Use latest SBI code from htsjdk PR (samtools/htsjdk#1138)

src/main/java/com/tom_e_white/disq/impl/formats/bam/BamSource.java

@@ -16,9 +16,9 @@
 import htsjdk.samtools.SAMFileHeader;
 import htsjdk.samtools.SAMFileSpan;
 import htsjdk.samtools.SAMRecord;
+import htsjdk.samtools.SBIIndex;
 import htsjdk.samtools.SamReader;
 import htsjdk.samtools.SamReader.PrimitiveSamReaderToSamReaderAdapter;
-import htsjdk.samtools.SplittingBAMIndex;
 import htsjdk.samtools.ValidationStringency;
 import htsjdk.samtools.seekablestream.SeekableStream;
 import htsjdk.samtools.util.BlockCompressedFilePointerUtil;
@@ -71,17 +71,16 @@ protected JavaRDD<PathChunk> getPathChunks(
       String referenceSourcePath)
       throws IOException {
 
-    String splittingBaiPath = path + SplittingBAMIndex.FILE_EXTENSION;
-    if (fileSystemWrapper.exists(jsc.hadoopConfiguration(), splittingBaiPath)) {
-      try (SeekableStream sbiStream =
-          fileSystemWrapper.open(jsc.hadoopConfiguration(), splittingBaiPath)) {
-        SplittingBAMIndex splittingBAMIndex = SplittingBAMIndex.load(sbiStream);
-        Broadcast<SplittingBAMIndex> splittingBAMIndexBroadcast = jsc.broadcast(splittingBAMIndex);
+    String sbiPath = path + SBIIndex.FILE_EXTENSION;
+    if (fileSystemWrapper.exists(jsc.hadoopConfiguration(), sbiPath)) {
+      try (SeekableStream sbiStream = fileSystemWrapper.open(jsc.hadoopConfiguration(), sbiPath)) {
+        SBIIndex sbiIndex = SBIIndex.load(sbiStream);
+        Broadcast<SBIIndex> sbiIndexBroadcast = jsc.broadcast(sbiIndex);
         pathSplitSource
             .getPathSplits(jsc, path, splitSize)
             .flatMap(
                 pathSplit -> {
-                  SplittingBAMIndex index = splittingBAMIndexBroadcast.getValue();
+                  SBIIndex index = sbiIndexBroadcast.getValue();
                   Chunk chunk = index.getChunk(pathSplit.getStart(), pathSplit.getEnd());
                   if (chunk == null) {
                     return Collections.emptyIterator();

src/main/java/htsjdk/samtools/BAMSBIIndexer.java

@@ -0,0 +1,77 @@
+package htsjdk.samtools;
+
+import htsjdk.samtools.cram.io.InputStreamUtils;
+import htsjdk.samtools.seekablestream.SeekablePathStream;
+import htsjdk.samtools.seekablestream.SeekableStream;
+import htsjdk.samtools.util.BlockCompressedInputStream;
+import htsjdk.samtools.util.IOUtil;
+import htsjdk.samtools.util.RuntimeEOFException;
+import java.io.EOFException;
+import java.io.IOException;
+import java.io.OutputStream;
+import java.nio.ByteBuffer;
+import java.nio.ByteOrder;
+import java.nio.file.Files;
+import java.nio.file.Path;
+
+/** Writes SBI files for BAM files, as understood by {@link SBIIndex}. */
+public final class BAMSBIIndexer {
+
+  /**
+   * Perform indexing on the given BAM file, at the granularity level specified.
+   *
+   * @param bamFile the path to the BAM file
+   * @param granularity write the offset of every n-th alignment to the index
+   * @throws IOException as per java IO contract
+   */
+  public static void createIndex(final Path bamFile, final long granularity) throws IOException {
+    Path splittingBaiFile = IOUtil.addExtension(bamFile, SBIIndex.FILE_EXTENSION);
+    try (SeekableStream in = new SeekablePathStream(bamFile);
+        OutputStream out = Files.newOutputStream(splittingBaiFile)) {
+      createIndex(in, out, granularity);
+    }
+  }
+
+  /**
+   * Perform indexing on the given BAM file, at the granularity level specified.
+   *
+   * @param in a seekable stream for reading the BAM file from
+   * @param out the stream to write the index to
+   * @param granularity write the offset of every n-th alignment to the index
+   * @throws IOException as per java IO contract
+   */
+  public static void createIndex(
+      final SeekableStream in, final OutputStream out, final long granularity) throws IOException {
+    long recordStart = findVirtualOffsetOfFirstRecordInBam(in);
+    try (BlockCompressedInputStream blockIn = new BlockCompressedInputStream(in)) {
+      blockIn.seek(recordStart);
+      final ByteBuffer byteBuffer =
+          ByteBuffer.allocate(4).order(ByteOrder.LITTLE_ENDIAN); // BAM is little-endian
+      SBIIndexWriter indexWriter = new SBIIndexWriter(out, granularity);
+      while (true) {
+        try {
+          recordStart = blockIn.getFilePointer();
+          InputStreamUtils.readFully(blockIn, byteBuffer.array(), 0, 4);
+          final int blockSize = byteBuffer.getInt(0); // length of remainder of alignment record
+          indexWriter.processRecord(recordStart);
+          InputStreamUtils.skipFully(blockIn, blockSize);
+        } catch (EOFException e) {
+          break;
+        }
+      }
+      indexWriter.finish(recordStart, in.length());
+    }
+  }
+
+  /**
+   * Returns the virtual file offset of the first record in a BAM file - i.e. the virtual file
+   * offset after skipping over the text header and the sequence records.
+   */
+  public static long findVirtualOffsetOfFirstRecordInBam(final SeekableStream seekableStream) {
+    try {
+      return BAMFileReader2.findVirtualOffsetOfFirstRecord(seekableStream);
+    } catch (final IOException ioe) {
+      throw new RuntimeEOFException(ioe);
+    }
+  }
+}