Package org.bdgenomics.convert.htsjdk

Class SamHeaderToReadGroups

java.lang.Object

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

org.bdgenomics.convert.htsjdk.SamHeaderToReadGroups

All Implemented Interfaces:

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

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

Convert a SAMFileHeader to a list of ReadGroups.

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor	Description
SamHeaderToReadGroups()	Create a new SAMFileHeader to a list of ReadGroups converter.
SamHeaderToReadGroups(Converter<htsjdk.samtools.SAMReadGroupRecord,org.bdgenomics.formats.avro.ReadGroup> readGroupConverter)	Create a new SAMFileHeader to a list of ReadGroups converter.

Method Summary

Modifier and Type	Method	Description
List<org.bdgenomics.formats.avro.ReadGroup>	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

SamHeaderToReadGroups

public SamHeaderToReadGroups()

Create a new SAMFileHeader to a list of ReadGroups converter.

SamHeaderToReadGroups

public SamHeaderToReadGroups(Converter<htsjdk.samtools.SAMReadGroupRecord,org.bdgenomics.formats.avro.ReadGroup> readGroupConverter)

Create a new SAMFileHeader to a list of ReadGroups converter.

Parameters:

readGroupConverter - read group converter, must not be null

Method Detail

convert

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

Throws:

ConversionException