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filter.cpp
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filter.cpp
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/* filter.c -- filter expressions.
Copyright (C) 2013-2015 Genome Research Ltd.
Author: Petr Danecek <pd3@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. */
#include <ctype.h>
#include <stdlib.h>
#include <errno.h>
#include <math.h>
#include <wordexp.h>
#include <regex.h>
//extern "C" {
//size_t hts_realloc_or_die(unsigned long, unsigned long, unsigned long, unsigned long, int, void**, char const*);
#include "filter.h"
#include <htslib/khash_str2int.h>
#include <htslib/hts_defs.h>
#include <htslib/vcfutils.h>
//}
#include "Error.h"
uint64_t bcf_double_missing = 0x7ff0000000000001;
uint64_t bcf_double_vector_end = 0x7ff0000000000002;
static inline void bcf_double_set(double *ptr, uint64_t value)
{
union { uint64_t i; double d; } u;
u.i = value;
*ptr = u.d;
}
static inline int bcf_double_test(double d, uint64_t value)
{
union { uint64_t i; double d; } u;
u.d = d;
return u.i==value ? 1 : 0;
}
#define bcf_double_set_vector_end(x) bcf_double_set(&(x),bcf_double_vector_end)
#define bcf_double_set_missing(x) bcf_double_set(&(x),bcf_double_missing)
#define bcf_double_is_vector_end(x) bcf_double_test((x),bcf_double_vector_end)
#define bcf_double_is_missing(x) bcf_double_test((x),bcf_double_missing)
typedef struct _token_t
{
// read-only values, same for all VCF lines
int tok_type; // one of the TOK_* keys below
char *key; // set only for string constants, otherwise NULL
char *tag; // for debugging and printout only, VCF tag name
double threshold; // filtering threshold
int hdr_id, type; // BCF header lookup ID and one of BCF_HT_* types
int idx; // 0-based index to VCF vectors, -1: not a vector, -2: any field ([*])
void (*setter)(filter_t *, bcf1_t *, struct _token_t *);
int (*comparator)(struct _token_t *, struct _token_t *, int op_type, bcf1_t *);
void *hash; // test presence of str value in the hash via comparator
regex_t *regex; // precompiled regex for string comparison
// modified on filter evaluation at each VCF line
double *values; // In case str_value is set, values[0] is one sample's string length
char *str_value; // and values[0]*nsamples gives the total length;
int is_str, is_missing; // is_missing is set only for constants, variables are controled via nvalues
int pass_site; // -1 not applicable, 0 fails, >0 pass
uint8_t *pass_samples; // status of individual samples
int nsamples; // number of samples
int nvalues, mvalues; // number of used values, n=0 for missing values, n=1 for scalars
// for strings, total length of str_value
}
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;
int max_unpack, mtmpi, mtmpf, nsamples;
};
#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
// 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
// ( ) [ < = > ] ! | & + - * / M m a A O ~ ^ S . l
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};
#define TOKEN_STRING "x()[<=>]!|&+-*/MmaAO~^f"
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,"MAX(",4) ) { (*str) += 3; return TOK_MAX; }
if ( !strncasecmp(tmp,"MIN(",4) ) { (*str) += 3; return TOK_MIN; }
if ( !strncasecmp(tmp,"AVG(",4) ) { (*str) += 3; return TOK_AVG; }
if ( !strncasecmp(tmp,"SUM(",4) ) { (*str) += 3; return TOK_SUM; }
if ( !strncasecmp(tmp,"ABS(",4) ) { (*str) += 3; return TOK_ABS; }
if ( !strncasecmp(tmp,"STRLEN(",7) ) { (*str) += 6; return TOK_LEN; }
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 ( tmp[0]=='@' ) // file name
{
while ( *tmp && !isspace(*tmp) && *tmp!='=' && *tmp!='!' ) tmp++;
*len = tmp - (*str);
return TOK_VAL;
}
while ( tmp[0] )
{
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;
// hacky: so that [*] is not split, the tokenizer does not recognise square brackets []
