Better support for specifying read filters to apply directly from the walkers.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1212 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/CommandLineExecutable.java

@@ -50,13 +50,8 @@ public abstract class CommandLineExecutable extends CommandLineProgram {
     /** the type of analysis to run - switch to the type of analysis */
     private String analysisName = "SomaticCoverageWalker";
 
-    // our walker manager
-    private WalkerManager walkerManager = null;
-
     // our genome analysis engine
-    private GenomeAnalysisEngine GATKEngine = null;
+    private GenomeAnalysisEngine GATKEngine = new GenomeAnalysisEngine();
-
-    public String pluginPathName = null;
 
     // get the analysis name
     protected abstract String getAnalysisName();
@@ -71,17 +66,7 @@ public abstract class CommandLineExecutable extends CommandLineProgram {
      * @return the return code to exit the program with
      */
     protected int execute() {
-
+        Walker<?,?> mWalker = GATKEngine.getWalkerByName(analysisName);
-        // create the walker
-        Walker<?, ?> mWalker = null;
-        try {
-            mWalker = walkerManager.createWalkerByName(analysisName);
-        } catch (InstantiationException ex) {
-            throw new RuntimeException("Unable to instantiate walker.", ex);
-        }
-        catch (IllegalAccessException ex) {
-            throw new RuntimeException("Unable to access walker", ex);
-        }
 
         // load the arguments into the walkers
         loadArgumentsIntoObject(argCollection);
@@ -93,7 +78,7 @@ public abstract class CommandLineExecutable extends CommandLineProgram {
         // set the analysis name in the argument collection
         this.argCollection.analysisName = this.analysisName;
         try {
-            GATKEngine = new GenomeAnalysisEngine(argCollection, mWalker);
+            GATKEngine.execute(argCollection, mWalker);
         }
         catch (ArgumentException ex) {
             // Rethrow argument exceptions.  Let the command-line argument do what it's designed to do.
@@ -124,20 +109,9 @@ public abstract class CommandLineExecutable extends CommandLineProgram {
      */
     @Override
     protected Class[] getArgumentSources() {
-        // get the analysis name from the overriding class
-        analysisName = this.getAnalysisName();
-        
-        // get any argument overrides they want to present
-        overrideArguments();
         // No walker info?  No plugins.
-        if (analysisName == null) return new Class[]{};
+        if (analysisName == null) return new Class[] {};
-
+        return new Class[] { GATKEngine.getWalkerByName(analysisName).getClass() };
-        walkerManager = new WalkerManager(pluginPathName);
-
-        if (!walkerManager.doesWalkerExist(analysisName))
-            throw new IllegalArgumentException("Invalid analysis name");
-
-        return new Class[]{walkerManager.getWalkerClassByName(analysisName)};
     }
 
 

java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java

@@ -1,7 +1,6 @@
 package org.broadinstitute.sting.gatk;
 
 import org.broadinstitute.sting.gatk.walkers.Walker;
-import org.broadinstitute.sting.gatk.traversals.TraversalEngine;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.xReadLines;
 import org.broadinstitute.sting.utils.cmdLine.*;
@@ -49,14 +48,8 @@ public class CommandLineGATK extends CommandLineProgram {
     @ArgumentCollection // our argument collection, the collection of command line args we accept
     public GATKArgumentCollection argCollection = new GATKArgumentCollection();
 
-    public String pluginPathName = null;
+    /** our genome analysis engine */
-
+    GenomeAnalysisEngine GATKEngine = new GenomeAnalysisEngine();
-    // our genome analysis engine
-    GenomeAnalysisEngine GATKEngine = null;
-
-    // our walker manager
-    private WalkerManager walkerManager = null;
-
 
     /** Required main method implementation. */
     public static void main(String[] argv) {
@@ -68,7 +61,6 @@ public class CommandLineGATK extends CommandLineProgram {
         }
     }
 
