text: #include <unistd.h>
  #include <stdlib.h>
  #include <math.h>
  #include <3rdparty/zlib/zlib.h>
  #include <errno.h>
  #include "bcf.h"
  #include "prob1.h"
  #include "kstring.h"
  #include "time.h"
  
  #ifdef _WIN32
  #define srand48(x) srand(x)
  #define lrand48() rand()
  #endif
  
  #include "kseq.h"
  KSTREAM_INIT( gzFile ,gzread, 16384)
  
  #define VC_NO_GENO 2
  #define VC_BCFOUT  4
  #define VC_CALL    8
  #define VC_VARONLY 16
  #define VC_VCFIN   32
  #define VC_UNCOMP  64
  #define VC_KEEPALT 256
  #define VC_ACGT_ONLY 512
  #define VC_QCALL   1024
  #define VC_CALL_GT 2048
  #define VC_ADJLD   4096
  #define VC_NO_INDEL 8192
  #define VC_ANNO_MAX 16384
  #define VC_FIX_PL   32768
  #define VC_EM       0x10000
  #define VC_PAIRCALL 0x20000
  #define VC_QCNT     0x40000
  
  typedef struct {
  	int flag, prior_type, n1, n_sub, *sublist, n_perm;
  	uint32_t *trio_aux;
  	char *prior_file, **subsam, *fn_dict;
  	uint8_t *ploidy;
  	double theta, pref, indel_frac, min_perm_p, min_smpl_frac, min_lrt;
  	void *bed;
  } viewconf_t;
  
  typedef struct {
      int    b_keepalt;
      int    b_fix_pl;
      int    b_no_geno;
      int    b_acgt_only;
      char * bcf_bed;
      int     b_qcall;
      char * samples;
      float   min_smpl_frac;
      int    b_call_gt;
      float   indel_frac;
      float   pref;
      char * ptype;
      float   theta;
      char * ccall;
      int     n1;
      int     n_perm;
      float   min_perm_p;
      int*    cancelFlag;
  } UGENE_bcf_view_settings;
  
  void *bed_read(const char *fn);
  void bed_destroy(void *_h);
  int bed_overlap(const void *_h, const char *chr, int beg, int end);
  
  typedef struct {
  	double p[4];
  	int mq, depth, is_tested, d[4];
  } anno16_t;
  
  static double ttest(int n1, int n2, int a[4])
  {
  	extern double kf_betai(double a, double b, double x);
  	double t, v, u1, u2;
  	if (n1 == 0 || n2 == 0 || n1 + n2 < 3) return 1.0;
  	u1 = (double)a[0] / n1; u2 = (double)a[2] / n2;
  	if (u1 <= u2) return 1.;
  	t = (u1 - u2) / sqrt(((a[1] - n1 * u1 * u1) + (a[3] - n2 * u2 * u2)) / (n1 + n2 - 2) * (1./n1 + 1./n2));
  	v = n1 + n2 - 2;
  //	printf("%d,%d,%d,%d,%lf,%lf,%lf\n", a[0], a[1], a[2], a[3], t, u1, u2);
  	return t < 0.? 1. : .5 * kf_betai(.5*v, .5, v/(v+t*t));
  }
  
  static int test16_core(int anno[16], anno16_t *a)
  {
  	extern double kt_fisher_exact(int n11, int n12, int n21, int n22, double *_left, double *_right, double *two);
  	double left, right;
  	int i;
  	a->p[0] = a->p[1] = a->p[2] = a->p[3] = 1.;
  	memcpy(a->d, anno, 4 * sizeof(int));
  	a->depth = anno[0] + anno[1] + anno[2] + anno[3];
  	a->is_tested = (anno[0] + anno[1] > 0 && anno[2] + anno[3] > 0);
  	if (a->depth == 0) return -1;
  	a->mq = (int)(sqrt((anno[9] + anno[11]) / (float)a->depth) + .499);
  	kt_fisher_exact(anno[0], anno[1], anno[2], anno[3], &left, &right, &a->p[0]);
  	for (i = 1; i < 4; ++i)
  		a->p[i] = ttest(anno[0] + anno[1], anno[2] + anno[3], anno+4*i);
  	return 0;
  }
  
  static int test16(bcf1_t *b, anno16_t *a)
  {
  	char *p;
  	int i, anno[16];
  	a->p[0] = a->p[1] = a->p[2] = a->p[3] = 1.;
  	a->d[0] = a->d[1] = a->d[2] = a->d[3] = 0.;
  	a->mq = a->depth = a->is_tested = 0;
  	if ((p = strstr(b->info, "I16=")) == 0) return -1;
  	p += 4;
  	for (i = 0; i < 16; ++i) {
  		errno = 0; anno[i] = strtol(p, &p, 10);
  		if (anno[i] == 0 && (errno == EINVAL || errno == ERANGE)) return -2;
  		++p;
  	}
  	return test16_core(anno, a);
  }
  
  static void rm_info(bcf1_t *b, const char *key)
  {
  	char *p, *q;
  	if ((p = strstr(b->info, key)) == 0) return;
  	for (q = p; *q && *q != ';'; ++q);
  	if (p > b->info && *(p-1) == ';') --p;
  	memmove(p, q, b->l_str - (q - b->str));
  	b->l_str -= q - p;
  	bcf_sync(b);
  }
  
  static int update_bcf1(bcf1_t *b, const bcf_p1aux_t *pa, const bcf_p1rst_t *pr, double pref, int flag, double em[10], int cons_llr, int64_t cons_gt)
  {
  	kstring_t s;
  	int has_I16, is_var;
  	double fq, r;
  	anno16_t a;
  
  	has_I16 = test16(b, &a) >= 0? 1 : 0;
  	rm_info(b, "I16="); // FIXME: probably this function has a bug. If I move it below, I16 will not be removed!
  
  	memset(&s, 0, sizeof(kstring_t));
  	kputc('\0', &s); kputs(b->ref, &s); kputc('\0', &s);
  	kputs(b->alt, &s); kputc('\0', &s); kputc('\0', &s);
  	kputs(b->info, &s);
  	if (b->info[0]) kputc(';', &s);
  	{ // print EM
  		if (em[0] >= 0) ksprintf(&s, "AF1=%.4g", 1 - em[0]);
  		if (em[4] >= 0 && em[4] <= 0.05) ksprintf(&s, ";G3=%.4g,%.4g,%.4g;HWE=%.3g", em[3], em[2], em[1], em[4]);
  		if (em[5] >= 0 && em[6] >= 0) ksprintf(&s, ";AF2=%.4g,%.4g", 1 - em[5], 1 - em[6]);
  		if (em[7] >= 0) ksprintf(&s, ";LRT=%.3g", em[7]);
  		if (em[8] >= 0) ksprintf(&s, ";LRT2=%.3g", em[8]);
  	}
  	if (cons_llr > 0) {
  		ksprintf(&s, ";CLR=%d", cons_llr);
  		if (cons_gt > 0)
  			ksprintf(&s, ";UGT=%c%c%c;CGT=%c%c%c", cons_gt&0xff, cons_gt>>8&0xff, cons_gt>>16&0xff,
  				     cons_gt>>32&0xff, cons_gt>>40&0xff, cons_gt>>48&0xff);
  	}
  	if (pr == 0) { // if pr is unset, return
  		kputc('\0', &s); kputs(b->fmt, &s); kputc('\0', &s);
  		free(b->str);
  		b->m_str = s.m; b->l_str = s.l; b->str = s.s;
  		bcf_sync(b);
  		return 1;
  	}
  
  	is_var = (pr->p_ref < pref);
  	r = is_var? pr->p_ref : pr->p_var;
  
  //	ksprintf(&s, ";CI95=%.4g,%.4g", pr->cil, pr->cih); // FIXME: when EM is not used, ";" should be omitted!
  	ksprintf(&s, ";AC1=%d", pr->ac);
  	if (has_I16) ksprintf(&s, ";DP4=%d,%d,%d,%d;MQ=%d", a.d[0], a.d[1], a.d[2], a.d[3], a.mq);
  	fq = pr->p_ref_folded < 0.5? -4.343 * log(pr->p_ref_folded) : 4.343 * log(pr->p_var_folded);
  	if (fq < -999) fq = -999;
  	if (fq > 999) fq = 999;
  	ksprintf(&s, ";FQ=%.3g", fq);
  	if (pr->cmp[0] >= 0.) { // two sample groups
  		int i, q[3];
  		for (i = 1; i < 3; ++i) {
  			double x = pr->cmp[i] + pr->cmp[0]/2.;
  			q[i] = x == 0? 255 : (int)(-4.343 * log(x) + .499);
  			if (q[i] > 255) q[i] = 255;
  		}
  		if (pr->perm_rank >= 0) ksprintf(&s, ";PR=%d", pr->perm_rank);
  		// ksprintf(&s, ";LRT3=%.3g", pr->lrt);
  		ksprintf(&s, ";PCHI2=%.3g;PC2=%d,%d", q[1], q[2], pr->p_chi2);
  	}
  	if (has_I16 && a.is_tested) ksprintf(&s, ";PV4=%.2g,%.2g,%.2g,%.2g", a.p[0], a.p[1], a.p[2], a.p[3]);
  	kputc('\0', &s);
  	kputs(b->fmt, &s); kputc('\0', &s);
  	free(b->str);
  	b->m_str = s.m; b->l_str = s.l; b->str = s.s;
  	b->qual = r < 1e-100? 999 : -4.343 * log(r);
  	if (b->qual > 999) b->qual = 999;
  	bcf_sync(b);
  	if (!is_var) bcf_shrink_alt(b, 1);
  	else if (!(flag&VC_KEEPALT))
  		bcf_shrink_alt(b, pr->rank0 < 2? 2 : pr->rank0+1);
  	if (is_var && (flag&VC_CALL_GT)) { // call individual genotype
  		int i, x, old_n_gi = b->n_gi;
  		s.m = b->m_str; s.l = b->l_str - 1; s.s = b->str;
  		kputs(":GT:GQ", &s); kputc('\0', &s);
  		b->m_str = s.m; b->l_str = s.l; b->str = s.s;
  		bcf_sync(b);
  		for (i = 0; i < b->n_smpl; ++i) {
  			x = bcf_p1_call_gt(pa, pr->f_exp, i);
  			((uint8_t*)b->gi[old_n_gi].data)[i] = (x&3) == 0? 1<<3|1 : (x&3) == 1? 1 : 0;
  			((uint8_t*)b->gi[old_n_gi+1].data)[i] = x>>2;
  		}
  	}
  	return is_var;
  }
  
