NCBI C++ ToolKit
Classes | Functions | Variables
agp_renumber.cpp File Reference
#include <ncbi_pch.hpp>
#include <corelib/ncbiapp.hpp>
#include <corelib/ncbiargs.hpp>
#include <corelib/ncbienv.hpp>
#include <corelib/ncbifile.hpp>
#include <objtools/readers/agp_util.hpp>
+ Include dependency graph for agp_renumber.cpp:

Go to the source code of this file.

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Classes

class  CCustomErrorHandler
 
class  CAgpRenumber
 

Functions

int ProcessStream (istream &in, ostream &out)
 
int main (int argc, char *argv[])
 

Variables

 USING_NCBI_SCOPE
 
const char * usage
 
const int MAX_BUF_LINES =100
 

Function Documentation

◆ main()

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

Definition at line 354 of file agp_renumber.cpp.

References in(), ProcessStream(), and usage.

◆ ProcessStream()

int ProcessStream ( istream &  in,
ostream &  out 
)

Variable Documentation

◆ MAX_BUF_LINES

const int MAX_BUF_LINES =100

Definition at line 62 of file agp_renumber.cpp.

Referenced by ProcessStream().

◆ usage

const char* usage ( void  )
Initial value:
=
"Clean up an AGP file:\n"
"https://www.ncbi.nlm.nih.gov/assembly/agp/AGP_Specification/\n"
"\n"
"USAGE: agp_renumber <in.agp >out.agp\n"
"\n"
" - Recalculate the object begin and end coordinates from\n"
" the length of the component span or gap length.\n"
" - Renumber the part numbers for each object.\n"
" - Lowercase gap type and linkage.\n"
" - Reorder linkage evidence terms: paired-ends;align_genus;align_xgenus;align_trnscpt;within_clone;clone_contig;map;strobe;pcr\n"
" - Reformat white space to conform to the AGP format specification:\n"
" - add missing tabs at the ends of gap lines;\n"
" - drop blank lines;\n"
" - remove extra tabs and spaces at the end of lines;\n"
" - add a missing line separator at the end of the file;\n"
" - replace spaces with tabs (except in comments).\n"

Definition at line 44 of file agp_renumber.cpp.

Referenced by CDBUDPriorityMapper::Add(), CCommandLineParser::AddCommand(), CGlRenderBuffer< T >::BufferData(), CGlBuffer20< T >::BufferData(), CCurrentProcess::GetMemoryUsage(), CProcess::GetMemoryUsage(), CArgAllow_Symbols::GetUsage(), CArgAllow_String::GetUsage(), CArgAllow_Int8s::GetUsage(), CArgAllow_Doubles::GetUsage(), CArgDesc::GetUsageConstraint(), main(), mbedtls_ssl_check_cert_usage_ncbicxx_2_28_3(), mbedtls_x509_crt_check_key_usage_ncbicxx_2_28_3(), psa_cipher_setup(), psa_get_and_lock_key_slot_with_policy(), psa_get_and_lock_transparent_key_slot_with_policy(), ReportMemoryUsage(), and s_Win_GetMemoryUsage().

◆ USING_NCBI_SCOPE

USING_NCBI_SCOPE

Definition at line 42 of file agp_renumber.cpp.

Modified on Wed Feb 28 07:14:15 2024 by modify_doxy.py rev. 669887