resolving some nitpicks from pr #1245 (#1246)

* resolving some nitpicks from pr #1245

src/main/java/htsjdk/samtools/SamStreams.java

@@ -66,7 +66,7 @@ public static boolean isBAMFile(final InputStream stream)
     /**
      * Checks whether the file is a gzipped sam file.  Returns true if it
      * is and false otherwise.
-     * @see @link IOUtil#isGZIPInputStream(InputStream)
+     * @deprecated use {@link IOUtil#isGZIPInputStream(InputStream)} instead
      */
     @Deprecated
     public static boolean isGzippedSAMFile(final InputStream stream) {

src/main/java/htsjdk/samtools/util/IOUtil.java

@@ -98,7 +98,6 @@ public class IOUtil {
     public static final String COMPRESSED_VCF_FILE_EXTENSION = ".vcf.gz";
     public static final String COMPRESSED_VCF_INDEX_EXTENSION = ".tbi";
 
-
     /** Possible extensions for VCF files and related formats. */
     public static final String[] VCF_EXTENSIONS = {VCF_FILE_EXTENSION, COMPRESSED_VCF_FILE_EXTENSION, BCF_FILE_EXTENSION};
 
@@ -110,6 +109,9 @@ public class IOUtil {
 
     public static final Set<String> BLOCK_COMPRESSED_EXTENSIONS = Collections.unmodifiableSet(new HashSet<String>(Arrays.asList(".gz", ".gzip", ".bgz", ".bgzf")));
 
+    /** number of bytes that will be read for the GZIP-header in the function {@link #isGZIPInputStream(InputStream)} */
+    public static final int GZIP_HEADER_READ_LENGTH = 8000;
+
     private static int compressionLevel = Defaults.COMPRESSION_LEVEL;
     /**
      * Sets the GZip compression level for subsequent GZIPOutputStream object creation.
@@ -1155,18 +1157,14 @@ public static List<Path> filesToPaths(Collection<File> files){
         return files.stream().map(File::toPath).collect(Collectors.toList());
     }
 
-    /** number of bytes that will be read for the GZIP-header in the function {@link #isGZIPInputStream(InputStream)} */
-    public static final int GZIP_HEADER_READ_LENGTH = 8000;
-
     /**
      * Test whether a input stream looks like a GZIP input.
+     * This identifies both gzip and bgzip streams as being GZIP.
      * @param stream the input stream.
-     * @return true if `stream` starts with a gzip signature
+     * @return true if `stream` starts with a gzip signature.
      * @throws IllegalArgumentException if `stream` cannot mark or reset the stream
-     * @see SamStreams#isGzippedSAMFile(InputStream)
      */
     public static boolean isGZIPInputStream(final InputStream stream) {
-        /* this function was previously implemented in SamStreams.isGzippedSAMFile */
         if (!stream.markSupported()) {
             throw new IllegalArgumentException("isGZIPInputStream() : Cannot test a stream that doesn't support marking.");
         }

src/main/java/htsjdk/variant/utils/VCFHeaderReader.java

@@ -3,6 +3,7 @@
 import htsjdk.samtools.SamStreams;
 import htsjdk.samtools.cram.io.InputStreamUtils;
 import htsjdk.samtools.seekablestream.SeekableStream;
+import htsjdk.samtools.util.IOUtil;
 import htsjdk.tribble.Feature;
 import htsjdk.tribble.FeatureCodec;
 import htsjdk.tribble.FeatureCodecHeader;
@@ -49,8 +50,8 @@ public static VCFHeader readHeaderFrom(final SeekableStream in) throws IOExcepti
 
     private static InputStream bufferAndDecompressIfNecessary(final InputStream in) throws IOException {
         BufferedInputStream bis = new BufferedInputStream(in);
-        // despite the name, SamStreams.isGzippedSAMFile looks for any gzipped stream (including block compressed)
-        return SamStreams.isGzippedSAMFile(bis) ? new GZIPInputStream(bis) : bis;
+        // IOUTil.isGZIPInputStream looks for any gzipped stream (including block compressed)
+        return IOUtil.isGZIPInputStream(bis) ? new GZIPInputStream(bis) : bis;
     }
 
