Package htsjdk.beta.codecs.reads.sam
Class SAMDecoder
java.lang.Object
htsjdk.beta.codecs.reads.sam.SAMDecoder
- All Implemented Interfaces:
HtsDecoder<SAMFileHeader,,SAMRecord> HtsQuery<SAMRecord>,ReadsDecoder,ReadsQuery<SAMRecord>,Closeable,AutoCloseable,Iterable<SAMRecord>
- Direct Known Subclasses:
SAMDecoderV1_0
InternalAPI
Base class for
BundleResourceType.READS_SAM decoders.-
Constructor Summary
ConstructorsConstructorDescriptionSAMDecoder(Bundle inputBundle, ReadsDecoderOptions readsDecoderOptions) Create a SAM decoder for the given input bundle. -
Method Summary
Modifier and TypeMethodDescriptionfinal StringGet a user-friendly display name for this decoder.final StringGet the name of the file format supported by this decoder.The format name defines the underlying format handled by this decoder, and also corresponds to the format of the primary bundle resource that is required when decoding (seeBundleResourceTypeandBundleResource.getFileFormat()).Get the inputBundlefor this decoder.Get theReadsDecoderOptionsfor this decoder.Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, waitMethods inherited from interface htsjdk.beta.plugin.HtsDecoder
close, getHeader, getVersionMethods inherited from interface htsjdk.beta.plugin.interval.HtsQuery
hasIndex, isQueryable, iterator, query, query, query, query, queryContained, queryContained, queryContained, queryOverlapping, queryOverlapping, queryOverlapping, queryStartMethods inherited from interface java.lang.Iterable
forEach, spliteratorMethods inherited from interface htsjdk.beta.plugin.reads.ReadsDecoder
queryMate, queryUnmapped
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Constructor Details
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SAMDecoder
Create a SAM decoder for the given input bundle. The primary resource in the bundle must have content typeBundleResourceType.ALIGNED_READS, and the resource must be an appropriate format and version for this encoder (to find an encoder for a bundle, seeReadsResolver.- Parameters:
inputBundle- inputBundleto decodereadsDecoderOptions-ReadsDecoderOptionsto use
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Method Details
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getFileFormat
Description copied from interface:HtsDecoderGet the name of the file format supported by this decoder.The format name defines the underlying format handled by this decoder, and also corresponds to the format of the primary bundle resource that is required when decoding (seeBundleResourceTypeandBundleResource.getFileFormat()).- Specified by:
getFileFormatin interfaceHtsDecoder<SAMFileHeader,SAMRecord> - Returns:
- the name of the underlying file format handled by this decoder
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getDisplayName
Description copied from interface:HtsDecoderGet a user-friendly display name for this decoder.- Specified by:
getDisplayNamein interfaceHtsDecoder<SAMFileHeader,SAMRecord> - Returns:
- a user-friendly display name for this decoder for use in error and warning messages
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getInputBundle
Get the inputBundlefor this decoder.- Returns:
- the input
Bundlefor this decoder
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getReadsDecoderOptions
Get theReadsDecoderOptionsfor this decoder.- Returns:
- the
ReadsDecoderOptionsfor this decoder.
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