| f09113d | Isaac Overcast | 09 May 2020, 18:03:35 UTC | "Updating ipyrad/__init__.py to version - 0.9.52 | 09 May 2020, 18:03:35 UTC |
| fd8e0d1 | Isaac Overcast | 09 May 2020, 18:03:16 UTC | Fix nasty off-by-one error in reference positions | 09 May 2020, 18:03:16 UTC |
| 5cdb266 | Isaac Overcast | 09 May 2020, 14:49:54 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 09 May 2020, 14:49:54 UTC |
| 29525fd | Isaac Overcast | 09 May 2020, 14:49:46 UTC | cosmetic | 09 May 2020, 14:49:46 UTC |
| fbd0d6a | eaton-lab | 08 May 2020, 05:28:32 UTC | multiple default clock models | 08 May 2020, 05:28:32 UTC |
| b52572e | eaton-lab | 08 May 2020, 05:27:11 UTC | multiple default clock models | 08 May 2020, 05:27:11 UTC |
| a290517 | eaton-lab | 08 May 2020, 03:45:53 UTC | multiple default clock models | 08 May 2020, 03:45:53 UTC |
| 7197557 | eaton-lab | 08 May 2020, 03:19:05 UTC | multiple default clock models | 08 May 2020, 03:19:05 UTC |
| e44caf6 | eaton-lab | 08 May 2020, 03:18:07 UTC | multiple default clock models | 08 May 2020, 03:18:07 UTC |
| 19d572f | eaton-lab | 08 May 2020, 03:11:59 UTC | multiple default clock models | 08 May 2020, 03:11:59 UTC |
| b2f9ce9 | eaton-lab | 08 May 2020, 02:57:37 UTC | multiple default clock models | 08 May 2020, 02:57:37 UTC |
| c71d1ba | eaton-lab | 07 May 2020, 19:37:27 UTC | wex concat name drop fix | 07 May 2020, 19:37:27 UTC |
| 03f7e13 | eaton-lab | 07 May 2020, 02:25:15 UTC | ts tmpdir renamed bootsdir | 07 May 2020, 02:25:15 UTC |
| f50a75f | eaton-lab | 06 May 2020, 22:46:14 UTC | umap learn conda instructions | 06 May 2020, 22:46:14 UTC |
| f6182e4 | eaton-lab | 06 May 2020, 22:35:03 UTC | ts: added dryrun method | 06 May 2020, 22:35:03 UTC |
| d8a02a2 | eaton-lab | 06 May 2020, 22:30:53 UTC | wex: remove print debug statement | 06 May 2020, 22:30:53 UTC |
| 799eaa6 | eaton-lab | 06 May 2020, 22:29:49 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 06 May 2020, 22:29:49 UTC |
| b483617 | Isaac Overcast | 04 May 2020, 20:37:47 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 04 May 2020, 20:37:47 UTC |
| 1a8dd23 | Isaac Overcast | 04 May 2020, 20:37:24 UTC | Fix baba cookbook docs | 04 May 2020, 20:37:24 UTC |
| e4cbb39 | eaton-lab | 02 May 2020, 14:37:54 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 02 May 2020, 14:37:54 UTC |
| f0d94bd | eaton-lab | 02 May 2020, 14:37:38 UTC | add umap option | 02 May 2020, 14:37:38 UTC |
| 57ab848 | eaton-lab | 02 May 2020, 14:36:47 UTC | added pseudocode for a further imputer in prog | 02 May 2020, 14:36:47 UTC |
| 007364b | eaton-lab | 02 May 2020, 14:36:17 UTC | prettier bpp plot | 02 May 2020, 14:36:17 UTC |
| ea04b8f | Isaac Overcast | 02 May 2020, 12:51:07 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 02 May 2020, 12:51:07 UTC |
| f03afbd | Isaac Overcast | 02 May 2020, 12:51:04 UTC | pca analysis tool passes through quiet flag to subfunctions | 02 May 2020, 12:51:04 UTC |
| 851f6a5 | eaton-lab | 01 May 2020, 22:21:43 UTC | warning about missing ref only up with no ref1 or ref2 | 01 May 2020, 22:21:43 UTC |
