public class RefSeqIdReader extends 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 and Description |
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RefSeqIdReader(int seqId,
int alignmentStart,
ValidationStringency validationStringency) |
Modifier and Type | Method and Description |
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java.util.Map<java.lang.Integer,AlignmentSpan> |
getReferenceSpans() |
void |
read() |
public RefSeqIdReader(int seqId, int alignmentStart, ValidationStringency validationStringency)
public java.util.Map<java.lang.Integer,AlignmentSpan> getReferenceSpans()
public void read()