Class MultiRefSliceAlignmentSpanReader
- java.lang.Object
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- htsjdk.samtools.cram.encoding.reader.CramRecordReader
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- htsjdk.samtools.cram.encoding.reader.MultiRefSliceAlignmentSpanReader
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public class MultiRefSliceAlignmentSpanReader extends CramRecordReader
A reader that only keeps track of alignment spans. The intended use is for CRAI indexing.
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Field Summary
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Fields inherited from class htsjdk.samtools.cram.encoding.reader.CramRecordReader
APDelta, validationStringency
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Constructor Summary
Constructors Constructor Description MultiRefSliceAlignmentSpanReader(BitInputStream coreInputStream, Map<Integer,ByteArrayInputStream> externalInputMap, CompressionHeader header, ValidationStringency validationStringency, int initialAlignmentStart, int recordCount)
Initializes a Multiple Reference Sequence ID Reader.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description Map<Integer,AlignmentSpan>
getReferenceSpans()
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Methods inherited from class htsjdk.samtools.cram.encoding.reader.CramRecordReader
read
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Constructor Detail
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MultiRefSliceAlignmentSpanReader
public MultiRefSliceAlignmentSpanReader(BitInputStream coreInputStream, Map<Integer,ByteArrayInputStream> externalInputMap, CompressionHeader header, ValidationStringency validationStringency, int initialAlignmentStart, int recordCount)
Initializes a Multiple Reference Sequence ID Reader. The intended use is for CRAI indexing.- Parameters:
coreInputStream
- Core data block bit stream, to be read by non-external EncodingsexternalInputMap
- External data block byte stream map, to be read by external Encodingsheader
- the associated Cram Compression HeadervalidationStringency
- how strict to be when reading this CRAM recordinitialAlignmentStart
- the alignmentStart used for initial calculation of spansrecordCount
- the number of CRAM records to read
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Method Detail
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getReferenceSpans
public Map<Integer,AlignmentSpan> getReferenceSpans()
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