//package org.broadinstitute.sting.gatk.refdata;
//
//import org.broadinstitute.sting.BaseTest;
//import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
//import org.broadinstitute.sting.utils.StingException;
//import org.broadinstitute.sting.utils.GenomeLocParser;
//import org.broadinstitute.sting.utils.GenomeLoc;
//import org.junit.BeforeClass;
//import org.junit.Test;
//import org.junit.Assert;
//
//import java.io.File;
//import java.io.FileNotFoundException;
//import java.io.BufferedReader;
//import java.io.FileReader;
//import java.util.*;
//
///**
// * Created by IntelliJ IDEA.
// * User: Ghost
// * Date: Jan 22, 2010
// * Time: 11:27:33 PM
// * To change this template use File | Settings | File Templates.
// */
//public class PlinkRodTest extends BaseTest {
//    private static IndexedFastaSequenceFile seq;
//
//    @BeforeClass
//    public static void beforeTests() {
//        try {
//            seq = new IndexedFastaSequenceFile(new File(oneKGLocation + "reference/human_b36_both.fasta"));
//        } catch (FileNotFoundException e) {
//            throw new StingException("unable to load the sequence dictionary");
//        }
//        GenomeLocParser.setupRefContigOrdering(seq);
//
//    }
//
//    public BufferedReader openFile(String filename) {
//        try {
//            return new BufferedReader(new FileReader(filename));
//        } catch (FileNotFoundException e) {
//            throw new StingException("Couldn't open file " + filename);
//        }
//
//    }
//
//    @Test
//    public void testStandardPedFile() {
//        PlinkRod rod = new PlinkRod("test");
//        try {
//            rod.initialize( new File("/humgen/gsa-hpprojects/GATK/data/Validation_Data/test/plink_rod_test/standard_plink_test.ped") );
//        } catch ( FileNotFoundException e ) {
//            throw new StingException("test file for testStandardPedFile() does not exist",e);
//        }
//
//        // test that the sample names are correct
//
//        List<String> rodNames = rod.getVariantSampleNames();
//        List<String> expectedNames = Arrays.asList("NA12887","NAMELY","COWBA");
//
//        Assert.assertEquals("That there are as many samples in the rod as in the expected list",expectedNames.size(),rodNames.size());
//
//        boolean namesCorrect = true;
//        for ( int i = 0; i < expectedNames.size(); i++ ) {
//            namesCorrect = namesCorrect && ( rodNames.get(i).equals(expectedNames.get(i)) );
//        }
//
//        Assert.assertTrue("That the names are correct and in the proper order",namesCorrect);
//
//        // test that rod can be iterated over
//
//        ArrayList<ArrayList<Genotype>> genotypesInRod = new ArrayList<ArrayList<Genotype>>();
//        ArrayList<ArrayList<String>> sampleNamesInRod = new ArrayList<ArrayList<String>>();
//        ArrayList<GenomeLoc> lociInRod = new ArrayList<GenomeLoc>();
//        do {
//            genotypesInRod.add(rod.getGenotypes());
//            sampleNamesInRod.add(rod.getVariantSampleNames());
//            lociInRod.add(rod.getLocation());
//        } while ( rod.parseLine(null,null) );
//
//        Assert.assertEquals("That there are three SNPs in the ROD",3,genotypesInRod.size());
//
//        ArrayList<Genotype> snp1 = genotypesInRod.get(0);
//        ArrayList<Genotype> snp3 = genotypesInRod.get(2);
//
//        Assert.assertEquals("That there are three Genotypes in SNP 1",3,snp1.size());
//        Assert.assertEquals("That there are three samples in SNP 2", 3, sampleNamesInRod.get(1).size());
//        Assert.assertEquals("That there are three Genotypes in SNP 3",3,snp3.size());
//
//
//        List<Allele> snp1_individual3_alleles = snp1.get(2).getAlleles();
//        List<Allele> snp3_individual2_alleles = snp3.get(1).getAlleles();
//
//        String alleleStr1 = snp1_individual3_alleles.get(0).getBases()+snp1_individual3_alleles.get(1).getBases();
//        String alleleStr2 = snp3_individual2_alleles.get(0).getBases()+snp3_individual2_alleles.get(1).getBases();
//
//        Assert.assertEquals("That the third genotype of snp 1 is correctly no-call","00",alleleStr1);
//        Assert.assertEquals("That the second genotype of snp 3 is correctly G G","GG",alleleStr2);
//
//        boolean name2isSame = true;
//
