RodWalkers are really fast and great. Is there any way to connect a BAM file to it and get the pileup in the given positions? If not, what is the appropriate way to get pileups for a small set of selection positions?
Is there anyway to generate a jar file to execute a single walker that I wrote?
Is there anyway to write a sliding window RodWalker? I've been try to look in your documentation, but I have not found a clue.