net.maizegenetics.analysis.gbs

Class ReadBarcodeResult

net.maizegenetics.analysis.gbs.ReadBarcodeResult

public class ReadBarcodeResult

Container class for returning the results of parsed barcoded sequencing read.

#unprocessedSequence is the original sequence with the barcode still attached

#processedSequence is the sequence with the barcode removed and cut down to the given length.

#paddedSequence is the #processedSequence padded with polyA to length if the #processedSequence was shorter than length.

Field Detail

unprocessedSequence

public java.lang.String unprocessedSequence

Original sequence from sequencer

processedSequence

public java.lang.String processedSequence

Processed sequence with barcode removed

paddedSequence

public java.lang.String paddedSequence

Processed sequence padded with polyA

Constructor Detail

ReadBarcodeResult

public ReadBarcodeResult(kotlin.Array[] read,
                         byte length,
                         java.lang.String taxon,
                         int taxonIndex)

ReadBarcodeResult

public ReadBarcodeResult(java.lang.String sequence)

Method Detail

toString

public java.lang.String toString()

getLength

public byte getLength()

getRead

public kotlin.Array[] getRead()

getTaxonName

public java.lang.String getTaxonName()

Return taxon name implied by the barcode sequence

getTaxonIndex

public int getTaxonIndex()