public class VCFUtil
public static int VCF_DEFAULT_MAX_NUM_ALLELES
public static kotlin.Array[] getScore(int i,
int j)
public static byte resolveVCFGeno(kotlin.Array[] alleles,
kotlin.Array[] allelesInTaxa,
int tx)
public static byte resolveVCFGeno(kotlin.Array[] alleles,
kotlin.Array[] alleleDepth)
public static kotlin.Array[] resolveRefSorted(kotlin.Array[] sortedAlleles,
byte refAllele)
public static boolean indelInKnownVariant(java.lang.String[] knownVariants)
public static boolean indelMinusInKnownVariant(java.lang.String[] knownVariants)
public static Tuple<kotlin.Array[],kotlin.Array[]> resolveSortedAndKnownVariantsExport(kotlin.Array[] sortedAllelesInput, java.lang.String[] knownVariantsInput)
public static kotlin.Array[] calcTop2Depths(kotlin.Array[] siteAlleleDepths)
public static java.util.List<htsjdk.variant.variantcontext.VariantContext> convertGenotypeTableToVariantContextList(GenotypeTable genotypeTable)
Method to convert a genotype table to a List of VariantContexts This is done by walking through the genotypeTable's positions in order. To Handle indels, we need to process a set of positions at a time It will start with the first position and hold its index temporarily Combine consecutive indel positions into this index list. A consecutive position is one where the chromosomes match, and the current position is less than 1 physical position away from the previous We need to check less than one as an insertion has the same physical reference position If the consecutive position also contains an indel character "+" or "-" we need to add it to the block Otherwise(either non indel or non-consecutive) process the previous block and setup a new block with the current site
genotypeTable - public static htsjdk.variant.variantcontext.VariantContext convertGenotypeTableSiteToVariantContext(GenotypeTable genotypeTable, java.util.List<java.lang.Integer> sites)
Method to convert a list of positions into a single variantContext record If sites only has one element, it will just create genotypes for that position(Fixing indels with missing information) If sites has multiple consecutive elements, it is likely an indel This needs to walk through the sites and combine the alleles together ignoring - and + nucleotides
genotypeTable - sites -