From c216584e710fde02e77964a295b49b971fd2aa62 Mon Sep 17 00:00:00 2001
From: Mengyao Zhao <mengyao.zhao@sbgenomics.com>
Date: Fri, 22 Jul 2016 16:36:58 -0400
Subject: [PATCH] mismatch function view upper and lower cases as mismatches

---
 src/ssw.c | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/ssw.c b/src/ssw.c
index b5f667f..250aa0d 100644
--- 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;