X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam_index.c;h=d6b94e2413e1dab2d2dc4ce2c91e471854ddd35a;hb=3a1bd4d97b4d58148b5a7fd845a3b6a023eecbed;hp=9b71bdbac9167ec38719be411ee6d42a276c927f;hpb=4d48006473298b62ee54f13d706f9f2e512e02bd;p=samtools.git

diff --git a/bam_index.c b/bam_index.c
index 9b71bdb..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;
@@ -176,7 +181,7 @@ bam_index_t *bam_index_core(bamFile fp)
 	off_beg = off_end = bam_tell(fp);
 	while ((ret = bam_read1(fp, b)) >= 0) {
 		if (c->tid < 0) ++n_no_coor;
-		if (last_tid < c->tid) { // change of chromosomes
+		if (last_tid < c->tid || (last_tid >= 0 && c->tid < 0)) { // change of chromosomes
 			last_tid = c->tid;
 			last_bin = 0xffffffffu;
 		} else if ((uint32_t)last_tid > (uint32_t)c->tid) {
@@ -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);