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vcfannotate.c
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/* vcfannotate.c -- Annotate and edit VCF/BCF files.
Copyright (C) 2013-2025 Genome Research Ltd.
Author: Petr Danecek <[email protected]>
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
THE SOFTWARE. */
#include <stdio.h>
#include <strings.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 <dirent.h>
#include <math.h>
#include <inttypes.h>
#include <htslib/vcf.h>
#include <htslib/synced_bcf_reader.h>
#include <htslib/kseq.h>
#include <htslib/khash_str2int.h>
#include "bcftools.h"
#include "vcmp.h"
#include "filter.h"
#include "convert.h"
#include "smpl_ilist.h"
#include "regidx.h"
#include "dbuf.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 (1<<0) // -c +TAG .. replace only missing values
#define REPLACE_ALL (1<<1) // -c TAG .. replace both missing and existing values
#define REPLACE_NON_MISSING (1<<2) // -c -TAG .. replace only if tgt is not missing
#define SET_OR_APPEND (1<<3) // -c =TAG .. set new value if missing or non-existent, append otherwise
#define MATCH_VALUE (1<<4) // -c ~ID .. do not set, just match the value
#define CARRY_OVER_MISSING (1<<5) // -c .TAG .. carry over source missing values as well
#define MM_FIRST 0 // if multiple annotation lines overlap a VCF record, use the first, discarding the rest
#define MM_APPEND 1 // append, possibly multiple times
#define MM_UNIQUE 2 // append, only unique values
#define MM_SUM 3
#define MM_AVG 4
#define MM_MIN 5
#define MM_MAX 6
#define MM_APPEND_MISSING 7 // missing values will be transferred as well
typedef struct _annot_col_t
{
int icol, replace, number; // number: one of BCF_VL_* types
char *hdr_key_src, *hdr_key_dst;
// The setters return 0 on successful update of the bcf record, negative value (bcf_update_* return status) on errors,
// or 1 on (repeated partial updates) concluded with a src=NULL call
int (*setter)(struct _args_t *, bcf1_t *dst, struct _annot_col_t *, void *src); // the last is the annotation line, either src bcf1_t or annot_line_t
int (*getter)(struct _args_t *, bcf1_t *src, struct _annot_col_t *, void **ptr, int *mptr);
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;
size_t
mm_dbl_nalloc, // the allocated size --merge-logic values array
mm_dbl_nused, // the number of used elements in the mm_dbl array
mm_dbl_ndat; // the number of merged rows (for calculating the average)
double
*mm_dbl;
void *ptr;
int mptr, done;
}
annot_col_t;
typedef struct
{
char *name; // column name
int ht_type; // type, one of BCF_HT_STR,BCF_HT_INT,BCF_HT_REAL
int icol; // index of the annotation column to use
union { // memory area with the current annotation value to pass to filter_test_ext
int i;
float f;
char *s;
};
}
ext_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, *tgts_hdr;
htsFile *out_fh;
int output_type, n_threads, clevel;
bcf_sr_regions_t *tgts;
char *index_fn;
int write_index;
regidx_t *tgt_idx; // keep everything in memory only with .tab annotation file and -c BEG,END columns
regitr_t *tgt_itr;
int tgt_is_bed;
filter_t *filter, *filter_ext; // only one is initialized, the latter contains external values to set dynamically on the fly
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
annot_line_t *aline_missing;
uint32_t *srt_alines; // sorted indexes (iALT<<16 || iAline)
int nalines, malines, nsrt_alines, msrt_alines;
