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vcf.c
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#include <zlib.h>
#include <stdio.h>
#include <ctype.h>
#include <assert.h>
#include <string.h>
#include <stdlib.h>
#include <limits.h>
#include "htslib/kstring.h"
#include "htslib/bgzf.h"
#include "htslib/vcf.h"
#include "htslib/tbx.h"
#include "htslib/hfile.h"
#include "htslib/khash.h"
KHASH_MAP_INIT_STR(vdict, bcf_idinfo_t)
typedef khash_t(vdict) vdict_t;
#include "htslib/kseq.h"
KSTREAM_DECLARE(gzFile, gzread)
uint32_t bcf_float_missing = 0x7F800001;
uint32_t bcf_float_vector_end = 0x7F800002;
uint8_t bcf_type_shift[] = { 0, 0, 1, 2, 0, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 };
static bcf_idinfo_t bcf_idinfo_def = { .info = { 15, 15, 15 }, .hrec = { NULL, NULL, NULL}, .id = -1 };
/*************************
*** VCF header parser ***
*************************/
int bcf_hdr_sync(bcf_hdr_t *h);
int bcf_hdr_add_sample(bcf_hdr_t *h, const char *s)
{
if ( !s )
{
bcf_hdr_sync(h);
return 0;
}
const char *ss = s;
while ( !*ss && isspace(*ss) ) ss++;
if ( !*ss )
{
fprintf(stderr,"[W::%s] Empty sample name: trailing spaces/tabs in the header line?\n", __func__);
abort();
}
vdict_t *d = (vdict_t*)h->dict[BCF_DT_SAMPLE];
int ret;
char *sdup = strdup(s);
int k = kh_put(vdict, d, sdup, &ret);
if (ret) { // absent
kh_val(d, k) = bcf_idinfo_def;
kh_val(d, k).id = kh_size(d) - 1;
} else {
if (hts_verbose >= 2)
fprintf(stderr, "[W::%s] Duplicated sample name '%s'. Skipped.\n", __func__, s);
free(sdup);
return -1;
}
int n = kh_size(d);
h->samples = (char**) realloc(h->samples,sizeof(char*)*n);
h->samples[n-1] = sdup;
return 0;
}
void bcf_hdr_parse_sample_line(bcf_hdr_t *h, const char *str)
{
int i = 0;
const char *p, *q;
// add samples
for (p = q = str;; ++q) {
if (*q != '\t' && *q != 0 && *q != '\n') continue;
if (++i > 9) {
char *s = (char*)malloc(q - p + 1);
strncpy(s, p, q - p);
s[q - p] = 0;
bcf_hdr_add_sample(h,s);
free(s);
}
if (*q == 0 || *q == '\n') break;
p = q + 1;
}
bcf_hdr_add_sample(h,NULL);
}
int bcf_hdr_sync(bcf_hdr_t *h)
{
int i;
for (i = 0; i < 3; i++)
{
vdict_t *d = (vdict_t*)h->dict[i];
khint_t k;
// find out the largest id, there may be holes because of IDX
int max_id = -1;
for (k=kh_begin(d); k<kh_end(d); k++)
{
if (!kh_exist(d,k)) continue;
if ( max_id < kh_val(d,k).id ) max_id = kh_val(d,k).id;
}
if ( max_id >= h->n[i] )
{
h->id[i] = (bcf_idpair_t*)realloc(h->id[i], (max_id+1)*sizeof(bcf_idpair_t));
for (k=h->n[i]; k<=max_id; k++)
{
h->id[i][k].key = NULL;
h->id[i][k].val = NULL;
}
h->n[i] = max_id+1;
}
for (k=kh_begin(d); k<kh_end(d); k++)
{
if (!kh_exist(d,k)) continue;
h->id[i][kh_val(d,k).id].key = kh_key(d,k);
h->id[i][kh_val(d,k).id].val = &kh_val(d,k);
}
}
return 0;
}
void bcf_hrec_destroy(bcf_hrec_t *hrec)
{
free(hrec->key);
if ( hrec->value ) free(hrec->value);
int i;
for (i=0; i<hrec->nkeys; i++)
{
free(hrec->keys[i]);
free(hrec->vals[i]);
}
free(hrec->keys);
free(hrec->vals);
free(hrec);
}
// Copies all fields except IDX.
