/**
* Extract reference sequence region for motif discovery in a fuzzy fashion.
*/
void CandidateRegionExtractor::extract_regions_by_fuzzy_alignment(bcf_hdr_t* h, bcf1_t* v, Variant& variant)
{
if (debug)
{
if (debug) std::cerr << "********************************************\n";
std::cerr << "EXTRACTIING REGION BY FUZZY ALIGNMENT\n\n";
}
VNTR& vntr = variant.vntr;
const char* chrom = bcf_get_chrom(h, v);
int32_t min_beg1 = bcf_get_pos1(v);
int32_t max_end1 = min_beg1;
//merge candidate search region
for (size_t i=1; i<bcf_get_n_allele(v); ++i)
{
std::string ref(bcf_get_alt(v, 0));
std::string alt(bcf_get_alt(v, i));
int32_t pos1 = bcf_get_pos1(v);
trim(pos1, ref, alt);
if (debug)
{
std::cerr << "indel fragment : " << (ref.size()<alt.size()? alt : ref) << "\n";
std::cerr << " : " << ref << ":" << alt << "\n";
}
min_beg1 = fuzzy_left_align(chrom, pos1, ref, alt, 3);
max_end1 = fuzzy_right_align(chrom, pos1 + ref.size() - 1, ref, alt, 3);
int32_t seq_len;
char* seq = faidx_fetch_seq(fai, chrom, min_beg1-1, max_end1-1, &seq_len);
if (debug)
{
std::cerr << "FUZZY REGION " << min_beg1 << "-" << max_end1 << " (" << max_end1-min_beg1+1 <<") " << "\n";
std::cerr << " " << seq << "\n";
}
if (seq_len) free(seq);
}
int32_t seq_len;
char* seq = faidx_fetch_seq(fai, chrom, min_beg1-1, max_end1-1, &seq_len);
if (debug)
{
std::cerr << "FINAL FUZZY REGION " << min_beg1 << "-" << max_end1 << " (" << max_end1-min_beg1+1 <<") " << "\n";
std::cerr << " " << seq << "\n";
}
vntr.exact_repeat_tract = seq;
vntr.exact_rbeg1 = min_beg1;
if (seq_len) free(seq);
}
/**
* Gets records for the most recent position and fills up the buffer from file i.
* returns true if buffer is filled or it is not necessary to fill buffer.
* returns false if no more records are found to fill buffer
*/
void BCFSyncedStreamReader::fill_buffer(int32_t i)
{
//not necessary to fill buffer
if (buffer[i].size()>=2)
return;
int32_t pos1 = buffer[i].size()==0 ? 0 : bcf_get_pos1(buffer[i].front());
if (ftypes[i]==FT_BCF_GZ)
{
bcf1_t *v = get_bcf1_from_pool();
bool populated = false;
while (itrs[i] && bcf_itr_next(vcfs[i], itrs[i], v) >= 0)
{
populated = true;
bcf_unpack(v, BCF_UN_STR);
buffer[i].push_back(v);
insert_into_pq(i, v);
if (pos1==0)
{
pos1 = bcf_get_pos1(v);
}
if (bcf_get_pos1(v)!=pos1)
{
break;
}
v = get_bcf1_from_pool();
populated = false;
}
if (!populated)
store_bcf1_into_pool(v);
}
else if (ftypes[i]==FT_VCF_GZ)
{
while (itrs[i] && tbx_itr_next(vcfs[i], tbxs[i], itrs[i], &s) >= 0)
{
bcf1_t *v = get_bcf1_from_pool();
vcf_parse(&s, hdrs[i], v);
bcf_unpack(v, BCF_UN_STR);
buffer[i].push_back(v);
insert_into_pq(i, v);
if (pos1==0)
{
pos1 = bcf_get_pos1(v);
}
if (bcf_get_pos1(v)!=pos1)
{
break;
}
}
}
}
/**
* Returns true if chrom:start1-end1 overlaps with a region in the file.
