htsjdk.samtools

Class BinningIndexBuilder

java.lang.Object

htsjdk.samtools.BinningIndexBuilder

public class BinningIndexBuilder
extends java.lang.Object

Builder for a BinningIndexContent object.

Nested Class Summary

Nested Classes

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

Constructor Summary

Constructors

Constructor and Description
BinningIndexBuilder(int referenceSequence)
BinningIndexBuilder(int referenceSequence, int sequenceLength)

Method Summary

Modifier and Type	Method and 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 Detail

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 Detail

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.