Commits · 0ecd6778c4df06f603497d277ee09d380a18ceb5 · Mirrors / biopet.biopet

04 Feb, 2016 2 commits
- 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 12 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
- Merge branch 'feature-update-cutadapt' into 'develop' · ac55539b
  Peter van 't Hof authored Jan 19, 2016
```
Update Cutadapt wrapper

Updated cutadapt wrapper to reflect cutadapt 1.9 and added missing options (which were already supported in 1.5 but not in extension)

Closes #243 

See merge request !310
```
  ac55539b
- add varscan test to shiva variantcalling test · 86ad2593
  Sander van der Zeeuw authored Jan 19, 2016
  
  86ad2593
- move varscan wrapper to extensions · ca40d875
  Sander van der Zeeuw authored Jan 19, 2016
  
  ca40d875
- Update Cutadapt wrapper and style change (camelCaps instead of _) · 3049d572
  Wai Yi Leung authored Jan 19, 2016
  
  3049d572
18 Jan, 2016 7 commits
- Update Cutadapt wrapper · 564081d7
  Wai Yi Leung authored Jan 18, 2016
  
  564081d7
- changes to get rid of reference calls · bb46c239
  Sander van der Zeeuw authored Jan 18, 2016
  
  bb46c239
- delete file name file on exit of pipeline · 59923a55
  Sander van der Zeeuw authored Jan 18, 2016
  
  59923a55
- change sample name in varscan vcf · 64325f97
  Sander van der Zeeuw authored Jan 18, 2016
  
  64325f97
- remove function removeEmptyPile() · a35c3c9c
  Sander van der Zeeuw authored Jan 18, 2016
  
  a35c3c9c
- added fix mpileup.py scripts to scripts dir in shiva · 7a5e1b5c
  Sander van der Zeeuw authored Jan 18, 2016
  
  7a5e1b5c
- added fixmpileup script and removeEmptypile function · 328be9a6
  Sander van der Zeeuw authored Jan 18, 2016
  
  328be9a6
17 Jan, 2016 2 commits
- Merge branch 'feature-core_unit_tests' into 'develop' · defe2788
  Wai Yi Leung authored Jan 17, 2016
```
Feature core unit tests

Fixes #253 

See merge request !307
```
  defe2788
- Merge branch 'fix-renames' into 'develop' · acf6fe14
  Peter van 't Hof authored Jan 17, 2016
```
Fix renames

Some naming fixes for consistency.

See merge request !309
```
  acf6fe14