*/
bool OrderedBCFOverlapMatcher::overlaps_with(std::string& chrom, int32_t start1, int32_t end1)
{
bool overlaps = false;
//moves to new chromosome
if (current_interval.seq!=chrom)
{
buffer.clear();
current_interval.set(chrom);
odr->jump_to_interval(current_interval);
std::cerr << "Jumped to chromosome " << chrom << "\n";
while (odr->read(v))
{
if (bcf_get_end_pos1(v)<start1) continue;
overlaps = overlaps || (bcf_get_pos1(v)<=end1);
buffer.push_back(v);
if (bcf_get_pos1(v)>end1) break;
v = bcf_init();
}
}
else
{
//scythe preceding bed records
std::list<bcf1_t*>::iterator i = buffer.begin();
while (i!=buffer.end())
{
if (bcf_get_end_pos1(*i)<start1)
{
bcf_destroy(*i);
i = buffer.erase(i);
continue;
}
overlaps = (bcf_get_pos1(*i)<=end1);
break;
}
if (!overlaps)
{
if (buffer.empty())
{
while (odr->read(v))
{
if (bcf_get_end_pos1(*i)<start1) continue;
overlaps = overlaps || (bcf_get_pos1(*i)<=end1);
buffer.push_back(v);
if (bcf_get_pos1(v)>end1) break;
v = bcf_init();
}
}
}
}
return overlaps;
};
/**
* Gets a sorted string representation of a variant.
*/
void bcf_variant2string_sorted(bcf_hdr_t *h, bcf1_t *v, kstring_t *var)
{
bcf_print_liten(h,v);
bcf_unpack(v, BCF_UN_STR);
var->l = 0;
kputs(bcf_get_chrom(h, v), var);
kputc(':', var);
kputw(bcf_get_pos1(v), var);
kputc(':', var);
if (v->n_allele==2)
{
kputs(bcf_get_alt(v, 0), var);
kputc(',', var);
kputs(bcf_get_alt(v, 1), var);
}
else
{
char** allele = bcf_get_allele(v);
char** temp = (char**) malloc((bcf_get_n_allele(v)-1)*sizeof(char*));
for (int32_t i=1; i<v->n_allele; ++i)
{
temp[i] = allele[i];
}
std::qsort(temp, bcf_get_n_allele(v), sizeof(char*), cmpstr);
kputs(bcf_get_alt(v, 0), var);
for (int32_t i=0; i<v->n_allele-1; ++i)
{
kputc(',', var);
kputs(temp[i], var);
}
free(temp);
}
}
/**
* Checks if a vntr is a homopolymer.
*/
bool CandidateRegionExtractor::is_homopolymer(bcf_hdr_t* h, bcf1_t* v)
{
bool is_homopolymer = false;
uint32_t ref_len = strlen(bcf_get_ref(v));
for (size_t i=1; i<bcf_get_n_allele(v); ++i)
{
std::string ref(bcf_get_alt(v, 0));
std::string alt(bcf_get_alt(v, i));
int32_t pos1 = bcf_get_pos1(v);
}
return is_homopolymer;
}
/**
* Gets a string representation of a variant.
*/
void bcf_variant2string(bcf_hdr_t *h, bcf1_t *v, kstring_t *var)
{
bcf_unpack(v, BCF_UN_STR);
var->l = 0;
kputs(bcf_get_chrom(h, v), var);
kputc(':', var);
kputw(bcf_get_pos1(v), var);
kputc(':', var);
for (int32_t i=0; i<v->n_allele; ++i)
{
if (i) kputc(',', var);
kputs(bcf_get_alt(v, i), var);
}
}
/**
* Gets a string representation of the variant.
*/
std::string Variant::get_variant_string()
{
kstring_t var = {0,0,0};
bcf_unpack(v, BCF_UN_STR);
var.l = 0;
kputs(bcf_get_chrom(h, v), &var);
kputc(':', &var);
kputw(bcf_get_pos1(v), &var);
kputc(':', &var);
for (size_t i=0; i<bcf_get_n_allele(v); ++i)
{
if (i) kputc('/', &var);
kputs(bcf_get_alt(v, i), &var);
}
std::string str(var.s);
if (var.m) free(var.s);
return str;
}
/**
* Pick candidate region.
*
* @mode - REFERENCE use refence field
* - ALLELE_EXACT by exact alignment
* - ALLELE_FUZZY by fuzzy alignment
*/
void CandidateRegionExtractor::pick_candidate_region(bcf_hdr_t* h, bcf1_t* v, Variant& variant, uint32_t mode)
{
if (mode==REFERENCE)
{
VNTR& vntr = variant.vntr;
vntr.exact_repeat_tract.assign(bcf_get_ref(v));
vntr.exact_rbeg1 = bcf_get_pos1(v);
char** alleles = bcf_get_allele(v);
vntr.exact_rend1 = strlen(alleles[0]);
vntr.fuzzy_rbeg1 = vntr.exact_rbeg1;
vntr.fuzzy_rend1 = vntr.exact_rend1;
}
else if (mode==EXACT_LEFT_RIGHT_ALIGNMENT)
{
extract_regions_by_exact_alignment(h, v, variant);
}
else if (mode==FUZZY_LEFT_RIGHT_ALIGNMENT)
{
extract_regions_by_fuzzy_alignment(h, v, variant);
}
}
/**
* Extract reference sequence region for motif discovery.