| 5f67637 | dereneaton | 01 May 2020, 18:29:29 UTC | merge fix | 01 May 2020, 18:29:29 UTC |
| 78e4193 | eaton-lab | 29 April 2020, 20:53:03 UTC | improving ipabpp summary funcs | 29 April 2020, 20:53:03 UTC |
| 3e8e85e | eaton-lab | 27 April 2020, 06:36:27 UTC | ensure conda ipcluster bin on stop | 27 April 2020, 06:36:27 UTC |
| 870bd8f | eaton-lab | 27 April 2020, 06:35:45 UTC | bpp prior checks, new ctl build for 4.0, parsing results funcs | 27 April 2020, 06:35:45 UTC |
| 2c1907b | eaton-lab | 24 April 2020, 21:30:46 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 24 April 2020, 21:30:46 UTC |
| 3289220 | Isaac Overcast | 24 April 2020, 18:52:21 UTC | Add a helpful message if merging assemblies with technical replicates beyond step 3. | 24 April 2020, 18:52:21 UTC |
| 02582ad | eaton-lab | 24 April 2020, 18:18:11 UTC | missing import | 24 April 2020, 18:18:11 UTC |
| 57ad9f7 | eaton-lab | 24 April 2020, 18:18:01 UTC | cosmetic | 24 April 2020, 18:18:01 UTC |
| 87a8beb | Isaac Overcast | 24 April 2020, 08:59:46 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 24 April 2020, 08:59:46 UTC |
| 2344061 | Isaac Overcast | 24 April 2020, 08:59:44 UTC | Handle empty imap population in snps_extractor | 24 April 2020, 08:59:44 UTC |
| a08f0e4 | eaton-lab | 24 April 2020, 07:57:09 UTC | binary fix | 24 April 2020, 07:57:09 UTC |
| 8e25d4b | eaton-lab | 24 April 2020, 07:53:11 UTC | syntaxerr on quiet | 24 April 2020, 07:53:11 UTC |
| 3b5e6ab | eaton-lab | 24 April 2020, 07:18:56 UTC | hide toytree dep in ast | 24 April 2020, 07:18:56 UTC |
| 5b86a65 | eaton-lab | 24 April 2020, 07:03:22 UTC | ast better error message | 24 April 2020, 07:03:22 UTC |
| 58a3181 | eaton-lab | 24 April 2020, 06:51:12 UTC | ip assemble shows cluster on run by default | 24 April 2020, 06:51:12 UTC |
| 5a4d9f2 | eaton-lab | 24 April 2020, 06:50:43 UTC | show_cluster func now listens to param arg | 24 April 2020, 06:50:43 UTC |
| 9e4b859 | eaton-lab | 24 April 2020, 06:49:44 UTC | big update for bpp 4.0, uses lex | 24 April 2020, 06:49:44 UTC |
| 9b20dd2 | eaton-lab | 24 April 2020, 06:48:54 UTC | wex and ts both use idxs in param name now | 24 April 2020, 06:48:54 UTC |
| b4c9487 | eaton-lab | 24 April 2020, 06:48:27 UTC | simple astral run tool | 24 April 2020, 06:48:27 UTC |
| 815e8bb | eaton-lab | 24 April 2020, 06:47:59 UTC | lex: imap/minmap filtering fix | 24 April 2020, 06:47:59 UTC |
| 8db3880 | eaton-lab | 24 April 2020, 06:47:40 UTC | wex: imap/minmap filtering fix | 24 April 2020, 06:47:40 UTC |
| a3ae29a | eaton-lab | 24 April 2020, 03:21:07 UTC | fixed warning message | 24 April 2020, 03:21:07 UTC |
| dc28661 | eaton-lab | 24 April 2020, 03:15:06 UTC | default minmap to 0 if imap and minmap empty | 24 April 2020, 03:15:06 UTC |
| 717e4d0 | eaton-lab | 24 April 2020, 03:05:52 UTC | hide toyplot dependency | 24 April 2020, 03:05:52 UTC |
| c268860 | eaton-lab | 24 April 2020, 02:58:01 UTC | simple option to keep treefiles in treeslider | 24 April 2020, 02:58:01 UTC |
