Field Detail

• INPUT

  @Argument(shortName="I",
            doc="Input SAM or BAM file.")
  public File INPUT

• OUTPUT

  @Argument(shortName="O",
            doc="Output metrics file.")
  public File OUTPUT

• MINIMUM_MAPPING_QUALITY

  @Argument(shortName="MQ",
            doc="Minimum mapping quality for a read to contribute coverage.")
  public int MINIMUM_MAPPING_QUALITY

• MINIMUM_BASE_QUALITY

  @Argument(shortName="Q",
            doc="Minimum base quality for a base to contribute coverage. N bases will be treated as having a base quality of negative infinity and will therefore be excluded from coverage regardless of the value of this parameter.")
  public int MINIMUM_BASE_QUALITY

• COVERAGE_CAP

  @Argument(shortName="CAP",
            doc="Treat positions with coverage exceeding this value as if they had coverage at this value (but calculate the difference for PCT_EXC_CAPPED).")
  public int COVERAGE_CAP

• LOCUS_ACCUMULATION_CAP

  @Argument(doc="At positions with coverage exceeding this value, completely ignore reads that accumulate beyond this value (so that they will not be considered for PCT_EXC_CAPPED).  Used to keep memory consumption in check, but could create bias if set too low")
  public int LOCUS_ACCUMULATION_CAP

• STOP_AFTER

  @Argument(doc="For debugging purposes, stop after processing this many genomic bases.")
  public long STOP_AFTER

• INCLUDE_BQ_HISTOGRAM

  @Argument(doc="Determines whether to include the base quality histogram in the metrics file.")
  public boolean INCLUDE_BQ_HISTOGRAM

• COUNT_UNPAIRED

  @Argument(doc="If true, count unpaired reads, and paired reads with one end unmapped")
  public boolean COUNT_UNPAIRED

• SAMPLE_SIZE

  @Argument(doc="Sample Size used for Theoretical Het Sensitivity sampling. Default is 10000.",
            optional=true)
  public int SAMPLE_SIZE

• intervalArugmentCollection

  @ArgumentCollection
  protected IntervalArgumentCollection intervalArugmentCollection

• USE_FAST_ALGORITHM

  @Argument(doc="If true, fast algorithm is used.")
  public boolean USE_FAST_ALGORITHM

• READ_LENGTH

  @Argument(doc="Average read length in the file. Default is 150.",
            optional=true)
  public int READ_LENGTH

• INTERVALS

  protected File INTERVALS

Constructor Detail

• CollectWgsMetrics

  public CollectWgsMetrics()

Method Detail

• requiresReference

  protected boolean requiresReference()

  Overrides:

  requiresReference in class CommandLineProgram

• makeIntervalArgumentCollection

  protected IntervalArgumentCollection makeIntervalArgumentCollection()

  Returns:

  An interval argument collection to be used for this tool. Subclasses can override this to provide an argument collection with alternative arguments or argument annotations.

• main

  public static void main​(String[] args)

• getSamReader

  protected htsjdk.samtools.SamReader getSamReader()

  Gets the SamReader from which records will be examined. This will also set the header so that it is available in

• doWork

  protected int doWork()

  Description copied from class: CommandLineProgram
  Do the work after command line has been parsed. RuntimeException may be thrown by this method, and are reported appropriately.

  Specified by:

  doWork in class CommandLineProgram

  Returns:

  program exit status.

• getIntervalsToExamine

  protected htsjdk.samtools.util.IntervalList getIntervalsToExamine()

  Gets the intervals over which we will calculate metrics.

• getSamFileHeader

  protected htsjdk.samtools.SAMFileHeader getSamFileHeader()

  This method should only be called after {@link this.getSamReader()} is called.

• generateWgsMetrics

  protected CollectWgsMetrics.WgsMetrics generateWgsMetrics​(htsjdk.samtools.util.IntervalList intervals,
                                                            htsjdk.samtools.util.Histogram<Integer> highQualityDepthHistogram,
                                                            htsjdk.samtools.util.Histogram<Integer> unfilteredDepthHistogram,
                                                            double pctExcludedByMapq,
                                                            double pctExcludedByDupes,
                                                            double pctExcludedByPairing,
                                                            double pctExcludedByBaseq,
                                                            double pctExcludedByOverlap,
                                                            double pctExcludedByCapping,
                                                            double pctTotal,
                                                            int coverageCap,
                                                            htsjdk.samtools.util.Histogram<Integer> unfilteredBaseQHistogram,
                                                            int theoreticalHetSensitivitySampleSize)

• getBasesExcludedBy

  protected long getBasesExcludedBy​(CountingFilter filter)

  If INTERVALS is specified, this will count bases beyond the interval list when the read overlaps the intervals and extends beyond the edge. Ideally INTERVALS should only include regions that have hard edges without reads that could extend beyond the boundary (such as a whole contig).

• getLocusIterator

  protected htsjdk.samtools.util.AbstractLocusIterator getLocusIterator​(htsjdk.samtools.SamReader in)

  Creates AbstractLocusIterator implementation according to {@link this#USE_FAST_ALGORITHM} value.

  Parameters:

  in - inner SamReader

  Returns:

  if {@link this#USE_FAST_ALGORITHM} is enabled, returns EdgeReadIterator implementation, otherwise default algorithm is used and SamLocusIterator is returned.

• getCollector

  protected AbstractWgsMetricsCollector getCollector​(int coverageCap,
                                                     htsjdk.samtools.util.IntervalList intervals)

  Creates AbstractWgsMetricsCollector implementation according to {@link this#USE_FAST_ALGORITHM} value.

  Parameters:

  coverageCap - the maximum depth/coverage to consider.

  intervals - the intervals over which metrics are collected.

  Returns:

  if {@link this#USE_FAST_ALGORITHM} is enabled, returns FastWgsMetricsCollector implementation, otherwise default algorithm is used and CollectWgsMetrics.WgsMetricsCollector is returned.