Commits · 09190f820a7858b7a28dac6a277cb51fe5329fa5 · Mirrors / biopet.biopet

27 May, 2014 1 commit
- Added general trait (BiopetQScript) that now have multisample functions · 09190f82
  Peter van 't Hof authored May 27, 2014
  
  09190f82
26 May, 2014 7 commits
- Moved aligners to own package · 5d0b4fc9
  Peter van 't Hof authored May 26, 2014
  
  5d0b4fc9
- Gatk now uses the mapping module · b3553528
  Peter van 't Hof authored May 26, 2014
  
  b3553528
- Small changes on config setup · 8d195010
  Peter van 't Hof authored May 26, 2014
  
  8d195010
- Added default_clip_mode option · b0317762
  Peter van 't Hof authored May 26, 2014
  
  b0317762
- Added scala files to jar and added a main class for each pipeline · 302c6fff
  Peter van 't Hof authored May 26, 2014
  
  302c6fff
- Added python parser to buildin python scripts · 2f38f1f1
  Peter van 't Hof authored May 26, 2014
  
  2f38f1f1
- Added python scripts to jar file · 9519ee04
  Peter van 't Hof authored May 26, 2014
  
  9519ee04
21 May, 2014 9 commits
- - Standerize config · 2fb73c96
  Peter van 't Hof authored May 21, 2014
  
  2fb73c96
- - Fixed output file for star · 30fe43b7
  Peter van 't Hof authored May 21, 2014
  
  30fe43b7
- - Fixed output file · bb158f36
  Peter van 't Hof authored May 21, 2014
  
  bb158f36
- - Added sub configs for gatk buildin modules · f95148c6
  Peter van 't Hof authored May 21, 2014
  
  f95148c6
- - Fixed scattercounts · 31ea0eee
  Peter van 't Hof authored May 21, 2014
  
  31ea0eee
- - Fixed scattercounts · 630092d5
  Peter van 't Hof authored May 21, 2014
  
  630092d5
- - Fixed scattercounts · 307c0b53
  Peter van 't Hof authored May 21, 2014
  
  307c0b53
- - output file for star · da6a6ef2
  Peter van 't Hof authored May 21, 2014
  
  da6a6ef2
- - output file for star · 23084ff1
  Peter van 't Hof authored May 21, 2014
  
  23084ff1
20 May, 2014 11 commits
- - fixed thread option for star · de498a26
  Peter van 't Hof authored May 20, 2014
  
  de498a26
- - fixed namespaceing in AddOrReplaceReadGroups · da66790f
  Peter van 't Hof authored May 20, 2014
  
  da66790f
- - fixed namespaceing in AddOrReplaceReadGroups · eb23b56e
  Peter van 't Hof authored May 20, 2014
  
  eb23b56e
- - Fixed output of star · 6ebb058a
  Peter van 't Hof authored May 20, 2014
  
  6ebb058a
- - Fixed input field on markduplicates in mapping module · 4785e578
  Peter van 't Hof authored May 20, 2014
  
  4785e578
- - Fixed scattercount in Variant Recalibration · 205355eb
  Peter van 't Hof authored May 20, 2014
  
  205355eb
- - Fixed memory issue in Variant Recalibration · 3f2913f8
  Peter van 't Hof authored May 20, 2014
  
  3f2913f8
- - Fixed Bwa on Gatk, did called the wrong config · 379c8474
  Peter van 't Hof authored May 20, 2014
  
  379c8474
- - Added referenceFile to catVariants · b1276a90
  Peter van 't Hof authored May 20, 2014
  
  b1276a90
- - Added nt and scattercount options to ApplyRecalibration · 08f3651d
  Peter van 't Hof authored May 20, 2014
  
  08f3651d
- - Added wrapper for Star · ca2905e5
  Peter van 't Hof authored May 20, 2014
```
- Added a mapping module (not yet used in Gatk)
- Added VariantRecalibrator to Gatk
```
  ca2905e5
15 May, 2014 3 commits
- Remove submodules · b26d817a
  Peter van 't Hof authored May 15, 2014
  
  b26d817a
- remove submodules · ffe46a1f
  Peter van 't Hof authored May 15, 2014
  
  ffe46a1f
- Remove submodules · 3634117a
  Peter van 't Hof authored May 15, 2014
  
  3634117a
14 May, 2014 8 commits
- fixed pom.xml · 08e40349
  Peter van 't Hof authored May 14, 2014
  
  08e40349
- Remove gatk-package · 453332de
  Peter van 't Hof authored May 14, 2014
  
  453332de
- Remove flexiprep-package · 3f1b94f5
  Peter van 't Hof authored May 14, 2014
  
  3f1b94f5
- add queue install script · 0c9ac7bd
  Peter van 't Hof authored May 14, 2014
  
  0c9ac7bd
- Added gatk package · c548969b
  Peter van 't Hof authored May 14, 2014
  
  c548969b
- First commit · 63939b51
  pjvan_thof authored May 14, 2014
  
  63939b51
- add submodules · b2b5e8fc
  Peter van 't Hof authored May 14, 2014
  
  b2b5e8fc
- First commit · d7457fe8
  pjvan_thof authored May 14, 2014
  
  d7457fe8