+++ /dev/null
-#include "pysam.h"
-
-#include <stdlib.h>
-#include <stdint.h>
-#include "bcf.h"
-
-#define MAX_GENO 359
-
-int8_t seq_bitcnt[] = { 4, 1, 1, 2, 1, 2, 2, 3, 1, 2, 2, 3, 2, 3, 3, 4 };
-char *seq_nt16rev = "XACMGRSVTWYHKDBN";
-
-uint32_t *bcf_trio_prep(int is_x, int is_son)
-{
- int i, j, k, n, map[10];
- uint32_t *ret;
- ret = calloc(MAX_GENO, 4);
- for (i = 0, k = 0; i < 4; ++i)
- for (j = i; j < 4; ++j)
- map[k++] = 1<<i|1<<j;
- for (i = 0, n = 1; i < 10; ++i) { // father
- if (is_x && seq_bitcnt[map[i]] != 1) continue;
- if (is_x && is_son) {
- for (j = 0; j < 10; ++j) // mother
- for (k = 0; k < 10; ++k) // child
- if (seq_bitcnt[map[k]] == 1 && (map[j]&map[k]))
- ret[n++] = j<<16 | i<<8 | k;
- } else {
- for (j = 0; j < 10; ++j) // mother
- for (k = 0; k < 10; ++k) // child
- if ((map[i]&map[k]) && (map[j]&map[k]) && ((map[i]|map[j])&map[k]) == map[k])
- ret[n++] = j<<16 | i<<8 | k;
- }
- }
- ret[0] = n - 1;
- return ret;
-}
-
-
-int bcf_trio_call(const uint32_t *prep, const bcf1_t *b, int *llr, int64_t *gt)
-{
- int i, j, k;
- const bcf_ginfo_t *PL;
- uint8_t *gl10;
- int map[10];
- if (b->n_smpl != 3) return -1; // not a trio
- 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
- gl10 = alloca(10 * b->n_smpl);
- if (bcf_gl10(b, gl10) < 0) {
- if (bcf_gl10_indel(b, gl10) < 0) return -1;
- }
- PL = b->gi + i;
- for (i = 0, k = 0; i < 4; ++i)
- for (j = i; j < 4; ++j)
- map[k++] = seq_nt16rev[1<<i|1<<j];
- for (j = 0; j < 3; ++j) // check if ref hom is the most probable in all members
- if (((uint8_t*)PL->data)[j * PL->len] != 0) break;
- if (j < 3) { // we need to go through the complex procedure
- uint8_t *g[3];
- int minc = 1<<30, minc_j = -1, minf = 0, gtf = 0, gtc = 0;
- g[0] = gl10;
- g[1] = gl10 + 10;
- g[2] = gl10 + 20;
- for (j = 1; j <= (int)prep[0]; ++j) { // compute LK with constraint
- int sum = g[0][prep[j]&0xff] + g[1][prep[j]>>8&0xff] + g[2][prep[j]>>16&0xff];
- if (sum < minc) minc = sum, minc_j = j;
- }
- gtc |= map[prep[minc_j]&0xff]; gtc |= map[prep[minc_j]>>8&0xff]<<8; gtc |= map[prep[minc_j]>>16]<<16;
- for (j = 0; j < 3; ++j) { // compute LK without constraint
- int min = 1<<30, min_k = -1;
- for (k = 0; k < 10; ++k)
- if (g[j][k] < min) min = g[j][k], min_k = k;
- gtf |= map[min_k]<<(j*8);
- minf += min;
- }
- *llr = minc - minf; *gt = (int64_t)gtc<<32 | gtf;
- } else *llr = 0, *gt = -1;
- return 0;
-}
-
-int bcf_pair_call(const bcf1_t *b)
-{
- int i, j, k;
- const bcf_ginfo_t *PL;
- if (b->n_smpl != 2) return -1; // not a pair
- 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 (j = 0; j < 2; ++j) // check if ref hom is the most probable in all members
- if (((uint8_t*)PL->data)[j * PL->len] != 0) break;
- if (j < 2) { // we need to go through the complex procedure
- uint8_t *g[2];
- int minc = 1<<30, minf = 0;
- g[0] = PL->data;
- g[1] = (uint8_t*)PL->data + PL->len;
- for (j = 0; j < PL->len; ++j) // compute LK with constraint
- minc = minc < g[0][j] + g[1][j]? minc : g[0][j] + g[1][j];
- for (j = 0; j < 2; ++j) { // compute LK without constraint
- int min = 1<<30;
- for (k = 0; k < PL->len; ++k)
- min = min < g[j][k]? min : g[j][k];
- minf += min;
- }
- return minc - minf;
- } else return 0;
-}
-
-int bcf_min_diff(const bcf1_t *b)
-{
- int i, min = 1<<30;
- const bcf_ginfo_t *PL;
- 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) {
- int m1, m2, j;
- const uint8_t *p = (uint8_t*)PL->data;
- m1 = m2 = 1<<30;
- for (j = 0; j < PL->len; ++j) {
- if ((int)p[j] < m1) m2 = m1, m1 = p[j];
- else if ((int)p[j] < m2) m2 = p[j];
- }
- min = min < m2 - m1? min : m2 - m1;
- }
- return min;
-}
projects / pysam.git / blobdiff