htsjdk.samtools

Class BamIndexValidator

java.lang.Object

htsjdk.samtools.BamIndexValidator

public class BamIndexValidator
extends java.lang.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].

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	BamIndexValidator.IndexValidationStringency

Constructor Summary

Constructors

Constructor and Description
BamIndexValidator()

Method Summary

Modifier and Type	Method and 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

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

BamIndexValidator

public BamIndexValidator()

Method Detail

exhaustivelyTestIndex

public static int exhaustivelyTestIndex(SamReader reader)

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