Hi guys,
What are the plans for the BamViews class. It looks like a useful
foundation. One thing that would be good to have in R is a way to calculate
"pileups" or base tallies for positions of interest. These counts could be
broken down by sample (bamfile), cycle (position in the read), etc. Results
returned as a DataFrame (in a format like that returned by as.data.frame on
a table) that could be aggregated() up as desired. Rles would save memory.
So there could be something like a alphabetFrequency() method for BamViews.
This is related to Steve's recent work with counting over XStringSets.
Surely there are many other features that could be added. The above is just
one that I would use often, across a number of contexts.
Thanks,
Michael
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