Commits · 13da13e9a6ab5bb4f8f43bbfb901ffc84f295076 · Mirrors / biopet.biopet

07 Oct, 2014 40 commits
- Simplify ToolCommand.toolName value · 13da13e9
  bow authored Oct 07, 2014
  
  13da13e9
- Remove strand option in WipeReads · 3a29a0ca
  bow authored Oct 07, 2014
  
  3a29a0ca
- Add explicit system exit points in main jar · 9c612125
  bow authored Oct 07, 2014
  
  9c612125
- Fix typo · e725e48b
  bow authored Oct 07, 2014
  
  e725e48b
- Add WipeReads to main command line interface · 179d9f01
  bow authored Oct 07, 2014
  
  179d9f01
- Improve main command line interface · 9e5f2608
  bow authored Oct 07, 2014
  
  9e5f2608
- Create interval tree map lazily in WipeReads · 46cfaf0e
  bow authored Oct 06, 2014
  
  46cfaf0e
- Update WipeReads to take splicing structure into account when finding overlaps · d5e6eb8c
  bow authored Oct 06, 2014
  
  d5e6eb8c
- Update SAMRecord equality test to test as file is iterated · c8e494d2
  bow authored Oct 06, 2014
  
  c8e494d2
- Code reformat + unused import removal in WipeReads · 657702dc
  bow authored Oct 06, 2014
  
  657702dc
- WipeReads docs wrap up · ca6ddab9
  bow authored Oct 06, 2014
  
  ca6ddab9
- Add test for filteredBAM output in WipeReads · c7c41ef6
  bow authored Oct 06, 2014
  
  c7c41ef6
- Initial complete main WipeReads function implementation · 3113399f
  bow authored Oct 05, 2014
  
  3113399f
- Allow for .bam.bai or .bai extension · cb1f06d1
  bow authored Oct 05, 2014
  
  cb1f06d1
- Add initial BAM writing function in WipeReads · 04599e18
  bow authored Oct 05, 2014
  
  04599e18
- Update WipeReads test cases · c16a5040
  bow authored Oct 05, 2014
  
  c16a5040
- Refactor set-creating function to output set membership function in WipeReads · 457d3655
  bow authored Oct 05, 2014
  
  457d3655
- Add more unit tests for WipeReads · e6fbe498
  bow authored Oct 05, 2014
  
  e6fbe498
- Update WipeReads mate query to propagate exceptions · 5b340f1e
  bow authored Oct 05, 2014
  
  5b340f1e
- Add tests for WipeReads overlap finders · 149f43d4
  bow authored Oct 04, 2014
  
  149f43d4
- Refactor query interval builder for fewer BAM objects · d502cf63
  bow authored Oct 03, 2014
  
  d502cf63
- Refactor set builder function in WipeReads · a748e6fa
  bow authored Oct 03, 2014
  
  a748e6fa
- Various small fixes for testing · 05959d3b
  bow authored Oct 02, 2014
  
  05959d3b
- Add function for set filtering in WipeReads · 1e0a70bb
  bow authored Oct 02, 2014
  
  1e0a70bb
- Nest interval file parser functions and case class · 2fe0577e
  bow authored Oct 02, 2014
  
  2fe0577e
- Add algebird dependency · 4ec31659
  bow authored Oct 02, 2014
  
  4ec31659
- Update rrna01.bed test dataset · e8659c03
  bow authored Oct 02, 2014
  
  e8659c03
- Update access modifiers for WipeReads functions · 7b78d005
  bow authored Oct 02, 2014
  
  7b78d005
- Update enumerated strand options · 9cd1b9d7
  bow authored Oct 02, 2014
  
  9cd1b9d7
- Add initial functions to parse interval from file · cbf4d93c
  bow authored Oct 02, 2014
  
  cbf4d93c
- Use Vector instead of Seq for multiple argument flag in WipeReads · ec703d07
  bow authored Oct 01, 2014
  
  ec703d07
- Update WipeReads usage message · f76745df
  bow authored Oct 01, 2014
  
  f76745df
- Use Seq instead of Array for immutability + easier comparison · b397262c
  bow authored Sep 30, 2014
  
  b397262c
- Finalize WipeReads command line parser and its tests · 337a2abe
  bow authored Sep 30, 2014
  
  337a2abe
- Add .gitattributes file · 41406ae4
  bow authored Sep 30, 2014
  
  41406ae4
- Add dependency for scalatest · f5b5eeb9
  bow authored Sep 30, 2014
  
  f5b5eeb9
- Initial app for WipeReads · 1ef79dd4
  bow authored Sep 29, 2014
  
  1ef79dd4
- Remove un deed lines for template · d1b18339
  Peter van 't Hof authored Oct 07, 2014
  
  d1b18339
- Fix small bugs · a4b640e8
  Peter van 't Hof authored Oct 07, 2014
  
  a4b640e8
- Added defaults example · 8a8fb7f7
  Peter van 't Hof authored Oct 07, 2014
  
  8a8fb7f7