All Implemented Interfaces:

java.lang.Runnable , net.maizegenetics.plugindef.Plugin , net.maizegenetics.plugindef.PluginListener , net.maizegenetics.util.ProgressListener
```
public class CreateIntervalsFileFromGffPlugin
extends AbstractPlugin
                    
```
This class creates the interval files needed for running GATK haplotype caller, and the csv files needed for loading reference sequence into the database. Two sets of files are created: one set has coordinates based just on the ref gene coordinates. The other is gene coordinates plus user-specified flanking regions Algorithm: 1. read gff file, grab gene coordinates 2. For each Chromosome: merge genes that overlap, toss genes that are embedded within another gene Store list as mergedGeneList. 3. Using the mergedGeneList in 3, create 2nd per-chrom coordinate lists that includes flanking regions 4. Write files: interval format (chrom:start-end): a. mergedGeneList; b. mergedGEneList with flanking csv format (chr,anchorstart,anchorend,geneStart,geneEnd,geneName) a. mergedGeneList; b. mergedGEneList with flanking debug files: List of merged, list of embedded files written for informational purposes NOTE: the csv files contain the name of all genes contained in an anchor. This data is not stored in the DB. IT is included because the biologists have at times asked for it and this is a good place for it to be stored and retrieved. INPUT: 1. refFile: String: path to reference genome. needed to find size of chromosomes for adding flanking regions to last chrom entry. 2. geneFile: String: path to single file containing all chrom gene data in GFF format; or path to directory containing per-chrom files with gene data in GFF format. These data files must consist of GFF gene data alone, not the full gff. 3. outputBase: String: directory, including trailing "/", where output files will be written. 4. numFlanking: int: number of flanking bps to add on each end of the anchors. OUTPUT: 1. intervals file based on gene coordinates. 2. intervals file based on gene coordinates + numflanking bps 3. csv file based on gene coordinates 4. csv file based on gene coordinates + numflanking bps

Nested Class Summary

Nested Classes
Modifier and Type	Class	Description

Field Summary

Fields
Modifier and Type	Field	Description
`public final static String`	`DEFAULT_CITATION`
`public final static String`	`POSITION_LIST_NONE`
`public final static String`	`TAXA_LIST_NONE`

Constructor Summary

Constructors
Constructor	Description
`CreateIntervalsFileFromGffPlugin()`
`CreateIntervalsFileFromGffPlugin(Frame parentFrame)`
`CreateIntervalsFileFromGffPlugin(Frame parentFrame, boolean isInteractive)`

Enum Constant Summary

Enum Constants
Enum Constant	Description

Method Summary

Modifier and Type	Method	Description
`DataSet`	`processData(DataSet input)`
`String`	`runPlugin(DataSet input)`	Convenience method to run plugin with one return object.
`ImageIcon`	`getIcon()`
`String`	`getButtonName()`
`String`	`getToolTipText()`
`String`	`refFile()`	Fasta file containing reference genome
`CreateIntervalsFileFromGffPlugin`	`refFile(String value)`	Set Ref Genome File.
`String`	`geneFile()`	Tab delimited .
`CreateIntervalsFileFromGffPlugin`	`geneFile(String value)`	Set Gene File.
`String`	`outputDir()`	Directory where output files will be written
`CreateIntervalsFileFromGffPlugin`	`outputDir(String value)`	Set Output Directory.
`Integer`	`numFlanking()`	Number of flanking basepairs to add at each end of the gene sequence
`CreateIntervalsFileFromGffPlugin`	`numFlanking(Integer value)`	Set Number of Flanking BPs.

Methods inherited from class net.maizegenetics.plugindef.AbstractPlugin
addListener, cancel, convert, dataSetReturned, getCitation, getInputs, getListeners, getMenu, getPanel, getParameter, getParentFrame, getUsage, getUsageHTML, hasListeners, isInteractive, isPluginParameter, performFunction, pluginDescription, pluginParameters, pluginUserManualURL, progress, receiveInput, reverseTrace, run, setConfigParameters, setParameter, setParameters, setParametersToDefault, setThreaded, trace, usageParameters, wasCancelled
Methods inherited from class net.maizegenetics.plugindef.Plugin
getPluginInstance, isPlugin
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - CreateIntervalsFileFromGffPlugin
```
CreateIntervalsFileFromGffPlugin()
```
  - CreateIntervalsFileFromGffPlugin
```
CreateIntervalsFileFromGffPlugin(Frame parentFrame)
```
  - CreateIntervalsFileFromGffPlugin
```
CreateIntervalsFileFromGffPlugin(Frame parentFrame, boolean isInteractive)
```
- Method Detail
  - processData
```
 DataSet processData(DataSet input)
```
  - runPlugin
```
 String runPlugin(DataSet input)
```
    Convenience method to run plugin with one return object.
  - getIcon
```
 ImageIcon getIcon()
```
  - getButtonName
```
 String getButtonName()
```
  - getToolTipText
```
 String getToolTipText()
```
  - refFile
```
 String refFile()
```
    Fasta file containing reference genome
  - refFile
```
 CreateIntervalsFileFromGffPlugin refFile(String value)
```
    Set Ref Genome File. Fasta file containing reference genome
    
    Parameters:
    
    value - Ref Genome File
  - geneFile
```
 String geneFile()
```
    Tab delimited .txt file containing gene-only GFF data from reference GFF file,
  - geneFile
```
 CreateIntervalsFileFromGffPlugin geneFile(String value)
```
    Set Gene File. Tab delimited .txt file containing gene-only GFF data from reference GFF file,
    
    Parameters:
    
    value - Gene File
  - outputDir
```
 String outputDir()
```
    Directory where output files will be written
  - outputDir
```
 CreateIntervalsFileFromGffPlugin outputDir(String value)
```
    Set Output Directory. Directory where output files will be written
    
    Parameters:
    
    value - Output Directory
  - numFlanking
```
 Integer numFlanking()
```
    Number of flanking basepairs to add at each end of the gene sequence
  - numFlanking
```
 CreateIntervalsFileFromGffPlugin numFlanking(Integer value)
```
    Set Number of Flanking BPs. Number of flanking basepairs to add at each end of the gene sequence
    
    Parameters:
    
    value - Number of Flanking BPs

Class CreateIntervalsFileFromGffPlugin

Nested Class Summary

Field Summary

Constructor Summary

Enum Constant Summary

Method Summary

Methods inherited from class net.maizegenetics.plugindef.AbstractPlugin

Methods inherited from class net.maizegenetics.plugindef.Plugin

Methods inherited from class java.lang.Object

Constructor Detail

CreateIntervalsFileFromGffPlugin

CreateIntervalsFileFromGffPlugin

CreateIntervalsFileFromGffPlugin

Method Detail

processData

runPlugin

getIcon

getButtonName

getToolTipText

refFile

refFile

geneFile

geneFile

outputDir

outputDir

numFlanking

numFlanking