/*****************************************************************************
#   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_part7


      else if ( soLowerCaseArg == "-ace" ) {
         bAceFileOnCommandLine = true;
         ++n;
         if ( n >= nArgc ) {
            cerr << "Fatal Error: -ace must be followed by a space and then the ace filename" << endl;
            exit( -1 );
         }
         filAceFileToOpen = argv[n];
      }
      else if ( soLowerCaseArg == "-socket" ) {
         bCreateSocketToControlConsed = true;
         ++n;
         if ( n >= nArgc ) {
            cerr << "Fatal Error: -socket must be followed by a space and then a number (the local port number)" << endl;
            exit( -1 );
         }
         soSocketToControlConsedLocalPortNumber = argv[n];
      }
      else if ( soLowerCaseArg == "-nophd" ) {
         bNoPhdFiles = true;
      }
      else if ( soLowerCaseArg == "-autofinish" ) {
         bAutomatedFinishProgram = true;
      }
      else if ( soLowerCaseArg == "-doexperiments" ) {
         bDoExperiments = true;
      }
      else if ( soLowerCaseArg == "-autopcramplify" ) {
         bAutoPCRAmplify = true;
         ++n;
         if ( n >= nArgc ) {
            cerr << "Fatal Error: -autoPCRAmplify must be followed by a space and then the name of the file of primer regions" << endl;
            exit( -1 );
         }
         filFileOfPrimerRegions = argv[n];
      }
      else if ( soLowerCaseArg == "-justcheckautofinishreads" ) {
         bJustCheckAutoFinishReads = true;
      }
      else if ( soLowerCaseArg == "-id" ) {
         bID = true;
         ++n;
         if ( n >= nArgc ) {
            cerr << "Fatal Error: -id must be followed by a space and then the id" << endl;
            exit( -1 );
         }
         soID = argv[n];
      }
      else if ( soLowerCaseArg == "-contig" ) {
         bContigSpecified = true;
         ++n;
         if ( n >= nArgc ) {
            cerr << "Fatal Error: -contig must be followed by a space and then the contig name" << endl;
            exit( -1 );
         }
         soContig = argv[n];
      }
      else if ( soLowerCaseArg == "-filenamesfile" ) {
         bFileNamesFile = true;
         ++n;
         if ( n >= nArgc ) {
            cerr << "Fatal Error: -filenamesFile must be followed by a space and then the name of the file to contain the filenames" << endl;
            exit( -1 );
         }
         soFilenamesFile = argv[n];
      }
      else if ( soLowerCaseArg == "-fileofphdfiles" ) {
         bFileOfPhdFiles = true;
         ++n;
         if ( n >= nArgc ) {
            cerr << "Fatal Error: -fileOfPhdFiles must be followed by a space and then the name of the file of phd files" << endl;
            exit( -1 );
         }
         filFileOfPhdFiles = argv[n];
      }
      else if ( soLowerCaseArg == "-terminate" ) {
         bTerminateAfterStartup = true;
      }
      else if ( soLowerCaseArg == "-read_only" ) {
         bReadOnly = true;
      }
      else if ( soLowerCaseArg == "-addnewreads" ) {
         bAddNewReads = true;
         ++n;
         if ( n >= nArgc ) {
            cerr << "Fatal Error: -addNewReads must be followed by a space and then the name of the file containing the reads to be added" << endl;
            exit( -1 );
         }
         filFileOfReadsOrPhdsToAdd = argv[n];
      }
      else if ( soLowerCaseArg == "-addreads" ) {
         bAddReads = true;
         ++n;
         if ( n >= nArgc ) {
            cerr << "Fatal Error: -addReads must be followed by a space and then the name of the file containing a list of the cross_match alignment files" << endl;
            exit( -1 );
         }
         filAddNewReadsAlignmentsFOF = argv[n];
      }
      else if ( soLowerCaseArg == "-chem" ) {
         bChem = true;
         ++n;
         if ( n >= nArgc ) {
            cerr << "Fatal Error: -chem must be followed by a space and then the chemistry which can be one of solexa, 454, or Sanger" << endl;
            exit( -1 );
         }
         soChemistry = argv[n];
      }
      else if ( soLowerCaseArg == "-autoedit" ) {
         bAutoEdit = true;
      }
      else if ( ( soLowerCaseArg == "-newacefilename" )  || ( soLowerCaseArg == "-newacefile" )
 ) {
         bNewAceFileName = true;
         ++n;
         if ( n >= nArgc ) {
            cerr << "Fatal Error: -newAceFilename must be followed by a space and then the name of the ace file to be created" << endl;
