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vcfstats.c
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/* vcfstats.c -- Produces stats which can be plotted using plot-vcfstats.
Copyright (C) 2012-2015 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. */
/*
Notes and known issues:
- SN ts/tv calculation includes all non-ref alleles listed in ALT while per-sample ts/tv
takes the first non-ref allele only, something to consider with many non-ref HETs.
*/
#include <stdio.h>
#include <stdarg.h>
#include <unistd.h>
#include <getopt.h>
#include <math.h>
#include <htslib/vcf.h>
#include <htslib/synced_bcf_reader.h>
#include <htslib/vcfutils.h>
#include <htslib/faidx.h>
#include <inttypes.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 HWE_STATS 1
#define QUAL_STATS 1
#define IRC_STATS 1
#define IRC_RLEN 10
#define NA_STRING "0"
typedef struct
{
char *tag;
float min, max;
uint64_t *vals_ts, *vals_tv;
void *val;
int nbins, type, m_val;
}
user_stats_t;
typedef struct
{
int min, max, step, m_vals;
uint64_t *vals;
}
idist_t;
typedef struct
{
double x;
double x2;
double y;
double y2;
double xy;
double n;
}
smpl_r_t;
typedef struct
{
int n_snps, n_indels, n_mnps, n_others, n_mals, n_snp_mals, n_records, n_noalts;
int *af_ts, *af_tv, *af_snps; // first bin of af_* stats are singletons
#if HWE_STATS
int *af_hwe;
#endif
#if IRC_STATS
int n_repeat[IRC_RLEN][4], n_repeat_na; // number of indels which are repeat-consistent, repeat-inconsistent (dels and ins), and not applicable
int *af_repeats[3];
#endif
int ts_alt1, tv_alt1;
#if QUAL_STATS
int *qual_ts, *qual_tv, *qual_snps, *qual_indels;
#endif
int *insertions, *deletions, m_indel; // maximum indel length
int in_frame, out_frame, na_frame, in_frame_alt1, out_frame_alt1, na_frame_alt1;
int subst[15];
int *smpl_hets, *smpl_homRR, *smpl_homAA, *smpl_ts, *smpl_tv, *smpl_indels, *smpl_ndp, *smpl_sngl;
int *smpl_indel_hets, *smpl_indel_homs;
int *smpl_frm_shifts; // not-applicable, in-frame, out-frame
unsigned long int *smpl_dp;
idist_t dp, dp_sites;
int nusr;
user_stats_t *usr;
}
stats_t;
typedef struct
{
uint64_t m[3], mm[3]; // number of hom, het and non-ref hom matches and mismatches
float r2sum;
uint32_t r2n;
}
gtcmp_t;
typedef struct
{
char *seq;
int pos, cnt, len;
}
_idc1_t;
typedef struct
{
faidx_t *ref;
_idc1_t *dat;
int ndat, mdat;
}
indel_ctx_t;
typedef struct
{
// stats
stats_t stats[3];
int *tmp_iaf, ntmp_iaf, m_af, m_qual, naf_hwe, mtmp_frm;
uint8_t *tmp_frm;
int dp_min, dp_max, dp_step;
gtcmp_t *af_gts_snps, *af_gts_indels, *smpl_gts_snps, *smpl_gts_indels; // first bin of af_* stats are singletons
// indel context
indel_ctx_t *indel_ctx;
char *ref_fname;
// user stats
int nusr;
user_stats_t *usr;
// other
bcf_srs_t *files;
bcf_sr_regions_t *exons;
char **argv, *exons_fname, *regions_list, *samples_list, *targets_list;
int argc, verbose_sites, first_allele_only, samples_is_file;
int split_by_id, nstats;
filter_t *filter[2];
char *filter_str;
int filter_logic; // include or exclude sites which match the filters? One of FLT_INCLUDE/FLT_EXCLUDE
// Per Sample r working data arrays of size equal to number of samples
smpl_r_t* smpl_r_snps;
smpl_r_t* smpl_r_indels;
}
args_t;
static int type2dosage[6], type2ploidy[6], type2stats[6];
