Commits · e79bb4103b4382c1bf10f11916fe2896e1497de7 · Mirrors / biopet.biopet

26 Oct, 2016 1 commit
- Merge branch 'feature-single_bed_sort' into 'develop' · e79bb410
  Sander Bollen authored Oct 26, 2016
```
For for BIOPET-389



See merge request !464
```
  e79bb410
25 Oct, 2016 1 commit
- For for BIOPET-389 · abb1f25e
  Peter van 't Hof authored Oct 25, 2016
  
  abb1f25e
24 Oct, 2016 3 commits
- Merge branch 'feature-sample_regex' into 'develop' · e6199e01
  Sander Bollen authored Oct 24, 2016
```
Added regex option



See merge request !458
```
  e6199e01
- Changed var name · d1e7b1f9
  Peter van 't Hof authored Oct 24, 2016
  
  d1e7b1f9
- Added text to args · 5ecbd595
  Peter van 't Hof authored Oct 24, 2016
  
  5ecbd595
13 Oct, 2016 2 commits
- Merge branch 'feature-convenience-version' into 'develop' · 4db54050
  Peter van 't Hof authored Oct 13, 2016
```
semantic version convenience methods

See #387

See merge request !459
```
  4db54050
- small extra com ment · 950fe55b
  Sander Bollen authored Oct 13, 2016
  
  950fe55b
12 Oct, 2016 3 commits
- Simplify regex fetching · 4c0e7a8b
  Peter van 't Hof authored Oct 12, 2016
  
  4c0e7a8b
- semantic version convenience methods · 5620069f
  Sander Bollen authored Oct 12, 2016
  
  5620069f
- Added regex option · 50d678ff
  Peter van 't Hof authored Oct 12, 2016
  
  50d678ff
05 Oct, 2016 3 commits
- Merge branch 'feature-centrifuge' into 'develop' · 2727f142
  bow authored Oct 05, 2016
```
Added base version of centrifuge extension

This is adding centrifuge, this will later on replace kraken.

See merge request !452
```
  2727f142
- Fix gzip · 290f37f6
  Peter van 't Hof authored Oct 05, 2016
  
  290f37f6
- Fixed unit test · a6f403df
  Peter van 't Hof authored Oct 05, 2016
  
  a6f403df
04 Oct, 2016 7 commits
- Merge branch 'fix-must-have-variant' into 'develop' · 0c7e6dae
  Peter van 't Hof authored Oct 04, 2016
```
Fix must have variant

Fixes #386 

See merge request !455
```
  0c7e6dae
- style changes · 87dad15a
  Sander Bollen authored Oct 04, 2016
  
  87dad15a
- extra safeguards. potential genotype 1/. is still a call. · 71ee4cab
  Sander Bollen authored Oct 04, 2016
```
 Tests in VcfUtils
```
  71ee4cab
- better way of finding these types of variants · 90ad4035
  Sander Bollen authored Oct 04, 2016
  
  90ad4035
- Remove default · a0ee046e
  Peter van 't Hof authored Oct 04, 2016
  
  a0ee046e
- Fixed output of centrifuge · 94ec5b1a
  Peter van 't Hof authored Oct 04, 2016
  
  94ec5b1a
- Merge branch 'feature-sage_unit_tests' into 'develop' · 3d9a0df1
  bow authored Oct 04, 2016
```
Added basic testing to sage



See merge request !457
```
  3d9a0df1
03 Oct, 2016 9 commits
- Fixed unit test · 83e1c12f
  Peter van 't Hof authored Oct 03, 2016
  
  83e1c12f
- Output centrifuge as gz files · a50fc782
  Peter van 't Hof authored Oct 03, 2016
  
  a50fc782
- Fix type · a8a0e1b0
  Peter van 't Hof authored Oct 03, 2016
  
  a8a0e1b0
- Fixed input files · 091a2657
  Peter van 't Hof authored Oct 03, 2016
  
  091a2657
- Fixed arg bug · 4245609f
  Peter van 't Hof authored Oct 03, 2016
  
  4245609f
- Make output name required · 35bd64d6
  Peter van 't Hof authored Oct 03, 2016
  
  35bd64d6
- Format fix · 05096c7d
  Peter van 't Hof authored Oct 03, 2016
  
  05096c7d
- Remove nulls · 9ec465f6
  Peter van 't Hof authored Oct 03, 2016
  
  9ec465f6
- Adding more testing · b8c07bd9
  Peter van 't Hof authored Oct 03, 2016
  
  b8c07bd9
29 Sep, 2016 1 commit
- Merge branch 'feature-basty_testing' into 'develop' · 3580cc2e
  bow authored Sep 29, 2016
```
Added testing to basty



See merge request !456
```
  3580cc2e
28 Sep, 2016 5 commits
- Remove some old code · 81797e5a
  Peter van 't Hof authored Sep 28, 2016
  
  81797e5a
- Added basic testing to sage · 6455b8d4
  Peter van 't Hof authored Sep 28, 2016
  
  6455b8d4
- Added testing to pipeline summary values · 2d9ade1e
  Peter van 't Hof authored Sep 28, 2016
  
  2d9ade1e
- Format fix · 81e75fbd
  Peter van 't Hof authored Sep 28, 2016
  
  81e75fbd
- Added more summary testing · 1aea2582
  Peter van 't Hof authored Sep 28, 2016
  
  1aea2582
27 Sep, 2016 5 commits
- Added more job testing · b4c7ded4
  Peter van 't Hof authored Sep 27, 2016
  
  b4c7ded4
- Added testing to basty · 6f2d19e0
  Peter van 't Hof authored Sep 27, 2016
  
  6f2d19e0
- Merge branch 'warning-do-note-remove' into 'develop' · d43c8265
  Peter van 't Hof authored Sep 27, 2016
```
Warning do note remove



See merge request !453
```
  d43c8265
- Merge branch 'feature-find_overlap' into 'develop' · 8a710c02
  bow authored Sep 27, 2016
```
Feature find overlap

This is a sample tool to find overlaping samples based on a matrix produces by vcfstats

See merge request !454
```
  8a710c02
- add test · af617116
  Sander Bollen authored Sep 27, 2016
  
  af617116