| e1532ad | isaacovercast | 28 June 2016, 16:01:45 UTC | "Updating ipyrad/__init__.py to version - 0.3.13 | 28 June 2016, 16:01:45 UTC |
| 3144b4e | isaacovercast | 28 June 2016, 16:01:04 UTC | Replaced direct call to with ipyrad.bins.vsearch | 28 June 2016, 16:01:04 UTC |
| 4bb37d3 | isaacovercast | 25 June 2016, 16:59:00 UTC | Fixed reference to old style assembly method reference_sub | 25 June 2016, 16:59:00 UTC |
| 7608a43 | isaacovercast | 24 June 2016, 22:14:07 UTC | Added ability to optionally pass in a flat file listing subsample names in a column. | 24 June 2016, 22:14:07 UTC |
| 1865db5 | isaacovercast | 24 June 2016, 21:19:23 UTC | Set a conditional to make sure params file is passed in if doing -b, -r, or -s | 24 June 2016, 21:19:23 UTC |
| 08b3d60 | isaacovercast | 24 June 2016, 21:06:18 UTC | Softened the warning about overlapping barcodes, and added a bit more explanation | 24 June 2016, 21:06:18 UTC |
| 15cb213 | isaacovercast | 24 June 2016, 20:53:36 UTC | Set default max barcode mismatch to 0 | 24 June 2016, 20:53:36 UTC |
| 715f5e7 | isaacovercast | 24 June 2016, 20:27:54 UTC | "Updating ipyrad/__init__.py to version - 0.3.12 | 24 June 2016, 20:27:54 UTC |
| 8b70d36 | isaacovercast | 24 June 2016, 20:25:11 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 24 June 2016, 20:25:11 UTC |
| 3cc63a2 | isaacovercast | 24 June 2016, 20:24:57 UTC | Fixed infinite while loop inside __name_from_file | 24 June 2016, 20:24:57 UTC |
| 4fd7813 | isaacovercast | 24 June 2016, 18:12:00 UTC | "Updating ipyrad/__init__.py to version - 0.3.11 | 24 June 2016, 18:12:00 UTC |
| a4c399d | isaacovercast | 24 June 2016, 18:11:37 UTC | Fixed commented call to cluster(), step 6 is working again | 24 June 2016, 18:11:37 UTC |
| 16367d5 | isaacovercast | 24 June 2016, 16:07:43 UTC | Added a check to ensure barcodes contain only IUPAC characters | 24 June 2016, 16:07:43 UTC |
| c2665c6 | isaacovercast | 23 June 2016, 21:59:00 UTC | Fixed demultiplex sorting progress bar | 23 June 2016, 21:59:00 UTC |
| d186067 | isaacovercast | 23 June 2016, 21:42:50 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 23 June 2016, 21:42:50 UTC |
| ce103f0 | isaacovercast | 23 June 2016, 21:42:48 UTC | append data.name to the tmp-chunks directory to prevent users from running multiple step1 and stepping on themselves | 23 June 2016, 21:42:48 UTC |
| d1eeb0f | Deren Eaton | 20 June 2016, 22:11:27 UTC | Update README.rst | 20 June 2016, 22:11:27 UTC |
| e3089e4 | isaacovercast | 20 June 2016, 16:57:42 UTC | Added force flag for merging CLI | 20 June 2016, 16:57:42 UTC |
| 273d106 | isaacovercast | 20 June 2016, 03:07:34 UTC | cosmetic changes | 20 June 2016, 03:07:34 UTC |
| 67e4780 | isaacovercast | 20 June 2016, 02:55:04 UTC | Bug in rawedit for merged assemblies | 20 June 2016, 02:55:04 UTC |
| f93b60a | dereneaton | 16 June 2016, 05:11:24 UTC | much faster indel entry in step6 | 16 June 2016, 05:11:24 UTC |
| 58e33a8 | dereneaton | 16 June 2016, 04:05:53 UTC | chunks size optimization | 16 June 2016, 04:05:53 UTC |
| 3a4f017 | dereneaton | 16 June 2016, 03:55:08 UTC | optimizing chunk size step6 | 16 June 2016, 03:55:08 UTC |
| ef751e5 | deren | 16 June 2016, 03:29:00 UTC | merge for lowmem fixes to step6 | 16 June 2016, 03:29:00 UTC |
| ff377fa | deren | 16 June 2016, 03:25:46 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 16 June 2016, 03:25:46 UTC |
