Write the correct ALT and PL in the SNP calling mode.

[samtools.git] / bcftools / bcfutils.c

diff --git a/bcftools/bcfutils.c b/bcftools/bcfutils.c
index 3010ef3435bb240fff5ee2a2fb1485701b1628a3..6908bc478bf7081409f9ef9f57b332ef9031ce39 100644 (file)
--- a/bcftools/bcfutils.c
+++ b/bcftools/bcfutils.c
@@ -1,4 +1,5 @@
 #include "bcf.h"
+#include "kstring.h"
 #include "khash.h"
 KHASH_MAP_INIT_STR(str2id, int)
 
@@ -46,3 +47,38 @@ int bcf_str2id_add(void *_hash, const char *str)
        kh_val(hash, k) = kh_size(hash) - 1;
        return kh_val(hash, k);
 }
+
+int bcf_shrink_alt(int n_smpl, bcf1_t *b, int n)
+{
+       char *p;
+       int i, j, k;
+       int *z;
+       if (b->n_alleles <= n) return -1;
+       if (n > 1) {
+               for (p = b->alt, k = 1; *p; ++p)
+                       if (*p == ',' && ++k == n) break;
+               *p = '\0';
+       } else p = b->alt, *p = '\0';
+       ++p;
+       memmove(p, b->flt, b->str + b->l_str - b->flt);
+       b->l_str -= b->flt - p;
+       z = alloca(sizeof(int) / 2 * n * (n+1));
+       for (i = k = 0; i < n; ++i)
+               for (j = 0; j < n - i; ++j)
+                       z[k++] = i * b->n_alleles + j;
+       for (i = 0; i < b->n_gi; ++i) {
+               bcf_ginfo_t *g = b->gi + i;
+               if (g->fmt == bcf_str2int("PL", 2)) {
+                       int l, x = b->n_alleles * (b->n_alleles + 1) / 2;
+                       uint8_t *d = (uint8_t*)g->data;
+                       g->len = n * (n + 1) / 2;
+                       for (l = k = 0; l < n_smpl; ++l) {
+                               uint8_t *dl = d + l * x;
+                               for (j = 0; j < g->len; ++j) d[k++] = dl[z[j]];
+                       }
+               } // FIXME: to add GL
+       }
+       b->n_alleles = n;
+       bcf_sync(n_smpl, b);
+       return 0;
+}