lower required match length for adapter check

jts · Sep 8, 2020 · 386f1a2 · 386f1a2
1 parent 6ffd46e
commit 386f1a2
Showing 1 changed file with 4 additions and 1 deletion.
diff --git a/bin/filter_residual_adapters.py b/bin/filter_residual_adapters.py
@@ -62,6 +62,9 @@ def filter_reads(filter_sequences, input_R1_fp, input_R2_fp, output_R1_fp, outpu
     # Illumina adapters that are occasionally leftover in reads
     S7 = "CCGAGCCCACGAGAC"
     P7 = "ATCTCGTATGCCGTCTTCTGCTTG"
-    filter_sequences = [ S7, P7 ]
+
+    # require a minimum match between read and adapter
+    min_length = 10
+    filter_sequences = [ S7[0:min_length], P7[0:min_length] ]
 
     filter_reads(filter_sequences, args.input_R1, args.input_R2, output_R1, output_R2)