| bcdeff1 | dereneaton | 16 June 2016, 03:02:53 UTC | decided against right anchoring method from rad muscle alignments. Improved step6 muscle align progress bar | 16 June 2016, 03:02:53 UTC |
| f9d4242 | deren | 16 June 2016, 02:19:34 UTC | reducing memory load in step6 | 16 June 2016, 02:19:34 UTC |
| 1824ab0 | deren | 15 June 2016, 13:50:47 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 15 June 2016, 13:50:47 UTC |
| 4056047 | isaacovercast | 13 June 2016, 16:29:42 UTC | "Updating ipyrad/__init__.py to version - 0.3.10 | 13 June 2016, 16:29:42 UTC |
| 9ef17ca | isaacovercast | 13 June 2016, 16:29:19 UTC | versioner now actually commits the releasenotes.rst | 13 June 2016, 16:29:19 UTC |
| 28b5016 | isaacovercast | 13 June 2016, 16:24:22 UTC | "Updating ipyrad/__init__.py to version - 0.3.9 | 13 June 2016, 16:24:22 UTC |
| 41c5f23 | isaacovercast | 13 June 2016, 16:23:49 UTC | Versioner now updates the docs/releasenotes.rst | 13 June 2016, 16:23:49 UTC |
| 7d425ea | isaacovercast | 13 June 2016, 02:02:08 UTC | cosmetic changes | 13 June 2016, 02:02:08 UTC |
| a92f2b5 | deren | 13 June 2016, 01:58:27 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 13 June 2016, 01:58:27 UTC |
| 42ffe8b | dereneaton | 13 June 2016, 01:50:06 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 13 June 2016, 01:50:06 UTC |
| a5740bf | deren | 13 June 2016, 01:49:32 UTC | debug merge fix | 13 June 2016, 01:49:32 UTC |
| b1899c9 | isaacovercast | 13 June 2016, 01:10:48 UTC | Eased back on the language in the performance expectations note | 13 June 2016, 01:10:48 UTC |
| 0dd9f74 | isaacovercast | 13 June 2016, 01:08:44 UTC | fixed all links to output formats file | 13 June 2016, 01:08:44 UTC |
| 61d84a2 | dereneaton | 13 June 2016, 01:00:12 UTC | "Updating ipyrad/__init__.py to version - 0.3.8 | 13 June 2016, 01:00:12 UTC |
| 738774a | isaacovercast | 13 June 2016, 00:59:42 UTC | blank page for recording different performance expectations | 13 June 2016, 00:59:42 UTC |
| 51de9ec | dereneaton | 13 June 2016, 00:53:04 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 13 June 2016, 00:53:04 UTC |
| 68bce12 | dereneaton | 13 June 2016, 00:52:51 UTC | much faster and lower memory concatenation and shuffling of consens files | 13 June 2016, 00:52:51 UTC |
| e1f5baa | isaacovercast | 13 June 2016, 00:52:24 UTC | fuck rst | 13 June 2016, 00:52:24 UTC |
| b103b87 | isaacovercast | 13 June 2016, 00:48:27 UTC | fuck rst | 13 June 2016, 00:48:27 UTC |
| b3cc4b9 | dereneaton | 13 June 2016, 00:47:02 UTC | max_alleles_consens filter now applied | 13 June 2016, 00:47:02 UTC |
| d1e28df | isaacovercast | 13 June 2016, 00:45:43 UTC | flesh out vcf and add a little blurb at the top | 13 June 2016, 00:45:43 UTC |
| a75fa32 | isaacovercast | 13 June 2016, 00:45:11 UTC | Changed the language in max_alleles_consens and tried to update the link to output_formats | 13 June 2016, 00:45:11 UTC |
| 37d6638 | isaacovercast | 13 June 2016, 00:24:40 UTC | oops forgot vcf | 13 June 2016, 00:24:40 UTC |
| 312d916 | isaacovercast | 13 June 2016, 00:22:04 UTC | Finished currently supported output formats. | 13 June 2016, 00:22:04 UTC |
| 0f024c5 | isaacovercast | 12 June 2016, 23:50:46 UTC | Added phylip | 12 June 2016, 23:50:46 UTC |
| bf9e4d8 | isaacovercast | 12 June 2016, 23:43:36 UTC | Filling in data types | 12 June 2016, 23:43:36 UTC |