     private static <FEATURE_TYPE extends Feature, SOURCE> VCFHeader readHeaderFrom(final InputStream in, final FeatureCodec<FEATURE_TYPE, SOURCE> featureCodec) throws IOException {

src/main/java/htsjdk/variant/vcf/VCFIteratorBuilder.java

@@ -78,18 +78,12 @@ public VCFIterator open(final InputStream in) throws IOException {
             }
         // wrap the input stream into a BufferedInputStream to reset/read a BCFHeader or a GZIP
         // buffer must be large enough to contain the BCF header and/or GZIP signature
-        BufferedInputStream  bufferedinput = new BufferedInputStream(in, Math.max(
-               BCF2Codec.SIZEOF_BCF_HEADER,
-               IOUtil.GZIP_HEADER_READ_LENGTH
-               ));
+        BufferedInputStream  bufferedinput = new BufferedInputStream(in, Math.max(BCF2Codec.SIZEOF_BCF_HEADER, IOUtil.GZIP_HEADER_READ_LENGTH));
         // test for gzipped inputstream
         if(IOUtil.isGZIPInputStream(bufferedinput)) {
             // this is a gzipped input stream, wrap it into GZIPInputStream
             // and re-wrap it into BufferedInputStream so we can test for the BCF header
-            bufferedinput = new BufferedInputStream(
-                    new GZIPInputStream(bufferedinput),
-                    BCF2Codec.SIZEOF_BCF_HEADER
-                    );
+            bufferedinput = new BufferedInputStream(new GZIPInputStream(bufferedinput), BCF2Codec.SIZEOF_BCF_HEADER);
         }
 
         // try to read a BCF header
@@ -190,9 +184,7 @@ public VCFHeader getHeader() {
 
         @Override
         protected VariantContext advance() {
-            return this.lineIterator.hasNext() ?
-                    this.codec.decode(this.lineIterator.next()) :
-                    null;
+            return this.lineIterator.hasNext() ? this.codec.decode(this.lineIterator.next()) : null;
         }
 
         @Override
@@ -225,9 +217,7 @@ public VCFHeader getHeader() {
 
         @Override
         protected VariantContext advance() {
-            return this.codec.isDone(this.inputStream) ?
-                    null :
-                    this.codec.decode(this.inputStream);
+            return this.codec.isDone(this.inputStream) ? null : this.codec.decode(this.inputStream);
         }
 
         @Override

src/test/java/htsjdk/samtools/SamStreamsTest.java

@@ -40,6 +40,7 @@ public class SamStreamsTest extends HtsjdkTest {
     private static final File TEST_DATA_DIR = new File("src/test/resources/htsjdk/samtools");
 
     @Test(dataProvider = "makeData")
+    @SuppressWarnings("deprecated") // we're testing a deprecated method here deliberately
     public void testDataFormat(final String inputFile, final boolean isGzippedSAMFile, final boolean isBAMFile, final boolean isCRAMFile) throws Exception {
         final File input = new File(TEST_DATA_DIR, inputFile);
         try(final InputStream fis = new BufferedInputStream(new FileInputStream(input))) { //must be buffered or the isGzippedSAMFile will blow up

src/test/java/htsjdk/samtools/util/IOUtilTest.java

@@ -733,8 +733,8 @@ private static byte[] gzipMessage(final byte[] message) throws IOException {
 
     @DataProvider
     public static Object[][] gzipTests() throws IOException {
-        final byte emptyMessage[]="".getBytes();
-        final byte message[]="Hello World".getBytes();
+        final byte[] emptyMessage = "".getBytes();
+        final byte[] message = "Hello World".getBytes();
 
         // Compressed version of the messages
         final byte[] gzippedMessage = gzipMessage(message);