Class CRAMDecoderV3_0
java.lang.Object
htsjdk.beta.codecs.reads.cram.CRAMDecoder
htsjdk.beta.codecs.reads.cram.cramV3_0.CRAMDecoderV3_0
- All Implemented Interfaces:
HtsDecoder<SAMFileHeader,
,SAMRecord> HtsQuery<SAMRecord>
,ReadsDecoder
,ReadsQuery<SAMRecord>
,Closeable
,AutoCloseable
,Iterable<SAMRecord>
CRAM v3.0 decoder.
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Constructor Summary
ConstructorsConstructorDescriptionCRAMDecoderV3_0
(Bundle bundle, ReadsDecoderOptions readsDecoderOptions) Create a new CRAM V3.0 decoder. -
Method Summary
Modifier and TypeMethodDescriptionGet the version of the file format supported by this decoder.Methods inherited from class htsjdk.beta.codecs.reads.cram.CRAMDecoder
close, getCRAMReferenceSource, getDisplayName, getFileFormat, getHeader, getInputBundle, getReadsDecoderOptions, hasIndex, isQueryable, iterator, query, queryMate, queryStart, queryUnmapped
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
Methods inherited from interface htsjdk.beta.plugin.interval.HtsQuery
query, query, query, queryContained, queryContained, queryContained, queryOverlapping, queryOverlapping, queryOverlapping
Methods inherited from interface java.lang.Iterable
forEach, spliterator
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Constructor Details
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CRAMDecoderV3_0
Create a new CRAM V3.0 decoder. The primary resource in the input bundle must have content typeBundleResourceType.CT_ALIGNED_READS
(to find a decoder for a bundle, seeReadsResolver
).- Parameters:
bundle
- inputBundle
to decodereadsDecoderOptions
-ReadsDecoderOptions
to use
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Method Details
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getVersion
Description copied from interface:HtsDecoder
Get the version of the file format supported by this decoder.
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