org.broadinstitute.hellbender.engine

Class FeatureInput<T extends htsjdk.tribble.Feature>

java.lang.Object

htsjdk.io.HtsPath

org.broadinstitute.hellbender.engine.GATKPath

org.broadinstitute.hellbender.engine.FeatureInput<T>

Type Parameters:

T - the type of Feature that this FeatureInput file contains (eg., VariantContext, BEDFeature, etc.)

All Implemented Interfaces:

htsjdk.io.IOPath, java.io.Serializable, org.broadinstitute.barclay.argparser.TaggedArgument

public final class FeatureInput<T extends htsjdk.tribble.Feature>
extends GATKPath
implements java.io.Serializable

Class to represent a Feature-containing input file. Tools should declare @Argument-annotated fields of this type (or Collections of this type), and the Feature management system will automatically discover them at runtime (provided that they are declared in the tool itself, a superclass of the tool, or an ArgumentCollection of the tool). DO NOT ATTEMPT TO INSTANTIATE THIS CLASS DIRECTLY! FeatureInputs must be instantiated by the argument-parsing system only in order to be recognized by the Feature management system. This is why the constructor is marked as protected. If you still want to instantiate this class directly, you will have to call GATKTool.addFeatureInputsAfterInitialization(String, String, Class, int) in order to register the FeatureInput with the engine. FeatureInputs can be assigned logical names on the command line using the syntax: --argument_name:logical_name feature_file These logical names can then be retrieved by the tool at runtime via getName() Furthermore, a list of comma-separated key=value pairs may be provided as follows: --argument_name:logical_name,key1=value1,key2=value2 feature_file the string value provided for a given key can be retrieved via getAttribute(String). Keys must be unique.

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	FEATURE_ARGUMENT_TAG_DELIMITER Delimiter between the logical name and the file name in the --argument_name logical_name:feature_file syntax
protected static org.apache.logging.log4j.Logger	logger

Fields inherited from class org.broadinstitute.hellbender.engine.GATKPath

HDFS_SCHEME

Constructor Summary

Constructors

Constructor and Description
FeatureInput(GATKPath gatkPath) Construct a FeatureInput from a GATKPath argument value.
FeatureInput(GATKPath gatkPath, java.lang.String name) Construct a FeatureInput from a GATKPath argument value.
FeatureInput(java.lang.String rawInputSpecifier, java.lang.String name, java.util.Map<java.lang.String,java.lang.String> keyValueMap) Construct a FeatureInput from raw components: name, key value pairs and the file.

Method Summary

Modifier and Type	Method and Description
boolean	equals(java.lang.Object other) Test FeatureInputs for equality
java.lang.String	getAttribute(java.lang.String key) Gets the value for the given key associated with this Feature source or null if no value is associated with a given key.
java.lang.Class<htsjdk.tribble.FeatureCodec<T,?>>	getFeatureCodecClass()
java.lang.String	getFeaturePath() Gets the file backing this source of Features
java.lang.String	getName() Gets the logical name of this Feature source.
int	hashCode() FeatureInputs will be hashed by the engine, so make an effort to produce a reasonable hash code
boolean	hasUserSuppliedName()
void	setFeatureCodecClass(java.lang.Class<htsjdk.tribble.FeatureCodec<T,?>> featureCodecClass) Remember the FeatureCodec class for this input the first time it is discovered so we can bypass dynamic codec discovery when multiple FeatureDataSources are created for the same input.
java.lang.String	toString() Returns a String representation of this FeatureInput.

Methods inherited from class org.broadinstitute.hellbender.engine.GATKPath

getInputStream, getOutputStream, getTag, getTagAttributes, isHadoopURL, setTag, setTagAttributes, toPath

Methods inherited from class htsjdk.io.HtsPath

getCachedPath, getRawInputString, getToPathFailureReason, getURI, getURIString, hasFileSystemProvider, isPath, setCachedPath

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface htsjdk.io.IOPath

getBaseName, getExtension, getScheme, hasExtension, isBam, isCram, isFasta, isSam

Field Detail

logger

protected static final org.apache.logging.log4j.Logger logger

FEATURE_ARGUMENT_TAG_DELIMITER

public static final java.lang.String FEATURE_ARGUMENT_TAG_DELIMITER

Delimiter between the logical name and the file name in the --argument_name logical_name:feature_file syntax

See Also:

Constant Field Values

Constructor Detail

FeatureInput

public FeatureInput(GATKPath gatkPath)

Construct a FeatureInput from a GATKPath argument value.

Parameters:

gatkPath - an existing GATKPath object

FeatureInput

public FeatureInput(GATKPath gatkPath,
                    java.lang.String name)

Construct a FeatureInput from a GATKPath argument value.

Parameters:

gatkPath - an existing GATKPath object

name - the tag name for this feature input

FeatureInput

public FeatureInput(java.lang.String rawInputSpecifier,
                    java.lang.String name,
                    java.util.Map<java.lang.String,java.lang.String> keyValueMap)

Construct a FeatureInput from raw components: name, key value pairs and the file. This constructor is meant to be called by the engine and test classes -- FeatureInputs constructed some other way will not be recognized by the engine.

Method Detail

setFeatureCodecClass

public void setFeatureCodecClass(java.lang.Class<htsjdk.tribble.FeatureCodec<T,?>> featureCodecClass)

Remember the FeatureCodec class for this input the first time it is discovered so we can bypass dynamic codec discovery when multiple FeatureDataSources are created for the same input.

getFeatureCodecClass

public java.lang.Class<htsjdk.tribble.FeatureCodec<T,?>> getFeatureCodecClass()

Returns:

The previously established FeatureCodec class to use for this input, if any. May return null.

getAttribute

public java.lang.String getAttribute(java.lang.String key)

Gets the value for the given key associated with this Feature source or null if no value is associated with a given key.

Throws:

java.lang.IllegalArgumentException - if the key is null.

getName

public java.lang.String getName()

Gets the logical name of this Feature source. This will be a user-provided value if the --argument_name logical_name:feature_file was used on the command line, otherwise it will default to the absolute path of the backing file

Returns:

logical name of this source of Features

hasUserSuppliedName

public boolean hasUserSuppliedName()

Returns:

true if the value for name does not match the default, indicating it was a user supplied name (i.e. foo:file.vcf)

getFeaturePath

public java.lang.String getFeaturePath()

Gets the file backing this source of Features

Returns:

file backing this source of Features

hashCode

public int hashCode()

FeatureInputs will be hashed by the engine, so make an effort to produce a reasonable hash code

Overrides:

hashCode in class GATKPath

Returns:

hash code for this FeatureInput (combination of hash code of the name and file)

equals

public boolean equals(java.lang.Object other)

Test FeatureInputs for equality

Overrides:

equals in class GATKPath

Parameters:

other - object to compare this FeatureInput with

Returns:

true if this FeatureInput equals other, otherwise false

toString

public java.lang.String toString()

Returns a String representation of this FeatureInput. Will be the absolute path to the featureFile if we have no logical name, or a String of the form "logical_name:absolute_path_to_featureFile" if we do have a logical name.

Overrides:

toString in class GATKPath

Returns:

String representation of this FeatureInput