diff --git a/cram/cram_decode.c b/cram/cram_decode.c
index dba7cf89c..6f1528dc0 100644
--- a/cram/cram_decode.c
+++ b/cram/cram_decode.c
@@ -1087,6 +1087,25 @@ static inline int add_md_char(cram_slice *s, int decode_md, char c, int32_t *md_
     return -1;
 }
 
+static int add_cigar(cram_slice *s, uint64_t cig_len, int cig_op) {
+    int nlen = 1 + cig_len/(1<<28);
+    if (s->ncigar +  nlen >= s->cigar_alloc) {
+        s->cigar_alloc = (s->ncigar + nlen) < 1024 ? 1024 : (s->ncigar + nlen)*2;
+        uint32_t *c2 = realloc(s->cigar, s->cigar_alloc * sizeof(*s->cigar));
+        if (!c2)
+            return -1;
+        s->cigar = c2;
+    }
+
+    while (cig_len) {
+        int sub_len = cig_len < (1<<28) ? cig_len : (1<<28)-1;
+        s->cigar[s->ncigar++] = (sub_len<<4) + cig_op;
+        cig_len -= sub_len;
+    }
+
+    return 0;
+}
+
 /*
  * Internal part of cram_decode_slice().
  * Generates the sequence, quality and cigar components.
@@ -1097,13 +1116,10 @@ static int cram_decode_seq(cram_fd *fd, cram_container *c, cram_slice *s,
                            int has_MD, int has_NM) {
     int prev_pos = 0, f, r = 0, out_sz = 1;
     int seq_pos = 1;
-    int cig_len = 0;
+    uint64_t cig_len = 0;
     int64_t ref_pos = cr->apos;
     int32_t fn, i32;
     enum cigar_op cig_op = BAM_CMATCH;
-    uint32_t *cigar = s->cigar;
-    uint32_t ncigar = s->ncigar;
-    uint32_t cigar_alloc = s->cigar_alloc;
     uint32_t nm = 0;
     int32_t md_dist = 0;
     int orig_aux = 0;
@@ -1134,7 +1150,7 @@ static int cram_decode_seq(cram_fd *fd, cram_container *c, cram_slice *s,
     }
 
     ref_pos--; // count from 0
-    cr->cigar = ncigar;
+    cr->cigar = s->ncigar;
 
     if (!(ds & (CRAM_FC | CRAM_FP)))
         goto skip_cigar;
@@ -1143,13 +1159,6 @@ static int cram_decode_seq(cram_fd *fd, cram_container *c, cram_slice *s,
         int32_t pos = 0;
         char op;
 
-        if (ncigar+2 >= cigar_alloc) {
-            cigar_alloc = cigar_alloc ? cigar_alloc*2 : 1024;
-            if (!(cigar = realloc(cigar, cigar_alloc * sizeof(*cigar))))
-                return -1;
-            s->cigar = cigar;
-        }
-
         if (ds & CRAM_FC) {
             if (!c->comp_hdr->codecs[DS_FC]) return -1;
             r |= c->comp_hdr->codecs[DS_FC]->decode(s,
@@ -1231,13 +1240,15 @@ static int cram_decode_seq(cram_fd *fd, cram_container *c, cram_slice *s,
             }
 #ifdef USE_X
             if (cig_len && cig_op != BAM_CBASE_MATCH) {
-                cigar[ncigar++] = (cig_len<<4) + cig_op;
+                if (add_cigar(s, cig_len, cig_op) < 0)
+                    goto err;
                 cig_len = 0;
             }
             cig_op = BAM_CBASE_MATCH;
 #else
             if (cig_len && cig_op != BAM_CMATCH) {
-                cigar[ncigar++] = (cig_len<<4) + cig_op;
+                if (add_cigar(s, cig_len, cig_op) < 0)
+                    goto err;
                 cig_len = 0;
             }
             cig_op = BAM_CMATCH;
@@ -1258,7 +1269,8 @@ static int cram_decode_seq(cram_fd *fd, cram_container *c, cram_slice *s,
             int have_sc = 0;
 
             if (cig_len) {
-                cigar[ncigar++] = (cig_len<<4) + cig_op;
+                if (add_cigar(s, cig_len, cig_op) < 0)
+                    goto err;
                 cig_len = 0;
             }
             switch (CRAM_MAJOR_VERS(fd->version)) {
@@ -1297,7 +1309,8 @@ static int cram_decode_seq(cram_fd *fd, cram_container *c, cram_slice *s,
             }
             if (have_sc) {
                 if (r) return r;
-                cigar[ncigar++] = (out_sz2<<4) + BAM_CSOFT_CLIP;
+                if (add_cigar(s, out_sz2, BAM_CSOFT_CLIP) < 0)
+                    goto err;
                 cig_op = BAM_CSOFT_CLIP;
                 seq_pos += out_sz2;
             }
@@ -1308,7 +1321,8 @@ static int cram_decode_seq(cram_fd *fd, cram_container *c, cram_slice *s,
             unsigned char base;
 #ifdef USE_X
             if (cig_len && cig_op != BAM_CBASE_MISMATCH) {
-                cigar[ncigar++] = (cig_len<<4) + cig_op;
+                if (add_cigar(s, cig_len, cig_op) < 0)
+                    goto err;
                 cig_len = 0;
             }
             if (ds & CRAM_BS) {
@@ -1323,7 +1337,8 @@ static int cram_decode_seq(cram_fd *fd, cram_container *c, cram_slice *s,
 #else
             int ref_base;
             if (cig_len && cig_op != BAM_CMATCH) {
-                cigar[ncigar++] = (cig_len<<4) + cig_op;
+                if (add_cigar(s, cig_len, cig_op) < 0)
+                    goto err;
                 cig_len = 0;
             }
             if (ds & CRAM_BS) {
@@ -1365,7 +1380,8 @@ static int cram_decode_seq(cram_fd *fd, cram_container *c, cram_slice *s,
 
         case 'D': { // Deletion; DL
             if (cig_len && cig_op != BAM_CDEL) {
-                cigar[ncigar++] = (cig_len<<4) + cig_op;
+                if (add_cigar(s, cig_len, cig_op) < 0)
+                    goto err;
                 cig_len = 0;
             }
             if (ds & CRAM_DL) {
@@ -1419,7 +1435,8 @@ static int cram_decode_seq(cram_fd *fd, cram_container *c, cram_slice *s,
             int32_t out_sz2 = 1;
 
             if (cig_len && cig_op != BAM_CINS) {
-                cigar[ncigar++] = (cig_len<<4) + cig_op;
+                if (add_cigar(s, cig_len, cig_op) < 0)
+                    goto err;
                 cig_len = 0;
             }
 
@@ -1441,7 +1458,8 @@ static int cram_decode_seq(cram_fd *fd, cram_container *c, cram_slice *s,
 
         case 'i': { // Insertion (single base); BA
             if (cig_len && cig_op != BAM_CINS) {
-                cigar[ncigar++] = (cig_len<<4) + cig_op;
+                if (add_cigar(s, cig_len, cig_op) < 0)
+                    goto err;
                 cig_len = 0;
             }
             if (ds & CRAM_BA) {
@@ -1463,7 +1481,8 @@ static int cram_decode_seq(cram_fd *fd, cram_container *c, cram_slice *s,
             int32_t len = 1;
 
             if (cig_len && cig_op != BAM_CMATCH) {
-                cigar[ncigar++] = (cig_len<<4) + cig_op;
+                if (add_cigar(s, cig_len, cig_op) < 0)
+                    goto err;
                 cig_len = 0;
             }
 
@@ -1513,7 +1532,8 @@ static int cram_decode_seq(cram_fd *fd, cram_container *c, cram_slice *s,
             int32_t len = 1;
 
             if (cig_len && cig_op != BAM_CMATCH) {
-                cigar[ncigar++] = (cig_len<<4) + cig_op;
+                if (add_cigar(s, cig_len, cig_op) < 0)
+                    goto err;
                 cig_len = 0;
             }
 
