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test_GAlignments_constructor <- function()
{
checkTrue(validObject(GAlignments()))
checkTrue(validObject(GAlignments(seqnames=factor("A"),
pos=1L, cigar="1M",
strand=strand("-"))))
}
test_GAlignments_seqlevels <- function()
{
gal0 <- GAlignments(seqnames=Rle(c("chr1", "chr2")),
pos=as.integer(c(10, 100)),
cigar=c("50M", "50M"),
strand=strand(c("*", "*")))
## Drop
gal <- gal0
seqlevels(gal, force=TRUE) <- "chr2"
checkIdentical("chr2", seqlevels(gal))
## Rename
gal <- gal0
seqlevels(gal)[seqlevels(gal) == "chr2"] <- "2"
checkIdentical(c("chr1", "2"), seqlevels(gal))
}
test_GAlignments_combine <- function()
{
galn <- GAlignments(seqnames=factor("A"),
pos=1L, cigar="1M",
strand=strand("-"))
galn_c <- GAlignments(seqnames=rep(factor("A"), 2),
pos=rep(1L, 2), cigar=rep("1M", 2),
strand=rep(strand("-"), 2))
checkIdentical(galn_c, c(galn, galn))
}
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