From 463af7143f6003e976daa5860369b10c8f44e6a4 Mon Sep 17 00:00:00 2001
From: Valentin Ruano-Rubio <valentin@broadinstitute.org>
Date: Wed, 19 Feb 2014 20:19:09 -0500
Subject: [PATCH] Activate reverse allele trimming in GVCF

Story:

https://www.pivotaltracker.com/s/projects/1007536

Changes:

1. HC's GenotypingEngine now invokes reverseAlleleTrimming on GVCF variant output lines.
2. GenotypeGVCFs also reverse trim after regenotyping as some alt. alleles are dropped (observed in real-data).
---
 .../sting/gatk/walkers/haplotypecaller/GenotypingEngine.java  | 3 +--
 .../sting/gatk/walkers/variantutils/GenotypeGVCFs.java        | 4 +++-
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java
index 26e4edc1a..d65251e58 100644
--- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java
+++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java
@@ -229,9 +229,8 @@ public class GenotypingEngine {
 
                     VariantContext annotatedCall = annotationEngine.annotateContextForActiveRegion(tracker, stratifiedReadMap, call);
 
-                    if( !emitReferenceConfidence && call.getAlleles().size() != mergedVC.getAlleles().size() ) { // some alleles were removed so reverseTrimming might be necessary!
+                    if( call.getAlleles().size() != mergedVC.getAlleles().size() )
                         annotatedCall = GATKVariantContextUtils.reverseTrimAlleles(annotatedCall);
-                    }
 
                     // maintain the set of all called haplotypes
                     for ( final Allele calledAllele : call.getAlleles() ) {
diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeGVCFs.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeGVCFs.java
index 59ac95771..a6d151df8 100644
--- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeGVCFs.java
+++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeGVCFs.java
@@ -202,10 +202,12 @@ public class GenotypeGVCFs extends RodWalker<VariantContext, VariantContextWrite
 
         // only re-genotype polymorphic sites
         if ( result.isVariant() ) {
-            final VariantContext regenotypedVC = genotypingEngine.calculateGenotypes(result);
+            VariantContext regenotypedVC = genotypingEngine.calculateGenotypes(result);
             if ( regenotypedVC == null )
                 return null;
 
+            regenotypedVC = GATKVariantContextUtils.reverseTrimAlleles(regenotypedVC);
+
             // we want to carry forward the attributes from the original VC but make sure to add the MLE-based annotations
             final Map<String, Object> attrs = new HashMap<>(originalVC.getAttributes());
             attrs.put(VCFConstants.MLE_ALLELE_COUNT_KEY, regenotypedVC.getAttribute(VCFConstants.MLE_ALLELE_COUNT_KEY));