public class CRAMCRAIIndexer
extends java.lang.Object
| Constructor and Description |
|---|
CRAMCRAIIndexer(java.io.OutputStream os,
SAMFileHeader samHeader)
Create a CRAMCRAIIndexer that writes to the given output stream.
|
| Modifier and Type | Method and Description |
|---|---|
void |
addEntry(CRAIEntry entry) |
void |
finish()
Finish creating the index by writing the accumulated entries out to the stream.
|
void |
processContainer(Container container)
Create index entries for a single container.
|
static CRAIIndex |
readIndex(java.io.InputStream is)
Read an input stream containing a .crai index and return a CRAIIndex object.
|
static void |
writeIndex(SeekableStream cramStream,
java.io.OutputStream craiStream)
Generate and write a CRAI index to an output stream from a CRAM input stream
|
public CRAMCRAIIndexer(java.io.OutputStream os,
SAMFileHeader samHeader)
os - output stream to which the index will be writtensamHeader - SAMFileHeader - user to verify sort orderpublic void processContainer(Container container)
container - the container to indexpublic void addEntry(CRAIEntry entry)
public void finish()
public static void writeIndex(SeekableStream cramStream, java.io.OutputStream craiStream)
cramStream - CRAM stream to index; must be coordinate sortedcraiStream - stream for output indexpublic static CRAIIndex readIndex(java.io.InputStream is)
is - Input stream to read