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vcfconvert.c
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/* vcfconvert.c -- convert between VCF/BCF and related formats.
Copyright (C) 2013-2023 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 <inttypes.h>
#include <htslib/faidx.h>
#include <htslib/vcf.h>
#include <htslib/bgzf.h>
#include <htslib/synced_bcf_reader.h>
#include <htslib/vcfutils.h>
#include <htslib/kseq.h>
#include "bcftools.h"
#include "filter.h"
#include "convert.h"
#include "tsv2vcf.h"
// Logic of the filters: include or exclude sites which match the filters?
#define FLT_INCLUDE 1
#define FLT_EXCLUDE 2
typedef struct _args_t args_t;
struct _args_t
{
faidx_t *ref;
filter_t *filter;
char *filter_str;
int filter_logic; // include or exclude sites which match the filters? One of FLT_INCLUDE/FLT_EXCLUDE
convert_t *convert;
bcf_srs_t *files;
bcf_hdr_t *header;
void (*convert_func)(struct _args_t *);
struct {
int total, skipped, hom_rr, het_ra, hom_aa, het_aa, missing;
} n;
kstring_t str;
int32_t *gts;
float *flt;
int rev_als, output_vcf_ids, hap2dip, gen_3N6;
int nsamples, *samples, sample_is_file, targets_is_file, regions_is_file, output_type;
int regions_overlap, targets_overlap;
char **argv, *sample_list, *targets_list, *regions_list, *tag, *columns;
char *outfname, *infname, *ref_fname, *sex_fname;
int argc, n_threads, record_cmd_line, keep_duplicates, clevel;
char *index_fn;
int write_index;
};
static void destroy_data(args_t *args)
{
if ( args->ref ) fai_destroy(args->ref);
if ( args->convert) convert_destroy(args->convert);
if ( args->filter ) filter_destroy(args->filter);
free(args->samples);
if ( args->files ) bcf_sr_destroy(args->files);
}
static void open_vcf(args_t *args, const char *format_str)
{
args->files = bcf_sr_init();
if ( args->n_threads && bcf_sr_set_threads(args->files, args->n_threads)!=0 )
error("Could not initialize --threads %d\n", args->n_threads);
if ( args->regions_list )
{
bcf_sr_set_opt(args->files,BCF_SR_REGIONS_OVERLAP,args->regions_overlap);
if ( bcf_sr_set_regions(args->files, args->regions_list, args->regions_is_file)<0 )
error("Failed to read the regions: %s\n", args->regions_list);
}
if ( args->targets_list )
{
bcf_sr_set_opt(args->files,BCF_SR_TARGETS_OVERLAP,args->targets_overlap);
if ( bcf_sr_set_targets(args->files, args->targets_list, args->targets_is_file, 0)<0 )
error("Failed to read the targets: %s\n", args->targets_list);
}
if ( !bcf_sr_add_reader(args->files, args->infname) )
error("Failed to open %s: %s\n", args->infname,bcf_sr_strerror(args->files->errnum));
args->header = args->files->readers[0].header;
if ( args->filter_str )
args->filter = filter_init(args->header, args->filter_str);
int i, nsamples = 0, *samples = NULL;
if ( args->sample_list && strcmp("-",args->sample_list) )
{
for (i=0; i<args->files->nreaders; i++)
{
int ret = bcf_hdr_set_samples(args->files->readers[i].header,args->sample_list,args->sample_is_file);
if ( ret<0 ) error("Error parsing the sample list\n");
else if ( ret>0 ) error("Sample name mismatch: sample #%d not found in the header\n", ret);
}
if ( args->sample_list[0]!='^' )
{
// the sample ordering may be different if not negated
int n;
char **smpls = hts_readlist(args->sample_list, args->sample_is_file, &n);
if ( !smpls ) error("Could not parse %s\n", args->sample_list);
if ( n!=bcf_hdr_nsamples(args->files->readers[0].header) )
error("The number of samples does not match, perhaps some are present multiple times?\n");
nsamples = bcf_hdr_nsamples(args->files->readers[0].header);
samples = (int*) malloc(sizeof(int)*nsamples);
for (i=0; i<n; i++)
{
samples[i] = bcf_hdr_id2int(args->files->readers[0].header, BCF_DT_SAMPLE,smpls[i]);
free(smpls[i]);
}
free(smpls);
}
}
if ( format_str ) args->convert = convert_init(args->header, samples, nsamples, format_str);
free(samples);
}
// Try to set CHROM:POS_REF_ALT[_END]. Return 0 on success, -1 on error
static int _set_chrom_pos_ref_alt(tsv_t *tsv, bcf1_t *rec, void *usr)
{
args_t *args = (args_t*) usr;
char tmp, *se = tsv->ss, *ss = tsv->ss;
while ( se < tsv->se && *se!=':' ) se++;
if ( *se!=':' ) return -1;
tmp = *se; *se = 0;
int rid = bcf_hdr_name2id(args->header,ss);
*se = tmp;
if ( rid<0 ) return -1;
// POS
hts_pos_t pos = strtol(se+1,&ss,10);
if ( ss==se+1 ) return -1;
pos--;
// REF,ALT
args->str.l = 0;
se = ++ss;
while ( se < tsv->se && *se!='_' ) se++;
if ( *se!='_' ) return -1;
kputsn(ss,se-ss,&args->str);
ss = ++se;
while ( se < tsv->se && *se!='_' && isspace(*tsv->se) ) se++;
if ( se < tsv->se && *se!='_' && isspace(*tsv->se) ) return -1;
kputc(',',&args->str);
kputsn(ss,se-ss,&args->str);
// END - optional
if (*se && *se=='_')
{
long end = strtol(se+1,&ss,10);
if ( ss==se+1 ) return -1;
bcf_update_info_int32(args->header, rec, "END", &end, 1);
}
rec->rid = rid;
rec->pos = pos;
bcf_update_alleles_str(args->header, rec, args->str.s);
return 0;
}
static int tsv_setter_chrom_pos_ref_alt_or_chrom(tsv_t *tsv, bcf1_t *rec, void *usr)
{
args_t *args = (args_t*)usr;
int ret = _set_chrom_pos_ref_alt(tsv,rec,usr);
if ( !ret ) return ret;
return tsv_setter_chrom(tsv,rec,args->header);
}
static int tsv_setter_chrom_pos_ref_alt(tsv_t *tsv, bcf1_t *rec, void *usr)
{
int ret = _set_chrom_pos_ref_alt(tsv,rec,usr);
if ( ret!=0 ) error("Could not parse the CHROM:POS_REF_ALT[_END] string: %s\n", tsv->ss);
return ret;
}
// This function must be called first, then tsv_setter_chrom_pos_ref_alt_id_or_die.
