public class DepthMask
extends java.lang.Object
Modifier and Type | Class | Description |
---|---|---|
static class |
DepthMask.Method |
Represents the method to be used to select genotypes to be masked
|
Constructor | Description |
---|---|
DepthMask(int[][][] depths,
int number,
int minDepth,
int maskTo,
DepthMask.Method method,
Caller caller) |
Masks a given number of genotypes to a given depth
|
DepthMask(int[][][] depths,
int number,
int minDepth,
int maskTo,
Caller caller) |
Masks a given number of genotypes to a given depth
|
DepthMask(int[][][] depths,
int number,
int minDepth,
ComparableDistribution<java.lang.Integer> maskToDistribution,
DepthMask.Method method,
java.util.List<SingleGenotypePosition> dontUse,
Caller caller) |
Masks a given number of genotypes to a given distribution of depths
|
DepthMask(int[][][] depths,
int number,
int minDepth,
ComparableDistribution<java.lang.Integer> maskToDistribution,
Caller caller) |
Masks a given number of genotypes to a given depth
|
Modifier and Type | Method | Description |
---|---|---|
int[][][] |
maskedArray() |
Get an array of masked reads.
|
java.util.List<SingleGenotypeMasked> |
maskedList() |
Get a list of masked reads
|
java.util.List<SingleGenotypePosition> |
maskedPositions() |
Get a list of masked positions
|
int |
size() |
Returns the number of genotypes masked
|
public DepthMask(int[][][] depths, int number, int minDepth, int maskTo, Caller caller) throws NotEnoughMaskableGenotypesException
depths
- The original read countsnumber
- The number of genotypes to maskminDepth
- Only mask genotypes with more than this read depthmaskTo
- Mask to read depthcaller
- The genotype callerNotEnoughMaskableGenotypesException
- If there is not
enough maskable genotypespublic DepthMask(int[][][] depths, int number, int minDepth, int maskTo, DepthMask.Method method, Caller caller) throws NotEnoughMaskableGenotypesException
depths
- The original read countsnumber
- The number of genotypes to maskminDepth
- Only mask genotypes with more than this read depthmaskTo
- Mask to read depthmethod
- The method to be used to mask genotypescaller
- The genotype callerNotEnoughMaskableGenotypesException
- If there is not
enough maskable genotypespublic DepthMask(int[][][] depths, int number, int minDepth, ComparableDistribution<java.lang.Integer> maskToDistribution, Caller caller) throws NotEnoughMaskableGenotypesException
depths
- The original read countsnumber
- The number of genotypes to maskminDepth
- Only mask genotypes with more than this read depthcaller
- The genotype callermaskToDistribution
- Mask to this distribution of read depthsNotEnoughMaskableGenotypesException
- If there is not
enough maskable genotypespublic DepthMask(int[][][] depths, int number, int minDepth, ComparableDistribution<java.lang.Integer> maskToDistribution, DepthMask.Method method, java.util.List<SingleGenotypePosition> dontUse, Caller caller) throws NotEnoughMaskableGenotypesException
depths
- The original read countsnumber
- The number of genotypes to maskminDepth
- Only mask genotypes with more than this number of readsmaskToDistribution
- Mask to this distribution of read depthsmethod
- The method to be used to mask genotypesdontUse
- A list of genotypes not to use for maskingcaller
- The genotype callerNotEnoughMaskableGenotypesException
- If there is not
enough maskable genotypespublic int[][][] maskedArray()
public java.util.List<SingleGenotypeMasked> maskedList()
public java.util.List<SingleGenotypePosition> maskedPositions()
public int size()