Imported Upstream version 0.1.10

[samtools.git] / bcftools / bcf.c

diff --git a/bcftools/bcf.c b/bcftools/bcf.c
index 9044b93b0b514fd9566f037a705f8769f60ecc54..fd5c0c9ae24971f15168f488452afe2077258dd0 100644 (file)
--- a/bcftools/bcf.c
+++ b/bcftools/bcf.c
@@ -13,7 +13,9 @@ bcf_t *bcf_open(const char *fn, const char *mode)
        } else {
                b->fp = strcmp(fn, "-")? bgzf_open(fn, mode) : bgzf_fdopen(fileno(stdin), mode);
        }
+#ifndef BCF_LITE
        b->fp->owned_file = 1;
+#endif
        return b;
 }
 
@@ -134,7 +136,9 @@ 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)) {
+               } 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))
+               {
                        b->gi[i].len = 1;
                } else if (b->gi[i].fmt == bcf_str2int("GL", 2)) {
                        b->gi[i].len = b->n_alleles * (b->n_alleles + 1) / 2 * 4;
@@ -236,7 +240,7 @@ 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)) {
+                       } else if (b->gi[i].fmt == bcf_str2int("GQ", 2) || b->gi[i].fmt == bcf_str2int("SP", 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];
@@ -304,3 +308,13 @@ int bcf_cpy(bcf1_t *r, const bcf1_t *b)
                memcpy(r->gi[i].data, b->gi[i].data, r->n_smpl * r->gi[i].len);
        return 0;
 }
+
+int bcf_is_indel(const bcf1_t *b)
+{
+       char *p;
+       if (strlen(b->ref) > 1) return 1;
+       for (p = b->alt; *p; ++p)
+               if (*p != ',' && p[1] != ',' && p[1] != '\0')
+                       return 1;
+       return 0;
+}