| c7c8cba | isaacovercast | 21 February 2017, 21:09:25 UTC | "Updating ipyrad/__init__.py to version - 0.6.5 | 21 February 2017, 21:09:25 UTC |
| 4ba137a | isaacovercast | 21 February 2017, 21:08:52 UTC | Fixed 2 errors in steps 3 and 4. | 21 February 2017, 21:08:52 UTC |
| 015456e | deren | 21 February 2017, 00:47:42 UTC | "Updating ipyrad/__init__.py to version - 0.6.4 | 21 February 2017, 00:47:42 UTC |
| 8166647 | deren | 21 February 2017, 00:47:19 UTC | left a debugging print statement in the code | 21 February 2017, 00:47:19 UTC |
| b2b7a06 | deren | 21 February 2017, 00:46:34 UTC | removed old bin | 21 February 2017, 00:46:34 UTC |
| 26649be | deren | 20 February 2017, 17:56:29 UTC | "Updating ipyrad/__init__.py to version - 0.6.4 | 20 February 2017, 17:56:29 UTC |
| 9bd7f8d | deren | 20 February 2017, 17:52:36 UTC | "Updating ipyrad/__init__.py to version - 0.6.4 | 20 February 2017, 17:52:36 UTC |
| 02ff2f8 | deren | 20 February 2017, 17:52:14 UTC | update to docs parameters | 20 February 2017, 17:52:14 UTC |
| fe963bb | deren | 20 February 2017, 17:51:22 UTC | bug fix for merging assemblies with a mix of same named and diff named samples | 20 February 2017, 17:51:22 UTC |
| 61fd3eb | Isaac Overcast | 18 February 2017, 22:49:37 UTC | cosmetic | 18 February 2017, 22:49:37 UTC |
| 4c31bbd | Isaac Overcast | 18 February 2017, 22:38:57 UTC | Cosmetic change. | 18 February 2017, 22:38:57 UTC |
| aa37ace | isaacovercast | 18 February 2017, 22:34:34 UTC | "Updating ipyrad/__init__.py to version - 0.6.3 | 18 February 2017, 22:34:34 UTC |
| c7a1d74 | isaacovercast | 18 February 2017, 22:30:32 UTC | Fixed a bug i introduced to assembly. Autotroll. | 18 February 2017, 22:30:32 UTC |
| 2d36fc9 | isaacovercast | 18 February 2017, 22:22:07 UTC | "Updating ipyrad/__init__.py to version - 0.6.2 | 18 February 2017, 22:22:07 UTC |
| 3a02e33 | isaacovercast | 18 February 2017, 22:21:50 UTC | Fix subtle bug with migration to trim_reads parameter. | 18 February 2017, 22:21:50 UTC |
| 5b48bce | isaacovercast | 18 February 2017, 21:13:38 UTC | "Updating ipyrad/__init__.py to version - 0.6.1 | 18 February 2017, 21:13:38 UTC |
| d449052 | isaacovercast | 18 February 2017, 21:12:46 UTC | Fixed malformed nexus output file. | 18 February 2017, 21:12:46 UTC |
| f207799 | deren | 16 February 2017, 20:58:36 UTC | cookbook updates to docs | 16 February 2017, 20:58:36 UTC |
| 6cb718d | deren | 16 February 2017, 20:32:48 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 16 February 2017, 20:32:48 UTC |
| 530f133 | deren | 16 February 2017, 20:32:43 UTC | updated cookbook structure pedicularis | 16 February 2017, 20:32:43 UTC |
| c7d27f7 | isaacovercast | 16 February 2017, 18:49:31 UTC | "Updating ipyrad/__init__.py to version - 0.6.0 | 16 February 2017, 18:49:31 UTC |
| 8a95c6c | deren | 15 February 2017, 19:46:11 UTC | trim reads default 0,0,0,0. Similar action to trim loci, but applied in step 2 to raws | 15 February 2017, 19:46:11 UTC |
| e5be300 | deren | 15 February 2017, 17:20:40 UTC | trim_reads default is 0,0 | 15 February 2017, 17:20:40 UTC |
| e66076d | deren | 15 February 2017, 17:20:22 UTC | raise default cov/minsl for gbs data to 0.5 from 0.33 | 15 February 2017, 17:20:22 UTC |
| 168ae0b | deren | 15 February 2017, 00:33:49 UTC | prettifying docs | 15 February 2017, 00:33:49 UTC |
