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filter.c
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/* filter.c -- filter expressions.
Copyright (C) 2013-2025 Genome Research Ltd.
Author: Petr Danecek <[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 <ctype.h>
#include <stdlib.h>
#include <strings.h>
#include <assert.h>
#include <errno.h>
#include <math.h>
#include <sys/types.h>
#include <stdint.h>
#include <inttypes.h>
#ifndef _WIN32
#include <pwd.h>
#endif
#include <regex.h>
#include <htslib/khash_str2int.h>
#include <htslib/hts_defs.h>
#include <htslib/vcfutils.h>
#include <htslib/kfunc.h>
#include <htslib/hts_endian.h>
#include "config.h"
#include "filter.h"
#include "bcftools.h"
#if ENABLE_PERL_FILTERS
// Work around clang warning problems
# if defined(__clang__)
# define PERL_GCC_BRACE_GROUPS_FORBIDDEN
# endif
# define filter_t perl_filter_t
# include <EXTERN.h>
# include <perl.h>
# undef filter_t
# define my_perl perl
static int filter_ninit = 0;
#endif
#ifndef __FUNCTION__
# define __FUNCTION__ __func__
#endif
typedef struct _token_t
{
// read-only values, same for all VCF lines
int tok_type; // one of the TOK_* keys below
int nargs; // with TOK_PERLSUB the first argument is the name of the subroutine
char *key; // set only for string constants, otherwise NULL
char *tag; // for debugging and printout only, VCF tag name
double threshold; // filtering threshold
int is_constant; // the threshold is set
int hdr_id, hl_type, ht_type, vl_len; // BCF header lookup ID and one of BCF_HL_*, BCF_HT_*, BCF_VL_* types
int idx; // 0-based index to VCF vectors,
// -2: list (e.g. [0,1,2] or [1..3] or [1..] or any field[*], which is equivalent to [0..])
// -3: select indices on the fly based on values in GT
int *idxs; // set indexes to 0 to exclude, to 1 to include, and last element negative if unlimited; used by VCF retrievers only
int nidxs, nuidxs; // size of idxs array and the number of elements set to 1
uint8_t *usmpl; // bitmask of used samples as set by idx, set for FORMAT fields, NULL otherwise
int nsamples; // number of samples for format fields, 0 for info and other fields
void (*setter)(filter_t *, bcf1_t *, struct _token_t *);
int (*func)(filter_t *, bcf1_t *, struct _token_t *rtok, struct _token_t **stack, int nstack);
void (*comparator)(struct _token_t *, struct _token_t *, struct _token_t *rtok, bcf1_t *);
void *hash; // test presence of str value in the hash via comparator
regex_t *regex; // precompiled regex for string comparison
int iext; // for the use with filter_test_ext(), 1-based index to external values, 0=don't use
// modified on filter evaluation at each VCF line
double *values;
kstring_t str_value;
int is_str, is_missing; // is_missing is set only for constants, variables are controlled via nvalues
int pass_site; // -1 not applicable, 0 fails, >0 pass
uint8_t *pass_samples; // status of individual samples
int nvalues, mvalues; // number of used values: n=0 for missing values, n=1 for scalars, for strings n=str_value.l
int nval1; // number of per-sample fields or string length
}
token_t;
struct _filter_t
{
bcf_hdr_t *hdr;
char *str;
int nfilters;
token_t *filters, **flt_stack; // filtering input tokens (in RPN) and evaluation stack
int32_t *tmpi;
float *tmpf;
kstring_t tmps;
int max_unpack, mtmpi, mtmpf, nsamples;
struct {
bcf1_t *line;
int32_t *buf, nbuf, mbuf; // GTs as obtained by bcf_get_genotypes()
uint64_t *mask; // GTs as mask, e.g 0/0 is 1; 0/1 is 3, max 63 unique alleles
} cached_GT;
#if ENABLE_PERL_FILTERS
PerlInterpreter *perl;
#endif
char **undef_tag, **used_tag;