-
     /**
      * this is the function that the inheriting class can expect to have called
      * when the command line system has initialized.
@@ -76,15 +68,8 @@ public class CommandLineGATK extends CommandLineProgram {
      * @return the return code to exit the program with
      */
     protected int execute() {
-        Walker<?, ?> mWalker = null;
+        Walker<?,?> mWalker = GATKEngine.getWalkerByName(analysisName);
-        try {
+
-            mWalker = walkerManager.createWalkerByName(analysisName);
-        } catch (InstantiationException ex) {
-            throw new RuntimeException("Unable to instantiate walker.", ex);
-        }
-        catch (IllegalAccessException ex) {
-            throw new RuntimeException("Unable to access walker", ex);
-        }
         loadArgumentsIntoObject(argCollection);
         loadArgumentsIntoObject(mWalker);
 
@@ -92,11 +77,11 @@ public class CommandLineGATK extends CommandLineProgram {
 
         this.argCollection.analysisName = this.analysisName;
         try {
-            GATKEngine = new GenomeAnalysisEngine(argCollection, mWalker);
+            GATKEngine.execute(argCollection, mWalker);
         }
         catch (ArgumentException ex) {
             // Rethrow argument exceptions.  Let the command-line argument do what it's designed to do.
-            throw ex;            
+            throw ex;
         }
         catch (StingException exp) {
             System.err.println("Caught StingException. It's message is " + exp.getMessage());
@@ -125,13 +110,7 @@ public class CommandLineGATK extends CommandLineProgram {
     protected Class[] getArgumentSources() {
         // No walker info?  No plugins.
         if (analysisName == null) return new Class[] {};
-
+        return new Class[] { GATKEngine.getWalkerByName(analysisName).getClass() };
-        walkerManager = new WalkerManager(pluginPathName);
-
-        if (!walkerManager.doesWalkerExist(analysisName))
-            throw new IllegalArgumentException("Invalid analysis name");
-
-        return new Class[]{walkerManager.getWalkerClassByName(analysisName)};
     }
 
     @Override

java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java

@@ -27,12 +27,14 @@ package org.broadinstitute.sting.gatk;
 
 import net.sf.picard.reference.ReferenceSequenceFile;
 import net.sf.picard.reference.ReferenceSequenceFileFactory;
+import net.sf.picard.filter.SamRecordFilter;
 import org.apache.log4j.Logger;
 import org.broadinstitute.sting.gatk.executive.MicroScheduler;
 import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData;
 import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
 import org.broadinstitute.sting.gatk.traversals.TraversalEngine;
 import org.broadinstitute.sting.gatk.walkers.*;
+import org.broadinstitute.sting.gatk.filters.ZeroMappingQualityReadFilter;
 import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.cmdLine.ArgumentException;
 
@@ -50,7 +52,7 @@ public class GenomeAnalysisEngine {
     private TraversalEngine engine = null;
 
     // our argument collection
-    private final GATKArgumentCollection argCollection;
+    private GATKArgumentCollection argCollection;
 
     /** Collection of output streams used by the walker. */
     private OutputTracker outputTracker = null;
@@ -58,8 +60,11 @@ public class GenomeAnalysisEngine {
     /** our log, which we want to capture anything from this class */
     private static Logger logger = Logger.getLogger(GenomeAnalysisEngine.class);
 
-    /** the return value from our walker */
+    /** our walker manager */
-    private Object walkerReturn = null;
+    private final WalkerManager walkerManager;
+
+    /** plugin path for the walker manager. */
+    public final String pluginPathName = null;
 
     /**
      * our constructor, where all the work is done
@@ -67,22 +72,31 @@ public class GenomeAnalysisEngine {
      * legacy traversal types are sent to legacyTraversal function; as we move more of the traversals to the
      * new MicroScheduler class we'll be able to delete that function.
      *
-     * @param args      the argument collection, where we get all our setup information from
-     * @param my_walker the walker we're running with
      */
-    public GenomeAnalysisEngine(GATKArgumentCollection args, Walker my_walker) {
+    public GenomeAnalysisEngine() {
+        // make sure our instance variable points to this analysis engine
+        instance = this;
+        walkerManager = new WalkerManager(pluginPathName);
+    }
+
+    /**
+     * Actually run the GATK with the specified walker.
+     * @param args      the argument collection, where we get all our setup information from
+     * @param my_walker Walker to run over the dataset.  Must not be null.
+     */
+    public Object execute(GATKArgumentCollection args, Walker<?,?> my_walker) {
+        // validate our parameters
+        if (args == null) {
+            throw new StingException("The GATKArgumentCollection passed to GenomeAnalysisEngine can be null.");
+        }
 
