Class RefSeqIdReader
- java.lang.Object
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- htsjdk.samtools.cram.encoding.reader.AbstractReader
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- htsjdk.samtools.cram.encoding.reader.RefSeqIdReader
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public class RefSeqIdReader extends AbstractReader
A reader that only keeps track of alignment spans. The intended use is for CRAI index.
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Field Summary
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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
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Constructor Summary
Constructors Constructor Description RefSeqIdReader(int seqId, int alignmentStart, ValidationStringency validationStringency)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description Map<Integer,AlignmentSpan>
getReferenceSpans()
void
read()
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Constructor Detail
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RefSeqIdReader
public RefSeqIdReader(int seqId, int alignmentStart, ValidationStringency validationStringency)
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Method Detail
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getReferenceSpans
public Map<Integer,AlignmentSpan> getReferenceSpans()
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read
public void read()
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