/** * Does this Slice contain reads placed on a single reference (whether their unmapped flags are set or not)? * @return true if all reads in the Slice are placed on a single reference */ public boolean isMappedSingleRef() { return ! isUnmapped() && ! isMultiref(); }
slice.containerOffset = container.offset; slice.index = sliceIndex++; if (slice.isMultiref()) { final ContainerParser parser = new ContainerParser(indexBuilder.bamHeader); final Map<Integer, AlignmentSpan> refSet = parser.getReferences(container, validationStringency);
slice.containerOffset = container.offset; slice.index = sliceIndex++; if (slice.isMultiref()) { final ContainerParser parser = new ContainerParser(indexBuilder.bamHeader); final Map<Integer, AlignmentSpan> refSet = parser.getReferences(container, validationStringency);