From: Heng Li <lh3@live.co.uk>
Date: Wed, 2 Feb 2011 16:28:24 +0000 (+0000)
Subject:  * fixed an out-of-boundary bug
X-Git-Url: https://git.donarmstrong.com/?p=samtools.git;a=commitdiff_plain;h=fee22b6b728d3f0115bec76f7b0e15cad330b7c0

 * fixed an out-of-boundary bug
 * improved sorting order checking in index
---

diff --git a/bam2bcf.c b/bam2bcf.c
index 46f534e..98acb5d 100644
--- a/bam2bcf.c
+++ b/bam2bcf.c
@@ -79,7 +79,7 @@ int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t
 		}
 		bca->bases[n++] = q<<5 | (int)bam1_strand(p->b)<<4 | b;
 		// collect annotations
-		r->qsum[b] += q;
+		if (b < 4) r->qsum[b] += q;
 		++r->anno[0<<2|is_diff<<1|bam1_strand(p->b)];
 		min_dist = p->b->core.l_qseq - 1 - p->qpos;
 		if (min_dist > p->qpos) min_dist = p->qpos;
diff --git a/bam_index.c b/bam_index.c
index 328f011..51c2701 100644
--- a/bam_index.c
+++ b/bam_index.c
@@ -217,8 +217,15 @@ bam_index_t *bam_index_core(bamFile fp)
 	}
 	merge_chunks(idx);
 	fill_missing(idx);
-	if (ret >= 0)
-		while ((ret = bam_read1(fp, b)) >= 0) ++n_no_coor;
+	if (ret >= 0) {
+		while ((ret = bam_read1(fp, b)) >= 0) {
+			++n_no_coor;
+			if (c->tid >= 0 && n_no_coor) {
+				fprintf(stderr, "[bam_index_core] the alignment is not sorted: reads without coordinates prior to reads with coordinates.\n");
+				exit(1);
+			}
+		}
+	}
 	if (ret < -1) fprintf(stderr, "[bam_index_core] truncated file? Continue anyway. (%d)\n", ret);
 	free(b->data); free(b);
 	idx->n_no_coor = n_no_coor;