Hi Stephen,

I was able to reproduce the error. It appears that you have unmapped reads
in your bam file which we always filter out during conversion of sam to bam
files using samtools view -S -F 4 -b -o out.bam in.sam (single end
sequening data). In case you filter your bam files accordingly, the error
message should disappear.  However, I will add an additional flag
scanBamFlag(isUnmappedQuery = F) to the according scanBam() function in
dev. Therefore, unmapped reads in a given bam file should be ignored in the
future (MEDIPS version >=1.11.1).

Lukas


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