  static char **read_samples(const char *fn, int *_n)
  {
  	gzFile fp;
  	kstream_t *ks;
  	kstring_t s;
  	int dret, n = 0, max = 0;
  	char **sam = 0;
  	*_n = 0;
  	s.l = s.m = 0; s.s = 0;
  	fp = gzopen(fn, "r");
  	if (fp == 0) return 0; // fail to open file
  	ks = ks_init(fp);
  	while (ks_getuntil(ks, 0, &s, &dret) >= 0) {
  		int l;
  		if (max == n) {
  			max = max? max<<1 : 4;
  			sam = (char **)realloc(sam, sizeof(void*)*max);
  		}
  		l = s.l;
  		sam[n] = (char *)malloc(s.l + 2);
  		strcpy(sam[n], s.s);
  		sam[n][l+1] = 2; // by default, diploid
  		if (dret != '\n') {
  			if (ks_getuntil(ks, 0, &s, &dret) >= 0) { // read ploidy, 1 or 2
  				int x = (int)s.s[0] - '0';
  				if (x == 1 || x == 2) sam[n][l+1] = x;
  				else fprintf(stderr, "(%s) ploidy can only be 1 or 2; assume diploid\n", __func__);
  			}
  			if (dret != '\n') ks_getuntil(ks, '\n', &s, &dret);
  		}
  		++n;
  	}
  	ks_destroy(ks);
  	gzclose(fp);
  	free(s.s);
  	*_n = n;
  	return sam;
  }
  
