static int mpileup_reg(mplp_conf_t *conf, uint32_t beg, uint32_t end)
{
bam_hdr_t *hdr = conf->mplp_data[0]->h; // header of first file in input list
int ret, i, tid, pos, ref_len;
char *ref;
while ( (ret=bam_mplp_auto(conf->iter, &tid, &pos, conf->n_plp, conf->plp)) > 0)
{
if ( end && (pos<beg || pos>end) ) continue;
if ( conf->bed && tid >= 0 )
{
int overlap = regidx_overlap(conf->bed, hdr->target_name[tid], pos, pos, NULL);
if ( !conf->bed_logic ) overlap = overlap ? 0 : 1;
if ( !overlap ) continue;
}
mplp_get_ref(conf->mplp_data[0], tid, &ref, &ref_len);
int total_depth, _ref0, ref16;
for (i = total_depth = 0; i < conf->nfiles; ++i) total_depth += conf->n_plp[i];
group_smpl(conf->gplp, conf->bsmpl, conf->nfiles, conf->n_plp, conf->plp);
_ref0 = (ref && pos < ref_len)? ref[pos] : 'N';
ref16 = seq_nt16_table[_ref0];
bcf_callaux_clean(conf->bca, &conf->bc);
for (i = 0; i < conf->gplp->n; ++i)
bcf_call_glfgen(conf->gplp->n_plp[i], conf->gplp->plp[i], ref16, conf->bca, conf->bcr + i);
conf->bc.tid = tid; conf->bc.pos = pos;
bcf_call_combine(conf->gplp->n, conf->bcr, conf->bca, ref16, &conf->bc);
bcf_clear1(conf->bcf_rec);
bcf_call2bcf(&conf->bc, conf->bcf_rec, conf->bcr, conf->fmt_flag, 0, 0);
flush_bcf_records(conf, conf->bcf_fp, conf->bcf_hdr, conf->bcf_rec);
// call indels; todo: subsampling with total_depth>max_indel_depth instead of ignoring?
// check me: rghash in bcf_call_gap_prep() should have no effect, reads mplp_func already excludes them
if (!(conf->flag&MPLP_NO_INDEL) && total_depth < conf->max_indel_depth
&& bcf_call_gap_prep(conf->gplp->n, conf->gplp->n_plp, conf->gplp->plp, pos, conf->bca, ref) >= 0)
{
bcf_callaux_clean(conf->bca, &conf->bc);
for (i = 0; i < conf->gplp->n; ++i)
bcf_call_glfgen(conf->gplp->n_plp[i], conf->gplp->plp[i], -1, conf->bca, conf->bcr + i);
if (bcf_call_combine(conf->gplp->n, conf->bcr, conf->bca, -1, &conf->bc) >= 0)
{
bcf_clear1(conf->bcf_rec);
bcf_call2bcf(&conf->bc, conf->bcf_rec, conf->bcr, conf->fmt_flag, conf->bca, ref);
flush_bcf_records(conf, conf->bcf_fp, conf->bcf_hdr, conf->bcf_rec);
}
}
}
return 0;
}
static void mask_region(args_t *args, char *seq, int len)
{
char *chr = (char*)bcf_hdr_id2name(args->hdr,args->rid);
int start = args->fa_src_pos - len;
int end = args->fa_src_pos;
regitr_t itr;
if ( !regidx_overlap(args->mask, chr,start,end, &itr) ) return;
int idx_start, idx_end, i;
while ( REGITR_OVERLAP(itr,start,end) )
{
idx_start = REGITR_START(itr) - start;
idx_end = REGITR_END(itr) - start;
if ( idx_start < 0 ) idx_start = 0;
if ( idx_end >= len ) idx_end = len - 1;
for (i=idx_start; i<=idx_end; i++) seq[i] = 'N';
itr.i++;
}
}
static void apply_variant(args_t *args, bcf1_t *rec)
{
if ( rec->n_allele==1 ) return;
