Package htsjdk.tribble.index.linear

Class LinearIndexCreator

java.lang.Object

htsjdk.tribble.index.TribbleIndexCreator

htsjdk.tribble.index.linear.LinearIndexCreator

All Implemented Interfaces:

IndexCreator

public class LinearIndexCreator
extends TribbleIndexCreator

For creating a LinearIndex from a stream of features.

Field Summary

Fields

Modifier and Type	Field	Description
static final int	DEFAULT_BIN_WIDTH

Fields inherited from class htsjdk.tribble.index.TribbleIndexCreator

properties

Constructor Summary

Constructors

Constructor	Description
LinearIndexCreator(File inputFile)
LinearIndexCreator(File inputFile, int binSize)
LinearIndexCreator(Path inputPath)
LinearIndexCreator(Path inputPath, int binSize)

Method Summary

Modifier and Type	Method	Description
void	addFeature(Feature feature, long filePosition)	add a feature to the index
int	defaultBinSize()	the current default bin size
Index	finalizeIndex(long finalFilePosition)	finalize the index; producing an index object
int	getBinSize()

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_BIN_WIDTH

public static final int DEFAULT_BIN_WIDTH

See Also:

• Constant Field Values

Constructor Details

LinearIndexCreator

public LinearIndexCreator(Path inputPath,
 int binSize)

LinearIndexCreator

public LinearIndexCreator(File inputFile,
 int binSize)

LinearIndexCreator

public LinearIndexCreator(File inputFile)

LinearIndexCreator

public LinearIndexCreator(Path inputPath)

Method Details

addFeature

public void addFeature(Feature feature,
 long filePosition)

add a feature to the index

Parameters:

feature - the feature, from which we use the contig, start, and stop

filePosition - the position of the file at the BEGINNING of the current feature

finalizeIndex

public Index finalizeIndex(long finalFilePosition)

finalize the index; producing an index object

Parameters:

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

Returns:

an Index object

defaultBinSize

public int defaultBinSize()

the current default bin size

Returns:

getBinSize

public int getBinSize()