b7eccb1 | Isaac Overcast | 08 March 2020, 14:03:01 UTC | "Updating ipyrad/__init__.py to version - 0.9.45 | 08 March 2020, 14:03:01 UTC |
4a20ebd | Isaac Overcast | 08 March 2020, 14:00:26 UTC | Allow more flexibility in sorted fastqs directory (DO NOT DELETE if it points to projectdir + _fastqs) | 08 March 2020, 14:00:26 UTC |
6ac3b17 | dereneaton | 05 March 2020, 21:51:08 UTC | window extracter fix for multiple loci w/ reduce | 05 March 2020, 21:51:08 UTC |
f3f1a9a | Isaac Overcast | 04 March 2020, 15:53:19 UTC | "Updating ipyrad/__init__.py to version - 0.9.44 | 04 March 2020, 15:53:19 UTC |
58511a4 | Isaac Overcast | 04 March 2020, 15:52:55 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 04 March 2020, 15:52:55 UTC |
4c3759f | Isaac Overcast | 04 March 2020, 15:52:49 UTC | Fix the treemix output so it actually generates. Took WAYYYY longer than I thought it would. | 04 March 2020, 15:52:49 UTC |
f9136b5 | Isaac Overcast | 04 March 2020, 14:42:39 UTC | Update faq.rst | 04 March 2020, 14:42:39 UTC |
a0c48a6 | Isaac Overcast | 04 March 2020, 14:40:22 UTC | Update faq.rst | 04 March 2020, 14:40:22 UTC |
28c7760 | Isaac Overcast | 26 February 2020, 16:57:06 UTC | "Updating ipyrad/__init__.py to version - 0.9.43 | 26 February 2020, 16:57:06 UTC |
11e34c3 | Isaac Overcast | 26 February 2020, 16:35:19 UTC | Fix off by 2 error in minsamp when using reference sequence | 26 February 2020, 16:35:19 UTC |
958b5d7 | dereneaton | 20 February 2020, 22:24:20 UTC | window extacter working for denovo loci | 20 February 2020, 22:24:20 UTC |
7dd08eb | Isaac Overcast | 20 February 2020, 13:17:53 UTC | cosmetic | 20 February 2020, 13:17:53 UTC |
5743bcd | Isaac Overcast | 20 February 2020, 13:06:24 UTC | cosmetic | 20 February 2020, 13:06:24 UTC |
94790ca | Isaac Overcast | 20 February 2020, 11:04:15 UTC | Cleaning up a TON of sphinx warnings from the docs and fixing a bunch of docs issues. | 20 February 2020, 11:04:15 UTC |
1652dfd | Isaac Overcast | 20 February 2020, 08:27:57 UTC | fix oops in baba.py (import sys) | 20 February 2020, 08:27:57 UTC |
776916e | Isaac Overcast | 19 February 2020, 20:49:04 UTC | "Updating ipyrad/__init__.py to version - 0.9.42 | 19 February 2020, 20:49:04 UTC |
824e4f4 | Isaac Overcast | 19 February 2020, 20:23:14 UTC | cosmetic | 19 February 2020, 20:23:14 UTC |
f17ce32 | Isaac Overcast | 19 February 2020, 19:57:08 UTC | cosmetic | 19 February 2020, 19:57:08 UTC |
4118a7e | Isaac Overcast | 19 February 2020, 19:55:51 UTC | Fix oops in step 6 which was leaving bad sample names hanging after alignment. | 19 February 2020, 19:55:51 UTC |
79d097f | Isaac Overcast | 18 February 2020, 22:15:35 UTC | "Updating ipyrad/__init__.py to version - 0.9.41 | 18 February 2020, 22:15:35 UTC |
6450927 | Isaac Overcast | 18 February 2020, 22:14:46 UTC | Set s6.data.ncpus value when routing around hierarchical clustering for ref based assemblies. | 18 February 2020, 22:14:46 UTC |
3d263f6 | dereneaton | 18 February 2020, 16:06:00 UTC | disable hierarchical clustering until further testing | 18 February 2020, 16:06:00 UTC |
cf2d064 | dereneaton | 18 February 2020, 15:55:42 UTC | split samples evenly among cgroups for hierarch clust | 18 February 2020, 15:55:42 UTC |
decd0e3 | dereneaton | 17 February 2020, 19:40:43 UTC | digest genomes uses qual score B instead of b | 17 February 2020, 19:40:43 UTC |
9d72986 | Isaac Overcast | 16 February 2020, 06:33:54 UTC | "Updating ipyrad/__init__.py to version - 0.9.40 | 16 February 2020, 06:33:54 UTC |
216e4ee | Isaac Overcast | 16 February 2020, 06:33:25 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 16 February 2020, 06:33:25 UTC |
44cfa92 | Isaac Overcast | 16 February 2020, 06:33:14 UTC | cosmetic | 16 February 2020, 06:33:14 UTC |
3e44567 | dereneaton | 16 February 2020, 00:55:27 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 16 February 2020, 00:55:27 UTC |
