Package Executable
Class Case
- java.lang.Object
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- Executable.Case
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public class Case extends java.lang.Object
Represent the LinkImputeR inputs for a single case (filters, caller, imputer and combiner)
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Constructor Summary
Constructors Constructor Description Case(java.lang.String name, java.util.List<VCFFilter> filters, Caller caller, ImputationOption imputer, CombinerOption combiner, PrintStats print, java.lang.String additional)
ConstructorCase(org.apache.commons.configuration2.HierarchicalConfiguration<org.apache.commons.configuration2.tree.ImmutableNode> params)
Constructor from a config (read in from a XML file)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
applyFilters(VCF vcf)
Apply the filters of this case to a VCFjava.lang.String
getAdditional()
Get the additional information for this caseCaller
getCaller()
Get the caller for this caseCombiner
getCombiner()
Get the combiner for this case if it doesn't require optimizing, else throw an errorCombiner
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 casejava.lang.String
getFilterSummary()
Get a summary of filters used in this caseorg.apache.commons.configuration2.tree.ImmutableNode
getImputeConfig(Caller caller, Imputer imputer, Combiner combiner)
Get the final imputation stage config for this caseImputer
getImputer()
Get the imputer for this case if it doesn't require optimizing, else throw an errorImputer
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 casePrintStats
getPrintStats()
Get the PrintStats object for this case
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Constructor Detail
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Case
public Case(java.lang.String name, java.util.List<VCFFilter> filters, Caller caller, ImputationOption imputer, CombinerOption combiner, PrintStats print, java.lang.String additional)
Constructor- Parameters:
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)
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Case
public Case(org.apache.commons.configuration2.HierarchicalConfiguration<org.apache.commons.configuration2.tree.ImmutableNode> params)
Constructor from a config (read in from a XML file)- Parameters:
params
- The config
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Method Detail
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applyFilters
public void applyFilters(VCF vcf) throws VCFDataException
Apply the filters of this case to a VCF- Parameters:
vcf
- The VCF- Throws:
VCFDataException
- If there is a problem with the data in the VCF
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getCaller
public Caller getCaller()
Get the caller for this case- Returns:
- The caller
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getImputer
public Imputer getImputer(double[][][] original, int[][][] readCounts, java.util.List<SingleGenotypeProbability> maskedprobs, java.util.List<SingleGenotypeMasked> list)
Get the imputer for this case. If the case imputer is optimizable return an optimized version else return the imputer- Parameters:
original
- The called genotype probabilitiesreadCounts
- The read countsmaskedprobs
- The masked genotype probabilitieslist
- List of masked positions- Returns:
- The imputer
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getImputer
public Imputer getImputer()
Get the imputer for this case if it doesn't require optimizing, else throw an error- Returns:
- The imputer
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getCombiner
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)
Get the combiner for this case. If the case combiner is optimizable return an optimized version else return the imputer- Parameters:
called
- The called genotype probabilitiesimputed
- The imputed genotype probabilitiesreads
- The read countscorrect
- The correct genotypesmasked
- A list of masked genotypes- Returns:
- The combiner
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getCombiner
public Combiner getCombiner()
Get the combiner for this case if it doesn't require optimizing, else throw an error- Returns:
- The combiner
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getPrintStats
public PrintStats getPrintStats()
Get the PrintStats object for this case- Returns:
- The print stats object
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getName
public java.lang.String getName()
Get the name of this case- Returns:
- The name
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getFilterSummary
public java.lang.String getFilterSummary()
Get a summary of filters used in this case- Returns:
- The summary
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getAdditional
public java.lang.String getAdditional()
Get the additional information for this case- Returns:
- The additional information
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getConfig
public org.apache.commons.configuration2.tree.ImmutableNode getConfig()
Get the config for this case- Returns:
- The config
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getImputeConfig
public org.apache.commons.configuration2.tree.ImmutableNode getImputeConfig(Caller caller, Imputer imputer, Combiner combiner)
Get the final imputation stage config for this case- Parameters:
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- Returns:
- The config
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