Commits · 72a96f7e5b377d20853d1d6b31f4aa9066b595c2 · Mirrors / biopet.biopet · GitLab

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Oct 30, 2015
- Adding Gears to summary output of Mapping · 72a96f7e
  Wai Yi Leung authored Oct 30, 2015
  
  72a96f7e
- Optimize code · 3cd8150f
  Peter van 't Hof authored Oct 30, 2015
  
  3cd8150f
- Added input file checking · 20cd7b6d
  Peter van 't Hof authored Oct 30, 2015
  
  20cd7b6d
Oct 29, 2015
- Simplify unmapped reads extraction · b7743a6e
  Wai Yi Leung authored Oct 29, 2015
  
  b7743a6e
- Fix resource copy for the report · 972ad0f3
  Wai Yi Leung authored Oct 29, 2015
  
  972ad0f3
- Fixed summary file name · 2f92eb6d
  Peter van 't Hof authored Oct 29, 2015
  
  2f92eb6d
- change pipeline test, not test on sambambaview, but on samtoolsview · 11fe02b4
  Wai Yi Leung authored Oct 29, 2015
  
  11fe02b4
- More style fixes · 755b864d
  Wai Yi Leung authored Oct 29, 2015
  
  755b864d
- Merge branch 'develop' of git.lumc.nl:biopet/biopet into feature-gears · 8a15fe3c
  Wai Yi Leung authored Oct 29, 2015
  
  8a15fe3c
- Style change · f5e66858
  Wai Yi Leung authored Oct 29, 2015
  
  f5e66858
- Remove sambamba and use samtools for extracting pairs of unmapped reads (not the advanced query) · 6483fd1f
  Wai Yi Leung authored Oct 29, 2015
  
  6483fd1f
- Style fixes and config for samtofastq · 705d9cd6
  Wai Yi Leung authored Oct 29, 2015
  
  705d9cd6
Oct 28, 2015
- Adding Scaladocs to KrakenReportToJson and remove redundant code · 4cb2adf1
  Wai Yi Leung authored Oct 28, 2015
  
  4cb2adf1
- Refactor the report generation a bit. Move pipeline specific report components... · 4c405315
  Wai Yi Leung authored Oct 28, 2015
  4c405315
- Merge branch 'fix-coverage_piping' into 'develop' · 9c5c1703
  Sander Bollen authored Oct 28, 2015
  9c5c1703
- Fixes for the comments made in the ticket #241 · 1b673dfa
  Wai Yi Leung authored Oct 28, 2015
  
  1b673dfa
Oct 27, 2015
- Merge branch 'develop' of git.lumc.nl:biopet/biopet into feature-gears · a464f561
  Wai Yi Leung authored Oct 27, 2015
  
  a464f561
- Merge branch 'feature-genotype_concordance' into 'develop' · 4258ac1b
  Sander Bollen authored Oct 27, 2015
  4258ac1b
- Change titles · 99a3ba0a
  Peter van 't Hof authored Oct 27, 2015
  
  99a3ba0a
- Switch -a and -b for bedtools coverage · e27c05d0
  Peter van 't Hof authored Oct 27, 2015
  
  e27c05d0
- Code style fixes · 41eade8b
  Peter van 't Hof authored Oct 27, 2015
  
  41eade8b
Oct 26, 2015
- Remove file checking · c40dda46
  Peter van 't Hof authored Oct 26, 2015
  
  c40dda46
- Fix summary key · 186db74d
  Peter van 't Hof authored Oct 26, 2015
  
  186db74d
- Fixed bcftools merge step · 779e8aa3
  Peter van 't Hof authored Oct 26, 2015
  
  779e8aa3
- Fixed unknown executables · 9156f68c
  Peter van 't Hof authored Oct 26, 2015
  
  9156f68c
- Style changes · db4dcbca
  Peter van 't Hof authored Oct 26, 2015
  
  db4dcbca
- Fix exist · 66f1b6ec
  Peter van 't Hof authored Oct 26, 2015
  
  66f1b6ec
- Fix case class · 21d0cae7
  Peter van 't Hof authored Oct 26, 2015
  
  21d0cae7
- Move Executable function outside of class · 311e596b
  Peter van 't Hof authored Oct 26, 2015
  
  311e596b
Oct 25, 2015
- Set defaults for gc limits · 595e482d
  Peter van 't Hof authored Oct 25, 2015
  
  595e482d
Oct 23, 2015
- Added GenotypeConcordance to shiva · 18e22c1b
  Peter van 't Hof authored Oct 23, 2015
  
  18e22c1b
- Added GenotypeConcordance · 05bff3ab
  Peter van 't Hof authored Oct 23, 2015
  
  05bff3ab
- Merge branch 'fix-Shiva_bcftools_calling' into 'develop' · fe9f50f7
  Sander Bollen authored Oct 23, 2015
  fe9f50f7
Oct 22, 2015
- Merge branch 'fix-sample-names' into 'develop' · 52a67c4b
  Peter van 't Hof authored Oct 22, 2015
  52a67c4b
- proper temp files · 4dcbb9cd
  Sander Bollen authored Oct 22, 2015
  
  4dcbb9cd
- fix for #222 · b4bb3fd3
  Sander Bollen authored Oct 22, 2015
  
  b4bb3fd3
- Bugfix in KrakenReportToJson, include Root and Unclassified in any case. · 0f4f1881
  Wai Yi Leung authored Oct 22, 2015
  
  0f4f1881
- POM definition fix. · 3ded0090
  Wai Yi Leung authored Oct 22, 2015
  
  3ded0090
- Merge remote-tracking branch 'remotes/origin/develop' into fix-Shiva_bcftools_calling · d4afc77f
  Sander van der Zeeuw authored Oct 22, 2015
  
  d4afc77f
- refactor memorylimit · a5a9f4b1
  Sander van der Zeeuw authored Oct 22, 2015
  
  a5a9f4b1