gb2ace.cpp File Reference

#include "gbseq.h"
#include <fstream>


Enumerations
enum	inftype { dna, protein }
Functions
void	processOneFile (string &infile, bool show, gbseq *seq)
void	getInputFiles (const char nameFile[], vector< string > &files)
void	usage ()
int	main (int argc, char *argv[])

Enumeration Type Documentation

enum inftype

Enumerator:

dna
protein

Function Documentation

void getInputFiles	(	const char	nameFile[],
		vector< string > &	files
	)

References ifstream().

Referenced by main().

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

References dna, feature::dumpGeneName(), Ref::dumpKey(), gbseq::dumpOrgmap(), feature::dumpSubseq(), getInputFiles(), gbseq::init(), inputFileType, feature::loadGeneName(), Ref::loadKey(), gbseq::loadOrgmap(), feature::loadSubseq(), processOneFile(), protein, feature::PRTOUT, gbdate::setup(), and usage.

void processOneFile	(	string &	infile,
		bool	show,
		gbseq *	seq
	)

References gbseq::getKey(), ifstream(), gbseq::read(), and gbseq::writeAce().

Referenced by main().

void usage ( )

given gmap summary format, this program converts it into combest archive format (*.car)

It can be used a pipe, or given specific file names.

this is a helper program to count distinct estids in the ESTId column of the combest result. So it is the actual number of ESTs mapped. This could be lower for deeply covered genome because of the coverage depth-dependent filtering.