public class CRAMIndexer
extends java.lang.Object
Constructor and Description |
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CRAMIndexer(java.io.File output,
SAMFileHeader fileHeader)
Create a CRAM indexer that writes BAI to a file.
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CRAMIndexer(java.io.OutputStream output,
SAMFileHeader fileHeader)
Create a CRAM indexer that writes BAI to a stream.
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Modifier and Type | Method and Description |
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static void |
createIndex(SeekableStream stream,
java.io.File output,
Log log)
Generates a BAI index file from an input CRAM stream
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void |
finish()
After all the slices have been processed, finish is called.
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void |
processAlignment(Slice slice)
Record any index information for a given CRAM slice.
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public CRAMIndexer(java.io.File output, SAMFileHeader fileHeader)
output
- binary BAM Index (.bai) filefileHeader
- header for the corresponding bam filepublic CRAMIndexer(java.io.OutputStream output, SAMFileHeader fileHeader)
output
- Index will be written here. output will be closed when finish() method is called.fileHeader
- header for the corresponding bam file.public void processAlignment(Slice slice)
slice
- The CRAM slicepublic void finish()
public static void createIndex(SeekableStream stream, java.io.File output, Log log) throws java.io.IOException
stream
- CRAM stream to indexoutput
- File for output index filelog
- optional Log
to output progressjava.io.IOException