AlleleCountStats |
Count singletons and other allele counts per sample
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Average |
A simple class that calculates averages
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AverageInt |
A simple class that calculates average of integer numbers
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BooleanMutable |
A mutable boolean
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ChrPosStats |
How many changes per position do we have in a chromosome.
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CountByKey<T> |
Counters indexed by key.
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CountByType |
Counters indexed by 'type' (type is a generic string that can mean anything)
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Counter |
A simple class that counts...
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CounterDouble |
A simple class that counts...
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CoverageByType |
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FloatStats |
A simple class that does some basic statistics on double numbers
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GeneCountByTypeTable |
Count for each 'type' and 'gene'.
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GenotypeStats |
Calculate statistics on genotype
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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
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IntStats |
A simple class that does some basic statistics on integer numbers
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MineMarkerIntervals |
Mine marker intervals: I.e.
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MineTwoMarkerIntervals |
Mine marker intervals: I.e.
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ObservedOverExpected |
Observed over expected values (o/e) ratios
E.g.: CpG dinucleotides in a sequence
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ObservedOverExpectedCHG |
Observed over expected values (o/e) of CHG in a sequence
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ObservedOverExpectedCHH |
Observed over expected values (o/e) of CHH in a sequence
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ObservedOverExpectedCpG |
Observed over expected values (o/e) of CpG in a sequence
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PosStats |
How many changes per position do we have in a chromosome.
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ReadsOnMarkersModel |
Calculate the maximum interval length by type, for all markers in a genome
Create a probability model based on binomial ditribution.
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TranslocationReport |
Pojo for translocation reports
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TsTvStats |
Calculate Ts/Tv rations per sample (transitions vs transversions)
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VariantEffectStats |
Variants effect statistics
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VariantStats |
Variants statistics
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VariantTypeStats |
Count variant types (SNP, MNP, INS, DEL)
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VcfStats |
VCF statistics: This are usually multi-sample statistics
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