Nothing

```
context("Counting mutations")
alns <- GenomicAlignments::GAlignments(seqnames=rep("1", 5),
pos=as.integer(rep(1,5)),
cigar=c("10M", "5M1D5M", "4M1D6M4D2M",
"1M2D3M4I", "2M3I2M3I2M"),
strand = S4Vectors::Rle(factor(rep("+", 5),
levels = c("+","-","*"))))
test_that("countDeletions returns the expected counts", {
expect_equal(countDeletions(alns), 1)
expect_equal(countDeletions(alns, multi.del = TRUE), 2)
expect_equal(countDeletions(alns, del.and.ins = TRUE), 2)
expect_equal(countDeletions(alns, multi.del = TRUE, del.and.ins = TRUE), 3)
expect_equal(countDeletions(alns, del.ops=c("N")), 0)
})
test_that("countInsertions returns the expected counts", {
expect_equal(countInsertions(alns), 0)
expect_equal(countInsertions(alns, multi.ins = TRUE), 1)
expect_equal(countInsertions(alns, ins.and.del = TRUE), 1)
expect_equal(countInsertions(alns, multi.ins = TRUE, ins.and.del = TRUE), 2)
})
test_that("countIndels returns the expected counts", {
expect_equal(countIndels(alns), 4)
})
test_that("indelPercent returns the expected value", {
expect_equal(indelPercent(alns), (4/5)*100)
})
context("Accessory plotting functions")
test_that("Extraploation of x-tick labels works correctly", {
tck <- .getAxisCoords(c(1:20), label.at = 10, lab.boundaries = c(-1,1))
# Only boundaries within the labels are included
expect_equal(tck$tick_labs, c(1,10,20))
# Error if labels aren't the same length as locations
expect_error(.getAxisCoords(c(1:20), "A"))
tck <- .getAxisCoords(c(1:23), labels = c(-17:-1, 1:6),
label.at = 2, lab.boundaries = c(-1,1))
tmp <- setdiff(c(seq(-16,6, by = 2), c(-1,1)),0)
exp_result <- tmp[order(tmp)]
expect_equal(tck$tick_labs, exp_result)
# If min.tick.sep is increased, ticks close to boundary
# should be removed
tck <- .getAxisCoords(c(1:23), labels = c(-17:-1, 1:6),
label.at = 2, lab.boundaries = c(-1,1),
min.tick.sep = 2)
expect_equal(tck$tick_labs, exp_result[!exp_result %in% c(-2,2)])
})
```

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