net.maizegenetics.analysis.gbs.v2

Class SAMToGBSdbPlugin

AbstractPlugin

net.maizegenetics.analysis.gbs.v2.SAMToGBSdbPlugin

All Implemented Interfaces:

Plugin, PluginListener, ProgressListener

public class SAMToGBSdbPlugin
extends AbstractPlugin

Reads SAM file formats to determine the potential positions of Tags against the reference genome.

Constructor Detail

SAMToGBSdbPlugin

public SAMToGBSdbPlugin()

SAMToGBSdbPlugin

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

Method Detail

processData

public DataSet processData(DataSet input)

mappingApproach

public SAMToGBSdbPlugin mappingApproach(java.lang.String value)

Set Mapper (one of 'Bowtie2', 'BWA', or 'bwaMem').

Parameters:

value - Mapper type

Returns:

org.jetbrains.dokka.NodeRenderContent@295df765: this plugin

mappingApproach

public java.lang.String mappingApproach()

Get Mapper (one of 'Bowtie2', 'BWA', or 'bwaMem').

Returns:

org.jetbrains.dokka.NodeRenderContent@6541bbb5: String for mapper type

runPlugin

public TagData runPlugin(DataSet input)

Convenience method to run plugin with one return object.

sAMInputFile

public java.lang.String sAMInputFile()

Name of input file in SAM text format

Returns:

org.jetbrains.dokka.NodeRenderContent@3d8f08e5: SAM Input File

sAMInputFile

public SAMToGBSdbPlugin sAMInputFile(java.lang.String value)

Set SAM Input File. Name of input file in SAM text format

Parameters:

value - SAM Input File

Returns:

org.jetbrains.dokka.NodeRenderContent@525663b4: this plugin

gBSDBFile

public java.lang.String gBSDBFile()

Name of output file (e.g. GBSv2.db)

Returns:

org.jetbrains.dokka.NodeRenderContent@14f65044: GBS DB File

gBSDBFile

public SAMToGBSdbPlugin gBSDBFile(java.lang.String value)

Set GBS DB File. Name of output file (e.g. GBSv2.db)

Parameters:

value - GBS DB File

Returns:

org.jetbrains.dokka.NodeRenderContent@7c82dd7c: this plugin

minAlignProportion

public java.lang.Double minAlignProportion()

Minimum proportion of sequence that must align to store the SAM entry

Returns:

org.jetbrains.dokka.NodeRenderContent@390f2a29: SAM Min Align Proportion

minAlignProportion

public SAMToGBSdbPlugin minAlignProportion(java.lang.Double value)

Set SAM Min Align Proportion. Minimum proportion of sequence that must align to store the SAM entry

Parameters:

value - SAM Min Align Proportion

Returns:

org.jetbrains.dokka.NodeRenderContent@58a5b57f: this plugin

minAlignLength

public java.lang.Integer minAlignLength()

Minimum length of bps aligning to store the SAM entry

Returns:

org.jetbrains.dokka.NodeRenderContent@7e77ba5f: SAM Min Align Length

minAlignLength

public SAMToGBSdbPlugin minAlignLength(java.lang.Integer value)

Set SAM Min Align Length. Minimum length of bps aligning to store the SAM entry

Parameters:

value - SAM Min Align Length

Returns:

org.jetbrains.dokka.NodeRenderContent@14f4f1d0: this plugin

minMAPQ

public java.lang.Integer minMAPQ()

Minimum value of MAPQ to store the SAM entry

Returns:

org.jetbrains.dokka.NodeRenderContent@546acf05: SAM minimum MAPQ value

minMAPQ

public SAMToGBSdbPlugin minMAPQ(java.lang.Integer value)

Set SAM minimum MAPQ value. Minimum value of MAPQ to store the SAM entry

Parameters:

value - SAM minimum MAPQ value

Returns:

org.jetbrains.dokka.NodeRenderContent@211196ba: this plugin

deleteOldData

public java.lang.Boolean deleteOldData()

Delete exisiting Alignment data from DB

Returns:

org.jetbrains.dokka.NodeRenderContent@62f76585: deleteOldData

deleteOldData

public SAMToGBSdbPlugin 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@513e727a: this plugin

getIcon

public javax.swing.ImageIcon getIcon()

getButtonName

public java.lang.String getButtonName()

getToolTipText

public java.lang.String getToolTipText()