/*****************************************************************************
#   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_part10


   if ( bAutomatedFinishProgram && !bAceFileOnCommandLine ) {
      cerr << "Error:  If you specify -autoFinish, you must also specify -ace (ace file)" << endl;
      exit( -1 );
   }
   if ( bAutoPCRAmplify && !bAceFileOnCommandLine ) {
      cerr << "Error:  If you specify -autoPCRAmplify, you must also specify -ace (ace file)" << endl;
      exit( -1 );
   }
   if ( bAddNewReads && !bAceFileOnCommandLine ) {
      cerr << "Error:  If you specify -addNewReads, you must also specify -ace (ace file)" << endl;
      exit( -1 );
   }
   if ( bAddReads && !bAceFileOnCommandLine ) {
      cerr << "Error:  If you specify -addReads, you must also specify -ace (ace file)" << endl;
      exit( -1 );
   }
   if ( bAutoEdit && !bAceFileOnCommandLine ) {
      cerr << "Error:  If you specify -autoEdit, you must also specify -ace (ace file)" << endl;
      exit( -1 );
   }
   if ( bNewAceFileName && !bAceFileOnCommandLine ) {
      cerr << "Error:  If you specify -newAceFileName, you must also specify -ace (ace file)" << endl;
      exit( -1 );
   }
   if ( bAddAlignedSequence && !bAceFileOnCommandLine ) {
      cerr << "Error:  If you specify -addAlignedSequence, you must also specify -ace (ace file)" << endl;
      exit( -1 );
   }
   if ( bTagSNPs && !bAceFileOnCommandLine ) {
      cerr << "Error:  If you specify -tagSNPs, you must also specify -ace (ace file)" << endl;
      exit( -1 );
   }
   if ( bAutoReport && !bAceFileOnCommandLine ) {
      cerr << "Error:  If you specify -autoReport, you must also specify -ace (ace file)" << endl;
      exit( -1 );
   }
   if ( bCustomNavigation && !bAceFileOnCommandLine ) {
      cerr << "Error:  If you specify -nav, you must also specify -ace (ace file)" << endl;
      exit( -1 );
   }
   if ( bPrintSingleSignal && !bAceFileOnCommandLine ) {
      cerr << "Error:  If you specify -singleSignal, you must also specify -ace (ace file)" << endl;
      exit( -1 );
   }
   if ( bMainContigPos && !bAceFileOnCommandLine ) {
      cerr << "Error:  If you specify -mainContigPos, you must also specify -ace (ace file)" << endl;
      exit( -1 );
   }
   if ( bSolexa2PhdBall && bAceFileOnCommandLine ) {
      cerr << "Error:  If you specify -solexa2PhdBall, you must not also specify -ace (ace file)" << endl;
      exit( -1 );
   }
   if ( bSelectRegions && !bAceFileOnCommandLine ) {
      cerr << "Error:  If you specify -selectRegions, you must also specify -ace (ace file)" << endl;
      exit( -1 );
   }
   if ( bAlignments && !bAceFileOnCommandLine ) {
      cerr << "Error:  If you specify -alignments, you must also specify -ace (ace file)" << endl;
      exit( -1 );
   }
   if ( bPhdBall2Fasta && bAceFileOnCommandLine ) {
      cerr << "Error:  If you specify -phdBall2Fasta, you must not also specify -ace (ace file)" << endl;
      exit( -1 );
   }
   if ( bFasta && bAceFileOnCommandLine ) {
      cerr << "Error:  If you specify -fasta, you must not also specify -ace (ace file)" << endl;
      exit( -1 );
   }
   if ( bFastq && bAceFileOnCommandLine ) {
      cerr << "Error:  If you specify -fastq, you must not also specify -ace (ace file)" << endl;
      exit( -1 );
   }
   if ( bTestReadPhdBall && bAceFileOnCommandLine ) {
      cerr << "Error:  If you specify -testReadPhdBall, you must not also specify -ace (ace file)" << endl;
      exit( -1 );
   }
   if ( bRemoveReads && !bAceFileOnCommandLine ) {
      cerr << "Error:  If you specify -removeReads, you must also specify -ace (ace file)" << endl;
