# Package org.snpeff.stats

package org.snpeff.stats

Related Packages
Package
Description
org.snpeff
org.snpeff.stats.plot
Class
Description
AlleleCountStats
Count singletons and other allele counts per sample
Average
A simple class that calculates averages
AverageInt
A simple class that calculates average of integer numbers
BooleanMutable
A mutable boolean
ChrPosStats
How many changes per position do we have in a chromosome.
CountByKey<T>
Counters indexed by key.
CountByType
Counters indexed by 'type' (type is a generic string that can mean anything)
Counter
A simple class that counts...
CounterDouble
A simple class that counts...
CoverageByType
FloatStats
A simple class that does some basic statistics on double numbers
GeneCountByTypeTable
Count for each 'type' and 'gene'.
GenotypeStats
Calculate statistics on genotype
HomHetStats
Count Hom/Het per sample From Pierre: For multiple ALT, I suggest to count the number of REF allele 0/1 => ALT1 0/2 => ALT1 1/1 => ALT2 2/2 => ALT2 1/2 => ALT2
IntStats
A simple class that does some basic statistics on integer numbers
MineMarkerIntervals
Mine marker intervals: I.e.
MineTwoMarkerIntervals
Mine marker intervals: I.e.
ObservedOverExpected
Observed over expected values (o/e) ratios E.g.: CpG dinucleotides in a sequence
ObservedOverExpectedCHG
Observed over expected values (o/e) of CHG in a sequence
ObservedOverExpectedCHH
Observed over expected values (o/e) of CHH in a sequence
ObservedOverExpectedCpG
Observed over expected values (o/e) of CpG in a sequence
PosStats
How many changes per position do we have in a chromosome.
ReadsOnMarkersModel
Calculate the maximum interval length by type, for all markers in a genome Create a probability model based on binomial ditribution.
SamplingStats<T>
Perform stats by analyzing some samples
TranslocationReport
Pojo for translocation reports
TsTvStats
Calculate Ts/Tv rations per sample (transitions vs transversions)
VariantEffectStats
Variants annotation statistics.
VariantStats
Variants statistics: These are statisticas at Variant level.
VariantTypeStats
Count variant types (SNP, MNP, INS, DEL)
VcfStats
VCF statistics: These are statisticas at VCF line (i.e.