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NCBI C++ ToolKit: src/app/gnomon/exon_selector.cpp Source File

list<pair<int, string>>

;

list<pair<int, char>>

;

<

T>

(!

.empty() &&

.front().first < 0)

(

.front().second ==

)

(!

.empty() &&

.back().first < 0)

(

.back().second ==

)

(

& cigar_string,

& MD_tag,

qfrom,

sfrom);

(!cigar_string.empty()) {

c = cigar_string[

];

(c !=

&& c !=

)

cigar_string.erase(0,

+1);

}

(c ==

) {

}

(c ==

|| c ==

|| c ==

) {

(

(MD_tag.front())) {

m = stoi(MD_tag, &idx);

(e.

.empty() || e.

.back().first <= 0)

MD_tag.erase(0, idx);

MD_tag = to_string(m-

)+MD_tag;

(e.

.empty() || e.

.back().first != 0)

e.

.emplace_back(0, MD_tag.substr(0, 1));

e.

.back().second += MD_tag.front();

}

(c ==

) {

}

(c ==

) {

(MD_tag.front() ==

) {

del = MD_tag.substr(1,

);

MD_tag.erase(0,

+1);

del = MD_tag.substr(0,

);

MD_tag.erase(0,

);

(e.

.empty() || e.

.back().first >= 0)

e.

.emplace_back(-1, del);

e.

.back().second += del;

cerr <<

<< endl;

length = seq.size();

: tA += 1;

;

: tC += 1;

;

: tG += 1;

;

: tT += 1;

;

entropy = -(tA*

(tA/length)+tC*

(tC/length)+tG*

(tG/length)+tT*

(tT/length))/(length*

(4.));

(

= 11;

< (

)tags.size() && (MD_tag.empty() || tstrand.empty()); ++

) {

&

= tags[

];

vector<string> fields;

(fields.size() != 3)

(fields[0] ==

&& fields[1] ==

)

((fields[0] ==

|| fields[0] ==

|| fields[0] ==

) && fields[1] ==

)

(MD_tag.empty()) {

cerr <<

<< endl;

cigar_string = tags[5];

sfrom = std::stoi(tags[3])-1;

(!cigar_string.empty()) {

align_exons.push_back(

(cigar_string, MD_tag, qfrom, sfrom));

align_exons.back().m_tstrand = tstrand;

qfrom = align_exons.back().m_qto+1;

sfrom = align_exons.back().m_sto+1;

& seq = tags[9];

(!align_exons.empty() &&

(seq.substr(align_exons.front().m_qfrom, align_exons.front().m_qto-align_exons.front().m_qfrom+1)) <

)

align_exons.erase(align_exons.begin());

(!align_exons.empty() &&

(seq.substr(align_exons.back().m_qfrom, align_exons.back().m_qto-align_exons.back().m_qfrom+1)) <

)

align_exons.pop_back();

exons.insert(exons.end(), align_exons.begin(), align_exons.end());

name+

+to_string(

);

(

& name,

&

) {

name+

+

;

name+

+

;

fields[0] = compart.

;

flag = 1+2+strand*16+(1-strand)*32+(mate+1)*64;

fields[1] = to_string(flag);

fields[3] = to_string(compart.

.first+1);

fields[8] = to_string(span);

fields[9] = compart.

;

fields.push_back(

(

, compart.

));

fields.push_back(

(

, compart.

));

fields.push_back(

(

,

));

fields.push_back(

(

, index));

(

= 1;

< fields.size(); ++

)

cout <<

<< fields[

];

fields[0] = compart.

;

flag = strand*16;

flag += 1+8+(mate+1)*64;

fields[1] = to_string(flag);

fields[3] = to_string(compart.

.first+1);

fields[9] = compart.

;

fields.push_back(

(

, compart.

));

fields.push_back(

(

, compart.

));

fields.push_back(

(

, compart.