00e3120 | dereneaton | 16 February 2020, 00:55:21 UTC | cosmetic | 16 February 2020, 00:55:21 UTC |
99618b3 | dereneaton | 16 February 2020, 00:55:08 UTC | cosmetic | 16 February 2020, 00:55:08 UTC |
b655034 | dereneaton | 15 February 2020, 23:20:25 UTC | subsample loci func added | 15 February 2020, 23:20:25 UTC |
1449f8d | dereneaton | 15 February 2020, 23:19:17 UTC | counts rm duplicates in denovo and works with step6 skipping alignment of loci w/ dups | 15 February 2020, 23:19:17 UTC |
a122119 | dereneaton | 15 February 2020, 23:18:34 UTC | denovo paired aligned separately again | 15 February 2020, 23:18:34 UTC |
0018eb1 | dereneaton | 15 February 2020, 23:17:54 UTC | cosmetic | 15 February 2020, 23:17:54 UTC |
06fdcb1 | dereneaton | 15 February 2020, 23:17:40 UTC | fastq qmax error in merge denovo fixed | 15 February 2020, 23:17:40 UTC |
19bf530 | Isaac Overcast | 15 February 2020, 20:20:47 UTC | "Updating ipyrad/__init__.py to version - 0.9.39 | 15 February 2020, 20:20:47 UTC |
f419b14 | Isaac Overcast | 15 February 2020, 20:19:33 UTC | Why can't i figure out how to comment out this plotting code right? wtf! | 15 February 2020, 20:19:33 UTC |
5d8c9ac | Isaac Overcast | 15 February 2020, 19:45:29 UTC | "Updating ipyrad/__init__.py to version - 0.9.38 | 15 February 2020, 19:45:29 UTC |
200058c | Isaac Overcast | 15 February 2020, 19:45:07 UTC | commented out the import of the baba_plot plotting function and the baba.plot() method as these are broken rn, and also the plotting/baba_plotting routine tries to access toyplot in a way that breaks the conda build since toyplot isn't a strict requirement. We could fix this in the future, but i'm tring to get the bioconda package to build successfully rn. | 15 February 2020, 19:45:07 UTC |
1e80b19 | Isaac Overcast | 15 February 2020, 18:23:17 UTC | "Updating ipyrad/__init__.py to version - 0.9.37 | 15 February 2020, 18:23:17 UTC |
bffa40a | Isaac Overcast | 15 February 2020, 18:23:00 UTC | fix import checking for baba_panel_plot.py | 15 February 2020, 18:23:00 UTC |
280f072 | Isaac Overcast | 15 February 2020, 18:06:07 UTC | "Updating ipyrad/__init__.py to version - 0.9.36 | 15 February 2020, 18:06:07 UTC |
1c18864 | Isaac Overcast | 15 February 2020, 18:05:39 UTC | Handle external imports in the baba module in the same way as the other analysis tools to fix the broken bioconda build. | 15 February 2020, 18:05:39 UTC |
61f4ef5 | Isaac Overcast | 13 February 2020, 08:33:09 UTC | Add a pops file to the ipsimdata.tar.gz because it's always useful. | 13 February 2020, 08:33:09 UTC |
538f909 | Isaac Overcast | 12 February 2020, 21:44:24 UTC | "Updating ipyrad/__init__.py to version - 0.9.35 | 12 February 2020, 21:44:24 UTC |
3bfc5e3 | Isaac Overcast | 12 February 2020, 21:44:09 UTC | "Updating ipyrad/__init__.py to version - 0.9.35 | 12 February 2020, 21:44:09 UTC |
3d80bb9 | Isaac Overcast | 12 February 2020, 17:21:35 UTC | Fix a bug in step 5 handling of RemoteError during indexing alleles. | 12 February 2020, 17:21:35 UTC |
25f1cfc | Isaac Overcast | 11 February 2020, 13:19:54 UTC | cosmetic | 11 February 2020, 13:19:54 UTC |
4ca03d3 | Isaac Overcast | 09 February 2020, 19:54:30 UTC | Report debug traceback for all crashes, not just API. This is essentially making the debug flag useless in v.0.9 | 09 February 2020, 19:54:30 UTC |
03a1d26 | Isaac Overcast | 09 February 2020, 19:00:11 UTC | "Updating ipyrad/__init__.py to version - 0.9.34 | 09 February 2020, 19:00:11 UTC |
8cfc6be | Isaac Overcast | 09 February 2020, 18:58:38 UTC | Roll back baba code to 0.7 version which doesn't use the current analysis format, but which still works. Saved ongoing baba code as baba.v0.9.py | 09 February 2020, 18:58:38 UTC |
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 |