if ( rec->pos <= args->fa_frz_pos )
{
fprintf(pysamerr,"The site %s:%d overlaps with another variant, skipping...\n", bcf_seqname(args->hdr,rec),rec->pos+1);
return;
}
if ( args->mask )
{
char *chr = (char*)bcf_hdr_id2name(args->hdr,args->rid);
int start = rec->pos;
int end = rec->pos + rec->rlen - 1;
if ( regidx_overlap(args->mask, chr,start,end,NULL) ) return;
}
int i, ialt = 1;
if ( args->isample >= 0 )
{
bcf_fmt_t *fmt = bcf_get_fmt(args->hdr, rec, "GT");
if ( !fmt ) return;
if ( args->haplotype )
{
if ( args->haplotype > fmt->n ) error("Can't apply %d-th haplotype at %s:%d\n", args->haplotype,bcf_seqname(args->hdr,rec),rec->pos+1);
uint8_t *ignore, *ptr = fmt->p + fmt->size*args->isample + args->haplotype - 1;
ialt = bcf_dec_int1(ptr, fmt->type, &ignore);
if ( bcf_gt_is_missing(ialt) || ialt==bcf_int32_vector_end ) return;
ialt = bcf_gt_allele(ialt);
}
else if ( args->output_iupac )
{
uint8_t *ignore, *ptr = fmt->p + fmt->size*args->isample;
ialt = bcf_dec_int1(ptr, fmt->type, &ignore);
if ( bcf_gt_is_missing(ialt) || ialt==bcf_int32_vector_end ) return;
ialt = bcf_gt_allele(ialt);
int jalt;
if ( fmt->n>1 )
{
ptr = fmt->p + fmt->size*args->isample + 1;
jalt = bcf_dec_int1(ptr, fmt->type, &ignore);
if ( bcf_gt_is_missing(jalt) || jalt==bcf_int32_vector_end ) jalt = ialt;
else jalt = bcf_gt_allele(jalt);
}
else jalt = ialt;
if ( rec->n_allele <= ialt || rec->n_allele <= jalt ) error("Broken VCF, too few alts at %s:%d\n", bcf_seqname(args->hdr,rec),rec->pos+1);
if ( ialt!=jalt && !rec->d.allele[ialt][1] && !rec->d.allele[jalt][1] ) // is this a het snp?
{
char ial = rec->d.allele[ialt][0];
char jal = rec->d.allele[jalt][0];
rec->d.allele[ialt][0] = gt2iupac(ial,jal);
}
}
else
{
for (i=0; i<fmt->n; i++)
{
uint8_t *ignore, *ptr = fmt->p + fmt->size*args->isample + i;
ialt = bcf_dec_int1(ptr, fmt->type, &ignore);
if ( bcf_gt_is_missing(ialt) || ialt==bcf_int32_vector_end ) return;
ialt = bcf_gt_allele(ialt);
if ( ialt ) break;
}
}
if ( !ialt ) return; // ref allele
if ( rec->n_allele <= ialt ) error("Broken VCF, too few alts at %s:%d\n", bcf_seqname(args->hdr,rec),rec->pos+1);
}
else if ( args->output_iupac && !rec->d.allele[0][1] && !rec->d.allele[1][1] )
{
char ial = rec->d.allele[0][0];
char jal = rec->d.allele[1][0];
rec->d.allele[1][0] = gt2iupac(ial,jal);
}
int idx = rec->pos - args->fa_ori_pos + args->fa_mod_off;
if ( idx<0 || idx>=args->fa_buf.l )
error("FIXME: %s:%d .. idx=%d, ori_pos=%d, len=%d, off=%d\n",bcf_seqname(args->hdr,rec),rec->pos+1,idx,args->fa_ori_pos,args->fa_buf.l,args->fa_mod_off);
// sanity check the reference base
int len_diff = 0, alen = 0;
if ( rec->d.allele[ialt][0]=='<' )
{
if ( strcasecmp(rec->d.allele[ialt], "<DEL>") )
