// ---------------------------------------------------------------------------------------------------------
//
// Public interface functions
//
// ---------------------------------------------------------------------------------------------------------
@Requires({"toolkit != null", "UAC != null"})
public UnifiedGenotyperEngine(GenomeAnalysisEngine toolkit, UnifiedArgumentCollection UAC) {
this(
toolkit,
UAC,
Logger.getLogger(UnifiedGenotyperEngine.class),
null,
null,
SampleUtils.getSAMFileSamples(toolkit.getSAMFileHeader()),
VariantContextUtils.DEFAULT_PLOIDY);
}
private void addWriter(
SAMReaderID id,
String outName,
SAMFileHeader.SortOrder order,
boolean presorted,
boolean indexOnTheFly,
boolean generateMD5,
SAMProgramRecord programRecord) {
File f = new File(outName);
SAMFileHeader header =
Utils.setupWriter(
toolkit, toolkit.getSAMFileHeader(id), KEEP_ALL_PG_RECORDS, programRecord);
SAMFileWriterFactory factory = new SAMFileWriterFactory();
factory.setCreateIndex(indexOnTheFly);
factory.setCreateMd5File(generateMD5);
SAMFileWriter sw = factory.makeSAMOrBAMWriter(header, presorted, f);
writerMap.put(id, sw);
}
public SAMFileHeader getFileHeader() {
return toolkit.getSAMFileHeader();
}