ProductionSNPCallerPluginV2 (net.maizegenetics:tassel 5.2.49 API)

java.lang.Object
- net.maizegenetics.plugindef.AbstractPlugin
- - net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2

All Implemented Interfaces:

Runnable, Plugin, PluginListener, ProgressListener
```
public class ProductionSNPCallerPluginV2
extends AbstractPlugin
```
This plugin converts all of the fastq (and/or qseq) files in the input folder and keyfile to genotypes and adds these to a genotype file in HDF5 format. We refer to this step as the "Production Pipeline". The output format is either HDF5 or VCF genotypes with allelic depth stored. Output file type is determined by presence of the ".h5" suffix. SNP calling is quantitative with the option of using either the Glaubitz/Buckler binomial method (pHet/pErr > 1 = het) (=default), or the Stacks method. Merging of samples with the same LibraryPrepID is handled by GenotypeTableBuilder.addTaxon(), with the genotypes re-called based upon the new depths. Therefore, if you want to keep adding genotypes to the same target HDF5 file in subsequent runs, use the -ko (keep open) option so that the output GenotypeTableBuilder will be mutable, using closeUnfinished() rather than build(). If the target output is HDF5, and that GenotypeTable file doesn't exist, it will be created. Each taxon in the output file is named "ShortName:LibraryPrepID" and is annotated with "Flowcell_Lanes" (=source seq data for current genotype). Requires a database with variants added from a previous "Discovery Pipeline" run. References to "tag" are being replaced by references to "kmer" as the pipeline is really a kmer alignment process. TODO add the Stacks likelihood method to BasicGenotypeMergeRule

Author:

Ed Buckler, Jeff Glaubitz

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

Constructor Summary

Constructors
Constructor and Description

ProductionSNPCallerPluginV2()

ProductionSNPCallerPluginV2(Frame parentFrame, boolean isInteractive)

Constructors
Constructor and Description
`ProductionSNPCallerPluginV2()`
`ProductionSNPCallerPluginV2(Frame parentFrame, boolean isInteractive)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`Double`	`aveSeqErrorRate()` Average sequencing error rate per base (used to decide between heterozygous and homozygous calls)
`ProductionSNPCallerPluginV2`	`aveSeqErrorRate(Double value)` Set Ave Seq Error Rate.
`Integer`	`batchSize()` Batch size for processing fastq files
`ProductionSNPCallerPluginV2`	`batchSize(Integer value)` Set number of Fastq files processed simultaneously
`Boolean`	`depthToOutput()` Output depth: write depths to the output hdf5 genotypes file
`ProductionSNPCallerPluginV2`	`depthToOutput(Boolean value)` User sets true or false, indicating if they do or do not want depth information written to the HDF5 file.
`String`	`enzyme()` Enzyme used to create the GBS library
`ProductionSNPCallerPluginV2`	`enzyme(String value)` Set Enzyme.
`String`	`getButtonName()` Button name for this plugin to be used in buttons, etc.
`ImageIcon`	`getIcon()` Icon for this plugin to be used in buttons, etc.
`String`	`getToolTipText()` Tool Tip Text for this plugin
`String`	`inputDirectory()` Input directory containing fastq AND/OR qseq files.
`ProductionSNPCallerPluginV2`	`inputDirectory(String value)` Set Input Directory.
`String`	`inputGBSDatabase()` Input Database file if using SQLite
`ProductionSNPCallerPluginV2`	`inputGBSDatabase(String value)` Set Input GBS Database.
`Boolean`	`keepGenotypesOpen()` Keep hdf5 genotypes open for future runs that add more taxa or more depth
`ProductionSNPCallerPluginV2`	`keepGenotypesOpen(Boolean value)` Set Keep Genotypes Open.
`String`	`keyFile()` Key file listing barcodes distinguishing the samples
`ProductionSNPCallerPluginV2`	`keyFile(String value)` Set Key File.
`Integer`	`kmerLength()` Maximum Tag Length
`ProductionSNPCallerPluginV2`	`kmerLength(Integer value)` Set Maximum Tag Length: User should set this value equivalent to what was used in GBSSeqToTagDBPlugin for maximum tag length when creating the database.
`Integer`	`maxDivergence()` Maximum divergence (edit distance) between new read and previously mapped read (Default: 0 = perfect matches only)
`ProductionSNPCallerPluginV2`	`maxDivergence(Integer value)` Set Max Divergence.
`Integer`	`minimumQualityScore()` Minimum quality score within the barcode and read length to be accepted
`ProductionSNPCallerPluginV2`	`minimumQualityScore(Integer value)` Set Minimum quality score.
`String`	`outputGenotypesFile()` Output (target) genotypes file to add new genotypes to (new file created if it doesn't exist)
`ProductionSNPCallerPluginV2`	`outputGenotypesFile(String value)` Set Output Genotypes File.
`Double`	`positionQualityScore()` Minimum Position Quality Score
`ProductionSNPCallerPluginV2`	`positionQualityScore(Double value)` Set Minimum quality score for position: This value is used to pull SNPs out of the snpposition table.
`void`	`postProcessParameters()`
`DataSet`	`processData(DataSet input)` For the new Generic Plugin Parameter design, performFunction() will automatically call this.
`TagData`	`runPlugin(DataSet input)` Convenience method to run plugin with one return object.
`void`	`setTagLenException()`

