WGS read-pairs are always from the same segment

[cerebis]

An oversight has been discovered in the simulation of WGS pairs.

Despite the possibility that real WGS pairs can span neighbouring contigs when occurring at contig-ends, during simulation in sim3C, these contig-spanning WGS pairs are never generated.

This is because no assumption is made regarding the orientation and order of non-contiguous sequences, even when defined as a single molecule group.

It would be possible to allow this as part of the community definition.

Two approaches:

1. stating explicitly that sim3C should consider the multi-fasta as defining the order and orientation
2. allow the user to specify collective ordering and orientations.

The second option would be more work to implement.