| f6fdb55 | Isaac Overcast | 06 February 2020, 17:50:08 UTC | "Updating ipyrad/__init__.py to version - 0.9.33 | 06 February 2020, 17:50:08 UTC |
| fe531be | Isaac Overcast | 06 February 2020, 17:49:49 UTC | Fix major oops in consens_se which failed step 5 every time. Bad! | 06 February 2020, 17:49:49 UTC |
| ec03ba7 | Isaac Overcast | 06 February 2020, 10:11:32 UTC | In step 6 use the sample.files.consens info, rather than data.dirs to allow for merging assemblies after step 5 where data.dirs is invalid/empty. | 06 February 2020, 10:11:32 UTC |
| 822ae39 | Isaac Overcast | 06 February 2020, 09:03:57 UTC | cosmetic | 06 February 2020, 09:03:57 UTC |
| 08bfde8 | Isaac Overcast | 04 February 2020, 08:37:54 UTC | "Updating ipyrad/__init__.py to version - 0.9.32 | 04 February 2020, 08:37:54 UTC |
| 8148218 | Isaac Overcast | 03 February 2020, 09:09:40 UTC | cosmetic | 03 February 2020, 09:09:40 UTC |
| a53379c | Isaac Overcast | 03 February 2020, 08:56:30 UTC | #392 allow scaffold names to be int | 03 February 2020, 08:56:30 UTC |
| df4603d | Isaac Overcast | 02 February 2020, 20:56:06 UTC | Add sensible error handling if only a few samples fail step 5. | 02 February 2020, 20:56:06 UTC |
| 1a30855 | Isaac Overcast | 02 February 2020, 18:20:42 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 02 February 2020, 18:20:42 UTC |
| 1fed7ea | Isaac Overcast | 02 February 2020, 18:20:40 UTC | add docs to clustmap_across | 02 February 2020, 18:20:40 UTC |
| fd59b96 | dereneaton | 30 January 2020, 19:19:23 UTC | fix for name re-ordering in window-extracter with multiple regions selected | 30 January 2020, 19:19:23 UTC |
| 3d7aba2 | eaton-lab | 30 January 2020, 17:54:31 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 30 January 2020, 17:54:31 UTC |
| 5e78018 | eaton-lab | 30 January 2020, 17:54:28 UTC | added comments | 30 January 2020, 17:54:28 UTC |
| be415a5 | eaton-lab | 30 January 2020, 17:54:15 UTC | added comments | 30 January 2020, 17:54:15 UTC |
| 4dcdf82 | eaton-lab | 30 January 2020, 17:53:58 UTC | cosmetic | 30 January 2020, 17:53:58 UTC |
| 05b4879 | eaton-lab | 30 January 2020, 17:53:38 UTC | added sys | 30 January 2020, 17:53:38 UTC |
| 1031c9b | Isaac Overcast | 30 January 2020, 17:10:51 UTC | Actually handle failed samples in step 2. | 30 January 2020, 17:10:51 UTC |
| e531fb1 | eaton-lab | 28 January 2020, 18:39:19 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 28 January 2020, 18:39:19 UTC |
| d234e73 | eaton-lab | 28 January 2020, 18:38:13 UTC | fix for new h5py warning | 28 January 2020, 18:38:13 UTC |
| 2204fb2 | eaton-lab | 28 January 2020, 18:37:59 UTC | fix for new sklearn warning | 28 January 2020, 18:37:59 UTC |
| a81456c | Isaac Overcast | 19 January 2020, 23:34:34 UTC | "Updating ipyrad/__init__.py to version - 0.9.31 | 19 January 2020, 23:34:34 UTC |
| e70b70d | isaacovercast | 19 January 2020, 23:32:50 UTC | Fix error in bucky (progressbar hell). | 19 January 2020, 23:32:50 UTC |
| f6a3ed3 | isaacovercast | 18 January 2020, 18:09:09 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 18 January 2020, 18:09:09 UTC |
| c1a983e | isaacovercast | 18 January 2020, 18:09:05 UTC | Add error handling in a couple cases if run() hasn't been called, e.g. before draw, and also add the pcs() function as a convenience. | 18 January 2020, 18:09:05 UTC |
| 7b38aff | Isaac Overcast | 17 January 2020, 12:44:21 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 17 January 2020, 12:44:21 UTC |
| 041050d | Isaac Overcast | 17 January 2020, 12:44:12 UTC | Removed support for legacy argument format from bpp.py and updated the docs. | 17 January 2020, 12:44:12 UTC |
| 82aea63 | isaacovercast | 16 January 2020, 18:52:17 UTC | Allow PCA() to import data as vcf. | 16 January 2020, 18:52:17 UTC |
| b657e5f | Isaac Overcast | 16 January 2020, 16:56:35 UTC | Add support for importing VCF into PCA | 16 January 2020, 16:56:35 UTC |
| 9b70b09 | Isaac Overcast | 16 January 2020, 15:31:28 UTC | "Updating ipyrad/__init__.py to version - 0.9.30 | 16 January 2020, 15:31:28 UTC |
| 5f6ba00 | Isaac Overcast | 16 January 2020, 15:30:48 UTC | Fix whoops with bucky progressbars | 16 January 2020, 15:30:48 UTC |
| ad5d1f6 | Isaac Overcast | 15 January 2020, 09:33:31 UTC | "Updating ipyrad/__init__.py to version - 0.9.29 | 15 January 2020, 09:33:31 UTC |
| 6f062ef | Isaac Overcast | 15 January 2020, 09:33:11 UTC | Fix bucky progressbar calls. | 15 January 2020, 09:33:11 UTC |
| 59e9ca5 | Isaac Overcast | 15 January 2020, 09:07:04 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 15 January 2020, 09:07:04 UTC |
| 26efacc | Isaac Overcast | 15 January 2020, 09:06:58 UTC | Fixed progressbar calls in bucky.py | 15 January 2020, 09:06:58 UTC |
| e0198c7 | Isaac Overcast | 14 January 2020, 12:49:14 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 14 January 2020, 12:49:14 UTC |
| eef08f7 | Isaac Overcast | 14 January 2020, 12:49:06 UTC | Conda install instructions were wrong. | 14 January 2020, 12:49:06 UTC |
| a1153c0 | Isaac Overcast | 14 January 2020, 10:34:24 UTC | cosmetic | 14 January 2020, 10:34:24 UTC |
| 8089b77 | Isaac Overcast | 13 January 2020, 08:43:44 UTC | add future print import to fasttree.py | 13 January 2020, 08:43:44 UTC |
| 1d4749d | Isaac Overcast | 12 January 2020, 18:48:53 UTC | Add releasenotes to the TOC | 12 January 2020, 18:48:53 UTC |
| 853b798 | Isaac Overcast | 12 January 2020, 18:46:45 UTC | cosmetic | 12 January 2020, 18:46:45 UTC |
| 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 |