bcf_hrec_t *bcf_hrec_dup(bcf_hrec_t *hrec)
{
bcf_hrec_t *out = (bcf_hrec_t*) calloc(1,sizeof(bcf_hrec_t));
out->type = hrec->type;
if ( hrec->key ) out->key = strdup(hrec->key);
if ( hrec->value ) out->value = strdup(hrec->value);
out->nkeys = hrec->nkeys;
out->keys = (char**) malloc(sizeof(char*)*hrec->nkeys);
out->vals = (char**) malloc(sizeof(char*)*hrec->nkeys);
int i, j = 0;
for (i=0; i<hrec->nkeys; i++)
{
if ( hrec->keys[i] && !strcmp("IDX",hrec->keys[i]) ) continue;
if ( hrec->keys[i] ) out->keys[j] = strdup(hrec->keys[i]);
if ( hrec->vals[i] ) out->vals[j] = strdup(hrec->vals[i]);
j++;
}
if ( i!=j ) out->nkeys--; // IDX was omitted
return out;
}
void bcf_hrec_debug(FILE *fp, bcf_hrec_t *hrec)
{
fprintf(fp, "key=[%s] value=[%s]", hrec->key, hrec->value?hrec->value:"");
int i;
for (i=0; i<hrec->nkeys; i++)
fprintf(fp, "\t[%s]=[%s]", hrec->keys[i],hrec->vals[i]);
fprintf(fp, "\n");
}
void bcf_header_debug(bcf_hdr_t *hdr)
{
int i, j;
for (i=0; i<hdr->nhrec; i++)
{
if ( !hdr->hrec[i]->value )
{
fprintf(stderr, "##%s=<", hdr->hrec[i]->key);
fprintf(stderr,"%s=%s", hdr->hrec[i]->keys[0], hdr->hrec[i]->vals[0]);
for (j=1; j<hdr->hrec[i]->nkeys; j++)
fprintf(stderr,",%s=%s", hdr->hrec[i]->keys[j], hdr->hrec[i]->vals[j]);
fprintf(stderr,">\n");
}
else
fprintf(stderr,"##%s=%s\n", hdr->hrec[i]->key,hdr->hrec[i]->value);
}
}
void bcf_hrec_add_key(bcf_hrec_t *hrec, const char *str, int len)
{
int n = ++hrec->nkeys;
hrec->keys = (char**) realloc(hrec->keys, sizeof(char*)*n);
hrec->vals = (char**) realloc(hrec->vals, sizeof(char*)*n);
assert( len );
hrec->keys[n-1] = (char*) malloc((len+1)*sizeof(char));
memcpy(hrec->keys[n-1],str,len);
hrec->keys[n-1][len] = 0;
hrec->vals[n-1] = NULL;
}
void bcf_hrec_set_val(bcf_hrec_t *hrec, int i, const char *str, int len, int is_quoted)
{
if ( !str ) { hrec->vals[i] = NULL; return; }
if ( hrec->vals[i] ) free(hrec->vals[i]);
if ( is_quoted )
{
hrec->vals[i] = (char*) malloc((len+3)*sizeof(char));
hrec->vals[i][0] = '"';
memcpy(&hrec->vals[i][1],str,len);
hrec->vals[i][len+1] = '"';
hrec->vals[i][len+2] = 0;
}
else
{
hrec->vals[i] = (char*) malloc((len+1)*sizeof(char));
memcpy(hrec->vals[i],str,len);
hrec->vals[i][len] = 0;
}
}
void hrec_add_idx(bcf_hrec_t *hrec, int idx)
{
int n = ++hrec->nkeys;
hrec->keys = (char**) realloc(hrec->keys, sizeof(char*)*n);
hrec->vals = (char**) realloc(hrec->vals, sizeof(char*)*n);
hrec->keys[n-1] = strdup("IDX");
kstring_t str = {0,0,0};
kputw(idx, &str);
hrec->vals[n-1] = str.s;
}
int bcf_hrec_find_key(bcf_hrec_t *hrec, const char *key)
{
int i;
for (i=0; i<hrec->nkeys; i++)
if ( !strcasecmp(key,hrec->keys[i]) ) return i;
return -1;
}
static inline int is_escaped(const char *min, const char *str)
{
int n = 0;
while ( --str>=min && *str=='\\' ) n++;
return n%2;
}
bcf_hrec_t *bcf_hdr_parse_line(const bcf_hdr_t *h, const char *line, int *len)
