Will merge sam_restore_seq.py, dedup_circular_sam.py & re_pair_circular_sam.py

Starting sam_undouble_circles.py as a copy of sam_restore_seq.py,
plan is to merge in functionality of dedup_circular_sam.py and
re_pair_circular_sam.py scripts.
Add command line API from dedup_circular_sam.py
Batch SAM lines by QNAME
Refactor SEQ restoration as iterator function
Update POS and PNEXT using logic from dedup_circular_sam.py
Bug fix, also update PNEXT when RNEXT was an equals sign.

Found while working on replacement script sam_undouble_circles.py
De-duplicate after un-doubling reads mapped to a circle
Remove now obsolete script, use sam_undouble_circles.py instead