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ANGSD-wrapper / angsd-wrapper

Utilities for analyzing next generation sequencing data.
MIT License
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Fst wrapper - graphing issue #2

Open chrisbalakrishnan opened 5 years ago

chrisbalakrishnan commented 5 years ago

Just want to report what I think is a bug in the code for the Fst wrapper. It seems that the FST.sh script moves the shared.pos file one directory up. However, at the stage where the script is preparing the files for graphing, it still calls the file from ${OUT}/shared.pos. If I'm reading this right, I think shared.pos is at the same level as ${OUT} rather than within it. This triggers an error at the end of the FST wrapper.

carte731 commented 5 years ago

Thank you, we'll look into it.

ChaochihL commented 5 years ago

Hi @chrisbalakrishnan , we did a test run and looked more into this issue. It looks like the parts you mentioned regarding the shared.pos file are part of deprecated code. We currently do not offer visualization for FST calculated by ANGSD. We have cleaned this up to reduce confusion, please pull the latest version of ANGSD-wrapper for the updates. Let us know if you have more questions.

chrisbalakrishnan commented 5 years ago

Thanks! perhaps I pulled the wrong version with git checkout ngsPopGen_Fst? or master? (I'm pretty sure my initial installation was the correct version) I'll admit I don't understand git checkout and what it did... I'll give it a go.