seekia/internal/genetics/createPersonGeneticAnalysis/createPersonGeneticAnalysis.go

// createPersonGeneticAnalysis provides functions to create a Person genetic analysis
// These analyses are performed on one or more genome files.
// They contain 3 categories of results: Monogenic Diseases, Polygenic Diseases and Traits
// Use createCoupleGeneticAnalysis.go to create Couple genetic analyses

package createPersonGeneticAnalysis

// Disclaimer: I am a novice in the ways of genetics. This package could be flawed in numerous ways.

// TODO: We want to eventually use neural nets for both trait and polygenic disease analysis (see geneticPrediction.go)
// These will be trained on a set of genomes and will output a probability analysis for each trait/disease
// This is only possible once we get access to the necessary training data

// TODO: Add the ability to weight different genome files based on their reliability.
//	Some files are much more accurate because they record each location many times.

import "seekia/resources/geneticReferences/locusMetadata"
import "seekia/resources/geneticReferences/monogenicDiseases"
import "seekia/resources/geneticReferences/polygenicDiseases"
import "seekia/resources/geneticReferences/traits"

import "seekia/internal/encoding"
import "seekia/internal/genetics/geneticAnalysis"
import "seekia/internal/genetics/locusValue"
import "seekia/internal/genetics/prepareRawGenomes"
import "seekia/internal/helpers"

import "errors"
import "slices"
import "maps"


//Outputs:
//	-bool: Process completed (it was not stopped manually before completion)
//	-string: New Genetic analysis string (Encoded in MessagePack)
//	-error
func CreatePersonGeneticAnalysis(genomesList []prepareRawGenomes.RawGenomeWithMetadata, updatePercentageCompleteFunction func(int)error, checkIfProcessIsStopped func()bool)(bool, string, error){

	prepareRawGenomesUpdatePercentageCompleteFunction := func(newPercentage int)error{

		newPercentageCompletion, err := helpers.ScaleNumberProportionally(true, newPercentage, 0, 100, 0, 50)
		if (err != nil){ return err }

		err = updatePercentageCompleteFunction(newPercentageCompletion)
		if (err != nil) { return err }

		return nil
	}

	genomesWithMetadataList, allRawGenomeIdentifiersList, multipleGenomesExist, onlyExcludeConflictsGenomeIdentifier, onlyIncludeSharedGenomeIdentifier, err := prepareRawGenomes.GetGenomesWithMetadataListFromRawGenomesList(genomesList, prepareRawGenomesUpdatePercentageCompleteFunction)
	if (err != nil) { return false, "", err }

	newGeneticAnalysisObject := geneticAnalysis.PersonAnalysis{
		AnalysisVersion: 1,
		CombinedGenomesExist: multipleGenomesExist,
		AllRawGenomeIdentifiersList: allRawGenomeIdentifiersList,
	}

	if (multipleGenomesExist == true){

		newGeneticAnalysisObject.OnlyExcludeConflictsGenomeIdentifier = onlyExcludeConflictsGenomeIdentifier
		newGeneticAnalysisObject.OnlyIncludeSharedGenomeIdentifier = onlyIncludeSharedGenomeIdentifier
	}

	processIsStopped := checkIfProcessIsStopped()
	if (processIsStopped == true){
		return false, "", nil
	}

	monogenicDiseasesList, err := monogenicDiseases.GetMonogenicDiseaseObjectsList()
	if (err != nil) { return false, "", err }

	// Map Structure: Disease Name -> PersonMonogenicDiseaseInfo
	analysisMonogenicDiseasesMap := make(map[string]geneticAnalysis.PersonMonogenicDiseaseInfo)

	for _, monogenicDiseaseObject := range monogenicDiseasesList{

		diseaseName := monogenicDiseaseObject.DiseaseName

		personDiseaseAnalysisObject, err := GetPersonMonogenicDiseaseAnalysis(genomesWithMetadataList, monogenicDiseaseObject)
		if (err != nil) { return false, "", err }

		analysisMonogenicDiseasesMap[diseaseName] = personDiseaseAnalysisObject
	}

	newGeneticAnalysisObject.MonogenicDiseasesMap = analysisMonogenicDiseasesMap

	polygenicDiseaseObjectsList, err := polygenicDiseases.GetPolygenicDiseaseObjectsList()
	if (err != nil) { return false, "", err }

	// Map Structure: Disease Name -> PersonPolygenicDiseaseInfo
	analysisPolygenicDiseasesMap := make(map[string]geneticAnalysis.PersonPolygenicDiseaseInfo)

	for _, diseaseObject := range polygenicDiseaseObjectsList{

		personDiseaseAnalysisObject, err := GetPersonPolygenicDiseaseAnalysis(genomesWithMetadataList, diseaseObject)
		if (err != nil) { return false, "", err }

		diseaseName := diseaseObject.DiseaseName

		analysisPolygenicDiseasesMap[diseaseName] = personDiseaseAnalysisObject
	}

	newGeneticAnalysisObject.PolygenicDiseasesMap = analysisPolygenicDiseasesMap

	traitObjectsList, err := traits.GetTraitObjectsList()
	if (err != nil) { return false, "", err }