error("Symbolic alleles other than <DEL> are currently not supported: %s at %s:%d\n",rec->d.allele[ialt],bcf_seqname(args->hdr,rec),rec->pos+1);
assert( rec->d.allele[0][1]==0 ); // todo: for now expecting strlen(REF) = 1
len_diff = 1-rec->rlen;
rec->d.allele[ialt] = rec->d.allele[0]; // according to VCF spec, REF must precede the event
alen = strlen(rec->d.allele[ialt]);
}
else if ( strncasecmp(rec->d.allele[0],args->fa_buf.s+idx,rec->rlen) )
{
// fprintf(pysamerr,"%d .. [%s], idx=%d ori=%d off=%d\n",args->fa_ori_pos,args->fa_buf.s,idx,args->fa_ori_pos,args->fa_mod_off);
char tmp = 0;
if ( args->fa_buf.l - idx > rec->rlen )
{
tmp = args->fa_buf.s[idx+rec->rlen];
args->fa_buf.s[idx+rec->rlen] = 0;
}
error(
"The fasta sequence does not match the REF allele at %s:%d:\n"
" .vcf: [%s]\n"
" .vcf: [%s] <- (ALT)\n"
" .fa: [%s]%c%s\n",
bcf_seqname(args->hdr,rec),rec->pos+1, rec->d.allele[0], rec->d.allele[ialt], args->fa_buf.s+idx,
tmp?tmp:' ',tmp?args->fa_buf.s+idx+rec->rlen+1:""
);
}
else
{
alen = strlen(rec->d.allele[ialt]);
len_diff = alen - rec->rlen;
}
if ( args->fa_case )
for (i=0; i<alen; i++) rec->d.allele[ialt][i] = toupper(rec->d.allele[ialt][i]);
else
for (i=0; i<alen; i++) rec->d.allele[ialt][i] = tolower(rec->d.allele[ialt][i]);
if ( len_diff <= 0 )
{
// deletion or same size event
for (i=0; i<alen; i++)
args->fa_buf.s[idx+i] = rec->d.allele[ialt][i];
if ( len_diff )
memmove(args->fa_buf.s+idx+alen,args->fa_buf.s+idx+rec->rlen,args->fa_buf.l-idx-rec->rlen);
}
else
{
// insertion
ks_resize(&args->fa_buf, args->fa_buf.l + len_diff);
memmove(args->fa_buf.s + idx + rec->rlen + len_diff, args->fa_buf.s + idx + rec->rlen, args->fa_buf.l - idx - rec->rlen);
for (i=0; i<alen; i++)
args->fa_buf.s[idx+i] = rec->d.allele[ialt][i];
}
if (args->chain && len_diff != 0)
{
// If first nucleotide of both REF and ALT are the same... (indels typically include the nucleotide before the variant)
if ( strncasecmp(rec->d.allele[0],rec->d.allele[ialt],1) == 0)
{
// ...extend the block by 1 bp: start is 1 bp further and alleles are 1 bp shorter
push_chain_gap(args->chain, rec->pos + 1, rec->rlen - 1, rec->pos + 1 + args->fa_mod_off, alen - 1);
}
else
{
// otherwise, just the coordinates of the variant as given
push_chain_gap(args->chain, rec->pos, rec->rlen, rec->pos + args->fa_mod_off, alen);
}
}
args->fa_buf.l += len_diff;
args->fa_mod_off += len_diff;
args->fa_frz_pos = rec->pos + rec->rlen - 1;
}
static int mplp_func(void *data, bam1_t *b)
{
char *ref;
mplp_aux_t *ma = (mplp_aux_t*)data;
int ret, ref_len;
while (1)
{
int has_ref;
ret = ma->iter? sam_itr_next(ma->fp, ma->iter, b) : sam_read1(ma->fp, ma->h, b);
if (ret < 0) break;
// The 'B' cigar operation is not part of the specification, considering as obsolete.
