| 8c557c4 | Isaac Overcast | 27 July 2017, 21:51:38 UTC | "Updating ipyrad/__init__.py to version - 0.7.7 | 27 July 2017, 21:51:38 UTC |
| 498dfb1 | Isaac Overcast | 27 July 2017, 21:50:32 UTC | Proper support for demux 2brad. | 27 July 2017, 21:50:32 UTC |
| 6796fe5 | Isaac Overcast | 27 July 2017, 21:25:37 UTC | "Updating ipyrad/__init__.py to version - 0.7.6 | 27 July 2017, 21:25:37 UTC |
| f85a3aa | Isaac Overcast | 27 July 2017, 21:23:28 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 27 July 2017, 21:23:28 UTC |
| 9e90504 | Isaac Overcast | 27 July 2017, 21:23:11 UTC | Fix very nasty refmap SE bug. | 27 July 2017, 21:23:11 UTC |
| 50b1260 | dereneaton | 27 July 2017, 21:08:55 UTC | update tutorials -- added APIs | 27 July 2017, 21:08:55 UTC |
| a7c0e16 | dereneaton | 27 July 2017, 20:39:42 UTC | update tutorials -- added APIs | 27 July 2017, 20:39:42 UTC |
| 88307ac | dereneaton | 27 July 2017, 18:29:12 UTC | cosmetic | 27 July 2017, 18:29:12 UTC |
| 05cd6ee | dereneaton | 27 July 2017, 18:22:39 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 27 July 2017, 18:22:39 UTC |
| a5be09e | dereneaton | 27 July 2017, 18:22:21 UTC | testing MBL slideshow | 27 July 2017, 18:22:21 UTC |
| 165381c | deren | 27 July 2017, 17:21:13 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 27 July 2017, 17:21:13 UTC |
| bc44aa7 | deren | 27 July 2017, 17:21:08 UTC | API cookbooks updated | 27 July 2017, 17:21:08 UTC |
| 837cc90 | dereneaton | 27 July 2017, 15:54:23 UTC | cosmetic | 27 July 2017, 15:54:23 UTC |
| dcd95d7 | dereneaton | 27 July 2017, 14:02:03 UTC | cleanup of badnames in sratools | 27 July 2017, 14:02:03 UTC |
| 8ceb872 | Isaac Overcast | 26 July 2017, 23:18:41 UTC | "Updating ipyrad/__init__.py to version - 0.7.5 | 26 July 2017, 23:18:41 UTC |
| 049dee4 | Isaac Overcast | 26 July 2017, 23:08:21 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 26 July 2017, 23:08:21 UTC |
| c3c4ee2 | Isaac Overcast | 26 July 2017, 23:08:07 UTC | Added error handling in persistent_popen_align3 | 26 July 2017, 23:08:07 UTC |
| e9888c6 | Isaac Overcast | 26 July 2017, 23:06:16 UTC | Catch bad seeds in step 6 sub_build_clustbits(). | 26 July 2017, 23:06:16 UTC |
| d48e6a7 | Isaac Overcast | 26 July 2017, 17:25:46 UTC | "Updating ipyrad/__init__.py to version - 0.7.4 | 26 July 2017, 17:25:46 UTC |
| 274456d | Isaac Overcast | 26 July 2017, 17:25:23 UTC | Actually fix the step 6 boolean mask error. | 26 July 2017, 17:25:23 UTC |
| 2a0c711 | Isaac Overcast | 26 July 2017, 15:32:36 UTC | Fix for boolean mask array length bug in step 6. | 26 July 2017, 15:32:36 UTC |
| 71c4efd | dereneaton | 25 July 2017, 14:30:59 UTC | add -noss option for treemix ipa | 25 July 2017, 14:30:59 UTC |
| 9647435 | dereneaton | 25 July 2017, 14:30:30 UTC | mods to tetrad and sratools ipa | 25 July 2017, 14:30:30 UTC |
| 5423ec5 | dereneaton | 25 July 2017, 02:44:30 UTC | ensure ints not floats for high depth base counts | 25 July 2017, 02:44:30 UTC |
| ede73f7 | dereneaton | 24 July 2017, 21:47:16 UTC | sratools updates | 24 July 2017, 21:47:16 UTC |
| a679337 | dereneaton | 24 July 2017, 21:23:46 UTC | improvements to sratools | 24 July 2017, 21:23:46 UTC |
| 759e1e3 | dereneaton | 24 July 2017, 21:04:42 UTC | added extra line ending to step7 final print statement | 24 July 2017, 21:04:42 UTC |
| 4d82271 | dereneaton | 24 July 2017, 21:03:34 UTC | add dask to environment.yaml | 24 July 2017, 21:03:34 UTC |
