net.maizegenetics.pangenome.hapcollapse

Class FindHaplotypeClustersPlugin

java.lang.Object

net.maizegenetics.plugindef.AbstractPlugin

net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin

All Implemented Interfaces:

Runnable, net.maizegenetics.plugindef.Plugin, net.maizegenetics.plugindef.PluginListener, net.maizegenetics.util.ProgressListener

public class FindHaplotypeClustersPlugin
extends net.maizegenetics.plugindef.AbstractPlugin

Processes a multi-haplotype VCF file from one region, and identifies haplotype clusters to be collapsed in future steps into a consensus haplotype.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	FindHaplotypeClustersPlugin.CLUSTER_METHOD

Field Summary

Fields inherited from class net.maizegenetics.plugindef.AbstractPlugin

DEFAULT_CITATION, POSITION_LIST_NONE, TAXA_LIST_NONE

Constructor Summary

Constructors

Constructor and Description
FindHaplotypeClustersPlugin(Frame parentFrame, boolean isInteractive)

Method Summary

Modifier and Type	Method and Description
FindHaplotypeClustersPlugin.CLUSTER_METHOD	clusterMethod() The method used to cluster taxa.
FindHaplotypeClustersPlugin	clusterMethod(FindHaplotypeClustersPlugin.CLUSTER_METHOD value) Set Cluster Method.
String	getButtonName()
ImageIcon	getIcon()
String	getToolTipText()
String	intervalFile() Interval File used to create the VCF file
FindHaplotypeClustersPlugin	intervalFile(String value) Set Interval File.
Double	maxDistFromFounder() Maximum genetic divergence from founder haplotype to cluster sequences
FindHaplotypeClustersPlugin	maxDistFromFounder(Double value) Set Max divergence from founder.
Double	maxError() Maximum error allowed to create a homozygous call.
FindHaplotypeClustersPlugin	maxError(Double value) Set Maximum error.
Integer	minSiteForComp() The minimum number of sites present in two taxa to compare genetic distance to evaluate similarity for clustering
FindHaplotypeClustersPlugin	minSiteForComp(Integer value) Set Min sites to cluster.
Double	minTaxaCoverage() The minimum proportion of sites present in a taxa to go into clustering
FindHaplotypeClustersPlugin	minTaxaCoverage(Double value) Set Min taxa coverage.
Integer	minTaxaInGroup() Minimum number of taxa to generate a haplotype
FindHaplotypeClustersPlugin	minTaxaInGroup(Integer value) Set Min taxa to generate a haplotype.
String	outFile() Output file directory name, or new directory path; Directory will be created, if doesn't exist.
FindHaplotypeClustersPlugin	outFile(String value) Set Donor dir/file basename.
String	pluginUserManualURL()
net.maizegenetics.plugindef.DataSet	processData(net.maizegenetics.plugindef.DataSet input) Method to create a consensus haplotype GenotypeTable object Method will now just create and return the GenotypeTable instead of doing additional work to create the fasta sequence.
net.maizegenetics.dna.map.GenomeSequence	referenceSequence() Reference Genome Sequence to use to extract the fasta
FindHaplotypeClustersPlugin	referenceSequence(net.maizegenetics.dna.map.GenomeSequence value) Set Reference Genome Sequence.
Boolean	replaceNsWithMajor() Boolean flag to replace any N calls with a Major Homozygous Diploid Value
FindHaplotypeClustersPlugin	replaceNsWithMajor(Boolean value) Set Replace N calls with Major Allele.
Double	seqErrorRate() Error rate used to merge alleles call hets versus homozygous
FindHaplotypeClustersPlugin	seqErrorRate(Double value) Set Sequencing error rate.
String	sequenceOutDir() Output Directory For storing the sequence files
FindHaplotypeClustersPlugin	sequenceOutDir(String value) Set Sequence Output Directory.
Boolean	useDepthForCalls() Boolean flag to have the clustering algorithm use depth information instead of allele counts
FindHaplotypeClustersPlugin	useDepthForCalls(Boolean value) Set Use Depth For Calls.
String	vcfDir() Input genotypes to generate haplotypes from.
FindHaplotypeClustersPlugin	vcfDir(String value) Set Target directory.

