Commits · 1043a54f4274c262f080bacb532c984fc3162958 · Mirrors / biopet.biopet

Oct 22, 2014
- 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
Oct 15, 2014
- Added FindRepeatsPacBio · e94e3dd5
  Peter van 't Hof authored 10 years ago
  
  e94e3dd5
- Added minBamAlternateDepth · e92dc5d4
  Peter van 't Hof authored 10 years ago
  
  e92dc5d4
Oct 14, 2014
- Parts for the SV calling pipeline, formatting and adding breakdancer as subpipeline · d980652c
  wyleung authored 10 years ago
  
  d980652c
- Netbeans config, automatic convert to LF instead of CRLF · 60c0ac17
  wyleung authored 10 years ago
  
  60c0ac17
- Added VcfFilter · b1943e5b
  Peter van 't Hof authored 10 years ago
  
  b1943e5b
- Changed arg parsing · 0425c5db
  Peter van 't Hof authored 10 years ago
  
  0425c5db
- Added vcfToTsv module · 7ff8ef5d
  Peter van 't Hof authored 10 years ago
  
  7ff8ef5d
- Fix missing variants · 6ef85c1b
  Peter van 't Hof authored 10 years ago
  
  6ef85c1b
- Add VcfToTsv · b8659593
  Peter van 't Hof authored 10 years ago
  
  b8659593
Oct 13, 2014
- Fix missed refactor (issue #29) · 1061798d
  bow authored 10 years ago
  
  1061798d
- Reorganize tools · d7260ac8
  Peter van 't Hof authored 10 years ago
  d7260ac8
- Fix args · 9e1bc3d0
  Peter van 't Hof authored 10 years ago
  
  9e1bc3d0