//        for ( ArrayList<String> names : sampleNamesInRod ) {
//            name2isSame = name2isSame && names.get(1).equals("NAMELY");
//        }
//
//        Assert.assertTrue("That the second name of all the genotypes is the same and is correct",name2isSame);
//
//        // test that the loci are correctly parsed and in order
//
//        List<String> expectedLoci = Arrays.asList("1:123456","2:13274","3:11111");
//        boolean lociCorrect = true;
//        for ( int i = 0; i < 3; i ++ ) {
//            lociCorrect = lociCorrect && lociInRod.get(i).toString().equals(expectedLoci.get(i));
//        }
//    }
//
//    @Test
//    public void testStandardPedFileWithIndels() {
//        PlinkRod rod = new PlinkRod("test");
//        try {
//            rod.initialize(new File("/humgen/gsa-hpprojects/GATK/data/Validation_Data/test/plink_rod_test/standard_plink_with_indels.ped") );
//        } catch ( FileNotFoundException e) {
//            throw new StingException("Test file for testStandardPedFileWithIndels() could not be found", e);
//        }
//
//        // Iterate through the rod
//
//        List<ArrayList<Genotype>> genotypesInRod = new ArrayList<ArrayList<Genotype>>();
//        ArrayList<ArrayList<String>> sampleNamesInRod = new ArrayList<ArrayList<String>>();
//        ArrayList<GenomeLoc> lociInRod = new ArrayList<GenomeLoc>();
//        ArrayList<Boolean> snpSites = new ArrayList<Boolean>();
//        do {
//            genotypesInRod.add(rod.getGenotypes());
//            sampleNamesInRod.add(rod.getVariantSampleNames());
//            lociInRod.add(rod.getLocation());
//            snpSites.add(rod.variantIsSNP());
//        } while ( rod.parseLine(null,null) );
//
//        boolean snpOrder = true;
//        List<Boolean> expectedOrder = Arrays.asList(true,false,true,false);
//        for ( int i = 0; i < 4; i ++ ) {
//            snpOrder = snpOrder && ( expectedOrder.get(i) == snpSites.get(i) );
//        }
//
//        Assert.assertTrue("That the variant type order is as expected", snpOrder);
//        Assert.assertTrue("That the second genotype of second variant is not a point mutation", ! genotypesInRod.get(1).get(1).isPointGenotype() );
//        Assert.assertTrue("That the second genotype of fourth variant is not a point mutation", ! genotypesInRod.get(3).get(1).isPointGenotype() );
//        Assert.assertTrue("That the second genotype of fourth variant is homozygous", genotypesInRod.get(3).get(1).isHom());
//        Assert.assertTrue("That the fourth genotype of fourth variant is heterozygous",genotypesInRod.get(3).get(3).isHet());
//        Assert.assertEquals("That the reference deletion genotype has the correct string", "ATTTAT",genotypesInRod.get(3).get(2).getAlleles().get(0).getBases());
//        Assert.assertEquals("That the insertion bases are correct","CTC",genotypesInRod.get(1).get(2).getAlleles().get(0).getBases());
//        Assert.assertEquals("That the snp bases are correct","GC",genotypesInRod.get(2).get(2).getAlleles().get(0).getBases()+genotypesInRod.get(2).get(2).getAlleles().get(1).getBases());
//    }
//
//    @Test
//    public void testBinaryPedFileNoIndels() {
//        PlinkRod rod = new PlinkRod("binaryTest1");
//        try {
//            rod.initialize(new File("/humgen/gsa-hpprojects/GATK/data/Validation_Data/test/plink_rod_test/binary_noindel_test.bed"));
//        } catch (FileNotFoundException e) {
//            throw new StingException("Test file for testBinaryPedFileNoIndels() could not be found",e);
//        }
//
//        // iterate through the ROD and get stuff
//        ArrayList<GenomeLoc> lociInRod = new ArrayList<GenomeLoc>();
//        ArrayList<ArrayList<Genotype>> genotypesInRod = new ArrayList<ArrayList<Genotype>>();
//        ArrayList<ArrayList<String>> samplesInRod = new ArrayList<ArrayList<String>>();
//
//        do {
//            lociInRod.add(rod.getLocation());
//            genotypesInRod.add(rod.getGenotypes());
//            samplesInRod.add(rod.getVariantSampleNames());
//        } while ( rod.parseLine(null,null) );
//
//        List<String> expecLoc = Arrays.asList("1:123456","1:14327877","2:22074511","3:134787","3:178678","4:829645","4:5234132","12:1268713");
//
//        for ( int i = 0; i < expecLoc.size(); i ++ ) {
