net.maizegenetics.analysis.gbs.v2

Class GBSSeqToTagDBPlugin

AbstractPlugin

net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin

All Implemented Interfaces:

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.

Field Detail

readEndCutSiteRemnantLength

protected static int readEndCutSiteRemnantLength

Constructor Detail

GBSSeqToTagDBPlugin

public GBSSeqToTagDBPlugin()

GBSSeqToTagDBPlugin

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

Method Detail

postProcessParameters

public void postProcessParameters()

processData

public DataSet processData(DataSet input)

setTagLenException

public void setTagLenException()

inputDirectory

public java.lang.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:

org.jetbrains.dokka.NodeRenderContent@3332d2f5: Input Directory

inputDirectory

public GBSSeqToTagDBPlugin inputDirectory(java.lang.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:

org.jetbrains.dokka.NodeRenderContent@5ddd13f7: this plugin

keyFile

public java.lang.String keyFile()

Key file listing barcodes distinguishing the samples

Returns:

org.jetbrains.dokka.NodeRenderContent@b7d33df: Key File

keyFile

public GBSSeqToTagDBPlugin keyFile(java.lang.String value)

Set Key File. Key file listing barcodes distinguishing the samples

Parameters:

value - Key File

Returns:

org.jetbrains.dokka.NodeRenderContent@547a8e91: this plugin

enzyme

public java.lang.String enzyme()

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

Returns:

org.jetbrains.dokka.NodeRenderContent@717a4b91: Enzyme

enzyme

public GBSSeqToTagDBPlugin enzyme(java.lang.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:

org.jetbrains.dokka.NodeRenderContent@440dace2: this plugin

kmerLength

public java.lang.Integer kmerLength()

Maximum Tag Length

Returns:

org.jetbrains.dokka.NodeRenderContent@260c8c77: Maximum Tag Length

kmerLength

public GBSSeqToTagDBPlugin kmerLength(java.lang.Integer value)

Set Maximum Tag Length. Maximum Tag Length

Parameters:

value - Maximum Tag Length

Returns:

org.jetbrains.dokka.NodeRenderContent@26029021: this plugin

minimumKmerLength

public java.lang.Integer minimumKmerLength()

Minimum Tag Length

Returns:

org.jetbrains.dokka.NodeRenderContent@58761b3: Minimum Tag Length

minimumKmerLength

public GBSSeqToTagDBPlugin minimumKmerLength(java.lang.Integer value)

Set Minimum Tag Length. Minimum Tag Length

Parameters:

value - Minimum Tag Length

Returns:

org.jetbrains.dokka.NodeRenderContent@2cc4b75d: this plugin

minKmerCount

public java.lang.Integer minKmerCount()

Minimum tag count

Returns:

org.jetbrains.dokka.NodeRenderContent@6e69e986: Min Tag Count

minKmerCount

public GBSSeqToTagDBPlugin minKmerCount(java.lang.Integer value)

Set Min Tag Count. Minimum tag count

Parameters:

value - Min Tag Count

Returns:

org.jetbrains.dokka.NodeRenderContent@5c58eff2: this plugin

outputDatabaseFile

public java.lang.String outputDatabaseFile()

Output Database File

Returns:

org.jetbrains.dokka.NodeRenderContent@62ec9733: Output Database File

outputDatabaseFile

public GBSSeqToTagDBPlugin outputDatabaseFile(java.lang.String value)

Set Output Database File. Output Database File

Parameters:

value - Output Database File

Returns:

org.jetbrains.dokka.NodeRenderContent@6b9bba6c: this plugin

minimumQualityScore

public java.lang.Integer minimumQualityScore()

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

Returns:

org.jetbrains.dokka.NodeRenderContent@4a1f4b40: Minimum quality score

minimumQualityScore

public GBSSeqToTagDBPlugin minimumQualityScore(java.lang.Integer value)

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

Parameters:

value - Minimum quality score

Returns:

org.jetbrains.dokka.NodeRenderContent@51a30a8e: this plugin

maximumKmerNumber

public GBSSeqToTagDBPlugin maximumKmerNumber(java.lang.Integer value)

Set maximum number of kmers

Parameters:

value -

Returns:

org.jetbrains.dokka.NodeRenderContent@57f05a86:

batchSize

public GBSSeqToTagDBPlugin batchSize(java.lang.Integer value)

Set number of Fastq files processed simultaneously

Parameters:

value -

Returns:

org.jetbrains.dokka.NodeRenderContent@610ec2ce:

deleteOldData

public java.lang.Boolean deleteOldData()

Delete exisiting DB

Returns:

org.jetbrains.dokka.NodeRenderContent@517bd0e4: deleteOldData

deleteOldData

public GBSSeqToTagDBPlugin deleteOldData(java.lang.Boolean value)

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

Parameters:

value - true/false - whether to delete data

Returns:

org.jetbrains.dokka.NodeRenderContent@18c5473f: this plugin

getIcon

public javax.swing.ImageIcon getIcon()

getButtonName

public java.lang.String getButtonName()

getToolTipText

public java.lang.String getToolTipText()