Imported Upstream version 0.5

[pysam.git] / samtools / bcftools / bcfutils.c.pysam.c

diff --git a/samtools/bcftools/bcfutils.c.pysam.c b/samtools/bcftools/bcfutils.c.pysam.c
index 110d0bb0855f59ec2e8eacb7fc0d144bd5ebb1b3..c48ab03c29cbcbd08c84f3cfd13ae1f8b1d81678 100644 (file)
--- a/samtools/bcftools/bcfutils.c.pysam.c
+++ b/samtools/bcftools/bcfutils.c.pysam.c
@@ -7,12 +7,6 @@
 #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;
@@ -316,77 +310,3 @@ 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;
-}