Class CollectRnaSeqMetrics


@DocumentedFeature public class CollectRnaSeqMetrics extends SinglePassSamProgram
  • Field Details

    • 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
    • END_BIAS_BASES

      @Argument(doc="The distance into a transcript over which 5\' and 3\' bias is calculated.") public int END_BIAS_BASES
  • Constructor Details

    • CollectRnaSeqMetrics

      public CollectRnaSeqMetrics()
  • 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 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
    • 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