| 8613ffe | dereneaton | 10 July 2017, 18:54:17 UTC | "Updating ipyrad/__init__.py to version - 0.7.2 | 10 July 2017, 18:54:17 UTC |
| e8f1312 | dereneaton | 10 July 2017, 18:47:36 UTC | bucky cookbook up | 10 July 2017, 18:47:36 UTC |
| aee7497 | dereneaton | 10 July 2017, 18:43:19 UTC | bucky cookbook up | 10 July 2017, 18:43:19 UTC |
| 008ec71 | dereneaton | 10 July 2017, 18:39:12 UTC | check multiple barcodes in samples that were merge of technical replicates | 10 July 2017, 18:39:12 UTC |
| 2c746aa | dereneaton | 10 July 2017, 18:38:51 UTC | merge technical replicates in demux | 10 July 2017, 18:38:51 UTC |
| 1a7e737 | dereneaton | 10 July 2017, 18:38:24 UTC | spacer fixing and fix for alleles output error | 10 July 2017, 18:38:24 UTC |
| 3347ff5 | dereneaton | 10 July 2017, 18:37:26 UTC | added checkpointing to step 6. Added cli detection for better spacer printing. Allow merging of technical replicates in barcodes file. | 10 July 2017, 18:37:26 UTC |
| 5189326 | dereneaton | 10 July 2017, 18:36:12 UTC | update spacers | 10 July 2017, 18:36:12 UTC |
| 7152a0f | dereneaton | 10 July 2017, 18:35:48 UTC | added bucky ipa code | 10 July 2017, 18:35:48 UTC |
| fd5b835 | dereneaton | 10 July 2017, 18:35:26 UTC | bpp bug fixes full path names | 10 July 2017, 18:35:26 UTC |
| 7e1fd27 | dereneaton | 10 July 2017, 18:33:11 UTC | API userguide merge | 10 July 2017, 18:33:11 UTC |
| 65e03f8 | dereneaton | 30 June 2017, 21:21:58 UTC | API user guide docs | 30 June 2017, 21:21:58 UTC |
| a56f123 | deren | 26 June 2017, 23:11:17 UTC | cookbook API userguide | 26 June 2017, 23:11:17 UTC |
| 19e041d | deren | 26 June 2017, 22:54:40 UTC | require >=11.2 pysam version | 26 June 2017, 22:54:40 UTC |
| 45161a3 | deren | 26 June 2017, 22:50:26 UTC | min checkpoint is actually 1 not 0 | 26 June 2017, 22:50:26 UTC |
| b623d6f | deren | 26 June 2017, 22:38:35 UTC | cosmetic -- spacers | 26 June 2017, 22:38:35 UTC |
| 66b0c9a | deren | 26 June 2017, 22:38:06 UTC | cosmetic -- spacers | 26 June 2017, 22:38:06 UTC |
| 46c3691 | deren | 26 June 2017, 22:31:14 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 26 June 2017, 22:31:14 UTC |
| 18391c6 | deren | 26 June 2017, 22:31:08 UTC | cookcook updates tetrad and treemix | 26 June 2017, 22:31:08 UTC |
| 32fd9fd | deren | 26 June 2017, 22:30:28 UTC | added some not-yet-implemented code, and some cosmetic changes | 26 June 2017, 22:30:28 UTC |
| dfc9af4 | deren | 26 June 2017, 22:25:00 UTC | cosmetic | 26 June 2017, 22:25:00 UTC |
| 65bf3b8 | deren | 26 June 2017, 22:24:34 UTC | new _cli, _checkpoint, and _spacer attributes, and new 'across' dir for step 6 | 26 June 2017, 22:24:34 UTC |
| ac37f49 | deren | 26 June 2017, 22:23:28 UTC | load sets cli=False by default, and it saves checkpoint info | 26 June 2017, 22:23:28 UTC |
| bbe437f | deren | 26 June 2017, 22:22:51 UTC | allow profile with ipcluster | 26 June 2017, 22:22:51 UTC |
| 5a6e571 | deren | 26 June 2017, 22:22:19 UTC | spacers for progress bars | 26 June 2017, 22:22:19 UTC |
| 14e0d35 | deren | 26 June 2017, 22:22:03 UTC | spacers for progress bars | 26 June 2017, 22:22:03 UTC |
| 5e3149b | deren | 26 June 2017, 22:21:45 UTC | built in checkpointing for step 6 | 26 June 2017, 22:21:45 UTC |
| b44a057 | deren | 26 June 2017, 22:21:09 UTC | spacers in progress bars | 26 June 2017, 22:21:09 UTC |
| 2fde7f9 | deren | 26 June 2017, 22:20:43 UTC | treemix report if no data is written (i.e., all filtered) | 26 June 2017, 22:20:43 UTC |
| bcf42c8 | deren | 26 June 2017, 22:20:04 UTC | fix to allow setting nquartets again. Better integration of API/CLI. Spacer for progress bars. Bug fix to Tree drawing when no boots. Fix for compatibility with new toytree rooting bug fix for saving features. | 26 June 2017, 22:20:04 UTC |
