Package htsjdk.samtools
Class BamIndexValidator
- java.lang.Object
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- htsjdk.samtools.BamIndexValidator
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public class BamIndexValidator extends Object
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
Nested Classes Modifier and Type Class Description static class
BamIndexValidator.IndexValidationStringency
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Constructor Summary
Constructors Constructor Description BamIndexValidator()
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description static 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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Method Detail
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exhaustivelyTestIndex
public static int exhaustivelyTestIndex(SamReader reader)
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lessExhaustivelyTestIndex
public 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- Parameters:
reader
-- Returns:
- # of chunks examined, or 0 if there is no browseable index for the reader
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