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Some ORFs are missing when --allScores option is used #7

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iljungr opened this Issue May 5, 2012 · 1 comment

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@iljungr @mlin
@iljungr
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iljungr commented May 5, 2012

Run with these arguments:
12flies -f3 --allScores --orf=ATGStop --minCodons=1 Bug.fa --species=dmel,dsim
Result:
Bug.fa orf_score(decibans) 14.5636 3 14
Bug.fa max_score(decibans) 20.6305 24 35

There are no orf_score's for the orfs at 24-35, 42-53, 63-74 (though one of them shows up in max_score). When PhyloCSF is run on these ORFs individually it is able to compute a score.

Here is Bug.fa:

dmel
aaaatgccctttgggtagcccaaaatgccctttggttagaaaatgccctttgggtagcccaaaatgccctttgggtag
dsim
aaaatgcctttcggatagcccaaaatgcctttcggatagaaaatgcctttcggatagcccaaaatgcctttcggatag

@mlin mlin added a commit that referenced this issue May 5, 2012

@mlin mlin fix --allScores (issues #7 and #8) 2ab5975
@mlin
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mlin commented May 5, 2012

Thanks, this and #8 were due to a lazy data structure that should have been eager. It arose only when using --allScores.

@mlin mlin closed this May 5, 2012

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