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convert.c
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convert.c
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/* convert.c -- functions for converting between VCF/BCF and related formats.
Copyright (C) 2013-2023 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 <stdio.h>
#include <unistd.h>
#include <getopt.h>
#include <assert.h>
#include <ctype.h>
#include <string.h>
#include <errno.h>
#include <sys/stat.h>
#include <sys/types.h>
#include <stdint.h>
#define __STDC_FORMAT_MACROS
#include <inttypes.h>
#include <math.h>
#include <htslib/vcf.h>
#include <htslib/synced_bcf_reader.h>
#include <htslib/vcfutils.h>
#include <htslib/kfunc.h>
#include <htslib/khash_str2int.h>
#include <htslib/hts_endian.h>
#include "bcftools.h"
#include "variantkey.h"
#include "convert.h"
#include "filter.h"
#define T_CHROM 1
#define T_POS 2
#define T_ID 3
#define T_REF 4
#define T_ALT 5
#define T_QUAL 6
#define T_FILTER 7
#define T_INFO 8
#define T_FORMAT 9
#define T_SAMPLE 10
#define T_SEP 11
#define T_IS_TS 12
#define T_TYPE 13
#define T_MASK 14
#define T_GT 15
#define T_TGT 16
#define T_LINE 17
#define T_CHROM_POS_ID 18 // not publicly advertised
#define T_GT_TO_PROB3 19 // not publicly advertised
#define T_PL_TO_PROB3 20 // not publicly advertised
#define T_GP_TO_PROB3 21 // not publicly advertised
#define T_FIRST_ALT 22 // not publicly advertised
#define T_IUPAC_GT 23
#define T_GT_TO_HAP 24 // not publicly advertised
#define T_GT_TO_HAP2 25 // not publicly advertised
#define T_TBCSQ 26
#define T_END 27
#define T_POS0 28
#define T_END0 29
#define T_RSX 30 // RSID HEX
#define T_VKX 31 // VARIANTKEY HEX
#define T_PBINOM 32
#define T_NPASS 33
typedef struct _fmt_t
{
int type, id, is_gt_field, ready, subscript;
char *key;
bcf_fmt_t *fmt;
void *usr; // user data (optional)
void (*handler)(convert_t *, bcf1_t *, struct _fmt_t *, int, kstring_t *);
void (*destroy)(void*); // clean user data (optional)
}
fmt_t;
struct _convert_t
{
fmt_t *fmt;
int nfmt, mfmt;
int nsamples, *samples;
bcf_hdr_t *header;
int max_unpack;
char *format_str;
bcf_srs_t *readers; // required only for %MASK
int nreaders;
void *dat;
int ndat;
char *undef_info_tag;
void *used_tags_hash;
char **used_tags_list;
char *print_filtered;
int nused_tags;
int allow_undef_tags;
int force_newline;
int header_samples;
uint8_t **subset_samples;
};
typedef struct
{
kstring_t hap1,hap2;
char **str;
int n, m;
}
bcsq_t;
static void process_chrom(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { kputs(convert->header->id[BCF_DT_CTG][line->rid].key, str); }
static void process_pos(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { kputw(line->pos+1, str); }
static void process_pos0(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { kputw(line->pos, str); }
static void process_end(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { kputw(line->pos+line->rlen, str); }
static void process_end0(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { kputw(line->pos+line->rlen-1, str); }
static void process_id(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { kputs(line->d.id, str); }
static void process_ref(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { kputs(line->d.allele[0], str); }
static void process_alt(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str)
{
int i;
if ( line->n_allele==1 )
{
kputc('.', str);
return;
}
if ( fmt->subscript>=0 )
{
if ( line->n_allele > fmt->subscript+1 )
kputs(line->d.allele[fmt->subscript+1], str);
else
kputc('.', str);
return;
}