{
const char *p = line;
if (p[0] != '#' || p[1] != '#') { *len = 0; return NULL; }
p += 2;
const char *q = p;
while ( *q && *q!='=' ) q++;
int n = q-p;
if ( *q!='=' || !n ) { *len = q-line+1; return NULL; } // wrong format
bcf_hrec_t *hrec = (bcf_hrec_t*) calloc(1,sizeof(bcf_hrec_t));
hrec->key = (char*) malloc(sizeof(char)*(n+1));
memcpy(hrec->key,p,n);
hrec->key[n] = 0;
p = ++q;
if ( *p!='<' ) // generic field, e.g. ##samtoolsVersion=0.1.18-r579
{
while ( *q && *q!='\n' ) q++;
hrec->value = (char*) malloc((q-p+1)*sizeof(char));
memcpy(hrec->value, p, q-p);
hrec->value[q-p] = 0;
*len = q-line+1;
return hrec;
}
// structured line, e.g. ##INFO=<ID=PV1,Number=1,Type=Float,Description="P-value for baseQ bias">
int nopen = 1;
while ( *q && *q!='\n' && nopen )
{
p = ++q;
while ( *q && isalnum(*q) ) q++;
n = q-p;
if ( *q!='=' || !n )
{
// wrong format
while ( *q && *q!='\n' ) q++;
kstring_t tmp = {0,0,0};
kputsn(line,q-line,&tmp);
fprintf(stderr,"Could not parse the header line: \"%s\"\n", tmp.s);
free(tmp.s);
*len = q-line+1;
bcf_hrec_destroy(hrec);
return NULL;
}
bcf_hrec_add_key(hrec, p, q-p);
p = ++q;
int quoted = *p=='"' ? 1 : 0;
if ( quoted ) p++, q++;
while (1)
{
if ( !*q ) break;
if ( quoted ) { if ( *q=='"' && !is_escaped(p,q) ) break; }
else
{
if ( *q=='<' ) nopen++;
if ( *q=='>' ) nopen--;
if ( !nopen ) break;
if ( *q==',' && nopen==1 ) break;
}
q++;
}
bcf_hrec_set_val(hrec, hrec->nkeys-1, p, q-p, quoted);
if ( quoted ) q++;
if ( *q=='>' ) { nopen--; q++; }
}
*len = q-line+1;
return hrec;
}
// returns: 1 when hdr needs to be synced, 0 otherwise
int bcf_hdr_register_hrec(bcf_hdr_t *hdr, bcf_hrec_t *hrec)
{
// contig
int i,j,k, ret;
char *str;
if ( !strcmp(hrec->key, "contig") )
{
hrec->type = BCF_HL_CTG;
// Get the contig ID ($str) and length ($j)
i = bcf_hrec_find_key(hrec,"length");
if ( i<0 ) return 0;
if ( sscanf(hrec->vals[i],"%d",&j)!=1 ) return 0;
i = bcf_hrec_find_key(hrec,"ID");
if ( i<0 ) return 0;
str = strdup(hrec->vals[i]);
// Register in the dictionary
vdict_t *d = (vdict_t*)hdr->dict[BCF_DT_CTG];
k = kh_put(vdict, d, str, &ret);
if ( !ret ) { free(str); return 0; } // already present
int idx = bcf_hrec_find_key(hrec,"IDX");
if ( idx!=-1 )
{
char *tmp = hrec->vals[idx];
idx = strtol(hrec->vals[idx], &tmp, 10);
if ( *tmp )
{
fprintf(stderr,"[%s:%d %s] Error parsing the IDX tag, skipping.\n", __FILE__,__LINE__,__FUNCTION__);
return 0;
}
}
else
{
idx = kh_size(d) - 1;
hrec_add_idx(hrec, idx);
}
kh_val(d, k) = bcf_idinfo_def;
kh_val(d, k).id = idx;
kh_val(d, k).info[0] = i;
kh_val(d, k).hrec[0] = hrec;
return 1;
}
if ( !strcmp(hrec->key, "INFO") ) hrec->type = BCF_HL_INFO;
else if ( !strcmp(hrec->key, "FILTER") ) hrec->type = BCF_HL_FLT;
else if ( !strcmp(hrec->key, "FORMAT") ) hrec->type = BCF_HL_FMT;
else if ( hrec->nkeys>0 ) { hrec->type = BCF_HL_STR; return 1; }
else return 0;
