public Map<Integer, AlignmentSpan> getReferences(final Container container, final ValidationStringency validationStringency) throws IOException { final Map<Integer, AlignmentSpan> containerSpanMap = new HashMap<>(); for (final Slice slice : container.slices) { addAllSpans(containerSpanMap, getReferences(slice, container.header, validationStringency)); } return containerSpanMap; }
public Map<Integer, AlignmentSpan> getReferences(final Container container, final ValidationStringency validationStringency) { final Map<Integer, AlignmentSpan> containerSpanMap = new HashMap<>(); for (final Slice slice : container.slices) { addAllSpans(containerSpanMap, getReferences(slice, container.header, validationStringency)); } return containerSpanMap; }
Map<Integer, AlignmentSpan> getReferences(final Slice slice, final CompressionHeader header, final ValidationStringency validationStringency) throws IOException { final Map<Integer, AlignmentSpan> spanMap = new HashMap<>(); switch (slice.sequenceId) { case SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX: spanMap.put(SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX, AlignmentSpan.UNMAPPED_SPAN); break; case Slice.MULTI_REFERENCE: final Map<Integer, AlignmentSpan> spans = slice.getMultiRefAlignmentSpans(header, validationStringency); addAllSpans(spanMap, spans); break; default: addSpan(slice.sequenceId, slice.alignmentStart, slice.alignmentSpan, slice.nofRecords, spanMap); break; } return spanMap; }
private Map<Integer, AlignmentSpan> getReferences(final Slice slice, final CompressionHeader header, final ValidationStringency validationStringency) { final Map<Integer, AlignmentSpan> spanMap = new HashMap<>(); switch (slice.sequenceId) { case SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX: spanMap.put(SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX, AlignmentSpan.UNMAPPED_SPAN); break; case Slice.MULTI_REFERENCE: final Map<Integer, AlignmentSpan> spans = slice.getMultiRefAlignmentSpans(header, validationStringency); addAllSpans(spanMap, spans); break; default: addSpan(slice.sequenceId, slice.alignmentStart, slice.alignmentSpan, slice.nofRecords, spanMap); break; } return spanMap; }