| a74d5c8 | Isaac Overcast | 24 December 2019, 15:08:31 UTC | "Updating ipyrad/__init__.py to version - 0.9.23 | 24 December 2019, 15:08:31 UTC |
| d0c8c97 | Isaac Overcast | 24 December 2019, 15:07:53 UTC | Regress baba.py | 24 December 2019, 15:07:53 UTC |
| aba941c | Isaac Overcast | 23 December 2019, 13:55:43 UTC | "Updating ipyrad/__init__.py to version - 0.9.22 | 23 December 2019, 13:55:43 UTC |
| b87aea0 | Isaac Overcast | 23 December 2019, 13:55:25 UTC | Add support for .ugeno file | 23 December 2019, 13:55:25 UTC |
| 77603a7 | Isaac Overcast | 23 December 2019, 13:29:32 UTC | Add support for .ustr format | 23 December 2019, 13:29:32 UTC |
| a927361 | Isaac Overcast | 23 December 2019, 12:53:38 UTC | Remove duplication of code in write_str() | 23 December 2019, 12:53:38 UTC |
| 6cb4d20 | Isaac Overcast | 23 December 2019, 11:18:29 UTC | Fix docs for output formats | 23 December 2019, 11:18:29 UTC |
| a612a22 | Isaac Overcast | 23 December 2019, 10:52:28 UTC | Add back output formats documentation | 23 December 2019, 10:52:28 UTC |
| 7c99f88 | Isaac Overcast | 23 December 2019, 10:39:11 UTC | "Updating ipyrad/__init__.py to version - 0.9.21 | 23 December 2019, 10:39:11 UTC |
| 9fbbb95 | Isaac Overcast | 23 December 2019, 10:38:54 UTC | Fix stupid bug introduced by fe8c2dfc282e177a7c18f6e2e23ef84d284a9e3f | 23 December 2019, 10:38:54 UTC |
| c0b5107 | Isaac Overcast | 18 December 2019, 19:12:07 UTC | "Updating ipyrad/__init__.py to version - 0.9.20 | 18 December 2019, 19:12:07 UTC |
| 6243086 | Isaac Overcast | 18 December 2019, 19:11:41 UTC | Expose analysis.baba for testing | 18 December 2019, 19:11:41 UTC |
| fe8c2df | Isaac Overcast | 09 December 2019, 22:42:18 UTC | Fix bug in handling sample names in the pops file. re: #375. | 09 December 2019, 22:42:18 UTC |
| b631bd5 | Isaac Overcast | 04 December 2019, 15:14:47 UTC | Allow faidict scaffold names to be int (cast to dtype=object) | 04 December 2019, 15:14:47 UTC |
| 5d8f164 | Isaac Overcast | 03 December 2019, 15:56:14 UTC | "Updating ipyrad/__init__.py to version - 0.9.19 | 03 December 2019, 15:56:14 UTC |
| ccc30ac | Isaac Overcast | 03 December 2019, 15:55:28 UTC | Fix step 6 with pop_assign_file | 03 December 2019, 15:55:28 UTC |
| ceb3809 | dereneaton | 01 December 2019, 22:32:11 UTC | fix for empty samples after align | 01 December 2019, 22:32:11 UTC |
| cc4fb0a | dereneaton | 30 November 2019, 05:05:08 UTC | list missing as ./. in VCF (like we used to) | 30 November 2019, 05:05:08 UTC |
| 96baf7e | Isaac Overcast | 23 November 2019, 12:00:45 UTC | "Updating ipyrad/__init__.py to version - 0.9.18 | 23 November 2019, 12:00:45 UTC |
| fe418f2 | Isaac Overcast | 23 November 2019, 11:59:21 UTC | Fix oops handling missing data in vcf to hdf5 | 23 November 2019, 11:59:21 UTC |
| e2931ef | eaton-lab | 14 November 2019, 17:09:29 UTC | mb binary path bugfix | 14 November 2019, 17:09:29 UTC |
| 29f6239 | eaton-lab | 14 November 2019, 17:06:04 UTC | treeslider mb bugfix | 14 November 2019, 17:06:04 UTC |
| 2c4848f | eaton-lab | 14 November 2019, 16:32:44 UTC | treeslider mb working | 14 November 2019, 16:32:44 UTC |
| 0ddde26 | eaton-lab | 14 November 2019, 15:47:56 UTC | treemix support for conda env installations | 14 November 2019, 15:47:56 UTC |
