org.broadinstitute.hellbender.utils.bwa

Class BwaMemIndexCache

java.lang.Object

org.broadinstitute.hellbender.utils.bwa.BwaMemIndexCache

public class BwaMemIndexCache
extends java.lang.Object

Manage a global collection of BwaMemIndex instances.

Constructor Summary

Constructors

Constructor and Description
BwaMemIndexCache()

Method Summary

Modifier and Type	Method and Description
static void	closeAllDistributedInstances(org.apache.spark.api.java.JavaSparkContext ctx) Closes all instances in all the VMs involved in the spark context provided.
static void	closeInstance(org.broadinstitute.hellbender.utils.bwa.BwaMemIndex instance) Closes an index instance.
static void	closeInstance(java.lang.String indexImageFile) Closes an index instance in the cache given its index file name.
static void	closeInstances() Closes all instances in the VM.
static org.broadinstitute.hellbender.utils.bwa.BwaMemIndex	getInstance(java.lang.String indexImageFile) Returns a BwaMemIndex instance that corresponds to given index image file.

Methods inherited from class java.lang.Object

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

Constructor Detail

BwaMemIndexCache

public BwaMemIndexCache()

Method Detail

getInstance

public static org.broadinstitute.hellbender.utils.bwa.BwaMemIndex getInstance(java.lang.String indexImageFile)

Returns a BwaMemIndex instance that corresponds to given index image file.

Parameters:

indexImageFile - the target image file.

Returns:

never null.

closeInstance

public static void closeInstance(java.lang.String indexImageFile)

Closes an index instance in the cache given its index file name.

Notice that you need to pass in exactly the same file name that was used when invoking getInstance(java.lang.String).

An attempt to close a missing instance, won't have any effect.

Parameters:

indexImageFile - the index file name of the instance to close.

closeInstance

public static void closeInstance(org.broadinstitute.hellbender.utils.bwa.BwaMemIndex instance)

Closes an index instance.

An attempt to close a instance that is not present in the cache, won't have any effect. Thus if the input instance is not part of the cache an is not closed, will remind unclosed.

Parameters:

instance - the instance ot close.

closeInstances

public static void closeInstances()

Closes all instances in the VM.

closeAllDistributedInstances

public static void closeAllDistributedInstances(org.apache.spark.api.java.JavaSparkContext ctx)

Closes all instances in all the VMs involved in the spark context provided.

Parameters:

ctx - the spark context.