net.maizegenetics.analysis.gbs

Class ParseBarcodeRead

net.maizegenetics.analysis.gbs.ParseBarcodeRead

Direct Known Subclasses:

PEParseBarcodeRead

public class ParseBarcodeRead

Takes a key file and then sets up the methods to decode a read from the sequencer. The key file decribes how barcodes are related to their taxon. Generally, a keyfile with all flowcells is included, and then the flowcell and lane to be processed are indicated in the constructor.

Field Detail

maximumMismatchInBarcodeAndOverhang

protected int maximumMismatchInBarcodeAndOverhang

initialCutSiteRemnant

protected static java.lang.String[] initialCutSiteRemnant

readEndCutSiteRemnantLength

protected static int readEndCutSiteRemnantLength

likelyReadEnd

protected static java.lang.String[] likelyReadEnd

theEnzyme

protected static java.lang.String theEnzyme

Constructor Detail

ParseBarcodeRead

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

Create the barcode parsing object

Parameters:

keyFile - file location for the keyfile

enzyme - name of the enzyme

flowcell - name of the flowcell to be processed

lane - name of the lane to be processed

Method Detail

chooseEnzyme

public static void chooseEnzyme(java.lang.String enzyme)

Determines which cut sites to look for, and sets them, based on the enzyme used to generate the GBS library. For two-enzyme GBS both enzymes MUST be specified and separated by a dash "-". e.g. PstI-MspI, SbfI-MspI

Parameters:

enzyme - The name of the enzyme (case insensitive)

removeSeqAfterSecondCutSite

public static ReadBarcodeResult removeSeqAfterSecondCutSite(java.lang.String seq,
                                                            byte maxLength)

The barcode libraries used for this study can include two types of extraneous sequence at the end of reads. The first are chimeras created with the free ends. These will recreate the restriction site. The second are short regions (less than 64bp), so that will they will contain a portion of site and the universal adapter. This finds the first of site in likelyReadEnd, keeps the restriction site overhang and then sets everything to polyA afterwards

Parameters:

seq - An unprocessed tag sequence.

maxLength - The maximum number of bp in the processed sequence.

Returns:

org.jetbrains.dokka.NodeRenderContent@346f70fa: returnValue A ReadBarcodeResult object containing the unprocessed tag, Cut site position, Processed tag, and Poly-A padded tag.

parseReadIntoTagAndTaxa

public ReadBarcodeResult parseReadIntoTagAndTaxa(java.lang.String seqS,
                                                 java.lang.String qualS,
                                                 boolean fastq,
                                                 int minQual)

Return a class ReadBarcodeResult that captures the processed read and taxa inferred by the barcode

Parameters:

seqS - DNA sequence from the sequencer

qualS - quality score string from the sequencer

fastq - (fastq = true?; qseq=false?)

minQual - minimum quality score

Returns:

org.jetbrains.dokka.NodeRenderContent@28b2c37d: If barcode and cut site was found returns the result and processed sequence, if the barcode and cut site were not found return null

See Also:

class ReadBarcodeResult

getBarCodeCount

public int getBarCodeCount()

Returns the number of barcodes for the flowcell and lane

getTheBarcodes

public Barcode getTheBarcodes(int index)

Returns the class Barcode for the flowcell and lane

See Also:

class Barcode

getTaxaNames

public java.lang.String[] getTaxaNames()

Returns the taxaNames for the flowcell and lane