Uses of Class
picard.fingerprint.Snp

Packages that use Snp

Package	Description
picard.fingerprint

Uses of Snp in picard.fingerprint

Methods in picard.fingerprint that return Snp

Modifier and Type	Method and Description
Snp	Snp.flip() Returns a new SNP object with the alleles swapped and MAF corrected.
Snp	HaplotypeBlock.getFirstSnp() Gets the arbitrarily first SNP in the haplotype.
abstract Snp	HaplotypeProbabilities.getRepresentativeSnp() Returns a representative SNP for this haplotype.
Snp	HaplotypeProbabilitiesFromGenotype.getRepresentativeSnp() Returns the SNP who's genotype was used to construct the likelihoods.
Snp	HaplotypeProbabilityOfNormalGivenTumor.getRepresentativeSnp()
Snp	HaplotypeBlock.getSnp(java.lang.String name) Gets a SNP by name if it belongs to this haplotype.
Snp	HaplotypeMap.getSnp(java.lang.String chrom, int pos) Queries a Snp by chromosome and position.

Methods in picard.fingerprint that return types with arguments of type Snp

Modifier and Type	Method and Description
java.util.Set<Snp>	HaplotypeMap.getAllSnps() Returns an unmodifiable collection of all SNPs in all Haplotype blocks.
java.util.Collection<Snp>	HaplotypeBlock.getSnps() Returns an unmodifiable, unordered, collection of all SNPs in this haplotype block.

Methods in picard.fingerprint with parameters of type Snp

Modifier and Type	Method and Description
void	HaplotypeBlock.addSnp(Snp snp) Adds a SNP to the haplotype.
void	HaplotypeProbabilitiesFromGenotypeLikelihoods.addToLogLikelihoods(Snp snp, java.util.List<htsjdk.variant.variantcontext.Allele> alleles, double[] logGenotypeLikelihoods) Adds a base observation with the observed quality to the evidence for this haplotype based on the fact that the SNP is part of the haplotype.
void	HaplotypeProbabilitiesFromContaminatorSequence.addToProbs(Snp snp, byte base, byte qual) Adds a base observation with the observed quality to the evidence for this haplotype based on the fact that the SNP is part of the haplotype.
void	HaplotypeProbabilitiesFromSequence.addToProbs(Snp snp, byte base, byte qual) Adds a base observation with the observed quality to the evidence for this haplotype based on the fact that the SNP is part of the haplotype.
int	Snp.compareTo(Snp that)
boolean	HaplotypeBlock.contains(Snp snp) Returns true if the SNP is contained within the haplotype block, false otherwise.
DiploidHaplotype	HaplotypeBlock.getDiploidHaplotype(Snp snp, DiploidGenotype gt) Gets the diploid haplotype for this haplotype block given the provided SNP and SNP genotype.
HaplotypeBlock	HaplotypeMap.getHaplotype(Snp snp) Queries a HaplotypeBlock by Snp object.
DiploidGenotype	HaplotypeProbabilities.getMostLikelyGenotype(Snp snp) Gets the genotype for this Snp given the most likely haplotype.
DiploidGenotype	HaplotypeBlock.getSnpGenotype(Snp snp, DiploidHaplotype haplotype) Gets the expected genotype of the provided SNP given the provided haplotype of this haplotype block.

Constructors in picard.fingerprint with parameters of type Snp

Constructor and Description
HaplotypeProbabilitiesFromGenotype(Snp snp, HaplotypeBlock haplotypeBlock, double AA, double Aa, double aa)