*
* The input is a VCF record that contains an indel.
*
* If the the indel has multiple alleles, it will examine all
* alleles.
*
* todo: is might be a good idea to combine this step with motif detection
* since there seems to be a need to have an iterative process here
* to ensure a good candidate motif is chosen. *
*/
void CandidateRegionExtractor::extract_regions_by_exact_alignment(bcf_hdr_t* h, bcf1_t* v, Variant& variant)
{
if (debug)
{
if (debug) std::cerr << "********************************************\n";
std::cerr << "EXTRACTIING REGION BY EXACT LEFT AND RIGHT ALIGNMENT\n\n";
}
VNTR& vntr = variant.vntr;
const char* chrom = bcf_get_chrom(h, v);
int32_t min_beg1 = bcf_get_pos1(v);
int32_t max_end1 = min_beg1;
if (debug)
{
bcf_print_liten(h, v);
}
//merge candidate search region
for (size_t i=1; i<bcf_get_n_allele(v); ++i)
{
std::string ref(bcf_get_alt(v, 0));
std::string alt(bcf_get_alt(v, i));
int32_t pos1 = bcf_get_pos1(v);
//this prevents introduction of flanks that do not harbour the repeat unit
trim(pos1, ref, alt);
int32_t end1 = pos1 + ref.size() - 1;
right_align(chrom, end1, ref, alt);
int32_t beg1 = end1 - ref.size() + 1;
left_align(chrom, beg1, ref, alt);
min_beg1 = beg1<min_beg1 ? beg1 : min_beg1;
max_end1 = end1>max_end1 ? end1 : max_end1;
int32_t seq_len;
char* seq = faidx_fetch_seq(fai, chrom, min_beg1-1, max_end1-1, &seq_len);
if (debug)
{
std::cerr << "EXACT REGION " << min_beg1 << "-" << max_end1 << " (" << max_end1-min_beg1+1 <<") from " << pos1 << ":" << ref << ":" << alt << "\n";
std::cerr << " " << seq << "\n";
}
if (seq_len) free(seq);
}
int32_t seq_len;
char* seq = faidx_fetch_seq(fai, chrom, min_beg1-1, max_end1-1, &seq_len);
if (debug)
{
std::cerr << "FINAL EXACT REGION " << min_beg1 << "-" << max_end1 << " (" << max_end1-min_beg1+1 <<") " << "\n";
std::cerr << " " << seq << "\n";
}
vntr.exact_repeat_tract = seq;
vntr.rid = bcf_get_rid(v);
vntr.exact_rbeg1 = min_beg1;
vntr.exact_rend1 = max_end1;
if (seq_len) free(seq);
}
/**
* Gets records for the most recent position and fills up the buffer from file i.
* returns true if buffer is filled or it is not necessary to fill buffer.
