Class CollectRnaSeqMetrics

    • Field Detail

      • REF_FLAT

        @Argument(doc="Gene annotations in refFlat form.  Format described here: http://genome.ucsc.edu/goldenPath/gbdDescriptionsOld.html#RefFlat")
        public File REF_FLAT
      • RIBOSOMAL_INTERVALS

        @Argument(doc="Location of rRNA sequences in genome, in interval_list format.  If not specified no bases will be identified as being ribosomal.  Format described <a href=\"http://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/util/IntervalList.html\">here</a>:",
                  optional=true)
        public File RIBOSOMAL_INTERVALS
      • STRAND_SPECIFICITY

        @Argument(shortName="STRAND",
                  doc="For strand-specific library prep. For unpaired reads, use FIRST_READ_TRANSCRIPTION_STRAND if the reads are expected to be on the transcription strand.")
        public RnaSeqMetricsCollector.StrandSpecificity STRAND_SPECIFICITY
      • MINIMUM_LENGTH

        @Argument(doc="When calculating coverage based values (e.g. CV of coverage) only use transcripts of this length or greater.")
        public int MINIMUM_LENGTH
      • CHART_OUTPUT

        @Argument(doc="The PDF file to write out a plot of normalized position vs. coverage.",
                  shortName="CHART",
                  optional=true)
        public File CHART_OUTPUT
      • IGNORE_SEQUENCE

        @Argument(doc="If a read maps to a sequence specified with this option, all the bases in the read are counted as ignored bases. These reads are not counted towards any metrics, except for the PF_BASES field.",
                  optional=true)
        public Set<String> IGNORE_SEQUENCE
      • RRNA_FRAGMENT_PERCENTAGE

        @Argument(doc="This percentage of the length of a fragment must overlap one of the ribosomal intervals for a read or read pair to be considered rRNA.")
        public double RRNA_FRAGMENT_PERCENTAGE
      • METRIC_ACCUMULATION_LEVEL

        @Argument(shortName="LEVEL",
                  doc="The level(s) at which to accumulate metrics.  ")
        public Set<MetricAccumulationLevel> METRIC_ACCUMULATION_LEVEL
    • Constructor Detail

      • CollectRnaSeqMetrics

        public CollectRnaSeqMetrics()
    • 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 refSeq)
        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