         // validate our parameters
-        if (args == null || my_walker == null) {
+        if (my_walker == null)
-            throw new StingException("Neither the GATKArgumentCollection or the Walker passed to GenomeAnalysisEngine can be null.");
+            throw new StingException("The walker passed to GenomeAnalysisEngine can be null.");
-        }
 
         // save our argument parameter
         this.argCollection = args;
 
-        // make sure our instance variable points to this analysis engine
-        instance = this;
-
         // our reference ordered data collection
         List<ReferenceOrderedData<? extends ReferenceOrderedDatum>> rods = new ArrayList<ReferenceOrderedData<? extends ReferenceOrderedDatum>>();
 
@@ -129,9 +143,26 @@ public class GenomeAnalysisEngine {
             locs = GenomeLocSortedSet.createSetFromList(parseIntervalRegion(argCollection.intervals));
         }
         // excute the microscheduler, storing the results
-        walkerReturn = microScheduler.execute(my_walker, locs, argCollection.maximumEngineIterations);
+        return microScheduler.execute(my_walker, locs, argCollection.maximumEngineIterations);
     }
 
+    /**
+     * Retrieves an instance of the walker based on the walker name.
+     * @param walkerName Name of the walker.  Must not be null.  If the walker cannot be instantiated, an exception will be thrown.
+     * @return An instance of the walker.
+     */
+    public Walker<?,?> getWalkerByName( String walkerName ) {
+        try {
+            return walkerManager.createWalkerByName(walkerName);
+        } catch (InstantiationException ex) {
+            throw new StingException("Unable to instantiate walker.", ex);
+        }
+        catch (IllegalAccessException ex) {
+            throw new StingException("Unable to access walker", ex);
+        }
+    }
+
+
     /**
      * setup a microscheduler
      *
@@ -147,12 +178,12 @@ public class GenomeAnalysisEngine {
         // we need to verify different parameter based on the walker type
         if (my_walker instanceof LocusWalker || my_walker instanceof LocusWindowWalker) {
             // create the MicroScheduler
-            microScheduler = MicroScheduler.create(my_walker, extractSourceInfoFromArguments(argCollection), argCollection.referenceFile, rods, argCollection.numberOfThreads);
+            microScheduler = MicroScheduler.create(my_walker, extractSourceInfo(my_walker,argCollection), argCollection.referenceFile, rods, argCollection.numberOfThreads);
             engine = microScheduler.getTraversalEngine();
         } else if (my_walker instanceof ReadWalker || my_walker instanceof DuplicateWalker) {
             if (argCollection.referenceFile == null)
                 Utils.scareUser(String.format("Read-based traversals require a reference file but none was given"));
-            microScheduler = MicroScheduler.create(my_walker, extractSourceInfoFromArguments(argCollection), argCollection.referenceFile, rods, argCollection.numberOfThreads);
+            microScheduler = MicroScheduler.create(my_walker, extractSourceInfo(my_walker,argCollection), argCollection.referenceFile, rods, argCollection.numberOfThreads);
             engine = microScheduler.getTraversalEngine();
         } else {
             Utils.scareUser(String.format("Unable to create the appropriate TraversalEngine for analysis type " + argCollection.analysisName));
@@ -191,18 +222,24 @@ public class GenomeAnalysisEngine {
     /**
      * Bundles all the source information about the reads into a unified data structure.
      *
+     * @param walker The walker for which to extract info.
      * @param argCollection The collection of arguments passed to the engine.
      *
      * @return The reads object providing reads source info.
      */
+    private Reads extractSourceInfo( Walker walker, GATKArgumentCollection argCollection ) {
+        List<SamRecordFilter> filters = new ArrayList<SamRecordFilter>();
 
