Commits · 928fbf79597a5479303eb23826634877a6c1b905 · Mirrors / biopet.biopet

Nov 08, 2014
- Added plugin to pom.xml · 928fbf79
  Peter van 't Hof authored 10 years ago
  
  928fbf79
Nov 05, 2014
- Rename package to workaround · 8035d76b
  Peter van 't Hof authored 10 years ago
  
  8035d76b
- Moved package because of implicit log appender · f4a40737
  Peter van 't Hof authored 10 years ago
  
  f4a40737
Nov 04, 2014
- Removed apps config, let the user decide on the settings · e5fa8f07
  wyleung authored 10 years ago
  
  e5fa8f07
- Remove mapping specific settings · 3ea7649d
  wyleung authored 10 years ago
  
  3ea7649d
- config json with executable used in biopet, SHARK specific config · e08e5820
  wyleung authored 10 years ago
  
  e08e5820
- Added genotypemergeoption option, needed since Gatk 3.3 · 137ecdb3
  Peter van 't Hof authored 10 years ago
  137ecdb3
- Fix layout · 4cf04751
  Peter van 't Hof authored 10 years ago
  
  4cf04751
- Changed warning · e1ae0698
  Peter van 't Hof authored 10 years ago
  
  e1ae0698
- Resolve name conflict · d0f1a12b
  Peter van 't Hof authored 10 years ago
  
  d0f1a12b
- Adding dirty warning · 5150c6c3
  Peter van 't Hof authored 10 years ago
  
  5150c6c3
- Extract logging in a trait · 45b639a2
  Peter van 't Hof authored 10 years ago
  
  45b639a2
Nov 03, 2014
- Added imports · 071c8031
  Peter van 't Hof authored 10 years ago
  
  071c8031
- Remove val in for loops · 10a2a09b
  Peter van 't Hof authored 10 years ago
  
  10a2a09b
- Changed to SamReaderFactory · da908cbb
  Peter van 't Hof authored 10 years ago
  
  da908cbb
- Added index as output file · 9cc92504
  Peter van 't Hof authored 10 years ago
  
  9cc92504
- Added version cache · 16068896
  Peter van 't Hof authored 10 years ago
  
  16068896
Oct 31, 2014
- More tests to guard against BAM query sorting error · 37bb8e35
  bow authored 10 years ago
  
  37bb8e35
- Fix for BAM query sorting order · 57145398
  bow authored 10 years ago
  
  57145398
- ExtractAlignedFastq fix for FASTQ records with descriptions · 1b93ce1c
  bow authored 10 years ago
  
  1b93ce1c
- Update refFlat parser to account for 0-based coordinate · 96d99632
  bow authored 10 years ago
  
  96d99632
- Add test for overlapping intervals · 92dd97f7
  bow authored 10 years ago
  
  92dd97f7
- Add test for unexpected interval file · deeadcca
  bow authored 10 years ago
  
  deeadcca
- Removing trait · d5ef9763
  wyleung authored 10 years ago
  
  d5ef9763
- Set test dependencies scope correctly · f8b9d901
  bow authored 10 years ago
  
  f8b9d901
- Add GTF support · 72584458
  bow authored 10 years ago
  
  72584458
- Added RAxml extension · 74f96c80
  Peter van 't Hof authored 10 years ago
  
  74f96c80
- Code cleanup · fd13448d
  bow authored 10 years ago
  
  fd13448d
- Add refFlat support · 9a00253e
  bow authored 10 years ago
  
  9a00253e
- Converting GATK VariantEval to Queue, wraps around to respect the · 0de6794f
  wyleung authored 10 years ago
  0de6794f
- Add test for different chromosome overlap · 94a2b3dd
  bow authored 10 years ago
  
  94a2b3dd
Oct 30, 2014
- Turn on deprecation warning and feature warning for the scala compiler · 8fe0a2bb
  bow authored 10 years ago
  
  8fe0a2bb
- prettify pom.xml · 4cc2d991
  bow authored 10 years ago
  
  4cc2d991
- Test updates · 97a3c3dc
  bow authored 10 years ago
  
  97a3c3dc
- Use mocks to avoid writing to disk when testing · 879c66bb
  bow authored 10 years ago
  
  879c66bb
- Add tests for CLI args parsing · 118f09c8
  bow authored 10 years ago
  
  118f09c8
- Remove explicit null use in WipeReads · 0fc60f0c
  bow authored 10 years ago
  
  0fc60f0c
- Refactor to use htsjdk in GATK 3.3 · 7dac383c
  bow authored 10 years ago
  
  7dac383c
Oct 29, 2014
- Initial switch to samtools.util.Interval from tribble.index.Interval · e7ee6eb0
  bow authored 10 years ago
  
  e7ee6eb0
- Remove all explicit null use in ExtractAlignedFastq · f4893563
  bow authored 10 years ago
  
  f4893563