From e322e71c2fe4365eac030a177acd919f7c33d141 Mon Sep 17 00:00:00 2001
From: fromer <fromer@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 29 Sep 2010 00:02:02 +0000
Subject: [PATCH] Restored SVN history for phasing

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4373 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/phasing/AllelePair.java     |  2 +-
 .../walkers/phasing/ReadBackedPhasingWalker.java   | 14 +++++++-------
 .../sting/gatk/walkers/phasing/SNPallelePair.java  |  2 +-
 3 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AllelePair.java b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AllelePair.java
index 4effa9767..f7e763d8c 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AllelePair.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AllelePair.java
@@ -21,7 +21,7 @@
  * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
  * OTHER DEALINGS IN THE SOFTWARE.
  */
-package org.broadinstitute.sting.playground.gatk.walkers.phasing;
+package org.broadinstitute.sting.gatk.walkers.phasing;
 
 import org.broad.tribble.util.variantcontext.Allele;
 import org.broad.tribble.util.variantcontext.Genotype;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
index 749ee83b8..33f1ebc18 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
@@ -22,7 +22,7 @@
  * OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.playground.gatk.walkers.phasing;
+package org.broadinstitute.sting.gatk.walkers.phasing;
 
 import org.broad.tribble.util.variantcontext.Allele;
 import org.broad.tribble.util.variantcontext.Genotype;
@@ -534,8 +534,8 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
 
                         edgeToReads.addRead(e, rdName);
 
-                        sitesWithEdges.add(e.v1);
-                        sitesWithEdges.add(e.v2);
+                        sitesWithEdges.add(e.getV1());
+                        sitesWithEdges.add(e.getV2());
                     }
                 }
             }
@@ -602,8 +602,8 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
                    Note that the path from prev ---> v1 will NOT contain v2, since we removed all of v2's edges,
                    and the path from v2 ---> cur will NOT contain v1.
                  */
-                boolean prevTo2and1ToCur = removedSiteSameCCAsPrev[e.v1].contains(e.v2) && removedSiteSameCCAsCur[e.v2].contains(e.v1);
-                boolean prevTo1and2ToCur = removedSiteSameCCAsPrev[e.v2].contains(e.v1) && removedSiteSameCCAsCur[e.v1].contains(e.v2);
+                boolean prevTo2and1ToCur = removedSiteSameCCAsPrev[e.getV1()].contains(e.getV2()) && removedSiteSameCCAsCur[e.getV2()].contains(e.getV1());
+                boolean prevTo1and2ToCur = removedSiteSameCCAsPrev[e.getV2()].contains(e.getV1()) && removedSiteSameCCAsCur[e.getV1()].contains(e.getV2());
 
                 if (prevTo2and1ToCur || prevTo1and2ToCur) {
                     for (String readName : edgeToReads.getReads(e)) {
@@ -611,9 +611,9 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
 
                         if (logger.isDebugEnabled()) {
                             if (prevTo2and1ToCur)
-                                logger.debug("Keep read " + readName + " due to path: " + prev + " ---> " + e.v2 + " -> " + e.v1 + " ---> " + cur);
+                                logger.debug("Keep read " + readName + " due to path: " + prev + " ---> " + e.getV2() + " -> " + e.getV1() + " ---> " + cur);
                             else
-                                logger.debug("Keep read " + readName + " due to path: " + prev + " ---> " + e.v1 + " -> " + e.v2 + " ---> " + cur);
+                                logger.debug("Keep read " + readName + " due to path: " + prev + " ---> " + e.getV1() + " -> " + e.getV2() + " ---> " + cur);
                         }
                     }
                 }
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/SNPallelePair.java b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/SNPallelePair.java
index 9b2ba6e5a..55a877c57 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/SNPallelePair.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/SNPallelePair.java
@@ -21,7 +21,7 @@
  * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
  * OTHER DEALINGS IN THE SOFTWARE.
  */
-package org.broadinstitute.sting.playground.gatk.walkers.phasing;
+package org.broadinstitute.sting.gatk.walkers.phasing;
 
 import org.broad.tribble.util.variantcontext.Allele;
 import org.broad.tribble.util.variantcontext.Genotype;