for (i=1; i<line->n_allele; i++)
{
if ( i>1 ) kputc(',', str);
kputs(line->d.allele[i], str);
}
}
static void process_first_alt(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str)
{
if ( line->n_allele==1 )
kputc('.', str);
else
kputs(line->d.allele[1], str);
}
static void process_qual(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str)
{
if ( bcf_float_is_missing(line->qual) ) kputc('.', str);
else kputd(line->qual, str);
}
static void process_filter(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str)
{
int i;
if ( line->d.n_flt )
{
for (i=0; i<line->d.n_flt; i++)
{
if (i) kputc(';', str);
kputs(convert->header->id[BCF_DT_ID][line->d.flt[i]].key, str);
}
}
else kputc('.', str);
}
static inline int32_t bcf_array_ivalue(uint8_t *bcf_array, int type, int idx)
{
if ( type==BCF_BT_INT8 )
{
int8_t val = le_to_i8(&bcf_array[idx * sizeof(val)]);
if ( val==bcf_int8_missing ) return bcf_int32_missing;
if ( val==bcf_int8_vector_end ) return bcf_int32_vector_end;
return val;
}
if ( type==BCF_BT_INT16 )
{
int16_t val = le_to_i16(&bcf_array[idx * sizeof(val)]);
if ( val==bcf_int16_missing ) return bcf_int32_missing;
if ( val==bcf_int16_vector_end ) return bcf_int32_vector_end;
return val;
}
return le_to_i32(&bcf_array[idx * sizeof(int32_t)]);
}
static inline void _copy_field(char *src, uint32_t len, int idx, kstring_t *str)
{
int n = 0, ibeg = 0;
while ( src[ibeg] && ibeg<len && n < idx )
{
if ( src[ibeg]==',' ) n++;
ibeg++;
}
if ( ibeg==len ) { kputc('.', str); return; }
int iend = ibeg;
while ( src[iend] && src[iend]!=',' && iend<len ) iend++;
if ( iend>ibeg )
kputsn(src+ibeg, iend-ibeg, str);
else
kputc('.', str);
}
static void process_info(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str)
{
int i;
if ( !fmt->key ) // the whole INFO column
{
int first = 1;
for (i=0; i<line->n_info; i++)
{
bcf_info_t *inf = &line->d.info[i];
if ( !inf->vptr ) continue;
if ( !first ) kputc(';', str);
first = 0;
if ( inf->key >= convert->header->n[BCF_DT_ID] ) continue;
kputs(convert->header->id[BCF_DT_ID][inf->key].key, str);
if ( inf->len <= 0 ) continue;
kputc('=', str);
if ( inf->len == 1 )
{
switch (inf->type)
{
case BCF_BT_INT8: if ( inf->v1.i==bcf_int8_missing ) kputc('.', str); else kputw(inf->v1.i, str); break;
case BCF_BT_INT16: if ( inf->v1.i==bcf_int16_missing ) kputc('.', str); else kputw(inf->v1.i, str); break;
case BCF_BT_INT32: if ( inf->v1.i==bcf_int32_missing ) kputc('.', str); else kputw(inf->v1.i, str); break;
case BCF_BT_FLOAT: if ( bcf_float_is_missing(inf->v1.f) ) kputc('.', str); else kputd(inf->v1.f, str); break;
case BCF_BT_CHAR: kputc(inf->v1.i, str); break;
default: error("Unexpected type %d", inf->type); break;
}
}
else bcf_fmt_array(str, inf->len, inf->type, inf->vptr);
}
if ( first ) kputc('.', str);
return;
}
if ( fmt->id<0 )
{
kputc('.', str);
return;
}
for (i=0; i<line->n_info; i++)
if ( line->d.info[i].key == fmt->id ) break;
// output "." if the tag is not present
if ( i==line->n_info )
{
kputc('.', str);
return;
}
bcf_info_t *info = &line->d.info[i];
// if this is a flag, output 1
if ( info->len <=0 )
{
kputc('1', str);
return;
}
if ( info->len == 1 )
{
switch (info->type)
{
case BCF_BT_INT8: if ( info->v1.i==bcf_int8_missing ) kputc('.', str); else kputw(info->v1.i, str); break;
case BCF_BT_INT16: if ( info->v1.i==bcf_int16_missing ) kputc('.', str); else kputw(info->v1.i, str); break;
case BCF_BT_INT32: if ( info->v1.i==bcf_int32_missing ) kputc('.', str); else kputw(info->v1.i, str); break;
case BCF_BT_FLOAT: if ( bcf_float_is_missing(info->v1.f) ) kputc('.', str); else kputd(info->v1.f, str); break;