// One of them is expected to find the CHROM:POS_REF_ALT[_END] string, if not, die.
static int tsv_setter_chrom_pos_ref_alt_or_id(tsv_t *tsv, bcf1_t *rec, void *usr)
{
args_t *args = (args_t*)usr;
if ( _set_chrom_pos_ref_alt(tsv,rec,usr)==0 ) return 0;
rec->pos = -1; // mark the record as unset
if ( !args->output_vcf_ids) return 0;
return tsv_setter_id(tsv,rec,usr);
}
static int tsv_setter_chrom_pos_ref_alt_id_or_die(tsv_t *tsv, bcf1_t *rec, void *usr)
{
args_t *args = (args_t*)usr;
if ( rec->pos!=-1 )
{
if ( !args->output_vcf_ids ) return 0;
return tsv_setter_id(tsv,rec,usr);
}
return tsv_setter_chrom_pos_ref_alt(tsv,rec,usr);
}
static int tsv_setter_verify_pos(tsv_t *tsv, bcf1_t *rec, void *usr)
{
char *se;
int pos = strtol(tsv->ss,&se,10);
if ( tsv->ss==se ) error("Could not parse POS: %s\n", tsv->ss);
if ( rec->pos != pos-1 ) error("POS mismatch: %s\n", tsv->ss);
return 0;
}
static int tsv_setter_verify_ref_alt(tsv_t *tsv, bcf1_t *rec, void *usr)
{
args_t *args = (args_t*) usr;
args->rev_als = 0;
char tmp = *tsv->se; *tsv->se = 0;
if ( strcmp(tsv->ss,rec->d.allele[0]) )
{
if ( strcmp(tsv->ss,rec->d.allele[1]) ) { *tsv->se = tmp; error("REF/ALT mismatch: [%s][%s]\n", tsv->ss,rec->d.allele[1]); }
args->rev_als = 1;
}
*tsv->se = tmp;
while ( *tsv->se && isspace(*tsv->se) ) tsv->se++;
tsv->ss = tsv->se;
while ( *tsv->se && !isspace(*tsv->se) ) tsv->se++;
tmp = *tsv->se; *tsv->se = 0;
if ( !args->rev_als && strcmp(tsv->ss,rec->d.allele[1]) ) { *tsv->se = tmp; error("REF/ALT mismatch: [%s][%s]\n", tsv->ss,rec->d.allele[1]); }
else if ( args->rev_als && strcmp(tsv->ss,rec->d.allele[0]) ) { *tsv->se = tmp; error("REF/ALT mismatch: [%s][%s]\n", tsv->ss,rec->d.allele[0]); }
*tsv->se = tmp;
return 0;
}
static int tsv_setter_gt_gp(tsv_t *tsv, bcf1_t *rec, void *usr)
{
args_t *args = (args_t*) usr;
int i, nsamples = bcf_hdr_nsamples(args->header);
for (i=0; i<nsamples; i++)
{
float aa,ab,bb;
aa = strtod(tsv->ss, &tsv->se);
if ( tsv->ss==tsv->se ) { fprintf(stderr,"Could not parse first value of %d-th sample\n", i+1); return -1; }
tsv->ss = tsv->se+1;
ab = strtod(tsv->ss, &tsv->se);
if ( tsv->ss==tsv->se ) { fprintf(stderr,"Could not parse second value of %d-th sample\n", i+1); return -1; }
tsv->ss = tsv->se+1;
bb = strtod(tsv->ss, &tsv->se);
if ( tsv->ss==tsv->se ) { fprintf(stderr,"Could not parse third value of %d-th sample\n", i+1); return -1; }
tsv->ss = tsv->se+1;
if ( args->rev_als ) { float tmp = bb; bb = aa; aa = tmp; }
args->flt[3*i+0] = aa;
args->flt[3*i+1] = ab;
args->flt[3*i+2] = bb;
if ( aa >= ab )
{
if ( aa >= bb ) args->gts[2*i+0] = args->gts[2*i+1] = bcf_gt_unphased(0);
else args->gts[2*i+0] = args->gts[2*i+1] = bcf_gt_unphased(1);
