def align_bam(in_bam, ref_file, names, align_dir, data):
    config = data["config"]
    out_file = os.path.join(align_dir, "{0}-sort.bam".format(names["lane"]))
    samtools = config_utils.get_program("samtools", config)
    bedtools = config_utils.get_program("bedtools", config)
    resources = config_utils.get_resources("samtools", config)
    num_cores = config["algorithm"].get("num_cores", 1)
    max_mem = config_utils.adjust_memory(resources.get("memory", "1G"),
                                         3, "decrease").upper()
    if not utils.file_exists(out_file):
        with tx_tmpdir(data) as work_dir:
            with postalign.tobam_cl(data, out_file, bam.is_paired(in_bam)) as (tobam_cl, tx_out_file):
                bwa_cmd = _get_bwa_mem_cmd(data, out_file, ref_file, "-")
                tx_out_prefix = os.path.splitext(tx_out_file)[0]
                prefix1 = "%s-in1" % tx_out_prefix
                cmd = ("unset JAVA_HOME && "
                       "{samtools} sort -n -o -l 1 -@ {num_cores} -m {max_mem} {in_bam} {prefix1} "
                       "| {bedtools} bamtofastq -i /dev/stdin -fq /dev/stdout -fq2 /dev/stdout "
                       "| {bwa_cmd} | ")
                cmd = cmd.format(**locals()) + tobam_cl
                do.run(cmd, "bwa mem alignment from BAM: %s" % names["sample"], None,
                       [do.file_nonempty(tx_out_file), do.file_reasonable_size(tx_out_file, in_bam)])
    return out_file