net.maizegenetics.analysis.gbs

Class PEParseBarcodeRead

ParseBarcodeRead

net.maizegenetics.analysis.gbs.PEParseBarcodeRead

public class PEParseBarcodeRead
extends ParseBarcodeRead

Constructor Detail

PEParseBarcodeRead

public PEParseBarcodeRead(java.lang.String keyFile,
                          java.lang.String enzyme,
                          java.lang.String flowcell,
                          java.lang.String lane)

Construct empty object from key file, enzyme and Illumina data from a lane. Set up likely end and barcode for parsing data

Parameters:

keyFile - the key file

enzyme - enzyme used

flowcell - flowcell name

lane - lane number

Method Detail

parseReadIntoTagAndTaxa

public PEReadBarcodeResult parseReadIntoTagAndTaxa(java.lang.String seqSF,
                                                   java.lang.String qualSF,
                                                   java.lang.String seqSB,
                                                   java.lang.String qualSB,
                                                   boolean fastq,
                                                   int minQual,
                                                   int tagLengthInLong)

Parse sequence pair to a PE tag and taxon.

Parameters:

seqSF - Forward sequence

qualSF - Quality string of forward sequence

seqSB - Backward sequence

qualSB - Quality string of backward sequence

fastq - Boolean value of if the data is fastq format

minQual - Minimum of quality value of sequence, default is 0 (quality is not controled)

tagLengthInLong - Tag length in Long primitive data type, defaut is 8 (8 * 32 = 256 bp)

Returns:

org.jetbrains.dokka.NodeRenderContent@4e3c760e: Parsed PE read (forward tag, backward tag and taxon)

removeSeqAfterSecondCutSite

public ShortReadBarcodeResult removeSeqAfterSecondCutSite(java.lang.String seq,
                                                          short maxLength,
                                                          int tagLengthInLong,
                                                          java.lang.String taxaName,
                                                          boolean ifForward)

Remove the sequence of the second cutsite

Parameters:

seq - sequence need to be processed

maxLength - maximum length of padded sequence, e.g. 32 * 8 = 256 bp. 256 is the maxLength

tagLengthInLong - PE Tag in Long primitive data type, e.g. 8

taxaName - taxon name

ifForward - Forward or backward sequence

Returns:

org.jetbrains.dokka.NodeRenderContent@48216ad4: