The approach taken for determining the placement of read pairs is the following:
- First, all the optimal placements for the two individual reads are found.
- Then, the allowed placements according to the paired options are found.
- If both reads can be placed independently but no pairs satisfy the paired criteria, the reads are treated as independent and not marked as a pair.
- If only one pair of placements satisfy the criteria, the reads are placed accordingly and marked as uniquely placed even if either read may have multiple optimal placements.
- If several placements satisfy the paired criteria, the read is treated according to the above described option for ambiguously placed reads. The number of places for the reads are reported as the possible number of placements of the whole pair, not the individual reads.