if elif else multiple options error - bash

Question

I have a .ini file, with one of the options being:
[LDdecay]
;determine if examining LD decay for SNPs
;"0" is false (no), "1" is true for GBS only, "2" is true for SoySNP50K only, "3" is true for Merge only, "4" is true for all (GBS, SoySNP50K and Merge)
decay=1
I am continuously getting the following error for lines 69, 72, 80, 88 and 96 (essentially anywhere there is an if or elif statement):
[: : integer expression expected
I'm clearly overlooking something as I have worked with if, elif and else successfully in the past, so anyone who can catch the glitch would be greatly appreaciated.
Thanks
#!/bin/bash
#################################################
# #
# A base directory must be created and #
# the config file must be placed in there #
# #
#################################################
#check if config file was supplied
if [ $# -ne 1 ]; then #if number of argument is different than 1
echo -e "Usage: run_pipeline_cfg.sh <configuration file>" #print error message
exit 1 #stop script execution
fi
#Parse the info from the ini file
ini=$(readlink -m "$1")
source <(grep="$ini" | \
sed -e "s/[[:space:]]*\=[[:space:]]*/=/g" \
-e "s/;.*$//" \
-e "s/[[:space:]]*$//" \
-e "s/^[[:space:]]*//" \
-e "s/^\(.*\)=\([^\"']*\)$/\1=\"\2\"/")
#ini="/home/directory/Initiator.ini" #debug
#Retrieve the base directory path
baseDir=$(dirname "$ini")
#Create required directory structure
logs="$baseDir/logs"
LDdecay="$baseDir/LDdecay"
imputed="$baseDir/imputed"
#dont create if already exists
[[ -d "$logs" ]] || mkdir "$logs"
[[ -d "$LDdecay" ]] || mkdir "$LDdecay"
[[ -d "$imputed" ]] || mkdir "$imputed"
#find imputed vcf files
if [ -e $imputed ] ; then
echo -e "Folder with imputed vcf files exists. Determining if calculating LD decay"
else
echo -e "Folder with imputed vcf files does not exist. Cannot calculate LD decay."
exit 1
fi
#######################################################
# #
# Create LD decay files for LD decay plots #
# #
#######################################################
#determine on which files to perform LD decay calculations
#"0" is false (no), "1" is true for GBS only, "2" is true for Microarray only, "3" is true for Integrated only, "4" is true for all (GBS, Microarray and Integrated)
if [ "$decay" -eq 0 ]; then
printf "LD decay rates not calculated" | tee -a $logs/log.txt;
elif [ "$decay" -eq 1 ]; then
#perform LD decay calculation for GBS only
zcat $imputed/GBS_MAF0.01.vcf.gz > $LDdecay/GBS_MAF0.01.vcf
plink --vcf $LDdecay/GBS_MAF0.01.vcf --r2 --ld-window 10000000 --ld-window-kb 10000 --ld-window-r2 0 --output $LDdecay/GBS_LD_decay
rm $LDdecay/GBS_MAF0.01.vcf
printf "LD decay for GBS dataset completed" | tee -a $logs/log.txt
elif [ "$decay" -eq 2 ]; then
#perform LD decay calculation for microarray only
zcat $imputed/microarray_MAF0.01.vcf.gz > $LDdecay/microarray_MAF0.01.vcf
plink --vcf $LDdecay/microarray_MAF0.01.vcf --r2 --ld-window 10000000 --ld-window-kb 10000 --ld-window-r2 0 --output $LDdecay/microarray_LD_decay
rm $LDdecay/microarray_MAF0.01.vcf
printf "LD decay for microarray dataset completed" | tee -a $logs/log.txt
elif [ "$decay" -eq 3 ]; then
#perform LD decay for Merged dataset only
zcat $imputed/Integrated_MAF0.01_sorted.vcf.gz > $LDdecay/Integrated_MAF0.01.vcf
plink --vcf $LDdecay/Integrated_MAF0.01.vcf --r2 --ld-window 10000000 --ld-window-kb 10000 --ld-window-r2 0 --output $LDdecay/Integrated_LD_decay
rm $LDdecay/Integrated_MAF0.01.vcf
printf "LD decay calculation for Integrated dataset complete" | tee -a $logs/log.txt
elif [ "$decay" -eq 4 ]; then
#perform LD decay for Merged, GBS and SoySNP50K datasets
zcat $imputed/Integrated_MAF0.01_sorted.vcf.gz > $LDdecay/Integrated_MAF0.01.vcf
plink --vcf $LDdecay/Integrated_MAF0.01.vcf --r2 --ld-window 10000000 --ld-window-kb 10000 --ld-window-r2 0 --output $LDdecay/Integrated_LD_decay
rm $LDdecay/Integrated_MAF0.01.vcf
zcat $imputed/microarray_MAF0.01.vcf.gz > $LDdecay/microarray_MAF0.01.vcf
plink --vcf $LDdecay/microarray_MAF0.01.vcf --r2 --ld-window 10000000 --ld-window-kb 10000 --ld-window-r2 0 --output $LDdecay/microarray_LD_decay
rm $LDdecay/microarray_MAF0.01.vcf
zcat $imputed/snp_imputed_GBS_MAF0.01.vcf.gz > $LDdecay/GBS_MAF0.01.vcf
plink --vcf $LDdecay/GBS_MAF0.01.vcf --r2 --ld-window 10000000 --ld-window-kb 10000 --ld-window-r2 0 --output $LDdecay/GBS_LD_decay
rm $LDdecay/GBS_MAF0.01.vcf
printf "LD decay calculation completed for Integrated, GBS and SoySNP50K datasets completed" | tee -a $logs/log.txt
else
echo "Wrong LD Decay calculation setup"
exit 1
fi

