Commits · 2a2a37fd6d5c5c420ee90e917dec807ac453387e · Mirrors / biopet.biopet

Jul 27, 2014
- Function to get encoding of the fastq file, replaces python script · 2a2a37fd
  Peter van 't Hof authored 10 years ago
  
  2a2a37fd
- Fix on output variable · 096d8a0e
  Peter van 't Hof authored 10 years ago
  
  096d8a0e
- - Moved constructor to function itself · 16a08dfd
  Peter van 't Hof authored 10 years ago
  
  - Add extract option to fastqc
  16a08dfd
Jul 23, 2014
- Update imports style order · bf372d9a
  bow authored 10 years ago
  
  bf372d9a
- Update code style using scalariform · 02b571a4
  bow authored 10 years ago
  
  02b571a4
Jul 22, 2014
- Changes in config class · 6294de9f
  Peter van 't Hof authored 10 years ago
  
  6294de9f
Jul 21, 2014
- Spelling error · 95ba716f
  Peter van 't Hof authored 10 years ago
  
  95ba716f
- Collected all gatk pipelines/artifacts into 1 maven project · 2f47af7e
  Peter van 't Hof authored 10 years ago
  
  2f47af7e
- Collected all gatk pipelines/artifacts into 1 maven project · 79435a29
  Peter van 't Hof authored 10 years ago
  
  79435a29
Jul 18, 2014
- update for Queue/GATK 3.2-2 · 62ed4c90
  Peter van 't Hof authored 10 years ago
  
  62ed4c90
Jul 15, 2014
- Update to Queue/GATK 3.2 · 0a33b3d3
  Peter van 't Hof authored 10 years ago
  
  0a33b3d3
- intial unzipped file is intermediate now · 2e45f064
  Peter van 't Hof authored 10 years ago
  
  2e45f064
- Option to skip summary · 9be7a784
  Peter van 't Hof authored 10 years ago
  
  9be7a784
Jul 03, 2014
- codestyle fix · e626880a
  Peter van 't Hof authored 10 years ago
  
  e626880a
- changed version command to def · c340b559
  Peter van 't Hof authored 10 years ago
  
  c340b559
Jun 27, 2014
- fix analysisName on Ln · 27db54a8
  Peter van 't Hof authored 10 years ago
  
  27db54a8
- Added chunking for mapping · b7690fca
  Peter van 't Hof authored 10 years ago
  
  b7690fca
Jun 26, 2014
- fixed call to sub pipeline · 6090fa33
  Peter van 't Hof authored 10 years ago
  
  6090fa33
Jun 23, 2014
- pom changes for start of 0.1.3 · 9e9e6022
  Peter van 't Hof authored 10 years ago
  
  9e9e6022
- Added bz2 support · 66dc8af2
  Peter van 't Hof authored 10 years ago
  
  66dc8af2
- Changed constructors · ea4f80e1
  Peter van 't Hof authored 10 years ago
  
  ea4f80e1
Jun 21, 2014
- Config changed · c22acb87
  Peter van 't Hof authored 10 years ago
  
  c22acb87
Jun 19, 2014
- Readme changed to README.md · cfee098a
  Peter van 't Hof authored 10 years ago
  
  cfee098a
- Readme changed to README.md · a33d9fd2
  Peter van 't Hof authored 10 years ago
  
  a33d9fd2
- Path to class for main class changed · 90e96f6c
  Peter van 't Hof authored 10 years ago
  
  90e96f6c
- Code style changes · a2c2e0fc
  Peter van 't Hof authored 10 years ago
  
  a2c2e0fc
- Packaging changed, no scala compiler anymore in jar · 27de6356
  Peter van 't Hof authored 10 years ago
  
  27de6356
Jun 17, 2014
- version changes · f0705ac8
  Peter van 't Hof authored 10 years ago
  
  removing source files from jar packaging
  f0705ac8
- No inline functions extending anymore · 69ba3389
  Peter van 't Hof authored 10 years ago
  
  69ba3389
- Added BiopetCommandlineFunction · bd8a2a63
  Peter van 't Hof authored 10 years ago
  
  All commandlinefunctions now extends from this trait
  bd8a2a63
Jun 13, 2014
- Rename directories and package identifiers for consistency with Queue · 4e14ca72
  bow authored 10 years ago
  
  4e14ca72
Jun 12, 2014
- Extends directly on Python · fcaccd90
  Peter van 't Hof authored 10 years ago
  
  fcaccd90
- Skipped compiling step at init phase of pipeline · e031256a
  Peter van 't Hof authored 10 years ago
  
  e031256a
Jun 10, 2014
- example jsons changed/added · 5b01a7d9
  Peter van 't Hof authored 10 years ago
  
  5b01a7d9
Jun 09, 2014
- deps not required · 50dc06bb
  Peter van 't Hof authored 10 years ago
  
  50dc06bb
- fixed bug on skip arguments · dc3bc04f
  Peter van 't Hof authored 10 years ago
  
  fixed output file when input file is not zipped skipping final seqstat and sha1sum when skipclip and skiptrim is true
  dc3bc04f
Jun 06, 2014
- Fixed bug on single end runs · 27ec36f7
  Peter van 't Hof authored 10 years ago
  
  27ec36f7
- Changed native linking · 539afc89
  Peter van 't Hof authored 10 years ago
  
  539afc89
- Added merge config · 5a4df715
  Peter van 't Hof authored 10 years ago
  
  5a4df715
Jun 04, 2014
- Added vmem option and uses by default 4G · f732e3ea
  Peter van 't Hof authored 10 years ago
  
  f732e3ea