net.maizegenetics.pangenome.hapcollapse

Class RunHapCollapsePipelinePlugin

java.lang.Object

net.maizegenetics.plugindef.AbstractPlugin

net.maizegenetics.pangenome.hapcollapse.RunHapCollapsePipelinePlugin

All Implemented Interfaces:

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

public class RunHapCollapsePipelinePlugin
extends net.maizegenetics.plugindef.AbstractPlugin

Simple plugin to run the full Haplotype Collapse plugin. Will do the following steps: Steps: 1. Loop through each reference range in the graph: 1.a Extract the HaplotypeNodes with the VariantContexts(We assume that the user has not pulled these yet for memory reasons) 1.b Merge all the VariantContext records for each BP of the reference range 1.c Export a GenotypeTable containing each bp 1.d Run HapCollapse Finding algorithm on this genotype table 2. For each VCF file exported, upload them to the DB as a consensus Created by zrm22 on 11/8/17.

Field Summary

Fields inherited from class net.maizegenetics.plugindef.AbstractPlugin

DEFAULT_CITATION, POSITION_LIST_NONE, TAXA_LIST_NONE

Constructor Summary

Constructors

Constructor and Description
RunHapCollapsePipelinePlugin(Frame parentFrame, boolean isInteractive)

Method Summary

Modifier and Type	Method and Description
FindHaplotypeClustersPlugin.CLUSTER_METHOD	clusterMethod() The method used to cluster taxa.
RunHapCollapsePipelinePlugin	clusterMethod(FindHaplotypeClustersPlugin.CLUSTER_METHOD value) Set Cluster Method.
String	collapseMethod() Name of the collapse method to be stored in the database
RunHapCollapsePipelinePlugin	collapseMethod(String value) Set Collapse Method.
String	collapseMethodDetails() Details for the collapse method to be stored in the database
RunHapCollapsePipelinePlugin	collapseMethodDetails(String value) Set Collapse Method Details.
String	consensusFastaOutputDir() Directory where you want to store the output fastas from the consensus process
RunHapCollapsePipelinePlugin	consensusFastaOutputDir(String value) Set Consensus Fasta Output Dir.
String	consensusVCFOutputDir() Directory where you want to store the output VCFs from the consensus process
RunHapCollapsePipelinePlugin	consensusVCFOutputDir(String value) Set Consensus VCF Output Dir.
String	dbConfigFile() File holding the DB config information
RunHapCollapsePipelinePlugin	dbConfigFile(String value) Set Db Config File.
String	getButtonName()
ImageIcon	getIcon()
String	getToolTipText()
FillIndelsIntoConsensus.INDEL_MERGE_RULE	mergeRule() The rule in which to resolve the conflicting Indels after consensus has been found.
RunHapCollapsePipelinePlugin	mergeRule(FillIndelsIntoConsensus.INDEL_MERGE_RULE value) Set Indel Merge Rule.
String	pluginDescription()
net.maizegenetics.plugindef.DataSet	processData(net.maizegenetics.plugindef.DataSet input)
String	reference() Input Reference Fasta
RunHapCollapsePipelinePlugin	reference(String value) Set Ref.
void	runCollapsePipeline(HaplotypeGraph graph, String referenceFasta) This method will loop through each reference range in the graph and will: 1.

Methods inherited from class net.maizegenetics.plugindef.AbstractPlugin

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

RunHapCollapsePipelinePlugin

public RunHapCollapsePipelinePlugin(Frame parentFrame,
                                    boolean isInteractive)

Method Detail

processData

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

Specified by:

processData in interface net.maizegenetics.plugindef.Plugin

Overrides:

processData in class net.maizegenetics.plugindef.AbstractPlugin

runCollapsePipeline

public void runCollapsePipeline(HaplotypeGraph graph,
                                String referenceFasta)

This method will loop through each reference range in the graph and will: 1. Merge all the gvcf records for a given haplotype method: 2. Cluster the haplotypes together into groups Then when done with all reference ranges, load the exported gvcfs and fastas to the db. This is the main function that processes each reference range in the graph

Parameters:

graph - haplotype graph

referenceFasta - reference fasta

getButtonName

public String getButtonName()

getToolTipText

public String getToolTipText()

pluginDescription

public String pluginDescription()

Specified by:

pluginDescription in interface net.maizegenetics.plugindef.Plugin

Overrides:

pluginDescription in class net.maizegenetics.plugindef.AbstractPlugin

getIcon

public ImageIcon getIcon()

reference

public String reference()

Input Reference Fasta

Returns:

Ref

reference

public RunHapCollapsePipelinePlugin reference(String value)

Set Ref. Input Reference Fasta

Parameters:

value - Ref

Returns:

this plugin

dbConfigFile

public String dbConfigFile()

File holding the DB config information

Returns:

Db Config File

dbConfigFile

public RunHapCollapsePipelinePlugin dbConfigFile(String value)

Set Db Config File. File holding the DB config information

Parameters:

value - Db Config File

Returns:

this plugin

consensusVCFOutputDir

public String consensusVCFOutputDir()

Directory where you want to store the output VCFs from the consensus process

Returns:

Consensus VCF Output Dir

consensusVCFOutputDir

public RunHapCollapsePipelinePlugin consensusVCFOutputDir(String value)

Set Consensus VCF Output Dir. Directory where you want to store the output VCFs from the consensus process

Parameters:

value - Consensus VCF Output Dir

Returns:

this plugin

consensusFastaOutputDir

public String consensusFastaOutputDir()

Directory where you want to store the output fastas from the consensus process

Returns:

Consensus Fasta Output Dir

consensusFastaOutputDir

public RunHapCollapsePipelinePlugin consensusFastaOutputDir(String value)

Set Consensus Fasta Output Dir. Directory where you want to store the output fastas from the consensus process

Parameters:

value - Consensus Fasta Output Dir

Returns:

this plugin

collapseMethod

public String collapseMethod()

Name of the collapse method to be stored in the database

Returns:

Collapse Method

collapseMethod

public RunHapCollapsePipelinePlugin collapseMethod(String value)

Set Collapse Method. Name of the collapse method to be stored in the database

Parameters:

value - Collapse Method

Returns:

this plugin

collapseMethodDetails

public String collapseMethodDetails()

Details for the collapse method to be stored in the database

Returns:

Collapse Method Details

collapseMethodDetails

public RunHapCollapsePipelinePlugin collapseMethodDetails(String value)

Set Collapse Method Details. Details for the collapse method to be stored in the database

Parameters:

value - Collapse Method Details

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 RunHapCollapsePipelinePlugin 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

mergeRule

public FillIndelsIntoConsensus.INDEL_MERGE_RULE mergeRule()

The rule in which to resolve the conflicting Indels after consensus has been found.

Returns:

Indel Merge Rule

mergeRule

public RunHapCollapsePipelinePlugin mergeRule(FillIndelsIntoConsensus.INDEL_MERGE_RULE value)

Set Indel Merge Rule. The rule in which to resolve the conflicting Indels after consensus has been found.

Parameters:

value - Indel Merge Rule

Returns:

this plugin