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
- Add GTF support · 72584458
  bow authored 10 years ago
  
  72584458
- Code cleanup · fd13448d
  bow authored 10 years ago
  
  fd13448d
- Add refFlat support · 9a00253e
  bow authored 10 years ago
  
  9a00253e
- 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
- 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
- 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
- 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
- Unit test updates · 4fb0abab
  bow authored 10 years ago
  
  4fb0abab
Oct 25, 2014
- Use DataProvider for testing multiple combinations · 6a492c14
  bow authored 10 years ago
  
  6a492c14
- Update tests and filter function name · 9c3639f6
  bow authored 10 years ago
  
  9c3639f6
- Initial working prototype · e6b0f47c
  bow authored 10 years ago
  
  e6b0f47c
Oct 23, 2014
- Short style update · 29cd9689
  bow authored 10 years ago
  
  29cd9689
Oct 22, 2014
- Comments update and code style refactor · 320f4a82
  bow authored 10 years ago
  
  320f4a82
- Update tests · f3ea203e
  bow authored 10 years ago
  
  f3ea203e
- Initial commit for ExtractAlignedFastq · 023de1ef
  bow authored 10 years ago
  
  023de1ef
Oct 21, 2014
- Expose bloom filter parameters in the command line · d4783368
  bow authored 10 years ago
  
  d4783368
Oct 20, 2014
- Fix missing test annotation import · 7ed44d6d
  bow authored 10 years ago
  
  7ed44d6d
- Move WipeReads test to correct directory · 6e48b13a
  bow authored 10 years ago
  
  6e48b13a
- Use htsjdk's BED reader and Feature object instead · a46706a1
  bow authored 10 years ago
  
  a46706a1
Oct 17, 2014
- Add record counting (excluded and included) · 84519616
  bow authored 10 years ago
  
  84519616
Oct 16, 2014
- Fix missed refactor (issue #29) · b4978ac1
  bow authored 10 years ago
  
  b4978ac1
Oct 13, 2014
- Fix missed refactor (issue #29) · 1061798d
  bow authored 10 years ago
  
  1061798d
- Use TestNGSuite and Matchers in Ln command test · 836eddf1
  bow authored 10 years ago
  
  836eddf1
- Use TestNGSuite and Matchers in WipeReads test · 57478950
  bow authored 10 years ago
  
  57478950
Oct 10, 2014
- Use common CLI argument parser for WipeReads · 0ea14304
  bow authored 10 years ago
  
  0ea14304
- More unit test for WipeReads · 634364dd
  bow authored 10 years ago
  
  634364dd