Commits · b5ec58457bd5a9b185097d50d811601f2b4c365a · Mirrors / biopet.biopet

17 Nov, 2014 8 commits
- Remove unused import · b5ec5845
  Peter van 't Hof authored Nov 17, 2014
  
  b5ec5845
- Added useIndelRealigner and useBaseRecalibration option · 9e565c2f
  Peter van 't Hof authored Nov 17, 2014
  
  9e565c2f
- Fix endlines in fasta files · 1f294e54
  Peter van 't Hof authored Nov 17, 2014
  
  1f294e54
- format · 6ac5e2c8
  Peter van 't Hof authored Nov 17, 2014
  
  6ac5e2c8
- Added collect consensus · 3b0bbaf7
  Peter van 't Hof authored Nov 17, 2014
  
  3b0bbaf7
- Fix reference name · d7e3156a
  Peter van 't Hof authored Nov 17, 2014
  
  d7e3156a
- Change defaults · ef67b6a8
  Peter van 't Hof authored Nov 12, 2014
  
  ef67b6a8
- fix queue args · 56df29e7
  Peter van 't Hof authored Nov 17, 2014
  
  56df29e7
12 Nov, 2014 7 commits
- Change util to utils · 9ba68d82
  Peter van 't Hof authored Nov 12, 2014
  
  9ba68d82
- Added consensus fastas to pipeline · c50d17a2
  Peter van 't Hof authored Nov 12, 2014
  
  c50d17a2
- Changed Queue wrapper · 54d818a2
  Peter van 't Hof authored Nov 12, 2014
  
  54d818a2
- Added consensus + variants builder · 48cfa704
  Peter van 't Hof authored Nov 12, 2014
  
  48cfa704
- Added consensus builder · 0eb984b0
  Peter van 't Hof authored Nov 12, 2014
  
  0eb984b0
- Added scala maxthread option · e3065aec
  Peter van 't Hof authored Nov 12, 2014
  
  e3065aec
- Added fillAllele function · 53855f50
  Peter van 't Hof authored Nov 12, 2014
  
  53855f50
11 Nov, 2014 3 commits
- Added checks · 20c25a0b
  Peter van 't Hof authored Nov 11, 2014
  
  20c25a0b
- Added general vcf utils · 0886c76f
  Peter van 't Hof authored Nov 11, 2014
  
  0886c76f
- Merge branch 'develop' into feature-basty_generate_fasta · 2150ef84
  Peter van 't Hof authored Nov 11, 2014
```
Conflicts:
	biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala
```
  2150ef84
10 Nov, 2014 9 commits
- Remove unused files · 4805a430
  Peter van 't Hof authored Nov 10, 2014
  
  4805a430
- Merge branch 'fixsamtofastq' into 'develop' · ba925f6c
  Peter van 't Hof authored Nov 10, 2014
```
Fixsamtofastq

Added java GC options to DEVELOP

See merge request !48
```
  ba925f6c
- Merge branch 'feature-merge_alleles' into 'develop' · e44e7e62
  bow authored Nov 10, 2014
```
Feature merge alleles

Extends from !44
Also added a tool MergeAlleles and implemented in the gatk-variantcalling pipeline

See merge request !46
```
  e44e7e62
- Merge branch 'feature-fixbedtools_cov_stats' into 'develop' · 933194d3
  Peter van 't Hof authored Nov 10, 2014
```
Feature fixbedtools cov stats

Please merge!@!@!
See also #68

See merge request !47
```
  933194d3
- Merge branch 'develop' into feature-merge_alleles · c405c4bb
  Peter van 't Hof authored Nov 10, 2014
```
Conflicts:
	biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala
```
  c405c4bb
- Fix typo and added exception · b8905325
  Peter van 't Hof authored Nov 10, 2014
  
  b8905325
- Change default threads to 1 · fbff5f3d
  Peter van 't Hof authored Nov 10, 2014
  
  fbff5f3d
- Merge branch 'feature-sample_config_create' into 'develop' · df33687d
  bow authored Nov 10, 2014
```
Feature sample config create

TsvToJson parsen, see also #66

See merge request !45
```
  df33687d
- Fix bedtools_cov_stats.py for plotting in new shark · efa7c989
  sajvanderzeeuw authored Nov 10, 2014
  
  efa7c989
08 Nov, 2014 13 commits
- Added index file as output file · b457ed22
  Peter van 't Hof authored Nov 08, 2014
  
  b457ed22
- Fix on output files · 2a998e22
  Peter van 't Hof authored Nov 08, 2014
  
  2a998e22
- Fix memory · 9aad81a3
  Peter van 't Hof authored Nov 08, 2014
  
  9aad81a3
- Style fix · bc3e6582
  Peter van 't Hof authored Nov 08, 2014
  
  bc3e6582
- Added mergeAlleles to executable · 384e5667
  Peter van 't Hof authored Nov 08, 2014
  
  384e5667
- Change to mergeAlleles · 7313c86d
  Peter van 't Hof authored Nov 08, 2014
  
  7313c86d
- Added constructor · 61128d4e
  Peter van 't Hof authored Nov 08, 2014
  
  61128d4e
- Added Queue wrapper · 2a789532
  Peter van 't Hof authored Nov 08, 2014
  
  2a789532
- Fix bugs on MergeAlleles · 2b4cb228
  Peter van 't Hof authored Nov 08, 2014
  
  2b4cb228
- Added MergeAlleles tool · c46b0592
  Peter van 't Hof authored Nov 08, 2014
  
  c46b0592
- Merge commit '6c473b65 ' into feature-merge_alleles · 6b492ea4
  Peter van 't Hof authored Nov 08, 2014
  
  6b492ea4
- Change name to SamplesTsvToJson · 1b39eb50
  Peter van 't Hof authored Nov 08, 2014
  
  1b39eb50
- Working version of ParseSamples · 480e70fb
  Peter van 't Hof authored Nov 08, 2014
  
  480e70fb