Constructor Detail

• AlleleSubsettingUtils

  public AlleleSubsettingUtils()

Method Detail

• subsetVCToMatchSnp

  public static htsjdk.variant.variantcontext.VariantContext subsetVCToMatchSnp​(htsjdk.variant.variantcontext.VariantContext ctx,
                                                                                Snp snp)

  Method to subset the alleles in the VariantContext to those in the input snp. Will also subset appropriately the AD and PL fields in all the genotypes, and in the case of a monomorphic variant with a NON_REF allele, will replace the NON_REF allele with the non-reference allele from snp.

  returns null if it is not possible to subset ctx to the alleles in snp.

  Parameters:

  ctx - The VariantContext to subset.

  snp - Snp whose alleles are used for subsetting ctx.

  Returns:

  a VariantContext subsetted to the alleles in snp, or null if unable.

• subsetAlleles

  public static htsjdk.variant.variantcontext.VariantContext subsetAlleles​(htsjdk.variant.variantcontext.VariantContext originalVc,
                                                                           List<htsjdk.variant.variantcontext.Allele> allelesToKeep)

• swapAlleles

  public static htsjdk.variant.variantcontext.VariantContext swapAlleles​(htsjdk.variant.variantcontext.VariantContext originalVc,
                                                                         htsjdk.variant.variantcontext.Allele oldAllele,
                                                                         htsjdk.variant.variantcontext.Allele newAllele)
                                                                  throws IllegalArgumentException

  Swaps one of the alleles in a VC (and its genotypes) with another.

  Parameters:

  originalVc - The VariantContext whose oldAllele will be swapped for newAllele.

  oldAllele - The Allele in originalVc that needs to be replaced.

  newAllele - The new Allele to use instead of oldAllele.

  Returns:

  A new VariantContext with newAllele swapped in for oldAllele.

  Throws:

  IllegalArgumentException - if originalVc doesn't contain oldAllele.

• subsetAlleles

  public static htsjdk.variant.variantcontext.GenotypesContext subsetAlleles​(htsjdk.variant.variantcontext.GenotypesContext originalGs,
                                                                             List<htsjdk.variant.variantcontext.Allele> originalAlleles,
                                                                             List<htsjdk.variant.variantcontext.Allele> allelesToKeep)

  Create the new GenotypesContext with the subsetted PLs and ADs Expects allelesToKeep to be in the same order in which they are in originalAlleles.

  Parameters:

  originalGs - the original GenotypesContext

  originalAlleles - the original alleles

  allelesToKeep - the subset of alleles to use with the new Genotypes

  Returns:

  a new non-null GenotypesContext

• subsettedPLIndices

  public static int[] subsettedPLIndices​(List<htsjdk.variant.variantcontext.Allele> originalAlleles,
                                         List<htsjdk.variant.variantcontext.Allele> newAlleles)

  Given a list of original alleles and a subset of new alleles to retain, find the array of old PL indices that correspond to new PL indices i.e. result[7] = old PL index of genotype containing same alleles as the new genotype with PL index 7.

  This method is written in terms f indices rather than subsetting PLs directly in order to produce output that can be recycled from sample to sample, provided that the ploidy is the same.

  Parameters:

  originalAlleles - List of original alleles

  newAlleles - New alleles -- must be a subset of originalAlleles

  Returns:

  old PL indices of new genotypes