Killing the final versions of old new VariantContext interface

public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java

@@ -122,7 +122,7 @@ public class BeagleOutputToVCFWalker  extends RodWalker<Integer, Integer> {
     protected static String line = null;
 
     private final double MIN_PROB_ERROR = 0.000001;
-    private final double MAX_GENOTYPE_QUALITY = 6.0;
+    private final double MAX_GENOTYPE_QUALITY = -6.0;
 
     public void initialize() {
 
@@ -292,7 +292,7 @@ public class BeagleOutputToVCFWalker  extends RodWalker<Integer, Integer> {
             if (probWrongGenotype < MIN_PROB_ERROR)
                 genotypeQuality = MAX_GENOTYPE_QUALITY;
             else
-                genotypeQuality = -log10(probWrongGenotype);
+                genotypeQuality = log10(probWrongGenotype);
 
             HashMap<String,Object> originalAttributes = new HashMap<String,Object>(g.getAttributes());
 

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

@@ -225,44 +225,6 @@ public class VariantContext implements Feature { // to enable tribble intergrati
     //
     // ---------------------------------------------------------------------------------------------------------
 
-    /**
-     * the complete constructor.  Makes a complete VariantContext from its arguments
-     * This is the only constructor that is able to create indels! DO NOT USE THE OTHER ONES.
-     *
-     * @param source          source
-     * @param contig          the contig
-     * @param start           the start base (one based)
-     * @param stop            the stop reference base (one based)
-     * @param alleles         alleles
-     * @param genotypes       genotypes map
-     * @param log10PError     qual
-     * @param filters         filters: use null for unfiltered and empty set for passes filters
-     * @param attributes      attributes
-     * @param referenceBaseForIndel   padded reference base
-     *
-     * @deprecated  replaced by {@link VariantContextBuilder}
-     */
-    @Deprecated
-    protected VariantContext(String source, String ID, String contig, long start, long stop, Collection<Allele> alleles, GenotypesContext genotypes, double log10PError, Set<String> filters, Map<String, Object> attributes, Byte referenceBaseForIndel) {
-        this(source, ID, contig, start, stop, alleles, genotypes, log10PError, filters, attributes, referenceBaseForIndel, false, ALL_VALIDATION);
-    }
-
-    /**
-     * Create a new variant context without genotypes and no Perror, no filters, and no attributes
-     *
-     * @param source          source
-     * @param contig          the contig
-     * @param start           the start base (one based)
-     * @param stop            the stop reference base (one based)
-     * @param alleles alleles
-     *
-     * @deprecated  replaced by {@link VariantContextBuilder}
-     */
-    @Deprecated
-    public VariantContext(String source, String ID, String contig, long start, long stop, Collection<Allele> alleles) {
-        this(source, ID, contig, start, stop, alleles, NO_GENOTYPES, CommonInfo.NO_LOG10_PERROR, null, null, null, false, ALL_VALIDATION);
-    }
-
     /**
      * Copy constructor
      *

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

@@ -375,8 +375,7 @@ public class VariantContextUtils {
                     genotypeAttributes, g.isPhased()));
         }
 
-        return new VariantContext(vc.getSource(), vc.getID(), vc.getChr(), vc.getStart(), vc.getEnd(),
+        return new VariantContextBuilder(vc).genotypes(genotypes).attributes(attributes).make();
-                vc.getAlleles(), genotypes, vc.getLog10PError(), vc.getFilters(), attributes, vc.getReferenceBaseForIndel());
     }
 
     public enum GenotypeMergeType {

public/java/test/org/broadinstitute/sting/gatk/refdata/RefMetaDataTrackerUnitTest.java

@@ -66,9 +66,9 @@ public class RefMetaDataTrackerUnitTest {
         C = Allele.create("C");
         G = Allele.create("G");
         T = Allele.create("T");
-        AC_SNP = new VariantContext("x", VCFConstants.EMPTY_ID_FIELD, "chr1", START_POS, START_POS, Arrays.asList(A, C));
+        AC_SNP = new VariantContextBuilder("x", "chr1", START_POS, START_POS, Arrays.asList(A, C).make());
-        AG_SNP = new VariantContext("x", VCFConstants.EMPTY_ID_FIELD, "chr1", START_POS, START_POS, Arrays.asList(A, G));
+        AG_SNP = new VariantContextBuilder("x", "chr1", START_POS, START_POS, Arrays.asList(A, G).make());
-        AT_SNP = new VariantContext("x", VCFConstants.EMPTY_ID_FIELD, "chr1", START_POS, START_POS, Arrays.asList(A, T));
+        AT_SNP = new VariantContextBuilder("x", "chr1", START_POS, START_POS, Arrays.asList(A, T).make());
         span10_10 = makeSpan(10, 10);
         span1_20 = makeSpan(1, 20);
         span10_20 = makeSpan(10, 20);

