First step in replacing the Hello, World! document. Revamped the HelloWalker and checked it into the source tree, created a special build file for it, and added it to the packaging tool.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1135 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/examples/HelloWalker.java

@@ -0,0 +1,76 @@
+/*
+ * 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.
+ */
+import org.broadinstitute.sting.gatk.walkers.LocusWalker;
+import org.broadinstitute.sting.gatk.LocusContext;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+
+/**
+ * An example walker for illustrative purposes.
+ */
+public class HelloWalker extends LocusWalker<Integer,Long> {
+    /**
+     * The map function runs once per single-base locus, and accepts a 'context', a
+     * data structure consisting of the reads which overlap the locus, the sites over
+     * which they fall, and the base from the reference that overlaps.
+     * @param tracker The accessor for reference metadata.
+     * @param ref The reference base that lines up with this locus.
+     * @param context Information about reads overlapping this locus.
+     * @return In this case, returns a count of how many loci were seen at this site (1).
+     */
+    @Override
+    public Integer map(RefMetaDataTracker tracker, char ref, LocusContext context) {
+        out.printf("Hello locus %s; your ref base is %c and you have %d reads%n", context.getLocation(), ref, context.getReads().size() );
+        return 1;
+    }
+
+    /**
+     * Provides an initial value for the reduce function.  Hello walker counts loci,
+     * so the base case for the inductive step is 0, indicating that the walker has seen 0 loci.
+     * @return 0.
+     */
+    @Override
+    public Long reduceInit() { return 0L; }
+
+    /**
+     * Combines the result of the latest map with the accumulator.  In inductive terms,
+     * this represents the step loci[x + 1] = loci[x] + 1
+     * @param value result of the map.
+     * @param sum accumulator for the reduce.
+     * @return The total count of loci processed so far.
+     */
+    @Override
+    public Long reduce(Integer value, Long sum) {
+        return sum + value;
+    }
+
+    /**
+     * Retrieves the final result of the traversal.
+     * @param result The ultimate value of the traversal, produced when map[n] is combined with reduce[n-1]
+     *               by the reduce function. 
+     */
+    @Override
+    public void onTraversalDone(Long result) {
+        out.println("Number of loci viewed is: " + result);
+    }
+}

java/src/org/broadinstitute/sting/gatk/examples/build.xml

@@ -0,0 +1,40 @@
+<!--
+  ~ 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.
+  -->
+
+<project name="BuildHelloWalker" default="dist" basedir=".">
+    <description>Build the GATK examples</description>
+    
+    <property name="gatk.home" value="${user.home}/GenomeAnalysisTK" />
+    <property name="walker.home" value="${gatk.home}/walkers" />
+
+    <target name="dist">
+      <mkdir dir="${walker.home}" />
+      <javac srcdir="${basedir}" destdir="${walker.home}">
+          <classpath>
+            <fileset dir="${gatk.home}" includes="GenomeAnalysisTK.jar" />
+          </classpath>
+      </javac>
+    </target>
+
+</project>

packages/GenomeAnalysisTK.xml

@@ -7,4 +7,8 @@
     <class>org.broadinstitute.sting.gatk.walkers.PileupWalker</class>
     <class>org.broadinstitute.sting.gatk.walkers.PrintReadsWalker</class>
   </dependencies>
+  <resources>
+    <file>java/src/org/broadinstitute/sting/gatk/examples/HelloWalker.java</file>
+    <file>java/src/org/broadinstitute/sting/gatk/examples/build.xml</file>
+  </resources>
 </package>