| 55706b0 | Kevin Bonham | 22 February 2020, 20:37:33 UTC | Add repo status badge | 22 February 2020, 20:37:33 UTC |
| de56423 | KEVIN BONHAM | 22 June 2017, 20:34:06 UTC | add travis badge to README | 22 June 2017, 20:34:06 UTC |
| 5fbc522 | KEVIN BONHAM | 22 June 2017, 20:31:18 UTC | improve logger implementation | 22 June 2017, 20:31:18 UTC |
| 62717ab | KEVIN BONHAM | 12 June 2017, 18:38:47 UTC | add docs link to README | 12 June 2017, 18:38:47 UTC |
| cf4c966 | KEVIN BONHAM | 12 June 2017, 18:36:06 UTC | Merge branch 'master' of github.com:kescobo/kvasir into docs | 12 June 2017, 18:36:06 UTC |
| 6c40fba | KEVIN BONHAM | 12 June 2017, 18:34:19 UTC | Update README with Badge | 12 June 2017, 18:34:19 UTC |
| 04858a2 | Kevin Bonham | 12 June 2017, 18:30:51 UTC | Merge pull request #28 from kescobo/docs Update Docs - checking to see if readthedocs.io updates | 12 June 2017, 18:30:51 UTC |
| 93af34d | KEVIN BONHAM | 12 June 2017, 18:26:48 UTC | some reformatting | 12 June 2017, 18:29:42 UTC |
| 7ade678 | KEVIN BONHAM | 12 June 2017, 18:20:45 UTC | Fix some formatting | 12 June 2017, 18:20:45 UTC |
| 20f591a | KEVIN BONHAM | 12 June 2017, 18:14:53 UTC | add docs index (formerly README) | 12 June 2017, 18:16:23 UTC |
| b07b5ed | KEVIN BONHAM | 12 June 2017, 18:14:53 UTC | add docs index (formerly README) | 12 June 2017, 18:14:53 UTC |
| ca96943 | KEVIN BONHAM | 12 June 2017, 16:45:59 UTC | add sphinx docs | 12 June 2017, 16:46:37 UTC |
| e4d10bd | KEVIN BONHAM | 12 June 2017, 15:32:04 UTC | update to google format docstrings | 12 June 2017, 15:32:04 UTC |
| 2f266a1 | Kevin Bonham | 08 June 2017, 22:34:36 UTC | Merge pull request #27 from kescobo/unit-tests Add Unit Tests | 08 June 2017, 22:34:36 UTC |
| 8d362f1 | KEVIN BONHAM | 08 June 2017, 22:18:56 UTC | fix number bug on travis | 08 June 2017, 22:18:56 UTC |
| 8685b2f | KEVIN BONHAM | 08 June 2017, 22:13:13 UTC | add database ops tests | 08 June 2017, 22:13:13 UTC |
| 48b1585 | KEVIN BONHAM | 08 June 2017, 21:27:13 UTC | more analysis tests | 08 June 2017, 21:27:13 UTC |
| 35fe21d | KEVIN BONHAM | 08 June 2017, 20:20:56 UTC | analysis tests, reorganize test folder | 08 June 2017, 20:20:56 UTC |
| bee09f1 | KEVIN BONHAM | 08 June 2017, 19:19:34 UTC | fix minor error | 08 June 2017, 19:19:34 UTC |
| 3ae3b22 | KEVIN BONHAM | 08 June 2017, 19:13:27 UTC | add tests for running blast | 08 June 2017, 19:13:27 UTC |
| 25c1675 | KEVIN BONHAM | 08 June 2017, 17:47:08 UTC | make tests for blastdb | 08 June 2017, 17:47:08 UTC |
| e9b43e9 | KEVIN BONHAM | 05 June 2017, 21:07:48 UTC | write genbank import test | 05 June 2017, 21:07:48 UTC |
| 94bc32a | KEVIN BONHAM | 05 June 2017, 20:57:13 UTC | Remove global variables | 05 June 2017, 21:02:09 UTC |
| 04e70a2 | KEVIN BONHAM | 05 June 2017, 19:52:53 UTC | updates to gitignore | 05 June 2017, 19:52:53 UTC |
| 1f5e7fc | KEVIN BONHAM | 05 June 2017, 19:51:53 UTC | minor doc fixes | 05 June 2017, 19:51:53 UTC |
| e263eb6 | KEVIN BONHAM | 05 June 2017, 19:51:40 UTC | replace import test with actual function | 05 June 2017, 19:51:40 UTC |
| e35c5a3 | KEVIN BONHAM | 05 June 2017, 19:50:39 UTC | add test data | 05 June 2017, 19:50:39 UTC |