static void idist_init(idist_t *d, int min, int max, int step)
{
d->min = min; d->max = max; d->step = step;
d->m_vals = 4 + (d->max - d->min)/d->step;
d->vals = (uint64_t*) calloc(d->m_vals,sizeof(uint64_t));
}
static void idist_destroy(idist_t *d)
{
if ( d->vals ) free(d->vals);
}
static inline uint64_t *idist(idist_t *d, int val)
{
if ( val < d->min ) return &d->vals[0];
if ( val > d->max ) return &d->vals[d->m_vals-1];
return &d->vals[1 + (val - d->min) / d->step];
}
static inline int idist_i2bin(idist_t *d, int i)
{
if ( i<=0 ) return d->min;
if ( i>= d->m_vals ) return d->max;
return i-1+d->min;
}
static inline int clip_nonnegative(float x, int limit)
{
if (x >= limit || isnan(x)) return limit - 1;
else if (x <= 0.0) return 0;
else return (int) x;
}
#define IC_DBG 0
#if IC_DBG
static void _indel_ctx_print1(_idc1_t *idc)
{
int i;
fprintf(stdout, "%d\t", idc->cnt);
for (i=0; i<idc->len; i++)
fputc(idc->seq[i], stdout);
fputc('\n', stdout);
}
static void _indel_ctx_print(indel_ctx_t *ctx)
{
int i;
for (i=0; i<ctx->ndat; i++)
_indel_ctx_print1(&ctx->dat[i]);
fputc('\n',stdout);
}
#endif
static int _indel_ctx_lookup(indel_ctx_t *ctx, char *seq, int seq_len, int *hit)
{
// binary search
int min = 0, max = ctx->ndat - 1;
while ( min<=max )
{
int i = (min+max)/2;
int cmp = strncmp(seq, ctx->dat[i].seq, seq_len);
if ( cmp<0 ) max = i - 1;
else if ( cmp>0 ) min = i + 1;
else
{
if ( seq_len==ctx->dat[i].len )
{
*hit = 1;
return i;
}
else if ( seq_len<ctx->dat[i].len ) max = i - 1;
else min = i + 1;
}
}
*hit = 0;
return max;
}
static void _indel_ctx_insert(indel_ctx_t *ctx, char *seq, int seq_len, int pos)
{
int idat, hit, i;
idat = _indel_ctx_lookup(ctx, seq, seq_len, &hit);
if ( !hit )
{
if ( pos>0 ) return;
idat++;
ctx->ndat++;
hts_expand(_idc1_t, ctx->ndat+1, ctx->mdat, ctx->dat);
if ( idat<ctx->ndat && ctx->ndat>1 )
memmove(&ctx->dat[idat+1], &ctx->dat[idat], (ctx->ndat - idat - 1)*sizeof(_idc1_t));
ctx->dat[idat].len = seq_len;
ctx->dat[idat].cnt = 1;
ctx->dat[idat].pos = pos;
ctx->dat[idat].seq = (char*) malloc(sizeof(char)*(seq_len+1));
for (i=0; i<seq_len; i++) ctx->dat[idat].seq[i] = seq[i];
ctx->dat[idat].seq[i] = 0;
return;
}
if ( ctx->dat[idat].pos + seq_len == pos )
{
ctx->dat[idat].cnt++;
ctx->dat[idat].pos = pos;
}
}
indel_ctx_t *indel_ctx_init(char *fa_ref_fname)
{
indel_ctx_t *ctx = (indel_ctx_t *) calloc(1,sizeof(indel_ctx_t));
ctx->ref = fai_load(fa_ref_fname);
if ( !ctx->ref )
{
free(ctx);
return NULL;
}
return ctx;
}
void indel_ctx_destroy(indel_ctx_t *ctx)
{
fai_destroy(ctx->ref);
if ( ctx->mdat ) free(ctx->dat);
free(ctx);
}
/**
* indel_ctx_type() - determine indel context type
* @ctx:
* @chr: chromosome name
* @pos: position of the first @ref base, 1-based
* @ref: reference allele
* @alt: alternate allele. Only first of multiple comma-separated alleles is
* considered
* @nrep: number of repeated elements (w)
* @nlen: length of a single repeat element (w)
*
* Returns the INDEL length, negative for deletions, positive for insertions
*/
int indel_ctx_type(indel_ctx_t *ctx, char *chr, int pos, char *ref, char *alt, int *nrep, int *nlen)
{
const int win_size = 50; // hard-wired for now
const int rep_len = IRC_RLEN; // hard-wired for now
int ref_len = strlen(ref);
int alt_len = 0;
while ( alt[alt_len] && alt[alt_len]!=',' ) alt_len++;
