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vcf.c
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/* vcf.c -- VCF/BCF API functions.
Copyright (C) 2012, 2013 Broad Institute.
Copyright (C) 2012-2017 Genome Research Ltd.
Portions copyright (C) 2014 Intel Corporation.
Author: Heng Li <[email protected]>
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
DEALINGS IN THE SOFTWARE. */
#include <config.h>
#include <stdio.h>
#include <assert.h>
#include <string.h>
#include <strings.h>
#include <stdlib.h>
#include <limits.h>
#include <stdint.h>
#include <errno.h>
#include "htslib/vcf.h"
#include "htslib/bgzf.h"
#include "htslib/tbx.h"
#include "htslib/hfile.h"
#include "hts_internal.h"
#include "htslib/hts_endian.h"
#include "htslib/khash_str2int.h"
#include "htslib/kstring.h"
#include "htslib/khash.h"
KHASH_MAP_INIT_STR(vdict, bcf_idinfo_t)
typedef khash_t(vdict) vdict_t;
#include "htslib/kseq.h"
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 };
static const char *dump_char(char *buffer, char c)
{
switch (c) {
case '\n': strcpy(buffer, "\\n"); break;
case '\r': strcpy(buffer, "\\r"); break;
case '\t': strcpy(buffer, "\\t"); break;
case '\'':
case '\"':
case '\\':
sprintf(buffer, "\\%c", c);
break;
default:
if (isprint_c(c)) sprintf(buffer, "%c", c);
else sprintf(buffer, "\\x%02X", (unsigned char) c);
break;
}
return buffer;
}
static char *find_chrom_header_line(char *s)
{
char *nl;
if (strncmp(s, "#CHROM\t", 7) == 0) return s;
else if ((nl = strstr(s, "\n#CHROM\t")) != NULL) return nl+1;
else return NULL;
}
/*************************
*** VCF header parser ***
*************************/
int bcf_hdr_add_sample(bcf_hdr_t *h, const char *s)
{
if ( !s ) return 0;
const char *ss = s;
while ( !*ss && isspace_c(*ss) ) ss++;
if ( !*ss )
{
hts_log_error("Empty sample name: trailing spaces/tabs in the header line?");
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 {
hts_log_error("Duplicated sample name '%s'", s);
free(sdup);
return -1;
}
int n = kh_size(d);
h->samples = (char**) realloc(h->samples,sizeof(char*)*n);
h->samples[n-1] = sdup;
h->dirty = 1;
return 0;
}
int bcf_hdr_parse_sample_line(bcf_hdr_t *h, const char *str)
{
int ret = 0;
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;
if ( bcf_hdr_add_sample(h,s) < 0 ) ret = -1;
free(s);
}
if (*q == 0 || *q == '\n') break;
p = q + 1;
}
bcf_hdr_add_sample(h,NULL);
return ret;
}
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;
if ( h->n[i] < kh_size(d) )
{
// this should be true only for i=2, BCF_DT_SAMPLE
h->n[i] = kh_size(d);
h->id[i] = (bcf_idpair_t*) realloc(h->id[i], kh_size(d)*sizeof(bcf_idpair_t));
}
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);
}
}
h->dirty = 0;
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 -= i-j; // 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 != '\n' ) 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 + (*q ? 1 : 0); // Skip \n but not \0
return hrec;
}
// structured line, e.g.
