Commits · fd4a3055c6aadf55d7fdfc9d287043960047b67f · Mirrors / biopet.biopet

Aug 25, 2015
- Fixed testing · 02733716
  Peter van 't Hof authored 9 years ago
  
  02733716
- Adding index file as output file for queue · 9ce8c169
  Peter van 't Hof authored 9 years ago
  
  9ce8c169
Aug 24, 2015
- 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
Aug 19, 2015
- Remove env value · 3b86133f
  Peter van 't Hof authored 9 years ago
  
  3b86133f
- Fix star output files · 17dbf930
  Peter van 't Hof authored 9 years ago
  
  17dbf930
- fixed bowtie command · 855bd500
  Peter van 't Hof authored 9 years ago
  
  855bd500
- Fixed typo · c3c0fc09
  Peter van 't Hof authored 9 years ago
  
  c3c0fc09
Aug 18, 2015
- Changed default mode for VepNormalizer · e493a90b
  Peter van 't Hof authored 9 years ago
  
  e493a90b
- Fix indexes location of bowtie · 5a13b740
  Peter van 't Hof authored 9 years ago
  
  5a13b740
- Fix output file · eedeeeeb
  Peter van 't Hof authored 9 years ago
  
  (cherry picked from commit fb2fc695)
  eedeeeeb
Aug 17, 2015
- Fix inversion · 92ae5a49
  Peter van 't Hof authored 9 years ago
  
  92ae5a49
- Style fix · 5a765da5
  Peter van 't Hof authored 9 years ago
  
  5a765da5
- Added reference trait for tophat · 2765ff0c
  Peter van 't Hof authored 9 years ago
  
  (cherry picked from commit 73990f01)
  2765ff0c
Aug 16, 2015
- Adding workaround for issue #180 · 6b9c8e37
  Peter van 't Hof authored 9 years ago
  
  6b9c8e37
- Added an exeption when lines has not the same columns as the header · 4b3972ae
  Peter van 't Hof authored 9 years ago
  
  4b3972ae
- Added exeption on duplicate sample/libs · cbd73126
  Peter van 't Hof authored 9 years ago
  
  cbd73126
- Switched library to an Option[String] · 6645955e
  Peter van 't Hof authored 9 years ago
  
  6645955e
Aug 15, 2015
- Skipping parts of report when they are skipped in the pipeline · e07267db
  Peter van 't Hof authored 9 years ago
  
  e07267db
Aug 14, 2015
- Added a option to not keep the last fastq file anymore · d4e45996
  Peter van 't Hof authored 9 years ago
  
  d4e45996
Aug 12, 2015
- Review refactor · d55c2684
  Peter van 't Hof authored 9 years ago
  
  d55c2684
- Added a better error handling on a missing reference. · 002dd1c3
  Peter van 't Hof authored 9 years ago
  
  002dd1c3
- Added unit test for #186. Unit test passes. · 8829cb1b
  Sander Bollen authored 9 years ago
  
  8829cb1b
Aug 06, 2015
- remove parallel data providers · 03d9db7b
  Peter van 't Hof authored 9 years ago
  
  03d9db7b
- enable parallel data providers · 907c8ddb
  Peter van 't Hof authored 9 years ago
  
  907c8ddb
- Multitreaded testing · 1c8e147d
  Peter van 't Hof authored 9 years ago
  
  1c8e147d
- Changed dependency · a9fbdf3f
  Peter van 't Hof authored 9 years ago
  
  a9fbdf3f
- VcfFilter addition for musthavegenotypes. See #186. · 1bbf15aa
  Sander Bollen authored 9 years ago
  
  Ended up using HTSJDK nomenclature for genotype types I.e: HET, HOM_REF, HOM_VAR, MIXED, NO_CALL and UNAVAILABLE
  1bbf15aa
Aug 04, 2015
- Upgrade shade plugin version · 35b7f2ee
  Peter van 't Hof authored 9 years ago
  
  35b7f2ee
Aug 03, 2015
- Fix gears in executables · 9d3bdc2a
  Peter van 't Hof authored 9 years ago
  
  9d3bdc2a
- Review changes · e667ee49
  Peter van 't Hof authored 9 years ago
  
  e667ee49
- Fix for #184 · 2196bd9d
  Peter van 't Hof authored 9 years ago
  
  2196bd9d
- Removed the trait, no need for it · bc53f7e3
  Peter van 't Hof authored 9 years ago
  
  bc53f7e3
- Review changes to kraken · 11f01f92
  Peter van 't Hof authored 9 years ago
  
  11f01f92
Aug 01, 2015
- Fix unit test · d05d08f9
  Peter van 't Hof authored 9 years ago
  
  d05d08f9
- Improved unit test · 7f682612
  Peter van 't Hof authored 9 years ago
  
  7f682612
- Fix unit test · 93080450
  Peter van 't Hof authored 9 years ago
  
  93080450
- Fix inspection warnings · 9b8e7dd8
  Peter van 't Hof authored 9 years ago
  
  9b8e7dd8
- Adding exac annotation step · 046d7d2b
  Peter van 't Hof authored 9 years ago
  
  046d7d2b