Nothing
test_mapqFilter <- function() {
fl <- system.file("extdata", "ex1.bam", package="Rsamtools")
p1 <- ScanBamParam(what="mapq")
p2 <- ScanBamParam(what="mapq", mapqFilter=74)
mapq1 <- scanBam(fl, param=p1)[[1]][["mapq"]]
mapq2 <- scanBam(fl, param=p2)[[1]][["mapq"]]
checkTrue(length(mapq1[!is.na(mapq1) & mapq1 == bamMapqFilter(p2)]) > 0)
checkIdentical(mapq2, mapq1[!is.na(mapq1) & mapq1 >= bamMapqFilter(p2)])
n <- countBam(fl, param=p2)
checkIdentical(n$records, length(mapq2))
checkException(ScanBamParam(mapqFilter=-1), silent=TRUE)
checkException(ScanBamParam(mapqFilter=1:2), silent=TRUE)
checkIdentical(bamMapqFilter(p2), 74L)
bamMapqFilter(p2) <- 75
checkIdentical(bamMapqFilter(p2), 75L)
bamMapqFilter(p2) <- "76.1"
checkIdentical(bamMapqFilter(p2), 76L)
}
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