| 18f2630 | deren | 15 February 2017, 00:26:33 UTC | pedicularis docs update v6 way way faster | 15 February 2017, 00:26:33 UTC |
| 2df15a6 | deren | 14 February 2017, 23:42:46 UTC | updated tutorial | 14 February 2017, 23:42:46 UTC |
| 9a29cd8 | deren | 14 February 2017, 23:31:35 UTC | fixing links in combining data docs | 14 February 2017, 23:31:35 UTC |
| 84bfb6f | deren | 14 February 2017, 23:30:07 UTC | updating tutorial for latest version/speed | 14 February 2017, 23:30:07 UTC |
| 43b9f22 | deren | 14 February 2017, 23:17:48 UTC | added docs for combining multiple plates | 14 February 2017, 23:17:48 UTC |
| 80e77e3 | deren | 14 February 2017, 22:54:00 UTC | added docs for combining multiple plates | 14 February 2017, 22:54:00 UTC |
| b091929 | deren | 14 February 2017, 22:43:31 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 14 February 2017, 22:43:31 UTC |
| 1d8c42c | deren | 14 February 2017, 22:41:26 UTC | added docs for combining multiple plates | 14 February 2017, 22:41:26 UTC |
| 52b29dd | isaacovercast | 14 February 2017, 16:16:11 UTC | cosmetic change to docs | 14 February 2017, 16:16:11 UTC |
| 7b545ef | isaacovercast | 14 February 2017, 16:14:50 UTC | Removed from output formats defaults (it doesn't do anything) | 14 February 2017, 16:14:50 UTC |
| 4c66ab4 | deren | 13 February 2017, 20:30:37 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 13 February 2017, 20:30:37 UTC |
| 3e8bcf3 | deren | 13 February 2017, 20:30:17 UTC | baba cookbooks [unfinished] up | 13 February 2017, 20:30:17 UTC |
| 621cceb | deren | 13 February 2017, 18:27:58 UTC | finally added osx QMC and fixed bug for same name and force flag rerun | 13 February 2017, 18:27:58 UTC |
| 3129873 | deren | 13 February 2017, 17:53:19 UTC | put back in a remove tmpdirs call | 13 February 2017, 17:53:19 UTC |
| 353e8e4 | deren | 13 February 2017, 03:41:02 UTC | removed a superfluous print statement | 13 February 2017, 03:41:02 UTC |
| de48991 | deren | 13 February 2017, 03:40:12 UTC | bug fix to mapfile, now compatible with tetrad | 13 February 2017, 03:40:12 UTC |
| c55f59d | deren | 12 February 2017, 00:23:59 UTC | paramsinfo for new trimreads param | 12 February 2017, 00:23:59 UTC |
| 6d016ab | deren | 12 February 2017, 00:23:45 UTC | branching fix for handling new param names and upgrading to them | 12 February 2017, 00:23:45 UTC |
| b30c124 | deren | 12 February 2017, 00:23:23 UTC | better handling of pairgbs no bcode trimming. Now handles --length arg | 12 February 2017, 00:23:23 UTC |
| 768f4a1 | deren | 12 February 2017, 00:22:54 UTC | better handling of KBD in demux. Faster compression. | 12 February 2017, 00:22:54 UTC |
| 7b9739f | deren | 08 February 2017, 19:14:23 UTC | forgot sname var in cutadaptit_single | 08 February 2017, 19:14:23 UTC |
| 66bff01 | deren | 08 February 2017, 19:12:16 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 08 February 2017, 19:12:16 UTC |
| 8c6a3e5 | isaacovercast | 08 February 2017, 01:18:01 UTC | cosmetic changes to rawedit | 08 February 2017, 01:18:01 UTC |
| 8656b00 | isaacovercast | 08 February 2017, 01:13:32 UTC | Fix step 2 for PE reads crashing during cutatapt. | 08 February 2017, 01:13:32 UTC |
| b5df196 | isaacovercast | 07 February 2017, 21:40:59 UTC | Test for bz2 files in sorted_fastq_path and nag the user bcz we don't support this format. | 07 February 2017, 21:40:59 UTC |
