Package htsjdk.samtools
Class BAMSBIIndexer
java.lang.Object
htsjdk.samtools.BAMSBIIndexer
Writes SBI files for BAM files, as understood by
SBIIndex
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionstatic void
createIndex
(SeekableStream in, OutputStream out, long granularity) Perform indexing on the given BAM file, at the granularity level specified.static void
createIndex
(Path bamFile, long granularity) Perform indexing on the given BAM file, at the granularity level specified.
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Constructor Details
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BAMSBIIndexer
public BAMSBIIndexer()
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Method Details
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createIndex
Perform indexing on the given BAM file, at the granularity level specified.- Parameters:
bamFile
- the path to the BAM filegranularity
- write the offset of every n-th alignment to the index- Throws:
IOException
- as per java IO contract
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createIndex
public static void createIndex(SeekableStream in, OutputStream out, long granularity) throws IOException Perform indexing on the given BAM file, at the granularity level specified.- Parameters:
in
- a seekable stream for reading the BAM file fromout
- the stream to write the index togranularity
- write the offset of every n-th alignment to the index- Throws:
IOException
- as per java IO contract
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