src/app/agp_validate/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.

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

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Function Documentation

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

Definition at line 314 of file agp_renumber.cpp. References ProcessStream(), and usage.

int ProcessStream (  istream &  in, ostream &  out )

Definition at line 206 of file agp_renumber.cpp. References buf, MAX_BUF_LINES, NcbiGetline(), and CAgpReader::ReadStream(). Referenced by main().

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Variable Documentation

const int MAX_BUF_LINES = 100

Definition at line 61 of file agp_renumber.cpp. Referenced by ProcessStream().

const char* usage

Initial value: "Clean up an AGP file:\n" "http://www.ncbi.nlm.nih.gov/genome/assembly/agp/AGP_Specification.shtml\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" " - 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 CArgDesc::GetUsageConstraint(), handle_option(), main(), and PercentOfWeightOverThresholdColumnScorer::PercentOfWeightOverThresholdColumnScorer().

USING_NCBI_SCOPE

Definition at line 42 of file agp_renumber.cpp.

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