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thelovelab / tximport

Transcript quantification import for modular pipelines
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`ignoreAfterBar` not used if `txOut=TRUE` #40

Closed csoneson closed 3 years ago

csoneson commented 4 years ago

It seems that ignoreAfterBar is not used if transcript-level output is requested. Am I overlooking a reason why this should not be supported (i.e., return only the part of the transcript ID before the first |)?

mikelove commented 4 years ago

You mean it doesn't alter the rownames?

I had initially just coded it up for fixing summarization when the tx2gene table didn't match the txp IDs, but I could rework it so it also alters the rownames. I don't see this as breaking any downstream code, right?

csoneson commented 4 years ago

Exactly.

I also can't see that it should break downstream code. The gene summarization should work regardless, it just wouldn't have anything to ignore if stuff after the '|' is already removed.

mikelove commented 4 years ago

sounds good, I'll work on it :)

mikelove commented 3 years ago

Oops! this fell off my list, just tried to address this in 18f39a7

csoneson commented 3 years ago

Looks good, thank you!