Dear Daniel,
do you plan implementing this kind of DAA merging option? It will be useful for creating one combined (instead of two - long read/contig & remained read level files) meganized daa file that contains alignment of de novo assembled contigs and non remappable reads with low abundance. I suppose that the result should be more consistent and contains less false positives / homologies with preserved sensitivity to single reads and unassembled, shorter genome fragments.
Bests: Balázs