// ##INFO=<ID=PV1,Number=1,Type=Float,Description="P-value for baseQ bias">
// ##PEDIGREE=<Name_0=G0-ID,Name_1=G1-ID,Name_3=GN-ID>
int nopen = 1;
while ( *q && *q!='\n' && nopen>0 )
{
p = ++q;
while ( *q && *q==' ' ) { p++; q++; }
// ^[A-Za-z_][0-9A-Za-z_.]*$
if (p==q && *q && (isalpha_c(*q) || *q=='_'))
{
q++;
while ( *q && (isalnum_c(*q) || *q=='_' || *q=='.') ) q++;
}
n = q-p;
int m = 0;
while ( *q && *q==' ' ) { q++; m++; }
if ( *q!='=' || !n )
{
// wrong format
while ( *q && *q!='\n' ) q++;
hts_log_error("Could not parse the header line: \"%.*s\"",
(int) (q - line), line);
*len = q - line + (*q ? 1 : 0);
bcf_hrec_destroy(hrec);
return NULL;
}
bcf_hrec_add_key(hrec, p, q-p-m);
p = ++q;
while ( *q && *q==' ' ) { p++; q++; }
int quoted = *p=='"' ? 1 : 0;
if ( quoted ) p++, q++;
while ( *q && *q != '\n' )
{
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++;
}
const char *r = q;
while ( r > p && r[-1] == ' ' ) r--;
bcf_hrec_set_val(hrec, hrec->nkeys-1, p, r-p, quoted);
if ( quoted && *q=='"' ) q++;
if ( *q=='>' ) { nopen--; q++; }
}
// Skip to end of line
int nonspace = 0;
p = q;
while ( *q && *q!='\n' ) { nonspace |= !isspace_c(*q); q++; }
if (nonspace) {
hts_log_warning("Dropped trailing junk from header line '%.*s'", (int) (q - line), line);
}
*len = q - line + (*q ? 1 : 0);
return hrec;
}
static int bcf_hdr_set_idx(bcf_hdr_t *hdr, int dict_type, const char *tag, bcf_idinfo_t *idinfo)
{
// If available, preserve existing IDX
if ( idinfo->id==-1 )
idinfo->id = hdr->n[dict_type]++;
else if ( idinfo->id < hdr->n[dict_type] && hdr->id[dict_type][idinfo->id].key )
{
hts_log_error("Conflicting IDX=%d lines in the header dictionary, the new tag is %s",
idinfo->id, tag);
exit(1);
}
if ( idinfo->id >= hdr->n[dict_type] ) hdr->n[dict_type] = idinfo->id+1;
hts_expand0(bcf_idpair_t,hdr->n[dict_type],hdr->m[dict_type],hdr->id[dict_type]);
// NB: the next kh_put call can invalidate the idinfo pointer, therefore
// we leave it unassigned here. It myst be set explicitly in bcf_hdr_sync.
hdr->id[dict_type][idinfo->id].key = tag;
return 0;
}
// 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, ret;
khint_t k;
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 ) j = 0;
else 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];
khint_t k = kh_get(vdict, d, str);
if ( k != kh_end(d) ) { free(str); return 0; } // already present
k = kh_put(vdict, d, str, &ret);
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 || idx < 0 || idx >= INT_MAX - 1)
{
hts_log_warning("Error parsing the IDX tag, skipping");
return 0;
}
}
kh_val(d, k) = bcf_idinfo_def;
kh_val(d, k).id = idx;
kh_val(d, k).info[0] = j;
kh_val(d, k).hrec[0] = hrec;
bcf_hdr_set_idx(hdr, BCF_DT_CTG, kh_key(d,k), &kh_val(d,k));
if ( idx==-1 ) hrec_add_idx(hrec, kh_val(d,k).id);
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;
uint32_t type = UINT32_MAX, var = UINT32_MAX;
int num = -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 || idx < 0 || idx >= INT_MAX - 1)
{
hts_log_warning("Error parsing the IDX tag, skipping");
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], "Character") ) type = BCF_HT_STR;
else if ( !strcmp(hrec->vals[i], "Flag") ) type = BCF_HT_FLAG;
else
{
hts_log_warning("The type \"%s\" is not supported, assuming \"String\"", 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;
}
}
if (hrec->type == BCF_HL_INFO || hrec->type == BCF_HL_FMT) {
if (type == -1) {
hts_log_warning("%s %s field has no Type defined. Assuming String",
*hrec->key == 'I' ? "An" : "A", hrec->key);
type = BCF_HT_STR;
}
if (var == -1) {
hts_log_warning("%s %s field has no Number defined. Assuming '.'",
*hrec->key == 'I' ? "An" : "A", hrec->key);
var = BCF_VL_VAR;
}
}
uint32_t info = ((((uint32_t)num) & 0xfffff)<<12 |
(var & 0xf) << 8 |
(type & 0xf) << 4 |
(((uint32_t) hrec->type) & 0xf));
if ( !id ) return 0;
str = strdup(id);
vdict_t *d = (vdict_t*)hdr->dict[BCF_DT_ID];
k = kh_get(vdict, d, str);
if ( k != kh_end(d) )
{
// 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;
if ( idx==-1 ) hrec_add_idx(hrec, kh_val(d, k).id);
return 1;
}
k = kh_put(vdict, d, str, &ret);
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;
bcf_hdr_set_idx(hdr, BCF_DT_ID, kh_key(d,k), &kh_val(d,k));
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;
hdr->dirty = 1;
return hrec->type==BCF_HL_GEN ? 0 : 1;
}
/*
* Note that while querying of FLT,INFO,FMT,CTG lines is fast (the keys are hashed),
* the STR,GEN lines are searched for linearly in a linked list of all header lines.
