BestHaplotypePathPlugin

net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin

```
public class BestHaplotypePathPlugin
```
Plugin that takes a haplotype graph and a set of read mappings to infer the best (most likely) path through the graph given the read mappings. Read mappings are a list of reads with a set of haplotypes to which that read aligned.
The plugin can (1) take a file of read mappings and return a file with a list of haplotypes or (2) take read mappings from a PHG DB and store the resulting list of haplotypes in the DB.
If (1) the input is a file, then the plugin can take either a file or a directory containing multiple files. If a directory, all read mapping files will be processed and the haplotype lists output as separate files to an output directory. If the output directory is not specified, then the lists will be written to the input directory. Any path files of the same name, will not be overwritten and a message will be written to the log to that effect, unless the overwrite flag is set to true.
If (2) the input comes from a PHG DB, an input read map method and the output path method must be supplied. In addition, a specific taxon or list of taxa for which paths are to be imputed can be supplied. If paths for any of the taxa and methods exist, the paths will not be imputed and a warning message will be written to the log. If an overwrite flag is set to true, any existing paths will be overwritten and a message to that effect written to the log.

- Constructor Detail
  - BestHaplotypePathPlugin
```
public BestHaplotypePathPlugin(@Nullable
                               java.awt.Frame parentFrame,
                               boolean isInteractive)
```
    Plugin that takes a haplotype graph and a set of read mappings to infer the best (most likely) path through the graph given the read mappings. Read mappings are a list of reads with a set of haplotypes to which that read aligned.
    The plugin can (1) take a file of read mappings and return a file with a list of haplotypes or (2) take read mappings from a PHG DB and store the resulting list of haplotypes in the DB.
    If (1) the input is a file, then the plugin can take either a file or a directory containing multiple files. If a directory, all read mapping files will be processed and the haplotype lists output as separate files to an output directory. If the output directory is not specified, then the lists will be written to the input directory. Any path files of the same name, will not be overwritten and a message will be written to the log to that effect, unless the overwrite flag is set to true.
    If (2) the input comes from a PHG DB, an input read map method and the output path method must be supplied. In addition, a specific taxon or list of taxa for which paths are to be imputed can be supplied. If paths for any of the taxa and methods exist, the paths will not be imputed and a warning message will be written to the log. If an overwrite flag is set to true, any existing paths will be overwritten and a message to that effect written to the log.
- Method Detail
  - preProcessParameters
```
protected void preProcessParameters(@Nullable
                                    net.maizegenetics.plugindef.DataSet input)
```
  - postProcessParameters
```
protected void postProcessParameters()
```
  - processData
```
@Nullable
public net.maizegenetics.plugindef.DataSet processData(@Nullable
                                                                 net.maizegenetics.plugindef.DataSet input)
```
  - processReadFile
```
public void processReadFile(@NotNull
                            java.lang.String readFileName,
                            @NotNull
                            HaplotypeGraph graph)
```
    Method to process a single read file and write the resulting path to the output directory. If overwrite = false, then the method will not overwrite an existing path file.
    
    Parameters:
    
    readFileName - The full path of the the file with read mappings
    
    graph - The HaplotypeGraph that will be used to infer a path as a list of haplotype ids
  - processReadDirectory
```
public void processReadDirectory(@NotNull
                                 java.io.File readDir,
                                 @NotNull
                                 HaplotypeGraph graph)
```
    Method that gets a list of read mapping files from the read directory and calls processReadFile for each of the files.
    
    Parameters:
    
    readDir - The directory containing the read mapping files to be processed
    
    graph - The HaplotypeGraph used to infer paths
    
    See Also:
    
    processReadFile
  - findPathsFromDBReadMappings
```
public void findPathsFromDBReadMappings(@NotNull
                                        HaplotypeGraph graph,
                                        @NotNull
                                        java.lang.String keyFile)
```
    Method that gets a list of read mappings from the database for a specific method and writes a path to the database for each read mapping record
    
