net.maizegenetics.analysis.gbs.repgen

Class RepGenLoadSeqToDBPlugin

AbstractPlugin

net.maizegenetics.analysis.gbs.repgen.RepGenLoadSeqToDBPlugin

All Implemented Interfaces:

Plugin, PluginListener, ProgressListener

public class RepGenLoadSeqToDBPlugin
extends AbstractPlugin

Develops a discovery rGBS database based on a folder of sequencing files Keeps only good reads having 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

qualityScoreBase

protected static int qualityScoreBase

Constructor Detail

RepGenLoadSeqToDBPlugin

public RepGenLoadSeqToDBPlugin()

RepGenLoadSeqToDBPlugin

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

Method Detail

postProcessParameters

public void postProcessParameters()

processData

public DataSet processData(DataSet input)

setTagLenException

public void setTagLenException()

calculateTagAveQS

public static java.util.Map<net.maizegenetics.dna.tag.Tag,net.maizegenetics.util.Tuple> calculateTagAveQS(net.maizegenetics.analysis.gbs.repgen.RepGenLoadSeqToDBPlugin.TagCountQualityScoreMap tagCntQSMap,
                                                                                                          int qualityScoreBase)

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@408312d7: Input Directory

inputDirectory

public RepGenLoadSeqToDBPlugin 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@637f4796: this plugin

keyFile

public java.lang.String keyFile()

Key file listing barcodes distinguishing the samples

Returns:

org.jetbrains.dokka.NodeRenderContent@7a38f6a2: Key File

keyFile

public RepGenLoadSeqToDBPlugin keyFile(java.lang.String value)

Set Key File. Key file listing barcodes distinguishing the samples

Parameters:

value - Key File

Returns:

org.jetbrains.dokka.NodeRenderContent@25ae22c0: this plugin

kmerLength

public java.lang.Integer kmerLength()

Maximum Tag Length

Returns:

org.jetbrains.dokka.NodeRenderContent@7d638908: Maximum Tag Length

kmerLength

public RepGenLoadSeqToDBPlugin kmerLength(java.lang.Integer value)

Set Maximum Tag Length. Maximum Tag Length

Parameters:

value - Maximum Tag Length

Returns:

org.jetbrains.dokka.NodeRenderContent@643932c5: this plugin

minimumKmerLength

public java.lang.Integer minimumKmerLength()

Minimum Tag Length

Returns:

org.jetbrains.dokka.NodeRenderContent@59095506: Minimum Tag Length

minimumKmerLength

public RepGenLoadSeqToDBPlugin minimumKmerLength(java.lang.Integer value)

Set Minimum Tag Length. Minimum Tag Length

Parameters:

value - Minimum Tag Length

Returns:

org.jetbrains.dokka.NodeRenderContent@d65d4c5: this plugin

minKmerCount

public java.lang.Integer minKmerCount()

Minimum tag count

Returns:

org.jetbrains.dokka.NodeRenderContent@6c2f37a8: Min Tag Count

minKmerCount

public RepGenLoadSeqToDBPlugin minKmerCount(java.lang.Integer value)

Set Min Tag Count. Minimum tag count

Parameters:

value - Min Tag Count

Returns:

org.jetbrains.dokka.NodeRenderContent@412d8ff2: this plugin

minTaxa

public java.lang.Integer minTaxa()

Minimum taxa containing tag

Returns:

org.jetbrains.dokka.NodeRenderContent@521f53b4: Min Taxa Count

minTaxa

public RepGenLoadSeqToDBPlugin minTaxa(java.lang.Integer value)

Set Min Taxa Count. Minimum Taxa count

Parameters:

value - Min Taxa containing a tag

Returns:

org.jetbrains.dokka.NodeRenderContent@71ff66ce: this plugin

outputDatabaseFile

public java.lang.String outputDatabaseFile()

Output Database File

Returns:

org.jetbrains.dokka.NodeRenderContent@64788d2e: Output Database File

outputDatabaseFile

public RepGenLoadSeqToDBPlugin outputDatabaseFile(java.lang.String value)

Set Output Database File. Output Database File

Parameters:

value - Output Database File

Returns:

org.jetbrains.dokka.NodeRenderContent@4987cc4c: 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@61ada43b: Minimum quality score

minimumQualityScore

public RepGenLoadSeqToDBPlugin 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@6bee77d6: this plugin

maximumKmerNumber

public RepGenLoadSeqToDBPlugin maximumKmerNumber(java.lang.Integer value)

Set maximum number of kmers

Parameters:

value -

Returns:

org.jetbrains.dokka.NodeRenderContent@4b5f8678:

batchSize

public RepGenLoadSeqToDBPlugin batchSize(java.lang.Integer value)

Set number of Fastq files processed simultaneously

Parameters:

value -

Returns:

org.jetbrains.dokka.NodeRenderContent@3c4dc6f3:

getIcon

public javax.swing.ImageIcon getIcon()

getButtonName

public java.lang.String getButtonName()

getToolTipText

public java.lang.String getToolTipText()