| cf0ebf4 | andrewjpage | 26 June 2015, 14:07:19 UTC | close file handles | 26 June 2015, 14:07:19 UTC |
| cd33a69 | andrewjpage | 26 June 2015, 13:40:24 UTC | convert more comparisions to filecmp | 26 June 2015, 13:40:24 UTC |
| 4e8ae80 | andrewjpage | 26 June 2015, 13:37:37 UTC | use file compare | 26 June 2015, 13:37:37 UTC |
| 4288856 | andrewjpage | 26 June 2015, 12:58:30 UTC | file open | 26 June 2015, 12:58:30 UTC |
| 4719b05 | andrewjpage | 26 June 2015, 12:44:41 UTC | new tree compare syntax | 26 June 2015, 12:44:41 UTC |
| 3bae85f | andrewjpage | 26 June 2015, 12:29:31 UTC | latest version of dendropy | 26 June 2015, 12:29:31 UTC |
| 3202a48 | andrewjpage | 26 June 2015, 12:27:34 UTC | set schema | 26 June 2015, 12:27:34 UTC |
| bed7256 | andrewjpage | 26 June 2015, 11:57:26 UTC | 2to3 python converter script | 26 June 2015, 11:57:26 UTC |
| 1730436 | andrewjpage | 11 June 2015, 14:10:29 UTC | Merge branch 'raxml_version_travis' | 11 June 2015, 14:10:29 UTC |
| 3f41db0 | andrewjpage | 11 June 2015, 14:10:09 UTC | update travis image | 11 June 2015, 14:10:09 UTC |
| be8089d | andrewjpage | 11 June 2015, 14:08:47 UTC | update raxml version for travis | 11 June 2015, 14:08:47 UTC |
| 9695a3d | andrewjpage | 11 June 2015, 14:08:28 UTC | Merge pull request #148 from andrewjpage/raxml_version_travis update raxml version for travis | 11 June 2015, 14:08:28 UTC |
| c34f5b4 | John Tate | 04 June 2015, 14:42:02 UTC | Merge pull request #147 from sanger-pathogens/travis Add build status to README | 04 June 2015, 14:42:02 UTC |
| fbd0c5e | Ben Taylor | 04 June 2015, 13:52:22 UTC | Add build status to README | 04 June 2015, 13:52:22 UTC |
| eb0c72b | John Tate | 04 June 2015, 13:31:50 UTC | Merge pull request #146 from sanger-pathogens/travis Add TravisCI support | 04 June 2015, 13:31:50 UTC |
| 9e38a6e | Ben Taylor | 04 June 2015, 13:16:00 UTC | Add .travis.yml for TravisCI | 04 June 2015, 13:16:00 UTC |
| 39c10df | Ben Taylor | 04 June 2015, 09:57:57 UTC | Add install_dependencies for TravisCI | 04 June 2015, 13:15:40 UTC |
| 1278cca | Ben Taylor | 28 May 2015, 15:25:55 UTC | Merge pull request #145 from aslett1/master Reference URL updated to final published version not early access | 28 May 2015, 15:25:55 UTC |
| 3cfd8c8 | Martin Aslett | 28 May 2015, 14:56:24 UTC | Reference URL updated to final published version not early access | 28 May 2015, 14:56:24 UTC |
| bc8d0ff | andrewjpage | 19 May 2015, 13:22:29 UTC | Merge branch 'master' of github.com:sanger-pathogens/gubbins | 19 May 2015, 13:22:29 UTC |
| eb2494f | andrewjpage | 19 May 2015, 13:22:07 UTC | use fastml3 | 19 May 2015, 13:22:07 UTC |
| 9a5e985 | andrewjpage | 18 May 2015, 14:21:59 UTC | Merge pull request #144 from andrewjpage/master Manually merge Aidan Delaneys pull request | 18 May 2015, 14:21:59 UTC |
| cf0d8a7 | andrewjpage | 18 May 2015, 14:21:21 UTC | Merge branch 'master' of github.com:sanger-pathogens/gubbins | 18 May 2015, 14:21:21 UTC |
| c9276d1 | andrewjpage | 18 May 2015, 14:20:20 UTC | install md | 18 May 2015, 14:20:20 UTC |
| c055bdf | andrewjpage | 18 May 2015, 14:19:37 UTC | Merge branch 'AidanDelaney-master' | 18 May 2015, 14:19:37 UTC |
| bffe70c | martinghunt | 18 May 2015, 14:14:16 UTC | Merge pull request #143 from andrewjpage/recombinations_at_root Detect blocks at end of sequence | 18 May 2015, 14:14:16 UTC |
