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-Add read length parameter. For dnase, it makes sense to just consider the reads at length 1, which is what I'm doing now. But this needs to be a parameter.
-Allow for noise supression. For really weak regions that are clearly clearly clearly not peaks, I should just eliminate the signal track alltogether, so save space (making the density output sparse).
-Maybe make a default setting for dnase, and one for chip? It looks like chip would do better with a wider window.
-for chip.
-add in background correction files for strange copy number cell lines? (like fseq)
-correct for mappability?
maybe I could have used binary file writing instead of extending to C.