Fixed bug in SelectVariants where maxIndelSize argument wasn't getting applied to deletions.

Added unit tests and docs.

public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java

@@ -507,7 +507,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
             if (!selectedTypes.contains(vc.getType()))
                 continue;
 
-            if ( badIndelSize(vc) )
+            if ( containsIndelLargerThan(vc, maxIndelSize) )
                 continue;
 
             VariantContext sub = subsetRecord(vc, EXCLUDE_NON_VARIANTS);
@@ -531,12 +531,20 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
         return 1;
     }
 
-    private boolean badIndelSize(final VariantContext vc) {
-        List<Integer> lengths = vc.getIndelLengths();
+    /*
+     * Determines if any of the alternate alleles are greater than the max indel size
+     *
+     * @param vc            the variant context to check
+     * @param maxIndelSize  the maximum size of allowed indels
+     * @return true if the VC contains an indel larger than maxIndelSize and false otherwise
+     */
+    protected static boolean containsIndelLargerThan(final VariantContext vc, final int maxIndelSize) {
+        final List<Integer> lengths = vc.getIndelLengths();
         if ( lengths == null )
-            return false; // VC does not harbor indel
-        for ( Integer indelLength : vc.getIndelLengths() ) {
-            if ( indelLength > maxIndelSize )
+            return false;
+
+        for ( Integer indelLength : lengths ) {
+            if ( Math.abs(indelLength) > maxIndelSize )
                 return true;
         }
 

public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsUnitTest.java

@@ -0,0 +1,88 @@
+/*
+* Copyright (c) 2012 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 org.broadinstitute.sting.gatk.walkers.variantutils;
+
+import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.variant.variantcontext.Allele;
+import org.broadinstitute.variant.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContextBuilder;
+import org.testng.Assert;
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
+
+public class SelectVariantsUnitTest extends BaseTest {
+
+    //////////////////////////////////////////
+    // Tests for maxIndelSize functionality //
+    //////////////////////////////////////////
+
+    @DataProvider(name = "MaxIndelSize")
+    public Object[][] MaxIndelSizeTestData() {
+
+        List<Object[]> tests = new ArrayList<Object[]>();
+
+        for ( final int size : Arrays.asList(1, 3, 10, 100) ) {
+            for ( final int otherSize : Arrays.asList(0, 1) ) {
+                for ( final int max : Arrays.asList(0, 1, 5, 50, 100000) ) {
+                    for ( final String op : Arrays.asList("D", "I") ) {
+                        tests.add(new Object[]{size, otherSize, max, op});
+                    }
+                }
+            }
+        }
+
+        return tests.toArray(new Object[][]{});
+    }
+
+    @Test(dataProvider = "MaxIndelSize")
+    public void maxIndelSizeTest(final int size, final int otherSize, final int max, final String op) {
+
+        final byte[] largerAllele = Utils.dupBytes((byte) 'A', size+1);
+        final byte[] smallerAllele = Utils.dupBytes((byte) 'A', 1);
+
+        final List<Allele> alleles = new ArrayList<Allele>(2);
+        final Allele ref = Allele.create(op.equals("I") ? smallerAllele : largerAllele, true);
+        final Allele alt = Allele.create(op.equals("D") ? smallerAllele : largerAllele, false);
+        alleles.add(ref);
+        alleles.add(alt);
+        if ( otherSize > 0 && otherSize != size ) {
+            final Allele otherAlt = Allele.create(op.equals("D") ? Utils.dupBytes((byte) 'A', size-otherSize+1) : Utils.dupBytes((byte) 'A', otherSize+1), false);
+            alleles.add(otherAlt);
+        }
+
+        final VariantContext vc = new VariantContextBuilder("test", "1", 10, 10 + ref.length() - 1, alleles).make();
+
+        boolean hasTooLargeIndel = SelectVariants.containsIndelLargerThan(vc, max);
+        Assert.assertEquals(hasTooLargeIndel, size > max);
+    }
+
+}