Package htsjdk.beta.codecs.reads
Class ReadsCodecUtils
java.lang.Object
htsjdk.beta.codecs.reads.ReadsCodecUtils
InternalAPI
Utilities for use by reads encoder/decoder implementations.
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionstatic 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 inputBundle
contains a reads index resourcestatic SamInputResource
bundleToSamInputResource
(Bundle inputBundle, ReadsDecoderOptions readsDecoderOptions) InternalAPI Convert an inputBundle
containing reads to aSamInputResource
.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 SamReaderstatic void
readsDecoderOptionsToSamReaderFactory
(ReadsDecoderOptions readsDecoderOptions, SamReaderFactory samReaderFactory) InternalAPII Propagate options from aReadsDecoderOptions
to a SamReaderFactory.
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Constructor Details
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ReadsCodecUtils
public ReadsCodecUtils()
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Method Details
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bundleToSamInputResource
@InternalAPI public static SamInputResource bundleToSamInputResource(Bundle inputBundle, ReadsDecoderOptions readsDecoderOptions) InternalAPI Convert an inputBundle
containing reads to aSamInputResource
.- Parameters:
inputBundle
- inputBundle
to convert (must contain a reads resource)readsDecoderOptions
-ReadsDecoderOptions
to use- Returns:
- a
SamInputResource
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readsDecoderOptionsToSamReaderFactory
@InternalAPI public static void readsDecoderOptionsToSamReaderFactory(ReadsDecoderOptions readsDecoderOptions, SamReaderFactory samReaderFactory) InternalAPII Propagate options from aReadsDecoderOptions
to a SamReaderFactory.- Parameters:
readsDecoderOptions
-ReadsDecoderOptions
to usesamReaderFactory
-SamReaderFactory
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bundleContainsIndex
InternalAPI Return true if the inputBundle
contains a reads index resource -
assertBundleContainsIndex
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
- inputBundle
to inspect
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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)
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