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

@@ -12,6 +12,7 @@ import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 import org.testng.Assert;
 
+import java.lang.reflect.Array;
 import java.util.*;
 
 
@@ -39,6 +40,8 @@ public class VariantContextUnitTest extends BaseTest {
     int mixedLocStart = 20;
     int mixedLocStop = 23;
 
+    VariantContextBuilder basicBuilder, snpBuilder, insBuilder;
+
     @BeforeSuite
     public void before() {
         del = Allele.create("-");
@@ -52,6 +55,10 @@ public class VariantContextUnitTest extends BaseTest {
 
         ATC = Allele.create("ATC");
         ATCref = Allele.create("ATC", true);
+
+        basicBuilder = new VariantContextBuilder("test", snpLoc,snpLocStart, snpLocStop, Arrays.asList(Aref, T)).referenceBaseForIndel((byte)'A');
+        snpBuilder = new VariantContextBuilder("test", snpLoc,snpLocStart, snpLocStop, Arrays.asList(Aref, T)).referenceBaseForIndel((byte)'A');
+        insBuilder = new VariantContextBuilder("test", insLoc, insLocStart, insLocStop, Arrays.asList(delRef, ATC)).referenceBaseForIndel((byte)'A');
     }
 
     @Test
@@ -68,68 +75,68 @@ public class VariantContextUnitTest extends BaseTest {
 
         // test REF
         List<Allele> alleles = Arrays.asList(Tref);
-        VariantContext vc = new VariantContext("test", VCFConstants.EMPTY_ID_FIELD, snpLoc,snpLocStart, snpLocStop, alleles);
+        VariantContext vc = snpBuilder.alleles(alleles).make();
         Assert.assertEquals(vc.getType(), VariantContext.Type.NO_VARIATION);
 
         // test SNPs
         alleles = Arrays.asList(Tref, A);
-        vc = new VariantContext("test", VCFConstants.EMPTY_ID_FIELD, snpLoc,snpLocStart, snpLocStop, alleles);
+        vc = snpBuilder.alleles(alleles).make();
         Assert.assertEquals(vc.getType(), VariantContext.Type.SNP);
 
         alleles = Arrays.asList(Tref, A, C);
-        vc = new VariantContext("test", VCFConstants.EMPTY_ID_FIELD, snpLoc,snpLocStart, snpLocStop, alleles);
+        vc = snpBuilder.alleles(alleles).make();
         Assert.assertEquals(vc.getType(), VariantContext.Type.SNP);
 
         // test MNPs
         alleles = Arrays.asList(ACref, TA);
-        vc = new VariantContext("test", VCFConstants.EMPTY_ID_FIELD, snpLoc,snpLocStart, snpLocStop+1, alleles);
+        vc = snpBuilder.alleles(alleles).stop(snpLocStop+1).make();
         Assert.assertEquals(vc.getType(), VariantContext.Type.MNP);
 
         alleles = Arrays.asList(ATCref, CAT, Allele.create("GGG"));
-        vc = new VariantContext("test", VCFConstants.EMPTY_ID_FIELD, snpLoc,snpLocStart, snpLocStop+2, alleles);
+        vc = basicBuilder.alleles(alleles).stop(snpLocStop+2).make();
         Assert.assertEquals(vc.getType(), VariantContext.Type.MNP);
 
         // test INDELs
         alleles = Arrays.asList(Aref, ATC);
-        vc = new VariantContext("test", VCFConstants.EMPTY_ID_FIELD, snpLoc,snpLocStart, snpLocStop, alleles, null, CommonInfo.NO_LOG10_PERROR, null, null, (byte)'A');
+        vc = basicBuilder.alleles(alleles).make();
         Assert.assertEquals(vc.getType(), VariantContext.Type.INDEL);
 
         alleles = Arrays.asList(ATCref, A);
-        vc = new VariantContext("test", VCFConstants.EMPTY_ID_FIELD, snpLoc,snpLocStart, snpLocStop+2, alleles, null, CommonInfo.NO_LOG10_PERROR, null, null, (byte)'A');
+        vc = basicBuilder.alleles(alleles).stop(snpLocStop+2).make();
         Assert.assertEquals(vc.getType(), VariantContext.Type.INDEL);
 