int nundef_tag, nused_tag;
int status, exit_on_error;
int n_ext; // number of external values to fill via filter_test_ext()
int *ext; // types of external values to fill via filter_test_ext()
};
#define TOK_VAL 0
#define TOK_LFT 1 // (
#define TOK_RGT 2 // )
#define TOK_LE 3 // less or equal
#define TOK_LT 4 // less than
#define TOK_EQ 5 // equal
#define TOK_BT 6 // bigger than
#define TOK_BE 7 // bigger or equal
#define TOK_NE 8 // not equal
#define TOK_OR 9 // |
#define TOK_AND 10 // &
#define TOK_ADD 11 // +
#define TOK_SUB 12 // -
#define TOK_MULT 13 // *
#define TOK_DIV 14 // /
#define TOK_MAX 15
#define TOK_MIN 16
#define TOK_AVG 17
#define TOK_AND_VEC 18 // && (operator applied in samples)
#define TOK_OR_VEC 19 // || (operator applied in samples)
#define TOK_LIKE 20 // ~ regular expression
#define TOK_NLIKE 21 // !~ regular expression
#define TOK_SUM 22
#define TOK_ABS 23
#define TOK_LEN 24
#define TOK_FUNC 25
#define TOK_CNT 26
#define TOK_PERLSUB 27
#define TOK_BINOM 28
#define TOK_PHRED 29
#define TOK_MEDIAN 30
#define TOK_STDEV 31
#define TOK_sMAX 32
#define TOK_sMIN 33
#define TOK_sAVG 34
#define TOK_sMEDIAN 35
#define TOK_sSTDEV 36
#define TOK_sSUM 37
#define TOK_IN 38 // contains, e.g. FILTER~"A"
#define TOK_NOT_IN 39 // does not contain, e.g. FILTER!~"A"
#define TOK_MODULO 40 // %
#define TOK_EXT 41 // external values set before each filter_test_ext() call, can be one of {},{str},{int},{float}
#define TOK_FISHER 42
// 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41
// ( ) [ < = > ] ! | & + - * / M m a A O ~ ^ S . l f c p b P i s %
static int op_prec[] = {0,1,1,5,5,5,5,5,5,2,3, 6, 6, 7, 7, 8, 8, 8, 3, 2, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 7, 0};
#define TOKEN_STRING "x()[<=>]!|&+-*/MmaAO~^S.lfcpis" // this is only for debugging, not maintained diligently
static void cmp_vector_strings(token_t *atok, token_t *btok, token_t *rtok);
inline static void tok_init_samples(token_t *atok, token_t *btok, token_t *rtok);
// Return negative values if it is a function with variable number of arguments
static int filters_next_token(char **str, int *len)
{
char *tmp = *str;
while ( *tmp && isspace(*tmp) ) tmp++;
*str = tmp;
*len = 0;
// test for doubles: d.ddde[+-]dd
if ( isdigit(*str[0]) || *str[0]=='.' ) // strtod would eat +/-
{
double HTS_UNUSED v = strtod(*str, &tmp);
if ( *str!=tmp && (!tmp[0] || !isalnum(tmp[0])) )
{
*len = tmp - (*str);
return TOK_VAL;
}
tmp = *str;
}
if ( !strncasecmp(tmp,"SMPL_MAX(",9) ) { (*str) += 8; return TOK_sMAX; }
if ( !strncasecmp(tmp,"SMPL_MIN(",9) ) { (*str) += 8; return TOK_sMIN; }
if ( !strncasecmp(tmp,"SMPL_MEAN(",10) ) { (*str) += 9; return TOK_sAVG; }
if ( !strncasecmp(tmp,"SMPL_MEDIAN(",12) ) { (*str) += 11; return TOK_sMEDIAN; }
if ( !strncasecmp(tmp,"SMPL_AVG(",9) ) { (*str) += 8; return TOK_sAVG; }
if ( !strncasecmp(tmp,"SMPL_STDEV(",11) ) { (*str) += 10; return TOK_sSTDEV; }
if ( !strncasecmp(tmp,"SMPL_SUM(",9) ) { (*str) += 8; return TOK_sSUM; }
if ( !strncasecmp(tmp,"sMAX(",5) ) { (*str) += 4; return TOK_sMAX; }
if ( !strncasecmp(tmp,"sMIN(",5) ) { (*str) += 4; return TOK_sMIN; }
if ( !strncasecmp(tmp,"sMEAN(",6) ) { (*str) += 5; return TOK_sAVG; }
if ( !strncasecmp(tmp,"sMEDIAN(",8) ) { (*str) += 7; return TOK_sMEDIAN; }
if ( !strncasecmp(tmp,"sAVG(",5) ) { (*str) += 4; return TOK_sAVG; }
if ( !strncasecmp(tmp,"sSTDEV(",7) ) { (*str) += 6; return TOK_sSTDEV; }
if ( !strncasecmp(tmp,"sSUM(",5) ) { (*str) += 4; return TOK_sSUM; }
if ( !strncasecmp(tmp,"MAX(",4) ) { (*str) += 3; return TOK_MAX; }
if ( !strncasecmp(tmp,"MIN(",4) ) { (*str) += 3; return TOK_MIN; }