	// Map Structure: Trait Name -> PersonTraitInfo
	analysisTraitsMap := make(map[string]geneticAnalysis.PersonTraitInfo)

	for _, traitObject := range traitObjectsList{

		personTraitAnalysisObject, err := GetPersonTraitAnalysis(genomesWithMetadataList, traitObject)
		if (err != nil) { return false, "", err }

		traitName := traitObject.TraitName

		analysisTraitsMap[traitName] = personTraitAnalysisObject
	}

	newGeneticAnalysisObject.TraitsMap = analysisTraitsMap

	analysisBytes, err := encoding.EncodeMessagePackBytes(newGeneticAnalysisObject)
	if (err != nil) { return false, "", err }

	analysisString := string(analysisBytes)

	return true, analysisString, nil
}


//Outputs:
//	-geneticAnalysis.PersonMonogenicDiseaseInfo: Monogenic disease analysis object
//	-error
func GetPersonMonogenicDiseaseAnalysis(inputGenomesWithMetadataList []prepareRawGenomes.GenomeWithMetadata, diseaseObject monogenicDiseases.MonogenicDisease)(geneticAnalysis.PersonMonogenicDiseaseInfo, error){

	emptyDiseaseInfoObject := geneticAnalysis.PersonMonogenicDiseaseInfo{}

	dominantOrRecessive := diseaseObject.DominantOrRecessive
	variantsList := diseaseObject.VariantsList

	// We use this map to keep track of which RSIDs corresponds to each variant
	// We also use it to have a map of all variants for the disease
	// Map Structure: Variant Identifier -> []rsID
	variantRSIDsMap := make(map[[3]byte][]int64)

	// This map stores all rsIDs for this monogenic disease
	// These are locations in the disease's gene which, if mutated, are known to cause the disease
	// We use this map to avoid duplicate rsIDs, because one rsID can have multiple variants which belong to it
	// We also store all alias rsIDs in this map
	allRSIDsMap := make(map[int64]struct{})

	for _, variantObject := range variantsList{

		variantIdentifierHex := variantObject.VariantIdentifier

		variantIdentifier, err := encoding.DecodeHexStringTo3ByteArray(variantIdentifierHex)
		if (err != nil) { return emptyDiseaseInfoObject, err }

		variantRSID := variantObject.VariantRSID

		variantRSIDsList := []int64{variantRSID}

		// We add aliases to variantRSIDsList

		anyAliasesExist, rsidAliasesList, err := locusMetadata.GetRSIDAliases(variantRSID)
		if (err != nil) { return emptyDiseaseInfoObject, err }
		if (anyAliasesExist == true){
			variantRSIDsList = append(variantRSIDsList, rsidAliasesList...)
		}

		variantRSIDsMap[variantIdentifier] = variantRSIDsList

		for _, rsID := range variantRSIDsList{
			allRSIDsMap[rsID] = struct{}{}
		}
	}

	// Now we create a new map without any rsID aliases
	// Each rsID in this map represents a unique locus on the genome
	// Each rsID may have aliases, but they are not included in this map
	allUniqueRSIDsMap := make(map[int64]struct{})

	for rsID, _ := range allRSIDsMap{

		anyAliasesExist, rsidAliasesList, err := locusMetadata.GetRSIDAliases(rsID)
		if (err != nil) { return emptyDiseaseInfoObject, err }
		if (anyAliasesExist == false){
			allUniqueRSIDsMap[rsID] = struct{}{}
			continue
		}

		// We see if we already added an alias of this rsID to the map

		checkIfAliasAlreadyExists := func()bool{

			for _, rsIDAlias := range rsidAliasesList{
				_, exists := allUniqueRSIDsMap[rsIDAlias]
				if (exists == true){
					return true
				}
			}
			return false
		}

		aliasAlreadyExists := checkIfAliasAlreadyExists()
		if (aliasAlreadyExists == true){
			// We already added this alias
			continue
		}
		allUniqueRSIDsMap[rsID] = struct{}{}
	}

	// Map Structure: Genome Identifier -> PersonGenomeMonogenicDiseaseInfo
	monogenicDiseaseInfoMap := make(map[[16]byte]geneticAnalysis.PersonGenomeMonogenicDiseaseInfo)

	for _, genomeWithMetadataObject := range inputGenomesWithMetadataList{

		genomeIdentifier := genomeWithMetadataObject.GenomeIdentifier
		genomeMap := genomeWithMetadataObject.GenomeMap

		// This stores all variant info for this genome
		// Map Structure: Variant Identifier -> PersonGenomeMonogenicDiseaseVariantInfo
		variantsInfoMap := make(map[[3]byte]geneticAnalysis.PersonGenomeMonogenicDiseaseVariantInfo)

		for _, variantObject := range variantsList{

			variantIdentifierHex := variantObject.VariantIdentifier

			variantIdentifier, err := encoding.DecodeHexStringTo3ByteArray(variantIdentifierHex)
			if (err != nil) { return emptyDiseaseInfoObject, err }

			variantRSID := variantObject.VariantRSID

			basePairValueFound, base1Value, base2Value, locusIsPhased, _, err := GetLocusValueFromGenomeMap(true, genomeMap, variantRSID)
			if (err != nil) { return emptyDiseaseInfoObject, err }
			if (basePairValueFound == false){

				// This genome does not contain info for this variant
				// We skip it
				continue
			}

