Retrieve command line for max coverage downsampling, fitting into bamsormadup output.

def get_maxcov_downsample_cl(data, in_pipe=None):
    """Retrieve command line for max coverage downsampling, fitting into bamsormadup output.
    """
    max_cov = _get_maxcov_downsample(data) if dd.get_aligner(data) not in ["snap"] else None
    if max_cov:
        if in_pipe == "bamsormadup":
            prefix = "level=0"
        elif in_pipe == "samtools":
            prefix = "-l 0"
        else:
            prefix = ""
        # Swap over to multiple cores until after testing
        #core_arg = "-t %s" % dd.get_num_cores(data)
        core_arg = ""
        return ("%s | variant - -b %s --mark-as-qc-fail --max-coverage %s"
                % (prefix, core_arg, max_cov))
    else:
        if in_pipe == "bamsormadup":
            prefix = "indexfilename={tx_out_file}.bai"
        else:
            prefix = ""
        return prefix