Position filtering

[csoneson]

• [x] sequence context (done in af66b27676da764d7226f055b3acd2fc91aeb435)
• [x] coverage (currently inside the calcReadStats function) (done in 26c7e41)
• [x] collapsing/pruning repeated positions (done in fe95936)
• [x] remove positions that are NA in all reads in all samples (done in 8ad2d22)
• [x] each of these go into a separate helper function
• [x] new function filterPositions() - calls one or more of the helper functions (done in b1e79e5)
• [ ] call read-NA-filtering in the end (by default turned on) to remove reads that are now all NA in the retained positions

[csoneson]

Some things to discuss:

• Currently, keeping positions matching sequence context TAG also retains (e.g.) NNN.
• Not totally sure if the current names for these filtering functions are the most intuitive.
• Should the coverage filter be applied to the sum across samples or to individual samples (e.g. require at least one sample to pass the coverage threshold)?
• For .removeAllNAPositions(), do we allow a summary assay (and if so, check for rowSums > 0 instead of presence of any non-NA values?