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vcfannotate.c
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/* vcfannotate.c -- Annotate and edit VCF/BCF files.
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 <stdio.h>
#include <strings.h>
#include <unistd.h>
#include <getopt.h>
#include <ctype.h>
#include <string.h>
#include <errno.h>
#include <sys/stat.h>
#include <sys/types.h>
#include <dirent.h>
#include <math.h>
#include <htslib/vcf.h>
#include <htslib/synced_bcf_reader.h>
#include <htslib/kseq.h>
#include <htslib/khash_str2int.h>
#include <dlfcn.h>
#include "bcftools.h"
#include "vcmp.h"
#include "filter.h"
#include "convert.h"
#include "smpl_ilist.h"
#include "regidx.h"
struct _args_t;
typedef struct _rm_tag_t
{
char *key;
int hdr_id;
void (*handler)(struct _args_t *, bcf1_t *, struct _rm_tag_t *);
}
rm_tag_t;
typedef struct
{
char **cols;
int ncols, mcols;
char **als;
int nals, mals;
kstring_t line;
int rid, start, end;
}
annot_line_t;
#define REPLACE_MISSING 0 // replace only missing values
#define REPLACE_ALL 1 // replace both missing and existing values
#define REPLACE_NON_MISSING 2 // replace only if tgt is not missing
#define SET_OR_APPEND 3 // set new value if missing or non-existent, append otherwise
#define MM_FIRST 0
#define MM_APPEND 1
#define MM_UNIQUE 2
#define MM_SUM 3
#define MM_AVG 4
#define MM_MIN 5
#define MM_MAX 6
typedef struct _annot_col_t
{
int icol, replace, number; // number: one of BCF_VL_* types
char *hdr_key_src, *hdr_key_dst;
int (*setter)(struct _args_t *, bcf1_t *, struct _annot_col_t *, void*);
int merge_method; // one of the MM_* defines
khash_t(str2int) *mm_str_hash; // lookup table to ensure uniqueness of added string values
kstring_t mm_kstr;
}
annot_col_t;
// Logic of the filters: include or exclude sites which match the filters?
#define FLT_INCLUDE 1
#define FLT_EXCLUDE 2
#define MARK_LISTED 1
#define MARK_UNLISTED 2
typedef struct _args_t
{
bcf_srs_t *files;
bcf_hdr_t *hdr, *hdr_out;
htsFile *out_fh;
int output_type, n_threads;
bcf_sr_regions_t *tgts;
regidx_t *tgt_idx;
regitr_t *tgt_itr;
int tgt_is_bed;
filter_t *filter;
char *filter_str;
int filter_logic; // include or exclude sites which match the filters? One of FLT_INCLUDE/FLT_EXCLUDE
int keep_sites;
rm_tag_t *rm; // tags scheduled for removal
int nrm;
int flt_keep_pass; // when all filters removed, reset to PASS
vcmp_t *vcmp; // for matching annotation and VCF lines by allele
annot_line_t *alines; // buffered annotation lines
int nalines, malines;
int ref_idx, alt_idx, chr_idx, beg_idx, end_idx; // -1 if not present
annot_col_t *cols; // column indexes and setters
int ncols;
char *set_ids_fmt;
convert_t *set_ids;
int set_ids_replace;
int nsmpl_annot;
int *sample_map, nsample_map, sample_is_file; // map[idst] -> isrc
uint8_t *src_smpl_pld, *dst_smpl_pld; // for Number=G format fields
int mtmpi, mtmpf, mtmps;
int mtmpi2, mtmpf2, mtmps2;
int mtmpi3, mtmpf3, mtmps3;
int32_t *tmpi, *tmpi2, *tmpi3;
float *tmpf, *tmpf2, *tmpf3;
char *tmps, *tmps2, **tmpp, **tmpp2;
kstring_t tmpks;
char **argv, *output_fname, *targets_fname, *regions_list, *header_fname;
char *remove_annots, *columns, *rename_chrs, *sample_names, *mark_sites;
char *merge_method_str;
int argc, drop_header, record_cmd_line, tgts_is_vcf, mark_sites_logic, force;
}
args_t;
char *msprintf(const char *fmt, ...);
int parse_with_payload(const char *line, char **chr_beg, char **chr_end, uint32_t *beg, uint32_t *end, void *payload, void *usr)
{
args_t *args = (args_t*) usr;
int ret = args->tgt_is_bed ? regidx_parse_bed(line, chr_beg, chr_end, beg, end, NULL, NULL) : regidx_parse_tab(line, chr_beg, chr_end, beg, end, NULL, NULL);
if ( ret<0 ) return ret;
*((char **)payload) = strdup(line);
return 0;
}
void free_payload(void *payload)
{
char *str = *((char**)payload);
free(str);
}
void remove_id(args_t *args, bcf1_t *line, rm_tag_t *tag)
{
bcf_update_id(args->hdr,line,NULL);
}
void remove_filter(args_t *args, bcf1_t *line, rm_tag_t *tag)
{
if ( tag->key && tag->hdr_id<0 )
{
assert(args->force);
tag->hdr_id = bcf_hdr_id2int(args->hdr, BCF_DT_ID, tag->key);
if ( !bcf_hdr_idinfo_exists(args->hdr,BCF_HL_FLT,tag->hdr_id) ) error("Error: parsing error\n"); // this should not happen
}
if ( !tag->key ) bcf_update_filter(args->hdr, line, NULL, args->flt_keep_pass);
else bcf_remove_filter(args->hdr, line, tag->hdr_id, args->flt_keep_pass);