    Parameters:
    
    graph - The HaplotypeGraph used to infer paths
  - findPathsFromDBReadMappingsMultithread
```
public void findPathsFromDBReadMappingsMultithread(@NotNull
                                                   HaplotypeGraph graph,
                                                   @NotNull
                                                   java.lang.String keyFile)
```
    Method to find paths by extracting the read mappings from the DB. Then it will aggregate the counts together by summing the counts for a given hapId set.
    The code will then find a path for those read mappings.
  - getToolTipText
```
@NotNull
public java.lang.String getToolTipText()
```
  - getIcon
```
@Nullable
public javax.swing.ImageIcon getIcon()
```
  - getButtonName
```
@NotNull
public java.lang.String getButtonName()
```
  - pluginDescription
```
@NotNull
public java.lang.String pluginDescription()
```
  - keyFile
```
@NotNull
public java.lang.String keyFile()
```
    KeyFile file name. Must be a tab separated file using the following headers: SampleName ReadMappingIds LikelyParents ReadMappingIds and LikelyParents need to be comma separated for multiple values
    
    Returns:
    
    KeyFile
  - keyFile
```
@NotNull
public BestHaplotypePathPlugin keyFile(@NotNull
                                                java.lang.String value)
```
    Set KeyFile. KeyFile file name. Must be a tab separated file using the following headers: SampleName ReadMappingIds LikelyParents ReadMappingIds and LikelyParents need to be comma separated for multiple values
    
    Parameters:
    
    value - KeyFile
    
    Returns:
    
    this plugin
  - readMapFilename
```
@Nullable
public java.lang.String readMapFilename()
```
    Filename of read mappings. Do not supply both a filename and a directory.
    
    Returns:
    
    Read Map File
  - readMapFilename
```
@NotNull
public BestHaplotypePathPlugin readMapFilename(@Nullable
                                                        java.lang.String value)
```
    Set Read Map File. Filename of read mappings. Do not supply both a filename and a directory.
    
    Parameters:
    
    value - Read Map File
    
    Returns:
    
    this plugin
  - readMapDirectory
```
@Nullable
public java.lang.String readMapDirectory()
```
    Directory of read mapping files. If this is supplied, do not also assign a read filename.
    
    Returns:
    
    Read Map Directory
  - readMapDirectory
```
@NotNull
public BestHaplotypePathPlugin readMapDirectory(@Nullable
                                                         java.lang.String value)
```
    Set Read Map Directory. Directory of read mapping files. If this is supplied, do not also assign a read filename.
    
    Parameters:
    
    value - Read Map Directory
    
    Returns:
    
    this plugin
  - pathOutDirectory
```
@Nullable
public java.lang.String pathOutDirectory()
```
    Directory to which path files will be written.
    
    Returns:
    
    Read Map Directory
  - pathOutDirectory
```
@NotNull
public BestHaplotypePathPlugin pathOutDirectory(@NotNull
                                                         java.lang.String value)
```
    Set Read Map Directory. Directory to which path files will be written.
    
    Parameters:
    
    value - Read Map Directory
    
    Returns:
    
    this plugin
  - readMethodName
```
@Nullable
public java.lang.String readMethodName()
```
    The name of the read method in the PHG DB
    
    Returns:
    
    Read Method
  - readMethodName
```
@NotNull
public BestHaplotypePathPlugin readMethodName(@NotNull
                                                       java.lang.String value)
```
    Set Read Method. The name of the read method in the PHG DB
    
    Parameters:
    
    value - Read Method
    
    Returns:
    
    this plugin
  - pathMethodName
```
@Nullable
public java.lang.String pathMethodName()
```
    The name of the path method used to write the results to the PHG DB
    
    Returns:
    
    Path Method
  - pathMethodName
```
@NotNull
public BestHaplotypePathPlugin pathMethodName(@NotNull
                                                       java.lang.String value)
```
    Set Path Method. The name of the path method used to write the results to the PHG DB
    
    Parameters:
    
    value - Path Method
    
    Returns:
    
    this plugin
  - pathMethodDescription
```
@Nullable
public java.lang.String pathMethodDescription()
```
    An additional description that will be stored with the path method name, if desired.
    
    Returns:
    
    Path Method Description
  - pathMethodDescription
```
@NotNull
public BestHaplotypePathPlugin pathMethodDescription(@NotNull
                                                              java.lang.String value)
```
    Set Path Method Description. An additional description that will be stored with the path method name, if desired.
    
