1. 01 Jul, 2015 5 commits
    • 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
    • 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
    • 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
    • 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
    • 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
  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 7 commits