Conform to updated interop test structure.

src/main/java/htsjdk/samtools/cram/compression/fqzcomp/FQZModels.java

@@ -17,7 +17,7 @@ public FQZModels(final FQZParams fqzParams) {
         }
         length = new ByteModel[4];
         for (int i = 0; i < 4; i++) {
-            length[i] = new ByteModel(256); //TODO: Magic 256 ?
+            length[i] = new ByteModel(256);
         }
         reverse = new ByteModel(2);
         duplicate = new ByteModel(2);

src/main/java/htsjdk/samtools/cram/compression/fqzcomp/FQZParams.java

@@ -5,7 +5,6 @@
 import java.util.List;
 
 public class FQZParams {
-    //TODO: share this with the decoder/encoder
     private static final int NUMBER_OF_SYMBOLS = 256;
 
     final FQZGlobalFlags fqzFlags;

src/main/java/htsjdk/samtools/cram/compression/fqzcomp/FQZState.java

@@ -38,7 +38,7 @@ public class FQZState {
     public void setSelector(int selector) { this.selector = selector; }
 
     //TODO: it is super confusing that this is called selectorTable, since that is also a thing in FQZParams as well,
-    // but there it is an array - is this the index ?
+    // but there it is an array
     public int getSelectorTable() { return selectorTable; }
     public void setSelectorTable(int selectorTable) { this.selectorTable = selectorTable; }
 

src/main/java/htsjdk/samtools/cram/compression/nametokenisation/TokenStreams.java

@@ -95,67 +95,14 @@ public TokenStreams(final ByteBuffer inputByteBuffer, final int useArith, final
                 final ByteBuffer uncompressedTokenStream;
                 if (useArith != 0) {
                     final RangeDecode rangeDecode = new RangeDecode();
-                    uncompressedTokenStream = rangeDecode.uncompress(ByteBuffer.wrap(compressedTokenStream));
+                    uncompressedTokenStream = rangeDecode.uncompress(CompressionUtils.wrap(compressedTokenStream));
                 } else {
                     final RANSNx16Decode ransDecode = new RANSNx16Decode();
-                    uncompressedTokenStream = ransDecode.uncompress(ByteBuffer.wrap(compressedTokenStream));
+                    uncompressedTokenStream = ransDecode.uncompress(CompressionUtils.wrap(compressedTokenStream));
                 }
                 getStreamsForPos(tokenPosition)[tokenType] = uncompressedTokenStream;
             }
         }
-        //displayTokenStreamSizes();
-    }
-
-    private void displayTokenStreamSizes() {
-        for (int t = 0; t < TOTAL_TOKEN_TYPES; t++) {
-            System.out.print(String.format("%s ", typeToString(t)));
-        }
-        System.out.println();
-        for (int pos = 0; pos < tokenStreams.length; pos++) {
-            System.out.print(String.format("Pos %2d: ", pos));
-            for (int typ = 0; typ < tokenStreams[pos].length; typ++) {
-                final ByteBuffer bf = tokenStreams[pos][typ];
-                if (bf == null) {
-                    System.out.print(String.format("%8s", "null"));
-                } else {
-                    System.out.print(String.format("%8d", bf.limit()));
-                }
-            }
-            System.out.println();
-        }
-    }
-
-   private String typeToString(int i) {
-        switch (i) {
-            case TOKEN_TYPE:
-                return "TOKEN_TYPE";
-            case TOKEN_STRING:
-                return "TOKEN_STRING";
-            case TOKEN_CHAR:
-                return "TOKEN_CHAR";
-            case TOKEN_DIGITS0:
-                return "TOKEN_DIGITS0";
-            case TOKEN_DZLEN:
-                return "TOKEN_DZLEN";
-            case TOKEN_DUP:
-                return "TOKEN_DUP";
-            case TOKEN_DIFF:
-                return "TOKEN_DIFF";
-            case TOKEN_DIGITS:
-                return "TOKEN_DIGITS";
-            case TOKEN_DELTA:
-                return "TOKEN_DELTA";
-            case TOKEN_DELTA0:
-                return "TOKEN_DELTA0";
-            case TOKEN_MATCH:
-                return "TOKEN_MATCH";
-            case TOKEN_END:
-                return "TOKEN_END";
-            case TOKEN_NOP:
-                return "NOP";
-            default:
-                throw new CRAMException("Invalid name tokenizer tokenType: " + i);
-        }
     }
 
