Class CRAMDecoderV2_1
java.lang.Object
htsjdk.beta.codecs.reads.cram.CRAMDecoder
htsjdk.beta.codecs.reads.cram.cramV2_1.CRAMDecoderV2_1
- All Implemented Interfaces:
HtsDecoder<SAMFileHeader,
,SAMRecord> HtsQuery<SAMRecord>
,ReadsDecoder
,ReadsQuery<SAMRecord>
,Closeable
,AutoCloseable
,Iterable<SAMRecord>
CRAM v2.1decoder.
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Constructor Summary
ConstructorDescriptionCRAMDecoderV2_1
(Bundle bundle, ReadsDecoderOptions readsDecoderOptions) Create a new V2.1 CRAM 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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CRAMDecoderV2_1
Create a new V2.1 CRAM decoder. The primary resource in the input bundle must have content typeBundleResourceType.ALIGNED_READS
(to find a decoder for a bundle, seeReadsResolver
).- Parameters:
bundle
- the inputBundle
to decodereadsDecoderOptions
- theReadsDecoderOptions
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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