Added more tests and documentation

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PhasingUtils.java

@@ -74,7 +74,7 @@ class PhasingUtils {
      * @param vc1 variant 1
      * @param vc2 variant 2
      * @param referenceFile sequence file containing the reference genome
-     * @param alleleMergeRule
+     * @param alleleMergeRule rule for merging variants
      * @return merged variant or null if the variants are NOT an SNP or MNP, on the same contig, variant location 1 is the same or after the  variant location 2,
      * their genotypes do NOT have the same number of chromosomes, haplotype, number of attributes as chromosomes, are both hetrozygous or do not abide by the merge rule
      */
@@ -98,7 +98,7 @@ class PhasingUtils {
     /**
      * Find the alleles with the same haplotype
      * assumes alleleSegregationIsKnown
-     * TODO - should alleleSegregationIsKnown be called within the method?
+     * TODO - should alleleSegregationIsKnown be called within this method?
      *
      * @param gt1 genotype 1
      * @param gt2 genotype 2
@@ -160,13 +160,13 @@ class PhasingUtils {
     }
 
     /**
+     * Merge variants into an MNP
      *
      * @param vc1 variant 1
      * @param vc2 variant 2
      * @param referenceFile sequence file containing the reference genome
      * @return variant with the merged MNP
      */
-
     static VariantContext reallyMergeIntoMNP(VariantContext vc1, VariantContext vc2, ReferenceSequenceFile referenceFile) {
         final int startInter = vc1.getEnd() + 1;
         final int endInter = vc2.getStart() - 1;
@@ -246,23 +246,28 @@ class PhasingUtils {
     }
 
     /**
+     * Get preset attributes and whether they are in vc1 or vc2
+     * TODO: Will always return an empty map because MERGE_OR_ATTRIBS is empty
      *
-     * @param vc1
+     * @param vc1 variant 1
-     * @param vc2
+     * @param vc2 variant 2
-     * @return merged variant attributes
+     * @return whether the preset attributes are in vc1 or vc2
      */
     static Map<String, Object> mergeVariantContextAttributes(VariantContext vc1, VariantContext vc2) {
+        // Map of attribute name to value
         Map<String, Object> mergedAttribs = new HashMap<String, Object>();
 
         final List<VariantContext> vcList = new LinkedList<VariantContext>();
         vcList.add(vc1);
         vcList.add(vc2);
 
+        // Attribute of interest
         //String[] MERGE_OR_ATTRIBS = {VCFConstants.DBSNP_KEY};
         final String[] MERGE_OR_ATTRIBS = {};
         for (String orAttrib : MERGE_OR_ATTRIBS) {
             boolean attribVal = false;
             for (VariantContext vc : vcList) {
+                // Does the variant have the attribute?
                 attribVal = vc.getAttributeAsBoolean(orAttrib, false);
                 if ( attribVal ) // already true, so no reason to continue:
                     break;
@@ -335,6 +340,8 @@ class PhasingUtils {
         // Check that each sample's genotype in vc2 is uniquely appendable onto its genotype in vc1
         for (final Genotype gt1 : vc1.getGenotypes()) {
             final Genotype gt2 = vc2.getGenotype(gt1.getSampleName());
+            if ( gt2 == null ) // gt2 does not have sample name
+                return false;
 
             if (!alleleSegregationIsKnown(gt1, gt2)) // can merge if: phased, or if either is a hom
                 return false;
@@ -385,7 +392,6 @@ class PhasingUtils {
      * @param vc2 variant 2
      * @return true if there is a sample with alternate alleles, false otherwise
      */
-
     static boolean someSampleHasDoubleNonReferenceAllele(VariantContext vc1, VariantContext vc2) {
         for (final Genotype gt1 : vc1.getGenotypes()) {
             final Genotype gt2 = vc2.getGenotype(gt1.getSampleName());
@@ -404,13 +410,12 @@ class PhasingUtils {
     }
 
     /**
-     * Check that Alleles at vc1 and at vc2 always segregate together in all samples (including reference
+     * Check that Alleles at vc1 and at vc2 always segregate together in all samples (including reference)
      *
      * @param vc1 variant 1
      * @param vc2 variant 2
      * @return true if
      */
-
     static boolean doubleAllelesSegregatePerfectlyAmongSamples(VariantContext vc1, VariantContext vc2) {
         final Map<Allele, Allele> allele1ToAllele2 = new HashMap<Allele, Allele>();
         final Map<Allele, Allele> allele2ToAllele1 = new HashMap<Allele, Allele>();
@@ -527,12 +532,12 @@ class PhasingUtils {
         private int intermediateLength;
 
