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#include "pysam.h"
#include <errno.h>
#include <math.h>
#include <string.h>
#include <stdlib.h>
#include "bcf.h"
static int8_t nt4_table[256] = {
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,
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, 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
};
static int read_I16(bcf1_t *b, int anno[16])
{
char *p;
int i;
if ((p = strstr(b->info, "I16=")) == 0) return -1;
p += 4;
for (i = 0; i < 16; ++i) {
anno[i] = strtol(p, &p, 10);
if (anno[i] == 0 && (errno == EINVAL || errno == ERANGE)) return -2;
++p;
}
return 0;
}
int bcf_2qcall(bcf_hdr_t *h, bcf1_t *b)
{
int a[4], k, g[10], l, map[4], k1, j, i, i0, anno[16], dp, mq, d_rest;
char *s;
if (b->ref[1] != 0 || b->n_alleles > 4) return -1; // ref is not a single base
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
if (read_I16(b, anno) != 0) return -1; // no I16; FIXME: can be improved
d_rest = dp = anno[0] + anno[1] + anno[2] + anno[3];
if (dp == 0) return -1; // depth is zero
mq = (int)(sqrt((double)(anno[9] + anno[11]) / dp) + .499);
i0 = i;
a[0] = nt4_table[(int)b->ref[0]];
if (a[0] > 3) 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;
}
for (k = 0; k < 4; ++k)
if (map[k] < 0) map[k] = k1;
for (i = 0; i < h->n_smpl; ++i) {
int d;
uint8_t *p = b->gi[i0].data + i * b->gi[i0].len;
for (j = 0; j < b->gi[i0].len; ++j)
if (p[j]) break;
d = (int)((double)d_rest / (h->n_smpl - i) + .499);
if (d == 0) d = 1;
if (j == b->gi[i0].len) d = 0;
d_rest -= d;
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; // swap
g[j++] = p[y * (y+1) / 2 + x];
}
}
printf("%s\t%d\t%c", h->ns[b->tid], b->pos+1, *b->ref);
printf("\t%d\t%d\t0", d, mq);
for (j = 0; j < 10; ++j)
printf("\t%d", g[j]);
printf("\t%s\n", h->sns[i]);
}
return 0;
}
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