public class FILLINFindHaplotypesPlugin
extends AbstractPlugin
Creates haplotypes by finding large IBS regions within GBS data. Starts with the highest coverage taxa and looks within windows of near perfect matches. Combines all matches together into one haplotype. The haplotype is named for the highest coverage sample.
public FILLINFindHaplotypesPlugin()
public FILLINFindHaplotypesPlugin(java.awt.Frame parentFrame,
boolean isInteractive)
protected void postProcessParameters()
public java.lang.String getCitation()
public static kotlin.Array[] divideChromosome(GenotypeTable a, int appoxSitesPerHaplotype, boolean verboseOutput)
Divides a genome up into roughly equally sized blocks of sites
a - appoxSitesPerHaplotype - verboseOutput - public static java.util.ArrayList<java.lang.Integer> maxMajorAllelesTaxa(GenotypeTable a, int numMaxTaxa, WHICH_ALLELE alleleNumber)
public javax.swing.ImageIcon getIcon()
public java.lang.String getButtonName()
public java.lang.String getToolTipText()
public java.lang.Boolean runPlugin(DataSet input)
Convenience method to run plugin with one return object.
public java.lang.String targetFile()
Input HapMap file of target genotypes to impute or all genotypes available for target taxon. Accepts all file types supported by TASSEL5.
public FILLINFindHaplotypesPlugin targetFile(java.lang.String value)
Set Target file. Input HapMap file of target genotypes to impute or all genotypes available for target taxon. Accepts all file types supported by TASSEL5.
value - Target filepublic java.lang.String outputFilename()
Output file; Use .gX in the output filename to denote the substring .gc#s# found in donor files, ie 'out.gX.hmp.txt'.
public FILLINFindHaplotypesPlugin outputFilename(java.lang.String value)
Set Output filename. Output file; Use .gX in the output filename to denote the substring .gc#s# found in donor files, ie 'out.gX.hmp.txt'.
value - Output filenamepublic java.lang.Double maxDivergenceFromFounder()
Maximum genetic divergence from founder haplotype to cluster sequences
public FILLINFindHaplotypesPlugin maxDivergenceFromFounder(java.lang.Double value)
Set Max divergence from founder. Maximum genetic divergence from founder haplotype to cluster sequences
value - Max divergence from founderpublic java.lang.Double maxHeterozygosityOfOutputHaplotypes()
Maximum heterozygosity of output haplotype. Heterozygosity results from clustering sequences that either have residual heterozygosity or clustering sequences that do not share all minor alleles.
public FILLINFindHaplotypesPlugin maxHeterozygosityOfOutputHaplotypes(java.lang.Double value)
Set Max heterozygosity of output haplotypes. Maximum heterozygosity of output haplotype. Heterozygosity results from clustering sequences that either have residual heterozygosity or clustering sequences that do not share all minor alleles.
value - Max heterozygosity of output haplotypespublic java.lang.Integer minSitesToCluster()
The minimum number of sites present in two taxa to compare genetic distance to evaluate similarity for clustering
public FILLINFindHaplotypesPlugin minSitesToCluster(java.lang.Integer value)
Set Min sites to cluster. The minimum number of sites present in two taxa to compare genetic distance to evaluate similarity for clustering
value - Min sites to clusterpublic java.lang.Double maxCombinedErrorToImputeTwoDonors()
The maximum genetic divergence allowable to cluster taxa
public FILLINFindHaplotypesPlugin maxCombinedErrorToImputeTwoDonors(java.lang.Double value)
Set Max combined error to impute two donors. The maximum genetic divergence allowable to cluster taxa
value - Max combined error to impute two donorspublic java.lang.Integer preferredHaplotypeSize()
Preferred haplotype block size in sites (minimum 64); will use the closest multiple of 64 at or below the supplied value
public FILLINFindHaplotypesPlugin preferredHaplotypeSize(java.lang.Integer value)
Set Preferred haplotype size. Preferred haplotype block size in sites (minimum 64); will use the closest multiple of 64 at or below the supplied value
value - Preferred haplotype sizepublic java.lang.Integer minSitesToTestMatch()
Minimum number of present sites within input sequence to do the search
public FILLINFindHaplotypesPlugin minSitesToTestMatch(java.lang.Integer value)
Set Min sites to test match. Minimum number of present sites within input sequence to do the search
value - Min sites to test matchpublic java.lang.Integer maxHaplotypesPerSegment()
Maximum number of haplotypes per segment
public FILLINFindHaplotypesPlugin maxHaplotypesPerSegment(java.lang.Integer value)
Set Max haplotypes per segment. Maximum number of haplotypes per segment
value - Max haplotypes per segmentpublic java.lang.Integer minTaxaToGenerateAHaplotype()
Minimum number of taxa to generate a haplotype
public FILLINFindHaplotypesPlugin minTaxaToGenerateAHaplotype(java.lang.Integer value)
Set Min taxa to generate a haplotype. Minimum number of taxa to generate a haplotype
value - Min taxa to generate a haplotypepublic java.lang.Double maxFrequencyMissingPerHaplotype()
Maximum frequency of missing data in the output haplotype
public FILLINFindHaplotypesPlugin maxFrequencyMissingPerHaplotype(java.lang.Double value)
Set Max frequency missing per haplotype. Maximum frequency of missing data in the output haplotype
value - Max frequency missing per haplotypepublic java.lang.Boolean supressSystemOut()
Supress system out
public FILLINFindHaplotypesPlugin supressSystemOut(java.lang.Boolean value)
Set Supress system out. Express system out
value - Express system outpublic java.lang.Boolean detailedSystemOutOnHaplotypes()
Details of taxa included in each haplotype to system out
public FILLINFindHaplotypesPlugin detailedSystemOutOnHaplotypes(java.lang.Boolean value)
Set Detailed system out on haplotypes. Details of taxa included in each haplotype to system out
value - Detailed system out on haplotypes