public class CRAMCRAIIndexer extends java.lang.Object implements CRAMIndexer
Constructor and Description |
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CRAMCRAIIndexer(java.io.OutputStream os,
SAMFileHeader samHeader)
Create a CRAMCRAIIndexer that writes to the given output stream.
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CRAMCRAIIndexer(java.io.OutputStream os,
SAMFileHeader samHeader,
java.util.Collection<CRAIEntry> entries)
Create a CRAMCRAIIndexer that writes to the given output stream,
initialized with a Collection of
CRAIEntry objects. |
Modifier and Type | Method and Description |
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void |
finish()
Finish creating the index by writing the accumulated entries out to the stream.
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void |
processContainer(Container container)
Create index entries for a single container.
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void |
processContainer(Container container,
ValidationStringency validationStringency)
Create index entries for a single container.
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static CRAIIndex |
readIndex(java.io.InputStream is)
Read an input stream containing a .crai index and return a CRAIIndex object.
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static void |
writeIndex(SeekableStream cramStream,
java.io.OutputStream craiStream)
Generate and write a CRAI index to an output stream from a CRAM input stream
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public CRAMCRAIIndexer(java.io.OutputStream os, SAMFileHeader samHeader)
os
- output stream to which the index will be writtensamHeader
- SAMFileHeader - user to verify sort orderpublic CRAMCRAIIndexer(java.io.OutputStream os, SAMFileHeader samHeader, java.util.Collection<CRAIEntry> entries)
CRAIEntry
objects.os
- output stream to which the index will be writtensamHeader
- SAMFileHeader - user to verify sort orderentries
- the CRAI entries to indexpublic void processContainer(Container container)
container
- the container to indexpublic void processContainer(Container container, ValidationStringency validationStringency)
CRAMIndexer
processContainer
in interface CRAMIndexer
container
- the container to indexvalidationStringency
- stringency for validating records (used when processing multi-reference slices,
since creating an index on a multi-ref slices requires actually decoding the
records in order to resove the constituent reference spans}public void finish()
finish
in interface CRAMIndexer
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