* samtools-0.1.9-6 (r803)

[samtools.git] / bcftools / bcf.c

diff --git a/bcftools/bcf.c b/bcftools/bcf.c
index 3531647e18775cd5049954385a1022d39a17ec6f..05eae5b7dc2bb8c54af062269950c679b9cddac8 100644 (file)
--- a/bcftools/bcf.c
+++ b/bcftools/bcf.c
@@ -134,7 +134,9 @@ 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 +238,7 @@ 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];
@@ -283,8 +285,7 @@ int bcf_append_info(bcf1_t *b, const char *info, int l)
        b->str[shift + l - 1] = '\0';
        b->fmt = b->str + shift + l;
        b->l_str += l;
-       bcf_sync(b);
-//     if (ori != b->str) bcf_sync(b); // synchronize when realloc changes the pointer
+       if (ori != b->str) bcf_sync(b); // synchronize when realloc changes the pointer
        return 0;
 }
 
@@ -305,3 +306,13 @@ 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;
+}