/*****************************************************************************
#   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.
#
#*****************************************************************************/
#include    "printChangedAutoFinishParameters.h"
#include    "consedResources.h"
#include    "fileDefines.h"
#include    "consedParameters.h"


void printChangedAutoFinishParameters() {

   fprintf( pAO, "PARAMETERS_CHANGED_FROM_DEFAULTS {\n" );


   if ( consedResources::pDefaultResources_->dAutoFinishMinNumberOfErrorsFixedByAnExp_
      != consedResources::pCurrentResources_->dAutoFinishMinNumberOfErrorsFixedByAnExp_ ) 
       fprintf( pAO, "consed.autoFinishMinNumberOfErrorsFixedByAnExp: %.3f\n",
        pCP->dAutoFinishMinNumberOfErrorsFixedByAnExp_ );


   if ( consedResources::pDefaultResources_->dAutoFinishRedundancy_
      != consedResources::pCurrentResources_->dAutoFinishRedundancy_ ) 
       fprintf( pAO, "consed.autoFinishRedundancy: %.3f\n",
        pCP->dAutoFinishRedundancy_ );


   if ( consedResources::pDefaultResources_->nAutoFinishAverageInsertSize_
      != consedResources::pCurrentResources_->nAutoFinishAverageInsertSize_ ) 
       fprintf( pAO, "consed.autoFinishAverageInsertSize: %d\n",
        pCP->nAutoFinishAverageInsertSize_ );


   if ( consedResources::pDefaultResources_->nPrimersMaxInsertSizeOfASubclone_
      != consedResources::pCurrentResources_->nPrimersMaxInsertSizeOfASubclone_ ) 
       fprintf( pAO, "consed.primersMaxInsertSizeOfASubclone: %d\n",
        pCP->nPrimersMaxInsertSizeOfASubclone_ );


   if ( consedResources::pDefaultResources_->nPrimersMaxMeltingTemp_
      != consedResources::pCurrentResources_->nPrimersMaxMeltingTemp_ ) 
       fprintf( pAO, "consed.primersMaxMeltingTemp: %d\n",
        pCP->nPrimersMaxMeltingTemp_ );


   if ( consedResources::pDefaultResources_->nPrimersMaxMeltingTempForPCR_
      != consedResources::pCurrentResources_->nPrimersMaxMeltingTempForPCR_ ) 
       fprintf( pAO, "consed.primersMaxMeltingTempForPCR: %d\n",
        pCP->nPrimersMaxMeltingTempForPCR_ );


   if ( consedResources::pDefaultResources_->bPrimersPickTemplatesForPrimers_
      != consedResources::pCurrentResources_->bPrimersPickTemplatesForPrimers_ ) 
       fprintf( pAO, "consed.primersPickTemplatesForPrimers: %s\n",
        ( pCP->bPrimersPickTemplatesForPrimers_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->soPrimersSubcloneFullPathnameOfFileOfSequencesForScreening_
      != consedResources::pCurrentResources_->soPrimersSubcloneFullPathnameOfFileOfSequencesForScreening_ ) 
        fprintf( pAO, "consed.primersSubcloneFullPathnameOfFileOfSequencesForScreening: %s\n",
              (char*)pCP->soPrimersSubcloneFullPathnameOfFileOfSequencesForScreening_.data() );


   if ( consedResources::pDefaultResources_->soPrimersCloneFullPathnameOfFileOfSequencesForScreening_
      != consedResources::pCurrentResources_->soPrimersCloneFullPathnameOfFileOfSequencesForScreening_ ) 
        fprintf( pAO, "consed.primersCloneFullPathnameOfFileOfSequencesForScreening: %s\n",
              (char*)pCP->soPrimersCloneFullPathnameOfFileOfSequencesForScreening_.data() );


   if ( consedResources::pDefaultResources_->nPrimersMinMeltingTemp_
      != consedResources::pCurrentResources_->nPrimersMinMeltingTemp_ ) 
       fprintf( pAO, "consed.primersMinMeltingTemp: %d\n",
        pCP->nPrimersMinMeltingTemp_ );


   if ( consedResources::pDefaultResources_->nPrimersMinMeltingTempForPCR_
      != consedResources::pCurrentResources_->nPrimersMinMeltingTempForPCR_ ) 
       fprintf( pAO, "consed.primersMinMeltingTempForPCR: %d\n",
        pCP->nPrimersMinMeltingTempForPCR_ );


   if ( consedResources::pDefaultResources_->bAutoFinishAllowHighQualityDiscrepanciesInTemplateIfConsistentForwardReversePair_
      != consedResources::pCurrentResources_->bAutoFinishAllowHighQualityDiscrepanciesInTemplateIfConsistentForwardReversePair_ ) 
       fprintf( pAO, "consed.autoFinishAllowHighQualityDiscrepanciesInTemplateIfConsistentForwardReversePair: %s\n",
        ( pCP->bAutoFinishAllowHighQualityDiscrepanciesInTemplateIfConsistentForwardReversePair_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoReportPrintReadNamesInRegion_
      != consedResources::pCurrentResources_->bAutoReportPrintReadNamesInRegion_ ) 
       fprintf( pAO, "consed.autoReportPrintReadNamesInRegion: %s\n",
        ( pCP->bAutoReportPrintReadNamesInRegion_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->soAutoReportPrintReadNamesInRegionContig_
      != consedResources::pCurrentResources_->soAutoReportPrintReadNamesInRegionContig_ ) 
        fprintf( pAO, "consed.autoReportPrintReadNamesInRegionContig: %s\n",
              (char*)pCP->soAutoReportPrintReadNamesInRegionContig_.data() );


   if ( consedResources::pDefaultResources_->nAutoReportPrintReadNamesInRegionLeftPos_
      != consedResources::pCurrentResources_->nAutoReportPrintReadNamesInRegionLeftPos_ ) 
       fprintf( pAO, "consed.autoReportPrintReadNamesInRegionLeftPos: %d\n",
        pCP->nAutoReportPrintReadNamesInRegionLeftPos_ );


   if ( consedResources::pDefaultResources_->nAutoReportPrintReadNamesInRegionRightPos_
      != consedResources::pCurrentResources_->nAutoReportPrintReadNamesInRegionRightPos_ ) 
       fprintf( pAO, "consed.autoReportPrintReadNamesInRegionRightPos: %d\n",
        pCP->nAutoReportPrintReadNamesInRegionRightPos_ );


   if ( consedResources::pDefaultResources_->bAutoReportPrintHighlyDiscrepantRegions_
      != consedResources::pCurrentResources_->bAutoReportPrintHighlyDiscrepantRegions_ ) 
       fprintf( pAO, "consed.autoReportPrintHighlyDiscrepantRegions: %s\n",
        ( pCP->bAutoReportPrintHighlyDiscrepantRegions_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoReportPrintScaffolds_
      != consedResources::pCurrentResources_->bAutoReportPrintScaffolds_ ) 
       fprintf( pAO, "consed.autoReportPrintScaffolds: %s\n",
        ( pCP->bAutoReportPrintScaffolds_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoReportPrintHighQualityDiscrepancies_
      != consedResources::pCurrentResources_->bAutoReportPrintHighQualityDiscrepancies_ ) 
       fprintf( pAO, "consed.autoReportPrintHighQualityDiscrepancies: %s\n",
        ( pCP->bAutoReportPrintHighQualityDiscrepancies_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoReportHighQualityDiscrepanciesExcludeCompressionOrG_dropoutTags_
      != consedResources::pCurrentResources_->bAutoReportHighQualityDiscrepanciesExcludeCompressionOrG_dropoutTags_ ) 
       fprintf( pAO, "consed.autoReportHighQualityDiscrepanciesExcludeCompressionOrG_dropoutTags: %s\n",
        ( pCP->bAutoReportHighQualityDiscrepanciesExcludeCompressionOrG_dropoutTags_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoReportHighQualityDiscrepanciesExcludeMostPads_
      != consedResources::pCurrentResources_->bAutoReportHighQualityDiscrepanciesExcludeMostPads_ ) 
       fprintf( pAO, "consed.autoReportHighQualityDiscrepanciesExcludeMostPads: %s\n",
        ( pCP->bAutoReportHighQualityDiscrepanciesExcludeMostPads_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoReportPrintLowConsensusQualityRegions_
      != consedResources::pCurrentResources_->bAutoReportPrintLowConsensusQualityRegions_ ) 
       fprintf( pAO, "consed.autoReportPrintLowConsensusQualityRegions: %s\n",
        ( pCP->bAutoReportPrintLowConsensusQualityRegions_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoReportPrintSingleSubcloneRegions_
      != consedResources::pCurrentResources_->bAutoReportPrintSingleSubcloneRegions_ ) 
       fprintf( pAO, "consed.autoReportPrintSingleSubcloneRegions: %s\n",
        ( pCP->bAutoReportPrintSingleSubcloneRegions_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoReportPrintSingleStrandedRegions_
      != consedResources::pCurrentResources_->bAutoReportPrintSingleStrandedRegions_ ) 
       fprintf( pAO, "consed.autoReportPrintSingleStrandedRegions: %s\n",
        ( pCP->bAutoReportPrintSingleStrandedRegions_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoReportPrintLinkingForwardReversePairs_
      != consedResources::pCurrentResources_->bAutoReportPrintLinkingForwardReversePairs_ ) 
       fprintf( pAO, "consed.autoReportPrintLinkingForwardReversePairs: %s\n",
        ( pCP->bAutoReportPrintLinkingForwardReversePairs_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoReportPrintFilteredInconsistentForwardReversePairs_
      != consedResources::pCurrentResources_->bAutoReportPrintFilteredInconsistentForwardReversePairs_ ) 
       fprintf( pAO, "consed.autoReportPrintFilteredInconsistentForwardReversePairs: %s\n",
        ( pCP->bAutoReportPrintFilteredInconsistentForwardReversePairs_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoReportPrintAssemblySummary_
      != consedResources::pCurrentResources_->bAutoReportPrintAssemblySummary_ ) 
       fprintf( pAO, "consed.autoReportPrintAssemblySummary: %s\n",
        ( pCP->bAutoReportPrintAssemblySummary_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->nAutoFinishDoNotDoPCRIfThisManyAvailableGapSpanningTemplates_
      != consedResources::pCurrentResources_->nAutoFinishDoNotDoPCRIfThisManyAvailableGapSpanningTemplates_ ) 
       fprintf( pAO, "consed.autoFinishDoNotDoPCRIfThisManyAvailableGapSpanningTemplates: %d\n",
        pCP->nAutoFinishDoNotDoPCRIfThisManyAvailableGapSpanningTemplates_ );


