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NCBI C++ ToolKit: src/algo/gnomon/variations.cpp Source File

indels.reserve(sam_indels.size());

(indl->GetInDelV().empty())

insertlen = indl->Len();

deletion = indl->GetInDelV();

}

(loc+insertlen == indl->Loc()) {

(indl->GetInDelV().empty())

insertlen += indl->Len();

deletion += indl->GetInDelV();

indels.push_back(

(loc, insertlen));

(!deletion.empty())

indels.push_back(

(loc+insertlen,(

)deletion.size(),deletion));

(indl->GetInDelV().empty()) {

insertlen = indl->Len();

deletion = indl->GetInDelV();

indels.push_back(

(loc, insertlen));

(!deletion.empty())

indels.push_back(

(loc+insertlen,(

)deletion.size(),deletion));

m_weight(

), m_ident(ident), m_range(range) {

first_element = cigar.find_first_not_of(

);

(first_element != string::npos && cigar[first_element] ==

)

cigar[first_element] =

;

(cigar[cigar.size()-1] ==

)

cigar[cigar.size()-1] =

;

istringstream istr_cigar(cigar);

& seq = ad.

;

(istr_cigar >>

>> c) {

(

= 0;

<

; ++

) {

(seq[seq_pos] != contig[gstop]) {

sam_indels.push_back(

(gstop+1,1,seq.substr(seq_pos,1)));

seq_pos +=

; align_len +=

; gstop +=

;

seq_pos +=

; align_len +=

; gstop +=

;

seq_pos +=

; align_len +=

;

align_len +=

; gstop +=

;

runtime_error(

);

= (double)matches/align_len;

seq = contig.substr(

,

-

);

seq += contig.substr(

,

-

);

length (sv.

());

(

= 0;

< (

)align.

().size(); ++

) {

(

->IntersectingWith(exon_lim.

(), exon_lim.

()))

corrections.push_back(*

);

(!corrections.empty() && corrections.front().Loc() == exon_lim.

()) {

exon_lim.

(corrections.front().InDelEnd());

corrections.erase(corrections.begin());

(!corrections.empty() && corrections.back().InDelEnd() == exon_lim.

()+1) {

exon_lim.

(corrections.back().Loc()-1);

corrections.pop_back();

errors += indl->Len();

(indl->IsDeletion())

align_len += indl->Len();

(!indl->IsInsertion()) {

s = indl->GetInDelV();

ns +=

(s.begin(), s.end(),

);

(indl->IsMismatch()) {

indels.push_back(

(indl->Loc(), indl->Len()));

indels.push_back(

(indl->InDelEnd(), indl->Len(), indl->GetInDelV()));

}

(indl->IsInsertion()) {

indels.push_back(

(indl->Loc(), indl->Len()));

indels.push_back(

(indl->Loc(), indl->Len(), indl->GetInDelV()));

map<TSignedSeqRange,TSIMap> variations;

list<TSignedSeqRange> confirmed_ranges;

(list<TSignedSeqRange>,

, confirmed_ranges) {

aligns.back().SetTargetId(*

);

& seq_counts =

->second;

(!correctionsonly) {

& seq = j->first;

= j->second;

aligns.back().SetTargetId(*

);

selected_weight = 0;

& seq = j->first;

= j->second;

(dist < selected_dist || (dist == selected_dist &&

> selected_weight)) {

selected_cigar = cigar;

selected_dist = dist;

selected_weight =

;

.SetWeight(selected_weight);

aligns.back().SetTargetId(*

);

read = al->TranscriptSeq(

);

base =

.substr(al->Limits().GetFrom(),al->Limits().GetLength());

all_alignsp.push_back(&(*al));

(

ir = 0; ir < (

)all_alignsp.size(); ++ir) {

(

ir = 0; ir < reads_num; ++ir) {

(

p =

[ir]->Limits().GetFrom(); p <=

[ir]->Limits().GetTo(); ++p)

((*indl)->IsDeletion()) {

= (*indl)->Len();

(indl != indels.begin()) {

TLiteInDelsP::const_iterator

= indl-1;

((*prev)->IsInsertion() && (*prev)->Loc()+(*prev)->Len() == (*indl)->Loc())

-= (*prev)->Len();

deletion_len[(*indl)->Loc()] =

(

, deletion_len[(*indl)->Loc()]);

contigp =

->first;

(del != deletion_len.

() && contigp == del->first) {

del_len = (del++)->second;

(

= 0;

< del_len; ++

)

alignp = contigp+shift;

total_deletion_len = 0;

total_deletion_len +=

->second;

.reserve(contig_len+total_deletion_len);

(

p = 0; p < contig_len; ++p) {

(rslt != deletion_len.

