From 6d7ec7377c40d94a01e79c176dd19acee92e0a85 Mon Sep 17 00:00:00 2001
From: Ron Levine <rlevine@broadinstitute.org>
Date: Fri, 11 Mar 2016 20:39:54 -0500
Subject: [PATCH] Set --reference_window_stop if homopolymer is greater than
 window size

---
 .../walkers/annotator/HomopolymerRun.java     | 20 ++++++++++++-------
 .../VariantAnnotatorIntegrationTest.java      | 18 +++++++++++++++++
 2 files changed, 31 insertions(+), 7 deletions(-)

diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/HomopolymerRun.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/HomopolymerRun.java
index d21dd1fbc..5b02cada2 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/HomopolymerRun.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/HomopolymerRun.java
@@ -51,6 +51,7 @@
 
 package org.broadinstitute.gatk.tools.walkers.annotator;
 
+import org.apache.log4j.Logger;
 import org.broadinstitute.gatk.utils.contexts.AlignmentContext;
 import org.broadinstitute.gatk.utils.contexts.ReferenceContext;
 import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker;
@@ -83,7 +84,11 @@ import java.util.Map;
  */
 public class HomopolymerRun extends InfoFieldAnnotation implements ExperimentalAnnotation {
 
+    private final static Logger logger = Logger.getLogger(HardyWeinberg.class);
+
     private boolean ANNOTATE_INDELS = true;
+    
+    private final static int BAD_RUN_LENGTH = -1;
 
     public Map<String, Object> annotate(final RefMetaDataTracker tracker,
                                         final AnnotatorCompatible walker,
@@ -103,6 +108,9 @@ public class HomopolymerRun extends InfoFieldAnnotation implements ExperimentalA
         } else {
             return null;
         }
+
+        if ( run == BAD_RUN_LENGTH )
+            return null;
         
         Map<String, Object> map = new HashMap<>();
         map.put(getKeyNames().get(0), String.format("%d", run));
@@ -149,15 +157,13 @@ public class HomopolymerRun extends InfoFieldAnnotation implements ExperimentalA
         GenomeLoc window = ref.getWindow();
         int refBasePos = (int) (locus.getStart() - window.getStart())+1;
         if ( vc.isSimpleDeletion() ) {
-            // check that deleted bases are the same
-            byte dBase = bases[refBasePos];
-            for ( int i = 0; i < vc.getReference().length(); i ++ ) {
-                if ( bases[refBasePos+i] != dBase ) {
-                    return 0;
-                }
+            if ( refBasePos + vc.getReference().length() - 1 >= bases.length ) {
+                logger.warn("Encountered a homopolymer at " + locus.toString() + " longer than the tool's default window size, so the position was skipped. " +
+                        "To process this position, add --reference_window_stop to your command with a value equal or greater than " + vc.getReference().length());
+                return BAD_RUN_LENGTH;
             }
 
-            return computeHomopolymerRun(dBase, ref);
+            return computeHomopolymerRun(bases[refBasePos], ref);
         } else {
             // check that inserted bases are the same
             byte insBase = vc.getAlternateAllele(0).getBases()[0];
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotatorIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotatorIntegrationTest.java
index f518fb468..b0f1ddc4e 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotatorIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotatorIntegrationTest.java
@@ -505,4 +505,22 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
         Assert.assertFalse(lineIterator.hasNext());
         Assert.assertFalse(lineIteratorAnn.hasNext());
     }
+
+    @Test
+    public void testHomopolymerRunWindow() {
+        WalkerTestSpec spec = new WalkerTestSpec(
+                "-T VariantAnnotator -R " + hg19ReferenceWithChrPrefixInChromosomeNames + " -A HomopolymerRun --variant:vcf " + privateTestDir + "problem_del.vcf  " +
+                        "-U ALLOW_SEQ_DICT_INCOMPATIBILITY -L chr18:44382010-44384010 --reference_window_stop 59 --no_cmdline_in_header -o %s", 1,
+                Arrays.asList("bda55495578147b2390d850d7fb25a12"));
+        executeTest("Testing testHomopolymerRunWindow", spec);
+    }
+
+    @Test
+    public void testHomopolymerRunTooBig() {
+        WalkerTestSpec spec = new WalkerTestSpec(
+                "-T VariantAnnotator -R " + hg19ReferenceWithChrPrefixInChromosomeNames + " -A HomopolymerRun --variant:vcf " + privateTestDir + "problem_del.vcf  " +
+                        "-U ALLOW_SEQ_DICT_INCOMPATIBILITY -L chr18:44382010-44384010 --no_cmdline_in_header -o %s", 1,
+                Arrays.asList("e20b12fd45f37a7bb31a2f2e91983477"));
+        executeTest("Testing HomopolymerRunTooBig", spec);
+    }
 }