Hi

When I excute mappy with paired ends like

aligner.map(seq1,seq2, MD=True):

MD string for second reads is wrong.
for example for 100nt length perfect match, it reports.
0T2A0G1C0T0C0A0T0T1T1T0T0G0C0C1A1G0C0T0G0G0A0G0T0G0C1G0T0G0G0T0G0T0G0A1C0T0C0G0G0C0T0C0A0C0T0G0C0A1C0C0C0C0C0A0A0C0C0C1C0A0C0T1C0C0C0A0G2T1A0A1C0G0A1T1T0C0C0T0G0C0C

I think, it maybe that second string is not reverse complemented when generating MD string.
(I put read FR oriented as instructed and mapping just works fine.)

Thanks in Advance.