@@ -1537,12 +1557,14 @@ static int cram_decode_seq(cram_fd *fd, cram_container *c, cram_slice *s,
         case 'B': { // Read base; BA, QS
 #ifdef USE_X
             if (cig_len && cig_op != BAM_CBASE_MISMATCH) {
-                cigar[ncigar++] = (cig_len<<4) + cig_op;
+                if (add_cigar(s, cig_len, cig_op) < 0)
+                    goto err;
                 cig_len = 0;
             }
 #else
             if (cig_len && cig_op != BAM_CMATCH) {
-                cigar[ncigar++] = (cig_len<<4) + cig_op;
+                if (add_cigar(s, cig_len, cig_op) < 0)
+                    goto err;
                 cig_len = 0;
             }
 #endif
@@ -1601,7 +1623,8 @@ static int cram_decode_seq(cram_fd *fd, cram_container *c, cram_slice *s,
 
         case 'H': { // hard clip; HC
             if (cig_len && cig_op != BAM_CHARD_CLIP) {
-                cigar[ncigar++] = (cig_len<<4) + cig_op;
+                if (add_cigar(s, cig_len, cig_op) < 0)
+                    goto err;
                 cig_len = 0;
             }
             if (ds & CRAM_HC) {
@@ -1618,7 +1641,8 @@ static int cram_decode_seq(cram_fd *fd, cram_container *c, cram_slice *s,
 
         case 'P': { // padding; PD
             if (cig_len && cig_op != BAM_CPAD) {
-                cigar[ncigar++] = (cig_len<<4) + cig_op;
+                if (add_cigar(s, cig_len, cig_op) < 0)
+                    goto err;
                 cig_len = 0;
             }
             if (ds & CRAM_PD) {
@@ -1635,7 +1659,8 @@ static int cram_decode_seq(cram_fd *fd, cram_container *c, cram_slice *s,
 
         case 'N': { // Ref skip; RS
             if (cig_len && cig_op != BAM_CREF_SKIP) {
-                cigar[ncigar++] = (cig_len<<4) + cig_op;
+                if (add_cigar(s, cig_len, cig_op) < 0)
+                    goto err;
                 cig_len = 0;
             }
             if (ds & CRAM_RS) {
@@ -1722,21 +1747,17 @@ static int cram_decode_seq(cram_fd *fd, cram_container *c, cram_slice *s,
             ref_pos += cr->len - seq_pos + 1;
         }
 
-        if (ncigar+1 >= cigar_alloc) {
-            cigar_alloc = cigar_alloc ? cigar_alloc*2 : 1024;
-            if (!(cigar = realloc(cigar, cigar_alloc * sizeof(*cigar))))
-                return -1;
-            s->cigar = cigar;
-        }
 #ifdef USE_X
         if (cig_len && cig_op != BAM_CBASE_MATCH) {
-            cigar[ncigar++] = (cig_len<<4) + cig_op;
+            if (add_cigar(s, cig_len, cig_op) < 0)
+                goto err;
             cig_len = 0;
         }
         cig_op = BAM_CBASE_MATCH;
 #else
         if (cig_len && cig_op != BAM_CMATCH) {
-            cigar[ncigar++] = (cig_len<<4) + cig_op;
+            if (add_cigar(s, cig_len, cig_op) < 0)
+                goto err;
             cig_len = 0;
         }
         cig_op = BAM_CMATCH;
@@ -1752,17 +1773,11 @@ static int cram_decode_seq(cram_fd *fd, cram_container *c, cram_slice *s,
     }
 
     if (cig_len) {
-        if (ncigar >= cigar_alloc) {
-            cigar_alloc = cigar_alloc ? cigar_alloc*2 : 1024;
-            if (!(cigar = realloc(cigar, cigar_alloc * sizeof(*cigar))))
-                return -1;
-            s->cigar = cigar;
-        }
-
-        cigar[ncigar++] = (cig_len<<4) + cig_op;
+        if (add_cigar(s, cig_len, cig_op) < 0)
+            goto err;
     }
 
-    cr->ncigar = ncigar - cr->cigar;
+    cr->ncigar = s->ncigar - cr->cigar;
     cr->aend = ref_pos;
 
     //printf("2: %.*s %d .. %d\n", cr->name_len, DSTRING_STR(name_ds) + cr->name, cr->apos, ref_pos);
@@ -1787,10 +1802,6 @@ static int cram_decode_seq(cram_fd *fd, cram_container *c, cram_slice *s,
         }
     }
 
-    s->cigar = cigar;
-    s->cigar_alloc = cigar_alloc;
-    s->ncigar = ncigar;
-
     if (cr->cram_flags & CRAM_FLAG_NO_SEQ)
         cr->len = 0;
 
