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guess-ploidy.c
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/*
Copyright (C) 2016-2021 Genome Research Ltd.
Author: Petr Danecek <pd3@sanger.ac.uk>
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
THE SOFTWARE.
*/
#include <stdio.h>
#include <stdlib.h>
#include <strings.h>
#include <getopt.h>
#include <stdarg.h>
#include <stdint.h>
#include <htslib/vcf.h>
#include <htslib/synced_bcf_reader.h>
#include <htslib/vcfutils.h>
#include <inttypes.h>
#include <unistd.h>
#include "bcftools.h"
#include "filter.h"
// Logic of the filters: include or exclude sites which match the filters?
#define FLT_INCLUDE 1
#define FLT_EXCLUDE 2
#define GUESS_GT 1
#define GUESS_PL 2
#define GUESS_GL 4
typedef struct
{
uint64_t ncount;
double phap, pdip;
}
count_t;
typedef struct
{
char *chr;
uint32_t start, end;
count_t *counts; // per-sample counts: counts[isample]
}
stats_t;
typedef struct
{
int argc;
char **argv, *af_tag;
double af_dflt;
stats_t stats;
filter_t *filter;
char *filter_str;
int filter_logic; // include or exclude sites which match the filters? One of FLT_INCLUDE/FLT_EXCLUDE
const uint8_t *smpl_pass;
int nsample, verbose, tag, include_indels;
int *counts, ncounts; // number of observed GTs with given ploidy, used when -g is not given
double *tmpf, *pl2p, gt_err_prob;
float *af;
int maf;
int32_t *arr, narr, nfarr;
float *farr;
bcf_srs_t *sr;
bcf_hdr_t *hdr;
}
args_t;
const char *about(void)
{
return "Determine sample sex by checking genotype likelihoods in haploid regions.\n";
}
static const char *usage_text(void)
{
return
"\n"
"About: Determine sample sex by checking genotype likelihoods (GL,PL) or genotypes (GT)\n"
" in the non-PAR region of chrX. The HWE is assumed, so given the alternate allele\n"
" frequency fA and the genotype likelihoods pRR,pRA,pAA, the probabilities are\n"
" calculated as\n"
" P(dip) = pRR*(1-fA)^2 + pAA*fA^2 + 2*pRA*(1-fA)*fA\n"
" P(hap) = pRR*(1-fA) + pAA*fA\n"
" When genotype likelihoods are not available, the -e option is used to account\n"
" for genotyping errors with -t GT. The alternate allele frequency fA is estimated\n"
" directly from the data (the default) or can be provided by an INFO tag.\n"
" The results can be visualized using the accompanied guess-ploidy.py script.\n"
" Note that this plugin is intended to replace the former vcf2sex plugin.\n"
"\n"
"Usage: bcftools +guess-ploidy <file.vcf.gz> [Plugin Options]\n"
"Plugin options:\n"
" --AF-dflt <float> the default alternate allele frequency [0.5]\n"
" --AF-tag <TAG> use TAG for allele frequency\n"
" -e, --error-rate <float> probability of GT being wrong (with -t GT) [1e-3]\n"
" --exclude <expr> exclude sites for which the expression is true\n"
" -i, --include-indels do not skip indel sites\n"
" --include <expr> include only sites for which the expression is true\n"
" -g, --genome <str> shortcut to select nonPAR region for common genomes b37|hg19|b38|hg38\n"
" -r, --regions <chr:beg-end> restrict to comma-separated list of regions\n"
" -R, --regions-file <file> restrict to regions listed in a file\n"
" -t, --tag <tag> genotype or genotype likelihoods: GT, PL, GL [PL]\n"
" -v, --verbose verbose output (specify twice to increase verbosity)\n"
