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NCBI C++ ToolKit: src/gui/widgets/loaders/columnar_vcf_reader.cpp Source File

edit::CParseTextOptions options;

options.SetStartText(

);

options.SetStopText(

);

= options.GetSelectedText(line);

options.SetStartText(

);

options.SetStopText(

);

= options.GetSelectedText(line);

options.SetStartText(

);

options.SetStopText(

);

nr_lines = 0;

(nr_lines % 200 == 0 && (canceled && canceled->

())) {

edit::CParseTextOptions options;

options.SetStartText(

);

options.SetStopText(

);

options.SetStopText(

);

}

(reader.

() ==

);

,

(header_line.find(

) !=

|| header_line.find(

) ==

) {

,

vector<string> col_names;

is_unique =

;

unique_strs(col_names.begin(), col_names.end());

is_unique = (col_names.size() == unique_strs.

());

,

it = col_names.begin();

(; it != col_names.end(); ++it) {

(; it != col_names.end(); ++it, ++index) {

,

placed = error_cont->

(err);

,

start = chrono::steady_clock::now();

nr_lines = 0;

lines_per_contig = 0;

previous_chrom;

vector<future<void>> async_calls;

JoinOptimization = [&async_calls]()

(

& task : async_calls) {

task_start = chrono::steady_clock::now();

opt_start = chrono::steady_clock::now();

var_map->FinalizeReading();

diff_opt = chrono::steady_clock::now() - opt_start;

(

<<

<< chr <<

<< chrono::duration_cast<chrono::milliseconds>(diff_opt).

() <<

);

(on_variants_list_ready) {

on_variants_list_ready(*var_map);

diff_opt = chrono::steady_clock::now() - task_start;

(

.good() && !

.eof()) {

(nr_lines % 1000 == 0 && (canceled && canceled->

())) {

(line.empty() || (!line.empty() && line[0] ==

)) {

(line.find(

) ==

) {

+ line,

pos = line.find(

);

chrom = line.substr(0, pos);

(chrom != previous_chrom) {

(!previous_chrom.empty()) {

async_calls.push_back(async(std::launch::async | std::launch::deferred, OptimizeVariantsList, std::ref(

.at(previous_chrom))));

previous_chrom = chrom;

lines_per_contig = 0;

vars_list = inserted.first->second.GetPointer();

chrom +

,

(prog_func && lines_per_contig > 0 && lines_per_contig % 500000 == 0) {

vars_list->ParseLine(line);

diff_parsing = chrono::steady_clock::now() - start;

(

<<

<< nr_lines <<

<< chrono::duration_cast<chrono::milliseconds>(diff_parsing).

() <<

);

(!

.eof() && !

.good()) {

(

<<

);

(on_variants_list_ready) {

(header_line.find(

) !=

|| header_line.find(

) ==

) {

,

kMandatoryCols = 8;

nr_tabs =

(

(header_line.begin(), header_line.end(),

));

(nr_tabs + 1 < kMandatoryCols) {

,

vector<CColumnarVCFReader::TSeqIdVarsListPair>

start = chrono::steady_clock::now();

nr_lines = 0;

lines_per_contig = 0;

search_chrs = chr_list.size();

vector<future<void>> async_calls;

JoinOptimization = [&async_calls]()

(

& task : async_calls) {

chr = var_map->GetChrName();

task_start = chrono::steady_clock::now();

opt_start = chrono::steady_clock::now();

var_map->FinalizeReading();

diff_opt = chrono::steady_clock::now() - opt_start;

(

<<

<< chr <<

<< chrono::duration_cast<chrono::milliseconds>(diff_opt).

() <<

);

(on_variants_list_ready) {

on_variants_list_ready(*var_map);

diff_opt = chrono::steady_clock::now() - task_start;

CallOptimizeVarsList = [&]() {

async_calls.push_back(async(std::launch::async | std::launch::deferred, OptimizeVariantsList, vcf_vars));

OptimizeVariantsList(vcf_vars);

(

.good() && !

.eof() && search_chrs > 0) {

(nr_lines % 1000 == 0 && (canceled && canceled->

())) {

variants_list.clear();

variants_list;

(line.empty() || (!line.empty() && line[0] ==

)) {

(line.find(

) ==

) {

+ line,

pos = line.find(

);

chrom = line.substr(0, pos);

(!vcf_vars || (vcf_vars && !