if ( tmp[0]=='*' && (tmp==*str || tmp[-1]!='[') ) break;
if ( tmp[0]=='-' ) break;
if ( tmp[0]=='/' ) break;
if ( tmp[0]=='~' ) break;
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; }
*len = tmp - (*str);
return TOK_VAL;
}
static void filters_set_qual(filter_t *flt, bcf1_t *line, token_t *tok)
{
float *ptr = &line->qual;
if ( bcf_float_is_missing(*ptr) )
tok->nvalues = 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 = 0;
else if ( line->d.info[i].type==BCF_BT_CHAR )
{
int n = line->d.info[i].len;
int m = (int)tok->values[0];
hts_expand(char,n+1,m,tok->str_value);
memcpy(tok->str_value,line->d.info[i].vptr,n);
tok->str_value[n] = 0;
tok->values[0] = m;
tok->nvalues = 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 = NULL;
}
else
{
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;
}
tok->str_value = NULL;
}
}
static int filters_cmp_bit_and(token_t *atok, token_t *btok, int op_type, bcf1_t *line)
{
int a = (int)(atok->nvalues?atok->values[0]:atok->threshold);
int b = (int)(btok->nvalues?btok->values[0]:btok->threshold);
if ( op_type==TOK_LIKE ) return a&b ? 1 : 0;
return a&b ? 0 : 1;
}
static int filters_cmp_filter(token_t *atok, token_t *btok, int op_type, bcf1_t *line)
{
int i;
if ( op_type==TOK_NE ) // AND logic: none of the filters can match
{
if ( !line->d.n_flt )
{
if ( atok->hdr_id==-1 ) return 0; // missing value
return 1; // no filter present, eval to true
}
for (i=0; i<line->d.n_flt; i++)
if ( atok->hdr_id==line->d.flt[i] ) return 0;
return 1;
}
// TOK_EQ with OR logic: at least one of the filters must match
if ( !line->d.n_flt )
{
if ( atok->hdr_id==-1 ) return 1;
return 0; // no filter present, eval to false
}
for (i=0; i<line->d.n_flt; i++)
if ( atok->hdr_id==line->d.flt[i] ) return 1;
return 0;
}
static int filters_cmp_id(token_t *atok, token_t *btok, int op_type, bcf1_t *line)
{
// multiple IDs not supported yet (easy to add though)
if ( btok->hash )
{
token_t *tmp = atok; atok = btok; btok = tmp;
}
if ( atok->hash )
{
int ret = khash_str2int_has_key(atok->hash, line->d.id);
if ( op_type==TOK_EQ ) return ret;
return ret ? 0 : 1;
}
if ( op_type==TOK_EQ ) return strcmp(btok->str_value,line->d.id) ? 0 : 1;
return strcmp(btok->str_value,line->d.id) ? 1 : 0;
}
/**
* 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 accomodate
* 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;
#define BRANCH(type_t, is_missing, is_vector_end, out_type_t) { \
type_t *p = (type_t *) info->vptr; \
for (j=0; j<ivec && j<info->len; j++) \
{ \
if ( is_vector_end ) return 0; \
} \
if ( is_missing ) return 0; \
*((out_type_t*)value) = p[j]; \
return 1; \
}
switch (info->type) {
case BCF_BT_INT8: BRANCH(int8_t, p[j]==bcf_int8_missing, p[j]==bcf_int8_vector_end, int64_t); break;
case BCF_BT_INT16: BRANCH(int16_t, p[j]==bcf_int16_missing, p[j]==bcf_int16_vector_end, int64_t); break;
case BCF_BT_INT32: BRANCH(int32_t, p[j]==bcf_int32_missing, p[j]==bcf_int32_vector_end, int64_t); break;
case BCF_BT_FLOAT: BRANCH(float, bcf_float_is_missing(p[j]), bcf_float_is_vector_end(p[j]), 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_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 )
{
int i;
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);
for (i=0; i<tok->nvalues; i++) tok->values[i] = flt->tmpi[i];
}
}
else
{
int64_t 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_float(filter_t *flt, bcf1_t *line, token_t *tok)
{
if ( tok->idx==-2 )
{
int i;
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);
for (i=0; i<tok->nvalues; i++)
if ( bcf_float_is_missing(flt->tmpf[i]) ) bcf_double_set_missing(tok->values[i]);
else tok->values[i] = flt->tmpf[i];
}
}
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)
{
int m = (int)tok->values[0];