   if ( consedResources::pDefaultResources_->nAutoFinishDoNotDoUnorientedPCRIfThisManyOrMoreUnorientedPCRReactions_
      != consedResources::pCurrentResources_->nAutoFinishDoNotDoUnorientedPCRIfThisManyOrMoreUnorientedPCRReactions_ ) 
       fprintf( pAO, "consed.autoFinishDoNotDoUnorientedPCRIfThisManyOrMoreUnorientedPCRReactions: %d\n",
        pCP->nAutoFinishDoNotDoUnorientedPCRIfThisManyOrMoreUnorientedPCRReactions_ );


   if ( consedResources::pDefaultResources_->nAutoFinishDoNotDoOrientedPCRIfGapSizeLargerThanThis_
      != consedResources::pCurrentResources_->nAutoFinishDoNotDoOrientedPCRIfGapSizeLargerThanThis_ ) 
       fprintf( pAO, "consed.autoFinishDoNotDoOrientedPCRIfGapSizeLargerThanThis: %d\n",
        pCP->nAutoFinishDoNotDoOrientedPCRIfGapSizeLargerThanThis_ );


   if ( consedResources::pDefaultResources_->bAutoFinishDoNotDoPCRIfEndIsExtendedByReads_
      != consedResources::pCurrentResources_->bAutoFinishDoNotDoPCRIfEndIsExtendedByReads_ ) 
       fprintf( pAO, "consed.autoFinishDoNotDoPCRIfEndIsExtendedByReads: %s\n",
        ( pCP->bAutoFinishDoNotDoPCRIfEndIsExtendedByReads_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->nAutoFinishMaxAcceptableErrorsPerMegabase_
      != consedResources::pCurrentResources_->nAutoFinishMaxAcceptableErrorsPerMegabase_ ) 
       fprintf( pAO, "consed.autoFinishMaxAcceptableErrorsPerMegabase: %d\n",
        pCP->nAutoFinishMaxAcceptableErrorsPerMegabase_ );


   if ( consedResources::pDefaultResources_->nAutoFinishIfNotEnoughFwdRevPairsUseThisPerCentOfInsertSize_
      != consedResources::pCurrentResources_->nAutoFinishIfNotEnoughFwdRevPairsUseThisPerCentOfInsertSize_ ) 
       fprintf( pAO, "consed.autoFinishIfNotEnoughFwdRevPairsUseThisPerCentOfInsertSize: %d\n",
        pCP->nAutoFinishIfNotEnoughFwdRevPairsUseThisPerCentOfInsertSize_ );


   if ( consedResources::pDefaultResources_->nPrimersNumberOfBasesToBackUpToStartLooking_
      != consedResources::pCurrentResources_->nPrimersNumberOfBasesToBackUpToStartLooking_ ) 
       fprintf( pAO, "consed.primersNumberOfBasesToBackUpToStartLooking: %d\n",
        pCP->nPrimersNumberOfBasesToBackUpToStartLooking_ );


   if ( consedResources::pDefaultResources_->nPrimersMakePCRPrimersThisManyBasesBackFromEndOfHighQualitySegment_
      != consedResources::pCurrentResources_->nPrimersMakePCRPrimersThisManyBasesBackFromEndOfHighQualitySegment_ ) 
       fprintf( pAO, "consed.primersMakePCRPrimersThisManyBasesBackFromEndOfHighQualitySegment: %d\n",
        pCP->nPrimersMakePCRPrimersThisManyBasesBackFromEndOfHighQualitySegment_ );


   if ( consedResources::pDefaultResources_->bPrimersOKToChoosePrimersInSingleSubcloneRegion_
      != consedResources::pCurrentResources_->bPrimersOKToChoosePrimersInSingleSubcloneRegion_ ) 
       fprintf( pAO, "consed.primersOKToChoosePrimersInSingleSubcloneRegion: %s\n",
        ( pCP->bPrimersOKToChoosePrimersInSingleSubcloneRegion_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bPrimersOKToChoosePrimersWhereHighQualityDiscrepancies_
      != consedResources::pCurrentResources_->bPrimersOKToChoosePrimersWhereHighQualityDiscrepancies_ ) 
       fprintf( pAO, "consed.primersOKToChoosePrimersWhereHighQualityDiscrepancies: %s\n",
        ( pCP->bPrimersOKToChoosePrimersWhereHighQualityDiscrepancies_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bPrimersOKToChoosePrimersWhereUnalignedHighQualityRegion_
      != consedResources::pCurrentResources_->bPrimersOKToChoosePrimersWhereUnalignedHighQualityRegion_ ) 
       fprintf( pAO, "consed.primersOKToChoosePrimersWhereUnalignedHighQualityRegion: %s\n",
        ( pCP->bPrimersOKToChoosePrimersWhereUnalignedHighQualityRegion_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoFinishCallReversesToFlankGaps_
      != consedResources::pCurrentResources_->bAutoFinishCallReversesToFlankGaps_ ) 
       fprintf( pAO, "consed.autoFinishCallReversesToFlankGaps: %s\n",
        ( pCP->bAutoFinishCallReversesToFlankGaps_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoFinishAllowWholeCloneReads_
      != consedResources::pCurrentResources_->bAutoFinishAllowWholeCloneReads_ ) 
       fprintf( pAO, "consed.autoFinishAllowWholeCloneReads: %s\n",
        ( pCP->bAutoFinishAllowWholeCloneReads_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoFinishAllowCustomPrimerSubcloneReads_
      != consedResources::pCurrentResources_->bAutoFinishAllowCustomPrimerSubcloneReads_ ) 
       fprintf( pAO, "consed.autoFinishAllowCustomPrimerSubcloneReads: %s\n",
        ( pCP->bAutoFinishAllowCustomPrimerSubcloneReads_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoFinishAllowResequencingReads_
      != consedResources::pCurrentResources_->bAutoFinishAllowResequencingReads_ ) 
       fprintf( pAO, "consed.autoFinishAllowResequencingReads: %s\n",
        ( pCP->bAutoFinishAllowResequencingReads_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoFinishAllowResequencingReadsOnlyForRunsAndStops_
      != consedResources::pCurrentResources_->bAutoFinishAllowResequencingReadsOnlyForRunsAndStops_ ) 
       fprintf( pAO, "consed.autoFinishAllowResequencingReadsOnlyForRunsAndStops: %s\n",
        ( pCP->bAutoFinishAllowResequencingReadsOnlyForRunsAndStops_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoFinishAllowDeNovoUniversalPrimerSubcloneReads_
      != consedResources::pCurrentResources_->bAutoFinishAllowDeNovoUniversalPrimerSubcloneReads_ ) 
       fprintf( pAO, "consed.autoFinishAllowDeNovoUniversalPrimerSubcloneReads: %s\n",
        ( pCP->bAutoFinishAllowDeNovoUniversalPrimerSubcloneReads_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoFinishAllowMinilibraries_
      != consedResources::pCurrentResources_->bAutoFinishAllowMinilibraries_ ) 
       fprintf( pAO, "consed.autoFinishAllowMinilibraries: %s\n",
        ( pCP->bAutoFinishAllowMinilibraries_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoFinishAllowPCR_
      != consedResources::pCurrentResources_->bAutoFinishAllowPCR_ ) 
       fprintf( pAO, "consed.autoFinishAllowPCR: %s\n",
        ( pCP->bAutoFinishAllowPCR_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoFinishAllowUnorientedPCRReactions_
      != consedResources::pCurrentResources_->bAutoFinishAllowUnorientedPCRReactions_ ) 
       fprintf( pAO, "consed.autoFinishAllowUnorientedPCRReactions: %s\n",
        ( pCP->bAutoFinishAllowUnorientedPCRReactions_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoFinishAllowResequencingAUniversalPrimerAutofinishRead_
      != consedResources::pCurrentResources_->bAutoFinishAllowResequencingAUniversalPrimerAutofinishRead_ ) 
       fprintf( pAO, "consed.autoFinishAllowResequencingAUniversalPrimerAutofinishRead: %s\n",
        ( pCP->bAutoFinishAllowResequencingAUniversalPrimerAutofinishRead_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoFinishAlwaysCloseGapsUsingMinilibraries_
      != consedResources::pCurrentResources_->bAutoFinishAlwaysCloseGapsUsingMinilibraries_ ) 
       fprintf( pAO, "consed.autoFinishAlwaysCloseGapsUsingMinilibraries: %s\n",
        ( pCP->bAutoFinishAlwaysCloseGapsUsingMinilibraries_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->nAutoFinishMaximumFinishingReadLength_
      != consedResources::pCurrentResources_->nAutoFinishMaximumFinishingReadLength_ ) 
       fprintf( pAO, "consed.autoFinishMaximumFinishingReadLength: %d\n",
        pCP->nAutoFinishMaximumFinishingReadLength_ );


   if ( consedResources::pDefaultResources_->nAutoFinishSuggestMinilibraryIfGapThisManyBasesOrLarger_
      != consedResources::pCurrentResources_->nAutoFinishSuggestMinilibraryIfGapThisManyBasesOrLarger_ ) 
       fprintf( pAO, "consed.autoFinishSuggestMinilibraryIfGapThisManyBasesOrLarger: %d\n",
        pCP->nAutoFinishSuggestMinilibraryIfGapThisManyBasesOrLarger_ );


   if ( consedResources::pDefaultResources_->bAutoFinishSuggestSpecialChemistryForRunsAndStops_
      != consedResources::pCurrentResources_->bAutoFinishSuggestSpecialChemistryForRunsAndStops_ ) 
       fprintf( pAO, "consed.autoFinishSuggestSpecialChemistryForRunsAndStops: %s\n",
        ( pCP->bAutoFinishSuggestSpecialChemistryForRunsAndStops_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->nAutoFinishSuggestThisManyMinilibrariesPerGap_
      != consedResources::pCurrentResources_->nAutoFinishSuggestThisManyMinilibrariesPerGap_ ) 
       fprintf( pAO, "consed.autoFinishSuggestThisManyMinilibrariesPerGap: %d\n",
        pCP->nAutoFinishSuggestThisManyMinilibrariesPerGap_ );


   if ( consedResources::pDefaultResources_->nPrimersWindowSizeInLooking_
      != consedResources::pCurrentResources_->nPrimersWindowSizeInLooking_ ) 
       fprintf( pAO, "consed.primersWindowSizeInLooking: %d\n",
        pCP->nPrimersWindowSizeInLooking_ );


