Constructor Detail

• SRAUnalignmentIterator

  public SRAUnalignmentIterator​(SRAAccession accession,
                                ngs.ReadCollection run,
                                SAMFileHeader header,
                                SRAIterator.RecordRangeInfo recordRangeInfo,
                                Chunk chunk)

  Parameters:

  run - opened read collection

  header - sam header

  recordRangeInfo - info about record ranges withing SRA archive

  chunk - used to determine which unaligned reads the iterator should return

Method Detail

• hasNext

  public boolean hasNext()

  Specified by:

  hasNext in interface Iterator<SAMRecord>

• next

  public SAMRecord next()

  Specified by:

  next in interface Iterator<SAMRecord>

• remove

  public void remove()

  Specified by:

  remove in interface Iterator<SAMRecord>

• setValidationStringency

  public void setValidationStringency​(ValidationStringency validationStringency)