Package org.bdgenomics.convert.htsjdk

Class SamHeaderToReferences

java.lang.Object

org.bdgenomics.convert.AbstractConverter<htsjdk.samtools.SAMFileHeader,List<org.bdgenomics.formats.avro.Reference>>

org.bdgenomics.convert.htsjdk.SamHeaderToReferences

All Implemented Interfaces:

Serializable, Converter<htsjdk.samtools.SAMFileHeader,List<org.bdgenomics.formats.avro.Reference>>

public final class SamHeaderToReferences
extends AbstractConverter<htsjdk.samtools.SAMFileHeader,List<org.bdgenomics.formats.avro.Reference>>

Convert a SAMFileHeader to a list of References.

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor	Description
SamHeaderToReferences()	Create a new SAMFileHeader to a list of References converter.

Method Summary

Modifier and Type	Method	Description
List<org.bdgenomics.formats.avro.Reference>	convert(htsjdk.samtools.SAMFileHeader header, ConversionStringency stringency, org.slf4j.Logger logger)

Methods inherited from class org.bdgenomics.convert.AbstractConverter

checkNotNull, checkNotNull, checkNotNull, getSourceClass, getTargetClass, warnOrThrow

Methods inherited from class java.lang.Object

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

Constructor Detail

SamHeaderToReferences

public SamHeaderToReferences()

Create a new SAMFileHeader to a list of References converter.

Method Detail

convert

public List<org.bdgenomics.formats.avro.Reference> convert(htsjdk.samtools.SAMFileHeader header,
                                                           ConversionStringency stringency,
                                                           org.slf4j.Logger logger)
                                                    throws ConversionException

Throws:

ConversionException