Methods inherited from class net.maizegenetics.plugindef.AbstractPlugin

addListener, cancel, convert, dataSetReturned, getCitation, getInputs, getMenu, getPanel, getParameter, getParameter, getParentFrame, getUsage, getUsageHTML, isInteractive, performFunction, pluginDescription, 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

FindHaplotypeClustersPlugin

public FindHaplotypeClustersPlugin(Frame parentFrame,
                                   boolean isInteractive)

Method Detail

processData

public net.maizegenetics.plugindef.DataSet processData(net.maizegenetics.plugindef.DataSet input)

Method to create a consensus haplotype GenotypeTable object Method will now just create and return the GenotypeTable instead of doing additional work to create the fasta sequence.

Specified by:

processData in interface net.maizegenetics.plugindef.Plugin

Overrides:

processData in class net.maizegenetics.plugindef.AbstractPlugin

Parameters:

input -

Returns:

pluginUserManualURL

public String pluginUserManualURL()

Specified by:

pluginUserManualURL in interface net.maizegenetics.plugindef.Plugin

Overrides:

pluginUserManualURL in class net.maizegenetics.plugindef.AbstractPlugin

getIcon

public ImageIcon getIcon()

getButtonName

public String getButtonName()

getToolTipText

public String getToolTipText()

vcfDir

public String vcfDir()

Input genotypes to generate haplotypes from. Usually best to use all available samples from a species. Accepts all file types supported by TASSEL5.

Returns:

Target directory

vcfDir

public FindHaplotypeClustersPlugin vcfDir(String value)

Set Target directory. Input genotypes to generate haplotypes from. Usually best to use all available samples from a species. Accepts all file types supported by TASSEL5.

Parameters:

value - Target directory

Returns:

this plugin

outFile

public String outFile()

Output file directory name, or new directory path; Directory will be created, if doesn't exist. Outfiles will be placed in the directory

Returns:

Donor dir/file basename

outFile

public FindHaplotypeClustersPlugin outFile(String value)

Set Donor dir/file basename. Output file directory name, or new directory path; Directory will be created, if doesn't exist. Outfiles will be placed in the directory

Parameters:

value - Donor dir/file basename

Returns:

this plugin

maxDistFromFounder

public Double maxDistFromFounder()

Maximum genetic divergence from founder haplotype to cluster sequences

Returns:

Max divergence from founder

maxDistFromFounder

public FindHaplotypeClustersPlugin maxDistFromFounder(Double value)

Set Max divergence from founder. Maximum genetic divergence from founder haplotype to cluster sequences

Parameters:

value - Max divergence from founder

Returns:

this plugin

seqErrorRate

public Double seqErrorRate()

Error rate used to merge alleles call hets versus homozygous

Returns:

Sequencing error rate

seqErrorRate

public FindHaplotypeClustersPlugin seqErrorRate(Double value)

Set Sequencing error rate. Error rate used to merge alleles call hets versus homozygous

Parameters:

value - Sequencing error rate

Returns:

this plugin

minSiteForComp

public Integer minSiteForComp()

The minimum number of sites present in two taxa to compare genetic distance to evaluate similarity for clustering

Returns:

Min sites to cluster

minSiteForComp

public FindHaplotypeClustersPlugin minSiteForComp(Integer value)

Set Min sites to cluster. The minimum number of sites present in two taxa to compare genetic distance to evaluate similarity for clustering

Parameters:

value - Min sites to cluster

Returns:

this plugin

minTaxaCoverage

public Double minTaxaCoverage()

The minimum proportion of sites present in a taxa to go into clustering

Returns:

