Package htsjdk.tribble.index.interval

Class IntervalIndexCreator

java.lang.Object

htsjdk.tribble.index.TribbleIndexCreator

htsjdk.tribble.index.interval.IntervalIndexCreator

All Implemented Interfaces:

IndexCreator

public class IntervalIndexCreator
extends TribbleIndexCreator

Creates interval indexes from a stream of features

Field Summary

Fields

Modifier and Type	Field	Description
static final int	DEFAULT_FEATURE_COUNT

Fields inherited from class htsjdk.tribble.index.TribbleIndexCreator

properties

Constructor Summary

Constructors

Constructor	Description
IntervalIndexCreator(File inputFile)
IntervalIndexCreator(File inputFile, int featuresPerInterval)
IntervalIndexCreator(Path inputPath)
IntervalIndexCreator(Path inputPath, int featuresPerInterval)

Method Summary

Modifier and Type	Method	Description
void	addFeature(Feature feature, long filePosition)	Add a feature to the index
Index	finalizeIndex(long finalFilePosition)	finalize the index; create a tree index given the feature list passed in so far
int	getFeaturesPerInterval()

Methods inherited from class htsjdk.tribble.index.TribbleIndexCreator

addProperty, setIndexSequenceDictionary

Methods inherited from class java.lang.Object

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

Field Details

DEFAULT_FEATURE_COUNT

public static final int DEFAULT_FEATURE_COUNT

See Also:

• Constant Field Values

Constructor Details

IntervalIndexCreator

public IntervalIndexCreator(Path inputPath,
 int featuresPerInterval)

IntervalIndexCreator

public IntervalIndexCreator(File inputFile,
 int featuresPerInterval)

IntervalIndexCreator

public IntervalIndexCreator(File inputFile)

IntervalIndexCreator

public IntervalIndexCreator(Path inputPath)

Method Details

addFeature

public void addFeature(Feature feature,
 long filePosition)

Description copied from interface: IndexCreator

Add a feature to the index

Parameters:

feature - the feature, of which start, end, and contig must be filled in

filePosition - the current file position, at the beginning of the specified feature

finalizeIndex

public Index finalizeIndex(long finalFilePosition)

finalize the index; create a tree index given the feature list passed in so far

Parameters:

finalFilePosition - the final file position, for indexes that have to close out with the final position

Returns:

a Tree Index

getFeaturesPerInterval

public int getFeaturesPerInterval()