| a8d643b | KEVIN BONHAM | 05 June 2017, 19:50:22 UTC | Turn off Travis e-mail notification | 05 June 2017, 19:50:22 UTC |
| f40b9c3 | KEVIN BONHAM | 05 June 2017, 18:23:57 UTC | attempt to fix pytest call for python 2.7 | 05 June 2017, 18:23:57 UTC |
| c99020b | KEVIN BONHAM | 05 June 2017, 17:27:08 UTC | explicitly call test file | 05 June 2017, 17:27:08 UTC |
| 786da7d | KEVIN BONHAM | 05 June 2017, 17:17:59 UTC | add travis config, test of mongodb | 05 June 2017, 17:17:59 UTC |
| 3b47cb1 | KEVIN BONHAM | 05 June 2017, 14:44:04 UTC | add doc strings for database functions | 05 June 2017, 14:44:04 UTC |
| 25d76c7 | KEVIN BONHAM | 05 June 2017, 14:36:34 UTC | add delete_loci() function | 05 June 2017, 14:36:34 UTC |
| 513e4c9 | KEVIN BONHAM | 29 May 2017, 20:39:57 UTC | fix list_contigs bugs | 29 May 2017, 20:39:57 UTC |
| 722b6ae | KEVIN BONHAM | 29 May 2017, 20:28:53 UTC | Add list_contigs | 29 May 2017, 20:28:53 UTC |
| 45659f7 | KEVIN BONHAM | 29 May 2017, 20:05:32 UTC | Reconsider dedupe | 29 May 2017, 20:05:32 UTC |
| 82df689 | KEVIN BONHAM | 29 May 2017, 20:02:41 UTC | Complete dedupe | 29 May 2017, 20:02:41 UTC |
| 1b0cfe2 | KEVIN BONHAM | 29 May 2017, 19:18:00 UTC | Add dedupe function | 29 May 2017, 19:18:00 UTC |
| d605019 | KEVIN BONHAM | 29 May 2017, 19:17:37 UTC | Fix minor errors in delete script | 29 May 2017, 19:17:37 UTC |
| fd66fc9 | KEVIN BONHAM | 29 May 2017, 18:11:32 UTC | begin database operations | 29 May 2017, 18:11:32 UTC |
| 69a8aae | KEVIN BONHAM | 29 May 2017, 17:21:19 UTC | add interupt if attempting to add species that already exists in DB | 29 May 2017, 17:22:38 UTC |
| de8152c | KEVIN BONHAM | 29 May 2017, 16:53:47 UTC | replace try/catch with if/else in gb_parse | 29 May 2017, 16:53:47 UTC |
| 0f51d31 | KEVIN BONHAM | 29 May 2017, 16:29:11 UTC | fix spelling and formatting of README | 29 May 2017, 16:29:11 UTC |
| 7f9df6b | KEVIN BONHAM | 25 May 2017, 20:56:19 UTC | pypi v0.6.7 | 25 May 2017, 20:56:19 UTC |
| 91bf780 | Kevin Bonham | 25 May 2017, 20:54:44 UTC | Bug fixes (#21) * Fix error in ANI script if no result is returned * remove last -c from README * add verbose tags to README to match output * Add pypi stuff to .gitignore * Add additional logging to get_ani() * Fix ani output * Attempt to fix issue with ani.rb * Minor README update * Minor changes to analysis script | 25 May 2017, 20:54:44 UTC |
| 446336e | KEVIN BONHAM | 18 May 2017, 22:44:59 UTC | I don't even... | 18 May 2017, 22:44:59 UTC |
| fce617d | KEVIN BONHAM | 27 April 2017, 18:57:51 UTC | Merge branch 'Bugfixes' | 27 April 2017, 19:01:09 UTC |
| ff831e2 | KEVIN BONHAM | 27 April 2017, 17:44:41 UTC | Fix error in single genbank file import | 27 April 2017, 17:44:41 UTC |
| ed76758 | Kevin Bonham | 16 March 2017, 23:33:27 UTC | V0.6.3 (#19) * modify scripts to include log file option * fix parsing and output * fix issues with logging * fixed output * remove -c from scripts, update README * little fixes * upversion pip, show compatibility with python 2.7 | 16 March 2017, 23:33:27 UTC |
| 079be8c | KEVIN BONHAM | 14 March 2017, 21:37:21 UTC | fix stray line in gbk_parse | 14 March 2017, 21:37:21 UTC |
| ebe0cbf | KEVIN BONHAM | 14 March 2017, 20:50:43 UTC | fix scripts to execute as python | 14 March 2017, 21:05:38 UTC |