| 9794732 | andrewjpage | 18 May 2015, 13:51:49 UTC | changelog | 18 May 2015, 13:51:49 UTC |
| afb6460 | andrewjpage | 18 May 2015, 13:50:03 UTC | inc version | 18 May 2015, 13:50:03 UTC |
| 75ebfd5 | andrewjpage | 18 May 2015, 13:45:34 UTC | close a block at the end of the genome | 18 May 2015, 13:49:28 UTC |
| ef7e20a | andrewjpage | 18 May 2015, 13:10:50 UTC | test to replicate bad data | 18 May 2015, 13:10:50 UTC |
| 3e7a7ce | andrewjpage | 15 May 2015, 10:49:54 UTC | display install file as markdown | 15 May 2015, 10:49:54 UTC |
| bc4edbc | andrewjpage | 15 May 2015, 08:49:32 UTC | tab between cells in stats | 15 May 2015, 08:49:32 UTC |
| a121363 | Aidan Delaney | 20 April 2015, 19:24:42 UTC | Updated documentation to fix Issue #130 - documentation should make it clear to run autoreconf before configure. | 20 April 2015, 19:24:42 UTC |
| 17c4924 | Aidan Delaney | 20 April 2015, 19:19:35 UTC | This time with valid URL for updated gubbins package. | 20 April 2015, 19:19:35 UTC |
| 98cf1bf | Aidan Delaney | 20 April 2015, 19:17:27 UTC | Updated version of gubbins package in install-userspace.sh | 20 April 2015, 19:17:27 UTC |
| 75e5a84 | andrewjpage | 16 April 2015, 15:10:13 UTC | Merge pull request #140 from andrewjpage/window_size_self_error Window size self error | 16 April 2015, 15:10:13 UTC |
| 374aa52 | andrewjpage | 16 April 2015, 15:09:40 UTC | max window size bug | 16 April 2015, 15:09:40 UTC |
| a1bb2b6 | andrewjpage | 16 April 2015, 15:08:24 UTC | max window size | 16 April 2015, 15:08:24 UTC |
| e8914d0 | andrewjpage | 16 April 2015, 15:02:09 UTC | Merge pull request #139 from andrewjpage/window_size_self_error Window size self error | 16 April 2015, 15:02:09 UTC |
| 0213034 | andrewjpage | 16 April 2015, 15:01:14 UTC | version 1.3.21 | 16 April 2015, 15:01:14 UTC |
| fdd2a32 | andrewjpage | 16 April 2015, 14:52:11 UTC | pass in self to Gubbins | 16 April 2015, 14:52:11 UTC |
| 5f9c17e | andrewjpage | 16 April 2015, 14:33:56 UTC | Merge pull request #138 from andrewjpage/recalculate_genome_length version 1.3.1 | 16 April 2015, 14:33:56 UTC |
| b5b73f6 | andrewjpage | 16 April 2015, 14:32:03 UTC | Merge pull request #137 from andrewjpage/recalculate_genome_length Recalculate genome length | 16 April 2015, 14:32:03 UTC |
| 4e83bb8 | andrewjpage | 16 April 2015, 14:11:37 UTC | version 1.3.1 | 16 April 2015, 14:11:37 UTC |
| ec5904e | andrewjpage | 16 April 2015, 14:09:25 UTC | output genome length minus gaps and recomb as separate stat | 16 April 2015, 14:09:25 UTC |
| 81368c3 | andrewjpage | 14 April 2015, 15:41:12 UTC | calculate genome length for branch as excluding parent recombinations | 14 April 2015, 15:41:12 UTC |
| d7f49b6 | andrewjpage | 14 April 2015, 13:17:24 UTC | Merge pull request #136 from andrewjpage/downstream_recombinations Downstream recombinations | 14 April 2015, 13:17:24 UTC |
| f905435 | andrewjpage | 14 April 2015, 13:14:26 UTC | check input values for window size | 14 April 2015, 13:14:26 UTC |
| 9914f1e | andrewjpage | 14 April 2015, 13:06:50 UTC | allow window size to be set in python | 14 April 2015, 13:06:50 UTC |
| 6eecfa3 | andrewjpage | 14 April 2015, 12:37:06 UTC | pass window max and min in | 14 April 2015, 12:37:06 UTC |