            exit( -1 );
         }
         filNewAceFile = argv[n];
      }
      else if ( soLowerCaseArg == "-addalignedsequence" ) {
         bAddAlignedSequence = true;
         ++n;
         if ( n >= nArgc ) {
            cerr << "Fatal Error: -addAlignedSequence must be followed by a space and then the name of the fasta file created by alignment2Ace.perl" << endl;
            exit( -1 );
         }
         filAlignmentFastaFile = argv[n];
      }
      else if ( soLowerCaseArg == "-tagsnps" ) {
         bTagSNPs = true;
         ++n;
         if ( n >= nArgc ) {
            cerr << "Fatal Error: -tagSNPs must be followed by a space and then the name of the fof of SNP reads" << endl;
            exit( -1 );
         }
         filFileOfReadsOrPhdsToAddForTagSNPs = argv[n];
      }
      else if ( soLowerCaseArg == "-phdwithwritem" ) {
         bPhdWithWRItem = true;
         ++n;
         if ( n >= nArgc ) {
            cerr << "Fatal Error: -phdWithWRItem must be followed by a space and then the name of the phd file containing the WR Item specifying the genomic region of the assembly" << endl;
            exit( -1 );
         }
         filPhdFileWithWRItem = argv[n];
      }
      else if ( soLowerCaseArg == "-autoreport" ) {
         bAutoReport = true;
      }
      else if ( soLowerCaseArg == "-nav" ) {
         bCustomNavigation = true;
         ++n;
         if ( n >= nArgc ) {
            cerr << "Fatal Error: -nav must be followed by a space and then the name of the custom navigation file" << endl;
            exit( -1 );
         }
         filCustomNavigation = argv[n];
      }
      else if ( soLowerCaseArg == "-allowtimestampmismatch" ) {
         bAllowTimestampMismatch = true;
      }
      else if ( soLowerCaseArg == "-singlesignal" ) {
         bPrintSingleSignal = true;
         ++n;
         if ( n >= nArgc ) {
            cerr << "Fatal Error: -singleSignal must be followed by a space and then the unpadded consensus position" << endl;
            exit( -1 );
         }
         soUnpaddedConsPosForSingleSignal = argv[n];
      }
      else if ( soLowerCaseArg == "-maincontigpos" ) {
         bMainContigPos = true;
         ++n;
         if ( n >= nArgc ) {
            cerr << "Fatal Error: -maincontigpos must be followed by a space and then the unpadded consensus position of the main contig" << endl;
            exit( -1 );
         }
         soUnpaddedConsPos = argv[n];
      }
      else if ( soLowerCaseArg == "-solexa2phdball" ) {
         bSolexa2PhdBall = true;
         ++n;
         if ( n >= nArgc ) {
            cerr << "Fatal Error: -solexa2PhdBall must be followed by a space and then the name of a file containing the name of the solexa fastq files." << endl;
            exit( -1 );
         }
         filSolexaFOF = argv[n];
      }
      else if ( soLowerCaseArg == "-phdballfof" ) {
         bNewPhdBallFOF = true;
         ++n;
         if ( n >= nArgc ) {
            cerr << "Fatal Error: -phdBallFOF must be followed by a space and then the name of the phdballfof to be created.  This file contains a list of all of the phdballs created." << endl;
            exit( -1 );
         }
         filNewPhdBallFOF = argv[n];
      }
      else if ( soLowerCaseArg == "-selectregions" ) {
         bSelectRegions = true;
         ++n;
         if ( n >= nArgc ) {
            cerr << "Fatal Error: -selectRegions must be followed by a space and then the name of the regions file" << endl;
            exit( -1 );
         }
         filRegionsFile = argv[n];
      }
      else if ( soLowerCaseArg == "-alignments" ) {
         bAlignments = true;
         ++n;
         if ( n >= nArgc ) {
            cerr << "Fatal Error: -alignments must be followed by a space and then the name of an fof of alignments files for -selectRegions" << endl;
            exit( -1 );
         }
         filSelectRegionsAlignmentsFOF = argv[n];
      }
      else if ( soLowerCaseArg == "-phdball2fasta" ) {
         bPhdBall2Fasta = true;
         ++n;
         if ( n >= nArgc ) {
            cerr << "Fatal Error: -phdBall2Fasta must be followed by a space and then the name of the phd ball" << endl;
            exit( -1 );
         }
         filPhdBall = argv[n];
      }
      else if ( soLowerCaseArg == "-fasta" ) {
         bFasta = true;
         ++n;
         if ( n >= nArgc ) {
            cerr << "Fatal Error: -fasta must be followed by a space and then the name of the output fasta file" << endl;