}
void remove_qual(args_t *args, bcf1_t *line, rm_tag_t *tag)
{
bcf_float_set_missing(line->qual);
}
void remove_info(args_t *args, bcf1_t *line, rm_tag_t *tag)
{
// remove all INFO fields
if ( !(line->unpacked & BCF_UN_INFO) ) bcf_unpack(line, BCF_UN_INFO);
int i;
for (i=0; i<line->n_info; i++)
{
bcf_info_t *inf = &line->d.info[i];
if ( inf->vptr_free )
{
free(inf->vptr - inf->vptr_off);
inf->vptr_free = 0;
}
line->d.shared_dirty |= BCF1_DIRTY_INF;
inf->vptr = NULL;
inf->vptr_off = inf->vptr_len = 0;
}
}
void remove_info_tag(args_t *args, bcf1_t *line, rm_tag_t *tag)
{
bcf_update_info(args->hdr, line, tag->key, NULL, 0, BCF_HT_INT); // the type does not matter with n=0
}
void remove_format_tag(args_t *args, bcf1_t *line, rm_tag_t *tag)
{
bcf_update_format(args->hdr, line, tag->key, NULL, 0, BCF_HT_INT); // the type does not matter with n=0
}
void remove_format(args_t *args, bcf1_t *line, rm_tag_t *tag)
{
// remove all FORMAT fields except GT
if ( !(line->unpacked & BCF_UN_FMT) ) bcf_unpack(line, BCF_UN_FMT);
int i;
for (i=0; i<line->n_fmt; i++)
{
bcf_fmt_t *fmt = &line->d.fmt[i];
const char *key = bcf_hdr_int2id(args->hdr,BCF_DT_ID,fmt->id);
if ( key[0]=='G' && key[1]=='T' && !key[2] ) continue;
if ( fmt->p_free )
{
free(fmt->p - fmt->p_off);
fmt->p_free = 0;
}
line->d.indiv_dirty = 1;
fmt->p = NULL;
}
}
#include "htslib/khash.h"
KHASH_MAP_INIT_STR(vdict, bcf_idinfo_t)
typedef khash_t(vdict) vdict_t;
static void remove_hdr_lines(bcf_hdr_t *hdr, int type)
{
int i = 0, nrm = 0;
while ( i<hdr->nhrec )
{
if ( hdr->hrec[i]->type!=type ) { i++; continue; }
bcf_hrec_t *hrec = hdr->hrec[i];
if ( type==BCF_HL_FMT || type==BCF_HL_INFO || type==BCF_HL_FMT || type== BCF_HL_CTG )
{
// everything except FORMAT/GT
int id = bcf_hrec_find_key(hrec, "ID");
if ( id>=0 )
{
if ( type==BCF_HL_FMT && !strcmp(hrec->vals[id],"GT") ) { i++; continue; }
vdict_t *d = type==BCF_HL_CTG ? (vdict_t*)hdr->dict[BCF_DT_CTG] : (vdict_t*)hdr->dict[BCF_DT_ID];
khint_t k = kh_get(vdict, d, hdr->hrec[i]->vals[id]);
kh_val(d, k).hrec[type==BCF_HL_CTG?0:type] = NULL;
kh_val(d, k).info[type] |= 0xf;
}
}
nrm++;
hdr->nhrec--;
if ( i < hdr->nhrec )
memmove(&hdr->hrec[i],&hdr->hrec[i+1],(hdr->nhrec-i)*sizeof(bcf_hrec_t*));
bcf_hrec_destroy(hrec);
}
if ( nrm ) {
if (bcf_hdr_sync(hdr) < 0)
error_errno("[%s] Failed to update header", __func__);
}
}
static void init_remove_annots(args_t *args)
{
int keep_info = 0, keep_fmt = 0, keep_flt = 0;
void *keep = khash_str2int_init();
kstring_t str = {0,0,0};
char *ss = args->remove_annots;
while ( *ss )
{
args->nrm++;
args->rm = (rm_tag_t*) realloc(args->rm,sizeof(rm_tag_t)*args->nrm);
rm_tag_t *tag = &args->rm[args->nrm-1];
tag->key = NULL;
int type = BCF_HL_GEN;
if ( !strncasecmp("INFO/",ss,5) ) { type = BCF_HL_INFO; ss += 5; }
else if ( !strncasecmp("INF/",ss,4) ) { type = BCF_HL_INFO; ss += 4; }
else if ( !strncasecmp("FORMAT/",ss,7) ) { type = BCF_HL_FMT; ss += 7; }
else if ( !strncasecmp("FMT/",ss,4) ) { type = BCF_HL_FMT; ss += 4; }
else if ( !strncasecmp("FILTER/",ss,7) ) { type = BCF_HL_FLT; ss += 7; }
else if ( !strncasecmp("^INFO/",ss,6) ) { type = BCF_HL_INFO; ss += 6; keep_info = 1; }
else if ( !strncasecmp("^INF/",ss,5) ) { type = BCF_HL_INFO; ss += 5; keep_info = 1; }
else if ( !strncasecmp("^FORMAT/",ss,8) ) { type = BCF_HL_FMT; ss += 8; keep_fmt = 1; }
else if ( !strncasecmp("^FMT/",ss,5) ) { type = BCF_HL_FMT; ss += 5; keep_fmt = 1; }
else if ( !strncasecmp("^FILTER/",ss,8) ) { type = BCF_HL_FLT; ss += 8; keep_flt = 1; }
char *se = ss;
while ( *se && *se!=',' ) se++;
str.l = 0;
kputsn(ss, se-ss, &str);
if ( type==BCF_HL_FLT )
{
if ( !keep_flt )
{
args->flt_keep_pass = 1;
tag->handler = remove_filter;
tag->key = strdup(str.s);
tag->hdr_id = bcf_hdr_id2int(args->hdr, BCF_DT_ID, tag->key);
if ( !bcf_hdr_idinfo_exists(args->hdr,BCF_HL_FLT,tag->hdr_id) )
{
if ( args->keep_sites )
error("Error: The filter \"%s\" is not defined in the header, cannot use the -k option\n", str.s);
else
fprintf(stderr,"Warning: The filter \"%s\" is not defined in the header\n", str.s);
}
else if ( !args->keep_sites ) bcf_hdr_remove(args->hdr_out,BCF_HL_FLT,tag->key);
}
else
{
int value, ret = khash_str2int_get(keep, str.s, &value);
if ( ret==-1 ) khash_str2int_set(keep, strdup(str.s),1<<BCF_HL_FLT);
else khash_str2int_set(keep, str.s, value | 1<<BCF_HL_FLT);
args->nrm--;
