| Interface | Description |
|---|---|
| GenotypeCallTable |
Interface for genotype calls for a table of taxa and sites. GenotypeCallTable only contain information on the genotype calls - the call table does not have the TaxaList or PositionList. The calls are diploid genotype calls stored and retrieved as bytes. Conversions to string are also provided.
|
| GenotypeMergeRule |
Defines the methods for merging the calls from two taxa. The merge rules need to be defined at the level of genotypic calls and for read depth. In general if depth is available, it will be used to merge.
|
| Class | Description |
|---|---|
| AlleleFreqCache |
Cache for allele frequency statistics. Allele frequency can be expensive to recalculate at large scale, so these class efficiently loops through blocks of sites and caches the statistics on them.
|
| BasicGenotypeMergeRule |
Defines the methods for merging the calls from two taxa. The merge rules need to be defined at the level of genotypic calls and for read depth. In general if depth is available, it will be used to merge.
|
| CombineGenotypeCallTable | |
| DifferenceGenotypeCallTable | |
| GOBIIAvroGenotypeCallTable | |
| GOBIIGenotypeCallTable | |
| GenotypeCallTableBuilder |
Builder to construct a GenotypeCallTable. This builder is generally only used in complex situations, where the GenotypeTableBuilder does not suffice.
|
| HighestDepthGenotypeMergeRule | |
| HybridGenotypeCallTable | |
| LineIndexHapmapGenotypeCallTable | |
| ListStats | |
| ListStatsFilterSite | |
| ListStatsFilterTaxa | |
| ListStatsSite | |
| ListStatsTaxa | |
| MaskGenotypeCallTable | |
| MaskedGenotypes | |
| MergedGenotypeCallTable | |
| ProjectionGenotypeCallTable |
Projection genotype use defined haplotypes and breakpoints that point to a high density genotypes (base GenotypeTable). These are used to efficiently store and connect low density maps with imputed high density genotypes.
|
| SetToNGenotypeMergeRule | |
| Stats |