			// This genome has at least 1 variant

			variantDefectiveBase := variantObject.DefectiveBase

			getBaseIsVariantMutationBool := func(inputBase string)bool{

				if (inputBase == variantDefectiveBase){
					return true
				}
				// Base could be mutated to a different unhealthy base
				// That mutation could be a neutral/healthier change
				// We only care about this specific variant
				return false
			}

			base1IsDefective := getBaseIsVariantMutationBool(base1Value)
			base2IsDefective := getBaseIsVariantMutationBool(base2Value)

			newDiseaseVariantInfoObject := geneticAnalysis.PersonGenomeMonogenicDiseaseVariantInfo{
				Base1HasVariant: base1IsDefective,
				Base2HasVariant: base2IsDefective,
				LocusIsPhased: locusIsPhased,
			}

			variantsInfoMap[variantIdentifier] = newDiseaseVariantInfoObject

			//TODO: Add LocusIsPhased to readGeneticAnalysis package
		}

		// We are done adding variant information for the genome
		// Now we determine probability that user will pass a disease variant to offspring, and if the user has the disease

		numberOfVariantsTested := len(variantsInfoMap)

		if (numberOfVariantsTested == 0){
			// We don't know anything about this genome's disease risk for this disease
			// We won't add any information to the map
			continue
		}

		// This stores the number of loci that were tested
		// Each locus can have multiple potential variants
		numberOfLociTested := 0

		// This stores the number of tested loci that are phased
		// A higher number means that the results are more potentially more accurate
		// It is only more accurate if multiple heterozygous variants on seperate loci exist.
		numberOfPhasedLoci := 0

		for rsID, _ := range allUniqueRSIDsMap{

			locusValueExists, _, _, locusIsPhased, _, err := GetLocusValueFromGenomeMap(true, genomeMap, rsID)
			if (err != nil) { return emptyDiseaseInfoObject, err }
			if (locusValueExists == false){
				continue
			}

			numberOfLociTested += 1

			if (locusIsPhased == true){
				numberOfPhasedLoci += 1
			}
		}

		// Outputs:
		//	-bool: Person has disease
		//	-float64: Probability Person will pass a defect (variant) to offspring (0-1)
		//	-error
		getPersonDiseaseInfo := func()(bool, float64, error){

			// These variables are used to count the number of defective variants that exist on each chromosome
			numberOfVariants_Chromosome1 := 0
			numberOfVariants_Chromosome2 := 0
			numberOfVariants_UnknownChromosome := 0

			// We use this map to keep track of how many mutations exist for each rsID
			// This allows us to know if 2 different variant mutations exist for a single rsID
			// For example, base1 is a different deleterious mutation than base2
			// If this ever happens, we know that the user has the disease,
			//		because both copies of the gene locus are defective.
			rsidMutationsMap := make(map[int64]int)

			for variantIdentifier, variantInfoObject := range variantsInfoMap{

				locusIsPhasedStatus := variantInfoObject.LocusIsPhased

				base1HasVariant := variantInfoObject.Base1HasVariant
				base2HasVariant := variantInfoObject.Base2HasVariant

				if (base1HasVariant == false && base2HasVariant == false){
					// Neither chromosome contains the variant mutation.
					continue
				}

				if (base1HasVariant == true && base2HasVariant == true){
					// Both chromosomes contain the same variant mutation.
					// Person has the disease.
					// Person will definitely pass disease variant to offspring.
					return true, 1, nil
				}

				// We know that this variant exists on 1 of the bases, but not both.

				variantRSIDsList, exists := variantRSIDsMap[variantIdentifier]
				if (exists == false){
					return false, 0, errors.New("variantRSIDsMap missing variantIdentifier.")
				}

				for _, rsID := range variantRSIDsList{
					rsidMutationsMap[rsID] += 1
				}

				if (locusIsPhasedStatus == true){

					if (base1HasVariant == true){
						numberOfVariants_Chromosome1 += 1
					}
					if (base2HasVariant == true){
						numberOfVariants_Chromosome2 += 1
					}
				} else {

					if (base1HasVariant == true || base2HasVariant == true){
						numberOfVariants_UnknownChromosome += 1
					}
				}
			}

			totalNumberOfVariants := numberOfVariants_Chromosome1 + numberOfVariants_Chromosome2 + numberOfVariants_UnknownChromosome

			if (totalNumberOfVariants == 0){
				// Person does not have any disease variants.
				// They do not have the disease, and have no chance of passing a disease variant
				return false, 0, nil
			}

			// Now we check to see if there are any loci which have 2 different variants, one for each base

			for _, numberOfMutations := range rsidMutationsMap{

				if (numberOfMutations >= 2){
					// Person has 2 mutations on the same location
					// They must have the disease, and will definitely pass a variant to their offspring
					return true, 1, nil
				}
			}

			// At this point, we know that there are no homozygous variant mutations
			// All variant mutations are heterozygous, meaning the other chromosome strand's base is healthy

			//Outputs:
			//	-bool: Person has disease
			getPersonHasDiseaseBool := func()bool{

				if (dominantOrRecessive == "Dominant"){
					// Only 1 variant is needed for the person to have the disease
					// We know they have at least 1 variant
					return true
				}

				// dominantOrRecessive == "Recessive"

				if (totalNumberOfVariants == 1){
					// There is only 1 variant in total.
					// This single variant cannot exist on both chromosomes.
					// The person does not have the disease
					return false
				}

				// We know that there are at least 2 variants

				if (numberOfVariants_Chromosome1 >= 1 && numberOfVariants_Chromosome2 >= 1){

					// We know there is at least 1 variant mutation on each chromosome
					// Therefore, the person has the disease
					return true
				}

				if (numberOfVariants_UnknownChromosome == 0){

					// We know that variants do not exist on both chromosomes, only on 1.
					// Thus, the person does not have the disease
					return false
				}

				// We know there are at least 2 variants
				// We know there is at least 1 variant whose phase is unknown

