Package org.snpeff.stats

Class VariantStats

java.lang.Object

org.snpeff.stats.VariantStats

All Implemented Interfaces:

SamplingStats<Variant>

public class VariantStats
extends java.lang.Object
implements SamplingStats<Variant>

Variants statistics

Field Summary

Fields

Modifier and Type	Field	Description
static java.lang.String	CHANGE_SEPARATOR

Constructor Summary

Constructors

Constructor	Description
VariantStats(Genome genome)

Method Summary

Modifier and Type	Method	Description
char[]	getBases()
java.lang.String	getBasesChangesColor(java.lang.String oldBase, java.lang.String newBase)	Background color used for base change table
long	getBasesChangesCount(java.lang.String oldBase, java.lang.String newBase)
Variant.VariantType[]	getChangeType()
int	getChangeTypeLength()
int	getChromosomeLength(java.lang.String chromoName)	Choromosome length
java.util.List<java.lang.String>	getChromosomeNamesEffective()	A list of chromosomes that had at least one change Note: Chromosome names are sorted.
ChrPosStats	getChrPosStats(java.lang.String chrName)
java.lang.String	getChrPosStatsChartUrl(java.lang.String chrName)
long	getCount()	Total number of variants
CountByType	getCountByChangeType()	Number of variants by type
int	getCountByChromosome(java.lang.String chromoName)	Number of changes by chromosome
long	getCountNonEmptyId()
long	getCountNonVariants()
long	getGenomeLen()	Genome length
long	getGenomeLenEffective()	Genome effective length: The sum of length of every chromosome that had a change (e.g.
IntStats	getIndelLen()
java.lang.String	getIndelLenHistoUrl()
double	getKnownRatio()	Ratio of known variants (the one with a non-empty ID) and total variants
long	getRateOfChange()	Rate of change
int	getRateOfChangeByChromosome(java.lang.String chromoName)	Rate of change by chromosome
boolean	hasData()	Does this statistic have any data?
void	sample(Variant variant)	Use this sample to perform statistics

Methods inherited from class java.lang.Object

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

Field Detail

CHANGE_SEPARATOR

public static final java.lang.String CHANGE_SEPARATOR

See Also:

Constant Field Values

Constructor Detail

VariantStats

public VariantStats(Genome genome)

Method Detail

getBases

public char[] getBases()

getBasesChangesColor

public java.lang.String getBasesChangesColor(java.lang.String oldBase,
                                             java.lang.String newBase)

Background color used for base change table

getBasesChangesCount

public long getBasesChangesCount(java.lang.String oldBase,
                                 java.lang.String newBase)

getChangeType

public Variant.VariantType[] getChangeType()

getChangeTypeLength

public int getChangeTypeLength()

getChromosomeLength

public int getChromosomeLength(java.lang.String chromoName)

Choromosome length

Parameters:

chromoName -

Returns:

getChromosomeNamesEffective

public java.util.List<java.lang.String> getChromosomeNamesEffective()

A list of chromosomes that had at least one change Note: Chromosome names are sorted.

Returns:

getChrPosStats

public ChrPosStats getChrPosStats(java.lang.String chrName)

getChrPosStatsChartUrl

public java.lang.String getChrPosStatsChartUrl(java.lang.String chrName)

getCount

public long getCount()

Total number of variants

Returns:

getCountByChangeType

public CountByType getCountByChangeType()

Number of variants by type

Returns:

getCountByChromosome

public int getCountByChromosome(java.lang.String chromoName)

Number of changes by chromosome

Parameters:

chromoName -

Returns:

getCountNonEmptyId

public long getCountNonEmptyId()

getCountNonVariants

public long getCountNonVariants()

getGenomeLen

public long getGenomeLen()

Genome length

Returns:

getGenomeLenEffective

public long getGenomeLenEffective()

Genome effective length: The sum of length of every chromosome that had a change (e.g. If there was no SNP in chromosome Y, then it doesn't count in the effective length)

Returns:

getIndelLen

public IntStats getIndelLen()

getIndelLenHistoUrl

public java.lang.String getIndelLenHistoUrl()

getKnownRatio

public double getKnownRatio()

Ratio of known variants (the one with a non-empty ID) and total variants

getRateOfChange

public long getRateOfChange()

Rate of change

Returns:

getRateOfChangeByChromosome

public int getRateOfChangeByChromosome(java.lang.String chromoName)

Rate of change by chromosome

Parameters:

chromoName -

Returns:

hasData

public boolean hasData()

Description copied from interface: SamplingStats

Does this statistic have any data?

Specified by:

hasData in interface SamplingStats<Variant>

Returns:

sample

public void sample(Variant variant)

Use this sample to perform statistics

Specified by:

sample in interface SamplingStats<Variant>