Fix an NPE in CRAMRecordReadFeatures.restoreReadBases #1655
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droazen
approved these changes
Feb 21, 2023
| final SAMRecord cramRecordEmbedded = cramEmbeddedIterator.next(); | ||
| Assert.assertEquals(cramRecordEmbedded, cramRecord); | ||
| } | ||
| Assert.assertEquals(count, 2); |
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Also assert that both iterators are exhausted after the loop
| final SAMRecord cramRecord = cramIterator.next(); | ||
| final SAMRecord cramRecordEmbedded = cramEmbeddedIterator.next(); | ||
| Assert.assertEquals(cramRecordEmbedded, cramRecord); | ||
| } | ||
| Assert.assertTrue( count >0); |
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Add text message for when assertion fails
lbergelson
changed the title
cmnbroad
approved these changes
Feb 21, 2023
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So I ran this in the debugger, and the reason the other embedded ref tests don't catch this issue is they have less interesting/varied read features than the other embedded ref tests (specifically this one has two read features with a gap between them). So I think this change is fine. We could use some better embedded ref tests.
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@cmnbroad This is a bug related to handling embedded references.