htsjdk.beta.plugin.reads

Class ReadsBundle<T extends IOPath>

java.lang.Object

htsjdk.beta.io.bundle.Bundle

htsjdk.beta.plugin.reads.ReadsBundle<T>

Type Parameters:

T - The type to use when creating a ReadsBundle new IOPathResources for a ReadsBundle. Note that resources that are put into a ReadsBundle using the {ReadsBundle(Collection)} constructor may have tIOPathResources that do not conform to this type.

All Implemented Interfaces:

java.io.Serializable, java.lang.Iterable<BundleResource>

public class ReadsBundle<T extends IOPath>
extends Bundle
implements java.io.Serializable

A Bundle specifically for reads and reads-related resources. A ReadsBundle has a primary resource with content type BundleResourceType.ALIGNED_READS; and an optional index resource. ReadsBundles can also contain other resources. ReadsBundle is primarily a convenience layer for the common case where a Bundle contains reads and related resources backed by IOPathResources. It provides convenient constructors, and validation for JSON interconversions. For reads sources that are backed by streams or other BundleResource types, the Bundle and BundleBuilder classes can be used directly.

See Also:

Serialized Form

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	ReadsBundle(java.util.Collection<BundleResource> resources) Create a ReadsBundle using the resources in an existing bundle.
	ReadsBundle(T reads) Create a ReadsBundle containing only a reads resource.
	ReadsBundle(T reads, T index) Create a ReadsBundle containing only reads and an index.

Method Summary

Modifier and Type	Method and Description
java.util.Optional<BundleResource>	getIndex() Get the optional BundleResourceType.READS_INDEX resource for this ReadsBundle.
BundleResource	getReads() return the BundleResourceType.ALIGNED_READS BundleResource for this ReadsBundle
static ReadsBundle<IOPath>	getReadsBundleFromPath(IOPath jsonPath) Create a ReadsBundle from a JSON string contained in jsonPath.
static ReadsBundle<IOPath>	getReadsBundleFromString(java.lang.String jsonString) Create a ReadsBundle from a JSON string.
static <T extends IOPath> ReadsBundle<T>	getReadsBundleFromString(java.lang.String jsonString, java.util.function.Function<java.lang.String,T> ioPathConstructor) Create a ReadsBundle from a JSON string with all IOPathResources using an IOPath-derived class of type T.
static boolean	looksLikeAReadsBundle(IOPath rawReadPath)
static ReadsBundle<IOPath>	resolveIndex(IOPath reads) Find the companion index for a reads source, and create a new ReadsBundle containing the reads and the companion index, if one can be found.
static <T extends IOPath> ReadsBundle<T>	resolveIndex(T reads, java.util.function.Function<java.lang.String,T> ioPathConstructor) Find the companion index for a reads source, and create a new ReadsBundle containing the reads and the companion index, if one can be found.

Methods inherited from class htsjdk.beta.io.bundle.Bundle

equals, get, getOrThrow, getPrimaryContentType, getPrimaryResource, getResources, hashCode, iterator, toString

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.lang.Iterable

forEach, spliterator

Constructor Detail

ReadsBundle

public ReadsBundle(T reads)

Create a ReadsBundle containing only a reads resource.

Parameters:

reads - An IOPath-derived object that represents a source of reads.

ReadsBundle

public ReadsBundle(T reads,
                   T index)

Create a ReadsBundle containing only reads and an index.

Parameters:

reads - An IOPath-derived object that represents a source of reads.

ReadsBundle

protected ReadsBundle(java.util.Collection<BundleResource> resources)

Create a ReadsBundle using the resources in an existing bundle. A resource with content type BundleResourceType.ALIGNED_READS must be present in the resources, or this constructor will throw. Note that this constructor allows existing IOPathResources that do not conform to the type T to be included in the resulting ReadsBundle.

Parameters:

resources - collection of BundleResource. the collection must include a resource with content type BundleResourceType.ALIGNED_READS.

Throws:

java.lang.IllegalArgumentException - if no resource with content type BundleResourceType.ALIGNED_READS is included in the input BundleResource collection

Method Detail

getReads

public BundleResource getReads()

return the BundleResourceType.ALIGNED_READS BundleResource for this ReadsBundle

Returns:

the BundleResourceType.ALIGNED_READS BundleResource for this ReadsBundle

getIndex

public java.util.Optional<BundleResource> getIndex()

Get the optional BundleResourceType.READS_INDEX resource for this ReadsBundle.

Returns:

the optional BundleResourceType.READS_INDEX resrouce for this ReadsBundle, or Optional.empty if no index resource is present in the bundle.

getReadsBundleFromPath

public static ReadsBundle<IOPath> getReadsBundleFromPath(IOPath jsonPath)

Create a ReadsBundle from a JSON string contained in jsonPath.

Parameters:

jsonPath - the path to a file that contains Bundle serialized to JSON. The bundle must contain a resource with content type READS.

Returns:

a ReadsBundle created from jsonPath

getReadsBundleFromString

public static ReadsBundle<IOPath> getReadsBundleFromString(java.lang.String jsonString)

Create a ReadsBundle from a JSON string.

Parameters:

jsonString - the jsonString to use to create the ReadsBundle

Returns:

a ReadsBundle

getReadsBundleFromString

public static <T extends IOPath> ReadsBundle<T> getReadsBundleFromString(java.lang.String jsonString,
                                                                         java.util.function.Function<java.lang.String,T> ioPathConstructor)

Create a ReadsBundle from a JSON string with all IOPathResources using an IOPath-derived class of type T.

Type Parameters:

T - the type of

Parameters:

jsonString - the string to use to create the ReadsBundle

ioPathConstructor - a function that takes a string and returns an IOPath-derived class of type T

Returns:

a newly created ReadsBundle

resolveIndex

public static ReadsBundle<IOPath> resolveIndex(IOPath reads)

Find the companion index for a reads source, and create a new ReadsBundle containing the reads and the companion index, if one can be found.

Parameters:

reads - the reads source to use

Returns:

a ReadsBundle containing reads and companion index, if it can be found

resolveIndex

public static <T extends IOPath> ReadsBundle<T> resolveIndex(T reads,
                                                             java.util.function.Function<java.lang.String,T> ioPathConstructor)

Find the companion index for a reads source, and create a new ReadsBundle containing the reads and the companion index, if one can be found. An index can only be resolved for an IOPath that represents on a file system for which an NIO provider is installed. Remote paths that use a protocol scheme for which no NIO file system is available will (silently) not be resolved.

Type Parameters:

T - the IOPath-derived type of the IOPathResources in the new bundle

Parameters:

reads - the reads source to use

ioPathConstructor - a function that takes a string and returns an IOPath-derived class of type

Returns:

a ReadsBundle containing reads and companion index, if it can be found

looksLikeAReadsBundle

public static boolean looksLikeAReadsBundle(IOPath rawReadPath)