int i, fai_ref_len;
char *fai_ref = faidx_fetch_seq(ctx->ref, chr, pos-1, pos+win_size, &fai_ref_len);
for (i=0; i<fai_ref_len; i++)
if ( (int)fai_ref[i]>96 ) fai_ref[i] -= 32;
// Sanity check: the reference sequence must match the REF allele
for (i=0; i<fai_ref_len && i<ref_len; i++)
if ( ref[i] != fai_ref[i] && ref[i] - 32 != fai_ref[i] )
error("\nSanity check failed, the reference sequence differs: %s:%d+%d .. %c vs %c\n", chr, pos, i, ref[i],fai_ref[i]);
// Count occurrences of all possible kmers
ctx->ndat = 0;
for (i=0; i<win_size; i++)
{
int k, kmax = rep_len <= i ? rep_len : i+1;
for (k=0; k<kmax; k++)
_indel_ctx_insert(ctx, &fai_ref[i-k+1], k+1, i-k);
}
#if IC_DBG
fprintf(stdout,"ref: %s\n", ref);
fprintf(stdout,"alt: %s\n", alt);
fprintf(stdout,"ctx: %s\n", fai_ref);
_indel_ctx_print(ctx);
#endif
int max_cnt = 0, max_len = 0;
for (i=0; i<ctx->ndat; i++)
{
if ( max_cnt < ctx->dat[i].cnt || (max_cnt==ctx->dat[i].cnt && max_len < ctx->dat[i].len) )
{
max_cnt = ctx->dat[i].cnt;
max_len = ctx->dat[i].len;
}
free(ctx->dat[i].seq);
}
free(fai_ref);
*nrep = max_cnt;
*nlen = max_len;
return alt_len - ref_len;
}
static void add_user_stats(args_t *args, char *str)
{
args->nusr++;
args->usr = (user_stats_t*) realloc(args->usr,sizeof(user_stats_t)*args->nusr);
user_stats_t *usr = &args->usr[args->nusr-1];
memset(usr,0,sizeof(*usr));
usr->min = 0;
usr->max = 1;
usr->nbins = 100;
char *tmp = str;
while ( *tmp && *tmp!=':' ) tmp++;
usr->tag = (char*)calloc(tmp-str+2,sizeof(char));
memcpy(usr->tag,str,tmp-str);
if ( *tmp )
{
char *ptr = ++tmp;
usr->min = strtod(tmp, &ptr);
if ( tmp==ptr ) error("Could not parse %s\n", str);
tmp = ptr+1;
}
if ( *tmp )
{
char *ptr = tmp;
usr->max = strtod(tmp, &ptr);
if ( tmp==ptr ) error("Could not parse %s\n", str);
tmp = ptr+1;
}
if ( *tmp )
{
char *ptr = tmp;
usr->nbins = strtol(tmp, &ptr, 10);
if ( tmp==ptr ) error("Could not parse %s\n", str);
if ( usr->nbins<=0 ) error("Number of bins does not make sense (%d): %s.\n", usr->nbins, str);
}
}
static void init_user_stats(args_t *args, bcf_hdr_t *hdr, stats_t *stats)
{
stats->nusr = args->nusr;
stats->usr = (user_stats_t*)malloc(sizeof(user_stats_t)*args->nusr);
memcpy(stats->usr,args->usr,args->nusr*sizeof(user_stats_t));
int i;
for (i=0; i<stats->nusr; i++)
{
user_stats_t *usr = &stats->usr[i];
usr->vals_ts = (uint64_t*)calloc(usr->nbins,sizeof(uint64_t));
usr->vals_tv = (uint64_t*)calloc(usr->nbins,sizeof(uint64_t));
int id = bcf_hdr_id2int(hdr,BCF_DT_ID,usr->tag);
if ( !bcf_hdr_idinfo_exists(hdr,BCF_HL_INFO,id) ) error("The INFO tag \"%s\" is not defined in the header\n", usr->tag);
usr->type = bcf_hdr_id2type(hdr,BCF_HL_INFO,id);
if ( usr->type!=BCF_HT_REAL && usr->type!=BCF_HT_INT ) error("The INFO tag \"%s\" is not of Float or Integer type (%d)\n", usr->type);
}
}
static void init_stats(args_t *args)
{
int i;
args->nstats = args->files->nreaders==1 ? 1 : 3;
if ( args->split_by_id ) args->nstats = 2;
if ( args->filter_str )
{
args->filter[0] = filter_init(bcf_sr_get_header(args->files,0), args->filter_str);
if ( args->files->nreaders==2 )
args->filter[1] = filter_init(bcf_sr_get_header(args->files,1), args->filter_str);
}
// AF corresponds to AC but is more robust for mixture of haploid and diploid GTs
args->m_af = 101;
