Commits · 38022912115b44c1e6b6abb530fcf4d5002561b6 · Mirrors / biopet.biopet

Sep 08, 2015
- Remove sumarizable from seqtk · 38022912
  Peter van 't Hof authored 9 years ago
  
  38022912
- Switch seqstat to init jobs · 94d9ba32
  Peter van 't Hof authored 9 years ago
  
  94d9ba32
- Adding stdin · 37e92018
  Peter van 't Hof authored 9 years ago
  
  37e92018
Sep 07, 2015
- Adding '>' method · 1b4d398c
  Peter van 't Hof authored 9 years ago
  
  1b4d398c
- Added '|' method · dda6094a
  Peter van 't Hof authored 9 years ago
  
  dda6094a
Sep 06, 2015
- Remove unneeded class. java and non-java jobs now both using def cmdLine · c8b89f97
  Peter van 't Hof authored 9 years ago
  
  c8b89f97
Sep 04, 2015
- Changing to SNAPSHOT version, this is following the maven convention · f550b637
  Peter van 't Hof authored 9 years ago
  
  f550b637
Sep 03, 2015

Fix strand-specific separation in Gentrap · 665bf70c

bow authored 9 years ago

This fixes a bug caused by incorrect creation of plus and minus strand BAM files.
It was caused by incorrectly specifying the SAM flags, causing the plus and minus
strand BAM files to still contain mixed strand reads.

665bf70c

Aug 31, 2015
- Scalariform needs a non empty src dir · 3a400454
  Peter van 't Hof authored 9 years ago
  
  3a400454
- Fix for #198 · 9253685c
  Sander Bollen authored 9 years ago
  
  9253685c
Aug 29, 2015
- Replace getCanonicalPath for getAbsolutePath · f7de2300
  Peter van 't Hof authored 9 years ago
  
  f7de2300
Aug 28, 2015
- No chunk_metrics when chunking is disabled · 04adff67
  Peter van 't Hof authored 9 years ago
  
  04adff67
- Now it does only the files of 1 module · 60ca1247
  Peter van 't Hof authored 9 years ago
  
  60ca1247
Aug 27, 2015
- Remove squish bed python script · 287e118d
  Peter van 't Hof authored 9 years ago
  
  287e118d
- 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
- Added picard R scipts as workaround till issue is resolved · 000e2882
  Peter van 't Hof authored 9 years ago
  
  000e2882
- 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
- Fixed testing · 02733716
  Peter van 't Hof authored 9 years ago
  
  02733716
- 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