def generate_contigs(args, run_params, graph_edges, out_folder, log_file, config_file, repeat_graph, reads_alignment):
    logger.debug('-----Begin contigger analyser log------')
    cmdline = [CONTIGGER_BIN, 'contigger', '--graph-edges', graph_edges, '--reads', ','.join(args.reads), '--out-dir', out_folder, '--config', config_file, '--repeat-graph', repeat_graph, '--graph-aln', reads_alignment, '--log', log_file, '--threads', str(args.threads)]
    if args.debug:
        cmdline.append('--debug')
    if args.keep_haplotypes:
        cmdline.append('--no-scaffold')
    cmdline.extend(['--min-ovlp', str(run_params['min_overlap'])])
    try:
        logger.debug(('Running: ' + ' '.join(cmdline)))
        subprocess.check_call(cmdline)
    except subprocess.CalledProcessError as e:
        if (e.returncode == (- 9)):
            logger.error('Looks like the system ran out of memory')
        raise RepeatException(str(e))
    except OSError as e:
        raise RepeatException(str(e))
def generate_contigs(args, run_params, graph_edges, out_folder, log_file, config_file, repeat_graph, reads_alignment):
    logger.debug('-----Begin contigger analyser log------')
    cmdline = [CONTIGGER_BIN, 'contigger', '--graph-edges', graph_edges, '--reads', ','.join(args.reads), '--out-dir', out_folder, '--config', config_file, '--repeat-graph', repeat_graph, '--graph-aln', reads_alignment, '--log', log_file, '--threads', str(args.threads)]
    if args.debug:
        cmdline.append('--debug')
    if args.keep_haplotypes:
        cmdline.append('--no-scaffold')
    cmdline.extend(['--min-ovlp', str(run_params['min_overlap'])])
    try:
        logger.debug(('Running: ' + ' '.join(cmdline)))
        subprocess.check_call(cmdline)
    except subprocess.CalledProcessError as e:
        if (e.returncode == (- 9)):
            logger.error('Looks like the system ran out of memory')
        raise RepeatException(str(e))
    except OSError as e:
        raise RepeatException(str(e))