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bcf.c

#include <string.h>
#include <ctype.h>
#include <stdio.h>
#include "kstring.h"
#include "bcf.h"

bcf_t *bcf_open(const char *fn, const char *mode)
{
      bcf_t *b;
      b = calloc(1, sizeof(bcf_t));
      if (strchr(mode, 'w')) {
            b->fp = strcmp(fn, "-")? bgzf_open(fn, mode) : bgzf_fdopen(fileno(stdout), mode);
      } else {
            b->fp = strcmp(fn, "-")? bgzf_open(fn, mode) : bgzf_fdopen(fileno(stdin), mode);
      }
#ifndef BCF_LITE
      b->fp->owned_file = 1;
#endif
      return b;
}

int bcf_close(bcf_t *b)
{
      int ret;
      if (b == 0) return 0;
      ret = bgzf_close(b->fp);
      free(b);
      return ret;
}

int bcf_hdr_write(bcf_t *b, const bcf_hdr_t *h)
{
      if (b == 0 || h == 0) return -1;
      bgzf_write(b->fp, "BCF\4", 4);
      bgzf_write(b->fp, &h->l_nm, 4);
      bgzf_write(b->fp, h->name, h->l_nm);
      bgzf_write(b->fp, &h->l_smpl, 4);
      bgzf_write(b->fp, h->sname, h->l_smpl);
      bgzf_write(b->fp, &h->l_txt, 4);
      bgzf_write(b->fp, h->txt, h->l_txt);
      bgzf_flush(b->fp);
      return 16 + h->l_nm + h->l_smpl + h->l_txt;
}

bcf_hdr_t *bcf_hdr_read(bcf_t *b)
{
      uint8_t magic[4];
      bcf_hdr_t *h;
      if (b == 0) return 0;
      h = calloc(1, sizeof(bcf_hdr_t));
      bgzf_read(b->fp, magic, 4);
      bgzf_read(b->fp, &h->l_nm, 4);
      h->name = malloc(h->l_nm);
      bgzf_read(b->fp, h->name, h->l_nm);
      bgzf_read(b->fp, &h->l_smpl, 4);
      h->sname = malloc(h->l_smpl);
      bgzf_read(b->fp, h->sname, h->l_smpl);
      bgzf_read(b->fp, &h->l_txt, 4);
      h->txt = malloc(h->l_txt);
      bgzf_read(b->fp, h->txt, h->l_txt);
      bcf_hdr_sync(h);
      return h;
}

void bcf_hdr_destroy(bcf_hdr_t *h)
{
      if (h == 0) return;
      free(h->name); free(h->sname); free(h->txt); free(h->ns); free(h->sns);
      free(h);
}

static inline char **cnt_null(int l, char *str, int *_n)
{
      int n = 0;
      char *p, **list;
      *_n = 0;
      if (l == 0 || str == 0) return 0;
      for (p = str; p != str + l; ++p)
            if (*p == 0) ++n;
      *_n = n;
      list = calloc(n, sizeof(void*));
      list[0] = str;
      for (p = str, n = 1; p < str + l - 1; ++p)
            if (*p == 0) list[n++] = p + 1;
      return list;
}

int bcf_hdr_sync(bcf_hdr_t *b)
{
      if (b == 0) return -1;
      if (b->ns) free(b->ns);
      if (b->sns) free(b->sns);
      if (b->l_nm) b->ns = cnt_null(b->l_nm, b->name, &b->n_ref);
      else b->ns = 0, b->n_ref = 0;
      b->sns = cnt_null(b->l_smpl, b->sname, &b->n_smpl);
      return 0;
}

