Package htsjdk.tribble.example

Class CountRecords

java.lang.Object

htsjdk.tribble.example.CountRecords

public class CountRecords
extends Object

An example of how to index a feature file, and then count all the records in the file. This is also useful for testing the feature reader

Constructor Summary

Constructors

Constructor	Description
CountRecords()

Method Summary

Modifier and Type	Method	Description
static Index	createAndWriteNewIndex(File featureFile, File indexFile, FeatureCodec codec)	creates a new index, given the feature file and the codec
static FeatureCodec	getFeatureCodec(File featureFile)	Return a FeatureCodec instance appropriate for the given featureFile.
static Index	loadIndex(File featureFile, FeatureCodec codec)
static void	main(String[] args)	The main method of this class: 1) checks to see that the feature file exists 2) loads an index from disk, if one doesn't exist, it creates it and writes it to disk 3) creates a FeatureSource 4) iterates over the records, emitting a final tally for the number of features seen
static void	printUsage()	print usage information
static long	runWithIndex(File featureInput, FeatureCodec codec, int optimizeThreshold)

Methods inherited from class java.lang.Object

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

Constructor Details

CountRecords

public CountRecords()

Method Details

main

public static void main(String[] args)

The main method of this class: 1) checks to see that the feature file exists 2) loads an index from disk, if one doesn't exist, it creates it and writes it to disk 3) creates a FeatureSource 4) iterates over the records, emitting a final tally for the number of features seen

Parameters:

args - a single parameter, the file name to load

runWithIndex

public static long runWithIndex(File featureInput,
 FeatureCodec codec,
 int optimizeThreshold)

Parameters:

featureInput - File containing features

codec - Codec used to read the features

optimizeThreshold - Threshold used to optimize the linear index

Returns:

See Also:

• LinearIndex.optimize(double)

printUsage

public static void printUsage()

print usage information

loadIndex

public static Index loadIndex(File featureFile,
 FeatureCodec codec)

Parameters:

featureFile - the feature file

codec - the codec to decode features with

Returns:

an index instance

createAndWriteNewIndex

public static Index createAndWriteNewIndex(File featureFile,
 File indexFile,
 FeatureCodec codec)

creates a new index, given the feature file and the codec

Parameters:

featureFile - the feature file (i.e. .vcf, .bed)

indexFile - the index file; the location we should be writing the index to

codec - the codec to read features with

Returns:

an index instance

getFeatureCodec

public static FeatureCodec getFeatureCodec(File featureFile)

Return a FeatureCodec instance appropriate for the given featureFile. Codec is generated based on file extension

Parameters:

featureFile -

Returns:

Throws:

IllegalArgumentException - If a codec cannot be found