| b605ad1 | isaac | 03 February 2017, 21:46:03 UTC | Step 1 create tmp file for estimating optim chunk size in project_dir not ./ | 03 February 2017, 21:46:03 UTC |
| 511bf4d | isaac | 03 February 2017, 21:41:27 UTC | Add force flag to mapreads(), mostly to save time on rerunning if it crashes during finalize_mapping. Also fixed a nasty bug in refmapping. | 03 February 2017, 21:41:27 UTC |
| 8997ab4 | isaacovercast | 02 February 2017, 20:50:54 UTC | Added text to faq about why PE original RAD is hard to assemble, cuz people always ask. | 02 February 2017, 20:50:54 UTC |
| 2f08ed2 | isaacovercast | 02 February 2017, 20:50:13 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 02 February 2017, 20:50:13 UTC |
| e8a8c11 | deren | 31 January 2017, 23:01:45 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 31 January 2017, 23:01:45 UTC |
| dbd43b0 | deren | 31 January 2017, 23:01:42 UTC | cosmetic | 31 January 2017, 23:01:42 UTC |
| 90885dd | isaac | 31 January 2017, 12:53:22 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 31 January 2017, 12:53:22 UTC |
| f924ec0 | isaac | 31 January 2017, 12:53:16 UTC | Better handling of loci w/ duplicate seqs per sample. | 31 January 2017, 12:53:16 UTC |
| b92265e | deren | 30 January 2017, 22:55:53 UTC | fkjd;afjd;ka | 30 January 2017, 22:55:53 UTC |
| e3501e3 | isaacovercast | 30 January 2017, 21:49:58 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 30 January 2017, 21:49:58 UTC |
| b743109 | isaacovercast | 30 January 2017, 21:49:56 UTC | Fix a bug that munged some names in branching. | 30 January 2017, 21:49:56 UTC |
| 2e378bf | deren | 30 January 2017, 21:14:08 UTC | merge conflict | 30 January 2017, 21:14:08 UTC |
| 9e89116 | deren | 30 January 2017, 21:12:28 UTC | modified for new trim param names | 30 January 2017, 21:12:28 UTC |
| d98b5a3 | deren | 30 January 2017, 21:12:13 UTC | support for new trim_loci param | 30 January 2017, 21:12:13 UTC |
| 6babeca | deren | 30 January 2017, 21:11:53 UTC | support for updated cutadapt | 30 January 2017, 21:11:53 UTC |
| 109104a | deren | 30 January 2017, 21:11:42 UTC | bugfix for hackerdict modify of cov | 30 January 2017, 21:11:42 UTC |
| 18f9055 | deren | 30 January 2017, 21:11:21 UTC | chrom only for paired data | 30 January 2017, 21:11:21 UTC |
| 39b3e18 | deren | 30 January 2017, 21:10:48 UTC | changed two parameter names (trims) | 30 January 2017, 21:10:48 UTC |
| b34e44d | deren | 30 January 2017, 20:49:56 UTC | tested out MPI checks | 30 January 2017, 20:49:56 UTC |
| 01545a1 | deren | 30 January 2017, 20:49:41 UTC | cutadapt upgrade allow for --length option | 30 January 2017, 20:49:41 UTC |
| f385ed5 | isaacovercast | 30 January 2017, 16:34:16 UTC | Moved log file reset from init to main to prevent -r from blanking the log >:{ | 30 January 2017, 16:34:16 UTC |
| 6d5feb9 | isaacovercast | 30 January 2017, 16:32:37 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 30 January 2017, 16:32:37 UTC |
| d6af59f | isaacovercast | 30 January 2017, 16:32:35 UTC | Moved log file reset from __init__ to __main__ | 30 January 2017, 16:32:35 UTC |
| 067536c | isaac | 29 January 2017, 16:15:52 UTC | Don't bother aligning clusters with duplicates in step 6. | 29 January 2017, 16:15:52 UTC |
| b828e9d | deren | 29 January 2017, 01:10:49 UTC | baba update | 29 January 2017, 01:10:49 UTC |
| 9e2d744 | deren | 28 January 2017, 22:45:17 UTC | remove print statement left in code | 28 January 2017, 22:45:17 UTC |
