Bug with read recruitment when targets have an ARC-like name

[samhunter]

Due to kind of a hack to stop ARC from recruiting reads which were already incorporated into a target, there exists a bug where ARC will refuse to recruit reads on the first iteration if the targets are named in a certain way

The code for this is in the mapper:

handle references built using assembled contigs:

if len(target.split(":")) == 3: target, status = target.split(":")[1:]

This keeps ARC from writing reads which mapped to finished contigs

if status.startswith("Contig") or status.startswith("isogroup"):
continue

[samhunter]

Unfortunately it isn't clear how to fix this bug without redesigning the strategy for limiting the number of targets a read can be mapped to.