@@ -1834,6 +1845,7 @@ static int cram_decode_seq(cram_fd *fd, cram_container *c, cram_slice *s,
     hts_log_error("CRAM CIGAR extends beyond slice reference extents");
     return -1;
 
+ err:
  block_err:
     return -1;
 }
diff --git a/cram/cram_encode.c b/cram/cram_encode.c
index 6c52c5892..8cbf9391c 100644
--- a/cram/cram_encode.c
+++ b/cram/cram_encode.c
@@ -2773,6 +2773,10 @@ static int process_one_read(cram_fd *fd, cram_container *c,
 
     c->num_bases   += cr->len;
     cr->apos        = bam_pos(b)+1;
+    if (cr->apos >= UINT32_MAX) {
+        hts_log_error("Sequence position out of valid range");
+        goto err;
+    }
     if (c->pos_sorted) {
         if (cr->apos < s->last_apos) {
             c->pos_sorted = 0;
diff --git a/header.c b/header.c
index 5a4a77d3d..e34168aac 100644
--- a/header.c
+++ b/header.c
@@ -47,7 +47,6 @@ typedef khash_t(rm) rmhash_t;
 static int sam_hdr_link_pg(sam_hdr_t *bh);
 
 static int sam_hrecs_vupdate(sam_hrecs_t *hrecs, sam_hrec_type_t *type, va_list ap);
-static int sam_hrecs_update(sam_hrecs_t *hrecs, sam_hrec_type_t *type, ...);
 
 
 #define MAX_ERROR_QUOTE 320 // Prevent over-long error messages
@@ -182,14 +181,10 @@ static int sam_hrecs_update_hashes(sam_hrecs_t *hrecs,
             if (hrecs->ref[nref].ty == NULL) {
                 // Attach header line to existing stub entry.
                 hrecs->ref[nref].ty = h_type;
-                // Check lengths match; correct if not.
-                if (len != hrecs->ref[nref].len) {
-                    char tmp[32];
-                    snprintf(tmp, sizeof(tmp), "%" PRIhts_pos,
-                             hrecs->ref[nref].len);
-                    if (sam_hrecs_update(hrecs, h_type, "LN", tmp, NULL) < 0)
-                        return -1;
-                }
+                // The old hrecs length may be incorrect as it is initially
+                // populated from h->target_len which has a max 32-bit size.
+                // We always take our latest data as canonical.
+                hrecs->ref[nref].len = len;
                 if (sam_hrecs_add_ref_altnames(hrecs, nref, altnames) < 0)
                     return -1;
 
@@ -749,6 +744,23 @@ static int sam_hrecs_rebuild_lines(const sam_hrecs_t *hrecs, kstring_t *ks) {
     return 0;
 }
 
+/*
+ * Reconstructs a kstring from the header hash table.
+ * Returns 0 on success
+ *        -1 on failure
+ */
+int sam_hrecs_rebuild_text(const sam_hrecs_t *hrecs, kstring_t *ks) {
+    ks->l = 0;
+
+    if (!hrecs->h || !hrecs->h->size) {
+        return kputsn("", 0, ks) >= 0 ? 0 : -1;
+    }
+    if (sam_hrecs_rebuild_lines(hrecs, ks) != 0)
+        return -1;
+
+    return 0;
+}
+
 static int sam_hrecs_parse_lines(sam_hrecs_t *hrecs, const char *hdr, size_t len) {
     size_t i, lno;
 
@@ -916,6 +928,8 @@ int sam_hdr_update_target_arrays(sam_hdr_t *bh, const sam_hrecs_t *hrecs,
     // hrecs->refs_changed is the first ref that has been updated, so ones
     // before that can be skipped.
     int i;
+    khint_t k;
+    khash_t(s2i) *long_refs = bh->sdict;
     for (i = refs_changed; i < hrecs->nref; i++) {
         if (i >= bh->n_targets
             || strcmp(bh->target_name[i], hrecs->ref[i].name) != 0) {
@@ -927,13 +941,38 @@ int sam_hdr_update_target_arrays(sam_hdr_t *bh, const sam_hrecs_t *hrecs,
         }
         if (hrecs->ref[i].len < UINT32_MAX) {
             bh->target_len[i] = hrecs->ref[i].len;
+
+            if (!long_refs)
+                continue;
+
+            // Check if we have an old length, if so remove it.
+            k = kh_get(s2i, long_refs, bh->target_name[i]);
+            if (k < kh_end(long_refs))
+                kh_del(s2i, long_refs, k);
         } else {
             bh->target_len[i] = UINT32_MAX;
+
+            if (!long_refs) {
+                if (!(bh->sdict = long_refs = kh_init(s2i)))
+                    return -1;
+            }
+
+            // Add / update length
+            int absent;
+            k = kh_put(s2i, long_refs, bh->target_name[i], &absent);
+            if (absent < 0)
+                return -1;
+            kh_val(long_refs, k) = hrecs->ref[i].len;
         }
     }
 