));

fields.push_back(

(

,

));

fields.push_back(

(

, index));

(

= 1;

< fields.size(); ++

)

cout <<

<< fields[

];

paired =

;

(

mate = 0; mate < 2; ++mate) {

(

strand = 0; strand < 2; ++strand) {

(

& compart : compact_aligns) {

(compart.m_matep !=

)

& contig = contig_aligns.first;

(

mate = 0; mate < 2; ++mate) {

& left_aligns = contig_aligns.second[mate][strand];

(

& compart : left_aligns) {

(compart, contig, mate, strand, mate_count[0], ++index,

);

(*compart.m_matep, contig, 1-mate, 1-strand, mate_count[0], index,

);

& contig = contig_aligns.first;

(

mate = 0; mate < 2; ++mate) {

(

strand = 0; strand < 2; ++strand) {

(

& compart : compact_aligns)

(compart, contig, mate, strand, mate_count[mate], ++mate_index[mate]);

(

mate = 0; mate < 2; ++mate) {

(

strand = 0; strand < 2; ++strand) {

(

& align : compact_aligns) {

mate_score[mate] =

(mate_score[mate], align.m_score);

(align.m_matep !=

)

pair_score =

(pair_score, align.m_score+align.m_matep->m_score);

compact_aligns.remove_if([](

&

){

!

.m_above_thresholds; });

paired = pair_score >=

(mate_score[0], mate_score[1]);

(

mate = 0; mate < 2; ++mate) {

(

strand = 0; strand < 2; ++strand) {

(

.m_matep ==

)

;

(

.m_score+

.m_matep->m_score == pair_score)

;

.m_matep->m_matep =

;

; });

compact_aligns.remove_if([&](

&

){

.m_matep =

;

.m_score != mate_score[mate]; });

vector<pair<int,int>> left_introns;

vector<pair<int,int>> right_introns;

(

= 1;

< left.

.size(); ++

) {

left_introns.emplace_back(left.

[

-1].m_sto+1, left.

[

].m_sfrom-1);

(

= 1;

< right.

.size(); ++

) {

right_introns.emplace_back(right.

[

-1].m_sto+1, right.

[

].m_sfrom-1);

left_introns == right_introns;

(

left_mate = 0; left_mate < 2; ++left_mate) {

right_mate = 1-left_mate;

right_strand = 1;

& left_aligns = contig_aligns.second[left_mate][left_strand];

& right_aligns = contig_aligns.second[right_mate][right_strand];

iright = right_aligns.begin();

(

ileft = left_aligns.begin(); ileft != left_aligns.end() && iright != right_aligns.end(); ++ileft) {

(iright != right_aligns.end() && iright->m_range.second < ileft->m_range.second)

(iright == right_aligns.end())

inext =

(ileft);

(inext != left_aligns.end() && inext->m_range.second < iright->m_range.second)

ileft->m_matep = &(*iright);

iright->m_matep = &(*ileft);

& contig = contig_aligns.first;

(

mate = 0; mate < 2; ++mate) {

(

strand = 0; strand < 2; ++strand) {

& orig_aligns = contig_aligns.second[mate][strand];

(orig_aligns.empty())

& read = orig_aligns.front()[0];

paired_read = stoi(orig_aligns.front()[1])&1;

& rseq = orig_aligns.front()[9];

read_len = rseq.size();

(

& oa : orig_aligns)

(exons.begin(), exons.end(), [](

& e1,

& e2){

if(e1.m_sto != e2.m_sto)

return e1.m_sto > e2.m_sto;

if(e1.m_sfrom != e2.m_sfrom)

return e1.m_sfrom < e2.m_sfrom;

if(e1.m_qto != e2.m_qto)

return e1.m_qto > e2.m_qto;

if(e1.m_qfrom != e2.m_qfrom)

return e1.m_qfrom < e2.m_qfrom;

if(e1.m_score != e2.m_score)

return e1.m_score > e2.m_score;

return e1.m_cigar < e2.m_cigar; });

tail = unique(exons.begin(), exons.end(), [](

& e1,

& e2){

return e1.m_sfrom == e2.m_sfrom && e1.m_sto == e2.m_sto && e1.m_qfrom == e2.m_qfrom && e1.m_qto == e2.m_qto; });

exons.erase(tail, exons.end());