Methods inherited from class net.maizegenetics.plugindef.AbstractPlugin
addListener, cancel, convert, dataSetReturned, getCitation, getInputs, getMenu, getPanel, getParameter, getParameter, getParentFrame, getUsage, getUsageHTML, isInteractive, performFunction, pluginDescription, 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
  - ProductionSNPCallerPluginV2
```
public ProductionSNPCallerPluginV2()
```
  - ProductionSNPCallerPluginV2
```
public ProductionSNPCallerPluginV2(Frame parentFrame,
                                   boolean isInteractive)
```
- Method Detail
  - postProcessParameters
```
public void postProcessParameters()
```
  - processData
```
public DataSet processData(DataSet input)
```
    Description copied from interface: Plugin
    
    For the new Generic Plugin Parameter design, performFunction() will automatically call this. Therefore, coders of Plugins should override this instead of performFunction().
    
    Specified by:
    
    processData in interface Plugin
    
    Overrides:
    
    processData in class AbstractPlugin
    
    Parameters:
    
    input - input
    
    Returns:
    
    resulting data set or null.
  - setTagLenException
```
public void setTagLenException()
```
  - getIcon
```
public ImageIcon getIcon()
```
    Description copied from interface: Plugin
    
    Icon for this plugin to be used in buttons, etc.
    
    Returns:
    
    ImageIcon
  - getButtonName
```
public String getButtonName()
```
    Description copied from interface: Plugin
    
    Button name for this plugin to be used in buttons, etc.
    
    Returns:
    
    String
  - getToolTipText
```
public String getToolTipText()
```
    Description copied from interface: Plugin
    
    Tool Tip Text for this plugin
    
    Returns:
    
    String
  - runPlugin
```
public TagData runPlugin(DataSet input)
```
    Convenience method to run plugin with one return object.
  - inputDirectory
```
public String inputDirectory()
```
    Input directory containing fastq AND/OR qseq files.
    
    Returns:
    
    Input Directory
  - inputDirectory
```
public ProductionSNPCallerPluginV2 inputDirectory(String value)
```
    Set Input Directory. Input directory containing fastq AND/OR qseq files.
    
    Parameters:
    
    value - Input Directory
    
    Returns:
    
    this plugin
  - keyFile
```
public String keyFile()
```
    Key file listing barcodes distinguishing the samples
    
    Returns:
    
    Key File
  - keyFile
```
public ProductionSNPCallerPluginV2 keyFile(String value)
```
    Set Key File. Key file listing barcodes distinguishing the samples
    
    Parameters:
    
    value - Key File
    
    Returns:
    
    this plugin
  - enzyme
```
public String enzyme()
```
    Enzyme used to create the GBS library
    
    Returns:
    
    Enzyme
  - enzyme
```
public ProductionSNPCallerPluginV2 enzyme(String value)
```
    Set Enzyme. Enzyme used to create the GBS library
    
    Parameters:
    
    value - Enzyme
    
    Returns:
    
    this plugin
  - inputGBSDatabase
```
public String inputGBSDatabase()
```
    Input Database file if using SQLite
    
    Returns:
    
    Input GBS Database
  - inputGBSDatabase
```
public ProductionSNPCallerPluginV2 inputGBSDatabase(String value)
```
    Set Input GBS Database. Input Database file if using SQLite
    
    Parameters:
    
    value - Input GBS Database
    
    Returns:
    
    this plugin
  - outputGenotypesFile
```
public String outputGenotypesFile()
```
    Output (target) genotypes file to add new genotypes to (new file created if it doesn't exist)
    
    Returns:
    
    Output file Genotypes File
  - outputGenotypesFile
```
public ProductionSNPCallerPluginV2 outputGenotypesFile(String value)
```
    Set Output Genotypes File. Output (target) genotypes file to add new genotypes to (new file created if it doesn't exist)
    
    Parameters:
    
    value - Output Genotypes File
    
    Returns:
    
    this plugin
  - aveSeqErrorRate
```
public Double aveSeqErrorRate()
```
    Average sequencing error rate per base (used to decide between heterozygous and homozygous calls)
    
