htsjdk.beta.codecs.reads.sam

Class SAMEncoder

java.lang.Object

htsjdk.beta.codecs.reads.sam.SAMEncoder

All Implemented Interfaces:

HtsEncoder<SAMFileHeader,SAMRecord>, ReadsEncoder, java.io.Closeable, java.lang.AutoCloseable

Direct Known Subclasses:

SAMEncoderV1_0

public abstract class SAMEncoder
extends java.lang.Object
implements ReadsEncoder

InternalAPI Base class for BundleResourceType.READS_SAM encoders.

Constructor Summary

Constructors

Constructor and Description
SAMEncoder(Bundle outputBundle, ReadsEncoderOptions readsEncoderOptions) InternalAPI Create a SAM encoder for the given output bundle.

Method Summary

Modifier and Type	Method and Description
java.lang.String	getDisplayName() Get a user-friendly display name for this encoder.
java.lang.String	getFileFormat() Get the name of the file format supported by this encoder.
Bundle	getOutputBundle() Get the output Bundle for this encoder.
ReadsEncoderOptions	getReadsEncoderOptions() Get the ReadsEncoderOptions for this encoder.

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.HtsEncoder

close, getVersion, setHeader, write

Constructor Detail

SAMEncoder

public SAMEncoder(Bundle outputBundle,
                  ReadsEncoderOptions readsEncoderOptions)

InternalAPI Create a SAM encoder for the given output bundle. The primary resource in the bundle must have content type BundleResourceType.ALIGNED_READS (to find a decoder for a bundle, see ReadsResolver). NOTE: callers that provide an output stream resource should provide a buffered output stream if buffering is desired, since the encoder does not provide an additional buffering layer.

Parameters:

outputBundle - output Bundle to encode

readsEncoderOptions - ReadsEncoderOptions to use

Method Detail

getFileFormat

public final java.lang.String getFileFormat()

Description copied from interface: HtsEncoder

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

Specified by:

getFileFormat in interface HtsEncoder<SAMFileHeader,SAMRecord>

Returns:

the name of the underlying file format handled by this encoder

getDisplayName

public final java.lang.String getDisplayName()

Description copied from interface: HtsEncoder

Get a user-friendly display name for this encoder.

Specified by:

getDisplayName in interface HtsEncoder<SAMFileHeader,SAMRecord>

Returns:

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

getOutputBundle

public Bundle getOutputBundle()

Get the output Bundle for this encoder.

Returns:

the output Bundle for this encoder

getReadsEncoderOptions

public ReadsEncoderOptions getReadsEncoderOptions()

Get the ReadsEncoderOptions for this encoder.

Returns:

the ReadsEncoderOptions for this encoder.