if ( !strncasecmp(tmp,"MEAN(",5) ) { (*str) += 4; return TOK_AVG; }
if ( !strncasecmp(tmp,"MEDIAN(",7) ) { (*str) += 6; return TOK_MEDIAN; }
if ( !strncasecmp(tmp,"AVG(",4) ) { (*str) += 3; return TOK_AVG; }
if ( !strncasecmp(tmp,"STDEV(",6) ) { (*str) += 5; return TOK_STDEV; }
if ( !strncasecmp(tmp,"SUM(",4) ) { (*str) += 3; return TOK_SUM; }
if ( !strncasecmp(tmp,"ABS(",4) ) { (*str) += 3; return TOK_ABS; }
if ( !strncasecmp(tmp,"COUNT(",6) ) { (*str) += 5; return TOK_CNT; }
if ( !strncasecmp(tmp,"STRLEN(",7) ) { (*str) += 6; return TOK_LEN; }
if ( !strncasecmp(tmp,"BINOM(",6) ) { (*str) += 5; return -TOK_BINOM; }
if ( !strncasecmp(tmp,"FISHER(",6) ) { (*str) += 6; return -TOK_FISHER; }
if ( !strncasecmp(tmp,"PHRED(",6) ) { (*str) += 5; return TOK_PHRED; }
if ( !strncasecmp(tmp,"%MAX(",5) ) { (*str) += 4; return TOK_MAX; } // for backward compatibility
if ( !strncasecmp(tmp,"%MIN(",5) ) { (*str) += 4; return TOK_MIN; } // for backward compatibility
if ( !strncasecmp(tmp,"%AVG(",5) ) { (*str) += 4; return TOK_AVG; } // for backward compatibility
if ( !strncasecmp(tmp,"%SUM(",5) ) { (*str) += 4; return TOK_SUM; } // for backward compatibility
if ( !strncasecmp(tmp,"INFO/",5) ) tmp += 5;
if ( !strncasecmp(tmp,"FORMAT/",7) ) tmp += 7;
if ( !strncasecmp(tmp,"FMT/",4) ) tmp += 4;
if ( !strncasecmp(tmp,"PERL.",5) ) { (*str) += 5; return -TOK_PERLSUB; }
if ( !strncasecmp(tmp,"N_PASS(",7) ) { *len = 6; (*str) += 6; return -TOK_FUNC; }
if ( !strncasecmp(tmp,"F_PASS(",7) ) { *len = 6; (*str) += 6; return -TOK_FUNC; }
if ( !strncasecmp(tmp,"%ILEN",5) ) { *len = 5; return TOK_VAL; } // to be able to distinguish between INFO/ILEN and on-the-fly ILEN
if ( !strncasecmp(tmp,"{}",2) ) { *len = 2; return TOK_EXT; }
if ( !strncasecmp(tmp,"{STR}",5) ) { *len = 5; return TOK_EXT; }
if ( !strncasecmp(tmp,"{INT}",5) ) { *len = 5; return TOK_EXT; }
if ( !strncasecmp(tmp,"{FLOAT}",7) ) { *len = 7; return TOK_EXT; }
if ( tmp[0]=='@' ) // file name
{
while ( *tmp && !isspace(*tmp) && *tmp!='=' && *tmp!='!' ) tmp++;
*len = tmp - (*str);
return TOK_VAL;
}
int square_brackets = 0;
while ( tmp[0] )
{
if ( !square_brackets )
{
if ( tmp[0]=='"' ) break;
if ( tmp[0]=='\'' ) break;
if ( isspace(tmp[0]) ) break;
if ( tmp[0]=='<' ) break;
if ( tmp[0]=='>' ) break;
if ( tmp[0]=='=' ) break;
if ( tmp[0]=='!' ) break;
if ( tmp[0]=='&' ) break;
if ( tmp[0]=='|' ) break;
if ( tmp[0]=='(' ) break;
if ( tmp[0]==')' ) break;
if ( tmp[0]=='+' ) break;
if ( tmp[0]=='*' ) break;
if ( tmp[0]=='-' ) break;
if ( tmp[0]=='/' ) break;
if ( tmp[0]=='~' ) break;
if ( tmp[0]=='%' ) break;
}
if ( tmp[0]==']' ) { if (square_brackets) tmp++; break; }
if ( tmp[0]=='[' ) square_brackets++;
tmp++;
}
if ( tmp > *str )
{
*len = tmp - (*str);
return TOK_VAL;
}
if ( tmp[0]=='"' || tmp[0]=='\'' )
{
int quote = tmp[0];
tmp++;
while ( *tmp && tmp[0]!=quote ) tmp++;
if ( !*tmp ) return -1; // missing quotes
*len = tmp - (*str) + 1;
return TOK_VAL;
}
if ( tmp[0]=='!' )
{
if ( tmp[1]=='=' ) { (*str) += 2; return TOK_NE; }
if ( tmp[1]=='~' ) { (*str) += 2; return TOK_NLIKE; }
}
if ( tmp[0]=='<' )
{
if ( tmp[1]=='=' ) { (*str) += 2; return TOK_LE; }
(*str) += 1; return TOK_LT;
}
if ( tmp[0]=='>' )
{
if ( tmp[1]=='=' ) { (*str) += 2; return TOK_BE; }
(*str) += 1; return TOK_BT;
}
if ( tmp[0]=='=' )
{
if ( tmp[1]=='=' ) { (*str) += 2; return TOK_EQ; }
(*str) += 1; return TOK_EQ;
}
if ( tmp[0]=='(' ) { (*str) += 1; return TOK_LFT; }
if ( tmp[0]==')' ) { (*str) += 1; return TOK_RGT; }
if ( tmp[0]=='&' && tmp[1]=='&' ) { (*str) += 2; return TOK_AND_VEC; }
