Merge pull request #1485 from broadinstitute/rhl_mv_samfilereader_samreaderfactory

Replace SAMFileReader with calls to SamReaderFactory

public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/AlignerTestHarness.java

@@ -35,6 +35,7 @@ import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
 
 import java.io.File;
 import java.io.FileNotFoundException;
+import java.io.IOException;
 
 /**
  * A test harness to ensure that the perfect aligner works.
@@ -63,8 +64,7 @@ public class AlignerTestHarness {
         Aligner aligner = new BWAJavaAligner(bwtFile,rbwtFile,suffixArrayFile,reverseSuffixArrayFile);
         int count = 0;
 
-        SAMFileReader reader = new SAMFileReader(bamFile);
+        final SamReader reader = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT).open(bamFile);
-        reader.setValidationStringency(ValidationStringency.SILENT);
 
         int mismatches = 0;
         int failures = 0;
@@ -160,6 +160,12 @@ public class AlignerTestHarness {
                 System.out.printf("%d reads examined.%n",count);                
         }
 
+        try {
+            reader.close();
+        } catch ( IOException ex ) {
+            throw new ReviewedGATKException("Unable to close " + bamFile , ex);
+        }
+
         System.out.printf("%d reads examined; %d mismatches; %d failures.%n",count,mismatches,failures);
     }
 

public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BlockInputStream.java

@@ -40,7 +40,7 @@ import java.util.LinkedList;
 import java.util.List;
 
 /**
- * Presents decompressed blocks to the SAMFileReader.
+ * Presents decompressed blocks to the SamReader.
  */
 public class BlockInputStream extends InputStream {
     /**

public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/BAMFileStat.java

@@ -25,15 +25,14 @@
 
 package org.broadinstitute.gatk.engine.datasources.reads.utilities;
 
-import htsjdk.samtools.BAMIndex;
+import htsjdk.samtools.*;
-import htsjdk.samtools.SAMFileReader;
-import htsjdk.samtools.ValidationStringency;
 import org.broadinstitute.gatk.utils.commandline.Argument;
 import org.broadinstitute.gatk.utils.commandline.CommandLineProgram;
 import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
 import org.broadinstitute.gatk.utils.instrumentation.Sizeof;
 
 import java.io.File;
+import java.io.IOException;
 import java.lang.reflect.Field;
 import java.util.List;
 import java.util.Map;
@@ -56,7 +55,7 @@ public class BAMFileStat extends CommandLineProgram {
     @Argument(doc="The range to inspect.",required=false)
     private String range;
 
-    public int execute() {
+    public int execute() throws IOException {
         switch(command) {
             case ShowBlocks:
                 throw new ReviewedGATKException("The BAM block inspector has been disabled.");
@@ -81,14 +80,11 @@ public class BAMFileStat extends CommandLineProgram {
         }
     }
 
-    private void showIndexBins(File bamFile,String contigName) {
+    private void showIndexBins(File bamFile,String contigName) throws IOException {
-        SAMFileReader reader;
-        BAMIndex index;
 
-        reader = new SAMFileReader(bamFile);
+        final SamReader reader = SamReaderFactory.makeDefault().enable(SamReaderFactory.Option.CACHE_FILE_BASED_INDEXES).
-        reader.setValidationStringency(ValidationStringency.SILENT);
+                validationStringency(ValidationStringency.SILENT).open(bamFile);
-        reader.enableIndexCaching(true);
+        final SamReader.Indexing index = reader.indexing();
-        index = reader.getIndex();
 
         reader.queryOverlapping(contigName,1,reader.getFileHeader().getSequence(contigName).getSequenceLength()).close();
 

public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/BAMTagRenamer.java

@@ -25,14 +25,17 @@
 
 package org.broadinstitute.gatk.engine.datasources.reads.utilities;
 
-import htsjdk.samtools.SAMFileReader;
+import htsjdk.samtools.SamReader;
+import htsjdk.samtools.SamReaderFactory;
 import htsjdk.samtools.SAMFileWriter;
 import htsjdk.samtools.SAMFileWriterFactory;
 import htsjdk.samtools.SAMRecord;
 import org.broadinstitute.gatk.utils.commandline.Argument;
 import org.broadinstitute.gatk.utils.commandline.CommandLineProgram;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
 
 import java.io.File;
+import java.io.IOException;
 
 /**
  * A simple utility written directly in Picard that will rename tags
@@ -62,7 +65,7 @@ public class BAMTagRenamer extends CommandLineProgram {
         long readsWritten = 0;
         long readsAltered = 0;
 
-        SAMFileReader reader = new SAMFileReader(input);
+        final SamReader reader = SamReaderFactory.makeDefault().open(input);
         SAMFileWriter writer = new SAMFileWriterFactory().makeBAMWriter(reader.getFileHeader(),true,output,compressionLevel);
 
         for(SAMRecord read: reader) {
@@ -79,7 +82,13 @@ public class BAMTagRenamer extends CommandLineProgram {
         }
 
         writer.close();
-        System.out.printf("%d reads written.  %d tag names updated from %s to %s.%n",readsWritten,readsAltered,sourceTagName,targetTagName);        
+        System.out.printf("%d reads written.  %d tag names updated from %s to %s.%n",readsWritten,readsAltered,sourceTagName,targetTagName);
+
+        try {
+            reader.close();
+        } catch ( IOException ex ) {
+            throw new ReviewedGATKException("Unable to close " + input , ex);
+        }
 
         return 0;
     }

public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/PrintBAMRegion.java

@@ -31,6 +31,7 @@ import org.broadinstitute.gatk.utils.commandline.CommandLineProgram;
 import org.broadinstitute.gatk.utils.exceptions.UserException;
 
 import java.io.File;
+import java.io.IOException;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
@@ -53,9 +54,8 @@ public class PrintBAMRegion extends CommandLineProgram {
     private static final int MIN_OFFSET_SIZE = 0;
     private static final int MAX_OFFSET_SIZE = (int)Math.pow(2,16)-1;
 
-    public int execute() {
+    public int execute() throws IOException {
-        SAMFileReader reader = new SAMFileReader(input);
+        final SamReader reader = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT).open(input);
-        reader.setValidationStringency(ValidationStringency.SILENT);
 
         Pattern regionPattern = Pattern.compile("(\\d+):(\\d+)-(\\d+):(\\d+)");
         Matcher matcher = regionPattern.matcher(region);
@@ -76,10 +76,10 @@ public class PrintBAMRegion extends CommandLineProgram {
         if(lastOffset < MIN_OFFSET_SIZE || lastOffset > MAX_OFFSET_SIZE)
             throw new UserException(String.format("Last offset is invalid; must be between %d and %d; actually is %d",MIN_OFFSET_SIZE,MAX_OFFSET_SIZE,lastOffset));
 
