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filter.c
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/* filter.c -- filter expressions.
Copyright (C) 2013-2018 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 <errno.h>
#include <math.h>
#include <sys/types.h>
#include <pwd.h>
#include <regex.h>
#include <htslib/khash_str2int.h>
#include <htslib/hts_defs.h>
#include <htslib/vcfutils.h>
#include <htslib/kfunc.h>
#include "config.h"
#include "filter.h"
#include "bcftools.h"
#if ENABLE_PERL_FILTERS
# 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
static const uint64_t bcf_double_missing = 0x7ff0000000000001;
static const 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)
#define bcf_double_is_missing_or_vector_end(x) (bcf_double_test((x),bcf_double_missing) || bcf_double_test((x),bcf_double_vector_end))
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, tag_type; // BCF header lookup ID and one of BCF_HL_* 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..])
int *idxs; // set indexes to 0 to exclude, to 1 to include, and last element negative if unlimited
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
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
// 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 controled 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;
#if ENABLE_PERL_FILTERS
PerlInterpreter *perl;
#endif
};
#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
// 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
// ( ) [ < = > ] ! | & + - * / 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};
#define TOKEN_STRING "x()[<=>]!|&+-*/MmaAO~^S.lfcpis"
// 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,"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(",4) ) { (*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,"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 ( 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]==']' ) { 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; }
*len = tmp - (*str);
return TOK_VAL;
}
/*
Simple path expansion, expands ~/, ~user, $var. The result must be freed by the caller.
Based on jkb's staden code with some adjustements.
https://sourceforge.net/p/staden/code/HEAD/tree/staden/trunk/src/Misc/getfile.c#l123
*/
char *expand_path(char *path)
{
#ifdef _WIN32
return strdup(path); // windows expansion: todo
#endif
kstring_t str = {0,0,0};
if ( path[0] == '~' )
{
if ( !path[1] || path[1] == '/' )
{
// ~ or ~/path
kputs(getenv("HOME"), &str);
if ( path[1] ) kputs(path+1, &str);
}
else
{
// user name: ~pd3/path
char *end = path;
while ( *end && *end!='/' ) end++;
kputsn(path+1, end-path-1, &str);
struct passwd *pwentry = getpwnam(str.s);
str.l = 0;
if ( !pwentry ) kputsn(path, end-path, &str);
else kputs(pwentry->pw_dir, &str);
kputs(end, &str);
}
return str.s;
}
if ( path[0] == '$' )
{
char *var = getenv(path+1);
if ( var ) path = var;
}
return strdup(path);
}
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)
{
int i;
if ( rtok->tok_type==TOK_NE ) // AND logic: none of the filters can match
{
if ( !line->d.n_flt )
{
if ( atok->hdr_id==-1 ) return; // missing value
