org.bdgenomics.convert.htsjdk

Interface AlignmentToSamRecordFactory

public interface AlignmentToSamRecordFactory

Factory for creating Alignment to htsjdk SAMRecord converters, which require late binding for a SAMFileHeader. Thus instead of a converter instance, a converter factory is available via injection:

 final class MyClass {
   private final AlignmentToSamRecordFactory alignmentToSamRecordFactory;

   @Inject
   MyClass(final AlignmentToSamRecordFactory alignmentToSamRecordFactory) {
     this.alignmentToSamRecordFactory = alignmentToSamRecordFactory;
   }

   void doIt() {
     Converter<Alignment, SAMRecord> converter = alignmentToSamRecordFactory.create(header);
     SAMRecord record = converter.convert(alignment, stringency, logger);
     // ...
 

Method Summary

Modifier and Type	Method and Description
Converter<org.bdgenomics.formats.avro.Alignment,htsjdk.samtools.SAMRecord>	create(htsjdk.samtools.SAMFileHeader header) Create a new Alignment to htsjdk SAMRecord converter with the specified header.

Method Detail

create

Converter<org.bdgenomics.formats.avro.Alignment,htsjdk.samtools.SAMRecord> create(htsjdk.samtools.SAMFileHeader header)

Create a new Alignment to htsjdk SAMRecord converter with the specified header.

Parameters:

header - header, must not be null

Returns:

a new Alignment to htsjdk SAMRecord converter with the specified header