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 String	BASE_URL
static String	CHROM
static String	FILTER
static String	ID
static String	INFO
static String	INTERNAL_ID
static String	NAME
static String	POS
static String	QUAL
static String	REF
static String	SAMPLES

Constructor Summary

Constructors

Constructor and Description
VcfRepository(File file, String entityName)

Method Summary

Modifier and Type	Method and Description
void	close()
EntityMetaData	getEntityMetaData()
Iterator<Entity>	iterator()

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

getName, getUrl, iterator

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

BASE_URL

public static final String BASE_URL

See Also:

Constant Field Values

CHROM

public static final String CHROM

See Also:

Constant Field Values

ALT

public static final String ALT

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Constant Field Values

POS

public static final String POS

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Constant Field Values

REF

public static final String REF

See Also:

Constant Field Values

FILTER

public static final String FILTER

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Constant Field Values

QUAL

public static final String QUAL

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Constant Field Values

ID

public static final String ID

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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

Constructor Detail

VcfRepository

public VcfRepository(File file,
                     String entityName)
              throws IOException

Throws:

IOException

Method Detail

iterator

public Iterator<Entity> iterator()

getEntityMetaData

public EntityMetaData getEntityMetaData()

close

public void close()
           throws IOException

Throws:

IOException