| bb46547 | eaton-lab | 13 November 2019, 21:34:38 UTC | additional drawing options for pca | 13 November 2019, 21:34:38 UTC |
| b4dbd18 | eaton-lab | 13 November 2019, 21:31:24 UTC | additional drawing options for pca | 13 November 2019, 21:31:24 UTC |
| f09f30b | eaton-lab | 06 November 2019, 20:10:59 UTC | raxml cookbook update | 06 November 2019, 20:10:59 UTC |
| 4e7c71e | dereneaton | 05 November 2019, 21:51:34 UTC | tetrad notebook | 05 November 2019, 21:51:34 UTC |
| b991f9a | eaton-lab | 05 November 2019, 21:26:52 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 05 November 2019, 21:26:52 UTC |
| 1695c06 | eaton-lab | 05 November 2019, 21:21:55 UTC | tetrad notebook updated | 05 November 2019, 21:21:55 UTC |
| 0efbf54 | Isaac Overcast | 05 November 2019, 17:55:20 UTC | Fix oops in params.py checking for lowercase overhangs seqs | 05 November 2019, 17:55:20 UTC |
| 7c57138 | Isaac Overcast | 05 November 2019, 16:42:21 UTC | Fix a nasty stupid bug setting the overhang sequence | 05 November 2019, 16:42:21 UTC |
| 10bb0a0 | Isaac Overcast | 05 November 2019, 15:27:33 UTC | Add back the docs about merging | 05 November 2019, 15:27:33 UTC |
| fb65bcf | Isaac Overcast | 05 November 2019, 14:13:05 UTC | Error checking in step 5. | 05 November 2019, 14:13:05 UTC |
| 4697825 | Isaac Overcast | 05 November 2019, 13:28:37 UTC | Forbid lowercase in overhang sequence | 05 November 2019, 13:28:37 UTC |
| 3361400 | Isaac Overcast | 04 November 2019, 13:50:23 UTC | "Updating ipyrad/__init__.py to version - 0.9.17 | 04 November 2019, 13:50:23 UTC |
| 6937de9 | Isaac Overcast | 04 November 2019, 13:49:48 UTC | Ooops. Allow popsfile w/o crashing, and allow populations to be integer values | 04 November 2019, 13:49:48 UTC |
| 8d9399d | eaton-lab | 03 November 2019, 17:58:21 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 03 November 2019, 17:58:21 UTC |
| e540e63 | eaton-lab | 03 November 2019, 17:58:13 UTC | cookbooks added link to nb | 03 November 2019, 17:58:13 UTC |
| fbb988a | eaton-lab | 03 November 2019, 17:57:38 UTC | pca stores results as attr instead or returning | 03 November 2019, 17:57:38 UTC |
| a575a17 | Isaac Overcast | 31 October 2019, 18:57:28 UTC | "Updating ipyrad/__init__.py to version - 0.9.16 | 31 October 2019, 18:57:28 UTC |
| 0062568 | Isaac Overcast | 31 October 2019, 18:55:45 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 31 October 2019, 18:55:45 UTC |
| ebeb82c | Isaac Overcast | 31 October 2019, 18:55:36 UTC | commented fix of optim chunksize calc | 31 October 2019, 18:55:36 UTC |
| 7f6e8c7 | eaton-lab | 30 October 2019, 21:12:24 UTC | treeslider now working with mb | 30 October 2019, 21:12:24 UTC |
| 017e993 | eaton-lab | 30 October 2019, 21:12:01 UTC | toggle to write in nexus | 30 October 2019, 21:12:01 UTC |
| 7c702c2 | eaton-lab | 30 October 2019, 21:11:37 UTC | note TODO | 30 October 2019, 21:11:37 UTC |
| 824ca06 | eaton-lab | 30 October 2019, 21:11:19 UTC | mb saves convergence stats as df | 30 October 2019, 21:11:19 UTC |
| cec6a00 | eaton-lab | 30 October 2019, 13:07:07 UTC | link fixed | 30 October 2019, 13:07:07 UTC |