-        GATKChunk chunk = new GATKChunk(firstBlock<<16 | firstOffset,lastBlock<<16 | lastOffset);
+        final GATKChunk chunk = new GATKChunk(firstBlock<<16 | firstOffset,lastBlock<<16 | lastOffset);
-        GATKBAMFileSpan fileSpan = new GATKBAMFileSpan(chunk);
+        final GATKBAMFileSpan fileSpan = new GATKBAMFileSpan(chunk);
 
-        SAMRecordIterator iterator = reader.iterator(fileSpan);
+        final SAMRecordIterator iterator = ((SamReader.PrimitiveSamReaderToSamReaderAdapter) reader).iterator(fileSpan);
         long readCount = 0;
         while(iterator.hasNext()) {
             System.out.printf("%s%n",iterator.next().format());

public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/PrintBGZFBounds.java

@@ -65,8 +65,6 @@ public class PrintBGZFBounds extends CommandLineProgram {
         float uncompressedSize = 0;
         long totalBlocks = 0;
 
-        //SAMFileReader reader = new SAMFileReader(input);
-
         while(true) {
             final long blockStart = fis.getChannel().position();
 

public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/OutputTracker.java

@@ -98,7 +98,7 @@ public abstract class OutputTracker implements ReferenceBacked {
             ArgumentSource targetField = io.getKey();
             Object targetValue = io.getValue();
 
-            // Ghastly hack: reaches in and finishes building out the SAMFileReader.
+            // Ghastly hack: reaches in and finishes building out the SameReader.
             // TODO: Generalize this, and move it to its own initialization step.
             if( targetValue instanceof SAMReaderBuilder) {
                 SAMReaderBuilder builder = (SAMReaderBuilder)targetValue;

public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/storage/SAMFileWriterStorage.java

@@ -31,6 +31,7 @@ import htsjdk.samtools.util.ProgressLoggerInterface;
 import htsjdk.samtools.util.RuntimeIOException;
 import org.apache.log4j.Logger;
 import org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub;
+import org.broadinstitute.gatk.utils.exceptions.GATKException;
 import org.broadinstitute.gatk.utils.exceptions.UserException;
 import org.broadinstitute.gatk.utils.sam.SimplifyingSAMFileWriter;
 
@@ -112,7 +113,7 @@ public class SAMFileWriterStorage implements SAMFileWriter, Storage<SAMFileWrite
     }
 
     public void mergeInto( SAMFileWriter targetStream ) {
-        SAMFileReader reader = new SAMFileReader( file );
+        final SamReader reader = SamReaderFactory.makeDefault().open(file);
         try {
             CloseableIterator<SAMRecord> iterator = reader.iterator();
             while( iterator.hasNext() )
@@ -120,7 +121,11 @@ public class SAMFileWriterStorage implements SAMFileWriter, Storage<SAMFileWrite
             iterator.close();
         }
         finally {
-            reader.close();
+            try {
+                reader.close();
+            } catch (IOException e ) {
+                throw new GATKException(e.getMessage());
+            }
             file.delete();
         }
     }

public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/stubs/SAMReaderArgumentTypeDescriptor.java

@@ -25,7 +25,7 @@
 
 package org.broadinstitute.gatk.engine.io.stubs;
 
-import htsjdk.samtools.SAMFileReader;
+import htsjdk.samtools.SamReader;
 import org.broadinstitute.gatk.utils.commandline.*;
 import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
 import org.broadinstitute.gatk.utils.exceptions.UserException;
@@ -43,7 +43,7 @@ public class SAMReaderArgumentTypeDescriptor extends ArgumentTypeDescriptor {
     private GenomeAnalysisEngine engine;
 
     /**
-     * Create a new SAMFileReader argument, notifying the given engine when that argument has been created.
+     * Create a new SamReader argument, notifying the given engine when that argument has been created.
      * @param engine engine
      */
     public SAMReaderArgumentTypeDescriptor(GenomeAnalysisEngine engine) {
@@ -52,7 +52,7 @@ public class SAMReaderArgumentTypeDescriptor extends ArgumentTypeDescriptor {
 
     @Override
     public boolean supports( Class type ) {
-        return SAMFileReader.class.isAssignableFrom(type);
+        return SamReader.class.isAssignableFrom(type);
     }
 
     @Override
@@ -69,7 +69,7 @@ public class SAMReaderArgumentTypeDescriptor extends ArgumentTypeDescriptor {
         // WARNING: Skipping required side-effect because stub is impossible to generate.
         engine.addInput(source, builder);
 
-        // MASSIVE KLUDGE!  SAMFileReader is tricky to implement and we don't yet have a stub.  Return null, then
+        // MASSIVE KLUDGE!  SamReader is tricky to implement and we don't yet have a stub.  Return null, then
         // let the output tracker load it in.
         // TODO: Add a stub for SAMReader.
         return null;

public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/CommandLineGATKUnitTest.java

@@ -25,7 +25,10 @@
 
 package org.broadinstitute.gatk.engine;
 
-import htsjdk.samtools.SAMFileReader;
+import htsjdk.samtools.SamInputResource;
+import htsjdk.samtools.SamReader;
+import htsjdk.samtools.SamReaderFactory;
+import htsjdk.samtools.ValidationStringency;
 import org.broadinstitute.gatk.utils.BaseTest;
 import org.testng.Assert;
 import org.testng.annotations.Test;
@@ -42,8 +45,11 @@ public class CommandLineGATKUnitTest extends BaseTest {
     public void testSamTextFileError1() {
         final File samFile = new File(publicTestDir + "testfile.sam");
         final File indexFile = new File(publicTestDir + "HiSeq.1mb.1RG.bai");
+        final SamInputResource samInputResource = SamInputResource.of(samFile);
+        samInputResource.index(indexFile);
         try {
-            final SAMFileReader reader = new SAMFileReader(samFile, indexFile, false);
+            final SamReader reader =
+                    SamReaderFactory.makeDefault().open(samInputResource);
 
             // we shouldn't get here
             Assert.fail("We should have exceptioned out when trying to create a reader with an index for a textual SAM file");
@@ -56,8 +62,9 @@ public class CommandLineGATKUnitTest extends BaseTest {
     public void testSamTextFileError2() {
         File samFile = new File(publicTestDir + "testfile.sam");
         try {
-            final SAMFileReader reader = new SAMFileReader(samFile);
+            final SamInputResource samInputResource = SamInputResource.of(samFile);
-            reader.getFilePointerSpanningReads();
+            final SamReader reader = SamReaderFactory.makeDefault().open(samInputResource);
+            reader.indexing().getFilePointerSpanningReads();
 