rtok->pass_site = 1;
return; // no filter present, eval to true
}
for (i=0; i<line->d.n_flt; i++)
if ( atok->hdr_id==line->d.flt[i] ) return;
rtok->pass_site = 1;
return;
}
else if ( rtok->tok_type==TOK_EQ ) // OR logic: at least one of the filters must match
{
if ( !line->d.n_flt )
{
if ( atok->hdr_id==-1 ) { rtok->pass_site = 1; return; }
return; // no filter present, eval to false
}
for (i=0; i<line->d.n_flt; i++)
if ( atok->hdr_id==line->d.flt[i] ) { rtok->pass_site = 1; return; }
return;
}
else
error("Only == and != operators are supported for FILTER\n");
return;
}
static void filters_cmp_id(token_t *atok, token_t *btok, token_t *rtok, bcf1_t *line)
{
// multiple IDs not supported yet (easy to add though)
if ( rtok->tok_type!=TOK_EQ && rtok->tok_type!=TOK_NE )
error("Only == and != operators are supported for ID\n");
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 ( rtok->tok_type==TOK_NE ) ret = ret ? 0 : 1;
rtok->pass_site = ret;
return;
}
if ( !btok->str_value.l ) error("Error occurred while evaluating the expression\n");
if ( rtok->tok_type==TOK_EQ )
rtok->pass_site = strcmp(btok->str_value.s,line->d.id) ? 0 : 1;
else
rtok->pass_site = strcmp(btok->str_value.s,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_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:%d .. %s, %d vs %d\n", bcf_seqname(flt->hdr,line),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
{
int kend = tok->idxs[tok->nidxs-1] < 0 ? tok->nval1 : tok->nidxs;
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<kend; k++)
{
if ( k<tok->nidxs && !tok->idxs[k] ) continue;
if ( src[k]==bcf_int32_missing )
bcf_double_set_missing(dst[j]);
else if ( src[k]==bcf_int32_vector_end )
bcf_double_set_vector_end(dst[j]);
else
dst[j] = src[k];
j++;
}
if ( j==0 )
{
bcf_double_set_missing(dst[j]);
j++;
}
while (j < tok->nval1)
{
bcf_double_set_vector_end(dst[j]);
j++;
}
}
}
}
static void filters_set_format_float(filter_t *flt, bcf1_t *line, token_t *tok)
{
if ( line->n_sample != tok->nsamples )
error("Incorrect number of FORMAT fields at %s:%d .. %s, %d vs %d\n", bcf_seqname(flt->hdr,line),line->pos+1,tok->tag,line->n_sample,tok->nsamples);
int nvals;
if ( (nvals=bcf_get_format_float(flt->hdr,line,tok->tag,&flt->tmpf,&flt->mtmpf))<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;
float *ptr = flt->tmpf + i*nsrc1;
if ( tok->idx>=nsrc1 || bcf_float_is_missing(ptr[tok->idx]) )
bcf_double_set_missing(tok->values[i]);
else if ( bcf_float_is_vector_end(ptr[tok->idx]) )
bcf_double_set_vector_end(tok->values[i]);
else
tok->values[i] = ptr[tok->idx];
}
}
else
{
int kend = tok->idxs[tok->nidxs-1] < 0 ? tok->nval1 : tok->nidxs;
for (i=0; i<tok->nsamples; i++)
{
if ( !tok->usmpl[i] ) continue;
float *src = flt->tmpf + i*nsrc1;
double *dst = tok->values + i*tok->nval1;
int k, j = 0;
for (k=0; k<kend; k++)
{
if ( k<tok->nidxs && !tok->idxs[k] ) continue;
if ( bcf_float_is_missing(src[k]) )
bcf_double_set_missing(dst[j]);
else if ( bcf_float_is_vector_end(src[k]) )
bcf_double_set_vector_end(dst[j]);
else
dst[j] = src[k];
j++;
}
if ( j==0 )
{
bcf_double_set_missing(dst[j]);
j++;
}
while (j < tok->nval1)
{
