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vcfstats.c
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/*
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 "bcftools.h"
#define HWE_STATS 1
#define QUAL_STATS 1
#define IRC_STATS 1
#define IRC_RLEN 10
typedef struct
{
int min, max, step, m_vals;
uint64_t *vals;
}
idist_t;
typedef struct
{
int n_snps, n_indels, n_mnps, n_others, n_mals, n_snp_mals;
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;
unsigned long int *smpl_dp;
idist_t dp;
}
stats_t;
typedef struct
{
int m[3], mm[3]; // number of hom, het and non-ref hom matches and mismatches
float r2sum;
int 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;
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;
// other
bcf_srs_t *files;
bcf_sr_regions_t *exons;
char **argv, *exons_fname, *regions_fname, *samples_fname, *targets_fname;
int argc, debug, first_allele_only;
int split_by_id, nstats;
}
args_t;
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;
}
#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);
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 init_stats(args_t *args)
{
int i;
args->nstats = args->files->nreaders==1 ? 1 : 3;
if ( args->split_by_id ) args->nstats = 2;
// 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 ( args->files->readers[i].header->n[BCF_DT_SAMPLE] + 1> args->m_af )
args->m_af = args->files->readers[i].header->n[BCF_DT_SAMPLE] + 1;
#if QUAL_STATS
args->m_qual = 999;
#endif
#if HWE_STATS
args->naf_hwe = 100;
#endif
if ( args->samples_fname )
{
if ( !bcf_sr_set_samples(args->files,args->samples_fname) ) error("Could not initialize samples: %s\n", args->samples_fname);
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));
}
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_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
}
idist_init(&stats->dp, args->dp_min,args->dp_max,args->dp_step);
}
if ( args->exons_fname )
{
args->exons = bcf_sr_regions_init(args->exons_fname);
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
}
static void destroy_stats(args_t *args)
{
int id;
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);
int j;
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
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_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);
}
if (args->tmp_iaf) free(args->tmp_iaf);
if (args->exons) bcf_sr_regions_destroy(args->exons);
if (args->af_gts_snps) free(args->af_gts_snps);
if (args->af_gts_indels) free(args->af_gts_indels);
if (args->smpl_gts_snps) free(args->smpl_gts_snps);
if (args->smpl_gts_indels) free(args->smpl_gts_indels);
if (args->indel_ctx) indel_ctx_destroy(args->indel_ctx);
}
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_fname ? 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 = line->qual >= args->m_qual || isnan(line->qual) ? args->m_qual - 1 : line->qual;
stats->qual_indels[iqual]++;
#endif
// Check if the indel is near an exon for the frameshift statistics
