GCcontent.cpp File Reference

#include <iostream>
#include <fstream>
#include "bioseq.h"

Functions
void	usage ()
void	writeResult (ostream &ous, long int A, long int C, long int G, long int T, long int N, long int genomiclen)
int	main (int argc, char *argv[])

---

Function Documentation

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

use fasta files to generate GC contesnt for all the sequences in one file

References A, C, G, DNA::GCContent(), bioseq::getName(), ifstream(), bioseq::length(), N, bioseq::read(), T, usage, and writeResult().

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.

void writeResult	(	ostream &	ous,
		long int	A,
		long int	C,
		long int	G,
		long int	T,
		long int	N,
		long int	genomiclen
	)