Nothing
# TODO: test indelDiff()
#
test_indelDiff <- 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')
## test deletion
deletionTest <- indelDiff(bam1,bam2,refFsa,'chr04',962501,1026983,pValueCutOff=1,gtDistCutOff=0,verbose=FALSE,nCores=2)
checkEquals(deletionTest$pos, 1026860)
checkEquals(deletionTest$ref, 'TCG')
checkEquals(deletionTest$altGt1, 'T')
## test insertion
insertionTest <- indelDiff(bam1,bam2,refFsa,'chr07',828514,828914,pValueCutOff=1,gtDistCutOff=0,nCores=2)
checkEquals(insertionTest$pos, c(828636,828714))
checkEquals(insertionTest$ref, c('GCCA','CAAAAAAA'))
checkEquals(insertionTest$altGt1, c('GCCACCA','CAAAAAAAA'))
## test NULL
checkTrue(is.null(indelDiff(bam1,bam2,refFsa,'chr04',962501,1026983,pValueCutOff=1,gtDistCutOff=2,verbose=FALSE,nCores=2)))
}
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