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cerebis / meta-sweeper

Parametric sweep of simulated microbial communities and metagenomic sequencing.
GNU General Public License v3.0
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A5 use of Unix "file" command is tricked by symbolic links #79

Closed cerebis closed 7 years ago

cerebis commented 7 years ago

When A5 is supplied compressed reads as input, it will auto-magically determine that the files are compressed. It does this by use of the Unix command, ie file $file. For a symbolic link however, the result will only report that it is a link, not that the referred to file is compressed.

I have changed A5 to deference symlinks as file -L $file, so that the type of the real file is reported instead.

koadman commented 7 years ago

good find! I will make a note to fix this in the A5 code repo as well

cerebis commented 7 years ago

Great. I wasn't sure whether to post it on SF.