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SystemsGenetics / KINC

Knowledge Independent Network Construction
MIT License
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filter-bias test overwrites input #149

Closed JohnHadish closed 4 years ago

JohnHadish commented 4 years ago

When performing the filter-bias test , one of the parameters is --out_prefix.

kinc-filter-bias.R \
    --threads 40 \
    --net "Network.txt" \
    --emx "/path/GEM.txt" \
    --out_prefix "Network"

To me, a "prefix" implies that multiple files will be created, and that some additional wording will be added to the name. In the case of the above example, KINC simply adds .txt to the name, which results in the input file being overwritten.

My suggestion is to change the --out_prefix parameter simply to --output. This would make it consistent with the KINC tools preceeding it, and prevent the user from accidently overwritting their input file.

JohnHadish commented 4 years ago

Looking at the code, this does not actually overwrite, it adds a "-filter" tag.