net.maizegenetics.analysis.gbs.v2

Class GBSUtils

net.maizegenetics.analysis.gbs.v2.GBSUtils

public class GBSUtils

This class contains methods and constants used by various classes in the GBSv2 pipeline.

Field Detail

inputFileGlob

public static java.lang.String inputFileGlob

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Constant Field Values

sampleNameField

public static java.lang.String sampleNameField

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Constant Field Values

flowcellField

public static java.lang.String flowcellField

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Constant Field Values

laneField

public static java.lang.String laneField

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Constant Field Values

barcodeField

public static java.lang.String barcodeField

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Constant Field Values

tissueNameField

public static java.lang.String tissueNameField

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Constant Field Values

fileNameField

public static java.lang.String fileNameField

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Constant Field Values

Method Detail

readFastQBlock

public static java.lang.String[] readFastQBlock(java.io.BufferedReader bw,
                                                int currentRead)

Method for reading FastQ four line structure, and returning a string array with [sequence, qualityScore]

readDeMultiPlexFastQBlock

public static java.lang.String[] readDeMultiPlexFastQBlock(java.io.BufferedReader bw,
                                                           int currentRead)

Method for reading FastQ four line structure, and returning a string array with [sequence, qualityScore]

determineQualityScoreBase

public static int determineQualityScoreBase(java.nio.file.Path fastqFile)

Method for reading FastQ four line structure, and returning a string array with [sequence, qualityScore]

getLaneAnnotatedTaxaList

public static java.util.ArrayList<net.maizegenetics.taxa.Taxon> getLaneAnnotatedTaxaList(java.nio.file.Path keyPath,
                                                                                         java.nio.file.Path fastQpath)

Returns an annotated taxaList based on a Keyfile for GBS

Parameters:

keyPath -

fastQpath -

Returns:

org.jetbrains.dokka.NodeRenderContent@3647d59c:

initializeBarcodeTrie

public static BarcodeTrie initializeBarcodeTrie(java.util.ArrayList<net.maizegenetics.taxa.Taxon> taxaList,
                                                TaxaList masterTaxaList,
                                                GBSEnzyme myEnzyme)

Produces a trie for sorting the read

Parameters:

taxaList - the taxaList of the current flowcell lanes that is annotated with barcode information

masterTaxaList - the mastertaxaList provides the taxaIndex

myEnzyme -

Returns:

org.jetbrains.dokka.NodeRenderContent@34c2076: Barcode trie for examining the prefixes

initializeBarcodeTrie

public static BarcodeTrie initializeBarcodeTrie(java.util.ArrayList<net.maizegenetics.taxa.Taxon> taxaList,
                                                TaxaList masterTaxaList,
                                                java.util.ArrayList masterTissueList,
                                                GBSEnzyme myEnzyme)

culledFiles

public static java.util.List<java.nio.file.Path> culledFiles(java.util.List<java.nio.file.Path> directoryFiles,
                                                             java.nio.file.Path keyFile)

Produces a list of fastq files that are represented by the plugin's keyfile

Parameters:

directoryFiles - : List of all the files in the directory

Returns:

org.jetbrains.dokka.NodeRenderContent@16e4f305: filesToProcess: List of only those files that should be processed

parseKeyfileIntoMap

public static com.google.common.collect.ListMultimap<java.lang.String,java.lang.String> parseKeyfileIntoMap(java.lang.String fileName)

Parses a tab-delimited keyFile storing the flow cell and lane values into a multimap. The flow cell is the key, which may have multiple associated lanes.

Returns:

org.jetbrains.dokka.NodeRenderContent@6bc8b8ae: