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vcf.c
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vcf.c
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/* vcf.c -- VCF/BCF API functions.
Copyright (C) 2012, 2013 Broad Institute.
Copyright (C) 2012-2024 Genome Research Ltd.
Portions copyright (C) 2014 Intel Corporation.
Author: Heng Li <lh3@sanger.ac.uk>
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. */
#define HTS_BUILDING_LIBRARY // Enables HTSLIB_EXPORT, see htslib/hts_defs.h
#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 <inttypes.h>
#include <errno.h>
#ifdef FUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION
#include "fuzz_settings.h"
#endif
#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/sam.h"
#include "htslib/khash.h"
#if 0
// This helps on Intel a bit, often 6-7% faster VCF parsing.
// Conversely sometimes harms AMD Zen4 as ~9% slower.
// Possibly related to IPC differences. However for now it's just a
// curiousity we ignore and stick with the simpler code.
//
// Left here as a hint for future explorers.
static inline int xstreq(const char *a, const char *b) {
while (*a && *a == *b)
a++, b++;
return *a == *b;
}
#define KHASH_MAP_INIT_XSTR(name, khval_t) \
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, xstreq)
KHASH_MAP_INIT_XSTR(vdict, bcf_idinfo_t)
#else
KHASH_MAP_INIT_STR(vdict, bcf_idinfo_t)
#endif
typedef khash_t(vdict) vdict_t;
KHASH_MAP_INIT_STR(hdict, bcf_hrec_t*)
typedef khash_t(hdict) hdict_t;
#include "htslib/kseq.h"
HTSLIB_EXPORT
uint32_t bcf_float_missing = 0x7F800001;
HTSLIB_EXPORT
uint32_t bcf_float_vector_end = 0x7F800002;
HTSLIB_EXPORT
uint8_t bcf_type_shift[] = { 0, 0, 1, 2, 3, 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 };
/*
Partial support for 64-bit POS and Number=1 INFO tags.
Notes:
- the support for 64-bit values is motivated by POS and INFO/END for large genomes
- the use of 64-bit values does not conform to the specification
- cannot output 64-bit BCF and if it does, it is not compatible with anything
- experimental, use at your risk
*/
#ifdef VCF_ALLOW_INT64
#define BCF_MAX_BT_INT64 (0x7fffffffffffffff) /* INT64_MAX, for internal use only */
#define BCF_MIN_BT_INT64 -9223372036854775800LL /* INT64_MIN + 8, for internal use only */
#endif
#define BCF_IS_64BIT (1<<30)
// Opaque structure with auxilary data which allows to extend bcf_hdr_t without breaking ABI.
// Note that this preserving API and ABI requires that the first element is vdict_t struct
// rather than a pointer, as user programs may (and in some cases do) access the dictionary
// directly as (vdict_t*)hdr->dict.
