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grl <- GRangesList(
A=GRanges("20", IRanges(14370, 17331)),
B=GRanges("20", IRanges(17330, width=1)),
C=GRanges("20", IRanges(1110696, width=1)),
D=GRanges("20", IRanges(1110696, width=2)))
test_summarizeOverlaps_ <- function()
{
fl <- system.file("extdata", "ex2.vcf", package="VariantAnnotation")
vcf <- readVcf(fl, "hg19")
sv <- summarizeVariants(grl, vcf, findOverlaps)
checkIdentical(ncol(vcf), ncol(sv))
checkIdentical(length(grl), nrow(sv))
target <- matrix(c(0, 0, 1, 1, 2, 1, 1, 1, 1, 0, 1, 1), ncol=3)
current <- unname(assays(sv)$counts)
checkIdentical(current, target)
}
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