htsjdk.samtools.cram.encoding.writer

Class CramRecordWriter

java.lang.Object

htsjdk.samtools.cram.encoding.writer.CramRecordWriter

public class CramRecordWriter
extends java.lang.Object

A writer that emits CRAMCompressionRecord into the various streams that represent a Slice's data series blocks. This essentially acts as a bridge between CRAMCompressionRecord fields and the various various data series streams associated with a Slice. It is the inverse of CramRecordReader.

Constructor Summary

Constructors

Constructor and Description
CramRecordWriter(Slice slice) Initializes a Cram Record Writer

Method Summary

Modifier and Type	Method and Description
SliceBlocks	writeToSliceBlocks(java.util.List<CRAMCompressionRecord> records, int initialAlignmentStart) Writes a series of Cram Compression Records to the underlying SliceBlocks, 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(Slice slice)

Initializes a Cram Record Writer

Parameters:

slice - the target slice to which the records will be written

Method Detail

writeToSliceBlocks

public SliceBlocks writeToSliceBlocks(java.util.List<CRAMCompressionRecord> records,
                                      int initialAlignmentStart)

Writes a series of Cram Compression Records to the underlying SliceBlocks, using this class's Encodings

Parameters:

records - the Cram Compression Records to write

initialAlignmentStart - the alignmentStart of the enclosing Slice, for delta calculation

Returns:

a SliceBlocks object