org.molgenis.data.vcf

Class VcfRepository

java.lang.Object

org.molgenis.data.support.AbstractRepository

org.molgenis.data.vcf.VcfRepository

All Implemented Interfaces:

Closeable, AutoCloseable, Iterable<Entity>, Repository

public class VcfRepository
extends AbstractRepository

Repository implementation for vcf files. The filename without the extension is considered to be the entityname

Field Summary

Fields

Modifier and Type	Field and Description
static String	ALT
static AttributeMetaData	ALT_META
static String	CHROM
static AttributeMetaData	CHROM_META
static String	FILTER
static AttributeMetaData	FILTER_META
static String	ID
static AttributeMetaData	ID_META
static String	INFO
static String	INTERNAL_ID
static String	NAME
static String	POS
static AttributeMetaData	POS_META
static String	PREFIX
static String	QUAL
static AttributeMetaData	QUAL_META
static String	REF
static AttributeMetaData	REF_META
static String	SAMPLES

Constructor Summary

Constructors

Constructor and Description
VcfRepository(File file, String entityName)

Method Summary

Modifier and Type	Method and Description
void	close()
long	count()
protected org.molgenis.vcf.VcfReader	createVcfReader()
Set<RepositoryCapability>	getCapabilities()
EntityMetaData	getEntityMetaData()
static String	getInfoPrefix() Prefix to make INFO column names safe-ish.
Iterator<Entity>	iterator()
Entity	toEntity(EntityMetaData emd, org.molgenis.vcf.VcfRecord vcfRecord, org.molgenis.vcf.meta.VcfMeta vcfMeta)

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

add, add, aggregate, clearCache, count, delete, delete, deleteAll, deleteById, deleteById, findAll, findAll, findOne, findOne, flush, getName, 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 java.lang.Iterable

forEach, spliterator

Field Detail

CHROM

public static final String CHROM

See Also:

Constant Field Values

ALT

public static final String ALT

See Also:

Constant Field Values

POS

public static final String POS

See Also:

Constant Field Values

REF

public static final String REF

See Also:

Constant Field Values

FILTER

public static final String FILTER

See Also:

Constant Field Values

QUAL

public static final String QUAL

See Also:

Constant Field Values

ID

public static final String ID

See Also:

Constant Field Values

INTERNAL_ID

public static final String INTERNAL_ID

See Also:

Constant Field Values

INFO

public static final String INFO

See Also:

Constant Field Values

SAMPLES

public static final String SAMPLES

See Also:

Constant Field Values

NAME

public static final String NAME

See Also:

Constant Field Values

PREFIX

public static final String PREFIX

See Also:

Constant Field Values

CHROM_META

public static final AttributeMetaData CHROM_META

ALT_META

public static final AttributeMetaData ALT_META

POS_META

public static final AttributeMetaData POS_META

REF_META

public static final AttributeMetaData REF_META

FILTER_META

public static final AttributeMetaData FILTER_META

QUAL_META

public static final AttributeMetaData QUAL_META

ID_META

public static final AttributeMetaData ID_META

Constructor Detail

VcfRepository

public VcfRepository(File file,
                     String entityName)
              throws IOException

Throws:

IOException

Method Detail

iterator

public Iterator<Entity> iterator()

toEntity

public Entity toEntity(EntityMetaData emd,
                       org.molgenis.vcf.VcfRecord vcfRecord,
                       org.molgenis.vcf.meta.VcfMeta vcfMeta)
                throws IOException

Throws:

IOException

getEntityMetaData

public EntityMetaData getEntityMetaData()

getInfoPrefix

public static String getInfoPrefix()

Prefix to make INFO column names safe-ish. For example, 'Samples' is sometimes used as an INFO field and clashes with the 'Samples' key used by Genotype-IO to store sample data in memory. By prefixing a tag we hope to create unique INFO field names that do not clash.

Returns:

createVcfReader

protected org.molgenis.vcf.VcfReader createVcfReader()
                                              throws IOException

Throws:

IOException

close

public void close()
           throws IOException

Specified by:

close in interface Closeable

Specified by:

close in interface AutoCloseable

Overrides:

close in class AbstractRepository

Throws:

IOException

getCapabilities

public Set<RepositoryCapability> getCapabilities()

count

public long count()

Specified by:

count in interface Repository

Overrides:

count in class AbstractRepository