if ( args->exons )
{
// New chromosome?
if ( !args->exons->seq || strcmp(args->exons->seq,reader->header->id[BCF_DT_CTG][line->rid].key) )
{
if ( bcf_sr_regions_seek(args->exons, reader->header->id[BCF_DT_CTG][line->rid].key)==0 )
bcf_sr_regions_next(args->exons);
}
if ( args->exons->start >= 0 )
{
while ( args->exons->start <= line->pos )
if ( bcf_sr_regions_next(args->exons)<0 ) break; // no more exons
}
}
int i;
for (i=1; i<line->n_allele; i++)
{
if ( args->first_allele_only && i>1 ) break;
if ( line->d.var[i].type!=VCF_INDEL ) continue;
int len = line->d.var[i].n;
#if IRC_STATS
// Indel repeat consistency
if ( args->indel_ctx && line->d.var[i].type==VCF_INDEL )
{
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] ]++;
}
}
}
#endif
// Check the frameshifts
int tlen = 0;
if ( args->exons && args->exons->start >= 0 ) // 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++;
else stats->in_frame++;
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_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 = line->qual >= args->m_qual || isnan(line->qual) ? args->m_qual - 1 : line->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 ( !(line->d.var[i].type&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
}
stats->af_ts[iaf]++;
}
else
{
if (i==1)
{
stats->tv_alt1++;
#if QUAL_STATS
stats->qual_tv[iqual]++;
#endif
}
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;
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;
int gt = bcf_gt_type(fmt_ptr, reader->samples[is], &ial);
if ( gt==GT_UNKN || gt==GT_HAPL_R || gt==GT_HAPL_A ) 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->d.var_type&VCF_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 )
{
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->d.var_type&VCF_INDEL )
{
if ( gt != GT_HOM_RR ) stats->smpl_indels[is]++;
}
}
if ( n_nref==1 ) stats->smpl_sngl[i_nref]++;
}
#if HWE_STATS
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;
gtcmp_t *af_stats = files->readers[0].buffer[0]->d.var_type&VCF_SNP ? args->af_gts_snps : args->af_gts_indels;
gtcmp_t *smpl_stats = files->readers[0].buffer[0]->d.var_type&VCF_SNP ? args->smpl_gts_snps : args->smpl_gts_indels;
int r2n = 0;
float r2a2 = 0, r2a = 0, r2b2 = 0, r2b = 0, r2ab = 0;
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 gt = bcf_gt_type(fmt0, files->readers[0].samples[is], NULL);
if ( gt == GT_UNKN ) continue;
int match = 1;
int gt2 = bcf_gt_type(fmt1, files->readers[1].samples[is], NULL);
if ( gt2 == GT_UNKN ) match = -1;
else if ( gt != gt2 ) match = 0;
if ( match == -1 ) continue;
if ( gt == GT_HET_AA ) gt = GT_HOM_AA; // rare case, treat as AA hom
if ( gt2 == GT_HET_AA ) gt2 = GT_HOM_AA;
if ( match )
{
af_stats[iaf].m[gt]++;
smpl_stats[is].m[gt]++;
}
else
{
af_stats[iaf].mm[gt]++;
smpl_stats[is].mm[gt]++;
}
r2a2 += gt*gt;
r2a += gt;
r2b2 += gt2*gt2;
r2b += gt2;
r2ab += gt*gt2;
r2n++;
}
if ( r2n )
{
float cov = r2ab - r2a*r2b/r2n;