"\n"
"Region shortcuts:\n"
" b37 .. -r X:2699521-154931043 # GRCh37 no-chr prefix\n"
" b38 .. -r X:2781480-155701381 # GRCh38 no-chr prefix\n"
" hg19 .. -r chrX:2699521-154931043 # GRCh37 chr prefix\n"
" hg38 .. -r chrX:2781480-155701381 # GRCh38 chr prefix\n"
"\n"
"Examples:\n"
" bcftools +guess-ploidy -g b37 in.vcf.gz\n"
" bcftools +guess-ploidy in.vcf.gz -t GL -r chrX:2699521-154931043\n"
" bcftools view file.vcf.gz -r chrX:2699521-154931043 | bcftools +guess-ploidy\n"
" bcftools +guess-ploidy in.bcf -v > ploidy.txt && guess-ploidy.py ploidy.txt img\n"
"\n";
}
static inline int smpl_pass(args_t *args, int ismpl)
{
if ( !args->smpl_pass ) return 1;
int pass = args->smpl_pass[ismpl];
if ( args->filter_logic & FLT_EXCLUDE ) pass = pass ? 0 : 1;
if ( pass ) return 1;
return 0;
}
void process_region_guess(args_t *args)
{
while ( bcf_sr_next_line(args->sr) )
{
bcf1_t *rec = bcf_sr_get_line(args->sr,0);
if ( rec->n_allele==1 ) continue;
if ( !args->include_indels && !(bcf_get_variant_types(rec)&VCF_SNP) ) continue;
if ( args->filter )
{
int pass = filter_test(args->filter, rec, &args->smpl_pass);
if ( args->filter_logic & FLT_EXCLUDE ) pass = pass ? 0 : 1;
if ( !args->smpl_pass && !pass ) continue; // site-level filtering, not per-sample filtering
}
double freq[2] = {0,0}, sum;
int ismpl,i;
if ( args->tag & GUESS_GT ) // use GTs to guess the ploidy, considering only one ALT
{
int ngt = bcf_get_genotypes(args->hdr,rec,&args->arr,&args->narr);
if ( ngt<=0 ) continue;
ngt /= args->nsample;
for (ismpl=0; ismpl<args->nsample; ismpl++)
{
if ( !smpl_pass(args,ismpl) ) continue;
int32_t *ptr = args->arr + ismpl*ngt;
double *tmp = args->tmpf + ismpl*3;
if ( ptr[0]==bcf_gt_missing )
{
tmp[0] = -1;
continue;
}
if ( ptr[1]==bcf_int32_vector_end )
{
if ( bcf_gt_allele(ptr[0])==0 ) // haploid R
{
tmp[0] = 1 - 2*args->gt_err_prob;
tmp[1] = tmp[2] = args->gt_err_prob;
}
else // haploid A
{
tmp[0] = tmp[1] = args->gt_err_prob;
tmp[2] = 1 - 2*args->gt_err_prob;
}
continue;
}
if ( bcf_gt_allele(ptr[0])==0 && bcf_gt_allele(ptr[1])==0 ) // RR
{
tmp[0] = 1 - 2*args->gt_err_prob;
tmp[1] = tmp[2] = args->gt_err_prob;
}
else if ( bcf_gt_allele(ptr[0])==bcf_gt_allele(ptr[1]) ) // AA
{
tmp[0] = tmp[1] = args->gt_err_prob;
tmp[2] = 1 - 2*args->gt_err_prob;
}
else // RA or hetAA, treating as RA
{
tmp[1] = 1 - 2*args->gt_err_prob;
tmp[0] = tmp[2] = args->gt_err_prob;
}
freq[0] += 2*tmp[0]+tmp[1];
freq[1] += tmp[1]+2*tmp[2];
}
}
else if ( args->tag & GUESS_PL ) // use PL guess the ploidy, restrict to first ALT allele
{
int npl = bcf_get_format_int32(args->hdr,rec,"PL",&args->arr,&args->narr);
if ( npl<=0 ) continue;
npl /= args->nsample;
int ndip_gt = rec->n_allele*(rec->n_allele+1)/2;
if ( npl==ndip_gt ) // diploid
{
for (ismpl=0; ismpl<args->nsample; ismpl++)
{
if ( !smpl_pass(args,ismpl) ) continue;
int32_t *ptr = args->arr + ismpl*npl;
double *tmp = args->tmpf + ismpl*3;
// restrict to first ALT
if ( ptr[0]==bcf_int32_missing || ptr[1]==bcf_int32_missing || ptr[2]==bcf_int32_missing )
{
tmp[0] = -1;
continue;
}
if ( ptr[0]==ptr[1] && ptr[0]==ptr[2] ) // non-informative
{
tmp[0] = -1;
continue;
}
if ( ptr[2]==bcf_int32_vector_end )
{
