htsjdk.tribble.index

Class IndexFactory

java.lang.Object

htsjdk.tribble.index.IndexFactory

public class IndexFactory
extends java.lang.Object

Factory class for creating indexes. It is the responsibility of this class to determine and create the correct index type from the input file or stream. Only LinearIndex and IntervalTreeIndex are supported by this factory.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	IndexFactory.IndexBalanceApproach We can optimize index-file-creation for different factors.
static class	IndexFactory.IndexType an enum that contains all of the information about the index types, and how to create them

Constructor Summary

Constructors

Constructor and Description
IndexFactory()

Method Summary

Modifier and Type	Method and Description
static <FEATURE_TYPE extends Feature,SOURCE_TYPE> Index	createDynamicIndex(java.io.File inputFile, FeatureCodec<FEATURE_TYPE,SOURCE_TYPE> codec) Create a dynamic index with the default balancing approach
static <FEATURE_TYPE extends Feature,SOURCE_TYPE> Index	createDynamicIndex(java.io.File inputFile, FeatureCodec<FEATURE_TYPE,SOURCE_TYPE> codec, IndexFactory.IndexBalanceApproach iba) create a dynamic index, given an input file, codec, and balance approach
static <FEATURE_TYPE extends Feature,SOURCE_TYPE> Index	createIndex(java.io.File inputFile, FeatureCodec<FEATURE_TYPE,SOURCE_TYPE> codec, IndexFactory.IndexType type) Create a index of the specified type with default binning parameters
static <FEATURE_TYPE extends Feature,SOURCE_TYPE> Index	createIndex(java.io.File inputFile, FeatureCodec<FEATURE_TYPE,SOURCE_TYPE> codec, IndexFactory.IndexType type, SAMSequenceDictionary sequenceDictionary) Create an index of the specified type with default binning parameters
static <FEATURE_TYPE extends Feature,SOURCE_TYPE> IntervalTreeIndex	createIntervalIndex(java.io.File inputFile, FeatureCodec<FEATURE_TYPE,SOURCE_TYPE> codec) create an interval-tree index with the default features per bin count
static <FEATURE_TYPE extends Feature,SOURCE_TYPE> IntervalTreeIndex	createIntervalIndex(java.io.File inputFile, FeatureCodec<FEATURE_TYPE,SOURCE_TYPE> codec, int featuresPerInterval) a helper method for creating an interval-tree index
static LinearIndex	createLinearIndex(java.io.File inputFile, FeatureCodec codec) a helper method for creating a linear binned index with default bin size
static <FEATURE_TYPE extends Feature,SOURCE_TYPE> LinearIndex	createLinearIndex(java.io.File inputFile, FeatureCodec<FEATURE_TYPE,SOURCE_TYPE> codec, int binSize) a helper method for creating a linear binned index
static <FEATURE_TYPE extends Feature,SOURCE_TYPE> TabixIndex	createTabixIndex(java.io.File inputFile, FeatureCodec<FEATURE_TYPE,SOURCE_TYPE> codec, SAMSequenceDictionary sequenceDictionary)
static <FEATURE_TYPE extends Feature,SOURCE_TYPE> TabixIndex	createTabixIndex(java.io.File inputFile, FeatureCodec<FEATURE_TYPE,SOURCE_TYPE> codec, TabixFormat tabixFormat, SAMSequenceDictionary sequenceDictionary)
static Index	loadIndex(java.lang.String indexFile) Load in index from the specified file.
static void	writeIndex(Index idx, java.io.File idxFile) Deprecated. use Index.write(File) instead

Methods inherited from class java.lang.Object

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

Constructor Detail

IndexFactory

public IndexFactory()

Method Detail

loadIndex

public static Index loadIndex(java.lang.String indexFile)

Load in index from the specified file. The type of index (LinearIndex or IntervalTreeIndex) is determined at run time by reading the type flag in the file.

