Ensure inputs to calling are indexed as expected.

def _prep_inputs(align_bams, ref_file, items):
    """Ensure inputs to calling are indexed as expected.
    """
    broad_runner = broad.runner_from_path("picard", items[0]["config"])
    broad_runner.run_fn("picard_index_ref", ref_file)
    for x in align_bams:
        bam.index(x, items[0]["config"])