https://github.com/sanger-pathogens/gubbins

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Revision Author Date Message Commit Date
e1df9fe Merge pull request #227 from puethe/segfault dynamically allocate memory to avoid stack overflow 30 July 2018, 15:30:49 UTC
06d3da2 dynamically allocate memory to avoid stack overflow 30 July 2018, 15:22:20 UTC
e1b4ec6 Merge pull request #226 from puethe/independent_docker Dockerfile independent from debian package 26 July 2018, 16:03:35 UTC
22fd2c5 clone from sanger-pathogens repo 25 July 2018, 09:44:14 UTC
f113ba6 dockerfile independent of the Debian package 25 July 2018, 09:30:16 UTC
b0a9969 Merge pull request #224 from puethe/master universal link 02 July 2018, 09:01:29 UTC
ec281b8 Update README.md 02 July 2018, 08:57:06 UTC
08e5213 Merge pull request #1 from sanger-pathogens/master link to install.md 02 July 2018, 08:55:19 UTC
87d65db Merge pull request #223 from puethe/link_to_install_file link to install.md 02 July 2018, 08:41:03 UTC
8e08591 link to install.md 02 July 2018, 08:34:53 UTC
2856b5e 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 Replaced the script gubbins_drawer.py with an empty script displaying only an info message. 15 June 2018, 11:42:44 UTC
7f334ce Merge pull request #220 from puethe/link_check_to_lsubunit Link check to lsubunit 15 June 2018, 07:47:37 UTC
41d3609 tell travis to install subunit 13 June 2018, 14:57:39 UTC
11e3a8c install libsubunit-dev 13 June 2018, 13:51:15 UTC
367d925 Link to 'subunit' to get check running on newer ubuntu/debian systems 13 June 2018, 13:25:06 UTC
87d8f83 Merge pull request #219 from puethe/correct_fasttree_typo corrected typo: 'fastree' -> 'fasttree' 08 June 2018, 15:19:09 UTC
f5afdd7 corrected typo: 'fastree' -> 'fasttree' 08 June 2018, 14:17:45 UTC
b38e643 Merge pull request #217 from ssjunnebo/625345_docker_instructions update instructions for Docker 31 May 2018, 14:29:08 UTC
bca8fec update instructions for Docker 31 May 2018, 14:23:53 UTC
8cd1870 Update README.md corrected spelling mistake 19 February 2018, 09:44:12 UTC
350e15a add example output data 24 January 2018, 09:54:53 UTC
523efaf accept install docker 15 January 2018, 12:40:51 UTC
1077ce6 remove installation instructions for homebrew 12 January 2018, 10:46:16 UTC
c677a77 Merge pull request #207 from schultzm/master added choices to `--tree_builder` and other args 27 November 2017, 07:35:34 UTC
8102d01 remove punctuation from choices 27 November 2017, 07:12:15 UTC
f7a8a41 added `choices` to all options with choices 27 November 2017, 07:09:39 UTC
20b10b6 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 Merge pull request #206 from ssjunnebo/master ignore ltmain.sh for language statistics 30 October 2017, 11:21:39 UTC
c460bd6 ignore ltmain.sh for language statistics 30 October 2017, 11:16:27 UTC
6be39ae Merge pull request #203 from andrewjpage/update_docs update manual 22 September 2017, 11:05:49 UTC
9dd5ae0 update manual 22 September 2017, 11:05:31 UTC
208a2ae Update README.md 22 September 2017, 10:59:26 UTC
b7b935d Merge branch 'internal_nodes' 22 September 2017, 10:57:33 UTC
5d8676e Merge branch 'master' of github.com:sanger-pathogens/gubbins into internal_nodes 22 September 2017, 10:56:03 UTC
abae76f fix changelog 22 September 2017, 10:55:46 UTC
3a276c0 Merge pull request #202 from andrewjpage/internal_nodes Internal nodes 22 September 2017, 10:54:52 UTC
b03434a test for internal labels 22 September 2017, 10:53:57 UTC
63134f3 inc version 22 September 2017, 10:02:33 UTC
e5c97f2 add internal node labels to the final tree 22 September 2017, 10:01:17 UTC
dbe0b71 Merge pull request #201 from andrewjpage/gubbins_drawer_help Gubbins drawer help text 21 September 2017, 14:33:23 UTC
c1305e7 assume 1 file 21 September 2017, 14:27:45 UTC
decfc5f Add helptext to gubbins drawer and require tree as a positional argument rather than an option. 21 September 2017, 14:02:31 UTC
0e6774a gubbins drawer to use argsparse 15 September 2017, 13:34:52 UTC
3ad41e8 Merge pull request #200 from andrewjpage/helptext Fix default extended help text. 15 September 2017, 13:04:25 UTC
