diff --git a/src/bisc_utils.c b/src/bisc_utils.c
index d27f5b2..6779270 100644
--- a/src/bisc_utils.c
+++ b/src/bisc_utils.c
@@ -86,6 +86,8 @@ uint32_t cnt_retention(refcache_t *rs, bam1_t *b, uint8_t bsstrand) {
         oplen = bam_cigar_oplen(bam_get_cigar(b)[i]);
         switch(op) {
             case BAM_CMATCH:
+            case BAM_CEQUAL:
+            case BAM_CDIFF:
                 for (j=0; j<oplen; ++j) {
                     rb = refcache_getbase_upcase(rs, rpos+j);
                     qb = bscall(b, qpos+j);
@@ -159,9 +161,7 @@ uint32_t get_mate_length(char *m_cigar) {
 }
 
 uint8_t infer_bsstrand(refcache_t *rs, bam1_t *b, uint32_t min_base_qual) {
-
     /* infer bsstrand from nC2T and nG2A on high quality bases */
-
     bam1_core_t *c = &b->core;
     uint32_t i, rpos = c->pos+1, qpos = 0;
     uint32_t op, oplen;
@@ -172,6 +172,8 @@ uint8_t infer_bsstrand(refcache_t *rs, bam1_t *b, uint32_t min_base_qual) {
         oplen = bam_cigar_oplen(bam_get_cigar(b)[i]);
         switch(op) {
             case BAM_CMATCH:
+            case BAM_CEQUAL:
+            case BAM_CDIFF:
                 for (j=0; j<oplen; ++j) {
                     rb = refcache_getbase_upcase(rs, rpos+j);
                     qb = bscall(b, qpos+j);
diff --git a/src/bsconv.c b/src/bsconv.c
index 860ae0f..a0ee771 100644
--- a/src/bsconv.c
+++ b/src/bsconv.c
@@ -65,6 +65,8 @@ int bsconv_func(bam1_t *b, samFile *out, bam_hdr_t *hdr, void *data) {
         uint32_t oplen = bam_cigar_oplen(bam_get_cigar(b)[i]);
         switch(op) {
             case BAM_CMATCH:
+            case BAM_CEQUAL:
+            case BAM_CDIFF:
                 for(j=0; j<oplen; ++j) {
                     rb = refcache_getbase_upcase(d->rs, rpos+j);
 
diff --git a/src/bsstrand.c b/src/bsstrand.c
index c617f51..f829e2e 100755
--- a/src/bsstrand.c
+++ b/src/bsstrand.c
@@ -82,6 +82,8 @@ int bsstrand_func(bam1_t *b, samFile *out, bam_hdr_t *header, void *data) {
         uint32_t oplen = bam_cigar_oplen(bam_get_cigar(b)[i]);
         switch(op) {
             case BAM_CMATCH:
+            case BAM_CEQUAL:
+            case BAM_CDIFF:
                 for(j=0; j<oplen; ++j) {
                     rbase = toupper(refcache_getbase(d->rs, rpos+j));
                     qbase = bscall(b, qpos+j);
diff --git a/src/cinread.c b/src/cinread.c
index f2ffa32..b1d0a20 100644
--- a/src/cinread.c
+++ b/src/cinread.c
@@ -72,6 +72,8 @@ int cinread_func(bam1_t *b, samFile *out, bam_hdr_t *hdr, void *data) {
         uint32_t oplen = bam_cigar_oplen(bam_get_cigar(b)[i]);
         switch(op) {
             case BAM_CMATCH:
+            case BAM_CEQUAL:
+            case BAM_CDIFF:
                 for(j=0; j<oplen; ++j) {
                     rb = refcache_getbase_upcase(d->rs, rpos+j);
 
diff --git a/src/epiread.c b/src/epiread.c
index f95c800..3a354ae 100644
--- a/src/epiread.c
+++ b/src/epiread.c
@@ -675,6 +675,8 @@ static void *process_func(void *data) {
                 uint32_t oplen = bam_cigar_oplen(bam_get_cigar(b)[i]);
                 switch(op) {
                     case BAM_CMATCH:
+                    case BAM_CEQUAL:
+                    case BAM_CDIFF:
                         for (j=0; j<oplen; ++j) {
                             // Query positions
                             qj = qpos + j;
diff --git a/src/pileup.c b/src/pileup.c
index aef6035..7fa8da0 100644
--- a/src/pileup.c
+++ b/src/pileup.c
@@ -752,6 +752,8 @@ static void *process_func(void *_result) {
                     char qb, rb;
                     switch(op) {
                         case BAM_CMATCH:
+                        case BAM_CEQUAL:
+                        case BAM_CDIFF:
                             for (j=0; j<oplen; ++j) {
 
                                 if (rpos+j<w.beg || rpos+j>=w.end) continue; /* include begin but not end */
diff --git a/src/tview.c b/src/tview.c
index 10c0018..c451b29 100644
--- a/src/tview.c
+++ b/src/tview.c
@@ -335,6 +335,8 @@ static void draw_read1(rnode_t *nd, btview_t *tv, int readattr, int bss) {
 
     switch(op) {
     case BAM_CMATCH:
+    case BAM_CEQUAL:
+    case BAM_CDIFF:
       for (j=0; j<oplen; ++j) {
         if (rpos + j < (unsigned) tv->left_pos) continue;
         qb = toupper(bscall(b, qpos + j));