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Created with Raphaël 2.2.07Mar632128Feb272421171615141310987653231Jan302928272625242322201918171614111097654226Dec242322212018171615141312109876542130Nov292827262524232221201918171614111098754231Oct282726Merge branch 'develop' into Fix_BIOPET_557Fixed compile errorChange version to varChanged VCFstats to check whether outputDir is a valid directory.Merge pull request #33 from biopet/fix-biopet-592Change sample and libraries to createOrUpdateRemove hard-coded settings in XhmmMatrix.Change utils to temp versionMerge remote-tracking branch 'remotes/origin/fix-BIOPET-591' into fix-BIOPET-587Remove Either objectSwitch templates to scalazFixed compile errorsBegin to convert to scalaz \/Merge remote-tracking branch 'remotes/origin/epic-summary_reformat' into fix-BIOPET-587Fixed last unit testsFixed unit tests for shivaFixed Kopisu unit testsFix name of methodFixed bammetrics testsStyle fixesFixed all core unit testsMerge pull request #30 from biopet/Improvement_BIOPET-561Merge branch 'develop' into Improvement_BIOPET-561Added varscan home page to the shiva pipeline documentationFixed three typos in READMEFixing code warningsMerge pull request #28 from biopet/fix-BIOPET-585Adding a lot of testing to summaryDBfix compile errordowngrade jdbc versionMerge branch 'develop' into fix-BIOPET-585Merge remote-tracking branch 'remotes/origin/develop' into fix-BIOPET-587Merge remote-tracking branch 'remotes/origin/develop' into epic-summary_reformatMerge pull request #29 from biopet/fix-BIOPET-590Merge branch 'develop' into fix-BIOPET-585Fixed that the timeout in on node time instead of including queue timeAdded separated outputDirs-Merge remote-tracking branch 'remotes/origin/develop' into fix-BIOPET-587added some if-s so that sv calling wouldn't fail when there's only one sample or when only one tool is being used for the analysis