Use duplexes to compute mutation candidate distance to ligation site (instead of doing it on a read by read basis), even if there are no Q2 duplexes (fall back on Q1 duplexes instead, if they are present).
Use duplexes to compute mutation candidate distance to ligation site (instead of doing it on a read by read basis), even if there are no Q2 duplexes (fall back on Q1 duplexes instead, if they are present).

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