| 7e2e9fa | isaacovercast | 12 June 2016, 23:26:20 UTC | finished polish on intro CLI tut | 12 June 2016, 23:26:20 UTC |
| e762570 | isaacovercast | 12 June 2016, 21:40:00 UTC | More polish on the intro_cli tut | 12 June 2016, 21:40:00 UTC |
| 7585d87 | isaacovercast | 12 June 2016, 20:03:44 UTC | polishing intro tutorial | 12 June 2016, 20:03:44 UTC |
| ce9fdab | isaacovercast | 12 June 2016, 19:30:30 UTC | "Updating ipyrad/__init__.py to version - 0.3.7 | 12 June 2016, 19:30:30 UTC |
| 5619fd2 | isaacovercast | 12 June 2016, 19:29:51 UTC | Fixed debug flag logging for CLI | 12 June 2016, 19:29:51 UTC |
| 265bc20 | deren | 12 June 2016, 18:04:45 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 12 June 2016, 18:04:45 UTC |
| f78c59a | dereneaton | 12 June 2016, 17:05:21 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 12 June 2016, 17:05:21 UTC |
| d3ad432 | dereneaton | 12 June 2016, 17:05:16 UTC | added an autosave feature for when running API steps | 12 June 2016, 17:05:16 UTC |
| 1c5b38c | isaacovercast | 12 June 2016, 01:17:02 UTC | Added some weak docs about branching with restricted # of samples | 12 June 2016, 01:17:02 UTC |
| 5c78117 | isaacovercast | 12 June 2016, 01:16:30 UTC | Added more refs for external tools we rely on | 12 June 2016, 01:16:30 UTC |
| b62219c | deren | 11 June 2016, 22:07:04 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 11 June 2016, 22:07:04 UTC |
| 53c7415 | isaacovercast | 11 June 2016, 21:59:19 UTC | "Updating ipyrad/__init__.py to version - 0.3.6 | 11 June 2016, 21:59:19 UTC |
| 904a444 | isaacovercast | 11 June 2016, 21:58:25 UTC | Support for the -m flag for merging assemblies | 11 June 2016, 21:58:25 UTC |
| 8047706 | isaacovercast | 11 June 2016, 21:43:25 UTC | Changed the way debug works so now it doesn't need to check the __loglevel__ before checkin | 11 June 2016, 21:43:25 UTC |
| d114258 | isaacovercast | 11 June 2016, 21:11:14 UTC | Fixed setting max_shared_Hs_locus for API | 11 June 2016, 21:11:14 UTC |
| f21e8c8 | deren | 11 June 2016, 20:56:48 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 11 June 2016, 20:56:48 UTC |
| 063fcd4 | dereneaton | 11 June 2016, 20:46:48 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 11 June 2016, 20:46:48 UTC |
| d202cc7 | dereneaton | 11 June 2016, 20:46:46 UTC | merge working, in step2 will concatenate multiple fastq files if present. But merges after step2 will not combine/merge data into the same Sample, but will work for joining Samples into the same Assembly. | 11 June 2016, 20:46:46 UTC |
| 4de4ce6 | isaacovercast | 11 June 2016, 18:45:44 UTC | "Updating ipyrad/__init__.py to version - 0.3.5 | 11 June 2016, 18:45:44 UTC |
| 40dfb81 | isaacovercast | 11 June 2016, 18:42:26 UTC | Fix merge conflict for casting max_shared_Hs locus | 11 June 2016, 18:42:26 UTC |
| 0b36bfb | isaacovercast | 11 June 2016, 18:41:08 UTC | Fixed bug with max_shared_Hs_locus not casting right, and step 7 would error out | 11 June 2016, 18:41:08 UTC |
| 0a67241 | deren | 11 June 2016, 00:03:35 UTC | improvement to debug flag. Much improved memory handling for demultiplexing | 11 June 2016, 00:03:35 UTC |
| dff65e5 | Isaac Overcast | 10 June 2016, 18:25:05 UTC | update readme to be more official | 10 June 2016, 18:25:05 UTC |
| b559665 | deren | 10 June 2016, 17:55:35 UTC | "Updating ipyrad/__init__.py to version - 0.3.4 | 10 June 2016, 17:55:35 UTC |
