Fix for picard issue 574: cram reader should look for the index file automatically

src/main/java/htsjdk/samtools/CRAMFileReader.java

@@ -26,7 +26,7 @@
 import htsjdk.samtools.seekablestream.SeekableStream;
 import htsjdk.samtools.util.CloseableIterator;
 import htsjdk.samtools.util.CloserUtil;
-import htsjdk.samtools.util.CoordMath;
+import htsjdk.samtools.util.Log;
 import htsjdk.samtools.util.RuntimeEOFException;
 
 import java.io.File;
@@ -57,6 +57,8 @@
 
     private ValidationStringency validationStringency;
 
+    private final static Log log = Log.getInstance(CRAMFileReader.class);
+
     /**
      * Create a CRAMFileReader from either a file or input stream using the reference source returned by
      * {@link ReferenceSource#getDefaultCRAMReferenceSource() getDefaultCRAMReferenceSource}.
@@ -95,6 +97,9 @@ public CRAMFileReader(final File cramFile, final InputStream inputStream,
         this.cramFile = cramFile;
         this.inputStream = inputStream;
         this.referenceSource = referenceSource;
+        if (cramFile != null) {
+            mIndexFile = findIndexForFile(null, cramFile);
+        }
         getIterator();
     }
 
@@ -117,7 +122,7 @@ public CRAMFileReader(final File cramFile, final File indexFile,
         }
 
         this.cramFile = cramFile;
-        this.mIndexFile = indexFile;
+        mIndexFile = findIndexForFile(indexFile, cramFile);
         this.referenceSource = referenceSource;
 
         getIterator();
@@ -140,6 +145,7 @@ public CRAMFileReader(final File cramFile, final CRAMReferenceSource referenceSo
 
         this.cramFile = cramFile;
         this.referenceSource = referenceSource;
+        mIndexFile = findIndexForFile(null, cramFile);
 
         getIterator();
     }
@@ -164,21 +170,8 @@ public CRAMFileReader(final InputStream inputStream, final SeekableStream indexI
         if (referenceSource == null) {
             throw new IllegalArgumentException("A reference is required for CRAM readers");
         }
-
-        this.inputStream = inputStream;
         this.referenceSource = referenceSource;
-        this.validationStringency = validationStringency;
-
-        iterator = new CRAMIterator(inputStream, referenceSource, validationStringency);
-        if (indexInputStream != null) {
-            SeekableStream baiStream = SamIndexes.asBaiSeekableStreamOrNull(indexInputStream, iterator.getSAMFileHeader().getSequenceDictionary());
-            if (null != baiStream)  {
-                mIndex = new CachingBAMFileIndex(baiStream, iterator.getSAMFileHeader().getSequenceDictionary());
-            }
-            else {
-                throw new IllegalArgumentException("CRAM index must be a BAI or CRAI stream");
-            }
-        }
+        initWithStreams(inputStream, indexInputStream, validationStringency);
     }
 
     /**
@@ -196,7 +189,7 @@ public CRAMFileReader(final InputStream inputStream, final SeekableStream indexI
     public CRAMFileReader(final InputStream stream,
                           final File indexFile, final CRAMReferenceSource referenceSource,
                           final ValidationStringency validationStringency) throws IOException {
-        this(stream, indexFile == null ? null: new SeekableFileStream(indexFile), referenceSource, validationStringency);
+        this(stream, indexFile == null ? null : new SeekableFileStream(indexFile), referenceSource, validationStringency);
     }
 
