Imported Upstream version 0.1.18

[samtools.git] / bcftools / bcfutils.c

diff --git a/bcftools/bcfutils.c b/bcftools/bcfutils.c
index d1b9668099be4e934bf0225cefb444370fdc7315..0eab4c1f322b398750fdda9da4caec6eea8e7579 100644 (file)
--- a/bcftools/bcfutils.c
+++ b/bcftools/bcfutils.c
@@ -5,6 +5,12 @@
 #include "khash.h"
 KHASH_MAP_INIT_STR(str2id, int)
 
+#ifdef _WIN32
+#define srand48(x) srand(x)
+#define drand48() ((double)rand() / RAND_MAX)
+#endif
+
+// FIXME: valgrind report a memory leak in this function. Probably it does not get deallocated...
 void *bcf_build_refhash(bcf_hdr_t *h)
 {
        khash_t(str2id) *hash;
@@ -308,3 +314,77 @@ int bcf_subsam(int n_smpl, int *list, bcf1_t *b)
        b->n_smpl = n_smpl;
        return 0;
 }
+
+static int8_t nt4_table[128] = {
+       4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
+       4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
+       4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4 /*'-'*/, 4, 4,
+       4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
+       4, 0, 4, 1,  4, 4, 4, 2,  4, 4, 4, 4,  4, 4, 4, 4, 
+       4, 4, 4, 4,  3, 4, 4, 4, -1, 4, 4, 4,  4, 4, 4, 4, 
+       4, 0, 4, 1,  4, 4, 4, 2,  4, 4, 4, 4,  4, 4, 4, 4, 
+       4, 4, 4, 4,  3, 4, 4, 4, -1, 4, 4, 4,  4, 4, 4, 4
+};
+
+int bcf_gl10(const bcf1_t *b, uint8_t *gl)
+{
+       int a[4], k, l, map[4], k1, j, i;
+       const bcf_ginfo_t *PL;
+       char *s;
+       if (b->ref[1] != 0 || b->n_alleles > 4) return -1; // ref is not a single base or >4 alleles
+       for (i = 0; i < b->n_gi; ++i)
+               if (b->gi[i].fmt == bcf_str2int("PL", 2)) break;
+       if (i == b->n_gi) return -1; // no PL
+       PL = b->gi + i;
+       a[0] = nt4_table[(int)b->ref[0]];
+       if (a[0] > 3 || a[0] < 0) return -1; // ref is not A/C/G/T
+       a[1] = a[2] = a[3] = -2; // -1 has a special meaning
+       if (b->alt[0] == 0) return -1; // no alternate allele
+       map[0] = map[1] = map[2] = map[3] = -2;
+       map[a[0]] = 0;
+       for (k = 0, s = b->alt, k1 = -1; k < 3 && *s; ++k, s += 2) {
+               if (s[1] != ',' && s[1] != 0) return -1; // ALT is not single base
+               a[k+1] = nt4_table[(int)*s];
+               if (a[k+1] >= 0) map[a[k+1]] = k+1;
+               else k1 = k + 1;
+               if (s[1] == 0) break; // the end of the ALT string
+       }
+       for (k = 0; k < 4; ++k)
+               if (map[k] < 0) map[k] = k1;
+       for (i = 0; i < b->n_smpl; ++i) {
+               const uint8_t *p = PL->data + i * PL->len; // the PL for the i-th individual
+               uint8_t *g = gl + 10 * i;
+               for (k = j = 0; k < 4; ++k) {
+                       for (l = k; l < 4; ++l) {
+                               int t, x = map[k], y = map[l];
+                               if (x > y) t = x, x = y, y = t; // make sure x is the smaller
+                               g[j++] = p[y * (y+1) / 2 + x];
+                       }
+               }
+       }
+       return 0;
+}
+
+int bcf_gl10_indel(const bcf1_t *b, uint8_t *gl)
+{
+       int k, l, j, i;
+       const bcf_ginfo_t *PL;
+       if (b->alt[0] == 0) return -1; // no alternate allele
+       for (i = 0; i < b->n_gi; ++i)
+               if (b->gi[i].fmt == bcf_str2int("PL", 2)) break;
+       if (i == b->n_gi) return -1; // no PL
+       PL = b->gi + i;
+       for (i = 0; i < b->n_smpl; ++i) {
+               const uint8_t *p = PL->data + i * PL->len; // the PL for the i-th individual
+               uint8_t *g = gl + 10 * i;
+               for (k = j = 0; k < 4; ++k) {
+                       for (l = k; l < 4; ++l) {
+                               int t, x = k, y = l;
+                               if (x > y) t = x, x = y, y = t; // make sure x is the smaller
+                               x = y * (y+1) / 2 + x;
+                               g[j++] = x < PL->len? p[x] : 255;
+                       }
+               }
+       }
+       return 0;
+}