   if ( consedResources::pDefaultResources_->bPrimersAssumeTemplatesAreDoubleStrandedUnlessSpecified_
      != consedResources::pCurrentResources_->bPrimersAssumeTemplatesAreDoubleStrandedUnlessSpecified_ ) 
       fprintf( pAO, "consed.primersAssumeTemplatesAreDoubleStrandedUnlessSpecified: %s\n",
        ( pCP->bPrimersAssumeTemplatesAreDoubleStrandedUnlessSpecified_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoFinishAllowResequencingReadsToExtendContigs_
      != consedResources::pCurrentResources_->bAutoFinishAllowResequencingReadsToExtendContigs_ ) 
       fprintf( pAO, "consed.autoFinishAllowResequencingReadsToExtendContigs: %s\n",
        ( pCP->bAutoFinishAllowResequencingReadsToExtendContigs_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->nAutoFinishCallHowManyReversesToFlankGaps_
      != consedResources::pCurrentResources_->nAutoFinishCallHowManyReversesToFlankGaps_ ) 
       fprintf( pAO, "consed.autoFinishCallHowManyReversesToFlankGaps: %d\n",
        pCP->nAutoFinishCallHowManyReversesToFlankGaps_ );


   if ( consedResources::pDefaultResources_->bAutoFinishCloseGaps_
      != consedResources::pCurrentResources_->bAutoFinishCloseGaps_ ) 
       fprintf( pAO, "consed.autoFinishCloseGaps: %s\n",
        ( pCP->bAutoFinishCloseGaps_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoFinishContinueEvenThoughReadInfoDoesNotMakeSense_
      != consedResources::pCurrentResources_->bAutoFinishContinueEvenThoughReadInfoDoesNotMakeSense_ ) 
       fprintf( pAO, "consed.autoFinishContinueEvenThoughReadInfoDoesNotMakeSense: %s\n",
        ( pCP->bAutoFinishContinueEvenThoughReadInfoDoesNotMakeSense_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->dAutoFinishCostOfResequencingUniversalPrimerSubcloneReaction_
      != consedResources::pCurrentResources_->dAutoFinishCostOfResequencingUniversalPrimerSubcloneReaction_ ) 
       fprintf( pAO, "consed.autoFinishCostOfResequencingUniversalPrimerSubcloneReaction: %.3f\n",
        pCP->dAutoFinishCostOfResequencingUniversalPrimerSubcloneReaction_ );


   if ( consedResources::pDefaultResources_->dAutoFinishCostOfCustomPrimerSubcloneReaction_
      != consedResources::pCurrentResources_->dAutoFinishCostOfCustomPrimerSubcloneReaction_ ) 
       fprintf( pAO, "consed.autoFinishCostOfCustomPrimerSubcloneReaction: %.3f\n",
        pCP->dAutoFinishCostOfCustomPrimerSubcloneReaction_ );


   if ( consedResources::pDefaultResources_->dAutoFinishCostOfCustomPrimerCloneReaction_
      != consedResources::pCurrentResources_->dAutoFinishCostOfCustomPrimerCloneReaction_ ) 
       fprintf( pAO, "consed.autoFinishCostOfCustomPrimerCloneReaction: %.3f\n",
        pCP->dAutoFinishCostOfCustomPrimerCloneReaction_ );


   if ( consedResources::pDefaultResources_->dAutoFinishCostOfDeNovoUniversalPrimerSubcloneReaction_
      != consedResources::pCurrentResources_->dAutoFinishCostOfDeNovoUniversalPrimerSubcloneReaction_ ) 
       fprintf( pAO, "consed.autoFinishCostOfDeNovoUniversalPrimerSubcloneReaction: %.3f\n",
        pCP->dAutoFinishCostOfDeNovoUniversalPrimerSubcloneReaction_ );


   if ( consedResources::pDefaultResources_->dAutoFinishCostOfMinilibrary_
      != consedResources::pCurrentResources_->dAutoFinishCostOfMinilibrary_ ) 
       fprintf( pAO, "consed.autoFinishCostOfMinilibrary: %.3f\n",
        pCP->dAutoFinishCostOfMinilibrary_ );


   if ( consedResources::pDefaultResources_->bAutoFinishCoverSingleSubcloneRegions_
      != consedResources::pCurrentResources_->bAutoFinishCoverSingleSubcloneRegions_ ) 
       fprintf( pAO, "consed.autoFinishCoverSingleSubcloneRegions: %s\n",
        ( pCP->bAutoFinishCoverSingleSubcloneRegions_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoFinishCoverLowConsensusQualityRegions_
      != consedResources::pCurrentResources_->bAutoFinishCoverLowConsensusQualityRegions_ ) 
       fprintf( pAO, "consed.autoFinishCoverLowConsensusQualityRegions: %s\n",
        ( pCP->bAutoFinishCoverLowConsensusQualityRegions_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->filAutoFinishDebugUniversalPrimerReadsFile_
      != consedResources::pCurrentResources_->filAutoFinishDebugUniversalPrimerReadsFile_ ) 
        fprintf( pAO, "consed.autoFinishDebugUniversalPrimerReadsFile: %s\n",
              (char*)pCP->filAutoFinishDebugUniversalPrimerReadsFile_.data() );


   if ( consedResources::pDefaultResources_->filAutoFinishDebugCustomPrimerReadsFile_
      != consedResources::pCurrentResources_->filAutoFinishDebugCustomPrimerReadsFile_ ) 
        fprintf( pAO, "consed.autoFinishDebugCustomPrimerReadsFile: %s\n",
              (char*)pCP->filAutoFinishDebugCustomPrimerReadsFile_.data() );


   if ( consedResources::pDefaultResources_->nAutoFinishDoNotAllowSubcloneCustomPrimerReadsCloserThanThisManyBases_
      != consedResources::pCurrentResources_->nAutoFinishDoNotAllowSubcloneCustomPrimerReadsCloserThanThisManyBases_ ) 
       fprintf( pAO, "consed.autoFinishDoNotAllowSubcloneCustomPrimerReadsCloserThanThisManyBases: %d\n",
        pCP->nAutoFinishDoNotAllowSubcloneCustomPrimerReadsCloserThanThisManyBases_ );


   if ( consedResources::pDefaultResources_->nAutoFinishDoNotAllowWholeCloneCustomPrimerReadsCloserThanThisManyBases_
      != consedResources::pCurrentResources_->nAutoFinishDoNotAllowWholeCloneCustomPrimerReadsCloserThanThisManyBases_ ) 
       fprintf( pAO, "consed.autoFinishDoNotAllowWholeCloneCustomPrimerReadsCloserThanThisManyBases: %d\n",
        pCP->nAutoFinishDoNotAllowWholeCloneCustomPrimerReadsCloserThanThisManyBases_ );


   if ( consedResources::pDefaultResources_->soAutoFinishDoNotFinishWhereTheseTagsAre_
      != consedResources::pCurrentResources_->soAutoFinishDoNotFinishWhereTheseTagsAre_ ) 
        fprintf( pAO, "consed.autoFinishDoNotFinishWhereTheseTagsAre: %s\n",
              (char*)pCP->soAutoFinishDoNotFinishWhereTheseTagsAre_.data() );


   if ( consedResources::pDefaultResources_->soAutoFinishDoNotExtendContigsWhereTheseTagsAre_
      != consedResources::pCurrentResources_->soAutoFinishDoNotExtendContigsWhereTheseTagsAre_ ) 
        fprintf( pAO, "consed.autoFinishDoNotExtendContigsWhereTheseTagsAre: %s\n",
              (char*)pCP->soAutoFinishDoNotExtendContigsWhereTheseTagsAre_.data() );


   if ( consedResources::pDefaultResources_->nAutoFinishDoNotExtendContigsIfTagsAreThisCloseToContigEnd_
      != consedResources::pCurrentResources_->nAutoFinishDoNotExtendContigsIfTagsAreThisCloseToContigEnd_ ) 
       fprintf( pAO, "consed.autoFinishDoNotExtendContigsIfTagsAreThisCloseToContigEnd: %d\n",
        pCP->nAutoFinishDoNotExtendContigsIfTagsAreThisCloseToContigEnd_ );


   if ( consedResources::pDefaultResources_->bAutoFinishDumpTemplates_
      != consedResources::pCurrentResources_->bAutoFinishDumpTemplates_ ) 
       fprintf( pAO, "consed.autoFinishDumpTemplates: %s\n",
        ( pCP->bAutoFinishDumpTemplates_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->nAutoFinishExcludeContigIfOnlyThisManyReadsOrLess_
      != consedResources::pCurrentResources_->nAutoFinishExcludeContigIfOnlyThisManyReadsOrLess_ ) 
       fprintf( pAO, "consed.autoFinishExcludeContigIfOnlyThisManyReadsOrLess: %d\n",
        pCP->nAutoFinishExcludeContigIfOnlyThisManyReadsOrLess_ );


   if ( consedResources::pDefaultResources_->dAutoFinishExcludeContigIfDepthOfCoverageGreaterThanThis_
      != consedResources::pCurrentResources_->dAutoFinishExcludeContigIfDepthOfCoverageGreaterThanThis_ ) 
       fprintf( pAO, "consed.autoFinishExcludeContigIfDepthOfCoverageGreaterThanThis: %.3f\n",
        pCP->dAutoFinishExcludeContigIfDepthOfCoverageGreaterThanThis_ );


   if ( consedResources::pDefaultResources_->nAutoFinishExcludeContigIfThisManyBasesOrLess_
      != consedResources::pCurrentResources_->nAutoFinishExcludeContigIfThisManyBasesOrLess_ ) 
       fprintf( pAO, "consed.autoFinishExcludeContigIfThisManyBasesOrLess: %d\n",
        pCP->nAutoFinishExcludeContigIfThisManyBasesOrLess_ );


   if ( consedResources::pDefaultResources_->nAutoFinishHowManyTemplatesYouIntendToUseForCustomPrimerSubcloneReactions_
      != consedResources::pCurrentResources_->nAutoFinishHowManyTemplatesYouIntendToUseForCustomPrimerSubcloneReactions_ ) 
       fprintf( pAO, "consed.autoFinishHowManyTemplatesYouIntendToUseForCustomPrimerSubcloneReactions: %d\n",
        pCP->nAutoFinishHowManyTemplatesYouIntendToUseForCustomPrimerSubcloneReactions_ );


