Commits · 4d479f00a203281961516f86df04c7181c24a753 · Mirrors / biopet.biopet

29 Oct, 2015 12 commits
- Style fixes · 4d479f00
  Peter van 't Hof authored Oct 29, 2015
  
  4d479f00
- Fixed intermediate files · bbaaa914
  Peter van 't Hof authored Oct 29, 2015
  
  bbaaa914
- Fix fai check · 09fe4d50
  Peter van 't Hof authored Oct 29, 2015
  
  09fe4d50
- Added reference to bamMetrics · 6ac2ce38
  Peter van 't Hof authored Oct 29, 2015
  
  6ac2ce38
- Merge remote-tracking branch 'remotes/origin/develop' into fix-shiva_fails · 25d38d41
  Peter van 't Hof authored Oct 29, 2015
  
  25d38d41
- Changed error handeling · cf4d0b82
  Peter van 't Hof authored Oct 29, 2015
  
  cf4d0b82
- Added bammetrics when start from bam file · ef5ea6ce
  Peter van 't Hof authored Oct 29, 2015
  
  ef5ea6ce
- Hide QC from report when flexiprep is not executed · 3d73d611
  Peter van 't Hof authored Oct 29, 2015
  
  3d73d611
- Fixed link to bai file · 55aba945
  Peter van 't Hof authored Oct 29, 2015
  
  55aba945
- Fixed library key · 740df971
  Peter van 't Hof authored Oct 29, 2015
  
  740df971
- No memory increase on first retry · e1795b9a
  Peter van 't Hof authored Oct 29, 2015
  
  e1795b9a
- Added a merge step · d222ae11
  Peter van 't Hof authored Oct 29, 2015
  
  d222ae11
28 Oct, 2015 6 commits
- Fixed sample settings · 5c207b0b
  Peter van 't Hof authored Oct 28, 2015
  
  5c207b0b
- Added args · ef3b8eb6
  Peter van 't Hof authored Oct 28, 2015
  
  ef3b8eb6
- Fixed md5 check · 974156b3
  Peter van 't Hof authored Oct 28, 2015
  
  974156b3
- Style change · 21d64302
  Peter van 't Hof authored Oct 28, 2015
  
  21d64302
- Merge branch 'fix-coverage_piping' into 'develop' · 9c5c1703
  Sander Bollen authored Oct 28, 2015
```
Fix coverage piping

Fixes #230 

still need testing

See merge request !257
```
  9c5c1703
- Fixed report · 2483b207
  Peter van 't Hof authored Oct 28, 2015
  
  2483b207
27 Oct, 2015 17 commits
- Merge remote-tracking branch 'remotes/origin/develop' into fix-shiva_fails · a6ff2665
  Peter van 't Hof authored Oct 27, 2015
  
  a6ff2665
- Merge branch 'feature-genotype_concordance' into 'develop' · 4258ac1b
  Sander Bollen authored Oct 27, 2015
```
Added GenotypeConcordance

Fixes #227, #228 and #229 

Adding here GenotypeConcordance of gatk. This can calculate concordance on multisample vcf files.

See merge request !260
```
  4258ac1b
- fixed missing key · 1a33022a
  Peter van 't Hof authored Oct 27, 2015
  
  1a33022a
- Removed double index · b00a8f2f
  Peter van 't Hof authored Oct 27, 2015
  
  b00a8f2f
- Fix sample flag · 1101daa7
  Peter van 't Hof authored Oct 27, 2015
  
  1101daa7
- Changed file name · 3921c5d9
  Peter van 't Hof authored Oct 27, 2015
  
  3921c5d9
- Fix type · 85735dd3
  Peter van 't Hof authored Oct 27, 2015
  
  85735dd3
- Added input files to summary of shiva · 5448ee58
  Peter van 't Hof authored Oct 27, 2015
  
  5448ee58
- Added more setting to the report · ba50ff98
  Peter van 't Hof authored Oct 27, 2015
  
  ba50ff98
- Hide variant report when multisample variantcalling is not executed · ffd2f2fa
  Peter van 't Hof authored Oct 27, 2015
  
  ffd2f2fa
- Raise default memory · 6a776170
  Peter van 't Hof authored Oct 27, 2015
  
  6a776170
- Added more settings to the summary · ad4b957a
  Peter van 't Hof authored Oct 27, 2015
  
  ad4b957a
- Style changes · f1011497
  Peter van 't Hof authored Oct 27, 2015
  
  f1011497
- Implemented sample specific settings in the summary · 7e1495dc
  Peter van 't Hof authored Oct 27, 2015
  
  7e1495dc
- Remove undeed trait · 59e750bf
  Peter van 't Hof authored Oct 27, 2015
  
  59e750bf
- Change titles · 99a3ba0a
  Peter van 't Hof authored Oct 27, 2015
  
  99a3ba0a
- Switch -a and -b for bedtools coverage · e27c05d0
  Peter van 't Hof authored Oct 27, 2015
  
  e27c05d0
26 Oct, 2015 5 commits
- Remove file checking · c40dda46
  Peter van 't Hof authored Oct 26, 2015
  
  c40dda46
- Fix summary key · 186db74d
  Peter van 't Hof authored Oct 26, 2015
  
  186db74d
- Fixed bcftools merge step · 779e8aa3
  Peter van 't Hof authored Oct 26, 2015
  
  779e8aa3
- Fixed unknown executables · 9156f68c
  Peter van 't Hof authored Oct 26, 2015
  
  9156f68c
- Style changes · db4dcbca
  Peter van 't Hof authored Oct 26, 2015
  
  db4dcbca