net.maizegenetics.util

Class ConvertOldFastqToModernFormatPlugin

AbstractPlugin

net.maizegenetics.util.ConvertOldFastqToModernFormatPlugin

All Implemented Interfaces:

Plugin, PluginListener, ProgressListener

public class ConvertOldFastqToModernFormatPlugin
extends AbstractPlugin

This plugin takes a single fastq or a directory of fastq files in the "old" format and converts them to the "modern" illumina format. The old format had multiple taxa combined in a single file, with barcodes attaached to each read sequence. The new fastQ format has the taxa (samples) each in individual files. THis method takes the old fastq and for each read block, subsets the sequence to start after the barcode (but including the initial cut site) and end after the ending cut site. The quality score is subsetted identically to the sequence so the 2 match. Files are written to a user defined directory.

Field Detail

inputFileGlob

public static java.lang.String inputFileGlob

See Also:

Constant Field Values

sampleNameField

public static java.lang.String sampleNameField

See Also:

Constant Field Values

flowcellField

public static java.lang.String flowcellField

See Also:

Constant Field Values

laneField

public static java.lang.String laneField

See Also:

Constant Field Values

barcodeField

public static java.lang.String barcodeField

See Also:

Constant Field Values

tissueNameField

public static java.lang.String tissueNameField

See Also:

Constant Field Values

fileNameField

public static java.lang.String fileNameField

See Also:

Constant Field Values

readEndCutSiteRemnantLength

protected static int readEndCutSiteRemnantLength

Constructor Detail

ConvertOldFastqToModernFormatPlugin

public ConvertOldFastqToModernFormatPlugin()

ConvertOldFastqToModernFormatPlugin

public ConvertOldFastqToModernFormatPlugin(java.awt.Frame parentFrame,
                                           boolean isInteractive)

Method Detail

postProcessParameters

protected void postProcessParameters()

processData

public DataSet processData(DataSet input)

determineKeyFormat

public static boolean determineKeyFormat(java.lang.String keyFile)

getLaneAnnotatedTaxaList

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

readOldTaxaAnnotationFile

public static TaxaList readOldTaxaAnnotationFile(java.lang.String fileName,
                                                 java.util.Map<java.lang.String,java.lang.String> filters,
                                                 boolean mergeSameNames)

readOldFormatKeyFile

public static java.util.ArrayList<net.maizegenetics.taxa.Taxon> readOldFormatKeyFile(java.lang.String fileName,
                                                                                     java.util.Map<java.lang.String,java.lang.String> filters,
                                                                                     boolean mergeSameNames)

processFastQFile

public static void processFastQFile(java.nio.file.Path keyPath,
                                    java.nio.file.Path fastQPath,
                                    java.lang.String enzymeName,
                                    TaxaList masterTaxaList,
                                    java.util.Map<net.maizegenetics.taxa.Taxon,net.maizegenetics.util.Tuple> taxaFileMap,
                                    java.lang.String outputDir,
                                    java.lang.String projectName,
                                    boolean keyFormatIsNew)

readAllFastQBlock

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

getIcon

public javax.swing.ImageIcon getIcon()

getButtonName

public java.lang.String getButtonName()

getToolTipText

public java.lang.String getToolTipText()

inputFile

public java.lang.String inputFile()

Input file or directory containing FASTQ files in text or gzipped text. NOTE: Directory will be searched recursively

Returns:

org.jetbrains.dokka.NodeRenderContent@3b2964bd: Input Directory

inputFile

public ConvertOldFastqToModernFormatPlugin inputFile(java.lang.String value)

Set Input Directory. Input file or directory containing FASTQ files in text or gzipped text. NOTE: Directory will be searched recursively

Parameters:

value - Input Directory

Returns:

org.jetbrains.dokka.NodeRenderContent@20bfa167: this plugin

keyFile

public java.lang.String keyFile()

Key file listing barcodes distinguishing the samples

Returns:

org.jetbrains.dokka.NodeRenderContent@6a4b1571: Key File

keyFile

public ConvertOldFastqToModernFormatPlugin keyFile(java.lang.String value)

Set Key File. Key file listing barcodes distinguishing the samples

Parameters:

value - Key File

Returns:

org.jetbrains.dokka.NodeRenderContent@3fcd21d5: this plugin

projectName

public java.lang.String projectName()

Name for this project. Project name becomes part of the newly created fastq file name

Returns:

org.jetbrains.dokka.NodeRenderContent@4fb1a61d: Project File

projectName

public ConvertOldFastqToModernFormatPlugin projectName(java.lang.String value)

Set Project File. Name for this project. Project name becomes part of the newly created fastq file name

Parameters:

value - Project File

Returns:

org.jetbrains.dokka.NodeRenderContent@12d88215: this plugin

outputDir

public java.lang.String outputDir()

Output directory where new fastQ files will be written

Returns:

org.jetbrains.dokka.NodeRenderContent@200aeda2: Output Directory

outputDir

public ConvertOldFastqToModernFormatPlugin outputDir(java.lang.String value)

Set Output Directory. Output directory where new fastQ files will be written

Parameters:

value - Output Directory

Returns:

org.jetbrains.dokka.NodeRenderContent@769fb3ff: this plugin

enzyme

public java.lang.String enzyme()

Enzyme used to create the GBS library

Returns:

org.jetbrains.dokka.NodeRenderContent@34dc627f: Enzyme

enzyme

public ConvertOldFastqToModernFormatPlugin enzyme(java.lang.String value)

Set Enzyme. Enzyme used to create the GBS library

Parameters:

value - Enzyme

Returns:

org.jetbrains.dokka.NodeRenderContent@624286db: this plugin