}
else if ( ab >= bb )
{
args->gts[2*i+0] = bcf_gt_unphased(0);
args->gts[2*i+1] = bcf_gt_unphased(1);
}
else args->gts[2*i+0] = args->gts[2*i+1] = bcf_gt_unphased(1);
}
if ( *tsv->se ) error("Could not parse: %s\n", tsv->ss);
if ( bcf_update_genotypes(args->header,rec,args->gts,nsamples*2) ) error("Could not update GT field\n");
if ( bcf_update_format_float(args->header,rec,"GP",args->flt,nsamples*3) ) error("Could not update GP field\n");
return 0;
}
static int tsv_setter_haps(tsv_t *tsv, bcf1_t *rec, void *usr)
{
args_t *args = (args_t*) usr;
int i, nsamples = bcf_hdr_nsamples(args->header);
int32_t a0, a1;
if ( args->rev_als ) { a0 = bcf_gt_phased(1); a1 = bcf_gt_phased(0); }
else { a0 = bcf_gt_phased(0); a1 = bcf_gt_phased(1); }
// up is short for "unphased"
int nup = 0;
for (i=0; i<nsamples; i++)
{
char *ss = tsv->ss + 4*i + nup;
int up = 0, all;
for (all=0; all < 2; all++){
// checking for premature ending
if ( !ss[0] || !ss[1] || !ss[2] ||
(up && (!ss[3] || !ss[4]) ) )
{
fprintf(stderr,"Wrong number of fields at %d-th sample ([%c][%c][%c]). ",i+1,ss[0],ss[1],ss[2]);
return -1;
}
switch(ss[all*2+up]){
case '0':
args->gts[2*i+all] = a0;
break;
case '1' :
args->gts[2*i+all] = a1;
break;
case '?' :
// there is no macro to express phased missing allele
args->gts[2*i+all] = bcf_gt_phased(-1);
break;
case '-' :
args->gts[2*i+all] = bcf_int32_vector_end;
break;
default :
fprintf(stderr,"Could not parse: [%c][%s]\n", ss[all*2+up],tsv->ss);
return -1;
}
if( ss[all*2+up+1]=='*' ) up = up + 1;
}
if(up && up != 2)
{
fprintf(stderr,"Missing unphased marker '*': [%c][%s]", ss[2+up], tsv->ss);
return -1;
}
// change alleles to unphased if the alleles are unphased
if ( up )
{
args->gts[2*i] = bcf_gt_unphased(bcf_gt_allele(args->gts[2*i]));
args->gts[2*i+1] = bcf_gt_unphased(bcf_gt_allele(args->gts[2*i+1]));
}
nup = nup + up;
}
if ( tsv->ss[(nsamples-1)*4+3+nup] )
{
fprintf(stderr,"nup: %d", nup);
fprintf(stderr,"Wrong number of fields (%d-th column = [%c]). ", nsamples*2,tsv->ss[(nsamples-1)*4+nup]);
return -1;
}
if ( bcf_update_genotypes(args->header,rec,args->gts,nsamples*2) ) error("Could not update GT field\n");
return 0;
}
static void gensample_to_vcf(args_t *args)
{
/*
* Inpute: IMPUTE2 output (indentation changed here for clarity):
*
* 20:62116619_C_T 20:62116619 62116619 C T 0.969 0.031 0 ...
* --- 20:62116698_C_A 62116698 C A 1 0 0 ...
*
* Second column is expected in the form of CHROM:POS_REF_ALT. We use second
* column because the first can be empty ("--") when filling sites from reference
* panel. When the option --vcf-ids is given, the first column is used to set the
* VCF ID.
