htsjdk.beta.codecs.reads

Class ReadsCodecUtils

java.lang.Object

htsjdk.beta.codecs.reads.ReadsCodecUtils

@InternalAPI
public final class ReadsCodecUtils
extends java.lang.Object

InternalAPI Utilities for use by reads encoder/decoder implementations.

Constructor Summary

Constructors

Constructor and Description
ReadsCodecUtils()

Method Summary

Modifier and Type	Method and Description
static void	assertBundleContainsIndex(Bundle inputBundle) InternalAPI The stated contract for decoders is that the index must be included in the bundle in order to use index queries, but some codecs use readers that *always* tries to resolve the index, which would violate that and allow some cases to work that shouldn't, so enforce the contract manually so that someday when we use a different implementation, no backward compatibility issue will be introduced.
static void	bamDecoderOptionsToSamReaderFactory(SamReaderFactory samReaderFactory, BAMDecoderOptions bamDecoderOptions)
static boolean	bundleContainsIndex(Bundle inputBundle) InternalAPI Return true if the input Bundle contains a reads index resource
static SamInputResource	bundleToSamInputResource(Bundle inputBundle, ReadsDecoderOptions readsDecoderOptions) InternalAPI Convert an input Bundle containing reads to a SamInputResource.
static SamReader	getSamReader(Bundle inputBundle, ReadsDecoderOptions readsDecoderOptions, SamReaderFactory samReaderFactory) Propagate all reads decoder options and all bam decoder options to either a SamReaderFactory or a SamInputResource, and return the resulting SamReader
static void	readsDecoderOptionsToSamReaderFactory(ReadsDecoderOptions readsDecoderOptions, SamReaderFactory samReaderFactory) InternalAPII Propagate options from a ReadsDecoderOptions to a SamReaderFactory.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

ReadsCodecUtils

public ReadsCodecUtils()

Method Detail

bundleToSamInputResource

@InternalAPI
public static SamInputResource bundleToSamInputResource(Bundle inputBundle,
                                                                     ReadsDecoderOptions readsDecoderOptions)

InternalAPI Convert an input Bundle containing reads to a SamInputResource.

Parameters:

inputBundle - input Bundle to convert (must contain a reads resource)

readsDecoderOptions - ReadsDecoderOptions to use

Returns:

a SamInputResource

readsDecoderOptionsToSamReaderFactory

@InternalAPI
public static void readsDecoderOptionsToSamReaderFactory(ReadsDecoderOptions readsDecoderOptions,
                                                                      SamReaderFactory samReaderFactory)

InternalAPII Propagate options from a ReadsDecoderOptions to a SamReaderFactory.

Parameters:

readsDecoderOptions - ReadsDecoderOptions to use

samReaderFactory - SamReaderFactory

bundleContainsIndex

@InternalAPI
public static boolean bundleContainsIndex(Bundle inputBundle)

InternalAPI Return true if the input Bundle contains a reads index resource

Parameters:

inputBundle - input Bundle to inspect

Returns:

true if input Bundle contains a reads index resource

assertBundleContainsIndex

@InternalAPI
public static void assertBundleContainsIndex(Bundle inputBundle)

InternalAPI The stated contract for decoders is that the index must be included in the bundle in order to use index queries, but some codecs use readers that *always* tries to resolve the index, which would violate that and allow some cases to work that shouldn't, so enforce the contract manually so that someday when we use a different implementation, no backward compatibility issue will be introduced.

Parameters:

inputBundle - input Bundle to inspect

getSamReader

@InternalAPI
public static SamReader getSamReader(Bundle inputBundle,
                                                  ReadsDecoderOptions readsDecoderOptions,
                                                  SamReaderFactory samReaderFactory)

Propagate all reads decoder options and all bam decoder options to either a SamReaderFactory or a SamInputResource, and return the resulting SamReader

bamDecoderOptionsToSamReaderFactory

@InternalAPI
public static void bamDecoderOptionsToSamReaderFactory(SamReaderFactory samReaderFactory,
                                                                    BAMDecoderOptions bamDecoderOptions)