Class CollectQualityYieldMetrics


  • @DocumentedFeature
    public class CollectQualityYieldMetrics
    extends SinglePassSamProgram
    Command line program to calculate quality yield metrics
    • Field Detail

      • USE_ORIGINAL_QUALITIES

        @Argument(shortName="OQ",
                  doc="If available in the OQ tag, use the original quality scores as inputs instead of the quality scores in the QUAL field.")
        public boolean USE_ORIGINAL_QUALITIES
      • INCLUDE_SECONDARY_ALIGNMENTS

        @Argument(doc="If true, include bases from secondary alignments in metrics. Setting to true may cause double-counting of bases if there are secondary alignments in the input file.")
        public boolean INCLUDE_SECONDARY_ALIGNMENTS
      • INCLUDE_SUPPLEMENTAL_ALIGNMENTS

        @Argument(doc="If true, include bases from supplemental alignments in metrics. Setting to true may cause double-counting of bases if there are supplemental alignments in the input file.")
        public boolean INCLUDE_SUPPLEMENTAL_ALIGNMENTS
      • FLOW_MODE

        @Argument(doc="If true, calculates flow-specific READ_LENGTH_AVG_Q metrics.")
        public boolean FLOW_MODE
    • Constructor Detail

      • CollectQualityYieldMetrics

        public CollectQualityYieldMetrics()
    • Method Detail

      • usesNoRefReads

        protected boolean usesNoRefReads()
        Ensure that we get all reads regardless of alignment status.
        Overrides:
        usesNoRefReads in class SinglePassSamProgram
      • 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