* This may become a problem for VCFs with huge headers, we might need to build a
* dictionary for these lines as well.
*/
bcf_hrec_t *bcf_hdr_get_hrec(const bcf_hdr_t *hdr, int type, const char *key, const char *value, const char *str_class)
{
int i;
if ( type==BCF_HL_GEN )
{
for (i=0; i<hdr->nhrec; i++)
{
if ( hdr->hrec[i]->type!=type ) continue;
if ( strcmp(hdr->hrec[i]->key,key) ) continue;
if ( !value || !strcmp(hdr->hrec[i]->value,value) ) return hdr->hrec[i];
}
return NULL;
}
else if ( type==BCF_HL_STR )
{
for (i=0; i<hdr->nhrec; i++)
{
if ( hdr->hrec[i]->type!=type ) continue;
if ( strcmp(hdr->hrec[i]->key,str_class) ) continue;
int j = bcf_hrec_find_key(hdr->hrec[i],key);
if ( j>=0 && !strcmp(hdr->hrec[i]->vals[j],value) ) 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, value);
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 )
{
hts_log_warning("PL should be declared as Number=G");
PL_warned = 1;
}
}
if ( !GL_warned )
{
int id = bcf_hdr_id2int(hdr, BCF_DT_ID, "GL");
if ( bcf_hdr_idinfo_exists(hdr,BCF_HL_FMT,id) && bcf_hdr_id2length(hdr,BCF_HL_FMT,id)!=BCF_VL_G )
{
hts_log_warning("GL should be declared as Number=G");
GL_warned = 1;
}
}
}
int bcf_hdr_parse(bcf_hdr_t *hdr, char *htxt)
{
int len, needs_sync = 0, done = 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") )
hts_log_warning("The first line should be ##fileformat; is the VCF/BCF header broken?");
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
do {
while (NULL != (hrec = bcf_hdr_parse_line(hdr, p, &len))) {
needs_sync += bcf_hdr_add_hrec(hdr, hrec);
p += len;
}
// Next should be the sample line. If not, it was a malformed
// header, in which case print a warning and skip (many VCF
// operations do not really care about a few malformed lines).
// In the future we may want to add a strict mode that errors in
// this case.
if ( strncmp("#CHROM\tPOS",p,10) != 0 ) {
char *eol = strchr(p, '\n');
if (*p != '\0') {
hts_log_warning("Could not parse header line: %.*s",
eol ? (int)(eol - p) : INT_MAX, p);
}
if (eol) {
p = eol + 1; // Try from the next line.
} else {
done = -1; // No more lines left, give up.
}
} else {
done = 1; // Sample line found
}
} while (!done);
if (done < 0) {
// No sample line is fatal.
