/***************************************************************************** # 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. # #*****************************************************************************/ saveAConsedParameter( bPrintPS ); saveAConsedParameter( soDefaultTagType ); saveAConsedParameter( bDefaultTagOnConsensusNotReads ); saveAConsedParameter( dAutoFinishMinNumberOfErrorsFixedByAnExp ); saveAConsedParameter( dAutoFinishRedundancy ); saveAConsedParameter( nAutoFinishAverageInsertSize ); saveAConsedParameter( nPrimersMaxInsertSizeOfASubclone ); saveAConsedParameter( nPrimersMaxMeltingTemp ); saveAConsedParameter( nPrimersMaxMeltingTempForPCR ); saveAConsedParameter( bPrimersPickTemplatesForPrimers ); saveAConsedParameter( soPrimersSubcloneFullPathnameOfFileOfSequencesForScreening ); saveAConsedParameter( soPrimersCloneFullPathnameOfFileOfSequencesForScreening ); saveAConsedParameter( nPrimersMinMeltingTemp ); saveAConsedParameter( nPrimersMinMeltingTempForPCR ); saveAConsedParameter( bSearchFunctionsUseUnalignedEndsOfReads ); saveAConsedParameter( bSearchFunctionsUseLowQualityEndsOfReads ); saveAConsedParameter( nInexactSearchForStringMaxPerCentMismatch ); saveAConsedParameter( bOnlyAllowOneReadWriteConsedAtATime ); saveAConsedParameter( bAutoFinishAllowHighQualityDiscrepanciesInTemplateIfConsistentForwardReversePair ); saveAConsedParameter( soPrintWindowCommand ); saveAConsedParameter( filFileOfTagTypes ); saveAConsedParameter( bAssemblyViewShowConsistentFwdRevPairs ); saveAConsedParameter( bAssemblyViewShowConsistentFwdRevPairDepth ); saveAConsedParameter( bAssemblyViewShowConsistentFwdRevPairsBetweenDifferentScaffolds ); saveAConsedParameter( bAssemblyViewShowLegsOnSquaresForConsistentFwdRevPairs ); saveAConsedParameter( bAssemblyViewShowGapSpanningFwdRevPairs ); saveAConsedParameter( soAssemblyViewShowWhichInconsistentFwdRevPairs ); saveAConsedParameter( bAssemblyViewShowReadDepth ); saveAConsedParameter( bAssemblyViewShowMultipleHighQualityDiscrepancies ); saveAConsedParameter( bAssemblyViewShowRestrictionDigestCutSites ); saveAConsedParameter( bAssemblyViewFilterSequenceMatchesBySize ); saveAConsedParameter( nAssemblyViewSequenceMatchesMinSize ); saveAConsedParameter( nAssemblyViewSequenceMatchesMaxSize ); saveAConsedParameter( bAssemblyViewAutomaticallyStartWithConsed ); saveAConsedParameter( soAssemblyViewDisplayTheseTagTypesOnTheseLines ); saveAConsedParameter( bAssemblyViewShowTags ); saveAConsedParameter( bAutoEditRecalculateHighQualitySegmentsOfReads ); saveAConsedParameter( bAutoEditConvertCloneEndBasesToXs ); saveAConsedParameter( bAutoEditTellPhrapNotToOverlapMultiplyDiscrepantReads ); saveAConsedParameter( bAutoEditTagEditableLowConsensusQualityRegions ); saveAConsedParameter( bAutoEditMakeFakeRead ); saveAConsedParameter( soAutoEditMakeFakeReadFromRead1 ); saveAConsedParameter( soAutoEditMakeFakeReadFromRead2 ); saveAConsedParameter( soAutoEditMakeFakeReadName ); saveAConsedParameter( filAutoEditMakeFakeReadFastaFilename ); saveAConsedParameter( bAutoEditMergeAssembly ); saveAConsedParameter( filAutoEditSecondaryAceFile ); saveAConsedParameter( bAutoEditFixRunsInConsensus ); saveAConsedParameter( bShowAllTracesJustShowGoodTraces ); saveAConsedParameter( nAddAlignedSequenceQualityOfBases ); saveAConsedParameter( bMakeLightBackgroundInAlignedReadsWindowAndTracesWindow ); saveAConsedParameter( bPutVerticalLineAtCursor ); saveAConsedParameter( bPutHorizontalLineAtCursor ); saveAConsedParameter( filHighlightedReadsFile ); saveAConsedParameter( bAutoReportPrintReadNamesInRegion ); saveAConsedParameter( soAutoReportPrintReadNamesInRegionContig ); saveAConsedParameter( nAutoReportPrintReadNamesInRegionLeftPos ); saveAConsedParameter( nAutoReportPrintReadNamesInRegionRightPos ); saveAConsedParameter( bAutoReportPrintHighlyDiscrepantRegions ); saveAConsedParameter( bAutoReportPrintScaffolds ); saveAConsedParameter( bNumberUnpaddedConsensusAtUserDefined ); saveAConsedParameter( bAutoReportPrintHighQualityDiscrepancies ); saveAConsedParameter( bAutoReportHighQualityDiscrepanciesExcludeCompressionOrG_dropoutTags ); saveAConsedParameter( bAutoReportHighQualityDiscrepanciesExcludeMostPads ); saveAConsedParameter( bAutoReportPrintLowConsensusQualityRegions ); saveAConsedParameter( bAutoReportPrintSingleSubcloneRegions ); saveAConsedParameter( bAutoReportPrintSingleStrandedRegions ); saveAConsedParameter( bAutoReportPrintLinkingForwardReversePairs ); saveAConsedParameter( bAutoReportPrintFilteredInconsistentForwardReversePairs ); saveAConsedParameter( bAutoReportPrintAssemblySummary ); saveAConsedParameter( soShowAllTracesDoNotShowTraceIfTheseTagsPresent ); saveAConsedParameter( bNameOfFakeJoiningReadsIncludesAceFileName ); saveAConsedParameter( nWhenUserScrollsOffWindowMillisecondsBetweenScrolling ); saveAConsedParameter( nWhenUserScrollsOffWindowBasesToScrollEachTime ); saveAConsedParameter( bCompareContigsUseBandedRatherThanFullSmithWaterman ); saveAConsedParameter( nCompareContigsBandSize ); saveAConsedParameter( nAssemblyViewShowFwdRevPairDepthsInRedIfOnlyThisMany ); saveAConsedParameter( bAssemblyViewShowSequenceMatches ); saveAConsedParameter( bAssemblyViewOKToShowSequenceMatchesBetweenContigs ); saveAConsedParameter( bAssemblyViewOKToShowSequenceMatchesWithinContigs ); saveAConsedParameter( bAssemblyViewOKToShowDirectSequenceMatches ); saveAConsedParameter( bAssemblyViewOKToShowInvertedSequenceMatches ); saveAConsedParameter( bAssemblyViewOnlyShowSequenceMatchesToAParticularRegion ); saveAConsedParameter( soAssemblyViewOnlyShowSequenceMatchesToThisContig ); saveAConsedParameter( nAssemblyViewOnlyShowSequenceMatchesToThisRegionLeft ); saveAConsedParameter( nAssemblyViewOnlyShowSequenceMatchesToThisRegionRight ); saveAConsedParameter( bAssemblyViewOnlyShowSequenceMatchesToEndsOfContigs ); saveAConsedParameter( nAssemblyViewOnlyShowSequenceMatchesToEndsOfContigsThisFar ); saveAConsedParameter( soDefaultReadPrefix ); saveAConsedParameter( filReadPrefixesFile ); saveAConsedParameter( nMaxCharsDisplayedForReadPrefix ); saveAConsedParameter( nAutoFinishDoNotDoPCRIfThisManyAvailableGapSpanningTemplates ); saveAConsedParameter( nAutoFinishDoNotDoUnorientedPCRIfThisManyOrMoreUnorientedPCRReactions ); saveAConsedParameter( nAutoFinishDoNotDoOrientedPCRIfGapSizeLargerThanThis ); saveAConsedParameter( bAutoFinishDoNotDoPCRIfEndIsExtendedByReads ); saveAConsedParameter( nAutoFinishMaxAcceptableErrorsPerMegabase ); saveAConsedParameter( nAutoFinishIfNotEnoughFwdRevPairsUseThisPerCentOfInsertSize ); saveAConsedParameter( nPrimersNumberOfBasesToBackUpToStartLooking ); saveAConsedParameter( nPrimersMakePCRPrimersThisManyBasesBackFromEndOfHighQualitySegment ); saveAConsedParameter( bPrimersOKToChoosePrimersInSingleSubcloneRegion ); saveAConsedParameter( bPrimersOKToChoosePrimersWhereHighQualityDiscrepancies ); saveAConsedParameter( bPrimersOKToChoosePrimersWhereUnalignedHighQualityRegion ); saveAConsedParameter( bAutoFinishCallReversesToFlankGaps ); saveAConsedParameter( bAutoFinishAllowWholeCloneReads ); saveAConsedParameter( bAutoFinishAllowCustomPrimerSubcloneReads ); saveAConsedParameter( bAutoFinishAllowResequencingReads ); saveAConsedParameter( bAutoFinishAllowResequencingReadsOnlyForRunsAndStops ); saveAConsedParameter( bAutoFinishAllowDeNovoUniversalPrimerSubcloneReads ); saveAConsedParameter( bAutoFinishAllowMinilibraries ); saveAConsedParameter( bAutoFinishAllowPCR ); saveAConsedParameter( bAutoFinishAllowUnorientedPCRReactions ); saveAConsedParameter( bAutoFinishAllowResequencingAUniversalPrimerAutofinishRead ); saveAConsedParameter( bAutoFinishAlwaysCloseGapsUsingMinilibraries ); saveAConsedParameter( nAutoFinishMaximumFinishingReadLength ); saveAConsedParameter( nAutoFinishSuggestMinilibraryIfGapThisManyBasesOrLarger ); saveAConsedParameter( bAutoFinishSuggestSpecialChemistryForRunsAndStops ); saveAConsedParameter( nAutoFinishSuggestThisManyMinilibrariesPerGap ); saveAConsedParameter( nPrimersWindowSizeInLooking ); saveAConsedParameter( bPrimersAssumeTemplatesAreDoubleStrandedUnlessSpecified ); saveAConsedParameter( nAlignedReadsWindowInitialCharsWide ); saveAConsedParameter( nAlignedReadsWindowInitialCharsHigh ); saveAConsedParameter( nAlignedReadsWindowMaxCharsForReadNames ); saveAConsedParameter( bAlignedReadsWindowAutomaticallyExpandRoomForReadNames ); saveAConsedParameter( bAutoFinishAllowResequencingReadsToExtendContigs ); saveAConsedParameter( nAutoFinishCallHowManyReversesToFlankGaps ); saveAConsedParameter( bAutoFinishCloseGaps ); saveAConsedParameter( bAutoFinishContinueEvenThoughReadInfoDoesNotMakeSense ); saveAConsedParameter( dAutoFinishCostOfResequencingUniversalPrimerSubcloneReaction ); saveAConsedParameter( dAutoFinishCostOfCustomPrimerSubcloneReaction ); saveAConsedParameter( dAutoFinishCostOfCustomPrimerCloneReaction ); saveAConsedParameter( dAutoFinishCostOfDeNovoUniversalPrimerSubcloneReaction ); saveAConsedParameter( dAutoFinishCostOfMinilibrary ); saveAConsedParameter( bAutoFinishCoverSingleSubcloneRegions ); saveAConsedParameter( bAutoFinishCoverLowConsensusQualityRegions ); saveAConsedParameter( filAutoFinishDebugUniversalPrimerReadsFile ); saveAConsedParameter( filAutoFinishDebugCustomPrimerReadsFile ); saveAConsedParameter( nAutoFinishDoNotAllowSubcloneCustomPrimerReadsCloserThanThisManyBases ); saveAConsedParameter( nAutoFinishDoNotAllowWholeCloneCustomPrimerReadsCloserThanThisManyBases ); saveAConsedParameter( soAutoFinishDoNotFinishWhereTheseTagsAre ); saveAConsedParameter( soAutoFinishDoNotExtendContigsWhereTheseTagsAre ); saveAConsedParameter( nAutoFinishDoNotExtendContigsIfTagsAreThisCloseToContigEnd ); saveAConsedParameter( filDumpContigOrderAndOrientationInfoToThisFile ); saveAConsedParameter( bAutoFinishDumpTemplates ); saveAConsedParameter( nAutoFinishExcludeContigIfOnlyThisManyReadsOrLess ); saveAConsedParameter( dAutoFinishExcludeContigIfDepthOfCoverageGreaterThanThis ); saveAConsedParameter( nAutoFinishExcludeContigIfThisManyBasesOrLess ); saveAConsedParameter( nAutoFinishHowManyTemplatesYouIntendToUseForCustomPrimerSubcloneReactions ); saveAConsedParameter( nPrimersMinNumberOfTemplatesForPrimers ); saveAConsedParameter( nAutoFinishMinBaseOverlapBetweenAReadAndHighQualitySegmentOfConsensus ); saveAConsedParameter( nAutoFinishNumberOfVectorBasesAtBeginningOfAUniveralPrimerRead ); saveAConsedParameter( bAutoFinishCDNANotGenomic ); saveAConsedParameter( nAutoFinishConfidenceThatReadWillCoverSingleSubcloneRegion ); saveAConsedParameter( bAutoFinishPrintForwardOrReverseStrandWhenPrintingSubcloneTemplatesForCustomPrimerReads ); saveAConsedParameter( bAutoFinishPrintMinilibrariesSummaryFile ); saveAConsedParameter( bAutoFinishNearGapsSuggestEachMissingReadOfReadPairs ); saveAConsedParameter( nAutoFinishDoNotIgnoreLCQIfThisManyBasesFromEndOfContigForLCQTagger ); saveAConsedParameter( bCheckIfTooManyWalks ); saveAConsedParameter( nNumberOfColumnsBeforeReadNameInAlignedReadsWindow ); saveAConsedParameter( nCompareContigsAlignsThisManyBasesMax ); saveAConsedParameter( soCompressedChromatExtension ); saveAConsedParameter( bDimLowQualityEndsOfReads ); saveAConsedParameter( bDimUnalignedEndsOfReads ); saveAConsedParameter( bFakeReadsSpecifiedByFilenameExtension ); saveAConsedParameter( filFullPathnameOfAddReads2ConsedScript ); saveAConsedParameter( filFullPathnameOfFixContigEndScript ); saveAConsedParameter( bFixContigEndsCleanUpTemporaryFiles ); saveAConsedParameter( nFixContigEndsMinSmithWatermanScoreToMakeJoin ); saveAConsedParameter( nFixContigEndsMinNumberOfReadsInContig ); saveAConsedParameter( filFullPathnameOfCrossMatch ); saveAConsedParameter( filFullPathnameOfPhred ); saveAConsedParameter( filFullPathnameOfMiniassemblyScript ); saveAConsedParameter( soGunzipFullPath ); saveAConsedParameter( filFullPathnameOfFilter454ReadsScript ); saveAConsedParameter( filFilter454ReadsAgainstThis ); saveAConsedParameter( fil454LinkerSequences ); saveAConsedParameter( bHideSomeTagTypesAtStartup ); saveAConsedParameter( nMaximumNumberOfTracesShown ); saveAConsedParameter( bNavigateAutomaticTracePopup ); saveAConsedParameter( bNavigateAutomaticAllTracesPopup ); saveAConsedParameter( nPrimersMinimumLengthOfAPrimer ); saveAConsedParameter( nPrimersMaximumLengthOfAPrimer ); saveAConsedParameter( nPrimersMinimumLengthOfAPrimerForPCR ); saveAConsedParameter( nPrimersMaximumLengthOfAPrimerForPCR ); saveAConsedParameter( dPrimersMaxMeltingTempDifferenceForPCR ); saveAConsedParameter( nPrimersMaxPCRPrimerPairsToDisplay ); saveAConsedParameter( bPrimersCheckJustSomePCRPrimerPairsRatherThanAll ); saveAConsedParameter( nPrimersNumberOfTemplatesToDisplayInFront ); saveAConsedParameter( nPrimersMaxLengthOfMononucleotideRepeat ); saveAConsedParameter( filPrimersBadLibrariesFile ); saveAConsedParameter( filPrimersLibrariesInfoFile ); saveAConsedParameter( filPrimersBadTemplatesFile ); saveAConsedParameter( bPrimersChooseTemplatesByPositionInsteadOfQuality ); saveAConsedParameter( nPrimersWhenChoosingATemplateMinPotentialReadLength ); saveAConsedParameter( nPrimersWindowSizeInLookingForPCR ); saveAConsedParameter( nQualityThresholdForFindingHighQualityDiscrepancies ); saveAConsedParameter( nQualityThresholdForNavigateByDepthOfCoverage ); saveAConsedParameter( bNavigateByHighDepthOfCoverageNotLow ); saveAConsedParameter( nMinDepthForNavigateByDepthOfCoverage ); saveAConsedParameter( filDefaultVectorPathnameForRestrictionFragments ); saveAConsedParameter( filFileOfAdditionalRestrictionEnzymes ); saveAConsedParameter( soCommonRestrictionEnzymes ); saveAConsedParameter( soDefaultSelectedRestrictionEnzymes ); saveAConsedParameter( filRestrictionEnzymesActualFragmentsFile ); saveAConsedParameter( nRestrictionDigestInitialWindowSizeInTextRows ); saveAConsedParameter( nRestrictionDigestDoNoShowAreaOfFragmentsOverThisSize ); saveAConsedParameter( bShowReadsAlphabetically ); saveAConsedParameter( bShowReadsInAlignedReadsWindowOrderedByFile ); saveAConsedParameter( filShowReadsInAlignedReadsWindowOrderedByThisFile ); saveAConsedParameter( soShowReadsAtCursorSortedHow ); saveAConsedParameter( bShowABIBasesInTraceWindow ); saveAConsedParameter( nTracesWindowInitialPixelHeight ); saveAConsedParameter( nAssemblyViewWindowInitialPixelHeight ); saveAConsedParameter( filAssemblyViewFileOfTemplatesToNotShow ); saveAConsedParameter( nAssemblyViewCrossMatchMinmatch ); saveAConsedParameter( nAssemblyViewCrossMatchMinscore ); saveAConsedParameter( filAssemblyViewFindSequenceMatchesForConsedScript ); saveAConsedParameter( nAssemblyViewCrossmatchMinmatch ); saveAConsedParameter( nAssemblyViewCrossmatchMinscore ); saveAConsedParameter( nAssemblyViewSequenceMatchesMinimumSimilarity ); saveAConsedParameter( nTracesWindowInitialPixelWidth ); saveAConsedParameter( nAssemblyViewWindowInitialPixelWidth ); saveAConsedParameter( bAutomaticallyScaleTraces ); saveAConsedParameter( dAutomaticallyScaleTracesSamplePeakHeightFractionOfWindowHeight ); saveAConsedParameter( nAutomaticallyScaleTracesSamplePeakPercentile ); saveAConsedParameter( nVerticalTraceMagnification ); saveAConsedParameter( soUserDefinedKeys ); saveAConsedParameter( soProgramsForUserDefinedKeys ); saveAConsedParameter( soArgumentsToPassToUserDefinedPrograms ); saveAConsedParameter( soTagsToApplyWithUserDefinedKeys ); saveAConsedParameter( bSnpGenomeUseInsertionPolymorphisms ); saveAConsedParameter( soListOfTagTypesToHide ); saveAConsedParameter( soListOfOptionalWordsToSaveInListOfReadNames ); saveAConsedParameter( bExtendConsensusWithHighQuality ); saveAConsedParameter( bFastStartup ); saveAConsedParameter( filFastStartupFile ); saveAConsedParameter( soAlwaysRunProgramToGetChromats ); saveAConsedParameter( filProgramToRunToGetChromats ); saveAConsedParameter( filProgramToRunToGetChromatsOf454Reads ); saveAConsedParameter( bCreateFakeChromatsForSolexaReads ); saveAConsedParameter( bAutoFinishUseLongModelReadRatherThanShort ); saveAConsedParameter( nAskAgainIfWantToQuitConsedIfThisManyReads ); saveAConsedParameter( soPrintWindowInstructions ); saveAConsedParameter( bAllowMultipleSearchForStringWindows ); saveAConsedParameter( nAutoPCRAmplifyFalseProductsOKIfLargerThanThis ); saveAConsedParameter( bAutoPCRAmplifyMakePrimerOutOfFirstRegion ); saveAConsedParameter( nAutoPCRAmplifyMaybeRejectPrimerIfThisCloseToDesiredProduct ); saveAConsedParameter( bAddNewReadsRecalculateConsensusQuality ); saveAConsedParameter( soAddNewReadsPutReadIntoItsOwnContig ); saveAConsedParameter( bAddNewReadsCheckThatCrossMatchRunCorrectly ); saveAConsedParameter( nAssemblyViewNumberOfRowsOfTags ); saveAConsedParameter( bWarnUserWhenTryingToEditAllReads ); saveAConsedParameter( filMaybeXKEYSYMDBPath ); saveAConsedParameter( filMaybeXKEYSYMDBPath2 ); saveAConsedParameter( nAmountToMoveWithBigLeftAndRightArrows ); saveAConsedParameter( nNavigateByHighlyDiscrepantPositionsMinDiscrepantReads ); saveAConsedParameter( nNavigateByHighlyDiscrepantPositionsMaxDepthOfCoverage ); saveAConsedParameter( nNavigateByHighlyDiscrepantPositionsIgnoreBasesBelowThisQuality ); saveAConsedParameter( bNavigateByHighlyDiscrepantPositionsJustListIndels ); saveAConsedParameter( bNavigateByHighlyDiscrepantPositionsIgnoreOtherReadsStartingAtSameLocation ); saveAConsedParameter( bNavigateByHighlyDiscrepantPositionsIgnoreIfListedBasesInConsensus ); saveAConsedParameter( soNavigateByHighlyDiscrepantPositionsIgnoreIfTheseBasesInConsensus ); saveAConsedParameter( filPhdBallDirectory ); saveAConsedParameter( filNewAceFileFOF ); saveAConsedParameter( nNavigateByHighOrLowDepthCoalesceRegionsIfThisClose ); saveAConsedParameter( bRemoveReadsDeleteNotJustPutInOwnContig ); saveAConsedParameter( soPaired454LeftReadExtension ); saveAConsedParameter( soPaired454RightReadExtension ); saveAConsedParameter( filSnpGenome1MSnps ); saveAConsedParameter( bDiffChromosomesExcludeDeletions ); saveAConsedParameter( bSnpGenomeFilterByWeight ); saveAConsedParameter( nWantReadsUpToThisFarFromSnps ); saveAConsedParameter( soPhaster2PhdBallSaveWhichMate ); saveAConsedParameter( bPhaster2PhdBallSaveInPhasterFormat ); saveAConsedParameter( bPhaster2PhdBallCalculateNewLocationsFile ); saveAConsedParameter( bPhdBall2FastaIgnoreLowQualityReads ); saveAConsedParameter( nPhdBall2FastaLowestAverageQuality ); saveAConsedParameter( filNextPhredPipelineControlFile ); saveAConsedParameter( filNextPhredPipelineTiffPerlScript ); saveAConsedParameter( filNextPhredPipelinePhasterPerlScript ); saveAConsedParameter( soNextPhredPipelineVersion ); saveAConsedParameter( soNextPhredPipelineMainDirectory ); saveAConsedParameter( nMaxNumberOfReadsPerPhdBall ); saveAConsedParameter( filUserWantsToSaveToThisAceFile ); saveAConsedParameter( bAutoFinishEmulate9_66Behavior ); saveAConsedParameter( nPrimersPCRPrimersGroupedIntoWindowOfThisManyBases ); saveAConsedParameter( nPrimersLookForThisManyPCRPrimerPairsPerPairOfGroups ); saveAConsedParameter( dAutoFinishStandardDeviationsFromMeanFromGapToLookForTemplatesForSuggestingEachMissingReadOfReadPairs ); saveAConsedParameter( bAutoFinishCheckThatReadsFromTheSameTemplateAreConsistent ); saveAConsedParameter( bAutoFinishDoNotAllowSubcloneCustomPrimerReadsCloseTogether ); saveAConsedParameter( bAutoFinishDoNotAllowWholeCloneCustomPrimerReadsCloseTogether ); saveAConsedParameter( dAutoFinishMinilibrariesPreferTemplateIfSizeThisManyStdDevsFromMean ); saveAConsedParameter( nAutoFinishMinNumberOfForwardReversePairsInLibraryToCalculateAverageInsertSize ); saveAConsedParameter( dAutoFinishIfEnoughFwdRevPairsUseThisManyStdDevBelowMeanForInsertSize ); saveAConsedParameter( nAutoFinishNewCustomPrimerReadThisFarFromOldCustomPrimerRead ); saveAConsedParameter( nAutoFinishMinNumberOfSingleSubcloneBasesFixedByAnExp ); saveAConsedParameter( nAutoFinishNumberOfBasesBetweenContigsAssumed ); saveAConsedParameter( nAutoFinishPotentialHighQualityPartOfReadStart ); saveAConsedParameter( nAutoFinishPotentialHighQualityPartOfReadEnd ); saveAConsedParameter( bAutoFinishPrintCustomNavigationFileForChosenReads ); saveAConsedParameter( nAutoFinishReversesForFlankingGapsTemplateMustProtrudeFromContigThisMuch ); saveAConsedParameter( bAutoFinishTagOligosWhenDoExperiments ); saveAConsedParameter( bCountPads ); saveAConsedParameter( nDebugging ); saveAConsedParameter( nDebugging2 ); saveAConsedParameter( nDebugging3 ); saveAConsedParameter( soDebuggingString ); saveAConsedParameter( nIgnoreHighQualityDiscrepanciesThisManyBasesFromEndOfAlignedRegion ); saveAConsedParameter( nIgnoreUnalignedHighQualitySegmentsShorterThanThis ); saveAConsedParameter( nPrimersLookThisFarForForwardVectorInsertJunction ); saveAConsedParameter( dPrimersDNAConcentrationNanomolar ); saveAConsedParameter( nPrimersMaxMatchElsewhereScore ); saveAConsedParameter( nPrimersMaxMatchElsewhereScoreForPCR ); saveAConsedParameter( nPrimersMaxSelfMatchScore ); saveAConsedParameter( nPrimersMaxPrimerDimerScoreForPCR ); saveAConsedParameter( nPrimersMinQuality ); saveAConsedParameter( bPrimersPrintInfoOnRejectedTemplates ); saveAConsedParameter( dPrimersSaltConcentrationMillimolar ); saveAConsedParameter( bPrimersScreenForVector ); saveAConsedParameter( nPrimersToleranceForDifferentBeginningLocationOfUniversalPrimerReads ); saveAConsedParameter( nPrimersTooManyVectorBasesInWalkingRead ); saveAConsedParameter( nQualityThresholdForLowConsensusQuality ); saveAConsedParameter( nTagColorPerCentOfBase ); saveAConsedParameter( soUncompressedChromatDirectory ); saveAConsedParameter( fil454sff2scfDirectory ); saveAConsedParameter( nWhenMakingFakeReadToJoinContigsAddThisManyBasesOnEitherSideOfAlignedRegion ); saveAConsedParameter( nWriteThisAceFormat ); saveAConsedParameter( bDumpCoreIfBoundsError ); saveAConsedParameter( nAutoFinishMinSmithWatermanScoreOfARun ); saveAConsedParameter( dAutoFinishDoNotComparePCRPrimersMoreThanThisManyTimes ); saveAConsedParameter( nRestrictionDigestMaximumBasesToCompareToVector ); saveAConsedParameter( dRestrictionDigestZoomFactor ); saveAConsedParameter( dRestrictionDigestZoomFactorForNavigate ); saveAConsedParameter( nRestrictionDigestToleranceInPositionUnits ); saveAConsedParameter( nAutoPCRAmplifyTooManySeriousFalseMatches ); saveAConsedParameter( dAssemblyViewZoomFactor ); saveAConsedParameter( nAssemblyViewFilterInconsistentFwdRevPairsIfThisClose ); saveAConsedParameter( dAssemblyViewGridCellWidthInPixels ); saveAConsedParameter( nAssemblyViewCursorSensitivityInPixels ); saveAConsedParameter( nAssemblyViewReadDepthQuality ); saveAConsedParameter( nShowAllTracesMaxNumberOfTracesToShowAtOnce ); saveAConsedParameter( nAllowFwdRevPairScaffoldsToBeMergedIfThisManyBasesIntersectionOrLess ); saveAConsedParameter( bJustForPrimateProject ); saveAConsedParameter( filSolexaFilesAreAssumedToBeHere ); saveAConsedParameter( nSolexaAlignmentFilesPerInsertingPadsCycle ); saveAConsedParameter( nSolexaAlignmentsPerAlignmentFile ); saveAConsedParameter( bSolexaFastqFilesArePhredQualityNotSolexaQuality ); saveAConsedParameter( soSolexa64FastqOrSanger33Fastq ); saveAConsedParameter( nMaximumReadsInReadList ); saveAConsedParameter( nMaxLengthOfReadsInapLocatedFragment2 ); saveAConsedParameter( nMaximumStartupErrorsToReport ); saveAConsedParameter( n454LinkerAlignmentMatchScore ); saveAConsedParameter( n454LinkerAlignmentMismatchScore ); saveAConsedParameter( n454LinkerAlignmentIndelScore ); saveAConsedParameter( bFilter454ReadsDeleteCrossMatchOutput ); saveAConsedParameter( nAutoReportAllNeededSpeciesCode ); saveAConsedParameter( bAutoReportUseCommasInBigNumbers ); saveAConsedParameter( bAutoReportPrintToCompareToReich ); saveAConsedParameter( bAutoReportOnlyAllowSitesThatAreBetweenAcceptableSites ); saveAConsedParameter( bAutoReportDeaminationMutationsDeterminedByMoreAccurateMethod ); saveAConsedParameter( bAutoReportChooseTreesUsingBadData ); saveAConsedParameter( bAutoReportChooseTreesByCountingDeaminationMutations ); saveAConsedParameter( bAutoReportChooseTreesUsingKimura ); saveAConsedParameter( bAutoReportPrintCrudeChimpHumanMutations ); saveAConsedParameter( bAutoReportPrintPositionsForGraham ); saveAConsedParameter( bAutoReportPrintAncestralCpGs ); saveAConsedParameter( bAutoReportPrintCpGMutations ); saveAConsedParameter( bAutoReportPrintMutationsWithContext ); saveAConsedParameter( bAutoReportCountAllMutationsML ); saveAConsedParameter( bAutoReportCountAllMutations ); saveAConsedParameter( bAutoReportIgnoreMultipleTrees ); saveAConsedParameter( bAutoReportCountAcceptableColumnsWithNoneOnLeft ); saveAConsedParameter( bAutoReportPrintFlankedColumns4 ); saveAConsedParameter( bAutoReportUseAnnotationFormat ); saveAConsedParameter( bAutoReportPrintFlankedColumns3 ); saveAConsedParameter( bAutoReportPrintFlankedColumns2 ); saveAConsedParameter( bAutoReportPrintFlankedColumns ); saveAConsedParameter( bAutoReportHighQualitySegmentData ); saveAConsedParameter( bAutoReportGoodReadsBug ); saveAConsedParameter( bAutoReportDiscrepancyRateInFlankedRegions ); saveAConsedParameter( bAutoReportDiscrepancyRateInFlankedRegions2 ); saveAConsedParameter( bAutoReportDiscrepancyRateInFlankedRegions4 ); saveAConsedParameter( bAutoReportDiscrepancyRateInFlankedRegions5 ); saveAConsedParameter( bAutoReportSingleSignalOrQuality ); saveAConsedParameter( bAutoReportLowQualityBasesInHQS ); saveAConsedParameter( bAutoReportCompareHQSWithLQS ); saveAConsedParameter( bAutoReportCountColumnsForGroupsOfSpecies ); saveAConsedParameter( bAutoReportSingleSignalInfo ); saveAConsedParameter( bAutoReportSingleSignalInfo2 ); saveAConsedParameter( bAutoReportCompareTopAndBottomStrands ); saveAConsedParameter( bAutoReportCompareTopAndBottomStrandsNoHuman ); saveAConsedParameter( bAutoReportCompareTopAndBottomStrands2 ); saveAConsedParameter( bAutoReportCompareTopAndBottomStrands3 ); saveAConsedParameter( bAutoReportCompareTopAndBottomStrands4 ); saveAConsedParameter( nAutoReportTopStrandPinnedPosition ); saveAConsedParameter( nAutoReportBottomStrandPinnedPosition ); saveAConsedParameter( bAutoReportCompareTopAndBottomStrandsWithHuman ); saveAConsedParameter( bAutoReportPrintLengthsOfAlignedSegmentsOfReads ); saveAConsedParameter( bAutoReportPrintLengthsOfUnalignedHighQualitySegmentsOfReads ); saveAConsedParameter( bAutoReportPrintIfReadsAreCorrectlyAligned ); saveAConsedParameter( bAutoReportCalculateErrorProbabilitiesByComparingPTroPPan ); saveAConsedParameter( bAutoReportPrintAgreeDisagreeBetweenPairsOfSpecies ); saveAConsedParameter( bAutoReportPrintAgreeDisagreeBetweenPairsOfSpecies2 ); saveAConsedParameter( bAutoReportFilterSingleSignal ); saveAConsedParameter( filAutoReportGoodHitReads ); saveAConsedParameter( nAutoReportQualityWindowLow ); saveAConsedParameter( nAutoReportQualityWindowHigh ); saveAConsedParameter( bAutoReportPrintNumberOfIsolatedPadsForEachSpecies ); saveAConsedParameter( bAutoReportPrintNumberOfIsolatedPads ); saveAConsedParameter( soAutoReportIsolatedPadsOfReadsWithThisPattern ); saveAConsedParameter( nAutoReportMinNumberOfPerfectlyAlignedBasesBeforeDiscrepancy ); saveAConsedParameter( nAutoReportMaxSizeOfDiscrepantRegion ); saveAConsedParameter( nAutoReportSizeOfDiscrepantRegion ); saveAConsedParameter( bAutoReportPrintMinimumQualityHistogram ); saveAConsedParameter( bAutoReportPrintDiscrepantRegions ); saveAConsedParameter( bAutoReportPrintBasesInDiscrepantRegions ); saveAConsedParameter( soAutoReportPrintDiscrepantRegionsButIgnoreReadsContainingThis ); saveAConsedParameter( soAutoReportBackboneReadHasThisStringInIt ); saveAConsedParameter( bAutoReportPrintDiscrepantRegionsButOnlyIfAboveQualityThreshold ); saveAConsedParameter( bAutoReportPrintSpeciesAlignment ); saveAConsedParameter( bAutoReportPrintReadAlignment ); saveAConsedParameter( filAutoReportPrintTheseReads ); saveAConsedParameter( bAutoReportPrintReadPositions ); saveAConsedParameter( bAutoReportPrintChosenReadName ); saveAConsedParameter( nAutoReportNumbersOfCharactersOfChosenReadNameToBePrinted ); saveAConsedParameter( soAutoReportPrefix ); saveAConsedParameter( bAutoReportUseOldCriteriaForDeletingColumnsOfPads ); saveAConsedParameter( bAutoReportDeleteColumnsOfPadsBeforeAdjustingReadQualityValues ); saveAConsedParameter( bAutoReportFlankingBasesMustBeSingleSignal ); saveAConsedParameter( nAutoReportMinimumQualityOfFlankingBases ); saveAConsedParameter( bAutoReportFlankingBasesMustBeInHighQualitySegment ); saveAConsedParameter( soAutoReportSpecies );