Addressing feedback from dec 5 - part 2

samtools · Jan 31, 2024 · 3233e39 · 3233e39
1 parent 67ad384
commit 3233e39
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Showing 2 changed files with 4 additions and 5 deletions.
diff --git a/src/main/java/htsjdk/samtools/cram/compression/nametokenisation/NameTokenisationEncode.java b/src/main/java/htsjdk/samtools/cram/compression/nametokenisation/NameTokenisationEncode.java
@@ -1,5 +1,6 @@
 package htsjdk.samtools.cram.compression.nametokenisation;
 
+import htsjdk.samtools.cram.compression.CompressionUtils;
 import htsjdk.samtools.cram.compression.nametokenisation.tokens.EncodeToken;
 import htsjdk.samtools.cram.compression.range.RangeEncode;
 import htsjdk.samtools.cram.compression.range.RangeParams;
@@ -16,8 +17,6 @@
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
-import static htsjdk.samtools.cram.compression.rans.Utils.writeUint7;
-
 public class NameTokenisationEncode {
 
     private int maxToken;
@@ -267,7 +266,7 @@ protected void serializeByteStreams(
             if (tokenStream.get(tokenType).remaining() > 0) {
                 outBuffer.put((byte) (tokenType + ((tokenType == 0) ? 128 : 0)));
                 ByteBuffer tempOutByteBuffer = tryCompress(tokenStream.get(tokenType), useArith);
-                writeUint7(tempOutByteBuffer.limit(),outBuffer);
+                CompressionUtils.writeUint7(tempOutByteBuffer.limit(),outBuffer);
                 outBuffer.put(tempOutByteBuffer);
             }
         }

diff --git a/src/main/java/htsjdk/samtools/cram/compression/nametokenisation/TokenStreams.java b/src/main/java/htsjdk/samtools/cram/compression/nametokenisation/TokenStreams.java
@@ -1,9 +1,9 @@
 package htsjdk.samtools.cram.compression.nametokenisation;
 
 import htsjdk.samtools.cram.CRAMException;
+import htsjdk.samtools.cram.compression.CompressionUtils;
 import htsjdk.samtools.cram.compression.range.RangeDecode;
 import htsjdk.samtools.cram.compression.rans.RANSDecode;
-import htsjdk.samtools.cram.compression.rans.Utils;
 import htsjdk.samtools.cram.compression.rans.ransnx16.RANSNx16Decode;
 
 import java.nio.ByteBuffer;
@@ -98,7 +98,7 @@ public TokenStreams(final ByteBuffer inputByteBuffer, final int useArith, final
                 final ByteBuffer dupTokenStream = tokenStreams.get(dupType).get(dupPosition).duplicate();
                 tokenStreams.get(tokenType).add(tokenPosition,dupTokenStream);
             } else {
-                final int clen = Utils.readUint7(inputByteBuffer);
+                final int clen = CompressionUtils.readUint7(inputByteBuffer);
                 final byte[] dataBytes = new byte[clen];
                 inputByteBuffer.get(dataBytes, 0, clen); // offset in the dst byte array
                 final ByteBuffer uncompressedDataByteBuffer;