Commits · 712422bb68b86e385e1810870014bc1702024cc3 · Mirrors / biopet.biopet

09 Feb, 2016 2 commits
- Merge branch 'fix-272' into 'develop' · 712422bb
  Peter van 't Hof authored Feb 09, 2016
```
Make inverse of the boolean to fix issue #272

Fixes #272 

See merge request !319
```
  712422bb
- Make inverse of the boolean to fix issue #272 · 0372b00e
  Wai Yi Leung authored Feb 09, 2016
  
  0372b00e
08 Feb, 2016 4 commits
- Merge branch 'fix-268' into 'develop' · eb605a1f
  Wai Yi Leung authored Feb 08, 2016
```
Fix 268

Fixes #268 

See merge request !318
```
  eb605a1f
- Raise memory of varscan · e16d2e05
  Peter van 't Hof authored Feb 08, 2016
  
  e16d2e05
- Remove unused imports · 2654e5c6
  Peter van 't Hof authored Feb 08, 2016
  
  2654e5c6
- Added extra check for forcing abolute paths for input files · 4fa85007
  Peter van 't Hof authored Feb 08, 2016
  
  4fa85007
05 Feb, 2016 6 commits
- Merge branch 'feature-qiime' into 'develop' · acbbc173
  Wai Yi Leung authored Feb 05, 2016
```
Feature qiime

Mainly for project 122

See merge request !287
```
  acbbc173
- Style fixes · 6e62a69e
  Peter van 't Hof authored Feb 05, 2016
  
  6e62a69e
- Added testing for qiime biom to krona method · 60d0fb74
  Peter van 't Hof authored Feb 05, 2016
  
  60d0fb74
- Added testing for kraken to krona method · 6b8b3a37
  Peter van 't Hof authored Feb 05, 2016
  
  6b8b3a37
- Fixed tests · 768f5596
  Peter van 't Hof authored Feb 05, 2016
  
  768f5596
- Added documentation · 2bfef3ed
  Peter van 't Hof authored Feb 05, 2016
  
  2bfef3ed
04 Feb, 2016 3 commits
- Added testing to gears pipeline · ff181760
  Peter van 't Hof authored Feb 04, 2016
  
  ff181760
- Added gears to multi mapping · 0ecd6778
  Peter van 't Hof authored Feb 04, 2016
  
  0ecd6778
- Added more methods to test · 95882d8e
  Peter van 't Hof authored Feb 04, 2016
  
  95882d8e
02 Feb, 2016 3 commits
- Fixed bug in Ln · 53cc2a4d
  Peter van 't Hof authored Feb 02, 2016
  
  53cc2a4d
- Added md5 check to pipeline · f941cb35
  Peter van 't Hof authored Feb 02, 2016
  
  f941cb35
- Merge remote-tracking branch 'remotes/origin/develop' into feature-qiime · b81ad8bb
  Peter van 't Hof authored Feb 02, 2016
  
  b81ad8bb
27 Jan, 2016 2 commits
- Merge branch 'feature-VarscanIntoShiva' into 'develop' · 52776123
  Wai Yi Leung authored Jan 27, 2016
```
Feature varscan into shiva

Fixes #246 

See merge request !308
```
  52776123
- Code improvement · 3427e4e1
  Peter van 't Hof authored Jan 27, 2016
  
  3427e4e1
25 Jan, 2016 4 commits
- Skipped flexiprep stats when flexiprep is not executed · 800ad479
  Peter van 't Hof authored Jan 25, 2016
  
  800ad479
- Fixed bug in report · b2156b2c
  Peter van 't Hof authored Jan 25, 2016
  
  b2156b2c
- Merge remote-tracking branch 'remotes/origin/develop' into feature-VarscanIntoShiva · 88c9300a
  Peter van 't Hof authored Jan 25, 2016
```
Conflicts:
	public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/Varscan.scala
```
  88c9300a
- Change version command · ae01e8be
  Peter van 't Hof authored Jan 25, 2016
  
  ae01e8be
20 Jan, 2016 8 commits
- Fix compile issue · 8afdecfc
  Peter van 't Hof authored Jan 20, 2016
  
  8afdecfc
- Merge remote-tracking branch 'remotes/origin/develop' into feature-qiime · ae8146ba
  Peter van 't Hof authored Jan 20, 2016
  
  ae8146ba
- Merge branch 'fix-260' into 'develop' · 6714a0ab
  Peter van 't Hof authored Jan 20, 2016
```
Fix 260

Closes #260 

See merge request !314
```
  6714a0ab
- Fix bwa bug using freeVar=false · 42b5a991
  Wai Yi Leung authored Jan 20, 2016
  
  42b5a991
- Revert "PindelVCF wrapper", does not belong to this branch · bba51033
  Wai Yi Leung authored Jan 20, 2016
```
This reverts commit 2b618795.
```
  bba51033
- PindelVCF wrapper · 2b618795
  Wai Yi Leung authored Jan 20, 2016
  
  2b618795
- Merge remote-tracking branch 'origin/feature-VarscanIntoShiva' into feature-VarscanIntoShiva · fcb1e2f5
  Sander van der Zeeuw authored Jan 20, 2016
  
  fcb1e2f5
- typo · 6073f6aa
  Sander van der Zeeuw authored Jan 20, 2016
  
  6073f6aa
19 Jan, 2016 8 commits
- Merge branch 'fix-259' into 'develop' · 19323af6
  Wai Yi Leung authored Jan 19, 2016
```
Fixed error message in bamutils

Fixes #259 

See merge request !311
```
  19323af6
- Fixed unit tests · 30696cab
  Peter van 't Hof authored Jan 19, 2016
  
  30696cab
- Added varscan_jar to test config · dd9a7060
  Peter van 't Hof authored Jan 19, 2016
  
  dd9a7060
- Raise default memory for varscan · 10835803
  Peter van 't Hof authored Jan 19, 2016
  
  10835803
- Added version to varscan · 3f85a446
  Peter van 't Hof authored Jan 19, 2016
```
(cherry picked from commit a13b0d1d)
```
  3f85a446
- Added version to varscan · a13b0d1d
  Peter van 't Hof authored Jan 19, 2016
  
  a13b0d1d
- Fixed error message in bamutils · 3fb6b5f8
  Peter van 't Hof authored Jan 19, 2016
  
  3fb6b5f8
- Fixed style · 8b099b94
  Peter van 't Hof authored Jan 19, 2016
  
  8b099b94