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bcf2qcall.c

#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;
                        g[j++] = p[x * b->n_alleles - x * (x-1) / 2 + (y - 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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