     /**
@@ -211,11 +204,44 @@ public CRAMFileReader(final InputStream stream,
      *
      * @throws IllegalArgumentException if the {@code cramFile} or the {@code CRAMReferenceSource} is null
      */
-    public CRAMFileReader(final File cramFile,
-                          final File indexFile, final CRAMReferenceSource referenceSource,
+    public CRAMFileReader(final File cramFile, final File indexFile, final CRAMReferenceSource referenceSource,
                           final ValidationStringency validationStringency) throws IOException {
-        this(new FileInputStream(cramFile), indexFile, referenceSource, validationStringency);
+        if (cramFile == null) {
+            throw new IllegalArgumentException("Input file can not be null for CRAM reader");
+        }
+        if (referenceSource == null) {
+            throw new IllegalArgumentException("A reference is required for CRAM readers");
+        }
         this.cramFile = cramFile;
+        this.referenceSource = referenceSource;
+        this.mIndexFile = findIndexForFile(indexFile, cramFile);
+        final SeekableFileStream indexStream = this.mIndexFile == null ? null : new SeekableFileStream(this.mIndexFile);
+        initWithStreams(new FileInputStream(cramFile), indexStream, validationStringency);
+    }
+
+    private void initWithStreams(final InputStream inputStream, final SeekableStream indexInputStream,
+                                 final ValidationStringency validationStringency) throws IOException {
+        this.inputStream = inputStream;
+        this.validationStringency = validationStringency;
+        iterator = new CRAMIterator(inputStream, referenceSource, validationStringency);
+        if (indexInputStream != null) {
+            SeekableStream baiStream = SamIndexes.asBaiSeekableStreamOrNull(indexInputStream, iterator.getSAMFileHeader().getSequenceDictionary());
+            if (null != baiStream)  {
+                mIndex = new CachingBAMFileIndex(baiStream, iterator.getSAMFileHeader().getSequenceDictionary());
+            }
+            else {
+                throw new IllegalArgumentException("CRAM index must be a BAI or CRAI stream");
+            }
+        }
+    }
+
+    private File findIndexForFile(File indexFile, final File cramFile) {
+        indexFile = indexFile == null ? SamFiles.findIndex(cramFile) : indexFile;
+        if (indexFile != null && indexFile.lastModified() < cramFile.lastModified()) {
+            log.warn("CRAM index file " + indexFile.getAbsolutePath() +
+                    " is older than CRAM " + cramFile.getAbsolutePath());
+        }
+        return indexFile;
     }
 
     @Override

src/test/java/htsjdk/samtools/CRAMFileReaderTest.java

@@ -27,6 +27,7 @@
 import htsjdk.samtools.reference.InMemoryReferenceSequenceFile;
 import htsjdk.samtools.seekablestream.SeekableFileStream;
 import htsjdk.samtools.util.Log;
+import org.testng.Assert;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
@@ -42,13 +43,18 @@
 public class CRAMFileReaderTest {
 
     private static final File TEST_DATA_DIR = new File("src/test/resources/htsjdk/samtools");
+    private static final File CRAM_WITH_CRAI = new File(TEST_DATA_DIR, "cram_with_crai_index.cram");
+    private static final File CRAM_WITHOUT_CRAI = new File(TEST_DATA_DIR, "cram_query_sorted.cram");
+    private static final ReferenceSource REFERENCE = createReferenceSource();
+    private static final File INDEX_FILE = new File(TEST_DATA_DIR, "cram_with_crai_index.cram.crai");
+
 
     @BeforeClass
     public void initClass() {
         Log.setGlobalLogLevel(Log.LogLevel.ERROR);
     }
 
-    private ReferenceSource createReferenceSource() {
+    private static ReferenceSource createReferenceSource() {
         byte[] refBases = new byte[10 * 10];
         Arrays.fill(refBases, (byte) 'A');
         InMemoryReferenceSequenceFile rsf = new InMemoryReferenceSequenceFile();
@@ -60,19 +66,17 @@ private ReferenceSource createReferenceSource() {
 
     @Test(description = "Test CRAMReader 1 reference required", expectedExceptions = IllegalStateException.class)
     public void testCRAMReader1_ReferenceRequired() {
-        File file = new File(TEST_DATA_DIR, "cram_with_crai_index.cram");
         InputStream bis = null;
         // assumes that reference_fasta property is not set and the download service is not enabled
-        new CRAMFileReader(file, bis);
+        new CRAMFileReader(CRAM_WITH_CRAI, bis);
     }
 