if ( tmp[0]=='|' && tmp[1]=='|' ) { (*str) += 2; return TOK_OR_VEC; }
if ( tmp[0]=='&' ) { (*str) += 1; return TOK_AND; }
if ( tmp[0]=='|' ) { (*str) += 1; return TOK_OR; }
if ( tmp[0]=='+' ) { (*str) += 1; return TOK_ADD; }
if ( tmp[0]=='-' ) { (*str) += 1; return TOK_SUB; }
if ( tmp[0]=='*' ) { (*str) += 1; return TOK_MULT; }
if ( tmp[0]=='/' ) { (*str) += 1; return TOK_DIV; }
if ( tmp[0]=='~' ) { (*str) += 1; return TOK_LIKE; }
if ( tmp[0]=='%' ) { (*str) += 1; return TOK_MODULO; }
*len = tmp - (*str);
return TOK_VAL;
}
static void filter_add_undef_tag(filter_t *filter, char *str)
{
int i;
for (i=0; i<filter->nundef_tag; i++)
if ( !strcmp(str,filter->undef_tag[i]) ) break;
if ( i<filter->nundef_tag ) return;
filter->nundef_tag++;
filter->undef_tag = (char**)realloc(filter->undef_tag,sizeof(*filter->undef_tag)*filter->nundef_tag);
if ( !filter->undef_tag ) error("Could not allocate memory\n");
filter->undef_tag[filter->nundef_tag-1] = strdup(str);
if ( !filter->undef_tag[filter->nundef_tag-1] ) error("Could not allocate memory\n");
}
const char **filter_list_undef_tags(filter_t *filter, int *ntags)
{
*ntags = filter->nundef_tag;
return (const char**)filter->undef_tag;
}
static void filter_add_used_tag(filter_t *filter, const char *prefix, char *str)
{
int i;
kstring_t tmp = {0,0,0};
if ( prefix ) kputs(prefix,&tmp);
kputs(str,&tmp);
for (i=0; i<filter->nused_tag; i++)
if ( !strcmp(tmp.s,filter->used_tag[i]) ) break;
if ( i<filter->nused_tag )
{
free(tmp.s);
return;
}
filter->nused_tag++;
filter->used_tag = (char**)realloc(filter->used_tag,sizeof(*filter->used_tag)*filter->nused_tag);
if ( !filter->used_tag ) error("Could not allocate memory\n");
filter->used_tag[filter->nused_tag-1] = tmp.s;
if ( !filter->used_tag[filter->nused_tag-1] ) error("Could not allocate memory\n");
}
const char **filter_list_used_tags(filter_t *filter, int *ntags)
{
*ntags = filter->nused_tag;
return (const char**)filter->used_tag;
}
/*
Simple path expansion, expands ~/, ~user, $var. The result must be freed by the caller.
Based on jkb's staden code with some adjustments.
https://sourceforge.net/p/staden/code/HEAD/tree/staden/trunk/src/Misc/getfile.c#l123
*/
char *expand_path(char *path)
{
kstring_t str = {0,0,0};
if ( path[0] == '~' )
{
if ( !path[1] || path[1] == '/' )
{
#ifdef _WIN32
kputs(getenv("HOMEDRIVE"), &str);
kputs(getenv("HOMEPATH"), &str);
#else
// ~ or ~/path
kputs(getenv("HOME"), &str);
if ( path[1] ) kputs(path+1, &str);
#endif
}
#ifndef _WIN32
else
{
// user name: ~pd3/path
char *end = path;
while ( *end && *end!='/' ) end++;
kputsn(path+1, end-path-1, &str);
struct passwd *pwentry = getpwnam(str.s);
str.l = 0;
if ( !pwentry ) kputsn(path, end-path, &str);
else kputs(pwentry->pw_dir, &str);
kputs(end, &str);
}
#endif
return ks_release(&str);
}
if ( path[0] == '$' )
{
char *var = getenv(path+1);
if ( var ) {
kputs(var, &str);
return ks_release(&str);
}
}
return strdup(path);
}
static int filters_cache_genotypes(filter_t *flt, bcf1_t *line)
{
if ( flt->cached_GT.line==line ) return flt->cached_GT.nbuf > 0 ? 0 : -1;
flt->cached_GT.line = line;
flt->cached_GT.nbuf = bcf_get_genotypes(flt->hdr, line, &flt->cached_GT.buf, &flt->cached_GT.mbuf);
if ( flt->cached_GT.nbuf<=0 ) return -1;
if ( !flt->cached_GT.mask )
{
flt->cached_GT.mask = (uint64_t*) malloc(sizeof(*flt->cached_GT.mask)*flt->nsamples);
if ( !flt->cached_GT.mask ) error("Could not alloc %zu bytes\n",sizeof(*flt->cached_GT.mask)*flt->nsamples);
}
int i,j, ngt1 = flt->cached_GT.nbuf / line->n_sample;
for (i=0; i<line->n_sample; i++)
{
int32_t *ptr = flt->cached_GT.buf + i*ngt1;
flt->cached_GT.mask[i] = 0;