   if ( consedResources::pDefaultResources_->nPrimersMinNumberOfTemplatesForPrimers_
      != consedResources::pCurrentResources_->nPrimersMinNumberOfTemplatesForPrimers_ ) 
       fprintf( pAO, "consed.primersMinNumberOfTemplatesForPrimers: %d\n",
        pCP->nPrimersMinNumberOfTemplatesForPrimers_ );


   if ( consedResources::pDefaultResources_->nAutoFinishMinBaseOverlapBetweenAReadAndHighQualitySegmentOfConsensus_
      != consedResources::pCurrentResources_->nAutoFinishMinBaseOverlapBetweenAReadAndHighQualitySegmentOfConsensus_ ) 
       fprintf( pAO, "consed.autoFinishMinBaseOverlapBetweenAReadAndHighQualitySegmentOfConsensus: %d\n",
        pCP->nAutoFinishMinBaseOverlapBetweenAReadAndHighQualitySegmentOfConsensus_ );


   if ( consedResources::pDefaultResources_->nAutoFinishNumberOfVectorBasesAtBeginningOfAUniveralPrimerRead_
      != consedResources::pCurrentResources_->nAutoFinishNumberOfVectorBasesAtBeginningOfAUniveralPrimerRead_ ) 
       fprintf( pAO, "consed.autoFinishNumberOfVectorBasesAtBeginningOfAUniveralPrimerRead: %d\n",
        pCP->nAutoFinishNumberOfVectorBasesAtBeginningOfAUniveralPrimerRead_ );


   if ( consedResources::pDefaultResources_->bAutoFinishCDNANotGenomic_
      != consedResources::pCurrentResources_->bAutoFinishCDNANotGenomic_ ) 
       fprintf( pAO, "consed.autoFinishCDNANotGenomic: %s\n",
        ( pCP->bAutoFinishCDNANotGenomic_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->nAutoFinishConfidenceThatReadWillCoverSingleSubcloneRegion_
      != consedResources::pCurrentResources_->nAutoFinishConfidenceThatReadWillCoverSingleSubcloneRegion_ ) 
       fprintf( pAO, "consed.autoFinishConfidenceThatReadWillCoverSingleSubcloneRegion: %d\n",
        pCP->nAutoFinishConfidenceThatReadWillCoverSingleSubcloneRegion_ );


   if ( consedResources::pDefaultResources_->bAutoFinishPrintForwardOrReverseStrandWhenPrintingSubcloneTemplatesForCustomPrimerReads_
      != consedResources::pCurrentResources_->bAutoFinishPrintForwardOrReverseStrandWhenPrintingSubcloneTemplatesForCustomPrimerReads_ ) 
       fprintf( pAO, "consed.autoFinishPrintForwardOrReverseStrandWhenPrintingSubcloneTemplatesForCustomPrimerReads: %s\n",
        ( pCP->bAutoFinishPrintForwardOrReverseStrandWhenPrintingSubcloneTemplatesForCustomPrimerReads_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoFinishPrintMinilibrariesSummaryFile_
      != consedResources::pCurrentResources_->bAutoFinishPrintMinilibrariesSummaryFile_ ) 
       fprintf( pAO, "consed.autoFinishPrintMinilibrariesSummaryFile: %s\n",
        ( pCP->bAutoFinishPrintMinilibrariesSummaryFile_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoFinishNearGapsSuggestEachMissingReadOfReadPairs_
      != consedResources::pCurrentResources_->bAutoFinishNearGapsSuggestEachMissingReadOfReadPairs_ ) 
       fprintf( pAO, "consed.autoFinishNearGapsSuggestEachMissingReadOfReadPairs: %s\n",
        ( pCP->bAutoFinishNearGapsSuggestEachMissingReadOfReadPairs_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->nAutoFinishDoNotIgnoreLCQIfThisManyBasesFromEndOfContigForLCQTagger_
      != consedResources::pCurrentResources_->nAutoFinishDoNotIgnoreLCQIfThisManyBasesFromEndOfContigForLCQTagger_ ) 
       fprintf( pAO, "consed.autoFinishDoNotIgnoreLCQIfThisManyBasesFromEndOfContigForLCQTagger: %d\n",
        pCP->nAutoFinishDoNotIgnoreLCQIfThisManyBasesFromEndOfContigForLCQTagger_ );


   if ( consedResources::pDefaultResources_->nPrimersMinimumLengthOfAPrimer_
      != consedResources::pCurrentResources_->nPrimersMinimumLengthOfAPrimer_ ) 
       fprintf( pAO, "consed.primersMinimumLengthOfAPrimer: %d\n",
        pCP->nPrimersMinimumLengthOfAPrimer_ );


   if ( consedResources::pDefaultResources_->nPrimersMaximumLengthOfAPrimer_
      != consedResources::pCurrentResources_->nPrimersMaximumLengthOfAPrimer_ ) 
       fprintf( pAO, "consed.primersMaximumLengthOfAPrimer: %d\n",
        pCP->nPrimersMaximumLengthOfAPrimer_ );


   if ( consedResources::pDefaultResources_->nPrimersMinimumLengthOfAPrimerForPCR_
      != consedResources::pCurrentResources_->nPrimersMinimumLengthOfAPrimerForPCR_ ) 
       fprintf( pAO, "consed.primersMinimumLengthOfAPrimerForPCR: %d\n",
        pCP->nPrimersMinimumLengthOfAPrimerForPCR_ );


   if ( consedResources::pDefaultResources_->nPrimersMaximumLengthOfAPrimerForPCR_
      != consedResources::pCurrentResources_->nPrimersMaximumLengthOfAPrimerForPCR_ ) 
       fprintf( pAO, "consed.primersMaximumLengthOfAPrimerForPCR: %d\n",
        pCP->nPrimersMaximumLengthOfAPrimerForPCR_ );


   if ( consedResources::pDefaultResources_->dPrimersMaxMeltingTempDifferenceForPCR_
      != consedResources::pCurrentResources_->dPrimersMaxMeltingTempDifferenceForPCR_ ) 
       fprintf( pAO, "consed.primersMaxMeltingTempDifferenceForPCR: %.3f\n",
        pCP->dPrimersMaxMeltingTempDifferenceForPCR_ );


   if ( consedResources::pDefaultResources_->nPrimersMaxPCRPrimerPairsToDisplay_
      != consedResources::pCurrentResources_->nPrimersMaxPCRPrimerPairsToDisplay_ ) 
       fprintf( pAO, "consed.primersMaxPCRPrimerPairsToDisplay: %d\n",
        pCP->nPrimersMaxPCRPrimerPairsToDisplay_ );


   if ( consedResources::pDefaultResources_->bPrimersCheckJustSomePCRPrimerPairsRatherThanAll_
      != consedResources::pCurrentResources_->bPrimersCheckJustSomePCRPrimerPairsRatherThanAll_ ) 
       fprintf( pAO, "consed.primersCheckJustSomePCRPrimerPairsRatherThanAll: %s\n",
        ( pCP->bPrimersCheckJustSomePCRPrimerPairsRatherThanAll_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->nPrimersNumberOfTemplatesToDisplayInFront_
      != consedResources::pCurrentResources_->nPrimersNumberOfTemplatesToDisplayInFront_ ) 
       fprintf( pAO, "consed.primersNumberOfTemplatesToDisplayInFront: %d\n",
        pCP->nPrimersNumberOfTemplatesToDisplayInFront_ );


   if ( consedResources::pDefaultResources_->nPrimersMaxLengthOfMononucleotideRepeat_
      != consedResources::pCurrentResources_->nPrimersMaxLengthOfMononucleotideRepeat_ ) 
       fprintf( pAO, "consed.primersMaxLengthOfMononucleotideRepeat: %d\n",
        pCP->nPrimersMaxLengthOfMononucleotideRepeat_ );


   if ( consedResources::pDefaultResources_->filPrimersBadLibrariesFile_
      != consedResources::pCurrentResources_->filPrimersBadLibrariesFile_ ) 
        fprintf( pAO, "consed.primersBadLibrariesFile: %s\n",
              (char*)pCP->filPrimersBadLibrariesFile_.data() );


   if ( consedResources::pDefaultResources_->filPrimersLibrariesInfoFile_
      != consedResources::pCurrentResources_->filPrimersLibrariesInfoFile_ ) 
        fprintf( pAO, "consed.primersLibrariesInfoFile: %s\n",
              (char*)pCP->filPrimersLibrariesInfoFile_.data() );


   if ( consedResources::pDefaultResources_->filPrimersBadTemplatesFile_
      != consedResources::pCurrentResources_->filPrimersBadTemplatesFile_ ) 
        fprintf( pAO, "consed.primersBadTemplatesFile: %s\n",
              (char*)pCP->filPrimersBadTemplatesFile_.data() );


   if ( consedResources::pDefaultResources_->bPrimersChooseTemplatesByPositionInsteadOfQuality_
      != consedResources::pCurrentResources_->bPrimersChooseTemplatesByPositionInsteadOfQuality_ ) 
       fprintf( pAO, "consed.primersChooseTemplatesByPositionInsteadOfQuality: %s\n",
        ( pCP->bPrimersChooseTemplatesByPositionInsteadOfQuality_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->nPrimersWhenChoosingATemplateMinPotentialReadLength_
      != consedResources::pCurrentResources_->nPrimersWhenChoosingATemplateMinPotentialReadLength_ ) 
       fprintf( pAO, "consed.primersWhenChoosingATemplateMinPotentialReadLength: %d\n",
        pCP->nPrimersWhenChoosingATemplateMinPotentialReadLength_ );


   if ( consedResources::pDefaultResources_->nPrimersWindowSizeInLookingForPCR_
      != consedResources::pCurrentResources_->nPrimersWindowSizeInLookingForPCR_ ) 
       fprintf( pAO, "consed.primersWindowSizeInLookingForPCR: %d\n",
        pCP->nPrimersWindowSizeInLookingForPCR_ );


   if ( consedResources::pDefaultResources_->nQualityThresholdForFindingHighQualityDiscrepancies_
      != consedResources::pCurrentResources_->nQualityThresholdForFindingHighQualityDiscrepancies_ ) 
       fprintf( pAO, "consed.qualityThresholdForFindingHighQualityDiscrepancies: %d\n",
        pCP->nQualityThresholdForFindingHighQualityDiscrepancies_ );


