encode.snp <- function(x)
{
base.shift <- integer(length(x$read_base))
base.shift[x$read_base=='A'] <- 0
base.shift[x$read_base=='C'] <- 1
base.shift[x$read_base=='G'] <- 2
base.shift[x$read_base=='T'] <- 3
x.code <- 4*(x$ref_pos - 1) + base.shift
x.code
}
decode.snv <- function(x)
{
locus <- floor(x/4)
shift <- x%%4
base <- character(length(x))
base[shift==0] <- 'A'
base[shift==1] <- 'C'
base[shift==2] <- 'G'
base[shift==3] <- 'T'
list(base=base, locus=locus)
}
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