X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=bcftools%2Fvcf.c;h=9daa845cba6c13b7d2190fbf77f4877b7979178c;hp=9b661ff5b4fbc29dde6a53b5e71c027f131a81f4;hb=c34624801b980425af68c3c431423c72b18c14fe;hpb=f2f3968e11eead9ce5601b01890bc2339ff951e9

diff --git a/bcftools/vcf.c b/bcftools/vcf.c
index 9b661ff..9daa845 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;
@@ -93,15 +120,14 @@ 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");
+		if (has_ver == 0) fprintf(v->fpout, "##fileformat=VCFv4.1\n");
 		fwrite(h->txt, 1, h->l_txt - 1, v->fpout);
-		if (strstr(h->txt, "##SQ=")) has_ref = 1;
 	}
-	if (has_ver == 0) fprintf(v->fpout, "##fileformat=VCFv4.0\n");
+	if (h->l_txt == 0) fprintf(v->fpout, "##fileformat=VCFv4.1\n");
 	fprintf(v->fpout, "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT");
 	for (i = 0; i < h->n_smpl; ++i)
 		fprintf(v->fpout, "\t%s", h->sns[i]);
@@ -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;
 			}
@@ -156,8 +182,10 @@ int vcf_read(bcf_t *bp, bcf_hdr_t *h, bcf1_t *b)
 				for (i = 0; i < b->n_gi; ++i) {
 					if (b->gi[i].fmt == bcf_str2int("GT", 2)) {
 						((uint8_t*)b->gi[i].data)[k-9] = 1<<7;
-					} else if (b->gi[i].fmt == bcf_str2int("GQ", 2) || b->gi[i].fmt == bcf_str2int("SP", 2)) {
+					} else if (b->gi[i].fmt == bcf_str2int("GQ", 2)) {
 						((uint8_t*)b->gi[i].data)[k-9] = 0;
+					} else if (b->gi[i].fmt == bcf_str2int("SP", 2)) {
+						((int32_t*)b->gi[i].data)[k-9] = 0;
 					} else if (b->gi[i].fmt == bcf_str2int("DP", 2)) {
 						((uint16_t*)b->gi[i].data)[k-9] = 0;
 					} else if (b->gi[i].fmt == bcf_str2int("PL", 2)) {
@@ -173,11 +201,15 @@ int vcf_read(bcf_t *bp, bcf_hdr_t *h, bcf1_t *b)
 			for (q = kstrtok(p, ":", &a2), i = 0; q && i < b->n_gi; q = kstrtok(0, 0, &a2), ++i) {
 				if (b->gi[i].fmt == bcf_str2int("GT", 2)) {
 					((uint8_t*)b->gi[i].data)[k-9] = (q[0] - '0')<<3 | (q[2] - '0') | (q[1] == '/'? 0 : 1) << 6;
-				} else if (b->gi[i].fmt == bcf_str2int("GQ", 2) || b->gi[i].fmt == bcf_str2int("SP", 2)) {
+				} else if (b->gi[i].fmt == bcf_str2int("GQ", 2)) {
 					double _x = strtod(q, &q);
 					int x = (int)(_x + .499);
 					if (x > 255) x = 255;
 					((uint8_t*)b->gi[i].data)[k-9] = x;
+				} else if (b->gi[i].fmt == bcf_str2int("SP", 2)) {
+					int x = strtol(q, &q, 10);
+					if (x > 0xffff) x = 0xffff;
+					((uint32_t*)b->gi[i].data)[k-9] = x;
 				} else if (b->gi[i].fmt == bcf_str2int("DP", 2)) {
 					int x = strtol(q, &q, 10);
 					if (x > 0xffff) x = 0xffff;
@@ -198,7 +230,7 @@ int vcf_read(bcf_t *bp, bcf_hdr_t *h, bcf1_t *b)
 					y = b->n_alleles * (b->n_alleles + 1) / 2;
 					for (j = 0; j < y; ++j) {
 						x = strtod(q, &q);
-						data[(k-9) * y + j] = x;
+						data[(k-9) * y + j] = x > 0? -x/10. : x;
 						++q;
 					}
 				}