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

diff --git a/bam2bcf.c b/bam2bcf.c
index 95532254a084caf3fbd6e05840819225848e952b..e55212ca98cbb28041fb6a6dfc46619ff595ee09 100644 (file)
--- 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 3393aad1edef67c24c548dbc290b15ac02c14caf..2fd1696eff466f4ad9490c041cdd0f6e09448e68 100644 (file)
--- 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 b52f36721d66a248530eef27c37d8881f1543a6a..92b2c0364e72503f189b0754da160e310cf034e3 100644 (file)
--- 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 dd1e89f16cf1c48ac8f90ceae35bae312d76ba54..4d6835da8206ea96542ce66e14124b4a388e70db 100644 (file)
--- 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 6b5c47bff1aecaa3d5eeefa1b865cbcdd8979ff3..5c6e477400845c743cb76016784297ec36e780d0 100644 (file)
--- 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 d441d7f0b278bf0d6d72eb05d0e641a0926b04ef..51ccb74521ead6cb7b59baa287b0f102a20683f1 100644 (file)
--- 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) {