Deleted useless memory allocation

Moved records correctness's checking from nextContainer() to next()

Moved records correctness's validation in the separate method

Added tests relate new functionality

Add inheriting from HtsjdkTest in new test

src/main/java/htsjdk/samtools/CRAMIterator.java

@@ -87,7 +87,7 @@ public CRAMIterator(final InputStream inputStream, final CRAMReferenceSource ref
         this.containerIterator = containerIterator;
 
         firstContainerOffset = this.countingInputStream.getCount();
-        records = new ArrayList<SAMRecord>(10000);
+        records = new ArrayList<SAMRecord>();
         normalizer = new CramNormalizer(cramHeader.getSamFileHeader(),
                 referenceSource);
         parser = new ContainerParser(cramHeader.getSamFileHeader());
@@ -106,7 +106,7 @@ public CRAMIterator(final SeekableStream seekableStream, final CRAMReferenceSour
         this.containerIterator = containerIterator;
 
         firstContainerOffset = containerIterator.getFirstContainerOffset();
-        records = new ArrayList<SAMRecord>(10000);
+        records = new ArrayList<SAMRecord>();
         normalizer = new CramNormalizer(cramHeader.getSamFileHeader(),
                 referenceSource);
         parser = new ContainerParser(cramHeader.getSamFileHeader());
@@ -131,6 +131,7 @@ void nextContainer() throws IOException, IllegalArgumentException,
                 nextRecord = null;
                 return;
             }
+
             container = containerIterator.next();
             if (container.isEOF()) {
                 records.clear();
@@ -146,10 +147,7 @@ void nextContainer() throws IOException, IllegalArgumentException,
             }
         }
 
-        if (records == null)
-            records = new ArrayList<SAMRecord>(container.nofRecords);
-        else
-            records.clear();
+        records.clear();
         if (cramRecords == null)
             cramRecords = new ArrayList<CramCompressionRecord>(container.nofRecords);
         else
@@ -175,8 +173,10 @@ void nextContainer() throws IOException, IllegalArgumentException,
 
         for (int i = 0; i < container.slices.length; i++) {
             final Slice slice = container.slices[i];
+
             if (slice.sequenceId < 0)
                 continue;
+
             if (!slice.validateRefMD5(refs)) {
                 final String msg = String.format(
                         "Reference sequence MD5 mismatch for slice: sequence id %d, start %d, span %d, expected MD5 %s",
@@ -204,12 +204,6 @@ void nextContainer() throws IOException, IllegalArgumentException,
 
             samRecord.setValidationStringency(validationStringency);
 
-            if (validationStringency != ValidationStringency.SILENT) {
-                final List<SAMValidationError> validationErrors = samRecord.isValid();
-                SAMUtils.processValidationErrors(validationErrors,
-                        samRecordIndex, validationStringency);
-            }
-
             if (mReader != null) {
                 final long chunkStart = (container.offset << 16) | cramRecord.sliceIndex;
                 final long chunkEnd = ((container.offset << 16) | cramRecord.sliceIndex) + 1;
@@ -271,7 +265,22 @@ public boolean hasNext() {
 
     @Override
     public SAMRecord next() {
-        return iterator.next();
+        SAMRecord samRecord = iterator.next();
+        if (validationStringency != ValidationStringency.SILENT) {
+            validateRecord(samRecord);
+        }
+        return samRecord;
+    }
+
+    /**
+     * Perform various validations of SAMRecord and handle
+     * found errors according to the validation stringency.
+     *
+     * @param samRecord - validated record
+     */
+    public void validateRecord(SAMRecord samRecord){
+        final List<SAMValidationError> validationErrors = samRecord.isValid();
+        SAMUtils.processValidationErrors(validationErrors, samRecordIndex, validationStringency);
     }
 
     @Override

src/test/java/htsjdk/samtools/CRAMIteratorTest.java

@@ -0,0 +1,53 @@
+package htsjdk.samtools;
+
+import htsjdk.HtsjdkTest;
+import htsjdk.samtools.cram.ref.ReferenceSource;
+import htsjdk.samtools.seekablestream.SeekableStream;
+import org.junit.Assert;
+import org.testng.annotations.Test;
+
+import java.io.File;
+
+
+/**
+ * @author [email protected], EPAM Systems, Inc.
+ *
+ * This test serve for verifying CRAMIterator records validation using strict validation strategy
+ **/
+
+public class CRAMIteratorTest extends HtsjdkTest {
+    private static final File refFile = new File("src/test/resources/htsjdk/samtools/cram/ce.fa");
+    private static final File cramFile = new File("src/test/resources/htsjdk/samtools/cram/ce#supp.3.0.cram");
+    ReferenceSource source = new ReferenceSource(refFile);
+
+    @Test()
+    public void shouldNotThrowsExceptionIfCRAMfileContainsInvalidRecords() {
+        SAMRecordIterator cramIter =
+                getCramFileIterator(cramFile, source, ValidationStringency.STRICT);
+
+        Assert.assertTrue(cramIter.hasNext());
+    }
+
+    @Test(expectedExceptions = SAMException.class)
+    public void shouldThrowExceptionIfCRAMFileContainsInvalidRecods() {
+        SAMRecordIterator cramIter =
+                getCramFileIterator(cramFile, source, ValidationStringency.STRICT);
+
+        while (cramIter.hasNext())
+        {
+            cramIter.next();
+        }
+    }
+
+    private SAMRecordIterator getCramFileIterator(File cramFile,
+                                                  ReferenceSource source,
+                                                  ValidationStringency valStrigency) {
+
+        CRAMFileReader cramFileReader = new CRAMFileReader(cramFile, (SeekableStream) null, source);
+        cramFileReader.setValidationStringency(valStrigency);
+        return cramFileReader.getIterator();
+    }
+}
+
+
+