(

= exons.begin();

!= exons.end(); ++

) {

(

->m_type ==

||

->m_qfrom > 10)

(

j =

(

); j != exons.end() && j->m_sto ==

->m_sto && j->m_qto ==

->m_qto; ++j)

exons.erase(

(exons.begin(), exons.end(), [](

& e){ return e.m_type == eBogus; }), exons.end());

(exons.begin(), exons.end(), [](

& e1,

& e2){

if(e1.m_sfrom != e2.m_sfrom)

return e1.m_sfrom < e2.m_sfrom;

if(e1.m_sto != e2.m_sto)

return e1.m_sto > e2.m_sto;

if(e1.m_qfrom != e2.m_qfrom)

return e1.m_qfrom < e2.m_qfrom;

return e1.m_qto > e2.m_qto; });

(

= exons.begin();

!= exons.end(); ++

) {

(

->m_type ==

|| read_len-

->m_qto-1 > 10)

(

j =

(

); j != exons.end() && j->m_sfrom ==

->m_sfrom && j->m_qfrom ==

->m_qfrom; ++j)

exons.erase(

(exons.begin(), exons.end(), [](

& e){ return e.m_type == eBogus; }), exons.end());

(

j =

(

); j != exons.end() && j->m_sfrom <=

->m_sto && !

; ++j) {

soverlap =

->m_sto-j->m_sfrom+1;

slen =

(

->m_sto-

->m_sfrom+1, j->m_sto-j->m_sfrom+1);

qoverlap =

->m_qto-j->m_qfrom+1;

qlen =

(

->m_qto-

->m_qfrom+1, j->m_qto-j->m_qfrom+1);

(soverlap > 0.5*slen && qoverlap < 0.1*qlen)

(

& e : exons) {

ident = double(matches)/align_len;

cov = double(qmax-qmin+1)/read_len;

log2factor = 0.25;

compart_penalty = ident*cov*

*read_len + 0.5;

exon_num = exons.size();

best_index = exon_num-1;

(

= exon_num-1;

>= 0; --

) {

& ei = exons[

];

iscore = ei.m_matches;

ei.m_chain_score = iscore;

(

j =

+1; j < exon_num; ++j) {

& ej = exons[j];

ijscore = ej.m_chain_score+iscore;

(ej.m_sfrom <= ei.m_sto)

overlap = ei.m_qto+1-ej.m_qfrom;

intron = ej.m_sfrom-ei.m_sto-1;

(overlap == 0 && intron > 20 && intron <=

) {

intron_len = ej.m_intron_len+intron;

deltas = score-ei.m_chain_score-log2factor*

((intron_len+1)/(ei.m_intron_len+1));

ei.m_chain_score = score;

ei.m_intron_len = intron_len;

overlap_penalty = 0;

overlap_penalty =

(2,

(ident*

(overlap)+0.5));

score = ijscore-overlap_penalty;

intron_len = ej.m_intron_len;

deltas = score-ei.m_chain_score-log2factor*

((intron_len+1)/(ei.m_intron_len+1));

ei.m_chain_score = score;

ei.m_intron_len = intron_len+intron;

}

(overlap > 0 && overlap < 10 && intron <=

) {

overlap_penalty = 0;

s = ei.m_script.size()-1;

(s >= 0 &&

> 0) {

(ei.m_script[s] ==

)

(ei.m_script[s] !=

)

(s < (

)ej.m_script.size() &&

> 0) {

(ej.m_script[s] ==

)