(vcf_vars->GetChrName(), chrom))) {

(prev_chrom == chrom)

(

& syn_it : chr_list) {

& seq_id = syn_it.first;

& synonyms = syn_it.second;

(find_if(synonyms.begin(), synonyms.end(),

[&chrom](

& elem) { return NStr::EqualCase(chrom, elem); }) != synonyms.end()) {

CallOptimizeVarsList();

lines_per_contig = 0;

(find_if(variants_list.begin(), variants_list.end(),

[&seq_id](

& elem) { return (seq_id->AsFastaString() == elem.first->AsFastaString()); }) == variants_list.end()) {

vcf_vars = variants_list.back().second;

chrom +

,

CallOptimizeVarsList();

vcf_vars.

(

);

lines_per_contig = 0;

(prog_func && lines_per_contig > 0 && lines_per_contig % 500000 == 0) {

vcf_vars->ParseLine(line);

diff_parsing = chrono::steady_clock::now() - start;

(

<<

<< nr_lines <<

<< chrono::duration_cast<chrono::milliseconds>(diff_parsing).

() <<

);

variants_list.clear();

variants_list;

(!

.good() && !

.eof()) {

(

<<

);

variants_list.clear();

OptimizeVariantsList(vcf_vars);

(chr_list.size() != variants_list.size()) {

(

& chr_it : chr_list) {

(find_if(variants_list.begin(), variants_list.end(),

{ return elem.first->Equals(*chr_it.first); }) == variants_list.end()) {

id_str = chr_it.first->AsFastaString();

+ id_str +

,

(!on_variants_list_ready) {

(

& var_it : variants_list) {

variants_list;

vector<string>

;

.push_back(it.first);

it.second->GetStatistics(

);

it.second->SerializeVariantData(prefix,

);

it.second->DeserializeAndCheck(prefix,

);

it.second->List(

, only_sv_cols);

it.second->ListPositionVectors(

);

Debugging functions (internal). Poorly documented, not well written.

Serialization for sparse_vector<>

void ListColumns(CNcbiOstream &out, bool only_sv_cols=false)

void SerializeToDisk(const string &prefix, CNcbiOstream *out=nullptr)

void GetStatistics(CNcbiOstream &out)

void Deserialize(const string &prefix, CNcbiOstream *out=nullptr)

void ListIndexVectors(CNcbiOstream &out)

bool m_LoadAllInfo

Flag to load every INFO field.

pair< CConstRef< objects::CSeq_id >, CRef< CVCFVariantList > > TSeqIdVarsListPair

void x_ProcessCriticalError(objects::CObjReaderLineException &err, objects::ILineErrorListener *error_cont)

vector< string > GetChromosomeNames() const

Returns a vector, holding the chrs/contigs identifiers, read from the file.

map< unsigned, string > m_SampleCols

List of SAMPLE columns parsed from the last line of the header, order is important.

unsigned x_ProcessHeaderLine(const string &header_line, unsigned line_nr, objects::ILineErrorListener *listener)

map< unsigned, string > m_LoadSamples

List of SAMPLES required to be loaded.

function< void(const string &)> TReportProgress

void x_ProcessError(objects::CObjReaderLineException &err, objects::ILineErrorListener *error_cont)

CRef< CVCFVariantList > GetVariantsForChr(const string &chr_name) const

Retrieves the variants list for a given chr/contig.

bool ReadHeader(CNcbiIstream &in, ICanceled *canceled=nullptr, objects::ILineErrorListener *listener=nullptr)

Reads only the header section of the file.

void x_GetSamplesToLoad(const string &header_line, objects::ILineErrorListener *listener, unsigned line_nr)

set< CConstRef< SVcfFieldData > > m_InfoFields

List of INFO fields parsed from the header of the file.

bool m_LoadAllSamples

Flag to load every SAMPLE column.

void x_ProcessWarning(objects::CObjReaderLineException &err, objects::ILineErrorListener *error_cont)

std::function< void(CVCFVariantList &)> TOnVCFVariantListReady

Defines a callable object, used when a variants list is processed by the reader.

