java.lang.Object

htsjdk.beta.codecs.variants.vcf.VCFDecoder

All Implemented Interfaces:: HtsDecoder<VCFHeader,VariantContext>, HtsQuery<VariantContext>, VariantsDecoder, Closeable, AutoCloseable, Iterable<VariantContext>

Direct Known Subclasses:: VCFDecoderV3_2, VCFDecoderV3_3, VCFDecoderV4_0, VCFDecoderV4_1, VCFDecoderV4_2, VCFDecoderV4_3

@InternalAPI public abstract class VCFDecoder extends Object implements VariantsDecoder

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

Constructor Summary

Constructors

Constructor

Description

VCFDecoder(Bundle inputBundle, AbstractVCFCodec vcfCodec, VariantsDecoderOptions variantsDecoderOptions)

InternalAPI Create a new VCF decoder.
Method Summary

Modifier and Type

Method

Description

void

close()

Close any resources associated with this decoder.

final String

getDisplayName()

Get a user-friendly display name for this decoder.

final 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(String queryString)

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

CloseableIterator<VariantContext>

query(List<HtsInterval> intervals, HtsQueryRule queryRule)

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

CloseableIterator<VariantContext>

queryStart(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 Details
- 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 Details
- getFileFormat
  
  public final 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 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 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(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(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(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 AutoCloseable
  
  Specified by:
  
  close in interface Closeable
  
  Specified by:
  
  close in interface HtsDecoder<VCFHeader,VariantContext>
- 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.

Class VCFDecoder

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Methods inherited from interface htsjdk.beta.plugin.HtsDecoder

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

Methods inherited from interface java.lang.Iterable

Constructor Details

VCFDecoder

Method Details

getFileFormat

getDisplayName

getHeader

iterator

isQueryable

hasIndex

query

query

queryStart

close

getInputBundle

getReadsDecoderOptions