Package htsjdk.beta.codecs.reads.htsget

Class HtsgetBAMDecoder

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.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.