Added check for null sequence dictionaries #6147
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droazen
requested changes
Sep 9, 2019
| @@ -146,6 +146,8 @@ public static void validateDictionaries( final String name1, | |||
| final SAMSequenceDictionary dict2, | |||
| final boolean requireSuperset, | |||
| final boolean checkContigOrdering ) { | |||
| Utils.nonNull(dict1, "Something went wrong with sequence dictionary detection, check that "+name1+" has a valid sequence dictionary"); | |||
| Utils.nonNull(dict2, "Something went wrong with sequence dictionary detection, check that "+name2+" has a valid sequence dictionary"); | |||
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Can you add a test that fails without this patch, and passes with it?
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@droazen added a test, back to you. |
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@droazen can this be merged? |
droazen
approved these changes
Sep 11, 2019
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One minor comment to address, then go ahead and merge once tests pass @jamesemery
| @Test (expectedExceptions = java.lang.IllegalArgumentException.class) | ||
| // test asserting that if the reference dictionary exists but is not valid we get a more helpful exception than a null pointer exception | ||
| public void testBrokenReferenceDictionaryErrorMessage() throws IOException { | ||
| createTempFile("reference", ".dict"); // file because we want an empty file that "exists" for the reference |
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Isn't this unnecessary given your creation of emptyDict below?
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its marking it for extermination later.
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fine, removed and will merge when tests pass
…at the reference diciotnary is called upon
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^ The failed build was evidently due to not having rebased the branch. |
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As a compromise fix, I have added a check to the validation code that asserts the dictionaries actually exist to save ourselves the potential null-pointer exceptions. @droazen
Fixes #6142