SAMFileWriterFactory.setDefaultCreateIndexWhileWriting(true);
SAMFileWriterFactory.setDefaultCreateIndexWhileWriting(true);
SAMFileWriterFactory.setDefaultCreateIndexWhileWriting(true);
if (null == SORT_ORDER) this.SORT_ORDER = inHeader.getSortOrder(); // same as the input outHeader.setSortOrder(SORT_ORDER); SAMFileWriterFactory.setDefaultCreateIndexWhileWriting(CREATE_INDEX); SAMFileWriterFactory.setDefaultCreateMd5File(CREATE_MD5_FILE); final SAMFileWriter out = new SAMFileWriterFactory().makeSAMOrBAMWriter(outHeader, false, OUTPUT);
if (null == SORT_ORDER) this.SORT_ORDER = inHeader.getSortOrder(); // same as the input outHeader.setSortOrder(SORT_ORDER); SAMFileWriterFactory.setDefaultCreateIndexWhileWriting(CREATE_INDEX); SAMFileWriterFactory.setDefaultCreateMd5File(CREATE_MD5_FILE); final SAMFileWriter out = new SAMFileWriterFactory().makeSAMOrBAMWriter(outHeader, false, OUTPUT);