case BCF_BT_CHAR: kputc(info->v1.i, str); break;
default: fprintf(stderr,"todo: type %d\n", info->type); exit(1); break;
}
}
else if ( fmt->subscript >=0 )
{
if ( info->len <= fmt->subscript )
{
kputc('.', str);
return;
}
#define BRANCH(type_t, convert, is_missing, is_vector_end, kprint) { \
type_t val = convert(&info->vptr[fmt->subscript * sizeof(type_t)]); \
if ( is_missing || is_vector_end ) kputc('.',str); \
else kprint; \
}
switch (info->type)
{
case BCF_BT_INT8: BRANCH(int8_t, le_to_i8, val==bcf_int8_missing, val==bcf_int8_vector_end, kputw(val, str)); break;
case BCF_BT_INT16: BRANCH(int16_t, le_to_i16, val==bcf_int16_missing, val==bcf_int16_vector_end, kputw(val, str)); break;
case BCF_BT_INT32: BRANCH(int32_t, le_to_i32, val==bcf_int32_missing, val==bcf_int32_vector_end, kputw(val, str)); break;
case BCF_BT_FLOAT: BRANCH(float, le_to_float, bcf_float_is_missing(val), bcf_float_is_vector_end(val), kputd(val, str)); break;
case BCF_BT_CHAR: _copy_field((char*)info->vptr, info->vptr_len, fmt->subscript, str); break;
default: fprintf(stderr,"todo: type %d\n", info->type); exit(1); break;
}
#undef BRANCH
}
else
bcf_fmt_array(str, info->len, info->type, info->vptr);
}
static void init_format(convert_t *convert, bcf1_t *line, fmt_t *fmt)
{
fmt->id = bcf_hdr_id2int(convert->header, BCF_DT_ID, fmt->key);
if ( !bcf_hdr_idinfo_exists(convert->header,BCF_HL_FMT,fmt->id) ) fmt->id = -1;
fmt->fmt = NULL;
if ( fmt->id >= 0 )
{
int i;
for (i=0; i<(int)line->n_fmt; i++)
if ( line->d.fmt[i].id==fmt->id ) { fmt->fmt = &line->d.fmt[i]; break; }
}
else if ( !convert->allow_undef_tags )
error("Error: no such tag defined in the VCF header: FORMAT/%s\n", fmt->key);
fmt->ready = 1;
}
static void process_complete_format(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str)
{
if ( convert->nsamples )
{
int i,j;
if ( line->n_fmt)
{
int gt_i = -1;
bcf_fmt_t *fmt = line->d.fmt;
int first = 1;
for (i=0; i<(int)line->n_fmt; i++)
{
if ( !fmt[i].p || fmt[i].id<0 ) continue;
if ( !first ) kputc(':', str);
first = 0;
kputs(convert->header->id[BCF_DT_ID][fmt[i].id].key, str);
if ( strcmp(convert->header->id[BCF_DT_ID][fmt[i].id].key, "GT") == 0) gt_i = i;
}
if ( first ) kputc('.', str);
for (j=0; j<convert->nsamples; j++)
{
kputc('\t', str);
first = 1;
for (i=0; i<(int)line->n_fmt; i++)
{
bcf_fmt_t *f = &fmt[i];
if ( !f->p ) continue;
if ( !first ) kputc(':', str);
first = 0;
if (gt_i == i)
bcf_format_gt(f,convert->samples[j],str);
else
bcf_fmt_array(str, f->n, f->type, f->p + convert->samples[j] * f->size);
}
if ( first ) kputc('.', str);
}
}
else
for (j=0; j<=line->n_sample; j++)
kputs("\t.", str);
}
else
kputc('.',str);
}
static void process_format(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str)
{
if ( !fmt->ready )
init_format(convert, line, fmt);
if ( fmt->fmt==NULL )
{
kputc('.', str);
return;
}
else if ( fmt->subscript >=0 )
{
if ( fmt->fmt->n <= fmt->subscript )
{
kputc('.', str);
return;
}
if ( fmt->fmt->type == BCF_BT_FLOAT )
{
uint8_t *ptr = fmt->fmt->p + isample*fmt->fmt->size;
float val = le_to_float(&ptr[fmt->subscript * sizeof(float)]);
if ( bcf_float_is_missing(val) || bcf_float_is_vector_end(val) )
kputc('.', str);
else
kputd(val, str);
}
else if ( fmt->fmt->type != BCF_BT_CHAR )
{
int32_t ival = bcf_array_ivalue(fmt->fmt->p+isample*fmt->fmt->size,fmt->fmt->type,fmt->subscript);
if ( ival==bcf_int32_missing || ival==bcf_int32_vector_end )
kputc('.', str);
else
kputw(ival, str);
}
else if ( fmt->fmt->type == BCF_BT_CHAR )
_copy_field((char*)(fmt->fmt->p + isample*fmt->fmt->size), fmt->fmt->size, fmt->subscript, str);
