Dear developers

In the following case countBam does not give the expected result:

>  param = ScanBamParam()
>  bamFlag(param) = scanBamFlag(isUnmappedQuery=TRUE)
>  cb = countBam(bamFile, param=param)
>  cb
   space start end width     file records nucleotides
1    NA    NA  NA    NA 4541.bam 3157955   133205755
>  bamReads = scanBam(bamFile, param=param)[[1]]$qname
>  scanBam(bamFile, param=param)[[1]]
named list()


There are no unmapped reads in my bamFile and so it should return 0, or am I wrong?

regards,
hubert



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