         /**
+         * Constructor
          *
-         * @param intermediateBases
+         * @param intermediateBases array of bases
          * @param vc1 variant 1
          * @param vc2 variant 2
          */
-
         public MergedAllelesData(byte[] intermediateBases, VariantContext vc1, VariantContext vc2) {
             this.mergedAlleles = new HashMap<AlleleOneAndTwo, Allele>(); // implemented equals() and hashCode() for AlleleOneAndTwo
             this.intermediateBases = intermediateBases;
@@ -545,7 +550,7 @@ class PhasingUtils {
          *
          * @param all1 allele 1
          * @param all2 allele 2
-         * @return
+         * @return merged allele
          */
         public Allele ensureMergedAllele(Allele all1, Allele all2) {
             return ensureMergedAllele(all1, all2, false); // false <-> since even if all1+all2 = reference, it was already created in the constructor

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/phasing/PhasingUtilsUnitTest.java

@@ -56,8 +56,8 @@ import htsjdk.variant.variantcontext.*;
 import java.io.File;
 import java.io.FileNotFoundException;
 import java.util.ArrayList;
-import java.util.Arrays;
 import java.util.List;
+
 import org.broadinstitute.gatk.utils.GenomeLocParser;
 import org.broadinstitute.gatk.utils.BaseTest;
 import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile;
@@ -79,54 +79,152 @@ public class PhasingUtilsUnitTest extends BaseTest  {
     @Test
     public void TestMatchHaplotypeAllelesKeyHP() {
 
-        final List<Allele> alleleList = new ArrayList<>();
+        final List<Allele> alleleList1 = new ArrayList<>();
-        alleleList.add(Allele.create("T", false));
+        alleleList1.add(Allele.create("T", false));
-        alleleList.add(Allele.create("C", false));
+        alleleList1.add(Allele.create("C", false));
-        String samelpName = "TC";
+        final Genotype genotype1 = new GenotypeBuilder("TC").attribute("HP", new String[]{"10-1", "10-2"}).alleles(alleleList1).make();
-        final Genotype genotypeALT = new GenotypeBuilder(samelpName).attribute("HP", new String[]{"10-1", "10-2"}).alleles(alleleList).make();
 
-        // Must match because the same genotype
+        // Attributes in different order
-        PhasingUtils.SameHaplotypeAlleles sameHaplotypeAlleles = PhasingUtils.matchHaplotypeAlleles(genotypeALT, genotypeALT);
+        final List<Allele> alleleList2 = new ArrayList<>();
+        alleleList2.add(Allele.create("G", false));
+        alleleList2.add(Allele.create("A", false));
+        final Genotype genotype2 = new GenotypeBuilder("GA").attribute("HP", new String[]{"10-2", "10-1"}).alleles(alleleList2).make();
+
+        PhasingUtils.SameHaplotypeAlleles sameHaplotypeAlleles = PhasingUtils.matchHaplotypeAlleles(genotype1, genotype2);
 
         PhasingUtils.SameHaplotypeAlleles sameHaplotypeAllelesAnswer = new PhasingUtils.SameHaplotypeAlleles();
-        sameHaplotypeAllelesAnswer.hapAlleles.add(new PhasingUtils.AlleleOneAndTwo(Allele.create("T", false), Allele.create("T", false)));
+        sameHaplotypeAllelesAnswer.hapAlleles.add(new PhasingUtils.AlleleOneAndTwo(Allele.create("T", false), Allele.create("A", false)));
-        sameHaplotypeAllelesAnswer.hapAlleles.add(new PhasingUtils.AlleleOneAndTwo(Allele.create("C", false), Allele.create("C", false)));
+        sameHaplotypeAllelesAnswer.hapAlleles.add(new PhasingUtils.AlleleOneAndTwo(Allele.create("C", false), Allele.create("G", false)));
+        sameHaplotypeAllelesAnswer.requiresSwap = true;
+
         Assert.assertEquals(sameHaplotypeAlleles.hapAlleles, sameHaplotypeAllelesAnswer.hapAlleles);
         Assert.assertEquals(sameHaplotypeAlleles.requiresSwap, sameHaplotypeAllelesAnswer.requiresSwap);
     }
 
     @Test
-    public void TestMatchHaplotypeAllelesNotKeyHP() {
+    public void TestMatchHaplotypeAllelesNoKeyHP() {
 
