Narrow output to specific positions

The pileup, sample-probs, summary, and extract sub commands have a --include-bed (or --include-positions) option that will restrict analysis to only positions that overlap with the intervals contained within the BED file.

In the case of pileup, summary, and sample-probs, the pass-threshold will be estimated with only base modification probabilities that are aligned to positions overlapping intervals in the BED. In the case of pileup and extract only positions will be reported if they overlap intervals in the BED.