kcibul

Integration tests are not passing as the gold files have not been updated. Understanding what "correct" looks like for spanning deletions beyond just unit tests is very complex, and fraught...

Initial support for spanning deletions and refactoring for testability

9

**Spanning Deletion Changes** 1. Created a new SpanningDeletionRecord as a subclass of ReferenceRecord but allows us to store GT and GQ 2. in handlePotentialSpanningDeletion when processing a deletion, we create...

Does CallMolecularConsensusReads handle overlapping fragments?

1

In the docs for `CallMolecularConsensusReads` it says: > Also, this tool calls each end of a pair independently, and does not jointly call bases that overlap within a pair However...