}
}
else if ( type!=BCF_HL_GEN )
{
int id = bcf_hdr_id2int(args->hdr,BCF_DT_ID,str.s);
if ( !bcf_hdr_idinfo_exists(args->hdr,type,id) )
{
if ( args->keep_sites )
error("Error: The tag \"%s\" is not defined in the header, cannot use the -k option\n", str.s);
else
fprintf(stderr,"Warning: The tag \"%s\" not defined in the header\n", str.s);
tag->key = strdup(str.s);
if ( type==BCF_HL_INFO ) tag->handler = remove_info_tag;
else if ( type==BCF_HL_FMT ) tag->handler = remove_format_tag;
}
else if ( (type==BCF_HL_FMT && keep_fmt) || (type==BCF_HL_INFO && keep_info) )
{
int value, ret = khash_str2int_get(keep, str.s, &value);
if ( ret==-1 ) khash_str2int_set(keep, strdup(str.s),1<<type);
else khash_str2int_set(keep, str.s, value | 1<<type);
args->nrm--;
}
else
{
tag->key = strdup(str.s);
if ( type==BCF_HL_INFO ) tag->handler = remove_info_tag;
else if ( type==BCF_HL_FMT ) tag->handler = remove_format_tag;
if ( !args->keep_sites ) bcf_hdr_remove(args->hdr_out,type,tag->key);
}
}
else if ( !strcasecmp("ID",str.s) ) tag->handler = remove_id;
else if ( !strcasecmp("FILTER",str.s) )
{
tag->handler = remove_filter;
if ( !args->keep_sites ) remove_hdr_lines(args->hdr_out,BCF_HL_FLT);
}
else if ( !strcasecmp("QUAL",str.s) ) tag->handler = remove_qual;
else if ( !strcasecmp("INFO",str.s) )
{
tag->handler = remove_info;
if ( !args->keep_sites ) remove_hdr_lines(args->hdr_out,BCF_HL_INFO);
}
else if ( !strcasecmp("FMT",str.s) || !strcasecmp("FORMAT",str.s) )
{
tag->handler = remove_format;
if ( !args->keep_sites ) remove_hdr_lines(args->hdr_out,BCF_HL_FMT);
}
else if ( str.l )
{
if ( !args->keep_sites )
{
if ( str.s[0]=='#' && str.s[1]=='#' )
bcf_hdr_remove(args->hdr_out,BCF_HL_GEN,str.s+2);
else
bcf_hdr_remove(args->hdr_out,BCF_HL_STR,str.s);
}
args->nrm--;
}
ss = *se ? se+1 : se;
}
free(str.s);
if ( keep_flt || keep_info || keep_fmt )
{
int j;
for (j=0; j<args->hdr->nhrec; j++)
{
bcf_hrec_t *hrec = args->hdr->hrec[j];
if ( hrec->type!=BCF_HL_FLT && hrec->type!=BCF_HL_INFO && hrec->type!=BCF_HL_FMT ) continue;
if ( !keep_flt && hrec->type==BCF_HL_FLT ) continue;
if ( !keep_info && hrec->type==BCF_HL_INFO ) continue;
if ( !keep_fmt && hrec->type==BCF_HL_FMT ) continue;
int k = bcf_hrec_find_key(hrec,"ID");
assert( k>=0 ); // this should always be true for valid VCFs
int value, ret = khash_str2int_get(keep,hrec->vals[k],&value);
if ( ret==0 && value>>hrec->type ) // keep
{
if ( hrec->type==BCF_HL_FLT && !strcmp("PASS",hrec->vals[k]) ) args->flt_keep_pass = 1;
continue;
}
args->nrm++;
args->rm = (rm_tag_t*) realloc(args->rm,sizeof(rm_tag_t)*args->nrm);
rm_tag_t *tag = &args->rm[args->nrm-1];
if ( hrec->type==BCF_HL_INFO ) tag->handler = remove_info_tag;
else if ( hrec->type==BCF_HL_FMT ) tag->handler = remove_format_tag;
else
{
tag->handler = remove_filter;
tag->hdr_id = bcf_hdr_id2int(args->hdr, BCF_DT_ID, hrec->vals[k]);
}
tag->key = strdup(hrec->vals[k]);
if ( !args->keep_sites ) bcf_hdr_remove(args->hdr_out,hrec->type,tag->key);
}
}
khash_str2int_destroy_free(keep);
if ( !args->nrm ) error("No matching tag in -x %s\n", args->remove_annots);
if (bcf_hdr_sync(args->hdr_out) < 0)
error_errno("[%s] Failed to update header", __func__);
}
static void init_header_lines(args_t *args)
{
htsFile *file = hts_open(args->header_fname, "rb");
if ( !file ) error("Error reading %s\n", args->header_fname);
kstring_t str = {0,0,0};
while ( hts_getline(file, KS_SEP_LINE, &str) > 0 )
{
if ( bcf_hdr_append(args->hdr_out,str.s) ) error("Could not parse %s: %s\n", args->header_fname, str.s);
bcf_hdr_append(args->hdr,str.s); // the input file may not have the header line if run with -h (and nothing else)
}
if ( hts_close(file)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,args->header_fname);
free(str.s);
if (bcf_hdr_sync(args->hdr_out) < 0)
error_errno("[%s] Failed to update output header", __func__);
if (bcf_hdr_sync(args->hdr) < 0)
error_errno("[%s] Failed to update input header", __func__);
}
static int setter_filter(args_t *args, bcf1_t *line, annot_col_t *col, void *data)
{
if ( !data ) error("Error: the --merge-logic option cannot be used with FILTER (yet?)\n");
// note: so far this works only with one filter, not a list of filters
annot_line_t *tab = (annot_line_t*) data;
if ( tab->cols[col->icol] && tab->cols[col->icol][0]=='.' && !tab->cols[col->icol][1] ) return 0; // don't replace with "."
