Constructor Detail

• SRAIterator

  public SRAIterator​(SRAAccession accession,
                     ngs.ReadCollection run,
                     SAMFileHeader header,
                     ReferenceCache cachedReferences,
                     SRAIterator.RecordRangeInfo recordRangeInfo,
                     List<Chunk> chunks)

  Parameters:

  run - opened read collection

  header - sam header

  cachedReferences - list of cached references shared among all iterators from a single SRAFileReader

  recordRangeInfo - info about record ranges withing SRA archive

  chunks - used to determine which records the iterator should return

Method Detail

• getRecordsRangeInfo

  public static SRAIterator.RecordRangeInfo getRecordsRangeInfo​(ngs.ReadCollection run)

  Loads record ranges needed for emulating BAM index

  Parameters:

  run - read collection

  Returns:

  record ranges

• hasNext

  public boolean hasNext()

  NGS iterators implement a single method "nextObject" which return true if the operation was successful or false if there are no more objects available. That means that there is no way to check "hasNext" without actually moving the iterator forward. Because of that all the logic of moving iterator forward is actually happens in "hasNext". Here is explanation of how it works: Iterator holds a list of chunks of requested records. Here we have chunksIterator that walks though that list. We walk though that list using chunksIterator. If current chunk can represent aligned fragments then we create SRAAlignmentIterator iterator, pass the chunk into it and ask if it can find any record. If record was found, we say that we have next; otherwise we check if the chunk can represent unaligned fragments and then create SRAUnalignmentIterator if so and do the same steps as with alignemnt iterator. If record was not found in both SRAAlignmentIterator and SRAUnalignmentIterator (it is possible that reference range has no alignments or that reads range has all aligned fragment), we try the next chunk. When there are no more chunks and both iterators have no more records we return false.

  Specified by:

  hasNext in interface Iterator<SAMRecord>

  Returns:

  true if there are more records available

• next

  public SAMRecord next()

  Call hasNext to make sure that one of inner iterators points to the next record, the retrieve the record from one of them.

  Specified by:

  next in interface Iterator<SAMRecord>

  Returns:

  lazy SRA record

• remove

  public void remove()

  Specified by:

  remove in interface Iterator<SAMRecord>

• close

  public void close()

  Description copied from interface: CloseableIterator
  Should be implemented to close/release any underlying resources.

  Specified by:

  close in interface AutoCloseable

  Specified by:

  close in interface Closeable

  Specified by:

  close in interface CloseableIterator<SAMRecord>

• assertSorted

  public SAMRecordIterator assertSorted​(SAMFileHeader.SortOrder sortOrder)

  Description copied from interface: SAMRecordIterator
  Establishes that records returned by this iterator are expected to be in the specified sort order. If this method has been called, then implementers must throw an IllegalStateException from next() when a record is read that violates the sort order. This method may be called multiple times over the course of an iteration, changing the expected sort, if desired -- from the time it is called, it validates whatever sort is set, or stops validating if it is set to null or SAMFileHeader.SortOrder.unsorted. If this method is not called, then no validation of the iterated records is done.

  Specified by:

  assertSorted in interface SAMRecordIterator

  Parameters:

  sortOrder - The order in which records are expected to be returned

  Returns:

  This SAMRecordIterator

• setValidationStringency

  public void setValidationStringency​(ValidationStringency validationStringency)