| 4d296db | Nick Croucher | 14 July 2022, 09:58:06 UTC | Add validation of datasets being combined | 14 July 2022, 09:58:06 UTC |
| 5f80ed7 | Nick Croucher | 24 May 2022, 09:51:01 UTC | Update for v3.2.1 | 24 May 2022, 09:51:01 UTC |
| 921856d | Nick Croucher | 24 May 2022, 09:46:10 UTC | Update manual with resume option | 24 May 2022, 09:46:10 UTC |
| 068d3c2 | Nick Croucher | 24 May 2022, 09:16:39 UTC | Update extracted clade alignment | 24 May 2022, 09:16:39 UTC |
| be7efe3 | Nick Croucher | 24 May 2022, 08:56:48 UTC | Update mutable seq processing | 24 May 2022, 08:56:48 UTC |
| 3cfc160 | Nick Croucher | 24 May 2022, 08:50:01 UTC | Update tree extraction | 24 May 2022, 08:50:01 UTC |
| 8c4d190 | Nick Croucher | 24 May 2022, 08:49:09 UTC | Update clade extraction test files | 24 May 2022, 08:49:09 UTC |
| c7fc555 | Nick Croucher | 24 May 2022, 08:27:20 UTC | Add model specification | 24 May 2022, 08:27:20 UTC |
| a05405a | Nick Croucher | 24 May 2022, 08:19:11 UTC | Update clade extraction test output | 24 May 2022, 08:19:11 UTC |
| ba08a1e | Nick Croucher | 24 May 2022, 08:00:46 UTC | Add resumption tests | 24 May 2022, 08:00:46 UTC |
| 49c4429 | Nick Croucher | 24 May 2022, 05:20:02 UTC | Enable resumption of stalled runs | 24 May 2022, 05:20:02 UTC |
| 892b663 | Nick Croucher | 23 May 2022, 10:35:54 UTC | Update test files | 23 May 2022, 10:35:54 UTC |
| e023ee7 | Nick Croucher | 23 May 2022, 10:00:27 UTC | Formatting adjustments | 23 May 2022, 10:00:27 UTC |
| 12e6cbc | Nick Croucher | 18 May 2022, 07:41:48 UTC | Enable writing to file | 18 May 2022, 07:41:48 UTC |
| 9f409dd | Nick Croucher | 18 May 2022, 05:37:45 UTC | Make tree outputs consistent | 18 May 2022, 05:37:45 UTC |
| 39b8ea9 | Nick Croucher | 03 May 2022, 11:58:36 UTC | Formatting change | 03 May 2022, 11:58:36 UTC |
| 68afff3 | Nick Croucher | 03 May 2022, 11:25:11 UTC | Update manual with new options and outputs | 03 May 2022, 11:25:11 UTC |
| a1699c4 | Nick Croucher | 03 May 2022, 11:11:30 UTC | Update column heading | 03 May 2022, 11:11:30 UTC |
| 5927bce | Nick Croucher | 03 May 2022, 11:09:10 UTC | Improve output of analysis statistics | 03 May 2022, 11:09:10 UTC |
| b1f63c9 | Nick Croucher | 03 May 2022, 07:37:51 UTC | Correct array size value | 03 May 2022, 07:37:51 UTC |
| ec6f712 | Nick Croucher | 03 May 2022, 05:22:12 UTC | Fix verbose timing messages | 03 May 2022, 05:22:12 UTC |
| d2a39b9 | Nick Croucher | 02 May 2022, 20:42:03 UTC | Modify boundary conditions | 02 May 2022, 20:42:03 UTC |
| 74e2061 | Nick Croucher | 02 May 2022, 20:29:47 UTC | Update rerooting file naming | 02 May 2022, 20:29:47 UTC |
| 568fd07 | Nick Croucher | 02 May 2022, 20:21:52 UTC | Update rerooted trees | 02 May 2022, 20:21:52 UTC |
| f1e6ebc | Nick Croucher | 02 May 2022, 19:38:13 UTC | Update tree files | 02 May 2022, 19:38:13 UTC |
| a1f6871 | Nick Croucher | 02 May 2022, 18:49:47 UTC | Update expected tree | 02 May 2022, 18:49:47 UTC |
| e171618 | Nick Croucher | 02 May 2022, 18:40:40 UTC | Update expected recombination count | 02 May 2022, 18:40:40 UTC |
