Commits · 66dc8af24f67b0d97027bcec74e06e7fd08f3ca5 · Mirrors / biopet.biopet

Jun 23, 2014
- 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
- Marked temp files as intermediate · 991903f5
  Peter van 't Hof authored 10 years ago
  
  991903f5
- Added dependencies list · b1a75245
  Peter van 't Hof authored 10 years ago
  
  b1a75245
- Removed Output annotation for stats file · 9a2897d8
  Peter van 't Hof authored 10 years ago
  
  9a2897d8
Jun 03, 2014
- Fixed package name · af1fde3f
  Peter van 't Hof authored 10 years ago
  
  af1fde3f
- Moved to flexiprep maven app · af141f38
  Peter van 't Hof authored 10 years ago
  
  af141f38
- No functional changes · 08a62d84
  Peter van 't Hof authored 10 years ago
  
  08a62d84
- Added dependencies for Flexiprep · d7fd1dad
  Peter van 't Hof authored 10 years ago
  
  d7fd1dad
- Changed filenames for compatible summarize script · 171522f4
  Peter van 't Hof authored 10 years ago
  
  171522f4
- Changed to make it compatible for new file structure · 97fd01f3
  Peter van 't Hof authored 10 years ago
  
  97fd01f3
- Added Summarize flexiprep wrapper · f9d9430b
  Peter van 't Hof authored 10 years ago
  
  f9d9430b
- Added Seqstat wrapper · a98ad7f7
  Peter van 't Hof authored 10 years ago
  
  a98ad7f7
May 27, 2014
- Added general trait (BiopetQScript) that now have multisample functions · 09190f82
  Peter van 't Hof authored 10 years ago
  
  09190f82
May 26, 2014
- Small changes on config setup · 8d195010
  Peter van 't Hof authored 10 years ago
  
  8d195010
- Added scala files to jar and added a main class for each pipeline · 302c6fff
  Peter van 't Hof authored 10 years ago
  
  302c6fff
- Added python parser to buildin python scripts · 2f38f1f1
  Peter van 't Hof authored 10 years ago
  
  2f38f1f1
- Added python scripts to jar file · 9519ee04
  Peter van 't Hof authored 10 years ago
  
  9519ee04
May 20, 2014

Peter van 't Hof authored 10 years ago

- Added a mapping module (not yet used in Gatk)
- Added VariantRecalibrator to Gatk

ca2905e5

May 15, 2014
- Remove submodules · b26d817a
  Peter van 't Hof authored 10 years ago
  
  b26d817a
- remove submodules · ffe46a1f
  Peter van 't Hof authored 10 years ago
  
  ffe46a1f