-        final List<Allele> alleleList = new ArrayList<>();
+        final List<Allele> alleleList1 = new ArrayList<>();
-        alleleList.add(Allele.create("T", false));
+        alleleList1.add(Allele.create("T", false));
-        alleleList.add(Allele.create("C", false));
+        alleleList1.add(Allele.create("C", false));
-        final Genotype genotypeALT = new GenotypeBuilder("TC").PL(new int[]{0, 100, 1000}).alleles(alleleList).make();
+        final Genotype genotype1 = new GenotypeBuilder("TC").alleles(alleleList1).make();
+
+        // Attributes in different order
+        final List<Allele> alleleList2 = new ArrayList<>();
+        alleleList2.add(Allele.create("G", false));
+        alleleList2.add(Allele.create("A", false));
+        final Genotype genotype2 = new GenotypeBuilder("GA").alleles(alleleList2).make();
 
         // Must match because the same genotype
-        PhasingUtils.SameHaplotypeAlleles sameHaplotypeAlleles = PhasingUtils.matchHaplotypeAlleles(genotypeALT, genotypeALT);
+        PhasingUtils.SameHaplotypeAlleles sameHaplotypeAlleles = PhasingUtils.matchHaplotypeAlleles(genotype1, genotype2);
 
         PhasingUtils.SameHaplotypeAlleles sameHaplotypeAllelesAnswer = new PhasingUtils.SameHaplotypeAlleles();
-        sameHaplotypeAllelesAnswer.hapAlleles.add(new PhasingUtils.AlleleOneAndTwo(Allele.create("T", false), Allele.create("T", false)));
+        sameHaplotypeAllelesAnswer.hapAlleles.add(new PhasingUtils.AlleleOneAndTwo(Allele.create("T", false), Allele.create("G", false)));
-        sameHaplotypeAllelesAnswer.hapAlleles.add(new PhasingUtils.AlleleOneAndTwo(Allele.create("C", false), Allele.create("C", false)));
+        sameHaplotypeAllelesAnswer.hapAlleles.add(new PhasingUtils.AlleleOneAndTwo(Allele.create("C", false), Allele.create("A", false)));
         Assert.assertEquals(sameHaplotypeAlleles.hapAlleles, sameHaplotypeAllelesAnswer.hapAlleles);
         Assert.assertEquals(sameHaplotypeAlleles.requiresSwap, sameHaplotypeAllelesAnswer.requiresSwap);
     }
 
     @Test
-    public void TestMergeIntoMNPvalidationCheck() {
+    public void TestMergeIntoMNPvalidationTrueCheck() {
-        String source = new String("test");
+        final String contig = new String("1");
-        String contig = new String("1");
         final List<Allele> alleleList1 = new ArrayList<>();
         alleleList1.add(Allele.create("T", true));
         alleleList1.add(Allele.create("C", false));
         final List<Allele> alleleList2 = new ArrayList<>();
         alleleList2.add(Allele.create("A", true));
-        alleleList2.add(Allele.create("CC", false));
+        alleleList2.add(Allele.create("C", false));
-        final VariantContext variantContext1 = new VariantContextBuilder(source, contig, start, start, alleleList1).make();
+        final VariantContext vc1 = new VariantContextBuilder("TC", contig, start, start, alleleList1).make();
-        final VariantContext variantContext2 = new VariantContextBuilder(source, contig, start, start, alleleList2).make();
+        final VariantContext vc2 = new VariantContextBuilder("AC", contig, start+1, start+1, alleleList2).make();
         GenomeLocParser genomeLocParser = new GenomeLocParser(referenceFile);
 