int n = bcf_get_info_string(flt->hdr,line,tok->tag,&tok->str_value,&m);
if ( n<0 ) { tok->nvalues = 0; return; }
tok->values[0] = m; // allocated length
if ( tok->idx>=0 )
{
// get ith field (i=tok->idx)
int i = 0;
char *ss = tok->str_value, *se = tok->str_value + n;
while ( ss<se && i<tok->idx )
{
if ( *ss==',' ) i++;
ss++;
}
if ( ss==se || i!=tok->idx ) { tok->nvalues = 0; return; }
se = ss;
while ( se-tok->str_value<n && *se!=',' ) se++;
if ( ss==tok->str_value ) *se = 0;
else
{
memmove(tok->str_value,ss,se-ss);
tok->str_value[se-ss] = 0;
}
tok->nvalues = se-ss;
}
else if ( tok->idx==-2 ) tok->nvalues = n;
}
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)
{
int i;
if ( (tok->nvalues=bcf_get_format_int32(flt->hdr,line,tok->tag,&flt->tmpi,&flt->mtmpi))<0 )
tok->nvalues = 0;
else
{
int is_missing = 1;
hts_expand(double,tok->nvalues,tok->mvalues,tok->values);
for (i=0; i<tok->nvalues; i++)
{
if ( flt->tmpi[i]==bcf_int32_missing || flt->tmpi[i]==bcf_int32_vector_end )
bcf_double_set_missing(tok->values[i]);
else
{
tok->values[i] = flt->tmpi[i];
is_missing = 0;
}
}
if ( is_missing ) tok->nvalues = 0;
else if ( tok->idx >= 0 )
{
int nsmpl = bcf_hdr_nsamples(flt->hdr);
int nvals = tok->nvalues / nsmpl;
if ( tok->idx >= nvals )
tok->nvalues = 0; // the index is too big
else
{
for (i=0; i<nsmpl; i++)
tok->values[i] = tok->values[i*nvals+tok->idx];
tok->nvalues = nsmpl;
}
}
}
tok->nsamples = tok->nvalues;
}
static void filters_set_format_float(filter_t *flt, bcf1_t *line, token_t *tok)
{
int i;
if ( (tok->nvalues=bcf_get_format_float(flt->hdr,line,tok->tag,&flt->tmpf,&flt->mtmpf))<=0 )
{
tok->nvalues = tok->nsamples = 0; // missing values
}
else
{
int is_missing = 1;
hts_expand(double,tok->nvalues,tok->mvalues,tok->values);
for (i=0; i<tok->nvalues; i++)
{
if ( bcf_float_is_missing(flt->tmpf[i]) || bcf_float_is_vector_end(flt->tmpf[i]) )
bcf_double_set_missing(tok->values[i]);
else
{
tok->values[i] = flt->tmpf[i];
is_missing = 0;
}
}
if ( is_missing ) tok->nvalues = 0;
else if ( tok->idx >= 0 )
{
int nsmpl = bcf_hdr_nsamples(flt->hdr);
int nvals = tok->nvalues / nsmpl;
if ( tok->idx >= nvals )
tok->nvalues = 0; // the index is too big
else
{
for (i=0; i<nsmpl; i++)
tok->values[i] = tok->values[i*nvals+tok->idx];
tok->nvalues = nsmpl;
}
}
}
tok->nsamples = tok->nvalues;
}
static void filters_set_format_string(filter_t *flt, bcf1_t *line, token_t *tok)
{
int ndim = tok->nsamples * (int)tok->values[0];
int ret = bcf_get_format_char(flt->hdr,line,tok->tag,&tok->str_value,&ndim);
int nsmpl = bcf_hdr_nsamples(flt->hdr);
ndim /= nsmpl;
tok->values[0] = ndim;
if ( ret<=0 )
{
tok->nvalues = 0;
return;
}
if ( tok->idx < 0 ) // scalar
{
tok->nvalues = tok->nsamples = nsmpl;
return;
}
// vector
int i;
for (i=0; i<nsmpl; i++)
{
char *ss = tok->str_value + i*ndim;
int is = 0, ivec = 0;
while ( ivec<tok->idx && is<ndim && ss[is] )
{
if ( ss[is]==',' ) ivec++;
is++;
}
if ( ivec!=tok->idx || is==ndim || !ss[is] )
{
ss[0] = '.';
ss[1] = 0;
continue;
}
int ie = is;
while ( ie<ndim && ss[ie] && ss[ie]!=',' ) ie++;
if ( is ) memmove(ss,&ss[is],ie-is);
if ( ndim-(ie-is) ) memset(ss+ie-is,0,ndim-(ie-is));
}
if ( !ndim )
{
tok->nvalues = 0;
return;
}
tok->nvalues = ret;
tok->nsamples = nsmpl;
}
static void filters_set_genotype_string(filter_t *flt, bcf1_t *line, token_t *tok)
{
bcf_fmt_t *fmt = bcf_get_fmt(flt->hdr, line, "GT");
if ( !fmt )
{
tok->nvalues = tok->nsamples = 0;
return;
}
int i, blen = 4, nsmpl = bcf_hdr_nsamples(flt->hdr);
kstring_t str;
gt_length_too_big:
str.s = tok->str_value; str.m = tok->values[0] * nsmpl; str.l = 0;
for (i=0; i<nsmpl; i++)
{
int plen = str.l;
bcf_format_gt(fmt, i, &str);
kputc_(0,&str);
if ( (int)str.l - plen > blen )
{
// too many alternate alleles or ploidy is too large, the genotype does not fit
// three characters ("0/0" vs "10/10").
