Normalize CRAM reference bases and throw on MD5 validation failure.

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

@@ -177,10 +177,14 @@ void nextContainer() throws IOException, IllegalArgumentException,
             final Slice slice = container.slices[i];
             if (slice.sequenceId < 0)
                 continue;
-            if (validationStringency != ValidationStringency.SILENT && !slice.validateRefMD5(refs)) {
-                log.error(String
-                        .format("Reference sequence MD5 mismatch for slice: seq id %d, start %d, span %d, expected MD5 %s", slice.sequenceId,
-                                slice.alignmentStart, slice.alignmentSpan, String.format("%032x", new BigInteger(1, slice.refMD5))));
+            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",
+                            slice.sequenceId,
+                            slice.alignmentStart,
+                            slice.alignmentSpan,
+                            String.format("%032x", new BigInteger(1, slice.refMD5)));
+                throw new CRAMException(msg);
             }
         }
 

src/main/java/htsjdk/samtools/cram/build/Utils.java

@@ -17,7 +17,9 @@
  */
 package htsjdk.samtools.cram.build;
 
-class Utils {
+final public class Utils {
+
+    private Utils() {};
 
     /**
      * CRAM operates with upper case bases, so both read and ref bases should be

src/main/java/htsjdk/samtools/cram/ref/CRAMReferenceSource.java

@@ -15,8 +15,8 @@
      *                        against the reference by using common name variations,
      *                        such as adding or removing a leading "chr" prefix
      *                        from the requested name. if false, use exact match
-     * @return the bases representing the requested sequence. or null if the sequence
-     *          cannot be found
+     * @return the upper cased, normalized (see {@link htsjdk.samtools.cram.build.Utils#normalizeBase})
+     * bases representing the requested sequence, or null if the sequence cannot be found
      */
     byte[] getReferenceBases(final SAMSequenceRecord sequenceRecord, final boolean tryNameVariants);
 }

src/main/java/htsjdk/samtools/cram/ref/ReferenceSource.java

@@ -20,6 +20,7 @@
 import htsjdk.samtools.Defaults;
 import htsjdk.samtools.SAMException;
 import htsjdk.samtools.SAMSequenceRecord;
+import htsjdk.samtools.cram.build.Utils;
 import htsjdk.samtools.cram.io.InputStreamUtils;
 import htsjdk.samtools.reference.ReferenceSequence;
 import htsjdk.samtools.reference.ReferenceSequenceFile;
@@ -123,13 +124,23 @@ public void clearCache() {
         return null;
     }
 
+    // Upper case and normalize (-> ACGTN) in-place, and add to the cache
+    private byte[] addToCache(final String sequenceName, final byte[] bases) {
+        for (int i = 0; i < bases.length; i++) {
+            bases[i] = Utils.normalizeBase(bases[i]);
+        }
+        cacheW.put(sequenceName, new WeakReference<byte[]>(bases));
+        return bases;
+    }
+
     public synchronized byte[] getReferenceBases(final SAMSequenceRecord record,
                                                  final boolean tryNameVariants) {
         { // check cache by sequence name:
             final String name = record.getSequenceName();
             final byte[] bases = findInCache(name);
-            if (bases != null)
+            if (bases != null) {
                 return bases;
+            }
         }
 
         final String md5 = record.getAttribute(SAMSequenceRecord.MD5_TAG);
@@ -152,10 +163,7 @@ public void clearCache() {
         { // try to fetch sequence by name:
             bases = findBasesByName(record.getSequenceName(), tryNameVariants);
             if (bases != null) {
-                SequenceUtil.upperCase(bases);
-                cacheW.put(record.getSequenceName(), new WeakReference<byte[]>(
-                        bases));
-                return bases;
+                return addToCache(record.getSequenceName(), bases);
             }
         }
 
@@ -169,9 +177,7 @@ public void clearCache() {
                     }
                 }
                 if (bases != null) {
-                    SequenceUtil.upperCase(bases);
-                    cacheW.put(md5, new WeakReference<byte[]>(bases));
-                    return bases;
+                    return addToCache(md5, bases);
                 }
             }
         }

src/test/java/htsjdk/samtools/CRAMCRAIIndexerTest.java

@@ -30,6 +30,11 @@ public void testCRAIIndexerFromContainer() throws IOException {
                 refSource,
                 ValidationStringency.STRICT);
         SAMFileHeader samHeader = reader.getFileHeader();
+        Iterator<SAMRecord> it = reader.getIterator();
+        while(it.hasNext()) {
+            SAMRecord samRec = it.next();
+        }
+
         reader.close();
 
         FileInputStream fis = new FileInputStream(CRAMFile);

src/test/java/htsjdk/samtools/cram/structure/SliceTests.java

@@ -1,10 +1,19 @@
 package htsjdk.samtools.cram.structure;
 
+import htsjdk.samtools.CRAMFileReader;
+import htsjdk.samtools.SAMFileHeader;
 import htsjdk.samtools.SAMRecord;
+import htsjdk.samtools.ValidationStringency;
+import htsjdk.samtools.cram.CRAMException;
+import htsjdk.samtools.cram.ref.ReferenceSource;
 import htsjdk.samtools.util.SequenceUtil;
 import org.testng.Assert;
 import org.testng.annotations.Test;
 
+import java.io.File;
+import java.io.IOException;
+import java.util.Iterator;
+
 /**
  * Created by vadim on 07/12/2015.
  */
@@ -33,4 +42,29 @@ public void test_validateRef() {
         Assert.assertEquals(slice.refMD5, md5);
         Assert.assertTrue(slice.validateRefMD5(ref));
     }
+
+    @Test(expectedExceptions= CRAMException.class)
+    public void testFailsMD5Check() throws IOException {
+        // auxf.alteredForMD5test.fa has been altered slightly from the original reference
+        // to cause the CRAM md5 check to fail
+        final File CRAMFile = new File("src/test/resources/htsjdk/samtools/cram/auxf#values.3.0.cram");
+        final File refFile = new File("src/test/resources/htsjdk/samtools/cram/auxf.alteredForMD5test.fa");
+        ReferenceSource refSource = new ReferenceSource(refFile);
+        CRAMFileReader reader = null;
+        try {
+            reader = new CRAMFileReader(
+                    CRAMFile,
+                    null,
+                    refSource,
+                    ValidationStringency.STRICT);
+            Iterator<SAMRecord> it = reader.getIterator();
+            while (it.hasNext()) {
+                it.next();
+            }
+        } finally {
+            if (reader != null) {
+                reader.close();
+            }
+        }
+    }
 }

src/test/resources/htsjdk/samtools/cram/auxf.alteredForMD5test.fa

@@ -0,0 +1,2 @@
+>Sheila
+CTAGCTCAGAAAAAAAAAA

src/test/resources/htsjdk/samtools/cram/auxf.alteredForMD5test.fa.fai

@@ -0,0 +1 @@
+Sheila	19	8	19	20