java.lang.Object

htsjdk.beta.codecs.reads.htsget.HtsgetBAMDecoder

All Implemented Interfaces:: HtsDecoder<SAMFileHeader,SAMRecord>, HtsQuery<SAMRecord>, ReadsDecoder, ReadsQuery<SAMRecord>, Closeable, AutoCloseable, Iterable<SAMRecord>

Direct Known Subclasses:: HtsgetBAMDecoderV1_2

public abstract class HtsgetBAMDecoder extends Object implements ReadsDecoder

Base class for concrete implementations of reads decoders that handle BundleResourceType.FMT_READS_HTSGET_BAM decoding.

Constructor Summary

Constructors

Constructor

Description

HtsgetBAMDecoder(Bundle inputBundle, ReadsDecoderOptions readsDecoderOptions)
Method Summary

Modifier and Type

Method

Description

final String

getDisplayName()

Get a user-friendly display name for this decoder.

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()).

Bundle

getInputBundle()

Get the input Bundle for this decoder.

ReadsDecoderOptions

getReadsDecoderOptions()

Get the ReadsDecoderOptions for this decoder.

HtsVersion

getVersion()

Get the version of the file format supported by this decoder.

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
close, getHeader

Methods inherited from interface htsjdk.beta.plugin.interval.HtsQuery
hasIndex, isQueryable, iterator, query, query, query, query, queryContained, queryContained, queryContained, queryOverlapping, queryOverlapping, queryOverlapping, queryStart

Methods inherited from interface java.lang.Iterable
forEach, spliterator

Methods inherited from interface htsjdk.beta.plugin.reads.ReadsDecoder
queryMate, queryUnmapped

Constructor Details
- HtsgetBAMDecoder
  
  public HtsgetBAMDecoder(Bundle inputBundle, ReadsDecoderOptions readsDecoderOptions)
Method Details
- getFileFormat
  
  public 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<SAMFileHeader,SAMRecord>
  
  Returns:
  
  the name of the underlying file format handled by this decoder
- getVersion
  
  public HtsVersion getVersion()
  
  Description copied from interface: HtsDecoder
  
  Get the version of the file format supported by this decoder.
  
  Specified by:
  
  getVersion in interface HtsDecoder<SAMFileHeader,SAMRecord>
- 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<SAMFileHeader,SAMRecord>
  
  Returns:
  
  a user-friendly display name for this decoder for use in error and warning messages
- getInputBundle
  
  public Bundle getInputBundle()
  
  Get the input Bundle for this decoder.
  
  Returns:
  
  the input Bundle for this decoder
- getReadsDecoderOptions
  
  public ReadsDecoderOptions getReadsDecoderOptions()
  
  Get the ReadsDecoderOptions for this decoder.
  
  Returns:
  
  the ReadsDecoderOptions for this decoder.

Class HtsgetBAMDecoder

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

Methods inherited from interface htsjdk.beta.plugin.reads.ReadsDecoder

Constructor Details

HtsgetBAMDecoder

Method Details

getFileFormat

getVersion

getDisplayName

getInputBundle

getReadsDecoderOptions