/*****************************************************************************
#   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.
#
#*****************************************************************************/
   checkPrintPS();
   checkDefaultTagType();
   checkDefaultTagOnConsensusNotReads();
   checkAutoFinishMinNumberOfErrorsFixedByAnExp();
   checkAutoFinishRedundancy();
   checkAutoFinishAverageInsertSize();
   checkPrimersMaxInsertSizeOfASubclone();
   checkPrimersMaxMeltingTemp();
   checkPrimersMaxMeltingTempForPCR();
   checkPrimersPickTemplatesForPrimers();
   checkPrimersSubcloneFullPathnameOfFileOfSequencesForScreening();
   checkPrimersCloneFullPathnameOfFileOfSequencesForScreening();
   checkPrimersMinMeltingTemp();
   checkPrimersMinMeltingTempForPCR();
   checkSearchFunctionsUseUnalignedEndsOfReads();
   checkSearchFunctionsUseLowQualityEndsOfReads();
   checkInexactSearchForStringMaxPerCentMismatch();
   checkOnlyAllowOneReadWriteConsedAtATime();
   checkAutoFinishAllowHighQualityDiscrepanciesInTemplateIfConsistentForwardReversePair();
   checkPrintWindowCommand();
   checkFileOfTagTypes();
   checkAssemblyViewShowConsistentFwdRevPairs();
   checkAssemblyViewShowConsistentFwdRevPairDepth();
   checkAssemblyViewShowConsistentFwdRevPairsBetweenDifferentScaffolds();
   checkAssemblyViewShowLegsOnSquaresForConsistentFwdRevPairs();
   checkAssemblyViewShowGapSpanningFwdRevPairs();
   checkAssemblyViewShowWhichInconsistentFwdRevPairs();
   checkAssemblyViewShowReadDepth();
   checkAssemblyViewShowMultipleHighQualityDiscrepancies();
   checkAssemblyViewShowRestrictionDigestCutSites();
   checkAssemblyViewFilterSequenceMatchesBySize();
   checkAssemblyViewSequenceMatchesMinSize();
   checkAssemblyViewSequenceMatchesMaxSize();
   checkAssemblyViewAutomaticallyStartWithConsed();
   checkAssemblyViewDisplayTheseTagTypesOnTheseLines();
   checkAssemblyViewShowTags();
   checkAutoEditRecalculateHighQualitySegmentsOfReads();
   checkAutoEditConvertCloneEndBasesToXs();
   checkAutoEditTellPhrapNotToOverlapMultiplyDiscrepantReads();
   checkAutoEditTagEditableLowConsensusQualityRegions();
   checkAutoEditMakeFakeRead();
   checkAutoEditMakeFakeReadFromRead1();
   checkAutoEditMakeFakeReadFromRead2();
   checkAutoEditMakeFakeReadName();
   checkAutoEditMakeFakeReadFastaFilename();
   checkAutoEditMergeAssembly();
   checkAutoEditSecondaryAceFile();
   checkAutoEditFixRunsInConsensus();
   checkShowAllTracesJustShowGoodTraces();
   checkAddAlignedSequenceQualityOfBases();
   checkMakeLightBackgroundInAlignedReadsWindowAndTracesWindow();
   checkPutVerticalLineAtCursor();
   checkPutHorizontalLineAtCursor();
   checkHighlightedReadsFile();
   checkAutoReportPrintReadNamesInRegion();
   checkAutoReportPrintReadNamesInRegionContig();
   checkAutoReportPrintReadNamesInRegionLeftPos();
   checkAutoReportPrintReadNamesInRegionRightPos();
   checkAutoReportPrintHighlyDiscrepantRegions();
   checkAutoReportPrintScaffolds();
   checkNumberUnpaddedConsensusAtUserDefined();
   checkAutoReportPrintHighQualityDiscrepancies();
