I found that samtools stats classifies dovetailed reads (share the same leftmost position) are classified as either outward- or inward-oriented depending on if read1 (blue in the image below) is on the forward or reverse strand.
The relevant code can be found here: https://github.com/samtools/samtools/blob/4224ee098020b8957bf19343ecbd45f9d7e76efa/stats.c#L1257C13-L1263C14
This results in that dovetailed read pairs are evenly split between being classified as outward or inward.
% samtools view -bh P33410_1001.bam -e 'pos == mpos' | samtools stats | grep orient
SN inward-oriented pairs: 245641
SN outward oriented pairs: 243434
For me, it would make more sense that these reads should rather all be classified as inward-oriented as the ends in fact do not protrude beyond the mate. What do you think?
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