//            Assert.assertEquals("That locus "+(i+1)+" in the rod is correct", expecLoc.get(i), lociInRod.get(i).toString());
//        }
//
//        List<String> expecAlleles = Arrays.asList("AA","AA","AA","GG","GG","GG","AA","TA","TT","CC","CC","GC","TC","CC","TT",
//                                                  "GG","GG","AG","TT","CC","CT","TG","GG","GG");
//        List<Boolean> expecHet = Arrays.asList(false,false,false,false,false,false,false,true,false,false,false,true,true,false,
//                    false,false,false,true,false,false,true,true,false,false);
//        List<String> expecName = Arrays.asList("NA12878","NA12890","NA07000","NA12878","NA12890","NA07000","NA12878","NA12890","NA07000",
//                    "NA12878","NA12890","NA07000","NA12878","NA12890","NA07000","NA12878","NA12890","NA07000","NA12878","NA12890","NA07000",
//                "NA12878","NA12890","NA07000");
//        int snpNo = 1;
//        int indiv = 1;
//        int alleleOffset = 0;
//        for ( ArrayList<Genotype> snp : genotypesInRod ) {
//            for ( Genotype gen : snp ) {
//                String alStr = gen.getAlleles().get(0).getBases()+gen.getAlleles().get(1).getBases();
//                Assert.assertEquals("That the allele of person "+indiv+" for snp "+snpNo+" is correct "+
//                                    "(allele offset "+alleleOffset+")", expecAlleles.get(alleleOffset),alStr);
//                Assert.assertEquals("That the genotype of person "+indiv+" for snp "+snpNo+" is properly set", expecHet.get(alleleOffset),gen.isHet());
//                Assert.assertEquals("That the name of person "+indiv+" for snp "+snpNo+" is correct", expecName.get(alleleOffset),samplesInRod.get(snpNo-1).get(indiv-1));
//                indiv++;
//                alleleOffset++;
//            }
//            indiv = 1;
//            snpNo++;
//        }
//    }
//
//    @Test
//    public void testIndelBinary() {
//        PlinkRod rod = new PlinkRod("binaryTest2");
//        try {
//            rod.initialize(new File("/humgen/gsa-hpprojects/GATK/data/Validation_Data/test/plink_rod_test/binary_indel_test.bed"));
//        } catch (FileNotFoundException e) {
//            throw new StingException("Test file for testBinaryPedFileNoIndels() could not be found",e);
//        }
//
//        ArrayList<ArrayList<Genotype>> genotypesInRod = new ArrayList<ArrayList<Genotype>>();
//        do {
//            genotypesInRod.add(rod.getGenotypes());
//        } while ( rod.parseLine(null,null) );
//
//        List<String> expecAlleles = Arrays.asList("ACCA","","ACCAACCA","GGGG","GG","","AA","TA","00","","CCTCCT","CCT",
//                    "TC","CC","TT","GG","GG","AG","","CTTGCTTG","CTTG","TG","GG","GG");
//        List<Boolean> expecDeletion = Arrays.asList(false,false,false,false,false,false,false,false,false,true,false,true,
//                    false,false,false,false,false,false,true,false,true,false,false,false);
//        List<Boolean> expecInsertion = Arrays.asList(true,false,true,true,true,false,false,false,false,false,false,false,
//                    false,false,false,false,false,false,false,false,false,false,false,false);
//
//        int al = 0;
//        for ( ArrayList<Genotype> snp : genotypesInRod ) {
//            for ( Genotype gen : snp ) {
//                String alStr = gen.getAlleles().get(0).getBases()+gen.getAlleles().get(1).getBases();
//                Allele firstAl = gen.getAlleles().get(0);
//                Allele secondAl = gen.getAlleles().get(1);
//                boolean isInsertion = ( firstAl.getType() == Allele.AlleleType.INSERTION || secondAl.getType() == Allele.AlleleType.INSERTION );
//                boolean isDeletion =  ( firstAl.getType() == Allele.AlleleType.DELETION || secondAl.getType() == Allele.AlleleType.DELETION );
//                Assert.assertEquals("That the indel file has the correct alleles for genotype "+al,expecAlleles.get(al), alStr);
//                Assert.assertEquals("That the insertion property of genotype "+al+" is correct",expecInsertion.get(al),isInsertion);
//                Assert.assertEquals("That the deletion property of genotype "+al+" is correct", expecDeletion.get(al), isDeletion);
//                al++;
//            }
//        }
//    }
//}