Package | Description |
---|---|
htsjdk.samtools | |
htsjdk.samtools.cram | |
htsjdk.samtools.cram.build | |
htsjdk.samtools.cram.structure |
Modifier and Type | Field and Description |
---|---|
Container |
CRAMIterator.container |
Modifier and Type | Method and Description |
---|---|
void |
CRAMIndexer.processContainer(Container container,
ValidationStringency validationStringency)
Index a container, any of mapped, unmapped and multiple references are allowed.
|
Modifier and Type | Method and Description |
---|---|
static List<CRAIEntry> |
CRAIEntry.fromContainer(Container container) |
Modifier and Type | Method and Description |
---|---|
Container |
ContainerFactory.buildContainer(List<CramCompressionRecord> records) |
Container |
CramContainerIterator.next() |
Container |
CramSpanContainerIterator.next() |
Modifier and Type | Method and Description |
---|---|
List<CramCompressionRecord> |
ContainerParser.getRecords(Container container,
ArrayList<CramCompressionRecord> records,
ValidationStringency validationStringency) |
Map<Integer,AlignmentSpan> |
ContainerParser.getReferences(Container container,
ValidationStringency validationStringency) |
Modifier and Type | Method and Description |
---|---|
static Container |
ContainerIO.readContainer(Version version,
InputStream inputStream)
Reads a CRAM container from the input stream.
|
static Container |
ContainerIO.readContainerHeader(int major,
InputStream inputStream)
Reads container header only from a
InputStream . |
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 int |
ContainerIO.writeContainer(Version version,
Container container,
OutputStream outputStream)
Writes a complete
Container with it's header to a OutputStream . |
static int |
ContainerIO.writeContainerHeader(int major,
Container container,
OutputStream outputStream)
Writes a
Container header information to a OutputStream . |