alnexon.cpp File Reference

#include <iostream>
#include <fstream>
#include <map>
#include <vector>
#include <list>
#include "GenModel.h"
#include <iterator>
#include "mysql++.h"
#include "dbinfo.h"
#include <string>

Classes
class	expair
class	idpair
Functions
float	fractionDifference (int x1, int x2)
bool	similarNumber (int x1, int x2, float frac=0.1)
int	alnex (const Noschain &ex1, const Noschain &ex2, vector< int > &countall, ostream &ous, ostream &oustab)
void	extendFront (const vector< int > &l1, const vector< int > &l2, int i, int j, list< expair > &res, ostream &ous)
void	extendBack (const vector< int > &l1, const vector< int > &l2, int i, int j, list< expair > &res, ostream &ous)
bool	perfectMatch (const list< expair > &res, int Eidx1, int Eidx2)
vector< int >	statMatch (const list< expair > &res, int Eidx1, int Eidx2)
void	showmatch (const vector< int > &l1, const vector< int > &l2, const list< expair > &res, ostream &ous)
void	makeExonLength (const Noschain &ex, vector< int > &exl, ostream &ous)
bool	loss2Intron (const vector< int > &l1, const vector< int > &l2, int i1, int i2)
bool	loss1Intron (const vector< int > &l1, const vector< int > &l2, int i1, int i2)
bool	loss1IntronFront (const vector< int > &l1, const vector< int > &l2, int i1, int i2)
bool	loss2IntronFront (const vector< int > &l1, const vector< int > &l2, int i1, int i2)
void	usage ()
int	main (int argc, char *argv[])
void	outputContainer (ostream &ous, const vector< int > &cc, char sep=',')

---

Function Documentation

int alnex	(	const Noschain &	ex1,
		const Noschain &	ex2,
		vector< int > &	countall,
		ostream &	ous,
		ostream &	oustab
	)

compare two exons with no concept of coding or non-coding use dot matrix diagonal indexing method

Parameters:

oustab

tabular output This function output the portion of table relating to the following columns: 1 exon length of model1, 2 exon length of model2, 3 exon align result detail = equal, ~ similar, 4 number of match, -5 number of mismatch, - 6 number of indel, 7 alignment include both ends, 8 alignment quality from 0-4

Returns:

quality. Alignment quality:

• 0: perfect,
• 1: almost perfect,
• 2: indels,
• 3: partial
• 4: no aln

References extendBack(), extendFront(), makeExonLength(), min, outputContainer(), perfectMatch(), showmatch(), and statMatch().

Referenced by main().

void extendBack	(	const vector< int > &	l1,
		const vector< int > &	l2,
		int	i,
		int	j,
		list< expair > &	res,
		ostream &	ous
	)

References fractionDifference(), loss1Intron(), loss2Intron(), and similarNumber().

Referenced by alnex().

void extendFront	(	const vector< int > &	l1,
		const vector< int > &	l2,
		int	i,
		int	j,
		list< expair > &	res,
		ostream &	ous
	)

References loss1IntronFront(), loss2IntronFront(), and min.

Referenced by alnex().

float fractionDifference	(	int	x1,
		int	x2
	)

References min.

Referenced by extendBack().

bool loss1Intron	(	const vector< int > &	l1,
		const vector< int > &	l2,
		int	i1,
		int	i2
	)

References similarNumber().

Referenced by extendBack().

bool loss1IntronFront	(	const vector< int > &	l1,
		const vector< int > &	l2,
		int	i1,
		int	i2
	)

References similarNumber().

Referenced by extendFront().

bool loss2Intron	(	const vector< int > &	l1,
		const vector< int > &	l2,
		int	i1,
		int	i2
	)

References similarNumber().

Referenced by extendBack().

bool loss2IntronFront	(	const vector< int > &	l1,
		const vector< int > &	l2,
		int	i1,
		int	i2
	)

References similarNumber().

Referenced by extendFront().

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

References alnex(), MysqlDBInfo::getAuthenInfo(), MysqlDBInfo::getPassword(), MysqlDBInfo::getUser(), passwd, qual(), Noschain::subchain(), usage, and user.

void makeExonLength	(	const Noschain &	ex,
		vector< int > &	exl,
		ostream &	ous
	)

References length, Range::length(), and Noschain::numberOfRanges().

Referenced by alnex().

void outputContainer	(	ostream &	ous,
		const vector< int > &	cc,
		char	sep = ','
	)

References sep.

Referenced by alnex().

bool perfectMatch	(	const list< expair > &	res,
		int	Eidx1,
		int	Eidx2
	)

Referenced by alnex().

void showmatch	(	const vector< int > &	l1,
		const vector< int > &	l2,
		const list< expair > &	res,
		ostream &	ous
	)

Referenced by alnex().

bool similarNumber	(	int	x1,
		int	x2,
		float	frac = 0.1
	)

References min.

Referenced by extendBack(), loss1Intron(), loss1IntronFront(), loss2Intron(), and loss2IntronFront().

vector< int > statMatch	(	const list< expair > &	res,
		int	Eidx1,
		int	Eidx2
	)

Returns:

a vector of integers

• 0 number of match,
• 1 number of mismatch,
• 2 number of indel 3
• 3 match Start (0 for false, 1 for true)
• 4 match end (0 for false, 1 for true)

References max.

Referenced by alnex().

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.