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Created with Raphaël 2.2.04Feb3230Jan292827262322212019161514131210986517Dec1611985432128Nov272524222120191817141211108765432131Oct30292827252423Ensure module name is not processed when parsing overrepresented sequencesFix bug caused by incorrect split regexStrip whitespace from encoding nameRefactor FastQC outputDir and dataFile to separate methodsMerge branch 'develop' into patch-flexiprep-parse-adaptersAdded thread scatteringMerge branch 'feature-fix_mapping' into 'develop'Change some optionsFix checksSkip extractIfNeeded on R2 when not pairedChange on empty string checkUse Option[File] for optional files and fix bug with adapter sequence from fastqc captureRemove todoChange to option typesNo null returns at files and stringsExpose sample ID and library ID as command line flags in mapping pipelineUse requirements check on mapping and flexiprep pipelineRename libraryId -> libId for consistencyMerge branch 'develop' of git.lumc.nl:biopet/biopet into feature-seqstat-scalaExpose Flexiprep sampleId and libraryId back to the command lineUse def again instead of lazy valsReducing the wrapper to take bam and chrom.sizes file onlyNo more manual definition of tdf and wig files. In the afterGraph, the paths are setMerge branch 'develop' of git.lumc.nl:biopet/biopet into feature-igvtoolsMerge branch 'develop' into feature-gentrapMerge branch 'feature-fix_only_sample' into 'develop'Name changeAdd documentation to FastQC flexiprep wrapperRefactor Cutadapt check in FlexiprepRefactor and document adapter retrieval from FastQCRefactor FastQC encoding retrievalRefactor and document fastqc data file parsing functionStyle update for FastQC wrapper and object in FlexiprepUpdate summary creation for Flexiprep FastQCMerge branch 'develop' of git.lumc.nl:biopet/biopet into feature-igvtoolsAdding all program arguments to the wrapper, cleaner file checkImplemented addMultisampleJobs methodSwitch to new multisample partAdded addMultisampleJobs methodSeqstat json output, also counts from nucleotides