htsjdk.samtools.cram.build

Class ContainerParser

java.lang.Object

htsjdk.samtools.cram.build.ContainerParser

public class ContainerParser
extends java.lang.Object

Constructor Summary

Constructors

Constructor and Description
ContainerParser(SAMFileHeader samFileHeader)

Method Summary

Modifier and Type	Method and Description
java.util.List<CramCompressionRecord>	getRecords(Container container, java.util.ArrayList<CramCompressionRecord> records, ValidationStringency validationStringency)
java.util.Map<java.lang.Integer,AlignmentSpan>	getReferences(Container container, ValidationStringency validationStringency)

Methods inherited from class java.lang.Object

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

Constructor Detail

ContainerParser

public ContainerParser(SAMFileHeader samFileHeader)

Method Detail

getRecords

public java.util.List<CramCompressionRecord> getRecords(Container container,
                                                        java.util.ArrayList<CramCompressionRecord> records,
                                                        ValidationStringency validationStringency)
                                                 throws java.lang.IllegalArgumentException,
                                                        java.lang.IllegalAccessException

Throws:

java.lang.IllegalArgumentException

java.lang.IllegalAccessException

getReferences

public java.util.Map<java.lang.Integer,AlignmentSpan> getReferences(Container container,
                                                                    ValidationStringency validationStringency)
                                                             throws java.io.IOException

Throws:

java.io.IOException