             // we shouldn't get here
             Assert.fail("We should have exceptioned out when trying to call getFilePointerSpanningReads() for a textual SAM file");

public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/EngineFeaturesIntegrationTest.java

@@ -344,7 +344,7 @@ public class EngineFeaturesIntegrationTest extends WalkerTest {
     // --------------------------------------------------------------------------------
 
     @Test
-    public void testGATKEngineConsolidatesCigars() {
+    public void testGATKEngineConsolidatesCigars() throws IOException {
         final WalkerTestSpec spec = new WalkerTestSpec(" -T TestPrintReadsWalker" +
                                                        " -R " + b37KGReference +
                                                        " -I " + privateTestDir + "zero_length_cigar_elements.bam" +
@@ -352,8 +352,7 @@ public class EngineFeaturesIntegrationTest extends WalkerTest {
                                                        1, Arrays.asList(""));  // No MD5s; we only want to check the cigar
 
         final File outputBam = executeTest("testGATKEngineConsolidatesCigars", spec).first.get(0);
-        final SAMFileReader reader = new SAMFileReader(outputBam);
+        final SamReader reader = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT).open(outputBam);
-        reader.setValidationStringency(ValidationStringency.SILENT);
 
         final SAMRecord read = reader.iterator().next();
         reader.close();
@@ -382,7 +381,7 @@ public class EngineFeaturesIntegrationTest extends WalkerTest {
                                                        1, Arrays.asList(""));  // No MD5s; we only want to check the read groups
 
         final File outputBam = executeTest("testOnTheFlySampleRenamingWithSingleBamFile", spec).first.get(0);
-        final SAMFileReader reader = new SAMFileReader(outputBam);
+        final SamReader reader = SamReaderFactory.makeDefault().open(outputBam);
 
         for ( final SAMReadGroupRecord readGroup : reader.getFileHeader().getReadGroups() ) {
             Assert.assertEquals(readGroup.getSample(), "myNewSampleName", String.format("Sample for read group %s not renamed correctly", readGroup.getId()));
@@ -402,12 +401,12 @@ public class EngineFeaturesIntegrationTest extends WalkerTest {
         final Map<String, String> readGroupToNewSampleMap = new HashMap<>();
         for ( String inputBamID : Arrays.asList("12878", "12891", "12892") ) {
             final File inputBam = new File(privateTestDir + String.format("CEUTrio.HiSeq.WGS.b37.NA%s.HEADERONLY.bam", inputBamID));
-            final SAMFileReader inputBamReader = new SAMFileReader(inputBam);
+            final SamReader reader = SamReaderFactory.makeDefault().open(inputBam);
             final String newSampleName = String.format("newSampleFor%s", inputBamID);
-            for ( final SAMReadGroupRecord readGroup : inputBamReader.getFileHeader().getReadGroups() ) {
+            for ( final SAMReadGroupRecord readGroup : reader.getFileHeader().getReadGroups() ) {
                 readGroupToNewSampleMap.put(readGroup.getId(), newSampleName);
             }
-            inputBamReader.close();
+            reader.close();
         }
 
         final WalkerTestSpec spec = new WalkerTestSpec(" -T TestPrintReadsWalker" +
@@ -420,10 +419,10 @@ public class EngineFeaturesIntegrationTest extends WalkerTest {
                                                        1, Arrays.asList(""));  // No MD5s; we only want to check the read groups
 
         final File outputBam = executeTest("testOnTheFlySampleRenamingWithMultipleBamFiles", spec).first.get(0);
-        final SAMFileReader outputBamReader = new SAMFileReader(outputBam);
+        final SamReader reader =  SamReaderFactory.makeDefault().open(outputBam);
 
         int totalReadGroupsSeen = 0;
-        for ( final SAMReadGroupRecord readGroup : outputBamReader.getFileHeader().getReadGroups() ) {
+        for ( final SAMReadGroupRecord readGroup : reader.getFileHeader().getReadGroups() ) {
             Assert.assertEquals(readGroup.getSample(), readGroupToNewSampleMap.get(readGroup.getId()),
                                 String.format("Wrong sample for read group %s after on-the-fly renaming", readGroup.getId()));
             totalReadGroupsSeen++;
@@ -431,7 +430,7 @@ public class EngineFeaturesIntegrationTest extends WalkerTest {
 
         Assert.assertEquals(totalReadGroupsSeen, readGroupToNewSampleMap.size(), "Wrong number of read groups encountered in output bam file");
 
-        outputBamReader.close();
+        reader.close();
     }
 
     // On-the-fly sample renaming test case: three single-sample bams with multiple read groups per bam,
@@ -446,15 +445,15 @@ public class EngineFeaturesIntegrationTest extends WalkerTest {
         final Map<String, String> readGroupToNewSampleMap = new HashMap<>();
         for ( String inputBamID : Arrays.asList("12878", "12891", "12892") ) {
             final File inputBam = new File(privateTestDir + String.format("CEUTrio.HiSeq.WGS.b37.NA%s.HEADERONLY.bam", inputBamID));
-            final SAMFileReader inputBamReader = new SAMFileReader(inputBam);
+            final SamReader reader = SamReaderFactory.makeDefault().open(inputBam);
 
             // Special-case NA12891, which we're not renaming:
             final String newSampleName = inputBamID.equals("12891") ? "NA12891" : String.format("newSampleFor%s", inputBamID);
 
-            for ( final SAMReadGroupRecord readGroup : inputBamReader.getFileHeader().getReadGroups() ) {
+            for ( final SAMReadGroupRecord readGroup : reader.getFileHeader().getReadGroups() ) {
                 readGroupToNewSampleMap.put(readGroup.getId(), newSampleName);
             }
-            inputBamReader.close();
+            reader.close();
         }
 
         final WalkerTestSpec spec = new WalkerTestSpec(" -T TestPrintReadsWalker" +
@@ -467,10 +466,10 @@ public class EngineFeaturesIntegrationTest extends WalkerTest {
                                                        1, Arrays.asList(""));  // No MD5s; we only want to check the read groups
 
         final File outputBam = executeTest("testOnTheFlySampleRenamingWithMultipleBamFilesPartialRename", spec).first.get(0);
-        final SAMFileReader outputBamReader = new SAMFileReader(outputBam);
+        final SamReader reader = SamReaderFactory.makeDefault().open(outputBam);
 
         int totalReadGroupsSeen = 0;
-        for ( final SAMReadGroupRecord readGroup : outputBamReader.getFileHeader().getReadGroups() ) {
+        for ( final SAMReadGroupRecord readGroup : reader.getFileHeader().getReadGroups() ) {
             Assert.assertEquals(readGroup.getSample(), readGroupToNewSampleMap.get(readGroup.getId()),
                                 String.format("Wrong sample for read group %s after on-the-fly renaming", readGroup.getId()));
             totalReadGroupsSeen++;
@@ -478,7 +477,7 @@ public class EngineFeaturesIntegrationTest extends WalkerTest {
 
