Allow for refs up to UINT32_MAX long in header

Quick update to push the ref length as far as possible without
making the bam_hdr_t target_len array bigger.

Author: daviesrob

sam.c

@@ -910,7 +910,7 @@ bam_hdr_t *sam_hdr_parse(int l_text, const char *text)
     for (p = text; *p; ++p) {
         if (strncmp(p, "@SQ\t", 4) == 0) {
             char *sn = 0;
-            int ln = -1;
+            int64_t ln = -1;
             for (q = p + 4;; ++q) {
                 if (strncmp(q, "SN:", 3) == 0) {
                     q += 3;
@@ -927,6 +927,10 @@ bam_hdr_t *sam_hdr_parse(int l_text, const char *text)
             if (sn && ln >= 0) {
                 khint_t k;
                 int absent;
+                if (ln > UINT32_MAX) {
+                    hts_log_error("Reference '%s' is too long", sn);
+                    return NULL; // FIXME: Leaks memory
+                }
                 k = kh_put(s2i, d, sn, &absent);
                 if (!absent) {
                     hts_log_warning("Duplicated sequence '%s'", sn);
@@ -1111,7 +1115,7 @@ int sam_hdr_write(htsFile *fp, const bam_hdr_t *h)
             for (i = 0; i < h->n_targets; ++i) {
                 fp->line.l = 0;
                 kputsn("@SQ\tSN:", 7, &fp->line); kputs(h->target_name[i], &fp->line);
-                kputsn("\tLN:", 4, &fp->line); kputw(h->target_len[i], &fp->line); kputc('\n', &fp->line);
+                kputsn("\tLN:", 4, &fp->line); kputuw(h->target_len[i], &fp->line); kputc('\n', &fp->line);
                 if ( hwrite(fp->fp.hfile, fp->line.s, fp->line.l) != fp->line.l ) return -1;
             }
         }