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expand <- VariantAnnotation::expand
test_expand_info_geno <- function()
{
fl <- system.file("unitTests", "cases", "expand.vcf",
package="VariantAnnotation")
vcf <- suppressWarnings(readVcf(fl, "hg19"))
exp <- expand(vcf)
names(mcols(rowData(exp)))
cnms <- c("paramRangeID", "REF", "ALT", "QUAL", "FILTER")
checkIdentical(cnms, names(mcols(rowData(exp))))
checkTrue(nrow(exp) == 22L)
checkIdentical(info(exp)$DP[5:6], c(10L, 10L))
checkIdentical(info(exp)$AF[5:6], c(0.333, 0.667))
checkIdentical(geno(exp)$AAP[6:11], c(2L, rep(1L, 4L), 3L))
}
test_expand_structural <- function()
{
fl <- system.file("extdata", "structural.vcf", package="VariantAnnotation")
vcf <- readVcf(fl, "hg19")
exp <- expand(vcf)
checkTrue(nrow(vcf) == nrow(exp))
checkTrue(ncol(vcf) == ncol(exp))
checkTrue(is.character(alt(exp)))
}
test_expand_structural <- function()
{
fl <- system.file("unitTests", "cases", "mixedStructural.vcf",
package="VariantAnnotation")
vcf <- readVcf(fl, "hg19")
exp <- expand(vcf)
checkTrue(nrow(exp) == 8L)
}
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