Package picard.util

Class BarcodeEditDistanceQuery

java.lang.Object
picard.util.BarcodeEditDistanceQuery

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

    • 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 Details

    • BarcodeEditDistanceQuery

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

    • getSingleBarcodeDistanceQuery

      public SingleBarcodeDistanceMetric getSingleBarcodeDistanceQuery(int index, int previousMismatchCount)