  static void write_header(bcf_hdr_t *h)
  {
  	kstring_t str;
  	str.l = h->l_txt? h->l_txt - 1 : 0;
  	str.m = str.l + 1; str.s = h->txt;
  	if (!strstr(str.s, "##INFO=<ID=DP,"))
  		kputs("##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Raw read depth\">\n", &str);
  	if (!strstr(str.s, "##INFO=<ID=DP4,"))
  		kputs("##INFO=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\n", &str);
  	if (!strstr(str.s, "##INFO=<ID=MQ,"))
  		kputs("##INFO=<ID=MQ,Number=1,Type=Integer,Description=\"Root-mean-square mapping quality of covering reads\">\n", &str);
  	if (!strstr(str.s, "##INFO=<ID=FQ,"))
  		kputs("##INFO=<ID=FQ,Number=1,Type=Float,Description=\"Phred probability of all samples being the same\">\n", &str);
  	if (!strstr(str.s, "##INFO=<ID=AF1,"))
  		kputs("##INFO=<ID=AF1,Number=1,Type=Float,Description=\"Max-likelihood estimate of the first ALT allele frequency (assuming HWE)\">\n", &str);
  	if (!strstr(str.s, "##INFO=<ID=AC1,"))
  		kputs("##INFO=<ID=AC1,Number=1,Type=Float,Description=\"Max-likelihood estimate of the first ALT allele count (no HWE assumption)\">\n", &str);
  	if (!strstr(str.s, "##INFO=<ID=G3,"))
  		kputs("##INFO=<ID=G3,Number=3,Type=Float,Description=\"ML estimate of genotype frequencies\">\n", &str);
  	if (!strstr(str.s, "##INFO=<ID=HWE,"))
  		kputs("##INFO=<ID=HWE,Number=1,Type=Float,Description=\"Chi^2 based HWE test P-value based on G3\">\n", &str);
  	if (!strstr(str.s, "##INFO=<ID=CLR,"))
  		kputs("##INFO=<ID=CLR,Number=1,Type=Integer,Description=\"Log ratio of genotype likelihoods with and without the constraint\">\n", &str);
  	if (!strstr(str.s, "##INFO=<ID=UGT,"))
  		kputs("##INFO=<ID=UGT,Number=1,Type=String,Description=\"The most probable unconstrained genotype configuration in the trio\">\n", &str);
  	if (!strstr(str.s, "##INFO=<ID=CGT,"))
  		kputs("##INFO=<ID=CGT,Number=1,Type=String,Description=\"The most probable constrained genotype configuration in the trio\">\n", &str);
  //	if (!strstr(str.s, "##INFO=<ID=CI95,"))
  //		kputs("##INFO=<ID=CI95,Number=2,Type=Float,Description=\"Equal-tail Bayesian credible interval of the site allele frequency at the 95% level\">\n", &str);
  	if (!strstr(str.s, "##INFO=<ID=PV4,"))
  		kputs("##INFO=<ID=PV4,Number=4,Type=Float,Description=\"P-values for strand bias, baseQ bias, mapQ bias and tail distance bias\">\n", &str);
      if (!strstr(str.s, "##INFO=<ID=INDEL,"))
          kputs("##INFO=<ID=INDEL,Number=0,Type=Flag,Description=\"Indicates that the variant is an INDEL.\">\n", &str);
      if (!strstr(str.s, "##INFO=<ID=PC2,"))
          kputs("##INFO=<ID=PC2,Number=2,Type=Integer,Description=\"Phred probability of the nonRef allele frequency in group1 samples being larger (,smaller) than in group2.\">\n", &str);
      if (!strstr(str.s, "##INFO=<ID=PCHI2,"))
          kputs("##INFO=<ID=PCHI2,Number=1,Type=Float,Description=\"Posterior weighted chi^2 P-value for testing the association between group1 and group2 samples.\">\n", &str);
      if (!strstr(str.s, "##INFO=<ID=QCHI2,"))
          kputs("##INFO=<ID=QCHI2,Number=1,Type=Integer,Description=\"Phred scaled PCHI2.\">\n", &str);
      if (!strstr(str.s, "##INFO=<ID=RP,"))
          kputs("##INFO=<ID=PR,Number=1,Type=Integer,Description=\"# permutations yielding a smaller PCHI2.\">\n", &str);
      if (!strstr(str.s, "##INFO=<ID=VDB,"))
          kputs("##INFO=<ID=VDB,Number=1,Type=Float,Description=\"Variant Distance Bias\">\n", &str);
      if (!strstr(str.s, "##FORMAT=<ID=GT,"))
          kputs("##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\n", &str);
      if (!strstr(str.s, "##FORMAT=<ID=GQ,"))
          kputs("##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\n", &str);
      if (!strstr(str.s, "##FORMAT=<ID=GL,"))
          kputs("##FORMAT=<ID=GL,Number=3,Type=Float,Description=\"Likelihoods for RR,RA,AA genotypes (R=ref,A=alt)\">\n", &str);
  	if (!strstr(str.s, "##FORMAT=<ID=DP,"))
  		kputs("##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"# high-quality bases\">\n", &str);
  	if (!strstr(str.s, "##FORMAT=<ID=SP,"))
  		kputs("##FORMAT=<ID=SP,Number=1,Type=Integer,Description=\"Phred-scaled strand bias P-value\">\n", &str);
  	if (!strstr(str.s, "##FORMAT=<ID=PL,"))
  		kputs("##FORMAT=<ID=PL,Number=G,Type=Integer,Description=\"List of Phred-scaled genotype likelihoods\">\n", &str);
  	h->l_txt = str.l + 1; h->txt = str.s;
  }
  
  double bcf_pair_freq(const bcf1_t *b0, const bcf1_t *b1, double f[4]);
  
  int bcfview(int argc, char *argv[], UGENE_bcf_view_settings* settings, const char* vcfOut)
  {
  	extern int bcf_2qcall(bcf_hdr_t *h, bcf1_t *b);
  	extern void bcf_p1_indel_prior(bcf_p1aux_t *ma, double x);
  	extern int bcf_fix_gt(bcf1_t *b);
  	extern int bcf_anno_max(bcf1_t *b);
  	extern int bcf_shuffle(bcf1_t *b, int seed);
  	extern uint32_t *bcf_trio_prep(int is_x, int is_son);
  	extern int bcf_trio_call(uint32_t *prep, const bcf1_t *b, int *llr, int64_t *gt);
  	extern int bcf_pair_call(const bcf1_t *b);
  	extern int bcf_min_diff(const bcf1_t *b);
  
  	bcf_t *bp, *bout = 0;
  	bcf1_t *b, *blast;
  	int c, *seeds = 0;
  	uint64_t n_processed = 0, qcnt[256];
  	viewconf_t vc;
  	bcf_p1aux_t *p1 = 0;
  	bcf_hdr_t *hin, *hout;
  	int tid, begin, end;
  	char moder[4], modew[4];
  
  	tid = begin = end = -1;
  	memset(&vc, 0, sizeof(viewconf_t));
  	vc.prior_type = vc.n1 = -1; vc.theta = 1e-3; vc.pref = 0.5; vc.indel_frac = -1.; vc.n_perm = 0; vc.min_perm_p = 0.01; vc.min_smpl_frac = 0; vc.min_lrt = 1;
  	memset(qcnt, 0, 8 * 256);
  
