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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;
/*==========================================================================
* Read
* represents an NGS machine read
* having some number of biological Fragments
*/
public interface Read
extends FragmentIterator
{
/**
* getReadId
* @return the ID-String of the Read
* @throws ErrorMsg upon an error accessing data
*/
String getReadId ()
throws ErrorMsg;
/*----------------------------------------------------------------------
* Fragment
*/
/**
* getNumFragments
* @return the number of biological Fragments contained in the read
* @throws ErrorMsg upon an error accessing data
*/
int getNumFragments ()
throws ErrorMsg;
/**
* fragmentIsAligned
* @param fragIdx is a zero-based and non-negative fragment index
* @return true if a fragment is aligned
* @throws ErrorMsg upon an error accessing data
*/
boolean fragmentIsAligned ( int fragIdx )
throws ErrorMsg;
/*----------------------------------------------------------------------
* read details
*/
/**
* ReadCategory
*/
static int fullyAligned = 1;
static int partiallyAligned = 2;
static int aligned = fullyAligned | partiallyAligned;
static int unaligned = 4;
static int all = aligned | unaligned;
/**
* getReadCategory
* @return the category of the read
* @throws ErrorMsg upon an error accessing data
*/
int getReadCategory ()
throws ErrorMsg;
/**
* getReadGroup
* @return the read-group of the read
* @throws ErrorMsg upon an error accessing data
*/
String getReadGroup ()
throws ErrorMsg;
/**
* getReadName
* @return the name of thethe read
* @throws ErrorMsg upon an error accessing data
*/
String getReadName ()
throws ErrorMsg;
/**
* getReadBases
* @return sequence bases
* @throws ErrorMsg upon an error accessing data
*/
String getReadBases ()
throws ErrorMsg;
/**
* getReadBases
* @param offset is zero-based and non-negative
* @return sequence bases
* @throws ErrorMsg upon an error accessing data
* @throws IndexOutOfBoundsException if offset is invalid
*/
String getReadBases ( long offset )
throws ErrorMsg, IndexOutOfBoundsException;
/**
* getReadBases
* @param offset is zero-based and non-negative
* @param length must be ≥ 0
* @return sequence bases
* @throws ErrorMsg upon an error accessing data
* @throws IndexOutOfBoundsException if offset/length are invalid
*/
String getReadBases ( long offset, long length )
throws ErrorMsg, IndexOutOfBoundsException;
/**
* getReadQualities
* @return phred quality values using ASCII offset of 33
* @throws ErrorMsg upon an error accessing data
*/
String getReadQualities ()
throws ErrorMsg;
/**
* getReadQualities
* @param offset is zero-based and non-negative
* @return phred quality values using ASCII offset of 33
* @throws ErrorMsg upon an error accessing data
* @throws IndexOutOfBoundsException if offset is invalid
*/
String getReadQualities ( long offset )
throws ErrorMsg, IndexOutOfBoundsException;
/**
* getReadQualities
* @param offset is zero-based and non-negative
* @param length must be ≥ 0
* @return phred quality values using ASCII offset of 33
* @throws ErrorMsg upon an error accessing data
* @throws IndexOutOfBoundsException if offset/length are invalid
*/
String getReadQualities ( long offset, long length )
throws ErrorMsg, IndexOutOfBoundsException;
}
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