Commits · 4b63e57c23511569dc858f783c9d85b9c612a702 · Mirrors / biopet.biopet

Jan 12, 2016
- Added empty implementations · 4b63e57c
  Peter van 't Hof authored 9 years ago
  
  4b63e57c
Jan 11, 2016
- Disable report · 621ccaf4
  Peter van 't Hof authored 9 years ago
  
  621ccaf4
Jan 08, 2016
- Fixed rna metrics · 565f3979
  Peter van 't Hof authored 9 years ago
  
  565f3979
Jan 06, 2016
- Switch to multisample mapping · d9c88772
  Peter van 't Hof authored 9 years ago
  
  d9c88772
Nov 24, 2015
- Bump version to 0.6.0-SNAPSHOT · ac785920
  Peter van 't Hof authored 9 years ago
  
  ac785920
- Bump version to 0.5.0 · c5303e8c
  Peter van 't Hof authored 9 years ago
  
  c5303e8c
Nov 23, 2015
- Bump to 0.5.0-RC2 · 16d2711f
  Peter van 't Hof authored 9 years ago
  
  16d2711f
Nov 19, 2015
- Bumb version to 0.5.0-RC1 · 19a93bbb
  Peter van 't Hof authored 9 years ago
  
  19a93bbb
- Fixed bug in loading the mainClass for biopet tools · 7f424eb9
  Peter van 't Hof authored 9 years ago
  
  7f424eb9
Nov 16, 2015
- Remove override method, now uses the bases class · d9d380c7
  Peter van 't Hof authored 9 years ago
  
  d9d380c7
- Fix samples dir · 7c57f730
  Peter van 't Hof authored 9 years ago
  
  7c57f730
Nov 09, 2015
- Fixed unit testing · 07b5f7bf
  Peter van 't Hof authored 9 years ago
  
  07b5f7bf
- Fixed small bug · 24205501
  Peter van 't Hof authored 9 years ago
  
  24205501
Nov 06, 2015
- Adding addError methods · 892540af
  Peter van 't Hof authored 9 years ago
  
  892540af
- Better error handeling on wrong values · abed23bb
  Peter van 't Hof authored 9 years ago
  
  abed23bb
- Fix null pointer on missing values · f861ddbb
  Peter van 't Hof authored 9 years ago
  
  f861ddbb
Nov 04, 2015
- adapters table was not filled correctly · 239b74f8
  Sander van der Zeeuw authored 9 years ago
  
  239b74f8
- num_reads_discarded changed into num_reads_discarded_total · 75e1b598
  Sander van der Zeeuw authored 9 years ago
  
  75e1b598
- fixes in gentrap report · e2a94705
  Sander van der Zeeuw authored 9 years ago
  
  e2a94705
Oct 16, 2015
- Style fix · c6ebdcae
  Peter van 't Hof authored 9 years ago
  
  c6ebdcae
Oct 15, 2015
- Gentrap test are now divided over 7 threads · 9cae1c11
  Peter van 't Hof authored 9 years ago
  
  9cae1c11
- added proper piping to bcftools and mpileup. [GENTRAP VARSCAN SHOULD BE TESTED] · 76da8883
  Sander van der Zeeuw authored 9 years ago
  
  76da8883
- Remove "reference" from testing · f4fb8907
  Peter van 't Hof authored 9 years ago
  
  (cherry picked from commit 8bf162ad)
  f4fb8907
- Remove "reference" from testing · 8bf162ad
  Peter van 't Hof authored 9 years ago
  
  8bf162ad
Oct 13, 2015
- Remove some testing · df83160f
  Peter van 't Hof authored 9 years ago
  
  df83160f
Sep 23, 2015
- Reference is not used in here · a2c583e8
  Peter van 't Hof authored 9 years ago
  
  a2c583e8
Sep 21, 2015
- Fix reference in varscan · 6b190fbd
  Peter van 't Hof authored 9 years ago
  
  6b190fbd
Sep 18, 2015
- Fixed unit tests · 6c7f4701
  Peter van 't Hof authored 9 years ago
  
  6c7f4701
- Add input files to pipelines · 4875e508
  Peter van 't Hof authored 9 years ago
  
  4875e508
Sep 13, 2015
- Fix pipeline without framework · f3343df9
  Peter van 't Hof authored 9 years ago
  
  f3343df9
Sep 11, 2015
- Tools split into new modules, core and utils are compileable now · eb97957f
  Peter van 't Hof authored 9 years ago
  
  eb97957f
Sep 10, 2015
- Moved config to utils · a81bce67
  Peter van 't Hof authored 9 years ago
  
  a81bce67
Sep 04, 2015
- Code style fix · 4ae12722
  Peter van 't Hof authored 9 years ago
  
  4ae12722
- Remove the need of merging the defaults anymore · 0586cbc2
  Peter van 't Hof authored 9 years ago
  
  0586cbc2
- Changing to SNAPSHOT version, this is following the maven convention · f550b637
  Peter van 't Hof authored 9 years ago
  
  f550b637
Sep 03, 2015

Fix strand-specific separation in Gentrap · 665bf70c

bow authored 9 years ago

This fixes a bug caused by incorrect creation of plus and minus strand BAM files.
It was caused by incorrectly specifying the SAM flags, causing the plus and minus
strand BAM files to still contain mixed strand reads.

665bf70c

Aug 11, 2015
- Adding gmap_build · 6deb5726
  Peter van 't Hof authored 9 years ago
  
  6deb5726
Aug 06, 2015
- remove parallel data providers · 03d9db7b
  Peter van 't Hof authored 9 years ago
  
  03d9db7b
- enable parallel data providers · 907c8ddb
  Peter van 't Hof authored 9 years ago
  
  907c8ddb
Jul 30, 2015
- Bumb version to 0.5.0-DEV · c3b83b90
  Peter van 't Hof authored 9 years ago
  
  c3b83b90