public class CombinerOption
extends java.lang.Object
Constructor | Description |
---|---|
CombinerOption(Combiner combiner) |
Constructor for when the combiner isn't optimizable.
|
CombinerOption(OptimizeCombiner combiner) |
Constructor for when the combiner is optimizable
|
CombinerOption(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 |
---|---|---|
Combiner |
getCombiner() |
Returns the combiner if the combiner option was for a non-optimizable
combiner, else throws an exception
|
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) |
Gets a combiner.
|
org.apache.commons.configuration2.tree.ImmutableNode |
getConfig() |
Get the combiner options config
|
public CombinerOption(Combiner combiner)
combiner
- The combinerpublic CombinerOption(OptimizeCombiner combiner)
combiner
- The combinerpublic CombinerOption(org.apache.commons.configuration2.HierarchicalConfiguration<org.apache.commons.configuration2.tree.ImmutableNode> params)
params
- The configpublic 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 readscorrect
- The correct genotypesmasked
- A list of masked genotypespublic Combiner getCombiner()
public org.apache.commons.configuration2.tree.ImmutableNode getConfig()