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Starting the work on next package update.
[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);
}
} else {
b->fp = strcmp(fn, "-")? bgzf_open(fn, mode) : bgzf_fdopen(fileno(stdin), mode);
}
+#ifndef BCF_LITE
b->fp->owned_file = 1;
b->fp->owned_file = 1;
+#endif
return b;
}
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;
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) {
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];
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;
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;
}
} 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;
}
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;
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);
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) {
} 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]);
}
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;
}
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;
+}