Fix LeftAlignAndTrimVariants args. (#5519)

broadinstitute · Jan 3, 2019 · e2cbab5 · e2cbab5
1 parent 1fb980c
commit e2cbab5
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Showing 2 changed files with 24 additions and 12 deletions.
diff --git a/...va/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants.java b/...va/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants.java
@@ -1,5 +1,6 @@
 package org.broadinstitute.hellbender.tools.walkers.variantutils;
 
+import com.google.common.annotations.VisibleForTesting;
 import htsjdk.samtools.Cigar;
 import htsjdk.samtools.CigarElement;
 import htsjdk.samtools.CigarOperator;
@@ -16,7 +17,6 @@
 import org.broadinstitute.hellbender.engine.ReadsContext;
 import org.broadinstitute.hellbender.engine.ReferenceContext;
 import org.broadinstitute.hellbender.engine.VariantWalker;
-import org.broadinstitute.hellbender.tools.walkers.annotator.ChromosomeCounts;
 import org.broadinstitute.hellbender.utils.variant.GATKVCFConstants;
 import org.broadinstitute.hellbender.utils.variant.GATKVCFHeaderLines;
 import org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils;
@@ -122,6 +122,12 @@ public class LeftAlignAndTrimVariants extends VariantWalker {
     public static final String SPLIT_MULTIALLELEICS_LONG_NAME = "split-multi-allelics";
     public static final String KEEP_ORIGINAL_AC_LONG_NAME = "keep-original-ac";
     public static final String MAX_INDEL_LENGTH_LONG_NAME = "max-indel-length";
+
+    private static final int DEFAULT_MAX_LEADING_BASES= 1000;
+
+    @VisibleForTesting
+    static final int DEFAULT_MAX_INDEL_SIZE = 200;
+
     public static final String MAX_LEADING_BASES_LONG_NAME = "max-leading-bases";
     /**
      * Output file to which to write left aligned variants
@@ -155,26 +161,28 @@ public class LeftAlignAndTrimVariants extends VariantWalker {
      * Maximum indel size to realign.  Indels larger than this will be left unadjusted.
      */
     @Argument(fullName = MAX_INDEL_LENGTH_LONG_NAME, doc = "Set maximum indel size to realign", optional = true)
-    protected static int maxIndelSize = 200;
+    protected int maxIndelSize = DEFAULT_MAX_INDEL_SIZE;
 
     /**
      * Distance in reference to look back before allele
      */
     @Argument(fullName = MAX_LEADING_BASES_LONG_NAME, doc = "Set max reference window size to look back before allele", optional = true)
-    protected static int maxLeadingBases = 1000;
+    protected int maxLeadingBases = DEFAULT_MAX_LEADING_BASES;
 
     @Hidden
     @Argument(fullName = "suppress-reference-path", optional = true,
             doc = "Suppress reference path in output for test result differencing")
     private boolean suppressReferencePath = false;
 
-    protected VariantContextWriter vcfWriter = null;
-    protected int numRealignedVariants;
-    protected int numVariantsSplit;
-    protected int numVariantsSplitTo;
-    protected int numVariantsTrimmed;
-    protected int numSkippedForLength;
-    protected int longestSkippedVariant;
+    private VariantContextWriter vcfWriter = null;
+    private int numRealignedVariants;
+    private int numVariantsSplit;
+    private int numVariantsSplitTo;
+    private int numVariantsTrimmed;
+    @VisibleForTesting
+    int numSkippedForLength;
+    @VisibleForTesting
+    int longestSkippedVariant;
     private int furthestEndOfEarlierVariant;
     private String currentContig;
 

diff --git a/...roadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariantsUnitTest.java b/...roadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariantsUnitTest.java
@@ -20,6 +20,10 @@
 import java.util.stream.*;
 import java.io.File;
 
+/**
+ * These tests should be refactored. They currently call LeftalignAndTrimVariants instance methods without
+ * putting it through the tool lifecycle.
+ */
 public class LeftAlignAndTrimVariantsUnitTest extends GATKBaseTest {
     final String refBases1 = "GCAGAGCTGACCCTCCCTCCCCTCTCCCAGTGCAACAGCACGGGCGGCGACTGCTTTTACCGAGGCTACACGTCAGGCGTGGCGGCTGTCCAGGACTGGTACCACTTCCACTATGTGGATCTCTGCTGAGGACCAGGAAAGCCAGCACCCGCAGAGACTCTTCCCCAGTGCTCCATACGATCACCATTCTCTGCAGAAGG";
     final String longStr = "AGTCGCTCGAGCTCGAGCTCGAGTGTGCGCTCTACAGCTCAGCTCGCTCGCACACAT";
@@ -96,7 +100,7 @@ public Object[][] LeftAlignTestData() throws UnsupportedEncodingException {
                     ReferenceContext ref = new ReferenceContext(refSource, interval);
 
                     final VariantContext vc = new VariantContextBuilder("test", artificialContig, indelIndex + 1, indelIndex + alleles.get(0).length(), alleles).make();
-                    final boolean expectRealigned = (indelIndex != repeatStart - 1) && (indelRepeats * strLength <= LeftAlignAndTrimVariants.maxIndelSize);
+                    final boolean expectRealigned = (indelIndex != repeatStart - 1) && (indelRepeats * strLength <= LeftAlignAndTrimVariants.DEFAULT_MAX_INDEL_SIZE);
                     final int expectedStart = expectRealigned ? repeatStart : indelIndex + 1;
                     tests.add(new Object[]{vc, ref, expectRealigned, expectedStart});
                 }
@@ -155,7 +159,7 @@ public void testSkipForLength(final VariantContext vc, final ReferenceContext re
         Assert.assertEquals(1, leftAligner.numSkippedForLength);
         leftAligner.longestSkippedVariant = 0;
         leftAligner.numSkippedForLength = 0;
-        LeftAlignAndTrimVariants.maxIndelSize = lengthSkippedVariant;
+        leftAligner.maxIndelSize = lengthSkippedVariant;
         leftAligner.leftAlign(vc, ref);
         Assert.assertEquals(0, leftAligner.longestSkippedVariant);
         Assert.assertEquals(0, leftAligner.numSkippedForLength);