org.molgenis.data.annotation.core.entity.impl.snpeff

Class SnpEffRunner

java.lang.Object

org.molgenis.data.annotation.core.entity.impl.snpeff.SnpEffRunner

@Component
public class SnpEffRunner
extends Object

Field Summary

Fields

Modifier and Type	Field and Description
static String	ANN
static String	ENTITY_NAME_SUFFIX
static String	NAME

Constructor Summary

Constructors

Constructor and Description
SnpEffRunner(JarRunner jarRunner, Entity snpEffAnnotatorSettings, IdGenerator idGenerator, VcfAttributes vcfAttributes, EffectsMetaData effectsMetaData, EntityTypeFactory entityTypeFactory, AttributeFactory attributeFactory)

Method Summary

Modifier and Type	Method and Description
File	getInputVcfFile(Iterator<Entity> source) Converts entities to a VCF file that can be passed to SnpEff.
Iterator<Entity>	getSnpEffects(Iterable<Entity> source)
Iterator<Entity>	getSnpEffects(Iterator<Entity> source, File inputVcf)
String	getSnpEffPath() Gets the path to the SnpEff JAR.
EntityType	getTargetEntityType(EntityType sourceEntityType)

Methods inherited from class java.lang.Object

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

Field Detail

ENTITY_NAME_SUFFIX

public static final String ENTITY_NAME_SUFFIX

See Also:

Constant Field Values

NAME

public static final String NAME

See Also:

Constant Field Values

ANN

public static final String ANN

See Also:

Constant Field Values

Constructor Detail

SnpEffRunner

@Autowired
public SnpEffRunner(JarRunner jarRunner,
                               Entity snpEffAnnotatorSettings,
                               IdGenerator idGenerator,
                               VcfAttributes vcfAttributes,
                               EffectsMetaData effectsMetaData,
                               EntityTypeFactory entityTypeFactory,
                               AttributeFactory attributeFactory)

Method Detail

getSnpEffects

public Iterator<Entity> getSnpEffects(Iterable<Entity> source)

getSnpEffects

public Iterator<Entity> getSnpEffects(Iterator<Entity> source,
                                      File inputVcf)

getInputVcfFile

public File getInputVcfFile(Iterator<Entity> source)
                     throws IOException

Converts entities to a VCF file that can be passed to SnpEff.

Parameters:

source - the Entities to convert to VCF

Returns:

a VCF file

Throws:

IOException

getSnpEffPath

public String getSnpEffPath()

Gets the path to the SnpEff JAR. Returns null when the path is not found or snpEffAnnotatorSettings is null.

Returns:

the path to the SnpEff JAR, or null

getTargetEntityType

public EntityType getTargetEntityType(EntityType sourceEntityType)

Parameters:

sourceEntityType - The entity type for the entity that is being annotated by snpEff

Returns:

entityType Returns the EntityType for the effect entity