Commits · f9649b70b16501377689fafb9464b22c0ec39e7b · Mirrors / biopet.biopet

26 Aug, 2015 1 commit
- Adding a scatter method · f9649b70
  Peter van 't Hof authored Aug 26, 2015
  
  f9649b70
25 Aug, 2015 13 commits
- Merge remote-tracking branch 'origin/develop' into feature-region_af_count · 0bc82cb9
  Peter van 't Hof authored Aug 25, 2015
  
  0bc82cb9
- Merge branch 'fix-aligners' into 'develop' · d3473e22
  Sander Bollen authored Aug 25, 2015
```
Fix aligners

Some aligner are failing in testing, this should fix those issues

See merge request !217
```
  d3473e22
- Merge branch 'fix-index_output_mergeSam' into 'develop' · 8b320e53
  Sander Bollen authored Aug 25, 2015
```
Adding index file as output file for queue

Small fix to add the index file as output file for queue

See merge request !219
```
  8b320e53
- changed error to warn · 33c54c0a
  Peter van 't Hof authored Aug 25, 2015
  
  33c54c0a
- Added more, now almost 100% coverage · f4e40a13
  Peter van 't Hof authored Aug 25, 2015
  
  f4e40a13
- Added write header to writeToFile · cac5d7d3
  Peter van 't Hof authored Aug 25, 2015
  
  cac5d7d3
- Adding index file as output file for queue · 9ce8c169
  Peter van 't Hof authored Aug 25, 2015
  
  9ce8c169
- Writing and removing test files · 3db7fce6
  Peter van 't Hof authored Aug 25, 2015
  
  3db7fce6
- Adding toSamInterval method · 09f73ff6
  Peter van 't Hof authored Aug 25, 2015
  
  09f73ff6
- Adding ExonIntronOverlap test · 7d95212a
  Peter van 't Hof authored Aug 25, 2015
  
  7d95212a
- Adde more test for BedRecord · 163192f0
  Peter van 't Hof authored Aug 25, 2015
  
  163192f0
- Adding basic testing · cd041e3f
  Peter van 't Hof authored Aug 25, 2015
  
  cd041e3f
- Change to IndexedSeq · 41a9e407
  Peter van 't Hof authored Aug 25, 2015
  
  41a9e407
24 Aug, 2015 16 commits
- Correct 1-based to 0 based · a99720fa
  Peter van 't Hof authored Aug 24, 2015
  
  a99720fa
- Switch wipereads to biopet bed reader · dc8933b8
  Peter van 't Hof authored Aug 24, 2015
  
  dc8933b8
- Switch to biopet bed parser · 02b7c60e
  Peter van 't Hof authored Aug 24, 2015
  
  02b7c60e
- Moved clode statement to finally · bb0853a7
  Peter van 't Hof authored Aug 24, 2015
  
  bb0853a7
- Added close to reader · 8faed309
  Peter van 't Hof authored Aug 24, 2015
  
  8faed309
- Change name · 6ede8254
  Peter van 't Hof authored Aug 24, 2015
  
  6ede8254
- Fixed statement · e9a3492b
  Peter van 't Hof authored Aug 24, 2015
  
  e9a3492b
- Added a check for tophat on index files · 9dca30a7
  Peter van 't Hof authored Aug 24, 2015
  
  9dca30a7
- Added auto detect on large indexes for bowtie · 27db07f0
  Peter van 't Hof authored Aug 24, 2015
  
  27db07f0
- Remove unused values · bfb88721
  Peter van 't Hof authored Aug 24, 2015
  
  bfb88721
- Refactor RegionAfCount, 10-20 times faster now · cedd54be
  Peter van 't Hof authored Aug 24, 2015
  
  cedd54be
- Sets utrs to None when not existing · 2b62e291
  Peter van 't Hof authored Aug 24, 2015
  
  2b62e291
- Move combine method inside class · 186b5775
  Peter van 't Hof authored Aug 24, 2015
  
  186b5775
- Fix match · 92f6a098
  Peter van 't Hof authored Aug 24, 2015
  
  92f6a098
- switch exons en introns to simple lists · 35315f22
  Peter van 't Hof authored Aug 24, 2015
  
  35315f22
- Added utr features · f365755d
  Peter van 't Hof authored Aug 24, 2015
  
  f365755d
23 Aug, 2015 6 commits
- Added UCSC header skipping · 68b01fdc
  Peter van 't Hof authored Aug 23, 2015
  
  68b01fdc
- Added validation · 2ecea204
  Peter van 't Hof authored Aug 23, 2015
  
  2ecea204
- Change _originals to val · 0e3d6e9f
  Peter van 't Hof authored Aug 23, 2015
  
  0e3d6e9f
- Added lengths · 38d3970e
  Peter van 't Hof authored Aug 23, 2015
  
  38d3970e
- cached sorting · 3483a1be
  Peter van 't Hof authored Aug 23, 2015
  
  3483a1be
- Full bed record output · 66ce14ba
  Peter van 't Hof authored Aug 23, 2015
  
  66ce14ba
22 Aug, 2015 4 commits
- Add nested option to originals · 22064e83
  Peter van 't Hof authored Aug 22, 2015
  
  22064e83
- Adding some logging · fb9e71f4
  Peter van 't Hof authored Aug 22, 2015
  
  fb9e71f4
- Switch to originals · 59ae18bd
  Peter van 't Hof authored Aug 22, 2015
  
  59ae18bd
- Fixed isSorted val · 31a37666
  Peter van 't Hof authored Aug 22, 2015
  
  31a37666