Coverdepth.cpp File Reference

#include "Coverdepth.h"
#include <cstring>
#include <limits>
#include <iomanip>
#include <cmath>
#include <strformat.h>

Functions
void	computeDerivative (const int *in, int *out, int L, int dx) throw (NegativeCoverage)
void	sumNumber (const int *A, int *&B, int L, int w)
ostream &	operator<< (ostream &ous, const Dip &v)
ostream &	operator<< (ostream &ous, const Coverdepth &cd)
void	averageIterator (list< pair< double, int > >::iterator &li1, list< pair< double, int > >::iterator &li2)
void	average3Iterator (list< pair< double, int > >::iterator &li1, list< pair< double, int > >::iterator &li2, list< pair< double, int > >::iterator &li3)
int	growZero (list< pair< double, int > > &seg)
int	joinNeighbor (list< pair< double, int > > &seg, double diff=2)
int	mergeTriple (list< pair< double, int > > &seg)
void	displaySegments (const list< pair< double, int > > &seg)

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Function Documentation

void average3Iterator	(	list< pair< double, int > >::iterator &	li1,
		list< pair< double, int > >::iterator &	li2,
		list< pair< double, int > >::iterator &	li3
	)

Referenced by Coverdepth::findLeftDropoff(), Coverdepth::findRightDropoff(), and mergeTriple().

void averageIterator	(	list< pair< double, int > >::iterator &	li1,
		list< pair< double, int > >::iterator &	li2
	)

Referenced by growZero(), and joinNeighbor().

void computeDerivative	(	const int *	in,
		int *	out,
		int	L,
		int	dx = 1
	)			throw (NegativeCoverage)

computes integer derivative dx determins the distance to use for X. Larger x tends to supress noise if there is a trend. out must have the same or longer length as in

References L.

Referenced by Coverdepth::derivative(), Coverdepth::findDip(), and Coverdepth::searchDip().

void displaySegments

(

const list< pair< double, int > > &

seg

)

References del().

int growZero

(

list< pair< double, int > > &

seg

)

References averageIterator(), and del().

Referenced by Coverdepth::searchDip().

int joinNeighbor	(	list< pair< double, int > > &	seg,
		double	diff = 2
	)

References averageIterator(), and del().

Referenced by Coverdepth::searchDip().

int mergeTriple

(

list< pair< double, int > > &

seg

)

References average3Iterator(), and del().

Referenced by Coverdepth::searchDip().

ostream& operator<<	(	ostream &	ous,
		const Coverdepth &	cd
	)

This is used by ESTAssembly::writeModel() to generate the last column of the tabular format Format: B-E (+/-) integer,.... B,E in genomic coordinate integer for the coverage of base at same index (0-based)

References Coverdepth::B, Coverdepth::dep, Coverdepth::direction, Coverdepth::E, and Coverdepth::length().

ostream& operator<<	(	ostream &	ous,
		const Dip &	v
	)

set this objecet into a right Dropoff

References Dip::BLH, Dip::bottomWidth(), Dip::BRH, Dip::LH, Dip::posBL, Dip::posBR, Dip::posTL, Dip::posTR, and Dip::RH.

void sumNumber	(	const int *	A,
		int *&	B,
		int	L,
		int	w
	)

w > 1 A and B should have the same length L elements B has memory allocated same or longer

References delta().

Referenced by testBaseProfile().