| 4c93f1a | deren | 28 January 2017, 22:41:36 UTC | same fix to names parser, better. | 28 January 2017, 22:41:36 UTC |
| e839443 | deren | 28 January 2017, 22:26:23 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 28 January 2017, 22:26:23 UTC |
| 1240bf9 | deren | 28 January 2017, 22:26:20 UTC | added comment ideas for chrompos in refmap | 28 January 2017, 22:26:20 UTC |
| 8aecf53 | deren | 28 January 2017, 22:21:24 UTC | bug fix, Sample names were being oversplit if they had '.' in them | 28 January 2017, 22:21:24 UTC |
| 3a25a86 | deren | 28 January 2017, 22:20:32 UTC | test labels, improved spacing, collapse_outgroups options added to baba plots | 28 January 2017, 22:20:32 UTC |
| 6c669f4 | isaac | 28 January 2017, 19:39:46 UTC | Fix debug message in refmap and don't raise on failure to parse reference sequence. | 28 January 2017, 19:39:46 UTC |
| 75df4f0 | deren | 27 January 2017, 16:45:30 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 27 January 2017, 16:45:30 UTC |
| 31ebbb0 | deren | 27 January 2017, 16:45:15 UTC | attempts to make better cleanup for interrupt in API | 27 January 2017, 16:45:15 UTC |
| 0ea41a9 | deren | 27 January 2017, 16:44:47 UTC | some cleanup to calling steps 1,2 funcs | 27 January 2017, 16:44:47 UTC |
| ef4cb4d | deren | 27 January 2017, 16:30:22 UTC | speed testing demux code with single vs multicore | 27 January 2017, 16:30:22 UTC |
| fb3a2ef | deren | 27 January 2017, 16:24:35 UTC | moved setting of ['merged'] to replace filepath names to Assembly instead of main so that it also works for the API | 27 January 2017, 16:24:35 UTC |
| cc7975b | deren | 27 January 2017, 16:13:45 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 27 January 2017, 16:13:45 UTC |
| e4ac3c7 | deren | 27 January 2017, 16:10:45 UTC | added a np dict-like arr to be used in baba, maybe in ref. | 27 January 2017, 16:10:45 UTC |
| d30d2ad | deren | 27 January 2017, 16:09:51 UTC | baba plotting functions added | 27 January 2017, 16:09:51 UTC |
| 15cd8e5 | isaacovercast | 26 January 2017, 18:42:40 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 26 January 2017, 18:42:40 UTC |
| 20bad3e | isaacovercast | 26 January 2017, 18:42:38 UTC | Better handling of tmpdir in step 6. | 26 January 2017, 18:42:38 UTC |
| d4a2ec4 | deren | 22 January 2017, 18:25:43 UTC | added baba cookbook | 22 January 2017, 18:25:43 UTC |
| 7e42e44 | deren | 22 January 2017, 18:25:33 UTC | only map chrom pos if in reference mode | 22 January 2017, 18:25:33 UTC |
| cd6228f | deren | 22 January 2017, 18:25:00 UTC | new batch and plotting functions | 22 January 2017, 18:25:00 UTC |
| 6961ab4 | deren | 21 January 2017, 22:21:45 UTC | trim .txt from new branch name if accidentally added to avoid Assembly name error | 21 January 2017, 22:21:45 UTC |
| 7aba9c6 | deren | 21 January 2017, 18:01:57 UTC | added a name-checker to the branch-drop CLI command | 21 January 2017, 18:01:57 UTC |
| 5ff1700 | Isaac | 17 January 2017, 01:25:06 UTC | Fixed legend on Pedicularis manuscript analysis trees. | 17 January 2017, 01:25:06 UTC |
| 98dcaef | Isaac | 17 January 2017, 01:13:36 UTC | Cosmetic change | 17 January 2017, 01:13:36 UTC |
| b9989b2 | Isaac | 17 January 2017, 01:10:53 UTC | Adding manuscript analysis tree plotting for empirical PE ddRAD refmap assemblies. | 17 January 2017, 01:10:53 UTC |