float var2 = (r2a2 - r2a*r2a/r2n) * (r2b2 - r2b*r2b/r2n);
af_stats[iaf].r2sum += var2==0 ? 1 : cov*cov/var2;
af_stats[iaf].r2n++;
}
if ( args->debug )
{
for (is=0; is<files->n_smpl; is++)
{
int gt = bcf_gt_type(fmt0, files->readers[0].samples[is], NULL);
if ( gt == GT_UNKN ) continue;
int gt2 = bcf_gt_type(fmt1, files->readers[1].samples[is], NULL);
if ( gt != gt2 )
{
bcf_sr_t *reader = &files->readers[0];
printf("DBG\t%s\t%d\t%s\t%d\t%d\n",reader->header->id[BCF_DT_CTG][reader->buffer[0]->rid].key,reader->buffer[0]->pos+1,files->samples[is],gt,gt2);
}
}
}
}
}
static void do_vcf_stats(args_t *args)
{
bcf_srs_t *files = args->files;
assert( sizeof(int)>files->nreaders );
while ( bcf_sr_next_line(files) )
{
bcf_sr_t *reader = NULL;
bcf1_t *line = NULL;
int ret = 0, i;
for (i=0; i<files->nreaders; i++)
{
if ( !bcf_sr_has_line(files,i) ) continue;
ret |= 1<<i;
if ( reader ) continue;
reader = &files->readers[i];
line = files->readers[i].buffer[0];
}
bcf_set_variant_types(line);
init_iaf(args, reader);
stats_t *stats = &args->stats[ret-1];
if ( args->split_by_id && line->d.id[0]=='.' && !line->d.id[1] )
stats = &args->stats[1];
if ( line->d.var_type&VCF_SNP )
do_snp_stats(args, stats, reader);
if ( line->d.var_type&VCF_INDEL )
do_indel_stats(args, stats, reader);
if ( line->d.var_type&VCF_MNP )
do_mnp_stats(args, stats, reader);
if ( line->d.var_type&VCF_OTHER )
do_other_stats(args, stats, reader);
if ( line->n_allele>2 )
{
stats->n_mals++;
if ( line->d.var_type == VCF_SNP ) stats->n_snp_mals++;
}
if ( files->n_smpl )
do_sample_stats(args, stats, reader, ret);
}
}
static void print_header(args_t *args)
{
int i;
printf("# This file was produced by vcfstats(%s) and can be plotted using plot-vcfstats.\n", bcftools_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#\n");
printf("# Definition of sets:\n# ID\t[2]id\t[3]tab-separated file names\n");
if ( args->files->nreaders==1 )
{
const char *fname = strcmp("-",args->files->readers[0].fname) ? args->files->readers[0].fname : "<STDIN>";
if ( args->split_by_id )
{
printf("ID\t0\t%s:known (sites with ID different from \".\")\n", fname);
printf("ID\t1\t%s:novel (sites where ID column is \".\")\n", fname);
}
else
printf("ID\t0\t%s\n", fname);
}
else
{
const char *fname0 = strcmp("-",args->files->readers[0].fname) ? args->files->readers[0].fname : "<STDIN>";
const char *fname1 = strcmp("-",args->files->readers[1].fname) ? args->files->readers[1].fname : "<STDIN>";
printf("ID\t0\t%s\n", fname0);
printf("ID\t1\t%s\n", fname1);
printf("ID\t2\t%s\t%s\n", fname0,fname1);
}
}
static void print_stats(args_t *args)
{
int i, id;
printf("# SN, Summary numbers:\n# SN\t[2]id\t[3]key\t[4]value\n");
for (id=0; id<args->files->nreaders; id++)
printf("SN\t%d\tnumber of samples:\t%d\n", id, args->files->readers[id].header->n[BCF_DT_SAMPLE]);
for (id=0; id<args->nstats; id++)
{
stats_t *stats = &args->stats[id];
printf("SN\t%d\tnumber of SNPs:\t%d\n", id, stats->n_snps);
