Package picard.analysis

Class FastWgsMetricsCollector

java.lang.Object
picard.analysis.AbstractWgsMetricsCollector<htsjdk.samtools.util.EdgingRecordAndOffset>
picard.analysis.FastWgsMetricsCollector
public class FastWgsMetricsCollector extends AbstractWgsMetricsCollector<htsjdk.samtools.util.EdgingRecordAndOffset>
Class represents fast algorithm for collecting data from AbstractLocusInfo with a list of aligned EdgingRecordAndOffset objects. According to the algorithm we receive only two EdgingRecordAndOffset objects for each alignment block of a read: one for the start of block and one for the end. When meeting a EdgingRecordAndOffset with type EdgingRecordAndOffset.Type.BEGIN, all information from the alignment block is accumulated in the collector, read name is added to a map holding the names of processed reads for detecting overlapping positions. When meeting a EdgingRecordAndOffset with type EdgingRecordAndOffset.Type.END, the read name is removed from the map with names of processed reads.

  • Constructor Details

    • FastWgsMetricsCollector

      public FastWgsMetricsCollector(CollectWgsMetrics collectWgsMetrics, int coverageCap, htsjdk.samtools.util.IntervalList intervals)
      Creates a collector and initializes the inner data structures
      Parameters:
      collectWgsMetrics - CollectWgsMetrics, that creates this collector
      coverageCap - coverage cap

  • Method Details

    • addInfo

      public void addInfo(htsjdk.samtools.util.AbstractLocusInfo<htsjdk.samtools.util.EdgingRecordAndOffset> info, htsjdk.samtools.reference.ReferenceSequence ref, boolean referenceBaseN)
      Description copied from class: AbstractWgsMetricsCollector
      Accumulates the data from AbstractLocusInfo in inner structures
      Specified by:
      addInfo in class AbstractWgsMetricsCollector<htsjdk.samtools.util.EdgingRecordAndOffset>
      Parameters:
      info - AbstractLocusInfo with aligned to reference position reads
      ref - ReferenceSequence
      referenceBaseN - true if current the value of reference base represents a no call