From f0b8a0228fef45f23478c1a12be1cd58633c0873 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Mon, 19 Nov 2012 09:57:55 -0500
Subject: [PATCH] Quick fix for HC refactoring: when copying over Haplotype
 objects, make sure to copy over the artificial allele used to create it too.

---
 .../gatk/walkers/haplotypecaller/SimpleDeBruijnAssembler.java | 2 ++
 public/java/src/org/broadinstitute/sting/utils/Haplotype.java | 4 ++++
 2 files changed, 6 insertions(+)

diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/SimpleDeBruijnAssembler.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/SimpleDeBruijnAssembler.java
index fd46e4e69..33fa49543 100755
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/SimpleDeBruijnAssembler.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/SimpleDeBruijnAssembler.java
@@ -369,6 +369,8 @@ public class SimpleDeBruijnAssembler extends LocalAssemblyEngine {
 
         h.setAlignmentStartHapwrtRef( swConsensus2.getAlignmentStart2wrt1() );
         h.setCigar( AlignmentUtils.leftAlignIndel(swConsensus2.getCigar(), ref, h.getBases(), swConsensus2.getAlignmentStart2wrt1(), 0) );
+        if ( haplotype.isArtificialHaplotype() )
+            h.setArtificialAllele(haplotype.getArtificialAllele());
         h.leftBreakPoint = leftBreakPoint;
         h.rightBreakPoint = rightBreakPoint;
         if( swConsensus2.getCigar().toString().contains("S") || swConsensus2.getCigar().getReferenceLength() != activeRegionStop - activeRegionStart ) { // protect against SW failures
diff --git a/public/java/src/org/broadinstitute/sting/utils/Haplotype.java b/public/java/src/org/broadinstitute/sting/utils/Haplotype.java
index 6de15e18b..af4e31698 100755
--- a/public/java/src/org/broadinstitute/sting/utils/Haplotype.java
+++ b/public/java/src/org/broadinstitute/sting/utils/Haplotype.java
@@ -185,6 +185,10 @@ public class Haplotype {
         return artificialAllele;
     }
 
+    public void setArtificialAllele(final Allele artificialAllele) {
+        this.artificialAllele = artificialAllele;
+    }
+
     @Requires({"refInsertLocation >= 0"})
     public Haplotype insertAllele( final Allele refAllele, final Allele altAllele, final int refInsertLocation ) {
         // refInsertLocation is in ref haplotype offset coordinates NOT genomic coordinates