tmp[0] = (ptr[0]<0 || ptr[0]>=256) ? args->pl2p[255] : args->pl2p[ptr[0]];
tmp[1] = args->pl2p[255];
tmp[2] = (ptr[1]<0 || ptr[1]>=256) ? args->pl2p[255] : args->pl2p[ptr[1]];
}
else
for (i=0; i<3; i++)
tmp[i] = (ptr[i]<0 || ptr[i]>=256) ? args->pl2p[255] : args->pl2p[ptr[i]];
sum = 0;
for (i=0; i<3; i++) sum += tmp[i];
for (i=0; i<3; i++) tmp[i] /= sum;
if ( ptr[2]==bcf_int32_vector_end )
{
freq[0] += tmp[0];
freq[1] += tmp[2];
}
else
{
freq[0] += 2*tmp[0]+tmp[1];
freq[1] += tmp[1]+2*tmp[2];
}
}
}
else if ( npl==rec->n_allele ) // all samples haploid
{
for (ismpl=0; ismpl<args->nsample; ismpl++)
{
if ( !smpl_pass(args,ismpl) ) continue;
int32_t *ptr = args->arr + ismpl*npl;
double *tmp = args->tmpf + ismpl*3;
// restrict to first ALT
if ( ptr[0]==bcf_int32_missing || ptr[1]==bcf_int32_missing )
{
tmp[0] = -1;
continue;
}
tmp[0] = (ptr[0]<0 || ptr[0]>=256) ? args->pl2p[255] : args->pl2p[ptr[0]];
tmp[1] = args->pl2p[255];
tmp[2] = (ptr[1]<0 || ptr[1]>=256) ? args->pl2p[255] : args->pl2p[ptr[1]];
sum = 0;
for (i=0; i<3; i++) sum += tmp[i];
for (i=0; i<3; i++) tmp[i] /= sum;
freq[0] += tmp[0];
freq[1] += tmp[2];
}
}
else
continue; // neither diploid nor haploid
}
else // use GL
{
int ngl = bcf_get_format_float(args->hdr,rec,"GL",&args->farr,&args->nfarr);
if ( ngl<=0 ) continue;
ngl /= args->nsample;
int ndip_gt = rec->n_allele*(rec->n_allele+1)/2;
if ( ngl==ndip_gt ) // diploid
{
for (ismpl=0; ismpl<args->nsample; ismpl++)
{
if ( !smpl_pass(args,ismpl) ) continue;
float *ptr = args->farr + ismpl*ngl;
double *tmp = args->tmpf + ismpl*3;
// restrict to first ALT
if ( bcf_float_is_missing(ptr[0]) || bcf_float_is_missing(ptr[1]) || bcf_float_is_missing(ptr[2]) )
{
tmp[0] = -1;
continue;
}
if ( ptr[0]==ptr[1] && ptr[0]==ptr[2] ) // non-informative
{
tmp[0] = -1;
continue;
}
if ( bcf_float_is_vector_end(ptr[2]) )
{
tmp[0] = pow(10.,ptr[0]);
tmp[1] = 1e-26; // arbitrary small value for a het
tmp[2] = pow(10.,ptr[1]);
}
else
for (i=0; i<3; i++)
tmp[i] = pow(10.,ptr[i]);
sum = 0;
for (i=0; i<3; i++) sum += tmp[i];
for (i=0; i<3; i++) tmp[i] /= sum;
if ( bcf_float_is_vector_end(ptr[2]) )
{
freq[0] += tmp[0];
freq[1] += tmp[2];
}
else
{
freq[0] += 2*tmp[0]+tmp[1];
freq[1] += tmp[1]+2*tmp[2];
}
}
}
else if ( ngl==rec->n_allele ) // all samples haploid
{
for (ismpl=0; ismpl<args->nsample; ismpl++)
{
if ( !smpl_pass(args,ismpl) ) continue;
float *ptr = args->farr + ismpl*ngl;
double *tmp = args->tmpf + ismpl*3;
// restrict to first ALT
if ( bcf_float_is_missing(ptr[0]) || bcf_float_is_missing(ptr[1]) )
{
tmp[0] = -1;
continue;
}
tmp[0] = pow(10.,ptr[0]);
tmp[1] = 1e-26;
tmp[2] = pow(10.,ptr[1]);
sum = 0;
for (i=0; i<3; i++) sum += tmp[i];
for (i=0; i<3; i++) tmp[i] /= sum;
freq[0] += tmp[0];
freq[1] += tmp[2];
}
}
else
continue; // neither diploid nor haploid
}
if ( args->af_tag )
{
int ret = bcf_get_info_float(args->hdr,rec,args->af_tag,&args->af, &args->maf);
if ( ret>0 ) { freq[0] = 1 - args->af[0]; freq[1] = args->af[0]; }
}
if ( !freq[0] && !freq[1] ) { freq[0] = 1 - args->af_dflt; freq[1] = args->af_dflt; }
sum = freq[0] + freq[1];
freq[0] /= sum;
freq[1] /= sum;
for (ismpl=0; ismpl<args->nsample; ismpl++)
{
if ( !smpl_pass(args,ismpl) ) continue;
count_t *counts = &args->stats.counts[ismpl];