else error("TODO: %s:%d .. fmt->type=%d\n", __FILE__,__LINE__, fmt->fmt->type);
}
else
bcf_fmt_array(str, fmt->fmt->n, fmt->fmt->type, fmt->fmt->p + isample*fmt->fmt->size);
}
static void process_gt(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str)
{
if ( !fmt->ready )
init_format(convert, line, fmt);
if ( fmt->fmt==NULL )
{
kputc('.', str);
return;
}
bcf_format_gt(fmt->fmt, isample, str);
}
static void process_tgt(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str)
{
if ( !fmt->ready )
init_format(convert, line, fmt);
if ( fmt->fmt==NULL )
{
kputc('.', str);
return;
}
assert( fmt->fmt->type==BCF_BT_INT8 );
int l;
int8_t *x = (int8_t*)(fmt->fmt->p + isample*fmt->fmt->size); // FIXME: does not work with n_alt >= 64
for (l = 0; l < fmt->fmt->n && x[l] != bcf_int8_vector_end; ++l)
{
if (l) kputc("/|"[x[l]&1], str);
if (x[l]>>1)
{
int ial = (x[l]>>1) - 1;
kputs(line->d.allele[ial], str);
}
else
kputc('.', str);
}
if (l == 0) kputc('.', str);
}
static void destroy_tbcsq(void *usr)
{
if ( !usr ) return;
bcsq_t *csq = (bcsq_t*) usr;
free(csq->hap1.s);
free(csq->hap2.s);
if ( csq->n )
free(csq->str[0]);
free(csq->str);
free(csq);
}
static void process_tbcsq(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str)
{
if ( !fmt->ready )
{
init_format(convert, line, fmt);
bcsq_t *csq;
if ( fmt->usr )
{
csq = (bcsq_t*) fmt->usr;
if ( csq->n )
free(csq->str[0]);
csq->n = 0;
}
else
csq = (bcsq_t*) calloc(1,sizeof(bcsq_t));
fmt->usr = csq;
int i=0, len = 0;
char *tmp = NULL;
if ( bcf_get_info_string(convert->header,line,fmt->key,&tmp,&len)<0 )
{
csq->n = 0;
return;
}
do
{
csq->n++;
hts_expand(char*, csq->n, csq->m, csq->str);
csq->str[ csq->n-1 ] = tmp + i;
while ( i<len && tmp[i]!=',' ) i++;
if ( i<len && tmp[i]==',' ) tmp[i++] = 0;
}
while ( i<len );
}
bcsq_t *csq = (bcsq_t*)fmt->usr;
if ( fmt->fmt==NULL || !csq->n ) return;
csq->hap1.l = 0;
csq->hap2.l = 0;
int mask = fmt->subscript==0 ? 3 : 1; // merge both haplotypes if subscript==0
#define BRANCH(type_t, convert, nbits) { \
uint8_t *x = fmt->fmt->p + isample*fmt->fmt->size; \
int i,j; \
if ( fmt->subscript<=0 || fmt->subscript==1 ) \
{ \
for (j=0; j < fmt->fmt->n; j++) \
{ \
type_t val = convert(&x[j * sizeof(type_t)]); \
if ( !val ) continue; \
for (i=0; i<nbits; i+=2) \
if ( val & (mask<<i) ) { kputs(csq->str[(j*30+i)/2], &csq->hap1); kputc_(',', &csq->hap1); } \
} \
} \
if ( fmt->subscript<0 || fmt->subscript==2 ) \
{ \
for (j=0; j < fmt->fmt->n; j++) \
{ \
type_t val = convert(&x[j * sizeof(type_t)]); \
if ( !val ) continue; \
for (i=1; i<nbits; i+=2) \
if ( val & (1<<i) ) { kputs(csq->str[(j*30+i)/2], &csq->hap2); kputc_(',', &csq->hap2); } \
} \
} \
}
switch (fmt->fmt->type)
{
case BCF_BT_INT8: BRANCH(uint8_t, le_to_u8, 8); break;
case BCF_BT_INT16: BRANCH(uint16_t, le_to_u16, 16); break;
case BCF_BT_INT32: BRANCH(uint32_t, le_to_u32, 30); break; // 2 bits unused to account for the reserved BCF values
default: error("Unexpected type: %d\n", fmt->fmt->type); exit(1); break;
}
#undef BRANCH
if ( !csq->hap1.l && !csq->hap2.l ) return;
if ( csq->hap1.l ) csq->hap1.s[--csq->hap1.l] = 0;
if ( csq->hap2.l ) csq->hap2.s[--csq->hap2.l] = 0;
if ( fmt->subscript<0 )
{
kputs(csq->hap1.l?csq->hap1.s:".", str);
kputc_('\t', str);
kputs(csq->hap2.l?csq->hap2.s:".", str);
}
else if ( fmt->subscript<2 )
kputs(csq->hap1.l?csq->hap1.s:".", str);
else
kputs(csq->hap2.l?csq->hap2.s:".", str);
}
static void init_format_iupac(convert_t *convert, bcf1_t *line, fmt_t *fmt)
{
init_format(convert, line, fmt);
if ( fmt->fmt==NULL ) return;
