/***************************************************************************** # 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. # #*****************************************************************************/ #include "printChangedAutoFinishParameters.h" #include "consedResources.h" #include "fileDefines.h" #include "consedParameters.h" void printChangedAutoFinishParameters() { fprintf( pAO, "PARAMETERS_CHANGED_FROM_DEFAULTS {\n" ); if ( consedResources::pDefaultResources_->dAutoFinishMinNumberOfErrorsFixedByAnExp_ != consedResources::pCurrentResources_->dAutoFinishMinNumberOfErrorsFixedByAnExp_ ) fprintf( pAO, "consed.autoFinishMinNumberOfErrorsFixedByAnExp: %.3f\n", pCP->dAutoFinishMinNumberOfErrorsFixedByAnExp_ ); if ( consedResources::pDefaultResources_->dAutoFinishRedundancy_ != consedResources::pCurrentResources_->dAutoFinishRedundancy_ ) fprintf( pAO, "consed.autoFinishRedundancy: %.3f\n", pCP->dAutoFinishRedundancy_ ); if ( consedResources::pDefaultResources_->nAutoFinishAverageInsertSize_ != consedResources::pCurrentResources_->nAutoFinishAverageInsertSize_ ) fprintf( pAO, "consed.autoFinishAverageInsertSize: %d\n", pCP->nAutoFinishAverageInsertSize_ ); if ( consedResources::pDefaultResources_->nPrimersMaxInsertSizeOfASubclone_ != consedResources::pCurrentResources_->nPrimersMaxInsertSizeOfASubclone_ ) fprintf( pAO, "consed.primersMaxInsertSizeOfASubclone: %d\n", pCP->nPrimersMaxInsertSizeOfASubclone_ ); if ( consedResources::pDefaultResources_->nPrimersMaxMeltingTemp_ != consedResources::pCurrentResources_->nPrimersMaxMeltingTemp_ ) fprintf( pAO, "consed.primersMaxMeltingTemp: %d\n", pCP->nPrimersMaxMeltingTemp_ ); if ( consedResources::pDefaultResources_->nPrimersMaxMeltingTempForPCR_ != consedResources::pCurrentResources_->nPrimersMaxMeltingTempForPCR_ ) fprintf( pAO, "consed.primersMaxMeltingTempForPCR: %d\n", pCP->nPrimersMaxMeltingTempForPCR_ ); if ( consedResources::pDefaultResources_->bPrimersPickTemplatesForPrimers_ != consedResources::pCurrentResources_->bPrimersPickTemplatesForPrimers_ ) fprintf( pAO, "consed.primersPickTemplatesForPrimers: %s\n", ( pCP->bPrimersPickTemplatesForPrimers_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->soPrimersSubcloneFullPathnameOfFileOfSequencesForScreening_ != consedResources::pCurrentResources_->soPrimersSubcloneFullPathnameOfFileOfSequencesForScreening_ ) fprintf( pAO, "consed.primersSubcloneFullPathnameOfFileOfSequencesForScreening: %s\n", (char*)pCP->soPrimersSubcloneFullPathnameOfFileOfSequencesForScreening_.data() ); if ( consedResources::pDefaultResources_->soPrimersCloneFullPathnameOfFileOfSequencesForScreening_ != consedResources::pCurrentResources_->soPrimersCloneFullPathnameOfFileOfSequencesForScreening_ ) fprintf( pAO, "consed.primersCloneFullPathnameOfFileOfSequencesForScreening: %s\n", (char*)pCP->soPrimersCloneFullPathnameOfFileOfSequencesForScreening_.data() ); if ( consedResources::pDefaultResources_->nPrimersMinMeltingTemp_ != consedResources::pCurrentResources_->nPrimersMinMeltingTemp_ ) fprintf( pAO, "consed.primersMinMeltingTemp: %d\n", pCP->nPrimersMinMeltingTemp_ ); if ( consedResources::pDefaultResources_->nPrimersMinMeltingTempForPCR_ != consedResources::pCurrentResources_->nPrimersMinMeltingTempForPCR_ ) fprintf( pAO, "consed.primersMinMeltingTempForPCR: %d\n", pCP->nPrimersMinMeltingTempForPCR_ ); if ( consedResources::pDefaultResources_->bAutoFinishAllowHighQualityDiscrepanciesInTemplateIfConsistentForwardReversePair_ != consedResources::pCurrentResources_->bAutoFinishAllowHighQualityDiscrepanciesInTemplateIfConsistentForwardReversePair_ ) fprintf( pAO, "consed.autoFinishAllowHighQualityDiscrepanciesInTemplateIfConsistentForwardReversePair: %s\n", ( pCP->bAutoFinishAllowHighQualityDiscrepanciesInTemplateIfConsistentForwardReversePair_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoReportPrintReadNamesInRegion_ != consedResources::pCurrentResources_->bAutoReportPrintReadNamesInRegion_ ) fprintf( pAO, "consed.autoReportPrintReadNamesInRegion: %s\n", ( pCP->bAutoReportPrintReadNamesInRegion_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->soAutoReportPrintReadNamesInRegionContig_ != consedResources::pCurrentResources_->soAutoReportPrintReadNamesInRegionContig_ ) fprintf( pAO, "consed.autoReportPrintReadNamesInRegionContig: %s\n", (char*)pCP->soAutoReportPrintReadNamesInRegionContig_.data() ); if ( consedResources::pDefaultResources_->nAutoReportPrintReadNamesInRegionLeftPos_ != consedResources::pCurrentResources_->nAutoReportPrintReadNamesInRegionLeftPos_ ) fprintf( pAO, "consed.autoReportPrintReadNamesInRegionLeftPos: %d\n", pCP->nAutoReportPrintReadNamesInRegionLeftPos_ ); if ( consedResources::pDefaultResources_->nAutoReportPrintReadNamesInRegionRightPos_ != consedResources::pCurrentResources_->nAutoReportPrintReadNamesInRegionRightPos_ ) fprintf( pAO, "consed.autoReportPrintReadNamesInRegionRightPos: %d\n", pCP->nAutoReportPrintReadNamesInRegionRightPos_ ); if ( consedResources::pDefaultResources_->bAutoReportPrintHighlyDiscrepantRegions_ != consedResources::pCurrentResources_->bAutoReportPrintHighlyDiscrepantRegions_ ) fprintf( pAO, "consed.autoReportPrintHighlyDiscrepantRegions: %s\n", ( pCP->bAutoReportPrintHighlyDiscrepantRegions_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoReportPrintScaffolds_ != consedResources::pCurrentResources_->bAutoReportPrintScaffolds_ ) fprintf( pAO, "consed.autoReportPrintScaffolds: %s\n", ( pCP->bAutoReportPrintScaffolds_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoReportPrintHighQualityDiscrepancies_ != consedResources::pCurrentResources_->bAutoReportPrintHighQualityDiscrepancies_ ) fprintf( pAO, "consed.autoReportPrintHighQualityDiscrepancies: %s\n", ( pCP->bAutoReportPrintHighQualityDiscrepancies_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoReportHighQualityDiscrepanciesExcludeCompressionOrG_dropoutTags_ != consedResources::pCurrentResources_->bAutoReportHighQualityDiscrepanciesExcludeCompressionOrG_dropoutTags_ ) fprintf( pAO, "consed.autoReportHighQualityDiscrepanciesExcludeCompressionOrG_dropoutTags: %s\n", ( pCP->bAutoReportHighQualityDiscrepanciesExcludeCompressionOrG_dropoutTags_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoReportHighQualityDiscrepanciesExcludeMostPads_ != consedResources::pCurrentResources_->bAutoReportHighQualityDiscrepanciesExcludeMostPads_ ) fprintf( pAO, "consed.autoReportHighQualityDiscrepanciesExcludeMostPads: %s\n", ( pCP->bAutoReportHighQualityDiscrepanciesExcludeMostPads_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoReportPrintLowConsensusQualityRegions_ != consedResources::pCurrentResources_->bAutoReportPrintLowConsensusQualityRegions_ ) fprintf( pAO, "consed.autoReportPrintLowConsensusQualityRegions: %s\n", ( pCP->bAutoReportPrintLowConsensusQualityRegions_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoReportPrintSingleSubcloneRegions_ != consedResources::pCurrentResources_->bAutoReportPrintSingleSubcloneRegions_ ) fprintf( pAO, "consed.autoReportPrintSingleSubcloneRegions: %s\n", ( pCP->bAutoReportPrintSingleSubcloneRegions_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoReportPrintSingleStrandedRegions_ != consedResources::pCurrentResources_->bAutoReportPrintSingleStrandedRegions_ ) fprintf( pAO, "consed.autoReportPrintSingleStrandedRegions: %s\n", ( pCP->bAutoReportPrintSingleStrandedRegions_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoReportPrintLinkingForwardReversePairs_ != consedResources::pCurrentResources_->bAutoReportPrintLinkingForwardReversePairs_ ) fprintf( pAO, "consed.autoReportPrintLinkingForwardReversePairs: %s\n", ( pCP->bAutoReportPrintLinkingForwardReversePairs_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoReportPrintFilteredInconsistentForwardReversePairs_ != consedResources::pCurrentResources_->bAutoReportPrintFilteredInconsistentForwardReversePairs_ ) fprintf( pAO, "consed.autoReportPrintFilteredInconsistentForwardReversePairs: %s\n", ( pCP->bAutoReportPrintFilteredInconsistentForwardReversePairs_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoReportPrintAssemblySummary_ != consedResources::pCurrentResources_->bAutoReportPrintAssemblySummary_ ) fprintf( pAO, "consed.autoReportPrintAssemblySummary: %s\n", ( pCP->bAutoReportPrintAssemblySummary_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->nAutoFinishDoNotDoPCRIfThisManyAvailableGapSpanningTemplates_ != consedResources::pCurrentResources_->nAutoFinishDoNotDoPCRIfThisManyAvailableGapSpanningTemplates_ ) fprintf( pAO, "consed.autoFinishDoNotDoPCRIfThisManyAvailableGapSpanningTemplates: %d\n", pCP->nAutoFinishDoNotDoPCRIfThisManyAvailableGapSpanningTemplates_ ); if ( consedResources::pDefaultResources_->nAutoFinishDoNotDoUnorientedPCRIfThisManyOrMoreUnorientedPCRReactions_ != consedResources::pCurrentResources_->nAutoFinishDoNotDoUnorientedPCRIfThisManyOrMoreUnorientedPCRReactions_ ) fprintf( pAO, "consed.autoFinishDoNotDoUnorientedPCRIfThisManyOrMoreUnorientedPCRReactions: %d\n", pCP->nAutoFinishDoNotDoUnorientedPCRIfThisManyOrMoreUnorientedPCRReactions_ ); if ( consedResources::pDefaultResources_->nAutoFinishDoNotDoOrientedPCRIfGapSizeLargerThanThis_ != consedResources::pCurrentResources_->nAutoFinishDoNotDoOrientedPCRIfGapSizeLargerThanThis_ ) fprintf( pAO, "consed.autoFinishDoNotDoOrientedPCRIfGapSizeLargerThanThis: %d\n", pCP->nAutoFinishDoNotDoOrientedPCRIfGapSizeLargerThanThis_ ); if ( consedResources::pDefaultResources_->bAutoFinishDoNotDoPCRIfEndIsExtendedByReads_ != consedResources::pCurrentResources_->bAutoFinishDoNotDoPCRIfEndIsExtendedByReads_ ) fprintf( pAO, "consed.autoFinishDoNotDoPCRIfEndIsExtendedByReads: %s\n", ( pCP->bAutoFinishDoNotDoPCRIfEndIsExtendedByReads_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->nAutoFinishMaxAcceptableErrorsPerMegabase_ != consedResources::pCurrentResources_->nAutoFinishMaxAcceptableErrorsPerMegabase_ ) fprintf( pAO, "consed.autoFinishMaxAcceptableErrorsPerMegabase: %d\n", pCP->nAutoFinishMaxAcceptableErrorsPerMegabase_ ); if ( consedResources::pDefaultResources_->nAutoFinishIfNotEnoughFwdRevPairsUseThisPerCentOfInsertSize_ != consedResources::pCurrentResources_->nAutoFinishIfNotEnoughFwdRevPairsUseThisPerCentOfInsertSize_ ) fprintf( pAO, "consed.autoFinishIfNotEnoughFwdRevPairsUseThisPerCentOfInsertSize: %d\n", pCP->nAutoFinishIfNotEnoughFwdRevPairsUseThisPerCentOfInsertSize_ ); if ( consedResources::pDefaultResources_->nPrimersNumberOfBasesToBackUpToStartLooking_ != consedResources::pCurrentResources_->nPrimersNumberOfBasesToBackUpToStartLooking_ ) fprintf( pAO, "consed.primersNumberOfBasesToBackUpToStartLooking: %d\n", pCP->nPrimersNumberOfBasesToBackUpToStartLooking_ ); if ( consedResources::pDefaultResources_->nPrimersMakePCRPrimersThisManyBasesBackFromEndOfHighQualitySegment_ != consedResources::pCurrentResources_->nPrimersMakePCRPrimersThisManyBasesBackFromEndOfHighQualitySegment_ ) fprintf( pAO, "consed.primersMakePCRPrimersThisManyBasesBackFromEndOfHighQualitySegment: %d\n", pCP->nPrimersMakePCRPrimersThisManyBasesBackFromEndOfHighQualitySegment_ ); if ( consedResources::pDefaultResources_->bPrimersOKToChoosePrimersInSingleSubcloneRegion_ != consedResources::pCurrentResources_->bPrimersOKToChoosePrimersInSingleSubcloneRegion_ ) fprintf( pAO, "consed.primersOKToChoosePrimersInSingleSubcloneRegion: %s\n", ( pCP->bPrimersOKToChoosePrimersInSingleSubcloneRegion_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bPrimersOKToChoosePrimersWhereHighQualityDiscrepancies_ != consedResources::pCurrentResources_->bPrimersOKToChoosePrimersWhereHighQualityDiscrepancies_ ) fprintf( pAO, "consed.primersOKToChoosePrimersWhereHighQualityDiscrepancies: %s\n", ( pCP->bPrimersOKToChoosePrimersWhereHighQualityDiscrepancies_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bPrimersOKToChoosePrimersWhereUnalignedHighQualityRegion_ != consedResources::pCurrentResources_->bPrimersOKToChoosePrimersWhereUnalignedHighQualityRegion_ ) fprintf( pAO, "consed.primersOKToChoosePrimersWhereUnalignedHighQualityRegion: %s\n", ( pCP->bPrimersOKToChoosePrimersWhereUnalignedHighQualityRegion_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoFinishCallReversesToFlankGaps_ != consedResources::pCurrentResources_->bAutoFinishCallReversesToFlankGaps_ ) fprintf( pAO, "consed.autoFinishCallReversesToFlankGaps: %s\n", ( pCP->bAutoFinishCallReversesToFlankGaps_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoFinishAllowWholeCloneReads_ != consedResources::pCurrentResources_->bAutoFinishAllowWholeCloneReads_ ) fprintf( pAO, "consed.autoFinishAllowWholeCloneReads: %s\n", ( pCP->bAutoFinishAllowWholeCloneReads_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoFinishAllowCustomPrimerSubcloneReads_ != consedResources::pCurrentResources_->bAutoFinishAllowCustomPrimerSubcloneReads_ ) fprintf( pAO, "consed.autoFinishAllowCustomPrimerSubcloneReads: %s\n", ( pCP->bAutoFinishAllowCustomPrimerSubcloneReads_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoFinishAllowResequencingReads_ != consedResources::pCurrentResources_->bAutoFinishAllowResequencingReads_ ) fprintf( pAO, "consed.autoFinishAllowResequencingReads: %s\n", ( pCP->bAutoFinishAllowResequencingReads_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoFinishAllowResequencingReadsOnlyForRunsAndStops_ != consedResources::pCurrentResources_->bAutoFinishAllowResequencingReadsOnlyForRunsAndStops_ ) fprintf( pAO, "consed.autoFinishAllowResequencingReadsOnlyForRunsAndStops: %s\n", ( pCP->bAutoFinishAllowResequencingReadsOnlyForRunsAndStops_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoFinishAllowDeNovoUniversalPrimerSubcloneReads_ != consedResources::pCurrentResources_->bAutoFinishAllowDeNovoUniversalPrimerSubcloneReads_ ) fprintf( pAO, "consed.autoFinishAllowDeNovoUniversalPrimerSubcloneReads: %s\n", ( pCP->bAutoFinishAllowDeNovoUniversalPrimerSubcloneReads_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoFinishAllowMinilibraries_ != consedResources::pCurrentResources_->bAutoFinishAllowMinilibraries_ ) fprintf( pAO, "consed.autoFinishAllowMinilibraries: %s\n", ( pCP->bAutoFinishAllowMinilibraries_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoFinishAllowPCR_ != consedResources::pCurrentResources_->bAutoFinishAllowPCR_ ) fprintf( pAO, "consed.autoFinishAllowPCR: %s\n", ( pCP->bAutoFinishAllowPCR_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoFinishAllowUnorientedPCRReactions_ != consedResources::pCurrentResources_->bAutoFinishAllowUnorientedPCRReactions_ ) fprintf( pAO, "consed.autoFinishAllowUnorientedPCRReactions: %s\n", ( pCP->bAutoFinishAllowUnorientedPCRReactions_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoFinishAllowResequencingAUniversalPrimerAutofinishRead_ != consedResources::pCurrentResources_->bAutoFinishAllowResequencingAUniversalPrimerAutofinishRead_ ) fprintf( pAO, "consed.autoFinishAllowResequencingAUniversalPrimerAutofinishRead: %s\n", ( pCP->bAutoFinishAllowResequencingAUniversalPrimerAutofinishRead_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoFinishAlwaysCloseGapsUsingMinilibraries_ != consedResources::pCurrentResources_->bAutoFinishAlwaysCloseGapsUsingMinilibraries_ ) fprintf( pAO, "consed.autoFinishAlwaysCloseGapsUsingMinilibraries: %s\n", ( pCP->bAutoFinishAlwaysCloseGapsUsingMinilibraries_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->nAutoFinishMaximumFinishingReadLength_ != consedResources::pCurrentResources_->nAutoFinishMaximumFinishingReadLength_ ) fprintf( pAO, "consed.autoFinishMaximumFinishingReadLength: %d\n", pCP->nAutoFinishMaximumFinishingReadLength_ ); if ( consedResources::pDefaultResources_->nAutoFinishSuggestMinilibraryIfGapThisManyBasesOrLarger_ != consedResources::pCurrentResources_->nAutoFinishSuggestMinilibraryIfGapThisManyBasesOrLarger_ ) fprintf( pAO, "consed.autoFinishSuggestMinilibraryIfGapThisManyBasesOrLarger: %d\n", pCP->nAutoFinishSuggestMinilibraryIfGapThisManyBasesOrLarger_ ); if ( consedResources::pDefaultResources_->bAutoFinishSuggestSpecialChemistryForRunsAndStops_ != consedResources::pCurrentResources_->bAutoFinishSuggestSpecialChemistryForRunsAndStops_ ) fprintf( pAO, "consed.autoFinishSuggestSpecialChemistryForRunsAndStops: %s\n", ( pCP->bAutoFinishSuggestSpecialChemistryForRunsAndStops_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->nAutoFinishSuggestThisManyMinilibrariesPerGap_ != consedResources::pCurrentResources_->nAutoFinishSuggestThisManyMinilibrariesPerGap_ ) fprintf( pAO, "consed.autoFinishSuggestThisManyMinilibrariesPerGap: %d\n", pCP->nAutoFinishSuggestThisManyMinilibrariesPerGap_ ); if ( consedResources::pDefaultResources_->nPrimersWindowSizeInLooking_ != consedResources::pCurrentResources_->nPrimersWindowSizeInLooking_ ) fprintf( pAO, "consed.primersWindowSizeInLooking: %d\n", pCP->nPrimersWindowSizeInLooking_ ); if ( consedResources::pDefaultResources_->bPrimersAssumeTemplatesAreDoubleStrandedUnlessSpecified_ != consedResources::pCurrentResources_->bPrimersAssumeTemplatesAreDoubleStrandedUnlessSpecified_ ) fprintf( pAO, "consed.primersAssumeTemplatesAreDoubleStrandedUnlessSpecified: %s\n", ( pCP->bPrimersAssumeTemplatesAreDoubleStrandedUnlessSpecified_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoFinishAllowResequencingReadsToExtendContigs_ != consedResources::pCurrentResources_->bAutoFinishAllowResequencingReadsToExtendContigs_ ) fprintf( pAO, "consed.autoFinishAllowResequencingReadsToExtendContigs: %s\n", ( pCP->bAutoFinishAllowResequencingReadsToExtendContigs_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->nAutoFinishCallHowManyReversesToFlankGaps_ != consedResources::pCurrentResources_->nAutoFinishCallHowManyReversesToFlankGaps_ ) fprintf( pAO, "consed.autoFinishCallHowManyReversesToFlankGaps: %d\n", pCP->nAutoFinishCallHowManyReversesToFlankGaps_ ); if ( consedResources::pDefaultResources_->bAutoFinishCloseGaps_ != consedResources::pCurrentResources_->bAutoFinishCloseGaps_ ) fprintf( pAO, "consed.autoFinishCloseGaps: %s\n", ( pCP->bAutoFinishCloseGaps_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoFinishContinueEvenThoughReadInfoDoesNotMakeSense_ != consedResources::pCurrentResources_->bAutoFinishContinueEvenThoughReadInfoDoesNotMakeSense_ ) fprintf( pAO, "consed.autoFinishContinueEvenThoughReadInfoDoesNotMakeSense: %s\n", ( pCP->bAutoFinishContinueEvenThoughReadInfoDoesNotMakeSense_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->dAutoFinishCostOfResequencingUniversalPrimerSubcloneReaction_ != consedResources::pCurrentResources_->dAutoFinishCostOfResequencingUniversalPrimerSubcloneReaction_ ) fprintf( pAO, "consed.autoFinishCostOfResequencingUniversalPrimerSubcloneReaction: %.3f\n", pCP->dAutoFinishCostOfResequencingUniversalPrimerSubcloneReaction_ ); if ( consedResources::pDefaultResources_->dAutoFinishCostOfCustomPrimerSubcloneReaction_ != consedResources::pCurrentResources_->dAutoFinishCostOfCustomPrimerSubcloneReaction_ ) fprintf( pAO, "consed.autoFinishCostOfCustomPrimerSubcloneReaction: %.3f\n", pCP->dAutoFinishCostOfCustomPrimerSubcloneReaction_ ); if ( consedResources::pDefaultResources_->dAutoFinishCostOfCustomPrimerCloneReaction_ != consedResources::pCurrentResources_->dAutoFinishCostOfCustomPrimerCloneReaction_ ) fprintf( pAO, "consed.autoFinishCostOfCustomPrimerCloneReaction: %.3f\n", pCP->dAutoFinishCostOfCustomPrimerCloneReaction_ ); if ( consedResources::pDefaultResources_->dAutoFinishCostOfDeNovoUniversalPrimerSubcloneReaction_ != consedResources::pCurrentResources_->dAutoFinishCostOfDeNovoUniversalPrimerSubcloneReaction_ ) fprintf( pAO, "consed.autoFinishCostOfDeNovoUniversalPrimerSubcloneReaction: %.3f\n", pCP->dAutoFinishCostOfDeNovoUniversalPrimerSubcloneReaction_ ); if ( consedResources::pDefaultResources_->dAutoFinishCostOfMinilibrary_ != consedResources::pCurrentResources_->dAutoFinishCostOfMinilibrary_ ) fprintf( pAO, "consed.autoFinishCostOfMinilibrary: %.3f\n", pCP->dAutoFinishCostOfMinilibrary_ ); if ( consedResources::pDefaultResources_->bAutoFinishCoverSingleSubcloneRegions_ != consedResources::pCurrentResources_->bAutoFinishCoverSingleSubcloneRegions_ ) fprintf( pAO, "consed.autoFinishCoverSingleSubcloneRegions: %s\n", ( pCP->bAutoFinishCoverSingleSubcloneRegions_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoFinishCoverLowConsensusQualityRegions_ != consedResources::pCurrentResources_->bAutoFinishCoverLowConsensusQualityRegions_ ) fprintf( pAO, "consed.autoFinishCoverLowConsensusQualityRegions: %s\n", ( pCP->bAutoFinishCoverLowConsensusQualityRegions_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->filAutoFinishDebugUniversalPrimerReadsFile_ != consedResources::pCurrentResources_->filAutoFinishDebugUniversalPrimerReadsFile_ ) fprintf( pAO, "consed.autoFinishDebugUniversalPrimerReadsFile: %s\n", (char*)pCP->filAutoFinishDebugUniversalPrimerReadsFile_.data() ); if ( consedResources::pDefaultResources_->filAutoFinishDebugCustomPrimerReadsFile_ != consedResources::pCurrentResources_->filAutoFinishDebugCustomPrimerReadsFile_ ) fprintf( pAO, "consed.autoFinishDebugCustomPrimerReadsFile: %s\n", (char*)pCP->filAutoFinishDebugCustomPrimerReadsFile_.data() ); if ( consedResources::pDefaultResources_->nAutoFinishDoNotAllowSubcloneCustomPrimerReadsCloserThanThisManyBases_ != consedResources::pCurrentResources_->nAutoFinishDoNotAllowSubcloneCustomPrimerReadsCloserThanThisManyBases_ ) fprintf( pAO, "consed.autoFinishDoNotAllowSubcloneCustomPrimerReadsCloserThanThisManyBases: %d\n", pCP->nAutoFinishDoNotAllowSubcloneCustomPrimerReadsCloserThanThisManyBases_ ); if ( consedResources::pDefaultResources_->nAutoFinishDoNotAllowWholeCloneCustomPrimerReadsCloserThanThisManyBases_ != consedResources::pCurrentResources_->nAutoFinishDoNotAllowWholeCloneCustomPrimerReadsCloserThanThisManyBases_ ) fprintf( pAO, "consed.autoFinishDoNotAllowWholeCloneCustomPrimerReadsCloserThanThisManyBases: %d\n", pCP->nAutoFinishDoNotAllowWholeCloneCustomPrimerReadsCloserThanThisManyBases_ ); if ( consedResources::pDefaultResources_->soAutoFinishDoNotFinishWhereTheseTagsAre_ != consedResources::pCurrentResources_->soAutoFinishDoNotFinishWhereTheseTagsAre_ ) fprintf( pAO, "consed.autoFinishDoNotFinishWhereTheseTagsAre: %s\n", (char*)pCP->soAutoFinishDoNotFinishWhereTheseTagsAre_.data() ); if ( consedResources::pDefaultResources_->soAutoFinishDoNotExtendContigsWhereTheseTagsAre_ != consedResources::pCurrentResources_->soAutoFinishDoNotExtendContigsWhereTheseTagsAre_ ) fprintf( pAO, "consed.autoFinishDoNotExtendContigsWhereTheseTagsAre: %s\n", (char*)pCP->soAutoFinishDoNotExtendContigsWhereTheseTagsAre_.data() ); if ( consedResources::pDefaultResources_->nAutoFinishDoNotExtendContigsIfTagsAreThisCloseToContigEnd_ != consedResources::pCurrentResources_->nAutoFinishDoNotExtendContigsIfTagsAreThisCloseToContigEnd_ ) fprintf( pAO, "consed.autoFinishDoNotExtendContigsIfTagsAreThisCloseToContigEnd: %d\n", pCP->nAutoFinishDoNotExtendContigsIfTagsAreThisCloseToContigEnd_ ); if ( consedResources::pDefaultResources_->bAutoFinishDumpTemplates_ != consedResources::pCurrentResources_->bAutoFinishDumpTemplates_ ) fprintf( pAO, "consed.autoFinishDumpTemplates: %s\n", ( pCP->bAutoFinishDumpTemplates_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->nAutoFinishExcludeContigIfOnlyThisManyReadsOrLess_ != consedResources::pCurrentResources_->nAutoFinishExcludeContigIfOnlyThisManyReadsOrLess_ ) fprintf( pAO, "consed.autoFinishExcludeContigIfOnlyThisManyReadsOrLess: %d\n", pCP->nAutoFinishExcludeContigIfOnlyThisManyReadsOrLess_ ); if ( consedResources::pDefaultResources_->dAutoFinishExcludeContigIfDepthOfCoverageGreaterThanThis_ != consedResources::pCurrentResources_->dAutoFinishExcludeContigIfDepthOfCoverageGreaterThanThis_ ) fprintf( pAO, "consed.autoFinishExcludeContigIfDepthOfCoverageGreaterThanThis: %.3f\n", pCP->dAutoFinishExcludeContigIfDepthOfCoverageGreaterThanThis_ ); if ( consedResources::pDefaultResources_->nAutoFinishExcludeContigIfThisManyBasesOrLess_ != consedResources::pCurrentResources_->nAutoFinishExcludeContigIfThisManyBasesOrLess_ ) fprintf( pAO, "consed.autoFinishExcludeContigIfThisManyBasesOrLess: %d\n", pCP->nAutoFinishExcludeContigIfThisManyBasesOrLess_ ); if ( consedResources::pDefaultResources_->nAutoFinishHowManyTemplatesYouIntendToUseForCustomPrimerSubcloneReactions_ != consedResources::pCurrentResources_->nAutoFinishHowManyTemplatesYouIntendToUseForCustomPrimerSubcloneReactions_ ) fprintf( pAO, "consed.autoFinishHowManyTemplatesYouIntendToUseForCustomPrimerSubcloneReactions: %d\n", pCP->nAutoFinishHowManyTemplatesYouIntendToUseForCustomPrimerSubcloneReactions_ ); if ( consedResources::pDefaultResources_->nPrimersMinNumberOfTemplatesForPrimers_ != consedResources::pCurrentResources_->nPrimersMinNumberOfTemplatesForPrimers_ ) fprintf( pAO, "consed.primersMinNumberOfTemplatesForPrimers: %d\n", pCP->nPrimersMinNumberOfTemplatesForPrimers_ ); if ( consedResources::pDefaultResources_->nAutoFinishMinBaseOverlapBetweenAReadAndHighQualitySegmentOfConsensus_ != consedResources::pCurrentResources_->nAutoFinishMinBaseOverlapBetweenAReadAndHighQualitySegmentOfConsensus_ ) fprintf( pAO, "consed.autoFinishMinBaseOverlapBetweenAReadAndHighQualitySegmentOfConsensus: %d\n", pCP->nAutoFinishMinBaseOverlapBetweenAReadAndHighQualitySegmentOfConsensus_ ); if ( consedResources::pDefaultResources_->nAutoFinishNumberOfVectorBasesAtBeginningOfAUniveralPrimerRead_ != consedResources::pCurrentResources_->nAutoFinishNumberOfVectorBasesAtBeginningOfAUniveralPrimerRead_ ) fprintf( pAO, "consed.autoFinishNumberOfVectorBasesAtBeginningOfAUniveralPrimerRead: %d\n", pCP->nAutoFinishNumberOfVectorBasesAtBeginningOfAUniveralPrimerRead_ ); if ( consedResources::pDefaultResources_->bAutoFinishCDNANotGenomic_ != consedResources::pCurrentResources_->bAutoFinishCDNANotGenomic_ ) fprintf( pAO, "consed.autoFinishCDNANotGenomic: %s\n", ( pCP->bAutoFinishCDNANotGenomic_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->nAutoFinishConfidenceThatReadWillCoverSingleSubcloneRegion_ != consedResources::pCurrentResources_->nAutoFinishConfidenceThatReadWillCoverSingleSubcloneRegion_ ) fprintf( pAO, "consed.autoFinishConfidenceThatReadWillCoverSingleSubcloneRegion: %d\n", pCP->nAutoFinishConfidenceThatReadWillCoverSingleSubcloneRegion_ ); if ( consedResources::pDefaultResources_->bAutoFinishPrintForwardOrReverseStrandWhenPrintingSubcloneTemplatesForCustomPrimerReads_ != consedResources::pCurrentResources_->bAutoFinishPrintForwardOrReverseStrandWhenPrintingSubcloneTemplatesForCustomPrimerReads_ ) fprintf( pAO, "consed.autoFinishPrintForwardOrReverseStrandWhenPrintingSubcloneTemplatesForCustomPrimerReads: %s\n", ( pCP->bAutoFinishPrintForwardOrReverseStrandWhenPrintingSubcloneTemplatesForCustomPrimerReads_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoFinishPrintMinilibrariesSummaryFile_ != consedResources::pCurrentResources_->bAutoFinishPrintMinilibrariesSummaryFile_ ) fprintf( pAO, "consed.autoFinishPrintMinilibrariesSummaryFile: %s\n", ( pCP->bAutoFinishPrintMinilibrariesSummaryFile_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoFinishNearGapsSuggestEachMissingReadOfReadPairs_ != consedResources::pCurrentResources_->bAutoFinishNearGapsSuggestEachMissingReadOfReadPairs_ ) fprintf( pAO, "consed.autoFinishNearGapsSuggestEachMissingReadOfReadPairs: %s\n", ( pCP->bAutoFinishNearGapsSuggestEachMissingReadOfReadPairs_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->nAutoFinishDoNotIgnoreLCQIfThisManyBasesFromEndOfContigForLCQTagger_ != consedResources::pCurrentResources_->nAutoFinishDoNotIgnoreLCQIfThisManyBasesFromEndOfContigForLCQTagger_ ) fprintf( pAO, "consed.autoFinishDoNotIgnoreLCQIfThisManyBasesFromEndOfContigForLCQTagger: %d\n", pCP->nAutoFinishDoNotIgnoreLCQIfThisManyBasesFromEndOfContigForLCQTagger_ ); if ( consedResources::pDefaultResources_->nPrimersMinimumLengthOfAPrimer_ != consedResources::pCurrentResources_->nPrimersMinimumLengthOfAPrimer_ ) fprintf( pAO, "consed.primersMinimumLengthOfAPrimer: %d\n", pCP->nPrimersMinimumLengthOfAPrimer_ ); if ( consedResources::pDefaultResources_->nPrimersMaximumLengthOfAPrimer_ != consedResources::pCurrentResources_->nPrimersMaximumLengthOfAPrimer_ ) fprintf( pAO, "consed.primersMaximumLengthOfAPrimer: %d\n", pCP->nPrimersMaximumLengthOfAPrimer_ ); if ( consedResources::pDefaultResources_->nPrimersMinimumLengthOfAPrimerForPCR_ != consedResources::pCurrentResources_->nPrimersMinimumLengthOfAPrimerForPCR_ ) fprintf( pAO, "consed.primersMinimumLengthOfAPrimerForPCR: %d\n", pCP->nPrimersMinimumLengthOfAPrimerForPCR_ ); if ( consedResources::pDefaultResources_->nPrimersMaximumLengthOfAPrimerForPCR_ != consedResources::pCurrentResources_->nPrimersMaximumLengthOfAPrimerForPCR_ ) fprintf( pAO, "consed.primersMaximumLengthOfAPrimerForPCR: %d\n", pCP->nPrimersMaximumLengthOfAPrimerForPCR_ ); if ( consedResources::pDefaultResources_->dPrimersMaxMeltingTempDifferenceForPCR_ != consedResources::pCurrentResources_->dPrimersMaxMeltingTempDifferenceForPCR_ ) fprintf( pAO, "consed.primersMaxMeltingTempDifferenceForPCR: %.3f\n", pCP->dPrimersMaxMeltingTempDifferenceForPCR_ ); if ( consedResources::pDefaultResources_->nPrimersMaxPCRPrimerPairsToDisplay_ != consedResources::pCurrentResources_->nPrimersMaxPCRPrimerPairsToDisplay_ ) fprintf( pAO, "consed.primersMaxPCRPrimerPairsToDisplay: %d\n", pCP->nPrimersMaxPCRPrimerPairsToDisplay_ ); if ( consedResources::pDefaultResources_->bPrimersCheckJustSomePCRPrimerPairsRatherThanAll_ != consedResources::pCurrentResources_->bPrimersCheckJustSomePCRPrimerPairsRatherThanAll_ ) fprintf( pAO, "consed.primersCheckJustSomePCRPrimerPairsRatherThanAll: %s\n", ( pCP->bPrimersCheckJustSomePCRPrimerPairsRatherThanAll_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->nPrimersNumberOfTemplatesToDisplayInFront_ != consedResources::pCurrentResources_->nPrimersNumberOfTemplatesToDisplayInFront_ ) fprintf( pAO, "consed.primersNumberOfTemplatesToDisplayInFront: %d\n", pCP->nPrimersNumberOfTemplatesToDisplayInFront_ ); if ( consedResources::pDefaultResources_->nPrimersMaxLengthOfMononucleotideRepeat_ != consedResources::pCurrentResources_->nPrimersMaxLengthOfMononucleotideRepeat_ ) fprintf( pAO, "consed.primersMaxLengthOfMononucleotideRepeat: %d\n", pCP->nPrimersMaxLengthOfMononucleotideRepeat_ ); if ( consedResources::pDefaultResources_->filPrimersBadLibrariesFile_ != consedResources::pCurrentResources_->filPrimersBadLibrariesFile_ ) fprintf( pAO, "consed.primersBadLibrariesFile: %s\n", (char*)pCP->filPrimersBadLibrariesFile_.data() ); if ( consedResources::pDefaultResources_->filPrimersLibrariesInfoFile_ != consedResources::pCurrentResources_->filPrimersLibrariesInfoFile_ ) fprintf( pAO, "consed.primersLibrariesInfoFile: %s\n", (char*)pCP->filPrimersLibrariesInfoFile_.data() ); if ( consedResources::pDefaultResources_->filPrimersBadTemplatesFile_ != consedResources::pCurrentResources_->filPrimersBadTemplatesFile_ ) fprintf( pAO, "consed.primersBadTemplatesFile: %s\n", (char*)pCP->filPrimersBadTemplatesFile_.data() ); if ( consedResources::pDefaultResources_->bPrimersChooseTemplatesByPositionInsteadOfQuality_ != consedResources::pCurrentResources_->bPrimersChooseTemplatesByPositionInsteadOfQuality_ ) fprintf( pAO, "consed.primersChooseTemplatesByPositionInsteadOfQuality: %s\n", ( pCP->bPrimersChooseTemplatesByPositionInsteadOfQuality_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->nPrimersWhenChoosingATemplateMinPotentialReadLength_ != consedResources::pCurrentResources_->nPrimersWhenChoosingATemplateMinPotentialReadLength_ ) fprintf( pAO, "consed.primersWhenChoosingATemplateMinPotentialReadLength: %d\n", pCP->nPrimersWhenChoosingATemplateMinPotentialReadLength_ ); if ( consedResources::pDefaultResources_->nPrimersWindowSizeInLookingForPCR_ != consedResources::pCurrentResources_->nPrimersWindowSizeInLookingForPCR_ ) fprintf( pAO, "consed.primersWindowSizeInLookingForPCR: %d\n", pCP->nPrimersWindowSizeInLookingForPCR_ ); if ( consedResources::pDefaultResources_->nQualityThresholdForFindingHighQualityDiscrepancies_ != consedResources::pCurrentResources_->nQualityThresholdForFindingHighQualityDiscrepancies_ ) fprintf( pAO, "consed.qualityThresholdForFindingHighQualityDiscrepancies: %d\n", pCP->nQualityThresholdForFindingHighQualityDiscrepancies_ ); if ( consedResources::pDefaultResources_->bAutoFinishUseLongModelReadRatherThanShort_ != consedResources::pCurrentResources_->bAutoFinishUseLongModelReadRatherThanShort_ ) fprintf( pAO, "consed.autoFinishUseLongModelReadRatherThanShort: %s\n", ( pCP->bAutoFinishUseLongModelReadRatherThanShort_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->nAutoPCRAmplifyFalseProductsOKIfLargerThanThis_ != consedResources::pCurrentResources_->nAutoPCRAmplifyFalseProductsOKIfLargerThanThis_ ) fprintf( pAO, "consed.autoPCRAmplifyFalseProductsOKIfLargerThanThis: %d\n", pCP->nAutoPCRAmplifyFalseProductsOKIfLargerThanThis_ ); if ( consedResources::pDefaultResources_->bAutoPCRAmplifyMakePrimerOutOfFirstRegion_ != consedResources::pCurrentResources_->bAutoPCRAmplifyMakePrimerOutOfFirstRegion_ ) fprintf( pAO, "consed.autoPCRAmplifyMakePrimerOutOfFirstRegion: %s\n", ( pCP->bAutoPCRAmplifyMakePrimerOutOfFirstRegion_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->nAutoPCRAmplifyMaybeRejectPrimerIfThisCloseToDesiredProduct_ != consedResources::pCurrentResources_->nAutoPCRAmplifyMaybeRejectPrimerIfThisCloseToDesiredProduct_ ) fprintf( pAO, "consed.autoPCRAmplifyMaybeRejectPrimerIfThisCloseToDesiredProduct: %d\n", pCP->nAutoPCRAmplifyMaybeRejectPrimerIfThisCloseToDesiredProduct_ ); if ( consedResources::pDefaultResources_->bAutoFinishEmulate9_66Behavior_ != consedResources::pCurrentResources_->bAutoFinishEmulate9_66Behavior_ ) fprintf( pAO, "consed.autoFinishEmulate9_66Behavior: %s\n", ( pCP->bAutoFinishEmulate9_66Behavior_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->nPrimersPCRPrimersGroupedIntoWindowOfThisManyBases_ != consedResources::pCurrentResources_->nPrimersPCRPrimersGroupedIntoWindowOfThisManyBases_ ) fprintf( pAO, "consed.primersPCRPrimersGroupedIntoWindowOfThisManyBases: %d\n", pCP->nPrimersPCRPrimersGroupedIntoWindowOfThisManyBases_ ); if ( consedResources::pDefaultResources_->nPrimersLookForThisManyPCRPrimerPairsPerPairOfGroups_ != consedResources::pCurrentResources_->nPrimersLookForThisManyPCRPrimerPairsPerPairOfGroups_ ) fprintf( pAO, "consed.primersLookForThisManyPCRPrimerPairsPerPairOfGroups: %d\n", pCP->nPrimersLookForThisManyPCRPrimerPairsPerPairOfGroups_ ); if ( consedResources::pDefaultResources_->dAutoFinishStandardDeviationsFromMeanFromGapToLookForTemplatesForSuggestingEachMissingReadOfReadPairs_ != consedResources::pCurrentResources_->dAutoFinishStandardDeviationsFromMeanFromGapToLookForTemplatesForSuggestingEachMissingReadOfReadPairs_ ) fprintf( pAO, "consed.autoFinishStandardDeviationsFromMeanFromGapToLookForTemplatesForSuggestingEachMissingReadOfReadPairs: %.3f\n", pCP->dAutoFinishStandardDeviationsFromMeanFromGapToLookForTemplatesForSuggestingEachMissingReadOfReadPairs_ ); if ( consedResources::pDefaultResources_->bAutoFinishCheckThatReadsFromTheSameTemplateAreConsistent_ != consedResources::pCurrentResources_->bAutoFinishCheckThatReadsFromTheSameTemplateAreConsistent_ ) fprintf( pAO, "consed.autoFinishCheckThatReadsFromTheSameTemplateAreConsistent: %s\n", ( pCP->bAutoFinishCheckThatReadsFromTheSameTemplateAreConsistent_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoFinishDoNotAllowSubcloneCustomPrimerReadsCloseTogether_ != consedResources::pCurrentResources_->bAutoFinishDoNotAllowSubcloneCustomPrimerReadsCloseTogether_ ) fprintf( pAO, "consed.autoFinishDoNotAllowSubcloneCustomPrimerReadsCloseTogether: %s\n", ( pCP->bAutoFinishDoNotAllowSubcloneCustomPrimerReadsCloseTogether_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoFinishDoNotAllowWholeCloneCustomPrimerReadsCloseTogether_ != consedResources::pCurrentResources_->bAutoFinishDoNotAllowWholeCloneCustomPrimerReadsCloseTogether_ ) fprintf( pAO, "consed.autoFinishDoNotAllowWholeCloneCustomPrimerReadsCloseTogether: %s\n", ( pCP->bAutoFinishDoNotAllowWholeCloneCustomPrimerReadsCloseTogether_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->dAutoFinishMinilibrariesPreferTemplateIfSizeThisManyStdDevsFromMean_ != consedResources::pCurrentResources_->dAutoFinishMinilibrariesPreferTemplateIfSizeThisManyStdDevsFromMean_ ) fprintf( pAO, "consed.autoFinishMinilibrariesPreferTemplateIfSizeThisManyStdDevsFromMean: %.3f\n", pCP->dAutoFinishMinilibrariesPreferTemplateIfSizeThisManyStdDevsFromMean_ ); if ( consedResources::pDefaultResources_->nAutoFinishMinNumberOfForwardReversePairsInLibraryToCalculateAverageInsertSize_ != consedResources::pCurrentResources_->nAutoFinishMinNumberOfForwardReversePairsInLibraryToCalculateAverageInsertSize_ ) fprintf( pAO, "consed.autoFinishMinNumberOfForwardReversePairsInLibraryToCalculateAverageInsertSize: %d\n", pCP->nAutoFinishMinNumberOfForwardReversePairsInLibraryToCalculateAverageInsertSize_ ); if ( consedResources::pDefaultResources_->dAutoFinishIfEnoughFwdRevPairsUseThisManyStdDevBelowMeanForInsertSize_ != consedResources::pCurrentResources_->dAutoFinishIfEnoughFwdRevPairsUseThisManyStdDevBelowMeanForInsertSize_ ) fprintf( pAO, "consed.autoFinishIfEnoughFwdRevPairsUseThisManyStdDevBelowMeanForInsertSize: %.3f\n", pCP->dAutoFinishIfEnoughFwdRevPairsUseThisManyStdDevBelowMeanForInsertSize_ ); if ( consedResources::pDefaultResources_->nAutoFinishNewCustomPrimerReadThisFarFromOldCustomPrimerRead_ != consedResources::pCurrentResources_->nAutoFinishNewCustomPrimerReadThisFarFromOldCustomPrimerRead_ ) fprintf( pAO, "consed.autoFinishNewCustomPrimerReadThisFarFromOldCustomPrimerRead: %d\n", pCP->nAutoFinishNewCustomPrimerReadThisFarFromOldCustomPrimerRead_ ); if ( consedResources::pDefaultResources_->nAutoFinishMinNumberOfSingleSubcloneBasesFixedByAnExp_ != consedResources::pCurrentResources_->nAutoFinishMinNumberOfSingleSubcloneBasesFixedByAnExp_ ) fprintf( pAO, "consed.autoFinishMinNumberOfSingleSubcloneBasesFixedByAnExp: %d\n", pCP->nAutoFinishMinNumberOfSingleSubcloneBasesFixedByAnExp_ ); if ( consedResources::pDefaultResources_->nAutoFinishNumberOfBasesBetweenContigsAssumed_ != consedResources::pCurrentResources_->nAutoFinishNumberOfBasesBetweenContigsAssumed_ ) fprintf( pAO, "consed.autoFinishNumberOfBasesBetweenContigsAssumed: %d\n", pCP->nAutoFinishNumberOfBasesBetweenContigsAssumed_ ); if ( consedResources::pDefaultResources_->nAutoFinishPotentialHighQualityPartOfReadStart_ != consedResources::pCurrentResources_->nAutoFinishPotentialHighQualityPartOfReadStart_ ) fprintf( pAO, "consed.autoFinishPotentialHighQualityPartOfReadStart: %d\n", pCP->nAutoFinishPotentialHighQualityPartOfReadStart_ ); if ( consedResources::pDefaultResources_->nAutoFinishPotentialHighQualityPartOfReadEnd_ != consedResources::pCurrentResources_->nAutoFinishPotentialHighQualityPartOfReadEnd_ ) fprintf( pAO, "consed.autoFinishPotentialHighQualityPartOfReadEnd: %d\n", pCP->nAutoFinishPotentialHighQualityPartOfReadEnd_ ); if ( consedResources::pDefaultResources_->bAutoFinishPrintCustomNavigationFileForChosenReads_ != consedResources::pCurrentResources_->bAutoFinishPrintCustomNavigationFileForChosenReads_ ) fprintf( pAO, "consed.autoFinishPrintCustomNavigationFileForChosenReads: %s\n", ( pCP->bAutoFinishPrintCustomNavigationFileForChosenReads_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->nAutoFinishReversesForFlankingGapsTemplateMustProtrudeFromContigThisMuch_ != consedResources::pCurrentResources_->nAutoFinishReversesForFlankingGapsTemplateMustProtrudeFromContigThisMuch_ ) fprintf( pAO, "consed.autoFinishReversesForFlankingGapsTemplateMustProtrudeFromContigThisMuch: %d\n", pCP->nAutoFinishReversesForFlankingGapsTemplateMustProtrudeFromContigThisMuch_ ); if ( consedResources::pDefaultResources_->bAutoFinishTagOligosWhenDoExperiments_ != consedResources::pCurrentResources_->bAutoFinishTagOligosWhenDoExperiments_ ) fprintf( pAO, "consed.autoFinishTagOligosWhenDoExperiments: %s\n", ( pCP->bAutoFinishTagOligosWhenDoExperiments_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->nPrimersLookThisFarForForwardVectorInsertJunction_ != consedResources::pCurrentResources_->nPrimersLookThisFarForForwardVectorInsertJunction_ ) fprintf( pAO, "consed.primersLookThisFarForForwardVectorInsertJunction: %d\n", pCP->nPrimersLookThisFarForForwardVectorInsertJunction_ ); if ( consedResources::pDefaultResources_->dPrimersDNAConcentrationNanomolar_ != consedResources::pCurrentResources_->dPrimersDNAConcentrationNanomolar_ ) fprintf( pAO, "consed.primersDNAConcentrationNanomolar: %.3f\n", pCP->dPrimersDNAConcentrationNanomolar_ ); if ( consedResources::pDefaultResources_->nPrimersMaxMatchElsewhereScore_ != consedResources::pCurrentResources_->nPrimersMaxMatchElsewhereScore_ ) fprintf( pAO, "consed.primersMaxMatchElsewhereScore: %d\n", pCP->nPrimersMaxMatchElsewhereScore_ ); if ( consedResources::pDefaultResources_->nPrimersMaxMatchElsewhereScoreForPCR_ != consedResources::pCurrentResources_->nPrimersMaxMatchElsewhereScoreForPCR_ ) fprintf( pAO, "consed.primersMaxMatchElsewhereScoreForPCR: %d\n", pCP->nPrimersMaxMatchElsewhereScoreForPCR_ ); if ( consedResources::pDefaultResources_->nPrimersMaxSelfMatchScore_ != consedResources::pCurrentResources_->nPrimersMaxSelfMatchScore_ ) fprintf( pAO, "consed.primersMaxSelfMatchScore: %d\n", pCP->nPrimersMaxSelfMatchScore_ ); if ( consedResources::pDefaultResources_->nPrimersMaxPrimerDimerScoreForPCR_ != consedResources::pCurrentResources_->nPrimersMaxPrimerDimerScoreForPCR_ ) fprintf( pAO, "consed.primersMaxPrimerDimerScoreForPCR: %d\n", pCP->nPrimersMaxPrimerDimerScoreForPCR_ ); if ( consedResources::pDefaultResources_->nPrimersMinQuality_ != consedResources::pCurrentResources_->nPrimersMinQuality_ ) fprintf( pAO, "consed.primersMinQuality: %d\n", pCP->nPrimersMinQuality_ ); if ( consedResources::pDefaultResources_->bPrimersPrintInfoOnRejectedTemplates_ != consedResources::pCurrentResources_->bPrimersPrintInfoOnRejectedTemplates_ ) fprintf( pAO, "consed.primersPrintInfoOnRejectedTemplates: %s\n", ( pCP->bPrimersPrintInfoOnRejectedTemplates_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->dPrimersSaltConcentrationMillimolar_ != consedResources::pCurrentResources_->dPrimersSaltConcentrationMillimolar_ ) fprintf( pAO, "consed.primersSaltConcentrationMillimolar: %.3f\n", pCP->dPrimersSaltConcentrationMillimolar_ ); if ( consedResources::pDefaultResources_->bPrimersScreenForVector_ != consedResources::pCurrentResources_->bPrimersScreenForVector_ ) fprintf( pAO, "consed.primersScreenForVector: %s\n", ( pCP->bPrimersScreenForVector_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->nPrimersToleranceForDifferentBeginningLocationOfUniversalPrimerReads_ != consedResources::pCurrentResources_->nPrimersToleranceForDifferentBeginningLocationOfUniversalPrimerReads_ ) fprintf( pAO, "consed.primersToleranceForDifferentBeginningLocationOfUniversalPrimerReads: %d\n", pCP->nPrimersToleranceForDifferentBeginningLocationOfUniversalPrimerReads_ ); if ( consedResources::pDefaultResources_->nPrimersTooManyVectorBasesInWalkingRead_ != consedResources::pCurrentResources_->nPrimersTooManyVectorBasesInWalkingRead_ ) fprintf( pAO, "consed.primersTooManyVectorBasesInWalkingRead: %d\n", pCP->nPrimersTooManyVectorBasesInWalkingRead_ ); if ( consedResources::pDefaultResources_->nAutoFinishMinSmithWatermanScoreOfARun_ != consedResources::pCurrentResources_->nAutoFinishMinSmithWatermanScoreOfARun_ ) fprintf( pAO, "consed.autoFinishMinSmithWatermanScoreOfARun: %d\n", pCP->nAutoFinishMinSmithWatermanScoreOfARun_ ); if ( consedResources::pDefaultResources_->dAutoFinishDoNotComparePCRPrimersMoreThanThisManyTimes_ != consedResources::pCurrentResources_->dAutoFinishDoNotComparePCRPrimersMoreThanThisManyTimes_ ) fprintf( pAO, "consed.autoFinishDoNotComparePCRPrimersMoreThanThisManyTimes: %.3f\n", pCP->dAutoFinishDoNotComparePCRPrimersMoreThanThisManyTimes_ ); if ( consedResources::pDefaultResources_->nAutoPCRAmplifyTooManySeriousFalseMatches_ != consedResources::pCurrentResources_->nAutoPCRAmplifyTooManySeriousFalseMatches_ ) fprintf( pAO, "consed.autoPCRAmplifyTooManySeriousFalseMatches: %d\n", pCP->nAutoPCRAmplifyTooManySeriousFalseMatches_ ); if ( consedResources::pDefaultResources_->nAutoReportAllNeededSpeciesCode_ != consedResources::pCurrentResources_->nAutoReportAllNeededSpeciesCode_ ) fprintf( pAO, "consed.autoReportAllNeededSpeciesCode: %d\n", pCP->nAutoReportAllNeededSpeciesCode_ ); if ( consedResources::pDefaultResources_->bAutoReportUseCommasInBigNumbers_ != consedResources::pCurrentResources_->bAutoReportUseCommasInBigNumbers_ ) fprintf( pAO, "consed.autoReportUseCommasInBigNumbers: %s\n", ( pCP->bAutoReportUseCommasInBigNumbers_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoReportPrintToCompareToReich_ != consedResources::pCurrentResources_->bAutoReportPrintToCompareToReich_ ) fprintf( pAO, "consed.autoReportPrintToCompareToReich: %s\n", ( pCP->bAutoReportPrintToCompareToReich_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoReportOnlyAllowSitesThatAreBetweenAcceptableSites_ != consedResources::pCurrentResources_->bAutoReportOnlyAllowSitesThatAreBetweenAcceptableSites_ ) fprintf( pAO, "consed.autoReportOnlyAllowSitesThatAreBetweenAcceptableSites: %s\n", ( pCP->bAutoReportOnlyAllowSitesThatAreBetweenAcceptableSites_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoReportDeaminationMutationsDeterminedByMoreAccurateMethod_ != consedResources::pCurrentResources_->bAutoReportDeaminationMutationsDeterminedByMoreAccurateMethod_ ) fprintf( pAO, "consed.autoReportDeaminationMutationsDeterminedByMoreAccurateMethod: %s\n", ( pCP->bAutoReportDeaminationMutationsDeterminedByMoreAccurateMethod_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoReportChooseTreesUsingBadData_ != consedResources::pCurrentResources_->bAutoReportChooseTreesUsingBadData_ ) fprintf( pAO, "consed.autoReportChooseTreesUsingBadData: %s\n", ( pCP->bAutoReportChooseTreesUsingBadData_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoReportChooseTreesByCountingDeaminationMutations_ != consedResources::pCurrentResources_->bAutoReportChooseTreesByCountingDeaminationMutations_ ) fprintf( pAO, "consed.autoReportChooseTreesByCountingDeaminationMutations: %s\n", ( pCP->bAutoReportChooseTreesByCountingDeaminationMutations_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoReportChooseTreesUsingKimura_ != consedResources::pCurrentResources_->bAutoReportChooseTreesUsingKimura_ ) fprintf( pAO, "consed.autoReportChooseTreesUsingKimura: %s\n", ( pCP->bAutoReportChooseTreesUsingKimura_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoReportPrintCrudeChimpHumanMutations_ != consedResources::pCurrentResources_->bAutoReportPrintCrudeChimpHumanMutations_ ) fprintf( pAO, "consed.autoReportPrintCrudeChimpHumanMutations: %s\n", ( pCP->bAutoReportPrintCrudeChimpHumanMutations_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoReportPrintPositionsForGraham_ != consedResources::pCurrentResources_->bAutoReportPrintPositionsForGraham_ ) fprintf( pAO, "consed.autoReportPrintPositionsForGraham: %s\n", ( pCP->bAutoReportPrintPositionsForGraham_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoReportPrintAncestralCpGs_ != consedResources::pCurrentResources_->bAutoReportPrintAncestralCpGs_ ) fprintf( pAO, "consed.autoReportPrintAncestralCpGs: %s\n", ( pCP->bAutoReportPrintAncestralCpGs_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoReportPrintCpGMutations_ != consedResources::pCurrentResources_->bAutoReportPrintCpGMutations_ ) fprintf( pAO, "consed.autoReportPrintCpGMutations: %s\n", ( pCP->bAutoReportPrintCpGMutations_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoReportPrintMutationsWithContext_ != consedResources::pCurrentResources_->bAutoReportPrintMutationsWithContext_ ) fprintf( pAO, "consed.autoReportPrintMutationsWithContext: %s\n", ( pCP->bAutoReportPrintMutationsWithContext_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoReportCountAllMutationsML_ != consedResources::pCurrentResources_->bAutoReportCountAllMutationsML_ ) fprintf( pAO, "consed.autoReportCountAllMutationsML: %s\n", ( pCP->bAutoReportCountAllMutationsML_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoReportCountAllMutations_ != consedResources::pCurrentResources_->bAutoReportCountAllMutations_ ) fprintf( pAO, "consed.autoReportCountAllMutations: %s\n", ( pCP->bAutoReportCountAllMutations_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoReportIgnoreMultipleTrees_ != consedResources::pCurrentResources_->bAutoReportIgnoreMultipleTrees_ ) fprintf( pAO, "consed.autoReportIgnoreMultipleTrees: %s\n", ( pCP->bAutoReportIgnoreMultipleTrees_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoReportCountAcceptableColumnsWithNoneOnLeft_ != consedResources::pCurrentResources_->bAutoReportCountAcceptableColumnsWithNoneOnLeft_ ) fprintf( pAO, "consed.autoReportCountAcceptableColumnsWithNoneOnLeft: %s\n", ( pCP->bAutoReportCountAcceptableColumnsWithNoneOnLeft_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoReportPrintFlankedColumns4_ != consedResources::pCurrentResources_->bAutoReportPrintFlankedColumns4_ ) fprintf( pAO, "consed.autoReportPrintFlankedColumns4: %s\n", ( pCP->bAutoReportPrintFlankedColumns4_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoReportUseAnnotationFormat_ != consedResources::pCurrentResources_->bAutoReportUseAnnotationFormat_ ) fprintf( pAO, "consed.autoReportUseAnnotationFormat: %s\n", ( pCP->bAutoReportUseAnnotationFormat_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoReportPrintFlankedColumns3_ != consedResources::pCurrentResources_->bAutoReportPrintFlankedColumns3_ ) fprintf( pAO, "consed.autoReportPrintFlankedColumns3: %s\n", ( pCP->bAutoReportPrintFlankedColumns3_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoReportPrintFlankedColumns2_ != consedResources::pCurrentResources_->bAutoReportPrintFlankedColumns2_ ) fprintf( pAO, "consed.autoReportPrintFlankedColumns2: %s\n", ( pCP->bAutoReportPrintFlankedColumns2_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoReportPrintFlankedColumns_ != consedResources::pCurrentResources_->bAutoReportPrintFlankedColumns_ ) fprintf( pAO, "consed.autoReportPrintFlankedColumns: %s\n", ( pCP->bAutoReportPrintFlankedColumns_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoReportHighQualitySegmentData_ != consedResources::pCurrentResources_->bAutoReportHighQualitySegmentData_ ) fprintf( pAO, "consed.autoReportHighQualitySegmentData: %s\n", ( pCP->bAutoReportHighQualitySegmentData_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoReportGoodReadsBug_ != consedResources::pCurrentResources_->bAutoReportGoodReadsBug_ ) fprintf( pAO, "consed.autoReportGoodReadsBug: %s\n", ( pCP->bAutoReportGoodReadsBug_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoReportDiscrepancyRateInFlankedRegions_ != consedResources::pCurrentResources_->bAutoReportDiscrepancyRateInFlankedRegions_ ) fprintf( pAO, "consed.autoReportDiscrepancyRateInFlankedRegions: %s\n", ( pCP->bAutoReportDiscrepancyRateInFlankedRegions_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoReportDiscrepancyRateInFlankedRegions2_ != consedResources::pCurrentResources_->bAutoReportDiscrepancyRateInFlankedRegions2_ ) fprintf( pAO, "consed.autoReportDiscrepancyRateInFlankedRegions2: %s\n", ( pCP->bAutoReportDiscrepancyRateInFlankedRegions2_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoReportDiscrepancyRateInFlankedRegions4_ != consedResources::pCurrentResources_->bAutoReportDiscrepancyRateInFlankedRegions4_ ) fprintf( pAO, "consed.autoReportDiscrepancyRateInFlankedRegions4: %s\n", ( pCP->bAutoReportDiscrepancyRateInFlankedRegions4_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoReportDiscrepancyRateInFlankedRegions5_ != consedResources::pCurrentResources_->bAutoReportDiscrepancyRateInFlankedRegions5_ ) fprintf( pAO, "consed.autoReportDiscrepancyRateInFlankedRegions5: %s\n", ( pCP->bAutoReportDiscrepancyRateInFlankedRegions5_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoReportSingleSignalOrQuality_ != consedResources::pCurrentResources_->bAutoReportSingleSignalOrQuality_ ) fprintf( pAO, "consed.autoReportSingleSignalOrQuality: %s\n", ( pCP->bAutoReportSingleSignalOrQuality_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoReportLowQualityBasesInHQS_ != consedResources::pCurrentResources_->bAutoReportLowQualityBasesInHQS_ ) fprintf( pAO, "consed.autoReportLowQualityBasesInHQS: %s\n", ( pCP->bAutoReportLowQualityBasesInHQS_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoReportCompareHQSWithLQS_ != consedResources::pCurrentResources_->bAutoReportCompareHQSWithLQS_ ) fprintf( pAO, "consed.autoReportCompareHQSWithLQS: %s\n", ( pCP->bAutoReportCompareHQSWithLQS_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoReportCountColumnsForGroupsOfSpecies_ != consedResources::pCurrentResources_->bAutoReportCountColumnsForGroupsOfSpecies_ ) fprintf( pAO, "consed.autoReportCountColumnsForGroupsOfSpecies: %s\n", ( pCP->bAutoReportCountColumnsForGroupsOfSpecies_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoReportSingleSignalInfo_ != consedResources::pCurrentResources_->bAutoReportSingleSignalInfo_ ) fprintf( pAO, "consed.autoReportSingleSignalInfo: %s\n", ( pCP->bAutoReportSingleSignalInfo_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoReportSingleSignalInfo2_ != consedResources::pCurrentResources_->bAutoReportSingleSignalInfo2_ ) fprintf( pAO, "consed.autoReportSingleSignalInfo2: %s\n", ( pCP->bAutoReportSingleSignalInfo2_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoReportCompareTopAndBottomStrands_ != consedResources::pCurrentResources_->bAutoReportCompareTopAndBottomStrands_ ) fprintf( pAO, "consed.autoReportCompareTopAndBottomStrands: %s\n", ( pCP->bAutoReportCompareTopAndBottomStrands_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoReportCompareTopAndBottomStrandsNoHuman_ != consedResources::pCurrentResources_->bAutoReportCompareTopAndBottomStrandsNoHuman_ ) fprintf( pAO, "consed.autoReportCompareTopAndBottomStrandsNoHuman: %s\n", ( pCP->bAutoReportCompareTopAndBottomStrandsNoHuman_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoReportCompareTopAndBottomStrands2_ != consedResources::pCurrentResources_->bAutoReportCompareTopAndBottomStrands2_ ) fprintf( pAO, "consed.autoReportCompareTopAndBottomStrands2: %s\n", ( pCP->bAutoReportCompareTopAndBottomStrands2_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoReportCompareTopAndBottomStrands3_ != consedResources::pCurrentResources_->bAutoReportCompareTopAndBottomStrands3_ ) fprintf( pAO, "consed.autoReportCompareTopAndBottomStrands3: %s\n", ( pCP->bAutoReportCompareTopAndBottomStrands3_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoReportCompareTopAndBottomStrands4_ != consedResources::pCurrentResources_->bAutoReportCompareTopAndBottomStrands4_ ) fprintf( pAO, "consed.autoReportCompareTopAndBottomStrands4: %s\n", ( pCP->bAutoReportCompareTopAndBottomStrands4_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->nAutoReportTopStrandPinnedPosition_ != consedResources::pCurrentResources_->nAutoReportTopStrandPinnedPosition_ ) fprintf( pAO, "consed.autoReportTopStrandPinnedPosition: %d\n", pCP->nAutoReportTopStrandPinnedPosition_ ); if ( consedResources::pDefaultResources_->nAutoReportBottomStrandPinnedPosition_ != consedResources::pCurrentResources_->nAutoReportBottomStrandPinnedPosition_ ) fprintf( pAO, "consed.autoReportBottomStrandPinnedPosition: %d\n", pCP->nAutoReportBottomStrandPinnedPosition_ ); if ( consedResources::pDefaultResources_->bAutoReportCompareTopAndBottomStrandsWithHuman_ != consedResources::pCurrentResources_->bAutoReportCompareTopAndBottomStrandsWithHuman_ ) fprintf( pAO, "consed.autoReportCompareTopAndBottomStrandsWithHuman: %s\n", ( pCP->bAutoReportCompareTopAndBottomStrandsWithHuman_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoReportPrintLengthsOfAlignedSegmentsOfReads_ != consedResources::pCurrentResources_->bAutoReportPrintLengthsOfAlignedSegmentsOfReads_ ) fprintf( pAO, "consed.autoReportPrintLengthsOfAlignedSegmentsOfReads: %s\n", ( pCP->bAutoReportPrintLengthsOfAlignedSegmentsOfReads_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoReportPrintLengthsOfUnalignedHighQualitySegmentsOfReads_ != consedResources::pCurrentResources_->bAutoReportPrintLengthsOfUnalignedHighQualitySegmentsOfReads_ ) fprintf( pAO, "consed.autoReportPrintLengthsOfUnalignedHighQualitySegmentsOfReads: %s\n", ( pCP->bAutoReportPrintLengthsOfUnalignedHighQualitySegmentsOfReads_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoReportPrintIfReadsAreCorrectlyAligned_ != consedResources::pCurrentResources_->bAutoReportPrintIfReadsAreCorrectlyAligned_ ) fprintf( pAO, "consed.autoReportPrintIfReadsAreCorrectlyAligned: %s\n", ( pCP->bAutoReportPrintIfReadsAreCorrectlyAligned_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoReportCalculateErrorProbabilitiesByComparingPTroPPan_ != consedResources::pCurrentResources_->bAutoReportCalculateErrorProbabilitiesByComparingPTroPPan_ ) fprintf( pAO, "consed.autoReportCalculateErrorProbabilitiesByComparingPTroPPan: %s\n", ( pCP->bAutoReportCalculateErrorProbabilitiesByComparingPTroPPan_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoReportPrintAgreeDisagreeBetweenPairsOfSpecies_ != consedResources::pCurrentResources_->bAutoReportPrintAgreeDisagreeBetweenPairsOfSpecies_ ) fprintf( pAO, "consed.autoReportPrintAgreeDisagreeBetweenPairsOfSpecies: %s\n", ( pCP->bAutoReportPrintAgreeDisagreeBetweenPairsOfSpecies_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoReportPrintAgreeDisagreeBetweenPairsOfSpecies2_ != consedResources::pCurrentResources_->bAutoReportPrintAgreeDisagreeBetweenPairsOfSpecies2_ ) fprintf( pAO, "consed.autoReportPrintAgreeDisagreeBetweenPairsOfSpecies2: %s\n", ( pCP->bAutoReportPrintAgreeDisagreeBetweenPairsOfSpecies2_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoReportFilterSingleSignal_ != consedResources::pCurrentResources_->bAutoReportFilterSingleSignal_ ) fprintf( pAO, "consed.autoReportFilterSingleSignal: %s\n", ( pCP->bAutoReportFilterSingleSignal_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->filAutoReportGoodHitReads_ != consedResources::pCurrentResources_->filAutoReportGoodHitReads_ ) fprintf( pAO, "consed.autoReportGoodHitReads: %s\n", (char*)pCP->filAutoReportGoodHitReads_.data() ); if ( consedResources::pDefaultResources_->nAutoReportQualityWindowLow_ != consedResources::pCurrentResources_->nAutoReportQualityWindowLow_ ) fprintf( pAO, "consed.autoReportQualityWindowLow: %d\n", pCP->nAutoReportQualityWindowLow_ ); if ( consedResources::pDefaultResources_->nAutoReportQualityWindowHigh_ != consedResources::pCurrentResources_->nAutoReportQualityWindowHigh_ ) fprintf( pAO, "consed.autoReportQualityWindowHigh: %d\n", pCP->nAutoReportQualityWindowHigh_ ); if ( consedResources::pDefaultResources_->bAutoReportPrintNumberOfIsolatedPadsForEachSpecies_ != consedResources::pCurrentResources_->bAutoReportPrintNumberOfIsolatedPadsForEachSpecies_ ) fprintf( pAO, "consed.autoReportPrintNumberOfIsolatedPadsForEachSpecies: %s\n", ( pCP->bAutoReportPrintNumberOfIsolatedPadsForEachSpecies_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoReportPrintNumberOfIsolatedPads_ != consedResources::pCurrentResources_->bAutoReportPrintNumberOfIsolatedPads_ ) fprintf( pAO, "consed.autoReportPrintNumberOfIsolatedPads: %s\n", ( pCP->bAutoReportPrintNumberOfIsolatedPads_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->soAutoReportIsolatedPadsOfReadsWithThisPattern_ != consedResources::pCurrentResources_->soAutoReportIsolatedPadsOfReadsWithThisPattern_ ) fprintf( pAO, "consed.autoReportIsolatedPadsOfReadsWithThisPattern: %s\n", (char*)pCP->soAutoReportIsolatedPadsOfReadsWithThisPattern_.data() ); if ( consedResources::pDefaultResources_->nAutoReportMinNumberOfPerfectlyAlignedBasesBeforeDiscrepancy_ != consedResources::pCurrentResources_->nAutoReportMinNumberOfPerfectlyAlignedBasesBeforeDiscrepancy_ ) fprintf( pAO, "consed.autoReportMinNumberOfPerfectlyAlignedBasesBeforeDiscrepancy: %d\n", pCP->nAutoReportMinNumberOfPerfectlyAlignedBasesBeforeDiscrepancy_ ); if ( consedResources::pDefaultResources_->nAutoReportMaxSizeOfDiscrepantRegion_ != consedResources::pCurrentResources_->nAutoReportMaxSizeOfDiscrepantRegion_ ) fprintf( pAO, "consed.autoReportMaxSizeOfDiscrepantRegion: %d\n", pCP->nAutoReportMaxSizeOfDiscrepantRegion_ ); if ( consedResources::pDefaultResources_->nAutoReportSizeOfDiscrepantRegion_ != consedResources::pCurrentResources_->nAutoReportSizeOfDiscrepantRegion_ ) fprintf( pAO, "consed.autoReportSizeOfDiscrepantRegion: %d\n", pCP->nAutoReportSizeOfDiscrepantRegion_ ); if ( consedResources::pDefaultResources_->bAutoReportPrintMinimumQualityHistogram_ != consedResources::pCurrentResources_->bAutoReportPrintMinimumQualityHistogram_ ) fprintf( pAO, "consed.autoReportPrintMinimumQualityHistogram: %s\n", ( pCP->bAutoReportPrintMinimumQualityHistogram_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoReportPrintDiscrepantRegions_ != consedResources::pCurrentResources_->bAutoReportPrintDiscrepantRegions_ ) fprintf( pAO, "consed.autoReportPrintDiscrepantRegions: %s\n", ( pCP->bAutoReportPrintDiscrepantRegions_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoReportPrintBasesInDiscrepantRegions_ != consedResources::pCurrentResources_->bAutoReportPrintBasesInDiscrepantRegions_ ) fprintf( pAO, "consed.autoReportPrintBasesInDiscrepantRegions: %s\n", ( pCP->bAutoReportPrintBasesInDiscrepantRegions_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->soAutoReportPrintDiscrepantRegionsButIgnoreReadsContainingThis_ != consedResources::pCurrentResources_->soAutoReportPrintDiscrepantRegionsButIgnoreReadsContainingThis_ ) fprintf( pAO, "consed.autoReportPrintDiscrepantRegionsButIgnoreReadsContainingThis: %s\n", (char*)pCP->soAutoReportPrintDiscrepantRegionsButIgnoreReadsContainingThis_.data() ); if ( consedResources::pDefaultResources_->soAutoReportBackboneReadHasThisStringInIt_ != consedResources::pCurrentResources_->soAutoReportBackboneReadHasThisStringInIt_ ) fprintf( pAO, "consed.autoReportBackboneReadHasThisStringInIt: %s\n", (char*)pCP->soAutoReportBackboneReadHasThisStringInIt_.data() ); if ( consedResources::pDefaultResources_->bAutoReportPrintDiscrepantRegionsButOnlyIfAboveQualityThreshold_ != consedResources::pCurrentResources_->bAutoReportPrintDiscrepantRegionsButOnlyIfAboveQualityThreshold_ ) fprintf( pAO, "consed.autoReportPrintDiscrepantRegionsButOnlyIfAboveQualityThreshold: %s\n", ( pCP->bAutoReportPrintDiscrepantRegionsButOnlyIfAboveQualityThreshold_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoReportPrintSpeciesAlignment_ != consedResources::pCurrentResources_->bAutoReportPrintSpeciesAlignment_ ) fprintf( pAO, "consed.autoReportPrintSpeciesAlignment: %s\n", ( pCP->bAutoReportPrintSpeciesAlignment_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoReportPrintReadAlignment_ != consedResources::pCurrentResources_->bAutoReportPrintReadAlignment_ ) fprintf( pAO, "consed.autoReportPrintReadAlignment: %s\n", ( pCP->bAutoReportPrintReadAlignment_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->filAutoReportPrintTheseReads_ != consedResources::pCurrentResources_->filAutoReportPrintTheseReads_ ) fprintf( pAO, "consed.autoReportPrintTheseReads: %s\n", (char*)pCP->filAutoReportPrintTheseReads_.data() ); if ( consedResources::pDefaultResources_->bAutoReportPrintReadPositions_ != consedResources::pCurrentResources_->bAutoReportPrintReadPositions_ ) fprintf( pAO, "consed.autoReportPrintReadPositions: %s\n", ( pCP->bAutoReportPrintReadPositions_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoReportPrintChosenReadName_ != consedResources::pCurrentResources_->bAutoReportPrintChosenReadName_ ) fprintf( pAO, "consed.autoReportPrintChosenReadName: %s\n", ( pCP->bAutoReportPrintChosenReadName_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->nAutoReportNumbersOfCharactersOfChosenReadNameToBePrinted_ != consedResources::pCurrentResources_->nAutoReportNumbersOfCharactersOfChosenReadNameToBePrinted_ ) fprintf( pAO, "consed.autoReportNumbersOfCharactersOfChosenReadNameToBePrinted: %d\n", pCP->nAutoReportNumbersOfCharactersOfChosenReadNameToBePrinted_ ); if ( consedResources::pDefaultResources_->soAutoReportPrefix_ != consedResources::pCurrentResources_->soAutoReportPrefix_ ) fprintf( pAO, "consed.autoReportPrefix: %s\n", (char*)pCP->soAutoReportPrefix_.data() ); if ( consedResources::pDefaultResources_->bAutoReportUseOldCriteriaForDeletingColumnsOfPads_ != consedResources::pCurrentResources_->bAutoReportUseOldCriteriaForDeletingColumnsOfPads_ ) fprintf( pAO, "consed.autoReportUseOldCriteriaForDeletingColumnsOfPads: %s\n", ( pCP->bAutoReportUseOldCriteriaForDeletingColumnsOfPads_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoReportDeleteColumnsOfPadsBeforeAdjustingReadQualityValues_ != consedResources::pCurrentResources_->bAutoReportDeleteColumnsOfPadsBeforeAdjustingReadQualityValues_ ) fprintf( pAO, "consed.autoReportDeleteColumnsOfPadsBeforeAdjustingReadQualityValues: %s\n", ( pCP->bAutoReportDeleteColumnsOfPadsBeforeAdjustingReadQualityValues_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->bAutoReportFlankingBasesMustBeSingleSignal_ != consedResources::pCurrentResources_->bAutoReportFlankingBasesMustBeSingleSignal_ ) fprintf( pAO, "consed.autoReportFlankingBasesMustBeSingleSignal: %s\n", ( pCP->bAutoReportFlankingBasesMustBeSingleSignal_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->nAutoReportMinimumQualityOfFlankingBases_ != consedResources::pCurrentResources_->nAutoReportMinimumQualityOfFlankingBases_ ) fprintf( pAO, "consed.autoReportMinimumQualityOfFlankingBases: %d\n", pCP->nAutoReportMinimumQualityOfFlankingBases_ ); if ( consedResources::pDefaultResources_->bAutoReportFlankingBasesMustBeInHighQualitySegment_ != consedResources::pCurrentResources_->bAutoReportFlankingBasesMustBeInHighQualitySegment_ ) fprintf( pAO, "consed.autoReportFlankingBasesMustBeInHighQualitySegment: %s\n", ( pCP->bAutoReportFlankingBasesMustBeInHighQualitySegment_ ? "true" : "false" ) ); if ( consedResources::pDefaultResources_->soAutoReportSpecies_ != consedResources::pCurrentResources_->soAutoReportSpecies_ ) fprintf( pAO, "consed.autoReportSpecies: %s\n", (char*)pCP->soAutoReportSpecies_.data() ); fprintf( pAO, "}\n" ); }