Hi all I think I am going insane. I have the following at the beginning of a bash script:
#!/bin/bash
while getopts i:o:c:p:g: flag
do
case "${flag}" in
g) genome=${OPTARG};;
p) poscol=${OPTARG};;
c) chromcol=${OPTARG};;
i) inf=${OPTARG};;
o) outf=${OPTARG};;
esac
done
echo ""
echo "This should be a list of the arguments:"
echo $inf
echo $outf
echo $poscol
echo $chromcol
echo $genome
echo "-----------------------"
Yet when I run a test of the code, eg:
bash Code.sh -i test.txt -o test.txt -c 0 -p 1 -g testgenome
bash returns:
This should be a list of the arguments:
-----------------------
I literally just copied this section of code from a script where the arguments work fine. Does anyone have any idea what could be going on here? Thanks in advance.