Class CramRecordReader
- java.lang.Object
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- htsjdk.samtools.cram.encoding.reader.CramRecordReader
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- Direct Known Subclasses:
MultiRefSliceAlignmentSpanReader
public class CramRecordReader extends Object
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Field Summary
Fields Modifier and Type Field Description protected boolean
APDelta
protected ValidationStringency
validationStringency
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Constructor Summary
Constructors Constructor Description CramRecordReader(BitInputStream coreInputStream, Map<Integer,ByteArrayInputStream> externalInputMap, CompressionHeader header, int refId, ValidationStringency validationStringency)
Initialize a Cram Record Reader
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
read(CramCompressionRecord cramRecord)
Read a Cram Compression Record, using this class's Encodings
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Field Detail
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validationStringency
protected final ValidationStringency validationStringency
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APDelta
protected final boolean APDelta
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Constructor Detail
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CramRecordReader
public CramRecordReader(BitInputStream coreInputStream, Map<Integer,ByteArrayInputStream> externalInputMap, CompressionHeader header, int refId, ValidationStringency validationStringency)
Initialize a Cram Record Reader- 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 HeaderrefId
- the reference sequence ID to assign to these recordsvalidationStringency
- how strict to be when reading this CRAM record
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Method Detail
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read
public void read(CramCompressionRecord cramRecord)
Read a Cram Compression Record, using this class's Encodings- Parameters:
cramRecord
- the Cram Compression Record to read into
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