
| 5c2767f | dereneaton | 13 June 2017, 17:08:34 UTC | ipa analysis updates | 13 June 2017, 17:08:34 UTC |
| c0ab851 | dereneaton | 13 June 2017, 17:08:08 UTC | cleaner API attr on structure object | 13 June 2017, 17:08:08 UTC |
| b08c142 | dereneaton | 13 June 2017, 17:07:49 UTC | cleaner API attr on raxml object | 13 June 2017, 17:07:49 UTC |
| 5e4ca60 | dereneaton | 13 June 2017, 17:07:30 UTC | cleaner API attr on bpp object | 13 June 2017, 17:07:30 UTC |
| a45c81c | Isaac Overcast | 09 June 2017, 19:06:46 UTC | Adding docs for the -t flag. | 09 June 2017, 19:06:46 UTC |
| 52d659e | dereneaton | 09 June 2017, 17:26:05 UTC | bpp notebook update: | 09 June 2017, 17:26:05 UTC |
| f87f0df | dereneaton | 09 June 2017, 17:20:47 UTC | bpp notebook update: | 09 June 2017, 17:20:47 UTC |
| ed3c915 | dereneaton | 09 June 2017, 16:58:18 UTC | updated tetrad notebook | 09 June 2017, 16:58:18 UTC |
| 372dd17 | dereneaton | 09 June 2017, 16:43:21 UTC | updated analysis notebooks | 09 June 2017, 16:43:21 UTC |
| 61a0fa7 | dereneaton | 09 June 2017, 16:42:14 UTC | merge conflict resolve | 09 June 2017, 16:42:14 UTC |
| b4224cd | dereneaton | 09 June 2017, 16:38:44 UTC | toying with new save/load structure | 09 June 2017, 16:38:44 UTC |
| 1ff323e | dereneaton | 09 June 2017, 16:38:22 UTC | cosmetic | 09 June 2017, 16:38:22 UTC |
| 6550302 | dereneaton | 09 June 2017, 16:37:58 UTC | consens bug fix | 09 June 2017, 16:37:58 UTC |
| 87607d2 | dereneaton | 09 June 2017, 16:37:32 UTC | added general Params object to utils. Currently used in analysis tools, future should replace the ObjDict object in ipyrad | 09 June 2017, 16:37:32 UTC |
| 61cfee4 | dereneaton | 09 June 2017, 16:36:44 UTC | cosmetic | 09 June 2017, 16:36:44 UTC |
| 90a41aa | dereneaton | 09 June 2017, 16:36:30 UTC | cosmetic | 09 June 2017, 16:36:30 UTC |
| 8d7ad1e | dereneaton | 09 June 2017, 15:27:37 UTC | replaced params object in structure analysis tools and fixed so rep jobs to do not overwrite | 09 June 2017, 15:27:37 UTC |
| ca36416 | dereneaton | 09 June 2017, 15:27:02 UTC | changed bpp command to run() in analysis tools | 09 June 2017, 15:27:02 UTC |
| 7fbf592 | dereneaton | 09 June 2017, 15:26:36 UTC | cleaner raxml object in analysis tools | 09 June 2017, 15:26:36 UTC |
| 485f89a | dereneaton | 09 June 2017, 15:26:04 UTC | cosmetic | 09 June 2017, 15:26:04 UTC |
| 286d7bd | dereneaton | 06 June 2017, 18:47:34 UTC | cosmetic | 06 June 2017, 18:47:34 UTC |
| 4dc3acf | Isaac Overcast | 05 June 2017, 20:20:34 UTC | Fix bad link in docs. | 05 June 2017, 20:20:34 UTC |
| 3878b06 | Isaac Overcast | 03 June 2017, 18:46:17 UTC | "Updating ipyrad/__init__.py to version - 0.6.27 | 03 June 2017, 18:46:17 UTC |
| 381118f | Isaac Overcast | 03 June 2017, 18:45:57 UTC | Step 6 import fullcomp from util. | 03 June 2017, 18:45:57 UTC |
| 8dbadd1 | Isaac Overcast | 01 June 2017, 18:42:00 UTC | "Updating ipyrad/__init__.py to version - 0.6.26 | 01 June 2017, 18:42:00 UTC |
| 4f5e112 | Isaac Overcast | 01 June 2017, 18:41:45 UTC | Step 4 - Handle the case where no clusters have sufficient depth for statistical basecalling. | 01 June 2017, 18:41:45 UTC |
| b3839d8 | Isaac Overcast | 30 May 2017, 20:44:44 UTC | "Updating ipyrad/__init__.py to version - 0.6.25 | 30 May 2017, 20:44:44 UTC |
| e2836b5 | isaacovercast | 30 May 2017, 18:21:05 UTC | Fix a bug in refmap that was retaining the reference sequence in the final clust file on rare occasions. | 30 May 2017, 18:21:05 UTC |
| fd262b7 | Isaac Overcast | 25 May 2017, 18:11:33 UTC | "Updating ipyrad/__init__.py to version - 0.6.24 | 25 May 2017, 18:11:33 UTC |
| 9e1a638 | Deren Eaton | 25 May 2017, 12:37:23 UTC | Bug fix for "numpq" nameerror fix for dumb typo error | 25 May 2017, 12:37:23 UTC |
| 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 |
| 222469f | deren | 17 May 2017, 19:21:39 UTC | better method to find raxml binary in analysis tools | 17 May 2017, 19:21:39 UTC |
| 380d500 | deren | 17 May 2017, 19:21:09 UTC | consens bugfix for new ipmlementation | 17 May 2017, 19:21:09 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 |
| 6d28b2f | deren | 15 May 2017, 17:30:11 UTC | ensure h5 files are closed after dask func | 15 May 2017, 17:30:11 UTC |
| 2525bba | deren | 15 May 2017, 17:29:41 UTC | fix to parse chrom pos info from new consens name format | 15 May 2017, 17:29:41 UTC |
| 0ab3d3c | deren | 15 May 2017, 16:52:30 UTC | removed deprecated align funcs | 15 May 2017, 16:52:30 UTC |
| a4332b3 | deren | 15 May 2017, 16:52:09 UTC | removed hardcoded path used in testing | 15 May 2017, 16:52:09 UTC |
| e9545ae | deren | 15 May 2017, 16:51:43 UTC | removed deprecated align funcs. Made it so build_clusters() does nothing for 'reference' method since there is a separate method in ref for chunking clusters | 15 May 2017, 16:51:43 UTC |
| 7b18e52 | deren | 15 May 2017, 15:59:58 UTC | some new simpler merge funcs | 15 May 2017, 15:59:58 UTC |
| efe0616 | deren | 15 May 2017, 15:59:25 UTC | make new ref funcs work with dag map | 15 May 2017, 15:59:25 UTC |
| 71ddf91 | deren | 15 May 2017, 15:59:03 UTC | new build funcs usign pysam | 15 May 2017, 15:59:03 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 |
