org.bdgenomics.convert.htsjdk

Class SamRecordToAlignment

java.lang.Object

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

org.bdgenomics.convert.htsjdk.SamRecordToAlignment

All Implemented Interfaces:

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

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

Convert htsjdk SAMRecord to Alignment.

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
SamRecordToAlignment() Create a new htsjdk SAMRecord to Alignment converter.

Method Summary

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

SamRecordToAlignment

public SamRecordToAlignment()

Create a new htsjdk SAMRecord to Alignment converter.

Method Detail

convert

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

Throws:

ConversionException