Commits · 5b01a7d9fbe7323dcdf0a694051040adfcccb164 · Mirrors / biopet.biopet

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
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
- Moved to mapping maven app · 525e2ecc
  Peter van 't Hof authored 10 years ago
  
  525e2ecc
- Merge branch 'master' of git.lumc.nl:biopet/biopet · 2038f3b7
  Peter van 't Hof authored 10 years ago
  
  2038f3b7
- 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
- Added VariantAnnotator step · 31460c83
  Peter van 't Hof authored 10 years ago
  
  31460c83
- Added shading for framework, Queue is now included in the jar of the framework · d5a50842
  Peter van 't Hof authored 10 years ago
  
  d5a50842
- Changed filenames for compatible summarize script · 171522f4
  Peter van 't Hof authored 10 years ago
  
  171522f4
- Added single QScript for for VariantAnnotator, not used in Gatk pipeline · 73053fa3
  Peter van 't Hof authored 10 years ago
  
  73053fa3
- BiopetQScript is now abstract · 80512eba
  Peter van 't Hof authored 10 years ago
  
  80512eba
- Changed to make it compatible for new file structure · 97fd01f3
  Peter van 't Hof authored 10 years ago
  
  97fd01f3
- Start up readme · 5967d0b9
  Sander van der Zeeuw authored 10 years ago
  
  5967d0b9
- 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
- Added Sha1sum wrapper · 157d6e8d
  Peter van 't Hof authored 10 years ago
  
  157d6e8d