Package | Description |
---|---|
htsjdk.tribble | |
htsjdk.tribble.example | |
htsjdk.tribble.index | |
htsjdk.tribble.index.interval | |
htsjdk.tribble.index.linear | |
htsjdk.tribble.index.tabix |
Modifier and Type | Method and Description |
---|---|
static <FEATURE extends Feature,SOURCE> |
AbstractFeatureReader.getFeatureReader(java.lang.String featureResource,
FeatureCodec<FEATURE,SOURCE> codec,
Index index)
Return a reader with a supplied index.
|
Constructor and Description |
---|
TribbleIndexedFeatureReader(java.lang.String featureFile,
FeatureCodec<T,SOURCE> codec,
Index index) |
Modifier and Type | Method and Description |
---|---|
static Index |
CountRecords.createAndWriteNewIndex(java.io.File featureFile,
java.io.File indexFile,
FeatureCodec codec)
creates a new index, given the feature file and the codec
|
static Index |
CountRecords.loadIndex(java.io.File featureFile,
FeatureCodec codec) |
static Index |
IndicesAreEqual.loadIndex(java.lang.String filename) |
Modifier and Type | Interface and Description |
---|---|
interface |
MutableIndex
Some Index implementations can be modified in memory.
|
Modifier and Type | Class and Description |
---|---|
class |
AbstractIndex
An abstract implementation of the index class.
|
Modifier and Type | Method and Description |
---|---|
static <FEATURE_TYPE extends Feature,SOURCE_TYPE> |
IndexFactory.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> |
IndexFactory.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> |
IndexFactory.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
|
Index |
IndexCreator.finalizeIndex(long finalFilePosition)
Create the index, given the stream of features passed in to this point
|
Index |
DynamicIndexCreator.finalizeIndex(long finalFilePosition) |
static Index |
IndexFactory.loadIndex(java.lang.String indexFile)
Load in index from the specified file.
|
Modifier and Type | Method and Description |
---|---|
static void |
IndexFactory.writeIndex(Index idx,
java.io.File idxFile)
Write the index to a file; little endian.
|
Modifier and Type | Class and Description |
---|---|
class |
IntervalTreeIndex
Index based on an interval tree
|
Modifier and Type | Method and Description |
---|---|
Index |
IntervalIndexCreator.finalizeIndex(long finalFilePosition)
finalize the index; create a tree index given the feature list passed in so far
|
Modifier and Type | Class and Description |
---|---|
class |
LinearIndex
Index defined by dividing the genome by chromosome, then each chromosome into bins of fixed width (in
genomic coordinates).
|
Modifier and Type | Method and Description |
---|---|
Index |
LinearIndexCreator.finalizeIndex(long finalFilePosition)
finalize the index; producing an index object
|
Index |
LinearIndex.optimize() |
Index |
LinearIndex.optimize(double threshold)
Adapative optimization of the linear index
|
Modifier and Type | Class and Description |
---|---|
class |
TabixIndex
This class represent a Tabix index that has been built in memory or read from a file.
|
Modifier and Type | Method and Description |
---|---|
Index |
TabixIndexCreator.finalizeIndex(long finalFilePosition) |