Package | Description |
---|---|
htsjdk.samtools.cram.build | |
htsjdk.samtools.cram.common | |
htsjdk.samtools.cram.structure |
Modifier and Type | Method and Description |
---|---|
static long |
CramIO.issueEOF(Version version,
java.io.OutputStream outputStream)
Write an end-of-file marker to the
OutputStream . |
static long |
CramIO.writeHeader(Version cramVersion,
java.io.OutputStream outStream,
SAMFileHeader samFileHeader,
java.lang.String cramID)
Write a CRAM File header and a SAM Header to an output stream.
|
Constructor and Description |
---|
Sam2CramRecordFactory(byte[] refBases,
SAMFileHeader samFileHeader,
Version version) |
Modifier and Type | Field and Description |
---|---|
static Version |
CramVersions.CRAM_v2_1 |
static Version |
CramVersions.CRAM_v3 |
static Version |
CramVersions.DEFAULT_CRAM_VERSION
The default CRAM version when creating a new CRAM output file or stream.
|
Modifier and Type | Method and Description |
---|---|
int |
Version.compareTo(Version o)
Compare with another version.
|
boolean |
Version.compatibleWith(Version version) |
static void |
CramVersionPolicies.eofNotFound(Version version)
The method holds the behaviour for when the EOF marker is not found.
|
Modifier and Type | Method and Description |
---|---|
Version |
CramHeader.getVersion() |
Modifier and Type | Method and Description |
---|---|
static long |
ContainerIO.getByteSize(Version version,
Container container)
Calculates the byte size of a container based on the CRAM version.
|
static Container |
ContainerIO.readContainer(Version version,
java.io.InputStream inputStream)
Reads a CRAM container from the input stream.
|
void |
CramHeader.setVersion(Version version) |
static int |
ContainerIO.writeContainer(Version version,
Container container,
java.io.OutputStream outputStream)
Writes a complete
Container with it's header to a OutputStream . |
Constructor and Description |
---|
CramHeader(Version version,
java.lang.String id,
SAMFileHeader samFileHeader)
Create a new
CramHeader object with the specified version, id and SAM file header. |