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

<

T>

istringstream icigar(cigar_string);

(icigar >>

>> c) {

}

(c ==

) {

cigar_string = cigar_string.substr(clip_pos);

}

(c ==

|| c ==

|| c ==

) {

(

(MD_tag.front())) {

m = stoi(MD_tag, &idx);

MD_tag.erase(0, idx);

MD_tag = to_string(m-

)+MD_tag;

}

(c ==

) {

}

(c ==

) {

(MD_tag.front() ==

)

MD_tag.erase(0,

+1);

MD_tag.erase(0,

);

cerr <<

<< endl;

clip_pos = icigar.tellg();

cigar_string.clear();

(

vector<string>& tags, vector<CCompactSAMApplication::Exon>& exons) {

mismatchpenalty = 1;

log2factor = 0.25;

intron_penalty = 0;

noncanonical_penalty = 8;

gcag_penalty = 4;

atac_penalty = 8;

(

= 11;

< (

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

) {

&

= tags[

];

vector<string> fields;

(fields.size() != 3)

(fields[0] ==

&& fields[1] ==

)

(fields[0] ==

&& fields[1] ==

)

(MD_tag.empty()) {

cerr <<

<< endl;

(jM_tag.empty()) {

cerr <<

<< endl;

cigar_string = tags[5];

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

(!cigar_string.empty()) {

exons.push_back(

(cigar_string, MD_tag, qfrom, sfrom));

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

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

pair<int, int> range(exons.front().m_sfrom, exons.back().m_sto);

align_score = -

(log2factor*

(

(range.second-range.first+1))+0.5);

(

& e : exons) {

gap_len = e.m_align_len-e.m_matches-e.m_mismatches;

e.m_score = e.m_matches*matchscore-e.m_mismatches*mismatchpenalty-e.m_indels*gapopen-gap_len*gapextend;

align_score += e.m_score;

(

(exons.begin()) != exons.end()) {

vector<string> splices;

(

& spl : splices) {

align_score -= intron_penalty;

align_score -= noncanonical_penalty;

(spl ==

|| spl ==

)

align_score -= gcag_penalty;

(spl ==

|| spl ==

)

align_score -= atac_penalty;

(

= 1;

< ai.

.size(); ++

)

name+

+to_string(

);

(

& name,

&

) {

name+

+

;

<

T>

itag = find_if(fields.begin()+11, fields.end(), [&](

&

){ return tag.substr(0,2) == name; });

(itag != fields.end())

fields.push_back(

(name,

));

(vector<string>& fields,

& name) {

itag = find_if(fields.begin()+11, fields.end(), [&](

&

){ return tag.substr(0,2) == name; });

(itag != fields.end())

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

fields[1] = to_string(flag);

fields[8] = to_string(span);

mismatches += e.m_mismatches;

mismatches += e.m_mismatches;

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

fields[1] = to_string(flag);

mismatches += e.m_mismatches;

paired =

;

(

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

(

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

(

& ai : compact_aligns) {

(ai.m_matep !=

)

(

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

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

(

& ai : left_aligns) {

(ai, mate, strand, mate_count[0], ++index,

);

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

);

all_aligned = mate_count[0] > 0 && mate_count[1] > 0;

(

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

(

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

(

& ai : compact_aligns)

(ai, mate, strand, mate_count[mate], ++mate_index[mate], all_aligned);

(

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) {

compact_aligns.remove_if([&](

&

){

(

.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);

(

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

(

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

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

(compact_aligns.empty())

read_len = compact_aligns.front().m_fields[9].size();

(

& ai : compact_aligns) {

& fields = ai.m_fields;

vector<Exon> align_exons;

align_score =

(fields, align_exons);

pair<int, int> align_range(align_exons.front().m_sfrom, align_exons.back().m_sto);

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

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

(

& e : align_exons) {

matches += e.m_matches;

align_len += e.m_align_len;

ai.m_range = align_range;

ai.m_score = align_score;

ai.m_above_thresholds = above_hresholds;

(align_exons, ai.m_exons);

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

& e1,

& e2){

if(e1.m_score == e2.m_score)

return e1.m_matches > e2.m_matches;

