Added makeWithShallowCopy to GenotypeBuilder

src/main/java/htsjdk/variant/variantcontext/FastGenotype.java

@@ -29,7 +29,10 @@
 import java.util.Map;
 
 /**
- * This class encompasses all the basic information about a genotype.  It is immutable.
+ * This class encompasses all the basic information about a genotype.
+ *
+ * For the sake of performance, it does not make a copy of the Collections/arrays it's constructed from, and so
+ * subsequent changes to those Collections/arrays will be reflected in the FastGenotype object
  *
  * A genotype has several key fields
  *

src/main/java/htsjdk/variant/variantcontext/GenotypeBuilder.java

@@ -28,6 +28,7 @@
 import htsjdk.tribble.util.ParsingUtils;
 import htsjdk.variant.vcf.VCFConstants;
 
+import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collections;
 import java.util.HashMap;
@@ -49,6 +50,11 @@
  * or with intervening sets to conveniently make similar Genotypes with
  * slight modifications.
  *
+ * Re-using the same GenotypeBuilder to build multiple Genotype objects via calls
+ * to make() is dangerous, since reference types in the builder (eg., Collections/arrays)
+ * don't get copied when making each Genotype. To safely re-use the same builder object
+ * multiple times, use makeWithShallowCopy() instead of make().
+ *
  * @author Mark DePristo
  * @since 06/12
  */
@@ -185,13 +191,34 @@ public final void reset(final boolean keepSampleName) {
      * created, althrough the contents of array values like PL should never be modified
      * inline as they are not copied for efficiency reasons.
      *
+     * Note: if attributes are added via this builder after a call to make(), the new Genotype will
+     * be modified. Use {@link #makeWithShallowCopy} to safely re-use the same builder object
+     * multiple times.
+     *
      * @return a newly minted Genotype object with values provided from this builder
      */
     public Genotype make() {
-        final Map<String, Object> ea = extendedAttributes == null ? NO_ATTRIBUTES : extendedAttributes;
+        final Map<String, Object> ea = (extendedAttributes == null) ? NO_ATTRIBUTES : extendedAttributes;
         return new FastGenotype(sampleName, alleles, isPhased, GQ, DP, AD, PL, filters, ea);
     }
 
+    /**
+     * Create a new Genotype object using the values set in this builder, and perform a
+     * shallow copy of reference types to allow safer re-use of this builder
+     *
+     * After creation the values in this builder can be modified and more Genotypes
+     * created.
+     *
+     * @return a newly minted Genotype object with values provided from this builder
+     */
+    public Genotype makeWithShallowCopy() {
+        final Map<String, Object> ea = (extendedAttributes == null) ? NO_ATTRIBUTES : new HashMap<>(extendedAttributes);
+        final List<Allele> al = new ArrayList<>(alleles);
+        final int[] copyAD = (AD == null) ? null : Arrays.copyOf(AD, AD.length);
+        final int[] copyPL = (PL == null) ? null : Arrays.copyOf(PL, PL.length);
+        return new FastGenotype(sampleName, al, isPhased, GQ, DP, copyAD, copyPL, filters, ea);
+    }
+
     /**
      * Set this genotype's name
      * @param sampleName
@@ -303,9 +330,9 @@ public GenotypeBuilder PL(final double[] GLs) {
     }
 
     /**
-     * This genotype has these attributes.
+     * This genotype has these attributes. Attributes are added to previous ones.
      *
-     * Cannot contain inline attributes (DP, AD, GQ, PL)
+     * Cannot contain inline attributes (DP, AD, GQ, PL). Note: this is not checked
      * @return
      */
     public GenotypeBuilder attributes(final Map<String, Object> attributes) {
@@ -327,7 +354,7 @@ public GenotypeBuilder noAttributes() {
     /**
      * This genotype has this attribute key / value pair.
      *
-     * Cannot contain inline attributes (DP, AD, GQ, PL)
+     * Cannot contain inline attributes (DP, AD, GQ, PL). Note: this is not checked
      * @return
      */
     public GenotypeBuilder attribute(final String key, final Object value) {

src/test/java/htsjdk/variant/variantcontext/GenotypeBuilderTest.java

@@ -0,0 +1,75 @@
+/*
+* Copyright (c) 2016 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.
+*/
+
+package htsjdk.variant.variantcontext;
+
+import htsjdk.variant.VariantBaseTest;
+import org.testng.Assert;
+import org.testng.annotations.Test;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
+public class GenotypeBuilderTest extends VariantBaseTest {
+
+    @Test
+    public void testMakeWithShallowCopy() {
+        final GenotypeBuilder gb = new GenotypeBuilder("test");
+        final List<Allele> alleles = new ArrayList<>(
+                Arrays.asList(Allele.create("A", true), Allele.create("T")));
+        final int[] ad = new int[]{1,5};
+        final int[] pl = new int[]{1,6};
+        final int[] first = new int[]{1, 2};
+        final int[] second = new int[]{3, 4};
+        final Genotype firstG = gb.alleles(alleles).attribute("first", first).makeWithShallowCopy();
+        final Genotype secondG = gb.AD(ad).PL(pl).attribute("second", second).makeWithShallowCopy();
+        // both genotypes have the first field
+        Assert.assertEquals(first, firstG.getExtendedAttribute("first"));
+        Assert.assertEquals(first, secondG.getExtendedAttribute("first"));
+        // both genotypes have the the alleles
+        Assert.assertEquals(alleles, firstG.getAlleles());
+        Assert.assertEquals(alleles, secondG.getAlleles());
+        // only the second genotype should have the AD field
+        Assert.assertNull(firstG.getAD());
+        Assert.assertEquals(ad, secondG.getAD());
+        // only the second genotype should have the PL field
+        Assert.assertNull(firstG.getPL());
+        Assert.assertEquals(pl, secondG.getPL());
+        // only the second genotype should have the second field
+        Assert.assertNull(firstG.getExtendedAttribute("second"));
+        Assert.assertEquals(second, secondG.getExtendedAttribute("second"));
+        // modification of alleles does not change the genotypes
+        alleles.add(Allele.create("C"));
+        Assert.assertNotEquals(alleles, firstG.getAlleles());
+        Assert.assertNotEquals(alleles, secondG.getAlleles());
+        // modification of ad or pl does not change the genotypes
+        ad[0] = 0;
+        pl[0] = 10;
+        Assert.assertNotEquals(ad, secondG.getAD());
+        Assert.assertNotEquals(pl, secondG.getPL());
+    }
+
+}