Add support for re-serializing (sharding and reassembling) CRAM conta…

…iners to a new stream.

src/main/java/htsjdk/samtools/CRAMContainerStreamRewriter.java

@@ -0,0 +1,92 @@
+package htsjdk.samtools;
+
+import htsjdk.samtools.cram.build.CramIO;
+import htsjdk.samtools.cram.structure.Container;
+import htsjdk.samtools.cram.structure.CramHeader;
+import htsjdk.samtools.util.RuntimeIOException;
+
+import java.io.IOException;
+import java.io.OutputStream;
+
+/**
+ * Rewrite a series of containers to a new stream. The CRAM header and SAMFileHeader containers are automatically
+ * written to the stream when this class is instantiated. An EOF container is automatically written when
+ * {@link #finish()} is called.
+ */
+public class CRAMContainerStreamRewriter {
+    private final OutputStream outputStream;
+    private final String outputStreamIdentifier;
+    private final CramHeader cramHeader;
+    private final SAMFileHeader samFileHeader;
+    private final CRAMIndexer cramIndexer;
+
+    private long streamOffset = 0L;
+    private long recordCounter = 0L;
+
+    /**
+     * Create a CRAMContainerStreamRewriter for writing a series of CRAM containers into an output
+     * stream, with an optional output index.
+     *
+     * @param outputStream where to write the CRAM stream.
+     * @param samFileHeader {@link SAMFileHeader} to be used. Sort order is determined by the sortOrder property of this arg.
+     * @param outputStreamIdentifier used for display in error message display
+     * @param indexer CRAM indexer. Can be null if no index is required.
+     */
+    public CRAMContainerStreamRewriter(
+            final OutputStream outputStream,
+            final CramHeader cramHeader,
+            final SAMFileHeader samFileHeader,
+            final String outputStreamIdentifier,
+            final CRAMIndexer indexer) {
+        this.outputStream = outputStream;
+        this.cramHeader = cramHeader;
+        this.samFileHeader = samFileHeader;
+        this.outputStreamIdentifier = outputStreamIdentifier;
+        this.cramIndexer = indexer;
+
+        streamOffset = CramIO.writeCramHeader(cramHeader, outputStream);
+        streamOffset += Container.writeSAMFileHeaderContainer(cramHeader.getCRAMVersion(), samFileHeader, outputStream);
+    }
+
+    /**
+     * Writes a container to a stream, updating the (stream-relative) global record counter and byte offsets.
+     *
+     * Since this method mutates the values in the container, the container is no longer valid in the context
+     * of the stream from which it originated.
+     *
+     * @param container the container to emit to the stream. the container must conform to the version and sort
+     *                  order specified in the CRAM header and SAM header provided to the constructor
+     *                  {@link #CRAMContainerStreamRewriter(OutputStream, CramHeader, SAMFileHeader, String, CRAMIndexer)}.
+     *                  All the containers serialized to a single stream using this method must have originated from the
+     *                  same original context(/stream), obtained via {@link htsjdk.samtools.cram.build.CramContainerIterator}.
+     */
+     public void rewriteContainer(final Container container) {
+         // update the container and slices with the correct global record counter and byte offsets
+         // (required for indexing)
+         container.relocateContainer(recordCounter, streamOffset);
+
+         // re-serialize the entire container and slice(s), block by block
+        streamOffset += container.write(cramHeader.getCRAMVersion(), outputStream);
+        recordCounter += container.getContainerHeader().getNumberOfRecords();
+
+        if (cramIndexer != null) {
+            cramIndexer.processContainer(container,  ValidationStringency.SILENT);
+        }
+    }
+
+    /**
+     * Finish writing to the stream. Flushes the record cache and optionally emits an EOF container.
+     */
+    public void finish() {
+        try {
+            CramIO.writeCramEOF(cramHeader.getCRAMVersion(), outputStream);
+            outputStream.flush();
+            if (cramIndexer != null) {
+                cramIndexer.finish();
+            }
+        } catch (final IOException e) {
+            throw new RuntimeIOException(String.format("IOException closing stream for %s", outputStreamIdentifier));
+        }
+    }
+
+}

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

@@ -1,6 +1,5 @@
 package htsjdk.samtools;
 
-import htsjdk.samtools.cram.structure.CompressorCache;
 import htsjdk.samtools.cram.structure.Container;
 
 /**

src/main/java/htsjdk/samtools/cram/structure/Container.java

@@ -49,7 +49,7 @@ public class Container {
     private final List<Slice> slices;
 
     // container's byte offset from the start of the containing stream, used for indexing
-    private final long containerByteOffset;
+    private long containerByteOffset;
 