         alleles = Arrays.asList(Tref, TA, TC);
-        vc = new VariantContext("test", VCFConstants.EMPTY_ID_FIELD, snpLoc,snpLocStart, snpLocStop, alleles, null, CommonInfo.NO_LOG10_PERROR, null, null, (byte)'A');
+        vc = basicBuilder.alleles(alleles).make();
         Assert.assertEquals(vc.getType(), VariantContext.Type.INDEL);
 
         alleles = Arrays.asList(ATCref, A, AC);
-        vc = new VariantContext("test", VCFConstants.EMPTY_ID_FIELD, snpLoc,snpLocStart, snpLocStop+2, alleles, null, CommonInfo.NO_LOG10_PERROR, null, null, (byte)'A');
+        vc = basicBuilder.alleles(alleles).stop(snpLocStop+2).make();
         Assert.assertEquals(vc.getType(), VariantContext.Type.INDEL);
 
         alleles = Arrays.asList(ATCref, A, Allele.create("ATCTC"));
-        vc = new VariantContext("test", VCFConstants.EMPTY_ID_FIELD, snpLoc,snpLocStart, snpLocStop+2, alleles, null, CommonInfo.NO_LOG10_PERROR, null, null, (byte)'A');
+        vc = basicBuilder.alleles(alleles).stop(snpLocStop+2).make();
         Assert.assertEquals(vc.getType(), VariantContext.Type.INDEL);
 
         // test MIXED
         alleles = Arrays.asList(TAref, T, TC);
-        vc = new VariantContext("test", VCFConstants.EMPTY_ID_FIELD, snpLoc,snpLocStart, snpLocStop+1, alleles, null, CommonInfo.NO_LOG10_PERROR, null, null, (byte)'A');
+        vc = basicBuilder.alleles(alleles).stop(snpLocStop+1).make();
         Assert.assertEquals(vc.getType(), VariantContext.Type.MIXED);
 
         alleles = Arrays.asList(TAref, T, AC);
-        vc = new VariantContext("test", VCFConstants.EMPTY_ID_FIELD, snpLoc,snpLocStart, snpLocStop+1, alleles, null, CommonInfo.NO_LOG10_PERROR, null, null, (byte)'A');
+        vc = basicBuilder.alleles(alleles).stop(snpLocStop+1).make();
         Assert.assertEquals(vc.getType(), VariantContext.Type.MIXED);
 
         alleles = Arrays.asList(ACref, ATC, AT);
-        vc = new VariantContext("test", VCFConstants.EMPTY_ID_FIELD, snpLoc,snpLocStart, snpLocStop+1, alleles, null, CommonInfo.NO_LOG10_PERROR, null, null, (byte)'A');
+        vc = basicBuilder.alleles(alleles).stop(snpLocStop+1).make();
         Assert.assertEquals(vc.getType(), VariantContext.Type.MIXED);
 
         alleles = Arrays.asList(Aref, T, symbolic);
-        vc = new VariantContext("test", VCFConstants.EMPTY_ID_FIELD, snpLoc,snpLocStart, snpLocStop, alleles, null, CommonInfo.NO_LOG10_PERROR, null, null, (byte)'A');
+        vc = basicBuilder.alleles(alleles).make();
         Assert.assertEquals(vc.getType(), VariantContext.Type.MIXED);
 
         // test SYMBOLIC
         alleles = Arrays.asList(Tref, symbolic);
-        vc = new VariantContext("test", VCFConstants.EMPTY_ID_FIELD, snpLoc,snpLocStart, snpLocStop, alleles, null, CommonInfo.NO_LOG10_PERROR, null, null, (byte)'A');
+        vc = basicBuilder.alleles(alleles).stop(snpLocStop+2).make();
         Assert.assertEquals(vc.getType(), VariantContext.Type.SYMBOLIC);
     }
 
@@ -137,8 +144,8 @@ public class VariantContextUnitTest extends BaseTest {
     public void testMultipleSNPAlleleOrdering() {
         final List<Allele> allelesNaturalOrder = Arrays.asList(Aref, C, T);
         final List<Allele> allelesUnnaturalOrder = Arrays.asList(Aref, T, C);
-        VariantContext naturalVC = new VariantContext("natural", VCFConstants.EMPTY_ID_FIELD, snpLoc, snpLocStart, snpLocStop, allelesNaturalOrder);
+        VariantContext naturalVC = snpBuilder.alleles(allelesNaturalOrder).make();
-        VariantContext unnaturalVC = new VariantContext("unnatural", VCFConstants.EMPTY_ID_FIELD, snpLoc, snpLocStart, snpLocStop, allelesUnnaturalOrder);
+        VariantContext unnaturalVC = snpBuilder.alleles(allelesUnnaturalOrder).make();
         Assert.assertEquals(new ArrayList<Allele>(naturalVC.getAlleles()), allelesNaturalOrder);
         Assert.assertEquals(new ArrayList<Allele>(unnaturalVC.getAlleles()), allelesUnnaturalOrder);
     }
@@ -147,7 +154,7 @@ public class VariantContextUnitTest extends BaseTest {
     public void testCreatingSNPVariantContext() {
 
