* parse PL

 * fixed a bug in parsing VCF

diff --git a/bcftools/vcf.c b/bcftools/vcf.c
index 50a73566a6d6e45dca212e909ca36d10580dcd0e..07e25315f7e69a529dcd4bcd4f89e3f47696dd60 100644 (file)
--- a/bcftools/vcf.c
+++ b/bcftools/vcf.c
@@ -132,7 +132,7 @@ int vcf_read(bcf_t *bp, bcf_hdr_t *h, bcf1_t *b)
                        int tid = bcf_str2id(v->refhash, p);
                        if (tid < 0) {
                                tid = bcf_str2id_add(v->refhash, p);
-                               kputs(p, &rn);
+                               kputs(p, &rn); kputc('\0', &rn);
                                sync = 1;
                        }
                        b->tid = tid;
@@ -156,6 +156,15 @@ int vcf_read(bcf_t *bp, bcf_hdr_t *h, bcf1_t *b)
                                        int x = strtol(q, &q, 10);
                                        if (x > 0xffff) x = 0xffff;
                                        ((uint16_t*)b->gi[i].data)[k-9] = x;
+                               } else if (b->gi[i].fmt == bcf_str2int("PL", 2)) {
+                                       int x, j;
+                                       uint8_t *data = (uint8_t*)b->gi[i].data;
+                                       for (j = 0; j < b->gi[i].len; ++j) {
+                                               x = strtol(q, &q, 10);
+                                               if (x > 255) x = 255;
+                                               data[i * b->gi[i].len + j] = x;
+                                               ++q;
+                                       }
                                }
                        }
                }