   if ( consedResources::pDefaultResources_->bAutoFinishUseLongModelReadRatherThanShort_
      != consedResources::pCurrentResources_->bAutoFinishUseLongModelReadRatherThanShort_ ) 
       fprintf( pAO, "consed.autoFinishUseLongModelReadRatherThanShort: %s\n",
        ( pCP->bAutoFinishUseLongModelReadRatherThanShort_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->nAutoPCRAmplifyFalseProductsOKIfLargerThanThis_
      != consedResources::pCurrentResources_->nAutoPCRAmplifyFalseProductsOKIfLargerThanThis_ ) 
       fprintf( pAO, "consed.autoPCRAmplifyFalseProductsOKIfLargerThanThis: %d\n",
        pCP->nAutoPCRAmplifyFalseProductsOKIfLargerThanThis_ );


   if ( consedResources::pDefaultResources_->bAutoPCRAmplifyMakePrimerOutOfFirstRegion_
      != consedResources::pCurrentResources_->bAutoPCRAmplifyMakePrimerOutOfFirstRegion_ ) 
       fprintf( pAO, "consed.autoPCRAmplifyMakePrimerOutOfFirstRegion: %s\n",
        ( pCP->bAutoPCRAmplifyMakePrimerOutOfFirstRegion_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->nAutoPCRAmplifyMaybeRejectPrimerIfThisCloseToDesiredProduct_
      != consedResources::pCurrentResources_->nAutoPCRAmplifyMaybeRejectPrimerIfThisCloseToDesiredProduct_ ) 
       fprintf( pAO, "consed.autoPCRAmplifyMaybeRejectPrimerIfThisCloseToDesiredProduct: %d\n",
        pCP->nAutoPCRAmplifyMaybeRejectPrimerIfThisCloseToDesiredProduct_ );


   if ( consedResources::pDefaultResources_->bAutoFinishEmulate9_66Behavior_
      != consedResources::pCurrentResources_->bAutoFinishEmulate9_66Behavior_ ) 
       fprintf( pAO, "consed.autoFinishEmulate9_66Behavior: %s\n",
        ( pCP->bAutoFinishEmulate9_66Behavior_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->nPrimersPCRPrimersGroupedIntoWindowOfThisManyBases_
      != consedResources::pCurrentResources_->nPrimersPCRPrimersGroupedIntoWindowOfThisManyBases_ ) 
       fprintf( pAO, "consed.primersPCRPrimersGroupedIntoWindowOfThisManyBases: %d\n",
        pCP->nPrimersPCRPrimersGroupedIntoWindowOfThisManyBases_ );


   if ( consedResources::pDefaultResources_->nPrimersLookForThisManyPCRPrimerPairsPerPairOfGroups_
      != consedResources::pCurrentResources_->nPrimersLookForThisManyPCRPrimerPairsPerPairOfGroups_ ) 
       fprintf( pAO, "consed.primersLookForThisManyPCRPrimerPairsPerPairOfGroups: %d\n",
        pCP->nPrimersLookForThisManyPCRPrimerPairsPerPairOfGroups_ );


   if ( consedResources::pDefaultResources_->dAutoFinishStandardDeviationsFromMeanFromGapToLookForTemplatesForSuggestingEachMissingReadOfReadPairs_
      != consedResources::pCurrentResources_->dAutoFinishStandardDeviationsFromMeanFromGapToLookForTemplatesForSuggestingEachMissingReadOfReadPairs_ ) 
       fprintf( pAO, "consed.autoFinishStandardDeviationsFromMeanFromGapToLookForTemplatesForSuggestingEachMissingReadOfReadPairs: %.3f\n",
        pCP->dAutoFinishStandardDeviationsFromMeanFromGapToLookForTemplatesForSuggestingEachMissingReadOfReadPairs_ );


   if ( consedResources::pDefaultResources_->bAutoFinishCheckThatReadsFromTheSameTemplateAreConsistent_
      != consedResources::pCurrentResources_->bAutoFinishCheckThatReadsFromTheSameTemplateAreConsistent_ ) 
       fprintf( pAO, "consed.autoFinishCheckThatReadsFromTheSameTemplateAreConsistent: %s\n",
        ( pCP->bAutoFinishCheckThatReadsFromTheSameTemplateAreConsistent_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoFinishDoNotAllowSubcloneCustomPrimerReadsCloseTogether_
      != consedResources::pCurrentResources_->bAutoFinishDoNotAllowSubcloneCustomPrimerReadsCloseTogether_ ) 
       fprintf( pAO, "consed.autoFinishDoNotAllowSubcloneCustomPrimerReadsCloseTogether: %s\n",
        ( pCP->bAutoFinishDoNotAllowSubcloneCustomPrimerReadsCloseTogether_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoFinishDoNotAllowWholeCloneCustomPrimerReadsCloseTogether_
      != consedResources::pCurrentResources_->bAutoFinishDoNotAllowWholeCloneCustomPrimerReadsCloseTogether_ ) 
       fprintf( pAO, "consed.autoFinishDoNotAllowWholeCloneCustomPrimerReadsCloseTogether: %s\n",
        ( pCP->bAutoFinishDoNotAllowWholeCloneCustomPrimerReadsCloseTogether_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->dAutoFinishMinilibrariesPreferTemplateIfSizeThisManyStdDevsFromMean_
      != consedResources::pCurrentResources_->dAutoFinishMinilibrariesPreferTemplateIfSizeThisManyStdDevsFromMean_ ) 
       fprintf( pAO, "consed.autoFinishMinilibrariesPreferTemplateIfSizeThisManyStdDevsFromMean: %.3f\n",
        pCP->dAutoFinishMinilibrariesPreferTemplateIfSizeThisManyStdDevsFromMean_ );


   if ( consedResources::pDefaultResources_->nAutoFinishMinNumberOfForwardReversePairsInLibraryToCalculateAverageInsertSize_
      != consedResources::pCurrentResources_->nAutoFinishMinNumberOfForwardReversePairsInLibraryToCalculateAverageInsertSize_ ) 
       fprintf( pAO, "consed.autoFinishMinNumberOfForwardReversePairsInLibraryToCalculateAverageInsertSize: %d\n",
        pCP->nAutoFinishMinNumberOfForwardReversePairsInLibraryToCalculateAverageInsertSize_ );


   if ( consedResources::pDefaultResources_->dAutoFinishIfEnoughFwdRevPairsUseThisManyStdDevBelowMeanForInsertSize_
      != consedResources::pCurrentResources_->dAutoFinishIfEnoughFwdRevPairsUseThisManyStdDevBelowMeanForInsertSize_ ) 
       fprintf( pAO, "consed.autoFinishIfEnoughFwdRevPairsUseThisManyStdDevBelowMeanForInsertSize: %.3f\n",
        pCP->dAutoFinishIfEnoughFwdRevPairsUseThisManyStdDevBelowMeanForInsertSize_ );


   if ( consedResources::pDefaultResources_->nAutoFinishNewCustomPrimerReadThisFarFromOldCustomPrimerRead_
      != consedResources::pCurrentResources_->nAutoFinishNewCustomPrimerReadThisFarFromOldCustomPrimerRead_ ) 
       fprintf( pAO, "consed.autoFinishNewCustomPrimerReadThisFarFromOldCustomPrimerRead: %d\n",
        pCP->nAutoFinishNewCustomPrimerReadThisFarFromOldCustomPrimerRead_ );


   if ( consedResources::pDefaultResources_->nAutoFinishMinNumberOfSingleSubcloneBasesFixedByAnExp_
      != consedResources::pCurrentResources_->nAutoFinishMinNumberOfSingleSubcloneBasesFixedByAnExp_ ) 
       fprintf( pAO, "consed.autoFinishMinNumberOfSingleSubcloneBasesFixedByAnExp: %d\n",
        pCP->nAutoFinishMinNumberOfSingleSubcloneBasesFixedByAnExp_ );


   if ( consedResources::pDefaultResources_->nAutoFinishNumberOfBasesBetweenContigsAssumed_
      != consedResources::pCurrentResources_->nAutoFinishNumberOfBasesBetweenContigsAssumed_ ) 
       fprintf( pAO, "consed.autoFinishNumberOfBasesBetweenContigsAssumed: %d\n",
        pCP->nAutoFinishNumberOfBasesBetweenContigsAssumed_ );


   if ( consedResources::pDefaultResources_->nAutoFinishPotentialHighQualityPartOfReadStart_
      != consedResources::pCurrentResources_->nAutoFinishPotentialHighQualityPartOfReadStart_ ) 
       fprintf( pAO, "consed.autoFinishPotentialHighQualityPartOfReadStart: %d\n",
        pCP->nAutoFinishPotentialHighQualityPartOfReadStart_ );


   if ( consedResources::pDefaultResources_->nAutoFinishPotentialHighQualityPartOfReadEnd_
      != consedResources::pCurrentResources_->nAutoFinishPotentialHighQualityPartOfReadEnd_ ) 
       fprintf( pAO, "consed.autoFinishPotentialHighQualityPartOfReadEnd: %d\n",
        pCP->nAutoFinishPotentialHighQualityPartOfReadEnd_ );


   if ( consedResources::pDefaultResources_->bAutoFinishPrintCustomNavigationFileForChosenReads_
      != consedResources::pCurrentResources_->bAutoFinishPrintCustomNavigationFileForChosenReads_ ) 
       fprintf( pAO, "consed.autoFinishPrintCustomNavigationFileForChosenReads: %s\n",
        ( pCP->bAutoFinishPrintCustomNavigationFileForChosenReads_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->nAutoFinishReversesForFlankingGapsTemplateMustProtrudeFromContigThisMuch_
      != consedResources::pCurrentResources_->nAutoFinishReversesForFlankingGapsTemplateMustProtrudeFromContigThisMuch_ ) 
       fprintf( pAO, "consed.autoFinishReversesForFlankingGapsTemplateMustProtrudeFromContigThisMuch: %d\n",
        pCP->nAutoFinishReversesForFlankingGapsTemplateMustProtrudeFromContigThisMuch_ );


   if ( consedResources::pDefaultResources_->bAutoFinishTagOligosWhenDoExperiments_
      != consedResources::pCurrentResources_->bAutoFinishTagOligosWhenDoExperiments_ ) 
       fprintf( pAO, "consed.autoFinishTagOligosWhenDoExperiments: %s\n",
        ( pCP->bAutoFinishTagOligosWhenDoExperiments_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->nPrimersLookThisFarForForwardVectorInsertJunction_
      != consedResources::pCurrentResources_->nPrimersLookThisFarForForwardVectorInsertJunction_ ) 
       fprintf( pAO, "consed.primersLookThisFarForForwardVectorInsertJunction: %d\n",
        pCP->nPrimersLookThisFarForForwardVectorInsertJunction_ );


