Field Detail

• INTERVALS

  @Argument(doc="An optional list of intervals to restrict analysis to.",
            optional=true)
  public File INTERVALS

• DB_SNP

  @Argument(doc="VCF format dbSNP file, used to exclude regions around known polymorphisms from analysis.",
            optional=true)
  public File DB_SNP

• MINIMUM_QUALITY_SCORE

  @Argument(shortName="Q",
            doc="The minimum base quality score for a base to be included in analysis.")
  public int MINIMUM_QUALITY_SCORE

• MINIMUM_MAPPING_QUALITY

  @Argument(shortName="MQ",
            doc="The minimum mapping quality score for a base to be included in analysis.")
  public int MINIMUM_MAPPING_QUALITY

• MINIMUM_INSERT_SIZE

  @Argument(shortName="MIN_INS",
            doc="The minimum insert size for a read to be included in analysis.")
  public int MINIMUM_INSERT_SIZE

• MAXIMUM_INSERT_SIZE

  @Argument(shortName="MAX_INS",
            doc="The maximum insert size for a read to be included in analysis. Set to 0 to have no maximum.")
  public int MAXIMUM_INSERT_SIZE

• INCLUDE_UNPAIRED

  @Argument(shortName="UNPAIRED",
            doc="Include unpaired reads. If set to true then all paired reads will be included as well - MINIMUM_INSERT_SIZE and MAXIMUM_INSERT_SIZE will be ignored.")
  public boolean INCLUDE_UNPAIRED

• INCLUDE_DUPLICATES

  @Argument(shortName="DUPES",
            doc="Include duplicate reads. If set to true then all reads flagged as duplicates will be included as well.")
  public boolean INCLUDE_DUPLICATES

• INCLUDE_NON_PF_READS

  @Argument(shortName="NON_PF",
            doc="Whether or not to include non-PF reads.")
  public boolean INCLUDE_NON_PF_READS

• TANDEM_READS

  @Argument(shortName="TANDEM",
            doc="Set to true if mate pairs are being sequenced from the same strand, i.e. they\'re expected to face the same direction.")
  public boolean TANDEM_READS

• USE_OQ

  @Argument(doc="When available, use original quality scores for filtering.")
  public boolean USE_OQ

• CONTEXT_SIZE

  @Argument(doc="The number of context bases to include on each side of the assayed base.")
  public int CONTEXT_SIZE

• CONTEXTS_TO_PRINT

  @Argument(doc="If specified, only print results for these contexts in the detail metrics output. However, the summary metrics output will still take all contexts into consideration.",
            optional=true)
  public Set<String> CONTEXTS_TO_PRINT

• FILE_EXTENSION

  @Argument(shortName="EXT",
            doc="Append the given file extension to all metric file names (ex. OUTPUT.pre_adapter_summary_metrics.EXT). None if null",
            optional=true)
  public String FILE_EXTENSION

Constructor Detail

• CollectSequencingArtifactMetrics

  public CollectSequencingArtifactMetrics()

Method Detail

• requiresReference

  protected boolean requiresReference()

  Overrides:

  requiresReference in class CommandLineProgram

• 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

• usesNoRefReads

  protected boolean usesNoRefReads()

  Description copied from class: SinglePassSamProgram
  Can be overridden and set to false if the section of unmapped reads at the end of the file isn't needed.

  Overrides:

  usesNoRefReads in class SinglePassSamProgram