int bcf_sync(bcf1_t *b)
{
      char *p, *tmp[5];
      int i, n, n_smpl = b->n_smpl;
      ks_tokaux_t aux;
      // set ref, alt, flt, info, fmt
      b->ref = b->alt = b->flt = b->info = b->fmt = 0;
      for (p = b->str, n = 0; p < b->str + b->l_str; ++p)
            if (*p == 0 && p+1 != b->str + b->l_str) tmp[n++] = p + 1;
      if (n != 5) {
            fprintf(stderr, "[%s] incorrect number of fields (%d != 5). Corrupted file?\n", __func__, n);
            return -1;
      }
      b->ref = tmp[0]; b->alt = tmp[1]; b->flt = tmp[2]; b->info = tmp[3]; b->fmt = tmp[4];
      // set n_alleles
      if (*b->alt == 0) b->n_alleles = 1;
      else {
            for (p = b->alt, n = 1; *p; ++p)
                  if (*p == ',') ++n;
            b->n_alleles = n + 1;
      }
      // set n_gi and gi[i].fmt
      for (p = b->fmt, n = 1; *p; ++p)
            if (*p == ':') ++n;
      if (n > b->m_gi) {
            int old_m = b->m_gi;
            b->m_gi = n;
            kroundup32(b->m_gi);
            b->gi = realloc(b->gi, b->m_gi * sizeof(bcf_ginfo_t));
            memset(b->gi + old_m, 0, (b->m_gi - old_m) * sizeof(bcf_ginfo_t));
      }
      b->n_gi = n;
      for (p = kstrtok(b->fmt, ":", &aux), n = 0; p; p = kstrtok(0, 0, &aux))
            b->gi[n++].fmt = bcf_str2int(p, aux.p - p);
      // set gi[i].len
      for (i = 0; i < b->n_gi; ++i) {
            if (b->gi[i].fmt == bcf_str2int("PL", 2)) {
                  b->gi[i].len = b->n_alleles * (b->n_alleles + 1) / 2;
            } else if (b->gi[i].fmt == bcf_str2int("DP", 2) || b->gi[i].fmt == bcf_str2int("HQ", 2)) {
                  b->gi[i].len = 2;
            } else if (b->gi[i].fmt == bcf_str2int("GQ", 2) || b->gi[i].fmt == bcf_str2int("GT", 2)
                           || b->gi[i].fmt == bcf_str2int("SP", 2))
            {
                  b->gi[i].len = 1;
            } else if (b->gi[i].fmt == bcf_str2int("GL", 2)) {
                  b->gi[i].len = b->n_alleles * (b->n_alleles + 1) / 2 * 4;
            }
            b->gi[i].data = realloc(b->gi[i].data, n_smpl * b->gi[i].len);
      }
      return 0;
}

int bcf_write(bcf_t *bp, const bcf_hdr_t *h, const bcf1_t *b)
{
      int i, l = 0;
      if (b == 0) return -1;
      bgzf_write(bp->fp, &b->tid, 4);
      bgzf_write(bp->fp, &b->pos, 4);
      bgzf_write(bp->fp, &b->qual, 4);
      bgzf_write(bp->fp, &b->l_str, 4);
      bgzf_write(bp->fp, b->str, b->l_str);
      l = 12 + b->l_str;
      for (i = 0; i < b->n_gi; ++i) {
            bgzf_write(bp->fp, b->gi[i].data, b->gi[i].len * h->n_smpl);
            l += b->gi[i].len * h->n_smpl;
      }
      return l;
}

int bcf_read(bcf_t *bp, const bcf_hdr_t *h, bcf1_t *b)
{
      int i, l = 0;
      if (b == 0) return -1;
      if (bgzf_read(bp->fp, &b->tid, 4) == 0) return -1;
      b->n_smpl = h->n_smpl;
      bgzf_read(bp->fp, &b->pos, 4);
      bgzf_read(bp->fp, &b->qual, 4);
      bgzf_read(bp->fp, &b->l_str, 4);
      if (b->l_str > b->m_str) {
            b->m_str = b->l_str;
            kroundup32(b->m_str);
            b->str = realloc(b->str, b->m_str);
      }
      bgzf_read(bp->fp, b->str, b->l_str);
      l = 12 + b->l_str;
      bcf_sync(b);
      for (i = 0; i < b->n_gi; ++i) {
            bgzf_read(bp->fp, b->gi[i].data, b->gi[i].len * h->n_smpl);
            l += b->gi[i].len * h->n_smpl;
      }
      return l;
}

int bcf_destroy(bcf1_t *b)
{
      int i;
      if (b == 0) return -1;
      free(b->str);
      for (i = 0; i < b->m_gi; ++i)
            free(b->gi[i].data);
      free(b->gi);
      free(b);
      return 0;
}

static inline void fmt_str(const char *p, kstring_t *s)
{
      if (*p == 0) kputc('.', s);
      else kputs(p, s);
}

