Package picard.analysis

Class CollectQualityYieldMetricsSNVQ

java.lang.Object
picard.cmdline.CommandLineProgram
picard.analysis.SinglePassSamProgram
picard.analysis.CollectQualityYieldMetricsSNVQ
@DocumentedFeature public class CollectQualityYieldMetricsSNVQ extends SinglePassSamProgram
Command line program to calculate SNV quality yield metrics for read files

  • Field Details

    • SNVQ_BASE_ORDER

      public static final String SNVQ_BASE_ORDER
      See Also:

    • qualityHistogram

      public htsjdk.samtools.util.Histogram<Integer> qualityHistogram

    • snvqHistogram

      public htsjdk.samtools.util.Histogram<Integer> snvqHistogram

    • ALTERNATE_QUALITY_ATTRIBUTE

      @Argument(shortName="AQA", doc="Use an alternative tag instead of base quality (QUAL) scores ", optional=true) public String ALTERNATE_QUALITY_ATTRIBUTE

    • 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

    • INCLUDE_BQ_HISTOGRAM

      @Argument(doc="Determines whether to include the base quality histogram in the metrics file.") public boolean INCLUDE_BQ_HISTOGRAM

  • Constructor Details

    • CollectQualityYieldMetricsSNVQ

      public CollectQualityYieldMetricsSNVQ()

  • Method Details

    • 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

    • finish

      protected void finish()
      Description copied from class: SinglePassSamProgram
      Should be implemented by subclasses to do one-time finalization work.
      Specified by:
      finish in class SinglePassSamProgram