      exit( -1 );
   }
   if ( bRemoveContigs && !bAceFileOnCommandLine ) {
      cerr << "Error:  If you specify -removeContigs, you must also specify -ace (ace file)" << endl;
      exit( -1 );
   }
   if ( bPrintDefaultResources && bAceFileOnCommandLine ) {
      cerr << "Error:  If you specify -printDefaultResources, you must not also specify -ace (ace file)" << endl;
      exit( -1 );
   }
   if ( bSff2PhdBall && bAceFileOnCommandLine ) {
      cerr << "Error:  If you specify -sff2PhdBall, you must not also specify -ace (ace file)" << endl;
      exit( -1 );
   }
   if ( bEditConsedrc && bAceFileOnCommandLine ) {
      cerr << "Error:  If you specify -editConsedrc, you must not also specify -ace (ace file)" << endl;
      exit( -1 );
   }
   if ( bChangeConsensus && !bAceFileOnCommandLine ) {
      cerr << "Error:  If you specify -changeConsensus, you must also specify -ace (ace file)" << endl;
      exit( -1 );
   }
   if ( bSnpGenome && bAceFileOnCommandLine ) {
      cerr << "Error:  If you specify -snpGenome, you must not also specify -ace (ace file)" << endl;
      exit( -1 );
   }
   if ( bGenome && bAceFileOnCommandLine ) {
      cerr << "Error:  If you specify -genome, you must not also specify -ace (ace file)" << endl;
      exit( -1 );
   }
   if ( bValid && bAceFileOnCommandLine ) {
      cerr << "Error:  If you specify -valid, you must not also specify -ace (ace file)" << endl;
      exit( -1 );
   }
   if ( bDiffChromosomes && bAceFileOnCommandLine ) {
      cerr << "Error:  If you specify -diffChromosomes, you must not also specify -ace (ace file)" << endl;
      exit( -1 );
   }
   if ( bAddFlowcells && bAceFileOnCommandLine ) {
      cerr << "Error:  If you specify -addFlowcells, you must not also specify -ace (ace file)" << endl;
      exit( -1 );
   }
   if ( bControlFile && bAceFileOnCommandLine ) {
      cerr << "Error:  If you specify -controlFile, you must not also specify -ace (ace file)" << endl;
      exit( -1 );
   }
   if ( bFixContigEnds && !bAceFileOnCommandLine ) {
      cerr << "Error:  If you specify -fixContigEnds, you must also specify -ace (ace file)" << endl;
      exit( -1 );
   }
   if ( bContigEndsFOF && !bAceFileOnCommandLine ) {
      cerr << "Error:  If you specify -contigEndsFOF, you must also specify -ace (ace file)" << endl;
      exit( -1 );
   }
   if ( bGeneClassifications && bAceFileOnCommandLine ) {
      cerr << "Error:  If you specify -geneClassifications, you must not also specify -ace (ace file)" << endl;
      exit( -1 );
   }
   if ( bChromosomesFOF && bAceFileOnCommandLine ) {
      cerr << "Error:  If you specify -chromosomesFOF, you must not also specify -ace (ace file)" << endl;
      exit( -1 );
   }
   if ( bKnownGene && bAceFileOnCommandLine ) {
      cerr << "Error:  If you specify -knownGene, you must not also specify -ace (ace file)" << endl;
      exit( -1 );
   }
   if ( bPhaster2PhdBall && bAceFileOnCommandLine ) {
      cerr << "Error:  If you specify -phaster2PhdBall, you must not also specify -ace (ace file)" << endl;
      exit( -1 );
   }
   if ( bPhasterLocations && bAceFileOnCommandLine ) {
      cerr << "Error:  If you specify -phasterLocations, you must not also specify -ace (ace file)" << endl;
      exit( -1 );
   }
   if ( bPhyloFOF && bAceFileOnCommandLine ) {
      cerr << "Error:  If you specify -phyloFOF, you must not also specify -ace (ace file)" << endl;
      exit( -1 );
   }
   if ( bMiscProgram && bAceFileOnCommandLine ) {
      cerr << "Error:  If you specify -miscProgram, you must not also specify -ace (ace file)" << endl;
      exit( -1 );
   }