diff --git a/cram/cram_encode.c b/cram/cram_encode.c
index 7ec3c003a..735784e89 100644
--- a/cram/cram_encode.c
+++ b/cram/cram_encode.c
@@ -1502,17 +1502,20 @@ int next_cigar_op(uint32_t *cigar, uint32_t ncigar, int *skip, int *spos,
 
 // Ensure ref and hist are large enough.
 static inline int extend_ref(char **ref, uint32_t (**hist)[5], hts_pos_t pos,
-                             hts_pos_t ref_start, hts_pos_t *ref_end) {
+                             hts_pos_t ref_start, hts_pos_t *ref_end,
+                             hts_pos_t *ref_end_alloc) {
+    if (*ref_end < pos)
+        *ref_end = pos;
     if (pos < ref_start)
         return -1;
-    if (pos < *ref_end)
+    if (pos < *ref_end_alloc)
         return 0;
 
     // realloc
     if (pos - ref_start > UINT_MAX)
         return -2; // protect overflow in new_end calculation
 
-    hts_pos_t old_end = *ref_end ? *ref_end : ref_start;
+    hts_pos_t old_end = *ref_end_alloc ? *ref_end_alloc : ref_start;
     hts_pos_t new_end = ref_start + 1000 + (pos-ref_start)*1.5;
 
     // Refuse to work on excessively large blocks.
@@ -1531,7 +1534,7 @@ static inline int extend_ref(char **ref, uint32_t (**hist)[5], hts_pos_t pos,
     if (!tmp5)
         return -1;
     *hist = tmp5;
-    *ref_end = new_end;
+    *ref_end_alloc = new_end;
 
     // initialise
     old_end -= ref_start;
@@ -1546,7 +1549,7 @@ static inline int extend_ref(char **ref, uint32_t (**hist)[5], hts_pos_t pos,
 // Returns 1 on success, <0 on failure
 static int cram_add_to_ref_MD(bam1_t *b, char **ref, uint32_t (**hist)[5],
                               hts_pos_t ref_start, hts_pos_t *ref_end,
-                              const uint8_t *MD) {
+                              hts_pos_t *ref_end_alloc, const uint8_t *MD) {
     uint8_t *seq = bam_get_seq(b);
     uint32_t *cigar = bam_get_cigar(b);
     uint32_t ncigar = b->core.n_cigar;
@@ -1558,7 +1561,7 @@ static int cram_add_to_ref_MD(bam1_t *b, char **ref, uint32_t (**hist)[5],
 
     // No sequence means extend based on CIGAR instead
     if (!b->core.l_qseq && extend_ref(ref, hist, rseq_end,
-                                      ref_start, ref_end) < 0)
+                                      ref_start, ref_end, ref_end_alloc) < 0)
         return -1;
 
     int iseq = 0, next_op;
@@ -1573,7 +1576,7 @@ static int cram_add_to_ref_MD(bam1_t *b, char **ref, uint32_t (**hist)[5],
             int len = hts_str2uint((char *)MD, (char **)&MD, 31, &overflow);
             if (overflow ||
                 extend_ref(ref, hist, iref+ref_start + len,
-                           ref_start, ref_end) < 0)
+                           ref_start, ref_end, ref_end_alloc) < 0)
                 return -1;
             while (iseq < b->core.l_qseq && len) {
                 // rewrite to have internal loops?
@@ -1605,7 +1608,7 @@ static int cram_add_to_ref_MD(bam1_t *b, char **ref, uint32_t (**hist)[5],
             MD++;
             while (isalpha(*MD)) {
                 if (extend_ref(ref, hist, iref+ref_start, ref_start,
-                               ref_end) < 0)
+                               ref_end, ref_end_alloc) < 0)
                     return -1;
                 if ((next_op = next_cigar_op(cigar, ncigar, cig_skip,
                                              &iseq, &cig_ind, &cig_op,
@@ -1621,7 +1624,8 @@ static int cram_add_to_ref_MD(bam1_t *b, char **ref, uint32_t (**hist)[5],
             }
         } else {
             // substitution
-            if (extend_ref(ref, hist, iref+ref_start, ref_start, ref_end) < 0)
+            if (extend_ref(ref, hist, iref+ref_start, ref_start, ref_end,
+                           ref_end_alloc) < 0)
                 return -1;
             if ((next_op = next_cigar_op(cigar, ncigar, cig_skip,
                                          &iseq, &cig_ind, &cig_op,
@@ -1650,12 +1654,14 @@ static int cram_add_to_ref_MD(bam1_t *b, char **ref, uint32_t (**hist)[5],
 // Returns >=0 on success,
 //         -1 on failure (eg inconsistent data)
 static int cram_add_to_ref(bam1_t *b, char **ref, uint32_t (**hist)[5],
-                           hts_pos_t ref_start, hts_pos_t *ref_end) {
+                           hts_pos_t ref_start, hts_pos_t *ref_end,
+                           hts_pos_t *ref_end_alloc) {
     const uint8_t *MD = bam_aux_get(b, "MD");
     int ret = 0;
     if (MD && *MD == 'Z') {
         // We can use MD to directly compute the reference
-        int ret = cram_add_to_ref_MD(b, ref, hist, ref_start, ref_end, MD+1);
+        int ret = cram_add_to_ref_MD(b, ref, hist, ref_start, ref_end,
+                                     ref_end_alloc, MD+1);
 
         if (ret > 0)
             return ret;
@@ -1683,7 +1689,7 @@ static int cram_add_to_ref(bam1_t *b, char **ref, uint32_t (**hist)[5],
             static uint8_t L16[16] = {4,0,1,4, 2,4,4,4, 3,4,4,4, 4,4,4,4};
 
             if (extend_ref(ref, hist, iref+ref_start + len,
-                           ref_start, ref_end) < 0)
+                           ref_start, ref_end, ref_end_alloc) < 0)
                 return -1;
             if (iseq + len <= b->core.l_qseq) {
                 // Nullify failed MD:Z if appropriate
@@ -1726,7 +1732,8 @@ static int cram_generate_reference(cram_container *c, cram_slice *s, int r1) {
     // user told us to do embed_ref=2.
     char *ref = NULL;
     uint32_t (*hist)[5] = NULL;
-    hts_pos_t ref_start = c->bams[r1]->core.pos, ref_end = 0;
+    hts_pos_t ref_start = c->bams[r1]->core.pos, ref_end = 0,
+        ref_end_alloc = 0;
     if (ref_start < 0)
         return -1; // cannot build consensus from unmapped data
 
@@ -1734,7 +1741,7 @@ static int cram_generate_reference(cram_container *c, cram_slice *s, int r1) {
     if (extend_ref(&ref, &hist,
                    c->bams[r1 + s->hdr->num_records-1]->core.pos +
                    c->bams[r1 + s->hdr->num_records-1]->core.l_qseq,
-                   ref_start, &ref_end) < 0)
+                   ref_start, &ref_end, &ref_end_alloc) < 0)
         return -1;
 
     // Add each bam file to the reference/consensus arrays
@@ -1746,7 +1753,8 @@ static int cram_generate_reference(cram_container *c, cram_slice *s, int r1) {
             goto err;
         }
         last_pos = c->bams[r1]->core.pos;
-        if (cram_add_to_ref(c->bams[r1], &ref, &hist, ref_start, &ref_end) < 0)
+        if (cram_add_to_ref(c->bams[r1], &ref, &hist, ref_start, &ref_end,
+                            &ref_end_alloc) < 0)
             goto err;
     }
 
@@ -1770,6 +1778,7 @@ static int cram_generate_reference(cram_container *c, cram_slice *s, int r1) {
     c->ref_start = ref_start+1;
     c->ref_end   = ref_end+1;
     c->ref_free  = 1;
+
     return 0;
 
  err:
@@ -2012,8 +2021,10 @@ int cram_encode_container(cram_fd *fd, cram_container *c) {
                 pthread_mutex_unlock(&fd->ref_lock);
             }
 
-            if (c->ref_end > fd->refs->ref_id[c->ref_id]->LN_length)
-                c->ref_end = fd->refs->ref_id[c->ref_id]->LN_length;
+            hts_pos_t rlen = MAX(fd->refs->ref_id[c->ref_id]->LN_length,
+                                 fd->refs->ref_id[c->ref_id]->length);
+            if (c->ref_end > rlen && rlen)
+                c->ref_end = rlen;
         }
 
         // Iterate through records creating the cram blocks for some
@@ -3927,7 +3938,8 @@ static int process_one_read(cram_fd *fd, cram_container *c,
             if (p->cram_flags & CRAM_FLAG_STATS_ADDED) {
                 cram_stats_del(c->stats[DS_NP], p->mate_pos);
                 cram_stats_del(c->stats[DS_MF], p->mate_flags);
-                if (!(p->cram_flags & CRAM_FLAG_EXPLICIT_TLEN))
+                if (!(p->cram_flags & CRAM_FLAG_EXPLICIT_TLEN)
+                    && !explicit_tlen)
                     cram_stats_del(c->stats[DS_TS], p->tlen);
                 cram_stats_del(c->stats[DS_NS], p->mate_ref_id);
             }
diff --git a/test/test.pl b/test/test.pl
index 8a68a658c..eaa65ea30 100755
--- a/test/test.pl
+++ b/test/test.pl
@@ -894,6 +894,16 @@ sub test_view
     testv $opts, "./test_view $tv_args -p $ersam2 $ercram";
     testv $opts, "./compare_sam.pl $ersam $ersam2";
 
+    # Embed_ref=2 with CRAM v4 uses explicit_len if it has to instead of
+    # breaking pairs with detached mode.
+    # Oddly this bug was only triggered when also specifying a reference.
+    $ersam = "xx#pair.sam";
+    $ercram = "xx#pair.tmp.cram";
+    $ersam2 = "${ercram}.sam";
+    testv $opts, "./test_view $tv_args -o version=4.0 -o embed_ref=2 -t xx.fa -C -p $ercram $ersam";
+    testv $opts, "./test_view $tv_args -p $ersam2 $ercram";
+    testv $opts, "./compare_sam.pl $ersam $ersam2";
+
     if ($test_view_failures == 0) {
         passed($opts, "embed_ref=2 tests");
     } else {