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