X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bcftools%2Fvcfout.c;h=827dcd232488b634ea7436ec26c7a3acfa0d669c;hb=f69357a6a9e701f12d1f01c52cc0d2893bb2ac7a;hp=51cfef1479f869d665417cfa2a837b86376a56ad;hpb=2bd87be64d80551809a35eea0a64f293c37059f8;p=samtools.git

diff --git a/bcftools/vcfout.c b/bcftools/vcfout.c
index 51cfef1..827dcd2 100644
--- a/bcftools/vcfout.c
+++ b/bcftools/vcfout.c
@@ -15,13 +15,15 @@ KSTREAM_INIT(gzFile, gzread, 16384)
 
 #define VC_NO_PL   1
 #define VC_NO_GENO 2
-#define VC_BCF     4
+#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;
+	char *fn_list, *prior_file;
 	double theta, pref;
 } viewconf_t;
 
@@ -75,22 +77,54 @@ static double test_hwe(const double g[3])
 	return kf_gammaq(.5, chi2 / 2.);
 }
 
-extern double kt_fisher_exact(int n11, int n12, int n21, int n22, double *_left, double *_right, double *two);
+typedef struct {
+	double p[4];
+	int mq, depth, is_tested, d[4];
+} anno16_t;
 
-static double test_fisher(bcf1_t *b, const char *key, int d[4])
+static double ttest(int n1, int n2, int a[4])
 {
-	double left, right, two;
-	char *p;
+	extern double kf_betai(double a, double b, double x);
+	double t, v;
+	if (n1 == 0 || n2 == 0 || n1 + n2 < 3) return 1.0;
+	t = (a[0] / n1 - a[2] / n2) / sqrt((a[1] + a[3]) / (n1 + n2 - 2) * (1./n1 + 1./n2));
+	v = n1 + n2 - 2;
+//	printf("%d,%d,%d,%d,%lf\n", a[0], a[1], a[2], a[3], t);
+	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;
-	if ((p = strstr(b->info, key)) == 0) return -1.;
+	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 < 4; ++i) {
-		d[i] = strtol(p, &p, 10);
-		if (errno == EINVAL || errno == ERANGE) return -2.;
+	for (i = 0; i < 16; ++i) {
+		anno[i] = strtol(p, &p, 10);
+		if (anno[i] == 0 && (errno == EINVAL || errno == ERANGE)) return -2;
 		++p;
 	}
-	kt_fisher_exact(d[0], d[1], d[2], d[3], &left, &right, &two);
-	return two;
+	return test16_core(anno, a);
 }
 
 static void rm_info(int n_smpl, bcf1_t *b, const char *key)
@@ -107,13 +141,13 @@ static void rm_info(int n_smpl, bcf1_t *b, const char *key)
 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 d[4], x, is_var = (pr->p_ref < pref);
-	double p_hwe, p_dp, p_ed, r = is_var? pr->p_ref : 1. - pr->p_ref;
+	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);
-	p_ed = test_fisher(b, "ED4=", d);
-	p_dp = test_fisher(b, "DP4=", d);
-	rm_info(n_smpl, b, "ED4=");
+	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);
@@ -122,19 +156,17 @@ static int update_bcf1(int n_smpl, bcf1_t *b, const bcf_p1aux_t *pa, const bcf_p
 	}
 	kputc('\0', &s); kputc('\0', &s);
 	kputs(b->info, &s);
-	if (p_dp >= 0. && d[2] + d[3] > 0) { // has at least one non-reference base
-		if (b->info[0]) kputc(';', &s);
-		ksprintf(&s, "AF1=%.3lf;AFE=%.3lf", 1.-pr->f_em, 1.-pr->f_exp);
-	}
-	if (p_hwe <= .2) ksprintf(&s, ";HWE=%.3lf", p_hwe);
-	if (p_dp >= 0. && p_dp <= .2) ksprintf(&s, ";TDP=%.3lf", p_dp);
-	if (p_ed >= 0. && p_ed <= .2) ksprintf(&s, ";TED=%.3lf", p_ed);
+	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;
-	x = (int)(r < 1e-100? 99 : -3.434 * log(r) + .499);
-	b->qual = x > 99? 99 : x;
+	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;
 }
@@ -149,46 +181,71 @@ int bcfview(int argc, char *argv[])
 	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:cGvLbP:t:p:")) >= 0) {
+	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_BCF; 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, "Usage: bcftools view [-cGPb] [-l list] <in.bcf> [reg]\n");
+		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));
-	bp = bcf_open(argv[optind], "r");
-	h = bcf_hdr_read(bp);
-	if (vc.flag & VC_BCF) {
-		bout = bcf_open("-", "w");
-		bcf_hdr_write(bout, h);
-	}
+	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);
-		bcf_p1_init_prior(p1, vc.prior_type, vc.theta);
+		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) {
+	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;
@@ -201,7 +258,7 @@ int bcfview(int argc, char *argv[])
 			}
 		}
 	}
-	while (bcf_read(bp, h, b) > 0) {
+	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);
@@ -220,23 +277,18 @@ int bcfview(int argc, char *argv[])
 			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_BCF) bcf_write(bout, h, b);
-		else {
-			char *vcf;
-			if (vc.flag & VC_NO_GENO) {
-				b->n_gi = 0;
-				b->fmt[0] = '\0';
-			}
-			vcf = bcf_fmt(h, b);
-			puts(vcf);
-			free(vcf);
+		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_close(bp); bcf_close(bout);
 	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);