     public ByteBuffer[] getStreamsForPos(final int pos) {

src/main/java/htsjdk/samtools/cram/compression/range/RangeDecode.java

@@ -107,7 +107,6 @@ private ByteBuffer uncompress(final ByteBuffer inBuffer, final int outSize) {
         }
         outBuffer.rewind();
         return outBuffer;
-
     }
 
     private void uncompressOrder0(

src/test/java/htsjdk/samtools/cram/CRAMInteropTestUtils.java

@@ -9,18 +9,60 @@
 import java.util.List;
 
 /**
- * Interop test data originates in a separate repository, currently at https://github.com/samtools/htslib, in htscodecs,
- * but we keep a copy in htsjdk so we can use it for round trip tests in CI without needing to clone a second repo.
+ * Interop test data originates in a separate repository, currently at hts-specs/test, so we keep a copy in
+ * htsjdk so we can use it for round trip tests in CI without needing to clone a second repo.
  */
 public class CRAMInteropTestUtils {
-    public static final String INTEROP_TEST_FILES_PATH = "src/test/resources/htsjdk/samtools/cram/htslib_interop/";
+    public static final String INTEROP_TEST_FILES_PATH = "src/test/resources/htsjdk/hts-specs/test/cram/codecs";
+    public static final String GZIP_PATH = "gzip/";
+    public static final String GZIP_SUFFIX = ".gz";
 
     /**
      * @return the name and location of the local interop test data as specified by the
      * variable INTEROP_TEST_FILES_PATH
      */
-    public static Path getCRAM31_Htslib_InteropTestDataLocation() {
-        return Paths.get(INTEROP_TEST_FILES_PATH + "cram31/");
+    public static Path getCRAMInteropTestDataLocation() {
+        return Paths.get(INTEROP_TEST_FILES_PATH);
+    }
+
+    // return a list of all encoded test data files in the interop/<compressedDir> directory
+    protected static List<Path> getCRAMInteropCompressedPaths(final String compressedDir) throws IOException {
+        final List<Path> paths = new ArrayList<>();
+        Files.newDirectoryStream(
+                        CRAMInteropTestUtils.getCRAMInteropTestDataLocation().resolve(compressedDir),
+                        path -> Files.isRegularFile(path))
+                .forEach(path -> paths.add(path));
+        return paths;
+    }
+
+    // Given a compressed test file path, return the corresponding uncompressed file path
+    protected static final Path getUnCompressedPathForCompressedPath(final Path compressedInteropPath) {
+        final String uncompressedFileName = getUncompressedFileName(compressedInteropPath);
+        return compressedInteropPath.getParent().getParent()
+                .resolve(CRAMInteropTestUtils.GZIP_PATH + uncompressedFileName);
+    }
+
+    private static final String getUncompressedFileName(final Path compressedPath) {
+        // Returns original filename from compressed file name
+        final String fileName = compressedPath.getFileName().toString();
+        final int lastDotIndex = fileName.lastIndexOf(".");
+        if (lastDotIndex >= 0) {
+            final String compressedFileName = fileName.substring(0, lastDotIndex);
+            return compressedFileName + CRAMInteropTestUtils.GZIP_SUFFIX;
+        } else {
+            throw new CRAMException("The name of the compressed file should contain a period followed by a number that" +
+                    "indicates the order of compression. Actual compressed file name = "+ fileName);
+        }
+    }
+
+    // return a list of all raw test files  in the hts-specs interop test directory (these files are raw in
+    // the sense that they are not compressed by any CRAM codec, although they ARE gzip compressed for inclusion
+    // in the repo)
+    protected static final List<Path> getRawCRAMInteropTestFiles() throws IOException {
+        final List<Path> paths = new ArrayList<>();
+        Files.newDirectoryStream(CRAMInteropTestUtils.getCRAMInteropTestDataLocation().resolve(GZIP_PATH))
+                .forEach(path -> paths.add(path));
+        return paths;
     }
 
