R/utils.R

In lawremi/VariantToolsData: Data for the VariantTools tutorial

sumDepths <- function(x) {
    ans <- unique(unlist(x, use.names=FALSE))
    ad.sum <- 0L
    td.sum <- 0L
    rd.sum <- 0L
    for (xi in as.list(x, use.names=FALSE)) {
        m <- match(ans, xi)
        td.sum <- td.sum + ifelse(is.na(m), 0L, totalDepth(xi)[m])
        ad.sum <- ad.sum + ifelse(is.na(m), 0L, altDepth(xi)[m])
        rd.sum <- rd.sum + ifelse(is.na(m), 0L, refDepth(xi)[m])
    }
    altDepth(ans) <- ad.sum
    totalDepth(ans) <- td.sum
    refDepth(ans) <- rd.sum
    ans
}