htsjdk.samtools.cram.build
Class ContainerFactory

java.lang.Object
  htsjdk.samtools.cram.build.ContainerFactory

public class ContainerFactory
extends java.lang.Object

Constructor Summary

ContainerFactory(SAMFileHeader samFileHeader, int recordsPerSlice)

Method Summary

Container	buildContainer(java.util.List<CramCompressionRecord> records)
Container	buildContainer(java.util.List<CramCompressionRecord> records, SubstitutionMatrix substitutionMatrix)
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)
                         throws java.lang.IllegalArgumentException,
                                java.lang.IllegalAccessException,
                                java.io.IOException

Throws:

java.lang.IllegalArgumentException

java.lang.IllegalAccessException

java.io.IOException

buildContainer

public Container buildContainer(java.util.List<CramCompressionRecord> records,
                                SubstitutionMatrix substitutionMatrix)
                         throws java.lang.IllegalArgumentException,
                                java.lang.IllegalAccessException,
                                java.io.IOException

Throws:

java.lang.IllegalArgumentException

java.lang.IllegalAccessException

java.io.IOException

isPreserveReadNames

public boolean isPreserveReadNames()

setPreserveReadNames

public void setPreserveReadNames(boolean preserveReadNames)