Imported Upstream version 0.1.18

[samtools.git] / bcftools / mut.c

diff --git a/bcftools/mut.c b/bcftools/mut.c
index 4b7cd104a60b7bc3d4fba7086b551ac72155f350..15ef265b25b38ce3b3894eebdd52e6496cb0135b 100644 (file)
--- 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)