addReadsSummary

[csoneson]

• [x] change default value of keep.reads in addReadsSummary to TRUE (6c70984)
• [x] summary assays should be sparse arrays (ec236ca): Decided to leave the assays dense, because:
  • Nmod, Nvalid and AvgConf are dense because rowSums is based on MatrixGenerics::rowSums, which returns a (dense) numeric vector
  • Nvalid typically has few zeros, and the SparseArray version would be larger in memory than the dense one
  • FracMod and Pmod have to be calculated using dense matrices and would have to be converted back to sparse objects (no "/" method for SparseArray objects, as the result wouldn't be sparse in general)
• [x] make sure that the output of readBedMethyl is consistent with the output of addReadsSummary (5fe339f)

[mbstadler]

I think this is done - feel free to reopen if you see any remaining issues