X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam_index.c;h=d6b94e2413e1dab2d2dc4ce2c91e471854ddd35a;hb=70c740facc966321754c6bfcc6d61ea056480638;hp=66d8eb8a896ab5a0a4decf612e65eac158e92cbf;hpb=3384f6c6c1642ada4edae9204ca1202672de7d5a;p=samtools.git

diff --git a/bam_index.c b/bam_index.c
index 66d8eb8..d6b94e2 100644
--- a/bam_index.c
+++ b/bam_index.c
@@ -159,9 +159,14 @@ bam_index_t *bam_index_core(bamFile fp)
 	bam1_core_t *c;
 	uint64_t save_off, last_off, n_mapped, n_unmapped, off_beg, off_end, n_no_coor;
 
+	h = bam_header_read(fp);
+	if(h == 0) {
+	    fprintf(stderr, "[bam_index_core] Invalid BAM header.");
+	    return NULL;
+	}
+
 	idx = (bam_index_t*)calloc(1, sizeof(bam_index_t));
 	b = (bam1_t*)calloc(1, sizeof(bam1_t));
-	h = bam_header_read(fp);
 	c = &b->core;
 
 	idx->n = h->n_targets;
@@ -188,7 +193,7 @@ bam_index_t *bam_index_core(bamFile fp)
 					bam1_qname(b), last_coor, c->pos, c->tid+1);
 			return NULL;
 		}
-		if (c->tid >= 0) insert_offset2(&idx->index2[b->core.tid], b, last_off);
+		if (c->tid >= 0 && !(c->flag & BAM_FUNMAP)) insert_offset2(&idx->index2[b->core.tid], b, last_off);
 		if (c->bin != last_bin) { // then possibly write the binning index
 			if (save_bin != 0xffffffffu) // save_bin==0xffffffffu only happens to the first record
 				insert_offset(idx->index[save_tid], save_bin, save_off, last_off);