From 529eecd4dc4337bc1ba4b46afec68b148495dc62 Mon Sep 17 00:00:00 2001
From: fromer <fromer@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 3 Sep 2010 13:38:46 +0000
Subject: [PATCH] Added phasing sub-directory to keep walkers directory clean

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4208 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/walkers/varianteval/GenotypePhasingEvaluator.java    | 4 ++--
 .../playground/gatk/walkers/ReadBackedPhasingWalker.java      | 3 ++-
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypePhasingEvaluator.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypePhasingEvaluator.java
index a396dc0f5..c64ce8205 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypePhasingEvaluator.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypePhasingEvaluator.java
@@ -4,7 +4,7 @@ import org.broad.tribble.util.variantcontext.Genotype;
 import org.broad.tribble.util.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.*;
 import org.broadinstitute.sting.gatk.refdata.*;
-import org.broadinstitute.sting.playground.gatk.walkers.Biallele;
+import org.broadinstitute.sting.playground.gatk.walkers.phasing.*;
 import org.broadinstitute.sting.playground.utils.report.tags.Analysis;
 import org.broadinstitute.sting.playground.utils.report.tags.DataPoint;
 import org.broadinstitute.sting.playground.utils.report.utils.TableType;
@@ -422,4 +422,4 @@ class SamplePhasingStatistics implements TableType {
         }
         return sb.toString();
     }
-}
\ No newline at end of file
+}
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/ReadBackedPhasingWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/ReadBackedPhasingWalker.java
index 016d7fbc7..0b3a98c68 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/ReadBackedPhasingWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/ReadBackedPhasingWalker.java
@@ -41,6 +41,7 @@ import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.vcf.VCFUtils;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
+import org.broadinstitute.sting.playground.gatk.walkers.phasing.*;
 
 import java.io.*;
 import java.util.*;
@@ -1212,4 +1213,4 @@ class PhasingQualityStatsWriter {
             }
         }
     }
-}
\ No newline at end of file
+}