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;
int match_id; // set iff `-c ~ID` given, -1 otherwise
int match_end; // set iff `-c ~INFO/END` is given, -1 otherwise
char *set_ids_fmt;
convert_t *set_ids;
int set_ids_replace;
// external values for dynamic -i/-e expressions
int n_ext;
ext_t *ext;
void **ext_ptr;
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, *rename_annots, *sample_names, *mark_sites;
char **rename_annots_map;
char *min_overlap_str;
float min_overlap_ann, min_overlap_vcf;
int rename_annots_nmap;
kstring_t merge_method_str;
int argc, drop_header, record_cmd_line, tgts_is_vcf, mark_sites_logic, force, single_overlaps;
int columns_is_file, has_append_mode, pair_logic;
dbuf_t *header_lines;
bcf1_t *current_rec; // current record for local setters
}
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 )
{
error("Error: Cannot proceed, not even with the --force option, bad things could happen.\n"
" Note that \"bcftools annotate -x FILTER\" can be used to remove ALL filters.\n"
" Even better, use \"bcftools view -h\" and \"bcftools reheader\" to fix the header!\n"
);
}
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 ( !strcmp("END",bcf_hdr_int2id(args->hdr,BCF_DT_ID,inf->key)) )
line->rlen = line->n_allele ? strlen(line->d.allele[0]) : 0;
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;
int i, ntags, needs_info = 0;
if ( args->set_ids )
{
const char **tags = convert_list_used_tags(args->set_ids,&ntags);
for (i=0; i<ntags; i++)
if ( !strncmp("INFO/",tags[i],4) ) needs_info = 1;
}
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;
if ( needs_info ) error("Error: `--remove INFO/%s` is executed first, cannot combine with `--set-id %s`\n",tag->key,args->set_ids_fmt);
}
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;
if ( needs_info ) error("Error: `--remove INFO/%s` is executed first, cannot combine with `--set-id %s`\n",tag->key,args->set_ids_fmt);
}
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) )
{
if ( needs_info ) error("Error: `--remove INFO` is executed first, cannot combine with `--set-id %s`\n",args->set_ids_fmt);
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 )
{
int id = bcf_hdr_id2int(args->hdr, BCF_DT_ID, str.s);
if ( bcf_hdr_idinfo_exists(args->hdr,BCF_HL_INFO,id) ) error("Error: did you mean INFO/%s?\n",str.s);
if ( bcf_hdr_idinfo_exists(args->hdr,BCF_HL_FMT,id) ) error("Error: did you mean FORMAT/%s?\n",str.s);
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)
{
if ( args->header_fname )
{
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 ( args->header_lines )
{
int i, n = dbuf_n(args->header_lines);
for (i=0; i<n; i++)
{
char *line = dbuf_ith(args->header_lines,i);
if ( bcf_hdr_append(args->hdr_out,line) ) error("Could not parse the header line: %s\n", line);
bcf_hdr_append(args->hdr,line); // the input file may not have the header line if run with -H (and nothing else)
}
dbuf_destroy_free(args->header_lines);
args->header_lines = NULL;
}
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 vcf_getter_info_str2str(args_t *args, bcf1_t *rec, annot_col_t *col, void **ptr, int *mptr)
{
return bcf_get_info_string(args->tgts_hdr,rec,col->hdr_key_src,ptr,mptr);
}
static int vcf_getter_id2str(args_t *args, bcf1_t *rec, annot_col_t *col, void **ptr, int *mptr)
{
char *str = *((char**)ptr);
int i, len = strlen(rec->d.id);
