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jts / sga

de novo sequence assembler using string graphs
http://genome.cshlp.org/content/22/3/549
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added prefix for fm-merge #42

Closed idot closed 11 years ago

idot commented 11 years ago

fm-merge does not accept the prefix option

jts commented 11 years ago

Hi,

Thanks for submitting the patch. FM-merge currently does not use -p because the output file can be specified in full using -o. I just want to check whether you considered using -o to specify the output file. If you think it is worth having -p as well let me know and I will merge the patch.

Cheers, Jared

idot commented 11 years ago

I need this for specifying the path to the index that fm-merge uses. I am calling fm-merge from a different folder (scripts) the data and the index is in like:

sga fm-merge --min-overlap=40 -t 1 --outfile=results/merged.fa results/filtered.fa

And the fm-merge looks in my workdir (where the scripts are) for filtered.index instead of in results.

thank you very much for your quick reply, ido

On Mar 12, 2013, at 4:57 PM, jts wrote:

Hi,

Thanks for submitting the patch. FM-merge currently does not use -p because the output file can be specified in full using -o. I just want to check whether you considered using -o to specify the output file. If you think it is worth having -p as well let me know and I will merge the patch.

Cheers, Jared

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jts commented 11 years ago

Ah, I see now, thanks for clarifying.