Commits · 292cae4e69145e9955eef59f8bba1c11fe5ab717 · Mirrors / biopet.biopet

Aug 27, 2015
- Switch to squishBed tool · 292cae4e
  Peter van 't Hof authored 9 years ago
  
  292cae4e
- Added squish bed extension · 63090796
  Peter van 't Hof authored 9 years ago
  
  63090796
- Code style fix · 3e58bd92
  Peter van 't Hof authored 9 years ago
  
  3e58bd92
- Change val name · bb5776d8
  Peter van 't Hof authored 9 years ago
  
  bb5776d8
- Added a method to validate contigs · 877f613f
  Peter van 't Hof authored 9 years ago
  
  877f613f
- Change to BedRecordsList for scattering · 9f7e5ddb
  Peter van 't Hof authored 9 years ago
  
  9f7e5ddb
- Added test to check for overlap between scatters · 5c583841
  Peter van 't Hof authored 9 years ago
  
  5c583841
Aug 26, 2015
- Adding method to test scatter · 63a27a65
  Peter van 't Hof authored 9 years ago
  
  63a27a65
- Adding method to test scatter · 451f437f
  Peter van 't Hof authored 9 years ago
  
  451f437f
- Added fromReference method · 8bf01dfa
  Peter van 't Hof authored 9 years ago
  
  8bf01dfa
- Adding a scatter method · f9649b70
  Peter van 't Hof authored 9 years ago
  
  f9649b70
- Raised memory for star · 0eabe6be
  Peter van 't Hof authored 9 years ago
  
  0eabe6be
Aug 25, 2015
- Fixed tophat unittests · 3644ce72
  Peter van 't Hof authored 9 years ago
  
  3644ce72
- changed error to warn · 33c54c0a
  Peter van 't Hof authored 9 years ago
  
  33c54c0a
- Added more, now almost 100% coverage · f4e40a13
  Peter van 't Hof authored 9 years ago
  
  f4e40a13
- Added write header to writeToFile · cac5d7d3
  Peter van 't Hof authored 9 years ago
  
  cac5d7d3
- Adding index file as output file for queue · 9ce8c169
  Peter van 't Hof authored 9 years ago
  
  9ce8c169
- Writing and removing test files · 3db7fce6
  Peter van 't Hof authored 9 years ago
  
  3db7fce6
- Adding toSamInterval method · 09f73ff6
  Peter van 't Hof authored 9 years ago
  
  09f73ff6
- Adding ExonIntronOverlap test · 7d95212a
  Peter van 't Hof authored 9 years ago
  
  7d95212a
- Adde more test for BedRecord · 163192f0
  Peter van 't Hof authored 9 years ago
  
  163192f0
- Adding basic testing · cd041e3f
  Peter van 't Hof authored 9 years ago
  
  cd041e3f
- Change to IndexedSeq · 41a9e407
  Peter van 't Hof authored 9 years ago
  
  41a9e407
Aug 24, 2015
- Correct 1-based to 0 based · a99720fa
  Peter van 't Hof authored 9 years ago
  
  a99720fa
- Switch wipereads to biopet bed reader · dc8933b8
  Peter van 't Hof authored 9 years ago
  
  dc8933b8
- Switch to biopet bed parser · 02b7c60e
  Peter van 't Hof authored 9 years ago
  
  02b7c60e
- Moved clode statement to finally · bb0853a7
  Peter van 't Hof authored 9 years ago
  
  bb0853a7
- Added close to reader · 8faed309
  Peter van 't Hof authored 9 years ago
  
  8faed309
- Change name · 6ede8254
  Peter van 't Hof authored 9 years ago
  
  6ede8254
- Fixed statement · e9a3492b
  Peter van 't Hof authored 9 years ago
  
  e9a3492b
- Added a check for tophat on index files · 9dca30a7
  Peter van 't Hof authored 9 years ago
  
  9dca30a7
- Added auto detect on large indexes for bowtie · 27db07f0
  Peter van 't Hof authored 9 years ago
  
  27db07f0
- Remove unused values · bfb88721
  Peter van 't Hof authored 9 years ago
  
  bfb88721
- Refactor RegionAfCount, 10-20 times faster now · cedd54be
  Peter van 't Hof authored 9 years ago
  
  cedd54be
- Sets utrs to None when not existing · 2b62e291
  Peter van 't Hof authored 9 years ago
  
  2b62e291
- Move combine method inside class · 186b5775
  Peter van 't Hof authored 9 years ago
  
  186b5775
- Fix match · 92f6a098
  Peter van 't Hof authored 9 years ago
  
  92f6a098
- switch exons en introns to simple lists · 35315f22
  Peter van 't Hof authored 9 years ago
  
  35315f22
- Added utr features · f365755d
  Peter van 't Hof authored 9 years ago
  
  f365755d
Aug 23, 2015
- Added UCSC header skipping · 68b01fdc
  Peter van 't Hof authored 9 years ago
  
  68b01fdc