htsjdk.samtools.cram.build

Class ContainerFactory

java.lang.Object

htsjdk.samtools.cram.build.ContainerFactory

public class ContainerFactory
extends java.lang.Object

Constructor Summary

Constructors

Constructor and Description
ContainerFactory(SAMFileHeader samFileHeader, int recordsPerSlice)

Method Summary

Modifier and Type	Method and Description
Container	buildContainer(java.util.List<CramCompressionRecord> records, long containerByteOffset) Build a Container (and its constituent Slices) from CramCompressionRecords.
boolean	isPreserveReadNames()
void	setPreserveReadNames(boolean preserveReadNames)

Methods inherited from class java.lang.Object

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

Constructor Detail

ContainerFactory

public ContainerFactory(SAMFileHeader samFileHeader,
                        int recordsPerSlice)

Method Detail

buildContainer

public Container buildContainer(java.util.List<CramCompressionRecord> records,
                                long containerByteOffset)

Build a Container (and its constituent Slices) from CramCompressionRecords. Note that this will always result in a single Container, regardless of how many Slices are created. It is up to the caller to divide the records into multiple Containers, if that is desired. TODO: enable a setting to automate this, perhaps "recordsPerContainer"

Parameters:

records - the records used to build the Container

containerByteOffset - the Container's byte offset from the start of the stream

Returns:

the container built from these records

isPreserveReadNames

public boolean isPreserveReadNames()

setPreserveReadNames

public void setPreserveReadNames(boolean preserveReadNames)