// Init mapping between alleles and IUPAC table
hts_expand(uint8_t, line->n_allele, convert->ndat, convert->dat);
int8_t *dat = (int8_t*)convert->dat;
int i;
for (i=0; i<line->n_allele; i++)
{
if ( line->d.allele[i][1] ) dat[i] = -1;
else
{
switch (line->d.allele[i][0])
{
case 'A': dat[i] = 0; break;
case 'C': dat[i] = 1; break;
case 'G': dat[i] = 2; break;
case 'T': dat[i] = 3; break;
case 'a': dat[i] = 0; break;
case 'c': dat[i] = 1; break;
case 'g': dat[i] = 2; break;
case 't': dat[i] = 3; break;
default: dat[i] = -1;
}
}
}
}
static void process_iupac_gt(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str)
{
if ( !fmt->ready )
init_format_iupac(convert, line, fmt);
if ( fmt->fmt==NULL )
{
kputc('.', str);
return;
}
assert( fmt->fmt->type==BCF_BT_INT8 );
static const char iupac[4][4] = { {'A','M','R','W'},{'M','C','S','Y'},{'R','S','G','K'},{'W','Y','K','T'} };
int8_t *dat = (int8_t*)convert->dat;
int8_t *x = (int8_t*)(fmt->fmt->p + isample*fmt->fmt->size); // FIXME: does not work with n_alt >= 64
int l = 0;
while ( l<fmt->fmt->n && x[l]!=bcf_int8_vector_end && x[l]!=bcf_int8_missing ) l++;
if ( l==2 )
{
// diploid
int ia = (x[0]>>1) - 1, ib = (x[1]>>1) - 1;
if ( ia>=0 && ia<line->n_allele && ib>=0 && ib<line->n_allele && dat[ia]>=0 && dat[ib]>=0 )
{
kputc(iupac[dat[ia]][dat[ib]], str);
return;
}
}
for (l = 0; l < fmt->fmt->n && x[l] != bcf_int8_vector_end; ++l)
{
if (l) kputc("/|"[x[l]&1], str);
if (x[l]>>1)
{
int ial = (x[l]>>1) - 1;
kputs(line->d.allele[ial], str);
}
else
kputc('.', str);
}
if (l == 0) kputc('.', str);
}
static void process_sample(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str)
{
kputs(convert->header->samples[isample], str);
}
static void process_sep(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { if (fmt->key) kputs(fmt->key, str); }
static void process_is_ts(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str)
{
int is_ts = 0;
if ( bcf_get_variant_types(line) & (VCF_SNP|VCF_MNP) )
is_ts = abs(bcf_acgt2int(*line->d.allele[0])-bcf_acgt2int(*line->d.allele[1])) == 2 ? 1 : 0;
kputc(is_ts ? '1' : '0', str);
}
static void process_type(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str)
{
int line_type = bcf_get_variant_types(line);
int i = 0;
if ( line_type == VCF_REF ) { kputs("REF", str); i++; }
if ( line_type & VCF_SNP ) { if (i) kputc(',',str); kputs("SNP", str); i++; }
if ( line_type & VCF_MNP ) { if (i) kputc(',',str); kputs("MNP", str); i++; }
if ( line_type & VCF_INDEL ) { if (i) kputc(',',str); kputs("INDEL", str); i++; }
if ( line_type & VCF_OTHER ) { if (i) kputc(',',str); kputs("OTHER", str); i++; }
if ( line_type & VCF_BND ) { if (i) kputc(',',str); kputs("BND", str); i++; }
if ( line_type & VCF_OVERLAP ) { if (i) kputc(',',str); kputs("OVERLAP", str); i++; }
}
static void process_line(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str)
{
vcf_format1(convert->header, line, str);
if ( str->s[str->l-1]=='\n' ) str->l--;
}
static void process_chrom_pos_id(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str)
{
if ( line->d.id[0]!='.' || line->d.id[1] )
{
// ID is present
kputs(line->d.id, str);
}
else
{
// use CHROM:POS instead of ID
kputs(convert->header->id[BCF_DT_CTG][line->rid].key, str);
kputc(':', str);
kputw(line->pos+1, str);
}
}
static void process_gt_to_prob3(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str)
{
int m,n,i;
m = convert->ndat / sizeof(int32_t);
n = bcf_get_genotypes(convert->header,line,&convert->dat,&m);
convert->ndat = m * sizeof(int32_t);
if ( n<=0 )
{
// Throw an error or silently proceed?
