Reads a given inputfile (tab delimited) and returns a matrix
    (list of list).
    arg: filename, the complete path to the inputfile to read

def read_input_file(filename, sep='\t', noquote=False):
    """Reads a given inputfile (tab delimited) and returns a matrix
    (list of list).
    arg: filename, the complete path to the inputfile to read
    """
    output = []
    stream = None
    try:
        stream = open(filename, 'r')
        for row in stream:
            row = row.strip()
            if noquote:
                row = row.replace('"', '')
            output.append(row.split(sep))
    except IOError as err:  # pragma: no cover
        LOG.info("Something wrong happend while reading the file %s "
                 % filename)
        LOG.debug("ERROR: %s" % err)
    finally:
        if stream:
            stream.close()
    return output