Class 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 Detail

      • 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 Detail

      • 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