tok->str_value = str.s;
blen *= 2;
goto gt_length_too_big;
}
plen = str.l - plen;
while ( plen<blen )
{
kputc_(0, &str);
plen++;
}
}
tok->nvalues = str.l;
tok->nsamples = nsmpl;
tok->values[0] = blen;
tok->str_value = str.s;
}
static void filters_set_ref_string(filter_t *flt, bcf1_t *line, token_t *tok)
{
kstring_t str; str.s = tok->str_value; str.m = tok->values[0]; str.l = 0;
kputs(line->d.allele[0], &str);
tok->nvalues = str.l;
tok->values[0] = str.m;
tok->str_value = str.s;
}
static void filters_set_alt_string(filter_t *flt, bcf1_t *line, token_t *tok)
{
kstring_t str; str.s = tok->str_value; str.m = tok->values[0]; str.l = 0;
if ( tok->idx>=0 )
{
if ( line->n_allele >= tok->idx )
kputs(line->d.allele[tok->idx], &str);
else
kputc('.', &str);
}
else if ( line->n_allele>1 )
{
kputs(line->d.allele[1], &str);
int i;
for (i=2; i<line->n_allele; i++)
{
kputc(',', &str);
kputs(line->d.allele[i], &str);
}
}
else if ( line->n_allele==1 )
kputc('.', &str);
tok->nvalues = str.l;
tok->values[0] = str.m;
tok->str_value = str.s;
}
static void filters_set_nalt(filter_t *flt, bcf1_t *line, token_t *tok)
{
tok->nvalues = 1;
tok->values[0] = line->n_allele - 1;
}
static void filters_set_ac(filter_t *flt, bcf1_t *line, token_t *tok)
{
hts_expand(int32_t, line->n_allele, flt->mtmpi, flt->tmpi);
if ( !bcf_calc_ac(flt->hdr, line, flt->tmpi, BCF_UN_INFO|BCF_UN_FMT) )
{
tok->nvalues = 0;
return;
}
int i, an = flt->tmpi[0];
for (i=1; i<line->n_allele; i++) an += flt->tmpi[i];
if ( !an )
{
tok->nvalues = 0;
return;
}
flt->tmpi[0] = an; // for filters_set_[mac|af|maf]
if ( tok->idx>=0 )
{
tok->nvalues = 1;
tok->values[0] = tok->idx+1<line->n_allele ? flt->tmpi[tok->idx+1] : 0;
}
else if ( line->n_allele==1 ) // no ALT
{
tok->nvalues = 1;
tok->values[0] = 0;
}
else
{
hts_expand(double,line->n_allele,tok->mvalues,tok->values);
for (i=1; i<line->n_allele; i++)
tok->values[i-1] = flt->tmpi[i];
tok->nvalues = line->n_allele - 1;
}
}
static void filters_set_an(filter_t *flt, bcf1_t *line, token_t *tok)
{
filters_set_ac(flt,line,tok);
tok->values[0] = tok->nvalues ? flt->tmpi[0] : 0;
tok->nvalues = 1;
}
static void filters_set_mac(filter_t *flt, bcf1_t *line, token_t *tok)
{
filters_set_ac(flt,line,tok);
if ( !tok->nvalues ) return;
int i, an = flt->tmpi[0];
for (i=0; i<tok->nvalues; i++)
if ( tok->values[i] > an*0.5 ) tok->values[i] = an - tok->values[i];
}
static void filters_set_af(filter_t *flt, bcf1_t *line, token_t *tok)
{
filters_set_ac(flt,line,tok);
if ( !tok->nvalues ) return;
int i, an = flt->tmpi[0];
for (i=0; i<tok->nvalues; i++)
tok->values[i] /= (double)an;
}
static void filters_set_maf(filter_t *flt, bcf1_t *line, token_t *tok)
{
filters_set_ac(flt,line,tok);
if ( !tok->nvalues ) return;
int i, an = flt->tmpi[0];
for (i=0; i<tok->nvalues; i++)
{
tok->values[i] /= (double)an;
