[Issue] Remove requirement for snp .bed when running epiread

[njspix]

I would call this more of a feature request than a bug, but would it be possible to remove the requirement for supplying a snp bed to biscuit epiread? Right now, if I want to get an epiread with SNP information in it, I have to do:

biscuit pileup /path/to/ref test.bam | bgzip > test.vcf.gz
biscuit vcf2bed -t snp test.vcf.gz | bgzip > test.bed.gz
biscuit epiread -B test.bed.gz /path/to/ref test.bam | sort -k1,1 -k2,2n | bgzip > test_epiread.bed.gz

I'm not sure how these tools work, but it seems like there is a fair bit of overlap between the pileup and epiread tools. Would it be possible to just run biscuit epiread directly, with a flag for adding in SNP information?

Thanks!
Nathan