Non-multiplexed Reference Assignment

[ZwFink]

The demux module should still be able to count probe occurrences when processing read data that is not multiplexed. In this mode, forward indexes, reverse indexes, and sample list arguments will not be used. The score for each probe will be written to a Default sample in the output matrix.

[jtladner]

This is reference-dependent generation of counts, but assuming that there is just a single sample in the run. Therefore, indexes are not relevant.