Package | Description |
---|---|
htsjdk.tribble | |
htsjdk.tribble.bed | |
htsjdk.tribble.example | |
htsjdk.tribble.gelitext | |
htsjdk.tribble.index | |
htsjdk.variant.bcf2 | |
htsjdk.variant.vcf |
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
canDecode(String) to indicate whether it can decode the file. |
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. |
Modifier and Type | Field and Description |
---|---|
protected FeatureCodec<T,SOURCE> |
AbstractFeatureReader.codec |
Modifier and Type | Method and Description |
---|---|
static <FEATURE extends Feature,SOURCE> |
AbstractFeatureReader.getFeatureReader(String featureFile,
FeatureCodec<FEATURE,SOURCE> codec)
Calls
AbstractFeatureReader.getFeatureReader(String, FeatureCodec, boolean) with requireIndex = true |
static <FEATURE extends Feature,SOURCE> |
AbstractFeatureReader.getFeatureReader(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(String featureResource,
FeatureCodec<FEATURE,SOURCE> codec,
Index index)
Return a reader with a supplied index.
|
static <FEATURE extends Feature,SOURCE> |
AbstractFeatureReader.getFeatureReader(String featureResource,
String indexResource,
FeatureCodec<FEATURE,SOURCE> codec,
boolean requireIndex) |
Constructor and Description |
---|
AbstractFeatureReader(String path,
FeatureCodec<T,SOURCE> codec) |
TribbleIndexedFeatureReader(String featurePath,
FeatureCodec<T,SOURCE> codec,
boolean requireIndex) |
TribbleIndexedFeatureReader(String featureFile,
FeatureCodec<T,SOURCE> codec,
Index index) |
TribbleIndexedFeatureReader(String featureFile,
String indexFile,
FeatureCodec<T,SOURCE> codec,
boolean requireIndex) |
Modifier and Type | Class and Description |
---|---|
class |
BEDCodec
Codec for parsing BED file, as described by UCSC
See https://genome.ucsc.edu/FAQ/FAQformat.html#format1
|
Modifier and Type | Class and Description |
---|---|
class |
ExampleBinaryCodec
An example binary codec that encodes / decodes contig / start / stop values via DataInputStreams
|
Modifier and Type | Method and Description |
---|---|
static FeatureCodec |
CountRecords.getFeatureCodec(File featureFile)
Return a
FeatureCodec instance appropriate for the given
featureFile . |
Modifier and Type | Method and Description |
---|---|
static <FEATURE_TYPE extends Feature> |
ExampleBinaryCodec.convertToBinaryTest(File source,
File dest,
FeatureCodec<FEATURE_TYPE,LineIterator> codec)
Convenience method that creates an ExampleBinaryCodec file from another feature file.
|
static Index |
CountRecords.createAndWriteNewIndex(File featureFile,
File indexFile,
FeatureCodec codec)
creates a new index, given the feature file and the codec
|
static Index |
CountRecords.loadIndex(File featureFile,
FeatureCodec codec) |
static long |
CountRecords.runWithIndex(File featureInput,
FeatureCodec codec,
int optimizeThreshold) |
Modifier and Type | Class and Description |
---|---|
class |
GeliTextCodec
Deprecated.
This is deprecated and unsupported.
|
Modifier and Type | Method and Description |
---|---|
static <FEATURE_TYPE extends Feature,SOURCE_TYPE> |
IndexFactory.createDynamicIndex(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(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(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(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(File inputFile,
FeatureCodec<FEATURE_TYPE,SOURCE_TYPE> codec,
int featuresPerInterval)
a helper method for creating an interval-tree index
|
static LinearIndex |
IndexFactory.createLinearIndex(File inputFile,
FeatureCodec codec)
a helper method for creating a linear binned index with default bin size
|
static <FEATURE_TYPE extends Feature,SOURCE_TYPE> |
IndexFactory.createLinearIndex(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(File inputFile,
FeatureCodec<FEATURE_TYPE,SOURCE_TYPE> codec,
TabixFormat tabixFormat,
SAMSequenceDictionary sequenceDictionary) |
Modifier and Type | Class and Description |
---|---|
class |
BCF2Codec
Decode BCF2 files
|
Modifier and Type | Class and Description |
---|---|
class |
AbstractVCFCodec |
class |
VCF3Codec
A feature codec for the VCF3 specification, to read older VCF files.
|
class |
VCFCodec
A feature codec for the VCF 4 specification
|