Commits · c75b0c16b2284db9e2a9ec9abf92743cd694a6fc · Mirrors / biopet.biopet

Feb 23, 2016
- Remove Yamsvp code and optimize BamUtils. · 628069f0
  Wai Yi Leung authored 9 years ago
  
  628069f0
Feb 22, 2016
- Adding pindel tests · 31982c15
  Wai Yi Leung authored 9 years ago
  
  31982c15
- Order fixes · 9ce0cde0
  Wai Yi Leung authored 9 years ago
  
  9ce0cde0
- Added test for bam arg · 30e7d8ce
  Peter van 't Hof authored 9 years ago
  
  30e7d8ce
- Added test for wrong caller · 1cafa1af
  Peter van 't Hof authored 9 years ago
  
  1cafa1af
- Added summary tests · 0d3f776d
  Peter van 't Hof authored 9 years ago
  
  0d3f776d
Feb 21, 2016
- Added testing for delly options · 4194de0a
  Peter van 't Hof authored 9 years ago
  
  4194de0a
- Added basic unit tests to sv calling · 08bedeee
  Peter van 't Hof authored 9 years ago
  
  08bedeee
Feb 12, 2016
- Simplyfy additional sections · 8215133a
  Peter van 't Hof authored 9 years ago
  
  8215133a
Feb 07, 2016
- Fix order is sections · 1fe8c904
  Peter van 't Hof authored 9 years ago
  
  1fe8c904
Jan 29, 2016
- Limit reporting of events in REF/ALT col to < SVTYPE > (saves space and post-processingpower) · 88adefce
  Wai Yi Leung authored 9 years ago
  
  88adefce
- Adding samplingSize to BamUtils - estimateInsertSize · 5164aa32
  Wai Yi Leung authored 9 years ago
  
  5164aa32
- Added insert size estimation. Fix pindel2vcf dependency (depend on pindel, use... · 75b7230c
  Wai Yi Leung authored 9 years ago
  
  Added insert size estimation. Fix pindel2vcf dependency (depend on pindel, use beforegraph to set outputpath)
  75b7230c
Jan 27, 2016
- Pindel update wrapper, specifing the output files (pindel generates more files) · eebab126
  Wai Yi Leung authored 9 years ago
  
  eebab126
Jan 20, 2016
- Add pindel2vcf to pipeline · d4901714
  Wai Yi Leung authored 9 years ago
  
  d4901714
- typo · 6073f6aa
  Sander van der Zeeuw authored 9 years ago
  
  6073f6aa
Jan 19, 2016
- Remove pindel from the list of default callers · 225b0cae
  Wai Yi Leung authored 9 years ago
  
  225b0cae
- Fixed unit tests · 30696cab
  Peter van 't Hof authored 9 years ago
  
  30696cab
- Added varscan_jar to test config · dd9a7060
  Peter van 't Hof authored 9 years ago
  
  dd9a7060
- Fixed style · 8b099b94
  Peter van 't Hof authored 9 years ago
  
  8b099b94
- add varscan test to shiva variantcalling test · 86ad2593
  Sander van der Zeeuw authored 9 years ago
  
  86ad2593
- move varscan wrapper to extensions · ca40d875
  Sander van der Zeeuw authored 9 years ago
  
  ca40d875
Jan 18, 2016
- changes to get rid of reference calls · bb46c239
  Sander van der Zeeuw authored 9 years ago
  
  bb46c239
- delete file name file on exit of pipeline · 59923a55
  Sander van der Zeeuw authored 9 years ago
  
  59923a55
- change sample name in varscan vcf · 64325f97
  Sander van der Zeeuw authored 9 years ago
  
  64325f97
- remove function removeEmptyPile() · a35c3c9c
  Sander van der Zeeuw authored 9 years ago
  
  a35c3c9c
- added fix mpileup.py scripts to scripts dir in shiva · 7a5e1b5c
  Sander van der Zeeuw authored 9 years ago
  
  7a5e1b5c
- added fixmpileup script and removeEmptypile function · 328be9a6
  Sander van der Zeeuw authored 9 years ago
  
  328be9a6
Jan 15, 2016
- generate dir for varscan · c22edcf3
  Sander van der Zeeuw authored 9 years ago
  
  c22edcf3
- add varscan to shiva variantcallers · 559881ed
  Sander van der Zeeuw authored 9 years ago
  
  559881ed
- Fix pindel caller (fixing null error with Option[File] = None instead of _) · de250d3f
  Wai Yi Leung authored 9 years ago
  
  de250d3f
- Fix input of bams to svcalling tools.. · 8af58a0b
  Wai Yi Leung authored 9 years ago
  
  8af58a0b
Jan 14, 2016
- Fix compile errors · e42f7355
  Wai Yi Leung authored 9 years ago
  
  e42f7355
- Adding Pindel to ShivaSVCalling · d1384de8
  Wai Yi Leung authored 9 years ago
  
  d1384de8
Jan 12, 2016
- Fix reference tag · 81d36084
  Peter van 't Hof authored 9 years ago
  
  81d36084
- Fixed report types · 9034e179
  Peter van 't Hof authored 9 years ago
  
  9034e179
Jan 11, 2016
- Change gentrap report to multisample mapping report · 56766d98
  Peter van 't Hof authored 9 years ago
  
  56766d98
- Switch shiva to general multisample report · b0f9d027
  Peter van 't Hof authored 9 years ago
  
  b0f9d027
- Remove outdated todo · d79733d1
  Peter van 't Hof authored 9 years ago
  
  d79733d1
Jan 10, 2016
- Fixed type · bf11fd13
  Peter van 't Hof authored 9 years ago
  
  bf11fd13