double *tmp = args->tmpf + ismpl*3;
if ( tmp[0] < 0 ) continue;
double phap = freq[0]*tmp[0] + freq[1]*tmp[2];
double pdip = freq[0]*freq[0]*tmp[0] + 2*freq[0]*freq[1]*tmp[1] + freq[1]*freq[1]*tmp[2];
counts->phap += log(phap);
counts->pdip += log(pdip);
counts->ncount++;
if ( args->verbose>1 )
printf("DBG\t%s\t%"PRId64"\t%s\t%e\t%e\t%e\t%e\t%e\t%e\n", bcf_seqname(args->hdr,rec),(int64_t) rec->pos+1,bcf_hdr_int2id(args->hdr,BCF_DT_SAMPLE,ismpl),
freq[1],tmp[0],tmp[1],tmp[2],phap,pdip);
}
}
}
int run(int argc, char **argv)
{
args_t *args = (args_t*) calloc(1,sizeof(args_t));
args->tag = GUESS_PL;
args->argc = argc; args->argv = argv;
args->gt_err_prob = 1e-3;
args->af_dflt = 0.5;
char *region = NULL;
int region_is_file = 0;
static struct option loptions[] =
{
{"AF-tag",required_argument,NULL,0},
{"AF-dflt",required_argument,NULL,1},
{"exclude",required_argument,NULL,2},
{"include",required_argument,NULL,3},
{"verbose",no_argument,NULL,'v'},
{"include-indels",no_argument,NULL,'i'},
{"error-rate",required_argument,NULL,'e'},
{"tag",required_argument,NULL,'t'},
{"genome",required_argument,NULL,'g'},
{"regions",required_argument,NULL,'r'},
{"regions-file",required_argument,NULL,'R'},
{"background",required_argument,NULL,'b'},
{NULL,0,NULL,0}
};
int c;
char *tmp;
while ((c = getopt_long(argc, argv, "vr:R:t:e:ig:",loptions,NULL)) >= 0)
{
switch (c)
{
case 0: args->af_tag = optarg; break;
case 1:
args->af_dflt = strtod(optarg,&tmp);
if ( *tmp ) error("Could not parse: --AF-dflt %s\n", optarg);
break;
case 2:
if ( args->filter_str ) error("Error: only one --include or --exclude expression can be given, and they cannot be combined\n");
args->filter_str = optarg; args->filter_logic |= FLT_EXCLUDE; break;
case 3:
if ( args->filter_str ) error("Error: only one --include or --exclude expression can be given, and they cannot be combined\n");
args->filter_str = optarg; args->filter_logic |= FLT_INCLUDE; break;
case 'i': args->include_indels = 1; break;
case 'e':
args->gt_err_prob = strtod(optarg,&tmp);
if ( *tmp ) error("Could not parse: -e %s\n", optarg);
if ( args->gt_err_prob<0 || args->gt_err_prob>1 ) error("Expected value from the interval [0,1]: -e %s\n", optarg);
break;
case 'g':
if ( !strcasecmp(optarg,"b37") ) region = "X:2699521-154931043";
else if ( !strcasecmp(optarg,"b38") ) region = "X:2781480-155701381";
else if ( !strcasecmp(optarg,"hg19") ) region = "chrX:2699521-154931043";
else if ( !strcasecmp(optarg,"hg38") ) region = "chrX:2781480-155701381";
else error("The argument not recognised, expected --genome b37, b38, hg19 or hg38: %s\n", optarg);
break;
case 'R': region_is_file = 1; // fall-through
case 'r': region = optarg; break;
case 'v': args->verbose++; break;
case 't':
if ( !strcasecmp(optarg,"GT") ) args->tag = GUESS_GT;
else if ( !strcasecmp(optarg,"PL") ) args->tag = GUESS_PL;
else if ( !strcasecmp(optarg,"GL") ) args->tag = GUESS_GL;
else error("The argument not recognised, expected --tag GT, PL or GL: %s\n", optarg);
break;
case 'h':
case '?':
default: error("%s", usage_text()); break;
}
}
if ( args->filter_logic == (FLT_EXCLUDE|FLT_INCLUDE) ) error("Only one of --include or --exclude can be given.\n");
char *fname = NULL;