// bam_remove_B(b);
if (b->core.tid < 0 || (b->core.flag&BAM_FUNMAP)) continue; // exclude unmapped reads
if (ma->conf->rflag_require && !(ma->conf->rflag_require&b->core.flag)) continue;
if (ma->conf->rflag_filter && ma->conf->rflag_filter&b->core.flag) continue;
if (ma->conf->bed)
{
// test overlap
regitr_t *itr = ma->conf->bed_itr;
int beg = b->core.pos, end = bam_endpos(b)-1;
int overlap = regidx_overlap(ma->conf->bed, ma->h->target_name[b->core.tid],beg,end, itr);
if ( !ma->conf->bed_logic && !overlap )
{
// exclude only reads which are fully contained in the region
while ( regitr_overlap(itr) )
{
if ( beg < itr->beg ) { overlap = 1; break; }
if ( end > itr->end ) { overlap = 1; break; }
}
}
if ( !overlap ) continue;
}
if ( bam_smpl_get_sample_id(ma->conf->bsmpl,ma->bam_id,b)<0 ) continue;
if (ma->conf->flag & MPLP_ILLUMINA13) {
int i;
uint8_t *qual = bam_get_qual(b);
for (i = 0; i < b->core.l_qseq; ++i)
qual[i] = qual[i] > 31? qual[i] - 31 : 0;
}
if (ma->conf->fai && b->core.tid >= 0) {
has_ref = mplp_get_ref(ma, b->core.tid, &ref, &ref_len);
if (has_ref && ref_len <= b->core.pos) { // exclude reads outside of the reference sequence
fprintf(stderr,"[%s] Skipping because %d is outside of %d [ref:%d]\n",
__func__, b->core.pos, ref_len, b->core.tid);
continue;
}
} else {
has_ref = 0;
}
if (has_ref && (ma->conf->flag&MPLP_REALN)) sam_prob_realn(b, ref, ref_len, (ma->conf->flag & MPLP_REDO_BAQ)? 7 : 3);
if (has_ref && ma->conf->capQ_thres > 10) {
int q = sam_cap_mapq(b, ref, ref_len, ma->conf->capQ_thres);
if (q < 0) continue; // skip
else if (b->core.qual > q) b->core.qual = q;
}
if (b->core.qual < ma->conf->min_mq) continue;
else if ((ma->conf->flag&MPLP_NO_ORPHAN) && (b->core.flag&BAM_FPAIRED) && !(b->core.flag&BAM_FPROPER_PAIR)) continue;
return ret;
};
return ret;
}
bcf1_t *process(bcf1_t *rec)
{
bcf1_t *dflt = args.mode&MODE_LIST_GOOD ? rec : NULL;
args.nrec++;
if ( rec->n_allele > 63 ) return dflt; // we use 64bit bitmask below
int ngt = bcf_get_genotypes(args.hdr, rec, &args.gt_arr, &args.ngt_arr);
if ( ngt<0 ) return dflt;
if ( ngt!=2*bcf_hdr_nsamples(args.hdr) && ngt!=bcf_hdr_nsamples(args.hdr) ) return dflt;
ngt /= bcf_hdr_nsamples(args.hdr);
int itr_set = regidx_overlap(args.rules, bcf_seqname(args.hdr,rec),rec->pos,rec->pos, args.itr_ori);
int i, has_bad = 0, needs_update = 0;
for (i=0; i<args.ntrios; i++)
{
int32_t a,b,c,d,e,f;
trio_t *trio = &args.trios[i];
a = args.gt_arr[ngt*trio->imother];
b = ngt==2 ? args.gt_arr[ngt*trio->imother+1] : bcf_int32_vector_end;
c = args.gt_arr[ngt*trio->ifather];
d = ngt==2 ? args.gt_arr[ngt*trio->ifather+1] : bcf_int32_vector_end;
e = args.gt_arr[ngt*trio->ichild];
f = ngt==2 ? args.gt_arr[ngt*trio->ichild+1] : bcf_int32_vector_end;
// skip sites with missing data in child
if ( bcf_gt_is_missing(e) || bcf_gt_is_missing(f) ) continue;
uint64_t mother = 0, father = 0,child1,child2;
int is_ok = 0;
if ( !itr_set )
{
if ( f==bcf_int32_vector_end ) { warn_ploidy(rec); continue; }
// All M,F,C genotypes are diploid. Missing data are considered consistent.