* returns false if no more records are found to fill buffer
*/
void BCFSyncedReader::fill_buffer(int32_t i)
{
if (buffer[i].size()>=2)
return;
if (random_access)
{
int32_t pos1 = buffer[i].size()==0 ? 0 : bcf_get_pos1(buffer[i].front());
if (ftypes[i].format==bcf)
{
bcf1_t *v = get_bcf1_from_pool();
bool populated = false;
while (itrs[i] && bcf_itr_next(files[i], itrs[i], v)>=0)
{
populated = true;
bcf_unpack(v, BCF_UN_STR);
//check to ensure order
if (!buffer[i].empty())
{
if (!bcf_is_in_order(buffer[i].back(), v))
{
fprintf(stderr, "[E:%s:%d %s] VCF file not in order: %s\n", __FILE__, __LINE__, __FUNCTION__, file_names[i].c_str());
exit(1);
}
}
buffer[i].push_back(v);
insert_into_pq(i, v);
if (pos1==0)
{
pos1 = bcf_get_pos1(v);
}
if (bcf_get_pos1(v)!=pos1)
{
break;
}
v = get_bcf1_from_pool();
populated = false;
}
if (!populated)
store_bcf1_into_pool(v);
}
else if (ftypes[i].format==vcf)
{
while (itrs[i] && tbx_itr_next(files[i], tbxs[i], itrs[i], &s)>=0)
{
bcf1_t *v = get_bcf1_from_pool();
vcf_parse(&s, hdrs[i], v);
bcf_unpack(v, BCF_UN_STR);
//check to ensure order
if (!buffer[i].empty())
{
if (!bcf_is_in_order(buffer[i].back(), v))
{
fprintf(stderr, "[E:%s:%d %s] VCF file not in order: %s\n", __FILE__, __LINE__, __FUNCTION__, file_names[i].c_str());
exit(1);
}
}
buffer[i].push_back(v);
insert_into_pq(i, v);
if (pos1==0)
{
pos1 = bcf_get_pos1(v);
}
if (bcf_get_pos1(v)!=pos1)
{
break;
}
}
}
}
else
{
int32_t rid = buffer[i].size()==0 ? -1 : bcf_get_rid(buffer[i].front());
int32_t pos1 = buffer[i].size()==0 ? 0 : bcf_get_pos1(buffer[i].front());
bcf1_t *v = get_bcf1_from_pool();
bool populated = false;
while (bcf_read(files[i], hdrs[i], v)>=0)
{
populated = true;
bcf_unpack(v, BCF_UN_STR);
//check to ensure order
if (!buffer[i].empty())
{
if (!bcf_is_in_order(buffer[i].back(), v))
{
fprintf(stderr, "[E:%s:%d %s] VCF file not in order: %s\n", __FILE__, __LINE__, __FUNCTION__, file_names[i].c_str());
exit(1);
}
}
buffer[i].push_back(v);
insert_into_pq(i, v);
if (rid==-1)
{
rid = bcf_get_rid(v);
pos1 = bcf_get_pos1(v);
}
if (bcf_get_rid(v)!=rid || bcf_get_pos1(v)!=pos1)
{
break;
}
v = get_bcf1_from_pool();
populated = false;
}
if (!populated)
store_bcf1_into_pool(v);
}
}
/**
* Constructor.
*/
Variant::Variant(bcf_hdr_t* h, bcf1_t* v)
{
this->h = h;
this->v = v;
type = classify(h, v);
chrom = bcf_get_chrom(h, v);
rid = bcf_get_rid(v);
pos1 = bcf_get_pos1(v);
no_overlapping_snps = 0;
no_overlapping_indels = 0;
no_overlapping_vntrs = 0;
is_new_multiallelic = false;
//attempts to update relevant information on variants
if (type==VT_SNP)
{
beg1 = bcf_get_pos1(v);
end1 = bcf_get_pos1(v);
}
else if (type==VT_INDEL)
{
beg1 = bcf_get_pos1(v);
end1 = bcf_get_info_int(h, v, "END", 0);
//annotate ends
if (!end1) end1 = bcf_get_end1(v);
}
//complex variants
else if (type & (VT_SNP|VT_MNP|VT_INDEL|VT_CLUMPED))
{
beg1 = bcf_get_pos1(v);
end1 = bcf_get_info_int(h, v, "END", 0);
if (!end1) end1 = bcf_get_end1(v);
}
else if (type==VT_VNTR)
{
beg1 = bcf_get_pos1(v);
end1 = bcf_get_info_int(h, v, "END", 0);
if (!end1) end1 = bcf_get_end1(v);
update_vntr_from_info_fields(h, v);
vs.push_back(v);
vntr_vs.push_back(v);
}
else if (type==VT_SV)
{
beg1 = bcf_get_pos1(v);
end1 = bcf_get_info_int(h, v, "END", 0);
if (!end1) end1 = bcf_get_end1(v);
}
else
{
std::cerr << "unexpected type in variant construction\n";
print();
exit(1);
}
}
/**
* Classifies variants.
