Class CRAMIterator

    • Method Detail

      • advanceToAlignmentInContainer

        public boolean advanceToAlignmentInContainer​(int refIndex,
                                                     int pos)
        Skip cached records until given alignment start position.
        Parameters:
        refIndex - reference sequence index
        pos - alignment start to skip to
      • getFirstContainerOffset

        public long getFirstContainerOffset()
      • 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
      • getCramHeader

        public CramHeader getCramHeader()
      • setValidationStringency

        public void setValidationStringency​(ValidationStringency validationStringency)
      • getFileSource

        public SamReader getFileSource()
      • setFileSource

        public void setFileSource​(SamReader mReader)