if ( tok->values[i] > 0.5 ) tok->values[i] = 1 - tok->values[i];
}
}
static void set_max(filter_t *flt, bcf1_t *line, token_t *tok)
{
double val = -HUGE_VAL;
int i;
for (i=0; i<tok->nvalues; i++)
{
if ( !bcf_double_is_missing(tok->values[i]) && val < tok->values[i] ) val = tok->values[i];
}
tok->values[0] = val;
tok->nvalues = 1;
tok->nsamples = 0;
}
static void set_min(filter_t *flt, bcf1_t *line, token_t *tok)
{
double val = HUGE_VAL;
int i;
for (i=0; i<tok->nvalues; i++)
if ( !bcf_double_is_missing(tok->values[i]) && val > tok->values[i] ) val = tok->values[i];
tok->values[0] = val;
tok->nvalues = 1;
tok->nsamples = 0;
}
static void set_avg(filter_t *flt, bcf1_t *line, token_t *tok)
{
double val = 0;
int i, n = 0;
for (i=0; i<tok->nvalues; i++)
if ( !bcf_double_is_missing(tok->values[i]) ) { val += tok->values[i]; n++; }
tok->values[0] = n ? val / n : 0;
tok->nvalues = 1;
tok->nsamples = 0;
}
static void set_sum(filter_t *flt, bcf1_t *line, token_t *tok)
{
double val = 0;
int i, n = 0;
for (i=0; i<tok->nvalues; i++)
if ( !bcf_double_is_missing(tok->values[i]) ) { val += tok->values[i]; n++; }
tok->values[0] = val;
tok->nvalues = 1;
tok->nsamples = 0;
}
static void set_abs(filter_t *flt, bcf1_t *line, token_t *tok)
{
if ( tok->is_str ) error("ABS() can be applied only on numeric values\n");
int i;
for (i=0; i<tok->nvalues; i++)
tok->values[i] = fabs(tok->values[i]);
}
static void set_strlen(filter_t *flt, bcf1_t *line, token_t *tok)
{
tok->is_str = 0;
if ( !tok->nvalues ) return;
if ( tok->idx==-2 )
{
int i = 0;
char *ss = tok->str_value;
while ( *ss )
{
char *se = ss;
while ( *se && *se!=',' ) se++;
if ( !*se ) tok->values[i] = strlen(ss);
else
{
*se = 0;
tok->values[i] = strlen(ss);
*se = ',';
}
ss = *se ? se + 1 : se;
i++;
}
tok->nvalues = i;
}
else
{
tok->values[0] = strlen(tok->str_value);
tok->nvalues = 1;
}
}
#define VECTOR_ARITHMETICS(atok,btok,AOP) \
{ \
int i, has_values = 0; \
if ( !(atok)->nvalues || !(btok)->nvalues ) /* missing values */ \
{ \
(atok)->nvalues = 0; (atok)->nsamples = 0; \
} \
else \
{ \
if ( ((atok)->nsamples && (btok)->nsamples) || (!(atok)->nsamples && !(btok)->nsamples)) \
{ \
for (i=0; i<(atok)->nvalues; i++) \
{ \
if ( bcf_double_is_missing((atok)->values[i]) ) continue; \
if ( bcf_double_is_missing((btok)->values[i]) ) { bcf_double_set_missing((atok)->values[i]); continue; } \
has_values = 1; \
(atok)->values[i] = (atok)->values[i] AOP (btok)->values[i]; \
} \
} \
else if ( (btok)->nsamples ) \
{ \
hts_expand(double,(btok)->nvalues,(atok)->mvalues,(atok)->values); \
for (i=0; i<(btok)->nvalues; i++) \
{ \
if ( bcf_double_is_missing((atok)->values[0]) || bcf_double_is_missing((btok)->values[i]) ) \
{ \
bcf_double_set_missing((atok)->values[i]); \
continue; \
} \
has_values = 1; \
(atok)->values[i] = (atok)->values[0] AOP (btok)->values[i]; \