| ee35d62 | Nick Croucher | 02 May 2022, 18:40:13 UTC | Update test comparison file | 02 May 2022, 18:40:13 UTC |
| 1112270 | Nick Croucher | 02 May 2022, 13:09:33 UTC | Update snp counts | 02 May 2022, 13:09:33 UTC |
| 455a2ef | Nick Croucher | 02 May 2022, 12:57:16 UTC | Update window end unit tests | 02 May 2022, 12:57:16 UTC |
| d72ea1a | Nick Croucher | 02 May 2022, 05:33:08 UTC | Add CI message | 02 May 2022, 05:33:08 UTC |
| becc66e | Nick Croucher | 01 May 2022, 06:15:28 UTC | Merge updates Merge branch 'update_rec' of https://github.com/nickjcroucher/gubbins into update_rec | 01 May 2022, 06:15:28 UTC |
| 10d9351 | Nick Croucher | 01 May 2022, 06:14:57 UTC | Correct inequality | 01 May 2022, 06:14:57 UTC |
| 6752347 | jdaeth274 | 29 April 2022, 11:55:50 UTC | merging more informative verbose | 29 April 2022, 11:55:50 UTC |
| a531c9a | jdaeth274 | 29 April 2022, 11:53:39 UTC | tweaking the verbose output | 29 April 2022, 11:53:39 UTC |
| 1102ae1 | Nick Croucher | 29 April 2022, 11:46:47 UTC | Avoid multiprocessing with one thread | 29 April 2022, 11:46:47 UTC |
| 305b208 | Nick Croucher | 29 April 2022, 08:01:42 UTC | Parallelise over sites independently | 29 April 2022, 08:01:42 UTC |
| d7fd18d | Nick Croucher | 25 April 2022, 16:05:10 UTC | Correct variable name for file checking | 25 April 2022, 16:05:10 UTC |
| 4b10cef | Nick Croucher | 21 April 2022, 15:50:06 UTC | Avoid unnecessary recombination searching | 21 April 2022, 15:50:06 UTC |
| 67047df | Nick Croucher | 21 April 2022, 13:54:23 UTC | Iteratively reduce window size in recombination search | 21 April 2022, 13:54:23 UTC |
| 4a15f70 | Nick Croucher | 14 April 2022, 10:24:08 UTC | Improve rerooting with outgroup | 14 April 2022, 10:24:08 UTC |
| eb34da7 | Nick Croucher | 13 April 2022, 21:25:33 UTC | Add flag for extensive search | 13 April 2022, 21:25:33 UTC |
| 5efcb38 | Nick Croucher | 13 April 2022, 21:09:23 UTC | Restore correct copy syntax | 13 April 2022, 21:09:23 UTC |
| 561fad2 | Nick Croucher | 13 April 2022, 21:04:32 UTC | Update multiple recombinations check | 13 April 2022, 21:04:32 UTC |
| b88c0ee | Nick Croucher | 13 April 2022, 15:28:32 UTC | Update trees for tests | 13 April 2022, 15:28:32 UTC |
| 8678024 | Nick Croucher | 13 April 2022, 15:21:18 UTC | Update recombination counting function | 13 April 2022, 15:21:18 UTC |
| 50330c6 | Nick Croucher | 13 April 2022, 15:20:10 UTC | Update test command | 13 April 2022, 15:20:10 UTC |
| 0f9f7e1 | Nick Croucher | 13 April 2022, 15:15:34 UTC | Update multiple recombination expected files | 13 April 2022, 15:15:34 UTC |
| 49c32be | Nick Croucher | 13 April 2022, 15:14:54 UTC | Update multiple recombination expected files | 13 April 2022, 15:14:54 UTC |
| c054532 | Nick Croucher | 13 April 2022, 13:59:24 UTC | Change taxon order in tab file | 13 April 2022, 13:59:24 UTC |
| 7acf3db | Nick Croucher | 13 April 2022, 13:48:05 UTC | Add internal nodes to tree | 13 April 2022, 13:48:05 UTC |
