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Jacquard expand should allow a "strict mode" that fails if a selected field regex is not found in the input VCF #7

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cgates opened this issue Jun 3, 2022 · 0 comments

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cgates commented Jun 3, 2022

You can invoke expand specifying a file of regex expressions to include as a subset of selected fields. As expand considers each regex, if it can't find any matching column, it logs a warning and continues. It is sometimes desirable that Jacquard should explicitly fail if a specified regex does not match any columns. By default, it would work as implemented - however if invoked in strict mode it would fail like so:
jacquard expand --strict_selected_column --selected_columns_file cols.txt foo.vcf foo.txt
Error: The selected_columns_file [cols.txt] could not match 5 of 25 specified regular expressions. See log for details.

Likely an adjustment in expand.py:_filter_column_list().
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