/*  File: acembly.h
 *  Author: Danielle et jean Thierry-Mieg (mieg@mrc-lmba.cam.ac.uk)
 *  Copyright (C) J Thierry-Mieg and R Durbin, 1995
 * -------------------------------------------------------------------
 * Acedb is free software; you can redistribute it and/or
 * modify it under the terms of the GNU General Public License
 * as published by the Free Software Foundation; either version 2
 * of the License, or (at your option) any later version.
 * 
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 * 
 * You should have received a copy of the GNU General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
 * or see the on-line version at http://www.gnu.org/copyleft/gpl.txt
 * -------------------------------------------------------------------
 * This file is part of the ACEDB genome database package, written by
 * 	Richard Durbin (MRC LMB, UK) rd@mrc-lmba.cam.ac.uk, and
 *	Jean Thierry-Mieg (CRBM du CNRS, France) mieg@frmop11.bitnet
 *
 * Description:
 * Exported functions:
 * HISTORY:
 * Last edited: Feb 13 23:04 1996 (mieg)
 * Created: Fri Oct 20 20:18:19 1995 (mieg)
 *-------------------------------------------------------------------
 */
/* $Id: acembly.h,v 1.11 2000/04/12 18:42:00 mieg Exp $ */
 
             /*********************************************/
             /* Acembly.h                                   */
             /* type definitions and size limits          */
             /*********************************************/
 
#ifndef DEF_Acembly_h
#define DEF_Acembly_h
 
#include "acedb.h"

enum  AcemblyMode { SHOTGUN = 0, MUTANT, CDNA} ;
extern int acemblyMode ;

extern KEY _Clips,
 _Later_part_of, _Hand_Clipping, 
_OriginalBaseCall, _Align_to_SCF, _SCF_Position,_Quality ;

Array blyDnaGet (KEY link, KEY contig, KEY mykey) ;
Array trackErrors (Array  dna1, int pos1, int *pp1, 
		   Array dna2, int pos2, int *pp2, int *NNp, Array err, int mode) ;
Array baseCallCptErreur (Array dnaD, Array dnaR, Array dnaCourt, BOOL isUp,
			 int x1, int x2, int x3, 
			 int *clipTopp, int *cEndp, int *cExp, int mode) ;

#endif