`lineage`

jennifer

import "@deckyard/forensicgenetics/lineage.j" as lineage;

mtDNA and Y-STR haplotypes. Independent of the rest of the deck. Signatures, constants and struct fields are in the Cheatsheet.

Conventions

Counts: N > 0, k in [0, N], confidence in (0.5, 1). The bound is exactly 1.0 at k == N, so the LR there is 1.
Positions are 1-based rCRS coordinates in [1, 999999]; insertion indices in [1, 9999]. Parsing ignores case and surrounding whitespace.
Differences sort by position, then insertion index.
mtMatches and mtDistance ignore sequenced ranges; mtRangesAgree compares them as sets.
align upper-cases its input, ignores whitespace, accepts IUPAC codes, and slides indels to the 3' end of homopolymer runs. No reference is bundled. EMPOP's phylogenetic alignment rules are not applied.
Y-STR multi-copy loci are written "11,14" or "11/14" and compared sorted. Only shared loci are compared.

Error{kind: "lineage"}, thrown for:

a non-positive N, a k outside [0, N], or a confidence outside (0.5, 1)
a malformed difference designation, a position outside [1, 999999], an insertion index of 0 or over four digits, or a deleted insertion
an unknown kind in formatDifference
in align and mtHaplotypeFrom: an empty sequence, a non-positive refStart, a non-IUPAC character, or a sequence longer than MAX_ALIGN_LENGTH
an empty locus name, a locus with no allele, or a Y-STR allele that is not a repeat count
two Y haplotypes sharing no locus, or with different copy counts at a shared locus
a negative steps