Package org.bdgenomics.convert.htsjdk

Class SamSequenceRecordToReference

java.lang.Object

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

org.bdgenomics.convert.htsjdk.SamSequenceRecordToReference

All Implemented Interfaces:

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

public final class SamSequenceRecordToReference
extends AbstractConverter<htsjdk.samtools.SAMSequenceRecord,org.bdgenomics.formats.avro.Reference>

Convert a SAMSequenceRecord to a Reference.

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor	Description
SamSequenceRecordToReference()	Create a new SAMSequenceRecord to a Reference converter.

Method Summary

Modifier and Type	Method	Description
org.bdgenomics.formats.avro.Reference	convert(htsjdk.samtools.SAMSequenceRecord record, 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

SamSequenceRecordToReference

public SamSequenceRecordToReference()

Create a new SAMSequenceRecord to a Reference converter.

Method Detail

convert

public org.bdgenomics.formats.avro.Reference convert(htsjdk.samtools.SAMSequenceRecord record,
                                                     ConversionStringency stringency,
                                                     org.slf4j.Logger logger)
                                              throws ConversionException

Throws:

ConversionException