Python handle_multiple_callersの例

コード例 #1

ファイル: joint.py プロジェクト: weizhiting/bcbio-nextgen

def square_off(samples, run_parallel):
    """Perform joint calling at all variants within a batch.
    """
    to_process = []
    extras = []
    for data in [x[0] for x in samples]:
        added = False
        if tz.get_in(("metadata", "batch"), data):
            for add in genotype.handle_multiple_callers(data, "jointcaller"):
                if _is_jointcaller_compatible(add):
                    added = True
                    to_process.append([add])
        if not added:
            extras.append([data])
    processed = grouped_parallel_split_combine(
        to_process, _split_by_callable_region, multi.group_batches_joint,
        run_parallel, "square_batch_region", "concat_variant_files",
        "vrn_file", ["region", "sam_ref", "config"])
    return _combine_to_jointcaller(processed) + extras

コード例 #2

ファイル: joint.py プロジェクト: bennyyu686/bcbio-nextgen

def square_off(samples, run_parallel):
    """Perform joint calling at all variants within a batch.
    """
    to_process = []
    extras = []
    for data in [x[0] for x in samples]:
        added = False
        if tz.get_in(("metadata", "batch"), data):
            for add in genotype.handle_multiple_callers(data, "jointcaller"):
                if _is_jointcaller_compatible(add):
                    added = True
                    to_process.append([add])
        if not added:
            extras.append([data])
    processed = grouped_parallel_split_combine(to_process, _split_by_callable_region,
                                               multi.group_batches_joint, run_parallel,
                                               "square_batch_region", "concat_variant_files",
                                               "vrn_file", ["region", "sam_ref", "config"])
    return _combine_to_jointcaller(processed) + extras