				// If all mutations are on the same chromosome, the person does not have the disease.
				// If at least 1 mutation exists on each chromosome, the person does have the disease.
				// Either way, we don't know enough to say if the person has the disease.
				// We will report that they do not, because their genome does not conclusively say that they do.
				// This is why phased genomes are useful and provide a more accurate reading
				// TODO: Explain this to the user in the GUI
				// We must explain that unphased genomes will not detect disease sometimes

				return false
			}

			personHasDiseaseBool := getPersonHasDiseaseBool()

			// Output:
			//	-float64: Probability person will pass a disease variant to their offspring (0-1)
			getPersonWillPassVariantProbability := func()float64{

				if (totalNumberOfVariants == 1){

					// There is only 1 variant on any chromosome
					// The probability of the person passing a variant is 50%.
					return 0.5
				}

				// We know that there are at least 2 variants

				if (numberOfVariants_Chromosome1 >= 1 && numberOfVariants_Chromosome2 >= 1){

					// We know there is at least 1 variant mutation on each chromosome
					// Therefore, the person will definitely pass a variant
					return 1
				}
				if (numberOfVariants_UnknownChromosome == 0){

					// We know that variants do not exist on both chromosomes, only on 1.
					// Thus, the person has a 50% probability of passing a variant
					return 0.5
				}

				// We know all variants are heterozygous

				// From Wikipeia:
				// The human genome contains somewhere between 19,000 and 20,000 protein-coding genes.
				// These genes contain an average of 10 introns and the average size of an intron is about 6 kb (6,000 base pairs)
				// This means that the average size of a protein-coding gene is about 62 kb (62,000 base pairs)

				// The probability of a recombination breakpoint occurring within the gene is very small
				// If there is 1 breakpoint every 100 million locations, on average, and each gene is 62,000 base pairs long, 
				//		then the probability of a breakpoint occurring within a gene is 62,000/100,000,000 = 0.00062 = .062%
				// Thus, we disregard the risk of a breakpoint occurring within a gene
				// I also read somewhere that breakpoints are less likely to occurr within genes, which makes this likelihood even smaller

				// At this point, we know there at at least 2 variants
				// We know that at least 1 of the variants has an unknown phase
				// We don't know if all of the variants belong to the same chromosome
				// If variants exist on both chromosomes, then the probability of passing a variant is 100%
				// If all variants exist on the same chromosome, then the probability of passing a variant is 50%
				// We know there is at least a 50% chance of passing a variant, and possibly higher

				return 0.5
			}

			personWillPassVariantProbability := getPersonWillPassVariantProbability()

			return personHasDiseaseBool, personWillPassVariantProbability, nil
		}

		personHasDisease, probabilityPersonWillPassAnyVariant, err := getPersonDiseaseInfo()
		if (err != nil) { return emptyDiseaseInfoObject, err }

		percentageProbabilityPersonWillPassADiseaseVariant := int(probabilityPersonWillPassAnyVariant * 100)

		diseaseAnalysisObject := geneticAnalysis.PersonGenomeMonogenicDiseaseInfo{
			PersonHasDisease: personHasDisease,
			NumberOfVariantsTested: numberOfVariantsTested,
			NumberOfLociTested: numberOfLociTested,
			NumberOfPhasedLoci: numberOfPhasedLoci,
			ProbabilityOfPassingADiseaseVariant: percentageProbabilityPersonWillPassADiseaseVariant,
			VariantsInfoMap: variantsInfoMap,
		}

		monogenicDiseaseInfoMap[genomeIdentifier] = diseaseAnalysisObject
	}

	personMonogenicDiseaseInfoObject := geneticAnalysis.PersonMonogenicDiseaseInfo{
		MonogenicDiseaseInfoMap: monogenicDiseaseInfoMap,
	}

	if (len(monogenicDiseaseInfoMap) <= 1){
		// We do not need to check for conflicts, there is only <=1 genome with disease information
		// Nothing left to do. Analysis is complete.
		return personMonogenicDiseaseInfoObject, nil
	}

	// We check for conflicts

	getConflictExistsBool := func()(bool, error){

		firstItemReached := false

		personHasDisease := false
		probabilityOfPassingAVariant := 0

		for _, currentGenomeDiseaseAnalysisObject := range monogenicDiseaseInfoMap{

			currentGenomePersonHasDisease := currentGenomeDiseaseAnalysisObject.PersonHasDisease
			currentGenomeProbabilityOfPassingAVariant := currentGenomeDiseaseAnalysisObject.ProbabilityOfPassingADiseaseVariant

			if (firstItemReached == false){
				personHasDisease = currentGenomePersonHasDisease
				probabilityOfPassingAVariant = currentGenomeProbabilityOfPassingAVariant
				firstItemReached = true
				continue
			}

			if (currentGenomePersonHasDisease != personHasDisease){
				return true, nil
			}
			if (currentGenomeProbabilityOfPassingAVariant != probabilityOfPassingAVariant){
				return true, nil
			}
		}

		// Now we test variants for conflicts
		// We are only doing this to see if there are variants which one genome has and another doesn't
		// For example, the analysis results say that you have a 50% chance of passing a variant for both genomes, but
		//		they have detected a different variant for each genome.
		//		This means that your real risk of passing a variant may actually be higher, and you are more likely to have the disease too

		for variantIdentifier, _ := range variantRSIDsMap{

			// Each variant base pair is either true/false, true/true, false/false, false/true

