/**
* 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;
}
/**
* is this base inside the adaptor of the read?