Package htsjdk.samtools

Class BinningIndexBuilder

java.lang.Object

htsjdk.samtools.BinningIndexBuilder

public class BinningIndexBuilder
extends Object

Builder for a BinningIndexContent object.

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static interface	BinningIndexBuilder.FeatureToBeIndexed	coordinates are 1-based, inclusive

Constructor Summary

Constructors

Constructor	Description
BinningIndexBuilder(int referenceSequence)
BinningIndexBuilder(int referenceSequence, int sequenceLength)
BinningIndexBuilder(int referenceSequence, int sequenceLength, boolean fillInUninitializedValues)

Method Summary

Modifier and Type	Method	Description
BinningIndexContent	generateIndexContent()	Creates the BAMIndexContent for this reference.
void	processFeature(BinningIndexBuilder.FeatureToBeIndexed feature)

Methods inherited from class java.lang.Object

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

Constructor Details

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 (see BAMIndexMerger)

BinningIndexBuilder

public BinningIndexBuilder(int referenceSequence,
 int sequenceLength)

Parameters:

referenceSequence -

sequenceLength - 0 implies unknown length. Known length will reduce memory use.

BinningIndexBuilder

public BinningIndexBuilder(int referenceSequence)

Method Details

processFeature

public void processFeature(BinningIndexBuilder.FeatureToBeIndexed feature)

generateIndexContent

public BinningIndexContent generateIndexContent()

Creates the BAMIndexContent for this reference. Requires all features of the reference have already been processed.