*/
int32_t Variant::classify(bcf_hdr_t *h, bcf1_t *v)
{
clear();
this->h = h;
this->v = v;
bcf_unpack(v, BCF_UN_STR);
chrom.assign(bcf_get_chrom(h, v));
rid = bcf_get_rid(v);
pos1 = bcf_get_pos1(v);
end1 = bcf_get_end1(v);
char** allele = bcf_get_allele(v);
int32_t n_allele = bcf_get_n_allele(v);
int32_t pos0 = pos1-1;
bool homogeneous_length = true;
char* ref = allele[0];
int32_t rlen = strlen(ref);
if (strchr(ref, 'N'))
{
contains_N = true;
}
//if only ref allele, skip this entire for loop
for (size_t i=1; i<n_allele; ++i)
{
int32_t allele_type = VT_REF;
//check for symbolic alternative alleles
if (strchr(allele[i],'<'))
{
size_t len = strlen(allele[i]);
if (len>=5)
{
//VN/d+
if (allele[i][0]=='<' && allele[i][1]=='V' && allele[i][2]=='N' && allele[i][len-1]=='>' )
{
for (size_t j=3; j<len-1; ++j)
{
if (allele[i][j]<'0' || allele[i][j]>'9')
{
allele_type = VT_VNTR;
}
}
}
//VNTR
else if (len==6 &&
allele[i][0]=='<' &&
allele[i][1]=='V' && allele[i][2]=='N' && allele[i][3]=='T' && allele[i][4]=='R' &&
allele[i][5]=='>' )
{
allele_type = VT_VNTR;
}
//STR
else if (len==5 &&
allele[i][0]=='<' &&
allele[i][1]=='S' && allele[i][2]=='T' && allele[i][3]=='R' &&
allele[i][4]=='>' )
{
allele_type = VT_VNTR;
}
//ST/d+
else if (allele[i][0]=='<' && allele[i][1]=='S' && allele[i][2]=='T' && allele[i][len-1]=='>' )
{
type = VT_VNTR;
for (size_t j=3; j<len-1; ++j)
{
if ((allele[i][j]<'0' || allele[i][j]>'9') && allele[i][j]!='.')
{
type = VT_SV;
}
}
}
}
if (allele_type==VT_VNTR)
{
allele_type = VT_VNTR;
type |= allele_type;
alleles.push_back(Allele(allele_type));
}
else
{
allele_type = VT_SV;
type |= allele_type;
std::string sv_type(allele[i]);
alleles.push_back(Allele(allele_type, sv_type));
}
}
//checks for chromosomal breakpoints
else if (strchr(allele[i],'[')||strchr(allele[i],']'))
{
allele_type = VT_SV;
type |= allele_type;
std::string sv_type("<BND>");
alleles.push_back(Allele(allele_type, sv_type));
}
//non variant record
else if (allele[i][0]=='.' || strcmp(allele[i],allele[0])==0)
{
type = VT_REF;
}
//explicit sequence of bases
else
{
kstring_t REF = {0,0,0};
kstring_t ALT = {0,0,0};
ref = allele[0];
char* alt = allele[i];
int32_t alen = strlen(alt);
if (strchr(alt, 'N'))
{
contains_N = true;
}
if (rlen!=alen)
{
homogeneous_length = false;
}
//trimming
//this is required in particular for the
//characterization of multiallelics and
//in general, any unnormalized variant
int32_t rl = rlen;
int32_t al = alen;
//trim right
while (rl!=1 && al!=1)
{
if (ref[rl-1]==alt[al-1])
{
--rl;
--al;
}
else
{
break;
}
}
//trim left
while (rl !=1 && al!=1)
{
if (ref[0]==alt[0])
{
++ref;
++alt;
--rl;
--al;
}
else
{
break;
}
}
kputsn(ref, rl, &REF);
kputsn(alt, al, &ALT);
ref = REF.s;
alt = ALT.s;
int32_t mlen = std::min(rl, al);
int32_t dlen = al-rl;
int32_t diff = 0;
int32_t ts = 0;
int32_t tv = 0;
if (mlen==1 && dlen)
{
char ls, le, ss;
if (rl>al)
{
ls = ref[0];
le = ref[rl-1];
ss = alt[0];
}
else
{
ls = alt[0];
le = alt[al-1];
ss = ref[0];
}
if (ls!=ss && le!=ss)
{
++diff;
if ((ls=='G' && ss=='A') ||
(ls=='A' && ss=='G') ||
(ls=='C' && ss=='T') ||
(ls=='T' && ss=='C'))
{
++ts;
}
else
{
++tv;
}
}
}
else
{
for (int32_t j=0; j<mlen; ++j)
{
if (ref[j]!=alt[j])
{
++diff;
if ((ref[j]=='G' && alt[j]=='A') ||
(ref[j]=='A' && alt[j]=='G') ||
(ref[j]=='C' && alt[j]=='T') ||
(ref[j]=='T' && alt[j]=='C'))
{
++ts;
}
else
{
++tv;
}
}
}
}
//substitution variants
if (mlen==diff)
{
allele_type |= mlen==1 ? VT_SNP : VT_MNP;
}
//indel variants
if (dlen)
{
allele_type |= VT_INDEL;
}
//clumped SNPs and MNPs
if (diff && diff < mlen) //internal gaps
{
allele_type |= VT_CLUMPED;
}
type |= allele_type;
alleles.push_back(Allele(type, diff, alen, dlen, mlen, ts, tv));
ts += ts;
tv += tv;
ins = dlen>0?1:0;
del = dlen<0?1:0;
if (REF.m) free(REF.s);
if (ALT.m) free(ALT.s);
}
}
if (type==VT_VNTR)
{
update_vntr_from_info_fields(h, v);
}
//additionally define MNPs by length of all alleles
if (!(type&(VT_VNTR|VT_SV)) && type!=VT_REF)
{
if (homogeneous_length && rlen>1 && n_allele>1)
{
type |= VT_MNP;
}
}
return type;
}
/**
* Annotates VNTR characteristics.
