Commits · a33d9fd2da78622c02748573be19d023cea8b2a4 · Mirrors / biopet.biopet

Jun 19, 2014
- 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
- now uses direct class file · a34d5672
  Peter van 't Hof authored 10 years ago
  
  a34d5672
- no merging when map is still empty · 667f417f
  Peter van 't Hof authored 10 years ago
  
  667f417f
- 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
- Better subprocess · 3f393b6d
  Peter van 't Hof authored 10 years ago
  
  3f393b6d
- Added BiopetCommandlineFunction · bd8a2a63
  Peter van 't Hof authored 10 years ago
  
  All commandlinefunctions now extends from this trait
  bd8a2a63
- Fixed env value · c4bdd49e
  Peter van 't Hof authored 10 years ago
  
  c4bdd49e
- Fixed default runname · 8c4f3b7c
  Peter van 't Hof authored 10 years ago
  
  8c4f3b7c
Jun 13, 2014
- Merge branch 'refactor_core-funcs' into 'master' · 02b6241f
  Peter van 't Hof authored 10 years ago
  
  Refactor core funcs
  02b6241f
- 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
- SplitNCigarReads now before indel realign · 35f10a6b
  Peter van 't Hof authored 10 years ago
  
  35f10a6b
- Changed filenames of bam files at star · 3990eb3f
  Peter van 't Hof authored 10 years ago
  
  3990eb3f
- Added outFileNamePrefix option · 7d08761a
  Peter van 't Hof authored 10 years ago
  
  7d08761a
Jun 09, 2014
- Added rna mode for inputtype · d46c0d7d
  Peter van 't Hof authored 10 years ago
  
  d46c0d7d
- Added star 2pass mode · 3c2d0da7
  Peter van 't Hof authored 10 years ago
  
  3c2d0da7
- Changed env variable for config to BIOPET_CONFIG · 4ca753b0
  Peter van 't Hof authored 10 years ago
  
  4ca753b0
- getThreads function implemented in gatk functions · 7e7762a9
  Peter van 't Hof authored 10 years ago
  
  7e7762a9
- 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
- Switched to InProcessFunction, no cluster job needed for ln commands · 709f5517
  Peter van 't Hof authored 10 years ago
  
  709f5517
Jun 06, 2014
- Fixed bug on single end runs · 27ec36f7
  Peter van 't Hof authored 10 years ago
  
  27ec36f7
- Changed key names of get functions · 8a3d69a0
  Peter van 't Hof authored 10 years ago
  
  8a3d69a0
- Changed native linking · 539afc89
  Peter van 't Hof authored 10 years ago
  
  539afc89
- Added getThreads function · 17ebb979
  Peter van 't Hof authored 10 years ago
  
  17ebb979
- Added merge config · 5a4df715
  Peter van 't Hof authored 10 years ago
  
  5a4df715
- Raise of an error at wrong JSON format · 03e66819
  Peter van 't Hof authored 10 years ago
  
  03e66819
- Merge branch 'master' of git.lumc.nl:biopet/biopet · 82cee4c6
  Peter van 't Hof authored 10 years ago
  
  82cee4c6
Jun 05, 2014
- Raise an error if the JSON file for configs is not properly formatted in JSON · 84c365c7
  wyleung authored 10 years ago
  
  84c365c7
- Changed glogal config to global config · 2cec3511
  sajvanderzeeuw authored 10 years ago
  
  2cec3511
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