for (j=0; j<ngt1; j++)
{
if ( bcf_gt_is_missing(ptr[j]) ) continue;
if ( ptr[j]==bcf_int32_vector_end ) break;
int allele = bcf_gt_allele(ptr[j]);
if ( allele > 63 )
{
static int warned = 0;
if ( !warned )
{
fprintf(stderr,"Too many alleles, skipping GT filtering at this site %s:%"PRId64". "
"(This warning is printed only once.)\n", bcf_seqname(flt->hdr,line),line->pos+1);
warned = 1;
}
flt->cached_GT.nbuf = 0;
return -1;
}
flt->cached_GT.mask[i] |= 1<<allele;
}
}
return 0;
}
static void filters_set_qual(filter_t *flt, bcf1_t *line, token_t *tok)
{
float *ptr = &line->qual;
if ( bcf_float_is_missing(*ptr) )
bcf_double_set_missing(tok->values[0]);
else
tok->values[0] = (double)line->qual;
tok->nvalues = 1;
}
static void filters_set_type(filter_t *flt, bcf1_t *line, token_t *tok)
{
tok->values[0] = bcf_get_variant_types(line);
if ( !tok->values[0] ) tok->values[0] = 1; // mistake in htslib: VCF_* should start with 1
else tok->values[0] = ((int)tok->values[0]) << 1;
tok->nvalues = 1;
}
static void filters_set_info(filter_t *flt, bcf1_t *line, token_t *tok)
{
assert( tok->hdr_id >=0 );
int i;
for (i=0; i<line->n_info; i++)
if ( line->d.info[i].key == tok->hdr_id ) break;
if ( i==line->n_info )
tok->nvalues = tok->str_value.l = 0;
else if ( line->d.info[i].type==BCF_BT_CHAR )
{
int n = line->d.info[i].len;
if ( n >= tok->str_value.m )
{
tok->str_value.m = n + 1;
tok->str_value.s = (char*) realloc(tok->str_value.s, tok->str_value.m);
if ( !tok->str_value.s ) error("Failed to alloc %d bytes\n", (int)tok->str_value.m);
}
memcpy(tok->str_value.s, line->d.info[i].vptr, n);
tok->str_value.s[n] = 0;
tok->nvalues = tok->str_value.l = n;
}
else if ( line->d.info[i].type==BCF_BT_FLOAT )
{
if ( bcf_float_is_missing(line->d.info[i].v1.f) ) tok->nvalues = 0;
else
{
tok->values[0] = line->d.info[i].v1.f;
tok->nvalues = 1;
}
tok->str_value.l = 0;
}
else
{
tok->str_value.l = 0;
if ( line->d.info[i].type==BCF_BT_INT8 && line->d.info[i].v1.i==bcf_int8_missing ) tok->nvalues = 0;
else if ( line->d.info[i].type==BCF_BT_INT16 && line->d.info[i].v1.i==bcf_int16_missing ) tok->nvalues = 0;
else if ( line->d.info[i].type==BCF_BT_INT32 && line->d.info[i].v1.i==bcf_int32_missing ) tok->nvalues = 0;
else
{
tok->values[0] = line->d.info[i].v1.i;
tok->nvalues = 1;
}
}
}
static void filters_cmp_bit_and(token_t *atok, token_t *btok, token_t *rtok, bcf1_t *line)
{
int a = (int)(atok->nvalues?atok->values[0]:atok->threshold);
int b = (int)(btok->nvalues?btok->values[0]:btok->threshold);
if ( rtok->tok_type==TOK_LIKE )
rtok->pass_site = a&b ? 1 : 0;
else
rtok->pass_site = a&b ? 0 : 1;
}
static void filters_cmp_filter(token_t *atok, token_t *btok, token_t *rtok, bcf1_t *line)
{
// the btok values contain FILTER ids obtained by parsing the user expression
int i,j;
if ( rtok->tok_type==TOK_NOT_IN ) // fail if the query expression is a subset of the VCF FILTER
{
if ( !btok->nvalues ) // the query expression is ".", pass everything unless the VCF is also "."
{
if ( line->d.n_flt ) rtok->pass_site = 1;
return;
}
if ( !line->d.n_flt ) // no filters at this VCF line and the query expression has a value
{
rtok->pass_site = 1;
return;
}
for (j=0; j<btok->nvalues; j++) // some query expression value must be absent from VCF in order to pass
{
for (i=0; i<line->d.n_flt; i++)
if ( btok->values[j]==line->d.flt[i] ) break;
if ( i==line->d.n_flt ) break; // the query is not in the VCF
}
if ( j!=btok->nvalues ) rtok->pass_site = 1;
return;
}
else if ( rtok->tok_type==TOK_IN )
{
if ( !btok->nvalues ) // the query expression is ".", fail everything unless the VCF is also "."
