Speed up genomecov

[arq5x]

Currently, even with sorted data, the algorithm is two-pass. It can reallty be done in one pass. As such, memory and runtime will be reduced.

[mdshw5]

I'll just put a +1 for this. Sorted BAM input is already a requirement, so this should be simple.

[ghuls]

Is this supported now for BED input? It would be nice if a sorted option would allow it with BED file as input.

bedtools genomecov -sorted -bg -i test.sorted.bed  -g hg38.chrom_sizes.tsv > test.sorted.bg