Parameters:

indexFile - from which to load the index

createLinearIndex

public static LinearIndex createLinearIndex(java.io.File inputFile,
                                            FeatureCodec codec)

a helper method for creating a linear binned index with default bin size

Parameters:

inputFile - the input file to load features from

codec - the codec to use for decoding records

createLinearIndex

public static <FEATURE_TYPE extends Feature,SOURCE_TYPE> LinearIndex createLinearIndex(java.io.File inputFile,
                                                                                       FeatureCodec<FEATURE_TYPE,SOURCE_TYPE> codec,
                                                                                       int binSize)

a helper method for creating a linear binned index

Parameters:

inputFile - the input file to load features from

codec - the codec to use for decoding records

binSize - the bin size

createIntervalIndex

public static <FEATURE_TYPE extends Feature,SOURCE_TYPE> IntervalTreeIndex createIntervalIndex(java.io.File inputFile,
                                                                                               FeatureCodec<FEATURE_TYPE,SOURCE_TYPE> codec)

create an interval-tree index with the default features per bin count

Parameters:

inputFile - the file containing the features

codec - to decode the features

createIntervalIndex

public static <FEATURE_TYPE extends Feature,SOURCE_TYPE> IntervalTreeIndex createIntervalIndex(java.io.File inputFile,
                                                                                               FeatureCodec<FEATURE_TYPE,SOURCE_TYPE> codec,
                                                                                               int featuresPerInterval)

a helper method for creating an interval-tree index

Parameters:

inputFile - the input file to load features from

codec - the codec to use for decoding records

featuresPerInterval -

createDynamicIndex

public static <FEATURE_TYPE extends Feature,SOURCE_TYPE> Index createDynamicIndex(java.io.File inputFile,
                                                                                  FeatureCodec<FEATURE_TYPE,SOURCE_TYPE> codec)

Create a dynamic index with the default balancing approach

Parameters:

inputFile - the input file to load features from

codec - the codec to use for decoding records

createIndex

public static <FEATURE_TYPE extends Feature,SOURCE_TYPE> Index createIndex(java.io.File inputFile,
                                                                           FeatureCodec<FEATURE_TYPE,SOURCE_TYPE> codec,
                                                                           IndexFactory.IndexType type)

Create a index of the specified type with default binning parameters

Parameters:

inputFile - the input file to load features from

codec - the codec to use for decoding records

type - the type of index to create

createIndex

public static <FEATURE_TYPE extends Feature,SOURCE_TYPE> Index createIndex(java.io.File inputFile,
                                                                           FeatureCodec<FEATURE_TYPE,SOURCE_TYPE> codec,
                                                                           IndexFactory.IndexType type,
                                                                           SAMSequenceDictionary sequenceDictionary)

Create an index of the specified type with default binning parameters

Parameters:

inputFile - the input file to load features from

codec - the codec to use for decoding records

type - the type of index to create

sequenceDictionary - May be null, but if present may reduce memory footprint for tabix index creation

writeIndex

@Deprecated
public static void writeIndex(Index idx,
                                          java.io.File idxFile)
                                   throws java.io.IOException

Deprecated. use Index.write(File) instead

Write the index to a file; little endian.

Parameters:

idx -

idxFile -

Throws:

java.io.IOException

createDynamicIndex

public static <FEATURE_TYPE extends Feature,SOURCE_TYPE> Index createDynamicIndex(java.io.File inputFile,
                                                                                  FeatureCodec<FEATURE_TYPE,SOURCE_TYPE> codec,
                                                                                  IndexFactory.IndexBalanceApproach iba)

create a dynamic index, given an input file, codec, and balance approach

Parameters:

inputFile - the input file to load features from

codec - the codec to use for decoding records

iba - the index balancing approach

createTabixIndex

public static <FEATURE_TYPE extends Feature,SOURCE_TYPE> TabixIndex createTabixIndex(java.io.File inputFile,
                                                                                     FeatureCodec<FEATURE_TYPE,SOURCE_TYPE> codec,
                                                                                     TabixFormat tabixFormat,
                                                                                     SAMSequenceDictionary sequenceDictionary)

Parameters:

inputFile - The file to be indexed.

codec - Mechanism for reading inputFile.

tabixFormat - Header fields for TabixIndex to be produced.

sequenceDictionary - May be null, but if present may reduce memory footprint for index creation. Features in inputFile must be in the order defined by sequenceDictionary, if it is present.

createTabixIndex

public static <FEATURE_TYPE extends Feature,SOURCE_TYPE> TabixIndex createTabixIndex(java.io.File inputFile,
                                                                                     FeatureCodec<FEATURE_TYPE,SOURCE_TYPE> codec,
                                                                                     SAMSequenceDictionary sequenceDictionary)

Parameters:

inputFile - The file to be indexed.

codec - the codec to use for decoding records

sequenceDictionary - May be null, but if present may reduce memory footprint for index creation. Features in inputFile must be in the order defined by sequenceDictionary, if it is present.