From 311dfa09989b2e98a0b1b6f4c063158e2e202d87 Mon Sep 17 00:00:00 2001
From: depristo <depristo@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 7 Jun 2011 00:13:44 +0000
Subject: [PATCH] Now builds examples, as I expected.  GATKPaperGenotyper lives
 again.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5953 348d0f76-0448-11de-a6fe-93d51630548a
---
 build.xml                                     |  8 ++---
 .../GATKPaperGenotyper.java                   |  2 +-
 .../examples/papergenotyper/SimpleCall.java   | 29 -------------------
 .../examples/papergenotyper/package-info.java |  4 ---
 4 files changed, 3 insertions(+), 40 deletions(-)
 rename java/src/org/broadinstitute/sting/gatk/examples/{papergenotyper => }/GATKPaperGenotyper.java (98%)
 delete mode 100644 java/src/org/broadinstitute/sting/gatk/examples/papergenotyper/SimpleCall.java
 delete mode 100644 java/src/org/broadinstitute/sting/gatk/examples/papergenotyper/package-info.java

diff --git a/build.xml b/build.xml
index f7ef3ba7c..549bf07b5 100644
--- a/build.xml
+++ b/build.xml
@@ -252,7 +252,6 @@
             description="compile the source">
         <!-- Compile the java code from ${src} into build -->
         <javac fork="true" memoryMaximumSize="512m" srcdir="${java.source.dir}" destdir="${java.classes}" debug="true" debuglevel="lines,vars,source" classpathref="external.dependencies" tempdir="${java.io.tmpdir}">
-            <exclude name="**/examples/**" />
             <exclude name="**/playground/**" unless="include.playground"/>
             <exclude name="**/oneoffprojects/**" unless="include.oneoffs"/>
             <compilerarg value="-proc:none"/>
@@ -268,7 +267,6 @@
 
     <target name="gatk.contracts" depends="gatk.compile.source" description="create GATK contracts" if="use.contracts">
         <javac fork="true" memoryMaximumSize="512m" srcdir="${java.source.dir}" destdir="${java.contracts}" debug="true" debuglevel="lines,vars,source" tempdir="${java.io.tmpdir}" >
-            <exclude name="**/examples/**" />
             <exclude name="**/playground/**" unless="include.playground"/>
             <exclude name="**/oneoffprojects/**" unless="include.oneoffs"/>
             <classpath>
@@ -679,10 +677,8 @@
                 <!-- needs to be if -->
                 <jvmarg value="-javaagent:lib/cofoja.jar"/>
                 <jvmarg value="-Dcom.google.java.contract.log.contract=false"/>
-<!-- 
-                <jvmarg value="-Xdebug"/>
-                <jvmarg value="-Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=5005"/>
- -->
+<!--                 <jvmarg value="-Xdebug"/> -->
+<!--                 <jvmarg value="-Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=5005"/> -->
                 <classpath>
                     <path refid="external.dependencies" />
                     <pathelement location="${java.classes}" />
diff --git a/java/src/org/broadinstitute/sting/gatk/examples/papergenotyper/GATKPaperGenotyper.java b/java/src/org/broadinstitute/sting/gatk/examples/GATKPaperGenotyper.java
similarity index 98%
rename from java/src/org/broadinstitute/sting/gatk/examples/papergenotyper/GATKPaperGenotyper.java
rename to java/src/org/broadinstitute/sting/gatk/examples/GATKPaperGenotyper.java
index 71043db75..b96d0ffbf 100644
--- a/java/src/org/broadinstitute/sting/gatk/examples/papergenotyper/GATKPaperGenotyper.java
+++ b/java/src/org/broadinstitute/sting/gatk/examples/GATKPaperGenotyper.java
@@ -23,7 +23,7 @@
  * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.gatk.examples.papergenotyper;
+package org.broadinstitute.sting.gatk.examples;
 
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
diff --git a/java/src/org/broadinstitute/sting/gatk/examples/papergenotyper/SimpleCall.java b/java/src/org/broadinstitute/sting/gatk/examples/papergenotyper/SimpleCall.java
deleted file mode 100644
index e1ba8379c..000000000
--- a/java/src/org/broadinstitute/sting/gatk/examples/papergenotyper/SimpleCall.java
+++ /dev/null
@@ -1,29 +0,0 @@
-package org.broadinstitute.sting.gatk.examples.papergenotyper;
-
-import org.broadinstitute.sting.utils.GenomeLoc;
-
-/**
- * Created by IntelliJ IDEA.
- * User: aaron
- * Date: Nov 19, 2009
- * Time: 2:07:25 AM
- *
- * This is a simple call class that stores the data for the per-locus calls of the GATKPaperGenotyper.
- *
- */
-class SimpleCall {
-    public String genotype;
-    public double LOD;
-    public GenomeLoc loc;
-    public char ref;
-    SimpleCall(GenomeLoc location, String gt, double lod, char reference) {
-        genotype = gt;
-        LOD = lod;
-        loc = location;
-        this.ref = reference;
-    }
-
-    public String toString() {
-        return String.format("%s\t%s\t%.4f\t%c", loc, genotype, LOD,ref);
-    }
-}
diff --git a/java/src/org/broadinstitute/sting/gatk/examples/papergenotyper/package-info.java b/java/src/org/broadinstitute/sting/gatk/examples/papergenotyper/package-info.java
deleted file mode 100644
index 976e4b469..000000000
--- a/java/src/org/broadinstitute/sting/gatk/examples/papergenotyper/package-info.java
+++ /dev/null
@@ -1,4 +0,0 @@
-/**
- * @help.display.name The GATK paper's Bayesian genotyper
- */
-package org.broadinstitute.sting.gatk.examples.papergenotyper;