FastqToHapCountPlugin (net.maizegenetics:phg 0.0.1 API)

java.lang.Object
- net.maizegenetics.plugindef.AbstractPlugin
- - net.maizegenetics.pangenome.hapCalling.FastqToHapCountPlugin

All Implemented Interfaces:

Runnable, net.maizegenetics.plugindef.Plugin, net.maizegenetics.plugindef.PluginListener, net.maizegenetics.util.ProgressListener
```
public class FastqToHapCountPlugin
extends net.maizegenetics.plugindef.AbstractPlugin
```
Plugin to run the read counting method based on bwa mem alignment. Need to input the connection parameters for the database, the method name, the reference genome file (indexed), the read file and the number of allowable alignment mistakes to be counted (default = 0). This plugin requires a HaplotypeGraph. Chain the running of HaplotypeGraphBuilderPlugin and this plugin. The output from HaplotypeGraphBuilderPlugin will be input to FastqToHapCountPlugin. Example: /tassel-5-standalone/run_pipeline.pl -Xmx5g -debug -HaplotypeGraphBuilderPlugin -configFile $CONFIGFILE -onlyAnchors true -consensusMethod $CONSENSUS_METHOD -includeVariantContexts true -endPlugin -FastqToHapCountPlugin -taxon $TAXON_NAME -configFile $CONFIGFILE -haplotypeFile $HAPLOTYPE_FASTA -method $HAP_COUNT_METHOD -refFile $REFERENCE_FILE -rawReadFile ${FASTQ_DIR}/${file}.fastq -exportHaploFile ${FASTQ_HAP_COUNT_DIR}/${file}.txt Assumptions made by this software:

Author:

Ed Buckler, Lynn Johnson

Field Summary
- Fields inherited from class net.maizegenetics.plugindef.AbstractPlugin
  DEFAULT_CITATION, POSITION_LIST_NONE, TAXA_LIST_NONE

Constructor Summary

Constructors
Constructor and Description

FastqToHapCountPlugin(Frame parentFrame, boolean isInteractive)

Constructors
Constructor and Description
`FastqToHapCountPlugin(Frame parentFrame, boolean isInteractive)`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`String`	`configFile()` ConfigFile name
`FastqToHapCountPlugin`	`configFile(String value)` Set ConfigFile Name.
`String`	`debugTaxon()` Debug taxon
`FastqToHapCountPlugin`	`debugTaxon(String value)` Set Debug Taxon.
`String`	`exportHaplotypeFile()` Text file to store haplotype scoring
`FastqToHapCountPlugin`	`exportHaplotypeFile(String value)` Set Export Haplo File.
`void`	`generateMetrics(com.google.common.collect.Multiset<HaplotypeNode> perfectHitSet, com.google.common.collect.Multiset<HaplotypeNode> exlusionSet)`
`String`	`getButtonName()`
`ImageIcon`	`getIcon()`
`String`	`getToolTipText()`
`String`	`haplotypesGenomeFile()` Fasta file and associated BWA indices for haplotypes
`FastqToHapCountPlugin`	`haplotypesGenomeFile(String value)` Set Haplotype File.
`static boolean`	`isPerfectMatch(htsjdk.samtools.SAMRecord samRecord)`
`Boolean`	`loadDb()` Whether to populate the haplotype_counts table - often false when testing
`FastqToHapCountPlugin`	`loadDb(Boolean value)` Set LoadDb.
`String`	`method()` Name of method used to create hap counts, for the haplotype_counts table.
`FastqToHapCountPlugin`	`method(String value)` Set Method.
`Integer`	`numErrorAllowed()` Maximum allowable error in order to count the read mapping
`FastqToHapCountPlugin`	`numErrorAllowed(Integer value)` Set Allowed Error.
`String`	`pluginUserManualURL()`
`net.maizegenetics.plugindef.DataSet`	`processData(net.maizegenetics.plugindef.DataSet input)`
`String`	`readFile()` Raw Read file aligned to the reference
`FastqToHapCountPlugin`	`readFile(String value)` Set Raw Read File.
`String`	`refGenomeFile()` Fasta file and associated BWA indices for haplotypes
`FastqToHapCountPlugin`	`refGenomeFile(String value)` Set Haplotype File.
`com.google.common.collect.Multiset<HaplotypeNode>`	`runPlugin(net.maizegenetics.plugindef.DataSet input)` Convenience method to run plugin with one return object.
`String`	`taxon()` Taxon
`FastqToHapCountPlugin`	`taxon(String value)` Set Taxon.