| 7531e7c | deren | 26 June 2017, 22:18:25 UTC | CLI now allows for profile name for ipcluster | 26 June 2017, 22:18:25 UTC |
| 7dd9bdd | deren | 26 June 2017, 22:17:40 UTC | cli is now an attribute of the Assembly object that is set to True by __main__ at runtime, otherwise 0. | 26 June 2017, 22:17:40 UTC |
| 9446d64 | deren | 26 June 2017, 22:16:45 UTC | cluster_info() now prints instead of return | 26 June 2017, 22:16:45 UTC |
| d221f0d | dereneaton | 22 June 2017, 16:49:24 UTC | rehaul of bucky ipa tools | 22 June 2017, 16:49:24 UTC |
| acf003a | dereneaton | 21 June 2017, 17:47:18 UTC | prin cluster_info now skips busy engines | 21 June 2017, 17:47:18 UTC |
| ca78d49 | dereneaton | 21 June 2017, 17:46:38 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 21 June 2017, 17:46:38 UTC |
| a620510 | dereneaton | 21 June 2017, 17:46:34 UTC | unroot tetrad tree on complete | 21 June 2017, 17:46:34 UTC |
| 8038c6b | deren | 20 June 2017, 21:14:35 UTC | cosmetic | 20 June 2017, 21:14:35 UTC |
| 93e97f7 | Isaac Overcast | 16 June 2017, 22:01:09 UTC | "Updating ipyrad/__init__.py to version - 0.7.1 | 16 June 2017, 22:01:09 UTC |
| 785ba8a | Isaac Overcast | 16 June 2017, 22:00:57 UTC | Actually handle SE reference sequence clustering. | 16 June 2017, 22:00:57 UTC |
| b0139ca | Isaac Overcast | 16 June 2017, 21:58:21 UTC | Prevent empty clust files from raising an error. Probably only impacts sim data. | 16 June 2017, 21:58:21 UTC |
| ab773b5 | Isaac Overcast | 16 June 2017, 21:02:28 UTC | If debug the retain the bed regions per sample as a file in the refmap directory. | 16 June 2017, 21:02:28 UTC |
| 0e49754 | dereneaton | 16 June 2017, 20:15:17 UTC | updated tunnel docs | 16 June 2017, 20:15:17 UTC |
| 8c9781c | dereneaton | 16 June 2017, 17:53:16 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 16 June 2017, 17:53:16 UTC |
| 59cabec | dereneaton | 16 June 2017, 17:53:14 UTC | HPC tunnel update | 16 June 2017, 17:53:14 UTC |
| 1c73471 | deren | 16 June 2017, 17:52:06 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 16 June 2017, 17:52:06 UTC |
| 29b9bac | deren | 16 June 2017, 17:51:46 UTC | cosmetic | 16 June 2017, 17:51:46 UTC |
| 0469f71 | deren | 16 June 2017, 17:51:33 UTC | support for parsing supervised structure analyses in ipa | 16 June 2017, 17:51:33 UTC |
| a7e4ed8 | dereneaton | 16 June 2017, 17:30:04 UTC | HPC tunnel docs update | 16 June 2017, 17:30:04 UTC |
| 9bb2321 | dereneaton | 16 June 2017, 17:04:18 UTC | update analysis docs | 16 June 2017, 17:04:18 UTC |
| bba05bb | dereneaton | 16 June 2017, 16:24:42 UTC | update analysis docs | 16 June 2017, 16:24:42 UTC |
| 414df13 | dereneaton | 16 June 2017, 16:14:30 UTC | update analysis docs | 16 June 2017, 16:14:30 UTC |
| 9ff06e6 | dereneaton | 16 June 2017, 16:09:32 UTC | update analysis docs | 16 June 2017, 16:09:32 UTC |
| 56630b9 | dereneaton | 16 June 2017, 07:03:15 UTC | ipa.treemix params | 16 June 2017, 07:03:15 UTC |
| c1fccc3 | dereneaton | 16 June 2017, 07:02:51 UTC | cosmetic | 16 June 2017, 07:02:51 UTC |
| 0c70d86 | dereneaton | 16 June 2017, 06:43:32 UTC | more params added to ipa.treemix | 16 June 2017, 06:43:32 UTC |
| f626ec0 | dereneaton | 16 June 2017, 06:42:53 UTC | cosmetic | 16 June 2017, 06:42:53 UTC |
| d6200fc | dereneaton | 16 June 2017, 06:38:37 UTC | cookbook update treemix | 16 June 2017, 06:38:37 UTC |
| f909397 | dereneaton | 16 June 2017, 05:04:00 UTC | fix to conda rec | 16 June 2017, 05:04:00 UTC |
| 1a93c47 | dereneaton | 15 June 2017, 23:25:55 UTC | treemix ipa updates | 15 June 2017, 23:25:55 UTC |
| 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 |
