Package org.snpeff.stats
Class ReadsOnMarkersModel
java.lang.Object
org.snpeff.stats.ReadsOnMarkersModel
Calculate the maximum interval length by type, for all markers in a genome
Create a probability model based on binomial ditribution.
- Author:
- pcingola
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
Count bases covered for each marker typegetProb()
void
Load data from a filevoid
randomSampling
(int iterations, int readLen, int numReads) Sample and calculate the probability of hitting each type of marker (marker.class).boolean
run()
Runvoid
Save model to filevoid
setMarkerTypes
(MarkerTypes markerTypes) void
setNumIterations
(int numIterations) void
setNumReads
(int numReads) void
setReadLength
(int readLength) void
setSnpEffectPredictor
(SnpEffectPredictor snpEffectPredictor) void
setVerbose
(boolean verbose) toString()
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Constructor Details
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ReadsOnMarkersModel
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Method Details
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countBases
public void countBases()Count bases covered for each marker type -
getCountBases
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getCountMarkers
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getProb
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getRawCountBases
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getRawCountMarkers
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load
Load data from a file- Parameters:
fileName
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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:
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save
Save model to file- Parameters:
fileName
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setMarkerTypes
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setNumIterations
public void setNumIterations(int numIterations) -
setNumReads
public void setNumReads(int numReads) -
setReadLength
public void setReadLength(int readLength) -
setSnpEffectPredictor
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setVerbose
public void setVerbose(boolean verbose) -
toString
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