calcObservedMutations return object is not consistent

[Jason Vander Heiden]

calcObservedMutations does not return R and S mutations, only total mutations if regionDefinition=NULL and/or frequency=TRUE. Meaning, we can't do selection on the full sequence. The behavior should be consistent, and return R and S in all cases. If we want the total mutation behavior, then we should add another flag for that.

[Namita Gupta]

This has been partially fixed with Susanna's creation of the null regionDefinition for the full sequence

[Namita Gupta]

Maybe still need to check behavior when frequency=TRUE

[ssnn]

Yes, the frequency needs to be checked. Also, I believe the frequency doesn't mean the same for observed and expected mutations. But I am not familiar with the code, I am reading it (pretty much all of it, thank you guys!) for the first time.

[Namita Gupta]

Frequency flag only exists with observed mutations, but now calcObservedMutations always returns the same region_R and region_S mutations, but it is either absolute counts or frequencies (divided by non-N bps in seq and gl in the region).