printf("SN\t%d\tnumber of MNPs:\t%d\n", id, stats->n_mnps);
printf("SN\t%d\tnumber of indels:\t%d\n", id, stats->n_indels);
printf("SN\t%d\tnumber of others:\t%d\n", id, stats->n_others);
printf("SN\t%d\tnumber of multiallelic sites:\t%d\n", id, stats->n_mals);
printf("SN\t%d\tnumber of multiallelic SNP sites:\t%d\n", id, stats->n_snp_mals);
}
printf("# TSTV, transitions/transversions:\n# TSTV\t[2]id\t[3]ts\t[4]tv\t[5]ts/tv\t[6]ts (1st ALT)\t[7]tv (1st ALT)\t[8]ts/tv (1st ALT)\n");
for (id=0; id<args->nstats; id++)
{
stats_t *stats = &args->stats[id];
int ts=0,tv=0;
for (i=0; i<args->m_af; i++) { ts += stats->af_ts[i]; tv += stats->af_tv[i]; }
printf("TSTV\t%d\t%d\t%d\t%.2f\t%d\t%d\t%.2f\n", id,ts,tv,tv?(float)ts/tv:0, stats->ts_alt1,stats->tv_alt1,stats->tv_alt1?(float)stats->ts_alt1/stats->tv_alt1:0);
}
if ( args->exons_fname )
{
printf("# FS, Indel frameshifts:\n# FS\t[2]id\t[3]in-frame\t[4]out-frame\t[5]not applicable\t[6]out/(in+out) ratio\t[7]in-frame (1st ALT)\t[8]out-frame (1st ALT)\t[9]not applicable (1st ALT)\t[10]out/(in+out) ratio (1st ALT)\n");
for (id=0; id<args->nstats; id++)
{
int in=args->stats[id].in_frame, out=args->stats[id].out_frame, na=args->stats[id].na_frame;
int in1=args->stats[id].in_frame_alt1, out1=args->stats[id].out_frame_alt1, na1=args->stats[id].na_frame_alt1;
printf("FS\t%d\t%d\t%d\t%d\t%.2f\t%d\t%d\t%d\t%.2f\n", id, in,out,na,out?(float)out/(in+out):0,in1,out1,na1,out1?(float)out1/(in1+out1):0);
}
}
if ( args->indel_ctx )
{
printf("# ICS, Indel context summary:\n# ICS\t[2]id\t[3]repeat-consistent\t[4]repeat-inconsistent\t[5]not applicable\t[6]c/(c+i) ratio\n");
for (id=0; id<args->nstats; id++)
{
int nc = 0, ni = 0, na = args->stats[id].n_repeat_na;
for (i=0; i<IRC_RLEN; i++)
{
nc += args->stats[id].n_repeat[i][0] + args->stats[id].n_repeat[i][2];
ni += args->stats[id].n_repeat[i][1] + args->stats[id].n_repeat[i][3];
}
printf("ICS\t%d\t%d\t%d\t%d\t%.4f\n", id, nc,ni,na,nc+ni ? (float)nc/(nc+ni) : 0.0);
}
printf("# ICL, Indel context by length:\n# ICL\t[2]id\t[3]length of repeat element\t[4]repeat-consistent deletions)\t[5]repeat-inconsistent deletions\t[6]consistent insertions\t[7]inconsistent insertions\t[8]c/(c+i) ratio\n");
for (id=0; id<args->nstats; id++)
{
for (i=1; i<IRC_RLEN; i++)
{
int nc = args->stats[id].n_repeat[i][0]+args->stats[id].n_repeat[i][2], ni = args->stats[id].n_repeat[i][1]+args->stats[id].n_repeat[i][3];
printf("ICL\t%d\t%d\t%d\t%d\t%d\t%d\t%.4f\n", id, i+1,
args->stats[id].n_repeat[i][0],args->stats[id].n_repeat[i][1],args->stats[id].n_repeat[i][2],args->stats[id].n_repeat[i][3],
nc+ni ? (float)nc/(nc+ni) : 0.0);
}
}
}
printf("# Sis, Singleton stats:\n# SiS\t[2]id\t[3]allele count\t[4]number of SNPs\t[5]number of transitions\t[6]number of transversions\t[7]number of indels\t[8]repeat-consistent\t[9]repeat-inconsistent\t[10]not applicable\n");
for (id=0; id<args->nstats; id++)
{
stats_t *stats = &args->stats[id];
