| 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 |
| 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 |
| 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 |
| 1b649e2 | dereneaton | 01 June 2016, 13:51:56 UTC | update to params defaults for getting rid of excludes/outgroup | 01 June 2016, 13:51:56 UTC |
| 99bed69 | dereneaton | 01 June 2016, 13:50:42 UTC | removed exclude and outgroup params options | 01 June 2016, 13:50:42 UTC |
| 1da9f90 | dereneaton | 01 June 2016, 13:50:06 UTC | prettier printing of skipping sample statements | 01 June 2016, 13:50:06 UTC |
| ddc25b2 | dereneaton | 01 June 2016, 13:48:47 UTC | store N alleles information | 01 June 2016, 13:48:47 UTC |
| 20109b5 | dereneaton | 01 June 2016, 13:47:28 UTC | raise warning if older params format | 01 June 2016, 13:47:28 UTC |
| 1fdc2e2 | dereneaton | 01 June 2016, 13:45:25 UTC | added anchored right side for 'rad' alignment | 01 June 2016, 13:45:25 UTC |
| 6efc57a | dereneaton | 01 June 2016, 13:44:52 UTC | fix for optim when small chunk sizes / changed successful check to completed and successful check / muscle alignment for 'rad' includes anchored right side / number of alleles is stored in database... but should we store the alleles proper?. | 01 June 2016, 13:44:52 UTC |
| aec4110 | isaacovercast | 31 May 2016, 18:21:08 UTC | fix link to datatypes | 31 May 2016, 18:21:08 UTC |
| ae597a0 | isaacovercast | 31 May 2016, 17:52:09 UTC | "Updating ipyrad/__init__.py to version - 0.2.11 | 31 May 2016, 17:52:09 UTC |
| 3cbe159 | isaacovercast | 31 May 2016, 17:51:20 UTC | Added support (weak) for multiple cutters | 31 May 2016, 17:51:20 UTC |
| 046e612 | isaacovercast | 31 May 2016, 17:50:40 UTC | Added support (weak) for multiple cutters, and removed an erroneous that was unnecessarily doubling the size of 'readlen' | 31 May 2016, 17:50:40 UTC |
| 31a8c4f | isaacovercast | 31 May 2016, 17:49:44 UTC | add a conditional to test for data.nloci < 100 and set chunk appropriately, to support running on small test datasets | 31 May 2016, 17:49:44 UTC |
| c3be239 | isaacovercast | 31 May 2016, 17:48:53 UTC | 3rad drop seqs w/ N in the i5 | 31 May 2016, 17:48:53 UTC |
| b058f96 | isaacovercast | 31 May 2016, 16:46:04 UTC | fixed a bug with pair data that was overallocating bcz of 2* max_fragment_length | 31 May 2016, 16:46:04 UTC |
| 67fc98e | isaacovercast | 31 May 2016, 16:30:07 UTC | added references for 3rad | 31 May 2016, 16:30:07 UTC |
| 4b6cdb5 | isaacovercast | 31 May 2016, 16:24:27 UTC | added declone_3rad() function. | 31 May 2016, 16:24:27 UTC |
| 54fe9da | isaacovercast | 30 May 2016, 18:44:09 UTC | Merge branch '3rad' of https://github.com/dereneaton/ipyrad into 3rad | 30 May 2016, 18:44:09 UTC |
| aea10ad | isaacovercast | 30 May 2016, 18:44:02 UTC | cosmetic | 30 May 2016, 18:44:02 UTC |
| f4433b7 | isaacovercast | 30 May 2016, 18:40:39 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad into 3rad | 30 May 2016, 18:40:39 UTC |
| 0cfbbb3 | isaacovercast | 30 May 2016, 18:40:07 UTC | 3rad support. Also some more robust error handling for s2 and 3 | 30 May 2016, 18:40:07 UTC |
| 5f260f7 | isaacovercast | 30 May 2016, 03:12:50 UTC | 3Rad update, support for more than 2 restriction_overhang values. Updated docs. | 30 May 2016, 03:12:50 UTC |
| 1b7728f | isaacovercast | 30 May 2016, 01:31:44 UTC | Fix bug that was appending to fastqs during step 1 w/ force flag. | 30 May 2016, 01:31:44 UTC |
| e363f73 | isaacovercast | 29 May 2016, 20:11:34 UTC | reset 3rad dtype to 'pair3rad'. Also fixed the assembly.stats function so it doesn't shit the bed on NaN | 29 May 2016, 20:11:34 UTC |
| b78a747 | dereneaton | 29 May 2016, 04:21:18 UTC | fix to merge conflict | 29 May 2016, 04:21:18 UTC |
| 2d83da6 | dereneaton | 29 May 2016, 04:19:55 UTC | fix for error reporting | 29 May 2016, 04:19:55 UTC |
| d0cfdb6 | dereneaton | 29 May 2016, 04:18:16 UTC | fix for error reporting | 29 May 2016, 04:18:16 UTC |
| 6e3de00 | dereneaton | 29 May 2016, 04:17:35 UTC | re-parallelized step1 | 29 May 2016, 04:17:35 UTC |