     /**
      * Create a Container with a {@link ReferenceContext} derived from its {@link Slice}s.
@@ -190,6 +190,7 @@ public int write(final CRAMVersion cramVersion, final OutputStream outputStream)
                 // landmark 0 = byte length of the compression header
                 // landmarks after 0 = byte length of the compression header plus all slices before this one
                 landmarks.add(tempOutputStream.size());
+                slice.byteOffsetOfContainer = containerByteOffset;
                 slice.write(cramVersion, tempOutputStream);
             }
             getContainerHeader().setLandmarks(landmarks);
@@ -335,6 +336,28 @@ public List<SAMRecord> getSAMRecords(
     public CompressionHeader getCompressionHeader() { return compressionHeader; }
     public AlignmentContext getAlignmentContext() { return containerHeader.getAlignmentContext(); }
     public long getContainerByteOffset() { return containerByteOffset; }
+
+    /**
+     * Update the stream-relative values (global record counter and stream byte offset) for this
+     * container. For use when re-serializing a container that has been read from an existing stream
+     * into a new stream. This method mutates the container and it's slices - the container is no
+     * longer valid in the context of it's original stream.
+     *
+     * @param containerRecordCounter the new global record counter for this container
+     * @param streamByteOffset the new stream byte offset counter for this container
+     * @return the updated global record counter
+     */
+    public long relocateContainer(final long containerRecordCounter, final long streamByteOffset) {
+        this.containerByteOffset = streamByteOffset;
+        this.getContainerHeader().setGlobalRecordCounter(containerRecordCounter);
+
+        long sliceRecordCounter = containerRecordCounter;
+        for (final Slice slice : getSlices()) {
+            sliceRecordCounter = slice.relocateSlice(sliceRecordCounter, streamByteOffset);
+        }
+        return sliceRecordCounter;
+    }
+
     public List<Slice> getSlices() { return slices; }
     public boolean isEOF() {
         return containerHeader.isEOF() && (getSlices() == null || getSlices().size() == 0);

src/main/java/htsjdk/samtools/cram/structure/ContainerHeader.java

@@ -42,7 +42,7 @@ public class ContainerHeader {
     // total length of all blocks in this container (total length of this container, minus the Container Header).
     private final AlignmentContext alignmentContext;
     private final int recordCount;
-    private final long globalRecordCounter;
+    private long globalRecordCounter;
     private final long baseCount;
     private final int blockCount;
 
@@ -249,4 +249,8 @@ public boolean isEOF() {
         return v3 || v2;
     }
 
+    void setGlobalRecordCounter(final long recordCounter) {
+        this.globalRecordCounter = recordCount;
+    }
+
 }

src/main/java/htsjdk/samtools/cram/structure/Slice.java

@@ -67,7 +67,7 @@ public class Slice {
     // Slice header components as defined in the spec
     private final AlignmentContext alignmentContext; // ref sequence, alignment start and span
     private final int nRecords;
-    private final long globalRecordCounter;
+    private long globalRecordCounter;
     private final int nSliceBlocks;              // includes the core block and external blocks, but not the header block
     private List<Integer> contentIDs;
     private int embeddedReferenceBlockContentID = EMBEDDED_REFERENCE_ABSENT_CONTENT_ID;
@@ -78,7 +78,7 @@ public class Slice {
 
     private final CompressionHeader compressionHeader;
     private final SliceBlocks sliceBlocks;
-    private final long byteOffsetOfContainer;
+    public long byteOffsetOfContainer;
 
     private Block sliceHeaderBlock;
 
@@ -518,6 +518,22 @@ public void normalizeCRAMRecords(final List<CRAMCompressionRecord> cramCompressi
         }
      }
 
+    /**
+     * Update the stream-relative values (global record counter and container stream byte offset) for
+     * this slice. For use when re-serializing a container that has been read from an existing stream
+     * into a new stream. This method mutates the container and it's slices - the container is no
+     * longer valid in the context of it's original stream.
+     *
+     * @param sliceRecordCounter the new global record counter for this slice
+     * @param containerByteOffset the new stream byte offset counter for this slice's enclosing container
+     * @return the updated global record counter
+     */
+    long relocateSlice(final long sliceRecordCounter, final long containerByteOffset) {
+        this.byteOffsetOfContainer = containerByteOffset;
+        this.globalRecordCounter = sliceRecordCounter;
+        return sliceRecordCounter + getNumberOfRecords();
+    }
+
     private int getReferenceOffset(final boolean hasEmbeddedReference) {
         final ReferenceContext sliceReferenceContext = getAlignmentContext().getReferenceContext();
         return sliceReferenceContext.isMappedSingleRef() && hasEmbeddedReference ?