    Parameters:
    
    value - Path Method Description
    
    Returns:
    
    this plugin
  - overwrite
```
public boolean overwrite()
```
    Overwrite
    
    Returns:
    
    Overwrite
  - overwrite
```
@NotNull
public BestHaplotypePathPlugin overwrite(boolean value)
```
    Set Overwrite. Overwrite
    
    Parameters:
    
    value - Overwrite
    
    Returns:
    
    this plugin
  - minTaxaPerRange
```
public int minTaxaPerRange()
```
    minimum number of taxa per anchor reference range. Ranges with fewer taxa will not be included in the output node list.
    
    Returns:
    
    Min Taxa
  - minTaxaPerRange
```
@NotNull
public BestHaplotypePathPlugin minTaxaPerRange(int value)
```
    Set Min Taxa. minimum number of taxa per anchor reference range. Ranges with fewer taxa will not be included in the output node list.
    
    Parameters:
    
    value - Min Taxa
    
    Returns:
    
    this plugin
  - minReads
```
public int minReads()
```
    minimum number of reads per anchor reference range. Ranges with fewer reads will not be included in the output node list.
    
    Returns:
    
    Min Reads
  - minReads
```
@NotNull
public BestHaplotypePathPlugin minReads(int value)
```
    Set Min Reads. minimum number of reads per anchor reference range. Ranges with fewer reads will not be included in the output node list.
    
    Parameters:
    
    value - Min Reads
    
    Returns:
    
    this plugin
  - maxReadsPerKB
```
public int maxReadsPerKB()
```
    maximum number of include counts per anchor reference range Kb. Ranges with more reads will not be included in the output node list.
    
    Returns:
    
    Max Reads
  - maxReadsPerKB
```
@NotNull
public BestHaplotypePathPlugin maxReadsPerKB(int value)
```
    Set Max Reads. maximum number of include counts per anchor reference range Kb. Ranges with more reads will not be included in the output node list.
    
    Parameters:
    
    value - Max Reads
    
    Returns:
    
    this plugin
  - maxNodesPerRange
```
public int maxNodesPerRange()
```
    maximum number of nodes per reference range. Ranges with more nodes will not be included in the output node list.
    
    Returns:
    
    Max Nodes
  - maxNodesPerRange
```
@NotNull
public BestHaplotypePathPlugin maxNodesPerRange(int value)
```
    Set Max Nodes. maximum number of nodes per reference range. Ranges with more nodes will not be included in the output node list.
    
    Parameters:
    
    value - Max Nodes
    
    Returns:
    
    this plugin
  - minTransitionProb
```
public double minTransitionProb()
```
    minimum probability of a transition between nodes at adjacent reference ranges.
    
    Returns:
    
    Min Transition Prob
  - minTransitionProb
```
@NotNull
public BestHaplotypePathPlugin minTransitionProb(double value)
```
    Set Min Transition Prob. minimum probability of a transition between nodes at adjacent reference ranges.
    
    Parameters:
    
    value - Min Transition Prob
    
    Returns:
    
    this plugin
  - probReadMappedCorrectly
```
public double probReadMappedCorrectly()
```
    minimum number of reads per anchor reference range. Ranges with fewer reads will not be included in the output node list.
    
    Returns:
    
    Prob Correct
  - probReadMappedCorrectly
```
@NotNull
public BestHaplotypePathPlugin probReadMappedCorrectly(double value)
```
    Set Prob Correct. minimum number of reads per anchor reference range. Ranges with fewer reads will not be included in the output node list.
    
    Parameters:
    
    value - Prob Correct
    
    Returns:
    
    this plugin
  - splitConsensusNodes
```
public boolean splitConsensusNodes()
```
    split consensus nodes into one node per taxon.
    
    Returns:
    
    Split Nodes
  - splitConsensusNodes
```
@NotNull
public BestHaplotypePathPlugin splitConsensusNodes(boolean value)
```
    Set Split Nodes. split consensus nodes into one node per taxon.
    
    Parameters:
    
    value - Split Nodes
    
    Returns:
    
    this plugin
  - splitTransitionProb
```
public double splitTransitionProb()
```
    When the consensus nodes are split by taxa, this is the transition probability for moving from a node to the next node of the same taxon. It equals 1 minus the probability of a recombination between adjacent nodes.
    
    Returns:
    
    Split Prob
  - splitTransitionProb
```
@NotNull
public BestHaplotypePathPlugin splitTransitionProb(double value)
```
    Set Split Prob. When the consensus nodes are split by taxa, this is the transition probability for moving from a node to the next node of the same taxon. It equals 1 minus the probability of a recombination between adjacent nodes.
    