-    private Reads extractSourceInfoFromArguments(GATKArgumentCollection argCollection) {
+        filters.addAll( WalkerManager.getReadFilters(walker) );
-        return new Reads(argCollection.samFiles,
+        if( argCollection.filterZeroMappingQualityReads != null && argCollection.filterZeroMappingQualityReads )
-                argCollection.strictnessLevel,
+            filters.add( new ZeroMappingQualityReadFilter() );
-                argCollection.downsampleFraction,
+
-                argCollection.downsampleCoverage,
+        return new Reads( argCollection.samFiles,
-                !argCollection.unsafe,
+                          argCollection.strictnessLevel,
-                argCollection.filterZeroMappingQualityReads);
+                          argCollection.downsampleFraction,
+                          argCollection.downsampleCoverage,
+                          !argCollection.unsafe,
+                          filters );
     }
 
     private void validateInputsAgainstWalker(Walker walker,
@@ -297,14 +334,4 @@ public class GenomeAnalysisEngine {
     public GATKArgumentCollection getArguments() {
         return this.argCollection;
     }
-
-    /**
-     * Get's the return value of the walker
-     *
-     * @return an Object representing the return value of the walker
-     */
-    public Object getWalkerReturn() {
-        return walkerReturn;
-    }
-
 }

java/src/org/broadinstitute/sting/gatk/Reads.java

@@ -1,13 +1,11 @@
 package org.broadinstitute.sting.gatk;
 
-import org.broadinstitute.sting.gatk.traversals.TraversalEngine;
-import org.broadinstitute.sting.utils.StingException;
-
 import java.io.File;
-import java.io.FileNotFoundException;
 import java.util.List;
+import java.util.ArrayList;
 
 import net.sf.samtools.SAMFileReader;
+import net.sf.picard.filter.SamRecordFilter;
 /**
  * User: hanna
  * Date: May 14, 2009
@@ -31,7 +29,7 @@ public class Reads {
     private Double downsamplingFraction = null;
     private Integer downsampleToCoverage = null;
     private Boolean beSafe = null;
-    private Boolean filterZeroMappingQualityReads = null;
+    private List<SamRecordFilter> supplementalFilters = null;
 
     /**
      * Gets a list of the files acting as sources of reads.
@@ -73,8 +71,8 @@ public class Reads {
         return beSafe;
     }
 
-    public Boolean getFilterZeroMappingQualityReads() {
+    public List<SamRecordFilter> getSupplementalFilters() {
-        return filterZeroMappingQualityReads;
+        return supplementalFilters;
     }
 
     /**
@@ -83,6 +81,7 @@ public class Reads {
      */
     public Reads( List<File> readsFiles ) {
         this.readsFiles = readsFiles;
+        this.supplementalFilters = new ArrayList<SamRecordFilter>();
     }
 
     /**
@@ -94,19 +93,19 @@ public class Reads {
      * @param downsampleFraction fraction of reads to downsample.
      * @param downsampleCoverage downsampling per-locus.
      * @param beSafe Whether to enable safety checking.
-     * @param filterZeroMappingQualityReads whether to filter zero mapping quality reads.
+     * @param supplementalFilters additional filters to dynamically apply.
      */
     Reads( List<File> samFiles,
            SAMFileReader.ValidationStringency strictness,
            Double downsampleFraction,
            Integer downsampleCoverage,
            Boolean beSafe,
-           Boolean filterZeroMappingQualityReads ) {
+           List<SamRecordFilter> supplementalFilters ) {
         this.readsFiles = samFiles;
         this.validationStringency = strictness;
         this.downsamplingFraction = downsampleFraction;
         this.downsampleToCoverage = downsampleCoverage;
         this.beSafe = beSafe;
-        this.filterZeroMappingQualityReads = filterZeroMappingQualityReads;
+        this.supplementalFilters = supplementalFilters;
     }
 }

java/src/org/broadinstitute/sting/gatk/WalkerManager.java

@@ -8,19 +8,14 @@ import java.util.HashMap;
 import java.util.Map;
 import java.util.Arrays;
 
