X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=bcftools%2Fmut.c;h=15ef265b25b38ce3b3894eebdd52e6496cb0135b;hp=4b7cd104a60b7bc3d4fba7086b551ac72155f350;hb=0f906dafb2ad22371a753557562ef95c3034480d;hpb=b301e959d73eee0955c57004f344f17af00703f4

diff --git a/bcftools/mut.c b/bcftools/mut.c
index 4b7cd10..15ef265 100644
--- a/bcftools/mut.c
+++ b/bcftools/mut.c
@@ -33,6 +33,7 @@ uint32_t *bcf_trio_prep(int is_x, int is_son)
 	return ret;
 }
 
+
 int bcf_trio_call(const uint32_t *prep, const bcf1_t *b, int *llr, int64_t *gt)
 {
 	int i, j, k;
@@ -44,7 +45,9 @@ int bcf_trio_call(const uint32_t *prep, const bcf1_t *b, int *llr, int64_t *gt)
 		if (b->gi[i].fmt == bcf_str2int("PL", 2)) break;
 	if (i == b->n_gi) return -1; // no PL
 	gl10 = alloca(10 * b->n_smpl);
-	if (bcf_gl10(b, gl10) < 0) return -1;
+	if (bcf_gl10(b, gl10) < 0) {
+		if (bcf_gl10_indel(b, gl10) < 0) return -1;
+	}
 	PL = b->gi + i;
 	for (i = 0, k = 0; i < 4; ++i)
 		for (j = i; j < 4; ++j)