* @mode -
*/
void VNTRAnnotator::annotate(bcf_hdr_t* h, bcf1_t* v, Variant& variant, std::string mode)
{
VNTR& vntr = variant.vntr;
//update chromosome and position
variant.rid = bcf_get_rid(v);
variant.pos1 = bcf_get_pos1(v);
//this is for reannotating an VNTR record
//this is more for the purpose of evaluation to
//check if vt's algorithm is concordant with
//VNTRs from other sources.
if (variant.type==VT_VNTR)
{
if (debug) std::cerr << "ANNOTATING VNTR/STR \n";
//1. pick candidate region
cre->pick_candidate_region(h, v, variant, REFERENCE);
//2. detect candidate motifs from a reference seqeuence
cmp->generate_candidate_motifs(h, v, variant);
cmp->next_motif(h, v, variant);
}
//main purpose - annotation of Indels.
else if (variant.type&VT_INDEL)
{
//the basic steps in annotating a TR
//
//1. extract a region that has a chance of containing the repeat units
//2. choose a set of candidate motifs and pick motif
//3. detect repeat region and evaluate
//4. iterate 2 and 3
//EXACT MODE
if (mode=="e")
{
if (debug) std::cerr << "============================================\n";
if (debug) std::cerr << "ANNOTATING INDEL EXACTLY\n";
//1. pick candidate region using exact left and right alignment
cre->pick_candidate_region(h, v, variant, EXACT_LEFT_RIGHT_ALIGNMENT);
//2. evaluate reference length
fd->detect_flanks(h, v, variant, CLIP_ENDS);
if (debug) std::cerr << "============================================\n";
return;
}
//FUZZY DETECTION
else if (mode=="f")
{
if (debug) std::cerr << "============================================\n";
if (debug) std::cerr << "ANNOTATING INDEL FUZZILY\n";
//1. selects candidate region by fuzzy left and right alignment
cre->pick_candidate_region(h, v, variant, EXACT_LEFT_RIGHT_ALIGNMENT);
//2. detect candidate motifs from a reference sequence
cmp->generate_candidate_motifs(h, v, variant);
if (!cmp->next_motif(h, v, variant))
{
std::cerr << "oops, no candidate motif for next step\n";
}
//3. evaluate reference length
fd->detect_flanks(h, v, variant, FRAHMM);
//introduce reiteration based on concordance and exact concordance.
if (debug) std::cerr << "============================================\n";
return;
}
}
}
/**
* Detects near by STRs.
*/
bool VariantManip::detect_str(bcf_hdr_t *h, bcf1_t *v, Variant& variant)
{
return detect_str(bcf_get_chrom(h, v), bcf_get_pos1(v), variant);
}
/**
* Inserts a record into pq.
*/
void BCFSyncedStreamReader::insert_into_pq(int32_t i, bcf1_t *v)
{
pq.push(new bcfptr(i, bcf_get_pos1(v), hdrs[i], v, sync_by_pos));
}
/**
* Classifies variants.