     // Free up any names that have been removed
     for (; i < bh->n_targets; i++) {
+        if (long_refs) {
+            k = kh_get(s2i, long_refs, bh->target_name[i]);
+            if (k < kh_end(long_refs))
+                kh_del(s2i, long_refs, k);
+        }
         free(bh->target_name[i]);
     }
 
@@ -941,7 +980,11 @@ int sam_hdr_update_target_arrays(sam_hdr_t *bh, const sam_hrecs_t *hrecs,
     return 0;
 }
 
-static int rebuild_target_arrays(sam_hdr_t *bh) {
+/*! Rebuild own target_name and target_len arrays from internal hrecs
+ *
+ *  @return 0 on success; -1 on failure
+ */
+static int sam_hdr_rebuild_target_arrays(sam_hdr_t *bh) {
     if (!bh || !bh->hrecs)
         return -1;
 
@@ -1102,7 +1145,7 @@ int sam_hdr_fill_hrecs(sam_hdr_t *bh) {
 
     bh->hrecs = hrecs;
 
-    if (hrecs->refs_changed >= 0 && rebuild_target_arrays(bh) != 0)
+    if (sam_hdr_rebuild_target_arrays(bh) != 0)
         return -1;
 
     return 0;
@@ -1197,11 +1240,9 @@ int sam_hdr_rebuild(sam_hdr_t *bh) {
     if (!(hrecs = bh->hrecs))
         return bh->text ? 0 : -1;
 
-    if (hrecs->refs_changed >= 0) {
-        if (rebuild_target_arrays(bh) < 0) {
-            hts_log_error("Header target array rebuild has failed");
-            return -1;
-        }
+    if (sam_hdr_rebuild_target_arrays(bh) < 0) {
+        hts_log_error("Header target array rebuild has failed");
+        return -1;
     }
 
     /* If header text wasn't changed or header is empty, don't rebuild it. */
@@ -1258,7 +1299,7 @@ int sam_hdr_add_lines(sam_hdr_t *bh, const char *lines, size_t len) {
     if (sam_hrecs_parse_lines(hrecs, lines, len) != 0)
         return -1;
 
-    if (hrecs->refs_changed >= 0 && rebuild_target_arrays(bh) != 0)
+    if (sam_hdr_rebuild_target_arrays(bh) != 0)
         return -1;
 
     hrecs->dirty = 1;
@@ -1293,7 +1334,7 @@ int sam_hdr_add_line(sam_hdr_t *bh, const char *type, ...) {
     va_end(args);
 
     if (ret == 0) {
-        if (hrecs->refs_changed >= 0 && rebuild_target_arrays(bh) != 0)
+        if (sam_hdr_rebuild_target_arrays(bh) != 0)
             return -1;
 
         if (hrecs->dirty)
@@ -1388,7 +1429,7 @@ int sam_hdr_remove_line_id(sam_hdr_t *bh, const char *type, const char *ID_key,
 
     int ret = sam_hrecs_remove_line(hrecs, type, type_found);
     if (ret == 0) {
-        if (hrecs->refs_changed >= 0 && rebuild_target_arrays(bh) != 0)
+        if (sam_hdr_rebuild_target_arrays(bh) != 0)
             return -1;
 
         if (hrecs->dirty)
@@ -1428,7 +1469,7 @@ int sam_hdr_remove_line_pos(sam_hdr_t *bh, const char *type, int position) {
 
     int ret = sam_hrecs_remove_line(hrecs, type, type_found);
     if (ret == 0) {
-        if (hrecs->refs_changed >= 0 && rebuild_target_arrays(bh) != 0)
+        if (sam_hdr_rebuild_target_arrays(bh) != 0)
             return -1;
 
