1. 01 Jul, 2015 7 commits
    • Wai Yi Leung's avatar
      Merge branch 'fix-temp_test_files' into 'develop' · 2b7a4f2f
      Wai Yi Leung authored
      Working dir for unit tests is now the target folder
      
      Fix for #150
      
      See merge request !176
      2b7a4f2f
    • Wai Yi Leung's avatar
      Merge branch 'small_fixes' into 'develop' · 448669b6
      Wai Yi Leung authored
      Small fixes
      
      Fixes two small issues
      
      1. Extra docs for target beds/regions of interest for Shiva
      2. Fixes integer overflow on WGS coverage statistics for report (Size of human genome > 2^31 -1 bases)
      
      See merge request !177
      448669b6
    • Wai Yi Leung's avatar
      Merge branch 'patch-picard_dependency_list' into 'develop' · 94afd24c
      Wai Yi Leung authored
      Patch picard dependency list
      
      This pull request deals with a recent change in pulling Picard's version number. Previously, the version number is generated only when the JAR is packaged. This means if we do `mvn test` or run tests on specific classes directly, we'll get `NullPointerException` since the dependency list is not created yet.
      
      To fix this, the pulled dependency list stream is wrapped properly in an `Option` class now (so we can run tests directly on classes).
      
      See merge request !180
      94afd24c
    • Wai Yi Leung's avatar
      Merge branch 'feature-gentrap_additions' into 'develop' · 20eefdf6
      Wai Yi Leung authored
      Feature gentrap additions
      
      This is the latest updates and fixes on the Gentrap pipeline to be compatible with the most recent framework updates.
      
      In particular:
      
      * Issue #156 is fixed ~ this was due to class initialization problems
      * Issue #157 is fixed
      * TopHat alignment results are now merged with its unmapped alignment file, producing the correct statistics
      * The pipeline is updated with the new reference module.
      * Redundant CollectRnaSeqMetrics is removed (now using the one from BamMetrics instead).
      
      See merge request !181
      20eefdf6
    • Wai Yi Leung's avatar
      Merge branch 'feature-seqstat_updates' into 'develop' · 3ec61eee
      Wai Yi Leung authored
      Feature seqstat updates
      
      Updates on SeqStat (per the commit messages).
      
      We still need to rely on FastQC since some other methods require further testing to be implemented. For example, to get the median base quality from all bases is not that straightforward since the container size may well exceet `Int.MaxValue` while the default containers' maximum sizes are all `Int.MaxValue`.
      
      See merge request !182
      3ec61eee
    • Wai Yi Leung's avatar
      Merge branch 'issue168' into 'develop' · 03c1cfa0
      Wai Yi Leung authored
      Shiva report messages
      
      Add messsages for Shiva report
      
      See #168
      
      See merge request !183
      03c1cfa0
    • Wai Yi Leung's avatar
      Merge branch 'feature-fix_java_version' into 'develop' · f62be586
      Wai Yi Leung authored
      Feature fix java version
      
      Fix for #144
      
      See merge request !185
      f62be586
  2. 30 Jun, 2015 4 commits
  3. 29 Jun, 2015 7 commits
  4. 28 Jun, 2015 6 commits
  5. 27 Jun, 2015 7 commits
  6. 26 Jun, 2015 4 commits
  7. 25 Jun, 2015 5 commits