I'm getting populated windows over an entire chromosome for a BAMPairedFragmentCollection, and the counts are a little low but not far off. I've dug into which fragments are missing from the counts and can't see a pattern. All types of mapped fragments seem to be represented in the missing fragments, including perfectly healthy fragments that pass filters and the mates do not overlap and are oriented as you would expect. Most fragments are included though.
I'm calling getPopulatedWindows() on a BAMPairedFragmentCollection. I'm passing in an entire chromosome as the region and getting 1kb windows over the whole chromosome.
I'm getting populated windows over an entire chromosome for a BAMPairedFragmentCollection, and the counts are a little low but not far off. I've dug into which fragments are missing from the counts and can't see a pattern. All types of mapped fragments seem to be represented in the missing fragments, including perfectly healthy fragments that pass filters and the mates do not overlap and are oriented as you would expect. Most fragments are included though.
I'm calling getPopulatedWindows() on a BAMPairedFragmentCollection. I'm passing in an entire chromosome as the region and getting 1kb windows over the whole chromosome.