printf("SiS\t%d\t%d\t%d\t%d\t%d\t%d\t%d\t%d\t%d\n", id,1,stats->af_snps[0],stats->af_ts[0],stats->af_tv[0],
stats->af_repeats[0][0]+stats->af_repeats[1][0]+stats->af_repeats[2][0],stats->af_repeats[0][0],stats->af_repeats[1][0],stats->af_repeats[2][0]);
// put the singletons stats into the first AF bin, note that not all of the stats is transferred (i.e. nrd mismatches)
stats->af_snps[1] += stats->af_snps[0];
stats->af_ts[1] += stats->af_ts[0];
stats->af_tv[1] += stats->af_tv[0];
stats->af_repeats[0][1] += stats->af_repeats[0][0];
stats->af_repeats[1][1] += stats->af_repeats[1][0];
stats->af_repeats[2][1] += stats->af_repeats[2][0];
}
printf("# AF, Stats by non-reference allele frequency:\n# AF\t[2]id\t[3]allele frequency\t[4]number of SNPs\t[5]number of transitions\t[6]number of transversions\t[7]number of indels\t[8]repeat-consistent\t[9]repeat-inconsistent\t[10]not applicable\n");
for (id=0; id<args->nstats; id++)
{
stats_t *stats = &args->stats[id];
for (i=1; i<args->m_af; i++) // note that af[1] now contains also af[0], see SiS stats output above
{
if ( stats->af_snps[i]+stats->af_ts[i]+stats->af_tv[i]+stats->af_repeats[0][i]+stats->af_repeats[1][i]+stats->af_repeats[2][i] == 0 ) continue;
printf("AF\t%d\t%f\t%d\t%d\t%d\t%d\t%d\t%d\t%d\n", id,100.*(i-1)/(args->m_af-2),stats->af_snps[i],stats->af_ts[i],stats->af_tv[i],
stats->af_repeats[0][i]+stats->af_repeats[1][i]+stats->af_repeats[2][i],stats->af_repeats[0][i],stats->af_repeats[1][i],stats->af_repeats[2][i]);
}
}
#if QUAL_STATS
printf("# QUAL, Stats by quality:\n# QUAL\t[2]id\t[3]Quality\t[4]number of SNPs\t[5]number of transitions (1st ALT)\t[6]number of transversions (1st ALT)\t[7]number of indels\n");
for (id=0; id<args->nstats; id++)
{
stats_t *stats = &args->stats[id];
for (i=0; i<args->m_qual; i++)
{
if ( stats->qual_snps[i]+stats->qual_ts[i]+stats->qual_tv[i]+stats->qual_indels[i] == 0 ) continue;
printf("QUAL\t%d\t%d\t%d\t%d\t%d\t%d\n", id,i,stats->qual_snps[i],stats->qual_ts[i],stats->qual_tv[i],stats->qual_indels[i]);
}
}
#endif
printf("# IDD, InDel distribution:\n# IDD\t[2]id\t[3]length (deletions negative)\t[4]count\n");
for (id=0; id<args->nstats; id++)
{
stats_t *stats = &args->stats[id];
for (i=stats->m_indel-1; i>=0; i--)
if ( stats->deletions[i] ) printf("IDD\t%d\t%d\t%d\n", id,-i-1,stats->deletions[i]);
for (i=0; i<stats->m_indel; i++)
if ( stats->insertions[i] ) printf("IDD\t%d\t%d\t%d\n", id,i+1,stats->insertions[i]);
}
printf("# ST, Substitution types:\n# ST\t[2]id\t[3]type\t[4]count\n");
for (id=0; id<args->nstats; id++)
{
int t;
for (t=0; t<15; t++)
{
if ( t>>2 == (t&3) ) continue;
printf("ST\t%d\t%c>%c\t%d\n", id, bcf_int2acgt(t>>2),bcf_int2acgt(t&3),args->stats[id].subst[t]);
}
}
if ( args->files->nreaders>1 && args->files->n_smpl )
{
printf("SN\t%d\tNumber of samples:\t%d\n", 2, args->files->n_smpl);
printf("# GCsAF, Genotype concordance by non-reference allele frequency (SNPs)\n# GCsAF\t[2]id\t[3]allele frequency\t[4]RR Hom matches\t[5]RA Het matches\t[6]AA Hom matches\t[7]RR Hom mismatches\t[8]RA Het mismatches\t[9]AA Hom mismatches\t[10]dosage r-squared\t[11]number of sites\n");
