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convert Runtime exceptions in the CRAM code into CRAMExceptions (also… #1557

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… runtime)

In the cram code the code throws an IllegalArgumentException when asked about the bases when a reference was not provided. This PR changes it to a CRAMException to be more informative and consistent.

@yfarjoun yfarjoun requested a review from cmnbroad July 25, 2021 20:25
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