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 Summary
Fields Modifier and Type Field Description byte[][]
barcodeBytes
list of barcodes (e.g.int
maximalInterestingDistance
maximal edit distance between reads and barcodes to be consideredint
minimumBaseQuality
minimal base quality to condiser informativebyte[][]
qualities
list of quality scores for readsbyte[][]
readSubsequence
list of barcode reads
-
Constructor Summary
Constructors Constructor Description BarcodeEditDistanceQuery(byte[][] barcodeBytes, byte[][] readSubsequence, byte[][] qualities, int minimumBaseQuality, int maximalInterestingDistance)
-
Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description SingleBarcodeDistanceMetric
getSingleBarcodeDistanceQuery(int index, int previousMismatchCount)
-
-
-
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
-
-
Method Detail
-
getSingleBarcodeDistanceQuery
public SingleBarcodeDistanceMetric getSingleBarcodeDistanceQuery(int index, int previousMismatchCount)
-
-