net.maizegenetics.analysis.gbs

Class QseqToPETagCountPlugin

AbstractPlugin

net.maizegenetics.analysis.gbs.QseqToPETagCountPlugin

All Implemented Interfaces:

Plugin, PluginListener, ProgressListener

public class QseqToPETagCountPlugin
extends AbstractPlugin

Derives a PETagCount list for a pair of Qseq files. The forward and backward tags are ordered during processing Keeps only good reads having a barcode and a cut site and no N's in the useful part of the sequence. For the barcoded end, trims off the barcodes and truncates sequences that (1) have a second cut site, or (2) read into the common adapter. For the unbarcoded end, trims off the barcodes and truncates sequences that (1) have a second cut site, or (2) read into the barcode adapter.

Constructor Detail

QseqToPETagCountPlugin

public QseqToPETagCountPlugin()

QseqToPETagCountPlugin

public QseqToPETagCountPlugin(java.awt.Frame parentFrame)

Method Detail

performFunction

public DataSet performFunction(DataSet input)

setParameters

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

countTags

public void countTags(java.lang.String keyFileS,
                      java.lang.String enzyme,
                      java.lang.String inputFileSWithBarcode,
                      java.lang.String inputFileSWithoutBarcode,
                      int minCount,
                      int tagLengthInLong)

Derives a PETagCount list for a pair of Qseq files.

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).

inputFileSWithBarcode - Filename of input Qseq file with barcode

inputFileSWithoutBarcode - Filename of input Qseq file without barcode

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

tagLengthInLong - Tag Length in Long primitive data type, the default is 8 (8*32=256 bp)

getIcon

public javax.swing.ImageIcon getIcon()

getButtonName

public java.lang.String getButtonName()

getToolTipText

public java.lang.String getToolTipText()