-        Assert.assertFalse(PhasingUtils.mergeIntoMNPvalidationCheck(genomeLocParser, variantContext1, variantContext1));
+        Assert.assertTrue(PhasingUtils.mergeIntoMNPvalidationCheck(genomeLocParser, vc1, vc2));
+    }
+
+    @Test
+    public void TestMergeIntoMNPvalidationCheckLocBefore() {
+        final String contig = new String("1");
+        final List<Allele> alleleList1 = new ArrayList<>();
+        alleleList1.add(Allele.create("T", true));
+        alleleList1.add(Allele.create("C", false));
+        final List<Allele> alleleList2 = new ArrayList<>();
+        alleleList2.add(Allele.create("A", true));
+        alleleList2.add(Allele.create("C", false));
+        final VariantContext vc1 = new VariantContextBuilder("TC", contig, start+1, start+1, alleleList1).make();
+        final VariantContext vc2 = new VariantContextBuilder("AC", contig, start, start, alleleList2).make();
+        GenomeLocParser genomeLocParser = new GenomeLocParser(referenceFile);
+
+        Assert.assertFalse(PhasingUtils.mergeIntoMNPvalidationCheck(genomeLocParser, vc1, vc2));
+    }
+
+    @Test
+    public void TestMergeIntoMNPvalidationDiffContigs() {
+        final String contig1 = new String("1");
+        final String contig2 = new String("2");
+        final List<Allele> alleleList1 = new ArrayList<>();
+        alleleList1.add(Allele.create("T", true));
+        alleleList1.add(Allele.create("C", false));
+        final List<Allele> alleleList2 = new ArrayList<>();
+        alleleList2.add(Allele.create("A", true));
+        alleleList2.add(Allele.create("C", false));
+        final VariantContext vc1 = new VariantContextBuilder("TC", contig1, start+1, start+1, alleleList1).make();
+        final VariantContext vc2 = new VariantContextBuilder("AC", contig2, start, start, alleleList2).make();
+        GenomeLocParser genomeLocParser = new GenomeLocParser(referenceFile);
+
+        Assert.assertFalse(PhasingUtils.mergeIntoMNPvalidationCheck(genomeLocParser, vc1, vc2));
+    }
+
+    @Test
+    public void TestMergeVariantContextNames() {
+        final String result = new String("A_B");
+        Assert.assertEquals(result, PhasingUtils.mergeVariantContextNames("A", "B"));
+    }
+
+    @Test
+    public void TestMergeVariantContextAttributes() {
+        final String contig = new String("1");
+        final List<Allele> alleleList1 = new ArrayList<>();
+        alleleList1.add(Allele.create("T", true));
+        alleleList1.add(Allele.create("C", false));
+        final List<Allele> alleleList2 = new ArrayList<>();
+        alleleList2.add(Allele.create("A", true));
+        alleleList2.add(Allele.create("C", false));
+        final VariantContext vc1 = new VariantContextBuilder("TC", contig, start, start, alleleList1).make();
+        final VariantContext vc2 = new VariantContextBuilder("AC", contig, start+1, start+1, alleleList2).make();
+
+        Assert.assertEquals(0, PhasingUtils.mergeVariantContextAttributes(vc1, vc2).size());
+    }
+
+    @Test
+    public void TestAllSamplesAreMergeableDiffSampleNames() {
+        final String contig = new String("1");
+        final List<Allele> alleleList1 = new ArrayList<>();
+        alleleList1.add(Allele.create("T", true));
+        alleleList1.add(Allele.create("C", false));
+        final List<Allele> alleleList2 = new ArrayList<>();
+        alleleList2.add(Allele.create("A", true));
+        alleleList2.add(Allele.create("C", false));
+
+        final Genotype g1 = new GenotypeBuilder().name("sample1").alleles(alleleList1).make();
+        final VariantContext vc1 = new VariantContextBuilder().chr(contig).id("id1").source("TC").start(start).stop(start).alleles(alleleList1).genotypes(g1).make();
+        Genotype g2 = new GenotypeBuilder().name("sample2").alleles(alleleList2).make();
+        final VariantContext vc2 = new VariantContextBuilder().chr(contig).id("i21").source("AC").start(start).stop(start).alleles(alleleList2).genotypes(g2).make();
+
+        Assert.assertFalse( PhasingUtils.allSamplesAreMergeable(vc1, vc2));
+    }
+
+    @Test
+    public void TestAlleleSegregationIsKnown(){
+
+    }
+
+    @Test
+    public void TestSomeSampleHasDoubleNonReferenceAllele(){
+
+    }
+
+    @Test
+    public void TestDoubleAllelesSegregatePerfectlyAmongSamples(){
+
     }
 }

public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/BaseTest.java

@@ -96,7 +96,6 @@ public abstract class BaseTest {
     public static final String hg18Reference = "/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta";
     public static final String hg19Reference = "/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta";
     public static final String b36KGReference = "/humgen/1kg/reference/human_b36_both.fasta";
-    //public static final String b37KGReference = "/Users/depristo/Desktop/broadLocal/localData/human_g1k_v37.fasta";
     public static final String b37KGReference = "/humgen/1kg/reference/human_g1k_v37.fasta";
     public static final String b37KGReferenceWithDecoy = "/humgen/gsa-hpprojects/GATK/bundle/current/b37/human_g1k_v37_decoy.fasta";
     public static final String hg19RefereneWithChrPrefixInChromosomeNames = "/humgen/gsa-hpprojects/GATK/bundle/current/hg19/ucsc.hg19.fasta";