net.maizegenetics.analysis.gbs

Class KmerToTagCountPlugin

AbstractPlugin

net.maizegenetics.analysis.gbs.KmerToTagCountPlugin

All Implemented Interfaces:

Plugin, PluginListener, ProgressListener

public class KmerToTagCountPlugin
extends AbstractPlugin

Derives a tagCount list for each fastq file in the input directory. Keeps only good reads having a barcode and a cut site and no N's in the useful part of the sequence. Trims off the barcodes and truncates sequences that (1) have a second cut site, or (2) read into the common adapter.

Constructor Detail

KmerToTagCountPlugin

public KmerToTagCountPlugin()

KmerToTagCountPlugin

public KmerToTagCountPlugin(java.awt.Frame parentFrame)

Method Detail

performFunction

public DataSet performFunction(DataSet input)

setParameters

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

countTags

public static void countTags(java.lang.String myInput,
                             java.lang.String myOutput,
                             int maxGoodReads,
                             int minCount,
                             int maxCount)

Derives a tagCount list for each fastq file in the fastqDirectory.

Parameters:

myInput - input file

myOutput - outputfile.

maxGoodReads - The maximum number of reads expected in a fastq file

minCount - The maximum number of kmer depth

getIcon

public javax.swing.ImageIcon getIcon()

getButtonName

public java.lang.String getButtonName()

getToolTipText

public java.lang.String getToolTipText()