RepGenAlignerPlugin (net.maizegenetics:tassel 5.2.49 API)

java.lang.Object
- net.maizegenetics.plugindef.AbstractPlugin
- - net.maizegenetics.analysis.gbs.repgen.RepGenAlignerPlugin

All Implemented Interfaces:

Runnable, Plugin, PluginListener, ProgressListener
```
public class RepGenAlignerPlugin
extends AbstractPlugin
```
This plugin takes an existing repGen db, grabs the tags whose depth meets that specified in the minCount parameter, makes kmer seeds from these tags. Window for kmer seeds is default 20. The ref genome is walked with a sliding window of 1. Reference tags are created based on peaks within clusters where kmer seeds align. The kmerLen field should match the length of the kmers stored as tags during the RepGenLoadSeqToDBPlugin step. The default is 150. The refKmerLen() should minimally be the length of the db kmer tags, but can be longer. Our defaults are 150 for kmer tags, and twice this length (300) for the refKmerLen. There are 2 count parameters: minTagCount specifies the minimum depth of a tag for it to be used when creating seed kmers. minHitCount specifies the number of "hits" that must occur within a sliding window (window size = refKmerLen) for the window to remain part of a cluser. When sliding, if the hit count drops below the minhitCount threshold, the cluster ends. A new cluster does not begin until the hit count is back up to threshold. See createRefTagsForAlignment() and storeRefTagPositions() for specifics. This plugin creates and stores the reference tags in the refTag table in the database. Both the tagMapping and the physicalMapPosition table will we populated with the reference tag information. Once the tables have been populated with the reference information, Smith Waterman is run to align all the nonreference tags in the db against each other; each non-reference tag against the reference tags; finally each refTag against all other refTags. ALignment data is stored in the tagAlignments table. Smith Waterman from SourceForge neobio project is used to determine alignment score. Settings for match rewards, mismatch penalty and gap penalty may be changed by user via plugin parameters.

Author:

lcj34

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

Constructor Summary

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

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`Integer`	`gap_penalty()` Parameter sent to Smith Waterman aligner for use in calculating penalty when when a gap is identified.
`RepGenAlignerPlugin`	`gap_penalty(Integer value)` Set Gap Penalty Amount.
`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`	`inputDB()` Input database file with tags and taxa distribution
`RepGenAlignerPlugin`	`inputDB(String value)` Set Input DB.
`Integer`	`kmerLen()` Length of kmers as tag sequences in the db
`RepGenAlignerPlugin`	`kmerLen(Integer value)` Set Kmer length.
`static void`	`main(String[] args)`
`Integer`	`match_reward()` Parameter sent to Smith Waterman aligner for use in calculating reward when base pairs match.
`RepGenAlignerPlugin`	`match_reward(Integer value)` Set Match Reward Amount.
`Integer`	`minHitCount()` Minimum count of hits in a cluster for a reference tag to be created for this cluster
`RepGenAlignerPlugin`	`minHitCount(Integer value)` Set Min Count.
`Integer`	`minTagCount()` Minimum count of reads for a tag to be output
`RepGenAlignerPlugin`	`minTagCount(Integer value)` Set Min Count.
`Integer`	`mismatch_penalty()` Parameter sent to Smith Waterman aligner for use in calculating penalty when base pairs are mis-matched.
`RepGenAlignerPlugin`	`mismatch_penalty(Integer value)` Set Mismatch Penalty Amount.
`void`	`postProcessParameters()`
`DataSet`	`processData(DataSet input)` For the new Generic Plugin Parameter design, performFunction() will automatically call this.
`String`	`refGenome()` Output fastq file to use as input for BWA or bowtie2
`RepGenAlignerPlugin`	`refGenome(String value)` Set Output File.
`Integer`	`refKmerLen()` Length of kmers as tag sequences in the db
`RepGenAlignerPlugin`	`refKmerLen(Integer value)` Set Kmer length.
`Integer`	`seedLen()` Length of seed kmers
`RepGenAlignerPlugin`	`seedLen(Integer value)` Set Seed kmer length.
`Integer`	`seedWindow()` Length of window between positions when creating seed from DB tags
`RepGenAlignerPlugin`	`seedWindow(Integer value)` Set Seed window length.
`static void`	`writeChrom9Bits(List<Integer> peakPositions)`
`static void`	`writePeakPositions(String chrom, int peak, List<Integer> peakPositions)`
`static void`	`writeToFile(String chrom, com.google.common.collect.Multimap<String,Integer> chromMaximaMap, int minCount)`