child1 = 1<<bcf_gt_allele(e);
child2 = 1<<bcf_gt_allele(f);
mother = bcf_gt_is_missing(a) ? child1|child2 : 1<<bcf_gt_allele(a);
mother |= bcf_gt_is_missing(b) || b==bcf_int32_vector_end ? child1|child2 : 1<<bcf_gt_allele(b);
father = bcf_gt_is_missing(c) ? child1|child2 : 1<<bcf_gt_allele(c);
father |= bcf_gt_is_missing(d) || d==bcf_int32_vector_end ? child1|child2 : 1<<bcf_gt_allele(d);
if ( (mother&child1 && father&child2) || (mother&child2 && father&child1) ) is_ok = 1;
}
else
{
child1 = 1<<bcf_gt_allele(e);
child2 = bcf_gt_is_missing(f) || f==bcf_int32_vector_end ? 0 : 1<<bcf_gt_allele(f);
mother |= bcf_gt_is_missing(a) ? 0 : 1<<bcf_gt_allele(a);
mother |= bcf_gt_is_missing(b) || b==bcf_int32_vector_end ? 0 : 1<<bcf_gt_allele(b);
father |= bcf_gt_is_missing(c) ? 0 : 1<<bcf_gt_allele(c);
father |= bcf_gt_is_missing(d) || d==bcf_int32_vector_end ? 0 : 1<<bcf_gt_allele(d);
regitr_copy(args.itr, args.itr_ori);
while ( !is_ok && regitr_overlap(args.itr) )
{
rule_t *rule = ®itr_payload(args.itr,rule_t);
if ( child1 && child2 )
{
if ( !rule->mal || !rule->fal ) continue; // wrong rule (haploid), but this is a diploid GT
if ( !mother ) mother = child1|child2;
if ( !father ) father = child1|child2;
if ( (mother&child1 && father&child2) || (mother&child2 && father&child1) ) is_ok = 1;
continue;
}
if ( rule->mal )
{
if ( mother && !(child1&mother) ) continue;
}
if ( rule->fal )
{
if ( father && !(child1&father) ) continue;
}
is_ok = 1;
}
}
if ( is_ok )
{
trio->nok++;
}
else
{
trio->nbad++;
has_bad = 1;
if ( args.mode&MODE_DELETE )
{
args.gt_arr[ngt*trio->imother] = bcf_gt_missing;
if ( b!=bcf_int32_vector_end ) args.gt_arr[ngt*trio->imother+1] = bcf_gt_missing; // should be always true
args.gt_arr[ngt*trio->ifather] = bcf_gt_missing;
if ( d!=bcf_int32_vector_end ) args.gt_arr[ngt*trio->ifather+1] = bcf_gt_missing;
args.gt_arr[ngt*trio->ichild] = bcf_gt_missing;
if ( f!=bcf_int32_vector_end ) args.gt_arr[ngt*trio->ichild+1] = bcf_gt_missing;
needs_update = 1;
}
}
}
if ( needs_update && bcf_update_genotypes(args.hdr,rec,args.gt_arr,ngt*bcf_hdr_nsamples(args.hdr)) )
error("Could not update GT field at %s:%d\n", bcf_seqname(args.hdr,rec),rec->pos+1);
if ( args.mode&MODE_DELETE ) return rec;
if ( args.mode&MODE_LIST_GOOD ) return has_bad ? NULL : rec;
if ( args.mode&MODE_LIST_BAD ) return has_bad ? rec : NULL;
return NULL;
}
static int query_regions(args_t *args, char *fname, char **regs, int nregs)
{
int i;
htsFile *fp = hts_open(fname,"r");
if ( !fp ) error("Could not read %s\n", fname);
enum htsExactFormat format = hts_get_format(fp)->format;
regidx_t *reg_idx = NULL;
if ( args->targets_fname )
{
reg_idx = regidx_init(args->targets_fname, NULL, NULL, 0, NULL);
if ( !reg_idx ) error("Could not read %s\n", args->targets_fname);
}
if ( format == bcf )
{
