[BioC] Computing the coverage on a bamfile with a huge amount of seqlevels

[Stefanie Tauber]

What is the best way to compute the coverage on a ReadGAlignments object
when I have many, many (about 50 000) seqlevels?

Just computing coverage(object) is terribly slow due to the huge amount of seqlevels.

At the moment, I am subsetting the ReadGAlignments object for each seqlevel,
 I omit the redundant seqlevels and calculate the coverage.
This is fast if you do it for a few seqlevels.
But if one really would like to compute the coverage for each seqlevel individually,
this really takes a long time..


I would appreciate any comments!

Best,
Stefanie