htsjdk.samtools.cram.encoding.reader

Class CramRecordReader

java.lang.Object

htsjdk.samtools.cram.encoding.reader.CramRecordReader

Direct Known Subclasses:

MultiRefSliceAlignmentSpanReader

public class CramRecordReader
extends java.lang.Object

Field Summary

Fields

Modifier and Type	Field and Description
protected boolean	APDelta
protected ValidationStringency	validationStringency

Constructor Summary

Constructors

Constructor and Description
CramRecordReader(BitInputStream coreInputStream, java.util.Map<java.lang.Integer,java.io.ByteArrayInputStream> externalInputMap, CompressionHeader header, ReferenceContext refContext, ValidationStringency validationStringency) Initialize a Cram Record Reader

Method Summary

Modifier and Type	Method and Description
int	read(CramCompressionRecord cramRecord, int prevAlignmentStart) Read a Cram Compression Record, using this class's Encodings

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

APDelta

protected final boolean APDelta

Constructor Detail

CramRecordReader

public CramRecordReader(BitInputStream coreInputStream,
                        java.util.Map<java.lang.Integer,java.io.ByteArrayInputStream> externalInputMap,
                        CompressionHeader header,
                        ReferenceContext refContext,
                        ValidationStringency validationStringency)

Initialize a Cram Record Reader

Parameters:

coreInputStream - Core data block bit stream, to be read by non-external Encodings

externalInputMap - External data block byte stream map, to be read by external Encodings

header - the associated Cram Compression Header

refContext - the reference context to assign to these records

validationStringency - how strict to be when reading this CRAM record

Method Detail

read

public int read(CramCompressionRecord cramRecord,
                int prevAlignmentStart)

Read a Cram Compression Record, using this class's Encodings

Parameters:

cramRecord - the Cram Compression Record to read into

prevAlignmentStart - the alignmentStart of the previous record, for delta calculation

Returns:

the alignmentStart of the newly-read record