Package picard.util

Class BarcodeEditDistanceQuery


  • public class BarcodeEditDistanceQuery
    extends Object
    A class for finding the distance between multiple (matched) barcodes and multiple barcode reads.
    • Field Detail

      • barcodeBytes

        public final byte[][] barcodeBytes
        list of barcodes (e.g. for dual-indexed barcodes)
      • readSubsequence

        public final byte[][] readSubsequence
        list of barcode reads
      • qualities

        public final byte[][] qualities
        list of quality scores for reads
      • minimumBaseQuality

        public final int minimumBaseQuality
        minimal base quality to condiser informative
      • maximalInterestingDistance

        public final int maximalInterestingDistance
        maximal edit distance between reads and barcodes to be considered
    • Constructor Detail

      • BarcodeEditDistanceQuery

        public BarcodeEditDistanceQuery​(byte[][] barcodeBytes,
                                        byte[][] readSubsequence,
                                        byte[][] qualities,
                                        int minimumBaseQuality,
                                        int maximalInterestingDistance)
    • Method Detail

      • getSingleBarcodeDistanceQuery

        public SingleBarcodeDistanceMetric getSingleBarcodeDistanceQuery​(int index,
                                                                         int previousMismatchCount)