Package org.snpeff.stats

Class GenotypeStats

java.lang.Object

org.snpeff.stats.GenotypeStats

All Implemented Interfaces:

SamplingStats<VcfEntry>

public class GenotypeStats
extends java.lang.Object
implements SamplingStats<VcfEntry>

Calculate statistics on genotype

Author:

pablocingolani

Constructor Summary

Constructors

Constructor	Description
GenotypeStats()

Method Summary

Modifier and Type	Method	Description
IntStats	getAlleleCount()
java.lang.String	getAlleleCountHistoUrl()
IntStats	getAlleleFrequency()
java.lang.String	getAlleleFrequencyHistoUrl()
java.lang.String	getHetBySampleUrl()
java.lang.String	getHomBySampleUrl()
java.lang.String	getHomHetTable()
java.lang.String	getMissingBySampleUrl()
boolean	hasData()	Does this statistic have any data?
void	sample(VcfEntry vcfEntry)	Update counters
java.lang.String	toString()	Show results to stdout

Methods inherited from class java.lang.Object

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

Constructor Detail

GenotypeStats

public GenotypeStats()

Method Detail

getAlleleCount

public IntStats getAlleleCount()

getAlleleCountHistoUrl

public java.lang.String getAlleleCountHistoUrl()

getAlleleFrequency

public IntStats getAlleleFrequency()

getAlleleFrequencyHistoUrl

public java.lang.String getAlleleFrequencyHistoUrl()

getHetBySampleUrl

public java.lang.String getHetBySampleUrl()

getHomBySampleUrl

public java.lang.String getHomBySampleUrl()

getHomHetTable

public java.lang.String getHomHetTable()

getMissingBySampleUrl

public java.lang.String getMissingBySampleUrl()

hasData

public boolean hasData()

Description copied from interface: SamplingStats

Does this statistic have any data?

Specified by:

hasData in interface SamplingStats<VcfEntry>

Returns:

sample

public void sample(VcfEntry vcfEntry)

Update counters

Specified by:

sample in interface SamplingStats<VcfEntry>

toString

public java.lang.String toString()

Show results to stdout

Overrides:

toString in class java.lang.Object