Commits · cb72d450e5f05da613d2904ea88194fbb564063b · Mirrors / biopet.biopet

Jun 26, 2014
- Added Intermediate files · cb72d450
  Peter van 't Hof authored 10 years ago
  
  cb72d450
Jun 23, 2014
- pom changes for start of 0.1.3 · 9e9e6022
  Peter van 't Hof authored 10 years ago
  
  9e9e6022
- memory multiples by the number of threads · a779a651
  Peter van 't Hof authored 10 years ago
  
  a779a651
- Added bz2 support · 66dc8af2
  Peter van 't Hof authored 10 years ago
  
  66dc8af2
- Also a class for JavaCommandLineTools · f54fc743
  Peter van 't Hof authored 10 years ago
  
  f54fc743
- Thread options does not work anymore from QScript · b9325173
  Peter van 't Hof authored 10 years ago
  
  b9325173
- Moved getThreads to BiopetCommandLineFunction · a4bacc87
  Peter van 't Hof authored 10 years ago
  
  a4bacc87
- Changed constructors · ea4f80e1
  Peter van 't Hof authored 10 years ago
  
  ea4f80e1
- Full funcional object now, root need to be in the constructor of class · c7abaef3
  Peter van 't Hof authored 10 years ago
  
  c7abaef3
- Move init msg out of the sub-constructor and changed to debug · 869e1851
  Peter van 't Hof authored 10 years ago
  
  869e1851
- General QScript with default configfiles, outputDir and outputFiles · d60a291a
  Peter van 't Hof authored 10 years ago
  
  d60a291a
- Separated multisample functions to an other class · 027a6ff3
  Peter van 't Hof authored 10 years ago
  
  027a6ff3
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
- 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