         List<Allele> alleles = Arrays.asList(Aref, T);
-        VariantContext vc = new VariantContext("test", VCFConstants.EMPTY_ID_FIELD, snpLoc,snpLocStart, snpLocStop, alleles);
+        VariantContext vc = snpBuilder.alleles(alleles).make();
 
         Assert.assertEquals(vc.getChr(), snpLoc);
         Assert.assertEquals(vc.getStart(), snpLocStart);
@@ -174,7 +181,7 @@ public class VariantContextUnitTest extends BaseTest {
     @Test
     public void testCreatingRefVariantContext() {
         List<Allele> alleles = Arrays.asList(Aref);
-        VariantContext vc = new VariantContext("test", VCFConstants.EMPTY_ID_FIELD, snpLoc,snpLocStart, snpLocStop, alleles);
+        VariantContext vc = snpBuilder.alleles(alleles).make();
 
         Assert.assertEquals(vc.getChr(), snpLoc);
         Assert.assertEquals(vc.getStart(), snpLocStart);
@@ -200,7 +207,7 @@ public class VariantContextUnitTest extends BaseTest {
     @Test
     public void testCreatingDeletionVariantContext() {
         List<Allele> alleles = Arrays.asList(ATCref, del);
-        VariantContext vc = new VariantContext("test", VCFConstants.EMPTY_ID_FIELD, delLoc, delLocStart, delLocStop, alleles, null, CommonInfo.NO_LOG10_PERROR, null, null, (byte)'A');
+        VariantContext vc = new VariantContextBuilder("test", delLoc, delLocStart, delLocStop, alleles).referenceBaseForIndel((byte)'A').make();
 
         Assert.assertEquals(vc.getChr(), delLoc);
         Assert.assertEquals(vc.getStart(), delLocStart);
@@ -227,7 +234,7 @@ public class VariantContextUnitTest extends BaseTest {
     @Test
     public void testCreatingInsertionVariantContext() {
         List<Allele> alleles = Arrays.asList(delRef, ATC);
-        VariantContext vc = new VariantContext("test", VCFConstants.EMPTY_ID_FIELD, insLoc, insLocStart, insLocStop, alleles, null, CommonInfo.NO_LOG10_PERROR, null, null, (byte)'A');
+        VariantContext vc = insBuilder.alleles(alleles).make();
 
         Assert.assertEquals(vc.getChr(), insLoc);
         Assert.assertEquals(vc.getStart(), insLocStart);
@@ -275,48 +282,48 @@ public class VariantContextUnitTest extends BaseTest {
 
     @Test (expectedExceptions = IllegalArgumentException.class)
     public void testBadConstructorArgs1() {
-        new VariantContext("test", VCFConstants.EMPTY_ID_FIELD, insLoc, insLocStart, insLocStop, Arrays.asList(delRef, ATCref));
+        new VariantContextBuilder("test", insLoc, insLocStart, insLocStop, Arrays.asList(delRef, ATCref)).make();
     }
 
     @Test (expectedExceptions = IllegalArgumentException.class)
     public void testBadConstructorArgs2() {
-        new VariantContext("test", VCFConstants.EMPTY_ID_FIELD, insLoc, insLocStart, insLocStop, Arrays.asList(delRef, del));
+        new VariantContextBuilder("test", insLoc, insLocStart, insLocStop, Arrays.asList(delRef, del)).make();
     }
 
     @Test (expectedExceptions = IllegalArgumentException.class)
     public void testBadConstructorArgs3() {
-        new VariantContext("test", VCFConstants.EMPTY_ID_FIELD, insLoc, insLocStart, insLocStop, Arrays.asList(del));
+        new VariantContextBuilder("test", insLoc, insLocStart, insLocStop, Arrays.asList(del)).make();
     }
 
