Package 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

      All Methods Instance Methods Abstract Methods 
      Modifier and Type Method 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