| 35ffb69 | isaacovercast | 29 May 2016, 03:07:16 UTC | Support for demux 3rad. adapters are hard coded at this point. | 29 May 2016, 03:07:16 UTC |
| b83664f | isaacovercast | 28 May 2016, 17:57:26 UTC | "Updating ipyrad/__init__.py to version - 0.2.10 | 28 May 2016, 17:57:26 UTC |
| 9fc0dcc | isaacovercast | 28 May 2016, 17:56:37 UTC | After all jobs complete test jobs.read() as well as jobs.successful() otherwise it dies on an assert if the job isn't ready | 28 May 2016, 17:56:37 UTC |
| 3f61711 | isaacovercast | 23 May 2016, 18:15:41 UTC | "Updating ipyrad/__init__.py to version - 0.2.9 | 23 May 2016, 18:15:41 UTC |
| 15007d5 | isaacovercast | 22 May 2016, 16:13:41 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 22 May 2016, 16:13:41 UTC |
| 36f90d7 | deren | 16 May 2016, 19:40:23 UTC | update to svd4tet to avoid nan errors on weights | 16 May 2016, 19:40:23 UTC |
| 4b8d23a | isaacovercast | 16 May 2016, 12:43:57 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 16 May 2016, 12:43:57 UTC |
| b5cc70a | dereneaton | 16 May 2016, 05:43:14 UTC | "Updating ipyrad/__init__.py to version - 0.2.8 | 16 May 2016, 05:43:14 UTC |
| 0c7bf1d | dereneaton | 16 May 2016, 05:42:43 UTC | fix to pairddrad edge trimming | 16 May 2016, 05:42:43 UTC |
| 0527f7c | isaacovercast | 15 May 2016, 23:42:57 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 15 May 2016, 23:42:57 UTC |
| 7f31641 | dereneaton | 15 May 2016, 22:26:21 UTC | docs updates | 15 May 2016, 22:26:21 UTC |
| c4cf441 | dereneaton | 15 May 2016, 21:55:20 UTC | docs update | 15 May 2016, 21:55:20 UTC |
| bfa0c60 | dereneaton | 15 May 2016, 19:04:15 UTC | "Updating ipyrad/__init__.py to version - 0.2.7 | 15 May 2016, 19:04:15 UTC |
| 4d1b16f | dereneaton | 15 May 2016, 19:04:06 UTC | fix to paired edge masking, still need minor fix to snp counting. | 15 May 2016, 19:04:06 UTC |
| 0c1da88 | isaacovercast | 15 May 2016, 15:14:24 UTC | Changed all docs to reflect the changed file names of the sim data | 15 May 2016, 15:14:24 UTC |
| 77b1733 | isaacovercast | 15 May 2016, 14:54:08 UTC | updated qscore offset docs | 15 May 2016, 14:54:08 UTC |
| 1e8bb4d | dereneaton | 14 May 2016, 19:45:02 UTC | docs updates | 14 May 2016, 19:45:02 UTC |
| 6826653 | dereneaton | 14 May 2016, 19:42:36 UTC | advanced tut update | 14 May 2016, 19:42:36 UTC |
| d33a62b | dereneaton | 14 May 2016, 19:40:47 UTC | advanced tut update | 14 May 2016, 19:40:47 UTC |
| 389f0e3 | dereneaton | 14 May 2016, 19:34:27 UTC | advanced tut update | 14 May 2016, 19:34:27 UTC |
| 8aef10a | dereneaton | 14 May 2016, 19:25:31 UTC | docs update | 14 May 2016, 19:25:31 UTC |
| d2afd5c | dereneaton | 14 May 2016, 19:20:52 UTC | docs update | 14 May 2016, 19:20:52 UTC |
| 655a2a9 | dereneaton | 14 May 2016, 19:19:15 UTC | docs update | 14 May 2016, 19:19:15 UTC |
| 84cf8fc | dereneaton | 14 May 2016, 19:15:10 UTC | docs update | 14 May 2016, 19:15:10 UTC |
| 0738f96 | dereneaton | 14 May 2016, 19:13:16 UTC | docs update | 14 May 2016, 19:13:16 UTC |
| a09f813 | dereneaton | 14 May 2016, 19:08:55 UTC | docs update | 14 May 2016, 19:08:55 UTC |
| 2ded41d | dereneaton | 14 May 2016, 19:08:14 UTC | docs update | 14 May 2016, 19:08:14 UTC |
| 375bd83 | dereneaton | 14 May 2016, 19:07:19 UTC | docs update | 14 May 2016, 19:07:19 UTC |
| ee42a14 | dereneaton | 14 May 2016, 19:05:36 UTC | docs update | 14 May 2016, 19:05:36 UTC |
| 0ac8220 | dereneaton | 14 May 2016, 19:03:30 UTC | docs update | 14 May 2016, 19:03:30 UTC |
| 8dffc68 | dereneaton | 14 May 2016, 19:01:04 UTC | docs update | 14 May 2016, 19:01:04 UTC |
| 810e514 | dereneaton | 14 May 2016, 18:49:07 UTC | docs update | 14 May 2016, 18:49:07 UTC |
| aca51e5 | dereneaton | 14 May 2016, 18:41:03 UTC | docs update | 14 May 2016, 18:41:03 UTC |
| 21586a5 | dereneaton | 14 May 2016, 18:40:33 UTC | docs update | 14 May 2016, 18:40:33 UTC |
| 9d252f8 | dereneaton | 14 May 2016, 18:37:19 UTC | docs update | 14 May 2016, 18:37:19 UTC |
| a311bf5 | dereneaton | 14 May 2016, 18:27:31 UTC | docs update | 14 May 2016, 18:27:31 UTC |
| b598c14 | dereneaton | 14 May 2016, 18:12:53 UTC | docs update | 14 May 2016, 18:12:53 UTC |