| 5bd1340 | eaton-lab | 29 October 2019, 21:51:08 UTC | single-end mapping infiles bugfix | 29 October 2019, 21:51:08 UTC |
| 82107f4 | eaton-lab | 29 October 2019, 19:42:49 UTC | pca cookbook update | 29 October 2019, 19:42:49 UTC |
| d412b60 | eaton-lab | 29 October 2019, 16:50:01 UTC | added fasttree tool | 29 October 2019, 16:50:01 UTC |
| 986f6ab | eaton-lab | 29 October 2019, 16:41:56 UTC | update cookbooks index | 29 October 2019, 16:41:56 UTC |
| aed37bf | eaton-lab | 29 October 2019, 16:35:58 UTC | cookbooks updated headers | 29 October 2019, 16:35:58 UTC |
| 1bb28f7 | eaton-lab | 29 October 2019, 16:23:10 UTC | warning about denovo-ref to use new param | 29 October 2019, 16:23:10 UTC |
| 129453d | eaton-lab | 29 October 2019, 16:21:05 UTC | clustmap keeps i5s and can do ref minus | 29 October 2019, 16:21:05 UTC |
| 3733867 | eaton-lab | 28 October 2019, 05:46:42 UTC | window extracter newdocs update | 28 October 2019, 05:46:42 UTC |
| 081ae76 | eaton-lab | 28 October 2019, 05:46:19 UTC | cosmetic | 28 October 2019, 05:46:19 UTC |
| 78efec5 | eaton-lab | 28 October 2019, 05:46:04 UTC | window extracter updated | 28 October 2019, 05:46:04 UTC |
| 2ca2ed7 | eaton-lab | 28 October 2019, 01:41:41 UTC | cosmetic | 28 October 2019, 01:41:41 UTC |
| 89bd878 | eaton-lab | 28 October 2019, 01:41:28 UTC | mb load existing results and bugfix result paths | 28 October 2019, 01:41:28 UTC |
| 0584faf | eaton-lab | 28 October 2019, 01:40:45 UTC | cosmetic | 28 October 2019, 01:40:45 UTC |
| cbf9f8e | eaton-lab | 28 October 2019, 01:40:32 UTC | cosmetic | 28 October 2019, 01:40:32 UTC |
| 22c0550 | eaton-lab | 28 October 2019, 01:37:50 UTC | update mb docs | 28 October 2019, 01:37:50 UTC |
| 90ece92 | eaton-lab | 27 October 2019, 21:24:04 UTC | update treemix and mb docs | 27 October 2019, 21:24:04 UTC |
| c6fdb52 | Isaac Overcast | 26 October 2019, 22:08:14 UTC | Fix calculation of optim during step 6 aligning. 3-4x speedup on this medium sized simulated data i'm working on. | 26 October 2019, 22:08:14 UTC |
| 44e2b3a | Isaac Overcast | 26 October 2019, 21:46:02 UTC | Fix oops in how optim was being counted. Was counting using _unsorted_ seed handle, I switched it to use sorted and now it works more like expected | 26 October 2019, 21:46:02 UTC |
| ec3574e | Isaac Overcast | 26 October 2019, 19:57:10 UTC | Clean up clust.txt files after step 3 finishes | 26 October 2019, 19:57:10 UTC |
| 3c6fbea | Isaac Overcast | 26 October 2019, 19:35:33 UTC | Update docs and parameter descriptions to reflect new reality of several params | 26 October 2019, 19:35:33 UTC |
| efdff88 | Isaac Overcast | 25 October 2019, 16:51:13 UTC | Add handlers for denovo +/- reference. | 25 October 2019, 16:51:13 UTC |
| da7d65d | eaton-lab | 24 October 2019, 20:31:36 UTC | vcf tool docs | 24 October 2019, 20:31:36 UTC |
| 2020158 | eaton-lab | 24 October 2019, 20:25:19 UTC | tools docs update | 24 October 2019, 20:25:19 UTC |
| ac17502 | eaton-lab | 24 October 2019, 20:24:57 UTC | enable vcf_to_hdf5 | 24 October 2019, 20:24:57 UTC |
| 4bd271e | eaton-lab | 24 October 2019, 20:24:40 UTC | pca reps legend looks nice | 24 October 2019, 20:24:40 UTC |
| 85d86fa | eaton-lab | 24 October 2019, 19:37:18 UTC | cosmetic | 24 October 2019, 19:37:18 UTC |
