From: Heng Li <lh3@live.co.uk>
Date: Tue, 31 Aug 2010 14:20:57 +0000 (+0000)
Subject:  * rename vcfout.c as call1.c
X-Git-Url: https://git.donarmstrong.com/?p=samtools.git;a=commitdiff_plain;h=082c52f3cb5517db50987bf1dc43aef845c45fd8

 * rename vcfout.c as call1.c
 * prepare to add two-sample comparison
---

diff --git a/bcftools/Makefile b/bcftools/Makefile
index 6a6bdb8..5a3dc76 100644
--- a/bcftools/Makefile
+++ b/bcftools/Makefile
@@ -3,7 +3,7 @@ CFLAGS=		-g -Wall -O2 #-m64 #-arch ppc
 DFLAGS=		-D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE
 LOBJS=		bcf.o vcf.o bcfutils.o prob1.o kfunc.o index.o fet.o
 OMISC=		..
-AOBJS=		vcfout.o main.o $(OMISC)/kstring.o $(OMISC)/bgzf.o $(OMISC)/knetfile.o
+AOBJS=		call1.o main.o $(OMISC)/kstring.o $(OMISC)/bgzf.o $(OMISC)/knetfile.o
 PROG=		bcftools
 INCLUDES=	
 SUBDIRS=	.
diff --git a/bcftools/call1.c b/bcftools/call1.c
new file mode 100644
index 0000000..75483e9
--- /dev/null
+++ b/bcftools/call1.c
@@ -0,0 +1,299 @@
+#include <unistd.h>
+#include <stdlib.h>
+#include <math.h>
+#include <zlib.h>
+#include <errno.h>
+#include "bcf.h"
+#include "prob1.h"
+#include "kstring.h"
+
+#include "khash.h"
+KHASH_SET_INIT_INT64(set64)
+
+#include "kseq.h"
+KSTREAM_INIT(gzFile, gzread, 16384)
+
+#define VC_NO_PL   1
+#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
+
+typedef struct {
+	int flag, prior_type;
+	char *fn_list, *prior_file;
+	double theta, pref;
+} viewconf_t;
+
+khash_t(set64) *bcf_load_pos(const char *fn, bcf_hdr_t *_h)
+{
+	void *str2id;
+	gzFile fp;
+	kstream_t *ks;
+	int ret, dret, lineno = 1;
+	kstring_t *str;
+	khash_t(set64) *hash = 0;
+
+	hash = kh_init(set64);
+	str2id = bcf_build_refhash(_h);
+	str = calloc(1, sizeof(kstring_t));
+	fp = strcmp(fn, "-")? gzopen(fn, "r") : gzdopen(fileno(stdin), "r");
+	ks = ks_init(fp);
+	while (ks_getuntil(ks, 0, str, &dret) >= 0) {
+		int tid = bcf_str2id(str2id, str->s);
+		if (tid >= 0 && dret != '\n') {
+			if (ks_getuntil(ks, 0, str, &dret) >= 0) {
+				uint64_t x = (uint64_t)tid<<32 | (atoi(str->s) - 1);
+				kh_put(set64, hash, x, &ret);
+			} else break;
+		} else fprintf(stderr, "[%s] %s is not a reference name (line %d).\n", __func__, str->s, lineno);
+		if (dret != '\n') while ((dret = ks_getc(ks)) > 0 && dret != '\n');
+		if (dret < 0) break;
+		++lineno;
+	}
+	bcf_str2id_destroy(str2id);
+	ks_destroy(ks);
+	gzclose(fp);
+	free(str->s); free(str);
+	return hash;
+}
+
+static double test_hwe(const double g[3])
+{
+	extern double kf_gammaq(double p, double x);
+	double fexp, chi2, f[3], n;
+	int i;
+	n = g[0] + g[1] + g[2];
+	fexp = (2. * g[2] + g[1]) / (2. * n);
+	if (fexp > 1. - 1e-10) fexp = 1. - 1e-10;
+	if (fexp < 1e-10) fexp = 1e-10;
+	f[0] = n * (1. - fexp) * (1. - fexp);
+	f[1] = n * 2. * fexp * (1. - fexp);
+	f[2] = n * fexp * fexp;
+	for (i = 0, chi2 = 0.; i < 3; ++i)
+		chi2 += (g[i] - f[i]) * (g[i] - f[i]) / f[i];
+	return kf_gammaq(.5, chi2 / 2.);
+}
+
+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]) / 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) {
