org.broadinstitute.hellbender.tools.genomicsdb

Class GenomicsDBOptions

java.lang.Object

org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBOptions

public final class GenomicsDBOptions
extends java.lang.Object

Encapsulates the GenomicsDB-specific options relevant to the FeatureDataSource

Constructor Summary

Constructors

Constructor and Description
GenomicsDBOptions()
GenomicsDBOptions(java.nio.file.Path reference)
GenomicsDBOptions(java.nio.file.Path reference, GenomicsDBArgumentCollection genomicsdbArgs)
GenomicsDBOptions(java.nio.file.Path reference, GenomicsDBArgumentCollection genomicsdbArgs, GenotypeCalculationArgumentCollection genotypeCalcArgs)

Method Summary

Modifier and Type	Method and Description
boolean	doCallGenotypes()
int	getMaxDiploidAltAllelesThatCanBeGenotyped()
int	getMaxGenotypeCount()
java.nio.file.Path	getReference()
boolean	useVCFCodec()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

GenomicsDBOptions

public GenomicsDBOptions()

GenomicsDBOptions

public GenomicsDBOptions(java.nio.file.Path reference)

GenomicsDBOptions

public GenomicsDBOptions(java.nio.file.Path reference,
                         GenomicsDBArgumentCollection genomicsdbArgs)

GenomicsDBOptions

public GenomicsDBOptions(java.nio.file.Path reference,
                         GenomicsDBArgumentCollection genomicsdbArgs,
                         GenotypeCalculationArgumentCollection genotypeCalcArgs)

Method Detail

getReference

public java.nio.file.Path getReference()

doCallGenotypes

public boolean doCallGenotypes()

getMaxDiploidAltAllelesThatCanBeGenotyped

public int getMaxDiploidAltAllelesThatCanBeGenotyped()

getMaxGenotypeCount

public int getMaxGenotypeCount()

useVCFCodec

public boolean useVCFCodec()