} \
(atok)->nvalues = (btok)->nvalues; \
(atok)->nsamples = (btok)->nsamples; \
} \
else if ( (atok)->nsamples ) \
{ \
for (i=0; i<(atok)->nvalues; i++) \
{ \
if ( bcf_double_is_missing((atok)->values[i]) || bcf_double_is_missing((btok)->values[0]) ) \
{ \
bcf_double_set_missing((atok)->values[i]); \
continue; \
} \
has_values = 1; \
(atok)->values[i] = (atok)->values[i] AOP (btok)->values[0]; \
} \
} \
} \
if ( !has_values ) { (atok)->nvalues = 0; (atok)->nsamples = 0; } \
}
static int vector_logic_and(token_t *atok, token_t *btok, int and_type)
{
// We are comparing either two scalars (result of INFO tag vs a threshold), two vectors (two FORMAT fields),
// or a vector and a scalar (FORMAT field vs threshold)
int i, pass_site = 0;
if ( !atok->nvalues || !btok->nvalues )
{
atok->nvalues = atok->nsamples = 0;
return 0;
}
if ( !atok->nsamples && !btok->nsamples ) return atok->pass_site && btok->pass_site;
if ( atok->nsamples && btok->nsamples )
{
if ( and_type==TOK_AND )
{
// perform AND within a sample
for (i=0; i<atok->nsamples; i++)
{
atok->pass_samples[i] = atok->pass_samples[i] && btok->pass_samples[i];
if ( !pass_site && atok->pass_samples[i] ) pass_site = 1;
}
}
else
{
// perform AND across samples
int pass_a = 0, pass_b = 0;
for (i=0; i<atok->nsamples; i++)
{
if ( atok->pass_samples[i] ) pass_a = 1;
atok->pass_samples[i] = atok->pass_samples[i] && btok->pass_samples[i];
}
for (i=0; i<btok->nsamples; i++)
{
if ( btok->pass_samples[i] ) { pass_b = 1; break; }
}
pass_site = pass_a && pass_b;
}
return pass_site;
}
if ( btok->nsamples )
{
for (i=0; i<btok->nsamples; i++)
{
atok->pass_samples[i] = atok->pass_site && btok->pass_samples[i];
if ( !pass_site && atok->pass_samples[i] ) pass_site = 1;
}
atok->nsamples = btok->nsamples;
return pass_site;
}
/* atok->nsamples!=0 */
for (i=0; i<atok->nsamples; i++)
{
atok->pass_samples[i] = atok->pass_samples[i] && btok->pass_site;
if ( !pass_site && atok->pass_samples[i] ) pass_site = 1;
}
return pass_site;
}
static int vector_logic_or(token_t *atok, token_t *btok, int or_type)
{
int i, pass_site = 0;
if ( !atok->nvalues && !btok->nvalues ) // missing sites in both
{
atok->nvalues = atok->nsamples = 0;
return 0;
}
if ( !atok->nvalues ) // missing value in a
{
for (i=0; i<btok->nsamples; i++)
atok->pass_samples[i] = btok->pass_samples[i];
atok->nsamples = btok->nsamples;
atok->nvalues = 1;
return btok->pass_site;
}
if ( !btok->nvalues ) // missing value in b
{
btok->nvalues = 1;
return atok->pass_site;
}
if ( !atok->nsamples && !btok->nsamples ) return atok->pass_site || btok->pass_site;
if ( !atok->nsamples )
{
if ( or_type==TOK_OR )
{
for (i=0; i<btok->nsamples; i++)
{
atok->pass_samples[i] = btok->pass_samples[i];
if ( atok->pass_site || atok->pass_samples[i] ) pass_site = 1;
}
}
else
{
for (i=0; i<btok->nsamples; i++)