Make CollectSamErrorMetrics understand lowercased reference (and read) bases

[yfarjoun]

• fix CollectSamErrorMetrics (ERROR accumulator) doesn't understand lowercased reference bases #1994
• modify tests to cover this case

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[yfarjoun]

@fleharty or @kachulis I suspect this would be in your interest...

[lbergelson]

Looks good to me. Thanks @yfarjoun

[yfarjoun]

🎉