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

[samtools.git] / bcftools / call1.c

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) {