1d7088c8b588859a39f3178c4415585e4bb1bd12,src/test/java/au/edu/wehi/idsv/sam/SAMFileUtilTest.java,SAMFileUtilTest,sort_should_copy_file_for_matching_sort_order,#,48
Before Change
createBAM(input, SortOrder.queryname,
Read(5, 1, "1M"),
Read(3, 3, "1M"),
Read(1, 5, "1M"));
SAMFileUtil.sort(getFSContext(), input, output, SortOrder.coordinate);
assertTrue(Ordering.from(SortOrder.coordinate.getComparatorInstance()).isOrdered(getRecords(output)));
}
After Change
createBAM(input, SortOrder.queryname,
withReadName("1", Read(5, 1, "1M"))[0],
withReadName("2", Read(3, 3, "1M"))[0],
withReadName("2", Read(1, 5, "1M"))[0]);
SAMFileUtil.sort(getFSContext(), input, output, SortOrder.coordinate);
assertTrue(Ordering.from(SortOrder.coordinate.getComparatorInstance()).isOrdered(getRecords(output)));
}