htsjdk.samtools.cram.encoding.reader

Class MultiRefSliceAlignmentSpanReader

java.lang.Object

htsjdk.samtools.cram.encoding.reader.CramRecordReader

htsjdk.samtools.cram.encoding.reader.MultiRefSliceAlignmentSpanReader

public class MultiRefSliceAlignmentSpanReader
extends CramRecordReader

A reader that only keeps track of alignment spans. The intended use is for CRAI indexing.

Field Summary

Fields inherited from class htsjdk.samtools.cram.encoding.reader.CramRecordReader

APDelta, validationStringency

Constructor Summary

Constructors

Constructor and Description
MultiRefSliceAlignmentSpanReader(BitInputStream coreInputStream, java.util.Map<java.lang.Integer,java.io.ByteArrayInputStream> externalInputMap, CompressionHeader header, ValidationStringency validationStringency, int initialAlignmentStart, int recordCount) Initializes a Multiple Reference Sequence ID Reader.

Method Summary

Modifier and Type	Method and Description
java.util.Map<ReferenceContext,AlignmentSpan>	getReferenceSpans()

Methods inherited from class htsjdk.samtools.cram.encoding.reader.CramRecordReader

read

Methods inherited from class java.lang.Object

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

Constructor Detail

MultiRefSliceAlignmentSpanReader

public MultiRefSliceAlignmentSpanReader(BitInputStream coreInputStream,
                                        java.util.Map<java.lang.Integer,java.io.ByteArrayInputStream> externalInputMap,
                                        CompressionHeader header,
                                        ValidationStringency validationStringency,
                                        int initialAlignmentStart,
                                        int recordCount)

Initializes a Multiple Reference Sequence ID Reader. The intended use is for CRAI indexing.

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

validationStringency - how strict to be when reading this CRAM record

initialAlignmentStart - the alignmentStart used for initial calculation of spans

recordCount - the number of CRAM records to read

Method Detail

getReferenceSpans

public java.util.Map<ReferenceContext,AlignmentSpan> getReferenceSpans()