mismatch function view upper and lower cases as mismatches

mengyao · Jul 22, 2016 · c216584 · c216584
1 parent 2dd739d
commit c216584
Showing 1 changed file with 2 additions and 0 deletions.
diff --git a/src/ssw.c b/src/ssw.c
@@ -912,8 +912,10 @@ int32_t mark_mismatch (int32_t ref_begin1,
 		length = cigar_int_to_len((*cigar)[i]);
 		if (op == 'M') {
 			for (j = 0; j < length; ++j) {
+				fprintf(stderr, "ref[%d]: %c\tread[%d]: %c\n", j, *ref, j, *read);
 				if (*ref != *read) {
 					++ mismatch_length;
+					fprintf(stderr, "length_m: %d\n", length_m);
 					// the previous is match; however the current one is mismatche
 					new_cigar = store_previous_m (2, &length_m, &length_x, &p, &s, new_cigar);			
 					++ length_x;