From 1515bf6de9c47d062b97c228e684b41ab1ee86dd Mon Sep 17 00:00:00 2001
From: fromer <fromer@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 2 Dec 2010 22:03:02 +0000
Subject: [PATCH] Merged common VCF writing logic into phasing/WriteVCF.java

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4776 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../walkers/phasing/AnnotateMNPsWalker.java   | 11 +----
 .../gatk/walkers/phasing/MergeMNPsWalker.java | 11 +----
 ...ergeSegregatingAlternateAllelesWalker.java | 11 +----
 .../phasing/ReadBackedPhasingWalker.java      | 11 +----
 .../sting/gatk/walkers/phasing/WriteVCF.java  | 44 +++++++++++++++++++
 5 files changed, 48 insertions(+), 40 deletions(-)
 create mode 100644 java/src/org/broadinstitute/sting/gatk/walkers/phasing/WriteVCF.java

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AnnotateMNPsWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AnnotateMNPsWalker.java
index 4121c5257..e1c1c1918 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AnnotateMNPsWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AnnotateMNPsWalker.java
@@ -305,16 +305,7 @@ public class AnnotateMNPsWalker extends RodWalker<Integer, Integer> {
     }
 
     private void writeVCF(VariantContext vc) {
-        byte refBase;
-        if (!vc.isIndel()) {
-            Allele varAllele = vc.getReference();
-            refBase = SNPallelePair.getSingleBase(varAllele);
-        }
-        else {
-            refBase = vc.getReferenceBaseForIndel();
-        }
-
-        writer.add(vc, refBase);
+        WriteVCF.writeVCF(vc, writer, logger);
     }
 
     /*
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeMNPsWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeMNPsWalker.java
index 2d5fd2d9a..5122e10c3 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeMNPsWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeMNPsWalker.java
@@ -111,16 +111,7 @@ public class MergeMNPsWalker extends RodWalker<Integer, Integer> {
     }
 
     private void writeVCF(VariantContext vc) {
-        byte refBase;
-        if (!vc.isIndel()) {
-            Allele varAllele = vc.getReference();
-            refBase = SNPallelePair.getSingleBase(varAllele);
-        }
-        else {
-            refBase = vc.getReferenceBaseForIndel();
-        }
-
-        vcMergerWriter.add(vc, refBase);
+        WriteVCF.writeVCF(vc, vcMergerWriter, logger);
     }
 
     public Integer reduce(Integer result, Integer total) {
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesWalker.java
index 7bbbd34d9..56a3b8b76 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesWalker.java
@@ -146,16 +146,7 @@ public class MergeSegregatingAlternateAllelesWalker extends RodWalker<Integer, I
     }
 
     private void writeVCF(VariantContext vc) {
-        byte refBase;
-        if (!vc.isIndel()) {
-            Allele varAllele = vc.getReference();
-            refBase = SNPallelePair.getSingleBase(varAllele);
-        }
-        else {
-            refBase = vc.getReferenceBaseForIndel();
-        }
-
-        vcMergerWriter.add(vc, refBase);
+        WriteVCF.writeVCF(vc, vcMergerWriter, logger);
     }
 
     public Integer reduce(Integer result, Integer total) {
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 956c6f57d..50466f5e0 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
@@ -980,16 +980,7 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
     }
 
     private void writeVCF(VariantContext vc) {
-        byte refBase;
-        if (!vc.isIndel()) {
-            Allele varAllele = vc.getReference();
-            refBase = SNPallelePair.getSingleBase(varAllele);
-        }
-        else {
-            refBase = vc.getReferenceBaseForIndel();
-        }
-
-        writer.add(vc, refBase);
+        WriteVCF.writeVCF(vc, writer, logger);
     }
 
     public static boolean processVariantInPhasing(VariantContext vc) {
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/WriteVCF.java b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/WriteVCF.java
new file mode 100644
index 000000000..ddeadee37
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/WriteVCF.java
@@ -0,0 +1,44 @@
+/*
+ * Copyright (c) 2010, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+package org.broadinstitute.sting.gatk.walkers.phasing;
+
+import org.apache.log4j.Logger;
+import org.broad.tribble.util.variantcontext.Allele;
+import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broad.tribble.vcf.VCFWriter;
+
+public class WriteVCF {
+    public static void writeVCF(VariantContext vc, VCFWriter writer, Logger logger) {
+        byte refBase;
+        if (!vc.isIndel()) {
+            Allele refAllele = vc.getReference();
+            refBase = SNPallelePair.getSingleBase(refAllele);
+        }
+        else {
+            refBase = vc.getReferenceBaseForIndel();
+        }
+
+        writer.add(vc, refBase);
+    }
+}