typedef struct
{
vdict_t dict; // bcf_hdr_t.dict[0] vdict_t dictionary which keeps bcf_idinfo_t for BCF_HL_FLT,BCF_HL_INFO,BCF_HL_FMT
hdict_t *gen; // hdict_t dictionary which keeps bcf_hrec_t* pointers for generic and structured fields
size_t *key_len;// length of h->id[BCF_DT_ID] strings
}
bcf_hdr_aux_t;
static inline bcf_hdr_aux_t *get_hdr_aux(const bcf_hdr_t *hdr)
{
return (bcf_hdr_aux_t *)hdr->dict[0];
}
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 ***
*************************/
static int bcf_hdr_add_sample_len(bcf_hdr_t *h, const char *s, size_t len)
{
const char *ss = s;
while ( *ss && isspace_c(*ss) && ss - s < len) ss++;
if ( !*ss || ss - s == len)
{
hts_log_error("Empty sample name: trailing spaces/tabs in the header line?");
return -1;
}
vdict_t *d = (vdict_t*)h->dict[BCF_DT_SAMPLE];
int ret;
char *sdup = malloc(len + 1);
if (!sdup) return -1;
memcpy(sdup, s, len);
sdup[len] = 0;
// Ensure space is available in h->samples
size_t n = kh_size(d);
char **new_samples = realloc(h->samples, sizeof(char*) * (n + 1));
if (!new_samples) {
free(sdup);
return -1;
}
h->samples = new_samples;
int k = kh_put(vdict, d, sdup, &ret);
if (ret < 0) {
free(sdup);
return -1;
}
if (ret) { // absent
kh_val(d, k) = bcf_idinfo_def;
kh_val(d, k).id = n;
} else {
hts_log_error("Duplicated sample name '%s'", sdup);
free(sdup);
return -1;
}
h->samples[n] = sdup;
h->dirty = 1;
return 0;
}
int bcf_hdr_add_sample(bcf_hdr_t *h, const char *s)
{
if (!s) {
// Allowed for backwards-compatibility, calling with s == NULL
// used to trigger bcf_hdr_sync(h);
return 0;
}
return bcf_hdr_add_sample_len(h, s, strlen(s));
}
int HTS_RESULT_USED bcf_hdr_parse_sample_line(bcf_hdr_t *hdr, const char *str)
{
const char *mandatory = "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO";
if ( strncmp(str,mandatory,strlen(mandatory)) )
{
hts_log_error("Could not parse the \"#CHROM..\" line, either the fields are incorrect or spaces are present instead of tabs:\n\t%s",str);
return -1;
}
const char *beg = str + strlen(mandatory), *end;
if ( !*beg || *beg=='\n' ) return 0;
if ( strncmp(beg,"\tFORMAT\t",8) )
{
hts_log_error("Could not parse the \"#CHROM..\" line, either FORMAT is missing or spaces are present instead of tabs:\n\t%s",str);
return -1;
}
beg += 8;
int ret = 0;
while ( *beg )
{
end = beg;
while ( *end && *end!='\t' && *end!='\n' ) end++;
if ( bcf_hdr_add_sample_len(hdr, beg, end-beg) < 0 ) ret = -1;
if ( !*end || *end=='\n' || ret<0 ) break;
beg = end + 1;
}
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) )
{
bcf_idpair_t *new_idpair;
// this should be true only for i=2, BCF_DT_SAMPLE
new_idpair = (bcf_idpair_t*) realloc(h->id[i], kh_size(d)*sizeof(bcf_idpair_t));
if (!new_idpair) return -1;
h->n[i] = kh_size(d);
h->id[i] = new_idpair;
}
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);
}
}
// Invalidate key length cache
bcf_hdr_aux_t *aux = get_hdr_aux(h);
if (aux && aux->key_len) {
free(aux->key_len);
aux->key_len = NULL;
}
h->dirty = 0;
return 0;
}
void bcf_hrec_destroy(bcf_hrec_t *hrec)
{
if (!hrec) return;
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)
{
int save_errno;
bcf_hrec_t *out = (bcf_hrec_t*) calloc(1,sizeof(bcf_hrec_t));
if (!out) return NULL;
out->type = hrec->type;
if ( hrec->key ) {
out->key = strdup(hrec->key);
if (!out->key) goto fail;
}
if ( hrec->value ) {
out->value = strdup(hrec->value);
if (!out->value) goto fail;
}
out->nkeys = hrec->nkeys;
out->keys = (char**) malloc(sizeof(char*)*hrec->nkeys);
if (!out->keys) goto fail;