   checkAutoReportHighQualityDiscrepanciesExcludeCompressionOrG_dropoutTags();
   checkAutoReportHighQualityDiscrepanciesExcludeMostPads();
   checkAutoReportPrintLowConsensusQualityRegions();
   checkAutoReportPrintSingleSubcloneRegions();
   checkAutoReportPrintSingleStrandedRegions();
   checkAutoReportPrintLinkingForwardReversePairs();
   checkAutoReportPrintFilteredInconsistentForwardReversePairs();
   checkAutoReportPrintAssemblySummary();
   checkShowAllTracesDoNotShowTraceIfTheseTagsPresent();
   checkNameOfFakeJoiningReadsIncludesAceFileName();
   checkWhenUserScrollsOffWindowMillisecondsBetweenScrolling();
   checkWhenUserScrollsOffWindowBasesToScrollEachTime();
   checkCompareContigsUseBandedRatherThanFullSmithWaterman();
   checkCompareContigsBandSize();
   checkAssemblyViewShowFwdRevPairDepthsInRedIfOnlyThisMany();
   checkAssemblyViewShowSequenceMatches();
   checkAssemblyViewOKToShowSequenceMatchesBetweenContigs();
   checkAssemblyViewOKToShowSequenceMatchesWithinContigs();
   checkAssemblyViewOKToShowDirectSequenceMatches();
   checkAssemblyViewOKToShowInvertedSequenceMatches();
   checkAssemblyViewOnlyShowSequenceMatchesToAParticularRegion();
   checkAssemblyViewOnlyShowSequenceMatchesToThisContig();
   checkAssemblyViewOnlyShowSequenceMatchesToThisRegionLeft();
   checkAssemblyViewOnlyShowSequenceMatchesToThisRegionRight();
   checkAssemblyViewOnlyShowSequenceMatchesToEndsOfContigs();
   checkAssemblyViewOnlyShowSequenceMatchesToEndsOfContigsThisFar();
   checkDefaultReadPrefix();
   checkReadPrefixesFile();
   checkMaxCharsDisplayedForReadPrefix();
   checkAutoFinishDoNotDoPCRIfThisManyAvailableGapSpanningTemplates();
   checkAutoFinishDoNotDoUnorientedPCRIfThisManyOrMoreUnorientedPCRReactions();
   checkAutoFinishDoNotDoOrientedPCRIfGapSizeLargerThanThis();
   checkAutoFinishDoNotDoPCRIfEndIsExtendedByReads();
   checkAutoFinishMaxAcceptableErrorsPerMegabase();
   checkAutoFinishIfNotEnoughFwdRevPairsUseThisPerCentOfInsertSize();
   checkPrimersNumberOfBasesToBackUpToStartLooking();
   checkPrimersMakePCRPrimersThisManyBasesBackFromEndOfHighQualitySegment();
   checkPrimersOKToChoosePrimersInSingleSubcloneRegion();
   checkPrimersOKToChoosePrimersWhereHighQualityDiscrepancies();
   checkPrimersOKToChoosePrimersWhereUnalignedHighQualityRegion();
   checkAutoFinishCallReversesToFlankGaps();
   checkAutoFinishAllowWholeCloneReads();
   checkAutoFinishAllowCustomPrimerSubcloneReads();
   checkAutoFinishAllowResequencingReads();
   checkAutoFinishAllowResequencingReadsOnlyForRunsAndStops();
   checkAutoFinishAllowDeNovoUniversalPrimerSubcloneReads();
   checkAutoFinishAllowMinilibraries();
   checkAutoFinishAllowPCR();
   checkAutoFinishAllowUnorientedPCRReactions();
   checkAutoFinishAllowResequencingAUniversalPrimerAutofinishRead();
   checkAutoFinishAlwaysCloseGapsUsingMinilibraries();
   checkAutoFinishMaximumFinishingReadLength();
   checkAutoFinishSuggestMinilibraryIfGapThisManyBasesOrLarger();
   checkAutoFinishSuggestSpecialChemistryForRunsAndStops();
   checkAutoFinishSuggestThisManyMinilibrariesPerGap();
   checkPrimersWindowSizeInLooking();
