Previously, the -f one-to-one filter plane-sweep filter was applied to all mappings at the same time. In cases where users are mapping multiple query genomes to one or more target sequences with the --skipPrefix # flag, the one-to-one filter would treat all query sequences as part of the same genome/group.
This patch makes it so that the one-to-one plane-sweep filter is applied to each pair of query and reference groups independently, ensuring that -n mappings are retained for each pair. A "group" of sequences is the set of sequences which contain the same prefix up until the last occurrence of the character c, where --skipPrefix c is specified.