Package htsjdk.samtools.reference
Class ReferenceSequenceFileWalker
- java.lang.Object
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- htsjdk.samtools.reference.ReferenceSequenceFileWalker
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- All Implemented Interfaces:
Closeable
,AutoCloseable
public class ReferenceSequenceFileWalker extends Object implements Closeable
Manages a ReferenceSequenceFile. Loads the requested sequence, ensuring that access is in order, and confirming that sequence name and index agree.
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Constructor Summary
Constructors Constructor Description ReferenceSequenceFileWalker(ReferenceSequenceFile referenceSequenceFile)
ReferenceSequenceFileWalker(File file)
ReferenceSequenceFileWalker(Path path)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
close()
ReferenceSequence
get(int sequenceIndex)
Get reference sequence without validating name or length.ReferenceSequence
get(int sequenceIndex, String sequenceName, int length)
Ensure that the requested sequence is loaded.SAMSequenceDictionary
getSequenceDictionary()
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Constructor Detail
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ReferenceSequenceFileWalker
public ReferenceSequenceFileWalker(ReferenceSequenceFile referenceSequenceFile)
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ReferenceSequenceFileWalker
public ReferenceSequenceFileWalker(Path path)
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ReferenceSequenceFileWalker
public ReferenceSequenceFileWalker(File file)
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Method Detail
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get
public ReferenceSequence get(int sequenceIndex, String sequenceName, int length)
Ensure that the requested sequence is loaded. Throws an exception if out-of-order request is made, or if there is a mismatch between the requested name and the name found in the ReferenceSequenceFile
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get
public ReferenceSequence get(int sequenceIndex)
Get reference sequence without validating name or length. This is OK if the entire sequence dictionary was validated before reading sequences.
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getSequenceDictionary
public SAMSequenceDictionary getSequenceDictionary()
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close
public void close() throws IOException
- Specified by:
close
in interfaceAutoCloseable
- Specified by:
close
in interfaceCloseable
- Throws:
IOException
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