X-Git-Url: https://git.donarmstrong.com/?p=samtools.git;a=blobdiff_plain;f=bcftools%2Fvcf.c;h=e8526a38706357c4aa2d067fcf9c64dadd8978f6;hp=23aad3c0c97b02c12d9643d18c87e68ef4d87dc2;hb=2fa4cde9b8806faceffb8677440b54ca4c90b6f7;hpb=39eb14826a5ef0de7f5982390e7e2b0d671848ee

diff --git a/bcftools/vcf.c b/bcftools/vcf.c
index 23aad3c..e8526a3 100644
--- a/bcftools/vcf.c
+++ b/bcftools/vcf.c
@@ -30,7 +30,12 @@ bcf_hdr_t *vcf_hdr_read(bcf_t *bp)
 	memset(&smpl, 0, sizeof(kstring_t));
 	while (ks_getuntil(v->ks, '\n', &v->line, &dret) >= 0) {
 		if (v->line.l < 2) continue;
-		if (v->line.s[0] != '#') return 0; // no sample line
+		if (v->line.s[0] != '#') {
+            free(meta.s);
+            free(smpl.s);
+            free(h);
+            return 0; // no sample line
+        }
 		if (v->line.s[0] == '#' && v->line.s[1] == '#') {
 			kputsn(v->line.s, v->line.l, &meta); kputc('\n', &meta);
 		} else if (v->line.s[0] == '#') {
@@ -72,6 +77,33 @@ 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 +116,7 @@ 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;
@@ -93,22 +125,14 @@ 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 (!has_ref) {
-		fprintf(v->fpout, "##SQ=");
-		for (i = 0; i < h->n_ref; ++i) {
-			fprintf(v->fpout, "%s", h->ns[i]);
-			fputc(i == h->n_ref - 1? '\n' : ',', v->fpout);
-		}
 	}
+	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]);
@@ -139,12 +163,13 @@ int vcf_read(bcf_t *bp, bcf_hdr_t *h, bcf1_t *b)
 	str.l = 0; str.m = b->m_str; str.s = b->str;
 	rn.l = rn.m = h->l_nm; rn.s = h->name;
 	if (ks_getuntil(v->ks, '\n', &v->line, &dret) < 0) return -1;
+	b->n_smpl = h->n_smpl;
 	for (p = kstrtok(v->line.s, "\t", &aux), k = 0; p; p = kstrtok(0, 0, &aux), ++k) {
 		*(char*)aux.p = 0;
 		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;
 			}
@@ -152,11 +177,11 @@ int vcf_read(bcf_t *bp, bcf_hdr_t *h, bcf1_t *b)
 		} else if (k == 1) { // pos
 			b->pos = atoi(p) - 1;
 		} else if (k == 5) { // qual
-			b->qual = (p[0] >= '0' && p[0] <= '9')? atoi(p) : 0;
+			b->qual = (p[0] >= '0' && p[0] <= '9')? atof(p) : 0;
 		} else if (k <= 8) { // variable length strings
 			kputs(p, &str); kputc('\0', &str);
 			b->l_str = str.l; b->m_str = str.m; b->str = str.s;
-			if (k == 8) bcf_sync(h->n_smpl, b);
+			if (k == 8) bcf_sync(b);
 		} else { // k > 9
 			if (strncmp(p, "./.", 3) == 0) {
 				for (i = 0; i < b->n_gi; ++i) {
@@ -164,7 +189,9 @@ int vcf_read(bcf_t *bp, bcf_hdr_t *h, bcf1_t *b)
 						((uint8_t*)b->gi[i].data)[k-9] = 1<<7;
 					} 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("DP", 2)) {
+					} 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) || b->gi[i].fmt == bcf_str2int("DV", 2)) {
 						((uint16_t*)b->gi[i].data)[k-9] = 0;
 					} else if (b->gi[i].fmt == bcf_str2int("PL", 2)) {
 						int y = b->n_alleles * (b->n_alleles + 1) / 2;
@@ -184,7 +211,11 @@ int vcf_read(bcf_t *bp, bcf_hdr_t *h, bcf1_t *b)
 					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("DP", 2)) {
+				} 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) || b->gi[i].fmt == bcf_str2int("DV", 2)) {
 					int x = strtol(q, &q, 10);
 					if (x > 0xffff) x = 0xffff;
 					((uint16_t*)b->gi[i].data)[k-9] = x;
@@ -204,7 +235,7 @@ 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;
 					}
 				}