Review and re-add coverage calculation

[kweav]

Issue Description

Coverage calculation used a hardcoded value not equal to the number of lines in the input file and so a more thorough review of the calculation in its original context needs to be undertaken in order to understand how to make a generalizable formula.

Inputs

For the desired generalizable function, the input should be a read count matrix where the number of samples is the number of columns and the number of paired guides is the number of rows. Alternatively, the reworked code used a counts_per_sample which sums the number of reads across the paired guides for each sample column.