org.broadinstitute.hellbender.tools.funcotator

Class FuncotatorConstants

java.lang.Object

org.broadinstitute.hellbender.tools.funcotator.FuncotatorConstants

public class FuncotatorConstants
extends java.lang.Object

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	B37_MITOCHONDRIAL_CONTIG_NAME Name of the Mitochondrial contig for the B37 human reference.
static java.lang.String	DATASOURCE_NAME_FOR_INPUT_VCFS Datasource name to use for Funcotations created from input variants from a VCF.
static java.lang.String	HG19_MITOCHONDRIAL_CONTIG_NAME Name of the Mitochondrial contig for the HG19 human reference.
static java.lang.String	HG38_MITOCHONDRIAL_CONTIG_NAME Name of the Mitochondrial contig for the HG38 human reference.
static char	MASKED_ANY_BASE A character representing any base as used in VCF files and IUPAC base standards.
static java.lang.String	MASKED_ANY_BASE_STRING A String representing any base as used in VCF files and IUPAC base standards.
static java.util.Set<java.lang.String>	MITOCHONDRIAL_CONTIG_NAMES Set containing known valid names for Mitochondrial chromosomes.
static java.lang.String	UNKNOWN_VALUE_STRING Value to insert into fields when the annotation is unspecified, but still required.

Constructor Summary

Constructors

Constructor and Description
FuncotatorConstants()

Method Summary

Methods inherited from class java.lang.Object

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

Field Detail

MASKED_ANY_BASE

public static final char MASKED_ANY_BASE

A character representing any base as used in VCF files and IUPAC base standards. NOTE: When HTSJDK with the fix for issue #1226 (https://github.com/samtools/htsjdk/issues/1226) is released we will want to remove this constant.

See Also:

Constant Field Values

MASKED_ANY_BASE_STRING

public static final java.lang.String MASKED_ANY_BASE_STRING

A String representing any base as used in VCF files and IUPAC base standards. NOTE: When HTSJDK with the fix for issue #1226 (https://github.com/samtools/htsjdk/issues/1226) is released we will want to remove this constant.

UNKNOWN_VALUE_STRING

public static final java.lang.String UNKNOWN_VALUE_STRING

Value to insert into fields when the annotation is unspecified, but still required.

See Also:

Constant Field Values

DATASOURCE_NAME_FOR_INPUT_VCFS

public static final java.lang.String DATASOURCE_NAME_FOR_INPUT_VCFS

Datasource name to use for Funcotations created from input variants from a VCF.

See Also:

Constant Field Values

B37_MITOCHONDRIAL_CONTIG_NAME

public static final java.lang.String B37_MITOCHONDRIAL_CONTIG_NAME

Name of the Mitochondrial contig for the B37 human reference.

See Also:

Constant Field Values

HG19_MITOCHONDRIAL_CONTIG_NAME

public static final java.lang.String HG19_MITOCHONDRIAL_CONTIG_NAME

Name of the Mitochondrial contig for the HG19 human reference.

See Also:

Constant Field Values

HG38_MITOCHONDRIAL_CONTIG_NAME

public static final java.lang.String HG38_MITOCHONDRIAL_CONTIG_NAME

Name of the Mitochondrial contig for the HG38 human reference.

See Also:

Constant Field Values

MITOCHONDRIAL_CONTIG_NAMES

public static final java.util.Set<java.lang.String> MITOCHONDRIAL_CONTIG_NAMES

Set containing known valid names for Mitochondrial chromosomes.

Constructor Detail

FuncotatorConstants

public FuncotatorConstants()