htsjdk.samtools

Class BinaryTagCodec

java.lang.Object

htsjdk.samtools.BinaryTagCodec

public class BinaryTagCodec
extends java.lang.Object

Converter between disk and in-memory representation of a SAMRecord tag.

Constructor Summary

Constructors

Constructor and Description
BinaryTagCodec(BinaryCodec binaryCodec) For writing tags.

Method Summary

Modifier and Type	Method and Description
static SAMBinaryTagAndValue	readTags(byte[] binaryRep, int offset, int length, ValidationStringency validationStringency) Convert tags from little-endian disk representation to in-memory representation.
void	writeTag(short tag, java.lang.Object value, boolean isUnsignedArray) Write the given tag name and value to disk.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

BinaryTagCodec

public BinaryTagCodec(BinaryCodec binaryCodec)

For writing tags. For reading tags, a BinaryCodec is not used. See readTags() below.

Parameters:

binaryCodec - where to write the file rep of the tags

Method Detail

writeTag

public void writeTag(short tag,
                     java.lang.Object value,
                     boolean isUnsignedArray)

Write the given tag name and value to disk.

readTags

public static SAMBinaryTagAndValue readTags(byte[] binaryRep,
                                            int offset,
                                            int length,
                                            ValidationStringency validationStringency)

Convert tags from little-endian disk representation to in-memory representation.

Parameters:

binaryRep - Byte buffer containing file representation of tags.

offset - Where in binaryRep tags start.

length - How many bytes in binaryRep are tag storage.