Empty unit tests for VariantContextUtils

-- will be expanded over the day

public/java/src/org/broadinstitute/sting/utils/variantcontext/Genotype.java

@@ -25,15 +25,32 @@ public class Genotype {
     protected boolean isPhased = false;
     protected boolean filtersWereAppliedToContext;
 
-    public Genotype(String sampleName, List<Allele> alleles, double negLog10PError, Set<String> filters, Map<String, ?> attributes, boolean isPhased) {
+    public Genotype(String sampleName, List<Allele> alleles, double negLog10PError, Set<String> filters, Map<String, ? super Object> attributes, boolean isPhased) {
+        this(sampleName, alleles, negLog10PError, filters, attributes, isPhased, null);
+    }
+
+    public Genotype(String sampleName, List<Allele> alleles, double negLog10PError, Set<String> filters, Map<String, ? super Object> attributes, boolean isPhased, double[] log10Likelihoods) {
         if ( alleles != null )
             this.alleles = Collections.unmodifiableList(alleles);
+        if ( log10Likelihoods != null )
+            attributes.put(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY, GenotypeLikelihoods.fromLog10Likelihoods(log10Likelihoods));
         commonInfo = new InferredGeneticContext(sampleName, negLog10PError, filters, attributes);
         filtersWereAppliedToContext = filters != null;
         this.isPhased = isPhased;
         validate();
     }
 
+    /**
+     * Creates a new Genotype for sampleName with genotype according to alleles.
+     * @param sampleName
+     * @param alleles
+     * @param negLog10PError the confidence in these alleles
+     * @param log10Likelihoods a log10 likelihoods for each of the genotype combinations possible for alleles, in the standard VCF ordering, or null if not known
+     */
+    public Genotype(String sampleName, List<Allele> alleles, double negLog10PError, double[] log10Likelihoods) {
+        this(sampleName, alleles, negLog10PError, null, null, false, log10Likelihoods);
+    }
+
     public Genotype(String sampleName, List<Allele> alleles, double negLog10PError) {
         this(sampleName, alleles, negLog10PError, null, null, false);
     }

public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUnitTest.java

@@ -5,6 +5,7 @@ package org.broadinstitute.sting.utils.variantcontext;
 // the imports for unit testing.
 
 
+import org.broadinstitute.sting.BaseTest;
 import org.testng.Assert;
 import org.testng.annotations.BeforeSuite;
 import org.testng.annotations.BeforeTest;
@@ -14,10 +15,7 @@ import java.util.Arrays;
 import java.util.List;
 
 
-/**
+public class VariantContextUnitTest extends BaseTest {
- * Basic unit test for RecalData
- */
-public class VariantContextUnitTest {
     Allele A, Aref, T, Tref;
     Allele del, delRef, ATC, ATCref;
 

public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUtilsUnitTest.java

@@ -0,0 +1,84 @@
+/*
+ * Copyright (c) 2011, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+// our package
+package org.broadinstitute.sting.utils.variantcontext;
+
+
+// the imports for unit testing.
+
+
+import net.sf.picard.reference.IndexedFastaSequenceFile;
+import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.sting.gatk.refdata.tracks.FeatureManager;
+import org.broadinstitute.sting.utils.GenomeLocParser;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
+import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
+import org.testng.Assert;
+import org.testng.annotations.BeforeSuite;
+import org.testng.annotations.Test;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.util.*;
+
+
+public class VariantContextUtilsUnitTest extends BaseTest {
+    Allele Aref, T, delRef, ATC;
+    Genotype snp1, snp2, indel1;
+    private GenomeLocParser genomeLocParser;
+
+    @BeforeSuite
+    public void setup() {
+        final File referenceFile = new File(b37KGReference);
+        try {
+            IndexedFastaSequenceFile seq = new CachingIndexedFastaSequenceFile(referenceFile);
+            genomeLocParser = new GenomeLocParser(seq);
+        }
+        catch(FileNotFoundException ex) {
+            throw new UserException.CouldNotReadInputFile(referenceFile,ex);
+        }
+
+        // alleles
+        Aref = Allele.create("A", true);
+        delRef = Allele.create("-", true);
+        T = Allele.create("T");
+        ATC = Allele.create("ATC");
+
+        snp1 = new Genotype("snp1", Arrays.asList(Aref,T), 10, new double[]{10, 0, 20});
+        snp2 = new Genotype("snp2", Arrays.asList(T,T), 15, new double[]{25, 15, 0});
+        indel1 = new Genotype("indel1", Arrays.asList(delRef,ATC), 20, new double[]{20, 0, 30});
+    }
+
+    private VariantContext makeVC(String source, List<Allele> alleles) {
+        return makeVC(source, alleles, null, null);
+    }
+
+    private VariantContext makeVC(String source, List<Allele> alleles, Collection<Genotype> genotypes, Set<String> filters) {
+        int start = 10;
+        int stop = alleles.contains(ATC) ? start + 3 : start;
+        return new VariantContext(source, "1", start, stop, alleles, genotypes, 1.0, filters, null);
+    }
+}