Class SRAFileReader

Method Details

• type

  public SamReader.Type type()

  Specified by:

  type in interface SamReader.PrimitiveSamReader

• hasIndex

  public boolean hasIndex()

  Specified by:

  hasIndex in interface SamReader.PrimitiveSamReader

• getIndex

  public BAMIndex getIndex()

  Description copied from interface: SamReader.Indexing

  Retrieves the index for the given file type. Ensure that the index is of the specified type.

  Specified by:

  getIndex in interface SamReader.Indexing

  Specified by:

  getIndex in interface SamReader.PrimitiveSamReader

  Returns:

  An index of the given type.

• getFileHeader

  public SAMFileHeader getFileHeader()

  Specified by:

  getFileHeader in interface SamReader.PrimitiveSamReader

• getIterator

  public CloseableIterator<SAMRecord> getIterator()

  Specified by:

  getIterator in interface SamReader.PrimitiveSamReader

• getIterator

  public CloseableIterator<SAMRecord> getIterator(SAMFileSpan chunks)

  Specified by:

  getIterator in interface SamReader.PrimitiveSamReader

• getFilePointerSpanningReads

  public SAMFileSpan getFilePointerSpanningReads()

  Description copied from interface: SamReader.Indexing

  Gets a pointer spanning all reads in the BAM file.

  Specified by:

  getFilePointerSpanningReads in interface SamReader.Indexing

  Specified by:

  getFilePointerSpanningReads in interface SamReader.PrimitiveSamReader

  Returns:

  Unbounded pointer to the first record, in chunk format.

• query

  public CloseableIterator<SAMRecord> query(QueryInterval[] intervals, boolean contained)

  Specified by:

  query in interface SamReader.PrimitiveSamReader

• queryAlignmentStart

  public CloseableIterator<SAMRecord> queryAlignmentStart(String sequence, int start)

  Specified by:

  queryAlignmentStart in interface SamReader.PrimitiveSamReader

• queryUnmapped

  public CloseableIterator<SAMRecord> queryUnmapped()

  Specified by:

  queryUnmapped in interface SamReader.PrimitiveSamReader

• close

  public void close()

  Specified by:

  close in interface SamReader.PrimitiveSamReader

• getValidationStringency

  public ValidationStringency getValidationStringency()

  Specified by:

  getValidationStringency in interface SamReader.PrimitiveSamReader

• hasBrowseableIndex

  public boolean hasBrowseableIndex()

  Returns true if the supported index is browseable, meaning the bins in it can be traversed and chunk data inspected and retrieved.

  Specified by:

  hasBrowseableIndex in interface SamReader.Indexing

  Returns:

  True if the index supports the BrowseableBAMIndex interface. False otherwise.

• getBrowseableIndex

  public BrowseableBAMIndex getBrowseableIndex()

  Gets an index tagged with the BrowseableBAMIndex interface. Throws an exception if no such index is available.

  Specified by:

  getBrowseableIndex in interface SamReader.Indexing

  Returns:

  An index with a browseable interface, if possible.

  Throws:

  SAMException - if no such index is available.

• iterator

  public SAMRecordIterator iterator(SAMFileSpan chunks)

  Iterate through the given chunks in the file.

  Specified by:

  iterator in interface SamReader.Indexing

  Parameters:

  chunks - List of chunks for which to retrieve data.

  Returns:

  An iterator over the given chunks.

• getRecordsRangeInfo

  protected SRAIterator.RecordRangeInfo getRecordsRangeInfo()