*/
int32_t VariantManip::classify_variant(bcf_hdr_t *h, bcf1_t *v, Variant& var)
{
bcf_unpack(v, BCF_UN_STR);
const char* chrom = bcf_get_chrom(h, v);
uint32_t pos1 = bcf_get_pos1(v);
char** allele = bcf_get_allele(v);
int32_t n_allele = bcf_get_n_allele(v);
int32_t pos0 = pos1-1;
var.ts = 0;
var.tv = 0;
var.ins = 0;
var.del = 0;
var.clear(); // this sets the type to VT_REF by default.
bool homogeneous_length = true;
char* ref = allele[0];
int32_t rlen = strlen(ref);
//if only ref allele, skip this entire for loop
for (size_t i=1; i<n_allele; ++i)
{
int32_t type = VT_REF;
//check for tags
if (strchr(allele[i],'<'))
{
size_t len = strlen(allele[i]);
if (len>=5)
{
//VN/d+
if (allele[i][0]=='<' && allele[i][1]=='V' && allele[i][2]=='N' && allele[i][len-1]=='>' )
{
for (size_t j=3; j<len-1; ++j)
{
if (allele[i][j]<'0' || allele[i][j]>'9')
{
type = VT_VNTR;
}
}
}
//VNTR
else if (len==6 &&
allele[i][0]=='<' &&
allele[i][1]=='V' && allele[i][2]=='N' && allele[i][3]=='T' && allele[i][4]=='R' &&
allele[i][5]=='>' )
{
type = VT_VNTR;
}
//ST/d+
else if (allele[i][0]=='<' && allele[i][1]=='S' && allele[i][2]=='T' && allele[i][len-1]=='>' )
{
for (size_t j=3; j<len-1; ++j)
{
if (allele[i][j]<'0' || allele[i][j]>'9')
{
type = VT_VNTR;
}
}
}
//STR
else if (len==5 &&
allele[i][0]=='<' &&
allele[i][1]=='S' && allele[i][2]=='T' && allele[i][3]=='R' &&
allele[i][4]=='>' )
{
type = VT_VNTR;
}
}
if (type==VT_VNTR)
{
type = VT_VNTR;
var.type |= type;
var.alleles.push_back(Allele(type));
}
else
{
type = VT_SV;
var.type |= type;
std::string sv_type(allele[i]);
var.alleles.push_back(Allele(type, sv_type));
}
}
else if (allele[i][0]=='.' || strcmp(allele[i],allele[0])==0)
{
type = VT_REF;
}
else
{
kstring_t REF = {0,0,0};
kstring_t ALT = {0,0,0};
ref = allele[0];
char* alt = allele[i];
int32_t alen = strlen(alt);
if (rlen!=alen)
{
homogeneous_length = false;
}
//trimming
//this is required in particular for the
//characterization of multiallelics and
//in general, any unnormalized variant
int32_t rl = rlen;
int32_t al = alen;
//trim right
while (rl!=1 && al!=1)
{
if (ref[rl-1]==alt[al-1])
{
--rl;
--al;
}
else
{
break;
}
}
//trim left
while (rl !=1 && al!=1)
{
if (ref[0]==alt[0])
{
++ref;
++alt;
--rl;
--al;
}
else
{
break;
}
}
kputsn(ref, rl, &REF);
kputsn(alt, al, &ALT);
ref = REF.s;
alt = ALT.s;
int32_t mlen = std::min(rl, al);
int32_t dlen = al-rl;
int32_t diff = 0;
int32_t ts = 0;
int32_t tv = 0;
if (mlen==1 && dlen)
{
char ls, le, ss;
if (rl>al)
{
ls = ref[0];
le = ref[rl-1];
ss = alt[0];
}
else
{
ls = alt[0];
le = alt[al-1];
ss = ref[0];
}
if (ls!=ss && le!=ss)
{
++diff;
if ((ls=='G' && ss=='A') ||
(ls=='A' && ss=='G') ||
(ls=='C' && ss=='T') ||
(ls=='T' && ss=='C'))
{
++ts;
}
else
{
++tv;
}
}
}
else
{
for (int32_t j=0; j<mlen; ++j)
{
if (ref[j]!=alt[j])
{
++diff;
if ((ref[j]=='G' && alt[j]=='A') ||
(ref[j]=='A' && alt[j]=='G') ||
(ref[j]=='C' && alt[j]=='T') ||
(ref[j]=='T' && alt[j]=='C'))
{
++ts;
}
else
{
++tv;
}
}
}
}
//substitution variants
if (mlen==diff)
{
type |= mlen==1 ? VT_SNP : VT_MNP;
}
//indel variants
if (dlen)
{
type |= VT_INDEL;
}
//clumped SNPs and MNPs
if (diff && diff < mlen) //internal gaps
{
type |= VT_CLUMPED;
}
var.type |= type;
var.alleles.push_back(Allele(type, diff, alen, dlen, mlen, ts, tv));
var.ts += ts;
var.tv += tv;
var.ins = dlen>0?1:0;
var.del = dlen<0?1:0;
if (REF.m) free(REF.s);
if (ALT.m) free(ALT.s);
}
}
if (var.type==VT_VNTR)
{
bcf_unpack(v, BCF_UN_INFO);
//populate motif, motif len etc. etc.