| 4fa5b95 | KEVIN BONHAM | 09 March 2017, 15:16:11 UTC | update README with pip install info | 09 March 2017, 15:16:11 UTC |
| 5dd77d1 | KEVIN BONHAM | 09 March 2017, 14:47:00 UTC | more pypi fixes | 09 March 2017, 14:49:18 UTC |
| 3487934 | KEVIN BONHAM | 09 March 2017, 14:03:53 UTC | fix setup.py | 09 March 2017, 14:42:27 UTC |
| 001550c | KEVIN BONHAM | 09 March 2017, 13:59:29 UTC | fix setup.py | 09 March 2017, 14:03:34 UTC |
| facb8ee | KEVIN BONHAM | 09 March 2017, 13:59:29 UTC | fix setup.py | 09 March 2017, 13:59:29 UTC |
| d6d470c | KEVIN BONHAM | 09 March 2017, 13:34:02 UTC | fix README | 09 March 2017, 13:35:00 UTC |
| dc160fc | KEVIN BONHAM | 09 March 2017, 13:22:18 UTC | final touches for pypi | 09 March 2017, 13:22:18 UTC |
| b790335 | KEVIN BONHAM | 08 March 2017, 23:53:45 UTC | fix merge conflict | 08 March 2017, 23:53:45 UTC |
| c3961b8 | KEVIN BONHAM | 08 March 2017, 23:46:44 UTC | add verbose and quiet args to scripts | 08 March 2017, 23:46:44 UTC |
| 3cfa8c7 | KEVIN BONHAM | 08 March 2017, 23:39:47 UTC | finish output groups script | 08 March 2017, 23:39:47 UTC |
| af07726 | KEVIN BONHAM | 03 March 2017, 22:38:09 UTC | outputs in progress | 03 March 2017, 22:38:09 UTC |
| 9b6b4b5 | KEVIN BONHAM | 27 February 2017, 19:14:11 UTC | finish distance script | 27 February 2017, 19:14:11 UTC |
| bfb3b0a | KEVIN BONHAM | 26 February 2017, 17:19:04 UTC | Additional work on species distances | 26 February 2017, 17:19:04 UTC |
| c19c155 | KEVIN BONHAM | 23 February 2017, 23:41:12 UTC | ani analysis | 23 February 2017, 23:41:42 UTC |
| 61fe717 | KEVIN BONHAM | 20 February 2017, 23:50:13 UTC | finish blast tools, begin analysis tools | 20 February 2017, 23:55:26 UTC |
| 58d615e | KEVIN BONHAM | 20 February 2017, 21:42:06 UTC | big changes - getting command line interface working | 20 February 2017, 21:42:06 UTC |
| b87cfae | KEVIN BONHAM | 20 February 2017, 17:25:10 UTC | more restucturing | 20 February 2017, 17:29:06 UTC |
| efced2c | KEVIN BONHAM | 17 February 2017, 00:09:39 UTC | continue reorg | 17 February 2017, 00:09:39 UTC |
| e6d8ffe | KEVIN BONHAM | 16 February 2017, 23:23:06 UTC | start reorg | 16 February 2017, 23:23:06 UTC |
| 740a285 | KEVIN BONHAM | 16 February 2017, 22:45:38 UTC | more tweaking | 16 February 2017, 22:45:38 UTC |
| 9a562b1 | KEVIN BONHAM | 25 January 2017, 14:55:34 UTC | Lots of changes, probably not all good | 25 January 2017, 14:55:34 UTC |
| 3fe341f | KEVIN BONHAM | 12 January 2017, 00:32:05 UTC | random fixes | 12 January 2017, 00:32:05 UTC |
| 43ee6a5 | Kevin Bonham, PhD | 28 December 2016, 16:49:08 UTC | fixed extraction of species name from file | 28 December 2016, 16:49:08 UTC |
| c7dd7b9 | Kevin Bonham, PhD | 28 December 2016, 16:37:40 UTC | minor fixes | 28 December 2016, 16:37:40 UTC |
| 91e33aa | Kevin Bonham, PhD | 16 September 2016, 18:00:59 UTC | minor mods | 16 September 2016, 18:00:59 UTC |
| 8173147 | Kevin Bonham, PhD | 14 August 2016, 16:00:22 UTC | trying to get species naming | 14 August 2016, 16:00:22 UTC |
| f586b29 | Kevin Bonham, PhD | 20 July 2016, 13:03:10 UTC | adjusted output to accomodate ani calculations | 20 July 2016, 13:03:10 UTC |
