Package htsjdk.samtools.cram.encoding.reader

Class CramRecordReader

java.lang.Object

htsjdk.samtools.cram.encoding.reader.CramRecordReader

public final class CramRecordReader
extends Object

A reader used to consume and populate encoded CRAMCompressionRecords 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 a Slice and the corresponding CRAMCompressionRecord fields.

Field Summary

Fields

Modifier and Type	Field	Description
protected final ValidationStringency	validationStringency

Constructor Summary

Constructors

Constructor	Description
CramRecordReader(Slice slice, CompressorCache compressorCache, ValidationStringency validationStringency)	Initialize a Cram Record Reader

Method Summary

Modifier and Type	Method	Description
CRAMCompressionRecord	readCRAMRecord(long sequentialIndex, int prevAlignmentStart)	Read a CRAMCompressionRecord, using this reader's data series readers.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details

validationStringency

protected final ValidationStringency validationStringency

Constructor Details

CramRecordReader

public CramRecordReader(Slice slice,
 CompressorCache compressorCache,
 ValidationStringency validationStringency)

Initialize a Cram Record Reader

Parameters:

slice - the slice into which the records should be read

validationStringency - how strict to be when reading this CRAM record

Method Details

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