dbaln_chimera.cpp File Reference

#include "mysql++.h"
#include <string>
#include "bioseq.h"
#include "dynaln.h"
#include <math.h>
#include <fstream>
#include "dbinfo.h"
#include <map>
#include "strformat.h"
#include "dbalnhelper.h"

Defines
#define	MYSQLPLUS2
Functions
void	alignProtein (const string &alnfile, Connection &conn)
void	usage ()
int	main (int argc, char *argv[])
Variables
string	user
string	passwd

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Define Documentation

#define MYSQLPLUS2

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Function Documentation

void alignProtein	(	const string &	alnfile,
		Connection &	conn
	)

References Dynaln::headers(), itos(), length, Dynaln::printAlign(), Dynaln::runlocal(), table2map(), table2pair(), tableFillMapFirst(), and Dynaln::toDelimitedString().

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

References alignProtein(), MysqlDBInfo::getAuthenInfo(), MysqlDBInfo::getPassword(), MysqlDBInfo::getUser(), passwd, usage, and user.

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.

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Variable Documentation

string passwd

string user

use three connections, the first connection provide the alignment pairs. the second and the third provided the raw sequences All three connections can be the same. each connection provide a table.

format I am adding a format for bootstrap where a vector of 0,1,2 are output that stands for mismatch, similar, and match respectively.