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First-pass implementation of MarkDuplicates downsampling always chooses a subset of chr1.

For targeted libraries which do not include chr1, this will not give useful results. (If zero reads aligned to chr1, Picard MarkDuplicates will exit with an error status.)

If MarkDuplicates downsampling is needed for a targeted sequencing library, read the target file and set the downsampled region(s) accordingly.