subcluster.cpp File Reference

#include "hatrees.h"
#include <map>
#include <set>
#include <algorithm>
#include <unistd.h>
#include <dirent.h>
#include "scorepair.h"
#include <iostream>
#include <iterator>
#include <cstdlib>
#include <cstring>


Enumerations
enum	quality { best, good, partial_good, ok, bad, good, bad, modify }
Functions
void	read (ifstream &in, multimap< int, int > &m, int cut)
quality	qual (ifstream &in, int cut)
void	usage ()
int	main (int argc, char *argv[])

Enumeration Type Documentation

enum quality

Enumerator:

best
good
partial_good
ok
bad
good
bad
modify

Function Documentation

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

References scorepair::addNewCluster(), scorepair::badMembers(), clusterIdCnt, deleteCluster(), ifstream(), scorepair::quality(), scorepair::read(), scorepair::showcluster(), string(), usage, and work.

quality qual	(	ifstream &	in,
		int	cut
	)

References bad, hatrees< T >::getNodeCount(), good, hatrees< T >::keyset(), modify, name, hatrees< T >::readFromMap(), and hatrees< T >::showClusterByLine().

Referenced by Gfeature::Gfeature(), and main().

void read	(	ifstream &	in,
		multimap< int, int > &	m,
		int	cut
	)

read the score file, discarding any pair with score < cut

References name.

Referenced by readGFSR().

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.