org.broadinstitute.hellbender.engine.spark

Class AssemblyRegionReadShardArgumentCollection

java.lang.Object

org.broadinstitute.hellbender.engine.spark.AssemblyRegionReadShardArgumentCollection

All Implemented Interfaces:

java.io.Serializable

public class AssemblyRegionReadShardArgumentCollection
extends java.lang.Object
implements java.io.Serializable

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static int	DEFAULT_READSHARD_PADDING_SIZE
static int	DEFAULT_READSHARD_SIZE
int	readShardPadding
int	readShardSize

Constructor Summary

Constructors

Constructor and Description
AssemblyRegionReadShardArgumentCollection()

Method Summary

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_READSHARD_SIZE

public static final int DEFAULT_READSHARD_SIZE

See Also:

Constant Field Values

DEFAULT_READSHARD_PADDING_SIZE

public static final int DEFAULT_READSHARD_PADDING_SIZE

See Also:

Constant Field Values

readShardSize

@Argument(fullName="read-shard-size",
          shortName="read-shard-size",
          doc="Maximum size of each read shard, in bases. For good performance, this should be much larger than the maximum assembly region size.",
          optional=true)
public int readShardSize

readShardPadding

@Argument(fullName="read-shard-padding",
          shortName="read-shard-padding",
          doc="Each read shard has this many bases of extra context on each side. Read shards must have as much or more padding than assembly regions.",
          optional=true)
public int readShardPadding

Constructor Detail

AssemblyRegionReadShardArgumentCollection

public AssemblyRegionReadShardArgumentCollection()