   if ( consedResources::pDefaultResources_->dPrimersDNAConcentrationNanomolar_
      != consedResources::pCurrentResources_->dPrimersDNAConcentrationNanomolar_ ) 
       fprintf( pAO, "consed.primersDNAConcentrationNanomolar: %.3f\n",
        pCP->dPrimersDNAConcentrationNanomolar_ );


   if ( consedResources::pDefaultResources_->nPrimersMaxMatchElsewhereScore_
      != consedResources::pCurrentResources_->nPrimersMaxMatchElsewhereScore_ ) 
       fprintf( pAO, "consed.primersMaxMatchElsewhereScore: %d\n",
        pCP->nPrimersMaxMatchElsewhereScore_ );


   if ( consedResources::pDefaultResources_->nPrimersMaxMatchElsewhereScoreForPCR_
      != consedResources::pCurrentResources_->nPrimersMaxMatchElsewhereScoreForPCR_ ) 
       fprintf( pAO, "consed.primersMaxMatchElsewhereScoreForPCR: %d\n",
        pCP->nPrimersMaxMatchElsewhereScoreForPCR_ );


   if ( consedResources::pDefaultResources_->nPrimersMaxSelfMatchScore_
      != consedResources::pCurrentResources_->nPrimersMaxSelfMatchScore_ ) 
       fprintf( pAO, "consed.primersMaxSelfMatchScore: %d\n",
        pCP->nPrimersMaxSelfMatchScore_ );


   if ( consedResources::pDefaultResources_->nPrimersMaxPrimerDimerScoreForPCR_
      != consedResources::pCurrentResources_->nPrimersMaxPrimerDimerScoreForPCR_ ) 
       fprintf( pAO, "consed.primersMaxPrimerDimerScoreForPCR: %d\n",
        pCP->nPrimersMaxPrimerDimerScoreForPCR_ );


   if ( consedResources::pDefaultResources_->nPrimersMinQuality_
      != consedResources::pCurrentResources_->nPrimersMinQuality_ ) 
       fprintf( pAO, "consed.primersMinQuality: %d\n",
        pCP->nPrimersMinQuality_ );


   if ( consedResources::pDefaultResources_->bPrimersPrintInfoOnRejectedTemplates_
      != consedResources::pCurrentResources_->bPrimersPrintInfoOnRejectedTemplates_ ) 
       fprintf( pAO, "consed.primersPrintInfoOnRejectedTemplates: %s\n",
        ( pCP->bPrimersPrintInfoOnRejectedTemplates_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->dPrimersSaltConcentrationMillimolar_
      != consedResources::pCurrentResources_->dPrimersSaltConcentrationMillimolar_ ) 
       fprintf( pAO, "consed.primersSaltConcentrationMillimolar: %.3f\n",
        pCP->dPrimersSaltConcentrationMillimolar_ );


   if ( consedResources::pDefaultResources_->bPrimersScreenForVector_
      != consedResources::pCurrentResources_->bPrimersScreenForVector_ ) 
       fprintf( pAO, "consed.primersScreenForVector: %s\n",
        ( pCP->bPrimersScreenForVector_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->nPrimersToleranceForDifferentBeginningLocationOfUniversalPrimerReads_
      != consedResources::pCurrentResources_->nPrimersToleranceForDifferentBeginningLocationOfUniversalPrimerReads_ ) 
       fprintf( pAO, "consed.primersToleranceForDifferentBeginningLocationOfUniversalPrimerReads: %d\n",
        pCP->nPrimersToleranceForDifferentBeginningLocationOfUniversalPrimerReads_ );


   if ( consedResources::pDefaultResources_->nPrimersTooManyVectorBasesInWalkingRead_
      != consedResources::pCurrentResources_->nPrimersTooManyVectorBasesInWalkingRead_ ) 
       fprintf( pAO, "consed.primersTooManyVectorBasesInWalkingRead: %d\n",
        pCP->nPrimersTooManyVectorBasesInWalkingRead_ );


   if ( consedResources::pDefaultResources_->nAutoFinishMinSmithWatermanScoreOfARun_
      != consedResources::pCurrentResources_->nAutoFinishMinSmithWatermanScoreOfARun_ ) 
       fprintf( pAO, "consed.autoFinishMinSmithWatermanScoreOfARun: %d\n",
        pCP->nAutoFinishMinSmithWatermanScoreOfARun_ );


   if ( consedResources::pDefaultResources_->dAutoFinishDoNotComparePCRPrimersMoreThanThisManyTimes_
      != consedResources::pCurrentResources_->dAutoFinishDoNotComparePCRPrimersMoreThanThisManyTimes_ ) 
       fprintf( pAO, "consed.autoFinishDoNotComparePCRPrimersMoreThanThisManyTimes: %.3f\n",
        pCP->dAutoFinishDoNotComparePCRPrimersMoreThanThisManyTimes_ );


   if ( consedResources::pDefaultResources_->nAutoPCRAmplifyTooManySeriousFalseMatches_
      != consedResources::pCurrentResources_->nAutoPCRAmplifyTooManySeriousFalseMatches_ ) 
       fprintf( pAO, "consed.autoPCRAmplifyTooManySeriousFalseMatches: %d\n",
        pCP->nAutoPCRAmplifyTooManySeriousFalseMatches_ );


   if ( consedResources::pDefaultResources_->nAutoReportAllNeededSpeciesCode_
      != consedResources::pCurrentResources_->nAutoReportAllNeededSpeciesCode_ ) 
       fprintf( pAO, "consed.autoReportAllNeededSpeciesCode: %d\n",
        pCP->nAutoReportAllNeededSpeciesCode_ );


