public class DepthMaskFactory
extends java.lang.Object
Constructor | Description |
---|---|
DepthMaskFactory(int number,
int minDepth,
int limitDist,
DepthMask.Method method) |
Default constructor
|
DepthMaskFactory(org.apache.commons.configuration2.HierarchicalConfiguration<org.apache.commons.configuration2.tree.ImmutableNode> params) |
Creates the factory from the given configuration
|
Modifier and Type | Method | Description |
---|---|---|
org.apache.commons.configuration2.tree.ImmutableNode |
getConfig() |
Get the config for the factory
|
DepthMask |
getDepthMask(int[][][] readCounts,
Caller caller) |
Get a depth mask
|
DepthMask |
getDepthMask(int[][][] readCounts,
java.util.List<SingleGenotypePosition> dontUse,
Caller caller) |
Get a depth mask
|
public DepthMaskFactory(int number, int minDepth, int limitDist, DepthMask.Method method)
number
- The number of genotypes to makes reads fromminDepth
- Only mask genotypes with a greater read depth than thislimitDist
- The distribution to mask the reads tomethod
- The method to be used to select genotypes to be maskedpublic DepthMaskFactory(org.apache.commons.configuration2.HierarchicalConfiguration<org.apache.commons.configuration2.tree.ImmutableNode> params)
params
- The configurationpublic DepthMask getDepthMask(int[][][] readCounts, java.util.List<SingleGenotypePosition> dontUse, Caller caller) throws NotEnoughMaskableGenotypesException
readCounts
- The reads to maskdontUse
- A list of genotypes not to maskcaller
- The genotype caller to useNotEnoughMaskableGenotypesException
- If there is not enough maskable genotypespublic DepthMask getDepthMask(int[][][] readCounts, Caller caller) throws NotEnoughMaskableGenotypesException
readCounts
- The reads to maskcaller
- The genotype caller to useNotEnoughMaskableGenotypesException
- If there is not enough maskable genotypespublic org.apache.commons.configuration2.tree.ImmutableNode getConfig()