void bcf_fmt_core(const bcf_hdr_t *h, bcf1_t *b, kstring_t *s)
{
      int i, j, x;
      s->l = 0;
      if (h->n_ref) kputs(h->ns[b->tid], s);
      else kputw(b->tid, s);
      kputc('\t', s);
      kputw(b->pos + 1, s); kputc('\t', s);
      fmt_str(b->str, s); kputc('\t', s);
      fmt_str(b->ref, s); kputc('\t', s);
      fmt_str(b->alt, s); kputc('\t', s);
      ksprintf(s, "%.3g", b->qual); kputc('\t', s);
      fmt_str(b->flt, s); kputc('\t', s);
      fmt_str(b->info, s);
      if (b->fmt[0]) {
            kputc('\t', s);
            fmt_str(b->fmt, s);
      }
      x = b->n_alleles * (b->n_alleles + 1) / 2;
      if (b->n_gi == 0) return;
      for (j = 0; j < h->n_smpl; ++j) {
            kputc('\t', s);
            for (i = 0; i < b->n_gi; ++i) {
                  if (i) kputc(':', s);
                  if (b->gi[i].fmt == bcf_str2int("PL", 2)) {
                        uint8_t *d = (uint8_t*)b->gi[i].data + j * x;
                        int k;
                        for (k = 0; k < x; ++k) {
                              if (k > 0) kputc(',', s);
                              kputw(d[k], s);
                        }
                  } else if (b->gi[i].fmt == bcf_str2int("DP", 2)) {
                        kputw(((uint16_t*)b->gi[i].data)[j], s);
                  } else if (b->gi[i].fmt == bcf_str2int("GQ", 2) || b->gi[i].fmt == bcf_str2int("SP", 2)) {
                        kputw(((uint8_t*)b->gi[i].data)[j], s);
                  } else if (b->gi[i].fmt == bcf_str2int("GT", 2)) {
                        int y = ((uint8_t*)b->gi[i].data)[j];
                        if (y>>7&1) {
                              kputsn("./.", 3, s);
                        } else {
                              kputc('0' + (y>>3&7), s);
                              kputc("/|"[y>>6&1], s);
                              kputc('0' + (y&7), s);
                        }
                  } else if (b->gi[i].fmt == bcf_str2int("GL", 2)) {
                        float *d = (float*)b->gi[i].data + j * x;
                        int k;
                        //printf("- %lx\n", d);
                        for (k = 0; k < x; ++k) {
                              if (k > 0) kputc(',', s);
                              ksprintf(s, "%.2f", d[k]);
                        }
                  }
            }
      }
}

char *bcf_fmt(const bcf_hdr_t *h, bcf1_t *b)
{
      kstring_t s;
      s.l = s.m = 0; s.s = 0;
      bcf_fmt_core(h, b, &s);
      return s.s;
}

int bcf_append_info(bcf1_t *b, const char *info, int l)
{
      int shift = b->fmt - b->str;
      int l_fmt = b->l_str - shift;
      char *ori = b->str;
      if (b->l_str + l > b->m_str) { // enlarge if necessary
            b->m_str = b->l_str + l;
            kroundup32(b->m_str);
            b->str = realloc(b->str, b->m_str);
      }
      memmove(b->str + shift + l, b->str + shift, l_fmt); // move the FORMAT field
      memcpy(b->str + shift - 1, info, l); // append to the INFO field
      b->str[shift + l - 1] = '\0';
      b->fmt = b->str + shift + l;
      b->l_str += l;
      if (ori != b->str) bcf_sync(b); // synchronize when realloc changes the pointer
      return 0;
}

int bcf_cpy(bcf1_t *r, const bcf1_t *b)
{
      char *t1 = r->str;
      bcf_ginfo_t *t2 = r->gi;
      int i, t3 = r->m_str, t4 = r->m_gi;
      *r = *b;
      r->str = t1; r->gi = t2; r->m_str = t3; r->m_gi = t4;
      if (r->m_str < b->m_str) {
            r->m_str = b->m_str;
            r->str = realloc(r->str, r->m_str);
      }
      memcpy(r->str, b->str, r->m_str);
      bcf_sync(r); // calling bcf_sync() is simple but inefficient
      for (i = 0; i < r->n_gi; ++i)
            memcpy(r->gi[i].data, b->gi[i].data, r->n_smpl * r->gi[i].len);
      return 0;
}

int bcf_is_indel(const bcf1_t *b)
{
      char *p;
      if (strlen(b->ref) > 1) return 1;
      for (p = b->alt; *p; ++p)
            if (*p != ',' && p[1] != ',' && p[1] != '\0')
                  return 1;
      return 0;
}

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