   if ( consedResources::pDefaultResources_->bAutoReportUseCommasInBigNumbers_
      != consedResources::pCurrentResources_->bAutoReportUseCommasInBigNumbers_ ) 
       fprintf( pAO, "consed.autoReportUseCommasInBigNumbers: %s\n",
        ( pCP->bAutoReportUseCommasInBigNumbers_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoReportPrintToCompareToReich_
      != consedResources::pCurrentResources_->bAutoReportPrintToCompareToReich_ ) 
       fprintf( pAO, "consed.autoReportPrintToCompareToReich: %s\n",
        ( pCP->bAutoReportPrintToCompareToReich_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoReportOnlyAllowSitesThatAreBetweenAcceptableSites_
      != consedResources::pCurrentResources_->bAutoReportOnlyAllowSitesThatAreBetweenAcceptableSites_ ) 
       fprintf( pAO, "consed.autoReportOnlyAllowSitesThatAreBetweenAcceptableSites: %s\n",
        ( pCP->bAutoReportOnlyAllowSitesThatAreBetweenAcceptableSites_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoReportDeaminationMutationsDeterminedByMoreAccurateMethod_
      != consedResources::pCurrentResources_->bAutoReportDeaminationMutationsDeterminedByMoreAccurateMethod_ ) 
       fprintf( pAO, "consed.autoReportDeaminationMutationsDeterminedByMoreAccurateMethod: %s\n",
        ( pCP->bAutoReportDeaminationMutationsDeterminedByMoreAccurateMethod_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoReportChooseTreesUsingBadData_
      != consedResources::pCurrentResources_->bAutoReportChooseTreesUsingBadData_ ) 
       fprintf( pAO, "consed.autoReportChooseTreesUsingBadData: %s\n",
        ( pCP->bAutoReportChooseTreesUsingBadData_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoReportChooseTreesByCountingDeaminationMutations_
      != consedResources::pCurrentResources_->bAutoReportChooseTreesByCountingDeaminationMutations_ ) 
       fprintf( pAO, "consed.autoReportChooseTreesByCountingDeaminationMutations: %s\n",
        ( pCP->bAutoReportChooseTreesByCountingDeaminationMutations_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoReportChooseTreesUsingKimura_
      != consedResources::pCurrentResources_->bAutoReportChooseTreesUsingKimura_ ) 
       fprintf( pAO, "consed.autoReportChooseTreesUsingKimura: %s\n",
        ( pCP->bAutoReportChooseTreesUsingKimura_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoReportPrintCrudeChimpHumanMutations_
      != consedResources::pCurrentResources_->bAutoReportPrintCrudeChimpHumanMutations_ ) 
       fprintf( pAO, "consed.autoReportPrintCrudeChimpHumanMutations: %s\n",
        ( pCP->bAutoReportPrintCrudeChimpHumanMutations_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoReportPrintPositionsForGraham_
      != consedResources::pCurrentResources_->bAutoReportPrintPositionsForGraham_ ) 
       fprintf( pAO, "consed.autoReportPrintPositionsForGraham: %s\n",
        ( pCP->bAutoReportPrintPositionsForGraham_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoReportPrintAncestralCpGs_
      != consedResources::pCurrentResources_->bAutoReportPrintAncestralCpGs_ ) 
       fprintf( pAO, "consed.autoReportPrintAncestralCpGs: %s\n",
        ( pCP->bAutoReportPrintAncestralCpGs_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoReportPrintCpGMutations_
      != consedResources::pCurrentResources_->bAutoReportPrintCpGMutations_ ) 
       fprintf( pAO, "consed.autoReportPrintCpGMutations: %s\n",
        ( pCP->bAutoReportPrintCpGMutations_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoReportPrintMutationsWithContext_
      != consedResources::pCurrentResources_->bAutoReportPrintMutationsWithContext_ ) 
       fprintf( pAO, "consed.autoReportPrintMutationsWithContext: %s\n",
        ( pCP->bAutoReportPrintMutationsWithContext_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoReportCountAllMutationsML_
      != consedResources::pCurrentResources_->bAutoReportCountAllMutationsML_ ) 
       fprintf( pAO, "consed.autoReportCountAllMutationsML: %s\n",
        ( pCP->bAutoReportCountAllMutationsML_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoReportCountAllMutations_
      != consedResources::pCurrentResources_->bAutoReportCountAllMutations_ ) 
       fprintf( pAO, "consed.autoReportCountAllMutations: %s\n",
        ( pCP->bAutoReportCountAllMutations_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoReportIgnoreMultipleTrees_
      != consedResources::pCurrentResources_->bAutoReportIgnoreMultipleTrees_ ) 
       fprintf( pAO, "consed.autoReportIgnoreMultipleTrees: %s\n",
        ( pCP->bAutoReportIgnoreMultipleTrees_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoReportCountAcceptableColumnsWithNoneOnLeft_
      != consedResources::pCurrentResources_->bAutoReportCountAcceptableColumnsWithNoneOnLeft_ ) 
       fprintf( pAO, "consed.autoReportCountAcceptableColumnsWithNoneOnLeft: %s\n",
        ( pCP->bAutoReportCountAcceptableColumnsWithNoneOnLeft_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoReportPrintFlankedColumns4_
      != consedResources::pCurrentResources_->bAutoReportPrintFlankedColumns4_ ) 
       fprintf( pAO, "consed.autoReportPrintFlankedColumns4: %s\n",
        ( pCP->bAutoReportPrintFlankedColumns4_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoReportUseAnnotationFormat_
      != consedResources::pCurrentResources_->bAutoReportUseAnnotationFormat_ ) 
       fprintf( pAO, "consed.autoReportUseAnnotationFormat: %s\n",
        ( pCP->bAutoReportUseAnnotationFormat_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoReportPrintFlankedColumns3_
      != consedResources::pCurrentResources_->bAutoReportPrintFlankedColumns3_ ) 
       fprintf( pAO, "consed.autoReportPrintFlankedColumns3: %s\n",
        ( pCP->bAutoReportPrintFlankedColumns3_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoReportPrintFlankedColumns2_
      != consedResources::pCurrentResources_->bAutoReportPrintFlankedColumns2_ ) 
       fprintf( pAO, "consed.autoReportPrintFlankedColumns2: %s\n",
        ( pCP->bAutoReportPrintFlankedColumns2_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoReportPrintFlankedColumns_
      != consedResources::pCurrentResources_->bAutoReportPrintFlankedColumns_ ) 
       fprintf( pAO, "consed.autoReportPrintFlankedColumns: %s\n",
        ( pCP->bAutoReportPrintFlankedColumns_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoReportHighQualitySegmentData_
      != consedResources::pCurrentResources_->bAutoReportHighQualitySegmentData_ ) 
       fprintf( pAO, "consed.autoReportHighQualitySegmentData: %s\n",
        ( pCP->bAutoReportHighQualitySegmentData_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoReportGoodReadsBug_
      != consedResources::pCurrentResources_->bAutoReportGoodReadsBug_ ) 
       fprintf( pAO, "consed.autoReportGoodReadsBug: %s\n",
        ( pCP->bAutoReportGoodReadsBug_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoReportDiscrepancyRateInFlankedRegions_
      != consedResources::pCurrentResources_->bAutoReportDiscrepancyRateInFlankedRegions_ ) 
       fprintf( pAO, "consed.autoReportDiscrepancyRateInFlankedRegions: %s\n",
        ( pCP->bAutoReportDiscrepancyRateInFlankedRegions_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoReportDiscrepancyRateInFlankedRegions2_
      != consedResources::pCurrentResources_->bAutoReportDiscrepancyRateInFlankedRegions2_ ) 
       fprintf( pAO, "consed.autoReportDiscrepancyRateInFlankedRegions2: %s\n",
        ( pCP->bAutoReportDiscrepancyRateInFlankedRegions2_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoReportDiscrepancyRateInFlankedRegions4_
      != consedResources::pCurrentResources_->bAutoReportDiscrepancyRateInFlankedRegions4_ ) 
       fprintf( pAO, "consed.autoReportDiscrepancyRateInFlankedRegions4: %s\n",
        ( pCP->bAutoReportDiscrepancyRateInFlankedRegions4_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoReportDiscrepancyRateInFlankedRegions5_
      != consedResources::pCurrentResources_->bAutoReportDiscrepancyRateInFlankedRegions5_ ) 
       fprintf( pAO, "consed.autoReportDiscrepancyRateInFlankedRegions5: %s\n",
        ( pCP->bAutoReportDiscrepancyRateInFlankedRegions5_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoReportSingleSignalOrQuality_
      != consedResources::pCurrentResources_->bAutoReportSingleSignalOrQuality_ ) 
       fprintf( pAO, "consed.autoReportSingleSignalOrQuality: %s\n",
        ( pCP->bAutoReportSingleSignalOrQuality_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoReportLowQualityBasesInHQS_
      != consedResources::pCurrentResources_->bAutoReportLowQualityBasesInHQS_ ) 
       fprintf( pAO, "consed.autoReportLowQualityBasesInHQS: %s\n",
        ( pCP->bAutoReportLowQualityBasesInHQS_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoReportCompareHQSWithLQS_
      != consedResources::pCurrentResources_->bAutoReportCompareHQSWithLQS_ ) 
       fprintf( pAO, "consed.autoReportCompareHQSWithLQS: %s\n",
        ( pCP->bAutoReportCompareHQSWithLQS_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoReportCountColumnsForGroupsOfSpecies_
      != consedResources::pCurrentResources_->bAutoReportCountColumnsForGroupsOfSpecies_ ) 
       fprintf( pAO, "consed.autoReportCountColumnsForGroupsOfSpecies: %s\n",
        ( pCP->bAutoReportCountColumnsForGroupsOfSpecies_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoReportSingleSignalInfo_
      != consedResources::pCurrentResources_->bAutoReportSingleSignalInfo_ ) 
       fprintf( pAO, "consed.autoReportSingleSignalInfo: %s\n",
        ( pCP->bAutoReportSingleSignalInfo_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoReportSingleSignalInfo2_
      != consedResources::pCurrentResources_->bAutoReportSingleSignalInfo2_ ) 
       fprintf( pAO, "consed.autoReportSingleSignalInfo2: %s\n",
        ( pCP->bAutoReportSingleSignalInfo2_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoReportCompareTopAndBottomStrands_
      != consedResources::pCurrentResources_->bAutoReportCompareTopAndBottomStrands_ ) 
       fprintf( pAO, "consed.autoReportCompareTopAndBottomStrands: %s\n",
        ( pCP->bAutoReportCompareTopAndBottomStrands_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoReportCompareTopAndBottomStrandsNoHuman_
      != consedResources::pCurrentResources_->bAutoReportCompareTopAndBottomStrandsNoHuman_ ) 
       fprintf( pAO, "consed.autoReportCompareTopAndBottomStrandsNoHuman: %s\n",
        ( pCP->bAutoReportCompareTopAndBottomStrandsNoHuman_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoReportCompareTopAndBottomStrands2_
      != consedResources::pCurrentResources_->bAutoReportCompareTopAndBottomStrands2_ ) 
       fprintf( pAO, "consed.autoReportCompareTopAndBottomStrands2: %s\n",
        ( pCP->bAutoReportCompareTopAndBottomStrands2_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoReportCompareTopAndBottomStrands3_
      != consedResources::pCurrentResources_->bAutoReportCompareTopAndBottomStrands3_ ) 
       fprintf( pAO, "consed.autoReportCompareTopAndBottomStrands3: %s\n",
        ( pCP->bAutoReportCompareTopAndBottomStrands3_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoReportCompareTopAndBottomStrands4_
      != consedResources::pCurrentResources_->bAutoReportCompareTopAndBottomStrands4_ ) 
       fprintf( pAO, "consed.autoReportCompareTopAndBottomStrands4: %s\n",
        ( pCP->bAutoReportCompareTopAndBottomStrands4_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->nAutoReportTopStrandPinnedPosition_
      != consedResources::pCurrentResources_->nAutoReportTopStrandPinnedPosition_ ) 
       fprintf( pAO, "consed.autoReportTopStrandPinnedPosition: %d\n",
        pCP->nAutoReportTopStrandPinnedPosition_ );


   if ( consedResources::pDefaultResources_->nAutoReportBottomStrandPinnedPosition_
      != consedResources::pCurrentResources_->nAutoReportBottomStrandPinnedPosition_ ) 
       fprintf( pAO, "consed.autoReportBottomStrandPinnedPosition: %d\n",
        pCP->nAutoReportBottomStrandPinnedPosition_ );


   if ( consedResources::pDefaultResources_->bAutoReportCompareTopAndBottomStrandsWithHuman_
      != consedResources::pCurrentResources_->bAutoReportCompareTopAndBottomStrandsWithHuman_ ) 
       fprintf( pAO, "consed.autoReportCompareTopAndBottomStrandsWithHuman: %s\n",
        ( pCP->bAutoReportCompareTopAndBottomStrandsWithHuman_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoReportPrintLengthsOfAlignedSegmentsOfReads_
      != consedResources::pCurrentResources_->bAutoReportPrintLengthsOfAlignedSegmentsOfReads_ ) 
       fprintf( pAO, "consed.autoReportPrintLengthsOfAlignedSegmentsOfReads: %s\n",
        ( pCP->bAutoReportPrintLengthsOfAlignedSegmentsOfReads_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoReportPrintLengthsOfUnalignedHighQualitySegmentsOfReads_
      != consedResources::pCurrentResources_->bAutoReportPrintLengthsOfUnalignedHighQualitySegmentsOfReads_ ) 
       fprintf( pAO, "consed.autoReportPrintLengthsOfUnalignedHighQualitySegmentsOfReads: %s\n",
        ( pCP->bAutoReportPrintLengthsOfUnalignedHighQualitySegmentsOfReads_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoReportPrintIfReadsAreCorrectlyAligned_
      != consedResources::pCurrentResources_->bAutoReportPrintIfReadsAreCorrectlyAligned_ ) 
       fprintf( pAO, "consed.autoReportPrintIfReadsAreCorrectlyAligned: %s\n",
        ( pCP->bAutoReportPrintIfReadsAreCorrectlyAligned_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoReportCalculateErrorProbabilitiesByComparingPTroPPan_
      != consedResources::pCurrentResources_->bAutoReportCalculateErrorProbabilitiesByComparingPTroPPan_ ) 
       fprintf( pAO, "consed.autoReportCalculateErrorProbabilitiesByComparingPTroPPan: %s\n",
        ( pCP->bAutoReportCalculateErrorProbabilitiesByComparingPTroPPan_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoReportPrintAgreeDisagreeBetweenPairsOfSpecies_
      != consedResources::pCurrentResources_->bAutoReportPrintAgreeDisagreeBetweenPairsOfSpecies_ ) 
       fprintf( pAO, "consed.autoReportPrintAgreeDisagreeBetweenPairsOfSpecies: %s\n",
        ( pCP->bAutoReportPrintAgreeDisagreeBetweenPairsOfSpecies_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoReportPrintAgreeDisagreeBetweenPairsOfSpecies2_
      != consedResources::pCurrentResources_->bAutoReportPrintAgreeDisagreeBetweenPairsOfSpecies2_ ) 
       fprintf( pAO, "consed.autoReportPrintAgreeDisagreeBetweenPairsOfSpecies2: %s\n",
        ( pCP->bAutoReportPrintAgreeDisagreeBetweenPairsOfSpecies2_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoReportFilterSingleSignal_
      != consedResources::pCurrentResources_->bAutoReportFilterSingleSignal_ ) 
       fprintf( pAO, "consed.autoReportFilterSingleSignal: %s\n",
        ( pCP->bAutoReportFilterSingleSignal_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->filAutoReportGoodHitReads_
      != consedResources::pCurrentResources_->filAutoReportGoodHitReads_ ) 
        fprintf( pAO, "consed.autoReportGoodHitReads: %s\n",
              (char*)pCP->filAutoReportGoodHitReads_.data() );