// char* str = NULL;
// int32_t n = 0;
// int32_t ret = bcf_get_info_string(h, v, "MOTIF", &str, &n);
// if (ret>0)
// {
// var.motif = std::string(str);
// var.mlen = var.motif.size();
// }
// ret = bcf_get_info_string(h, v, "RU", &str, &n);
// if (ret>0)
// {
// var.ru = std::string(str);
// var.mlen = var.ru.size();
// }
// if (n) free(str);
//
// int32_t* no = NULL;
// n = 0;
// ret = bcf_get_info_int32(h, v, "RL", &no, &n);
// if (ret>0) var.rlen = *no;
// if (n) free(no);
//
// int32_t* fl = NULL;
// n = 0;
// ret = bcf_get_info_int32(h, v, "REF", &fl, &n);
// if (ret>0) var.rcn = *fl;
// if (n) free(fl);
}
//additionally define MNPs by length of all alleles
if (!(var.type&(VT_VNTR|VT_SV)) && var.type!=VT_REF)
{
if (homogeneous_length && rlen>1 && n_allele>1)
{
var.type |= VT_MNP;
}
}
return var.type;
}
/**
* Constructor.
* @v - VCF record.
*/
GenotypingRecord::GenotypingRecord(bcf_hdr_t *h, bcf1_t *v, int32_t vtype)
{
clear();
this->h = h;
this->v = v;
rid = bcf_get_rid(v);
pos1 = bcf_get_pos1(v);
this->vtype = vtype;
int32_t n_allele = bcf_get_n_allele(v);
if (vtype==VT_SNP && n_allele==2)
{
rid = bcf_get_rid(v);
beg1 = bcf_get_pos1(v);
end1 = beg1;
}
else if (vtype==VT_INDEL && bcf_get_n_allele(v)==2)
{
rid = bcf_get_rid(v);
char** alleles = bcf_get_allele(v);
dlen = strlen(alleles[1])-strlen(alleles[0]);
len = abs(dlen);
int32_t *flanks = NULL;
int32_t n = 0;
if (bcf_get_info_int32(h, v, "FLANKS", &flanks, &n)>0)
{
lend1 = flanks[0];
rbeg1 = flanks[1];
free(flanks);
}
else
{
lend1 = bcf_get_pos1(v) - 1;
rbeg1 = bcf_get_end_pos1(v) + 1;
}
int32_t *fuzzy_flanks = NULL;
n = 0;
if (bcf_get_info_int32(h, v, "FZ_FLANKS", &fuzzy_flanks, &n)>0)
{
fuzzy_lend1 = fuzzy_flanks[0];
fuzzy_rbeg1 = fuzzy_flanks[1];
free(fuzzy_flanks);
}
else
{
fuzzy_lend1 = bcf_get_pos1(v) - 1;
fuzzy_rbeg1 = bcf_get_end_pos1(v) + 1;
}
beg1 = std::min(lend1-2, fuzzy_lend1-2);
end1 = std::max(rbeg1+2, fuzzy_rbeg1+2);
//construct alleles
//get reference sequence
// char* ref_seq = NULL;
// int32_t ref_len = 0;
//// ref_seq = faidx_fetch_seq(fai, bcf_get_chrom(h,v), lend1+1-1, rbeg1-1-1, &ref_len);
//
// for (uint32_t i=0; i<n_allele; ++i)
// {
//
// }
// for ()
// {
// }
//
if (dlen>0)
{
indel.append(&alleles[1][1]);
}
else
{
indel.append(&alleles[0][1]);
}
}
else if (vtype==VT_VNTR)
{
rid = bcf_get_rid(v);
beg1 = bcf_get_pos1(v) - 1;
end1 = bcf_get_end_pos1(v) + 1;
char *motif = NULL;
int32_t n = 0;
if (bcf_get_info_string(h, v, "MOTIF", &motif, &n)>0)
{
this->motif.assign(motif);
free(motif);
}
}
}