+		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(int n_smpl, 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(n_smpl, b);
+}
+
+static int update_bcf1(int n_smpl, bcf1_t *b, const bcf_p1aux_t *pa, const bcf_p1rst_t *pr, double pref, int flag)
+{
+	kstring_t s;
+	int is_var = (pr->p_ref < pref);
+	double p_hwe, r = is_var? pr->p_ref : 1. - pr->p_ref;
+	anno16_t a;
+
+	p_hwe = test_hwe(pr->g);
+	test16(b, &a);
+	rm_info(n_smpl, b, "I16=");
+
+	memset(&s, 0, sizeof(kstring_t));
+	kputc('\0', &s); kputs(b->ref, &s); kputc('\0', &s);
+	if (is_var) {
+		kputs(b->alt, &s);
+	}
+	kputc('\0', &s); kputc('\0', &s);
+	kputs(b->info, &s);
+	if (b->info[0]) kputc(';', &s);
+	ksprintf(&s, "AF1=%.3lf;AFE=%.3lf", 1.-pr->f_em, 1.-pr->f_exp);
+	ksprintf(&s, ";DP4=%d,%d,%d,%d;MQ=%d", a.d[0], a.d[1], a.d[2], a.d[3], a.mq);
+	if (a.is_tested) ksprintf(&s, ";PV4=%.2lg,%.2lg,%.2lg,%.2lg", a.p[0], a.p[1], a.p[2], a.p[3]);
+	if (p_hwe <= .2) ksprintf(&s, ";GC=%.2lf,%.2lf,%.2lf;HWE=%.3lf", pr->g[2], pr->g[1], pr->g[0], p_hwe);
+	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? 99 : -3.434 * log(r);
+	if (b->qual > 99) b->qual = 99;
+	bcf_sync(n_smpl, b);
+	return is_var;
+}
+
+int bcfview(int argc, char *argv[])
+{
+	bcf_t *bp, *bout = 0;
+	bcf1_t *b;
+	int c;
+	uint64_t n_processed = 0;
+	viewconf_t vc;
+	bcf_p1aux_t *p1 = 0;
+	bcf_hdr_t *h;
+	int tid, begin, end;
+	char moder[4], modew[4];
+	khash_t(set64) *hash = 0;
+
+	tid = begin = end = -1;
+	memset(&vc, 0, sizeof(viewconf_t));
+	vc.prior_type = -1; vc.theta = 1e-3; vc.pref = 0.9;
+	while ((c = getopt(argc, argv, "l:cGvLbSuP:t:p:")) >= 0) {
+		switch (c) {
+		case 'l': vc.fn_list = strdup(optarg); break;
+		case 'G': vc.flag |= VC_NO_GENO; break;
+		case 'L': vc.flag |= VC_NO_PL; break;
+		case 'b': vc.flag |= VC_BCFOUT; break;
+		case 'S': vc.flag |= VC_VCFIN; break;
+		case 'c': vc.flag |= VC_CALL; break;
+		case 'v': vc.flag |= VC_VARONLY; break;
+		case 'u': vc.flag |= VC_UNCOMP | VC_BCFOUT; break;
+		case 't': vc.theta = atof(optarg); break;
+		case 'p': vc.pref = atof(optarg); 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;
+		}
+	}
+	if (argc == optind) {
+		fprintf(stderr, "\n");
+		fprintf(stderr, "Usage:   bcftools view [options] <in.bcf> [reg]\n\n");
+		fprintf(stderr, "Options: -c        SNP calling\n");
+		fprintf(stderr, "         -b        output BCF instead of VCF\n");
+		fprintf(stderr, "         -u        uncompressed BCF output\n");
+		fprintf(stderr, "         -S        input is VCF\n");
+		fprintf(stderr, "         -G        suppress all individual genotype information\n");
+		fprintf(stderr, "         -L        discard the PL genotype field\n");
+		fprintf(stderr, "         -v        output potential variant sites only\n");
+		fprintf(stderr, "         -l FILE   list of sites to output [all sites]\n");
+		fprintf(stderr, "         -t FLOAT  scaled mutation rate [%.4lg]\n", vc.theta);
+		fprintf(stderr, "         -p FLOAT  variant if P(ref|D)<FLOAT [%.3lg]\n", vc.pref);
+		fprintf(stderr, "         -P STR    type of prior: full, cond2, flat [full]\n");