//
// for (i=0; i<convert->nsamples; i++) kputs(" 0.33 0.33 0.33", str);
// return;
error("Error parsing GT tag at %s:%"PRId64"\n", bcf_seqname(convert->header,line),(int64_t) line->pos+1);
}
n /= convert->nsamples;
for (i=0; i<convert->nsamples; i++)
{
int32_t *ptr = (int32_t*)convert->dat + i*n;
int j;
for (j=0; j<n; j++)
if ( ptr[j]==bcf_int32_vector_end ) break;
if ( j==2 )
{
// diploid
if ( bcf_gt_is_missing(ptr[0]) )
kputs(" 0.33 0.33 0.33", str);
else if ( bcf_gt_allele(ptr[0])!=bcf_gt_allele(ptr[1]) )
kputs(" 0 1 0", str); // HET
else if ( bcf_gt_allele(ptr[0])==1 )
kputs(" 0 0 1", str); // ALT HOM, first ALT allele
else
kputs(" 1 0 0", str); // REF HOM or something else than first ALT
}
else if ( j==1 )
{
// haploid
if ( bcf_gt_is_missing(ptr[0]) )
kputs(" 0.5 0.0 0.5", str);
else if ( bcf_gt_allele(ptr[0])==1 )
kputs(" 0 0 1", str); // first ALT allele
else
kputs(" 1 0 0", str); // REF or something else than first ALT
}
else error("FIXME: not ready for ploidy %d\n", j);
}
}
static void process_pl_to_prob3(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str)
{
int m,n,i;
m = convert->ndat / sizeof(int32_t);
n = bcf_get_format_int32(convert->header,line,"PL",&convert->dat,&m);
convert->ndat = m * sizeof(int32_t);
if ( n<=0 )
{
// Throw an error or silently proceed?
//
// for (i=0; i<convert->nsamples; i++) kputs(" 0.33 0.33 0.33", str);
// return;
error("Error parsing PL tag at %s:%"PRId64"\n", bcf_seqname(convert->header,line),(int64_t) line->pos+1);
}
n /= convert->nsamples;
for (i=0; i<convert->nsamples; i++)
{
int32_t *ptr = (int32_t*)convert->dat + i*n;
int j;
float sum = 0;
for (j=0; j<n; j++)
{
if ( ptr[j]==bcf_int32_vector_end ) break;
sum += pow(10,-0.1*ptr[j]);
}
if ( j==line->n_allele )
{
// haploid
kputc(' ',str);
ksprintf(str,"%f",pow(10,-0.1*ptr[0])/sum);
kputs(" 0 ", str);
ksprintf(str,"%f",pow(10,-0.1*ptr[1])/sum);
}
else
{
// diploid
kputc(' ',str);
ksprintf(str,"%f",pow(10,-0.1*ptr[0])/sum);
kputc(' ',str);
ksprintf(str,"%f",pow(10,-0.1*ptr[1])/sum);
kputc(' ',str);
ksprintf(str,"%f",pow(10,-0.1*ptr[2])/sum);
}
}
}
static void process_gp_to_prob3(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str)
{
int m,n,i;
m = convert->ndat / sizeof(float);
n = bcf_get_format_float(convert->header,line,"GP",&convert->dat,&m);
convert->ndat = m * sizeof(float);
if ( n<=0 )
{
// Throw an error or silently proceed?
//
// for (i=0; i<convert->nsamples; i++) kputs(" 0.33 0.33 0.33", str);
// return;
error("Error parsing GP tag at %s:%"PRId64"\n", bcf_seqname(convert->header,line),(int64_t) line->pos+1);
}
n /= convert->nsamples;
for (i=0; i<convert->nsamples; i++)
{
float *ptr = (float*)convert->dat + i*n;
int j;
for (j=0; j<n; j++)
{
if ( bcf_float_is_vector_end(ptr[j]) ) break;
if ( bcf_float_is_missing(ptr[j]) ) { ptr[j]=0; continue; }
if ( ptr[j]<0 || ptr[j]>1 ) error("[%s:%"PRId64":%f] GP value outside range [0,1]; bcftools convert expects the VCF4.3+ spec for the GP field encoding genotype posterior probabilities", bcf_seqname(convert->header,line),(int64_t) line->pos+1,ptr[j]);
}
if ( j==line->n_allele )
ksprintf(str," %f %f %f",ptr[0],0.,ptr[1]); // haploid
else
ksprintf(str," %f %f %f",ptr[0],ptr[1],ptr[2]); // diploid
}
}
static void process_gt_to_hap(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str)
{
// https://mathgen.stats.ox.ac.uk/impute/impute_v2.html#-known_haps_g
// File containing known haplotypes for the study cohort. The format
// is the same as the output format from IMPUTE2's -phase option:
// five header columns (as in the -g file) followed by two columns
// (haplotypes) per individual. Allowed values in the haplotype
// columns are 0, 1, and ?.
// If your study dataset is fully phased, you can replace the -g file
// with a -known_haps_g file. This will cause IMPUTE2 to perform
// haploid imputation, although it will still report diploid imputation
// probabilities in the main output file. If any genotypes are missing,
// they can be marked as '? ?' (two question marks separated by one
// space) in the input file. (The program does not allow just one
// allele from a diploid genotype to be missing.) If the reference
// panels are also phased, IMPUTE2 will perform a single, fast
// imputation step rather than its standard MCMC module this is how
// the program imputes into pre-phased GWAS haplotypes.