hts_expand(int,1,args->mtmpi,args->tmpi);
args->tmpi[0] = bcf_hdr_id2int(args->hdr_out, BCF_DT_ID, tab->cols[col->icol]);
if ( args->tmpi[0]<0 ) error("The FILTER is not defined in the header: %s\n", tab->cols[col->icol]);
if ( col->replace==SET_OR_APPEND ) { bcf_add_filter(args->hdr_out,line,args->tmpi[0]); return 0; }
if ( col->replace!=REPLACE_MISSING )
{
bcf_update_filter(args->hdr_out,line,NULL,0);
bcf_update_filter(args->hdr_out,line,args->tmpi,1);
return 0;
}
// only update missing FILTER
if ( !(line->unpacked & BCF_UN_FLT) ) bcf_unpack(line, BCF_UN_FLT);
if ( !line->d.n_flt )
bcf_update_filter(args->hdr_out,line,args->tmpi,1);
return 0;
}
static int vcf_setter_filter(args_t *args, bcf1_t *line, annot_col_t *col, void *data)
{
int i;
bcf1_t *rec = (bcf1_t*) data;
if ( !(rec->unpacked & BCF_UN_FLT) ) bcf_unpack(rec, BCF_UN_FLT);
if ( !(line->unpacked & BCF_UN_FLT) ) bcf_unpack(line, BCF_UN_FLT);
if ( !rec->d.n_flt ) return 0; // don't overwrite with a missing value
if ( col->replace==SET_OR_APPEND || col->replace==REPLACE_MISSING )
{
if ( col->replace==REPLACE_MISSING && line->d.n_flt ) return 0; // only update missing FILTER
for (i=0; i<rec->d.n_flt; i++)
{
const char *flt = bcf_hdr_int2id(args->files->readers[1].header, BCF_DT_ID, rec->d.flt[i]);
bcf_add_filter(args->hdr_out,line,bcf_hdr_id2int(args->hdr_out, BCF_DT_ID, flt));
}
return 0;
}
hts_expand(int,rec->d.n_flt,args->mtmpi,args->tmpi);
for (i=0; i<rec->d.n_flt; i++)
{
const char *flt = bcf_hdr_int2id(args->files->readers[1].header, BCF_DT_ID, rec->d.flt[i]);
args->tmpi[i] = bcf_hdr_id2int(args->hdr_out, BCF_DT_ID, flt);
}
bcf_update_filter(args->hdr_out,line,NULL,0);
bcf_update_filter(args->hdr_out,line,args->tmpi,rec->d.n_flt);
return 0;
}
static int setter_id(args_t *args, bcf1_t *line, annot_col_t *col, void *data)
{
if ( !data ) error("Error: the --merge-logic option cannot be used with ID (yet?)\n");
// possible cases:
// IN ANNOT OUT ACHIEVED_BY
// x y x -c +ID
// x y y -c ID
// x y x,y -c =ID
// x . x -c +ID, ID
// x . . -x ID
// . y y -c +ID, -c ID
//
annot_line_t *tab = (annot_line_t*) data;
if ( tab->cols[col->icol] && tab->cols[col->icol][0]=='.' && !tab->cols[col->icol][1] ) return 0; // don't replace with "."
if ( col->replace==SET_OR_APPEND ) return bcf_add_id(args->hdr_out,line,tab->cols[col->icol]);
if ( col->replace!=REPLACE_MISSING ) return bcf_update_id(args->hdr_out,line,tab->cols[col->icol]);
// running with +ID, only update missing ids
if ( !line->d.id || (line->d.id[0]=='.' && !line->d.id[1]) )
return bcf_update_id(args->hdr_out,line,tab->cols[col->icol]);
return 0;
}
static int vcf_setter_id(args_t *args, bcf1_t *line, annot_col_t *col, void *data)
{
bcf1_t *rec = (bcf1_t*) data;
if ( rec->d.id && rec->d.id[0]=='.' && !rec->d.id[1] ) return 0; // don't replace with "."
