htsjdk.beta.codecs.reads.cram

Class CRAMEncoder

java.lang.Object

htsjdk.beta.codecs.reads.cram.CRAMEncoder

All Implemented Interfaces:

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

Direct Known Subclasses:

CRAMEncoderV2_1, CRAMEncoderV3_0

@InternalAPI
public abstract class CRAMEncoder
extends java.lang.Object
implements ReadsEncoder

InternalAPI Base class for BundleResourceType.READS_CRAM decoders.

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method and Description
void	close() Close any resources associated with this decoder.
static CRAMReferenceSource	getCRAMReferenceSource(CRAMEncoderOptions cramEncoderOptions) Return a CRAMReferenceSource using the ReadsEncoderOptions, or a default source.
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.
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 java.lang.Object

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

Methods inherited from interface htsjdk.beta.plugin.HtsEncoder

getVersion

Constructor Detail

CRAMEncoder

@InternalAPI
public CRAMEncoder(Bundle outputBundle,
                                ReadsEncoderOptions readsEncoderOptions)

InternalAPI Create a CRAM 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

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

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.

Specified by:

setHeader in interface HtsEncoder<SAMFileHeader,SAMRecord>

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.

Specified by:

write in interface HtsEncoder<SAMFileHeader,SAMRecord>

Parameters:

record - record to write

close

public void close()

Description copied from interface: HtsEncoder

Close any resources associated with this decoder.

Specified by:

close in interface HtsEncoder<SAMFileHeader,SAMRecord>

Specified by:

close in interface java.io.Closeable

Specified by:

close in interface java.lang.AutoCloseable

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.

getCRAMReferenceSource

@InternalAPI
public static CRAMReferenceSource getCRAMReferenceSource(CRAMEncoderOptions cramEncoderOptions)

Return a CRAMReferenceSource using the ReadsEncoderOptions, or a default source.

Parameters:

cramEncoderOptions - CRAMEncoderOptions options to use

Returns:

a CRAMReferenceSource