// The -known_haps_g file can also be used to specify study
// genotypes that are "partially" phased, in the sense that some
// genotypes are phased relative to a fixed reference point while
// others are not. We anticipate that this will be most useful when
// trying to phase resequencing data onto a scaffold of known
// haplotypes. To mark a known genotype as unphased, place an
// asterisk immediately after each allele, with no space between
// the allele (0/1) and the asterisk (*); e.g., "0* 1*" for a
// heterozygous genotype of unknown phase.
int i, gt_id = bcf_hdr_id2int(convert->header, BCF_DT_ID, "GT");
if ( !bcf_hdr_idinfo_exists(convert->header,BCF_HL_FMT,gt_id) )
error("FORMAT/GT tag not present at %s:%"PRId64"\n", bcf_seqname(convert->header, line),(int64_t) line->pos+1);
if ( !(line->unpacked & BCF_UN_FMT) ) bcf_unpack(line, BCF_UN_FMT);
bcf_fmt_t *fmt_gt = NULL;
for (i=0; i<line->n_fmt; i++)
if ( line->d.fmt[i].id==gt_id ) { fmt_gt = &line->d.fmt[i]; break; }
if ( !fmt_gt )
error("FORMAT/GT tag not present at %s:%"PRId64"\n", bcf_seqname(convert->header, line),(int64_t) line->pos+1);
// Alloc all memory in advance to avoid kput routines. The biggest allowed allele index is 99
if ( line->n_allele > 100 )
error("Too many alleles (%d) at %s:%"PRId64"\n", line->n_allele, bcf_seqname(convert->header, line),(int64_t) line->pos+1);
if ( ks_resize(str, str->l+convert->nsamples*8) != 0 )
error("Could not alloc %" PRIu64 " bytes\n", (uint64_t)(str->l + convert->nsamples*8));
if ( fmt_gt->type!=BCF_BT_INT8 ) // todo: use BRANCH_INT if the VCF is valid
error("Uh, too many alleles (%d) or redundant BCF representation at %s:%"PRId64"\n", line->n_allele, bcf_seqname(convert->header, line),(int64_t) line->pos+1);
if ( fmt_gt->n!=1 && fmt_gt->n!=2 )
error("Uh, ploidy of %d not supported, see %s:%"PRId64"\n", fmt_gt->n, bcf_seqname(convert->header, line),(int64_t) line->pos+1);
int8_t *ptr = ((int8_t*) fmt_gt->p) - fmt_gt->n;
for (i=0; i<convert->nsamples; i++)
{
ptr += fmt_gt->n;
if ( fmt_gt->n==1 ) // haploid genotypes
{
if ( ptr[0]==2 ) /* 0 */
{
str->s[str->l++] = '0'; str->s[str->l++] = ' '; str->s[str->l++] = '-'; str->s[str->l++] = ' ';
}
else if ( ptr[0]==bcf_int8_missing ) /* . */
{
str->s[str->l++] = '?'; str->s[str->l++] = ' '; str->s[str->l++] = '?'; str->s[str->l++] = ' ';
}
else if ( ptr[0]==4 ) /* 1 */
{
str->s[str->l++] = '1'; str->s[str->l++] = ' '; str->s[str->l++] = '-'; str->s[str->l++] = ' ';
}
else
{
kputw(bcf_gt_allele(ptr[0]),str); str->s[str->l++] = ' '; str->s[str->l++] = '-'; str->s[str->l++] = ' ';
}
}
else if ( ptr[0]==2 )
{
if ( ptr[1]==3 ) /* 0|0 */
{
str->s[str->l++] = '0'; str->s[str->l++] = ' '; str->s[str->l++] = '0'; str->s[str->l++] = ' ';
}
else if ( ptr[1]==5 ) /* 0|1 */
{
str->s[str->l++] = '0'; str->s[str->l++] = ' '; str->s[str->l++] = '1'; str->s[str->l++] = ' ';
}
else if ( ptr[1]==bcf_int8_vector_end ) /* 0 */
{
str->s[str->l++] = '0'; str->s[str->l++] = ' '; str->s[str->l++] = '-'; str->s[str->l++] = ' ';
}
else if ( ptr[1]==2 ) /* 0/0 */
{
str->s[str->l++] = '0'; str->s[str->l++] = '*'; str->s[str->l++] = ' '; str->s[str->l++] = '0'; str->s[str->l++] = '*'; str->s[str->l++] = ' ';
}
else if ( ptr[1]==4 ) /* 0/1 */