bcf_double_set_vector_end(dst[j]);
j++;
}
}
}
}
static void filters_set_format_string(filter_t *flt, bcf1_t *line, token_t *tok)
{
if ( line->n_sample != tok->nsamples )
error("Incorrect number of FORMAT fields at %s:%d .. %s, %d vs %d\n", bcf_seqname(flt->hdr,line),line->pos+1,tok->tag,line->n_sample,tok->nsamples);
int i, ndim = tok->str_value.m;
int nstr = bcf_get_format_char(flt->hdr, line, tok->tag, &tok->str_value.s, &ndim);
tok->str_value.m = ndim;
tok->str_value.l = tok->nvalues = 0;
if ( nstr<0 ) return;
tok->nvalues = tok->str_value.l = nstr;
tok->nval1 = nstr / tok->nsamples;
for (i=0; i<tok->nsamples; i++)
{
if ( !tok->usmpl[i] ) continue;
char *src = tok->str_value.s + i*tok->nval1, *dst = src;
int ibeg = 0, idx = 0;
while ( ibeg < tok->nval1 )
{
int iend = ibeg;
while ( iend < tok->nval1 && src[iend] && src[iend]!=',' ) iend++;
int keep = 0;
if ( tok->idx >= 0 )
{
if ( tok->idx==idx ) keep = 1;
}
else if ( idx < tok->nidxs )
{
if ( tok->idxs[idx] != 0 ) keep = 1;
}
else if ( tok->idxs[tok->nidxs-1] < 0 )
keep = 1;
if ( keep )
{
if ( ibeg!=0 ) memmove(dst, src+ibeg, iend-ibeg+1);
dst += iend - ibeg + 1;
if ( tok->idx>=0 ) break;
}
if ( !src[iend] ) break;
ibeg = iend + 1;
idx++;
}
if ( dst==src ) { dst[0] = '.'; dst+=2; }
if ( dst - src < tok->nval1 ) memset(dst-1, 0, tok->nval1 - (dst - src));
}
}
static void _filters_set_genotype(filter_t *flt, bcf1_t *line, token_t *tok, int type)
{
bcf_fmt_t *fmt = bcf_get_fmt(flt->hdr, line, "GT");
if ( !fmt )
{
tok->nvalues = tok->str_value.l = 0;
return;
}
int i,j, nsmpl = bcf_hdr_nsamples(flt->hdr), nvals1 = type==2 ? 3 : 4;
if ( tok->str_value.m <= nvals1*nsmpl )
{
tok->str_value.m = nvals1*nsmpl + 1;
tok->str_value.s = (char*)realloc(tok->str_value.s, tok->str_value.m);
}
#define BRANCH_INT(type_t,vector_end) \
{ \
for (i=0; i<line->n_sample; i++) \
{ \
type_t *ptr = (type_t*) (fmt->p + i*fmt->size); \
int is_het = 0, has_ref = 0, missing = 0; \
for (j=0; j<fmt->n; j++) \
{ \
if ( ptr[j]==vector_end ) break; /* smaller ploidy */ \
if ( bcf_gt_is_missing(ptr[j]) ) { missing=1; break; } /* missing allele */ \
int ial = ptr[j]; \
if ( bcf_gt_allele(ial)==0 ) has_ref = 1; \
if ( j>0 ) \
{ \
int jal = ptr[j-1]; \
if ( bcf_gt_allele(ial)!=bcf_gt_allele(jal) ) is_het = 1; \
} \
} \
char *dst = &tok->str_value.s[nvals1*i]; \
if ( type==4 ) \
{ \
if ( !j || missing ) dst[0]='m', dst[1]='i', dst[2]='s', dst[3] = 0; /* mis, missing genotype */ \
else if ( !has_ref ) dst[0]='a', dst[1]='l', dst[2]='t', dst[3] = 0; /* alt, no ref, must have alt allele */ \
else if ( !is_het ) dst[0]='r', dst[1]='e', dst[2]='f', dst[3] = 0; /* ref, must be ref-only, no alt alelle */ \
else dst[0]='a', dst[1]='l', dst[2]='t', dst[3] = 0; /* alt, is het, has alt allele */ \
} \
else if ( !j || missing ) dst[0]='.', dst[1]=0; /* ., missing genotype */ \
else if ( type==3 ) \
{ \
if ( j==1 ) dst[0]='h', dst[1]='a', dst[2]='p', dst[3] = 0; /* hap, haploid */ \
else if ( !is_het ) dst[0]='h', dst[1]='o', dst[2]='m', dst[3] = 0; /* hom */ \
else dst[0]='h', dst[1]='e', dst[2]='t', dst[3] = 0; /* het */ \
} \
else \
{ \
if ( j==1 ) \
{ \
if ( has_ref ) dst[0]='r', dst[1]=0; /* r, haploid */ \
