Package org.snpeff.stats
package org.snpeff.stats
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ClassDescriptionCount singletons and other allele counts per sampleA simple class that calculates averagesA simple class that calculates average of integer numbersA mutable booleanHow many changes per position do we have in a chromosome.CountByKey<T>Counters indexed by key.Counters indexed by 'type' (type is a generic string that can mean anything)A simple class that counts...A simple class that counts...A simple class that does some basic statistics on double numbersCount for each 'type' and 'gene'.Calculate statistics on genotypeCount 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 => ALT2A simple class that does some basic statistics on integer numbersMine marker intervals: I.e.Mine marker intervals: I.e.Observed over expected values (o/e) ratios E.g.: CpG dinucleotides in a sequenceObserved over expected values (o/e) of CHG in a sequenceObserved over expected values (o/e) of CHH in a sequenceObserved over expected values (o/e) of CpG in a sequenceHow many changes per position do we have in a chromosome.Calculate the maximum interval length by type, for all markers in a genome Create a probability model based on binomial ditribution.Perform stats by analyzing some samplesPojo for translocation reportsCalculate Ts/Tv rations per sample (transitions vs transversions)Variants effect statisticsVariants statisticsCount variant types (SNP, MNP, INS, DEL)VCF statistics: This are usually multi-sample statistics