/** * Uses a Multiple Reference Slice Alignment Reader to determine the Reference Spans of a Slice. * The intended use is for CRAI indexing. * * @param header the associated Cram Compression Header * @param validationStringency how strict to be when reading CRAM records */ public Map<Integer, AlignmentSpan> getMultiRefAlignmentSpans(final CompressionHeader header, final ValidationStringency validationStringency) { final MultiRefSliceAlignmentSpanReader reader = new MultiRefSliceAlignmentSpanReader(getCoreBlockInputStream(), getExternalBlockInputMap(), header, validationStringency, alignmentStart, nofRecords); return reader.getReferenceSpans(); }
/** * Uses a Multiple Reference Slice Alignment Reader to determine the Reference Spans of a Slice. * The intended use is for CRAI indexing. * * @param header the associated Cram Compression Header * @param validationStringency how strict to be when reading CRAM records */ public Map<Integer, AlignmentSpan> getMultiRefAlignmentSpans(final CompressionHeader header, final ValidationStringency validationStringency) { final MultiRefSliceAlignmentSpanReader reader = new MultiRefSliceAlignmentSpanReader(getCoreBlockInputStream(), getExternalBlockInputMap(), header, validationStringency, alignmentStart, nofRecords); return reader.getReferenceSpans(); }
final BitInputStream bis = new DefaultBitInputStream(is)) { final MultiRefSliceAlignmentSpanReader reader = new MultiRefSliceAlignmentSpanReader(bis, inputMap, header, ValidationStringency.DEFAULT_STRINGENCY, 0, initialRecords.size()); final Map<Integer, AlignmentSpan> spans = reader.getReferenceSpans();