Class SRAIndexedSequenceFile

Method Details

• getSequenceDictionary

  public SAMSequenceDictionary getSequenceDictionary()

  Description copied from interface: ReferenceSequenceFile

  Must return a sequence dictionary with at least the following fields completed for each sequence: name, length.

  Specified by:

  getSequenceDictionary in interface ReferenceSequenceFile

  Returns:

  a list of sequence records representing the sequences in this reference file

• nextSequence

  public ReferenceSequence nextSequence()

  Description copied from interface: ReferenceSequenceFile

  Retrieves the next whole sequences from the file.

  Specified by:

  nextSequence in interface ReferenceSequenceFile

  Returns:

  a ReferenceSequence or null if at the end of the file

• reset

  public void reset()

  Description copied from interface: ReferenceSequenceFile

  Resets the ReferenceSequenceFile so that the next call to nextSequence() will return the first sequence in the file.

  Specified by:

  reset in interface ReferenceSequenceFile

• isIndexed

  public boolean isIndexed()

  Specified by:

  isIndexed in interface ReferenceSequenceFile

  Returns:

  true if getSequence and getSubsequenceAt methods are allowed.

• getSequence

  public ReferenceSequence getSequence(String contig)

  Description copied from interface: ReferenceSequenceFile

  Retrieves the complete sequence described by this contig.

  Specified by:

  getSequence in interface ReferenceSequenceFile

  Parameters:

  contig - contig whose data should be returned.

  Returns:

  The full sequence associated with this contig.

• getSubsequenceAt

  public ReferenceSequence getSubsequenceAt(String contig, long start, long stop)

  Description copied from interface: ReferenceSequenceFile

  Gets the subsequence of the contig in the range [start,stop]

  Specified by:

  getSubsequenceAt in interface ReferenceSequenceFile

  Parameters:

  contig - Contig whose subsequence to retrieve.

  start - inclusive, 1-based start of region.

  stop - inclusive, 1-based stop of region.

  Returns:

  The partial reference sequence associated with this range.

• close

  public void close() throws IOException

  Specified by:

  close in interface AutoCloseable

  Specified by:

  close in interface Closeable

  Specified by:

  close in interface ReferenceSequenceFile

  Throws:

  IOException

• loadSequenceDictionary

  protected SAMSequenceDictionary loadSequenceDictionary() throws ngs.ErrorMsg

  Throws:

  ngs.ErrorMsg