| Interface | Description |
|---|---|
| Allele |
Defines Allele present at a genomic Position
|
| Filter | |
| GenotypeTable |
A representation of the SNP and indel variation for a set of taxa and genomic positions.
|
| MaskMatrix |
| Class | Description |
|---|---|
| AbstractMaskMatrix | |
| CombineGenotypeTable |
Combines multiple GenotypeTables together.
|
| CoreGenotypeTable |
Basic implementation of a
|
| ExportUtils |
Exports Genotype Tables to various file formats.
|
| FilterAndMaskGVCFGenomeSequence |
Created by zrm22 on 4/3/17.
|
| FilterGenotypeTable |
Taxa and site filtering of GenotypeTables. The class essentially creates views of the baseGenotypeTable through arrays for indirection.
|
| FilterList | |
| FilterSite | |
| FilterTableReport | |
| FilterTaxa | |
| GenotypeTableBuilder |
Builder for GenotypeTables. New genotypeTables are built from a minimum of TaxaList, PositionList, and GenotypeCallTable. Depth and Scores are optional features of GenotypeTables.
|
| GenotypeTableUtils |
Utility methods for comparing, sorting, and counting genotypes.
|
| HapMapHDF5Constants |
Definition of fields and directories of the GenotypeTable in a HDF5 file format.
|
| ImportUtils |
Methods for importing GenotypeTables from various file formats.
|
| MaskGenotypeMatrix | |
| MaskGenotypeStatsMatrix | |
| MaskMatrixBuilder | |
| MaskSiteMatrix | |
| MaskTaxaMatrix | |
| MergedGenotypeTable | |
| NucleotideAlignmentConstants | |
| ProjectionBuilder |
Builder for a projection alignment. Projection alignments use defined haplotypes and breakpoints that point to high density genotypes (base GenotypeTable). These are used to efficiently store and connect low density maps with imputed high density genotypes.
|
| ReadSequenceAlignmentUtils |
reads aligned sequence data from plain text files.
|
| SimpleAllele |
Basic implementation of allele. TODO: Consider whether this should be kept. TODO: Should there be a builder? TODO: Should there simple nucleotide one versus other states. Memory could be an important consideration.
|
| TOPMGenotypeTable | |
| Translate |
This translates filtered taxa and sites. Also indicates masking, but this implementation has no mask.
|
| TranslateBuilder | |
| TranslateIndex |
No translation to index.
|
| TranslateIndexBuilder | |
| TranslateIndexRange | |
| TranslateIndexRedirect |
Translation redirects index to corresponding index in base genotype table.
|
| TranslateIndexRedirectUnordered | |
| TranslateNegative |