     // constructor 2: CRAMFileReader(final File cramFile, final InputStream inputStream, final ReferenceSource referenceSource)
 
     @Test(description = "Test CRAMReader 2 reference required", expectedExceptions = IllegalArgumentException.class)
     public void testCRAMReader2ReferenceRequired() {
-        File file = new File(TEST_DATA_DIR, "cram_with_crai_index.cram");
         InputStream bis =  null;
-        new CRAMFileReader(file, bis, null);
+        new CRAMFileReader(CRAM_WITH_CRAI, bis, null);
     }
 
     @Test(description = "Test CRAMReader 2 input required", expectedExceptions = IllegalArgumentException.class)
@@ -82,31 +86,66 @@ public void testCRAMReader2_InputRequired() {
         new CRAMFileReader(file, bis, createReferenceSource());
     }
 
+    @Test
+    public void testCRAMReader2_ShouldAutomaticallyFindCRAMIndex() {
+        InputStream inputStream = null;
+        CRAMFileReader reader = new CRAMFileReader(CRAM_WITH_CRAI, inputStream, REFERENCE);
+        reader.getIndex();
+        Assert.assertTrue(reader.hasIndex(), "Can't find CRAM existing index.");
+    }
+
+    @Test(expectedExceptions = SAMException.class)
+    public void testCRAMReader2_WithoutCRAMIndex() {
+        InputStream inputStream = null;
+        CRAMFileReader reader = new CRAMFileReader(CRAM_WITHOUT_CRAI, inputStream, REFERENCE);
+        reader.getIndex();
+    }
+
     // constructor 3: CRAMFileReader(final File cramFile, final File indexFile, final ReferenceSource referenceSource)
 
     @Test(description = "Test CRAMReader 3 reference required", expectedExceptions = IllegalArgumentException.class)
     public void testCRAMReader3_RequiredReference() {
-        File inputFile = new File(TEST_DATA_DIR, "cram_with_crai_index.cram");
         File indexFile = null;
         ReferenceSource refSource = null;
-        new CRAMFileReader(inputFile, indexFile, refSource);
+        new CRAMFileReader(CRAM_WITH_CRAI, indexFile, refSource);
     }
 
     @Test(description = "Test CRAMReader 3 input required", expectedExceptions = IllegalArgumentException.class)
-    public void testCRAMReader3_InputRequirted() {
+    public void testCRAMReader3_InputRequired() {
         File inputFile = null;
         File indexFile = null;
         ReferenceSource refSource = null;
         new CRAMFileReader(inputFile, indexFile, refSource);
     }
 
+    @Test
+    public void testCRAMReader3_ShouldAutomaticallyFindCRAMIndex() {
+        File indexFile = null;
+        CRAMFileReader reader = new CRAMFileReader(CRAM_WITH_CRAI, indexFile, REFERENCE);
+        reader.getIndex();
+        Assert.assertTrue(reader.hasIndex(), "Can't find existing CRAM index.");
+    }
+
+    @Test
+    public void testCRAMReader3_ShouldUseCRAMIndex() {
+        CRAMFileReader reader = new CRAMFileReader(CRAM_WITH_CRAI, INDEX_FILE, REFERENCE);
+        reader.getIndex();
+        Assert.assertTrue(reader.hasIndex(), "Can't find existing CRAM index.");
+    }
+
+    @Test(expectedExceptions = SAMException.class)
+    public void testCRAMReader3_WithoutCRAMIndex() {
+        File indexFile = null;
+        CRAMFileReader reader = new CRAMFileReader(CRAM_WITHOUT_CRAI, indexFile, REFERENCE);
+        reader.getIndex();
+    }
+
     // constructor 4: CRAMFileReader(final File cramFile, final ReferenceSource referenceSource)
 
