| 1e390a3 | Isaac Overcast | 13 April 2017, 07:48:52 UTC | "Updating ipyrad/__init__.py to version - 0.6.13 | 13 April 2017, 07:48:52 UTC |
| 92e9190 | Isaac Overcast | 13 April 2017, 07:48:25 UTC | Fix gphocs output format. | 13 April 2017, 07:48:25 UTC |
| a122555 | Isaac Overcast | 10 April 2017, 16:59:29 UTC | If the user removes the population assignment file blank out the data.populations dictionary. | 10 April 2017, 16:59:29 UTC |
| 9e5f564 | Isaac Overcast | 10 April 2017, 16:26:18 UTC | "Updating ipyrad/__init__.py to version - 0.6.12 | 10 April 2017, 16:26:18 UTC |
| 6440dfd | Isaac Overcast | 10 April 2017, 16:25:53 UTC | Prevent versioner from including merge commits in the release notes cuz they are annoying. | 10 April 2017, 16:25:53 UTC |
| 7012f19 | Isaac Overcast | 10 April 2017, 16:21:38 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 10 April 2017, 16:21:38 UTC |
| 231a034 | Isaac Overcast | 10 April 2017, 16:21:34 UTC | Add the date of each version to the releasenotes docs, for convenience. | 10 April 2017, 16:21:34 UTC |
| ddf0c33 | Isaac Overcast | 10 April 2017, 16:15:32 UTC | Experimenting with adding date to releasenotes.rst | 10 April 2017, 16:15:32 UTC |
| 6edbd03 | deren | 09 April 2017, 22:56:18 UTC | added more attributres to tree | 09 April 2017, 22:56:18 UTC |
| 2af18b1 | deren | 09 April 2017, 22:55:31 UTC | change alpha to >= | 09 April 2017, 22:55:31 UTC |
| 8440a22 | deren | 09 April 2017, 22:54:59 UTC | tip label and node label attributes added to tree | 09 April 2017, 22:54:59 UTC |
| 8cfae6f | deren | 09 April 2017, 22:54:22 UTC | tetrad ensure minrank is int | 09 April 2017, 22:54:22 UTC |
| ba0ae8f | deren | 09 April 2017, 22:53:31 UTC | fix structure obj removing old files | 09 April 2017, 22:53:31 UTC |
| 920d1b8 | deren | 09 April 2017, 22:52:57 UTC | lots of cleanup to baba code | 09 April 2017, 22:52:57 UTC |
| 86fbf9b | deren | 09 April 2017, 20:46:42 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 09 April 2017, 20:46:42 UTC |
| fc07b94 | deren | 09 April 2017, 20:46:34 UTC | edit to analysis docs | 09 April 2017, 20:46:34 UTC |
| 8b6a7f8 | Isaac Overcast | 09 April 2017, 09:45:52 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 09 April 2017, 09:45:52 UTC |
| fd00785 | Isaac Overcast | 09 April 2017, 09:45:44 UTC | Handle pop assignment file w/o the min sample per pop line. | 09 April 2017, 09:45:44 UTC |
| 2f61e53 | deren | 05 April 2017, 21:16:29 UTC | merge conflict resolved | 05 April 2017, 21:16:29 UTC |
| 9562ad3 | deren | 05 April 2017, 21:13:32 UTC | bug fix for tuples in output formats json | 05 April 2017, 21:13:32 UTC |
| 488144d | deren | 05 April 2017, 21:11:45 UTC | sim notebook started | 05 April 2017, 21:11:45 UTC |
| 67cb19f | deren | 05 April 2017, 21:11:02 UTC | cookbook abba-baba updated | 05 April 2017, 21:11:02 UTC |
| c7c564f | deren | 05 April 2017, 21:10:21 UTC | tetrad cookbook api added | 05 April 2017, 21:10:21 UTC |
| 1b07a92 | deren | 05 April 2017, 21:09:15 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 05 April 2017, 21:09:15 UTC |
