breakcl.cpp File Reference

#include <iostream>
#include <cstring>
#include <pqxx>
#include <string>
#include <list>
#include <map>
#include <functional>
#include <algorithm>
#include <set>
#include "stddev.h"
#include "hatrees.h"
#include "strformat.h"
#include <sstream>

Classes
class	Relrow
class	Relrow_less
class	Relrow_lessScore
class	Relrow_lessSmcov
class	Relrow_lessLgcov
class	Relrow_lessMatchlen
class	Relrow_eq2
class	Relrow_eq1
class	Relrow_eq1Score
class	Relrow_eq1Smcov
class	Relrow_eq1Lgcov
class	Relrow_eq1Matchlen
struct	Relmin
struct	Subclparam
Functions
Relmin	trim (list< Relrow > &rel)
void	list2map (const list< Relrow > &rel, multimap< string, string > &mm)
void	usage ()
void	breakonecl (connection &pgdb, const string &clidstr, const Subclparam &subparam)
set< string >	getClusterMembers (const list< Relrow > &rel)
bool	isParent (const string &clid, const Subclparam &subparam, work &TR)
int	main (int argc, char *argv[])
Variables
bool	UPDATE_DB = false

---

Function Documentation

void breakonecl	(	connection &	pgdb,
		const string &	clidstr,
		const Subclparam &	subparam
	)

References Subclparam::alntab, avgstd(), Relmin::bad(), hatrees< T >::clear(), Subclparam::cltab, hatrees< T >::clusterArray(), find(), getClusterMembers(), stddev::getMean(), stddev::getSampleStd(), itos(), Relmin::lgcov, list2map(), Relmin::ngiden, Relrow::query, hatrees< T >::readFromMap(), Relrow::Relrow(), stddev::result(), hatrees< T >::showClusterIntId(), Relmin::smcov, Subclparam::treetab, trim(), UPDATE_DB, and work.

Referenced by main().

set< string > getClusterMembers

(

const list< Relrow > &

rel

)

Referenced by breakonecl().

bool isParent	(	const string &	clid,
		const Subclparam &	subparam,
		work &	TR
	)

References Relrow::query, and Subclparam::treetab.

Referenced by main().

void list2map	(	const list< Relrow > &	rel,
		multimap< string, string > &	mm
	)

Referenced by breakonecl().

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

References Subclparam::alntab, breakonecl(), Subclparam::cltab, isParent(), Subclparam::matchlencutoffstr, Subclparam::treetab, UPDATE_DB, and work.

Relmin trim

(

list< Relrow > &

rel

)

References Relrow::lgcov(), Relmin::lgcov, Relrow::matchlen, Relmin::matchlen, Relmin::ngiden, Relrow::ngidentity, Relrow::smcov(), and Relmin::smcov.

Referenced by breakonecl(), gbseq::getType(), and feature::next().

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.

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.

---

Variable Documentation

bool UPDATE_DB = false

Referenced by breakonecl(), and main().