X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bcftools%2Fbcfutils.c;h=4d6835da8206ea96542ce66e14124b4a388e70db;hb=168ad095c3483f195ae3e404b3cd1fe949681909;hp=6908bc478bf7081409f9ef9f57b332ef9031ce39;hpb=6418571502ba9c6bd4eb930c7ae0309f7f251b4e;p=samtools.git

diff --git a/bcftools/bcfutils.c b/bcftools/bcfutils.c
index 6908bc4..4d6835d 100644
--- a/bcftools/bcfutils.c
+++ b/bcftools/bcfutils.c
@@ -48,11 +48,10 @@ int bcf_str2id_add(void *_hash, const char *str)
 	return kh_val(hash, k);
 }
 
-int bcf_shrink_alt(int n_smpl, bcf1_t *b, int n)
+int bcf_shrink_alt(bcf1_t *b, int n)
 {
 	char *p;
-	int i, j, k;
-	int *z;
+	int i, j, k, *z, n_smpl = b->n_smpl;
 	if (b->n_alleles <= n) return -1;
 	if (n > 1) {
 		for (p = b->alt, k = 1; *p; ++p)
@@ -79,6 +78,32 @@ int bcf_shrink_alt(int n_smpl, bcf1_t *b, int n)
 		} // FIXME: to add GL
 	}
 	b->n_alleles = n;
-	bcf_sync(n_smpl, b);
+	bcf_sync(b);
+	return 0;
+}
+
+int bcf_gl2pl(bcf1_t *b)
+{
+	char *p;
+	int i, n_smpl = b->n_smpl;
+	bcf_ginfo_t *g;
+	float *d0;
+	uint8_t *d1;
+	if (strstr(b->fmt, "PL")) return -1;
+	if ((p = strstr(b->fmt, "GL")) == 0) return -1;
+	*p = 'P';
+	for (i = 0; i < b->n_gi; ++i)
+		if (b->gi[i].fmt == bcf_str2int("GL", 2))
+			break;
+	g = b->gi + i;
+	g->fmt = bcf_str2int("PL", 2);
+	g->len /= 4; // 4 == sizeof(float)
+	d0 = (float*)g->data; d1 = (uint8_t*)g->data;
+	for (i = 0; i < n_smpl * g->len; ++i) {
+		int x = (int)(-10. * d0[i] + .499);
+		if (x > 255) x = 255;
+		if (x < 0) x = 0;
+		d1[i] = x;
+	}
 	return 0;
 }