+		fprintf(stderr, "\n");
+		return 1;
+	}
+
+	b = 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);
+	h = vcf_hdr_read(bp);
+	bout = vcf_open("-", modew);
+	vcf_hdr_write(bout, h);
+	if (vc.flag & VC_CALL) {
+		p1 = bcf_p1_init(h->n_smpl);
+		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.fn_list) hash = bcf_load_pos(vc.fn_list, h);
+	if (optind + 1 < argc && !(vc.flag&VC_VCFIN)) {
+		void *str2id = bcf_build_refhash(h);
+		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, end);
+				bgzf_seek(bp->fp, off, SEEK_SET);
+				bcf_idx_destroy(idx);
+			}
+		}
+	}
+	while (vcf_read(bp, h, b) > 0) {
+		if (hash) {
+			uint64_t x = (uint64_t)b->tid<<32 | b->pos;
+			khint_t k = kh_get(set64, hash, x);
+			if (k == kh_end(hash)) 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;
+		}
+		if (vc.flag & VC_CALL) {
+			bcf_p1rst_t pr;
+			bcf_p1_cal(b, p1, &pr);
+			if ((n_processed + 1) % 50000 == 0) bcf_p1_dump_afs(p1);
+			if (pr.p_ref >= vc.pref && (vc.flag & VC_VARONLY)) continue;
+			update_bcf1(h->n_smpl, b, p1, &pr, vc.pref, vc.flag);
+		}
+		if (vc.flag & VC_NO_GENO) {
+			b->n_gi = 0;
+			b->fmt[0] = '\0';
+		}
+		vcf_write(bout, h, b);
+		++n_processed;
+	}
+	if (vc.prior_file) free(vc.prior_file);
+	if (vc.flag & VC_CALL) bcf_p1_dump_afs(p1);
+	bcf_hdr_destroy(h);
+	bcf_destroy(b);
+	vcf_close(bp); vcf_close(bout);
+	if (hash) kh_destroy(set64, hash);
+	if (vc.fn_list) free(vc.fn_list);
+	if (p1) bcf_p1_destroy(p1);
+	return 0;
+}
+
diff --git a/bcftools/prob1.c b/bcftools/prob1.c
index 4611af1..e124b0f 100644
--- a/bcftools/prob1.c
+++ b/bcftools/prob1.c
@@ -32,7 +32,7 @@ unsigned char seq_nt4_table[256] = {
 };
 
 struct __bcf_p1aux_t {
-	int n, M;
+	int n, M, n1;
 	double *q2p, *pdg; // pdg -> P(D|g)
 	double *phi;
 	double *z, *zswap; // aux for afs
@@ -100,6 +100,7 @@ bcf_p1aux_t *bcf_p1_init(int n) // FIXME: assuming diploid
 	bcf_p1aux_t *ma;
 	int i;
 	ma = calloc(1, sizeof(bcf_p1aux_t));
+	ma->n1 = -1;
 	ma->n = n; ma->M = 2 * n;
 	ma->q2p = calloc(256, sizeof(double));
 	ma->pdg = calloc(3 * ma->n, sizeof(double));
@@ -114,6 +115,13 @@ bcf_p1aux_t *bcf_p1_init(int n) // FIXME: assuming diploid
 	return ma;
 }
 
+int bcf_p1_set_n1(bcf_p1aux_t *b, int n1)
+{
+	if (n1 == 0 || n1 >= b->n) return -1;
+	b->n1 = n1;
+	return 0;
+}
+
 void bcf_p1_destroy(bcf_p1aux_t *ma)
 {
 	if (ma) {
diff --git a/bcftools/vcfout.c b/bcftools/vcfout.c
deleted file mode 100644
index 75483e9..0000000
--- a/bcftools/vcfout.c
+++ /dev/null
@@ -1,299 +0,0 @@
-#include <unistd.h>
-#include <stdlib.h>
-#include <math.h>
-#include <zlib.h>
-#include <errno.h>
-#include "bcf.h"
-#include "prob1.h"
-#include "kstring.h"
-
-#include "khash.h"
-KHASH_SET_INIT_INT64(set64)
-
-#include "kseq.h"
-KSTREAM_INIT(gzFile, gzread, 16384)
-
-#define VC_NO_PL   1
-#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
-
-typedef struct {
-	int flag, prior_type;
-	char *fn_list, *prior_file;
-	double theta, pref;
-} viewconf_t;
-
-khash_t(set64) *bcf_load_pos(const char *fn, bcf_hdr_t *_h)
