org.bdgenomics.convert.htsjdk

Class AlignmentToSamRecord

java.lang.Object

org.bdgenomics.convert.AbstractConverter<org.bdgenomics.formats.avro.Alignment,htsjdk.samtools.SAMRecord>

org.bdgenomics.convert.htsjdk.AlignmentToSamRecord

All Implemented Interfaces:

Serializable, Converter<org.bdgenomics.formats.avro.Alignment,htsjdk.samtools.SAMRecord>

public final class AlignmentToSamRecord
extends AbstractConverter<org.bdgenomics.formats.avro.Alignment,htsjdk.samtools.SAMRecord>

Convert Alignment to htsjdk SAMRecord.

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
AlignmentToSamRecord(htsjdk.samtools.SAMFileHeader header) Create a new Alignment to htsjdk SAMRecord converter with the specified header.

Method Summary

Modifier and Type	Method and Description
htsjdk.samtools.SAMRecord	convert(org.bdgenomics.formats.avro.Alignment alignment, 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

AlignmentToSamRecord

@Inject
public AlignmentToSamRecord(htsjdk.samtools.SAMFileHeader header)

Create a new Alignment to htsjdk SAMRecord converter with the specified header.

Parameters:

header - header, must not be null

Method Detail

convert

public htsjdk.samtools.SAMRecord convert(org.bdgenomics.formats.avro.Alignment alignment,
                                         ConversionStringency stringency,
                                         org.slf4j.Logger logger)
                                  throws ConversionException

Throws:

ConversionException