Major change to chimeric blacklist handling of chimeric reads (3 alignments)...

Major change to chimeric blacklist handling of chimeric reads (3 alignments) with one MAPQ 0. Used to go into Normal Paired with the MAPQ 0 read discarded, now goes into low mapq collisions; this is more consistent with Juicer 1.5 behavior. Added flag for including MAPQ 0 reads when calling Juicer.