net.maizegenetics.analysis.gbs

Class FastqToTBTPlugin

AbstractPlugin

net.maizegenetics.analysis.gbs.FastqToTBTPlugin

All Implemented Interfaces:

Plugin, PluginListener, ProgressListener

public class FastqToTBTPlugin
extends AbstractPlugin

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

Constructor Detail

FastqToTBTPlugin

public FastqToTBTPlugin()

FastqToTBTPlugin

public FastqToTBTPlugin(java.awt.Frame parentFrame)

Method Detail

performFunction

public DataSet performFunction(DataSet input)

setParameters

public void setParameters(java.lang.String[] args)

matchTagsToTaxa

public static void matchTagsToTaxa(java.lang.String[] fastqFileS,
                                   java.lang.String keyFileS,
                                   java.lang.String enzyme,
                                   Tags theMasterTags,
                                   java.lang.String outputDir,
                                   int minCount,
                                   boolean useTBTByte,
                                   boolean useTBTShort)

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

outputDir - String containing the path of the output directory to contain tags-by-taxa files

minCount - The minimum number of times a tag must show up in a fastq file before it is included in the corresponding TBT file

getIcon

public javax.swing.ImageIcon getIcon()

getButtonName

public java.lang.String getButtonName()

getToolTipText

public java.lang.String getToolTipText()