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When you run vcfSampleCompare on a file that is missing DP, AO, and/or RO in the FORMAT column, all you get are warnings about undefined values. GT is checked and generates an error (automatically changing the mode to not use genotype information, I believe - regardless, it's gracefully handled and provides an error that describes the problem well).
Problem
Users don't know what the warnings are about. The fact that they are warnings instead of errors suggests you can ignore them.
Suggested Resolution
Implement an input format check and issue a fatal error if the input does not include values for AO, RO, or DP.
Inspiration
When you run vcfSampleCompare on a file that is missing
DP
,AO
, and/orRO
in theFORMAT
column, all you get are warnings about undefined values.GT
is checked and generates an error (automatically changing the mode to not use genotype information, I believe - regardless, it's gracefully handled and provides an error that describes the problem well).Problem
Users don't know what the warnings are about. The fact that they are warnings instead of errors suggests you can ignore them.
Suggested Resolution
Implement an input format check and issue a fatal error if the input does not include values for AO, RO, or DP.
Comment
See issue #26
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