Add CRAIIndexMerger

src/main/java/htsjdk/samtools/cram/CRAIIndexMerger.java

@@ -0,0 +1,37 @@
+package htsjdk.samtools.cram;
+
+import htsjdk.samtools.IndexMerger;
+
+import java.io.BufferedOutputStream;
+import java.io.IOException;
+import java.io.OutputStream;
+import java.util.zip.GZIPOutputStream;
+
+public class CRAIIndexMerger extends IndexMerger<CRAIIndex> {
+
+  private GZIPOutputStream compressedOut;
+  private long offset;
+
+  public CRAIIndexMerger(final OutputStream out, final long headerLength) throws IOException {
+    super(out, headerLength);
+    this.compressedOut = new GZIPOutputStream(new BufferedOutputStream(out));
+    this.offset = headerLength;
+  }
+
+  @Override
+  public void processIndex(CRAIIndex index, long partLength) {
+    index.getCRAIEntries()
+        .forEach(e -> shift(e, offset).writeToStream(compressedOut));
+    offset += partLength;
+  }
+
+  private static CRAIEntry shift(CRAIEntry entry, long offset) {
+    return new CRAIEntry(entry.getSequenceId(), entry.getAlignmentStart(), entry.getAlignmentSpan(), entry.getContainerStartByteOffset() + offset, entry.getSliceByteOffsetFromCompressionHeaderStart(), entry.getSliceByteSize());
+  }
+
+  @Override
+  public void finish(long dataFileLength) throws IOException {
+    compressedOut.flush();
+    compressedOut.close();
+  }
+}