Fix bug when loading indexed bgzip fasta file. (#1311)

* There was a bug that prevented loading an indexed bgzip fasta file if the index location was specified but wasn't next to the fasta in the file system.
* Fixes #1290

src/main/java/htsjdk/samtools/reference/BlockCompressedIndexedFastaSequenceFile.java

@@ -26,19 +26,15 @@
 
 import htsjdk.samtools.SAMException;
 import htsjdk.samtools.SAMSequenceDictionary;
-import htsjdk.samtools.seekablestream.ReadableSeekableStreamByteChannel;
 import htsjdk.samtools.seekablestream.SeekablePathStream;
 import htsjdk.samtools.seekablestream.SeekableStream;
 import htsjdk.samtools.util.BlockCompressedInputStream;
 import htsjdk.samtools.util.GZIIndex;
 import htsjdk.samtools.util.IOUtil;
 
-import java.io.BufferedInputStream;
 import java.io.FileNotFoundException;
 import java.io.IOException;
-import java.io.InputStream;
 import java.nio.ByteBuffer;
-import java.nio.file.Files;
 import java.nio.file.Path;
 
 /**
@@ -55,7 +51,7 @@ public class BlockCompressedIndexedFastaSequenceFile extends AbstractIndexedFast
 
     public BlockCompressedIndexedFastaSequenceFile(final Path path)
             throws FileNotFoundException {
-        this(path,new FastaSequenceIndex((findRequiredFastaIndexFile(path))));
+        this(path, new FastaSequenceIndex((findRequiredFastaIndexFile(path))));
     }
 
     public BlockCompressedIndexedFastaSequenceFile(final Path path, final FastaSequenceIndex index) {
@@ -67,9 +63,7 @@ public BlockCompressedIndexedFastaSequenceFile(final Path path, final FastaSeque
         if (gziIndex == null) {
             throw new IllegalArgumentException("null gzi index");
         }
-        if (!canCreateBlockCompresedIndexedFastaSequence(path)) {
-            throw new SAMException("Invalid block-compressed Fasta file");
-        }
+        assertIsBlockCompressed(path);
         try {
             stream = new BlockCompressedInputStream(new SeekablePathStream(path));
             gzindex = gziIndex;
@@ -103,12 +97,14 @@ private static GZIIndex loadFastaGziIndex(final Path path) {
         }
     }
 
-    private static boolean canCreateBlockCompresedIndexedFastaSequence(final Path path) {
+    private static void assertIsBlockCompressed(final Path path) {
         try {
             // check if the it is a valid block-compressed file and if the .gzi index exits
-            return IOUtil.isBlockCompressed(path, true) && Files.exists(GZIIndex.resolveIndexNameForBgzipFile(path));
+            if (!IOUtil.isBlockCompressed(path, true)) {
+                throw new SAMException("Invalid block-compressed Fasta file: " + path);
+            }
         } catch (IOException e) {
-            return false;
+            throw new SAMException("Invalid block-compressed Fasta file: " + path, e);
         }
     }
 

src/test/java/htsjdk/samtools/reference/AbstractIndexedFastaSequenceFileTest.java

@@ -29,6 +29,7 @@
 import htsjdk.samtools.seekablestream.SeekableFileStream;
 import htsjdk.samtools.util.CloserUtil;
 import htsjdk.samtools.util.GZIIndex;
+import htsjdk.samtools.util.IOUtil;
 import htsjdk.samtools.util.RuntimeIOException;
 import htsjdk.samtools.util.StringUtil;
 import org.testng.Assert;
@@ -39,6 +40,9 @@
 import java.io.FileInputStream;
 import java.io.FileNotFoundException;
 import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.StandardCopyOption;
 
 /**
  * Test the indexed fasta sequence file reader.
@@ -353,4 +357,16 @@ public void testBadInputForIndexedFastaSequenceFile() throws Exception {
     public void testBadInputForBlockCompressedIndexedFastaSequenceFile() throws Exception {
         new BlockCompressedIndexedFastaSequenceFile(SEQUENCE_FILE.toPath());
     }
+
+    @Test
+    public void testCanCreateBlockCompressedIndexedWithSpecifiedGZIAndDict() throws IOException {
+        final Path moved = Files.createTempFile("moved", ".fasta.gz");
+        Files.copy(SEQUENCE_FILE_BGZ.toPath(), moved, StandardCopyOption.REPLACE_EXISTING);
+        IOUtil.deleteOnExit(moved);
+        try (ReferenceSequenceFile withNoAdacentIndex = new BlockCompressedIndexedFastaSequenceFile(moved, new FastaSequenceIndex(SEQUENCE_FILE_INDEX), GZIIndex.loadIndex(SEQUENCE_FILE_GZI.toPath()));
+             ReferenceSequenceFile withFilesAdjacent = new BlockCompressedIndexedFastaSequenceFile(SEQUENCE_FILE_BGZ.toPath())) {
+            Assert.assertEquals(withNoAdacentIndex.getSubsequenceAt("chrM", 100, 1000).getBases(),
+                    withFilesAdjacent.getSubsequenceAt("chrM", 100, 1000).getBases());
+        }
+    }
 }