         Assert.assertEquals(totalReadGroupsSeen, readGroupToNewSampleMap.size(), "Wrong number of read groups encountered in output bam file");
 
-        outputBamReader.close();
+        reader.close();
     }
 
     // On-the-fly sample renaming test case: two single-sample bams with read group collisions
@@ -489,11 +488,11 @@ public class EngineFeaturesIntegrationTest extends WalkerTest {
                               privateTestDir + "CEUTrio.HiSeq.WGS.b37.READ_GROUP_COLLISIONS_WITH_NA12878.HEADERONLY.bam  newSampleForNot12878"));
 
         final Set<String> na12878ReadGroups = new HashSet<>();
-        final SAMFileReader inputBamReader = new SAMFileReader(new File(privateTestDir + "CEUTrio.HiSeq.WGS.b37.NA12878.HEADERONLY.bam"));
+        final SamReader inpuBAMreader = SamReaderFactory.makeDefault().open(new File(privateTestDir + "CEUTrio.HiSeq.WGS.b37.NA12878.HEADERONLY.bam"));
-        for ( final SAMReadGroupRecord readGroup : inputBamReader.getFileHeader().getReadGroups() ) {
+        for ( final SAMReadGroupRecord readGroup : inpuBAMreader.getFileHeader().getReadGroups() ) {
             na12878ReadGroups.add(readGroup.getId());
         }
-        inputBamReader.close();
+        inpuBAMreader.close();
 
         final WalkerTestSpec spec = new WalkerTestSpec(" -T TestPrintReadsWalker" +
                                                        " -R " + b37KGReference +
@@ -504,10 +503,10 @@ public class EngineFeaturesIntegrationTest extends WalkerTest {
                                                        1, Arrays.asList(""));  // No MD5s; we only want to check the read groups
 
         final File outputBam = executeTest("testOnTheFlySampleRenamingWithReadGroupCollisions", spec).first.get(0);
-        final SAMFileReader outputBamReader = new SAMFileReader(outputBam);
+        final SamReader outputBAMreader = SamReaderFactory.makeDefault().open(outputBam);
 
         int totalReadGroupsSeen = 0;
-        for ( final SAMReadGroupRecord readGroup : outputBamReader.getFileHeader().getReadGroups() ) {
+        for ( final SAMReadGroupRecord readGroup : outputBAMreader.getFileHeader().getReadGroups() ) {
             String expectedSampleName = "";
             if ( na12878ReadGroups.contains(readGroup.getId()) ) {
                 expectedSampleName = "newSampleFor12878";
@@ -523,7 +522,7 @@ public class EngineFeaturesIntegrationTest extends WalkerTest {
 
         Assert.assertEquals(totalReadGroupsSeen, na12878ReadGroups.size() * 2, "Wrong number of read groups encountered in output bam file");
 
-        outputBamReader.close();
+        outputBAMreader.close();
     }
 
     // On-the-fly sample renaming test case: a multi-sample bam (this should generate a UserException)

public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/DownsamplerBenchmark.java

@@ -55,12 +55,12 @@ public class DownsamplerBenchmark extends ReadProcessingBenchmark {
 
 //    public void timeDownsampling(int reps) {
 //        for(int i = 0; i < reps; i++) {
-//            SAMFileReader reader = new SAMFileReader(inputFile);
+//            SamReader reader = SamReaderFactory.makeDefault().open(inputFile);
 //            ReadProperties readProperties = new ReadProperties(Collections.<SAMReaderID>singletonList(new SAMReaderID(inputFile,new Tags())),
 //                    reader.getFileHeader(),
 //                    SAMFileHeader.SortOrder.coordinate,
 //                    false,
-//                    SAMFileReader.ValidationStringency.SILENT,
+//                    ValidationStringency.SILENT,
 //                    downsampling.create(),
 //                    new ValidationExclusion(Collections.singletonList(ValidationExclusion.TYPE.ALL)),
 //                    Collections.<ReadFilter>emptyList(),

public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/GATKBAMIndexFromDataSourceUnitTest.java

@@ -25,7 +25,6 @@
 
 package org.broadinstitute.gatk.engine.datasources.reads;
 
-import htsjdk.samtools.SAMFileReader;
 import htsjdk.samtools.SamReader;
 import htsjdk.samtools.SamReaderFactory;
 import org.broadinstitute.gatk.utils.BaseTest;
@@ -50,8 +49,7 @@ public class GATKBAMIndexFromDataSourceUnitTest extends BaseTest {
 
     @BeforeClass
     public void init() throws IOException {
-        final SAMFileReader reader = new SAMFileReader(bamFile);
+        final SamReader reader = SamReaderFactory.makeDefault().enable(SamReaderFactory.Option.CACHE_FILE_BASED_INDEXES).open(bamFile);
-        reader.enableIndexCaching(true); // needed ot get BrowseableBAMIndex
         Assert.assertTrue(reader.hasIndex());
         Assert.assertTrue(reader.indexing().hasBrowseableIndex());
 

public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/GATKBAMIndexFromFileUnitTest.java

@@ -25,8 +25,9 @@
 
 package org.broadinstitute.gatk.engine.datasources.reads;
 
-import htsjdk.samtools.SAMFileReader;
 import htsjdk.samtools.SAMSequenceDictionary;
+import htsjdk.samtools.SamReader;
+import htsjdk.samtools.SamReaderFactory;
 import org.broadinstitute.gatk.utils.BaseTest;
 import org.broadinstitute.gatk.utils.exceptions.UserException;
 import org.testng.Assert;
@@ -34,7 +35,7 @@ import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
 import java.io.File;
-import java.io.FileNotFoundException;
+import java.io.IOException;
 
 /**
  * Test basic functionality in the GATK's implementation of the BAM index classes.
@@ -59,8 +60,8 @@ public class GATKBAMIndexFromFileUnitTest extends BaseTest {
 
 
     @BeforeClass
-    public void init() throws FileNotFoundException {
+    public void init() throws IOException {
-        final SAMFileReader reader = new SAMFileReader(bamFile);
+        final SamReader reader = SamReaderFactory.makeDefault().enable(SamReaderFactory.Option.CACHE_FILE_BASED_INDEXES).open(bamFile);
         sequenceDictionary = reader.getFileHeader().getSequenceDictionary();
         reader.close();
 

public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/PicardBaselineBenchmark.java

