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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/columnar__vcf__variants_8cpp_source.html below:

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

:

(load_all_info, info_fields, sample_cols), m_ChrName(chr_name)

* buf_ptr = (

*)

.data();

skip_max_feat_length =

;

(!found_end_col) {

(

() > 100000) {

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

end_it = end_vector.

();

end_stop_it = end_vector.end();

(; end_it != end_stop_it; ++end_it) {

(!end_it.is_null()) {

tmp_delta = end_point - start_point + 1;

tmp_delta = tmp_delta * (-1);

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

(

<<

<<

() <<

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

() <<

);

* write_ptr =

->data();

buf_ptr = (

*)

.data();

memcpy(write_ptr, &idx_size,

(idx_size));

write_ptr +=

(idx_size);

buf_ptr +=

(idx_size);

memcpy(write_ptr, &nr_cols,

(nr_cols));

write_ptr +=

(nr_cols);

buf_ptr +=

(nr_cols);

memcpy(write_ptr, buf_ptr,

.size() -

(idx_size) -

(nr_cols));

pos = line.find(

);

remainder = line;

added = (errno == 0);

vector<string> var_ids;

var_ids.push_back(

);

(

& it : var_ids) {

(var_ids.begin(), var_ids.end());

var_ids.erase(unique(var_ids.begin(), var_ids.end()), var_ids.end());

col_it = col_names.begin();

(var_ids.size() == 1) {

(++col_it; col_it != col_names.end() - 1; ++col_it) {

= remainder.substr(pos + 1,

);

vector<string> tmp_values;

(++col_it; col_it != col_names.end() - 1; ++col_it) {

tmp_values.push_back(

);

= remainder.substr(pos + 1,

);

tmp_values.push_back(

);

(

index = 1; index < var_ids.size(); ++index) {

col_it = col_names.begin();

(++col_it; col_it != col_names.end() &&

< tmp_values.size(); ++col_it, ++

) {

line = line.substr(pos + 1,

);

pos = line.find(

);

line.substr(0, pos);

(; it != it_end; ++it) {

ret =

.insert(*it);

(ret.second ==

) {

copies_it = find_if(copies.begin(), copies.end(),

[&search](

pair<string, unsigned>& elem) { return elem.first == search; });

(copies_it == copies.end()) {

copies.emplace_back(search, 2);

(copies.empty());

(indices.count() > 0) {

(positions.begin(), positions.end());

positions.erase(unique(positions.begin(), positions.end()), positions.end());

<< var_iter.GetPosition() <<

<< var_iter.GetVariantID() <<

<< var_iter.GetRef() <<

<< var_iter.GetAlt();

<<

<< var_iter.GetQual() <<

<< var_iter.GetFilter()

<<

<< var_iter.GetInfo() <<

<< var_iter.GetFormat();

(

& it : samples) {

<< var_iter.GetPosition() <<

<< var_iter.GetVariantID() <<

;

(

& it : samples) {

<< var_iter.GetSample(it) <<

;

vector<string> variants;

variants.push_back(var_iter.GetVariantID());

<<

<< endl;

Jaccard_index =

;

(

& it : col_names) {

<<

<< it <<

<< endl;

(

<<

<< it <<

);

str_vector, Jaccard_index);

cum_memory_used = 0;

cum_layout_size = 0;

*

<<

<<

<< endl;

(

& it : col_names) {

(

& it : info_fields) {

(

& it : samples) {

*

<< endl <<

<< cum_memory_used << endl << endl;

*

<<

<< cum_layout_size << endl;

(

exception& e) {

*

<<

<<

<< endl;

(

& it : col_names) {

(

& it : info_fields) {

(

& it : samples) {

(

exception& e) {

(

& it : col_names) {

(

& it : info_fields) {

(

& it : samples) {

(

exception& e) {

: m_ColsDecode(cols_to_decode)

, m_BufferPtr(

)

(positions.begin(), positions.end());

positions.erase(unique(positions.begin(), positions.end()), positions.end());

(indices.count() > 0) {

<< var_iter.GetPosition() <<

<< var_iter.GetVariantID() <<

<< var_iter.GetRef() <<

<< var_iter.GetAlt() <<

<< var_iter.GetQual() <<

<< var_iter.GetFilter() <<

<< var_iter.GetInfo();

(var_iter.IsSetFormat()) {

<<

<< var_iter.GetFormat() <<

<< var_iter.GetSampleCols();

#define BM_SCALAR_VERSION

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

Class for support low level input/output for files.

void GetStatistics(bm::bv_statistics &stat_sum, bool Jaccard_index, CNcbiOstream &out)

void DeserializeVectors(const string &prefix, CNcbiOstream *out)

void FinalizeReading()

Flushes the insert iterators after which it remaps and optimizes each vector.

unsigned GetPositionForIndex(const size_t &index) const

void Lookup(const TSparseStrVector::bvector_type &values, vector< unsigned > &indices) const

const size_t & GetMaxIndex() const

bool Add(const unsigned &index, const unsigned &value)

void SerializeVectors(const string &prefix, CNcbiOstream *out, unsigned &cum_memory_used, unsigned &cum_layout_size)

bool RemoveSerializedOutput(const string &prefix)

