StreamBasedTabixIndexCreator

src/main/java/htsjdk/tribble/index/tabix/StreamBasedTabixIndexCreator.java

@@ -0,0 +1,55 @@
+package htsjdk.tribble.index.tabix;
+
+import htsjdk.samtools.BinningIndexContent;
+import htsjdk.samtools.SAMSequenceDictionary;
+import htsjdk.samtools.util.BlockCompressedOutputStream;
+import htsjdk.tribble.index.Index;
+import htsjdk.tribble.util.LittleEndianOutputStream;
+
+import java.io.IOException;
+import java.io.OutputStream;
+import java.nio.file.Path;
+import java.util.List;
+
+public class StreamBasedTabixIndexCreator extends TabixIndexCreator {
+
+  static class StreamBasedTabixIndex extends TabixIndex {
+    private final OutputStream out;
+
+    StreamBasedTabixIndex(
+        TabixFormat formatSpec,
+        List<String> sequenceNames,
+        BinningIndexContent[] indices,
+        OutputStream out) {
+      super(formatSpec, sequenceNames, indices);
+      this.out = out;
+    }
+
+    @Override
+    public void writeBasedOnFeaturePath(final Path featurePath) throws IOException {
+      try (final LittleEndianOutputStream los =
+          new LittleEndianOutputStream(new BlockCompressedOutputStream(out, (Path) null))) {
+        write(los);
+      }
+    }
+  }
+
+  private final OutputStream out;
+
+  public StreamBasedTabixIndexCreator(
+          SAMSequenceDictionary sequenceDictionary, TabixFormat formatSpec, OutputStream out) {
+    super(sequenceDictionary, formatSpec);
+    this.out = out;
+  }
+
+  @Override
+  public Index finalizeIndex(long finalFilePosition) {
+    Index index = super.finalizeIndex(finalFilePosition);
+    TabixIndex tabixIndex = (TabixIndex) index;
+    return new StreamBasedTabixIndex(
+        tabixIndex.getFormatSpec(),
+        tabixIndex.getSequenceNames(),
+        tabixIndex.getIndices(),
+        out);
+  }
+}