Fix build problems with tests

public/java/src/org/broadinstitute/sting/utils/baq/ReadTransformingIterator.java

@@ -19,7 +19,7 @@ public class ReadTransformingIterator implements StingSAMIterator {
     /**
      * Creates a new ReadTransforming iterator
      */
-    @Requires({"it != null", "engine != null", "transformer != null", "transformer.isInitialized()"})
+    @Requires({"it != null", "transformer != null", "transformer.isInitialized()"})
     public ReadTransformingIterator(final StingSAMIterator it, final ReadTransformer transformer) {
         if ( ! transformer.isInitialized() )
             throw new IllegalStateException("Creating a read transformer stream for an uninitialized read transformer: " + transformer);

public/java/test/org/broadinstitute/sting/gatk/datasources/reads/DownsamplerBenchmark.java

@@ -36,8 +36,8 @@ import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
 import org.broadinstitute.sting.gatk.filters.ReadFilter;
 import org.broadinstitute.sting.gatk.filters.UnmappedReadFilter;
 import org.broadinstitute.sting.gatk.iterators.LocusIteratorByState;
+import org.broadinstitute.sting.gatk.iterators.ReadTransformer;
 import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.baq.BAQ;
 
 import java.util.Collections;
 import java.util.Iterator;
@@ -69,18 +69,15 @@ public class DownsamplerBenchmark extends ReadProcessingBenchmark {
         for(int i = 0; i < reps; i++) {
             SAMFileReader reader = new SAMFileReader(inputFile);
             ReadProperties readProperties = new ReadProperties(Collections.<SAMReaderID>singletonList(new SAMReaderID(inputFile,new Tags())),
-                                                               reader.getFileHeader(),
+                    reader.getFileHeader(),
-                                                               false,
+                    false,
-                                                               SAMFileReader.ValidationStringency.SILENT,
+                    SAMFileReader.ValidationStringency.SILENT,
-                                                               downsampling.create(),
+                    downsampling.create(),
-                                                               new ValidationExclusion(Collections.singletonList(ValidationExclusion.TYPE.ALL)),
+                    new ValidationExclusion(Collections.singletonList(ValidationExclusion.TYPE.ALL)),
-                                                               Collections.<ReadFilter>emptyList(),
+                    Collections.<ReadFilter>emptyList(),
-                                                               false,
+                    Collections.<ReadTransformer>emptyList(),
-                                                               BAQ.CalculationMode.OFF,
+                    false,
-                                                               BAQ.QualityMode.DONT_MODIFY,
+                    (byte)0);
-                                                               null, // no BAQ
-                                                               null, // no BQSR
-                                                               (byte)0);
 
             GenomeLocParser genomeLocParser = new GenomeLocParser(reader.getFileHeader().getSequenceDictionary());
             // Filter unmapped reads.  TODO: is this always strictly necessary?  Who in the GATK normally filters these out?

public/java/test/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSourceUnitTest.java

@@ -24,9 +24,6 @@
 
 package org.broadinstitute.sting.gatk.datasources.reads;
 
-import static org.testng.Assert.assertEquals;
-import static org.testng.Assert.assertTrue;
-import static org.testng.Assert.fail;
 import net.sf.picard.reference.IndexedFastaSequenceFile;
 import net.sf.samtools.SAMFileReader;
 import net.sf.samtools.SAMProgramRecord;
@@ -35,24 +32,25 @@ import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.commandline.Tags;
 import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
 import org.broadinstitute.sting.gatk.filters.ReadFilter;
+import org.broadinstitute.sting.gatk.iterators.ReadTransformer;
 import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
 import org.broadinstitute.sting.gatk.resourcemanagement.ThreadAllocation;
-import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.baq.BAQ;
+import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
 import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
 import org.testng.annotations.AfterMethod;
 import org.testng.annotations.BeforeMethod;
-
 import org.testng.annotations.Test;
 
 import java.io.File;
 import java.io.FileNotFoundException;
 import java.util.ArrayList;
-import java.util.Iterator;
+import java.util.Collections;
 import java.util.List;
 
+import static org.testng.Assert.*;
+
 /**
  * @author aaron
  * @version 1.0
@@ -183,11 +181,8 @@ public class SAMDataSourceUnitTest extends BaseTest {
                 null,
                 new ValidationExclusion(),
                 new ArrayList<ReadFilter>(),
+                Collections.<ReadTransformer>emptyList(),
                 false,
-                BAQ.CalculationMode.OFF,
-                BAQ.QualityMode.DONT_MODIFY,
-                null, // no BAQ
-                null, // no BQSR
                 (byte) -1,
                 removeProgramRecords);
 
@@ -205,11 +200,8 @@ public class SAMDataSourceUnitTest extends BaseTest {
                 null,
                 new ValidationExclusion(),
                 new ArrayList<ReadFilter>(),
+                Collections.<ReadTransformer>emptyList(),
                 false,
-                BAQ.CalculationMode.OFF,
-                BAQ.QualityMode.DONT_MODIFY,
-                null, // no BAQ
-                null, // no BQSR
                 (byte) -1,
                 removeProgramRecords);
 

public/java/test/org/broadinstitute/sting/gatk/iterators/LocusIteratorByStateUnitTest.java

@@ -4,25 +4,27 @@ import net.sf.samtools.SAMFileHeader;
 import net.sf.samtools.SAMFileReader;
 import net.sf.samtools.SAMRecord;
 import net.sf.samtools.util.CloseableIterator;
-import org.broadinstitute.sting.gatk.filters.ReadFilter;
-import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.pileup.PileupElement;
-import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
-import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
-import org.testng.Assert;
 import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.gatk.ReadProperties;
 import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
-import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID;
+import org.broadinstitute.sting.gatk.filters.ReadFilter;
 import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.baq.BAQ;
+import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.sting.utils.pileup.PileupElement;
+import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+import org.testng.Assert;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
-import java.util.*;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.Iterator;
+import java.util.List;
 
 /**
  * testing of the LocusIteratorByState
@@ -349,11 +351,8 @@ public class LocusIteratorByStateUnitTest extends BaseTest {
                 null,
                 new ValidationExclusion(),
                 Collections.<ReadFilter>emptyList(),
+                Collections.<ReadTransformer>emptyList(),
                 false,
-                BAQ.CalculationMode.OFF,
-                BAQ.QualityMode.DONT_MODIFY,
-                null, // no BAQ
-                null, // no BQSR
                 (byte) -1
         );
     }