From: Heng Li <lh3@live.co.uk>
Date: Fri, 17 Sep 2010 13:15:53 +0000 (+0000)
Subject:  * put n_smpl to "bcf1_t" to simplify API a little
X-Git-Url: https://git.donarmstrong.com/?p=samtools.git;a=commitdiff_plain;h=4fe4b27b44d067c21948870d9e48976662dec397

 * put n_smpl to "bcf1_t" to simplify API a little
---

diff --git a/bam2bcf.c b/bam2bcf.c
index 9553225..e55212c 100644
--- a/bam2bcf.c
+++ b/bam2bcf.c
@@ -158,6 +158,7 @@ int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b)
 {
 	kstring_t s;
 	int i;
+	b->n_smpl = bc->n;
 	b->tid = tid; b->pos = pos; b->qual = 0;
 	s.s = b->str; s.m = b->m_str; s.l = 0;
 	kputc('\0', &s);
@@ -179,7 +180,7 @@ int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b)
 	// FMT
 	kputs("PL", &s); kputc('\0', &s);
 	b->m_str = s.m; b->str = s.s; b->l_str = s.l;
-	bcf_sync(bc->n, b);
+	bcf_sync(b);
 	memcpy(b->gi[0].data, bc->PL, b->gi[0].len * bc->n);
 	return 0;
 }
diff --git a/bcftools/bcf.c b/bcftools/bcf.c
index 3393aad..2fd1696 100644
--- a/bcftools/bcf.c
+++ b/bcftools/bcf.c
@@ -100,10 +100,10 @@ int bcf_hdr_sync(bcf_hdr_t *b)
 	return 0;
 }
 
-int bcf_sync(int n_smpl, bcf1_t *b)
+int bcf_sync(bcf1_t *b)
 {
 	char *p, *tmp[5];
-	int i, n;
+	int i, n, n_smpl = b->n_smpl;
 	ks_tokaux_t aux;
 	// set ref, alt, flt, info, fmt
 	b->ref = b->alt = b->flt = b->info = b->fmt = 0;
@@ -172,6 +172,7 @@ int bcf_read(bcf_t *bp, const bcf_hdr_t *h, bcf1_t *b)
 	int i, l = 0;
 	if (b == 0) return -1;
 	if (bgzf_read(bp->fp, &b->tid, 4) == 0) return -1;
+	b->n_smpl = h->n_smpl;
 	bgzf_read(bp->fp, &b->pos, 4);
 	bgzf_read(bp->fp, &b->qual, 4);
 	bgzf_read(bp->fp, &b->l_str, 4);
@@ -182,7 +183,7 @@ int bcf_read(bcf_t *bp, const bcf_hdr_t *h, bcf1_t *b)
 	}
 	bgzf_read(bp->fp, b->str, b->l_str);
 	l = 12 + b->l_str;
-	bcf_sync(h->n_smpl, b);
+	bcf_sync(b);
 	for (i = 0; i < b->n_gi; ++i) {
 		bgzf_read(bp->fp, b->gi[i].data, b->gi[i].len * h->n_smpl);
 		l += b->gi[i].len * h->n_smpl;
@@ -219,7 +220,7 @@ void bcf_fmt_core(const bcf_hdr_t *h, bcf1_t *b, kstring_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);
-	ksprintf(s, "%.3g", b->qual); /*kputw(b->qual, s);*/ kputc('\t', s);
+	ksprintf(s, "%.3g", b->qual); kputc('\t', s);
 	fmt_str(b->flt, s); kputc('\t', s);
 	fmt_str(b->info, s);
 	if (b->fmt[0]) {
diff --git a/bcftools/bcf.h b/bcftools/bcf.h
index b52f367..92b2c03 100644
--- a/bcftools/bcf.h
+++ b/bcftools/bcf.h
@@ -19,7 +19,7 @@ typedef struct {
 	char *str, *ref, *alt, *flt, *info, *fmt; // fmt, ref, alt and info point to str
 	int n_gi, m_gi;
 	bcf_ginfo_t *gi;
-	int n_alleles;
+	int n_alleles, n_smpl;
 	// derived info: ref, alt, flt, info, fmt, n_gi, n_alleles
 } bcf1_t;
 
@@ -49,7 +49,7 @@ extern "C" {
 	bcf_t *bcf_open(const char *fn, const char *mode);
 	int bcf_close(bcf_t *b);
 	int bcf_read(bcf_t *bp, const bcf_hdr_t *h, bcf1_t *b);
-	int bcf_sync(int n_smpl, bcf1_t *b);
+	int bcf_sync(bcf1_t *b);
 	int bcf_write(bcf_t *bp, const bcf_hdr_t *h, const bcf1_t *b);
 	bcf_hdr_t *bcf_hdr_read(bcf_t *b);
 	int bcf_hdr_write(bcf_t *b, const bcf_hdr_t *h);
@@ -65,8 +65,8 @@ extern "C" {
 	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);
 
