public class DiscoverySNPCallerPluginV2
extends AbstractPlugin
This class aligns tags at the same physical location against one another, calls SNPs, and then outputs the SNPs to a HapMap file. It is multi-threaded, as there are substantial speed increases with it.
public DiscoverySNPCallerPluginV2()
public DiscoverySNPCallerPluginV2(java.awt.Frame parentFrame,
boolean isInteractive)
public void postProcessParameters()
public javax.swing.ImageIcon getIcon()
public java.lang.String getButtonName()
public java.lang.String getToolTipText()
public java.lang.String inputDB()
Input TagsByTaxa file (if hdf5 format, use .hdf or .h5 extension)
public DiscoverySNPCallerPluginV2 inputDB(java.lang.String value)
Set Input Tags by Taxa File. Input TagsByTaxa file (if hdf5 format, use .hdf or .h5 extension)
value - Input Tags by Taxa Filepublic java.lang.Double minMinorAlleleFreq()
Minimum minor allele frequency
public DiscoverySNPCallerPluginV2 minMinorAlleleFreq(java.lang.Double value)
Set Min Minor Allele Freq. Minimum minor allele frequency
value - Min Minor Allele Freqpublic java.lang.Double minLocusCoverage()
Minimum locus coverage (proportion of Taxa with a genotype)
public DiscoverySNPCallerPluginV2 minLocusCoverage(java.lang.Double value)
Set Min Locus Coverage. Minimum locus coverage (proportion of Taxa with a genotype)
value - Min Locus Coveragepublic java.lang.String referenceGenomeFile()
Path to reference genome in fasta format. Ensures that a tag from the reference genome is always included when the tags at a locus are aligned against each other to call SNPs. The reference allele for each site is then provided in the output HapMap files, under the taxon name "REFERENCE_GENOME" (first taxon). DEFAULT: Don't use reference genome.
public DiscoverySNPCallerPluginV2 referenceGenomeFile(java.lang.String value)
Set Reference Genome File. Path to reference genome in fasta format. Ensures that a tag from the reference genome is always included when the tags at a locus are aligned against each other to call SNPs. The reference allele for each site is then provided in the output HapMap files, under the taxon name "REFERENCE_GENOME" (first taxon). DEFAULT: Don't use reference genome.
value - Reference Genome Filepublic Chromosome startChromosome()
Start Chromosome
public DiscoverySNPCallerPluginV2 startChromosome(Chromosome value)
Set Start Chromosome. Start Chromosome
value - Start Chromosomepublic Chromosome endChromosome()
End Chromosome
public DiscoverySNPCallerPluginV2 endChromosome(Chromosome value)
Set End Chromosome. End Chromosome
value - End Chromosomepublic java.lang.Boolean includeGaps()
Include sites where major or minor allele is a GAP
public DiscoverySNPCallerPluginV2 includeGaps(java.lang.Boolean value)
Set Include Gaps. Include sites where major or minor allele is a GAP
value - Include Gapspublic java.lang.Double gapAlignmentThreshold()
Maximum gap alignment allowed from the equation: IndelContrast / (IndelContrast/Non-IndelContrast) IC=Indel contrasts=Sum the number ACGT vs - NC=non-indel constrasts = Sum the number of ACGT vs ACGT ignore = - vs - Gapped Alignment ratio = IC/(IC+NC)
public DiscoverySNPCallerPluginV2 gapAlignmentThreshold(java.lang.Double value)
Maximum gap alignment allowed from the equation: IndelContrast / (IndelContrast/Non-IndelContrast) IC=Indel contrasts=Sum the number ACGT vs - NC=non-indel constrasts = Sum the number of ACGT vs ACGT ignore = - vs - Gapped Alignment ratio = IC/(IC+NC)
value - Max gap alignment ratiopublic java.lang.Integer maxTagsPerCutSite()
Maximum number of tags per cut site (for alignment)
public DiscoverySNPCallerPluginV2 maxTagsPerCutSite(java.lang.Integer value)
Set maxTagsPerCutSite. This is the maximum number of tags allowed per cute site when performaing an alignment. Too many tags and biojava 4 getMultipleSequenceAlignment grinds to a halt.
value - Max number of tags per cut sitepublic static void setKeyFileStringToInt(java.util.Map<java.lang.String,java.lang.Integer> inputKeyFile)
public java.lang.Boolean deleteOldData()
Delete exisiting Discovery data from DB
public DiscoverySNPCallerPluginV2 deleteOldData(java.lang.Boolean value)
Set Delete old data flag. True indicates we want the db tables cleared
value - true/false - whether to delete datapublic static int keyFileReturnChromInt(java.lang.String chromosome)
GIven a chromosome string value, search for it's corresponding number from the keyFileStringToInt map