uninitialized variables...

[martin-raden]

Hi @PatrickRWright

the script blast2homfile.pl shows two uninitialized variables (skip_sort and evalcorr) in if statements

CopraRNA/coprarna_aux/blast2homfile.pl

Line 9 in 6097464

if (! $skip_sort) {

as far as I get it, perl variables are initialized "undefined", which is considered FALSE.
thus the current script will

• always run the sorting (!$skip_sort)
• and ignore the eval correction ($evalcorr)

is the following (default) initialization correct:

$skip_sort=0 # ie. FALSE
$evalcorr=0 # ie. FALSE

which I would like to add to the top of the script..

Thanks for feedback,
Martin

[martin-raden]

I eventually just found the evalcorr triggered statement to be wrong anyway since it uses len that is neither a variable or anything

CopraRNA/coprarna_aux/blast2homfile.pl

Line 34 in 6097464

$eval *= len

so I think I can remove the evalcorr part completely, right?

[martin-raden]

see commit a9115b9

[PatrickRWright]

This script is provided by domclust. If I remember correctly I had to make some adjustments to make everything work for bioconda.

[martin-raden]

mhh.. so I guess the changes are fine!?!