diff --git a/src/main/java/htsjdk/samtools/cram/compression/nametokenisation/NameTokenisationEncode.java b/src/main/java/htsjdk/samtools/cram/compression/nametokenisation/NameTokenisationEncode.java index e67df2d99b..4a07f8422f 100644 --- 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 index 52ab03a052..deed459022 100644 --- 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;