htsFile *out = hts_open("-","w");
if ( !out ) error("Could not open stdout\n", fname);
hts_idx_t *idx = bcf_index_load(fname);
if ( !idx ) error("Could not load .csi index of %s\n", fname);
bcf_hdr_t *hdr = bcf_hdr_read(fp);
if ( !hdr ) error("Could not read the header: %s\n", fname);
if ( args->print_header )
bcf_hdr_write(out,hdr);
if ( !args->header_only )
{
bcf1_t *rec = bcf_init();
for (i=0; i<nregs; i++)
{
hts_itr_t *itr = bcf_itr_querys(idx,hdr,regs[i]);
while ( bcf_itr_next(fp, itr, rec) >=0 )
{
if ( reg_idx && !regidx_overlap(reg_idx, bcf_seqname(hdr,rec),rec->pos,rec->pos+rec->rlen-1, NULL) ) continue;
bcf_write(out,hdr,rec);
}
tbx_itr_destroy(itr);
}
bcf_destroy(rec);
}
if ( hts_close(out) ) error("hts_close returned non-zero status for stdout\n");
bcf_hdr_destroy(hdr);
hts_idx_destroy(idx);
}
else if ( format==vcf || format==sam || format==unknown_format )
{
tbx_t *tbx = tbx_index_load(fname);
if ( !tbx ) error("Could not load .tbi/.csi index of %s\n", fname);
kstring_t str = {0,0,0};
if ( args->print_header )
{
while ( hts_getline(fp, KS_SEP_LINE, &str) >= 0 )
{
if ( !str.l || str.s[0]!=tbx->conf.meta_char ) break;
puts(str.s);
}
}
if ( !args->header_only )
{
int nseq;
const char **seq = NULL;
if ( reg_idx ) seq = tbx_seqnames(tbx, &nseq);
for (i=0; i<nregs; i++)
{
hts_itr_t *itr = tbx_itr_querys(tbx, regs[i]);
if ( !itr ) continue;
while (tbx_itr_next(fp, tbx, itr, &str) >= 0)
{
if ( reg_idx && !regidx_overlap(reg_idx,seq[itr->curr_tid],itr->curr_beg,itr->curr_end, NULL) ) continue;
puts(str.s);
}
tbx_itr_destroy(itr);
}
free(seq);
}
free(str.s);
tbx_destroy(tbx);
}
else if ( format==bam )
error("Please use \"samtools view\" for querying BAM files.\n");
if ( reg_idx ) regidx_destroy(reg_idx);
if ( hts_close(fp) ) error("hts_close returned non-zero status: %s\n", fname);
for (i=0; i<nregs; i++) free(regs[i]);
free(regs);
return 0;
}
int run(int argc, char **argv)
{
args_t *args = (args_t*) calloc(1,sizeof(args_t));
args->nsites = 10;
args->min_hets = 0.3;
args->background = "X:60001-2699520";
static struct option loptions[] =
{
{"verbose",1,0,'v'},
{"ploidy",1,0,'p'},
{"nsites",1,0,'n'},
{"guess",1,0,'g'},
{"min-hets",1,0,'m'},
{"background",1,0,'b'},
{0,0,0,0}
};
char c, *tmp, *ploidy_fname = NULL;
while ((c = getopt_long(argc, argv, "p:n:g:m:vb:",loptions,NULL)) >= 0)
{
switch (c) {
case 'b':
if ( !strcmp("-",optarg) ) args->background = NULL;
else args->background = optarg;
break;
case 'v': args->verbose = 1; break;
case 'g':
if ( !strcasecmp(optarg,"GT") ) args->guess = GUESS_GT;
else if ( !strcasecmp(optarg,"PL") ) args->guess = GUESS_PL;
else if ( !strcasecmp(optarg,"GL") ) args->guess = GUESS_GL;
else error("The argument not recognised, expected --guess GT, --guess PL or --guess GL: %s\n", optarg);
break;
case 'm':
args->min_hets = strtod(optarg,&tmp);
