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tyjo / coptr

Accurate and robust inference of microbial growth dynamics from metagenomic sequencing
GNU General Public License v3.0
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CoPTR should throw an error on invalid parameter choices #10

Open brendanwee opened 2 years ago

brendanwee commented 2 years ago

I ran an experiment trying min-cov to be .3, .4, .5, .6 and .75 on 10 datasets. Each data set had the same exact result for each value of min-cov.

Also just a small nitpick: the --min-cov parameter should error out or complain if the user provides an argument greater than one.

brendanwee commented 2 years ago

Closing this because I think I just have some questions around how to run this tool.

tyjo commented 2 years ago

The --min-cov flag gives the proportion of the genome that to be covered by at least 1 read. This is more for quality filtering to remove genomes with many reads that mapped to a conserved region, but may not be present in the sample.

I'm going to reopen this issue because I agree with your nitpick. Invalid parameter combinations should throw an error.