| 2e64072 | eaton-lab | 24 October 2019, 19:37:04 UTC | cosmetic | 24 October 2019, 19:37:04 UTC |
| 3260328 | eaton-lab | 24 October 2019, 19:36:41 UTC | cosmetic | 24 October 2019, 19:36:41 UTC |
| dd47619 | eaton-lab | 24 October 2019, 19:36:24 UTC | added replicate clouds to pca | 24 October 2019, 19:36:24 UTC |
| 3a5a190 | eaton-lab | 24 October 2019, 19:35:59 UTC | cosmetic | 24 October 2019, 19:35:59 UTC |
| 4b74dcb | eaton-lab | 24 October 2019, 19:35:21 UTC | vcf to hdf5 converter tested empirically | 24 October 2019, 19:35:21 UTC |
| 0a4231a | eaton-lab | 24 October 2019, 15:29:16 UTC | cosmetic | 24 October 2019, 15:29:16 UTC |
| c739cd9 | Isaac Overcast | 23 October 2019, 20:35:30 UTC | Add hils.py from the hotfix branch | 23 October 2019, 20:35:30 UTC |
| 72a5c26 | Isaac Overcast | 23 October 2019, 19:42:47 UTC | Pull from the correct repo inside meta.yaml | 23 October 2019, 19:42:47 UTC |
| b0fcf38 | eaton-lab | 22 October 2019, 16:44:24 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 22 October 2019, 16:44:24 UTC |
| 9e80825 | eaton-lab | 22 October 2019, 16:44:05 UTC | VCF 9's fixed to be . | 22 October 2019, 16:44:05 UTC |
| 0122416 | Isaac Overcast | 20 October 2019, 16:14:31 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 20 October 2019, 16:14:31 UTC |
| e1a0b27 | Isaac Overcast | 20 October 2019, 16:14:14 UTC | Add back tetrad docs | 20 October 2019, 16:14:14 UTC |
| 167efd1 | dereneaton | 16 October 2019, 19:02:33 UTC | default hackers set to yes merge tech reps, and cleanup | 16 October 2019, 19:02:33 UTC |
| 6f7517a | dereneaton | 16 October 2019, 19:01:02 UTC | behavior for duplicates in barcodes file | 16 October 2019, 19:01:02 UTC |
| eaa8353 | dereneaton | 16 October 2019, 19:00:31 UTC | bugfix: error reporting for barcodes within n | 16 October 2019, 19:00:31 UTC |
| 249b912 | eaton-lab | 16 October 2019, 17:42:39 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 16 October 2019, 17:42:39 UTC |
| c40d12d | eaton-lab | 15 October 2019, 19:41:39 UTC | find binary from env or user arg | 15 October 2019, 19:41:39 UTC |
| 767116e | eaton-lab | 15 October 2019, 19:39:24 UTC | find binary from env or user arg | 15 October 2019, 19:39:24 UTC |
| 7358fb9 | eaton-lab | 15 October 2019, 19:36:07 UTC | find binary from env or user arg | 15 October 2019, 19:36:07 UTC |
| 473a218 | eaton-lab | 15 October 2019, 19:33:24 UTC | find binary from env or user entered | 15 October 2019, 19:33:24 UTC |
| 788adcf | eaton-lab | 15 October 2019, 17:47:13 UTC | find ipcluster from conda env bin | 15 October 2019, 17:47:13 UTC |
| 112b58e | eaton-lab | 15 October 2019, 17:44:14 UTC | bugfix: allow demux i7s even if datatype=pair3rad | 15 October 2019, 17:44:14 UTC |
| aa9117e | Isaac Overcast | 13 October 2019, 15:29:52 UTC | add the notebook tunnel docs back | 13 October 2019, 15:29:52 UTC |
| 7767da0 | eaton-lab | 13 October 2019, 14:56:43 UTC | API docs update | 13 October 2019, 14:56:43 UTC |
| 88c1c73 | eaton-lab | 13 October 2019, 14:56:23 UTC | new api tutorial | 13 October 2019, 14:56:23 UTC |
| 41e636b | eaton-lab | 13 October 2019, 14:56:07 UTC | image in docs | 13 October 2019, 14:56:07 UTC |