for (i=0; i<args->files->nreaders; i++)
if ( bcf_hdr_nsamples(args->files->readers[i].header) + 1> args->m_af )
args->m_af = bcf_hdr_nsamples(args->files->readers[i].header) + 1;
#if QUAL_STATS
args->m_qual = 999;
#endif
#if HWE_STATS
args->naf_hwe = 100;
#endif
if ( args->samples_list )
{
if ( !bcf_sr_set_samples(args->files,args->samples_list,args->samples_is_file) )
{
if ( !bcf_hdr_nsamples(args->files->readers[0].header) )
error("No sample columns in %s\n", args->files->readers[0].fname);
error("Unable to parse the samples: \"%s\"\n", args->samples_list);
}
args->af_gts_snps = (gtcmp_t *) calloc(args->m_af,sizeof(gtcmp_t));
args->af_gts_indels = (gtcmp_t *) calloc(args->m_af,sizeof(gtcmp_t));
args->smpl_gts_snps = (gtcmp_t *) calloc(args->files->n_smpl,sizeof(gtcmp_t));
args->smpl_gts_indels = (gtcmp_t *) calloc(args->files->n_smpl,sizeof(gtcmp_t));
args->smpl_r_snps = (smpl_r_t*) calloc(args->files->n_smpl, sizeof(smpl_r_t));
args->smpl_r_indels = (smpl_r_t*) calloc(args->files->n_smpl, sizeof(smpl_r_t));
}
for (i=0; i<args->nstats; i++)
{
stats_t *stats = &args->stats[i];
stats->m_indel = 60;
stats->insertions = (int*) calloc(stats->m_indel,sizeof(int));
stats->deletions = (int*) calloc(stats->m_indel,sizeof(int));
stats->af_ts = (int*) calloc(args->m_af,sizeof(int));
stats->af_tv = (int*) calloc(args->m_af,sizeof(int));
stats->af_snps = (int*) calloc(args->m_af,sizeof(int));
int j;
for (j=0; j<3; j++) stats->af_repeats[j] = (int*) calloc(args->m_af,sizeof(int));
#if QUAL_STATS
stats->qual_ts = (int*) calloc(args->m_qual,sizeof(int));
stats->qual_tv = (int*) calloc(args->m_qual,sizeof(int));
stats->qual_snps = (int*) calloc(args->m_qual,sizeof(int));
stats->qual_indels = (int*) calloc(args->m_qual,sizeof(int));
#endif
if ( args->files->n_smpl )
{
stats->smpl_hets = (int *) calloc(args->files->n_smpl,sizeof(int));
stats->smpl_homAA = (int *) calloc(args->files->n_smpl,sizeof(int));
stats->smpl_homRR = (int *) calloc(args->files->n_smpl,sizeof(int));
stats->smpl_indel_hets = (int *) calloc(args->files->n_smpl,sizeof(int));
stats->smpl_indel_homs = (int *) calloc(args->files->n_smpl,sizeof(int));
stats->smpl_ts = (int *) calloc(args->files->n_smpl,sizeof(int));
stats->smpl_tv = (int *) calloc(args->files->n_smpl,sizeof(int));
stats->smpl_indels = (int *) calloc(args->files->n_smpl,sizeof(int));
stats->smpl_dp = (unsigned long int *) calloc(args->files->n_smpl,sizeof(unsigned long int));
stats->smpl_ndp = (int *) calloc(args->files->n_smpl,sizeof(int));
stats->smpl_sngl = (int *) calloc(args->files->n_smpl,sizeof(int));
#if HWE_STATS
stats->af_hwe = (int*) calloc(args->m_af*args->naf_hwe,sizeof(int));
#endif
if ( args->exons_fname )
stats->smpl_frm_shifts = (int*) calloc(args->files->n_smpl*3,sizeof(int));
}
idist_init(&stats->dp, args->dp_min,args->dp_max,args->dp_step);
idist_init(&stats->dp_sites, args->dp_min,args->dp_max,args->dp_step);
init_user_stats(args, i!=1 ? args->files->readers[0].header : args->files->readers[1].header, stats);
}
if ( args->exons_fname )
{
args->exons = bcf_sr_regions_init(args->exons_fname,1,0,1,2);
if ( !args->exons )
error("Error occurred while reading, was the file compressed with bgzip: %s?\n", args->exons_fname);
}
#if IRC_STATS
if ( args->ref_fname )
args->indel_ctx = indel_ctx_init(args->ref_fname);
