independent while processing, and only merged back in a priority queue if necessary in a special
variant of the ReadBackedPileup. This code is not live yet except in the case of naive deduping.
Downsampling by sample temporarily disabled, and the ReadBackedPileup variant is sketchy and
not well integrated with StratifiedAlignmentContext or the walkers. Cleanup to follow.
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as walker attributes or from the command-line. Not ready yet! Downsampling/deduping
works in a general sense, but this approach has not been completely optimized or validated.
Use with caution.
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the reference implementation. Also implemented a heap size monitor that can
be used to programmatically report the current heap size.
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from a stream (see Vitter 1985). Thanks to Eric and Andrey for the pointer.
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depristo
hanna