   checkPrimersAssumeTemplatesAreDoubleStrandedUnlessSpecified();
   checkAlignedReadsWindowInitialCharsWide();
   checkAlignedReadsWindowInitialCharsHigh();
   checkAlignedReadsWindowMaxCharsForReadNames();
   checkAlignedReadsWindowAutomaticallyExpandRoomForReadNames();
   checkAutoFinishAllowResequencingReadsToExtendContigs();
   checkAutoFinishCallHowManyReversesToFlankGaps();
   checkAutoFinishCloseGaps();
   checkAutoFinishContinueEvenThoughReadInfoDoesNotMakeSense();
   checkAutoFinishCostOfResequencingUniversalPrimerSubcloneReaction();
   checkAutoFinishCostOfCustomPrimerSubcloneReaction();
   checkAutoFinishCostOfCustomPrimerCloneReaction();
   checkAutoFinishCostOfDeNovoUniversalPrimerSubcloneReaction();
   checkAutoFinishCostOfMinilibrary();
   checkAutoFinishCoverSingleSubcloneRegions();
   checkAutoFinishCoverLowConsensusQualityRegions();
   checkAutoFinishDebugUniversalPrimerReadsFile();
   checkAutoFinishDebugCustomPrimerReadsFile();
   checkAutoFinishDoNotAllowSubcloneCustomPrimerReadsCloserThanThisManyBases();
   checkAutoFinishDoNotAllowWholeCloneCustomPrimerReadsCloserThanThisManyBases();
   checkAutoFinishDoNotFinishWhereTheseTagsAre();
   checkAutoFinishDoNotExtendContigsWhereTheseTagsAre();
   checkAutoFinishDoNotExtendContigsIfTagsAreThisCloseToContigEnd();
   checkDumpContigOrderAndOrientationInfoToThisFile();
   checkAutoFinishDumpTemplates();
   checkAutoFinishExcludeContigIfOnlyThisManyReadsOrLess();
   checkAutoFinishExcludeContigIfDepthOfCoverageGreaterThanThis();
   checkAutoFinishExcludeContigIfThisManyBasesOrLess();
   checkAutoFinishHowManyTemplatesYouIntendToUseForCustomPrimerSubcloneReactions();
   checkPrimersMinNumberOfTemplatesForPrimers();
   checkAutoFinishMinBaseOverlapBetweenAReadAndHighQualitySegmentOfConsensus();
   checkAutoFinishNumberOfVectorBasesAtBeginningOfAUniveralPrimerRead();
   checkAutoFinishCDNANotGenomic();
   checkAutoFinishConfidenceThatReadWillCoverSingleSubcloneRegion();
   checkAutoFinishPrintForwardOrReverseStrandWhenPrintingSubcloneTemplatesForCustomPrimerReads();
   checkAutoFinishPrintMinilibrariesSummaryFile();
   checkAutoFinishNearGapsSuggestEachMissingReadOfReadPairs();
   checkAutoFinishDoNotIgnoreLCQIfThisManyBasesFromEndOfContigForLCQTagger();
   checkCheckIfTooManyWalks();
   checkNumberOfColumnsBeforeReadNameInAlignedReadsWindow();
   checkCompareContigsAlignsThisManyBasesMax();
   checkCompressedChromatExtension();
   checkDimLowQualityEndsOfReads();
   checkDimUnalignedEndsOfReads();
   checkFakeReadsSpecifiedByFilenameExtension();
   checkFullPathnameOfAddReads2ConsedScript();
   checkFullPathnameOfFixContigEndScript();
   checkFixContigEndsCleanUpTemporaryFiles();
   checkFixContigEndsMinSmithWatermanScoreToMakeJoin();
   checkFixContigEndsMinNumberOfReadsInContig();
   checkFullPathnameOfCrossMatch();
   checkFullPathnameOfPhred();
   checkFullPathnameOfMiniassemblyScript();
   checkGunzipFullPath();
   checkFullPathnameOfFilter454ReadsScript();
   checkFilter454ReadsAgainstThis();
   check454LinkerSequences();
   checkHideSomeTagTypesAtStartup();