out->vals = (char**) malloc(sizeof(char*)*hrec->nkeys);
if (!out->vals) goto fail;
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 (!out->keys[j]) goto fail;
}
if ( hrec->vals[i] ) {
out->vals[j] = strdup(hrec->vals[i]);
if (!out->vals[j]) goto fail;
}
j++;
}
if ( i!=j ) out->nkeys -= i-j; // IDX was omitted
return out;
fail:
save_errno = errno;
hts_log_error("%s", strerror(errno));
bcf_hrec_destroy(out);
errno = save_errno;
return NULL;
}
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);
}
}
int bcf_hrec_add_key(bcf_hrec_t *hrec, const char *str, size_t len)
{
char **tmp;
size_t n = hrec->nkeys + 1;
assert(len > 0 && len < SIZE_MAX);
tmp = realloc(hrec->keys, sizeof(char*)*n);
if (!tmp) return -1;
hrec->keys = tmp;
tmp = realloc(hrec->vals, sizeof(char*)*n);
if (!tmp) return -1;
hrec->vals = tmp;
hrec->keys[hrec->nkeys] = (char*) malloc((len+1)*sizeof(char));
if (!hrec->keys[hrec->nkeys]) return -1;
memcpy(hrec->keys[hrec->nkeys],str,len);
hrec->keys[hrec->nkeys][len] = 0;
hrec->vals[hrec->nkeys] = NULL;
hrec->nkeys = n;
return 0;
}
int bcf_hrec_set_val(bcf_hrec_t *hrec, int i, const char *str, size_t len, int is_quoted)
{
if ( hrec->vals[i] ) {
free(hrec->vals[i]);
hrec->vals[i] = NULL;
}
if ( !str ) return 0;
if ( is_quoted )
{
if (len >= SIZE_MAX - 3) {
errno = ENOMEM;
return -1;
}
hrec->vals[i] = (char*) malloc((len+3)*sizeof(char));
if (!hrec->vals[i]) return -1;
hrec->vals[i][0] = '"';
memcpy(&hrec->vals[i][1],str,len);
hrec->vals[i][len+1] = '"';
hrec->vals[i][len+2] = 0;
}
else
{
if (len == SIZE_MAX) {
errno = ENOMEM;
return -1;
}
hrec->vals[i] = (char*) malloc((len+1)*sizeof(char));
if (!hrec->vals[i]) return -1;
memcpy(hrec->vals[i],str,len);
hrec->vals[i][len] = 0;
}
return 0;
}
int hrec_add_idx(bcf_hrec_t *hrec, int idx)
{
int n = hrec->nkeys + 1;
char **tmp = (char**) realloc(hrec->keys, sizeof(char*)*n);
if (!tmp) return -1;
hrec->keys = tmp;
tmp = (char**) realloc(hrec->vals, sizeof(char*)*n);
if (!tmp) return -1;
hrec->vals = tmp;
hrec->keys[hrec->nkeys] = strdup("IDX");
if (!hrec->keys[hrec->nkeys]) return -1;
kstring_t str = {0,0,0};
if (kputw(idx, &str) < 0) {
free(hrec->keys[hrec->nkeys]);
return -1;
}
hrec->vals[hrec->nkeys] = str.s;
hrec->nkeys = n;
return 0;
}
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 void bcf_hrec_set_type(bcf_hrec_t *hrec)
{
if ( !strcmp(hrec->key, "contig") ) hrec->type = BCF_HL_CTG;
else 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;
else hrec->type = BCF_HL_GEN;
}
/**
The arrays were generated with
valid_ctg:
perl -le '@v = (split(//,q[!#$%&*+./:;=?@^_|~-]),"a"..."z","A"..."Z","0"..."9"); @a = (0) x 256; foreach $c (@v) { $a[ord($c)] = 1; } print join(", ",@a)' | fold -w 48
valid_tag:
perl -le '@v = (split(//,q[_.]),"a"..."z","A"..."Z","0"..."9"); @a = (0) x 256; foreach $c (@v) { $a[ord($c)] = 1; } print join(", ",@a)' | fold -w 48
*/
static const uint8_t valid_ctg[256] =
{
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 1, 0, 1, 1, 1, 1, 0, 0, 0, 1, 1, 0, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 0, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1,
0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 0, 1, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
};
static const uint8_t valid_tag[256] =
{
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0,
0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 1,
0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
};
/**
bcf_hrec_check() - check the validity of structured header lines
Returns 0 on success or negative value on error.
