htsjdk.beta.plugin

Interface HtsEncoder<H extends HtsHeader,R extends HtsRecord>

Type Parameters:

H - type param for the header for this encoder's format (i.e. SAMFileHeader)

R - type param for the record for this encoder's format (i.e. SAMRecord)

All Superinterfaces:

java.lang.AutoCloseable, java.io.Closeable

All Known Subinterfaces:

HaploidReferenceEncoder, ReadsEncoder, VariantsEncoder

All Known Implementing Classes:

BAMEncoder, BAMEncoderV1_0, CRAMEncoder, CRAMEncoderV2_1, CRAMEncoderV3_0, SAMEncoder, SAMEncoderV1_0, VCFEncoder, VCFEncoderV3_2, VCFEncoderV3_3, VCFEncoderV4_0, VCFEncoderV4_1, VCFEncoderV4_2

public interface HtsEncoder<H extends HtsHeader,R extends HtsRecord>
extends java.io.Closeable

Base interface for encoders.

Method Summary

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

Method Detail

getFileFormat

java.lang.String getFileFormat()

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()).

Returns:

the name of the underlying file format handled by this encoder

getVersion

HtsVersion getVersion()

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

getDisplayName

java.lang.String getDisplayName()

Get a user-friendly display name for this encoder.

Returns:

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

setHeader

void setHeader(H header)

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

Parameters:

header - to use

write

void write(R record)

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

Parameters:

record - record to write

close

void close()

Close any resources associated with this decoder.

Specified by:

close in interface java.lang.AutoCloseable

Specified by:

close in interface java.io.Closeable