@@ -26,13 +26,13 @@
 package org.broadinstitute.gatk.engine.datasources.reads;
 
 import com.google.caliper.Param;
-import com.google.caliper.SimpleBenchmark;
+import htsjdk.samtools.SamReader;
+import htsjdk.samtools.SamReaderFactory;
 import htsjdk.samtools.util.SamLocusIterator;
-import htsjdk.samtools.SAMFileReader;
 import htsjdk.samtools.SAMRecord;
 import htsjdk.samtools.util.CloseableIterator;
 
-import java.io.File;
+import java.io.IOException;
 import java.util.Iterator;
 
 /**
@@ -55,9 +55,9 @@ public class PicardBaselineBenchmark extends ReadProcessingBenchmark {
     @Override
     public Integer getMaxReads() { return maxReads; }
     
-    public void timeDecompressBamFile(int reps) {
+    public void timeDecompressBamFile(int reps) throws IOException {
         for(int i = 0; i < reps; i++) {
-            SAMFileReader reader = new SAMFileReader(inputFile);
+            final SamReader reader = SamReaderFactory.makeDefault().open(inputFile);
             CloseableIterator<SAMRecord> iterator = reader.iterator();
             while(iterator.hasNext())
                 iterator.next();
@@ -66,9 +66,9 @@ public class PicardBaselineBenchmark extends ReadProcessingBenchmark {
         }
     }
 
-    public void timeExtractTag(int reps) {
+    public void timeExtractTag(int reps) throws IOException {
         for(int i = 0; i < reps; i++) {
-            SAMFileReader reader = new SAMFileReader(inputFile);
+            final SamReader reader = SamReaderFactory.makeDefault().open(inputFile);
             CloseableIterator<SAMRecord> iterator = reader.iterator();
             while(iterator.hasNext()) {
                 SAMRecord read = iterator.next();
@@ -79,9 +79,9 @@ public class PicardBaselineBenchmark extends ReadProcessingBenchmark {
         }
     }
 
-    public void timeSamLocusIterator(int reps) {
+    public void timeSamLocusIterator(int reps) throws IOException {
         for(int i = 0; i < reps; i++) {
-            SAMFileReader reader = new SAMFileReader(inputFile);
+            final SamReader reader = SamReaderFactory.makeDefault().open(inputFile);
             long loci = 0;
 
             SamLocusIterator samLocusIterator = new SamLocusIterator(reader);

public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/ReadProcessingBenchmark.java

@@ -25,11 +25,11 @@
 
 package org.broadinstitute.gatk.engine.datasources.reads;
 
-import com.google.caliper.Param;
 import com.google.caliper.SimpleBenchmark;
-import htsjdk.samtools.SAMFileReader;
 import htsjdk.samtools.SAMFileWriter;
 import htsjdk.samtools.SAMFileWriterFactory;
+import htsjdk.samtools.SamReader;
+import htsjdk.samtools.SamReaderFactory;
 import htsjdk.samtools.SAMRecord;
 import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
 
@@ -51,7 +51,7 @@ public abstract class ReadProcessingBenchmark extends SimpleBenchmark {
 
     @Override
     public void setUp() {
-        SAMFileReader fullInputFile = new SAMFileReader(new File(getBAMFile()));
+        SamReader reader = SamReaderFactory.makeDefault().open(new File(getBAMFile()));
 
         File tempFile = null;
         try {
@@ -62,15 +62,20 @@ public abstract class ReadProcessingBenchmark extends SimpleBenchmark {
         }
         SAMFileWriterFactory factory = new SAMFileWriterFactory();
         factory.setCreateIndex(true);
-        SAMFileWriter writer = factory.makeBAMWriter(fullInputFile.getFileHeader(),true,tempFile);
+        SAMFileWriter writer = factory.makeBAMWriter(reader.getFileHeader(),true,tempFile);
 
         long numReads = 0;
-        for(SAMRecord read: fullInputFile) {
+        for(SAMRecord read: reader) {
             if(numReads++ >= getMaxReads())
                 break;
             writer.addAlignment(read);
         }
 
+        try {
+            reader.close();
+        } catch ( IOException ex ) {
+            throw new ReviewedGATKException("Unable to close " + getBAMFile() , ex);
+        }
         writer.close();
 
         inputFile = tempFile;

public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/TheoreticalMinimaBenchmark.java

@@ -28,11 +28,13 @@ package org.broadinstitute.gatk.engine.datasources.reads;
 import com.google.caliper.Param;
 import htsjdk.samtools.Cigar;
 import htsjdk.samtools.CigarElement;
-import htsjdk.samtools.SAMFileReader;
+import htsjdk.samtools.SamReader;
+import htsjdk.samtools.SamReaderFactory;
 import htsjdk.samtools.SAMRecord;
 import htsjdk.samtools.util.CloseableIterator;
 
 import java.io.File;
+import java.io.IOException;
 
 /**
  * Created by IntelliJ IDEA.
@@ -54,10 +56,10 @@ public class TheoreticalMinimaBenchmark extends ReadProcessingBenchmark {
     @Override
     public Integer getMaxReads() { return maxReads; }
 
-    public void timeIterateOverEachBase(int reps) {
+    public void timeIterateOverEachBase(int reps) throws IOException {
         System.out.printf("Processing " + inputFile);
         for(int i = 0; i < reps; i++) {
-            SAMFileReader reader = new SAMFileReader(inputFile);
+            final SamReader reader = SamReaderFactory.makeDefault().open((inputFile));
             CloseableIterator<SAMRecord> iterator = reader.iterator();
 
             long As=0,Cs=0,Gs=0,Ts=0;
@@ -78,14 +80,14 @@ public class TheoreticalMinimaBenchmark extends ReadProcessingBenchmark {
         }
     }
 
-    public void timeIterateOverCigarString(int reps) {
+    public void timeIterateOverCigarString(int reps) throws IOException {
         for(int i = 0; i < reps; i++) {
             long matchMismatches = 0;
             long insertions = 0;
             long deletions = 0;
             long others = 0;
 
-            SAMFileReader reader = new SAMFileReader(inputFile);
+            final SamReader reader = SamReaderFactory.makeDefault().open(inputFile);
             CloseableIterator<SAMRecord> iterator = reader.iterator();
             while(iterator.hasNext()) {
                 SAMRecord read = iterator.next();

public/gatk-queue-extensions-generator/src/main/java/org/broadinstitute/gatk/queue/extensions/gatk/ArgumentField.java

@@ -25,7 +25,7 @@
 
 package org.broadinstitute.gatk.queue.extensions.gatk;
 