| d795b25 | Nick Croucher | 13 April 2022, 13:37:07 UTC | Include node names in trees | 13 April 2022, 13:37:07 UTC |
| fbe31f1 | Nick Croucher | 13 April 2022, 12:37:40 UTC | Update JAR alignment for test | 13 April 2022, 12:37:40 UTC |
| 9e9387d | Nick Croucher | 13 April 2022, 12:26:45 UTC | Update tree for test | 13 April 2022, 12:26:45 UTC |
| 7f3d2a6 | Nick Croucher | 13 April 2022, 12:19:51 UTC | Updated expected result | 13 April 2022, 12:19:51 UTC |
| 2c14e59 | Nick Croucher | 13 April 2022, 11:03:46 UTC | Update multiple recombinations check | 13 April 2022, 11:03:46 UTC |
| ac4fb33 | Nick Croucher | 13 April 2022, 10:31:41 UTC | Update cutoff calculation | 13 April 2022, 10:31:41 UTC |
| e8fbb8c | Nick Croucher | 12 April 2022, 19:52:55 UTC | Fix recombinations at end of genome | 12 April 2022, 19:53:50 UTC |
| a97d3a7 | Nick Croucher | 12 April 2022, 10:42:09 UTC | Reformat function | 12 April 2022, 10:42:09 UTC |
| da4f26f | Nick Croucher | 08 April 2022, 09:11:04 UTC | Update run_gubbins calls | 08 April 2022, 09:11:04 UTC |
| 4503076 | Nick Croucher | 08 April 2022, 09:02:24 UTC | Add extensive search mode | 08 April 2022, 09:02:24 UTC |
| 826a282 | Nick Croucher | 08 April 2022, 08:18:24 UTC | Update threshold calculation | 08 April 2022, 08:18:24 UTC |
| 14072db | Nick Croucher | 08 April 2022, 07:12:11 UTC | Reformat likelihood calculation function | 08 April 2022, 07:12:11 UTC |
| 62ee040 | Nick Croucher | 08 April 2022, 05:33:22 UTC | Update usage information | 08 April 2022, 05:33:22 UTC |
| 04edbee | Nick Croucher | 07 April 2022, 19:37:11 UTC | Update installation instructions | 07 April 2022, 19:37:11 UTC |
| e6f546f | Nick Croucher | 07 April 2022, 16:52:50 UTC | Change ratio definition | 07 April 2022, 16:52:50 UTC |
| 5eba4da | Nick Croucher | 07 April 2022, 14:18:09 UTC | Bump version | 07 April 2022, 14:18:09 UTC |
| fe3641d | Nick Croucher | 07 April 2022, 13:42:25 UTC | Fix typo | 07 April 2022, 13:42:25 UTC |
| 16b647f | Nick Croucher | 07 April 2022, 13:32:52 UTC | Fix command line syntax | 07 April 2022, 13:32:52 UTC |
| 2fbeb39 | Nick Croucher | 07 April 2022, 13:29:04 UTC | Fix gubbins command test | 07 April 2022, 13:29:04 UTC |
| 508710e | Nick Croucher | 07 April 2022, 13:17:29 UTC | Convert float to str | 07 April 2022, 13:17:29 UTC |
| 4943a2a | Nick Croucher | 07 April 2022, 12:53:04 UTC | Update gubbins command test | 07 April 2022, 12:53:04 UTC |
| 093c760 | Nick Croucher | 07 April 2022, 12:45:01 UTC | Add tests for new options | 07 April 2022, 12:45:01 UTC |
| a132395 | Nick Croucher | 07 April 2022, 12:33:27 UTC | Update interface with C code | 07 April 2022, 12:33:27 UTC |
| f22a9c9 | Nick Croucher | 07 April 2022, 12:24:05 UTC | Update run_gubbins arguments | 07 April 2022, 12:24:05 UTC |
| 2f9e1a4 | Nick Croucher | 07 April 2022, 12:22:13 UTC | Change formatting of main function | 07 April 2022, 12:22:13 UTC |
| b3544e0 | Nick Croucher | 07 April 2022, 12:17:36 UTC | Enable alteration of trimming ratio | 07 April 2022, 12:17:36 UTC |