*
* Output: VCF with filled GT,GP
*
*/
kstring_t line = {0,0,0};
char *gen_fname = NULL, *sample_fname = NULL;
sample_fname = strchr(args->infname,',');
if ( !sample_fname )
{
args->str.l = 0;
ksprintf(&args->str,"%s.gen.gz", args->infname);
gen_fname = strdup(args->str.s);
args->str.l = 0;
ksprintf(&args->str,"%s.samples", args->infname);
sample_fname = strdup(args->str.s);
}
else
{
*sample_fname = 0;
gen_fname = strdup(args->infname);
sample_fname = strdup(sample_fname+1);
}
htsFile *gen_fh = hts_open(gen_fname, "r");
if ( !gen_fh ) error("Could not read: %s\n", gen_fname);
if ( hts_getline(gen_fh, KS_SEP_LINE, &line) <= 0 ) error("Empty file: %s\n", gen_fname);
// Find out the chromosome name, depending on the format variant (--3N6 or plain) and the ordering
// of the columns (CHROM:POS_REF_ALT comes first or second)
args->str.l = 0;
char *sb = line.s, *se = line.s;
while ( *se && !isspace(*se) ) se++;
if ( !*se ) error("Could not determine CHROM in %s: %s\n", gen_fname,line.s);
if ( args->gen_3N6 ) // first column, just CHROM
kputsn(sb, se-sb, &args->str);
else // first or second column, part of CHROM:POS_REF_ALT
{
char *sc = strchr(sb,':');
if ( !sc || sc > se )
{
while ( *se && !isspace(*se) ) se++;
if ( !*se ) error("Could not determine CHROM in %s: %s\n", gen_fname,line.s);
sb = ++se;
sc = strchr(sb,':');
if ( !sc ) error("Could not determine CHROM in %s: %s\n", gen_fname,line.s);
}
kputsn(sb, sc-sb, &args->str);
}
// Initialize and print the VCF header, args->str.s contains the chr name
args->header = bcf_hdr_init("w");
bcf_hdr_append(args->header, "##INFO=<ID=END,Number=1,Type=Integer,Description=\"End position of the variant described in this record\">");
bcf_hdr_append(args->header, "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">");
bcf_hdr_append(args->header, "##FORMAT=<ID=GP,Number=G,Type=Float,Description=\"Genotype Probabilities\">");
bcf_hdr_printf(args->header, "##contig=<ID=%s,length=%d>", args->str.s,0x7fffffff); // MAX_CSI_COOR
if (args->record_cmd_line) bcf_hdr_append_version(args->header, args->argc, args->argv, "bcftools_convert");
tsv_t *tsv;
if ( args->gen_3N6 )
{
tsv = tsv_init("CHROM,CHROM_POS_REF_ALT,ID,POS,REF_ALT,GT_GP");
tsv_register(tsv, "CHROM", tsv_setter_chrom, args->header);
}
else
tsv = tsv_init("CHROM_POS_REF_ALT,ID,POS,REF_ALT,GT_GP");
tsv_register(tsv, "CHROM_POS_REF_ALT", tsv_setter_chrom_pos_ref_alt_or_id, args);
tsv_register(tsv, "ID", tsv_setter_chrom_pos_ref_alt_id_or_die, args);
tsv_register(tsv, "POS", tsv_setter_verify_pos, NULL);
tsv_register(tsv, "REF_ALT", tsv_setter_verify_ref_alt, args);
tsv_register(tsv, "GT_GP", tsv_setter_gt_gp, args);
// Find out sample names
int i, nsamples;
char **samples = hts_readlist(sample_fname, 1, &nsamples);
if ( !samples ) error("Could not read %s\n", sample_fname);
for (i=2; i<nsamples; i++)
{
se = samples[i]; while ( *se && !isspace(*se) ) se++;
*se = 0;
bcf_hdr_add_sample(args->header,samples[i]);
}
for (i=0; i<nsamples; i++) free(samples[i]);
free(samples);
char wmode[8];
set_wmode(wmode,args->output_type,args->outfname,args->clevel);
htsFile *out_fh = hts_open(args->outfname ? args->outfname : "-", wmode);
if ( out_fh == NULL ) error("Can't write to \"%s\": %s\n", args->outfname, strerror(errno));
if ( args->n_threads ) hts_set_threads(out_fh, args->n_threads);
if ( bcf_hdr_write(out_fh,args->header)!=0 ) error("[%s] Error: cannot write the header to %s\n", __func__,args->outfname);
if ( args->write_index && init_index(out_fh,args->header,args->outfname,&args->index_fn)<0 ) error("Error: failed to initialise index for %s\n",args->outfname);
bcf1_t *rec = bcf_init();
nsamples -= 2;
args->gts = (int32_t *) malloc(sizeof(int32_t)*nsamples*2);
args->flt = (float *) malloc(sizeof(float)*nsamples*3);
do
{
bcf_clear(rec);
args->n.total++;
if ( !tsv_parse(tsv, rec, line.s) )
{
if ( bcf_write(out_fh, args->header, rec)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->outfname);
}
else
error("Error occurred while parsing: %s\n", line.s);
}
while ( hts_getline(gen_fh, KS_SEP_LINE, &line)>0 );
if ( args->write_index )
{
if ( bcf_idx_save(out_fh)<0 )
{
if ( hts_close(out_fh) ) error("Close failed: %s\n", args->outfname);
error("Error: cannot write to index %s\n", args->index_fn);
}
free(args->index_fn);
}
if ( hts_close(out_fh) ) error("Close failed: %s\n", args->outfname);
if ( hts_close(gen_fh) ) error("Close failed: %s\n", gen_fname);
bcf_hdr_destroy(args->header);
bcf_destroy(rec);
free(sample_fname);
free(gen_fname);
free(args->str.s);
free(line.s);
free(args->gts);
free(args->flt);
tsv_destroy(tsv);
fprintf(stderr,"Number of processed rows: \t%d\n", args->n.total);
}
static void haplegendsample_to_vcf(args_t *args)
{
/*
* Convert from IMPUTE2 hap/legend/sample output files to VCF
*
* hap:
* 0 1 0 1
* legend:
* id position a0 a1
* 1:186946386_G_T 186946386 G T
* sample:
* sample population group sex
* sample1 sample1 sample1 2
* sample2 sample2 sample2 2
*
* Output: VCF with filled GT
*/
kstring_t line = {0,0,0};
if ( args->output_vcf_ids )
error(