-import org.broadinstitute.sting.gatk.walkers.Walker;
+import org.broadinstitute.sting.gatk.walkers.*;
-import org.broadinstitute.sting.gatk.walkers.WalkerName;
-import org.broadinstitute.sting.gatk.walkers.DataSource;
-import org.broadinstitute.sting.gatk.walkers.By;
-import org.broadinstitute.sting.gatk.walkers.Allows;
-import org.broadinstitute.sting.gatk.walkers.Requires;
-import org.broadinstitute.sting.gatk.walkers.RMD;
 import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
 import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData;
 import org.broadinstitute.sting.utils.JVMUtils;
 import org.broadinstitute.sting.utils.PathUtils;
 import org.broadinstitute.sting.utils.StingException;
 import org.apache.log4j.Logger;
+import net.sf.picard.filter.SamRecordFilter;
 
 /**
  * Created by IntelliJ IDEA.
@@ -185,6 +180,30 @@ public class WalkerManager {
         return Arrays.asList(requiresDataSource.referenceMetaData());
     }
 
+    /**
+     * Extracts filters that the walker has requested be run on the dataset.
+     * @param walker Walker to inspect for filtering requests.
+     * @return A non-empty list of filters to apply to the reads.
+     */
+    public static List<SamRecordFilter> getReadFilters(Walker walker) {
+        Class<? extends SamRecordFilter>[] filterTypes = getReadFilterTypes(walker);
+        List<SamRecordFilter> filters = new ArrayList<SamRecordFilter>();
+
+        for( Class<? extends SamRecordFilter> filterType: filterTypes ) {
+            try {
+                filters.add(filterType.newInstance());
+            }
+            catch( InstantiationException ex ) {
+                throw new StingException("Unable to instantiate filter: " + filterType, ex);
+            }
+            catch( IllegalAccessException ex ) {
+                throw new StingException("Unable to access filter: " + filterType, ex);                
+            }
+        }
+
+        return filters;
+    }
+
     /**
      * Load classes internal to the classpath from an arbitrary location.
      *
@@ -280,4 +299,16 @@ public class WalkerManager {
         Allows allowsDataSource = walkerClass.getAnnotation(Allows.class);
         return allowsDataSource;
     }
+
+    /**
+     * Gets the list of filtering classes specified as walker annotations.
+     * @param walker The walker to inspect.
+     * @return An array of types extending from SamRecordFilter.  Will never be null.
+     */
+    private static Class<? extends SamRecordFilter>[] getReadFilterTypes(Walker walker) {
+        Class<? extends Walker> walkerClass = walker.getClass();
+        if( !walkerClass.isAnnotationPresent(ReadFilters.class) )
+            return new Class[0];
+        return walkerClass.getAnnotation(ReadFilters.class).value();
+    }
 }

java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMDataSource.java

@@ -16,6 +16,7 @@ import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.sam.SAMReadViolationHistogram;
 
 import java.io.File;
+import java.util.List;
 
