Imported Upstream version 0.1.13

[samtools.git] / bcftools / bcf.c

diff --git a/bcftools/bcf.c b/bcftools/bcf.c
index 6e45695cfb8c35a22dc4699728e445129293a699..080b6fefcfc6ba8af057bd0a9792f620ac061f7a 100644 (file)
--- a/bcftools/bcf.c
+++ b/bcftools/bcf.c
@@ -106,7 +106,7 @@ int bcf_sync(bcf1_t *b)
        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) {
-               fprintf(stderr, "[%s] incorrect number of fields (%d != 5). Corrupted file?\n", __func__, n);
+               fprintf(stderr, "[%s] incorrect number of fields (%d != 5) at %d:%d\n", __func__, n, b->tid, b->pos);
                return -1;
        }
        b->ref = tmp[0]; b->alt = tmp[1]; b->flt = tmp[2]; b->info = tmp[3]; b->fmt = tmp[4];
@@ -136,10 +136,10 @@ int bcf_sync(bcf1_t *b)
                        b->gi[i].len = b->n_alleles * (b->n_alleles + 1) / 2;
                } 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 == bcf_str2int("GQ", 2) || b->gi[i].fmt == bcf_str2int("GT", 2)
-                                  || b->gi[i].fmt == bcf_str2int("SP", 2))
-               {
+               } 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("SP", 2)) {
+                       b->gi[i].len = 4;
                } else if (b->gi[i].fmt == bcf_str2int("GL", 2)) {
                        b->gi[i].len = b->n_alleles * (b->n_alleles + 1) / 2 * 4;
                }
@@ -240,8 +240,10 @@ void bcf_fmt_core(const bcf_hdr_t *h, bcf1_t *b, kstring_t *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) || b->gi[i].fmt == bcf_str2int("SP", 2)) {
+                       } 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("SP", 2)) {
+                               kputw(((int32_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];
                                if (y>>7&1) {
@@ -259,7 +261,7 @@ void bcf_fmt_core(const bcf_hdr_t *h, bcf1_t *b, kstring_t *s)
                                        if (k > 0) kputc(',', s);
                                        ksprintf(s, "%.2f", d[k]);
                                }
-                       }
+                       } else kputc('.', s); // custom fields
                }
        }
 }