Min taxa coverage

minTaxaCoverage

public FindHaplotypeClustersPlugin minTaxaCoverage(Double value)

Set Min taxa coverage. The minimum proportion of sites present in a taxa to go into clustering

Parameters:

value - Min taxa coverage

Returns:

this plugin

minTaxaInGroup

public Integer minTaxaInGroup()

Minimum number of taxa to generate a haplotype

Returns:

Min taxa to generate a haplotype

minTaxaInGroup

public FindHaplotypeClustersPlugin minTaxaInGroup(Integer value)

Set Min taxa to generate a haplotype. Minimum number of taxa to generate a haplotype

Parameters:

value - Min taxa to generate a haplotype

Returns:

this plugin

referenceSequence

public net.maizegenetics.dna.map.GenomeSequence referenceSequence()

Reference Genome Sequence to use to extract the fasta

Returns:

Reference Genome Sequence

referenceSequence

public FindHaplotypeClustersPlugin referenceSequence(net.maizegenetics.dna.map.GenomeSequence value)

Set Reference Genome Sequence. Reference Genome Sequence to use to extract the fasta

Parameters:

value - Reference Genome Sequence

Returns:

this plugin

sequenceOutDir

public String sequenceOutDir()

Output Directory For storing the sequence files

Returns:

Sequence Output Directory

sequenceOutDir

public FindHaplotypeClustersPlugin sequenceOutDir(String value)

Set Sequence Output Directory. Output Directory For storing the sequence files

Parameters:

value - Sequence Output Directory

Returns:

this plugin

intervalFile

public String intervalFile()

Interval File used to create the VCF file

Returns:

Interval File

intervalFile

public FindHaplotypeClustersPlugin intervalFile(String value)

Set Interval File. Interval File used to create the VCF file

Parameters:

value - Interval File

Returns:

this plugin

clusterMethod

public FindHaplotypeClustersPlugin.CLUSTER_METHOD clusterMethod()

The method used to cluster taxa. Coverage seeds the first cluster with the highest coverage taxon. UPGMA builds a UPGMA tree then cuts it at maxDistance.

Returns:

Cluster Method

clusterMethod

public FindHaplotypeClustersPlugin clusterMethod(FindHaplotypeClustersPlugin.CLUSTER_METHOD value)

Set Cluster Method. The method used to cluster taxa. Coverage seeds the first cluster with the highest coverage taxon. UPGMA builds a UPGMA tree then cuts it at maxDistance.

Parameters:

value - Cluster Method

Returns:

this plugin

maxError

public Double maxError()

Maximum error allowed to create a homozygous call. If the error rate is above this value N or Major allele will be exported for that site

Returns:

Maximum error

maxError

public FindHaplotypeClustersPlugin maxError(Double value)

Set Maximum error. Maximum error allowed to create a homozygous call. If the error rate is above this value N or Major allele will be exported for that site

Parameters:

value - Maximum error

Returns:

this plugin

replaceNsWithMajor

public Boolean replaceNsWithMajor()

Boolean flag to replace any N calls with a Major Homozygous Diploid Value

Returns:

Replace N calls with Major Allele

replaceNsWithMajor

public FindHaplotypeClustersPlugin replaceNsWithMajor(Boolean value)

Set Replace N calls with Major Allele. Boolean flag to replace any N calls with a Major Homozygous Diploid Value

Parameters:

value - Replace N calls with Major Allele

Returns:

this plugin

useDepthForCalls

public Boolean useDepthForCalls()

Boolean flag to have the clustering algorithm use depth information instead of allele counts

Returns:

Use Depth For Calls

useDepthForCalls

public FindHaplotypeClustersPlugin useDepthForCalls(Boolean value)

Set Use Depth For Calls. Boolean flag to have the clustering algorithm use depth information instead of allele counts

Parameters:

value - Use Depth For Calls

Returns:

this plugin