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?
I found that
samtools statsclassifies 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.
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?