Column merging

[bschilder]

extract_snpvar.py

For scenarios where someone's summary stats file has both SNP and CHR/POS, I modified the merging procedure so that column names don't get duplicated.
lines 66-76

#merge the dfs
    # BMS edits
    print('Merging metadata files by...')
    if all(x in df_snps.columns for x in ['SNP', 'BP', 'CHR']):
        logging.info('   SNP and position.')
        df = df_meta.merge(df_snps, on=['SNP', 'A1', 'A2', 'SNP', 'BP', 'CHR'], how='inner')
    elif 'SNP' in df_snps.columns:
        print('   SNP.')
        df = df_meta.merge(df_snps, on=['SNP', 'A1', 'A2'], how='inner')
    else:
        print('   position.')
        df = df_meta.merge(df_snps, on=['CHR', 'BP', 'A1', 'A2'], how='inner')

[omerwe]

Great suggestion! Committed (with slight modifications)