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

[samtools.git] / bcftools / bcf.c

diff --git a/bcftools/bcf.c b/bcftools/bcf.c
index 8801cea00a23feaea70e7cc40a736f580e9f17c1..2fd1696eff466f4ad9490c041cdd0f6e09448e68 100644 (file)
--- a/bcftools/bcf.c
+++ b/bcftools/bcf.c
@@ -100,21 +100,27 @@ 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;
        for (p = b->str, n = 0; p < b->str + b->l_str; ++p)
                if (*p == 0 && p+1 != b->str + b->l_str) tmp[n++] = p + 1;
-       if (n != 5) return -1;
+       if (n != 5) {
+               fprintf(stderr, "[bcf_sync] incorrect number of fields (%d != 5)\n", n);
+               return -1;
+       }
        b->ref = tmp[0]; b->alt = tmp[1]; b->flt = tmp[2]; b->info = tmp[3]; b->fmt = tmp[4];
        // set n_alleles
-       for (p = b->alt, n = 1; *p; ++p)
-               if (*p == ',') ++n;
-       b->n_alleles = n + 1;
+       if (*b->alt == 0) b->n_alleles = 1;
+       else {
+               for (p = b->alt, n = 1; *p; ++p)
+                       if (*p == ',') ++n;
+               b->n_alleles = n + 1;
+       }
        // set n_gi and gi[i].fmt
        for (p = b->fmt, n = 1; *p; ++p)
                if (*p == ':') ++n;
@@ -137,7 +143,7 @@ int bcf_sync(int n_smpl, bcf1_t *b)
                } 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 == bcf_str2int("GL", 2)) {
-                       b->gi[i].len = 4;
+                       b->gi[i].len = b->n_alleles * (b->n_alleles + 1) / 2 * 4;
                }
                b->gi[i].data = realloc(b->gi[i].data, n_smpl * b->gi[i].len);
        }
@@ -166,6 +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);
@@ -176,7 +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;
@@ -213,7 +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]) {
@@ -239,9 +246,21 @@ void bcf_fmt_core(const bcf_hdr_t *h, bcf1_t *b, kstring_t *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);
+                               if (y>>7&1) {
+                                       kputsn("./.", 3, s);
+                               } else {
+                                       kputc('0' + (y>>3&7), s);
+                                       kputc("/|"[y>>6&1], s);
+                                       kputc('0' + (y&7), s);
+                               }
+                       } else if (b->gi[i].fmt == bcf_str2int("GL", 2)) {
+                               float *d = (float*)b->gi[i].data + j * x;
+                               int k;
+                               //printf("- %lx\n", d);
+                               for (k = 0; k < x; ++k) {
+                                       if (k > 0) kputc(',', s);
+                                       ksprintf(s, "%.2f", d[k]);
+                               }
                        }
                }
        }