| 01a22fa | deren | 10 June 2016, 17:55:20 UTC | bug fix for failure when project_dir is ./ | 10 June 2016, 17:55:20 UTC |
| 41db082 | deren | 10 June 2016, 17:54:55 UTC | simplified debug flag, and works better with API | 10 June 2016, 17:54:55 UTC |
| be391c4 | deren | 09 June 2016, 23:51:38 UTC | fix to nan error in s7 output. Removed optim//2 from demulti. Testing larger buffer size for demultiplexing | 09 June 2016, 23:51:38 UTC |
| df877b7 | deren | 09 June 2016, 21:46:45 UTC | "Updating ipyrad/__init__.py to version - 0.3.3 | 09 June 2016, 21:46:45 UTC |
| 93408c9 | deren | 09 June 2016, 21:46:18 UTC | simplified demultiplexing with zcat_make_temps. handles interrupts. name splitting on link_fastqs bug fix | 09 June 2016, 21:46:18 UTC |
| 72b6520 | dereneaton | 06 June 2016, 18:37:08 UTC | "Updating ipyrad/__init__.py to version - 0.3.2 | 06 June 2016, 18:37:08 UTC |
| 44a2eb2 | dereneaton | 06 June 2016, 18:36:36 UTC | int/float fix for bug in trying to make an int from a string of the max_shared_Hs_locus param | 06 June 2016, 18:36:36 UTC |
| 0fb8eeb | isaacovercast | 06 June 2016, 16:25:47 UTC | "Updating ipyrad/__init__.py to version - 0.3.1 | 06 June 2016, 16:25:47 UTC |
| 6fe0f90 | dereneaton | 06 June 2016, 14:19:15 UTC | working on debugging | 06 June 2016, 14:19:15 UTC |
| 1b67594 | dereneaton | 06 June 2016, 14:15:01 UTC | "Updating ipyrad/__init__.py to version - 0.3.0 | 06 June 2016, 14:15:01 UTC |
| 3681daa | dereneaton | 06 June 2016, 14:14:51 UTC | debug flag is working, sets to INFO | 06 June 2016, 14:14:51 UTC |
| d6dc4ed | dereneaton | 06 June 2016, 13:34:55 UTC | init indent error | 06 June 2016, 13:34:55 UTC |
| 8411001 | dereneaton | 06 June 2016, 13:25:03 UTC | "Updating ipyrad/__init__.py to version - 0.3.0 | 06 June 2016, 13:25:03 UTC |
| 80f81fe | dereneaton | 06 June 2016, 13:22:56 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 06 June 2016, 13:22:56 UTC |
| 2cc10e8 | dereneaton | 06 June 2016, 13:22:37 UTC | bug fix to step7 filters that were not applying | 06 June 2016, 13:22:37 UTC |
| 6018f11 | isaacovercast | 03 June 2016, 19:45:14 UTC | Finished fixing support for the debug flag. Works good. | 03 June 2016, 19:45:14 UTC |
| b9774ac | isaacovercast | 03 June 2016, 16:12:21 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 03 June 2016, 16:12:21 UTC |
| b4bc6a4 | isaacovercast | 03 June 2016, 16:12:18 UTC | Added the debug flag -d though it isn't working right yet | 03 June 2016, 16:12:18 UTC |
| acb904b | dereneaton | 03 June 2016, 15:40:01 UTC | merge conflict resolve | 03 June 2016, 15:40:01 UTC |
| 4e7fc3e | dereneaton | 03 June 2016, 15:38:17 UTC | update to 0.30 pre-push update | 03 June 2016, 15:38:17 UTC |
| 00f0bca | isaacovercast | 02 June 2016, 21:31:45 UTC | test if job.ready() before calling job.successful() | 02 June 2016, 21:31:45 UTC |
| 3e3216c | isaacovercast | 02 June 2016, 21:31:23 UTC | test if job.ready() before calling job.successful() | 02 June 2016, 21:31:23 UTC |
| 16ff150 | isaacovercast | 02 June 2016, 21:30:19 UTC | Nasty bug where max_shared_Hs_locus was not getting actually used | 02 June 2016, 21:30:19 UTC |
| 92fe6be | dereneaton | 01 June 2016, 13:52:53 UTC | add some logger error printing | 01 June 2016, 13:52:53 UTC |
| 847378c | dereneaton | 01 June 2016, 13:52:27 UTC | skip excludes if in params file | 01 June 2016, 13:52:27 UTC |
