Package org.snpeff.stats

Class ReadsOnMarkersModel

java.lang.Object

org.snpeff.stats.ReadsOnMarkersModel

public class ReadsOnMarkersModel
extends java.lang.Object

Calculate the maximum interval length by type, for all markers in a genome Create a probability model based on binomial ditribution.

Author:

pcingola

Constructor Summary

Constructors

Constructor	Description
ReadsOnMarkersModel(SnpEffectPredictor snpEffectPredictor)

Method Summary

Modifier and Type	Method	Description
void	countBases()	Count bases covered for each marker type
CountByType	getCountBases()
CountByType	getCountMarkers()
CountByType	getProb()
CountByType	getRawCountBases()
CountByType	getRawCountMarkers()
void	load(java.lang.String fileName)	Load data from a file
void	randomSampling(int iterations, int readLen, int numReads)	Sample and calculate the probability of hitting each type of marker (marker.class).
boolean	run()	Run
void	save(java.lang.String fileName)	Save model to file
void	setMarkerTypes(MarkerTypes markerTypes)
void	setNumIterations(int numIterations)
void	setNumReads(int numReads)
void	setReadLength(int readLength)
void	setSnpEffectPredictor(SnpEffectPredictor snpEffectPredictor)
void	setVerbose(boolean verbose)
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

ReadsOnMarkersModel

public ReadsOnMarkersModel(SnpEffectPredictor snpEffectPredictor)

Method Detail

countBases

public void countBases()

Count bases covered for each marker type

getCountBases

public CountByType getCountBases()

getCountMarkers

public CountByType getCountMarkers()

getProb

public CountByType getProb()

getRawCountBases

public CountByType getRawCountBases()

getRawCountMarkers

public CountByType getRawCountMarkers()

load

public void load(java.lang.String fileName)

Load data from a file

Parameters:

fileName -

randomSampling

public void randomSampling(int iterations,
                           int readLen,
                           int numReads)

Sample and calculate the probability of hitting each type of marker (marker.class). Creates 'numReads' reads of size 'readLen' and count how many of them hit each marker type. Iterate 'iterations' times to obtain a distribution.

run

public boolean run()

Run

Returns:

save

public void save(java.lang.String fileName)

Save model to file

Parameters:

fileName -

setMarkerTypes

public void setMarkerTypes(MarkerTypes markerTypes)

setNumIterations

public void setNumIterations(int numIterations)

setNumReads

public void setNumReads(int numReads)

setReadLength

public void setReadLength(int readLength)

setSnpEffectPredictor

public void setSnpEffectPredictor(SnpEffectPredictor snpEffectPredictor)

setVerbose

public void setVerbose(boolean verbose)

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object