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

tail =

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

& e){

bool r1 = !lefts.insert(e.m_sfrom).second; bool r2 = !rights.insert(e.m_sto).second;

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

(

& e : exons) {

hit->SetQueryId(readid);

hit->SetSubjId(contigid);

hit->SetQueryStart(e.m_qfrom);

hit->SetQueryStop(e.m_qto);

hit->SetSubjStart(e.m_sfrom);

hit->SetSubjStop(e.m_sto);

hit->SetLength(e.m_align_len);

hit->SetMismatches(e.m_mismatches);

hit->SetGaps(e.m_indels);

hit->SetScore(e.m_score);

hit->SetRawScore(e.m_score);

hit->SetIdentity(

(e.m_matches)/e.m_align_len);

hitrefs.push_back(hit);

TAccessor::TCoord TCoord;

TCoord penalty_bps (TCoord(

*read_len + 0.5));

TCoord min_matches (TCoord(

*read_len + 0.5));

TCoord min_singleton_matches (

(msm1, msm2));

TAccessor ca (penalty_bps, min_matches, min_singleton_matches,

);

ca.Run(hitrefs.begin(), hitrefs.end());

(

b0 (ca.GetFirst(comp)); b0 ; b0 = ca.GetNext(comp)) {

pair<int, int> range(span[2], span[3]);

selected_ranges.

(range);

compact_aligns.remove_if([&](

&

){

selected_ranges.count(

.m_range) == 0; });

(

it = compact_aligns.begin(); it != compact_aligns.end(); ++it) {

(

inext =

(it); inext != compact_aligns.end() && inext->m_range == it->m_range; )

inext = compact_aligns.erase(inext);

argdescr->SetUsageContext(

().GetProgramBasename(),

);

argdescr->AddDefaultKey(

,

,

,

argdescr->AddDefaultKey(

,

,

,

argdescr->AddDefaultKey(

,

,

,

argdescr->AddDefaultKey (

,

,

,

argdescr->AddDefaultKey(

,

,

,

argdescr->AddFlag(

,

);

argdescr->SetConstraint(

, constrain01);

argdescr->SetConstraint(

, constrain01);

argdescr->SetConstraint(

, constrain01);

argdescr->SetConstraint(

, constrain_minqlen);

= args[

].AsDouble();

= !args[

];

(getline(cin, line)) {

(line[0] ==

) {

cout << line << endl;

vector<string> fields;

read = fields[0];

(read != read_old) {

(

&& !previous_reads.

(read_old).second) {

cerr <<

<< endl;

contig = fields[2];

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

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

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

(ais.back().m_fields, fields);

(

&& !previous_reads.

(read_old).second) {

cerr <<

<< endl;

(

argc,

* argv[])

void remove_if(Container &c, Predicate *__pred)

void SelectBestLocations()

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

vector< THitRef > THitRefs

double m_min_singleton_idty

virtual int Run()

Run the application.

int m_min_singleton_idty_bps

virtual void Init()

Initialize the application.

list< AlignInfo > TAlignInfoList

map< string, TMatrix< TAlignInfoList > > m_compact_aligns

list< TSamFields > TSplitAligns

vector< string > TSamFields

iterator_bool insert(const value_type &val)

void FormatSingle(CCompactSAMApplication::AlignInfo &ai, int mate, int strand, int count, int index, bool all_aligned)

void FormatPaired(CCompactSAMApplication::AlignInfo &ai, int mate, int strand, int count, int index, bool left)

string Tag(const string &name, int value)

int ProcessSAM(const vector< string > &tags, vector< CCompactSAMApplication::Exon > &exons)

void Print(const CCompactSAMApplication::AlignInfo &ai)

void ReplaceTag(vector< string > &fields, const string &name, const T &value)

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

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

void RemoveTag(vector< string > &fields, const string &name)

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

static void s_GetSpan(const THitRefs &hitrefs, TCoord span[4])

Get sequence span for a set of alignments (hits).

unsigned int TSeqPos

Type for sequence locations and lengths.

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.

const CNcbiArguments & GetArguments(void) const

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

void swap(NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair1, NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair2)

@ 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:

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