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bcfutils.c

#include "bcf.h"
#include "kstring.h"
#include "khash.h"
KHASH_MAP_INIT_STR(str2id, int)

void *bcf_build_refhash(bcf_hdr_t *h)
{
      khash_t(str2id) *hash;
      int i, ret;
      hash = kh_init(str2id);
      for (i = 0; i < h->n_ref; ++i) {
            khint_t k;
            k = kh_put(str2id, hash, h->ns[i], &ret); // FIXME: check ret
            kh_val(hash, k) = i;
      }
      return hash;
}

void *bcf_str2id_init()
{
      return kh_init(str2id);
}

void bcf_str2id_destroy(void *_hash)
{
      khash_t(str2id) *hash = (khash_t(str2id)*)_hash;
      if (hash) kh_destroy(str2id, hash); // Note that strings are not freed.
}

int bcf_str2id(void *_hash, const char *str)
{
      khash_t(str2id) *hash = (khash_t(str2id)*)_hash;
      khint_t k;
      if (!hash) return -1;
      k = kh_get(str2id, hash, str);
      return k == kh_end(hash)? -1 : kh_val(hash, k);
}

int bcf_str2id_add(void *_hash, const char *str)
{
      khint_t k;
      int ret;
      khash_t(str2id) *hash = (khash_t(str2id)*)_hash;
      if (!hash) return -1;
      k = kh_put(str2id, hash, str, &ret);
      if (ret == 0) return kh_val(hash, k);
      kh_val(hash, k) = kh_size(hash) - 1;
      return kh_val(hash, k);
}

int bcf_shrink_alt(bcf1_t *b, int n)
{
      char *p;
      int i, j, k, *z, n_smpl = b->n_smpl;
      if (b->n_alleles <= n) return -1;
      if (n > 1) {
            for (p = b->alt, k = 1; *p; ++p)
                  if (*p == ',' && ++k == n) break;
            *p = '\0';
      } else p = b->alt, *p = '\0';
      ++p;
      memmove(p, b->flt, b->str + b->l_str - b->flt);
      b->l_str -= b->flt - p;
      z = alloca(sizeof(int) / 2 * n * (n+1));
      for (i = k = 0; i < n; ++i)
            for (j = 0; j < n - i; ++j)
                  z[k++] = i * b->n_alleles + j;
      for (i = 0; i < b->n_gi; ++i) {
            bcf_ginfo_t *g = b->gi + i;
            if (g->fmt == bcf_str2int("PL", 2)) {
                  int l, x = b->n_alleles * (b->n_alleles + 1) / 2;
                  uint8_t *d = (uint8_t*)g->data;
                  g->len = n * (n + 1) / 2;
                  for (l = k = 0; l < n_smpl; ++l) {
                        uint8_t *dl = d + l * x;
                        for (j = 0; j < g->len; ++j) d[k++] = dl[z[j]];
                  }
            } // FIXME: to add GL
      }
      b->n_alleles = n;
      bcf_sync(b);
      return 0;
}

int bcf_gl2pl(bcf1_t *b)
{
      char *p;
      int i, n_smpl = b->n_smpl;
      bcf_ginfo_t *g;
      float *d0;
      uint8_t *d1;
      if (strstr(b->fmt, "PL")) return -1;
      if ((p = strstr(b->fmt, "GL")) == 0) return -1;
      *p = 'P';
      for (i = 0; i < b->n_gi; ++i)
            if (b->gi[i].fmt == bcf_str2int("GL", 2))
                  break;
      g = b->gi + i;
      g->fmt = bcf_str2int("PL", 2);
      g->len /= 4; // 4 == sizeof(float)
      d0 = (float*)g->data; d1 = (uint8_t*)g->data;
      for (i = 0; i < n_smpl * g->len; ++i) {
            int x = (int)(-10. * d0[i] + .499);
            if (x > 255) x = 255;
            if (x < 0) x = 0;
            d1[i] = x;
      }
      return 0;
}

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