			// Two different genomes have true/false and false/true, it will not count as a conflict
			// If the locus is unphased, then there is no difference between true/false and false/true
			// If the locus is phased, then this flip is only meaningful if it effects the probability of disease/passing a variant
			// We already checked those probabilities for conflicts earlier
			// Therefore, any flip is not considered a conflict
			// We only care about conflicts where 1 genome says you have a variant and the other says you don't, or 
			//		one says you have only 1 mutation and the other says you have 2 at that location

			firstItemReached := false

			base1HasVariant := false
			base2HasVariant := false

			for _, currentGenomeDiseaseAnalysisObject := range monogenicDiseaseInfoMap{

				variantsInfoMap := currentGenomeDiseaseAnalysisObject.VariantsInfoMap

				variantInfoObject, exists := variantsInfoMap[variantIdentifier]
				if (exists == false){
					if (firstItemReached == true){
						// A previous genome has information for this variant, and the current one does not
						return true, nil
					}
					continue
				}

				currentBase1HasVariant := variantInfoObject.Base1HasVariant
				currentBase2HasVariant := variantInfoObject.Base2HasVariant

				if (firstItemReached == false){
					base1HasVariant = currentBase1HasVariant
					base2HasVariant = currentBase2HasVariant
					firstItemReached = true
					continue
				}

				if (base1HasVariant == currentBase1HasVariant && base2HasVariant == currentBase2HasVariant){
					// No conflict exists
					continue
				}
				if (base1HasVariant == currentBase2HasVariant && base2HasVariant == currentBase1HasVariant){
					// We don't count this as a conflict
					continue
				}

				// A conflict exists
				return true, nil
			}
		}

		return false, nil
	}

	conflictExists, err := getConflictExistsBool()
	if (err != nil) { return emptyDiseaseInfoObject, err }

	personMonogenicDiseaseInfoObject.ConflictExists = conflictExists

	return personMonogenicDiseaseInfoObject, nil
}


//Outputs:
//	-bool: Any loci tested
//	-int: Person genome risk score (value between 0-10)
//	-int: Person Genome Number of loci tested
//	-map[[3]byte]geneticAnalysis.PersonGenomePolygenicDiseaseLocusInfo: Person disease locus info map
//		Map Structure: Locus Identifier -> PersonGenomePolygenicDiseaseLocusInfo
//	-error
func GetPersonGenomePolygenicDiseaseInfo(diseaseLociList []polygenicDiseases.DiseaseLocus, personLocusValuesMap map[int64]locusValue.LocusValue, lookForLocusAliases bool)(bool, int, int, map[[3]byte]geneticAnalysis.PersonGenomePolygenicDiseaseLocusInfo, error){

	if (len(personLocusValuesMap) == 0){
		return false, 0, 0, nil, nil
	}

	// Map Structure: Locus Identifier -> PersonGenomePolygenicDiseaseLocusInfo
	genomeLociInfoMap := make(map[[3]byte]geneticAnalysis.PersonGenomePolygenicDiseaseLocusInfo)

	summedDiseaseRiskWeight := 0

	minimumPossibleRiskWeightSum := 0
	maximumPossibleRiskWeightSum := 0

	for _, locusObject := range diseaseLociList{

		locusRSID := locusObject.LocusRSID
		locusRiskWeightsMap := locusObject.RiskWeightsMap
		locusOddsRatiosMap := locusObject.OddsRatiosMap
		locusMinimumWeight := locusObject.MinimumRiskWeight
		locusMaximumWeight := locusObject.MaximumRiskWeight

		locusValueFound, locusBase1Value, locusBase2Value, _, _, err := GetLocusValueFromGenomeMap(lookForLocusAliases, personLocusValuesMap, locusRSID)	
		if (err != nil) { return false, 0, 0, nil, err }
		if (locusValueFound == false){
			continue
		}

		locusRiskWeight, locusOddsRatioIsKnown, locusOddsRatio, err := GetGenomePolygenicDiseaseLocusRiskInfo(locusRiskWeightsMap, locusOddsRatiosMap, locusBase1Value, locusBase2Value)
		if (err != nil) { return false, 0, 0, nil, err }

		newLocusInfoObject := geneticAnalysis.PersonGenomePolygenicDiseaseLocusInfo{
			RiskWeight: locusRiskWeight,
			OddsRatioIsKnown: locusOddsRatioIsKnown,
		}

		if (locusOddsRatioIsKnown == true){
			newLocusInfoObject.OddsRatio = locusOddsRatio
		}

		locusIdentifierHex := locusObject.LocusIdentifier

		locusIdentifier, err := encoding.DecodeHexStringTo3ByteArray(locusIdentifierHex)
		if (err != nil) { return false, 0, 0, nil, err }

		genomeLociInfoMap[locusIdentifier] = newLocusInfoObject

		minimumPossibleRiskWeightSum += locusMinimumWeight
		maximumPossibleRiskWeightSum += locusMaximumWeight

		summedDiseaseRiskWeight += locusRiskWeight
	}

	numberOfLociTested := len(genomeLociInfoMap)
	if (numberOfLociTested == 0){
		// We have no information about this disease for this genome
		return false, 0, 0, nil, nil
	}

	diseaseRiskScore, err := helpers.ScaleNumberProportionally(true, summedDiseaseRiskWeight, minimumPossibleRiskWeightSum, maximumPossibleRiskWeightSum, 0, 10)
	if (err != nil) { return false, 0, 0, nil, err }

	return true, diseaseRiskScore, numberOfLociTested, genomeLociInfoMap, nil
}


//Outputs:
//	-geneticAnalysis.PersonPolygenicDiseaseInfo
//	-error
func GetPersonPolygenicDiseaseAnalysis(inputGenomesWithMetadataList []prepareRawGenomes.GenomeWithMetadata, diseaseObject polygenicDiseases.PolygenicDisease)(geneticAnalysis.PersonPolygenicDiseaseInfo, error){

