RetroSearch Browse

Home - News ( United States | United Kingdom | Italy | Germany ) - Football scores

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/demoreadlarge__vcf_8cpp_source.html below:

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

50 virtual void Init

(

void

);

51 virtual int Run

(

void

);

52 virtual void Exit

(

void

);

57 bool x_ListErrors

(objects::ILineErrorListener* errCont);

60 void x_ReadVCFBlob

(

const string

& fname, vector<char>& vcf_blob);

66

arg_desc->SetUsageContext(

GetArguments

().GetProgramBasename(),

"Demo application to read VCF files"

);

74

arg_desc->AddFlag(

"sv_cols"

"Output only the first five columns from the data section of the input file"

);

80

arg_desc->AddFlag(

"deserialize_and_compare"

"Deserialize data and compare it with the existing variant data"

);

82

arg_desc->AddOptionalKey(

"range"

"GenomicRange"

"Specify the genomic range for which to extract the data"

CArgDescriptions::eString

);

104

cout <<

"Starting to read file: "

<< fname << endl;

109 bool

has_errors =

false

;

110 bool

read_data =

false

;

113

read_data = reader.

ReadData

(

file

.GetIstream(

false

nullptr

, err_cont, progress);

117

cout <<

"Loading VCF file "

<< fname <<

" failed: "

<< e.

GetMsg

();

120 catch

(

const

exception& e) {

121

cout <<

"Loading VCF file "

<< fname <<

" failed: "

<< e.

what

();

128

cout <<

"VCF file was successfully loaded into memory"

<< endl;

131 for

(

const auto

& it : chr_names) {

133

cout << it <<

"\t"

<< var->Count() <<

" variants\n"

;

138 if

(args[

"serial"

]) {

139 const string

& serial_fname = args[

"serial"

].AsString();

140 auto

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

141 for

(

const auto

& it : chr_names) {

143

var->WriteSerializedData(it +

"_"

+ serial_fname);

145 auto

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

146

cout <<

"Serialization of all data took: "

147

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

" ms"

<< endl;

149 if

(args[

"deserialize_and_compare"

]) {

150 for

(

const auto

& it : chr_names) {

154 if

(*orig_var == *new_variant) {

155

cout << it <<

"\t"

"are the same\n"

;

158

cout << it <<

"\t"

"are not the same\n"

;

167 for

(

const auto

& it : chr_names) {

169 string

out_fname = it +

"_"

+ args[

"o"

].AsString();

171

var->List(

out

, args[

"sv_cols"

]);

173

cout <<

"Finished listing columns"

<< endl;

176

cout <<

"Listing data columns has failed: "

<< e.

GetMsg

() << endl;

181 if

(args[

"index"

]) {

183 for

(

const auto

& it : chr_names) {

185 string

out_fname = it +

"_"

+ args[

"index"

].AsString();

187

var->ListPositionVectors(

out

);

189

cout <<

"Finished listing index vectors "

<< endl;

192

cout <<

"Listing index vectors has failed: "

<< e.

GetMsg

() << endl;

202

cout <<

text

<< endl;

207 bool

has_errors = (errCont && errCont->Count() > 0);

209 for

(

size_t i

= 0;

< errCont->Count(); ++

) {

210 const auto

& lerror = errCont->GetError(

);

211

cerr <<

"Line "

<< lerror.Line() <<

". "

<< lerror.Message() << endl;

224 if

(!args[

"range"

]) {

228

cout <<

"Number of variants read: "

<< new_variant->Count() << endl;

231

cout <<

"Failed to load data from "

<< fname <<

": "

<< e.

GetMsg

() << endl;

241 if

(args[

"range"

]) {

246

vector<char> vcf_blob;

250 CVCFSlicedVariants

variants((

const unsigned char

*)vcf_blob.data(), &range, data_cols);

252

cout <<

"There are "

<< variants.

Count

(range) <<

" variants in the specified range"

;

264 if

(range_str.empty())

267

vector<string> positions;

269 if

(positions.size() != 2) {

285

cout <<

"Parsed: "

<< from <<

" and "

<< to << endl;

286

range.

Set

(from, to);

287

cout <<

"Range: "

<< range.

GetFrom

() <<

" and "

<< range.

GetTo

() << endl;

298

cerr <<

"Cannot open "

+ fname +

"\nas: "

+ e.

GetMsg

() << endl;

303 char

buf

= vcf_blob.data();

318 else if

(args[

"iserial"

]) {

354

cout <<

"Press any key to end the demo app"

<< endl;

bool x_ListErrors(objects::ILineErrorListener *errCont)

bool x_LoadVCFFile(const string &fname)

void x_ReadVCFBlob(const string &fname, vector< char > &vcf_blob)

virtual void Exit(void)

Cleanup on application exit.

bool x_LoadSerializedData(const string &fname)

virtual int Run(void)

Run the application.

TSeqRange x_ParseRange(const string &range_str)

virtual void Init(void)

Initialize the application.

void x_UpdateProgress(const string &text)

Class responsible to read VCF files.

vector< string > GetChromosomeNames() const

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

function< void(const string &)> TReportProgress

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

Retrieves the variants list for a given chr/contig.

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.

Class for support low level input/output for files.

void List(CNcbiOstream &out) const

static const vector< string > & s_GetAllColNames()

contains sm_INFO, sm_SAMPLES

int NcbiSys_main(int argc, ncbi::TXChar *argv[])

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

main entry point for tests

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.

@ eInputFile

Name of file (must exist and be readable)

@ eString

An arbitrary string.

@ eOutputFile

Name of file (must be writable)

void SetDiagStream(CNcbiOstream *os, bool quick_flush=true, FDiagCleanup cleanup=0, void *cleanup_data=0, const string &stream_name="")

Set diagnostic stream.

const string & GetMsg(void) const

Get message string.

virtual const char * what(void) const noexcept

Standard report (includes full backlog).

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.

void Reset(void)

Reset reference object.

TThisType & Set(position_type from, position_type to)

IO_PREFIX::ofstream CNcbiOfstream

Portable alias for ofstream.

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 Uint8 StringToUInt8(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to Uint8.

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

Convert UInt8 to string.

@ fSplit_MergeDelimiters

Merge adjacent delimiters.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

static void text(MDB_val *v)

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

Process information in the NCBI Registry, including working with configuration files.

C++ I/O stream wrappers to compress/decompress data on-the-fly.

RetroSearch is an open source project built by @garambo | Open a GitHub Issue

Search and Browse the WWW like it's 1997 | Search results from DuckDuckGo

HTML: 3.2 | Encoding: UTF-8 | Version: 0.7.4

Home - News ( United States | United Kingdom | Italy | Germany ) - Football scores

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/demo__read__large__vcf_8cpp_source.html below:

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

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/demoreadlarge__vcf_8cpp_source.html below: