Package picard.analysis

Class QualityScoreDistribution

  • @DocumentedFeature
public class QualityScoreDistribution
extends SinglePassSamProgram
    Charts quality score distribution within a BAM file.

    • 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 mean quality over aligned reads only.")
public boolean ALIGNED_READS_ONLY

      • PF_READS_ONLY

        @Argument(shortName="PF",
          doc="If set to true calculate mean quality over PF reads only.")
public boolean PF_READS_ONLY

      • INCLUDE_NO_CALLS

        @Argument(doc="If set to true, include quality for no-call bases in the distribution.")
public boolean INCLUDE_NO_CALLS

    • Constructor Detail

      • QualityScoreDistribution

        public QualityScoreDistribution()

    • 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