/*****************************************************************************
#   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_part4



int main(int nArgc, char* argv[]) {

   bool bAceFileOnCommandLine = false;
   FileName filAceFileToOpen;
   bool bCreateSocketToControlConsed = false;
   RWCString soSocketToControlConsedLocalPortNumber;
   bool bNoPhdFiles = false;
   bool bAutomatedFinishProgram = false;
   bool bDoExperiments = false;
   bool bAutoPCRAmplify = false;
   FileName filFileOfPrimerRegions;
   bool bJustCheckAutoFinishReads = false;
   bool bID = false;
   RWCString soID;
   bool bContigSpecified = false;
   RWCString soContig;
   bool bFileNamesFile = false;
   RWCString soFilenamesFile;
   bool bFileOfPhdFiles = false;
   FileName filFileOfPhdFiles;
   bool bTerminateAfterStartup = false;
   bool bReadOnly = false;
   bool bAddNewReads = false;
   FileName filFileOfReadsOrPhdsToAdd;
   bool bAddReads = false;
   FileName filAddNewReadsAlignmentsFOF;
   bool bChem = false;
   RWCString soChemistry;
   bool bAutoEdit = false;
   bool bNewAceFileName = false;
   FileName filNewAceFile;
   bool bAddAlignedSequence = false;
   FileName filAlignmentFastaFile;
   bool bTagSNPs = false;
   FileName filFileOfReadsOrPhdsToAddForTagSNPs;
   bool bPhdWithWRItem = false;
   FileName filPhdFileWithWRItem;
   bool bAutoReport = false;
   bool bCustomNavigation = false;
   FileName filCustomNavigation;
   bool bAllowTimestampMismatch = false;
   bool bPrintSingleSignal = false;
   RWCString soUnpaddedConsPosForSingleSignal;
   bool bMainContigPos = false;
   RWCString soUnpaddedConsPos;
   bool bSolexa2PhdBall = false;
   FileName filSolexaFOF;
   bool bNewPhdBallFOF = false;
   FileName filNewPhdBallFOF;
   bool bSelectRegions = false;
   FileName filRegionsFile;
   bool bAlignments = false;
   FileName filSelectRegionsAlignmentsFOF;
   bool bPhdBall2Fasta = false;
   FileName filPhdBall;
   bool bFasta = false;
   FileName filFasta;
   bool bFastq = false;
   FileName filFastq;
   bool bTestReadPhdBall = false;
   FileName filPhdBallForTestRead;
   bool bRemoveReads = false;
   FileName filReadsToBeRemoved;
   bool bRemoveContigs = false;
   FileName filContigsToBeRemoved;
   bool bPrintDefaultResources = false;
   bool bSff2PhdBall = false;
   FileName filSffFile;
   bool bPhdBall = false;
   FileName filNewPhdBall;
   bool bFOF = false;
   FileName filFOF;
   bool bEditConsedrc = false;
   bool bChangeConsensus = false;
   FileName filChangeConsensus;
   bool bSnpGenome = false;
   FileName filSnps;
   bool bGenome = false;
   FileName filGenome;
   bool bValid = false;
   FileName filValidation;
   bool bDiffChromosomes = false;
   FileName filOtherDirectory;
   bool bAddFlowcells = false;
   FileName filFlowcellsToAdd;
   bool bControlFile = false;
   FileName filControlFile;
   bool bFixContigEnds = false;
   bool bContigEndsFOF = false;
   FileName filContigEndsFOF;
   bool bGeneClassifications = false;
   FileName filGenomicLocations;
   bool bChromosomesFOF = false;
   FileName filChromosomesFOF;
   bool bKnownGene = false;
   FileName filKnownGene;
   bool bPhaster2PhdBall = false;
   FileName filPhasterFOF;
   bool bPhasterLocations = false;
   FileName filPhasterLocations;
   bool bPhyloFOF = false;
   FileName filPhyloFOF;
   bool bMiscProgram = false;