// INFO/FILTER/FORMAT
char *id = NULL;
int type = -1, num = -1, var = -1, idx = -1;
for (i=0; i<hrec->nkeys; i++)
{
if ( !strcmp(hrec->keys[i], "ID") ) id = hrec->vals[i];
else if ( !strcmp(hrec->keys[i], "IDX") )
{
char *tmp = hrec->vals[i];
idx = strtol(hrec->vals[i], &tmp, 10);
if ( *tmp )
{
fprintf(stderr,"[%s:%d %s] Error parsing the IDX tag, skipping.\n", __FILE__,__LINE__,__FUNCTION__);
return 0;
}
}
else if ( !strcmp(hrec->keys[i], "Type") )
{
if ( !strcmp(hrec->vals[i], "Integer") ) type = BCF_HT_INT;
else if ( !strcmp(hrec->vals[i], "Float") ) type = BCF_HT_REAL;
else if ( !strcmp(hrec->vals[i], "String") ) type = BCF_HT_STR;
else if ( !strcmp(hrec->vals[i], "Flag") ) type = BCF_HT_FLAG;
else
{
fprintf(stderr, "[E::%s] The type \"%s\" not supported, assuming \"String\"\n", __func__, hrec->vals[i]);
type = BCF_HT_STR;
}
}
else if ( !strcmp(hrec->keys[i], "Number") )
{
if ( !strcmp(hrec->vals[i],"A") ) var = BCF_VL_A;
else if ( !strcmp(hrec->vals[i],"R") ) var = BCF_VL_R;
else if ( !strcmp(hrec->vals[i],"G") ) var = BCF_VL_G;
else if ( !strcmp(hrec->vals[i],".") ) var = BCF_VL_VAR;
else
{
sscanf(hrec->vals[i],"%d",&num);
var = BCF_VL_FIXED;
}
if (var != BCF_VL_FIXED) num = 0xfffff;
}
}
uint32_t info = (uint32_t)num<<12 | var<<8 | type<<4 | hrec->type;
if ( !id ) return 0;
str = strdup(id);
vdict_t *d = (vdict_t*)hdr->dict[BCF_DT_ID];
k = kh_put(vdict, d, str, &ret);
if ( !ret )
{
// already present
free(str);
if ( kh_val(d, k).hrec[info&0xf] ) return 0;
kh_val(d, k).info[info&0xf] = info;
kh_val(d, k).hrec[info&0xf] = hrec;
return 1;
}
kh_val(d, k) = bcf_idinfo_def;
kh_val(d, k).info[info&0xf] = info;
kh_val(d, k).hrec[info&0xf] = hrec;
kh_val(d, k).id = idx==-1 ? kh_size(d) - 1 : idx;
if ( idx==-1 ) hrec_add_idx(hrec, kh_val(d, k).id);
return 1;
}
int bcf_hdr_add_hrec(bcf_hdr_t *hdr, bcf_hrec_t *hrec)
{
if ( !hrec ) return 0;
hrec->type = BCF_HL_GEN;
if ( !bcf_hdr_register_hrec(hdr,hrec) )
{
// If one of the hashed field, then it is already present
if ( hrec->type != BCF_HL_GEN )
{
bcf_hrec_destroy(hrec);
return 0;
}
// Is one of the generic fields and already present?
int i;
for (i=0; i<hdr->nhrec; i++)
{
if ( hdr->hrec[i]->type!=BCF_HL_GEN ) continue;
if ( !strcmp(hdr->hrec[i]->key,hrec->key) && !strcmp(hrec->key,"fileformat") ) break;
if ( !strcmp(hdr->hrec[i]->key,hrec->key) && !strcmp(hdr->hrec[i]->value,hrec->value) ) break;
}
if ( i<hdr->nhrec )
{
bcf_hrec_destroy(hrec);
return 0;
}
}
// New record, needs to be added
int n = ++hdr->nhrec;
hdr->hrec = (bcf_hrec_t**) realloc(hdr->hrec, n*sizeof(bcf_hrec_t*));
hdr->hrec[n-1] = hrec;
return hrec->type==BCF_HL_GEN ? 0 : 1;
}
bcf_hrec_t *bcf_hdr_get_hrec(const bcf_hdr_t *hdr, int type, const char *id)
{
int i;
if ( type==BCF_HL_GEN )
{
for (i=0; i<hdr->nhrec; i++)
{
if ( hdr->hrec[i]->type!=BCF_HL_GEN ) continue;