 /*
  * Copyright (c) 2009 The Broad Institute
@@ -133,15 +134,15 @@ public class SAMDataSource implements SimpleDataSource {
             iterator = applyDecoratingIterators(true,
                     iterator,
                     reads.getDownsamplingFraction(),
-                    reads.getFilterZeroMappingQualityReads(),
+                    reads.getSafetyChecking(),
-                    reads.getSafetyChecking());
+                    reads.getSupplementalFilters());
         } else if (shard.getShardType() == Shard.ShardType.LOCUS || shard.getShardType() == Shard.ShardType.INTERVAL) {
             iterator = seekLocus(shard.getGenomeLoc());
             iterator = applyDecoratingIterators(false,
                     iterator,
                     reads.getDownsamplingFraction(),
-                    reads.getFilterZeroMappingQualityReads(),
+                    reads.getSafetyChecking(),
-                    reads.getSafetyChecking());
+                    reads.getSupplementalFilters());
         } else {
             throw new StingException("seek: Unknown shard type");
         }
@@ -362,15 +363,15 @@ public class SAMDataSource implements SimpleDataSource {
      * @param enableVerification Verify the order of reads.
      * @param wrappedIterator the raw data source.
      * @param downsamplingFraction whether and how much to downsample the reads themselves (not at a locus).
-     * @param filterZeroMappingQualityReads whether to filter zero mapping quality reads.
      * @param beSafeP Another trigger for the verifying iterator?  TODO: look into this.
+     * @param supplementalFilters additional filters to apply to the reads.
      * @return An iterator wrapped with filters reflecting the passed-in parameters.  Will not be null.
      */
     private StingSAMIterator applyDecoratingIterators(boolean enableVerification,
                                                       StingSAMIterator wrappedIterator,
                                                       Double downsamplingFraction,
-                                                      Boolean filterZeroMappingQualityReads,
+                                                      Boolean beSafeP,
-                                                      Boolean beSafeP) {
+                                                      List<SamRecordFilter> supplementalFilters) {
         // NOTE: this (and other filtering) should be done before on-the-fly sorting
         //  as there is no reason to sort something that we will end of throwing away
         if (downsamplingFraction != null)
@@ -379,19 +380,12 @@ public class SAMDataSource implements SimpleDataSource {
         if (beSafeP != null && beSafeP && enableVerification)
             wrappedIterator = new VerifyingSamIterator(wrappedIterator);
 
-        if ( filterZeroMappingQualityReads != null && filterZeroMappingQualityReads )
+        for( SamRecordFilter supplementalFilter: supplementalFilters )
             wrappedIterator = StingSAMIteratorAdapter.adapt(wrappedIterator.getSourceInfo(),
-                    new FilteringIterator(wrappedIterator, new ZeroMappingQualityReadFilterFunc()));
+                                                            new FilteringIterator(wrappedIterator,supplementalFilter));
 
         return wrappedIterator;
     }
-
-    private static class ZeroMappingQualityReadFilterFunc implements SamRecordFilter {
-        public boolean filterOut(SAMRecord rec) {
-            return (rec.getMappingQuality() == 0);
-        }
-    }
-    
 }
 
 

java/src/org/broadinstitute/sting/gatk/filters/ZeroMappingQualityReadFilter.java

@@ -0,0 +1,42 @@
+/*
+ * 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.
+ */
+
+package org.broadinstitute.sting.gatk.filters;
+
+import net.sf.picard.filter.SamRecordFilter;
+import net.sf.samtools.SAMRecord;
+
+/**
+ * Filter out zero mapping quality reads.
+ *
+ * @author hanna
+ * @version 0.1
+ */
+
+public class ZeroMappingQualityReadFilter implements SamRecordFilter {
+    public boolean filterOut(SAMRecord rec) {
+        return (rec.getMappingQuality() == 0);
+    }
+}
+

java/src/org/broadinstitute/sting/gatk/filters/package.html

@@ -0,0 +1,34 @@
+<!--
+  ~ 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.
+  -->
+
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"
+        "http://www.w3.org/TR/html4/loose.dtd">
+<html>
+<head>
+    <title></title>
+</head>
+<body>
+Provides a commonly used set of filters for determining which data should and should not be applied.
+</body>
+</html>

java/src/org/broadinstitute/sting/gatk/walkers/PrintLocusContextWalker.java

@@ -1,12 +1,10 @@
 package org.broadinstitute.sting.gatk.walkers;
 
 import org.broadinstitute.sting.gatk.LocusContext;
-import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 
 import java.util.List;
 import java.util.Arrays;
-import java.util.ArrayList;
 
 import net.sf.samtools.SAMRecord;
 
