/*****************************************************************************
#   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.
#
#*****************************************************************************/


// main.cpp_part8
     else if ( soLowerCaseArg == "-dumpdefaultresources" ) {
        bPrintDefaultResources = true;
     }
     else if ( soLowerCaseArg == "-printconsedresources" ) {
        bPrintDefaultResources = true;
     }
     else if ( soLowerCaseArg == "-printconsedrcresources" ) {
        bPrintDefaultResources = true;
     }
     else if ( soLowerCaseArg == "-printconsedparameters" ) {
        bPrintDefaultResources = true;
     }
     else if ( soLowerCaseArg == "-printconsedrcparameters" ) {
        bPrintDefaultResources = true;
     }
     else {
        cerr << "Error:  do not recognize argument " << argv[n] << " lowercase: " << soLowerCaseArg << endl;
        cout << soUsage << endl;
        _exit( -1 );
     }
        
   } // for(  n = 0; n < nArgc; ++n ) {


   if ( bAddReads && !bChem ) {
      cerr << "Fatal Error:  if you specify -addReads, you must also specify -chem to give the type of chemistry of reads being added.  At this time, each chemistry of reads must be added one at a time." << endl;
      _exit( -1 );
   }

   if ( bSolexa2PhdBall && !bNewPhdBallFOF ) {
      cerr << "Fatal Error: if you specify -solexa2PhdBall, you must also specify -phdBallFOF (file for this program to write the phdball filenames)" << endl;
      _exit( -1 );
   }

   if ( bSelectRegions && !bAlignments ) {
      cerr << "Fatal Error: if you specify -selectRegions, you must also specify -alignments (alignments file)" << endl;
      _exit( -1 );
   }

   if ( bPhdBall2Fasta && !bFasta && !bFastq ) {
      cerr << "Fatal Error:  if you specify -phdBall2Fasta, you must also specify -fasta (fasta file) or -fastq (fastq file)" << endl;
      _exit( -1 );
   }

   if ( bSff2PhdBall && !bPhdBall ) {
      cerr << "Fatal Error:  if you specify -sff2PhdBall, must also specify -phdBall (phdball full path)" << endl;
      _exit( -1 );
   }

   if ( bSnpGenome && !bGenome ) {
      cerr << "Fatal Error:  if you specify -snpGenome, you must also specify -genome" << endl;
      _exit( -1 );
   }

   if ( bSnpGenome && !bValid ) {
      cerr << "Fatal Error:  if you specify -snpGenome, you must also specify -valid" << endl;
      _exit( -1 );
   }

   if ( bGeneClassifications && ! bChromosomesFOF ) {
      cerr << "Fatal Error:  if you specify -geneClassifications, you must also specify -chromosomesFOF" << endl;
      _exit( -1 );
   }
   
   if ( bGeneClassifications && !bKnownGene ) {
      cerr << "Fatal Error:  if you specify -geneClassifications, you must also specify -knownGene" << endl;
      _exit( -1 );
   }

   if ( bPhaster2PhdBall && !bPhasterLocations ) {
      cerr << "Fatal Error: if you specify -phaster2PhdBall, you must also specify -phasterLocations" << endl;
      _exit( -1 );
   }

   if ( bPhaster2PhdBall && !bNewPhdBallFOF ) {
      cerr << "Fatal Error:  if you specify -phaster2PhdBall, you must also specify -phdBallFOF (file for this program to write the phdball filenames)" << endl;
      _exit( -1 );
   }
      

   

   if ( bNoPhdFiles ) {
      cout << "Not using phd files" << endl;
   }


   if ( bAddFlowcells && !bControlFile ) {
      cerr << "Fatal Error:  if you specify -addFlowCell, you must also specify -controlFile" << endl;
      _exit( -1 );
   }