   if ( consedResources::pDefaultResources_->nAutoReportQualityWindowLow_
      != consedResources::pCurrentResources_->nAutoReportQualityWindowLow_ ) 
       fprintf( pAO, "consed.autoReportQualityWindowLow: %d\n",
        pCP->nAutoReportQualityWindowLow_ );


   if ( consedResources::pDefaultResources_->nAutoReportQualityWindowHigh_
      != consedResources::pCurrentResources_->nAutoReportQualityWindowHigh_ ) 
       fprintf( pAO, "consed.autoReportQualityWindowHigh: %d\n",
        pCP->nAutoReportQualityWindowHigh_ );


   if ( consedResources::pDefaultResources_->bAutoReportPrintNumberOfIsolatedPadsForEachSpecies_
      != consedResources::pCurrentResources_->bAutoReportPrintNumberOfIsolatedPadsForEachSpecies_ ) 
       fprintf( pAO, "consed.autoReportPrintNumberOfIsolatedPadsForEachSpecies: %s\n",
        ( pCP->bAutoReportPrintNumberOfIsolatedPadsForEachSpecies_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoReportPrintNumberOfIsolatedPads_
      != consedResources::pCurrentResources_->bAutoReportPrintNumberOfIsolatedPads_ ) 
       fprintf( pAO, "consed.autoReportPrintNumberOfIsolatedPads: %s\n",
        ( pCP->bAutoReportPrintNumberOfIsolatedPads_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->soAutoReportIsolatedPadsOfReadsWithThisPattern_
      != consedResources::pCurrentResources_->soAutoReportIsolatedPadsOfReadsWithThisPattern_ ) 
        fprintf( pAO, "consed.autoReportIsolatedPadsOfReadsWithThisPattern: %s\n",
              (char*)pCP->soAutoReportIsolatedPadsOfReadsWithThisPattern_.data() );


   if ( consedResources::pDefaultResources_->nAutoReportMinNumberOfPerfectlyAlignedBasesBeforeDiscrepancy_
      != consedResources::pCurrentResources_->nAutoReportMinNumberOfPerfectlyAlignedBasesBeforeDiscrepancy_ ) 
       fprintf( pAO, "consed.autoReportMinNumberOfPerfectlyAlignedBasesBeforeDiscrepancy: %d\n",
        pCP->nAutoReportMinNumberOfPerfectlyAlignedBasesBeforeDiscrepancy_ );


   if ( consedResources::pDefaultResources_->nAutoReportMaxSizeOfDiscrepantRegion_
      != consedResources::pCurrentResources_->nAutoReportMaxSizeOfDiscrepantRegion_ ) 
       fprintf( pAO, "consed.autoReportMaxSizeOfDiscrepantRegion: %d\n",
        pCP->nAutoReportMaxSizeOfDiscrepantRegion_ );


   if ( consedResources::pDefaultResources_->nAutoReportSizeOfDiscrepantRegion_
      != consedResources::pCurrentResources_->nAutoReportSizeOfDiscrepantRegion_ ) 
       fprintf( pAO, "consed.autoReportSizeOfDiscrepantRegion: %d\n",
        pCP->nAutoReportSizeOfDiscrepantRegion_ );


   if ( consedResources::pDefaultResources_->bAutoReportPrintMinimumQualityHistogram_
      != consedResources::pCurrentResources_->bAutoReportPrintMinimumQualityHistogram_ ) 
       fprintf( pAO, "consed.autoReportPrintMinimumQualityHistogram: %s\n",
        ( pCP->bAutoReportPrintMinimumQualityHistogram_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoReportPrintDiscrepantRegions_
      != consedResources::pCurrentResources_->bAutoReportPrintDiscrepantRegions_ ) 
       fprintf( pAO, "consed.autoReportPrintDiscrepantRegions: %s\n",
        ( pCP->bAutoReportPrintDiscrepantRegions_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoReportPrintBasesInDiscrepantRegions_
      != consedResources::pCurrentResources_->bAutoReportPrintBasesInDiscrepantRegions_ ) 
       fprintf( pAO, "consed.autoReportPrintBasesInDiscrepantRegions: %s\n",
        ( pCP->bAutoReportPrintBasesInDiscrepantRegions_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->soAutoReportPrintDiscrepantRegionsButIgnoreReadsContainingThis_
      != consedResources::pCurrentResources_->soAutoReportPrintDiscrepantRegionsButIgnoreReadsContainingThis_ ) 
        fprintf( pAO, "consed.autoReportPrintDiscrepantRegionsButIgnoreReadsContainingThis: %s\n",
              (char*)pCP->soAutoReportPrintDiscrepantRegionsButIgnoreReadsContainingThis_.data() );


   if ( consedResources::pDefaultResources_->soAutoReportBackboneReadHasThisStringInIt_
      != consedResources::pCurrentResources_->soAutoReportBackboneReadHasThisStringInIt_ ) 
        fprintf( pAO, "consed.autoReportBackboneReadHasThisStringInIt: %s\n",
              (char*)pCP->soAutoReportBackboneReadHasThisStringInIt_.data() );


   if ( consedResources::pDefaultResources_->bAutoReportPrintDiscrepantRegionsButOnlyIfAboveQualityThreshold_
      != consedResources::pCurrentResources_->bAutoReportPrintDiscrepantRegionsButOnlyIfAboveQualityThreshold_ ) 
       fprintf( pAO, "consed.autoReportPrintDiscrepantRegionsButOnlyIfAboveQualityThreshold: %s\n",
        ( pCP->bAutoReportPrintDiscrepantRegionsButOnlyIfAboveQualityThreshold_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoReportPrintSpeciesAlignment_
      != consedResources::pCurrentResources_->bAutoReportPrintSpeciesAlignment_ ) 
       fprintf( pAO, "consed.autoReportPrintSpeciesAlignment: %s\n",
        ( pCP->bAutoReportPrintSpeciesAlignment_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoReportPrintReadAlignment_
      != consedResources::pCurrentResources_->bAutoReportPrintReadAlignment_ ) 
       fprintf( pAO, "consed.autoReportPrintReadAlignment: %s\n",
        ( pCP->bAutoReportPrintReadAlignment_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->filAutoReportPrintTheseReads_
      != consedResources::pCurrentResources_->filAutoReportPrintTheseReads_ ) 
        fprintf( pAO, "consed.autoReportPrintTheseReads: %s\n",
              (char*)pCP->filAutoReportPrintTheseReads_.data() );


   if ( consedResources::pDefaultResources_->bAutoReportPrintReadPositions_
      != consedResources::pCurrentResources_->bAutoReportPrintReadPositions_ ) 
       fprintf( pAO, "consed.autoReportPrintReadPositions: %s\n",
        ( pCP->bAutoReportPrintReadPositions_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoReportPrintChosenReadName_
      != consedResources::pCurrentResources_->bAutoReportPrintChosenReadName_ ) 
       fprintf( pAO, "consed.autoReportPrintChosenReadName: %s\n",
        ( pCP->bAutoReportPrintChosenReadName_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->nAutoReportNumbersOfCharactersOfChosenReadNameToBePrinted_
      != consedResources::pCurrentResources_->nAutoReportNumbersOfCharactersOfChosenReadNameToBePrinted_ ) 
       fprintf( pAO, "consed.autoReportNumbersOfCharactersOfChosenReadNameToBePrinted: %d\n",
        pCP->nAutoReportNumbersOfCharactersOfChosenReadNameToBePrinted_ );


   if ( consedResources::pDefaultResources_->soAutoReportPrefix_
      != consedResources::pCurrentResources_->soAutoReportPrefix_ ) 
        fprintf( pAO, "consed.autoReportPrefix: %s\n",
              (char*)pCP->soAutoReportPrefix_.data() );


   if ( consedResources::pDefaultResources_->bAutoReportUseOldCriteriaForDeletingColumnsOfPads_
      != consedResources::pCurrentResources_->bAutoReportUseOldCriteriaForDeletingColumnsOfPads_ ) 
       fprintf( pAO, "consed.autoReportUseOldCriteriaForDeletingColumnsOfPads: %s\n",
        ( pCP->bAutoReportUseOldCriteriaForDeletingColumnsOfPads_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoReportDeleteColumnsOfPadsBeforeAdjustingReadQualityValues_
      != consedResources::pCurrentResources_->bAutoReportDeleteColumnsOfPadsBeforeAdjustingReadQualityValues_ ) 
       fprintf( pAO, "consed.autoReportDeleteColumnsOfPadsBeforeAdjustingReadQualityValues: %s\n",
        ( pCP->bAutoReportDeleteColumnsOfPadsBeforeAdjustingReadQualityValues_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->bAutoReportFlankingBasesMustBeSingleSignal_
      != consedResources::pCurrentResources_->bAutoReportFlankingBasesMustBeSingleSignal_ ) 
       fprintf( pAO, "consed.autoReportFlankingBasesMustBeSingleSignal: %s\n",
        ( pCP->bAutoReportFlankingBasesMustBeSingleSignal_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->nAutoReportMinimumQualityOfFlankingBases_
      != consedResources::pCurrentResources_->nAutoReportMinimumQualityOfFlankingBases_ ) 
       fprintf( pAO, "consed.autoReportMinimumQualityOfFlankingBases: %d\n",
        pCP->nAutoReportMinimumQualityOfFlankingBases_ );


   if ( consedResources::pDefaultResources_->bAutoReportFlankingBasesMustBeInHighQualitySegment_
      != consedResources::pCurrentResources_->bAutoReportFlankingBasesMustBeInHighQualitySegment_ ) 
       fprintf( pAO, "consed.autoReportFlankingBasesMustBeInHighQualitySegment: %s\n",
        ( pCP->bAutoReportFlankingBasesMustBeInHighQualitySegment_ ? "true" : "false" ) );


   if ( consedResources::pDefaultResources_->soAutoReportSpecies_
      != consedResources::pCurrentResources_->soAutoReportSpecies_ ) 
        fprintf( pAO, "consed.autoReportSpecies: %s\n",
              (char*)pCP->soAutoReportSpecies_.data() );



    fprintf( pAO, "}\n" );

}