f63458a827952f14b1b1465a6da88c19d4facb9b
markd
  Mon Oct 16 15:20:32 2017 -0700
fixed compile error when CRAM enabled

diff --git src/htslib/sam.c src/htslib/sam.c
index 0508aca..6ec84ab 100644
--- src/htslib/sam.c
+++ src/htslib/sam.c
@@ -103,37 +103,37 @@
     h->target_len = (uint32_t*)malloc(sizeof(uint32_t) * h->n_targets);
     h->target_name = (char**)malloc(sizeof(char*) * h->n_targets);
     for (k = kh_begin(d); k != kh_end(d); ++k) {
         if (!kh_exist(d, k)) continue;
         h->target_name[kh_val(d, k)>>32] = (char*)kh_key(d, k);
         h->target_len[kh_val(d, k)>>32]  = kh_val(d, k)<<32>>32;
         kh_val(d, k) >>= 32;
     }
     return h;
 }
 
 bam_hdr_t *bam_hdr_read(BGZF *fp)
 {
     bam_hdr_t *h;
     char buf[4];
-    int magic_len; // has_EOF;
+    int magic_len;
     int32_t i, name_len, num_names = 0;
     size_t bufsize;
     ssize_t bytes;
 #ifndef UCSC_CRAM
     // check EOF
-    has_EOF = bgzf_check_EOF(fp);
+    int has_EOF = bgzf_check_EOF(fp);
     if (has_EOF < 0) {
         perror("[W::bam_hdr_read] bgzf_check_EOF");
     } else if (has_EOF == 0 && hts_verbose >= 2)
         fprintf(stderr, "[W::%s] EOF marker is absent. The input is probably truncated.\n", __func__);
 #endif
     // read "BAM1"
     magic_len = bgzf_read(fp, buf, 4);
     if (magic_len != 4 || strncmp(buf, "BAM\1", 4)) {
         if (hts_verbose >= 1) fprintf(stderr, "[E::%s] invalid BAM binary header\n", __func__);
         return 0;
     }
     h = bam_hdr_init();
     if (!h) goto nomem;
 
     // read plain text and the number of reference sequences