def _check_sample_config(items, in_file, config):
    """Identify common problems in input sample configuration files.
    """
    logger.info("Checking sample YAML configuration: %s" % in_file)
    _check_quality_format(items)
    _check_for_duplicates(items, "lane")
    _check_for_duplicates(items, "description")
    _check_for_degenerate_interesting_groups(items)
    _check_for_batch_clashes(items)
    _check_for_problem_somatic_batches(items, config)
    _check_for_misplaced(items, "algorithm",
                         ["resources", "metadata", "analysis",
                          "description", "genome_build", "lane", "files"])

    [_check_toplevel_misplaced(x) for x in items]
    [_check_algorithm_keys(x) for x in items]
    [_check_algorithm_values(x) for x in items]
    [_check_aligner(x) for x in items]
    [_check_variantcaller(x) for x in items]
    [_check_svcaller(x) for x in items]
    [_check_hetcaller(x) for x in items]
    [_check_indelcaller(x) for x in items]
    [_check_jointcaller(x) for x in items]
    [_check_hlacaller(x) for x in items]
    [_check_realign(x) for x in items]
    [_check_trim(x) for x in items]
def _check_sample_config ( items , in_file , config ) : logger . info ( "Checking sample YAML configuration: %s" % in_file ) _check_quality_format ( items ) _check_for_duplicates ( items , "lane" ) _check_for_duplicates ( items , "description" ) _check_for_degenerate_interesting_groups ( items ) _check_for_batch_clashes ( items ) _check_for_problem_somatic_batches ( items , config ) _check_for_misplaced ( items , "algorithm" , [ "resources" , "metadata" , "analysis" , "description" , "genome_build" , "lane" , "files" ] ) [ _check_toplevel_misplaced ( x ) for x in items ] [ _check_algorithm_keys ( x ) for x in items ] [ _check_algorithm_values ( x ) for x in items ] [ _check_aligner ( x ) for x in items ] [ _check_variantcaller ( x ) for x in items ] [ _check_svcaller ( x ) for x in items ] [ _check_hetcaller ( x ) for x in items ] [ _check_indelcaller ( x ) for x in items ] [ _check_jointcaller ( x ) for x in items ] [ _check_hlacaller ( x ) for x in items ] [ _check_realign ( x ) for x in items ] [ _check_trim ( x ) for x in items ]
Identify common problems in input sample configuration files.