faster for large sample size (in principle)

[samtools.git] / bcftools / bcf.c

diff --git a/bcftools/bcf.c b/bcftools/bcf.c
index 2cd6423558c6e3e15459f8beeeb56acc40d6be54..c3313881ef90fc2930c72d218c090b35e5cf9466 100644 (file)
--- a/bcftools/bcf.c
+++ b/bcftools/bcf.c
@@ -100,12 +100,11 @@ int bcf_hdr_sync(bcf_hdr_t *b)
        return 0;
 }
 
-#define char2int(s) (((int)s[0])<<8|s[1])
-
 int bcf_sync(int n_smpl, bcf1_t *b)
 {
-       char *p, *tmp[5], *s;
+       char *p, *tmp[5];
        int i, n;
+       ks_tokaux_t aux;
        // set ref, alt, flt, info, fmt
        b->ref = b->alt = b->flt = b->info = b->fmt = 0;
        for (p = b->str, n = 0; p < b->str + b->l_str; ++p)
@@ -127,23 +126,17 @@ int bcf_sync(int n_smpl, bcf1_t *b)
                memset(b->gi + old_m, 0, (b->m_gi - old_m) * sizeof(bcf_ginfo_t));
        }
        b->n_gi = n;
-       for (p = s = b->fmt, n = 0; *p; ++p) {
-               if (*p == ':' || *(p+1) == 0) {
-                       char *q = *p == ':'? p : p + 1;
-                       if ((q - s) != 2) return -2;
-                       b->gi[n].fmt = char2int(s);
-                       s = q;
-               }
-       }
+       for (p = kstrtok(b->fmt, ":", &aux), n = 0; p; p = kstrtok(0, 0, &aux))
+               b->gi[n++].fmt = bcf_str2int(p, aux.p - p);
        // set gi[i].len
        for (i = 0; i < b->n_gi; ++i) {
-               if (b->gi[i].fmt == char2int("PL")) {
+               if (b->gi[i].fmt == bcf_str2int("PL", 2)) {
                        b->gi[i].len = b->n_alleles * (b->n_alleles + 1) / 2;
-               } else if (b->gi[i].fmt == char2int("DP") || b->gi[i].fmt == char2int("HQ")) {
+               } else if (b->gi[i].fmt == bcf_str2int("DP", 2) || b->gi[i].fmt == bcf_str2int("HQ", 2)) {
                        b->gi[i].len = 2;
-               } else if (b->gi[i].fmt == char2int("GQ") || b->gi[i].fmt == char2int("GT")) {
+               } else if (b->gi[i].fmt == bcf_str2int("GQ", 2) || b->gi[i].fmt == bcf_str2int("GT", 2)) {
                        b->gi[i].len = 1;
-               } else if (b->gi[i].fmt == char2int("GL")) {
+               } else if (b->gi[i].fmt == bcf_str2int("GL", 2)) {
                        b->gi[i].len = 4;
                }
                b->gi[i].data = realloc(b->gi[i].data, n_smpl * b->gi[i].len);
@@ -211,41 +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 (b->gi[i].fmt == char2int("PL")) {
+                       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 == char2int("DP")) {
-                               kputw(((uint16_t*)b->gi[i].data)[j], &s);
-                       } else if (b->gi[i].fmt == char2int("GQ")) {
-                               kputw(((uint8_t*)b->gi[i].data)[j], &s);
+                       } else if (b->gi[i].fmt == bcf_str2int("DP", 2)) {
+                               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);
+                       } 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;
 }