"The option --haplegendsample2vcf cannot be combined with --vcf-ids. This is because the\n"
"ID column must be formatted as \"CHROM:POS_REF_ALT\" to check sanity of the operation\n");
char *hap_fname = NULL, *leg_fname = NULL, *sample_fname = NULL;
sample_fname = strchr(args->infname,',');
if ( !sample_fname )
{
args->str.l = 0;
ksprintf(&args->str,"%s.hap.gz", args->infname);
hap_fname = strdup(args->str.s);
args->str.l = 0;
ksprintf(&args->str,"%s.samples", args->infname);
sample_fname = strdup(args->str.s);
args->str.l = 0;
ksprintf(&args->str,"%s.legend.gz", args->infname);
leg_fname = strdup(args->str.s);
}
else
{
char *ss = sample_fname, *se = strchr(ss+1,',');
if ( !se ) error("Could not parse hap/legend/sample file names: %s\n", args->infname);
*ss = 0;
*se = 0;
hap_fname = strdup(args->infname);
leg_fname = strdup(ss+1);
sample_fname = strdup(se+1);
}
htsFile *hap_fh = hts_open(hap_fname, "r");
if ( !hap_fh ) error("Could not read: %s\n", hap_fname);
htsFile *leg_fh = hts_open(leg_fname,"r");
if ( !leg_fh ) error("Could not read: %s\n", leg_fname);
// Eat up first legend line, then determine chromosome name
if ( hts_getline(leg_fh, KS_SEP_LINE, &line) <= 0 ) error("Empty file: %s\n", leg_fname);
if ( hts_getline(leg_fh, KS_SEP_LINE, &line) <= 0 ) error("Empty file: %s\n", leg_fname);
// Find out the chromosome name, sample names, init and print the VCF header
args->str.l = 0;
char *se = strchr(line.s,':');
if ( !se ) error("Expected CHROM:POS_REF_ALT in first column of %s\n", leg_fname);
kputsn(line.s, se-line.s, &args->str);
tsv_t *leg_tsv = tsv_init("CHROM_POS_REF_ALT,POS,REF_ALT");
tsv_register(leg_tsv, "CHROM_POS_REF_ALT", tsv_setter_chrom_pos_ref_alt, args);
tsv_register(leg_tsv, "POS", tsv_setter_verify_pos, NULL);
tsv_register(leg_tsv, "REF_ALT", tsv_setter_verify_ref_alt, args);
tsv_t *hap_tsv = tsv_init("HAPS");
tsv_register(hap_tsv, "HAPS", tsv_setter_haps, args);
args->header = bcf_hdr_init("w");
bcf_hdr_append(args->header, "##INFO=<ID=END,Number=1,Type=Integer,Description=\"End position of the variant described in this record\">");
bcf_hdr_append(args->header, "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">");
bcf_hdr_printf(args->header, "##contig=<ID=%s,length=%d>", args->str.s,0x7fffffff); // MAX_CSI_COOR
if (args->record_cmd_line) bcf_hdr_append_version(args->header, args->argc, args->argv, "bcftools_convert");
int i, nrows, nsamples;
char **samples = hts_readlist(sample_fname, 1, &nrows);
if ( !samples ) error("Could not read %s\n", sample_fname);
nsamples = nrows - 1;
// sample_fname should contain a header line, so need to ignore first row
// returned from hts_readlist (i=1, and not i=0)
for (i=1; i<nrows; i++)
{
se = samples[i]; while ( *se && !isspace(*se) ) se++;
*se = 0;
bcf_hdr_add_sample(args->header,samples[i]);
}
bcf_hdr_add_sample(args->header,NULL);
for (i=0; i<nrows; i++) free(samples[i]);
free(samples);
char wmode[8];
set_wmode(wmode,args->output_type,args->outfname,args->clevel);
htsFile *out_fh = hts_open(args->outfname ? args->outfname : "-", wmode);
if ( out_fh == NULL ) error("Can't write to \"%s\": %s\n", args->outfname, strerror(errno));
if ( args->n_threads ) hts_set_threads(out_fh, args->n_threads);
if ( bcf_hdr_write(out_fh,args->header)!=0 ) error("[%s] Error: cannot write the header to %s\n", __func__,args->outfname);
if ( args->write_index && init_index(out_fh,args->header,args->outfname,&args->index_fn)<0 ) error("Error: failed to initialise index for %s\n",args->outfname);
bcf1_t *rec = bcf_init();
args->gts = (int32_t *) malloc(sizeof(int32_t)*nsamples*2);
while (1)
{
bcf_clear(rec);
args->n.total++;
if ( tsv_parse(leg_tsv, rec, line.s) )
error("Error occurred while parsing %s: %s\n", leg_fname,line.s);
if ( hts_getline(hap_fh, KS_SEP_LINE, &line)<=0 )
error("Different number of records in %s and %s?\n", leg_fname,hap_fname);
if ( tsv_parse(hap_tsv, rec, line.s) )
error("Error occurred while parsing %s: %s\n", hap_fname,line.s);
if ( bcf_write(out_fh, args->header, rec)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->outfname);
if ( hts_getline(leg_fh, KS_SEP_LINE, &line)<=0 )
{
if ( hts_getline(hap_fh, KS_SEP_LINE, &line)>0 )
error("Different number of records in %s and %s?\n", leg_fname,hap_fname);
break;
}
}
if ( args->write_index )
{
if ( bcf_idx_save(out_fh)<0 )
{
if ( hts_close(out_fh) ) error("Close failed: %s\n", args->outfname);
error("Error: cannot write to index %s\n", args->index_fn);
}
free(args->index_fn);
}
if ( hts_close(out_fh) ) error("Close failed: %s\n", args->outfname);
if ( hts_close(hap_fh) ) error("Close failed: %s\n", hap_fname);
if ( hts_close(leg_fh) ) error("Close failed: %s\n", leg_fname);
bcf_hdr_destroy(args->header);
bcf_destroy(rec);
free(sample_fname);
free(hap_fname);
free(leg_fname);
free(args->str.s);
free(line.s);
free(args->gts);
tsv_destroy(hap_tsv);
tsv_destroy(leg_tsv);
fprintf(stderr,"Number of processed rows: \t%d\n", args->n.total);
}
static void hapsample_to_vcf(args_t *args)
{
/*
* Input: SHAPEIT output
*
* 20:19995888_A_G rsid1 19995888 A G 0 0 0 0 ...
