org.molgenis.data.annotation.core.resources.impl.tabix

Class TabixVcfRepository

java.lang.Object

org.molgenis.data.support.AbstractRepository

org.molgenis.data.vcf.VcfRepository

org.molgenis.data.annotation.core.resources.impl.tabix.TabixVcfRepository

All Implemented Interfaces:

Closeable, AutoCloseable, Iterable<Entity>, Repository<Entity>

public class TabixVcfRepository
extends VcfRepository

An indexed VCF Repository

Field Summary

Fields inherited from class org.molgenis.data.vcf.VcfRepository

DEFAULT_ATTRIBUTE_DESCRIPTION, NAME, ORIGINAL_NAME, PREFIX, vcfToEntitySupplier

Constructor Summary

Constructors

Constructor and Description
TabixVcfRepository(File file, String entityTypeId, VcfAttributes vcfAttributes, EntityTypeFactory entityTypeFactory, AttributeFactory attrMetaFactory)

Method Summary

Modifier and Type	Method and Description
Stream<Entity>	findAll(Query<Entity> q)
Set<RepositoryCapability>	getCapabilities()
protected Collection<String>	getLines(TabixReader.Iterator iterator) Collect the lines returned in a TabixReader.Iterator.
List<Entity>	query(String chrom, int posFrom, int posTo) Queries the tabix reader.

Methods inherited from class org.molgenis.data.vcf.VcfRepository

close, count, getEntityType, iterator

Methods inherited from class org.molgenis.data.support.AbstractRepository

add, add, aggregate, count, delete, delete, deleteAll, deleteAll, deleteById, findAll, findAll, findOne, findOneById, findOneById, forEachBatched, getName, getQueryOperators, query, update, update

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.Repository

forEachBatched, getExistingIDs, upsertBatch

Methods inherited from interface java.lang.Iterable

forEach, spliterator

Constructor Detail

TabixVcfRepository

public TabixVcfRepository(File file,
                          String entityTypeId,
                          VcfAttributes vcfAttributes,
                          EntityTypeFactory entityTypeFactory,
                          AttributeFactory attrMetaFactory)
                   throws IOException

Throws:

IOException

Method Detail

getCapabilities

public Set<RepositoryCapability> getCapabilities()

Specified by:

getCapabilities in interface Repository<Entity>

Overrides:

getCapabilities in class VcfRepository

findAll

public Stream<Entity> findAll(Query<Entity> q)

Specified by:

findAll in interface Repository<Entity>

Overrides:

findAll in class AbstractRepository

query

public List<Entity> query(String chrom,
                          int posFrom,
                          int posTo)

Queries the tabix reader.

Parameters:

chrom - Name of chromosome

posFrom - position lower bound (inclusive)

posTo - position upper bound (inclusive)

Returns:

ImmutableList of entities found

getLines

protected Collection<String> getLines(TabixReader.Iterator iterator)

Collect the lines returned in a TabixReader.Iterator.

Parameters:

iterator - the iterator from which the lines are collected, may be null.

Returns:

Collection of lines, is empty if the iterator was null.