net.maizegenetics.analysis.gbs

Class QseqToTagCountPlugin

AbstractPlugin

net.maizegenetics.analysis.gbs.QseqToTagCountPlugin

All Implemented Interfaces:

Plugin, PluginListener, ProgressListener

public class QseqToTagCountPlugin
extends AbstractPlugin

Derives a tagCount list for each qseq file in the qseqDirectory. 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

QseqToTagCountPlugin

public QseqToTagCountPlugin()

QseqToTagCountPlugin

public QseqToTagCountPlugin(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 keyFileS,
                             java.lang.String enzyme,
                             java.lang.String qseqDirectory,
                             java.lang.String outputDir,
                             int maxGoodReads,
                             int minCount)

Derives a tagCount list for each qseq file in the qseqDirectory.

Parameters:

keyFileS - A key file (a sample key by barcode, with a plate map included).

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

qseqDirectory - Directory containing the qseq files (will be recursively searched).

outputDir - Directory to which the tagCounts files (one per qseq file) will be written.

maxGoodReads - The maximum number of barcoded reads expected in a qseq file

minCount - The minimum number of occurrences of a tag in a qseq file for it to be included in the output tagCounts file

getIcon

public javax.swing.ImageIcon getIcon()

getButtonName

public java.lang.String getButtonName()

getToolTipText

public java.lang.String getToolTipText()