/*****************************************************************************
#   Copyright (C) 1994-2008 by David Gordon.
#   All rights reserved.                           
#                                                                           
#   This software is part of a beta-test version of the Consed/Autofinish
#   package.  It should not be redistributed or
#   used for any commercial purpose, including commercially funded
#   sequencing, without written permission from the author and the
#   University of Washington.
#   
#   This software is provided ``AS IS'' and any express or implied
#   warranties, including, but not limited to, the implied warranties of
#   merchantability and fitness for a particular purpose, are disclaimed.
#   In no event shall the authors or the University of Washington be
#   liable for any direct, indirect, incidental, special, exemplary, or
#   consequential damages (including, but not limited to, procurement of
#   substitute goods or services; loss of use, data, or profits; or
#   business interruption) however caused and on any theory of liability,
#   whether in contract, strict liability, or tort (including negligence
#   or otherwise) arising in any way out of the use of this software, even
#   if advised of the possibility of such damage.
#
#   Building Consed from source is error prone and not simple which is
#   why I provide executables.  Due to time limitations I cannot
#   provide any assistance in building Consed.  Even if you do not
#   modify the source, you may introduce errors due to using a
#   different version of the compiler, a different version of motif,
#   different versions of other libraries than I used, etc.  For this
#   reason, if you discover Consed bugs, I can only offer help with
#   those bugs if you first reproduce those bugs with an executable
#   provided by me--not an executable you have built.
# 
#   Modifying Consed is also difficult.  Although Consed is modular,
#   some modules are used by many other modules.  Thus making a change
#   in one place can have unforeseen effects on many other features.
#   It may takes months for you to notice these other side-effects
#   which may not seen connected at all.  It is not feasable for me to
#   provide help with modifying Consed sources because of the
#   potentially huge amount of time involved.
#
#*****************************************************************************/
//
// readPHD.h
//
// PURPOSE:  reads PHD file
//
//

#ifndef READPHD_INCLUDED
#define READPHD_INCLUDED


#ifdef SCCS_ID
static const char* readPHDSccsId = "@(#)readPHD.h	1.16 08/10/99 02:00:54";
#endif


#include    "rwcstring.h"
#include    "filename.h"


void  readPHDFileAndMaybeComplement( 
            FileName filPHD,
            bool bComplement,
            LocatedFragment* pLocFrag,
            int nArraySize, 
            char* pBaseArray,
            int* pQualityArray, 
            int* pPointPositionArray,
            RWCString& soTimestampFromPHDFile,
            RWCString& soABIThumbprint, 
            RWCString& soPhredVersion,
            RWCString& soCallMethod, 
            RWCString& soChemistry, 
            RWCString& soDye,
            int& nTraceArrayMinIndex,
            int& nTraceArrayMaxIndex,
            bool& bFoundTraceArrayMaxIndex,
            int& nQualityLevels,
            int& nNumberOfUnpaddedBases,
            const bool bIgnoreTags );



// used internally
void  readPHDFile( 
                  const FileName& filPHD, 
                  LocatedFragment* pLocFrag,
                  int nArraySize, 
                  char* pBaseArray,
                  int* pQualityArray, 
                  int* pPointPositionArray,
                  RWCString& soTimestampFromPHDFile,
                  RWCString& soABIThumbprint, 
                  RWCString& soPhredVersion,
                  RWCString& soCallMethod, 
                  RWCString& soChemistry,
                  RWCString& soDye,
                  int& nTraceArrayMinIndex,
                  int& nTraceArrayMaxIndex,
                  bool& bFoundTraceArrayMaxIndex,
                  int& nQualityLevels,
                  int& nNumberOfUnpaddedBases,
                  const bool bIgnoreTags );

// used before reading phred calls to decide how
// big the arrays should be

int nReadPHDFileForSize( const FileName& filPHD );



void  readPHDFileToSetQualitiesAndPeakPositions2( 
                  LocatedFragment* pLocFrag,
                  const bool bIgnoreTags );

// This is used for addNewReads function which first reads just the phred
// calls, then does the alignment to put in pads, and then reads the tags
// in order to determine their padded positions.
   
void  readPHDFileJustForTagsAndWholeReadItems( 
                  LocatedFragment* pLocFrag );

#endif