()) {

= rslt->second;

(

p = 0; p < (

)

.length(); ++p) {

(

[p] ==

) {

(

< reads_num &&

[

]+dashes == p)

(

ir = 0; ir < reads_num; ++ir) {

list<pair<int,int> > indel_pos_length;

((*indl)->IsDeletion()) {

(!indel_pos_length.empty() && indel_pos_length.back().first-indel_pos_length.back().second == (*indl)->Loc()) {

(indel_pos_length.back().second < 0);

new_len = indel_pos_length.back().second+(*indl)->Len();

indel_pos_length.back().second = new_len;

}

(new_len > 0) {

indel_pos_length.back().first = (*indl)->Loc();

indel_pos_length.back().second = new_len;

indel_pos_length.pop_back();

indel_pos_length.push_back(make_pair((*indl)->Loc(), (*indl)->Len()));

indel_pos_length.push_back(make_pair((*indl)->Loc(), -(*indl)->Len()));

list<pair<int,int> >::iterator indl = indel_pos_length.begin();

(

p = start+1; p <

&& p < start+(

)read.size(); ) {

(

[p] ==

) {

insertp = p-start;

(indl != indel_pos_length.end() && indl->second > 0 &&

[indl->first] == p) {

read.insert(insertp,

,

);

}

(indl != indel_pos_length.end() && indl->second < 0 &&

[indl->first] == p) {

read.

(p-start,

,

);

(

ir = 0; ir < reads_num; ++ir) {

& read =

[ir];

(

p = legit_range.

(); p <= legit_range.

(); ++p) {

c = read[p-start];

vector<const CLiteAlign*> all_alignsp;

aligns_size = (

)all_alignsp.size();

(

(read_range,two_word_range)) {

seq_counts[read_seq] += w;

& read =

[ir];

end = start+(

)read.size()-1;

first_legit_match = start;

(shift <

|| (first_legit_match <= end && (read[first_legit_match-start] ==

|| read[first_legit_match-start] !=

[first_legit_match]))) {

(

[first_legit_match] !=

)

last_legit_match = end;

(shift <

|| (last_legit_match >= start && (read[last_legit_match-start] ==

|| read[last_legit_match-start] !=

[last_legit_match]))) {

(

[last_legit_match] !=

)

maximal_bases(

.size(),

);

(

p = 0; p < (

)

.size(); ++p) {

maximal_bases[p] =

;

(

->second > w) {

maximal_bases[p] =

;

maximal_bases[p] = c;

prev_strong_word;

(

p = 0; p < (

)maximal_bases.size(); ) {

(maximal_bases[p] ==

) {

(strong_word_range.

())

p = strong_word_range.

()+1;

same_as_contig =

;

(

pos = strong_word_range.

(); pos <= strong_word_range.

() && same_as_contig; ++pos)

same_as_contig = (maximal_bases[pos] ==

[pos]);

(!same_as_contig) {

}

(first_gap >= 0) {

there_is_weak_range = prev_strong_word_range.

() && prev_strong_word_range.

()+1 < strong_word_range.

();

(there_is_weak_range) {

accepted_cross = 0;

(prev_strong_word_range, prev_strong_word, strong_word_range, strong_word, seq_counts, total_cross, accepted_cross);

(!seq_counts.

()) {

(

->second > most_frequent_variant->second)

most_frequent_variant =

;

var_seq = prev_strong_word+it->first+strong_word;

var_counts[var_seq] = it->second;

(!var_counts.

()) {

base_posr = swordr;

(var_counts.

() == 1 && var_counts.

()->first ==

.substr(base_posl,base_posr-base_posl+1)) {

confirmed_ranges.back().SetTo(base_posr);

there_is_weak_range =

;

variations.insert(var);

prev_strong_word_range = strong_word_range;

prev_strong_word = strong_word;

(confirmed_ranges.empty() || there_is_weak_range || confirmed_ranges.back().GetTo()+1 < swordl)

confirmed_ranges.back().

(swordr);

& read =

[ir];

stop = start+(

)read.size()-1;

(read[

-start] !=

)

read_word.push_back(read[

-start]);

(

= word_range.

();

<= word_range.

(); ++

) {

read_word.push_back(

[

]);

(

(legit_range,word_range)) {

(word == read_word)

(nextp < (

)maximal_bases.size()) {

word_start = nextp;

word_end = nextp;

low_complexity =

;

( ; word_end < (

)maximal_bases.size() && (

)word.size() <

&& maximal_bases[word_end] !=

; ++word_end) {

(maximal_bases[word_end] !=

) {

word.push_back(

(maximal_bases[word_end]));

(

(maximal_bases[word_end]))

low_complexity =

;

((

)word.size() <

) {

(maximal_bases[word_end] ==

) {

(first_gap < 0) first_gap = word_end;

(!low_complexity &&

(word_range,word)) {

strong_word_range = word_range;

= args[

].AsInteger();

= args[

].AsInteger();

int Distance(const char *query, const char *subject) const

TInDels GetInDels(int sstart, const char *const query, const char *subject) const

const TExons & Exons() const

TSignedSeqRange Limits() const

CLiteAlign(TSignedSeqRange range, const TLiteInDels &indels, set< CLiteIndel > &indel_holder, double weight, double ident)

string TranscriptSeq(const string &contig) const

void InsertDashesInBase()

void InsertDashesInReads()

static void SetupArgDescriptions(CArgDescriptions *arg_desc)

int m_min_abs_support_for_variant

bool CheckWord(const TSignedSeqRange &word_range, const string &word)

void SelectAligns(vector< const CLiteAlign * > &all_alignsp)

string EmitSequenceFromBase(const TSignedSeqRange &word_range)

set< CLiteIndel > m_indel_holder

void ProcessArgs(const CArgs &args)

map< int, TCharIntMap > m_counts

void AddAlignment(const SSamData &align)

TAlignModelList GetVariationAlignList(bool correctionsonly)

TSignedSeqRange LegitRange(int ir)

void SetGenomic(const CConstRef< CSeq_id > &seqid, CScope &scope)

vector< const CLiteAlign * > m_alignsp

TIntMap m_contig_to_align

double m_min_rel_support_for_variant

int FindNextStrongWord(int nextp, const string &maximal_bases, string &strong_word, TSignedSeqRange &strong_word_range, int &first_gap)

string EmitSequenceFromRead(int ir, const TSignedSeqRange &word_range)

void SeqCountsBetweenTwoStrongWords(const TSignedSeqRange &prev_strong_word_range, const string &prev_strong_word, const TSignedSeqRange &strong_word_range, const string &strong_word, TSIMap &seq_counts, int &total_cross, int &accepted_cross)

void Variations(map< TSignedSeqRange, TSIMap > &variations, list< TSignedSeqRange > &confirmed_ranges)

double m_strong_consensus

void PrepareReads(const vector< const CLiteAlign * > &all_alignsp)

TIntMap m_align_to_contig

container_type::const_iterator const_iterator

container_type::iterator iterator

const_iterator begin() const

const_iterator end() const

iterator_bool insert(const value_type &val)

container_type::value_type value_type

const_iterator find(const key_type &key) const

iterator_bool insert(const value_type &val)

static int base_length[29]

static DLIST_TYPE *DLIST_NAME() prev(DLIST_LIST_TYPE *list, DLIST_TYPE *item)

double Entropy(const string &seq)

CCigar GlbAlign(const char *query, int querylen, const char *subject, int subjectlen, int gopen, int gapextend, const char delta[256][256])

list< CAlignModel > TAlignModelList

bool Include(TSignedSeqRange big, TSignedSeqRange small)

vector< CInDelInfo > TInDels

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

int TSignedSeqPos

Type for signed sequence position.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

void AddDefaultKey(const string &name, const string &synopsis, const string &comment, EType type, const string &default_value, TFlags flags=0, const string &env_var=kEmptyStr, const char *display_value=nullptr)

Add description for optional key with default value.

@ eDouble

Convertible into a floating point number (double)

@ eInteger

Convertible into an integer number (int or Int8)

string GetSeqIdString(bool with_version=false) const

Return seqid string with optional version for text seqid type.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

CSeqVector GetSeqVector(EVectorCoding coding, ENa_strand strand=eNa_strand_plus) const

Get sequence: Iupacna or Iupacaa if use_iupac_coding is true.

@ eCoding_Iupac

Set coding to printable coding (Iupacna or Iupacaa)

void GetSeqData(TSeqPos start, TSeqPos stop, string &buffer) const

Fill the buffer string with the sequence data for the interval [start, stop).

position_type GetLength(void) const

bool NotEmpty(void) const

static TThisType GetEmpty(void)

CRange< TSignedSeqPos > TSignedSeqRange

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

static string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

void SetFrom(TFrom value)

Assign a value to From data member.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

void SetTo(TTo value)

Assign a value to To data member.

unsigned int

A callback function used to compare two keys in a database.

constexpr auto sort(_Init &&init)

const struct ncbi::grid::netcache::search::fields::SIZE size

Int4 delta(size_t dimension_, const Int4 *score_)

double r(size_t dimension_, const Int4 *score_, const double *prob_, double theta_)

static int match(PCRE2_SPTR start_eptr, PCRE2_SPTR start_ecode, uint16_t top_bracket, PCRE2_SIZE frame_size, pcre2_match_data *match_data, match_block *mb)

static SLJIT_INLINE sljit_ins l(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

TLiteInDels GroupInDels(const TLiteInDels &sam_indels)

#define ENTROPY_LEVEL_FOR_ALIGNS

vector< const CLiteIndel * > TLiteInDelsP

vector< CLiteIndel > TLiteInDels

list< CLiteAlign > TLiteAlignList

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