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Created with Raphaël 2.2.03Feb230Jan292827262322212019161514131210986517Dec1611985432128Nov272524222120191817141211108765432131Oct3029282725242322Merge 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 nucleotidesFix for -sample commandline argumentPrep for paralyzationMerge branch 'feature-Chipcap' into 'develop'Merge branch 'develop' into feature-ChipcapMerge branch 'develop' into feature-Chipcapmade creating bam file with function createFile(*.bam)Update Gentrap with new multisample classesAdd default values to HtseqCount extensionAdd default values to Gsnap extensionMerge branch 'feature-cnvpipeline' into 'develop'Merge branch 'feature-typofixes' into 'develop'Fix verion to versionAligner BWA typo and Mapping clean pathsMerge from origin masterMove SVcallers into the toplevel extensions directoryRefactor Yamsvp to new sample/lib modelfixed output_dir name bugMerge branch 'develop' of git.lumc.nl:biopet/biopet into feature-yamsvpMerge branch 'develop' of git.lumc.nl:biopet/biopet into feature-igvtoolsSupport multiple output for igvtoolsMerge branch 'develop' into feature-gentrapMerge branch 'feature-fastq_sync' into 'develop'Add notes on input - output compressionUse AsyncFastqWriter instead of BasicFastqWriter