gtcmp_t *stats = args->af_gts_snps;
int nrd_m[3] = {0,0,0}, nrd_mm[3] = {0,0,0};
for (i=0; i<args->m_af; i++)
{
int j, n = 0;
for (j=0; j<3; j++)
{
n += stats[i].m[j] + stats[i].mm[j];
nrd_m[j] += stats[i].m[j];
nrd_mm[j] += stats[i].mm[j];
}
if ( !i || !n ) continue; // skip singleton stats and empty bins
printf("GCsAF\t2\t%f", 100.*(i-1)/(args->m_af-2));
printf("\t%d\t%d\t%d", stats[i].m[GT_HOM_RR],stats[i].m[GT_HET_RA],stats[i].m[GT_HOM_AA]);
printf("\t%d\t%d\t%d", stats[i].mm[GT_HOM_RR],stats[i].mm[GT_HET_RA],stats[i].mm[GT_HOM_AA]);
printf("\t%f\t%d\n", stats[i].r2n ? stats[i].r2sum/stats[i].r2n : -1.0, stats[i].r2n);
}
int m = nrd_m[GT_HET_RA] + nrd_m[GT_HOM_AA];
int mm = nrd_mm[GT_HOM_RR] + nrd_mm[GT_HET_RA] + nrd_mm[GT_HOM_AA];
printf("# Non-Reference Discordance (NRD)\n# NRD\t[2]id\t[3]NRD\t[4]Ref/Ref discordance\t[5]Ref/Alt discordance\t[6]Alt/Alt discordance\n");
printf("NRD\t2\t%f\t%f\t%f\t%f\n",
m+mm ? mm*100.0/(m+mm) : 0,
nrd_m[GT_HOM_RR]+nrd_mm[GT_HOM_RR] ? nrd_mm[GT_HOM_RR]*100.0/(nrd_m[GT_HOM_RR]+nrd_mm[GT_HOM_RR]) : 0,
nrd_m[GT_HET_RA]+nrd_mm[GT_HET_RA] ? nrd_mm[GT_HET_RA]*100.0/(nrd_m[GT_HET_RA]+nrd_mm[GT_HET_RA]) : 0,
nrd_m[GT_HOM_AA]+nrd_mm[GT_HOM_AA] ? nrd_mm[GT_HOM_AA]*100.0/(nrd_m[GT_HOM_AA]+nrd_mm[GT_HOM_AA]) : 0
);
printf("# GCcS, Genotype concordance by sample (SNPs)\n# GCsS\t[2]id\t[3]sample\t[4]non-reference discordance rate\t[5]RR Hom matches\t[6]RA Het matches\t[7]AA Hom matches\t[8]RR Hom mismatches\t[9]RA Het mismatches\t[10]AA Hom mismatches\n");
stats = args->smpl_gts_snps;
for (i=0; i<args->files->n_smpl; i++)
{
int m = stats[i].m[GT_HET_RA] + stats[i].m[GT_HOM_AA];
int mm = stats[i].mm[GT_HOM_RR] + stats[i].mm[GT_HET_RA] + stats[i].mm[GT_HOM_AA];
printf("GCsS\t2\t%s\t%.3f", args->files->samples[i], m+mm ? mm*100.0/(m+mm) : 0);
printf("\t%d\t%d\t%d", stats[i].m[GT_HOM_RR],stats[i].m[GT_HET_RA],stats[i].m[GT_HOM_AA]);
printf("\t%d\t%d\t%d\n", stats[i].mm[GT_HOM_RR],stats[i].mm[GT_HET_RA],stats[i].mm[GT_HOM_AA]);
}
}
if ( args->files->n_smpl )
{
printf("# PSC, Per-sample counts\n# PSC\t[2]id\t[3]sample\t[4]nRefHom\t[5]nNonRefHom\t[6]nHets\t[7]nTransitions\t[8]nTransversions\t[9]nIndels\t[10]average depth\t[11]nSingletons\n");
for (id=0; id<args->nstats; id++)
{
stats_t *stats = &args->stats[id];
for (i=0; i<args->files->n_smpl; i++)
{
float dp = stats->smpl_ndp[i] ? stats->smpl_dp[i]/(float)stats->smpl_ndp[i] : 0;
printf("PSC\t%d\t%s\t%d\t%d\t%d\t%d\t%d\t%d\t%.1f\t%d\n", id,args->files->samples[i],
stats->smpl_homRR[i], stats->smpl_homAA[i], stats->smpl_hets[i], stats->smpl_ts[i],
stats->smpl_tv[i], stats->smpl_indels[i],dp, stats->smpl_sngl[i]);
}
}
printf("# DP, Depth distribution\n# DP\t[2]id\t[3]bin\t[4]number of genotypes\t[5]fraction of genotypes (%%)\n");
for (id=0; id<args->nstats; id++)
{
stats_t *stats = &args->stats[id];