     @Test(description = "Test CRAMReader 4 reference required", expectedExceptions = IllegalArgumentException.class)
     public void testCRAMReader4_ReferenceRequired() {
-        File inputFile = new File(TEST_DATA_DIR, "cram_with_crai_index.cram");
         ReferenceSource refSource = null;
-        new CRAMFileReader(inputFile, refSource);
+        new CRAMFileReader(CRAM_WITH_CRAI, refSource);
     }
 
     @Test(description = "Test CRAMReader 4 input required", expectedExceptions = IllegalArgumentException.class)
@@ -115,6 +154,19 @@ public void testCRAMReader4_InputRequired() {
         new CRAMFileReader(inputFile, createReferenceSource());
     }
 
+    @Test
+    public void testCRAMReader4_ShouldAutomaticallyFindCRAMIndex() {
+        CRAMFileReader reader = new CRAMFileReader(CRAM_WITH_CRAI, REFERENCE);
+        reader.getIndex();
+        Assert.assertTrue(reader.hasIndex(), "Can't find existing CRAM index.");
+    }
+
+    @Test(expectedExceptions = SAMException.class)
+    public void testCRAMReader4_WithoutCRAMIndex() {
+        CRAMFileReader reader = new CRAMFileReader(CRAM_WITHOUT_CRAI, REFERENCE);
+        reader.getIndex();
+    }
+
     // constructor 5: CRAMFileReader(final InputStream inputStream, final SeekableStream indexInputStream,
     //          final ReferenceSource referenceSource, final ValidationStringency validationStringency)
     @Test(description = "Test CRAMReader 5 reference required", expectedExceptions = IllegalArgumentException.class)
@@ -146,18 +198,34 @@ public void testCRAMReader6_ReferenceRequired() throws IOException {
     public void testCRAMReader6_InputRequired() throws IOException {
         InputStream bis = null;
         File file = null;
-        ReferenceSource refSource = null;
         new CRAMFileReader(bis, file, createReferenceSource(), ValidationStringency.STRICT);
     }
 
     // constructor 7: CRAMFileReader(final File cramFile, final File indexFile, final ReferenceSource referenceSource,
     //                final ValidationStringency validationStringency)
     @Test(description = "Test CRAMReader 7 reference required", expectedExceptions = IllegalArgumentException.class)
     public void testCRAMReader7_ReferenceRequired() throws IOException {
-        InputStream bis = new ByteArrayInputStream(new byte[0]);
-        File file = new File(TEST_DATA_DIR, "cram_with_crai_index.cram");
         ReferenceSource refSource = null;
-        new CRAMFileReader(file, file, refSource, ValidationStringency.STRICT);
+        new CRAMFileReader(CRAM_WITH_CRAI, CRAM_WITH_CRAI, refSource, ValidationStringency.STRICT);
     }
 
+    @Test
+    public void testCRAMReader7_ShouldAutomaticallyFindCRAMIndex()throws IOException {
+        File indexFile = null;
+        CRAMFileReader reader = new CRAMFileReader(CRAM_WITH_CRAI, indexFile, REFERENCE, ValidationStringency.STRICT);
+        Assert.assertTrue(reader.hasIndex(), "Can't find existing CRAM index.");
+    }
+
+    @Test
+    public void testCRAMReader7_ShouldUseCRAMIndex() throws IOException {
+        CRAMFileReader reader = new CRAMFileReader(CRAM_WITH_CRAI, INDEX_FILE, REFERENCE, ValidationStringency.STRICT);
+        Assert.assertTrue(reader.hasIndex(), "Can't find existing CRAM index.");
+    }
+
+    @Test(expectedExceptions = SAMException.class)
+    public void testCRAMReader7_WithoutCRAMIndex() throws IOException {
+        File indexFile = null;
+        CRAMFileReader reader = new CRAMFileReader(CRAM_WITHOUT_CRAI, indexFile, REFERENCE, ValidationStringency.STRICT);
+        reader.getIndex();
+    }
 }