htsjdk.samtools.cram.encoding.reader

Class CramRecordReader

java.lang.Object

htsjdk.samtools.cram.encoding.reader.CramRecordReader

public final class CramRecordReader
extends java.lang.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 and Description
protected ValidationStringency	validationStringency

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method and 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 Detail

validationStringency

protected final ValidationStringency validationStringency

Constructor Detail

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 Detail

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