| Class | Description |
|---|---|
| BuilderFromGVCF |
Created by zrm22 on 3/24/17.
|
| BuilderFromGenotypeHDF5 |
Provides Builder and methods to build HDF5 files. The methods for merging files work, but they are far from optimal. It appears that they are taking twice the memory that they should. Ed has looked for the memory leak with a profiler but cannot find it yet. Todo: TAS-70 Details the issues with apparent memory leak.
|
| BuilderFromHapMap | |
| BuilderFromHapMapLIX | |
| BuilderFromPLINK | |
| BuilderFromVCF |
Create an alignment based on VCF format file (either .txt or compressed). Alleles are set as global reference. e.g. code
|
| BuilderFromVCFUsingHTSJDK |
This builder reads a VCF formatted file and creates a
|
| FilterJSONUtils | |
| FlapjackUtils | |
| JSONUtils | |
| LineIndex | |
| LineIndexBuilder | |
| ProjectionGenotypeIO |
Methods for reading and writing ProjectionGenotypes to files. ProjectionGenotypes have two parts - one is the Projection file that has the names of high density genotyped taxa and the recombination breakpoints for each of the low density taxa that point to the high density taxa.
|
| ReadBedfile | |
| ReadNumericMarkerUtils | |
| SiteScoresIO | |
| VCFUtil |