   checkMaximumNumberOfTracesShown();
   checkNavigateAutomaticTracePopup();
   checkNavigateAutomaticAllTracesPopup();
   checkPrimersMinimumLengthOfAPrimer();
   checkPrimersMaximumLengthOfAPrimer();
   checkPrimersMinimumLengthOfAPrimerForPCR();
   checkPrimersMaximumLengthOfAPrimerForPCR();
   checkPrimersMaxMeltingTempDifferenceForPCR();
   checkPrimersMaxPCRPrimerPairsToDisplay();
   checkPrimersCheckJustSomePCRPrimerPairsRatherThanAll();
   checkPrimersNumberOfTemplatesToDisplayInFront();
   checkPrimersMaxLengthOfMononucleotideRepeat();
   checkPrimersBadLibrariesFile();
   checkPrimersLibrariesInfoFile();
   checkPrimersBadTemplatesFile();
   checkPrimersChooseTemplatesByPositionInsteadOfQuality();
   checkPrimersWhenChoosingATemplateMinPotentialReadLength();
   checkPrimersWindowSizeInLookingForPCR();
   checkQualityThresholdForFindingHighQualityDiscrepancies();
   checkQualityThresholdForNavigateByDepthOfCoverage();
   checkNavigateByHighDepthOfCoverageNotLow();
   checkMinDepthForNavigateByDepthOfCoverage();
   checkDefaultVectorPathnameForRestrictionFragments();
   checkFileOfAdditionalRestrictionEnzymes();
   checkCommonRestrictionEnzymes();
   checkDefaultSelectedRestrictionEnzymes();
   checkRestrictionEnzymesActualFragmentsFile();
   checkRestrictionDigestInitialWindowSizeInTextRows();
   checkRestrictionDigestDoNoShowAreaOfFragmentsOverThisSize();
   checkShowReadsAlphabetically();
   checkShowReadsInAlignedReadsWindowOrderedByFile();
   checkShowReadsInAlignedReadsWindowOrderedByThisFile();
   checkShowReadsAtCursorSortedHow();
   checkShowABIBasesInTraceWindow();
   checkTracesWindowInitialPixelHeight();
   checkAssemblyViewWindowInitialPixelHeight();
   checkAssemblyViewFileOfTemplatesToNotShow();
   checkAssemblyViewCrossMatchMinmatch();
   checkAssemblyViewCrossMatchMinscore();
   checkAssemblyViewFindSequenceMatchesForConsedScript();
   checkAssemblyViewCrossmatchMinmatch();
   checkAssemblyViewCrossmatchMinscore();
   checkAssemblyViewSequenceMatchesMinimumSimilarity();
   checkTracesWindowInitialPixelWidth();
   checkAssemblyViewWindowInitialPixelWidth();
   checkAutomaticallyScaleTraces();
   checkAutomaticallyScaleTracesSamplePeakHeightFractionOfWindowHeight();
   checkAutomaticallyScaleTracesSamplePeakPercentile();
   checkVerticalTraceMagnification();
   checkUserDefinedKeys();
   checkProgramsForUserDefinedKeys();
   checkArgumentsToPassToUserDefinedPrograms();
   checkTagsToApplyWithUserDefinedKeys();
   checkSnpGenomeUseInsertionPolymorphisms();
   checkListOfTagTypesToHide();
   checkListOfOptionalWordsToSaveInListOfReadNames();
   checkExtendConsensusWithHighQuality();
   checkFastStartup();
   checkFastStartupFile();
   checkAlwaysRunProgramToGetChromats();
   checkProgramToRunToGetChromats();
   checkProgramToRunToGetChromatsOf454Reads();
   checkCreateFakeChromatsForSolexaReads();
   checkAutoFinishUseLongModelReadRatherThanShort();
   checkAskAgainIfWantToQuitConsedIfThisManyReads();
   checkPrintWindowInstructions();
   checkAllowMultipleSearchForStringWindows();
   checkAutoPCRAmplifyFalseProductsOKIfLargerThanThis();
