//read input files, insert your own

controlFile = INPUT(path="control.ped")
familyCaseFile = INPUT(path="family.chr")

controlHaplotypes = SNPHaplotypeMatrix(genotypeMatrix=controlFile, inputType="ped", 
						haploRec="PATH_TO/haplorecv2_3/haplorec")

caseHaplotypes = SNPHaplotypeMatrix(genotypeMatrix=familyCaseFile, inputType="family", 
						haploRec="PATH_TO/haplorecv2_3/haplorec")

chromosome = 12

snpMap = INPUT(path= chromosome+".map")
alleleFreqFile = INPUT(path= chromosome+".allfr")

sharedHaplotypes = HaplotypeScan(haplotypeMatrix1=caseHaplotypes,
                                haplotypeMatrix2=controlHaplotypes,
                                lociFile=snpMap,
                                alleleFrequenceFile=alleleFreqFile,
                                chromosome=chromosome,
                                w=100,
                                m=1,
                                l=80,
                                t=1,
                                markerList="A,B")

//sample names
caseRegexp="case\\d"
controlRegexp="control\\d{6}"

//filter haplotypes

filteredHaplotypes = HaploFilter(haplotypes=sharedHaplotypes,
                                snpMap=snpMap,
                                alleleFreq=alleleFreqFile,
                                haplotypeMatrix1=caseHaplotypes,
                                haplotypeMatrix2=controlHaplotypes,
                                caseRegexp=caseRegexp,
                                controlRegexp=controlRegexp,
                                infThreshold=1,
                                caseHomots=1,
                                caseHeterots=4,
				caseMethod="OR",
                                controlHomots=1,
                                controlHeterots=4,
                                controlMethod="OR",
                                compoundHomots=20,  //no compounds
                                compounds=20,
				markerList="A,B")

//score haplotypes
scores = HaplotypeScore(haplotypes = filteredHaplotypes, 
			snpMap=snpMap, 
			alleleFreq=alleleFreqFile, 
			chromosome=chromosome, 
			caseRegexp=caseRegexp, 
			controlRegexp=controlRegexp)

OUTPUT(scores.scoredHaplotypes)