net.maizegenetics.analysis.gbs

Class FastqToTagCountPlugin

AbstractPlugin

net.maizegenetics.analysis.gbs.FastqToTagCountPlugin

All Implemented Interfaces:

Plugin, PluginListener, ProgressListener

public class FastqToTagCountPlugin
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

FastqToTagCountPlugin

public FastqToTagCountPlugin()

FastqToTagCountPlugin

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

Method Detail

processData

public DataSet processData(DataSet input)

countTags

public static void countTags(java.lang.String keyFileS,
                             java.lang.String enzyme,
                             java.lang.String fastqDirectory,
                             java.lang.String outputDir,
                             int maxGoodReads,
                             int minCount)

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

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).

fastqDirectory - Directory containing the fastq files (will be recursively searched).

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

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

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

inputDir

public FastqToTagCountPlugin inputDir(java.lang.String value)

inputDir

public java.lang.String inputDir()

keyFile

public FastqToTagCountPlugin keyFile(java.lang.String value)

keyFile

public java.lang.String keyFile()

enzyme

public FastqToTagCountPlugin enzyme(java.lang.String value)

enzyme

public java.lang.String enzyme()

maxGoodReads

public FastqToTagCountPlugin maxGoodReads(java.lang.Integer value)

maxGoodReads

public java.lang.Integer maxGoodReads()

minTagCount

public FastqToTagCountPlugin minTagCount(java.lang.Integer value)

minTagCount

public java.lang.Integer minTagCount()

outputDir

public FastqToTagCountPlugin outputDir(java.lang.String value)

outputDir

public java.lang.String outputDir()

getIcon

public javax.swing.ImageIcon getIcon()

getButtonName

public java.lang.String getButtonName()

getToolTipText

public java.lang.String getToolTipText()