{
if ( !line->d.n_flt ) rtok->pass_site = 1;
return;
}
if ( !line->d.n_flt ) return; // no filters at this VCF line and the query expression has a value
for (j=0; j<btok->nvalues; j++) // all of the query values must be present in the VCF in order to pass
{
for (i=0; i<line->d.n_flt; i++)
if ( btok->values[j]==line->d.flt[i] ) break;
if ( i==line->d.n_flt ) break; // the query is not in the VCF
}
if ( j==btok->nvalues ) rtok->pass_site = 1;
return;
}
else if ( rtok->tok_type==TOK_NE ) // require anything but exact match
{
if ( btok->nvalues != line->d.n_flt )
{
rtok->pass_site = 1;
return;
}
if ( !btok->nvalues ) return;
for (j=0; j<btok->nvalues; j++) // some of the query values must be absent from the VCF in order to pass
{
for (i=0; i<line->d.n_flt; i++)
if ( btok->values[j]==line->d.flt[i] ) break;
if ( i==line->d.n_flt ) break; // the query is not in the VCF
}
if ( j!=btok->nvalues ) rtok->pass_site = 1;
return;
}
else if ( rtok->tok_type==TOK_EQ ) // require exact match
{
if ( btok->nvalues != line->d.n_flt ) return;
if ( !btok->nvalues )
{
rtok->pass_site = 1;
return;
}
for (j=0; j<btok->nvalues; j++) // all of the query values must be present in the VCF in order to pass
{
for (i=0; i<line->d.n_flt; i++)
if ( btok->values[j]==line->d.flt[i] ) break;
if ( i==line->d.n_flt ) break; // the query is not in the VCF
}
if ( j==btok->nvalues ) rtok->pass_site = 1;
return;
}
else
error("Only ==, !=, ~, and !~ operators are supported for FILTER\n");
return;
}
static void filters_cmp_string_hash(token_t *atok, token_t *btok, token_t *rtok, bcf1_t *line)
{
if ( btok->hash )
{
token_t *tmp = atok; atok = btok; btok = tmp;
}
if ( rtok->tok_type!=TOK_EQ && rtok->tok_type!=TOK_NE )
error("Only == and != operators are supported for strings read from a file\n");
// INFO
if ( !btok->nsamples )
{
// there is only one string value, e.g. STR[1][email protected]
if ( btok->idx >= 0 )
{
int ret = btok->str_value.s ? khash_str2int_has_key(atok->hash, btok->str_value.s) : 0;
if ( rtok->tok_type==TOK_NE ) ret = ret ? 0 : 1;
rtok->pass_site = ret;
return;
}
// there can be multiple comma-separated string values, e.g. [email protected] or STR[*][email protected]
int ret = 0;
char *ptr = btok->str_value.s;
while ( *ptr )
{
char *eptr = ptr + 1;
while ( *eptr && *eptr!=',' ) eptr++;
char keep = *eptr;
*eptr = 0;
ret |= khash_str2int_has_key(atok->hash, ptr);
*eptr = keep;
if ( !keep ) break;
ptr = eptr + 1;
}
if ( rtok->tok_type==TOK_NE ) ret = ret ? 0 : 1;
rtok->pass_site = ret;
return;
}
// FORMAT
tok_init_samples(atok, btok, rtok);
rtok->pass_site = 0;
int i;
// there is only one string value, e.g. FMT/STR[*:1][email protected]
if ( btok->idx >= 0 )
{
for (i=0; i<btok->nsamples; i++)
{
if ( !rtok->usmpl[i] ) continue;
char *str = btok->str_value.s + i*btok->nval1;
char keep = str[btok->nval1];
str[btok->nval1] = 0;
int ret = khash_str2int_has_key(atok->hash, str);
str[btok->nval1] = keep;
if ( rtok->tok_type==TOK_NE ) ret = ret ? 0 : 1;
rtok->pass_samples[i] = ret;
rtok->pass_site |= ret;
}
return;
}
// there can be multiple comma-separated string values, e.g. FMT/[email protected]
for (i=0; i<btok->nsamples; i++)
{
if ( !rtok->usmpl[i] ) continue;
char *str = btok->str_value.s + i*btok->nval1;
char keep = str[btok->nval1];
str[btok->nval1] = 0;
// now str contains the block of per-sample comma-separated strings to loop over
int ret = 0;
char *ptr = str;
while ( *ptr )
{
char *eptr = ptr + 1;
while ( *eptr && *eptr!=',' ) eptr++;
char keep0 = *eptr;
*eptr = 0;
ret |= khash_str2int_has_key(atok->hash, ptr);
*eptr = keep0;
if ( !keep0 ) break;
ptr = eptr + 1;
}
str[btok->nval1] = keep;
if ( rtok->tok_type==TOK_NE ) ret = ret ? 0 : 1;
rtok->pass_samples[i] = ret;
rtok->pass_site |= ret;
}
}
static void filters_cmp_id(token_t *atok, token_t *btok, token_t *rtok, bcf1_t *line)
{
if ( btok->hash )
{
token_t *tmp = atok; atok = btok; btok = tmp;
}
char *id = line->d.id;
int pass = 0;
while ( id )
{
char *ep = strchr(id,';');
if ( ep ) *ep = 0;
if ( atok->hash )
{
if ( rtok->tok_type!=TOK_EQ && rtok->tok_type!=TOK_NE )
error("Only == and != operators are supported for strings read from a file\n");
pass = khash_str2int_has_key(atok->hash, id);
}
else
{
if ( !btok->str_value.l ) error("Error occurred while evaluating the expression\n");
if ( rtok->tok_type==TOK_EQ || rtok->tok_type==TOK_NE )
pass = strcmp(btok->str_value.s,id) ? 0 : 1;
else
{
if ( rtok->tok_type!=TOK_LIKE && rtok->tok_type!=TOK_NLIKE )
error("Only the following operators are supported for querying ID: ==, !=, ~, !~; the operator type %d is not supported (%p %p)\n",
rtok->tok_type,atok->regex,btok->regex);
regex_t *regex = atok->regex ? atok->regex : (btok->regex ? btok->regex : NULL);
if ( !regex ) error("fixme: regex initialization failed\n");
pass = regexec(regex,id, 0,NULL,0) ? 0 : 1;
}
}
if ( ep )
{
*ep = ';';
id = ep + 1;
}
if ( pass || !ep ) break;
}
if ( rtok->tok_type==TOK_NE || rtok->tok_type==TOK_NE) pass = pass ? 0 : 1;
rtok->pass_site = pass;
}
/**
* bcf_get_info_value() - get single INFO value, int64_t or double
* @line: BCF line
* @info_id: tag ID, as returned by bcf_hdr_id2int
* @ivec: 0-based index to retrieve, -1 when single value is expected
* @vptr: pointer to memory location of sufficient size to accommodate
* info_id's type
*
* The returned value is -1 if tag is not present, 0 if present but
* values is missing or ivec is out of range, and 1 on success.
