/** * As {@link #createSAMFileWriter(String, org.broadinstitute.gatk.engine.GenomeAnalysisEngine)}, but also sets the header */ public static SAMFileWriter createSAMFileWriter(final String file, final GenomeAnalysisEngine engine, final SAMFileHeader header) { final SAMFileWriterStub output = (SAMFileWriterStub) createSAMFileWriter(file, engine); output.writeHeader(header); return output; }