   checkAutoPCRAmplifyMakePrimerOutOfFirstRegion();
   checkAutoPCRAmplifyMaybeRejectPrimerIfThisCloseToDesiredProduct();
   checkAddNewReadsRecalculateConsensusQuality();
   checkAddNewReadsPutReadIntoItsOwnContig();
   checkAddNewReadsCheckThatCrossMatchRunCorrectly();
   checkAssemblyViewNumberOfRowsOfTags();
   checkWarnUserWhenTryingToEditAllReads();
   checkMaybeXKEYSYMDBPath();
   checkMaybeXKEYSYMDBPath2();
   checkAmountToMoveWithBigLeftAndRightArrows();
   checkNavigateByHighlyDiscrepantPositionsMinDiscrepantReads();
   checkNavigateByHighlyDiscrepantPositionsMaxDepthOfCoverage();
   checkNavigateByHighlyDiscrepantPositionsIgnoreBasesBelowThisQuality();
   checkNavigateByHighlyDiscrepantPositionsJustListIndels();
   checkNavigateByHighlyDiscrepantPositionsIgnoreOtherReadsStartingAtSameLocation();
   checkNavigateByHighlyDiscrepantPositionsIgnoreIfListedBasesInConsensus();
   checkNavigateByHighlyDiscrepantPositionsIgnoreIfTheseBasesInConsensus();
   checkPhdBallDirectory();
   checkNewAceFileFOF();
   checkNavigateByHighOrLowDepthCoalesceRegionsIfThisClose();
   checkRemoveReadsDeleteNotJustPutInOwnContig();
   checkPaired454LeftReadExtension();
   checkPaired454RightReadExtension();
   checkSnpGenome1MSnps();
   checkDiffChromosomesExcludeDeletions();
   checkSnpGenomeFilterByWeight();
   checkWantReadsUpToThisFarFromSnps();
   checkPhaster2PhdBallSaveWhichMate();
   checkPhaster2PhdBallSaveInPhasterFormat();
   checkPhaster2PhdBallCalculateNewLocationsFile();
   checkPhdBall2FastaIgnoreLowQualityReads();
   checkPhdBall2FastaLowestAverageQuality();
   checkNextPhredPipelineControlFile();
   checkNextPhredPipelineTiffPerlScript();
   checkNextPhredPipelinePhasterPerlScript();
   checkNextPhredPipelineVersion();
   checkNextPhredPipelineMainDirectory();
   checkMaxNumberOfReadsPerPhdBall();
   checkUserWantsToSaveToThisAceFile();
   checkAutoFinishEmulate9_66Behavior();
   checkPrimersPCRPrimersGroupedIntoWindowOfThisManyBases();
   checkPrimersLookForThisManyPCRPrimerPairsPerPairOfGroups();
   checkAutoFinishStandardDeviationsFromMeanFromGapToLookForTemplatesForSuggestingEachMissingReadOfReadPairs();
   checkAutoFinishCheckThatReadsFromTheSameTemplateAreConsistent();
   checkAutoFinishDoNotAllowSubcloneCustomPrimerReadsCloseTogether();
   checkAutoFinishDoNotAllowWholeCloneCustomPrimerReadsCloseTogether();
   checkAutoFinishMinilibrariesPreferTemplateIfSizeThisManyStdDevsFromMean();
   checkAutoFinishMinNumberOfForwardReversePairsInLibraryToCalculateAverageInsertSize();
   checkAutoFinishIfEnoughFwdRevPairsUseThisManyStdDevBelowMeanForInsertSize();
   checkAutoFinishNewCustomPrimerReadThisFarFromOldCustomPrimerRead();
   checkAutoFinishMinNumberOfSingleSubcloneBasesFixedByAnExp();
   checkAutoFinishNumberOfBasesBetweenContigsAssumed();
   checkAutoFinishPotentialHighQualityPartOfReadStart();
   checkAutoFinishPotentialHighQualityPartOfReadEnd();
   checkAutoFinishPrintCustomNavigationFileForChosenReads();
   checkAutoFinishReversesForFlankingGapsTemplateMustProtrudeFromContigThisMuch();
   checkAutoFinishTagOligosWhenDoExperiments();