void x_InterruptReading()

void x_GatherSampleColNames(const string &header_line, objects::ILineErrorListener *listener, unsigned line_nr)

unordered_map< string, CRef< CVCFVariantList > > m_ChromosomeMap

set< string > m_LoadInfoFields

List of INFO fields required to be loaded.

vector< TSeqIdVarsListPair > ReadVariantsForChrs(CNcbiIstream &in, const vector< pair< CConstRef< objects::CSeq_id >, vector< string >>> &chr_list, ICanceled *canceled=nullptr, objects::ILineErrorListener *listener=nullptr, TReportProgress prog_func=TReportProgress(), TOnVCFVariantListReady on_variants_list_ready=TOnVCFVariantListReady())

Reads a list of variants.

bool ReadData(CNcbiIstream &in, ICanceled *canceled=nullptr, objects::ILineErrorListener *listener=nullptr, TReportProgress prog_func=TReportProgress(), TOnVCFVariantListReady on_variants_list_ready=TOnVCFVariantListReady())

Reads only the data section of the file.

void Throw(void) const

this function to throw this object.

static CObjReaderLineException * Create(EDiagSev eSeverity, unsigned int uLine, const std::string &strMessage, EProblem eProblem=eProblem_GeneralParsingError, const std::string &strSeqId=string(""), const std::string &strFeatureName=string(""), const std::string &strQualifierName=string(""), const std::string &strQualifierValue=string(""), CObjReaderLineException::EErrCode eErrCode=eFormat, const TVecOfLines &vecOfOtherLines=TVecOfLines())

Please use this instead of the constructor because the ctor is protected.

std::string Message() const

Simple implementation of ILineReader for i(o)streams.

CTempString implements a light-weight string on top of a storage buffer whose lifetime management is ...

const string & GetChrName() const

static const string sm_FORMAT

Interface for testing cancellation request in a long lasting operation.

virtual bool PutError(const ILineError &)=0

Store error in the container, and return true if error was stored fine, and return false if the calle...

@ eProblem_GeneralParsingError

string SeverityStr() const

iterator_bool insert(const value_type &val)

const_iterator begin() const

const_iterator end() const

const Uint8 kAsyncVarsThreshold

std::ofstream out("events_result.xml")

main entry point for tests

static const struct name_t names[]

#define LOG_POST(message)

This macro is deprecated and it's strongly recomended to move in all projects (except tests) to macro...

@ eDiag_Warning

Warning message.

@ eDiag_Critical

Critical error message.

void Error(CExceptionArgs_Base &args)

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

const string & GetMsg(void) const

Get message string.

void Info(CExceptionArgs_Base &args)

char PeekChar(void) const

Returns the first character of the next string without consuming it.

Uint8 GetLineNumber(void) const

Returns the current line number (counting from 1, not 0).

void Reset(void)

Reset reference object.

TObjectType * Release(void)

Release a reference to the object and return a pointer to the object.

uint64_t Uint8

8-byte (64-bit) unsigned integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

virtual bool IsCanceled(void) const =0

CNcbiIstream & NcbiGetlineEOL(CNcbiIstream &is, string &str, string::size_type *count=NULL)

Read from "is" to "str" the next line (taking into account platform specifics of End-of-Line)

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

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.

static bool EqualCase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-sensitive equality of a substring with another string.

bool empty(void) const

Return true if the represented string is empty (i.e., the length is zero)

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

Convert UInt to string.

static bool StartsWith(const CTempString str, const CTempString start, ECase use_case=eCase)

Check if a string starts with a specified prefix value.

CTempString substr(size_type pos) const

Obtain a substring from this string, beginning at a given offset.

static string UInt8ToString(Uint8 value, TNumToStringFlags flags=0, int base=10)

Convert UInt8 to string.

Lightweight interface for getting lines of data with minimal memory copying.

Compressed bitset (entry point to bm.h)

std::istream & in(std::istream &in_, double &x_)

Structure to store characteristics of an INFO field It is constructed from an INFO meta-information l...

string m_Name

INFO ID (name)

string m_Description

INFO Description.

SVcfFieldData(const string &line)

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