Package htsjdk.samtools
Class BinningIndexBuilder
- java.lang.Object
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- htsjdk.samtools.BinningIndexBuilder
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public class BinningIndexBuilder extends Object
Builder for a BinningIndexContent object.
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Nested Class Summary
Nested Classes Modifier and Type Class Description static interface
BinningIndexBuilder.FeatureToBeIndexed
coordinates are 1-based, inclusive
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Constructor Summary
Constructors Constructor Description BinningIndexBuilder(int referenceSequence)
BinningIndexBuilder(int referenceSequence, int sequenceLength)
BinningIndexBuilder(int referenceSequence, int sequenceLength, boolean fillInUninitializedValues)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description BinningIndexContent
generateIndexContent()
Creates the BAMIndexContent for this reference.void
processFeature(BinningIndexBuilder.FeatureToBeIndexed feature)
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Constructor Detail
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BinningIndexBuilder
public BinningIndexBuilder(int referenceSequence, int sequenceLength, boolean fillInUninitializedValues)
- Parameters:
referenceSequence
-sequenceLength
- 0 implies unknown length. Known length will reduce memory use.fillInUninitializedValues
- if true, set uninitialized values (-1) to the last non-zero offset; if false, leave uninitialized values as -1, which is required when merging index files (seeBAMIndexMerger
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BinningIndexBuilder
public BinningIndexBuilder(int referenceSequence, int sequenceLength)
- Parameters:
referenceSequence
-sequenceLength
- 0 implies unknown length. Known length will reduce memory use.
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BinningIndexBuilder
public BinningIndexBuilder(int referenceSequence)
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Method Detail
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processFeature
public void processFeature(BinningIndexBuilder.FeatureToBeIndexed feature)
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generateIndexContent
public BinningIndexContent generateIndexContent()
Creates the BAMIndexContent for this reference. Requires all features of the reference have already been processed.
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