Currently the return status is not checked by the caller
and only a warning is printed on stderr. This should be improved
to propagate the error all the way up to the caller and let it
decide what to do: throw an error or proceed anyway.
*/
static int bcf_hrec_check(bcf_hrec_t *hrec)
{
int i;
bcf_hrec_set_type(hrec);
if ( hrec->type==BCF_HL_CTG )
{
i = bcf_hrec_find_key(hrec,"ID");
if ( i<0 ) goto err_missing_id;
char *val = hrec->vals[i];
if ( val[0]=='*' || val[0]=='=' || !valid_ctg[(uint8_t)val[0]] ) goto err_invalid_ctg;
while ( *(++val) )
if ( !valid_ctg[(uint8_t)*val] ) goto err_invalid_ctg;
return 0;
}
if ( hrec->type==BCF_HL_INFO )
{
i = bcf_hrec_find_key(hrec,"ID");
if ( i<0 ) goto err_missing_id;
char *val = hrec->vals[i];
if ( !strcmp(val,"1000G") ) return 0;
if ( val[0]=='.' || (val[0]>='0' && val[0]<='9') || !valid_tag[(uint8_t)val[0]] ) goto err_invalid_tag;
while ( *(++val) )
if ( !valid_tag[(uint8_t)*val] ) goto err_invalid_tag;
return 0;
}
if ( hrec->type==BCF_HL_FMT )
{
i = bcf_hrec_find_key(hrec,"ID");
if ( i<0 ) goto err_missing_id;
char *val = hrec->vals[i];
if ( val[0]=='.' || (val[0]>='0' && val[0]<='9') || !valid_tag[(uint8_t)val[0]] ) goto err_invalid_tag;
while ( *(++val) )
if ( !valid_tag[(uint8_t)*val] ) goto err_invalid_tag;
return 0;
}
return 0;
err_missing_id:
hts_log_warning("Missing ID attribute in one or more header lines");
return -1;
err_invalid_ctg:
hts_log_warning("Invalid contig name: \"%s\"", hrec->vals[i]);
return -1;
err_invalid_tag:
hts_log_warning("Invalid tag name: \"%s\"", hrec->vals[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)
{
bcf_hrec_t *hrec = NULL;
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++;
ptrdiff_t n = q-p;
if ( *q!='=' || !n ) // wrong format
goto malformed_line;
hrec = (bcf_hrec_t*) calloc(1,sizeof(bcf_hrec_t));
if (!hrec) { *len = -1; return NULL; }
hrec->key = (char*) malloc(sizeof(char)*(n+1));
if (!hrec->key) goto fail;
memcpy(hrec->key,p,n);
hrec->key[n] = 0;
hrec->type = -1;
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));
if (!hrec->value) goto fail;
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 )
goto malformed_line;
if (bcf_hrec_add_key(hrec, p, q-p-m) < 0) goto fail;
p = ++q;
while ( *q && *q==' ' ) { p++; q++; }
int quoted = 0;
char ending = '\0';
switch (*p) {
case '"':
quoted = 1;
ending = '"';
p++;
break;
case '[':
quoted = 1;
ending = ']';
break;
}
if ( quoted ) q++;
while ( *q && *q != '\n' )
{
if ( quoted ) { if ( *q==ending && !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;
if (quoted && ending == ']') {
if (*q == ending) {
r++;
q++;
quoted = 0;
} else {
char buffer[320];
hts_log_error("Missing ']' in header line %s",
hts_strprint(buffer, sizeof(buffer), '"',
line, q-line));
goto fail;
}
}
while ( r > p && r[-1] == ' ' ) r--;
if (bcf_hrec_set_val(hrec, hrec->nkeys-1, p, r-p, quoted) < 0)
goto fail;
if ( quoted && *q==ending ) q++;
if ( *q=='>' )
{
if (nopen) nopen--; // this can happen with nested angle brackets <>
q++;
}
}
if ( nopen )
hts_log_warning("Incomplete header line, trying to proceed anyway:\n\t[%s]\n\t[%d]",line,q[0]);
// Skip to end of line
int nonspace = 0;
p = q;
while ( *q && *q!='\n' ) { nonspace |= !isspace_c(*q); q++; }
if (nonspace) {
char buffer[320];
hts_log_warning("Dropped trailing junk from header line '%s'",
hts_strprint(buffer, sizeof(buffer),
'"', line, q - line));
}
*len = q - line + (*q ? 1 : 0);
return hrec;
fail:
*len = -1;
bcf_hrec_destroy(hrec);
return NULL;
malformed_line:
{
char buffer[320];
while ( *q && *q!='\n' ) q++; // Ensure *len includes full line
hts_log_error("Could not parse the header line: %s",
hts_strprint(buffer, sizeof(buffer),
'"', line, q - line));
*len = q - line + (*q ? 1 : 0);
bcf_hrec_destroy(hrec);
return NULL;
}
}
static int bcf_hdr_set_idx(bcf_hdr_t *hdr, int dict_type, const char *tag, bcf_idinfo_t *idinfo)
{
size_t new_n;
// 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);
errno = EINVAL;
return -1;
}
new_n = idinfo->id >= hdr->n[dict_type] ? idinfo->id+1 : hdr->n[dict_type];
#ifdef FUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION
// hts_resize() can attempt to allocate up to 2 * requested items
if (new_n > FUZZ_ALLOC_LIMIT/(2 * sizeof(bcf_idpair_t)))
return -1;
#endif
if (hts_resize(bcf_idpair_t, new_n, &hdr->m[dict_type],
&hdr->id[dict_type], HTS_RESIZE_CLEAR)) {
return -1;
}
hdr->n[dict_type] = new_n;
// NB: the next kh_put call can invalidate the idinfo pointer, therefore
// we leave it unassigned here. It must 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, -1 on error, 0 otherwise
static int bcf_hdr_register_hrec(bcf_hdr_t *hdr, bcf_hrec_t *hrec)
{
// contig
int i, ret, replacing = 0;
khint_t k;
char *str = NULL;
bcf_hrec_set_type(hrec);
if ( hrec->type==BCF_HL_CTG )
{
hts_pos_t len = 0;
// Get the contig ID ($str) and length ($j)
i = bcf_hrec_find_key(hrec,"length");
if ( i<0 ) len = 0;
else {
char *end = hrec->vals[i];
len = strtoll(hrec->vals[i], &end, 10);
if (end == hrec->vals[i] || len < 0) return 0;
}
i = bcf_hrec_find_key(hrec,"ID");
if ( i<0 ) return 0;
str = strdup(hrec->vals[i]);
if (!str) return -1;
// 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) ) { // already present
free(str); str=NULL;
if (kh_val(d, k).hrec[0] != NULL) // and not removed
return 0;
replacing = 1;
} else {
k = kh_put(vdict, d, str, &ret);
if (ret < 0) { free(str); return -1; }
}
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)
{
if (!replacing) {
kh_del(vdict, d, k);
free(str);
}
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] = len;
kh_val(d, k).hrec[0] = hrec;
if (bcf_hdr_set_idx(hdr, BCF_DT_CTG, kh_key(d,k), &kh_val(d,k)) < 0) {
if (!replacing) {
kh_del(vdict, d, k);
free(str);
}
return -1;
}
if ( idx==-1 ) {