-import htsjdk.samtools.SAMFileReader;
+import htsjdk.samtools.SamReader;
 import htsjdk.samtools.SAMFileWriter;
 import org.apache.commons.lang.StringEscapeUtils;
 import org.apache.commons.lang.StringUtils;
@@ -245,7 +245,7 @@ public abstract class ArgumentField {
 
     protected static Class<?> mapType(Class<?> clazz) {
         if (InputStream.class.isAssignableFrom(clazz)) return File.class;
-        if (SAMFileReader.class.isAssignableFrom(clazz)) return File.class;
+        if (SamReader.class.isAssignableFrom(clazz)) return File.class;
         if (OutputStream.class.isAssignableFrom(clazz)) return File.class;
         if (VariantContextWriter.class.isAssignableFrom(clazz)) return File.class;
         if (SAMFileWriter.class.isAssignableFrom(clazz)) return File.class;

public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/QScriptUtils.scala

@@ -27,7 +27,7 @@ package org.broadinstitute.gatk.queue.util
 
 import java.io.File
 import io.Source._
-import htsjdk.samtools.{SAMReadGroupRecord, SAMFileReader}
+import htsjdk.samtools.{SamReaderFactory, SAMReadGroupRecord}
 
 import collection.JavaConversions._
 
@@ -87,8 +87,10 @@ object QScriptUtils {
    * Returns the number of contigs in the BAM file header.
    */
   def getNumberOfContigs(bamFile: File): Int = {
-    val samReader = new SAMFileReader(bamFile)
+    val samReader = SamReaderFactory.makeDefault().open(bamFile)
-    samReader.getFileHeader.getSequenceDictionary.getSequences.size()
+    val size = samReader.getFileHeader.getSequenceDictionary.getSequences.size()
+    samReader.close
+    return size
   }
 
   /**
@@ -112,11 +114,12 @@ object QScriptUtils {
    * @return    a set with all distinct samples (in no particular order)
    */
   def getSamplesFromBAM(bam: File) : Set[String] = {
-    val reader = new SAMFileReader(bam)
+    val reader = SamReaderFactory.makeDefault().open(bam);
     var samples: Set[String] = Set()
     for (rg <- reader.getFileHeader.getReadGroups) {
       samples += rg.getSample
     }
+    reader.close
     samples
   }
 }

public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/VCF_BAM_utilities.scala

@@ -28,7 +28,7 @@ package org.broadinstitute.gatk.queue.util
 import java.io.File
 import org.apache.commons.io.FilenameUtils
 import scala.io.Source._
-import htsjdk.samtools.SAMFileReader
+import htsjdk.samtools.{SamReaderFactory}
 import htsjdk.variant.vcf.{VCFHeader, VCFCodec}
 import scala.collection.JavaConversions._
 import htsjdk.tribble.AbstractFeatureReader
@@ -40,7 +40,7 @@ object VCF_BAM_utilities {
   }
 
   def getSamplesInBAM(bam: File): List[String] = {
-    return new SAMFileReader(bam).getFileHeader().getReadGroups().toList.map(srgr => srgr.getSample()).toSet.toList
+    return SamReaderFactory.makeDefault().open(bam).getFileHeader().getReadGroups().toList.map(srgr => srgr.getSample()).toSet.toList
   }
 
   def parseBAMsInput(bamsIn: File): List[File] = FilenameUtils.getExtension(bamsIn.getPath) match {

public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/BAMDiffableReader.java

@@ -25,11 +25,13 @@
 
 package org.broadinstitute.gatk.utils.diffengine;
 
-import htsjdk.samtools.SAMFileReader;
+import htsjdk.samtools.SamReader;
+import htsjdk.samtools.SamReaderFactory;
 import htsjdk.samtools.SAMRecord;
 import htsjdk.samtools.SAMRecordIterator;
 import htsjdk.samtools.ValidationStringency;
 import htsjdk.samtools.util.BlockCompressedInputStream;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
 
 import java.io.*;
 import java.util.Arrays;
@@ -49,8 +51,7 @@ public class BAMDiffableReader implements DiffableReader {
 
     @Override
     public DiffElement readFromFile(File file, int maxElementsToRead) {
-        final SAMFileReader reader = new SAMFileReader(file, null); // null because we don't want it to look for the index
+        final SamReader reader = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT).open(file);
-        reader.setValidationStringency(ValidationStringency.SILENT);
 
         DiffNode root = DiffNode.rooted(file.getName());
         SAMRecordIterator iterator = reader.iterator();
@@ -93,7 +94,11 @@ public class BAMDiffableReader implements DiffableReader {
                 break;
         }
 
-        reader.close();
+        try {
+            reader.close();
+        } catch (final IOException ex ) {
+            throw new ReviewedGATKException("Unable to close " + file , ex);
+        }
 
         return root.getBinding();
     }

public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LIBSPerformance.java

@@ -25,7 +25,8 @@
 
 package org.broadinstitute.gatk.utils.locusiterator;
 
-import htsjdk.samtools.SAMFileReader;
+import htsjdk.samtools.SamReader;
+import htsjdk.samtools.SamReaderFactory;
 import htsjdk.samtools.SAMReadGroupRecord;
 import htsjdk.samtools.SAMRecordIterator;
 import htsjdk.samtools.reference.ReferenceSequenceFile;
@@ -65,7 +66,7 @@ public class LIBSPerformance extends CommandLineProgram {
         final ReferenceSequenceFile reference = new CachingIndexedFastaSequenceFile(referenceFile);
         final GenomeLocParser genomeLocParser = new GenomeLocParser(reference);
 
-        final SAMFileReader reader = new SAMFileReader(samFile);
+        final SamReader reader = SamReaderFactory.makeDefault().open(samFile);
 
         SAMRecordIterator rawIterator;
         if ( location == null )
@@ -81,6 +82,8 @@ public class LIBSPerformance extends CommandLineProgram {
         for ( final SAMReadGroupRecord rg : reader.getFileHeader().getReadGroups() )
             samples.add(rg.getSample());
 
+        reader.close();
+
         final LIBSDownsamplingInfo ds = new LIBSDownsamplingInfo(downsample, 250);
 
         final LocusIteratorByState libs =

public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByState.java

@@ -28,7 +28,7 @@ package org.broadinstitute.gatk.utils.locusiterator;
 import com.google.java.contract.Ensures;
 import com.google.java.contract.Requires;
 import htsjdk.samtools.CigarOperator;
-import htsjdk.samtools.SAMFileReader;
+import htsjdk.samtools.SamReader;
 import htsjdk.samtools.SAMRecord;
 import htsjdk.samtools.util.CloseableIterator;
 import org.apache.log4j.Logger;
@@ -149,7 +149,7 @@ public final class LocusIteratorByState extends LocusIterator {
     }
 