    Parameters:
    
    value - Split Prob
    
    Returns:
    
    this plugin
  - useBackwardForward
```
public boolean useBackwardForward()
```
    Use the Backward-Forward algorithm instead of the Viterbi algorithm for the HMM.
    
    Returns:
    
    Usebf
  - useBackwardForward
```
@NotNull
public BestHaplotypePathPlugin useBackwardForward(boolean value)
```
    Set Usebf. Use the Backward-Forward algorithm instead of the Viterbi algorithm for the HMM.
    
    Parameters:
    
    value - Usebf
    
    Returns:
    
    this plugin
  - minProbBF
```
public double minProbBF()
```
    Only nodes with minP or greater probability will be kept in the path when using the Backward-Forward algorithm,
    
    Returns:
    
    Min P
  - minProbBF
```
@NotNull
public BestHaplotypePathPlugin minProbBF(double value)
```
    Set Min P. Only nodes with minP or greater probability will be kept in the path when using the Backward-Forward algorithm,
    
    Parameters:
    
    value - Min P
    
    Returns:
    
    this plugin
  - bfInfoFilename
```
@Nullable
public java.lang.String bfInfoFilename()
```
    The base name of the file to node probabilities from the backward-forward algorithm will be written. taxonName.txt will be appended to each file.
    
    Returns:
    
    Bf Info File
  - bfInfoFilename
```
@NotNull
public BestHaplotypePathPlugin bfInfoFilename(@Nullable
                                                       java.lang.String value)
```
    Set Bf Info File. The base name of the file to node probabilities from the backward-forward algorithm will be written. taxonName.txt will be appended to each file.
    
    Parameters:
    
    value - Bf Info File
    
    Returns:
    
    this plugin
  - removeRangesWithEqualCounts
```
public boolean removeRangesWithEqualCounts()
```
    Ranges with equal read counts for all haplotypes should be removed from the graph. Defaults to true but will be always be false if minReads = 0.
    
    Returns:
    
    Remove Equal
  - removeRangesWithEqualCounts
```
@NotNull
public BestHaplotypePathPlugin removeRangesWithEqualCounts(boolean value)
```
    Set Remove Equal. Ranges with equal read counts for all haplotypes should be removed from the graph. Defaults to true but will be always be false if minReads = 0.
    
    Parameters:
    
    value - Remove Equal
    
    Returns:
    
    this plugin
  - numThreads
```
public int numThreads()
```
    Number of threads used to upload
    
    Returns:
    
    Num Threads
  - numThreads
```
@NotNull
public BestHaplotypePathPlugin numThreads(int value)
```
    Set Num Threads. Number of threads used to upload
    
    Parameters:
    
    value - Num Threads
    
    Returns:
    
    this plugin
  - requiredTaxaList
```
@Nullable
public net.maizegenetics.taxa.TaxaList requiredTaxaList()
```
    Optional list of taxa required to have haplotypes. Any reference range that does not have a haplotype for one of these taxa will not be used for path finding. This can be a comma separated list of taxa (no spaces unless surrounded by quotes), file (.txt) with list of taxa names to include, or a taxa list file (.json or .json.gz). By default, all taxa will be included.
    
    Returns:
    
    Required Taxa
  - requiredTaxaList
```
@NotNull
public BestHaplotypePathPlugin requiredTaxaList(@NotNull
                                                         net.maizegenetics.taxa.TaxaList value)
```
    Set Required Taxa. Optional list of taxa required to be have haplotypes. Any reference range that does not have a haplotype for one of these taxa will not be used for path finding. This can be a comma separated list of taxa (no spaces unless surrounded by quotes), file (.txt) with list of taxa names to include, or a taxa list file (.json or .json.gz). By default, all taxa will be included.
    
    Parameters:
    
    value - Required Taxa
    
    Returns:
    
    this plugin
  - algorithmType
```
@NotNull
public net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin.ALGORITHM_TYPE algorithmType()
```
    the type of algorithm. Choices are classic, which is the original implementation describe by Rabiner 1989, or efficient, which is modified for improved computational efficiency.
    
