public class Case
extends java.lang.Object
Constructor | Description |
---|---|
Case(java.lang.String name,
java.util.List<VCFFilter> filters,
Caller caller,
ImputationOption imputer,
CombinerOption combiner,
PrintStats print,
java.lang.String additional) |
Constructor
|
Case(org.apache.commons.configuration2.HierarchicalConfiguration<org.apache.commons.configuration2.tree.ImmutableNode> params) |
Constructor from a config (read in from a XML file)
|
Modifier and Type | Method | Description |
---|---|---|
void |
applyFilters(VCF vcf) |
Apply the filters of this case to a VCF
|
java.lang.String |
getAdditional() |
Get the additional information for this case
|
Caller |
getCaller() |
Get the caller for this case
|
Combiner |
getCombiner() |
Get the combiner for this case if it doesn't require optimizing, else throw
an error
|
Combiner |
getCombiner(java.util.List<SingleGenotypeProbability> called,
java.util.List<SingleGenotypeProbability> imputed,
java.util.List<SingleGenotypeReads> reads,
java.util.List<SingleGenotypeCall> correct,
java.util.List<SingleGenotypeMasked> masked) |
Get the combiner for this case.
|
org.apache.commons.configuration2.tree.ImmutableNode |
getConfig() |
Get the config for this case
|
java.lang.String |
getFilterSummary() |
Get a summary of filters used in this case
|
org.apache.commons.configuration2.tree.ImmutableNode |
getImputeConfig(Caller caller,
Imputer imputer,
Combiner combiner) |
Get the final imputation stage config for this case
|
Imputer |
getImputer() |
Get the imputer for this case if it doesn't require optimizing, else throw
an error
|
Imputer |
getImputer(double[][][] original,
int[][][] readCounts,
java.util.List<SingleGenotypeProbability> maskedprobs,
java.util.List<SingleGenotypeMasked> list) |
Get the imputer for this case.
|
java.lang.String |
getName() |
Get the name of this case
|
PrintStats |
getPrintStats() |
Get the PrintStats object for this case
|
public Case(java.lang.String name, java.util.List<VCFFilter> filters, Caller caller, ImputationOption imputer, CombinerOption combiner, PrintStats print, java.lang.String additional)
name
- The name of the casefilters
- The filters to be appliedcaller
- The caller to useimputer
- The imputer optionscombiner
- The combiner optionsprint
- The stats printing optionsadditional
- Additional string to be used in output (currently
used to show minimum read depth)public Case(org.apache.commons.configuration2.HierarchicalConfiguration<org.apache.commons.configuration2.tree.ImmutableNode> params)
params
- The configpublic void applyFilters(VCF vcf) throws VCFDataException
vcf
- The VCFVCFDataException
- If there is a problem with the
data in the VCFpublic Caller getCaller()
public Imputer getImputer(double[][][] original, int[][][] readCounts, java.util.List<SingleGenotypeProbability> maskedprobs, java.util.List<SingleGenotypeMasked> list)
original
- The called genotype probabilitiesreadCounts
- The read countsmaskedprobs
- The masked genotype probabilitieslist
- List of masked positionspublic Imputer getImputer()
public Combiner getCombiner(java.util.List<SingleGenotypeProbability> called, java.util.List<SingleGenotypeProbability> imputed, java.util.List<SingleGenotypeReads> reads, java.util.List<SingleGenotypeCall> correct, java.util.List<SingleGenotypeMasked> masked)
called
- The called genotype probabilitiesimputed
- The imputed genotype probabilitiesreads
- The read countscorrect
- The correct genotypesmasked
- A list of masked genotypespublic Combiner getCombiner()
public PrintStats getPrintStats()
public java.lang.String getName()
public java.lang.String getFilterSummary()
public java.lang.String getAdditional()
public org.apache.commons.configuration2.tree.ImmutableNode getConfig()
public org.apache.commons.configuration2.tree.ImmutableNode getImputeConfig(Caller caller, Imputer imputer, Combiner combiner)
caller
- The caller to be used in the final imputation stageimputer
- The optimized imputer to be used in the final imputation stagecombiner
- The optimized combiner to be used in the final imputation stage