     /**
-     * Create a new LocusIteratorByState based on a SAMFileReader using reads in an iterator it
+     * Create a new LocusIteratorByState based on a SamReader using reads in an iterator it
      *
      * Simple constructor that uses the samples in the reader, doesn't do any downsampling,
      * and makes a new GenomeLocParser using the reader.  This constructor will be slow(ish)
@@ -158,7 +158,7 @@ public final class LocusIteratorByState extends LocusIterator {
      * @param reader a non-null reader
      * @param it an iterator from reader that has the reads we want to use to create ReadBackPileups
      */
-    public LocusIteratorByState(final SAMFileReader reader, final CloseableIterator<SAMRecord> it) {
+    public LocusIteratorByState(final SamReader reader, final CloseableIterator<SAMRecord> it) {
         this(new GATKSAMRecordIterator(it),
                 new LIBSDownsamplingInfo(false, 0),
                 true,

public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMFileReader.java

@@ -26,16 +26,19 @@
 package org.broadinstitute.gatk.utils.sam;
 
 import htsjdk.samtools.*;
+import htsjdk.samtools.SamReader.Indexing;
 import org.broadinstitute.gatk.utils.GenomeLoc;
 import org.broadinstitute.gatk.utils.GenomeLocParser;
 import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
 
 import java.io.ByteArrayInputStream;
+import java.io.IOException;
 import java.io.InputStream;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Iterator;
 import java.util.List;
+
 /**
  * User: hanna
  * Date: Jun 11, 2009
@@ -53,7 +56,13 @@ import java.util.List;
  * Pass specified reads into the given walker.
  */
 
-public class ArtificialSAMFileReader extends SAMFileReader {
+public class ArtificialSAMFileReader implements SamReader, Indexing {
+
+    /**
+     * The reader of SamRecords
+     */
+    private SamReader reader;
+
     /**
      * The parser, for GenomeLocs.
      */
@@ -64,15 +73,20 @@ public class ArtificialSAMFileReader extends SAMFileReader {
      */
     private final List<SAMRecord> reads;
 
+    /**
+     * Input/custom SAM file header
+     */
     private SAMFileHeader customHeader = null;
 
     /**
      * Construct an artificial SAM file reader.
+     *
      * @param sequenceDictionary sequence dictionary used to initialize our GenomeLocParser
      * @param reads Reads to use as backing data source.
      */
     public ArtificialSAMFileReader(SAMSequenceDictionary sequenceDictionary,SAMRecord... reads) {
-        super( createEmptyInputStream(),true );
+        final SamInputResource samInputResource = SamInputResource.of(createEmptyInputStream());
+        reader = SamReaderFactory.makeDefault().open(samInputResource);
         this.genomeLocParser = new GenomeLocParser(sequenceDictionary);
         this.reads = Arrays.asList(reads);
     }
@@ -84,30 +98,75 @@ public class ArtificialSAMFileReader extends SAMFileReader {
      * @param reads Reads to use as backing data source.
      */
     public ArtificialSAMFileReader( SAMFileHeader customHeader, SAMRecord... reads ) {
-        super(createEmptyInputStream(),true);
+        final SamInputResource samInputResource = SamInputResource.of(createEmptyInputStream());
+        reader = SamReaderFactory.makeDefault().open(samInputResource);
 
         this.customHeader = customHeader;
         this.genomeLocParser = new GenomeLocParser(customHeader.getSequenceDictionary());
         this.reads = Arrays.asList(reads);
     }
 
+    @Override
+    public String getResourceDescription() {
+        return this.toString();
+    }
 
     @Override
-    public SAMFileHeader getFileHeader() {
+    public boolean hasIndex() {
-        if ( customHeader != null ) {
+        return this.reader.hasIndex();
-            return customHeader;
+    }
-        }
 
-        return super.getFileHeader();
+    @Override
+    public Indexing indexing() {
+        return this;
+    }
+
+    @Override
+    public BrowseableBAMIndex getBrowseableIndex() {
+        BAMIndex index = this.getIndex();
+        if(!(index instanceof BrowseableBAMIndex)) {
+            throw new SAMException("Cannot return index: index created by BAM is not browseable.");
+        } else {
+            return BrowseableBAMIndex.class.cast(index);
+        }
+    }
+
+    @Override
+    public boolean hasBrowseableIndex() {
+        return this.hasIndex() && this.getIndex() instanceof BrowseableBAMIndex;
+    }
+
+    @Override
+    public BAMIndex getIndex() {
+        throw new UnsupportedOperationException();
+    }
+
+    @Override
+    public SAMRecordIterator iterator() {
+        return new SAMRecordIterator() {
+            private final Iterator<SAMRecord> iterator = reads.iterator();
+            public boolean hasNext() { return iterator.hasNext(); }
+            public SAMRecord next() { return iterator.next(); }
+            public void close() {}
+            public void remove() { iterator.remove(); }
+            public SAMRecordIterator assertSorted(SAMFileHeader.SortOrder sortOrder) { return this; }
+        };
     }
 
     /**
-     * @{inheritDoc}
+     * Iterate through the the file.
+     *
+     * @param chunks List of chunks for which to retrieve data.
+     * @return An iterator.
      */
     @Override
+    public SAMRecordIterator iterator(SAMFileSpan chunks) {
+        return new SamReader.AssertingIterator(this.reader.iterator());
+    }
+
     public SAMRecordIterator query(final String sequence, final int start, final int end, final boolean contained) {
         GenomeLoc region = genomeLocParser.createGenomeLoc(sequence, start, end);
-        List<SAMRecord> coveredSubset = new ArrayList<SAMRecord>();
+        List<SAMRecord> coveredSubset = new ArrayList<>();
 
         for( SAMRecord read: reads ) {
             GenomeLoc readPosition = genomeLocParser.createGenomeLoc(read);
@@ -126,15 +185,116 @@ public class ArtificialSAMFileReader extends SAMFileReader {
     }
 
