From: Heng Li <lh3@live.co.uk>
Date: Mon, 9 Aug 2010 16:49:23 +0000 (+0000)
Subject:  * fixed a bug in kstrtok@kstring.c
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=86329087668959dbb63af0e0ca97597c23c9678e;p=samtools.git

 * fixed a bug in kstrtok@kstring.c
 * preliminary VCF parser (not parse everything for now)
 * improved view interface
---

diff --git a/bcftools/bcf.c b/bcftools/bcf.c
index f6c26f2..fdc13b8 100644
--- a/bcftools/bcf.c
+++ b/bcftools/bcf.c
@@ -204,41 +204,52 @@ static inline void fmt_str(const char *p, kstring_t *s)
 	else kputs(p, s);
 }
 
-char *bcf_fmt(const bcf_hdr_t *h, bcf1_t *b)
+void bcf_fmt_core(const bcf_hdr_t *h, bcf1_t *b, kstring_t *s)
 {
-	kstring_t s;
 	int i, j, x;
-	memset(&s, 0, sizeof(kstring_t));
-	kputs(h->ns[b->tid], &s); kputc('\t', &s);
-	kputw(b->pos + 1, &s); kputc('\t', &s);
-	fmt_str(b->str, &s); kputc('\t', &s);
-	fmt_str(b->ref, &s); kputc('\t', &s);
-	fmt_str(b->alt, &s); kputc('\t', &s);
-	kputw(b->qual, &s); kputc('\t', &s);
-	fmt_str(b->flt, &s); kputc('\t', &s);
-	fmt_str(b->info, &s);
+	s->l = 0;
+	kputs(h->ns[b->tid], s); kputc('\t', s);
+	kputw(b->pos + 1, s); kputc('\t', s);
+	fmt_str(b->str, s); kputc('\t', s);
+	fmt_str(b->ref, s); kputc('\t', s);
+	fmt_str(b->alt, s); kputc('\t', s);
+	kputw(b->qual, s); kputc('\t', s);
+	fmt_str(b->flt, s); kputc('\t', s);
+	fmt_str(b->info, s);
 	if (b->fmt[0]) {
-		kputc('\t', &s);
-		fmt_str(b->fmt, &s);
+		kputc('\t', s);
+		fmt_str(b->fmt, s);
 	}
 	x = b->n_alleles * (b->n_alleles + 1) / 2;
 	for (j = 0; j < h->n_smpl; ++j) {
-		kputc('\t', &s);
+		kputc('\t', s);
 		for (i = 0; i < b->n_gi; ++i) {
-			if (i) kputc(':', &s);
+			if (i) kputc(':', s);
 			if (b->gi[i].fmt == bcf_str2int("PL", 2)) {
 				uint8_t *d = (uint8_t*)b->gi[i].data + j * x;
 				int k;
 				for (k = 0; k < x; ++k) {
-					if (k > 0) kputc(',', &s);
-					kputw(d[k], &s);
+					if (k > 0) kputc(',', s);
+					kputw(d[k], s);
 				}
 			} else if (b->gi[i].fmt == bcf_str2int("DP", 2)) {
-				kputw(((uint16_t*)b->gi[i].data)[j], &s);
+				kputw(((uint16_t*)b->gi[i].data)[j], s);
 			} else if (b->gi[i].fmt == bcf_str2int("GQ", 2)) {
-				kputw(((uint8_t*)b->gi[i].data)[j], &s);
+				kputw(((uint8_t*)b->gi[i].data)[j], s);
+			} else if (b->gi[i].fmt == bcf_str2int("GT", 2)) {
+				int y = ((uint8_t*)b->gi[i].data)[j];
+				kputc('0' + (y>>3&7), s);
+				kputc("/|"[y>>6&1], s);
+				kputc('0' + (y&7), s);
 			}
 		}
 	}
+}
+
+char *bcf_fmt(const bcf_hdr_t *h, bcf1_t *b)
+{
+	kstring_t s;
+	s.l = s.m = 0; s.s = 0;
+	bcf_fmt_core(h, b, &s);
 	return s.s;
 }
diff --git a/bcftools/bcf.h b/bcftools/bcf.h
index 3c0ab2c..c317440 100644
--- a/bcftools/bcf.h
+++ b/bcftools/bcf.h
@@ -58,11 +58,18 @@ extern "C" {
 	int bcf_destroy(bcf1_t *b);
 	char *bcf_fmt(const bcf_hdr_t *h, bcf1_t *b);
 