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
  - RepGenAlignerPlugin
```
public RepGenAlignerPlugin()
```
  - RepGenAlignerPlugin
```
public RepGenAlignerPlugin(Frame parentFrame)
```
  - RepGenAlignerPlugin
```
public RepGenAlignerPlugin(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.
  - writeToFile
```
public static void writeToFile(String chrom,
                               com.google.common.collect.Multimap<String,Integer> chromMaximaMap,
                               int minCount)
```
  - writePeakPositions
```
public static void writePeakPositions(String chrom,
                                      int peak,
                                      List<Integer> peakPositions)
```
  - writeChrom9Bits
```
public static void writeChrom9Bits(List<Integer> peakPositions)
```
  - 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
  - main
```
public static void main(String[] args)
```
  - inputDB
```
public String inputDB()
```
    Input database file with tags and taxa distribution
    
    Returns:
    
    Input DB
  - inputDB
```
public RepGenAlignerPlugin inputDB(String value)
```
    Set Input DB. Input database file with tags and taxa distribution
    
    Parameters:
    
    value - Input DB
    
    Returns:
    
    this plugin
  - refGenome
```
public String refGenome()
```
    Output fastq file to use as input for BWA or bowtie2
    
    Returns:
    
    Output File
  - refGenome
```
public RepGenAlignerPlugin refGenome(String value)
```
    Set Output File. Output fastq file to use as input for BWA or bowtie2
    
    Parameters:
    
    value - Output File
    
    Returns:
    
    this plugin
  - minTagCount
```
public Integer minTagCount()
```
    Minimum count of reads for a tag to be output
    
    Returns:
    
    Min Count
  - minTagCount
```
public RepGenAlignerPlugin minTagCount(Integer value)
```
    Set Min Count. Minimum count of reads for a tag to be output
    
    Parameters:
    
    value - Min Count
    
    Returns:
    
    this plugin
  - minHitCount
```
public Integer minHitCount()
```
    Minimum count of hits in a cluster for a reference tag to be created for this cluster
    
    Returns:
    
    Min Count
  - minHitCount
```
public RepGenAlignerPlugin minHitCount(Integer value)
```
    Set Min Count. Minimum count of hits in a cluster for a reference tag to be created fro this cluster
    
    Parameters:
    
    value - Min Count
    
    Returns:
    
    this plugin
  - seedLen
```
public Integer seedLen()
```
    Length of seed kmers
    
    Returns:
    
    seed len
  - seedLen
```
public RepGenAlignerPlugin seedLen(Integer value)
```
    Set Seed kmer length. Length of seeds to use in aligning.
    
    Parameters:
    
    value - seed length
    
    Returns:
    
    this plugin
  - seedWindow
```
public Integer seedWindow()
```
    Length of window between positions when creating seed from DB tags
    
    Returns:
    
    seed window
  - seedWindow
```
public RepGenAlignerPlugin seedWindow(Integer value)
```
    Set Seed window length. Length of window between positions when creating seed from DB tags
    
    Parameters:
    
    value - seed length
    
    Returns:
    
    this plugin
  - kmerLen
```
public Integer kmerLen()
```
    Length of kmers as tag sequences in the db
    
    Returns:
    
    kmerLen
  - kmerLen
```
public RepGenAlignerPlugin kmerLen(Integer value)
```
    Set Kmer length. Length of kmers to be stored as tag sequences in the db
    
    Parameters:
    
    value - kmer length
    
    Returns:
    
    this plugin
  - refKmerLen
```
public Integer refKmerLen()
```
    Length of kmers as tag sequences in the db
    
    Returns:
    
    kmerLen
  - refKmerLen
```
public RepGenAlignerPlugin refKmerLen(Integer value)
```
    Set Kmer length. Length of kmers to be stored as tag sequences in the db
    
    Parameters:
    
    value - kmer length
    
    Returns:
    
    this plugin
  - match_reward
```
public Integer match_reward()
```
    Parameter sent to Smith Waterman aligner for use in calculating reward when base pairs match.
    
    Returns:
    
    Match Reward Amount
  - match_reward
```
public RepGenAlignerPlugin match_reward(Integer value)
```
    Set Match Reward Amount. Parameter sent to Smith Waterman aligner for use in calculating reward when base pairs match.
    
    Parameters:
    
    value - Match Reward Amount
    
    Returns:
    
    this plugin
  - mismatch_penalty
```
public Integer mismatch_penalty()
```
    Parameter sent to Smith Waterman aligner for use in calculating penalty when base pairs are mis-matched.
    
    Returns:
    
    Mismatch Penalty Amount
  - mismatch_penalty
```
public RepGenAlignerPlugin mismatch_penalty(Integer value)
```
    Set Mismatch Penalty Amount. Parameter sent to Smith Waterman aligner for use in calculating penalty when base pairs are mis-matched.
    
    Parameters:
    
    value - Mismatch Penalty Amount
    
    Returns:
    
    this plugin
  - gap_penalty
```
public Integer gap_penalty()
```
    Parameter sent to Smith Waterman aligner for use in calculating penalty when when a gap is identified.
    
    Returns:
    
    Gap Penalty Amount
  - gap_penalty
```
public RepGenAlignerPlugin gap_penalty(Integer value)
```
    Set Gap Penalty Amount. Parameter sent to Smith Waterman aligner for use in calculating penalty when when a gap is identified.
    
    Parameters:
    
    value - Gap Penalty Amount
    
    Returns:
    
    this plugin

Class RepGenAlignerPlugin

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

RepGenAlignerPlugin

RepGenAlignerPlugin

RepGenAlignerPlugin

Method Detail

postProcessParameters

processData

writeToFile

writePeakPositions

writeChrom9Bits

getIcon

getButtonName

getToolTipText

main

inputDB

inputDB

refGenome

refGenome

minTagCount

minTagCount

minHitCount

minHitCount

seedLen

seedLen

seedWindow

seedWindow

kmerLen

kmerLen

refKmerLen

refKmerLen

match_reward

match_reward

mismatch_penalty

mismatch_penalty

gap_penalty

gap_penalty