htsjdk.samtools.cram.encoding.reader

Class CramRecordReader

java.lang.Object

htsjdk.samtools.cram.encoding.reader.AbstractReader

htsjdk.samtools.cram.encoding.reader.CramRecordReader

public class CramRecordReader
extends AbstractReader

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
CramRecordReader(ValidationStringency validationStringency)

Method Summary

Modifier and Type	Method and Description
void	read(CramCompressionRecord cramRecord)

Methods inherited from class java.lang.Object

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

Constructor Detail

CramRecordReader

public CramRecordReader(ValidationStringency validationStringency)

Method Detail

read

public void read(CramCompressionRecord cramRecord)