Package org.bdgenomics.convert.htsjdk

Class SamReadGroupRecordToReadGroup

java.lang.Object

org.bdgenomics.convert.AbstractConverter<htsjdk.samtools.SAMReadGroupRecord,org.bdgenomics.formats.avro.ReadGroup>

org.bdgenomics.convert.htsjdk.SamReadGroupRecordToReadGroup

All Implemented Interfaces:

Serializable, Converter<htsjdk.samtools.SAMReadGroupRecord,org.bdgenomics.formats.avro.ReadGroup>

public final class SamReadGroupRecordToReadGroup
extends AbstractConverter<htsjdk.samtools.SAMReadGroupRecord,org.bdgenomics.formats.avro.ReadGroup>

Convert a SAMReadGroup to a ReadGroup.

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor	Description
SamReadGroupRecordToReadGroup()	Create a new SAMReadGroupRecord to a ReadGroup converter.

Method Summary

Modifier and Type	Method	Description
org.bdgenomics.formats.avro.ReadGroup	convert(htsjdk.samtools.SAMReadGroupRecord 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

SamReadGroupRecordToReadGroup

public SamReadGroupRecordToReadGroup()

Create a new SAMReadGroupRecord to a ReadGroup converter.

Method Detail

convert

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

Throws:

ConversionException