Prevent negative rlen on erroneous INFO/END when reading BCF

This is an extension of ea879e1 which added checks for reading
VCF.

Resolves samtools/bcftools#1154

vcf.c

@@ -3895,6 +3895,8 @@ int bcf_get_variant_type(bcf1_t *rec, int ith_allele)
 
 int bcf_update_info(const bcf_hdr_t *hdr, bcf1_t *line, const char *key, const void *values, int n, int type)
 {
+    static int negative_rlen_warned = 0;
+
     // Is the field already present?
     int i, inf_id = bcf_hdr_id2int(hdr,BCF_DT_ID,key);
     if ( !bcf_hdr_idinfo_exists(hdr,BCF_HL_INFO,inf_id) ) return -1;    // No such INFO field in the header
@@ -3991,7 +3993,16 @@ int bcf_update_info(const bcf_hdr_t *hdr, bcf1_t *line, const char *key, const v
     if ( n==1 && !strcmp("END",key) ) {
         assert(type == BCF_HT_INT || type == BCF_HT_LONG);
         int64_t end = type == BCF_HT_INT ? *(int32_t *) values : *(int64_t *) values;
-        line->rlen = end - line->pos;
+        if ( end <= line->pos )
+        {
+            if ( !negative_rlen_warned )
+            {
+                hts_log_warning("INFO/END=%"PRIhts_pos" is smaller than POS at %s:%"PRIhts_pos,end,bcf_seqname(hdr,line),line->pos+1);
+                negative_rlen_warned = 1;
+            }
+        }
+        else
+            line->rlen = end - line->pos;
     }
     return 0;
 }