htsjdk.beta.codecs.variants.vcf

Class VCFDecoder

java.lang.Object

htsjdk.beta.codecs.variants.vcf.VCFDecoder

All Implemented Interfaces:

HtsDecoder<VCFHeader,VariantContext>, HtsQuery<VariantContext>, VariantsDecoder, java.io.Closeable, java.lang.AutoCloseable, java.lang.Iterable<VariantContext>

Direct Known Subclasses:

VCFDecoderV3_2, VCFDecoderV3_3, VCFDecoderV4_0, VCFDecoderV4_1, VCFDecoderV4_2, VCFDecoderV4_3

@InternalAPI
public abstract class VCFDecoder
extends java.lang.Object
implements VariantsDecoder

InternalAPII Base class for concrete implementations of HtsContentType.VARIANT_CONTEXTS decoders.

Constructor Summary

Constructors

Constructor and Description
VCFDecoder(Bundle inputBundle, AbstractVCFCodec vcfCodec, VariantsDecoderOptions variantsDecoderOptions) InternalAPI Create a new VCF decoder.

Method Summary

Modifier and Type	Method and Description
void	close() Close any resources associated with this decoder.
java.lang.String	getDisplayName() Get a user-friendly display name for this decoder.
java.lang.String	getFileFormat() Get the name of the file format supported by this decoder.The format name defines the underlying format handled by this decoder, and also corresponds to the format of the primary bundle resource that is required when decoding (see BundleResourceType and BundleResource.getFileFormat()).
VCFHeader	getHeader() Get the file header for this decoder.
Bundle	getInputBundle() Get the input Bundle for this decoder.
VariantsDecoderOptions	getReadsDecoderOptions() Get the VariantsDecoderOptions for this decoder.
boolean	hasIndex() Return true if the underlying resource has an index.
boolean	isQueryable() Gte true if the underlying resource is queryable.
CloseableIterator<VariantContext>	iterator() Get an iterator of all records in the underlying resource.
CloseableIterator<VariantContext>	query(java.util.List<HtsInterval> intervals, HtsQueryRule queryRule) Get an iterator over all records from the underlying resource that match the query arguments.
CloseableIterator<VariantContext>	query(java.lang.String queryString) Get an iterator over all records from the underlying resource that match the query string
CloseableIterator<VariantContext>	queryStart(java.lang.String queryName, long start) Get an iterator over all records from the underlying resource that overlap the start position

Methods inherited from class java.lang.Object

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

Methods inherited from interface htsjdk.beta.plugin.HtsDecoder

getVersion

Methods inherited from interface htsjdk.beta.plugin.interval.HtsQuery

query, query, queryContained, queryContained, queryContained, queryOverlapping, queryOverlapping, queryOverlapping

Methods inherited from interface java.lang.Iterable

forEach, spliterator

Constructor Detail

VCFDecoder

@InternalAPI
public VCFDecoder(Bundle inputBundle,
                               AbstractVCFCodec vcfCodec,
                               VariantsDecoderOptions variantsDecoderOptions)

InternalAPI Create a new VCF decoder.

Parameters:

inputBundle - the input Bundle to decode

vcfCodec - the AbstractVCFCodec to use for this decoder

variantsDecoderOptions - the VariantsDecoderOptions for this decoder

Method Detail

getFileFormat

public final java.lang.String getFileFormat()

Description copied from interface: HtsDecoder

Get the name of the file format supported by this decoder.The format name defines the underlying format handled by this decoder, and also corresponds to the format of the primary bundle resource that is required when decoding (see BundleResourceType and BundleResource.getFileFormat()).

Specified by:

getFileFormat in interface HtsDecoder<VCFHeader,VariantContext>

Returns:

the name of the underlying file format handled by this decoder

getDisplayName

public final java.lang.String getDisplayName()

Description copied from interface: HtsDecoder

Get a user-friendly display name for this decoder.

Specified by:

getDisplayName in interface HtsDecoder<VCFHeader,VariantContext>

Returns:

a user-friendly display name for this decoder for use in error and warning messages

getHeader

public VCFHeader getHeader()

Description copied from interface: HtsDecoder

Get the file header for this decoder.

Specified by:

getHeader in interface HtsDecoder<VCFHeader,VariantContext>

Returns:

the file header for this decoder, of type H

iterator

public CloseableIterator<VariantContext> iterator()

Description copied from interface: HtsQuery

Get an iterator of all records in the underlying resource.

Specified by:

iterator in interface HtsQuery<VariantContext>

Specified by:

iterator in interface java.lang.Iterable<VariantContext>

Returns:

an iterator of all records in the underlying resource

isQueryable

public boolean isQueryable()

Description copied from interface: HtsQuery

Gte true if the underlying resource is queryable.

Specified by:

isQueryable in interface HtsQuery<VariantContext>

Returns:

true if the underlying resource is queryable. this may be true even if the underlying resource returns false for HtsQuery.hasIndex()

hasIndex

public boolean hasIndex()

Description copied from interface: HtsQuery

Return true if the underlying resource has an index.

Specified by:

hasIndex in interface HtsQuery<VariantContext>

Returns:

true if the underlying resource has an index

query

public CloseableIterator<VariantContext> query(java.util.List<HtsInterval> intervals,
                                               HtsQueryRule queryRule)

Description copied from interface: HtsQuery

Get an iterator over all records from the underlying resource that match the query arguments. Callers much ensure that the intervals are in increasing order and do not overlap or abut.

Specified by:

query in interface HtsQuery<VariantContext>

Parameters:

intervals - list of intervals to match

queryRule - query rule to use, from HtsQueryRule

Returns:

an iterator over all records from the underlying resource that match the query arguments

query

public CloseableIterator<VariantContext> query(java.lang.String queryString)

Description copied from interface: HtsQuery

Get an iterator over all records from the underlying resource that match the query string

Specified by:

query in interface HtsQuery<VariantContext>

Parameters:

queryString - decoder specific query string

Returns:

an iterator over all records from the underlying resource that match the query string

queryStart

public CloseableIterator<VariantContext> queryStart(java.lang.String queryName,
                                                    long start)

Description copied from interface: HtsQuery

Get an iterator over all records from the underlying resource that overlap the start position

Specified by:

queryStart in interface HtsQuery<VariantContext>

Parameters:

queryName - name to match

start - start position to overlap

Returns:

an iterator over all records from the underlying resource that overlap the start position

close

public void close()

Description copied from interface: HtsDecoder

Close any resources associated with this decoder.

Specified by:

close in interface HtsDecoder<VCFHeader,VariantContext>

Specified by:

close in interface java.io.Closeable

Specified by:

close in interface java.lang.AutoCloseable

getInputBundle

public Bundle getInputBundle()

Get the input Bundle for this decoder.

Returns:

the input Bundle for this decoder

getReadsDecoderOptions

public VariantsDecoderOptions getReadsDecoderOptions()

Get the VariantsDecoderOptions for this decoder.

Returns:

the VariantsDecoderOptions for this decoder.