*/
static int bcf_get_info_value(bcf1_t *line, int info_id, int ivec, void *value)
{
int j;
for (j=0; j<line->n_info; j++)
if ( line->d.info[j].key == info_id ) break;
if ( j==line->n_info ) return -1;
bcf_info_t *info = &line->d.info[j];
if ( info->len == 1 )
{
if ( info->type==BCF_BT_FLOAT ) *((double*)value) = info->v1.f;
else if ( info->type==BCF_BT_INT8 || info->type==BCF_BT_INT16 || info->type==BCF_BT_INT32 ) *((int64_t*)value) = info->v1.i;
return 1;
}
if ( ivec<0 ) ivec = 0;
if ( ivec>=info->len) return 0;
#define BRANCH(type_t, convert, is_missing, is_vector_end, out_type_t) { \
uint8_t *p = info->vptr; \
for (j=0; j<ivec; j++) \
{ \
type_t val = convert(&p[j * sizeof(type_t)]); \
if ( is_vector_end ) return 0; \
} \
type_t val = convert(&p[ivec * sizeof(type_t)]); \
if ( is_missing ) return 0; \
*((out_type_t*)value) = val; \
return 1; \
}
switch (info->type) {
case BCF_BT_INT8: BRANCH(int8_t, le_to_i8, val==bcf_int8_missing, val==bcf_int8_vector_end, int64_t); break;
case BCF_BT_INT16: BRANCH(int16_t, le_to_i16, val==bcf_int16_missing, val==bcf_int16_vector_end, int64_t); break;
case BCF_BT_INT32: BRANCH(int32_t, le_to_i32, val==bcf_int32_missing, val==bcf_int32_vector_end, int64_t); break;
case BCF_BT_FLOAT: BRANCH(float, le_to_float, bcf_float_is_missing(val), bcf_float_is_vector_end(val), double); break;
default: fprintf(stderr,"todo: type %d\n", info->type); exit(1); break;
}
#undef BRANCH
return -1; // this shouldn't happen
}
static void filters_set_chrom(filter_t *flt, bcf1_t *line, token_t *tok)
{
tok->str_value.l = 0;
kputs(bcf_seqname(flt->hdr,line), &tok->str_value);
tok->nvalues = tok->str_value.l;
tok->is_str = 1;
}
static void filters_set_pos(filter_t *flt, bcf1_t *line, token_t *tok)
{
tok->values[0] = line->pos+1;
tok->nvalues = 1;
}
static void filters_set_info_int(filter_t *flt, bcf1_t *line, token_t *tok)
{
if ( tok->idx==-2 )
{
tok->nvalues = bcf_get_info_int32(flt->hdr,line,tok->tag,&flt->tmpi,&flt->mtmpi);
if ( tok->nvalues<=0 ) tok->nvalues = 0;
else
{
hts_expand(double,tok->nvalues,tok->mvalues,tok->values);
int i, j = 0, end = tok->idxs[tok->nidxs-1] < 0 ? tok->nvalues - 1 : tok->nidxs - 1;
if ( end >= tok->nvalues ) end = tok->nvalues - 1;
for (i=0; i<=end; i++)
if ( i>=tok->nidxs || tok->idxs[i] ) tok->values[j++] = flt->tmpi[i];
tok->nvalues = j;
}
}
else
{
int64_t value = 0;
if ( bcf_get_info_value(line,tok->hdr_id,tok->idx,&value) <= 0 )
tok->nvalues = 0;
else
{
tok->values[0] = value;
tok->nvalues = 1;
}
}
}
static void filters_set_info_float(filter_t *flt, bcf1_t *line, token_t *tok)
{
if ( tok->idx==-2 )
{
tok->nvalues = bcf_get_info_float(flt->hdr,line,tok->tag,&flt->tmpf,&flt->mtmpf);
if ( tok->nvalues<=0 ) tok->nvalues = 0;
else
{
hts_expand(double,tok->nvalues,tok->mvalues,tok->values);
int i, j = 0, end = tok->idxs[tok->nidxs-1] < 0 ? tok->nvalues - 1 : tok->nidxs - 1;
if ( end >= tok->nvalues ) end = tok->nvalues - 1;
for (i=0; i<=end; i++)
if ( i>=tok->nidxs || tok->idxs[i] )
{
if ( bcf_float_is_missing(flt->tmpf[i]) ) bcf_double_set_missing(tok->values[j]);
else tok->values[j] = flt->tmpf[i];
j++;
}
tok->nvalues = j;
}
}
else
{
double value;
if ( bcf_get_info_value(line,tok->hdr_id,tok->idx,&value) <= 0 )
