net.maizegenetics.analysis.gbs

Class SeqToTBTHDF5Plugin

AbstractPlugin

net.maizegenetics.analysis.gbs.SeqToTBTHDF5Plugin

All Implemented Interfaces:

Plugin, PluginListener, ProgressListener

public class SeqToTBTHDF5Plugin
extends AbstractPlugin

This pipeline converts a series of fastq or qseq files to a single TagsByTaxa HDF5 file. It requires a list of existing tags (Tags object), which may come from a TagCounts file or TOPM file.

Constructor Detail

SeqToTBTHDF5Plugin

public SeqToTBTHDF5Plugin()

SeqToTBTHDF5Plugin

public SeqToTBTHDF5Plugin(java.awt.Frame parentFrame,
                          boolean isInteractive)

Method Detail

processData

public DataSet processData(DataSet input)

postProcessParameters

public void postProcessParameters()

matchTagsToTaxa

public void matchTagsToTaxa(java.lang.String[] fastqFileS,
                            java.lang.String keyFileS,
                            java.lang.String enzyme,
                            Tags theMasterTags,
                            java.lang.String outputTBT,
                            java.lang.String outputLog)

Uses an existing Tags object to create one TagsByTaxa file for each fastq file in the input directory. Output TBT files written to the outputDir, using fastq file names with extension changed to .tbt.bin (or .tbt.txt)

Parameters:

fastqFileS - Array of fastq file names (Illumina-created files with raw read sequence, quality score, machine name, etc.)

keyFileS - A key file (list of taxa by barcode, lane & flow cell, including plate maps)

enzyme - The enzyme used to make the library (currently ApeKI or PstI)

theMasterTags - A Tags object: list of tags to be included in the final TBT

getIcon

public javax.swing.ImageIcon getIcon()

getButtonName

public java.lang.String getButtonName()

getToolTipText

public java.lang.String getToolTipText()

inputDirectory

public java.lang.String inputDirectory()

Input directory containing .fastq files

Returns:

org.jetbrains.dokka.NodeRenderContent@515274e3: Input Directory

inputDirectory

public SeqToTBTHDF5Plugin inputDirectory(java.lang.String value)

Set Input Directory. Input directory containing .fastq files

Parameters:

value - Input Directory

Returns:

org.jetbrains.dokka.NodeRenderContent@f3d9b3f: this plugin

keyFile

public java.lang.String keyFile()

Barcode key file

Returns:

org.jetbrains.dokka.NodeRenderContent@5337741a: Key File

keyFile

public SeqToTBTHDF5Plugin keyFile(java.lang.String value)

Set Key File. Barcode key file

Parameters:

value - Key File

Returns:

org.jetbrains.dokka.NodeRenderContent@7936c9e7: this plugin

enzyme

public java.lang.String enzyme()

Enzyme used to create the GBS library, if it differs from the one listed in the key file.

Returns:

org.jetbrains.dokka.NodeRenderContent@3b014f4e: Enzyme

enzyme

public SeqToTBTHDF5Plugin enzyme(java.lang.String value)

Set Enzyme. Enzyme used to create the GBS library, if it differs from the one listed in the key file.

Parameters:

value - Enzyme

Returns:

org.jetbrains.dokka.NodeRenderContent@5886cf72: this plugin

outputFile

public java.lang.String outputFile()

Output HDF5 file

Returns:

org.jetbrains.dokka.NodeRenderContent@3079f7dc: Output File

outputFile

public SeqToTBTHDF5Plugin outputFile(java.lang.String value)

Set Output File. Output HDF5 file

Parameters:

value - Output File

Returns:

org.jetbrains.dokka.NodeRenderContent@7f4f79c5: this plugin

maxGoodReads

public java.lang.Integer maxGoodReads()

Max good reads per lane.

Returns:

org.jetbrains.dokka.NodeRenderContent@4e05325d: Max Good Reads

maxGoodReads

public SeqToTBTHDF5Plugin maxGoodReads(java.lang.Integer value)

Set Max Good Reads. Max good reads per lane.

Parameters:

value - Max Good Reads

Returns:

org.jetbrains.dokka.NodeRenderContent@209699b0: this plugin

logFile

public java.lang.String logFile()

Output log file

Returns:

org.jetbrains.dokka.NodeRenderContent@5fae4d69: Log File

logFile

public SeqToTBTHDF5Plugin logFile(java.lang.String value)

Set Log File. Output log file

Parameters:

value - Log File

Returns:

org.jetbrains.dokka.NodeRenderContent@5b2b8608: this plugin

tagCountFile

public java.lang.String tagCountFile()

Tag count file. (Only -t or -m allowed)

Returns:

org.jetbrains.dokka.NodeRenderContent@3cdbd0ea: Tag Count File

tagCountFile

public SeqToTBTHDF5Plugin tagCountFile(java.lang.String value)

Set Tag Count File. Tag count file. (Only -t or -m allowed)

Parameters:

value - Tag Count File

Returns:

org.jetbrains.dokka.NodeRenderContent@281485d8: this plugin

physicalMapFile

public java.lang.String physicalMapFile()

Physical map file containing alignments. (Only -t or -m allowed)

Returns:

org.jetbrains.dokka.NodeRenderContent@57c40b6: Physical Map File

physicalMapFile

public SeqToTBTHDF5Plugin physicalMapFile(java.lang.String value)

Set Physical Map File. Physical map file containing alignments. (Only -t or -m allowed)

Parameters:

value - Physical Map File

Returns:

org.jetbrains.dokka.NodeRenderContent@2e08dd7: this plugin