e1df9fe | Christoph Püthe | 30 July 2018, 15:30:49 UTC | Merge pull request #227 from puethe/segfault dynamically allocate memory to avoid stack overflow | 30 July 2018, 15:30:49 UTC |
06d3da2 | puethe | 30 July 2018, 15:22:20 UTC | dynamically allocate memory to avoid stack overflow | 30 July 2018, 15:22:20 UTC |
e1b4ec6 | Christoph Püthe | 26 July 2018, 16:03:35 UTC | Merge pull request #226 from puethe/independent_docker Dockerfile independent from debian package | 26 July 2018, 16:03:35 UTC |
22fd2c5 | puethe | 25 July 2018, 09:44:14 UTC | clone from sanger-pathogens repo | 25 July 2018, 09:44:14 UTC |
f113ba6 | puethe | 25 July 2018, 09:30:16 UTC | dockerfile independent of the Debian package | 25 July 2018, 09:30:16 UTC |
b0a9969 | Christoph Püthe | 02 July 2018, 09:01:29 UTC | Merge pull request #224 from puethe/master universal link | 02 July 2018, 09:01:29 UTC |
ec281b8 | Christoph Püthe | 02 July 2018, 08:57:06 UTC | Update README.md | 02 July 2018, 08:57:06 UTC |
08e5213 | Christoph Püthe | 02 July 2018, 08:55:19 UTC | Merge pull request #1 from sanger-pathogens/master link to install.md | 02 July 2018, 08:55:19 UTC |
87d65db | Christoph Püthe | 02 July 2018, 08:41:03 UTC | Merge pull request #223 from puethe/link_to_install_file link to install.md | 02 July 2018, 08:41:03 UTC |
8e08591 | Christoph Püthe | 02 July 2018, 08:34:53 UTC | link to install.md | 02 July 2018, 08:34:53 UTC |
2856b5e | Christoph Püthe | 15 June 2018, 11:48:19 UTC | Merge pull request #221 from puethe/remove_gubbins_drawer Replaced the script gubbins_drawer.py with an empty script displaying an info message. | 15 June 2018, 11:48:19 UTC |
0ad9e88 | puethe | 15 June 2018, 11:42:44 UTC | Replaced the script gubbins_drawer.py with an empty script displaying only an info message. | 15 June 2018, 11:42:44 UTC |
7f334ce | Christoph Püthe | 15 June 2018, 07:47:37 UTC | Merge pull request #220 from puethe/link_check_to_lsubunit Link check to lsubunit | 15 June 2018, 07:47:37 UTC |
41d3609 | puethe | 13 June 2018, 14:57:39 UTC | tell travis to install subunit | 13 June 2018, 14:57:39 UTC |
11e3a8c | puethe | 13 June 2018, 13:51:15 UTC | install libsubunit-dev | 13 June 2018, 13:51:15 UTC |
367d925 | puethe | 13 June 2018, 13:25:06 UTC | Link to 'subunit' to get check running on newer ubuntu/debian systems | 13 June 2018, 13:25:06 UTC |
87d8f83 | Christoph Püthe | 08 June 2018, 15:19:09 UTC | Merge pull request #219 from puethe/correct_fasttree_typo corrected typo: 'fastree' -> 'fasttree' | 08 June 2018, 15:19:09 UTC |
f5afdd7 | puethe | 08 June 2018, 14:17:45 UTC | corrected typo: 'fastree' -> 'fasttree' | 08 June 2018, 14:17:45 UTC |
b38e643 | Sara Sjunnebo | 31 May 2018, 14:29:08 UTC | Merge pull request #217 from ssjunnebo/625345_docker_instructions update instructions for Docker | 31 May 2018, 14:29:08 UTC |
bca8fec | Sara Sjunnebo | 31 May 2018, 14:23:53 UTC | update instructions for Docker | 31 May 2018, 14:23:53 UTC |
8cd1870 | Simon Harris | 19 February 2018, 09:44:12 UTC | Update README.md corrected spelling mistake | 19 February 2018, 09:44:12 UTC |
350e15a | andrewjpage | 24 January 2018, 09:54:53 UTC | add example output data | 24 January 2018, 09:54:53 UTC |
523efaf | andrewjpage | 15 January 2018, 12:40:51 UTC | accept install docker | 15 January 2018, 12:40:51 UTC |
1077ce6 | andrewjpage | 12 January 2018, 10:46:16 UTC | remove installation instructions for homebrew | 12 January 2018, 10:46:16 UTC |