Answer 1

Consider changing the elsif chain to a case statement. It should side-step the need for the tests to have integer arguments and it is both clearer and more easy to extend:
case $decay in
0)
printf "LD decay rates not calculated" | tee -a $logs/log.txt;
;;
1)
#perform LD decay calculation for GBS only
zcat $imputed/GBS_MAF0.01.vcf.gz > $LDdecay/GBS_MAF0.01.vcf
plink --vcf $LDdecay/GBS_MAF0.01.vcf --r2 --ld-window 10000000 --ld-window-kb 10000 --ld-window-r2 0 --output $LDdecay/GBS_LD_decay
rm $LDdecay/GBS_MAF0.01.vcf
printf "LD decay for GBS dataset completed" | tee -a $logs/log.txt
;;
2)
#perform LD decay calculation for microarray only
zcat $imputed/microarray_MAF0.01.vcf.gz > $LDdecay/microarray_MAF0.01.vcf
plink --vcf $LDdecay/microarray_MAF0.01.vcf --r2 --ld-window 10000000 --ld-window-kb 10000 --ld-window-r2 0 --output $LDdecay/microarray_LD_decay
rm $LDdecay/microarray_MAF0.01.vcf
printf "LD decay for microarray dataset completed" | tee -a $logs/log.txt
;;
3)
#perform LD decay for Merged dataset only
zcat $imputed/Integrated_MAF0.01_sorted.vcf.gz > $LDdecay/Integrated_MAF0.01.vcf
plink --vcf $LDdecay/Integrated_MAF0.01.vcf --r2 --ld-window 10000000 --ld-window-kb 10000 --ld-window-r2 0 --output $LDdecay/Integrated_LD_decay
rm $LDdecay/Integrated_MAF0.01.vcf
printf "LD decay calculation for Integrated dataset complete" | tee -a $logs/log.txt
;;
4)
#perform LD decay for Merged, GBS and SoySNP50K datasets
zcat $imputed/Integrated_MAF0.01_sorted.vcf.gz > $LDdecay/Integrated_MAF0.01.vcf
plink --vcf $LDdecay/Integrated_MAF0.01.vcf --r2 --ld-window 10000000 --ld-window-kb 10000 --ld-window-r2 0 --output $LDdecay/Integrated_LD_decay
rm $LDdecay/Integrated_MAF0.01.vcf
zcat $imputed/microarray_MAF0.01.vcf.gz > $LDdecay/microarray_MAF0.01.vcf
plink --vcf $LDdecay/microarray_MAF0.01.vcf --r2 --ld-window 10000000 --ld-window-kb 10000 --ld-window-r2 0 --output $LDdecay/microarray_LD_decay
rm $LDdecay/microarray_MAF0.01.vcf
zcat $imputed/snp_imputed_GBS_MAF0.01.vcf.gz > $LDdecay/GBS_MAF0.01.vcf
plink --vcf $LDdecay/GBS_MAF0.01.vcf --r2 --ld-window 10000000 --ld-window-kb 10000 --ld-window-r2 0 --output $LDdecay/GBS_LD_decay
rm $LDdecay/GBS_MAF0.01.vcf
printf "LD decay calculation completed for Integrated, GBS and SoySNP50K datasets completed" | tee -a $logs/log.txt
;;
*)
echo "Wrong LD Decay calculation setup"
exit 1
;;
esac