tok->nvalues = 0;
else
{
tok->values[0] = value;
tok->nvalues = 1;
}
}
}
static void filters_set_info_string(filter_t *flt, bcf1_t *line, token_t *tok)
{
int32_t m = tok->str_value.m;
int n = bcf_get_info_string(flt->hdr,line,tok->tag,&tok->str_value.s,&m);
tok->str_value.m = m;
if ( n<0 ) { tok->nvalues = tok->str_value.l = 0; return; }
if ( tok->idx>=0 )
{
// get ith field (i=tok->idx)
int i = 0;
char *ss = tok->str_value.s, *se = tok->str_value.s + n;
while ( ss<se && i<tok->idx )
{
if ( *ss==',' ) i++;
ss++;
}
if ( ss==se || i!=tok->idx ) { tok->nvalues = tok->str_value.l = 0; return; }
se = ss;
while ( se - tok->str_value.s < n && *se!=',' ) se++;
if ( ss==tok->str_value.s ) *se = 0;
else
{
memmove(tok->str_value.s, ss, se-ss);
tok->str_value.s[se-ss] = 0;
}
tok->str_value.l = se - ss;
}
else if ( tok->idx==-2 && tok->idxs[0]==-1 ) // keep all values, TAG[*]
tok->str_value.l = n;
else if ( tok->idx==-2 )
{
flt->tmps.l = 0;
ks_resize(&flt->tmps, n);
int i, iend = tok->idxs[tok->nidxs-1] < 0 ? n - 1 : tok->nidxs - 1;
if ( iend >= n ) iend = n - 1;
char *beg = tok->str_value.s, *dst = flt->tmps.s;
for (i=0; i<=iend; i++)
{
char *end = beg;
while ( *end && *end!=',' ) end++;
if ( i>=tok->nidxs || tok->idxs[i] )
{
memcpy(dst, beg, end - beg);
dst += end - beg;
dst[0] = ',';
dst++;
}
beg = end+1;
}
dst[0] = 0;
tok->str_value.l = dst - flt->tmps.s;
#define SWAP(type_t, a, b) { type_t t = a; a = b; b = t; }
SWAP(char *, flt->tmps.s, tok->str_value.s);
SWAP(size_t, flt->tmps.m, tok->str_value.m);
}
tok->nvalues = tok->str_value.l;
}
static void filters_set_info_flag(filter_t *flt, bcf1_t *line, token_t *tok)
{
int j;
for (j=0; j<line->n_info; j++)
if ( line->d.info[j].key == tok->hdr_id ) break;
tok->values[0] = j==line->n_info ? 0 : 1;
tok->nvalues = 1;
}
static void filters_set_format_int(filter_t *flt, bcf1_t *line, token_t *tok)
{
if ( line->n_sample != tok->nsamples )
error("Incorrect number of FORMAT fields at %s:%"PRId64" .. %s, %d vs %d\n", bcf_seqname(flt->hdr,line),(int64_t) line->pos+1,tok->tag,line->n_sample,tok->nsamples);
int nvals;
if ( (nvals=bcf_get_format_int32(flt->hdr,line,tok->tag,&flt->tmpi,&flt->mtmpi))<0 )
{
tok->nvalues = 0;
return;
}
int i, nsrc1 = nvals / tok->nsamples;
tok->nval1 = tok->idx >= 0 ? 1 : (tok->nuidxs ? tok->nuidxs : nsrc1);
tok->nvalues = tok->nval1*tok->nsamples;
hts_expand(double, tok->nvalues, tok->mvalues, tok->values);
if ( tok->idx >= 0 ) // scalar or vector index
{
for (i=0; i<tok->nsamples; i++)
{
if ( !tok->usmpl[i] ) continue;
int32_t *ptr = flt->tmpi + i*nsrc1;
if ( tok->idx>=nsrc1 || ptr[tok->idx]==bcf_int32_missing )
bcf_double_set_missing(tok->values[i]);
else if ( ptr[tok->idx]==bcf_int32_vector_end )
bcf_double_set_vector_end(tok->values[i]);
else
tok->values[i] = ptr[tok->idx];
}
}
else if ( tok->idx==-3 )
{
if ( filters_cache_genotypes(flt,line)!=0 )
{
tok->nvalues = 0;
return;
}
for (i=0; i<tok->nsamples; i++)
{
if ( !tok->usmpl[i] ) continue;
int32_t *src = flt->tmpi + i*nsrc1;
double *dst = tok->values + i*tok->nval1;
int k, j = 0;
for (k=0; k<nsrc1; k++) // source values are AD[0..nsrc1]
{
if ( !(flt->cached_GT.mask[i] & (1<<k)) ) continue;
dst[j++] = src[k];