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:

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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
	)

Definition at line 228 of file agp_renumber.cpp.

References buf, CAgpRenumber::custom_err, CAgpReader::eFinalize_No, CAgpReader::Finalize(), CAgpReader::GetErrorMessage(), CAgpRenumber::had_empty_line, CCustomErrorHandler::had_missing_tab, i, in(), MAX_BUF_LINES, NcbiGetline(), CAgpRenumber::no_renum_objs, out(), CAgpReader::ReadStream(), CAgpRenumber::renum_objs, CAgpRenumber::reordered_ln_ev, and tolower().

Referenced by main().

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(), psa_get_key_usage_flags(), psa_set_key_usage_flags(), ReportMemoryUsage(), and s_Win_GetMemoryUsage().

USING_NCBI_SCOPE

USING_NCBI_SCOPE

Definition at line 42 of file agp_renumber.cpp.