From f092e1438d4385dc3b06b385cc0d64045a2e0748 Mon Sep 17 00:00:00 2001
From: Ron Levine <rlevine@broadinstitute.org>
Date: Fri, 6 Jan 2017 09:19:21 -0500
Subject: [PATCH] Allow disabling of BadMateFilter in HaplotypeCaller

---
 .../tools/walkers/haplotypecaller/HaplotypeCaller.java | 10 ++++++++--
 .../HaplotypeCallerIntegrationTest.java                |  7 ++++++-
 2 files changed, 14 insertions(+), 3 deletions(-)

diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java
index 491abf6fc..8bf63f494 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java
@@ -530,7 +530,6 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
      */
     private static final int MINIMUM_PUTATIVE_PLOIDY_FOR_ACTIVE_REGION_DISCOVERY = 2;
 
-
     /**
      * Reads with length lower than this number, after clipping off overhands outside the active region,
      * won't be considered for genotyping.
@@ -550,6 +549,11 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
 
     ReferenceConfidenceModel referenceConfidenceModel = null;
 
+    /*
+     * Is the bad mate filter disabled by the argument -drf BadMate?
+     */
+    private boolean isBadMateFilterDisabled = false;
+
 
     ////////////////////////////////////////////////////////////////////////
     //// Deprecated Arguments					                        ////
@@ -735,6 +739,8 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
 
         trimmer.initialize(getToolkit().getGenomeLocParser(), HCAC.DEBUG,
                 HCAC.genotypingOutputMode == GenotypingOutputMode.GENOTYPE_GIVEN_ALLELES,emitReferenceConfidence());
+
+        isBadMateFilterDisabled = toolkit.getArguments().disabledReadFilters.contains("BadMate");
     }
 
     private void initializeReferenceConfidenceModel(final SampleList samples, final Set<VCFHeaderLine> headerInfo) {
@@ -1226,7 +1232,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
     private Set<GATKSAMRecord> filterNonPassingReads( final ActiveRegion activeRegion ) {
         final Set<GATKSAMRecord> readsToRemove = new LinkedHashSet<>();
         for( final GATKSAMRecord rec : activeRegion.getReads() ) {
-            if( rec.getReadLength() < READ_LENGTH_FILTER_THRESHOLD || rec.getMappingQuality() < READ_QUALITY_FILTER_THRESHOLD || BadMateFilter.hasBadMate(rec) || (keepRG != null && !rec.getReadGroup().getId().equals(keepRG)) ) {
+            if( rec.getReadLength() < READ_LENGTH_FILTER_THRESHOLD || rec.getMappingQuality() < READ_QUALITY_FILTER_THRESHOLD || (!isBadMateFilterDisabled && BadMateFilter.hasBadMate(rec)) || (keepRG != null && !rec.getReadGroup().getId().equals(keepRG)) ) {
                 readsToRemove.add(rec);
             }
         }
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
index 9cb90c06e..befb87b39 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
@@ -117,6 +117,11 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
         HCTest(CEUTRIO_BAM, "", "ad472fbd63864caacf5bc018dcae9df9");
     }
 
+    @Test
+    public void testHaplotypeCallerMultiSampleNoBadMateFilter() throws IOException {
+        HCTest(CEUTRIO_BAM, "-drf BadMate", "bb6b14675d62ff5b86430508ed688776");
+    }
+
     @Test
     public void testHaplotypeCallerSingleSample() throws IOException {
 
@@ -471,7 +476,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
                         1, UserException.CommandLineException.class));
     }
 
-    @Test 
+    @Test
     public void testHaplotypeCallerMergeVariantsViaLDException(){
         executeTest("HaplotypeCallerMergeVariantsViaLDException",
                 new WalkerTest.WalkerTestSpec(