Release samtools-0.1.11

[samtools.git] / bcftools / bcfutils.c

diff --git a/bcftools/bcfutils.c b/bcftools/bcfutils.c
index 6908bc478bf7081409f9ef9f57b332ef9031ce39..4d6835da8206ea96542ce66e14124b4a388e70db 100644 (file)
--- 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;
 }