    Returns:
    
    Ave Seq Error Rate
  - aveSeqErrorRate
```
public ProductionSNPCallerPluginV2 aveSeqErrorRate(Double value)
```
    Set Ave Seq Error Rate. Average sequencing error rate per base (used to decide between heterozygous and homozygous calls)
    
    Parameters:
    
    value - Ave Seq Error Rate
    
    Returns:
    
    this plugin
  - maxDivergence
```
public Integer maxDivergence()
```
    Maximum divergence (edit distance) between new read and previously mapped read (Default: 0 = perfect matches only)
    
    Returns:
    
    Max Divergence
  - maxDivergence
```
public ProductionSNPCallerPluginV2 maxDivergence(Integer value)
```
    Set Max Divergence. Maximum divergence (edit distance) between new read and previously mapped read (Default: 0 = perfect matches only)
    
    Parameters:
    
    value - Max Divergence
    
    Returns:
    
    this plugin
  - keepGenotypesOpen
```
public Boolean keepGenotypesOpen()
```
    Keep hdf5 genotypes open for future runs that add more taxa or more depth
    
    Returns:
    
    Keep Genotypes Open
  - keepGenotypesOpen
```
public ProductionSNPCallerPluginV2 keepGenotypesOpen(Boolean value)
```
    Set Keep Genotypes Open. Keep hdf5 genotypes open for future runs that add more taxa or more depth
    
    Parameters:
    
    value - Keep Genotypes Open
    
    Returns:
    
    this plugin
  - depthToOutput
```
public Boolean depthToOutput()
```
    Output depth: write depths to the output hdf5 genotypes file
    
    Returns:
    
    Depth to Output - true or false
  - depthToOutput
```
public ProductionSNPCallerPluginV2 depthToOutput(Boolean value)
```
    User sets true or false, indicating if they do or do not want depth information written to the HDF5 file.
    
    Parameters:
    
    value - Write depth to output file
    
    Returns:
    
    this plugin
  - kmerLength
```
public Integer kmerLength()
```
    Maximum Tag Length
    
    Returns:
    
    Maximum Tag Length
  - kmerLength
```
public ProductionSNPCallerPluginV2 kmerLength(Integer value)
```
    Set Maximum Tag Length: User should set this value equivalent to what was used in GBSSeqToTagDBPlugin for maximum tag length when creating the database. If the two values are not equal inconsistent results may occur.
    
    Parameters:
    
    value - Maximum Tag Length
    
    Returns:
    
    this plugin
  - positionQualityScore
```
public Double positionQualityScore()
```
    Minimum Position Quality Score
    
    Returns:
    
    Minimum position quality score
  - positionQualityScore
```
public ProductionSNPCallerPluginV2 positionQualityScore(Double value)
```
    Set Minimum quality score for position: This value is used to pull SNPs out of the snpposition table. Only snps with quality scores meeting or exceeding the specified value will be processed.
    
    Parameters:
    
    value - Minimum position quality score
    
    Returns:
    
    this plugin
  - batchSize
```
public Integer batchSize()
```
    Batch size for processing fastq files
    
    Returns:
    
    batchSize
  - batchSize
```
public ProductionSNPCallerPluginV2 batchSize(Integer value)
```
    Set number of Fastq files processed simultaneously
    
    Parameters:
    
    value -
    
    Returns:
  - minimumQualityScore
```
public Integer minimumQualityScore()
```
    Minimum quality score within the barcode and read length to be accepted
    
    Returns:
    
    Minimum quality score
  - minimumQualityScore
```
public ProductionSNPCallerPluginV2 minimumQualityScore(Integer value)
```
    Set Minimum quality score. Minimum quality score within the barcode and read length to be accepted
    
    Parameters:
    
    value - Minimum quality score
    
    Returns:
    
    this plugin

Class ProductionSNPCallerPluginV2

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

ProductionSNPCallerPluginV2

ProductionSNPCallerPluginV2

Method Detail

postProcessParameters

processData

setTagLenException

getIcon

getButtonName

getToolTipText

runPlugin

inputDirectory

inputDirectory

keyFile

keyFile

enzyme

enzyme

inputGBSDatabase

inputGBSDatabase

outputGenotypesFile

outputGenotypesFile

aveSeqErrorRate

aveSeqErrorRate

maxDivergence

maxDivergence

keepGenotypesOpen

keepGenotypesOpen

depthToOutput

depthToOutput

kmerLength

kmerLength

positionQualityScore

positionQualityScore

batchSize

batchSize

minimumQualityScore

minimumQualityScore