hts_log_error("Could not parse the header, sample line not found");
return -1;
}
int ret = bcf_hdr_parse_sample_line(hdr,p);
bcf_hdr_sync(hdr);
bcf_hdr_check_sanity(hdr);
return ret;
}
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;
bcf_hdr_add_hrec(hdr, hrec);
return 0;
}
void bcf_hdr_remove(bcf_hdr_t *hdr, int type, const char *key)
{
int i = 0;
bcf_hrec_t *hrec;
if ( !key )
{
while ( i<hdr->nhrec )
{
if ( hdr->hrec[i]->type!=type ) { i++; continue; }
hrec = hdr->hrec[i];
if ( type==BCF_HL_FLT || type==BCF_HL_INFO || type==BCF_HL_FMT || type== BCF_HL_CTG )
{
int j = bcf_hrec_find_key(hdr->hrec[i], "ID");
if ( j>=0 )
{
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, hdr->hrec[i]->vals[j]);
kh_val(d, k).hrec[type==BCF_HL_CTG?0:type] = NULL;
}
}
hdr->dirty = 1;
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);
}
return;
}
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, "ID", key, NULL);
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 ( type==BCF_HL_GEN )
{
if ( !strcmp(hdr->hrec[i]->key,key) ) break;
}
else
{
// not all structured lines have ID, we could be more sophisticated as in bcf_hdr_get_hrec()
int j = bcf_hrec_find_key(hdr->hrec[i], "ID");
if ( j>=0 && !strcmp(hdr->hrec[i]->vals[j],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);
hdr->dirty = 1;
}
}
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", NULL, NULL);
if ( !hrec )
{
hts_log_warning("No version string found, assuming VCFv4.2");
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", NULL, NULL);
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);
}
hdr->dirty = 1;
}
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));
if (!h) return NULL;
for (i = 0; i < 3; ++i)
if ((h->dict[i] = kh_init(vdict)) == NULL) goto fail;
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;
fail:
for (i = 0; i < 3; ++i)
kh_destroy(vdict, h->dict[i]);
free(h);
return NULL;
}
void bcf_hdr_destroy(bcf_hdr_t *h)
{
int i;
khint_t k;
if (!h) return;
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->format.format == vcf)
return vcf_hdr_read(hfp);
if (hfp->format.format != bcf) {
hts_log_error("Input is not detected as bcf or vcf format");
return NULL;
}
assert(hfp->is_bgzf);
BGZF *fp = hfp->fp.bgzf;
uint8_t magic[5];
bcf_hdr_t *h;
h = bcf_hdr_init("r");
if (!h) {
hts_log_error("Failed to allocate bcf header");
return NULL;
}
if (bgzf_read(fp, magic, 5) != 5)
{
hts_log_error("Failed to read the header (reading BCF in text mode?)");
bcf_hdr_destroy(h);
return NULL;
}
if (strncmp((char*)magic, "BCF\2\2", 5) != 0)
{
if (!strncmp((char*)magic, "BCF", 3))
hts_log_error("Invalid BCF2 magic string: only BCFv2.2 is supported");
else
hts_log_error("Invalid BCF2 magic string");
bcf_hdr_destroy(h);
return NULL;
}
uint8_t buf[4];
size_t hlen;
char *htxt = NULL;
if (bgzf_read(fp, buf, 4) != 4) goto fail;
hlen = buf[0] | (buf[1] << 8) | (buf[2] << 16) | (buf[3] << 24);
if (hlen >= SIZE_MAX) { errno = ENOMEM; goto fail; }
htxt = (char*)malloc(hlen + 1);
if (!htxt) goto fail;
if (bgzf_read(fp, htxt, hlen) != hlen) goto fail;
htxt[hlen] = '\0'; // Ensure htxt is terminated
if ( bcf_hdr_parse(h, htxt) < 0 ) goto fail;
free(htxt);
return h;
fail:
hts_log_error("Failed to read BCF header");
free(htxt);
bcf_hdr_destroy(h);
return NULL;
}
int bcf_hdr_write(htsFile *hfp, bcf_hdr_t *h)
{
if (!h) {
errno = EINVAL;
return -1;
}
if ( h->dirty ) bcf_hdr_sync(h);
if (hfp->format.format == vcf || hfp->format.format == text_format)
return vcf_hdr_write(hfp, h);
kstring_t htxt = {0,0,0};
bcf_hdr_format(h, 1, &htxt);
kputc('\0', &htxt); // include the \0 byte
BGZF *fp = hfp->fp.bgzf;
if ( bgzf_write(fp, "BCF\2\2", 5) !=5 ) return -1;
uint8_t hlen[4];
u32_to_le(htxt.l, hlen);
if ( bgzf_write(fp, hlen, 4) !=4 ) return -1;
if ( bgzf_write(fp, htxt.s, htxt.l) != htxt.l ) return -1;
free(htxt.s);
return 0;
}
/********************
*** BCF site I/O ***
********************/
bcf1_t *bcf_init()
{
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_empty(bcf1_t *v)
{
bcf_clear1(v);
free(v->d.id);