| 8fcf950 | Isaac Overcast | 12 January 2020, 18:42:30 UTC | "Updating ipyrad/__init__.py to version - 0.9.28 | 12 January 2020, 18:42:30 UTC |
| af9db3a | Isaac Overcast | 12 January 2020, 18:42:08 UTC | Fix versioner.py to actually record releasenotes | 12 January 2020, 18:42:08 UTC |
| d89fb35 | Isaac Overcast | 12 January 2020, 18:40:03 UTC | Fix releasenotes in versioner script | 12 January 2020, 18:40:03 UTC |
| ca251da | Isaac Overcast | 12 January 2020, 18:30:40 UTC | Fix releasenotes | 12 January 2020, 18:30:40 UTC |
| ea9bc83 | Isaac Overcast | 12 January 2020, 18:27:38 UTC | "Updating ipyrad/__init__.py to version - 0.9.27 | 12 January 2020, 18:27:38 UTC |
| ac038da | Isaac Overcast | 12 January 2020, 18:13:46 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 12 January 2020, 18:13:46 UTC |
| 904421d | Isaac Overcast | 12 January 2020, 18:13:37 UTC | Add all the old commit info that has been blanked since the switch to v.0.9 | 12 January 2020, 18:13:37 UTC |
| bb2deb9 | Isaac Overcast | 11 January 2020, 16:45:18 UTC | Update index.rst | 11 January 2020, 16:45:18 UTC |
| 843d501 | Isaac Overcast | 11 January 2020, 16:44:03 UTC | Update README.rst | 11 January 2020, 16:44:03 UTC |
| 6865d60 | Isaac Overcast | 11 January 2020, 16:43:03 UTC | Update README.rst | 11 January 2020, 16:43:03 UTC |
| 49753b5 | Isaac Overcast | 09 January 2020, 15:38:23 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 09 January 2020, 15:38:23 UTC |
| 4d2d65a | Isaac Overcast | 09 January 2020, 15:37:56 UTC | Tweek install directions to support new no change /home/isaac/miniconda3/condabin/conda no change /home/isaac/miniconda3/bin/conda no change /home/isaac/miniconda3/bin/conda-env no change /home/isaac/miniconda3/bin/activate no change /home/isaac/miniconda3/bin/deactivate no change /home/isaac/miniconda3/etc/profile.d/conda.sh no change /home/isaac/miniconda3/etc/fish/conf.d/conda.fish no change /home/isaac/miniconda3/shell/condabin/Conda.psm1 no change /home/isaac/miniconda3/shell/condabin/conda-hook.ps1 no change /home/isaac/miniconda3/lib/python3.7/site-packages/xontrib/conda.xsh no change /home/isaac/miniconda3/etc/profile.d/conda.csh no change /home/isaac/.bashrc No action taken. process | 09 January 2020, 15:37:56 UTC |
| b4d1e26 | Isaac Overcast | 08 January 2020, 15:08:52 UTC | Make hackersonly.exclude_reference default to True, since in most cases the reference sequence isn't 'real' data, and people won't want it included in downstream. | 08 January 2020, 15:08:52 UTC |
| 0306f25 | eaton-lab | 03 January 2020, 14:31:12 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 03 January 2020, 14:31:12 UTC |
| d12e720 | eaton-lab | 03 January 2020, 14:31:01 UTC | estimated inner mate distance does not work well for small and weird libraries, like digested reference samples, but seems to work well enough for real data. But maybe a default of 1000 would be reasonable unless overridden by hackers... leaving for now as estimate unless set by hackers. | 03 January 2020, 14:31:01 UTC |
| 5bc1f59 | eaton-lab | 03 January 2020, 14:25:14 UTC | digest genomes update after empiciral testing | 03 January 2020, 14:25:14 UTC |
| 0aaec41 | Isaac Overcast | 01 January 2020, 17:51:53 UTC | "Updating ipyrad/__init__.py to version - 0.9.26 | 01 January 2020, 17:51:53 UTC |
| 13947ec | Isaac Overcast | 01 January 2020, 17:51:26 UTC | During steps 5 & 6 honor the filter_min_trim_len parameter, which is useful in some cases (2brad). | 01 January 2020, 17:51:26 UTC |
| 116b58a | Isaac Overcast | 01 January 2020, 17:04:46 UTC | In step 3, force vsearch to honor the filter_min_trim_len param, otherwise it defaults to --minseqlength 32, which can be undesirable in some cases. | 01 January 2020, 17:04:46 UTC |
| eddfc9c | Isaac Overcast | 31 December 2019, 15:34:16 UTC | "Updating ipyrad/__init__.py to version - 0.9.25 | 31 December 2019, 15:34:16 UTC |
| ade66ba | Isaac Overcast | 31 December 2019, 15:33:00 UTC | concatedits files now write to the tmpdir, rather than edits (#378), also handle refmap samples with no reads that map to the reference, also change where edits files are pulling from during PE merging to allow for assembly merging after step 2. phew. | 31 December 2019, 15:33:00 UTC |
| 4a67db3 | eaton-lab | 30 December 2019, 23:37:07 UTC | cosmetic | 30 December 2019, 23:37:07 UTC |
| 827bc34 | eaton-lab | 30 December 2019, 23:36:44 UTC | digested genome bugfix - check each fbit 0 and -1 | 30 December 2019, 23:36:44 UTC |
| 57b73e7 | eaton-lab | 27 December 2019, 19:45:50 UTC | digest genomes nscaffolds arg support | 27 December 2019, 19:45:50 UTC |
| b3134c4 | eaton-lab | 27 December 2019, 19:45:33 UTC | digest genomes nscaffolds arg support | 27 December 2019, 19:45:33 UTC |
| 871d10e | eaton-lab | 27 December 2019, 19:00:59 UTC | docs cookbook updates | 27 December 2019, 19:00:59 UTC |
| b9a6154 | eaton-lab | 27 December 2019, 19:00:07 UTC | new consens sampling function and support for window extracter to concatenate | 27 December 2019, 19:00:07 UTC |
| 2d4022f | eaton-lab | 27 December 2019, 18:59:13 UTC | cosmetic | 27 December 2019, 18:59:13 UTC |
| b1c5949 | eaton-lab | 27 December 2019, 15:45:08 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 27 December 2019, 15:45:08 UTC |
| 70cbaab | eaton-lab | 27 December 2019, 15:45:06 UTC | comment about zlib | 27 December 2019, 15:45:06 UTC |
| 3b03d69 | Isaac Overcast | 24 December 2019, 15:28:42 UTC | "Updating ipyrad/__init__.py to version - 0.9.24 | 24 December 2019, 15:28:42 UTC |
| 19ceeba | Isaac Overcast | 24 December 2019, 15:28:17 UTC | Fix IPyradError import | 24 December 2019, 15:28:17 UTC |
| 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 |
| 25d4685 | eaton-lab | 18 December 2019, 17:26:54 UTC | fasterq-dump seems to be only avail on linux | 18 December 2019, 17:26:54 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 |
