Package picard.analysis

Class QualityScoreDistribution

java.lang.Object
picard.cmdline.CommandLineProgram
picard.analysis.SinglePassSamProgram
picard.analysis.QualityScoreDistribution
@DocumentedFeature public class QualityScoreDistribution extends SinglePassSamProgram
Charts quality score distribution within a BAM file.

  • Field Details

    • 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 Details

    • QualityScoreDistribution

      public QualityScoreDistribution()

  • Method Details

    • 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

    • 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