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poseidon-framework / poseidon-analysis-hs

A tool to analyse genotype data (optionally in the poseidon data format)
MIT License
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Poseidon hs upgrade #19

Closed stschiff closed 1 year ago

stschiff commented 1 year ago

OK, I have made all the changes necessary to work with the latest poseidon-hs. I am not yet ready quite yet, as I would like to also implement the stats block output. But I wanted to make this available for your review @nevrome, whenever you have time, since there are also changes to AdmixPop which need to be reviewed by you.

nevrome commented 1 year ago

This doesn't compile for me:

[ 5 of 11] Compiling Poseidon.Analysis.CLI.FStats

/home/schmid/agora/poseidon-analysis-hs/src/Poseidon/Analysis/CLI/FStats.hs:196:34: error:
    Variable not in scope: popLefts :: [a0]
    |
196 |                 forM_ (zip [0..] popLefts) $ \(i, popLeft) ->
    |                                  ^^^^^^^^

/home/schmid/agora/poseidon-analysis-hs/src/Poseidon/Analysis/CLI/FStats.hs:197:38: error:
    Variable not in scope: popRights :: [a1]
    |
197 |                     forM_ (zip [0..] popRights) $ \(j, popRight) ->
    |                                      ^^^^^^^^^

/home/schmid/agora/poseidon-analysis-hs/src/Poseidon/Analysis/CLI/FStats.hs:198:51: error:
    • Variable not in scope: blockData :: [BlockData]
    • Perhaps you meant data constructor ‘BlockData’ (line 84)
    |
198 |                         forM_ (zip [(0 :: Int)..] blockData) $ \(k, block) ->
    |                                                   ^^^^^^^^^

/home/schmid/agora/poseidon-analysis-hs/src/Poseidon/Analysis/CLI/FStats.hs:201:108: error:
    Variable not in scope: blockVals :: BlockData -> [[a3]]
    |
201 |                                 show (snd . blockEndPos $ block), show (blockSiteCount block !! i), show ((blockVals block !! i) !! j)]
    |                                                                                                            ^^^^^^^^^

I'll look into the changes now without running anything.

stschiff commented 1 year ago

Yes, I'm sorry it doesn't compile. I started adding stuff after I started the PR, my bad. Thanks for reviewing the bits you did. I'll finalize now and make ready for review/merge.

stschiff commented 1 year ago

OK, I've followed your advice and removed the block output stuff from this branch for now. If you give green-light, @nevrome, I will merge this and then make another PR with the block-output feature.

codecov[bot] commented 1 year ago

Codecov Report

:exclamation: No coverage uploaded for pull request base (main@fedf433). Click here to learn what that means. Patch has no changes to coverable lines.

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nevrome commented 1 year ago

Excellent! Can be merged now :+1:

nevrome commented 1 year ago

I think this PR will close #8 and #10, right?