      //from UGENE
  
      if(settings->b_keepalt == 1) vc.flag |= VC_KEEPALT;
      if(settings->b_fix_pl == 1) vc.flag |= VC_FIX_PL;
      if(settings->b_no_geno == 1) vc.flag |= VC_NO_GENO;
      if(settings->b_acgt_only == 1) vc.flag |= VC_ACGT_ONLY;
      if(settings->bcf_bed && strlen(settings->bcf_bed) != 0) vc.bed = bed_read(settings->bcf_bed);
      if(settings->b_qcall == 1) vc.flag |= VC_QCALL;
      if(settings->samples && strlen(settings->samples) != 0) vc.subsam = read_samples(settings->samples, &vc.n_sub);
      vc.min_smpl_frac = settings->min_smpl_frac;
      if(settings->b_call_gt == 1) vc.flag |= VC_CALL_GT | VC_CALL;
      vc.indel_frac = settings->indel_frac;
      vc.pref = settings->pref;
  
      if(settings->ptype && strlen(settings->ptype) != 0){
          if (strcmp(settings->ptype, "full") == 0) vc.prior_type = MC_PTYPE_FULL;
          else if (strcmp(settings->ptype, "cond2") == 0) vc.prior_type = MC_PTYPE_COND2;
          else if (strcmp(settings->ptype, "flat") == 0) vc.prior_type = MC_PTYPE_FLAT;
          else vc.prior_file = strdup(settings->ptype);
      }
  
      vc.theta = settings->theta;
      if(settings->ccall && strlen(settings->ccall) != 0){
          if (strcmp(settings->ccall, "trioauto") == 0) vc.trio_aux = bcf_trio_prep(0, 0);
          else if (strcmp(settings->ccall, "trioxd") == 0) vc.trio_aux = bcf_trio_prep(1, 0);
          else if (strcmp(settings->ccall, "trioxs") == 0) vc.trio_aux = bcf_trio_prep(1, 1);
          else if (strcmp(settings->ccall, "pair") == 0) vc.flag |= VC_PAIRCALL;
          else {
              fprintf(stderr, "[%s] Option '-T' can only take value trioauto, trioxd or trioxs.\n", __func__);
              return 1;
          }
      }
  
      vc.n1 = settings->n1;
      vc.n_perm = settings->n_perm;
      vc.min_perm_p = settings->min_perm_p;
  
  	/*while ((c = getopt(argc, argv, "FN1:l:cC:eHAGvbSuP:t:p:QgLi:IMs:D:U:X:d:T:Y")) >= 0) {
  		switch (c) {
  		case '1': vc.n1 = atoi(optarg); break;
  		case 'l': vc.bed = bed_read(optarg); break;
  		case 'D': vc.fn_dict = strdup(optarg); break;
  		case 'F': vc.flag |= VC_FIX_PL; break;
  		case 'N': vc.flag |= VC_ACGT_ONLY; break;
  		case 'G': vc.flag |= VC_NO_GENO; break;
  		case 'A': vc.flag |= VC_KEEPALT; break;
  		case 'b': vc.flag |= VC_BCFOUT; break;
  		case 'S': vc.flag |= VC_VCFIN; break;
  		case 'c': vc.flag |= VC_CALL; break;
  		case 'e': vc.flag |= VC_EM; break;
  		case 'v': vc.flag |= VC_VARONLY | VC_CALL; break;
  		case 'u': vc.flag |= VC_UNCOMP | VC_BCFOUT; break;
  		case 'g': vc.flag |= VC_CALL_GT | VC_CALL; break;
  		case 'I': vc.flag |= VC_NO_INDEL; break;
  		case 'M': vc.flag |= VC_ANNO_MAX; break;
  		case 'Y': vc.flag |= VC_QCNT; break;
  		case 't': vc.theta = atof(optarg); break;
  		case 'p': vc.pref = atof(optarg); break;
  		case 'i': vc.indel_frac = atof(optarg); break;
  		case 'Q': vc.flag |= VC_QCALL; break;
  		case 'L': vc.flag |= VC_ADJLD; break;
  		case 'U': vc.n_perm = atoi(optarg); break;
  		case 'C': vc.min_lrt = atof(optarg); break;
  		case 'X': vc.min_perm_p = atof(optarg); break;
  		case 'd': vc.min_smpl_frac = atof(optarg); break;
  		case 's': vc.subsam = read_samples(optarg, &vc.n_sub);
  			vc.ploidy = calloc(vc.n_sub + 1, 1);
  			for (tid = 0; tid < vc.n_sub; ++tid) vc.ploidy[tid] = vc.subsam[tid][strlen(vc.subsam[tid]) + 1];
  			tid = -1;
  			break;
  		case 'T':
  			if (strcmp(optarg, "trioauto") == 0) vc.trio_aux = bcf_trio_prep(0, 0);
  			else if (strcmp(optarg, "trioxd") == 0) vc.trio_aux = bcf_trio_prep(1, 0);
  			else if (strcmp(optarg, "trioxs") == 0) vc.trio_aux = bcf_trio_prep(1, 1);
  			else if (strcmp(optarg, "pair") == 0) vc.flag |= VC_PAIRCALL;
  			else {
  				fprintf(stderr, "[%s] Option '-T' can only take value trioauto, trioxd or trioxs.\n", __func__);
  				return 1;
  			}
  			break;
  		case 'P':
  			if (strcmp(optarg, "full") == 0) vc.prior_type = MC_PTYPE_FULL;
  			else if (strcmp(optarg, "cond2") == 0) vc.prior_type = MC_PTYPE_COND2;
  			else if (strcmp(optarg, "flat") == 0) vc.prior_type = MC_PTYPE_FLAT;
  			else vc.prior_file = strdup(optarg);
  			break;
  		}
  	}*/
      vc.flag |= VC_VARONLY | VC_CALL;
  
