org.broadinstitute.hellbender.tools.genomicsdb

Class GenomicsDBArgumentCollection

java.lang.Object

org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBArgumentCollection

All Implemented Interfaces:

java.io.Serializable

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

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
boolean	callGenotypes Not full-fledged arguments for now.
int	maxDiploidAltAllelesThatCanBeGenotyped
static java.lang.String	USE_VCF_CODEC_LONG_NAME
boolean	useVCFCodec Currently there is no support for 64-bit fields in BCFCodec.

Constructor Summary

Constructors

Constructor and Description
GenomicsDBArgumentCollection()

Method Summary

Methods inherited from class java.lang.Object

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

Field Detail

USE_VCF_CODEC_LONG_NAME

public static final java.lang.String USE_VCF_CODEC_LONG_NAME

See Also:

Constant Field Values

callGenotypes

public boolean callGenotypes

Not full-fledged arguments for now.

maxDiploidAltAllelesThatCanBeGenotyped

public int maxDiploidAltAllelesThatCanBeGenotyped

useVCFCodec

@Advanced
 @Argument(fullName="genomicsdb-use-vcf-codec",
          doc="Use VCF Codec Streaming for data from GenomicsDB instead of the default BCF",
          optional=true)
public boolean useVCFCodec

Currently there is no support for 64-bit fields in BCFCodec. Specifying this option will allow for 64-bit width positions and INFO fields and for computed annotation sizes to exceed the 32-bit integer space while encoding/decoding with GenomicsDB.

Constructor Detail

GenomicsDBArgumentCollection

public GenomicsDBArgumentCollection()