| 0bc86c3 | eaton-lab | 24 April 2020, 02:57:05 UTC | under the hood mods to pca draw func to make it more atomic | 24 April 2020, 02:57:05 UTC |
| 050127e | Isaac Overcast | 23 April 2020, 12:48:15 UTC | Update faq.rst | 23 April 2020, 12:48:15 UTC |
| a7140ae | Isaac Overcast | 21 April 2020, 19:48:49 UTC | Set default filter_adapters parameter to 2 | 21 April 2020, 19:48:49 UTC |
| 2acf129 | Isaac Overcast | 17 April 2020, 16:19:01 UTC | "Updating ipyrad/__init__.py to version - 0.9.51 | 17 April 2020, 16:19:01 UTC |
| 44df1c8 | Isaac Overcast | 17 April 2020, 16:18:38 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 17 April 2020, 16:18:38 UTC |
| db5a731 | Isaac Overcast | 17 April 2020, 16:18:25 UTC | 1 index POS in vcf output | 17 April 2020, 16:18:25 UTC |
| 772949c | eaton-lab | 15 April 2020, 02:13:13 UTC | minmap default is 0 | 15 April 2020, 02:13:13 UTC |
| deb11f0 | eaton-lab | 14 April 2020, 16:52:18 UTC | bugfix: apply imapdrop only when imap | 14 April 2020, 16:52:18 UTC |
| 261f14b | eaton-lab | 14 April 2020, 16:45:50 UTC | faster extraction and mincov after minmap in lex | 14 April 2020, 16:45:50 UTC |
| e92c182 | eaton-lab | 14 April 2020, 16:45:03 UTC | mincov applies after minmap in wex | 14 April 2020, 16:45:03 UTC |
| 144877c | eaton-lab | 14 April 2020, 16:44:34 UTC | scaff arg entered later in cov tool | 14 April 2020, 16:44:34 UTC |
| 4d8a25f | eaton-lab | 13 April 2020, 16:44:58 UTC | rmincov added to ts | 13 April 2020, 16:44:58 UTC |
| 7b7404b | eaton-lab | 13 April 2020, 05:16:17 UTC | option to keep all tmp files in treeslider | 13 April 2020, 05:16:17 UTC |
| ec445b9 | eaton-lab | 13 April 2020, 04:47:09 UTC | major fix to names sorting in wex | 13 April 2020, 04:47:09 UTC |
| 5186544 | eaton-lab | 13 April 2020, 04:46:32 UTC | names offset by scaff length in cov plot | 13 April 2020, 04:46:32 UTC |
| dab9280 | eaton-lab | 13 April 2020, 04:46:06 UTC | cosmetic | 13 April 2020, 04:46:06 UTC |
| 9ffbd1e | eaton-lab | 13 April 2020, 04:45:29 UTC | set default inner mate to 500 and use it unless user changes to None, in which case we estimate from reads | 13 April 2020, 04:45:29 UTC |
| 3623af9 | eaton-lab | 12 April 2020, 19:08:20 UTC | tmp working baba update | 12 April 2020, 19:08:20 UTC |
| d86f332 | eaton-lab | 12 April 2020, 19:07:24 UTC | added locus extracter | 12 April 2020, 19:07:24 UTC |
| d0a7bc8 | eaton-lab | 12 April 2020, 19:03:11 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 12 April 2020, 19:03:11 UTC |
| c7395f9 | eaton-lab | 12 April 2020, 19:03:00 UTC | option to keep all files in treeslider | 12 April 2020, 19:03:00 UTC |
| 6d7929a | eaton-lab | 12 April 2020, 19:02:31 UTC | added cov plot tool | 12 April 2020, 19:02:31 UTC |
| 3752f48 | dereneaton | 09 April 2020, 23:08:42 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 09 April 2020, 23:08:42 UTC |
| 33a8625 | dereneaton | 09 April 2020, 23:08:20 UTC | raise warning if ref+ or ref- and method not ref | 09 April 2020, 23:08:20 UTC |
| 9f05179 | dereneaton | 09 April 2020, 23:07:42 UTC | notes on window extracter | 09 April 2020, 23:07:42 UTC |