if ( col->replace==SET_OR_APPEND ) return bcf_add_id(args->hdr_out,line,rec->d.id);
if ( col->replace!=REPLACE_MISSING ) return bcf_update_id(args->hdr_out,line,rec->d.id);
// running with +ID, only update missing ids
if ( !line->d.id || (line->d.id[0]=='.' && !line->d.id[1]) )
return bcf_update_id(args->hdr_out,line,rec->d.id);
return 0;
}
static int vcf_setter_ref(args_t *args, bcf1_t *line, annot_col_t *col, void *data)
{
bcf1_t *rec = (bcf1_t*) data;
if ( !strcmp(rec->d.allele[0],line->d.allele[0]) ) return 0; // no update necessary
const char **als = (const char**) malloc(sizeof(char*)*line->n_allele);
als[0] = rec->d.allele[0];
int i;
for (i=1; i<line->n_allele; i++) als[i] = line->d.allele[i];
bcf_update_alleles(args->hdr_out, line, als, line->n_allele);
free(als);
return 0;
}
static int vcf_setter_alt(args_t *args, bcf1_t *line, annot_col_t *col, void *data)
{
bcf1_t *rec = (bcf1_t*) data;
int i;
if ( rec->n_allele==line->n_allele )
{
for (i=1; i<rec->n_allele; i++) if ( strcmp(rec->d.allele[i],line->d.allele[i]) ) break;
if ( i==rec->n_allele ) return 0; // no update necessary
}
const char **als = (const char**) malloc(sizeof(char*)*rec->n_allele);
als[0] = line->d.allele[0];
for (i=1; i<rec->n_allele; i++) als[i] = rec->d.allele[i];
bcf_update_alleles(args->hdr_out, line, als, rec->n_allele);
free(als);
return 0;
}
static int setter_qual(args_t *args, bcf1_t *line, annot_col_t *col, void *data)
{
if ( !data ) error("Error: the --merge-logic option cannot be used with QUAL (yet?)\n");
annot_line_t *tab = (annot_line_t*) data;
char *str = tab->cols[col->icol];
if ( str[0]=='.' && str[1]==0 ) return 0; // empty
if ( col->replace==REPLACE_MISSING && !bcf_float_is_missing(line->qual) ) return 0;
line->qual = strtod(str, &str);
if ( str == tab->cols[col->icol] )
error("Could not parse %s at %s:%d .. [%s]\n", col->hdr_key_src,bcf_seqname(args->hdr,line),line->pos+1,tab->cols[col->icol]);
return 0;
}
static int vcf_setter_qual(args_t *args, bcf1_t *line, annot_col_t *col, void *data)
{
bcf1_t *rec = (bcf1_t*) data;
if ( bcf_float_is_missing(rec->qual) ) return 0;
if ( col->replace==REPLACE_MISSING && !bcf_float_is_missing(line->qual) ) return 0;
line->qual = rec->qual;
return 0;
}
static int setter_info_flag(args_t *args, bcf1_t *line, annot_col_t *col, void *data)
{
if ( !data ) error("Error: the --merge-logic option cannot be used with INFO type=Flag (yet?)\n");
annot_line_t *tab = (annot_line_t*) data;
char *str = tab->cols[col->icol];
if ( str[0]=='.' && str[1]==0 ) return 0;
if ( str[0]=='1' && str[1]==0 ) return bcf_update_info_flag(args->hdr_out,line,col->hdr_key_dst,NULL,1);
if ( str[0]=='0' && str[1]==0 ) return bcf_update_info_flag(args->hdr_out,line,col->hdr_key_dst,NULL,0);
error("Could not parse %s at %s:%d .. [%s]\n", col->hdr_key_src,bcf_seqname(args->hdr,line),line->pos+1,tab->cols[col->icol]);
return -1;
}
static int vcf_setter_info_flag(args_t *args, bcf1_t *line, annot_col_t *col, void *data)
{
bcf1_t *rec = (bcf1_t*) data;
int flag = bcf_get_info_flag(args->files->readers[1].header,rec,col->hdr_key_src,NULL,NULL);
bcf_update_info_flag(args->hdr_out,line,col->hdr_key_dst,NULL,flag);
return 0;
}
static int setter_ARinfo_int32(args_t *args, bcf1_t *line, annot_col_t *col, int nals, char **als, int ntmpi)
{
if ( col->number==BCF_VL_A && ntmpi!=nals-1 && (ntmpi!=1 || args->tmpi[0]!=bcf_int32_missing || args->tmpi[1]!=bcf_int32_vector_end) )
error("Incorrect number of values (%d) for the %s tag at %s:%d\n", ntmpi,col->hdr_key_src,bcf_seqname(args->hdr,line),line->pos+1);
else if ( col->number==BCF_VL_R && ntmpi!=nals && (ntmpi!=1 || args->tmpi[0]!=bcf_int32_missing || args->tmpi[1]!=bcf_int32_vector_end) )
error("Incorrect number of values (%d) for the %s tag at %s:%d\n", ntmpi,col->hdr_key_src,bcf_seqname(args->hdr,line),line->pos+1);
int ndst = col->number==BCF_VL_A ? line->n_allele - 1 : line->n_allele;
int *map = vcmp_map_ARvalues(args->vcmp,ndst,nals,als,line->n_allele,line->d.allele);
if ( !map ) error("REF alleles not compatible at %s:%d\n", bcf_seqname(args->hdr,line),line->pos+1);
// fill in any missing values in the target VCF (or all, if not present)
int ntmpi2 = bcf_get_info_float(args->hdr, line, col->hdr_key_dst, &args->tmpi2, &args->mtmpi2);
if ( ntmpi2 < ndst ) hts_expand(int32_t,ndst,args->mtmpi2,args->tmpi2);
int i;
for (i=0; i<ndst; i++)
{
if ( map[i]<0 )
{