if ( len >= *mptr ) str = realloc(str, len+1);
for (i=0; i<len; i++)
str[i] = rec->d.id[i]==';' ? ',' : rec->d.id[i];
str[len] = 0;
*((char**)ptr) = str;
*mptr = len+1;
return len;
}
inline static int vcf_getter_filter2str_core(bcf_hdr_t *hdr, bcf1_t *rec, char **ptr, int *mptr)
{
if ( !(rec->unpacked & BCF_UN_FLT) ) bcf_unpack(rec, BCF_UN_FLT);
kstring_t str;
str.s = *ptr;
str.m = *mptr;
str.l = 0;
int i;
if ( rec->d.n_flt )
{
for (i=0; i<rec->d.n_flt; i++)
{
if (i) kputc(',', &str);
kputs(bcf_hdr_int2id(hdr,BCF_DT_ID,rec->d.flt[i]), &str);
}
}
else kputc('.', &str);
*ptr = str.s;
*mptr = str.m;
return str.l;
}
static int vcf_getter_filter2str_local(args_t *args, bcf1_t *rec, annot_col_t *col, void **ptr, int *mptr)
{
return vcf_getter_filter2str_core(args->hdr_out, args->current_rec, (char**)ptr, mptr);
}
static int vcf_getter_filter2str(args_t *args, bcf1_t *rec, annot_col_t *col, void **ptr, int *mptr)
{
return vcf_getter_filter2str_core(args->tgts_hdr, rec, (char**)ptr, mptr);
}
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][0]=='.' && !tab->cols[col->icol][1] ) // don't overwrite with a missing value unless asked
{
if ( (col->replace & CARRY_OVER_MISSING) && (col->replace & (REPLACE_ALL|REPLACE_NON_MISSING)) ) bcf_update_filter(args->hdr_out,line,NULL,0);
return 0;
}
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 \"%s\" is not defined in the header, was the -h option provided?\n", tab->cols[col->icol]);
if ( col->replace & SET_OR_APPEND ) return bcf_add_filter(args->hdr_out,line,args->tmpi[0]);
if ( !(col->replace & REPLACE_MISSING) )
{
bcf_update_filter(args->hdr_out,line,NULL,0);
return bcf_update_filter(args->hdr_out,line,args->tmpi,1);
}
// only update missing FILTER
if ( !(line->unpacked & BCF_UN_FLT) ) bcf_unpack(line, BCF_UN_FLT);
if ( !line->d.n_flt )
return 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, ret = 0;
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 ) // don't overwrite with a missing value unless asked
{
if ( (col->replace & CARRY_OVER_MISSING) && (col->replace & (REPLACE_ALL|REPLACE_NON_MISSING)) ) bcf_update_filter(args->hdr_out,line,NULL,0);
return 0;
}
if ( col->replace & (SET_OR_APPEND|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]);
if ( bcf_add_filter(args->hdr_out,line,bcf_hdr_id2int(args->hdr_out, BCF_DT_ID, flt)) < 0 ) ret = -1;
}
return ret;
}
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);
return bcf_update_filter(args->hdr_out,line,args->tmpi,rec->d.n_flt);
}
static int setter_pos(args_t *args, bcf1_t *line, annot_col_t *col, void *data)
{
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 "."
char *tmp;
int pos = strtol(tab->cols[col->icol], &tmp, 10);
if ( tmp==tab->cols[col->icol] )
error("Could not parse -POS at %s:%"PRId64" .. [%s]\n",bcf_seqname(args->hdr,line),(int64_t)line->pos+1,tab->cols[col->icol]);
line->pos = pos - 1;
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");
if ( col->replace & MATCH_VALUE ) return 0;
// 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)
{
if ( col->replace & MATCH_VALUE ) return 0;
bcf1_t *rec = (bcf1_t*) data;
char *id;
if ( col->getter )
{
int nret = col->getter(args,rec,col,&col->ptr,&col->mptr);
id = (char*) col->ptr;
if ( nret<=0 || (nret==1 && *id=='.') ) return 0; // don't replace with "."
}
else
{
if ( rec->d.id && rec->d.id[0]=='.' && !rec->d.id[1] ) return 0; // don't replace with "."