     // the input files have embedded newlines that the test remove before round-tripping...
@@ -45,43 +87,4 @@ protected static final byte[] filterEmbeddedNewlines(final byte[] rawBytes) thro
         }
     }
 
-    // return a list of all encoded test data files in the htscodecs/tests/dat/<compressedDir> directory
-    protected static List<Path> getInteropCompressedFilePaths(final String compressedDir) throws IOException {
-        final List<Path> paths = new ArrayList<>();
-        Files.newDirectoryStream(
-                        CRAMInteropTestUtils.getCRAM31_Htslib_InteropTestDataLocation().resolve("dat/"+compressedDir),
-                        path -> Files.isRegularFile(path))
-                .forEach(path -> paths.add(path));
-        return paths;
-    }
-
-    // Given a compressed test file path, return the corresponding uncompressed file path
-    protected static final Path getUnCompressedFilePath(final Path compressedInteropPath) {
-        final String uncompressedFileName = getUncompressedFileName(compressedInteropPath.getFileName().toString());
-        // Example compressedInteropPath: ../dat/r4x8/q4.1 => unCompressedFilePath: ../dat/q4
-        return compressedInteropPath.getParent().getParent().resolve(uncompressedFileName);
-    }
-
-    private static final String getUncompressedFileName(final String compressedFileName) {
-        // Returns original filename from compressed file name
-        final int lastDotIndex = compressedFileName.lastIndexOf(".");
-        if (lastDotIndex >= 0) {
-            return compressedFileName.substring(0, lastDotIndex);
-        } else {
-            throw new CRAMException("The format of the compressed File Name is not as expected. " +
-                    "The name of the compressed file should contain a period followed by a number that" +
-                    "indicates the order of compression. Actual compressed file name = "+ compressedFileName);
-        }
-    }
-
-    // return a list of all raw test files in the htscodecs/tests/dat directory
-    protected static final List<Path> getInteropRawTestFiles() throws IOException {
-        final List<Path> paths = new ArrayList<>();
-        Files.newDirectoryStream(
-                        CRAMInteropTestUtils.getCRAM31_Htslib_InteropTestDataLocation().resolve("dat"),
-                        path -> (Files.isRegularFile(path)) && !Files.isHidden(path))
-                .forEach(path -> paths.add(path));
-        return paths;
-    }
-
 }

src/test/java/htsjdk/samtools/cram/FQZCompInteropTest.java

@@ -18,6 +18,7 @@
 import java.nio.file.Path;
 import java.util.ArrayList;
 import java.util.List;
+import java.util.zip.GZIPInputStream;
 
 public class FQZCompInteropTest extends HtsjdkTest {
 
@@ -31,10 +32,10 @@ public Object[][] getDecodeOnlyTestCases() throws IOException {
         // compressed testfile path, uncompressed testfile path,
         // FQZComp decoder
         final List<Object[]> testCases = new ArrayList<>();
-        for (Path path : CRAMInteropTestUtils.getInteropCompressedFilePaths(COMPRESSED_FQZCOMP_DIR)) {
+        for (Path path : CRAMInteropTestUtils.getCRAMInteropCompressedPaths(COMPRESSED_FQZCOMP_DIR)) {
             Object[] objects = new Object[]{
                     path,
-                    CRAMInteropTestUtils.getUnCompressedFilePath(path),
+                    CRAMInteropTestUtils.getUnCompressedPathForCompressedPath(path),
                     new FQZCompDecode()
             };
             testCases.add(objects);
@@ -49,7 +50,8 @@ public void testDecodeOnly(
             final Path compressedFilePath,
             final Path uncompressedInteropPath,
             final FQZCompDecode fqzcompDecode) throws IOException {
-        try (final InputStream uncompressedInteropStream = Files.newInputStream(uncompressedInteropPath);
+        try (final InputStream uncompressedInteropStream =
+                     new GZIPInputStream(Files.newInputStream(uncompressedInteropPath));
              final InputStream preCompressedInteropStream = Files.newInputStream(compressedFilePath)
         ) {
             // preprocess the uncompressed data (to match what the htscodecs-library test harness does)