/***************************************************************************** # 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. # #*****************************************************************************/ aConsedResources_.insert("consed.printPS" ); aConsedResources_.insert("consed.defaultTagType" ); aConsedResources_.insert("consed.defaultTagOnConsensusNotReads" ); aConsedResources_.insert("consed.autoFinishMinNumberOfErrorsFixedByAnExp" ); aConsedResources_.insert("consed.autoFinishRedundancy" ); aConsedResources_.insert("consed.autoFinishAverageInsertSize" ); aConsedResources_.insert("consed.primersMaxInsertSizeOfASubclone" ); aConsedResources_.insert("consed.primersMaxMeltingTemp" ); aConsedResources_.insert("consed.primersMaxMeltingTempForPCR" ); aConsedResources_.insert("consed.primersPickTemplatesForPrimers" ); aConsedResources_.insert("consed.primersSubcloneFullPathnameOfFileOfSequencesForScreening" ); aConsedResources_.insert("consed.primersCloneFullPathnameOfFileOfSequencesForScreening" ); aConsedResources_.insert("consed.primersMinMeltingTemp" ); aConsedResources_.insert("consed.primersMinMeltingTempForPCR" ); aConsedResources_.insert("consed.searchFunctionsUseUnalignedEndsOfReads" ); aConsedResources_.insert("consed.searchFunctionsUseLowQualityEndsOfReads" ); aConsedResources_.insert("consed.inexactSearchForStringMaxPerCentMismatch" ); aConsedResources_.insert("consed.onlyAllowOneReadWriteConsedAtATime" ); aConsedResources_.insert("consed.autoFinishAllowHighQualityDiscrepanciesInTemplateIfConsistentForwardReversePair" ); aConsedResources_.insert("consed.printWindowCommand" ); aConsedResources_.insert("consed.fileOfTagTypes" ); aConsedResources_.insert("consed.assemblyViewShowConsistentFwdRevPairs" ); aConsedResources_.insert("consed.assemblyViewShowConsistentFwdRevPairDepth" ); aConsedResources_.insert("consed.assemblyViewShowConsistentFwdRevPairsBetweenDifferentScaffolds" ); aConsedResources_.insert("consed.assemblyViewShowLegsOnSquaresForConsistentFwdRevPairs" ); aConsedResources_.insert("consed.assemblyViewShowGapSpanningFwdRevPairs" ); aConsedResources_.insert("consed.assemblyViewShowWhichInconsistentFwdRevPairs" ); aConsedResources_.insert("consed.assemblyViewShowReadDepth" ); aConsedResources_.insert("consed.assemblyViewShowMultipleHighQualityDiscrepancies" ); aConsedResources_.insert("consed.assemblyViewShowRestrictionDigestCutSites" ); aConsedResources_.insert("consed.assemblyViewFilterSequenceMatchesBySize" ); aConsedResources_.insert("consed.assemblyViewSequenceMatchesMinSize" ); aConsedResources_.insert("consed.assemblyViewSequenceMatchesMaxSize" ); aConsedResources_.insert("consed.assemblyViewAutomaticallyStartWithConsed" ); aConsedResources_.insert("consed.assemblyViewDisplayTheseTagTypesOnTheseLines" ); aConsedResources_.insert("consed.assemblyViewShowTags" ); aConsedResources_.insert("consed.autoEditRecalculateHighQualitySegmentsOfReads" ); aConsedResources_.insert("consed.autoEditConvertCloneEndBasesToXs" ); aConsedResources_.insert("consed.autoEditTellPhrapNotToOverlapMultiplyDiscrepantReads" ); aConsedResources_.insert("consed.autoEditTagEditableLowConsensusQualityRegions" ); aConsedResources_.insert("consed.autoEditMakeFakeRead" ); aConsedResources_.insert("consed.autoEditMakeFakeReadFromRead1" ); aConsedResources_.insert("consed.autoEditMakeFakeReadFromRead2" ); aConsedResources_.insert("consed.autoEditMakeFakeReadName" ); aConsedResources_.insert("consed.autoEditMakeFakeReadFastaFilename" ); aConsedResources_.insert("consed.autoEditMergeAssembly" ); aConsedResources_.insert("consed.autoEditSecondaryAceFile" ); aConsedResources_.insert("consed.autoEditFixRunsInConsensus" ); aConsedResources_.insert("consed.showAllTracesJustShowGoodTraces" ); aConsedResources_.insert("consed.addAlignedSequenceQualityOfBases" ); aConsedResources_.insert("consed.makeLightBackgroundInAlignedReadsWindowAndTracesWindow" ); aConsedResources_.insert("consed.putVerticalLineAtCursor" ); aConsedResources_.insert("consed.putHorizontalLineAtCursor" ); aConsedResources_.insert("consed.highlightedReadsFile" ); aConsedResources_.insert("consed.autoReportPrintReadNamesInRegion" ); aConsedResources_.insert("consed.autoReportPrintReadNamesInRegionContig" ); aConsedResources_.insert("consed.autoReportPrintReadNamesInRegionLeftPos" ); aConsedResources_.insert("consed.autoReportPrintReadNamesInRegionRightPos" ); aConsedResources_.insert("consed.autoReportPrintHighlyDiscrepantRegions" ); aConsedResources_.insert("consed.autoReportPrintScaffolds" ); aConsedResources_.insert("consed.numberUnpaddedConsensusAtUserDefined" ); aConsedResources_.insert("consed.autoReportPrintHighQualityDiscrepancies" ); aConsedResources_.insert("consed.autoReportHighQualityDiscrepanciesExcludeCompressionOrG_dropoutTags" ); aConsedResources_.insert("consed.autoReportHighQualityDiscrepanciesExcludeMostPads" ); aConsedResources_.insert("consed.autoReportPrintLowConsensusQualityRegions" ); aConsedResources_.insert("consed.autoReportPrintSingleSubcloneRegions" ); aConsedResources_.insert("consed.autoReportPrintSingleStrandedRegions" ); aConsedResources_.insert("consed.autoReportPrintLinkingForwardReversePairs" ); aConsedResources_.insert("consed.autoReportPrintFilteredInconsistentForwardReversePairs" ); aConsedResources_.insert("consed.autoReportPrintAssemblySummary" ); aConsedResources_.insert("consed.showAllTracesDoNotShowTraceIfTheseTagsPresent" ); aConsedResources_.insert("consed.nameOfFakeJoiningReadsIncludesAceFileName" ); aConsedResources_.insert("consed.whenUserScrollsOffWindowMillisecondsBetweenScrolling" ); aConsedResources_.insert("consed.whenUserScrollsOffWindowBasesToScrollEachTime" ); aConsedResources_.insert("consed.compareContigsUseBandedRatherThanFullSmithWaterman" ); aConsedResources_.insert("consed.compareContigsBandSize" ); aConsedResources_.insert("consed.assemblyViewShowFwdRevPairDepthsInRedIfOnlyThisMany" ); aConsedResources_.insert("consed.assemblyViewShowSequenceMatches" ); aConsedResources_.insert("consed.assemblyViewOKToShowSequenceMatchesBetweenContigs" ); aConsedResources_.insert("consed.assemblyViewOKToShowSequenceMatchesWithinContigs" ); aConsedResources_.insert("consed.assemblyViewOKToShowDirectSequenceMatches" ); aConsedResources_.insert("consed.assemblyViewOKToShowInvertedSequenceMatches" ); aConsedResources_.insert("consed.assemblyViewOnlyShowSequenceMatchesToAParticularRegion" ); aConsedResources_.insert("consed.assemblyViewOnlyShowSequenceMatchesToThisContig" ); aConsedResources_.insert("consed.assemblyViewOnlyShowSequenceMatchesToThisRegionLeft" ); aConsedResources_.insert("consed.assemblyViewOnlyShowSequenceMatchesToThisRegionRight" ); aConsedResources_.insert("consed.assemblyViewOnlyShowSequenceMatchesToEndsOfContigs" ); aConsedResources_.insert("consed.assemblyViewOnlyShowSequenceMatchesToEndsOfContigsThisFar" ); aConsedResources_.insert("consed.defaultReadPrefix" ); aConsedResources_.insert("consed.readPrefixesFile" ); aConsedResources_.insert("consed.maxCharsDisplayedForReadPrefix" ); aConsedResources_.insert("consed.autoFinishDoNotDoPCRIfThisManyAvailableGapSpanningTemplates" ); aConsedResources_.insert("consed.autoFinishDoNotDoUnorientedPCRIfThisManyOrMoreUnorientedPCRReactions" ); aConsedResources_.insert("consed.autoFinishDoNotDoOrientedPCRIfGapSizeLargerThanThis" ); aConsedResources_.insert("consed.autoFinishDoNotDoPCRIfEndIsExtendedByReads" ); aConsedResources_.insert("consed.autoFinishMaxAcceptableErrorsPerMegabase" ); aConsedResources_.insert("consed.autoFinishIfNotEnoughFwdRevPairsUseThisPerCentOfInsertSize" ); aConsedResources_.insert("consed.primersNumberOfBasesToBackUpToStartLooking" ); aConsedResources_.insert("consed.primersMakePCRPrimersThisManyBasesBackFromEndOfHighQualitySegment" ); aConsedResources_.insert("consed.primersOKToChoosePrimersInSingleSubcloneRegion" ); aConsedResources_.insert("consed.primersOKToChoosePrimersWhereHighQualityDiscrepancies" ); aConsedResources_.insert("consed.primersOKToChoosePrimersWhereUnalignedHighQualityRegion" ); aConsedResources_.insert("consed.autoFinishCallReversesToFlankGaps" ); aConsedResources_.insert("consed.autoFinishAllowWholeCloneReads" ); aConsedResources_.insert("consed.autoFinishAllowCustomPrimerSubcloneReads" ); aConsedResources_.insert("consed.autoFinishAllowResequencingReads" ); aConsedResources_.insert("consed.autoFinishAllowResequencingReadsOnlyForRunsAndStops" ); aConsedResources_.insert("consed.autoFinishAllowDeNovoUniversalPrimerSubcloneReads" ); aConsedResources_.insert("consed.autoFinishAllowMinilibraries" ); aConsedResources_.insert("consed.autoFinishAllowPCR" ); aConsedResources_.insert("consed.autoFinishAllowUnorientedPCRReactions" ); aConsedResources_.insert("consed.autoFinishAllowResequencingAUniversalPrimerAutofinishRead" ); aConsedResources_.insert("consed.autoFinishAlwaysCloseGapsUsingMinilibraries" ); aConsedResources_.insert("consed.autoFinishMaximumFinishingReadLength" ); aConsedResources_.insert("consed.autoFinishSuggestMinilibraryIfGapThisManyBasesOrLarger" ); aConsedResources_.insert("consed.autoFinishSuggestSpecialChemistryForRunsAndStops" ); aConsedResources_.insert("consed.autoFinishSuggestThisManyMinilibrariesPerGap" ); aConsedResources_.insert("consed.primersWindowSizeInLooking" ); aConsedResources_.insert("consed.primersAssumeTemplatesAreDoubleStrandedUnlessSpecified" ); aConsedResources_.insert("consed.alignedReadsWindowInitialCharsWide" ); aConsedResources_.insert("consed.alignedReadsWindowInitialCharsHigh" ); aConsedResources_.insert("consed.alignedReadsWindowMaxCharsForReadNames" ); aConsedResources_.insert("consed.alignedReadsWindowAutomaticallyExpandRoomForReadNames" ); aConsedResources_.insert("consed.autoFinishAllowResequencingReadsToExtendContigs" ); aConsedResources_.insert("consed.autoFinishCallHowManyReversesToFlankGaps" ); aConsedResources_.insert("consed.autoFinishCloseGaps" ); aConsedResources_.insert("consed.autoFinishContinueEvenThoughReadInfoDoesNotMakeSense" ); aConsedResources_.insert("consed.autoFinishCostOfResequencingUniversalPrimerSubcloneReaction" ); aConsedResources_.insert("consed.autoFinishCostOfCustomPrimerSubcloneReaction" ); aConsedResources_.insert("consed.autoFinishCostOfCustomPrimerCloneReaction" ); aConsedResources_.insert("consed.autoFinishCostOfDeNovoUniversalPrimerSubcloneReaction" ); aConsedResources_.insert("consed.autoFinishCostOfMinilibrary" ); aConsedResources_.insert("consed.autoFinishCoverSingleSubcloneRegions" ); aConsedResources_.insert("consed.autoFinishCoverLowConsensusQualityRegions" ); aConsedResources_.insert("consed.autoFinishDebugUniversalPrimerReadsFile" ); aConsedResources_.insert("consed.autoFinishDebugCustomPrimerReadsFile" ); aConsedResources_.insert("consed.autoFinishDoNotAllowSubcloneCustomPrimerReadsCloserThanThisManyBases" ); aConsedResources_.insert("consed.autoFinishDoNotAllowWholeCloneCustomPrimerReadsCloserThanThisManyBases" ); aConsedResources_.insert("consed.autoFinishDoNotFinishWhereTheseTagsAre" ); aConsedResources_.insert("consed.autoFinishDoNotExtendContigsWhereTheseTagsAre" ); aConsedResources_.insert("consed.autoFinishDoNotExtendContigsIfTagsAreThisCloseToContigEnd" ); aConsedResources_.insert("consed.dumpContigOrderAndOrientationInfoToThisFile" ); aConsedResources_.insert("consed.autoFinishDumpTemplates" ); aConsedResources_.insert("consed.autoFinishExcludeContigIfOnlyThisManyReadsOrLess" ); aConsedResources_.insert("consed.autoFinishExcludeContigIfDepthOfCoverageGreaterThanThis" ); aConsedResources_.insert("consed.autoFinishExcludeContigIfThisManyBasesOrLess" ); aConsedResources_.insert("consed.autoFinishHowManyTemplatesYouIntendToUseForCustomPrimerSubcloneReactions" ); aConsedResources_.insert("consed.primersMinNumberOfTemplatesForPrimers" ); aConsedResources_.insert("consed.autoFinishMinBaseOverlapBetweenAReadAndHighQualitySegmentOfConsensus" ); aConsedResources_.insert("consed.autoFinishNumberOfVectorBasesAtBeginningOfAUniveralPrimerRead" ); aConsedResources_.insert("consed.autoFinishCDNANotGenomic" ); aConsedResources_.insert("consed.autoFinishConfidenceThatReadWillCoverSingleSubcloneRegion" ); aConsedResources_.insert("consed.autoFinishPrintForwardOrReverseStrandWhenPrintingSubcloneTemplatesForCustomPrimerReads" ); aConsedResources_.insert("consed.autoFinishPrintMinilibrariesSummaryFile" ); aConsedResources_.insert("consed.autoFinishNearGapsSuggestEachMissingReadOfReadPairs" ); aConsedResources_.insert("consed.autoFinishDoNotIgnoreLCQIfThisManyBasesFromEndOfContigForLCQTagger" ); aConsedResources_.insert("consed.checkIfTooManyWalks" ); aConsedResources_.insert("consed.numberOfColumnsBeforeReadNameInAlignedReadsWindow" ); aConsedResources_.insert("consed.compareContigsAlignsThisManyBasesMax" ); aConsedResources_.insert("consed.compressedChromatExtension" ); aConsedResources_.insert("consed.dimLowQualityEndsOfReads" ); aConsedResources_.insert("consed.dimUnalignedEndsOfReads" ); aConsedResources_.insert("consed.fakeReadsSpecifiedByFilenameExtension" ); aConsedResources_.insert("consed.fullPathnameOfAddReads2ConsedScript" ); aConsedResources_.insert("consed.fullPathnameOfFixContigEndScript" ); aConsedResources_.insert("consed.fixContigEndsCleanUpTemporaryFiles" ); aConsedResources_.insert("consed.fixContigEndsMinSmithWatermanScoreToMakeJoin" ); aConsedResources_.insert("consed.fixContigEndsMinNumberOfReadsInContig" ); aConsedResources_.insert("consed.fullPathnameOfCrossMatch" ); aConsedResources_.insert("consed.fullPathnameOfPhred" ); aConsedResources_.insert("consed.fullPathnameOfMiniassemblyScript" ); aConsedResources_.insert("consed.gunzipFullPath" ); aConsedResources_.insert("consed.fullPathnameOfFilter454ReadsScript" ); aConsedResources_.insert("consed.filter454ReadsAgainstThis" ); aConsedResources_.insert("consed.454LinkerSequences" ); aConsedResources_.insert("consed.hideSomeTagTypesAtStartup" ); aConsedResources_.insert("consed.maximumNumberOfTracesShown" ); aConsedResources_.insert("consed.navigateAutomaticTracePopup" ); aConsedResources_.insert("consed.navigateAutomaticAllTracesPopup" ); aConsedResources_.insert("consed.primersMinimumLengthOfAPrimer" ); aConsedResources_.insert("consed.primersMaximumLengthOfAPrimer" ); aConsedResources_.insert("consed.primersMinimumLengthOfAPrimerForPCR" ); aConsedResources_.insert("consed.primersMaximumLengthOfAPrimerForPCR" ); aConsedResources_.insert("consed.primersMaxMeltingTempDifferenceForPCR" ); aConsedResources_.insert("consed.primersMaxPCRPrimerPairsToDisplay" ); aConsedResources_.insert("consed.primersCheckJustSomePCRPrimerPairsRatherThanAll" ); aConsedResources_.insert("consed.primersNumberOfTemplatesToDisplayInFront" ); aConsedResources_.insert("consed.primersMaxLengthOfMononucleotideRepeat" ); aConsedResources_.insert("consed.primersBadLibrariesFile" ); aConsedResources_.insert("consed.primersLibrariesInfoFile" ); aConsedResources_.insert("consed.primersBadTemplatesFile" ); aConsedResources_.insert("consed.primersChooseTemplatesByPositionInsteadOfQuality" ); aConsedResources_.insert("consed.primersWhenChoosingATemplateMinPotentialReadLength" ); aConsedResources_.insert("consed.primersWindowSizeInLookingForPCR" ); aConsedResources_.insert("consed.qualityThresholdForFindingHighQualityDiscrepancies" ); aConsedResources_.insert("consed.qualityThresholdForNavigateByDepthOfCoverage" ); aConsedResources_.insert("consed.navigateByHighDepthOfCoverageNotLow" ); aConsedResources_.insert("consed.MinDepthForNavigateByDepthOfCoverage" ); aConsedResources_.insert("consed.defaultVectorPathnameForRestrictionFragments" ); aConsedResources_.insert("consed.fileOfAdditionalRestrictionEnzymes" ); aConsedResources_.insert("consed.commonRestrictionEnzymes" ); aConsedResources_.insert("consed.defaultSelectedRestrictionEnzymes" ); aConsedResources_.insert("consed.restrictionEnzymesActualFragmentsFile" ); aConsedResources_.insert("consed.restrictionDigestInitialWindowSizeInTextRows" ); aConsedResources_.insert("consed.restrictionDigestDoNoShowAreaOfFragmentsOverThisSize" ); aConsedResources_.insert("consed.showReadsAlphabetically" ); aConsedResources_.insert("consed.showReadsInAlignedReadsWindowOrderedByFile" ); aConsedResources_.insert("consed.showReadsInAlignedReadsWindowOrderedByThisFile" ); aConsedResources_.insert("consed.showReadsAtCursorSortedHow" ); aConsedResources_.insert("consed.showABIBasesInTraceWindow" ); aConsedResources_.insert("consed.tracesWindowInitialPixelHeight" ); aConsedResources_.insert("consed.assemblyViewWindowInitialPixelHeight" ); aConsedResources_.insert("consed.assemblyViewFileOfTemplatesToNotShow" ); aConsedResources_.insert("consed.assemblyViewCrossMatchMinmatch" ); aConsedResources_.insert("consed.assemblyViewCrossMatchMinscore" ); aConsedResources_.insert("consed.assemblyViewFindSequenceMatchesForConsedScript" ); aConsedResources_.insert("consed.assemblyViewCrossmatchMinmatch" ); aConsedResources_.insert("consed.assemblyViewCrossmatchMinscore" ); aConsedResources_.insert("consed.assemblyViewSequenceMatchesMinimumSimilarity" ); aConsedResources_.insert("consed.tracesWindowInitialPixelWidth" ); aConsedResources_.insert("consed.assemblyViewWindowInitialPixelWidth" ); aConsedResources_.insert("consed.automaticallyScaleTraces" ); aConsedResources_.insert("consed.automaticallyScaleTracesSamplePeakHeightFractionOfWindowHeight" ); aConsedResources_.insert("consed.automaticallyScaleTracesSamplePeakPercentile" ); aConsedResources_.insert("consed.verticalTraceMagnification" ); aConsedResources_.insert("consed.userDefinedKeys" ); aConsedResources_.insert("consed.programsForUserDefinedKeys" ); aConsedResources_.insert("consed.argumentsToPassToUserDefinedPrograms" ); aConsedResources_.insert("consed.tagsToApplyWithUserDefinedKeys" ); aConsedResources_.insert("consed.snpGenomeUseInsertionPolymorphisms" ); aConsedResources_.insert("consed.listOfTagTypesToHide" ); aConsedResources_.insert("consed.listOfOptionalWordsToSaveInListOfReadNames" ); aConsedResources_.insert("consed.extendConsensusWithHighQuality" ); aConsedResources_.insert("consed.fastStartup" ); aConsedResources_.insert("consed.fastStartupFile" ); aConsedResources_.insert("consed.alwaysRunProgramToGetChromats" ); aConsedResources_.insert("consed.programToRunToGetChromats" ); aConsedResources_.insert("consed.programToRunToGetChromatsOf454Reads" ); aConsedResources_.insert("consed.createFakeChromatsForSolexaReads" ); aConsedResources_.insert("consed.autoFinishUseLongModelReadRatherThanShort" ); aConsedResources_.insert("consed.askAgainIfWantToQuitConsedIfThisManyReads" ); aConsedResources_.insert("consed.printWindowInstructions" ); aConsedResources_.insert("consed.allowMultipleSearchForStringWindows" ); aConsedResources_.insert("consed.autoPCRAmplifyFalseProductsOKIfLargerThanThis" ); aConsedResources_.insert("consed.autoPCRAmplifyMakePrimerOutOfFirstRegion" ); aConsedResources_.insert("consed.autoPCRAmplifyMaybeRejectPrimerIfThisCloseToDesiredProduct" ); aConsedResources_.insert("consed.addNewReadsRecalculateConsensusQuality" ); aConsedResources_.insert("consed.addNewReadsPutReadIntoItsOwnContig" ); aConsedResources_.insert("consed.addNewReadsCheckThatCrossMatchRunCorrectly" ); aConsedResources_.insert("consed.assemblyViewNumberOfRowsOfTags" ); aConsedResources_.insert("consed.warnUserWhenTryingToEditAllReads" ); aConsedResources_.insert("consed.maybeXKEYSYMDBPath" ); aConsedResources_.insert("consed.maybeXKEYSYMDBPath2" ); aConsedResources_.insert("consed.amountToMoveWithBigLeftAndRightArrows" ); aConsedResources_.insert("consed.navigateByHighlyDiscrepantPositionsMinDiscrepantReads" ); aConsedResources_.insert("consed.navigateByHighlyDiscrepantPositionsMaxDepthOfCoverage" ); aConsedResources_.insert("consed.navigateByHighlyDiscrepantPositionsIgnoreBasesBelowThisQuality" ); aConsedResources_.insert("consed.navigateByHighlyDiscrepantPositionsJustListIndels" ); aConsedResources_.insert("consed.navigateByHighlyDiscrepantPositionsIgnoreOtherReadsStartingAtSameLocation" ); aConsedResources_.insert("consed.navigateByHighlyDiscrepantPositionsIgnoreIfListedBasesInConsensus" ); aConsedResources_.insert("consed.navigateByHighlyDiscrepantPositionsIgnoreIfTheseBasesInConsensus" ); aConsedResources_.insert("consed.phdBallDirectory" ); aConsedResources_.insert("consed.newAceFileFOF" ); aConsedResources_.insert("consed.navigateByHighOrLowDepthCoalesceRegionsIfThisClose" ); aConsedResources_.insert("consed.removeReadsDeleteNotJustPutInOwnContig" ); aConsedResources_.insert("consed.paired454LeftReadExtension" ); aConsedResources_.insert("consed.paired454RightReadExtension" ); aConsedResources_.insert("consed.snpGenome1MSnps" ); aConsedResources_.insert("consed.diffChromosomesExcludeDeletions" ); aConsedResources_.insert("consed.snpGenomeFilterByWeight" ); aConsedResources_.insert("consed.wantReadsUpToThisFarFromSnps" ); aConsedResources_.insert("consed.phaster2PhdBallSaveWhichMate" ); aConsedResources_.insert("consed.phaster2PhdBallSaveInPhasterFormat" ); aConsedResources_.insert("consed.phaster2PhdBallCalculateNewLocationsFile" ); aConsedResources_.insert("consed.phdBall2FastaIgnoreLowQualityReads" ); aConsedResources_.insert("consed.phdBall2FastaLowestAverageQuality" ); aConsedResources_.insert("consed.nextPhredPipelineControlFile" ); aConsedResources_.insert("consed.nextPhredPipelineTiffPerlScript" ); aConsedResources_.insert("consed.nextPhredPipelinePhasterPerlScript" ); aConsedResources_.insert("consed.nextPhredPipelineVersion" ); aConsedResources_.insert("consed.nextPhredPipelineMainDirectory" ); aConsedResources_.insert("consed.maxNumberOfReadsPerPhdBall" ); aConsedResources_.insert("consed.userWantsToSaveToThisAceFile" ); aConsedResources_.insert("consed.autoFinishEmulate9_66Behavior" ); aConsedResources_.insert("consed.primersPCRPrimersGroupedIntoWindowOfThisManyBases" ); aConsedResources_.insert("consed.primersLookForThisManyPCRPrimerPairsPerPairOfGroups" ); aConsedResources_.insert("consed.autoFinishStandardDeviationsFromMeanFromGapToLookForTemplatesForSuggestingEachMissingReadOfReadPairs" ); aConsedResources_.insert("consed.autoFinishCheckThatReadsFromTheSameTemplateAreConsistent" ); aConsedResources_.insert("consed.autoFinishDoNotAllowSubcloneCustomPrimerReadsCloseTogether" ); aConsedResources_.insert("consed.autoFinishDoNotAllowWholeCloneCustomPrimerReadsCloseTogether" ); aConsedResources_.insert("consed.autoFinishMinilibrariesPreferTemplateIfSizeThisManyStdDevsFromMean" ); aConsedResources_.insert("consed.autoFinishMinNumberOfForwardReversePairsInLibraryToCalculateAverageInsertSize" ); aConsedResources_.insert("consed.autoFinishIfEnoughFwdRevPairsUseThisManyStdDevBelowMeanForInsertSize" ); aConsedResources_.insert("consed.autoFinishNewCustomPrimerReadThisFarFromOldCustomPrimerRead" ); aConsedResources_.insert("consed.autoFinishMinNumberOfSingleSubcloneBasesFixedByAnExp" ); aConsedResources_.insert("consed.autoFinishNumberOfBasesBetweenContigsAssumed" ); aConsedResources_.insert("consed.autoFinishPotentialHighQualityPartOfReadStart" ); aConsedResources_.insert("consed.autoFinishPotentialHighQualityPartOfReadEnd" ); aConsedResources_.insert("consed.autoFinishPrintCustomNavigationFileForChosenReads" ); aConsedResources_.insert("consed.autoFinishReversesForFlankingGapsTemplateMustProtrudeFromContigThisMuch" ); aConsedResources_.insert("consed.autoFinishTagOligosWhenDoExperiments" ); aConsedResources_.insert("consed.countPads" ); aConsedResources_.insert("consed.debugging" ); aConsedResources_.insert("consed.debugging2" ); aConsedResources_.insert("consed.debugging3" ); aConsedResources_.insert("consed.debuggingString" ); aConsedResources_.insert("consed.ignoreHighQualityDiscrepanciesThisManyBasesFromEndOfAlignedRegion" ); aConsedResources_.insert("consed.ignoreUnalignedHighQualitySegmentsShorterThanThis" ); aConsedResources_.insert("consed.primersLookThisFarForForwardVectorInsertJunction" ); aConsedResources_.insert("consed.primersDNAConcentrationNanomolar" ); aConsedResources_.insert("consed.primersMaxMatchElsewhereScore" ); aConsedResources_.insert("consed.primersMaxMatchElsewhereScoreForPCR" ); aConsedResources_.insert("consed.primersMaxSelfMatchScore" ); aConsedResources_.insert("consed.primersMaxPrimerDimerScoreForPCR" ); aConsedResources_.insert("consed.primersMinQuality" ); aConsedResources_.insert("consed.primersPrintInfoOnRejectedTemplates" ); aConsedResources_.insert("consed.primersSaltConcentrationMillimolar" ); aConsedResources_.insert("consed.primersScreenForVector" ); aConsedResources_.insert("consed.primersToleranceForDifferentBeginningLocationOfUniversalPrimerReads" ); aConsedResources_.insert("consed.primersTooManyVectorBasesInWalkingRead" ); aConsedResources_.insert("consed.qualityThresholdForLowConsensusQuality" ); aConsedResources_.insert("consed.tagColorPerCentOfBase" ); aConsedResources_.insert("consed.uncompressedChromatDirectory" ); aConsedResources_.insert("consed.454sff2scfDirectory" ); aConsedResources_.insert("consed.whenMakingFakeReadToJoinContigsAddThisManyBasesOnEitherSideOfAlignedRegion" ); aConsedResources_.insert("consed.writeThisAceFormat" ); aConsedResources_.insert("consed.dumpCoreIfBoundsError" ); aConsedResources_.insert("consed.autoFinishMinSmithWatermanScoreOfARun" ); aConsedResources_.insert("consed.autoFinishDoNotComparePCRPrimersMoreThanThisManyTimes" ); aConsedResources_.insert("consed.restrictionDigestMaximumBasesToCompareToVector" ); aConsedResources_.insert("consed.restrictionDigestZoomFactor" ); aConsedResources_.insert("consed.restrictionDigestZoomFactorForNavigate" ); aConsedResources_.insert("consed.restrictionDigestToleranceInPositionUnits" ); aConsedResources_.insert("consed.autoPCRAmplifyTooManySeriousFalseMatches" ); aConsedResources_.insert("consed.assemblyViewZoomFactor" ); aConsedResources_.insert("consed.assemblyViewFilterInconsistentFwdRevPairsIfThisClose" ); aConsedResources_.insert("consed.assemblyViewGridCellWidthInPixels" ); aConsedResources_.insert("consed.assemblyViewCursorSensitivityInPixels" ); aConsedResources_.insert("consed.assemblyViewReadDepthQuality" ); 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aConsedResources_.insert("consed.autoReportMinNumberOfPerfectlyAlignedBasesBeforeDiscrepancy" ); aConsedResources_.insert("consed.autoReportMaxSizeOfDiscrepantRegion" ); aConsedResources_.insert("consed.autoReportSizeOfDiscrepantRegion" ); aConsedResources_.insert("consed.autoReportPrintMinimumQualityHistogram" ); aConsedResources_.insert("consed.autoReportPrintDiscrepantRegions" ); aConsedResources_.insert("consed.autoReportPrintBasesInDiscrepantRegions" ); aConsedResources_.insert("consed.autoReportPrintDiscrepantRegionsButIgnoreReadsContainingThis" ); aConsedResources_.insert("consed.autoReportBackboneReadHasThisStringInIt" ); aConsedResources_.insert("consed.autoReportPrintDiscrepantRegionsButOnlyIfAboveQualityThreshold" ); aConsedResources_.insert("consed.autoReportPrintSpeciesAlignment" ); aConsedResources_.insert("consed.autoReportPrintReadAlignment" ); aConsedResources_.insert("consed.autoReportPrintTheseReads" ); aConsedResources_.insert("consed.autoReportPrintReadPositions" ); aConsedResources_.insert("consed.autoReportPrintChosenReadName" ); aConsedResources_.insert("consed.autoReportNumbersOfCharactersOfChosenReadNameToBePrinted" ); aConsedResources_.insert("consed.autoReportPrefix" ); aConsedResources_.insert("consed.autoReportUseOldCriteriaForDeletingColumnsOfPads" ); aConsedResources_.insert("consed.autoReportDeleteColumnsOfPadsBeforeAdjustingReadQualityValues" ); aConsedResources_.insert("consed.autoReportFlankingBasesMustBeSingleSignal" ); aConsedResources_.insert("consed.autoReportMinimumQualityOfFlankingBases" ); aConsedResources_.insert("consed.autoReportFlankingBasesMustBeInHighQualitySegment" ); aConsedResources_.insert("consed.autoReportSpecies" );