| 4567683 | Kevin Bonham, PhD | 27 June 2016, 18:35:51 UTC | new analysis (not finished) | 27 June 2016, 18:35:51 UTC |
| a97cacf | Kevin Bonham, PhD | 27 June 2016, 18:34:30 UTC | All kind of mess | 27 June 2016, 18:34:30 UTC |
| 1d3446c | Kevin Bonham, PhD | 01 June 2016, 22:17:26 UTC | fix bug in pulling sp. name from filename | 01 June 2016, 22:17:26 UTC |
| 547277f | Kevin Bonham | 31 May 2016, 15:58:34 UTC | Update README to include new DOI | 31 May 2016, 15:58:34 UTC |
| 43fb8ae | Kevin Bonham | 28 May 2016, 16:17:32 UTC | Add status updates (#17) * Added status for multi-species GenBank files * added status for blast import * More progress indicators, bug fix in run.analyze() | 28 May 2016, 16:17:32 UTC |
| a672cca | Kevin Bonham | 28 May 2016, 00:31:21 UTC | Bug fixes (#16) * fix import for folder * More bug fixes | 28 May 2016, 00:31:21 UTC |
| 1c0226a | Kevin Bonham | 27 May 2016, 17:01:18 UTC | Update README to include DOI | 27 May 2016, 21:01:32 UTC |
| 47c75d8 | Kevin Bonham | 27 May 2016, 16:35:31 UTC | Clean-up (#14) * Clean-up * fixed tab in output.py * removed old code/ folder * more cleanup | 27 May 2016, 16:35:31 UTC |
| be74847 | Kevin Bonham | 26 May 2016, 20:27:54 UTC | Merge pull request #13 from kescobo/analysis_2 continue cleanup | 26 May 2016, 20:27:54 UTC |
| 117fc4c | Kevin Bonham, PhD | 26 May 2016, 20:26:57 UTC | continue cleanup | 26 May 2016, 20:26:57 UTC |
| 46cc9b3 | Kevin Bonham | 26 May 2016, 20:25:51 UTC | Merge pull request #12 from kescobo/analysis_2 Analysis 2 | 26 May 2016, 20:25:51 UTC |
| 44fa399 | Kevin Bonham | 26 May 2016, 20:25:34 UTC | Merge pull request #11 from kescobo/analysis_1 Analysis 1 | 26 May 2016, 20:25:34 UTC |
| 4070552 | Kevin Bonham, PhD | 26 May 2016, 20:22:30 UTC | getting back on this horse | 26 May 2016, 20:22:30 UTC |
| cd90ac7 | Kevin Bonham, PhD | 26 February 2016, 22:04:23 UTC | update to return blast record as well | 26 February 2016, 22:04:23 UTC |
| e60e630 | Kevin Bonham, PhD | 23 February 2016, 17:57:37 UTC | revert `settings` and `run` to general | 23 February 2016, 17:57:37 UTC |
| 45ed1d0 | Kevin Bonham, PhD | 23 February 2016, 17:49:20 UTC | finish minimal circos outputs - generate conf and karyotype files - generate GC plot files and include in main conf | 23 February 2016, 17:49:20 UTC |
| f275e79 | Kevin Bonham, PhD | 22 February 2016, 22:03:56 UTC | Merge branch 'analysis_1' into analysis_2 # Conflicts: # run.py # settings.py | 22 February 2016, 22:03:56 UTC |
| fb42d35 | Kevin Bonham, PhD | 22 February 2016, 22:01:31 UTC | Fix `settings` and `run` | 22 February 2016, 22:01:31 UTC |
| 8cdf88c | Kevin Bonham, PhD | 22 February 2016, 21:51:12 UTC | Merge branch 'master' into analysis_1 # Conflicts: # run.py | 22 February 2016, 21:51:12 UTC |
| 2e52d1d | Kevin Bonham, PhD | 22 February 2016, 19:07:59 UTC | Merge branch 'analysis_1' into analysis_2 # Conflicts: # run.py | 22 February 2016, 19:07:59 UTC |
| 1d5a055 | Kevin Bonham, PhD | 22 February 2016, 19:03:41 UTC | Merge remote-tracking branch 'origin/analysis_1' into analysis_1 # Conflicts: # run.py | 22 February 2016, 19:03:41 UTC |
| 554b8ef | Kevin Bonham, PhD | 16 February 2016, 22:20:51 UTC | remove unused files | 22 February 2016, 19:01:07 UTC |