* 20 20:19995888_A_G 19995888 A G 0 0 0 0 ...
*
* First column is expected in the form of CHROM:POS_REF_ALT
*
* Output: VCF with filled GT
*
*/
kstring_t line = {0,0,0};
char *hap_fname = NULL, *sample_fname = NULL;
sample_fname = strchr(args->infname,',');
if ( !sample_fname )
{
args->str.l = 0;
ksprintf(&args->str,"%s.hap.gz", args->infname);
hap_fname = strdup(args->str.s);
args->str.l = 0;
ksprintf(&args->str,"%s.samples", args->infname);
sample_fname = strdup(args->str.s);
}
else
{
*sample_fname = 0;
hap_fname = strdup(args->infname);
sample_fname = strdup(sample_fname+1);
}
htsFile *hap_fh = hts_open(hap_fname, "r");
if ( !hap_fh ) error("Could not read: %s\n", hap_fname);
if ( hts_getline(hap_fh, KS_SEP_LINE, &line) <= 0 ) error("Empty file: %s\n", hap_fname);
// Find out the chromosome name, it can be either in the first or second column
args->str.l = 0;
char *sb = line.s, *se = line.s;
while ( *se && !isspace(*se) ) se++;
if ( !*se ) error("Could not determine CHROM in %s: %s\n", hap_fname,line.s);
if ( !args->output_vcf_ids )
{
// first column should be just CHROM, but the second must be CHROM:POS_REF_ALT, use that
sb = ++se;
while ( *se && !isspace(*se) ) se++;
if ( !*se ) error("Could not determine CHROM in %s: %s\n", hap_fname,line.s);
if ( !strchr(sb,':') )
error("Could not determine CHROM in the second column of %s: %s\n", hap_fname,line.s);
}
// Parse CHROM:POS_REF_ALT
char *sc = strchr(sb,':');
if ( !sc || sc > se )
error("Could not determine CHROM in %s: %s\n", hap_fname,line.s);
kputsn(sb, sc-sb, &args->str);
// Initialize and print the VCF header, args->str.s contains the chr name
args->header = bcf_hdr_init("w");
bcf_hdr_append(args->header, "##INFO=<ID=END,Number=1,Type=Integer,Description=\"End position of the variant described in this record\">");
bcf_hdr_append(args->header, "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">");
bcf_hdr_printf(args->header, "##contig=<ID=%s,length=%d>", args->str.s,0x7fffffff); // MAX_CSI_COOR
if (args->record_cmd_line) bcf_hdr_append_version(args->header, args->argc, args->argv, "bcftools_convert");
tsv_t *tsv;
if ( args->output_vcf_ids )
{
tsv = tsv_init("CHROM_POS_REF_ALT,ID,POS,REF_ALT,HAPS");
tsv_register(tsv, "ID", tsv_setter_id, args);
}
else
{
tsv = tsv_init("CHROM,CHROM_POS_REF_ALT,POS,REF_ALT,HAPS");
tsv_register(tsv, "CHROM", tsv_setter_chrom_pos_ref_alt_or_chrom, args);
}
tsv_register(tsv, "CHROM_POS_REF_ALT", tsv_setter_chrom_pos_ref_alt, args);
tsv_register(tsv, "POS", tsv_setter_verify_pos, NULL);
tsv_register(tsv, "REF_ALT", tsv_setter_verify_ref_alt, args);
tsv_register(tsv, "HAPS", tsv_setter_haps, args);
int i, nsamples;
char **samples = hts_readlist(sample_fname, 1, &nsamples);
if ( !samples ) error("Could not read %s\n", sample_fname);
for (i=2; i<nsamples; i++)
{
se = samples[i]; while ( *se && !isspace(*se) ) se++;
*se = 0;
bcf_hdr_add_sample(args->header,samples[i]);
}
bcf_hdr_add_sample(args->header,NULL);
for (i=0; i<nsamples; i++) free(samples[i]);
free(samples);
char wmode[8];
set_wmode(wmode,args->output_type,args->outfname,args->clevel);
htsFile *out_fh = hts_open(args->outfname ? args->outfname : "-", wmode);
if ( out_fh == NULL ) error("Can't write to \"%s\": %s\n", args->outfname, strerror(errno));
if ( args->n_threads ) hts_set_threads(out_fh, args->n_threads);
if ( bcf_hdr_write(out_fh,args->header)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->outfname);
if ( args->write_index && init_index(out_fh,args->header,args->outfname,&args->index_fn)<0 ) error("Error: failed to initialise index for %s\n",args->outfname);
bcf1_t *rec = bcf_init();
nsamples -= 2;
args->gts = (int32_t *) malloc(sizeof(int32_t)*nsamples*2);
do
