From 35e013ed7e32dd64f1fe9fdc44497b180271c305 Mon Sep 17 00:00:00 2001
From: Tom White <tom.e.white@gmail.com>
Date: Mon, 21 Jan 2019 14:48:33 +0000
Subject: [PATCH] StreamBasedTabixIndexCreator

---
 .../tabix/StreamBasedTabixIndexCreator.java   | 55 +++++++++++++++++++
 1 file changed, 55 insertions(+)
 create mode 100644 src/main/java/htsjdk/tribble/index/tabix/StreamBasedTabixIndexCreator.java

diff --git a/src/main/java/htsjdk/tribble/index/tabix/StreamBasedTabixIndexCreator.java b/src/main/java/htsjdk/tribble/index/tabix/StreamBasedTabixIndexCreator.java
new file mode 100644
index 0000000000..c638fc9cf1
--- /dev/null
+++ b/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);
+  }
+}