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test_readGAlignmentsFromBam <- function()
{
fl <- system.file("extdata", "ex1.bam", package="Rsamtools")
which <- RangesList(seq1=IRanges(1, width=100))
param <- ScanBamParam(which=which)
result <- readGAlignmentsFromBam(fl, param=param)
checkTrue(validObject(result))
checkIdentical(c(seq1=1575L, seq2=1584L), seqlengths(result))
}
test_readGAlignmentsFromBam_missing_param <- function()
{
fl <- system.file("unitTests", "cases", "ex1_noindex.bam",
package="Rsamtools")
result0 <- readGAlignmentsFromBam(fl)
checkTrue(validObject(result0))
bf <- open(BamFile(fl, character()))
result1 <- readGAlignmentsFromBam(bf)
checkIdentical(result1, result0)
}
test_readGAlignmentsFromBam_length0 <- function()
{
fl <- system.file("extdata", "ex1.bam", package="Rsamtools")
which <- RangesList(seq1=IRanges(100000, width=100))
param <- ScanBamParam(which=which)
result <- readGAlignmentsFromBam(fl, param=param)
checkTrue(validObject(result))
which <- RangesList(seq1=IRanges(c(1, 100000), width=100))
param <- ScanBamParam(which=which)
result <- readGAlignmentsFromBam(fl, param=param)
checkTrue(validObject(result))
}
test_readGAlignmentsFromBam_tag <- function()
{
fl <- system.file("extdata", "ex1.bam", package="Rsamtools")
## valid
param <- ScanBamParam(tag=("NM"))
gal <- readGAlignmentsFromBam(fl, param=param)
checkIdentical(924L, sum(mcols(gal)[["NM"]]))
## empty
param <- ScanBamParam(tag=("FO"))
gal <- readGAlignmentsFromBam(fl, param=param)
checkIdentical(rep.int(NA, length(gal)), mcols(gal)[["FO"]])
}
test_readGAlignmentsFromBam_BamViews <- function()
{
checkTrue(validObject(readGAlignmentsFromBam(BamViews())))
src <- system.file("unitTests", "cases", package="Rsamtools")
fl <- c(system.file("extdata", "ex1.bam", package="Rsamtools"),
file.path(src, "ex1_shuf1000.bam"))
bv <- BamViews(fl, auto.range=TRUE)
rng <- bamRanges(bv)
aln <- readGAlignmentsFromBam(bv)
checkEquals(length(bamPaths(bv)), length(aln))
fl <- c(fl, tempfile())
bv <- BamViews(fl, bamRanges=rng)
msg <- NULL
suppressWarnings({
tryCatch({
aln <- readGAlignmentsFromBam(bv)
}, error=function(err) {
msg <<- conditionMessage(err)
})
})
tst <- sprintf("'readGAlignmentsFromBam' failed on '%s'",
names(bv)[3])
checkIdentical(tst, msg)
}
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