Support writing a CRAI index from CRAMContainerStreamWriter

src/main/java/htsjdk/samtools/CRAMBAIIndexer.java

@@ -79,7 +79,7 @@
  * but it is unused.  This would be accomplished via {@link #createIndex(SeekableStream, File, Log, ValidationStringency)}.
  *
  */
-public class CRAMBAIIndexer {
+public class CRAMBAIIndexer implements CRAMIndexer {
 
     // The number of references (chromosomes) in the BAM file
     private final int numReferences;
@@ -130,7 +130,8 @@ public CRAMBAIIndexer(final OutputStream output, final SAMFileHeader fileHeader)
      *
      * @param container container to be indexed
      */
-    void processContainer(final Container container, final ValidationStringency validationStringency) {
+    @Override
+    public void processContainer(final Container container, final ValidationStringency validationStringency) {
         if (container == null || container.isEOF()) {
             return;
         }
@@ -226,6 +227,7 @@ public void processAsSingleReferenceSlice(final Slice slice) {
      * After all the slices have been processed, finish is called.
      * Writes any final information and closes the output file.
      */
+    @Override
     public void finish() {
         // process any remaining references
         advanceToReference(numReferences);

src/main/java/htsjdk/samtools/CRAMCRAIIndexer.java

@@ -26,7 +26,7 @@
  * <li>read an existing index from an input stream</li>
  * </ul><p>
  */
-public class CRAMCRAIIndexer {
+public class CRAMCRAIIndexer implements CRAMIndexer {
 
     final private CRAIIndex craiIndex = new CRAIIndex();
     final private GZIPOutputStream os;
@@ -72,9 +72,15 @@ public void processContainer(final Container container) {
         craiIndex.processContainer(container);
     }
 
+    @Override
+    public void processContainer(final Container container, final ValidationStringency validationStringency) {
+        processContainer(container);
+    }
+
     /**
      * Finish creating the index by writing the accumulated entries out to the stream.
      */
+    @Override
     public void finish() {
         try {
             craiIndex.writeIndex(os);

src/main/java/htsjdk/samtools/CRAMContainerStreamWriter.java

@@ -59,7 +59,7 @@ public class CRAMContainerStreamWriter {
     private Set<String> captureTags = new TreeSet<>();
     private Set<String> ignoreTags = new TreeSet<>();
 
-    private CRAMBAIIndexer indexer;
+    private CRAMIndexer indexer;
     private long offset;
 
     /**
@@ -78,14 +78,31 @@ public CRAMContainerStreamWriter(
             final CRAMReferenceSource source,
             final SAMFileHeader samFileHeader,
             final String cramId) {
+        this(outputStream, source, samFileHeader, cramId, indexStream == null ? null : new CRAMBAIIndexer(indexStream, samFileHeader));
+    }
+
+    /**
+     * Create a CRAMContainerStreamWriter for writing SAM records into a series of CRAM
+     * containers on output stream, with an optional index.
+     *
+     * @param outputStream where to write the CRAM stream.
+     * @param source reference source
+     * @param samFileHeader {@link SAMFileHeader} to be used. Sort order is determined by the sortOrder property of this arg.
+     * @param cramId used for display in error message display
+     * @param indexer CRAM indexer. Can be null if no index is required.
+     */
+    public CRAMContainerStreamWriter(
+            final OutputStream outputStream,
+            final CRAMReferenceSource source,
+            final SAMFileHeader samFileHeader,
+            final String cramId,
+            final CRAMIndexer indexer) {
         this.outputStream = outputStream;
+        this.source = source;
         this.samFileHeader = samFileHeader;
         this.cramID = cramId;
-        this.source = source;
+        this.indexer = indexer;
         containerFactory = new ContainerFactory(samFileHeader, recordsPerSlice);
-        if (indexStream != null) {
-            indexer = new CRAMBAIIndexer(indexStream, samFileHeader);
-        }
     }
 
     /**

src/main/java/htsjdk/samtools/CRAMIndexer.java

@@ -0,0 +1,20 @@
+package htsjdk.samtools;
+
+import htsjdk.samtools.cram.structure.Container;
+
+/**
+ * Interface for indexing CRAM.
+ */
+public interface CRAMIndexer {
+    /**
+     * Create index entries for a single container.
+     * @param container the container to index
+     * @param validationStringency stringency for validating records, passed to {@link Container#getSpans(ValidationStringency)}
+     */
+    void processContainer(final Container container, final ValidationStringency validationStringency);
+
+    /**
+     * Finish creating the index by writing the accumulated entries out.
+     */
+    void finish();
+}

