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iqbal-lab-org / pandora

Pan-genome inference and genotyping with long noisy or short accurate reads
MIT License
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Put sample pangraphs in separate directory #259

Open mbhall88 opened 3 years ago

mbhall88 commented 3 years ago

https://github.com/rmcolq/pandora/blob/815da22867f2bdaa3e3bf40f382be830c1506b0a/src/compare_main.cpp#L275

We output a directory for each sample in the --outdir. This does not scale well with the number of samples. i.e.with 150 samples, my output directory is full of directories for each sample.

I would suggest we instead create a directory outdir/pangraphs/ and put each directory in here

leoisl commented 3 years ago

Not sure I understand this issue. The issue is that you have 150 entries in the pandora compare output directory, each one corresponding to a sample? And you are just interested on the main output (i.e. files pandora_multisample*), so the output directory is filled with not-so-interesting entries?

mbhall88 commented 3 years ago

Exactly...