  
  	if (argc == optind) {
  		fprintf(stderr, "\n");
  		fprintf(stderr, "Usage: bcftools view [options] <in.bcf> [reg]\n\n");
  		fprintf(stderr, "Input/output options:\n\n");
  		fprintf(stderr, "       -A        keep all possible alternate alleles at variant sites\n");
  		fprintf(stderr, "       -b        output BCF instead of VCF\n");
  		fprintf(stderr, "       -D FILE   sequence dictionary for VCF->BCF conversion [null]\n");
  		fprintf(stderr, "       -F        PL generated by r921 or before (which generate old ordering)\n");
  		fprintf(stderr, "       -G        suppress all individual genotype information\n");
  		fprintf(stderr, "       -l FILE   list of sites (chr pos) or regions (BED) to output [all sites]\n");
  		fprintf(stderr, "       -L        calculate LD for adjacent sites\n");
  		fprintf(stderr, "       -N        skip sites where REF is not A/C/G/T\n");
  		fprintf(stderr, "       -Q        output the QCALL likelihood format\n");
  		fprintf(stderr, "       -s FILE   list of samples to use [all samples]\n");
  		fprintf(stderr, "       -S        input is VCF\n");
  		fprintf(stderr, "       -u        uncompressed BCF output (force -b)\n");
  		fprintf(stderr, "\nConsensus/variant calling options:\n\n");
  		fprintf(stderr, "       -c        SNP calling (force -e)\n");
  		fprintf(stderr, "       -d FLOAT  skip loci where less than FLOAT fraction of samples covered [0]\n");
  		fprintf(stderr, "       -e        likelihood based analyses\n");
  		fprintf(stderr, "       -g        call genotypes at variant sites (force -c)\n");
  		fprintf(stderr, "       -i FLOAT  indel-to-substitution ratio [%.4g]\n", vc.indel_frac);
  		fprintf(stderr, "       -I        skip indels\n");
  		fprintf(stderr, "       -p FLOAT  variant if P(ref|D)<FLOAT [%.3g]\n", vc.pref);
  		fprintf(stderr, "       -P STR    type of prior: full, cond2, flat [full]\n");
  		fprintf(stderr, "       -t FLOAT  scaled substitution mutation rate [%.4g]\n", vc.theta);
  		fprintf(stderr, "       -T STR    constrained calling; STR can be: pair, trioauto, trioxd and trioxs (see manual) [null]\n");
  		fprintf(stderr, "       -v        output potential variant sites only (force -c)\n");
  		fprintf(stderr, "\nContrast calling and association test options:\n\n");
  		fprintf(stderr, "       -1 INT    number of group-1 samples [0]\n");
  		fprintf(stderr, "       -C FLOAT  posterior constrast for LRT<FLOAT and P(ref|D)<0.5 [%g]\n", vc.min_lrt);
  		fprintf(stderr, "       -U INT    number of permutations for association testing (effective with -1) [0]\n");
  		fprintf(stderr, "       -X FLOAT  only perform permutations for P(chi^2)<FLOAT [%g]\n", vc.min_perm_p);
  		fprintf(stderr, "\n");
  		return 1;
  	}
  
