Fix bug: snps-within-gene using location

Author: tayaza

codes3d/codes3d.py

@@ -747,7 +747,7 @@ def log_settings(args, logger):
     if args.gene_input:
         logger.write(f'--gene-input:\t{", ".join(args.gene_input)}')
     if args.snps_within_gene:
-        logger.write(f'--snps-within-gebe:\t{args.snps_within_gene}')
+        logger.write(f'--snps-within-gene:\t{args.snps_within_gene}')
     logger.write('\n')
 
 

codes3d/genes.py

@@ -207,7 +207,7 @@ def get_gene_by_id(
 def get_gene_by_position(df, db):
     gene_df = []
     omitted_genes = []
-    sql = '''SELECT * FROM genes where chrom = '{}' and start= {} and "end" = {};'''
+    sql = '''SELECT * FROM genes where chrom = '{}' and start >= {} and "end" <= {};'''
     with db.connect() as con:
         for idx, row in df.iterrows():
             try: