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.noGaps <- GAlignments(
Rle(factor(c("chr1", "chr2", "chr1", "chr3")),
c(1, 3, 2, 4)),
pos=1:10, cigar=paste0(10:1, "M"),
strand=Rle(strand(c("-", "+", "*", "+", "-")),
c(1, 2, 2, 3, 2)),
names=head(letters, 10), score=1:10)
.Gaps <- GAlignments(
Rle(factor(c("chr2", "chr4")), c(3, 4)), pos=1:7,
cigar=c("5M", "3M2N3M2N3M", "5M", "10M", "5M1N4M", "8M2N1M", "5M"),
strand=Rle(strand(c("-", "+")), c(4, 3)),
names=tail(letters, 7), score=1:7)
test_GAlignments_qnarrow <- function()
{
gal <- GAlignments(seqnames=rep(factor("A"), 8),
pos=10:17,
cigar=c("5M", "5X", "3M2I3M", "3M2D3M",
"3M2N3M", "3M2S3M", "3M2H3M", "3M2P3M"),
strand=Rle(strand(rep("+", 8))))
n1 <- narrow(gal, start=3)
q1 <- qnarrow(gal, start=3)
checkIdentical(qwidth(n1), qwidth(q1))
checkIdentical(width(n1), width(q1))
n2 <- narrow(gal, start=4)
q2 <- qnarrow(gal, start=4)
checkIdentical(width(n2), width(q2))
## M and X
checkIdentical(qwidth(n2[1:2]), qwidth(q2[1:2]))
## I
checkIdentical(qwidth(q2[3]), width(q2[3]) + 2L)
## D, N and P
checkIdentical(qwidth(q2[c(4,5,8)]), width(q2[c(4,5,8)]))
## S and H
checkIdentical(qwidth(q2[6]), width(q2[6]) + 2L)
checkIdentical(qwidth(q2[7]), width(q2[7]))
}
test_GAlignmentsList_qnarrow <- function()
{
galist <- GAlignmentsList(.noGaps[1:6], .Gaps)
qn <- qnarrow(galist, end=-4)
checkIdentical(qnarrow(galist[[1]], end=-4), qn[[1]])
checkIdentical(qnarrow(galist[[2]], end=-4), qn[[2]])
}
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