htsjdk.beta.codecs.reads.sam.samV1_0

Class SAMEncoderV1_0

java.lang.Object

htsjdk.beta.codecs.reads.sam.SAMEncoder

htsjdk.beta.codecs.reads.sam.samV1_0.SAMEncoderV1_0

All Implemented Interfaces:

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

@InternalAPI
public class SAMEncoderV1_0
extends SAMEncoder

SAM v1.0 encoder.

Constructor Summary

Constructors

Constructor and Description
SAMEncoderV1_0(Bundle outputBundle, ReadsEncoderOptions readsEncoderOptions) Create a V1.0 SAM encoder for the given output bundle.

Method Summary

Modifier and Type	Method and Description
void	close() Close any resources associated with this decoder.
HtsVersion	getVersion() Get the version of the file format supported by this encoder.
void	setHeader(SAMFileHeader samFileHeader) Set the file format header for this decoder, of type H.
void	write(SAMRecord record) Write a single record to the underlying output.

Methods inherited from class htsjdk.beta.codecs.reads.sam.SAMEncoder

getDisplayName, getFileFormat, getOutputBundle, getReadsEncoderOptions

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

SAMEncoderV1_0

public SAMEncoderV1_0(Bundle outputBundle,
                      ReadsEncoderOptions readsEncoderOptions)

Create a V1.0 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).

Parameters:

outputBundle - bundle to encode

readsEncoderOptions - options to use

Method Detail

getVersion

public HtsVersion getVersion()

Description copied from interface: HtsEncoder

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

setHeader

public void setHeader(SAMFileHeader samFileHeader)

Description copied from interface: HtsEncoder

Set the file format header for this decoder, of type H. HtsEncoder.setHeader(HtsHeader) must be called before HtsEncoder.write(HtsRecord) can be called.

Parameters:

samFileHeader - to use

write

public void write(SAMRecord record)

Description copied from interface: HtsEncoder

Write a single record to the underlying output. HtsEncoder.write(HtsRecord) may only called after HtsEncoder.setHeader(HtsHeader) has been called.

Parameters:

record - record to write

close

public void close()

Description copied from interface: HtsEncoder

Close any resources associated with this decoder.