   checkCountPads();
   checkDebugging();
   checkDebugging2();
   checkDebugging3();
   checkDebuggingString();
   checkIgnoreHighQualityDiscrepanciesThisManyBasesFromEndOfAlignedRegion();
   checkIgnoreUnalignedHighQualitySegmentsShorterThanThis();
   checkPrimersLookThisFarForForwardVectorInsertJunction();
   checkPrimersDNAConcentrationNanomolar();
   checkPrimersMaxMatchElsewhereScore();
   checkPrimersMaxMatchElsewhereScoreForPCR();
   checkPrimersMaxSelfMatchScore();
   checkPrimersMaxPrimerDimerScoreForPCR();
   checkPrimersMinQuality();
   checkPrimersPrintInfoOnRejectedTemplates();
   checkPrimersSaltConcentrationMillimolar();
   checkPrimersScreenForVector();
   checkPrimersToleranceForDifferentBeginningLocationOfUniversalPrimerReads();
   checkPrimersTooManyVectorBasesInWalkingRead();
   checkQualityThresholdForLowConsensusQuality();
   checkTagColorPerCentOfBase();
   checkUncompressedChromatDirectory();
   check454sff2scfDirectory();
   checkWhenMakingFakeReadToJoinContigsAddThisManyBasesOnEitherSideOfAlignedRegion();
   checkWriteThisAceFormat();
   checkDumpCoreIfBoundsError();
   checkAutoFinishMinSmithWatermanScoreOfARun();
   checkAutoFinishDoNotComparePCRPrimersMoreThanThisManyTimes();
   checkRestrictionDigestMaximumBasesToCompareToVector();
   checkRestrictionDigestZoomFactor();
   checkRestrictionDigestZoomFactorForNavigate();
   checkRestrictionDigestToleranceInPositionUnits();
   checkAutoPCRAmplifyTooManySeriousFalseMatches();
   checkAssemblyViewZoomFactor();
   checkAssemblyViewFilterInconsistentFwdRevPairsIfThisClose();
   checkAssemblyViewGridCellWidthInPixels();
   checkAssemblyViewCursorSensitivityInPixels();
   checkAssemblyViewReadDepthQuality();
   checkShowAllTracesMaxNumberOfTracesToShowAtOnce();
   checkAllowFwdRevPairScaffoldsToBeMergedIfThisManyBasesIntersectionOrLess();
   checkJustForPrimateProject();
   checkSolexaFilesAreAssumedToBeHere();
   checkSolexaAlignmentFilesPerInsertingPadsCycle();
   checkSolexaAlignmentsPerAlignmentFile();
   checkSolexaFastqFilesArePhredQualityNotSolexaQuality();
   checkSolexa64FastqOrSanger33Fastq();
   checkMaximumReadsInReadList();
   checkMaxLengthOfReadsInapLocatedFragment2();
   checkMaximumStartupErrorsToReport();
   check454LinkerAlignmentMatchScore();
   check454LinkerAlignmentMismatchScore();
   check454LinkerAlignmentIndelScore();
   checkFilter454ReadsDeleteCrossMatchOutput();
   checkAutoReportAllNeededSpeciesCode();
   checkAutoReportUseCommasInBigNumbers();
   checkAutoReportPrintToCompareToReich();
   checkAutoReportOnlyAllowSitesThatAreBetweenAcceptableSites();
   checkAutoReportDeaminationMutationsDeterminedByMoreAccurateMethod();
   checkAutoReportChooseTreesUsingBadData();
   checkAutoReportChooseTreesByCountingDeaminationMutations();
   checkAutoReportChooseTreesUsingKimura();
   checkAutoReportPrintCrudeChimpHumanMutations();
   checkAutoReportPrintPositionsForGraham();
   checkAutoReportPrintAncestralCpGs();
   checkAutoReportPrintCpGMutations();
   checkAutoReportPrintMutationsWithContext();
   checkAutoReportCountAllMutationsML();