| 63f49ed | deren | 05 April 2017, 21:09:12 UTC | added option to change line spacing on progress bar | 05 April 2017, 21:09:12 UTC |
| 0c858c6 | deren | 05 April 2017, 21:08:27 UTC | major overhaul to ipyrad.analysis and plotting | 05 April 2017, 21:08:27 UTC |
| 2bc1f84 | deren | 05 April 2017, 21:07:05 UTC | option to buffer line spacing on cluster report | 05 April 2017, 21:07:05 UTC |
| 4d35ca7 | Isaac Overcast | 04 April 2017, 07:17:00 UTC | Removed confusing punctuation in warning message | 04 April 2017, 07:17:00 UTC |
| 5fa27f2 | Isaac Overcast | 04 April 2017, 05:41:13 UTC | Make vcf and loci output files agree about CHROM number per locus. | 04 April 2017, 05:41:13 UTC |
| e18ad7c | Isaac Overcast | 04 April 2017, 05:39:58 UTC | Cosmetic change to debug output. | 04 April 2017, 05:39:58 UTC |
| 17fcef6 | Isaac Overcast | 03 April 2017, 12:14:32 UTC | Make the new debug info append instead of overwrite. | 03 April 2017, 12:14:32 UTC |
| 61b05be | Isaac Overcast | 03 April 2017, 10:22:34 UTC | Fix annoying bug with output_format param I introduced recently. | 03 April 2017, 10:22:34 UTC |
| a0e6cf4 | Isaac Overcast | 03 April 2017, 09:25:14 UTC | Add platform info to default log output on startup. | 03 April 2017, 09:25:14 UTC |
| 12de7a8 | deren | 31 March 2017, 20:30:06 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 31 March 2017, 20:30:06 UTC |
| 333459f | Isaac Overcast | 30 March 2017, 00:21:06 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 30 March 2017, 00:21:06 UTC |
| b6c0d9b | Isaac Overcast | 30 March 2017, 00:20:56 UTC | Actually write the error to the log file on cutadapt failure. | 30 March 2017, 00:20:56 UTC |
| b4a70cd | Isaac Overcast | 29 March 2017, 22:50:48 UTC | Write the version and the args used to the log file for each run. This might be annoying, but it could be useful. | 29 March 2017, 22:50:48 UTC |
| f91fd64 | deren | 29 March 2017, 21:58:51 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 29 March 2017, 21:58:51 UTC |
| e982575 | deren | 29 March 2017, 21:58:35 UTC | bpp randomize option added to write | 29 March 2017, 21:58:35 UTC |
| 7cdc49a | deren | 29 March 2017, 21:55:53 UTC | adding bpp cookbook update | 29 March 2017, 21:55:53 UTC |
| 3775d6d | deren | 29 March 2017, 21:55:26 UTC | updating analysis tools for new bpp baba and tree | 29 March 2017, 21:55:26 UTC |
| bd7a840 | deren | 29 March 2017, 20:26:11 UTC | merge resolved | 29 March 2017, 20:26:11 UTC |
| 20793ed | deren | 29 March 2017, 20:10:28 UTC | analysis init update for new funcs | 29 March 2017, 20:10:28 UTC |
| bd75281 | deren | 29 March 2017, 20:09:36 UTC | apitest update | 29 March 2017, 20:09:36 UTC |
| 082a286 | deren | 29 March 2017, 20:06:01 UTC | abba cookbook update | 29 March 2017, 20:06:01 UTC |
| 13eec90 | deren | 29 March 2017, 20:05:22 UTC | update bpp cookbook | 29 March 2017, 20:05:22 UTC |
| d54d9b8 | deren | 27 March 2017, 16:16:09 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 27 March 2017, 16:16:09 UTC |
| 9a09104 | deren | 27 March 2017, 16:16:02 UTC | small edit to HPC docs | 27 March 2017, 16:16:02 UTC |
