Modifier and Type | Class and Description |
---|---|
class |
AbstractFeatureCodec<FEATURE_TYPE extends Feature,SOURCE>
Simple basic class providing much of the basic functionality of codecs
Every concrete subclass must implement
FeatureCodec.canDecode(String) to indicate whether it can decode the file. |
class |
AbstractFeatureReader<T extends Feature,SOURCE>
jrobinso
the feature reader class, which uses indices and codecs to read in Tribble file formats.
|
class |
AsciiFeatureCodec<T extends Feature>
A convenience base class for codecs that want to read in features from ASCII lines.
|
class |
BinaryFeatureCodec<T extends Feature>
Implements common methods of
FeatureCodec s that read from PositionalBufferedStream s. |
interface |
CloseableTribbleIterator<T extends Feature>
The basic iterator we use in Tribble, which allows closing and basic iteration.
|
interface |
FeatureCodec<FEATURE_TYPE extends Feature,SOURCE>
The base interface for classes that read in features.
|
interface |
FeatureReader<T extends Feature>
the basic interface that feature sources need to match
|
class |
TabixFeatureReader<T extends Feature,SOURCE> |
class |
TribbleIndexedFeatureReader<T extends Feature,SOURCE>
A reader for text feature files (i.e.
|
Modifier and Type | Class and Description |
---|---|
class |
SimpleFeature
A simple concrete Feature.
|
Modifier and Type | Method and Description |
---|---|
static <FEATURE extends Feature,SOURCE> |
AbstractFeatureReader.getFeatureReader(java.lang.String featureFile,
FeatureCodec<FEATURE,SOURCE> codec)
Calls
AbstractFeatureReader.getFeatureReader(String, FeatureCodec, boolean) with requireIndex = true |
static <FEATURE extends Feature,SOURCE> |
AbstractFeatureReader.getFeatureReader(java.lang.String featureResource,
FeatureCodec<FEATURE,SOURCE> codec,
boolean requireIndex)
AbstractFeatureReader.getFeatureReader(String, String, FeatureCodec, boolean) with null for indexResource |
static <FEATURE extends Feature,SOURCE> |
AbstractFeatureReader.getFeatureReader(java.lang.String featureResource,
FeatureCodec<FEATURE,SOURCE> codec,
Index index)
Return a reader with a supplied index.
|
static <FEATURE extends Feature,SOURCE> |
AbstractFeatureReader.getFeatureReader(java.lang.String featureResource,
java.lang.String indexResource,
FeatureCodec<FEATURE,SOURCE> codec,
boolean requireIndex) |
Modifier and Type | Method and Description |
---|---|
Feature |
FeatureCodec.decodeLoc(SOURCE source)
Decode a line to obtain just its FeatureLoc for indexing -- contig, start, and stop.
|
Feature |
AbstractFeatureCodec.decodeLoc(SOURCE source) |
Modifier and Type | Interface and Description |
---|---|
interface |
BEDFeature |
Modifier and Type | Class and Description |
---|---|
class |
FullBEDFeature
Object for full BED file.
|
class |
SimpleBEDFeature
Feature from a BED file without exon blocks.
|
Modifier and Type | Method and Description |
---|---|
static <FEATURE_TYPE extends Feature> |
ExampleBinaryCodec.convertToBinaryTest(FeatureReader<FEATURE_TYPE> reader,
java.io.OutputStream out)
Convenience method that creates an ExampleBinaryCodec file from another feature file.
|
static <FEATURE_TYPE extends Feature> |
ExampleBinaryCodec.convertToBinaryTest(java.io.File source,
java.io.File dest,
FeatureCodec<FEATURE_TYPE,LineIterator> codec)
Convenience method that creates an ExampleBinaryCodec file from another feature file.
|
Modifier and Type | Method and Description |
---|---|
Feature |
ExampleBinaryCodec.decode(PositionalBufferedStream stream) |
Feature |
ExampleBinaryCodec.decodeLoc(PositionalBufferedStream stream) |
Modifier and Type | Method and Description |
---|---|
java.lang.Class<Feature> |
ExampleBinaryCodec.getFeatureType() |
Modifier and Type | Class and Description |
---|---|
class |
GeliTextFeature
Deprecated.
this is deprecated and no longer supported
|
Modifier and Type | Method and Description |
---|---|
Feature |
GeliTextCodec.decodeLoc(java.lang.String line)
Deprecated.
|
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
|
static <FEATURE_TYPE extends Feature,SOURCE_TYPE> |
IndexFactory.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> |
IndexFactory.createIntervalIndex(java.io.File inputFile,
FeatureCodec<FEATURE_TYPE,SOURCE_TYPE> codec,
int featuresPerInterval)
a helper method for creating an interval-tree index
|
static <FEATURE_TYPE extends Feature,SOURCE_TYPE> |
IndexFactory.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> |
IndexFactory.createTabixIndex(java.io.File inputFile,
FeatureCodec<FEATURE_TYPE,SOURCE_TYPE> codec,
TabixFormat tabixFormat,
SAMSequenceDictionary sequenceDictionary) |
Modifier and Type | Method and Description |
---|---|
void |
IndexCreator.addFeature(Feature feature,
long filePosition)
Add a feature to the index
|
void |
DynamicIndexCreator.addFeature(Feature f,
long filePosition) |
Modifier and Type | Method and Description |
---|---|
void |
IntervalIndexCreator.addFeature(Feature feature,
long filePosition) |
Modifier and Type | Method and Description |
---|---|
void |
LinearIndexCreator.addFeature(Feature feature,
long filePosition)
add a feature to the index
|
Modifier and Type | Method and Description |
---|---|
void |
TabixIndexCreator.addFeature(Feature feature,
long filePosition) |
Modifier and Type | Method and Description |
---|---|
Feature |
BCF2Codec.decodeLoc(PositionalBufferedStream inputStream) |
Modifier and Type | Class and Description |
---|---|
class |
VariantContext
High-level overview
|
Modifier and Type | Method and Description |
---|---|
Feature |
AbstractVCFCodec.decodeLoc(java.lang.String line)
the fast decode function
|