Better organization of AnalysisTK modules

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6 348d0f76-0448-11de-a6fe-93d51630548a

lib/edu/mit/broad/picard/filter/FilteringIterator.java

@@ -86,7 +86,7 @@ public class FilteringIterator implements CloseableIterator<SAMRecord> {
         while (iterator.hasNext()) {
             SAMRecord record = iterator.next();
             if (!filter.filterOut(record)) {
-                return next;
+                return record;
             }
         }
         return null;

src/edu/mit/broad/sting/atk/AnalysisTK.java

@@ -19,7 +19,7 @@ public class AnalysisTK extends CommandLineProgram {
     @Option(shortName="R", doc="Reference sequence file", optional=true) public File REF_FILE_ARG = null;
     @Option(shortName="B", doc="Debugging output", optional=true) public String DEBUGGING_STR = null;
     @Option(shortName="L", doc="Genome region to operation on: from chr:start-end", optional=true) public String REGION_STR = null;
-    @Option(shortName="T", doc="Type of analysis to run") public String AnalysisName = null;
+    @Option(shortName="T", doc="Type of analysis to run") public String Analysis_Name = null;
 
     public static HashMap<String, Object> MODULES = new HashMap<String,Object>();
     public static void addModule(final String name, final Object walker) {
@@ -28,13 +28,13 @@ public class AnalysisTK extends CommandLineProgram {
     }
 
     static {
-        addModule("EmptyLocusWalker", new EmptyLocusWalker());
-        addModule("PileupWalker", new PileupWalker());
+        addModule("Empty_Locus_Walker", new EmptyLocusWalker());
+        addModule("Pileup", new PileupWalker());
+        addModule("Empty_Read_Walker", new EmptyReadWalker());
+        addModule("Base_Quality_Histogram", new BaseQualityHistoWalker());
     }
 
     private TraversalEngine engine = null;
-    private int nSkippedIndels = 0;
-
     public boolean DEBUGGING = false;
 
     /** Required main method implementation. */
@@ -45,7 +45,7 @@ public class AnalysisTK extends CommandLineProgram {
     protected int doWork() {
         this.engine = new TraversalEngine(INPUT_FILE, REF_FILE_ARG);
 
-        ValidationStringency strictness = ValidationStringency.STRICT;
+        ValidationStringency strictness;
     	if ( STRICTNESS_ARG == null ) {
             strictness = ValidationStringency.STRICT;
     	}
@@ -64,10 +64,17 @@ public class AnalysisTK extends CommandLineProgram {
         engine.setDebugging(! ( DEBUGGING_STR == null || DEBUGGING_STR.toLowerCase().equals("true")));
         engine.setMaxReads(Integer.parseInt(MAX_READS_ARG));
 
-        //LocusWalker<Integer,Integer> walker = new EmptyLocusWalker();
-        LocusWalker<?, ?> walker = (LocusWalker<?, ?>)MODULES.get(AnalysisName);
+        //LocusWalker<Integer,Integer> walker = new PileupWalker();
         engine.initialize();
-        engine.traverseByLoci(walker);
+        try {
+            LocusWalker<?, ?> walker = (LocusWalker<?, ?>)MODULES.get(Analysis_Name);
+            engine.traverseByLoci(walker);
+        }
+        catch ( java.lang.ClassCastException e ) {
+            // I guess we're a read walker LOL
+            ReadWalker<?, ?> walker = (ReadWalker<?, ?>)MODULES.get(Analysis_Name);
+            engine.traverseByRead(walker);
+        }
 
         return 0;
     }

src/edu/mit/broad/sting/atk/modules/BaseQualityHistoWalker.java

@@ -11,7 +11,7 @@ import edu.mit.broad.sting.atk.LocusContext;
  * Time: 3:22:14 PM
  * To change this template use File | Settings | File Templates.
  */
-public class ReadWalkerTest implements ReadWalker<Integer, Integer> {
+public class BaseQualityHistoWalker implements ReadWalker<Integer, Integer> {
     long[] qualCounts = new long[100];
 
     public void initialize() {
@@ -44,8 +44,16 @@ public class ReadWalkerTest implements ReadWalker<Integer, Integer> {
     }
 
     public void onTraveralDone() {
-        for ( int i = 0; i < this.qualCounts.length; i++ ) {
+        int lastNonZero = -1;
+        for ( int i = this.qualCounts.length-1; i >= 0; i-- ) {
+            if ( this.qualCounts[i] > 0 ) {
+                lastNonZero = i;
+                break;
+            }
+        }
+
+        for ( int i = 0; i < lastNonZero+1; i++ ) {
             System.out.printf("%3d : %10d%n", i, this.qualCounts[i]);
         }
     }
-}
+}

src/edu/mit/broad/sting/atk/modules/EmptyReadWalker.java

@@ -0,0 +1,38 @@
+package edu.mit.broad.sting.atk.modules;
+
+import edu.mit.broad.sam.SAMRecord;
+import edu.mit.broad.sting.atk.ReadWalker;
+import edu.mit.broad.sting.atk.LocusContext;
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: mdepristo
+ * Date: Feb 22, 2009
+ * Time: 3:22:14 PM
+ * To change this template use File | Settings | File Templates.
+ */
+public class EmptyReadWalker implements ReadWalker<Integer, Integer> {
+
+    public void initialize() { }
+
+    public String walkerType() { return "ByRead"; }
+
+    // Do we actually want to operate on the context?
+    public boolean filter(LocusContext context, SAMRecord read) {
+        return true;    // We are keeping all the reads
+    }
+
+    // Map over the edu.mit.broad.sting.atk.LocusContext
+    public Integer map(LocusContext context, SAMRecord read) {
+        return 1;
+    }
+
+    // Given result of map function
+    public Integer reduceInit() { return 0; }
+    public Integer reduce(Integer value, Integer sum) {
+        return value + sum;
+    }
+
+    public void onTraveralDone() {
+    }
+}

src/scripts/TraverseTest.sh

@@ -1 +1 @@
-java -cp out/production/AnalysisTK:../../jars/broad.jar edu.mit.broad.sting.atk.AnalysisTK $*
+java -Xmx1024m -cp out/production/AnalysisTK:../../jars/broad.jar edu.mit.broad.sting.atk.AnalysisTK $*

src/scripts/TraverseTestProf.sh

@@ -1 +1 @@
-java -agentlib:hprof=cpu=samples -cp out/production/AnalysisTK:../../jars/broad.jar edu.mit.broad.sting.atk.AnalysisTK $*
+java -Xmx1024m -agentlib:hprof=cpu=samples -cp out/production/AnalysisTK:../../jars/broad.jar edu.mit.broad.sting.atk.AnalysisTK $*