-{
-	void *str2id;
-	gzFile fp;
-	kstream_t *ks;
-	int ret, dret, lineno = 1;
-	kstring_t *str;
-	khash_t(set64) *hash = 0;
-
-	hash = kh_init(set64);
-	str2id = bcf_build_refhash(_h);
-	str = calloc(1, sizeof(kstring_t));
-	fp = strcmp(fn, "-")? gzopen(fn, "r") : gzdopen(fileno(stdin), "r");
-	ks = ks_init(fp);
-	while (ks_getuntil(ks, 0, str, &dret) >= 0) {
-		int tid = bcf_str2id(str2id, str->s);
-		if (tid >= 0 && dret != '\n') {
-			if (ks_getuntil(ks, 0, str, &dret) >= 0) {
-				uint64_t x = (uint64_t)tid<<32 | (atoi(str->s) - 1);
-				kh_put(set64, hash, x, &ret);
-			} else break;
-		} else fprintf(stderr, "[%s] %s is not a reference name (line %d).\n", __func__, str->s, lineno);
-		if (dret != '\n') while ((dret = ks_getc(ks)) > 0 && dret != '\n');
-		if (dret < 0) break;
-		++lineno;
-	}
-	bcf_str2id_destroy(str2id);
-	ks_destroy(ks);
-	gzclose(fp);
-	free(str->s); free(str);
-	return hash;
-}
-
-static double test_hwe(const double g[3])
-{
-	extern double kf_gammaq(double p, double x);
-	double fexp, chi2, f[3], n;
-	int i;
-	n = g[0] + g[1] + g[2];
-	fexp = (2. * g[2] + g[1]) / (2. * n);
-	if (fexp > 1. - 1e-10) fexp = 1. - 1e-10;
-	if (fexp < 1e-10) fexp = 1e-10;
-	f[0] = n * (1. - fexp) * (1. - fexp);
-	f[1] = n * 2. * fexp * (1. - fexp);
-	f[2] = n * fexp * fexp;
-	for (i = 0, chi2 = 0.; i < 3; ++i)
-		chi2 += (g[i] - f[i]) * (g[i] - f[i]) / f[i];
-	return kf_gammaq(.5, chi2 / 2.);
-}
-
-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]) / 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) {
-		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(int n_smpl, 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(n_smpl, b);
-}
-
-static int update_bcf1(int n_smpl, bcf1_t *b, const bcf_p1aux_t *pa, const bcf_p1rst_t *pr, double pref, int flag)
-{
-	kstring_t s;
-	int is_var = (pr->p_ref < pref);
-	double p_hwe, r = is_var? pr->p_ref : 1. - pr->p_ref;
-	anno16_t a;
-
-	p_hwe = test_hwe(pr->g);
-	test16(b, &a);
-	rm_info(n_smpl, b, "I16=");
-
-	memset(&s, 0, sizeof(kstring_t));
-	kputc('\0', &s); kputs(b->ref, &s); kputc('\0', &s);
-	if (is_var) {
-		kputs(b->alt, &s);
-	}
-	kputc('\0', &s); kputc('\0', &s);
-	kputs(b->info, &s);
-	if (b->info[0]) kputc(';', &s);
-	ksprintf(&s, "AF1=%.3lf;AFE=%.3lf", 1.-pr->f_em, 1.-pr->f_exp);
-	ksprintf(&s, ";DP4=%d,%d,%d,%d;MQ=%d", a.d[0], a.d[1], a.d[2], a.d[3], a.mq);
-	if (a.is_tested) ksprintf(&s, ";PV4=%.2lg,%.2lg,%.2lg,%.2lg", a.p[0], a.p[1], a.p[2], a.p[3]);
-	if (p_hwe <= .2) ksprintf(&s, ";GC=%.2lf,%.2lf,%.2lf;HWE=%.3lf", pr->g[2], pr->g[1], pr->g[0], p_hwe);
-	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? 99 : -3.434 * log(r);
-	if (b->qual > 99) b->qual = 99;
-	bcf_sync(n_smpl, b);
-	return is_var;
-}
-
-int bcfview(int argc, char *argv[])
-{
-	bcf_t *bp, *bout = 0;
-	bcf1_t *b;
-	int c;
-	uint64_t n_processed = 0;
-	viewconf_t vc;
-	bcf_p1aux_t *p1 = 0;
-	bcf_hdr_t *h;
-	int tid, begin, end;
-	char moder[4], modew[4];
-	khash_t(set64) *hash = 0;
-
-	tid = begin = end = -1;
-	memset(&vc, 0, sizeof(viewconf_t));