if (hrec_add_idx(hrec, kh_val(d,k).id) < 0) {
return -1;
}
}
return 1;
}
if ( hrec->type==BCF_HL_STR ) return 1;
if ( hrec->type!=BCF_HL_INFO && hrec->type!=BCF_HL_FLT && hrec->type!=BCF_HL_FMT ) 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;
}
if ( type==BCF_HT_FLAG && (var!=BCF_VL_FIXED || num!=0) )
{
hts_log_warning("The definition of Flag \"%s/%s\" is invalid, forcing Number=0", hrec->key,id);
var = BCF_VL_FIXED;
num = 0;
}
}
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);
if (!str) return -1;
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 ) {
if (hrec_add_idx(hrec, kh_val(d, k).id) < 0) {
return -1;
}
}
return 1;
}
k = kh_put(vdict, d, str, &ret);
if (ret < 0) {
free(str);
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;
if (bcf_hdr_set_idx(hdr, BCF_DT_ID, kh_key(d,k), &kh_val(d,k)) < 0) {
kh_del(vdict, d, k);
free(str);
return -1;
}
if ( idx==-1 ) {
if (hrec_add_idx(hrec, kh_val(d,k).id) < 0) {
return -1;
}
}
return 1;
}
static void bcf_hdr_unregister_hrec(bcf_hdr_t *hdr, bcf_hrec_t *hrec)
{
if (hrec->type == BCF_HL_FLT ||
hrec->type == BCF_HL_INFO ||
hrec->type == BCF_HL_FMT ||
hrec->type == BCF_HL_CTG) {
int id = bcf_hrec_find_key(hrec, "ID");
if (id < 0 || !hrec->vals[id])
return;
vdict_t *dict = (hrec->type == BCF_HL_CTG
? (vdict_t*)hdr->dict[BCF_DT_CTG]
: (vdict_t*)hdr->dict[BCF_DT_ID]);
khint_t k = kh_get(vdict, dict, hrec->vals[id]);
if (k != kh_end(dict))
kh_val(dict, k).hrec[hrec->type==BCF_HL_CTG ? 0 : hrec->type] = NULL;
}
}
static void bcf_hdr_remove_from_hdict(bcf_hdr_t *hdr, bcf_hrec_t *hrec)
{
kstring_t str = KS_INITIALIZE;
bcf_hdr_aux_t *aux = get_hdr_aux(hdr);
khint_t k;
int id;
switch (hrec->type) {
case BCF_HL_GEN:
if (ksprintf(&str, "##%s=%s", hrec->key,hrec->value) < 0)
str.l = 0;
break;
case BCF_HL_STR:
id = bcf_hrec_find_key(hrec, "ID");
if (id < 0)
return;
if (!hrec->vals[id] ||
ksprintf(&str, "##%s=<ID=%s>", hrec->key, hrec->vals[id]) < 0)
str.l = 0;
break;
default:
return;
}
if (str.l) {
k = kh_get(hdict, aux->gen, str.s);
} else {
// Couldn't get a string for some reason, so try the hard way...
for (k = kh_begin(aux->gen); k < kh_end(aux->gen); k++) {
if (kh_exist(aux->gen, k) && kh_val(aux->gen, k) == hrec)
break;
}
}
if (k != kh_end(aux->gen) && kh_val(aux->gen, k) == hrec) {
kh_val(aux->gen, k) = NULL;
free((char *) kh_key(aux->gen, k));
kh_key(aux->gen, k) = NULL;
kh_del(hdict, aux->gen, k);
}
free(str.s);
}
int bcf_hdr_update_hrec(bcf_hdr_t *hdr, bcf_hrec_t *hrec, const bcf_hrec_t *tmp)
{
// currently only for bcf_hdr_set_version
assert( hrec->type==BCF_HL_GEN );
int ret;
khint_t k;
bcf_hdr_aux_t *aux = get_hdr_aux(hdr);
for (k=kh_begin(aux->gen); k<kh_end(aux->gen); k++)
{
if ( !kh_exist(aux->gen,k) ) continue;
if ( hrec!=(bcf_hrec_t*)kh_val(aux->gen,k) ) continue;
break;
}
assert( k<kh_end(aux->gen) ); // something went wrong, should never happen
free((char*)kh_key(aux->gen,k));