Fixing PrintRODs. Now has input and only prints out one copy of each record

public/java/src/org/broadinstitute/sting/gatk/walkers/PrintRODsWalker.java

@@ -26,21 +26,23 @@
 package org.broadinstitute.sting.gatk.walkers;
 
 import org.broad.tribble.Feature;
+import org.broadinstitute.sting.commandline.Input;
 import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.commandline.RodBinding;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.refdata.VariantContextAdaptors;
-import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
 
 import java.io.PrintStream;
-import java.util.Iterator;
 
 /**
  * Prints out all of the RODs in the input data set. Data is rendered using the toString() method
  * of the given ROD.
  */
 public class PrintRODsWalker extends RodWalker<Integer, Integer> {
+    @Input(fullName="input", shortName = "input", doc="The input ROD which should be printed out.", required=true)
+    public RodBinding<Feature> input;
+
     @Output
     PrintStream out;
 
@@ -62,7 +64,7 @@ public class PrintRODsWalker extends RodWalker<Integer, Integer> {
         if ( tracker == null )
             return 0;
 
-        for ( Feature feature : tracker.getValues(Feature.class) ) {
+        for ( Feature feature : tracker.getValues(Feature.class, context.getLocation()) ) {
             out.println(feature.toString());
         }
 

public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java

@@ -32,24 +32,6 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
         executeTest("test MultiSample Pilot1", spec);
     }
 
-    //    @Test
-    // todo - currently not working because when calling indels, using GENOTYPE_GIVEN_ALLELES yields a different result than in normal mode. To be fixed when extended events are removed.
-    public void testMultiSamplePilot2AndRecallingWithAlleles() {
-        String md5 = "b45636b29891f9df573ad2af6f507ee0";
-
-        WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
-                baseCommand + " -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,050,000", 1,
-                Arrays.asList(md5));
-        List<File> result = executeTest("test MultiSample Pilot2", spec1).getFirst();
-
-        GenomeAnalysisEngine.resetRandomGenerator();
-
-        WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
-                baseCommand + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + result.get(0).getAbsolutePath() + " -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,050,000", 1,
-                Arrays.asList(md5));
-        executeTest("test MultiSample Pilot2 with alleles passed in", spec2);       
-    }
-
     @Test
     public void testWithAllelesPassedIn() {
         WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
@@ -87,15 +69,6 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
         executeTest("test compressed output", spec);
     }
 
-    // todo -- fixme
-//    @Test
-//    public void testCompressedOutputParallel() {
-//        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-//                baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,100,000 -nt 4", 1,
-//                Arrays.asList("gz"), Arrays.asList(COMPRESSED_OUTPUT_MD5));
-//        executeTest("testCompressedOutput-nt4", spec);
-//    }
-
     // --------------------------------------------------------------------------------------------------------------
     //
     // testing parallelization
@@ -296,6 +269,13 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
                         "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1,
                 Arrays.asList("94977d6e42e764280e9deaf4e3ac8c80"));
         executeTest("test MultiSample Pilot2 indels with alleles passed in and emitting all sites", spec2);
+
+        WalkerTest.WalkerTestSpec spec3 = new WalkerTest.WalkerTestSpec(
+                baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "indelAllelesForUG.vcf -I " + validationDataLocation +
+                        "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1,
+                Arrays.asList("408d3aba4d094c067fc00a43992c2292"));
+        executeTest("test MultiSample Pilot2 indels with complicated records", spec3);
+
     }