    Returns:
    
    Algorithm Type
  - algorithmType
```
@NotNull
public BestHaplotypePathPlugin algorithmType(@NotNull
                                                      net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin.ALGORITHM_TYPE value)
```
    Set Algorithm Type. the type of algorithm. Choices are classic, which is the original implementation describe by Rabiner 1989, or efficient, which is modified for improved computational efficiency.
    
    Parameters:
    
    value - Algorithm Type
    
    Returns:
    
    this plugin
  - maxParents
```
public int maxParents()
```
    To restrict path finding to the most likely parents, the number of parents used will not be greater than maxParents. The number of parents used will be the minimum of maxParents and the number of parents needed to reach minCoverage. If both maxParents and minCoverage are left at the default, all parents in the input HaplotypeGraph will be used.
    
    Returns:
    
    Max Parents
  - maxParents
```
@NotNull
public BestHaplotypePathPlugin maxParents(int value)
```
    Set Max Parents. To restrict path finding to the most likely parents, the number of parents used will not be greater than maxParents. The number of parents used will be the minimum of maxParents and the number of parents needed to reach minCoverage. If both maxParents and minCoverage are left at the default, all parents in the input HaplotypeGraph will be used.
    
    Parameters:
    
    value - Max Parents
    
    Returns:
    
    this plugin
  - minCoverage
```
public double minCoverage()
```
    To restrict path finding to the most likely parents, the smallest number of parents needed to provide read coverage greater than or equal to minCoverage will be used to find paths. If maxParents is smaller, that number of parents will be used.
    
    Returns:
    
    Min Coverage
  - minCoverage
```
@NotNull
public BestHaplotypePathPlugin minCoverage(double value)
```
    Set Min Coverage. To restrict path finding to the most likely parents, the smallest number of parents needed to provide read coverage greater than or equal to minCoverage will be used to find paths. If maxParents is smaller, that number of parents will be used.
    
    Parameters:
    
    value - Min Coverage
    
    Returns:
    
    this plugin
  - likelyParentFile
```
@Nullable
public java.lang.String likelyParentFile()
```
    The name and path of the file of likely parents and their read counts.
    
    Returns:
    
    Parent Output File
  - likelyParentFile
```
@NotNull
public BestHaplotypePathPlugin likelyParentFile(@NotNull
                                                         java.lang.String value)
```
    Set Parent Output File. The name and path of the file of likely parents and their read counts.
    
    Parameters:
    
    value - Parent Output File
    
    Returns:
    
    this plugin
  - isTestMethod
```
public boolean isTestMethod()
```
    Indication if the data is to be loaded against a test method. Data loaded with test methods are not cached with the PHG ktor server
    
    Returns:
    
    Is Test Method
  - isTestMethod
```
@NotNull
public BestHaplotypePathPlugin isTestMethod(boolean value)
```
    Set Is Test Method. Indication if the data is to be loaded against a test method. Data loaded with test methods are not cached with the PHG ktor server
    
    Parameters:
    
    value - Is Test Method
    
    Returns:
    
    this plugin

Class BestHaplotypePathPlugin

Constructor Detail

BestHaplotypePathPlugin

Method Detail

preProcessParameters

postProcessParameters

processData

processReadFile

processReadDirectory

findPathsFromDBReadMappings

findPathsFromDBReadMappingsMultithread

getToolTipText

getIcon

getButtonName

pluginDescription

keyFile

keyFile

readMapFilename

readMapFilename

readMapDirectory

readMapDirectory

pathOutDirectory

pathOutDirectory

readMethodName

readMethodName

pathMethodName

pathMethodName

pathMethodDescription

pathMethodDescription

overwrite

overwrite

minTaxaPerRange

minTaxaPerRange

minReads

minReads

maxReadsPerKB

maxReadsPerKB

maxNodesPerRange

maxNodesPerRange

minTransitionProb

minTransitionProb

probReadMappedCorrectly

probReadMappedCorrectly

splitConsensusNodes

splitConsensusNodes

splitTransitionProb

splitTransitionProb

useBackwardForward

useBackwardForward

minProbBF

minProbBF

bfInfoFilename

bfInfoFilename

removeRangesWithEqualCounts

removeRangesWithEqualCounts

numThreads

numThreads

requiredTaxaList

requiredTaxaList

algorithmType

algorithmType

maxParents

maxParents

minCoverage

minCoverage

likelyParentFile

likelyParentFile

isTestMethod

isTestMethod