{
str->s[str->l++] = '0'; str->s[str->l++] = '*'; str->s[str->l++] = ' '; str->s[str->l++] = '1'; str->s[str->l++] = '*'; str->s[str->l++] = ' ';
}
else if ( bcf_gt_is_missing(ptr[1]) ) /* 0/. */
{
str->s[str->l++] = '?'; str->s[str->l++] = ' '; str->s[str->l++] = '?'; str->s[str->l++] = ' ';
}
else if ( bcf_gt_is_phased(ptr[1]) ) /* 0|x */
{
str->s[str->l++] = '0'; str->s[str->l++] = ' ';
kputw(bcf_gt_allele(ptr[1]),str);
str->s[str->l++] = ' ';
}
else /* 0/x */
{
str->s[str->l++] = '0'; str->s[str->l++] = '*'; str->s[str->l++] = ' ';
kputw(bcf_gt_allele(ptr[1]),str);
str->s[str->l++] = '*'; str->s[str->l++] = ' ';
}
}
else if ( ptr[0]==4 )
{
if ( ptr[1]==3 ) /* 1|0 */
{
str->s[str->l++] = '1'; str->s[str->l++] = ' '; str->s[str->l++] = '0'; str->s[str->l++] = ' ';
}
else if ( ptr[1]==5 ) /* 1|1 */
{
str->s[str->l++] = '1'; str->s[str->l++] = ' '; str->s[str->l++] = '1'; str->s[str->l++] = ' ';
}
else if ( ptr[1]==bcf_int8_vector_end ) /* 1 */
{
str->s[str->l++] = '1'; str->s[str->l++] = ' '; str->s[str->l++] = '-'; str->s[str->l++] = ' ';
}
else if ( ptr[1]==2 ) /* 1/0 */
{
str->s[str->l++] = '1'; str->s[str->l++] = '*'; str->s[str->l++] = ' '; str->s[str->l++] = '0'; str->s[str->l++] = '*'; str->s[str->l++] = ' ';
}
else if ( ptr[1]==4 ) /* 1/1 */
{
str->s[str->l++] = '1'; str->s[str->l++] = '*'; str->s[str->l++] = ' '; str->s[str->l++] = '1'; str->s[str->l++] = '*'; str->s[str->l++] = ' ';
}
else if ( bcf_gt_is_missing(ptr[1]) ) /* 1/. */
{
str->s[str->l++] = '?'; str->s[str->l++] = ' '; str->s[str->l++] = '?'; str->s[str->l++] = ' ';
}
else if ( bcf_gt_is_phased(ptr[1]) ) /* 1|x */
{
str->s[str->l++] = '1'; str->s[str->l++] = ' ';
kputw(bcf_gt_allele(ptr[1]),str);
str->s[str->l++] = ' ';
}
else /* 1/x */
{
str->s[str->l++] = '1'; str->s[str->l++] = '*'; str->s[str->l++] = ' ';
kputw(bcf_gt_allele(ptr[1]),str);
str->s[str->l++] = '*'; str->s[str->l++] = ' ';
}
}
else if ( bcf_gt_is_missing(ptr[0]) )
{
if ( ptr[1]==bcf_int8_vector_end )
{
str->s[str->l++] = '?'; str->s[str->l++] = ' '; str->s[str->l++] = '-'; str->s[str->l++] = ' ';
}
else
{
str->s[str->l++] = '?'; str->s[str->l++] = ' '; str->s[str->l++] = '?'; str->s[str->l++] = ' ';
}
}
else if ( ptr[1]==bcf_int8_vector_end )
{
/* use REF for something else than first ALT */
str->s[str->l++] = '0'; str->s[str->l++] = ' '; str->s[str->l++] = '-'; str->s[str->l++] = ' ';
}
else
{
kputw(bcf_gt_allele(ptr[0]),str);
if ( bcf_gt_is_phased(ptr[1]) ) str->s[str->l++] = '*';
str->s[str->l++] = ' ';
kputw(bcf_gt_allele(ptr[1]),str);
if ( bcf_gt_is_phased(ptr[1]) ) str->s[str->l++] = '*';
str->s[str->l++] = ' ';
}
}
str->s[--str->l] = 0; // delete the last space
}
static void process_gt_to_hap2(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str)
{
// same as process_gt_to_hap but converts haploid genotypes into diploid
int i, gt_id = bcf_hdr_id2int(convert->header, BCF_DT_ID, "GT");
if ( !bcf_hdr_idinfo_exists(convert->header,BCF_HL_FMT,gt_id) )
error("FORMAT/GT tag not present at %s:%"PRId64"\n", bcf_seqname(convert->header, line),(int64_t) line->pos+1);
if ( !(line->unpacked & BCF_UN_FMT) ) bcf_unpack(line, BCF_UN_FMT);
bcf_fmt_t *fmt_gt = NULL;
for (i=0; i<line->n_fmt; i++)