SAMFileWriterFactory factory = new SAMFileWriterFactory(); if (stub.getFileHeader().getSortOrder().equals(SAMFileHeader.SortOrder.coordinate) && stub.getIndexOnTheFly()) factory.setCreateIndex(true); if (stub.getGenerateMD5())
SAMFileWriterFactory factory = new SAMFileWriterFactory(); if (stub.getFileHeader().getSortOrder().equals(SAMFileHeader.SortOrder.coordinate) && stub.getIndexOnTheFly()) factory.setCreateIndex(true); if (stub.getGenerateMD5())