Commits · f0eb1866e8f8ced9b830a4961ffd2fb952139ddc · Mirrors / biopet.biopet

Oct 27, 2014
- Revert back to JDK 1.7 due to regression in GATK 3.3 · 4548f60c
  bow authored 10 years ago
  
  4548f60c
Oct 25, 2014
- Update tests and filter function name · 9c3639f6
  bow authored 10 years ago
  
  9c3639f6
Oct 24, 2014
- Added FastqSplitter to exe · b7fbb9c2
  Peter van 't Hof authored 10 years ago
  
  b7fbb9c2
- Added MpileupToVcf to exe · 844c1f10
  Peter van 't Hof authored 10 years ago
  
  844c1f10
- Added BedToInterval to exe · 9be3b0ef
  Peter van 't Hof authored 10 years ago
  
  9be3b0ef
Oct 23, 2014
- Added metrics when pipeline starts with bamfile · e43efd94
  Peter van 't Hof authored 10 years ago
  
  e43efd94
- Add IntelliJ project files · 7edebc62
  bow authored 10 years ago
  
  7edebc62
- Refactor set creation with fold · e9338525
  bow authored 10 years ago
  
  e9338525
Oct 22, 2014
- Comments update and code style refactor · 320f4a82
  bow authored 10 years ago
  
  320f4a82
- Fix on bamADfilter · 917ed16d
  Peter van 't Hof authored 10 years ago
  
  917ed16d
- Fix on Queue header · 82bfba46
  Peter van 't Hof authored 10 years ago
  
  82bfba46
- Added versions and commit hash to commandline programs · fe661dad
  Peter van 't Hof authored 10 years ago
  
  fe661dad
- Begin 0.2.0-DEV · 1043a54f
  Peter van 't Hof authored 10 years ago
  
  1043a54f
- Commit changes before removing branch · fb266355
  Wai Yi Leung authored 10 years ago
  
  fb266355
- Added version to usage of main executeble · c7646d66
  Peter van 't Hof authored 10 years ago
  
  c7646d66
Oct 21, 2014
- Added git hash and version to final jar file, jar will also now contain a git.properties file · cabe8d0c
  Peter van 't Hof authored 10 years ago
  
  cabe8d0c
- Fix arg parsing · 1c669861
  Peter van 't Hof authored 10 years ago
  
  1c669861
- Expose bloom filter parameters in the command line · d4783368
  bow authored 10 years ago
  
  d4783368
- Fix queue wrapper · 70865194
  Peter van 't Hof authored 10 years ago
  
  70865194
- Added file to warning · 08eb14a4
  Peter van 't Hof authored 10 years ago
  
  08eb14a4
- Fix on knownSites option · f1396c89
  Peter van 't Hof authored 10 years ago
  
  f1396c89
Oct 20, 2014
- Fix missing test annotation import · 7ed44d6d
  bow authored 10 years ago
  
  7ed44d6d
- Move WipeReads test to correct directory · 6e48b13a
  bow authored 10 years ago
  
  6e48b13a
- Use htsjdk's BED reader and Feature object instead · a46706a1
  bow authored 10 years ago
  
  a46706a1
- Added all options and sort function · 4c0d4e42
  Peter van 't Hof authored 10 years ago
  
  4c0d4e42
- Bugfix in yamsvp (concerns multiple library merging), Adding Sambamba tool wrappers · 18f4992e
  wyleung authored 10 years ago
  
  18f4992e
- Removing Python version of seqstat and add the wrapper for the dQual/FastDtools version · 6eec9fed
  wyleung authored 10 years ago
  
  6eec9fed
- Adding pindel and removing seqstat (python version) · 5165c95f
  wyleung authored 10 years ago
  
  5165c95f
- format of script changed · 3513524a
  sajvanderzeeuw authored 10 years ago
  
  3513524a
- Remove unused type · 1e3ba0ee
  bow authored 10 years ago
  
  1e3ba0ee
Oct 17, 2014
- Use vars for better memory footprint · ea87604b
  bow authored 10 years ago
  
  ea87604b
- Fix boolean flags limit_removal and no_make_index · 1532236b
  bow authored 10 years ago
  
  1532236b
- Fix BAM writing memory overhead · 2b7acedf
  bow authored 10 years ago
  
  2b7acedf
- Add simple log messages · 3b094512
  bow authored 10 years ago
  
  3b094512
- Add command line flag to output BAM file containing discarded reads · 3ed4520f
  bow authored 10 years ago
  
  3ed4520f
- Add record counting (excluded and included) · 84519616
  bow authored 10 years ago
  
  84519616
- Refactor set-related functions · d646d680
  bow authored 10 years ago
  
  d646d680
- Change the format of the output table · 43aaa401
  sajvanderzeeuw authored 10 years ago
  
  43aaa401
Oct 16, 2014
- Add Header to the output · a7917974
  sajvanderzeeuw authored 10 years ago
  
  a7917974
- Fix missed refactor (issue #29) · b4978ac1
  bow authored 10 years ago
  
  b4978ac1