| 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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