Class CollectGcBiasMetrics


  • @DocumentedFeature
    public class CollectGcBiasMetrics
    extends SinglePassSamProgram
    Tool to collect information about GC bias in the reads in a given BAM file. Computes the number of windows (of size specified by SCAN_WINDOW_SIZE) in the genome at each GC% and counts the number of read starts in each GC bin. What is output and plotted is the "normalized coverage" in each bin - i.e. the number of reads per window normalized to the average number of reads per window across the whole genome.
    • Field Detail

      • CHART_OUTPUT

        @Argument(shortName="CHART",
                  doc="The PDF file to render the chart to.")
        public File CHART_OUTPUT
      • SUMMARY_OUTPUT

        @Argument(shortName="S",
                  doc="The text file to write summary metrics to.")
        public File SUMMARY_OUTPUT
      • SCAN_WINDOW_SIZE

        @Argument(shortName="WINDOW_SIZE",
                  doc="The size of the scanning windows on the reference genome that are used to bin reads.")
        public int SCAN_WINDOW_SIZE
      • MINIMUM_GENOME_FRACTION

        @Argument(shortName="MGF",
                  doc="For summary metrics, exclude GC windows that include less than this fraction of the genome.")
        public double MINIMUM_GENOME_FRACTION
      • IS_BISULFITE_SEQUENCED

        @Argument(shortName="BS",
                  doc="Whether the SAM or BAM file consists of bisulfite sequenced reads.")
        public boolean IS_BISULFITE_SEQUENCED
      • METRIC_ACCUMULATION_LEVEL

        @Argument(shortName="LEVEL",
                  doc="The level(s) at which to accumulate metrics.")
        public Set<MetricAccumulationLevel> METRIC_ACCUMULATION_LEVEL
      • ALSO_IGNORE_DUPLICATES

        @Argument(shortName="ALSO_IGNORE_DUPLICATES",
                  doc="Use to get additional results without duplicates. This option allows to gain two plots per level at the same time: one is the usual one and the other excludes duplicates.")
        public boolean ALSO_IGNORE_DUPLICATES
    • Constructor Detail

      • CollectGcBiasMetrics

        public CollectGcBiasMetrics()
    • Method Detail

      • customCommandLineValidation

        protected String[] customCommandLineValidation()
        Description copied from class: CommandLineProgram
        Put any custom command-line validation in an override of this method. clp is initialized at this point and can be used to print usage and access argv. Any options set by command-line parser can be validated.
        Overrides:
        customCommandLineValidation in class CommandLineProgram
        Returns:
        null if command line is valid. If command line is invalid, returns an array of error message to be written to the appropriate place.
      • 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