Patched the example makefile to not use samtools pileup, deprecated.

[samtools.git] / bcftools / bcf.c

diff --git a/bcftools/bcf.c b/bcftools/bcf.c
index 9044b93b0b514fd9566f037a705f8769f60ecc54..84a8e767ec58adb397630f609a52670779f99c89 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;
 }
 
@@ -101,10 +103,16 @@ int bcf_sync(bcf1_t *b)
        ks_tokaux_t aux;
        // set ref, alt, flt, info, fmt
        b->ref = b->alt = b->flt = b->info = b->fmt = 0;
-       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;
+       for (p = b->str, n = 0; p < b->str + b->l_str; ++p) {
+               if (*p == 0 && p+1 != b->str + b->l_str) {
+                       if (n == 5) {
+                               ++n;
+                               break;
+                       } else 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];
@@ -136,6 +144,8 @@ int bcf_sync(bcf1_t *b)
                        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].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;
                }
@@ -177,7 +187,7 @@ int bcf_read(bcf_t *bp, const bcf_hdr_t *h, bcf1_t *b)
        }
        bgzf_read(bp->fp, b->str, b->l_str);
        l = 12 + b->l_str;
-       bcf_sync(b);
+       if (bcf_sync(b) < 0) return -2;
        for (i = 0; i < b->n_gi; ++i) {
                bgzf_read(bp->fp, b->gi[i].data, b->gi[i].len * h->n_smpl);
                l += b->gi[i].len * h->n_smpl;
@@ -238,6 +248,8 @@ void bcf_fmt_core(const bcf_hdr_t *h, bcf1_t *b, kstring_t *s)
                                kputw(((uint16_t*)b->gi[i].data)[j], s);
                        } 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) {
@@ -255,7 +267,7 @@ 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
                }
        }
 }
@@ -304,3 +316,13 @@ 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;
+}