Initial checkin of skeleton code for AnalyzeAnnotations

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2605 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/analyzecovariates/AnalysisDataManager.java

@@ -5,6 +5,31 @@ import org.broadinstitute.sting.utils.NestedHashMap;
 
 import java.util.ArrayList;
 
+/*
+ * Copyright (c) 2009 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.
+ */
+
 /**
  * Created by IntelliJ IDEA.
  * User: rpoplin

java/src/org/broadinstitute/sting/analyzecovariates/AnalyzeCovariates.java

@@ -12,6 +12,31 @@ import java.util.Map;
 import java.util.regex.Pattern;
 import java.io.*;
 
+/*
+ * Copyright (c) 2009 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.
+ */
+
 /**
  * Created by IntelliJ IDEA.
  * User: rpoplin

java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnalyzeAnnotationsWalker.java

@@ -0,0 +1,86 @@
+package org.broadinstitute.sting.playground.gatk.walkers.variantoptimizer;
+
+import org.broadinstitute.sting.gatk.walkers.RodWalker;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+
+/*
+ * 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.
+ */
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: rpoplin
+ * Date: Jan 15, 2010
+ */
+
+public class AnalyzeAnnotationsWalker extends RodWalker<Integer, Integer> {
+
+    /////////////////////////////
+    // Command Line Arguments
+    /////////////////////////////
+
+    /////////////////////////////
+    // Private Member Variables
+    /////////////////////////////
+    
+    //---------------------------------------------------------------------------------------------------------------
+    //
+    // initialize
+    //
+    //---------------------------------------------------------------------------------------------------------------
+
+    public void initialize() {
+    }
+
+    //---------------------------------------------------------------------------------------------------------------
+    //
+    // map
+    //
+    //---------------------------------------------------------------------------------------------------------------
+
+    public Integer map( RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context ) {
+        // Add each VCF record to eacn annotation's data structure
+        return 1; // This value isn't actually used for anything
+    }
+
+    //---------------------------------------------------------------------------------------------------------------
+    //
+    // reduce
+    //
+    //---------------------------------------------------------------------------------------------------------------
+
+    public Integer reduceInit() {
+        return 0; // Nothing to do here
+    }
+
+    public Integer reduce( Integer value, Integer sum ) {
+        return 0; // Nothing to do here
+    }
+
+    public void onTraversalDone( Integer sum ) {
+        // For each annotation, decide how to cut up the data, output intermediate cumulative p(true) tables, and call RScript to plot the tables
+    }
+}