Commits · master · Klinische Genetica / prinia

11 Oct, 2018 4 commits
- always end param dir with a slash. · d24fc710
  Sander Bollen authored Oct 11, 2018
  
  d24fc710
- thermodynamic params in tool. · 0f4f8bd0
  Sander Bollen authored Oct 11, 2018
  
  0f4f8bd0
- add test for thermodynamic params · ec1b3935
  Sander Bollen authored Oct 11, 2018
  
  ec1b3935
- add optional thermodynamics parameters option in jinja template · c3006d80
  Sander Bollen authored Oct 11, 2018
  
  c3006d80
10 Oct, 2018 6 commits
- update readme · 25a43952
  Sander Bollen authored Oct 10, 2018
  
  25a43952
- Set python 3.7 to use xenial and sudo, since 3.7 doesn't work on travis out of the box 😢 · 30d2b433
  Sander Bollen authored Oct 10, 2018
```
See https://github.com/travis-ci/travis-ci/issues/9815
```
  30d2b433
- add missing primer_internal_opt_gc_percent parameter. · 39fbaa2c
  Sander Bollen authored Oct 10, 2018
  
  39fbaa2c
- add a travis yml · 74d516ea
  Sander Bollen authored Oct 10, 2018
  
  74d516ea
- add example line in readme · 1f818ba2
  Sander Bollen authored Oct 10, 2018
  
  1f818ba2
- add a few more primer3 settings · 79eb5c59
  Sander Bollen authored Oct 10, 2018
  
  79eb5c59
27 Sep, 2018 1 commit
- explicity check primer3_core executable in test · c77faac1
  Sander Bollen authored Sep 27, 2018
  
  c77faac1
26 Sep, 2018 2 commits
- update readme · 3244f77d
  Sander Bollen authored Sep 26, 2018
  
  3244f77d
- rewrite interface to use settings json in stead of flat arguments when designing primers · 097bfea5
  Sander Bollen authored Sep 26, 2018
  
  097bfea5
25 Sep, 2018 4 commits
- make Primer3 object use settings json · 195f6d48
  Sander Bollen authored Sep 25, 2018
  
  195f6d48
- add jinja2 to requirements.txt · 6cb64c2e
  Sander Bollen authored Sep 25, 2018
  
  6cb64c2e
- create primer3 configuration from template. · 7e51d455
  Sander Bollen authored Sep 25, 2018
  
  7e51d455
- add more tests for settings dict · 5560f6d0
  Sander Bollen authored Sep 25, 2018
  
  5560f6d0
24 Sep, 2018 1 commit
- Generate settings dict from supplied json, with defaults from schema · a02c84e1
  Sander Bollen authored Sep 24, 2018
  
  a02c84e1
20 Sep, 2018 3 commits
- add more constraints to schema and add schema tests · 646885c5
  Sander Bollen authored Sep 20, 2018
  
  646885c5
- add stub for settings schema for primer3 · 73f7434e
  Sander Bollen authored Sep 20, 2018
  
  73f7434e
- add conda environment yaml · d228cd87
  Sander Bollen authored Sep 20, 2018
  
  d228cd87
11 Sep, 2018 1 commit
- fix missing return statement · 1dc01b41
  Sander Bollen authored Sep 11, 2018
  
  1dc01b41
10 Sep, 2018 1 commit
- flake8 fixes · 2ce69ed4
  Sander Bollen authored Sep 10, 2018
  
  2ce69ed4
05 Sep, 2018 5 commits
- setup.py: Add MANIFEST.in and force static files to be included at install stage · d860edaf
  Damien Zammit authored Jan 31, 2018
  
  d860edaf
- add rudimentary testing · a4da9b23
  Sander Bollen authored Sep 05, 2018
  
  a4da9b23
- update year in license · e5a5710c
  Sander Bollen authored Sep 05, 2018
  
  e5a5710c
- use setuptools find_packages · 19e7f76a
  Sander Bollen authored Sep 05, 2018
  
  19e7f76a
- fetch samtools version with regex, so that it handles version · 81878f97
  Sander Bollen authored Sep 05, 2018
```
strings with suffixes. Warn in stead of fail when version cannot be
determined.
```
  81878f97
11 Jul, 2018 3 commits
- dbsnp is not per se required · c2c6fee7
  Sander Bollen authored Jul 11, 2018
  
  c2c6fee7
- fix read mode on region reeader. · 86cbe6d0
  Sander Bollen authored Jul 11, 2018
  
  86cbe6d0
- remove fastools from requirements · 204024b5
  Sander Bollen authored Jul 11, 2018
  
  204024b5
18 Oct, 2017 1 commit
- reverse complement for reverse sequence · 63ef0435
  Sander Bollen authored Oct 18, 2017
  
  63ef0435
21 Aug, 2017 1 commit
- samtools 1.3 removed old-style sort arguments · e2996a03
  Sander Bollen authored Aug 21, 2017
  
  e2996a03
14 Aug, 2017 3 commits
- mode = w for python3 · 9cc41c4e
  Sander Bollen authored Aug 14, 2017
  
  9cc41c4e
- hashes must be encoded in python3 · 498d3487
  Sander Bollen authored Aug 14, 2017
  
  498d3487
- mode w for config (python 3) · 02cddf6c
  Sander Bollen authored Aug 14, 2017
  
  02cddf6c
09 Aug, 2017 3 commits
- remove redundant code · 0aa9d54a
  Sander Bollen authored Aug 09, 2017
  
  0aa9d54a
- expose new options in primerdesign · e451eef4
  Sander Bollen authored Aug 09, 2017
  
  e451eef4
- use subprocess in design · 8e4ba82e
  Sander Bollen authored Aug 09, 2017
  
  8e4ba82e
08 Aug, 2017 1 commit
- parse output when outpath is specified for primer3 · e35d806b
  Sander Bollen authored Aug 08, 2017
  
  e35d806b