| 1cf5c80 | andrewjpage | 13 April 2015, 14:28:24 UTC | revert to per branch | 13 April 2015, 14:28:24 UTC |
| 16eafeb | andrewjpage | 13 April 2015, 14:05:07 UTC | number of blocks includes all parents | 13 April 2015, 14:05:07 UTC |
| 9967faf | andrewjpage | 13 April 2015, 13:41:22 UTC | update number of snps stats | 13 April 2015, 13:41:22 UTC |
| ed3551f | andrewjpage | 13 April 2015, 13:19:09 UTC | version 1.3.0 | 13 April 2015, 13:19:09 UTC |
| 2ad5336 | andrewjpage | 13 April 2015, 13:15:24 UTC | convert from coords to index in single block test | 13 April 2015, 13:15:24 UTC |
| dd0a537 | andrewjpage | 13 April 2015, 13:05:53 UTC | use merged coords | 13 April 2015, 13:05:53 UTC |
| 03b8935 | andrewjpage | 13 April 2015, 11:04:31 UTC | include the current nodes blocks | 13 April 2015, 11:04:31 UTC |
| 7b7c3af | andrewjpage | 13 April 2015, 10:32:18 UTC | make output array big enough to hold all snps | 13 April 2015, 10:32:18 UTC |
| a20b101 | andrewjpage | 13 April 2015, 10:26:48 UTC | pass through length of snp_locations array | 13 April 2015, 10:26:48 UTC |
| d460593 | andrewjpage | 09 April 2015, 11:11:02 UTC | extra test for a single block | 09 April 2015, 11:11:02 UTC |
| 9482d25 | andrewjpage | 07 April 2015, 10:19:48 UTC | order of indices depends on order of blocks | 07 April 2015, 10:19:48 UTC |
| b99bd75 | andrewjpage | 07 April 2015, 10:15:53 UTC | initialise snp index list | 07 April 2015, 10:15:53 UTC |
| 9ce983d | andrewjpage | 07 April 2015, 10:06:41 UTC | non overlapping block | 07 April 2015, 10:06:41 UTC |
| 0655286 | andrewjpage | 07 April 2015, 10:01:45 UTC | remove debugging | 07 April 2015, 10:01:45 UTC |
| c39864a | andrewjpage | 07 April 2015, 10:01:04 UTC | remove duplicate indices | 07 April 2015, 10:01:04 UTC |
| 0011076 | andrewjpage | 07 April 2015, 09:46:03 UTC | version 1.2.5 | 07 April 2015, 09:46:03 UTC |
| 93f4ec0 | andrewjpage | 07 April 2015, 09:45:03 UTC | block out snps in downstream recombinations | 07 April 2015, 09:45:03 UTC |
| 4d193d8 | andrewjpage | 31 March 2015, 14:02:24 UTC | Merge pull request #135 from andrewjpage/script_version_number output version in python script | 31 March 2015, 14:02:24 UTC |
| f41a877 | andrewjpage | 31 March 2015, 14:01:56 UTC | output version in python script | 31 March 2015, 14:01:56 UTC |
| bdd1854 | andrewjpage | 30 March 2015, 13:59:12 UTC | Merge branch 'master' of github.com:sanger-pathogens/gubbins | 30 March 2015, 13:59:12 UTC |
| 329306d | andrewjpage | 30 March 2015, 13:58:47 UTC | eggs werent included in deb | 30 March 2015, 13:58:47 UTC |
| 15dede9 | andrewjpage | 30 March 2015, 13:18:52 UTC | Merge pull request #134 from andrewjpage/master include last element of array | 30 March 2015, 13:18:52 UTC |
| 6ec565c | andrewjpage | 30 March 2015, 13:18:11 UTC | include last element of array | 30 March 2015, 13:18:11 UTC |
| 7b597ff | andrewjpage | 30 March 2015, 10:37:55 UTC | Merge pull request #133 from andrewjpage/correct_vcf_format Correct vcf format and EMBL format | 30 March 2015, 10:37:55 UTC |
| c10301f | andrewjpage | 30 March 2015, 10:36:52 UTC | update version | 30 March 2015, 10:36:52 UTC |
| 3b68a20 | andrewjpage | 30 March 2015, 10:35:06 UTC | add quotes to tab files test | 30 March 2015, 10:35:06 UTC |
