Package htsjdk.samtools
Class BamIndexValidator
java.lang.Object
htsjdk.samtools.BamIndexValidator
Class to validate (at two different levels of thoroughness) the index for a BAM file.
This class is [not] thread safe [because it is immutable].
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Nested Class Summary
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionstatic int
exhaustivelyTestIndex
(SamReader reader) static int
lessExhaustivelyTestIndex
(SamReader reader) A less time-consuming index validation that only looks at the first and last references in the index and the first and last chunks in each of those
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Constructor Details
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BamIndexValidator
public BamIndexValidator()
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Method Details
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exhaustivelyTestIndex
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lessExhaustivelyTestIndex
A less time-consuming index validation that only looks at the first and last references in the index and the first and last chunks in each of those- Parameters:
reader
-- Returns:
- # of chunks examined, or 0 if there is no browseable index for the reader
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