         if (hrecs->dirty)
@@ -1558,7 +1599,7 @@ int sam_hdr_update_line(sam_hdr_t *bh, const char *type,
     ret = sam_hrecs_update_hashes(hrecs, TYPEKEY(type), ty);
 
     if (!ret && hrecs->refs_changed >= 0)
-        ret = rebuild_target_arrays(bh);
+        ret = sam_hdr_rebuild_target_arrays(bh);
 
     if (!ret && hrecs->dirty)
         redact_header_text(bh);
@@ -1905,23 +1946,6 @@ int sam_hdr_remove_tag_id(sam_hdr_t *bh,
     return ret;
 }
 
-/*
- * Reconstructs a kstring from the header hash table.
- * Returns 0 on success
- *        -1 on failure
- */
-int sam_hrecs_rebuild_text(const sam_hrecs_t *hrecs, kstring_t *ks) {
-    ks->l = 0;
-
-    if (!hrecs->h || !hrecs->h->size) {
-        return kputsn("", 0, ks) >= 0 ? 0 : -1;
-    }
-    if (sam_hrecs_rebuild_lines(hrecs, ks) != 0)
-        return -1;
-
-    return 0;
-}
-
 /*
  * Looks up a reference sequence by name and returns the numerical ID.
  * Returns -1 if unknown reference; -2 if header could not be parsed.
@@ -2485,25 +2509,6 @@ int sam_hrecs_vupdate(sam_hrecs_t *hrecs, sam_hrec_type_t *type, va_list ap) {
     return 0;
 }
 
-/*
- * Adds or updates tag key,value pairs in a header line.
- * Eg for adding M5 tags to @SQ lines or updating sort order for the
- * @HD line.
- *
- * Specify multiple key,value pairs ending in NULL.
- *
- * Returns 0 on success
- *        -1 on failure
- */
-static int sam_hrecs_update(sam_hrecs_t *hrecs, sam_hrec_type_t *type, ...) {
-    va_list args;
-    int res;
-    va_start(args, type);
-    res = sam_hrecs_vupdate(hrecs, type, args);
-    va_end(args);
-    return res;
-}
-
 /*
  * Looks for a specific key in a single sam header line identified by *type.
  * If prev is non-NULL it also fills this out with the previous tag, to
diff --git a/header.h b/header.h
index 810a3dda1..c6fbd7f5f 100644
--- a/header.h
+++ b/header.h
@@ -249,7 +249,7 @@ sam_hrecs_t *sam_hrecs_new(void);
  */
 sam_hrecs_t *sam_hrecs_dup(sam_hrecs_t *hrecs);
 
-/*! Update sam_hdr_t target_name and target_len arrays
+/*! Update sam_hdr_t target_name and target_len arrays from source sam_hrecs_t
  *
  *  sam_hdr_t and sam_hrecs_t are specified separately so that sam_hdr_dup
  *  can use it to construct target arrays from the source header.
diff --git a/test/test.pl b/test/test.pl
index ca0d766c1..69cc7b5e1 100755
--- a/test/test.pl
+++ b/test/test.pl
@@ -645,6 +645,12 @@ sub test_view
     testv $opts, "./test_view $tv_args -p longrefs/longref.tmp.sam_ longrefs/longref.tmp.sam.gz";
     testv $opts, "./compare_sam.pl longrefs/longref.sam longrefs/longref.tmp.sam_";
 
+    # CRAM disabled for now as the positions cannot be 32-bit.  (These tests are useful for
+    # checking SQ headers only.)
+    # testv $opts, "./test_view $tv_args -C -o no_ref -p longrefs/longref.tmp.cram longrefs/longref.sam";
+    # testv $opts, "./test_view $tv_args -p longrefs/longref.tmp.sam_ longrefs/longref.tmp.cram";
+    # testv $opts, "./compare_sam.pl longrefs/longref.sam longrefs/longref.tmp.sam_";
+
     # Build index and compare with on-the-fly one made earlier.
     test_compare $opts, "$$opts{path}/test_index -c longrefs/longref.tmp.sam.gz", "longrefs/longref.tmp.sam.gz.csi.otf", "longrefs/longref.tmp.sam.gz.csi", gz=>1;