Package picard.util
Class BarcodeEditDistanceQuery
java.lang.Object
picard.util.BarcodeEditDistanceQuery
A class for finding the distance between multiple (matched) barcodes and multiple barcode reads.
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Field Summary
FieldsModifier and TypeFieldDescriptionfinal byte[][]
list of barcodes (e.g.final int
maximal edit distance between reads and barcodes to be consideredfinal int
minimal base quality to condiser informativefinal byte[][]
list of quality scores for readsfinal byte[][]
list of barcode reads -
Constructor Summary
ConstructorsConstructorDescriptionBarcodeEditDistanceQuery
(byte[][] barcodeBytes, byte[][] readSubsequence, byte[][] qualities, int minimumBaseQuality, int maximalInterestingDistance) -
Method Summary
Modifier and TypeMethodDescriptiongetSingleBarcodeDistanceQuery
(int index, int previousMismatchCount)
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Field Details
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barcodeBytes
public final byte[][] barcodeByteslist of barcodes (e.g. for dual-indexed barcodes) -
readSubsequence
public final byte[][] readSubsequencelist of barcode reads -
qualities
public final byte[][] qualitieslist of quality scores for reads -
minimumBaseQuality
public final int minimumBaseQualityminimal base quality to condiser informative -
maximalInterestingDistance
public final int maximalInterestingDistancemaximal edit distance between reads and barcodes to be considered
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Constructor Details
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BarcodeEditDistanceQuery
public BarcodeEditDistanceQuery(byte[][] barcodeBytes, byte[][] readSubsequence, byte[][] qualities, int minimumBaseQuality, int maximalInterestingDistance)
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Method Details
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getSingleBarcodeDistanceQuery
public SingleBarcodeDistanceMetric getSingleBarcodeDistanceQuery(int index, int previousMismatchCount)
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