+	bcf_t *vcf_open(const char *fn, const char *mode);
 	int vcf_close(bcf_t *bp);
+	bcf_hdr_t *vcf_hdr_read(bcf_t *bp);
+	int vcf_hdr_write(bcf_t *bp, const bcf_hdr_t *h);
+	int vcf_write(bcf_t *bp, bcf_hdr_t *h, bcf1_t *b);
+	int vcf_read(bcf_t *bp, bcf_hdr_t *h, bcf1_t *b);
 
 	void *bcf_build_refhash(bcf_hdr_t *h);
 	void bcf_str2id_destroy(void *_hash);
+	int bcf_str2id_add(void *_hash, const char *str);
 	int bcf_str2id(void *_hash, const char *str);
+	void *bcf_str2id_init();
 
 	int bcf_idx_build(const char *fn);
 	uint64_t bcf_idx_query(const bcf_idx_t *idx, int tid, int beg, int end);
diff --git a/bcftools/bcfutils.c b/bcftools/bcfutils.c
index 861e33f..3010ef3 100644
--- a/bcftools/bcfutils.c
+++ b/bcftools/bcfutils.c
@@ -20,11 +20,6 @@ void *bcf_str2id_init()
 	return kh_init(str2id);
 }
 
-int bcf_str2id_put(void *_hash, const char *str, int id)
-{
-	return 0;
-}
-
 void bcf_str2id_destroy(void *_hash)
 {
 	khash_t(str2id) *hash = (khash_t(str2id)*)_hash;
@@ -40,3 +35,14 @@ int bcf_str2id(void *_hash, const char *str)
 	return k == kh_end(hash)? -1 : kh_val(hash, k);
 }
 
+int bcf_str2id_add(void *_hash, const char *str)
+{
+	khint_t k;
+	int ret;
+	khash_t(str2id) *hash = (khash_t(str2id)*)_hash;
+	if (!hash) return -1;
+	k = kh_put(str2id, hash, str, &ret);
+	if (ret == 0) return kh_val(hash, k);
+	kh_val(hash, k) = kh_size(hash) - 1;
+	return kh_val(hash, k);
+}
diff --git a/bcftools/main.c b/bcftools/main.c
index 21d9eec..e271efd 100644
--- a/bcftools/main.c
+++ b/bcftools/main.c
@@ -4,7 +4,6 @@
 
 int bcfview(int argc, char *argv[]);
 int bcf_main_index(int argc, char *argv[]);
-int vcf_test(int argc, char *argv[]);
 
 int main(int argc, char *argv[])
 {
@@ -18,7 +17,6 @@ int main(int argc, char *argv[])
 	}
 	if (strcmp(argv[1], "view") == 0) return bcfview(argc-1, argv+1);
 	if (strcmp(argv[1], "index") == 0) return bcf_main_index(argc-1, argv+1);
-	if (strcmp(argv[1], "test") == 0) return vcf_test(argc-1, argv+1);
 	else {
 		fprintf(stderr, "[main] Unrecognized command.\n");
 		return 1;
diff --git a/bcftools/vcf.c b/bcftools/vcf.c
index 81a5777..50a7356 100644
--- a/bcftools/vcf.c
+++ b/bcftools/vcf.c
@@ -22,7 +22,7 @@ bcf_hdr_t *vcf_hdr_read(bcf_t *bp)
 	int dret;
 	vcf_t *v;
 	bcf_hdr_t *h;
-	if (!bp->is_vcf) return 0;
+	if (!bp->is_vcf) return bcf_hdr_read(bp);
 	h = calloc(1, sizeof(bcf_hdr_t));
 	v = (vcf_t*)bp->v;
 	v->line.l = 0;
@@ -35,15 +35,12 @@ bcf_hdr_t *vcf_hdr_read(bcf_t *bp)
 			kputsn(v->line.s, v->line.l, &meta); kputc('\n', &meta);
 		} else if (v->line.s[0] == '#') {
 			int k;
-			char *p, *q, *r;
-			for (q = v->line.s, p = q + 1, k = 0; *p; ++p) {
-				if (*p == '\t' || *(p+1) == 0) {
-					r = *(p+1) == 0? p+1 : p;
-					if (k >= 9) {
-						kputsn(q, r - q, &smpl);
-						kputc('\0', &smpl);
-					}
-					q = p + 1; ++k;
+			ks_tokaux_t aux;
+			char *p;
+			for (p = kstrtok(v->line.s, "\t\n", &aux), k = 0; p; p = kstrtok(0, 0, &aux), ++k) {
+				if (k >= 9) {
+					kputsn(p, aux.p - p, &smpl);
+					kputc('\0', &smpl);
 				}
 			}
 			break;
@@ -61,25 +58,25 @@ bcf_t *vcf_open(const char *fn, const char *mode)
 {
 	bcf_t *bp;
 	vcf_t *v;
+	if (strchr(mode, 'b')) return bcf_open(fn, mode);
 	bp = calloc(1, sizeof(bcf_t));
 	v = calloc(1, sizeof(vcf_t));
 	bp->is_vcf = 1;
 	bp->v = v;
+	v->refhash = bcf_str2id_init();
 	if (strchr(mode, 'r')) {
 		v->fp = strcmp(fn, "-")? gzopen(fn, "r") : gzdopen(fileno(stdin), "r");
 		v->ks = ks_init(v->fp);
 	} else if (strchr(mode, 'w'))
-		v->fpout = strcmp(fn, "-")? fopen(fn, "w") : fdopen(fileno(stdout), "w");
+		v->fpout = strcmp(fn, "-")? fopen(fn, "w") : stdout;
 	return bp;
 }
 
