Class CollectBaseDistributionByCycle

    • Field Detail

      • CHART_OUTPUT

        @Argument(shortName="CHART",
                  doc="A file (with .pdf extension) to write the chart to.")
        public File CHART_OUTPUT
      • ALIGNED_READS_ONLY

        @Argument(doc="If set to true, calculate the base distribution over aligned reads only.")
        public boolean ALIGNED_READS_ONLY
      • PF_READS_ONLY

        @Argument(doc="If set to true, calculate the base distribution over PF reads only (Illumina specific). PF reads are reads that passed the internal quality filters applied by Illumina sequencers.")
        public boolean PF_READS_ONLY
    • Constructor Detail

      • CollectBaseDistributionByCycle

        public CollectBaseDistributionByCycle()
    • Method Detail

      • setup

        protected void setup​(htsjdk.samtools.SAMFileHeader header,
                             File samFile)
        Description copied from class: SinglePassSamProgram
        Should be implemented by subclasses to do one-time initialization work.
        Specified by:
        setup in class SinglePassSamProgram
      • acceptRead

        protected void acceptRead​(htsjdk.samtools.SAMRecord rec,
                                  htsjdk.samtools.reference.ReferenceSequence ref)
        Description copied from class: SinglePassSamProgram
        Should be implemented by subclasses to accept SAMRecords one at a time. If the read has a reference sequence and a reference sequence file was supplied to the program it will be passed as 'ref'. Otherwise 'ref' may be null.
        Specified by:
        acceptRead in class SinglePassSamProgram