| 8f45129 | Isaac Overcast | 05 April 2020, 13:58:11 UTC | "Updating ipyrad/__init__.py to version - 0.9.50 | 05 April 2020, 13:58:11 UTC |
| 8d25487 | Isaac Overcast | 05 April 2020, 13:57:53 UTC | Actually fix FASTQ+64 problem. Max fastq_qmax is 126, so this is set to 93 now (93+33=126) | 05 April 2020, 13:57:53 UTC |
| 6d3c454 | Isaac Overcast | 02 April 2020, 15:52:39 UTC | "Updating ipyrad/__init__.py to version - 0.9.49 | 02 April 2020, 15:52:39 UTC |
| 47a91ac | Isaac Overcast | 02 April 2020, 15:52:10 UTC | Allow high fastq_qmax in pair merging to allow FASTQ+64 data | 02 April 2020, 15:52:10 UTC |
| 352eb9b | Isaac Overcast | 01 April 2020, 21:05:25 UTC | "Updating ipyrad/__init__.py to version - 0.9.48 | 01 April 2020, 21:05:25 UTC |
| 1d6a4a4 | Isaac Overcast | 30 March 2020, 17:19:11 UTC | Record refseq mapped/unmapped for both SE & PE | 30 March 2020, 17:19:11 UTC |
| 5bed66a | eaton-lab | 27 March 2020, 18:08:06 UTC | wextract minmap+consred minmap default added | 27 March 2020, 18:08:06 UTC |
| 3068ae2 | eaton-lab | 27 March 2020, 17:57:34 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 27 March 2020, 17:57:34 UTC |
| c003575 | eaton-lab | 27 March 2020, 17:57:10 UTC | treeslider default args typed | 27 March 2020, 17:57:10 UTC |
| 3016254 | eaton-lab | 27 March 2020, 17:56:42 UTC | tested working wextracter | 27 March 2020, 17:56:42 UTC |
| 6e97c3d | Isaac Overcast | 24 March 2020, 21:15:22 UTC | "Updating ipyrad/__init__.py to version - 0.9.47 | 24 March 2020, 21:15:22 UTC |
| 2563125 | Isaac Overcast | 24 March 2020, 21:13:48 UTC | Fix snpstring length oops in .alleles outputs so they line up right. | 24 March 2020, 21:13:48 UTC |
| 28143f2 | Isaac Overcast | 24 March 2020, 16:14:43 UTC | "Updating ipyrad/__init__.py to version - 0.9.46 | 24 March 2020, 16:14:43 UTC |
| b65829a | Isaac Overcast | 24 March 2020, 16:11:07 UTC | Fix pd.as_matrix() call which is deprecated. | 24 March 2020, 16:11:07 UTC |
| 2284869 | eaton-lab | 21 March 2020, 19:20:56 UTC | baba merge | 21 March 2020, 19:20:56 UTC |
| d4ee2eb | eaton-lab | 21 March 2020, 16:37:02 UTC | new dict for translation | 21 March 2020, 16:37:02 UTC |
| c493485 | eaton-lab | 21 March 2020, 16:36:25 UTC | updating bpp for 4.0 | 21 March 2020, 16:36:25 UTC |
| d258e2d | Isaac Overcast | 16 March 2020, 19:10:51 UTC | Force pca.draw() to honor the length of the color list if it is sufficiently long to color all samples in the imap, or at least use the length of the color list to set the value of the variable. | 16 March 2020, 19:10:51 UTC |
| 1bdb8f2 | Isaac Overcast | 12 March 2020, 15:31:50 UTC | Fix oops in baba.py for importing msprime. Pushed it to Sim.__init__, since if you want to do baba, and don't care about sims, then you shouldn't have to install msprime. | 12 March 2020, 15:31:50 UTC |
| 52b1253 | dereneaton | 09 March 2020, 15:05:28 UTC | h5py warning fix | 09 March 2020, 15:05:28 UTC |
| 3f30d92 | dereneaton | 09 March 2020, 15:05:15 UTC | use _pnames to use filtered names in run() | 09 March 2020, 15:05:15 UTC |
| 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 |
