Commits · 1b93ce1c44350f98cc98c2d5dbb9e8c732356589 · Mirrors / biopet.biopet

Oct 31, 2014
- 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
- 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
- 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
- More main test · 1f5b341b
  bow authored 10 years ago
  
  1f5b341b
- Initial test for main function · c1fd16a8
  bow authored 10 years ago
  
  c1fd16a8
- Use Option typeclass for optional CLI flag · ddd29d64
  bow authored 10 years ago
  
  ddd29d64
Oct 28, 2014
- Remove redundant validation · 47decd35
  bow authored 10 years ago
  
  47decd35
- Removing ticks surrounding filenames.. causing command to fail · 5af8e333
  wyleung authored 10 years ago
  
  5af8e333
- Build with scaliform · cc8b2760
  Peter van 't Hof authored 10 years ago
  
  cc8b2760
- #57, tool is now feature complete · b3957406
  wyleung authored 10 years ago
  
  b3957406
- Moved Sage tools to nl.lumc.biopet.tools · 6f44aea3
  Peter van 't Hof authored 10 years ago
  
  6f44aea3
- Breakdancer, scaliform reformat · 24f1405c
  wyleung authored 10 years ago
  
  24f1405c
- make intermediate fastq · d09f9f9d
  sajvanderzeeuw authored 10 years ago
  
  d09f9f9d
- fix on R2 output name · 3f86e487
  sajvanderzeeuw authored 10 years ago
  
  3f86e487
- fix on main class · ad12312d
  sajvanderzeeuw authored 10 years ago
  
  ad12312d
- Update to htsjdk use in GATK 3.3 · ef2a9acd
  bow authored 10 years ago
  
  ef2a9acd
Oct 27, 2014
- Add unit tests for file writing · cc6a184f
  bow authored 10 years ago
  
  cc6a184f
- Update write function to accept FASTQ readers and writers · 717bf892
  bow authored 10 years ago
  
  717bf892
- Add more CLI validation · bce349be
  bow authored 10 years ago
  
  bce349be
- Unit test updates · 4fb0abab
  bow authored 10 years ago
  
  4fb0abab
- Add functions to main · 7930bcb4
  bow authored 10 years ago
  
  7930bcb4
- Update input and output FASTQs argument flag names · b91de099
  bow authored 10 years ago
  
  b91de099
- Expose read suffix length argument to command line · 28c8e585
  bow authored 10 years ago
  
  28c8e585
- Add logging message when writing · b9ad17e8
  bow authored 10 years ago
  
  b9ad17e8
- Filter on MAPQ instead of read groups · fd7e403b
  bow authored 10 years ago
  
  fd7e403b