test_rangesTo <- function() {
gds <- SeqVarTools:::.testData()
ranges <- GRanges("1", IRanges(start=c(1e6,3e6), end=c(2e6,4e6)))
checkEquals(1:7, SeqVarTools:::.rangesToSel(gds, ranges))
checkEquals(1:7, SeqVarTools:::.rangesToID(gds, ranges))
# check empty ranges
ranges <- GRanges("X", IRanges(start=c(1e6,3e6), end=c(2e6,4e6)))
checkEquals(0, length(SeqVarTools:::.rangesToSel(gds, ranges)))
seqClose(gds)
}
test_nSamp <- function() {
gds <- SeqVarTools:::.testData()
n <- sum(seqGetFilter(gds)$sample.sel)
checkEquals(n, SeqVarTools:::.nSamp(gds))
n <- 10
seqSetFilter(gds, sample.sel=1:n)
checkEquals(n, SeqVarTools:::.nSamp(gds))
seqClose(gds)
}
test_nVar <- function() {
gds <- SeqVarTools:::.testData()
n <- sum(seqGetFilter(gds)$variant.sel)
checkEquals(n, SeqVarTools:::.nVar(gds))
n <- 10
seqSetFilter(gds, variant.sel=1:n)
checkEquals(n, SeqVarTools:::.nVar(gds))
seqClose(gds)
}
test_nSampUnfiltered <- function() {
gds <- SeqVarTools:::.testData()
n <- SeqVarTools:::.nSamp(gds)
seqSetFilter(gds, sample.sel=1:10)
checkEquals(n, SeqVarTools:::.nSampUnfiltered(gds))
seqClose(gds)
}
test_nVarUnfiltered <- function() {
gds <- SeqVarTools:::.testData()
n <- SeqVarTools:::.nVar(gds)
seqSetFilter(gds, sample.sel=1:10)
checkEquals(n, SeqVarTools:::.nVarUnfiltered(gds))
seqClose(gds)
}
test_emptyGenoMatrix <- function() {
gds <- SeqVarTools:::.testData()
SeqVarTools:::.emptyVarFilter(gds)
checkTrue(SeqVarTools:::.emptyDim(gds))
m <- SeqVarTools:::.emptyGenoMatrix(gds, use.names=TRUE)
checkEquals(SeqVarTools:::.nSamp(gds), nrow(m))
checkEquals(0, ncol(m))
checkEquals(seqGetData(gds, "sample.id"), rownames(m))
seqResetFilter(gds, verbose=FALSE)
SeqVarTools:::.emptySampFilter(gds)
checkTrue(SeqVarTools:::.emptyDim(gds))
m <- SeqVarTools:::.emptyGenoMatrix(gds, use.names=TRUE)
checkEquals(SeqVarTools:::.nVar(gds), ncol(m))
checkEquals(0, nrow(m))
checkEquals(as.character(seqGetData(gds, "variant.id")), colnames(m))
seqClose(gds)
}
test_nSampObserved <- function() {
gds <- SeqVarTools:::.testData()
nso <- SeqVarTools:::.nSampObserved(gds)
checkEquals(SeqVarTools:::.nVar(gds), length(nso))
checkEquals(SeqVarTools:::.nSamp(gds), max(nso))
seqClose(gds)
}
test_nSamp_empty <- function() {
gds <- SeqVarTools:::.testData()
seqSetFilter(gds, sample.sel=rep(SeqVarTools:::.nSamp(gds), FALSE), verbose=FALSE)
checkEquals(0, SeqVarTools:::.nSamp(gds))
checkEquals(rep(0, SeqVarTools:::.nVar(gds)), SeqVarTools:::.nSampObserved(gds))
seqClose(gds)
}
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