            exit( -1 );
         }
         filFasta = argv[n];
      }
      else if ( soLowerCaseArg == "-fastq" ) {
         bFastq = true;
         ++n;
         if ( n >= nArgc ) {
            cerr << "Fatal Error: -fastq must be followed by a space and then the name of the output fastq file" << endl;
            exit( -1 );
         }
         filFastq = argv[n];
      }
      else if ( soLowerCaseArg == "-testreadphdball" ) {
         bTestReadPhdBall = true;
         ++n;
         if ( n >= nArgc ) {
            cerr << "Fatal Error: -testReadPhdBall must be followed by a space and then the phdball to be read for testing purposes" << endl;
            exit( -1 );
         }
         filPhdBallForTestRead = argv[n];
      }
      else if ( soLowerCaseArg == "-removereads" ) {
         bRemoveReads = true;
         ++n;
         if ( n >= nArgc ) {
            cerr << "Fatal Error: -removeReads must be followed by a space and then the file containing the reads to be removed.  Use consed.removeReadsPutIntoOwnContig: true/false to determine whether the removed reads are just put into their own contigs or completely removed" << endl;
            exit( -1 );
         }
         filReadsToBeRemoved = argv[n];
      }
      else if ( soLowerCaseArg == "-removecontigs" ) {
         bRemoveContigs = true;
         ++n;
         if ( n >= nArgc ) {
            cerr << "Fatal Error: -removeContigs must be followed by a space and then the file containing the contigs to be removed.  Use consed.removeReadsPutIntoOwnContig: true/false to determine whether the removed reads are just put into their own contigs or completely removed" << endl;
            exit( -1 );
         }
         filContigsToBeRemoved = argv[n];
      }
      else if ( soLowerCaseArg == "-printdefaultresources" ) {
         bPrintDefaultResources = true;
      }
      else if ( soLowerCaseArg == "-sff2phdball" ) {
         bSff2PhdBall = true;
         ++n;
         if ( n >= nArgc ) {
            cerr << "Fatal Error: -sff2PhdBall must be followed by a space and then full path of the sff file" << endl;
            exit( -1 );
         }
         filSffFile = argv[n];
      }
      else if ( soLowerCaseArg == "-phdball" ) {
         bPhdBall = true;
         ++n;
         if ( n >= nArgc ) {
            cerr << "Fatal Error: -phdBall must be followed by a space and then the full path of the phd ball" << endl;
            exit( -1 );
         }
         filNewPhdBall = argv[n];
      }
      else if ( soLowerCaseArg == "-fof" ) {
         bFOF = true;
         ++n;
         if ( n >= nArgc ) {
            cerr << "Fatal Error: -fof must be followed by a space and then the name of a file containing read names" << endl;
            exit( -1 );
         }
         filFOF = argv[n];
      }
      else if ( soLowerCaseArg == "-editconsedrc" ) {
         bEditConsedrc = true;
      }
      else if ( soLowerCaseArg == "-changeconsensus" ) {
         bChangeConsensus = true;
         ++n;
         if ( n >= nArgc ) {
            cerr << "Fatal Error: -changeConsensus must be followed by a space and then the name of the file with lines like this:  Contig21 28-30 x where Contig21 is the contig, 28-30 are the unpadded positions and x is the new base.  To change a pad (let's say at padded position 35, specify this as *35 as in Contig21 *35-*40 c" << endl;
            exit( -1 );
         }
         filChangeConsensus = argv[n];
      }
      else if ( soLowerCaseArg == "-snpgenome" ) {
         bSnpGenome = true;
         ++n;
         if ( n >= nArgc ) {
            cerr << "Fatal Error: -snpGenome must be followed by a space and then the full path of the snp table in ucsc format" << endl;
            exit( -1 );
         }
         filSnps = argv[n];
      }
      else if ( soLowerCaseArg == "-genome" ) {
         bGenome = true;
         ++n;
         if ( n >= nArgc ) {
            cerr << "Fatal Error: -genome is used by -snpGenome.  It must be followed by a space and then a file that has 3 columns for each chromosome:  the name of the chromosome in the snp file, the full path of the corresponding chromosome in fasta format, and the full path of the snp-annotated chromosome to be created." << endl;
            exit( -1 );
         }
         filGenome = argv[n];
      }
      else if ( soLowerCaseArg == "-valid" ) {
         bValid = true;
         ++n;
         if ( n >= nArgc ) {
