public class BinningIndexBuilder
extends java.lang.Object
Modifier and Type | Class and Description |
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static interface |
BinningIndexBuilder.FeatureToBeIndexed
coordinates are 1-based, inclusive
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Constructor and Description |
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BinningIndexBuilder(int referenceSequence) |
BinningIndexBuilder(int referenceSequence,
int sequenceLength) |
BinningIndexBuilder(int referenceSequence,
int sequenceLength,
boolean fillInUninitializedValues) |
Modifier and Type | Method and Description |
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BinningIndexContent |
generateIndexContent()
Creates the BAMIndexContent for this reference.
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void |
processFeature(BinningIndexBuilder.FeatureToBeIndexed feature) |
public BinningIndexBuilder(int referenceSequence, int sequenceLength, boolean fillInUninitializedValues)
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
(see BAMIndexMerger
)public BinningIndexBuilder(int referenceSequence, int sequenceLength)
referenceSequence
- sequenceLength
- 0 implies unknown length. Known length will reduce memory use.public BinningIndexBuilder(int referenceSequence)
public void processFeature(BinningIndexBuilder.FeatureToBeIndexed feature)
public BinningIndexContent generateIndexContent()