	// We use this when returning errors
	emptyDiseaseInfoObject := geneticAnalysis.PersonPolygenicDiseaseInfo{}

	diseaseLociList := diseaseObject.LociList

	// This map stores the polygenic disease for each of the person's genomes
	// Map Structure: Genome Identifier -> PersonGenomePolygenicDiseaseInfo
	personPolygenicDiseaseInfoMap := make(map[[16]byte]geneticAnalysis.PersonGenomePolygenicDiseaseInfo)

	// We construct polygenic disease probability info for each genome

	for _, genomeWithMetadataObject := range inputGenomesWithMetadataList{

		genomeIdentifier := genomeWithMetadataObject.GenomeIdentifier
		genomeMap := genomeWithMetadataObject.GenomeMap

		// This map stores the loci for this disease and does not contain loci which do not belong to this disease
		// Map Structure: rsID -> Locus Value
		genomeLocusValuesMap := make(map[int64]locusValue.LocusValue)

		for _, locusObject := range diseaseLociList{

			locusRSID := locusObject.LocusRSID

			locusValueFound, _, _, _, locusValueObject, err := GetLocusValueFromGenomeMap(true, genomeMap, locusRSID)	
			if (err != nil) { return emptyDiseaseInfoObject, err }
			if (locusValueFound == false){
				continue
			}

			genomeLocusValuesMap[locusRSID] = locusValueObject
		}

		anyLociTested, personDiseaseRiskScore, genomeNumberOfLociTested, genomeLociInfoMap, err := GetPersonGenomePolygenicDiseaseInfo(diseaseLociList, genomeLocusValuesMap, false)
		if (err != nil) { return emptyDiseaseInfoObject, err }
		if (anyLociTested == false){
			continue
		}

		newDiseaseInfoObject := geneticAnalysis.PersonGenomePolygenicDiseaseInfo{
			NumberOfLociTested: genomeNumberOfLociTested,
			RiskScore: personDiseaseRiskScore,
			LocusValuesMap: genomeLocusValuesMap,
			LociInfoMap: genomeLociInfoMap,
		}

		personPolygenicDiseaseInfoMap[genomeIdentifier] = newDiseaseInfoObject
	}

	newPersonPolygenicDiseaseInfoObject := geneticAnalysis.PersonPolygenicDiseaseInfo{
		PolygenicDiseaseInfoMap: personPolygenicDiseaseInfoMap,
	}

	if (len(personPolygenicDiseaseInfoMap) <= 1){
		// We do not need to check for conflicts, there is only <=1 genome with disease information
		// Nothing left to do. Analysis is complete.
		return newPersonPolygenicDiseaseInfoObject, nil
	}

	// We check for conflicts between the different genome's results

	getConflictExistsBool := func()(bool, error){

		// First we check to see if any of the genomes have different risk scores or NumberOfLociTested

		genomeRiskScore := 0
		genomeNumberOfLociTested := 0

		firstItemReached := false

		for _, personGenomeDiseaseInfoObject := range personPolygenicDiseaseInfoMap{

			currentGenomeRiskScore := personGenomeDiseaseInfoObject.RiskScore
			currentGenomeNumberOfLociTested := personGenomeDiseaseInfoObject.NumberOfLociTested

			if (firstItemReached == false){
				genomeRiskScore = currentGenomeRiskScore
				genomeNumberOfLociTested = currentGenomeNumberOfLociTested
				firstItemReached = true
				continue
			}

			if (genomeRiskScore != currentGenomeRiskScore){
				return true, nil
			}
			if (genomeNumberOfLociTested != currentGenomeNumberOfLociTested){
				return true, nil
			}
		}

		// Now we check for conflicts between the different locus values
		// We consider a conflict any time the same locus has different weights/odds ratios
		// We don't care if the loci have different base pair values, so long as those base pairs have the same risk weights/odds ratios

		for _, locusObject := range diseaseLociList{

			locusIdentifierHex := locusObject.LocusIdentifier

			locusIdentifier, err := encoding.DecodeHexStringTo3ByteArray(locusIdentifierHex)
			if (err != nil) { return false, err }

			locusRiskWeight := 0
			locusOddsRatio := float64(0)

			firstItemReached := false

			for _, personGenomeDiseaseInfoObject := range personPolygenicDiseaseInfoMap{

				genomeLociInfoMap := personGenomeDiseaseInfoObject.LociInfoMap

				genomeLocusObject, exists := genomeLociInfoMap[locusIdentifier]
				if (exists == false){
					if (firstItemReached == true){
						// A previous genome has information for this locus, and the current one does not
						return true, nil
					}
					continue
				}

				genomeLocusRiskWeight := genomeLocusObject.RiskWeight
				genomeLocusOddsRatio := genomeLocusObject.OddsRatio

				if (firstItemReached == false){
					locusRiskWeight = genomeLocusRiskWeight
					locusOddsRatio = genomeLocusOddsRatio
					firstItemReached = true
					continue
				}
				if (locusRiskWeight == genomeLocusRiskWeight && locusOddsRatio == genomeLocusOddsRatio){
					// No conflict exists for this locus on the genomes we have already checked
					continue
				}

