import logging
from . import run_settings

def update_variants(variant_df):
    '''
    This function logs information to the run_settings.log_filename to indicate
    any newly identified variants from the most recent iteration of the
    alignment. Each variant that was identifies gets its own line

    INPUT:

    variants_df: a dataFrame of variants identifying newly identified in the
    most recent alignment. This dataFrame must contain the following columns:
        * reference - the reference name as it is contained in the bam
        * position - the position (in zero-based coordinates) of the variable
        position from the reference in the bam
        * ref_base - the reference base, as present in the bam
        * var_base - the variant base, with frququency above threshold

    RETURN:
    a boolean that is True if the data was logged properly and false
    otherwise
    '''

def log_result(final_filename):
    '''
    This function should be called at completion. It simply reports the
    location of the final filename containing the corrected sequences.

    INPUT:

    final_filename: the filename of the fasta consensus sequences

    RETURN:

    a boolean that is True if the final result  was logged properly and false
    otherwise

    '''

