rename avg_unique_mapped_coverage
to effective_coverage
. #217
Description
In #211, I 'coined' the term avg_unique_mapped_coverage
for the coverage of only the bases that were actually mapped.
then I got curious if I was badly reinventing existing terms, much like we did with detection. so I asked on the microbial bioinformatics slack, and got this nice response from Lee Katz:
I think we call this effective coverage
and using that as google bait I found this paper, "Understand Effective Coverage by Mapped Reads using Genome Repeat Complexity", with the definition:
The effective coverage of a chromosome is defined as the actual amount of bases covered by reads.
which (from text later on) I infer to mean weighted by the number of times the base is actually covered by a read.
So I think we should rename avg_unique_mapped_coverage
to effective_coverage
.