#endif
type2dosage[GT_HOM_RR] = 0;
type2dosage[GT_HET_RA] = 1;
type2dosage[GT_HOM_AA] = 2;
type2dosage[GT_HET_AA] = 2;
type2dosage[GT_HAPL_R] = 0;
type2dosage[GT_HAPL_A] = 1;
type2ploidy[GT_HOM_RR] = 1;
type2ploidy[GT_HET_RA] = 1;
type2ploidy[GT_HOM_AA] = 1;
type2ploidy[GT_HET_AA] = 1;
type2ploidy[GT_HAPL_R] = -1;
type2ploidy[GT_HAPL_A] = -1;
type2stats[GT_HOM_RR] = 0;
type2stats[GT_HET_RA] = 1;
type2stats[GT_HOM_AA] = 2;
type2stats[GT_HET_AA] = 1;
type2stats[GT_HAPL_R] = 0;
type2stats[GT_HAPL_A] = 2;
}
static void destroy_stats(args_t *args)
{
int id, j;
for (id=0; id<args->nstats; id++)
{
stats_t *stats = &args->stats[id];
if (stats->af_ts) free(stats->af_ts);
if (stats->af_tv) free(stats->af_tv);
if (stats->af_snps) free(stats->af_snps);
for (j=0; j<3; j++)
if (stats->af_repeats[j]) free(stats->af_repeats[j]);
#if QUAL_STATS
if (stats->qual_ts) free(stats->qual_ts);
if (stats->qual_tv) free(stats->qual_tv);
if (stats->qual_snps) free(stats->qual_snps);
if (stats->qual_indels) free(stats->qual_indels);
#endif
#if HWE_STATS
//if ( args->files->n_smpl ) free(stats->af_hwe);
free(stats->af_hwe);
#endif
free(stats->insertions);
free(stats->deletions);
if (stats->smpl_hets) free(stats->smpl_hets);
if (stats->smpl_homAA) free(stats->smpl_homAA);
if (stats->smpl_homRR) free(stats->smpl_homRR);
if (stats->smpl_indel_homs) free(stats->smpl_indel_homs);
if (stats->smpl_indel_hets) free(stats->smpl_indel_hets);
if (stats->smpl_ts) free(stats->smpl_ts);
if (stats->smpl_tv) free(stats->smpl_tv);
if (stats->smpl_indels) free(stats->smpl_indels);
if (stats->smpl_dp) free(stats->smpl_dp);
if (stats->smpl_ndp) free(stats->smpl_ndp);
if (stats->smpl_sngl) free(stats->smpl_sngl);
idist_destroy(&stats->dp);
idist_destroy(&stats->dp_sites);
for (j=0; j<stats->nusr; j++)
{
free(stats->usr[j].vals_ts);
free(stats->usr[j].vals_tv);
free(stats->usr[j].val);
}
free(stats->usr);
if ( args->exons ) free(stats->smpl_frm_shifts);
}
for (j=0; j<args->nusr; j++) free(args->usr[j].tag);
free(args->usr);
free(args->tmp_frm);
free(args->tmp_iaf);
if (args->exons) bcf_sr_regions_destroy(args->exons);
free(args->af_gts_snps);
free(args->af_gts_indels);
free(args->smpl_gts_snps);
free(args->smpl_gts_indels);
free(args->smpl_r_snps);
free(args->smpl_r_indels);
if (args->indel_ctx) indel_ctx_destroy(args->indel_ctx);
if (args->filter[0]) filter_destroy(args->filter[0]);
if (args->filter[1]) filter_destroy(args->filter[1]);
}
static void init_iaf(args_t *args, bcf_sr_t *reader)
{
bcf1_t *line = reader->buffer[0];
if ( args->ntmp_iaf < line->n_allele )
{
args->tmp_iaf = (int*)realloc(args->tmp_iaf, line->n_allele*sizeof(int));
args->ntmp_iaf = line->n_allele;
}
// tmp_iaf is first filled with AC counts in calc_ac and then transformed to
// an index to af_gts_snps
int i, ret = bcf_calc_ac(reader->header, line, args->tmp_iaf, args->samples_list ? BCF_UN_INFO|BCF_UN_FMT : BCF_UN_INFO);
if ( ret )
{
int an=0;
for (i=0; i<line->n_allele; i++)
an += args->tmp_iaf[i];
args->tmp_iaf[0] = 0;
for (i=1; i<line->n_allele; i++)
{
if ( args->tmp_iaf[i]==1 )
args->tmp_iaf[i] = 0; // singletons into the first bin
else if ( !an )
args->tmp_iaf[i] = 1; // no genotype at all, put to the AF=0 bin
else
args->tmp_iaf[i] = 1 + args->tmp_iaf[i] * (args->m_af-2.0) / an;
}
}
else
