mergefootprint.cpp File Reference

#include <mysql++.h>
#include <iostream>
#include <fstream>
#include <list>
#include "Range.h"
#include <string>
#include "strformat.h"

Classes
struct	ProgParam
Functions
bool	createSummaryTable (Connection &dbh, const string &tab)
void	topfp (Connection &conn, Connection &conn2, const ProgParam &par)
void	usage ()
void	mergeNeighbor (Connection &conn, Connection &conn2, const ProgParam &par)
int	main (int argc, char *argv[])
ostream &	operator<< (ostream &ous, const ProgParam &par)

---

Function Documentation

bool createSummaryTable	(	Connection &	dbh,
		const string &	tab
	)

always drop existing table create a summary table Here the exon is the merged homology part, not strictly.

Referenced by mergeNeighbor().

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

References ProgParam::fpdetailtab, ProgParam::fptoptab, mergeNeighbor(), ProgParam::oufile, ProgParam::outab, and user.

void mergeNeighbor	(	Connection &	conn,
		Connection &	conn2,
		const ProgParam &	par
	)

this version deals with multiple target databases Normally you don't do this. It is one search db. I am using this test case to develope this application

References ProgParam::avgidencut, RangeChain::begin(), createSummaryTable(), RangeChain::end(), ProgParam::exolpcut, ProgParam::exolpfrcut, RangeChain::exonMerge(), RangeChain::exonOverlap(), ProgParam::fpdetailtab, ProgParam::fptoptab, itos(), RangeChain::numberOfRanges(), ProgParam::oufile, ProgParam::outab, string(), RangeChain::sumLength(), and RangeChain::tableRows().

Referenced by main().

ostream& operator<<	(	ostream &	ous,
		const ProgParam &	par
	)

only check intab and outab for not emptyness

References ProgParam::avgidencut, ProgParam::exolpcut, ProgParam::exolpfrcut, ProgParam::fpdetailtab, ProgParam::fptoptab, ProgParam::oufile, and ProgParam::outab.

void topfp	(	Connection &	conn,
		Connection &	conn2,
		const ProgParam &	par
	)

this version deals with multiple target databases Normally you don't do this. It is one search db. I am using this test case to develope this application

Make sure the quality of the table has been set to non-null. This program will only pick quality >= 0.

References Range::begin(), createUniqueTable(), del(), Range::end(), ProgParam::fpmaxlen, ProgParam::intab, Range::merge(), ProgParam::oufile, ProgParam::outab, Range::output(), Range::overlap(), and string().

Referenced by main().

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.