Package org.snpeff.coverage

Class Coverage

java.lang.Object

org.snpeff.coverage.Coverage

All Implemented Interfaces:

java.io.Serializable

public class Coverage
extends java.lang.Object
implements java.io.Serializable

Base by base coverage (one chromsome)

Author:

pcingola

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor	Description
Coverage()

Method Summary

Modifier and Type	Method	Description
double	avgCoverage(Marker m)	Calculate average coverage per base
static Coverage	calculateFromSam(java.lang.String samFile, boolean verbose)	Calculate coverage from a SAM file
long	coverage(Marker m)	Calculate total coverage per base
void	createChr(java.lang.String chr, int len)	Create new chromosome coverage
CoverageChr	get(java.lang.String chr)
void	inc(java.lang.String chr, int start, int end)	Increment a region
java.lang.String	toString()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

Coverage

public Coverage()

Method Detail

calculateFromSam

public static Coverage calculateFromSam(java.lang.String samFile,
                                        boolean verbose)

Calculate coverage from a SAM file

Parameters:

samFile -

verbose -

Returns:

avgCoverage

public double avgCoverage(Marker m)

Calculate average coverage per base

Parameters:

m - : A marker interval

Returns:

coverage

public long coverage(Marker m)

Calculate total coverage per base

Parameters:

m - : A marker interval

Returns:

createChr

public void createChr(java.lang.String chr,
                      int len)

Create new chromosome coverage

Parameters:

chr -

len -

get

public CoverageChr get(java.lang.String chr)

inc

public void inc(java.lang.String chr,
                int start,
                int end)

Increment a region

Parameters:

start -

end -

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object