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thelovelab / fishpond

Differential expression and allelic analysis, nonparametric statistics
https://thelovelab.github.io/fishpond
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Fix bug salmonEC: internally address indexing discrepancy #31

Closed jgilis closed 1 year ago

jgilis commented 1 year ago

Fix bug where salmonEC did not correct equivalence class names for going from 0-indexing to 1-indexing internally. In prior versions, to correctly link equivalence classes to gene names, users would have needed to manually add a value of 1 to the equivalence class names, which was erroneously not mentioned in the man files. After this bug fix, if the equivalence class identifier reads 1|2|8, then the equivalence class is immediately compatible with the transcripts and their respective genes in rows 1, 2 and 8 of 'tx2gene_matched', without any further user intervention.

mikelove commented 1 year ago

Thanks @jgilis I've pushed this to release and devel branches of Bioc