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, boolean callGenotypes, int maxAlternateAlleles)

Method Summary

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

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,
                         boolean callGenotypes,
                         int maxAlternateAlleles)

Parameters:

reference - Path to a reference. May be null. Needed only for reading from GenomicsDB.

callGenotypes - Indicates whether GenomicsDB should return called genotypes

maxAlternateAlleles - The maximum number of alternative alleles to return in query results

Method Detail

getReference

public java.nio.file.Path getReference()

doCallGenotypes

public boolean doCallGenotypes()

getMaxAlternateAlleles

public int getMaxAlternateAlleles()