-	int bcf_shrink_alt(int n_smpl, bcf1_t *b, int n);
-	int bcf_gl2pl(int n_smpl, bcf1_t *b);
+	int bcf_shrink_alt(bcf1_t *b, int n);
+	int bcf_gl2pl(bcf1_t *b);
 
 	void *bcf_build_refhash(bcf_hdr_t *h);
 	void bcf_str2id_destroy(void *_hash);
diff --git a/bcftools/bcfutils.c b/bcftools/bcfutils.c
index dd1e89f..4d6835d 100644
--- a/bcftools/bcfutils.c
+++ b/bcftools/bcfutils.c
@@ -48,11 +48,10 @@ int bcf_str2id_add(void *_hash, const char *str)
 	return kh_val(hash, k);
 }
 
-int bcf_shrink_alt(int n_smpl, bcf1_t *b, int n)
+int bcf_shrink_alt(bcf1_t *b, int n)
 {
 	char *p;
-	int i, j, k;
-	int *z;
+	int i, j, k, *z, n_smpl = b->n_smpl;
 	if (b->n_alleles <= n) return -1;
 	if (n > 1) {
 		for (p = b->alt, k = 1; *p; ++p)
@@ -79,14 +78,14 @@ int bcf_shrink_alt(int n_smpl, bcf1_t *b, int n)
 		} // FIXME: to add GL
 	}
 	b->n_alleles = n;
-	bcf_sync(n_smpl, b);
+	bcf_sync(b);
 	return 0;
 }
 
-int bcf_gl2pl(int n_smpl, bcf1_t *b)
+int bcf_gl2pl(bcf1_t *b)
 {
 	char *p;
-	int i;
+	int i, n_smpl = b->n_smpl;
 	bcf_ginfo_t *g;
 	float *d0;
 	uint8_t *d1;
diff --git a/bcftools/call1.c b/bcftools/call1.c
index 6b5c47b..5c6e477 100644
--- a/bcftools/call1.c
+++ b/bcftools/call1.c
@@ -133,7 +133,7 @@ static int test16(bcf1_t *b, anno16_t *a)
 	return test16_core(anno, a);
 }
 
-static void rm_info(int n_smpl, bcf1_t *b, const char *key)
+static void rm_info(bcf1_t *b, const char *key)
 {
 	char *p, *q;
 	if ((p = strstr(b->info, key)) == 0) return;
@@ -141,7 +141,7 @@ static void rm_info(int n_smpl, bcf1_t *b, const char *key)
 	if (p > b->info && *(p-1) == ';') --p;
 	memmove(p, q, b->l_str - (q - b->str));
 	b->l_str -= q - p;
-	bcf_sync(n_smpl, b);
+	bcf_sync(b);
 }
 
 static int update_bcf1(int n_smpl, bcf1_t *b, const bcf_p1aux_t *pa, const bcf_p1rst_t *pr, double pref, int flag)
@@ -153,7 +153,7 @@ static int update_bcf1(int n_smpl, bcf1_t *b, const bcf_p1aux_t *pa, const bcf_p
 
 	p_hwe = pr->g[0] >= 0.? test_hwe(pr->g) : 1.0; // only do HWE g[] is calculated
 	test16(b, &a);
-	rm_info(n_smpl, b, "I16=");
+	rm_info(b, "I16=");
 
 	memset(&s, 0, sizeof(kstring_t));
 	kputc('\0', &s); kputs(b->ref, &s); kputc('\0', &s);
@@ -174,10 +174,10 @@ static int update_bcf1(int n_smpl, bcf1_t *b, const bcf_p1aux_t *pa, const bcf_p
 	b->m_str = s.m; b->l_str = s.l; b->str = s.s;
 	b->qual = r < 1e-100? 99 : -4.343 * log(r);
 	if (b->qual > 99) b->qual = 99;
-	bcf_sync(n_smpl, b);
-	if (!is_var) bcf_shrink_alt(n_smpl, b, 1);
+	bcf_sync(b);
+	if (!is_var) bcf_shrink_alt(b, 1);
 	else if (!(flag&VC_KEEPALT))
-		bcf_shrink_alt(n_smpl, b, pr->rank0 < 2? 2 : pr->rank0+1);
+		bcf_shrink_alt(b, pr->rank0 < 2? 2 : pr->rank0+1);
 	return is_var;
 }
 
@@ -314,7 +314,7 @@ int bcfview(int argc, char *argv[])
 		}
 		if (vc.flag & VC_CALL) { // call variants
 			bcf_p1rst_t pr;
-			bcf_gl2pl(h->n_smpl, b);
+			bcf_gl2pl(b);
 			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) {
diff --git a/bcftools/vcf.c b/bcftools/vcf.c
index d441d7f..51ccb74 100644
--- a/bcftools/vcf.c
+++ b/bcftools/vcf.c
@@ -139,6 +139,7 @@ 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
@@ -156,7 +157,7 @@ int vcf_read(bcf_t *bp, bcf_hdr_t *h, bcf1_t *b)
 		} 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) {