Constructor Detail

• MergingSamRecordIterator

  @Deprecated
  public MergingSamRecordIterator​(SamFileHeaderMerger headerMerger,
                                  boolean forcePresorted)

  Deprecated.

  replaced by MergingSamRecordIterator(SamFileHeaderMerger, Collection, boolean)
  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.

Method Detail

• close

  public void close()

  Close down all open iterators.

  Specified by:

  close in interface AutoCloseable

  Specified by:

  close in interface Closeable

  Specified by:

  close in interface CloseableIterator<SAMRecord>

• hasNext

  public boolean hasNext()

  Returns true if any of the underlying iterators has more records, otherwise false.

  Specified by:

  hasNext in interface Iterator<SAMRecord>

• next

  public SAMRecord next()

  Returns the next record from the top most iterator during merging.

  Specified by:

  next in interface Iterator<SAMRecord>

• remove

  public void remove()

  Unsupported operation.

  Specified by:

  remove in interface Iterator<SAMRecord>

• getMergedHeader

  public SAMFileHeader getMergedHeader()

  Returns the merged header that the merging iterator is working from.