From: Heng Li <lh3@live.co.uk>
Date: Fri, 11 Feb 2011 03:59:47 +0000 (+0000)
Subject: finished VCF->BCF conversion
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=06021e30abb66d5631a0cd5daadb8f45878e90a3;p=samtools.git

finished VCF->BCF conversion
---

diff --git a/bcftools/bcf.h b/bcftools/bcf.h
index 6932f35..f545a91 100644
--- a/bcftools/bcf.h
+++ b/bcftools/bcf.h
@@ -129,6 +129,8 @@ extern "C" {
 	int vcf_close(bcf_t *bp);
 	// read the VCF/BCF header
 	bcf_hdr_t *vcf_hdr_read(bcf_t *bp);
+	// read the sequence dictionary from a separate file; required for VCF->BCF conversion
+	int vcf_dictread(bcf_t *bp, bcf_hdr_t *h, const char *fn);
 	// read a VCF/BCF record; return -1 on end-of-file and <-1 for errors
 	int vcf_read(bcf_t *bp, bcf_hdr_t *h, bcf1_t *b);
 	// write the VCF header
diff --git a/bcftools/call1.c b/bcftools/call1.c
index c9df3c0..286c014 100644
--- a/bcftools/call1.c
+++ b/bcftools/call1.c
@@ -30,7 +30,7 @@ KSTREAM_INIT(gzFile, gzread, 16384)
 
 typedef struct {
 	int flag, prior_type, n1, n_sub, *sublist;
-	char *fn_list, *prior_file, **subsam;
+	char *fn_list, *prior_file, **subsam, *fn_dict;
 	double theta, pref, indel_frac;
 } viewconf_t;
 
@@ -286,10 +286,11 @@ int bcfview(int argc, char *argv[])
 	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_sub = 0; vc.subsam = 0; vc.sublist = 0;
-	while ((c = getopt(argc, argv, "N1:l:cHAGvbSuP:t:p:QgLi:IMs:")) >= 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;
@@ -332,6 +333,7 @@ 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);
@@ -343,6 +345,10 @@ int bcfview(int argc, char *argv[])
 		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");
@@ -352,6 +358,8 @@ int bcfview(int argc, char *argv[])
 	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("-", modew);
 	if (!(vc.flag & VC_QCALL)) {
 		if (vc.n_sub) {
@@ -462,6 +470,7 @@ int bcfview(int argc, char *argv[])
 	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]);
diff --git a/bcftools/vcf.c b/bcftools/vcf.c
index b3832e7..6d3abaa 100644
--- a/bcftools/vcf.c
+++ b/bcftools/vcf.c
@@ -72,6 +72,33 @@ bcf_t *vcf_open(const char *fn, const char *mode)
 	return bp;
 }
 
+int vcf_dictread(bcf_t *bp, bcf_hdr_t *h, const char *fn)
+{
+	vcf_t *v;
+	gzFile fp;
+	kstream_t *ks;
+	kstring_t s, rn;
+	int dret;
+	if (bp == 0) return -1;
+	if (!bp->is_vcf) return 0;
+	s.l = s.m = 0; s.s = 0;
+	rn.m = rn.l = h->l_nm; rn.s = h->name;
+	v = (vcf_t*)bp->v;
+	fp = gzopen(fn, "r");
+	ks = ks_init(fp);
+	while (ks_getuntil(ks, 0, &s, &dret) >= 0) {
+		bcf_str2id_add(v->refhash, strdup(s.s));
+		kputs(s.s, &rn); kputc('\0', &rn);
+		if (dret != '\n') ks_getuntil(ks, '\n', &s, &dret);
+	}
+	ks_destroy(ks);
+	gzclose(fp);
+	h->l_nm = rn.l; h->name = rn.s;
+	bcf_hdr_sync(h);
+	free(s.s);
+	return 0;
+}
+
 int vcf_close(bcf_t *bp)
 {
 	vcf_t *v;
@@ -84,7 +111,7 @@ int vcf_close(bcf_t *bp)
 	}
 	if (v->fpout) fclose(v->fpout);
 	free(v->line.s);
-	bcf_str2id_destroy(v->refhash);
+	bcf_str2id_thorough_destroy(v->refhash);
 	free(v);
 	free(bp);
 	return 0;
@@ -93,13 +120,12 @@ int vcf_close(bcf_t *bp)
 int vcf_hdr_write(bcf_t *bp, const bcf_hdr_t *h)
 {
 	vcf_t *v = (vcf_t*)bp->v;
-	int i, has_ref = 0, has_ver = 0;
+	int i, has_ver = 0;
 	if (!bp->is_vcf) return bcf_hdr_write(bp, h);
 	if (h->l_txt > 0) {
 		if (strstr(h->txt, "##fileformat=")) has_ver = 1;
 		if (has_ver == 0) fprintf(v->fpout, "##fileformat=VCFv4.0\n");
 		fwrite(h->txt, 1, h->l_txt - 1, v->fpout);
-		if (strstr(h->txt, "##SQ=")) has_ref = 1;
 	}
 	if (h->l_txt == 0) fprintf(v->fpout, "##fileformat=VCFv4.0\n");
 	fprintf(v->fpout, "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT");
@@ -138,7 +164,7 @@ int vcf_read(bcf_t *bp, bcf_hdr_t *h, bcf1_t *b)
 		if (k == 0) { // ref
 			int tid = bcf_str2id(v->refhash, p);
 			if (tid < 0) {
-				tid = bcf_str2id_add(v->refhash, p);
+				tid = bcf_str2id_add(v->refhash, strdup(p));
 				kputs(p, &rn); kputc('\0', &rn);
 				sync = 1;
 			}