text: #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);
  	}
  	b->fp->owned_file = 1;
  	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].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)) {
  				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;
  }
  