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Solve the following problem using Python, implementing the functions described below, one line at a time
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Description:
 def _handle_special_inputs(inputs, variables):
 """Adjust input variables based on special cases. This case handles inputs where we are optional or can have flexible choices. XXX Need to better expose this at a top level definition. """

    from bcbio import structural
    optional = [["config", "algorithm", "coverage"],
                ["config", "algorithm", "variant_regions"],
                ["config", "algorithm", "sv_regions"],
                ["config", "algorithm", "validate"],
                ["config", "algorithm", "validate_regions"]]
    all_vs = set([get_base_id(v["id"]) for v in variables])
    out = []
    for input in inputs:
        if input == ["reference", "aligner", "indexes"]:
            for v in variables:
                vid = get_base_id(v["id"]).split("__")
                if vid[0] == "reference" and vid[1] in alignment.TOOLS:
                    out.append(vid)
        elif input == ["reference", "snpeff", "genome_build"]:
            found_indexes = False
            for v in variables:
                vid = get_base_id(v["id"]).split("__")
                if vid[0] == "reference" and vid[1] == "snpeff":
                    out.append(vid)
                    found_indexes = True
            assert found_indexes, "Found no snpEff indexes in %s" % [v["id"] for v in variables]
        elif input == ["config", "algorithm", "background", "cnv_reference"]:
            for v in variables:
                vid = get_base_id(v["id"]).split("__")
                if (vid[:4] == ["config", "algorithm", "background", "cnv_reference"] and
                      structural.supports_cnv_reference(vid[4])):
                    out.append(vid)
        elif input in optional:
            if _get_string_vid(input) in all_vs:
                out.append(input)
        else:
            out.append(input)
    return out