Parse the output from Picard's CollectAlignmentSummaryMetrics and return as
    pandas Dataframe.

    Parameters
    ----------
    filename : str of filename or file handle
        Filename of the Picard output you want to parse.

    Returns
    -------
    df : pandas.DataFrame
        Data from output file.

def parse_alignment_summary_metrics(fn):
    """
    Parse the output from Picard's CollectAlignmentSummaryMetrics and return as
    pandas Dataframe.

    Parameters
    ----------
    filename : str of filename or file handle
        Filename of the Picard output you want to parse.

    Returns
    -------
    df : pandas.DataFrame
        Data from output file.

    """
    df = pd.read_table(fn, index_col=0, skiprows=range(6) + [10, 11]).T
    return df