id = rec->d.id;
}
if ( col->replace & SET_OR_APPEND ) return bcf_add_id(args->hdr_out,line,id);
if ( !(col->replace & REPLACE_MISSING) ) return bcf_update_id(args->hdr_out,line,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,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];
int ret = bcf_update_alleles(args->hdr_out, line, als, line->n_allele);
free(als);
return ret;
}
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 ( line->n_allele>1 && (col->replace & REPLACE_MISSING) ) return 0;
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];
int ret = bcf_update_alleles(args->hdr_out, line, als, rec->n_allele);
free(als);
return ret;
}
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 ) // don't overwrite with a missing value unless asked
{
if ( (col->replace & CARRY_OVER_MISSING) && (col->replace & (REPLACE_ALL|REPLACE_NON_MISSING)) ) bcf_float_set_missing(line->qual);
return 0;
}
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:%"PRId64" .. [%s]\n", col->hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) 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) ) // don't overwrite with a missing value unless asked
{
if ( (col->replace & CARRY_OVER_MISSING) && (col->replace & (REPLACE_ALL|REPLACE_NON_MISSING)) ) bcf_float_set_missing(line->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 ) // don't overwrite with a missing value unless asked
{
if ( (col->replace & CARRY_OVER_MISSING) && (col->replace & (REPLACE_ALL|REPLACE_NON_MISSING)) ) bcf_update_info_flag(args->hdr_out,line,col->hdr_key_dst,NULL,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:%"PRId64" .. [%s]\n", col->hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) 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 ( !nals ) error("Cannot fill Number=R,A tags without --columns ..,REF,ALT,..\n");
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:%"PRId64"\n", ntmpi,col->hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) 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:%"PRId64"\n", ntmpi,col->hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) 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:%"PRId64"\n", bcf_seqname(args->hdr,line),(int64_t) 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] ];
}
return bcf_update_info_int32(args->hdr_out,line,col->hdr_key_dst,args->tmpi2,ndst);
}
static int setter_info_int(args_t *args, bcf1_t *line, annot_col_t *col, void *data)
{
annot_line_t *tab = (annot_line_t*) data;
// This is a bit hacky, only to reuse existing code with minimal changes:
// -c =TAG will now behave as -l TAG:APPEND for integers
if ( col->replace & SET_OR_APPEND ) col->merge_method=MM_APPEND;
if ( !tab )
{
if ( col->merge_method!=MM_SUM && col->merge_method!=MM_AVG &&
col->merge_method!=MM_MIN && col->merge_method!=MM_MAX &&
col->merge_method!=MM_APPEND &&
col->merge_method!=MM_APPEND_MISSING )
error("Error: at the moment only the sum,avg,min,max,append,append-missing options are supported with --merge-logic for INFO type=Integer\n");
}
int i,ntmpi = 0;
if ( (col->replace & SET_OR_APPEND) && !col->mm_dbl_nused )
{
ntmpi = bcf_get_info_int32(args->hdr, line, col->hdr_key_dst, &args->tmpi, &args->mtmpi);
if ( ntmpi>0 && (args->tmpi[0]!=bcf_int32_missing || (col->replace & CARRY_OVER_MISSING)) )
{
col->mm_dbl_nused = col->mm_dbl_ndat = ntmpi;
hts_expand(double,col->mm_dbl_nused,col->mm_dbl_nalloc,col->mm_dbl);
for (i=0; i<ntmpi; i++)
col->mm_dbl[i] = args->tmpi[i];
col->mm_dbl_ndat = 1;
}
ntmpi = 0;
}
if ( tab ) // has data, not flushing yet
{
char *str = tab->cols[col->icol], *end = str;
if ( str[0]=='.' && str[1]==0 && col->merge_method!=MM_APPEND_MISSING && !(col->replace & CARRY_OVER_MISSING) ) return 1;
while ( *end )
{
ntmpi++;
hts_expand(int32_t,ntmpi,args->mtmpi,args->tmpi);
if ( str[0]=='.' && (str[1]==0 || str[1]==',') )
{
if ( col->merge_method==MM_APPEND_MISSING || (col->replace & CARRY_OVER_MISSING) )
args->tmpi[ntmpi-1] = bcf_int32_missing;
else
ntmpi--;
if ( str[1]==0 ) end = str+1;
str += 2;
