Using a bash array in an awk and also quoted variable: conflicting syntax issue

I have a script the aim of which is:

• For a list of files, obtain a specific number for each file (this is sequencing data, to be specific) and store these into array1
• Using array1, find the smallest number is array1
• Based on smallest number in array1, divide all it by all numbers in array1 to make array2.

My script looks as follows:

#!/usr/bin/bash



USAGE() { echo "Usage: bash $0 [-b <in-bam-files-dir>] [-o <out-dir>] [-c <chromlen>]" 1>&2; exit 1; }

if (($# == 0))
then
    USAGE
fi



while getopts ":b:o:c:h" opt
do
    case $opt in
        b ) BAMFILES=$OPTARG
        ;;
        o ) OUTDIR=$OPTARG
        ;;
        c ) CHROMLEN=$OPTARG
        ;;
        h ) USAGE
        ;;
        \? ) echo "Invalid option: -$OPTARG exiting" >&2
        exit
        ;;
        : ) echo "Option -$OPTARG requires an argument" >&2
        exit
        ;;
    esac
done



if [ ! -d ${OUTDIR} ]
then
    mkdir ${OUTDIR}
fi

if [ ! -d ${OUTDIR}/temp ]
then
    mkdir ${OUTDIR}/temp
fi

if [ -d ${BAMFILES} ]
then
    echo -e "\nProcessing BAM files from following directory: ${BAMFILES} \n "
fi



module purge
module load samtools
module load bedtools
module load ucsctools
echo -e "Modules are loaded\n"



FIRSTBAM=$(ls $BAMFILES/*bam | head -1)
MIN=$(samtools view -c -F 260 ${FIRSTBAM} )
echo -e "Minimum number of reads is currently set to $MIN from $FIRSTBAM (first bam in directory)\n"



declare -A BAMREADS
echo "BAMREADS array is initialized"

for i in $(ls $BAMFILES/*bam)
do
    echo "Counting reads in $i "
    BAMREADS[$i]=$(samtools view -c -F 260 $i)
done



for i in ${BAMREADS[@]}
do
    if [[ $i -lt $MIN ]]
    then
        MIN=$i
    fi
done

echo -e "Minimum number of reads that will be used for scaling is $MIN \n"



declare -A BAMFRACS
echo -e "BAMFRACS array is initialized"

for i in ${!BAMREADS[@]}
do
    BAMFRACS[$i]=$(awk -v var1=${MIN} -v var2=${BAMREADS[$i]} 'BEGIN { x= var1 / var2; printf "%.8f", x }')
done



for i in $(ls $BAMFILES/*bam)
do

    SAMPLE=`basename $i`
    SAMPLE=${SAMPLE%.bam}
    echo $SAMPLE

    if [[ ${BAMREADS[$i]} -eq $MIN ]]
    then

        echo "Sample $i does not need scaling"

        command="cp $i ${OUTDIR}/temp/${SAMPLE}.scaled.bam;
        genomeCoverageBed -bg -split -ibam ${OUTDIR}/temp/${SAMPLE}.scaled.bam > ${OUTDIR}/temp/${SAMPLE}.bedgraph;
        sed -e 's/^/chr/g;s/MT/M/g' ${OUTDIR}/temp/${SAMPLE}.bedgraph > ${OUTDIR}/temp/${SAMPLE}.modified.bedgraph;
        sort -k1,1 -k2,2n ${OUTDIR}/temp/${SAMPLE}.modified.bedgraph > ${OUTDIR}/temp/${SAMPLE}.sorted.bedgraph;
        bedGraphToBigWig ${OUTDIR}/temp/${SAMPLE}.sorted.bedgraph $CHROMLEN ${OUTDIR}/${SAMPLE}.bw"
        #rm ${OUTDIR}/temp/${SAMPLE}.*

    else

        command="samtools view -s ${BAMFRACS[$i]} -b $i > ${OUTDIR}/temp/${SAMPLE}.scaled.bam;
        genomeCoverageBed -bg -split -ibam ${OUTDIR}/temp/${SAMPLE}.scaled.bam > ${OUTDIR}/temp/${SAMPLE}.bedgraph;
        sed -e 's/^/chr/g;s/MT/M/g' ${OUTDIR}/temp/${SAMPLE}.bedgraph > ${OUTDIR}/temp/${SAMPLE}.modified.bedgraph;
        sort -k1,1 -k2,2n ${OUTDIR}/temp/${SAMPLE}.modified.bedgraph > ${OUTDIR}/temp/${SAMPLE}.sorted.bedgraph;
        bedGraphToBigWig ${OUTDIR}/temp/${SAMPLE}.sorted.bedgraph $CHROMLEN ${OUTDIR}/${SAMPLE}.bw"
        #rm ${OUTDIR}/temp/${SAMPLE}.*

    fi

    echo $command | qsub -V -cwd -o $OUTDIR -e $OUTDIR -l tmem=10G -l h_vmem=10G -l h_rt=3600 -N bigwig_${SAMPLE}

 done

 echo "Task completed: conversion jobs submitted to cluster"

I have 2 questions:

• From what I understand, bash is not very good at doing arithmetic maths: i.e. doing any kind of operation (addition, division etc) involving float numbers. However, given the fact that var1 and var2 are always integers in my script (see $MIN and all array1 values), do we agree that this is not a problem? I.e. my operation results in float numbers, but it uses integers, so it's not a problem right?

• It's not very clear in StackExchange because there is no syntax highlighting here, but I noticed that the var2=${BAMREADS[$i]} part of my script isn't quite right. I use nano and in my terminal, instead of having all of the ${BAMREADS[$i]} in red, like the other variables (like ${MIN}), only the ${BAMREADS[$i part of the script is appearing in red, i.e. the ending ]} are not red. The script seems to be behaving as I expect and everything seems to be working.. So I don't quite understand why it's not all in red.

This is how my script looks like in nano (notice how the ]} in ${BAMREADS[$i]} in the awk command AND later on in the second $command is not in red as it should be):

However, if you paste this code into https://www.shellcheck.net/, you don't get any problem in terms of highlighting in this part of the script. So how come nano and shellcheck are not telling me the same thing? I have used this script and it seems to work for me but I am concerned by this highlighting issue..

Thanks