filterblast.cpp File Reference

#include <iostream>
#include <fstream>
#include <vector>
#include "strformat.h"
#include <sys/types.h>
#include <dirent.h>
#include <cmath>
#include <cstring>

Functions
pair< int, int >	parseOneFile (istream &ins, ostream &ous, bool rmslf, bool rmtwz)
void	parseAllFilesIntoOne (const char pat[], ostream &ous, bool rmslf, bool rmtwz)
void	parseMultipleFiles (const vector< string > &files, bool rmslf, bool rmtwz)
int	main (int argc, char *argv[])
void	usage ()
Variables
const char	sep = '\t'
double	identityCut = 50

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Function Documentation

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

References files, identityCut, parseAllFilesIntoOne(), and parseMultipleFiles().

void parseAllFilesIntoOne	(	const char	pat[],
		ostream &	ous,
		bool	rmslf,
		bool	rmtwz
	)

References ifstream(), and parseOneFile().

Referenced by main().

void parseMultipleFiles	(	const vector< string > &	files,
		bool	rmslf,
		bool	rmtwz
	)

References ifstream(), and parseOneFile().

Referenced by main().

pair< int, int > parseOneFile	(	istream &	ins,
		ostream &	ous,
		bool	rmslf,
		bool	rmtwz
	)

References dissect(), and identityCut.

Referenced by parseAllFilesIntoOne(), and parseMultipleFiles().

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.

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Variable Documentation

double identityCut = 50

Referenced by main(), and parseOneFile().

const char sep = '\t'

Referenced by buildGeneInfo(), rangePair::genomicInfo(), operator<<(), outputContainer(), split(), and writeBase().