}
else
{
args->tmpi[ntmpi-1] = strtol(str, &end, 10);
if ( end==str || (*end && *end!=',') )
error("Could not parse %s (Type=Integer) at %s:%"PRId64" .. [%s]\n", col->hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1,tab->cols[col->icol]);
str = end+1;
}
}
if ( col->merge_method!=MM_FIRST )
{
if ( !col->mm_dbl_nused )
{
col->mm_dbl_nused = ntmpi;
hts_expand(double,col->mm_dbl_nused,col->mm_dbl_nalloc,col->mm_dbl);
for (i=0; i<ntmpi; i++)
col->mm_dbl[i] = args->tmpi[i];
}
else
{
if ( col->merge_method==MM_APPEND || col->merge_method==MM_APPEND_MISSING )
{
int nori = col->mm_dbl_nused;
col->mm_dbl_nused += ntmpi;
hts_expand(double,col->mm_dbl_nused,col->mm_dbl_nalloc,col->mm_dbl);
for (i=0; i<ntmpi; i++)
col->mm_dbl[i+nori] = args->tmpi[i];
}
else
{
if ( ntmpi!=col->mm_dbl_nused ) error("Error: cannot merge fields of unequal length\n");
if ( col->merge_method==MM_SUM || col->merge_method==MM_AVG )
for (i=0; i<ntmpi; i++) col->mm_dbl[i] += args->tmpi[i];
else if ( col->merge_method==MM_MIN )
for (i=0; i<ntmpi; i++) { if ( col->mm_dbl[i] > args->tmpi[i] ) col->mm_dbl[i] = args->tmpi[i]; }
else if ( col->merge_method==MM_MAX )
for (i=0; i<ntmpi; i++) { if ( col->mm_dbl[i] < args->tmpi[i] ) col->mm_dbl[i] = args->tmpi[i]; }
}
}
col->mm_dbl_ndat++;
return 1;
}
}
else if ( col->merge_method==MM_SUM || col->merge_method==MM_MIN || col->merge_method==MM_MAX || col->merge_method==MM_APPEND || col->merge_method==MM_APPEND_MISSING )
{
ntmpi = col->mm_dbl_nused;
hts_expand(int32_t,ntmpi,args->mtmpi,args->tmpi);
for (i=0; i<ntmpi; i++) args->tmpi[i] = col->mm_dbl[i];
col->mm_dbl_nused = col->mm_dbl_ndat = 0;
}
else if ( col->merge_method==MM_AVG )
{
ntmpi = col->mm_dbl_nused;
hts_expand(int32_t,ntmpi,args->mtmpi,args->tmpi);
for (i=0; i<ntmpi; i++) args->tmpi[i] = col->mm_dbl[i]/col->mm_dbl_ndat;
col->mm_dbl_nused = col->mm_dbl_ndat = 0;
}
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;
}
return bcf_update_info_int32(args->hdr_out,line,col->hdr_key_dst,args->tmpi,ntmpi);
}
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;
}
return bcf_update_info_int32(args->hdr_out,line,col->hdr_key_dst,args->tmpi,ntmpi);
}
static int setter_ARinfo_real(args_t *args, bcf1_t *line, annot_col_t *col, int nals, char **als, int ntmpf)
{
if ( !nals ) error("Cannot fill Number=R,A tags without --columns ..,REF,ALT,..\n");
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:%"PRId64"\n", ntmpf,col->hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) 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:%"PRId64"\n", ntmpf,col->hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) 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:%"PRId64"\n", bcf_seqname(args->hdr,line),(int64_t) 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] ];
}
return bcf_update_info_float(args->hdr_out,line,col->hdr_key_dst,args->tmpf2,ndst);
}
static int setter_info_real(args_t *args, bcf1_t *line, annot_col_t *col, void *data)
{
annot_line_t *tab = (annot_line_t*) data;
// This is a bit hacky, only to reuse existing code with minimal changes:
// -c =TAG will now behave as -l TAG:APPEND for floats
if ( col->replace & SET_OR_APPEND ) col->merge_method=MM_APPEND;
if ( !tab )
{
if ( col->merge_method!=MM_SUM && col->merge_method!=MM_AVG &&
col->merge_method!=MM_MIN && col->merge_method!=MM_MAX &&
col->merge_method!=MM_APPEND &&
col->merge_method!=MM_APPEND_MISSING )
error("Error: at the moment only the sum,avg,min,max,append,append-missing options are supported with --merge-logic for INFO type=Float\n");
}
int i,ntmpf = 0;
if ( (col->replace & SET_OR_APPEND) && !col->mm_dbl_nused )
{
ntmpf = bcf_get_info_float(args->hdr, line, col->hdr_key_dst, &args->tmpf, &args->mtmpf);
if ( ntmpf>0 && (!bcf_float_is_missing(args->tmpf[0]) || (col->replace & CARRY_OVER_MISSING)) )
{
col->mm_dbl_nused = ntmpf;
hts_expand(double,col->mm_dbl_nused,col->mm_dbl_nalloc,col->mm_dbl);
for (i=0; i<ntmpf; i++)
if ( bcf_float_is_missing(args->tmpf[i]) )
bcf_double_set_missing(col->mm_dbl[i]);
else