  	if (vc.flag & VC_CALL) vc.flag |= VC_EM;
  	if ((vc.flag & VC_VCFIN) && (vc.flag & VC_BCFOUT) && vc.fn_dict == 0) {
  		fprintf(stderr, "[%s] For VCF->BCF conversion please specify the sequence dictionary with -D\n", __func__);
  		return 1;
  	}
  	if (vc.n1 <= 0) vc.n_perm = 0; // TODO: give a warning here!
  	if (vc.n_perm > 0) {
  		seeds = (int *)malloc(vc.n_perm * sizeof(int));
  		srand48(time(0));
  		for (c = 0; c < vc.n_perm; ++c) seeds[c] = lrand48();
  	}
  	b = (bcf1_t *)calloc(1, sizeof(bcf1_t));
  	blast = (bcf1_t *)calloc(1, sizeof(bcf1_t));
  	strcpy(moder, "r");
  	if (!(vc.flag & VC_VCFIN)) strcat(moder, "b");
  	strcpy(modew, "w");
  	if (vc.flag & VC_BCFOUT) strcat(modew, "b");
  	if (vc.flag & VC_UNCOMP) strcat(modew, "u");
  	bp = vcf_open(argv[optind], moder);
  	hin = hout = vcf_hdr_read(bp);
  	if (vc.fn_dict && (vc.flag & VC_VCFIN))
  		vcf_dictread(bp, hin, vc.fn_dict);
      bout = vcf_open(vcfOut, modew);
  	if (!(vc.flag & VC_QCALL)) {
  		if (vc.n_sub) {
  			vc.sublist = (int*)calloc(vc.n_sub, sizeof(int));
  			hout = bcf_hdr_subsam(hin, vc.n_sub, vc.subsam, vc.sublist);
  		}
  		if (vc.flag & VC_CALL) write_header(hout);
  		vcf_hdr_write(bout, hout);
  	}
  	if (vc.flag & VC_CALL) {
  		p1 = bcf_p1_init(hout->n_smpl, vc.ploidy);
  		if (vc.prior_file) {
  			if (bcf_p1_read_prior(p1, vc.prior_file) < 0) {
  				fprintf(stderr, "[%s] fail to read the prior AFS.\n", __func__);
  				return 1;
  			}
  		} else bcf_p1_init_prior(p1, vc.prior_type, vc.theta);
  		if (vc.n1 > 0 && vc.min_lrt > 0.) { // set n1
  			bcf_p1_set_n1(p1, vc.n1);
  			bcf_p1_init_subprior(p1, vc.prior_type, vc.theta);
  		}
  		if (vc.indel_frac > 0.) bcf_p1_indel_prior(p1, vc.indel_frac); // otherwise use the default indel_frac
  	}
  	if (optind + 1 < argc && !(vc.flag&VC_VCFIN)) {
  		void *str2id = bcf_build_refhash(hout);
  		if (bcf_parse_region(str2id, argv[optind+1], &tid, &begin, &end) >= 0) {
  			bcf_idx_t *idx;
  			idx = bcf_idx_load(argv[optind]);
  			if (idx) {
  				uint64_t off;
  				off = bcf_idx_query(idx, tid, begin);
  				if (off == 0) {
  					fprintf(stderr, "[%s] no records in the query region.\n", __func__);
  					return 1; // FIXME: a lot of memory leaks...
  				}
  				bgzf_seek(bp->fp, off, SEEK_SET);
  				bcf_idx_destroy(idx);
  			}
  		}
  	}
  	while (vcf_read(bp, hin, b) > 0) {
  		int is_indel, cons_llr = -1;
  		int64_t cons_gt = -1;
  		double em[10];
          if (*(settings->cancelFlag)) {
              break;
          }
  