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
  - FastqToHapCountPlugin
```
public FastqToHapCountPlugin(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
  - generateMetrics
```
public void generateMetrics(com.google.common.collect.Multiset<HaplotypeNode> perfectHitSet,
                            com.google.common.collect.Multiset<HaplotypeNode> exlusionSet)
```
  - isPerfectMatch
```
public static boolean isPerfectMatch(htsjdk.samtools.SAMRecord samRecord)
```
  - 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()
```
  - runPlugin
```
public com.google.common.collect.Multiset<HaplotypeNode> runPlugin(net.maizegenetics.plugindef.DataSet input)
```
    Convenience method to run plugin with one return object.
  - configFile
```
public String configFile()
```
    ConfigFile name
    
    Returns:
    
    ConfigFile Name
  - configFile
```
public FastqToHapCountPlugin configFile(String value)
```
    Set ConfigFile Name. ConfigFile name
    
    Parameters:
    
    value - ConfigFile Name
    
    Returns:
    
    this plugin
  - haplotypesGenomeFile
```
public String haplotypesGenomeFile()
```
    Fasta file and associated BWA indices for haplotypes
    
    Returns:
    
    Haplotype File
  - haplotypesGenomeFile
```
public FastqToHapCountPlugin haplotypesGenomeFile(String value)
```
    Set Haplotype File. Fasta file and associated BWA indices for haplotypes
    
    Parameters:
    
    value - Haplotype File
    
    Returns:
    
    this plugin
  - refGenomeFile
```
public String refGenomeFile()
```
    Fasta file and associated BWA indices for haplotypes
    
    Returns:
    
    Haplotype File
  - refGenomeFile
```
public FastqToHapCountPlugin refGenomeFile(String value)
```
    Set Haplotype File. Fasta file and associated BWA indices for haplotypes
    
    Parameters:
    
    value - Reference Genome File
    
    Returns:
    
    this plugin
  - readFile
```
public String readFile()
```
    Raw Read file aligned to the reference
    
    Returns:
    
    Raw Read File
  - readFile
```
public FastqToHapCountPlugin readFile(String value)
```
    Set Raw Read File. Raw Read file aligned to the reference
    
    Parameters:
    
    value - Raw Read File
    
    Returns:
    
    this plugin
  - numErrorAllowed
```
public Integer numErrorAllowed()
```
    Maximum allowable error in order to count the read mapping
    
    Returns:
    
    Allowed Error
  - numErrorAllowed
```
public FastqToHapCountPlugin numErrorAllowed(Integer value)
```
    Set Allowed Error. Maximum allowable error in order to count the read mapping
    
    Parameters:
    
    value - Allowed Error
    
    Returns:
    
    this plugin
  - exportHaplotypeFile
```
public String exportHaplotypeFile()
```
    Text file to store haplotype scoring
    
    Returns:
    
    Export Haplo File
  - exportHaplotypeFile
```
public FastqToHapCountPlugin exportHaplotypeFile(String value)
```
    Set Export Haplo File. Text file to store haplotype scoring
    
    Parameters:
    
    value - Export Haplo File
    
    Returns:
    
    this plugin
  - taxon
```
public String taxon()
```
    Taxon
    
    Returns:
    
    Taxon
  - taxon
```
public FastqToHapCountPlugin taxon(String value)
```
    Set Taxon. Set taxon name for laoding into genotypes table
    
    Parameters:
    
    value - Taxon
    
    Returns:
    
    this plugin
  - debugTaxon
```
public String debugTaxon()
```
    Debug taxon
    
    Returns:
    
    Debug Taxon
  - debugTaxon
```
public FastqToHapCountPlugin debugTaxon(String value)
```
    Set Debug Taxon. Debut taxon
    
    Parameters:
    
    value - Debug Taxon
    
    Returns:
    
    this plugin
  - method
```
public String method()
```
    Name of method used to create hap counts, for the haplotype_counts table.
    
    Returns:
    
    Method
  - method
```
public FastqToHapCountPlugin method(String value)
```
    Set Method. Name of method used to create hap counts, for the haplotype_counts table.
    
    Parameters:
    
    value - Method
    
    Returns:
    
    this plugin
  - loadDb
```
public Boolean loadDb()
```
    Whether to populate the haplotype_counts table - often false when testing
    
    Returns:
    
    LoadDb
  - loadDb
```
public FastqToHapCountPlugin loadDb(Boolean value)
```
    Set LoadDb. Whether to populate the haplotype_counts table - often false when testing
    
    Parameters:
    
    value - LoadDb
    
    Returns:
    
    this plugin

Class FastqToHapCountPlugin

Field Summary

Fields inherited from class net.maizegenetics.plugindef.AbstractPlugin

Constructor Summary

Method Summary

Methods inherited from class net.maizegenetics.plugindef.AbstractPlugin

Methods inherited from class java.lang.Object

Methods inherited from interface net.maizegenetics.plugindef.Plugin

Constructor Detail

FastqToHapCountPlugin

Method Detail

processData

generateMetrics

isPerfectMatch

pluginUserManualURL

getIcon

getButtonName

getToolTipText

runPlugin

configFile

configFile

haplotypesGenomeFile

haplotypesGenomeFile

refGenomeFile

refGenomeFile

readFile

readFile

numErrorAllowed

numErrorAllowed

exportHaplotypeFile

exportHaplotypeFile

taxon

taxon

debugTaxon

debugTaxon

method

method

loadDb

loadDb