fixed a bug in indexing

[samtools.git] / bcftools / bcf.c

diff --git a/bcftools/bcf.c b/bcftools/bcf.c
index 19969eb5d4a4f15ad0e4e9f2486123794e8b7410..3393aad1edef67c24c548dbc290b15ac02c14caf 100644 (file)
--- a/bcftools/bcf.c
+++ b/bcftools/bcf.c
@@ -143,7 +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);
        }
@@ -245,9 +245,21 @@ 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]);
+                               }
                        }
                }
        }