Properly handle cases in which both reads in a pair map to the same coordinate.
Properly handle cases in which both reads in a pair map to the same
coordinate.

If paired-end sequencing is used and a fragment has length less than
or equal to the read length, then both reads from that fragment should
map to the same coordinate. Previously, filter_remapped_reads.py skipped
over remapped pairs in which both reads map to the same location,
leading the original SNP-overlapping reads to be discarded. Now such
pairs should be properly handled.

bmvdgeijn/WASP,bmvdgeijn/WASP,gmcvicker/WASP,gmcvicker/WASP,gmcvicker/WASP,bmvdgeijn/WASP,bmvdgeijn/WASP,gmcvicker/WASP