Commits · b808493584a7de36bd63d54e356584720dbc4e98 · Mirrors / biopet.biopet

Feb 09, 2015
- Remove required from config calls · b8084935
  Peter van 't Hof authored 10 years ago
  
  b8084935
- Removed required argument for config, now handled by conversions, not a option means required · b7fe37de
  Peter van 't Hof authored 10 years ago
  
  b7fe37de
Feb 06, 2015
- Fix for error handling · e3964450
  Peter van 't Hof authored 10 years ago
  
  e3964450
- Refactor code · 2757c868
  Peter van 't Hof authored 10 years ago
  
  2757c868
- Added inverted output file · 4d20276b
  Peter van 't Hof authored 10 years ago
  
  4d20276b
- Add --id and --id-file option · 14300afa
  Peter van 't Hof authored 10 years ago
  
  14300afa
- Add --no-bgfs option · 0999885a
  Peter van 't Hof authored 10 years ago
  
  0999885a
- Fix NullPointerException caused by Option[File] being null · c78ca1be
  bow authored 10 years ago
  
  c78ca1be
Feb 05, 2015
- Remove redundant check on outputDir character · 700ced12
  bow authored 10 years ago
  
  700ced12
- Make setting the tdf/wig less restrictive and no default names anymore · e929b76a
  Wai Yi Leung authored 10 years ago
  
  e929b76a
- Fix bug on vmem · fb215ab1
  Peter van 't Hof authored 10 years ago
  
  fb215ab1
- Making the output files Option[File], and use Some() to verify whether it was set or not · b2da50cb
  Wai Yi Leung authored 10 years ago
  
  b2da50cb
- Enables manual set of jobOutputFile · b36e7c85
  Peter van 't Hof authored 10 years ago
  
  b36e7c85
- Added basic testing · 74f11c8e
  Peter van 't Hof authored 10 years ago
  
  74f11c8e
- Switch to case classes · 0c2b2242
  Peter van 't Hof authored 10 years ago
  
  0c2b2242
- Fix warning on max color · a4a4697f
  Peter van 't Hof authored 10 years ago
  
  a4a4697f
- Fix typo bug · a12e3ec3
  Peter van 't Hof authored 10 years ago
  
  a12e3ec3
- Added more general stats · 0f888fd4
  Peter van 't Hof authored 10 years ago
  
  0f888fd4
- Added scala docs · f913516e
  Peter van 't Hof authored 10 years ago
  
  f913516e
Feb 04, 2015
- Fix bug in gubbins output · e5e7978f
  Peter van 't Hof authored 10 years ago
  
  e5e7978f
- Added vcfstats to gatk pipeline · 5121ff20
  Peter van 't Hof authored 10 years ago
  
  5121ff20
- Added queue wrapper · 3ce22c45
  Peter van 't Hof authored 10 years ago
  
  3ce22c45
- Change name · 9c0409f6
  Peter van 't Hof authored 10 years ago
  
  9c0409f6
- Added general stats · 11a6c2db
  Peter van 't Hof authored 10 years ago
  
  11a6c2db
- Reverse colors on heatmap · 612be8f7
  Peter van 't Hof authored 10 years ago
  
  612be8f7
- Added better debug information for the R scripts · 2945cb4a
  Peter van 't Hof authored 10 years ago
  
  2945cb4a
- Added AD fields · 41064621
  Peter van 't Hof authored 10 years ago
  
  41064621
- Added thread scattering · fd22b885
  Peter van 't Hof authored 10 years ago
  
  fd22b885
- Change some options · fa32164f
  Peter van 't Hof authored 10 years ago
  
  fa32164f
Feb 03, 2015
- Fix checks · fd8a4043
  Peter van 't Hof authored 10 years ago
  
  fd8a4043
- Skip extractIfNeeded on R2 when not paired · 481a7a96
  Peter van 't Hof authored 10 years ago
  
  481a7a96
- Change on empty string check · 2838b39a
  Peter van 't Hof authored 10 years ago
  
  2838b39a
- Remove todo · 33a8edef
  Peter van 't Hof authored 10 years ago
  
  33a8edef
- Change to option types · 71eb5183
  Peter van 't Hof authored 10 years ago
  
  71eb5183
- No null returns at files and strings · ffc5158b
  Peter van 't Hof authored 10 years ago
  
  ffc5158b
- Expose sample ID and library ID as command line flags in mapping pipeline · 904a99b9
  bow authored 10 years ago
  
  904a99b9
- Use requirements check on mapping and flexiprep pipeline · a9c9dfbd
  bow authored 10 years ago
  
  a9c9dfbd
- Rename libraryId -> libId for consistency · ad0c55bc
  bow authored 10 years ago
  
  ad0c55bc
- Expose Flexiprep sampleId and libraryId back to the command line · daf3d591
  bow authored 10 years ago
  
  daf3d591
- Reducing the wrapper to take bam and chrom.sizes file only · 92fd93df
  Wai Yi Leung authored 10 years ago
  
  92fd93df