Proportional coverage is trivial to compute and can be done on the fly if really necessary (e.g., for plotting? When else do we need it?). Only allowing raw read counts will make the interface for the CoveragePanelOfNormals simpler, among other things.
If we want to keep pcov output around, we could move it into NormalizeSomaticReadCounts (which seems like a more natural home for it anyway).
samuelklee
commented
7 years ago
Proportional coverage is trivial to compute and can be done on the fly if really necessary (e.g., for plotting? When else do we need it?). Only allowing raw read counts will make the interface for the CoveragePanelOfNormals simpler, among other things.
If we want to keep pcov output around, we could move it into NormalizeSomaticReadCounts (which seems like a more natural home for it anyway).