docs: def parseFilteringOptions(cls, args, filterRead=None, storeQueryIds=False):
          """
          Parse command line options (added in C{addSAMFilteringOptions}.
  
          @param args: The command line arguments, as returned by
              C{argparse.parse_args}.
          @param filterRead: A one-argument function that accepts a read
              and returns C{None} if the read should be omitted in filtering
              or else a C{Read} instance.
          @param storeQueryIds: If C{True}, query ids will be stored as the
              SAM/BAM file is read.
          @return: A C{SAMFilter} instance.
          """
          referenceIds = (set(chain.from_iterable(args.referenceId))
                          if args.referenceId else None)
  
          return cls(
              args.samfile,
              filterRead=filterRead,
              referenceIds=referenceIds,
              storeQueryIds=storeQueryIds,
              dropUnmapped=args.dropUnmapped,
              dropSecondary=args.dropSecondary,
              dropSupplementary=args.dropSupplementary,
              dropDuplicates=args.dropDuplicates,
              keepQCFailures=args.keepQCFailures,
              minScore=args.minScore,
              maxScore=args.maxScore)