if ( !strcmp(hdr->hrec[i]->key,id) ) return hdr->hrec[i];
}
return NULL;
}
vdict_t *d = type==BCF_HL_CTG ? (vdict_t*)hdr->dict[BCF_DT_CTG] : (vdict_t*)hdr->dict[BCF_DT_ID];
khint_t k = kh_get(vdict, d, id);
if ( k == kh_end(d) ) return NULL;
return kh_val(d, k).hrec[type==BCF_HL_CTG?0:type];
}
void bcf_hdr_check_sanity(bcf_hdr_t *hdr)
{
static int PL_warned = 0, GL_warned = 0;
if ( !PL_warned )
{
int id = bcf_hdr_id2int(hdr, BCF_DT_ID, "PL");
if ( bcf_hdr_idinfo_exists(hdr,BCF_HL_FMT,id) && bcf_hdr_id2length(hdr,BCF_HL_FMT,id)!=BCF_VL_G )
{
fprintf(stderr,"[W::%s] PL should be declared as Number=G\n", __func__);
PL_warned = 1;
}
}
if ( !GL_warned )
{
int id = bcf_hdr_id2int(hdr, BCF_HL_FMT, "GL");
if ( bcf_hdr_idinfo_exists(hdr,BCF_HL_FMT,id) && bcf_hdr_id2length(hdr,BCF_HL_FMT,id)!=BCF_VL_G )
{
fprintf(stderr,"[W::%s] GL should be declared as Number=G\n", __func__);
PL_warned = 1;
}
}
}
int bcf_hdr_parse(bcf_hdr_t *hdr, char *htxt)
{
int len, needs_sync = 0;
char *p = htxt;
// Check sanity: "fileformat" string must come as first
bcf_hrec_t *hrec = bcf_hdr_parse_line(hdr,p,&len);
if ( !hrec || !hrec->key || strcasecmp(hrec->key,"fileformat") )
fprintf(stderr, "[W::%s] The first line should be ##fileformat; is the VCF/BCF header broken?\n", __func__);
needs_sync += bcf_hdr_add_hrec(hdr, hrec);
// The filter PASS must appear first in the dictionary
hrec = bcf_hdr_parse_line(hdr,"##FILTER=<ID=PASS,Description=\"All filters passed\">",&len);
needs_sync += bcf_hdr_add_hrec(hdr, hrec);
// Parse the whole header
while ( (hrec=bcf_hdr_parse_line(hdr,p,&len)) )
{
needs_sync += bcf_hdr_add_hrec(hdr, hrec);
p += len;
}
bcf_hdr_parse_sample_line(hdr,p); // calls hdr_sync
bcf_hdr_check_sanity(hdr);
return 0;
}
int bcf_hdr_append(bcf_hdr_t *hdr, const char *line)
{
int len;
bcf_hrec_t *hrec = bcf_hdr_parse_line(hdr, (char*) line, &len);
if ( !hrec ) return -1;
if ( bcf_hdr_add_hrec(hdr, hrec) )
bcf_hdr_sync(hdr);
return 0;
}
void bcf_hdr_remove(bcf_hdr_t *hdr, int type, const char *key)
{
int i;
bcf_hrec_t *hrec;
while (1)
{
if ( type==BCF_HL_FLT || type==BCF_HL_INFO || type==BCF_HL_FMT || type== BCF_HL_CTG )
{
hrec = bcf_hdr_get_hrec(hdr, type, key);
if ( !hrec ) return;
for (i=0; i<hdr->nhrec; i++)
if ( hdr->hrec[i]==hrec ) break;
assert( i<hdr->nhrec );
vdict_t *d = type==BCF_HL_CTG ? (vdict_t*)hdr->dict[BCF_DT_CTG] : (vdict_t*)hdr->dict[BCF_DT_ID];
khint_t k = kh_get(vdict, d, key);
kh_val(d, k).hrec[type==BCF_HL_CTG?0:type] = NULL;
}
else
{
for (i=0; i<hdr->nhrec; i++)
{
if ( hdr->hrec[i]->type!=type ) continue;
if ( !strcmp(hdr->hrec[i]->key,key) ) break;
}
if ( i==hdr->nhrec ) return;
hrec = hdr->hrec[i];
}
hdr->nhrec--;
if ( i < hdr->nhrec )
memmove(&hdr->hrec[i],&hdr->hrec[i+1],(hdr->nhrec-i)*sizeof(bcf_hrec_t*));
bcf_hrec_destroy(hrec);
bcf_hdr_sync(hdr);
}
}
int bcf_hdr_printf(bcf_hdr_t *hdr, const char *fmt, ...)