-void bcf_hdr_clear(bcf_hdr_t *b);
-
 int vcf_close(bcf_t *bp)
 {
 	vcf_t *v;
 	if (bp == 0) return -1;
-	if (bp->v == 0) return -1;
+	if (!bp->is_vcf) return bcf_close(bp);
 	v = (vcf_t*)bp->v;
 	if (v->fp) {
 		ks_destroy(v->ks);
@@ -87,6 +84,7 @@ int vcf_close(bcf_t *bp)
 	}
 	if (v->fpout) fclose(v->fpout);
 	free(v->line.s);
+	bcf_str2id_destroy(v->refhash);
 	free(v);
 	free(bp);
 	return 0;
@@ -96,52 +94,73 @@ int vcf_hdr_write(bcf_t *bp, const bcf_hdr_t *h)
 {
 	vcf_t *v = (vcf_t*)bp->v;
 	int i;
-	if (v == 0 || v->fpout == 0) return -1;
-	fwrite(h->txt, 1, h->l_txt, v->fpout);
-	fprintf(v->fpout, "#CHROM\tPOS\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT");
+	if (!bp->is_vcf) return bcf_hdr_write(bp, h);
+	if (h->l_txt > 0) fwrite(h->txt, 1, h->l_txt - 1, v->fpout);
+	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]);
 	fputc('\n', v->fpout);
 	return 0;
 }
 
+int vcf_write(bcf_t *bp, bcf_hdr_t *h, bcf1_t *b)
+{
+	vcf_t *v = (vcf_t*)bp->v;
+	extern void bcf_fmt_core(const bcf_hdr_t *h, bcf1_t *b, kstring_t *s);
+	if (!bp->is_vcf) return bcf_write(bp, h, b);
+	bcf_fmt_core(h, b, &v->line);
+	fwrite(v->line.s, 1, v->line.l, v->fpout);
+	fputc('\n', v->fpout);
+	return v->line.l + 1;
+}
+
 int vcf_read(bcf_t *bp, bcf_hdr_t *h, bcf1_t *b)
 {
-	int dret, k;
+	int dret, k, i, sync = 0;
 	vcf_t *v = (vcf_t*)bp->v;
-	char *p, *q, *r;
-	kstring_t str;
+	char *p, *q;
+	kstring_t str, rn;
+	ks_tokaux_t aux, a2;
+	if (!bp->is_vcf) return bcf_read(bp, h, b);
 	v->line.l = 0;
 	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;
-	for (q = v->line.s, p = q + 1, k = 0; *p; ++p) {
-		if (*p == '\t' || *(p+1) == '\0') {
-			++k;
-			r = *(p+1)? p : p + 1;
-			*r = '\0';
-			if (k == 1) { // ref
-			} else if (k == 2) {
-				b->pos = atoi(q);
-			} else if (k == 3 || k == 4 || k == 5 || k == 7 || k == 8 || k == 9) {
-				kputsn(q, r - q + 1, &str);
-				if (k == 9) bcf_sync(h->n_smpl, b);
-			} else if (k == 6) {
-				b->qual = (q[0] >= '0' && q[0] <= '9')? atoi(q) : 0;
+	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);
+				kputs(p, &rn);
+				sync = 1;
+			}
+			b->tid = tid;
+		} else if (k == 1) { // pos
+			b->pos = atoi(p);
+		} else if (k == 5) { // qual
+			b->qual = (p[0] >= '0' && p[0] <= '9')? atoi(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);
+		} else {
+			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)) {
+					int x = strtol(q, &q, 10);
+					if (x > 255) x = 255;
+					((uint8_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;
+					((uint16_t*)b->gi[i].data)[k-9] = x;
+				}
 			}
-			q = p + 1;
 		}
 	}
+	h->l_nm = rn.l; h->name = rn.s;
+	if (sync) bcf_hdr_sync(h);
 	return v->line.l + 1;
 }
-
-int vcf_test(int argc, char *argv[])
-{
-	bcf_t *bp, *bpout;
-	bcf_hdr_t *h;
-	bp = vcf_open(argv[1], "r");
-	bpout = vcf_open("-", "w");
-	h = vcf_hdr_read(bpout);
-	vcf_hdr_write(bpout, h);
-	vcf_close(bp);
-	return 0;
-}
diff --git a/bcftools/vcfout.c b/bcftools/vcfout.c
index dfcb25a..58f11a2 100644
--- a/bcftools/vcfout.c
+++ b/bcftools/vcfout.c
@@ -15,9 +15,11 @@ KSTREAM_INIT(gzFile, gzread, 16384)
 
