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Created with Raphaël 2.2.020Aug19181514121187654130Jul29282724232221181514327Jun26232119171312109654327May2621201514Added BamOutput Option to HaplotypecallerMerge commit 'feeafebb314e1a73877c2b2ad665d3a6cc5875ad' into sanderFix bug on single end library'schanged mem limit to 4gbMerge commit '18e080e150289ce602782bdfc112f99e9af6ff60' into sanderadded all BWA optionsMoved Flexiprep val to root op mapping classRemove version command for picardDebug sickle wrapperFix bug when json parse failedFix bug on single end bam filesChanged one option in BWA.scala so mapping had to be changed as wellAdded all Sickle OptionsAdded all BWA mem optionsChange chunk directorySpelling fixChanges actions for BedToIntervals testsChanged run to libraryRemoved the Gatk-Old from the pom.xmlChanged Int to LongFix bug on VariantEval -L optionAdded a default vmemSkipping lines that are not correct bed entry'sAdded targetBed optionAdded Vcf sample compare moduleAdded targetBait config optionFix array on json fileFix on end files on flexiprep, not intermediate anymoreAdded md5sums for excuteblesFix class name for reportFastqc now compatible to version 0.11.2Fix compile errorsAdded Float optionMerge commit 'dd952f2e87d58c2dd919d1510a43d0539885290c'Add unit tests to Ln extensionAdd initial cufflinks wrapperUpdate Sha1sum documentationRemoved unused importsMerge commit 'fa3bbb631e31ecac993939a8397d965f0a5b85de' into peterRelative path calculation fix