{
va_list ap;
va_start(ap, fmt);
int n = vsnprintf(NULL, 0, fmt, ap) + 2;
va_end(ap);
char *line = (char*)malloc(n);
va_start(ap, fmt);
vsnprintf(line, n, fmt, ap);
va_end(ap);
int ret = bcf_hdr_append(hdr, line);
free(line);
return ret;
}
/**********************
*** BCF header I/O ***
**********************/
const char *bcf_hdr_get_version(const bcf_hdr_t *hdr)
{
bcf_hrec_t *hrec = bcf_hdr_get_hrec(hdr, BCF_HL_GEN, "fileformat");
if ( !hrec )
{
fprintf(stderr,"No version string found, assuming VCFv4.2\n");
return "VCFv4.2";
}
return hrec->value;
}
void bcf_hdr_set_version(bcf_hdr_t *hdr, const char *version)
{
bcf_hrec_t *hrec = bcf_hdr_get_hrec(hdr, BCF_HL_GEN, "fileformat");
if ( !hrec )
{
int len;
kstring_t str = {0,0,0};
ksprintf(&str,"##fileformat=%s", version);
hrec = bcf_hdr_parse_line(hdr, str.s, &len);
free(str.s);
}
else
{
free(hrec->value);
hrec->value = strdup(version);
}
bcf_hdr_sync(hdr);
}
bcf_hdr_t *bcf_hdr_init(const char *mode)
{
int i;
bcf_hdr_t *h;
h = (bcf_hdr_t*)calloc(1, sizeof(bcf_hdr_t));
for (i = 0; i < 3; ++i)
h->dict[i] = kh_init(vdict);
if ( strchr(mode,'w') )
{
bcf_hdr_append(h, "##fileformat=VCFv4.2");
// The filter PASS must appear first in the dictionary
bcf_hdr_append(h, "##FILTER=<ID=PASS,Description=\"All filters passed\">");
}
return h;
}
void bcf_hdr_destroy(bcf_hdr_t *h)
{
int i;
khint_t k;
for (i = 0; i < 3; ++i) {
vdict_t *d = (vdict_t*)h->dict[i];
if (d == 0) continue;
for (k = kh_begin(d); k != kh_end(d); ++k)
if (kh_exist(d, k)) free((char*)kh_key(d, k));
kh_destroy(vdict, d);
free(h->id[i]);
}
for (i=0; i<h->nhrec; i++)
bcf_hrec_destroy(h->hrec[i]);
if (h->nhrec) free(h->hrec);
if (h->samples) free(h->samples);
free(h->keep_samples);
free(h->transl[0]); free(h->transl[1]);
free(h->mem.s);
free(h);
}
bcf_hdr_t *bcf_hdr_read(htsFile *hfp)
{
if (!hfp->is_bin)
return vcf_hdr_read(hfp);
BGZF *fp = hfp->fp.bgzf;
uint8_t magic[5];
bcf_hdr_t *h;
h = bcf_hdr_init("r");
if ( bgzf_read(fp, magic, 5)<0 )
{
fprintf(stderr,"[%s:%d %s] Failed to read the header (reading BCF in text mode?)\n", __FILE__,__LINE__,__FUNCTION__);
return NULL;
}
if (strncmp((char*)magic, "BCF\2\2", 5) != 0)
{
if (!strncmp((char*)magic, "BCF", 3))
fprintf(stderr,"[%s:%d %s] invalid BCF2 magic string: only BCFv2.2 is supported.\n", __FILE__,__LINE__,__FUNCTION__);
else if (hts_verbose >= 2)
fprintf(stderr, "[E::%s] invalid BCF2 magic string\n", __func__);
bcf_hdr_destroy(h);
return 0;
}
int hlen;
char *htxt;
bgzf_read(fp, &hlen, 4);
htxt = (char*)malloc(hlen);
bgzf_read(fp, htxt, hlen);
bcf_hdr_parse(h, htxt);
free(htxt);
return h;
}
int bcf_hdr_write(htsFile *hfp, const bcf_hdr_t *h)
{
if (!hfp->is_bin) return vcf_hdr_write(hfp, h);
int hlen;
char *htxt = bcf_hdr_fmt_text(h, 1, &hlen);
hlen++; // include the \0 byte
BGZF *fp = hfp->fp.bgzf;
if ( bgzf_write(fp, "BCF\2\2", 5) !=5 ) return -1;
if ( bgzf_write(fp, &hlen, 4) !=4 ) return -1;
if ( bgzf_write(fp, htxt, hlen) != hlen ) return -1;
free(htxt);
return 0;
}
/********************
*** BCF site I/O ***
********************/
bcf1_t *bcf_init1()
{
bcf1_t *v;
v = (bcf1_t*)calloc(1, sizeof(bcf1_t));
return v;
}
void bcf_clear(bcf1_t *v)
{
int i;
for (i=0; i<v->d.m_info; i++)
{
if ( v->d.info[i].vptr_free )
{
free(v->d.info[i].vptr - v->d.info[i].vptr_off);