{
bcf_clear(rec);
args->n.total++;
if ( !tsv_parse(tsv, rec, line.s) )
{
if ( bcf_write(out_fh, args->header, rec)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->outfname);
}
else
error("Error occurred while parsing: %s\n", line.s);
}
while ( hts_getline(hap_fh, KS_SEP_LINE, &line)>0 );
if ( args->write_index )
{
if ( bcf_idx_save(out_fh)<0 )
{
if ( hts_close(out_fh) ) error("Close failed: %s\n", args->outfname);
error("Error: cannot write to index %s\n", args->index_fn);
}
free(args->index_fn);
}
if ( hts_close(out_fh) ) error("Close failed: %s\n", args->outfname);
if ( hts_close(hap_fh) ) error("Close failed: %s\n", hap_fname);
bcf_hdr_destroy(args->header);
bcf_destroy(rec);
free(sample_fname);
free(hap_fname);
free(args->str.s);
free(line.s);
free(args->gts);
tsv_destroy(tsv);
fprintf(stderr,"Number of processed rows: \t%d\n", args->n.total);
}
char *init_sample2sex(bcf_hdr_t *hdr, char *sex_fname)
{
int i, nlines;
char *sample2sex = (char*) calloc(bcf_hdr_nsamples(hdr),1);
char **lines = hts_readlist(sex_fname, 1, &nlines);
if ( !lines ) error("Could not read %s\n", sex_fname);
for (i=0; i<nlines; i++)
{
char *se = lines[i]; while ( *se && !isspace(*se) ) se++;
char tmp = *se;
*se = 0;
int id = bcf_hdr_id2int(hdr, BCF_DT_SAMPLE, lines[i]);
*se = tmp;
if ( id<0 ) continue;
while ( *se && isspace(*se) ) se++;
if ( *se=='M' ) sample2sex[id] = '1';
else if ( *se=='F' ) sample2sex[id] = '2';
else error("Could not parse %s: %s\n", sex_fname,lines[i]);
}
for (i=0; i<nlines; i++) free(lines[i]);
free(lines);
for (i=0; i<bcf_hdr_nsamples(hdr); i++)
if ( !sample2sex[i] ) error("Missing sex for sample %s in %s\n", bcf_hdr_int2id(hdr, BCF_DT_SAMPLE, i),sex_fname);
return sample2sex;
}
static void vcf_to_gensample(args_t *args)
{
kstring_t str = {0,0,0};
// insert chrom as first column if needed
if ( args->gen_3N6 )
kputs("%CHROM ", &str);
kputs("%CHROM:%POS\\_%REF\\_%FIRST_ALT ", &str);
// insert rsid as second column if needed
if ( args->output_vcf_ids )
kputs("%ID ", &str);
else
kputs("%CHROM:%POS\\_%REF\\_%FIRST_ALT ", &str);
kputs("%POS %REF %FIRST_ALT", &str);
if ( !args->tag || !strcmp(args->tag,"GT") ) kputs("%_GT_TO_PROB3",&str);
else if ( !strcmp(args->tag,"PL") ) kputs("%_PL_TO_PROB3",&str);
else if ( !strcmp(args->tag,"GP") ) kputs("%_GP_TO_PROB3",&str);
else error("todo: --tag %s\n", args->tag);
kputs("\n", &str);
open_vcf(args,str.s);
int ret, gen_compressed = 1, sample_compressed = 0;
char *gen_fname = NULL, *sample_fname = NULL;
str.l = 0;
kputs(args->outfname,&str);
int n_files = 0, i;
char **files = hts_readlist(str.s, 0, &n_files);
if ( n_files==1 )
{
int l = str.l;
kputs(".samples",&str);
sample_fname = strdup(str.s);
str.l = l;
kputs(".gen.gz",&str);
gen_fname = strdup(str.s);
}
else if ( n_files==2 )
{
if (strlen(files[0]) && strcmp(files[0],".")!=0) gen_fname = strdup(files[0]);
if (strlen(files[1]) && strcmp(files[1],".")!=0) sample_fname = strdup(files[1]);
}
else
{
error("Error parsing --gensample filenames: %s\n", args->outfname);
}
for (i=0; i<n_files; i++) free(files[i]);
free(files);
if ( gen_fname && (strlen(gen_fname)<3 || strcasecmp(".gz",gen_fname+strlen(gen_fname)-3)) ) gen_compressed = 0;
if ( sample_fname && strlen(sample_fname)>3 && strcasecmp(".gz",sample_fname+strlen(sample_fname)-3)==0 ) sample_compressed = 0;
if (gen_fname) fprintf(stderr, "Gen file: %s\n", gen_fname);
if (sample_fname) fprintf(stderr, "Sample file: %s\n", sample_fname);
// write samples file
if (sample_fname)
{
char *sample2sex = NULL;
if ( args->sex_fname ) sample2sex = init_sample2sex(args->header,args->sex_fname);
int i;
BGZF *sout = bgzf_open(sample_fname, sample_compressed ? "wg" : "wu");
str.l = 0;