for (i=0; i<line->n_allele; i++)
args->tmp_iaf[i] = 0;
// todo: otherwise use AF
}
static inline void do_mnp_stats(args_t *args, stats_t *stats, bcf_sr_t *reader)
{
stats->n_mnps++;
}
static inline void do_other_stats(args_t *args, stats_t *stats, bcf_sr_t *reader)
{
stats->n_others++;
}
static void do_indel_stats(args_t *args, stats_t *stats, bcf_sr_t *reader)
{
stats->n_indels++;
bcf1_t *line = reader->buffer[0];
#if QUAL_STATS
int iqual = clip_nonnegative(line->qual, args->m_qual);
stats->qual_indels[iqual]++;
#endif
// Check if the indel is near an exon for the frameshift statistics
int i, exon_overlap = 0;
if ( args->exons )
{
if ( !bcf_sr_regions_overlap(args->exons, bcf_seqname(reader->header,line),line->pos,line->pos) ) exon_overlap = 1;
hts_expand(uint8_t,line->n_allele,args->mtmp_frm,args->tmp_frm);
for (i=0; i<line->n_allele; i++) args->tmp_frm[i] = 0;
}
for (i=1; i<line->n_allele; i++)
{
if ( args->first_allele_only && i>1 ) break;
if ( bcf_get_variant_type(line,i)!=VCF_INDEL ) continue;
int len = line->d.var[i].n;
#if IRC_STATS
// Indel repeat consistency
if ( args->indel_ctx )
{
int nrep, nlen, ndel;
ndel = indel_ctx_type(args->indel_ctx, (char*)reader->header->id[BCF_DT_CTG][line->rid].key, line->pos+1, line->d.allele[0], line->d.allele[i], &nrep, &nlen);
if ( nlen<=1 || nrep<=1 )
{
// not a repeat or a single base repeat
stats->n_repeat_na++;
stats->af_repeats[2][ args->tmp_iaf[i] ]++;
}
else
{
if ( abs(ndel) % nlen )
{
// the length of the inserted/deleted sequence is not consistent with the repeat element
stats->n_repeat[nlen-1][ndel<0 ? 1 : 3]++;
stats->af_repeats[1][ args->tmp_iaf[i] ]++;
}
else
{
// the length consistent with the repeat
stats->n_repeat[nlen-1][ndel<0 ? 0 : 2]++;
stats->af_repeats[0][ args->tmp_iaf[i] ]++;
}
}
}
else
stats->af_repeats[2][ args->tmp_iaf[i] ]++;
#endif
// Check the frameshifts
int tlen = 0;
if ( args->exons && exon_overlap ) // there is an exon
{
if ( len>0 )
{
// insertion
if ( args->exons->start <= line->pos && args->exons->end > line->pos ) tlen = abs(len);
}
else if ( args->exons->start <= line->pos + abs(len) )
{
// deletion
tlen = abs(len);
if ( line->pos < args->exons->start ) // trim the beginning
tlen -= args->exons->start - line->pos + 1;
if ( args->exons->end < line->pos + abs(len) ) // trim the end
tlen -= line->pos + abs(len) - args->exons->end;
}
}
if ( tlen ) // there are some deleted/inserted bases in the exon
{
if ( tlen%3 ) { stats->out_frame++; args->tmp_frm[i] = 2; }
else { stats->in_frame++; args->tmp_frm[i] = 1; }
if ( i==1 )
{
if ( tlen%3 ) stats->out_frame_alt1++;
else stats->in_frame_alt1++;
}
}
else // no exon affected
{
if ( i==1 ) stats->na_frame_alt1++;
stats->na_frame++;
}
// Indel length distribution
int *ptr = stats->insertions;
if ( len<0 )
{
len *= -1;
ptr = stats->deletions;
}
if ( --len >= stats->m_indel ) len = stats->m_indel-1;
ptr[len]++;
}
}
static void do_user_stats(stats_t *stats, bcf_sr_t *reader, int is_ts)
{
int i;
for (i=0; i<stats->nusr; i++)
{
user_stats_t *usr = &stats->usr[i];
uint64_t *vals = is_ts ? usr->vals_ts : usr->vals_tv;
float val;
if ( usr->type==BCF_HT_REAL )
{
if ( bcf_get_info_float(reader->header,reader->buffer[0],usr->tag,&usr->val,&usr->m_val)<=0 ) continue;
val = ((float*)usr->val)[0];
}
else
{