CVCFSlicedVariants(const unsigned char *data, const TSeqRange *range=nullptr, const set< string > &cols_to_decode=set< string >(), bool only_start=false)

void List(CNcbiOstream &out) const

virtual void GetPositionsForMissingVarID(vector< unsigned > &positions)

const unsigned char * m_BufferPtr

size_t m_NrCols

number of data columns to be deserialized

virtual bool GetPositionsForVariant(const string &variant_id, vector< unsigned > &positions)

set< string > m_ColsDecode

the name of data columns to be deserialized

virtual bool GetPositionsForVariant(const string &variant_id, vector< unsigned > &positions)

void ParseLine(const string &line)

void GetStatistics(CNcbiOstream &out)

CVCFVariantList(const string &chr_name, bool load_all_info=true, const set< string > &info_fields=set< string >(), const map< unsigned, string > &sample_cols=map< unsigned, string >())

bool RemoveSerializedOutput(const string &prefix)

void List(CNcbiOstream &out, bool only_sv_cols=false) const

virtual void GetPositionsForMissingVarID(vector< unsigned > &positions)

const vector< char > & GetSerializedData() const

bool AreVariantIdsUnique(vector< pair< string, unsigned >> &copies)

void WriteSerializedData(const string &filename)

bool operator==(const CVCFVariantList &other) const

string x_GetFilePrefix(const string &prefix) const

string x_ParseNextColumn(string &line, size_t &pos)

void ListSamples(CNcbiOstream &out) const

vector< string > GetAllVariantIDS() const

bool SerializeVariantData(const string &prefix, CNcbiOstream *out=nullptr)

bool DeserializeAndCheck(const string &prefix, CNcbiOstream *out=nullptr)

bool x_DeserializeColumn(const string &col_name, const unsigned char *buf_ptr, const size_t &nr_cols)

static const string sm_ID

void x_DeserializeIndexVectors(const unsigned char *&buf_ptr, size_t &nr_cols, bool skip_feat_length=false)

size_t GetNumberOfIndexVecs() const

void x_DeserializeDescr_Range(const unsigned char *buf_ptr, const size_t &nr_cols, const TSeqRange *range=nullptr, const set< string > &cols_to_decode=set< string >(), bool only_start=false)

static const vector< string > & s_GetAllColNames()

contains sm_INFO, sm_SAMPLES

static string s_GetPreviousVersion()

static const vector< string > & s_GetColNames()

does not contain sm_INFO and sm_SAMPLES

TSeqPos m_StartPos

in genomic coordinates (1-based)

CPosToIndex m_Posindexmap

void x_DeserializeAllData()

static const string sm_MissingValue

vector< char > * m_Buffer

TSeqPos m_StopPos

in genomic coordinates (1-based)

void x_SerializeData() const

unsigned m_MaxFeatLength

maximum feature variant length

CVariantDescriptors m_Descriptors

bool GetIndicesForVariant(const string &variant_id, TSparseStrVector::bvector_type &indices) const

bool AreInsertersReady() const

const TSparseOptVector & GetSample(const string &name) const

TSparseOptVector & SetSample(const string &name)

const TSparseOptVector & GetInfoField(const string &field_name) const

TSparseOptVector & SetInfoField(const string &field_name)

vector< string > GetInfoFieldNames() const

void FinalizeReading()

Flushes the insert iterators after which it remaps and optimizes each vector.

void PushBackPos(const unsigned &value)

Push back starting position of a variant.

vector< string > GetSampleNames() const

unsigned GetMaxFeatureLength()

Returns the maximum feature length within the set or 0 if the end points are not specified.

void PushBack(const string &label, const string &value)

Push back 'value' into the vector identified by 'label' The 'value' is not actually stored in the vec...

void GetIndicesForMissingVarID(TSparseStrVector::bvector_type &indices) const

const_iterator begin() const noexcept

Provide const iterator access to container content.

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

main entry point for tests

#define LOG_POST(message)

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

#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.

virtual const char * what(void) const noexcept

Standard report (includes full backlog).

void Info(CExceptionArgs_Base &args)

void Close(void)

Close file.

void Open(const string &filename, EOpenMode open_mode, EAccessMode access_mode, EShareMode share_mode=eShare)

Open file.

Uint8 GetFileSize(void) const

Get file size.

size_t Read(void *buf, size_t count) const

Read file.

@ eRead

File can be read.

@ eOpen

Open an existing file, or create a new one.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

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 void TruncateSpacesInPlace(string &str, ETrunc where=eTrunc_Both)

Truncate whitespace in a string (in-place)

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

Convert UInt to string.

static unsigned int StringToUInt(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to unsigned int.

@ fConvErr_NoThrow

Do not throw an exception on error.

static const char label[]

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

bool RemoveFile(const string &fname)

void SerializeColumn(SV &vec, const string &prefix, const string &col_name, CNcbiOstream *out, unsigned &cum_memory_used, unsigned &cum_layout_size)

void PrintStats(const bm::bv_statistics &sum, CNcbiOstream &out)

void AddStats(bm::bv_statistics &sum, SV &vec, CNcbiOstream &out)

void DeserializeColumn(SV &vec, const string &prefix, const string &col_name, CNcbiOstream *out)

void PrintToFile(const char *buff, size_t size, const string &fname)

string GenerateColFileName(const string &prefix, const string &col_name)

void print_svector_stat(TOut &tout, const SV &svect, bool print_sim=false)

constexpr auto sort(_Init &&init)

const string version

version string

const GenericPointer< typename T::ValueType > T2 value

Compressed bitset (entry point to bm.h)

static sljit_uw total_size

Structure with statistical information about memory allocation footprint, serialization projection,...

void reset() noexcept

Reset statisctics.

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