				// Conflict exists
				return true, nil
			}
		}

		return false, nil
	}

	conflictExists, err := getConflictExistsBool()
	if (err != nil) { return emptyDiseaseInfoObject, err }

	newPersonPolygenicDiseaseInfoObject.ConflictExists = conflictExists

	return newPersonPolygenicDiseaseInfoObject, nil
}


//Outputs:
//	-geneticAnalysis.PersonTraitInfo: Trait analysis object
//	-error
func GetPersonTraitAnalysis(inputGenomesWithMetadataList []prepareRawGenomes.GenomeWithMetadata, traitObject traits.Trait)(geneticAnalysis.PersonTraitInfo, error){

	// We use this when returning errors
	emptyPersonTraitInfo := geneticAnalysis.PersonTraitInfo{}

	traitLociList := traitObject.LociList
	traitRulesList := traitObject.RulesList

	// Map Structure: Genome Identifier -> PersonGenomeTraitInfo
	newPersonTraitInfoMap := make(map[[16]byte]geneticAnalysis.PersonGenomeTraitInfo)

	for _, genomeWithMetadataObject := range inputGenomesWithMetadataList{

		genomeIdentifier := genomeWithMetadataObject.GenomeIdentifier
		genomeMap := genomeWithMetadataObject.GenomeMap

		// This map contains the locus values for the genome
		// If an locus's entry doesn't exist, its value is unknown
		// Map Structure: Locus rsID -> Locus Value
		genomeLocusValuesMap := make(map[int64]locusValue.LocusValue)

		for _, locusRSID := range traitLociList{

			locusBasePairKnown, _, _, _, locusValueObject, err := GetLocusValueFromGenomeMap(true, genomeMap, locusRSID)
			if (err != nil) { return emptyPersonTraitInfo, err }
			if (locusBasePairKnown == false){
				continue
			}

			genomeLocusValuesMap[locusRSID] = locusValueObject
		}

		// This map contains the trait outcome scores for the genome
		// Map Structure: Outcome Name -> Score
		// Example: "Intolerant" -> 5
		traitOutcomeScoresMap := make(map[string]int)

		// Map Structure: Rule Identifier -> Genome Passes rule (true if the genome passes the rule)
		personPassesRulesMap := make(map[[3]byte]bool)

		if (len(traitRulesList) != 0){

			// At least 1 rule exists for this trait

			for _, ruleObject := range traitRulesList{

				ruleIdentifierHex := ruleObject.RuleIdentifier

				ruleIdentifier, err := encoding.DecodeHexStringTo3ByteArray(ruleIdentifierHex)
				if (err != nil) { return emptyPersonTraitInfo, err }

				ruleLociList := ruleObject.LociList

				genomePassesRuleIsKnown, genomePassesRule, err := GetGenomePassesTraitRuleStatus(ruleLociList, genomeMap, false)
				if (err != nil) { return emptyPersonTraitInfo, err }
				if (genomePassesRuleIsKnown == false){
					continue
				}

				personPassesRulesMap[ruleIdentifier] = genomePassesRule

				// The rule has been passed by this genome
				// We add the outcome points for the rule to the traitOutcomeScoresMap

				ruleOutcomePointsMap := ruleObject.OutcomePointsMap

				for traitOutcome, pointsChange := range ruleOutcomePointsMap{

					traitOutcomeScoresMap[traitOutcome] += pointsChange
				}
			}
		}

		traitOutcomesList := traitObject.OutcomesList

		// We add all outcomes for which there were no points

		for _, traitOutcome := range traitOutcomesList{

			_, exists := traitOutcomeScoresMap[traitOutcome]
			if (exists == false){
				traitOutcomeScoresMap[traitOutcome] = 0
			}
		}

		numberOfRulesTested := len(personPassesRulesMap)

		newPersonGenomeTraitInfo := geneticAnalysis.PersonGenomeTraitInfo{
			NumberOfRulesTested: numberOfRulesTested,
			LocusValuesMap: genomeLocusValuesMap,
			OutcomeScoresMap: traitOutcomeScoresMap,
			GenomePassesRulesMap: personPassesRulesMap,
		}

		newPersonTraitInfoMap[genomeIdentifier] = newPersonGenomeTraitInfo
	}

	newPersonTraitInfoObject := geneticAnalysis.PersonTraitInfo{
		TraitInfoMap: newPersonTraitInfoMap,
	}

	if (len(newPersonTraitInfoMap) <= 1){
		// We do not need to check for conflicts, there is only <=1 genome with trait information
		// Nothing left to do. Analysis is complete.
		return newPersonTraitInfoObject, nil
	}

	// We check for conflicts

	getConflictExistsBool := func()(bool, error){

		//TODO: Check for locus value conflicts once locus values are used in neural network prediction.