          if ((vc.flag & VC_VARONLY) && strcmp(b->alt, "X") == 0) continue;
  		if ((vc.flag & VC_VARONLY) && vc.min_smpl_frac > 0.) {
  			extern int bcf_smpl_covered(const bcf1_t *b);
  			int n = bcf_smpl_covered(b);
  			if ((double)n / b->n_smpl < vc.min_smpl_frac) continue;
  		}
  		if (vc.n_sub) bcf_subsam(vc.n_sub, vc.sublist, b);
  		if (vc.flag & VC_FIX_PL) bcf_fix_pl(b);
  		is_indel = bcf_is_indel(b);
  		if ((vc.flag & VC_NO_INDEL) && is_indel) continue;
  		if ((vc.flag & VC_ACGT_ONLY) && !is_indel) {
  			int x;
  			if (b->ref[0] == 0 || b->ref[1] != 0) continue;
  			x = toupper(b->ref[0]);
  			if (x != 'A' && x != 'C' && x != 'G' && x != 'T') continue;
  		}
  		if (vc.bed && !bed_overlap(vc.bed, hin->ns[b->tid], b->pos, b->pos + strlen(b->ref))) continue;
  		if (tid >= 0) {
  			int l = strlen(b->ref);
  			l = b->pos + (l > 0? l : 1);
  			if (b->tid != tid || b->pos >= end) break;
  			if (!(l > begin && end > b->pos)) continue;
  		}
  		++n_processed;
  		if ((vc.flag & VC_QCNT) && !is_indel) { // summarize the difference
  			int x = bcf_min_diff(b);
  			if (x > 255) x = 255;
  			if (x >= 0) ++qcnt[x];
  		}
  		if (vc.flag & VC_QCALL) { // output QCALL format; STOP here
  			bcf_2qcall(hout, b);
  			continue;
  		}
  		if (vc.trio_aux) // do trio calling
  			bcf_trio_call(vc.trio_aux, b, &cons_llr, &cons_gt);
  		else if (vc.flag & VC_PAIRCALL)
  			cons_llr = bcf_pair_call(b);
  		if (vc.flag & (VC_CALL|VC_ADJLD|VC_EM)) bcf_gl2pl(b);
  		if (vc.flag & VC_EM) bcf_em1(b, vc.n1, 0x1ff, em);
  		else {
  			int i;
  			for (i = 0; i < 9; ++i) em[i] = -1.;
  		}
  		if (vc.flag & VC_CALL) { // call variants
  			bcf_p1rst_t pr;
  			int calret = bcf_p1_cal(b, (em[7] >= 0 && em[7] < vc.min_lrt), p1, &pr);
  			if (n_processed % 100000 == 0) {
  				fprintf(stderr, "[%s] %ld sites processed.\n", __func__, (long)n_processed);
  				bcf_p1_dump_afs(p1);
  			}
  			if (pr.p_ref >= vc.pref && (vc.flag & VC_VARONLY)) continue;
  			if (vc.n_perm && vc.n1 > 0 && pr.p_chi2 < vc.min_perm_p) { // permutation test
  				bcf_p1rst_t r;
  				int i, n = 0;
  				for (i = 0; i < vc.n_perm; ++i) {
  #ifdef BCF_PERM_LRT // LRT based permutation is much faster but less robust to artifacts
  					double x[10];
  					bcf_shuffle(b, seeds[i]);
  					bcf_em1(b, vc.n1, 1<<7, x);
  					if (x[7] < em[7]) ++n;
  #else
  					bcf_shuffle(b, seeds[i]);
  					bcf_p1_cal(b, 1, p1, &r);
  					if (pr.p_chi2 >= r.p_chi2) ++n;
  #endif
  				}
  				pr.perm_rank = n;
  			}
  			if (calret >= 0) update_bcf1(b, p1, &pr, vc.pref, vc.flag, em, cons_llr, cons_gt);
  		} else if (vc.flag & VC_EM) update_bcf1(b, 0, 0, 0, vc.flag, em, cons_llr, cons_gt);
  		if (vc.flag & VC_ADJLD) { // compute LD
  			double f[4], r2;
  			if ((r2 = bcf_pair_freq(blast, b, f)) >= 0) {
  				kstring_t s;
  				s.m = s.l = 0; s.s = 0;
  				if (*b->info) kputc(';', &s);
  				ksprintf(&s, "NEIR=%.3f;NEIF4=%.3f,%.3f,%.3f,%.3f", r2, f[0], f[1], f[2], f[3]);
  				bcf_append_info(b, s.s, s.l);
  				free(s.s);
  			}
  			bcf_cpy(blast, b);
  		}
  		if (vc.flag & VC_ANNO_MAX) bcf_anno_max(b);
  		if (vc.flag & VC_NO_GENO) { // do not output GENO fields
  			b->n_gi = 0;
  			b->fmt[0] = '\0';
  			b->l_str = b->fmt - b->str + 1;
  		} else bcf_fix_gt(b);
  		vcf_write(bout, hout, b);
  	}
  	if (vc.prior_file) free(vc.prior_file);
  	if (vc.flag & VC_CALL) bcf_p1_dump_afs(p1);
  	if (hin != hout) bcf_hdr_destroy(hout);
  	bcf_hdr_destroy(hin);
  	bcf_destroy(b); bcf_destroy(blast);
  	vcf_close(bp); vcf_close(bout);
  	if (vc.fn_dict) free(vc.fn_dict);
  	if (vc.ploidy) free(vc.ploidy);
  	if (vc.trio_aux) free(vc.trio_aux);
  	if (vc.n_sub) {
  		int i;
  		for (i = 0; i < vc.n_sub; ++i) free(vc.subsam[i]);
  		free(vc.subsam); free(vc.sublist);
  	}
  	if (vc.bed) bed_destroy(vc.bed);
  	if (vc.flag & VC_QCNT)
  		for (c = 0; c < 256; ++c)
  			fprintf(stderr, "QT\t%d\t%lld\n", c, (long long)qcnt[c]);
  	if (seeds) free(seeds);
  	if (p1) bcf_p1_destroy(p1);
  	return 0;
  }
  