| c8955e2 | andrewjpage | 30 March 2015, 10:27:44 UTC | Merge branch 'correct_vcf_format' of github.com:andrewjpage/gubbins into correct_vcf_format | 30 March 2015, 10:27:44 UTC |
| 8e4bb9c | andrewjpage | 30 March 2015, 10:26:16 UTC | quote out digits in embl format | 30 March 2015, 10:26:16 UTC |
| f6d28f6 | andrewjpage | 30 March 2015, 10:23:49 UTC | corrected vcf test output | 30 March 2015, 10:23:49 UTC |
| edc31b2 | andrewjpage | 30 March 2015, 10:12:49 UTC | pass length of genome through | 30 March 2015, 10:12:49 UTC |
| 6ae3471 | andrewjpage | 30 March 2015, 10:10:17 UTC | add contig line and remove trailing tab | 30 March 2015, 10:10:17 UTC |
| dbe580a | andrewjpage | 30 March 2015, 09:17:27 UTC | Merge pull request #132 from andrewjpage/gap_filling debian changelog | 30 March 2015, 09:17:27 UTC |
| cfd26de | andrewjpage | 30 March 2015, 09:17:01 UTC | debian changelog | 30 March 2015, 09:17:01 UTC |
| fc84f9e | andrewjpage | 30 March 2015, 09:13:58 UTC | Merge pull request #131 from andrewjpage/gap_filling Dont fill in gaps in parent with bases from child | 30 March 2015, 09:13:58 UTC |
| 061e2b8 | andrewjpage | 30 March 2015, 09:06:55 UTC | Dont fill in gaps in parent with bases from child | 30 March 2015, 09:06:55 UTC |
| 4b7486a | andrewjpage | 06 March 2015, 11:30:39 UTC | Merge pull request #128 from andrewjpage/update_robustness Update robustness | 06 March 2015, 11:30:39 UTC |
| 5cbe0f7 | andrewjpage | 06 March 2015, 11:29:30 UTC | Fix warnings | 06 March 2015, 11:29:30 UTC |
| c2fab08 | andrewjpage | 06 March 2015, 09:46:24 UTC | fix gff format and better error messages | 06 March 2015, 09:46:24 UTC |
| c3daaaa | andrewjpage | 26 January 2015, 10:21:52 UTC | make sure ntp is available | 26 January 2015, 10:21:52 UTC |
| 5fb9599 | andrewjpage | 26 January 2015, 10:04:05 UTC | further debian changelog syntax fix | 26 January 2015, 10:04:05 UTC |
| 49ef9ae | andrewjpage | 26 January 2015, 10:00:51 UTC | fix debian changelog syntax | 26 January 2015, 10:00:51 UTC |
| 9aad71c | andrewjpage | 23 January 2015, 16:03:08 UTC | Merge pull request #127 from andrewjpage/error_message_with_outgroup_not_clade message about invalid outgroups | 23 January 2015, 16:03:08 UTC |
| 6499829 | andrewjpage | 23 January 2015, 16:02:50 UTC | message about invalid outgroups | 23 January 2015, 16:02:50 UTC |
| 404203e | andrewjpage | 23 January 2015, 15:27:40 UTC | Merge pull request #126 from andrewjpage/clade_as_outgroup Clade as outgroup | 23 January 2015, 15:27:40 UTC |
| d06e3fd | andrewjpage | 23 January 2015, 15:27:19 UTC | make tests past split | 23 January 2015, 15:27:19 UTC |
| 5450158 | andrewjpage | 23 January 2015, 15:06:13 UTC | allow for multiple outgroups | 23 January 2015, 15:06:13 UTC |
| 5f07d92 | andrewjpage | 20 January 2015, 09:10:33 UTC | Merge pull request #125 from andrewjpage/remove_internal_nodes_from_final_tree test data | 20 January 2015, 09:10:33 UTC |
| 9e2dd9c | andrewjpage | 20 January 2015, 09:09:12 UTC | test data | 20 January 2015, 09:09:12 UTC |
| 6353400 | andrewjpage | 20 January 2015, 09:06:02 UTC | Merge pull request #124 from andrewjpage/remove_internal_nodes_from_final_tree Remove internal nodes from final tree | 20 January 2015, 09:06:02 UTC |
| 8005e71 | andrewjpage | 20 January 2015, 09:04:34 UTC | version 1.0.12 | 20 January 2015, 09:04:34 UTC |