		if (len(traitRulesList) == 0){
			return false, nil
		}

		// We check to see if the outcome scores are the same for all genomes
		// We also check each rule result

		firstItemReached := false

		outcomeScoresMap := make(map[string]int)
		passesRulesMap := make(map[[3]byte]bool)

		for _, genomeTraitInfoObject := range newPersonTraitInfoMap{

			currentGenomeOutcomeScoresMap := genomeTraitInfoObject.OutcomeScoresMap
			currentGenomePassesRulesMap := genomeTraitInfoObject.GenomePassesRulesMap

			if (firstItemReached == false){
				outcomeScoresMap = currentGenomeOutcomeScoresMap
				passesRulesMap = currentGenomePassesRulesMap
				firstItemReached = true
				continue
			}

			areEqual := maps.Equal(currentGenomeOutcomeScoresMap, outcomeScoresMap)
			if (areEqual == false){
				// A conflict exists
				return true, nil
			}
			areEqual = maps.Equal(currentGenomePassesRulesMap, passesRulesMap)
			if (areEqual == false){
				// A conflict exists
				return true, nil
			}
		}

		return false, nil
	}

	conflictExists, err := getConflictExistsBool()
	if (err != nil) { return emptyPersonTraitInfo, err }

	newPersonTraitInfoObject.ConflictExists = conflictExists

	return newPersonTraitInfoObject, nil
}


//Outputs:
//	-int: Base pair disease locus risk weight
//	-bool: Base pair disease locus odds ratio known
//	-float64: Base pair disease locus odds ratio
//	-error
func GetGenomePolygenicDiseaseLocusRiskInfo(locusRiskWeightsMap map[string]int, locusOddsRatiosMap map[string]float64, locusBase1Value string, locusBase2Value string)(int, bool, float64, error){

	locusBasePairJoined := locusBase1Value + ";" + locusBase2Value

	riskWeight, exists := locusRiskWeightsMap[locusBasePairJoined]
	if (exists == false){
		// This is an unknown base combination
		// We will treat it as a 0 risk weight
		return 0, true, 1, nil
	}

	if (riskWeight == 0){
		return 0, true, 1, nil
	}

	oddsRatio, exists := locusOddsRatiosMap[locusBasePairJoined]
	if (exists == false){
		return riskWeight, false, 0, nil
	}

	return riskWeight, true, oddsRatio, nil
}

// This function checks to see if a genome will pass a trait rule
// Outputs:
//	-bool: Genome passes trait rule status is known
//	-bool: Genome passes trait rule
//	-error
func GetGenomePassesTraitRuleStatus(ruleLociList []traits.RuleLocus, genomeMap map[int64]locusValue.LocusValue, checkForAliases bool)(bool, bool, error){

	// We check to see if genome passes all rule loci
	// To pass a rule, all of the rule's loci must be passed by the provided genome
	// We consider a rule Known if the genome either passes all loci, or fails to pass 1 locus
	// We consider a rule Unknown if any loci are unknown, and there are no rules which are known not to be passed

	anyLocusIsUnknown := false

	for _, locusObject := range ruleLociList{

		locusRSID := locusObject.LocusRSID

		locusBasePairKnown, locusBase1, locusBase2, _, _, err := GetLocusValueFromGenomeMap(checkForAliases, genomeMap, locusRSID)
		if (err != nil) { return false, false, err }
		if (locusBasePairKnown == false){
			anyLocusIsUnknown = true
			// We keep searching to see if any of the rule's loci are known to not pass
			continue
		}

		locusBasePairJoined := locusBase1 + ";" + locusBase2

		locusBasePairsList := locusObject.BasePairsList

		genomePassesRuleLocus := slices.Contains(locusBasePairsList, locusBasePairJoined)
		if (genomePassesRuleLocus == false){
			// The genome has failed to pass a single rule locus, thus, the rule is not passed
			return true, false, nil
		}
	}

	if (anyLocusIsUnknown == true){
		// The rule is not passed, but it's status is unknown
		// There were no rules which were known not to pass
		return false, false, nil
	}

	// All rules were passed

	return true, true, nil
}


// This function will retrieve the base pair of the locus from the input genome map
// We use this function because each rsID has aliases, so we must sometimes check those aliases to find locus values
//
// Outputs:
//	-bool: Valid base pair value found
//	-string: Base 1 Value (Nucleotide base for the SNP)
//	-string: Base 2 Value (Nucleotide base for the SNP)
//	-bool: Locus base pair is phased
//	-locusValue.LocusValue
//	-error
func GetLocusValueFromGenomeMap(checkForAliases bool, inputGenomeMap map[int64]locusValue.LocusValue, locusRSID int64)(bool, string, string, bool, locusValue.LocusValue, error){

	// Outputs:
	//	-bool: Locus value found
	//	-locusValue.LocusValue
	//	-error
	getLocusValue := func()(bool, locusValue.LocusValue, error){

		currentLocusValue, exists := inputGenomeMap[locusRSID]
		if (exists == true){
			return true, currentLocusValue, nil
		}

		if (checkForAliases == false){
			return false, locusValue.LocusValue{}, nil
		}

		// We check for aliases

		anyAliasesExist, rsidAliasesList, err := locusMetadata.GetRSIDAliases(locusRSID)
		if (err != nil) { return false, locusValue.LocusValue{}, err }
		if (anyAliasesExist == false){
			return false, locusValue.LocusValue{}, nil
		}

		for _, rsidAlias := range rsidAliasesList{

			currentLocusValue, exists := inputGenomeMap[rsidAlias]
			if (exists == true){
				return true, currentLocusValue, nil
			}
		}

		return false, locusValue.LocusValue{}, nil
	}

	locusValueFound, locusValueObject, err := getLocusValue()
	if (err != nil) { return false, "", "", false, locusValue.LocusValue{}, err }
	if (locusValueFound == false){
		return false, "", "", false, locusValue.LocusValue{}, nil
	}

	base1Value := locusValueObject.Base1Value
	base2Value := locusValueObject.Base2Value
	locusIsPhased := locusValueObject.LocusIsPhased

	return true, base1Value, base2Value, locusIsPhased, locusValueObject, nil
}