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/*===========================================================================
*
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information
*
* This software/database is a "United States Government Work" under the
* terms of the United States Copyright Act. It was written as part of
* the author's official duties as a United States Government employee and
* thus cannot be copyrighted. This software/database is freely available
* to the public for use. The National Library of Medicine and the U.S.
* Government have not placed any restriction on its use or reproduction.
*
* Although all reasonable efforts have been taken to ensure the accuracy
* and reliability of the software and data, the NLM and the U.S.
* Government do not and cannot warrant the performance or results that
* may be obtained by using this software or data. The NLM and the U.S.
* Government disclaim all warranties, express or implied, including
* warranties of performance, merchantability or fitness for any particular
* purpose.
*
* Please cite the author in any work or product based on this material.
*
* ===========================================================================
*
*/
package ngs;
/**
* Represents a slice through a stack of Alignments at a given position on the Reference
*/
public interface Pileup
extends PileupEventIterator
{
/*----------------------------------------------------------------------
* Reference
*/
/**
* getReferenceSpec
* @return name of the Reference
* @throws ErrorMsg upon an error accessing data
*/
String getReferenceSpec ()
throws ErrorMsg;
/**
* getReferencePosition
* @return current position on the Reference
* @throws ErrorMsg upon an error accessing data
*/
long getReferencePosition ()
throws ErrorMsg;
/**
* @return base at current Reference position
* @throws ErrorMsg upon an error accessing data
*/
char getReferenceBase ()
throws ErrorMsg;
/*----------------------------------------------------------------------
* details of this pileup row
*/
/**
* getPileupDepth
* @return the coverage depth at the current reference position
* @throws ErrorMsg upon an error accessing data
*/
int getPileupDepth ()
throws ErrorMsg;
}
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