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 as ")
  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

• main

  public static void main​(String[] argv)

  Required main method implementation.

• 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