if ( optind==argc )
{
if ( !isatty(fileno((FILE *)stdin)) ) fname = "-"; // reading from stdin
else { error("%s",usage_text()); }
}
else if ( optind+1!=argc ) error("%s",usage_text());
else fname = argv[optind];
args->sr = bcf_sr_init();
if ( strcmp("-",fname) )
{
if ( region )
{
args->sr->require_index = 1;
if ( bcf_sr_set_regions(args->sr, region, region_is_file)<0 )
error("Failed to read the regions: %s\n",region);
}
}
else
{
if ( region )
{
if ( bcf_sr_set_targets(args->sr, region, region_is_file, 0)<0 )
error("Failed to read the targets: %s\n",region);
}
}
if ( !bcf_sr_add_reader(args->sr,fname) ) error("Error: %s\n", bcf_sr_strerror(args->sr->errnum));
args->hdr = args->sr->readers[0].header;
args->nsample = bcf_hdr_nsamples(args->hdr);
args->stats.counts = (count_t*) calloc(args->nsample,sizeof(count_t));
if ( args->filter_str )
args->filter = filter_init(args->hdr, args->filter_str);
if ( args->af_tag && !bcf_hdr_idinfo_exists(args->hdr,BCF_HL_INFO,bcf_hdr_id2int(args->hdr,BCF_DT_ID,args->af_tag)) )
error("No such INFO tag: %s\n", args->af_tag);
if ( args->tag&GUESS_PL && bcf_hdr_id2int(args->hdr, BCF_DT_ID, "PL")<0 )
{
fprintf(stderr, "Warning: PL tag not found in header, switching to GL\n");
args->tag = GUESS_GL;
}
if ( args->tag&GUESS_GL && bcf_hdr_id2int(args->hdr, BCF_DT_ID, "GL")<0 )
{
fprintf(stderr, "Warning: GL tag not found in header, switching to GT\n");
args->tag = GUESS_GT;
}
if ( args->tag&GUESS_GT && bcf_hdr_id2int(args->hdr, BCF_DT_ID, "GT")<0 )
error("Error: GT tag not found in header\n");
int i;
if ( args->tag&GUESS_PL )
{
args->pl2p = (double*) calloc(256,sizeof(double));
for (i=0; i<256; i++) args->pl2p[i] = pow(10., -i/10.);
}
if ( args->tag&GUESS_PL || args->tag&GUESS_GL || args->tag&GUESS_GT )
args->tmpf = (double*) malloc(sizeof(*args->tmpf)*3*args->nsample);
if ( args->verbose )
{
printf("# This file was produced by: bcftools +guess-ploidy(%s+htslib-%s)\n", bcftools_version(),hts_version());
printf("# The command line was:\tbcftools +%s", args->argv[0]);
for (i=1; i<args->argc; i++)
printf(" %s",args->argv[i]);
printf("\n");
printf("# [1]SEX\t[2]Sample\t[3]Predicted sex\t[4]log P(Haploid)/nSites\t[5]log P(Diploid)/nSites\t[6]nSites\t[7]Score: F < 0 < M ($4-$5)\n");
if ( args->verbose>1 )
printf("# [1]DBG\t[2]Chr\t[3]Pos\t[4]Sample\t[5]AF\t[6]pRR\t[7]pRA\t[8]pAA\t[9]P(Haploid)\t[10]P(Diploid)\n");
}
process_region_guess(args);
for (i=0; i<args->nsample; i++)
{
double phap = args->stats.counts[i].ncount ? args->stats.counts[i].phap / args->stats.counts[i].ncount : 0.5;
double pdip = args->stats.counts[i].ncount ? args->stats.counts[i].pdip / args->stats.counts[i].ncount : 0.5;
char predicted_sex = 'U';
if (phap>pdip) predicted_sex = 'M';
else if (phap<pdip) predicted_sex = 'F';
if ( args->verbose )
{
printf("SEX\t%s\t%c\t%f\t%f\t%"PRId64"\t%f\n", args->hdr->samples[i],predicted_sex,
phap,pdip,args->stats.counts[i].ncount,phap-pdip);
}
else
printf("%s\t%c\n", args->hdr->samples[i],predicted_sex);
}
if ( args->filter )
filter_destroy(args->filter);
bcf_sr_destroy(args->sr);
free(args->pl2p);
free(args->tmpf);
free(args->counts);
free(args->stats.counts);
free(args->arr);
free(args->farr);
free(args->af);
free(args);
return 0;
}