cnvkit.py coverage does not honor -q option

[ishida-md]

Hi, I am running the latest cnvkit image on the docker hub.
I get spurious calls where many reads with mapq = 0. I tried cnvkit.py coverage with the -q option, but it does not do anything. Is this a bug?

Here is the snippet:
singularity exec -e --env OMP_NUM_THREADS=1 --bind /home cnvkit_0.9.11.sif cnvkit.py coverage -o mapq0.cnn test.bam xgen.t750.bed

singularity exec -e --env OMP_NUM_THREADS=1 --bind /home cnvkit_0.9.11.sif cnvkit.py coverage -o mapq60.cnn -q 60 test.markdup.bam xgen.t750.bed

mapq0.cnn and mapq60.cnn are identical although I see a lot of mapq = 0 reads on IGV.