net.maizegenetics.analysis.gbs.v2

Class GBSSeqToTagDBPlugin

java.lang.Object

net.maizegenetics.plugindef.AbstractPlugin

net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin

All Implemented Interfaces:

Runnable, Plugin, PluginListener, ProgressListener

public class GBSSeqToTagDBPlugin
extends AbstractPlugin

Develops a discovery TBT file from a set of GBS sequence files. 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. Originally the reference throughout was to "tag". This is being changed to "kmer" as the pipeline is a kmer alignment process.

Author:

Ed Buckler

Field Summary

Fields inherited from class net.maizegenetics.plugindef.AbstractPlugin

DEFAULT_CITATION, POSITION_LIST_NONE, TAXA_LIST_NONE

Constructor Summary

Constructors

Constructor and Description
GBSSeqToTagDBPlugin()
GBSSeqToTagDBPlugin(Frame parentFrame, boolean isInteractive)

Method Summary

Modifier and Type	Method and Description
GBSSeqToTagDBPlugin	batchSize(Integer value) Set number of Fastq files processed simultaneously
Boolean	deleteOldData() Delete exisiting DB
GBSSeqToTagDBPlugin	deleteOldData(Boolean value) Set Delete old data flag.
String	enzyme() Enzyme used to create the GBS library, if it differs from the one listed in the key file
GBSSeqToTagDBPlugin	enzyme(String value) Set Enzyme.
String	getButtonName() Button name for this plugin to be used in buttons, etc.
ImageIcon	getIcon() Icon for this plugin to be used in buttons, etc.
String	getToolTipText() Tool Tip Text for this plugin
String	inputDirectory() Input directory containing FASTQ files in text or gzipped text.
GBSSeqToTagDBPlugin	inputDirectory(String value) Set Input Directory.
String	keyFile() Key file listing barcodes distinguishing the samples
GBSSeqToTagDBPlugin	keyFile(String value) Set Key File.
Integer	kmerLength() Maximum Tag Length
GBSSeqToTagDBPlugin	kmerLength(Integer value) Set Maximum Tag Length.
GBSSeqToTagDBPlugin	maximumKmerNumber(Integer value) Set maximum number of kmers
Integer	minimumKmerLength() Minimum Tag Length
GBSSeqToTagDBPlugin	minimumKmerLength(Integer value) Set Minimum Tag Length.
Integer	minimumQualityScore() Minimum quality score within the barcode and read length to be accepted
GBSSeqToTagDBPlugin	minimumQualityScore(Integer value) Set Minimum quality score.
Integer	minKmerCount() Minimum tag count
GBSSeqToTagDBPlugin	minKmerCount(Integer value) Set Min Tag Count.
String	outputDatabaseFile() Output Database File
GBSSeqToTagDBPlugin	outputDatabaseFile(String value) Set Output Database File.
void	postProcessParameters()
DataSet	processData(DataSet input) For the new Generic Plugin Parameter design, performFunction() will automatically call this.
void	setTagLenException()

Methods inherited from class net.maizegenetics.plugindef.AbstractPlugin

addListener, cancel, convert, dataSetReturned, getCitation, getInputs, getMenu, getPanel, getParameter, getParameter, getParentFrame, getUsage, getUsageHTML, isInteractive, performFunction, pluginDescription, pluginUserManualURL, progress, progress, receiveInput, reverseTrace, run, setConfigParameters, setParameter, setParameter, setParameter, setParameters, setParametersToDefault, setThreaded, trace, wasCancelled

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface net.maizegenetics.plugindef.Plugin

getPluginInstance, getPluginInstance, isPlugin

Constructor Detail

GBSSeqToTagDBPlugin

public GBSSeqToTagDBPlugin()

GBSSeqToTagDBPlugin

public GBSSeqToTagDBPlugin(Frame parentFrame,
                           boolean isInteractive)

Method Detail

postProcessParameters

public void postProcessParameters()

processData

public DataSet processData(DataSet input)

Description copied from interface: Plugin

For the new Generic Plugin Parameter design, performFunction() will automatically call this. Therefore, coders of Plugins should override this instead of performFunction().

