From 30a19a00fed99e8f6d69dc3a3bf6bf0d22d3e3fe Mon Sep 17 00:00:00 2001
From: rpoplin <rpoplin@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 12 Apr 2011 20:07:06 +0000
Subject: [PATCH] Fix for when running with EMIT_ALL_SITES but not
 GENOTYPE_GIVEN_ALLELES. Still want to emit a site even when over the deletion
 fraction for example.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5617 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../genotyper/UnifiedGenotyperEngine.java     | 23 +++++++++++--------
 .../UnifiedGenotyperIntegrationTest.java      |  2 +-
 2 files changed, 14 insertions(+), 11 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
index db860029b..a89ce0ba0 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
@@ -151,9 +151,10 @@ public class UnifiedGenotyperEngine {
         }
 
         Map<String, AlignmentContext> stratifiedContexts = getFilteredAndStratifiedContexts(UAC, refContext, rawContext, model);
-        if ( stratifiedContexts == null )
-            return (UAC.OutputMode != OUTPUT_MODE.EMIT_ALL_SITES ? null : generateEmptyContext(tracker, refContext, stratifiedContexts, rawContext));
-
+        if ( stratifiedContexts == null ) {
+            return (UAC.OutputMode == OUTPUT_MODE.EMIT_ALL_SITES && UAC.GenotypingMode != GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES ? generateEmptyContext(tracker, refContext, stratifiedContexts, rawContext) : null);
+        }
+        
         VariantContext vc = calculateLikelihoods(tracker, refContext, stratifiedContexts, AlignmentContextUtils.ReadOrientation.COMPLETE, null, true, model);
 
         if ( vc == null )
@@ -459,7 +460,7 @@ public class UnifiedGenotyperEngine {
             ReadBackedExtendedEventPileup pileup = rawPileup.getMappingFilteredPileup(UAC.MIN_MAPPING_QUALTY_SCORE);
 
             // don't call when there is no coverage
-            if ( pileup.size() == 0 && UAC.OutputMode != OUTPUT_MODE.EMIT_ALL_SITES )
+            if ( pileup.size() == 0 && !(UAC.OutputMode == OUTPUT_MODE.EMIT_ALL_SITES && UAC.GenotypingMode != GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES) )
                 return null;
 
             // stratify the AlignmentContext and cut by sample
@@ -473,12 +474,14 @@ public class UnifiedGenotyperEngine {
             // stratify the AlignmentContext and cut by sample
             stratifiedContexts = AlignmentContextUtils.splitContextBySampleName(rawContext.getBasePileup(), UAC.ASSUME_SINGLE_SAMPLE);
 
-            int numDeletions = 0;
-            for( final PileupElement p : rawContext.getBasePileup() ) {
-                if( p.isDeletion() ) { numDeletions++; }
-            }
-            if( ((double) numDeletions) / ((double) rawContext.getBasePileup().size()) > UAC.MAX_DELETION_FRACTION ) {
-                return null;
+            if( !(UAC.OutputMode == OUTPUT_MODE.EMIT_ALL_SITES && UAC.GenotypingMode != GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES) ) {
+                int numDeletions = 0;
+                for( final PileupElement p : rawContext.getBasePileup() ) {
+                    if( p.isDeletion() ) { numDeletions++; }
+                }
+                if( ((double) numDeletions) / ((double) rawContext.getBasePileup().size()) > UAC.MAX_DELETION_FRACTION ) {
+                    return null;
+                }
             }
         }
 
diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
index ad49221c5..9ce58665b 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
@@ -153,7 +153,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
         HashMap<String, String> e = new HashMap<String, String>();
         e.put( "-sites_only", "63b76c4d26edf8cbb5bd91dafc81fee1" );
         e.put( "--output_mode EMIT_ALL_CONFIDENT_SITES", "5bf0268945d953377ea3a811b20ff1bc" );
-        e.put( "--output_mode EMIT_ALL_SITES", "a1730ea5ae5e1aa57d85d9d2372facc8" );
+        e.put( "--output_mode EMIT_ALL_SITES", "78eeff5b2277877954e4985934077d3f" );
 
         for ( Map.Entry<String, String> entry : e.entrySet() ) {
             WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(