v->d.info[i].vptr_free = 0;
}
}
for (i=0; i<v->d.m_fmt; i++)
{
if ( v->d.fmt[i].p_free )
{
free(v->d.fmt[i].p - v->d.fmt[i].p_off);
v->d.fmt[i].p_free = 0;
}
}
v->rid = v->pos = v->rlen = v->unpacked = 0;
bcf_float_set_missing(v->qual);
v->n_info = v->n_allele = v->n_fmt = v->n_sample = 0;
v->shared.l = v->indiv.l = 0;
v->d.var_type = -1;
v->d.shared_dirty = 0;
v->d.indiv_dirty = 0;
v->d.n_flt = 0;
v->errcode = 0;
if (v->d.m_als) v->d.als[0] = 0;
if (v->d.m_id) v->d.id[0] = 0;
}
void bcf_empty1(bcf1_t *v)
{
bcf_clear1(v);
free(v->d.id);
free(v->d.als);
free(v->d.allele); free(v->d.flt); free(v->d.info); free(v->d.fmt);
if (v->d.var ) free(v->d.var);
free(v->shared.s); free(v->indiv.s);
}
void bcf_destroy1(bcf1_t *v)
{
bcf_empty1(v);
free(v);
}
static inline int bcf_read1_core(BGZF *fp, bcf1_t *v)
{
uint32_t x[8];
int ret;
if ((ret = bgzf_read(fp, x, 32)) != 32) {
if (ret == 0) return -1;
return -2;
}
bcf_clear1(v);
x[0] -= 24; // to exclude six 32-bit integers
ks_resize(&v->shared, x[0]);
ks_resize(&v->indiv, x[1]);
memcpy(v, x + 2, 16);
v->n_allele = x[6]>>16; v->n_info = x[6]&0xffff;
v->n_fmt = x[7]>>24; v->n_sample = x[7]&0xffffff;
v->shared.l = x[0], v->indiv.l = x[1];
// silent fix of broken BCFs produced by earlier versions of bcf_subset, prior to and including bd6ed8b4
if ( (!v->indiv.l || !v->n_sample) && v->n_fmt ) v->n_fmt = 0;
bgzf_read(fp, v->shared.s, v->shared.l);
bgzf_read(fp, v->indiv.s, v->indiv.l);
return 0;
}
#define bit_array_size(n) ((n)/8+1)
#define bit_array_set(a,i) ((a)[(i)/8] |= 1 << ((i)%8))
#define bit_array_clear(a,i) ((a)[(i)/8] &= ~(1 << ((i)%8)))
#define bit_array_test(a,i) ((a)[(i)/8] & (1 << ((i)%8)))
static inline uint8_t *bcf_unpack_fmt_core1(uint8_t *ptr, int n_sample, bcf_fmt_t *fmt);
int bcf_subset_format(const bcf_hdr_t *hdr, bcf1_t *rec)
{
if ( !hdr->keep_samples ) return 0;
if ( !bcf_hdr_nsamples(hdr) )
{
rec->indiv.l = rec->n_sample = 0;
return 0;
}
int i, j;
uint8_t *ptr = (uint8_t*)rec->indiv.s, *dst = NULL, *src;
bcf_dec_t *dec = &rec->d;
hts_expand(bcf_fmt_t, rec->n_fmt, dec->m_fmt, dec->fmt);
for (i=0; i<dec->m_fmt; ++i) dec->fmt[i].p_free = 0;
for (i=0; i<rec->n_fmt; i++)
{
ptr = bcf_unpack_fmt_core1(ptr, rec->n_sample, &dec->fmt[i]);
src = dec->fmt[i].p - dec->fmt[i].size;
if ( dst )
{
memmove(dec->fmt[i-1].p + dec->fmt[i-1].p_len, dec->fmt[i].p - dec->fmt[i].p_off, dec->fmt[i].p_off);
dec->fmt[i].p = dec->fmt[i-1].p + dec->fmt[i-1].p_len + dec->fmt[i].p_off;
}
dst = dec->fmt[i].p;
for (j=0; j<hdr->nsamples_ori; j++)
{
src += dec->fmt[i].size;
if ( !bit_array_test(hdr->keep_samples,j) ) continue;
memmove(dst, src, dec->fmt[i].size);
dst += dec->fmt[i].size;
}
rec->indiv.l -= dec->fmt[i].p_len - (dst - dec->fmt[i].p);
dec->fmt[i].p_len = dst - dec->fmt[i].p;
}
rec->unpacked |= BCF_UN_FMT;
rec->n_sample = bcf_hdr_nsamples(hdr);
return 0;
}
int bcf_read(htsFile *fp, const bcf_hdr_t *h, bcf1_t *v)
{
if (!fp->is_bin) return vcf_read(fp,h,v);
int ret = bcf_read1_core(fp->fp.bgzf, v);
if ( ret!=0 || !h->keep_samples ) return ret;
return bcf_subset_format(h,v);
}
int bcf_readrec(BGZF *fp, void *null, void *vv, int *tid, int *beg, int *end)
{
bcf1_t *v = (bcf1_t *) vv;
int ret;
if ((ret = bcf_read1_core(fp, v)) >= 0)
*tid = v->rid, *beg = v->pos, *end = v->pos + v->rlen;