c677a77 | andrewjpage | 27 November 2017, 07:35:34 UTC | Merge pull request #207 from schultzm/master added choices to `--tree_builder` and other args | 27 November 2017, 07:35:34 UTC |
8102d01 | Mark Schultz | 27 November 2017, 07:12:15 UTC | remove punctuation from choices | 27 November 2017, 07:12:15 UTC |
f7a8a41 | Mark Schultz | 27 November 2017, 07:09:39 UTC | added `choices` to all options with choices | 27 November 2017, 07:09:39 UTC |
20b10b6 | Mark Schultz | 27 November 2017, 07:07:18 UTC | choices for tree building Without choices under `-t`, there is nothing to protect the user from doing e.g., `-t 16`. This would happen if the end-user tried to use `-t` to mean `--threads` (which it doesn't). Without the choices, the error is uninformative (try for example `run_gubbins.py -v -t 2 alignment.fasta`). | 27 November 2017, 07:07:18 UTC |
4266187 | Sara Sjunnebo | 30 October 2017, 11:21:39 UTC | Merge pull request #206 from ssjunnebo/master ignore ltmain.sh for language statistics | 30 October 2017, 11:21:39 UTC |
c460bd6 | Sara Sjunnebo | 30 October 2017, 11:16:27 UTC | ignore ltmain.sh for language statistics | 30 October 2017, 11:16:27 UTC |
6be39ae | andrewjpage | 22 September 2017, 11:05:49 UTC | Merge pull request #203 from andrewjpage/update_docs update manual | 22 September 2017, 11:05:49 UTC |
9dd5ae0 | andrewjpage | 22 September 2017, 11:05:31 UTC | update manual | 22 September 2017, 11:05:31 UTC |
208a2ae | andrewjpage | 22 September 2017, 10:59:26 UTC | Update README.md | 22 September 2017, 10:59:26 UTC |
b7b935d | andrewjpage | 22 September 2017, 10:57:33 UTC | Merge branch 'internal_nodes' | 22 September 2017, 10:57:33 UTC |
5d8676e | andrewjpage | 22 September 2017, 10:56:03 UTC | Merge branch 'master' of github.com:sanger-pathogens/gubbins into internal_nodes | 22 September 2017, 10:56:03 UTC |
abae76f | andrewjpage | 22 September 2017, 10:55:46 UTC | fix changelog | 22 September 2017, 10:55:46 UTC |
3a276c0 | andrewjpage | 22 September 2017, 10:54:52 UTC | Merge pull request #202 from andrewjpage/internal_nodes Internal nodes | 22 September 2017, 10:54:52 UTC |
b03434a | andrewjpage | 22 September 2017, 10:53:57 UTC | test for internal labels | 22 September 2017, 10:53:57 UTC |
63134f3 | andrewjpage | 22 September 2017, 10:02:33 UTC | inc version | 22 September 2017, 10:02:33 UTC |
e5c97f2 | andrewjpage | 22 September 2017, 10:01:17 UTC | add internal node labels to the final tree | 22 September 2017, 10:01:17 UTC |
dbe0b71 | andrewjpage | 21 September 2017, 14:33:23 UTC | Merge pull request #201 from andrewjpage/gubbins_drawer_help Gubbins drawer help text | 21 September 2017, 14:33:23 UTC |
c1305e7 | andrewjpage | 21 September 2017, 14:27:45 UTC | assume 1 file | 21 September 2017, 14:27:45 UTC |
decfc5f | andrewjpage | 21 September 2017, 14:02:31 UTC | Add helptext to gubbins drawer and require tree as a positional argument rather than an option. | 21 September 2017, 14:02:31 UTC |
0e6774a | andrewjpage | 15 September 2017, 13:34:52 UTC | gubbins drawer to use argsparse | 15 September 2017, 13:34:52 UTC |
3ad41e8 | andrewjpage | 15 September 2017, 13:04:25 UTC | Merge pull request #200 from andrewjpage/helptext Fix default extended help text. | 15 September 2017, 13:04:25 UTC |
30b8cb0 | andrewjpage | 15 September 2017, 13:03:47 UTC | changelog version | 15 September 2017, 13:03:47 UTC |
d983d0b | andrewjpage | 15 September 2017, 12:58:55 UTC | force defaults to always print | 15 September 2017, 12:58:55 UTC |
f796262 | andrewjpage | 04 September 2017, 10:10:32 UTC | Update CHANGELOG | 04 September 2017, 10:10:32 UTC |
