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phac-nml / staramr

Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.
Apache License 2.0
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Fixed exclude phenotype column command #67

Closed jennifertran closed 5 years ago

jennifertran commented 5 years ago

Based on Issue #65

Problem

When you include the --exclude-resistance-phenotypes in the command line, the Predicted Phenotypes Column is still included in the summary and detailed_summary file

Solution

Take advantage of polymorphism and overriding to dynamically remove the Predicted Phenotypes Column

Implementation

Create getter methods to return the proper column names and values

Testing

Ran through the staramr tests and refactored the unit tests to use the AMRDetectionSummaryResistance method rather than the AMRDetectionSummary

jennifertran commented 5 years ago

@apetkau The command error is coming from including the negatives method, I forgot to add an if/else case if the phenotype command is enabled, which is now fixed.

apetkau commented 5 years ago

Thanks so much. I'm merging this in.