Example on how to reconstruct alignment from pysam aligned segment

pysam_alignedpairs.py

# assuming:
# - refsq is set and always the same
# - bamfh is an open pysam samfile
for r in bamfh:
    if r.is_unmapped:
      continue

    for (qapos, rpos) in r.get_aligned_pairs():
        # qapos is the aligned index, i.e. this ignores clipping. add that
        if qapos is None:
            qpos = None
        else:
            qpos = qapos + r.query_alignment_start
        # qpos and rpos now safe to use, but might be None (indel)

        rbase = qbase = "-"
        if rpos is not None:
            rbase = refsq[rpos].upper()
        if qpos is not None:
            qbase = r.seq[qpos].upper()
        # now you can use rbase and qbase

        # ...