79501ae | andrewjpage | 04 September 2017, 10:09:27 UTC | Merge pull request #197 from andrewjpage/avx2 allow for AVX2 | 04 September 2017, 10:09:27 UTC |
b907ad4 | andrewjpage | 04 September 2017, 10:05:21 UTC | allow for AVX2 | 04 September 2017, 10:05:21 UTC |
1d13185 | ssjunnebo | 02 August 2017, 12:10:44 UTC | Merge pull request #193 from ssjunnebo/master updated manual | 02 August 2017, 12:10:44 UTC |
d8a2b9d | Sara Sjunnebo | 02 August 2017, 12:08:41 UTC | updated manual | 02 August 2017, 12:08:41 UTC |
8e6109c | andrewjpage | 21 June 2017, 15:39:59 UTC | Update README.md | 21 June 2017, 15:39:59 UTC |
933d50e | andrewjpage | 21 June 2017, 13:29:38 UTC | Update INSTALL.md | 21 June 2017, 13:29:38 UTC |
b1a1186 | ssjunnebo | 13 March 2017, 14:02:36 UTC | Merge pull request #188 from ssjunnebo/master Manual in docx format | 13 March 2017, 14:02:36 UTC |
5a1ff3a | ssjunnebo | 13 March 2017, 13:57:06 UTC | Added latest manual in docx format | 13 March 2017, 13:57:06 UTC |
863d44f | ssjunnebo | 20 February 2017, 15:04:07 UTC | Merge pull request #186 from ssjunnebo/master Fixed biopython sub_features bug | 20 February 2017, 15:04:07 UTC |
6f3af4a | Sara Sjunnebo | 20 February 2017, 15:02:37 UTC | change version nr | 20 February 2017, 15:02:37 UTC |
f0eb50f | Sara Sjunnebo | 20 February 2017, 14:51:21 UTC | Merge branch '516666' | 20 February 2017, 14:51:21 UTC |
cef2dcc | Sara Sjunnebo | 20 February 2017, 14:49:57 UTC | gubbins_drawer.py fixed biopython error | 20 February 2017, 14:49:57 UTC |
dbb278c | andrewjpage | 31 October 2016, 13:45:01 UTC | Update CHANGELOG | 31 October 2016, 13:45:01 UTC |
5bb1896 | andrewjpage | 31 October 2016, 13:12:07 UTC | Merge pull request #180 from andrewjpage/dont_filter_identical_sequences_by_default dont filter out identical sequences by default | 31 October 2016, 13:12:07 UTC |
3472753 | andrewjpage | 31 October 2016, 13:09:09 UTC | dont filter out identical sequences by default | 31 October 2016, 13:09:09 UTC |
8a12ae7 | andrewjpage | 01 August 2016, 15:05:52 UTC | Merge branch 'master' of github.com:sanger-pathogens/gubbins | 01 August 2016, 15:05:52 UTC |
c2eb532 | andrewjpage | 01 August 2016, 15:05:27 UTC | Dockerfile | 01 August 2016, 15:05:27 UTC |
28b83fc | andrewjpage | 25 July 2016, 12:43:03 UTC | Update README.md | 25 July 2016, 12:43:03 UTC |
599c7e1 | andrewjpage | 22 July 2016, 13:58:50 UTC | Update README.md | 22 July 2016, 13:58:50 UTC |
ff12945 | andrewjpage | 22 July 2016, 13:57:43 UTC | Update README.md | 22 July 2016, 13:57:43 UTC |
cd83da2 | andrewjpage | 22 July 2016, 13:57:23 UTC | Update README.md | 22 July 2016, 13:57:23 UTC |
99d6756 | andrewjpage | 22 July 2016, 13:32:22 UTC | Merge pull request #175 from andrewjpage/speedup Use GTRCAT by default with RAxML | 22 July 2016, 13:32:22 UTC |
18cbead | andrewjpage | 22 July 2016, 13:23:18 UTC | raxml 7.8 doesnt like missing blank line at end of test fasta | 22 July 2016, 13:23:18 UTC |
8ac5ceb | andrewjpage | 22 July 2016, 13:11:48 UTC | GTRCAT by default in RAxML | 22 July 2016, 13:11:48 UTC |
3487292 | andrewjpage | 22 July 2016, 10:57:50 UTC | remove unnessisary loops when finding recombination bases | 22 July 2016, 10:57:50 UTC |
b868e40 | andrewjpage | 22 July 2016, 09:49:10 UTC | Update INSTALL.md | 22 July 2016, 09:49:10 UTC |
a5f4fc0 | andrewjpage | 15 July 2016, 17:13:08 UTC | Merge pull request #172 from andrewjpage/raxml_reconstruction Raxml reconstruction | 15 July 2016, 17:13:08 UTC |