src/test/java/htsjdk/samtools/CRAMContainerStreamWriterTest.java

@@ -3,11 +3,9 @@
 import htsjdk.HtsjdkTest;
 import htsjdk.samtools.cram.ref.ReferenceSource;
 import htsjdk.samtools.reference.InMemoryReferenceSequenceFile;
-import htsjdk.samtools.seekablestream.SeekableMemoryStream;
 import htsjdk.samtools.util.CloseableIterator;
 import htsjdk.samtools.util.Log;
 import htsjdk.samtools.util.Log.LogLevel;
-import htsjdk.samtools.util.RuntimeIOException;
 import org.testng.Assert;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
@@ -18,7 +16,6 @@
 import java.io.FileOutputStream;
 import java.io.IOException;
 import java.io.OutputStream;
-import java.io.StringWriter;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collections;
@@ -75,6 +72,19 @@ private void doTest(final List<SAMRecord> samRecords, final ByteArrayOutputStrea
         final CRAMContainerStreamWriter containerStream = new CRAMContainerStreamWriter(outStream, indexStream, refSource, header, "test");
         containerStream.writeHeader(header);
 
+        writeThenReadRecords(samRecords, outStream, refSource, containerStream);
+    }
+
+    private void doTestWithIndexer(final List<SAMRecord> samRecords, final ByteArrayOutputStream outStream, final SAMFileHeader header, final CRAMIndexer indexer) {
+        final ReferenceSource refSource = createReferenceSource();
+
+        final CRAMContainerStreamWriter containerStream = new CRAMContainerStreamWriter(outStream, refSource, header, "test", indexer);
+        containerStream.writeHeader(header);
+
+        writeThenReadRecords(samRecords, outStream, refSource, containerStream);
+    }
+
+    private void writeThenReadRecords(List<SAMRecord> samRecords, ByteArrayOutputStream outStream, ReferenceSource refSource, CRAMContainerStreamWriter containerStream) {
         for (SAMRecord record : samRecords) {
             containerStream.writeAlignment(record);
         }
@@ -144,15 +154,32 @@ public void testCRAMContainerAggregatePartitions() throws IOException {
         Assert.assertEquals(count, nRecs);
     }
 
-    @Test(description = "Test CRAMContainerStream with index")
-    public void testCRAMContainerStreamWithIndex() throws IOException {
+    @Test(description = "Test CRAMContainerStream with bai index")
+    public void testCRAMContainerStreamWithBaiIndex() throws IOException {
         final List<SAMRecord> samRecords = createRecords(100);
-        final ByteArrayOutputStream outStream = new ByteArrayOutputStream();
-        final ByteArrayOutputStream indexStream = new ByteArrayOutputStream();
-        doTest(samRecords, outStream, indexStream);
-        outStream.close();
-        indexStream.close();
+        try (ByteArrayOutputStream outStream = new ByteArrayOutputStream();
+             ByteArrayOutputStream indexStream = new ByteArrayOutputStream()) {
+            doTest(samRecords, outStream, indexStream);
+            outStream.flush();
+            indexStream.flush();
+            checkCRAMContainerStream(outStream, indexStream, ".bai");
+        }
+    }
+
+    @Test(description = "Test CRAMContainerStream with crai index")
+    public void testCRAMContainerStreamWithCraiIndex() throws IOException {
+        final List<SAMRecord> samRecords = createRecords(100);
+        final SAMFileHeader header = createSAMHeader(SAMFileHeader.SortOrder.coordinate);
+        try (ByteArrayOutputStream outStream = new ByteArrayOutputStream();
+             ByteArrayOutputStream indexStream = new ByteArrayOutputStream()) {
+            doTestWithIndexer(samRecords, outStream, header, new CRAMCRAIIndexer(indexStream, header));
+            outStream.flush();
+            indexStream.flush();
+            checkCRAMContainerStream(outStream, indexStream, ".crai");
+        }
+    }
 
+    private void checkCRAMContainerStream(ByteArrayOutputStream outStream, ByteArrayOutputStream indexStream, String indexExtension) throws IOException {
         // write the file out
         final File cramTempFile = File.createTempFile("cramContainerStreamTest", ".cram");
         cramTempFile.deleteOnExit();
@@ -161,7 +188,7 @@ public void testCRAMContainerStreamWithIndex() throws IOException {
         cramFileStream.close();
 
         // write the index out
-        final File indexTempFile = File.createTempFile("cramContainerStreamTest", ".bai");
+        final File indexTempFile = File.createTempFile("cramContainerStreamTest", indexExtension);
         indexTempFile.deleteOnExit();
         OutputStream indexFileStream = new FileOutputStream(indexTempFile);
         indexFileStream.write(indexStream.toByteArray());