Package org.bdgenomics.convert.htsjdk

Class SamHeaderToProcessingSteps

java.lang.Object

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

org.bdgenomics.convert.htsjdk.SamHeaderToProcessingSteps

All Implemented Interfaces:

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

public final class SamHeaderToProcessingSteps
extends AbstractConverter<htsjdk.samtools.SAMFileHeader,List<org.bdgenomics.formats.avro.ProcessingStep>>

Convert a SAMFileHeader to a list of ProcessingSteps.

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor	Description
SamHeaderToProcessingSteps()	Create a new SAMFileHeader to a list of ProcessingSteps converter.

Method Summary

Modifier and Type	Method	Description
List<org.bdgenomics.formats.avro.ProcessingStep>	convert(htsjdk.samtools.SAMFileHeader header, 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

SamHeaderToProcessingSteps

public SamHeaderToProcessingSteps()

Create a new SAMFileHeader to a list of ProcessingSteps converter.

Method Detail

convert

public List<org.bdgenomics.formats.avro.ProcessingStep> convert(htsjdk.samtools.SAMFileHeader header,
                                                                ConversionStringency stringency,
                                                                org.slf4j.Logger logger)
                                                         throws ConversionException

Throws:

ConversionException