return ret;
}
static inline void bcf1_sync_id(bcf1_t *line, kstring_t *str)
{
// single typed string
if ( line->d.id && strcmp(line->d.id, ".") ) bcf_enc_vchar(str, strlen(line->d.id), line->d.id);
else bcf_enc_size(str, 0, BCF_BT_CHAR);
}
static inline void bcf1_sync_alleles(bcf1_t *line, kstring_t *str)
{
// list of typed strings
int i;
for (i=0; i<line->n_allele; i++)
bcf_enc_vchar(str, strlen(line->d.allele[i]), line->d.allele[i]);
if ( !line->rlen && line->n_allele ) line->rlen = strlen(line->d.allele[0]);
}
static inline void bcf1_sync_filter(bcf1_t *line, kstring_t *str)
{
// typed vector of integers
if ( line->d.n_flt ) bcf_enc_vint(str, line->d.n_flt, line->d.flt, -1);
else bcf_enc_vint(str, 0, 0, -1);
}
static inline void bcf1_sync_info(bcf1_t *line, kstring_t *str)
{
// pairs of typed vectors
int i, irm = -1;
for (i=0; i<line->n_info; i++)
{
bcf_info_t *info = &line->d.info[i];
if ( !info->vptr )
{
// marked for removal
if ( irm < 0 ) irm = i;
continue;
}
kputsn_(info->vptr - info->vptr_off, info->vptr_len + info->vptr_off, str);
if ( irm >=0 )
{
bcf_info_t tmp = line->d.info[irm]; line->d.info[irm] = line->d.info[i]; line->d.info[i] = tmp;
while ( irm<=i && line->d.info[irm].vptr ) irm++;
}
}
if ( irm>=0 ) line->n_info = irm;
}
static int bcf1_sync(bcf1_t *line)
{
char *shared_ori = line->shared.s;
size_t prev_len;
kstring_t tmp = {0,0,0};
if ( !line->shared.l )
{
// New line created via API, BCF data blocks do not exist. Get it ready for BCF output
tmp = line->shared;
bcf1_sync_id(line, &tmp);
line->unpack_size[0] = tmp.l; prev_len = tmp.l;
bcf1_sync_alleles(line, &tmp);
line->unpack_size[1] = tmp.l - prev_len; prev_len = tmp.l;
bcf1_sync_filter(line, &tmp);
line->unpack_size[2] = tmp.l - prev_len;
bcf1_sync_info(line, &tmp);
line->shared = tmp;
}
else if ( line->d.shared_dirty )
{
// The line was edited, update the BCF data block, ptr_ori points
// to the original unchanged BCF data.
uint8_t *ptr_ori = (uint8_t *) line->shared.s;
assert( line->unpacked & BCF_UN_STR );
// ID: single typed string
if ( line->d.shared_dirty & BCF1_DIRTY_ID )
bcf1_sync_id(line, &tmp);
else
kputsn_(ptr_ori, line->unpack_size[0], &tmp);
ptr_ori += line->unpack_size[0];
line->unpack_size[0] = tmp.l; prev_len = tmp.l;
// REF+ALT: list of typed strings
if ( line->d.shared_dirty & BCF1_DIRTY_ALS )
bcf1_sync_alleles(line, &tmp);
else
{
kputsn_(ptr_ori, line->unpack_size[1], &tmp);
if ( !line->rlen && line->n_allele ) line->rlen = strlen(line->d.allele[0]);
}
ptr_ori += line->unpack_size[1];
line->unpack_size[1] = tmp.l - prev_len; prev_len = tmp.l;
if ( line->unpacked & BCF_UN_FLT )
{
// FILTER: typed vector of integers
if ( line->d.shared_dirty & BCF1_DIRTY_FLT )
bcf1_sync_filter(line, &tmp);
else if ( line->d.n_flt )
kputsn_(ptr_ori, line->unpack_size[2], &tmp);
else
bcf_enc_vint(&tmp, 0, 0, -1);
ptr_ori += line->unpack_size[2];
line->unpack_size[2] = tmp.l - prev_len;
if ( line->unpacked & BCF_UN_INFO )
{
// INFO: pairs of typed vectors
if ( line->d.shared_dirty & BCF1_DIRTY_INF )
{
bcf1_sync_info(line, &tmp);
ptr_ori = (uint8_t*)line->shared.s + line->shared.l;
}
}
}
int size = line->shared.l - (size_t)ptr_ori + (size_t)line->shared.s;
if ( size ) kputsn_(ptr_ori, size, &tmp);
free(line->shared.s);