if ( *tmp ) error("Unexpected argument to --min-hets: %s\n", optarg);
break;
case 'p': ploidy_fname = optarg; break;
case 'n':
args->nsites = strtol(optarg,&tmp,10);
if (*tmp) error("Unexpected argument to --nsites: %s\n", optarg); break;
case 'h':
case '?':
default: error("%s", usage()); break;
}
}
args->sr = bcf_sr_init();
args->sr->require_index = 1;
if ( !argv[0] ) error("%s", usage());
if ( !bcf_sr_add_reader(args->sr,argv[0]) ) 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->dflt_ploidy = 2;
if ( ploidy_fname )
{
args->ploidy = ploidy_init(ploidy_fname, args->dflt_ploidy);
if ( !args->ploidy ) error("Could not read %s\n", ploidy_fname);
}
else
{
args->ploidy = ploidy_init_string(
"X 1 60000 M 1\n"
"X 2699521 154931043 M 1\n"
"Y 1 59373566 M 1\n"
"Y 1 59373566 F 0\n", args->dflt_ploidy);
}
args->nsex = ploidy_nsex(args->ploidy);
args->sex2ploidy = (int*) malloc(sizeof(int)*args->nsex);
args->max_ploidy = ploidy_max(args->ploidy);
if ( args->guess && args->max_ploidy > 2 ) error("Sorry, ploidy %d not supported with -g\n", args->max_ploidy);
args->ncounts = args->nsample * ((args->max_ploidy>2 ? args->max_ploidy : 2)+1);
args->counts = (int*) malloc(sizeof(int)*args->ncounts);
args->bg_counts = (count_t*) calloc(args->nsample,sizeof(count_t));
args->sex2prob = (float*) calloc(args->nsample*args->nsex,sizeof(float));
int i, nseq;
for (i=0; i<args->nsample*args->nsex; i++) args->sex2prob[i] = 1;
if ( args->verbose && args->guess )
printf("# [1]REG\t[2]Region\t[3]Sample\t[4]Het fraction\t[5]nHet\t[6]nHom\t[7]nMissing\n");
// First get the counts from expected haploid regions
regidx_t *idx = ploidy_regions(args->ploidy);
char **seqs = regidx_seq_names(idx, &nseq);
for (i=0; i<nseq; i++)
{
regitr_t itr;
regidx_overlap(idx, seqs[i], 0, UINT32_MAX, &itr);
while ( itr.i < itr.n )
{
if ( args->guess )
itr.i += process_region_guess(args, seqs[i], &itr);
else
itr.i += process_region_precise(args, seqs[i], &itr);
}
}
// Get the counts from a PAR (the background diploid region) and see if the fraction
// of hets is different
if ( args->guess ) sex2prob_guess(args);
for (i=0; i<args->nsample; i++)
{
int j, jmax = 0;
float max = 0, sum = 0;
for (j=0; j<args->nsex; j++)
{
sum += args->sex2prob[i*args->nsex+j];
if ( max < args->sex2prob[i*args->nsex+j] )
{
jmax = j;
max = args->sex2prob[i*args->nsex+j];
}
}
if ( args->verbose )
printf("%s\t%s\t%f\n", args->hdr->samples[i],ploidy_id2sex(args->ploidy,jmax),args->sex2prob[i*args->nsex+jmax]/sum);
else
printf("%s\t%s\n", args->hdr->samples[i],ploidy_id2sex(args->ploidy,jmax));
}
bcf_sr_destroy(args->sr);
ploidy_destroy(args->ploidy);
destroy_regs(args);
free(args->sex2ploidy);
free(args->counts);
free(args->bg_counts);
free(args->gts);
free(args->pls);
free(args->sex2prob);
free(args);
return 0;
}