def _get_jar(self, command, alts=None, allow_missing=False):
        """Retrieve the jar for running the specified command.
        """
        dirs = []
        for bdir in [self._gatk_dir, self._picard_ref]:
            dirs.extend([bdir,
                         os.path.join(bdir, os.pardir, "gatk")])
        if alts is None: alts = []
        for check_cmd in [command] + alts:
            for dir_check in dirs:
                try:
                    check_file = config_utils.get_jar(check_cmd, dir_check)
                    return check_file
                except ValueError as msg:
                    if str(msg).find("multiple") > 0:
                        raise
                    else:
                        pass
        if allow_missing:
            return None
        else:
            raise ValueError("Could not find jar %s in %s:%s" % (command, self._picard_ref, self._gatk_dir))
Retrieve the jar for running the specified command.