test fix. if the start is out of bounds and the end is in bounds, then the code will return the available nucleotides. An exception is thrown ONLY if both are out of bounds.
@@ -74,13 +74,9 @@ public class CellBaseNormalizerSequenceAdaptorTest extends GenericMongoDBAdapto
@Test
public void testGenomicSequenceQueryStartOutOfLeftBound() throws Exception {
- Throwable exception = assertThrows(RuntimeException.class, () -> {
- cellBaseNormalizerSequenceAdaptor.query("17", 63960000, 63969999);
- });
- // TODO FIXME What should happen here?
- // the left coordinate is out of bounds, but the right one is not. Should this fail?
- // previously the test coordinates were 1:-100-1999 but that's an illegal value now.
- assertEquals("Unable to find entry for 17:63960000-63970000", exception.getMessage());
+ // the left coordinate is out of bounds, but the right one is not.
+ String result = cellBaseNormalizerSequenceAdaptor.query("17", 63969989, 63970000);
+ assertEquals("GGAGAGAGAAA", result);
}
}
\ No newline at end of file
