htsjdk.samtools.cram.encoding.reader

Class RefSeqIdReader

java.lang.Object

htsjdk.samtools.cram.encoding.reader.AbstractReader

htsjdk.samtools.cram.encoding.reader.RefSeqIdReader

public class RefSeqIdReader
extends AbstractReader

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

Field Summary

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

alignmentStartCodec, APDelta, baseCodec, basesCodec, baseSubstitutionCodec, bitFlagsCodec, captureReadNames, compressionBitFlagsCodec, deletionLengthCodec, distanceToNextFragmentCodec, hardClipCodec, insertionCodec, insertSizeCodec, mappingScoreCodec, mateAlignmentStartCodec, mateBitFlagCodec, mateReferenceIdCodec, numberOfReadFeaturesCodec, paddingCodec, qualityScoreCodec, qualityScoresCodec, readFeatureCodeCodec, readFeaturePositionCodec, readGroupCodec, readLengthCodec, readNameCodec, refId, refIdCodec, refSkipCodec, scoresCodec, softClipCodec, tagIdDictionary, tagIdListCodec, tagValueCodecs

Constructor Summary

Constructors

Constructor and Description
RefSeqIdReader(int seqId, int alignmentStart, ValidationStringency validationStringency)

Method Summary

Modifier and Type	Method and Description
java.util.Map<java.lang.Integer,AlignmentSpan>	getReferenceSpans()
void	read()

Methods inherited from class java.lang.Object

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

Constructor Detail

RefSeqIdReader

public RefSeqIdReader(int seqId,
                      int alignmentStart,
                      ValidationStringency validationStringency)

Method Detail

getReferenceSpans

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

read

public void read()