Fix CRAM embed_ref=2 with seqs overlapping ref end.

If the sequences align off the end of the reference and we are
creating consensus on the fly, then the consensus generated also steps
beyond the reference length.  Although this longer reference is
embedded, it is trimmed back by the CRAM decoder which validates
against the declared reference length in SQ LN, leading to Ns
appearing in the decoder.

Therefore we now validate in the encoder too, which also needed
refs_from_header updates to work when not given any externals (such as
.fai).

cram/cram_encode.c

@@ -1761,7 +1761,6 @@ 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:
@@ -1997,6 +1996,9 @@ int cram_encode_container(cram_fd *fd, cram_container *c) {
                 fd->no_ref_counter -= (fd->no_ref_counter > 0);
                 pthread_mutex_unlock(&fd->ref_lock);
             }
+
+            if (c->ref_end > fd->refs->ref_id[c->ref_id]->length)
+                c->ref_end = fd->refs->ref_id[c->ref_id]->length;
         }
 
         // Iterate through records creating the cram blocks for some

cram/cram_io.c

@@ -2734,7 +2734,7 @@ int refs2id(refs_t *r, sam_hdr_t *hdr) {
  * Returns 0 on success
  *         -1 on failure
  */
-static int refs_from_header(cram_fd *fd) {
+ int refs_from_header(cram_fd *fd) {
     if (!fd)
         return -1;
 
@@ -2787,10 +2787,11 @@ static int refs_from_header(cram_fd *fd) {
 
         /* Initialise likely filename if known */
         if ((ty = sam_hrecs_find_type_id(h->hrecs, "SQ", "SN", h->hrecs->ref[i].name))) {
-            if ((tag = sam_hrecs_find_key(ty, "M5", NULL))) {
+            if ((tag = sam_hrecs_find_key(ty, "M5", NULL)))
                 r->ref_id[j]->fn = string_dup(r->pool, tag->str+3);
-                //fprintf(stderr, "Tagging @SQ %s / %s\n", r->ref_id[h]->name, r->ref_id[h]->fn);
-            }
+
+            if ((tag = sam_hrecs_find_key(ty, "LN", NULL)))
+                r->ref_id[j]->length = strtol(tag->str+3, NULL, 0);
         }
 
         k = kh_put(refs, r->h_meta, r->ref_id[j]->name, &n);