net.maizegenetics.analysis.gbs.v2

Class TagExportToFastqPlugin

AbstractPlugin

net.maizegenetics.analysis.gbs.v2.TagExportToFastqPlugin

All Implemented Interfaces:

Plugin, PluginListener, ProgressListener

public class TagExportToFastqPlugin
extends AbstractPlugin

Converts a TagCounts binary (*.cnt) file (presumably a master tag list) to a fastq file that can be used as input for BWA or bowtie2 (and possibly additional aligners). The same function can be performed with MergeMultipleTagCountPlugin using the -t option and a single Master Tag List file in the input directory, but having a separate plugin to do this reduces confusion and eliminates the risk of merging the master tag list back on itself.

Constructor Detail

TagExportToFastqPlugin

public TagExportToFastqPlugin()

TagExportToFastqPlugin

public TagExportToFastqPlugin(java.awt.Frame parentFrame)

TagExportToFastqPlugin

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

Method Detail

processData

public DataSet processData(DataSet input)

getToolTipText

public java.lang.String getToolTipText()

getIcon

public javax.swing.ImageIcon getIcon()

getButtonName

public java.lang.String getButtonName()

runPlugin

public java.lang.String runPlugin(DataSet input)

Convenience method to run plugin with one return object.

inputDB

public java.lang.String inputDB()

Input database file with tags and taxa distribution

Returns:

org.jetbrains.dokka.NodeRenderContent@7a640a27: Input DB

inputDB

public TagExportToFastqPlugin inputDB(java.lang.String value)

Set Input DB. Input database file with tags and taxa distribution

Parameters:

value - Input DB

Returns:

org.jetbrains.dokka.NodeRenderContent@71ce29d0: this plugin

outputFile

public java.lang.String outputFile()

Output fastq file to use as input for BWA or bowtie2

Returns:

org.jetbrains.dokka.NodeRenderContent@73db3e39: Output File

outputFile

public TagExportToFastqPlugin outputFile(java.lang.String value)

Set Output File. Output fastq file to use as input for BWA or bowtie2

Parameters:

value - Output File

Returns:

org.jetbrains.dokka.NodeRenderContent@6415832e: this plugin

minCount

public java.lang.Integer minCount()

Minimum count of reads for a tag to be output

Returns:

org.jetbrains.dokka.NodeRenderContent@3efa88b9: Min Count

minCount

public TagExportToFastqPlugin minCount(java.lang.Integer value)

Set Min Count. Minimum count of reads for a tag to be output

Parameters:

value - Min Count

Returns:

org.jetbrains.dokka.NodeRenderContent@3e7ab61f: this plugin