else dst[0]='a', dst[1]=0; /* a, haploid */ \
} \
else if ( !is_het ) \
{ \
if ( has_ref ) dst[0]='r', dst[1]='r', dst[2] = 0; /* rr */ \
else dst[0]='a', dst[1]='a', dst[2] = 0; /* aa */ \
} \
else \
{ \
if ( has_ref ) dst[0]='r', dst[1]='a', dst[2] = 0; /* ra */ \
else dst[0]='a', dst[1]='A', dst[2] = 0; /* aA */ \
} \
} \
} \
}
switch (fmt->type) {
case BCF_BT_INT8: BRANCH_INT(int8_t, bcf_int8_vector_end); break;
case BCF_BT_INT16: BRANCH_INT(int16_t, bcf_int16_vector_end); break;
case BCF_BT_INT32: BRANCH_INT(int32_t, bcf_int32_vector_end); break;
default: error("The GT type is not lineognised: %d at %s:%d\n",fmt->type, bcf_seqname(flt->hdr,line),line->pos+1); break;
}
#undef BRANCH_INT
assert( tok->nsamples == nsmpl );
tok->nvalues = tok->str_value.l = nvals1*nsmpl;
tok->str_value.s[tok->str_value.l] = 0;
tok->nval1 = nvals1;
}
static void filters_set_genotype2(filter_t *flt, bcf1_t *line, token_t *tok) { _filters_set_genotype(flt, line, tok, 2); }
static void filters_set_genotype3(filter_t *flt, bcf1_t *line, token_t *tok) { _filters_set_genotype(flt, line, tok, 3); }
static void filters_set_genotype4(filter_t *flt, bcf1_t *line, token_t *tok) { _filters_set_genotype(flt, line, tok, 4); }
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 = 0;
return;
}
int i, blen = 4, nsmpl = line->n_sample;
gt_length_too_big:
tok->str_value.l = 0;
for (i=0; i<nsmpl; i++)
{
size_t plen = tok->str_value.l;
bcf_format_gt(fmt, i, &tok->str_value);
kputc_(0, &tok->str_value);
if ( tok->str_value.l - plen > blen )
{
// too many alternate alleles or ploidy is too large, the genotype does not fit
// three characters ("0/0" vs "10/10").
blen *= 2;
goto gt_length_too_big;
}
plen = tok->str_value.l - plen;
while ( plen < blen )
{
kputc_(0, &tok->str_value);
plen++;
}
}
assert( tok->nsamples == nsmpl );
tok->nvalues = tok->str_value.l;
tok->nval1 = blen;
}
static void filters_set_ilen(filter_t *flt, bcf1_t *line, token_t *tok)
{
tok->nvalues = line->n_allele - 1;
hts_expand(double,tok->nvalues,tok->mvalues,tok->values);
int i, rlen = strlen(line->d.allele[0]);
for (i=1; i<line->n_allele; i++)
{
int alen = strlen(line->d.allele[i]);
if ( rlen==alen ) bcf_double_set_missing(tok->values[i-1]);
else tok->values[i-1] = alen - rlen;
}
}
static void filters_set_ref_string(filter_t *flt, bcf1_t *line, token_t *tok)
{
tok->str_value.l = 0;
kputs(line->d.allele[0], &tok->str_value);
tok->nvalues = tok->str_value.l;
}
static void filters_set_alt_string(filter_t *flt, bcf1_t *line, token_t *tok)
{
tok->str_value.l = 0;
if ( tok->idx>=0 )
{
if ( line->n_allele > tok->idx + 1 )
kputs(line->d.allele[tok->idx + 1], &tok->str_value);
else
kputc('.', &tok->str_value);
}
else if ( tok->idx==-2 )
{
int i, end = tok->nuidxs ? tok->nuidxs : line->n_allele - 1;
if ( end >= line->n_allele - 1 ) end = line->n_allele - 2;
for (i=0; i<=end; i++)
if ( i>=tok->nidxs || tok->idxs[i] )
{
if ( tok->str_value.l ) kputc(',', &tok->str_value);
kputs(line->d.allele[i+1], &tok->str_value);
}
}
else if ( line->n_allele>1 )
{
kputs(line->d.allele[1], &tok->str_value);
int i;
for (i=2; i<line->n_allele; i++)