| 2e6bfcb | dereneaton | 24 July 2017, 21:03:13 UTC | added sratools to ipyrad.analysis | 24 July 2017, 21:03:13 UTC |
| f3ce615 | Isaac Overcast | 23 July 2017, 22:28:30 UTC | "Updating ipyrad/__init__.py to version - 0.7.3 | 23 July 2017, 22:28:30 UTC |
| 231e94f | Isaac Overcast | 23 July 2017, 22:28:11 UTC | Better handling for restarting jobs in substeps of step 6. | 23 July 2017, 22:28:11 UTC |
| c721ebb | Isaac Overcast | 23 July 2017, 19:21:35 UTC | Fixed the fscking pysam conda-build scripts for osx. | 23 July 2017, 19:21:35 UTC |
| dc3c3e2 | Isaac Overcast | 23 July 2017, 01:35:10 UTC | Add patch for pysam build on osx | 23 July 2017, 01:35:10 UTC |
| f4fb80a | Isaac Overcast | 23 July 2017, 01:05:31 UTC | Fix for conda-build v3 breaking meta.yaml | 23 July 2017, 01:05:31 UTC |
| f426352 | Isaac Overcast | 22 July 2017, 23:02:34 UTC | Using htslib internal to pysam and removing bcftools/htslib/samtools direct dependencies. | 22 July 2017, 23:02:34 UTC |
| 3ce2589 | Isaac Overcast | 22 July 2017, 18:13:54 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 22 July 2017, 18:13:54 UTC |
| ceb49ca | Isaac Overcast | 22 July 2017, 18:13:49 UTC | Add force flag to force building clusters if utemp exists. | 22 July 2017, 18:13:49 UTC |
| 3a6f6a0 | dereneaton | 20 July 2017, 19:15:16 UTC | conda recipe updates | 20 July 2017, 19:15:16 UTC |
| 0861d3d | dereneaton | 20 July 2017, 18:02:50 UTC | updateing conda recipe | 20 July 2017, 18:02:50 UTC |
| ba62bd7 | dereneaton | 14 July 2017, 17:32:51 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 14 July 2017, 17:32:51 UTC |
| 16ff54f | dereneaton | 14 July 2017, 17:32:40 UTC | ensure stats are saved as floats | 14 July 2017, 17:32:40 UTC |
| 2a11172 | dereneaton | 14 July 2017, 17:32:14 UTC | fix to bug introduced just now to track progress during s6 clustering | 14 July 2017, 17:32:14 UTC |
| 5b9aa7c | Isaac Overcast | 12 July 2017, 20:27:56 UTC | Fix an issue with merged assemblies and 3rad. | 12 July 2017, 20:27:56 UTC |
| 62b4bd7 | dereneaton | 11 July 2017, 20:54:55 UTC | fix for step 6 checkpoints for reference-based analyses | 11 July 2017, 20:54:55 UTC |
| ede163f | dereneaton | 11 July 2017, 19:43:10 UTC | conda recipe tweaking | 11 July 2017, 19:43:10 UTC |
| de70f18 | dereneaton | 11 July 2017, 19:03:02 UTC | conda recipe updates | 11 July 2017, 19:03:02 UTC |
| b4bf8be | dereneaton | 11 July 2017, 18:17:52 UTC | fix to conda recipes | 11 July 2017, 18:17:52 UTC |
| 19227c1 | dereneaton | 11 July 2017, 14:46:09 UTC | cosmetic | 11 July 2017, 14:46:09 UTC |
| 4ded84a | dereneaton | 11 July 2017, 14:41:11 UTC | update bucky cookbook | 11 July 2017, 14:41:11 UTC |
| edf4f50 | deren | 11 July 2017, 14:29:20 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 11 July 2017, 14:29:20 UTC |
| 07324ed | deren | 11 July 2017, 14:00:04 UTC | added shareplot code | 11 July 2017, 14:00:04 UTC |
| 111463d | dereneaton | 10 July 2017, 20:58:13 UTC | bucky ipa update remove old files | 10 July 2017, 20:58:13 UTC |
| c48bf6d | dereneaton | 10 July 2017, 20:57:22 UTC | conda recipe updated | 10 July 2017, 20:57:22 UTC |
| 4b9eea6 | dereneaton | 10 July 2017, 20:52:21 UTC | "Updating ipyrad/__init__.py to version - 0.7.2 | 10 July 2017, 20:52:21 UTC |
| 1a77758 | dereneaton | 10 July 2017, 19:38:08 UTC | update conda recipe | 10 July 2017, 19:38:08 UTC |
| 98da62f | dereneaton | 10 July 2017, 19:18:39 UTC | update pysam to correct version | 10 July 2017, 19:18:39 UTC |
| 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 |
