reader now takes an argument for the maximum number of elements to read from the file.

public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/BAMDiffableReader.java

@@ -51,12 +51,11 @@ import java.util.zip.GZIPInputStream;
  * Class implementing diffnode reader for VCF
  */
 public class BAMDiffableReader implements DiffableReader {
-    private final static int MAX_RECORDS_TO_READ = 1000;
     @Override
     public String getName() { return "BAM"; }
 
     @Override
-    public DiffElement readFromFile(File file) {
+    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
         reader.setValidationStringency(SAMFileReader.ValidationStringency.SILENT);
 
@@ -65,7 +64,7 @@ public class BAMDiffableReader implements DiffableReader {
 
         int count = 0;
         while ( iterator.hasNext() ) {
-            if ( count++ > MAX_RECORDS_TO_READ )
+            if ( count++ > maxElementsToRead && maxElementsToRead != -1)
                 break;
             final SAMRecord record = iterator.next();
 

public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java

@@ -385,12 +385,17 @@ public class DiffEngine {
         return findReaderForFile(file) != null;
     }
 
+
     public DiffElement createDiffableFromFile(File file) {
+        return createDiffableFromFile(file, -1);
+    }
+
+    public DiffElement createDiffableFromFile(File file, int maxElementsToRead) {
         DiffableReader reader = findReaderForFile(file);
         if ( reader == null )
             throw new UserException("Unsupported file type: " + file);
         else
-            return reader.readFromFile(file);
+            return reader.readFromFile(file, maxElementsToRead);
     }
 
     public static boolean simpleDiffFiles(File masterFile, File testFile, DiffEngine.SummaryReportParams params) {

public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsWalker.java

@@ -48,11 +48,14 @@ public class DiffObjectsWalker extends RodWalker<Integer, Integer> {
     @Output(doc="File to which results should be written",required=true)
     protected PrintStream out;
 
-    @Argument(fullName="maxRecords", shortName="M", doc="Max. number of records to process", required=false)
+    @Argument(fullName="maxObjectsToRead", shortName="motr", doc="Max. number of objects to read from the files.  -1 [default] means unlimited", required=false)
-    int MAX_RECORDS = 0;
+    int MAX_OBJECTS_TO_READ = -1;
 
-    @Argument(fullName="maxCount1Records", shortName="M1", doc="Max. number of records occuring exactly once in the file to process", required=false)
+    @Argument(fullName="maxDiffs", shortName="M", doc="Max. number of diffs to process", required=false)
-    int MAX_COUNT1_RECORDS = 0;
+    int MAX_DIFFS = 0;
+
+    @Argument(fullName="maxCount1Diffs", shortName="M1", doc="Max. number of diffs occuring exactly once in the file to process", required=false)
+    int MAX_COUNT1_DIFFS = 0;
 
     @Argument(fullName="minCountForDiff", shortName="MCFD", doc="Min number of observations for a records to display", required=false)
     int minCountForDiff = 1;
@@ -91,9 +94,9 @@ public class DiffObjectsWalker extends RodWalker<Integer, Integer> {
     @Override
     public void onTraversalDone(Integer sum) {
         out.printf("Reading master file %s%n", masterFile);
-        DiffElement master = diffEngine.createDiffableFromFile(masterFile);
+        DiffElement master = diffEngine.createDiffableFromFile(masterFile, MAX_OBJECTS_TO_READ);
         out.printf("Reading test file %s%n", testFile);
-        DiffElement test = diffEngine.createDiffableFromFile(testFile);
+        DiffElement test = diffEngine.createDiffableFromFile(testFile, MAX_OBJECTS_TO_READ);
 
 //        out.printf("Master diff objects%n");
 //        out.println(master.toString());
@@ -107,7 +110,7 @@ public class DiffObjectsWalker extends RodWalker<Integer, Integer> {
                 out.printf("DIFF: %s%n", diff.toString());
         }
 
-        DiffEngine.SummaryReportParams params = new DiffEngine.SummaryReportParams(out, MAX_RECORDS, MAX_COUNT1_RECORDS, minCountForDiff);
+        DiffEngine.SummaryReportParams params = new DiffEngine.SummaryReportParams(out, MAX_DIFFS, MAX_COUNT1_DIFFS, minCountForDiff);
         diffEngine.reportSummarizedDifferences(diffs, params);
     }
 }

public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReader.java

@@ -43,7 +43,7 @@ public interface DiffableReader {
 
     @Ensures("result != null")
     @Requires("file != null")
-    public DiffElement readFromFile(File file);
+    public DiffElement readFromFile(File file, int maxElementsToRead);
 
     @Requires("file != null")
     public boolean canRead(File file);

public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java

@@ -51,15 +51,21 @@ public class VCFDiffableReader implements DiffableReader {
     public String getName() { return "VCF"; }
 
     @Override
-    public DiffElement readFromFile(File file) {
+    public DiffElement readFromFile(File file, int maxElementsToRead) {
         DiffNode root = DiffNode.rooted(file.getName());
         try {
             LineReader lineReader = new AsciiLineReader(new FileInputStream(file));
             VCFCodec vcfCodec = new VCFCodec();
-            VCFHeader header = (VCFHeader)vcfCodec.readHeader(lineReader);
+
+            // must be read as state is stored in reader itself
+            vcfCodec.readHeader(lineReader);
 
             String line = lineReader.readLine();
+            int count = 0;
             while ( line != null ) {
+                if ( count++ > maxElementsToRead && maxElementsToRead != -1)
+                    break;
+
                 VariantContext vc = (VariantContext)vcfCodec.decode(line);
                 String name = vc.getChr() + ":" + vc.getStart();
                 DiffNode vcRoot = DiffNode.empty(name, root);

public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReaderUnitTest.java

@@ -80,7 +80,7 @@ public class DiffableReaderUnitTest extends BaseTest {
         Assert.assertTrue(vcfReader.canRead(vcfFile));
         Assert.assertFalse(vcfReader.canRead(bamFile));
 
-        DiffElement diff = vcfReader.readFromFile(vcfFile);
+        DiffElement diff = vcfReader.readFromFile(vcfFile, -1);
         Assert.assertNotNull(diff);
 
         Assert.assertEquals(diff.getName(), vcfFile.getName());
@@ -110,7 +110,7 @@ public class DiffableReaderUnitTest extends BaseTest {
         Assert.assertTrue(bamReader.canRead(bamFile));
         Assert.assertFalse(bamReader.canRead(vcfFile));
 
-        DiffElement diff = bamReader.readFromFile(bamFile);
+        DiffElement diff = bamReader.readFromFile(bamFile, -1);
         Assert.assertNotNull(diff);
 
         Assert.assertEquals(diff.getName(), bamFile.getName());