[ADAM-777] Add validation stringency flag for BQSR.

[fnothaft]

Resolves #777.

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[heuermh]

The code looks reasonable to me. Could you add the the failing read (or a similar one) as a test case to demonstrate the fix?

[fnothaft]

@beaunorgeot can you test with this patch to see if this passes on your end?

[fnothaft]

@heuermh I am working on unit tests.

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[heuermh]

+1

[beaunorgeot]

@fnothaft this patched worked successfully for me on the same file that generated issue 777. Well done!

[heuermh]

Thanks @fnothaft, @beaunorgeot