From 94ea9e99aad80f64c871a192e78559619f96f6d5 Mon Sep 17 00:00:00 2001
From: yash-puligundla <yasasvini.puligundla@ga4gh.org>
Date: Wed, 7 Feb 2024 13:50:59 -0500
Subject: [PATCH] Use CompressionUtils

---
 .../samtools/cram/compression/fqzcomp/FQZCompDecode.java    | 6 +++---
 .../htsjdk/samtools/cram/compression/range/RangeCoder.java  | 4 ++--
 src/test/java/htsjdk/samtools/cram/FQZCompInteropTest.java  | 5 +++--
 3 files changed, 8 insertions(+), 7 deletions(-)

diff --git a/src/main/java/htsjdk/samtools/cram/compression/fqzcomp/FQZCompDecode.java b/src/main/java/htsjdk/samtools/cram/compression/fqzcomp/FQZCompDecode.java
index 332c37cbd5..5933a7bcaf 100644
--- a/src/main/java/htsjdk/samtools/cram/compression/fqzcomp/FQZCompDecode.java
+++ b/src/main/java/htsjdk/samtools/cram/compression/fqzcomp/FQZCompDecode.java
@@ -1,9 +1,9 @@
 package htsjdk.samtools.cram.compression.fqzcomp;
 
 import htsjdk.samtools.cram.CRAMException;
+import htsjdk.samtools.cram.compression.CompressionUtils;
 import htsjdk.samtools.cram.compression.range.ByteModel;
 import htsjdk.samtools.cram.compression.range.RangeCoder;
-import htsjdk.samtools.cram.compression.rans.Utils;
 
 import java.nio.ByteBuffer;
 import java.util.ArrayList;
@@ -13,7 +13,7 @@ public class FQZCompDecode {
     private static final int NUMBER_OF_SYMBOLS = 256;
 
     public static ByteBuffer uncompress( final ByteBuffer inBuffer) {
-        final int bufferLength = Utils.readUint7(inBuffer);
+        final int bufferLength = CompressionUtils.readUint7(inBuffer);
         final int version = inBuffer.get() & 0xFF;
         if (version != 5) {
             throw new CRAMException("Invalid FQZComp format version number: " + version);
@@ -52,7 +52,7 @@ public static ByteBuffer uncompress( final ByteBuffer inBuffer) {
         FQZParam params = null;
         int last = 0;
         final int[] rev = null;
-        final ByteBuffer outBuffer = ByteBuffer.allocate(bufferLength);
+        final ByteBuffer outBuffer = CompressionUtils.allocateByteBuffer(bufferLength);
         while (i<bufferLength){
             if (fqzState.getBases()==0) {
                 decodeFQZNewRecord(
diff --git a/src/main/java/htsjdk/samtools/cram/compression/range/RangeCoder.java b/src/main/java/htsjdk/samtools/cram/compression/range/RangeCoder.java
index a7d7b21828..f0d7d82911 100644
--- a/src/main/java/htsjdk/samtools/cram/compression/range/RangeCoder.java
+++ b/src/main/java/htsjdk/samtools/cram/compression/range/RangeCoder.java
@@ -11,7 +11,7 @@ public class RangeCoder {
     private boolean carry;
     private int cache;
 
-    protected RangeCoder() {
+    public RangeCoder() {
         // Spec: RangeEncodeStart
         this.low = 0;
         this.range = Constants.MAX_RANGE; // 4 bytes of all 1's
@@ -21,7 +21,7 @@ protected RangeCoder() {
         this.cache = 0;
     }
 
-    protected void rangeDecodeStart(final ByteBuffer inBuffer){
+    public void rangeDecodeStart(final ByteBuffer inBuffer){
         for (int i = 0; i < 5; i++){
             code = (code << 8) + (inBuffer.get() & 0xFF);
         }
diff --git a/src/test/java/htsjdk/samtools/cram/FQZCompInteropTest.java b/src/test/java/htsjdk/samtools/cram/FQZCompInteropTest.java
index d07317bb3d..ab9ad4a517 100644
--- a/src/test/java/htsjdk/samtools/cram/FQZCompInteropTest.java
+++ b/src/test/java/htsjdk/samtools/cram/FQZCompInteropTest.java
@@ -1,6 +1,7 @@
 package htsjdk.samtools.cram;
 
 import htsjdk.HtsjdkTest;
+import htsjdk.samtools.cram.compression.CompressionUtils;
 import htsjdk.samtools.cram.compression.fqzcomp.FQZCompDecode;
 import org.apache.commons.compress.utils.IOUtils;
 import org.testng.Assert;
@@ -62,8 +63,8 @@ public void testDecodeOnly(
             // preprocess the uncompressed data (to match what the htscodecs-library test harness does)
             // by filtering out the embedded newlines, and then round trip through FQZComp codec
             // and compare the results
-            final ByteBuffer uncompressedInteropBytes = ByteBuffer.wrap(CRAMInteropTestUtils.filterEmbeddedNewlines(IOUtils.toByteArray(uncompressedInteropStream)));
-            final ByteBuffer preCompressedInteropBytes = ByteBuffer.wrap(IOUtils.toByteArray(preCompressedInteropStream));
+            final ByteBuffer uncompressedInteropBytes = CompressionUtils.wrap(CRAMInteropTestUtils.filterEmbeddedNewlines(IOUtils.toByteArray(uncompressedInteropStream)));
+            final ByteBuffer preCompressedInteropBytes = CompressionUtils.wrap(IOUtils.toByteArray(preCompressedInteropStream));
 
             // Use htsjdk to uncompress the precompressed file from htscodecs repo
             final ByteBuffer uncompressedHtsjdkBytes = fqzcompDecode.uncompress(preCompressedInteropBytes);