(ej.m_script[s] !=

)

overlap_penalty =

(2, overlap_penalty);

score = ijscore-overlap_penalty;

intron_len = ej.m_intron_len+intron;

deltas = score-ei.m_chain_score-log2factor*

((intron_len+1)/(ei.m_intron_len+1));

ei.m_chain_score = score;

ei.m_intron_len = intron_len;

score = ijscore-compart_penalty;

intron_len = ej.m_intron_len;

deltas = score-ei.m_chain_score-log2factor*

((intron_len+1)/(ei.m_intron_len+1));

ei.m_chain_score = score;

ei.m_intron_len = intron_len;

deltas = ei.m_chain_score-exons[best_index].m_chain_score-log2factor*

((

)(ei.m_intron_len+1)/(exons[best_index].m_intron_len+1));

(

* p = &exons[best_index]; p !=

; p = p->

) {

(compartments.empty() || compartments.back().m_exons.back().m_type !=

)

compartments.emplace_back();

compartments.back().m_exons.push_back(*p);

(

iloop = compartments.begin(); iloop != compartments.end(); ) {

(!it->m_exons.empty()) {

(it->m_exons.front().m_align_len == 0)

it->m_exons.erase(it->m_exons.begin());

(!it->m_exons.empty()) {

(it->m_exons.back().m_align_len == 0)

it->m_exons.pop_back();

(it->m_exons.empty())

compartments.erase(it);

(

& compartment : compartments) {

& cigar = compartment.m_cigar;

(compartment.m_exons.front().m_qfrom > 0)

cigar += to_string(compartment.m_exons.front().m_qfrom)+

;

& tstrand = compartment.m_tstrand;

tstrand = compartment.m_exons.front().m_tstrand;

(

= 0;

< (

)compartment.m_exons.size(); ++

) {

& e = compartment.m_exons[

];

intron = compartment.m_exons[

].m_sfrom-compartment.m_exons[

-1].m_sto-1;

cigar += to_string(intron)+

;

(

& elem : compartment.m_exons[

].m_cigar)

cigar += to_string(elem.first)+elem.second;

(!tstrand.empty() && e.

!= tstrand)

md.insert(md.end(), e.

.begin(), e.

.end());

tail = rseq.size()-compartment.m_exons.back().m_qto-1;

cigar += to_string(tail)+

;

(compartment.m_exons.size() == 1)

& md_tag = compartment.m_md;

(

= md.begin();

!= md.end(); ++

) {

(

j =

(

); j != md.end(); j =

(

)) {

(

->first > 0 && j->first > 0)

->first += j->first;

(

->first == j->first)

->second += j->second;

md_tag += to_string(

->first);

(

->first == 0)

md_tag +=

->second;

md_tag +=

+

->second;

compartment.m_range.first = compartment.m_exons.front().m_sfrom;

compartment.m_range.second = compartment.m_exons.back().m_sto;

read_span = compartment.m_exons.back().m_qto-compartment.m_exons.front().m_qfrom+1;

compartment.m_read = read;

compartment.m_rseq = rseq;

compartment.m_paired_read = paired_read;

list<TAlignCompartments::iterator> erased;

TAlignCompartments::reverse_iterator keeper = compartments.rbegin();

(

=

(keeper);

!= compartments.rend(); ++

) {

(

->m_score > keeper->m_score) {

erased.push_back(

(keeper.base()));

erased.push_back(

(

.base()));

(

: erased)

compartments.erase(

);

argdescr->SetUsageContext(

().GetProgramBasename(),

);

argdescr->AddDefaultKey (

,

,

,

,

);

argdescr->AddDefaultKey(

,

,

,

,

);

argdescr->AddFlag(

,

);

argdescr->AddFlag(

,

);

argdescr->AddOptionalKey(

,

,

,

);

argdescr->AddOptionalKey(

,

,

,

);

argdescr->AddOptionalKey(

,

,

,

);

argdescr->AddFlag(

,

);

argdescr->AddFlag(

,

);

argdescr->SetConstraint(

, constrain01);

argdescr->SetConstraint(

, constrain01);

argdescr->SetConstraint(

, constrain01);

argdescr->SetConstraint(

, constrain_minqlen);

argdescr->SetConstraint(

, constrain_score);

argdescr->SetConstraint(

, constrain_score);

argdescr->SetConstraint(

, constrain_score);

argdescr->SetConstraint(

, constrain_score);

argdescr->SetConstraint(

, constrain_score);

argdescr->SetConstraint(

, constrain_score);

