/***************************************************************************** # 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. # #*****************************************************************************/ // consed.printPS if ( resources_.bPrintPS_ != CONDEF->bPrintPS_ ) { fprintf( pFileToWrite, "consed.printPS: %s\n", ( resources_.bPrintPS_ ? "true" : "false" ) ); } // consed.defaultTagType if ( resources_.soDefaultTagType_ != CONDEF->soDefaultTagType_ ) { fprintf( pFileToWrite, "consed.defaultTagType: %s\n", resources_.soDefaultTagType_.data() ); } // consed.defaultTagOnConsensusNotReads if ( resources_.bDefaultTagOnConsensusNotReads_ != CONDEF->bDefaultTagOnConsensusNotReads_ ) { fprintf( pFileToWrite, "consed.defaultTagOnConsensusNotReads: %s\n", ( resources_.bDefaultTagOnConsensusNotReads_ ? "true" : "false" ) ); } // consed.autoFinishMinNumberOfErrorsFixedByAnExp if ( resources_.dAutoFinishMinNumberOfErrorsFixedByAnExp_ != CONDEF->dAutoFinishMinNumberOfErrorsFixedByAnExp_ ) { fprintf( pFileToWrite, "consed.autoFinishMinNumberOfErrorsFixedByAnExp: %f\n", resources_.dAutoFinishMinNumberOfErrorsFixedByAnExp_ ); } // consed.autoFinishRedundancy if ( resources_.dAutoFinishRedundancy_ != CONDEF->dAutoFinishRedundancy_ ) { fprintf( pFileToWrite, "consed.autoFinishRedundancy: %f\n", resources_.dAutoFinishRedundancy_ ); } // consed.autoFinishAverageInsertSize if ( resources_.nAutoFinishAverageInsertSize_ != CONDEF->nAutoFinishAverageInsertSize_ ) { fprintf( pFileToWrite, "consed.autoFinishAverageInsertSize: %d\n", resources_.nAutoFinishAverageInsertSize_ ); } // consed.primersMaxInsertSizeOfASubclone if ( resources_.nPrimersMaxInsertSizeOfASubclone_ != CONDEF->nPrimersMaxInsertSizeOfASubclone_ ) { fprintf( pFileToWrite, "consed.primersMaxInsertSizeOfASubclone: %d\n", resources_.nPrimersMaxInsertSizeOfASubclone_ ); } // consed.primersMaxMeltingTemp if ( resources_.nPrimersMaxMeltingTemp_ != CONDEF->nPrimersMaxMeltingTemp_ ) { fprintf( pFileToWrite, "consed.primersMaxMeltingTemp: %d\n", resources_.nPrimersMaxMeltingTemp_ ); } // consed.primersMaxMeltingTempForPCR if ( resources_.nPrimersMaxMeltingTempForPCR_ != CONDEF->nPrimersMaxMeltingTempForPCR_ ) { fprintf( pFileToWrite, "consed.primersMaxMeltingTempForPCR: %d\n", resources_.nPrimersMaxMeltingTempForPCR_ ); } // consed.primersPickTemplatesForPrimers if ( resources_.bPrimersPickTemplatesForPrimers_ != CONDEF->bPrimersPickTemplatesForPrimers_ ) { fprintf( pFileToWrite, "consed.primersPickTemplatesForPrimers: %s\n", ( resources_.bPrimersPickTemplatesForPrimers_ ? "true" : "false" ) ); } // consed.primersSubcloneFullPathnameOfFileOfSequencesForScreening if ( resources_.soPrimersSubcloneFullPathnameOfFileOfSequencesForScreening_ != CONDEF->soPrimersSubcloneFullPathnameOfFileOfSequencesForScreening_ ) { fprintf( pFileToWrite, "consed.primersSubcloneFullPathnameOfFileOfSequencesForScreening: %s\n", resources_.soPrimersSubcloneFullPathnameOfFileOfSequencesForScreening_.data() ); } // consed.primersCloneFullPathnameOfFileOfSequencesForScreening if ( resources_.soPrimersCloneFullPathnameOfFileOfSequencesForScreening_ != CONDEF->soPrimersCloneFullPathnameOfFileOfSequencesForScreening_ ) { fprintf( pFileToWrite, "consed.primersCloneFullPathnameOfFileOfSequencesForScreening: %s\n", resources_.soPrimersCloneFullPathnameOfFileOfSequencesForScreening_.data() ); } // consed.primersMinMeltingTemp if ( resources_.nPrimersMinMeltingTemp_ != CONDEF->nPrimersMinMeltingTemp_ ) { fprintf( pFileToWrite, "consed.primersMinMeltingTemp: %d\n", resources_.nPrimersMinMeltingTemp_ ); } // consed.primersMinMeltingTempForPCR if ( resources_.nPrimersMinMeltingTempForPCR_ != CONDEF->nPrimersMinMeltingTempForPCR_ ) { fprintf( pFileToWrite, "consed.primersMinMeltingTempForPCR: %d\n", resources_.nPrimersMinMeltingTempForPCR_ ); } // consed.searchFunctionsUseUnalignedEndsOfReads if ( resources_.bSearchFunctionsUseUnalignedEndsOfReads_ != CONDEF->bSearchFunctionsUseUnalignedEndsOfReads_ ) { fprintf( pFileToWrite, "consed.searchFunctionsUseUnalignedEndsOfReads: %s\n", ( resources_.bSearchFunctionsUseUnalignedEndsOfReads_ ? "true" : "false" ) ); } // consed.searchFunctionsUseLowQualityEndsOfReads if ( resources_.bSearchFunctionsUseLowQualityEndsOfReads_ != CONDEF->bSearchFunctionsUseLowQualityEndsOfReads_ ) { fprintf( pFileToWrite, "consed.searchFunctionsUseLowQualityEndsOfReads: %s\n", ( resources_.bSearchFunctionsUseLowQualityEndsOfReads_ ? "true" : "false" ) ); } // consed.inexactSearchForStringMaxPerCentMismatch if ( resources_.nInexactSearchForStringMaxPerCentMismatch_ != CONDEF->nInexactSearchForStringMaxPerCentMismatch_ ) { fprintf( pFileToWrite, "consed.inexactSearchForStringMaxPerCentMismatch: %d\n", resources_.nInexactSearchForStringMaxPerCentMismatch_ ); } // consed.onlyAllowOneReadWriteConsedAtATime if ( resources_.bOnlyAllowOneReadWriteConsedAtATime_ != CONDEF->bOnlyAllowOneReadWriteConsedAtATime_ ) { fprintf( pFileToWrite, "consed.onlyAllowOneReadWriteConsedAtATime: %s\n", ( resources_.bOnlyAllowOneReadWriteConsedAtATime_ ? "true" : "false" ) ); } // consed.autoFinishAllowHighQualityDiscrepanciesInTemplateIfConsistentForwardReversePair if ( resources_.bAutoFinishAllowHighQualityDiscrepanciesInTemplateIfConsistentForwardReversePair_ != CONDEF->bAutoFinishAllowHighQualityDiscrepanciesInTemplateIfConsistentForwardReversePair_ ) { fprintf( pFileToWrite, "consed.autoFinishAllowHighQualityDiscrepanciesInTemplateIfConsistentForwardReversePair: %s\n", ( resources_.bAutoFinishAllowHighQualityDiscrepanciesInTemplateIfConsistentForwardReversePair_ ? "true" : "false" ) ); } // consed.printWindowCommand if ( resources_.soPrintWindowCommand_ != CONDEF->soPrintWindowCommand_ ) { fprintf( pFileToWrite, "consed.printWindowCommand: %s\n", resources_.soPrintWindowCommand_.data() ); } // consed.fileOfTagTypes if ( resources_.filFileOfTagTypes_ != CONDEF->filFileOfTagTypes_ ) { fprintf( pFileToWrite, "consed.fileOfTagTypes: %s\n", resources_.filFileOfTagTypes_.data() ); } // consed.assemblyViewShowConsistentFwdRevPairs if ( resources_.bAssemblyViewShowConsistentFwdRevPairs_ != CONDEF->bAssemblyViewShowConsistentFwdRevPairs_ ) { fprintf( pFileToWrite, "consed.assemblyViewShowConsistentFwdRevPairs: %s\n", ( resources_.bAssemblyViewShowConsistentFwdRevPairs_ ? "true" : "false" ) ); } // consed.assemblyViewShowConsistentFwdRevPairDepth if ( resources_.bAssemblyViewShowConsistentFwdRevPairDepth_ != CONDEF->bAssemblyViewShowConsistentFwdRevPairDepth_ ) { fprintf( pFileToWrite, "consed.assemblyViewShowConsistentFwdRevPairDepth: %s\n", ( resources_.bAssemblyViewShowConsistentFwdRevPairDepth_ ? "true" : "false" ) ); } // consed.assemblyViewShowConsistentFwdRevPairsBetweenDifferentScaffolds if ( resources_.bAssemblyViewShowConsistentFwdRevPairsBetweenDifferentScaffolds_ != CONDEF->bAssemblyViewShowConsistentFwdRevPairsBetweenDifferentScaffolds_ ) { fprintf( pFileToWrite, "consed.assemblyViewShowConsistentFwdRevPairsBetweenDifferentScaffolds: %s\n", ( resources_.bAssemblyViewShowConsistentFwdRevPairsBetweenDifferentScaffolds_ ? "true" : "false" ) ); } // consed.assemblyViewShowLegsOnSquaresForConsistentFwdRevPairs if ( resources_.bAssemblyViewShowLegsOnSquaresForConsistentFwdRevPairs_ != CONDEF->bAssemblyViewShowLegsOnSquaresForConsistentFwdRevPairs_ ) { fprintf( pFileToWrite, "consed.assemblyViewShowLegsOnSquaresForConsistentFwdRevPairs: %s\n", ( resources_.bAssemblyViewShowLegsOnSquaresForConsistentFwdRevPairs_ ? "true" : "false" ) ); } // consed.assemblyViewShowGapSpanningFwdRevPairs if ( resources_.bAssemblyViewShowGapSpanningFwdRevPairs_ != CONDEF->bAssemblyViewShowGapSpanningFwdRevPairs_ ) { fprintf( pFileToWrite, "consed.assemblyViewShowGapSpanningFwdRevPairs: %s\n", ( resources_.bAssemblyViewShowGapSpanningFwdRevPairs_ ? "true" : "false" ) ); } // consed.assemblyViewShowWhichInconsistentFwdRevPairs if ( resources_.soAssemblyViewShowWhichInconsistentFwdRevPairs_ != CONDEF->soAssemblyViewShowWhichInconsistentFwdRevPairs_ ) { fprintf( pFileToWrite, "consed.assemblyViewShowWhichInconsistentFwdRevPairs: %s\n", resources_.soAssemblyViewShowWhichInconsistentFwdRevPairs_.data() ); } // consed.assemblyViewShowReadDepth if ( resources_.bAssemblyViewShowReadDepth_ != CONDEF->bAssemblyViewShowReadDepth_ ) { fprintf( pFileToWrite, "consed.assemblyViewShowReadDepth: %s\n", ( resources_.bAssemblyViewShowReadDepth_ ? "true" : "false" ) ); } // consed.assemblyViewShowMultipleHighQualityDiscrepancies if ( resources_.bAssemblyViewShowMultipleHighQualityDiscrepancies_ != CONDEF->bAssemblyViewShowMultipleHighQualityDiscrepancies_ ) { fprintf( pFileToWrite, "consed.assemblyViewShowMultipleHighQualityDiscrepancies: %s\n", ( resources_.bAssemblyViewShowMultipleHighQualityDiscrepancies_ ? "true" : "false" ) ); } // consed.assemblyViewShowRestrictionDigestCutSites if ( resources_.bAssemblyViewShowRestrictionDigestCutSites_ != CONDEF->bAssemblyViewShowRestrictionDigestCutSites_ ) { fprintf( pFileToWrite, "consed.assemblyViewShowRestrictionDigestCutSites: %s\n", ( resources_.bAssemblyViewShowRestrictionDigestCutSites_ ? "true" : "false" ) ); } // consed.assemblyViewFilterSequenceMatchesBySize if ( resources_.bAssemblyViewFilterSequenceMatchesBySize_ != CONDEF->bAssemblyViewFilterSequenceMatchesBySize_ ) { fprintf( pFileToWrite, "consed.assemblyViewFilterSequenceMatchesBySize: %s\n", ( resources_.bAssemblyViewFilterSequenceMatchesBySize_ ? "true" : "false" ) ); } // consed.assemblyViewSequenceMatchesMinSize if ( resources_.nAssemblyViewSequenceMatchesMinSize_ != CONDEF->nAssemblyViewSequenceMatchesMinSize_ ) { fprintf( pFileToWrite, "consed.assemblyViewSequenceMatchesMinSize: %d\n", resources_.nAssemblyViewSequenceMatchesMinSize_ ); } // consed.assemblyViewSequenceMatchesMaxSize if ( resources_.nAssemblyViewSequenceMatchesMaxSize_ != CONDEF->nAssemblyViewSequenceMatchesMaxSize_ ) { fprintf( pFileToWrite, "consed.assemblyViewSequenceMatchesMaxSize: %d\n", resources_.nAssemblyViewSequenceMatchesMaxSize_ ); } // consed.assemblyViewAutomaticallyStartWithConsed if ( resources_.bAssemblyViewAutomaticallyStartWithConsed_ != CONDEF->bAssemblyViewAutomaticallyStartWithConsed_ ) { fprintf( pFileToWrite, "consed.assemblyViewAutomaticallyStartWithConsed: %s\n", ( resources_.bAssemblyViewAutomaticallyStartWithConsed_ ? "true" : "false" ) ); } // consed.assemblyViewDisplayTheseTagTypesOnTheseLines if ( resources_.soAssemblyViewDisplayTheseTagTypesOnTheseLines_ != CONDEF->soAssemblyViewDisplayTheseTagTypesOnTheseLines_ ) { fprintf( pFileToWrite, "consed.assemblyViewDisplayTheseTagTypesOnTheseLines: %s\n", resources_.soAssemblyViewDisplayTheseTagTypesOnTheseLines_.data() ); } // consed.assemblyViewShowTags if ( resources_.bAssemblyViewShowTags_ != CONDEF->bAssemblyViewShowTags_ ) { fprintf( pFileToWrite, "consed.assemblyViewShowTags: %s\n", ( resources_.bAssemblyViewShowTags_ ? "true" : "false" ) ); } // consed.autoEditRecalculateHighQualitySegmentsOfReads if ( resources_.bAutoEditRecalculateHighQualitySegmentsOfReads_ != CONDEF->bAutoEditRecalculateHighQualitySegmentsOfReads_ ) { fprintf( pFileToWrite, "consed.autoEditRecalculateHighQualitySegmentsOfReads: %s\n", ( resources_.bAutoEditRecalculateHighQualitySegmentsOfReads_ ? "true" : "false" ) ); } // consed.autoEditConvertCloneEndBasesToXs if ( resources_.bAutoEditConvertCloneEndBasesToXs_ != CONDEF->bAutoEditConvertCloneEndBasesToXs_ ) { fprintf( pFileToWrite, "consed.autoEditConvertCloneEndBasesToXs: %s\n", ( resources_.bAutoEditConvertCloneEndBasesToXs_ ? "true" : "false" ) ); } // consed.autoEditTellPhrapNotToOverlapMultiplyDiscrepantReads if ( resources_.bAutoEditTellPhrapNotToOverlapMultiplyDiscrepantReads_ != CONDEF->bAutoEditTellPhrapNotToOverlapMultiplyDiscrepantReads_ ) { fprintf( pFileToWrite, "consed.autoEditTellPhrapNotToOverlapMultiplyDiscrepantReads: %s\n", ( resources_.bAutoEditTellPhrapNotToOverlapMultiplyDiscrepantReads_ ? "true" : "false" ) ); } // consed.autoEditTagEditableLowConsensusQualityRegions if ( resources_.bAutoEditTagEditableLowConsensusQualityRegions_ != CONDEF->bAutoEditTagEditableLowConsensusQualityRegions_ ) { fprintf( pFileToWrite, "consed.autoEditTagEditableLowConsensusQualityRegions: %s\n", ( resources_.bAutoEditTagEditableLowConsensusQualityRegions_ ? "true" : "false" ) ); } // consed.autoEditMakeFakeRead if ( resources_.bAutoEditMakeFakeRead_ != CONDEF->bAutoEditMakeFakeRead_ ) { fprintf( pFileToWrite, "consed.autoEditMakeFakeRead: %s\n", ( resources_.bAutoEditMakeFakeRead_ ? "true" : "false" ) ); } // consed.autoEditMakeFakeReadFromRead1 if ( resources_.soAutoEditMakeFakeReadFromRead1_ != CONDEF->soAutoEditMakeFakeReadFromRead1_ ) { fprintf( pFileToWrite, "consed.autoEditMakeFakeReadFromRead1: %s\n", resources_.soAutoEditMakeFakeReadFromRead1_.data() ); } // consed.autoEditMakeFakeReadFromRead2 if ( resources_.soAutoEditMakeFakeReadFromRead2_ != CONDEF->soAutoEditMakeFakeReadFromRead2_ ) { fprintf( pFileToWrite, "consed.autoEditMakeFakeReadFromRead2: %s\n", resources_.soAutoEditMakeFakeReadFromRead2_.data() ); } // consed.autoEditMakeFakeReadName if ( resources_.soAutoEditMakeFakeReadName_ != CONDEF->soAutoEditMakeFakeReadName_ ) { fprintf( pFileToWrite, "consed.autoEditMakeFakeReadName: %s\n", resources_.soAutoEditMakeFakeReadName_.data() ); } // consed.autoEditMakeFakeReadFastaFilename if ( resources_.filAutoEditMakeFakeReadFastaFilename_ != CONDEF->filAutoEditMakeFakeReadFastaFilename_ ) { fprintf( pFileToWrite, "consed.autoEditMakeFakeReadFastaFilename: %s\n", resources_.filAutoEditMakeFakeReadFastaFilename_.data() ); } // consed.autoEditMergeAssembly if ( resources_.bAutoEditMergeAssembly_ != CONDEF->bAutoEditMergeAssembly_ ) { fprintf( pFileToWrite, "consed.autoEditMergeAssembly: %s\n", ( resources_.bAutoEditMergeAssembly_ ? "true" : "false" ) ); } // consed.autoEditSecondaryAceFile if ( resources_.filAutoEditSecondaryAceFile_ != CONDEF->filAutoEditSecondaryAceFile_ ) { fprintf( pFileToWrite, "consed.autoEditSecondaryAceFile: %s\n", resources_.filAutoEditSecondaryAceFile_.data() ); } // consed.autoEditFixRunsInConsensus if ( resources_.bAutoEditFixRunsInConsensus_ != CONDEF->bAutoEditFixRunsInConsensus_ ) { fprintf( pFileToWrite, "consed.autoEditFixRunsInConsensus: %s\n", ( resources_.bAutoEditFixRunsInConsensus_ ? "true" : "false" ) ); } // consed.showAllTracesJustShowGoodTraces if ( resources_.bShowAllTracesJustShowGoodTraces_ != CONDEF->bShowAllTracesJustShowGoodTraces_ ) { fprintf( pFileToWrite, "consed.showAllTracesJustShowGoodTraces: %s\n", ( resources_.bShowAllTracesJustShowGoodTraces_ ? "true" : "false" ) ); } // consed.addAlignedSequenceQualityOfBases if ( resources_.nAddAlignedSequenceQualityOfBases_ != CONDEF->nAddAlignedSequenceQualityOfBases_ ) { fprintf( pFileToWrite, "consed.addAlignedSequenceQualityOfBases: %d\n", resources_.nAddAlignedSequenceQualityOfBases_ ); } // consed.makeLightBackgroundInAlignedReadsWindowAndTracesWindow if ( resources_.bMakeLightBackgroundInAlignedReadsWindowAndTracesWindow_ != CONDEF->bMakeLightBackgroundInAlignedReadsWindowAndTracesWindow_ ) { fprintf( pFileToWrite, "consed.makeLightBackgroundInAlignedReadsWindowAndTracesWindow: %s\n", ( resources_.bMakeLightBackgroundInAlignedReadsWindowAndTracesWindow_ ? "true" : "false" ) ); } // consed.putVerticalLineAtCursor if ( resources_.bPutVerticalLineAtCursor_ != CONDEF->bPutVerticalLineAtCursor_ ) { fprintf( pFileToWrite, "consed.putVerticalLineAtCursor: %s\n", ( resources_.bPutVerticalLineAtCursor_ ? "true" : "false" ) ); } // consed.putHorizontalLineAtCursor if ( resources_.bPutHorizontalLineAtCursor_ != CONDEF->bPutHorizontalLineAtCursor_ ) { fprintf( pFileToWrite, "consed.putHorizontalLineAtCursor: %s\n", ( resources_.bPutHorizontalLineAtCursor_ ? "true" : "false" ) ); } // consed.highlightedReadsFile if ( resources_.filHighlightedReadsFile_ != CONDEF->filHighlightedReadsFile_ ) { fprintf( pFileToWrite, "consed.highlightedReadsFile: %s\n", resources_.filHighlightedReadsFile_.data() ); } // consed.autoReportPrintReadNamesInRegion if ( resources_.bAutoReportPrintReadNamesInRegion_ != CONDEF->bAutoReportPrintReadNamesInRegion_ ) { fprintf( pFileToWrite, "consed.autoReportPrintReadNamesInRegion: %s\n", ( resources_.bAutoReportPrintReadNamesInRegion_ ? "true" : "false" ) ); } // consed.autoReportPrintReadNamesInRegionContig if ( resources_.soAutoReportPrintReadNamesInRegionContig_ != CONDEF->soAutoReportPrintReadNamesInRegionContig_ ) { fprintf( pFileToWrite, "consed.autoReportPrintReadNamesInRegionContig: %s\n", resources_.soAutoReportPrintReadNamesInRegionContig_.data() ); } // consed.autoReportPrintReadNamesInRegionLeftPos if ( resources_.nAutoReportPrintReadNamesInRegionLeftPos_ != CONDEF->nAutoReportPrintReadNamesInRegionLeftPos_ ) { fprintf( pFileToWrite, "consed.autoReportPrintReadNamesInRegionLeftPos: %d\n", resources_.nAutoReportPrintReadNamesInRegionLeftPos_ ); } // consed.autoReportPrintReadNamesInRegionRightPos if ( resources_.nAutoReportPrintReadNamesInRegionRightPos_ != CONDEF->nAutoReportPrintReadNamesInRegionRightPos_ ) { fprintf( pFileToWrite, "consed.autoReportPrintReadNamesInRegionRightPos: %d\n", resources_.nAutoReportPrintReadNamesInRegionRightPos_ ); } // consed.autoReportPrintHighlyDiscrepantRegions if ( resources_.bAutoReportPrintHighlyDiscrepantRegions_ != CONDEF->bAutoReportPrintHighlyDiscrepantRegions_ ) { fprintf( pFileToWrite, "consed.autoReportPrintHighlyDiscrepantRegions: %s\n", ( resources_.bAutoReportPrintHighlyDiscrepantRegions_ ? "true" : "false" ) ); } // consed.autoReportPrintScaffolds if ( resources_.bAutoReportPrintScaffolds_ != CONDEF->bAutoReportPrintScaffolds_ ) { fprintf( pFileToWrite, "consed.autoReportPrintScaffolds: %s\n", ( resources_.bAutoReportPrintScaffolds_ ? "true" : "false" ) ); } // consed.numberUnpaddedConsensusAtUserDefined if ( resources_.bNumberUnpaddedConsensusAtUserDefined_ != CONDEF->bNumberUnpaddedConsensusAtUserDefined_ ) { fprintf( pFileToWrite, "consed.numberUnpaddedConsensusAtUserDefined: %s\n", ( resources_.bNumberUnpaddedConsensusAtUserDefined_ ? "true" : "false" ) ); } // consed.autoReportPrintHighQualityDiscrepancies if ( resources_.bAutoReportPrintHighQualityDiscrepancies_ != CONDEF->bAutoReportPrintHighQualityDiscrepancies_ ) { fprintf( pFileToWrite, "consed.autoReportPrintHighQualityDiscrepancies: %s\n", ( resources_.bAutoReportPrintHighQualityDiscrepancies_ ? "true" : "false" ) ); } // consed.autoReportHighQualityDiscrepanciesExcludeCompressionOrG_dropoutTags if ( resources_.bAutoReportHighQualityDiscrepanciesExcludeCompressionOrG_dropoutTags_ != CONDEF->bAutoReportHighQualityDiscrepanciesExcludeCompressionOrG_dropoutTags_ ) { fprintf( pFileToWrite, "consed.autoReportHighQualityDiscrepanciesExcludeCompressionOrG_dropoutTags: %s\n", ( resources_.bAutoReportHighQualityDiscrepanciesExcludeCompressionOrG_dropoutTags_ ? "true" : "false" ) ); } // consed.autoReportHighQualityDiscrepanciesExcludeMostPads if ( resources_.bAutoReportHighQualityDiscrepanciesExcludeMostPads_ != CONDEF->bAutoReportHighQualityDiscrepanciesExcludeMostPads_ ) { fprintf( pFileToWrite, "consed.autoReportHighQualityDiscrepanciesExcludeMostPads: %s\n", ( resources_.bAutoReportHighQualityDiscrepanciesExcludeMostPads_ ? "true" : "false" ) ); } // consed.autoReportPrintLowConsensusQualityRegions if ( resources_.bAutoReportPrintLowConsensusQualityRegions_ != CONDEF->bAutoReportPrintLowConsensusQualityRegions_ ) { fprintf( pFileToWrite, "consed.autoReportPrintLowConsensusQualityRegions: %s\n", ( resources_.bAutoReportPrintLowConsensusQualityRegions_ ? "true" : "false" ) ); } // consed.autoReportPrintSingleSubcloneRegions if ( resources_.bAutoReportPrintSingleSubcloneRegions_ != CONDEF->bAutoReportPrintSingleSubcloneRegions_ ) { fprintf( pFileToWrite, "consed.autoReportPrintSingleSubcloneRegions: %s\n", ( resources_.bAutoReportPrintSingleSubcloneRegions_ ? "true" : "false" ) ); } // consed.autoReportPrintSingleStrandedRegions if ( resources_.bAutoReportPrintSingleStrandedRegions_ != CONDEF->bAutoReportPrintSingleStrandedRegions_ ) { fprintf( pFileToWrite, "consed.autoReportPrintSingleStrandedRegions: %s\n", ( resources_.bAutoReportPrintSingleStrandedRegions_ ? "true" : "false" ) ); } // consed.autoReportPrintLinkingForwardReversePairs if ( resources_.bAutoReportPrintLinkingForwardReversePairs_ != CONDEF->bAutoReportPrintLinkingForwardReversePairs_ ) { fprintf( pFileToWrite, "consed.autoReportPrintLinkingForwardReversePairs: %s\n", ( resources_.bAutoReportPrintLinkingForwardReversePairs_ ? "true" : "false" ) ); } // consed.autoReportPrintFilteredInconsistentForwardReversePairs if ( resources_.bAutoReportPrintFilteredInconsistentForwardReversePairs_ != CONDEF->bAutoReportPrintFilteredInconsistentForwardReversePairs_ ) { fprintf( pFileToWrite, "consed.autoReportPrintFilteredInconsistentForwardReversePairs: %s\n", ( resources_.bAutoReportPrintFilteredInconsistentForwardReversePairs_ ? "true" : "false" ) ); } // consed.autoReportPrintAssemblySummary if ( resources_.bAutoReportPrintAssemblySummary_ != CONDEF->bAutoReportPrintAssemblySummary_ ) { fprintf( pFileToWrite, "consed.autoReportPrintAssemblySummary: %s\n", ( resources_.bAutoReportPrintAssemblySummary_ ? "true" : "false" ) ); } // consed.showAllTracesDoNotShowTraceIfTheseTagsPresent if ( resources_.soShowAllTracesDoNotShowTraceIfTheseTagsPresent_ != CONDEF->soShowAllTracesDoNotShowTraceIfTheseTagsPresent_ ) { fprintf( pFileToWrite, "consed.showAllTracesDoNotShowTraceIfTheseTagsPresent: %s\n", resources_.soShowAllTracesDoNotShowTraceIfTheseTagsPresent_.data() ); } // consed.nameOfFakeJoiningReadsIncludesAceFileName if ( resources_.bNameOfFakeJoiningReadsIncludesAceFileName_ != CONDEF->bNameOfFakeJoiningReadsIncludesAceFileName_ ) { fprintf( pFileToWrite, "consed.nameOfFakeJoiningReadsIncludesAceFileName: %s\n", ( resources_.bNameOfFakeJoiningReadsIncludesAceFileName_ ? "true" : "false" ) ); } // consed.whenUserScrollsOffWindowMillisecondsBetweenScrolling if ( resources_.nWhenUserScrollsOffWindowMillisecondsBetweenScrolling_ != CONDEF->nWhenUserScrollsOffWindowMillisecondsBetweenScrolling_ ) { fprintf( pFileToWrite, "consed.whenUserScrollsOffWindowMillisecondsBetweenScrolling: %d\n", resources_.nWhenUserScrollsOffWindowMillisecondsBetweenScrolling_ ); } // consed.whenUserScrollsOffWindowBasesToScrollEachTime if ( resources_.nWhenUserScrollsOffWindowBasesToScrollEachTime_ != CONDEF->nWhenUserScrollsOffWindowBasesToScrollEachTime_ ) { fprintf( pFileToWrite, "consed.whenUserScrollsOffWindowBasesToScrollEachTime: %d\n", resources_.nWhenUserScrollsOffWindowBasesToScrollEachTime_ ); } // consed.compareContigsUseBandedRatherThanFullSmithWaterman if ( resources_.bCompareContigsUseBandedRatherThanFullSmithWaterman_ != CONDEF->bCompareContigsUseBandedRatherThanFullSmithWaterman_ ) { fprintf( pFileToWrite, "consed.compareContigsUseBandedRatherThanFullSmithWaterman: %s\n", ( resources_.bCompareContigsUseBandedRatherThanFullSmithWaterman_ ? "true" : "false" ) ); } // consed.compareContigsBandSize if ( resources_.nCompareContigsBandSize_ != CONDEF->nCompareContigsBandSize_ ) { fprintf( pFileToWrite, "consed.compareContigsBandSize: %d\n", resources_.nCompareContigsBandSize_ ); } // consed.assemblyViewShowFwdRevPairDepthsInRedIfOnlyThisMany if ( resources_.nAssemblyViewShowFwdRevPairDepthsInRedIfOnlyThisMany_ != CONDEF->nAssemblyViewShowFwdRevPairDepthsInRedIfOnlyThisMany_ ) { fprintf( pFileToWrite, "consed.assemblyViewShowFwdRevPairDepthsInRedIfOnlyThisMany: %d\n", resources_.nAssemblyViewShowFwdRevPairDepthsInRedIfOnlyThisMany_ ); } // consed.assemblyViewShowSequenceMatches if ( resources_.bAssemblyViewShowSequenceMatches_ != CONDEF->bAssemblyViewShowSequenceMatches_ ) { fprintf( pFileToWrite, "consed.assemblyViewShowSequenceMatches: %s\n", ( resources_.bAssemblyViewShowSequenceMatches_ ? "true" : "false" ) ); } // consed.assemblyViewOKToShowSequenceMatchesBetweenContigs if ( resources_.bAssemblyViewOKToShowSequenceMatchesBetweenContigs_ != CONDEF->bAssemblyViewOKToShowSequenceMatchesBetweenContigs_ ) { fprintf( pFileToWrite, "consed.assemblyViewOKToShowSequenceMatchesBetweenContigs: %s\n", ( resources_.bAssemblyViewOKToShowSequenceMatchesBetweenContigs_ ? "true" : "false" ) ); } // consed.assemblyViewOKToShowSequenceMatchesWithinContigs if ( resources_.bAssemblyViewOKToShowSequenceMatchesWithinContigs_ != CONDEF->bAssemblyViewOKToShowSequenceMatchesWithinContigs_ ) { fprintf( pFileToWrite, "consed.assemblyViewOKToShowSequenceMatchesWithinContigs: %s\n", ( resources_.bAssemblyViewOKToShowSequenceMatchesWithinContigs_ ? "true" : "false" ) ); } // consed.assemblyViewOKToShowDirectSequenceMatches if ( resources_.bAssemblyViewOKToShowDirectSequenceMatches_ != CONDEF->bAssemblyViewOKToShowDirectSequenceMatches_ ) { fprintf( pFileToWrite, "consed.assemblyViewOKToShowDirectSequenceMatches: %s\n", ( resources_.bAssemblyViewOKToShowDirectSequenceMatches_ ? "true" : "false" ) ); } // consed.assemblyViewOKToShowInvertedSequenceMatches if ( resources_.bAssemblyViewOKToShowInvertedSequenceMatches_ != CONDEF->bAssemblyViewOKToShowInvertedSequenceMatches_ ) { fprintf( pFileToWrite, "consed.assemblyViewOKToShowInvertedSequenceMatches: %s\n", ( resources_.bAssemblyViewOKToShowInvertedSequenceMatches_ ? "true" : "false" ) ); } // consed.assemblyViewOnlyShowSequenceMatchesToAParticularRegion if ( resources_.bAssemblyViewOnlyShowSequenceMatchesToAParticularRegion_ != CONDEF->bAssemblyViewOnlyShowSequenceMatchesToAParticularRegion_ ) { fprintf( pFileToWrite, "consed.assemblyViewOnlyShowSequenceMatchesToAParticularRegion: %s\n", ( resources_.bAssemblyViewOnlyShowSequenceMatchesToAParticularRegion_ ? "true" : "false" ) ); } // consed.assemblyViewOnlyShowSequenceMatchesToThisContig if ( resources_.soAssemblyViewOnlyShowSequenceMatchesToThisContig_ != CONDEF->soAssemblyViewOnlyShowSequenceMatchesToThisContig_ ) { fprintf( pFileToWrite, "consed.assemblyViewOnlyShowSequenceMatchesToThisContig: %s\n", resources_.soAssemblyViewOnlyShowSequenceMatchesToThisContig_.data() ); } // consed.assemblyViewOnlyShowSequenceMatchesToThisRegionLeft if ( resources_.nAssemblyViewOnlyShowSequenceMatchesToThisRegionLeft_ != CONDEF->nAssemblyViewOnlyShowSequenceMatchesToThisRegionLeft_ ) { fprintf( pFileToWrite, "consed.assemblyViewOnlyShowSequenceMatchesToThisRegionLeft: %d\n", resources_.nAssemblyViewOnlyShowSequenceMatchesToThisRegionLeft_ ); } // consed.assemblyViewOnlyShowSequenceMatchesToThisRegionRight if ( resources_.nAssemblyViewOnlyShowSequenceMatchesToThisRegionRight_ != CONDEF->nAssemblyViewOnlyShowSequenceMatchesToThisRegionRight_ ) { fprintf( pFileToWrite, "consed.assemblyViewOnlyShowSequenceMatchesToThisRegionRight: %d\n", resources_.nAssemblyViewOnlyShowSequenceMatchesToThisRegionRight_ ); } // consed.assemblyViewOnlyShowSequenceMatchesToEndsOfContigs if ( resources_.bAssemblyViewOnlyShowSequenceMatchesToEndsOfContigs_ != CONDEF->bAssemblyViewOnlyShowSequenceMatchesToEndsOfContigs_ ) { fprintf( pFileToWrite, "consed.assemblyViewOnlyShowSequenceMatchesToEndsOfContigs: %s\n", ( resources_.bAssemblyViewOnlyShowSequenceMatchesToEndsOfContigs_ ? "true" : "false" ) ); } // consed.assemblyViewOnlyShowSequenceMatchesToEndsOfContigsThisFar if ( resources_.nAssemblyViewOnlyShowSequenceMatchesToEndsOfContigsThisFar_ != CONDEF->nAssemblyViewOnlyShowSequenceMatchesToEndsOfContigsThisFar_ ) { fprintf( pFileToWrite, "consed.assemblyViewOnlyShowSequenceMatchesToEndsOfContigsThisFar: %d\n", resources_.nAssemblyViewOnlyShowSequenceMatchesToEndsOfContigsThisFar_ ); } // consed.defaultReadPrefix if ( resources_.soDefaultReadPrefix_ != CONDEF->soDefaultReadPrefix_ ) { fprintf( pFileToWrite, "consed.defaultReadPrefix: %s\n", resources_.soDefaultReadPrefix_.data() ); } // consed.readPrefixesFile if ( resources_.filReadPrefixesFile_ != CONDEF->filReadPrefixesFile_ ) { fprintf( pFileToWrite, "consed.readPrefixesFile: %s\n", resources_.filReadPrefixesFile_.data() ); } // consed.maxCharsDisplayedForReadPrefix if ( resources_.nMaxCharsDisplayedForReadPrefix_ != CONDEF->nMaxCharsDisplayedForReadPrefix_ ) { fprintf( pFileToWrite, "consed.maxCharsDisplayedForReadPrefix: %d\n", resources_.nMaxCharsDisplayedForReadPrefix_ ); } // consed.autoFinishDoNotDoPCRIfThisManyAvailableGapSpanningTemplates if ( resources_.nAutoFinishDoNotDoPCRIfThisManyAvailableGapSpanningTemplates_ != CONDEF->nAutoFinishDoNotDoPCRIfThisManyAvailableGapSpanningTemplates_ ) { fprintf( pFileToWrite, "consed.autoFinishDoNotDoPCRIfThisManyAvailableGapSpanningTemplates: %d\n", resources_.nAutoFinishDoNotDoPCRIfThisManyAvailableGapSpanningTemplates_ ); } // consed.autoFinishDoNotDoUnorientedPCRIfThisManyOrMoreUnorientedPCRReactions if ( resources_.nAutoFinishDoNotDoUnorientedPCRIfThisManyOrMoreUnorientedPCRReactions_ != CONDEF->nAutoFinishDoNotDoUnorientedPCRIfThisManyOrMoreUnorientedPCRReactions_ ) { fprintf( pFileToWrite, "consed.autoFinishDoNotDoUnorientedPCRIfThisManyOrMoreUnorientedPCRReactions: %d\n", resources_.nAutoFinishDoNotDoUnorientedPCRIfThisManyOrMoreUnorientedPCRReactions_ ); } // consed.autoFinishDoNotDoOrientedPCRIfGapSizeLargerThanThis if ( resources_.nAutoFinishDoNotDoOrientedPCRIfGapSizeLargerThanThis_ != CONDEF->nAutoFinishDoNotDoOrientedPCRIfGapSizeLargerThanThis_ ) { fprintf( pFileToWrite, "consed.autoFinishDoNotDoOrientedPCRIfGapSizeLargerThanThis: %d\n", resources_.nAutoFinishDoNotDoOrientedPCRIfGapSizeLargerThanThis_ ); } // consed.autoFinishDoNotDoPCRIfEndIsExtendedByReads if ( resources_.bAutoFinishDoNotDoPCRIfEndIsExtendedByReads_ != CONDEF->bAutoFinishDoNotDoPCRIfEndIsExtendedByReads_ ) { fprintf( pFileToWrite, "consed.autoFinishDoNotDoPCRIfEndIsExtendedByReads: %s\n", ( resources_.bAutoFinishDoNotDoPCRIfEndIsExtendedByReads_ ? "true" : "false" ) ); } // consed.autoFinishMaxAcceptableErrorsPerMegabase if ( resources_.nAutoFinishMaxAcceptableErrorsPerMegabase_ != CONDEF->nAutoFinishMaxAcceptableErrorsPerMegabase_ ) { fprintf( pFileToWrite, "consed.autoFinishMaxAcceptableErrorsPerMegabase: %d\n", resources_.nAutoFinishMaxAcceptableErrorsPerMegabase_ ); } // consed.autoFinishIfNotEnoughFwdRevPairsUseThisPerCentOfInsertSize if ( resources_.nAutoFinishIfNotEnoughFwdRevPairsUseThisPerCentOfInsertSize_ != CONDEF->nAutoFinishIfNotEnoughFwdRevPairsUseThisPerCentOfInsertSize_ ) { fprintf( pFileToWrite, "consed.autoFinishIfNotEnoughFwdRevPairsUseThisPerCentOfInsertSize: %d\n", resources_.nAutoFinishIfNotEnoughFwdRevPairsUseThisPerCentOfInsertSize_ ); } // consed.primersNumberOfBasesToBackUpToStartLooking if ( resources_.nPrimersNumberOfBasesToBackUpToStartLooking_ != CONDEF->nPrimersNumberOfBasesToBackUpToStartLooking_ ) { fprintf( pFileToWrite, "consed.primersNumberOfBasesToBackUpToStartLooking: %d\n", resources_.nPrimersNumberOfBasesToBackUpToStartLooking_ ); } // consed.primersMakePCRPrimersThisManyBasesBackFromEndOfHighQualitySegment if ( resources_.nPrimersMakePCRPrimersThisManyBasesBackFromEndOfHighQualitySegment_ != CONDEF->nPrimersMakePCRPrimersThisManyBasesBackFromEndOfHighQualitySegment_ ) { fprintf( pFileToWrite, "consed.primersMakePCRPrimersThisManyBasesBackFromEndOfHighQualitySegment: %d\n", resources_.nPrimersMakePCRPrimersThisManyBasesBackFromEndOfHighQualitySegment_ ); } // consed.primersOKToChoosePrimersInSingleSubcloneRegion if ( resources_.bPrimersOKToChoosePrimersInSingleSubcloneRegion_ != CONDEF->bPrimersOKToChoosePrimersInSingleSubcloneRegion_ ) { fprintf( pFileToWrite, "consed.primersOKToChoosePrimersInSingleSubcloneRegion: %s\n", ( resources_.bPrimersOKToChoosePrimersInSingleSubcloneRegion_ ? "true" : "false" ) ); } // consed.primersOKToChoosePrimersWhereHighQualityDiscrepancies if ( resources_.bPrimersOKToChoosePrimersWhereHighQualityDiscrepancies_ != CONDEF->bPrimersOKToChoosePrimersWhereHighQualityDiscrepancies_ ) { fprintf( pFileToWrite, "consed.primersOKToChoosePrimersWhereHighQualityDiscrepancies: %s\n", ( resources_.bPrimersOKToChoosePrimersWhereHighQualityDiscrepancies_ ? "true" : "false" ) ); } // consed.primersOKToChoosePrimersWhereUnalignedHighQualityRegion if ( resources_.bPrimersOKToChoosePrimersWhereUnalignedHighQualityRegion_ != CONDEF->bPrimersOKToChoosePrimersWhereUnalignedHighQualityRegion_ ) { fprintf( pFileToWrite, "consed.primersOKToChoosePrimersWhereUnalignedHighQualityRegion: %s\n", ( resources_.bPrimersOKToChoosePrimersWhereUnalignedHighQualityRegion_ ? "true" : "false" ) ); } // consed.autoFinishCallReversesToFlankGaps if ( resources_.bAutoFinishCallReversesToFlankGaps_ != CONDEF->bAutoFinishCallReversesToFlankGaps_ ) { fprintf( pFileToWrite, "consed.autoFinishCallReversesToFlankGaps: %s\n", ( resources_.bAutoFinishCallReversesToFlankGaps_ ? "true" : "false" ) ); } // consed.autoFinishAllowWholeCloneReads if ( resources_.bAutoFinishAllowWholeCloneReads_ != CONDEF->bAutoFinishAllowWholeCloneReads_ ) { fprintf( pFileToWrite, "consed.autoFinishAllowWholeCloneReads: %s\n", ( resources_.bAutoFinishAllowWholeCloneReads_ ? "true" : "false" ) ); } // consed.autoFinishAllowCustomPrimerSubcloneReads if ( resources_.bAutoFinishAllowCustomPrimerSubcloneReads_ != CONDEF->bAutoFinishAllowCustomPrimerSubcloneReads_ ) { fprintf( pFileToWrite, "consed.autoFinishAllowCustomPrimerSubcloneReads: %s\n", ( resources_.bAutoFinishAllowCustomPrimerSubcloneReads_ ? "true" : "false" ) ); } // consed.autoFinishAllowResequencingReads if ( resources_.bAutoFinishAllowResequencingReads_ != CONDEF->bAutoFinishAllowResequencingReads_ ) { fprintf( pFileToWrite, "consed.autoFinishAllowResequencingReads: %s\n", ( resources_.bAutoFinishAllowResequencingReads_ ? "true" : "false" ) ); } // consed.autoFinishAllowResequencingReadsOnlyForRunsAndStops if ( resources_.bAutoFinishAllowResequencingReadsOnlyForRunsAndStops_ != CONDEF->bAutoFinishAllowResequencingReadsOnlyForRunsAndStops_ ) { fprintf( pFileToWrite, "consed.autoFinishAllowResequencingReadsOnlyForRunsAndStops: %s\n", ( resources_.bAutoFinishAllowResequencingReadsOnlyForRunsAndStops_ ? "true" : "false" ) ); } // consed.autoFinishAllowDeNovoUniversalPrimerSubcloneReads if ( resources_.bAutoFinishAllowDeNovoUniversalPrimerSubcloneReads_ != CONDEF->bAutoFinishAllowDeNovoUniversalPrimerSubcloneReads_ ) { fprintf( pFileToWrite, "consed.autoFinishAllowDeNovoUniversalPrimerSubcloneReads: %s\n", ( resources_.bAutoFinishAllowDeNovoUniversalPrimerSubcloneReads_ ? "true" : "false" ) ); } // consed.autoFinishAllowMinilibraries if ( resources_.bAutoFinishAllowMinilibraries_ != CONDEF->bAutoFinishAllowMinilibraries_ ) { fprintf( pFileToWrite, "consed.autoFinishAllowMinilibraries: %s\n", ( resources_.bAutoFinishAllowMinilibraries_ ? "true" : "false" ) ); } // consed.autoFinishAllowPCR if ( resources_.bAutoFinishAllowPCR_ != CONDEF->bAutoFinishAllowPCR_ ) { fprintf( pFileToWrite, "consed.autoFinishAllowPCR: %s\n", ( resources_.bAutoFinishAllowPCR_ ? "true" : "false" ) ); } // consed.autoFinishAllowUnorientedPCRReactions if ( resources_.bAutoFinishAllowUnorientedPCRReactions_ != CONDEF->bAutoFinishAllowUnorientedPCRReactions_ ) { fprintf( pFileToWrite, "consed.autoFinishAllowUnorientedPCRReactions: %s\n", ( resources_.bAutoFinishAllowUnorientedPCRReactions_ ? "true" : "false" ) ); } // consed.autoFinishAllowResequencingAUniversalPrimerAutofinishRead if ( resources_.bAutoFinishAllowResequencingAUniversalPrimerAutofinishRead_ != CONDEF->bAutoFinishAllowResequencingAUniversalPrimerAutofinishRead_ ) { fprintf( pFileToWrite, "consed.autoFinishAllowResequencingAUniversalPrimerAutofinishRead: %s\n", ( resources_.bAutoFinishAllowResequencingAUniversalPrimerAutofinishRead_ ? "true" : "false" ) ); } // consed.autoFinishAlwaysCloseGapsUsingMinilibraries if ( resources_.bAutoFinishAlwaysCloseGapsUsingMinilibraries_ != CONDEF->bAutoFinishAlwaysCloseGapsUsingMinilibraries_ ) { fprintf( pFileToWrite, "consed.autoFinishAlwaysCloseGapsUsingMinilibraries: %s\n", ( resources_.bAutoFinishAlwaysCloseGapsUsingMinilibraries_ ? "true" : "false" ) ); } // consed.autoFinishMaximumFinishingReadLength if ( resources_.nAutoFinishMaximumFinishingReadLength_ != CONDEF->nAutoFinishMaximumFinishingReadLength_ ) { fprintf( pFileToWrite, "consed.autoFinishMaximumFinishingReadLength: %d\n", resources_.nAutoFinishMaximumFinishingReadLength_ ); } // consed.autoFinishSuggestMinilibraryIfGapThisManyBasesOrLarger if ( resources_.nAutoFinishSuggestMinilibraryIfGapThisManyBasesOrLarger_ != CONDEF->nAutoFinishSuggestMinilibraryIfGapThisManyBasesOrLarger_ ) { fprintf( pFileToWrite, "consed.autoFinishSuggestMinilibraryIfGapThisManyBasesOrLarger: %d\n", resources_.nAutoFinishSuggestMinilibraryIfGapThisManyBasesOrLarger_ ); } // consed.autoFinishSuggestSpecialChemistryForRunsAndStops if ( resources_.bAutoFinishSuggestSpecialChemistryForRunsAndStops_ != CONDEF->bAutoFinishSuggestSpecialChemistryForRunsAndStops_ ) { fprintf( pFileToWrite, "consed.autoFinishSuggestSpecialChemistryForRunsAndStops: %s\n", ( resources_.bAutoFinishSuggestSpecialChemistryForRunsAndStops_ ? "true" : "false" ) ); } // consed.autoFinishSuggestThisManyMinilibrariesPerGap if ( resources_.nAutoFinishSuggestThisManyMinilibrariesPerGap_ != CONDEF->nAutoFinishSuggestThisManyMinilibrariesPerGap_ ) { fprintf( pFileToWrite, "consed.autoFinishSuggestThisManyMinilibrariesPerGap: %d\n", resources_.nAutoFinishSuggestThisManyMinilibrariesPerGap_ ); } // consed.primersWindowSizeInLooking if ( resources_.nPrimersWindowSizeInLooking_ != CONDEF->nPrimersWindowSizeInLooking_ ) { fprintf( pFileToWrite, "consed.primersWindowSizeInLooking: %d\n", resources_.nPrimersWindowSizeInLooking_ ); } // consed.primersAssumeTemplatesAreDoubleStrandedUnlessSpecified if ( resources_.bPrimersAssumeTemplatesAreDoubleStrandedUnlessSpecified_ != CONDEF->bPrimersAssumeTemplatesAreDoubleStrandedUnlessSpecified_ ) { fprintf( pFileToWrite, "consed.primersAssumeTemplatesAreDoubleStrandedUnlessSpecified: %s\n", ( resources_.bPrimersAssumeTemplatesAreDoubleStrandedUnlessSpecified_ ? "true" : "false" ) ); } // consed.alignedReadsWindowInitialCharsWide if ( resources_.nAlignedReadsWindowInitialCharsWide_ != CONDEF->nAlignedReadsWindowInitialCharsWide_ ) { fprintf( pFileToWrite, "consed.alignedReadsWindowInitialCharsWide: %d\n", resources_.nAlignedReadsWindowInitialCharsWide_ ); } // consed.alignedReadsWindowInitialCharsHigh if ( resources_.nAlignedReadsWindowInitialCharsHigh_ != CONDEF->nAlignedReadsWindowInitialCharsHigh_ ) { fprintf( pFileToWrite, "consed.alignedReadsWindowInitialCharsHigh: %d\n", resources_.nAlignedReadsWindowInitialCharsHigh_ ); } // consed.alignedReadsWindowMaxCharsForReadNames if ( resources_.nAlignedReadsWindowMaxCharsForReadNames_ != CONDEF->nAlignedReadsWindowMaxCharsForReadNames_ ) { fprintf( pFileToWrite, "consed.alignedReadsWindowMaxCharsForReadNames: %d\n", resources_.nAlignedReadsWindowMaxCharsForReadNames_ ); } // consed.alignedReadsWindowAutomaticallyExpandRoomForReadNames if ( resources_.bAlignedReadsWindowAutomaticallyExpandRoomForReadNames_ != CONDEF->bAlignedReadsWindowAutomaticallyExpandRoomForReadNames_ ) { fprintf( pFileToWrite, "consed.alignedReadsWindowAutomaticallyExpandRoomForReadNames: %s\n", ( resources_.bAlignedReadsWindowAutomaticallyExpandRoomForReadNames_ ? "true" : "false" ) ); } // consed.autoFinishAllowResequencingReadsToExtendContigs if ( resources_.bAutoFinishAllowResequencingReadsToExtendContigs_ != CONDEF->bAutoFinishAllowResequencingReadsToExtendContigs_ ) { fprintf( pFileToWrite, "consed.autoFinishAllowResequencingReadsToExtendContigs: %s\n", ( resources_.bAutoFinishAllowResequencingReadsToExtendContigs_ ? "true" : "false" ) ); } // consed.autoFinishCallHowManyReversesToFlankGaps if ( resources_.nAutoFinishCallHowManyReversesToFlankGaps_ != CONDEF->nAutoFinishCallHowManyReversesToFlankGaps_ ) { fprintf( pFileToWrite, "consed.autoFinishCallHowManyReversesToFlankGaps: %d\n", resources_.nAutoFinishCallHowManyReversesToFlankGaps_ ); } // consed.autoFinishCloseGaps if ( resources_.bAutoFinishCloseGaps_ != CONDEF->bAutoFinishCloseGaps_ ) { fprintf( pFileToWrite, "consed.autoFinishCloseGaps: %s\n", ( resources_.bAutoFinishCloseGaps_ ? "true" : "false" ) ); } // consed.autoFinishContinueEvenThoughReadInfoDoesNotMakeSense if ( resources_.bAutoFinishContinueEvenThoughReadInfoDoesNotMakeSense_ != CONDEF->bAutoFinishContinueEvenThoughReadInfoDoesNotMakeSense_ ) { fprintf( pFileToWrite, "consed.autoFinishContinueEvenThoughReadInfoDoesNotMakeSense: %s\n", ( resources_.bAutoFinishContinueEvenThoughReadInfoDoesNotMakeSense_ ? "true" : "false" ) ); } // consed.autoFinishCostOfResequencingUniversalPrimerSubcloneReaction if ( resources_.dAutoFinishCostOfResequencingUniversalPrimerSubcloneReaction_ != CONDEF->dAutoFinishCostOfResequencingUniversalPrimerSubcloneReaction_ ) { fprintf( pFileToWrite, "consed.autoFinishCostOfResequencingUniversalPrimerSubcloneReaction: %f\n", resources_.dAutoFinishCostOfResequencingUniversalPrimerSubcloneReaction_ ); } // consed.autoFinishCostOfCustomPrimerSubcloneReaction if ( resources_.dAutoFinishCostOfCustomPrimerSubcloneReaction_ != CONDEF->dAutoFinishCostOfCustomPrimerSubcloneReaction_ ) { fprintf( pFileToWrite, "consed.autoFinishCostOfCustomPrimerSubcloneReaction: %f\n", resources_.dAutoFinishCostOfCustomPrimerSubcloneReaction_ ); } // consed.autoFinishCostOfCustomPrimerCloneReaction if ( resources_.dAutoFinishCostOfCustomPrimerCloneReaction_ != CONDEF->dAutoFinishCostOfCustomPrimerCloneReaction_ ) { fprintf( pFileToWrite, "consed.autoFinishCostOfCustomPrimerCloneReaction: %f\n", resources_.dAutoFinishCostOfCustomPrimerCloneReaction_ ); } // consed.autoFinishCostOfDeNovoUniversalPrimerSubcloneReaction if ( resources_.dAutoFinishCostOfDeNovoUniversalPrimerSubcloneReaction_ != CONDEF->dAutoFinishCostOfDeNovoUniversalPrimerSubcloneReaction_ ) { fprintf( pFileToWrite, "consed.autoFinishCostOfDeNovoUniversalPrimerSubcloneReaction: %f\n", resources_.dAutoFinishCostOfDeNovoUniversalPrimerSubcloneReaction_ ); } // consed.autoFinishCostOfMinilibrary if ( resources_.dAutoFinishCostOfMinilibrary_ != CONDEF->dAutoFinishCostOfMinilibrary_ ) { fprintf( pFileToWrite, "consed.autoFinishCostOfMinilibrary: %f\n", resources_.dAutoFinishCostOfMinilibrary_ ); } // consed.autoFinishCoverSingleSubcloneRegions if ( resources_.bAutoFinishCoverSingleSubcloneRegions_ != CONDEF->bAutoFinishCoverSingleSubcloneRegions_ ) { fprintf( pFileToWrite, "consed.autoFinishCoverSingleSubcloneRegions: %s\n", ( resources_.bAutoFinishCoverSingleSubcloneRegions_ ? "true" : "false" ) ); } // consed.autoFinishCoverLowConsensusQualityRegions if ( resources_.bAutoFinishCoverLowConsensusQualityRegions_ != CONDEF->bAutoFinishCoverLowConsensusQualityRegions_ ) { fprintf( pFileToWrite, "consed.autoFinishCoverLowConsensusQualityRegions: %s\n", ( resources_.bAutoFinishCoverLowConsensusQualityRegions_ ? "true" : "false" ) ); } // consed.autoFinishDebugUniversalPrimerReadsFile if ( resources_.filAutoFinishDebugUniversalPrimerReadsFile_ != CONDEF->filAutoFinishDebugUniversalPrimerReadsFile_ ) { fprintf( pFileToWrite, "consed.autoFinishDebugUniversalPrimerReadsFile: %s\n", resources_.filAutoFinishDebugUniversalPrimerReadsFile_.data() ); } // consed.autoFinishDebugCustomPrimerReadsFile if ( resources_.filAutoFinishDebugCustomPrimerReadsFile_ != CONDEF->filAutoFinishDebugCustomPrimerReadsFile_ ) { fprintf( pFileToWrite, "consed.autoFinishDebugCustomPrimerReadsFile: %s\n", resources_.filAutoFinishDebugCustomPrimerReadsFile_.data() ); } // consed.autoFinishDoNotAllowSubcloneCustomPrimerReadsCloserThanThisManyBases if ( resources_.nAutoFinishDoNotAllowSubcloneCustomPrimerReadsCloserThanThisManyBases_ != CONDEF->nAutoFinishDoNotAllowSubcloneCustomPrimerReadsCloserThanThisManyBases_ ) { fprintf( pFileToWrite, "consed.autoFinishDoNotAllowSubcloneCustomPrimerReadsCloserThanThisManyBases: %d\n", resources_.nAutoFinishDoNotAllowSubcloneCustomPrimerReadsCloserThanThisManyBases_ ); } // consed.autoFinishDoNotAllowWholeCloneCustomPrimerReadsCloserThanThisManyBases if ( resources_.nAutoFinishDoNotAllowWholeCloneCustomPrimerReadsCloserThanThisManyBases_ != CONDEF->nAutoFinishDoNotAllowWholeCloneCustomPrimerReadsCloserThanThisManyBases_ ) { fprintf( pFileToWrite, "consed.autoFinishDoNotAllowWholeCloneCustomPrimerReadsCloserThanThisManyBases: %d\n", resources_.nAutoFinishDoNotAllowWholeCloneCustomPrimerReadsCloserThanThisManyBases_ ); } // consed.autoFinishDoNotFinishWhereTheseTagsAre if ( resources_.soAutoFinishDoNotFinishWhereTheseTagsAre_ != CONDEF->soAutoFinishDoNotFinishWhereTheseTagsAre_ ) { fprintf( pFileToWrite, "consed.autoFinishDoNotFinishWhereTheseTagsAre: %s\n", resources_.soAutoFinishDoNotFinishWhereTheseTagsAre_.data() ); } // consed.autoFinishDoNotExtendContigsWhereTheseTagsAre if ( resources_.soAutoFinishDoNotExtendContigsWhereTheseTagsAre_ != CONDEF->soAutoFinishDoNotExtendContigsWhereTheseTagsAre_ ) { fprintf( pFileToWrite, "consed.autoFinishDoNotExtendContigsWhereTheseTagsAre: %s\n", resources_.soAutoFinishDoNotExtendContigsWhereTheseTagsAre_.data() ); } // consed.autoFinishDoNotExtendContigsIfTagsAreThisCloseToContigEnd if ( resources_.nAutoFinishDoNotExtendContigsIfTagsAreThisCloseToContigEnd_ != CONDEF->nAutoFinishDoNotExtendContigsIfTagsAreThisCloseToContigEnd_ ) { fprintf( pFileToWrite, "consed.autoFinishDoNotExtendContigsIfTagsAreThisCloseToContigEnd: %d\n", resources_.nAutoFinishDoNotExtendContigsIfTagsAreThisCloseToContigEnd_ ); } // consed.dumpContigOrderAndOrientationInfoToThisFile if ( resources_.filDumpContigOrderAndOrientationInfoToThisFile_ != CONDEF->filDumpContigOrderAndOrientationInfoToThisFile_ ) { fprintf( pFileToWrite, "consed.dumpContigOrderAndOrientationInfoToThisFile: %s\n", resources_.filDumpContigOrderAndOrientationInfoToThisFile_.data() ); } // consed.autoFinishDumpTemplates if ( resources_.bAutoFinishDumpTemplates_ != CONDEF->bAutoFinishDumpTemplates_ ) { fprintf( pFileToWrite, "consed.autoFinishDumpTemplates: %s\n", ( resources_.bAutoFinishDumpTemplates_ ? "true" : "false" ) ); } // consed.autoFinishExcludeContigIfOnlyThisManyReadsOrLess if ( resources_.nAutoFinishExcludeContigIfOnlyThisManyReadsOrLess_ != CONDEF->nAutoFinishExcludeContigIfOnlyThisManyReadsOrLess_ ) { fprintf( pFileToWrite, "consed.autoFinishExcludeContigIfOnlyThisManyReadsOrLess: %d\n", resources_.nAutoFinishExcludeContigIfOnlyThisManyReadsOrLess_ ); } // consed.autoFinishExcludeContigIfDepthOfCoverageGreaterThanThis if ( resources_.dAutoFinishExcludeContigIfDepthOfCoverageGreaterThanThis_ != CONDEF->dAutoFinishExcludeContigIfDepthOfCoverageGreaterThanThis_ ) { fprintf( pFileToWrite, "consed.autoFinishExcludeContigIfDepthOfCoverageGreaterThanThis: %f\n", resources_.dAutoFinishExcludeContigIfDepthOfCoverageGreaterThanThis_ ); } // consed.autoFinishExcludeContigIfThisManyBasesOrLess if ( resources_.nAutoFinishExcludeContigIfThisManyBasesOrLess_ != CONDEF->nAutoFinishExcludeContigIfThisManyBasesOrLess_ ) { fprintf( pFileToWrite, "consed.autoFinishExcludeContigIfThisManyBasesOrLess: %d\n", resources_.nAutoFinishExcludeContigIfThisManyBasesOrLess_ ); } // consed.autoFinishHowManyTemplatesYouIntendToUseForCustomPrimerSubcloneReactions if ( resources_.nAutoFinishHowManyTemplatesYouIntendToUseForCustomPrimerSubcloneReactions_ != CONDEF->nAutoFinishHowManyTemplatesYouIntendToUseForCustomPrimerSubcloneReactions_ ) { fprintf( pFileToWrite, "consed.autoFinishHowManyTemplatesYouIntendToUseForCustomPrimerSubcloneReactions: %d\n", resources_.nAutoFinishHowManyTemplatesYouIntendToUseForCustomPrimerSubcloneReactions_ ); } // consed.primersMinNumberOfTemplatesForPrimers if ( resources_.nPrimersMinNumberOfTemplatesForPrimers_ != CONDEF->nPrimersMinNumberOfTemplatesForPrimers_ ) { fprintf( pFileToWrite, "consed.primersMinNumberOfTemplatesForPrimers: %d\n", resources_.nPrimersMinNumberOfTemplatesForPrimers_ ); } // consed.autoFinishMinBaseOverlapBetweenAReadAndHighQualitySegmentOfConsensus if ( resources_.nAutoFinishMinBaseOverlapBetweenAReadAndHighQualitySegmentOfConsensus_ != CONDEF->nAutoFinishMinBaseOverlapBetweenAReadAndHighQualitySegmentOfConsensus_ ) { fprintf( pFileToWrite, "consed.autoFinishMinBaseOverlapBetweenAReadAndHighQualitySegmentOfConsensus: %d\n", resources_.nAutoFinishMinBaseOverlapBetweenAReadAndHighQualitySegmentOfConsensus_ ); } // consed.autoFinishNumberOfVectorBasesAtBeginningOfAUniveralPrimerRead if ( resources_.nAutoFinishNumberOfVectorBasesAtBeginningOfAUniveralPrimerRead_ != CONDEF->nAutoFinishNumberOfVectorBasesAtBeginningOfAUniveralPrimerRead_ ) { fprintf( pFileToWrite, "consed.autoFinishNumberOfVectorBasesAtBeginningOfAUniveralPrimerRead: %d\n", resources_.nAutoFinishNumberOfVectorBasesAtBeginningOfAUniveralPrimerRead_ ); } // consed.autoFinishCDNANotGenomic if ( resources_.bAutoFinishCDNANotGenomic_ != CONDEF->bAutoFinishCDNANotGenomic_ ) { fprintf( pFileToWrite, "consed.autoFinishCDNANotGenomic: %s\n", ( resources_.bAutoFinishCDNANotGenomic_ ? "true" : "false" ) ); } // consed.autoFinishConfidenceThatReadWillCoverSingleSubcloneRegion if ( resources_.nAutoFinishConfidenceThatReadWillCoverSingleSubcloneRegion_ != CONDEF->nAutoFinishConfidenceThatReadWillCoverSingleSubcloneRegion_ ) { fprintf( pFileToWrite, "consed.autoFinishConfidenceThatReadWillCoverSingleSubcloneRegion: %d\n", resources_.nAutoFinishConfidenceThatReadWillCoverSingleSubcloneRegion_ ); } // consed.autoFinishPrintForwardOrReverseStrandWhenPrintingSubcloneTemplatesForCustomPrimerReads if ( resources_.bAutoFinishPrintForwardOrReverseStrandWhenPrintingSubcloneTemplatesForCustomPrimerReads_ != CONDEF->bAutoFinishPrintForwardOrReverseStrandWhenPrintingSubcloneTemplatesForCustomPrimerReads_ ) { fprintf( pFileToWrite, "consed.autoFinishPrintForwardOrReverseStrandWhenPrintingSubcloneTemplatesForCustomPrimerReads: %s\n", ( resources_.bAutoFinishPrintForwardOrReverseStrandWhenPrintingSubcloneTemplatesForCustomPrimerReads_ ? "true" : "false" ) ); } // consed.autoFinishPrintMinilibrariesSummaryFile if ( resources_.bAutoFinishPrintMinilibrariesSummaryFile_ != CONDEF->bAutoFinishPrintMinilibrariesSummaryFile_ ) { fprintf( pFileToWrite, "consed.autoFinishPrintMinilibrariesSummaryFile: %s\n", ( resources_.bAutoFinishPrintMinilibrariesSummaryFile_ ? "true" : "false" ) ); } // consed.autoFinishNearGapsSuggestEachMissingReadOfReadPairs if ( resources_.bAutoFinishNearGapsSuggestEachMissingReadOfReadPairs_ != CONDEF->bAutoFinishNearGapsSuggestEachMissingReadOfReadPairs_ ) { fprintf( pFileToWrite, "consed.autoFinishNearGapsSuggestEachMissingReadOfReadPairs: %s\n", ( resources_.bAutoFinishNearGapsSuggestEachMissingReadOfReadPairs_ ? "true" : "false" ) ); } // consed.autoFinishDoNotIgnoreLCQIfThisManyBasesFromEndOfContigForLCQTagger if ( resources_.nAutoFinishDoNotIgnoreLCQIfThisManyBasesFromEndOfContigForLCQTagger_ != CONDEF->nAutoFinishDoNotIgnoreLCQIfThisManyBasesFromEndOfContigForLCQTagger_ ) { fprintf( pFileToWrite, "consed.autoFinishDoNotIgnoreLCQIfThisManyBasesFromEndOfContigForLCQTagger: %d\n", resources_.nAutoFinishDoNotIgnoreLCQIfThisManyBasesFromEndOfContigForLCQTagger_ ); } // consed.checkIfTooManyWalks if ( resources_.bCheckIfTooManyWalks_ != CONDEF->bCheckIfTooManyWalks_ ) { fprintf( pFileToWrite, "consed.checkIfTooManyWalks: %s\n", ( resources_.bCheckIfTooManyWalks_ ? "true" : "false" ) ); } // consed.numberOfColumnsBeforeReadNameInAlignedReadsWindow if ( resources_.nNumberOfColumnsBeforeReadNameInAlignedReadsWindow_ != CONDEF->nNumberOfColumnsBeforeReadNameInAlignedReadsWindow_ ) { fprintf( pFileToWrite, "consed.numberOfColumnsBeforeReadNameInAlignedReadsWindow: %d\n", resources_.nNumberOfColumnsBeforeReadNameInAlignedReadsWindow_ ); } // consed.compareContigsAlignsThisManyBasesMax if ( resources_.nCompareContigsAlignsThisManyBasesMax_ != CONDEF->nCompareContigsAlignsThisManyBasesMax_ ) { fprintf( pFileToWrite, "consed.compareContigsAlignsThisManyBasesMax: %d\n", resources_.nCompareContigsAlignsThisManyBasesMax_ ); } // consed.compressedChromatExtension if ( resources_.soCompressedChromatExtension_ != CONDEF->soCompressedChromatExtension_ ) { fprintf( pFileToWrite, "consed.compressedChromatExtension: %s\n", resources_.soCompressedChromatExtension_.data() ); } // consed.dimLowQualityEndsOfReads if ( resources_.bDimLowQualityEndsOfReads_ != CONDEF->bDimLowQualityEndsOfReads_ ) { fprintf( pFileToWrite, "consed.dimLowQualityEndsOfReads: %s\n", ( resources_.bDimLowQualityEndsOfReads_ ? "true" : "false" ) ); } // consed.dimUnalignedEndsOfReads if ( resources_.bDimUnalignedEndsOfReads_ != CONDEF->bDimUnalignedEndsOfReads_ ) { fprintf( pFileToWrite, "consed.dimUnalignedEndsOfReads: %s\n", ( resources_.bDimUnalignedEndsOfReads_ ? "true" : "false" ) ); } // consed.fakeReadsSpecifiedByFilenameExtension if ( resources_.bFakeReadsSpecifiedByFilenameExtension_ != CONDEF->bFakeReadsSpecifiedByFilenameExtension_ ) { fprintf( pFileToWrite, "consed.fakeReadsSpecifiedByFilenameExtension: %s\n", ( resources_.bFakeReadsSpecifiedByFilenameExtension_ ? "true" : "false" ) ); } // consed.fullPathnameOfAddReads2ConsedScript if ( resources_.filFullPathnameOfAddReads2ConsedScript_ != CONDEF->filFullPathnameOfAddReads2ConsedScript_ ) { fprintf( pFileToWrite, "consed.fullPathnameOfAddReads2ConsedScript: %s\n", resources_.filFullPathnameOfAddReads2ConsedScript_.data() ); } // consed.fullPathnameOfFixContigEndScript if ( resources_.filFullPathnameOfFixContigEndScript_ != CONDEF->filFullPathnameOfFixContigEndScript_ ) { fprintf( pFileToWrite, "consed.fullPathnameOfFixContigEndScript: %s\n", resources_.filFullPathnameOfFixContigEndScript_.data() ); } // consed.fixContigEndsCleanUpTemporaryFiles if ( resources_.bFixContigEndsCleanUpTemporaryFiles_ != CONDEF->bFixContigEndsCleanUpTemporaryFiles_ ) { fprintf( pFileToWrite, "consed.fixContigEndsCleanUpTemporaryFiles: %s\n", ( resources_.bFixContigEndsCleanUpTemporaryFiles_ ? "true" : "false" ) ); } // consed.fixContigEndsMinSmithWatermanScoreToMakeJoin if ( resources_.nFixContigEndsMinSmithWatermanScoreToMakeJoin_ != CONDEF->nFixContigEndsMinSmithWatermanScoreToMakeJoin_ ) { fprintf( pFileToWrite, "consed.fixContigEndsMinSmithWatermanScoreToMakeJoin: %d\n", resources_.nFixContigEndsMinSmithWatermanScoreToMakeJoin_ ); } // consed.fixContigEndsMinNumberOfReadsInContig if ( resources_.nFixContigEndsMinNumberOfReadsInContig_ != CONDEF->nFixContigEndsMinNumberOfReadsInContig_ ) { fprintf( pFileToWrite, "consed.fixContigEndsMinNumberOfReadsInContig: %d\n", resources_.nFixContigEndsMinNumberOfReadsInContig_ ); } // consed.fullPathnameOfCrossMatch if ( resources_.filFullPathnameOfCrossMatch_ != CONDEF->filFullPathnameOfCrossMatch_ ) { fprintf( pFileToWrite, "consed.fullPathnameOfCrossMatch: %s\n", resources_.filFullPathnameOfCrossMatch_.data() ); } // consed.fullPathnameOfPhred if ( resources_.filFullPathnameOfPhred_ != CONDEF->filFullPathnameOfPhred_ ) { fprintf( pFileToWrite, "consed.fullPathnameOfPhred: %s\n", resources_.filFullPathnameOfPhred_.data() ); } // consed.fullPathnameOfMiniassemblyScript if ( resources_.filFullPathnameOfMiniassemblyScript_ != CONDEF->filFullPathnameOfMiniassemblyScript_ ) { fprintf( pFileToWrite, "consed.fullPathnameOfMiniassemblyScript: %s\n", resources_.filFullPathnameOfMiniassemblyScript_.data() ); } // consed.gunzipFullPath if ( resources_.soGunzipFullPath_ != CONDEF->soGunzipFullPath_ ) { fprintf( pFileToWrite, "consed.gunzipFullPath: %s\n", resources_.soGunzipFullPath_.data() ); } // consed.fullPathnameOfFilter454ReadsScript if ( resources_.filFullPathnameOfFilter454ReadsScript_ != CONDEF->filFullPathnameOfFilter454ReadsScript_ ) { fprintf( pFileToWrite, "consed.fullPathnameOfFilter454ReadsScript: %s\n", resources_.filFullPathnameOfFilter454ReadsScript_.data() ); } // consed.filter454ReadsAgainstThis if ( resources_.filFilter454ReadsAgainstThis_ != CONDEF->filFilter454ReadsAgainstThis_ ) { fprintf( pFileToWrite, "consed.filter454ReadsAgainstThis: %s\n", resources_.filFilter454ReadsAgainstThis_.data() ); } // consed.454LinkerSequences if ( resources_.fil454LinkerSequences_ != CONDEF->fil454LinkerSequences_ ) { fprintf( pFileToWrite, "consed.454LinkerSequences: %s\n", resources_.fil454LinkerSequences_.data() ); } // consed.hideSomeTagTypesAtStartup if ( resources_.bHideSomeTagTypesAtStartup_ != CONDEF->bHideSomeTagTypesAtStartup_ ) { fprintf( pFileToWrite, "consed.hideSomeTagTypesAtStartup: %s\n", ( resources_.bHideSomeTagTypesAtStartup_ ? "true" : "false" ) ); } // consed.maximumNumberOfTracesShown if ( resources_.nMaximumNumberOfTracesShown_ != CONDEF->nMaximumNumberOfTracesShown_ ) { fprintf( pFileToWrite, "consed.maximumNumberOfTracesShown: %d\n", resources_.nMaximumNumberOfTracesShown_ ); } // consed.navigateAutomaticTracePopup if ( resources_.bNavigateAutomaticTracePopup_ != CONDEF->bNavigateAutomaticTracePopup_ ) { fprintf( pFileToWrite, "consed.navigateAutomaticTracePopup: %s\n", ( resources_.bNavigateAutomaticTracePopup_ ? "true" : "false" ) ); } // consed.navigateAutomaticAllTracesPopup if ( resources_.bNavigateAutomaticAllTracesPopup_ != CONDEF->bNavigateAutomaticAllTracesPopup_ ) { fprintf( pFileToWrite, "consed.navigateAutomaticAllTracesPopup: %s\n", ( resources_.bNavigateAutomaticAllTracesPopup_ ? "true" : "false" ) ); } // consed.primersMinimumLengthOfAPrimer if ( resources_.nPrimersMinimumLengthOfAPrimer_ != CONDEF->nPrimersMinimumLengthOfAPrimer_ ) { fprintf( pFileToWrite, "consed.primersMinimumLengthOfAPrimer: %d\n", resources_.nPrimersMinimumLengthOfAPrimer_ ); } // consed.primersMaximumLengthOfAPrimer if ( resources_.nPrimersMaximumLengthOfAPrimer_ != CONDEF->nPrimersMaximumLengthOfAPrimer_ ) { fprintf( pFileToWrite, "consed.primersMaximumLengthOfAPrimer: %d\n", resources_.nPrimersMaximumLengthOfAPrimer_ ); } // consed.primersMinimumLengthOfAPrimerForPCR if ( resources_.nPrimersMinimumLengthOfAPrimerForPCR_ != CONDEF->nPrimersMinimumLengthOfAPrimerForPCR_ ) { fprintf( pFileToWrite, "consed.primersMinimumLengthOfAPrimerForPCR: %d\n", resources_.nPrimersMinimumLengthOfAPrimerForPCR_ ); } // consed.primersMaximumLengthOfAPrimerForPCR if ( resources_.nPrimersMaximumLengthOfAPrimerForPCR_ != CONDEF->nPrimersMaximumLengthOfAPrimerForPCR_ ) { fprintf( pFileToWrite, "consed.primersMaximumLengthOfAPrimerForPCR: %d\n", resources_.nPrimersMaximumLengthOfAPrimerForPCR_ ); } // consed.primersMaxMeltingTempDifferenceForPCR if ( resources_.dPrimersMaxMeltingTempDifferenceForPCR_ != CONDEF->dPrimersMaxMeltingTempDifferenceForPCR_ ) { fprintf( pFileToWrite, "consed.primersMaxMeltingTempDifferenceForPCR: %f\n", resources_.dPrimersMaxMeltingTempDifferenceForPCR_ ); } // consed.primersMaxPCRPrimerPairsToDisplay if ( resources_.nPrimersMaxPCRPrimerPairsToDisplay_ != CONDEF->nPrimersMaxPCRPrimerPairsToDisplay_ ) { fprintf( pFileToWrite, "consed.primersMaxPCRPrimerPairsToDisplay: %d\n", resources_.nPrimersMaxPCRPrimerPairsToDisplay_ ); } // consed.primersCheckJustSomePCRPrimerPairsRatherThanAll if ( resources_.bPrimersCheckJustSomePCRPrimerPairsRatherThanAll_ != CONDEF->bPrimersCheckJustSomePCRPrimerPairsRatherThanAll_ ) { fprintf( pFileToWrite, "consed.primersCheckJustSomePCRPrimerPairsRatherThanAll: %s\n", ( resources_.bPrimersCheckJustSomePCRPrimerPairsRatherThanAll_ ? "true" : "false" ) ); } // consed.primersNumberOfTemplatesToDisplayInFront if ( resources_.nPrimersNumberOfTemplatesToDisplayInFront_ != CONDEF->nPrimersNumberOfTemplatesToDisplayInFront_ ) { fprintf( pFileToWrite, "consed.primersNumberOfTemplatesToDisplayInFront: %d\n", resources_.nPrimersNumberOfTemplatesToDisplayInFront_ ); } // consed.primersMaxLengthOfMononucleotideRepeat if ( resources_.nPrimersMaxLengthOfMononucleotideRepeat_ != CONDEF->nPrimersMaxLengthOfMononucleotideRepeat_ ) { fprintf( pFileToWrite, "consed.primersMaxLengthOfMononucleotideRepeat: %d\n", resources_.nPrimersMaxLengthOfMononucleotideRepeat_ ); } // consed.primersBadLibrariesFile if ( resources_.filPrimersBadLibrariesFile_ != CONDEF->filPrimersBadLibrariesFile_ ) { fprintf( pFileToWrite, "consed.primersBadLibrariesFile: %s\n", resources_.filPrimersBadLibrariesFile_.data() ); } // consed.primersLibrariesInfoFile if ( resources_.filPrimersLibrariesInfoFile_ != CONDEF->filPrimersLibrariesInfoFile_ ) { fprintf( pFileToWrite, "consed.primersLibrariesInfoFile: %s\n", resources_.filPrimersLibrariesInfoFile_.data() ); } // consed.primersBadTemplatesFile if ( resources_.filPrimersBadTemplatesFile_ != CONDEF->filPrimersBadTemplatesFile_ ) { fprintf( pFileToWrite, "consed.primersBadTemplatesFile: %s\n", resources_.filPrimersBadTemplatesFile_.data() ); } // consed.primersChooseTemplatesByPositionInsteadOfQuality if ( resources_.bPrimersChooseTemplatesByPositionInsteadOfQuality_ != CONDEF->bPrimersChooseTemplatesByPositionInsteadOfQuality_ ) { fprintf( pFileToWrite, "consed.primersChooseTemplatesByPositionInsteadOfQuality: %s\n", ( resources_.bPrimersChooseTemplatesByPositionInsteadOfQuality_ ? "true" : "false" ) ); } // consed.primersWhenChoosingATemplateMinPotentialReadLength if ( resources_.nPrimersWhenChoosingATemplateMinPotentialReadLength_ != CONDEF->nPrimersWhenChoosingATemplateMinPotentialReadLength_ ) { fprintf( pFileToWrite, "consed.primersWhenChoosingATemplateMinPotentialReadLength: %d\n", resources_.nPrimersWhenChoosingATemplateMinPotentialReadLength_ ); } // consed.primersWindowSizeInLookingForPCR if ( resources_.nPrimersWindowSizeInLookingForPCR_ != CONDEF->nPrimersWindowSizeInLookingForPCR_ ) { fprintf( pFileToWrite, "consed.primersWindowSizeInLookingForPCR: %d\n", resources_.nPrimersWindowSizeInLookingForPCR_ ); } // consed.qualityThresholdForFindingHighQualityDiscrepancies if ( resources_.nQualityThresholdForFindingHighQualityDiscrepancies_ != CONDEF->nQualityThresholdForFindingHighQualityDiscrepancies_ ) { fprintf( pFileToWrite, "consed.qualityThresholdForFindingHighQualityDiscrepancies: %d\n", resources_.nQualityThresholdForFindingHighQualityDiscrepancies_ ); } // consed.qualityThresholdForNavigateByDepthOfCoverage if ( resources_.nQualityThresholdForNavigateByDepthOfCoverage_ != CONDEF->nQualityThresholdForNavigateByDepthOfCoverage_ ) { fprintf( pFileToWrite, "consed.qualityThresholdForNavigateByDepthOfCoverage: %d\n", resources_.nQualityThresholdForNavigateByDepthOfCoverage_ ); } // consed.navigateByHighDepthOfCoverageNotLow if ( resources_.bNavigateByHighDepthOfCoverageNotLow_ != CONDEF->bNavigateByHighDepthOfCoverageNotLow_ ) { fprintf( pFileToWrite, "consed.navigateByHighDepthOfCoverageNotLow: %s\n", ( resources_.bNavigateByHighDepthOfCoverageNotLow_ ? "true" : "false" ) ); } // consed.MinDepthForNavigateByDepthOfCoverage if ( resources_.nMinDepthForNavigateByDepthOfCoverage_ != CONDEF->nMinDepthForNavigateByDepthOfCoverage_ ) { fprintf( pFileToWrite, "consed.MinDepthForNavigateByDepthOfCoverage: %d\n", resources_.nMinDepthForNavigateByDepthOfCoverage_ ); } // consed.defaultVectorPathnameForRestrictionFragments if ( resources_.filDefaultVectorPathnameForRestrictionFragments_ != CONDEF->filDefaultVectorPathnameForRestrictionFragments_ ) { fprintf( pFileToWrite, "consed.defaultVectorPathnameForRestrictionFragments: %s\n", resources_.filDefaultVectorPathnameForRestrictionFragments_.data() ); } // consed.fileOfAdditionalRestrictionEnzymes if ( resources_.filFileOfAdditionalRestrictionEnzymes_ != CONDEF->filFileOfAdditionalRestrictionEnzymes_ ) { fprintf( pFileToWrite, "consed.fileOfAdditionalRestrictionEnzymes: %s\n", resources_.filFileOfAdditionalRestrictionEnzymes_.data() ); } // consed.commonRestrictionEnzymes if ( resources_.soCommonRestrictionEnzymes_ != CONDEF->soCommonRestrictionEnzymes_ ) { fprintf( pFileToWrite, "consed.commonRestrictionEnzymes: %s\n", resources_.soCommonRestrictionEnzymes_.data() ); } // consed.defaultSelectedRestrictionEnzymes if ( resources_.soDefaultSelectedRestrictionEnzymes_ != CONDEF->soDefaultSelectedRestrictionEnzymes_ ) { fprintf( pFileToWrite, "consed.defaultSelectedRestrictionEnzymes: %s\n", resources_.soDefaultSelectedRestrictionEnzymes_.data() ); } // consed.restrictionEnzymesActualFragmentsFile if ( resources_.filRestrictionEnzymesActualFragmentsFile_ != CONDEF->filRestrictionEnzymesActualFragmentsFile_ ) { fprintf( pFileToWrite, "consed.restrictionEnzymesActualFragmentsFile: %s\n", resources_.filRestrictionEnzymesActualFragmentsFile_.data() ); } // consed.restrictionDigestInitialWindowSizeInTextRows if ( resources_.nRestrictionDigestInitialWindowSizeInTextRows_ != CONDEF->nRestrictionDigestInitialWindowSizeInTextRows_ ) { fprintf( pFileToWrite, "consed.restrictionDigestInitialWindowSizeInTextRows: %d\n", resources_.nRestrictionDigestInitialWindowSizeInTextRows_ ); } // consed.restrictionDigestDoNoShowAreaOfFragmentsOverThisSize if ( resources_.nRestrictionDigestDoNoShowAreaOfFragmentsOverThisSize_ != CONDEF->nRestrictionDigestDoNoShowAreaOfFragmentsOverThisSize_ ) { fprintf( pFileToWrite, "consed.restrictionDigestDoNoShowAreaOfFragmentsOverThisSize: %d\n", resources_.nRestrictionDigestDoNoShowAreaOfFragmentsOverThisSize_ ); } // consed.showReadsAlphabetically if ( resources_.bShowReadsAlphabetically_ != CONDEF->bShowReadsAlphabetically_ ) { fprintf( pFileToWrite, "consed.showReadsAlphabetically: %s\n", ( resources_.bShowReadsAlphabetically_ ? "true" : "false" ) ); } // consed.showReadsInAlignedReadsWindowOrderedByFile if ( resources_.bShowReadsInAlignedReadsWindowOrderedByFile_ != CONDEF->bShowReadsInAlignedReadsWindowOrderedByFile_ ) { fprintf( pFileToWrite, "consed.showReadsInAlignedReadsWindowOrderedByFile: %s\n", ( resources_.bShowReadsInAlignedReadsWindowOrderedByFile_ ? "true" : "false" ) ); } // consed.showReadsInAlignedReadsWindowOrderedByThisFile if ( resources_.filShowReadsInAlignedReadsWindowOrderedByThisFile_ != CONDEF->filShowReadsInAlignedReadsWindowOrderedByThisFile_ ) { fprintf( pFileToWrite, "consed.showReadsInAlignedReadsWindowOrderedByThisFile: %s\n", resources_.filShowReadsInAlignedReadsWindowOrderedByThisFile_.data() ); } // consed.showReadsAtCursorSortedHow if ( resources_.soShowReadsAtCursorSortedHow_ != CONDEF->soShowReadsAtCursorSortedHow_ ) { fprintf( pFileToWrite, "consed.showReadsAtCursorSortedHow: %s\n", resources_.soShowReadsAtCursorSortedHow_.data() ); } // consed.showABIBasesInTraceWindow if ( resources_.bShowABIBasesInTraceWindow_ != CONDEF->bShowABIBasesInTraceWindow_ ) { fprintf( pFileToWrite, "consed.showABIBasesInTraceWindow: %s\n", ( resources_.bShowABIBasesInTraceWindow_ ? "true" : "false" ) ); } // consed.tracesWindowInitialPixelHeight if ( resources_.nTracesWindowInitialPixelHeight_ != CONDEF->nTracesWindowInitialPixelHeight_ ) { fprintf( pFileToWrite, "consed.tracesWindowInitialPixelHeight: %d\n", resources_.nTracesWindowInitialPixelHeight_ ); } // consed.assemblyViewWindowInitialPixelHeight if ( resources_.nAssemblyViewWindowInitialPixelHeight_ != CONDEF->nAssemblyViewWindowInitialPixelHeight_ ) { fprintf( pFileToWrite, "consed.assemblyViewWindowInitialPixelHeight: %d\n", resources_.nAssemblyViewWindowInitialPixelHeight_ ); } // consed.assemblyViewFileOfTemplatesToNotShow if ( resources_.filAssemblyViewFileOfTemplatesToNotShow_ != CONDEF->filAssemblyViewFileOfTemplatesToNotShow_ ) { fprintf( pFileToWrite, "consed.assemblyViewFileOfTemplatesToNotShow: %s\n", resources_.filAssemblyViewFileOfTemplatesToNotShow_.data() ); } // consed.assemblyViewCrossMatchMinmatch if ( resources_.nAssemblyViewCrossMatchMinmatch_ != CONDEF->nAssemblyViewCrossMatchMinmatch_ ) { fprintf( pFileToWrite, "consed.assemblyViewCrossMatchMinmatch: %d\n", resources_.nAssemblyViewCrossMatchMinmatch_ ); } // consed.assemblyViewCrossMatchMinscore if ( resources_.nAssemblyViewCrossMatchMinscore_ != CONDEF->nAssemblyViewCrossMatchMinscore_ ) { fprintf( pFileToWrite, "consed.assemblyViewCrossMatchMinscore: %d\n", resources_.nAssemblyViewCrossMatchMinscore_ ); } // consed.assemblyViewFindSequenceMatchesForConsedScript if ( resources_.filAssemblyViewFindSequenceMatchesForConsedScript_ != CONDEF->filAssemblyViewFindSequenceMatchesForConsedScript_ ) { fprintf( pFileToWrite, "consed.assemblyViewFindSequenceMatchesForConsedScript: %s\n", resources_.filAssemblyViewFindSequenceMatchesForConsedScript_.data() ); } // consed.assemblyViewCrossmatchMinmatch if ( resources_.nAssemblyViewCrossmatchMinmatch_ != CONDEF->nAssemblyViewCrossmatchMinmatch_ ) { fprintf( pFileToWrite, "consed.assemblyViewCrossmatchMinmatch: %d\n", resources_.nAssemblyViewCrossmatchMinmatch_ ); } // consed.assemblyViewCrossmatchMinscore if ( resources_.nAssemblyViewCrossmatchMinscore_ != CONDEF->nAssemblyViewCrossmatchMinscore_ ) { fprintf( pFileToWrite, "consed.assemblyViewCrossmatchMinscore: %d\n", resources_.nAssemblyViewCrossmatchMinscore_ ); } // consed.assemblyViewSequenceMatchesMinimumSimilarity if ( resources_.nAssemblyViewSequenceMatchesMinimumSimilarity_ != CONDEF->nAssemblyViewSequenceMatchesMinimumSimilarity_ ) { fprintf( pFileToWrite, "consed.assemblyViewSequenceMatchesMinimumSimilarity: %d\n", resources_.nAssemblyViewSequenceMatchesMinimumSimilarity_ ); } // consed.tracesWindowInitialPixelWidth if ( resources_.nTracesWindowInitialPixelWidth_ != CONDEF->nTracesWindowInitialPixelWidth_ ) { fprintf( pFileToWrite, "consed.tracesWindowInitialPixelWidth: %d\n", resources_.nTracesWindowInitialPixelWidth_ ); } // consed.assemblyViewWindowInitialPixelWidth if ( resources_.nAssemblyViewWindowInitialPixelWidth_ != CONDEF->nAssemblyViewWindowInitialPixelWidth_ ) { fprintf( pFileToWrite, "consed.assemblyViewWindowInitialPixelWidth: %d\n", resources_.nAssemblyViewWindowInitialPixelWidth_ ); } // consed.automaticallyScaleTraces if ( resources_.bAutomaticallyScaleTraces_ != CONDEF->bAutomaticallyScaleTraces_ ) { fprintf( pFileToWrite, "consed.automaticallyScaleTraces: %s\n", ( resources_.bAutomaticallyScaleTraces_ ? "true" : "false" ) ); } // consed.automaticallyScaleTracesSamplePeakHeightFractionOfWindowHeight if ( resources_.dAutomaticallyScaleTracesSamplePeakHeightFractionOfWindowHeight_ != CONDEF->dAutomaticallyScaleTracesSamplePeakHeightFractionOfWindowHeight_ ) { fprintf( pFileToWrite, "consed.automaticallyScaleTracesSamplePeakHeightFractionOfWindowHeight: %f\n", resources_.dAutomaticallyScaleTracesSamplePeakHeightFractionOfWindowHeight_ ); } // consed.automaticallyScaleTracesSamplePeakPercentile if ( resources_.nAutomaticallyScaleTracesSamplePeakPercentile_ != CONDEF->nAutomaticallyScaleTracesSamplePeakPercentile_ ) { fprintf( pFileToWrite, "consed.automaticallyScaleTracesSamplePeakPercentile: %d\n", resources_.nAutomaticallyScaleTracesSamplePeakPercentile_ ); } // consed.verticalTraceMagnification if ( resources_.nVerticalTraceMagnification_ != CONDEF->nVerticalTraceMagnification_ ) { fprintf( pFileToWrite, "consed.verticalTraceMagnification: %d\n", resources_.nVerticalTraceMagnification_ ); } // consed.userDefinedKeys if ( resources_.soUserDefinedKeys_ != CONDEF->soUserDefinedKeys_ ) { fprintf( pFileToWrite, "consed.userDefinedKeys: %s\n", resources_.soUserDefinedKeys_.data() ); } // consed.programsForUserDefinedKeys if ( resources_.soProgramsForUserDefinedKeys_ != CONDEF->soProgramsForUserDefinedKeys_ ) { fprintf( pFileToWrite, "consed.programsForUserDefinedKeys: %s\n", resources_.soProgramsForUserDefinedKeys_.data() ); } // consed.argumentsToPassToUserDefinedPrograms if ( resources_.soArgumentsToPassToUserDefinedPrograms_ != CONDEF->soArgumentsToPassToUserDefinedPrograms_ ) { fprintf( pFileToWrite, "consed.argumentsToPassToUserDefinedPrograms: %s\n", resources_.soArgumentsToPassToUserDefinedPrograms_.data() ); } // consed.tagsToApplyWithUserDefinedKeys if ( resources_.soTagsToApplyWithUserDefinedKeys_ != CONDEF->soTagsToApplyWithUserDefinedKeys_ ) { fprintf( pFileToWrite, "consed.tagsToApplyWithUserDefinedKeys: %s\n", resources_.soTagsToApplyWithUserDefinedKeys_.data() ); } // consed.snpGenomeUseInsertionPolymorphisms if ( resources_.bSnpGenomeUseInsertionPolymorphisms_ != CONDEF->bSnpGenomeUseInsertionPolymorphisms_ ) { fprintf( pFileToWrite, "consed.snpGenomeUseInsertionPolymorphisms: %s\n", ( resources_.bSnpGenomeUseInsertionPolymorphisms_ ? "true" : "false" ) ); } // consed.listOfTagTypesToHide if ( resources_.soListOfTagTypesToHide_ != CONDEF->soListOfTagTypesToHide_ ) { fprintf( pFileToWrite, "consed.listOfTagTypesToHide: %s\n", resources_.soListOfTagTypesToHide_.data() ); } // consed.listOfOptionalWordsToSaveInListOfReadNames if ( resources_.soListOfOptionalWordsToSaveInListOfReadNames_ != CONDEF->soListOfOptionalWordsToSaveInListOfReadNames_ ) { fprintf( pFileToWrite, "consed.listOfOptionalWordsToSaveInListOfReadNames: %s\n", resources_.soListOfOptionalWordsToSaveInListOfReadNames_.data() ); } // consed.extendConsensusWithHighQuality if ( resources_.bExtendConsensusWithHighQuality_ != CONDEF->bExtendConsensusWithHighQuality_ ) { fprintf( pFileToWrite, "consed.extendConsensusWithHighQuality: %s\n", ( resources_.bExtendConsensusWithHighQuality_ ? "true" : "false" ) ); } // consed.fastStartup if ( resources_.bFastStartup_ != CONDEF->bFastStartup_ ) { fprintf( pFileToWrite, "consed.fastStartup: %s\n", ( resources_.bFastStartup_ ? "true" : "false" ) ); } // consed.fastStartupFile if ( resources_.filFastStartupFile_ != CONDEF->filFastStartupFile_ ) { fprintf( pFileToWrite, "consed.fastStartupFile: %s\n", resources_.filFastStartupFile_.data() ); } // consed.alwaysRunProgramToGetChromats if ( resources_.soAlwaysRunProgramToGetChromats_ != CONDEF->soAlwaysRunProgramToGetChromats_ ) { fprintf( pFileToWrite, "consed.alwaysRunProgramToGetChromats: %s\n", resources_.soAlwaysRunProgramToGetChromats_.data() ); } // consed.programToRunToGetChromats if ( resources_.filProgramToRunToGetChromats_ != CONDEF->filProgramToRunToGetChromats_ ) { fprintf( pFileToWrite, "consed.programToRunToGetChromats: %s\n", resources_.filProgramToRunToGetChromats_.data() ); } // consed.programToRunToGetChromatsOf454Reads if ( resources_.filProgramToRunToGetChromatsOf454Reads_ != CONDEF->filProgramToRunToGetChromatsOf454Reads_ ) { fprintf( pFileToWrite, "consed.programToRunToGetChromatsOf454Reads: %s\n", resources_.filProgramToRunToGetChromatsOf454Reads_.data() ); } // consed.createFakeChromatsForSolexaReads if ( resources_.bCreateFakeChromatsForSolexaReads_ != CONDEF->bCreateFakeChromatsForSolexaReads_ ) { fprintf( pFileToWrite, "consed.createFakeChromatsForSolexaReads: %s\n", ( resources_.bCreateFakeChromatsForSolexaReads_ ? "true" : "false" ) ); } // consed.autoFinishUseLongModelReadRatherThanShort if ( resources_.bAutoFinishUseLongModelReadRatherThanShort_ != CONDEF->bAutoFinishUseLongModelReadRatherThanShort_ ) { fprintf( pFileToWrite, "consed.autoFinishUseLongModelReadRatherThanShort: %s\n", ( resources_.bAutoFinishUseLongModelReadRatherThanShort_ ? "true" : "false" ) ); } // consed.askAgainIfWantToQuitConsedIfThisManyReads if ( resources_.nAskAgainIfWantToQuitConsedIfThisManyReads_ != CONDEF->nAskAgainIfWantToQuitConsedIfThisManyReads_ ) { fprintf( pFileToWrite, "consed.askAgainIfWantToQuitConsedIfThisManyReads: %d\n", resources_.nAskAgainIfWantToQuitConsedIfThisManyReads_ ); } // consed.printWindowInstructions if ( resources_.soPrintWindowInstructions_ != CONDEF->soPrintWindowInstructions_ ) { fprintf( pFileToWrite, "consed.printWindowInstructions: %s\n", resources_.soPrintWindowInstructions_.data() ); } // consed.allowMultipleSearchForStringWindows if ( resources_.bAllowMultipleSearchForStringWindows_ != CONDEF->bAllowMultipleSearchForStringWindows_ ) { fprintf( pFileToWrite, "consed.allowMultipleSearchForStringWindows: %s\n", ( resources_.bAllowMultipleSearchForStringWindows_ ? "true" : "false" ) ); } // consed.autoPCRAmplifyFalseProductsOKIfLargerThanThis if ( resources_.nAutoPCRAmplifyFalseProductsOKIfLargerThanThis_ != CONDEF->nAutoPCRAmplifyFalseProductsOKIfLargerThanThis_ ) { fprintf( pFileToWrite, "consed.autoPCRAmplifyFalseProductsOKIfLargerThanThis: %d\n", resources_.nAutoPCRAmplifyFalseProductsOKIfLargerThanThis_ ); } // consed.autoPCRAmplifyMakePrimerOutOfFirstRegion if ( resources_.bAutoPCRAmplifyMakePrimerOutOfFirstRegion_ != CONDEF->bAutoPCRAmplifyMakePrimerOutOfFirstRegion_ ) { fprintf( pFileToWrite, "consed.autoPCRAmplifyMakePrimerOutOfFirstRegion: %s\n", ( resources_.bAutoPCRAmplifyMakePrimerOutOfFirstRegion_ ? "true" : "false" ) ); } // consed.autoPCRAmplifyMaybeRejectPrimerIfThisCloseToDesiredProduct if ( resources_.nAutoPCRAmplifyMaybeRejectPrimerIfThisCloseToDesiredProduct_ != CONDEF->nAutoPCRAmplifyMaybeRejectPrimerIfThisCloseToDesiredProduct_ ) { fprintf( pFileToWrite, "consed.autoPCRAmplifyMaybeRejectPrimerIfThisCloseToDesiredProduct: %d\n", resources_.nAutoPCRAmplifyMaybeRejectPrimerIfThisCloseToDesiredProduct_ ); } // consed.addNewReadsRecalculateConsensusQuality if ( resources_.bAddNewReadsRecalculateConsensusQuality_ != CONDEF->bAddNewReadsRecalculateConsensusQuality_ ) { fprintf( pFileToWrite, "consed.addNewReadsRecalculateConsensusQuality: %s\n", ( resources_.bAddNewReadsRecalculateConsensusQuality_ ? "true" : "false" ) ); } // consed.addNewReadsPutReadIntoItsOwnContig if ( resources_.soAddNewReadsPutReadIntoItsOwnContig_ != CONDEF->soAddNewReadsPutReadIntoItsOwnContig_ ) { fprintf( pFileToWrite, "consed.addNewReadsPutReadIntoItsOwnContig: %s\n", resources_.soAddNewReadsPutReadIntoItsOwnContig_.data() ); } // consed.addNewReadsCheckThatCrossMatchRunCorrectly if ( resources_.bAddNewReadsCheckThatCrossMatchRunCorrectly_ != CONDEF->bAddNewReadsCheckThatCrossMatchRunCorrectly_ ) { fprintf( pFileToWrite, "consed.addNewReadsCheckThatCrossMatchRunCorrectly: %s\n", ( resources_.bAddNewReadsCheckThatCrossMatchRunCorrectly_ ? "true" : "false" ) ); } // consed.assemblyViewNumberOfRowsOfTags if ( resources_.nAssemblyViewNumberOfRowsOfTags_ != CONDEF->nAssemblyViewNumberOfRowsOfTags_ ) { fprintf( pFileToWrite, "consed.assemblyViewNumberOfRowsOfTags: %d\n", resources_.nAssemblyViewNumberOfRowsOfTags_ ); } // consed.warnUserWhenTryingToEditAllReads if ( resources_.bWarnUserWhenTryingToEditAllReads_ != CONDEF->bWarnUserWhenTryingToEditAllReads_ ) { fprintf( pFileToWrite, "consed.warnUserWhenTryingToEditAllReads: %s\n", ( resources_.bWarnUserWhenTryingToEditAllReads_ ? "true" : "false" ) ); } // consed.maybeXKEYSYMDBPath if ( resources_.filMaybeXKEYSYMDBPath_ != CONDEF->filMaybeXKEYSYMDBPath_ ) { fprintf( pFileToWrite, "consed.maybeXKEYSYMDBPath: %s\n", resources_.filMaybeXKEYSYMDBPath_.data() ); } // consed.maybeXKEYSYMDBPath2 if ( resources_.filMaybeXKEYSYMDBPath2_ != CONDEF->filMaybeXKEYSYMDBPath2_ ) { fprintf( pFileToWrite, "consed.maybeXKEYSYMDBPath2: %s\n", resources_.filMaybeXKEYSYMDBPath2_.data() ); } // consed.amountToMoveWithBigLeftAndRightArrows if ( resources_.nAmountToMoveWithBigLeftAndRightArrows_ != CONDEF->nAmountToMoveWithBigLeftAndRightArrows_ ) { fprintf( pFileToWrite, "consed.amountToMoveWithBigLeftAndRightArrows: %d\n", resources_.nAmountToMoveWithBigLeftAndRightArrows_ ); } // consed.navigateByHighlyDiscrepantPositionsMinDiscrepantReads if ( resources_.nNavigateByHighlyDiscrepantPositionsMinDiscrepantReads_ != CONDEF->nNavigateByHighlyDiscrepantPositionsMinDiscrepantReads_ ) { fprintf( pFileToWrite, "consed.navigateByHighlyDiscrepantPositionsMinDiscrepantReads: %d\n", resources_.nNavigateByHighlyDiscrepantPositionsMinDiscrepantReads_ ); } // consed.navigateByHighlyDiscrepantPositionsMaxDepthOfCoverage if ( resources_.nNavigateByHighlyDiscrepantPositionsMaxDepthOfCoverage_ != CONDEF->nNavigateByHighlyDiscrepantPositionsMaxDepthOfCoverage_ ) { fprintf( pFileToWrite, "consed.navigateByHighlyDiscrepantPositionsMaxDepthOfCoverage: %d\n", resources_.nNavigateByHighlyDiscrepantPositionsMaxDepthOfCoverage_ ); } // consed.navigateByHighlyDiscrepantPositionsIgnoreBasesBelowThisQuality if ( resources_.nNavigateByHighlyDiscrepantPositionsIgnoreBasesBelowThisQuality_ != CONDEF->nNavigateByHighlyDiscrepantPositionsIgnoreBasesBelowThisQuality_ ) { fprintf( pFileToWrite, "consed.navigateByHighlyDiscrepantPositionsIgnoreBasesBelowThisQuality: %d\n", resources_.nNavigateByHighlyDiscrepantPositionsIgnoreBasesBelowThisQuality_ ); } // consed.navigateByHighlyDiscrepantPositionsJustListIndels if ( resources_.bNavigateByHighlyDiscrepantPositionsJustListIndels_ != CONDEF->bNavigateByHighlyDiscrepantPositionsJustListIndels_ ) { fprintf( pFileToWrite, "consed.navigateByHighlyDiscrepantPositionsJustListIndels: %s\n", ( resources_.bNavigateByHighlyDiscrepantPositionsJustListIndels_ ? "true" : "false" ) ); } // consed.navigateByHighlyDiscrepantPositionsIgnoreOtherReadsStartingAtSameLocation if ( resources_.bNavigateByHighlyDiscrepantPositionsIgnoreOtherReadsStartingAtSameLocation_ != CONDEF->bNavigateByHighlyDiscrepantPositionsIgnoreOtherReadsStartingAtSameLocation_ ) { fprintf( pFileToWrite, "consed.navigateByHighlyDiscrepantPositionsIgnoreOtherReadsStartingAtSameLocation: %s\n", ( resources_.bNavigateByHighlyDiscrepantPositionsIgnoreOtherReadsStartingAtSameLocation_ ? "true" : "false" ) ); } // consed.navigateByHighlyDiscrepantPositionsIgnoreIfListedBasesInConsensus if ( resources_.bNavigateByHighlyDiscrepantPositionsIgnoreIfListedBasesInConsensus_ != CONDEF->bNavigateByHighlyDiscrepantPositionsIgnoreIfListedBasesInConsensus_ ) { fprintf( pFileToWrite, "consed.navigateByHighlyDiscrepantPositionsIgnoreIfListedBasesInConsensus: %s\n", ( resources_.bNavigateByHighlyDiscrepantPositionsIgnoreIfListedBasesInConsensus_ ? "true" : "false" ) ); } // consed.navigateByHighlyDiscrepantPositionsIgnoreIfTheseBasesInConsensus if ( resources_.soNavigateByHighlyDiscrepantPositionsIgnoreIfTheseBasesInConsensus_ != CONDEF->soNavigateByHighlyDiscrepantPositionsIgnoreIfTheseBasesInConsensus_ ) { fprintf( pFileToWrite, "consed.navigateByHighlyDiscrepantPositionsIgnoreIfTheseBasesInConsensus: %s\n", resources_.soNavigateByHighlyDiscrepantPositionsIgnoreIfTheseBasesInConsensus_.data() ); } // consed.phdBallDirectory if ( resources_.filPhdBallDirectory_ != CONDEF->filPhdBallDirectory_ ) { fprintf( pFileToWrite, "consed.phdBallDirectory: %s\n", resources_.filPhdBallDirectory_.data() ); } // consed.newAceFileFOF if ( resources_.filNewAceFileFOF_ != CONDEF->filNewAceFileFOF_ ) { fprintf( pFileToWrite, "consed.newAceFileFOF: %s\n", resources_.filNewAceFileFOF_.data() ); } // consed.navigateByHighOrLowDepthCoalesceRegionsIfThisClose if ( resources_.nNavigateByHighOrLowDepthCoalesceRegionsIfThisClose_ != CONDEF->nNavigateByHighOrLowDepthCoalesceRegionsIfThisClose_ ) { fprintf( pFileToWrite, "consed.navigateByHighOrLowDepthCoalesceRegionsIfThisClose: %d\n", resources_.nNavigateByHighOrLowDepthCoalesceRegionsIfThisClose_ ); } // consed.removeReadsDeleteNotJustPutInOwnContig if ( resources_.bRemoveReadsDeleteNotJustPutInOwnContig_ != CONDEF->bRemoveReadsDeleteNotJustPutInOwnContig_ ) { fprintf( pFileToWrite, "consed.removeReadsDeleteNotJustPutInOwnContig: %s\n", ( resources_.bRemoveReadsDeleteNotJustPutInOwnContig_ ? "true" : "false" ) ); } // consed.paired454LeftReadExtension if ( resources_.soPaired454LeftReadExtension_ != CONDEF->soPaired454LeftReadExtension_ ) { fprintf( pFileToWrite, "consed.paired454LeftReadExtension: %s\n", resources_.soPaired454LeftReadExtension_.data() ); } // consed.paired454RightReadExtension if ( resources_.soPaired454RightReadExtension_ != CONDEF->soPaired454RightReadExtension_ ) { fprintf( pFileToWrite, "consed.paired454RightReadExtension: %s\n", resources_.soPaired454RightReadExtension_.data() ); } // consed.snpGenome1MSnps if ( resources_.filSnpGenome1MSnps_ != CONDEF->filSnpGenome1MSnps_ ) { fprintf( pFileToWrite, "consed.snpGenome1MSnps: %s\n", resources_.filSnpGenome1MSnps_.data() ); } // consed.diffChromosomesExcludeDeletions