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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;
}
return ret;
}
+
int bcf_trio_call(const uint32_t *prep, const bcf1_t *b, int *llr, int64_t *gt)
{
int i, j, k;
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 (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)
PL = b->gi + i;
for (i = 0, k = 0; i < 4; ++i)
for (j = i; j < 4; ++j)