39e8852 | andrewjpage | 14 July 2016, 09:59:13 UTC | change permissions on test | 14 July 2016, 09:59:13 UTC |
ce5bc10 | andrewjpage | 14 July 2016, 09:27:25 UTC | use teardown for tests, rename internal node prefix | 14 July 2016, 09:27:25 UTC |
07175a3 | andrewjpage | 13 July 2016, 10:47:19 UTC | print internal tree command in verbose mode | 13 July 2016, 10:47:19 UTC |
bbd7720 | andrewjpage | 12 July 2016, 14:58:50 UTC | tests pass | 12 July 2016, 14:58:50 UTC |
4c117f4 | andrewjpage | 11 July 2016, 15:42:44 UTC | wip | 12 July 2016, 14:44:58 UTC |
fc1c04e | andrewjpage | 27 May 2016, 10:28:06 UTC | base sequence reconstruction | 06 July 2016, 13:10:51 UTC |
5404925 | andrewjpage | 21 April 2016, 13:33:55 UTC | ubuntu 16.04 | 21 April 2016, 13:33:55 UTC |
a4b6c1d | andrewjpage | 15 April 2016, 12:27:52 UTC | Merge pull request #166 from andrewjpage/duplicate_sequences Duplicate sequences | 15 April 2016, 12:27:52 UTC |
5f48483 | andrewjpage | 14 April 2016, 15:26:46 UTC | fix tests which werent running remove duplicates and missing data move some fasta validation to new file changelog description of change update versions for travis rename fasttree arch make variables rename fastml dir add v before version number | 15 April 2016, 12:26:54 UTC |
d0ea1bb | andrewjpage | 14 April 2016, 10:37:32 UTC | hash input sequences | 14 April 2016, 10:37:32 UTC |
677be48 | andrewjpage | 13 April 2016, 09:59:20 UTC | update version number | 13 April 2016, 09:59:20 UTC |
ee61719 | andrewjpage | 13 April 2016, 09:55:06 UTC | Merge branch 'master' of github.com:sanger-pathogens/gubbins | 13 April 2016, 09:55:06 UTC |
88c91d2 | andrewjpage | 12 April 2016, 17:58:19 UTC | Merge pull request #164 from harvardinformatics/master Convert the proc output from bytes to strings | 12 April 2016, 17:58:19 UTC |
74de8b9 | Aaron Kitzmiller | 12 April 2016, 14:49:25 UTC | Convert the proc output from bytes to strings so that comparisons will work. | 12 April 2016, 14:49:25 UTC |
d9dfff8 | andrewjpage | 09 March 2016, 10:28:32 UTC | remove homebrew directory | 09 March 2016, 10:28:32 UTC |
fe094b0 | andrewjpage | 01 March 2016, 09:49:02 UTC | Merge branch 'master' of github.com:sanger-pathogens/gubbins | 01 March 2016, 09:49:02 UTC |
baa595b | andrewjpage | 01 March 2016, 09:48:42 UTC | more informative changelog | 01 March 2016, 09:48:42 UTC |
3f9e92c | andrewjpage | 01 March 2016, 09:06:07 UTC | Update README.md | 01 March 2016, 09:06:07 UTC |
ce39645 | andrewjpage | 01 March 2016, 09:01:03 UTC | midpoint rerooting | 01 March 2016, 09:01:03 UTC |
e2adff3 | andrewjpage | 29 February 2016, 16:16:22 UTC | update version | 29 February 2016, 16:16:22 UTC |
1b4b312 | andrewjpage | 29 February 2016, 16:15:14 UTC | Merge pull request #161 from jeromekelleher/fix-stack-allocation2 Fix allocation from stack bug. | 29 February 2016, 16:15:14 UTC |
49db81e | andrewjpage | 29 February 2016, 16:15:02 UTC | Merge pull request #163 from andrewjpage/master midpoint rerooting by default | 29 February 2016, 16:15:02 UTC |
bcc3b87 | andrewjpage | 29 February 2016, 15:19:27 UTC | update version | 29 February 2016, 15:19:27 UTC |
5a29de8 | andrewjpage | 29 February 2016, 15:18:48 UTC | midpoint rerooting by default | 29 February 2016, 15:18:48 UTC |
3960753 | Jerome Kelleher | 19 February 2016, 23:00:15 UTC | Fix allocation from stack bug. For large numbers of SNPs allocating from the stack caused a segfault. This fixes the issue by allocating from the heap with malloc. | 19 February 2016, 23:00:15 UTC |