            cerr << "Fatal Error: -valid is used by -snpGenome.  It must be followed by a space and then a file that lists, one per line, each validation combination for which *no* snps are to be used." << endl;
            exit( -1 );
         }
         filValidation = argv[n];
      }
      else if ( soLowerCaseArg == "-diffchromosomes" ) {
         bDiffChromosomes = true;
         ++n;
         if ( n >= nArgc ) {
            cerr << "Fatal Error: -diffChromosomes must be followed by a space and then the full or relative path of the other directory containing the chromosome files" << endl;
            exit( -1 );
         }
         filOtherDirectory = argv[n];
      }
      else if ( soLowerCaseArg == "-addflowcells" ) {
         bAddFlowcells = true;
         ++n;
         if ( n >= nArgc ) {
            cerr << "Fatal Error: -addFlowcells must be followed by a space and then the full or relative path of file containing flowcell lines" << endl;
            exit( -1 );
         }
         filFlowcellsToAdd = argv[n];
      }
      else if ( soLowerCaseArg == "-controlfile" ) {
         bControlFile = true;
         ++n;
         if ( n >= nArgc ) {
            cerr << "Fatal Error: -controlFile must be followed by a space and then the full or relative path of the control file" << endl;
            exit( -1 );
         }
         filControlFile = argv[n];
      }
      else if ( soLowerCaseArg == "-fixcontigends" ) {
         bFixContigEnds = true;
      }
      else if ( soLowerCaseArg == "-contigendsfof" ) {
         bContigEndsFOF = true;
         ++n;
         if ( n >= nArgc ) {
            cerr << "Fatal Error: -contigEndsFOF must be followed by a space and then the full or relative path of a file which each line having (contig name) (left or right)" << endl;
            exit( -1 );
         }
         filContigEndsFOF = argv[n];
      }
      else if ( soLowerCaseArg == "-geneclassifications" ) {
         bGeneClassifications = true;
         ++n;
         if ( n >= nArgc ) {
            cerr << "Fatal Error: -geneClassifications must be followed by a space and then the full or relative path of the list of genomic locations in the format chr1 345671" << endl;
            exit( -1 );
         }
         filGenomicLocations = argv[n];
      }
      else if ( soLowerCaseArg == "-chromosomesfof" ) {
         bChromosomesFOF = true;
         ++n;
         if ( n >= nArgc ) {
            cerr << "Fatal Error: -chromosomesFOF must be followed by a space and then the full or relative path of a file containing the full or relative paths of the chromosomes in fasta format" << endl;
            exit( -1 );
         }
         filChromosomesFOF = argv[n];
      }
      else if ( soLowerCaseArg == "-knowngene" ) {
         bKnownGene = true;
         ++n;
         if ( n >= nArgc ) {
            cerr << "Fatal Error: -knownGene must be followed by a space and then the full or relative path of a file containing the full or relative paths of the knownGene.txt file" << endl;
            exit( -1 );
         }
         filKnownGene = argv[n];
      }
      else if ( soLowerCaseArg == "-phaster2phdball" ) {
         bPhaster2PhdBall = true;
         ++n;
         if ( n >= nArgc ) {
            cerr << "Fatal Error: -phaster2PhdBall must be followed by a space and then the full or relative path of a file containing a list of phaster output files (assumes cref2 and -report_type:2 )" << endl;
            exit( -1 );
         }
         filPhasterFOF = argv[n];
      }
      else if ( soLowerCaseArg == "-phasterlocations" ) {
         bPhasterLocations = true;
         ++n;
         if ( n >= nArgc ) {
            cerr << "Fatal Error: -phasterLocations must be followed by a space and then the full or relative path of a file containing a list of locations in the form (full phaster genomic location) (chromosome) (1-based chromosome position)" << endl;
            exit( -1 );
         }
         filPhasterLocations = argv[n];
      }
      else if ( soLowerCaseArg == "-phylofof" ) {
         bPhyloFOF = true;
         ++n;
         if ( n >= nArgc ) {
            cerr << "Fatal Error: -phyloFOF must be followed by a space and then the full or relative path of a file containing the full or relative path of phyloP conservation score files in wig format such as chr11.phyloP44way.wigFix.gz" << endl;
            exit( -1 );
         }
         filPhyloFOF = argv[n];
      }
      else if ( soLowerCaseArg == "-miscprogram" ) {
         bMiscProgram = true;
      }