30b8cb0 changelog version 15 September 2017, 13:03:47 UTC
d983d0b force defaults to always print 15 September 2017, 12:58:55 UTC
f796262 Update CHANGELOG 04 September 2017, 10:10:32 UTC
79501ae Merge pull request #197 from andrewjpage/avx2 allow for AVX2 04 September 2017, 10:09:27 UTC
b907ad4 allow for AVX2 04 September 2017, 10:05:21 UTC
1d13185 Merge pull request #193 from ssjunnebo/master updated manual 02 August 2017, 12:10:44 UTC
d8a2b9d updated manual 02 August 2017, 12:08:41 UTC
8e6109c Update README.md 21 June 2017, 15:39:59 UTC
933d50e Update INSTALL.md 21 June 2017, 13:29:38 UTC
b1a1186 Merge pull request #188 from ssjunnebo/master Manual in docx format 13 March 2017, 14:02:36 UTC
5a1ff3a Added latest manual in docx format 13 March 2017, 13:57:06 UTC
863d44f Merge pull request #186 from ssjunnebo/master Fixed biopython sub_features bug 20 February 2017, 15:04:07 UTC
6f3af4a change version nr 20 February 2017, 15:02:37 UTC
f0eb50f Merge branch '516666' 20 February 2017, 14:51:21 UTC
cef2dcc gubbins_drawer.py fixed biopython error 20 February 2017, 14:49:57 UTC
dbb278c Update CHANGELOG 31 October 2016, 13:45:01 UTC
5bb1896 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 dont filter out identical sequences by default 31 October 2016, 13:09:09 UTC
8a12ae7 Merge branch 'master' of github.com:sanger-pathogens/gubbins 01 August 2016, 15:05:52 UTC
c2eb532 Dockerfile 01 August 2016, 15:05:27 UTC
28b83fc Update README.md 25 July 2016, 12:43:03 UTC
599c7e1 Update README.md 22 July 2016, 13:58:50 UTC
ff12945 Update README.md 22 July 2016, 13:57:43 UTC
cd83da2 Update README.md 22 July 2016, 13:57:23 UTC
99d6756 Merge pull request #175 from andrewjpage/speedup Use GTRCAT by default with RAxML 22 July 2016, 13:32:22 UTC
18cbead raxml 7.8 doesnt like missing blank line at end of test fasta 22 July 2016, 13:23:18 UTC
8ac5ceb GTRCAT by default in RAxML 22 July 2016, 13:11:48 UTC
3487292 remove unnessisary loops when finding recombination bases 22 July 2016, 10:57:50 UTC
b868e40 Update INSTALL.md 22 July 2016, 09:49:10 UTC
a5f4fc0 Merge pull request #172 from andrewjpage/raxml_reconstruction Raxml reconstruction 15 July 2016, 17:13:08 UTC
39e8852 change permissions on test 14 July 2016, 09:59:13 UTC
ce5bc10 use teardown for tests, rename internal node prefix 14 July 2016, 09:27:25 UTC
07175a3 print internal tree command in verbose mode 13 July 2016, 10:47:19 UTC
bbd7720 tests pass 12 July 2016, 14:58:50 UTC
4c117f4 wip 12 July 2016, 14:44:58 UTC
fc1c04e base sequence reconstruction 06 July 2016, 13:10:51 UTC
5404925 ubuntu 16.04 21 April 2016, 13:33:55 UTC
a4b6c1d Merge pull request #166 from andrewjpage/duplicate_sequences Duplicate sequences 15 April 2016, 12:27:52 UTC
5f48483 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 hash input sequences 14 April 2016, 10:37:32 UTC
677be48 update version number 13 April 2016, 09:59:20 UTC
ee61719 Merge branch 'master' of github.com:sanger-pathogens/gubbins 13 April 2016, 09:55:06 UTC
88c91d2 Merge pull request #164 from harvardinformatics/master Convert the proc output from bytes to strings 12 April 2016, 17:58:19 UTC
74de8b9 Convert the proc output from bytes to strings so that comparisons will work. 12 April 2016, 14:49:25 UTC
d9dfff8 remove homebrew directory 09 March 2016, 10:28:32 UTC
fe094b0 Merge branch 'master' of github.com:sanger-pathogens/gubbins 01 March 2016, 09:49:02 UTC
baa595b more informative changelog 01 March 2016, 09:48:42 UTC
3f9e92c Update README.md 01 March 2016, 09:06:07 UTC
ce39645 midpoint rerooting 01 March 2016, 09:01:03 UTC
e2adff3 update version 29 February 2016, 16:16:22 UTC
1b4b312 Merge pull request #161 from jeromekelleher/fix-stack-allocation2 Fix allocation from stack bug. 29 February 2016, 16:15:14 UTC
49db81e Merge pull request #163 from andrewjpage/master midpoint rerooting by default 29 February 2016, 16:15:02 UTC
bcc3b87 update version 29 February 2016, 15:19:27 UTC
5a29de8 midpoint rerooting by default 29 February 2016, 15:18:48 UTC
3960753 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
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