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

;

& header,

list<string>& body);

arg_desc->AddKey(

,

,

,

arg_desc->AddOptionalKey(

,

,

dirname = args[

].AsString();

output_dir(dirname);

(!output_dir.

()) {

err_msg = dirname

+

;

output_dir =

;

(

& key_val : id_map) {

filename = output_dir +

unique_ptr<CNcbiOfstream> ostr(

(filename.c_str()));

id_map[

[0]].push_back(line);

( !

.AtEOF() ) {

(line.size() > 2 &&

& header,

list<string>& body)

ostr << header <<

;

(

& line : body) {

ostr << line <<

;

(

argc,

* argv[])

void xProcessFile(CNcbiIstream &istr)

void xProcessLine(const string &line, TIdmap &id_map)

void xReadFile(CNcbiIstream &istr, string &header, TIdmap &id_map)

int Run(void)

Run the application.

void xWriteFile(CNcbiOfstream &ostr, const string &header, const list< string > &body)

void xSetExtension(const string &input_filename)

void Init(void)

Initialize the application.

NCBI_EXCEPTION_DEFAULT(CGffDeconcatException, CException)

virtual const char * GetErrCodeString() const override

Get error code interpreted as text.

Simple implementation of ILineReader for i(o)streams.

Include a standard set of the NCBI C++ Toolkit most basic headers.

static const column_t columns[]

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

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.

void SetVersion(const CVersionInfo &version)

Set the version number for the program.

@ eInputFile

Name of file (must exist and be readable)

@ eOutputFile

Name of file (must be writable)

@ eDS_ToStderr

To standard error stream.

TErrCode GetErrCode(void) const

Get error code.

#define NCBI_THROW(exception_class, err_code, message)

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

EErrCode

Error types that an application can generate.

virtual const char * GetErrCodeString(void) const

Get error code interpreted as text.

static string CreateAbsolutePath(const string &path, ERelativeToWhat rtw=eRelativeToCwd)

Get an absolute path from some, possibly relative, path.

static bool IsAbsolutePath(const string &path)

Check if a "path" is absolute for the current OS.

virtual bool Exists(void) const

Check if directory "dirname" exists.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

IO_PREFIX::ofstream CNcbiOfstream

Portable alias for ofstream.

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 IsBlank(const CTempString str, SIZE_TYPE pos=0)

Check if a string is blank (has no text).

static double StringToDouble(const CTempStringEx str, TStringToNumFlags flags=0)

Convert string to double.

@ fSplit_MergeDelimiters

Merge adjacent delimiters.

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

#define NCBI_SC_VERSION_PROXY

#define NCBI_TEAMCITY_BUILD_NUMBER_PROXY

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

Defines command line argument related classes.

Defines NCBI C++ exception handling.

Defines classes: CDirEntry, CFile, CDir, CSymLink, CMemoryFile, CFileUtil, CFileLock,...

static SLJIT_INLINE sljit_ins lr(sljit_gpr dst, sljit_gpr src)

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