When counting fragments (paired end reads) overlapping a genomic window that I got by calling getPopulatedWindows() on an entire chromosome, we only count a fragment if the actual reads overlap the window. We don't count it if the insert (not captured in reads) overlaps the window. Is that the behavior we want?
Specifically, I'm calling getAnnotationsInWindow() on a PopulatedWindow<PairedMappedFragment>.
When counting fragments (paired end reads) overlapping a genomic window that I got by calling getPopulatedWindows() on an entire chromosome, we only count a fragment if the actual reads overlap the window. We don't count it if the insert (not captured in reads) overlaps the window. Is that the behavior we want?
Specifically, I'm calling getAnnotationsInWindow() on a PopulatedWindow<PairedMappedFragment>.