- checkAllele
check to make sure the allele is an acceptable allele
- createGenotypeMap
create a genotype map
- decodeInts
- generateException
- generateExceptionTextForBadAlleleBases
Generates the exception text for the case where the allele string contains
unacceptable bases.
- getCachedString
Return a cached copy of the supplied string.
- getName
get the name of this codec
- isSymbolicAllele
return true if this is a symbolic allele (e.g. ) or structural variation
breakend (with [ or ]), oth
- isVCFStream
- oneAllele
create a an allele from an index and an array of alleles
- parseAlleles
parse out the alleles
- parseFilters
parse the filter string, first checking to see if we already have parsed it in a
previous attempt