Add filter for not primary alignment or at least document it?

[mmterpstra]

Using bwa also outputs not primary alignments. These reads are flagged by the 256 flag (https://broadinstitute.github.io/picard/explain-flags.html). Preferably you would also filter them with the readcounter tool or you want the step being described in the manual.

There is a filter for duplicate alignment here (ideally the best place to insert it):
https://github.com/shahcompbio/hmmcopy_utils/blob/29a8d1d18dfd301600d5d91832e5fe231935058c/src/bin/readCounter.cpp#L194C1-L194C63

or update documentation in the README.md around here with a note.