faster for large sample size (in principle)

[samtools.git] / bcftools / bcf.c

diff --git a/bcftools/bcf.c b/bcftools/bcf.c
index f6c26f2db2e248c05ffefe34642a5a68b33ae95b..c3313881ef90fc2930c72d218c090b35e5cf9466 100644 (file)
--- a/bcftools/bcf.c
+++ b/bcftools/bcf.c
@@ -204,41 +204,55 @@ 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;
+       if (h->n_ref) kputs(h->ns[b->tid], s);
+       else kputw(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;
+       if (b->n_gi == 0) return;
        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;
 }