if ( resources_.bDiffChromosomesExcludeDeletions_ != CONDEF->bDiffChromosomesExcludeDeletions_ ) { fprintf( pFileToWrite, "consed.diffChromosomesExcludeDeletions: %s\n", ( resources_.bDiffChromosomesExcludeDeletions_ ? "true" : "false" ) ); } // consed.snpGenomeFilterByWeight if ( resources_.bSnpGenomeFilterByWeight_ != CONDEF->bSnpGenomeFilterByWeight_ ) { fprintf( pFileToWrite, "consed.snpGenomeFilterByWeight: %s\n", ( resources_.bSnpGenomeFilterByWeight_ ? "true" : "false" ) ); } // consed.wantReadsUpToThisFarFromSnps if ( resources_.nWantReadsUpToThisFarFromSnps_ != CONDEF->nWantReadsUpToThisFarFromSnps_ ) { fprintf( pFileToWrite, "consed.wantReadsUpToThisFarFromSnps: %d\n", resources_.nWantReadsUpToThisFarFromSnps_ ); } // consed.phaster2PhdBallSaveWhichMate if ( resources_.soPhaster2PhdBallSaveWhichMate_ != CONDEF->soPhaster2PhdBallSaveWhichMate_ ) { fprintf( pFileToWrite, "consed.phaster2PhdBallSaveWhichMate: %s\n", resources_.soPhaster2PhdBallSaveWhichMate_.data() ); } // consed.phaster2PhdBallSaveInPhasterFormat if ( resources_.bPhaster2PhdBallSaveInPhasterFormat_ != CONDEF->bPhaster2PhdBallSaveInPhasterFormat_ ) { fprintf( pFileToWrite, "consed.phaster2PhdBallSaveInPhasterFormat: %s\n", ( resources_.bPhaster2PhdBallSaveInPhasterFormat_ ? "true" : "false" ) ); } // consed.phaster2PhdBallCalculateNewLocationsFile if ( resources_.bPhaster2PhdBallCalculateNewLocationsFile_ != CONDEF->bPhaster2PhdBallCalculateNewLocationsFile_ ) { fprintf( pFileToWrite, "consed.phaster2PhdBallCalculateNewLocationsFile: %s\n", ( resources_.bPhaster2PhdBallCalculateNewLocationsFile_ ? "true" : "false" ) ); } // consed.phdBall2FastaIgnoreLowQualityReads if ( resources_.bPhdBall2FastaIgnoreLowQualityReads_ != CONDEF->bPhdBall2FastaIgnoreLowQualityReads_ ) { fprintf( pFileToWrite, "consed.phdBall2FastaIgnoreLowQualityReads: %s\n", ( resources_.bPhdBall2FastaIgnoreLowQualityReads_ ? "true" : "false" ) ); } // consed.phdBall2FastaLowestAverageQuality if ( resources_.nPhdBall2FastaLowestAverageQuality_ != CONDEF->nPhdBall2FastaLowestAverageQuality_ ) { fprintf( pFileToWrite, "consed.phdBall2FastaLowestAverageQuality: %d\n", resources_.nPhdBall2FastaLowestAverageQuality_ ); } // consed.nextPhredPipelineControlFile if ( resources_.filNextPhredPipelineControlFile_ != CONDEF->filNextPhredPipelineControlFile_ ) { fprintf( pFileToWrite, "consed.nextPhredPipelineControlFile: %s\n", resources_.filNextPhredPipelineControlFile_.data() ); } // consed.nextPhredPipelineTiffPerlScript if ( resources_.filNextPhredPipelineTiffPerlScript_ != CONDEF->filNextPhredPipelineTiffPerlScript_ ) { fprintf( pFileToWrite, "consed.nextPhredPipelineTiffPerlScript: %s\n", resources_.filNextPhredPipelineTiffPerlScript_.data() ); } // consed.nextPhredPipelinePhasterPerlScript if ( resources_.filNextPhredPipelinePhasterPerlScript_ != CONDEF->filNextPhredPipelinePhasterPerlScript_ ) { fprintf( pFileToWrite, "consed.nextPhredPipelinePhasterPerlScript: %s\n", resources_.filNextPhredPipelinePhasterPerlScript_.data() ); } // consed.nextPhredPipelineVersion if ( resources_.soNextPhredPipelineVersion_ != CONDEF->soNextPhredPipelineVersion_ ) { fprintf( pFileToWrite, "consed.nextPhredPipelineVersion: %s\n", resources_.soNextPhredPipelineVersion_.data() ); } // consed.nextPhredPipelineMainDirectory if ( resources_.soNextPhredPipelineMainDirectory_ != CONDEF->soNextPhredPipelineMainDirectory_ ) { fprintf( pFileToWrite, "consed.nextPhredPipelineMainDirectory: %s\n", resources_.soNextPhredPipelineMainDirectory_.data() ); } // consed.maxNumberOfReadsPerPhdBall if ( resources_.nMaxNumberOfReadsPerPhdBall_ != CONDEF->nMaxNumberOfReadsPerPhdBall_ ) { fprintf( pFileToWrite, "consed.maxNumberOfReadsPerPhdBall: %d\n", resources_.nMaxNumberOfReadsPerPhdBall_ ); } // consed.userWantsToSaveToThisAceFile if ( resources_.filUserWantsToSaveToThisAceFile_ != CONDEF->filUserWantsToSaveToThisAceFile_ ) { fprintf( pFileToWrite, "consed.userWantsToSaveToThisAceFile: %s\n", resources_.filUserWantsToSaveToThisAceFile_.data() ); } // consed.autoFinishEmulate9_66Behavior if ( resources_.bAutoFinishEmulate9_66Behavior_ != CONDEF->bAutoFinishEmulate9_66Behavior_ ) { fprintf( pFileToWrite, "consed.autoFinishEmulate9_66Behavior: %s\n", ( resources_.bAutoFinishEmulate9_66Behavior_ ? "true" : "false" ) ); } // consed.primersPCRPrimersGroupedIntoWindowOfThisManyBases if ( resources_.nPrimersPCRPrimersGroupedIntoWindowOfThisManyBases_ != CONDEF->nPrimersPCRPrimersGroupedIntoWindowOfThisManyBases_ ) { fprintf( pFileToWrite, "consed.primersPCRPrimersGroupedIntoWindowOfThisManyBases: %d\n", resources_.nPrimersPCRPrimersGroupedIntoWindowOfThisManyBases_ ); } // consed.primersLookForThisManyPCRPrimerPairsPerPairOfGroups if ( resources_.nPrimersLookForThisManyPCRPrimerPairsPerPairOfGroups_ != CONDEF->nPrimersLookForThisManyPCRPrimerPairsPerPairOfGroups_ ) { fprintf( pFileToWrite, "consed.primersLookForThisManyPCRPrimerPairsPerPairOfGroups: %d\n", resources_.nPrimersLookForThisManyPCRPrimerPairsPerPairOfGroups_ ); } // consed.autoFinishStandardDeviationsFromMeanFromGapToLookForTemplatesForSuggestingEachMissingReadOfReadPairs if ( resources_.dAutoFinishStandardDeviationsFromMeanFromGapToLookForTemplatesForSuggestingEachMissingReadOfReadPairs_ != CONDEF->dAutoFinishStandardDeviationsFromMeanFromGapToLookForTemplatesForSuggestingEachMissingReadOfReadPairs_ ) { fprintf( pFileToWrite, "consed.autoFinishStandardDeviationsFromMeanFromGapToLookForTemplatesForSuggestingEachMissingReadOfReadPairs: %f\n", resources_.dAutoFinishStandardDeviationsFromMeanFromGapToLookForTemplatesForSuggestingEachMissingReadOfReadPairs_ ); } // consed.autoFinishCheckThatReadsFromTheSameTemplateAreConsistent if ( resources_.bAutoFinishCheckThatReadsFromTheSameTemplateAreConsistent_ != CONDEF->bAutoFinishCheckThatReadsFromTheSameTemplateAreConsistent_ ) { fprintf( pFileToWrite, "consed.autoFinishCheckThatReadsFromTheSameTemplateAreConsistent: %s\n", ( resources_.bAutoFinishCheckThatReadsFromTheSameTemplateAreConsistent_ ? "true" : "false" ) ); } // consed.autoFinishDoNotAllowSubcloneCustomPrimerReadsCloseTogether if ( resources_.bAutoFinishDoNotAllowSubcloneCustomPrimerReadsCloseTogether_ != CONDEF->bAutoFinishDoNotAllowSubcloneCustomPrimerReadsCloseTogether_ ) { fprintf( pFileToWrite, "consed.autoFinishDoNotAllowSubcloneCustomPrimerReadsCloseTogether: %s\n", ( resources_.bAutoFinishDoNotAllowSubcloneCustomPrimerReadsCloseTogether_ ? "true" : "false" ) ); } // consed.autoFinishDoNotAllowWholeCloneCustomPrimerReadsCloseTogether if ( resources_.bAutoFinishDoNotAllowWholeCloneCustomPrimerReadsCloseTogether_ != CONDEF->bAutoFinishDoNotAllowWholeCloneCustomPrimerReadsCloseTogether_ ) { fprintf( pFileToWrite, "consed.autoFinishDoNotAllowWholeCloneCustomPrimerReadsCloseTogether: %s\n", ( resources_.bAutoFinishDoNotAllowWholeCloneCustomPrimerReadsCloseTogether_ ? "true" : "false" ) ); } // consed.autoFinishMinilibrariesPreferTemplateIfSizeThisManyStdDevsFromMean if ( resources_.dAutoFinishMinilibrariesPreferTemplateIfSizeThisManyStdDevsFromMean_ != CONDEF->dAutoFinishMinilibrariesPreferTemplateIfSizeThisManyStdDevsFromMean_ ) { fprintf( pFileToWrite, "consed.autoFinishMinilibrariesPreferTemplateIfSizeThisManyStdDevsFromMean: %f\n", resources_.dAutoFinishMinilibrariesPreferTemplateIfSizeThisManyStdDevsFromMean_ ); } // consed.autoFinishMinNumberOfForwardReversePairsInLibraryToCalculateAverageInsertSize if ( resources_.nAutoFinishMinNumberOfForwardReversePairsInLibraryToCalculateAverageInsertSize_ != CONDEF->nAutoFinishMinNumberOfForwardReversePairsInLibraryToCalculateAverageInsertSize_ ) { fprintf( pFileToWrite, "consed.autoFinishMinNumberOfForwardReversePairsInLibraryToCalculateAverageInsertSize: %d\n", resources_.nAutoFinishMinNumberOfForwardReversePairsInLibraryToCalculateAverageInsertSize_ ); } // consed.autoFinishIfEnoughFwdRevPairsUseThisManyStdDevBelowMeanForInsertSize if ( resources_.dAutoFinishIfEnoughFwdRevPairsUseThisManyStdDevBelowMeanForInsertSize_ != CONDEF->dAutoFinishIfEnoughFwdRevPairsUseThisManyStdDevBelowMeanForInsertSize_ ) { fprintf( pFileToWrite, "consed.autoFinishIfEnoughFwdRevPairsUseThisManyStdDevBelowMeanForInsertSize: %f\n", resources_.dAutoFinishIfEnoughFwdRevPairsUseThisManyStdDevBelowMeanForInsertSize_ ); } // consed.autoFinishNewCustomPrimerReadThisFarFromOldCustomPrimerRead if ( resources_.nAutoFinishNewCustomPrimerReadThisFarFromOldCustomPrimerRead_ != CONDEF->nAutoFinishNewCustomPrimerReadThisFarFromOldCustomPrimerRead_ ) { fprintf( pFileToWrite, "consed.autoFinishNewCustomPrimerReadThisFarFromOldCustomPrimerRead: %d\n", resources_.nAutoFinishNewCustomPrimerReadThisFarFromOldCustomPrimerRead_ ); } // consed.autoFinishMinNumberOfSingleSubcloneBasesFixedByAnExp if ( resources_.nAutoFinishMinNumberOfSingleSubcloneBasesFixedByAnExp_ != CONDEF->nAutoFinishMinNumberOfSingleSubcloneBasesFixedByAnExp_ ) { fprintf( pFileToWrite, "consed.autoFinishMinNumberOfSingleSubcloneBasesFixedByAnExp: %d\n", resources_.nAutoFinishMinNumberOfSingleSubcloneBasesFixedByAnExp_ ); } // consed.autoFinishNumberOfBasesBetweenContigsAssumed if ( resources_.nAutoFinishNumberOfBasesBetweenContigsAssumed_ != CONDEF->nAutoFinishNumberOfBasesBetweenContigsAssumed_ ) { fprintf( pFileToWrite, "consed.autoFinishNumberOfBasesBetweenContigsAssumed: %d\n", resources_.nAutoFinishNumberOfBasesBetweenContigsAssumed_ ); } // consed.autoFinishPotentialHighQualityPartOfReadStart if ( resources_.nAutoFinishPotentialHighQualityPartOfReadStart_ != CONDEF->nAutoFinishPotentialHighQualityPartOfReadStart_ ) { fprintf( pFileToWrite, "consed.autoFinishPotentialHighQualityPartOfReadStart: %d\n", resources_.nAutoFinishPotentialHighQualityPartOfReadStart_ ); } // consed.autoFinishPotentialHighQualityPartOfReadEnd if ( resources_.nAutoFinishPotentialHighQualityPartOfReadEnd_ != CONDEF->nAutoFinishPotentialHighQualityPartOfReadEnd_ ) { fprintf( pFileToWrite, "consed.autoFinishPotentialHighQualityPartOfReadEnd: %d\n", resources_.nAutoFinishPotentialHighQualityPartOfReadEnd_ ); } // consed.autoFinishPrintCustomNavigationFileForChosenReads if ( resources_.bAutoFinishPrintCustomNavigationFileForChosenReads_ != CONDEF->bAutoFinishPrintCustomNavigationFileForChosenReads_ ) { fprintf( pFileToWrite, "consed.autoFinishPrintCustomNavigationFileForChosenReads: %s\n", ( resources_.bAutoFinishPrintCustomNavigationFileForChosenReads_ ? "true" : "false" ) ); } // consed.autoFinishReversesForFlankingGapsTemplateMustProtrudeFromContigThisMuch if ( resources_.nAutoFinishReversesForFlankingGapsTemplateMustProtrudeFromContigThisMuch_ != CONDEF->nAutoFinishReversesForFlankingGapsTemplateMustProtrudeFromContigThisMuch_ ) { fprintf( pFileToWrite, "consed.autoFinishReversesForFlankingGapsTemplateMustProtrudeFromContigThisMuch: %d\n", resources_.nAutoFinishReversesForFlankingGapsTemplateMustProtrudeFromContigThisMuch_ ); } // consed.autoFinishTagOligosWhenDoExperiments if ( resources_.bAutoFinishTagOligosWhenDoExperiments_ != CONDEF->bAutoFinishTagOligosWhenDoExperiments_ ) { fprintf( pFileToWrite, "consed.autoFinishTagOligosWhenDoExperiments: %s\n", ( resources_.bAutoFinishTagOligosWhenDoExperiments_ ? "true" : "false" ) ); } // consed.countPads if ( resources_.bCountPads_ != CONDEF->bCountPads_ ) { fprintf( pFileToWrite, "consed.countPads: %s\n", ( resources_.bCountPads_ ? "true" : "false" ) ); } // consed.debugging if ( resources_.nDebugging_ != CONDEF->nDebugging_ ) { fprintf( pFileToWrite, "consed.debugging: %d\n", resources_.nDebugging_ ); } // consed.debugging2 if ( resources_.nDebugging2_ != CONDEF->nDebugging2_ ) { fprintf( pFileToWrite, "consed.debugging2: %d\n", resources_.nDebugging2_ ); } // consed.debugging3 if ( resources_.nDebugging3_ != CONDEF->nDebugging3_ ) { fprintf( pFileToWrite, "consed.debugging3: %d\n", resources_.nDebugging3_ ); } // consed.debuggingString if ( resources_.soDebuggingString_ != CONDEF->soDebuggingString_ ) { fprintf( pFileToWrite, "consed.debuggingString: %s\n", resources_.soDebuggingString_.data() ); } // consed.ignoreHighQualityDiscrepanciesThisManyBasesFromEndOfAlignedRegion if ( resources_.nIgnoreHighQualityDiscrepanciesThisManyBasesFromEndOfAlignedRegion_ != CONDEF->nIgnoreHighQualityDiscrepanciesThisManyBasesFromEndOfAlignedRegion_ ) { fprintf( pFileToWrite, "consed.ignoreHighQualityDiscrepanciesThisManyBasesFromEndOfAlignedRegion: %d\n", resources_.nIgnoreHighQualityDiscrepanciesThisManyBasesFromEndOfAlignedRegion_ ); } // consed.ignoreUnalignedHighQualitySegmentsShorterThanThis if ( resources_.nIgnoreUnalignedHighQualitySegmentsShorterThanThis_ != CONDEF->nIgnoreUnalignedHighQualitySegmentsShorterThanThis_ ) { fprintf( pFileToWrite, "consed.ignoreUnalignedHighQualitySegmentsShorterThanThis: %d\n", resources_.nIgnoreUnalignedHighQualitySegmentsShorterThanThis_ ); } // consed.primersLookThisFarForForwardVectorInsertJunction if ( resources_.nPrimersLookThisFarForForwardVectorInsertJunction_ != CONDEF->nPrimersLookThisFarForForwardVectorInsertJunction_ ) { fprintf( pFileToWrite, "consed.primersLookThisFarForForwardVectorInsertJunction: %d\n", resources_.nPrimersLookThisFarForForwardVectorInsertJunction_ ); } // consed.primersDNAConcentrationNanomolar if ( resources_.dPrimersDNAConcentrationNanomolar_ != CONDEF->dPrimersDNAConcentrationNanomolar_ ) { fprintf( pFileToWrite, "consed.primersDNAConcentrationNanomolar: %f\n", resources_.dPrimersDNAConcentrationNanomolar_ ); } // consed.primersMaxMatchElsewhereScore if ( resources_.nPrimersMaxMatchElsewhereScore_ != CONDEF->nPrimersMaxMatchElsewhereScore_ ) { fprintf( pFileToWrite, "consed.primersMaxMatchElsewhereScore: %d\n", resources_.nPrimersMaxMatchElsewhereScore_ ); } // consed.primersMaxMatchElsewhereScoreForPCR if ( resources_.nPrimersMaxMatchElsewhereScoreForPCR_ != CONDEF->nPrimersMaxMatchElsewhereScoreForPCR_ ) { fprintf( pFileToWrite, "consed.primersMaxMatchElsewhereScoreForPCR: %d\n", resources_.nPrimersMaxMatchElsewhereScoreForPCR_ ); } // consed.primersMaxSelfMatchScore if ( resources_.nPrimersMaxSelfMatchScore_ != CONDEF->nPrimersMaxSelfMatchScore_ ) { fprintf( pFileToWrite, "consed.primersMaxSelfMatchScore: %d\n", resources_.nPrimersMaxSelfMatchScore_ ); } // consed.primersMaxPrimerDimerScoreForPCR if ( resources_.nPrimersMaxPrimerDimerScoreForPCR_ != CONDEF->nPrimersMaxPrimerDimerScoreForPCR_ ) { fprintf( pFileToWrite, "consed.primersMaxPrimerDimerScoreForPCR: %d\n", resources_.nPrimersMaxPrimerDimerScoreForPCR_ ); } // consed.primersMinQuality if ( resources_.nPrimersMinQuality_ != CONDEF->nPrimersMinQuality_ ) { fprintf( pFileToWrite, "consed.primersMinQuality: %d\n", resources_.nPrimersMinQuality_ ); } // consed.primersPrintInfoOnRejectedTemplates if ( resources_.bPrimersPrintInfoOnRejectedTemplates_ != CONDEF->bPrimersPrintInfoOnRejectedTemplates_ ) { fprintf( pFileToWrite, "consed.primersPrintInfoOnRejectedTemplates: %s\n", ( resources_.bPrimersPrintInfoOnRejectedTemplates_ ? "true" : "false" ) ); } // consed.primersSaltConcentrationMillimolar if ( resources_.dPrimersSaltConcentrationMillimolar_ != CONDEF->dPrimersSaltConcentrationMillimolar_ ) { fprintf( pFileToWrite, "consed.primersSaltConcentrationMillimolar: %f\n", resources_.dPrimersSaltConcentrationMillimolar_ ); } // consed.primersScreenForVector if ( resources_.bPrimersScreenForVector_ != CONDEF->bPrimersScreenForVector_ ) { fprintf( pFileToWrite, "consed.primersScreenForVector: %s\n", ( resources_.bPrimersScreenForVector_ ? "true" : "false" ) ); } // consed.primersToleranceForDifferentBeginningLocationOfUniversalPrimerReads if ( resources_.nPrimersToleranceForDifferentBeginningLocationOfUniversalPrimerReads_ != CONDEF->nPrimersToleranceForDifferentBeginningLocationOfUniversalPrimerReads_ ) { fprintf( pFileToWrite, "consed.primersToleranceForDifferentBeginningLocationOfUniversalPrimerReads: %d\n", resources_.nPrimersToleranceForDifferentBeginningLocationOfUniversalPrimerReads_ ); } // consed.primersTooManyVectorBasesInWalkingRead if ( resources_.nPrimersTooManyVectorBasesInWalkingRead_ != CONDEF->nPrimersTooManyVectorBasesInWalkingRead_ ) { fprintf( pFileToWrite, "consed.primersTooManyVectorBasesInWalkingRead: %d\n", resources_.nPrimersTooManyVectorBasesInWalkingRead_ ); } // consed.qualityThresholdForLowConsensusQuality if ( resources_.nQualityThresholdForLowConsensusQuality_ != CONDEF->nQualityThresholdForLowConsensusQuality_ ) { fprintf( pFileToWrite, "consed.qualityThresholdForLowConsensusQuality: %d\n", resources_.nQualityThresholdForLowConsensusQuality_ ); } // consed.tagColorPerCentOfBase if ( resources_.nTagColorPerCentOfBase_ != CONDEF->nTagColorPerCentOfBase_ ) { fprintf( pFileToWrite, "consed.tagColorPerCentOfBase: %d\n", resources_.nTagColorPerCentOfBase_ ); } // consed.uncompressedChromatDirectory if ( resources_.soUncompressedChromatDirectory_ != CONDEF->soUncompressedChromatDirectory_ ) { fprintf( pFileToWrite, "consed.uncompressedChromatDirectory: %s\n", resources_.soUncompressedChromatDirectory_.data() ); } // consed.454sff2scfDirectory if ( resources_.fil454sff2scfDirectory_ != CONDEF->fil454sff2scfDirectory_ ) { fprintf( pFileToWrite, "consed.454sff2scfDirectory: %s\n", resources_.fil454sff2scfDirectory_.data() ); } // consed.whenMakingFakeReadToJoinContigsAddThisManyBasesOnEitherSideOfAlignedRegion if ( resources_.nWhenMakingFakeReadToJoinContigsAddThisManyBasesOnEitherSideOfAlignedRegion_ != CONDEF->nWhenMakingFakeReadToJoinContigsAddThisManyBasesOnEitherSideOfAlignedRegion_ ) { fprintf( pFileToWrite, "consed.whenMakingFakeReadToJoinContigsAddThisManyBasesOnEitherSideOfAlignedRegion: %d\n", resources_.nWhenMakingFakeReadToJoinContigsAddThisManyBasesOnEitherSideOfAlignedRegion_ ); } // consed.writeThisAceFormat if ( resources_.nWriteThisAceFormat_ != CONDEF->nWriteThisAceFormat_ ) { fprintf( pFileToWrite, "consed.writeThisAceFormat: %d\n", resources_.nWriteThisAceFormat_ ); } // consed.dumpCoreIfBoundsError if ( resources_.bDumpCoreIfBoundsError_ != CONDEF->bDumpCoreIfBoundsError_ ) { fprintf( pFileToWrite, "consed.dumpCoreIfBoundsError: %s\n", ( resources_.bDumpCoreIfBoundsError_ ? "true" : "false" ) ); } // consed.autoFinishMinSmithWatermanScoreOfARun if ( resources_.nAutoFinishMinSmithWatermanScoreOfARun_ != CONDEF->nAutoFinishMinSmithWatermanScoreOfARun_ ) { fprintf( pFileToWrite, "consed.autoFinishMinSmithWatermanScoreOfARun: %d\n", resources_.nAutoFinishMinSmithWatermanScoreOfARun_ ); } // consed.autoFinishDoNotComparePCRPrimersMoreThanThisManyTimes if ( resources_.dAutoFinishDoNotComparePCRPrimersMoreThanThisManyTimes_ != CONDEF->dAutoFinishDoNotComparePCRPrimersMoreThanThisManyTimes_ ) { fprintf( pFileToWrite, "consed.autoFinishDoNotComparePCRPrimersMoreThanThisManyTimes: %f\n", resources_.dAutoFinishDoNotComparePCRPrimersMoreThanThisManyTimes_ ); } // consed.restrictionDigestMaximumBasesToCompareToVector if ( resources_.nRestrictionDigestMaximumBasesToCompareToVector_ != CONDEF->nRestrictionDigestMaximumBasesToCompareToVector_ ) { fprintf( pFileToWrite, "consed.restrictionDigestMaximumBasesToCompareToVector: %d\n", resources_.nRestrictionDigestMaximumBasesToCompareToVector_ ); } // consed.restrictionDigestZoomFactor if ( resources_.dRestrictionDigestZoomFactor_ != CONDEF->dRestrictionDigestZoomFactor_ ) { fprintf( pFileToWrite, "consed.restrictionDigestZoomFactor: %f\n", resources_.dRestrictionDigestZoomFactor_ ); } // consed.restrictionDigestZoomFactorForNavigate if ( resources_.dRestrictionDigestZoomFactorForNavigate_ != CONDEF->dRestrictionDigestZoomFactorForNavigate_ ) { fprintf( pFileToWrite, "consed.restrictionDigestZoomFactorForNavigate: %f\n", resources_.dRestrictionDigestZoomFactorForNavigate_ ); } // consed.restrictionDigestToleranceInPositionUnits if ( resources_.nRestrictionDigestToleranceInPositionUnits_ != CONDEF->nRestrictionDigestToleranceInPositionUnits_ ) { fprintf( pFileToWrite, "consed.restrictionDigestToleranceInPositionUnits: %d\n", resources_.nRestrictionDigestToleranceInPositionUnits_ ); } // consed.autoPCRAmplifyTooManySeriousFalseMatches if ( resources_.nAutoPCRAmplifyTooManySeriousFalseMatches_ != CONDEF->nAutoPCRAmplifyTooManySeriousFalseMatches_ ) { fprintf( pFileToWrite, "consed.autoPCRAmplifyTooManySeriousFalseMatches: %d\n", resources_.nAutoPCRAmplifyTooManySeriousFalseMatches_ ); } // consed.assemblyViewZoomFactor if ( resources_.dAssemblyViewZoomFactor_ != CONDEF->dAssemblyViewZoomFactor_ ) { fprintf( pFileToWrite, "consed.assemblyViewZoomFactor: %f\n", resources_.dAssemblyViewZoomFactor_ ); } // consed.assemblyViewFilterInconsistentFwdRevPairsIfThisClose if ( resources_.nAssemblyViewFilterInconsistentFwdRevPairsIfThisClose_ != CONDEF->nAssemblyViewFilterInconsistentFwdRevPairsIfThisClose_ ) { fprintf( pFileToWrite, "consed.assemblyViewFilterInconsistentFwdRevPairsIfThisClose: %d\n", resources_.nAssemblyViewFilterInconsistentFwdRevPairsIfThisClose_ ); } // consed.assemblyViewGridCellWidthInPixels if ( resources_.dAssemblyViewGridCellWidthInPixels_ != CONDEF->dAssemblyViewGridCellWidthInPixels_ ) { fprintf( pFileToWrite, "consed.assemblyViewGridCellWidthInPixels: %f\n", resources_.dAssemblyViewGridCellWidthInPixels_ ); } // consed.assemblyViewCursorSensitivityInPixels if ( resources_.nAssemblyViewCursorSensitivityInPixels_ != CONDEF->nAssemblyViewCursorSensitivityInPixels_ ) { fprintf( pFileToWrite, "consed.assemblyViewCursorSensitivityInPixels: %d\n", resources_.nAssemblyViewCursorSensitivityInPixels_ ); } // consed.assemblyViewReadDepthQuality if ( resources_.nAssemblyViewReadDepthQuality_ != CONDEF->nAssemblyViewReadDepthQuality_ ) { fprintf( pFileToWrite, "consed.assemblyViewReadDepthQuality: %d\n", resources_.nAssemblyViewReadDepthQuality_ ); } // consed.showAllTracesMaxNumberOfTracesToShowAtOnce if ( resources_.nShowAllTracesMaxNumberOfTracesToShowAtOnce_ != CONDEF->nShowAllTracesMaxNumberOfTracesToShowAtOnce_ ) { fprintf( pFileToWrite, "consed.showAllTracesMaxNumberOfTracesToShowAtOnce: %d\n", resources_.nShowAllTracesMaxNumberOfTracesToShowAtOnce_ ); } // consed.allowFwdRevPairScaffoldsToBeMergedIfThisManyBasesIntersectionOrLess if ( resources_.nAllowFwdRevPairScaffoldsToBeMergedIfThisManyBasesIntersectionOrLess_ != CONDEF->nAllowFwdRevPairScaffoldsToBeMergedIfThisManyBasesIntersectionOrLess_ ) { fprintf( pFileToWrite, "consed.allowFwdRevPairScaffoldsToBeMergedIfThisManyBasesIntersectionOrLess: %d\n", resources_.nAllowFwdRevPairScaffoldsToBeMergedIfThisManyBasesIntersectionOrLess_ ); } // consed.justForPrimateProject if ( resources_.bJustForPrimateProject_ != CONDEF->bJustForPrimateProject_ ) { fprintf( pFileToWrite, "consed.justForPrimateProject: %s\n", ( resources_.bJustForPrimateProject_ ? "true" : "false" ) ); } // consed.solexaFilesAreAssumedToBeHere if ( resources_.filSolexaFilesAreAssumedToBeHere_ != CONDEF->filSolexaFilesAreAssumedToBeHere_ ) { fprintf( pFileToWrite, "consed.solexaFilesAreAssumedToBeHere: %s\n", resources_.filSolexaFilesAreAssumedToBeHere_.data() ); } // consed.solexaAlignmentFilesPerInsertingPadsCycle if ( resources_.nSolexaAlignmentFilesPerInsertingPadsCycle_ != CONDEF->nSolexaAlignmentFilesPerInsertingPadsCycle_ ) { fprintf( pFileToWrite, "consed.solexaAlignmentFilesPerInsertingPadsCycle: %d\n", resources_.nSolexaAlignmentFilesPerInsertingPadsCycle_ ); } // consed.solexaAlignmentsPerAlignmentFile if ( resources_.nSolexaAlignmentsPerAlignmentFile_ != CONDEF->nSolexaAlignmentsPerAlignmentFile_ ) { fprintf( pFileToWrite, "consed.solexaAlignmentsPerAlignmentFile: %d\n", resources_.nSolexaAlignmentsPerAlignmentFile_ ); } // consed.solexaFastqFilesArePhredQualityNotSolexaQuality if ( resources_.bSolexaFastqFilesArePhredQualityNotSolexaQuality_ != CONDEF->bSolexaFastqFilesArePhredQualityNotSolexaQuality_ ) { fprintf( pFileToWrite, "consed.solexaFastqFilesArePhredQualityNotSolexaQuality: %s\n", ( resources_.bSolexaFastqFilesArePhredQualityNotSolexaQuality_ ? "true" : "false" ) ); } // consed.solexa64FastqOrSanger33Fastq if ( resources_.soSolexa64FastqOrSanger33Fastq_ != CONDEF->soSolexa64FastqOrSanger33Fastq_ ) { fprintf( pFileToWrite, "consed.solexa64FastqOrSanger33Fastq: %s\n", resources_.soSolexa64FastqOrSanger33Fastq_.data() ); } // consed.maximumReadsInReadList if ( resources_.nMaximumReadsInReadList_ != CONDEF->nMaximumReadsInReadList_ ) { fprintf( pFileToWrite, "consed.maximumReadsInReadList: %d\n", resources_.nMaximumReadsInReadList_ ); } // consed.maxLengthOfReadsInapLocatedFragment2 if ( resources_.nMaxLengthOfReadsInapLocatedFragment2_ != CONDEF->nMaxLengthOfReadsInapLocatedFragment2_ ) { fprintf( pFileToWrite, "consed.maxLengthOfReadsInapLocatedFragment2: %d\n", resources_.nMaxLengthOfReadsInapLocatedFragment2_ ); } // consed.maximumStartupErrorsToReport if ( resources_.nMaximumStartupErrorsToReport_ != CONDEF->nMaximumStartupErrorsToReport_ ) { fprintf( pFileToWrite, "consed.maximumStartupErrorsToReport: %d\n", resources_.nMaximumStartupErrorsToReport_ ); } // consed.454LinkerAlignmentMatchScore if ( resources_.n454LinkerAlignmentMatchScore_ != CONDEF->n454LinkerAlignmentMatchScore_ ) { fprintf( pFileToWrite, "consed.454LinkerAlignmentMatchScore: %d\n", resources_.n454LinkerAlignmentMatchScore_ ); } // consed.454LinkerAlignmentMismatchScore if ( resources_.n454LinkerAlignmentMismatchScore_ != CONDEF->n454LinkerAlignmentMismatchScore_ ) { fprintf( pFileToWrite, "consed.454LinkerAlignmentMismatchScore: %d\n", resources_.n454LinkerAlignmentMismatchScore_ ); } // consed.454LinkerAlignmentIndelScore if ( resources_.n454LinkerAlignmentIndelScore_ != CONDEF->n454LinkerAlignmentIndelScore_ ) { fprintf( pFileToWrite, "consed.454LinkerAlignmentIndelScore: %d\n", resources_.n454LinkerAlignmentIndelScore_ ); } // consed.filter454ReadsDeleteCrossMatchOutput if ( resources_.bFilter454ReadsDeleteCrossMatchOutput_ != CONDEF->bFilter454ReadsDeleteCrossMatchOutput_ ) { fprintf( pFileToWrite, "consed.filter454ReadsDeleteCrossMatchOutput: %s\n", ( resources_.bFilter454ReadsDeleteCrossMatchOutput_ ? "true" : "false" ) ); } // consed.autoReportAllNeededSpeciesCode if ( resources_.nAutoReportAllNeededSpeciesCode_ != CONDEF->nAutoReportAllNeededSpeciesCode_ ) { fprintf( pFileToWrite, "consed.autoReportAllNeededSpeciesCode: %d\n", resources_.nAutoReportAllNeededSpeciesCode_ ); } // consed.autoReportUseCommasInBigNumbers if ( resources_.bAutoReportUseCommasInBigNumbers_ != CONDEF->bAutoReportUseCommasInBigNumbers_ ) { fprintf( pFileToWrite, "consed.autoReportUseCommasInBigNumbers: %s\n", ( resources_.bAutoReportUseCommasInBigNumbers_ ? "true" : "false" ) ); } // consed.autoReportPrintToCompareToReich if ( resources_.bAutoReportPrintToCompareToReich_ != CONDEF->bAutoReportPrintToCompareToReich_ ) { fprintf( pFileToWrite, "consed.autoReportPrintToCompareToReich: %s\n", ( resources_.bAutoReportPrintToCompareToReich_ ? "true" : "false" ) ); } // consed.autoReportOnlyAllowSitesThatAreBetweenAcceptableSites if ( resources_.bAutoReportOnlyAllowSitesThatAreBetweenAcceptableSites_ != CONDEF->bAutoReportOnlyAllowSitesThatAreBetweenAcceptableSites_ ) { fprintf( pFileToWrite, "consed.autoReportOnlyAllowSitesThatAreBetweenAcceptableSites: %s\n", ( resources_.bAutoReportOnlyAllowSitesThatAreBetweenAcceptableSites_ ? "true" : "false" ) ); } // consed.autoReportDeaminationMutationsDeterminedByMoreAccurateMethod if ( resources_.bAutoReportDeaminationMutationsDeterminedByMoreAccurateMethod_ != CONDEF->bAutoReportDeaminationMutationsDeterminedByMoreAccurateMethod_ ) { fprintf( pFileToWrite, "consed.autoReportDeaminationMutationsDeterminedByMoreAccurateMethod: %s\n", ( resources_.bAutoReportDeaminationMutationsDeterminedByMoreAccurateMethod_ ? "true" : "false" ) ); } // consed.autoReportChooseTreesUsingBadData if ( resources_.bAutoReportChooseTreesUsingBadData_ != CONDEF->bAutoReportChooseTreesUsingBadData_ ) { fprintf( pFileToWrite, "consed.autoReportChooseTreesUsingBadData: %s\n", ( resources_.bAutoReportChooseTreesUsingBadData_ ? "true" : "false" ) ); } // consed.autoReportChooseTreesByCountingDeaminationMutations if ( resources_.bAutoReportChooseTreesByCountingDeaminationMutations_ != CONDEF->bAutoReportChooseTreesByCountingDeaminationMutations_ ) { fprintf( pFileToWrite, "consed.autoReportChooseTreesByCountingDeaminationMutations: %s\n", ( resources_.bAutoReportChooseTreesByCountingDeaminationMutations_ ? "true" : "false" ) ); } // consed.autoReportChooseTreesUsingKimura if ( resources_.bAutoReportChooseTreesUsingKimura_ != CONDEF->bAutoReportChooseTreesUsingKimura_ ) { fprintf( pFileToWrite, "consed.autoReportChooseTreesUsingKimura: %s\n", ( resources_.bAutoReportChooseTreesUsingKimura_ ? "true" : "false" ) ); } // consed.autoReportPrintCrudeChimpHumanMutations if ( resources_.bAutoReportPrintCrudeChimpHumanMutations_ != CONDEF->bAutoReportPrintCrudeChimpHumanMutations_ ) { fprintf( pFileToWrite, "consed.autoReportPrintCrudeChimpHumanMutations: %s\n", ( resources_.bAutoReportPrintCrudeChimpHumanMutations_ ? "true" : "false" ) ); } // consed.autoReportPrintPositionsForGraham if ( resources_.bAutoReportPrintPositionsForGraham_ != CONDEF->bAutoReportPrintPositionsForGraham_ ) { fprintf( pFileToWrite, "consed.autoReportPrintPositionsForGraham: %s\n", ( resources_.bAutoReportPrintPositionsForGraham_ ? "true" : "false" ) ); } // consed.autoReportPrintAncestralCpGs if ( resources_.bAutoReportPrintAncestralCpGs_ != CONDEF->bAutoReportPrintAncestralCpGs_ ) { fprintf( pFileToWrite, "consed.autoReportPrintAncestralCpGs: %s\n", ( resources_.bAutoReportPrintAncestralCpGs_ ? "true" : "false" ) ); } // consed.autoReportPrintCpGMutations if ( resources_.bAutoReportPrintCpGMutations_ != CONDEF->bAutoReportPrintCpGMutations_ ) { fprintf( pFileToWrite, "consed.autoReportPrintCpGMutations: %s\n", ( resources_.bAutoReportPrintCpGMutations_ ? "true" : "false" ) ); } // consed.autoReportPrintMutationsWithContext if ( resources_.bAutoReportPrintMutationsWithContext_ != CONDEF->bAutoReportPrintMutationsWithContext_ ) { fprintf( pFileToWrite, "consed.autoReportPrintMutationsWithContext: %s\n", ( resources_.bAutoReportPrintMutationsWithContext_ ? "true" : "false" ) ); } // consed.autoReportCountAllMutationsML if ( resources_.bAutoReportCountAllMutationsML_ != CONDEF->bAutoReportCountAllMutationsML_ ) { fprintf( pFileToWrite, "consed.autoReportCountAllMutationsML: %s\n", ( resources_.bAutoReportCountAllMutationsML_ ? "true" : "false" ) ); } // consed.autoReportCountAllMutations if ( resources_.bAutoReportCountAllMutations_ != CONDEF->bAutoReportCountAllMutations_ ) { fprintf( pFileToWrite, "consed.autoReportCountAllMutations: %s\n", ( resources_.bAutoReportCountAllMutations_ ? "true" : "false" ) ); } // consed.autoReportIgnoreMultipleTrees if ( resources_.bAutoReportIgnoreMultipleTrees_ != CONDEF->bAutoReportIgnoreMultipleTrees_ ) { fprintf( pFileToWrite, "consed.autoReportIgnoreMultipleTrees: %s\n", ( resources_.bAutoReportIgnoreMultipleTrees_ ? "true" : "false" ) ); } // consed.autoReportCountAcceptableColumnsWithNoneOnLeft if ( resources_.bAutoReportCountAcceptableColumnsWithNoneOnLeft_ != CONDEF->bAutoReportCountAcceptableColumnsWithNoneOnLeft_ ) { fprintf( pFileToWrite, "consed.autoReportCountAcceptableColumnsWithNoneOnLeft: %s\n", ( resources_.bAutoReportCountAcceptableColumnsWithNoneOnLeft_ ? "true" : "false" ) ); } // consed.autoReportPrintFlankedColumns4 if ( resources_.bAutoReportPrintFlankedColumns4_ != CONDEF->bAutoReportPrintFlankedColumns4_ ) { fprintf( pFileToWrite, "consed.autoReportPrintFlankedColumns4: %s\n", ( resources_.bAutoReportPrintFlankedColumns4_ ? "true" : "false" ) ); } // consed.autoReportUseAnnotationFormat if ( resources_.bAutoReportUseAnnotationFormat_ != CONDEF->bAutoReportUseAnnotationFormat_ ) { fprintf( pFileToWrite, "consed.autoReportUseAnnotationFormat: %s\n", ( resources_.bAutoReportUseAnnotationFormat_ ? "true" : "false" ) ); } // consed.autoReportPrintFlankedColumns3 if ( resources_.bAutoReportPrintFlankedColumns3_ != CONDEF->bAutoReportPrintFlankedColumns3_ ) { fprintf( pFileToWrite, "consed.autoReportPrintFlankedColumns3: %s\n", ( resources_.bAutoReportPrintFlankedColumns3_ ? "true" : "false" ) ); } // consed.autoReportPrintFlankedColumns2 if ( resources_.bAutoReportPrintFlankedColumns2_ != CONDEF->bAutoReportPrintFlankedColumns2_ ) { fprintf( pFileToWrite, "consed.autoReportPrintFlankedColumns2: %s\n", ( resources_.bAutoReportPrintFlankedColumns2_ ? "true" : "false" ) ); } // consed.autoReportPrintFlankedColumns if ( resources_.bAutoReportPrintFlankedColumns_ != CONDEF->bAutoReportPrintFlankedColumns_ ) { fprintf( pFileToWrite, "consed.autoReportPrintFlankedColumns: %s\n", ( resources_.bAutoReportPrintFlankedColumns_ ? "true" : "false" ) ); } // consed.autoReportHighQualitySegmentData if ( resources_.bAutoReportHighQualitySegmentData_ != CONDEF->bAutoReportHighQualitySegmentData_ ) { fprintf( pFileToWrite, "consed.autoReportHighQualitySegmentData: %s\n", ( resources_.bAutoReportHighQualitySegmentData_ ? "true" : "false" ) ); } // consed.autoReportGoodReadsBug if ( resources_.bAutoReportGoodReadsBug_ != CONDEF->bAutoReportGoodReadsBug_ ) { fprintf( pFileToWrite, "consed.autoReportGoodReadsBug: %s\n", ( resources_.bAutoReportGoodReadsBug_ ? "true" : "false" ) ); } // consed.autoReportDiscrepancyRateInFlankedRegions if ( resources_.bAutoReportDiscrepancyRateInFlankedRegions_ != CONDEF->bAutoReportDiscrepancyRateInFlankedRegions_ ) { fprintf( pFileToWrite, "consed.autoReportDiscrepancyRateInFlankedRegions: %s\n", ( resources_.bAutoReportDiscrepancyRateInFlankedRegions_ ? "true" : "false" ) ); } // consed.autoReportDiscrepancyRateInFlankedRegions2 if ( resources_.bAutoReportDiscrepancyRateInFlankedRegions2_ != CONDEF->bAutoReportDiscrepancyRateInFlankedRegions2_ ) { fprintf( pFileToWrite, "consed.autoReportDiscrepancyRateInFlankedRegions2: %s\n", ( resources_.bAutoReportDiscrepancyRateInFlankedRegions2_ ? "true" : "false" ) ); } // consed.autoReportDiscrepancyRateInFlankedRegions4 if ( resources_.bAutoReportDiscrepancyRateInFlankedRegions4_ != CONDEF->bAutoReportDiscrepancyRateInFlankedRegions4_ ) { fprintf( pFileToWrite, "consed.autoReportDiscrepancyRateInFlankedRegions4: %s\n", ( resources_.bAutoReportDiscrepancyRateInFlankedRegions4_ ? "true" : "false" ) ); } // consed.autoReportDiscrepancyRateInFlankedRegions5 if ( resources_.bAutoReportDiscrepancyRateInFlankedRegions5_ != CONDEF->bAutoReportDiscrepancyRateInFlankedRegions5_ ) { fprintf( pFileToWrite, "consed.autoReportDiscrepancyRateInFlankedRegions5: %s\n", ( resources_.bAutoReportDiscrepancyRateInFlankedRegions5_ ? "true" : "false" ) ); } // consed.autoReportSingleSignalOrQuality if ( resources_.bAutoReportSingleSignalOrQuality_ != CONDEF->bAutoReportSingleSignalOrQuality_ ) { fprintf( pFileToWrite, "consed.autoReportSingleSignalOrQuality: %s\n", ( resources_.bAutoReportSingleSignalOrQuality_ ? "true" : "false" ) ); } // consed.autoReportLowQualityBasesInHQS if ( resources_.bAutoReportLowQualityBasesInHQS_ != CONDEF->bAutoReportLowQualityBasesInHQS_ ) { fprintf( pFileToWrite, "consed.autoReportLowQualityBasesInHQS: %s\n", ( resources_.bAutoReportLowQualityBasesInHQS_ ? "true" : "false" ) ); } // consed.autoReportCompareHQSWithLQS if ( resources_.bAutoReportCompareHQSWithLQS_ != CONDEF->bAutoReportCompareHQSWithLQS_ ) { fprintf( pFileToWrite, "consed.autoReportCompareHQSWithLQS: %s\n", ( resources_.bAutoReportCompareHQSWithLQS_ ? "true" : "false" ) ); } // consed.autoReportCountColumnsForGroupsOfSpecies if ( resources_.bAutoReportCountColumnsForGroupsOfSpecies_ != CONDEF->bAutoReportCountColumnsForGroupsOfSpecies_ ) { fprintf( pFileToWrite, "consed.autoReportCountColumnsForGroupsOfSpecies: %s\n", ( resources_.bAutoReportCountColumnsForGroupsOfSpecies_ ? "true" : "false" ) ); } // consed.autoReportSingleSignalInfo if ( resources_.bAutoReportSingleSignalInfo_ != CONDEF->bAutoReportSingleSignalInfo_ ) { fprintf( pFileToWrite, "consed.autoReportSingleSignalInfo: %s\n", ( resources_.bAutoReportSingleSignalInfo_ ? "true" : "false" ) ); } // consed.autoReportSingleSignalInfo2 if ( resources_.bAutoReportSingleSignalInfo2_ != CONDEF->bAutoReportSingleSignalInfo2_ ) { fprintf( pFileToWrite, "consed.autoReportSingleSignalInfo2: %s\n", ( resources_.bAutoReportSingleSignalInfo2_ ? "true" : "false" ) ); } // consed.autoReportCompareTopAndBottomStrands if ( resources_.bAutoReportCompareTopAndBottomStrands_ != CONDEF->bAutoReportCompareTopAndBottomStrands_ ) { fprintf( pFileToWrite, "consed.autoReportCompareTopAndBottomStrands: %s\n", ( resources_.bAutoReportCompareTopAndBottomStrands_ ? "true" : "false" ) ); } // consed.autoReportCompareTopAndBottomStrandsNoHuman if ( resources_.bAutoReportCompareTopAndBottomStrandsNoHuman_ != CONDEF->bAutoReportCompareTopAndBottomStrandsNoHuman_ ) { fprintf( pFileToWrite, "consed.autoReportCompareTopAndBottomStrandsNoHuman: %s\n", ( resources_.bAutoReportCompareTopAndBottomStrandsNoHuman_ ? "true" : "false" ) ); } // consed.autoReportCompareTopAndBottomStrands2 if ( resources_.bAutoReportCompareTopAndBottomStrands2_ != CONDEF->bAutoReportCompareTopAndBottomStrands2_ ) { fprintf( pFileToWrite, "consed.autoReportCompareTopAndBottomStrands2: %s\n", ( resources_.bAutoReportCompareTopAndBottomStrands2_ ? "true" : "false" ) ); } // consed.autoReportCompareTopAndBottomStrands3 if ( resources_.bAutoReportCompareTopAndBottomStrands3_ != CONDEF->bAutoReportCompareTopAndBottomStrands3_ ) { fprintf( pFileToWrite, "consed.autoReportCompareTopAndBottomStrands3: %s\n", ( resources_.bAutoReportCompareTopAndBottomStrands3_ ? "true" : "false" ) ); } // consed.autoReportCompareTopAndBottomStrands4 if ( resources_.bAutoReportCompareTopAndBottomStrands4_ != CONDEF->bAutoReportCompareTopAndBottomStrands4_ ) { fprintf( pFileToWrite, "consed.autoReportCompareTopAndBottomStrands4: %s\n", ( resources_.bAutoReportCompareTopAndBottomStrands4_ ? "true" : "false" ) ); } // consed.autoReportTopStrandPinnedPosition if ( resources_.nAutoReportTopStrandPinnedPosition_ != CONDEF->nAutoReportTopStrandPinnedPosition_ ) { fprintf( pFileToWrite, "consed.autoReportTopStrandPinnedPosition: %d\n", resources_.nAutoReportTopStrandPinnedPosition_ ); } // consed.autoReportBottomStrandPinnedPosition if ( resources_.nAutoReportBottomStrandPinnedPosition_ != CONDEF->nAutoReportBottomStrandPinnedPosition_ ) { fprintf( pFileToWrite, "consed.autoReportBottomStrandPinnedPosition: %d\n", resources_.nAutoReportBottomStrandPinnedPosition_ ); } // consed.autoReportCompareTopAndBottomStrandsWithHuman if ( resources_.bAutoReportCompareTopAndBottomStrandsWithHuman_ != CONDEF->bAutoReportCompareTopAndBottomStrandsWithHuman_ ) { fprintf( pFileToWrite, "consed.autoReportCompareTopAndBottomStrandsWithHuman: %s\n", ( resources_.bAutoReportCompareTopAndBottomStrandsWithHuman_ ? "true" : "false" ) ); } // consed.autoReportPrintLengthsOfAlignedSegmentsOfReads if ( resources_.bAutoReportPrintLengthsOfAlignedSegmentsOfReads_ != CONDEF->bAutoReportPrintLengthsOfAlignedSegmentsOfReads_ ) { fprintf( pFileToWrite, "consed.autoReportPrintLengthsOfAlignedSegmentsOfReads: %s\n", ( resources_.bAutoReportPrintLengthsOfAlignedSegmentsOfReads_ ? "true" : "false" ) ); } // consed.autoReportPrintLengthsOfUnalignedHighQualitySegmentsOfReads if ( resources_.bAutoReportPrintLengthsOfUnalignedHighQualitySegmentsOfReads_ != CONDEF->bAutoReportPrintLengthsOfUnalignedHighQualitySegmentsOfReads_ ) { fprintf( pFileToWrite, "consed.autoReportPrintLengthsOfUnalignedHighQualitySegmentsOfReads: %s\n", ( resources_.bAutoReportPrintLengthsOfUnalignedHighQualitySegmentsOfReads_ ? "true" : "false" ) ); } // consed.autoReportPrintIfReadsAreCorrectlyAligned if ( resources_.bAutoReportPrintIfReadsAreCorrectlyAligned_ != CONDEF->bAutoReportPrintIfReadsAreCorrectlyAligned_ ) { fprintf( pFileToWrite, "consed.autoReportPrintIfReadsAreCorrectlyAligned: %s\n", ( resources_.bAutoReportPrintIfReadsAreCorrectlyAligned_ ? "true" : "false" ) ); } // consed.autoReportCalculateErrorProbabilitiesByComparingPTroPPan if ( resources_.bAutoReportCalculateErrorProbabilitiesByComparingPTroPPan_ != CONDEF->bAutoReportCalculateErrorProbabilitiesByComparingPTroPPan_ ) { fprintf( pFileToWrite, "consed.autoReportCalculateErrorProbabilitiesByComparingPTroPPan: %s\n", ( resources_.bAutoReportCalculateErrorProbabilitiesByComparingPTroPPan_ ? "true" : "false" ) ); } // consed.autoReportPrintAgreeDisagreeBetweenPairsOfSpecies if ( resources_.bAutoReportPrintAgreeDisagreeBetweenPairsOfSpecies_ != CONDEF->bAutoReportPrintAgreeDisagreeBetweenPairsOfSpecies_ ) { fprintf( pFileToWrite, "consed.autoReportPrintAgreeDisagreeBetweenPairsOfSpecies: %s\n", ( resources_.bAutoReportPrintAgreeDisagreeBetweenPairsOfSpecies_ ? "true" : "false" ) ); } // consed.autoReportPrintAgreeDisagreeBetweenPairsOfSpecies2 if ( resources_.bAutoReportPrintAgreeDisagreeBetweenPairsOfSpecies2_ != CONDEF->bAutoReportPrintAgreeDisagreeBetweenPairsOfSpecies2_ ) { fprintf( pFileToWrite, "consed.autoReportPrintAgreeDisagreeBetweenPairsOfSpecies2: %s\n", ( resources_.bAutoReportPrintAgreeDisagreeBetweenPairsOfSpecies2_ ? "true" : "false" ) ); } // consed.autoReportFilterSingleSignal if ( resources_.bAutoReportFilterSingleSignal_ != CONDEF->bAutoReportFilterSingleSignal_ ) { fprintf( pFileToWrite, "consed.autoReportFilterSingleSignal: %s\n", ( resources_.bAutoReportFilterSingleSignal_ ? "true" : "false" ) ); } // consed.autoReportGoodHitReads if ( resources_.filAutoReportGoodHitReads_ != CONDEF->filAutoReportGoodHitReads_ ) { fprintf( pFileToWrite, "consed.autoReportGoodHitReads: %s\n", resources_.filAutoReportGoodHitReads_.data() ); } // consed.autoReportQualityWindowLow if ( resources_.nAutoReportQualityWindowLow_ != CONDEF->nAutoReportQualityWindowLow_ ) { fprintf( pFileToWrite, "consed.autoReportQualityWindowLow: %d\n", resources_.nAutoReportQualityWindowLow_ ); } // consed.autoReportQualityWindowHigh if ( resources_.nAutoReportQualityWindowHigh_ != CONDEF->nAutoReportQualityWindowHigh_ ) { fprintf( pFileToWrite, "consed.autoReportQualityWindowHigh: %d\n", resources_.nAutoReportQualityWindowHigh_ ); } // consed.autoReportPrintNumberOfIsolatedPadsForEachSpecies if ( resources_.bAutoReportPrintNumberOfIsolatedPadsForEachSpecies_ != CONDEF->bAutoReportPrintNumberOfIsolatedPadsForEachSpecies_ ) { fprintf( pFileToWrite, "consed.autoReportPrintNumberOfIsolatedPadsForEachSpecies: %s\n", ( resources_.bAutoReportPrintNumberOfIsolatedPadsForEachSpecies_ ? "true" : "false" ) ); } // consed.autoReportPrintNumberOfIsolatedPads if ( resources_.bAutoReportPrintNumberOfIsolatedPads_ != CONDEF->bAutoReportPrintNumberOfIsolatedPads_ ) { fprintf( pFileToWrite, "consed.autoReportPrintNumberOfIsolatedPads: %s\n", ( resources_.bAutoReportPrintNumberOfIsolatedPads_ ? "true" : "false" ) ); } // consed.autoReportIsolatedPadsOfReadsWithThisPattern if ( resources_.soAutoReportIsolatedPadsOfReadsWithThisPattern_ != CONDEF->soAutoReportIsolatedPadsOfReadsWithThisPattern_ ) { fprintf( pFileToWrite, "consed.autoReportIsolatedPadsOfReadsWithThisPattern: %s\n", resources_.soAutoReportIsolatedPadsOfReadsWithThisPattern_.data() ); } // consed.autoReportMinNumberOfPerfectlyAlignedBasesBeforeDiscrepancy if ( resources_.nAutoReportMinNumberOfPerfectlyAlignedBasesBeforeDiscrepancy_ != CONDEF->nAutoReportMinNumberOfPerfectlyAlignedBasesBeforeDiscrepancy_ ) { fprintf( pFileToWrite, "consed.autoReportMinNumberOfPerfectlyAlignedBasesBeforeDiscrepancy: %d\n", resources_.nAutoReportMinNumberOfPerfectlyAlignedBasesBeforeDiscrepancy_ ); } // consed.autoReportMaxSizeOfDiscrepantRegion if ( resources_.nAutoReportMaxSizeOfDiscrepantRegion_ != CONDEF->nAutoReportMaxSizeOfDiscrepantRegion_ ) { fprintf( pFileToWrite, "consed.autoReportMaxSizeOfDiscrepantRegion: %d\n", resources_.nAutoReportMaxSizeOfDiscrepantRegion_ ); } // consed.autoReportSizeOfDiscrepantRegion if ( resources_.nAutoReportSizeOfDiscrepantRegion_ != CONDEF->nAutoReportSizeOfDiscrepantRegion_ ) { fprintf( pFileToWrite, "consed.autoReportSizeOfDiscrepantRegion: %d\n", resources_.nAutoReportSizeOfDiscrepantRegion_ ); } // consed.autoReportPrintMinimumQualityHistogram if ( resources_.bAutoReportPrintMinimumQualityHistogram_ != CONDEF->bAutoReportPrintMinimumQualityHistogram_ ) { fprintf( pFileToWrite, "consed.autoReportPrintMinimumQualityHistogram: %s\n", ( resources_.bAutoReportPrintMinimumQualityHistogram_ ? "true" : "false" ) ); } // consed.autoReportPrintDiscrepantRegions if ( resources_.bAutoReportPrintDiscrepantRegions_ != CONDEF->bAutoReportPrintDiscrepantRegions_ ) { fprintf( pFileToWrite, "consed.autoReportPrintDiscrepantRegions: %s\n", ( resources_.bAutoReportPrintDiscrepantRegions_ ? "true" : "false" ) ); } // consed.autoReportPrintBasesInDiscrepantRegions if ( resources_.bAutoReportPrintBasesInDiscrepantRegions_ != CONDEF->bAutoReportPrintBasesInDiscrepantRegions_ ) { fprintf( pFileToWrite, "consed.autoReportPrintBasesInDiscrepantRegions: %s\n", ( resources_.bAutoReportPrintBasesInDiscrepantRegions_ ? "true" : "false" ) ); } // consed.autoReportPrintDiscrepantRegionsButIgnoreReadsContainingThis if ( resources_.soAutoReportPrintDiscrepantRegionsButIgnoreReadsContainingThis_ != CONDEF->soAutoReportPrintDiscrepantRegionsButIgnoreReadsContainingThis_ ) { fprintf( pFileToWrite, "consed.autoReportPrintDiscrepantRegionsButIgnoreReadsContainingThis: %s\n", resources_.soAutoReportPrintDiscrepantRegionsButIgnoreReadsContainingThis_.data() ); } // consed.autoReportBackboneReadHasThisStringInIt if ( resources_.soAutoReportBackboneReadHasThisStringInIt_ != CONDEF->soAutoReportBackboneReadHasThisStringInIt_ ) { fprintf( pFileToWrite, "consed.autoReportBackboneReadHasThisStringInIt: %s\n", resources_.soAutoReportBackboneReadHasThisStringInIt_.data() ); } // consed.autoReportPrintDiscrepantRegionsButOnlyIfAboveQualityThreshold if ( resources_.bAutoReportPrintDiscrepantRegionsButOnlyIfAboveQualityThreshold_ != CONDEF->bAutoReportPrintDiscrepantRegionsButOnlyIfAboveQualityThreshold_ ) { fprintf( pFileToWrite, "consed.autoReportPrintDiscrepantRegionsButOnlyIfAboveQualityThreshold: %s\n", ( resources_.bAutoReportPrintDiscrepantRegionsButOnlyIfAboveQualityThreshold_ ? "true" : "false" ) ); } // consed.autoReportPrintSpeciesAlignment if ( resources_.bAutoReportPrintSpeciesAlignment_ != CONDEF->bAutoReportPrintSpeciesAlignment_ ) { fprintf( pFileToWrite, "consed.autoReportPrintSpeciesAlignment: %s\n", ( resources_.bAutoReportPrintSpeciesAlignment_ ? "true" : "false" ) ); } // consed.autoReportPrintReadAlignment if ( resources_.bAutoReportPrintReadAlignment_ != CONDEF->bAutoReportPrintReadAlignment_ ) { fprintf( pFileToWrite, "consed.autoReportPrintReadAlignment: %s\n", ( resources_.bAutoReportPrintReadAlignment_ ? "true" : "false" ) ); } // consed.autoReportPrintTheseReads if ( resources_.filAutoReportPrintTheseReads_ != CONDEF->filAutoReportPrintTheseReads_ ) { fprintf( pFileToWrite, "consed.autoReportPrintTheseReads: %s\n", resources_.filAutoReportPrintTheseReads_.data() ); } // consed.autoReportPrintReadPositions if ( resources_.bAutoReportPrintReadPositions_ != CONDEF->bAutoReportPrintReadPositions_ ) { fprintf( pFileToWrite, "consed.autoReportPrintReadPositions: %s\n", ( resources_.bAutoReportPrintReadPositions_ ? "true" : "false" ) ); } // consed.autoReportPrintChosenReadName if ( resources_.bAutoReportPrintChosenReadName_ != CONDEF->bAutoReportPrintChosenReadName_ ) { fprintf( pFileToWrite, "consed.autoReportPrintChosenReadName: %s\n", ( resources_.bAutoReportPrintChosenReadName_ ? "true" : "false" ) ); } // consed.autoReportNumbersOfCharactersOfChosenReadNameToBePrinted if ( resources_.nAutoReportNumbersOfCharactersOfChosenReadNameToBePrinted_ != CONDEF->nAutoReportNumbersOfCharactersOfChosenReadNameToBePrinted_ ) { fprintf( pFileToWrite, "consed.autoReportNumbersOfCharactersOfChosenReadNameToBePrinted: %d\n", resources_.nAutoReportNumbersOfCharactersOfChosenReadNameToBePrinted_ ); } // consed.autoReportPrefix if ( resources_.soAutoReportPrefix_ != CONDEF->soAutoReportPrefix_ ) { fprintf( pFileToWrite, "consed.autoReportPrefix: %s\n", resources_.soAutoReportPrefix_.data() ); } // consed.autoReportUseOldCriteriaForDeletingColumnsOfPads if ( resources_.bAutoReportUseOldCriteriaForDeletingColumnsOfPads_ != CONDEF->bAutoReportUseOldCriteriaForDeletingColumnsOfPads_ ) { fprintf( pFileToWrite, "consed.autoReportUseOldCriteriaForDeletingColumnsOfPads: %s\n", ( resources_.bAutoReportUseOldCriteriaForDeletingColumnsOfPads_ ? "true" : "false" ) ); } // consed.autoReportDeleteColumnsOfPadsBeforeAdjustingReadQualityValues if ( resources_.bAutoReportDeleteColumnsOfPadsBeforeAdjustingReadQualityValues_ != CONDEF->bAutoReportDeleteColumnsOfPadsBeforeAdjustingReadQualityValues_ ) { fprintf( pFileToWrite, "consed.autoReportDeleteColumnsOfPadsBeforeAdjustingReadQualityValues: %s\n", ( resources_.bAutoReportDeleteColumnsOfPadsBeforeAdjustingReadQualityValues_ ? "true" : "false" ) ); } // consed.autoReportFlankingBasesMustBeSingleSignal if ( resources_.bAutoReportFlankingBasesMustBeSingleSignal_ != CONDEF->bAutoReportFlankingBasesMustBeSingleSignal_ ) { fprintf( pFileToWrite, "consed.autoReportFlankingBasesMustBeSingleSignal: %s\n", ( resources_.bAutoReportFlankingBasesMustBeSingleSignal_ ? "true" : "false" ) ); } // consed.autoReportMinimumQualityOfFlankingBases if ( resources_.nAutoReportMinimumQualityOfFlankingBases_ != CONDEF->nAutoReportMinimumQualityOfFlankingBases_ ) { fprintf( pFileToWrite, "consed.autoReportMinimumQualityOfFlankingBases: %d\n", resources_.nAutoReportMinimumQualityOfFlankingBases_ ); } // consed.autoReportFlankingBasesMustBeInHighQualitySegment if ( resources_.bAutoReportFlankingBasesMustBeInHighQualitySegment_ != CONDEF->bAutoReportFlankingBasesMustBeInHighQualitySegment_ ) { fprintf( pFileToWrite, "consed.autoReportFlankingBasesMustBeInHighQualitySegment: %s\n", ( resources_.bAutoReportFlankingBasesMustBeInHighQualitySegment_ ? "true" : "false" ) ); } // consed.autoReportSpecies if ( resources_.soAutoReportSpecies_ != CONDEF->soAutoReportSpecies_ ) { fprintf( pFileToWrite, "consed.autoReportSpecies: %s\n", resources_.soAutoReportSpecies_.data() ); }