if ( bcf_get_info_int32(reader->header,reader->buffer[0],usr->tag,&usr->val,&usr->m_val)<=0 ) continue;
val = ((int32_t*)usr->val)[0];
}
int idx;
if ( val<=usr->min ) idx = 0;
else if ( val>=usr->max ) idx = usr->nbins - 1;
else idx = (val - usr->min)/(usr->max - usr->min) * (usr->nbins-1);
vals[idx]++;
}
}
static void do_snp_stats(args_t *args, stats_t *stats, bcf_sr_t *reader)
{
stats->n_snps++;
bcf1_t *line = reader->buffer[0];
int ref = bcf_acgt2int(*line->d.allele[0]);
if ( ref<0 ) return;
#if QUAL_STATS
int iqual = clip_nonnegative(line->qual, args->m_qual);
stats->qual_snps[iqual]++;
#endif
int i;
for (i=1; i<line->n_allele; i++)
{
if ( args->first_allele_only && i>1 ) break;
if ( !(bcf_get_variant_type(line,i)&VCF_SNP) ) continue;
int alt = bcf_acgt2int(*line->d.allele[i]);
if ( alt<0 || ref==alt ) continue;
stats->subst[ref<<2|alt]++;
int iaf = args->tmp_iaf[i];
stats->af_snps[iaf]++;
if ( abs(ref-alt)==2 )
{
if (i==1)
{
stats->ts_alt1++;
#if QUAL_STATS
stats->qual_ts[iqual]++;
#endif
do_user_stats(stats, reader, 1);
}
stats->af_ts[iaf]++;
}
else
{
if (i==1)
{
stats->tv_alt1++;
#if QUAL_STATS
stats->qual_tv[iqual]++;
#endif
do_user_stats(stats, reader, 0);
}
stats->af_tv[iaf]++;
}
}
}
static void do_sample_stats(args_t *args, stats_t *stats, bcf_sr_t *reader, int matched)
{
bcf_srs_t *files = args->files;
bcf1_t *line = reader->buffer[0];
bcf_fmt_t *fmt_ptr;
int nref_tot = 0, nhet_tot = 0, nalt_tot = 0;
int line_type = bcf_get_variant_types(line);
if ( (fmt_ptr = bcf_get_fmt(reader->header,reader->buffer[0],"GT")) )
{
int ref = bcf_acgt2int(*line->d.allele[0]);
int is, n_nref = 0, i_nref = 0;
for (is=0; is<args->files->n_smpl; is++)
{
int ial, jal;
int gt = bcf_gt_type(fmt_ptr, reader->samples[is], &ial, &jal);
if ( gt==GT_UNKN ) continue;
if ( gt==GT_HAPL_R || gt==GT_HAPL_A )
{
if ( line_type&VCF_INDEL && stats->smpl_frm_shifts )
{
assert( ial<line->n_allele );
stats->smpl_frm_shifts[is*3 + args->tmp_frm[ial]]++;
}
continue;
}
if ( gt != GT_HOM_RR ) { n_nref++; i_nref = is; }
#if HWE_STATS
switch (gt)
{
case GT_HOM_RR: nref_tot++; break;
case GT_HET_RA: nhet_tot++; break;
case GT_HET_AA:
case GT_HOM_AA: nalt_tot++; break;
}
#endif
if ( line_type&VCF_SNP || line_type==VCF_REF ) // count ALT=. as SNP
{
if ( gt == GT_HET_RA ) stats->smpl_hets[is]++;
else if ( gt == GT_HET_AA ) stats->smpl_hets[is]++;
else if ( gt == GT_HOM_RR ) stats->smpl_homRR[is]++;
else if ( gt == GT_HOM_AA ) stats->smpl_homAA[is]++;
if ( gt != GT_HOM_RR && line->d.var[ial].type&VCF_SNP ) // this is safe, bcf_get_variant_types has been already called
{
int alt = bcf_acgt2int(*line->d.allele[ial]);
if ( alt<0 ) continue;
if ( abs(ref-alt)==2 )
stats->smpl_ts[is]++;
else
stats->smpl_tv[is]++;
}
}
if ( line_type&VCF_INDEL )
{
if ( gt != GT_HOM_RR )
{
stats->smpl_indels[is]++;
if ( gt==GT_HET_RA || gt==GT_HET_AA ) stats->smpl_indel_hets[is]++;
else if ( gt==GT_HOM_AA ) stats->smpl_indel_homs[is]++;
}
if ( stats->smpl_frm_shifts )
{
assert( ial<line->n_allele && jal<line->n_allele );
stats->smpl_frm_shifts[is*3 + args->tmp_frm[ial]]++;
stats->smpl_frm_shifts[is*3 + args->tmp_frm[jal]]++;
}
}
}
if ( n_nref==1 ) stats->smpl_sngl[i_nref]++;
}
#if HWE_STATS
if ( nhet_tot + nref_tot + nalt_tot )
{
float het_frac = (float)nhet_tot/(nhet_tot + nref_tot + nalt_tot);