| 0776aa2 | Nick Croucher | 07 April 2022, 12:07:15 UTC | Remove debug statement | 07 April 2022, 12:07:15 UTC |
| 339177f | Nick Croucher | 07 April 2022, 12:05:35 UTC | Enable customisation of p values used for detection | 07 April 2022, 12:05:35 UTC |
| 5a71d2c | Nick Croucher | 07 April 2022, 11:02:00 UTC | Change formatting of move_blocks function | 07 April 2022, 11:02:00 UTC |
| a9d5dcd | nickjcroucher | 02 March 2022, 17:16:28 UTC | Merge pull request #334 from nickjcroucher/fix_tests Fixes to ensure code passes CI tests | 02 March 2022, 17:16:28 UTC |
| 2f9f80c | jdaeth274 | 02 March 2022, 09:16:34 UTC | Merge branch 'fix_tests' of https://github.com/sanger-pathogens/gubbins into fix_tests | 02 March 2022, 09:16:34 UTC |
| 0a4f4b3 | jdaeth274 | 02 March 2022, 09:16:15 UTC | switching array_max calculation | 02 March 2022, 09:16:15 UTC |
| 35fface | Nick Croucher | 01 March 2022, 15:53:17 UTC | Add spec definition | 01 March 2022, 15:53:17 UTC |
| 30894eb | Nick Croucher | 01 March 2022, 15:11:58 UTC | Merge branch 'fix_tests' of https://github.com/nickjcroucher/gubbins into fix_tests | 01 March 2022, 15:11:58 UTC |
| e937425 | Nick Croucher | 01 March 2022, 15:11:13 UTC | Clarify file copy | 01 March 2022, 15:11:13 UTC |
| 54223da | Nick Croucher | 01 March 2022, 15:10:14 UTC | Restore test file | 01 March 2022, 15:10:14 UTC |
| 8ff3905 | jdaeth274 | 28 February 2022, 16:56:42 UTC | reverting test_dependencies script | 28 February 2022, 16:56:42 UTC |
| 7a68a71 | jdaeth274 | 28 February 2022, 15:37:39 UTC | Switching to previous working test_dependencies.py file | 28 February 2022, 15:37:39 UTC |
| b8acc83 | jdaeth274 | 23 February 2022, 11:19:32 UTC | swtiching to Counter for alignment checking | 23 February 2022, 11:19:32 UTC |
| 516f635 | Nick Croucher | 23 February 2022, 09:38:18 UTC | Simplify pool commands | 23 February 2022, 09:38:18 UTC |
| b59dee6 | Nick Croucher | 23 February 2022, 09:37:30 UTC | Remove need for directory changing | 23 February 2022, 09:37:30 UTC |
| f4104f6 | Nick Croucher | 23 February 2022, 08:53:01 UTC | Update test for masking | 23 February 2022, 08:53:01 UTC |
| 1262cd5 | Nick Croucher | 23 February 2022, 08:30:34 UTC | Update python installation command | 23 February 2022, 08:30:34 UTC |
| 8cfb4d9 | Nick Croucher | 23 February 2022, 06:28:03 UTC | Change alignment checking script name | 23 February 2022, 06:28:03 UTC |
| 2f04b60 | Nick Croucher | 23 February 2022, 06:25:58 UTC | Change file permissions | 23 February 2022, 06:25:58 UTC |
| ccb9ed0 | jdaeth274 | 22 February 2022, 11:56:46 UTC | allowing single core pyjar runs | 22 February 2022, 11:56:46 UTC |
| 2f7ed9a | jdaeth274 | 22 February 2022, 10:49:16 UTC | allowing for single threaded testing of generate_ska_alignment | 22 February 2022, 10:49:16 UTC |
| 5b8888b | jdaeth274 | 22 February 2022, 09:59:59 UTC | No pool runs on single threads in generate_ska_alignment.py | 22 February 2022, 09:59:59 UTC |
| d58f5e3 | jdaeth274 | 22 February 2022, 09:18:50 UTC | removing bash script from test_generate_ska_alignment | 22 February 2022, 09:18:50 UTC |
