org.molgenis.data.annotation.core.utils

Class EffectStructureConverter

java.lang.Object

org.molgenis.data.annotation.core.utils.EffectStructureConverter

@Component
public class EffectStructureConverter
extends Object

This class is used to convert from (MOLGENIS)SnpEff annotated VCF files to the entity structure expected by Effects annotators (for example GAVIN), and the other way around

An effect is an entity containing information about the combination of a variant (CHROM POS REF ALT(single allele)) in a specific GENE

Constructor Summary

Constructors

Constructor and Description
EffectStructureConverter(EntityTypeFactory entityTypeFactory, AttributeFactory attributeFactory)

Method Summary

Modifier and Type	Method and Description
Stream<Entity>	createVariantEffectStructure(String effectAttributeName, List<Attribute> annotatorAttributes, VcfRepository vcfRepository)
Iterator<Entity>	createVcfEntityStructure(Iterator<Entity> annotatedRecords)
String	getEffectDescription(Attribute effectAttributeToParse)

Methods inherited from class java.lang.Object

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

Constructor Detail

EffectStructureConverter

@Autowired
public EffectStructureConverter(EntityTypeFactory entityTypeFactory,
                                           AttributeFactory attributeFactory)

Method Detail

createVcfEntityStructure

public Iterator<Entity> createVcfEntityStructure(Iterator<Entity> annotatedRecords)

createVariantEffectStructure

public Stream<Entity> createVariantEffectStructure(String effectAttributeName,
                                                   List<Attribute> annotatorAttributes,
                                                   VcfRepository vcfRepository)

getEffectDescription

public String getEffectDescription(Attribute effectAttributeToParse)