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 | Description |
---|---|
RefSeqIdReader(int seqId,
int alignmentStart,
ValidationStringency validationStringency) |
Modifier and Type | Method | Description |
---|---|---|
Map<Integer,AlignmentSpan> |
getReferenceSpans() |
|
void |
read() |
public RefSeqIdReader(int seqId, int alignmentStart, ValidationStringency validationStringency)
public Map<Integer,AlignmentSpan> getReferenceSpans()
public void read()