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[pygenomeworks] evalute_paf does not properly report the number of incorrect starts/ends #560

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edawson opened this issue Sep 15, 2020 · 0 comments

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edawson commented Sep 15, 2020

The evaluate_paf script in pygenomeworks/bin reports a number of correct query/target starts and ends. However, the numbers reported currently are not accurate, as each searched interval increments these variables:
https://github.com/clara-parabricks/GenomeWorks/blob/88dcc74b17a659e1baf21139920a41d9e0cac7f6/pygenomeworks/bin/evaluate_paf#L195-L198

The proper behavior should instead be to only report the correctness of starts/ends only for the best match.

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[pygenomeworks] Fix counts of incorrect starts and ends in evaluate_paf #562

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