Waypoint check-in: a couple of changes to for Tribble, and adding some options to the integration test for passing in auxillary files that aren’t “%s” command line options.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2925 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/refdata/tracks/FeatureReaderTrack.java

@@ -72,6 +72,16 @@ public class FeatureReaderTrack extends RMDTrack implements QueryableTrack {
         }
     }
 
+    /**
+     * do we support the query interface?
+     *
+     * @return true
+     */
+    @Override
+    public boolean supportsQuery() {
+        return true;
+    }
+
     @Override
     public Iterator<GATKFeature> query(GenomeLoc interval) throws IOException {
         return new FeatureToGATKFeatureIterator(reader.query(interval.getContig(),(int)interval.getStart(),(int)interval.getStop()),this.getName());

java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrack.java

@@ -85,4 +85,10 @@ public abstract class RMDTrack {
     public boolean matches(String name, String type) {
         return (name.equals(this.name) && type.equals(this.type.getSimpleName()));
     }
+
+    /**
+     * do we support the query interface?
+     * @return true if we can be cast to the QueryableTrack interface 
+     */
+    public abstract boolean supportsQuery();
 }

java/src/org/broadinstitute/sting/gatk/refdata/tracks/RODRMDTrack.java

@@ -24,7 +24,6 @@
 package org.broadinstitute.sting.gatk.refdata.tracks;
 
 import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData;
-import org.broadinstitute.sting.gatk.refdata.SeekableRODIterator;
 import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
 import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODIterator;
 import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
@@ -40,7 +39,7 @@ import java.util.Iterator;
  * 
  * Class RODRMDTrack
  *
- * wrap a reference ordered data object in the new track style. This will hopefully be phased-out as we move to
+ * wrap a reference ordered data object in the new track style. This track will hopefully be phased-out as we move to
  * a FeatureReader based system.
  */
 public class RODRMDTrack extends RMDTrack {
@@ -67,15 +66,29 @@ public class RODRMDTrack extends RMDTrack {
      */
     @Override
     public Iterator<GATKFeature> getIterator() {
-        return new SRIToIterator(data.iterator());
+        return new RODIteratorToRMDIterator(data.iterator());
+    }
+
+    /**
+     * do we support the query interface?
+     *
+     * @return false
+     */
+    @Override
+    public boolean supportsQuery() {
+        return false; // sadly no, we don't
     }
 }
 
-class SRIToIterator implements Iterator<GATKFeature> {
+/**
+ * this class wraps a ROD iterator, so that it produces GATKFeatures (basicly features that can generate a GenomeLoc
+ * for its position).  
+ */
+class RODIteratorToRMDIterator implements Iterator<GATKFeature> {
     private RODRecordList list = null;
     private LocationAwareSeekableRODIterator iterator = null;
 
-    SRIToIterator(LocationAwareSeekableRODIterator iter) {
+    RODIteratorToRMDIterator(LocationAwareSeekableRODIterator iter) {
             iterator = iter;
     }
 

java/test/org/broadinstitute/sting/WalkerTest.java

@@ -15,8 +15,7 @@ import java.io.IOException;
 import java.io.InputStream;
 import java.math.BigInteger;
 import java.security.MessageDigest;
-import java.util.ArrayList;
-import java.util.List;
+import java.util.*;
 
 public class WalkerTest extends BaseTest {
     public String assertMatchingMD5(final String name, final File resultsFile, final String expectedMD5 ) {
@@ -90,6 +89,8 @@ public class WalkerTest extends BaseTest {
         List<String> md5s = null;
         List<String> exts = null;
 
+        Map<String,File> auxillaryFiles = new HashMap<String,File>();
+
         public WalkerTestSpec(String args, int nOutputFiles, List<String> md5s) {
             this.args = args;
             this.nOutputFiles = nOutputFiles;
@@ -102,6 +103,10 @@ public class WalkerTest extends BaseTest {
             this.md5s = md5s;
             this.exts = exts;
         }
+
+        public void addAuxFile(String expectededMD5sum, File outputfile) {
+            auxillaryFiles.put(expectededMD5sum,outputfile);
+        }
     }
 
     protected boolean parameterize() {
@@ -125,6 +130,28 @@ public class WalkerTest extends BaseTest {
         System.out.println(Utils.dupString('-', 80));
         System.out.println(String.format("Executing test %s with GATK arguments: %s", name, args));
 
+        List<String> md5s = new LinkedList<String>();
+        md5s.addAll(spec.md5s);
+
+        // check to see if they included any auxillary files, if so add them to the list
+        for (String md5 : spec.auxillaryFiles.keySet()) {
+            md5s.add(md5);
+            tmpFiles.add(spec.auxillaryFiles.get(md5));
+        }
+
+        return executeTest(name, md5s, tmpFiles, args);
+    }
+
+
+    /**
+     * execute the test, given the following:
+     * @param name the name of the test
+     * @param md5s the list of md5s
+     * @param tmpFiles the temp file corresponding to the md5 list
+     * @param args the argument list
+     * @return a pair of file and string lists
+     */
+    private Pair<List<File>, List<String>> executeTest(String name, List<String> md5s, List<File> tmpFiles, String args) {
         CommandLineGATK instance = new CommandLineGATK();
         String[] command;
 
@@ -142,8 +169,8 @@ public class WalkerTest extends BaseTest {
             throw new RuntimeException("Error running the GATK with arguments: " + args);
         }
 
-        return new Pair<List<File>, List<String>>(tmpFiles, assertMatchingMD5s(name, tmpFiles, spec.md5s));
-    }    
+        return new Pair<List<File>, List<String>>(tmpFiles, assertMatchingMD5s(name, tmpFiles, md5s));
+    }
 
     private static String[] escapeExpressions(String args, String delimiter) {
         String[] command = {};