| 3dd4daf | Isaac Overcast | 27 March 2017, 12:26:11 UTC | "Updating ipyrad/__init__.py to version - 0.6.11 | 27 March 2017, 12:26:11 UTC |
| ee57ad3 | Isaac Overcast | 27 March 2017, 12:25:47 UTC | Fix a bug in PE refmapping. | 27 March 2017, 12:25:47 UTC |
| 408c8b0 | Isaac Overcast | 26 March 2017, 19:08:45 UTC | Fix error reporting if when testing for existence of the clust_database file at beginning of step 7. | 26 March 2017, 19:08:45 UTC |
| 7e53211 | Isaac Overcast | 25 March 2017, 18:55:31 UTC | Fix bug reading output formats from params file. | 25 March 2017, 18:55:31 UTC |
| 2894ea4 | Isaac Overcast | 25 March 2017, 18:03:02 UTC | cosmetic | 25 March 2017, 18:03:02 UTC |
| 5971c2d | Isaac Overcast | 25 March 2017, 17:54:25 UTC | Add docs for dealing with long running jobs due to quality issues. | 25 March 2017, 17:54:25 UTC |
| 206ce4e | deren | 23 March 2017, 22:17:16 UTC | tetrad formatting changing | 23 March 2017, 22:17:16 UTC |
| 1a02c3d | deren | 23 March 2017, 22:16:42 UTC | updated analysis tools cookbooks | 23 March 2017, 22:16:42 UTC |
| fb765ad | deren | 23 March 2017, 18:28:59 UTC | bug fix for output format empty | 23 March 2017, 18:28:59 UTC |
| 2449b44 | deren | 23 March 2017, 18:28:26 UTC | structure cookbook update | 23 March 2017, 18:28:26 UTC |
| 1369882 | deren | 23 March 2017, 00:23:21 UTC | pushing analysis tools | 23 March 2017, 00:23:21 UTC |
| d19f91a | deren | 22 March 2017, 18:29:54 UTC | svg struct plot added | 22 March 2017, 18:29:54 UTC |
| 0b4d04b | deren | 22 March 2017, 18:27:32 UTC | structure cookbook updates | 22 March 2017, 18:27:32 UTC |
| d05106f | deren | 22 March 2017, 18:26:18 UTC | struct image added for docs | 22 March 2017, 18:26:18 UTC |
| 6b575d6 | deren | 22 March 2017, 18:03:45 UTC | update structure cookbook for new code | 22 March 2017, 18:03:45 UTC |
| fecf493 | isaacovercast | 21 March 2017, 20:13:24 UTC | Actually fix the output_format default if blank. | 21 March 2017, 20:13:24 UTC |
| 5c27e9e | isaacovercast | 21 March 2017, 20:09:18 UTC | Set blank output formats in params to default to all formats. | 21 March 2017, 20:09:18 UTC |
| d14ab21 | Isaac Overcast | 13 March 2017, 23:06:04 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 13 March 2017, 23:06:04 UTC |
| 7c5d1a6 | Isaac Overcast | 13 March 2017, 23:05:43 UTC | Add a filter flag for samtools to push secondary alignments to the unmapped file. | 13 March 2017, 23:05:43 UTC |
| c30a64a | deren | 13 March 2017, 05:59:09 UTC | docs analysis page fix | 13 March 2017, 05:59:09 UTC |
| 90ca782 | deren | 13 March 2017, 05:00:52 UTC | rm old files | 13 March 2017, 05:00:52 UTC |
| e01d24f | deren | 13 March 2017, 04:59:47 UTC | shareplot code in progress | 13 March 2017, 04:59:47 UTC |
| 025afee | deren | 13 March 2017, 04:58:37 UTC | work in progress baba code notebook | 13 March 2017, 04:58:37 UTC |
| 775404e | deren | 13 March 2017, 04:57:32 UTC | a decent api intro but bland | 13 March 2017, 04:57:32 UTC |
| eb3ffcb | deren | 13 March 2017, 04:55:31 UTC | beginnings of a migrate script | 13 March 2017, 04:55:31 UTC |