Specified by:

processData in interface Plugin

Overrides:

processData in class AbstractPlugin

Parameters:

input - input

Returns:

resulting data set or null.

setTagLenException

public void setTagLenException()

inputDirectory

public String inputDirectory()

Input directory containing FASTQ files in text or gzipped text. NOTE: Directory will be searched recursively and should be written WITHOUT a slash after its name.

Returns:

Input Directory

inputDirectory

public GBSSeqToTagDBPlugin inputDirectory(String value)

Set Input Directory. Input directory containing FASTQ files in text or gzipped text. NOTE: Directory will be searched recursively and should be written WITHOUT a slash after its name.

Parameters:

value - Input Directory

Returns:

this plugin

keyFile

public String keyFile()

Key file listing barcodes distinguishing the samples

Returns:

Key File

keyFile

public GBSSeqToTagDBPlugin keyFile(String value)

Set Key File. Key file listing barcodes distinguishing the samples

Parameters:

value - Key File

Returns:

this plugin

enzyme

public String enzyme()

Enzyme used to create the GBS library, if it differs from the one listed in the key file

Returns:

Enzyme

enzyme

public GBSSeqToTagDBPlugin enzyme(String value)

Set Enzyme. Enzyme used to create the GBS library, if it differs from the one listed in the key file

Parameters:

value - Enzyme

Returns:

this plugin

kmerLength

public Integer kmerLength()

Maximum Tag Length

Returns:

Maximum Tag Length

kmerLength

public GBSSeqToTagDBPlugin kmerLength(Integer value)

Set Maximum Tag Length. Maximum Tag Length

Parameters:

value - Maximum Tag Length

Returns:

this plugin

minimumKmerLength

public Integer minimumKmerLength()

Minimum Tag Length

Returns:

Minimum Tag Length

minimumKmerLength

public GBSSeqToTagDBPlugin minimumKmerLength(Integer value)

Set Minimum Tag Length. Minimum Tag Length

Parameters:

value - Minimum Tag Length

Returns:

this plugin

minKmerCount

public Integer minKmerCount()

Minimum tag count

Returns:

Min Tag Count

minKmerCount

public GBSSeqToTagDBPlugin minKmerCount(Integer value)

Set Min Tag Count. Minimum tag count

Parameters:

value - Min Tag Count

Returns:

this plugin

outputDatabaseFile

public String outputDatabaseFile()

Output Database File

Returns:

Output Database File

outputDatabaseFile

public GBSSeqToTagDBPlugin outputDatabaseFile(String value)

Set Output Database File. Output Database File

Parameters:

value - Output Database File

Returns:

this plugin

minimumQualityScore

public Integer minimumQualityScore()

Minimum quality score within the barcode and read length to be accepted

Returns:

Minimum quality score

minimumQualityScore

public GBSSeqToTagDBPlugin minimumQualityScore(Integer value)

Set Minimum quality score. Minimum quality score within the barcode and read length to be accepted

Parameters:

value - Minimum quality score

Returns:

this plugin

maximumKmerNumber

public GBSSeqToTagDBPlugin maximumKmerNumber(Integer value)

Set maximum number of kmers

Parameters:

value -

Returns:

batchSize

public GBSSeqToTagDBPlugin batchSize(Integer value)

Set number of Fastq files processed simultaneously

Parameters:

value -

Returns:

deleteOldData

public Boolean deleteOldData()

Delete exisiting DB

Returns:

deleteOldData

deleteOldData

public GBSSeqToTagDBPlugin deleteOldData(Boolean value)

Set Delete old data flag. True indicates we want the db tables cleared

Parameters:

value - true/false - whether to delete data

Returns:

this plugin

getIcon

public ImageIcon getIcon()

Description copied from interface: Plugin

Icon for this plugin to be used in buttons, etc.

Returns:

ImageIcon

getButtonName

public String getButtonName()

Description copied from interface: Plugin

Button name for this plugin to be used in buttons, etc.

Returns:

String

getToolTipText

public String getToolTipText()

Description copied from interface: Plugin

Tool Tip Text for this plugin

Returns:

String