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Update benchmarking script with new CLI #56
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PR closes #27 |
- add option for verbose printing - fix error when tmp_dir exists
one step closer to custom parameters
proportions rounded to 4 decimal points
I was able to do most of the finalizing work for this today. A few more unit tests that I'm figuring out how to implement since it doesn't seem like The updated README is mostly technical without much insight on the biological context; @ababaian if you have any comments/suggestions feel free to modify directly or let me know! |
Hey @victorlin, can you remove the fq files from the repo and instead host them on the s3 bucket. There is a -- I'm a bit tied up at the moment, I'll do a proper review tomorrow |
A lot has happened since this was started. Is the benchmarker still needed? The last task is unit testing |
IMO we don't need a mapping benchmark for the main Serratus search, we have settled on how to run bowtie2 and are not likely to revisit benchmarking of mappers. |
Ironically enough I do think we /should/ revisit this as there will be ways to improve on |
Opening this PR to track progress for #27. Keeping as draft until ready.
TODO:
cov_benchmark.py
msbar
,art_illumina
,bowtie2
)pangenome_cov_benchmark.py
cov_benchmark.py
with predefined parameters.csv
file