= args[

].AsDouble();

= !args[

];

(args[

])

(args[

] && args[

]) {

cerr <<

<< endl;

(args[

] || !args[

]) {

(args[

]) {

(args[

])

(args[

])

(args[

])

(args[

])

(args[

])

(args[

])

(args[

])

paired_read =

;

(getline(cin, line)) {

(line[0] ==

) {

cout << line << endl;

vector<string> fields;

read = fields[0];

(

&& !previous_reads.

(read_old).second) {

cerr <<

<< endl;

paired_read = stoi(fields[1])&1;

contig = fields[2];

flag = std::stoi(fields[1]);

strand = (flag&16) ? 1 : 0;

mate = (flag&128) ? 1 : 0;

(

&& !previous_reads.

(read_old).second) {

cerr <<

<< endl;

(

argc,

* argv[])

void remove_if(Container &c, Predicate *__pred)

virtual void Init()

Initialize the application.

bool CompatiblePair(const AlignCompartment &left, const AlignCompartment &right)

map< string, TMatrix< TAlignCompartments > > m_compartments

list< pair< int, char > > TCigar

void FormatSingle(AlignCompartment &compart, const string &contig, int mate, int strand, int count, int index)

list< TSamFields > TSplitAligns

map< string, TMatrix< TSplitAligns > > m_read_aligns

void ExtractExonsFromSAM(const TSamFields &tags, TExons &exons)

Exon GetNextExon(string &cigar_string, string &MD_tag, int qfrom, int sfrom)

virtual int Run()

Run the application.

list< pair< int, string > > TMDTag

vector< string > TSamFields

void SelectBestLocations()

list< AlignCompartment > TAlignCompartments

void FormatPaired(AlignCompartment &compart, const string &contig, int mate, int strand, int count, int index, bool left)

iterator_bool insert(const value_type &val)

double Entropy(const string &seq)

string Tag(const string &name, int value)

int main(int argc, const char *argv[])

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

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

virtual const CArgs & GetArgs(void) const

Get parsed command line arguments.

int AppMain(int argc, const char *const *argv, const char *const *envp=0, EAppDiagStream diag=eDS_Default, const char *conf=NcbiEmptyCStr, const string &name=NcbiEmptyString)

Main function (entry point) for the NCBI application.

virtual void SetupArgDescriptions(CArgDescriptions *arg_desc)

Setup the command line argument descriptions.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

const CNcbiArguments & GetArguments(void) const

Get the application's cached unprocessed command-line arguments.

@ eDouble

Convertible into a floating point number (double)

@ eInteger

Convertible into an integer number (int or Int8)

EDiagSev SetDiagPostLevel(EDiagSev post_sev=eDiag_Error)

Set the threshold severity for posting the messages.

@ eDS_ToStderr

To standard error stream.

@ eDiag_Info

Informational message.

static list< string > & Split(const CTempString str, const CTempString delim, list< string > &arr, TSplitFlags flags=0, vector< SIZE_TYPE > *token_pos=NULL)

Split a string using specified delimiters.

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

const GenericPointer< typename T::ValueType > T2 value

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

Defines command line argument related classes.

Defines unified interface to application:

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

AlignCompartment * m_matep

void RemoveLeftIndels(int gapopen1, int gapextend1, int gapopen2, int gapextend2)

void RemoveRightIndels(int gapopen1, int gapextend1, int gapopen2, int gapextend2)

static Uint4 letter(char c)

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