Class MergingSamRecordIterator

    • Constructor Detail

      • MergingSamRecordIterator

        @Deprecated
        public MergingSamRecordIterator​(SamFileHeaderMerger headerMerger,
                                        boolean forcePresorted)
        Constructs a new merging iterator with the same set of readers and sort order as provided by the header merger parameter.
        Parameters:
        headerMerger - The merged header and contents of readers.
        forcePresorted - True to ensure that the iterator checks the headers of the readers for appropriate sort order.
      • MergingSamRecordIterator

        public MergingSamRecordIterator​(SamFileHeaderMerger headerMerger,
                                        Collection<SamReader> readers,
                                        boolean assumeSorted)
        Constructs a new merging iterator with the same set of readers and sort order as provided by the header merger parameter.
        Parameters:
        headerMerger - The merged header and contents of readers.
        assumeSorted - false ensures that the iterator checks the headers of the readers for appropriate sort order.
      • MergingSamRecordIterator

        public MergingSamRecordIterator​(SamFileHeaderMerger headerMerger,
                                        Map<SamReader,​CloseableIterator<SAMRecord>> iterators,
                                        boolean assumeSorted)
        Add a set of SAM file iterators to the merging iterator. Use this to restrict the merged iteration to a given genomic interval, rather than iterating over every read in the backing file or stream.
        Parameters:
        headerMerger - The merged header and contents of readers.
        iterators - Iterator traversing over reader contents.