Class CramRecordReader
- java.lang.Object
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- htsjdk.samtools.cram.encoding.reader.CramRecordReader
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public final class CramRecordReader extends Object
A reader used to consume and populate encodedCRAMCompressionRecord
s from a set of streams representing data series/blocks in a Slice. This is essentially a bridge between the various data series streams associated in aSlice
and the correspondingCRAMCompressionRecord
fields.
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Field Summary
Fields Modifier and Type Field Description protected ValidationStringency
validationStringency
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Constructor Summary
Constructors Constructor Description CramRecordReader(Slice slice, CompressorCache compressorCache, ValidationStringency validationStringency)
Initialize a Cram Record Reader
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description CRAMCompressionRecord
readCRAMRecord(long sequentialIndex, int prevAlignmentStart)
Read a CRAMCompressionRecord, using this reader's data series readers.
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Field Detail
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validationStringency
protected final ValidationStringency validationStringency
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Constructor Detail
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CramRecordReader
public CramRecordReader(Slice slice, CompressorCache compressorCache, ValidationStringency validationStringency)
Initialize a Cram Record Reader- Parameters:
slice
- the slice into which the records should be readvalidationStringency
- how strict to be when reading this CRAM record
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Method Detail
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readCRAMRecord
public CRAMCompressionRecord readCRAMRecord(long sequentialIndex, int prevAlignmentStart)
Read a CRAMCompressionRecord, using this reader's data series readers.- Parameters:
prevAlignmentStart
- the alignmentStart of the previous record, for position delta calculation- Returns:
- the newly-read CRAMCompressionRecord
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