-	vc.prior_type = -1; vc.theta = 1e-3; vc.pref = 0.9;
-	while ((c = getopt(argc, argv, "l:cGvLbSuP:t:p:")) >= 0) {
-		switch (c) {
-		case 'l': vc.fn_list = strdup(optarg); break;
-		case 'G': vc.flag |= VC_NO_GENO; break;
-		case 'L': vc.flag |= VC_NO_PL; break;
-		case 'b': vc.flag |= VC_BCFOUT; break;
-		case 'S': vc.flag |= VC_VCFIN; break;
-		case 'c': vc.flag |= VC_CALL; break;
-		case 'v': vc.flag |= VC_VARONLY; break;
-		case 'u': vc.flag |= VC_UNCOMP | VC_BCFOUT; break;
-		case 't': vc.theta = atof(optarg); break;
-		case 'p': vc.pref = atof(optarg); 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;
-		}
-	}
-	if (argc == optind) {
-		fprintf(stderr, "\n");
-		fprintf(stderr, "Usage:   bcftools view [options] <in.bcf> [reg]\n\n");
-		fprintf(stderr, "Options: -c        SNP calling\n");
-		fprintf(stderr, "         -b        output BCF instead of VCF\n");
-		fprintf(stderr, "         -u        uncompressed BCF output\n");
-		fprintf(stderr, "         -S        input is VCF\n");
-		fprintf(stderr, "         -G        suppress all individual genotype information\n");
-		fprintf(stderr, "         -L        discard the PL genotype field\n");
-		fprintf(stderr, "         -v        output potential variant sites only\n");
-		fprintf(stderr, "         -l FILE   list of sites to output [all sites]\n");
-		fprintf(stderr, "         -t FLOAT  scaled mutation rate [%.4lg]\n", vc.theta);
-		fprintf(stderr, "         -p FLOAT  variant if P(ref|D)<FLOAT [%.3lg]\n", vc.pref);
-		fprintf(stderr, "         -P STR    type of prior: full, cond2, flat [full]\n");
-		fprintf(stderr, "\n");
-		return 1;
-	}
-
-	b = 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);
-	h = vcf_hdr_read(bp);
-	bout = vcf_open("-", modew);
-	vcf_hdr_write(bout, h);
-	if (vc.flag & VC_CALL) {
-		p1 = bcf_p1_init(h->n_smpl);
-		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.fn_list) hash = bcf_load_pos(vc.fn_list, h);
-	if (optind + 1 < argc && !(vc.flag&VC_VCFIN)) {
-		void *str2id = bcf_build_refhash(h);
-		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, end);
-				bgzf_seek(bp->fp, off, SEEK_SET);
-				bcf_idx_destroy(idx);
-			}
-		}
-	}
-	while (vcf_read(bp, h, b) > 0) {
-		if (hash) {
-			uint64_t x = (uint64_t)b->tid<<32 | b->pos;
-			khint_t k = kh_get(set64, hash, x);
-			if (k == kh_end(hash)) 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;
-		}
-		if (vc.flag & VC_CALL) {
-			bcf_p1rst_t pr;
-			bcf_p1_cal(b, p1, &pr);
-			if ((n_processed + 1) % 50000 == 0) bcf_p1_dump_afs(p1);
-			if (pr.p_ref >= vc.pref && (vc.flag & VC_VARONLY)) continue;
-			update_bcf1(h->n_smpl, b, p1, &pr, vc.pref, vc.flag);
-		}
-		if (vc.flag & VC_NO_GENO) {
-			b->n_gi = 0;
-			b->fmt[0] = '\0';
-		}
-		vcf_write(bout, h, b);
-		++n_processed;
-	}
-	if (vc.prior_file) free(vc.prior_file);
-	if (vc.flag & VC_CALL) bcf_p1_dump_afs(p1);
-	bcf_hdr_destroy(h);
-	bcf_destroy(b);
-	vcf_close(bp); vcf_close(bout);
-	if (hash) kh_destroy(set64, hash);
-	if (vc.fn_list) free(vc.fn_list);
-	if (p1) bcf_p1_destroy(p1);
-	return 0;
-}
-