X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=bcftools%2Fcall1.c;h=286c0141856f0f7f2bac22f4e7f8ab80f52afa2c;hp=f293a6cf94e611a9f9ff50d83ab1b69c660e15d7;hb=c34624801b980425af68c3c431423c72b18c14fe;hpb=f2f3968e11eead9ce5601b01890bc2339ff951e9

diff --git a/bcftools/call1.c b/bcftools/call1.c
index f293a6c..286c014 100644
--- a/bcftools/call1.c
+++ b/bcftools/call1.c
@@ -26,11 +26,11 @@ KSTREAM_INIT(gzFile, gzread, 16384)
 #define VC_CALL_GT 2048
 #define VC_ADJLD   4096
 #define VC_NO_INDEL 8192
-#define VC_FOLDED 16384
+#define VC_ANNO_MAX 16384
 
 typedef struct {
-	int flag, prior_type, n1;
-	char *fn_list, *prior_file;
+	int flag, prior_type, n1, n_sub, *sublist;
+	char *fn_list, *prior_file, **subsam, *fn_dict;
 	double theta, pref, indel_frac;
 } viewconf_t;
 
@@ -151,7 +151,7 @@ static int update_bcf1(int n_smpl, bcf1_t *b, const bcf_p1aux_t *pa, const bcf_p
 {
 	kstring_t s;
 	int is_var = (pr->p_ref < pref);
-	double p_hwe, r = is_var? pr->p_ref : 1. - pr->p_ref;
+	double p_hwe, r = is_var? pr->p_ref : pr->p_var, fq;
 	anno16_t a;
 
 	p_hwe = pr->g[0] >= 0.? test_hwe(pr->g) : 1.0; // only do HWE g[] is calculated
@@ -164,20 +164,24 @@ static int update_bcf1(int n_smpl, bcf1_t *b, const bcf_p1aux_t *pa, const bcf_p
 	kputs(b->info, &s);
 	if (b->info[0]) kputc(';', &s);
 //	ksprintf(&s, "AF1=%.4lg;AFE=%.4lg;CI95=%.4lg,%.4lg", 1.-pr->f_em, 1.-pr->f_exp, pr->cil, pr->cih);
-	ksprintf(&s, "AF1=%.4lg;CI95=%.4lg,%.4lg", 1.-pr->f_em, pr->cil, pr->cih);
+	ksprintf(&s, "AF1=%.4g;CI95=%.4g,%.4g", 1.-pr->f_em, pr->cil, pr->cih);
 	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 (a.is_tested) {
-		if (pr->pc[0] >= 0.) ksprintf(&s, ";PC4=%lg,%lg,%lg,%lg", pr->pc[0], pr->pc[1], pr->pc[2], pr->pc[3]);
-		ksprintf(&s, ";PV4=%.2lg,%.2lg,%.2lg,%.2lg", a.p[0], a.p[1], a.p[2], a.p[3]);
+		if (pr->pc[0] >= 0.) ksprintf(&s, ";PC4=%g,%g,%g,%g", pr->pc[0], pr->pc[1], pr->pc[2], pr->pc[3]);
+		ksprintf(&s, ";PV4=%.2g,%.2g,%.2g,%.2g", a.p[0], a.p[1], a.p[2], a.p[3]);
 	}
 	if (pr->g[0] >= 0. && p_hwe <= .2)
-		ksprintf(&s, ";GC=%.2lf,%.2lf,%.2lf;HWE=%.3lf", pr->g[2], pr->g[1], pr->g[0], p_hwe);
+		ksprintf(&s, ";GC=%.2f,%.2f,%.2f;HWE=%.3f", 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 : -4.343 * log(r);
-	if (b->qual > 99) b->qual = 99;
+	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))
@@ -197,19 +201,83 @@ static int update_bcf1(int n_smpl, bcf1_t *b, const bcf_p1aux_t *pa, const bcf_p
 	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) {
+		if (max == n) {
+			max = max? max<<1 : 4;
+			sam = realloc(sam, sizeof(void*)*max);
+		}
+		sam[n++] = strdup(s.s);
+	}
+	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 that sample chromosomes are not all 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 site allele frequency of the first ALT allele\">\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=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=-1,Type=Integer,Description=\"List of Phred-scaled genotype likelihoods, number of values is (#ALT+1)*(#ALT+2)/2\">\n", &str);
+	h->l_txt = str.l + 1; h->txt = str.s;
+}
+
 double bcf_ld_freq(const bcf1_t *b0, const bcf1_t *b1, double f[4]);
 