int idx = het_frac*(args->naf_hwe - 1);
if ( line->n_allele>1 ) idx += args->naf_hwe*args->tmp_iaf[1];
stats->af_hwe[idx]++;
}
#endif
if ( (fmt_ptr = bcf_get_fmt(reader->header,reader->buffer[0],"DP")) )
{
#define BRANCH_INT(type_t,missing,vector_end) { \
int is; \
for (is=0; is<args->files->n_smpl; is++) \
{ \
type_t *p = (type_t *) (fmt_ptr->p + fmt_ptr->size*is); \
if ( *p==vector_end ) continue; \
if ( *p!=missing ) \
{ \
(*idist(&stats->dp, *p))++; \
stats->smpl_ndp[is]++; \
stats->smpl_dp[is] += *p; \
} \
} \
}
switch (fmt_ptr->type) {
case BCF_BT_INT8: BRANCH_INT(int8_t, bcf_int8_missing, bcf_int8_vector_end); break;
case BCF_BT_INT16: BRANCH_INT(int16_t, bcf_int16_missing, bcf_int16_vector_end); break;
case BCF_BT_INT32: BRANCH_INT(int32_t, bcf_int32_missing, bcf_int32_vector_end); break;
default: fprintf(stderr, "[E::%s] todo: %d\n", __func__, fmt_ptr->type); exit(1); break;
}
#undef BRANCH_INT
}
if ( matched==3 )
{
int is;
bcf_fmt_t *fmt0, *fmt1;
fmt0 = bcf_get_fmt(files->readers[0].header,files->readers[0].buffer[0],"GT"); if ( !fmt0 ) return;
fmt1 = bcf_get_fmt(files->readers[1].header,files->readers[1].buffer[0],"GT"); if ( !fmt1 ) return;
// only the first ALT allele is considered
int iaf = line->n_allele>1 ? args->tmp_iaf[1] : 1;
int line_type = bcf_get_variant_types(files->readers[0].buffer[0]);
gtcmp_t *af_stats = line_type&VCF_SNP ? args->af_gts_snps : args->af_gts_indels;
gtcmp_t *smpl_stats = line_type&VCF_SNP ? args->smpl_gts_snps : args->smpl_gts_indels;
//
// Calculates r squared
// x is mean dosage of x at given site
// x2 is mean squared dosage of x at given site
// y is mean dosage of x at given site
// y2 is mean squared dosage of x at given site
// xy is mean dosage of x*y at given site
// r2sum += (xy - x*y)^2 / ( (x2 - x^2) * (y2 - y^2) )
// r2n is number of sites considered
// output as r2sum/r2n for each AF bin
int r2n = 0;
float x = 0, y = 0, xy = 0, x2 = 0, y2 = 0;
// Select smpl_r
smpl_r_t *smpl_r = NULL;
if (line_type&VCF_SNP)
{
smpl_r = args->smpl_r_snps;
}
else if (line_type&VCF_INDEL)
{
smpl_r = args->smpl_r_indels;
}
for (is=0; is<files->n_smpl; is++)
{
// Simplified comparison: only 0/0, 0/1, 1/1 is looked at as the identity of
// actual alleles can be enforced by running without the -c option.
int gt0 = bcf_gt_type(fmt0, files->readers[0].samples[is], NULL, NULL);
if ( gt0 == GT_UNKN ) continue;
int gt1 = bcf_gt_type(fmt1, files->readers[1].samples[is], NULL, NULL);
if ( gt1 == GT_UNKN ) continue;
if ( type2ploidy[gt0]*type2ploidy[gt1] == -1 ) continue; // cannot compare diploid and haploid genotypes
int dsg0 = type2dosage[gt0];
int dsg1 = type2dosage[gt1];
x += dsg0;
x2 += dsg0*dsg0;
y += dsg1;
y2 += dsg1*dsg1;
xy += dsg0*dsg1;
r2n++;
int idx = type2stats[gt0];
if ( gt0==gt1 )
{
af_stats[iaf].m[idx]++;
smpl_stats[is].m[idx]++;
}
else
{
af_stats[iaf].mm[idx]++;
smpl_stats[is].mm[idx]++;
}
// Now do it across samples
if (smpl_r) {
smpl_r[is].xy += dsg0*dsg1;
smpl_r[is].x += dsg0;
smpl_r[is].x2 += dsg0*dsg0;
smpl_r[is].y += dsg1;
smpl_r[is].y2 += dsg1*dsg1;
++(smpl_r[is].n);
}
}
if ( r2n )
{
x /= r2n; y /= r2n; x2 /= r2n; y2 /= r2n; xy /= r2n;
float cov = xy - x*y;
float var2 = (x2 - x*x) * (y2 - y*y);
if ( var2!=0 )
{
af_stats[iaf].r2sum += cov*cov/var2;
af_stats[iaf].r2n++;