org.bdgenomics.convert.htsjdk

Class SamProgramRecordToProcessingStep

java.lang.Object

org.bdgenomics.convert.AbstractConverter<htsjdk.samtools.SAMProgramRecord,org.bdgenomics.formats.avro.ProcessingStep>

org.bdgenomics.convert.htsjdk.SamProgramRecordToProcessingStep

All Implemented Interfaces:

Serializable, Converter<htsjdk.samtools.SAMProgramRecord,org.bdgenomics.formats.avro.ProcessingStep>

public final class SamProgramRecordToProcessingStep
extends AbstractConverter<htsjdk.samtools.SAMProgramRecord,org.bdgenomics.formats.avro.ProcessingStep>

Convert a SAMProgramRecord to a ProcessingStep.

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
SamProgramRecordToProcessingStep() Create a new SAMProgramRecord to a ProcessingStep converter.

Method Summary

Modifier and Type	Method and Description
org.bdgenomics.formats.avro.ProcessingStep	convert(htsjdk.samtools.SAMProgramRecord 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

SamProgramRecordToProcessingStep

public SamProgramRecordToProcessingStep()

Create a new SAMProgramRecord to a ProcessingStep converter.

Method Detail

convert

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

Throws:

ConversionException