Package htsjdk.beta.codecs.reads.cram
Class CRAMEncoder
java.lang.Object
htsjdk.beta.codecs.reads.cram.CRAMEncoder
- All Implemented Interfaces:
HtsEncoder<SAMFileHeader,,SAMRecord> ReadsEncoder,Closeable,AutoCloseable
- Direct Known Subclasses:
CRAMEncoderV2_1,CRAMEncoderV3_0
InternalAPI
Base class for
BundleResourceType.READS_CRAM decoders.-
Constructor Summary
ConstructorsConstructorDescriptionCRAMEncoder(Bundle outputBundle, ReadsEncoderOptions readsEncoderOptions) InternalAPI Create a CRAM encoder for the given output bundle. -
Method Summary
Modifier and TypeMethodDescriptionvoidclose()Close any resources associated with this decoder.static CRAMReferenceSourcegetCRAMReferenceSource(CRAMEncoderOptions cramEncoderOptions) Return aCRAMReferenceSourceusing theReadsEncoderOptions, or a default source.final StringGet a user-friendly display name for this encoder.final StringGet the name of the file format supported by this encoder.Get the outputBundlefor this encoder.Get theReadsEncoderOptionsfor this encoder.voidsetHeader(SAMFileHeader samFileHeader) Set the file format header for this decoder, of typeHtsEncoder.voidWrite a single record to the underlying output.Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, waitMethods inherited from interface htsjdk.beta.plugin.HtsEncoder
getVersion
-
Constructor Details
-
CRAMEncoder
InternalAPI Create a CRAM encoder for the given output bundle. The primary resource in the bundle must have content typeBundleResourceType.ALIGNED_READS(to find a decoder for a bundle, seeReadsResolver).- Parameters:
outputBundle- bundle to encodereadsEncoderOptions- options to use
-
-
Method Details
-
getFileFormat
Description copied from interface:HtsEncoderGet 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 (seeBundleResourceTypeandBundleResource.getFileFormat()).- Specified by:
getFileFormatin interfaceHtsEncoder<SAMFileHeader,SAMRecord> - Returns:
- the name of the underlying file format handled by this encoder
-
getDisplayName
Description copied from interface:HtsEncoderGet a user-friendly display name for this encoder.- Specified by:
getDisplayNamein interfaceHtsEncoder<SAMFileHeader,SAMRecord> - Returns:
- a user-friendly display name for this encoder for use in error and warning messages
-
setHeader
Description copied from interface:HtsEncoderSet the file format header for this decoder, of typeHtsEncoder.HtsEncoder.setHeader(HtsHeader)must be called beforeHtsEncoder.write(HtsRecord)can be called.- Specified by:
setHeaderin interfaceHtsEncoder<SAMFileHeader,SAMRecord> - Parameters:
samFileHeader- to use
-
write
Description copied from interface:HtsEncoderWrite a single record to the underlying output.HtsEncoder.write(HtsRecord)may only called afterHtsEncoder.setHeader(HtsHeader)has been called.- Specified by:
writein interfaceHtsEncoder<SAMFileHeader,SAMRecord> - Parameters:
record- record to write
-
close
public void close()Description copied from interface:HtsEncoderClose any resources associated with this decoder.- Specified by:
closein interfaceAutoCloseable- Specified by:
closein interfaceCloseable- Specified by:
closein interfaceHtsEncoder<SAMFileHeader,SAMRecord>
-
getOutputBundle
Get the outputBundlefor this encoder.- Returns:
- the output
Bundlefor this encoder
-
getReadsEncoderOptions
Get theReadsEncoderOptionsfor this encoder.- Returns:
- the
ReadsEncoderOptionsfor this encoder.
-
getCRAMReferenceSource
@InternalAPI public static CRAMReferenceSource getCRAMReferenceSource(CRAMEncoderOptions cramEncoderOptions) Return aCRAMReferenceSourceusing theReadsEncoderOptions, or a default source.- Parameters:
cramEncoderOptions- CRAMEncoderOptions options to use- Returns:
- a
CRAMReferenceSource
-