 #define VC_NO_PL   1
 #define VC_NO_GENO 2
-#define VC_BCF     4
+#define VC_BCFOUT  4
 #define VC_CALL    8
 #define VC_VARONLY 16
+#define VC_VCFIN   32
+#define VC_UNCOMP  64
 
 typedef struct {
 	int flag, prior_type;
@@ -149,19 +151,22 @@ int bcfview(int argc, char *argv[])
 	bcf_p1aux_t *p1 = 0;
 	bcf_hdr_t *h;
 	int tid, begin, end;
+	char moder[4], modew[4];
 	khash_t(set64) *hash = 0;
 
 	tid = begin = end = -1;
 	memset(&vc, 0, sizeof(viewconf_t));
 	vc.prior_type = -1; vc.theta = 1e-3; vc.pref = 0.9;
-	while ((c = getopt(argc, argv, "l:cGvLbP:t:p:")) >= 0) {
+	while ((c = getopt(argc, argv, "l:cGvLbSuP:t:p:")) >= 0) {
 		switch (c) {
 		case 'l': vc.fn_list = strdup(optarg); break;
 		case 'G': vc.flag |= VC_NO_GENO; break;
 		case 'L': vc.flag |= VC_NO_PL; break;
-		case 'b': vc.flag |= VC_BCF; break;
+		case 'b': vc.flag |= VC_BCFOUT; break;
+		case 'S': vc.flag |= VC_VCFIN; break;
 		case 'c': vc.flag |= VC_CALL; break;
 		case 'v': vc.flag |= VC_VARONLY; break;
+		case 'u': vc.flag |= VC_UNCOMP | VC_BCFOUT; break;
 		case 't': vc.theta = atof(optarg); break;
 		case 'p': vc.pref = atof(optarg); break;
 		case 'P':
@@ -176,6 +181,8 @@ int bcfview(int argc, char *argv[])
 		fprintf(stderr, "Usage:   bcftools view [options] <in.bcf> [reg]\n\n");
 		fprintf(stderr, "Options: -c        SNP calling\n");
 		fprintf(stderr, "         -b        output BCF instead of VCF\n");
+		fprintf(stderr, "         -u        uncompressed BCF output\n");
+		fprintf(stderr, "         -S        input is VCF\n");
 		fprintf(stderr, "         -G        suppress all individual genotype information\n");
 		fprintf(stderr, "         -L        discard the PL genotype field\n");
 		fprintf(stderr, "         -v        output potential variant sites only\n");
@@ -188,18 +195,21 @@ int bcfview(int argc, char *argv[])
 	}
 