if ( ntmpi2 < ndst ) args->tmpi2[i] = bcf_int32_missing;
continue;
}
if ( ntmpi2==ndst && col->replace==REPLACE_MISSING
&& args->tmpi2[i]!=bcf_int32_missing
&& args->tmpi2[i]!=bcf_int32_vector_end ) continue;
args->tmpi2[i] = args->tmpi[ map[i] ];
}
bcf_update_info_int32(args->hdr_out,line,col->hdr_key_dst,args->tmpi2,ndst);
return 0;
}
static int setter_info_int(args_t *args, bcf1_t *line, annot_col_t *col, void *data)
{
if ( !data ) error("Error: the --merge-logic option cannot be used with INFO type=Integer (yet?)\n");
annot_line_t *tab = (annot_line_t*) data;
char *str = tab->cols[col->icol], *end = str;
if ( str[0]=='.' && str[1]==0 ) return 0;
int ntmpi = 0;
while ( *end )
{
int val = strtol(str, &end, 10);
if ( end==str )
error("Could not parse %s at %s:%d .. [%s]\n", col->hdr_key_src,bcf_seqname(args->hdr,line),line->pos+1,tab->cols[col->icol]);
ntmpi++;
hts_expand(int32_t,ntmpi,args->mtmpi,args->tmpi);
args->tmpi[ntmpi-1] = val;
str = end+1;
}
if ( col->number==BCF_VL_A || col->number==BCF_VL_R )
return setter_ARinfo_int32(args,line,col,tab->nals,tab->als,ntmpi);
if ( col->replace==REPLACE_MISSING )
{
int ret = bcf_get_info_int32(args->hdr, line, col->hdr_key_dst, &args->tmpi2, &args->mtmpi2);
if ( ret>0 && args->tmpi2[0]!=bcf_int32_missing ) return 0;
}
bcf_update_info_int32(args->hdr_out,line,col->hdr_key_dst,args->tmpi,ntmpi);
return 0;
}
static int vcf_setter_info_int(args_t *args, bcf1_t *line, annot_col_t *col, void *data)
{
bcf1_t *rec = (bcf1_t*) data;
int ntmpi = bcf_get_info_int32(args->files->readers[1].header,rec,col->hdr_key_src,&args->tmpi,&args->mtmpi);
if ( ntmpi < 0 ) return 0; // nothing to add
if ( col->number==BCF_VL_A || col->number==BCF_VL_R )
return setter_ARinfo_int32(args,line,col,rec->n_allele,rec->d.allele,ntmpi);
if ( col->replace==REPLACE_MISSING )
{
int ret = bcf_get_info_int32(args->hdr, line, col->hdr_key_dst, &args->tmpi2, &args->mtmpi2);
if ( ret>0 && args->tmpi2[0]!=bcf_int32_missing ) return 0;
}
bcf_update_info_int32(args->hdr_out,line,col->hdr_key_dst,args->tmpi,ntmpi);
return 0;
}
static int setter_ARinfo_real(args_t *args, bcf1_t *line, annot_col_t *col, int nals, char **als, int ntmpf)
{
if ( col->number==BCF_VL_A && ntmpf!=nals-1 && (ntmpf!=1 || !bcf_float_is_missing(args->tmpf[0]) || !bcf_float_is_vector_end(args->tmpf[0])) )
error("Incorrect number of values (%d) for the %s tag at %s:%d\n", ntmpf,col->hdr_key_src,bcf_seqname(args->hdr,line),line->pos+1);
else if ( col->number==BCF_VL_R && ntmpf!=nals && (ntmpf!=1 || !bcf_float_is_missing(args->tmpf[0]) || !bcf_float_is_vector_end(args->tmpf[0])) )
error("Incorrect number of values (%d) for the %s tag at %s:%d\n", ntmpf,col->hdr_key_src,bcf_seqname(args->hdr,line),line->pos+1);
int ndst = col->number==BCF_VL_A ? line->n_allele - 1 : line->n_allele;
int *map = vcmp_map_ARvalues(args->vcmp,ndst,nals,als,line->n_allele,line->d.allele);
if ( !map ) error("REF alleles not compatible at %s:%d\n", bcf_seqname(args->hdr,line),line->pos+1);
// fill in any missing values in the target VCF (or all, if not present)
int ntmpf2 = bcf_get_info_float(args->hdr, line, col->hdr_key_dst, &args->tmpf2, &args->mtmpf2);
if ( ntmpf2 < ndst ) hts_expand(float,ndst,args->mtmpf2,args->tmpf2);
int i;
for (i=0; i<ndst; i++)
{
if ( map[i]<0 )
{
if ( ntmpf2 < ndst ) bcf_float_set_missing(args->tmpf2[i]);
continue;
}
if ( ntmpf2==ndst && col->replace==REPLACE_MISSING
&& !bcf_float_is_missing(args->tmpf2[i])
&& !bcf_float_is_vector_end(args->tmpf2[i]) ) continue;
args->tmpf2[i] = args->tmpf[ map[i] ];
}
bcf_update_info_float(args->hdr_out,line,col->hdr_key_dst,args->tmpf2,ndst);
return 0;
}
static int setter_info_real(args_t *args, bcf1_t *line, annot_col_t *col, void *data)
{
if ( !data ) error("Error: the --merge-logic option cannot be used with INFO type=Float (yet?)\n");
annot_line_t *tab = (annot_line_t*) data;
char *str = tab->cols[col->icol], *end = str;
if ( str[0]=='.' && str[1]==0 ) return 0;
int ntmpf = 0;
while ( *end )
{
double val = strtod(str, &end);
if ( end==str )
error("Could not parse %s at %s:%d .. [%s]\n", col->hdr_key_src,bcf_seqname(args->hdr,line),line->pos+1,tab->cols[col->icol]);
ntmpf++;
hts_expand(float,ntmpf,args->mtmpf,args->tmpf);
args->tmpf[ntmpf-1] = val;
str = end+1;
}
if ( col->number==BCF_VL_A || col->number==BCF_VL_R )
return setter_ARinfo_real(args,line,col,tab->nals,tab->als,ntmpf);
if ( col->replace==REPLACE_MISSING )