@@ -17,8 +15,8 @@ import net.sf.samtools.SAMRecord;
  * Time: 11:23:14 AM
  * To change this template use File | Settings | File Templates.
  */
-public class PrintLocusContextWalker extends LocusWindowWalker<LocusContext, Integer> implements TreeReducible<Integer> {
+public class PrintLocusContextWalker extends LocusWalker<LocusContext, Integer> implements TreeReducible<Integer> {
-    public LocusContext map(RefMetaDataTracker tracker, String ref, LocusContext context) {
+    public LocusContext map(RefMetaDataTracker tracker, char ref, LocusContext context) {
         out.printf( "In map: ref = %s, loc = %s, reads = %s%n", ref,
                                                                 context.getLocation(),
                                                                 Arrays.deepToString( getReadNames(context.getReads()) ) );

java/src/org/broadinstitute/sting/gatk/walkers/RMD.java

@@ -1,6 +1,8 @@
 package org.broadinstitute.sting.gatk.walkers;
 
 import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
+
+import java.lang.annotation.*;
 /**
  * User: hanna
  * Date: May 19, 2009
@@ -17,7 +19,10 @@ import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
 /**
  * A data type representing reference-ordered data.
  */
-
+@Documented
+@Inherited
+@Retention(RetentionPolicy.RUNTIME)
+@Target(ElementType.TYPE)
 public @interface RMD {
     String name();    
     Class<? extends ReferenceOrderedDatum> type();

java/src/org/broadinstitute/sting/gatk/walkers/ReadFilters.java

@@ -0,0 +1,43 @@
+/*
+ * 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.
+ */
+
+package org.broadinstitute.sting.gatk.walkers;
+
+import net.sf.picard.filter.SamRecordFilter;
+
+import java.lang.annotation.*;
+
+/**
+ * An annotation to describe what kind of data will be filtered out.
+ *
+ * @author hanna
+ * @version 0.1
+ */
+@Documented
+@Inherited
+@Retention(RetentionPolicy.RUNTIME)
+@Target(ElementType.TYPE)
+public @interface ReadFilters {
+    public Class<? extends SamRecordFilter>[] value() default {};
+}

java/src/org/broadinstitute/sting/playground/gatk/walkers/SingleSampleGenotyper.java

@@ -3,8 +3,10 @@ package org.broadinstitute.sting.playground.gatk.walkers;
 import net.sf.samtools.SAMReadGroupRecord;
 import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.LocusContext;
+import org.broadinstitute.sting.gatk.filters.ZeroMappingQualityReadFilter;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.LocusWalker;
+import org.broadinstitute.sting.gatk.walkers.ReadFilters;
 import org.broadinstitute.sting.playground.utils.AlleleFrequencyEstimate;
 import org.broadinstitute.sting.playground.utils.AlleleMetrics;
 import org.broadinstitute.sting.playground.utils.GenotypeLikelihoods;
@@ -20,6 +22,7 @@ import java.io.FileNotFoundException;
 import java.io.PrintStream;
 import java.util.List;
 
+@ReadFilters(ZeroMappingQualityReadFilter.class)
 public class SingleSampleGenotyper extends LocusWalker<AlleleFrequencyEstimate, String> {
     // Control output settings
     @Argument(fullName="variants_out", shortName="varout", doc="File to which variants should be written", required=true) public File VARIANTS_FILE;

java/src/org/broadinstitute/sting/utils/cmdLine/CommandLineProgram.java

@@ -151,6 +151,11 @@ public abstract class CommandLineProgram {
         return null;
     }
 
+    static {
+        // setup a basic log configuration
+        BasicConfigurator.configure();
+    }
+
     /**
      * This function is called to start processing the command line, and kick
      * off the execute message of the program.
@@ -161,9 +166,6 @@ public abstract class CommandLineProgram {
     public static void start(CommandLineProgram clp, String[] args) {
 
         try {
-            // setup a basic log configuration
-            BasicConfigurator.configure();
-
             // setup our log layout
             PatternLayout layout = new PatternLayout();