     @Override
-    public SAMRecordIterator iterator() {
+    public SAMRecordIterator queryOverlapping(final String sequence, final int start, final int end) {
-        return new SAMRecordIterator() {
+        return this.query(sequence, start, end, false);
-            private final Iterator<SAMRecord> iterator = reads.iterator();
+    }
-            public boolean hasNext() { return iterator.hasNext(); }
+
-            public SAMRecord next() { return iterator.next(); }
+    @Override
-            public void close() {}
+    public SAMRecordIterator queryContained(final String sequence, final int start, final int end) {
-            public void remove() { iterator.remove(); }
+        return this.query(sequence, start, end, true);
-            public SAMRecordIterator assertSorted(SAMFileHeader.SortOrder sortOrder) { return this; }
+    }
-        };
+
+    @Override
+    public SAMRecordIterator query(final QueryInterval[] intervals, final boolean contained) {
+        return new AssertingIterator(this.reader.query(intervals, contained));
+    }
+
+    @Override
+    public SAMRecordIterator queryOverlapping(final QueryInterval[] intervals) {
+        return this.query(intervals, false);
+    }
+
+    @Override
+    public SAMRecordIterator queryContained(final QueryInterval[] intervals) {
+        return this.query(intervals, true);
+    }
+
+    @Override
+    public SAMRecordIterator queryUnmapped() {
+        return new AssertingIterator(this.reader.queryUnmapped());
+    }
+
+    @Override
+    public SAMRecordIterator queryAlignmentStart(final String sequence, final int start) {
+        return new AssertingIterator(this.reader.queryAlignmentStart(sequence, start));
+    }
+
+    @Override
+    public SAMRecord queryMate(final SAMRecord rec) {
+        if(!rec.getReadPairedFlag()) {
+            throw new IllegalArgumentException("queryMate called for unpaired read.");
+        } else if(rec.getFirstOfPairFlag() == rec.getSecondOfPairFlag()) {
+            throw new IllegalArgumentException("SAMRecord must be either first and second of pair, but not both.");
+        } else {
+            boolean firstOfPair = rec.getFirstOfPairFlag();
+            SAMRecordIterator it;
+            if(rec.getMateReferenceIndex() == -1) {
+                it = this.queryUnmapped();
+            } else {
+                it = this.queryAlignmentStart(rec.getMateReferenceName(), rec.getMateAlignmentStart());
+            }
+
+            try {
+                SAMRecord mateRec = null;
+
+                while(true) {
+                    SAMRecord next;
+                    while(it.hasNext()) {
+                        next = it.next();
+                        if(!next.getReadPairedFlag()) {
+                            if(rec.getReadName().equals(next.getReadName())) {
+                                throw new SAMFormatException("Paired and unpaired reads with same name: " + rec.getReadName());
+                            }
+                        } else {
+                            if(firstOfPair) {
+                                if(next.getFirstOfPairFlag()) {
+                                    continue;
+                                }
+                            } else if(next.getSecondOfPairFlag()) {
+                                continue;
+                            }
+
+                            if(rec.getReadName().equals(next.getReadName())) {
+                                if(mateRec != null) {
+                                    throw new SAMFormatException("Multiple SAMRecord with read name " + rec.getReadName() + " for " + (firstOfPair?"second":"first") + " end.");
+                                }
+
+                                mateRec = next;
+                            }
+                        }
+                    }
+
+                    next = mateRec;
+                    return next;
+                }
+            } finally {
+                it.close();
+            }
+        }
+    }
+
+    @Override
+    public SAMFileSpan getFilePointerSpanningReads() {
+        return this.reader.indexing().getFilePointerSpanningReads();
+    }
+
+    @Override
+    public void close() throws IOException{
+        if(this.reader != null) {
+            this.reader.close();
+        }
+
+        this.reader = null;
+    }
+
+    @Override
+    public Type type() {
+        return this.reader.type();
+    }
+
+    @Override
+    public SAMFileHeader getFileHeader() {
+        return customHeader != null ? customHeader : this.reader.getFileHeader();
     }
 
     /**

public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/ExampleToCopyUnitTest.java

@@ -30,9 +30,11 @@ package org.broadinstitute.gatk.utils;
 
 
 import htsjdk.samtools.SAMFileHeader;
-import htsjdk.samtools.SAMFileReader;
+import htsjdk.samtools.SamReader;
+import htsjdk.samtools.SamReaderFactory;
 import htsjdk.samtools.SAMRecord;
 import htsjdk.samtools.reference.ReferenceSequenceFile;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
 import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile;
 import org.broadinstitute.gatk.utils.pileup.PileupElement;
 import org.broadinstitute.gatk.utils.pileup.ReadBackedPileup;
@@ -50,6 +52,7 @@ import org.testng.annotations.Test;
 
 import java.io.File;
 import java.io.FileNotFoundException;
+import java.io.IOException;
 import java.util.*;
 
 public class ExampleToCopyUnitTest extends BaseTest {
@@ -217,13 +220,18 @@ public class ExampleToCopyUnitTest extends BaseTest {
         // create a fake BAM file, and iterate through it
         final ArtificialBAMBuilder bamBuilder = new ArtificialBAMBuilder(seq, 20, 10);
         final File bam = bamBuilder.makeTemporarilyBAMFile();
-        final SAMFileReader reader = new SAMFileReader(bam);
+        final SamReader reader = SamReaderFactory.makeDefault().open(bam);
 
         final Iterator<SAMRecord> bamIt = reader.iterator();
         while ( bamIt.hasNext() ) {
             final SAMRecord read = bamIt.next(); // all reads are actually GATKSAMRecords
             // TODO -- add some tests that use reads from a BAM
         }
+        try {
+            reader.close();
+        } catch ( IOException ex ) {
+            throw new ReviewedGATKException("Unable to close " + bam , ex);
+        }
     }
 
     /**

public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialBAMBuilderUnitTest.java

@@ -25,14 +25,17 @@
 
 package org.broadinstitute.gatk.utils.sam;
 
-import htsjdk.samtools.SAMFileReader;
 import htsjdk.samtools.SAMRecord;
+import htsjdk.samtools.SamReader;
+import htsjdk.samtools.SamReaderFactory;
 import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
 import org.testng.Assert;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
 import java.io.File;
+import java.io.IOException;
 import java.util.Arrays;
 import java.util.Iterator;
 import java.util.LinkedList;
@@ -94,7 +97,7 @@ public class ArtificialBAMBuilderUnitTest extends BaseTest {
         }
 
         final File bam = bamBuilder.makeTemporarilyBAMFile();
-        final SAMFileReader reader = new SAMFileReader(bam);
+        final SamReader reader = SamReaderFactory.makeDefault().open(bam);
         Assert.assertTrue(reader.hasIndex());
         final Iterator<SAMRecord> bamIt = reader.iterator();
         int nReadsFromBam = 0;
@@ -106,6 +109,11 @@ public class ArtificialBAMBuilderUnitTest extends BaseTest {
             Assert.assertTrue(read.getAlignmentStart() >= lastStart);
             lastStart = read.getAlignmentStart();
         }
+        try {
+            reader.close();
+        } catch ( IOException ex ) {
+            throw new ReviewedGATKException("Unable to close " + bam , ex);
+        }
         Assert.assertEquals(nReadsFromBam, bamBuilder.expectedNumberOfReads());
     }