{
int ret = bcf_get_info_float(args->hdr, line, col->hdr_key_dst, &args->tmpf2, &args->mtmpf2);
if ( ret>0 && !bcf_float_is_missing(args->tmpf2[0]) ) return 0;
}
bcf_update_info_float(args->hdr_out,line,col->hdr_key_dst,args->tmpf,ntmpf);
return 0;
}
static int vcf_setter_info_real(args_t *args, bcf1_t *line, annot_col_t *col, void *data)
{
bcf1_t *rec = (bcf1_t*) data;
int ntmpf = bcf_get_info_float(args->files->readers[1].header,rec,col->hdr_key_src,&args->tmpf,&args->mtmpf);
if ( ntmpf < 0 ) return 0; // nothing to add
if ( col->number==BCF_VL_A || col->number==BCF_VL_R )
return setter_ARinfo_real(args,line,col,rec->n_allele,rec->d.allele,ntmpf);
if ( col->replace==REPLACE_MISSING )
{
int ret = bcf_get_info_float(args->hdr, line, col->hdr_key_dst, &args->tmpf2, &args->mtmpf2);
if ( ret>0 && !bcf_float_is_missing(args->tmpf2[0]) ) return 0;
}
bcf_update_info_float(args->hdr_out,line,col->hdr_key_dst,args->tmpf,ntmpf);
return 0;
}
int copy_string_field(char *src, int isrc, int src_len, kstring_t *dst, int idst); // see vcfmerge.c
static int setter_ARinfo_string(args_t *args, bcf1_t *line, annot_col_t *col, int nals, char **als)
{
assert( col->merge_method==MM_FIRST );
int nsrc = 1, lsrc = 0;
while ( args->tmps[lsrc] )
{
if ( args->tmps[lsrc]==',' ) nsrc++;
lsrc++;
}
if ( col->number==BCF_VL_A && nsrc!=nals-1 && (nsrc!=1 || args->tmps[0]!='.' || args->tmps[1]!=0 ) )
error("Incorrect number of values (%d) for the %s tag at %s:%d\n", nsrc,col->hdr_key_src,bcf_seqname(args->hdr,line),line->pos+1);
else if ( col->number==BCF_VL_R && nsrc!=nals && (nsrc!=1 || args->tmps[0]!='.' || args->tmps[1]!=0 ) )
error("Incorrect number of values (%d) for the %s tag at %s:%d\n", nsrc,col->hdr_key_src,bcf_seqname(args->hdr,line),line->pos+1);
int ndst = col->number==BCF_VL_A ? line->n_allele - 1 : line->n_allele;
int *map = vcmp_map_ARvalues(args->vcmp,ndst,nals,als,line->n_allele,line->d.allele);
if ( !map ) error("REF alleles not compatible at %s:%d\n", bcf_seqname(args->hdr,line),line->pos+1);
// fill in any missing values in the target VCF (or all, if not present)
int i, empty = 0, nstr, mstr = args->tmpks.m;
nstr = bcf_get_info_string(args->hdr, line, col->hdr_key_dst, &args->tmpks.s, &mstr);
args->tmpks.m = mstr;
if ( nstr<0 || (nstr==1 && args->tmpks.s[0]=='.' && args->tmpks.s[1]==0) )
{
empty = 0;
args->tmpks.l = 0;
kputc('.',&args->tmpks);
for (i=1; i<ndst; i++) kputs(",.",&args->tmpks);
}
else args->tmpks.l = nstr;
for (i=0; i<ndst; i++)
{
if ( map[i]<0 )
{
if ( empty ) copy_string_field(".",0,1,&args->tmpks,i);
continue;
}
if ( col->replace==REPLACE_MISSING )
{
// Do not replace filled values. The field must be looked up again because
// of realloc in copy_string_field
int n = 0;
char *str = args->tmpks.s;
while ( *str && n<i )
{
if ( *str==',' ) n++;
str++;
}
if ( str[0]!='.' || (str[1]!=',' && str[1]!=0) ) continue; // value already set
}
int ret = copy_string_field(args->tmps,map[i],lsrc,&args->tmpks,i);
assert( ret==0 );
}
bcf_update_info_string(args->hdr_out,line,col->hdr_key_dst,args->tmpks.s);
return 0;
}
void khash_str2int_clear_free(void *_hash)
{
khash_t(str2int) *hash = (khash_t(str2int)*)_hash;
khint_t k;
if (hash == 0) return;
for (k = 0; k < kh_end(hash); ++k)
if (kh_exist(hash, k)) free((char*)kh_key(hash, k));
kh_clear(str2int, hash);
}
static int setter_info_str(args_t *args, bcf1_t *line, annot_col_t *col, void *data)
{
if ( col->replace==REPLACE_MISSING && col->number!=BCF_VL_A && col->number!=BCF_VL_R )
{
int ret = bcf_get_info_string(args->hdr, line, col->hdr_key_dst, &args->tmps2, &args->mtmps2);
if ( ret>0 && (args->tmps2[0]!='.' || args->tmps2[1]!=0) ) return 0;
}
annot_line_t *tab = (annot_line_t*) data;
int len = 0;
if ( tab )
{
len = strlen(tab->cols[col->icol]);
if ( !len ) return 0;
if ( len==1 && tab->cols[col->icol][0]=='.' ) return 0;
}
if ( col->merge_method!=MM_FIRST )
{
if ( col->number==BCF_VL_A || col->number==BCF_VL_R )
error("Error: the --merge-logic option cannot be used with INFO tags Type=String,Number={A,R,G}\n");
if ( data )
{
assert( col->merge_method==MM_APPEND || col->merge_method==MM_UNIQUE );
if ( col->merge_method==MM_UNIQUE )
{
if ( !col->mm_str_hash ) col->mm_str_hash = khash_str2int_init();
if ( khash_str2int_has_key(col->mm_str_hash, tab->cols[col->icol]) ) return 0;
khash_str2int_inc(col->mm_str_hash, strdup(tab->cols[col->icol]));
}
if ( col->mm_kstr.l ) kputc(',',&col->mm_kstr);
kputs(tab->cols[col->icol], &col->mm_kstr);
return 0;
}
hts_expand(char,col->mm_kstr.l+1,args->mtmps,args->tmps);
memcpy(args->tmps,col->mm_kstr.s,col->mm_kstr.l+1);
if ( !data )
{
if ( col->merge_method==MM_UNIQUE )
khash_str2int_clear_free(col->mm_str_hash);
col->mm_kstr.l = 0;
}
}
else
{
assert(tab);
hts_expand(char,len+1,args->mtmps,args->tmps);
memcpy(args->tmps,tab->cols[col->icol],len+1);
if ( col->number==BCF_VL_A || col->number==BCF_VL_R )
return setter_ARinfo_string(args,line,col,tab->nals,tab->als);
}
bcf_update_info_string(args->hdr_out,line,col->hdr_key_dst,args->tmps);
return 0;
}
static int vcf_setter_info_str(args_t *args, bcf1_t *line, annot_col_t *col, void *data)
{
bcf1_t *rec = (bcf1_t*) data;
int ntmps = bcf_get_info_string(args->files->readers[1].header,rec,col->hdr_key_src,&args->tmps,&args->mtmps);
if ( ntmps < 0 ) return 0; // nothing to add
if ( col->number==BCF_VL_A || col->number==BCF_VL_R )
return setter_ARinfo_string(args,line,col,rec->n_allele,rec->d.allele);
if ( col->replace==REPLACE_MISSING )
{
int ret = bcf_get_info_string(args->hdr, line, col->hdr_key_dst, &args->tmps2, &args->mtmps2);
if ( ret>0 && (args->tmps2[0]!='.' || args->tmps2[1]!=0) ) return 0;
}
bcf_update_info_string(args->hdr_out,line,col->hdr_key_dst,args->tmps);
return 0;
}
static int genotypes_to_string(args_t *args, int nsrc1, int32_t *src, int nsmpl_dst, kstring_t *str)
{
int i, isrc, idst;
int blen = nsrc1 > 1 ? nsrc1 + 1 : 1; // typically the genotypes take three bytes 0/1, no 0-termination is needed
gt_length_too_big:
str->l = 0;
for (idst=0; idst<nsmpl_dst; idst++)
{
isrc = args->sample_map ? args->sample_map[idst] : idst;
if ( isrc==-1 )
{
kputc_('.', str);
for (i=1; i < blen; i++) kputc_(0, str);
continue;
}
size_t plen = str->l;
int32_t *ptr = src + isrc*nsrc1;
for (i=0; i<nsrc1 && ptr[i]!=bcf_int32_vector_end; i++)
{
if ( i ) kputc("/|"[bcf_gt_is_phased(ptr[i])], str);
if ( bcf_gt_is_missing(ptr[i]) ) kputc('.', str);
else kputw(bcf_gt_allele(ptr[i]), str);
}
if ( i==0 ) kputc('.', str);
if ( 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").
blen *= 2;
goto gt_length_too_big;
}
plen = str->l - plen;
while ( plen < blen )
{
kputc_(0, str);
plen++;
}
}
return 0;
}
static int vcf_setter_format_gt(args_t *args, bcf1_t *line, annot_col_t *col, void *data)
{
bcf1_t *rec = (bcf1_t*) data;
int nsrc = bcf_get_genotypes(args->files->readers[1].header,rec,&args->tmpi,&args->mtmpi);
if ( nsrc==-3 ) return 0; // the tag is not present
if ( nsrc<=0 ) return 1; // error
// Genotypes are internally represented as integers. This is a complication when
// adding as a different Type=String field, such as FMT/newGT:=GT
if ( strcmp(col->hdr_key_src,col->hdr_key_dst) )
{
int nsmpl_dst = bcf_hdr_nsamples(args->hdr_out);
int nsmpl_src = bcf_hdr_nsamples(args->files->readers[1].header);
genotypes_to_string(args,nsrc/nsmpl_src,args->tmpi,nsmpl_dst,&args->tmpks);
return bcf_update_format_char(args->hdr_out,line,col->hdr_key_dst,args->tmpks.s,args->tmpks.l);
}
if ( !args->sample_map )
return bcf_update_genotypes(args->hdr_out,line,args->tmpi,nsrc);
int i, j, ndst = bcf_get_genotypes(args->hdr,line,&args->tmpi2,&args->mtmpi2);
if ( ndst > 0 ) ndst /= bcf_hdr_nsamples(args->hdr_out);
nsrc /= bcf_hdr_nsamples(args->files->readers[1].header);
if ( ndst<=0 ) // field not present in dst file
{
if ( col->replace==REPLACE_NON_MISSING ) return 0;
hts_expand(int32_t, nsrc*bcf_hdr_nsamples(args->hdr_out), args->mtmpi2, args->tmpi2);
for (i=0; i<bcf_hdr_nsamples(args->hdr_out); i++)
{
int32_t *dst = args->tmpi2 + nsrc*i;
if ( args->sample_map[i]==-1 )
{
dst[0] = bcf_gt_missing;
for (j=1; j<nsrc; j++) dst[j] = bcf_int32_vector_end;
}
else
{
int32_t *src = args->tmpi + nsrc*args->sample_map[i];
for (j=0; j<nsrc; j++) dst[j] = src[j];
}
}
return bcf_update_genotypes(args->hdr_out,line,args->tmpi2,nsrc*bcf_hdr_nsamples(args->hdr_out));
}
else if ( ndst >= nsrc )
{
for (i=0; i<bcf_hdr_nsamples(args->hdr_out); i++)
{
if ( args->sample_map[i]==-1 ) continue;
int32_t *src = args->tmpi + nsrc*args->sample_map[i];
int32_t *dst = args->tmpi2 + ndst*i;
if ( col->replace==REPLACE_NON_MISSING && bcf_gt_is_missing(dst[0]) ) continue;
if ( col->replace==REPLACE_MISSING && !bcf_gt_is_missing(dst[0]) ) continue;
for (j=0; j<nsrc; j++) dst[j] = src[j];
for (; j<ndst; j++) dst[j] = bcf_int32_vector_end;