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Created with Raphaël 2.2.09Jan86517Dec1611985432128Nov272524222120191817141211108765432131Oct30292827252423222120171615141310987630Sep29262217161512Extended sample handing in multisample qscriptAdded sample and library option to configRefactor getValueFromMap methodAdd test for default valueSmall optimizations after unit testsFix bug on freevarAdded unit tests to ConfigurableSmall optimizations after unit testingSwitch to optionsSwitch to case classAdded unit tests to configvalue classAdded unit tests at config classadded initial carp setupadded MACS2 wrappersRefactor getValueFromPathRenameAdded more scaladocsAdded getValueFromPath method and let getMapFromPath use new methodAdded more unit testsMove getMapFromPath to utilsFix small bugs after unit testingAdded more testsSmall fixes after unit testingAdded tests to util config methodsAdding IGVTools for creation of TDF files (Wiggle for IGV)Merge branch 'develop' of git.lumc.nl:biopet/biopet into feature-yamsvpUpdate yamsvp pipeline, link filesAdded scala docs to config classremove dirstructure from configRemove the indexing requirement from sambamba, since this does this on the fly since version v0.5.0Added scala docs to config utilsMerge branch 'develop' into feature-gentrapMerge branch 'feature-fastq_sync' of git.lumc.nl:biopet/biopet into feature-fastq_syncMerge branch 'develop' into feature-fastq_syncAdd fetch IDs and slight rewrite of previous commitMerge branch 'develop' of git.lumc.nl:biopet/biopet into feature-seqstat-scalaRefactor seqstatFinished method fetchVCFFrequencyAdd some method stubs to frequency annotatorChange pom version