org.hammerlab.guacamole.jointcaller
the contig (chromosome)
the position of the allele
reference allele, must be nonempty
alternate allele, may be equal to reference
alternate allele, may be equal to reference
the contig (chromosome)
Zero-based exclusive end site on the reference genome.
reference allele, must be nonempty
the position of the allele
Apply a transformation function to the alleles (ref and alt) and also the start and end coordinates, returning a new AlleleAtLocus.
Apply a transformation function to the alleles (ref and alt) and also the start and end coordinates, returning a new AlleleAtLocus.
This is used when we need to change the number of bases of reference context used, e.g. to change the variant "A>C" to "GA>GC", as part of harmonizing it with other variants of different lengths at the same site.
transformation function on alleles
transformation function on (start, end) pairs.
a new AlleleAtLocus instance
An allele (alt) at a site in the genome. We also keep track of the reference allele (ref) at this site.
Usually alt != ref, but in some cases, such as force calling positions with no variant reads, we can have alt == ref.
Indels are supported in the usual VCF style, in which ref.length != alt.length. ref.length and alt.length are > 0 (e.g. an insertion is represented as A -> ACC) and therefore end > start. The length of the reference allele determines the size of the region.
NOTE: We currently evaluate only a single alternate at each site at a time, i.e. the mixtures whose likelihoods we compute are always just a reference and at most one alternate allele. If we extend this to mixtures with multiple alts, we should change this class to contain any nuber of alts.
the contig (chromosome)
the position of the allele
reference allele, must be nonempty
alternate allele, may be equal to reference