   checkAutoReportCountAllMutations();
   checkAutoReportIgnoreMultipleTrees();
   checkAutoReportCountAcceptableColumnsWithNoneOnLeft();
   checkAutoReportPrintFlankedColumns4();
   checkAutoReportUseAnnotationFormat();
   checkAutoReportPrintFlankedColumns3();
   checkAutoReportPrintFlankedColumns2();
   checkAutoReportPrintFlankedColumns();
   checkAutoReportHighQualitySegmentData();
   checkAutoReportGoodReadsBug();
   checkAutoReportDiscrepancyRateInFlankedRegions();
   checkAutoReportDiscrepancyRateInFlankedRegions2();
   checkAutoReportDiscrepancyRateInFlankedRegions4();
   checkAutoReportDiscrepancyRateInFlankedRegions5();
   checkAutoReportSingleSignalOrQuality();
   checkAutoReportLowQualityBasesInHQS();
   checkAutoReportCompareHQSWithLQS();
   checkAutoReportCountColumnsForGroupsOfSpecies();
   checkAutoReportSingleSignalInfo();
   checkAutoReportSingleSignalInfo2();
   checkAutoReportCompareTopAndBottomStrands();
   checkAutoReportCompareTopAndBottomStrandsNoHuman();
   checkAutoReportCompareTopAndBottomStrands2();
   checkAutoReportCompareTopAndBottomStrands3();
   checkAutoReportCompareTopAndBottomStrands4();
   checkAutoReportTopStrandPinnedPosition();
   checkAutoReportBottomStrandPinnedPosition();
   checkAutoReportCompareTopAndBottomStrandsWithHuman();
   checkAutoReportPrintLengthsOfAlignedSegmentsOfReads();
   checkAutoReportPrintLengthsOfUnalignedHighQualitySegmentsOfReads();
   checkAutoReportPrintIfReadsAreCorrectlyAligned();
   checkAutoReportCalculateErrorProbabilitiesByComparingPTroPPan();
   checkAutoReportPrintAgreeDisagreeBetweenPairsOfSpecies();
   checkAutoReportPrintAgreeDisagreeBetweenPairsOfSpecies2();
   checkAutoReportFilterSingleSignal();
   checkAutoReportGoodHitReads();
   checkAutoReportQualityWindowLow();
   checkAutoReportQualityWindowHigh();
   checkAutoReportPrintNumberOfIsolatedPadsForEachSpecies();
   checkAutoReportPrintNumberOfIsolatedPads();
   checkAutoReportIsolatedPadsOfReadsWithThisPattern();
   checkAutoReportMinNumberOfPerfectlyAlignedBasesBeforeDiscrepancy();
   checkAutoReportMaxSizeOfDiscrepantRegion();
   checkAutoReportSizeOfDiscrepantRegion();
   checkAutoReportPrintMinimumQualityHistogram();
   checkAutoReportPrintDiscrepantRegions();
   checkAutoReportPrintBasesInDiscrepantRegions();
   checkAutoReportPrintDiscrepantRegionsButIgnoreReadsContainingThis();
   checkAutoReportBackboneReadHasThisStringInIt();
   checkAutoReportPrintDiscrepantRegionsButOnlyIfAboveQualityThreshold();
   checkAutoReportPrintSpeciesAlignment();
   checkAutoReportPrintReadAlignment();
   checkAutoReportPrintTheseReads();
   checkAutoReportPrintReadPositions();
   checkAutoReportPrintChosenReadName();
   checkAutoReportNumbersOfCharactersOfChosenReadNameToBePrinted();
   checkAutoReportPrefix();
   checkAutoReportUseOldCriteriaForDeletingColumnsOfPads();
   checkAutoReportDeleteColumnsOfPadsBeforeAdjustingReadQualityValues();
   checkAutoReportFlankingBasesMustBeSingleSignal();
   checkAutoReportMinimumQualityOfFlankingBases();
   checkAutoReportFlankingBasesMustBeInHighQualitySegment();
   checkAutoReportSpecies();