kputs(sample2sex ? "ID_1 ID_2 missing sex\n0 0 0 0\n" : "ID_1 ID_2 missing\n0 0 0\n", &str);
ret = bgzf_write(sout, str.s, str.l);
if ( ret != str.l ) error("Error writing %s: %s\n", sample_fname, strerror(errno));
for (i=0; i<bcf_hdr_nsamples(args->header); i++)
{
str.l = 0;
if ( sample2sex )
ksprintf(&str, "%s %s 0 %c\n", args->header->samples[i],args->header->samples[i],sample2sex[i]);
else
ksprintf(&str, "%s %s 0\n", args->header->samples[i],args->header->samples[i]);
ret = bgzf_write(sout, str.s, str.l);
if ( ret != str.l ) error("Error writing %s: %s\n", sample_fname, strerror(errno));
}
if ( bgzf_close(sout)!=0 ) error("Error closing %s: %s\n", sample_fname, strerror(errno));
free(sample_fname);
free(sample2sex);
}
if (!gen_fname) {
if ( str.m ) free(str.s);
return;
}
int prev_rid = -1, prev_pos = -1;
int no_alt = 0, non_biallelic = 0, filtered = 0, ndup = 0, nok = 0;
BGZF *gout = bgzf_open(gen_fname, gen_compressed ? "wg" : "wu");
while ( bcf_sr_next_line(args->files) )
{
bcf1_t *line = bcf_sr_get_line(args->files,0);
if ( args->filter )
{
int pass = filter_test(args->filter, line, NULL);
if ( args->filter_logic & FLT_EXCLUDE ) pass = pass ? 0 : 1;
if ( !pass ) { filtered++; continue; }
}
// ALT allele is required
if ( line->n_allele<2 ) { no_alt++; continue; }
// biallelic required
if ( line->n_allele>2 ) {
if (!non_biallelic)
fprintf(stderr, "Warning: non-biallelic records are skipped. Consider splitting multi-allelic records into biallelic records using 'bcftools norm -m-'.\n");
non_biallelic++;
continue;
}
// skip duplicate lines, or otherwise shapeit complains
if ( !args->keep_duplicates && prev_rid==line->rid && prev_pos==line->pos ) { ndup++; continue; }
prev_rid = line->rid;
prev_pos = line->pos;
str.l = 0;
convert_line(args->convert, line, &str);
if ( str.l )
{
int ret = bgzf_write(gout, str.s, str.l);
if ( ret!= str.l ) error("Error writing %s: %s\n", gen_fname,strerror(errno));
nok++;
}
}
fprintf(stderr, "%d records written, %d skipped: %d/%d/%d/%d no-ALT/non-biallelic/filtered/duplicated\n",
nok, no_alt+non_biallelic+filtered+ndup, no_alt, non_biallelic, filtered, ndup);
if ( str.m ) free(str.s);
if ( bgzf_close(gout)!=0 ) error("Error closing %s: %s\n", gen_fname,strerror(errno));
free(gen_fname);
}
static void vcf_to_haplegendsample(args_t *args)
{
kstring_t str = {0,0,0};
if ( args->hap2dip )
kputs("%_GT_TO_HAP2\n", &str);
else
kputs("%_GT_TO_HAP\n", &str);
open_vcf(args,str.s);
int ret, hap_compressed = 1, legend_compressed = 1, sample_compressed = 0;
char *hap_fname = NULL, *legend_fname = NULL, *sample_fname = NULL;
str.l = 0;
kputs(args->outfname,&str);
int n_files = 0, i;
char **files = hts_readlist(str.s, 0, &n_files);
if ( n_files==1 )
{
int l = str.l;
kputs(".samples",&str);
sample_fname = strdup(str.s);
str.l = l;
kputs(".legend.gz",&str);
legend_fname = strdup(str.s);
str.l = l;
kputs(".hap.gz",&str);
hap_fname = strdup(str.s);
}
else if ( n_files==3 )
{
if (strlen(files[0]) && strcmp(files[0],".")!=0) hap_fname = strdup(files[0]);
if (strlen(files[1]) && strcmp(files[1],".")!=0) legend_fname = strdup(files[1]);
if (strlen(files[2]) && strcmp(files[2],".")!=0) sample_fname = strdup(files[2]);
}
else
{
error("Error parsing --hapslegendsample filenames: %s\n", args->outfname);
}
for (i=0; i<n_files; i++) free(files[i]);
free(files);
if ( hap_fname && (strlen(hap_fname)<3 || strcasecmp(".gz",hap_fname+strlen(hap_fname)-3)) ) hap_compressed = 0;
if ( legend_fname && (strlen(legend_fname)<3 || strcasecmp(".gz",legend_fname+strlen(legend_fname)-3)) ) legend_compressed = 0;
if ( sample_fname && strlen(sample_fname)>3 && strcasecmp(".gz",sample_fname+strlen(sample_fname)-3)==0 ) sample_compressed = 0;