org.molgenis.data.annotation.impl

Class CaddServiceAnnotator

java.lang.Object

org.molgenis.data.annotation.AbstractRepositoryAnnotator

org.molgenis.data.annotation.LocusAnnotator

org.molgenis.data.annotation.VariantAnnotator

org.molgenis.data.annotation.impl.CaddServiceAnnotator

All Implemented Interfaces:

EventListener, RepositoryAnnotator, org.springframework.context.ApplicationListener<org.springframework.context.event.ContextRefreshedEvent>

@Component(value="caddService")
public class CaddServiceAnnotator
extends VariantAnnotator

This class performs a system call to cross reference a chromosome and genomic location with a tabix indexed file. A match can result in 1, 2 or 3 hits. These matches are reduced to one based on a reference and alternative nucleotide base. The remaining hit will be used to parse two CADD scores.

CADD returns: CADD score Absolute, CADD score Scaled

Author:

mdehaan

Field Summary

Fields

Modifier and Type	Field and Description
static String	CADD_ABS
static String	CADD_FILE_LOCATION_PROPERTY
static String	CADD_SCALED

Fields inherited from class org.molgenis.data.annotation.VariantAnnotator

ALTERNATIVE, REFERENCE

Fields inherited from class org.molgenis.data.annotation.LocusAnnotator

CHROMOSOME, POSITION

Fields inherited from interface org.molgenis.data.annotation.RepositoryAnnotator

ANNOTATOR_PREFIX

Constructor Summary

Constructors

Constructor and Description
CaddServiceAnnotator(File caddTsvGzFile, File inputVcfFile, File outputVCFFile)
CaddServiceAnnotator(MolgenisSettings molgenisSettings, AnnotationService annotatorService)

Method Summary

Modifier and Type	Method and Description
List<Entity>	annotateEntity(Entity entity)
boolean	annotationDataExists() Checks if folder and files that were set with a runtime property actually exist, or if a webservice can be reached
String	getDescription()
EntityMetaData	getOutputMetaData()
String	getSimpleName()
void	onApplicationEvent(org.springframework.context.event.ContextRefreshedEvent event)

Methods inherited from class org.molgenis.data.annotation.VariantAnnotator

getInputMetaData

Methods inherited from class org.molgenis.data.annotation.AbstractRepositoryAnnotator

annotate, canAnnotate, getFullName

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.molgenis.data.annotation.RepositoryAnnotator

annotate, canAnnotate, getFullName

Field Detail

CADD_SCALED

public static final String CADD_SCALED

See Also:

Constant Field Values

CADD_ABS

public static final String CADD_ABS

See Also:

Constant Field Values

CADD_FILE_LOCATION_PROPERTY

public static final String CADD_FILE_LOCATION_PROPERTY

See Also:

Constant Field Values

Constructor Detail

CaddServiceAnnotator

@Autowired
public CaddServiceAnnotator(MolgenisSettings molgenisSettings,
                                       AnnotationService annotatorService)
                                throws IOException

Throws:

IOException

CaddServiceAnnotator

public CaddServiceAnnotator(File caddTsvGzFile,
                            File inputVcfFile,
                            File outputVCFFile)
                     throws Exception

Throws:

Exception

Method Detail

onApplicationEvent

public void onApplicationEvent(org.springframework.context.event.ContextRefreshedEvent event)

Specified by:

onApplicationEvent in interface org.springframework.context.ApplicationListener<org.springframework.context.event.ContextRefreshedEvent>

Overrides:

onApplicationEvent in class AbstractRepositoryAnnotator

annotationDataExists

public boolean annotationDataExists()

Description copied from class: AbstractRepositoryAnnotator

Checks if folder and files that were set with a runtime property actually exist, or if a webservice can be reached

Specified by:

annotationDataExists in class AbstractRepositoryAnnotator

Returns:

boolean

getSimpleName

public String getSimpleName()

annotateEntity

public List<Entity> annotateEntity(Entity entity)
                            throws IOException,
                                   InterruptedException

Specified by:

annotateEntity in class AbstractRepositoryAnnotator

Throws:

IOException

InterruptedException

getOutputMetaData

public EntityMetaData getOutputMetaData()

getDescription

public String getDescription()