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Below are my understandings:
bcf_gt_phased
andbcf_gt_unphased
encodeidx
toval
bcf_gt_is_phased
andbcf_gt_allele
decodeval
to phase info andidx
For instance,
idx = 0(ref), 1, 2, 3(alt)
when phased(
|
), the corresponding values areval = 3, 5, 7, 9;
when unphased (
\
), the corresponding values areval = 2, 4, 6, 8;
According to vcf: line 1168, I believe
val
is what the author refers to.