| 1afdcfe | deren | 13 March 2017, 04:54:49 UTC | raxml docs updated, needs work still | 13 March 2017, 04:54:49 UTC |
| 3f5e340 | deren | 13 March 2017, 04:53:39 UTC | analysis docs page update | 13 March 2017, 04:53:39 UTC |
| 052608d | deren | 13 March 2017, 04:52:35 UTC | cosmetic changes | 13 March 2017, 04:52:35 UTC |
| 90e4556 | deren | 12 March 2017, 19:52:33 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 12 March 2017, 19:52:33 UTC |
| 030e3bf | deren | 12 March 2017, 19:50:19 UTC | structure parallel wrapper scripts up in analysis | 12 March 2017, 19:50:19 UTC |
| 21a63b3 | deren | 12 March 2017, 19:49:42 UTC | cosmetic | 12 March 2017, 19:49:42 UTC |
| ed75c16 | deren | 12 March 2017, 19:49:21 UTC | simplifying analysis imports | 12 March 2017, 19:49:21 UTC |
| ad84dbd | deren | 12 March 2017, 19:46:30 UTC | cleanup top imports | 12 March 2017, 19:46:30 UTC |
| 4c1b818 | isaac | 12 March 2017, 00:22:34 UTC | Adding support for G-PhoCS output format. | 12 March 2017, 00:22:34 UTC |
| 74b0bc9 | isaac | 11 March 2017, 23:40:46 UTC | Fix wacky reporting of mapped/unmapped reads for PE. | 11 March 2017, 23:40:46 UTC |
| dae2b73 | Isaac Overcast | 11 March 2017, 21:20:16 UTC | Document why we don't write out the alleles format currently. | 11 March 2017, 21:20:16 UTC |
| 3cf065f | deren | 11 March 2017, 17:21:05 UTC | added header to bpp convert script | 11 March 2017, 17:21:05 UTC |
| c99743d | deren | 10 March 2017, 00:33:33 UTC | module init headers | 10 March 2017, 00:33:33 UTC |
| 8eb0c4b | deren | 09 March 2017, 20:02:32 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 09 March 2017, 20:02:32 UTC |
| c05a838 | deren | 09 March 2017, 20:02:27 UTC | added loci2cf script | 09 March 2017, 20:02:27 UTC |
| e54926f | deren | 09 March 2017, 19:48:43 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 09 March 2017, 19:48:43 UTC |
| 9bf2ebd | deren | 09 March 2017, 19:32:19 UTC | update structure notebook with conda recipes | 09 March 2017, 19:32:19 UTC |
| 4a740df | deren | 09 March 2017, 19:24:13 UTC | fileconversions updated | 09 March 2017, 19:24:13 UTC |
| 668a36c | deren | 09 March 2017, 19:22:06 UTC | loci2cf func added | 09 March 2017, 19:22:06 UTC |
| abae994 | deren | 09 March 2017, 19:20:28 UTC | cookbook bucky docs up | 09 March 2017, 19:20:28 UTC |
| 8b9d839 | deren | 09 March 2017, 19:18:18 UTC | loci2multinex and bucky notebook updated | 09 March 2017, 19:18:18 UTC |
| 1bf0992 | deren | 09 March 2017, 19:12:21 UTC | BUCKy cookbook updated | 09 March 2017, 19:12:21 UTC |
| 960e70e | deren | 06 March 2017, 16:57:11 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 06 March 2017, 16:57:11 UTC |
| 849efca | deren | 06 March 2017, 16:53:53 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 06 March 2017, 16:53:53 UTC |
| e0a907f | deren | 06 March 2017, 16:52:31 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 06 March 2017, 16:52:31 UTC |
| 9a751b5 | deren | 06 March 2017, 00:56:59 UTC | bucky conda recipe up | 06 March 2017, 00:56:59 UTC |
| a41aa68 | deren | 05 March 2017, 20:54:33 UTC | fix to API access hint | 05 March 2017, 20:54:33 UTC |
