Nothing
# TODO: test snpDiff() using RUnit
## for normal test
test_snpDiff <- function(){
bam1 <- system.file(package='SICtools','extdata','example1.bam')
bam2 <- system.file(package='SICtools','extdata','example2.bam')
refFsa <- system.file(package='SICtools','extdata','example.ref.fasta')
## check
snpTest <- snpDiff(bam1,bam2,refFsa,'chr04',1,1531933,pValueCutOff=1,baseDistCutOff=0,nCores=2)
checkEquals(nrow(snpTest),17)
checkEquals(subset(snpTest,p.value < 1e-10)$pos,c(962801,1026683))
checkEquals(subset(snpTest, A1 == 16)$pos,c(963005,1026599))
## check NULL
checkTrue(is.null(snpDiff(bam1,bam2,refFsa,'chr04',962501,1026983,pValueCutOff=0,baseDistCutOff=0,nCores=2)))
}
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