 int bcfview(int argc, char *argv[])
 {
 	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);
 	bcf_t *bp, *bout = 0;
 	bcf1_t *b, *blast;
 	int c;
 	uint64_t n_processed = 0;
 	viewconf_t vc;
 	bcf_p1aux_t *p1 = 0;
-	bcf_hdr_t *h;
+	bcf_hdr_t *hin, *hout;
 	int tid, begin, end;
 	char moder[4], modew[4];
 	khash_t(set64) *hash = 0;
@@ -217,11 +285,12 @@ int bcfview(int argc, char *argv[])
 	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.;
-	while ((c = getopt(argc, argv, "fN1:l:cHAGvbSuP:t:p:QgLi:I")) >= 0) {
+	vc.n_sub = 0; vc.subsam = 0; vc.sublist = 0;
+	while ((c = getopt(argc, argv, "N1:l:cHAGvbSuP:t:p:QgLi:IMs:D:")) >= 0) {
 		switch (c) {
-		case 'f': vc.flag |= VC_FOLDED; break;
 		case '1': vc.n1 = atoi(optarg); break;
 		case 'l': vc.fn_list = strdup(optarg); break;
+		case 'D': vc.fn_dict = strdup(optarg); break;
 		case 'N': vc.flag |= VC_ACGT_ONLY; break;
 		case 'G': vc.flag |= VC_NO_GENO; break;
 		case 'A': vc.flag |= VC_KEEPALT; break;
@@ -233,11 +302,13 @@ int bcfview(int argc, char *argv[])
 		case 'H': vc.flag |= VC_HWE; 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 '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 's': vc.subsam = read_samples(optarg, &vc.n_sub); 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;
@@ -262,17 +333,22 @@ int bcfview(int argc, char *argv[])
 		fprintf(stderr, "         -Q        output the QCALL likelihood format\n");
 		fprintf(stderr, "         -L        calculate LD for adjacent sites\n");
 		fprintf(stderr, "         -I        skip indels\n");
-		fprintf(stderr, "         -f        reference-free variant calling\n");
+		fprintf(stderr, "         -D FILE   sequence dictionary for VCF->BCF conversion [null]\n");
 		fprintf(stderr, "         -1 INT    number of group-1 samples [0]\n");
 		fprintf(stderr, "         -l FILE   list of sites to output [all sites]\n");
-		fprintf(stderr, "         -t FLOAT  scaled substitution mutation rate [%.4lg]\n", vc.theta);
-		fprintf(stderr, "         -i FLOAT  indel-to-substitution ratio [%.4lg]\n", vc.indel_frac);
-		fprintf(stderr, "         -p FLOAT  variant if P(ref|D)<FLOAT [%.3lg]\n", vc.pref);
+		fprintf(stderr, "         -t FLOAT  scaled substitution mutation rate [%.4g]\n", vc.theta);
+		fprintf(stderr, "         -i FLOAT  indel-to-substitution ratio [%.4g]\n", vc.indel_frac);
+		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, "         -s FILE   list of samples to use [all samples]\n");
 		fprintf(stderr, "\n");
 		return 1;
 	}
 
+	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;
+	}
 	b = calloc(1, sizeof(bcf1_t));
 	blast = calloc(1, sizeof(bcf1_t));
 	strcpy(moder, "r");
@@ -281,11 +357,20 @@ int bcfview(int argc, char *argv[])
 	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);
+	hin = hout = vcf_hdr_read(bp);
+	if (vc.fn_dict && (vc.flag & VC_VCFIN))
+		vcf_dictread(bp, hin, vc.fn_dict);
 	bout = vcf_open("-", modew);
-	if (!(vc.flag & VC_QCALL)) vcf_hdr_write(bout, h);
+	if (!(vc.flag & VC_QCALL)) {
+		if (vc.n_sub) {
+			vc.sublist = 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(h->n_smpl);
+		p1 = bcf_p1_init(hout->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__);
@@ -297,11 +382,10 @@ int bcfview(int argc, char *argv[])
 			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 (vc.flag & VC_FOLDED) bcf_p1_set_folded(p1);
 	}
-	if (vc.fn_list) hash = bcf_load_pos(vc.fn_list, h);
+	if (vc.fn_list) hash = bcf_load_pos(vc.fn_list, hin);
 	if (optind + 1 < argc && !(vc.flag&VC_VCFIN)) {
-		void *str2id = bcf_build_refhash(h);
+		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]);
@@ -317,8 +401,10 @@ int bcfview(int argc, char *argv[])
 			}
 		}
 	}
-	while (vcf_read(bp, h, b) > 0) {
-		int is_indel = bcf_is_indel(b);
+	while (vcf_read(bp, hin, b) > 0) {
+		int is_indel;
+		if (vc.n_sub) bcf_subsam(vc.n_sub, vc.sublist, 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;
@@ -341,7 +427,7 @@ int bcfview(int argc, char *argv[])
 		}
 		++n_processed;
 		if (vc.flag & VC_QCALL) { // output QCALL format; STOP here
-			bcf_2qcall(h, b);
+			bcf_2qcall(hout, b);
 			continue;
 		}
 		if (vc.flag & (VC_CALL|VC_ADJLD)) bcf_gl2pl(b);
@@ -354,7 +440,7 @@ int bcfview(int argc, char *argv[])
 				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);
+			update_bcf1(hout->n_smpl, b, p1, &pr, vc.pref, vc.flag);
 		}
 		if (vc.flag & VC_ADJLD) { // compute LD
 			double f[4], r2;
@@ -362,25 +448,34 @@ int bcfview(int argc, char *argv[])
 				kstring_t s;
 				s.m = s.l = 0; s.s = 0;
 				if (*b->info) kputc(';', &s);
-				ksprintf(&s, "NEIR=%.3lf;NEIF=%.3lf,%.3lf", r2, f[0]+f[2], f[0]+f[1]);
+				ksprintf(&s, "NEIR=%.3f;NEIF=%.3f,%.3f", r2, f[0]+f[2], f[0]+f[1]);
 				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';
-		}
-		vcf_write(bout, h, b);
+			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);
-	bcf_hdr_destroy(h);
+	if (hin != hout) bcf_hdr_destroy(hout);
+	bcf_hdr_destroy(hin);
 	bcf_destroy(b); bcf_destroy(blast);
 	vcf_close(bp); vcf_close(bout);
 	if (hash) kh_destroy(set64, hash);
 	if (vc.fn_list) free(vc.fn_list);
+	if (vc.fn_dict) free(vc.fn_dict);
+	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 (p1) bcf_p1_destroy(p1);
 	return 0;
 }