htsjdk.beta.codecs.reads.sam

Class SAMDecoder

java.lang.Object

htsjdk.beta.codecs.reads.sam.SAMDecoder

All Implemented Interfaces:

HtsDecoder<SAMFileHeader,SAMRecord>, HtsQuery<SAMRecord>, ReadsDecoder, ReadsQuery<SAMRecord>, java.io.Closeable, java.lang.AutoCloseable, java.lang.Iterable<SAMRecord>

Direct Known Subclasses:

SAMDecoderV1_0

@InternalAPI
public abstract class SAMDecoder
extends java.lang.Object
implements ReadsDecoder

InternalAPI Base class for BundleResourceType.READS_SAM decoders.

Constructor Summary

Constructors

Constructor and Description
SAMDecoder(Bundle inputBundle, ReadsDecoderOptions readsDecoderOptions) Create a SAM decoder for the given input bundle.

Method Summary

Modifier and Type	Method and Description
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()).
Bundle	getInputBundle() Get the input Bundle for this decoder.
ReadsDecoderOptions	getReadsDecoderOptions() Get the ReadsDecoderOptions for 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.reads.ReadsDecoder

queryMate, queryUnmapped

Methods inherited from interface htsjdk.beta.plugin.HtsDecoder

close, getHeader, getVersion

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

Constructor Detail

SAMDecoder

@InternalAPI
public SAMDecoder(Bundle inputBundle,
                               ReadsDecoderOptions readsDecoderOptions)

Create a SAM decoder for the given input bundle. The primary resource in the bundle must have content type BundleResourceType.ALIGNED_READS, and the resource must be an appropriate format and version for this encoder (to find an encoder for a bundle, see ReadsResolver.

Parameters:

inputBundle - input Bundle to decode

readsDecoderOptions - ReadsDecoderOptions to use

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<SAMFileHeader,SAMRecord>

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<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.