Class MeanQualityByCycle


  • @DocumentedFeature
    public class MeanQualityByCycle
    extends SinglePassSamProgram
    Program to generate a data table and chart of mean quality by cycle from a BAM file. Works best on a single lane/run of data, but can be applied to merged BAMs - the output may just be a little confusing.
    • 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(doc="If set to true calculate mean quality over PF reads only.")
        public boolean PF_READS_ONLY
    • Constructor Detail

      • MeanQualityByCycle

        public MeanQualityByCycle()
    • 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