htsjdk.samtools.cram.encoding.writer

Class CramRecordWriter

java.lang.Object

htsjdk.samtools.cram.encoding.writer.CramRecordWriter

public class CramRecordWriter
extends java.lang.Object

Constructor Summary

Constructors

Constructor and Description
CramRecordWriter(BitOutputStream coreOutputStream, java.util.Map<java.lang.Integer,java.io.ByteArrayOutputStream> externalOutputMap, CompressionHeader header, int refId) Initializes a Cram Record Writer

Method Summary

Modifier and Type	Method and Description
void	writeCramCompressionRecords(java.util.List<CramCompressionRecord> records, int prevAlignmentStart) Writes a series of Cram Compression Records, using this class's Encodings

Methods inherited from class java.lang.Object

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

Constructor Detail

CramRecordWriter

public CramRecordWriter(BitOutputStream coreOutputStream,
                        java.util.Map<java.lang.Integer,java.io.ByteArrayOutputStream> externalOutputMap,
                        CompressionHeader header,
                        int refId)

Initializes a Cram Record Writer

Parameters:

coreOutputStream - Core data block bit stream, to be written by non-external Encodings

externalOutputMap - External data block byte stream map, to be written by external Encodings

header - the associated Cram Compression Header

refId - the reference sequence ID to assign to these records

Method Detail

writeCramCompressionRecords

public void writeCramCompressionRecords(java.util.List<CramCompressionRecord> records,
                                        int prevAlignmentStart)
                                 throws java.io.IOException

Writes a series of Cram Compression Records, using this class's Encodings

Parameters:

records - the Cram Compression Records to write

prevAlignmentStart - the alignmentStart of the previous record, for delta calculation

Throws:

java.io.IOException