     @Test (expectedExceptions = IllegalArgumentException.class)
     public void testBadConstructorArgs4() {
-        new VariantContext("test", VCFConstants.EMPTY_ID_FIELD, insLoc, insLocStart, insLocStop, Collections.<Allele>emptyList());
+        new VariantContextBuilder("test", insLoc, insLocStart, insLocStop, Collections.<Allele>emptyList()).make();
     }
 
     @Test (expectedExceptions = IllegalArgumentException.class)
     public void testBadConstructorArgsDuplicateAlleles1() {
-        new VariantContext("test", VCFConstants.EMPTY_ID_FIELD, insLoc, insLocStart, insLocStop, Arrays.asList(Aref, T, T));
+        new VariantContextBuilder("test", insLoc, insLocStart, insLocStop, Arrays.asList(Aref, T, T)).make();
     }
 
     @Test (expectedExceptions = IllegalArgumentException.class)
     public void testBadConstructorArgsDuplicateAlleles2() {
-        new VariantContext("test", VCFConstants.EMPTY_ID_FIELD, insLoc, insLocStart, insLocStop, Arrays.asList(Aref, A));
+        new VariantContextBuilder("test", insLoc, insLocStart, insLocStop, Arrays.asList(Aref, A)).make();
     }
 
     @Test (expectedExceptions = IllegalStateException.class)
     public void testBadLoc1() {
         List<Allele> alleles = Arrays.asList(Aref, T, del);
-        new VariantContext("test", VCFConstants.EMPTY_ID_FIELD, delLoc, delLocStart, delLocStop, alleles);
+        new VariantContextBuilder("test", delLoc, delLocStart, delLocStop, alleles).make();
     }
 
     @Test (expectedExceptions = IllegalArgumentException.class)
     public void testBadID1() {
-        new VariantContext("test", null, delLoc, delLocStart, delLocStop, Arrays.asList(Aref, T));
+        new VariantContextBuilder("test", delLoc, delLocStart, delLocStop, Arrays.asList(Aref, T)).id(null).make();
     }
 
     @Test (expectedExceptions = IllegalArgumentException.class)
     public void testBadID2() {
-        new VariantContext("test", "", delLoc, delLocStart, delLocStop, Arrays.asList(Aref, T));
+        new VariantContextBuilder("test", delLoc, delLocStart, delLocStop, Arrays.asList(Aref, T)).id("");
     }
 
     @Test
@@ -550,7 +557,7 @@ public class VariantContextUnitTest extends BaseTest {
     @Test(dataProvider = "getAlleles")
     public void testMergeAlleles(GetAllelesTest cfg) {
         final List<Allele> altAlleles = cfg.alleles.subList(1, cfg.alleles.size());
-        final VariantContext vc = new VariantContext("test", VCFConstants.EMPTY_ID_FIELD, snpLoc, snpLocStart, snpLocStop, cfg.alleles, null, CommonInfo.NO_LOG10_PERROR, null, null, (byte)'A');
+        final VariantContext vc = snpBuilder.alleles(cfg.alleles).make();
 
         Assert.assertEquals(vc.getAlleles(), cfg.alleles, "VC alleles not the same as input alleles");
         Assert.assertEquals(vc.getNAlleles(), cfg.alleles.size(), "VC getNAlleles not the same as input alleles size");

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

@@ -99,8 +99,7 @@ public class VariantContextUtilsUnitTest extends BaseTest {
     private VariantContext makeVC(String source, List<Allele> alleles, Collection<Genotype> genotypes, Set<String> filters) {
         int start = 10;
         int stop = start; // alleles.contains(ATC) ? start + 3 : start;
-        return new VariantContext(source, VCFConstants.EMPTY_ID_FIELD, "1", start, stop, alleles,
+        return new VariantContextBuilder(source, "1", start, stop, alleles).genotypes(genotypes).filters(filters).referenceBaseForIndel(Cref.getBases()[0]).make();
-                GenotypesContext.copy(genotypes), 1.0, filters, null, Cref.getBases()[0]);
     }
 
     // --------------------------------------------------------------------------------

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

@@ -144,7 +144,7 @@ public class VariantJEXLContextUnitTest extends BaseTest {
     private JEXLMap getVarContext() {
         List<Allele> alleles = Arrays.asList(Aref, T);
 
-        VariantContext vc = new VariantContext("test", VCFConstants.EMPTY_ID_FIELD, snpLoc.getContig(), snpLoc.getStart(), snpLoc.getStop(), alleles);
+        VariantContext vc = new VariantContextBuilder("test", snpLoc.getContig(), snpLoc.getStart(), snpLoc.getStop(), alleles).make();
         return new JEXLMap(Arrays.asList(exp),vc);
     }