X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bcftools%2Fcall1.c;h=9c0b498c18cb46e2dd673f0527f7c02d2e76dc3d;hb=f528e7da717a1a2a6ab2672c7c55f37d315452f3;hp=2308607ab6d9de176570282f32a4797a275b6f7c;hpb=bc2ecad90ddee39dd8ce4378134063cfbfcae220;p=samtools.git

diff --git a/bcftools/call1.c b/bcftools/call1.c
index 2308607..9c0b498 100644
--- a/bcftools/call1.c
+++ b/bcftools/call1.c
@@ -19,7 +19,6 @@ KSTREAM_INIT(gzFile, gzread, 16384)
 #define VC_VARONLY 16
 #define VC_VCFIN   32
 #define VC_UNCOMP  64
-#define VC_HWE     128
 #define VC_KEEPALT 256
 #define VC_ACGT_ONLY 512
 #define VC_QCALL   1024
@@ -29,8 +28,9 @@ KSTREAM_INIT(gzFile, gzread, 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;
+	uint8_t *ploidy;
 	double theta, pref, indel_frac;
 } viewconf_t;
 
@@ -67,23 +67,6 @@ khash_t(set64) *bcf_load_pos(const char *fn, bcf_hdr_t *_h)
 	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];
@@ -151,10 +134,9 @@ 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 : pr->p_var, fq;
+	double 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
 	test16(b, &a);
 	rm_info(b, "I16=");
 
@@ -174,8 +156,6 @@ static int update_bcf1(int n_smpl, bcf1_t *b, const bcf_p1aux_t *pa, const bcf_p
 		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=%.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);
@@ -201,6 +181,45 @@ 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) {
+		int l;
+		if (max == n) {
+			max = max? max<<1 : 4;
+			sam = realloc(sam, sizeof(void*)*max);
+		}
+		l = s.l;
+		sam[n] = 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;
@@ -221,7 +240,7 @@ static void write_header(bcf_hdr_t *h)
 	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,Descriptin=\"Indicates that the variant is an INDEL.\">\n", &str);
+        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,"))
@@ -251,7 +270,7 @@ int bcfview(int argc, char *argv[])
 	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;
@@ -259,10 +278,11 @@ 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, "N1:l:cHAGvbSuP:t:p:QgLi:IM")) >= 0) {
+	while ((c = getopt(argc, argv, "N1:l:cHAGvbSuP:t:p:QgLi:IMs:D:")) >= 0) {
 		switch (c) {
 		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;
@@ -271,7 +291,6 @@ int bcfview(int argc, char *argv[])
 		case 'c': vc.flag |= VC_CALL; break;
 		case 'v': vc.flag |= VC_VARONLY | VC_CALL; break;
 		case 'u': vc.flag |= VC_UNCOMP | VC_BCFOUT; break;
-		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;
@@ -280,6 +299,11 @@ int bcfview(int argc, char *argv[])
 		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);
+			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 'P':
 			if (strcmp(optarg, "full") == 0) vc.prior_type = MC_PTYPE_FULL;
 			else if (strcmp(optarg, "cond2") == 0) vc.prior_type = MC_PTYPE_COND2;
@@ -304,16 +328,22 @@ 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, "         -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 [%.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");
@@ -322,14 +352,20 @@ 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)) {
-		if (vc.flag & VC_CALL) write_header(h);
-		vcf_hdr_write(bout, h);
+		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, 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__);
@@ -342,9 +378,9 @@ int bcfview(int argc, char *argv[])
 		}
 		if (vc.indel_frac > 0.) bcf_p1_indel_prior(p1, vc.indel_frac); // otherwise use the default indel_frac
 	}
-	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]);
@@ -360,8 +396,10 @@ 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;
@@ -384,20 +422,19 @@ 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);
 		if (vc.flag & VC_CALL) { // call variants
 			bcf_p1rst_t pr;
 			bcf_p1_cal(b, p1, &pr); // pr.g[3] is not calculated here
-			if (vc.flag&VC_HWE) bcf_p1_cal_g3(p1, pr.g);
 			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;
-			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;
@@ -417,15 +454,23 @@ int bcfview(int argc, char *argv[])
 			b->fmt[0] = '\0';
 			b->l_str = b->fmt - b->str + 1;
 		} else bcf_fix_gt(b);
-		vcf_write(bout, h, 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.ploidy) free(vc.ploidy);
+	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;
 }