 	b = calloc(1, sizeof(bcf1_t));
-	bp = bcf_open(argv[optind], "r");
-	h = bcf_hdr_read(bp);
-	if (vc.flag & VC_BCF) {
-		bout = bcf_open("-", "w");
-		bcf_hdr_write(bout, h);
-	}
+	strcpy(moder, "r");
+	if (!(vc.flag & VC_VCFIN)) strcat(moder, "b");
+	strcpy(modew, "w");
+	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);
+	bout = vcf_open("-", modew);
+	vcf_hdr_write(bout, h);
 	if (vc.flag & VC_CALL) {
 		p1 = bcf_p1_init(h->n_smpl);
 		bcf_p1_init_prior(p1, vc.prior_type, vc.theta);
 	}
 	if (vc.fn_list) hash = bcf_load_pos(vc.fn_list, h);
-	if (optind + 1 < argc) {
+	if (optind + 1 < argc && !(vc.flag&VC_VCFIN)) {
 		void *str2id = bcf_build_refhash(h);
 		if (bcf_parse_region(str2id, argv[optind+1], &tid, &begin, &end) >= 0) {
 			bcf_idx_t *idx;
@@ -212,7 +222,7 @@ int bcfview(int argc, char *argv[])
 			}
 		}
 	}
-	while (bcf_read(bp, h, b) > 0) {
+	while (vcf_read(bp, h, b) > 0) {
 		if (hash) {
 			uint64_t x = (uint64_t)b->tid<<32 | b->pos;
 			khint_t k = kh_get(set64, hash, x);
@@ -231,23 +241,17 @@ int bcfview(int argc, char *argv[])
 			if (pr.p_ref >= vc.pref && (vc.flag & VC_VARONLY)) continue;
 			update_bcf1(h->n_smpl, b, p1, &pr, vc.pref, vc.flag);
 		}
-		if (vc.flag & VC_BCF) bcf_write(bout, h, b);
-		else {
-			char *vcf;
-			if (vc.flag & VC_NO_GENO) {
-				b->n_gi = 0;
-				b->fmt[0] = '\0';
-			}
-			vcf = bcf_fmt(h, b);
-			puts(vcf);
-			free(vcf);
+		if (vc.flag & VC_NO_GENO) {
+			b->n_gi = 0;
+			b->fmt[0] = '\0';
 		}
+		vcf_write(bout, h, b);
 		++n_processed;
 	}
 	if (vc.flag & VC_CALL) bcf_p1_dump_afs(p1);
 	bcf_hdr_destroy(h);
-	bcf_close(bp); bcf_close(bout);
 	bcf_destroy(b);
+	vcf_close(bp); vcf_close(bout);
 	if (hash) kh_destroy(set64, hash);
 	if (vc.fn_list) free(vc.fn_list);
 	if (p1) bcf_p1_destroy(p1);
diff --git a/bgzf.c b/bgzf.c
index a6923da..66d6b02 100644
--- a/bgzf.c
+++ b/bgzf.c
@@ -177,7 +177,7 @@ BGZF*
 bgzf_open(const char* __restrict path, const char* __restrict mode)
 {
     BGZF* fp = NULL;
-    if (mode[0] == 'r' || mode[0] == 'R') { /* The reading mode is preferred. */
+    if (strchr(mode, 'r') || strchr(mode, 'R')) { /* The reading mode is preferred. */
 #ifdef _USE_KNETFILE
 		knetFile *file = knet_open(path, mode);
 		if (file == 0) return 0;
@@ -194,14 +194,14 @@ bgzf_open(const char* __restrict path, const char* __restrict mode)
 		if (fd == -1) return 0;
         fp = open_read(fd);
 #endif
-    } else if (mode[0] == 'w' || mode[0] == 'W') {
+    } else if (strchr(mode, 'w') || strchr(mode, 'W')) {
 		int fd, oflag = O_WRONLY | O_CREAT | O_TRUNC;
 #ifdef _WIN32
 		oflag |= O_BINARY;
 #endif
 		fd = open(path, oflag, 0666);
 		if (fd == -1) return 0;
-        fp = open_write(fd, strstr(mode, "u")? 1 : 0);
+        fp = open_write(fd, strchr(mode, 'u')? 1 : 0);
     }
     if (fp != NULL) fp->owned_file = 1;
     return fp;
diff --git a/kstring.c b/kstring.c
index a09180b..43d524c 100644
--- a/kstring.c
+++ b/kstring.c
@@ -36,7 +36,7 @@ char *kstrtok(const char *str, const char *sep, ks_tokaux_t *aux)
 	if (str) aux->p = str - 1, aux->tab[0] &= ~1ull;
 	else if (aux->tab[0]&1) return 0;
 	for (p = start = aux->p + 1; *p; ++p)
-		if (aux->tab[*p/64]>>(*p%64)) break;
+		if (aux->tab[*p/64]>>(*p%64)&1) break;
 	aux->p = p; // end of token
 	if (*p == 0) aux->tab[0] |= 1; // no more tokens
 	return (char*)start;